Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_014043
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 379236
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:41304 original size:13 final size:14
Alignment explanation
Indices: 41286--41315 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
41276 TGATTATGTG
41286 AGAAGTCAGT-TCA
1 AGAAGTCAGTCTCA
41299 AGAAGTCAGTCTCA
1 AGAAGTCAGTCTCA
41313 AGA
1 AGA
41316 CTGTCCCGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (14 bp):
AGAAGTCAGTCTCA
Left flanking sequence: Indices 40786 -- 41285
CTGGAAAGCCTAAACCCTCACTCTTCCAAGCGGACATCAATCCCGGAAAAAAAAATAGTGTAAGT
AAGAAGAAGACCGGTTAGGATCACACTAGTCCTGGCTGGCCTATTATGAACTATTTTCCCTCAGA
ACAAGAATAAAAGAGGCTTGCAGGTCTAGTCGCATACCCCTATCGTCTTATTGTTCTATTCGTTG
CAGTGGTAAACTCATTGAATACTCAAATATGGTTTAGTCACACCCTTCAAGAGTGTACATTCTGA
TTCAATAGCAAACAGAGCATTCTTTGCTTCTGATTCCATTCCTGAAAACAATTCTATCACACACG
GCGAATCGAGTTCAAAGAACTCTCCCCACAGCTTATTCGTGCAAAGATCCAGCATTCCTTCACTT
ATCATATAGAATAACGATCGACAAGTCCAGAGTGTGCACCAACGAGAGATTGAAGTACGCTTGCA
AGATTCTCCGAATCGCAGCATTCTTCTCTACTATGTGATTATGTG
Right flanking sequence: Indices 41316 -- 41815
CTGTCCCGGCACAGAAGGCATTGAATACGGCTGTTCAGGCTAGCAACAGATTCTCCGGTAAGATA
GATTCAGTCAGTTCCGGCCGGCATTCAATCAAGAAAGAAAAGAAATGGGCATTGCTTGAGCTAAG
TCAAGCTTTTTTTCCAAGTGTTGTAAAGACGGGCTACAACGAAAGTCAACAAAACAAGAAAGATG
AAAACTTCCGTCACTGCGCACCACTTTGCTTTGGGCTCTGGTCCACTTTCGCTCCGTTTACGCGA
ATCGGTTGTATCTGCCCGCTAGGAACGCTGGCATCAGGATTGTTGACAACAGTCCCGCTAAAGGC
CGCAGTCTCTTCCACATTCGGCAAGGTAAGTCAAGTAGTTCATGAGGAATCATCATTAGCATTAG
CAGTCGGTGAAGCTTTTTCTAATGTTGTTCTTGATCATGGCACAGATGTATTTGGTTGGGCGCTG
CTGCTCAAGAAGGAAAAAGTGCTAAAGCTTTAGCTGCTTGTAGAA
Found at i:43538 original size:75 final size:75
Alignment explanation
Indices: 43432--43653 Score: 444
Period size: 75 Copynumber: 3.0 Consensus size: 75
43422 GAGTGCTAGC
43432 GCTGCAATCACATCTGGGTTATTGTTATTTTCGGGGGCTGGGCCCGCGGATGTACCCACTGAAGC
1 GCTGCAATCACATCTGGGTTATTGTTATTTTCGGGGGCTGGGCCCGCGGATGTACCCACTGAAGC
43497 TGGTGCCCCT
66 TGGTGCCCCT
43507 GCTGCAATCACATCTGGGTTATTGTTATTTTCGGGGGCTGGGCCCGCGGATGTACCCACTGAAGC
1 GCTGCAATCACATCTGGGTTATTGTTATTTTCGGGGGCTGGGCCCGCGGATGTACCCACTGAAGC
43572 TGGTGCCCCT
66 TGGTGCCCCT
43582 GCTGCAATCACATCTGGGTTATTGTTATTTTCGGGGGCTGGGCCCGCGGATGTACCCACTGAAGC
1 GCTGCAATCACATCTGGGTTATTGTTATTTTCGGGGGCTGGGCCCGCGGATGTACCCACTGAAGC
43647 TGGTGCC
66 TGGTGCC
43654 ACATTCGAGG
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 147 1.00
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (75 bp):
GCTGCAATCACATCTGGGTTATTGTTATTTTCGGGGGCTGGGCCCGCGGATGTACCCACTGAAGC
TGGTGCCCCT
Left flanking sequence: Indices 42932 -- 43431
CATGGGAGTCTTTGGGCATTGCTTCGGATAAAAGAAAACGGAAATGCCCACCCTTTCTTTTTTTC
CTTGTCAATGATCGAACTTAAAGATATGAACTGAGTGCCATTTTCTGAGTAACGTAGAAAAAAAG
AGGAAAATCGAAAGGATGAAATAATTCAAGAAGAAGTCAAATCAAATCAATGTTCTAATTAGCAC
TTTTATTGCAGGTTGAAGAACCTTCTATCTTCTCTCAGTTACCCCACCTTTGTCTCACCCACTGG
CGGATCTCCGCCTTAAGGAAATTTCTATCAGACTGGAATCTGGAAAGAAACTCCTGCAGGATAGC
GGGGTTTAGTTCATCATCTAGTTCGAGTTCCACCAGTAATTGATGGGCGGCATCTTGGTGGTATG
GGGTCATCCAATGGGGGAATAGGCGGGAAAGCGGGGCCCGGAGAACCTTATCGCTTTCCACCCGG
AAGCGCTCCTCTATTAAAGCACGAATCTCTGAACGGAGTGCTAGC
Right flanking sequence: Indices 43654 -- 44153
ACATTCGAGGGCCCCGCTCCCTCCACACTGGGCATCGGTTGATTGACAGATGGGAGACTTCCACT
ACGTCCCGAACTGGCCGAATCATCGTCAAAATCCGAAGTATAAGTGAACCATTCGGACGAGGTGG
AGGGAGTCCTATTATCATTATCAAAAAAAGTCTTGAATCCTCCAAAAAATACAAAATCTGAATCA
GAATAAAATAAAAGTGTCCTCAGACAATGTAAAAAGAGTGGGATGAACGGAAGGGCTCGTTGAAA
CAGACAACAAATTCGAGAGCCCGATTTTGGATAAGAAAAATCCGTCAATAAATGACGAACCCCAT
TATACAGATGATAGGACAGGGCTAAGGCAGTAATCTCGGCGGAGATTAGGATGAGCTTTGATGAA
TAAAAGAAGAATCTGTAGAAATTCGAATAGGTGAAGCAAATCAAACCCATTTTCAGACAAAGAAG
ATAAAAAAACAAAACGAGAGTGGCTAGGAAAGCCCCGGAGATTCT
Found at i:44239 original size:6 final size:6
Alignment explanation
Indices: 44228--44268 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
44218 CGCAGGATAT
44228 TCATTC TCATTC TCATTC TCATTC TCATTC TCATTC TCATT
1 TCATTC TCATTC TCATTC TCATTC TCATTC TCATTC TCATT
44269 GGTGAGATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (6 bp):
TCATTC
Left flanking sequence: Indices 43728 -- 44227
ACTGGCCGAATCATCGTCAAAATCCGAAGTATAAGTGAACCATTCGGACGAGGTGGAGGGAGTCC
TATTATCATTATCAAAAAAAGTCTTGAATCCTCCAAAAAATACAAAATCTGAATCAGAATAAAAT
AAAAGTGTCCTCAGACAATGTAAAAAGAGTGGGATGAACGGAAGGGCTCGTTGAAACAGACAACA
AATTCGAGAGCCCGATTTTGGATAAGAAAAATCCGTCAATAAATGACGAACCCCATTATACAGAT
GATAGGACAGGGCTAAGGCAGTAATCTCGGCGGAGATTAGGATGAGCTTTGATGAATAAAAGAAG
AATCTGTAGAAATTCGAATAGGTGAAGCAAATCAAACCCATTTTCAGACAAAGAAGATAAAAAAA
CAAAACGAGAGTGGCTAGGAAAGCCCCGGAGATTCTATGGGAAATAGGAAACGTAGAAGTGAGCT
GTGGCTTATAAATAGGAAGATGAGGAGATAACGGACGCAGGATAT
Right flanking sequence: Indices 44269 -- 44768
GGTGAGATTGAGAGTTTCTTGCTCCTTAATCGCGGAGCAGCATACCGAAAAAAAAAAAGGCCCTG
TAGGTTCAAGTCACACTTTTGGCTTGCTACAAGCTGGGCTCAGGGACAGCAGTCAGCCGCTTCCC
CTCCCTGTAGTCGTCAGCTCCCTCGTGATCTTGACAGATCCGATCGGGTGTGAATAATCTGGAGT
AAAAGGATTCGAACCTTTGCATGCCGGTACCAAAAACCGATGCCTTACCACTTGGCTATACTCCA
TACGGCCTTGTTTTGGACGGTAGAACGGGGAGAGGGGGAAGGGAGAAGCAGGGCTCGAAGAACGA
GCCGAGCCGTGCAAGAACGCGGGATATAGCAAGTAAGCAGCAAGATTCTCTCTTGTTTGTTGACC
GACTACAACAAGCTCGCGACTCTAATAGAAACAAACGGTAAGCTCTCCTCTGTTCTATTTGCTTG
CAATGCTATACCTATCAAAGTTGGCGAACGCTTCTGTAACCTTAG
Found at i:58769 original size:29 final size:29
Alignment explanation
Indices: 58727--58882 Score: 312
Period size: 29 Copynumber: 5.4 Consensus size: 29
58717 ATCACCTGCT
58727 TCCTCTCCCTATCGGTCGAGCTGCGAAGC
1 TCCTCTCCCTATCGGTCGAGCTGCGAAGC
58756 TCCTCTCCCTATCGGTCGAGCTGCGAAGC
1 TCCTCTCCCTATCGGTCGAGCTGCGAAGC
58785 TCCTCTCCCTATCGGTCGAGCTGCGAAGC
1 TCCTCTCCCTATCGGTCGAGCTGCGAAGC
58814 TCCTCTCCCTATCGGTCGAGCTGCGAAGC
1 TCCTCTCCCTATCGGTCGAGCTGCGAAGC
58843 TCCTCTCCCTATCGGTCGAGCTGCGAAGC
1 TCCTCTCCCTATCGGTCGAGCTGCGAAGC
58872 TCCTCTCCCTA
1 TCCTCTCCCTA
58883 GTGAATGCAA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 127 1.00
ACGTcount: A:0.13, C:0.39, G:0.22, T:0.25
Consensus pattern (29 bp):
TCCTCTCCCTATCGGTCGAGCTGCGAAGC
Left flanking sequence: Indices 58227 -- 58726
TCTTCCTATTTGAATATTATTACAATCTTCCAACATAGAGAAGGAAGAGTTTTTTGATTCCAATC
CTATATCATTATCATTTGTTGATAGATAGGGCCGATAGCCACCTGACGAGAGAGGTCCTTAAGGA
TATTGTGGGGAGAGCGGAGGCTCTCGTTTTTTCTTCTCGCTAACGATCGGCATTCTTTTCTTCCT
CATTCCGGCATGATCAAAGAAGCTATGACTGACCTGGTCCCCTTTGAAGACAAGACCCTCTTTTT
TCTTTCTGTGTTTTTCAGCTTTTTAATTGGGAATCAACCCCCTCTGCTCCTCTTTCTTTCCTAGC
GCACAGCTTTATTGCACGCATTTGGTGCGCTATTGAATAACATTCCTATAAGTGGTCAAACGAGA
TCCCCATCTCAAGGAGGTCCTCCACTTTGGTTGGCTAGTCGATCTTCCTCTCTCCGAATTGCAAT
TTTGATCATCCTCGTTGTACTTACTCTTTCGAAGGATCACCTGCT
Right flanking sequence: Indices 58883 -- 59382
GTGAATGCAATCTATACTTGATTCTACTCTTCTATATGAGTAGAATTCACTTGAGTGATTCTTCC
TTTCAGTTGATGGACCGAGAAGCTTCTCCCCTATCAGTGATAATAAGGTATCATAGAACAGCTTT
TAAGTACTAAAGATAGAAAGAAGTGATGCTGTGCTAACAAAGCTAGGTGTTCGAGGATTGAATGA
ACACCAGGATTGAACTACCTCTTATGGGTGTATATACTCCTGTGTAGCTACAACTTACCATTAGC
TGTGGGAATAGGGTAACCGTACTTAACGCGGGAATAAAGCTCATCTCTTTCAGACTCTTCGACTT
ACGGCTCTTCATCGGAACTCACTGCCCAAAATCTTAGGGCTGACAATGTGCCTTGAAGTGCCTCG
GACATAGGATTCATCGTGGGACCCCCCAAACGCTCGTTTAAGCGCACTACAATGGCCTTCTCGAA
CGATCCACCATCAGACTTGCCTCAAGCTGAAGCAATATTGGACAA
Found at i:61757 original size:14 final size:14
Alignment explanation
Indices: 61738--61767 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61728 GAGGGGAAAG
61738 AAGGATTTCGAAGA
1 AAGGATTTCGAAGA
*
61752 AAGGATTTCGGAGA
1 AAGGATTTCGAAGA
61766 AA
1 AA
61768 AGAATGGCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.30, T:0.20
Consensus pattern (14 bp):
AAGGATTTCGAAGA
Left flanking sequence: Indices 61238 -- 61737
GAATAAGATGCCGATAGGCTCAGAGGACGAAGGAGTAAGTAAGGCGAAGAGGACAAAGTCAAGTA
GTTCGTTCCGCTATACCAAAAGGAGGGGCTTTAGAGGCGACTTGACTTCTCCGCTTCGTGGGACT
CCGCTCCTAAAGAAAGGGTGCTTTCATTCAAGAAGAGATCCATATCTCTATAGAGCTTCGAAGGG
ACAGCACGAAGGTTACAAGGAAAAAGCCTTGCTACGAGCTCGTATATGGATATCCAGCCTTAGTC
AAAACCTTACCTTAATATCGTGGATAACGTTGATTCCTCCTTACCTCCCCTTCTCCGCCTAAAAT
GAAGTAAGTGTCTCAATAGCGAGAAAATCATAGCCCTGGCACTGAAACAAGAGAGGAACCTCCTC
CAAGACAACGAGAGAGGAATCAGTCGTTTACCACTTTCAACTGAATTGCTACTTTTTTCTTGTTA
TTGATAGAGTTGTCTTCCCCGCCCCTGATAAATACGAGGGGAAAG
Right flanking sequence: Indices 61768 -- 62267
AGAATGGCTGACACGTTGACTCGAGACTATAAGAATTAGAGGACTTTTTTCCCGGTCTAGTGCCA
AGCGAGCCGGACCCAAACCGAATACTCCATAATCAGTAAACAGCATAGATGCGAAGCATGTTATG
CCGCCGCTTAAGGACTCTTCCCAAACGACTCTGAATCTCAAGTATAGAGAGGCTGTTTCATATAG
TTTGAAAAGTGCTTCAGTGACTGACGATGTTGAAAGTCGTGTATGGCTTTCTAAAGAAGACGAAC
AACAACTAGCGGCGAACAAGCATAAATGCAACTCTCATTTCATCATTTCTAGTTCAAATCCCTTA
TTGCCTAGTTCAACCACGAACCATCAAAGGTAGTCGGCGAAGATGCGCAGCGGCGAACAGTCCTG
GGCCCGAGGTAGGTGCTTTGTTTGTGAGCCGGAAATTCGAAGATTAGTGATCCCACCGATTTTGA
TGTTGGAGTGCTTAAAGGCGTAACCAGTGTTGTCGGAAGTTCTTT
Found at i:96650 original size:39 final size:39
Alignment explanation
Indices: 96595--96673 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
96585 CCGATCCATT
*
96595 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
96634 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
96673 A
1 A
96674 TAGAAAATCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.22
Consensus pattern (39 bp):
AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
Left flanking sequence: Indices 96095 -- 96594
CAGCGATTGATTCTTTTCTCCACTAATAACCCCTTCCCAACCAGCCCGCCCGATCGATTTTGTAA
GATCGGCTAATTCAAAGGGGTTAATCTGGTCCGAAGTTGTCGGAACGAATCGTTTGCTTTATCGA
ACAAAGCTTTATTAGGGGGTCTTGGTTGGCCCCCTATTTTCAACCATTACAGCTGGCGTCGACCA
GCTTTGCGATACGGACGGACACAAAAAAGAACGCTGGCAGCGGAAATGCAAAAGAGAAGAGCAAA
GATTCCCGACCCAGAGCATGTTATTGACTCAACCACAAATCTGTTGAATGAAGGTAGCTTGCTTA
CTCTCAGCCGCTAGTTAGAAGGAAATCCGTTGACTTCGTTTATGCCCTTATGCAGTAAAGAAAGC
AAGTGAGGCGGGCTAAGCTTCCATTCGAAGTAAGGTAAGAGGATTCGATCTTGCACCATCTTCAA
CTCTTCTCGGGATCCGGTGTTTTTCGAGAAAAGGTCCGATCCATT
Right flanking sequence: Indices 96674 -- 97173
TAGAAAATCGAAAACGTACATAGCAGTCCCAGCTGAAATACTTGGAATAATTCTACCACTTCTAC
TAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAGGGT
CCTGATGTAGTGGGATCGTTCGGATTGTTACAACCTCTAGCAGATGGTTTGAAATTGATTCTAAA
AGAACCTCTTTCACCAAGTAGTGCAAATTTCTCCCTTTTTAGAATGGCTCCAGTGGCTACATTTA
TGTTAAGTCTGGTCGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATCCGAAC
ATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCGGGTTG
GTCTAGTAATTAGGGGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTCAAAAATGGG
TTTGTGCCGCAGGTGTTGAACGATCTACTCTACACAGGTGTGGGC
Found at i:107727 original size:22 final size:22
Alignment explanation
Indices: 107699--107777 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
107689 ATGCACTTAC
107699 AGGTGCTAGTTCTCTAGTTTAG
1 AGGTGCTAGTTCTCTAGTTTAG
* * *
107721 AGGTGCTAGTTTTGTAGTTTAC
1 AGGTGCTAGTTCTCTAGTTTAG
107743 AGGTGCTAGTTCTCTAGTTTAG
1 AGGTGCTAGTTCTCTAGTTTAG
107765 AGGTGCTAGTTCT
1 AGGTGCTAGTTCT
107778 TGTTTCCCGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGTGCTAGTTCTCTAGTTTAG
Left flanking sequence: Indices 107199 -- 107698
AGAGTGACTTGTTCTCTCGGTAACAGAGTTGGTAACATAGAACATTACAGATAGAACAGGTATTC
TTCTTCATCTTCTTCTTTACAGGTAAAAGTACAGGTAAAAGAAATTTCCCTATAGTGTTTTCCCG
GTAAAATCAGTAGTTTTCATACTCCTTTACGGATAGAACATTACTTCTTCACTTACTTTAAGTTA
CAGGTCAAAGAAAGAAAGCATACTCCTGGACTAGGTGTAAGAGAACAGATAGTTAGTTGTTCTAG
AACCTCTAGTTAGTTTACAGGGAAGAGAGAGTTAGTTAACGGATAGTCTTCTTTACAGGTAATAG
CTGTTGAGGAGTTGTTGTTAAGAACTGATATTGTTAACACTGTAACAGAGTTGGCACATGGAGCA
TTACTTCTTATTTCATTTATTCTTCCACCTCGGTAAAATCAATGGAAGATATAACATTTCTTCTT
CTATTTCATCTTCTTCATCTTCTTTCCCTGGTATGATGCACTTAC
Right flanking sequence: Indices 107778 -- 108277
TGTTTCCCGGTATTTTCAATAGAACAAGTATAAGCCCCTGGTAAACTCGGTAAAGCAGCGGAGAT
CCCTATCGGTCGAGTGGCTCCTTTCCCTATCGGTCTCGTTGCTTCGCTCCCTTCGGCTTTTTGGC
TTTGCTTCTTTCCCTATATGGGTTGCAAAGTTCCTCTGCCTTGTAATCGGCAGGGCGTAGATCCG
GCTTCTTCCCAATTAAACTAGGTAAAGCATATAAGCCCCTTTCCTTTACAGTTGAGCAGCTTTGA
GCCTTTACAGGAGAGTAAATTGAATCGATCCTTGTAATTGTCTTTGCAGCTTTTCCCCTTTACAG
TTGAGGATATTCAACCCTTTCCCTTGTAAACTACTCGGGTTTTTGGCTTCGCCCCGATCCCCTCG
TACCTTTACAGGGGACCCTATTGTTATTACACCTGTAAATCAGAATAAATGTTCTATCTGTAAAA
GAGTATGTGAAATAGCTGTTACAGTTATAACAATATCTTTTCTTT
Found at i:107758 original size:44 final size:45
Alignment explanation
Indices: 107695--107780 Score: 165
Period size: 44 Copynumber: 1.9 Consensus size: 45
107685 TATGATGCAC
107695 TTACAGGTGCTAGTTCTCTAGTTTAGAGGTGCTAGTT-TTGTAGT
1 TTACAGGTGCTAGTTCTCTAGTTTAGAGGTGCTAGTTCTTGTAGT
107739 TTACAGGTGCTAGTTCTCTAGTTTAGAGGTGCTAGTTCTTGT
1 TTACAGGTGCTAGTTCTCTAGTTTAGAGGTGCTAGTTCTTGT
107781 TTCCCGGTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 37 0.90
45 4 0.10
ACGTcount: A:0.17, C:0.13, G:0.27, T:0.43
Consensus pattern (45 bp):
TTACAGGTGCTAGTTCTCTAGTTTAGAGGTGCTAGTTCTTGTAGT
Left flanking sequence: Indices 107195 -- 107694
TAGCAGAGTGACTTGTTCTCTCGGTAACAGAGTTGGTAACATAGAACATTACAGATAGAACAGGT
ATTCTTCTTCATCTTCTTCTTTACAGGTAAAAGTACAGGTAAAAGAAATTTCCCTATAGTGTTTT
CCCGGTAAAATCAGTAGTTTTCATACTCCTTTACGGATAGAACATTACTTCTTCACTTACTTTAA
GTTACAGGTCAAAGAAAGAAAGCATACTCCTGGACTAGGTGTAAGAGAACAGATAGTTAGTTGTT
CTAGAACCTCTAGTTAGTTTACAGGGAAGAGAGAGTTAGTTAACGGATAGTCTTCTTTACAGGTA
ATAGCTGTTGAGGAGTTGTTGTTAAGAACTGATATTGTTAACACTGTAACAGAGTTGGCACATGG
AGCATTACTTCTTATTTCATTTATTCTTCCACCTCGGTAAAATCAATGGAAGATATAACATTTCT
TCTTCTATTTCATCTTCTTCATCTTCTTTCCCTGGTATGATGCAC
Right flanking sequence: Indices 107781 -- 108280
TTCCCGGTATTTTCAATAGAACAAGTATAAGCCCCTGGTAAACTCGGTAAAGCAGCGGAGATCCC
TATCGGTCGAGTGGCTCCTTTCCCTATCGGTCTCGTTGCTTCGCTCCCTTCGGCTTTTTGGCTTT
GCTTCTTTCCCTATATGGGTTGCAAAGTTCCTCTGCCTTGTAATCGGCAGGGCGTAGATCCGGCT
TCTTCCCAATTAAACTAGGTAAAGCATATAAGCCCCTTTCCTTTACAGTTGAGCAGCTTTGAGCC
TTTACAGGAGAGTAAATTGAATCGATCCTTGTAATTGTCTTTGCAGCTTTTCCCCTTTACAGTTG
AGGATATTCAACCCTTTCCCTTGTAAACTACTCGGGTTTTTGGCTTCGCCCCGATCCCCTCGTAC
CTTTACAGGGGACCCTATTGTTATTACACCTGTAAATCAGAATAAATGTTCTATCTGTAAAAGAG
TATGTGAAATAGCTGTTACAGTTATAACAATATCTTTTCTTTTCC
Found at i:114573 original size:21 final size:21
Alignment explanation
Indices: 114549--114617 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
114539 TTATCGCAGT
114549 ACTAGTTCCGAATGGATTAAG
1 ACTAGTTCCGAATGGATTAAG
* * **
114570 ACTAG-TCTC-ACTGGTAGTACT
1 ACTAGTTC-CGAATGG-ATTAAG
114591 ACTAGTTCCGAATGGATTAAG
1 ACTAGTTCCGAATGGATTAAG
114612 ACTAGT
1 ACTAGT
114618 CTCACTGGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
20 6 0.17
21 24 0.67
22 6 0.17
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (21 bp):
ACTAGTTCCGAATGGATTAAG
Left flanking sequence: Indices 114049 -- 114548
ATTCTCAAATGGTCTCGAGTCAAGGGAGAATGCCGCTGCTGTAAAGACTAAGATGTTCTCTTTCA
CATTACCGAGCTGGTAATTCTAGTTAGAAGCTTCACAGCTTCCTCCCAATACCAACTCTGCAAAC
CATGAAGTGAAAGATCGGACAAGACGTCGCTTAGATAAGAGGGGTCTTGAACCACCTCTTCCCCA
ATCACCGTACGGGAAAATTCTTGGATAGACCATTCGGCTGGCAAGGCCGTTCCGGTCGTTTCCAA
ATAGAAAGAAAAATGATCACAGATCGCAGTCAAAAGACTTTCTGGGTCATCGAAAGCAATAATGT
TACGATCATCTCCCATGTCCGGAAGGTGGGGTGAATTTTCAACATCGTCGGATCCTTCTGCAAGA
CCCGGAAAATCCTCAAAAAGACCATGAGTGTTGGCCAGAGTCTCGGATGATTGAGAACTCAAATC
GTTAATAGTCGTCGTCGGCTGATCCGTAGTATTCGTTATCGCAGT
Right flanking sequence: Indices 114618 -- 115117
CTCACTGGAACTAGAACTTGATGATCTCAATCTCAACATGATTGATTTTGATCAAAACAATTCCC
TCCAGACAGACCGTCAAGCCTGTAGGAGTAGTGAAGAAGAAATAGAGAATGGTTGGTTGTTGACC
AACAAAAGACATTTTTGGGCGTTCTCGATTCTCTTCTCTTACGCAATAAAGAGTTGGATGAAGCT
CCTAAACTCTCTTCCATCCCGCGGTTAAGCTCTCGGCCCGGACCTTGCTGATCTTGCTCCTGACT
CCTCTCTTTGCCTTTAGTGGGAGCTCTTATCAGACTGACGAATTGGTTAAGATTCTTTTCTTATT
AAGGTAAGGTCATCCAAGTAGAATAGATAGCATAGGCCTATGCCTTAGACTTATCCCCGCTAAAG
CTTCTACCTCCACAGGGGATTCGTTTCCAAGAGGTTGCTCGTCGACAATGGCAGTGCAGTGAACC
TGATAACTTGGGATACCTTTAAAGCAATGAAGGGATCATCTATTG
Found at i:150247 original size:18 final size:18
Alignment explanation
Indices: 150207--150248 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
150197 ACCGCCCCGC
150207 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
150226 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
150243 CATAGT
1 CATAGT
150249 TAACAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.24
17 1 0.05
18 15 0.71
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 149707 -- 150206
CTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACCATGCCTGTCTGTT
GGAGCGAATAGGATGATCGGGCCGAGGGCAGCCCCCTCTTCCCCTCACTCTCCTTTCCCTAATAT
GAACCTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGTCCGGTCGCCCTACGCGACTGGCGCGG
CCGAAAGGCGAAACTCTCGTCGTAGTTTGGCGACCTAAGGGGCGGACACCTTTTTTTGTTATCTA
AAGGCGAAGACTCTGAAGTGGGCGAACACTCGGCCCAGCGGGCGAACATGGCGGGCTCCGGCTCC
GCGCACCTGCTGACACCTTTCGAAGCACTTTCGAGTGTGCGCTTTCGTTTTCGAATGTGTCGTTC
AGCCTCACGAGTCTACAAGCCTTTCTCATTCCAGTGCTCGCCTTTTAGTAGGGGCCTTTAGTCTT
TTGATTAGAGTAGGGGTCCCGAGAGAGCGGAGCGTACCGCCCCGC
Right flanking sequence: Indices 150249 -- 150748
TAACAAGGTTGAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGAC
CGTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGA
AGGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGA
AAGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACA
CGATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTG
AATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCG
CATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGA
AATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGT
Found at i:221920 original size:29 final size:29
Alignment explanation
Indices: 221878--221997 Score: 195
Period size: 29 Copynumber: 4.1 Consensus size: 29
221868 CAGGAGACGA
*
221878 AGGAGCAAAGCAGCTCGACCGATAGGGAG
1 AGGAACAAAGCAGCTCGACCGATAGGGAG
* ***
221907 AGGAGCTTCGCAGCTCGACCGATAGGGAG
1 AGGAACAAAGCAGCTCGACCGATAGGGAG
221936 AGGAACAAAGCAGCTCGACCGATAGGGAG
1 AGGAACAAAGCAGCTCGACCGATAGGGAG
221965 AGGAACAAAGCAGCTCGACCGATAGGGAG
1 AGGAACAAAGCAGCTCGACCGATAGGGAG
221994 AGGA
1 AGGA
221998 GCTGTTTAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.34, C:0.21, G:0.37, T:0.08
Consensus pattern (29 bp):
AGGAACAAAGCAGCTCGACCGATAGGGAG
Left flanking sequence: Indices 221378 -- 221877
CGAACTAATGTTCATGGACACGTAAGAGAAGCAAAGCAAATAAGGTAGGTATATAGCGCCAAACG
AGGCTAAGAAGAAGATAGCATTAAGGAAGAGAGCAACTACGAGCGATGAAAGCGGAAGATTGAAT
ATGAATAAAAGAAGGACGCAACAAAATGAAAGATGAGAGCTGCTAGTTGTTGCCCTCCCGCGCCC
TTTGTATATAAAGGTAAGGATCTTCTTTTGCGAGACTCCATCAAAATCCGCCACTCGTTGGTTGG
AACTCAATTTTTTTTATTGAGACTATGCCTTCAATTCCATTCTTCGTTTCCCTAGTCGCTGTATT
CTTGCTCAACCCAACATGCATTTTATAGTGCCGTGCCGGGGCGATAGGCGCGCCGCAGTCACGCA
TTCGAGTAAGAGCTTTTGCCTTTCTTCGCTATGTAAATATAGGGCCGGAATAAGTGCAAGACCCT
CAACAAAAGAATGGATTAAGGTGATAGAATGTTATCAGGAGACGA
Right flanking sequence: Indices 221998 -- 222497
GCTGTTTAAAAAAAAGCTCTTTTTTTTTTCGTCAGCGGATTTCGCTCATCAAGTTCTTGTTTGAT
CTGCCACTCTTAGAACACCACAATATTCGTTGGGGTTAATGCTCTCTCCCCTCTCAATGGTGAAT
CGATCATTCGATATCCTTTTCCTTATGAGAGGACGGAATGGAATAAAAGTAATGAAACCCGCGAT
GGCTACTGAATAACCTCCTTTGACTTTCTCAATAATAAAGCCTTTGACTTTTGTATTCGTTTGCC
AAATCTTGTTCAGTTCCATCCAAGCTCGGTTTTGTCTGAATCTTCGTGGAAGAAGAAAAAGCGGT
TCACCAGCCACTACATCTGTGGATCCCACCAAATCATTAAACCTGGCGGCAGCTCGCTCTTTGAT
CAGTGATTCGCCGGCCACTAGATCGATGAAGAATCTCTCCAAAATTTGATCTTTGATCAGTGATT
CACCGGCCACTAGATCCAGGGATCCCACCTTATTCTCAAACCTGG
Found at i:240204 original size:6 final size:6
Alignment explanation
Indices: 240195--240235 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
240185 CAATCTCACC
240195 AATGAG AATGAG AATGAG AATGAG AATGAG AATGAG AATGA
1 AATGAG AATGAG AATGAG AATGAG AATGAG AATGAG AATGA
240236 ATATCCTGCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.32, T:0.17
Consensus pattern (6 bp):
AATGAG
Left flanking sequence: Indices 239695 -- 240194
CTAAGGTTACAGAAGCGTTCGCCAACTTTGATAGGTATAGCATTGCAAGCAAATAGAACAGAGGA
GAGCTTACCGTTTGTTTCTATTAGAGTCGCGAGCTTGTTGTAGTCGGTCAACAAACAAGAGAGAA
TCTTGCTGCTTACTTGCTATATCCCGCGTTCTTGCACGGCTCGGCTCGTTCTTCGAGCCCTGCTT
CTCCCTTCCCCCTCTCCCCGTTCTACCGTCCAAAACAAGGCCGTATGGAGTATAGCCAAGTGGTA
AGGCATCGGTTTTTGGTACCGGCATGCAAAGGTTCGAATCCTTTTACTCCAGATTATTCACACCC
GATCGGATCTGTCAAGATCACGAGGGAGCTGACGACTACAGGGAGGGGAAGCGGCTGACTGCTGT
CCCTGAGCCCAGCTTGTAGCAAGCCAAAAGTGTGACTTGAACCTACAGGGCCTTTTTTTTTTTCG
GTATGCTGCTCCGCGATTAAGGAGCAAGAAACTCTCAATCTCACC
Right flanking sequence: Indices 240236 -- 240735
ATATCCTGCGTCCGTTATCTCCTCATCTTCCTATTTATAAGCCACAGCTCACTTCTACGTTTCCT
ATTTCCCATAGAATCTCCGGGGCTTTCCTAGCCACTCTCGTTTTGTTTTTTTATCTTCTTTGTCT
GAAAATGGGTTTGATTTGCTTCACCTATTCGAATTTCTACAGATTCTTCTTTTATTCATCAAAGC
TCATCCTAATCTCCGCCGAGATTACTGCCTTAGCCCTGTCCTATCATCTGTATAATGGGGTTCGT
CATTTATTGACGGATTTTTCTTATCCAAAATCGGGCTCTCGAATTTGTTGTCTGTTTCAACGAGC
CCTTCCGTTCATCCCACTCTTTTTACATTGTCTGAGGACACTTTTATTTTATTCTGATTCAGATT
TTGTATTTTTTGGAGGATTCAAGACTTTTTTTGATAATGATAATAGGACTCCCTCCACCTCGTCC
GAATGGTTCACTTATACTTCGGATTTTGACGATGATTCGGCCAGT
Found at i:241048 original size:75 final size:75
Alignment explanation
Indices: 240810--241031 Score: 444
Period size: 75 Copynumber: 3.0 Consensus size: 75
240800 CCTCGAATGT
240810 GGCACCAGCTTCAGTGGGTACATCCGCGGGCCCAGCCCCCGAAAATAACAATAACCCAGATGTGA
1 GGCACCAGCTTCAGTGGGTACATCCGCGGGCCCAGCCCCCGAAAATAACAATAACCCAGATGTGA
240875 TTGCAGCAGG
66 TTGCAGCAGG
240885 GGCACCAGCTTCAGTGGGTACATCCGCGGGCCCAGCCCCCGAAAATAACAATAACCCAGATGTGA
1 GGCACCAGCTTCAGTGGGTACATCCGCGGGCCCAGCCCCCGAAAATAACAATAACCCAGATGTGA
240950 TTGCAGCAGG
66 TTGCAGCAGG
240960 GGCACCAGCTTCAGTGGGTACATCCGCGGGCCCAGCCCCCGAAAATAACAATAACCCAGATGTGA
1 GGCACCAGCTTCAGTGGGTACATCCGCGGGCCCAGCCCCCGAAAATAACAATAACCCAGATGTGA
241025 TTGCAGC
66 TTGCAGC
241032 GCTAGCACTC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 147 1.00
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (75 bp):
GGCACCAGCTTCAGTGGGTACATCCGCGGGCCCAGCCCCCGAAAATAACAATAACCCAGATGTGA
TTGCAGCAGG
Left flanking sequence: Indices 240310 -- 240809
AGAATCTCCGGGGCTTTCCTAGCCACTCTCGTTTTGTTTTTTTATCTTCTTTGTCTGAAAATGGG
TTTGATTTGCTTCACCTATTCGAATTTCTACAGATTCTTCTTTTATTCATCAAAGCTCATCCTAA
TCTCCGCCGAGATTACTGCCTTAGCCCTGTCCTATCATCTGTATAATGGGGTTCGTCATTTATTG
ACGGATTTTTCTTATCCAAAATCGGGCTCTCGAATTTGTTGTCTGTTTCAACGAGCCCTTCCGTT
CATCCCACTCTTTTTACATTGTCTGAGGACACTTTTATTTTATTCTGATTCAGATTTTGTATTTT
TTGGAGGATTCAAGACTTTTTTTGATAATGATAATAGGACTCCCTCCACCTCGTCCGAATGGTTC
ACTTATACTTCGGATTTTGACGATGATTCGGCCAGTTCGGGACGTAGTGGAAGTCTCCCATCTGT
CAATCAACCGATGCCCAGTGTGGAGGGAGCGGGGCCCTCGAATGT
Right flanking sequence: Indices 241032 -- 241531
GCTAGCACTCCGTTCAGAGATTCGTGCTTTAATAGAGGAGCGCTTCCGGGTGGAAAGCGATAAGG
TTCTCCGGGCCCCGCTTTCCCGCCTATTCCCCCATTGGATGACCCCATACCACCAAGATGCCGCC
CATCAATTACTGGTGGAACTCGAACTAGATGATGAACTAAACCCCGCTATCCTGCAGGAGTTTCT
TTCCAGATTCCAGTCTGATAGAAATTTCCTTAAGGCGGAGATCCGCCAGTGGGTGAGACAAAGGT
GGGGTAACTGAGAGAAGATAGAAGGTTCTTCAACCTGCAATAAAAGTGCTAATTAGAACATTGAT
TTGATTTGACTTCTTCTTGAATTATTTCATCCTTTCGATTTTCCTCTTTTTTTCTACGTTACTCA
GAAAATGGCACTCAGTTCATATCTTTAAGTTCGATCATTGACAAGGAAAAAAAGAAAGGGTGGGC
ATTTCCGTTTTCTTTTATCCGAAGCAATGCCCAAAGACTCCCATG
Found at i:295207 original size:16 final size:16
Alignment explanation
Indices: 295173--295211 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
295163 TTTCCTTTGC
* *
295173 AAGCCTCTTTCGTTGAT
1 AAGCC-CTTCCGTTCAT
295190 AAGCCCTTCCGTTCAT
1 AAGCCCTTCCGTTCAT
295206 AAGCCC
1 AAGCCC
295212 ATGAAATTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (16 bp):
AAGCCCTTCCGTTCAT
Left flanking sequence: Indices 294673 -- 295172
AATTTGCTTACCACTGGTAAGTATAAATTCATCTTTCTCAAAGTAATAGGCTCTTGGTTACGCTG
TTAGAGTGGCAGCTAAAGCGGTTCCCGCACTGAGGGATTTCGTTAAAAGTGGTAGAAGTTCCTCT
CCAGCTAAAGGAACTAAAAGAACAGCAGTAGCAACAGTAGCTATTGGAAGGGATCTCAGTTCTGC
AAAAGCAACAGAAACCACATCATCAGCAAAAGAAAGTCCTTCAGCAGCAACTCGTAACTCTCCAA
AGGAAGGGAAGGGGAATTGCTCCCCCAAACAAAGCCCCTACCCCTATTTATTGTGTTTACTTACT
GAACTTGTTAGTCCCTCGCTAAAGTGTCAACATCCTTAGCAAGATGAGCTGACTGGGCTGGCTTG
TCTGAAAAGGCTTTTATATGGGCTTGTATATGGCCCTCATATAGCGTGGATAAAGCTTTGATAGG
GTGGCTCCCTGTAATACCAGTAATAGCAAGAATTCTTTCCTTTGC
Right flanking sequence: Indices 295212 -- 295711
ATGAAATTCCAAGGCCTTCCACTAAGAATGGTGGATGAAGGTCAAATGAGAGAATTTCCCCTTGT
ACCTTTGAAGGAGCTATTGAGTTCTCTTTCCCCGAGTAACTCACTAGGGGGACAAGAGCTAAAAT
GAGACCACGAAAGAGCAATCCTGCGAGCAAGGAAGCTAGTGGGTTATCTGGGTAGAGTGCGGCAT
ATCTGGAAACTGAGGATTGTTACAACCTCCAGGCAGCGGAAGCGAAGAGTGAAATGAGAGGAAGC
GAAAACTATGGTTTTCTATAGGAAGTAGTGTGTAGGCTAGCACTTCGGGAGTCCAAGCTGGACCC
ATTGTCTCACTAGCTTCTGAAAGACGAAGAAGTATAACTCCCGTAGTATTGCTGCATGCATCTAC
TGAAAGAGAAGGGGGCTACCTTCAAATAAGCTGGATCATCCGGAGTGGCAAATTACCTCACTCAG
AATGGTATTCCCCCGATCCGATTGAGTCGTTTTTGTAGACCATTC
Done.