Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_048499
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: 301823
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Found at i:18192 original size:17 final size:17
Alignment explanation
Indices: 18170--18203 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18160 AAGAAAACTG
18170 TCTTAGTACAGCTTTAA
1 TCTTAGTACAGCTTTAA
18187 TCTTAGTACAGCTTTAA
1 TCTTAGTACAGCTTTAA
18204 GTGGTCCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (17 bp):
TCTTAGTACAGCTTTAA
Left flanking sequence: Indices 17670 -- 18169
CGATCACAGCCTCAGCTAGGATATATATGTAACCTTATATATATCTCAAGAGAGGACTGCTACTA
CACGGACTCTATACCAAGTCATGAGCGATAGCGAAGCCAAGCCGCCATCCCGGTGCCTTCCCGAT
GAAGCTTCCTTTGATTTGAATGAATGAGGAAGGAAGGCGCATGCAAGAGAAAAGAAAGCCCCTAT
TTGGGCATTCGGATTCGGAAGTTAGAGACTCAAGAGGTTGTTTGCCTGTGACAGGCTTATTGCTC
TTATGGTAAGGCAGTAGCAAGAAGCCTCCATCCATAGGGCTTAAATGCTACGGATTATATTATAA
GTGACTACTCAATCGATTAGCATAAACTAAGGGAAGAGGATTTTATCCGGTAACCTTCGGAAGGT
TTGTTCTCTAATGTGATATATAAGTAACTAACTTATTACTGCTTGCTTTAAAACCTCGAGAGACT
TGAGTATATAGGGCTCTGGAACATTTTACAGAGATAAGAAAACTG
Right flanking sequence: Indices 18204 -- 18703
GTGGTCCCTTTAATTTAACCGGTTGTCATACATGATGACAGAAAGCTTACATCGATGTTACTTTC
ACTTAGCCCGGAGATACCTGCCATCTTCAATGCTGGGAGGTGCTACTGCACATTCTACTTCCTCT
TTCTCCGTTTGACTTCTCATCTTTGTCATACTCTGACACTTGCTCTTGCTTGAGTATTTTTACCA
TTTTGGAGATTCCTTCATCTTATAAAGGTATATAAAACAGGATTGAGACTACGATCTCCGGTTAA
ATTAGCCACGTTCCAGCTAAAAGCTAGTCGAACGTTAGCCTGCCTTACGAGGGAGAATTCCCACT
GTTAACCAAAGCGCTGATCCTAGTGAGTCATATTCCACTTCCACTTTGTCTGCTATTCCAGTCTT
CCTCTTTCTTGTCGGCATAAGGACTGCCTACGGTTAGCTCTTCTTCAACTCCTGGCATAGTGTAC
AATAGACAATCTCAAAAAGAGAGAGTATCCACCCTTCCTACAATA
Found at i:18812 original size:14 final size:16
Alignment explanation
Indices: 18776--18812 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
18766 TCCCTCCCAT
18776 GGCTTTCTGCACGCAC
1 GGCTTTCTGCACGCAC
*
18792 AGCTTTC-GCAC-CAC
1 GGCTTTCTGCACGCAC
18806 GGCTTTC
1 GGCTTTC
18813 CTAGAGCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 9 0.47
15 4 0.21
16 6 0.32
ACGTcount: A:0.14, C:0.38, G:0.22, T:0.27
Consensus pattern (16 bp):
GGCTTTCTGCACGCAC
Left flanking sequence: Indices 18276 -- 18775
CCGGAGATACCTGCCATCTTCAATGCTGGGAGGTGCTACTGCACATTCTACTTCCTCTTTCTCCG
TTTGACTTCTCATCTTTGTCATACTCTGACACTTGCTCTTGCTTGAGTATTTTTACCATTTTGGA
GATTCCTTCATCTTATAAAGGTATATAAAACAGGATTGAGACTACGATCTCCGGTTAAATTAGCC
ACGTTCCAGCTAAAAGCTAGTCGAACGTTAGCCTGCCTTACGAGGGAGAATTCCCACTGTTAACC
AAAGCGCTGATCCTAGTGAGTCATATTCCACTTCCACTTTGTCTGCTATTCCAGTCTTCCTCTTT
CTTGTCGGCATAAGGACTGCCTACGGTTAGCTCTTCTTCAACTCCTGGCATAGTGTACAATAGAC
AATCTCAAAAAGAGAGAGTATCCACCCTTCCTACAATACTTGAATCAGTAAGAGCCCTTTCTACG
GGAACTCCATCAACAAGAAATTCCCTTTCGCCTGCTCCCTCCCAT
Right flanking sequence: Indices 18813 -- 19312
CTAGAGCTGTAGCTCTAATGTCTATATGTTCGAGGTTCCAGACAACAAGTGTCCAATTACCGCTG
GTTTCAACCGGTGTGAAGTGTGAAGTTTCGCGCACGCAACCCACCCGCCCAGCTAGAAGCAATGT
AGGCAAGTCACATTGCTTACCCTTGGAGTTAGTCGAACCGGAGGCGAAAGAGATCGGGTCGAGCC
GCTACAAACAGATCAAAAAGACCTATCTCGTAGGTCACATGCATGGTTTAGAGAAGGATGATGAT
CTATTGTGTATGCAGGGATCGATACTGTGATAAAAGAAAAGAGTAGGATCTAGGCTCGCGCTTGC
TGACTCAGATGCTTAGGATCCATTTATTATGGAGGAGGAAGTCTTTGATGAGGTGGGGCCCCACT
TCAGGGGGAACATGGGCGAGGAAAATCCTTTCTCTTAGAAGAGGATTTCATACCTTTTTCAGGGC
CAGCAGAGAAGAGGAGTAATCGCATGCGAGGGGGAGTCTTATAAC
Found at i:54626 original size:5 final size:5
Alignment explanation
Indices: 54616--54648 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
54606 GGGAAGAGAA
54616 TATTC TATTC TATTC TATTC TATTC TATTC TAT
1 TATTC TATTC TATTC TATTC TATTC TATTC TAT
54649 AAAGGCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTC
Left flanking sequence: Indices 54116 -- 54615
TTGGAGCTTTTAAAACACCAGTTGCAGTAGGAAGACCCCCTGACCCCAGGGAAAACATCTGTCCT
TATCGCTTTATAGTGCCACAAGAAGTGACAGAGGTAGAGGGAGAGGGTCAATTCTCACTAAACGT
TCCTCTAGCTCTAGTAAGGCACCATCACCAGCGCACATGAGAAAAGGCCAAGGAGAAGGTGAGAG
GAAGGTTCAAACACCAGGCTACACAGCCCTAAACTCAAGCAATGATTTATTGTAGCTATTGAGTT
TAGTACACCGTACTCAAACCTATACCCACTCTCATACCCTACGGTAAGTGAAAGGAAGCAGTACA
TTCCACTTTTAAGGGAGGAGCTGAAAGATAGACCTTCCTCTTGAAACATGGGGTGAAGTATTGGG
GAGTTACACAGCCACAGTTGGTCTTATATCCCTACCACCAAGACCAACAGCTGCGGATTCAATAG
AGAGAGAGAGAATTCCTATTGAGTTAGCTTTCCTGGGGAAGAGAA
Right flanking sequence: Indices 54649 -- 55148
AAAGGCTATACCACCCCAGAAGATCAGACATCATTCTCGAAAAGCAGCTACCGGGTGATAATTAC
AAACTACCAGCTGACAGCTACACGGATTCACCACTACTTATGACTTATTACTCCTGCTCCTAGAC
AAACTAAGAAGCAAGGAAAGAGGAACTATATATATAAGATATCAGATCTGTTATCCGCAACAACT
CTAACTCCTTACTCAGGAACTACCTAGCTACCGGTAAATCCGAGATTGGATTGAGATAGGCCAAG
ACTGGATTGAATGCATCTCTCCTGTAATGGGTTCACTCGGGTCTAAGACCGCACGGGAATGCATC
TAGTCAATTCATGGTCATCAACATTTCTTAGACCTTGATCTTAAGATCTTAAAGCGGTGACTTCA
GCGACTTGCTCTCATTCTTTTCTCAAACAAAGGACTTCGAACTCAATAATGCTAGTTTAGTTCCA
CCCTTGATCGCCCGTCTGTAATCTGTAATAGGGCACTCTGGGAAG
Found at i:133751 original size:15 final size:15
Alignment explanation
Indices: 133731--133779 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
133721 CAAACGGCCG
133731 TTAAAAGAAAGGCGT
1 TTAAAAGAAAGGCGT
*
133746 TTAAAA-AACGGCCG-
1 TTAAAAGAAAGG-CGT
133760 TTAAAAGAAAGGCGT
1 TTAAAAGAAAGGCGT
133775 TTAAA
1 TTAAA
133780 CGGCCCGGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.20
Consensus pattern (15 bp):
TTAAAAGAAAGGCGT
Left flanking sequence: Indices 133231 -- 133730
CCTAGCCCTTGACTCATGGTAGAGAACACCAAAGGGTACTGCTCGCTTTGTTTCTCTTTATGTGG
GGACGAGAACAAACTGACTATAAATCTGCAGAATCCACTACCCGCTCCTGCTTCTTGGTCACCAG
AAGGGTAATTAGGATCTGCTGCTGAACCAGATATCCCGCCCCTTACGACCAGTAATCGATATCCC
TCACAGCGAGCCAACAAAGAATGAAAGAAGGAAAGGTAGGCAGGCTCAACAAAAGCTGCAAACTA
AGGCTCAGAAAACTTGTGCAATCTAAAGAAGAAAGAGTTAAAAATAATCTAATTGATCGAATCTA
TTCGTGGAATTAGAGGAGGGGCTATCTATCTAATTCAAAAAAGTAATTCGTACCGGTACCGCACT
CTTTCAATCAAATACCGCTGGCAGATCCTGGTAATTATAACAGGCACATCTTATCTTCCTTAAAC
TTCACTCCTGAGACCTACCTTAAACAGCCAGCCATCAAACGGCCG
Right flanking sequence: Indices 133780 -- 134279
CGGCCCGGCCGGGCTTGAAACCAACTTCATGGGCTTCCTTCCCTGCTCGTGCTATCATTGGGGCC
ATATTCTCCTATACTATCTTCATGACGAGCACTTACATTACTAGCTCCCTCAACGTAAAAGGGAA
AGAAACAAGGACTTACTCAACTCTATTGACTCTACTTACTTCCCTTACTGGACAGGATTATCAAC
TAAACTAACGACTGACTCGCTTGAGAGCTTAACTACATTACTACAATTTTCACACTTAGAAAACT
CACCTACTAACTAGCCCTTATACTCGTTCCATTTATTCCACTCGCTGACTTTTCTATTAAAATAG
TCTGTATTGACAAGAGGTTTTATCCTCGATCCTTCAGTTAGCTTGCCCAATCACTGGCAACTATT
TCATAGCCTCCTCTGGCAACAGGTTCCTCTTCTTTATGTAACTATACTTTATCTCTCTGCACTGG
CTTGGCTTTCTAATAATCTCTTTCCTTGCCTACGGGATGTGTACA
Found at i:133755 original size:29 final size:29
Alignment explanation
Indices: 133722--133779 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
133712 GCCAGCCATC
133722 AAACGGCCGTTAAAAGAAAGGCGTTTAAA
1 AAACGGCCGTTAAAAGAAAGGCGTTTAAA
133751 AAACGGCCGTTAAAAGAAAGGCGTTTAAA
1 AAACGGCCGTTAAAAGAAAGGCGTTTAAA
133780 CGGCCCGGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.24, T:0.17
Consensus pattern (29 bp):
AAACGGCCGTTAAAAGAAAGGCGTTTAAA
Left flanking sequence: Indices 133222 -- 133721
CAGTGGATTCCTAGCCCTTGACTCATGGTAGAGAACACCAAAGGGTACTGCTCGCTTTGTTTCTC
TTTATGTGGGGACGAGAACAAACTGACTATAAATCTGCAGAATCCACTACCCGCTCCTGCTTCTT
GGTCACCAGAAGGGTAATTAGGATCTGCTGCTGAACCAGATATCCCGCCCCTTACGACCAGTAAT
CGATATCCCTCACAGCGAGCCAACAAAGAATGAAAGAAGGAAAGGTAGGCAGGCTCAACAAAAGC
TGCAAACTAAGGCTCAGAAAACTTGTGCAATCTAAAGAAGAAAGAGTTAAAAATAATCTAATTGA
TCGAATCTATTCGTGGAATTAGAGGAGGGGCTATCTATCTAATTCAAAAAAGTAATTCGTACCGG
TACCGCACTCTTTCAATCAAATACCGCTGGCAGATCCTGGTAATTATAACAGGCACATCTTATCT
TCCTTAAACTTCACTCCTGAGACCTACCTTAAACAGCCAGCCATC
Right flanking sequence: Indices 133780 -- 134279
CGGCCCGGCCGGGCTTGAAACCAACTTCATGGGCTTCCTTCCCTGCTCGTGCTATCATTGGGGCC
ATATTCTCCTATACTATCTTCATGACGAGCACTTACATTACTAGCTCCCTCAACGTAAAAGGGAA
AGAAACAAGGACTTACTCAACTCTATTGACTCTACTTACTTCCCTTACTGGACAGGATTATCAAC
TAAACTAACGACTGACTCGCTTGAGAGCTTAACTACATTACTACAATTTTCACACTTAGAAAACT
CACCTACTAACTAGCCCTTATACTCGTTCCATTTATTCCACTCGCTGACTTTTCTATTAAAATAG
TCTGTATTGACAAGAGGTTTTATCCTCGATCCTTCAGTTAGCTTGCCCAATCACTGGCAACTATT
TCATAGCCTCCTCTGGCAACAGGTTCCTCTTCTTTATGTAACTATACTTTATCTCTCTGCACTGG
CTTGGCTTTCTAATAATCTCTTTCCTTGCCTACGGGATGTGTACA
Found at i:133763 original size:14 final size:14
Alignment explanation
Indices: 133722--133765 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
133712 GCCAGCCATC
133722 AAACGGCCGTTAAA
1 AAACGGCCGTTAAA
*
133736 AGAAAGG-CGTTTAAA
1 A-AACGGCCG-TTAAA
133751 AAACGGCCGTTAAA
1 AAACGGCCGTTAAA
133765 A
1 A
133766 GAAAGGCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (14 bp):
AAACGGCCGTTAAA
Left flanking sequence: Indices 133222 -- 133721
CAGTGGATTCCTAGCCCTTGACTCATGGTAGAGAACACCAAAGGGTACTGCTCGCTTTGTTTCTC
TTTATGTGGGGACGAGAACAAACTGACTATAAATCTGCAGAATCCACTACCCGCTCCTGCTTCTT
GGTCACCAGAAGGGTAATTAGGATCTGCTGCTGAACCAGATATCCCGCCCCTTACGACCAGTAAT
CGATATCCCTCACAGCGAGCCAACAAAGAATGAAAGAAGGAAAGGTAGGCAGGCTCAACAAAAGC
TGCAAACTAAGGCTCAGAAAACTTGTGCAATCTAAAGAAGAAAGAGTTAAAAATAATCTAATTGA
TCGAATCTATTCGTGGAATTAGAGGAGGGGCTATCTATCTAATTCAAAAAAGTAATTCGTACCGG
TACCGCACTCTTTCAATCAAATACCGCTGGCAGATCCTGGTAATTATAACAGGCACATCTTATCT
TCCTTAAACTTCACTCCTGAGACCTACCTTAAACAGCCAGCCATC
Right flanking sequence: Indices 133766 -- 134265
GAAAGGCGTTTAAACGGCCCGGCCGGGCTTGAAACCAACTTCATGGGCTTCCTTCCCTGCTCGTG
CTATCATTGGGGCCATATTCTCCTATACTATCTTCATGACGAGCACTTACATTACTAGCTCCCTC
AACGTAAAAGGGAAAGAAACAAGGACTTACTCAACTCTATTGACTCTACTTACTTCCCTTACTGG
ACAGGATTATCAACTAAACTAACGACTGACTCGCTTGAGAGCTTAACTACATTACTACAATTTTC
ACACTTAGAAAACTCACCTACTAACTAGCCCTTATACTCGTTCCATTTATTCCACTCGCTGACTT
TTCTATTAAAATAGTCTGTATTGACAAGAGGTTTTATCCTCGATCCTTCAGTTAGCTTGCCCAAT
CACTGGCAACTATTTCATAGCCTCCTCTGGCAACAGGTTCCTCTTCTTTATGTAACTATACTTTA
TCTCTCTGCACTGGCTTGGCTTTCTAATAATCTCTTTCCTTGCCT
Found at i:133775 original size:14 final size:14
Alignment explanation
Indices: 133729--133775 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
133719 ATCAAACGGC
133729 CGTTAAAAGAAAGG
1 CGTTAAAAGAAAGG
*
133743 CGTTTAAAA-AACGG
1 CG-TTAAAAGAAAGG
133757 CCGTTAAAAGAAAGG
1 -CGTTAAAAGAAAGG
133772 CGTT
1 CGTT
133776 TAAACGGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.19
Consensus pattern (14 bp):
CGTTAAAAGAAAGG
Left flanking sequence: Indices 133229 -- 133728
TTCCTAGCCCTTGACTCATGGTAGAGAACACCAAAGGGTACTGCTCGCTTTGTTTCTCTTTATGT
GGGGACGAGAACAAACTGACTATAAATCTGCAGAATCCACTACCCGCTCCTGCTTCTTGGTCACC
AGAAGGGTAATTAGGATCTGCTGCTGAACCAGATATCCCGCCCCTTACGACCAGTAATCGATATC
CCTCACAGCGAGCCAACAAAGAATGAAAGAAGGAAAGGTAGGCAGGCTCAACAAAAGCTGCAAAC
TAAGGCTCAGAAAACTTGTGCAATCTAAAGAAGAAAGAGTTAAAAATAATCTAATTGATCGAATC
TATTCGTGGAATTAGAGGAGGGGCTATCTATCTAATTCAAAAAAGTAATTCGTACCGGTACCGCA
CTCTTTCAATCAAATACCGCTGGCAGATCCTGGTAATTATAACAGGCACATCTTATCTTCCTTAA
ACTTCACTCCTGAGACCTACCTTAAACAGCCAGCCATCAAACGGC
Right flanking sequence: Indices 133776 -- 134275
TAAACGGCCCGGCCGGGCTTGAAACCAACTTCATGGGCTTCCTTCCCTGCTCGTGCTATCATTGG
GGCCATATTCTCCTATACTATCTTCATGACGAGCACTTACATTACTAGCTCCCTCAACGTAAAAG
GGAAAGAAACAAGGACTTACTCAACTCTATTGACTCTACTTACTTCCCTTACTGGACAGGATTAT
CAACTAAACTAACGACTGACTCGCTTGAGAGCTTAACTACATTACTACAATTTTCACACTTAGAA
AACTCACCTACTAACTAGCCCTTATACTCGTTCCATTTATTCCACTCGCTGACTTTTCTATTAAA
ATAGTCTGTATTGACAAGAGGTTTTATCCTCGATCCTTCAGTTAGCTTGCCCAATCACTGGCAAC
TATTTCATAGCCTCCTCTGGCAACAGGTTCCTCTTCTTTATGTAACTATACTTTATCTCTCTGCA
CTGGCTTGGCTTTCTAATAATCTCTTTCCTTGCCTACGGGATGTG
Found at i:166293 original size:21 final size:21
Alignment explanation
Indices: 166267--166308 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
166257 CATACCCTGT
166267 TACGGATATTACAGATGTAGA
1 TACGGATATTACAGATGTAGA
166288 TACGGATATTACAGATGTAGA
1 TACGGATATTACAGATGTAGA
166309 GACAGATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
TACGGATATTACAGATGTAGA
Left flanking sequence: Indices 165767 -- 166266
CAGATTTTTTCTTTGCCGATATCCGGAACAAGGGAATCCGAGATGCCGACCTTGACGGATATAAC
TTTCTTGAATCGTGATAATGTTGGGAATTGCTGTATTTCATAGTTATTTAAAAGTTAGCGTCTTA
TTTGGGAGCCGCCTCGGGATCCCCGGGATTCGGGATCCTCCACATTTTATTCTATTTATGACTTT
TTTTTGTAACTATCTTAATCCTTAATTTTGAAATAAGGATCTGAGCGATGAGCGATCTTGTGATA
AAAAGTCCCGCTTAGTCCGTCACCTCGTCCTCACTTACCACCAACCCACTCGCCTCCAATACTTT
CTTACCTCTCCGAGAATTGAGGTTGAGCGAGATTCAGTCTTCGATAAGCCAGCCAGCCCTTATGA
TGATGGGCGTGATCCATAGCCGATGTTGGCTATAAGCAGTATCAGTTGAAGCTATGGAGCACCCA
CCCCTTCCTTCCAGTTTCAGATCGATATTGAGTTCCATACCCTGT
Right flanking sequence: Indices 166309 -- 166808
GACAGATCCAAAGCCATTTGATCGAGATCGAGTAGCTATAGCAGATCCATTTAGAGATCGGAACC
TGGGTACACCCATTTTTGTATAAACAGCCCCTAAGCCGGTAGGTCTCGTTCAAAAGCCACTTTTG
TTGATGTGTCCCAATCCATGTGCTCGGTAATGATGTTGTCATCGCTGATGCGCAAGTTGCTGAAG
TTTATTTTCAGTGTCTTCATAAACTAAAAAATATCTTATTTCTTACACTGGTGCATTTGAGTTTG
CTAAGCGCTTTTGCGTCAAGGGTGGATTTATCTGCCATGTCTGCTCGTTGTTTGCTTGCTTACCA
TCATCCATATGGTCTGATGGCTATATTTAAATAATTTCCATTCATTACGAGGGTTCTCTACCTTA
GTAAGGATAGGTGGTGGAGGGGGTCCTTGCCAAACTCAGTCATACAAGATCTCGTCACTTTGAGC
GGGTTCTTGCTATGTACACCAAGCCTCGGGGGTGTAGCGGTTGCT
Found at i:171938 original size:18 final size:19
Alignment explanation
Indices: 171904--171939 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
171894 GAAAGAAGAA
*
171904 TGCACCAAAATGCAGGTGC
1 TGCACCAAAACGCAGGTGC
171923 TGCACC-AAACGCAGGTG
1 TGCACCAAAACGCAGGTG
171940 GTTGTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (19 bp):
TGCACCAAAACGCAGGTGC
Left flanking sequence: Indices 171404 -- 171903
AAAAACAAAGCAATGCCAAGAGCTCCGTCAATCCGCTGTTCATCGATAGACGAAGCTCTCTCTTT
ATCATATCGTGCCAGATGCAACAAAGGATGAGTCCTTCTTTTTCCTTCTCGCGAACCACGGGAGC
GCCTAGCACCCAGAGGAGCTAAGCTAATTATCCTTTCAGGGTAAAGCGGCGCATAAAAAAGGGCT
GGCCCGTCAAACGTTCGGTTCCGGGAGAGATAGAATGGAGTTCTTCACGAAGTTCGAGACAAAGT
CATACAAAACTTCTCTATGGCCTCCTCGTTTTGAGACATTATGGCTTTGGGGTCGACCCCGGTAA
CAAAGAAGGAATCCATAAAAACGTGGGATCCGACACCATGATAAAATACTACCCTCATGATTAGA
CCATGTCCCTGAGATTTGATAAAAGAAAGGTGCATTAGCGGTTAATACGTTGTAATTGGATAAGT
TATTAGGAATATGACGGAACGAAAGACCGAGGAAAGAAAGAAGAA
Right flanking sequence: Indices 171940 -- 172439
GTTGTTTCTTGTTGTAAGTGAATGCAACGAAAAGACCCGGAAATAACGATAAATGAAAGAATTCA
TATATTATGTACATTTCGTGCTCTGCTCATTTTTAAATTTCTGCTTTGTTATTCCCATCATCCGG
TAACCACAGGATGATCCACAAGAAAGGTGGCAGGATTCGAACCTATGGCCGGCCCGCCCCTGACC
TGCTCTGCTGGGTTGGGTGGCCGGGTTAGCACCCCTCGTCGCCCCTGTACCCGAAACAGATGCGC
TGCGCTACCCAGCGCGTAACCTTGTCTCCCCTACTCCTCTTCTGGTTGGTTATGCCATTACCAAT
CGCGGGCCGGGCCGGCCGCCCCTGACCTAATAAGATAAGAACTATTATCCTTATGACCAAACAGC
GATAGTTTCACGATCCCGACCAGCAACTTGTTGGGAGTAGGGGCATCCAAGCTTGCCCAACCTAG
ACATTGTAACTGAAAGTCCTGCCTACTTGTAGGCTTAGGGTAGTC
Found at i:177732 original size:19 final size:19
Alignment explanation
Indices: 177708--177747 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
177698 AACCGAAGTC
177708 AATATTATAACAGAACTGG
1 AATATTATAACAGAACTGG
177727 AATATTATAACAGAACTGG
1 AATATTATAACAGAACTGG
177746 AA
1 AA
177748 AGGGCATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (19 bp):
AATATTATAACAGAACTGG
Left flanking sequence: Indices 177208 -- 177707
TCTAGCTATGCTTGGAGCTTGCAATCCTTGAAAAAGCCCAACCCGCACATTGCTCTATTAACTGC
ACCTGCCTTCGGTCTTAGTTCGTAATGACAAAATTTATTCTTTGAAGGAAGAAAGCTTGGGGACT
GATTCACTGACTTCACCACCAGCAGCGGATAGGAAAAAGTCTTTGACTCTTCTTCTAGCTAACCA
CTGCTTTAGACTATTCCTACTATTCATAGTTCTCAATCTTACTTTTATCGTCCAAGTCTTTTAGA
GTATTGTCTTATATAGTAAGGTAAGTATATAAAGAAAGAATAAAGTAAAGCTTTCCTAAAGGGAA
AGGAGTGAATTATTTGAATACTTCTTCCTCTTTCCCTTCTTTTCAAGCTCTTACTCTTACTGGCG
CAGATAAAGTCTTTCTTACGGCCAGACGACTTAAACACAGCGCTCTGATCTCCGACCTCCAAGGA
CCCAAGCAAAGGATTGACTTCGCTAACCTCAGCTTAACCGAAGTC
Right flanking sequence: Indices 177748 -- 178247
AGGGCATACCTTGAATACAGATCAAGATTCACTCATGCACTCTGGAACTGACTTAGGAAAGCTAG
CCTTAGCCCTAAAATAAAGGAAGGCGGCCGAGCCGAAAGCCCTACAAAGAATATCGCTTATGAAC
AGGCCCAGGGGTTGTCAGTTGAGAAGGAAGTCTTTATTGAATTGATCATAGAAAAAAAGGATAGA
AATGGAATCGGTTGTTTAAGTCGGAAGATCTGATGTTTTGAGCGGAGAATCGGGTTCTGCTAAGC
AGAAAAGCCTTCTCTAATCTAACGGGTCGATTCGAAATGGGAATGGAGTTTGAGGCTAGTGGAGC
AAGCATGAATAATAAAAGGAAAAAGCCAAAATGAGTGGAAAGAAATTCAAAGCAAAGCCACCACC
GCCGAATAGAACCGACGAGTAATATCCTGTCCTTCCCTACCTACTGTATTCAAGCGAACAAGCTA
TAGCACTTGAGAATGAAGGGGGGAAAAAGCCACAACTGGATGATA
Found at i:258141 original size:30 final size:30
Alignment explanation
Indices: 258107--258178 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
258097 CTAAAACCGG
* *
258107 AACCTCCGGGGCAGCGGGGGGTAATTCCCA
1 AACCTCCGGGGCAGCGGGGGGCAATCCCCA
258137 AACCTCCGGGGCAGCGGGGGGCAATCCCCA
1 AACCTCCGGGGCAGCGGGGGGCAATCCCCA
258167 AACCTCCGGGGC
1 AACCTCCGGGGC
258179 TACCCGAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.19, C:0.35, G:0.36, T:0.10
Consensus pattern (30 bp):
AACCTCCGGGGCAGCGGGGGGCAATCCCCA
Left flanking sequence: Indices 257607 -- 258106
AAGTTTTCATTTTACCCGTATGGAGCACTTAGTCAAAAACGTTACGTTACGATATTAAACAGGCA
GGTTGCCCCCCGTCCTTTCTTGCTATCGGTCCCACACAGTGCAGTGCCGCTACCCACCTCTACTC
TGATCTATTCCTATAGCCATAGATCATAGTTTCTTACCGCCGTCATAAGACGTTGGAAGGCCCGT
GTGTCTCGGGTACCCAACCGGTAGATACTTCGTAGATGGGAGCGGTACTGCCGCAAGGATAGTGC
CCTGCCTTGAGGGTAAAAAACAATCCCTCTTATCCGGTGTCGGTTAAGCAAGATCCGACTCGGAT
TGAACCCGCCATGGACTAAAGCGGCTTCTATTAACCTCTCGATCTGGCTTTGGACCGATATAGTT
TCCGCTATTCGCCGTAGGGGCGGGTTTTCCCCTAGAGTATTGACCAAGAACCGAGCGTAAAGCTC
GGCCTCCCTTTGGGGGTCCGGTATCATTAGATGTGCTAAAACCGG
Right flanking sequence: Indices 258179 -- 258678
TACCCGAACCCCCACAACAGGCGGTGAAGGAGGTCCCTCCACACCTCCCACCCCATCGCTACATG
CGATGTCCCCGGCAGCGAGACCAAATAAAAATAAAAAAAGAATATAAATTTCGAAACTCGTAAAA
TAAAAAAGGGCTATTCTAGCCCTGTGGAAAGCTAGTAAAACTTGTCGTTTCACATTTCCACCTAT
TTGTTCGTTTACCAGGTTCGGCACGAAATCATAAATAAGCTCTACCAAGGATTGCCAAGCATTGG
GTACTGACTTTCCTCCTCCCTTTTTAGTAACAAAATGAACCAGCAGTAAGACCAAACTGAGAGTG
AGCAGCATAAACAAAGAGGGATTTGTGAATGAGAAATACAAGTCACCTATCTTCATAGGAAGAAA
AGGGATTATCTCAAATTGTTCAAGAGGGCTGGGTATAGGAAACACCCCCGACTCTAAGTAAAAGT
CTAAGTAAAAAAAGTTCATCTTGACGGCAAGTTAAGTTAAAATTC
Found at i:298969 original size:3 final size:3
Alignment explanation
Indices: 298961--298995 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
298951 TCTAACGCAT
298961 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
298996 TGGGAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Left flanking sequence: Indices 298461 -- 298960
AAGCCAGTGTCAACCAACCGGACTCTCCCAACCCTAGTGAGCCCCCGGCGCCAGCGACTGAATAT
AACCCCTTGCTGGGGGACGGGCAGAGGCGCCAAGAACTCAAGGATCGTCTCGCTATTAACTTAGT
CGGGAATACCCTTGGTGTTCGGGAAAATGACATACTGGATACACAATACGAGATAGAGATTCGTA
TTGAAAAAGCACTAAGGTGGGACAGATTTTCGGATAATTCCCTTATAGAGAGCCGGCATCGTATA
AGGGGGGTCCTATTCTACCCCTATGGCCGGCCCCTCTCATTGAACACCTATCAACGGCACCTCCA
ATTCATGGATAACTATGGAACGCACCACAGCGTGCCCTATAAGCGGGTGATGGACGCGGTTTATT
CCAAGTATTCCATAAATCTAAATAAGGGTTAGTTGGAGAACCATCGTTCCAGACTTATTAACAGA
TTGCCCCATTCATTCTTGAATCTGATGCTAACAGTTCTAACGCAT
Right flanking sequence: Indices 298996 -- 299495
TGGGAATATAAAAGAACTCCCACACTAAGTGAATAGTCTTCCCCCTACCTATCTATCTGTTTTGC
TTTCTTCTAGATCACAGACGTTTTAATAACCACCTGTCTTGCTGCCAAGAGGGGGGTATTCGAGA
ATAAGCTAAACAAGCCCTGGTTCGGTTAACAGGTAATGAAGGTAGTCCCTAGGAGAGGATTGAAT
CCCTTTCATACGCTATTCCTCGATGCGCACTTGACACGCAAAGAAAGATAAAAAGCAGTATAGAA
GACATTAGATCCTGCGGTACATAAAACTTTTATTAGATCCTGCTTAGGGGTTCAGTACCACCATT
AGGTCCAGGTACTTAGTGCTCCCATTTCCGTTGATTGGACAACTGGCCTGCATTAATGGTGCTCC
CTTACCTTCTCTCGTTGGGAAGTCATTGAGGTGCTTTCATTTTGGTGAGCAGTAGATAGATACCA
AGGTTCTCCTTTCTTTGCCAGGAGATAGGAAATACTTGGTGTAGC
Done.