Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_065223
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: 290970
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Found at i:33527 original size:31 final size:29
Alignment explanation
Indices: 33474--33549 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 29
33464 GTTGGAAAAA
* *
33474 AAGTAAAACTCCCTCTCCCTAAC-AGTCGAGT
1 AAGT-AAACTCCCT-TCCCTAACAAGT-AAGC
*
33505 AAGTGAAACTCCCTTACTCTAACAAGTAAGC
1 AAGT-AAACTCCCTT-CCCTAACAAGTAAGC
33536 AAGTAAACTCCCTT
1 AAGTAAACTCCCTT
33550 TGAATCTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 11 0.28
31 25 0.64
32 3 0.08
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.24
Consensus pattern (29 bp):
AAGTAAACTCCCTTCCCTAACAAGTAAGC
Left flanking sequence: Indices 32974 -- 33473
ACTTTAGGAGAGTCATATTTTCTGGTACGTCCATCTACTTATAAGCGGCCGGCTATGTTCTCTAA
ACTCATCTATTTCCTCTCGGCTCTCAGCGCAACGAGAAAGGATTCCCCAATAGCTGAGATTGGTA
CTAGAATTCGCGAATCTAGAGAGCACCAACGATGTTGACCGGGAGGGAAAGGAGCAATTAAAGCC
TTTCATCTCAATCAAATGACCGAAATGGAGACTCTATTCTTGTTGGCAAATGCAAATACGAATCC
ACTGATTTCCATCCCCATGTTCTCTGAGCAATGACCTTTGTTTCCAACAGTAATGGAGATTTGTT
GCAAACTGTCTCCGAATCCCGTGCTTTTCAAGTAAGCACCAACTCCTGTGATGTGTATTCCCCTC
CAGAGTCTGTCCTCAAACATGGCTTTCTTTGCCTTGACTTTATAAGTTTCATTCTCCACTAAGCT
TCTGAACTCTATGAATTTTTGAAAGATTTCGGACCGTTGGAAAAA
Right flanking sequence: Indices 33550 -- 34049
TGAATCTTATCCATTGAAGAAGACAGACTTCAAGACTGAAACCCGCCCTTTATTATTATATTATT
AGTAAGATAGGTTTGGAACTCGGGCTATAGTTATACTATATGCCCGGGCTTTTCTCGCTTGTTGC
TTTCTTTCTTCGCATGCTTTCGCGCATTTTTAAAAAATTTTTCTTCTGGGGCGAACTCCCTATCT
TGATCGAAGTCCTGAAAGGCTTGGTTATGGTAGTCCCTCGGTCTATAAGATGTAGGCTTATCAAG
CTGAGGGAATTGCATAGTCAAGAGGAACTAAGTGCTGGTGATCGGAGCGTGGGGAACTCAGGCCG
CTGGTAGTAGAGGCAATGCAATTGAACCAATTTCCTTACACTCTAGCTGAGGGAGAGACTTTACC
TTTACTTAGAGAGGGGCAGCAATACTACTATGCTCTTCGGTGCTCGTAGGTTGACTTCCCTTATG
CACCCAGCCGCTTCACTAATGTGAATAGGTTATACAGAAGGGTGA
Found at i:36108 original size:39 final size:39
Alignment explanation
Indices: 36065--36143 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
36055 CGATTTTCTA
* *
36065 TTCACTCATGATCTGGCCTGGTCGACTCGATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
36104 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
36143 T
1 T
36144 GAAGGATGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (39 bp):
TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
Left flanking sequence: Indices 35565 -- 36064
GCCCACACCTGTGTAGAGTAGATCGTTCAACACCTGCGGCACAAACCTATTTTTGACCTATTGGT
CCTAGTATCATAGGCGACCGAACGGCCGCCCCCTAATTACTAGACCAACCTGCTATAATAATTCC
ATAAACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATGTTCGAATCTGACAATACCA
TACCATAATCAAAAGGTACAACGGCCCGAGCAACCAGACTTAACATAAATGTAGTCACTGGAGCC
ATTCTAAAAAGGGAGAAATTAGCACTACTTGGTGAAATAGGTTCTTTTAGAATCAATTTCAAACC
ATCCGCTAGAGGTTGTAACAATCCGAACGCTCCCACTACATCAGGACCCTTTCGACGTTGCACAA
AAGCCATTACTTTACGTTCAGCTAGCACTAAAAAGGCTACTCCTAGTAGAAGTGGTAGAATTATT
CCAAGTATTTCGGCTGGAACAGCTATGTACGTTTTCGATTTTCTA
Right flanking sequence: Indices 36144 -- 36643
GAAGGATGGGACCTTTTCTCGAAAAACTCCGGATCGAGTTGAAGGTGGTGCAACATCGAATCTTG
TTACCTTACTTCGAATGGAATCTTAGCCCGCCTCACTTGCTTTCTGTACTGCATAAGGTTCTGAA
AGAAAGTAAAGGGATTTCCTTCTAACTAGTGGCTGAGAGTAAGCAAGCTACCTTCATTCAACAGA
TTTGTGGTTGAGTCAATAAGGGTCGGGAATCTTTGCTCTTCTCTTTTGCATTTCCGCTGCCTGCG
TTCTTCTTCGTGTCCGTACGTATCGCAAAGCTGGTCGACGCCAGCTGTAATGGTTCATTTCGGGA
GTTTGAACACCATCCCAAAAATACAACCCTGTCAAAGGTATTTAACCTTCCTTCCTTCTGAGTGG
AAATCCAATCCCGTTTTGTCTTTTTTGCATAAAAACCAAACTAATAATATATATATATATTTCTT
TTAAACCCGTTCTTCCGACCCCTCCAAAAATGACCTTCTCCAGTG
Found at i:98782 original size:18 final size:18
Alignment explanation
Indices: 98761--98797 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
98751 GTCACGGCCG
98761 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
98779 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
98797 A
1 A
98798 CAAGAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATCGTCACTATCATCA
Left flanking sequence: Indices 98261 -- 98760
TACTAATCGATAGGGCCTCATCGGTAAGTGCTACAAGATCTCGTACATTGGAACCCATGGTTATG
GACCCGAATCCATTAGTATAGAACATTTTCTTTTCCAAGTGAAATCCCCTAGTATATGAAAGAGT
GAAAAAGTGCTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCATGTATTTAATTTAT
TCGGAGCTATTAGAGCGGGATCCACTTTTTGGGGAATATGAGTCGAAGCAATAACAAGAATATTT
CTAGTGGAACATCTTTCACAATCCCTGGAGAGATAGTTCACTAATAAACCGAGGGATAAGTAATT
CGACTCATTCACATCCAGATCATGAATGTTTGGAATCCATATTATGCAAGGAGACATTGCTTTTG
CTAATTCGAATTGAAGGGTGATATAAAATAGGTCTATTTCCGGCATCATATCCATAGTTAGCGCA
TTCATCATAGTTAGAAGCTCCAGCTCCGTATCAAGGTCACGGCCG
Right flanking sequence: Indices 98798 -- 99297
CAAGAAAACCCTTGGGCTTGTTATCCAGGAACTTGTTCAGAAATACTGTAATGAAAGGAACATAG
GAGTTTGTCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCTATCACTAAAAT
ACCCCTAGAGAGGGATAGGGCTAAACGGAGCGAAAAGGGTTTTCCATGAGATGGGAAATGAAAAC
TATTAGCCCCACAGGAGGTTTGTGAATAAGTGATTGTCTGATAATGAGCAAGGAATATCCGCCTT
TCTGCTAAACAGGATGTATTGAACTCATAATTCATTAGATACTTTTTATGAATGTCAACTAAGTA
TCGTAAGTAAATTGCTCCCGGTTGTTCAATCATTTGATAACCAGAGTCATTCTTTGATAAATGAT
CACTATGAGTCAGACTCAATAGAATTTGATCAATCCTTTTTTCTGTCGTTAAGGTGGAGAACTGA
ACCAAGAATTCTCTTTCTTTATCACCAATCGAATCACTGTTCGAG
Found at i:110829 original size:18 final size:18
Alignment explanation
Indices: 110789--110831 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
110779 ACCGCCCTGC
110789 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
110808 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
110825 CATAGTC
1 CATAGTC
110832 AACAAGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 110289 -- 110788
GAAAGCTTTTTTTTCAAGTGTCAGTAGCGGAACGTTCTGTCAATCGGGGAAGGTTTTTGGTGACA
ACACCTGGAGATATCAGAAGTGAGAATGCTGACATGAGTAACGAAAAATCCTGTGAAAAACACGA
TCGCCTGCCAGTGGAAGGCTTTCTGCGTTCAGTCAATCTACGCAGAGTGAATCGGTCCCTAAGGA
ACCCCCGAAAGGGCTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACC
ATGCCTGTCTGTTGGAGCGAATTGAATGATCGGGCCGAGGGCAGCCCCCTCTTCCCCTCACTCTC
CTTTCCCTAATATGAACCTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGCCCGGTCGCCCTAC
GCGACTGGCGCTTCAAAAGACGAAACTCTCGTCGTAGTTTGGCGACCTAAGGGGCCTTTACTCTT
TTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 110832 -- 111331
AACAAGGTTTAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:117592 original size:26 final size:23
Alignment explanation
Indices: 117544--117596 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
117534 AGGAATGGGT
117544 GAACGGGAAACCTGTTGTTAGGA
1 GAACGGGAAACCTGTTGTTAGGA
117567 GAACGGGAAACCTGTTGTTAGGA
1 GAACGGGAAACCTGTTGTTAGGA
*
117590 GGACGGG
1 GAACGGG
117597 GCCTGTTGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.40, T:0.19
Consensus pattern (23 bp):
GAACGGGAAACCTGTTGTTAGGA
Left flanking sequence: Indices 117044 -- 117543
GTTATTTAAAACCAATAACAACGTAAAAAACACGTGGTTTTGCATGTAGGTGAAGGGTCAAATTG
ATCAAAAAAGGAACGCTCTCACTAAGTAAAACGGCTTTTCTAGGTTTTGTAGCTAGGGCTAGATG
GATTTCGTGTCAAAAGAAAAACGAGTGAAAAGACCATTTCAAGCAAAAAAGACGGGGTTTTAGAC
TTTTTTCCAAAAAGCATGCCACTTCACTTCTTATTCACTTCCTCACTTTGTTTACTTCGTAACCT
TTGGTATTGCGTCTCATCCAGGTGATTAATATCACGTCATAGCATTTCTTCCCCTGCTTCTGAAA
GAAAAGAATCATATGACTTACCTAGGCGGTTGTACCACTTGAAAGGTGACATTGAAGAAGCTGAA
TCGAAACTTATACGATATTGTAGAGAACCACTCTGAGTCTTTATTCCCCTAGTCTTCTTCGCATC
CTTACTTACCTCCTTATACTACTGTAAGCATATGAAGGAATGGGT
Right flanking sequence: Indices 117597 -- 118096
GCCTGTTGCCAAGGAGAACGGATAACATGGAAAGACAAGGAATACAAGGAAAGACAAGGAAAGCG
TGGGAGTTGCCGGGGTAACCTCCCTCTCCGGTCGAGTAACCTTCTACCTCTCCTTGTTGCCGAGG
AATGGAATTCCTATTAAAATTCCCGGGAAAGTCGACTTTGTTCGATAGTTCCCATCTCTCGATCA
CCCCACAAGAGAAGCCACTCGAACGAATAGCTCCTTTCTTGCCGTGGAATTCCTCAAAGCTATAA
TATAAATGGAATTCTCCCTTGACTCGATCTTTAAAAAAATTATGGAATTCTCTACAAGAGCTGCG
GAACTAACGACTCTATTAGAAAGTAGAATTACCAACTTTTACACGAATTTTCAAGTGGATGAGAT
CGGTCGAGTGGTCTCAGTTGGAGATGGGATTGCACGTGTTTATGGATTGAATGAGATTCAAGCTG
GGGAAATGGTTGAATTTGCCAGCGGTGTGAAAGGAATAGCGTTGA
Found at i:117653 original size:10 final size:10
Alignment explanation
Indices: 117625--117659 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
117615 CGGATAACAT
117625 GGAAAGACAA
1 GGAAAGACAA
*
117635 GG-AATACAA
1 GGAAAGACAA
117644 GGAAAGACAA
1 GGAAAGACAA
117654 GGAAAG
1 GGAAAG
117660 CGTGGGAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.57, C:0.09, G:0.31, T:0.03
Consensus pattern (10 bp):
GGAAAGACAA
Left flanking sequence: Indices 117125 -- 117624
TCTCACTAAGTAAAACGGCTTTTCTAGGTTTTGTAGCTAGGGCTAGATGGATTTCGTGTCAAAAG
AAAAACGAGTGAAAAGACCATTTCAAGCAAAAAAGACGGGGTTTTAGACTTTTTTCCAAAAAGCA
TGCCACTTCACTTCTTATTCACTTCCTCACTTTGTTTACTTCGTAACCTTTGGTATTGCGTCTCA
TCCAGGTGATTAATATCACGTCATAGCATTTCTTCCCCTGCTTCTGAAAGAAAAGAATCATATGA
CTTACCTAGGCGGTTGTACCACTTGAAAGGTGACATTGAAGAAGCTGAATCGAAACTTATACGAT
ATTGTAGAGAACCACTCTGAGTCTTTATTCCCCTAGTCTTCTTCGCATCCTTACTTACCTCCTTA
TACTACTGTAAGCATATGAAGGAATGGGTGAACGGGAAACCTGTTGTTAGGAGAACGGGAAACCT
GTTGTTAGGAGGACGGGGCCTGTTGCCAAGGAGAACGGATAACAT
Right flanking sequence: Indices 117660 -- 118159
CGTGGGAGTTGCCGGGGTAACCTCCCTCTCCGGTCGAGTAACCTTCTACCTCTCCTTGTTGCCGA
GGAATGGAATTCCTATTAAAATTCCCGGGAAAGTCGACTTTGTTCGATAGTTCCCATCTCTCGAT
CACCCCACAAGAGAAGCCACTCGAACGAATAGCTCCTTTCTTGCCGTGGAATTCCTCAAAGCTAT
AATATAAATGGAATTCTCCCTTGACTCGATCTTTAAAAAAATTATGGAATTCTCTACAAGAGCTG
CGGAACTAACGACTCTATTAGAAAGTAGAATTACCAACTTTTACACGAATTTTCAAGTGGATGAG
ATCGGTCGAGTGGTCTCAGTTGGAGATGGGATTGCACGTGTTTATGGATTGAATGAGATTCAAGC
TGGGGAAATGGTTGAATTTGCCAGCGGTGTGAAAGGAATAGCGTTGAATCTTGAGAATGAGAATG
TAGGGATTGTTGTCTTTGGTAGTGATACCGCTATTAAAGAAGGAG
Found at i:196474 original size:17 final size:17
Alignment explanation
Indices: 196447--196479 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
196437 ACTTGTGTCA
196447 GGGTAAAGCCCCCTTTAT
1 GGGTAAAG-CCCCTTTAT
196465 GGGT-AAGCCCCTTTA
1 GGGTAAAGCCCCTTTA
196480 GAGATAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 3 0.20
18 4 0.27
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (17 bp):
GGGTAAAGCCCCTTTAT
Left flanking sequence: Indices 195947 -- 196446
ATCGATCCTTAGTAATCGCGGGCCCCTAGTTGTTCACATAGATTTTTGCAGGCTCGAATAGGTGG
TTGGCTGCTGCGTCGTCGGAAGGGTCTTTTCCTTTGCTTGCGTAAGTTACCCTGCTTGCTATTCT
ATCACCCCTCGCCCGGCCTTTACTTGATTGATAGGGCTCCTTCACCAGGATCAATAGCCCAGCTA
CACTACCACTACCCGTAAGATAGAAGTAGGGCACTTCACTCACCTCAGAGAATGCACTACCTATC
TGTAATCAGTTCAGCTTAGAGTTGTTTGCTGACACACGCTACTATCACGCTGGTTGCTGCTTTCA
CTCGGATTCTCCTCGGGCGGATCAAGGGATATTGGCTTGGCTTGCGAAAGAACTTATAGTTGCAG
GATGGTTGGTTGACAGGTGTCTGGCTAGCAAAGAACCAGACAAAAAAAAACAAGTACAGTAGCGC
TATAGGCTATTTGATATAGTATAGCCGCGGAGACTACTTGTGTCA
Right flanking sequence: Indices 196480 -- 196979
GAGATAGGAAAACGGCCTAGCTGCTTTATTGAGGCAACATTGAGAATTTTAAAAAGAATTTGCTG
CTATTTCAGTGGTTGAAGTGCCGGTCGGCATTGCCTAAGTAACGTCCGACACTGTTTGCGCGCTT
CTCTCCTCTTCATTCAATGCAAAGACAACCGCCTGAGCGTCGCGTCTGACTCCAGCATCAGAGAA
GAAAGGCCCATATCTAATGCTTGCTTCAACCCGCACGAGATTGCCAAAATCTCAACGAGAGGAAA
CTCCGGCGCCCATACCTTTTGGTCTACACACCAAATCCTAATTAGCAAGATGGATCTTCCTCTTA
TTTTTACCAAAAAAAGTTTTTCTGTTTAGCTTGTCAAGCCTAGAGCACACAGAAATAAGCAACTT
GCCTATCGATATTAGGAGAACATAAGATATTCTATTTCTCAAAGCGCCCTGAAACCATGCAAAAA
TCATCCAAACACTTTCTCTCAGCTTGAGAGCCTCAGAGAAACTGA
Found at i:224249 original size:28 final size:28
Alignment explanation
Indices: 224217--224327 Score: 172
Period size: 28 Copynumber: 4.0 Consensus size: 28
224207 TGTGCCAATT
224217 GATAATAAATCGAGGGATGCAAGAGCTC
1 GATAATAAATCGAGGGATGCAAGAGCTC
224245 GATAATAAATCGAGGGATGCAAGAGCTC
1 GATAATAAATCGAGGGATGCAAGAGCTC
224273 GATAATAAATCGAGGGATGCAAGAGCTC
1 GATAATAAATCGAGGGATGCAAGAGCTC
** *
224301 --TAATATTTGAGAGGGATGCAAGAGCTC
1 GATAATAAAT-CGAGGGATGCAAGAGCTC
224328 TAATATTTGA
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.08
27 17 0.22
28 56 0.71
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.20
Consensus pattern (28 bp):
GATAATAAATCGAGGGATGCAAGAGCTC
Left flanking sequence: Indices 223717 -- 224216
GGATCAAGATGCCCATTTACGATGCGGAGTTTACGAGTCAAAAGCCTGAAAGGGAGGATGAAGCA
GCTGAGTCCATTGAAGCATTGATTGGCCGTGGATTGGGTGGCATTGGTTGCAATAAGTGCTTGTT
GTTCTGGGGGCAGAAAGAGAATGAATATATCTCTTAAATAATGTCATATTAAGGTGCCTTGCATC
CTCTCCATAACCAACTACCCCCGGTTAAAACAGCTTATTACTTTATTTCATTCCAGTTTCATCTG
CTGCTCAAACAACTGCCCCCGCTCGTCGAGCCTCGCATCCCTGAGCCTCTGCCCGTATGCGGAAG
AGAATCTGTTCTGACGAATCAATCTCTTTATGAGAGAAAACCCACGGTAAAGTACGCTTTTGGTC
AAAAGATAAACTCGTTTACGAGGAAATCCATTGAAAAACCACGGAGATTGGTGGCAATGTGCGCT
GAAGGAGATGCTTAAAATGCCGCTCTCGAATCCGCTGTGCCAATT
Right flanking sequence: Indices 224328 -- 224827
TAATATTTGAGAGGGATGCTCTGTTGTTAAGCGGAAAGCTGTTAAAGAATCTTATTAAACTATGT
CAAGCGTTGTTGATTATAATGCTTACAGAGACGAATGTAGGCCCTTTAAAGTCAATCTTTCCCAG
CCTTGTGTATCTTTCGCTATCGAGTACTAAAAAGTGGCATAAAAAGCCCGGTATTACTTCACTTC
GTCAGCGCCTTTCACTACGTTATTGAGCTTACGATCACATGAACGGTATTGATCAATTCAGATGC
ATAAAACCTTAGGATGCGGATATTACACTTTCAGTGCGTTTAAATGCACTGATTTTCATCGTGTC
AATTCTTGTTATGTTGCTATACGCCCTACAACCAGTCGCAGTTGTTTAGCTTTAATATTCTTACT
AACCGGAGGGGGGTTTGTCTAATTCTCTGATCCCGGCGACTATTGTGAAATACCGGCATAGATAA
ATCTTTCTTTCGGGCGGTTCATAAAAATCATACTGCTTACCCACG
Found at i:224322 original size:27 final size:27
Alignment explanation
Indices: 224218--224346 Score: 145
Period size: 28 Copynumber: 4.7 Consensus size: 27
224208 GTGCCAATTG
*
224218 ATAATAAATCGAGGGATGCAAGAGCTC
1 ATAATAAATAGAGGGATGCAAGAGCTC
*
224245 GATAATAAATCGAGGGATGCAAGAGCTC
1 -ATAATAAATAGAGGGATGCAAGAGCTC
*
224273 GATAATAAATCGAGGGATGCAAGAGCTC
1 -ATAATAAATAGAGGGATGCAAGAGCTC
**
224301 -TAATATTTGAGAGGGATGCAAGAGCTC
1 ATAATAAAT-AGAGGGATGCAAGAGCTC
**
224328 -TAATATTTGAGAGGGATGC
1 ATAATAAAT-AGAGGGATGC
224347 TCTGTTGTTA
Statistics
Matches: 97, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
26 6 0.06
27 36 0.37
28 55 0.57
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (27 bp):
ATAATAAATAGAGGGATGCAAGAGCTC
Left flanking sequence: Indices 223718 -- 224217
GATCAAGATGCCCATTTACGATGCGGAGTTTACGAGTCAAAAGCCTGAAAGGGAGGATGAAGCAG
CTGAGTCCATTGAAGCATTGATTGGCCGTGGATTGGGTGGCATTGGTTGCAATAAGTGCTTGTTG
TTCTGGGGGCAGAAAGAGAATGAATATATCTCTTAAATAATGTCATATTAAGGTGCCTTGCATCC
TCTCCATAACCAACTACCCCCGGTTAAAACAGCTTATTACTTTATTTCATTCCAGTTTCATCTGC
TGCTCAAACAACTGCCCCCGCTCGTCGAGCCTCGCATCCCTGAGCCTCTGCCCGTATGCGGAAGA
GAATCTGTTCTGACGAATCAATCTCTTTATGAGAGAAAACCCACGGTAAAGTACGCTTTTGGTCA
AAAGATAAACTCGTTTACGAGGAAATCCATTGAAAAACCACGGAGATTGGTGGCAATGTGCGCTG
AAGGAGATGCTTAAAATGCCGCTCTCGAATCCGCTGTGCCAATTG
Right flanking sequence: Indices 224347 -- 224846
TCTGTTGTTAAGCGGAAAGCTGTTAAAGAATCTTATTAAACTATGTCAAGCGTTGTTGATTATAA
TGCTTACAGAGACGAATGTAGGCCCTTTAAAGTCAATCTTTCCCAGCCTTGTGTATCTTTCGCTA
TCGAGTACTAAAAAGTGGCATAAAAAGCCCGGTATTACTTCACTTCGTCAGCGCCTTTCACTACG
TTATTGAGCTTACGATCACATGAACGGTATTGATCAATTCAGATGCATAAAACCTTAGGATGCGG
ATATTACACTTTCAGTGCGTTTAAATGCACTGATTTTCATCGTGTCAATTCTTGTTATGTTGCTA
TACGCCCTACAACCAGTCGCAGTTGTTTAGCTTTAATATTCTTACTAACCGGAGGGGGGTTTGTC
TAATTCTCTGATCCCGGCGACTATTGTGAAATACCGGCATAGATAAATCTTTCTTTCGGGCGGTT
CATAAAAATCATACTGCTTACCCACGGTACTACTGAGCTAACTCC
Found at i:271444 original size:21 final size:21
Alignment explanation
Indices: 271418--271458 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
271408 CCATAACCAA
*
271418 CTCGAGAAAAGAGTTTATAGC
1 CTCGAGAAAAGAGTCTATAGC
271439 CTCGAGAAAAGAGTCTATAG
1 CTCGAGAAAAGAGTCTATAG
271459 TGGTATCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (21 bp):
CTCGAGAAAAGAGTCTATAGC
Left flanking sequence: Indices 270918 -- 271417
TCGATCATGGCATACGAAACTGCCCTTCGTATGTCTTCTTTATTAACCAATATGTTTTTTTGCAC
TAAGAGTACATATGCTTTTTCAATCATATTATCTTCGATCCCCTTACACCGATCCATTATACCAG
CTATCTGCTGATACACGGGGTCCTCGACCCCCCCACGCTGTTCGTGCGCCGCGTGGATATTCGCC
TGGATGAAGATGTCCGCCCAGTCGCCTACCTCTAGGTTAGGCATCGGCATTGCTTTTTGAGGGGC
AGTGACCCCTGTTTTTATGAAGGGGCTTAGGGCATCCCATAATAGGCCTCCCCCGCGCCCACTCT
GCGAAGAAGAAGAGGGGTCCTGTGGCGCGATTTTCGATGGTTCTTTCTCTTTCCGTTCGATCGAT
GTCTCCGGCGAAGAGTTCAAATATTTTTTCCAATCGCCGGAGTTTCCATTCGAAGTTGTCGGTTG
AGAAGGCCCCCCTTCTTCCATTAGCAAGGGCCTCCCCATAACCAA
Right flanking sequence: Indices 271459 -- 271958
TGGTATCACATTTGACACCTGAGGAAGGTACAGCCCAACTATGAGGTACATCAGCAGGTGTTACA
ATAATACGTAGATGAGTTTTGGCTGGTACAACCACTCTATTGTCCACTTCTAATAAACGTGATTG
ACCCAATTCTAGATCATCTTCTGGAATCGTATAACTGTCAAAAGTGAGTGACTGTTCATCGGAAC
TGTTATAGTCTGAATACTCATAAGTCCGATACCATTGATGTCCATAGCTTTGATAGTAATGGCTG
GATCGACTACTACCTCGTCCATTGAGTATAACAGAGCAAATGATGGTATAGCAATGAACATCGGG
ATGATACTAGGAATATGGTCCGAAGAATCTCGATAGTAGTTCCATGAACAATCCTTTGCGGGATT
GGATTTTTTTTATAGTGGAAATGCCATAAAGCGCGAACCAAGATCCGTGATACGAAAACAAAATA
AGAATGAGGAGAAAAAGATATCGTGATGTAAGTCCATTATTCCTT
Found at i:281929 original size:11 final size:12
Alignment explanation
Indices: 281910--281935 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
281900 GTAACCGGTG
281910 AAATAAAAAAGA
1 AAATAAAAAAGA
281922 AAATAAAAAAGA
1 AAATAAAAAAGA
281934 AA
1 AA
281936 GAAATTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAATAAAAAAGA
Left flanking sequence: Indices 281410 -- 281909
TAAATGATGTTAGGATCGGCCGGCTCGTTCTCGGAATCCTAAAATAAAACAGAGACAGAACGGAT
TGTTTCAATGACATATCTAATCAGACTGAATAGGATTTGAAGAGCTGTCACGATCATTCACATCA
ATTTCAGCAGGCAGGAAGGGCGCGGAAGCTACCGTTTCTAGAATGCAAGCAAGGTAGCTTGCTTA
CTCTCCTAGTAGCGTACGTTGGCGGCAAGGAAGGAGGCATTGGAAAAACTAGACCATACTAAAGT
AAAGAGGCATTCGGGAAGCTACTAGTCGCTTCTGGCGAAGCTTATAGAAGGCCGACCGCTACATA
GAGAGATCCATATACTATACCAGTCATGAGCGATAGCGAAGCCTAGAGAGGCGGAAGCAGTAGCT
TCTAGGACGAAGCCGAGCCTATAGTCGGGCGAAGGAAGCGAGACCAAGCCGAGCCACTAGTGGAG
TGGCGAAGGAGGCCTACTATACGTATACTGGATTAGTAACCGGTG
Right flanking sequence: Indices 281936 -- 282435
GAAATTTCAGTGAACTATTGAACAGTGTGATTGATCAGACAAGTACCAAGGGCTTTCGGTAGACT
TCTTTCATTTCCGAATTAGCTTGCGAAAAGTCCTTGCATTAGTATGAGTTCGTTGACCGCGTAAG
GGCAATCCATCTTGATGACGAATTCCACGATAACAAGAAATAGAAATTAATCGTTCGATGTCTGC
TCGTTCTCCCCTCTTCAATTCCCAATGAACAACATGATCTTGACCTATCATTTGTTCAATTTGGT
CGATCTGATACTTAGTTAACTCTTTTATCTTTATGTTCCCACTGATACCTAATCGATAACGAACC
TGAATGGCTTTTTTAGGTCCAATTCCATCAATTTTTGTTGAGGCAATTCTTACTTGTTCATCGGC
AACTGATCTAGCTCCTGAAATATATGACATTCTTGATCCTTCCTTTTACTAGTCTTCTCGGCTGG
AATCAAAAATGGGGTGTCTCCTCTCTGATGATCTTTTCTATAGGT
Done.