Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3290
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42336
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:6868 original size:39 final size:40
Alignment explanation
Indices: 6823--7046 Score: 224
Period size: 40 Copynumber: 5.7 Consensus size: 40
6813 GCTCCTCGTT
* * * *
6823 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
6863 C-AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
6902 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
6942 CAAAGGCCTTCGGG-CTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
6981 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
7022 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
7047 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.01
39 65 0.42
40 77 0.50
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:6916 original size:40 final size:38
Alignment explanation
Indices: 6790--7046 Score: 200
Period size: 40 Copynumber: 6.5 Consensus size: 38
6780 AAATCACGTA
* * *
6790 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCG--CACAATG
* * * *
6829 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAATG
*
6868 CCTTCGGGACTTAACCCGGATTTAATGACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCAC-AATG
*
6908 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCAC-AATG
*
6948 CCTTCGGG-CTTAACCCGGAACTT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCAC-AATG
** * * * *
6987 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAATG
*
7027 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
7047 CAGCATTCAA
Statistics
Matches: 180, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
38 4 0.02
39 78 0.43
40 89 0.49
41 9 0.05
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (38 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAATG
Found at i:6979 original size:79 final size:78
Alignment explanation
Indices: 6823--7046 Score: 213
Period size: 79 Copynumber: 2.8 Consensus size: 78
6813 GCTCCTCGTT
* * *
6823 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGA
6888 TTTAATGACTCGCA
66 TTTAAT-ACTCGCA
* * * *
6902 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACTTAACCCGG
6966 AACTTGT-AT-CTCGCA
65 -A-TT-TAATACTCGCA
* ** * * * * * *
6981 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAACTCA-CACAAGGCCTTCGGGACTTAACCCG
7045 GA
64 GA
7047 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
78 3 0.03
79 88 0.73
80 24 0.20
81 4 0.03
82 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGA
TTTAATACTCGCA
Found at i:7055 original size:41 final size:41
Alignment explanation
Indices: 6978--7055 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
6968 CTTGTATCTC
* * *
6978 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
7019 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
7056 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:8980 original size:45 final size:44
Alignment explanation
Indices: 8916--9080 Score: 179
Period size: 45 Copynumber: 3.7 Consensus size: 44
8906 GATCAGAGAG
*
8916 TGCCATGGTGTCTTTCAACCATGGTCTTATTTATTCTCGTCTTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATT-TCGTCTTGA
* * *
8961 TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTTCGTCGTGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATT--TATTTCGTCTTGA
* * *
9007 TCCCATAGTGTCTTTCAACTATGGTCTTATTTATTT-GATTTGTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTTCG-TCT-TGA
* * * *
9052 TGCTATAGCGTCTTTCAGCTATGGTCTTA
1 TGCCATAGTGTCTTTCAACCATGGTCTTA
9081 CTCGATAGAA
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
43 1 0.01
44 5 0.05
45 57 0.56
46 36 0.35
47 3 0.03
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (44 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTTCGTCTTGA
Found at i:9019 original size:46 final size:46
Alignment explanation
Indices: 8918--9042 Score: 180
Period size: 46 Copynumber: 2.7 Consensus size: 46
8908 TCAGAGAGTG
* * *
8918 CCATGGTGTCTTTCAACCATGGTCTTATTTA-TTCTCGTCTTGATG
1 CCATAGTGTCTTTCAACCATGGTCTTATTTATTTCTCGTCGTGATC
* * *
8963 CCATAGTGTCTTTCAACCATGGTCTTATTCATTTTTCGTCGTGTTC
1 CCATAGTGTCTTTCAACCATGGTCTTATTTATTTCTCGTCGTGATC
*
9009 CCATAGTGTCTTTCAACTATGGTCTTATTTATTT
1 CCATAGTGTCTTTCAACCATGGTCTTATTTATTT
9043 GATTTGTGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 29 0.41
46 42 0.59
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (46 bp):
CCATAGTGTCTTTCAACCATGGTCTTATTTATTTCTCGTCGTGATC
Found at i:9097 original size:45 final size:45
Alignment explanation
Indices: 9062--9219 Score: 235
Period size: 45 Copynumber: 3.5 Consensus size: 45
9052 TGCTATAGCG
*
9062 TCTTTCAGCTATGGTCTTACTCGATAGAATCGTGATGCCATAACA
1 TCTTTCAGCTATGGTCTTACTCGATAGAATCGTGATGACATAACA
* * * *
9107 TCTTTCACCTATGGTCTTACTCAATAGAATCATGATGACATAACG
1 TCTTTCAGCTATGGTCTTACTCGATAGAATCGTGATGACATAACA
** *
9152 TCTTTCAGCTATGGTCTTACTCGATAGAATTTTTATGACATAACA
1 TCTTTCAGCTATGGTCTTACTCGATAGAATCGTGATGACATAACA
*
9197 TCTTTCAGCTATAGTCTTACTCG
1 TCTTTCAGCTATGGTCTTACTCG
9220 TTTCTAGTAT
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 101 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (45 bp):
TCTTTCAGCTATGGTCTTACTCGATAGAATCGTGATGACATAACA
Found at i:20573 original size:27 final size:27
Alignment explanation
Indices: 20543--20750 Score: 167
Period size: 27 Copynumber: 7.7 Consensus size: 27
20533 TTACCCTATG
*
20543 GGGGTATTTCAATAATTTTACCCATTA
1 GGGGTATTTCGATAATTTTACCCATTA
*
20570 GGGGTATTT-TAGTAATTTTACCC-TTCA
1 GGGGTATTTCGA-TAATTTTACCCATT-A
* * * *
20597 AGGGTATTTTGATAATTTTAGCCA-TC
1 GGGGTATTTCGATAATTTTACCCATTA
* *
20623 GAGGGTATTTCGATAATTTTATCC-TTCG
1 G-GGGTATTTCGATAATTTTACCCATT-A
* * **
20651 GGGGAATTTTGATAATTTTACCCATCG
1 GGGGTATTTCGATAATTTTACCCATTA
* *
20678 GGGGTATTTCGGTAATTTTACCCA-TC
1 GGGGTATTTCGATAATTTTACCCATTA
*
20704 GAGGGTATTTCGGTAATTTTACCC-TTCA
1 G-GGGTATTTCGATAATTTTACCCATT-A
* *
20732 AGGGTATTTCAATAATTTT
1 GGGGTATTTCGATAATTTT
20751 TACGACCTTT
Statistics
Matches: 148, Mismatches: 22, Indels: 22
0.77 0.11 0.11
Matches are distributed among these distances:
26 4 0.03
27 141 0.95
28 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (27 bp):
GGGGTATTTCGATAATTTTACCCATTA
Found at i:20614 original size:54 final size:54
Alignment explanation
Indices: 20544--20750 Score: 213
Period size: 54 Copynumber: 3.8 Consensus size: 54
20534 TACCCTATGG
* * *
20544 GGGTATTTCAATAATTTTACCCATTAGGGGTATTTTAGTAATTTTACCCTTCAA
1 GGGTATTTCGATAATTTTACCCATTAGGGGTATTTCAGTAATTTTACCCTTCGA
* * * * *
20598 GGGTATTTTGATAATTTTAGCCA-TCGAGGGTATTTC-GATAATTTTATCCTTCGG
1 GGGTATTTCGATAATTTTACCCATTAG-GGGTATTTCAG-TAATTTTACCCTTCGA
* * ** * *
20652 GGGAATTTTGATAATTTTACCCATCGGGGGTATTTCGGTAATTTTACCCATCGA
1 GGGTATTTCGATAATTTTACCCATTAGGGGTATTTCAGTAATTTTACCCTTCGA
* * *
20706 GGGTATTTCGGTAATTTTACCC-TTCAAGGGTATTTCAATAATTTT
1 GGGTATTTCGATAATTTTACCCATT-AGGGGTATTTCAGTAATTTT
20751 TACGACCTTT
Statistics
Matches: 125, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
53 4 0.03
54 119 0.95
55 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (54 bp):
GGGTATTTCGATAATTTTACCCATTAGGGGTATTTCAGTAATTTTACCCTTCGA
Found at i:20683 original size:81 final size:81
Alignment explanation
Indices: 20544--20750 Score: 247
Period size: 81 Copynumber: 2.6 Consensus size: 81
20534 TACCCTATGG
* * * *
20544 GGGTATTTCAATAATTTTACCCATT-AGGGGTATTTTAGTAATTTTACCCTTCAAGGGTATTTTG
1 GGGTATTTCGATAATTTTACCC-TTCAGGGGAATTTTAGTAATTTTACCCATCAAGGGTATTTCG
*
20608 ATAATTTTAGCCATCGA
65 ATAATTTTACCCATCGA
* * **
20625 GGGTATTTCGATAATTTTATCCTTCGGGGGAATTTT-GATAATTTTACCCATCGGGGGTATTTCG
1 GGGTATTTCGATAATTTTACCCTTCAGGGGAATTTTAG-TAATTTTACCCATCAAGGGTATTTCG
*
20689 GTAATTTTACCCATCGA
65 ATAATTTTACCCATCGA
* * * * *
20706 GGGTATTTCGGTAATTTTACCCTTCAAGGGTATTTCAATAATTTT
1 GGGTATTTCGATAATTTTACCCTTCAGGGGAATTTTAGTAATTTT
20751 TACGACCTTT
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
80 3 0.03
81 103 0.97
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (81 bp):
GGGTATTTCGATAATTTTACCCTTCAGGGGAATTTTAGTAATTTTACCCATCAAGGGTATTTCGA
TAATTTTACCCATCGA
Found at i:20979 original size:17 final size:18
Alignment explanation
Indices: 20957--20991 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20947 TATCTGTGTG
*
20957 GGGCCCACGA-GCCCATT
1 GGGCCCACAAGGCCCATT
20974 GGGCCCACAAGGCCCATT
1 GGGCCCACAAGGCCCATT
20992 TCGGCCCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.20, C:0.40, G:0.29, T:0.11
Consensus pattern (18 bp):
GGGCCCACAAGGCCCATT
Found at i:22168 original size:25 final size:25
Alignment explanation
Indices: 22119--22172 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
22109 TGAACCTCTA
*
22119 ACCTCCTTACCACACCTGTGACGCC
1 ACCTCCTTACCACACCTATGACGCC
* **
22144 ACCTCCTTGCCACACCTATTTCGCC
1 ACCTCCTTACCACACCTATGACGCC
22169 ACCT
1 ACCT
22173 TGCCACTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.19, C:0.48, G:0.09, T:0.24
Consensus pattern (25 bp):
ACCTCCTTACCACACCTATGACGCC
Found at i:23946 original size:21 final size:21
Alignment explanation
Indices: 23905--23946 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23895 CATTTGAGTG
* **
23905 TGTTGATTGTAGTTCTGTTGT
1 TGTTGATTGTAATTCCCTTGT
23926 TGTTGATTGTAATTCCCTTGT
1 TGTTGATTGTAATTCCCTTGT
23947 CTAGGATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.24, T:0.55
Consensus pattern (21 bp):
TGTTGATTGTAATTCCCTTGT
Found at i:26302 original size:681 final size:679
Alignment explanation
Indices: 24987--27015 Score: 3373
Period size: 681 Copynumber: 3.0 Consensus size: 679
24977 CTCAACTTTC
* *
24987 TAAATTTATGGTCGGCCACCCATGGAAGATGATTCAAAAGATGGAAACTCCTATTTTTAGCAAAC
1 TAAA-TTATGGCCGGCCACCCATGGAAGATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAAC
*
25052 TATCTCTCTCTCCTCACCTATAAATAAGACCCTCTCATCCCTCAAGCGTCAATCAAGCATCATTC
65 TATCTCTCTCTCCTCACCTATAAATAAGACCCTCTCATCCCTCAAGCATCAATCAAGCATCATTC
* *
25117 TCTCTTTTTGTCTTAGCCTTTTCCATTCCCACGCCTAGCATCATCTCTTT-ATAGAGATTTTAAC
130 TCTCTTTTTCTCTTAGCCTTTTCCATTCCCACGCCTAG-ATCAT-T-TTTCATAGAGATTTTAGC
*
25181 AATTAAGCCTCTTTAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGCAAAGCA
192 AATTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGCAAAGCA
* * *
25246 AAGCAACGAAGGAATCTCGTCAGTTAGAGTCTTGGGGGCCACTTTGAATTGGGTTTAATCTTTCT
257 AAGCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGAGCCACTCTGAATTGGGTTTAATCTTTCT
* * *
25311 TTTCTTTAAATTAATATAAAGATATTTGCTATGTGTTCTTTGTTCTTGTTGATAACAATGTTAGC
322 TTTCTTTAAATTAATATAAAGATGTTTGCTATGTGTTCTTTGTTCTTGTTTACAACAATGTTAGC
*
25376 TTAACTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGCTTATAA
387 TTAATTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGCTTATAA
* * *
25441 TGTTTGTGCTTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATACGAGAAT
452 TGTTTGTGCCTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATACGTGATT
* * * *
25506 GAAGTACACCTAAATTAGCTGAGCGATCCTAACCAGATGACGGCTAATGGACGCATAATTGAAAT
517 GAAATACACCTGAATTAGCTGAGCGATCCTAACTAGACGACGGCTAATGGACGCATAATTGAAAT
*
25571 GTGCATGCTTAATTTAGATCCTAACATGATTAAATTGTAGGTTGCATAACAACTCCAACCAAGCT
582 GTGCATGCTTAATTTAGATCCTAACATGATTAAATTGTAGGTTGCATAACAACTCTAACCAAGCT
*
25636 TTGTTATCTGCATAGTTTTTACATTTGTGTGAT
647 TTGTTATCTGCATAGTTTTTAGATTTGTGTGAT
25669 TAAATTATGGCCGGCCACCCATGGAAGATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACT
1 TAAATTATGGCCGGCCACCCATGGAAGATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACT
* * * *
25734 CTCTCTCTCTCCTCACCTATAAAGAAGACCCTCTCATCCCTCAAGCATCAATCAAACATCATTCC
66 ATCTCTCTCTCCTCACCTATAAATAAGACCCTCTCATCCCTCAAGCATCAATCAAGCATCATTCT
*
25799 CTCTCTTTCTCTTAGCCTTTTCCATTCCCACGCCTAGTATCATTTTTTCATAGAGATTTTAGCAA
131 CTCTTTTTCTCTTAGCCTTTTCCATTCCCACGCCTAG-ATCA-TTTTTCATAGAGATTTTAGCAA
*
25864 TTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAATGAGCAAAGCAAA
194 TTAAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGCAAAGCAAA
* *
25929 GCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGAGAGCCACTCTAAATTGGGTTTAATCTTTCTTT
259 GCAACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGAGCCACTCTGAATTGGGTTTAATCTTTCTTT
* * *
25994 TCTTTAAATTAATATAAAGATGTTTTCTTTGTGTTCTTTGTTCTTGTTTACAACAATTTTAGCTT
324 TCTTTAAATTAATATAAAGATGTTTGCTATGTGTTCTTTGTTCTTGTTTACAACAATGTTAGCTT
* *
26059 AATTTTATTTAAGCCAGGATGATTACTTTGATTAAATAATATTTATTTGATTCATGCTTATAATG
389 AATTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGCTTATAATG
*
26124 TTTGTGCCTCAATCGATCATGTTTTTAATTAAAATCAAGTCTGTATTTCATTCATACGTGATTGA
454 TTTGTGCCTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATACGTGATTGA
* * *
26189 AATACACCTGAATTAGCTGAGCGATACTAACTAGACAACGGCTAATGGACGCATAATTGAATTGT
519 AATACACCTGAATTAGCTGAGCGATCCTAACTAGACGACGGCTAATGGACGCATAATTGAAATGT
26254 GCATGCTTAATTTAGATCCTAACATGATTAAATTGTAGGTTGCATAACAACTCTAACCAAGCTTT
584 GCATGCTTAATTTAGATCCTAACATGATTAAATTGTAGGTTGCATAACAACTCTAACCAAGCTTT
*
26319 GTTATCTGCATAGTTTTTGGATTTGTGTGAT
649 GTTATCTGCATAGTTTTTAGATTTGTGTGAT
*
26350 TAAATTATGGCCGACCACCCATGGAAGATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACT
1 TAAATTATGGCCGGCCACCCATGGAAGATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACT
26415 ATCTCTCTCTCCTCACCTATAAATAAGACCCTCTCATCCCTCAAGCATCAATCAAGCATCATTCT
66 ATCTCTCTCTCCTCACCTATAAATAAGACCCTCTCATCCCTCAAGCATCAATCAAGCATCATTCT
26480 CTCTTTTTCTCTTAGCCTTTTCCATTCCCA---C--G---------C-----G--TTTAGCAATT
131 CTCTTTTTCTCTTAGCCTTTTCCATTCCCACGCCTAGATCATTTTTCATAGAGATTTTAGCAATT
* *
26524 AAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAACAAAGGAGCAAAGCAAAGG
196 AAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGCAAAGCAAAGC
* *
26589 AACGAAGGAGTCCCGTCAGTTAGAGTCTTGGGAGCCACTCTGAATTGGGTTTAATATTTCTTTTC
261 AACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGAGCCACTCTGAATTGGGTTTAATCTTTCTTTTC
*
26654 TTTAAATTAATATAAAGATGTTTGCTATGTGTTCTTTGCTCTTGTTTACAACAATGTTAGCTTAA
326 TTTAAATTAATATAAAGATGTTTGCTATGTGTTCTTTGTTCTTGTTTACAACAATGTTAGCTTAA
*
26719 TTTTTTTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGCTTATAATGTT
391 TTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGCTTATAATGTT
*
26784 TATGCCTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATACGTGATTGAAA
456 TGTGCCTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATACGTGATTGAAA
*
26849 TACACTTGAATTAGCTGAGCGATCCTAACTAGACGACGGCTAATGGACGCATAATTGAAATGTGC
521 TACACCTGAATTAGCTGAGCGATCCTAACTAGACGACGGCTAATGGACGCATAATTGAAATGTGC
* * * *
26914 ATGCTCAATTTAGATCCTAACACGATTAAATTGTAGGTTGCATAACAACTCTAACCATGGTTTGT
586 ATGCTTAATTTAGATCCTAACATGATTAAATTGTAGGTTGCATAACAACTCTAACCAAGCTTTGT
26979 TATCTGCATAGTTTTTAGATTTGTGTGAT
651 TATCTGCATAGTTTTTAGATTTGTGTGAT
27008 TAAATTAT
1 TAAATTAT
27016 TTCAAACCTA
Statistics
Matches: 1273, Mismatches: 72, Indels: 28
0.93 0.05 0.02
Matches are distributed among these distances:
658 477 0.37
660 1 0.00
665 1 0.00
676 1 0.00
678 1 0.00
680 3 0.00
681 784 0.62
682 5 0.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (679 bp):
TAAATTATGGCCGGCCACCCATGGAAGATGCTTCAAAAGATGGAAACTCCTATTTTTAGCAAACT
ATCTCTCTCTCCTCACCTATAAATAAGACCCTCTCATCCCTCAAGCATCAATCAAGCATCATTCT
CTCTTTTTCTCTTAGCCTTTTCCATTCCCACGCCTAGATCATTTTTCATAGAGATTTTAGCAATT
AAGCCTCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAACCATCAGCAAAGGAGCAAAGCAAAGC
AACGAAGGAGTCTCGTCAGTTAGAGTCTTGGGAGCCACTCTGAATTGGGTTTAATCTTTCTTTTC
TTTAAATTAATATAAAGATGTTTGCTATGTGTTCTTTGTTCTTGTTTACAACAATGTTAGCTTAA
TTTTATTTAAGCTAGGATGATTGCTTTGATTAAATAATATTTATTTGATTCATGCTTATAATGTT
TGTGCCTCAATCGATCATGTTTTCAATTAAAATCAAGTCTGTATTTCATTCATACGTGATTGAAA
TACACCTGAATTAGCTGAGCGATCCTAACTAGACGACGGCTAATGGACGCATAATTGAAATGTGC
ATGCTTAATTTAGATCCTAACATGATTAAATTGTAGGTTGCATAACAACTCTAACCAAGCTTTGT
TATCTGCATAGTTTTTAGATTTGTGTGAT
Found at i:31537 original size:13 final size:13
Alignment explanation
Indices: 31519--31543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31509 CCGAAACTAG
31519 AAAGAAAAAAAAC
1 AAAGAAAAAAAAC
31532 AAAGAAAAAAAA
1 AAAGAAAAAAAA
31544 ATGCTCATCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAC
Found at i:32633 original size:40 final size:40
Alignment explanation
Indices: 32549--32732 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
32539 TTGAATGCTG
* * * *
32549 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
32588 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * **
32629 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACCAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
32669 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
32709 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
32733 GAATGAGTTA
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 110 0.91
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:32753 original size:39 final size:39
Alignment explanation
Indices: 32629--32779 Score: 117
Period size: 40 Copynumber: 3.8 Consensus size: 39
32619 AGTTATTAAT
* ** * * *
32629 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATAC-CAAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAG-TTCTAAAA
** *
32669 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
32709 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
32749 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
32780 GAGCTATATC
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
39 29 0.31
40 64 0.69
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:40554 original size:39 final size:40
Alignment explanation
Indices: 40459--40588 Score: 172
Period size: 40 Copynumber: 3.3 Consensus size: 40
40449 GGACTAAGAT
* *
40459 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATAAATTCCGGGTTAAGTC
* * **
40499 CCGAAGGCCTTTGTGCGAGATACCAATTCCGGGTT-AGTC
1 CCGAAGGCATTTGTGCGAGTTATAAATTCCGGGTTAAGTC
* * *
40538 CCGAAGGCATTCGTGCGAGTTTTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATAAATTCCGGGTTAAGTC
40578 CCGAAGGCATT
1 CCGAAGGCATT
40589 GAATGAGTTA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 32 0.42
40 45 0.58
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTATAAATTCCGGGTTAAGTC
Found at i:40618 original size:79 final size:79
Alignment explanation
Indices: 40459--40625 Score: 187
Period size: 79 Copynumber: 2.1 Consensus size: 79
40449 GGACTAAGAT
* * * * **
40459 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACCA
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACCA
* *
40524 ATTCCGGGTTAGTC
66 ATACCGGGCTAGTC
* *
40538 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGG-CATTGAATGAGTTA-C
1 CCGAAGGCATTCGTGCGAGTTATT-AAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACC
*
40600 TATGACCGGGCTATGTC
65 AAT-ACCGGGCTA-GTC
40617 CCGAAGGCA
1 CCGAAGGCA
40626 CTTGAACGAG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
77 3 0.04
78 18 0.24
79 53 0.72
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACCA
ATACCGGGCTAGTC
Done.