Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3112.1
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: 161243
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.31
Warning! 2320 characters in sequence are not A, C, G, or T
Found at i:1084 original size:40 final size:40
Alignment explanation
Indices: 999--1183 Score: 189
Period size: 40 Copynumber: 4.6 Consensus size: 40
989 ATTGAATGCT
* * * *
999 TTCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-A
1 TTCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAA
**
1038 TATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAA
1 T-TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAA
* * * *
1079 TTCCGGGTTAAGTCCCGAAGGCCTTTGTACGAGATACTAA
1 TTCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAA
* *
1119 TTCCGGGTTAAGTGCCGAAGGCATTCGTGCGAGTT-TTAAA
1 TTCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AA
*
1159 ATCCGGGTTAAGTCCCGAAGGCATT
1 TTCCGGGTTAAGTCCCGAAGGCATT
1184 GTATGAGTTA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.02
40 109 0.89
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TTCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAA
Found at i:8922 original size:40 final size:40
Alignment explanation
Indices: 8872--9013 Score: 171
Period size: 40 Copynumber: 3.5 Consensus size: 40
8862 TTGAATGCTG
* * *
8872 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATA
* *
8912 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
* *
8952 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* *
8992 ACCGGGCTATGTCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCA
9014 CTTGAACGAG
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 78 0.90
41 8 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:19422 original size:60 final size:60
Alignment explanation
Indices: 19329--19447 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
19319 AATCTATACA
*
19329 CAACCGGACCAACTCGTTCGGAGATTTCGTACGGCCCAATGAATCTCGGGCTCAACTTGG
1 CAACCGGACCAACTCGTTCAGAGATTTCGTACGGCCCAATGAATCTCGGGCTCAACTTGG
19389 CAACCGGACCAACTCGTTCAGAGATTTCGTACGGCCCAATGAATCTCGGGCTCAACTTG
1 CAACCGGACCAACTCGTTCAGAGATTTCGTACGGCCCAATGAATCTCGGGCTCAACTTG
19448 CCCTTACGGC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (60 bp):
CAACCGGACCAACTCGTTCAGAGATTTCGTACGGCCCAATGAATCTCGGGCTCAACTTGG
Found at i:26699 original size:20 final size:20
Alignment explanation
Indices: 26674--26714 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
26664 CAAAGTAAGC
26674 TTCATAACTTAGTAAACTCG
1 TTCATAACTTAGTAAACTCG
*
26694 TTCATAGCTTAGTAAACTCG
1 TTCATAACTTAGTAAACTCG
26714 T
1 T
26715 ATTATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (20 bp):
TTCATAACTTAGTAAACTCG
Found at i:33231 original size:93 final size:93
Alignment explanation
Indices: 33100--33274 Score: 350
Period size: 93 Copynumber: 1.9 Consensus size: 93
33090 TACATTTATC
33100 AAACATGCTTCAGAAGTGATTCGAGACTAAACCGATAACATATGAAAATTTTGGAAACTTAGAAA
1 AAACATGCTTCAGAAGTGATTCGAGACTAAACCGATAACATATGAAAATTTTGGAAACTTAGAAA
33165 AATTTCAGCCATACAGGTACGAGGCCTT
66 AATTTCAGCCATACAGGTACGAGGCCTT
33193 AAACATGCTTCAGAAGTGATTCGAGACTAAACCGATAACATATGAAAATTTTGGAAACTTAGAAA
1 AAACATGCTTCAGAAGTGATTCGAGACTAAACCGATAACATATGAAAATTTTGGAAACTTAGAAA
33258 AATTTCAGCCATACAGG
66 AATTTCAGCCATACAGG
33275 GAACGCGGAC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.25
Consensus pattern (93 bp):
AAACATGCTTCAGAAGTGATTCGAGACTAAACCGATAACATATGAAAATTTTGGAAACTTAGAAA
AATTTCAGCCATACAGGTACGAGGCCTT
Found at i:37893 original size:93 final size:93
Alignment explanation
Indices: 37762--37936 Score: 350
Period size: 93 Copynumber: 1.9 Consensus size: 93
37752 TACATTTATC
37762 AAACATGCTTCAGAAGTGATTCGAGACTAAACCGATAACATATGAAAATTTTGGAAACTTAGAAA
1 AAACATGCTTCAGAAGTGATTCGAGACTAAACCGATAACATATGAAAATTTTGGAAACTTAGAAA
37827 AATTTCAGCCATACAGGTACGAGGCCTT
66 AATTTCAGCCATACAGGTACGAGGCCTT
37855 AAACATGCTTCAGAAGTGATTCGAGACTAAACCGATAACATATGAAAATTTTGGAAACTTAGAAA
1 AAACATGCTTCAGAAGTGATTCGAGACTAAACCGATAACATATGAAAATTTTGGAAACTTAGAAA
37920 AATTTCAGCCATACAGG
66 AATTTCAGCCATACAGG
37937 GGTCACACAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.25
Consensus pattern (93 bp):
AAACATGCTTCAGAAGTGATTCGAGACTAAACCGATAACATATGAAAATTTTGGAAACTTAGAAA
AATTTCAGCCATACAGGTACGAGGCCTT
Found at i:38248 original size:29 final size:28
Alignment explanation
Indices: 38197--38290 Score: 125
Period size: 28 Copynumber: 3.3 Consensus size: 28
38187 ATTGCATGAC
*
38197 TATGAATGTGATTGGGCCTAATGCGCCA
1 TATGAATGTGATTGGGCCTAATGGGCCA
*
38225 TATGAATTTGATTTGGGCCTAATGGGCCA
1 TATGAATGTGA-TTGGGCCTAATGGGCCA
* * *
38254 TATGAAAGAGATTGGGCCTAGTGGGCCA
1 TATGAATGTGATTGGGCCTAATGGGCCA
*
38282 TATGCATGT
1 TATGAATGT
38291 ATGTAGACTT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 32 0.57
29 24 0.43
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTAATGGGCCA
Found at i:39699 original size:30 final size:30
Alignment explanation
Indices: 39650--39706 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39640 TCACCAAGGG
*
39650 ATACACGGCTGTGTAACATGACCGTGTGTC
1 ATACACGGCTGAGTAACATGACCGTGTGTC
*
39680 ATACACGGCTGAG-ACACATGCCCGTGT
1 ATACACGGCTGAGTA-ACATGACCGTGT
39707 CTCTAACCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (30 bp):
ATACACGGCTGAGTAACATGACCGTGTGTC
Found at i:40609 original size:28 final size:28
Alignment explanation
Indices: 40560--40615 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
40550 ATGCCGTTGA
*
40560 ATACTCAATGTCTAGCACACTAAGTGCC
1 ATACTCAATGTCTAGCACACTAACTGCC
* *
40588 ATACTCAATTTCTCA-CAGACTAACTGCC
1 ATACTCAATGTCT-AGCACACTAACTGCC
40616 GTACATAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (28 bp):
ATACTCAATGTCTAGCACACTAACTGCC
Found at i:40650 original size:40 final size:41
Alignment explanation
Indices: 40617--40713 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 41
40607 CTAACTGCCG
*
40617 TACATAGTCGAAGCTATCTCAAACCACACACTAAGTGCCATA
1 TACATAGCCGAAGCTATCTCAAACCACACACTAAGTGCCA-A
* * * *
40659 TATATAGCCGAAGCTATGTCAAATCGCACACTAAGTGCC-A
1 TACATAGCCGAAGCTATCTCAAACCACACACTAAGTGCCAA
* *
40699 TATATAGCTGAAGCT
1 TACATAGCCGAAGCT
40714 GTATTATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
40 15 0.31
42 34 0.69
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (41 bp):
TACATAGCCGAAGCTATCTCAAACCACACACTAAGTGCCAA
Found at i:40671 original size:42 final size:42
Alignment explanation
Indices: 40620--40704 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
40610 ACTGCCGTAC
*
40620 ATAGTCGAAGCTATCTCAAACCACACACTAAGTGCCATATAT
1 ATAGCCGAAGCTATCTCAAACCACACACTAAGTGCCATATAT
* * *
40662 ATAGCCGAAGCTATGTCAAATCGCACACTAAGTGCCATATAT
1 ATAGCCGAAGCTATCTCAAACCACACACTAAGTGCCATATAT
40704 A
1 A
40705 GCTGAAGCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.24
Consensus pattern (42 bp):
ATAGCCGAAGCTATCTCAAACCACACACTAAGTGCCATATAT
Found at i:40728 original size:40 final size:40
Alignment explanation
Indices: 40606--40738 Score: 131
Period size: 40 Copynumber: 3.3 Consensus size: 40
40596 TTTCTCACAG
* * * * * * *
40606 ACTAACTGCCGTACATAGTCGAAGCTATCTCAAACCACAC
1 ACTAAGTGCCATATATAGCCGAAGCTATATCAAATCGCAC
*
40646 ACTAAGTGCCATATATATAGCCGAAGCTATGTCAAATCGCAC
1 ACTAAGTGCC--ATATATAGCCGAAGCTATATCAAATCGCAC
* * * * *
40688 ACTAAGTGCCATATATAGCTGAAGCTGTATTATATTGCAC
1 ACTAAGTGCCATATATAGCCGAAGCTATATCAAATCGCAC
40728 ACTAAGTGCCA
1 ACTAAGTGCCA
40739 CAAATAATCG
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 44 0.56
42 34 0.44
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
ACTAAGTGCCATATATAGCCGAAGCTATATCAAATCGCAC
Found at i:44791 original size:25 final size:25
Alignment explanation
Indices: 44754--44801 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
44744 TAAACTTGAG
*
44754 AATTCTCTGAAAAGCCTTTGTGGAA
1 AATTCTCTAAAAAGCCTTTGTGGAA
* *
44779 AATTCTTTAAAAAGCTTTTGTGG
1 AATTCTCTAAAAAGCCTTTGTGG
44802 TGTACCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (25 bp):
AATTCTCTAAAAAGCCTTTGTGGAA
Found at i:44862 original size:50 final size:50
Alignment explanation
Indices: 44808--44928 Score: 131
Period size: 50 Copynumber: 2.4 Consensus size: 50
44798 GTGGTGTACC
* *
44808 ATTTGGAAAGCCTTTATAGTG-AA-TTCTCTAGAAAGT-CTTTATGGCATATT
1 ATTTGGAAAGCCTTTAT-G-GCAAGTTCTCTAGAAAATCCTTTATGGC-TAAT
* *
44858 ATTTGGAAAGTCTTTGTGGCAAGTTCTCTAGAAAATCCTTTATGGCTAAT
1 ATTTGGAAAGCCTTTATGGCAAGTTCTCTAGAAAATCCTTTATGGCTAAT
* *
44908 CTTGTGAAAAGCCTTTATGGC
1 ATT-TGGAAAGCCTTTATGGC
44929 GTGTTATCTG
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
48 1 0.02
49 3 0.05
50 32 0.54
51 23 0.39
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (50 bp):
ATTTGGAAAGCCTTTATGGCAAGTTCTCTAGAAAATCCTTTATGGCTAAT
Found at i:44891 original size:25 final size:25
Alignment explanation
Indices: 44830--44903 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
44820 TTTATAGTGA
44830 ATTCTCTAGAAAGTCTTTATGGCAT
1 ATTCTCTAGAAAGTCTTTATGGCAT
* * * *
44855 ATTATTTGGAAAGTCTTTGTGGCA-
1 ATTCTCTAGAAAGTCTTTATGGCAT
*
44879 AGTTCTCTAGAAAATCCTTTATGGC
1 A-TTCTCTAGAAAGT-CTTTATGGC
44904 TAATCTTGTG
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
24 1 0.03
25 29 0.76
26 8 0.21
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (25 bp):
ATTCTCTAGAAAGTCTTTATGGCAT
Found at i:46904 original size:43 final size:43
Alignment explanation
Indices: 46763--46929 Score: 153
Period size: 43 Copynumber: 3.9 Consensus size: 43
46753 ACATCAGCTG
* * * * *
46763 TACAATGCC-ATATCCCAGATATGGTCTTACATGTTACCACAA
1 TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCTCAA
* * * * *
46805 -ATCAATGCCACTGTCCCAAACAGGGTTTTACATG-AA-ATCAA
1 TA-CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCTCAA
* * *
46846 TTAACGATGCTAATGTCCCAGACATGGTCTTACACGTAATCTCAA
1 -T-ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCTCAA
*
46891 TACAATGCCAATGTCCCAGACATGGTCTCACATGTAATC
1 TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATC
46930 ACAACTCGAT
Statistics
Matches: 97, Mismatches: 21, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
41 4 0.04
42 8 0.08
43 77 0.79
44 4 0.04
45 4 0.04
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (43 bp):
TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATCTCAA
Found at i:54442 original size:40 final size:40
Alignment explanation
Indices: 54398--54661 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
54388 GCTCCTCGTT
* *
54398 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
54438 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
54478 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
54518 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
54558 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
54597 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
54638 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54662 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:70135 original size:43 final size:42
Alignment explanation
Indices: 70054--70155 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 42
70044 GATGCTACTA
* *
70054 TCCCAGACAGGGTCTTACACGAAATCGATTAACGATGCCAATG
1 TCCCAGACATGGTCTTACACGAAATC-ATTAACAATGCCAATG
* *
70097 TCCCAAACATGGTCTTACACGTAATC-TTAATACAATGCCAATG
1 TCCCAGACATGGTCTTACACGAAATCATT-A-ACAATGCCAATG
70140 TCCCAGACATGGTCTT
1 TCCCAGACATGGTCTT
70156 CCATGTAAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.04
42 1 0.02
43 49 0.94
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAAATCATTAACAATGCCAATG
Found at i:72048 original size:24 final size:25
Alignment explanation
Indices: 72021--72070 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
72011 AGTTCCGACC
72021 TCACTATGCCATCCTACCT-CCTCT
1 TCACTATGCCATCCTACCTCCCTCT
72045 TCACTATGCCATCCTACCTCCCTCT
1 TCACTATGCCATCCTACCTCCCTCT
72070 T
1 T
72071 ACTCCCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.16, C:0.46, G:0.04, T:0.34
Consensus pattern (25 bp):
TCACTATGCCATCCTACCTCCCTCT
Found at i:83502 original size:43 final size:43
Alignment explanation
Indices: 83441--83525 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
83431 TGAGGTATGT
*
83441 AGCATCCAAGCTCATTGAGAGGTCTGAGTTCATTATGGATGCA
1 AGCATCCAAGCTCATTGAGAGGTCTGAGTTCATGATGGATGCA
* *
83484 AGCATCGAAGCTCATTGAGTGGTCTGAGTTCATGATGGATGC
1 AGCATCCAAGCTCATTGAGAGGTCTGAGTTCATGATGGATGC
83526 GATTCATGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (43 bp):
AGCATCCAAGCTCATTGAGAGGTCTGAGTTCATGATGGATGCA
Found at i:86625 original size:22 final size:22
Alignment explanation
Indices: 86597--86641 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
86587 ATTATGATGA
86597 TTGATATG-ATGAGACTGATATT
1 TTGATATGTATGAGA-TGATATT
*
86619 TTGATATGTATGAGATTATATT
1 TTGATATGTATGAGATGATATT
86641 T
1 T
86642 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (22 bp):
TTGATATGTATGAGATGATATT
Found at i:95204 original size:48 final size:48
Alignment explanation
Indices: 95148--95310 Score: 193
Period size: 48 Copynumber: 3.4 Consensus size: 48
95138 CTAAATGCTC
* * ** * *
95148 ATATCATGGCCTGAAGCCAACTTAATGTATCTCGCACCCGAAGTACTA
1 ATATCATGGCCCGAAGCCAAATTAATAAAGCTCGCACCCAAAGTACTA
* *
95196 ATATCATGGCCCGAAGCCAAATTAATAAAGCTCGCACCCAAAGTGCTG
1 ATATCATGGCCCGAAGCCAAATTAATAAAGCTCGCACCCAAAGTACTA
* * * *
95244 ATATCATGGTCCGAAGACAAATCAATAAAGCTCGCACCCAAAGTACTG
1 ATATCATGGCCCGAAGCCAAATTAATAAAGCTCGCACCCAAAGTACTA
*
95292 ATAT-AGTGGCCCAAAGCCA
1 ATATCA-TGGCCCGAAGCCA
95311 TCAAAGTATC
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
47 1 0.01
48 98 0.99
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (48 bp):
ATATCATGGCCCGAAGCCAAATTAATAAAGCTCGCACCCAAAGTACTA
Found at i:97523 original size:8 final size:8
Alignment explanation
Indices: 97510--97540 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
97500 GTGCTTGGTA
97510 GGAAAGAT
1 GGAAAGAT
*
97518 GGAAAGTT
1 GGAAAGAT
97526 GGAAAGAT
1 GGAAAGAT
97534 GGAAAGA
1 GGAAAGA
97541 AAATGTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.39, T:0.13
Consensus pattern (8 bp):
GGAAAGAT
Found at i:120284 original size:20 final size:19
Alignment explanation
Indices: 120250--120289 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
120240 ATGTTTTTAT
120250 AAATATTTTTTTAAT-ATA
1 AAATATTTTTTTAATCATA
120268 AAATATTTTCATTTAATCATA
1 AAATATTTT--TTTAATCATA
120289 A
1 A
120290 TGTGAGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
20 6 0.32
21 4 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATATTTTTTTAATCATA
Found at i:123572 original size:27 final size:27
Alignment explanation
Indices: 123542--123662 Score: 188
Period size: 27 Copynumber: 4.5 Consensus size: 27
123532 TAAATGATAG
*
123542 AATGACTATTTTGCCCTTATGTGGTAA
1 AATGACTGTTTTGCCCTTATGTGGTAA
*
123569 AATGATTGTTTTGCCCTTATGTGGTAA
1 AATGACTGTTTTGCCCTTATGTGGTAA
*
123596 AATGACTGTTTTGCCCATATGTGGTAA
1 AATGACTGTTTTGCCCTTATGTGGTAA
*
123623 AATGACTGGTTTGCCCTTATGTGGTAA
1 AATGACTGTTTTGCCCTTATGTGGTAA
* *
123650 GATGACTGCTTTG
1 AATGACTGTTTTG
123663 ATCCTATATG
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (27 bp):
AATGACTGTTTTGCCCTTATGTGGTAA
Found at i:129134 original size:16 final size:16
Alignment explanation
Indices: 129065--129132 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
129055 TTTGGTTCGC
129065 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
129081 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
129097 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
129113 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
129129 TGTA
1 TGTA
129133 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:129167 original size:45 final size:44
Alignment explanation
Indices: 129113--129207 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
129103 GGATTAGAGG
* *
129113 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
129158 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
129202 TGTAAT
1 TGTAAT
129208 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:129377 original size:25 final size:25
Alignment explanation
Indices: 129345--129399 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
129335 TAATTTAATC
*
129345 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
129369 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
129394 ATATAT
1 ATATAT
129400 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:129581 original size:47 final size:46
Alignment explanation
Indices: 129530--129690 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
129520 GATTTAATAA
129530 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
129577 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
129618 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
129665 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
129691 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:140682 original size:19 final size:19
Alignment explanation
Indices: 140631--140689 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
140621 AATTTTTAAA
140631 AAATTAACCAATAAT-TTT
1 AAATTAACCAATAATATTT
140649 -AATTAA--AATAAAATATTT
1 AAATTAACCAAT--AATATTT
140667 AAATTAACCAATAATATTAT
1 AAATTAACCAATAATATT-T
140687 AAA
1 AAA
140690 AGTTAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
15 3 0.09
17 9 0.26
18 3 0.09
19 12 0.35
20 4 0.12
21 3 0.09
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTAACCAATAATATTT
Found at i:141242 original size:13 final size:13
Alignment explanation
Indices: 141224--141248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
141214 AACATACAAT
141224 AAGTAAGAAAATG
1 AAGTAAGAAAATG
141237 AAGTAAGAAAAT
1 AAGTAAGAAAAT
141249 ATAATATCAT
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:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (13 bp):
AAGTAAGAAAATG
Found at i:145406 original size:7 final size:7
Alignment explanation
Indices: 145396--145422 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
145386 GATAATACCC
145396 GATAAAT
1 GATAAAT
145403 GATAAAT
1 GATAAAT
145410 GATAAAT
1 GATAAAT
145417 GATAAA
1 GATAAA
145423 AATGTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (7 bp):
GATAAAT
Found at i:145948 original size:16 final size:15
Alignment explanation
Indices: 145927--145976 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
145917 CTTGAAGTAC
*
145927 ATGAAAATGATGATAT
1 ATGAAAAT-ATGAAAT
145943 ATG-AAATATGAAAT
1 ATGAAAATATGAAAT
*
145957 ATGAAAGTATGAAATT
1 ATGAAAATATGAAA-T
145973 ATGA
1 ATGA
145977 TATACGGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.30
15 13 0.43
16 8 0.27
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (15 bp):
ATGAAAATATGAAAT
Found at i:145969 original size:8 final size:7
Alignment explanation
Indices: 145931--145976 Score: 56
Period size: 7 Copynumber: 6.1 Consensus size: 7
145921 AAGTACATGA
145931 AAATGATG
1 AAAT-ATG
*
145939 ATATATG
1 AAATATG
145946 AAATATG
1 AAATATG
145953 AAATATG
1 AAATATG
145960 AAAGTATG
1 AAA-TATG
145968 AAATTATG
1 AAA-TATG
145976 A
1 A
145977 TATACGGACA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
7 19 0.56
8 15 0.44
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.30
Consensus pattern (7 bp):
AAATATG
Found at i:157860 original size:6 final size:6
Alignment explanation
Indices: 157849--157887 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
157839 GGTTTCAAAT
157849 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATG
1 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATG
157888 AATCATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.33, T:0.18
Consensus pattern (6 bp):
ATGGAA
Done.