Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006283.1 Hibiscus syriacus cultivar Beakdansim tig00014996_pilon, whole genome shotgun sequence
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: 92542
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:8616 original size:31 final size:31
Alignment explanation
Indices: 8578--8642 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
8568 AGAGTCGAGG
*
8578 GTTTACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
** * *
8609 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
8640 GTT
1 GTT
8643 ACCGAGGATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGACA
Found at i:8662 original size:30 final size:30
Alignment explanation
Indices: 8601--8697 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
8591 CTAAGGAACA
* * ***
8601 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
8632 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* * *
8662 TCTGGATAGTTATCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
8692 TCTGGA
1 TATGGA
8698 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 49 0.84
31 9 0.16
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:8698 original size:30 final size:30
Alignment explanation
Indices: 8628--8700 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
8618 GGTTCTTCGG
* *
8628 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
8658 GACCTCTGGATAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
8688 GACCTCTGGATAG
1 GACCTCTGGATAG
8701 GTCCTTCGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:13401 original size:30 final size:30
Alignment explanation
Indices: 13367--13439 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
13357 GGTTCTTCGG
*
13367 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
13397 GACCTCTGGATAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
13427 GACCTCTGGATAG
1 GACCTCTGGATAG
13440 GTCTTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:22700 original size:41 final size:41
Alignment explanation
Indices: 22643--22727 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
22633 CGGAGGCACT
* *
22643 CCCCATCTGTTTTCGGACTAAAGTGG-CTCGAAGACGTGAAC
1 CCCCACCTGTTTTCGGACTAAAG-GGACTCGAAGACATGAAC
**
22684 CCCCACCTGTTTTCGGACTCGAGGGACTCGAAGACATGAAC
1 CCCCACCTGTTTTCGGACTAAAGGGACTCGAAGACATGAAC
22725 CCC
1 CCC
22728 ACCGTCAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 2 0.05
41 37 0.95
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (41 bp):
CCCCACCTGTTTTCGGACTAAAGGGACTCGAAGACATGAAC
Found at i:23441 original size:12 final size:12
Alignment explanation
Indices: 23426--23450 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23416 GTTATTTAAA
23426 CGGGTATCGGGC
1 CGGGTATCGGGC
23438 CGGGTATCGGGC
1 CGGGTATCGGGC
23450 C
1 C
23451 AAATTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.28, G:0.48, T:0.16
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:40564 original size:118 final size:118
Alignment explanation
Indices: 40337--40567 Score: 277
Period size: 118 Copynumber: 2.0 Consensus size: 118
40327 TTCACAGATG
* * * * *
40337 AAGTAAAATGTAAAAGTAACACCAAAGTAGAAAGGGAGATGCAACTTATTAATGGATAATAGTCT
1 AAGTAAAATGTAAAAGAAACACCAAAGTAGAAAGAGAGATGCAACTTAGTAATGGATAACAGCCT
* * * * * *
40402 AAAAGAGAATGTTTAGTATTAAACAAATATCAGTGCGGCCCTTGGGTGTGCAC
66 AAAAGAGAAAGTTCAGTATAAAACAAATACCAGTGCAGCACTTGGGTGTGCAC
* * *
40455 AAGTAAAATGTAAAAGAAATACCGAAGTAG-AAGAGAGATGCAACCTTAGTAATTGATAACAGCC
1 AAGTAAAATGTAAAAGAAACACCAAAGTAGAAAGAGAGATGCAA-CTTAGTAATGGATAACAGCC
* * *
40519 TGAAAA-AGAAAGTTCAGTATAAAATAGATACCGGTGCAGCACTTGGGTG
65 T-AAAAGAGAAAGTTCAGTATAAAACAAATACCAGTGCAGCACTTGGGTG
40568 AGTACATTTC
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
117 12 0.13
118 78 0.83
119 4 0.04
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.23
Consensus pattern (118 bp):
AAGTAAAATGTAAAAGAAACACCAAAGTAGAAAGAGAGATGCAACTTAGTAATGGATAACAGCCT
AAAAGAGAAAGTTCAGTATAAAACAAATACCAGTGCAGCACTTGGGTGTGCAC
Found at i:42595 original size:2 final size:2
Alignment explanation
Indices: 42588--42617 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42578 TGTATTCTTC
42588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42618 GATCCTCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42887 original size:24 final size:24
Alignment explanation
Indices: 42860--42907 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
42850 TATTTGATTT
* *
42860 TTTAGAAGAAAAAAATATTGAAAA
1 TTTAAAAGAAAAAAATATTCAAAA
* *
42884 TTTAAAATATAAAAATATTCAAAA
1 TTTAAAAGAAAAAAATATTCAAAA
42908 AAAATAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (24 bp):
TTTAAAAGAAAAAAATATTCAAAA
Found at i:42945 original size:21 final size:22
Alignment explanation
Indices: 42907--42964 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
42897 AATATTCAAA
42907 AAAAATAAATATAATAAAATGGC-
1 AAAAATAAA-A-AATAAAATGGCT
*
42930 AAAAATAAAAAAT-AAATTGCT
1 AAAAATAAAAAATAAAATGGCT
*
42951 AAAAATTAAAAATA
1 AAAAATAAAAAATA
42965 TATATTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 6 0.19
21 15 0.48
22 1 0.03
23 9 0.29
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (22 bp):
AAAAATAAAAAATAAAATGGCT
Found at i:61168 original size:49 final size:49
Alignment explanation
Indices: 61042--61186 Score: 177
Period size: 49 Copynumber: 2.9 Consensus size: 49
61032 AACCAGCACT
*
61042 TCATGTTCAAGGGGGTATCTTGGATGCCTAGCACTAATTGTGCTAAAATC
1 TCATGTTCAAGGAGGTATCTTGG-TGCCTAGCACTAATTGTGCTAAAATC
* * * *
61092 TCATGTTCTAGGTGGT-TCATTGTGTGCCTAGCATTTATTGTGCT-AAATC
1 TCATGTTCAAGGAGGTATC-TTG-GTGCCTAGCACTAATTGTGCTAAAATC
**
61141 TCATGTTCAAGGAGGTATCTTAGGTGCCTAATACTAATTGTGCTAA
1 TCATGTTCAAGGAGGTATCTT-GGTGCCTAGCACTAATTGTGCTAA
61187 GGTTTCATGT
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
49 40 0.50
50 39 0.49
51 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (49 bp):
TCATGTTCAAGGAGGTATCTTGGTGCCTAGCACTAATTGTGCTAAAATC
Found at i:61221 original size:99 final size:99
Alignment explanation
Indices: 61042--61226 Score: 234
Period size: 99 Copynumber: 1.9 Consensus size: 99
61032 AACCAGCACT
* *
61042 TCATGTTCAAGGGGGTATCTTGGATGCCTAGCACTAATTGTGCTAAAATCTCATGTTCTAGGTGG
1 TCATGTTCAAGGAGGTATCTTGGATGCCTAACACTAATTGTGCTAAAATCTCATGTTCTAGGTGG
* *
61107 TTCATTGTGTGCCTAGCATTTATTGTGCTAAATC
66 TGCATTGTGTACCTAGCATTTATTGTGCTAAATC
* ** *
61141 TCATGTTCAAGGAGGTATCTTAGG-TGCCTAATACTAATTGTGCTAAGGTTTCATGTT-TAAGG-
1 TCATGTTCAAGGAGGTATCTT-GGATGCCTAACACTAATTGTGCTAAAATCTCATGTTCT-AGGT
61203 GG-GCACTTCGTGTACCTAGCATTT
64 GGTGCA-TT-GTGTACCTAGCATTT
61227 TATGTGTTCC
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
97 2 0.03
98 5 0.07
99 65 0.88
100 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (99 bp):
TCATGTTCAAGGAGGTATCTTGGATGCCTAACACTAATTGTGCTAAAATCTCATGTTCTAGGTGG
TGCATTGTGTACCTAGCATTTATTGTGCTAAATC
Found at i:62544 original size:171 final size:169
Alignment explanation
Indices: 62342--62736 Score: 524
Period size: 171 Copynumber: 2.3 Consensus size: 169
62332 AGCTGAATAG
* ** * *
62342 AATCGAACTCGACA-GTTTTTGTTGACAGATAACTTTTTCTTGACTTAAGCTATGCTGTAAATTT
1 AATCGAACTCGA-AGGTTTTTATTGACAGATAAC-CCTTCTCGACTTAAGCTATGATGTAAATTT
* *
62406 GATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGG-TTTTTGTTGACAGATAACCATTCTCGC
64 GATATGCCATTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTATTGACAGATAACCATTCTCGC
62470 CTTGAGCTATGCTATAAATTTGATATGCCCTTGAGATGAATGT
129 CTTGAGCTATGCTATAAATTTG--ATGCCCTTGAGATGAATGT
* * * *
62513 AATCGAACTGGAAGGTTTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGA
1 AATCGAACTCGAAGGTTTTTATTGACAGATAACCCTTCTCGACTTAAGCTATGATGTAAATTTGA
* *
62578 TATGTCATTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTATTGACAGATAACCCTTCTCGCCT
66 TATGCCATTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTATTGACAGATAACCATTCTCGCCT
* * *
62643 TGAGTTATGCTATAAATTTGATGTCCTTGAGCTGAATGT
131 TGAGCTATGCTATAAATTTGATGCCCTTGAGATGAATGT
* * * * * *
62682 AATTGAACTCGAAGATTTTTTTGCTGACAGATAGCCCTTCTCGTCTTGAGCTATG
1 AATCGAACTCGAAGGTTTTTAT--TGACAGATAACCCTTCTCGACTTAAGCTATG
62737 CTGTGAATAG
Statistics
Matches: 197, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
169 35 0.18
170 59 0.30
171 103 0.52
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (169 bp):
AATCGAACTCGAAGGTTTTTATTGACAGATAACCCTTCTCGACTTAAGCTATGATGTAAATTTGA
TATGCCATTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTATTGACAGATAACCATTCTCGCCT
TGAGCTATGCTATAAATTTGATGCCCTTGAGATGAATGT
Found at i:62660 original size:86 final size:85
Alignment explanation
Indices: 62331--62738 Score: 527
Period size: 85 Copynumber: 4.8 Consensus size: 85
62321 ATATGTTATC
* ** * * *
62331 GAGCTGAATAG-AATCGAACTCGACA-GTTTTTGTTGACAGATAACTTTTTCTTGACTTAAGCTA
1 GAGCTGAAT-GTAATCGAACTCGA-AGGTTTTTATTGACAGATAAC-CCTTCTCGCCTTGAGCTA
* *
62394 TGCTGTAAATTTGATATGCCCTT
63 TGCTATAAATTTGATATGTCCTT
* *
62417 GAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCATTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTATTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
62482 TATAAATTTGATATGCCCTT
66 TATAAATTTGATATGTCCTT
* * * *
62502 GAGATGAATGTAATCGAACTGGAAGGTTTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGA
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTATTGACAGATAACCCTTCTCGCCTTGAGCTATGC
* *
62567 TGTAAATTTGATATGTCATT
66 TATAAATTTGATATGTCCTT
*
62587 GAGCTGAATGTAATCGAACTCGAAGGTTTTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGG-TTTTTATTGACAGATAACCCTTCTCGCCTTGAGCTATG
62652 CTATAAATTTG--ATGTCCTT
65 CTATAAATTTGATATGTCCTT
* * * * *
62671 GAGCTGAATGTAATTGAACTCGAAGATTTTTTTGCTGACAGATAGCCCTTCTCGTCTTGAGCTAT
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTAT--TGACAGATAACCCTTCTCGCCTTGAGCTAT
62736 GCT
64 GCT
62739 GTGAATAGTT
Statistics
Matches: 291, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
83 6 0.02
84 31 0.11
85 167 0.57
86 87 0.30
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTTTTTATTGACAGATAACCCTTCTCGCCTTGAGCTATGC
TATAAATTTGATATGTCCTT
Found at i:67178 original size:16 final size:16
Alignment explanation
Indices: 67154--67189 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
67144 ATAAATGATA
67154 AAAATAAAATGAAA-G
1 AAAATAAAATGAAAGG
67169 AAAATAAAAATGAAAGG
1 AAAAT-AAAATGAAAGG
67186 AAAA
1 AAAA
67190 AGTTAGTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 5 0.26
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (16 bp):
AAAATAAAATGAAAGG
Found at i:68174 original size:12 final size:13
Alignment explanation
Indices: 68157--68185 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
68147 TTAATTGTGA
68157 AAAATCAAAA-TT
1 AAAATCAAAATTT
68169 AAAATCAAAATTT
1 AAAATCAAAATTT
68182 AAAA
1 AAAA
68186 ACTCGATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATCAAAATTT
Found at i:70279 original size:23 final size:22
Alignment explanation
Indices: 70226--70280 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
70216 TATAAAACGT
*
70226 TAAATTATAAAATATTAAAAGTA
1 TAAA-TATAAAATATTAAAAATA
* * *
70249 TAATTATAAATTAGTTAAAAATC
1 TAAATATAAAATA-TTAAAAATA
70272 TAAATATAA
1 TAAATATAA
70281 TTTTAATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (22 bp):
TAAATATAAAATATTAAAAATA
Found at i:70800 original size:23 final size:23
Alignment explanation
Indices: 70774--70824 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
70764 TGGACCACTA
*
70774 AATTTGTCTAGTATATATAACAT
1 AATTTGTCTAGTATATAAAACAT
70797 AATTTGTCTAGTATATAAAACAT
1 AATTTGTCTAGTATATAAAACAT
70820 AATTT
1 AATTT
70825 ATATAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (23 bp):
AATTTGTCTAGTATATAAAACAT
Found at i:70836 original size:23 final size:23
Alignment explanation
Indices: 70785--70837 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
70775 ATTTGTCTAG
* * * *
70785 TATATATAACATAATTTGTCTAG
1 TATATAAAACATAATTTATATAA
70808 TATATAAAACATAATTTATATAA
1 TATATAAAACATAATTTATATAA
*
70831 TTTATAA
1 TATATAA
70838 TATAGTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (23 bp):
TATATAAAACATAATTTATATAA
Found at i:72152 original size:16 final size:16
Alignment explanation
Indices: 72131--72161 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
72121 ATAAATTAAT
*
72131 TTAATGGTGCTCATCG
1 TTAATGATGCTCATCG
72147 TTAATGATGCTCATC
1 TTAATGATGCTCATC
72162 CATGCTCGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (16 bp):
TTAATGATGCTCATCG
Found at i:79834 original size:2 final size:2
Alignment explanation
Indices: 79829--79858 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
79819 ACACACACAC
79829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79859 GGGTAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80590 original size:21 final size:21
Alignment explanation
Indices: 80566--80606 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
80556 TATATTTCTT
80566 TAGATTAAAAAAAGTTAATTA
1 TAGATTAAAAAAAGTTAATTA
* *
80587 TAGATTTAAAATAGTTAATT
1 TAGATTAAAAAAAGTTAATT
80607 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (21 bp):
TAGATTAAAAAAAGTTAATTA
Found at i:81982 original size:37 final size:37
Alignment explanation
Indices: 81892--81993 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 37
81882 CATTTTCGTC
*
81892 CTACTAGGATTCAAACTCCTAAAAATAGAATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGAATAGAATT
* * *
81929 TTGCTAGGATTCAAACTCCTAAAAATATG-ATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATA-GAATAGAATT
* * *
81966 CTACTATGATTTAAACTCCTAAAGATAG
1 CTACTAGGATTCAAACTCCTAAAAATAG
81994 GATCCACAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
36 1 0.02
37 53 0.96
38 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGAATAGAATT
Found at i:82543 original size:22 final size:21
Alignment explanation
Indices: 82454--82571 Score: 71
Period size: 22 Copynumber: 5.3 Consensus size: 21
82444 TTTTCAATTG
*
82454 ATTTTTTACACTATATATTATT
1 ATTTTTTATACTATAT-TTATT
* * *
82476 ATTATCTATACATATATTTTTT
1 ATTTTTTATAC-TATATTTATT
*
82498 ATTTATTTATA-T-TCATTTGGTT
1 ATTT-TTTATACTAT-ATTT-ATT
82520 ATTTTTTAATACTATATTTATT
1 ATTTTTT-ATACTATATTTATT
* *
82542 ATTTATATATA-TATATATATAT
1 ATTT-TTTATACTATATTTAT-T
82564 ACTTTTTT
1 A-TTTTTT
82572 TTAAATATTT
Statistics
Matches: 75, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
20 1 0.01
21 16 0.21
22 37 0.49
23 20 0.27
24 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTTATACTATATTTATT
Found at i:82554 original size:19 final size:19
Alignment explanation
Indices: 82465--82555 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
82455 TTTTTTACAC
*
82465 TATATAT-TA-TTATTATC
1 TATATATATATTTATTATT
* *
82482 TATACATATATTTTTTATT
1 TATATATATATTTATTATT
* *
82501 TATTTATATTCATTTGGTTATTT
1 TATATATA-T-ATTT-ATTA-TT
*
82524 TTTAATACTATATTTATTATT
1 TAT-ATA-TATATTTATTATT
82545 TATATATATAT
1 TATATATATAT
82556 ATATATATAC
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
17 6 0.11
18 2 0.04
19 17 0.30
20 4 0.07
21 8 0.14
22 6 0.11
23 8 0.14
24 3 0.05
25 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TATATATATATTTATTATT
Found at i:82778 original size:18 final size:19
Alignment explanation
Indices: 82752--82787 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
82742 GTTTTTGGTT
*
82752 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
82770 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
82788 TATTGTTATG
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:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:82831 original size:2 final size:2
Alignment explanation
Indices: 82824--82850 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
82814 TTTACTCATT
82824 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
82851 TAATATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82867 original size:4 final size:4
Alignment explanation
Indices: 82854--82883 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
82844 TATATATTAA
82854 TATT TCATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT T
82884 TTCCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:82892 original size:16 final size:16
Alignment explanation
Indices: 82873--82913 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
82863 TATTTATTTA
*
82873 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
82889 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
82904 TATT-TTTATT
1 T-TTATTTATT
82914 CTTCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:87505 original size:19 final size:19
Alignment explanation
Indices: 87461--87531 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
87451 ACAAAAAGGG
* *
87461 CAAAAATAAAA-AAGAAAT
1 CAAAAAAAAAAGAAGAAAA
* *
87479 GAAGAAAAAAAGAAGAAAA
1 CAAAAAAAAAAGAAGAAAA
* *
87498 CAAAAAAAAAGGAACAAAAA
1 CAAAAAAAAAAGAA-GAAAA
87518 TCAAAAAGAAAAAG
1 -CAAAAA-AAAAAG
87532 TGAAAAAAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 8 0.20
19 17 0.43
20 4 0.10
21 6 0.15
22 5 0.12
ACGTcount: A:0.77, C:0.06, G:0.13, T:0.04
Consensus pattern (19 bp):
CAAAAAAAAAAGAAGAAAA
Found at i:88206 original size:22 final size:22
Alignment explanation
Indices: 88134--88209 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
88124 CTACCTCATT
* *
88134 AAACCATTGAGCATCAAATACC
1 AAACCTTTGAGCATCAAATGCC
*
88156 AAACCTATGAGCATCAAATGCC
1 AAACCTTTGAGCATCAAATGCC
88178 AAACCTTTGAGCATCAAATGCC
1 AAACCTTTGAGCATCAAATGCC
88200 AAACCTTTGA
1 AAACCTTTGA
88210 CCAAACATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (22 bp):
AAACCTTTGAGCATCAAATGCC
Found at i:88430 original size:24 final size:24
Alignment explanation
Indices: 88401--88463 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
88391 GGGACAATAT
88401 TTTCAAAACTTTTAATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
* *
88425 TTTCAAAACTCTTGATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
88449 TTTCAAAACTCTTTA
1 TTTCAAAACT-TTTA
88464 TTGATATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 32 0.94
25 2 0.06
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTCAAAACTTTTAATTAAACATC
Found at i:88671 original size:30 final size:32
Alignment explanation
Indices: 88614--88674 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
88604 AGAAATGAGG
88614 AATATTTGGGGCATCTTTGAAGATTCAACATAA
1 AATATTTGGGGCATCTTTG-AGATTCAACATAA
*
88647 AATA-TTGGGGCATTTTTG-GATTCAACAT
1 AATATTTGGGGCATCTTTGAGATTCAACAT
88675 CCTAATGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.37
32 13 0.48
33 4 0.15
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (32 bp):
AATATTTGGGGCATCTTTGAGATTCAACATAA
Found at i:89194 original size:106 final size:106
Alignment explanation
Indices: 89069--90197 Score: 1611
Period size: 106 Copynumber: 10.7 Consensus size: 106
89059 ATTCACAATA
* *
89069 AAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAA
1 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
*
89134 GGATATTGGACTCCAGGCAACGCAAGTTCAACTTCACGACG
66 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
89175 AAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAAAGCCAATTTCAACTTCACAGCGAA
1 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
* *
89240 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAATG
66 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
89281 AAGGGACCGCTGGTTGTCAACAAACAACTACTTAATTTTAGAGCCAATTTCAACTTCACAGCGAA
1 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
*
89346 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACG
66 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
89387 AAGGGACCGATGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACTA-CGA
1 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCAC-AGCGA
* *
89451 AGGTTATTGGACTCCAGACAATGCAAGTTCAACTTCACGACG
65 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * * * *
89493 AAGGAACCGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAA
1 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
* *
89558 GGATATTGGACTCAAGACAATGCAAGTTCAACTTCACGACG
66 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
89599 AAGGGACCGCTGGTTGTCAATAAATAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
1 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
*
89664 GGATATTGGACTCCAGACAAAGCAAGTTCAACTTCACGACG
66 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
89705 AAGGGACCG-TGGTTGTCAACAAACAACTTCTC-ATTTCAGAGCCAATTTCAACTTCACAACGAA
1 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
89768 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
66 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * * *
89809 AAGGGA-CGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGTA
1 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
*
89873 GGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACG
66 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * * *
89914 AAGGGACCGCTGGTTGTCAATAAATAATTTC-CTAATTTCAGAGCCAATTTCAACTTCTCAGCGA
1 AAGGGACCGCTGGTTGTCAACAAACAACTTCTC-AATTTCAGAGCCAATTTCAACTTCACAGCGA
* * *
89978 AGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTCACGACG
65 AGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACG
* * * **
90020 AAGAGG-CGGTTGATTGTCAAC-AA-AA-TT-TC-A-TTCAGAGTTAATTTCAACTTCACAGCGA
1 AAG-GGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGA
* * *
90078 AGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACG
65 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * * * * ** * *
90120 AAGGGACGGCTGGTTGTTAACAAATAATTTCCCGGTTCCAGAGCCAATTTCAACTTCAC-GACGG
1 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAG-CGA
90184 AGGATATTGGACTC
65 AGGATATTGGACTC
90198 GGAACAATGC
Statistics
Matches: 930, Mismatches: 75, Indels: 36
0.89 0.07 0.03
Matches are distributed among these distances:
99 2 0.00
100 76 0.08
101 4 0.00
102 2 0.00
103 7 0.01
104 99 0.11
105 101 0.11
106 636 0.68
107 3 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (106 bp):
AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
Found at i:91491 original size:21 final size:22
Alignment explanation
Indices: 91460--91504 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
91450 ATTGATTTTT
91460 TACACTATATATTTATTATCTA
1 TACACTATATATTTATTATCTA
*
91482 TACA-TATATATTTATTATTTA
1 TACACTATATATTTATTATCTA
91503 TA
1 TA
91505 TTCATTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (22 bp):
TACACTATATATTTATTATCTA
Found at i:91569 original size:15 final size:15
Alignment explanation
Indices: 91536--91569 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
91526 ATAATAGTTT
*
91536 ATATATATATTATAT
1 ATATATATATTATAA
*
91551 ATATATATATTTTAA
1 ATATATATATTATAA
91566 ATAT
1 ATAT
91570 TTTACTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATATATTATAA
Found at i:91569 original size:17 final size:17
Alignment explanation
Indices: 91535--91569 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
91525 AATAATAGTT
*
91535 TATATATATATTATATA
1 TATATATATATTAAATA
*
91552 TATATATATTTTAAATA
1 TATATATATATTAAATA
91569 T
1 T
91570 TTTACTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATATATATTAAATA
Found at i:91782 original size:19 final size:19
Alignment explanation
Indices: 91743--91783 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
91733 GGTTTTTTTA
*
91743 TATTATATTATATTTTCAT
1 TATTATATTATATTATCAT
* *
91762 TATTATATTATGTTATGAT
1 TATTATATTATATTATCAT
91781 TAT
1 TAT
91784 ATTTTCTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (19 bp):
TATTATATTATATTATCAT
Found at i:91816 original size:2 final size:2
Alignment explanation
Indices: 91803--91837 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
91793 TTTACTCATT
*
91803 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
91838 CTATTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:91877 original size:23 final size:22
Alignment explanation
Indices: 91851--91893 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
91841 TTAATATTCA
*
91851 TTTATTTATTATTTTATTTTTCC
1 TTTATTTATTA-CTTATTTTTCC
*
91874 TTTATTTTTTACTTATTTTT
1 TTTATTTATTACTTATTTTT
91894 ATTCTTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTATTTATTACTTATTTTTCC
Done.