Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003322.1 Hibiscus syriacus cultivar Beakdansim tig00006994_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: 54880
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2343 original size:3 final size:3
Alignment explanation
Indices: 2337--2370 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2327 TAATAATAAA
2337 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2371 ATTTATACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2866 original size:6 final size:6
Alignment explanation
Indices: 2857--2887 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2847 TTAATGTTAA
2857 TAATAT TAATAT TAATAT TAATAT TAATAT T
1 TAATAT TAATAT TAATAT TAATAT TAATAT T
2888 TTTTAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Found at i:4178 original size:60 final size:60
Alignment explanation
Indices: 4073--4197 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
4063 CATAACACAT
***** *
4073 TTAAAAAAAGTTAATTTTTAATTTAATTCTTATTTTTTTTTAAATCTCTC-ATCTAAACCA
1 TTAAAAAAAGTTAATTTTTAATTTAATTCTTAAACACTTTAAAATCTCTCAAT-TAAACCA
* *
4133 TTAAAAAGAGTTAATTTTTAATTTAATTCTTAAACACTTTAAAATCTCTCAATTAAACCC
1 TTAAAAAAAGTTAATTTTTAATTTAATTCTTAAACACTTTAAAATCTCTCAATTAAACCA
4193 TTAAA
1 TTAAA
4198 CACCCGACAC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 54 0.96
61 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (60 bp):
TTAAAAAAAGTTAATTTTTAATTTAATTCTTAAACACTTTAAAATCTCTCAATTAAACCA
Found at i:16676 original size:50 final size:51
Alignment explanation
Indices: 16617--16721 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 51
16607 CAAGTTTTTT
* * ** * * * *
16617 TTTTTCAAGATAAGTCGAGTTGAAAGGATT-ATTTTTTAGGTCGAGTAAAA
1 TTTTTCAAGACAAATCGAGCGGAAAAGATTGATTTTTCAAGTCGAATAAAA
*
16667 TTTTTCAAGACAAATCGAGCGGAAAAGATTGATTTTTCAAGTCGAATAGAA
1 TTTTTCAAGACAAATCGAGCGGAAAAGATTGATTTTTCAAGTCGAATAAAA
16718 TTTT
1 TTTT
16722 GCTCAGCTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
50 25 0.56
51 20 0.44
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (51 bp):
TTTTTCAAGACAAATCGAGCGGAAAAGATTGATTTTTCAAGTCGAATAAAA
Found at i:17498 original size:5 final size:5
Alignment explanation
Indices: 17488--17515 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
17478 CTCTTCATAC
17488 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
17516 TTCTCTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:18909 original size:18 final size:18
Alignment explanation
Indices: 18886--18920 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18876 TTTTGGAGAG
* *
18886 TTGAAATAAAATTAAGAT
1 TTGAAAGAAAATAAAGAT
18904 TTGAAAGAAAATAAAGA
1 TTGAAAGAAAATAAAGA
18921 AACTAAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (18 bp):
TTGAAAGAAAATAAAGAT
Found at i:20430 original size:118 final size:118
Alignment explanation
Indices: 20219--20444 Score: 348
Period size: 118 Copynumber: 1.9 Consensus size: 118
20209 GGGCTCCTAA
*
20219 TTTTTATATTTATAGTAGGGTCCCTAATTTTTATAATTCCATAAAATTCTTAGTTTTTGACCCTC
1 TTTTTATATTTATAGTAGGGACCCTAATTTTTATAATTCCATAAAATTCTTAGTTTTTGACCCTC
* *
20284 TTTTTTCATATCTCTTATTAATTCATTCAATTTTGAATTAAATTTAACCATTT
66 TTTTGTCATATATCTTATTAATTCATTCAATTTTGAATTAAATTTAACCATTT
* *
20337 TTTTTATATTTATAATTA-GGACCCTAATTTTTATAATTTCATAAAATGT-TTAGTTTTTGACCC
1 TTTTTATATTTAT-AGTAGGGACCCTAATTTTTATAATTCCATAAAAT-TCTTAGTTTTTGACCC
* * *
20400 TCTTTTGTCATTTATCTTATTTATTTATTCAATTTTGAATTAAAT
64 TCTTTTGTCATATATCTTATTAATTCATTCAATTTTGAATTAAAT
20445 CAAATCATAT
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
118 94 0.96
119 4 0.04
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.53
Consensus pattern (118 bp):
TTTTTATATTTATAGTAGGGACCCTAATTTTTATAATTCCATAAAATTCTTAGTTTTTGACCCTC
TTTTGTCATATATCTTATTAATTCATTCAATTTTGAATTAAATTTAACCATTT
Found at i:23376 original size:7 final size:7
Alignment explanation
Indices: 23364--23388 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
23354 AATTATGAAG
23364 TGAATAA
1 TGAATAA
23371 TGAATAA
1 TGAATAA
23378 TGAATAA
1 TGAATAA
23385 TGAA
1 TGAA
23389 CGGTACATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (7 bp):
TGAATAA
Found at i:25306 original size:32 final size:31
Alignment explanation
Indices: 25270--25338 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
25260 TTGGTTAAAT
* *
25270 AAATTTCAGTTCGATTAATGGTTATAGAAAAA
1 AAATTT-AGTTCGATTAACGGTTAAAGAAAAA
*
25302 AAATTTGGTTCGATTAACGGTTAAAGAAAAA
1 AAATTTAGTTCGATTAACGGTTAAAGAAAAA
*
25333 ATATTT
1 AAATTT
25339 TATTTGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 27 0.82
32 6 0.18
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (31 bp):
AAATTTAGTTCGATTAACGGTTAAAGAAAAA
Found at i:25314 original size:31 final size:31
Alignment explanation
Indices: 25278--25338 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
25268 ATAAATTTCA
* *
25278 GTTCGATTAATGGTTATAGAAAAAAAATTTG
1 GTTCGATTAACGGTTAAAGAAAAAAAATTTG
*
25309 GTTCGATTAACGGTTAAAGAAAAAATATTT
1 GTTCGATTAACGGTTAAAGAAAAAAAATTT
25339 TATTTGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (31 bp):
GTTCGATTAACGGTTAAAGAAAAAAAATTTG
Found at i:25438 original size:94 final size:92
Alignment explanation
Indices: 25337--25680 Score: 419
Period size: 94 Copynumber: 3.8 Consensus size: 92
25327 GAAAAAATAT
25337 TTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTCTTTAA-CATTAATCGAACC
1 TTTATTTGAAAATTATTAACCGAACCAAATTAA---ATTTTTTTTCTTTAACCATTAATCGAACC
25401 AAAATTATTTGACCGTTAATCGAACCAAAA
63 AAAATTATTTGACCGTTAATCGAACCAAAA
25431 TTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTTCTTT-ACCATTAATCGAACC
1 TTTATTTGAAAATTATTAACCGAACCAAATTAA---ATTTTTTTTCTTTAACCATTAATCGAACC
* * * *
25495 AAAATTATTTGACTGTTACTCAAACCGAAA
63 AAAATTATTTGACCGTTAATCGAACCAAAA
*
25525 TTTATTTGAAAATTATT-----AACC-----AAA-TTTTTTTCTTTAACCATTAATCGAACCGAA
1 TTTATTTGAAAATTATTAACCGAACCAAATTAAATTTTTTTTCTTTAACCATTAATCGAACCAAA
*
25579 ATTATTTGACCGTTAATCGAACCCAAA
66 ATTATTTGACCGTTAATCGAACCAAAA
* * * *
25606 TTTATTTGAAAATTATTAACCGAA-TAAAATAAATTATTTTTTCTTTAACCGTTAATTGAACCGA
1 TTTATTTGAAAATTATTAACCGAACCAAATTAAATT-TTTTTTCTTTAACCATTAATCGAACC-A
*
25670 AATTTATTTGA
64 AAATTATTTGA
25681 AAATTATTAA
Statistics
Matches: 221, Mismatches: 14, Indels: 31
0.83 0.05 0.12
Matches are distributed among these distances:
80 11 0.05
81 58 0.26
84 2 0.01
86 2 0.01
89 4 0.02
90 3 0.01
91 1 0.00
92 24 0.11
93 11 0.05
94 105 0.48
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.39
Consensus pattern (92 bp):
TTTATTTGAAAATTATTAACCGAACCAAATTAAATTTTTTTTCTTTAACCATTAATCGAACCAAA
ATTATTTGACCGTTAATCGAACCAAAA
Found at i:25569 original size:175 final size:173
Alignment explanation
Indices: 25365--25680 Score: 485
Period size: 175 Copynumber: 1.8 Consensus size: 173
25355 ACCGAACCAA
* *
25365 ATTAACCGATTTTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAAA
1 ATTAACCAAATTTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAAA
*
25430 ATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATT-TTTTTTCTTT-ACCATTAATCGAA
66 ATTTATTTGAAAATTATTAACCGAA-CAAAATAA---ATTATTTTTTCTTTAACCATTAATCGAA
25493 CC-AAAATTATTTGACTGTTACTCAAACCGAAATTTATTTGAAAATT
127 CCGAAAATTATTTGACTGTTACTCAAACCGAAATTTATTTGAAAATT
* *
25539 ATTAACCAAATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCCA
1 ATTAACCAAATTTTTTTCTTTAA-CATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAA
* * *
25604 AATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCTTTAACCGTTAATTGAACCG
65 AATTTATTTGAAAATTATTAACCGAACAAAATAAATTATTTTTTCTTTAACCATTAATCGAACCG
*
25669 AAATTTATTTGA
130 AAAATTATTTGA
25681 AAATTATTAA
Statistics
Matches: 129, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
171 3 0.02
172 10 0.08
173 13 0.10
174 38 0.29
175 65 0.50
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.39
Consensus pattern (173 bp):
ATTAACCAAATTTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAAA
ATTTATTTGAAAATTATTAACCGAACAAAATAAATTATTTTTTCTTTAACCATTAATCGAACCGA
AAATTATTTGACTGTTACTCAAACCGAAATTTATTTGAAAATT
Found at i:25581 original size:81 final size:80
Alignment explanation
Indices: 25459--25626 Score: 264
Period size: 81 Copynumber: 2.1 Consensus size: 80
25449 ACCGAACCAA
* * * * *
25459 ATTAACCGATTTTTTTTCTTTACCATTAATCGAACCAAAATTATTTGACTGTTACTCAAACCGAA
1 ATTAACCAAATTTTTTTCTTTACCATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAA
25524 ATTTATTTGAAAATT
66 ATTTATTTGAAAATT
* *
25539 ATTAACCAAATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCCA
1 ATTAACCAAATTTTTTTCTTT-ACCATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCA
25604 AATTTATTTGAAAATT
65 AATTTATTTGAAAATT
25620 ATTAACC
1 ATTAACC
25627 GAATAAAATA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 19 0.24
81 61 0.76
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.39
Consensus pattern (80 bp):
ATTAACCAAATTTTTTTCTTTACCATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAA
ATTTATTTGAAAATT
Found at i:25667 original size:66 final size:66
Alignment explanation
Indices: 25587--25830 Score: 276
Period size: 66 Copynumber: 3.7 Consensus size: 66
25577 AAATTATTTG
25587 ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCTTT
1 ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCTTT
25652 A
66 A
* * ** ***
25653 ACCGTTAATTGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCT
1 ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAATAAAAT-AAATTA-TTTTTTCT
25718 TTA
64 TTA
* * *** * * * *
25721 ACCATTAATCGAA-CCAAAATTATTTGACCGTTAATCGAATCGAATAAAATAAATT-CTTTTTCC
1 ACCGTTAATCGAACCCAAATTTATTTGAAAATT-AT-TAACCGAATAAAATAAATTATTTTTTCT
25784 TTA
64 TTA
* *
25787 CCCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAAT
1 ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAAT
25831 CGAATTAACC
Statistics
Matches: 141, Mismatches: 32, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
65 7 0.05
66 67 0.48
67 31 0.22
68 26 0.18
69 10 0.07
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (66 bp):
ACCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCTTT
A
Found at i:25734 original size:134 final size:137
Alignment explanation
Indices: 25591--25882 Score: 378
Period size: 134 Copynumber: 2.2 Consensus size: 137
25581 TATTTGACCG
* * *
25591 TTAATCGAACCCAAATTTATTTGAAAATT-AT-TAACCGAATAAAATAAATTATTTTTTCTTTAA
1 TTAATCGAACCCAAATTTATTTGAAAATTAATCGAACCGAATAAAATAAATT-CTTTTTCCTTAA
* *
25654 CCGTTAATTGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCG-A-TTTTTTTC
65 CCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGAATTTTTTTTC
**
25717 TTTAACCA
130 TGGAACCA
* *** * *
25725 TTAATCGAA-CCAAAATTATTTGACCGTTAATCGAATCGAATAAAATAAATTCTTTTTCCTTACC
1 TTAATCGAACCCAAATTTATTTGAAAATTAATCGAACCGAATAAAATAAATTCTTTTTCCTTAAC
* * *
25789 CGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAATCGAATTAACCGAATTTTTTTTCT
66 CGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGAATTTTTTTTCT
25854 GGAACCA
131 GGAACCA
**
25861 TTAATCGAACTGAAATTTATTT
1 TTAATCGAACCCAAATTTATTT
25883 AACCAAATAA
Statistics
Matches: 134, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
133 15 0.11
134 69 0.51
135 18 0.13
136 23 0.17
137 9 0.07
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (137 bp):
TTAATCGAACCCAAATTTATTTGAAAATTAATCGAACCGAATAAAATAAATTCTTTTTCCTTAAC
CGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGAATTTTTTTTCT
GGAACCA
Found at i:26763 original size:30 final size:30
Alignment explanation
Indices: 26718--26809 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
26708 AAAATTTAAA
*
26718 AACAG-AAAATAAAAGGGC-TGAAATATAAAT
1 AACAGAAAAAT-AAAGGGCAT-AAATACAAAT
*
26748 ATA-AGAAAAATAAAGGGCATAAATGCAAAT
1 A-ACAGAAAAATAAAGGGCATAAATACAAAT
* * *
26778 AACAGAAAAATAAAGTGTATAAATATAAAT
1 AACAGAAAAATAAAGGGCATAAATACAAAT
26808 AA
1 AA
26810 ACGAAAGTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 1 0.02
30 44 0.85
31 7 0.13
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.18
Consensus pattern (30 bp):
AACAGAAAAATAAAGGGCATAAATACAAAT
Found at i:27162 original size:2 final size:2
Alignment explanation
Indices: 27150--27198 Score: 55
Period size: 2 Copynumber: 24.0 Consensus size: 2
27140 TATTACTCCC
* *
27150 AT AT AT GAT AT AT A- AC AT AT GAA 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 AT AT AT AT AT AT
27193 AT AT AT
1 AT AT AT
27199 GATTATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 1 0.02
2 37 0.90
3 3 0.07
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:27205 original size:16 final size:15
Alignment explanation
Indices: 27150--27205 Score: 73
Period size: 14 Copynumber: 3.9 Consensus size: 15
27140 TATTACTCCC
27150 ATATATGATATATA-
1 ATATATGATATATAT
* *
27164 ACATATGAAATATAT
1 ATATATGATATATAT
27179 ATATAT-ATATATAT
1 ATATATGATATATAT
27193 ATATATGAT-TATA
1 ATATATGATATATA
27206 AAAGATCGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 29 0.81
15 7 0.19
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (15 bp):
ATATATGATATATAT
Found at i:27630 original size:18 final size:18
Alignment explanation
Indices: 27607--27645 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
27597 TTTTCAATGA
27607 AAAATACATAAAAATTTT
1 AAAATACATAAAAATTTT
* * *
27625 AAAATATATGACAATTTT
1 AAAATACATAAAAATTTT
27643 AAA
1 AAA
27646 TTTCAAGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAATACATAAAAATTTT
Found at i:27962 original size:20 final size:20
Alignment explanation
Indices: 27926--27981 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
27916 AAATCTCAAT
27926 TGAGTCTTAGG--TATGCTC
1 TGAGTCTTAGGTATATGCTC
27944 TGAGTCTTAGGTATATGCTC
1 TGAGTCTTAGGTATATGCTC
*
27964 TGAGTATTAGGTATATGC
1 TGAGTCTTAGGTATATGC
27982 ATCACTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 11 0.31
20 24 0.69
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.39
Consensus pattern (20 bp):
TGAGTCTTAGGTATATGCTC
Found at i:31515 original size:23 final size:23
Alignment explanation
Indices: 31452--31517 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
31442 CTGAATGATT
* * *
31452 CAGTGCTGACTGATTCAACAAAA
1 CAGTGTTGAATGATTCAGCAAAA
31475 CAGTGTTGAATGATTCAGCAAAA
1 CAGTGTTGAATGATTCAGCAAAA
31498 CAGTGTTGAATGATTCAGCA
1 CAGTGTTGAATGATTCAGCA
31518 CAGAAGTACA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (23 bp):
CAGTGTTGAATGATTCAGCAAAA
Found at i:34530 original size:2 final size:2
Alignment explanation
Indices: 34523--34555 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34513 ATCGATGATT
34523 TA TA TA 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 T
34556 TTAATATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35321 original size:18 final size:18
Alignment explanation
Indices: 35298--35333 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35288 TGGTTTGATC
*
35298 CGTCTCGAGTCTAAGGGA
1 CGTCTCAAGTCTAAGGGA
35316 CGTCTCAAGTCTAAGGGA
1 CGTCTCAAGTCTAAGGGA
35334 ATCGACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (18 bp):
CGTCTCAAGTCTAAGGGA
Found at i:37269 original size:13 final size:12
Alignment explanation
Indices: 37251--37301 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
37241 TTTTTAATAA
37251 AAAAAGTATATTT
1 AAAAAGTAT-TTT
*
37264 AAAAAGTGATGTT
1 AAAAAGT-ATTTT
37277 AAAAAGTATTTT
1 AAAAAGTATTTT
*
37289 TAAAAGTGATTTT
1 AAAAAGT-ATTTT
37302 GAAAGTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 10 0.30
13 21 0.64
14 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (12 bp):
AAAAAGTATTTT
Found at i:38539 original size:2 final size:2
Alignment explanation
Indices: 38532--38577 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
38522 TAATAATCTC
*
38532 AT AT AT AT AT AT AT CT 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 AT AT AT AT AT AT
38574 AT AT
1 AT AT
38578 CGATTTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38719 original size:2 final size:2
Alignment explanation
Indices: 38712--38752 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
38702 GAATAATTTC
38712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38753 AACTCAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45135 original size:2 final size:2
Alignment explanation
Indices: 45128--45153 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45118 TCCAGTCCCA
45128 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
45154 GTGCTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:53126 original size:16 final size:15
Alignment explanation
Indices: 53071--53137 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
53061 TGATTTTATA
* *
53071 ATTAATTTAAAATTT
1 ATTATTTTAATATTT
* *
53086 ATTATGTAAATATTT
1 ATTATTTTAATATTT
*
53101 ATTTAATTTAATATTTT
1 A-TTATTTTAATA-TTT
* *
53118 ATTATTTTAAAATTA
1 ATTATTTTAATATTT
53133 ATTAT
1 ATTAT
53138 ATACACAGCT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
15 19 0.47
16 17 0.43
17 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (15 bp):
ATTATTTTAATATTT
Done.