Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003951.1 Hibiscus syriacus cultivar Beakdansim tig00008539_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: 102818
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5586 original size:2 final size:2
Alignment explanation
Indices: 5574--5607 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5564 TGATTTTCTG
*
5574 AT AT AT GT 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
5608 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5612 original size:2 final size:2
Alignment explanation
Indices: 5607--5655 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5597 TATATATATA
5607 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5649 TG TG TG T
1 TG TG TG T
5656 TTATCGTATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:6140 original size:21 final size:21
Alignment explanation
Indices: 6093--6133 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6083 TGTCACCGCG
6093 AGATCC-TCCTATTTCGCATGT
1 AGATCCAT-CTATTTCGCATGT
*
6114 AGATCCATCTATTTCTCATG
1 AGATCCATCTATTTCGCATG
6134 ATGATCCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.39
Consensus pattern (21 bp):
AGATCCATCTATTTCGCATGT
Found at i:10429 original size:20 final size:22
Alignment explanation
Indices: 10391--10431 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
10381 TATATAAAAT
*
10391 TATATATGTTCATCGATATAAG
1 TATATATGTTCATCAATATAAG
10413 TATATATG-TCAT-AATATAA
1 TATATATGTTCATCAATATAA
10432 CCATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (22 bp):
TATATATGTTCATCAATATAAG
Found at i:10516 original size:23 final size:24
Alignment explanation
Indices: 10489--10533 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
10479 ACATAACTAA
10489 ATATAA-TAACTAATAAT-TAACTC
1 ATATAATTAA-TAATAATATAACTC
10512 ATATAATTAATAATAATATAAC
1 ATATAATTAATAATAATATAAC
10534 ATATGAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATAATTAATAATAATATAACTC
Found at i:20548 original size:17 final size:16
Alignment explanation
Indices: 20526--20559 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
20516 TAAAAACAGT
20526 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
20543 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
20559 A
1 A
20560 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:21078 original size:24 final size:24
Alignment explanation
Indices: 21034--21080 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21024 ATAAAGAACC
*
21034 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
21058 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
21081 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:24388 original size:19 final size:20
Alignment explanation
Indices: 24366--24409 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
24356 GAGAAAAGGT
24366 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
24385 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
24405 AAAAG
1 AAAAG
24410 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:30783 original size:17 final size:16
Alignment explanation
Indices: 30761--30794 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
30751 TAAAAACAGT
30761 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
30778 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
30794 A
1 A
30795 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:31313 original size:24 final size:24
Alignment explanation
Indices: 31269--31315 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31259 ATAAAGAACC
*
31269 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
31293 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
31316 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:48221 original size:23 final size:24
Alignment explanation
Indices: 48194--48238 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
48184 GCATAACTAA
48194 ATATAA-TAACTAATAAT-TAACCC
1 ATATAATTAA-TAATAATATAACCC
48217 ATATAATTAATAATAATATAAC
1 ATATAATTAATAATAATATAAC
48239 ATATGAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (24 bp):
ATATAATTAATAATAATATAACCC
Found at i:48774 original size:3 final size:3
Alignment explanation
Indices: 48766--48804 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
48756 TAAATTTCTA
48766 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
48805 AGGGTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:50586 original size:17 final size:17
Alignment explanation
Indices: 50564--50601 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
50554 AAAATCCAAT
50564 CCCTTATCAGAAAACCA
1 CCCTTATCAGAAAACCA
50581 CCCTTATCAGAAAACCA
1 CCCTTATCAGAAAACCA
50598 CCCT
1 CCCT
50602 CAAATTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.39, G:0.05, T:0.18
Consensus pattern (17 bp):
CCCTTATCAGAAAACCA
Found at i:55200 original size:28 final size:28
Alignment explanation
Indices: 55164--55220 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
55154 AATTTGACAG
55164 AACTCGTATCAGGACGGACATGATGAAC
1 AACTCGTATCAGGACGGACATGATGAAC
55192 AACTCGTATCAGGACGGACATGATGAAC
1 AACTCGTATCAGGACGGACATGATGAAC
55220 A
1 A
55221 TGTAATGTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.18
Consensus pattern (28 bp):
AACTCGTATCAGGACGGACATGATGAAC
Found at i:57058 original size:21 final size:21
Alignment explanation
Indices: 57032--57076 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57022 GATTTCTGGG
* *
57032 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
57053 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
57074 CAA
1 CAA
57077 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:57679 original size:18 final size:18
Alignment explanation
Indices: 57656--57690 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
57646 CTAGGAGATT
57656 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
57674 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
57691 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:57776 original size:21 final size:22
Alignment explanation
Indices: 57747--57790 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
57737 GTTGTATGAT
57747 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
57768 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
57790 A
1 A
57791 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:59012 original size:149 final size:149
Alignment explanation
Indices: 58549--59001 Score: 870
Period size: 149 Copynumber: 3.0 Consensus size: 149
58539 GAGTCGAGGG
* *
58549 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
58614 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
58679 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
58698 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
58763 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
58828 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
58847 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
58912 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
58977 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
58996 TCTACG
1 TCTACG
59002 GGGCACTTCG
Statistics
Matches: 300, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 300 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:59024 original size:23 final size:23
Alignment explanation
Indices: 58980--59024 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
58970 ATCATTATAT
*
58980 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
59003 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
59025 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:60251 original size:21 final size:20
Alignment explanation
Indices: 60224--60322 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
60214 AATTAGTTTC
60224 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
60245 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
60266 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
60286 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
60307 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
60323 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:60313 original size:20 final size:19
Alignment explanation
Indices: 60287--60359 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
60277 TGCGATTTTC
*
60287 CAAAATCGCAACGCGAATA
1 CAAAATCGCAACGCGAACA
*
60306 TGAAAATCGCAACGCGAACA
1 -CAAAATCGCAACGCGAACA
*
60326 CATAAATCGCAACGCGTATC-
1 CA-AAATCGCAACGCG-AACA
60346 CATAAATCGCAACG
1 CA-AAATCGCAACG
60360 TGTATCCGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.94
21 2 0.04
ACGTcount: A:0.42, C:0.27, G:0.16, T:0.14
Consensus pattern (19 bp):
CAAAATCGCAACGCGAACA
Found at i:60338 original size:40 final size:39
Alignment explanation
Indices: 60289--60483 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 39
60279 CGATTTTCCA
* * *
60289 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATACGTAAATCGCAACGCGAAC-CAT
* * * * *
60329 AAATCGCAACGCGTATCCATAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATACGTAAATCGCAACGCG-AACCAT
** * *
60369 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCAT
1 AAATCGCAACGCGTATACGTAAATCGCAACGCG-AACCAT
* * ** *
60409 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATACGTAAATCGCAACGCGAA-CCAT
*
60449 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATACGTAAATCGCAACGCGA
60484 TATTTAAAGC
Statistics
Matches: 127, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 93 0.73
41 33 0.26
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATACGTAAATCGCAACGCGAACCAT
Found at i:60364 original size:20 final size:20
Alignment explanation
Indices: 60309--60482 Score: 199
Period size: 20 Copynumber: 8.7 Consensus size: 20
60299 GCGAATATGA
*
60309 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CAT
60329 AAATCGCAACGCGTATCCAT
1 AAATCGCAACGCGTATCCAT
* *
60349 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCAT
***
60369 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCAT
*
60389 AAATCGCAATGCGTATCCAT
1 AAATCGCAACGCGTATCCAT
* *
60409 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCAT
* *
60429 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCAT
*
60449 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCAT
60470 AAATCGCAACGCG
1 AAATCGCAACGCG
60483 ATATTTAAAG
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.01
20 111 0.85
21 17 0.13
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCAT
Found at i:60373 original size:60 final size:60
Alignment explanation
Indices: 60285--60482 Score: 245
Period size: 60 Copynumber: 3.3 Consensus size: 60
60275 ATTGCGATTT
* ** * *
60285 TCCA-AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTA
1 TCCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTA
* * *** *
60344 TCCATAAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTA
1 TCCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTA
* **
60404 TCCATATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTA
1 TCCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTA
*
60465 TCCGTAAATCGCAACGCG
1 TCCATAAATCGCAACGCG
60483 ATATTTAAAG
Statistics
Matches: 115, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
59 4 0.03
60 81 0.70
61 30 0.26
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.19
Consensus pattern (60 bp):
TCCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTA
Found at i:60904 original size:33 final size:33
Alignment explanation
Indices: 60865--60935 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
60855 TTCACTTAGA
*
60865 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
60898 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
60931 TTTCA
1 TTTCA
60936 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:61059 original size:20 final size:20
Alignment explanation
Indices: 61015--61124 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
61005 TGCAGAAGAG
*
61015 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
61036 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
61056 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
61077 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
61091 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
61110 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
61125 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:61072 original size:41 final size:38
Alignment explanation
Indices: 61008--61124 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
60998 TTCAATTTGC
* *
61008 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
61046 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
61087 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
61120 AGAAT
1 AGAAT
61125 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:61094 original size:14 final size:14
Alignment explanation
Indices: 61075--61131 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
61065 GAGAAATGAA
61075 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
61089 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
61108 AATCGCAACGAGAG
1 AATCGCAACGAGAG
61122 AATCGCAACG
1 AATCGCAACG
61132 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:61107 original size:33 final size:33
Alignment explanation
Indices: 61067--61147 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
61057 CGCAACGAGA
61067 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
61100 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
61133 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
61148 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:61184 original size:14 final size:14
Alignment explanation
Indices: 61165--61254 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
61155 TTTAATTTCG
61165 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
61179 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
61198 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
61212 CGTTGCGATTGTCATTTT
1 CGTTGCGA-T-TC--TCT
61230 GCGTTGCGATTCTCT
1 -CGTTGCGATTCTCT
61245 CGTTGCGATT
1 CGTTGCGATT
61255 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 3 0.05
16 5 0.08
17 5 0.08
18 3 0.05
19 18 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:61190 original size:33 final size:33
Alignment explanation
Indices: 61148--61262 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
61138 CAAAATCGCA
*
61148 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
61181 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
61214 TTGCGATTGTCATTTTGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
61247 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
61263 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:61203 original size:19 final size:19
Alignment explanation
Indices: 61143--61240 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
61133 GAAACCAAAA
* *
61143 TCGCATTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
61162 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
61176 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
61195 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
61209 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
*
61228 TTGCGTTGCGATT
1 TCGCGTTGCGATT
61241 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
16 5 0.08
17 5 0.08
19 31 0.51
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:63440 original size:12 final size:12
Alignment explanation
Indices: 63423--63447 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63413 TCTTCGGGGA
63423 CTTTTTCTTCTT
1 CTTTTTCTTCTT
63435 CTTTTTCTTCTT
1 CTTTTTCTTCTT
63447 C
1 C
63448 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:64375 original size:20 final size:20
Alignment explanation
Indices: 64347--64576 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
64337 AAATTTCAGT
* * *
64347 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
64367 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
64387 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
64407 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
64427 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
64447 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
64467 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
64487 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
64507 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
64527 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
64547 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
64567 GTTGCGATTT
1 GTTGCGATTT
64577 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:64577 original size:20 final size:20
Alignment explanation
Indices: 64543--64619 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
64533 ATTTATGTGT
*
64543 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAA
* *
64563 TCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTT-CATAA
* *
64584 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTC-ATAA
64605 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
64620 GGAAACTGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 15 0.31
21 33 0.69
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAA
Found at i:64592 original size:21 final size:21
Alignment explanation
Indices: 64543--64659 Score: 98
Period size: 20 Copynumber: 5.7 Consensus size: 21
64533 ATTTATGTGT
* * *
64543 TCGCGTTGCGATTTT-CATAT
1 TCGCGTTGCGATTTTGGAAAA
64563 TCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGGAAAA
* *
64584 TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGGAA-AA
*
64605 TCGCGTTGCGATTTTGGAAAC
1 TCGCGTTGCGATTTTGGAAAA
** * **
64626 T-GATTTGCGATTCTGG-GGA
1 TCGCGTTGCGATTTTGGAAAA
64645 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
64660 TATTTCGCGT
Statistics
Matches: 76, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.01
20 39 0.51
21 34 0.45
22 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTGGAAAA
Found at i:64634 original size:41 final size:41
Alignment explanation
Indices: 64543--64659 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 41
64533 ATTTATGTGT
* * *
64543 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTCAGAATCGCGTTGCGATTTTGGAAAA
*
64584 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAAC
1 TCGCATTGCGATTTTC-AGAATCGCGTTGCGATTTTGGAAAA
* ** *
64626 T-G-ATTTGCGATTCTGGGGATCGCGTTGCGATTTT
1 TCGCA-TTGCGATTTTCAGAATCGCGTTGCGATTTT
64660 TATTTCGCGT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
40 18 0.27
41 25 0.38
42 23 0.35
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (41 bp):
TCGCATTGCGATTTTCAGAATCGCGTTGCGATTTTGGAAAA
Found at i:64659 original size:40 final size:42
Alignment explanation
Indices: 64563--64659 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
64553 ATTTTCATAT
*
64563 TCGCGTTGCGATTTTGGAAAATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTGGAAAATCGCATTGCGATTCTCAAGAA
* ** *
64605 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCT-GGGGA
1 TCGCGTTGCGATTTTGGAAAATCGCA-TTGCGATTCTCAAGAA
64645 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
64660 TATTTCGCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 18 0.37
41 10 0.20
42 21 0.43
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (42 bp):
TCGCGTTGCGATTTTGGAAAATCGCATTGCGATTCTCAAGAA
Found at i:64931 original size:6 final size:6
Alignment explanation
Indices: 64920--64954 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
64910 TCAGTTCATG
64920 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
64955 TTTATCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:65052 original size:2 final size:2
Alignment explanation
Indices: 65040--65071 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
65030 TTATTATTAT
65040 TA TA T- 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
65072 TATTAGCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:65088 original size:3 final size:3
Alignment explanation
Indices: 64989--65076 Score: 88
Period size: 3 Copynumber: 27.0 Consensus size: 3
64979 ATATTACGTT
*
64989 TTA TTA TTA TTA TATA TGTT TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65036 TTA TTA -TA TTA TATA TATA TATA TATA TATA TATA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA T-TA T-TA T-TA T-TA TTA TTA
65077 GCTGTTATTA
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.03
3 49 0.62
4 28 0.35
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:65423 original size:19 final size:20
Alignment explanation
Indices: 65390--65437 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
65380 CTTTATTTGA
*
65390 TTTTTTAGTATTTTTTCTTAT-
1 TTTTTTA-TATTTTTAC-TATG
65411 TTTTTTATA-TTTTACTATG
1 TTTTTTATATTTTTACTATG
65430 TTTTTTAT
1 TTTTTTAT
65438 TTGGTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 13 0.52
20 2 0.08
21 7 0.28
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTTTATATTTTTACTATG
Found at i:65598 original size:21 final size:20
Alignment explanation
Indices: 65575--65612 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65565 TTATTTTTGT
65575 TTTTA-TTTATGTTATTTTCC
1 TTTTATTTTA-GTTATTTTCC
65595 TTTTATTTTAGTTATTTT
1 TTTTATTTTAGTTATTTT
65613 ACTTACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTATTTTAGTTATTTTCC
Found at i:70389 original size:110 final size:110
Alignment explanation
Indices: 70247--70756 Score: 757
Period size: 110 Copynumber: 4.7 Consensus size: 110
70237 GTCGAGAAAA
* **
70247 ACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
* * *
70312 ATTGGACTCGAGACAACAC-AGACCCAACTTCATAGCGAATGGGAG
66 ATTGGACTCGAGACAACACAAG-CTCAACTTCACAGCGAAGGGGAG
* * * * *
70357 ACTGAATGTCAAAAAACAACTTTTCAATTTCATTCAGAGTTAATTTCAACTTCACAATGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
*
70422 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGTGAA-GGGACG
66 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGA-G
* *
70467 ACTGACTGTCAACAAACAACTTTTCAG-TT--TT---ATTCAATTTCAACTTCACAGCGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
* *
70526 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGAGAAGGGGCG
66 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGAG
*
70571 ACTGACTGTAAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
*
70636 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCG
66 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGAG
*
70681 ACTGACTGTTAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
* *
70746 TTTGAACTCGA
66 ATTGGACTCGA
70757 AGCGACAAAA
Statistics
Matches: 366, Mismatches: 25, Indels: 18
0.89 0.06 0.04
Matches are distributed among these distances:
104 89 0.24
105 5 0.01
107 4 0.01
109 6 0.02
110 260 0.71
111 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (110 bp):
ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
ATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGAG
Found at i:70622 original size:214 final size:214
Alignment explanation
Indices: 70247--70716 Score: 710
Period size: 214 Copynumber: 2.2 Consensus size: 214
70237 GTCGAGAAAA
* * *
70247 ACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAG-TT--TT---ATTCAATTTCAACTTCACAGCGAAGGAT
* * *
70312 ATTGGACTCGAGACAACACAGACCCAACTTCATAGCGAATGGGAGACTGAATGTCAAAAAACAAC
60 ATTGGACTCGAGACAACACAGACCCAACTTCACAGAGAAGGGGAGACTGAATGTCAAAAAACAAC
* *
70377 TTTTCAATTTCATTCAGAGTTAATTTCAACTTCACAATGAAGGATATTGGACTCGAGACAACACA
125 TTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
*
70442 AGCTCAACTTCACAGTGAAGGGACG
190 AGCTCAACTTCACAGCGAAGGGACG
70467 ACTGACTGTCAACAAACAACTTTTCAGTTTTATTCAATTTCAACTTCACAGCGAAGGATATTGGA
1 ACTGACTGTCAACAAACAACTTTTCAGTTTTATTCAATTTCAACTTCACAGCGAAGGATATTGGA
* * *
70532 CTCGAGACAACACA-AGCTCAACTTCACAGAGAAGGGGCGACTGACTGT-AAACAAACAACTTTT
66 CTCGAGACAACACAGA-CCCAACTTCACAGAGAAGGGGAGACTGAATGTCAAA-AAACAACTTTT
*
70595 CAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCT
129 CAATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCT
*
70660 CAACTTCACAGCGAAGGGGCG
194 CAACTTCACAGCGAAGGGACG
* *
70681 ACTGACTGTTAACAAACAACTTTTCAGTTTCATTCA
1 ACTGACTGTCAACAAACAACTTTTCAGTTTTATTCA
70717 GAGTCAATTT
Statistics
Matches: 232, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
213 4 0.02
214 198 0.85
217 2 0.01
219 2 0.01
220 26 0.11
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (214 bp):
ACTGACTGTCAACAAACAACTTTTCAGTTTTATTCAATTTCAACTTCACAGCGAAGGATATTGGA
CTCGAGACAACACAGACCCAACTTCACAGAGAAGGGGAGACTGAATGTCAAAAAACAACTTTTCA
ATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCA
ACTTCACAGCGAAGGGACG
Found at i:72911 original size:2 final size:2
Alignment explanation
Indices: 72906--72945 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
72896 TATGTTTTAT
72906 TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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 TA TA TA T
72946 TAACGTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:73382 original size:14 final size:15
Alignment explanation
Indices: 73363--73398 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
73353 TTACTATTGT
73363 TTTCTTTTTTA-TTA
1 TTTCTTTTTTACTTA
73377 TTTC-TTTTTACTTA
1 TTTCTTTTTTACTTA
73391 TTT-TTTTT
1 TTTCTTTTT
73399 CTTTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTTTTTTACTTA
Found at i:73404 original size:13 final size:13
Alignment explanation
Indices: 73374--73424 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
73364 TTCTTTTTTA
73374 TTATTTCTTTTTAC-
1 TTATTT-TTTTT-CT
73388 TTATTTTTTTTCT
1 TTATTTTTTTTCT
* *
73401 TTATTTTTATCCT
1 TTATTTTTTTTCT
*
73414 TAATTTTTTTT
1 TTATTTTTTTT
73425 TTCTGTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 1 0.03
13 24 0.77
14 6 0.19
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTTTTTCT
Found at i:73407 original size:23 final size:25
Alignment explanation
Indices: 73367--73424 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 25
73357 TATTGTTTTC
*
73367 TTTTTTATTATTTCTTTTTA-CTT-A
1 TTTTTT-TTATTTATTTTTACCTTAA
*
73391 TTTTTTTTCTTTATTTTTATCCTTAA
1 TTTTTTTTATTTATTTTTA-CCTTAA
73417 TTTTTTTT
1 TTTTTTTT
73425 TTCTGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 11 0.38
24 6 0.21
25 3 0.10
26 9 0.31
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTTTTATTTATTTTTACCTTAA
Found at i:73455 original size:9 final size:9
Alignment explanation
Indices: 73440--73522 Score: 64
Period size: 9 Copynumber: 9.0 Consensus size: 9
73430 TTATTTTCCT
73440 TTTATTTTA
1 TTTATTTTA
*
73449 GTTATTTTA
1 TTTATTTTA
* *
73458 CTTACTTTA
1 TTTATTTTA
73467 TCTT-TTGTTA
1 T-TTATT-TTA
*
73477 -TTATTTTC
1 TTTATTTTA
73485 TTTATTTTA
1 TTTATTTTA
73494 TTTA-TTTA
1 TTTATTTTA
73502 TTTTATTTTCCA
1 -TTTATTTT--A
73514 TTTATTTTA
1 TTTATTTTA
73523 AGTTATTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
8 8 0.14
9 34 0.58
10 8 0.14
11 8 0.14
12 1 0.02
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTATTTTA
Found at i:73489 original size:22 final size:22
Alignment explanation
Indices: 73430--73505 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
73420 TTTTTTTCTG
*
73430 TTATTTTCCTTTTATTTTAGTTATT
1 TTATTTT-C-TTTATTTTATTTA-T
* *
73455 TTACTTACTTTATCTTT-TGTTA-
1 TTATTTTCTTTAT-TTTAT-TTAT
73477 TTATTTTCTTTATTTTATTTAT
1 TTATTTTCTTTATTTTATTTAT
73499 TTATTTT
1 TTATTTT
73506 ATTTTCCATT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
21 6 0.14
22 19 0.45
23 5 0.12
24 7 0.17
25 5 0.12
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (22 bp):
TTATTTTCTTTATTTTATTTAT
Found at i:73493 original size:27 final size:28
Alignment explanation
Indices: 73450--73522 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
73440 TTTATTTTAG
* *
73450 TTATTTTAC-TTACTTTATCT-TTTGTT
1 TTATTTTACTTTATTTTATCTATTTATT
*
73476 ATTATTTT-CTTTATTTTATTTATTTATT
1 -TTATTTTACTTTATTTTATCTATTTATT
*
73504 TTATTTTCCATTTATTTTA
1 TTATTTTAC-TTTATTTTA
73523 AGTTATTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 1 0.03
27 23 0.59
28 6 0.15
29 9 0.23
ACGTcount: A:0.19, C:0.08, G:0.01, T:0.71
Consensus pattern (28 bp):
TTATTTTACTTTATTTTATCTATTTATT
Found at i:73503 original size:13 final size:13
Alignment explanation
Indices: 73485--73509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73475 TATTATTTTC
73485 TTTATTTTATTTA
1 TTTATTTTATTTA
73498 TTTATTTTATTT
1 TTTATTTTATTT
73510 TCCATTTATT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:78561 original size:22 final size:23
Alignment explanation
Indices: 78536--78578 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
78526 TTATTTGCTA
78536 TTATTAATTAATAC-TATTAATG
1 TTATTAATTAATACTTATTAATG
* *
78558 TTATTATTTATTACTTATTAA
1 TTATTAATTAATACTTATTAA
78579 CTACTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (23 bp):
TTATTAATTAATACTTATTAATG
Found at i:82408 original size:18 final size:18
Alignment explanation
Indices: 82385--82428 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
82375 ACATTCCCAG
*
82385 TAATCTTATTCCCGCCGA
1 TAATCTTATTCCCACCGA
* *
82403 TAATCTTATTCTCACTGA
1 TAATCTTATTCCCACCGA
82421 TAATCTTA
1 TAATCTTA
82429 CATTCCGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.41
Consensus pattern (18 bp):
TAATCTTATTCCCACCGA
Found at i:84365 original size:6 final size:6
Alignment explanation
Indices: 84250--84362 Score: 163
Period size: 6 Copynumber: 18.8 Consensus size: 6
84240 GTATGTATGT
* * * * * *
84250 GTGTGT GTGCGC GCGTGC GTGTGT GTGTGT GCGTGC GTGTGC GTGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
84298 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
*
84346 GTGTGC GTGTGT GTGTG
1 GTGTGC GTGTGC GTGTG
84363 TGTCATAATG
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 97 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
GTGTGC
Found at i:84477 original size:117 final size:117
Alignment explanation
Indices: 84346--84584 Score: 460
Period size: 117 Copynumber: 2.0 Consensus size: 117
84336 GTGCGTGTGC
84346 GTGTGCGTGTGTGTGTGTGTCATAATGACTTACATGGCCTGCCAGCATGTAGAGCATCAAGTTAT
1 GTGTGCGTGTGTGTGTGTGTCATAATGACTTACATGGCCTGCCAGCATGTAGAGCATCAAGTTAT
84411 ATGCAGCGCCAGCCCATGCTGTTTCGGTCACAACACCAGTGGCATTGACAAT
66 ATGCAGCGCCAGCCCATGCTGTTTCGGTCACAACACCAGTGGCATTGACAAT
*
84463 GTGTGTGTGTGTGTGTGTGTCATAATGACTTACATGGCCTGCCAGCATGTAGAGCATCAAGTTAT
1 GTGTGCGTGTGTGTGTGTGTCATAATGACTTACATGGCCTGCCAGCATGTAGAGCATCAAGTTAT
84528 ATGCAGCGCCAGCCCATGCTGTTTCGGTCACAACACCAGTGGCATTGACAAT
66 ATGCAGCGCCAGCCCATGCTGTTTCGGTCACAACACCAGTGGCATTGACAAT
*
84580 TTGTG
1 GTGTG
84585 ATGACAAAGG
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 120 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (117 bp):
GTGTGCGTGTGTGTGTGTGTCATAATGACTTACATGGCCTGCCAGCATGTAGAGCATCAAGTTAT
ATGCAGCGCCAGCCCATGCTGTTTCGGTCACAACACCAGTGGCATTGACAAT
Found at i:98173 original size:21 final size:21
Alignment explanation
Indices: 98122--98183 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
98112 AGGGTTACAT
*
98122 AAGTCCTTCGGGACGT--ATG
1 AAGTCCTTCGGGACATAGATG
*
98141 ACAGGTCATTCGGGACATAGATG
1 A-A-GTCCTTCGGGACATAGATG
98164 AAGTCCTTCGGGACATAGAT
1 AAGTCCTTCGGGACATAGAT
98184 TTCACATGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 29 0.81
22 1 0.03
23 4 0.11
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (21 bp):
AAGTCCTTCGGGACATAGATG
Found at i:101261 original size:25 final size:25
Alignment explanation
Indices: 101227--101279 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
101217 GTTGGAAATC
*
101227 TAAATTCTAAATGATATTAGGATAA
1 TAAATTCTAAATGAGATTAGGATAA
101252 TAAATTCTAAATGAGATTAGGATAA
1 TAAATTCTAAATGAGATTAGGATAA
101277 TAA
1 TAA
101280 TTACACATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (25 bp):
TAAATTCTAAATGAGATTAGGATAA
Found at i:102700 original size:2 final size:2
Alignment explanation
Indices: 102689--102717 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
102679 AATAGTCTTG
102689 AT AT -T 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
102718 GATAAGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.