Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002317.1 Hibiscus syriacus cultivar Beakdansim tig00004719_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: 118665
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1038 original size:21 final size:22
Alignment explanation
Indices: 994--1057 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
984 AAAGTTTAGG
*
994 TTTTTTACAAATAAATTAAGTT
1 TTTTTTACAAATAAATTAAATT
1016 TTTTTTA-AAATAAA-TAATATT
1 TTTTTTACAAATAAATTAA-ATT
* * *
1037 TTTATTATTAAAAAAATTAAA
1 TTTTTTA-CAAATAAATTAAA
1058 AAAATATAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 3 0.09
21 15 0.43
22 7 0.20
23 7 0.20
24 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTTACAAATAAATTAAATT
Found at i:4473 original size:29 final size:30
Alignment explanation
Indices: 4422--4478 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
4412 TATTTTAAGT
* *
4422 AACGAAATGAAATATTAGGCACTAAACTAA
1 AACGAAATGAAACATTAGACACTAAACTAA
4452 AACGAAAT-AAACATTAGACACTAAACT
1 AACGAAATGAAACATTAGACACTAAACT
4479 GTAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (30 bp):
AACGAAATGAAACATTAGACACTAAACTAA
Found at i:9712 original size:44 final size:45
Alignment explanation
Indices: 9621--9723 Score: 172
Period size: 44 Copynumber: 2.3 Consensus size: 45
9611 GCTCAATGAC
9621 TAATGATGTAATTTATAGAAAAGAAAGTGTCACATTATCATGTCTT
1 TAATGATGTAATTTATAGAAAAGAAAG-GTCACATTATCATGTCTT
9667 TAATGATGTAATTTATAGAAAAGAAA-GTCACATTATCATGTCTT
1 TAATGATGTAATTTATAGAAAAGAAAGGTCACATTATCATGTCTT
* *
9711 TAAAGATTTAATT
1 TAATGATGTAATT
9724 GTCAAGTGAC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
44 29 0.53
46 26 0.47
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (45 bp):
TAATGATGTAATTTATAGAAAAGAAAGGTCACATTATCATGTCTT
Found at i:10422 original size:2 final size:2
Alignment explanation
Indices: 10415--10442 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10405 CAAGCGTGTT
10415 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10443 ATGAAGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17160 original size:23 final size:23
Alignment explanation
Indices: 17128--17171 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
17118 GTTATCTCCG
*
17128 TTAACTTTCTTCTTCCTCTTCCA
1 TTAACCTTCTTCTTCCTCTTCCA
17151 TTAACCTTCTTCTTCCTCTTC
1 TTAACCTTCTTCTTCCTCTTC
17172 TTCTTCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.36, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAACCTTCTTCTTCCTCTTCCA
Found at i:22961 original size:22 final size:22
Alignment explanation
Indices: 22935--22978 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
22925 TTCTGGGCTA
* *
22935 GGGGAATCGGTACCCATTCAAG
1 GGGGAACCGATACCCATTCAAG
*
22957 GGGGAACCGATACCCCTTCAAG
1 GGGGAACCGATACCCATTCAAG
22979 CGAATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (22 bp):
GGGGAACCGATACCCATTCAAG
Found at i:23048 original size:23 final size:22
Alignment explanation
Indices: 23004--23048 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
22994 AATGTCATGG
*
23004 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
23026 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
23049 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:24596 original size:103 final size:103
Alignment explanation
Indices: 24417--24630 Score: 401
Period size: 103 Copynumber: 2.1 Consensus size: 103
24407 AGGGTCTATA
24417 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
24482 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATG
66 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATG
*
24520 TGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
* *
24585 TCTCTAGTATATGTATATGATTCTTAAGGAATGATCTG
66 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATG
24623 TGGTCCTT
1 TGGTCCTT
24631 ATGGACATTT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
TCCCTAGTATATGTATATGATTCTTAAGGAATGATATG
Found at i:24696 original size:23 final size:23
Alignment explanation
Indices: 24642--24714 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
24632 TGGACATTTT
*
24642 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
*** *
24665 TACGCGGCACTACGTTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
24688 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
24709 TATATG
1 TATATG
24715 AGATGTGGTG
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 6 0.15
22 3 0.08
23 31 0.77
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:28487 original size:22 final size:22
Alignment explanation
Indices: 28453--28494 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28443 TCTGGGCTAG
* *
28453 GGGAATCGGTACCCATTCAAAA
1 GGGAACCGATACCCATTCAAAA
*
28475 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
28495 GCGAATAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.17
Consensus pattern (22 bp):
GGGAACCGATACCCATTCAAAA
Found at i:28565 original size:23 final size:22
Alignment explanation
Indices: 28521--28565 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28511 AATGTCATGG
*
28521 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
28543 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
28566 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:30110 original size:103 final size:103
Alignment explanation
Indices: 29931--30145 Score: 394
Period size: 103 Copynumber: 2.1 Consensus size: 103
29921 GTCGAGGGTC
*
29931 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
29996 TTAATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTAATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
30034 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
30099 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTAATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
30137 TCTGTGGTC
1 TATGTGGTC
30146 CTTATGGACA
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTAATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:30214 original size:23 final size:23
Alignment explanation
Indices: 30160--30232 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
30150 TGGACATTTT
*
30160 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
***
30183 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
30206 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
30227 TATATG
1 TATATG
30233 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 33 0.79
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:33996 original size:22 final size:22
Alignment explanation
Indices: 33970--34013 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
33960 TTCTGGGCTA
* *
33970 GGGGAATCGGTACCCATTCAAG
1 GGGGAACCGATACCCATTCAAG
*
33992 GGGGAACCGATACCCCTTCAAG
1 GGGGAACCGATACCCATTCAAG
34014 CGAATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (22 bp):
GGGGAACCGATACCCATTCAAG
Found at i:35676 original size:103 final size:103
Alignment explanation
Indices: 35451--35668 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
35441 GTCGAGGGTC
35451 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
35516 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
* *
35554 TATGTGGTCCTTCGGGACATATTTGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
35619 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
35657 TATGTGGTCCTT
1 TATGTGGTCCTT
35669 ATGGACATTT
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:35734 original size:23 final size:23
Alignment explanation
Indices: 35680--35752 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
35670 TGGACATTTT
* *
35680 TATATGGCACTACAGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
***
35703 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
35726 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
35747 TATATG
1 TATATG
35753 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 6 0.15
22 3 0.07
23 32 0.78
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:37380 original size:22 final size:22
Alignment explanation
Indices: 37353--37394 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37343 GAATTAATTT
* *
37353 TATATTAAATTTGATATGATCA
1 TATATTAAAGTTGAAATGATCA
*
37375 TATATTTAAGTTGAAATGAT
1 TATATTAAAGTTGAAATGAT
37395 ATTTTCTATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (22 bp):
TATATTAAAGTTGAAATGATCA
Found at i:41031 original size:30 final size:27
Alignment explanation
Indices: 40991--41052 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
40981 TAATGTATGT
40991 ATTTTATATCTGTGTAATGATGTATTTTA
1 ATTTTATATC--TGTAATGATGTATTTTA
*
41020 ATTTATATATCTGTAGTGATGTATTTTA
1 ATTT-TATATCTGTAATGATGTATTTTA
*
41048 TTTTT
1 ATTTT
41053 GCATTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.03
28 19 0.63
29 4 0.13
30 6 0.20
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (27 bp):
ATTTTATATCTGTAATGATGTATTTTA
Found at i:41034 original size:28 final size:28
Alignment explanation
Indices: 40993--41047 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
40983 ATGTATGTAT
* *
40993 TTTATATCTGTGTAATGATGTATTTTAA
1 TTTATATATCTGTAATGATGTATTTTAA
*
41021 TTTATATATCTGTAGTGATGTATTTTA
1 TTTATATATCTGTAATGATGTATTTTA
41048 TTTTTGCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.04, G:0.15, T:0.55
Consensus pattern (28 bp):
TTTATATATCTGTAATGATGTATTTTAA
Found at i:41190 original size:2 final size:2
Alignment explanation
Indices: 41183--41208 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41173 ATATTGTCCC
41183 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
41209 TCTCAACATG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41674 original size:3 final size:3
Alignment explanation
Indices: 41666--41691 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41656 ATTAAAGTTT
41666 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
41692 GTTACTCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:47207 original size:3 final size:3
Alignment explanation
Indices: 47199--47235 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
47189 CCATATTGAT
* *
47199 TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
47236 ATATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:47366 original size:16 final size:16
Alignment explanation
Indices: 47347--47387 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
47337 CTCTAACCCT
*
47347 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTAC
47363 AGCCGCCTCTGCCTAC
1 AGCCGCCTCTGCCTAC
*
47379 AACCGCCTC
1 AGCCGCCTC
47388 AGCCAATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.12, C:0.54, G:0.17, T:0.17
Consensus pattern (16 bp):
AGCCGCCTCTGCCTAC
Found at i:48560 original size:13 final size:13
Alignment explanation
Indices: 48544--48583 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
48534 ATATAATAAA
48544 TAAATATTTATTT
1 TAAATATTTATTT
*
48557 TAAATAAATTATTT
1 TAAAT-ATTTATTT
48571 T-AATATTTATTT
1 TAAATATTTATTT
48583 T
1 T
48584 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:53025 original size:22 final size:22
Alignment explanation
Indices: 53000--53042 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
52990 GAAAGTCAAC
53000 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
53022 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
53043 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:53057 original size:9 final size:9
Alignment explanation
Indices: 53039--53156 Score: 83
Period size: 9 Copynumber: 12.3 Consensus size: 9
53029 GGTCGGGTCG
*
53039 GGTCAGACC
1 GGTCAAACC
53048 GGTCAAACC
1 GGTCAAACC
*
53057 GGTTCAGACC
1 GG-TCAAACC
*
53067 GGTCAAGCC
1 GGTCAAACC
* *
53076 GATTCAGACC
1 G-GTCAAACC
*
53086 GGACAAACC
1 GGTCAAACC
*
53095 GGTTCGAACC
1 GG-TCAAACC
*
53105 GGTTGAAACC
1 GG-TCAAACC
53115 GGTCAAACC
1 GGTCAAACC
53124 GGTCAGAACC
1 GGTCA-AACC
*
53134 GGTTGAAAACC
1 GG-T-CAAACC
*
53145 GGTTAAACC
1 GGTCAAACC
53154 GGT
1 GGT
53157 TTCCAGCAGC
Statistics
Matches: 86, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
9 42 0.49
10 36 0.42
11 7 0.08
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:53063 original size:19 final size:19
Alignment explanation
Indices: 53041--53157 Score: 112
Period size: 19 Copynumber: 6.1 Consensus size: 19
53031 TCGGGTCGGG
53041 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
53060 TCAGACCGGTCAAGCCGAT
1 TCAGACCGGTCAAACCGGT
*
53079 TCAGACCGGACAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
53098 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
53117 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
53137 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
53157 T
1 T
53158 TCCAGCAGCC
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
18 3 0.04
19 53 0.65
20 16 0.20
21 9 0.11
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:53115 original size:29 final size:31
Alignment explanation
Indices: 53083--53157 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
53073 GCCGATTCAG
*
53083 ACCGGACAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
53112 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
53142 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
53158 TCCAGCAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.56
30 15 0.37
31 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:60331 original size:7 final size:7
Alignment explanation
Indices: 60319--60349 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
60309 GTCAAAGAAA
60319 GTCAACG
1 GTCAACG
60326 GTCAACG
1 GTCAACG
60333 GTCAACG
1 GTCAACG
60340 GTCAACG
1 GTCAACG
60347 GTC
1 GTC
60350 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:60394 original size:27 final size:24
Alignment explanation
Indices: 60338--60381 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
60328 CAACGGTCAA
60338 CGGTC-AACGGTCGGGTCGGGTCG
1 CGGTCAAACGGTCGGGTCGGGTCG
*
60361 -GG-GAAACGGTCGGGTCGGGTC
1 CGGTCAAACGGTCGGGTCGGGTC
60382 AGACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.11, C:0.23, G:0.50, T:0.16
Consensus pattern (24 bp):
CGGTCAAACGGTCGGGTCGGGTCG
Found at i:60402 original size:19 final size:19
Alignment explanation
Indices: 60380--60515 Score: 132
Period size: 19 Copynumber: 7.1 Consensus size: 19
60370 TCGGGTCGGG
60380 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
60399 TCAGACCGATCAAGCCGGT
1 TCAGACCGGTCAAACCGGT
**
60418 TCAGACCGGTCATGCCGGT
1 TCAGACCGGTCAAACCGGT
*
60437 TCAGACCGGACAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
60456 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
60475 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
60495 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
60515 T
1 T
60516 TCCAGCAGCC
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.03
19 70 0.71
20 16 0.16
21 9 0.09
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:60464 original size:29 final size:29
Alignment explanation
Indices: 60432--60514 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
60422 ACCGGTCATG
*
60432 CCGGTTCAGACCGGACAAACCGGTTC-GAA
1 CCGGTTCAAACCGGACAAACCGG-TCAGAA
* *
60461 CCGGTTGAAACCGGTCAAACCGGTCAGAA
1 CCGGTTCAAACCGGACAAACCGGTCAGAA
* **
60490 CCGGTTGAAAACCGGTTAAACCGGT
1 CCGGTT-CAAACCGGACAAACCGGT
60515 TTCCAGCAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
28 2 0.04
29 29 0.62
30 16 0.34
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (29 bp):
CCGGTTCAAACCGGACAAACCGGTCAGAA
Found at i:60515 original size:9 final size:10
Alignment explanation
Indices: 60448--60515 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 10
60438 CAGACCGGAC
60448 AAACCGGTTCG
1 AAACCGGTT-G
60459 -AACCGGTTG
1 AAACCGGTTG
*
60468 AAACCGG-TC
1 AAACCGGTTG
*
60477 AAACCGG-TC
1 AAACCGGTTG
60486 AGAACCGGTTG
1 A-AACCGGTTG
60497 AAAACCGGTT-
1 -AAACCGGTTG
60507 AAACCGGTT
1 AAACCGGTT
60516 TCCAGCAGCC
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
9 21 0.41
10 20 0.39
11 9 0.18
12 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (10 bp):
AAACCGGTTG
Found at i:70274 original size:10 final size:10
Alignment explanation
Indices: 70259--70356 Score: 98
Period size: 10 Copynumber: 9.9 Consensus size: 10
70249 TATTATGCTT
70259 GAAGAAAAAA
1 GAAGAAAAAA
70269 GAAGAAAAAA
1 GAAGAAAAAA
70279 GAAAGAAAAAA
1 G-AAGAAAAAA
70290 -AA-AAAAAA
1 GAAGAAAAAA
70298 -AA-AAAAGAA
1 GAAGAAAA-AA
*
70307 AAAGAAAAAA
1 GAAGAAAAAA
*
70317 GAAAAAAGAAA
1 GAAGAAA-AAA
*
70328 AAAGAAAAAA
1 GAAGAAAAAA
70338 -AGAGAAAAAA
1 GA-AGAAAAAA
70348 GAAGAAAAA
1 GAAGAAAAA
70357 GGGGGGGTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
8 12 0.16
9 5 0.06
10 38 0.49
11 22 0.29
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
GAAGAAAAAA
Found at i:70285 original size:21 final size:19
Alignment explanation
Indices: 70260--70356 Score: 108
Period size: 21 Copynumber: 4.9 Consensus size: 19
70250 ATTATGCTTG
70260 AAGAAAAAAGAAGAAAAAAGA
1 AAGAAAAAA-AAGAAAAAA-A
70281 AAGAAAAAAAA-AAAAAAA
1 AAGAAAAAAAAGAAAAAAA
70299 AA-AAAGAAAAAGAAAAAAGA
1 AAGAAA-AAAAAGAAAAAA-A
*
70319 AAAAAGAAAAAAGAAAAAAA
1 AAGAA-AAAAAAGAAAAAAA
*
70339 GAGAAAAAAGAAGAAAAA
1 AAGAAAAAA-AAGAAAAA
70357 GGGGGGGTCA
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
17 3 0.04
18 8 0.12
19 16 0.24
20 17 0.25
21 23 0.34
22 1 0.01
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAAGAAAAAAA
Found at i:70293 original size:27 final size:25
Alignment explanation
Indices: 70263--70356 Score: 118
Period size: 27 Copynumber: 3.6 Consensus size: 25
70253 ATGCTTGAAG
*
70263 AAAAAAGAAGAAAAAAGAAAGAAAAA
1 AAAAAAAAAGAAAAAAGAAA-AAAAA
70289 AAAAAAAAA-AAAAAAGAAAAAGAAA
1 AAAAAAAAAGAAAAAAGAAAAA-AAA
70314 AAAGAAAAAAGAAAAAAGAAAAAAAGA
1 AAA-AAAAAAGAAAAAAGAAAAAAA-A
*
70341 GAAAAAAGAAGAAAAA
1 -AAAAAAAAAGAAAAA
70357 GGGGGGGTCA
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
24 2 0.03
25 16 0.26
26 16 0.26
27 24 0.39
28 3 0.05
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAGAAAAAAGAAAAAAAA
Found at i:70312 original size:38 final size:38
Alignment explanation
Indices: 70265--70355 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 38
70255 GCTTGAAGAA
70265 AAAAGAAGAAAAAAGAAAGAAAAAAAAAAAAAAAAAAAAG
1 AAAA-AAGAAAAAAGAAA-AAAAAAAAAAAAAAAAAAAAG
* * *
70305 -AAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAAGAG
1 AAAAAAGAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAG
70342 AAAAAAGAAGAAAA
1 AAAAAAGAA-AAAA
70356 AGGGGGGGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
37 18 0.39
38 21 0.46
39 7 0.15
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (38 bp):
AAAAAAGAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAG
Found at i:70350 original size:7 final size:7
Alignment explanation
Indices: 70260--70337 Score: 106
Period size: 7 Copynumber: 11.3 Consensus size: 7
70250 ATTATGCTTG
70260 AAGAAAA
1 AAGAAAA
70267 AAGAAGAA
1 AAGAA-AA
*
70275 AA-AAGA
1 AAGAAAA
70281 AAGAAAA
1 AAGAAAA
*
70288 AAAAAAA
1 AAGAAAA
*
70295 AAAAAAA
1 AAGAAAA
70302 AAG-AAA
1 AAGAAAA
70308 AAGAAAA
1 AAGAAAA
70315 AAGAAAA
1 AAGAAAA
70322 AAGAAAA
1 AAGAAAA
70329 AAGAAAA
1 AAGAAAA
70336 AA
1 AA
70338 AGAGAAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
6 9 0.14
7 51 0.80
8 4 0.06
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:70356 original size:1 final size:1
Alignment explanation
Indices: 70263--70338 Score: 71
Period size: 1 Copynumber: 76.0 Consensus size: 1
70253 ATGCTTGAAG
* * * * * * * *
70263 AAAAAAGAAGAAAAAAGAAAGAAAAAAAAAAAAAAAAAAAAGAAAAAGAAAAAAGAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
70328 AAAGAAAAAAA
1 AAAAAAAAAAA
70339 GAGAAAAAAG
Statistics
Matches: 57, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:72141 original size:83 final size:83
Alignment explanation
Indices: 71494--72136 Score: 1223
Period size: 83 Copynumber: 7.7 Consensus size: 83
71484 AAACATTAAA
*
71494 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTGGTTTAGC
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
71559 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
71577 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
71642 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
* *
71660 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGC
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
71725 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
71743 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
71808 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
*
71826 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAAC
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
71891 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
71909 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
71974 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
* *
71992 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
72057 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
*
72075 TGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
72137 GGTAGGAACT
Statistics
Matches: 550, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 550 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (83 bp):
TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
AGAACCAATCATTGAATT
Found at i:73069 original size:113 final size:113
Alignment explanation
Indices: 72882--73485 Score: 880
Period size: 113 Copynumber: 5.4 Consensus size: 113
72872 TAGATTGACA
*
72882 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
72947 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAACT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
*
72995 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
73060 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
73108 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G--GAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
73170 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
* *
73218 TTTCCAGAAAAAGTTCATAATGA-AATGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAG
1 TTTCCAGAGAAAGTTCATAATGAGAA-GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * *
73282 AAGAATTTGTTCAACCTTTTG-CTCAAATTTATCACTTGATAGATTAGCT
65 AAGAATTTGTTCAACCTTTTGCCT-GAATTCATCACTTGATGGATCAGCT
**** * * *
73331 TTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAATGATGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
73396 AGAATTTGTTCAGA-TTTTTG-CTCAAATCCATCACTTGATGAATCAACT
66 AGAATTTGTTCA-ACCTTTTGCCT-GAATTCATCACTTGATGGATCAGCT
*
73444 TTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
73486 AGAACTTGTT
Statistics
Matches: 448, Mismatches: 36, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
109 2 0.00
110 102 0.23
111 1 0.00
112 3 0.01
113 337 0.75
114 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
Found at i:73273 original size:223 final size:225
Alignment explanation
Indices: 72882--73485 Score: 887
Period size: 223 Copynumber: 2.7 Consensus size: 225
72872 TAGATTGACA
72882 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGA
*
72947 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCA
65 AGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCA
*
73012 TAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
130 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
* *
73077 TTGC-CTGAATTCATCACTTGATGGATCAGCT
195 TTGCTC-AAATTCATCACTTGATAGATCAGCT
*
73108 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-GAAGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAA
* * * * *
73171 GAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCCTTTCCAGAAAAAGTTCAT
66 GAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCAT
* *
73236 AATGA-AATGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
131 AATGAGAA-GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
* *
73300 TTGCTCAAATTTATCACTTGATAGATTAGCT
195 TTGCTCAAATTCATCACTTGATAGATCAGCT
**** *
73331 TTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAATGATGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA-GAAGAAGTTCATAATGAGA
** * * * *
73396 AGAATTTGTTCAGA--TTTTTGCTCAAATCCATCACTTGATGAATCAACTTTTCTAGAGAAAGTT
65 AGAATTTGTTCA-ACCTTTTACCT-GAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTT
73459 CATAATGAGAAGAACTCATCTGAAGAA
128 CATAATGAGAAGAACTCATCTGAAGAA
73486 AGAACTTGTT
Statistics
Matches: 340, Mismatches: 30, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
222 2 0.01
223 199 0.59
224 2 0.01
225 7 0.02
226 127 0.37
227 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (225 bp):
TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAA
GAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCAT
AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
TGCTCAAATTCATCACTTGATAGATCAGCT
Found at i:73840 original size:3 final size:3
Alignment explanation
Indices: 73832--73927 Score: 129
Period size: 3 Copynumber: 32.0 Consensus size: 3
73822 CCATATTGAT
* * * * *
73832 TTA TTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA CTA TAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
73880 TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
73928 AATATATATA
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:73866 original size:30 final size:30
Alignment explanation
Indices: 73832--73927 Score: 165
Period size: 30 Copynumber: 3.2 Consensus size: 30
73822 CCATATTGAT
* *
73832 TTATTATTATAATTATAATTATTATTATTA
1 TTATTATTATAAATATTATTATTATTATTA
*
73862 TTATTACTATAAATATTATTATTATTATTA
1 TTATTATTATAAATATTATTATTATTATTA
73892 TTATTATTATAAATATTATTATTATTATTA
1 TTATTATTATAAATATTATTATTATTATTA
73922 TTATTA
1 TTATTA
73928 AATATATATA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (30 bp):
TTATTATTATAAATATTATTATTATTATTA
Found at i:74059 original size:16 final size:16
Alignment explanation
Indices: 74040--74080 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
74030 CTCTAACCCT
74040 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
74056 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
*
74072 AACCGCCTC
1 AGCCGCCTC
74081 AGCCAATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.56, G:0.17, T:0.17
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Found at i:75302 original size:13 final size:13
Alignment explanation
Indices: 75286--75325 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
75276 ATATAATAAA
75286 TAAATATTTATTT
1 TAAATATTTATTT
*
75299 TAAATAAATTATTT
1 TAAAT-ATTTATTT
75313 T-AATATTTATTT
1 TAAATATTTATTT
75325 T
1 T
75326 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:91828 original size:21 final size:20
Alignment explanation
Indices: 91798--91849 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
91788 GCTGGAAACC
* *
91798 GGTTTAACCGGTTTTCAACT
1 GGTTTGACCGGTTTTCAACA
91818 GGTTCTGACCGG-TTTCAACA
1 GGTT-TGACCGGTTTTCAACA
91838 GGTTTGACCGGT
1 GGTTTGACCGGT
91850 CTGAACCGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.25
20 15 0.54
21 6 0.21
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (20 bp):
GGTTTGACCGGTTTTCAACA
Found at i:91847 original size:19 final size:19
Alignment explanation
Indices: 91798--91865 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
91788 GCTGGAAACC
* *
91798 GGTTTAACCGGTTTTCAACT
1 GGTTTGACCGG-TTTCAACA
91818 GGTTCTGACCGGTTTCAACA
1 GGTT-TGACCGGTTTCAACA
* * *
91838 GGTTTGACCGGTCTGAACC
1 GGTTTGACCGGTTTCAACA
91857 GGTTTGACC
1 GGTTTGACC
91866 AGTCCGACCC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 21 0.50
20 15 0.36
21 6 0.14
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (19 bp):
GGTTTGACCGGTTTCAACA
Found at i:91879 original size:5 final size:5
Alignment explanation
Indices: 91869--91911 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
91859 TTTGACCAGT
*
91869 CCGAC CCGAC CCGAC CCGAC CGTTGAC CCGAC CCGAC CCGAC C
1 CCGAC CCGAC CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC C
91912 GTTGACCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 30 0.88
7 4 0.12
ACGTcount: A:0.19, C:0.56, G:0.21, T:0.05
Consensus pattern (5 bp):
CCGAC
Found at i:91896 original size:22 final size:22
Alignment explanation
Indices: 91871--91918 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
91861 TGACCAGTCC
91871 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
91893 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
91915 GACC
1 GACC
91919 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCCGACCGTT
Found at i:97753 original size:43 final size:43
Alignment explanation
Indices: 97705--97794 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
97695 CCATCTTCAA
97705 AACATATACGTTTTATCGTTATGATATTAATTCAAAACAATTT
1 AACATATACGTTTTATCGTTATGATATTAATTCAAAACAATTT
97748 AACATATACGTTTTATCGTTATGATATTAATTCAAAACAATTT
1 AACATATACGTTTTATCGTTATGATATTAATTCAAAACAATTT
97791 AACA
1 AACA
97795 AGTTCAACTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (43 bp):
AACATATACGTTTTATCGTTATGATATTAATTCAAAACAATTT
Found at i:107129 original size:2 final size:2
Alignment explanation
Indices: 107122--107157 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
107112 AATAATTATT
107122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
107158 TAATAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107193 original size:21 final size:21
Alignment explanation
Indices: 107169--107212 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
107159 AATAAATTTA
107169 ATTTAAATAAAAAATATATAT
1 ATTTAAATAAAAAATATATAT
* * *
107190 ATTTAATTTAAATATATATAT
1 ATTTAAATAAAAAATATATAT
107211 AT
1 AT
107213 ACCCGACCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTAAATAAAAAATATATAT
Found at i:107255 original size:12 final size:12
Alignment explanation
Indices: 107211--107276 Score: 73
Period size: 12 Copynumber: 5.6 Consensus size: 12
107201 ATATATATAT
*
107211 ATACCCGACCCG
1 ATACCCGACCCA
*
107223 ATTCCC-AGCCCA
1 ATACCCGA-CCCA
107235 ATA-CCGACCCA
1 ATACCCGACCCA
107246 ATACCCGACCCA
1 ATACCCGACCCA
* *
107258 ATACCTGGCCCA
1 ATACCCGACCCA
107270 ATACCCG
1 ATACCCG
107277 TTTAAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
11 10 0.22
12 35 0.78
ACGTcount: A:0.29, C:0.47, G:0.12, T:0.12
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:109351 original size:2 final size:2
Alignment explanation
Indices: 109344--109375 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
109334 GGTAATTTTA
109344 AT 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 AT
109376 CTTTCAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110108 original size:31 final size:33
Alignment explanation
Indices: 110036--110108 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
110026 GCGAAGAAAA
* **
110036 AAATATTAAATTTAGATACTAAATTAATCTAAG
1 AAATTTTAAATTTAGATACTAAATTAAAATAAG
*
110069 AAATTTTAAATTTAGATACT-AA-TAAAATAAT
1 AAATTTTAAATTTAGATACTAAATTAAAATAAG
*
110100 TAATTTTAA
1 AAATTTTAA
110109 TTAATATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 14 0.40
32 2 0.06
33 19 0.54
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (33 bp):
AAATTTTAAATTTAGATACTAAATTAAAATAAG
Found at i:110200 original size:2 final size:2
Alignment explanation
Indices: 110193--110217 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
110183 TATCATAAGT
110193 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 T
110218 TTAAGTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:110723 original size:12 final size:12
Alignment explanation
Indices: 110706--110733 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
110696 ATCGTTAAAA
110706 AATTAAATTTAT
1 AATTAAATTTAT
110718 AATTAAATTTAT
1 AATTAAATTTAT
110730 AATT
1 AATT
110734 TATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTAAATTTAT
Found at i:111587 original size:22 final size:20
Alignment explanation
Indices: 111541--111580 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
111531 CAGTGACTAA
111541 TTTAAAAATTATATTAAAAT
1 TTTAAAAATTATATTAAAAT
111561 TTTAAAAATTCA-ATTAAAAT
1 TTTAAAAATT-ATATTAAAAT
111581 ATTTTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAAAATTATATTAAAAT
Found at i:117965 original size:2 final size:2
Alignment explanation
Indices: 117952--117985 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
117942 AGAAAAGGTT
*
117952 TG TG TG TT TG TG TG -G TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
117986 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:118514 original size:24 final size:25
Alignment explanation
Indices: 118471--118518 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
118461 ATTATTTAAT
*
118471 TTCGTATTTCATATGATTTTAATAA
1 TTCGTATATCATATGATTTTAATAA
*
118496 TTCGTATATC-TATGTTTTTAATA
1 TTCGTATATCATATGATTTTAATA
118519 TAATTCTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.54
Consensus pattern (25 bp):
TTCGTATATCATATGATTTTAATAA
Done.