Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007483.1 Hibiscus syriacus cultivar Beakdansim tig00020637_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: 104192
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2522 original size:18 final size:18
Alignment explanation
Indices: 2500--2589 Score: 155
Period size: 18 Copynumber: 5.1 Consensus size: 18
2490 TCGAGGGATT
* *
2500 ATAGTGGTCCTTCGGGAT
1 ATAGTGGTCATTCGGGAC
2518 ATAGTGGTCATTCGGGAC
1 ATAGTGGTCATTCGGGAC
2536 ATAGTGGTCATTCGGGAC
1 ATAGTGGTCATTCGGGAC
2554 ATAGTGGTCATTC-GGAC
1 ATAGTGGTCATTCGGGAC
2571 ATAGTGGTCATTCGGGAC
1 ATAGTGGTCATTCGGGAC
2589 A
1 A
2590 AATATTCATG
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
17 17 0.25
18 52 0.75
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (18 bp):
ATAGTGGTCATTCGGGAC
Found at i:6303 original size:20 final size:20
Alignment explanation
Indices: 6248--6293 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
6238 TGAACCCAAG
*
6248 GAACCGTTCAAACCGGCTTT
1 GAACCGTTCGAACCGGCTTT
6268 GAACCGTTCGAACCGGCTTT
1 GAACCGTTCGAACCGGCTTT
6288 GAACCG
1 GAACCG
6294 CTTGAGCCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (20 bp):
GAACCGTTCGAACCGGCTTT
Found at i:10107 original size:2 final size:2
Alignment explanation
Indices: 10023--10098 Score: 75
Period size: 2 Copynumber: 38.5 Consensus size: 2
10013 CGTCCCACTG
* * *
10023 TA TA TA TCA TA TA TA TA TA TA TA TA TA TA -A GA -A AA AA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
10064 AA GA AA 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 TA T
10099 TTGTATATAA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
1 2 0.03
2 62 0.94
3 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (2 bp):
TA
Found at i:15345 original size:2 final size:2
Alignment explanation
Indices: 15338--15377 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
15328 ATGTATAATC
15338 TA TA TA TA TA TA 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 TA TA TA TA TA TA
15378 CTTGTCTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19743 original size:23 final size:23
Alignment explanation
Indices: 19692--19743 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
19682 TGTCGTTGTC
*
19692 GATATTTTTAATAATTCTTATTT
1 GATATTTTTAATAATTCTTATAT
**
19715 TTTATTTTTAATAATTCTTATAT
1 GATATTTTTAATAATTCTTATAT
19738 GATATT
1 GATATT
19744 GAGTGGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (23 bp):
GATATTTTTAATAATTCTTATAT
Found at i:22358 original size:24 final size:22
Alignment explanation
Indices: 22312--22376 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 22
22302 AGCGTTAATT
*
22312 TTTTTTAAATATGTTATTTTTAA
1 TTTTTTAAATAT-TTTTTTTTAA
22335 TTTTTTAAATATTTTTTATATTAA
1 TTTTTTAAATATTTTTT-T-TTAA
* * *
22359 ATTTATAAAGATTTTTTT
1 TTTTTTAAATATTTTTTT
22377 CTCTCAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.11
23 14 0.39
24 18 0.50
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (22 bp):
TTTTTTAAATATTTTTTTTTAA
Found at i:24770 original size:37 final size:37
Alignment explanation
Indices: 24720--24796 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
24710 CGTTCCTTTA
24720 AAAACACGTTTAAGTGCAGTCGACATACTGCTGCTAG
1 AAAACACGTTTAAGTGCAGTCGACATACTGCTGCTAG
24757 AAAACACGTTTAAGTGCAGTCGACATACTGCTGCTAG
1 AAAACACGTTTAAGTGCAGTCGACATACTGCTGCTAG
24794 AAA
1 AAA
24797 TGCGGGTGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (37 bp):
AAAACACGTTTAAGTGCAGTCGACATACTGCTGCTAG
Found at i:30471 original size:3 final size:3
Alignment explanation
Indices: 30459--30501 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
30449 AATATGTAAT
*
30459 TAA T-A TAA TAA TAA TAA TAAA TAA CAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA T-AA TAA TAA TAA TAA
30502 AATTAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 27 0.77
4 6 0.17
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:30487 original size:10 final size:10
Alignment explanation
Indices: 30463--30498 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
30453 TGTAATTAAT
30463 ATAAT-AATA
1 ATAATAAATA
30472 ATAATAAATA
1 ATAATAAATA
*
30482 ACAATAAATA
1 ATAATAAATA
30492 ATAATAA
1 ATAATAA
30499 TAAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAATAAATA
Found at i:30487 original size:13 final size:14
Alignment explanation
Indices: 30459--30501 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 14
30449 AATATGTAAT
30459 TAATATAATAATAA
1 TAATATAATAATAA
*
30473 TAATA-AATAACAA
1 TAATATAATAATAA
30486 TAA-ATAATAATAA
1 TAATATAATAATAA
30499 TAA
1 TAA
30502 AATTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 1 0.04
13 20 0.77
14 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:30770 original size:43 final size:41
Alignment explanation
Indices: 30722--31085 Score: 222
Period size: 40 Copynumber: 8.6 Consensus size: 41
30712 AAAAGTGATA
* * *
30722 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GATCTGG--ATCTAGGGTTG
* *
30765 ACACGGCTCCTACGTGATAAGGAGATCTGG-TCT-GGGAATG
1 ACACGGCTCCTACGTGATGAGGAGATCTGGATCTAGGG-TTG
* * * * *
30805 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGATCTGG--ATCT--AGG-GTTG
* * *
30851 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GATCTGG--ATCTAGGGTTG
* *
30894 ACACGGCTCCTACGTGATAAGGAGATCTGG-TCT-GGGAATG
1 ACACGGCTCCTACGTGATGAGGAGATCTGGATCTAGGG-TTG
* * * * *
30934 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGATCTGG--ATC-T-AGG-GTTG
* * *
30980 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GATCTGG--ATCTAGGGTTG
* * *
31023 ACACGGCTCCTACGTGATGAAGAGATCTGG-TCTGGGGATG
1 ACACGGCTCCTACGTGATGAGGAGATCTGGATCTAGGGTTG
* * *
31063 ACACGGTTCCTACATGATAAGGA
1 ACACGGCTCCTACGTGATGAGGA
31086 CGGCTGGCCA
Statistics
Matches: 252, Mismatches: 48, Indels: 45
0.73 0.14 0.13
Matches are distributed among these distances:
39 4 0.02
40 88 0.35
42 3 0.01
43 84 0.33
44 5 0.02
45 1 0.00
46 63 0.25
47 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (41 bp):
ACACGGCTCCTACGTGATGAGGAGATCTGGATCTAGGGTTG
Found at i:30905 original size:129 final size:129
Alignment explanation
Indices: 30675--31068 Score: 700
Period size: 129 Copynumber: 3.1 Consensus size: 129
30665 TGTTGGGGAC
* * * * * *
30675 GACACTGCTCATACATGATGAAGAGTTTTGGTCGTCTAAAAGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
30740 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAAT
66 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAAT
30804 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
30869 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAAT
66 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAAT
*
30933 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
*
30998 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAA-GAGATCTGGTCTGGGGAT
66 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGAT-AAGGAGATCTGGTCTGGGAAT
31062 GACACGG
1 GACACGG
31069 TTCCTACATG
Statistics
Matches: 256, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
129 254 0.99
130 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (129 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAAT
Found at i:31043 original size:89 final size:83
Alignment explanation
Indices: 30718--31092 Score: 237
Period size: 83 Copynumber: 4.4 Consensus size: 83
30708 GTCTAAAAGT
* * *
30718 GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGAT
1 GATAACACGGTTCCTACATGATAAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGAT
30783 -AAGGAGATCTGGTCTGGG
66 GAA-GAGATCTGGTCTGGG
* * * * * * ** * * * *
30801 AATGACACGGCTCATACGTGATGAA-GA-GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTAC
1 GATAACACGGTTCCTACATGAT-AAGGACG-GCTGGTTATCT-ATGGT--TGACACGGCTCATAC
* * **
30864 GTGATGAGGACG-GCTGGTTATCTATG
61 GTGATGAAGA-GATCTGG---TCTGGG
* * * * * * *
30890 GTTGACACGGCTCCTACGTGATAAGGA-GATCTGG---TCT-GGGAATGACACGGCTCATACGTG
1 GATAACACGGTTCCTACATGATAAGGACG-GCTGGTTATCTATGG-TTGACACGGCTCATACGTG
* *
30950 ATGAAGAGTTCTGGCCATCTTAAGGT
64 ATGAAGAGATCTGG---TC-T--GGG
* * *
30976 GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGAT
1 GATAACACGGTTCCTACATGATAAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGAT
31041 GAAGAGATCTGGTCTGGG
66 GAAGAGATCTGGTCTGGG
*
31059 GATGACACGGTTCCTACATGATAAGGACGGCTGG
1 GATAACACGGTTCCTACATGATAAGGACGGCTGG
31093 CCATCTTTAG
Statistics
Matches: 227, Mismatches: 44, Indels: 42
0.73 0.14 0.13
Matches are distributed among these distances:
82 2 0.01
83 89 0.39
84 8 0.04
85 1 0.00
86 56 0.25
87 3 0.01
88 2 0.01
89 64 0.28
90 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (83 bp):
GATAACACGGTTCCTACATGATAAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGAT
GAAGAGATCTGGTCTGGG
Found at i:31152 original size:28 final size:29
Alignment explanation
Indices: 31111--31199 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
31101 AGGAGTTATG
* **
31111 GTTTCAAGAGAAACCAAA-TTAAAGATTT
1 GTTTCAAGAAAAACCAAACCCAAAGATTT
*
31139 GTTTCAA-AAAAAACAAACCCAAAGATTT
1 GTTTCAAGAAAAACCAAACCCAAAGATTT
* *
31167 GTTTCAAGAAAAA-CATACTCAAAGACTTT
1 GTTTCAAGAAAAACCAAACCCAAAGA-TTT
31196 GTTT
1 GTTT
31200 GTTTTGTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
27 8 0.15
28 32 0.62
29 12 0.23
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (29 bp):
GTTTCAAGAAAAACCAAACCCAAAGATTT
Found at i:31196 original size:29 final size:28
Alignment explanation
Indices: 31131--31199 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
31121 AAACCAAATT
31131 AAAGATTTGTTTCAAAAAAAACAAACCC
1 AAAGATTTGTTTCAAAAAAAACAAACCC
* * *
31159 AAAGATTTGTTTCAAGAAAAACATACTC
1 AAAGATTTGTTTCAAAAAAAACAAACCC
31187 AAAGACTTTGTTT
1 AAAGA-TTTGTTT
31200 GTTTTGTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 30 0.81
29 7 0.19
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.29
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAAAAACAAACCC
Found at i:32059 original size:30 final size:30
Alignment explanation
Indices: 32023--32086 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
32013 AGAGACAAAA
* *
32023 TTTTGTTTCCAAAGAAATAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
**
32053 TTTTGTTTCAAAAGAAACACTCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
32083 TTTT
1 TTTT
32087 TCACAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:32148 original size:52 final size:53
Alignment explanation
Indices: 32074--32176 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
32064 AAGAAACACT
*
32074 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAACACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
32127 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
32177 AAATAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 40 0.83
53 8 0.17
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:32203 original size:28 final size:28
Alignment explanation
Indices: 32172--32297 Score: 137
Period size: 28 Copynumber: 4.5 Consensus size: 28
32162 CAAAACTTTG
* *
32172 TTTCAAAATAAATAGACTCAAAGATTTT
1 TTTCAAAAGAAACAGACTCAAAGATTTT
32200 TTTCAAAAGAAACA-ACTCAAAGATATTT
1 TTTCAAAAGAAACAGACTCAAAGAT-TTT
* * * *
32228 ATTCAAAAGGAACAAACTCCAAGATTTT
1 TTTCAAAAGAAACAGACTCAAAGATTTT
* *
32256 TATTCAAAAGGAACAGACTCAAAGATTTA
1 T-TTCAAAAGAAACAGACTCAAAGATTTT
* *
32285 TCTCAAGAGAAAC
1 TTTCAAAAGAAAC
32298 TGTCTCCAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
27 10 0.12
28 39 0.47
29 34 0.41
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTT
Found at i:32246 original size:29 final size:28
Alignment explanation
Indices: 32187--32283 Score: 133
Period size: 29 Copynumber: 3.4 Consensus size: 28
32177 AAATAAATAG
* *
32187 ACTCAAAGATTTTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTATTCAAAAGGAACAA
32214 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTTATTCAAAAGGAACAA
* *
32243 ACTCCAAGATTTTTATTCAAAAGGAACAG
1 ACTCAAAGA-TTTTATTCAAAAGGAACAA
32272 ACTCAAAGATTT
1 ACTCAAAGATTT
32284 ATCTCAAGAG
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.16
28 17 0.27
29 34 0.55
30 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.28
Consensus pattern (28 bp):
ACTCAAAGATTTTATTCAAAAGGAACAA
Found at i:32679 original size:36 final size:36
Alignment explanation
Indices: 32595--32698 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
32585 AAAGGAAAAA
* * *
32595 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
32629 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
32665 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
32699 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:32726 original size:36 final size:36
Alignment explanation
Indices: 32591--32714 Score: 112
Period size: 36 Copynumber: 3.5 Consensus size: 36
32581 TCTCAAAGGA
* * * *
32591 AAAATGTCTCAAGCGAGACGAAATTTG-CTTTA-AG
1 AAAACGTCTCAAGTGAGACAAAATTTGTTTTTAGAG
* *
32625 ATATA-GTCTCAAATGAGACAAAATTTGTTTTTAGAG
1 A-AAACGTCTCAAGTGAGACAAAATTTGTTTTTAGAG
** * *
32661 AAATTGTCTCAAGCGAGACAAAGTTTGTTTTT-GAG
1 AAAACGTCTCAAGTGAGACAAAATTTGTTTTTAGAG
32696 AAAACGATCTCAAGTGAGA
1 AAAACG-TCTCAAGTGAGA
32715 TCAACTTTGT
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
34 20 0.28
35 14 0.19
36 38 0.53
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (36 bp):
AAAACGTCTCAAGTGAGACAAAATTTGTTTTTAGAG
Found at i:32845 original size:105 final size:101
Alignment explanation
Indices: 32666--32898 Score: 292
Period size: 105 Copynumber: 2.3 Consensus size: 101
32656 TAGAGAAATT
*
32666 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
* *
32730 GTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
32768 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
32832 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
32873 GTCTCAAGCGAGACGAAGTTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
32899 AAGAGAATTT
Statistics
Matches: 115, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 4 0.03
105 78 0.68
106 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:32912 original size:36 final size:36
Alignment explanation
Indices: 32872--32953 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
32862 AAAGGAAAAA
* * *
32872 TGTCTCAAGCGAGACGAAGTTTG-TTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAA-AGAAAT
* * *
32908 TGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAAT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
32944 TGTCTCAAGC
1 TGTCTCAAGC
32954 AAAACAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
Found at i:32961 original size:36 final size:36
Alignment explanation
Indices: 32872--32966 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
32862 AAAGGAAAAA
* * * *
32872 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
* * * *
32908 TGTCTTAAGTGATACAAACTTTGTTTTTAA-AGAAAT
1 TGTCTCAAGCGAAACAAAATTTG-TTTTAAGAGAAAT
*
32944 TGTCTCAAGCAAAACAAAATTTG
1 TGTCTCAAGCGAAACAAAATTTG
32967 AGAAAACGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
36 41 0.87
37 6 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
Found at i:33009 original size:168 final size:166
Alignment explanation
Indices: 32814--33132 Score: 423
Period size: 167 Copynumber: 1.9 Consensus size: 166
32804 ACAATCTAAG
* *
32814 GTGAGATTAATTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCA
1 GTGAGATCAACTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTC-AAGGAAAAATGTCTCA
* ** * *
32879 AGCGAGAC-GAAGTTTG-TTTT-AAGAGAATTTGTCTTAAGTGATACAAACTTTGTTTTTAAAGA
65 AGCGAGACGGAA-TTTGTTTTTCAAGA-AA-TTGTCTCAAACGAGACAAAATTTGTTTTT--AGA
*
32941 AA-TTGTCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
125 AAGCTGTCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
* *
32982 GTGAGATCAACTTTG-TTTAATGTGAATCAAATTCGAAATTTGTATCTCAAGGAAAAATGTCTCC
1 GTGAGATCAACTTTGTTTTAA-GTGAATCAAATTCAAAATTTGTATCTCAAGGAAAAATGTCTCA
*
33046 AGTGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGCT
65 AGCGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGCT
* *
33111 GTCTCAAGCGAGACAAAATTTG
130 GTCTCAAGCAAAACAAAATTTG
33133 CTTTGAAAGA
Statistics
Matches: 133, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
165 5 0.04
166 21 0.16
167 55 0.41
168 48 0.36
169 4 0.03
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (166 bp):
GTGAGATCAACTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTCAAGGAAAAATGTCTCAA
GCGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGCTG
TCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
Found at i:33031 original size:273 final size:266
Alignment explanation
Indices: 32435--33065 Score: 797
Period size: 273 Copynumber: 2.3 Consensus size: 266
32425 TTTTGAAAAA
* * * * *
32435 CTCAAGTGATATTAATTTTGTTTCAA-GT-ACAACAAATT-TAAATTTGTATCTC-AGAGAAAAT
1 CTCAAGTGAGATCAACTTTGTTT-AATGTGA-AACAAATTCGAAATTTGTATCTCAAGGGAAAAT
* * * *
32496 ATCTCAAGCGAAACGAAATTTGTTTCGAAATAAACACAATATCAAGTGAGATTTTGTTTTAAGTG
64 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACACAATATCAAGTGAGATTTTGTTTTAAGTG
32561 AAACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTTTAAGA
129 AAACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTTTAAGA
* * * * *
32626 TATAGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACAAAGTTTGTTT
194 AATAGTCTCAAATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAA-----TAT
32691 TTGAGAAAACGAT
254 TTGAGAAAACGAT
* *
32704 CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAGG
1 CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTC-AAGGGAAAATG
*
32769 TCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTTT
65 TCTCAAGCGAGACGAAATTTGTTTTGAAAGAAAC-ACAATATCAA-GTGAG----ATTTTGTTTT
* * * *
32833 AAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAGTTTGTTT
124 AAGTGAAACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTT
* * * * *
32898 TAAGAGAATTTGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAA-
189 TAAGA-AA-TAGTCTCAAATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAAT
32962 ATTTGAGAAAACGAT
252 ATTTGAGAAAACGAT
* *
32977 CTCAAGTGAGATCAACTTTGTTTAATGTGAATCAAATTCGAAATTTGTATCTCAAGGAAAAATGT
1 CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAGGGAAAATGT
* * *
33042 CTCCAGTGAGACGGAATTTGTTTT
66 CTCAAGCGAGACGAAATTTGTTTT
33066 TCAAGAAATT
Statistics
Matches: 316, Mismatches: 33, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
268 2 0.01
269 30 0.09
270 13 0.04
272 71 0.22
273 76 0.24
277 76 0.24
278 1 0.00
279 47 0.15
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (266 bp):
CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAGGGAAAATGT
CTCAAGCGAGACGAAATTTGTTTTGAAAGAAACACAATATCAAGTGAGATTTTGTTTTAAGTGAA
ACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTTTAAGAAA
TAGTCTCAAATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAATATTTGAGAA
AACGAT
Found at i:33089 original size:36 final size:35
Alignment explanation
Indices: 33056--33173 Score: 157
Period size: 36 Copynumber: 3.3 Consensus size: 35
33046 AGTGAGACGG
*
33056 AATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAGCGAGACAA
*
33092 AATTTGTTTTT-AGAAAGCTGTCTCAAGCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAGCGAGACAA
**
33127 AATTTGCTTTGAAAGAAATTGTCTCAAGCGAGACAAA
1 AATTTG-TTTTTAAGAAATTGTCTCAAGCGAGAC-AA
33164 AATTTGTTTT
1 AATTTGTTTT
33174 AAAATTCTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
34 5 0.07
35 22 0.31
36 32 0.44
37 13 0.18
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAGCGAGACAA
Found at i:33533 original size:4 final size:4
Alignment explanation
Indices: 33524--33589 Score: 82
Period size: 4 Copynumber: 17.0 Consensus size: 4
33514 TTTATGTATC
* *
33524 ATGT ATGT A--T ATGT ATGT ATGT ATAT ATGT ATGT ATGT ACGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
33570 ATAT ACGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT
33590 GTATACTCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
4 50 0.96
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:34796 original size:14 final size:13
Alignment explanation
Indices: 34766--34852 Score: 53
Period size: 12 Copynumber: 7.1 Consensus size: 13
34756 TCTTTGTCAT
34766 CTTTTGTTCTTTG
1 CTTTTGTTCTTTG
*
34779 CTTTTTTTCTTTG
1 CTTTTGTTCTTTG
34792 ACTTTTG--CTTTG
1 -CTTTTGTTCTTTG
*
34804 -ATTT-TTCTTTG
1 CTTTTGTTCTTTG
*
34815 TTTTTGCTT-TTTG
1 CTTTTG-TTCTTTG
*
34828 -TTTTTTTCTTTG
1 CTTTTGTTCTTTG
* *
34840 -GTTTGATCTTTG
1 CTTTTGTTCTTTG
34852 C
1 C
34853 ACTCTGCGTC
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
10 3 0.05
11 7 0.12
12 25 0.43
13 16 0.28
14 7 0.12
ACGTcount: A:0.03, C:0.13, G:0.14, T:0.70
Consensus pattern (13 bp):
CTTTTGTTCTTTG
Found at i:34808 original size:11 final size:11
Alignment explanation
Indices: 34775--34824 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
34765 TCTTTTGTTC
34775 TTTGCTTT--T
1 TTTGCTTTGAT
34784 TTT-CTTTGACT
1 TTTGCTTTGA-T
34795 TTTGCTTTGAT
1 TTTGCTTTGAT
* *
34806 TTTTCTTTGTT
1 TTTGCTTTGAT
34817 TTTGCTTT
1 TTTGCTTT
34825 TTGTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 4 0.12
9 3 0.09
11 21 0.62
12 6 0.18
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.72
Consensus pattern (11 bp):
TTTGCTTTGAT
Found at i:34832 original size:23 final size:23
Alignment explanation
Indices: 34782--34824 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
34772 TTCTTTGCTT
34782 TTTTTCTTTGACTTTTGCTTTGA
1 TTTTTCTTTGACTTTTGCTTTGA
*
34805 TTTTTCTTTG-TTTTTGCTTT
1 TTTTTCTTTGACTTTTGCTTT
34825 TTGTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.05, C:0.12, G:0.12, T:0.72
Consensus pattern (23 bp):
TTTTTCTTTGACTTTTGCTTTGA
Found at i:40774 original size:3 final size:3
Alignment explanation
Indices: 40762--40804 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
40752 AATATGTAAT
*
40762 TAA T-A TAA TAA TAA TAA TAAA TAA CAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA T-AA TAA TAA TAA TAA
40805 AATTAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 27 0.77
4 6 0.17
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:40790 original size:10 final size:10
Alignment explanation
Indices: 40766--40801 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
40756 TGTAATTAAT
40766 ATAAT-AATA
1 ATAATAAATA
40775 ATAATAAATA
1 ATAATAAATA
*
40785 ACAATAAATA
1 ATAATAAATA
40795 ATAATAA
1 ATAATAA
40802 TAAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAATAAATA
Found at i:40790 original size:13 final size:14
Alignment explanation
Indices: 40762--40804 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 14
40752 AATATGTAAT
40762 TAATATAATAATAA
1 TAATATAATAATAA
*
40776 TAATA-AATAACAA
1 TAATATAATAATAA
40789 TAA-ATAATAATAA
1 TAATATAATAATAA
40802 TAA
1 TAA
40805 AATTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 1 0.04
13 20 0.77
14 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:43290 original size:40 final size:41
Alignment explanation
Indices: 43246--43326 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
43236 GTATCTAAAT
*
43246 TATTAAAATATTAAAATAATA-TATTAAAGACACTTAACAA
1 TATTAAAAGATTAAAATAATATTATTAAAGACACTTAACAA
* * *
43286 TATTAAAAGATTAAAATAGTATTATTAAAGGCATTTAACAA
1 TATTAAAAGATTAAAATAATATTATTAAAGACACTTAACAA
43327 GACATTTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 19 0.53
41 17 0.47
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.33
Consensus pattern (41 bp):
TATTAAAAGATTAAAATAATATTATTAAAGACACTTAACAA
Found at i:45510 original size:20 final size:20
Alignment explanation
Indices: 45475--45512 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
45465 TTTTTCACCA
* *
45475 TCTCTTTTTTCTTTCTTTTC
1 TCTCTTTTTACCTTCTTTTC
45495 TCTCTTTTTACCTTCTTT
1 TCTCTTTTTACCTTCTTT
45513 ATAAAGTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTCTTTTTACCTTCTTTTC
Found at i:45843 original size:8 final size:10
Alignment explanation
Indices: 45821--45851 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
45811 GAAGGTAAAA
45821 CTCTCATTTT
1 CTCTCATTTT
45831 CTCTCATTTT
1 CTCTCATTTT
45841 CTCTCATTTT
1 CTCTCATTTT
45851 C
1 C
45852 GACTTTTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.10, C:0.32, G:0.00, T:0.58
Consensus pattern (10 bp):
CTCTCATTTT
Found at i:46972 original size:21 final size:22
Alignment explanation
Indices: 46905--46980 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 22
46895 TGATTCATGG
* *
46905 GGTATCGATACCTGTAT-AAATA
1 GGTATCGATACCT-TATGGAAGA
46927 -GTATCGATACCTTATGGAAGA
1 GGTATCGATACCTTATGGAAGA
*
46948 GGTATCGATACC-TATGTGGAG-
1 GGTATCGATACCTTATG-GAAGA
46969 GGTATCGATACC
1 GGTATCGATACC
46981 CGAGGATTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
20 3 0.06
21 31 0.65
22 14 0.29
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (22 bp):
GGTATCGATACCTTATGGAAGA
Found at i:48073 original size:2 final size:2
Alignment explanation
Indices: 48061--48090 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
48051 AGGTAAAATG
*
48061 AT AT GT 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
48091 GACTATGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48639 original size:18 final size:18
Alignment explanation
Indices: 48608--48646 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
48598 TATATGATAT
**
48608 GTGGTCCTTTGGGACATA
1 GTGGTCCTCCGGGACATA
*
48626 GTGGTCCTCCGGGATATA
1 GTGGTCCTCCGGGACATA
48644 GTG
1 GTG
48647 ATCATTCGGG
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:0.15, C:0.18, G:0.36, T:0.31
Consensus pattern (18 bp):
GTGGTCCTCCGGGACATA
Found at i:53224 original size:17 final size:17
Alignment explanation
Indices: 53202--53249 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
53192 CTTTGATTGA
53202 AAAAGTCAATTTTTTTG
1 AAAAGTCAATTTTTTTG
53219 AAAAGTCAATTTTTTTG
1 AAAAGTCAATTTTTTTG
53236 AAAAGTCATATTTT
1 AAAAGTCA-ATTTT
53250 ATATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 25 0.83
18 5 0.17
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (17 bp):
AAAAGTCAATTTTTTTG
Found at i:55963 original size:159 final size:160
Alignment explanation
Indices: 55632--55999 Score: 578
Period size: 159 Copynumber: 2.3 Consensus size: 160
55622 CGGAAAATGT
* * *
55632 TTATGGAGTGTTCGGTTGGAGGAATTACTATGGTTTTTTATAAATGTTTTATGGGAGGGTGTTGT
1 TTATGGAGTGTTCGGTTGGAGGGATTAATATGGTTTTTGATAAATGTTTTATGGGAGGGTGTTGT
* *
55697 TGGAGGAAGTTACCGTTACTGTTACTACAAGCTCCTCTGCTTTCTGCTCAGGGCCTTACTTGGTG
66 TGGAGGAAGTTACCGTTACTG----T-CAAGCTCCTCTACTTTCTGCTCAGGGCCTTACTTAGTG
*
55762 TGTAGGTGGGTGTATGGTTCTGGGGAACCTACACA
126 TGTAAGTGGGTGTATGGTTCTGGGGAACCTACACA
*
55797 TTTTGGAGTGTTCGGTTGGAGGGATTAATATGGTTTTTGATAAATGTTTTATGGGAGGGTGTTGT
1 TTATGGAGTGTTCGGTTGGAGGGATTAATATGGTTTTTGATAAATGTTTTATGGGAGGGTGTTGT
* *
55862 TGGAGGAAGTTACCGTTACTG-CAGGCTCCTCTACTTTGTGCTCAGGGCCTTACTTAGTGTGTAA
66 TGGAGGAAGTTACCGTTACTGTCAAGCTCCTCTACTTTCTGCTCAGGGCCTTACTTAGTGTGTAA
*
55926 GTGGGTGTATGGTTCTGGGGAACCTACATA
131 GTGGGTGTATGGTTCTGGGGAACCTACACA
55956 TTATGGAGTGTTCGGTTGGA-GGATTAATATGGTTTTTGAATAAA
1 TTATGGAGTGTTCGGTTGGAGGGATTAATATGGTTTTTG-ATAAA
56000 AATATGTTTT
Statistics
Matches: 191, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
158 18 0.09
159 91 0.48
165 82 0.43
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.38
Consensus pattern (160 bp):
TTATGGAGTGTTCGGTTGGAGGGATTAATATGGTTTTTGATAAATGTTTTATGGGAGGGTGTTGT
TGGAGGAAGTTACCGTTACTGTCAAGCTCCTCTACTTTCTGCTCAGGGCCTTACTTAGTGTGTAA
GTGGGTGTATGGTTCTGGGGAACCTACACA
Found at i:65740 original size:15 final size:15
Alignment explanation
Indices: 65720--65756 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
65710 GAGACATTAC
*
65720 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
65735 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
65750 CCCGCCC
1 CCCGCCC
65757 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:68323 original size:16 final size:16
Alignment explanation
Indices: 68294--68328 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
68284 AATAATGCTA
*
68294 AGGTGAAGGCGCATCT
1 AGGTGAAGGAGCATCT
*
68310 AGGTGCAGGAGCATCT
1 AGGTGAAGGAGCATCT
68326 AGG
1 AGG
68329 CGCACACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.40, T:0.17
Consensus pattern (16 bp):
AGGTGAAGGAGCATCT
Found at i:69123 original size:6 final size:6
Alignment explanation
Indices: 69109--69141 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
69099 GGGAATTGAA
*
69109 CCATCT CCATGT CCATGT CCATGT CCATGT CCA
1 CCATGT CCATGT CCATGT CCATGT CCATGT CCA
69142 CCCCTAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.39, G:0.12, T:0.30
Consensus pattern (6 bp):
CCATGT
Found at i:71584 original size:21 final size:21
Alignment explanation
Indices: 71546--71585 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
71536 TCATATAAAA
71546 AAATAATTTCATAAGAATATT
1 AAATAATTTCATAAGAATATT
*
71567 AAATGAATTT-ATATGAATA
1 AAAT-AATTTCATAAGAATA
71586 AAATCTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATAATTTCATAAGAATATT
Found at i:73438 original size:2 final size:2
Alignment explanation
Indices: 73431--73497 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
73421 ATTTTCCTAT
* *
73431 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73473 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
73498 TTTTTATCTA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:73677 original size:26 final size:27
Alignment explanation
Indices: 73635--73695 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
73625 TTTTCATTTA
73635 TTTATTATTATTAATAC-TATTTAGTA-T
1 TTTA-TATTATTAATACATATTTA-TATT
*
73662 TTTATATTA-TACATACATTTTTATATT
1 TTTATATTATTA-ATACATATTTATATT
73689 TTTATAT
1 TTTATAT
73696 ATTTTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.07
26 11 0.37
27 17 0.57
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTATATTATTAATACATATTTATATT
Found at i:73710 original size:12 final size:13
Alignment explanation
Indices: 73687--73725 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
73677 CATTTTTATA
73687 TTTTTATATATTT
1 TTTTTATATATTT
73700 TTTTTAT-TATTT
1 TTTTTATATATTT
*
73712 TATTTATACTATTT
1 TTTTTATA-TATTT
73726 ATTTATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 11 0.48
13 7 0.30
14 5 0.22
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTATATATTT
Found at i:73713 original size:21 final size:21
Alignment explanation
Indices: 73679--73746 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
73669 TATACATACA
73679 TTTTTA-TATTTTTATATATTT
1 TTTTTATTA-TTTTATATATTT
* **
73700 TTTTTATTATTTTATTTATAC
1 TTTTTATTATTTTATATATTT
*
73721 TATTTATTTATTTTCATTATATTT
1 TTTTTA-TTATTTT-A-TATATTT
73745 TT
1 TT
73747 AGTTTTTTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 20 0.57
22 9 0.26
23 1 0.03
24 5 0.14
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTATTATTTTATATATTT
Found at i:73728 original size:13 final size:12
Alignment explanation
Indices: 73614--73731 Score: 51
Period size: 13 Copynumber: 10.2 Consensus size: 12
73604 AGTTAATATA
73614 TATATATTTATT
1 TATATATTTATT
73626 T-T-TCATTTATT
1 TATAT-ATTTATT
73637 TAT-TA-TTA-T
1 TATATATTTATT
*
73646 TA-ATA-CTATT
1 TATATATTTATT
73656 TAGTAT-TTTATAT
1 TA-TATATTTAT-T
* **
73669 TATACATACATT
1 TATATATTTATT
*
73681 TTTATA-TT-TT
1 TATATATTTATT
73691 TATATATTT-TT
1 TATATATTTATT
*
73702 TTTATTATTTTATT
1 TATA-TA-TTTATT
73716 TATACTATTTATT
1 TATA-TATTTATT
73729 TAT
1 TAT
73732 TTTCATTATA
Statistics
Matches: 80, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
9 7 0.09
10 14 0.17
11 17 0.21
12 17 0.21
13 18 0.22
14 7 0.09
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (12 bp):
TATATATTTATT
Found at i:74867 original size:4 final size:4
Alignment explanation
Indices: 74858--74885 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
74848 TCCTTTCGTC
74858 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
74886 TACTAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:78212 original size:16 final size:14
Alignment explanation
Indices: 78191--78256 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 14
78181 AAAGGACAAA
78191 AACAAAAAAGAAAAG
1 AACAAAAAA-AAAAG
78206 AAGCAAAAAAAAAAG
1 AA-CAAAAAAAAAAG
78221 AAAACAAAAAAAAGAAAG
1 --AAC-AAAAAAA-AAAG
78239 AACAAAAATCAAAAAG
1 AACAAAAA--AAAAAG
78255 AA
1 AA
78257 AAAGGGACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
15 12 0.27
16 17 0.39
17 11 0.25
18 4 0.09
ACGTcount: A:0.80, C:0.08, G:0.11, T:0.02
Consensus pattern (14 bp):
AACAAAAAAAAAAG
Found at i:78219 original size:20 final size:19
Alignment explanation
Indices: 78189--78260 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 19
78179 AAAAAGGACA
*
78189 AAAACAAAAAAGAAAAGAAGC
1 AAAA-AAAAAAGAAAA-AAAC
*
78210 AAAAAAAAAAGAAAACAA-
1 AAAAAAAAAAGAAAAAAAC
*
78228 AAAAAAGAAAGAACAAAAATC
1 AAAAAAAAAAGAA-AAAAA-C
78249 AAAAAGAAAAAG
1 AAAAA-AAAAAG
78261 GGACAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
18 12 0.29
19 5 0.12
20 11 0.26
21 9 0.21
22 5 0.12
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.01
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAAAAC
Found at i:78232 original size:34 final size:33
Alignment explanation
Indices: 78189--78258 Score: 99
Period size: 32 Copynumber: 2.1 Consensus size: 33
78179 AAAAAGGACA
*
78189 AAAACAAAAAAGA-AAAGAAGCAAAAA-AAAAAG
1 AAAACAAAAAAAAGAAAGAA-CAAAAACAAAAAG
78221 AAAACAAAAAAAAGAAAGAACAAAAATCAAAAAG
1 AAAACAAAAAAAAGAAAGAACAAAAA-CAAAAAG
78255 AAAA
1 AAAA
78259 AGGGACAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
32 18 0.53
33 6 0.18
34 10 0.29
ACGTcount: A:0.81, C:0.07, G:0.10, T:0.01
Consensus pattern (33 bp):
AAAACAAAAAAAAGAAAGAACAAAAACAAAAAG
Found at i:78245 original size:15 final size:15
Alignment explanation
Indices: 78194--78246 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 15
78184 GGACAAAAAC
78194 AAAAAAGAAAAGAAGCA
1 AAAAAAG-AAAGAA-CA
78211 AAAAAA-AAAGAAAACAA
1 AAAAAAGAAAG--AAC-A
78228 AAAAAAGAAAGAACA
1 AAAAAAGAAAGAACA
78243 AAAA
1 AAAA
78247 TCAAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 9 0.28
16 4 0.12
17 15 0.47
18 4 0.12
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAGAACA
Found at i:78891 original size:22 final size:22
Alignment explanation
Indices: 78863--78917 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
78853 GCTACCCTAT
78863 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
78885 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
78907 CAAACCTTTGA
1 CAAACCTTTGA
78918 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:80008 original size:106 final size:106
Alignment explanation
Indices: 79883--81357 Score: 2233
Period size: 106 Copynumber: 14.0 Consensus size: 106
79873 GTGCCACTCG
* * ** * *
79883 AGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAACTTCCCAAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
79948 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
* * * * *
79989 AGACAACGCAAGTTCAACTTCACGACGAATGGACTGATGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
* *
80054 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
*
80095 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
*
80160 CAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGAC-TC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
* *
80200 AAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATT
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATT
* * *
80265 TCAGAGCCAATTTCAACTTCACATCGAAAGATATTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
*
80307 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
*
80372 CAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGAC-TC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
* *
80412 AAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATT
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATT
* * *
80477 TCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
* * *
80519 AGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
** *
80584 CAGAGCCAATTTCAACTTCACAAAGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
*
80625 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
80690 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC-TC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
80730 GAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATT
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATT
* * *
80795 TCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
80837 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC--A-AA-----CAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
* * *
80894 CGGAGCCAATTTCAAATTCACAACGAAGGATATTGGAC-TC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
* * *
80934 TAGACAACGCAAGTTCAACTTCACGACGAAGGGACCTCTGGTTGTCAACAAACAACTTCTCAATT
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATT
* * * *
80999 TCAAAGCCAATTTCAACTTCACAACGAAGGATACTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
* * *
81041 ATACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
*
81106 CAGAGCCAATTTCAACTTCATAGCGAAGGATATTGGAC-TC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
*
81146 GAGACAACGCAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAACAAACAATTTCCCAATT
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATT
* * *
81211 TCGGAGCCAATTTCAACTTCACAACAAAGGATATTGGAC-TC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
* * * *
81252 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATT
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATT
* *
81317 CCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTT
65 TCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTT
81358 GGAACAATGC
Statistics
Matches: 1261, Mismatches: 89, Indels: 37
0.91 0.06 0.03
Matches are distributed among these distances:
97 1 0.00
98 88 0.07
100 1 0.00
101 2 0.00
103 2 0.00
104 1 0.00
105 4 0.00
106 1157 0.92
107 5 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTC
Found at i:82722 original size:2 final size:2
Alignment explanation
Indices: 82715--82741 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
82705 CTATTATTAT
82715 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
82742 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82944 original size:24 final size:22
Alignment explanation
Indices: 82914--82969 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
82904 CTATTTAGTA
82914 TTTTATTATATTATACATACATT
1 TTTTATTAT-TTATACATACATT
* *
82937 TTTATATT-TTTATATATATATT
1 TTT-TATTATTTATACATACATT
82959 TTTTATTATTT
1 TTTTATTATTT
82970 TATTTATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 17 0.59
23 4 0.14
24 4 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATTATTTATACATACATT
Found at i:82949 original size:22 final size:21
Alignment explanation
Indices: 82914--82992 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 21
82904 CTATTTAGTA
82914 TTTTATTATATTATACATACATT
1 TTTTATT-T-TTATACATACATT
* *
82937 TTTATATTTTTATATATATATT
1 TTT-TATTTTTATACATACATT
**
82959 TTTTATTATTTTATTTATACTATT
1 TTTTA-T-TTTTATACATAC-ATT
82983 TATTTATTTT
1 T-TTTATTTT
82993 CATTATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.04
22 15 0.32
23 17 0.36
24 9 0.19
25 4 0.09
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTTTTATACATACATT
Found at i:82965 original size:21 final size:21
Alignment explanation
Indices: 82935--83004 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 21
82925 TATACATACA
82935 TTTTTATATTTTTATATATATAT
1 TTTTTATA-TTTTAT-TATATAT
82958 TTTTTATTATTTTATTTATACTAT
1 TTTTTA-TATTTTA-TTATA-TAT
*
82982 TTATTTAT-TTTCATTATAT-T
1 TT-TTTATATTTTATTATATAT
83002 TTT
1 TTT
83005 AATTTTTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 1 0.02
22 5 0.12
23 19 0.45
24 9 0.21
25 4 0.10
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATATTTTATTATATAT
Found at i:83000 original size:45 final size:44
Alignment explanation
Indices: 82914--83004 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 44
82904 CTATTTAGTA
*
82914 TTTTATTATATTATACATACATTTTTATATTTTTATATATATATT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATAT-TT
* **
82959 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATATTT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATTT
83003 TT
1 TT
83005 AATTTTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
44 4 0.10
45 22 0.55
46 12 0.30
47 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (44 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATTT
Found at i:83001 original size:28 final size:27
Alignment explanation
Indices: 82945--83002 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
82935 TTTTTATATT
* *
82945 TTTATATATATATTTTTTATTATTTTA
1 TTTATATATATATTTTTTATCATTATA
*
82972 TTTATACTATTTATTTATTT-TCATTATA
1 TTTATA-TATATATTT-TTTATCATTATA
83000 TTT
1 TTT
83003 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTATATATATATTTTTTATCATTATA
Found at i:83009 original size:22 final size:22
Alignment explanation
Indices: 82953--83014 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
82943 TTTTTATATA
82953 TATATTTTT-TATTATTTT-ATT
1 TATATTTTTAT-TTATTTTCATT
*
82974 TATACTATTTATTTATTTTCA-T
1 TATA-TTTTTATTTATTTTCATT
82996 TATATTTTTAATTT-TTTTC
1 TATATTTTT-ATTTATTTTC
83015 CTCTTATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 13 0.37
22 20 0.57
23 2 0.06
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
TATATTTTTATTTATTTTCATT
Found at i:83116 original size:20 final size:19
Alignment explanation
Indices: 83089--83144 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
83079 TTTTATCTTT
83089 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
83108 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
83128 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
83145 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:88723 original size:18 final size:20
Alignment explanation
Indices: 88686--88723 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
88676 TTTAATAAAC
*
88686 TATTGTATTTTTAATTTGAA
1 TATTGTATTTTTAATATGAA
88706 TATT-TATTTTT-ATATGAA
1 TATTGTATTTTTAATATGAA
88724 CCAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (20 bp):
TATTGTATTTTTAATATGAA
Found at i:93569 original size:68 final size:68
Alignment explanation
Indices: 93485--93619 Score: 270
Period size: 68 Copynumber: 2.0 Consensus size: 68
93475 ATATATTCAT
93485 GTATTCATGTCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATGTGCATTTG
1 GTATTCATGTCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATGTGCATTTG
93550 AAA
66 AAA
93553 GTATTCATGTCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATGTGCATTTG
1 GTATTCATGTCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATGTGCATTTG
93618 AA
66 AA
93620 TCTATTCACA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (68 bp):
GTATTCATGTCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATGTGCATTTG
AAA
Found at i:93659 original size:68 final size:67
Alignment explanation
Indices: 93494--93635 Score: 187
Period size: 68 Copynumber: 2.1 Consensus size: 67
93484 TGTATTCATG
* * *
93494 TCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATGTGCATTTGAAAGTATTC
1 TCATATCTCTTGTAATCATATAAC-CATATCACTTACCATGTAACATGTGCATTTGAAACTATTC
**
93559 ATG
65 ACA
* * *
93562 TCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATGTGCATTTGAATCTATTC
1 TCATATCTCTTGTAATCATATAAC-CATATCACTTACCATGTAACATGTGCATTTGAAACTATTC
93627 ACA
65 ACA
93630 T-ATATC
1 TCATATC
93636 ATTTATTAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 4 0.06
68 65 0.94
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (67 bp):
TCATATCTCTTGTAATCATATAACCATATCACTTACCATGTAACATGTGCATTTGAAACTATTCA
CA
Found at i:98049 original size:68 final size:68
Alignment explanation
Indices: 97960--98094 Score: 234
Period size: 68 Copynumber: 2.0 Consensus size: 68
97950 ATATATTCAT
* * *
97960 GTATTCATGTCATTTCTCTTGTGATCATATAACTCATATCATTTACCATGTAACATATGTATTTG
1 GTATACATGTCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATATGCATTTG
98025 AAA
66 AAA
*
98028 GTATACATGTCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATGTGCATTTG
1 GTATACATGTCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATATGCATTTG
98093 AA
66 AA
98095 TCTATTTACA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (68 bp):
GTATACATGTCATTTCTCTTGTGATCATATAACTCATATCACTTACCATGTAACATATGCATTTG
AAA
Found at i:100011 original size:22 final size:22
Alignment explanation
Indices: 99986--100033 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
99976 ACGCTGATAT
99986 TGAACGGTTCAACATTCAACGA
1 TGAACGGTTCAACATTCAACGA
*
100008 TGAACGGTTCAGCATTCAACGA
1 TGAACGGTTCAACATTCAACGA
100030 TGAA
1 TGAA
100034 TGATTCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (22 bp):
TGAACGGTTCAACATTCAACGA
Found at i:101169 original size:24 final size:23
Alignment explanation
Indices: 101134--101179 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
101124 GATAAAATGT
101134 AACTTCTACACAAATAAAATTATA
1 AACTTCTACAC-AATAAAATTATA
*
101158 AACTCTCT-CACATTAAAATTAT
1 AACT-TCTACACAATAAAATTAT
101180 TGATTGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 7 0.35
25 3 0.15
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.33
Consensus pattern (23 bp):
AACTTCTACACAATAAAATTATA
Done.