Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 176 of 186
Found at i:58463406 original size:26 final size:26
Alignment explanation
Indices: 58463377--58463451 Score: 132
Period size: 26 Copynumber: 2.9 Consensus size: 26
58463367 AGCGGTGTAA
* *
58463377 TAGGTTTGGTTGCTGGTTTGTTTGGT
1 TAGGTTTGGTTGTTGGTTCGTTTGGT
58463403 TAGGTTTGGTTGTTGGTTCGTTTGGT
1 TAGGTTTGGTTGTTGGTTCGTTTGGT
58463429 TAGGTTTGGTTGTTGGTTCGTTT
1 TAGGTTTGGTTGTTGGTTCGTTT
58463452 TATTTGATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.04, C:0.04, G:0.37, T:0.55
Consensus pattern (26 bp):
TAGGTTTGGTTGTTGGTTCGTTTGGT
Found at i:58463411 original size:10 final size:9
Alignment explanation
Indices: 58463390--58463440 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 9
58463380 GTTTGGTTGC
*
58463390 TGGTTTGTT
1 TGGTTGGTT
58463399 TGGTTAGGTT
1 TGGTT-GGTT
58463409 TGGTT-G-T
1 TGGTTGGTT
*
58463416 TGGTTCGTT
1 TGGTTGGTT
58463425 TGGTTAGGTT
1 TGGTT-GGTT
58463435 TGGTTG
1 TGGTTG
58463441 TTGGTTCGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 6 0.17
8 2 0.06
9 12 0.33
10 16 0.44
ACGTcount: A:0.04, C:0.02, G:0.39, T:0.55
Consensus pattern (9 bp):
TGGTTGGTT
Found at i:58463420 original size:7 final size:9
Alignment explanation
Indices: 58463390--58463451 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 9
58463380 GTTTGGTTGC
*
58463390 TGGTTTGTT
1 TGGTTAGTT
58463399 TGGTTAGGTT
1 TGGTTA-GTT
58463409 TGGTT-G-T
1 TGGTTAGTT
*
58463416 TGGTTCGTT
1 TGGTTAGTT
58463425 TGGTTAGGTT
1 TGGTTA-GTT
58463435 TGGTT-G-T
1 TGGTTAGTT
*
58463442 TGGTTCGTT
1 TGGTTAGTT
58463451 T
1 T
58463452 TATTTGATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
7 12 0.27
8 4 0.09
9 13 0.29
10 16 0.36
ACGTcount: A:0.03, C:0.03, G:0.37, T:0.56
Consensus pattern (9 bp):
TGGTTAGTT
Found at i:58464700 original size:11 final size:11
Alignment explanation
Indices: 58464684--58464709 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
58464674 TCATTCGTAC
58464684 AATTTTGATGT
1 AATTTTGATGT
58464695 AATTTTGATGT
1 AATTTTGATGT
58464706 AATT
1 AATT
58464710 ATTTTTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (11 bp):
AATTTTGATGT
Found at i:58472679 original size:16 final size:16
Alignment explanation
Indices: 58472642--58472677 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
58472632 GTGCATAGAT
58472642 GTAAATAACATGAAAA
1 GTAAATAACATGAAAA
*
58472658 GTAAATAACTTG-AAA
1 GTAAATAACATGAAAA
58472673 GTAAA
1 GTAAA
58472678 ATGAAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (16 bp):
GTAAATAACATGAAAA
Found at i:58474626 original size:50 final size:50
Alignment explanation
Indices: 58474570--58474669 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
58474560 AAAATGAATG
58474570 AAAAAACTAATGTTTGTTAACTTTGCTGACGTGATATACACGTGAATTGC
1 AAAAAACTAATGTTTGTTAACTTTGCTGACGTGATATACACGTGAATTGC
* *
58474620 AAAAAACTAATGTTTGTTAATTTTGCTGACGTGATATACACGTGGATTGC
1 AAAAAACTAATGTTTGTTAACTTTGCTGACGTGATATACACGTGAATTGC
58474670 TATGTGGATG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (50 bp):
AAAAAACTAATGTTTGTTAACTTTGCTGACGTGATATACACGTGAATTGC
Found at i:58474747 original size:20 final size:20
Alignment explanation
Indices: 58474722--58474760 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58474712 TAAAAAAATT
*
58474722 TAATTTTTATACTTTTTTAA
1 TAATTTTAATACTTTTTTAA
*
58474742 TAATTTTAATAGTTTTTTA
1 TAATTTTAATACTTTTTTA
58474761 TTTTTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TAATTTTAATACTTTTTTAA
Found at i:58482895 original size:158 final size:156
Alignment explanation
Indices: 58482609--58482921 Score: 563
Period size: 158 Copynumber: 2.0 Consensus size: 156
58482599 ACAATAAAAA
*
58482609 GAATTCAAAACCCCAAAAAGAACAAATCTTGCAGAGACCCAAAATTAAAAAAAAATGAAACATGA
1 GAATTCAAAACCCCAAAAAGAACAAATCTTGCAGAGACCCAAAATTAAAAAAAAAGGAAACATGA
*
58482674 TTACATATGGCTTGTAAATTGAAGGTTTAGTTAACCTGTAATGAATATGGATTTCCTTTGAAATA
66 TTACATATGGCTTGTAAATTGAAGGTTTAGTTAACCTGTAATGAATATGGATTTCCATTGAAATA
*
58482739 GATTGAAGCCTTGAGTGGAGCCTGGG
131 AATTGAAGCCTTGAGTGGAGCCTGGG
*
58482765 GAATTTAAAACCCCAAAAAGAACAAATCTTGCAGAGACCCAAAATTAAAAAAAAAAAGGAAACAT
1 GAATTCAAAACCCCAAAAAGAACAAATCTTGCAGAGACCCAAAATT--AAAAAAAAAGGAAACAT
*
58482830 GATTACATATGGCTTGTAAATTGAAGGTTTAGTTGACCTGTAATGAATATGGATTTCCATTGAAA
64 GATTACATATGGCTTGTAAATTGAAGGTTTAGTTAACCTGTAATGAATATGGATTTCCATTGAAA
58482895 TAAATTGAAGCCTTGAGTGGAGCCTGG
129 TAAATTGAAGCCTTGAGTGGAGCCTGG
58482922 AAAGAATCAG
Statistics
Matches: 150, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
156 45 0.30
158 105 0.70
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (156 bp):
GAATTCAAAACCCCAAAAAGAACAAATCTTGCAGAGACCCAAAATTAAAAAAAAAGGAAACATGA
TTACATATGGCTTGTAAATTGAAGGTTTAGTTAACCTGTAATGAATATGGATTTCCATTGAAATA
AATTGAAGCCTTGAGTGGAGCCTGGG
Found at i:58484381 original size:21 final size:21
Alignment explanation
Indices: 58484356--58484395 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58484346 GATGTCAGGG
*
58484356 GACGTGTCAGCAAATCGCGCT
1 GACGTGGCAGCAAATCGCGCT
58484377 GACGTGGCAGCAAATCGCG
1 GACGTGGCAGCAAATCGCG
58484396 TCCACGTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.28, G:0.33, T:0.15
Consensus pattern (21 bp):
GACGTGGCAGCAAATCGCGCT
Found at i:58484906 original size:126 final size:125
Alignment explanation
Indices: 58484656--58485340 Score: 908
Period size: 126 Copynumber: 5.5 Consensus size: 125
58484646 GATAAAATCA
* * * * * * * * *
58484656 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCACACCCACGTATACGCGCTTTTGCTACAGT
1 AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTAGACGTGCTTTTGCTACAGT
58484721 AGGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
*
58484781 AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTAGACGTGCTTTTGCTACAGT
1 AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTAGACGTGCTTTTGCTACAGT
*
58484846 TGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCCTGGAA-AAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
*
58484907 AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTAGACGTGCTTTTGCTACAGT
1 AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTAGACGTGCTTTTGCTACAGT
* *
58484972 TGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATA-TTTAAAAAATGCTTC
66 AGGTCCTGGAA-AAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* * *
58485032 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGTGCTTTTGCTACAGT
1 AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTAGACGTGCTTTTGCTACAGT
* * * *
58485097 AGGTCCTGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAACAACGCTGT-
66 AGGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAA-AACGCT-TC
* * *
58485158 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGTCCAC---G-C-TG---TTGCTATAG
1 AAGCAGGATG-TTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTAGACGTGCTTTTGCTACAG
* * * * *
58485214 TAGGTCCTGGAAAAATAATTTCGACTTGATGTTTCTGAGCAAATAGTAT-AAAATCGCTTC
65 TAGGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* * * * ** * *
58485274 TAGCAGGATGCTATATGAGAAGAATTTGTGAAATTGTACCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTAGACGTGCTTTTGCTACAGT
58485339 AG
66 AG
58485341 CATGTTTGGG
Statistics
Matches: 503, Mismatches: 42, Indels: 31
0.87 0.07 0.05
Matches are distributed among these distances:
115 2 0.00
116 38 0.08
117 3 0.01
118 53 0.11
119 1 0.00
120 1 0.00
121 3 0.01
122 1 0.00
123 1 0.00
124 42 0.08
125 155 0.31
126 200 0.40
127 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (125 bp):
AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTAGACGTGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
Found at i:58485104 original size:251 final size:249
Alignment explanation
Indices: 58484656--58485340 Score: 915
Period size: 251 Copynumber: 2.8 Consensus size: 249
58484646 GATAAAATCA
* * * * * * * * *
58484656 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCACACCCACGTATACGCGCTTTTGCTACAGT
1 AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTACACG-GCTTTTGCTACAGT
*
58484721 AGGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTCAAGCA
65 AGGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATA-TTTAAAAAATGCTTCAAGCA
* * * * *
58484786 GGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTAGACGTGCTTTTGCTACAGTTGGTC
129 GGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGTGCTTTTGCTACAGTAGGTC
* * * *
58484851 CTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTTTAAAA-AACGCT-T
194 CT-GAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAACAACGCTGT
*
58484906 CAAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTAGACGTGCTTTTGCTACAG
1 -AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTACACG-GCTTTTGCTACAG
*
58484971 TTGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATATTTAAAAAATGCTTCAAGC
64 TAGGTCCTGGAA-AAATAATTTTGAGTTGACGTTTCTGAGCAAATATTTAAAAAATGCTTCAAGC
58485036 AGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGTGCTTTTGCTACAGTAGGT
128 AGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGTGCTTTTGCTACAGTAGGT
58485101 CCTGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAACAACGCTGT
193 CCTGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAACAACGCTGT
* * *
58485158 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCG---TC---CAC-GCTGTTGCTATAGT
1 AAGCAGGATG-TTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTACACGGCTTTTGCTACAGT
* * * * * *
58485215 AGGTCCTGGAAAAATAATTTCGACTTGATGTTTCTGAGCAAATA-GTATAAAATCGCTTCTAGCA
65 AGGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATATTTAAAAAAT-GCTTCAAGCA
* * * *
58485279 GGATGCTATATGAGAAGAATTTGTGAAATTGTACCCACGTGGACGCGCTTTTGCTACAGTAG
129 GGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGTGCTTTTGCTACAGTAG
58485341 CATGTTTGGG
Statistics
Matches: 393, Mismatches: 36, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
241 7 0.02
242 97 0.25
243 22 0.06
245 2 0.01
248 2 0.01
250 41 0.10
251 185 0.47
252 37 0.09
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (249 bp):
AAGCAGGATGTTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTACACGGCTTTTGCTACAGTA
GGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATATTTAAAAAATGCTTCAAGCAGG
ATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCACGTGGACGTGCTTTTGCTACAGTAGGTCCT
GAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAACAACGCTGT
Found at i:58485237 original size:118 final size:116
Alignment explanation
Indices: 58485087--58485307 Score: 336
Period size: 118 Copynumber: 1.9 Consensus size: 116
58485077 GGACGTGCTT
*
58485087 TTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAACAA
1 TTGCTACAGTAGGTCCTGAAAAAATAATTTCGACTTGACATTTCTGAGCAAATAGTAT-AAA-AA
*
58485152 CGCTGT-AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGTCCACGCTG
64 CGCT-TCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCGCGTCCACGCTG
* * ** *
58485205 TTGCTATAGTAGGTCCTGGAAAAATAATTTCGACTTGATGTTTCTGAGCAAATAGTATAAAATCG
1 TTGCTACAGTAGGTCCTGAAAAAATAATTTCGACTTGACATTTCTGAGCAAATAGTATAAAAACG
*
58485270 CTTCTAGCAGGATGCTATATGAGAAGAATTTGTGAAAT
66 CTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAAT
58485308 TGTACCCACG
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
115 1 0.01
116 37 0.39
117 3 0.03
118 53 0.56
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (116 bp):
TTGCTACAGTAGGTCCTGAAAAAATAATTTCGACTTGACATTTCTGAGCAAATAGTATAAAAACG
CTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAATCGCGTCCACGCTG
Found at i:58488554 original size:21 final size:22
Alignment explanation
Indices: 58488514--58488839 Score: 317
Period size: 21 Copynumber: 15.0 Consensus size: 22
58488504 TCAAATTATA
58488514 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
58488536 TTTAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
58488557 TTTTATTTAAGGG-TTACGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
58488578 TTAAAGTTAAGAGTTTAGGGTA
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
58488600 TTTAATTTAAGGG-TTACGATT
1 TTTAAGTTAAGGGTTTAGGGTT
*
58488621 TTTAAGTTAAGGG-TTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
58488642 TTTAAGTTAAGGGGTTTTGGATT
1 TTTAAGTTAA-GGGTTTAGGGTT
*
58488665 TTTAAGTTAATGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * **
58488686 TTTCATTTAAGGG-TTACAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
58488707 TTTAAGTTAAAGGTTTACGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
58488729 TTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
58488750 TTAAAGTTAAAGGTTTAGAG-T
1 TTTAAGTTAAGGGTTTAGGGTT
* *
58488771 TTTAAGGTTTTAGGGTTTATGGTT
1 TTTAA-G-TTAAGGGTTTAGGGTT
*
58488795 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
58488817 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
58488839 T
1 T
58488840 AGGGCTTTAG
Statistics
Matches: 245, Mismatches: 51, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
21 122 0.50
22 92 0.38
23 25 0.10
24 6 0.02
ACGTcount: A:0.26, C:0.02, G:0.27, T:0.46
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:58488596 original size:43 final size:43
Alignment explanation
Indices: 58488514--58488936 Score: 304
Period size: 43 Copynumber: 9.6 Consensus size: 43
58488504 TCAAATTATA
* * *
58488514 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGTG-TTAGGGTT
1 TTTAATTTAAGGG-TTACGGTTTTTAAGTTAAGAGTTTAGGGTT
* * *
58488557 TTTTATTTAAGGGTTACGGTTTTAAAGTTAAGAGTTTAGGGTA
1 TTTAATTTAAGGGTTACGGTTTTTAAGTTAAGAGTTTAGGGTT
* * *
58488600 TTTAATTTAAGGGTTACGATTTTTAAGTTAAG-GGTTAGAGTT
1 TTTAATTTAAGGGTTACGGTTTTTAAGTTAAGAGTTTAGGGTT
* **
58488642 TTTAAGTTAAGGGGTTTTGGATTTTTAAGTTAATG-G-TTAGGGTT
1 TTTAATTTAA-GGGTTACGG-TTTTTAAGTTAA-GAGTTTAGGGTT
* * *
58488686 TTTCATTTAAGGGTTACAGTTTTTAAGTTAA-AGGTTTACGGTT
1 TTTAATTTAAGGGTTACGGTTTTTAAGTTAAGA-GTTTAGGGTT
* * * * *
58488729 TTAAAGTTAAGGGTTAGGGTTTTAAAGTTAA-AGGTTTAGAG-T
1 TTTAATTTAAGGGTTACGGTTTTTAAGTTAAGA-GTTTAGGGTT
* * * *
58488771 TTTAAGGTTTTAGGGTTTATGGTTTTTAATTTAAGGGTTTAGGGTT
1 TTTAA--TTTAAGGG-TTACGGTTTTTAAGTTAAGAGTTTAGGGTT
* * * * * **
58488817 TTTAAGTTAAGGGTTTAAGGTTTAGGGCTTTAGGGCTTTAGGGTTTAAAGTT
1 TTTAATTTAAGGG-TTACGG-TT-----TTTA-AG-TTAAGAGTTTAGGGTT
*
58488869 TTTAATTTAAGGGTTTAGGGTTTTTAAGTTAAGAGTTTAGGG-T
1 TTTAATTTAAGGG-TTACGGTTTTTAAGTTAAGAGTTTAGGGTT
* *
58488912 TTTAATTTAAAGGTTTAGGGTTTTT
1 TTTAATTT-AAGGGTTACGGTTTTT
58488937 CAGTAATAAC
Statistics
Matches: 304, Mismatches: 55, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
42 52 0.17
43 119 0.39
44 59 0.19
45 27 0.09
46 10 0.03
50 4 0.01
51 2 0.01
52 31 0.10
ACGTcount: A:0.25, C:0.02, G:0.27, T:0.46
Consensus pattern (43 bp):
TTTAATTTAAGGGTTACGGTTTTTAAGTTAAGAGTTTAGGGTT
Found at i:58488623 original size:64 final size:64
Alignment explanation
Indices: 58488514--58488831 Score: 311
Period size: 64 Copynumber: 4.9 Consensus size: 64
58488504 TCAAATTATA
* * *
58488514 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGTGTTAGGGTTTTTTATTTAAGGGTTACGGTT
1 TTTAAGTTAAGAGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAGGGTTACGGTT
* * * * * *
58488578 TTAAAGTTAAGAGTTTAGGGTATTTAATTTAAGGGTTACGATTTTTAAGTTAAGGGTTA-GAGTT
1 TTTAAGTTAAGAGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAGGGTTACG-GTT
* * * * * *
58488642 TTTAAGTTAAGGGGTTTTGGATTTTTAAGTTAATGGTTAGGGTTTTTCATTTAAGGGTTACAGTT
1 TTTAAGTTAA-GAGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAGGGTTACGGTT
* * * * *
58488707 TTTAAGTTAA-AGGTTTACGGTTTTAAAGTTAAGGGTTAGGGTTTTAAAGTTAAAGGTTTA-GAG
1 TTTAAGTTAAGA-GTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAA-TTTAAGGGTTACG-G
58488770 -T
63 TT
* * * * *
58488771 TTTAAGGTTTTAGGGTTTATGGTTTTTAATTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTT
1 TTTAA-G-TTAAGAGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAATTTAAGGGTT
58488832 TAAGGTTTAG
Statistics
Matches: 203, Mismatches: 41, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
63 1 0.00
64 97 0.48
65 63 0.31
66 30 0.15
67 12 0.06
ACGTcount: A:0.26, C:0.02, G:0.27, T:0.46
Consensus pattern (64 bp):
TTTAAGTTAAGAGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAAGGGTTACGGTT
Found at i:58488832 original size:37 final size:37
Alignment explanation
Indices: 58488792--58488906 Score: 123
Period size: 37 Copynumber: 3.1 Consensus size: 37
58488782 AGGGTTTATG
58488792 GTTTTTAATTTAAGGGTTTAGGGTTTTTAAGTTAAG-
1 GTTTTTAATTTAAGGGTTTAGGGTTTTTAAGTTAAGA
* * *
58488828 G-GTTTAAGGTTT-AGGGCTTTAGGG-CTTTAGGGTTTAA-A
1 GTTTTTAA--TTTAAGGG-TTTAGGGTTTTTA-AG-TTAAGA
58488866 GTTTTTAATTTAAGGGTTTAGGGTTTTTAAGTTAAGA
1 GTTTTTAATTTAAGGGTTTAGGGTTTTTAAGTTAAGA
58488903 GTTT
1 GTTT
58488907 AGGGTTTTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
35 5 0.08
36 13 0.21
37 27 0.43
38 13 0.21
39 5 0.08
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (37 bp):
GTTTTTAATTTAAGGGTTTAGGGTTTTTAAGTTAAGA
Found at i:58488836 original size:8 final size:7
Alignment explanation
Indices: 58488804--58488863 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
58488794 TTTTAATTTA
58488804 AGGGTTT
1 AGGGTTT
58488811 AGGGTTTTT
1 AGGG--TTT
* *
58488820 A-AGTTA
1 AGGGTTT
58488826 AGGGTTT
1 AGGGTTT
*
58488833 AAGGTTT
1 AGGGTTT
58488840 AGGGCTTT
1 AGGG-TTT
58488848 AGGGCTTT
1 AGGG-TTT
58488856 AGGGTTT
1 AGGGTTT
58488863 A
1 A
58488864 AAGTTTTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 3 0.07
7 20 0.47
8 16 0.37
9 4 0.09
ACGTcount: A:0.20, C:0.03, G:0.35, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:58488857 original size:74 final size:74
Alignment explanation
Indices: 58488750--58488913 Score: 240
Period size: 74 Copynumber: 2.2 Consensus size: 74
58488740 GGTTAGGGTT
* * * **
58488750 TTAA-AGTTAAAGGTTTAGAGTTTTAAGGTTTTAGGGTTTATGGTTTTTAATTTAAGGGTTTAGG
1 TTAAGAGTTTAAGGTTTAGAGCTTTAAGGCTTTAGGGTTTAAAGTTTTTAATTTAAGGGTTTAGG
58488814 GTTTTTAAG
66 GTTTTTAAG
* * *
58488823 TTAAGGGTTTAAGGTTTAGGGCTTTAGGGCTTTAGGGTTTAAAGTTTTTAATTTAAGGGTTTAGG
1 TTAAGAGTTTAAGGTTTAGAGCTTTAAGGCTTTAGGGTTTAAAGTTTTTAATTTAAGGGTTTAGG
58488888 GTTTTTAAG
66 GTTTTTAAG
*
58488897 TTAAGAGTTTAGGGTTT
1 TTAAGAGTTTAAGGTTT
58488914 TAATTTAAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
73 4 0.05
74 76 0.95
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.46
Consensus pattern (74 bp):
TTAAGAGTTTAAGGTTTAGAGCTTTAAGGCTTTAGGGTTTAAAGTTTTTAATTTAAGGGTTTAGG
GTTTTTAAG
Found at i:58488883 original size:22 final size:22
Alignment explanation
Indices: 58488856--58488936 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
58488846 TTAGGGCTTT
*
58488856 AGGGTTTAAAGTTTTTAATTTA
1 AGGGTTTAAGGTTTTTAATTTA
* *
58488878 AGGGTTTAGGGTTTTTAAGTTA
1 AGGGTTTAAGGTTTTTAATTTA
* *
58488900 AGAGTTT-AGGGTTTTAATTTA
1 AGGGTTTAAGGTTTTTAATTTA
* *
58488921 AAGGTTTAGGGTTTTT
1 AGGGTTTAAGGTTTTT
58488937 CAGTAATAAC
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
21 16 0.34
22 31 0.66
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (22 bp):
AGGGTTTAAGGTTTTTAATTTA
Found at i:58488892 original size:21 final size:21
Alignment explanation
Indices: 58488868--58488935 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
58488858 GGTTTAAAGT
58488868 TTTTAATTTAAGGGTTTAGGG
1 TTTTAATTTAAGGGTTTAGGG
* *
58488889 TTTTTAAGTTAAGAGTTTAGGG
1 -TTTTAATTTAAGGGTTTAGGG
*
58488911 TTTTAATTTAAAGGTTTAGGG
1 TTTTAATTTAAGGGTTTAGGG
58488932 TTTT
1 TTTT
58488936 TCAGTAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 22 0.54
22 19 0.46
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (21 bp):
TTTTAATTTAAGGGTTTAGGG
Found at i:58490443 original size:20 final size:20
Alignment explanation
Indices: 58490406--58490443 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58490396 TTTATTTTTA
*
58490406 AAAATCTACATAATAATTAT
1 AAAATCTACATAAAAATTAT
58490426 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
58490444 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTAT
Found at i:58491774 original size:21 final size:20
Alignment explanation
Indices: 58491735--58491783 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
58491725 TACATGTAAT
* **
58491735 TATTTTTTTAATAGGAGCTA
1 TATTTTTTAAATAAAAGCTA
58491755 CTATTTTTTAAATAAAAGCTA
1 -TATTTTTTAAATAAAAGCTA
58491776 T-TTTTTTA
1 TATTTTTTA
58491784 TTTTTAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.28
20 1 0.04
21 17 0.68
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (20 bp):
TATTTTTTAAATAAAAGCTA
Found at i:58500868 original size:16 final size:16
Alignment explanation
Indices: 58500847--58500878 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58500837 ATTCTGGTTT
*
58500847 ACTAATGTTTGGGCTG
1 ACTAATATTTGGGCTG
58500863 ACTAATATTTGGGCTG
1 ACTAATATTTGGGCTG
58500879 TTGAGCAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (16 bp):
ACTAATATTTGGGCTG
Found at i:58505268 original size:28 final size:27
Alignment explanation
Indices: 58505232--58505423 Score: 154
Period size: 28 Copynumber: 6.8 Consensus size: 27
58505222 ATGTCCTTTG
*
58505232 TTTTTTAGATTTTGTAGTTTTCCCCTTA
1 TTTTTTAGATTTTATAGTTTT-CCCTTA
*
58505260 TTTTTTAGATTTTATTGTTTTACCCTTA
1 TTTTTTAGATTTTATAGTTTT-CCCTTA
* *
58505288 TTTTTAAAAAATTTTATAGTTTTGCCCTTA
1 TTTTT--TAGATTTTATAGTTTT-CCCTTA
* * *
58505318 TTTTTTTAGATTTTACAATTTTTCCTCTA
1 -TTTTTTAGATTTTATAGTTTTCCCT-TA
* **
58505347 TTTTTTAAATTTTATTTTTTTGTCCC-TA
1 TTTTTTAGATTTTA-TAGTTT-TCCCTTA
58505375 TTTTTTAGATTTTATAGTTTTTCTCC-TA
1 TTTTTTAGATTTTATAG-TTTTC-CCTTA
* * *
58505403 TTTTTCAAATTTTATAATTTT
1 TTTTTTAGATTTTATAGTTTT
58505424 TTCCAAAAAT
Statistics
Matches: 133, Mismatches: 23, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
27 7 0.05
28 82 0.62
29 17 0.13
30 22 0.17
31 5 0.04
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (27 bp):
TTTTTTAGATTTTATAGTTTTCCCTTA
Found at i:58505377 original size:87 final size:85
Alignment explanation
Indices: 58505232--58505395 Score: 197
Period size: 87 Copynumber: 1.9 Consensus size: 85
58505222 ATGTCCTTTG
** *
58505232 TTTTTTAGATTTTGTAGTTTTCCCCTTATTTTTTAGATTTTATTGTTTTACCCTTATTTTTAAAA
1 TTTTTTAGATTTTCAAGTTTTCCCCTTATTTTTTAAATTTTATTGTTTTACCCTTATTTTT--AA
58505297 AATTTTATAGTTTTGCCCTTAT
64 AATTTTATAGTTTTGCCCTTAT
* * * * *
58505319 TTTTTTAGATTTTACAATTTTTCCTC-TATTTTTTAAATTTTATTTTTTTGTCCC-TATTTTTTA
1 TTTTTTAGATTTT-CAAGTTTTCCCCTTATTTTTTAAATTTTATTGTTTT-ACCCTTATTTTTAA
*
58505382 GATTTTATAGTTTT
64 AATTTTATAGTTTT
58505396 TCTCCTATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
85 14 0.21
87 41 0.62
88 11 0.17
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.63
Consensus pattern (85 bp):
TTTTTTAGATTTTCAAGTTTTCCCCTTATTTTTTAAATTTTATTGTTTTACCCTTATTTTTAAAA
TTTTATAGTTTTGCCCTTAT
Found at i:58505404 original size:56 final size:55
Alignment explanation
Indices: 58505240--58505423 Score: 199
Period size: 56 Copynumber: 3.2 Consensus size: 55
58505230 TGTTTTTTAG
* * * *
58505240 ATTTTGTAGTTTTCCCCTTATTTTTTAGATTTTATTGTTTTACCCTTATTTTTAAAAA
1 ATTTTATAGTTTTGCCCTTATTTTTTAGATTTTATAGTTTTTCCC-TATTTTT--AAA
* * *
58505298 ATTTTATAGTTTTGCCCTTATTTTTTTAGATTTTACAATTTTTCCTCTATTTTTTAA
1 ATTTTATAGTTTTGCCCTTA-TTTTTTAGATTTTATAGTTTTTCC-CTATTTTTAAA
** *
58505355 ATTTTATTTTTTTGTCCC-TATTTTTTAGATTTTATAGTTTTTCTCCTATTTTTCAA
1 ATTTTATAGTTTTG-CCCTTATTTTTTAGATTTTATAGTTTTTC-CCTATTTTTAAA
*
58505411 ATTTTATAATTTT
1 ATTTTATAGTTTT
58505424 TTCCAAAAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
56 42 0.39
57 17 0.16
58 21 0.19
59 27 0.25
60 1 0.01
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.62
Consensus pattern (55 bp):
ATTTTATAGTTTTGCCCTTATTTTTTAGATTTTATAGTTTTTCCCTATTTTTAAA
Found at i:58512703 original size:22 final size:22
Alignment explanation
Indices: 58512665--58512708 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
58512655 CAATGTATAT
*
58512665 ATTTTATATGTATTATTAATTA
1 ATTTTAAATGTATTATTAATTA
*
58512687 ATTTTAAAT-TATATATTTATTA
1 ATTTTAAATGTAT-TATTAATTA
58512709 TTTATTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTTTAAATGTATTATTAATTA
Found at i:58513066 original size:16 final size:16
Alignment explanation
Indices: 58513045--58513096 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
58513035 TTTGGTTCGC
58513045 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
58513061 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
58513077 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
58513093 TGTA
1 TGTA
58513097 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:58513352 original size:16 final size:16
Alignment explanation
Indices: 58513312--58513366 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
58513302 TTAATCATAT
*
58513312 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
58513328 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
58513343 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
58513361 -TAAAAT
1 TTAAAAT
58513367 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:58513359 original size:18 final size:17
Alignment explanation
Indices: 58513332--58513366 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58513322 TTTTTATTAA
*
58513332 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
58513350 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
58513367 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:58513479 original size:18 final size:17
Alignment explanation
Indices: 58513452--58513486 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58513442 TTACTATTAA
*
58513452 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
58513470 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
58513487 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:58513532 original size:61 final size:60
Alignment explanation
Indices: 58513347--58513537 Score: 155
Period size: 61 Copynumber: 3.2 Consensus size: 60
58513337 TTTTAATTAA
* *
58513347 AATATATAATTTAATAAAATTCTTAATAATT-AATATTCTTATATTAATTTACTGAAATCAT
1 AATATATAATTTAATAAAATTCTTAAT-ATTAAATATTCTTATATAAATTTTCT-AAATCAT
* * * * * *
58513408 AATATATGATACT-GTAAAA-T-ATAA-ATTAACATAATTAC-TAT-TAAATATATT-TTAATTA
1 AATATATAAT-TTAATAAAATTCTTAATATTAA-AT-ATT-CTTATATAAAT-T-TTCTAAATCA
*
58513466 A
60 T
*
58513467 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCT-AAATCAT
58513528 AATATATAAT
1 AATATATAAT
58513538 ACTATGAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
57 3 0.03
58 2 0.02
59 30 0.31
60 18 0.18
61 39 0.40
62 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCTAAATCAT
Found at i:58513615 original size:120 final size:120
Alignment explanation
Indices: 58513310--58513593 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
58513300 ATTTAATCAT
*
58513310 ATTTAAACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAAT-
* * * *
58513375 ATT-AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
64 ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
* *
58513431 AATTAACATAATTACTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
* *
58513496 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATGAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
*
58513551 ATTTAACATAATTATTATTAAATATAATTTAA-TAAAATATATA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATA
58513594 TTTTCAATTA
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 133 0.89
121 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
Found at i:58515707 original size:27 final size:27
Alignment explanation
Indices: 58515677--58515729 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
58515667 TACAATTTTT
* *
58515677 AATTA-TTCTCCATGTGATTGATTAAAA
1 AATTATTTATCCAAGTG-TTGATTAAAA
58515704 AATTATTTATCCAAGTGTTGATTAAA
1 AATTATTTATCCAAGTGTTGATTAAA
58515730 CAAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (27 bp):
AATTATTTATCCAAGTGTTGATTAAAA
Found at i:58517702 original size:25 final size:25
Alignment explanation
Indices: 58517660--58517708 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
58517650 GATTGAAAAA
*
58517660 ATTAAAATAATATAAATTTTTAATT
1 ATTAAAATAATATAAATTTGTAATT
*
58517685 ATTAAAATTATGAT-AATTTGTAAT
1 ATTAAAATAAT-ATAAATTTGTAAT
58517709 ATGGTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
ATTAAAATAATATAAATTTGTAATT
Found at i:58519425 original size:43 final size:43
Alignment explanation
Indices: 58519354--58519532 Score: 234
Period size: 43 Copynumber: 4.2 Consensus size: 43
58519344 TAAAAGTACT
* * **
58519354 CCGCT-AAGAACAAGACCTTTAGCGGCGCTTCTCCCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTATCACAAACG
** *
58519396 CAACTAAAGACCAAGACCTTTAACGGCGCTTTTATCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTATCACAAACG
* * *
58519439 CCGCTATAGACTATGACCTTTAGCGGCGCTTTTATCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTATCACAAACG
* * *
58519482 CCGCTATAGACTATGACCTTTAGCGGCGCTTTTATCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTATCACAAACG
58519525 CCGCTAAA
1 CCGCTAAA
58519533 AACATAATCT
Statistics
Matches: 122, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 3 0.02
43 119 0.98
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTATCACAAACG
Found at i:58522865 original size:24 final size:24
Alignment explanation
Indices: 58522838--58522885 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
58522828 AATGATGCCG
*
58522838 TTTTGTTATGCTAAATATT-TTTTA
1 TTTTG-TATGCTAAAAATTATTTTA
*
58522862 TTTTGTCTGCTAAAAATTATTTTA
1 TTTTGTATGCTAAAAATTATTTTA
58522886 AAGTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.58
Consensus pattern (24 bp):
TTTTGTATGCTAAAAATTATTTTA
Found at i:58523459 original size:7 final size:7
Alignment explanation
Indices: 58523444--58523521 Score: 66
Period size: 7 Copynumber: 11.0 Consensus size: 7
58523434 AACCTTAAAC
58523444 CCCCATAA
1 CCCC-TAA
58523452 CCCCTAA
1 CCCCTAA
*
58523459 CCTCTAA
1 CCCCTAA
58523466 CCCCTAA
1 CCCCTAA
58523473 CCCCTAA
1 CCCCTAA
* *
58523480 ACCTTAA
1 CCCCTAA
*
58523487 ACCCTAA
1 CCCCTAA
*
58523494 CCCTTAA
1 CCCCTAA
* *
58523501 ACCATAA
1 CCCCTAA
*
58523508 TCCCTAA
1 CCCCTAA
*
58523515 TCCCTAA
1 CCCCTAA
58523522 ACACATAATC
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
7 55 0.93
8 4 0.07
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCCTAA
Found at i:58523475 original size:21 final size:21
Alignment explanation
Indices: 58523433--58523523 Score: 94
Period size: 21 Copynumber: 4.2 Consensus size: 21
58523423 CTAGCTTTAC
58523433 AAACCTTAAACCCCCATAACCCCT
1 AAACCTT-AA-CCCC-TAACCCCT
58523457 -AACCTCTAACCCCTAACCCCT
1 AAACCT-TAACCCCTAACCCCT
* *
58523478 AAACCTTAAACCCTAACCCTT
1 AAACCTTAACCCCTAACCCCT
* * *
58523499 AAACCATAATCCCTAATCCCT
1 AAACCTTAACCCCTAACCCCT
58523520 AAAC
1 AAAC
58523524 ACATAATCCC
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
21 42 0.71
22 9 0.15
23 7 0.12
24 1 0.02
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACCTTAACCCCTAACCCCT
Found at i:58523544 original size:22 final size:21
Alignment explanation
Indices: 58523467--58523544 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
58523457 AACCTCTAAC
* * * *
58523467 CCCTAACCCCTAAACCTTAAA
1 CCCTAAACCTTAAACCATAAT
*
58523488 CCCTAACCCTTAAACCATAAT
1 CCCTAAACCTTAAACCATAAT
* *
58523509 CCCTAATCCCTAAACACATAAT
1 CCCTAAACCTTAAAC-CATAAT
58523531 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
58523545 ATCATTTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 31 0.63
22 18 0.37
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCTAAACCTTAAACCATAAT
Found at i:58524227 original size:7 final size:7
Alignment explanation
Indices: 58524215--58524251 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
58524205 CCTTAAACCA
58524215 CATAATC
1 CATAATC
58524222 CATAATC
1 CATAATC
58524229 CATAATC
1 CATAATC
*
58524236 CATAAAC
1 CATAATC
58524243 ACATAATC
1 -CATAATC
58524251 C
1 C
58524252 CTAAATTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (7 bp):
CATAATC
Found at i:58524249 original size:15 final size:15
Alignment explanation
Indices: 58524208--58524256 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
58524198 CCACAACCCT
58524208 TAAACCACATAATCCA
1 TAAA-CACATAATCCA
*
58524224 TAATC-CATAATCCA
1 TAAACACATAATCCA
*
58524238 TAAACACATAATCCC
1 TAAACACATAATCCA
58524253 TAAA
1 TAAA
58524257 TTATCTTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 13 0.45
15 13 0.45
16 3 0.10
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAACACATAATCCA
Found at i:58524761 original size:21 final size:21
Alignment explanation
Indices: 58524735--58524774 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58524725 CTTAAAATAG
* *
58524735 TAACCCCTATACCTTAAACTC
1 TAACCCATATACCCTAAACTC
58524756 TAACCCATATACCCTAAAC
1 TAACCCATATACCCTAAAC
58524775 CAAAAACCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (21 bp):
TAACCCATATACCCTAAACTC
Found at i:58524961 original size:41 final size:41
Alignment explanation
Indices: 58524911--58525066 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
58524901 TATGATAAAT
*
58524911 CTGAGCATTAGCGGCGCTTCTTTAAAAACGCCGCTAAATCC
1 CTGAGCATTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGCC
* * * *
58524952 CTGAGCATTAGTGGCGCTTCTTCAGAAACACCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGCC
* *
58524993 CTGAGCATTAGCGGTGCTTCTTTAAAAATGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGCC
* * *
58525034 CTGAGCATTAGCGGTGCTTTTTTGAAAACGCCG
1 CTGAGCATTAGCGGCGCTTCTTTAAAAACGCCG
58525067 TTATGCTCAT
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 101 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGCC
Found at i:58525093 original size:38 final size:39
Alignment explanation
Indices: 58525051--58525173 Score: 135
Period size: 40 Copynumber: 3.2 Consensus size: 39
58525041 TTAGCGGTGC
* *
58525051 TTTTTTGAAAA-CGCCG-TTATGCTCATTTTTAGCGGC-
1 TTTTTTTAAAAGCGCCGCTAATGCTCATTTTTAGCGGCA
* * * *
58525087 GTTTTTTAAAAGGCGCCGCTAATACTCGATCTTTAGTGGCA
1 TTTTTTTAAAA-GCGCCGCTAATGCTC-ATTTTTAGCGGCA
*
58525128 TTTTTTTAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCA
1 TTTTTTTAAAAGCGCCGCTAATGC-TCATTTTTAGCGGCA
58525168 TTTTTT
1 TTTTTT
58525174 ATCCAAACGC
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
36 9 0.13
38 5 0.07
39 6 0.09
40 39 0.56
41 11 0.16
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (39 bp):
TTTTTTTAAAAGCGCCGCTAATGCTCATTTTTAGCGGCA
Found at i:58526323 original size:22 final size:22
Alignment explanation
Indices: 58526297--58526339 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
58526287 AATTTTATAT
58526297 AATTTAATGAAT-AAAATAAAAA
1 AATTTAAT-AATCAAAATAAAAA
*
58526319 AATTTAATCATCAAAATAAAA
1 AATTTAATAATCAAAATAAAA
58526340 TGTCTTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (22 bp):
AATTTAATAATCAAAATAAAAA
Found at i:58537011 original size:27 final size:26
Alignment explanation
Indices: 58536976--58537087 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
58536966 AGCATGGCTG
* *
58536976 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
58537002 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
58537030 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
58537057 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
58537084 CCAG
1 CCAG
58537088 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:58537068 original size:54 final size:54
Alignment explanation
Indices: 58536976--58537087 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
58536966 AGCATGGCTG
* *
58536976 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
58537030 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
58537084 CCAG
1 CCAG
58537088 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:58538533 original size:24 final size:24
Alignment explanation
Indices: 58538506--58538552 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
58538496 CTAGATTTCC
**
58538506 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
58538530 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
58538553 CTCCTGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:58540259 original size:75 final size:75
Alignment explanation
Indices: 58540059--58540260 Score: 280
Period size: 75 Copynumber: 2.7 Consensus size: 75
58540049 ATATCTGTCA
* * *
58540059 ATTTATCTGACTAGCGTTGGGCGCAACCTTCGTCAGTTTATCTGACTAGTACAAGCCACACTATT
1 ATTTATCCGACTAGCGCTGGGCGCAACCTTCGTCAGTTTATCTGACTAGTGCAAGCCACACTATT
58540124 ATATTTTCTG
66 ATATTTTCTG
* * * * **
58540134 ATTTATCCGACTAGTGCTGGGCACAACCTTCGTTAGTTTATCTGACTAGTGCAGGGTACACTATT
1 ATTTATCCGACTAGCGCTGGGCGCAACCTTCGTCAGTTTATCTGACTAGTGCAAGCCACACTATT
58540199 ATATTTGTC-G
66 ATATTT-TCTG
* * *
58540209 GTTTATCCGACTAGCGCTGGGCGCAACCTTGGTCAGTTTATCTGAATAGTGC
1 ATTTATCCGACTAGCGCTGGGCGCAACCTTCGTCAGTTTATCTGACTAGTGC
58540261 TAGACACATC
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
75 109 0.98
76 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (75 bp):
ATTTATCCGACTAGCGCTGGGCGCAACCTTCGTCAGTTTATCTGACTAGTGCAAGCCACACTATT
ATATTTTCTG
Found at i:58540655 original size:2 final size:2
Alignment explanation
Indices: 58540648--58540716 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
58540638 GTGATGTACT
*
58540648 TC TC TC TC TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
58540690 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
58540717 TGTATTTTGG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:58542435 original size:13 final size:13
Alignment explanation
Indices: 58542417--58542444 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
58542407 AAGAAATATG
58542417 TCAGGGAACTATA
1 TCAGGGAACTATA
58542430 TCAGGGAACTATA
1 TCAGGGAACTATA
58542443 TC
1 TC
58542445 TCGATGATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (13 bp):
TCAGGGAACTATA
Found at i:58546613 original size:69 final size:69
Alignment explanation
Indices: 58546531--58546663 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 69
58546521 CTCAATATCC
*
58546531 TCACCTCTTTTCAAGTAAATTTCGAGGATAAAATTTTTTAAAAGGG-AAAGAATTGTAATGATTC
1 TCACCTCTTTTCAAGTAAATTTCGAGGATAAAATTTTCT-AAAGGGAAAAGAATTGTAATGATTC
58546595 AAAAT
65 AAAAT
* * *
58546600 TCACCTCTTTTCAAGTAAATTTTGGGGATGAAATTTTCTAAAGGGAAAAGAATTGTAATGATTC
1 TCACCTCTTTTCAAGTAAATTTCGAGGATAAAATTTTCTAAAGGGAAAAGAATTGTAATGATTC
58546664 GAAAGTCAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 6 0.10
69 53 0.90
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (69 bp):
TCACCTCTTTTCAAGTAAATTTCGAGGATAAAATTTTCTAAAGGGAAAAGAATTGTAATGATTCA
AAAT
Found at i:58548041 original size:75 final size:75
Alignment explanation
Indices: 58547918--58548205 Score: 351
Period size: 75 Copynumber: 3.8 Consensus size: 75
58547908 TGTAATTATG
* * ** * * *
58547918 TATATCTGTCAGTTTATCTGACTAGGATTGGGCGCAACCTTCGTCAATTTATCTGACTAGTGCAG
1 TATATCTATCGGTTTATCCAACTAGCACTGGGCACAACCTTCGTCAATTTATCTGACTAGTGCAG
58547983 GGCACACTGT
66 GGCACACTGT
* * * * *
58547993 TATATTTATCGGTTTATCCAACTAGCACTAGGTACAACTTTCGTCAATTTATTTGACTAGTGCAG
1 TATATCTATCGGTTTATCCAACTAGCACTGGGCACAACCTTCGTCAATTTATCTGACTAGTGCAG
*
58548058 GACACACTGT
66 GGCACACTGT
* * * * *
58548068 TATATCTATCGGTTTATCTAACTAGCGCTGGGCACAACCTTTGTTAGTTTATCTGACTAGTGCAG
1 TATATCTATCGGTTTATCCAACTAGCACTGGGCACAACCTTCGTCAATTTATCTGACTAGTGCAG
*
58548133 GGCACACTAT
66 GGCACACTGT
* * * * * *
58548143 TATATCTGTCGGTTTATCCTACTAGCATTGGGCGCAACCTTCGTCAGTTTATTTGACTAGTGC
1 TATATCTATCGGTTTATCCAACTAGCACTGGGCACAACCTTCGTCAATTTATCTGACTAGTGC
58548206 TAAGAACATC
Statistics
Matches: 179, Mismatches: 34, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 179 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (75 bp):
TATATCTATCGGTTTATCCAACTAGCACTGGGCACAACCTTCGTCAATTTATCTGACTAGTGCAG
GGCACACTGT
Found at i:58548194 original size:150 final size:150
Alignment explanation
Indices: 58547918--58548205 Score: 398
Period size: 150 Copynumber: 1.9 Consensus size: 150
58547908 TGTAATTATG
* * * *
58547918 TATATCTGTCAGTTTATCTGACTAGGATTGGGCGCAACCTTCGTCAATTTATCTGACTAGTGCAG
1 TATATCTATCAGTTTATCTAACTAGGACTGGGCACAACCTTCGTCAATTTATCTGACTAGTGCAG
* * * *
58547983 GGCACACTGTTATATTTATCGGTTTATCCAACTAGCACTAGGTACAACTTTCGTCAATTTATTTG
66 GGCACACTATTATATCTATCGGTTTATCCAACTAGCACTAGGCACAACCTTCGTCAATTTATTTG
58548048 ACTAGTGCAGGACACACTGT
131 ACTAGTGCAGGACACACTGT
* * * *
58548068 TATATCTATCGGTTTATCTAACTAGCG-CTGGGCACAACCTTTGTTAGTTTATCTGACTAGTGCA
1 TATATCTATCAGTTTATCTAACTAG-GACTGGGCACAACCTTCGTCAATTTATCTGACTAGTGCA
* * * * * *
58548132 GGGCACACTATTATATCTGTCGGTTTATCCTACTAGCATTGGGCGCAACCTTCGTCAGTTTATTT
65 GGGCACACTATTATATCTATCGGTTTATCCAACTAGCACTAGGCACAACCTTCGTCAATTTATTT
58548197 GACTAGTGC
130 GACTAGTGC
58548206 TAAGAACATC
Statistics
Matches: 119, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
150 118 0.99
151 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (150 bp):
TATATCTATCAGTTTATCTAACTAGGACTGGGCACAACCTTCGTCAATTTATCTGACTAGTGCAG
GGCACACTATTATATCTATCGGTTTATCCAACTAGCACTAGGCACAACCTTCGTCAATTTATTTG
ACTAGTGCAGGACACACTGT
Found at i:58550488 original size:25 final size:26
Alignment explanation
Indices: 58550449--58550509 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
58550439 TTAAAGTTTA
*
58550449 TATTTTTTTT-GTT-AATTTGACCTT
1 TATTTTTTTTAGTTAAATTTGACCCT
* *
58550473 TCTTTTTTTTATTTAAATTTGACCCT
1 TATTTTTTTTAGTTAAATTTGACCCT
58550499 TATTTTTTTTA
1 TATTTTTTTTA
58550510 AAAAAAGTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 9 0.29
25 2 0.06
26 20 0.65
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.67
Consensus pattern (26 bp):
TATTTTTTTTAGTTAAATTTGACCCT
Found at i:58550694 original size:16 final size:18
Alignment explanation
Indices: 58550663--58550699 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
58550653 TTCATGAACT
*
58550663 TTTTATAATTTTTTTA-A
1 TTTTATAATATTTTTATA
58550680 TTTTA-AATATTTTTATA
1 TTTTATAATATTTTTATA
58550697 TTT
1 TTT
58550700 ATTGACTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATAATATTTTTATA
Found at i:58552006 original size:22 final size:22
Alignment explanation
Indices: 58551980--58552056 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
58551970 GTCCCTGGCC
58551980 CACACGGGCGTGTGCCTCCCTT
1 CACACGGGCGTGTGCCTCCCTT
58552002 CACACGGGCGTGTGCCTCCCTT
1 CACACGGGCGTGTGCCTCCCTT
*
58552024 CACATGGGCGTGTGCC-CCTCTT
1 CACACGGGCGTGTGCCTCC-CTT
*
58552046 CACATGGGCGT
1 CACACGGGCGT
58552057 TTGACCTCTC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
21 2 0.04
22 51 0.96
ACGTcount: A:0.10, C:0.38, G:0.29, T:0.23
Consensus pattern (22 bp):
CACACGGGCGTGTGCCTCCCTT
Found at i:58556328 original size:33 final size:32
Alignment explanation
Indices: 58556266--58556328 Score: 74
Period size: 33 Copynumber: 1.9 Consensus size: 32
58556256 TGTGCTATCA
*
58556266 TTTTTAACTTTCAAGACTTACTTTGTGTTGCT
1 TTTTTAACTTTCAAGACTTACTTTATGTTGCT
* *
58556298 TTTTTAAACTTTTAAGA-TTTCTTCTATGTTG
1 TTTTT-AACTTTCAAGACTTACTT-TATGTTG
58556329 TCATAGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 10 0.38
33 16 0.62
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.56
Consensus pattern (32 bp):
TTTTTAACTTTCAAGACTTACTTTATGTTGCT
Found at i:58557534 original size:38 final size:40
Alignment explanation
Indices: 58557455--58557542 Score: 108
Period size: 38 Copynumber: 2.2 Consensus size: 40
58557445 TTAAAAATAT
* * * *
58557455 TTATATTAAAAATACTACCATACATTTGATAAATGTTTTA
1 TTATATTAAAAATACTACAATAAATATAATAAATGTTTTA
*
58557495 TTATATTAAAAATAC-A-AATAAATATAATAAATTTTTTA
1 TTATATTAAAAATACTACAATAAATATAATAAATGTTTTA
*
58557533 TTTTATTAAA
1 TTATATTAAA
58557543 TATTATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 26 0.62
39 1 0.02
40 15 0.36
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (40 bp):
TTATATTAAAAATACTACAATAAATATAATAAATGTTTTA
Found at i:58559453 original size:213 final size:210
Alignment explanation
Indices: 58559055--58559484 Score: 655
Period size: 213 Copynumber: 2.0 Consensus size: 210
58559045 TTTCTTTAAT
* * *
58559055 TTTCAGCAAGAGCCATCATTTCCACAGAAAAACTTCTAAACATCACAAATCATCCTGGCTTTTCA
1 TTTC-GCAAGAGCCATCATTTCCAAAAAAAAACTTCCAAACATCACAAATCATCCTGGCTTTTCA
* *
58559120 AACTTCATCCTAAATCTTTCCAACAGCAAATCCAACGATTCAGTCCCCCAAAGAAACCCTCCAAC
65 AACTTCATCCAAAAACTTTCCAACAGCAAATCCAACGATTCAGTCCCCCAAAGAAACCCTCCAAC
* * *
58559185 TTTGATCGGCCACCATAGCTTCCTTCGCTCCAATCAAAACCATGCCCAGCAGATAAGTTGATTTG
130 TTCGATCGGCCACCATAGCTTCCTCCGCTCCAATCAAAACCATGCCCAACAGATAAGTTGATTTG
58559250 TTCTTCTATAATCCCTC
195 TTCTTCTATAA-CCCTC
* *
58559267 TTTCGCAGGAGCCATCATTTCCATAAAAAAAACTTCCAAATATCACAAATCATCCTGGCTTTTCA
1 TTTCGCAAGAGCCATCATTTCCA-AAAAAAAACTTCCAAACATCACAAATCATCCTGGCTTTTCA
* * * *
58559332 ACCTTCATCCCAAAAACTTTCCGACAGTAAATCCAACGATTCAGTCCCCCCAAA-AAACCTTCCA
65 AACTTCAT-CCAAAAACTTTCCAACAGCAAATCCAACGATTCAGT-CCCCCAAAGAAACCCTCCA
58559396 ACTTCGATCGGCCACCATAGCTTCCTCCGCTCCAATCAAAACCATGCCCAACAGATAAGTTGATT
128 ACTTCGATCGGCCACCATAGCTTCCTCCGCTCCAATCAAAACCATGCCCAACAGATAAGTTGATT
* * *
58559461 TGTTCTTTTGTAAGCCTC
193 TGTTCTTCTATAACCCTC
58559479 TTTCGC
1 TTTCGC
58559485 TATGAAATGA
Statistics
Matches: 198, Mismatches: 17, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
211 18 0.09
212 58 0.29
213 114 0.58
214 8 0.04
ACGTcount: A:0.31, C:0.32, G:0.10, T:0.27
Consensus pattern (210 bp):
TTTCGCAAGAGCCATCATTTCCAAAAAAAAACTTCCAAACATCACAAATCATCCTGGCTTTTCAA
ACTTCATCCAAAAACTTTCCAACAGCAAATCCAACGATTCAGTCCCCCAAAGAAACCCTCCAACT
TCGATCGGCCACCATAGCTTCCTCCGCTCCAATCAAAACCATGCCCAACAGATAAGTTGATTTGT
TCTTCTATAACCCTC
Found at i:58565752 original size:15 final size:17
Alignment explanation
Indices: 58565727--58565760 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
58565717 ATCAACTAAT
58565727 TTTTTTGATATATA-TA
1 TTTTTTGATATATAGTA
58565743 TTTTTT-ATATATAGTA
1 TTTTTTGATATATAGTA
58565759 TT
1 TT
58565761 CATATGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTTTGATATATAGTA
Found at i:58566442 original size:23 final size:23
Alignment explanation
Indices: 58566387--58566456 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
58566377 TTATTAACAT
*
58566387 TGTTCGTGAACATGCTT-AATTATA
1 TGTTCGTGAACATG-TTCGATTA-A
*
58566411 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
* *
58566434 TGTTTGTGAGCATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
58566457 GTTAAATGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
23 23 0.57
24 17 0.43
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:58567108 original size:3 final size:3
Alignment explanation
Indices: 58567100--58567133 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
58567090 ATTTCAAGCT
*
58567100 TTA TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
58567134 GTTTGACCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:58567389 original size:6 final size:7
Alignment explanation
Indices: 58567370--58567399 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
58567360 GTCTATCATC
58567370 AATTTTT
1 AATTTTT
58567377 AATTTTT
1 AATTTTT
58567384 AATTTTT
1 AATTTTT
58567391 AATTTTT
1 AATTTTT
58567398 AA
1 AA
58567400 AGAAAGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
AATTTTT
Found at i:58569222 original size:14 final size:15
Alignment explanation
Indices: 58569203--58569231 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58569193 TAAAAATATT
58569203 AAATAAAAT-TTAAA
1 AAATAAAATATTAAA
58569217 AAATAAAATATTAAA
1 AAATAAAATATTAAA
58569232 GTCATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAAAATATTAAA
Found at i:58569413 original size:18 final size:18
Alignment explanation
Indices: 58569390--58569426 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
58569380 AAGTTATTTG
58569390 TTTAAAATTATTTTAAAT
1 TTTAAAATTATTTTAAAT
58569408 TTTAAAATTATTTTAAAT
1 TTTAAAATTATTTTAAAT
58569426 T
1 T
58569427 GTCTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAAAATTATTTTAAAT
Found at i:58571614 original size:16 final size:17
Alignment explanation
Indices: 58571583--58571615 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
58571573 CATAAGTATA
58571583 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
58571600 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
58571616 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:58571955 original size:46 final size:46
Alignment explanation
Indices: 58571890--58572133 Score: 285
Period size: 46 Copynumber: 5.3 Consensus size: 46
58571880 TTATCTTTGA
* * * * *
58571890 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCTAT
* **
58571936 CATGTTGCCATGGTATCTTTCAACCATGTTCTTATTCATTTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTT-CTAT
* * *
58571983 CGTGTTGCCATGGTATCTTTCAAACATGGTCTTATTCA-TTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTC-TAT
* * *
58572029 CACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCTTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCTAT
* * **
58572075 CATGTTACCATGGTATCTTTCAACCATGGTCCTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTC-TAT
58572121 CATGTTGCCATGG
1 CATGTTGCCATGG
58572134 ATAGGATCAT
Statistics
Matches: 169, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
45 5 0.03
46 123 0.73
47 41 0.24
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCTAT
Found at i:58572054 original size:93 final size:92
Alignment explanation
Indices: 58571890--58572133 Score: 312
Period size: 93 Copynumber: 2.6 Consensus size: 92
58571880 TTATCTTTGA
* * *
58571890 CATGATGCCATAGTGTCTTTC-AACTATGGTCTTACTCATTTTC-TATCATGTTGCCATGGTATC
1 CATGTTGCCATGGTATCTTTCAAAC-ATGGTCTTACTCA-TTTCATATCATGTTGCCATGGTATC
*
58571953 TTTCAACCATGTTCTTATTCATTTTCCCGT
64 TTTCAACCATGGTCTTATTCATTTT-CCGT
* * * * *
58571983 CGTGTTGCCATGGTATCTTTCAAACATGGTCTTATTCATTTCATGTCACGCTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAAACATGGTCTTACTCATTTCATATCATGTTGCCATGGTATCTT
**
58572048 TCAACCATGGTCTTATTCATTTTCTTT
66 TCAACCATGGTCTTATTCATTTTCCGT
* * * *
58572075 CATGTTACCATGGTATCTTTCAACCATGGTCCTACACATTTCATATCATGTTGCCATGG
1 CATGTTGCCATGGTATCTTTCAAACATGGTCTTACTCATTTCATATCATGTTGCCATGG
58572134 ATAGGATCAT
Statistics
Matches: 129, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
92 56 0.43
93 70 0.54
94 3 0.02
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (92 bp):
CATGTTGCCATGGTATCTTTCAAACATGGTCTTACTCATTTCATATCATGTTGCCATGGTATCTT
TCAACCATGGTCTTATTCATTTTCCGT
Found at i:58573970 original size:21 final size:20
Alignment explanation
Indices: 58573931--58573980 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
58573921 ATAATATAAT
58573931 TATTTAAT-TAATAAATATC
1 TATTTAATATAATAAATATC
*
58573950 TTTTATAATATAATAAATATC
1 TATT-TAATATAATAAATATC
58573971 TATTTAATAT
1 TATTTAATAT
58573981 CTAATACATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 10 0.37
21 14 0.52
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTTAATATAATAAATATC
Found at i:58574149 original size:29 final size:27
Alignment explanation
Indices: 58574078--58574149 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 27
58574068 TATCATATAA
* *
58574078 ATATCTTATAATATAATTATAATAAATT
1 ATATTTTATAAT-TTATTATAATAAATT
*
58574106 A-ATTTAATATCATTTATTACTAATAAATAT
1 ATATTT--TATAATTTATTA-TAATAAAT-T
58574136 ATATTTTATAATTT
1 ATATTTTATAATTT
58574150 GAAATCTAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
27 3 0.09
28 6 0.17
29 20 0.57
30 2 0.06
31 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (27 bp):
ATATTTTATAATTTATTATAATAAATT
Found at i:58576028 original size:11 final size:11
Alignment explanation
Indices: 58576012--58576050 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
58576002 TAAAAAGAAG
58576012 AAAGAAACGAA
1 AAAGAAACGAA
58576023 AAAGAAA--AA
1 AAAGAAACGAA
58576032 GAAAGAAACGAA
1 -AAAGAAACGAA
58576044 AAAGAAA
1 AAAGAAA
58576051 AAAAAAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.08
10 7 0.28
11 14 0.56
12 2 0.08
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAACGAA
Found at i:58576029 original size:15 final size:17
Alignment explanation
Indices: 58576003--58576050 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 17
58575993 TCAAAGAAGT
58576003 AAAAAGAAGAAAGAAACG
1 AAAAAGAA-AAAGAAACG
58576021 AAAAAGAAAAAGAAA-G
1 AAAAAGAAAAAGAAACG
*
58576037 -AAACGAAAAAGAAA
1 AAAAAGAAAAAGAAA
58576051 AAAAAAGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 13 0.45
16 1 0.03
17 7 0.24
18 8 0.28
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAACG
Found at i:58576035 original size:21 final size:21
Alignment explanation
Indices: 58576009--58576058 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
58575999 AAGTAAAAAG
58576009 AAGAAAGAAACGAAAAAGAAA
1 AAGAAAGAAACGAAAAAGAAA
58576030 AAGAAAGAAACGAAAAAGAAA
1 AAGAAAGAAACGAAAAAGAAA
*
58576051 AAAAAAGA
1 AAGAAAGA
58576059 GTACAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAACGAAAAAGAAA
Found at i:58576058 original size:25 final size:24
Alignment explanation
Indices: 58576003--58576055 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 24
58575993 TCAAAGAAGT
*
58576003 AAAAAGAAGAAAGAAACGAAAAAG
1 AAAAAAAAGAAAGAAACGAAAAAG
58576027 ---AAAAAGAAAGAAACGAAAAAG
1 AAAAAAAAGAAAGAAACGAAAAAG
58576048 AAAAAAAA
1 AAAAAAAA
58576056 AGAGTACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 20 0.80
24 5 0.20
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (24 bp):
AAAAAAAAGAAAGAAACGAAAAAG
Found at i:58583865 original size:18 final size:18
Alignment explanation
Indices: 58583842--58583884 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
58583832 TTTGGTGCAT
*
58583842 CTTTCTTAACTATCGATG
1 CTTTCTTAACTATAGATG
58583860 CTTTCTTAACTATAGATG
1 CTTTCTTAACTATAGATG
*
58583878 CTGTCTT
1 CTTTCTT
58583885 GGTGCAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (18 bp):
CTTTCTTAACTATAGATG
Found at i:58585933 original size:16 final size:16
Alignment explanation
Indices: 58585907--58585945 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
58585897 AGAAAAATTA
58585907 TATTTTTCAT-CTTTC
1 TATTTTTCATCCTTTC
58585922 TATTTTTCCATCCTTTC
1 TATTTTT-CATCCTTTC
*
58585939 AATTTTT
1 TATTTTT
58585946 TTTTCTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 3 0.14
17 11 0.52
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTTTCATCCTTTC
Found at i:58585953 original size:16 final size:18
Alignment explanation
Indices: 58585934--58585967 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
58585924 TTTTTCCATC
58585934 CTTT-CAATTTT-TTTTT
1 CTTTCCAATTTTCTTTTT
58585950 CTTTCCAATTTTCTTTTT
1 CTTTCCAATTTTCTTTTT
58585968 ACTCTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTCCAATTTTCTTTTT
Found at i:58587048 original size:17 final size:17
Alignment explanation
Indices: 58587023--58587056 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
58587013 TCTTTTAATG
58587023 TGTAATAAAAAAAATTA
1 TGTAATAAAAAAAATTA
*
58587040 TGTATTAAAAAAAATTA
1 TGTAATAAAAAAAATTA
58587057 ATATTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
TGTAATAAAAAAAATTA
Found at i:58587064 original size:17 final size:17
Alignment explanation
Indices: 58587028--58587061 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
58587018 TAATGTGTAA
*
58587028 TAAAAAAAATTATGTAT
1 TAAAAAAAATTATATAT
58587045 TAAAAAAAATTA-ATAT
1 TAAAAAAAATTATATAT
58587061 T
1 T
58587062 TAATACGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TAAAAAAAATTATATAT
Found at i:58611662 original size:7 final size:7
Alignment explanation
Indices: 58611650--58611676 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
58611640 ATAATCATCA
58611650 GAAAAAT
1 GAAAAAT
58611657 GAAAAAT
1 GAAAAAT
58611664 GAAAAAT
1 GAAAAAT
58611671 GAAAAA
1 GAAAAA
58611677 CAAGCTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (7 bp):
GAAAAAT
Found at i:58616089 original size:26 final size:26
Alignment explanation
Indices: 58616058--58616107 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
58616048 TTTTATATTA
*
58616058 AAAAAAATA-TATT-TTTTGTTTTTT
1 AAAAAAATATTATTATTTTATTTTTT
58616082 AAATAAAATATTATTATTTTATTTTT
1 AAA-AAAATATTATTATTTTATTTTT
58616108 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 6 0.27
26 4 0.18
27 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
AAAAAAATATTATTATTTTATTTTTT
Found at i:58616108 original size:26 final size:25
Alignment explanation
Indices: 58616055--58616118 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
58616045 TTTTTTTATA
*
58616055 TTAAAAAAAATATATTTTTTGTTTT
1 TTAAAAAAAATATATTTTTTGATTT
*
58616080 TTAAATAAAATATTATTATTTT-ATTT
1 TTAAAAAAAATA-TATT-TTTTGATTT
**
58616106 TTATTAAAAATAT
1 TTAAAAAAAATAT
58616119 TTAAATTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
25 12 0.38
26 16 0.50
27 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTAAAAAAAATATATTTTTTGATTT
Found at i:58616112 original size:29 final size:26
Alignment explanation
Indices: 58616045--58616115 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
58616035 GCACAACACC
*
58616045 TTTTTTTATATTAAAAAAAATATATT
1 TTTTTTTTTATTAAAAAAAATATATT
* *
58616071 TTTTGTTTT-TTAAATAAAATATTATT
1 TTTTTTTTTATTAAAAAAAATA-TATT
58616097 ATTTTATTTTTATTAAAAA
1 -TTTT-TTTTTATTAAAAA
58616116 TATTTAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 11 0.31
26 11 0.31
27 4 0.11
28 4 0.11
29 6 0.17
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTTTTTTTTATTAAAAAAAATATATT
Found at i:58616429 original size:4 final size:4
Alignment explanation
Indices: 58616417--58616479 Score: 51
Period size: 4 Copynumber: 15.5 Consensus size: 4
58616407 CACCCACCGG
* *
58616417 AAGA GAGA AAGAA AAGA AAGA AATGA GAAG- AA-A AAGA AAAA GAAGA
1 AAGA AAGA AAG-A AAGA AAGA AA-GA -AAGA AAGA AAGA AAGA -AAGA
58616463 AAGA AAGA AA-A AAGA AA
1 AAGA AAGA AAGA AAGA AA
58616480 ATTATTATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
3 7 0.15
4 29 0.60
5 10 0.21
6 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:58616436 original size:9 final size:9
Alignment explanation
Indices: 58616422--58616472 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
58616412 ACCGGAAGAG
58616422 AGAAAGAAA
1 AGAAAGAAA
58616431 AGAAAGAAA
1 AGAAAGAAA
*
58616440 TGAGAAGAAAA
1 AGA-AAG-AAA
58616451 AGAAA-AAGA
1 AGAAAGAA-A
58616460 AGAAAG-AA
1 AGAAAGAAA
58616468 AGAAA
1 AGAAA
58616473 AAAGAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 8 0.22
9 18 0.50
10 5 0.14
11 5 0.14
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (9 bp):
AGAAAGAAA
Found at i:58616458 original size:22 final size:19
Alignment explanation
Indices: 58616417--58616479 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 19
58616407 CACCCACCGG
*
58616417 AAGAGAGAAAGAAAAGAAAGA
1 AAGAAAGAAA-AAAA-AAAGA
58616438 AATGAGAAGAAAAAGAAAAAG-
1 AA-GA-AAGAAAAA-AAAAAGA
*
58616459 AAGAAAGAAAGAAAAAAGA
1 AAGAAAGAAAAAAAAAAGA
58616478 AA
1 AA
58616480 ATTATTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 6 0.17
19 9 0.25
20 2 0.06
21 4 0.11
22 8 0.22
23 7 0.19
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (19 bp):
AAGAAAGAAAAAAAAAAGA
Found at i:58616704 original size:60 final size:61
Alignment explanation
Indices: 58616629--58616748 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 61
58616619 GTAATTTATT
* * *
58616629 TTTTGTAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATAATGTTATAAATTTTTGTA
1 TTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGAATAATGTTATAAATTGTTGTA
*
58616690 TTTT-TAATTATTTTAAAATTAATTTATTAGTAATTTAGAATTATGTTATAAATTGTTGT
1 TTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGAATAATGTTATAAATTGTTGT
58616749 GTTTACTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
60 51 0.93
61 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (61 bp):
TTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGAATAATGTTATAAATTGTTGTA
Found at i:58616732 original size:33 final size:32
Alignment explanation
Indices: 58616635--58616743 Score: 93
Period size: 33 Copynumber: 3.5 Consensus size: 32
58616625 TATTTTTTGT
*
58616635 AATTATTTTAAAATTAATTTGTTAGTAATTTAG
1 AATTATGTTAAAATTAATTT-TTAGTAATTTAG
* * * **
58616668 GATAATGTT---ATAAATTTTT-GT-ATTTTT
1 AATTATGTTAAAATTAATTTTTAGTAATTTAG
*
58616695 AATTATTTTAAAATTAATTTATTAGTAATTTAG
1 AATTATGTTAAAATTAATTT-TTAGTAATTTAG
58616728 AATTATGTTATAAATT
1 AATTATGTTA-AAATT
58616744 GTTGTGTTTA
Statistics
Matches: 56, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
27 10 0.18
28 2 0.04
29 2 0.04
30 14 0.25
31 2 0.04
32 2 0.04
33 19 0.34
34 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (32 bp):
AATTATGTTAAAATTAATTTTTAGTAATTTAG
Found at i:58618995 original size:24 final size:24
Alignment explanation
Indices: 58618939--58618984 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
58618929 TTCTGTTCTG
*
58618939 CTAAATTTTGTGTCTGTTGCTCTT
1 CTAAATTTTGTGTCTATTGCTCTT
58618963 CTAAATTTTGTGTCTATTGCTC
1 CTAAATTTTGTGTCTATTGCTC
58618985 ATTTGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.52
Consensus pattern (24 bp):
CTAAATTTTGTGTCTATTGCTCTT
Found at i:58619060 original size:22 final size:22
Alignment explanation
Indices: 58619032--58619083 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
58619022 AAGCACCAAA
* *
58619032 CGCGTCTGTAGGCCCTATCAGT
1 CGCGTCTATAGGCCCTACCAGT
58619054 CGCGTCTATAGGCCCTACCAGT
1 CGCGTCTATAGGCCCTACCAGT
58619076 CGCGTCTA
1 CGCGTCTA
58619084 GCAGATAGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (22 bp):
CGCGTCTATAGGCCCTACCAGT
Found at i:58621494 original size:24 final size:24
Alignment explanation
Indices: 58621454--58621522 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
58621444 TTCTTCGTCT
* * *
58621454 TCATCTTCACCTTCACCCTCGTAC
1 TCATCTTCATCTCCACCCTCATAC
* **
58621478 TCATCTTCATCTCCACCATCATTT
1 TCATCTTCATCTCCACCCTCATAC
* *
58621502 TTATCTTTATCTCCACCCTCA
1 TCATCTTCATCTCCACCCTCA
58621523 GCTTCGTCTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.19, C:0.41, G:0.01, T:0.39
Consensus pattern (24 bp):
TCATCTTCATCTCCACCCTCATAC
Found at i:58625571 original size:19 final size:21
Alignment explanation
Indices: 58625543--58625586 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
58625533 CATGTGAGCA
*
58625543 TTTAATAAATT-TTTTAA-AT
1 TTTAAAAAATTCTTTTAATAT
58625562 TTTAAAAAATTCTTTTAATAT
1 TTTAAAAAATTCTTTTAATAT
58625583 TTTA
1 TTTA
58625587 TAATATTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 6 0.27
21 6 0.27
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAAAAAATTCTTTTAATAT
Found at i:58626521 original size:27 final size:27
Alignment explanation
Indices: 58626469--58626527 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
58626459 AAATTTTCCC
*
58626469 TTTTTTTCTAAATAGATACTTAAAACTTT
1 TTTTTTTCTAAATAGAAAC-T-AAACTTT
58626498 TTTTTTTCTCAAATAGAAAC-AAACTTT
1 TTTTTTTCT-AAATAGAAACTAAACTTT
58626525 TTT
1 TTT
58626528 AGTCCAAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 10 0.36
29 9 0.32
30 9 0.32
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (27 bp):
TTTTTTTCTAAATAGAAACTAAACTTT
Found at i:58633990 original size:29 final size:29
Alignment explanation
Indices: 58633957--58634043 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
58633947 AATTGTTAAC
58633957 GCCACATGGTCATGTGCCAGGCCGTGTAA
1 GCCACATGGTCATGTGCCAGGCCGTGTAA
58633986 GCCACATGGTCATGTGCCAGGCCGTGTAA
1 GCCACATGGTCATGTGCCAGGCCGTGTAA
* * *
58634015 GCCACATGGCCATGTGTCAGGCCATGTAA
1 GCCACATGGTCATGTGCCAGGCCGTGTAA
58634044 CTCACTATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.22, C:0.28, G:0.30, T:0.21
Consensus pattern (29 bp):
GCCACATGGTCATGTGCCAGGCCGTGTAA
Found at i:58635497 original size:42 final size:42
Alignment explanation
Indices: 58635438--58635547 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 42
58635428 ATGCCAAAAA
* *
58635438 CCCAGCTATGGTCTTACACGAAGTCTCTTATCGATGTCATAT
1 CCCAGATATGGTCTTACACGAAGTCTCATATCGATGTCATAT
* *
58635480 CTCAGATATGGTCTTACACGAAGTCTCATATTGATGTCATAT
1 CCCAGATATGGTCTTACACGAAGTCTCATATCGATGTCATAT
*
58635522 CCCAGATATGGTCTTACACGTAGTCT
1 CCCAGATATGGTCTTACACGAAGTCT
58635548 TAGTAACCCT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (42 bp):
CCCAGATATGGTCTTACACGAAGTCTCATATCGATGTCATAT
Found at i:58643070 original size:42 final size:42
Alignment explanation
Indices: 58642963--58643071 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 42
58642953 TTACCAATGT
* * *
58642963 CATATCCCAAATATGGTCATACATGAGATTCTCGTATCTATGC
1 CATATCCC-AATATGGTCTTACATGAGAGTCTCATATCTATGC
* *
58643006 CAATAGCCCAACTATAGTCTTACATGA-AGTCTCATA-CTGATGC
1 C-ATATCCCAA-TATGGTCTTACATGAGAGTCTCATATCT-ATGC
58643049 CATATCCCAGATATGGTCTTACA
1 CATATCCCA-ATATGGTCTTACA
58643072 CGTAGTCTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
42 20 0.36
43 16 0.29
44 19 0.35
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (42 bp):
CATATCCCAATATGGTCTTACATGAGAGTCTCATATCTATGC
Found at i:58644776 original size:46 final size:46
Alignment explanation
Indices: 58644709--58644926 Score: 391
Period size: 46 Copynumber: 4.7 Consensus size: 46
58644699 AACCCACCCC
*
58644709 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
58644755 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCATTCACATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
58644801 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
58644847 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
58644893 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
58644927 TGCTCAACCA
Statistics
Matches: 163, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 163 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:58647506 original size:49 final size:48
Alignment explanation
Indices: 58647376--58647519 Score: 189
Period size: 49 Copynumber: 2.9 Consensus size: 48
58647366 TCTATTGTGA
* *
58647376 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CC--AGACTGT
* * * * *
58647427 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTG-T
58647476 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
58647520 TAGCTTCGGC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
48 5 0.06
49 40 0.50
50 2 0.03
51 33 0.41
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (48 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACTGT
Found at i:58653680 original size:15 final size:15
Alignment explanation
Indices: 58653645--58653681 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
58653635 TAGTTCATAT
58653645 ATTTTTATTTTTTAA
1 ATTTTTATTTTTTAA
* *
58653660 AATTTTATTTTTTTA
1 ATTTTTATTTTTTAA
58653675 ATTTTTA
1 ATTTTTA
58653682 AATTTCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTTATTTTTTAA
Found at i:58657318 original size:96 final size:96
Alignment explanation
Indices: 58657154--58657345 Score: 375
Period size: 96 Copynumber: 2.0 Consensus size: 96
58657144 AAGAGATGGA
*
58657154 ATCACTCCACAAAAACAGAACATGGGACCTTGTGAAACTTCCTAAAGTTAAAAAGGTTGTTTGTT
1 ATCACTCCACAAAAACAGAACATGGGACCTTGTGAAACTTCCTAAAGGTAAAAAGGTTGTTTGTT
58657219 GTAAATGGGTGTTTAAAAAGAAAGAAGGGAC
66 GTAAATGGGTGTTTAAAAAGAAAGAAGGGAC
58657250 ATCACTCCACAAAAACAGAACATGGGACCTTGTGAAACTTCCTAAAGGTAAAAAGGTTGTTTGTT
1 ATCACTCCACAAAAACAGAACATGGGACCTTGTGAAACTTCCTAAAGGTAAAAAGGTTGTTTGTT
58657315 GTAAATGGGTGTTTAAAAAGAAAGAAGGGAC
66 GTAAATGGGTGTTTAAAAAGAAAGAAGGGAC
58657346 TCCAGGAGTT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (96 bp):
ATCACTCCACAAAAACAGAACATGGGACCTTGTGAAACTTCCTAAAGGTAAAAAGGTTGTTTGTT
GTAAATGGGTGTTTAAAAAGAAAGAAGGGAC
Found at i:58659912 original size:22 final size:21
Alignment explanation
Indices: 58659874--58659936 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
58659864 TTACACCACA
*
58659874 TTGTGGATGAAACCACTCATCG
1 TTGTAGAT-AAACCACTCATCG
*
58659896 TTGTAGATAAACACACTCATTG
1 TTGTAGATAAAC-CACTCATCG
*
58659918 TTGTAGATAAACTACTCAT
1 TTGTAGATAAACCACTCAT
58659937 AATAAAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.27
22 27 0.73
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (21 bp):
TTGTAGATAAACCACTCATCG
Found at i:58662413 original size:15 final size:15
Alignment explanation
Indices: 58662393--58662422 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58662383 CTATGTATGC
*
58662393 AAAATATAAAAGACA
1 AAAATACAAAAGACA
58662408 AAAATACAAAAGACA
1 AAAATACAAAAGACA
58662423 TAATAGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATACAAAAGACA
Found at i:58663662 original size:20 final size:20
Alignment explanation
Indices: 58663625--58663664 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
58663615 CTTGTACGGA
* * *
58663625 TTGCACTTTGGTGTCTCTGT
1 TTGCACTTCGATGCCTCTGT
58663645 TTGCACTTCGATGCCTCTGT
1 TTGCACTTCGATGCCTCTGT
58663665 ATTTGCACTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.45
Consensus pattern (20 bp):
TTGCACTTCGATGCCTCTGT
Found at i:58666500 original size:11 final size:11
Alignment explanation
Indices: 58666464--58666506 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
58666454 AAAAAATTAA
58666464 AAATATATATAT
1 AAATATATAT-T
58666476 AAATAT-T-TT
1 AAATATATATT
*
58666485 CAATATATATT
1 AAATATATATT
58666496 AAATATATATT
1 AAATATATATT
58666507 TATAAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 6 0.22
10 2 0.07
11 13 0.48
12 6 0.22
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
AAATATATATT
Found at i:58666581 original size:21 final size:19
Alignment explanation
Indices: 58666532--58666593 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
58666522 TCTTGATTCT
* *
58666532 ATTTTTATATATTTTTTAAG
1 ATTTTTAT-TATTTTTGAAA
*
58666552 ATTATTA-T-TTTTTGAAA
1 ATTTTTATTATTTTTGAAA
*
58666569 TTTTTTATATATTTTTGAAA
1 ATTTTTAT-TATTTTTGAAA
58666589 ATTTT
1 ATTTT
58666594 AGAATTAGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
17 12 0.36
18 1 0.03
19 1 0.03
20 19 0.58
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
ATTTTTATTATTTTTGAAA
Found at i:58667559 original size:19 final size:20
Alignment explanation
Indices: 58667535--58667572 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58667525 ATTTAAAAAA
*
58667535 ATTTTAA-AAAAATCTTAAT
1 ATTTTAATAAAAATATTAAT
58667554 ATTTTAATAAAAATATTAA
1 ATTTTAATAAAAATATTAA
58667573 AAAAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTTAATAAAAATATTAAT
Found at i:58667885 original size:6 final size:6
Alignment explanation
Indices: 58667874--58667913 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
58667864 TCTTCCTCCC
*
58667874 CCCAAA CCCAAA CCCAAA CCCAAA CCCCAAC CCCAAA CCC
1 CCCAAA CCCAAA CCCAAA CCCAAA -CCCAAA CCCAAA CCC
58667914 CTCCTTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.42, C:0.57, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAA
Found at i:58667908 original size:13 final size:13
Alignment explanation
Indices: 58667873--58667914 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
58667863 TTCTTCCTCC
58667873 CCCCAAACCCAAA
1 CCCCAAACCCAAA
58667886 -CCCAAACCCAAA
1 CCCCAAACCCAAA
*
58667898 CCCCAACCCCAAA
1 CCCCAAACCCAAA
58667911 CCCC
1 CCCC
58667915 TCCTTTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (13 bp):
CCCCAAACCCAAA
Found at i:58669574 original size:6 final size:6
Alignment explanation
Indices: 58669565--58669595 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
58669555 GGAATTGCAT
58669565 GTTGAA GTTGAA GTTGAA GTTGAA GTTGAA G
1 GTTGAA GTTGAA GTTGAA GTTGAA GTTGAA G
58669596 ATGCTTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (6 bp):
GTTGAA
Found at i:58674519 original size:19 final size:18
Alignment explanation
Indices: 58674483--58674517 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58674473 ATAGGAACTA
58674483 TATAAAATTTAAAAAAAT
1 TATAAAATTTAAAAAAAT
*
58674501 TATACAATTTAAAAAAA
1 TATAAAATTTAAAAAAA
58674518 ATAGCGAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TATAAAATTTAAAAAAAT
Found at i:58676654 original size:117 final size:117
Alignment explanation
Indices: 58676506--58676739 Score: 380
Period size: 117 Copynumber: 2.0 Consensus size: 117
58676496 GATGAGGAAG
*
58676506 AAGGATACTTAATTTATTACCTTAATTAAAGCTTTCTCTCTTTAACCCATA-TTTTCTCTCACTA
1 AAGGATACTTAATTTATTACCTTAATTAAAGCTTTCTCTCTTTAACCCAAACTTTT-TCTCACTA
* *
58676570 TACTATAGAAACCATAAGCTTCAATGGAGAGATTAAGGATGTAAACATGCTTA
65 TACTATAGAAACCATAAACTTCAACGGAGAGATTAAGGATGTAAACATGCTTA
*
58676623 AAGGATACTTAATTTTTTACCTTAATTAAAGCTTTCTCTCTTTAACCCAAACTTTTTCTCACTAT
1 AAGGATACTTAATTTATTACCTTAATTAAAGCTTTCTCTCTTTAACCCAAACTTTTTCTCACTAT
* * * *
58676688 ACTATAGGAACCCTAAACTTTAACGGAGAGATTGAGGATGTAAACATGCTTA
66 ACTATAGAAACCATAAACTTCAACGGAGAGATTAAGGATGTAAACATGCTTA
58676740 GGAGGTGATT
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
117 104 0.96
118 4 0.04
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (117 bp):
AAGGATACTTAATTTATTACCTTAATTAAAGCTTTCTCTCTTTAACCCAAACTTTTTCTCACTAT
ACTATAGAAACCATAAACTTCAACGGAGAGATTAAGGATGTAAACATGCTTA
Found at i:58678595 original size:13 final size:13
Alignment explanation
Indices: 58678577--58678606 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
58678567 CTACCTAGAG
58678577 ATATTTAGAAGAT
1 ATATTTAGAAGAT
58678590 ATATTTAGAAGAT
1 ATATTTAGAAGAT
58678603 ATAT
1 ATAT
58678607 AAAACAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (13 bp):
ATATTTAGAAGAT
Found at i:58681199 original size:8 final size:8
Alignment explanation
Indices: 58681186--58681214 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
58681176 TTATGTTTAG
58681186 TATATTAT
1 TATATTAT
58681194 TATATTAT
1 TATATTAT
58681202 TATATTAT
1 TATATTAT
58681210 TATAT
1 TATAT
58681215 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:58681247 original size:5 final size:5
Alignment explanation
Indices: 58681237--58681272 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
58681227 TTATGTTTTA
58681237 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
58681273 AAACTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:58681971 original size:5 final size:5
Alignment explanation
Indices: 58681961--58682073 Score: 219
Period size: 5 Copynumber: 22.8 Consensus size: 5
58681951 GTGAGACAAG
58681961 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
58682011 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
58682061 ATATT ATA-T ATAT
1 ATATT ATATT ATAT
58682074 GAACTAAAGA
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.04
5 103 0.96
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:58682732 original size:801 final size:801
Alignment explanation
Indices: 58681237--58682761 Score: 2908
Period size: 801 Copynumber: 1.9 Consensus size: 801
58681227 TTATGTTTTA
58681237 ATTATATTATATTATATTATATTATATTATATATATAAACTAAAGAAGCAAATGAAAGGAAATAG
1 ATTATATTATATTATATTATATTATATTATATATATAAACTAAAGAAGCAAATGAAAGGAAATAG
58681302 AAACAGAATGAAACGAAACAGAGAGCAGGGGAGAAAAAGAAAGAAAGAAGGGGAGAAAAGGGAAA
66 AAACAGAATGAAACGAAACAGAGAGCAGGGGAGAAAAAGAAAGAAAGAAGGGGAGAAAAGGGAAA
*
58681367 ATTGAAGGTTTGAAGCTTTAAGCTTTAATAGGTAAGTCAATCAAGCCCTTTTTACTTAATTTTGA
131 ATTCAAGGTTTGAAGCTTTAAGCTTTAATAGGTAAGTCAATCAAGCCCTTTTTACTTAATTTTGA
58681432 TGTTTTAGAAGTTTTAGAACAAAGTTTTGATGAAATTAAGTTGATATTTTGATAGTTATTAGATT
196 TGTTTTAGAAGTTTTAGAACAAAGTTTTGATGAAATTAAGTTGATATTTTGATAGTTATTAGATT
58681497 TCTAGATATTGTCCATGTTAAATAAAATGATGAATTAAGGGCTAAATTGATAGAAATTCAAGTTA
261 TCTAGATATTGTCCATGTTAAATAAAATGATGAATTAAGGGCTAAATTGATAGAAATTCAAGTTA
58681562 AAAATGATACAAGGATTGAATTGTAAAGTGATTCATAAGTTTTATGCTTTAAGGACTAAATTGAA
326 AAAATGATACAAGGATTGAATTGTAAAGTGATTCATAAGTTTTATGCTTTAAGGACTAAATTGAA
58681627 AGAATTTCGAAATTATGGTTTTATGATGAAAAATAGATAATTATGTCTAAGTTTGGTTAAAAATT
391 AGAATTTCGAAATTATGGTTTTATGATGAAAAATAGATAATTATGTCTAAGTTTGGTTAAAAATT
58681692 GAGTAGAAATAAAGTATGAATTAAGATAGAAAAGTAAGTGAATTTAGTTAGAATTAAATTGAAAT
456 GAGTAGAAATAAAGTATGAATTAAGATAGAAAAGTAAGTGAATTTAGTTAGAATTAAATTGAAAT
* *
58681757 TAAAGTAAATCAACATTTTGTACTAAGACTATTTTGGACAGCAGCAGTAGTCTAAGTTTGAAAAA
521 TAAAGTAAATCAACATTTTGGACTAAGACTATTTTGGACAGCAGCAGTAGTCTAAATTTGAAAAA
*
58681822 TCACCAAAAATTGTAGAAATTGAATTAGAGGATGAATAAAATATGGAATTAAATACTATTGAGTC
586 TCACCAAAAATTGTAGAAATTGAATTAGAGGATGAATAAAATATGGAATTAAATACTATTGAGTA
*
58681887 TAGTTTCCTATAGAAGAAACGATATAAGCAATTGAATTGTAAATTATGAGATATAATGAATTTTG
651 TAGTTTCCTATAGAAGAAACGATATAAGAAATTGAATTGTAAATTATGAGATATAATGAATTTTG
58681952 TGAGACAAGATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTA
716 TGAGACAAGATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTA
58682017 TATTATATTATATTATATTAT
781 TATTATATTATATTATATTAT
*
58682038 ATTATATTATATTATATTATATTATATTATATATATGAACTAAAGAAGCAAATGAAAGGAAATAG
1 ATTATATTATATTATATTATATTATATTATATATATAAACTAAAGAAGCAAATGAAAGGAAATAG
* *
58682103 AAACAGAATGAAACGAAACTGATAGCAGGGGAGAAAAAGAAAGAAAGAAGGGGAGAAAAGGGAAA
66 AAACAGAATGAAACGAAACAGAGAGCAGGGGAGAAAAAGAAAGAAAGAAGGGGAGAAAAGGGAAA
58682168 ATTCAAGGTTTGAAGCTTTAAGCTTTAATAGGTAAGTCAATCAAGCCCTTTTTACTTAATTTTGA
131 ATTCAAGGTTTGAAGCTTTAAGCTTTAATAGGTAAGTCAATCAAGCCCTTTTTACTTAATTTTGA
58682233 TGTTTTAGAAGTTTTAGAACAAAGTTTTGATGAAATTAAGTTGATATTTTGATAGTTATTAGATT
196 TGTTTTAGAAGTTTTAGAACAAAGTTTTGATGAAATTAAGTTGATATTTTGATAGTTATTAGATT
58682298 TCTAGATATTGTCCATGTTAAATAAAATGATGAATTAAGGGCTAAATTGATAGAAATTCAAGTTA
261 TCTAGATATTGTCCATGTTAAATAAAATGATGAATTAAGGGCTAAATTGATAGAAATTCAAGTTA
* *
58682363 AAAATGATACAAGGATTGAATTGTAAATTGATTCTTAAGTTTTATGCTTTAAGGACTAAATTGAA
326 AAAATGATACAAGGATTGAATTGTAAAGTGATTCATAAGTTTTATGCTTTAAGGACTAAATTGAA
58682428 AGAATTTCGAAATTATGGTTTTATGATGAAAAATAGATAATTATGTCTAAGTTTGGTTAAAAATT
391 AGAATTTCGAAATTATGGTTTTATGATGAAAAATAGATAATTATGTCTAAGTTTGGTTAAAAATT
58682493 GAGTAGAAATAAAGTATGAATTAAGATAGAAAAGTAAGTGAATTTAGTTAGAATTAAATTGAAAT
456 GAGTAGAAATAAAGTATGAATTAAGATAGAAAAGTAAGTGAATTTAGTTAGAATTAAATTGAAAT
*
58682558 TAAAGTAAATCAACATTTTGGACTAAGACTATTTTGGACAGTAGCAGTAGTCTAAATTTGAAAAA
521 TAAAGTAAATCAACATTTTGGACTAAGACTATTTTGGACAGCAGCAGTAGTCTAAATTTGAAAAA
58682623 TCACCAAAAATTGTAGAAATTGAATTAGAGGATGAATAAAATATGGAATTAAAT-CTTATTGAGT
586 TCACCAAAAATTGTAGAAATTGAATTAGAGGATGAATAAAATATGGAATTAAATAC-TATTGAGT
* * *
58682687 ATAGTTTCTTATAGAAGAAACGGTATAAGAAATTGAGTTGTAAATTATGAGATATAATGAATTTT
650 ATAGTTTCCTATAGAAGAAACGATATAAGAAATTGAATTGTAAATTATGAGATATAATGAATTTT
58682752 GTGAGACAAG
715 GTGAGACAAG
58682762 GTTAGGATGA
Statistics
Matches: 709, Mismatches: 14, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
800 1 0.00
801 708 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.34
Consensus pattern (801 bp):
ATTATATTATATTATATTATATTATATTATATATATAAACTAAAGAAGCAAATGAAAGGAAATAG
AAACAGAATGAAACGAAACAGAGAGCAGGGGAGAAAAAGAAAGAAAGAAGGGGAGAAAAGGGAAA
ATTCAAGGTTTGAAGCTTTAAGCTTTAATAGGTAAGTCAATCAAGCCCTTTTTACTTAATTTTGA
TGTTTTAGAAGTTTTAGAACAAAGTTTTGATGAAATTAAGTTGATATTTTGATAGTTATTAGATT
TCTAGATATTGTCCATGTTAAATAAAATGATGAATTAAGGGCTAAATTGATAGAAATTCAAGTTA
AAAATGATACAAGGATTGAATTGTAAAGTGATTCATAAGTTTTATGCTTTAAGGACTAAATTGAA
AGAATTTCGAAATTATGGTTTTATGATGAAAAATAGATAATTATGTCTAAGTTTGGTTAAAAATT
GAGTAGAAATAAAGTATGAATTAAGATAGAAAAGTAAGTGAATTTAGTTAGAATTAAATTGAAAT
TAAAGTAAATCAACATTTTGGACTAAGACTATTTTGGACAGCAGCAGTAGTCTAAATTTGAAAAA
TCACCAAAAATTGTAGAAATTGAATTAGAGGATGAATAAAATATGGAATTAAATACTATTGAGTA
TAGTTTCCTATAGAAGAAACGATATAAGAAATTGAATTGTAAATTATGAGATATAATGAATTTTG
TGAGACAAGATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTA
TATTATATTATATTATATTAT
Found at i:58683725 original size:21 final size:21
Alignment explanation
Indices: 58683701--58683753 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
58683691 TATGTGTCGT
58683701 ATTTCAGGCACCTCGTGTGTC
1 ATTTCAGGCACCTCGTGTGTC
58683722 ATTTCAGGCACCTCGTGTGTC
1 ATTTCAGGCACCTCGTGTGTC
* *
58683743 GTTTTAGGCAC
1 ATTTCAGGCAC
58683754 TTTATGTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.34
Consensus pattern (21 bp):
ATTTCAGGCACCTCGTGTGTC
Found at i:58683761 original size:21 final size:21
Alignment explanation
Indices: 58683683--58683765 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
58683673 TTTATCGATC
* *
58683683 AGGCACTTTATGTGTCGTATTT
1 AGGCACCTCATGTGTCGT-TTT
* * *
58683705 CAGGCACCTCGTGTGTCATTTC
1 -AGGCACCTCATGTGTCGTTTT
*
58683727 AGGCACCTCGTGTGTCGTTTT
1 AGGCACCTCATGTGTCGTTTT
* *
58683748 AGGCACTTTATGTGTCGT
1 AGGCACCTCATGTGTCGT
58683766 ATACTGATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 34 0.68
22 2 0.04
23 14 0.28
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (21 bp):
AGGCACCTCATGTGTCGTTTT
Done.