Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 21
Found at i:163116 original size:17 final size:18
Alignment explanation
Indices: 163072--163116 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
163062 ATACATATTT
163072 AAAGGGTATCGATACTTTTC
1 AAAGGGTATCGATAC--TTC
*
163092 ATAGGGTATCGATAC-TC
1 AAAGGGTATCGATACTTC
163109 AAAGGGTA
1 AAAGGGTA
163117 GTATCGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
20 14 0.61
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (18 bp):
AAAGGGTATCGATACTTC
Found at i:164119 original size:16 final size:16
Alignment explanation
Indices: 164094--164131 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
164084 GAGTCATAAC
*
164094 TGTTTTTTGAAACAAT
1 TGTTTATTGAAACAAT
164110 TGTTTATTGAAACAAT
1 TGTTTATTGAAACAAT
164126 TGTTTA
1 TGTTTA
164132 AAACATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (16 bp):
TGTTTATTGAAACAAT
Found at i:164413 original size:14 final size:15
Alignment explanation
Indices: 164394--164428 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
164384 GTTTTGCAAT
164394 ATAAAAGTGA-AAGA
1 ATAAAAGTGATAAGA
*
164408 ATAAAAGTGATGAGA
1 ATAAAAGTGATAAGA
164423 ATAAAA
1 ATAAAA
164429 CAAAGGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (15 bp):
ATAAAAGTGATAAGA
Found at i:168874 original size:9 final size:9
Alignment explanation
Indices: 168860--168903 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
168850 ATTTTTATTA
168860 ATATTTTTC
1 ATATTTTTC
*
168869 ATATTTTTAAA
1 ATATTTTT--C
168880 ATATTTTTC
1 ATATTTTTC
168889 ATATTTTT-
1 ATATTTTTC
168897 ATATTTT
1 ATATTTT
168904 AAATATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 7 0.23
9 16 0.52
11 8 0.26
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (9 bp):
ATATTTTTC
Found at i:168877 original size:28 final size:27
Alignment explanation
Indices: 168857--168909 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
168847 TTAATTTTTA
168857 TTAATATTTTTCATATTTTTAAAATATTT
1 TTAATATTTTT-ATATTTTT-AAATATTT
*
168886 TTCATATTTTTATA-TTTTAAATAT
1 TTAATATTTTTATATTTTTAAATAT
168910 AAAATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 4 0.17
28 3 0.13
29 10 0.43
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (27 bp):
TTAATATTTTTATATTTTTAAATATTT
Found at i:168882 original size:20 final size:20
Alignment explanation
Indices: 168859--168897 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
168849 AATTTTTATT
168859 AATATTTTTCATATTTTTAA
1 AATATTTTTCATATTTTTAA
168879 AATATTTTTCATATTTTTA
1 AATATTTTTCATATTTTTA
168898 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
AATATTTTTCATATTTTTAA
Found at i:168884 original size:26 final size:25
Alignment explanation
Indices: 168855--168934 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 25
168845 ATTTAATTTT
168855 TATTAATATTTTTCATATTTTTAAAA
1 TATTAATATTTTT-ATATTTTTAAAA
*
168881 TATTTTTCATATTTTTATA-TTTT-AAA
1 TA---TTAATATTTTTATATTTTTAAAA
*
168907 TATAAAATAATTTTTA-ATTTTTAAAA
1 TAT-TAAT-ATTTTTATATTTTTAAAA
168933 TA
1 TA
168935 ATAAATAAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
23 1 0.02
24 3 0.07
25 11 0.25
26 12 0.27
27 4 0.09
28 3 0.07
29 10 0.23
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTAATATTTTTATATTTTTAAAA
Found at i:170215 original size:30 final size:31
Alignment explanation
Indices: 170181--170245 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
170171 GACCGGTCAC
*
170181 GACCCAACCCGTTGACCCGGCCCGA-CCGTT
1 GACCCAACCCGTTGACCCGACCCGACCCGTT
*
170211 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCAACCCGTTGACCCGACCCGACCCGTT
170242 GACC
1 GACC
170246 GGTACTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (31 bp):
GACCCAACCCGTTGACCCGACCCGACCCGTT
Found at i:170234 original size:18 final size:18
Alignment explanation
Indices: 170180--170245 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 18
170170 TGACCGGTCA
*
170180 CGACCCAACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
170198 CGGCCCGA-CCGTT----
1 CGACCCGACCCGTTGACC
170211 -GACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
170228 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
170246 GGTACTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
12 6 0.15
13 5 0.13
17 5 0.13
18 23 0.59
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:170245 original size:13 final size:13
Alignment explanation
Indices: 170201--170234 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
170191 GTTGACCCGG
170201 CCCGA-CCGTTGA
1 CCCGACCCGTTGA
170213 CCCGACCCGTTGA
1 CCCGACCCGTTGA
170226 CCCGACCCG
1 CCCGACCCG
170235 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.15, C:0.50, G:0.24, T:0.12
Consensus pattern (13 bp):
CCCGACCCGTTGA
Found at i:170292 original size:29 final size:29
Alignment explanation
Indices: 170250--170388 Score: 197
Period size: 29 Copynumber: 4.7 Consensus size: 29
170240 TTGACCGGTA
* *
170250 CTATTTTGGTAAATAATTCGGTTTTGATG
1 CTATTCTGGTAAATAATTCGGTTTTGGTG
**
170279 CTATTCTGGTAAATAATTTAGTTTTGGTG
1 CTATTCTGGTAAATAATTCGGTTTTGGTG
*
170308 CTATTCTGGTAAATAATTCAGTTTTGGTG
1 CTATTCTGGTAAATAATTCGGTTTTGGTG
170337 CTATTCTGGTAAATAATTCGGGTTTTTTGGTG
1 CTATTCTGGTAAATAATTC-GG--TTTTGGTG
*
170369 CTATTCTGGTAATTAATTCG
1 CTATTCTGGTAAATAATTCG
170389 AAATGGTTGC
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
29 72 0.72
30 1 0.01
31 1 0.01
32 26 0.26
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (29 bp):
CTATTCTGGTAAATAATTCGGTTTTGGTG
Found at i:170400 original size:61 final size:58
Alignment explanation
Indices: 170250--170409 Score: 160
Period size: 58 Copynumber: 2.7 Consensus size: 58
170240 TTGACCGGTA
* * *** * *
170250 CTATTTTGGTAAATAATTCGGTTTTGATGCTATTCTGGTAAATAATTTAGTTTTGGTG
1 CTATTCTGGTAAATAATTCAGAAATGGTGCTATTCTGGTAAATAATTGAGTTTTGGTG
*** *
170308 CTATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGGGTTTTTTGGTG
1 CTATTCTGGTAAATAATTCAGAAATGGTGCTATTCTGGTAAATAATT-GAG--TTTTGGTG
* *
170369 CTATTCTGGTAATTAATTC-GAAATGGTTGCTATTTTGGTAA
1 CTATTCTGGTAAATAATTCAGAAATGG-TGCTATTCTGGTAA
170410 TTATTTTAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
58 44 0.50
59 1 0.01
60 4 0.05
61 39 0.44
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.46
Consensus pattern (58 bp):
CTATTCTGGTAAATAATTCAGAAATGGTGCTATTCTGGTAAATAATTGAGTTTTGGTG
Found at i:170437 original size:28 final size:28
Alignment explanation
Indices: 170365--170437 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
170355 CGGGTTTTTT
* *
170365 GGTGCTATTCTG-GTAATTAATTCGAAAT
1 GGTGCTATT-TGTGTAATTAATTCAAAAA
* *
170393 GGTTGCTATTT-TGGTAATTATTTTAAAAA
1 GG-TGCTATTTGT-GTAATTAATTCAAAAA
170422 GGTGCTATTTGTGTAA
1 GGTGCTATTTGTGTAA
170438 AATGTTCAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 15 0.41
29 22 0.59
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (28 bp):
GGTGCTATTTGTGTAATTAATTCAAAAA
Found at i:177716 original size:30 final size:29
Alignment explanation
Indices: 177597--177736 Score: 190
Period size: 29 Copynumber: 4.8 Consensus size: 29
177587 ACCGTTGACC
* *
177597 GGTGCTATTTTAGTAAATAATTCGATTTT
1 GGTGCTATTCTGGTAAATAATTCGATTTT
* *
177626 GGTGTTATTCTGATAAATAATTCGATTTT
1 GGTGCTATTCTGGTAAATAATTCGATTTT
* *
177655 GGGGCTATTCTGGTAAATAATTCAATTTT
1 GGTGCTATTCTGGTAAATAATTCGATTTT
* *
177684 GGTGCTATTATGGTAAATAATTCGGTTTTT
1 GGTGCTATTCTGGTAAATAATTC-GATTTT
*
177714 GGTGCTATTCTGGTAATTAATTC
1 GGTGCTATTCTGGTAAATAATTC
177737 TAACTGGATG
Statistics
Matches: 96, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
29 71 0.74
30 25 0.26
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.46
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGATTTT
Found at i:177749 original size:59 final size:57
Alignment explanation
Indices: 177600--177758 Score: 158
Period size: 58 Copynumber: 2.7 Consensus size: 57
177590 GTTGACCGGT
* * * * * * *
177600 GCTATTTTAGTAAATAATTCGATTTTGGTGTTATTCTGATAAATAATTCGATTTTGGG
1 GCTATTCTGGTAAATAATTC-AATCTGGTGCTATTATGGTAAATAATTCGATTTTGGG
* * *
177658 GCTATTCTGGTAAATAATTCAATTTTGGTGCTATTATGGTAAATAATTCGGTTTTTGGT
1 GCTATTCTGGTAAATAATTCAA-TCTGGTGCTATTATGGTAAATAATTC-GATTTTGGG
* *
177717 GCTATTCTGGTAATTAATTCTAA-CTGGATGCTATTTTGGTAA
1 GCTATTCTGGTAAATAATTC-AATCTGG-TGCTATTATGGTAA
177759 TTATTTTAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 44 0.51
59 39 0.45
60 2 0.02
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.45
Consensus pattern (57 bp):
GCTATTCTGGTAAATAATTCAATCTGGTGCTATTATGGTAAATAATTCGATTTTGGG
Found at i:177777 original size:29 final size:29
Alignment explanation
Indices: 177714--177781 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
177704 TTCGGTTTTT
* **
177714 GGTGCTATTCTGGTAATTAATTCTAACTG
1 GGTGCTATTTTGGTAATTAATTCTAAAAG
* *
177743 GATGCTATTTTGGTAATT-ATTTTAAAAAG
1 GGTGCTATTTTGGTAATTAATTCT-AAAAG
177772 GGTGCTATTT
1 GGTGCTATTT
177782 GTGTAAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTCTAAAAG
Found at i:180362 original size:26 final size:23
Alignment explanation
Indices: 180321--180367 Score: 58
Period size: 26 Copynumber: 1.9 Consensus size: 23
180311 AGTTTTCACA
180321 TTCCTTTATCTACATTTCTTTTGT
1 TTCCTTTATCTACATTT-TTTTGT
*
180345 TTCCTTTAATTCTTCATTTTTTT
1 TTCCTTT-A-TCTACATTTTTTT
180368 ATCCCTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 5 0.25
26 8 0.40
ACGTcount: A:0.13, C:0.19, G:0.02, T:0.66
Consensus pattern (23 bp):
TTCCTTTATCTACATTTTTTTGT
Found at i:185298 original size:2 final size:2
Alignment explanation
Indices: 185291--185328 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
185281 TACGATAAAC
185291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
185329 TAGAAAACCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:189705 original size:29 final size:30
Alignment explanation
Indices: 189673--189735 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
189663 AATATTCTAG
*
189673 AATCATAAATCATATACA-AAAAATACAA-A
1 AATCAGAAATCATAT-CAGAAAAATACAATA
* *
189702 AATCAGAGATCATATCAGAAAAGTACAATA
1 AATCAGAAATCATATCAGAAAAATACAATA
189732 AATC
1 AATC
189736 CAATATCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.07
29 22 0.76
30 5 0.17
ACGTcount: A:0.59, C:0.14, G:0.06, T:0.21
Consensus pattern (30 bp):
AATCAGAAATCATATCAGAAAAATACAATA
Found at i:190357 original size:14 final size:14
Alignment explanation
Indices: 190338--190364 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
190328 TCGATTAACG
190338 GTCAATGGTCAACC
1 GTCAATGGTCAACC
190352 GTCAATGGTCAAC
1 GTCAATGGTCAAC
190365 GGCCATTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (14 bp):
GTCAATGGTCAACC
Found at i:198808 original size:20 final size:21
Alignment explanation
Indices: 198785--198867 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
198775 TTGGTGCAGA
198785 GGGAATCGATCCCCCCATGA-
1 GGGAATCGATCCCCCCATGAG
* **
198805 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGA-TCCCCCCATG-AG
*
198828 GGGAATCGATCCCCCCCA-CAG
1 GGGAATCGAT-CCCCCCATGAG
*
198849 GGGAATCGATACCCCCATG
1 GGGAATCGATCCCCCCATG
198868 GGGTTCTGTT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
20 14 0.29
21 20 0.41
22 2 0.04
23 13 0.27
ACGTcount: A:0.24, C:0.35, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAATCGATCCCCCCATGAG
Found at i:203761 original size:31 final size:31
Alignment explanation
Indices: 203711--203771 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
203701 CTAAATAAGT
203711 CCTCAAACTTTCAAAAAATCAATT-AGTCCC
1 CCTCAAACTTTCAAAAAATCAATTAAGTCCC
203741 CCTCAAACTTGGT-AAAAAATCAATTAAGTCC
1 CCTCAAACTT--TCAAAAAATCAATTAAGTCC
203772 ATCTATCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 10 0.36
31 12 0.43
32 6 0.21
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (31 bp):
CCTCAAACTTTCAAAAAATCAATTAAGTCCC
Found at i:205010 original size:17 final size:17
Alignment explanation
Indices: 204988--205028 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
204978 GATAGCATGG
204988 CCGGTTCGCTAACCGAT
1 CCGGTTCGCTAACCGAT
*
205005 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGAT
205022 CCGGTTC
1 CCGGTTC
205029 TGAAAACCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.37, G:0.27, T:0.24
Consensus pattern (17 bp):
CCGGTTCGCTAACCGAT
Found at i:211719 original size:96 final size:96
Alignment explanation
Indices: 211590--211789 Score: 220
Period size: 96 Copynumber: 2.1 Consensus size: 96
211580 AATCATGATT
** * * *
211590 TACTGGTTTATAAACTATGACTACATGGTATATGTTCTATGGTTACCTATTTTCACAGTAAAATA
1 TACTGGTTTATAAACTATGACTACATGAAATATGTTATATGATTACCTATTTTCACAGGAAAATA
* * *
211655 TGATCGTTTATGATTTACAGATTATGGAATC
66 TGATCGTTCATGATTTACAGATCATGAAATC
* ** * * * * **
211686 TACTGGTTTATGAACTATGGTTACCTGAAATATGTTATCTGATTTCCTGTTTTCATTGGAAAATA
1 TACTGGTTTATAAACTATGACTACATGAAATATGTTATATGATTACCTATTTTCACAGGAAAATA
* **
211751 TGATCGTTCCTGATTTATGGATCATGAAATC
66 TGATCGTTCATGATTTACAGATCATGAAATC
211782 TACTGGTT
1 TACTGGTT
211790 ACTACTTGAA
Statistics
Matches: 84, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
96 84 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (96 bp):
TACTGGTTTATAAACTATGACTACATGAAATATGTTATATGATTACCTATTTTCACAGGAAAATA
TGATCGTTCATGATTTACAGATCATGAAATC
Found at i:214609 original size:27 final size:26
Alignment explanation
Indices: 214571--214634 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
214561 CTTTTAAAAA
*
214571 TAAA-TATGAAAATATTGAATTTATTT
1 TAAATTAT-AAAATATTAAATTTATTT
214597 TAGAATTATAAAATATTAAATTTATTT
1 TA-AATTATAAAATATTAAATTTATTT
*
214624 TAAATTTTAAA
1 TAAATTATAAA
214635 TTTCACATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 10 0.29
27 21 0.62
28 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
TAAATTATAAAATATTAAATTTATTT
Found at i:214988 original size:44 final size:44
Alignment explanation
Indices: 214938--215024 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
214928 TGTAAGTAGT
* *
214938 TTGATATCGCTTAAG-CAGAGTTTCAGGTTTGAATCCTTATGTAC
1 TTGATATCGCTTAAGAAAG-GTTTCAGGTTTCAATCCTTATGTAC
*
214982 TTGATATCGCTTAAGAAAGGTTTCAGGTTTCAATCCTTGTGTA
1 TTGATATCGCTTAAGAAAGGTTTCAGGTTTCAATCCTTATGTA
215025 TGCAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 37 0.95
45 2 0.05
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (44 bp):
TTGATATCGCTTAAGAAAGGTTTCAGGTTTCAATCCTTATGTAC
Found at i:216748 original size:2 final size:2
Alignment explanation
Indices: 216736--216830 Score: 68
Period size: 2 Copynumber: 52.5 Consensus size: 2
216726 AATATTATTA
* * * *
216736 AT AT A- AT AT AT AT A- AT A- AT A- AT GT AT AT A- AT AA AA AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
216773 AT AT AT GAT -T A- AT A- AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
216812 AT AT AT AT AT A- AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
216831 AACAGATAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
1 11 0.14
2 63 0.83
3 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:216756 original size:15 final size:15
Alignment explanation
Indices: 216718--216828 Score: 99
Period size: 15 Copynumber: 7.6 Consensus size: 15
216708 ATATTATTTA
*
216718 ATAATACTAATAT-T
1 ATAATAATAATATAT
216732 ATTAAT-ATAATATAT
1 A-TAATAATAATATAT
*
216747 ATAATAATAATGTAT
1 ATAATAATAATATAT
* *
216762 ATAATAAAAACATAT
1 ATAATAATAATATAT
*
216777 ATGATTAATAATATAT
1 AT-AATAATAATATAT
*
216793 AT-ATTAT-ATATAT
1 ATAATAATAATATAT
216806 AT-AT-ATATATATAT
1 ATAATAATA-ATATAT
216820 ATAATAATA
1 ATAATAATA
216829 TAAACAGATA
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
12 2 0.03
13 10 0.13
14 22 0.28
15 30 0.38
16 15 0.19
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
ATAATAATAATATAT
Found at i:217089 original size:42 final size:42
Alignment explanation
Indices: 217038--217119 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
217028 AAGGACTTAT
* *
217038 CATCTTGCTCAAAAGACTGACAGATAACCCGAAGGATTTAAA
1 CATCATGCTCAAAAGACTGACAGATAACCCGAAGAATTTAAA
* * * * *
217080 CATCATGCTCGAAGGACTTACAGATGACCCGGAGAATTTA
1 CATCATGCTCAAAAGACTGACAGATAACCCGAAGAATTTA
217120 CAAATTCGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
CATCATGCTCAAAAGACTGACAGATAACCCGAAGAATTTAAA
Found at i:218033 original size:65 final size:64
Alignment explanation
Indices: 217937--218076 Score: 181
Period size: 65 Copynumber: 2.2 Consensus size: 64
217927 CCACGTCCGT
* * * * *
217937 TCTGATTTGACTCTTGAAACACTTCATAAGAAAGATTTATCCTAATTCCTTTTATGTCTCCACA
1 TCTGATTAGACTCTTGAAACACATCACAAGAAAGATTTATCCTAATTCATTTCATGTCTCCACA
* * * *
218001 TCTGATTAGATCTCTTGTAATACATCACAAGAAGGTTTTATCCTAATTCATTTCATGTCTCCACA
1 TCTGATTAGA-CTCTTGAAACACATCACAAGAAAGATTTATCCTAATTCATTTCATGTCTCCACA
*
218066 TCTAATTAGAC
1 TCTGATTAGAC
218077 CTCGAACAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 10 0.15
65 55 0.85
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (64 bp):
TCTGATTAGACTCTTGAAACACATCACAAGAAAGATTTATCCTAATTCATTTCATGTCTCCACA
Found at i:218828 original size:42 final size:42
Alignment explanation
Indices: 218765--218849 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
218755 AATACCATGT
* * * * *
218765 TAGATTATTTTTATCTGAAATGGGCCTTCAGCATGCCCCACA
1 TAGATTATTTCTAACTAAAATGGGCCTTCAACATGCCCAACA
218807 TAGATTATTTCTAACTAAAATGGGCCTTCAACATGCCCAACA
1 TAGATTATTTCTAACTAAAATGGGCCTTCAACATGCCCAACA
218849 T
1 T
218850 TAAAATGCCT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (42 bp):
TAGATTATTTCTAACTAAAATGGGCCTTCAACATGCCCAACA
Found at i:219145 original size:22 final size:22
Alignment explanation
Indices: 219117--219168 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
219107 AGTGATCAAT
219117 TCTTCTGACTGAGATATGTGCA
1 TCTTCTGACTGAGATATGTGCA
219139 TCTTCTGACTGAGATATGTGCA
1 TCTTCTGACTGAGATATGTGCA
219161 TCTTCTGA
1 TCTTCTGA
219169 ATGAAGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (22 bp):
TCTTCTGACTGAGATATGTGCA
Found at i:224842 original size:18 final size:18
Alignment explanation
Indices: 224797--224850 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
224787 AATTATGAAT
*
224797 TATAATAATAATCCTAA-GG
1 TATAATAATAAT--TAATCG
224816 TACTAATAATAATTAATCG
1 TA-TAATAATAATTAATCG
224835 TATAATAATAATTAAT
1 TATAATAATAATTAAT
224851 ATTTAAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 17 0.53
19 5 0.16
20 10 0.31
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (18 bp):
TATAATAATAATTAATCG
Found at i:226143 original size:2 final size:2
Alignment explanation
Indices: 226131--226236 Score: 67
Period size: 2 Copynumber: 59.5 Consensus size: 2
226121 AATATTATTA
* * *
226131 AT AT A- AT AT AT AT A- AT A- AT A- AC AT AT AT A- AT A- AA AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
226167 AT AT AT A- AT -T A- AT A- AT AT AT AT A- AT -T AA AT AA AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
226203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
226237 AACAGAAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
1 13 0.16
2 69 0.84
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:226146 original size:14 final size:14
Alignment explanation
Indices: 226113--226237 Score: 114
Period size: 14 Copynumber: 8.6 Consensus size: 14
226103 ATATTATTTA
226113 ATAATACTAATAT-T
1 ATAATA-TAATATAT
226127 ATTAATATAATATAT
1 A-TAATATAATATAT
*
226142 ATAATAATAACATAT
1 ATAAT-ATAATATAT
* *
226157 ATAATAAAACATAT
1 ATAATATAATATAT
226171 ATAATTAATAATATAT
1 ATAA-T-ATAATATAT
*
226187 ATAAT-TAA-ATAA
1 ATAATATAATATAT
226199 ATAA-ATATATATAT
1 ATAATATA-ATATAT
226213 ATATATATATATATAT
1 ATA-ATATA-ATATAT
226229 ATAATATAA
1 ATAATATAA
226238 ACAGAAAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 20
0.79 0.05 0.17
Matches are distributed among these distances:
12 9 0.09
13 4 0.04
14 30 0.32
15 28 0.29
16 24 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATATAATATAT
Found at i:231064 original size:15 final size:15
Alignment explanation
Indices: 231044--231083 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
231034 GGTAGGCTAT
231044 TCACAAGAATTTAGC
1 TCACAAGAATTTAGC
231059 TCACAAGAATTTAGC
1 TCACAAGAATTTAGC
231074 TCACAAGAAT
1 TCACAAGAAT
231084 AAAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (15 bp):
TCACAAGAATTTAGC
Found at i:234489 original size:14 final size:15
Alignment explanation
Indices: 234465--234493 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
234455 AACCCCTTTA
234465 TAAAGAAAAGAAATG
1 TAAAGAAAAGAAATG
234480 TAAA-AAAAGAAATG
1 TAAAGAAAAGAAATG
234494 CTCTTAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (15 bp):
TAAAGAAAAGAAATG
Found at i:235209 original size:2 final size:2
Alignment explanation
Indices: 235202--235229 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
235192 ATATAGTTCA
235202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
235230 TCTATTAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:238615 original size:3 final size:3
Alignment explanation
Indices: 238602--238652 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
238592 AGACCCGTTT
* *
238602 TTA TT- TTA TTA TTA TTA TCA TTA TTA TTTA ATA TTA TCTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA
238648 TTA TT
1 TTA TT
238653 TTTGTCTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 6 0.15
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:238629 original size:23 final size:24
Alignment explanation
Indices: 238602--238654 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
238592 AGACCCGTTT
*
238602 TTATTTTATTATTAT-TATCATTA
1 TTATTTTAATATTATCTATCATTA
*
238625 TTA-TTTAATATTATCTATTATTA
1 TTATTTTAATATTATCTATCATTA
238648 TTATTTT
1 TTATTTT
238655 TGTCTGTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 13 0.50
24 3 0.12
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATTTTAATATTATCTATCATTA
Found at i:239667 original size:14 final size:15
Alignment explanation
Indices: 239648--239677 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
239638 AAATAAATGA
239648 AAAAAT-GAAAAAAT
1 AAAAATGGAAAAAAT
239662 AAAAATGGAAAAAAT
1 AAAAATGGAAAAAAT
239677 A
1 A
239678 TGATATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAAATGGAAAAAAT
Found at i:244916 original size:15 final size:15
Alignment explanation
Indices: 244896--244934 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
244886 ATATTAATTA
*
244896 ATAAATCTAATTAAT
1 ATAAATATAATTAAT
244911 ATAAATATAATTAAT
1 ATAAATATAATTAAT
244926 A-AAATATAA
1 ATAAATATAA
244935 AAACCCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAATATAATTAAT
Found at i:244932 original size:14 final size:14
Alignment explanation
Indices: 244876--244934 Score: 68
Period size: 14 Copynumber: 4.2 Consensus size: 14
244866 ACAATTTATT
*
244876 TAATTAA-ACAATA
1 TAATTAATAAAATA
*
244889 TTAATTAAT-AAATC
1 -TAATTAATAAAATA
244903 TAATTAATATAAATA
1 TAATTAATA-AAATA
244918 TAATTAATAAAATA
1 TAATTAATAAAATA
244932 TAA
1 TAA
244935 AAACCCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
13 8 0.21
14 18 0.46
15 13 0.33
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATTAATAAAATA
Found at i:245156 original size:55 final size:55
Alignment explanation
Indices: 245051--245202 Score: 189
Period size: 55 Copynumber: 2.8 Consensus size: 55
245041 AAAACGAGTC
* * *
245051 CGCTCCTTCTTCTTTCAAGGACTATTGGACTTGAACAATTTTCAAAAAATGGGTA
1 CGCTCCTTCTTCTTTCAAGGAGTATAGGACTTGAACAATCTTCAAAAAATGGGTA
* *** * *
245106 TGCTCCTTCTTCTTTCAAGGAGTATAGGACTTGAACAATCTTCGGTAAATGTGTC
1 CGCTCCTTCTTCTTTCAAGGAGTATAGGACTTGAACAATCTTCAAAAAATGGGTA
* *
245161 CGCTCCCTT-TTCTTTCAAGGAGTATAAGACTCGAACAATCTT
1 CGCT-CCTTCTTCTTTCAAGGAGTATAGGACTTGAACAATCTT
245203 TGGAAAACTA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
55 80 0.95
56 4 0.05
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (55 bp):
CGCTCCTTCTTCTTTCAAGGAGTATAGGACTTGAACAATCTTCAAAAAATGGGTA
Found at i:264692 original size:44 final size:44
Alignment explanation
Indices: 264629--264849 Score: 307
Period size: 44 Copynumber: 5.0 Consensus size: 44
264619 TGTTATCGAA
* * *
264629 ATAAATGAAAATTCATAACGGTGCATTATTGGAAGAAATATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
* *
264673 ATAAATGAAAATGCATAACGGTGCTTTAATGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
* * *
264717 ATAAATGAAAATGCATAACAGTGCATTATTGGCATAAATGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
** **
264761 ATAAATGAAAATGCATAACAATGCATTATTGGCAGAAGGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
* * *
264805 ATAAATGAAAATACATAACGGTGCATTATTTGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
264849 A
1 A
264850 CTCATGGTAT
Statistics
Matches: 157, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 157 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
Found at i:270891 original size:44 final size:44
Alignment explanation
Indices: 270822--270906 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
270812 TAATTAGGAA
* *
270822 CATAAATGAAAATGCATAACAGTGCATTATTTGCATAAAGGCGC
1 CATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGCGC
**
270866 CATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGG
1 CATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGG
270907 TGTCACTCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (44 bp):
CATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGCGC
Found at i:275360 original size:34 final size:34
Alignment explanation
Indices: 275314--275380 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
275304 CCTTTACAGC
* *
275314 TCCCTAGTTTTTCACGGGCTAAACTAGAACCTTA
1 TCCCTAGCTTTTCAAGGGCTAAACTAGAACCTTA
* *
275348 TCCCTAGCTTTTCAAGGGCTCAGCTAGAACCTT
1 TCCCTAGCTTTTCAAGGGCTAAACTAGAACCTT
275381 TCCTTTTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTCAAGGGCTAAACTAGAACCTTA
Found at i:275864 original size:22 final size:22
Alignment explanation
Indices: 275839--275885 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
275829 GATGTTTGAG
* *
275839 CAGTCATAGGGGTATTGATACC
1 CAGTCACAGGGGTATCGATACC
275861 CAGTCACAGGGGTATCGATACC
1 CAGTCACAGGGGTATCGATACC
275883 CAG
1 CAG
275886 GGTAAAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (22 bp):
CAGTCACAGGGGTATCGATACC
Found at i:277906 original size:22 final size:22
Alignment explanation
Indices: 277881--277923 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
277871 AATGTTTGAG
* * *
277881 AAGTCATAGGGGTATTGATACC
1 AAGTCACAAGGGTATCGATACC
277903 AAGTCACAAGGGTATCGATAC
1 AAGTCACAAGGGTATCGATAC
277924 ACAGGGTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (22 bp):
AAGTCACAAGGGTATCGATACC
Found at i:283276 original size:17 final size:17
Alignment explanation
Indices: 283254--283289 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
283244 GGTAAATCGG
283254 TTTGGGTCAAGTTAATT
1 TTTGGGTCAAGTTAATT
*
283271 TTTGGGTCAGGTTAATT
1 TTTGGGTCAAGTTAATT
283288 TT
1 TT
283290 CAGGTCGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (17 bp):
TTTGGGTCAAGTTAATT
Found at i:283758 original size:32 final size:32
Alignment explanation
Indices: 283685--283758 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
283675 GTTGTTTTTT
* * * **
283685 GGTTCAGGTTATTTTTGGTTTGGATTGTTTTC
1 GGTTCAGGTTAATTTCGGTTCGGATTACTTTC
*
283717 GAATT-AGGTTAATTTCGGTTCGGATTACTTTC
1 G-GTTCAGGTTAATTTCGGTTCGGATTACTTTC
283749 GGTTCAGGTT
1 GGTTCAGGTT
283759 GTTTTCTATG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
31 2 0.06
32 29 0.88
33 2 0.06
ACGTcount: A:0.15, C:0.09, G:0.27, T:0.49
Consensus pattern (32 bp):
GGTTCAGGTTAATTTCGGTTCGGATTACTTTC
Found at i:283764 original size:16 final size:16
Alignment explanation
Indices: 283680--283764 Score: 50
Period size: 16 Copynumber: 5.3 Consensus size: 16
283670 TTTAGGTTGT
*
283680 TTTTTGGTTCAGGTTA
1 TTTTCGGTTCAGGTTA
* * *
283696 TTTTTGGTT-TGGATTG
1 TTTTCGGTTCAGG-TTA
*
283712 TTTTCGAATT-AGGTTA
1 TTTTCG-GTTCAGGTTA
*
283728 ATTTCGGTTC-GGATTA
1 TTTTCGGTTCAGG-TTA
* *
283744 CTTTCGGTTCAGGTTG
1 TTTTCGGTTCAGGTTA
283760 TTTTC
1 TTTTC
283765 TATGCGGATC
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
15 6 0.11
16 41 0.77
17 6 0.11
ACGTcount: A:0.13, C:0.09, G:0.25, T:0.53
Consensus pattern (16 bp):
TTTTCGGTTCAGGTTA
Found at i:284015 original size:5 final size:5
Alignment explanation
Indices: 284007--284193 Score: 374
Period size: 5 Copynumber: 37.4 Consensus size: 5
283997 ATATCATATC
284007 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG
1 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG
284057 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG
1 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG
284107 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG
1 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG
284157 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG AT
1 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG AT
284194 ATTATATTAT
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 182 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
ATGTG
Found at i:285787 original size:16 final size:14
Alignment explanation
Indices: 285768--285808 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
285758 TTATTTATTA
285768 TTTCTTTTTTTTCTAT
1 TTTCTTTTTTTTC--T
*
285784 TTTCTTTTTCTTCT
1 TTTCTTTTTTTTCT
285798 TTTCTTTTTTT
1 TTTCTTTTTTT
285809 CTTACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
16 12 0.52
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTCTTTTTTTTCT
Found at i:285809 original size:16 final size:17
Alignment explanation
Indices: 285766--285811 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
285756 TTTTATTTAT
285766 TATTTC-TTTTTT-TTC
1 TATTTCTTTTTTTCTTC
*
285781 TATTT-TCTTTTTCTTC
1 TATTTCTTTTTTTCTTC
285797 T-TTTCTTTTTTTCTT
1 TATTTCTTTTTTTCTT
285812 ACTTATTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (17 bp):
TATTTCTTTTTTTCTTC
Found at i:293189 original size:77 final size:78
Alignment explanation
Indices: 293075--293222 Score: 178
Period size: 78 Copynumber: 1.9 Consensus size: 78
293065 TTAATAAATA
*
293075 AAATATTATTTAATTAATTCAAATTAAATATACATT-AAAGACTTATAATCTGAATTACAGTCTT
1 AAATATTATTTAATTAATTCAAATTAAATATACATTAAAAGACTTATAATCTAAATTACAGTCTT
293139 -TAATGTTTATTT
66 ATAATGTTTATTT
* ** * * *
293151 AAATATTTATTTAATT-ATTCTGAATTATGTAT-CAATTAAAAGAGTTGTAATCTAAATTACATT
1 AAATA-TTATTTAATTAATTC-AAATTAAATATAC-ATTAAAAGACTTATAATCTAAATTACAGT
293214 CTTATAATG
63 CTTATAATG
293223 CTTACTTACT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
76 10 0.17
77 21 0.35
78 24 0.40
79 5 0.08
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (78 bp):
AAATATTATTTAATTAATTCAAATTAAATATACATTAAAAGACTTATAATCTAAATTACAGTCTT
ATAATGTTTATTT
Found at i:295088 original size:18 final size:18
Alignment explanation
Indices: 295065--295104 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
295055 ACACGCTATA
295065 GGTTTGACCCCTTCAAGT
1 GGTTTGACCCCTTCAAGT
295083 GGTTTGACCCCTTCAAGT
1 GGTTTGACCCCTTCAAGT
295101 GGTT
1 GGTT
295105 CAACAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (18 bp):
GGTTTGACCCCTTCAAGT
Found at i:302499 original size:18 final size:19
Alignment explanation
Indices: 302461--302499 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
302451 ACCTGTTTTC
*
302461 TACCCAAAACATTTAGAAT
1 TACCCAAAACACTTAGAAT
302480 TACCCAAAACACTT-GAAT
1 TACCCAAAACACTTAGAAT
302498 TA
1 TA
302500 GGGAAACGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (19 bp):
TACCCAAAACACTTAGAAT
Found at i:304045 original size:2 final size:2
Alignment explanation
Indices: 304040--304074 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
304030 AAAAAAGTAT
304040 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
304075 TAAAAGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:306114 original size:18 final size:17
Alignment explanation
Indices: 305993--306127 Score: 65
Period size: 18 Copynumber: 7.7 Consensus size: 17
305983 GCATACGTGA
* * *
305993 ATATAATATAATATAAT
1 ATATTATATATTATATT
* * *
306010 ATAATATAATATAATATA
1 ATATTAT-ATATTATATT
* * *
306028 ATATAATATAATATAAT
1 ATATTATATATTATATT
* * *
306045 ATAATATAATATAATATA
1 ATATTAT-ATATTATATT
* * *
306063 ATATAATATAATATAAT
1 ATATTATATATTATATT
* *
306080 ATAATATAATATAATATT
1 ATATTAT-ATATTATATT
306098 CA-ATTATTATATTATATT
1 -ATATTA-TATATTATATT
306116 ATATTATATATT
1 ATATTATATATT
306128 TAGAAAACCA
Statistics
Matches: 81, Mismatches: 31, Indels: 12
0.65 0.25 0.10
Matches are distributed among these distances:
17 34 0.42
18 45 0.56
19 2 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATTATATATTATATT
Found at i:306116 original size:5 final size:5
Alignment explanation
Indices: 305992--306096 Score: 210
Period size: 5 Copynumber: 21.0 Consensus size: 5
305982 AGCATACGTG
305992 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
306042 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
306092 AATAT
1 AATAT
306097 TCAATTATTA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 100 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:309202 original size:51 final size:53
Alignment explanation
Indices: 309128--309255 Score: 172
Period size: 54 Copynumber: 2.4 Consensus size: 53
309118 ATCGAATAAT
* *
309128 AAAAGCAGCAACATTTAGCAAAATTT-AAG-AAAAACTAAAAATTATTTTGTA
1 AAAAGAAGCAACGTTTAGCAAAATTTAAAGAAAAAACTAAAAATTATTTTGTA
*
309179 AAAAGAAGCAACGTTTAGCAAAATTTAAAAGAAAAAACTAACAATTATTTTGTA
1 AAAAGAAGCAACGTTTAGCAAAATTT-AAAGAAAAAACTAAAAATTATTTTGTA
* *
309233 AAAA-ACAACAACGTTTAACAAAA
1 AAAAGA-AGCAACGTTTAGCAAAA
309256 AATCAGAAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
51 24 0.35
53 4 0.06
54 40 0.59
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.24
Consensus pattern (53 bp):
AAAAGAAGCAACGTTTAGCAAAATTTAAAGAAAAAACTAAAAATTATTTTGTA
Found at i:309540 original size:21 final size:22
Alignment explanation
Indices: 309499--309542 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
309489 TTTGTCCGGG
**
309499 ATTTTTATTTTTTATTGTTATT
1 ATTTTTATTTTTTATAATTATT
309521 ATTTTTA-TTTTTATAATTATT
1 ATTTTTATTTTTTATAATTATT
309542 A
1 A
309543 AGTATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTTTATTTTTTATAATTATT
Found at i:318141 original size:2 final size:2
Alignment explanation
Indices: 318136--318182 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
318126 ATACATACAA
318136 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
318178 AT AT A
1 AT AT A
318183 CACTTTTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:320090 original size:20 final size:20
Alignment explanation
Indices: 320067--320112 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 20
320057 CTACTAGAAC
*
320067 AGTACCGATGATGTTCAAGA
1 AGTATCGATGATGTTCAAGA
320087 AGTATC---GATGTTCAAGA
1 AGTATCGATGATGTTCAAGA
320104 AGTATCGAT
1 AGTATCGAT
320113 ACAGATATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
17 17 0.77
20 5 0.23
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (20 bp):
AGTATCGATGATGTTCAAGA
Found at i:320098 original size:17 final size:17
Alignment explanation
Indices: 320076--320112 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
320066 CAGTACCGAT
320076 GATGTTCAAGAAGTATC
1 GATGTTCAAGAAGTATC
320093 GATGTTCAAGAAGTATC
1 GATGTTCAAGAAGTATC
320110 GAT
1 GAT
320113 ACAGATATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (17 bp):
GATGTTCAAGAAGTATC
Found at i:330751 original size:31 final size:31
Alignment explanation
Indices: 330715--330776 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
330705 TCAACTTCCC
330715 TTTGCGTCCAAACCGCAATACTTTCTTCTAA
1 TTTGCGTCCAAACCGCAATACTTTCTTCTAA
330746 TTTGCGTCCAAACCGCAATACTTTCTTCTAA
1 TTTGCGTCCAAACCGCAATACTTTCTTCTAA
330777 GGCGATACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.10, T:0.35
Consensus pattern (31 bp):
TTTGCGTCCAAACCGCAATACTTTCTTCTAA
Found at i:340463 original size:43 final size:44
Alignment explanation
Indices: 340250--340519 Score: 310
Period size: 44 Copynumber: 6.2 Consensus size: 44
340240 TTGTAAGTCT
* * * * *
340250 TTACCGTTACCGCATGCTCCTATGCTATATGCAAGGCTAAGTCC
1 TTACCGTTACCGCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* * *
340294 TTACCGTTACCACAGGCTCCTTTGCTATGTTCAAGAATAAGACC
1 TTACCGTTACCGCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
340338 TTACCGTTACCGCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
1 TTACCGTTACCGCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* * *
340382 TTACTGTTACCGCATGCTCCTTTGCTATTTGCAAGGATAAGACC
1 TTACCGTTACCGCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* * ** ** * *
340426 TTACCATT-TCTTAGGCTTGTTTGCTATGTCCAAGGATACGACC
1 TTACCGTTACCGCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
* * ** *
340469 TTACCGTTTCC-CAGGCTCTTTTGCTATGTTTAAGGGTAAGACC
1 TTACCGTTACCGCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
340512 TTACCGTT
1 TTACCGTT
340520 TTTACATGCT
Statistics
Matches: 191, Mismatches: 34, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
43 66 0.35
44 125 0.65
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (44 bp):
TTACCGTTACCGCAGGCTCCTTTGCTATGTGCAAGGATAAGACC
Found at i:344357 original size:15 final size:15
Alignment explanation
Indices: 344337--344371 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
344327 CGGTAGTCCT
344337 CAATGCATACATCCA
1 CAATGCATACATCCA
344352 CAATGCATACATCCA
1 CAATGCATACATCCA
344367 CAATG
1 CAATG
344372 AAACAGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (15 bp):
CAATGCATACATCCA
Found at i:345364 original size:15 final size:15
Alignment explanation
Indices: 345344--345378 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
345334 CGGTAGTCCT
345344 CAATGCATACATCCA
1 CAATGCATACATCCA
345359 CAATGCATACATCCA
1 CAATGCATACATCCA
*
345374 AAATG
1 CAATG
345379 AAACAAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.29, G:0.09, T:0.20
Consensus pattern (15 bp):
CAATGCATACATCCA
Found at i:349331 original size:22 final size:22
Alignment explanation
Indices: 349280--349333 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
349270 CTTTTGGATA
* * *
349280 ATTCTACGCGGTCTTTCGGGAC
1 ATTCTATGTGGTCCTTCGGGAC
349302 A-TCTATGTGGTCCTTCGGGAC
1 ATTCTATGTGGTCCTTCGGGAC
349323 ATTCTATGTGG
1 ATTCTATGTGG
349334 AACTTCGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.15, C:0.22, G:0.28, T:0.35
Consensus pattern (22 bp):
ATTCTATGTGGTCCTTCGGGAC
Found at i:349347 original size:22 final size:22
Alignment explanation
Indices: 349294--349341 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
349284 TACGCGGTCT
**
349294 TTCGGGACA-TCTATGTGGTCC
1 TTCGGGACATTCTATGTGGAAC
349315 TTCGGGACATTCTATGTGGAAC
1 TTCGGGACATTCTATGTGGAAC
349337 TTCGG
1 TTCGG
349342 TGCATTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (22 bp):
TTCGGGACATTCTATGTGGAAC
Found at i:355948 original size:22 final size:22
Alignment explanation
Indices: 355897--355975 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 22
355887 TTTCAAGATA
* *
355897 ATTCTATGCGGTCCTTCGAGAC
1 ATTCTATGTGGTCCTTCGGGAC
355919 A-TCTATGTGGTCCTTCGGGAC
1 ATTCTATGTGGTCCTTCGGGAC
355940 ATTCTATGTGG-CACTTCGGTG-C
1 ATTCTATGTGGTC-CTTCGG-GAC
355962 ATTTTCTATGTGGT
1 A--TTCTATGTGGT
355976 ACTTAGGTGC
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
21 20 0.41
22 18 0.37
23 1 0.02
24 10 0.20
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (22 bp):
ATTCTATGTGGTCCTTCGGGAC
Found at i:355973 original size:24 final size:24
Alignment explanation
Indices: 355941--355986 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
355931 CTTCGGGACA
*
355941 TTCTATGTGGCACTTCGGTGCATT
1 TTCTATGTGGCACTTAGGTGCATT
*
355965 TTCTATGTGGTACTTAGGTGCA
1 TTCTATGTGGCACTTAGGTGCA
355987 ATTTATACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.26, T:0.41
Consensus pattern (24 bp):
TTCTATGTGGCACTTAGGTGCATT
Found at i:356742 original size:18 final size:18
Alignment explanation
Indices: 356729--356786 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
356719 TGTGCCATGA
*
356729 CAACTTCACTTGCCACGG
1 CAACTTTACTTGCCACGG
*
356747 TAACTTTACTTGCCACGG
1 CAACTTTACTTGCCACGG
356765 CAACTTTACTTGCCACGG
1 CAACTTTACTTGCCACGG
356783 CAAC
1 CAAC
356787 GTCATTAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (18 bp):
CAACTTTACTTGCCACGG
Found at i:356804 original size:27 final size:27
Alignment explanation
Indices: 356766--356839 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
356756 TTGCCACGGC
356766 AACTTTACTTGCCACGGCAACGTCATT
1 AACTTTACTTGCCACGGCAACGTCATT
* * *
356793 AACTCTACTTGCCTCGACAACGTCATT
1 AACTTTACTTGCCACGGCAACGTCATT
*
356820 AACTTTACCTGCCACGGCAA
1 AACTTTACTTGCCACGGCAA
356840 ATTGTCATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (27 bp):
AACTTTACTTGCCACGGCAACGTCATT
Found at i:358703 original size:51 final size:51
Alignment explanation
Indices: 358648--358816 Score: 250
Period size: 51 Copynumber: 3.3 Consensus size: 51
358638 ATACTTTCAA
*
358648 TTTATGCATTTTAGTCATTGTTTATTTCTGATTTAGCTACTGTTCTTCTAT
1 TTTATGCATTTTAGTCATTGTTTATTTCTGATTTAGCTATTGTTCTTCTAT
* * *
358699 TTTATGCATTTTAGTCACTATTTATTTCTGATTTGGCTATTGTTCTTCTAT
1 TTTATGCATTTTAGTCATTGTTTATTTCTGATTTAGCTATTGTTCTTCTAT
* * * *
358750 TTTATTCATTTTAGTTATTG-TTATTTCTGATTTAGCTATTATACTTCTAT
1 TTTATGCATTTTAGTCATTGTTTATTTCTGATTTAGCTATTGTTCTTCTAT
*
358800 TTTATGCATTTTGGTCA
1 TTTATGCATTTTAGTCA
358817 CTTTTTGTCT
Statistics
Matches: 104, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 41 0.39
51 63 0.61
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.57
Consensus pattern (51 bp):
TTTATGCATTTTAGTCATTGTTTATTTCTGATTTAGCTATTGTTCTTCTAT
Found at i:362766 original size:14 final size:14
Alignment explanation
Indices: 362747--362807 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
362737 ATAGCGAGAA
*
362747 AAAAAAGAGAAGAG
1 AAAAAAGAAAAGAG
**
362761 AAAAAAGGCAAG-G
1 AAAAAAGAAAAGAG
*
362774 AAAAAAGAAAAAAG
1 AAAAAAGAAAAGAG
362788 AAAAAAAGAAAAGAG
1 -AAAAAAGAAAAGAG
362803 AAAAA
1 AAAAA
362808 TAAAGAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
13 10 0.26
14 16 0.41
15 13 0.33
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAGAG
Found at i:362766 original size:15 final size:15
Alignment explanation
Indices: 362746--362825 Score: 76
Period size: 15 Copynumber: 5.3 Consensus size: 15
362736 CATAGCGAGA
*
362746 AAAAAAAGAGAAGAG
1 AAAAAAAGAAAAGAG
**
362761 -AAAAAAGGCAAG-G
1 AAAAAAAGAAAAGAG
*
362774 -AAAAAAGAAAAAAG
1 AAAAAAAGAAAAGAG
362788 AAAAAAAGAAAAGAG
1 AAAAAAAGAAAAGAG
362803 AAAAATAAAGAAAAAGAG
1 -AAAA-AAAG-AAAAGAG
362821 AAAAA
1 AAAAA
362826 TGGATCAAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 10 0.19
14 11 0.20
15 13 0.24
16 5 0.09
17 8 0.15
18 7 0.13
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (15 bp):
AAAAAAAGAAAAGAG
Found at i:362785 original size:7 final size:7
Alignment explanation
Indices: 362773--362807 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
362763 AAAAGGCAAG
362773 GAAAAAA
1 GAAAAAA
362780 GAAAAAA
1 GAAAAAA
362787 GAAAAAAA
1 G-AAAAAA
*
362795 GAAAAGA
1 GAAAAAA
362802 GAAAAA
1 GAAAAA
362808 TAAAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:362792 original size:8 final size:8
Alignment explanation
Indices: 362774--362825 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
362764 AAAGGCAAGG
362774 AAAAAAG-
1 AAAAAAGA
362781 AAAAAAGA
1 AAAAAAGA
362789 AAAAAAGA
1 AAAAAAGA
362797 AAAGAGAA-A
1 AAA-A-AAGA
*
362806 AATAAAGA
1 AAAAAAGA
*
362814 AAAAGAGA
1 AAAAAAGA
362822 AAAA
1 AAAA
362826 TGGATCAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
7 9 0.24
8 23 0.61
9 4 0.11
10 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:362823 original size:40 final size:40
Alignment explanation
Indices: 362746--362825 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 40
362736 CATAGCGAGA
*
362746 AAAAAAAGAGAAGAGAAAAAAGGCAAGGAAAAAAGAAAAAAG
1 AAAAAAAGAAAAGAGAAAAAA-G-AAGGAAAAAAGAAAAAAG
362788 AAAAAAAGAAAAGAGAAAAATA-AA-GAAAAAGAGAAAAA
1 AAAAAAAGAAAAGAGAAAAA-AGAAGGAAAAA-AGAAAAA
362826 TGGATCAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
39 6 0.17
40 9 0.26
42 19 0.54
43 1 0.03
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (40 bp):
AAAAAAAGAAAAGAGAAAAAAGAAGGAAAAAAGAAAAAAG
Found at i:365453 original size:67 final size:67
Alignment explanation
Indices: 365363--365535 Score: 233
Period size: 67 Copynumber: 2.6 Consensus size: 67
365353 TAAAAAAAAA
* * * *
365363 TTTGTCTCGCTTGAGACAGTTTCTCTTCAAACATAAAATTTTGAGATTATTTCTCTCCAAATAAA
1 TTTGTCTCGCTTGAAACATTTTCTCTTGAAACATAAAATTTTGAGATTATTTCTCTCCAAACAAA
365428 GT
66 GT
* ** * *
365430 TTTGTCTCGCTTAAAACATTTTCTCTTGAAACATAAAGCTTTGAGATTGTTTCTCTCGAAACAAA
1 TTTGTCTCGCTTGAAACATTTTCTCTTGAAACATAAAATTTTGAGATTATTTCTCTCCAAACAAA
365495 GT
66 GT
*
365497 TTTGTCTCGTTTGAAACAGTTTT-TCTTGAAACA-AAAATT
1 TTTGTCTCGCTTGAAACA-TTTTCTCTTGAAACATAAAATT
365536 GATCTCACTT
Statistics
Matches: 92, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
66 4 0.04
67 84 0.91
68 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (67 bp):
TTTGTCTCGCTTGAAACATTTTCTCTTGAAACATAAAATTTTGAGATTATTTCTCTCCAAACAAA
GT
Found at i:366421 original size:137 final size:137
Alignment explanation
Indices: 366035--366422 Score: 467
Period size: 137 Copynumber: 2.8 Consensus size: 137
366025 TAAAGTACAA
* * * * * * *
366035 CTAGACATCTTCAACATAAAGAAACAATGTTATCCACCGAACAGATCTCCTCAATGTAAAGGAGC
1 CTAGACATCCTCAACACAAAGAAACAATGTCATCCACTGACCAGATCTCCTCAACGCAAAGGAGC
* * * * * **
366100 AGCGTCATCTTTAGACAATCAAACTTCCTCAACATAAAGGAATTATGTTGTCTCCAAATTATCCA
66 AGTGTCATCCTCAGACAATCAGACTTCCTCAACGTAAAGGAATCGTGTTGTCTCCAAATTATCCA
366165 AATACGG
131 AATACGG
* *
366172 CTAGACATCCTCAACACGAAGGAACAATGTCATCCA-TCGACCAGATCTCCTCAACGCAAAGGAG
1 CTAGACATCCTCAACACAAAGAAACAATGTCATCCACT-GACCAGATCTCCTCAACGCAAAGGAG
* *
366236 CAATGTCATCCTCAGACAATCAGACGTCCTCAACACG-AAA-GAATCGTGTTGTCTCCAAATTAT
65 CAGTGTCATCCTCAGACAATCAGACTTCCTC-A-ACGTAAAGGAATCGTGTTGTCTCCAAATTAT
366299 CCAAATACGG
128 CCAAATACGG
* * ** * *
366309 GTAGACGTCCTCAATTCAAAGAAACAATGTCATCAACTGACCAGATCTCCTCAACGCGAAGGAGC
1 CTAGACATCCTCAACACAAAGAAACAATGTCATCCACTGACCAGATCTCCTCAACGCAAAGGAGC
* * * * *
366374 AGTGTCATCCTCAGATAATTAGACTTTCTCAATGTAAAGGAACCGTGTT
66 AGTGTCATCCTCAGACAATCAGACTTCCTCAACGTAAAGGAATCGTGTT
366423 ACCTTTAAAT
Statistics
Matches: 212, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
135 2 0.01
136 4 0.02
137 199 0.94
138 5 0.02
139 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.23
Consensus pattern (137 bp):
CTAGACATCCTCAACACAAAGAAACAATGTCATCCACTGACCAGATCTCCTCAACGCAAAGGAGC
AGTGTCATCCTCAGACAATCAGACTTCCTCAACGTAAAGGAATCGTGTTGTCTCCAAATTATCCA
AATACGG
Found at i:366927 original size:13 final size:13
Alignment explanation
Indices: 366909--366949 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
366899 CTGAGTTGTC
366909 TTTATTATTATCA
1 TTTATTATTATCA
*
366922 TTTATTATTATTA
1 TTTATTATTATCA
366935 TTATATT-TTA-CA
1 TT-TATTATTATCA
366947 TTT
1 TTT
366950 TTAGGCTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 1 0.04
12 3 0.12
13 17 0.68
14 4 0.16
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTATTATTATCA
Found at i:368278 original size:51 final size:51
Alignment explanation
Indices: 368223--368438 Score: 297
Period size: 51 Copynumber: 4.2 Consensus size: 51
368213 ATACTTTCAA
* * * * *
368223 TTTATGCATTTTGGTTAATGCTTATTTCTAATTTAGCTATTGTTCTTCTAT
1 TTTATGCATTTTAGTCACTGTTTATTTCTAATTTGGCTATTGTTCTTCTAT
* *
368274 TTTATGCATTTTAGTCATTGTTTATTTTTAATTTGGCTATTGTTCTTCTAT
1 TTTATGCATTTTAGTCACTGTTTATTTCTAATTTGGCTATTGTTCTTCTAT
* * *
368325 TTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGATATTATTCTTCTAT
1 TTTATGCATTTTAGTCACTGTTTATTTCTAATTTGGCTATTGTTCTTCTAT
* * * * *
368376 TTTACGCATTTTAGTCACTGTTTATTTTTTATTTGGCCACTGTTCTTCTAT
1 TTTATGCATTTTAGTCACTGTTTATTTCTAATTTGGCTATTGTTCTTCTAT
368427 TTTATGCATTTT
1 TTTATGCATTTT
368439 GGTTACTTTT
Statistics
Matches: 146, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 146 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (51 bp):
TTTATGCATTTTAGTCACTGTTTATTTCTAATTTGGCTATTGTTCTTCTAT
Found at i:368293 original size:29 final size:29
Alignment explanation
Indices: 368261--368346 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
368251 TAATTTAGCT
368261 ATTGTTCTTCTATTTTATGCATTTTAGTC
1 ATTGTTCTTCTATTTTATGCATTTTAGTC
* *
368290 ATTG---TT-TATTTT-T--AATTT-GGC
1 ATTGTTCTTCTATTTTATGCATTTTAGTC
368311 TATTGTTCTTCTATTTTATGCATTTTAGTC
1 -ATTGTTCTTCTATTTTATGCATTTTAGTC
*
368341 ACTGTT
1 ATTGTT
368347 TATTTCTGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
24 1 0.02
25 8 0.19
26 8 0.19
27 1 0.02
29 13 0.30
30 2 0.05
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.59
Consensus pattern (29 bp):
ATTGTTCTTCTATTTTATGCATTTTAGTC
Found at i:368738 original size:2 final size:2
Alignment explanation
Indices: 368731--368784 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
368721 TATATCATGT
368731 TA 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 TA
368773 TA TA TA TA -A TA T
1 TA TA TA TA TA TA T
368785 TCTCAACCCT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:371104 original size:20 final size:21
Alignment explanation
Indices: 371074--371113 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
371064 TGTTATAATA
371074 TGATGGAATTTAATGTTAGAG
1 TGATGGAATTTAATGTTAGAG
*
371095 TGAT-GAATTTGATGTTAGA
1 TGATGGAATTTAATGTTAGA
371114 ATGCGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.40
Consensus pattern (21 bp):
TGATGGAATTTAATGTTAGAG
Found at i:372945 original size:19 final size:19
Alignment explanation
Indices: 372921--372964 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
372911 AATATGATAA
372921 GATTATTATGTTTGATATT
1 GATTATTATGTTTGATATT
372940 GATTATTATGTTTGATATT
1 GATTATTATGTTTGATATT
372959 GATTAT
1 GATTAT
372965 CATGGTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.57
Consensus pattern (19 bp):
GATTATTATGTTTGATATT
Found at i:374590 original size:15 final size:15
Alignment explanation
Indices: 374570--374600 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
374560 CTCTCCTCTA
374570 TTAATTAATTTATTT
1 TTAATTAATTTATTT
374585 TTAATTAATTTATTT
1 TTAATTAATTTATTT
374600 T
1 T
374601 AGAGTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTAATTAATTTATTT
Found at i:379400 original size:15 final size:15
Alignment explanation
Indices: 379369--379402 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
379359 ATAAATTACA
379369 TTTCTGAAAAATGTT
1 TTTCTGAAAAATGTT
*
379384 TTTC-GAAAAATATT
1 TTTCTGAAAAATGTT
379398 TTTCT
1 TTTCT
379403 TTAAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (15 bp):
TTTCTGAAAAATGTT
Found at i:379953 original size:55 final size:55
Alignment explanation
Indices: 379829--379954 Score: 131
Period size: 55 Copynumber: 2.3 Consensus size: 55
379819 AAAAATTAGT
*
379829 ATATATTTATTA-AA-A-TAAAAATATAATATCTTATATTATTATAATATAATTGA
1 ATATA-TTATTATAATATTAAAAATATAATATCTTATATTATTATAATATAATTAA
* *
379882 TTATTTTATTATAATATTAAAAATATAATAT-TATATTATTATTATAAATATTAA-TAA
1 ATATATTATTATAATATTAAAAATATAATATCT-TA-TATTATTAT-AATA-TAATTAA
379939 ATATATT-TTA-AATATT
1 ATATATTATTATAATATT
379955 TTAATAATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
52 6 0.10
53 5 0.08
54 2 0.03
55 22 0.36
56 12 0.20
57 11 0.18
58 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (55 bp):
ATATATTATTATAATATTAAAAATATAATATCTTATATTATTATAATATAATTAA
Found at i:380228 original size:41 final size:42
Alignment explanation
Indices: 380168--380256 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 42
380158 TTCCTCCAAC
*
380168 CAAACACTGAAAAACATTTTCCGGAAAACGAATTACGTGAAA
1 CAAACACTGAAAAACATTTTCCGGAAAACGAATTACATGAAA
* * *
380210 CAAACAC-GAAAAATATTTTTCGGAAAACGAATTACATTAAA
1 CAAACACTGAAAAACATTTTCCGGAAAACGAATTACATGAAA
380251 CAAACA
1 CAAACA
380257 TGGGATTTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 36 0.84
42 7 0.16
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (42 bp):
CAAACACTGAAAAACATTTTCCGGAAAACGAATTACATGAAA
Found at i:381768 original size:63 final size:63
Alignment explanation
Indices: 381653--381876 Score: 340
Period size: 63 Copynumber: 3.6 Consensus size: 63
381643 ATGATGATCG
* * * * * *
381653 TGCAGAATGCAAAGATGCAAATACAGATGCAAAACTGATAATCCTCTAAAATGCAATGCATTA
1 TGCAAAATGCGAAGATGCAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCA
* * * *
381716 TGCAGAATGCGAAGATGCAAATGCATATGCAAAATTGATGATACTCTGAAATGCAATGCATCA
1 TGCAAAATGCGAAGATGCAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCA
381779 TGCAAAATGCGAAGATGCAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCA
1 TGCAAAATGCGAAGATGCAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCA
* *
381842 TGAAAAATGCGAAGATGCAAATGCATATGCAAAAT
1 TGCAAAATGCGAAGATGCAAATGCAGATGCAAAAT
381877 GCAAAGATGC
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 147 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (63 bp):
TGCAAAATGCGAAGATGCAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCA
Found at i:381782 original size:36 final size:37
Alignment explanation
Indices: 381730--381849 Score: 104
Period size: 36 Copynumber: 3.6 Consensus size: 37
381720 GAATGCGAAG
381730 ATGCAAATGCAT-ATGCAAAATTGATGATACTCTGAA
1 ATGCAAATGCATCATGCAAAATTGATGATACTCTGAA
*
381766 ATGC-AATGCATCATGCAAAA-TG-CGA-A----G--
1 ATGCAAATGCATCATGCAAAATTGATGATACTCTGAA
* * *
381793 ATGCAAATGCA-GATGCAAAATTGATGATCCTCTAAA
1 ATGCAAATGCATCATGCAAAATTGATGATACTCTGAA
*
381829 ATGC-AATGCATCATGAAAAAT
1 ATGCAAATGCATCATGCAAAAT
381850 GCGAAGATGC
Statistics
Matches: 65, Mismatches: 7, Indels: 24
0.68 0.07 0.25
Matches are distributed among these distances:
27 12 0.18
28 8 0.12
29 3 0.05
33 1 0.02
34 2 0.03
35 15 0.23
36 24 0.37
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.24
Consensus pattern (37 bp):
ATGCAAATGCATCATGCAAAATTGATGATACTCTGAA
Found at i:381871 original size:6 final size:6
Alignment explanation
Indices: 381846--381901 Score: 58
Period size: 6 Copynumber: 8.5 Consensus size: 6
381836 GCATCATGAA
*
381846 AAATGC GAAGATGC AAATGC ATATGC AAAATGC AAAGATGC AAATGC AAATGC
1 AAATGC -AA-ATGC AAATGC AAATGC -AAATGC -AA-ATGC AAATGC AAATGC
381899 AAA
1 AAA
381902 AATGTTGATC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
6 22 0.50
7 14 0.32
8 8 0.18
ACGTcount: A:0.50, C:0.14, G:0.20, T:0.16
Consensus pattern (6 bp):
AAATGC
Found at i:381875 original size:27 final size:27
Alignment explanation
Indices: 381829--381902 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
381819 ATCCTCTAAA
* *
381829 ATGC-AATGCATCATGAAAAATGCGAAG
1 ATGCAAATGCAT-ATGCAAAATGCAAAG
381856 ATGCAAATGCATATGCAAAATGCAAAG
1 ATGCAAATGCATATGCAAAATGCAAAG
*
381883 ATGCAAATGCAAATGCAAAA
1 ATGCAAATGCATATGCAAAA
381903 ATGTTGATCC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 36 0.84
28 7 0.16
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.18
Consensus pattern (27 bp):
ATGCAAATGCATATGCAAAATGCAAAG
Found at i:387755 original size:27 final size:26
Alignment explanation
Indices: 387692--387755 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
387682 ATGTTAGATA
* * *
387692 AAAAGGTAAGAAATAAATAATTAAAT
1 AAAAGATAAGAAAAAAAAAATTAAAT
*
387718 TAAA-ATGAAGAAAAAAACAAATTAAAT
1 AAAAGAT-AAGAAAAAAA-AAATTAAAT
387745 AAAAGATAAGA
1 AAAAGATAAGA
387756 TAAGGAAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 1 0.03
26 12 0.40
27 15 0.50
28 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.11, T:0.19
Consensus pattern (26 bp):
AAAAGATAAGAAAAAAAAAATTAAAT
Found at i:387807 original size:9 final size:9
Alignment explanation
Indices: 387793--387860 Score: 59
Period size: 9 Copynumber: 7.4 Consensus size: 9
387783 TAAAGTAAAT
387793 ATAAAAAAA
1 ATAAAAAAA
387802 AT-AAAAAA
1 ATAAAAAAA
387810 ATAAAGAAAA
1 ATAAA-AAAA
*
387820 AGAAGAAAAA
1 ATAA-AAAAA
* *
387830 A-ATATATAA
1 ATA-AAAAAA
*
387839 ATAAAACAA
1 ATAAAAAAA
387848 ATAAAAAAA
1 ATAAAAAAA
387857 ATAA
1 ATAA
387861 TAATAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
8 8 0.17
9 25 0.52
10 14 0.29
11 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.04, T:0.13
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:387843 original size:46 final size:49
Alignment explanation
Indices: 387793--387908 Score: 132
Period size: 50 Copynumber: 2.4 Consensus size: 49
387783 TAAAGTAAAT
*
387793 ATAAAAAAAATAAAAAAATAA-AGA-AAAAGAAG-AAA-AAAATATATAA
1 ATAAAAAAAATAAAAAAATAATA-ATAAAAAAAGTAAATAAAATATATAA
* * *
387839 ATAAAACAAATAAAAAAAATAATAATAAAAAAAGTAAATATAATATATAT
1 ATAAAAAAAAT-AAAAAAATAATAATAAAAAAAGTAAATAAAATATATAA
* *
387889 ATATAATAAATAAAAAAATA
1 ATAAAAAAAATAAAAAAATA
387909 GAAAAATAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
46 10 0.17
47 11 0.19
48 8 0.14
49 12 0.20
50 18 0.31
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (49 bp):
ATAAAAAAAATAAAAAAATAATAATAAAAAAAGTAAATAAAATATATAA
Found at i:387844 original size:25 final size:24
Alignment explanation
Indices: 387788--387908 Score: 81
Period size: 25 Copynumber: 4.9 Consensus size: 24
387778 GTTAGTAAAG
387788 TAAATATAAAAAA-AATAAAAA-A-A
1 TAAATA-AAAAAAGAA-AAAAATATA
*
387811 TAAAGAAAAAGAAGAAAAAAATATA
1 TAAATAAAAA-AAGAAAAAAATATA
*
387836 TAAATAAAACAAATAAAAAAA-ATA
1 TAAATAAAA-AAAGAAAAAAATATA
*
387860 -ATAATAAAAAAAGTAAATATAATATA
1 TA-AATAAAAAAAG-AAA-AAAATATA
* * *
387886 TATATATAATAAATAAAAAAATA
1 TAAATA-AAAAAAGAAAAAAATA
387909 GAAAAATAGT
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
22 4 0.05
23 16 0.21
24 16 0.21
25 26 0.33
26 10 0.13
27 6 0.08
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (24 bp):
TAAATAAAAAAAGAAAAAAATATA
Found at i:387857 original size:29 final size:27
Alignment explanation
Indices: 387795--387871 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 27
387785 AAGTAAATAT
*
387795 AAAAAAAATAAAAAAATAAAGAAAAAGAA
1 AAAAAAAAT-AATAAATAAA-AAAAAGAA
* * *
387824 GAAAAAAATATATAAATAAAACAAATAA
1 AAAAAAAATA-ATAAATAAAAAAAAGAA
387852 AAAAAATAATAATAAA-AAAA
1 AAAAAA-AATAATAAATAAAA
387872 GTAAATATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
27 4 0.10
28 17 0.41
29 20 0.49
ACGTcount: A:0.82, C:0.01, G:0.04, T:0.13
Consensus pattern (27 bp):
AAAAAAAATAATAAATAAAAAAAAGAA
Found at i:387901 original size:38 final size:38
Alignment explanation
Indices: 387859--387944 Score: 113
Period size: 36 Copynumber: 2.3 Consensus size: 38
387849 TAAAAAAAAT
*
387859 AATAATAAAAAAAGTAAATATAATATATATATATA-ATA
1 AATAATAAAAAAAG-AAAAATAATATATATATATATATA
* *
387897 AATAA-AAAAATAGAAAAATAGTATATATATATATATA
1 AATAATAAAAAAAGAAAAATAATATATATATATATATA
387934 AATTAATAAAA
1 AA-TAATAAAA
387945 CTGATAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 18 0.43
37 12 0.29
38 8 0.19
39 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.30
Consensus pattern (38 bp):
AATAATAAAAAAAGAAAAATAATATATATATATATATA
Found at i:387965 original size:42 final size:42
Alignment explanation
Indices: 387854--387973 Score: 113
Period size: 42 Copynumber: 2.8 Consensus size: 42
387844 ACAAATAAAA
* *
387854 AAAATAATAATAAAAAAAGTAAATATAATATATATATATAATAAAT
1 AAAAT-ATAAT-AAAAAA-TAAATAT-ATATATATATACAATTAAT
*
387900 AAAA-A-AATAGAAAAATAGTATATATATATATATA-AATTAAT
1 AAAATATAATA-AAAAATA-AATATATATATATATACAATTAAT
387941 AAAACTGATAATAAAAAA-AAATATATATATATA
1 AAAA-T-ATAATAAAAAATAAATATATATATATA
387974 ATCTAAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
41 10 0.15
42 27 0.42
43 13 0.20
44 7 0.11
45 4 0.06
46 4 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (42 bp):
AAAATATAATAAAAAATAAATATATATATATATACAATTAAT
Found at i:389443 original size:110 final size:105
Alignment explanation
Indices: 389270--389573 Score: 396
Period size: 110 Copynumber: 2.8 Consensus size: 105
389260 CTCCATCCTA
* * * *
389270 AAGTTGAAATTGGA-TCTGGAACTGGGAAATTATTTGTTGACAGCCAGTCGCCCCTTCGCTGTGA
1 AAGTTGAAATT-GACTCTGAAACT-GGAAAATGTTTGTTGACAGCCAGTCGCCCCTTCGTTGTGA
* *
389334 AGTTGAGCTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTG
64 AGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCCTCGCTGTG
**
389376 AAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTTGTTTGTTGACAATCAGTCGCCCCTTCGTT
1 AAGTTGAAATTGACTC----TGAAACTGGAAAA--TGTTTGTTGACAGCCAGTCGCCCCTTCGTT
*
389440 GTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCCTCGCTGTG
60 GTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCCTCGCTGTG
* * *
389486 AAGTTGAAATTGGCTCTGAAACTGGGAAAATGTTTGTTGACAGCCAGTCGTCCCTTCGTTGTGGA
1 AAGTTGAAATTGACTCTGAAACT-GGAAAATGTTTGTTGACAGCCAGTCGCCCCTTCGTTGTGAA
*
389551 GTTGAACTTGTGTTGTCTCGAGT
65 GTTGAGCTTGTGTTGTCTCGAGT
389574 GACATGATAT
Statistics
Matches: 173, Mismatches: 16, Indels: 18
0.84 0.08 0.09
Matches are distributed among these distances:
105 2 0.01
106 72 0.42
108 9 0.05
110 90 0.52
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AAGTTGAAATTGACTCTGAAACTGGAAAATGTTTGTTGACAGCCAGTCGCCCCTTCGTTGTGAAG
TTGAGCTTGTGTTGTCTCGAGTCCAATATCCCTCGCTGTG
Found at i:390192 original size:32 final size:32
Alignment explanation
Indices: 390151--390238 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
390141 TTTGTATCAG
*
390151 GATGTTGAAT-TCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCT-CCAAAGATGCCCCAACATTC
* * *
390183 GATGTTGAATCTCAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
* *
390215 GATGTTAAATCTTCAAAGATGCCC
1 GATGTTGAATCTCCAAAGATGCCC
390239 TCATTGTTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 46 0.98
33 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTC
Found at i:395733 original size:26 final size:26
Alignment explanation
Indices: 395671--395733 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
395661 ATGTTAGATA
* *
395671 AAAAGGTAAGAAATAAATAATTAAAT
1 AAAAGATAAGAAATAAAAAATTAAAT
*
395697 TAAA-ATAAAGAAA-AAACAAATTAAAT
1 AAAAGAT-AAGAAATAAA-AAATTAAAT
395723 AAAAGATAAGA
1 AAAAGATAAGA
395734 TAAAGAAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
25 4 0.13
26 24 0.80
27 2 0.07
ACGTcount: A:0.70, C:0.02, G:0.10, T:0.19
Consensus pattern (26 bp):
AAAAGATAAGAAATAAAAAATTAAAT
Found at i:395854 original size:2 final size:2
Alignment explanation
Indices: 395847--395962 Score: 59
Period size: 2 Copynumber: 60.5 Consensus size: 2
395837 AGTAAAAATA
* * * * * *
395847 AT AT AT AT AT AT AT AT AT A- AT AA AA AA AT A- AA AA AT AGT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
395888 AT AT AT AT AT AT AT AT AT AT AT AT AA AT -T A- AT A- AA ACT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT
* *
395929 A- AT AA AA AT A- AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
395963 ATCTAAAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
1 8 0.09
2 81 0.87
3 3 0.03
4 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (2 bp):
AT
Found at i:395900 original size:49 final size:48
Alignment explanation
Indices: 395843--395975 Score: 157
Period size: 49 Copynumber: 2.8 Consensus size: 48
395833 TAAAAGTAAA
*
395843 AATA-ATATATATATATATATATAA-TAAAAAAATAAAAAATAGTAAAT
1 AATATATATATATATATATATATAATTAAAAAAATAAAAAATA-AAAAT
* * *
395890 -ATATATATATATATATATATATAAATTAATAAAACT-GATAATAAAAAT
1 AATATATATATATATATATATAT-AATTAA-AAAAATAAAAAATAAAAAT
395938 AATATATATATATATATATAATATAATCTAAAAAAATA
1 AATATATATATATATATAT-ATATAAT-TAAAAAAATA
395976 CAAATATATA
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
46 3 0.04
47 18 0.25
48 6 0.08
49 34 0.47
50 12 0.16
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (48 bp):
AATATATATATATATATATATATAATTAAAAAAATAAAAAATAAAAAT
Found at i:396901 original size:13 final size:13
Alignment explanation
Indices: 396883--396916 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
396873 ATTTGGGTCT
*
396883 ACTGGATTCTGTA
1 ACTGGATCCTGTA
396896 ACTGGATCCTGTA
1 ACTGGATCCTGTA
396909 ACTGGATC
1 ACTGGATC
396917 ACTGGTTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTGGATCCTGTA
Found at i:397024 original size:3 final size:3
Alignment explanation
Indices: 397004--397042 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
396994 CATGTAAATC
* *
397004 AAT AAC AAT AATT AAT AAT AAT AAT ATT AAT AAT AAT AA
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AA
397043 ATATATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:399023 original size:21 final size:21
Alignment explanation
Indices: 398997--399040 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
398987 TTAGGGTTTA
398997 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
399018 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
399039 AT
1 AT
399041 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:399048 original size:28 final size:28
Alignment explanation
Indices: 399017--399070 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
399007 TAGTATAAAT
*
399017 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTA
399045 TATTAGTTTATTAGTTTAAGTTATAT
1 TATTAGTTTATTAGTTTAAGTTATAT
399071 ATTATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAGTTTATTAGTTTAAGTTATATTA
Found at i:399111 original size:45 final size:44
Alignment explanation
Indices: 399046--399148 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 44
399036 GTTATATTAT
*
399046 ATTAGTTTATTAGTTTAAGTTA-TATATTATATAAAAAATTAGTTA
1 ATTAGTTTATTAGTTAAAGTTATTATA-TATAT-AAAAATTAGTTA
* * * *
399091 ATTAGTTTCTTTGTTAAAGTTATTATATGTATAAAAATTATTTA
1 ATTAGTTTATTAGTTAAAGTTATTATATATATAAAAATTAGTTA
* *
399135 ATTAATTTGTTAGT
1 ATTAGTTTATTAGT
399149 GGGTTTAAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 22 0.45
45 23 0.47
46 4 0.08
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.51
Consensus pattern (44 bp):
ATTAGTTTATTAGTTAAAGTTATTATATATATAAAAATTAGTTA
Found at i:399573 original size:17 final size:17
Alignment explanation
Indices: 399551--399610 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
399541 AGTTATTCCC
*
399551 GTTTAAAAAAATATTAT
1 GTTTAAAAAAATATTTT
*
399568 GTTTAAAAATATTTATTGTT
1 GTTTAAAAA-A-ATATT-TT
399588 GTTTAAAAAAATATTTT
1 GTTTAAAAAAATATTTT
399605 GTTTAA
1 GTTTAA
399611 TTTATAATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 17 0.46
18 5 0.14
19 5 0.14
20 10 0.27
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.48
Consensus pattern (17 bp):
GTTTAAAAAAATATTTT
Found at i:399656 original size:17 final size:17
Alignment explanation
Indices: 399636--399691 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
399626 TTGAACAAAT
399636 TTTAATAAATTTGATTG
1 TTTAATAAATTTGATTG
*
399653 TTTAATAAATTTGA-TA
1 TTTAATAAATTTGATTG
*
399669 TTTAACAAATTTGATTG
1 TTTAATAAATTTGATTG
*
399686 ATTAAT
1 TTTAAT
399692 TAACAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 14 0.42
17 19 0.58
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (17 bp):
TTTAATAAATTTGATTG
Found at i:399678 original size:16 final size:16
Alignment explanation
Indices: 399636--399683 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
399626 TTGAACAAAT
*
399636 TTTAATAAATTTGATTG
1 TTTAATAAATTTGA-TA
399653 TTTAATAAATTTGATA
1 TTTAATAAATTTGATA
*
399669 TTTAACAAATTTGAT
1 TTTAATAAATTTGAT
399684 TGATTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (16 bp):
TTTAATAAATTTGATA
Found at i:399720 original size:21 final size:20
Alignment explanation
Indices: 399662--399714 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
399652 GTTTAATAAA
*
399662 TTTGATATTTAACAAATTTG
1 TTTGATATTTAACAAATTTC
* *
399682 ATTGATTAATTAACAAATTTC
1 TTTGA-TATTTAACAAATTTC
399703 TTTGATATTTAA
1 TTTGATATTTAA
399715 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (20 bp):
TTTGATATTTAACAAATTTC
Found at i:403078 original size:26 final size:25
Alignment explanation
Indices: 402942--403078 Score: 111
Period size: 26 Copynumber: 5.4 Consensus size: 25
402932 TAATAATTAT
* *
402942 ATGATTTAGTAATGATTTGATAATA
1 ATGATATAATAATGATTTGATAATA
* * *
402967 ATGAT-T-TTAAT-ATTTCATGATTTA
1 ATGATATAATAATGATTTGAT-A-ATA
* *
402991 ATGATTTAGTAATGATTTGATAATA
1 ATGATATAATAATGATTTGATAATA
*
403016 ATCATTATAATAATGATTT-AGTAATA
1 ATGA-TATAATAATGATTTGA-TAATA
*
403042 ATCATTATAATAATGATTTGATAATA
1 ATGA-TATAATAATGATTTGATAATA
403068 ATGATAGTAAT
1 ATGATA-TAAT
403079 GATTTAATAA
Statistics
Matches: 93, Mismatches: 10, Indels: 17
0.77 0.08 0.14
Matches are distributed among these distances:
22 6 0.06
23 5 0.05
24 8 0.09
25 14 0.15
26 53 0.57
27 7 0.08
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.45
Consensus pattern (25 bp):
ATGATATAATAATGATTTGATAATA
Done.