Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008258.1 Hibiscus syriacus cultivar Beakdansim tig00110911_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: 1617810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1237116 original size:23 final size:26
Alignment explanation
Indices: 1237068--1237118 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
1237058 AAGTTTCTTA
*
1237068 TTTTATTTTATTATTTTTTCTCTACT
1 TTTTATTTTATTATTTTTACTCTACT
1237094 TTTTA-TTT-TTATTTTTACT-TACT
1 TTTTATTTTATTATTTTTACTCTACT
1237117 TT
1 TT
1237119 CAAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 10 0.42
25 3 0.12
26 5 0.21
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTATTTTATTATTTTTACTCTACT
Found at i:1237283 original size:4 final size:4
Alignment explanation
Indices: 1237274--1237319 Score: 62
Period size: 4 Copynumber: 12.0 Consensus size: 4
1237264 ATAACCTTTC
1237274 ATTT ATTT ATTT ATTT ATTT A-TT ATTT CA--T ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT ATTT
1237320 TTATACTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 1 0.03
3 4 0.11
4 32 0.84
5 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:1237416 original size:13 final size:13
Alignment explanation
Indices: 1237398--1237427 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1237388 TGAATCGAGT
1237398 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
1237411 TTTTAATTTTTAA
1 TTTTAAATTTTAA
1237424 TTTT
1 TTTT
1237428 CGCAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1242804 original size:85 final size:85
Alignment explanation
Indices: 1242661--1243317 Score: 926
Period size: 85 Copynumber: 7.7 Consensus size: 85
1242651 TGTTCCCAGT
* * * *
1242661 ATAGCTCAAGGCAAGAAGGGTTATATGTCAACAAAAACCATCGAGTTCGATTACATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
*
1242726 AGGCATATCAAATTTAC-GAC
66 GGGCATATCAAATTTACAG-C
* * * *
1242746 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCAATTCCATTCAGCTAAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
1242811 GGGCATATCAAATTTACAGC
66 GGGCATATCAAATTTACAGC
* * * * *
1242831 ATAACTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTTGAGTT-GATTTCATTCAGCTCCA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
* *
1242895 GGCCATATCAATTTTACAGC
66 GGGCATATCAAATTTACAGC
* * * * *
1242915 ATATCTCAAGGCGAGAAGAGCTCTCTGTCAAGAAAAACCTTCGAGTTCGTTTACATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
*
1242980 GGGCATATCAAATTTACAAC
66 GGGCATATCAAATTTACAGC
* * * *
1243000 ATAGCTCAAGGCAAAAAGGACTATCTGTCAATAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
1243065 GGGCATATCAAATTTACAGC
66 GGGCATATCAAATTTACAGC
* *
1243085 ATAGCTTAAGACGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
1243150 GGGCATATCAAATTTACAGC
66 GGGCATATCAAATTTACAGC
* * * * * *
1243170 ATAGCTCAAGGAGAGAAGGGCTATC-GTCAACAAAAAATCTTTGAGTTCGATTCCATTTAGTTCA
1 ATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAAACCTTCGAGTTCGATTACATTCAGCTCA
*
1243234 AGGGCATATCCAATTTACAGC
65 AGGGCATATCAAATTTACAGC
* *
1243255 ATAGCTCAAGGCGAG-AGGAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTTCATTTAGCTC
1 ATAGCTCAAGGCGAGAAGG-GCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTC
1243318 GATGACAGTG
Statistics
Matches: 509, Mismatches: 58, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
84 81 0.16
85 421 0.83
86 7 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (85 bp):
ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
GGGCATATCAAATTTACAGC
Found at i:1243118 original size:254 final size:254
Alignment explanation
Indices: 1242661--1243317 Score: 888
Period size: 254 Copynumber: 2.6 Consensus size: 254
1242651 TGTTCCCAGT
* * * * *
1242661 ATAGCTCAAGGCA-AGAAGGGTTATATGTCAACAAAAACCATCGAGTTCGATTACATTCAGCTCA
1 ATAGCTCAAGG-AGAGAAGAGCTATCTGTCAAAAAAAACCTTCGAGTTCGATTACATTCAGCTCA
* * * **
1242725 AAGGCATATCAAATTTACGACATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGA
65 AGGGCATATCAAATTTACAACATAGCTCAAGGC-AAAAGGACTATCTGTCAACAAAAACCTTCGA
* * * *
1242790 GTTCAATTCCATTCAGCTAAAGGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGCTAT
129 GTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCATAACTCAAGACGAGAAGGGCTAT
* * * *
1242855 CTATCAACAAAAACCTTTGAGTT-GATTTCATTCAGCTCCAGGCCATATCAATTTTACAGC
194 CTATCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGCCATATCAAATTTACAGC
* * * * *
1242915 ATATCTCAAGGCGAGAAGAGCTCTCTGTCAAGAAAAACCTTCGAGTTCGTTTACATTCAGCTCAA
1 ATAGCTCAAGGAGAGAAGAGCTATCTGTCAAAAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
*
1242980 GGGCATATCAAATTTACAACATAGCTCAAGGCAAAAAGGACTATCTGTCAATAAAAACCTTCGAG
66 GGGCATATCAAATTTACAACATAGCTCAAGGC-AAAAGGACTATCTGTCAACAAAAACCTTCGAG
* *
1243045 TTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCATAGCTTAAGACGAGAAGGGCTATC
130 TTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCATAACTCAAGACGAGAAGGGCTATC
* *
1243110 TGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGC
195 TATCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGCCATATCAAATTTACAGC
* * * * * *
1243170 ATAGCTCAAGGAGAGAAGGGCTATC-GTCAACAAAAAATCTTTGAGTTCGATTCCATTTAGTTCA
1 ATAGCTCAAGGAGAGAAGAGCTATCTGTCAA-AAAAAACCTTCGAGTTCGATTACATTCAGCTCA
* * * *
1243234 AGGGCATATCCAATTTACAGCATAGCTCAAGGCGAGAGGAGCTATCTGTCAACAAAAACCTTCGA
65 AGGGCATATCAAATTTACAACATAGCTCAAGGCAAAAGGA-CTATCTGTCAACAAAAACCTTCGA
* *
1243299 GTTCGATTTCATTTAGCTC
129 GTTCGATTACATTCAGCTC
1243318 GATGACAGTG
Statistics
Matches: 353, Mismatches: 46, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
254 202 0.57
255 151 0.43
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (254 bp):
ATAGCTCAAGGAGAGAAGAGCTATCTGTCAAAAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
GGGCATATCAAATTTACAACATAGCTCAAGGCAAAAGGACTATCTGTCAACAAAAACCTTCGAGT
TCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCATAACTCAAGACGAGAAGGGCTATCT
ATCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGCCATATCAAATTTACAGC
Found at i:1243991 original size:28 final size:28
Alignment explanation
Indices: 1243938--1243991 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1243928 AAAAAATCGG
* * *
1243938 TTTTTGAAACATATTTATAATGTATAGT
1 TTTTTAAAACATATTTAAAATATATAGT
1243966 TTTTTAAAACAT-TTTGAAAATATATA
1 TTTTTAAAACATATTT-AAAATATATA
1243992 TAATATATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 3 0.14
28 19 0.86
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (28 bp):
TTTTTAAAACATATTTAAAATATATAGT
Found at i:1244072 original size:75 final size:74
Alignment explanation
Indices: 1243938--1244216 Score: 375
Period size: 75 Copynumber: 3.7 Consensus size: 74
1243928 AAAAAATCGG
* * *
1243938 TTTTTGAAACATATTTATAATGTATAGTTTTTTAAAACATTTTG-AAAATATATATAATATATAG
1 TTTTTGAAA-ATATATATAATATATAG-TTTTGAAAACATTTTGAAAAATATATATAATATATAG
1244002 TTTTGAAAACA
64 TTTTGAAAACA
*
1244013 TTTTTGAAAATATATATATTATATAGTTTTGAAAACATTTTGAAAACATATATATAATATATAGT
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAA-ATATATATAATATATAG-
1244078 TTTTGAAAACA
64 TTTTGAAAACA
* * *
1244089 -TTTTAAAAATATATATAATATATAGTTTTTAAAA-ATGTTTTAAAAATATATATAATATATAGT
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACAT-TTTGAAAAATATATATAATATATAGT
*
1244152 TTTGAAAAATA
65 TTTG-AAAACA
* *
1244163 TTTTTGAAAATGTATATAATATATAGTTTTGAAAATATTTTTGAAAACATATAT
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA-TTTTGAAAA-ATATAT
1244217 CTTTTAAAGT
Statistics
Matches: 182, Mismatches: 13, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
73 20 0.11
74 41 0.23
75 95 0.52
76 19 0.10
77 7 0.04
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (74 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAAATATATATAATATATAGTT
TTGAAAACA
Found at i:1244080 original size:112 final size:113
Alignment explanation
Indices: 1243938--1244216 Score: 397
Period size: 112 Copynumber: 2.5 Consensus size: 113
1243928 AAAAAATCGG
* * *
1243938 TTTTTGAAACATATTTATAATGTATAGTTTTTTAAAACATTTTGAAAATATATATAATATATAGT
1 TTTTTGAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGT
* *
1244003 TTTGAAAACAT-TTTTGAAAATATATATATTATATAGTTTTG-AAAACA
66 TTTGAAAA-ATGTTTTAAAAATATATATAATATATAGTTTTGAAAAACA
*
1244050 -TTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAATATATAG
1 TTTTTG-AAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAG
* *
1244114 TTTTTAAAAATGTTTTAAAAATATATATAATATATAGTTTTGAAAAATA
65 TTTTGAAAAATGTTTTAAAAATATATATAATATATAGTTTTGAAAAACA
* * *
1244163 TTTTTGAAA-ATGTATATAATATATAG-TTTTGAAAATATTTTTGAAAACATATAT
1 TTTTTGAAACATATATATAATATATAGTTTTTGAAAACA-TTTTGAAAATATATAT
1244217 CTTTTAAAGT
Statistics
Matches: 150, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
111 17 0.11
112 120 0.80
113 8 0.05
114 5 0.03
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (113 bp):
TTTTTGAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGT
TTTGAAAAATGTTTTAAAAATATATATAATATATAGTTTTGAAAAACA
Found at i:1244099 original size:28 final size:28
Alignment explanation
Indices: 1244050--1244103 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1244040 TTTGAAAACA
*
1244050 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACATATATAAAATATATAGT
*
1244078 TTTTGAAAACAT-TTTAAAAATATATA
1 TTTTGAAAACATATAT-AAAATATATA
1244104 TAATATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (28 bp):
TTTTGAAAACATATATAAAATATATAGT
Found at i:1244228 original size:37 final size:37
Alignment explanation
Indices: 1243938--1244216 Score: 368
Period size: 37 Copynumber: 7.5 Consensus size: 37
1243928 AAAAAATCGG
* * *
1243938 TTTTTGAAACATATTTATAATGTATAGTTTTTTAAAACA
1 TTTTTGAAA-ATATATATAATATATAG-TTTTGAAAACA
1243977 -TTTTGAAAATATATATAATATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
1244013 TTTTTGAAAATATATATATTATATAGTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
1244050 -TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
1 TTTTTG-AAA-ATATATATAATATATAG-TTTTGAAAACA
* *
1244089 -TTTTAAAAATATATATAATATATAGTTTTTAAAA-A
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
* *
1244124 TGTTTTAAAAATATATATAATATATAGTTTTGAAAAATA
1 T-TTTTGAAAATATATATAATATATAGTTTTG-AAAACA
* *
1244163 TTTTTGAAAATGTATATAATATATAGTTTTGAAAATA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
*
1244200 TTTTTGAAAACATATAT
1 TTTTTGAAAATATATAT
1244217 CTTTTAAAGT
Statistics
Matches: 220, Mismatches: 12, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
35 1 0.00
36 23 0.10
37 120 0.55
38 59 0.27
39 17 0.08
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAACA
Found at i:1245336 original size:31 final size:30
Alignment explanation
Indices: 1245298--1245361 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
1245288 TTCTTTAAGT
*
1245298 TTTTTA-TTTTATTTTATTATTTTTTCTCTAC
1 TTTTTATTTTTATTTTATT-TTTTTACT-TAC
*
1245329 TTTTTATTTTTATTTTGTTTTTTTACTTAC
1 TTTTTATTTTTATTTTATTTTTTTACTTAC
1245359 TTT
1 TTT
1245362 CAAAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 6 0.20
31 13 0.43
32 11 0.37
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.77
Consensus pattern (30 bp):
TTTTTATTTTTATTTTATTTTTTTACTTAC
Found at i:1245456 original size:12 final size:12
Alignment explanation
Indices: 1245441--1245469 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1245431 ACTCTTTTTA
1245441 TTATTTATTTGT
1 TTATTTATTTGT
1245453 TTATTTATTTGT
1 TTATTTATTTGT
1245465 TTATT
1 TTATT
1245470 CTCTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
TTATTTATTTGT
Found at i:1245456 original size:52 final size:54
Alignment explanation
Indices: 1245316--1245459 Score: 149
Period size: 52 Copynumber: 2.7 Consensus size: 54
1245306 TTATTTTATT
* *
1245316 ATTTTTTCTCTACTTTTTATT-TTTATTTTGTTTTTTTACTTACTTTCAAAATTTAAC
1 ATTTTTTC-CT-CTTTTTATTATTTA-TTTGTTTATTTACTTA-TTTCAAAAATTAAC
*
1245373 ATTTCTTT-CT-TTTATT-TTATTTATTTATTTATTT-CTT-TTT-AAAAATTAAC
1 ATTT-TTTCCTCTTT-TTATTATTTATTTGTTTATTTACTTATTTCAAAAATTAAC
1245423 ATTTTTTCACTCTTTTTATTATTTATTTGTTTATTTA
1 ATTTTTTC-CTCTTTTTATTATTTATTTGTTTATTTA
1245460 TTTGTTTATT
Statistics
Matches: 75, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
49 3 0.04
50 13 0.17
51 7 0.09
52 20 0.27
53 3 0.04
54 14 0.19
55 6 0.08
56 2 0.03
57 4 0.05
58 3 0.04
ACGTcount: A:0.22, C:0.10, G:0.01, T:0.67
Consensus pattern (54 bp):
ATTTTTTCCTCTTTTTATTATTTATTTGTTTATTTACTTATTTCAAAAATTAAC
Found at i:1246751 original size:17 final size:18
Alignment explanation
Indices: 1246710--1246751 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1246700 ATTTTAATGT
1246710 ATTTTTATCTATCTTGTA
1 ATTTTTATCTATCTTGTA
1246728 A-TTTTATCTA-CTTG-A
1 ATTTTTATCTATCTTGTA
1246743 ATTTATTAT
1 ATTT-TTAT
1246752 ATTATGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 6 0.27
17 13 0.59
18 1 0.05
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTTTTATCTATCTTGTA
Found at i:1246869 original size:23 final size:24
Alignment explanation
Indices: 1246843--1246888 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1246833 AAAAAAAGGA
1246843 AAAG-AAAAAGAAAATAAC-AAAAG
1 AAAGTAAAAA-AAAATAACTAAAAG
*
1246866 AAAGTAAAAAAATATAACTAAAA
1 AAAGTAAAAAAAAATAACTAAAA
1246889 CCAAAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (24 bp):
AAAGTAAAAAAAAATAACTAAAAG
Found at i:1249522 original size:15 final size:15
Alignment explanation
Indices: 1249499--1249552 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
1249489 GATTTTCTAA
1249499 AAAAT-AATTTACTT
1 AAAATGAATTTACTT
1249513 AAAATGAA-TTATCTT
1 AAAATGAATTTA-CTT
* *
1249528 AAAACTG-TTTTACGT
1 AAAA-TGAATTTACTT
1249543 AAAATGAATT
1 AAAATGAATT
1249553 ACATGAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 10 0.31
15 17 0.53
16 5 0.16
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (15 bp):
AAAATGAATTTACTT
Found at i:1249540 original size:30 final size:29
Alignment explanation
Indices: 1249506--1249609 Score: 133
Period size: 30 Copynumber: 3.6 Consensus size: 29
1249496 TAAAAAATAA
*
1249506 TTTACTTAAAATGAATTATCTTAAAACTGT
1 TTTACGTAAAATGAATTA-CTTAAAACTGT
*
1249536 TTTACGTAAAATGAATTACATGAAAACTGT
1 TTTACGTAAAATGAATTAC-TTAAAACTGT
*
1249566 TTTACGTAAAAT--ATTAC-TAAAATTGT
1 TTTACGTAAAATGAATTACTTAAAACTGT
*
1249592 TTTATGTAAAATGAATTA
1 TTTACGTAAAATGAATTA
1249610 TTTTCTGGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
26 18 0.27
28 9 0.14
29 1 0.02
30 38 0.58
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (29 bp):
TTTACGTAAAATGAATTACTTAAAACTGT
Found at i:1249576 original size:15 final size:15
Alignment explanation
Indices: 1249527--1249576 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1249517 TGAATTATCT
1249527 TAAAACTGTTTTACG
1 TAAAACTGTTTTACG
** *
1249542 TAAAA-TGAATTACA
1 TAAAACTGTTTTACG
1249556 TGAAAACTGTTTTACG
1 T-AAAACTGTTTTACG
1249572 TAAAA
1 TAAAA
1249577 TATTACTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 7 0.26
15 13 0.48
16 7 0.26
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (15 bp):
TAAAACTGTTTTACG
Found at i:1250076 original size:25 final size:22
Alignment explanation
Indices: 1250047--1250105 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
1250037 TATTAATATC
*
1250047 ATATATTATTATAATATACTTGAGA
1 ATATATTATTAT-A-ATA-TTGAAA
* **
1250072 ATATACTAACATAATATTGAAA
1 ATATATTATTATAATATTGAAA
1250094 ATATATTATTAT
1 ATATATTATTAT
1250106 TTAAATTATA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
22 14 0.52
23 3 0.11
24 1 0.04
25 9 0.33
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (22 bp):
ATATATTATTATAATATTGAAA
Found at i:1250389 original size:36 final size:38
Alignment explanation
Indices: 1250335--1250410 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 38
1250325 AGGTCTATGA
* * * *
1250335 TACATAATTCACATATAAAA-TT-TAAAAATTTAAAAT
1 TACATAATTAAAAGATAAAACTTATAAAAATATAAAAT
*
1250371 TACATAATTAAAAGATAAAACTTATTAAAATATAAAAT
1 TACATAATTAAAAGATAAAACTTATAAAAATATAAAAT
1250409 TA
1 TA
1250411 AAGAAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 17 0.52
37 2 0.06
38 14 0.42
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.34
Consensus pattern (38 bp):
TACATAATTAAAAGATAAAACTTATAAAAATATAAAAT
Found at i:1253529 original size:25 final size:26
Alignment explanation
Indices: 1253501--1253553 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
1253491 ACTTAGTGCA
*
1253501 TATGGTGGG-ACGACCTTATGTGTAT
1 TATGGTGGGTACGACCTTATGTGAAT
1253526 TATGGTGGGTACGACCTTATGTGAAT
1 TATGGTGGGTACGACCTTATGTGAAT
1253552 TA
1 TA
1253554 GCACTTCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (26 bp):
TATGGTGGGTACGACCTTATGTGAAT
Found at i:1255833 original size:31 final size:31
Alignment explanation
Indices: 1255795--1255858 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1255785 GTTAATTACA
1255795 GTTAACATTATCACGCACAATAACATATTAG
1 GTTAACATTATCACGCACAATAACATATTAG
1255826 GTTAACATTATCACGCACAATAACATATTAG
1 GTTAACATTATCACGCACAATAACATATTAG
1255857 GT
1 GT
1255859 AACGCTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (31 bp):
GTTAACATTATCACGCACAATAACATATTAG
Found at i:1256062 original size:118 final size:119
Alignment explanation
Indices: 1255829--1256062 Score: 321
Period size: 120 Copynumber: 2.0 Consensus size: 119
1255819 ATATTAGGTT
* * * *
1255829 AACATTATCACGCACAATAACATATTAGGTAACGCTTATATAACGTAATAGCTAGCGCCTTTTTA
1 AACATTATCAAGCACAATAAAAAATTAGGTAACGCTTATATAACGTAATAGCTAGCACCTTTTTA
** * * *
1255894 AAGCTGATGGGGCTTTTGGAAATTCGACGATAACATAATCGGTTAATTACTGGA
66 AAGCTGACAGGGCTTTTGGAAATCCGACGATAACAAAATAGGTTAATTACTGGA
* * *
1255948 AACATTATCAAGCATAATAAAAAAATTAGGTAGCG-TTGATATAACGTAATAGGTAGCACCTTTT
1 AACATTATCAAGCACAAT-AAAAAATTAGGTAACGCTT-ATATAACGTAATAGCTAGCACCTTTT
1256012 T-AAGCTGACAGGGC-TTTGGAAATCCGACGATAACAAAATAGGTTAATTACT
64 TAAAGCTGACAGGGCTTTTGGAAATCCGACGATAACAAAATAGGTTAATTACT
1256063 TAATTTGTTA
Statistics
Matches: 101, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
118 34 0.34
119 29 0.29
120 38 0.38
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (119 bp):
AACATTATCAAGCACAATAAAAAATTAGGTAACGCTTATATAACGTAATAGCTAGCACCTTTTTA
AAGCTGACAGGGCTTTTGGAAATCCGACGATAACAAAATAGGTTAATTACTGGA
Found at i:1260149 original size:20 final size:20
Alignment explanation
Indices: 1260102--1260163 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 20
1260092 ATTCCCCTGT
1260102 GGGGGGAATCGATTCCCCTTCAAA
1 GGGGGG-ATCGATT-CCC-TC-AA
*
1260126 GGGGGGATCGGTTCCCTCAA
1 GGGGGGATCGATTCCCTCAA
1260146 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
1260164 TGCACTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 19 0.53
21 2 0.06
22 3 0.08
23 6 0.17
24 6 0.17
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.21
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAA
Found at i:1264017 original size:22 final size:21
Alignment explanation
Indices: 1263977--1264016 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1263967 GAGTTTGTTT
1263977 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
1263998 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1264017 ATAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1267861 original size:23 final size:23
Alignment explanation
Indices: 1267826--1267874 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1267816 GGTCATCATC
*
1267826 TTCGCGAAAAAATGTTTATTTAA
1 TTCGAGAAAAAATGTTTATTTAA
*
1267849 TTCGAGAAGAAATGTTTATTTAA
1 TTCGAGAAAAAATGTTTATTTAA
1267872 TTC
1 TTC
1267875 AAAAACACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (23 bp):
TTCGAGAAAAAATGTTTATTTAA
Found at i:1269138 original size:333 final size:344
Alignment explanation
Indices: 1268628--1269394 Score: 979
Period size: 333 Copynumber: 2.2 Consensus size: 344
1268618 ACCATTTTTG
* * * * * *
1268628 TTATATTGAAACTGGTTTTATCAATTTTGAACATGTTATATTATCATGTATTGATACATGTGTCA
1 TTATATTGAAACCGGTTTTGTCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTCA
* * * *
1268693 CAGGTATCGATACTTCCTACGTGCATTTTGTTTGGGAACATACATGACAAAAAGTATCGATACAT
66 TAGGTAT-GATACTTCCTACGTACATCTTGTTTGAGAACATACATGACAAAAAGTATCGATACAT
* *
1268758 ATACCAAAAGTATAAATACTTTATATAAATGTATTTTACCATTAAACTGGTATATTTTTACAGTT
130 ATACCAAAAGTATAAATACTTTATATAAACGTATTTTACCATTAAACTGGTATATTTTTACAGCT
*
1268823 TACATTGTATATTTACCTGTTAATTTAAAGT-A-A-TTG-G-TTT-CAA-A-A-TTTT-A-A-GA
195 TACATTGTATATCTACCTGTTAATTTAAAGTAACATTTGAGTTTTACAACATACTTTTCATACGA
* * * *
1268876 ACCGATACTTTT-ATACGTGTATCGATACTTTATAAGCGTTGTTATGCAAACCAGTTTTGTCAA-
260 ACCGATACTTTTCATACGTGTATCGATAATTTATAAGCGTAGTTATGCAAACCAGTTTCGCCAAT
1268939 TTTTTTACCCGTTAAGTTAT
325 TTTTTTACCCGTTAAGTTAT
* *
1268959 TTATATTGAACCCGTTTTTGTCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTCA
1 TTATATTGAAACCGGTTTTGTCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTCA
**
1269024 TAGGTATAGATACTTCCTACGTACATCTTGTTTGAGAAGCAT-GTTGGACAAAAAAGTATCGATA
66 TAGGTAT-GATACTTCCTACGTACATCTTGTTTGAGAA-CATACAT-GAC-AAAAAGTATCGATA
** * *
1269088 CATATACCAAAAGTATCGATACTTTATATAAACGTATTTTATCATTAAACTGGTATATTTTTATA
127 CATATACCAAAAGTATAAATACTTTATATAAACGTATTTTACCATTAAACTGGTATATTTTTACA
*
1269153 GCTTACATTGTATATCTACCTGTTAATTTAAAGTAATCAGTTTTGAAGTTTTAAGAATCGATACT
192 GCTTACATTGTATATCTACCTGTTAATTTAAAGTAA-CA--TTTG-AGTTTT-ACAA-C-ATACT
* * *
1269218 TTTCATACGTGTATCGATACTTTTCATACGTGTATCGATAATTTATAAGCGTAGTTATGGAAACC
250 TTTCATAC--GAACCGATACTTTTCATACGTGTATCGATAATTTATAAGCGTAGTTATGCAAACC
***
1269283 AGTTTCGCCAATTTTTTTATTTGTTAAGTTAT
313 AGTTTCGCCAATTTTTTTACCCGTTAAGTTAT
* * *
1269315 TTATATTGAAATCGGTTTTGTCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTTTCT
1 TTATATTGAAACCGGTTTTGTCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTCA
1269380 TAGGTACTGATACTT
66 TAGGTA-TGATACTT
1269395 TATAGGCGTA
Statistics
Matches: 371, Mismatches: 38, Indels: 29
0.85 0.09 0.07
Matches are distributed among these distances:
331 91 0.25
332 6 0.02
333 106 0.29
334 1 0.00
336 1 0.00
339 3 0.01
341 1 0.00
342 3 0.01
344 2 0.01
347 1 0.00
348 1 0.00
349 4 0.01
350 1 0.00
351 1 0.00
354 12 0.03
355 46 0.12
356 90 0.24
357 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (344 bp):
TTATATTGAAACCGGTTTTGTCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTCA
TAGGTATGATACTTCCTACGTACATCTTGTTTGAGAACATACATGACAAAAAGTATCGATACATA
TACCAAAAGTATAAATACTTTATATAAACGTATTTTACCATTAAACTGGTATATTTTTACAGCTT
ACATTGTATATCTACCTGTTAATTTAAAGTAACATTTGAGTTTTACAACATACTTTTCATACGAA
CCGATACTTTTCATACGTGTATCGATAATTTATAAGCGTAGTTATGCAAACCAGTTTCGCCAATT
TTTTTACCCGTTAAGTTAT
Found at i:1269233 original size:21 final size:21
Alignment explanation
Indices: 1269209--1269257 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1269199 AGTTTTAAGA
1269209 ATCGATACTTTTCATACGTGT
1 ATCGATACTTTTCATACGTGT
1269230 ATCGATACTTTTCATACGTGT
1 ATCGATACTTTTCATACGTGT
1269251 ATCGATA
1 ATCGATA
1269258 ATTTATAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (21 bp):
ATCGATACTTTTCATACGTGT
Found at i:1270850 original size:24 final size:24
Alignment explanation
Indices: 1270831--1270886 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1270821 CGAAATTTAT
1270831 ATTGAAATTCAAACTCAAATTGAA
1 ATTGAAATTCAAACTCAAATTGAA
* *
1270855 ATTGAAATTCAAACTCCAATTAAA
1 ATTGAAATTCAAACTCAAATTGAA
*
1270879 AATGAAAT
1 ATTGAAAT
1270887 GAACATGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTGAA
Found at i:1270854 original size:18 final size:18
Alignment explanation
Indices: 1270831--1270867 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1270821 CGAAATTTAT
1270831 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1270849 ATTGAAATTGAAATTCAA
1 ATTGAAATTCAAACTCAA
1270867 A
1 A
1270868 CTCCAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1274070 original size:179 final size:178
Alignment explanation
Indices: 1273759--1274130 Score: 559
Period size: 179 Copynumber: 2.1 Consensus size: 178
1273749 ATACAAATTA
* *
1273759 AAAAAGTATCGATACTTTTTTC-TCACCTATTCTCTCATTAAACTATATATTTTTACC-GATTAC
1 AAAAAGTATCGATACTTTTTTCAT-ACATATTCTCTCATTAAACAATATATTTTTACCAG-TTAC
* * *
1273822 ATTGTAAATTTACCTATTACGTTATAATTGTCAGTTTCGATGTTTTAAGGATCGATATTTATCAT
64 ATTGTAAATTTACCTATTACGTTATAATTATCGGTTTCGATGTTTTAAGGATCGATACTTATCAT
* * *
1273887 ACATGTATCGATACTTTATGCGTTCATCTCGTTTGGGATTCATACTAGAC
129 ACATGTATCGATACTTTATGCATCCATCTCGTTTGGGATTCATACTGGAC
* * * *
1273937 AAAAAGTATCGATACTTTTTTCTTATATATTCTCTTATTAAACAAGTATATTTGTACCAGTTACA
1 AAAAAGTATCGATACTTTTTTCATACATATTCTCTCATTAAACAA-TATATTTTTACCAGTTACA
* * *
1274002 TTGTAAATTTACGTATTACGTTATAATTACCGGTTTCGATGTTTTAAGGATCGATACTTATAATA
65 TTGTAAATTTACCTATTACGTTATAATTATCGGTTTCGATGTTTTAAGGATCGATACTTATCATA
*
1274067 CATGTATCGATAATTTATGCATCCATCTCGTTTGGGATTCATACTGGAC
130 CATGTATCGATACTTTATGCATCCATCTCGTTTGGGATTCATACTGGAC
1274116 AAAAAGTATCGATAC
1 AAAAAGTATCGATAC
1274131 AAATTATAAA
Statistics
Matches: 176, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
178 39 0.22
179 136 0.77
180 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.41
Consensus pattern (178 bp):
AAAAAGTATCGATACTTTTTTCATACATATTCTCTCATTAAACAATATATTTTTACCAGTTACAT
TGTAAATTTACCTATTACGTTATAATTATCGGTTTCGATGTTTTAAGGATCGATACTTATCATAC
ATGTATCGATACTTTATGCATCCATCTCGTTTGGGATTCATACTGGAC
Found at i:1274226 original size:199 final size:200
Alignment explanation
Indices: 1273938--1274329 Score: 633
Period size: 199 Copynumber: 2.0 Consensus size: 200
1273928 ATACTAGACA
* * *
1273938 AAAAGTATCGATACTTTTTTCTTATATATTCTCTTATTAAACAAGTATATTTGTACCAGTTACAT
1 AAAAGTATCGATACCTTTTTCTTACATATTCTCTCATTAAACAAGTATATTTGTACCAGTTACAT
*
1274003 TGTAAATTTACGTATTACGTTATAATTACCGGTTTCGATGTTTTAAGGATCGATACTTATAATAC
66 TGTAAATTTACCTATTACGTTATAATTACCGGTTTCGATGTTTTAAGGATCGATACTTATAATAC
*
1274068 ATGTATCGATAATTTATGCATCCATCTCGTTTGGGATTCATACTGGACAAAAAGTATCGATACAA
131 ATGTATCGATAATTTATGCATCCACCTCGTTTGGGATTCATACTGGACAAAAAGTATCGATACAA
1274133 ATTAT
196 ATTAT
* * * * *
1274138 AAAAGTATCGATACCTTTTTCTTACCTATTCTCTCGTTAAACCA-TATATTTTTACCGGTTACAT
1 AAAAGTATCGATACCTTTTTCTTACATATTCTCTCATTAAACAAGTATATTTGTACCAGTTACAT
** * *
1274202 TGTAAATTTACCTATTACGTTATAATTATTGGTTTCGATGTTTTAAGGATTGATACTTATCATAC
66 TGTAAATTTACCTATTACGTTATAATTACCGGTTTCGATGTTTTAAGGATCGATACTTATAATAC
* *
1274267 ATGTATCGATACTTTATGCATCCACCTCGTTTGGGATTCATATTGGACAAAAAGTATCGATAC
131 ATGTATCGATAATTTATGCATCCACCTCGTTTGGGATTCATACTGGACAAAAAGTATCGATAC
1274330 TTTTTTATAC
Statistics
Matches: 176, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
199 138 0.78
200 38 0.22
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (200 bp):
AAAAGTATCGATACCTTTTTCTTACATATTCTCTCATTAAACAAGTATATTTGTACCAGTTACAT
TGTAAATTTACCTATTACGTTATAATTACCGGTTTCGATGTTTTAAGGATCGATACTTATAATAC
ATGTATCGATAATTTATGCATCCACCTCGTTTGGGATTCATACTGGACAAAAAGTATCGATACAA
ATTAT
Found at i:1274482 original size:176 final size:177
Alignment explanation
Indices: 1274138--1274505 Score: 596
Period size: 176 Copynumber: 2.1 Consensus size: 177
1274128 TACAAATTAT
* * *
1274138 AAAAGTATCGATACCTTTTTCTTACCTATTCTCTCGTTAAACCATATATTTTTACCGGTTACATT
1 AAAAGTATCGATA-CTTTTTCTTACCTATTCTCTCATTAAACAATATATTTTTACAGGTTACATT
* * *
1274203 GTAAATTTACCTATTACGTTATAATTATTGGTTTCGATGTTTTAAGGATTGATACTTATCATACA
65 GTAAACTTACCTATTACGTTATAATTATTCGTTTCGATGTTTTAAGGATCGATACTTATCATACA
* *
1274268 TGTATCGATACTTTATGCATCCACCTCGTTTGGGATTCATATTGGACA
130 TATATCGATACTTTATGCATCCACCTCGTTTGGGATTCATACTGGACA
1274316 AAAAGTATCGATACTTTTT-TATACCTATTCTCTCATTAAACAATATATTTTTACAGGTTACATT
1 AAAAGTATCGATACTTTTTCT-TACCTATTCTCTCATTAAACAATATATTTTTACAGGTTACATT
1274380 GTAAACTTACCTATTACGTTATAATTA-TCGTTTCGATGTTTTAAGGATCGATACTTATCATACA
65 GTAAACTTACCTATTACGTTATAATTATTCGTTTCGATGTTTTAAGGATCGATACTTATCATACA
** * *
1274444 TATATCGATACTTTATGTGTCCATCTCTTTTGGGATTCATACTGGACA
130 TATATCGATACTTTATGCATCCACCTCGTTTGGGATTCATACTGGACA
1274492 AAAAGTATCGATAC
1 AAAAGTATCGATAC
1274506 AAATTAAAAA
Statistics
Matches: 177, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
176 92 0.52
177 72 0.41
178 13 0.07
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (177 bp):
AAAAGTATCGATACTTTTTCTTACCTATTCTCTCATTAAACAATATATTTTTACAGGTTACATTG
TAAACTTACCTATTACGTTATAATTATTCGTTTCGATGTTTTAAGGATCGATACTTATCATACAT
ATATCGATACTTTATGCATCCACCTCGTTTGGGATTCATACTGGACA
Found at i:1274601 original size:198 final size:199
Alignment explanation
Indices: 1274315--1274784 Score: 723
Period size: 199 Copynumber: 2.4 Consensus size: 199
1274305 CATATTGGAC
* * * *
1274315 AAAAAGTATCGATACTTTTTT-ATACCTATTCTCTCATTAAACAATATATTTTTACAGGTTACAT
1 AAAAAGTATCGAAACTTTTTTCTTACCTATTCTCTCATTAAACGATATATTTTTACCGGTTACAT
* *
1274379 TGTAAACTTACCTATTACGTTATAATTATC-GTTTCGATGTTTTAAGGATCGATACTTATCATAC
66 TGTAAATTTACCTATTACGTTATAATTATCGGTTTCGATGTTTTAAGGATCGATACTTATCAAAC
* *
1274443 ATATATCGATACTTTATGTGTCCATCTCTTTTGGGATTCATACTGGACAAAAAGTATCGATACAA
131 ATATATCGATACTTTATGCGTCCATCTCGTTTGGGATTCATACTGGACAAAAAGTATCGATACAA
1274508 ATT-
196 ATTA
* *
1274511 AAAAAGTATCAAAACTTTTTTCTTACCTATTCTCTTATTAAACCGATA-ATTTTTTACCGGTTAC
1 AAAAAGTATCGAAACTTTTTTCTTACCTATTCTCTCATTAAA-CGATATA-TTTTTACCGGTTAC
* * *
1274575 ATTGTAAATTTACTTATTATGTTATAATTATCGGTTTCGATGTTTTAAGGATTGATACTTATCAA
64 ATTGTAAATTTACCTATTACGTTATAATTATCGGTTTCGATGTTTTAAGGATCGATACTTATCAA
* *
1274640 ACATGTATCGATACTTTATGCGTCCATCTCGTTTGGGATTCATATTGGACAAAAAGTATCGATAC
129 ACATATATCGATACTTTATGCGTCCATCTCGTTTGGGATTCATACTGGACAAAAAGTATCGATAC
1274705 AAATTA
194 AAATTA
* *
1274711 AAAAAGTATCGAAACTTTTTTCTTACCTATTCTCCCATTAAATCGGTATATTTTTACCGGTTACA
1 AAAAAGTATCGAAACTTTTTTCTTACCTATTCTCTCATTAAA-CGATATATTTTTACCGGTTACA
*
1274776 TTATAAATT
65 TTGTAAATT
1274785 GAGAAAATAA
Statistics
Matches: 247, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
196 19 0.08
197 19 0.08
198 46 0.19
199 96 0.39
200 66 0.27
201 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (199 bp):
AAAAAGTATCGAAACTTTTTTCTTACCTATTCTCTCATTAAACGATATATTTTTACCGGTTACAT
TGTAAATTTACCTATTACGTTATAATTATCGGTTTCGATGTTTTAAGGATCGATACTTATCAAAC
ATATATCGATACTTTATGCGTCCATCTCGTTTGGGATTCATACTGGACAAAAAGTATCGATACAA
ATTA
Found at i:1274603 original size:375 final size:377
Alignment explanation
Indices: 1273731--1274704 Score: 1553
Period size: 375 Copynumber: 2.6 Consensus size: 377
1273721 TGTAATATCA
*
1273731 ACTGGACAAAAAGTATCGATACAAATTAAAAAAGTATCGATACTTTTTTCTCACCTATTCTCTCA
1 ACTGGACAAAAAGTATCGATACAAATT-AAAAAGTATCGATACTTTTTTCTTACCTATTCTCTCA
* * * *
1273796 TTAAACTATATATTTTTACCGATTACATTGTAAATTTACCTATTACGTTATAATTGTCAGTTTCG
65 TTAAACCATATATTTTTACCGGTTACATTGTAAATTTACCTATTACGTTATAATTATCGGTTTCG
* * *
1273861 ATGTTTTAAGGATCGATATTTATCATACATGTATCGATACTTTATGCGTTCATCTCGTTTGGGAT
130 ATGTTTTAAGGATTGATACTTATCATACATGTATCGATACTTTATGCGTCCATCTCGTTTGGGAT
* * * * *
1273926 TCATACTAGACAAAAAGTATCGATACTTTTTTCTTATATATTCTCTTATTAAACAAGTATATTTG
195 TCATATTGGACAAAAAGTATCGATACTTTTTTCATACATATTCTCTCATTAAACAAGTATATTTG
* *
1273991 TACCAGTTACATTGTAAATTTACGTATTACGTTATAATTACCGGTTTCGATGTTTTAAGGATCGA
260 TACCAGTTACATTGTAAACTTACCTATTACGTTATAATTACCGGTTTCGATGTTTTAAGGATCGA
*
1274056 TACTTATAATACATGTATCGATAATTTATGCATCCATCTCGTTTGGGATTCAT
325 TACTTATAATACATATATCGATAATTTATGCATCCATCTCGTTTGGGATTCAT
* *
1274109 ACTGGACAAAAAGTATCGATACAAATTATAAAAGTATCGATACCTTTTTCTTACCTATTCTCTCG
1 ACTGGACAAAAAGTATCGATACAAATTA-AAAAGTATCGATACTTTTTTCTTACCTATTCTCTCA
*
1274174 TTAAACCATATATTTTTACCGGTTACATTGTAAATTTACCTATTACGTTATAATTATTGGTTTCG
65 TTAAACCATATATTTTTACCGGTTACATTGTAAATTTACCTATTACGTTATAATTATCGGTTTCG
* *
1274239 ATGTTTTAAGGATTGATACTTATCATACATGTATCGATACTTTATGCATCCACCTCGTTTGGGAT
130 ATGTTTTAAGGATTGATACTTATCATACATGTATCGATACTTTATGCGTCCATCTCGTTTGGGAT
* *
1274304 TCATATTGGACAAAAAGTATCGATACTTTTTT-ATACCTATTCTCTCATTAAACAA-TATATTTT
195 TCATATTGGACAAAAAGTATCGATACTTTTTTCATACATATTCTCTCATTAAACAAGTATATTTG
*
1274367 TA-CAGGTTACATTGTAAACTTACCTATTACGTTATAATTATC-GTTTCGATGTTTTAAGGATCG
260 TACCA-GTTACATTGTAAACTTACCTATTACGTTATAATTACCGGTTTCGATGTTTTAAGGATCG
* * ** *
1274430 ATACTTATCATACATATATCGATACTTTATGTGTCCATCTCTTTTGGGATTCAT
324 ATACTTATAATACATATATCGATAATTTATGCATCCATCTCGTTTGGGATTCAT
* * *
1274484 ACTGGACAAAAAGTATCGATACAAATTAAAAAGTATCAAAACTTTTTTCTTACCTATTCTCTTAT
1 ACTGGACAAAAAGTATCGATACAAATTAAAAAGTATCGATACTTTTTTCTTACCTATTCTCTCAT
* *
1274549 TAAACCGATA-ATTTTTTACCGGTTACATTGTAAATTTACTTATTATGTTATAATTATCGGTTTC
66 TAAACC-ATATA-TTTTTACCGGTTACATTGTAAATTTACCTATTACGTTATAATTATCGGTTTC
*
1274613 GATGTTTTAAGGATTGATACTTATCAAACATGTATCGATACTTTATGCGTCCATCTCGTTTGGGA
129 GATGTTTTAAGGATTGATACTTATCATACATGTATCGATACTTTATGCGTCCATCTCGTTTGGGA
1274678 TTCATATTGGACAAAAAGTATCGATAC
194 TTCATATTGGACAAAAAGTATCGATAC
1274705 AAATTAAAAA
Statistics
Matches: 552, Mismatches: 40, Indels: 11
0.92 0.07 0.02
Matches are distributed among these distances:
374 39 0.07
375 240 0.43
376 43 0.08
377 20 0.04
378 210 0.38
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (377 bp):
ACTGGACAAAAAGTATCGATACAAATTAAAAAGTATCGATACTTTTTTCTTACCTATTCTCTCAT
TAAACCATATATTTTTACCGGTTACATTGTAAATTTACCTATTACGTTATAATTATCGGTTTCGA
TGTTTTAAGGATTGATACTTATCATACATGTATCGATACTTTATGCGTCCATCTCGTTTGGGATT
CATATTGGACAAAAAGTATCGATACTTTTTTCATACATATTCTCTCATTAAACAAGTATATTTGT
ACCAGTTACATTGTAAACTTACCTATTACGTTATAATTACCGGTTTCGATGTTTTAAGGATCGAT
ACTTATAATACATATATCGATAATTTATGCATCCATCTCGTTTGGGATTCAT
Found at i:1274892 original size:19 final size:19
Alignment explanation
Indices: 1274868--1274904 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1274858 ATGACCAACA
*
1274868 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1274887 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1274905 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1275909 original size:24 final size:24
Alignment explanation
Indices: 1275858--1275911 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1275848 GTATTCGAAA
*
1275858 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1275882 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1275906 TTTGAT
1 TTTGAT
1275912 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1276121 original size:15 final size:15
Alignment explanation
Indices: 1276101--1276136 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1276091 AGAAAAAGAA
1276101 AAGAAAAAATCCCCG
1 AAGAAAAAATCCCCG
*
1276116 AAG-AAAAGTCCCCG
1 AAGAAAAAATCCCCG
1276130 AAGAAAA
1 AAGAAAA
1276137 TGCCACGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.56, C:0.22, G:0.17, T:0.06
Consensus pattern (15 bp):
AAGAAAAAATCCCCG
Found at i:1278511 original size:140 final size:140
Alignment explanation
Indices: 1278259--1278541 Score: 548
Period size: 140 Copynumber: 2.0 Consensus size: 140
1278249 GCAAATGTTG
1278259 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1278324 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1278389 CGAATTTGAC
131 CGAATTTGAC
1278399 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1278464 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAATG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1278529 CGAATTTGAC
131 CGAATTTGAC
1278539 TAT
1 TAT
1278542 CGCAACGCGA
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 141 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:1278537 original size:20 final size:20
Alignment explanation
Indices: 1278512--1278688 Score: 300
Period size: 20 Copynumber: 8.8 Consensus size: 20
1278502 TTACACATTC
* *
1278512 ATTTGAATATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
1278532 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1278552 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1278572 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1278592 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1278612 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1278632 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
1278652 ATTTGATTATCGCAATGGGA
1 ATTTGACTATCGCAACGCGA
1278672 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
1278689 AGAAAATTGC
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 149 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1283663 original size:66 final size:65
Alignment explanation
Indices: 1283520--1283664 Score: 182
Period size: 66 Copynumber: 2.2 Consensus size: 65
1283510 AACCACTCCT
* *
1283520 ATCACCCCCTAAGTTCACCCCTCAATTCCAAAACTTCCTCCACCACTCCATCAATATTTCCACCC
1 ATCACCCCTTAAGTTCACCCCTCAATTCCAAAACTACCTCCACCACTCCATCAATATTTCCACCC
* * * * * * *
1283585 ATCACCATCTTAAGTTCACCCTTCAATTCCACAACTACTTTCACCACTCCATCTATTTTTCCACC
1 ATCACC-CCTTAAGTTCACCCCTCAATTCCAAAACTACCTCCACCACTCCATCAATATTTCCACC
1283650 C
65 C
*
1283651 ACTTACCCCTTAAG
1 A-TCACCCCTTAAG
1283665 CTTCTCAATT
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
65 6 0.09
66 57 0.85
67 4 0.06
ACGTcount: A:0.27, C:0.42, G:0.02, T:0.29
Consensus pattern (65 bp):
ATCACCCCTTAAGTTCACCCCTCAATTCCAAAACTACCTCCACCACTCCATCAATATTTCCACCC
Found at i:1283832 original size:18 final size:17
Alignment explanation
Indices: 1283809--1283844 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1283799 CTTATTTATT
*
1283809 CTCCTCTTCCTCCTCTGC
1 CTCCTCTACCTCCT-TGC
1283827 CTCCTCTACCTCCTTGC
1 CTCCTCTACCTCCTTGC
1283844 C
1 C
1283845 AATAACCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.03, C:0.56, G:0.06, T:0.36
Consensus pattern (17 bp):
CTCCTCTACCTCCTTGC
Found at i:1284103 original size:25 final size:24
Alignment explanation
Indices: 1284073--1284122 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1284063 AACTACATTT
*
1284073 ATAATTAAATTTATCATTTTATATA
1 ATAATTAAA-CTATCATTTTATATA
* *
1284098 ATAATTATACTCTCATTTTATATA
1 ATAATTAAACTATCATTTTATATA
1284122 A
1 A
1284123 AAAAAACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (24 bp):
ATAATTAAACTATCATTTTATATA
Found at i:1286418 original size:183 final size:183
Alignment explanation
Indices: 1286109--1286885 Score: 1206
Period size: 183 Copynumber: 4.3 Consensus size: 183
1286099 GCGCTTTACC
1286109 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
1 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
* * *
1286174 TTTATAGGCGATATTAATG-TATTTCTTTTAAATTCCAAAAGTATCGATGCTTATTTGAATGATA
66 TTTATAGGCGATATTATTGCT-TTTCTTTTAAATTCAAAAAGTATCGATACTTATTTGAATGATA
*
1286238 TCGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACC-
130 TCGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATATTG-AACCT
* * ** *
1286292 AGTTTTGTCATATTTTTACATGTTATATCATTATGTATCGATACATGTTTATAAAGTATCAATAC
1 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
* *
1286357 TTTATAGGCGCTATTATTGCTTTTCTTTTAAATTAAAAAAGTATCGATACTTATTTGAATGATAT
66 TTTATAGGCGATATTATTGCTTTTCTTTTAAATTCAAAAAGTATCGATACTTATTTGAATGATAT
*
1286422 CGATATCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATATTGAACCT
131 CGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATATTGAACCT
1286475 GGTTTTGTCATATTTTTACCTG--ATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
1 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
* * * *
1286538 TTTATAGGCGATATTACTGCTTTTTTTTTTAAATTCAACAAGTATCGATACTTATTTGAATGGTA
66 TTTATAGGCGATATTATTGC-TTTTCTTTTAAATTCAAAAAGTATCGATACTTATTTGAATGATA
* *
1286603 TCGATACCTTCAACATATTCGGTAGCTCTTTACCGGTTTTGTCATATTGAACCC
130 TCGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATATTGAACCT
* *
1286657 GGTTTTGTCATATTTTTACCTGATATATTGTTATATATC-AGTACATGTTTATAAAGTATCGATA
1 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGA-TACATGTTTATAAAGTATCGATA
* * * *
1286721 CTTTATAGGCGCTATTATTGCTTTTCTTTAAAATTCCAAAAGTATCGATACATATTTGAATGGA-
65 CTTTATAGGCGATATTATTGCTTTTCTTTTAAATTCAAAAAGTATCGATACTTATTTGAAT-GAT
* *
1286785 ATCGATACCTTCAACATATCCGGTAGCGCTTTACTGGTTTTGTCATATTGAACCT
129 ATCGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATATTGAACCT
* * *
1286840 GGTTCTGTCATATTTTTACCTATTATATTGTTATGCATCGATACAT
1 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACAT
1286886 ATTAGAATTG
Statistics
Matches: 542, Mismatches: 44, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
181 56 0.10
182 117 0.22
183 310 0.57
184 59 0.11
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (183 bp):
GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
TTTATAGGCGATATTATTGCTTTTCTTTTAAATTCAAAAAGTATCGATACTTATTTGAATGATAT
CGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATATTGAACCT
Found at i:1286618 original size:365 final size:364
Alignment explanation
Indices: 1286109--1286885 Score: 1236
Period size: 365 Copynumber: 2.1 Consensus size: 364
1286099 GCGCTTTACC
1286109 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
1 GGTTTTGTCATATTTTTACCTG--ATATTGTTATGTATCGATACATGTTTATAAAGTATCGATAC
*
1286174 TTTATAGGCGATATTAATGTATTTCTTTTAAATTCCAAAAGTATCGATGCTTATTTGAATGATAT
64 TTTATAGGCGATATTAATGTATTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGATAT
1286239 CGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACCAGTTTTGTCATA
129 CGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACCAGTTTTGTCATA
* *
1286304 TTTTTACATGTTATATCATTATGTATC-GATACATGTTTATAAAGTATCAATACTTTATAGGCGC
194 TTTTTACATGATATATCATTATATATCAG-TACATGTTTATAAAGTATCAATACTTTATAGGCGC
* * *
1286368 TATTATTGCTTTTCTTTTAAATTAAAAAAGTATCGATACTTATTTGAAT-GATATCGATATCTTC
258 TATTATTGCTTTTCTTTAAAATTAAAAAAGTATCGATACATATTTGAATGGA-ATCGATACCTTC
*
1286432 AACATATCCGGTAGCTCTTTACCGGTTTTGTCATATTGAACCT
322 AACATATCCGGTAGCGCTTTACCGGTTTTGTCATATTGAACCT
1286475 GGTTTTGTCATATTTTTACCTGATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTT
1 GGTTTTGTCATATTTTTACCTGATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTT
* * * *
1286540 TATAGGCGATATTACTGCTTTTTTTTTTAAATT-CAACAAGTATCGATACTTATTTGAATGGTAT
66 TATAGGCGATATTAATG-TATTTCTTTTAAATTCCAA-AAGTATCGATACTTATTTGAATGATAT
* * * *
1286604 CGATACCTTCAACATATTCGGTAGCTCTTTACCGGTTTTGTCATATTGAACCCGGTTTTGTCATA
129 CGATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACCAGTTTTGTCATA
* ** *
1286669 TTTTTACCTGATATATTGTTATATATCAGTACATGTTTATAAAGTATCGATACTTTATAGGCGCT
194 TTTTTACATGATATATCATTATATATCAGTACATGTTTATAAAGTATCAATACTTTATAGGCGCT
**
1286734 ATTATTGCTTTTCTTTAAAATTCCAAAAGTATCGATACATATTTGAATGGAATCGATACCTTCAA
259 ATTATTGCTTTTCTTTAAAATTAAAAAAGTATCGATACATATTTGAATGGAATCGATACCTTCAA
*
1286799 CATATCCGGTAGCGCTTTACTGGTTTTGTCATATTGAACCT
324 CATATCCGGTAGCGCTTTACCGGTTTTGTCATATTGAACCT
* * *
1286840 GGTTCTGTCATATTTTTACCTATTATATTGTTATGCATCGATACAT
1 GGTTTTGTCATATTTTTACC--TGATATTGTTATGTATCGATACAT
1286886 ATTAGAATTG
Statistics
Matches: 380, Mismatches: 25, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
364 62 0.16
365 271 0.71
366 25 0.07
367 22 0.06
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (364 bp):
GGTTTTGTCATATTTTTACCTGATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTT
TATAGGCGATATTAATGTATTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGATATCG
ATACCTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACCAGTTTTGTCATATT
TTTACATGATATATCATTATATATCAGTACATGTTTATAAAGTATCAATACTTTATAGGCGCTAT
TATTGCTTTTCTTTAAAATTAAAAAAGTATCGATACATATTTGAATGGAATCGATACCTTCAACA
TATCCGGTAGCGCTTTACCGGTTTTGTCATATTGAACCT
Found at i:1286902 original size:21 final size:21
Alignment explanation
Indices: 1286876--1286925 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1286866 ATTGTTATGC
*
1286876 ATCGATACATATTAGAATTGT
1 ATCGATACATATTAGAATGGT
*
1286897 TTCGATACATATTAGAATGGT
1 ATCGATACATATTAGAATGGT
1286918 ATCGATAC
1 ATCGATAC
1286926 GTACCGACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (21 bp):
ATCGATACATATTAGAATGGT
Found at i:1287080 original size:11 final size:11
Alignment explanation
Indices: 1287064--1287088 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1287054 TTCTGTTAAC
1287064 GTCGTATATTA
1 GTCGTATATTA
1287075 GTCGTATATTA
1 GTCGTATATTA
1287086 GTC
1 GTC
1287089 CGTCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (11 bp):
GTCGTATATTA
Found at i:1287133 original size:22 final size:22
Alignment explanation
Indices: 1287102--1287143 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1287092 CTTTCCTGAG
* *
1287102 ACAACTCACTAAAATTCAAAAT
1 ACAACCCACTAAAAATCAAAAT
1287124 ACAACCCACTAAAAATCAAA
1 ACAACCCACTAAAAATCAAA
1287144 GAATTAGGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (22 bp):
ACAACCCACTAAAAATCAAAAT
Found at i:1292075 original size:3 final size:3
Alignment explanation
Indices: 1292069--1292114 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
1292059 CTAAATGATG
** * *
1292069 ATA ATA ATA ATA ATA ATA ATA GCA GTG ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1292115 AAACTTCATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1295290 original size:33 final size:34
Alignment explanation
Indices: 1295253--1295321 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
1295243 TTTACAACTT
*
1295253 CCTAG-TTTTTCACGGGA-TAAACTAGAACCTTTC
1 CCTAGCTTTTACAC-GGACTAAACTAGAACCTTTC
*
1295286 CCTAGCTTTTACACGGACTAAGCTAGAACCTTTC
1 CCTAGCTTTTACACGGACTAAACTAGAACCTTTC
1295320 CC
1 CC
1295322 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 8 0.25
34 24 0.75
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.30
Consensus pattern (34 bp):
CCTAGCTTTTACACGGACTAAACTAGAACCTTTC
Found at i:1295811 original size:20 final size:20
Alignment explanation
Indices: 1295783--1295838 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1295773 TCGATGCACC
1295783 AGTGTATGGATACACTGCAG
1 AGTGTATGGATACACTGCAG
* *
1295803 AGTGCATGGATACACTGTAG
1 AGTGTATGGATACACTGCAG
* *
1295823 GGTATATGGATACACT
1 AGTGTATGGATACACT
1295839 TTGACACCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (20 bp):
AGTGTATGGATACACTGCAG
Found at i:1296866 original size:29 final size:29
Alignment explanation
Indices: 1296804--1296868 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1296794 TCAAATGTTG
* * *
1296804 CCAAAATGTTTTTAGATGTGAAGTTCCTT
1 CCAAAATGTTTGTAGATGTGAAGTTCATC
*
1296833 TCAAAATGTTTGTAGATGTGAAGCTT-ATC
1 CCAAAATGTTTGTAGATGTGAAG-TTCATC
1296862 CCAAAAT
1 CCAAAAT
1296869 ATCAAGTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (29 bp):
CCAAAATGTTTGTAGATGTGAAGTTCATC
Found at i:1299054 original size:20 final size:20
Alignment explanation
Indices: 1299031--1299133 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
1299021 ACATAGTCTC
*
1299031 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
* * *
1299051 CAAATTCGTAACTCGATTTT
1 CAAATTCGCAACACGAATTT
*
1299071 AACAATTTCGCAACACGAATTT
1 --CAAATTCGCAACACGAATTT
*** *
1299093 CTTTTTCGCAAAAC-AATTTT
1 CAAATTCGCAACACGAA-TTT
* *
1299113 TAAATTCGCAACACGAGTTT
1 CAAATTCGCAACACGAATTT
1299133 C
1 C
1299134 CTTTTCGCAA
Statistics
Matches: 62, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
19 2 0.03
20 43 0.69
21 1 0.02
22 16 0.26
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:1299140 original size:20 final size:20
Alignment explanation
Indices: 1299035--1299145 Score: 62
Period size: 20 Copynumber: 5.5 Consensus size: 20
1299025 AGTCTCCAAA
* **
1299035 TTCGCAACGCGAATTTCAAA
1 TTCGCAACACGAATTTCATT
* * * *
1299055 TTCGTAACTCGATTTTAACAAT
1 TTCGCAACACGAATTT--CATT
*
1299077 TTCGCAACACGAATTTCTTT
1 TTCGCAACACGAATTTCATT
* * **
1299097 TTCGCAAAAC-AATTTTTAAA
1 TTCGCAACACGAA-TTTCATT
* *
1299117 TTCGCAACACGAGTTTCCTT
1 TTCGCAACACGAATTTCATT
1299137 TTCGCAACA
1 TTCGCAACA
1299146 AGATTTTCTA
Statistics
Matches: 67, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
19 2 0.03
20 48 0.72
21 1 0.01
22 16 0.24
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (20 bp):
TTCGCAACACGAATTTCATT
Found at i:1299242 original size:20 final size:20
Alignment explanation
Indices: 1299074--1299266 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
1299064 CGATTTTAAC
1299074 AATTTCGCAACACGAATTTCT
1 AATTTCGCAACACGAATTT-T
* *
1299095 -TTTTCGCAAAAC-AATTTTT
1 AATTTCGCAACACGAA-TTTT
* * *
1299114 AAATTCGCAACACGAGTTTC
1 AATTTCGCAACACGAATTTT
** * *
1299134 CTTTTCGCAACAAGATTTTCT
1 AATTTCGCAACACGAATTT-T
* ** *
1299155 AA-TTCACAA-AGCGCGTTTC
1 AATTTCGCAACA-CGAATTTT
**
1299174 AATTTCGCAACGGGAATTTT
1 AATTTCGCAACACGAATTTT
* * * * *
1299194 ATTTTCGAAACTC-TATTTCCG
1 AATTTCGCAACACGAATTT--T
1299215 AA-TTCGCAACACGAATTTT
1 AATTTCGCAACACGAATTTT
*
1299234 AATTTCGCAAAAC-AACTTTT
1 AATTTCGCAACACGAA-TTTT
*
1299254 ATTTTCGCAACAC
1 AATTTCGCAACAC
1299267 AAATGTTTTT
Statistics
Matches: 120, Mismatches: 40, Indels: 25
0.65 0.22 0.14
Matches are distributed among these distances:
19 14 0.12
20 100 0.83
21 6 0.05
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (20 bp):
AATTTCGCAACACGAATTTT
Found at i:1300048 original size:12 final size:12
Alignment explanation
Indices: 1300031--1300064 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1300021 ACTACATTTC
1300031 CAATATCAAACA
1 CAATATCAAACA
1300043 CAATATCAAACA
1 CAATATCAAACA
*
1300055 CAATCTCAAA
1 CAATATCAAA
1300065 ATCCACAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1302493 original size:18 final size:18
Alignment explanation
Indices: 1302470--1302505 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1302460 AAGCAAAAGG
*
1302470 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1302488 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1302506 CAACCGCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1302907 original size:20 final size:20
Alignment explanation
Indices: 1302867--1302941 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1302857 TCGCAACACG
* *
1302867 AAAA-TCGCAACTTGATGTT
1 AAAATTCGCAACTCGATATT
*
1302886 AAAATTCACAACTCGATATT
1 AAAATTCGCAACTCGATATT
1302906 AAAATTCGCAACTCGATATT
1 AAAATTCGCAACTCGATATT
1302926 AAAATTCGCAACTCGA
1 AAAATTCGCAACTCGA
1302942 AAATATAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 4 0.08
20 47 0.92
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (20 bp):
AAAATTCGCAACTCGATATT
Found at i:1302928 original size:40 final size:40
Alignment explanation
Indices: 1302867--1302959 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 40
1302857 TCGCAACACG
* * * *
1302867 AAAA-TCGCAACTTGATGTTAAAATTCACAACTCGATATT
1 AAAATTCGCAACTCGATATTAAAATTCACAACTCGAAAAT
*
1302906 AAAATTCGCAACTCGATATTAAAATTCGCAACTCGAAAAT
1 AAAATTCGCAACTCGATATTAAAATTCACAACTCGAAAAT
* *
1302946 ATAATTCGTAACTC
1 AAAATTCGCAACTC
1302960 AAAAATGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 4 0.09
40 42 0.91
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (40 bp):
AAAATTCGCAACTCGATATTAAAATTCACAACTCGAAAAT
Found at i:1302951 original size:20 final size:20
Alignment explanation
Indices: 1302793--1302984 Score: 105
Period size: 20 Copynumber: 9.9 Consensus size: 20
1302783 TTCGTAACTC
* *
1302793 AAATTCGCAACTCG-AATTCC
1 AAATTCGCAACTCGAAAAT-A
* *
1302813 AAATTCGCAACTCAAAAATC
1 AAATTCGCAACTCGAAAATA
* * *
1302833 AAATTC-CTAATTCGAAACTC
1 AAATTCGC-AACTCGAAAATA
*
1302853 AAATTCGCAACACG-----A
1 AAATTCGCAACTCGAAAATA
* ***
1302868 AAA-TCGCAACTTGATGTTA
1 AAATTCGCAACTCGAAAATA
* * *
1302887 AAATTCACAACTCGATATTA
1 AAATTCGCAACTCGAAAATA
* *
1302907 AAATTCGCAACTCGATATTA
1 AAATTCGCAACTCGAAAATA
1302927 AAATTCGCAACTCGAAAATA
1 AAATTCGCAACTCGAAAATA
* * * *
1302947 TAATTCGTAACTCAAAAATG
1 AAATTCGCAACTCGAAAATA
*
1302967 AAATTCGTAACTC-AAAAT
1 AAATTCGCAACTCGAAAAT
1302985 TGATTTCGAT
Statistics
Matches: 142, Mismatches: 21, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
14 8 0.06
15 3 0.02
19 10 0.07
20 117 0.82
21 4 0.03
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (20 bp):
AAATTCGCAACTCGAAAATA
Found at i:1302965 original size:94 final size:94
Alignment explanation
Indices: 1302793--1302965 Score: 199
Period size: 94 Copynumber: 1.8 Consensus size: 94
1302783 TTCGTAACTC
* * * * *
1302793 AAATTCGCAACTCGAATTCCAAATTCGCAACTCAAAAATCAAATTCCTAATTCGAAACTCAAATT
1 AAATTCACAACTCGAATTCAAAATTCGCAACTCAAAAATAAAATTCCTAACTCGAAAATCAAATT
*
1302858 CGCAACACGAAAATCGCAACTTGATGTTA
66 CGCAACACAAAAATCGCAACTTGATGTTA
* * *
1302887 AAATTCACAACTCGATATT-AAAATTCGCAACTCGATATTAAAATTCGC-AACTCGAAAAT-ATA
1 AAATTCACAACTCGA-ATTCAAAATTCGCAACTCAAAAATAAAATTC-CTAACTCGAAAATCA-A
* *
1302949 ATTCGTAACTCAAAAAT
63 ATTCGCAACACAAAAAT
1302966 GAAATTCGTA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
93 1 0.02
94 60 0.92
95 4 0.06
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (94 bp):
AAATTCACAACTCGAATTCAAAATTCGCAACTCAAAAATAAAATTCCTAACTCGAAAATCAAATT
CGCAACACAAAAATCGCAACTTGATGTTA
Found at i:1303080 original size:74 final size:74
Alignment explanation
Indices: 1302999--1303178 Score: 211
Period size: 74 Copynumber: 2.4 Consensus size: 74
1302989 TTCGATTTTC
* *
1302999 ATTTTCGCGTTGCGGATTTAAATATT-GAGTTAG-GATTTTCCTATTGCGAATTTGATTTTTGAA
1 ATTTTCGCGTTGC-GAATTAAATATTCGAGTT-GCGATTTTCCTATTGCGAATTTGATTTTCGAA
1303062 TTGCGAAAACG
64 TTGCGAAAACG
** * * *
1303073 ATTTTCGCGTTGCGAATTCGATTTTCGAGTTGCGATTTTCGTGTTGCGAATTTGATTTTCGAATT
1 ATTTTCGCGTTGCGAATTAAATATTCGAGTTGCGATTTTCCTATTGCGAATTTGATTTTCGAATT
* *
1303138 GTGAAATCG
66 GCGAAAACG
* * * *
1303147 ATTTTCGCGTTGCAAATTCAATTTTAGAGTTG
1 ATTTTCGCGTTGCGAATTAAATATTCGAGTTG
1303179 TGAATTTGAA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
73 9 0.10
74 83 0.90
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (74 bp):
ATTTTCGCGTTGCGAATTAAATATTCGAGTTGCGATTTTCCTATTGCGAATTTGATTTTCGAATT
GCGAAAACG
Found at i:1303085 original size:20 final size:20
Alignment explanation
Indices: 1303052--1303107 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1303042 TTGCGAATTT
* *
1303052 GATTTTTGAATTGCGAAAAC
1 GATTTTCGAGTTGCGAAAAC
* **
1303072 GATTTTCGCGTTGCGAATTC
1 GATTTTCGAGTTGCGAAAAC
1303092 GATTTTCGAGTTGCGA
1 GATTTTCGAGTTGCGA
1303108 TTTTCGTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (20 bp):
GATTTTCGAGTTGCGAAAAC
Found at i:1303110 original size:14 final size:14
Alignment explanation
Indices: 1303091--1303121 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1303081 GTTGCGAATT
1303091 CGATTTTCGAGTTG
1 CGATTTTCGAGTTG
*
1303105 CGATTTTCGTGTTG
1 CGATTTTCGAGTTG
1303119 CGA
1 CGA
1303122 ATTTGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.42
Consensus pattern (14 bp):
CGATTTTCGAGTTG
Found at i:1303131 original size:20 final size:20
Alignment explanation
Indices: 1303105--1303212 Score: 81
Period size: 20 Copynumber: 5.4 Consensus size: 20
1303095 TTTCGAGTTG
*
1303105 CGATTTTCGTGTTGCGAATT
1 CGATTTTCGAGTTGCGAATT
* * * *
1303125 TGATTTTCGAATTGTGAAAT
1 CGATTTTCGAGTTGCGAATT
* *
1303145 CGATTTTCGCGTTGCAAATT
1 CGATTTTCGAGTTGCGAATT
* * *
1303165 CAATTTTAGAGTTGTGAATT
1 CGATTTTCGAGTTGCGAATT
* * * *
1303185 TGAATATCGTGTTGCGAATT
1 CGATTTTCGAGTTGCGAATT
*
1303205 TGATTTTC
1 CGATTTTC
1303213 TTAAAGGTAG
Statistics
Matches: 63, Mismatches: 25, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.44
Consensus pattern (20 bp):
CGATTTTCGAGTTGCGAATT
Found at i:1303153 original size:40 final size:40
Alignment explanation
Indices: 1303032--1303212 Score: 158
Period size: 40 Copynumber: 4.7 Consensus size: 40
1303022 ATTGAGTTAG
* * * * *
1303032 GATTTTCCTATTGCGAATTTGATTTTTGAATTGCGAAAAC
1 GATTTTCGTGTTGCGAATTTGATTTTCGAATTGTGAAATC
* * *
1303072 GATTTTCGCGTTGCGAATTCGATTTTCG-AGT-TG----C
1 GATTTTCGTGTTGCGAATTTGATTTTCGAATTGTGAAATC
1303106 GATTTTCGTGTTGCGAATTTGATTTTCGAATTGTGAAATC
1 GATTTTCGTGTTGCGAATTTGATTTTCGAATTGTGAAATC
* * ** * * * *
1303146 GATTTTCGCGTTGCAAATTCAATTTTAGAGTTGTGAATTT
1 GATTTTCGTGTTGCGAATTTGATTTTCGAATTGTGAAATC
* *
1303186 GAATATCGTGTTGCGAATTTGATTTTC
1 GATTTTCGTGTTGCGAATTTGATTTTC
1303213 TTAAAGGTAG
Statistics
Matches: 110, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
34 27 0.25
35 2 0.02
36 2 0.02
38 1 0.01
39 2 0.02
40 76 0.69
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.44
Consensus pattern (40 bp):
GATTTTCGTGTTGCGAATTTGATTTTCGAATTGTGAAATC
Found at i:1305086 original size:21 final size:21
Alignment explanation
Indices: 1305062--1305108 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1305052 AGGTAGACCC
**
1305062 TGAACGATAGGAAGGGCCTCT
1 TGAACGATAGGAAGGGAATCT
* *
1305083 TGAACGATGGGAGGGGAATCT
1 TGAACGATAGGAAGGGAATCT
1305104 TGAAC
1 TGAAC
1305109 AATGAGAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.36, T:0.19
Consensus pattern (21 bp):
TGAACGATAGGAAGGGAATCT
Found at i:1305117 original size:21 final size:21
Alignment explanation
Indices: 1305080--1305144 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
1305070 AGGAAGGGCC
*
1305080 TCTTGAACGATGGGAGG-GGAA
1 TCTTGAACAATGGGAGGTGG-A
*
1305101 TCTTGAACAATGAGAGGTGGA
1 TCTTGAACAATGGGAGGTGGA
*
1305122 TCCTGAACAATGGGAGGTGGA
1 TCTTGAACAATGGGAGGTGGA
1305143 TC
1 TC
1305145 AGGGTTCTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 37 0.95
22 2 0.05
ACGTcount: A:0.29, C:0.12, G:0.37, T:0.22
Consensus pattern (21 bp):
TCTTGAACAATGGGAGGTGGA
Found at i:1305297 original size:12 final size:12
Alignment explanation
Indices: 1305278--1305318 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1305268 GGTCCGCTAA
1305278 AAATAAATTAAT
1 AAATAAATTAAT
* *
1305290 ACATAAATTAGT
1 AAATAAATTAAT
*
1305302 AAATAAATAAAT
1 AAATAAATTAAT
1305314 AAATA
1 AAATA
1305319 GTGTCAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:1305546 original size:62 final size:63
Alignment explanation
Indices: 1305439--1305596 Score: 164
Period size: 63 Copynumber: 2.5 Consensus size: 63
1305429 CACATAGAGC
* * *
1305439 ACCTACCTCATCACGTAAAGTA-GCTACCTCACCACGTAAAGCACCATT-TCATAACGTAAA-A
1 ACCTACCTCATCACGTAAAG-ACCCTACCTCATCACGCAAAGCACCATTGTCATAACGTAAACA
* * * *
1305500 CAGCTACCTCACCACGTAAAGACCCTACCTCATCACGCCATA-CACCATTGTCATCACGTAAACA
1 -ACCTACCTCATCACGTAAAGACCCTACCTCATCACG-CAAAGCACCATTGTCATAACGTAAACA
* *
1305564 ACCGACCTCATCACGTAAAG-CACCTAACTCATC
1 ACCTACCTCATCACGTAAAGAC-CCTACCTCATC
1305597 CTGTGGAGGT
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
61 1 0.01
62 38 0.47
63 40 0.50
64 1 0.01
ACGTcount: A:0.35, C:0.36, G:0.09, T:0.20
Consensus pattern (63 bp):
ACCTACCTCATCACGTAAAGACCCTACCTCATCACGCAAAGCACCATTGTCATAACGTAAACA
Found at i:1305594 original size:21 final size:21
Alignment explanation
Indices: 1305436--1305596 Score: 116
Period size: 21 Copynumber: 7.7 Consensus size: 21
1305426 TCTCACATAG
1305436 AGCACCTACCTCATCACGTAA
1 AGCACCTACCTCATCACGTAA
* * *
1305457 AGTAGCTACCTCACCACGTAA
1 AGCACCTACCTCATCACGTAA
** *
1305478 AGCACC-ATTTCATAACGTAA
1 AGCACCTACCTCATCACGTAA
* * *
1305498 AACAGCTACCTCACCACGTAA
1 AGCACCTACCTCATCACGTAA
* *
1305519 AG-ACCCTACCTCATCACGCCAT
1 AGCA-CCTACCTCATCACG-TAA
**
1305541 A-CACC-ATTGTCATCACGTAA
1 AGCACCTA-CCTCATCACGTAA
*
1305561 A-CAACCGACCTCATCACGTAA
1 AGC-ACCTACCTCATCACGTAA
*
1305582 AGCACCTAACTCATC
1 AGCACCTACCTCATC
1305597 CTGTGGAGGT
Statistics
Matches: 104, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
20 19 0.18
21 80 0.77
22 5 0.05
ACGTcount: A:0.35, C:0.36, G:0.10, T:0.19
Consensus pattern (21 bp):
AGCACCTACCTCATCACGTAA
Found at i:1305783 original size:42 final size:41
Alignment explanation
Indices: 1305697--1305838 Score: 153
Period size: 42 Copynumber: 3.5 Consensus size: 41
1305687 TGATGGAATA
* * *
1305697 GGTGTCGAGGCGTAGAGTCGGCT--ATAGGTGATGGTTCTC
1 GGTGTCGAGGTGTAGAATCGGCTCGATAGGTGATGGATCTC
* *
1305736 AGTGTCGAGGTGTAAAATCGGCTCGATCAGGTGATGGATCTC
1 GGTGTCGAGGTGTAGAATCGGCTCGAT-AGGTGATGGATCTC
* * * *
1305778 GGTGTCGAAGTGGAGAATCGACACGATGAGGTGATGGATCTC
1 GGTGTCGAGGTGTAGAATCGGCTCGAT-AGGTGATGGATCTC
* *
1305820 GGTGTCGAAGTGAAGAATC
1 GGTGTCGAGGTGTAGAATC
1305839 CACTCGATGA
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 19 0.22
41 2 0.02
42 66 0.76
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.25
Consensus pattern (41 bp):
GGTGTCGAGGTGTAGAATCGGCTCGATAGGTGATGGATCTC
Found at i:1305847 original size:42 final size:42
Alignment explanation
Indices: 1305722--1305848 Score: 166
Period size: 42 Copynumber: 3.0 Consensus size: 42
1305712 AGTCGGCTAT
* * * * *
1305722 AGGTGATGGTTCTCAGTGTCGAGGTGTAA-AATCGGCTCGATC
1 AGGTGATGGATCTCGGTGTCGAAGTG-AAGAATCGACTCGATG
* *
1305764 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACACGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGAAGAATCGACTCGATG
*
1305806 AGGTGATGGATCTCGGTGTCGAAGTGAAGAATCCACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGAAGAATCGACTCGATG
1305848 A
1 A
1305849 AAAAGTGGGG
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 1 0.01
42 73 0.99
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCGAAGTGAAGAATCGACTCGATG
Found at i:1307372 original size:34 final size:32
Alignment explanation
Indices: 1307326--1307417 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 32
1307316 AGTTTATTCT
1307326 TGAAACATAAATTCGCAACACGAAAATCGCAAAA
1 TGAAA-ATAAATTCGCAACACGAAAATCGC-AAA
* *
1307360 TGAAAATAAAATTCGCAACATGAAAATCGCAAG
1 TGAAAAT-AAATTCGCAACACGAAAATCGCAAA
*
1307393 TCGAAAATGAAATTCGCAATACGAA
1 T-GAAAAT-AAATTCGCAACACGAA
1307418 TTTTGAATTC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
33 5 0.10
34 46 0.90
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (32 bp):
TGAAAATAAATTCGCAACACGAAAATCGCAAA
Found at i:1307377 original size:20 final size:19
Alignment explanation
Indices: 1307348--1307386 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1307338 TCGCAACACG
1307348 AAAATCGCAAAATGAAAAT
1 AAAATCGCAAAATGAAAAT
*
1307367 AAAATTCGCAACATGAAAAT
1 AAAA-TCGCAAAATGAAAAT
1307387 CGCAAGTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.59, C:0.13, G:0.10, T:0.18
Consensus pattern (19 bp):
AAAATCGCAAAATGAAAAT
Found at i:1307426 original size:20 final size:20
Alignment explanation
Indices: 1307403--1307440 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1307393 TCGAAAATGA
1307403 AATTCGCAA-TACGAATTTTG
1 AATTCGCAACT-CGAATTTTG
1307423 AATTCGCAACTCGAATTT
1 AATTCGCAACTCGAATTT
1307441 CTTTTTCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (20 bp):
AATTCGCAACTCGAATTTTG
Found at i:1307461 original size:20 final size:20
Alignment explanation
Indices: 1307438--1307483 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1307428 GCAACTCGAA
* *
1307438 TTTCTTTTTCGTGTTGCGAT
1 TTTCGTTTTCGCGTTGCGAT
1307458 TTTCGTTTTCGCGTTGCGAT
1 TTTCGTTTTCGCGTTGCGAT
1307478 TTTCGT
1 TTTCGT
1307484 GTTGCGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.04, C:0.17, G:0.22, T:0.57
Consensus pattern (20 bp):
TTTCGTTTTCGCGTTGCGAT
Found at i:1307486 original size:34 final size:34
Alignment explanation
Indices: 1307443--1307520 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
1307433 TCGAATTTCT
* * *
1307443 TTTTCGTGTTGCGATTTTCGTTTTCGCGTTGCGA
1 TTTTCGTGTTGCGAATTTCATTTTCGAGTTGCGA
**
1307477 TTTTCGTGTTGCGAATTTCATTTTTTAGTTGCGA
1 TTTTCGTGTTGCGAATTTCATTTTCGAGTTGCGA
1307511 TTTTCGTGTT
1 TTTTCGTGTT
1307521 ACAAATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.54
Consensus pattern (34 bp):
TTTTCGTGTTGCGAATTTCATTTTCGAGTTGCGA
Found at i:1307499 original size:20 final size:20
Alignment explanation
Indices: 1307434--1307500 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
1307424 ATTCGCAACT
*
1307434 CGAATTTCTTTTTCGTGTTG
1 CGAATTTCATTTTCGTGTTG
* * *
1307454 CGATTTTCGTTTTCGCGTTG
1 CGAATTTCATTTTCGTGTTG
1307474 CG------ATTTTCGTGTTG
1 CGAATTTCATTTTCGTGTTG
1307488 CGAATTTCATTTT
1 CGAATTTCATTTT
1307501 TTAGTTGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
14 12 0.33
20 24 0.67
ACGTcount: A:0.10, C:0.16, G:0.21, T:0.52
Consensus pattern (20 bp):
CGAATTTCATTTTCGTGTTG
Found at i:1307904 original size:22 final size:22
Alignment explanation
Indices: 1307879--1307928 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1307869 GATGGAGGGG
*
1307879 GTCGCCGGATATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
1307901 GTCGCCGGAGATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
1307923 GTCGCC
1 GTCGCC
1307929 ATAGAGAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACGGAT
Found at i:1308084 original size:20 final size:20
Alignment explanation
Indices: 1308059--1308106 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1308049 TGAAAATTGA
*
1308059 GTTGCGAAAATAAAATTCGC
1 GTTGCGAAAATAAAATGCGC
* *
1308079 GTTGCGAAATTGAAATGCGC
1 GTTGCGAAAATAAAATGCGC
*
1308099 TTTGCGAA
1 GTTGCGAA
1308107 TTATAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (20 bp):
GTTGCGAAAATAAAATGCGC
Found at i:1308240 original size:20 final size:20
Alignment explanation
Indices: 1308217--1308254 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1308207 AATTTTACTT
*
1308217 CTGTGTTGCGAATTTGGAAA
1 CTGTGTTGCGAAATTGGAAA
1308237 CTGTGTTGCGAAATTGGA
1 CTGTGTTGCGAAATTGGA
1308255 GTTCGTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.34
Consensus pattern (20 bp):
CTGTGTTGCGAAATTGGAAA
Found at i:1309025 original size:2 final size:2
Alignment explanation
Indices: 1309020--1309063 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1309010 ACACACACAC
1309020 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
1309062 AT
1 AT
1309064 TCATTCTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1315231 original size:64 final size:64
Alignment explanation
Indices: 1315159--1315285 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 64
1315149 ATCTCACTTG
* **
1315159 AGATTGTTTCTATTTTAACAAAATTCTGTCTCGCTCAAGACAATTTCCCTTGAAACACAAGCAT
1 AGATTGTTTATATTGAAACAAAATTCTGTCTCGCTCAAGACAATTTCCCTTGAAACACAAGCAT
* * *
1315223 AGATTGTTTATCTTGAAACAAAATTTTGTCTCGCTCGAGACAATTTCCCTTGAAACACAAGCA
1 AGATTGTTTATATTGAAACAAAATTCTGTCTCGCTCAAGACAATTTCCCTTGAAACACAAGCA
1315286 CATATCTAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (64 bp):
AGATTGTTTATATTGAAACAAAATTCTGTCTCGCTCAAGACAATTTCCCTTGAAACACAAGCAT
Found at i:1347352 original size:20 final size:21
Alignment explanation
Indices: 1347327--1347366 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1347317 TGTTAATAAT
1347327 TTAGGGATGAAATT-GAAAGA
1 TTAGGGATGAAATTAGAAAGA
1347347 TTAGGGATGAAATTAGAAAG
1 TTAGGGATGAAATTAGAAAG
1347367 TTTAAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (21 bp):
TTAGGGATGAAATTAGAAAGA
Found at i:1348222 original size:21 final size:21
Alignment explanation
Indices: 1348196--1348254 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1348186 AGATGGCGAA
1348196 GCTCTTCCTGCACTCTCATTT
1 GCTCTTCCTGCACTCTCATTT
1348217 GCTCTTCCTGCACTCTCATTT
1 GCTCTTCCTGCACTCTCATTT
*
1348238 GCTCTTCCTGCAATCTC
1 GCTCTTCCTGCACTCTC
1348255 TTCCTCAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.10, C:0.39, G:0.10, T:0.41
Consensus pattern (21 bp):
GCTCTTCCTGCACTCTCATTT
Found at i:1351588 original size:51 final size:51
Alignment explanation
Indices: 1351506--1351602 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
1351496 TACCTAAATC
* * *
1351506 ATTAATCCCATCAGTATAGTCTTGAATTGGAACTGGATTCTTTGACTTTGA
1 ATTAATCCCATCAGTAGAGTCCTGAACTGGAACTGGATTCTTTGACTTTGA
* *
1351557 ATTAATCTCATCAGTAGAGTCCTGAACTGGAACTGTATTCTTTGAC
1 ATTAATCCCATCAGTAGAGTCCTGAACTGGAACTGGATTCTTTGAC
1351603 AGCTTCAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (51 bp):
ATTAATCCCATCAGTAGAGTCCTGAACTGGAACTGGATTCTTTGACTTTGA
Found at i:1359344 original size:21 final size:20
Alignment explanation
Indices: 1359306--1359389 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 20
1359296 TTTTGTCCGG
*
1359306 TTATAAATATAATATTATAA
1 TTATTAATATAATATTATAA
*
1359326 TTATTAATATAACTATTATTA
1 TTATTAATATAA-TATTATAA
* *
1359347 TTATTATAACAATTAAAATTATAA
1 TTA-T-TAA-TA-TAATATTATAA
*
1359371 TTATTATTAGTAATATTAT
1 TTATTAATA-TAATATTAT
1359390 TAATATTGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
20 11 0.22
21 19 0.38
22 3 0.06
23 4 0.08
24 10 0.20
25 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (20 bp):
TTATTAATATAATATTATAA
Found at i:1359348 original size:18 final size:18
Alignment explanation
Indices: 1359325--1359361 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1359315 TAATATTATA
*
1359325 ATTATTAATATAACTATT
1 ATTATTAATATAACAATT
*
1359343 ATTATTATTATAACAATT
1 ATTATTAATATAACAATT
1359361 A
1 A
1359362 AAATTATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTATTAATATAACAATT
Found at i:1359379 original size:12 final size:12
Alignment explanation
Indices: 1359318--1359391 Score: 57
Period size: 12 Copynumber: 6.4 Consensus size: 12
1359308 ATAAATATAA
1359318 TATTATAATTAT
1 TATTATAATTAT
* *
1359330 TAATATAACTAT
1 TATTATAATTAT
1359342 TA-T-T-ATTAT
1 TATTATAATTAT
* * *
1359351 TATAACAATTAA
1 TATTATAATTAT
*
1359363 AATTATAATTAT
1 TATTATAATTAT
1359375 TATTAGTAA-TAT
1 TATTA-TAATTAT
1359387 TATTA
1 TATTA
1359392 ATATTGTTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
9 6 0.13
10 1 0.02
11 1 0.02
12 36 0.77
13 3 0.06
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (12 bp):
TATTATAATTAT
Found at i:1359538 original size:14 final size:14
Alignment explanation
Indices: 1359519--1359548 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1359509 GAGCTACAGC
*
1359519 TGTCCTAATTGCCT
1 TGTCCTAACTGCCT
1359533 TGTCCTAACTGCCT
1 TGTCCTAACTGCCT
1359547 TG
1 TG
1359549 ATAACTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.30, G:0.17, T:0.40
Consensus pattern (14 bp):
TGTCCTAACTGCCT
Found at i:1360551 original size:21 final size:21
Alignment explanation
Indices: 1360522--1360574 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1360512 ATTCTGACTA
1360522 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1360543 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1360564 TCGCAATGCGA
1 TCGCATTGCGA
1360575 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1362722 original size:493 final size:477
Alignment explanation
Indices: 1361772--1362741 Score: 1760
Period size: 493 Copynumber: 2.0 Consensus size: 477
1361762 TAAATTAAAA
1361772 GTGTATCCCATTAGTGACACCTAAAAATTGATTCATCACTTTAAAATTTGGGAACAAAAGAAAAG
1 GTGTATCCCATTAGTGACACCTAAAAATTGATTCATCACTTTAAAATTTGGGAACAAAAGAAAAG
1361837 GAAATGTTCGGTTATATAAATTTATCGAGAAAAGGTTGTTATAGCTTTTAAGATCTAGTCTCGAT
66 GAAATGTTCGGTTATATAAATTTATCGAGAAAAGGTTGTTATAGCTTTTAAGATCTAGTCTCGAT
1361902 ATTTGTAAATAATCGAACATTCTTATCTTTCTAAAATGACTTGGTAATTTTAATTTAATTAATTT
131 ATTTGTAAATAATCGAACATTCTTATCTTTCTAAAATGACTTGGTAATTTTAATTTAATTAATTT
* *
1361967 TTTTGAGTTCTTTTGAATGTTTTTAAACATCTTTGTTTTGGGATCAAAAGTCAAATTAAAGTCGA
196 ATTTGAGTGCTTTTGAATGTTTTTAAACATCTTTGTTTTGGGATCAAAAGTCAAATTAAAGTCGA
*
1362032 TTTGAAATTTCATTGCAAAGACGTTAATTCGACTAGGTACCGATTAGGCGTTGTGGGGGTTCTAA
261 TTTGAAATTTCATTGCAAAGACGTTAATTCGACTAGGTACCGATTAGGCATTGTGGGGGTTCTAA
1362097 TCCTTCTCCACACGTAACCGACTCCCGAACTCGGATTTTGGTAACGTAGACTTTAATTTATTGTT
326 TCCTTCTCCACACGTAACCGACTCCCGAACTCGGATTTTGGTAACGTAGACTTTAATTTATTGTT
1362162 TTAATTAAAATTAATTTTTATTTAAAATAACAAACATTTTTTGGGTGCCCAATCACACCCTAATC
391 TTAATTAAAATTAATTTTTATTTAAAATAACAAACATTTTTTGGGTGCCCAATCACACCCTAATC
1362227 AAAGATTGGTGACGACTCTTTT
456 AAAGATTGGTGACGACTCTTTT
1362249 GTGTATCCCCATTAGTGACACCTAAAAATTGATTCATCACTTTAAAATTTGGGAACAAAAGAAAA
1 GTGTAT-CCCATTAGTGACACCTAAAAATTGATTCATCACTTTAAAATTTGGGAACAAAAGAAAA
1362314 GGAAATGTTCGGTTATATAAATTTATCGAGAAAAGGTTGTTATAGCTTTTAAGATCTAGTCTCGA
65 GGAAATGTTCGGTTATATAAATTTATCGAGAAAAGGTTGTTATAGCTTTTAAGATCTAGTCTCGA
1362379 TATTTGTAAATAATCGAACATTCTTTATCTTTCTAAAATGACTTGGTAATTTTAATTTAATTTAA
130 TATTTGTAAATAATCGAACATTC-TTATCTTTCTAAAATGACTTGGTAATTTTAATTTAA-TTAA
1362444 TTTATTTGAGTGCTTTTGAATGTTTTTAAATTTACATCTTTGTTTTATGGGATCAAAAGTCAAAT
193 TTTATTTGAGTGCTTTTGAATGTTTTT-AA---ACATCTTTG-TTT-TGGGATCAAAAGTCAAAT
*
1362509 TAAAGTCGAATTTGTAAATTTCATTGCAAAGACGTTAATTAATCGACTAGGTACTGATTTAGGGC
252 TAAAGTCG-ATTTG-AAATTTCATTGCAAAGACGTTAA-T--TCGACTAGGTACCGA-TTA-GGC
1362574 ATTGTGGGGGTTCTAATCCTTCTCCACACGTAACCGACTCCCGAACTCGGATTTTGGTAACGTAG
310 ATTGTGGGGGTTCTAATCCTTCTCCACACGTAACCGACTCCCGAACTCGGATTTTGGTAACGTAG
1362639 ACTTTAATTTATTGTTTTAATTAAAATTAATTTTTATTTAAAATAACAAACATTTTTTGGGTGCC
375 ACTTTAATTTATTGTTTTAATTAAAATTAATTTTTATTTAAAATAACAAACATTTTTTGGGTGCC
1362704 CAATCACACCCTAATCAAAGATTGGTGACGACTCTTTT
440 CAATCACACCCTAATCAAAGATTGGTGACGACTCTTTT
1362742 AACCGTATTT
Statistics
Matches: 473, Mismatches: 4, Indels: 16
0.96 0.01 0.03
Matches are distributed among these distances:
477 6 0.01
478 146 0.31
479 36 0.08
480 29 0.06
481 2 0.00
484 9 0.02
485 3 0.01
486 26 0.05
487 5 0.01
488 23 0.05
489 1 0.00
491 14 0.03
492 3 0.01
493 170 0.36
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (477 bp):
GTGTATCCCATTAGTGACACCTAAAAATTGATTCATCACTTTAAAATTTGGGAACAAAAGAAAAG
GAAATGTTCGGTTATATAAATTTATCGAGAAAAGGTTGTTATAGCTTTTAAGATCTAGTCTCGAT
ATTTGTAAATAATCGAACATTCTTATCTTTCTAAAATGACTTGGTAATTTTAATTTAATTAATTT
ATTTGAGTGCTTTTGAATGTTTTTAAACATCTTTGTTTTGGGATCAAAAGTCAAATTAAAGTCGA
TTTGAAATTTCATTGCAAAGACGTTAATTCGACTAGGTACCGATTAGGCATTGTGGGGGTTCTAA
TCCTTCTCCACACGTAACCGACTCCCGAACTCGGATTTTGGTAACGTAGACTTTAATTTATTGTT
TTAATTAAAATTAATTTTTATTTAAAATAACAAACATTTTTTGGGTGCCCAATCACACCCTAATC
AAAGATTGGTGACGACTCTTTT
Found at i:1370769 original size:13 final size:13
Alignment explanation
Indices: 1370751--1370775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1370741 TGAAGCAAAT
1370751 CCATCAGTAAGTG
1 CCATCAGTAAGTG
1370764 CCATCAGTAAGT
1 CCATCAGTAAGT
1370776 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:1370822 original size:42 final size:41
Alignment explanation
Indices: 1370763--1370908 Score: 141
Period size: 44 Copynumber: 3.5 Consensus size: 41
1370753 ATCAGTAAGT
1370763 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGAT-AAATCCTTCGG
* * *
1370805 GCCATCAGTAAGTCTTTCAAGCATGATGATTAAAAATCATTCGT
1 GCCATCAGTAAGTCTTTCGAGCATGATGA-T--AAATCCTTCGG
** * * * *
1370849 GCCATTTGTGAGTCTTTTGAGTAAGATGATAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGG
* *
1370890 GTCATCCA-TAAGTCATTCG
1 GCCAT-CAGTAAGTCTTTCG
1370909 GGTAGGATAT
Statistics
Matches: 82, Mismatches: 19, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
41 21 0.26
42 28 0.34
43 2 0.02
44 31 0.38
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (41 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGG
Found at i:1370865 original size:44 final size:42
Alignment explanation
Indices: 1370763--1370853 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
1370753 ATCAGTAAGT
* * *
1370763 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCAAGCATGATGATAAAATCATTCGG
*
1370805 GCCATCAGTAAGTCTTTCAAGCATGATGATTAAAAATCATTCGT
1 GCCATCAGTAAGTCTTTCAAGCATGATGA-T-AAAATCATTCGG
1370849 GCCAT
1 GCCAT
1370854 TTGTGAGTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 28 0.65
43 1 0.02
44 14 0.33
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCAAGCATGATGATAAAATCATTCGG
Found at i:1371064 original size:53 final size:53
Alignment explanation
Indices: 1371001--1371158 Score: 246
Period size: 53 Copynumber: 3.0 Consensus size: 53
1370991 AGGAAAATTG
*
1371001 TTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTA
1 TTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTA
* *
1371054 TTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGACTG
1 TTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTA
* * *
1371107 TTTGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCGCTAGTC-GAAGATT
1 TTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGGCAGAAGATT
1371159 GTTCAAAGAA
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
53 93 0.96
54 4 0.04
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (53 bp):
TTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAGATTA
Found at i:1371367 original size:62 final size:62
Alignment explanation
Indices: 1371301--1371421 Score: 206
Period size: 62 Copynumber: 2.0 Consensus size: 62
1371291 TAGACACCCG
**
1371301 TTTTTGTCTGGTTATAAATATAATATTAAAATTATTAATATTATAATATAAATATTATTCCA
1 TTTTTGTCCAGTTATAAATATAATATTAAAATTATTAATATTATAATATAAATATTATTCCA
* *
1371363 TTTTTGTCCAGTTATAAATATAATATTATAATTATTAATATTATAATATAACTATTATT
1 TTTTTGTCCAGTTATAAATATAATATTAAAATTATTAATATTATAATATAAATATTATT
1371422 ATTATTATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (62 bp):
TTTTTGTCCAGTTATAAATATAATATTAAAATTATTAATATTATAATATAAATATTATTCCA
Found at i:1371411 original size:23 final size:24
Alignment explanation
Indices: 1371381--1371468 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 24
1371371 CAGTTATAAA
*
1371381 TATAATATTA-TAATTATTAATAT
1 TATAATATTACTAATTATTATTAT
*
1371404 TATAATATAACT-ATTATTATTAT
1 TATAATATTACTAATTATTATTAT
*
1371427 TATAAGAATTA--AATTATTATTAT
1 TATAA-TATTACTAATTATTATTAT
*
1371450 TAT--TATTATTAATATATTA
1 TATAATATTACTAAT-TATTA
1371469 GTTTATTTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
20 4 0.07
22 3 0.06
23 43 0.80
24 4 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
TATAATATTACTAATTATTATTAT
Found at i:1371423 original size:3 final size:3
Alignment explanation
Indices: 1371386--1371480 Score: 56
Period size: 3 Copynumber: 33.3 Consensus size: 3
1371376 ATAAATATAA
* * * * * * *
1371386 TAT TAT AAT TAT TAA TAT TA- TAA TAT AAC TAT TAT TAT TAT TAT AAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
1371433 AAT TA- AAT TAT TAT TAT TAT TAT TAT TAA TA- TAT TAG T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1371477 TAT T
1 TAT T
1371481 TCTTGCAGGC
Statistics
Matches: 69, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
2 8 0.12
3 61 0.88
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:1371467 original size:20 final size:20
Alignment explanation
Indices: 1371374--1371468 Score: 70
Period size: 20 Copynumber: 4.7 Consensus size: 20
1371364 TTTTGTCCAG
* *
1371374 TTATAAATATAATATTATAA
1 TTATTAATATATTATTATAA
*
1371394 TTATTAATAT-TATAATATAA
1 TTATTAATATAT-TATTATAA
*
1371414 CTATT-AT-TATTATTATAA
1 TTATTAATATATTATTATAA
** *
1371432 GAATTAAATTATTATTATTATTA
1 TTATT-AA-TA-TATTATTATAA
1371455 TTATTAATATATTA
1 TTATTAATATATTA
1371469 GTTTATTTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
18 11 0.19
19 3 0.05
20 26 0.45
21 3 0.05
22 2 0.03
23 13 0.22
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (20 bp):
TTATTAATATATTATTATAA
Found at i:1371609 original size:14 final size:14
Alignment explanation
Indices: 1371590--1371619 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1371580 GAGCTACAGC
*
1371590 TGTCCTAATTGCCT
1 TGTCCTAACTGCCT
1371604 TGTCCTAACTGCCT
1 TGTCCTAACTGCCT
1371618 TG
1 TG
1371620 ATAACTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.30, G:0.17, T:0.40
Consensus pattern (14 bp):
TGTCCTAACTGCCT
Found at i:1373356 original size:21 final size:22
Alignment explanation
Indices: 1373297--1373357 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
1373287 ATATAAGTTT
1373297 ATATATTATA-TACT-TGTATTC
1 ATATATTATATTA-TGTGTATTC
* * *
1373318 ATATGTTAGTATAATGTGTA-TG
1 ATATATTA-TATTATGTGTATTC
1373340 ATATATTATATTATGTGT
1 ATATATTATATTATGTGT
1373358 GTTAAATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 16 0.50
22 11 0.34
23 5 0.16
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (22 bp):
ATATATTATATTATGTGTATTC
Found at i:1373477 original size:2 final size:2
Alignment explanation
Indices: 1373470--1373572 Score: 192
Period size: 2 Copynumber: 52.5 Consensus size: 2
1373460 GTGTAAAGGT
1373470 TA TA TA TA TA T- 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
1373511 TA TA TA 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 TA TA TA TA
1373552 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1373573 TTTTCATTAC
Statistics
Matches: 99, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 97 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1375156 original size:45 final size:48
Alignment explanation
Indices: 1375079--1375176 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 48
1375069 TTTATTTTCG
*
1375079 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAATGCATACGAACTAGATATCATGCGGTTAGGATTTA
* * *
1375126 TTTTTCGAA-CAA-GCATACGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTCGAATAAATGCATACGAACTAGATATCATGCGGTTAGGATTTA
1375172 TTTTT
1 TTTTT
1375177 TAATAACAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
45 27 0.59
46 10 0.22
47 9 0.20
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATACGAACTAGATATCATGCGGTTAGGATTTA
Found at i:1381783 original size:16 final size:16
Alignment explanation
Indices: 1381757--1381790 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1381747 TTGTCCTGAA
1381757 AAGGGTAACAAA-AAG
1 AAGGGTAACAAACAAG
1381772 AAGGGATAACAAACAAG
1 AAGGG-TAACAAACAAG
1381789 AA
1 AA
1381791 AAGGCTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.62, C:0.09, G:0.24, T:0.06
Consensus pattern (16 bp):
AAGGGTAACAAACAAG
Found at i:1384552 original size:42 final size:42
Alignment explanation
Indices: 1384478--1384559 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1384468 ACACTCATCC
* *
1384478 TCATTTCTTGTTAAAGTGCATGAGTCGATTCTCTTGTTTCCT
1 TCATTTCTTGTTAAAGTGCATGAATCGATTCTCTTATTTCCT
* * *
1384520 TCATTTAC-TGTTGAAGTGCATGAATTGTTTCTCTTATTTC
1 TCATTT-CTTGTTAAAGTGCATGAATCGATTCTCTTATTTC
1384560 TTGTTGAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.49
Consensus pattern (42 bp):
TCATTTCTTGTTAAAGTGCATGAATCGATTCTCTTATTTCCT
Found at i:1384575 original size:33 final size:33
Alignment explanation
Indices: 1384511--1384575 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
1384501 GTCGATTCTC
* *
1384511 TTGTTTCCTTCATTTACTGTTGAAGTGCATGAA
1 TTGTTTCCTTCATTTACTGTTGAAATACATGAA
1384544 TTGTTTCTCTT-ATTT-CTTGTTGAAATACATGA
1 TTGTTTC-CTTCATTTAC-TGTTGAAATACATGA
1384576 GTAGAGTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 24 0.86
34 3 0.11
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (33 bp):
TTGTTTCCTTCATTTACTGTTGAAATACATGAA
Found at i:1385692 original size:30 final size:30
Alignment explanation
Indices: 1385656--1385715 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1385646 ATTAGAATCT
1385656 CGATATTAAGGAAATAAAAGTAAAATGGGG
1 CGATATTAAGGAAATAAAAGTAAAATGGGG
1385686 CGATATTAAGGAAATAAAAGTAAAATGGGG
1 CGATATTAAGGAAATAAAAGTAAAATGGGG
1385716 GGTTGCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.27, T:0.20
Consensus pattern (30 bp):
CGATATTAAGGAAATAAAAGTAAAATGGGG
Found at i:1386494 original size:16 final size:16
Alignment explanation
Indices: 1386473--1386506 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1386463 TAAATCATAT
* *
1386473 AAAGAAAGTTAAAATA
1 AAAGAAAATCAAAATA
1386489 AAAGAAAATCAAAATA
1 AAAGAAAATCAAAATA
1386505 AA
1 AA
1386507 CAAAGTCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.15
Consensus pattern (16 bp):
AAAGAAAATCAAAATA
Found at i:1387529 original size:15 final size:15
Alignment explanation
Indices: 1387509--1387541 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1387499 TTAGCTGGGT
1387509 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
1387524 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
1387539 GGG
1 GGG
1387542 TAATGTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.70, T:0.06
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:1388785 original size:3 final size:3
Alignment explanation
Indices: 1388737--1388772 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1388727 ATGATATTTG
*
1388737 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1388773 TTTCTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1391567 original size:63 final size:63
Alignment explanation
Indices: 1391490--1391609 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
1391480 TATTTGTTAC
* *
1391490 CTATTTAACTTTGAATATTAAAGA-T-AATTATATCATTTTGAATATTTCAAATTAAAATAATAT
1 CTATTTAACTTTGAATAGTAAAAAGTGAATT-TAT-ATTTTGAATATTTCAAATTAAAATAATAT
* * *
1391553 CTATTTTAGTTTGAATAGTAAAAAGTGACTTTATATTTTGAATATTTCAAATTAAAA
1 CTATTTAACTTTGAATAGTAAAAAGTGAATTTATATTTTGAATATTTCAAATTAAAA
1391610 GGTATTATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 43 0.86
64 4 0.08
65 3 0.06
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (63 bp):
CTATTTAACTTTGAATAGTAAAAAGTGAATTTATATTTTGAATATTTCAAATTAAAATAATAT
Found at i:1401226 original size:18 final size:18
Alignment explanation
Indices: 1401203--1401237 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1401193 ACATGTAGAC
1401203 TGAGA-TATGATAGTCATT
1 TGAGATTATGATA-TCATT
1401221 TGAGATTATGATATCAT
1 TGAGATTATGATATCAT
1401238 ATTTTATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (18 bp):
TGAGATTATGATATCATT
Found at i:1405315 original size:21 final size:21
Alignment explanation
Indices: 1405285--1405326 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1405275 GGTATTAATC
1405285 TAGTCCAAGTTCGCATTGCGA
1 TAGTCCAAGTTCGCATTGCGA
* *
1405306 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCCAAGTTCGCATTGCGA
1405327 ATCTGGAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (21 bp):
TAGTCCAAGTTCGCATTGCGA
Found at i:1406345 original size:18 final size:18
Alignment explanation
Indices: 1406322--1406368 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1406312 GTTTAAAAAA
1406322 TATTATTATTTAT-TTTAT
1 TATTATTATTTATGTTT-T
*
1406340 TATTATTATTAATGTTTT
1 TATTATTATTTATGTTTT
*
1406358 TATTAATATTT
1 TATTATTATTT
1406369 TTACAGACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TATTATTATTTATGTTTT
Found at i:1406348 original size:21 final size:21
Alignment explanation
Indices: 1406320--1406367 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1406310 GGGTTTAAAA
*
1406320 AATATTATT-ATTTATTTTATT
1 AATATTATTAATGT-TTTTATT
*
1406341 ATTATTATTAATGTTTTTATT
1 AATATTATTAATGTTTTTATT
1406362 AATATT
1 AATATT
1406368 TTTACAGACC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
AATATTATTAATGTTTTTATT
Found at i:1409943 original size:28 final size:27
Alignment explanation
Indices: 1409912--1409986 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 27
1409902 CAGTCAGAAC
1409912 AAAAAGAAAAAAAAGAAAAAAAACAAAG
1 AAAAA-AAAAAAAAGAAAAAAAACAAAG
*
1409940 AAAAAACAAAAAAGAAATAAAAACAAAG
1 AAAAAAAAAAAAAGAAA-AAAAACAAAG
* *
1409968 AAATAAAAACAAAGAAAAA
1 AAAAAAAAAAAAAGAAAAA
1409987 GGGACAAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 13 0.31
28 29 0.69
ACGTcount: A:0.84, C:0.05, G:0.08, T:0.03
Consensus pattern (27 bp):
AAAAAAAAAAAAAGAAAAAAAACAAAG
Found at i:1409944 original size:14 final size:14
Alignment explanation
Indices: 1409912--1409986 Score: 91
Period size: 14 Copynumber: 5.4 Consensus size: 14
1409902 CAGTCAGAAC
*
1409912 AAAAAGAAAAAAAAG
1 AAAAA-AAAACAAAG
1409927 -AAAAAAAACAAAG
1 AAAAAAAAACAAAG
1409940 AAAAAACAAA-AAAG
1 AAAAAA-AAACAAAG
*
1409954 AAATAAAAACAAAG
1 AAAAAAAAACAAAG
*
1409968 AAATAAAAACAAAG
1 AAAAAAAAACAAAG
1409982 AAAAA
1 AAAAA
1409987 GGGACAAGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
13 11 0.20
14 40 0.74
15 3 0.06
ACGTcount: A:0.84, C:0.05, G:0.08, T:0.03
Consensus pattern (14 bp):
AAAAAAAAACAAAG
Found at i:1414261 original size:3 final size:3
Alignment explanation
Indices: 1414248--1414282 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1414238 GGTTTAAAAA
*
1414248 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1414283 ATGTTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Done.