Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008298.1 Hibiscus syriacus cultivar Beakdansim tig00110984_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: 1334650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1054106 original size:15 final size:15
Alignment explanation
Indices: 1054075--1054114 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1054065 AGGGTGTAGG
*
1054075 GTTTAAGG-TTTATA
1 GTTTAAGGTTTTAAA
1054089 GTTTAAGGTTTTAAA
1 GTTTAAGGTTTTAAA
*
1054104 GTTTATGGTTT
1 GTTTAAGGTTT
1054115 AGAGTTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (15 bp):
GTTTAAGGTTTTAAA
Found at i:1054156 original size:22 final size:21
Alignment explanation
Indices: 1054062--1054157 Score: 70
Period size: 22 Copynumber: 4.5 Consensus size: 21
1054052 TGGTTTGTGA
* *
1054062 TTTAGGGTGTAGGGTTTAAGG
1 TTTATGGTCTAGGGTTTAAGG
* * * *
1054083 TTTATAGTTTAAGGTTTTAAAG
1 TTTATGGTCT-AGGGTTTAAGG
* * *
1054105 TTTATGGTTTAGAGTTT-AGTA
1 TTTATGGTCTAGGGTTTAAG-G
1054126 TTTA-GGTCTAGGGTTTAAGG
1 TTTATGGTCTAGGGTTTAAGG
1054146 TTTCATGGTCTA
1 TTT-ATGGTCTA
1054158 AGGTGTGTAG
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
20 14 0.25
21 19 0.33
22 24 0.42
ACGTcount: A:0.23, C:0.03, G:0.28, T:0.46
Consensus pattern (21 bp):
TTTATGGTCTAGGGTTTAAGG
Found at i:1054416 original size:15 final size:14
Alignment explanation
Indices: 1054407--1054448 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
1054397 TAAGTCTTAG
1054407 GGTTTAAAGTTTAA
1 GGTTTAAAGTTTAA
*
1054421 GGTTT-AAGGTTAA
1 GGTTTAAAGTTTAA
*
1054434 GGTTTAAGGTTTAA
1 GGTTTAAAGTTTAA
1054448 G
1 G
1054449 AGTTCATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (14 bp):
GGTTTAAAGTTTAA
Found at i:1054435 original size:6 final size:7
Alignment explanation
Indices: 1054407--1054487 Score: 83
Period size: 7 Copynumber: 11.3 Consensus size: 7
1054397 TAAGTCTTAG
1054407 GGTTTAA
1 GGTTTAA
*
1054414 AGTTTAA
1 GGTTTAA
1054421 GGTTTAA
1 GGTTTAA
1054428 GG-TTAA
1 GGTTTAA
1054434 GGTTTAA
1 GGTTTAA
1054441 GGTTTAA
1 GGTTTAA
* *
1054448 GAGTTCAT
1 G-GTTTAA
1054456 GGTTTATA
1 GGTTTA-A
1054464 GGTTTAA
1 GGTTTAA
* *
1054471 GTTTTTAG
1 G-GTTTAA
1054479 GGTTTAA
1 GGTTTAA
1054486 GG
1 GG
1054488 CTTATGATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
6 6 0.10
7 38 0.63
8 16 0.27
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.43
Consensus pattern (7 bp):
GGTTTAA
Found at i:1054438 original size:20 final size:21
Alignment explanation
Indices: 1054410--1054471 Score: 81
Period size: 20 Copynumber: 2.9 Consensus size: 21
1054400 GTCTTAGGGT
*
1054410 TTAAAGTTTAAGGTTTAAG-G
1 TTAAGGTTTAAGGTTTAAGAG
1054430 TTAAGGTTTAAGGTTTAAGAG
1 TTAAGGTTTAAGGTTTAAGAG
*
1054451 TTCATGGTTTATAGGTTTAAG
1 TT-AAGGTTTA-AGGTTTAAG
1054472 TTTTTAGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.49
21 3 0.08
22 7 0.19
23 9 0.24
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.42
Consensus pattern (21 bp):
TTAAGGTTTAAGGTTTAAGAG
Found at i:1054479 original size:14 final size:15
Alignment explanation
Indices: 1054395--1054486 Score: 54
Period size: 15 Copynumber: 6.4 Consensus size: 15
1054385 GGTTTTATAA
*
1054395 TTTAAGTCT-TAGGG
1 TTTAAGTTTATAGGG
1054409 TTTAAAGTTTA-A-GG
1 TTT-AAGTTTATAGGG
*
1054423 TTTAAGGTTA-A-GG
1 TTTAAGTTTATAGGG
*
1054436 TTTAAGGTTTA-AGAG
1 TTTAA-GTTTATAGGG
* *
1054451 TTCATGGTTTATA-GG
1 TTTA-AGTTTATAGGG
*
1054466 TTTAAGTTTTTAGGG
1 TTTAAGTTTATAGGG
1054481 TTTAAG
1 TTTAAG
1054487 GCTTATGATT
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
13 14 0.23
14 19 0.31
15 27 0.44
16 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.26, T:0.45
Consensus pattern (15 bp):
TTTAAGTTTATAGGG
Found at i:1054534 original size:29 final size:29
Alignment explanation
Indices: 1054474--1054541 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1054464 GGTTTAAGTT
* * *
1054474 TTTAGGGTTTAAGGCTTATGATTTTAGGG
1 TTTAGGTTTTAAGGCTTAGGATTTTAGCG
** *
1054503 TTTAGGTTTTAAGTTTTAGGATTTTATCG
1 TTTAGGTTTTAAGGCTTAGGATTTTAGCG
1054532 TTTATGGTTT
1 TTTA-GGTTT
1054542 AGGTTTTTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.19, C:0.03, G:0.25, T:0.53
Consensus pattern (29 bp):
TTTAGGTTTTAAGGCTTAGGATTTTAGCG
Found at i:1056916 original size:7 final size:7
Alignment explanation
Indices: 1056914--1056941 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1056904 TCTAAAAATT
1056914 AAAATAA
1 AAAATAA
1056921 AAAATAA
1 AAAATAA
1056928 AAAATAA
1 AAAATAA
1056935 AAAATAA
1 AAAATAA
1056942 CTCTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:1058025 original size:22 final size:22
Alignment explanation
Indices: 1057997--1058040 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1057987 ATAAGGTGTT
1057997 GGGAGCTTTACACCTTGTCCAA
1 GGGAGCTTTACACCTTGTCCAA
1058019 GGGAGCTTTACACCTTGTCCAA
1 GGGAGCTTTACACCTTGTCCAA
1058041 CTTCCATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (22 bp):
GGGAGCTTTACACCTTGTCCAA
Found at i:1059381 original size:21 final size:21
Alignment explanation
Indices: 1059351--1059392 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1059341 TTCTTCCCAT
1059351 CCCCAGTTCACTCTTCTTCAC
1 CCCCAGTTCACTCTTCTTCAC
*
1059372 CCCCATTTCACTCTTCTTCAC
1 CCCCAGTTCACTCTTCTTCAC
1059393 TCATTTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.48, G:0.02, T:0.36
Consensus pattern (21 bp):
CCCCAGTTCACTCTTCTTCAC
Found at i:1060345 original size:19 final size:19
Alignment explanation
Indices: 1060321--1060365 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1060311 TAGAATTTAG
*
1060321 GGTTTATGATTAGGATTAA
1 GGTTTATGATTAAGATTAA
1060340 GGTTTATGATTAAGATTAA
1 GGTTTATGATTAAGATTAA
1060359 GGTTTAT
1 GGTTTAT
1060366 TGTTTATGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.44
Consensus pattern (19 bp):
GGTTTATGATTAAGATTAA
Found at i:1060402 original size:21 final size:22
Alignment explanation
Indices: 1060367--1060408 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1060357 AAGGTTTATT
* *
1060367 GTTTATGGTTTTAGGGTTTAAG
1 GTTTATGGATTTAGGATTTAAG
1060389 GTTTA-GGATTTAGGATTTAA
1 GTTTATGGATTTAGGATTTAA
1060409 TGTTAGAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.48
Consensus pattern (22 bp):
GTTTATGGATTTAGGATTTAAG
Found at i:1065130 original size:16 final size:16
Alignment explanation
Indices: 1065106--1065137 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1065096 TATCGTCGAC
*
1065106 CAAATTTTACTATTCA
1 CAAAATTTACTATTCA
1065122 CAAAATTTACTATTCA
1 CAAAATTTACTATTCA
1065138 TGTGCATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (16 bp):
CAAAATTTACTATTCA
Found at i:1068654 original size:22 final size:22
Alignment explanation
Indices: 1068606--1068648 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1068596 AAAGGTTTAG
1068606 AGTTTTAAGGTTTAGTATATAA
1 AGTTTTAAGGTTTAGTATATAA
*
1068628 AGTTTT-AGAGTTTATTATATA
1 AGTTTTAAG-GTTTAGTATATA
1068649 TGGTTTATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (22 bp):
AGTTTTAAGGTTTAGTATATAA
Found at i:1068778 original size:14 final size:14
Alignment explanation
Indices: 1068761--1068797 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1068751 AGTTTAAGAG
1068761 TTAGGGTTTAGAT-T
1 TTAGGGTTT-GATGT
1068775 TTAGGGTTTGATGT
1 TTAGGGTTTGATGT
1068789 TTAGGGTTT
1 TTAGGGTTT
1068798 TAGTATTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.51
Consensus pattern (14 bp):
TTAGGGTTTGATGT
Found at i:1068800 original size:22 final size:21
Alignment explanation
Indices: 1068773--1068843 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
1068763 AGGGTTTAGA
1068773 TTTTAGGGTTTGATGTTTAGGG
1 TTTTAGGGTTTGA-GTTTAGGG
** *
1068795 TTTTAGTATTTAGAATTTAGGG
1 TTTTAGGGTTT-GAGTTTAGGG
* * *
1068817 TTTTATGGCTTAAGGTTTAGGG
1 TTTTAGGGTTTGA-GTTTAGGG
1068839 TTTTA
1 TTTTA
1068844 TTTCAAAGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
21 1 0.03
22 35 0.92
23 2 0.05
ACGTcount: A:0.20, C:0.01, G:0.28, T:0.51
Consensus pattern (21 bp):
TTTTAGGGTTTGAGTTTAGGG
Found at i:1069034 original size:29 final size:29
Alignment explanation
Indices: 1069002--1069058 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1068992 GATTTTTATG
1069002 GTTTATGATTAT-AG-GTTTCAGGGTTTAGT
1 GTTTATG-TTATAAGTGTTT-AGGGTTTAGT
*
1069031 GTTTATGTTGTAAGTGTTTAGGGTTTAG
1 GTTTATGTTATAAGTGTTTAGGGTTTAG
1069059 GGTTCATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 3 0.12
29 18 0.72
30 4 0.16
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.49
Consensus pattern (29 bp):
GTTTATGTTATAAGTGTTTAGGGTTTAGT
Found at i:1070500 original size:25 final size:25
Alignment explanation
Indices: 1070451--1070500 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1070441 GGGAATGAAT
*
1070451 TTATAAAACTTTAAAGAGACGAAAC
1 TTATAAAACTTTAAAGAGACAAAAC
*
1070476 TTATAAAACTTTAAAGAGGCAAAAC
1 TTATAAAACTTTAAAGAGACAAAAC
1070501 AAGTTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (25 bp):
TTATAAAACTTTAAAGAGACAAAAC
Found at i:1075939 original size:202 final size:201
Alignment explanation
Indices: 1075239--1076575 Score: 1918
Period size: 202 Copynumber: 6.7 Consensus size: 201
1075229 ATAATGTATC
* * * ***
1075239 AAAACATCGAAA-TCCATAATTATAATATAATAGATAATTTTT-AATGTAATTAGTATAAATATA
1 AAAATATCGAAACT-CATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
** * * *
1075302 TTGATTTTATGTA-AGAATATGTCTACATAATGTATCAAAACTTTTTAAGTTTGTGTCGATA-TT
65 CCGGTTTTATG-AGAGAATATGTCTACATAATGTATCGACACTTTTTAAGTTTGTGTCGATACTT
* * * * *
1075365 TCTTGTCTAGAATGAATGCCCAAACTA-GTGCACGTATCAAGTGTCGATACATTTATGAAAAGTA
129 T-TTGTCCAGAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTA
*
1075429 TCGATCGCA
193 TCGATCCCA
*
1075438 AAAACATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
1 AAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
* * *
1075503 CGGTTTTAAGAGAGAATATGTCTACATAATGTATCGAAACTTTTTATGTTTGTGTCGATACTTTT
66 CGGTTTTATGAGAGAATATGTCTACATAATGTATCGACACTTTTTAAGTTTGTGTCGATACTTTT
* *
1075568 TGACCAGAATGAATGCTCAAACTAGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTATCG
131 TGTCCAGAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTATCG
1075633 ATCCCA
196 ATCCCA
*
1075639 AAAATATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
1 AAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
* *
1075704 TGGTTTTATGAGAGAATATGTCTACATAATGTATCAACACTTTTTAAGTTTGTGTCGATACTTTT
66 CGGTTTTATGAGAGAATATGTCTACATAATGTATCGACACTTTTTAAGTTTGTGTCGATACTTTT
* * * *
1075769 CGTCTAGAATGAATGCCCAAACTAGGTGCACGTATAAAGTGTCGATATATTTATAAAAAAATATC
131 TGTCCAGAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCGATATATTTAT-AAAAAGTATC
*
1075834 GATCCTA
195 GATCCCA
** *
1075841 AAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATAAAACCAGTATAAATATAC
1 AAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
*
1075906 CGGTTTTATGAGAGAATA-GATCTACATAATGTATCGACATTTTTTAAGTTTGTGTCGATACTTT
66 CGGTTTTATGAGAGAATATG-TCTACATAATGTATCGACACTTTTTAAGTTTGTGTCGATACTTT
* ** * * * *
1075970 TCG-CCAGAACAAATTCCCGAACTAGGTACACACATAAAGTGTCGATATATTTATAAAAAGTATC
130 TTGTCCAGAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTATC
1076034 GATCCCA
195 GATCCCA
* *
1076041 AAAATATCGAAACACATAATTATAATGTAATAGGTAATTTTTTAATGTAACCGGTATAAATATAC
1 AAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
* * *
1076106 CAGTTTTATGAGAGGATATGTCTACATAATGTATCGATACTTTTTTAAGTTTGTGTCGATACTTT
66 CGGTTTTATGAGAGAATATGTCTACATAATGTATCGACAC-TTTTTAAGTTTGTGTCGATACTTT
* * *
1076171 TTGTCCAGAATAAATACTCAAACTAGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTATC
130 TTGTCCAGAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTATC
*
1076236 GATCCTA
195 GATCCCA
* * *
1076243 AAAATA-CTAAAACCCATTATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
1 AAAATATC-GAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
* *
1076307 CCGGTTTTATGAGATAATAGGTCTACATAATGTATCGACACTTTTTTAAGTTTGTGTCGATACTT
65 CCGGTTTTATGAGAGAATATGTCTACATAATGTATCGACAC-TTTTTAAGTTTGTGTCGATACTT
* * * *
1076372 TTTATCCAGAATGAATGCCCAAACTAGGTGCACACATAAAGTGTCGATACATTTATAAAAAATAT
129 TTTGTCCAGAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTAT
1076437 CGATCCCA
194 CGATCCCA
* * * *
1076445 AAAACT-TCAAAAATCATAATTATAATGTAATAGGTACTTTTTTAATGTAACCGGTATAAATATA
1 AAAA-TATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATA
* * * *
1076509 TCGGTTTTAAGAGAGAATATGTGTACATAATGTATCGACACTTTTTATGTTTGTGTCGATACTTT
65 CCGGTTTTATGAGAGAATATGTCTACATAATGTATCGACACTTTTTAAGTTTGTGTCGATACTTT
1076574 TT
130 TT
1076576 TAAATTTCGC
Statistics
Matches: 1030, Mismatches: 95, Indels: 24
0.90 0.08 0.02
Matches are distributed among these distances:
199 39 0.04
200 203 0.20
201 313 0.30
202 473 0.46
203 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (201 bp):
AAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
CGGTTTTATGAGAGAATATGTCTACATAATGTATCGACACTTTTTAAGTTTGTGTCGATACTTTT
TGTCCAGAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTATCG
ATCCCA
Found at i:1076090 original size:402 final size:400
Alignment explanation
Indices: 1075239--1076575 Score: 1956
Period size: 402 Copynumber: 3.3 Consensus size: 400
1075229 ATAATGTATC
* * * ***
1075239 AAAACATCGAAATC-CATAATTATAATATAATAGATAA-TTTTTAATGTAATTAGTATAAATATA
1 AAAATATCGAAA-CACATAATTATAATGTAATAGGTAATTTTTTAATGTAACCGGTATAAATATA
* * *
1075302 TTGATTTTATGTA-AGAATATGTCTACATAATGTATCAAAACTTTTTAAGTTTGTGTCGATA-TT
65 CTGGTTTTATG-AGAGAATATGTCTACATAATGTATCAACACTTTTTAAGTTTGTGTCGATACTT
* * *
1075365 TCTTGTCTAGAATGAATGCCCAAACTA-GTGCACGTATCAAGTGTCGATACATTTATGAAAAGTA
129 T-TTGTCTAGAATGAATGCCCAAACTAGGTGCACGTATAAAGTGTCGATATATTTATAAAAAGTA
*
1075429 TCGATCGC-AAAAACATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGT
193 TCGATC-CTAAAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGT
* * * *
1075493 ATAAATATACCGGTTTTAAGAGAGAATATGTCTACATAATGTATCGAAACTTTTTATGTTTGTGT
257 ATAAATATACCGGTTTTATGAGAGAATA-GTCTACATAATGTATCGACATTTTTTAAGTTTGTGT
* * *
1075558 CGATACTTTTTGACCAGAATGAATGCTCAAACTAGGTGCACGCATAAAGTGTCGATATATTTATA
321 CGATACTTTTAG-CCAGAATGAATGCCCAAACTAGGTGCACACATAAAGTGTCGATATATTTATA
1075623 AAAAGTATCGATCCCA
385 AAAAGTATCGATCCCA
* *
1075639 AAAATATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATAC
1 AAAATATCGAAACACATAATTATAATGTAATAGGTAATTTTTTAATGTAACCGGTATAAATATAC
1075704 TGGTTTTATGAGAGAATATGTCTACATAATGTATCAACACTTTTTAAGTTTGTGTCGATACTTTT
66 TGGTTTTATGAGAGAATATGTCTACATAATGTATCAACACTTTTTAAGTTTGTGTCGATACTTTT
* *
1075769 CGTCTAGAATGAATGCCCAAACTAGGTGCACGTATAAAGTGTCGATATATTTATAAAAAAATATC
131 TGTCTAGAATGAATGCCCAAACTAGGTGCACGTATAAAGTGTCGATATATTTAT-AAAAAGTATC
** *
1075834 GATCCTAAAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATAAAACCAGTATA
195 GATCCTAAAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATA
1075899 AATATACCGGTTTTATGAGAGAATAGATCTACATAATGTATCGACATTTTTTAAGTTTGTGTCGA
260 AATATACCGGTTTTATGAGAGAATAG-TCTACATAATGTATCGACATTTTTTAAGTTTGTGTCGA
* ** * * *
1075964 TACTTTTCGCCAGAACAAATTCCCGAACTAGGTACACACATAAAGTGTCGATATATTTATAAAAA
324 TACTTTTAGCCAGAATGAATGCCCAAACTAGGTGCACACATAAAGTGTCGATATATTTATAAAAA
1076029 GTATCGATCCCA
389 GTATCGATCCCA
1076041 AAAATATCGAAACACATAATTATAATGTAATAGGTAATTTTTTAATGTAACCGGTATAAATATAC
1 AAAATATCGAAACACATAATTATAATGTAATAGGTAATTTTTTAATGTAACCGGTATAAATATAC
** * * *
1076106 CAGTTTTATGAGAGGATATGTCTACATAATGTATCGATACTTTTTTAAGTTTGTGTCGATACTTT
66 TGGTTTTATGAGAGAATATGTCTACATAATGTATCAACAC-TTTTTAAGTTTGTGTCGATACTTT
* * * * *
1076171 TTGTCCAGAATAAATACTCAAACTAGGTGCACGCATAAAGTGTCGATATATTTATAAAAAGTATC
130 TTGTCTAGAATGAATGCCCAAACTAGGTGCACGTATAAAGTGTCGATATATTTATAAAAAGTATC
* * *
1076236 GATCCTAAAAATA-CTAAAACCCATTATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTAT
195 GATCCTAAAAATATC-GAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTAT
*
1076300 AAATATACCGGTTTTATGAGATAATAGGTCTACATAATGTATCGACACTTTTTTAAGTTTGTGTC
259 AAATATACCGGTTTTATGAGAGAATA-GTCTACATAATGTATCGACA-TTTTTTAAGTTTGTGTC
* *
1076365 GATACTTTTTATCCAGAATGAATGCCCAAACTAGGTGCACACATAAAGTGTCGATACATTTATAA
322 GATAC-TTTTAGCCAGAATGAATGCCCAAACTAGGTGCACACATAAAGTGTCGATATATTTATAA
*
1076430 AAAATATCGATCCCA
386 AAAGTATCGATCCCA
* *
1076445 AAAACT-TC-AAAAATCATAATTATAATGTAATAGGTACTTTTTTAATGTAACCGGTATAAATAT
1 AAAA-TATCGAAACA-CATAATTATAATGTAATAGGTAATTTTTTAATGTAACCGGTATAAATAT
* * * *
1076508 A-TCGGTTTTAAGAGAGAATATGTGTACATAATGTATCGACACTTTTTATGTTTGTGTCGATACT
64 ACT-GGTTTTATGAGAGAATATGTCTACATAATGTATCAACACTTTTTAAGTTTGTGTCGATACT
1076572 TTTT
128 TTTT
1076576 TAAATTTCGC
Statistics
Matches: 851, Mismatches: 70, Indels: 29
0.90 0.07 0.03
Matches are distributed among these distances:
399 1 0.00
400 33 0.04
401 103 0.12
402 300 0.35
403 259 0.30
404 154 0.18
405 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (400 bp):
AAAATATCGAAACACATAATTATAATGTAATAGGTAATTTTTTAATGTAACCGGTATAAATATAC
TGGTTTTATGAGAGAATATGTCTACATAATGTATCAACACTTTTTAAGTTTGTGTCGATACTTTT
TGTCTAGAATGAATGCCCAAACTAGGTGCACGTATAAAGTGTCGATATATTTATAAAAAGTATCG
ATCCTAAAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAA
ATATACCGGTTTTATGAGAGAATAGTCTACATAATGTATCGACATTTTTTAAGTTTGTGTCGATA
CTTTTAGCCAGAATGAATGCCCAAACTAGGTGCACACATAAAGTGTCGATATATTTATAAAAAGT
ATCGATCCCA
Found at i:1080561 original size:17 final size:18
Alignment explanation
Indices: 1080539--1080574 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1080529 GTGCACTAAG
1080539 AGTGCA-TCGATGCTTCA
1 AGTGCATTCGATGCTTCA
*
1080556 AGTGCATTCGATGTTTCA
1 AGTGCATTCGATGCTTCA
1080574 A
1 A
1080575 AATAGCCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (18 bp):
AGTGCATTCGATGCTTCA
Found at i:1081697 original size:18 final size:18
Alignment explanation
Indices: 1081674--1081719 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
1081664 AGGCATTTGA
1081674 TCCTCTCGCT-GTGCTTAT
1 TCCTCT-GCTCGTGCTTAT
1081692 TCCTCTGCTCGTGCTTAT
1 TCCTCTGCTCGTGCTTAT
1081710 TCCTCGTGCT
1 TCCTC-TGCT
1081720 GTTTTGGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.04, C:0.35, G:0.17, T:0.43
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTAT
Found at i:1083333 original size:23 final size:22
Alignment explanation
Indices: 1083294--1083365 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
1083284 GGGGTGTCGA
*
1083294 TTCCCCTACAAGGGGGAATCGG
1 TTCCCCTTCAAGGGGGAATCGG
1083316 TTCCCCTTCAAAGGGGGAATCGG
1 TTCCCCTTC-AAGGGGGAATCGG
* *
1083339 TTCCCCTTCAAGGGGGTATCGA
1 TTCCCCTTCAAGGGGGAATCGG
1083361 TTCCC
1 TTCCC
1083366 TCTGCACTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 24 0.52
23 22 0.48
ACGTcount: A:0.19, C:0.29, G:0.28, T:0.24
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGAATCGG
Found at i:1087220 original size:22 final size:21
Alignment explanation
Indices: 1087178--1087217 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1087168 GAGTTTGTTT
*
1087178 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1087199 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1087218 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1089212 original size:65 final size:64
Alignment explanation
Indices: 1089079--1089224 Score: 172
Period size: 65 Copynumber: 2.2 Consensus size: 64
1089069 TGCACTAAGA
* *
1089079 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCATCAGTGCATCGATGCATGGTAT
* * *
1089144 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCAT-AGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-A-TAAAATCATCAGTGCATCGATGCATGG-T
*
1089207 TT
63 AT
1089209 GTGCATC-AGTGCATCA
1 GTGCATCGA-TGCATCA
1089225 CTCTGAAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
63 3 0.04
64 18 0.26
65 49 0.70
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCATCAGTGCATCGATGCATGGTAT
Found at i:1091246 original size:198 final size:199
Alignment explanation
Indices: 1090783--1091278 Score: 635
Period size: 200 Copynumber: 2.5 Consensus size: 199
1090773 AATATGTATC
* * * * *
1090783 GATACATTTTCTAAAAGTATCGACCCCAAAAATATCGAAACCAATAATTATAATGTAATAGGTAT
1 GATACA-TTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
* * * *
1090848 ATTAACAATGTAACCAGTATAAATATACCGGTTAATTACAAAACAGGCAAACATAATGTATCGAC
65 ATTTACAATGTAACCGGTATAAATATACCGATTAATGACAAAACAGGCAAACATAATGTATCGAC
* *
1090913 ACTTTTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACACATAAA
130 ACTTTTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACACATAAA
1090978 GTGCT
195 GTGCT
* * *
1090983 GATACATTTATTAAAAGTATCGATCCTAAAAACATCGAAACCGAAAATTATGATGTAATAGGTAA
1 GATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
* * * * *
1091048 ATTTACAATATAACCGGTATAAATATACCGATTATATGAGAGAATAGATC-AACATAATGTATCG
65 ATTTACAATGTAACCGGTATAAATATACCGATTA-ATGACAAAACAG-GCAAACATAATGTATCG
* * * *
1091112 ACACTTTTTAAATATGTGTCGATACTT-TTTTCTAGAATGAATGCCC-AACGAGGTGCACGCATA
128 ACACTTTTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACACATA
1091175 AAGTG-T
193 AAGTGCT
*
1091181 CGATACATTTA-AAATTA-TATCGATCCCAAAAACATCGAAAACGATAATTATAATGTAATAGGT
1 -GATACATTTATAAA--AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
* * * *
1091244 AAATTTGCAATGTTATCGGTATAAATAAACCGATT
63 AAATTTACAATGTAACCGGTATAAATATACCGATT
1091279 TAGTTAGAAA
Statistics
Matches: 258, Mismatches: 32, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
197 3 0.01
198 73 0.28
199 35 0.14
200 100 0.39
201 46 0.18
202 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (199 bp):
GATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAA
TTTACAATGTAACCGGTATAAATATACCGATTAATGACAAAACAGGCAAACATAATGTATCGACA
CTTTTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACACATAAAG
TGCT
Found at i:1091396 original size:23 final size:23
Alignment explanation
Indices: 1091370--1091421 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1091360 TCCGGTTAAA
**
1091370 TACCTATTTTATTATATAAGAGC
1 TACCTATTACATTATATAAGAGC
*
1091393 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGAGC
1091416 TACCTA
1 TACCTA
1091422 ATATGTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAGAGC
Found at i:1091417 original size:87 final size:86
Alignment explanation
Indices: 1091297--1091457 Score: 268
Period size: 87 Copynumber: 1.9 Consensus size: 86
1091287 AAATAGGTCA
* *
1091297 ATATAAGCGCTACCTATACATTATATAAACGCTACCTAATATGTTATTGTACTTCATAATATTTC
1 ATATAAGAGCTACCTATACATTATATAAACGCTACCTAATATGTTATTGAACTTCATAATATTTC
1091362 CGGTTAAATACCTATTTTATT
66 CGGTTAAATACCTATTTTATT
* * *
1091383 ATATAAGAGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGAACTTGATGATATTT
1 ATATAAGAGCTACCTA-TACATTATATAAACGCTACCTAATATGTTATTGAACTTCATAATATTT
1091448 CCGGTTAAAT
65 CCGGTTAAAT
1091458 GATACAACAT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
86 15 0.22
87 54 0.78
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (86 bp):
ATATAAGAGCTACCTATACATTATATAAACGCTACCTAATATGTTATTGAACTTCATAATATTTC
CGGTTAAATACCTATTTTATT
Found at i:1092668 original size:89 final size:89
Alignment explanation
Indices: 1092514--1092679 Score: 271
Period size: 89 Copynumber: 1.9 Consensus size: 89
1092504 CCTAACACAC
*
1092514 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
*
1092579 TTTAATTAATTAGAATTTAATAAT
66 TATAATTAATTAGAATTTAATAAT
* *
1092603 CCTTTTATATCCAAGTTTCCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAA-ATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATAT
*
1092667 ATATATTTAATTA
65 ATATAATTAATTA
1092680 ATTGAAATTA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
89 47 0.66
90 24 0.34
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
TATAATTAATTAGAATTTAATAAT
Found at i:1092679 original size:23 final size:22
Alignment explanation
Indices: 1092652--1092695 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1092642 TATTATTTCA
*
1092652 AATTAATTAAAATATATATATTT
1 AATTAATTAAAAT-TAAATATTT
*
1092675 AATTAATTGAAATTAAATATT
1 AATTAATTAAAATTAAATATT
1092696 CGGGATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATTAATTAAAATTAAATATTT
Found at i:1099657 original size:21 final size:21
Alignment explanation
Indices: 1099631--1099688 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
1099621 TTTTGACTTG
1099631 GAGTATCGATACTGCCAAAGA
1 GAGTATCGATACTGCCAAAGA
1099652 GAGTATCGATACTGCCAAAGA
1 GAGTATCGATACTGCCAAAGA
1099673 GAGTATCGATACTGCC
1 GAGTATCGATACTGCC
1099689 CCTACAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (21 bp):
GAGTATCGATACTGCCAAAGA
Found at i:1099718 original size:21 final size:21
Alignment explanation
Indices: 1099692--1099745 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1099682 TACTGCCCCT
*
1099692 ACAATATCGATACTCAGGGTA
1 ACAATATCAATACTCAGGGTA
1099713 ACAATATCAATACTCAGGGTA
1 ACAATATCAATACTCAGGGTA
1099734 ACAATATCAATA
1 ACAATATCAATA
1099746 TTGTTCTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (21 bp):
ACAATATCAATACTCAGGGTA
Found at i:1102702 original size:28 final size:28
Alignment explanation
Indices: 1102662--1102716 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1102652 GAAGAAGAAC
1102662 AAAATCTAGTTACACAAAACAGAGGAAT
1 AAAATCTAGTTACACAAAACAGAGGAAT
1102690 AAAATCTAGTTACACAAAACAGAGGAA
1 AAAATCTAGTTACACAAAACAGAGGAA
1102717 AGTAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.16
Consensus pattern (28 bp):
AAAATCTAGTTACACAAAACAGAGGAAT
Found at i:1106743 original size:60 final size:61
Alignment explanation
Indices: 1106658--1106808 Score: 170
Period size: 60 Copynumber: 2.5 Consensus size: 61
1106648 ACCCATAATC
* * *
1106658 TTTTAAACATCTT-AATTTATCCCCTAAACTAC-GACTATTATTTTAAATTAGTC-CTTAAA-A
1 TTTTAAATAT-TTCAATTTAT-CCCTAAACTACTAACTATTATTCTAAATTAGTCTC-TAAACA
* *
1106718 TTTTAAATATTTCAATTCTATCCCTAAACT-CTAACTTTTATTCTAAATTAGTCTCTAAACT
1 TTTTAAATATTTCAATT-TATCCCTAAACTACTAACTATTATTCTAAATTAGTCTCTAAACA
1106779 TTTTAAATATTTCAATTTCAT-CCTAAACTA
1 TTTTAAATATTTCAATTT-ATCCCTAAACTA
1106809 TATGTATATA
Statistics
Matches: 79, Mismatches: 5, Indels: 13
0.81 0.05 0.13
Matches are distributed among these distances:
59 3 0.04
60 53 0.67
61 23 0.29
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (61 bp):
TTTTAAATATTTCAATTTATCCCTAAACTACTAACTATTATTCTAAATTAGTCTCTAAACA
Found at i:1112020 original size:6 final size:6
Alignment explanation
Indices: 1112011--1112035 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1112001 GGGATGATAA
1112011 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
1112036 AAACCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:1112135 original size:12 final size:13
Alignment explanation
Indices: 1112099--1112142 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
1112089 GCCCCGATTA
1112099 CCCGATTACCCGC
1 CCCGATTACCCGC
1112112 CCCGATTACCCGC
1 CCCGATTACCCGC
*
1112125 CCCGA-TACCCGA
1 CCCGATTACCCGC
1112137 CCCGAT
1 CCCGAT
1112143 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:1112196 original size:32 final size:33
Alignment explanation
Indices: 1112160--1112245 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 33
1112150 AAAAATAATT
*
1112160 ATTTATATATATATATA-ATATTAATAAATTTA
1 ATTTAAATATATATATATATATTAATAAATTTA
* * * *
1112192 ATTTAAATA-AAAAATATATATTTATATATTTA
1 ATTTAAATATATATATATATATTAATAAATTTA
1112224 ATTTAAATATATATATATATAT
1 ATTTAAATATATATATATATAT
1112246 ACCCGACCCG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 5 0.11
32 30 0.67
33 10 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
ATTTAAATATATATATATATATTAATAAATTTA
Found at i:1112276 original size:24 final size:24
Alignment explanation
Indices: 1112244--1112298 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
1112234 ATATATATAT
* * *
1112244 ATACCCGACCCGATTCTCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
1112268 ATACCCGACCCAATACCCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
1112292 ATACCCG
1 ATACCCG
1112299 TTTAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:1112281 original size:12 final size:12
Alignment explanation
Indices: 1112244--1112298 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
1112234 ATATATATAT
*
1112244 ATACCCGACCCG
1 ATACCCGACCCA
* * *
1112256 ATTCTCGGCCCA
1 ATACCCGACCCA
1112268 ATACCCGACCCA
1 ATACCCGACCCA
*
1112280 ATACCCGGCCCA
1 ATACCCGACCCA
1112292 ATACCCG
1 ATACCCG
1112299 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.25, C:0.47, G:0.15, T:0.13
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:1118770 original size:21 final size:21
Alignment explanation
Indices: 1118744--1118786 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1118734 CCGTTAGACA
*
1118744 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAAACGGTACCCCCTG
*
1118765 GGGGGGAAACTGTACCCCCTG
1 GGGGGGAAACGGTACCCCCTG
1118786 G
1 G
1118787 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.28, G:0.42, T:0.14
Consensus pattern (21 bp):
GGGGGGAAACGGTACCCCCTG
Found at i:1119238 original size:16 final size:17
Alignment explanation
Indices: 1119202--1119245 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1119192 TTAAAATTAG
1119202 ATATTATTTTTAAATAA
1 ATATTATTTTTAAATAA
*
1119219 ATA-TATTTTTACAAT-C
1 ATATTATTTTTA-AATAA
1119235 ATATTATTTTT
1 ATATTATTTTT
1119246 TACCTCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTATTTTTAAATAA
Found at i:1128590 original size:6 final size:6
Alignment explanation
Indices: 1128581--1128605 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1128571 GGGATGATAA
1128581 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
1128606 AAACCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:1128705 original size:12 final size:13
Alignment explanation
Indices: 1128669--1128712 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
1128659 GCCCCGATTA
1128669 CCCGATTACCCGC
1 CCCGATTACCCGC
1128682 CCCGATTACCCGC
1 CCCGATTACCCGC
*
1128695 CCCGA-TACCCGA
1 CCCGATTACCCGC
1128707 CCCGAT
1 CCCGAT
1128713 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:1128795 original size:23 final size:23
Alignment explanation
Indices: 1128746--1128803 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
1128736 ATATAATATT
*
1128746 AATAAATTTA-ATTTAAATAAAA
1 AATATATTTATATTTAAATAAAA
* *
1128768 AATATATTTATATTTAATTTAAA
1 AATATATTTATATTTAAATAAAA
* *
1128791 TATATATATATAT
1 AATATATTTATAT
1128804 ACCCGACCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 9 0.30
23 21 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATATATTTATATTTAAATAAAA
Found at i:1128828 original size:23 final size:24
Alignment explanation
Indices: 1128802--1128855 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
1128792 ATATATATAT
* *
1128802 ATACCCGACCC-ATTCTCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
1128825 ATACCCGACCCAATACCCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
1128849 ATACCCG
1 ATACCCG
1128856 TTTAAATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.26, C:0.48, G:0.13, T:0.13
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:1128838 original size:12 final size:12
Alignment explanation
Indices: 1128802--1128855 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
1128792 ATATATATAT
1128802 ATACCCGACCC-
1 ATACCCGACCCA
* * *
1128813 ATTCTCGGCCCA
1 ATACCCGACCCA
1128825 ATACCCGACCCA
1 ATACCCGACCCA
*
1128837 ATACCCGGCCCA
1 ATACCCGACCCA
1128849 ATACCCG
1 ATACCCG
1128856 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
11 8 0.23
12 27 0.77
ACGTcount: A:0.26, C:0.48, G:0.13, T:0.13
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:1135137 original size:22 final size:22
Alignment explanation
Indices: 1135110--1135153 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1135100 CCGTTAGACA
*
1135110 GGGGGGAATCGGTACCCCCTGG
1 GGGGGGAAACGGTACCCCCTGG
*
1135132 GGGGGGAAACTGTACCCCCTGG
1 GGGGGGAAACGGTACCCCCTGG
1135154 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.43, T:0.14
Consensus pattern (22 bp):
GGGGGGAAACGGTACCCCCTGG
Found at i:1135605 original size:16 final size:17
Alignment explanation
Indices: 1135569--1135612 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1135559 TTAAAATTAG
1135569 ATATTATTTTTAAATAA
1 ATATTATTTTTAAATAA
*
1135586 ATA-TATTTTTACAAT-C
1 ATATTATTTTTA-AATAA
1135602 ATATTATTTTT
1 ATATTATTTTT
1135613 TACCTCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTATTTTTAAATAA
Found at i:1167206 original size:94 final size:94
Alignment explanation
Indices: 1167045--1167232 Score: 313
Period size: 94 Copynumber: 2.0 Consensus size: 94
1167035 AAAGGTATTT
*
1167045 TAAAAGTAATCCACTTGAAAAGATGGTTTTAGGCATTGAGAAAACAACTAACATTTGTAGCAAGA
1 TAAAAGTAATCCACCTGAAAAGATGGTTTTAGGCATTGAGAAAACAACTAACATTTGTAGCAAGA
1167110 AACAACTATGGCACCTTCAATAGGTTGTG
66 AACAACTATGGCACCTTCAATAGGTTGTG
* * * **
1167139 TAAAAGTTATCCACCTGAAAAGATGGTTTTGGGCATTGGGAAAACTTCTAACATTTGTAGCAAGA
1 TAAAAGTAATCCACCTGAAAAGATGGTTTTAGGCATTGAGAAAACAACTAACATTTGTAGCAAGA
*
1167204 AACAACTATGGCATCTTCAATAGGTTGTG
66 AACAACTATGGCACCTTCAATAGGTTGTG
1167233 CTAATTGTTA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (94 bp):
TAAAAGTAATCCACCTGAAAAGATGGTTTTAGGCATTGAGAAAACAACTAACATTTGTAGCAAGA
AACAACTATGGCACCTTCAATAGGTTGTG
Found at i:1171363 original size:26 final size:26
Alignment explanation
Indices: 1171334--1171390 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1171324 GCTGAGGTAA
1171334 GCATCATGGTGTAGTCAGAGGGTTCT
1 GCATCATGGTGTAGTCAGAGGGTTCT
1171360 GCATCATGGTGTAGTCAGAGGGTTCT
1 GCATCATGGTGTAGTCAGAGGGTTCT
1171386 GCATC
1 GCATC
1171391 TTGGGATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (26 bp):
GCATCATGGTGTAGTCAGAGGGTTCT
Found at i:1171840 original size:20 final size:21
Alignment explanation
Indices: 1171801--1171842 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1171791 TATGGTACCA
* *
1171801 ATACTAAGCCTTTTAGTATCG
1 ATACTAAGCATTTGAGTATCG
1171822 ATACTAA-CATTTGAGTATCG
1 ATACTAAGCATTTGAGTATCG
1171842 A
1 A
1171843 CACTCACCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (21 bp):
ATACTAAGCATTTGAGTATCG
Found at i:1174242 original size:287 final size:282
Alignment explanation
Indices: 1173610--1174257 Score: 785
Period size: 283 Copynumber: 2.3 Consensus size: 282
1173600 TGGATAAAAT
* * * * *
1173610 ATAGGGATTAAATTGAAACAATT-TTAAATCGTAAATCT-AAATAAATATCAAATTGGACTAAAT
1 ATAGTGATCAAATTGAAACAATTGTAAAAT-GTAAAACTGAAATTAATATCAAATTGGACTAAAT
* * *
1173673 TGCATTCATTTGAAAAGTTGTTGAACAAAAGTTTACAAGGCTGAAGGTTATGATATAATTTATAG
65 TGCATTCATTT-AAAAATTGTTAAACAAAAGTTTACAAGGCTGAAGATTATGATATAATTTATAG
* *
1173738 GGTTTGAAATGAAATTTATAATGTGGTTTATAAGGTTTAGAGTAAAATACAAAATAGAAATAATT
129 GGTTTGAAATGAAATTTATAATGTGATTTATAAGGTTTAGAGTAAAATACAAAATAAAAATAATT
* * * *
1173803 ATGAGCTAGTTTTGGATAAAAATATTTTTAAGGACTAACTTGAATAAACATGAAATTATAAAGTG
194 ATGAGCTAGTTTTAGATAAAAATATTTTTAAGGACTAAATTAAATAAACATGAAATTATAAAGTA
1173868 AAATTTAAATAAATTAAACAACAC
259 AAATTTAAATAAATTAAACAACAC
* * * *
1173892 ACA-TGGATCAAATTAAAACAATTGTAAAATGTAAAGCTGGAATTAATATCAAATTGGACTAAAT
1 ATAGT-GATCAAATTGAAACAATTGTAAAATGTAAAACTGAAATTAATATCAAATTGGACTAAAT
* * * *
1173956 TGTATTCATTTAAAAATATAG-TAAAGAAAAGTTTA-TAGGTTTGAAGATTATGATATAATTTAT
65 TGCATTCATTTAAAAAT-T-GTTAAACAAAAGTTTACAAGG-CTGAAGATTATGATATAATTTAT
* *
1174019 AGGGTTTGAAATGAAATTTATGATGTGATTTAT-AGGATTTGGAGTAAATTATA-AAAATAAAAA
127 AGGGTTTGAAATGAAATTTATAATGTGATTTATAAGG-TTTAGAGTAAA--ATACAAAATAAAAA
* * * *
1174082 TAATTATGGGAC-ATTTTTAGATAAAAAAATATACTTTTAAGGATTAAATTAAATAAATATGAAA
189 TAATTATGAG-CTAGTTTTAGAT--AAAAATAT--TTTTAAGGACTAAATTAAATAAACATGAAA
**
1174146 TTATAAA-TAAAATTTAAATAAATTAAGGAACAC
249 TTATAAAGTAAAATTTAAATAAATTAAACAACAC
* * **
1174179 ATAGTGATCAAATTGGAACAATTGTAAAATGTAAAACTGAAATTAATATAAAATTAAACTAAATT
1 ATAGTGATCAAATTGAAACAATTGTAAAATGTAAAACTGAAATTAATATCAAATTGGACTAAATT
*
1174244 -CATTCATTTTAAAA
66 GCATTCATTTAAAAA
1174258 GTTTTAATTA
Statistics
Matches: 312, Mismatches: 39, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
282 36 0.12
283 113 0.36
284 27 0.09
285 4 0.01
286 20 0.06
287 78 0.25
288 34 0.11
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (282 bp):
ATAGTGATCAAATTGAAACAATTGTAAAATGTAAAACTGAAATTAATATCAAATTGGACTAAATT
GCATTCATTTAAAAATTGTTAAACAAAAGTTTACAAGGCTGAAGATTATGATATAATTTATAGGG
TTTGAAATGAAATTTATAATGTGATTTATAAGGTTTAGAGTAAAATACAAAATAAAAATAATTAT
GAGCTAGTTTTAGATAAAAATATTTTTAAGGACTAAATTAAATAAACATGAAATTATAAAGTAAA
ATTTAAATAAATTAAACAACAC
Found at i:1174363 original size:20 final size:22
Alignment explanation
Indices: 1174330--1174371 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1174320 ATAAAATTAA
*
1174330 TTTAATGATTATAAATA-AATT
1 TTTAATGATAATAAATATAATT
1174351 TTTAATG-TAATAAATATAATT
1 TTTAATGATAATAAATATAATT
1174372 ACTATAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTAATGATAATAAATATAATT
Found at i:1174436 original size:27 final size:27
Alignment explanation
Indices: 1174384--1174436 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1174374 TATAGAAGAA
* * *
1174384 AATTTATTAATTTAATGGTTAGAATTT
1 AATTTATTAATCTAATGATCAGAATTT
*
1174411 AATTTATTAATCTAATGATCATAATT
1 AATTTATTAATCTAATGATCAGAATT
1174437 AATAATTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (27 bp):
AATTTATTAATCTAATGATCAGAATTT
Found at i:1188059 original size:15 final size:17
Alignment explanation
Indices: 1188039--1188070 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1188029 TTCATATGAG
1188039 TGCTTTT-GTTC-TTCT
1 TGCTTTTAGTTCATTCT
1188054 TGCTTTTAGTTCATTCT
1 TGCTTTTAGTTCATTCT
1188071 CAGGATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.06, C:0.19, G:0.12, T:0.62
Consensus pattern (17 bp):
TGCTTTTAGTTCATTCT
Found at i:1190578 original size:84 final size:84
Alignment explanation
Indices: 1190431--1190595 Score: 222
Period size: 84 Copynumber: 2.0 Consensus size: 84
1190421 ATATACTCTC
* * * * *
1190431 TGACACACAATGTGTGTCATTTTCATTTATGATGGGGGCTTCAATGACACACAATGTAAGTCATA
1 TGACACACAATGTGTGTCATCTTAATTTATGACGAGGGCTTCAATGACACACAATGCAAGTCATA
* *
1190496 TATGCGTGTCATAAATTTA
66 AATGCGCGTCATAAATTTA
** * * *
1190515 TGACACACAATGTGTGTTGTCTTAATTTATGACGAGGGCTTCAATGACGCTCAATGCACGTCATA
1 TGACACACAATGTGTGTCATCTTAATTTATGACGAGGGCTTCAATGACACACAATGCAAGTCATA
1190580 AATGCGCGTCATAAAT
66 AATGCGCGTCATAAAT
1190596 GCGTGTCATA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (84 bp):
TGACACACAATGTGTGTCATCTTAATTTATGACGAGGGCTTCAATGACACACAATGCAAGTCATA
AATGCGCGTCATAAATTTA
Found at i:1190589 original size:13 final size:13
Alignment explanation
Indices: 1190567--1190617 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
1190557 AATGACGCTC
*
1190567 AATGCACGTCATA
1 AATGCGCGTCATA
1190580 AATGCGCGTCATA
1 AATGCGCGTCATA
*
1190593 AATGCGTGTCATA
1 AATGCGCGTCATA
*
1190606 AATGCTCGTCAT
1 AATGCGCGTCAT
1190618 CAAAAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:1192377 original size:25 final size:25
Alignment explanation
Indices: 1192343--1192394 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1192333 ATTTACATAG
1192343 CCTATTACATGTCATTCTTAGTATT
1 CCTATTACATGTCATTCTTAGTATT
1192368 CCTATTACATGTCATTCTTAGTATT
1 CCTATTACATGTCATTCTTAGTATT
1192393 CC
1 CC
1192395 CTGCAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (25 bp):
CCTATTACATGTCATTCTTAGTATT
Found at i:1198427 original size:32 final size:32
Alignment explanation
Indices: 1198354--1198430 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
1198344 AAAAAAAAAC
*
1198354 AGTTTAAGGACTTAAAACAAAAACAAAAACAT
1 AGTTTAAGGGCTTAAAACAAAAACAAAAACAT
*
1198386 AGTTTAAGGGCTTAAAATAAAAACAAAAACAT
1 AGTTTAAGGGCTTAAAACAAAAACAAAAACAT
1198418 AGTTTAAGGGCTT
1 AGTTTAAGGGCTT
1198431 TTTTTACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.23
Consensus pattern (32 bp):
AGTTTAAGGGCTTAAAACAAAAACAAAAACAT
Found at i:1205066 original size:78 final size:79
Alignment explanation
Indices: 1204913--1205074 Score: 186
Period size: 78 Copynumber: 2.1 Consensus size: 79
1204903 TTAATATAAG
* * *
1204913 ATTAAGGAATAATAGAAAATTGATGTAATCGAAAATATTATAAAAATATAAAATTATCGGTTTGA
1 ATTAAGGAACAATAGAAAATTGATGTAACCGAAAATATTATAAAAACATAAAATTATCGGTTTGA
*
1204978 CGTAATCT-AAAAT
66 CGCAATCTAAAAAT
* * * * * * *
1204991 ATTAAGGAACAGTAGAGAATTGGTGTAACCGAAAATGTTATAAAAAACATAATATTTTTGGTTAT
1 ATTAAGGAACAATAGAAAATTGATGTAACCGAAAATATTAT-AAAAACATAAAATTATCGGTT-T
1205056 G-CGCAA-CTAAAAAT
64 GACGCAATCTAAAAAT
1205070 ATTAA
1 ATTAA
1205075 TCTTTTTCTA
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
78 37 0.53
79 31 0.44
80 2 0.03
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.31
Consensus pattern (79 bp):
ATTAAGGAACAATAGAAAATTGATGTAACCGAAAATATTATAAAAACATAAAATTATCGGTTTGA
CGCAATCTAAAAAT
Found at i:1205224 original size:38 final size:39
Alignment explanation
Indices: 1205182--1205266 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 39
1205172 AATCTTTTTC
* *
1205182 TAACATTCTCGGTTG-AACAAAAAATATTATCAAGAATG
1 TAACATTCTCAGTTGCAACAAAAAATATTATCAAAAATG
* ** *
1205220 TAACATTTTCAGTTGCCAACCGAAAATATTATTAAAAATG
1 TAACATTCTCAGTTG-CAACAAAAAATATTATCAAAAATG
1205260 TAACATT
1 TAACATT
1205267 TTCGATTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 13 0.33
40 26 0.67
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (39 bp):
TAACATTCTCAGTTGCAACAAAAAATATTATCAAAAATG
Found at i:1206882 original size:7 final size:7
Alignment explanation
Indices: 1206870--1206898 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1206860 ATAAATAAAA
1206870 TTTATTT
1 TTTATTT
1206877 TTTATTT
1 TTTATTT
1206884 TTTATTT
1 TTTATTT
1206891 TTTATTT
1 TTTATTT
1206898 T
1 T
1206899 AGTTGATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:1207741 original size:36 final size:35
Alignment explanation
Indices: 1207693--1207788 Score: 131
Period size: 36 Copynumber: 2.7 Consensus size: 35
1207683 ATATATAACA
1207693 ATATATAGTATAGTTTTTGAAAATATTTTTGAAAAC
1 ATATATA-TATAGTTTTTGAAAATATTTTTGAAAAC
* ***
1207729 ATATAGTATATAGTTTTAGAAACGGTTTTTGAAAAC
1 ATATA-TATATAGTTTTTGAAAATATTTTTGAAAAC
1207765 ATAT-TATATAGTTTTTGAAAATAT
1 ATATATATATAGTTTTTGAAAATAT
1207789 AATATATATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 16 0.31
36 33 0.65
37 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (35 bp):
ATATATATATAGTTTTTGAAAATATTTTTGAAAAC
Found at i:1207781 original size:22 final size:22
Alignment explanation
Indices: 1207753--1207796 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1207743 TTTAGAAACG
*
1207753 GTTTTTGAAAACATATTATATA
1 GTTTTTGAAAACATAATATATA
*
1207775 GTTTTTGAAAATATAATATATA
1 GTTTTTGAAAACATAATATATA
1207797 TTATATAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (22 bp):
GTTTTTGAAAACATAATATATA
Found at i:1207793 original size:20 final size:22
Alignment explanation
Indices: 1207753--1207794 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
1207743 TTTAGAAACG
*
1207753 GTTTTTGAAAACATATTATATA
1 GTTTTTGAAAACATATAATATA
1207775 GTTTTTG-AAA-ATATAATATA
1 GTTTTTGAAAACATATAATATA
1207795 TATTATATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 3 0.16
22 7 0.37
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (22 bp):
GTTTTTGAAAACATATAATATA
Found at i:1207805 original size:29 final size:26
Alignment explanation
Indices: 1207765--1207822 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 26
1207755 TTTTGAAAAC
*
1207765 ATATTATATAGTTTTTGAAAATATAATAT
1 ATATTATATAGTTTAT--AAATA-AATAT
1207794 ATATTATATAGTTTATAAATAAATAT
1 ATATTATATAGTTTATAAATAAATAT
1207820 ATA
1 ATA
1207823 GTACATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 8 0.29
27 5 0.18
29 15 0.54
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
ATATTATATAGTTTATAAATAAATAT
Found at i:1207867 original size:17 final size:17
Alignment explanation
Indices: 1207847--1207893 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1207837 TATAGTGTTA
1207847 TTTATTATTTTCA-TTAC
1 TTTATTATTTT-ATTTAC
1207864 TTTATTCA-TTTATTTAC
1 TTTATT-ATTTTATTTAC
*
1207881 TTAATTATTTTAT
1 TTTATTATTTTAT
1207894 ATTCATTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 2 0.08
17 23 0.88
18 1 0.04
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATTATTTTATTTAC
Found at i:1207977 original size:19 final size:19
Alignment explanation
Indices: 1207955--1207994 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1207945 ACTGAGCTAT
1207955 GCCAGCCTGACCCAACAAA
1 GCCAGCCTGACCCAACAAA
*
1207974 GCCAGCCTGACCCAGCAAA
1 GCCAGCCTGACCCAACAAA
1207993 GC
1 GC
1207995 AGGCTCAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.42, G:0.20, T:0.05
Consensus pattern (19 bp):
GCCAGCCTGACCCAACAAA
Found at i:1217115 original size:22 final size:22
Alignment explanation
Indices: 1217087--1217140 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1217077 ACTTGAACCT
1217087 ACCCCACTATAATCCCAATCAA
1 ACCCCACTATAATCCCAATCAA
*
1217109 ACCCCACTATAATCCCACTCAA
1 ACCCCACTATAATCCCAATCAA
*
1217131 ACACCACTAT
1 ACCCCACTAT
1217141 TCGAACTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.19
Consensus pattern (22 bp):
ACCCCACTATAATCCCAATCAA
Found at i:1220418 original size:12 final size:12
Alignment explanation
Indices: 1220374--1220427 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
1220364 GATCAACAGT
*
1220374 TTTGCATCTGTA
1 TTTGCATCTGCA
*
1220386 TTTACATCTTTGCA
1 TTTGCATC--TGCA
1220400 TTTTGCATCTGCA
1 -TTTGCATCTGCA
*
1220413 TTTGCATATGCA
1 TTTGCATCTGCA
1220425 TTT
1 TTT
1220428 ACATATTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 21 0.60
13 4 0.11
14 3 0.09
15 7 0.20
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.50
Consensus pattern (12 bp):
TTTGCATCTGCA
Found at i:1223149 original size:7 final size:7
Alignment explanation
Indices: 1223137--1223284 Score: 115
Period size: 7 Copynumber: 19.9 Consensus size: 7
1223127 GAGTTCTTCG
1223137 AGAAAAA
1 AGAAAAA
1223144 AGAAAAAA
1 AG-AAAAA
*
1223152 AGAGAAA
1 AGAAAAA
*
1223159 AG-AAGA
1 AGAAAAA
*
1223165 A-AAAAG
1 AGAAAAA
1223171 AGAAAAGA
1 AGAAAA-A
1223179 AGAAAAAA
1 AG-AAAAA
1223187 AGAAAAA
1 AGAAAAA
1223194 AGAGGAAAA
1 AGA--AAAA
1223203 A-AAGGAAA
1 AGAA--AAA
*
1223211 A-AAGAA
1 AGAAAAA
1223217 AGAAAAA
1 AGAAAAA
1223224 AGAAAAAA
1 AG-AAAAA
1223232 GAGAAAAA
1 -AGAAAAA
1223240 AGAAAAGA
1 AGAAAA-A
1223248 AGAAAAAA
1 AG-AAAAA
1223256 GAGAAAAA
1 -AGAAAAA
1223264 AGAAAAGA
1 AGAAAA-A
1223272 AGAAAAA
1 AGAAAAA
1223279 AGAAAA
1 AGAAAA
1223285 TGAATCAAGA
Statistics
Matches: 117, Mismatches: 8, Indels: 32
0.75 0.05 0.20
Matches are distributed among these distances:
6 10 0.09
7 45 0.38
8 45 0.38
9 17 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:1223152 original size:8 final size:8
Alignment explanation
Indices: 1223139--1223284 Score: 152
Period size: 8 Copynumber: 17.4 Consensus size: 8
1223129 GTTCTTCGAG
1223139 AAAAAAGA
1 AAAAAAGA
1223147 AAAAAAGA
1 AAAAAAGA
1223155 GAAAAGAAGA
1 -AAAA-AAGA
1223165 AAAAAGAGA
1 AAAAA-AGA
*
1223174 AAAGAAGA
1 AAAAAAGA
1223182 AAAAAAGA
1 AAAAAAGA
1223190 AAAAAGAGGA
1 AAAAA-A-GA
*
1223200 AAAAAAGG
1 AAAAAAGA
1223208 AAAAAAGA
1 AAAAAAGA
*
1223216 AAGAAAAAA
1 AA-AAAAGA
1223225 GAAAAAAGA
1 -AAAAAAGA
1223234 GAAAAAAGA
1 -AAAAAAGA
*
1223243 AAAGAAG-
1 AAAAAAGA
1223250 AAAAAAGA
1 AAAAAAGA
1223258 GAAAAAAGA
1 -AAAAAAGA
*
1223267 AAAGAAG-
1 AAAAAAGA
1223274 AAAAAAGA
1 AAAAAAGA
1223282 AAA
1 AAA
1223285 TGAATCAAGA
Statistics
Matches: 118, Mismatches: 10, Indels: 20
0.80 0.07 0.14
Matches are distributed among these distances:
7 12 0.10
8 49 0.42
9 44 0.37
10 13 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1223158 original size:17 final size:17
Alignment explanation
Indices: 1223136--1223284 Score: 168
Period size: 17 Copynumber: 8.8 Consensus size: 17
1223126 AGAGTTCTTC
1223136 GAGAAAAAAGAAAAAAA
1 GAGAAAAAAGAAAAAAA
1223153 GAGAAAAGAAG-AAAAAA
1 GAGAAAA-AAGAAAAAAA
1223170 GAGAAAAGAAGAAAAAAA
1 GAGAAAA-AAGAAAAAAA
1223188 GA-AAAAAGAGGAAAAAAA
1 GAGAAAAA-A-GAAAAAAA
1223206 G-GAAAAAAGAAAGAAAA
1 GAGAAAAAAGAAA-AAAA
*
1223223 AAGAAAAAAGAGAAAAAA
1 GAGAAAAAAGA-AAAAAA
*
1223241 GA-AAAGAAG-AAAAAA
1 GAGAAAAAAGAAAAAAA
*
1223256 GAGAAAAAAG-AAAAGA
1 GAGAAAAAAGAAAAAAA
1223272 -AGAAAAAAGAAAA
1 GAGAAAAAAGAAAA
1223285 TGAATCAAGA
Statistics
Matches: 117, Mismatches: 5, Indels: 21
0.82 0.03 0.15
Matches are distributed among these distances:
15 17 0.15
16 19 0.16
17 40 0.34
18 39 0.33
19 2 0.02
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAGAAAAAAGAAAAAAA
Found at i:1225483 original size:43 final size:43
Alignment explanation
Indices: 1225422--1225569 Score: 219
Period size: 43 Copynumber: 3.5 Consensus size: 43
1225412 GCCTAATTTT
* *
1225422 TAGGGGTTCCTTGATGACAAGCTTTAGAGACCAACGTGATATG
1 TAGGGGTTCCTTGATGACAAGCTTGAGGGACCAACGTGATATG
*
1225465 TAGGGGTTCCTTGATGACAAGCTTGAGGGATCAACGTGATATG
1 TAGGGGTTCCTTGATGACAAGCTTGAGGGACCAACGTGATATG
* *
1225508 TAGGGGTTCATTAATGA-ACA-CTTGAGGGACCAACGTGATATG
1 TAGGGGTTCCTTGATGACA-AGCTTGAGGGACCAACGTGATATG
*
1225550 TAGGGGTTCCTTGGTGACAA
1 TAGGGGTTCCTTGATGACAA
1225570 CTAAGAAACT
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
42 37 0.39
43 57 0.61
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (43 bp):
TAGGGGTTCCTTGATGACAAGCTTGAGGGACCAACGTGATATG
Found at i:1225633 original size:20 final size:20
Alignment explanation
Indices: 1225608--1225669 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
1225598 TTTCTTGATG
1225608 AGTAAGTCCTTCGGGCCATC
1 AGTAAGTCCTTCGGGCCATC
* * *
1225628 AGTAAGTCTTTCGAG-CATG
1 AGTAAGTCCTTCGGGCCATC
1225647 ATGTGTAAGTCCTTCGGGCCATC
1 A---GTAAGTCCTTCGGGCCATC
1225670 CATAAGACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 4 0.12
20 13 0.41
22 12 0.38
23 3 0.09
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (20 bp):
AGTAAGTCCTTCGGGCCATC
Found at i:1225903 original size:90 final size:90
Alignment explanation
Indices: 1225645--1226308 Score: 981
Period size: 90 Copynumber: 7.3 Consensus size: 90
1225635 CTTTCGAGCA
* * * *
1225645 TGATGTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGATTTCAAATGAGATTTA
1 TGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
1225710 AGAAACTAAGCCTTCGGGGGTTTCT
66 AGAAACTAAGCCTTCGGGGGTTTCT
* * * *
1225735 TGGTTTGTAAGTCCTTC-GGTCATCCATAAGACCTTCAGTGCAAGATGATTTCAAATGAGATTTA
1 TGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
*
1225799 AGAAACTAAGCCTTCGAGGGTTTCT
66 AGAAACTAAGCCTTCGGGGGTTTCT
* * * *
1225824 TGATTTGTAAGTCCTTCGGGCCATCCATAATACCTTCAGTGCAGGATGATTTCAAATGAGATTTA
1 TGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
* *
1225889 AAAAAGTAAGCCTTCGGGGGTTTCT
66 AGAAACTAAGCCTTCGGGGGTTTCT
* *
1225914 TGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTACATGATGTTTTCAAATGAGATTTT
1 TGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
1225979 AGAAACTAAGCCTTC-GGGGTTTCT
66 AGAAACTAAGCCTTCGGGGGTTTCT
**
1226003 TGATTTGTAAGTCCTTTTGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
1 TGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
1226068 AGAAACTAAGCCTTCGGGGGTTTCT
66 AGAAACTAAGCCTTCGGGGGTTTCT
* *
1226093 TGATTTGTAAGTCCTTTGGGACATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
1 TGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
1226158 AGAAACTAAGCCTTCGGGGGTTTCT
66 AGAAACTAAGCCTTCGGGGGTTTCT
* *
1226183 TGATTTGTAAGTCCTTTGGGACATCCATGGGACATCCATAAGACCTTCAGTGCATGATGTTTTCA
1 TGATTTGTAAGTCC--T------T-C--GGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCA
**
1226248 AATGAGATTTTAGAAACTAAGCCTTCGAAGGTTTCT
55 AATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCT
*
1226284 TGATTTTTAAGTCCTTCGGGTCATC
1 TGATTTGTAAGTCCTTCGGGTCATC
1226309 AGTAAGTCTT
Statistics
Matches: 529, Mismatches: 32, Indels: 26
0.90 0.05 0.04
Matches are distributed among these distances:
89 170 0.32
90 271 0.51
92 2 0.00
93 1 0.00
98 1 0.00
99 1 0.00
101 83 0.16
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (90 bp):
TGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
AGAAACTAAGCCTTCGGGGGTTTCT
Found at i:1226001 original size:179 final size:179
Alignment explanation
Indices: 1225645--1226308 Score: 988
Period size: 179 Copynumber: 3.6 Consensus size: 179
1225635 CTTTCGAGCA
*
1225645 TGATGTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGATTTCAAATGAGATTTA
1 TGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGATTTCAAATGAGATTTA
*
1225710 AGAAACTAAGCCTTCGGGGGTTTCTTGGTTTGTAAGTCCTTC-GGTCATCCATAAGACCTTCAGT
66 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGT
* *
1225774 GCAAGATGATTTCAAATGAGATTTAAGAAACTAAGCCTTCGAGGGTTTCT
131 GCAAGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCG-GGGTTTCT
*
1225824 TGATTTGTAAGTCCTTCGGGCCATCCATAATACCTTCAGTGCAGGATGATTTCAAATGAGATTTA
1 TGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGATTTCAAATGAGATTTA
* *
1225889 AAAAAGTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGT
66 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGT
* *
1225954 ACATGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGTTTCT
131 GCAAGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGTTTCT
** * * *
1226003 TGATTTGTAAGTCCTTTTGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
1 TGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGATTTCAAATGAGATTTA
* *
1226068 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTTGGGACATCCATAAGACCTTCAGT
66 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGT
*
1226133 GCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCT
131 GCAAGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTC-GGGGTTTCT
* * *
1226183 TGATTTGTAAGTCCTTTGGGACATCCATGGGACATCCATAAGACCTTCAGTGCATGATGTTTTCA
1 TGATTTGTAAGTCC--T------T-C--GGGCCATCCATAAGACCTTCAGTGCAGGATGATTTCA
* ** *
1226248 AATGAGATTTTAGAAACTAAGCCTTCGAAGGTTTCTTGATTTTTAAGTCCTTCGGGTCATC
55 AATGAGATTTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATC
1226309 AGTAAGTCTT
Statistics
Matches: 442, Mismatches: 30, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
179 268 0.61
180 82 0.19
182 1 0.00
188 1 0.00
191 90 0.20
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (179 bp):
TGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGATTTCAAATGAGATTTA
AGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGT
GCAAGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGTTTCT
Found at i:1226130 original size:269 final size:269
Alignment explanation
Indices: 1225645--1226308 Score: 990
Period size: 269 Copynumber: 2.4 Consensus size: 269
1225635 CTTTCGAGCA
* * * * *
1225645 TGATGTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGATTTCAAATGAGATTTA
1 TGATTTGTAAGTCCTTCGGGACATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTT
*
1225710 AGAAACTAAGCCTTCGGGGGTTTCTTGGTTTGTAAGTCC-TTCGGTCATCCATAAGACCTTCAGT
66 AGAAACTAAGCCTTC-GGGGTTTCTTGATTTGTAAGTCCTTTCGGTCATCCATAAGACCTTCAGT
1225774 GCAAGATGATTTCAAATGAGATTTAAGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCT
130 GCAAGATGATTTCAAATGAGATTTAAGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCT
* * *
1225839 TCGGGCCATCCATAATACCTTCAGTGCAGGATGATTTCAAATGAGATTTAAAAAAGTAAGCCTTC
195 TCGGGACATCCATAAGACCTTCAGTGCAGGATGATTTCAAATGAGATTTAAAAAACTAAGCCTTC
1225904 GGGGGTTTCT
260 GGGGGTTTCT
* *
1225914 TGATTTGTAAGTCCTTCGGGTCATCCATAAGACCTTCAGTACATGATGTTTTCAAATGAGATTTT
1 TGATTTGTAAGTCCTTCGGGACATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTT
*
1225979 AGAAACTAAGCCTTCGGGGTTTCTTGATTTGTAAGTCCTTTTGGTCATCCATAAGACCTTCAGTG
66 AGAAACTAAGCCTTCGGGGTTTCTTGATTTGTAAGTCCTTTCGGTCATCCATAAGACCTTCAGTG
* * * *
1226044 CAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTT
131 CAAGATGATTTCAAATGAGATTTAAGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTT
* * * *
1226109 TGGGACATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCG
196 CGGGACATCCATAAGACCTTCAGTGCAGGATGATTTCAAATGAGATTTAAAAAACTAAGCCTTCG
1226174 GGGGTTTCT
261 GGGGTTTCT
1226183 TGATTTGTAAGTCCTTTGGGACATCCATGGGACATCCATAAGACCTTCAGTGCATGATGTTTTCA
1 TGATTTGTAAGTCC--T------T-C--GGGACATCCATAAGACCTTCAGTGCATGATGTTTTCA
* *
1226248 AATGAGATTTTAGAAACTAAGCCTTCGAAGGTTTCTTGATTTTTAAGTCC-TTCGGGTCATC
55 AATGAGATTTTAGAAACTAAGCCTTCG-GGGTTTCTTGATTTGTAAGTCCTTTC-GGTCATC
1226309 AGTAAGTCTT
Statistics
Matches: 357, Mismatches: 24, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
268 22 0.06
269 241 0.68
271 1 0.00
277 1 0.00
278 1 0.00
280 64 0.18
281 27 0.08
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (269 bp):
TGATTTGTAAGTCCTTCGGGACATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTT
AGAAACTAAGCCTTCGGGGTTTCTTGATTTGTAAGTCCTTTCGGTCATCCATAAGACCTTCAGTG
CAAGATGATTTCAAATGAGATTTAAGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTT
CGGGACATCCATAAGACCTTCAGTGCAGGATGATTTCAAATGAGATTTAAAAAACTAAGCCTTCG
GGGGTTTCT
Found at i:1226284 original size:101 final size:101
Alignment explanation
Indices: 1226109--1226308 Score: 346
Period size: 101 Copynumber: 2.0 Consensus size: 101
1226099 GTAAGTCCTT
1226109 TGGGACATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCG
1 TGGGACATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCG
** *
1226174 GGGGTTTCTTGATTTGTAAGTCCTTTGGGACATCCA
66 AAGGTTTCTTGATTTGTAAGTCCTTCGGGACATCCA
*
1226210 TGGGACATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCG
1 TGGGACATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCG
* *
1226275 AAGGTTTCTTGATTTTTAAGTCCTTCGGGTCATC
66 AAGGTTTCTTGATTTGTAAGTCCTTCGGGACATC
1226309 AGTAAGTCTT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 93 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (101 bp):
TGGGACATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCG
AAGGTTTCTTGATTTGTAAGTCCTTCGGGACATCCA
Found at i:1226356 original size:42 final size:42
Alignment explanation
Indices: 1226290--1226372 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
1226280 TTCTTGATTT
* * *
1226290 TTAAGTCCTTCGGGTCATCAGTAAGTCTTTCAAGCATGATGC
1 TTAAATCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGC
* * *
1226332 TTAAATCCTTCGTGTCATCTGTAAGCCTTTCGAGCAAGATG
1 TTAAATCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATG
1226373 ATAAGTCTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (42 bp):
TTAAATCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGC
Found at i:1226866 original size:14 final size:17
Alignment explanation
Indices: 1226847--1226883 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1226837 AGGATAAAAA
1226847 TATTATA-T-TTAT-AT
1 TATTATATTATTATGAT
1226861 TATTATATTATTATGAT
1 TATTATATTATTATGAT
1226878 TATTAT
1 TATTAT
1226884 TAATATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 1 0.05
16 4 0.20
17 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTATATTATTATGAT
Found at i:1227315 original size:22 final size:22
Alignment explanation
Indices: 1227287--1227337 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1227277 TGAACCTACT
1227287 CCACTATAATCCCACTCAAACA
1 CCACTATAATCCCACTCAAACA
1227309 CCACTATAATCCCACTCAAACA
1 CCACTATAATCCCACTCAAACA
1227331 CCACTAT
1 CCACTAT
1227338 TCAAACTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (22 bp):
CCACTATAATCCCACTCAAACA
Found at i:1230861 original size:2 final size:2
Alignment explanation
Indices: 1230854--1230879 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1230844 CATTGTTATG
1230854 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
1230880 GTGTGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1231285 original size:2 final size:2
Alignment explanation
Indices: 1231278--1231312 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1231268 AATTAAAATA
1231278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1231313 AAGTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1233096 original size:23 final size:23
Alignment explanation
Indices: 1233070--1233122 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1233060 GAAGATGAAT
1233070 GAGTCCCGTCTTTAATTGAAACG
1 GAGTCCCGTCTTTAATTGAAACG
*
1233093 GAGTACCGTCTTTAATTGAAACG
1 GAGTCCCGTCTTTAATTGAAACG
*
1233116 TAGTCCC
1 GAGTCCC
1233123 ACCACTAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (23 bp):
GAGTCCCGTCTTTAATTGAAACG
Found at i:1234359 original size:24 final size:24
Alignment explanation
Indices: 1234323--1234430 Score: 84
Period size: 24 Copynumber: 4.6 Consensus size: 24
1234313 AAATCCTAAT
* *
1234323 TAAAACACTTAAAACTATTTAAAC
1 TAAAATACCTAAAACTATTTAAAC
* *
1234347 TAAAATACCTAAAAAAATATTTAAAA
1 TAAAATACCT--AAAACTATTTAAAC
* * *
1234373 TAATAT-CCT-AAA-T-CTT-AAT
1 TAAAATACCTAAAACTATTTAAAC
1234392 TAAAATA-CTAAAACCTATTTAAAC
1 TAAAATACCTAAAA-CTATTTAAAC
1234416 TAAAATACCTAAAAC
1 TAAAATACCTAAAAC
1234431 AAAGATAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
19 9 0.14
20 5 0.08
21 1 0.02
22 4 0.06
23 2 0.03
24 18 0.28
25 9 0.14
26 17 0.26
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAATACCTAAAACTATTTAAAC
Found at i:1234369 original size:26 final size:25
Alignment explanation
Indices: 1234333--1234384 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
1234323 TAAAACACTT
* *
1234333 AAAACTATTTAAACTAAAATACCTAA
1 AAAAATATTTAAAATAAAAT-CCTAA
*
1234359 AAAAATATTTAAAATAATATCCTAA
1 AAAAATATTTAAAATAAAATCCTAA
1234384 A
1 A
1234385 TCTTAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAAATATTTAAAATAAAATCCTAA
Found at i:1237196 original size:43 final size:43
Alignment explanation
Indices: 1237149--1237321 Score: 224
Period size: 43 Copynumber: 4.0 Consensus size: 43
1237139 TGACGATATA
*
1237149 TAGCGGCATTTGTCAT-ACAAACGCCACAATATGTGTTGATG-TT
1 TAGCGGCATTTTTC-TCACAAACGCCACAATATGTGTTGA-GATT
* * *
1237192 TAGCGGCGTTTTTCCCACAAAAGCCACAATATGTGTTGAGATT
1 TAGCGGCATTTTTCTCACAAACGCCACAATATGTGTTGAGATT
* *
1237235 TAGCGGCATTTTTCTCACAAACGCCACAATAAGTTTTGAGATT
1 TAGCGGCATTTTTCTCACAAACGCCACAATATGTGTTGAGATT
** * *
1237278 TAGCGGTGTTTTTCTCAAAAACGCCACAATAGGTGTTGAGATT
1 TAGCGGCATTTTTCTCACAAACGCCACAATATGTGTTGAGATT
1237321 T
1 T
1237322 CGTGGAATTT
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.01
43 113 0.99
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (43 bp):
TAGCGGCATTTTTCTCACAAACGCCACAATATGTGTTGAGATT
Found at i:1237255 original size:86 final size:86
Alignment explanation
Indices: 1237122--1237321 Score: 253
Period size: 86 Copynumber: 2.3 Consensus size: 86
1237112 TTTTTTAACG
* ** * * *
1237122 AAAAACGCCAAAATAGGTGACGATATATAGCGGCATTTGTCATACAAACGCCACAATATGTGTTG
1 AAAAACGCCACAATAGGTGTTGAGATTTAGCGGCATTTGTCATACAAACGCCACAATAAGTGTTG
1237187 ATG-TTTAGCGGCGTTTTTCCC
66 A-GATTTAGCGGCGTTTTTCCC
* * *
1237208 ACAAAA-GCCACAATATGTGTTGAGATTTAGCGGCATTTTTC-TCACAAACGCCACAATAAGTTT
1 A-AAAACGCCACAATAGGTGTTGAGATTTAGCGGCATTTGTCAT-ACAAACGCCACAATAAGTGT
* *
1237271 TGAGATTTAGCGGTGTTTTTCTC
64 TGAGATTTAGCGGCGTTTTTCCC
1237294 AAAAACGCCACAATAGGTGTTGAGATTT
1 AAAAACGCCACAATAGGTGTTGAGATTT
1237322 CGTGGAATTT
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
85 6 0.06
86 88 0.90
87 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (86 bp):
AAAAACGCCACAATAGGTGTTGAGATTTAGCGGCATTTGTCATACAAACGCCACAATAAGTGTTG
AGATTTAGCGGCGTTTTTCCC
Found at i:1237333 original size:43 final size:43
Alignment explanation
Indices: 1237122--1237321 Score: 208
Period size: 43 Copynumber: 4.7 Consensus size: 43
1237112 TTTTTTAACG
* * ** * * *
1237122 AAAAACGCCAAAATAGGTGACGATATATAGCGGCATTTGTCAT-
1 AAAAACGCCACAATATGTGTTGAGATTTAGCGGCATTTTTC-TC
* * *
1237165 ACAAACGCCACAATATGTGTTGATG-TTTAGCGGCGTTTTTCCC
1 AAAAACGCCACAATATGTGTTGA-GATTTAGCGGCATTTTTCTC
1237208 ACAAAA-GCCACAATATGTGTTGAGATTTAGCGGCATTTTTCTC
1 A-AAAACGCCACAATATGTGTTGAGATTTAGCGGCATTTTTCTC
* * * **
1237251 ACAAACGCCACAATAAGTTTTGAGATTTAGCGGTGTTTTTCTC
1 AAAAACGCCACAATATGTGTTGAGATTTAGCGGCATTTTTCTC
*
1237294 AAAAACGCCACAATAGGTGTTGAGATTT
1 AAAAACGCCACAATATGTGTTGAGATTT
1237322 CGTGGAATTT
Statistics
Matches: 131, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
42 4 0.03
43 124 0.95
44 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (43 bp):
AAAAACGCCACAATATGTGTTGAGATTTAGCGGCATTTTTCTC
Found at i:1237368 original size:86 final size:86
Alignment explanation
Indices: 1237192--1237376 Score: 189
Period size: 86 Copynumber: 2.2 Consensus size: 86
1237182 TGTTGATGTT
* *
1237192 TAGCGGCGTTTTTCCCACAAAAGCCACAATATGTGTTGAGATTTAGCGGCATTTTTCTCACAAAC
1 TAGCGGCGTTTTTCCCACAAAAGCCACAATAGGTGTTGAGATTTAGCGGAATTTTTCTCACAAAC
* * * *
1237257 GCCACAATAAGTTTTGAGATT
66 GCAACAATAAGATCTGAGATA
* * * * *
1237278 TAGCGGTGTTTTTCTCA-AAAACGCCACAATAGGTGTTGAGATTTCGTGGAATTTTT-TGATACA
1 TAGCGGCGTTTTTCCCACAAAA-GCCACAATAGGTGTTGAGATTTAGCGGAATTTTTCT--CACA
*
1237341 AACGCAACTAT-AGATCTG-GTATA
63 AACGCAACAATAAGATCTGAG-ATA
*
1237364 TAGCGGCATTTTT
1 TAGCGGCGTTTTT
1237377 AGGATACAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
85 6 0.07
86 63 0.78
87 12 0.15
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (86 bp):
TAGCGGCGTTTTTCCCACAAAAGCCACAATAGGTGTTGAGATTTAGCGGAATTTTTCTCACAAAC
GCAACAATAAGATCTGAGATA
Found at i:1237436 original size:44 final size:44
Alignment explanation
Indices: 1237335--1237484 Score: 165
Period size: 44 Copynumber: 3.4 Consensus size: 44
1237325 GGAATTTTTT
** * * *
1237335 GATACAAACGCAACTATAGATCTGGTATATAGCGGCATTTTTAG
1 GATACAAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAG
*
1237379 GATACAAAAGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAG
1 GATACAAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAG
* * * * * **
1237423 GATACAAACGCCGCTACATGTATGGTATATTGCAGCGTTTTTTT
1 GATACAAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAG
* *
1237467 GTTACAAGCGCCGCTAAA
1 GATACAAACGCCGCTAAA
1237485 TAACACAGAA
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 89 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
GATACAAACGCCGCTAAAGGTCTGGTATATAGCGGCGTTTTTAG
Found at i:1237854 original size:23 final size:21
Alignment explanation
Indices: 1237801--1237853 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1237791 ATTGATATGT
1237801 TGCTTCTCTCTGTGCTATCAC
1 TGCTTCTCTCTGTGCTATCAC
* *
1237822 TGCTTCTCTCTGTGCTGTCGC
1 TGCTTCTCTCTGTGCTATCAC
1237843 TGCTTCTCTCT
1 TGCTTCTCTCT
1237854 CTAATTCTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.04, C:0.34, G:0.17, T:0.45
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTATCAC
Found at i:1245099 original size:80 final size:81
Alignment explanation
Indices: 1244971--1245137 Score: 264
Period size: 80 Copynumber: 2.1 Consensus size: 81
1244961 TAACGATGGC
* * *
1244971 GGTGATCACGAGCAGCAGCAGGAACGACAGCTTCAAGCGGCGATGACCAGCAGCAGTTGAGTA-C
1 GGTGATAACGAGCAGCAGCAGGAACGACAGCTTCAAGCGGCGACGACCAGCAACAGTTGAGTACC
**
1245035 GGGCAGCGACGGTGTA
66 AAGCAGCGACGGTGTA
* *
1245051 GGTGATAACGAGCAGCAGCAGGAACGACGGCTTCAAGCGGCGGCGACCAGCAACAGTTGAGTACC
1 GGTGATAACGAGCAGCAGCAGGAACGACAGCTTCAAGCGGCGACGACCAGCAACAGTTGAGTACC
1245116 AAGCAGCGACGGTGTA
66 AAGCAGCGACGGTGTA
1245132 GGTGAT
1 GGTGAT
1245138 GACGGCTTCG
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 58 0.73
81 21 0.27
ACGTcount: A:0.28, C:0.23, G:0.36, T:0.13
Consensus pattern (81 bp):
GGTGATAACGAGCAGCAGCAGGAACGACAGCTTCAAGCGGCGACGACCAGCAACAGTTGAGTACC
AAGCAGCGACGGTGTA
Found at i:1247764 original size:11 final size:11
Alignment explanation
Indices: 1247750--1247774 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1247740 CGTCTCTTTT
1247750 CATCATCTTCA
1 CATCATCTTCA
1247761 CATCATCTTCA
1 CATCATCTTCA
1247772 CAT
1 CAT
1247775 GCACCACCTC
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:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (11 bp):
CATCATCTTCA
Found at i:1251074 original size:75 final size:76
Alignment explanation
Indices: 1250927--1251156 Score: 381
Period size: 76 Copynumber: 3.0 Consensus size: 76
1250917 TGGTTATCGT
* *
1250927 ATTATTTTTTCTCTCAATGTGACTCTCCAATTCAAAAAATAAACCAAATGTGGCCCTTTGATCAA
1 ATTATTTTTTCTCTCAATGTGACTCTCCAATTCAAAAAATAAACCCAATGTGACCCTTTGATCAA
*
1250992 TGTTTTTCACC
66 CGTTTTTCACC
* *
1251003 ATTATTTTCTCTCTCAACGTGACTCTCCAATTC-AAAAATAAACCCAATGTGACCCTTTGATCAA
1 ATTATTTTTTCTCTCAATGTGACTCTCCAATTCAAAAAATAAACCCAATGTGACCCTTTGATCAA
1251067 CGTTTTTCACC
66 CGTTTTTCACC
* *
1251078 ATTATTTTTTCTCTCAATGTGACTCTCTAATTCAAAAAATAAACTCAATGTGACCCTTTGATCAA
1 ATTATTTTTTCTCTCAATGTGACTCTCCAATTCAAAAAATAAACCCAATGTGACCCTTTGATCAA
*
1251143 CATTTTTCACC
66 CGTTTTTCACC
1251154 ATT
1 ATT
1251157 GACTGTTAAG
Statistics
Matches: 143, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
75 69 0.48
76 74 0.52
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (76 bp):
ATTATTTTTTCTCTCAATGTGACTCTCCAATTCAAAAAATAAACCCAATGTGACCCTTTGATCAA
CGTTTTTCACC
Found at i:1257199 original size:2 final size:2
Alignment explanation
Indices: 1257192--1257262 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1257182 TCAATCTACA
1257192 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
1257234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1257263 CAACATACAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1257435 original size:13 final size:13
Alignment explanation
Indices: 1257414--1257468 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
1257404 AATGACGCGC
*
1257414 AATGAGCGTCATA
1 AATGCGCGTCATA
*
1257427 AATGTGCGTCATA
1 AATGCGCGTCATA
*
1257440 AATGCGTGTCATA
1 AATGCGCGTCATA
*
1257453 AATGCGCATCATA
1 AATGCGCGTCATA
1257466 AAT
1 AAT
1257469 TTATGACGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:1260413 original size:68 final size:68
Alignment explanation
Indices: 1260329--1260728 Score: 667
Period size: 68 Copynumber: 5.9 Consensus size: 68
1260319 AAATAAAATA
*
1260329 TTGATGGCCTAGTTGTGCATTTGAAAGAAA-GATGTCAATTATGCCAGTTAGATGAAAGGCTAAG
1 TTGA-GGCCTAGTTGTGCATTTGACAGAAATG-TGTCAATTATGCCAGTTAGATGAAAGGCTAAG
1260393 TGCCT
64 TGCCT
* * *
1260398 TTGAGGCCTAGTTGTGCATTTGACAGAAATGTGGCAATTATGCCAGCTAGATGAAAGACTAAGTG
1 TTGAGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1260463 CCT
66 CCT
*
1260466 TTGAGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1 TTGAGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1260531 CCT
66 CCT
***
1260534 TTGATATCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1 TTGAGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1260599 CCT
66 CCT
* **
1260602 TTGAGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGTCAACTAGATGAAAGGCTAAGTG
1 TTGAGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1260667 CCT
66 CCT
*
1260670 TTGAGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGC
1 TTGAGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGC
1260729 GTGTCACAAA
Statistics
Matches: 308, Mismatches: 22, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
68 303 0.98
69 5 0.02
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.30
Consensus pattern (68 bp):
TTGAGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
CCT
Found at i:1260829 original size:47 final size:45
Alignment explanation
Indices: 1260736--1260979 Score: 190
Period size: 45 Copynumber: 5.4 Consensus size: 45
1260726 GGCGTGTCAC
* *
1260736 AAATGAAATGTATAATAGTGTATAAAAGGCATGAAAGTATGTCAT
1 AAATGAAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCAT
1260781 AAATGAAATGTATAATAGTGTATAAAAAAGGCATGAAAGGATGCCAT
1 AAATGAAATGTATAATAGTGTAT--AAAAGGCATGAAAGGATGCCAT
* * * * ** *
1260828 AAATGAAATGCAT-ATGGGTGCATTATTGGCATGAAAGGATTCCAT
1 AAATGAAATGTATAAT-AGTGTATAAAAGGCATGAAAGGATGCCAT
* * * * **
1260873 AAATGAAATGTAT-GTGGGTGCATTATCGGCATGAAATGG-TGCCAT
1 AAATGAAATGTATAAT-AGTGTATAAAAGGCATGAAA-GGATGCCAT
* * * * ** * *
1260918 AATTGAAATGCAT-ATAGGTGCATTATTGGTATGAAAGAATGCCAT
1 AAATGAAATGTATAATA-GTGTATAAAAGGCATGAAAGGATGCCAT
1260963 AAATGAAAATGTATAAT
1 AAATG-AAATGTATAAT
1260980 GGTGCATTAT
Statistics
Matches: 169, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
44 1 0.01
45 118 0.70
46 11 0.07
47 39 0.23
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (45 bp):
AAATGAAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCAT
Found at i:1260891 original size:45 final size:45
Alignment explanation
Indices: 1260810--1260989 Score: 238
Period size: 45 Copynumber: 4.0 Consensus size: 45
1260800 GTATAAAAAA
1260810 GGCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATT
1 GGCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATT
* * * *
1260855 GGCATGAAAGGATTCCATAAATGAAATGTATGTGGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATT
* *
1260900 GGCATGAAATGG-TGCCATAATTGAAATGCATATAGGTGCATTATT
1 GGCATGAAA-GGATGCCATAAATGAAATGCATATGGGTGCATTATT
* * *
1260945 GGTATGAAAGAATGCCATAAATGAAAATGTATAAT-GGTGCATTAT
1 GGCATGAAAGGATGCCATAAATG-AAATGCAT-ATGGGTGCATTAT
1260990 AAGTATGAAG
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
44 1 0.01
45 95 0.81
46 19 0.16
47 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATT
Found at i:1260929 original size:90 final size:91
Alignment explanation
Indices: 1260763--1260989 Score: 273
Period size: 90 Copynumber: 2.5 Consensus size: 91
1260753 GTGTATAAAA
* * * * * **
1260763 GGCATGAAAGTATGTCATAAATG-AAATGTATAATAGTGTATAAAAAAGGCATGAAAGGATGCCA
1 GGCATGAAAGAATGCCATAAATGAAAATGTATAATGGTGCAT--TATCGGCATGAAAGGATGCCA
*
1260827 TAAATGAAATGCATATGGGTGCATTATT
64 TAAATGAAATGCATATAGGTGCATTATT
* * *
1260855 GGCATGAAAGGATTCCATAAATG-AAATGTAT-GTGGGTGCATTATCGGCATGAAATGG-TGCCA
1 GGCATGAAAGAATGCCATAAATGAAAATGTATAAT-GGTGCATTATCGGCATGAAA-GGATGCCA
*
1260917 TAATTGAAATGCATATAGGTGCATTATT
64 TAAATGAAATGCATATAGGTGCATTATT
*
1260945 GGTATGAAAGAATGCCATAAATGAAAATGTATAATGGTGCATTAT
1 GGCATGAAAGAATGCCATAAATGAAAATGTATAATGGTGCATTAT
1260990 AAGTATGAAG
Statistics
Matches: 116, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
90 61 0.53
91 21 0.18
92 34 0.29
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.29
Consensus pattern (91 bp):
GGCATGAAAGAATGCCATAAATGAAAATGTATAATGGTGCATTATCGGCATGAAAGGATGCCATA
AATGAAATGCATATAGGTGCATTATT
Found at i:1274063 original size:155 final size:155
Alignment explanation
Indices: 1273795--1274100 Score: 436
Period size: 155 Copynumber: 2.0 Consensus size: 155
1273785 ATTTTGGGTT
*
1273795 ATCTTAATGAGAAGAACTTGATGAATTTACTAACGTAAAGGTTGAATAACTACTCTTAATGAATT
1 ATCTTAATGAGAAGAACTTGATGAATTTACTAACATAAAGGTTGAATAACTACTCTTAATGAATT
* * *
1273860 CATATTTAAAATTGTTTGGAAATCTTAGTGAGAGGAAAATTGACGAATTCATCAATTTAGAACTA
66 CATATTTAAAATTGTTTGGAAATCCTAGTGAGAGGAAAATCGAAGAATTCATCAATTTAGAACTA
* *
1273925 TAGTTCATATTTCATTATTTGAGTG
131 TAGTTCACATCTCATTATTTGAGTG
* * *
1273950 ATCTTAATGAGAAGGACTTGATGAATTTACTAACATAAATGTTGAATAATTACTCTTAATGAATT
1 ATCTTAATGAGAAGAACTTGATGAATTTACTAACATAAAGGTTGAATAACTACTCTTAATGAATT
* * ** * *
1274015 TAT-TTCTCAAATTGTTTGGACGGTCCTAGTGAGA-GAAAATCGAAGAATTCATCGATTTTGAAC
66 CATATT-TAAAATTGTTTGGA-AATCCTAGTGAGAGGAAAATCGAAGAATTCATCAATTTAGAAC
*
1274078 TATAGTTTACATCTCATTATTTG
129 TATAGTTCACATCTCATTATTTG
1274101 GGTGGTCCTA
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
154 2 0.02
155 121 0.91
156 10 0.08
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (155 bp):
ATCTTAATGAGAAGAACTTGATGAATTTACTAACATAAAGGTTGAATAACTACTCTTAATGAATT
CATATTTAAAATTGTTTGGAAATCCTAGTGAGAGGAAAATCGAAGAATTCATCAATTTAGAACTA
TAGTTCACATCTCATTATTTGAGTG
Found at i:1280341 original size:296 final size:296
Alignment explanation
Indices: 1279807--1280399 Score: 1134
Period size: 296 Copynumber: 2.0 Consensus size: 296
1279797 ACTCTACCCT
1279807 ATTCAAATTCAGTAGTGGAAATGAGACAAGATAACTATGAACTTTATGATCAGGTTATGAATTAC
1 ATTCAAATTCAGTAGTGGAAATGAGACAAGATAACTATGAACTTTATGATCAGGTTATGAATTAC
1279872 TAGATAGAGACATGACGCGGTATAAATTATAATAGACTGATTGAACAAGTCATCTCAATTTCTTC
66 TAGATAGAGACATGACGCGGTATAAATTATAATAGACTGATTGAACAAGTCATCTCAATTTCTTC
1279937 CAATTTGGATGGACGATACCTTAGAGAGGTTGACTCAGTTGTACATCTACAAGATTTTGAGATTA
131 CAATTTGGATGGACGATACCTTAGAGAGGTTGACTCAGTTGTACATCTACAAGATTTTGAGATTA
1280002 CATATGATACTAATTTGAATCATCTTTGAAAGAGACCTCGTTTAACCTCACGATTTTAGAAAAGC
196 CATATGATACTAATTTGAATCATCTTTGAAAGAGACCTCGTTTAACCTCACGATTTTAGAAAAGC
1280067 TTCATGAACCCCTAGGCACTAAACTTCTTTTTAACA
261 TTCATGAACCCCTAGGCACTAAACTTCTTTTTAACA
*
1280103 ATTCAAATTCAGTAGTGGAAATGAGACAAGGTAACTATGAACTTTATGATCAGGTTATGAATTAC
1 ATTCAAATTCAGTAGTGGAAATGAGACAAGATAACTATGAACTTTATGATCAGGTTATGAATTAC
1280168 TAGATAGAGACATGACGCGGATATAAATTATAATAGACTGATTGAACAAGTCATCTCAATTTCTT
66 TAGATAGAGACATGACGCGG-TATAAATTATAATAGACTGATTGAACAAGTCATCTCAATTTCTT
*
1280233 CCAATTTGGATGGACTATACCTTAGAGAGGTTGACTCAGTTGTACATCTACAAGATTTTGAGATT
130 CCAATTTGGATGGACGATACCTTAGAGAGGTTGACTCAGTTGTACATCTACAAGATTTTGAGATT
* *
1280298 ATATGTGATACTAATTT-AATCATCTTTGAAAGAGACCTCGTTTAACCTCACGATTTTAGAAAAG
195 ACATATGATACTAATTTGAATCATCTTTGAAAGAGACCTCGTTTAACCTCACGATTTTAGAAAAG
1280362 CTTCATGAACCCCTAGGCACTAAACTTCTTTTTAACA
260 CTTCATGAACCCCTAGGCACTAAACTTCTTTTTAACA
1280399 A
1 A
1280400 CTTTTTCATC
Statistics
Matches: 292, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
296 169 0.58
297 123 0.42
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (296 bp):
ATTCAAATTCAGTAGTGGAAATGAGACAAGATAACTATGAACTTTATGATCAGGTTATGAATTAC
TAGATAGAGACATGACGCGGTATAAATTATAATAGACTGATTGAACAAGTCATCTCAATTTCTTC
CAATTTGGATGGACGATACCTTAGAGAGGTTGACTCAGTTGTACATCTACAAGATTTTGAGATTA
CATATGATACTAATTTGAATCATCTTTGAAAGAGACCTCGTTTAACCTCACGATTTTAGAAAAGC
TTCATGAACCCCTAGGCACTAAACTTCTTTTTAACA
Found at i:1284497 original size:30 final size:31
Alignment explanation
Indices: 1284449--1284514 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
1284439 GTTTCAAAAC
* * * *
1284449 TAACAAATCAATTACTAACGTTATTGATTTG
1 TAACAAATCAACTACTAACATTATTAATTTA
1284480 TAACAAATC-ACTACTAACATTATTAATTTA
1 TAACAAATCAACTACTAACATTATTAATTTA
1284510 TAACA
1 TAACA
1284515 CATAGGTCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (31 bp):
TAACAAATCAACTACTAACATTATTAATTTA
Found at i:1286184 original size:31 final size:32
Alignment explanation
Indices: 1286125--1286185 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1286115 TCATTGTAAC
* *
1286125 AATTATTAACATTAAGTGTCCAATTTATTATA
1 AATTAATAACATTAAGTGACCAATTTATTATA
*
1286157 AATTAATAACATT-AGTGACTAATTTATTA
1 AATTAATAACATTAAGTGACCAATTTATTA
1286186 ATTTTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (32 bp):
AATTAATAACATTAAGTGACCAATTTATTATA
Found at i:1296965 original size:16 final size:17
Alignment explanation
Indices: 1296944--1296976 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1296934 CGGATATCTG
1296944 ATCCGAA-ATTTTGGAT
1 ATCCGAATATTTTGGAT
*
1296960 ATCCGAATTTTTTGGAT
1 ATCCGAATATTTTGGAT
1296977 CGGATACGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (17 bp):
ATCCGAATATTTTGGAT
Found at i:1297032 original size:16 final size:17
Alignment explanation
Indices: 1297000--1297033 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1296990 TTACTTTAGG
*
1297000 TATCCGAAATTTTCGGA
1 TATCCGAAATATTCGGA
1297017 TATCCGAAA-ATTCGGA
1 TATCCGAAATATTCGGA
1297033 T
1 T
1297034 CGGATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (17 bp):
TATCCGAAATATTCGGA
Found at i:1301486 original size:15 final size:15
Alignment explanation
Indices: 1301468--1301521 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
1301458 GTTAGTGGGC
*
1301468 GGGTAGATGTGAGAT
1 GGGTGGATGTGAGAT
1301483 GGGTGGATGTGAGAT
1 GGGTGGATGTGAGAT
* *
1301498 GAGTGGATGTGAGAC
1 GGGTGGATGTGAGAT
*
1301513 AGGTGGATG
1 GGGTGGATG
1301522 CGGTGAGGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.24, C:0.02, G:0.50, T:0.24
Consensus pattern (15 bp):
GGGTGGATGTGAGAT
Found at i:1302792 original size:19 final size:19
Alignment explanation
Indices: 1302768--1302825 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
1302758 TTTTTAATAT
**
1302768 TAAAAAATAATTTTTTCAAA
1 TAAAAAATAAAATTTT-AAA
1302788 TAAAAAATAAAATTTTAAA
1 TAAAAAATAAAATTTTAAA
1302807 TAAAAAATAAACATTTTAA
1 TAAAAAATAAA-ATTTTAA
1302826 TGGGGGAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.40
20 21 0.60
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAAAATAAAATTTTAAA
Found at i:1304525 original size:20 final size:20
Alignment explanation
Indices: 1304502--1304541 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1304492 TTTCAATTGA
1304502 ATTAAAGTAAATTTAAAAAT
1 ATTAAAGTAAATTTAAAAAT
* * *
1304522 ATTAAATTAAGTTTGAAAAT
1 ATTAAAGTAAATTTAAAAAT
1304542 GTGTAAATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (20 bp):
ATTAAAGTAAATTTAAAAAT
Found at i:1312599 original size:13 final size:13
Alignment explanation
Indices: 1312581--1312624 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
1312571 GTCATAAATC
*
1312581 TATGACGTGCATT
1 TATGACGCGCATT
*
1312594 TATGACACGCATT
1 TATGACGCGCATT
1312607 TATGACGCGCATT
1 TATGACGCGCATT
1312620 TATGA
1 TATGA
1312625 TGCTAATTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:1317105 original size:20 final size:19
Alignment explanation
Indices: 1317082--1317128 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
1317072 CGATATACCA
1317082 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1317102 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1317122 GGTAAAA
1 GGTAAAA
1317129 CGTTATCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1317216 original size:181 final size:182
Alignment explanation
Indices: 1316870--1317342 Score: 678
Period size: 181 Copynumber: 2.6 Consensus size: 182
1316860 GATCCAAATT
* * * **
1316870 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAATTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * *
1316935 AAATCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGAATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGAATCGACACTTC
* * * *
1317000 GTGAATTTAAAATAGAAGCAGTTTTAAATCCTATAAAGTGTCGATAATTTTA
131 GTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATAATTTAA
* *
1317052 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
1317117 AAACCGGTAAAACGTTATCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGAATCGACACTTC
** * *
1317181 GTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATAATTTAA
* *
1317233 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
1317298 AAACCGGTAAAATGATACCGGATATATTGAAAGTGCCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1317343 CGTAAGTACG
Statistics
Matches: 259, Mismatches: 32, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
181 163 0.63
182 96 0.37
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGAATCGACACTTC
GTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATAATTTAA
Found at i:1317286 original size:20 final size:19
Alignment explanation
Indices: 1317263--1317309 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1317253 CGATATAACA
1317263 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1317283 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1317303 GGTAAAA
1 GGTAAAA
1317310 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1317311 original size:17 final size:19
Alignment explanation
Indices: 1317272--1317314 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1317262 AGGTAAAAAT
1317272 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1317292 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1317309 ATGATA
1 ATGATA
1317315 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1319565 original size:21 final size:21
Alignment explanation
Indices: 1319539--1319603 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1319529 AAGACAATCA
*
1319539 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
*
1319560 AGAGTCGAAGAGAAACTTAAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1319581 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1319602 AG
1 AG
1319604 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1319682 original size:33 final size:33
Alignment explanation
Indices: 1319637--1319702 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1319627 AAATAGATGG
* *
1319637 AGTGGTGGAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1319670 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1319703 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.50, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1321517 original size:19 final size:19
Alignment explanation
Indices: 1321493--1321541 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1321483 AATGTAGGGT
1321493 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1321512 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1321531 TAATTTTGTAT
1 TAATTTTGTAT
1321542 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1321997 original size:200 final size:199
Alignment explanation
Indices: 1321654--1322343 Score: 1202
Period size: 200 Copynumber: 3.4 Consensus size: 199
1321644 AATTTACAAT
* * *
1321654 ATGGCAAACAGAATGCAACAATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAG-GTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
1321719 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCAGTTTT
65 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
*
1321784 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAG
130 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1321849 AATGA
195 AATGA
*
1321854 ATGGCAAACAAGGTGCAACCATACAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAAC-AGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1321919 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
65 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
1321984 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
130 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1322049 AATGA
195 AATGA
1322054 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACA-GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1322119 CG-AAACCTAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTT
65 CGAAAACC-AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTT
* *
1322183 TATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
129 TATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
1322248 GAATGA
194 GAATGA
* *
1322254 ATGGAAAACAGGCTGCAACCATAAAGTGTCAATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGG-TGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1322319 CGAAACCCAAAAGTATAATGTAATA
65 CGAAAACCAAAAGTATAATGTAATA
1322344 GGTATTGCTT
Statistics
Matches: 469, Mismatches: 16, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
199 8 0.02
200 455 0.97
201 6 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (199 bp):
ATGGCAAACAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATC
GAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTTA
TGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGA
ATGA
Done.