Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold333
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: 1398653
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.32
Warning! 76431 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1179599 original size:147 final size:147
Alignment explanation
Indices: 1179343--1179639 Score: 531
Period size: 147 Copynumber: 2.0 Consensus size: 147
1179333 TCAGAGCAAA
1179343 TACTTTCTTTTATTCATCATGTTGATTATGTATGTGCTATGTGATGTGTGATGTACTGGCTACTT
1 TACTTTCTTTTATTCATCATGTTGATTATGTATGTGCTATGTGATGTGTGATGTACTGGCTACTT
*
1179408 CACTGACATTTTCTTTAATATGTTTTACATAATGTTTTCAGTTTCTAAGTAACTGTCCATTTTTC
66 CACTGACATTTTCTTTAATATGCTTTACATAATGTTTTCAGTTTCTAAGTAACTGTCCATTTTTC
1179473 TTCATTCTTAGATATGG
131 TTCATTCTTAGATATGG
*
1179490 TACTTTCTTTTATTCATCATGTTGATTATTTATGTGCTATGTGATGTGTGATGTACTGGCTACTT
1 TACTTTCTTTTATTCATCATGTTGATTATGTATGTGCTATGTGATGTGTGATGTACTGGCTACTT
* * *
1179555 CACTGACATTTTCTTTAATTTGCTTTACATAATGTTTTCTGTTTCTAAGTAACTGTCCGTTTTTC
66 CACTGACATTTTCTTTAATATGCTTTACATAATGTTTTCAGTTTCTAAGTAACTGTCCATTTTTC
* *
1179620 TTCTTTCTTGGATATGG
131 TTCATTCTTAGATATGG
1179637 TAC
1 TAC
1179640 ATGCGGTTAG
Statistics
Matches: 143, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 143 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (147 bp):
TACTTTCTTTTATTCATCATGTTGATTATGTATGTGCTATGTGATGTGTGATGTACTGGCTACTT
CACTGACATTTTCTTTAATATGCTTTACATAATGTTTTCAGTTTCTAAGTAACTGTCCATTTTTC
TTCATTCTTAGATATGG
Found at i:1180402 original size:1 final size:1
Alignment explanation
Indices: 1180396--1180425 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1180386 TCAAAGGTCC
1180396 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1180426 CACAGATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1181806 original size:13 final size:13
Alignment explanation
Indices: 1181788--1181815 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1181778 AGTCAGCTTC
1181788 ATTAATATATTTA
1 ATTAATATATTTA
1181801 ATTAATATATTTA
1 ATTAATATATTTA
1181814 AT
1 AT
1181816 ACAACAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTAATATATTTA
Found at i:1192404 original size:50 final size:51
Alignment explanation
Indices: 1192324--1192421 Score: 153
Period size: 50 Copynumber: 1.9 Consensus size: 51
1192314 TCAGGACATT
* * *
1192324 AGATAGAGAGGTCCCATGTACGACCATGTCTGGGACATGGCGTTGGCACCG
1 AGATAGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCCTTGGCACCG
*
1192375 AGAT-GAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCCTTGGCA
1 AGATAGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCCTTGGCA
1192422 TGTTATTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 39 0.91
51 4 0.09
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.19
Consensus pattern (51 bp):
AGATAGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCCTTGGCACCG
Found at i:1192550 original size:99 final size:99
Alignment explanation
Indices: 1192379--1192574 Score: 347
Period size: 99 Copynumber: 2.0 Consensus size: 99
1192369 GCACCGAGAT
* *
1192379 GAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCCTTGGCATGTTATTATCATAAGAGACCCG
1 GAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCCTTGGCATGTTATTATCATAAGAGACCCG
1192444 AGTATCCTTATTATTCCAATGTAGCTCAACGGTA
66 AGTATCCTTATTATTCCAATGTAGCTCAACGGTA
* *
1192478 GAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCCTTGGCATGTTATTATCATAAGATACCCG
1 GAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCCTTGGCATGTTATTATCATAAGAGACCCG
*
1192543 AGTATCCTTATTATTCTAATGTAGCTCAACGG
66 AGTATCCTTATTATTCCAATGTAGCTCAACGG
1192575 GCTAATAAAC
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (99 bp):
GAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCCTTGGCATGTTATTATCATAAGAGACCCG
AGTATCCTTATTATTCCAATGTAGCTCAACGGTA
Found at i:1206442 original size:3 final size:3
Alignment explanation
Indices: 1206434--1206459 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1206424 ATCATTAAGA
1206434 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1206460 TGGTTCACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1207816 original size:22 final size:23
Alignment explanation
Indices: 1207775--1207818 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1207765 TATTAATTTT
**
1207775 AAAAATATTAAATTTATTTGTAA
1 AAAAATATTAAAAATATTTGTAA
1207798 AAAAATATTAAAAAT-TTTGTA
1 AAAAATATTAAAAATATTTGTA
1207819 CATTTTCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
AAAAATATTAAAAATATTTGTAA
Found at i:1207967 original size:39 final size:39
Alignment explanation
Indices: 1207924--1208003 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
1207914 ACGCTATAAA
* **
1207924 ATTTTAAAATTTATTAGTTAA-TATATGTTTTA-ATTAATT
1 ATTTTAAAAATTATTA--TAAGTATAACTTTTATATTAATT
1207963 ATTTTAAAAATTATTATAAGTATAACTTTTATATTAATT
1 ATTTTAAAAATTATTATAAGTATAACTTTTATATTAATT
1208002 AT
1 AT
1208004 AATCCTTGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 3 0.08
38 9 0.25
39 24 0.67
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (39 bp):
ATTTTAAAAATTATTATAAGTATAACTTTTATATTAATT
Found at i:1209685 original size:2 final size:2
Alignment explanation
Indices: 1209678--1209702 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1209668 ATAAACATAC
1209678 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1209703 GAGTACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1211095 original size:16 final size:17
Alignment explanation
Indices: 1211054--1211096 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1211044 GATACACATA
*
1211054 TTTTTATAATTTATAAT
1 TTTTTATATTTTATAAT
1211071 TTCTTTATATTTTA-AAT
1 TT-TTTATATTTTATAAT
1211088 TTTTTATAT
1 TTTTTATAT
1211097 ATTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 10 0.42
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTATATTTTATAAT
Found at i:1211101 original size:18 final size:19
Alignment explanation
Indices: 1211054--1211101 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
1211044 GATACACATA
1211054 TTTTTATA-A-TTTATAAT
1 TTTTTATATATTTTATAAT
*
1211071 TTCTT-TATATTTTA-AAT
1 TTTTTATATATTTTATAAT
1211088 TTTTTATATATTTT
1 TTTTTATATATTTT
1211102 CTTTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 2 0.08
17 12 0.46
18 12 0.46
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTATATATTTTATAAT
Found at i:1212431 original size:16 final size:17
Alignment explanation
Indices: 1212389--1212432 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
1212379 TAAGTAATCA
*
1212389 GTATAGGCGAACCCCCT
1 GTATATGCGAACCCCCT
1212406 GTAGTATGCGAACCCCCT
1 GTA-TATGCGAACCCCCT
1212424 GT-TATGCGA
1 GTATATGCGA
1212433 CCCTCTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 7 0.28
17 3 0.12
18 15 0.60
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (17 bp):
GTATATGCGAACCCCCT
Found at i:1215755 original size:124 final size:124
Alignment explanation
Indices: 1215534--1215910 Score: 533
Period size: 124 Copynumber: 3.0 Consensus size: 124
1215524 TTAGGGTTTT
* *** * * * *
1215534 TAGGTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGATCAAATAGTATAAAATCGCTTTTAGC
1 TAGGTCATGGAAGAAATAATTT-TTTTTTACTTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * * * *
1215599 AGGATGTTATTTTAGAAGAATTTGTGAAATCGCGCCCTCGTAGACGCGCTTTTACTACAG
65 AGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
1215659 TAGGTCATGGAAGAAATAATTTTTTTTTACTTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
1 TAGGTCATGGAAGAAATAATTTTTTTTTACTTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
*
1215724 GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGTTTTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* *
1215783 TCGGTCATGGAAGAAAT-ATTTTTTTTTGA-TGTTTCTGAGCTAATAGTATAAAATCGCTTCTAG
1 TAGGTCATGGAAGAAATAATTTTTTTTT-ACT-TTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* * *
1215846 CAGGATGCTATTTGAAAAGAAATTGTGAAAATCGCGCCCTTGTGGACGCGCTTTTGCTACAG
64 CAGGATGCTATTTGAGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
1215908 TAG
1 TAG
1215911 CATGTTTGGG
Statistics
Matches: 228, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
123 11 0.05
124 161 0.71
125 56 0.25
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (124 bp):
TAGGTCATGGAAGAAATAATTTTTTTTTACTTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
GGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:1219211 original size:23 final size:23
Alignment explanation
Indices: 1219185--1219835 Score: 585
Period size: 23 Copynumber: 29.6 Consensus size: 23
1219175 TAGTTTAATT
*
1219185 TTTTTAA-TTAACTTAGTTTAGGG
1 TTTTTAAGTTAA-TTAGGTTAGGG
* *
1219208 TTTTAAAGTTAA--GGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219229 TTTTTAAGTTAA--GGGTTTAGGG
1 TTTTTAAGTTAATTAGG-TTAGGG
* **
1219251 TTTTTAAGTTAA--GGGTTAATG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219272 TTTTTAATTTAATTAGGTTAGGTTAGGG
1 TTTTTAAGTT-A--A--TTAGGTTAGGG
1219300 TTTTTAAGTTAATTAGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219323 TTTTTAA-TTAA--A--ATAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
* *
1219341 TGTTTAATTTAATTAGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219364 TTTTTAAGTTAA--GGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219385 TTTTTAATTTAATTAGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219408 TTTTTAATTTAATTAGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
1219431 TTTTTTAAGTTAATTAGGTTAGGG
1 -TTTTTAAGTTAATTAGGTTAGGG
*
1219455 TTTTTAA-TTAA--A--ATAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219473 TTTTTAA-TTAAATTAGGTTAGTGT
1 TTTTTAAGTT-AATTAGGTTAG-GG
* *
1219497 TTTTTAAGTTAATAAGGTTAGAG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219520 TTTTTAA-TTAA--A--ATAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
**
1219538 TTTTTACTTTAATTAGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
1219561 TTTTTAAGTTAA-T-GGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219582 TTTTTAATTTAATTAGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219605 TTTTTAA-TTAA--A--ATAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219623 TTTTTAA-TTAAATTAGGTTAGGAT
1 TTTTTAAGTT-AATTAGGTTAGG-G
1219647 TTTTTAAGTTAATTAGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219670 TTTTTAA-TTAA--A--ATAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
* *
1219688 TGTTTAATTTAATTAGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219711 TTTTTAAGTTAA--GGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219732 TTTTTAATTTAATTAGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
*
1219755 TTTTTAAATTTAATTAGGTTAGGG
1 TTTTT-AAGTTAATTAGGTTAGGG
*
1219779 TTTTTAAGTTAA--GGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
* **
1219800 TTGTTACTTTAATTAGGTTAGGG
1 TTTTTAAGTTAATTAGGTTAGGG
1219823 TTTTTAAGTTAAT
1 TTTTTAAGTTAAT
1219836 GGTTTTAAGT
Statistics
Matches: 526, Mismatches: 54, Indels: 96
0.78 0.08 0.14
Matches are distributed among these distances:
18 60 0.11
19 16 0.03
20 5 0.01
21 113 0.21
22 44 0.08
23 180 0.34
24 87 0.17
25 5 0.01
27 1 0.00
28 15 0.03
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.48
Consensus pattern (23 bp):
TTTTTAAGTTAATTAGGTTAGGG
Found at i:1219295 original size:28 final size:28
Alignment explanation
Indices: 1219264--1219321 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
1219254 TTAAGTTAAG
* *
1219264 GGTTAATGTTTTTAATTTAATTAGGTTA
1 GGTTAAGGTTTTTAAGTTAATTAGGTTA
*
1219292 GGTTAGGGTTTTTAAGTTAATTAGGTTA
1 GGTTAAGGTTTTTAAGTTAATTAGGTTA
1219320 GG
1 GG
1219322 GTTTTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (28 bp):
GGTTAAGGTTTTTAAGTTAATTAGGTTA
Found at i:1219484 original size:150 final size:147
Alignment explanation
Indices: 1219187--1219977 Score: 751
Period size: 150 Copynumber: 5.2 Consensus size: 147
1219177 GTTTAATTTT
* * * *
1219187 TTTAA-TTAACTTAGTTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTTTAAGTTAA--GGGTTTAG
1 TTTAATTTAA-TTAGGTTAGGGTTTTTAAGTTAA--GTTAGGGTTTTTAATTTAATTAGG-TTAG
* **
1219249 GGTTTTTAAGTTAAGGGTTAATGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTTAAGTTAATT
62 GGTTTTTAAGTTAAAGGTTAGGGTTTTTAA-TT-A--A--TTAGGTTAGGGTTTTTAAGTTAA-T
1219314 AGGTTAGGGTTTTTAATTAAAATAGGGTG
120 A-GTTAGGGTTTTTAATTAAAATAGGGTG
1219343 TTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGG
1 TTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--GTTAGGGTTTTTAATTTAATTAGGTTAGGG
* *
1219408 TTTTTAATTTAATTAGGTTAGGGTTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TTAA-A-ATA
64 TTTTTAAGTTAA--AGGTTAGGG-TTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTAATAGTTA
*
1219470 GGGTTTTTAATTAAATTAGGTTAGTG
125 GGGTTTTTAATTAAAATAGG---GTG
* * * ** *
1219496 TTTTTTAAGTTAATAAGGTTAGAGTTTTTAA-TTAAAATAGGGTTTTTACTTTAATTAGGTTAGG
1 ---TTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGTTAGGGTTTTTAATTTAATTAGGTTAGG
* *
1219560 GTTTTTAAGTTAATGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAA-A-ATAGG
63 GTTTTTAAGTTAAAGGTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTAATAGTTAGG
* *
1219622 GTTTTTAATTAAATTAGGTTAGGATTT
127 GTTTTTAATTAAA--A---TAGG-GTG
* ** *
1219649 TTTAAGTTAATTAGGTTAGGGTTTTTAA-TTAAAATAGGGTGTTTAATTTAATTAGGTTAGGGTT
1 TTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGTTAGGGTTTTTAATTTAATTAGGTTAGGGTT
* *
1219713 TTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAATTTAATTAGGTTAGG
66 TTTAAGTTAAAGGTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTT-AAGTTAA-TA-GTTAGG
**
1219778 GTTTTTAAGTTAAGGGTTAGGGT-
127 GTTTTTAA-TTAA--AATAGGGTG
* * *
1219801 TGTTACTTTAATTAGGTTAGGGTTTTTAAGTTAA--T--GG-TTTTAAGTTAA-TAGGTTAGGTT
1 T-TTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGTTAGGGTTTTTAATTTAATTAGGTTAGGGT
* *
1219860 TTTTAATTTAAA---TAGGGTTTTTAATTAAATTAGGGTAGGGTTTTTTAAGTTAATTAGGTTAG
65 TTTTAAGTTAAAGGTTAGGGTTTTTAATT-AATTAGGTTAGGG-TTTTTAAGTTAA-TA-GTTAG
1219922 GGTTTTTAATTAAAATAGGGTG
126 GGTTTTTAATTAAAATAGGGTG
1219944 TTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
1 TTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
1219978 GGTATTAATG
Statistics
Matches: 559, Mismatches: 44, Indels: 77
0.82 0.06 0.11
Matches are distributed among these distances:
142 37 0.07
143 1 0.00
144 6 0.01
145 48 0.09
146 5 0.01
148 20 0.04
149 9 0.02
150 181 0.32
151 10 0.02
152 7 0.01
153 69 0.12
154 13 0.02
155 26 0.05
156 83 0.15
157 26 0.05
158 2 0.00
159 7 0.01
160 9 0.02
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.48
Consensus pattern (147 bp):
TTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGTTAGGGTTTTTAATTTAATTAGGTTAGGGTT
TTTAAGTTAAAGGTTAGGGTTTTTAATTAATTAGGTTAGGGTTTTTAAGTTAATAGTTAGGGTTT
TTAATTAAAATAGGGTG
Found at i:1219485 original size:17 final size:18
Alignment explanation
Indices: 1219450--1219639 Score: 92
Period size: 18 Copynumber: 9.2 Consensus size: 18
1219440 TTAATTAGGT
1219450 TAGGGTTTTTAATTAAAA
1 TAGGGTTTTTAATTAAAA
1219468 TAGGGTTTTTAATTAAATTA
1 TAGGGTTTTTAATTAAA--A
*
1219488 GGTTAGTGTTTTTTAAGTTAATAA
1 ---TAG-GGTTTTTAA-TTAA-AA
*
1219512 GGTTAGAGTTTTTAATTAAAA
1 ---TAGGGTTTTTAATTAAAA
* *
1219533 TAGGGTTTTTACTTTAATTAGGT
1 TAGGGTTTTTA-ATTAA--A--A
**
1219556 TAGGGTTTTTAAGTTAATGGT
1 TAGGGTTTTTAA-TTAA--AA
*
1219577 TAGGGTTTTTAATTTAATTAGGT
1 TAGGGTTTTTAA-TTAA--A--A
1219600 TAGGGTTTTTAATTAAAA
1 TAGGGTTTTTAATTAAAA
*
1219618 TAGGGTTTTTAATTAAAT
1 TAGGGTTTTTAATTAAAA
1219636 TAGG
1 TAGG
1219640 TTAGGATTTT
Statistics
Matches: 142, Mismatches: 14, Indels: 32
0.76 0.07 0.17
Matches are distributed among these distances:
18 48 0.34
19 4 0.03
20 2 0.01
21 21 0.15
22 8 0.06
23 39 0.27
24 15 0.11
25 4 0.03
26 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.48
Consensus pattern (18 bp):
TAGGGTTTTTAATTAAAA
Found at i:1219848 original size:14 final size:15
Alignment explanation
Indices: 1219824--1219854 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1219814 AGGTTAGGGT
1219824 TTTTAAGTTAAT-GG
1 TTTTAAGTTAATAGG
1219838 TTTTAAGTTAATAGG
1 TTTTAAGTTAATAGG
1219853 TT
1 TT
1219855 AGGTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (15 bp):
TTTTAAGTTAATAGG
Found at i:1219853 original size:36 final size:38
Alignment explanation
Indices: 1219753--1219919 Score: 142
Period size: 44 Copynumber: 4.1 Consensus size: 38
1219743 ATTAGGTTAG
1219753 GGTTTTTAAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTA
1 GGTTTTT-AA-TTAATTAGGTTAGGGTTTTTAAGTTAA----TA
* *
1219797 GGGTTGTTACTTTAATTAGGTTAGGGTTTTTAAGTTAAT-
1 -GGTTTTTA-ATTAATTAGGTTAGGGTTTTTAAGTTAATA
* *
1219836 GG-TTTTAAGTTAA-TAGGTTAGGTTTTTTAATTTAAATA
1 GGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTT-AATA
*
1219874 GGGTTTTTAATTAAATTAGGGTAGGGTTTTTTAAGTTAATTA
1 -GGTTTTTAATT-AATTAGGTTAGGG-TTTTTAAGTTAA-TA
1219916 GGTT
1 GGTT
1219920 AGGGTTTTTA
Statistics
Matches: 103, Mismatches: 9, Indels: 24
0.76 0.07 0.18
Matches are distributed among these distances:
36 18 0.17
37 11 0.11
38 2 0.02
39 4 0.04
40 9 0.09
41 14 0.14
42 11 0.11
44 28 0.27
45 6 0.06
ACGTcount: A:0.27, C:0.01, G:0.24, T:0.49
Consensus pattern (38 bp):
GGTTTTTAATTAATTAGGTTAGGGTTTTTAAGTTAATA
Found at i:1219880 original size:18 final size:18
Alignment explanation
Indices: 1219853--1219895 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1219843 AGTTAATAGG
*
1219853 TTAGGTTTTTTAATTTAAA
1 TTAGGGTTTTTAA-TTAAA
1219872 -TAGGGTTTTTAATTAAA
1 TTAGGGTTTTTAATTAAA
1219889 TTAGGGT
1 TTAGGGT
1219896 AGGGTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (18 bp):
TTAGGGTTTTTAATTAAA
Found at i:1219898 original size:23 final size:23
Alignment explanation
Indices: 1219872--1219976 Score: 114
Period size: 23 Copynumber: 4.7 Consensus size: 23
1219862 TTAATTTAAA
*
1219872 TAGGGTTTTTAATTAAATTAGGG
1 TAGGGTTTTTAATTAAATTAGGT
1219895 TAGGGTTTTTTAAGTT-AATTAGGT
1 TAGGG-TTTTTAA-TTAAATTAGGT
1219919 TAGGGTTTTTAATTAAA--A---
1 TAGGGTTTTTAATTAAATTAGGT
* *
1219937 TAGGGTGTTTAATTTAATTAGGT
1 TAGGGTTTTTAATTAAATTAGGT
1219960 TAGGGTTTTTAAGTTAA
1 TAGGGTTTTTAA-TTAA
1219977 GGGTATTAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 17
0.76 0.06 0.19
Matches are distributed among these distances:
18 15 0.22
20 1 0.01
21 1 0.01
22 2 0.03
23 25 0.37
24 22 0.32
25 2 0.03
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.47
Consensus pattern (23 bp):
TAGGGTTTTTAATTAAATTAGGT
Found at i:1219930 original size:18 final size:18
Alignment explanation
Indices: 1219909--1219971 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
1219899 GTTTTTTAAG
1219909 TTAATTAGGTTAGGGTTT
1 TTAATTAGGTTAGGGTTT
***
1219927 TTAATTAAAATAGGGTGTTTAAT
1 TTAATTAGGTTA-GG-G-TT--T
1219950 TTAATTAGGTTAGGGTTT
1 TTAATTAGGTTAGGGTTT
1219968 TTAA
1 TTAA
1219972 GTTAAGGGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
18 14 0.41
19 2 0.06
20 3 0.09
21 3 0.09
22 2 0.06
23 10 0.29
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (18 bp):
TTAATTAGGTTAGGGTTT
Found at i:1219956 original size:65 final size:63
Alignment explanation
Indices: 1219295--1219976 Score: 528
Period size: 65 Copynumber: 10.6 Consensus size: 63
1219285 TAGGTTAGGT
* * *
1219295 TAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TTAA-A--ATAGGGTGTTTAATTTAATTA
1 TAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAA-TTAA--A
*
1219356 GGT
63 --A
* * *
1219359 TAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATT
1 TAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA-TAGGTTAGGGTTTTTAA-TTAA--
*
1219422 AGGT
62 A--A
* *
1219426 TAGGGTTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TTAA-A--ATAGGGTTTTTAATTAAATT
1 TAGGG-TTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAATTAAA--
1219487 A
63 A
* * * * * *
1219488 GGTTAGTGTTTTTTAAGTTAATAAGGTTAGAGTTTTTAA-TTAA-A--ATAGGGTTTTTACTTTA
1 ---TAG-GGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTA-ATTA
*
1219549 ATTAGGT
61 A--A--A
* *
1219556 TAGGGTTTTTAAGTTAA-T-GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTAAAA
1 TAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA-TAGGTTAGGGTTTTTAATTAAAA
* *
1219618 TAGGGTTTTTAATTAAATTAGGTTAGGATTTTTTAAGTTAATTAGGTTAGGGTTTTTAATTAAAA
1 TAGGGTTTTTAATTTAATTAGGTTAGG-GTTTTTAAGTTAA-TAGGTTAGGGTTTTTAATTAAAA
* *
1219683 TAGGGTGTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAATTTAATTA
1 TAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAA-TTAA--A
*
1219747 GGT
63 --A
* * * * *
1219750 TAGGGTTTTTAAATTTAATTAGGTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTGTTACTTTAAT
1 TAGGGTTTTT-AATTTAATTAGGTTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAATTAAAA
**** * * * *
1219813 TA-GG-TTAGGGTTT--TTAAGTTAATGG-TTTTAAGTTAATAGGTTAGGTTTTTTAATTTAAA
1 TAGGGTTTTTAATTTAATTAGGTT-AGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAATTAAAA
* *
1219872 TAGGGTTTTTAATTAAATTAGGGTAGGGTTTTTTAAGTTAATTAGGTTAGGGTTTTTAATTAAAA
1 TAGGGTTTTTAATTTAATTAGGTTAGGG-TTTTTAAGTTAA-TAGGTTAGGGTTTTTAATTAAAA
*
1219937 TAGGGTGTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
1 TAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA
1219977 GGGTATTAAT
Statistics
Matches: 522, Mismatches: 58, Indels: 76
0.80 0.09 0.12
Matches are distributed among these distances:
58 17 0.03
59 22 0.04
60 5 0.01
61 6 0.01
62 65 0.12
63 21 0.04
64 77 0.15
65 173 0.33
66 9 0.02
67 51 0.10
68 57 0.11
69 4 0.01
70 15 0.03
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (63 bp):
TAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATAGGTTAGGGTTTTTAATTAAAA
Found at i:1220018 original size:145 final size:143
Alignment explanation
Indices: 1219727--1220018 Score: 331
Period size: 145 Copynumber: 2.0 Consensus size: 143
1219717 AGTTAAGGGT
* * *
1219727 TAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAATTTAATTAGGTTAGGGTTTTTAAGTTAAG
1 TAGGGTTTTTAATTAAATTAGGGTAGGGTTTTTAAAGTTAATTAGGTTAGGGTTTTTAAGTTAA-
** * * * *
1219792 GGTTAGGGTTGTTACTTTAATTAGGTTAGGGTTTTTAAGTTAATGGTTTTAAGTTAATAGGTTAG
65 GAATAGGGTTGTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTATTAAGTTAATAGATTA-
* **** *
1219857 GTTTTTTAATTTAAA
129 CTCAAATAATTAAAA
*
1219872 TAGGGTTTTTAATTAAATTAGGGTAGGGTTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TTAA-
1 TAGGGTTTTTAATTAAATTAGGGTAGGGTTTTTAAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
*
1219935 AATAGGG-TGTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTATTAATGGTTAGTAGAAT
66 AATAGGGTTG-TTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTATTAA--GTTAATAG-AT
1219999 T-CTCAAATAATATCAAAA
127 TACTCAAATAAT-T-AAAA
1220017 TA
1 TA
1220019 TTCAAAATAT
Statistics
Matches: 124, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
141 2 0.02
142 43 0.35
143 5 0.04
144 12 0.10
145 62 0.50
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.46
Consensus pattern (143 bp):
TAGGGTTTTTAATTAAATTAGGGTAGGGTTTTTAAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
AATAGGGTTGTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTATTAAGTTAATAGATTACT
CAAATAATTAAAA
Found at i:1220035 original size:18 final size:16
Alignment explanation
Indices: 1220007--1220042 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 16
1219997 ATTCTCAAAT
1220007 AATATCAAAATATTCAA
1 AATATCAAAATATT-AA
1220024 AATATGCAAAATATTAA
1 AATAT-CAAAATATTAA
1220041 AA
1 AA
1220043 AATTTCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.28
Consensus pattern (16 bp):
AATATCAAAATATTAA
Found at i:1220043 original size:18 final size:17
Alignment explanation
Indices: 1220007--1220043 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1219997 ATTCTCAAAT
*
1220007 AATATCAAAATATTCAA
1 AATATCAAAATATTAAA
1220024 AATATGCAAAATATTAAA
1 AATAT-CAAAATATTAAA
1220042 AA
1 AA
1220044 ATTTCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (17 bp):
AATATCAAAATATTAAA
Found at i:1220520 original size:18 final size:18
Alignment explanation
Indices: 1220497--1220536 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1220487 GACTCGGAAA
*
1220497 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
1220515 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
1220533 AGGA
1 AGGA
1220537 AACGCACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:1222411 original size:50 final size:51
Alignment explanation
Indices: 1222356--1222470 Score: 198
Period size: 50 Copynumber: 2.3 Consensus size: 51
1222346 TATTTTAAAA
1222356 AAGGAAATTGAGAGCAA-ATGGAAATTAAATATGGA-TTTAGAGAATTTTGG
1 AAGGAAATTGAGAG-AATATGGAAATTAAATATGGATTTTAGAGAATTTTGG
*
1222406 AAGGAAATTGAGAGAATATTGAAATTAAATATGGATTTTAGAGAATTTTGG
1 AAGGAAATTGAGAGAATATGGAAATTAAATATGGATTTTAGAGAATTTTGG
1222457 AAGGAAATTGAGAG
1 AAGGAAATTGAGAG
1222471 GAATTTGAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
49 2 0.03
50 31 0.50
51 29 0.47
ACGTcount: A:0.44, C:0.01, G:0.26, T:0.29
Consensus pattern (51 bp):
AAGGAAATTGAGAGAATATGGAAATTAAATATGGATTTTAGAGAATTTTGG
Found at i:1222421 original size:22 final size:22
Alignment explanation
Indices: 1222394--1222488 Score: 59
Period size: 22 Copynumber: 4.0 Consensus size: 22
1222384 ATATGGATTT
1222394 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
* * **
1222416 AGAGAATATTGAAATTAAATATGG
1 AGAGAATTTTGGAAGGAAAT-T-G
1222440 ATTTTAGAGAATTTTGGAAGGAAATTG
1 -----AGAGAATTTTGGAAGGAAATTG
1222467 AGAGGAA-TTT-GAGAGGAAATTG
1 AGA-GAATTTTGGA-AGGAAATTG
1222489 GGAGGAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
21 2 0.04
22 31 0.55
23 4 0.07
24 1 0.02
27 1 0.02
28 1 0.02
29 16 0.29
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.29
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:1222467 original size:51 final size:50
Alignment explanation
Indices: 1222356--1222478 Score: 196
Period size: 51 Copynumber: 2.4 Consensus size: 50
1222346 TATTTTAAAA
*
1222356 AAGGAAATTGAGAGCAA-ATGGAAATTAAATATGGATTTAGAGAATTTTGG
1 AAGGAAATTGAGAG-AATATTGAAATTAAATATGGATTTAGAGAATTTTGG
1222406 AAGGAAATTGAGAGAATATTGAAATTAAATATGGATTTTAGAGAATTTTGG
1 AAGGAAATTGAGAGAATATTGAAATTAAATATGGA-TTTAGAGAATTTTGG
1222457 AAGGAAATTGAGAGGAAT-TTGA
1 AAGGAAATTGAGA-GAATATTGA
1222479 GAGGAAATTG
Statistics
Matches: 69, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
49 2 0.03
50 31 0.45
51 32 0.46
52 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.26, T:0.29
Consensus pattern (50 bp):
AAGGAAATTGAGAGAATATTGAAATTAAATATGGATTTAGAGAATTTTGG
Found at i:1222478 original size:11 final size:11
Alignment explanation
Indices: 1222458--1222504 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
1222448 GAATTTTGGA
1222458 AGGAAATTGAG
1 AGGAAATTGAG
*
1222469 AGGAATTTGAG
1 AGGAAATTGAG
*
1222480 AGGAAATTGGG
1 AGGAAATTGAG
1222491 AGGAAATATGAG
1 AGGAAAT-TGAG
1222503 AG
1 AG
1222505 AGGATTAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 26 0.84
12 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.19
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:1225264 original size:25 final size:25
Alignment explanation
Indices: 1225235--1225288 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
1225225 TCTGCTGGTT
*
1225235 CTCTGCTGGTGCTGGTTCTTTGTTC
1 CTCTGCTGGCGCTGGTTCTTTGTTC
1225260 CTCTGCTGGCGCTGGTTCTTTGTTC
1 CTCTGCTGGCGCTGGTTCTTTGTTC
1225285 CTCT
1 CTCT
1225289 TTTCCACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.00, C:0.28, G:0.26, T:0.46
Consensus pattern (25 bp):
CTCTGCTGGCGCTGGTTCTTTGTTC
Found at i:1225939 original size:13 final size:13
Alignment explanation
Indices: 1225889--1225939 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
1225879 ACACTCAAAG
*
1225889 TTTTCAAAAACAC
1 TTTTCAAAAGCAC
*
1225902 TCTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
1225915 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
1225928 TTTTCAAAAGCA
1 TTTTCAAAAGCA
1225940 ATGAAGAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 5 0.16
13 22 0.71
14 4 0.13
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:1248061 original size:105 final size:105
Alignment explanation
Indices: 1247939--1248150 Score: 266
Period size: 105 Copynumber: 2.0 Consensus size: 105
1247929 TATAGGTAAT
*
1247939 AACATCGGGCTCAATGCCTCGTTTTATCATTGTGTCAACAATATCCT-CAGCTTTAGAAACCATC
1 AACATCGGGCTCAATGCCTCGCTTTATCATTGTGTCAACAATAT-CTACAGCTTTAGAAACCATC
** *
1248003 CCTTCTTTGCA-ATGTGCATCAACCAATGTAGAATACGTGAC
65 CCTTCCGTGCACA-GTGCATCAACCAATATAGAATACGTGAC
* * * * * * * *
1248044 AACATTGGGTTCAATGCCTTGCTTTCTCATTGTGTCAACGATCTCTACAGCTTTAGAAATCATTC
1 AACATCGGGCTCAATGCCTCGCTTTATCATTGTGTCAACAATATCTACAGCTTTAGAAACCATCC
* *
1248109 CTTCCGTGCACAGTGCATCAACCAATATGGTATACGTGAC
66 CTTCCGTGCACAGTGCATCAACCAATATAGAATACGTGAC
1248149 AA
1 AA
1248151 TATCAAGTGA
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
104 2 0.02
105 88 0.97
106 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (105 bp):
AACATCGGGCTCAATGCCTCGCTTTATCATTGTGTCAACAATATCTACAGCTTTAGAAACCATCC
CTTCCGTGCACAGTGCATCAACCAATATAGAATACGTGAC
Found at i:1249731 original size:30 final size:30
Alignment explanation
Indices: 1249697--1249755 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
1249687 GGGTCAGGCC
1249697 TAACAATTGGGCCTAGCCTATGAACACCTA
1 TAACAATTGGGCCTAGCCTATGAACACCTA
1249727 TAACAATTGGGCCTAGCCTATGAACACCT
1 TAACAATTGGGCCTAGCCTATGAACACCT
1249756 CTCGTTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (30 bp):
TAACAATTGGGCCTAGCCTATGAACACCTA
Found at i:1252297 original size:55 final size:55
Alignment explanation
Indices: 1252238--1252356 Score: 238
Period size: 55 Copynumber: 2.2 Consensus size: 55
1252228 ATATATTAAA
1252238 AATATTAACAATAAGTTATAATAAATTATTTTTTATATTCTTGCTAAAATAGCAT
1 AATATTAACAATAAGTTATAATAAATTATTTTTTATATTCTTGCTAAAATAGCAT
1252293 AATATTAACAATAAGTTATAATAAATTATTTTTTATATTCTTGCTAAAATAGCAT
1 AATATTAACAATAAGTTATAATAAATTATTTTTTATATTCTTGCTAAAATAGCAT
1252348 AATATTAAC
1 AATATTAAC
1252357 TAATTTGAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (55 bp):
AATATTAACAATAAGTTATAATAAATTATTTTTTATATTCTTGCTAAAATAGCAT
Found at i:1254753 original size:23 final size:23
Alignment explanation
Indices: 1254723--1254786 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
1254713 TTTTATGCAC
1254723 GCAAGTGATAGTGGCACTACGAT
1 GCAAGTGATAGTGGCACTACGAT
* *** * *
1254746 GCAAGTGAAAGCAACACTATGGT
1 GCAAGTGATAGTGGCACTACGAT
*
1254769 GCAAGTGTTAGTGGCACT
1 GCAAGTGATAGTGGCACT
1254787 TTTGTGCAAA
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (23 bp):
GCAAGTGATAGTGGCACTACGAT
Found at i:1267505 original size:45 final size:44
Alignment explanation
Indices: 1267440--1267530 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
1267430 CTAAATTTAA
* *
1267440 TTTAATTGTTTTGTTATTTATTTTGAAGCAAATAAAATTATATTT
1 TTTAATTATTTTATTATTTATTTTGAAGCAAATAAAATTAT-TTT
* *
1267485 TTTAATTATTTTATTTTTTATTTTGAAGCAAATAAGATTATTTT
1 TTTAATTATTTTATTATTTATTTTGAAGCAAATAAAATTATTTT
1267529 TT
1 TT
1267531 AGGTGAGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 5 0.12
45 37 0.88
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (44 bp):
TTTAATTATTTTATTATTTATTTTGAAGCAAATAAAATTATTTT
Found at i:1269556 original size:16 final size:16
Alignment explanation
Indices: 1269535--1269566 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1269525 TTCTCATTAG
1269535 TAGATGGTACAGTTTA
1 TAGATGGTACAGTTTA
1269551 TAGATGGTACAGTTTA
1 TAGATGGTACAGTTTA
1269567 GGGCCACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (16 bp):
TAGATGGTACAGTTTA
Found at i:1273347 original size:343 final size:344
Alignment explanation
Indices: 1272714--1273400 Score: 1367
Period size: 343 Copynumber: 2.0 Consensus size: 344
1272704 AATTAAATTT
1272714 TTATTCAAAAATACAATTTTATTTGAAAACATTTTCCATTTTACGCCCCTGCTCAGTCTCCACAG
1 TTATTCAAAAATACAATTTTATTTGAAAACATTTTCCATTTTACGCCCCTGCTCAGTCTCCACAG
1272779 TCTCCCCCTTATAAATGGCAGTCAAAAATGAGAGTAAGATGACGACGTCTCATCGTTACACATGA
66 TCTCCCCCTTATAAATGGCAGTCAAAAATGAGAGTAAGATGACGACGTCTCATCGTTACACATGA
1272844 GCACACCAACCAAAGCAATACTTTTATAACACCAAACCCACTTCCACCCATCATTCAGACCCATG
131 GCACACCAACCAAAGCAATACTTTTATAACACCAAACCCACTTCCACCCATCATTCAGACCCATG
1272909 TCTGCTCTTACTTTACCATGAACTAACGTTTCGGAAAGTAATCCATGTCGCAAGCCACGACCTTA
196 TCTGCTCTTACTTTACCATGAACTAACGTTTCGGAAAGTAATCCATGTCGCAAGCCACGACCTTA
1272974 AGCAGACCATTTGTCAATTTTGCTCCCACCCACCATCTCTCCAACACTCCACAATCCATCCGCCC
261 AGCAGACCATTTGTCAATTTTGCTCCCACCCACCATCTCTCCAACACTCCACAATCCATCCGCCC
1273039 AAGCCCCACATATTTTCTC
326 AAGCCCCACATATTTTCTC
1273058 TTATTC-AAAATACAATTTTATTTGAAAACATTTTCCATTTTACGCCCCTGCTCAGTCTCCACAG
1 TTATTCAAAAATACAATTTTATTTGAAAACATTTTCCATTTTACGCCCCTGCTCAGTCTCCACAG
1273122 TCTCCCCCTTATAAATGGCAGTCAAAAATGAGAGTAAGATGACGACGTCTCATCGTTACACATGA
66 TCTCCCCCTTATAAATGGCAGTCAAAAATGAGAGTAAGATGACGACGTCTCATCGTTACACATGA
1273187 GCACACCAACCAAAGCAATACTTTTATAACACCAAACCCACTTCCACCCATCATTCAGACCCATG
131 GCACACCAACCAAAGCAATACTTTTATAACACCAAACCCACTTCCACCCATCATTCAGACCCATG
1273252 TCTGCTCTTACTTTACCATGAACTAACGTTTCGGAAAGTAATCCATGTCGCAAGCCACGACCTTA
196 TCTGCTCTTACTTTACCATGAACTAACGTTTCGGAAAGTAATCCATGTCGCAAGCCACGACCTTA
1273317 AGCAGACCATTTGTCAATTTTGCTCCCACCCACCATCTCTCCAACACTCCACAATCCATCCGCCC
261 AGCAGACCATTTGTCAATTTTGCTCCCACCCACCATCTCTCCAACACTCCACAATCCATCCGCCC
1273382 AAGCCCCACATATTTTCTC
326 AAGCCCCACATATTTTCTC
1273401 CTCAACACCT
Statistics
Matches: 343, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
343 337 0.98
344 6 0.02
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (344 bp):
TTATTCAAAAATACAATTTTATTTGAAAACATTTTCCATTTTACGCCCCTGCTCAGTCTCCACAG
TCTCCCCCTTATAAATGGCAGTCAAAAATGAGAGTAAGATGACGACGTCTCATCGTTACACATGA
GCACACCAACCAAAGCAATACTTTTATAACACCAAACCCACTTCCACCCATCATTCAGACCCATG
TCTGCTCTTACTTTACCATGAACTAACGTTTCGGAAAGTAATCCATGTCGCAAGCCACGACCTTA
AGCAGACCATTTGTCAATTTTGCTCCCACCCACCATCTCTCCAACACTCCACAATCCATCCGCCC
AAGCCCCACATATTTTCTC
Found at i:1278491 original size:12 final size:12
Alignment explanation
Indices: 1278474--1278500 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1278464 AAATTTAAAG
1278474 TTTTTTATAATT
1 TTTTTTATAATT
1278486 TTTTTTATAATT
1 TTTTTTATAATT
1278498 TTT
1 TTT
1278501 ATAATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTATAATT
Found at i:1279081 original size:2 final size:2
Alignment explanation
Indices: 1279074--1279107 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1279064 CTAACAGCTT
1279074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1279108 TACCAGTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1287529 original size:193 final size:194
Alignment explanation
Indices: 1287154--1287540 Score: 505
Period size: 195 Copynumber: 2.0 Consensus size: 194
1287144 TAAAAGGTTA
1287154 AATAATATTCTCAAGATCTATCTGATTATTAGTCTCTAAGATTAAGCGATAGGTACCAATAACTA
1 AATAATATTCTCAAGATCTATCTGATTATTAGTCTCTAAGATTAAGCGATAGGTACCAATAACTA
* *
1287219 TCACGTCCTCTTTGAGATGGTTCCTATATAGATGAATTTCTCACTTTCTTTCAGTGCCCTGCTTG
66 TCACGTCCGCTTTGAGATGGTTCCTATATAGATGAA-TCCTCACTTTCTTTCAGTGCCCTGCTTG
*
1287284 CAAGGAATCCTTACGTTAAATTAGTAATATGAGTAGTGACACCAAAATCAATCCACCAAGTATTT
130 CAAGGAATCCTTACATTAAATTAGTAATATGAGTAGTGACACCAAAATCAATCCACCAAGTATTT
* * * * *
1287349 AATAATCTTCTCAAGAGTC-ATTTGATTATTAGTCTCTAAGATTAAGCGTTAGGTTCCAATAGCT
1 AATAATATTCTCAAGA-TCTATCTGATTATTAGTCTCTAAGATTAAGCGATAGGTACCAATAACT
* * * ** * *
1287413 ATTACTTCCGCTTTGAGATGGTTCCTCATGTAGATG-A-CCTCACTTTCTTTC-GATTTCTTGGT
65 ATCACGTCCGCTTTGAGATGGTTCCT-ATATAGATGAATCCTCACTTTCTTTCAG-TGCCCTGCT
* ** * * *
1287475 TGTAAGGAATCCTTACATTGGATTAGTAATGTGAGTAGT-AGCTCCAGAATCAATCCACCAAGTA
128 TGCAAGGAATCCTTACATTAAATTAGTAATATGAGTAGTGA-CACCAAAATCAATCCACCAAGTA
1287539 TT
192 TT
1287541 AGAAAGATCT
Statistics
Matches: 167, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
192 2 0.01
193 75 0.45
195 80 0.48
196 10 0.06
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (194 bp):
AATAATATTCTCAAGATCTATCTGATTATTAGTCTCTAAGATTAAGCGATAGGTACCAATAACTA
TCACGTCCGCTTTGAGATGGTTCCTATATAGATGAATCCTCACTTTCTTTCAGTGCCCTGCTTGC
AAGGAATCCTTACATTAAATTAGTAATATGAGTAGTGACACCAAAATCAATCCACCAAGTATTT
Found at i:1291669 original size:2 final size:2
Alignment explanation
Indices: 1291662--1291688 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1291652 GAATGTATGC
1291662 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 A
1291689 GGCAACAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1295448 original size:164 final size:165
Alignment explanation
Indices: 1295266--1295596 Score: 655
Period size: 164 Copynumber: 2.0 Consensus size: 165
1295256 CTTAATTTAT
1295266 TATTTTAGCTATTAAAATAAAATATTTAAAATATTTTTTACATTTAATTTTGTCTTCAAATTATT
1 TATTTTAGCTATTAAAATAAAATATTTAAAATATTTTTTACATTTAATTTTGTCTTCAAATTATT
1295331 TTAAATTGAAATTGAATAGAAATTGTAAAAAATAAAAATAAAAAAATTAATATATAGTAAAAGTA
66 TTAAATTGAAATTGAATAGAAATTGTAAAAAATAAAAATAAAAAAATTAATATATAGTAAAAGTA
1295396 TAGTCCTAAATTTAGATGTCAATTAATGCAAAATA
131 TAGTCCTAAATTTAGATGTCAATTAATGCAAAATA
1295431 TATTTTAGCTA-TAAAATAAAATATTTAAAATATTTTTTACATTTAATTTTGTCTTCAAATTATT
1 TATTTTAGCTATTAAAATAAAATATTTAAAATATTTTTTACATTTAATTTTGTCTTCAAATTATT
1295495 TTAAATTGAAATTGAATAGAAATTGTAAAAAATAAAAATAAAAAAATTAATATATAGTAAAAGTA
66 TTAAATTGAAATTGAATAGAAATTGTAAAAAATAAAAATAAAAAAATTAATATATAGTAAAAGTA
1295560 TAGTCCTAAATTTAGATGTCAATTAATGCAAAATA
131 TAGTCCTAAATTTAGATGTCAATTAATGCAAAATA
1295595 TA
1 TA
1295597 GTGTTAAATT
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
164 155 0.93
165 11 0.07
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (165 bp):
TATTTTAGCTATTAAAATAAAATATTTAAAATATTTTTTACATTTAATTTTGTCTTCAAATTATT
TTAAATTGAAATTGAATAGAAATTGTAAAAAATAAAAATAAAAAAATTAATATATAGTAAAAGTA
TAGTCCTAAATTTAGATGTCAATTAATGCAAAATA
Found at i:1305616 original size:1 final size:1
Alignment explanation
Indices: 1305610--1305644 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
1305600 TGGAGTGTAC
1305610 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1305645 GGGTGTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1310625 original size:13 final size:13
Alignment explanation
Indices: 1310607--1310635 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1310597 AAACAATGGA
1310607 TTTATTTTTATTT
1 TTTATTTTTATTT
1310620 TTTATTTTTATTT
1 TTTATTTTTATTT
1310633 TTT
1 TTT
1310636 CAGAGCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTATTTTTATTT
Found at i:1312627 original size:22 final size:22
Alignment explanation
Indices: 1312601--1312642 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1312591 TGAAATTATA
1312601 AATATATTAAAATATATAATAT
1 AATATATTAAAATATATAATAT
*
1312623 AATATATTAATATATATAAT
1 AATATATTAAAATATATAAT
1312643 CATATCGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATATTAAAATATATAATAT
Found at i:1313192 original size:22 final size:22
Alignment explanation
Indices: 1313166--1313207 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1313156 CGAAATTATA
1313166 AATATATTAAAATATATAATAT
1 AATATATTAAAATATATAATAT
*
1313188 AATATATTAATATATATAAT
1 AATATATTAAAATATATAAT
1313208 CATATCGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATATTAAAATATATAATAT
Found at i:1322201 original size:6 final size:6
Alignment explanation
Indices: 1322192--1322225 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1322182 ACTTTTTGCT
* *
1322192 TTTTGA TTTTGA TTGTGA TTTTGA TTTTAA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
1322226 TGATGTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:1326053 original size:19 final size:19
Alignment explanation
Indices: 1326029--1326065 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1326019 TAAATTTGAT
1326029 ATTATTACTGTTATTATTA
1 ATTATTACTGTTATTATTA
* *
1326048 ATTATTATTGTTGTTATT
1 ATTATTACTGTTATTATT
1326066 TGTTCATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (19 bp):
ATTATTACTGTTATTATTA
Found at i:1326213 original size:2 final size:2
Alignment explanation
Indices: 1326154--1326196 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1326144 TTTTATAATT
* *
1326154 TA TA TC TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1326196 T
1 T
1326197 TTTTTTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1326996 original size:189 final size:191
Alignment explanation
Indices: 1326660--1327041 Score: 529
Period size: 189 Copynumber: 2.0 Consensus size: 191
1326650 TTTTAAATGA
* * * * *
1326660 TCTCGGAAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCCCTTTTTTTTAATCCGA
1 TCTCGGAAATTAACAAAAGATCATGTCCTAACTTACGGGGCATGATCCCC-TTTTTCTAAACCGA
*
1326725 GATAGCTAAATATCTTTTAAATAAGTAAATTTTTGGCATCCATTTCGCGCATCGGGAATTCAAGA
65 GATAACTAAATATCTTTTAAATAAGTAAATTTTTGGCATCCATTTCGCGCATCGGGAATTCAAGA
* * * *
1326790 CATTGTGTGCTAACTTACTGGATATAATTCTCTTTCTCGATTAACGTAAAATATGCCC-TTT
130 CATTGTGTCCTAACTTACGGGATATAATTCTCTTTCCCGATTAACGTAAAACATGCCCATTT
* *
1326851 TCTCGGGAATTAACAAAAGATCATGTTCTAACTTACGGGGCATGAT-CCC-TTTTCTAAACCTGA
1 TCTCGGAAATTAACAAAAGATCATGTCCTAACTTACGGGGCATGATCCCCTTTTTCTAAACC-GA
* * * ** *
1326914 GATAATTAAATATCTTTTTAAATAAGTAAGTTTTTGGCGTTTA-TTCGCGTATCGGGAATTCAAG
65 GATAACTAAATATC-TTTTAAATAAGTAAATTTTTGGCATCCATTTCGCGCATCGGGAATTCAAG
* *
1326978 ACATTGTGTCCTAACTTACGGGATATAATTTTCTTTCCCGATTAACGTGAAACATGCCCATTT
129 ACATTGTGTCCTAACTTACGGGATATAATTCTCTTTCCCGATTAACGTAAAACATGCCCATTT
1327041 T
1 T
1327042 TCTCAAAAAA
Statistics
Matches: 168, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
188 9 0.05
189 87 0.52
190 31 0.18
191 41 0.24
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (191 bp):
TCTCGGAAATTAACAAAAGATCATGTCCTAACTTACGGGGCATGATCCCCTTTTTCTAAACCGAG
ATAACTAAATATCTTTTAAATAAGTAAATTTTTGGCATCCATTTCGCGCATCGGGAATTCAAGAC
ATTGTGTCCTAACTTACGGGATATAATTCTCTTTCCCGATTAACGTAAAACATGCCCATTT
Found at i:1329555 original size:25 final size:25
Alignment explanation
Indices: 1329504--1329585 Score: 92
Period size: 25 Copynumber: 3.3 Consensus size: 25
1329494 AGCTCTTCCA
* * * *
1329504 AGCTGAATAATGGTAAACTCCTCCG
1 AGCTGAATAACGGTAAGCTCATACG
*
1329529 AGTTGAATAACGGTAAGCTCATACG
1 AGCTGAATAACGGTAAGCTCATACG
* * *
1329554 AGCTGAGTATCGGTAAGCTCATAAG
1 AGCTGAATAACGGTAAGCTCATACG
1329579 AGCTGAA
1 AGCTGAA
1329586 GTCGGTAACC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (25 bp):
AGCTGAATAACGGTAAGCTCATACG
Found at i:1331229 original size:6 final size:6
Alignment explanation
Indices: 1331215--1331296 Score: 74
Period size: 6 Copynumber: 13.7 Consensus size: 6
1331205 TGAGGATAGG
* * * * *
1331215 ATCTTT ATCTGT ATCCGT ATCTGT TTCTGC ATCTGT ATCTGT AACTGT
1 ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT
* * * * *
1331263 ATATGT ATTTAT ATCTAT AACTGT ATCTGT ATCT
1 ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCT
1331297 AAAATTTTCT
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49
Consensus pattern (6 bp):
ATCTGT
Found at i:1336543 original size:23 final size:25
Alignment explanation
Indices: 1336517--1336565 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1336507 AAATAATTTT
1336517 TGAAAAAT-GAAAAT-AAAAATATG
1 TGAAAAATAGAAAATAAAAAATATG
* *
1336540 TGAAAATTAGAGAATAAAAAATATG
1 TGAAAAATAGAAAATAAAAAATATG
1336565 T
1 T
1336566 TTTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 5 0.23
25 10 0.45
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.24
Consensus pattern (25 bp):
TGAAAAATAGAAAATAAAAAATATG
Found at i:1338374 original size:17 final size:17
Alignment explanation
Indices: 1338352--1338386 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1338342 AACCTTCAAA
1338352 TGAAGGCTGGTTAAAGT
1 TGAAGGCTGGTTAAAGT
1338369 TGAAGGCTGGTTAAAGT
1 TGAAGGCTGGTTAAAGT
1338386 T
1 T
1338387 TAACGGTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.34, T:0.31
Consensus pattern (17 bp):
TGAAGGCTGGTTAAAGT
Found at i:1349247 original size:105 final size:104
Alignment explanation
Indices: 1349088--1349300 Score: 232
Period size: 105 Copynumber: 2.0 Consensus size: 104
1349078 ACCATTAACT
* *
1349088 AATGCACTATAGGTAACAACATCAGGCTCAATGCCTCGCTTTATCAATGCGTCAATGATATCCT-
1 AATGCACTATACGTAACAACATCAGGCTCAATGCCTCGCTTTATCAAT-CGTCAACGATAT-CTA
* * *
1349152 CAGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACC
64 CAGCTTCAGAAACCATCCCTTCCTTGCAAAGAGCATCAACC
* * * * * * *
1349193 AATGTACTATACGTGACAACATTAGGCTCAATGCCTTGCTTTCTC-ATCATGTCAACGGTCTCTA
1 AATGCACTATACGTAACAACATCAGGCTCAATGCCTCGCTTTATCAATC--GTCAACGATATCTA
* * * *
1349257 CAGCTTTAGAAATCATTCCTTCCTTGCAAAGAGCATCAATC
64 CAGCTTCAGAAACCATCCCTTCCTTGCAAAGAGCATCAACC
1349298 AAT
1 AAT
1349301 AGTTTGATAT
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
103 1 0.01
104 4 0.04
105 84 0.94
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (104 bp):
AATGCACTATACGTAACAACATCAGGCTCAATGCCTCGCTTTATCAATCGTCAACGATATCTACA
GCTTCAGAAACCATCCCTTCCTTGCAAAGAGCATCAACC
Found at i:1349580 original size:8 final size:8
Alignment explanation
Indices: 1349569--1349614 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
1349559 GCAGGGCAGC
1349569 AGAAAAGA
1 AGAAAAGA
1349577 AGAAAAGA
1 AGAAAAGA
*
1349585 AAAAAAGA
1 AGAAAAGA
* *
1349593 AAAAAAAA
1 AGAAAAGA
1349601 GAGAAAAGA
1 -AGAAAAGA
1349610 AGAAA
1 AGAAA
1349615 TGGACATATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 27 0.82
9 6 0.18
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:1349587 original size:13 final size:13
Alignment explanation
Indices: 1349569--1349610 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1349559 GCAGGGCAGC
1349569 AGAAAAGAAGAAA
1 AGAAAAGAAGAAA
*
1349582 AGAAAAAAAGAAA
1 AGAAAAGAAGAAA
*
1349595 AAAAAAG-AGAAA
1 AGAAAAGAAGAAA
1349607 AGAA
1 AGAA
1349611 GAAATGGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAGAAA
Found at i:1352836 original size:23 final size:25
Alignment explanation
Indices: 1352810--1352858 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1352800 AAATAATTTT
1352810 TGAAAAAT-GAAAATAAAAA-TATG
1 TGAAAAATAGAAAATAAAAAGTATG
* *
1352833 TGAAAACTAGAGAATAAAAAGTATG
1 TGAAAAATAGAAAATAAAAAGTATG
1352858 T
1 T
1352859 TTTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 10 0.45
25 5 0.23
ACGTcount: A:0.59, C:0.02, G:0.16, T:0.22
Consensus pattern (25 bp):
TGAAAAATAGAAAATAAAAAGTATG
Found at i:1363706 original size:22 final size:23
Alignment explanation
Indices: 1363677--1363732 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
1363667 AACGTTAGAA
*
1363677 AATATTATAAAA-A-ATATACAT
1 AATATTATAAAATACATATAAAT
1363698 ATATATTATAAAATACATATAAAT
1 A-ATATTATAAAATACATATAAAT
*
1363722 AATATAATAAA
1 AATATTATAAA
1363733 TGATGCAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.03
22 11 0.37
23 10 0.33
24 8 0.27
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (23 bp):
AATATTATAAAATACATATAAAT
Found at i:1363730 original size:18 final size:18
Alignment explanation
Indices: 1363692--1363730 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1363682 TATAAAAAAT
* *
1363692 ATACATATATATTATAAA
1 ATACATATAAATAATAAA
*
1363710 ATACATATAAATAATATA
1 ATACATATAAATAATAAA
1363728 ATA
1 ATA
1363731 AATGATGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
ATACATATAAATAATAAA
Found at i:1364303 original size:10 final size:10
Alignment explanation
Indices: 1364268--1364326 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
1364258 TATTTTAGGT
*
1364268 GAAACAAAAA
1 GAAATAAAAA
1364278 GAAA-ATAAAA
1 GAAATA-AAAA
1364288 GAAAATAAAAA
1 G-AAATAAAAA
1364299 GAAATATAAAA
1 GAAATA-AAAA
*
1364310 -AAATAAACA
1 GAAATAAAAA
1364319 GAAATAAA
1 GAAATAAA
1364327 CGATGAACAC
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
9 4 0.09
10 26 0.60
11 12 0.28
12 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.10
Consensus pattern (10 bp):
GAAATAAAAA
Found at i:1365481 original size:132 final size:132
Alignment explanation
Indices: 1365302--1365904 Score: 936
Period size: 132 Copynumber: 4.6 Consensus size: 132
1365292 CTGCTGACCG
* * *
1365302 GGGAAATAGAATTACTAGCTTCAATATACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCT
1 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCT
* * * * *
1365367 TTGATCTACTCCACTATTGCTTAGGGAGATAATATCTGTAATCTTCAATCTATTCCGCTGCAGCC
66 TTGATCTGCCCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCGCTGCTGCC
*
1365432 CA
131 TA
*
1365434 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCTTAGGGAGGTAAAATCCACCATCT
1 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCT
1365499 TTGATCTGCCCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCGCTGCTGCC
66 TTGATCTGCCCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCGCTGCTGCC
1365564 TA
131 TA
* * *
1365566 GGGAAGTAGAATTACTGGCTTCAATGTCCTCCACTGCAACCTTAGGGAGGGAAAATCCACCATCT
1 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCT
*
1365631 TTGATTTGCCCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCGCTGCTGCC
66 TTGATCTGCCCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCGCTGCTGCC
1365696 TA
131 TA
* *
1365698 GGGAAGTAGAATTACTGGCTTCAATGTCCTCCACTGCAACCTCAGGGAGGTAAAATCTACCATCT
1 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCT
* ** * ** * ** * *
1365763 TCGATCTGCTTCACTATTTATGTAGGAAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGC
66 TTGATCTGCCCCACTACTGCT-TAGGGAGATAAAATCTGTAATCTTCAATCTATTCCGCTGCTGC
1365828 CTA
130 CTA
*
1365831 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCTACCATCT
1 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCT
*
1365896 TCGATCTGC
66 TTGATCTGC
1365905 TATGACATGT
Statistics
Matches: 441, Mismatches: 29, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
132 327 0.74
133 114 0.26
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (132 bp):
GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCT
TTGATCTGCCCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCGCTGCTGCC
TA
Found at i:1376701 original size:30 final size:30
Alignment explanation
Indices: 1376665--1376895 Score: 288
Period size: 30 Copynumber: 7.7 Consensus size: 30
1376655 TGTATTTAAA
* *
1376665 ATTTTAAAAATAAAAAAATATATGTAATGG
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
1376695 ATTTTAAAAATAAAAAAATACT-TGTAGTGT
1 ATTTTAAAAATAAAAAAATA-TATGTAGTGT
* * * *
1376725 ATTTT-AATATATATATATATATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
1376754 ATTTTAAAAAT-AAAAAATATATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
* * *
1376783 ATTCTAGAAATAAAAAAATATATGTAGTCT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
* * * * *
1376813 ATTTTAATATATATATATATATATGAAGTGT
1 ATTTTAA-AAATAAAAAAATATATGTAGTGT
*
1376844 ATTTTAAAAGTAAAAAAATATATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGT
1376874 ATTTTAAAAATAAAAAAATATA
1 ATTTTAAAAATAAAAAAATATA
1376896 AAGTAGTCAA
Statistics
Matches: 168, Mismatches: 28, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
28 1 0.01
29 47 0.28
30 95 0.57
31 25 0.15
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.39
Consensus pattern (30 bp):
ATTTTAAAAATAAAAAAATATATGTAGTGT
Found at i:1376816 original size:88 final size:91
Alignment explanation
Indices: 1376665--1376895 Score: 362
Period size: 88 Copynumber: 2.6 Consensus size: 91
1376655 TGTATTTAAA
* * *
1376665 ATTTTAAAAATAAAAAAATATATGTAATGGATTTTAAAAATAAAAAAATACT-TGTAGTGTATTT
1 ATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAATA-TATGTAGTCTATTT
*
1376729 T-A-ATATATATATATATATGTAGTGT
65 TAATATATATATATATATATGAAGTGT
* *
1376754 ATTTTAAAAAT-AAAAAATATATGTAGTGTATTCTAGAAATAAAAAAATATATGTAGTCTATTTT
1 ATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAATATATGTAGTCTATTTT
1376818 AATATATATATATATATATGAAGTGT
66 AATATATATATATATATATGAAGTGT
*
1376844 ATTTTAAAAGTAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAATATA
1 ATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAATATA
1376896 AAGTAGTCAA
Statistics
Matches: 129, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
87 1 0.01
88 46 0.36
89 12 0.09
90 32 0.25
91 38 0.29
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.39
Consensus pattern (91 bp):
ATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAATATATGTAGTCTATTTT
AATATATATATATATATATGAAGTGT
Found at i:1376845 original size:61 final size:59
Alignment explanation
Indices: 1376669--1376899 Score: 245
Period size: 59 Copynumber: 3.9 Consensus size: 59
1376659 TTTAAAATTT
* * * * *
1376669 TAAAAATAAAAAAATATATGTAATGGATTTTAAAAATAAAAAA-ATACTTGTAGTGTATTT
1 TAAAAGTAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATA--TGAAGTGTATTC
* * * * *
1376729 TAATA-TATATATATATATGTAGTGTATTTTAAAAATAAAAAATATATGTAGTGTATTC
1 TAAAAGTAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGAAGTGTATTC
* * * * *
1376787 TAGAAA-TAAAAAAATATATGTAGTCTATTTTAATATATATATATATATATGAAGTGTATTT
1 TA-AAAGTAAAAAAATATATGTAGTGTATTTTAA-AAATA-AAAAATATATGAAGTGTATTC
*
1376848 TAAAAGTAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAA-ATATAAAGT
1 TAAAAGTAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGAAGT
1376900 AGTCAATTAA
Statistics
Matches: 144, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
58 21 0.15
59 60 0.42
60 18 0.12
61 45 0.31
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (59 bp):
TAAAAGTAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAATATATGAAGTGTATTC
Found at i:1377365 original size:21 final size:21
Alignment explanation
Indices: 1377313--1377367 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1377303 ACCATTGTTT
* *
1377313 CTAATCTCACAGCTACAGTAT
1 CTAATCTCACCGCTACAGTAA
*
1377334 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAGTAA
1377355 CTAATCTCACCGC
1 CTAATCTCACCGC
1377368 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.36, G:0.09, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:1378643 original size:36 final size:36
Alignment explanation
Indices: 1378565--1378643 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
1378555 TAAAGGAAAC
*
1378565 TAAATATTTCTAATAATCATTTTCACCAAATATTTAA
1 TAAA-ATTTCTAATAATCATTTTCACCAAATACTTAA
* *
1378602 TAAAATTTCTAATAAAT-ATTTTTACTAAATGACTTAA
1 TAAAATTTCTAAT-AATCATTTTCACCAAAT-ACTTAA
1378639 -AAAAT
1 TAAAAT
1378644 ATAAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 25 0.68
37 12 0.32
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (36 bp):
TAAAATTTCTAATAATCATTTTCACCAAATACTTAA
Found at i:1379942 original size:105 final size:105
Alignment explanation
Indices: 1379784--1379999 Score: 236
Period size: 105 Copynumber: 2.1 Consensus size: 105
1379774 ACTATAGGTA
** *
1379784 ACAACATTAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATATCCTCAGCTTCAGAGACCAT
1 ACAACATTAGGCTCAATGCCTCGCTTTATCATCACGTCAACAATATCCTCAGCTTCAGAAACCAT
* * *
1379849 CCCTTCCTTGCAATGCGCATCAACCAATGTATTATACGTG
66 CCCTTCCTTGCAAAGCGCATCAACCAATATATTATAAGTG
* * * *** * * * *
1379889 ACAACATTAGGCTCAATGCCTTGCTTTCTCATCATGTCAATGGTCT-CTACAGCTTTAGAAATCG
1 ACAACATTAGGCTCAATGCCTCGCTTTATCATCACGTCAACAATATCCT-CAGCTTCAGAAACCA
* * *
1379953 TTCCTTCCTTGCAAAGTGCATCAATCAATATATTATAAGTG
65 TCCCTTCCTTGCAAAGCGCATCAACCAATATATTATAAGTG
*
1379994 TCAACA
1 ACAACA
1380000 AGTGAAATAT
Statistics
Matches: 90, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
104 2 0.02
105 88 0.98
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (105 bp):
ACAACATTAGGCTCAATGCCTCGCTTTATCATCACGTCAACAATATCCTCAGCTTCAGAAACCAT
CCCTTCCTTGCAAAGCGCATCAACCAATATATTATAAGTG
Found at i:1381519 original size:18 final size:19
Alignment explanation
Indices: 1381481--1381534 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1381471 AATACAAAAT
1381481 AATTCAAAATCATTT-TAAA
1 AATTCAAAAT-ATTTATAAA
1381500 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
1381519 AATTCCAAA-ATTTATA
1 AATTCAAAATATTTATA
1381535 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:1389600 original size:5 final size:5
Alignment explanation
Indices: 1389592--1389641 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
1389582 TTTAATTATC
* * *
1389592 ATAAT ATAAT ATAAT ATAATT ATAAT ATAAT -TATT ATAAT TTAAC ATAAT
1 ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1389642 TAAATTTATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
4 3 0.08
5 29 0.78
6 5 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (5 bp):
ATAAT
Found at i:1389617 original size:16 final size:16
Alignment explanation
Indices: 1389592--1389643 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
1389582 TTTAATTATC
1389592 ATAA-TATAATATAAT
1 ATAATTATAATATAAT
1389607 ATAATTATAATATAAT
1 ATAATTATAATATAAT
* *
1389623 -T-ATTATAATTTAAC
1 ATAATTATAATATAAT
1389637 ATAATTA
1 ATAATTA
1389644 AATTTATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 11 0.34
15 6 0.19
16 15 0.47
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTATAATATAAT
Found at i:1389631 original size:35 final size:36
Alignment explanation
Indices: 1389550--1389641 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 36
1389540 GTTGACGTAT
* * *
1389550 TAATTAATATAA-ATAAATAA-ATTAGTTATAAATT
1 TAATTATTATAATATAAATAATATTAATTATAAATA
*
1389584 TAATTATCATAATATAATATAATA-TAATTAT-AATA
1 TAATTATTATAATATAA-ATAATATTAATTATAAATA
*
1389619 TAATTATTATAATTTAACATAAT
1 TAATTATTATAATATAA-ATAAT
1389642 TAAATTTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 10 0.21
35 27 0.56
36 10 0.21
37 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (36 bp):
TAATTATTATAATATAAATAATATTAATTATAAATA
Found at i:1390375 original size:6 final size:6
Alignment explanation
Indices: 1390357--1390396 Score: 71
Period size: 6 Copynumber: 6.5 Consensus size: 6
1390347 GAAACAGGGG
1390357 AAAGGA GAAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAA
1 AAAGGA -AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAA
1390397 ATTAGGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:1391944 original size:19 final size:19
Alignment explanation
Indices: 1391916--1391953 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1391906 ATTGCATATG
*
1391916 AATTGAAATGAGATTGAAA
1 AATTGAAATGAAATTGAAA
*
1391935 AATTGCAATGAAATTGAAA
1 AATTGAAATGAAATTGAAA
1391954 TAGTGAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (19 bp):
AATTGAAATGAAATTGAAA
Found at i:1392524 original size:18 final size:17
Alignment explanation
Indices: 1392485--1392641 Score: 147
Period size: 18 Copynumber: 8.8 Consensus size: 17
1392475 TTTTTAAAAA
1392485 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
1392502 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
*
1392519 TGCGTGTTTTCAAAAAATTC
1 T-CGTG-TTTC-AAAAATTT
1392539 TCGTGTTT-AAAAATTT
1 TCGTGTTTCAAAAATTT
*
1392555 TCGCAT-TTTCAAAAAATT
1 TCG--TGTTTCAAAAATTT
*
1392573 TCAGTGCTTCAAAAATTT
1 TC-GTGTTTCAAAAATTT
* * *
1392591 TCTTATTTTCAAAAAATTA
1 TCGT-GTTTC-AAAAATTT
1392610 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
* *
1392627 CCATGTTTTCAAAAA
1 TCGTG-TTTCAAAAA
1392642 AAATTATTAT
Statistics
Matches: 115, Mismatches: 14, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.09
17 33 0.29
18 45 0.39
19 19 0.17
20 8 0.07
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:1392532 original size:36 final size:35
Alignment explanation
Indices: 1392485--1392696 Score: 178
Period size: 36 Copynumber: 5.8 Consensus size: 35
1392475 TTTTTAAAAA
1392485 TCGTG-TTTCAAAAATTTTCGTGTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTTTCGTGTTTCAAAAATTT
*
1392519 TGCGTGTTTTCAAAAAATTCTCGTGTTT-AAAAATTT
1 T-CGTGTTTTC-AAAAATTTTCGTGTTTCAAAAATTT
** * *
1392555 TCGCATTTTCAAAAAATTTCAGTGCTTCAAAAATTT
1 TCGTGTTTTCAAAAATTTTC-GTGTTTCAAAAATTT
* * *
1392591 TCTTATTTTCAAAAAATTATCGTGTTTCAAAAATTT
1 TCGTGTTTTC-AAAAATTTTCGTGTTTCAAAAATTT
* * * *
1392627 CCATGTTTTCAAAAAAAATTATTATGGTGTTTC-AAAATTC
1 TCGTGTTTTC---AAAAA-T-TT-TCGTGTTTCAAAAATTT
* *
1392667 TCGTGTTTTAAAAAAATTCTCGTGTTTCAA
1 TCGTGTTTT-CAAAAATTTTCGTGTTTCAA
1392697 TCGGATCACG
Statistics
Matches: 143, Mismatches: 22, Indels: 24
0.76 0.12 0.13
Matches are distributed among these distances:
34 9 0.06
35 24 0.17
36 52 0.36
37 24 0.17
38 11 0.08
39 1 0.01
40 14 0.10
41 8 0.06
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (35 bp):
TCGTGTTTTCAAAAATTTTCGTGTTTCAAAAATTT
Found at i:1392675 original size:40 final size:40
Alignment explanation
Indices: 1392606--1392682 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
1392596 TTTTCAAAAA
1392606 ATTATCGTGTTTCAAAAATTTCCATGTTTTCAAAAAAAATT
1 ATTATCGTGTTTCAAAAATTTCCATGTTTT-AAAAAAAATT
* *
1392647 ATTATGGTGTTTC-AAAA-TTCTCGTGTTTTAAAAAAA
1 ATTATCGTGTTTCAAAAATTTC-CATGTTTTAAAAAAA
1392683 TTCTCGTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 10 0.30
40 11 0.33
41 12 0.36
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (40 bp):
ATTATCGTGTTTCAAAAATTTCCATGTTTTAAAAAAAATT
Found at i:1393814 original size:21 final size:19
Alignment explanation
Indices: 1393765--1393815 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
1393755 TGTAATAACT
*
1393765 ATAAAGAAAGAAAGAGAAG
1 ATAAAGAAAAAAAGAGAAG
1393784 A-AAAGGGAAAAAAATGAGAAG
1 ATAAA--GAAAAAAA-GAGAAG
1393805 ATTAAAGAAAA
1 A-TAAAGAAAA
1393816 GAAGTAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 3 0.12
19 1 0.04
20 7 0.27
21 12 0.46
23 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
ATAAAGAAAAAAAGAGAAG
Found at i:1395092 original size:105 final size:105
Alignment explanation
Indices: 1394910--1395270 Score: 650
Period size: 105 Copynumber: 3.4 Consensus size: 105
1394900 TTCTAGCTTT
1394910 ATTCCTTCCTTGCAAAGTGCATCAACCAATGTACTATACGTGACAACATCGGGCTCAATGCCTTG
1 ATTCCTTCCTTGCAAAGTGCATCAACCAATGTACTATACGTGACAACATCGGGCTCAATGCCTTG
1394975 CTTTCTCATCATGTCAACGGTCTCTACAGCTTTAGAAATC
66 CTTTCTCATCATGTCAACGGTCTCTACAGCTTTAGAAATC
* **
1395015 ATTCCTTCCTTGCAAAGTGCATCAACCAATGTACTATATGTGACAACATTAGGCTCAATGCCTTG
1 ATTCCTTCCTTGCAAAGTGCATCAACCAATGTACTATACGTGACAACATCGGGCTCAATGCCTTG
1395080 CTTTCTCATCATGTCAACGGTCTCTACAGCTTTAGAAATC
66 CTTTCTCATCATGTCAACGGTCTCTACAGCTTTAGAAATC
1395120 ATTCCTTCCTTGCAAAGTGCATCAACCAATGTACTATACGTGACAACATCGGGCTCAATGCCTTG
1 ATTCCTTCCTTGCAAAGTGCATCAACCAATGTACTATACGTGACAACATCGGGCTCAATGCCTTG
1395185 CTTTCTCATCATGTCAACGGTCTCTACAGCTTTAGAAATC
66 CTTTCTCATCATGTCAACGGTCTCTACAGCTTTAGAAATC
* ** * *
1395225 GTTCCTTCCTTGCAAAGAACATCAACCAATGTATTATACATGACAA
1 ATTCCTTCCTTGCAAAGTGCATCAACCAATGTACTATACGTGACAA
1395271 TATGAAGTGA
Statistics
Matches: 245, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 245 1.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (105 bp):
ATTCCTTCCTTGCAAAGTGCATCAACCAATGTACTATACGTGACAACATCGGGCTCAATGCCTTG
CTTTCTCATCATGTCAACGGTCTCTACAGCTTTAGAAATC
Found at i:1397124 original size:21 final size:18
Alignment explanation
Indices: 1397081--1397117 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1397071 AATACTTTTG
1397081 AATTTTTTTTATGAACAT
1 AATTTTTTTTATGAACAT
1397099 AATTTTTTTTATGAACAT
1 AATTTTTTTTATGAACAT
1397117 A
1 A
1397118 CTAATTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
AATTTTTTTTATGAACAT
Done.