Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 7 of 125
Found at i:2256669 original size:15 final size:16
Alignment explanation
Indices: 2256635--2256671 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2256625 TTGGAAAAGT
2256635 TTTTAAATATATATGG
1 TTTTAAATATATATGG
2256651 TTTTAAAT-T-TATGGG
1 TTTTAAATATATAT-GG
2256666 TTTTAA
1 TTTTAA
2256672 CATGAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 9 0.45
16 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (16 bp):
TTTTAAATATATATGG
Found at i:2259712 original size:9 final size:9
Alignment explanation
Indices: 2259698--2259723 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2259688 GAATGTACTA
2259698 ACCAATACG
1 ACCAATACG
2259707 ACCAATACG
1 ACCAATACG
2259716 ACCAATAC
1 ACCAATAC
2259724 TAATACGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.35, G:0.08, T:0.12
Consensus pattern (9 bp):
ACCAATACG
Found at i:2263357 original size:20 final size:20
Alignment explanation
Indices: 2263332--2263423 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
2263322 ATTATATTGT
* *
2263332 TGTTTTGGTATTTTTTTTGC
1 TGTTTTGGTGTTTTTTTTAC
* * *
2263352 TGTTTTGGTTGCTATTTTTGC
1 TGTTTTGG-TGTTTTTTTTAC
* *
2263373 TGTTTTTGTGTTATGTTTTTAT
1 TGTTTTGGTGTT-T-TTTTTAC
*
2263395 TATTTTGGTGTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
2263415 TGTTTTGGT
1 TGTTTTGGT
2263424 TGCTGTTTTG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
20 25 0.44
21 17 0.30
22 15 0.26
ACGTcount: A:0.07, C:0.04, G:0.21, T:0.68
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:2263432 original size:21 final size:21
Alignment explanation
Indices: 2263345--2263432 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 21
2263335 TTTGGTATTT
* *
2263345 TTTTTGCTGTTTTGGTTGCTA
1 TTTTTACTGTTTTGGTTGCTG
* *
2263366 TTTTTGCTGTTTTTGTGTT-ATG
1 TTTTTACTG-TTTTG-GTTGCTG
* * * *
2263388 TTTTTATTATTTTGG-TGTTT
1 TTTTTACTGTTTTGGTTGCTG
2263408 TTTTTACTGTTTTGGTTGCTG
1 TTTTTACTGTTTTGGTTGCTG
2263429 TTTT
1 TTTT
2263433 GGTGTTATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
19 1 0.02
20 15 0.29
21 21 0.40
22 12 0.23
23 3 0.06
ACGTcount: A:0.06, C:0.06, G:0.20, T:0.68
Consensus pattern (21 bp):
TTTTTACTGTTTTGGTTGCTG
Found at i:2263453 original size:53 final size:54
Alignment explanation
Indices: 2263369--2263471 Score: 163
Period size: 53 Copynumber: 1.9 Consensus size: 54
2263359 GTTGCTATTT
* * *
2263369 TTGCTGTTTTTGTGTTATGTTTTTATTATTTTGGTGTTTTTTTTACTGTTTTGG
1 TTGCTGTTTTGGTGTTATGTTTTTACTATTTTGGTGTTGTTTTTACTGTTTTGG
*
2263423 TTGCTGTTTTGGTGTTAT-TTTTTACTATTTTGGTGTTGTTTTTATTGTT
1 TTGCTGTTTTGGTGTTATGTTTTTACTATTTTGGTGTTGTTTTTACTGTT
2263472 ATTTTTTCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 28 0.62
54 17 0.38
ACGTcount: A:0.08, C:0.04, G:0.20, T:0.68
Consensus pattern (54 bp):
TTGCTGTTTTGGTGTTATGTTTTTACTATTTTGGTGTTGTTTTTACTGTTTTGG
Found at i:2263472 original size:33 final size:33
Alignment explanation
Indices: 2263397--2263483 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 33
2263387 GTTTTTATTA
* *
2263397 TTTTGGTGTT-TTTTTTACTGTTTTGGTTGCTG
1 TTTTAGTGTTATTTTTTACTATTTTGGTTGCTG
* *
2263429 TTTTGGTGTTATTTTTTACTATTTTGG-TGTTG
1 TTTTAGTGTTATTTTTTACTATTTTGGTTGCTG
*
2263461 TTTTTATTGTTATTTTTT-CTATT
1 -TTTTAGTGTTATTTTTTACTATT
2263484 ATTTTTGCTG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 19 0.39
33 30 0.61
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (33 bp):
TTTTAGTGTTATTTTTTACTATTTTGGTTGCTG
Found at i:2263477 original size:32 final size:32
Alignment explanation
Indices: 2263397--2263483 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 32
2263387 GTTTTTATTA
* * *
2263397 TTTTGGTGTTTTTTTTACTGTTTTGGTTGCTG
1 TTTTAGTGTTATTTTTACTATTTTGGTTGCTG
* *
2263429 TTTTGGTGTTATTTTTTACTATTTTGG-TGTTG
1 TTTTAGTGTTA-TTTTTACTATTTTGGTTGCTG
* *
2263461 TTTTTATTGTTATTTTTTCTATT
1 -TTTTAGTGTTATTTTTACTATT
2263484 ATTTTTGCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 24 0.51
33 23 0.49
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (32 bp):
TTTTAGTGTTATTTTTACTATTTTGGTTGCTG
Found at i:2266252 original size:27 final size:27
Alignment explanation
Indices: 2266220--2266306 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 27
2266210 TTTTTACGAT
*
2266220 AATAAAAATGTATTTTTTAAAATGTTA
1 AATAAAAATTTATTTTTTAAAATGTTA
2266247 AATAAAAAATTTATTATTTTTAGAGAATG-TA
1 AAT-AAAAATTTA-T-TTTTTA-A-AATGTTA
* *
2266278 AAGTATAATTTTATTTTTTAAAAT-TTA
1 AA-TAAAAATTTATTTTTTAAAATGTTA
2266305 AA
1 AA
2266307 AGTTTAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
27 10 0.20
28 9 0.18
29 7 0.14
30 7 0.14
31 12 0.24
32 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (27 bp):
AATAAAAATTTATTTTTTAAAATGTTA
Found at i:2266323 original size:17 final size:16
Alignment explanation
Indices: 2266297--2266331 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2266287 TTTATTTTTT
*
2266297 AAAATTTAAAAGTTTA
1 AAAATTTAAAAATTTA
2266313 AAAATTTTAAAAATTTA
1 AAAA-TTTAAAAATTTA
2266330 AA
1 AA
2266332 TAGAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AAAATTTAAAAATTTA
Found at i:2271404 original size:21 final size:20
Alignment explanation
Indices: 2271358--2271408 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2271348 AACCCTATTG
*
2271358 TTTTTATTGTTGTTTTTCTA
1 TTTTTTTTGTTGTTTTTCTA
*
2271378 TGTTTTGTTGTTGTTTTT-TCA
1 T-TTTTTTTGTTGTTTTTCT-A
2271399 TTTTTTTTGT
1 TTTTTTTTGT
2271409 CATTTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.06, C:0.04, G:0.14, T:0.76
Consensus pattern (20 bp):
TTTTTTTTGTTGTTTTTCTA
Found at i:2275575 original size:22 final size:23
Alignment explanation
Indices: 2275535--2275579 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2275525 AATTTGATAA
2275535 AATTATTTACAAATATAAAAATT
1 AATTATTTACAAATATAAAAATT
* *
2275558 AATTTTTTA-AAATTTAAAAATT
1 AATTATTTACAAATATAAAAATT
2275580 TTATCAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTATTTACAAATATAAAAATT
Found at i:2277508 original size:3 final size:3
Alignment explanation
Indices: 2277493--2277556 Score: 74
Period size: 3 Copynumber: 21.3 Consensus size: 3
2277483 AGGTGGGAAT
* * *
2277493 GAG GAG GAT GAG GAG GAG GAG GAG GAG GGG GAG GAT GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
* * *
2277541 GAA AAG GAA GAG GAG G
1 GAG GAG GAG GAG GAG G
2277557 GTCAAATGAG
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.36, C:0.00, G:0.61, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:2287391 original size:12 final size:12
Alignment explanation
Indices: 2287374--2287400 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2287364 TTATTTCAGG
2287374 TTATTTTTAAAA
1 TTATTTTTAAAA
2287386 TTATTTTTAAAA
1 TTATTTTTAAAA
2287398 TTA
1 TTA
2287401 CGTATTTTTT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATTTTTAAAA
Found at i:2290212 original size:6 final size:6
Alignment explanation
Indices: 2290201--2290233 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2290191 ATTATTGTTT
2290201 CCAATC CCAATC CCAATC CCAATC CCAATC CCA
1 CCAATC CCAATC CCAATC CCAATC CCAATC CCA
2290234 CTACCACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (6 bp):
CCAATC
Found at i:2295293 original size:14 final size:13
Alignment explanation
Indices: 2295275--2295322 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
2295265 AATGTGTTTT
2295275 TAAAAATAATATA
1 TAAAAATAATATA
2295288 TAAAAAT-ATAT-
1 TAAAAATAATATA
2295299 TAAAAATAATATA
1 TAAAAATAATATA
*
2295312 AAATAAATAAT
1 TAA-AAATAAT
2295323 GAAACATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 7 0.23
12 8 0.26
13 9 0.29
14 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAAATAATATA
Found at i:2295298 original size:12 final size:12
Alignment explanation
Indices: 2295275--2295314 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
2295265 AATGTGTTTT
2295275 TAAAAATAATATA
1 TAAAAAT-ATATA
2295288 TAAAAATATAT-
1 TAAAAATATATA
2295299 TAAAAATA-ATA
1 TAAAAATATATA
2295310 TAAAA
1 TAAAA
2295315 TAAATAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.08
11 13 0.50
12 4 0.15
13 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TAAAAATATATA
Found at i:2295306 original size:24 final size:25
Alignment explanation
Indices: 2295274--2295320 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
2295264 AAATGTGTTT
*
2295274 TTAAAAATAATATATAA-AAATATA
1 TTAAAAATAATATAAAATAAATATA
2295298 TTAAAAATAATATAAAATAAATA
1 TTAAAAATAATATAAAATAAATA
2295321 ATGAAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
TTAAAAATAATATAAAATAAATATA
Found at i:2298012 original size:85 final size:85
Alignment explanation
Indices: 2297857--2298012 Score: 183
Period size: 85 Copynumber: 1.8 Consensus size: 85
2297847 TAAAATTTTA
* * *
2297857 AATTAATAATAATAAAATTATATTTTAATTTCGTAAAAATAATAAAAAATTAATTTAATCATTTA
1 AATTAATAATAATAAAATTACATTTTAATATCGTAAAAATAATAAAAAATTAATTTAATCATTAA
*
2297922 TAAATTATAAAGATATCGAC
66 AAAATTATAAAGATATCGAC
* * * * *
2297942 AATTAA-AATAATGAAATTACATTTTTACTATCGTAAAAAT-AT-ACAATTTAATTTCTATCATT
1 AATTAATAATAATAAAATTACA-TTTTAATATCGTAAAAATAATAAAAAATTAATTT-AATCATT
2298004 CAAAAAATT
64 -AAAAAATT
2298013 TTTTGACTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
83 10 0.17
84 21 0.36
85 28 0.47
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (85 bp):
AATTAATAATAATAAAATTACATTTTAATATCGTAAAAATAATAAAAAATTAATTTAATCATTAA
AAAATTATAAAGATATCGAC
Found at i:2302432 original size:116 final size:115
Alignment explanation
Indices: 2302228--2302463 Score: 409
Period size: 116 Copynumber: 2.0 Consensus size: 115
2302218 AATACTTGTG
* *
2302228 ACACGGGCTGTCACACAACCATGTATCATATTTAGGTGCAGAGCAGTTTACACTGACAGACACAC
1 ACACGGGCTATCACACAACCATGTATCATATTTAGGTGCAGAGCAGTTTACACGGACAGACACAC
*
2302293 GGGCTGTTACACGGTCGTGTGGCCCTTTTTCGAGTAGACACACGGTCTGGC
66 GGGCTGTTACACGGCCGTGTGGCCC-TTTTCGAGTAGACACACGGTCTGGC
***
2302344 ACACGGGCTATCACATGGCCATGTATCATATTTAGGTGCAGAGCAGTTTACACGGACAGACACAC
1 ACACGGGCTATCACACAACCATGTATCATATTTAGGTGCAGAGCAGTTTACACGGACAGACACAC
2302409 GGGCTGTTACACGGCCGTGTGGCCCTTTTCGAGTAGACACACGGTCTGGC
66 GGGCTGTTACACGGCCGTGTGGCCCTTTTCGAGTAGACACACGGTCTGGC
2302459 ACACG
1 ACACG
2302464 ATCATACCCA
Statistics
Matches: 114, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
115 30 0.26
116 84 0.74
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.23
Consensus pattern (115 bp):
ACACGGGCTATCACACAACCATGTATCATATTTAGGTGCAGAGCAGTTTACACGGACAGACACAC
GGGCTGTTACACGGCCGTGTGGCCCTTTTCGAGTAGACACACGGTCTGGC
Found at i:2311571 original size:39 final size:36
Alignment explanation
Indices: 2311515--2311596 Score: 92
Period size: 39 Copynumber: 2.2 Consensus size: 36
2311505 TGATAAACTC
*
2311515 AAAAATAAAAATTTAACCTAAAAATCCAACATAAAAAAT
1 AAAAA-AAAAATCTAACC-AAAAATCCAA-ATAAAAAAT
* **
2311554 AAAAAAATAAATCTAACCCAAAATCCAAATAAAATGT
1 AAAAAAA-AAATCTAACCAAAAATCCAAATAAAAAAT
2311591 AAAAAA
1 AAAAAA
2311597 GTACAACACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 13 0.34
38 11 0.29
39 14 0.37
ACGTcount: A:0.67, C:0.13, G:0.01, T:0.18
Consensus pattern (36 bp):
AAAAAAAAAATCTAACCAAAAATCCAAATAAAAAAT
Found at i:2311866 original size:47 final size:47
Alignment explanation
Indices: 2311797--2311886 Score: 153
Period size: 47 Copynumber: 1.9 Consensus size: 47
2311787 CATGGCTACA
* *
2311797 AATCCGACTCAACCCAAGTCACTTATAATCTATCTTTCGTCTAAAGG
1 AATCCAACTCAACCCAAGTCACTTATAATCCATCTTTCGTCTAAAGG
*
2311844 AATCCAACTCAACCCAGGTCACTTATAATCCATCTTTCGTCTA
1 AATCCAACTCAACCCAAGTCACTTATAATCCATCTTTCGTCTA
2311887 CAGGGCAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.30
Consensus pattern (47 bp):
AATCCAACTCAACCCAAGTCACTTATAATCCATCTTTCGTCTAAAGG
Found at i:2319306 original size:3 final size:3
Alignment explanation
Indices: 2319298--2319348 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
2319288 ATATTCAAAC
2319298 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2319345 AAT A
1 AAT A
2319349 GTAAAATGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2320194 original size:14 final size:14
Alignment explanation
Indices: 2320177--2320214 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2320167 AACTTGAACT
2320177 TTGAATCTTGGATC
1 TTGAATCTTGGATC
*
2320191 TTGAATCTTGGATT
1 TTGAATCTTGGATC
*
2320205 TTGAACCTTG
1 TTGAATCTTG
2320215 AACCATAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (14 bp):
TTGAATCTTGGATC
Found at i:2320233 original size:21 final size:21
Alignment explanation
Indices: 2320181--2320234 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
2320171 TGAACTTTGA
* * * *
2320181 ATCTTGGATCTTGAATCTTGG
1 ATCTTGGACCTTGAACCATAG
* *
2320202 ATTTTGAACCTTGAACCATAG
1 ATCTTGGACCTTGAACCATAG
2320223 ATCTTGGACCTT
1 ATCTTGGACCTT
2320235 AAAACTGAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (21 bp):
ATCTTGGACCTTGAACCATAG
Found at i:2320407 original size:21 final size:22
Alignment explanation
Indices: 2320383--2320430 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
2320373 AGATTTAGAG
*
2320383 TTTAAGATCCT-AGGTCTAAAA
1 TTTAAGATCCTAAAGTCTAAAA
**
2320404 TTT-AGATTTTAAAGTCTAAAA
1 TTTAAGATCCTAAAGTCTAAAA
2320425 TTTAAG
1 TTTAAG
2320431 GTTTACGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (22 bp):
TTTAAGATCCTAAAGTCTAAAA
Found at i:2327190 original size:15 final size:15
Alignment explanation
Indices: 2327170--2327199 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2327160 CAATTGATAA
2327170 ATTGAAAAATTAAGT
1 ATTGAAAAATTAAGT
*
2327185 ATTGAAAATTTAAGT
1 ATTGAAAAATTAAGT
2327200 GATAAATATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (15 bp):
ATTGAAAAATTAAGT
Found at i:2331807 original size:23 final size:22
Alignment explanation
Indices: 2331777--2331819 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
2331767 GTTAATTTTT
2331777 GCAAGGGTCGAATGCTCTAGGGA
1 GCAAGGGTCGAATGC-CTAGGGA
2331800 GCAAGGGTCGAATGCCTAGG
1 GCAAGGGTCGAATGCCTAGG
2331820 CCGATTCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.26, C:0.19, G:0.40, T:0.16
Consensus pattern (22 bp):
GCAAGGGTCGAATGCCTAGGGA
Found at i:2338849 original size:28 final size:29
Alignment explanation
Indices: 2338818--2338878 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
2338808 CAACTTAGAT
* *
2338818 TTTAATTTAAGTTTGAA-TTAATTTTAAA
1 TTTAATTTAAATTTAAATTTAATTTTAAA
**
2338846 TTT-ATTTAAATTTAAATTTTGTTTTAAA
1 TTTAATTTAAATTTAAATTTAATTTTAAA
2338874 TTTAA
1 TTTAA
2338879 ATACATTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 11 0.41
28 15 0.56
29 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (29 bp):
TTTAATTTAAATTTAAATTTAATTTTAAA
Found at i:2340041 original size:20 final size:20
Alignment explanation
Indices: 2340016--2340055 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2340006 GCTGAGCTTG
*
2340016 GTCGGAG-GTGAGCCGAGGGC
1 GTCGGAGCGTG-GCCCAGGGC
2340036 GTCGGAGCGTGGCCCAGGGC
1 GTCGGAGCGTGGCCCAGGGC
2340056 ACCGACGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.12, C:0.25, G:0.53, T:0.10
Consensus pattern (20 bp):
GTCGGAGCGTGGCCCAGGGC
Found at i:2340684 original size:29 final size:28
Alignment explanation
Indices: 2340652--2340744 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 28
2340642 AAAACTTTCC
2340652 AAAATCCCATTTAAACCCCGCTTTCACCA
1 AAAATCCCATTT-AACCCCGCTTTCACCA
* *
2340681 AAAATTACCATTTTACCCCTGAACTTT--CC-
1 AAAA-TCCCATTTAACCCC-G--CTTTCACCA
*
2340710 AAAATCCCATTTTTAACCCCGATTTCACCA
1 AAAATCCCA--TTTAACCCCGCTTTCACCA
2340740 AAAAT
1 AAAAT
2340745 TACCATTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
27 3 0.06
28 4 0.08
29 16 0.32
30 23 0.46
32 4 0.08
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.29
Consensus pattern (28 bp):
AAAATCCCATTTAACCCCGCTTTCACCA
Found at i:2340711 original size:58 final size:59
Alignment explanation
Indices: 2340633--2340757 Score: 207
Period size: 59 Copynumber: 2.1 Consensus size: 59
2340623 AAAAATTATT
*
2340633 TTTTACCCCAAAACTTTCCAAAATCCCA-TTTAAACCCCGCTTTCACCAAAAATTACCA
1 TTTTACCCCAAAACTTTCCAAAATCCCATTTTAAACCCCGATTTCACCAAAAATTACCA
** *
2340691 TTTTACCCCTGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTACCCCAAAACTTTCCAAAATCCCATTTTAAACCCCGATTTCACCAAAAATTACCA
2340750 TTTTACCC
1 TTTTACCC
2340758 TCGAAAGTCG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 26 0.42
59 36 0.58
ACGTcount: A:0.33, C:0.34, G:0.02, T:0.31
Consensus pattern (59 bp):
TTTTACCCCAAAACTTTCCAAAATCCCATTTTAAACCCCGATTTCACCAAAAATTACCA
Found at i:2340757 original size:29 final size:29
Alignment explanation
Indices: 2340666--2340757 Score: 93
Period size: 29 Copynumber: 3.1 Consensus size: 29
2340656 TCCCATTTAA
*
2340666 ACCCCGCTTTCACCAAAAATTACCATTTT
1 ACCCCGATTTCACCAAAAATTACCATTTT
*
2340695 ACCCCTGAACTTT--CC-AAAA-TCCCATTTTT
1 ACCCC-G-A-TTTCACCAAAAATTACCA-TTTT
2340724 AACCCCGATTTCACCAAAAATTACCATTTT
1 -ACCCCGATTTCACCAAAAATTACCATTTT
2340754 ACCC
1 ACCC
2340758 TCGAAAGTCG
Statistics
Matches: 51, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
27 3 0.06
28 5 0.10
29 20 0.39
30 16 0.31
31 4 0.08
32 3 0.06
ACGTcount: A:0.32, C:0.35, G:0.03, T:0.30
Consensus pattern (29 bp):
ACCCCGATTTCACCAAAAATTACCATTTT
Found at i:2340779 original size:59 final size:59
Alignment explanation
Indices: 2340649--2340780 Score: 162
Period size: 59 Copynumber: 2.3 Consensus size: 59
2340639 CCCAAAACTT
* * * **
2340649 TCCAAAATCCCA-TTTAAACCCCGCTTTCACCAAAAATTACCATTTTACCCCTGAACTT
1 TCCAAAATACCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTGAACAG
*
2340707 TCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTA-CCCTCGAA-AG
1 TCCAAAATACCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCT-GAACAG
*
2340765 TCGAAAATTACCATTT
1 TCCAAAA-TACCATTT
2340781 CACACCCGAG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
58 22 0.34
59 43 0.66
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (59 bp):
TCCAAAATACCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTGAACAG
Found at i:2346829 original size:25 final size:23
Alignment explanation
Indices: 2346788--2346833 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
2346778 CCAATTAAGG
2346788 AATTATTATTTAGATTTAATTCT
1 AATTATTATTTAGATTTAATTCT
*
2346811 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
2346834 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCT
Found at i:2347906 original size:10 final size:11
Alignment explanation
Indices: 2347889--2347920 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
2347879 TACTTTAGCC
2347889 ATTTTATTATT
1 ATTTTATTATT
2347900 A-TTTATTATT
1 ATTTTATTATT
2347910 ATTTTATTATT
1 ATTTTATTATT
2347921 TGCATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:2350775 original size:11 final size:11
Alignment explanation
Indices: 2350761--2350785 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2350751 CATTTTTTTG
2350761 AAAAAAATTGA
1 AAAAAAATTGA
2350772 AAAAAAATTGA
1 AAAAAAATTGA
2350783 AAA
1 AAA
2350786 GTTCAAAAAA
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:2350836 original size:11 final size:11
Alignment explanation
Indices: 2350806--2350851 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
2350796 AAATAATTTA
*
2350806 TTTATTTCATT
1 TTTATTTTATT
*
2350817 TTTAGTTTTAGT
1 TTTA-TTTTATT
2350829 TTTATTTTATT
1 TTTATTTTATT
2350840 TTTATTTT-TT
1 TTTATTTTATT
2350850 TT
1 TT
2350852 AATTATGCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 4 0.13
11 18 0.58
12 9 0.29
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.78
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:2351823 original size:26 final size:26
Alignment explanation
Indices: 2351794--2351843 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2351784 AAGTCGAAAA
2351794 GAAAAAAA-TGAAGAAAAAAAAGAATT
1 GAAAAAAATTGAA-AAAAAAAAGAATT
*
2351820 GAAAAAAATTGAAAAGAAAAAGAA
1 GAAAAAAATTGAAAAAAAAAAGAA
2351844 AAAGAAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (26 bp):
GAAAAAAATTGAAAAAAAAAAGAATT
Found at i:2352887 original size:23 final size:25
Alignment explanation
Indices: 2352861--2352906 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2352851 CCAATTAAGG
2352861 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
2352884 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
2352907 TGGATCGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:2360420 original size:25 final size:23
Alignment explanation
Indices: 2360392--2360437 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
2360382 GTTGGATCCA
2360392 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
2360417 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
2360438 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:2361498 original size:24 final size:25
Alignment explanation
Indices: 2361457--2361503 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2361447 TGTCTTCTTT
2361457 TTCTTTTTTTTTCAATTTTTTTCAA
1 TTCTTTTTTTTTCAATTTTTTTCAA
2361482 TTCTTTTTTTTTC-ATTTTTTTC
1 TTCTTTTTTTTTCAATTTTTTTC
2361504 TTTTCGACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.77
Consensus pattern (25 bp):
TTCTTTTTTTTTCAATTTTTTTCAA
Found at i:2361502 original size:14 final size:15
Alignment explanation
Indices: 2361472--2361520 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
2361462 TTTTTTTCAA
*
2361472 TTTTTTTCAATTCTT
1 TTTTTTTCAATTTTT
2361487 TTTTTTTC-ATTTTT
1 TTTTTTTCAATTTTT
* *
2361501 TTCTTTTCGACTTTTT
1 TTTTTTTC-AATTTTT
2361517 TTTT
1 TTTT
2361521 CTAAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 12 0.43
15 8 0.29
16 8 0.29
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTTTTCAATTTTT
Found at i:2365346 original size:16 final size:16
Alignment explanation
Indices: 2365325--2365356 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2365315 TGCCAGAAAC
2365325 AATTAAAAGAGAAAAA
1 AATTAAAAGAGAAAAA
*
2365341 AATTAAAATAGAAAAA
1 AATTAAAAGAGAAAAA
2365357 TTAAATTAAA
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:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (16 bp):
AATTAAAAGAGAAAAA
Found at i:2365355 original size:15 final size:15
Alignment explanation
Indices: 2365319--2365361 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
2365309 AGAACTTGCC
*
2365319 AGAAACAATTAAAAG
1 AGAAAAAATTAAAAG
*
2365334 AGAAAAAAATTAAAAT
1 AG-AAAAAATTAAAAG
2365350 AG-AAAAATTAAA
1 AGAAAAAATTAAA
2365362 TTAAAAATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.40
15 2 0.08
16 13 0.52
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (15 bp):
AGAAAAAATTAAAAG
Found at i:2365357 original size:14 final size:14
Alignment explanation
Indices: 2365319--2365361 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2365309 AGAACTTGCC
2365319 AGAAACAATTAAAAG
1 AGAAA-AATTAAAAG
*
2365334 AGAAAAAAATTAAAAT
1 AG--AAAAATTAAAAG
2365350 AGAAAAATTAAA
1 AGAAAAATTAAA
2365362 TTAAAAATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 2 0.08
16 10 0.40
17 3 0.12
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (14 bp):
AGAAAAATTAAAAG
Found at i:2366522 original size:25 final size:24
Alignment explanation
Indices: 2366469--2366514 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2366459 GTTGGATCTA
2366469 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAAGATAATTAG
*
2366494 AATTAAATCTAAACA-ATAATT
1 AATTAAATCTAAAAAGATAATT
2366515 CCGTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (24 bp):
AATTAAATCTAAAAAGATAATTAG
Found at i:2372232 original size:23 final size:25
Alignment explanation
Indices: 2372205--2372250 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2372195 CTAATTAAGA
2372205 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
2372228 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
2372251 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:2373373 original size:14 final size:15
Alignment explanation
Indices: 2373354--2373387 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2373344 ATTATTTGCA
2373354 TTTTTAATTT-AATT
1 TTTTTAATTTAAATT
*
2373368 TTTTTATTTTAAATT
1 TTTTTAATTTAAATT
2373383 TTTTT
1 TTTTT
2373388 CCCTTTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTAATTTAAATT
Found at i:2376204 original size:12 final size:10
Alignment explanation
Indices: 2376174--2376200 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2376164 TCATGTTTTT
2376174 AAAAAAATTG
1 AAAAAAATTG
2376184 AAAAAAATTG
1 AAAAAAATTG
2376194 AAAAAAA
1 AAAAAAA
2376201 AATTAGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:2376238 original size:24 final size:22
Alignment explanation
Indices: 2376211--2376254 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
2376201 AATTAGCATA
2376211 TTTATTTTCATTTGCATTTTTAGT
1 TTTATTTT-ATTT-CATTTTTAGT
*
2376235 TTTATTTTATTTTATTTTTA
1 TTTATTTTATTTCATTTTTA
2376255 ATTATGCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (22 bp):
TTTATTTTATTTCATTTTTAGT
Found at i:2377229 original size:14 final size:12
Alignment explanation
Indices: 2377190--2377232 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
2377180 TAAAAAAGAC
*
2377190 AAAAAAAATCGA
1 AAAAAAAATTGA
2377202 AAAAAAAATTGA
1 AAAAAAAATTGA
*
2377214 AATAAAAATTGA
1 AAAAAAAATTGA
2377226 GAAAAAA
1 -AAAAAA
2377233 GAAAAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 22 0.81
13 5 0.19
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:2379988 original size:29 final size:28
Alignment explanation
Indices: 2379927--2379980 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2379917 AAATAATAAC
*
2379927 ATAAGTGACTAAAACGTAACATTTGAAAT
1 ATAAGTGACTAAAACGTAACA-TTGAAAA
*
2379956 ATAAGTGACTAAAATGTAAC-TTGAA
1 ATAAGTGACTAAAACGTAACATTGAA
2379981 GCAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.21
29 19 0.79
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (28 bp):
ATAAGTGACTAAAACGTAACATTGAAAA
Found at i:2380362 original size:30 final size:32
Alignment explanation
Indices: 2380308--2380371 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
2380298 TAGAAAAAAT
2380308 AAAATTATATTTAGATTCTTTTAAAAATGATA
1 AAAATTATATTTAGATTCTTTTAAAAATGATA
*
2380340 AAAATT-TGATTTA-ATT-TTTTAAAAATTATA
1 AAAATTAT-ATTTAGATTCTTTTAAAAATGATA
2380370 AA
1 AA
2380372 GACATAGACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 15 0.50
31 4 0.13
32 11 0.37
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (32 bp):
AAAATTATATTTAGATTCTTTTAAAAATGATA
Found at i:2383395 original size:21 final size:20
Alignment explanation
Indices: 2383370--2383423 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2383360 TCTCTCTCAA
2383370 CAAAAGTTACAAAATAATTTT
1 CAAAA-TTACAAAATAATTTT
*
2383391 CAAAATTTCAAAATAATTTT
1 CAAAATTACAAAATAATTTT
* *
2383411 TAATATTA-AAAAT
1 CAAAATTACAAAAT
2383424 GATTATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 5 0.17
20 19 0.66
21 5 0.17
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (20 bp):
CAAAATTACAAAATAATTTT
Found at i:2384665 original size:17 final size:18
Alignment explanation
Indices: 2384638--2384671 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2384628 GCTGCATATG
2384638 TAAATTTTTAATATTAAT
1 TAAATTTTTAATATTAAT
2384656 TAAA-TTTTAATATTAA
1 TAAATTTTTAATATTAA
2384672 AAATTTATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAATTTTTAATATTAAT
Found at i:2384882 original size:3 final size:3
Alignment explanation
Indices: 2384874--2384938 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
2384864 TTTAATTTAC
2384874 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2384922 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
2384939 AGCAATTAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2385442 original size:16 final size:17
Alignment explanation
Indices: 2385421--2385454 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2385411 AAAAAAAAAA
*
2385421 ATCAAA-ACCAGAGAGT
1 ATCAAAGACCAAAGAGT
2385437 ATCAAAGACCAAAGAGT
1 ATCAAAGACCAAAGAGT
2385454 A
1 A
2385455 GTCCAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.18, G:0.18, T:0.12
Consensus pattern (17 bp):
ATCAAAGACCAAAGAGT
Found at i:2386080 original size:13 final size:13
Alignment explanation
Indices: 2386062--2386087 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2386052 TACCTCCAAG
2386062 ATTGCATGAAATT
1 ATTGCATGAAATT
2386075 ATTGCATGAAATT
1 ATTGCATGAAATT
2386088 CTTCTTTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
ATTGCATGAAATT
Found at i:2393037 original size:157 final size:157
Alignment explanation
Indices: 2392751--2393073 Score: 628
Period size: 157 Copynumber: 2.1 Consensus size: 157
2392741 GTGTGATCAG
2392751 TGCGTCTATAGGGTTGGTTATAGTTGTCTTAATTCTAGCTCAAAGAATCTGGCTTAAATTGTAAG
1 TGCGTCTATAGGGTTGGTTATAGTTGTCTTAATTCTAGCTCAAAGAATCTGGCTTAAATTGTAAG
2392816 ACGATTTTTTTGACAAGCATTGTTCTTCTGATTGGAGGTTTATTCTAAATTGGTGCTGTATAGAA
66 ACGATTTTTTTGACAAGCATTGTTCTTCTGATTGGAGGTTTATTCTAAATTGGTGCTGTATAGAA
2392881 ATGCTTATATATGCCTGCACATGAACC
131 ATGCTTATATATGCCTGCACATGAACC
*
2392908 TGCGTCTATAGGGTTGGTTATAGTTGTTTTAATTCTAGCTCAAAGAATCTGGCTTAAATTGTAAG
1 TGCGTCTATAGGGTTGGTTATAGTTGTCTTAATTCTAGCTCAAAGAATCTGGCTTAAATTGTAAG
2392973 ACGATTTTTTTGACAAGCATTGTTCTTCTGATTGGAGGTTTATTCTAAATTGGTGCTGTATAGAA
66 ACGATTTTTTTGACAAGCATTGTTCTTCTGATTGGAGGTTTATTCTAAATTGGTGCTGTATAGAA
2393038 ATGCTTATATATGCCTGCACATGAACC
131 ATGCTTATATATGCCTGCACATGAACC
*
2393065 TGCATCTAT
1 TGCGTCTAT
2393074 TCTGCTTTGT
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 164 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (157 bp):
TGCGTCTATAGGGTTGGTTATAGTTGTCTTAATTCTAGCTCAAAGAATCTGGCTTAAATTGTAAG
ACGATTTTTTTGACAAGCATTGTTCTTCTGATTGGAGGTTTATTCTAAATTGGTGCTGTATAGAA
ATGCTTATATATGCCTGCACATGAACC
Found at i:2418919 original size:15 final size:15
Alignment explanation
Indices: 2418899--2418929 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2418889 CTTGATTGGT
2418899 ACGAATATAAATTAG
1 ACGAATATAAATTAG
2418914 ACGAATATAAATTAG
1 ACGAATATAAATTAG
2418929 A
1 A
2418930 TAGCATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (15 bp):
ACGAATATAAATTAG
Found at i:2424590 original size:3 final size:3
Alignment explanation
Indices: 2424577--2424605 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2424567 TTTTTACTAT
2424577 TGA TG- TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
2424606 AATTGTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:2429341 original size:31 final size:29
Alignment explanation
Indices: 2429267--2429342 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
2429257 CAATCCAAGC
* * *
2429267 TTCATGTATATAATTACACTAAATCAAAG
1 TTCATGTATAAAATTGCACTAAAACAAAG
*
2429296 -TCTATGTATCAAATTGCACATGAAAACAAAG
1 TTC-ATGTATAAAATTGCAC-T-AAAACAAAG
2429327 TTCATGTATAAAATTG
1 TTCATGTATAAAATTG
2429343 ATATTTGTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.05
29 13 0.34
30 1 0.03
31 20 0.53
32 2 0.05
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (29 bp):
TTCATGTATAAAATTGCACTAAAACAAAG
Found at i:2447106 original size:2 final size:2
Alignment explanation
Indices: 2447093--2447128 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2447083 CAGGAAGATA
*
2447093 AT AT AA 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
2447129 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2452723 original size:4 final size:4
Alignment explanation
Indices: 2452714--2452740 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2452704 GGCTTTAATG
2452714 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2452741 ATTGTGCGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2453181 original size:16 final size:15
Alignment explanation
Indices: 2453157--2453221 Score: 51
Period size: 16 Copynumber: 4.2 Consensus size: 15
2453147 TTATATGTGT
*
2453157 AATATTAAATTTTAGA
1 AATAATAAATTTTA-A
*
2453173 AATAATAAAATTTAA
1 AATAATAAATTTTAA
*
2453188 ATTAATAAA-TTTAA
1 AATAATAAATTTTAA
* *
2453202 CTATACAAAAATTTTAA
1 -AATA-ATAAATTTTAA
2453219 AAT
1 AAT
2453222 TAAAAAGGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
14 5 0.13
15 11 0.28
16 18 0.46
17 5 0.13
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (15 bp):
AATAATAAATTTTAA
Found at i:2456030 original size:25 final size:25
Alignment explanation
Indices: 2455994--2456063 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
2455984 TCAGGTCTTA
*
2455994 CATCTCTCTATTATTATTTTTATTC
1 CATCTCTCTATTATTATTATTATTC
2456019 CATCTCGT-TATTATTATTATTATT-
1 CATCTC-TCTATTATTATTATTATTC
*
2456043 -AT-TAT-TATTATTATTATTATT
1 CATCTCTCTATTATTATTATTATT
2456064 ATTATTGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 17 0.40
22 1 0.02
23 2 0.05
25 21 0.50
26 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.61
Consensus pattern (25 bp):
CATCTCTCTATTATTATTATTATTC
Found at i:2456034 original size:3 final size:3
Alignment explanation
Indices: 2456026--2456069 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2456016 TTCCATCTCG
2456026 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2456070 GATTTAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2462395 original size:17 final size:20
Alignment explanation
Indices: 2462361--2462400 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
2462351 CATCTATTTT
*
2462361 AAATATAATTTGATAAA-TA
1 AAATATAATTTGAAAAATTA
2462380 AAATA-AATTT-AAAAATTA
1 AAATATAATTTGAAAAATTA
2462398 AAA
1 AAA
2462401 GAAACAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 4 0.21
18 10 0.53
19 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAATATAATTTGAAAAATTA
Found at i:2463166 original size:17 final size:16
Alignment explanation
Indices: 2463139--2463170 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2463129 TCTCTTATAA
2463139 AAGAGAAAATTCTTAC
1 AAGAGAAAATTCTTAC
2463155 AAGAGTAAAATTCTTA
1 AAGAG-AAAATTCTTA
2463171 TAAAAGCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (16 bp):
AAGAGAAAATTCTTAC
Found at i:2468994 original size:24 final size:23
Alignment explanation
Indices: 2468949--2468997 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
2468939 AAATGACACC
* *
2468949 AAAATAGTGACAAAACAACAACA
1 AAAATAATGAAAAAACAACAACA
2468972 AAAATAATGAAAACAACAACAACA
1 AAAATAATGAAAA-AACAACAACA
2468996 AA
1 AA
2468998 TTTGTGTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.69, C:0.16, G:0.06, T:0.08
Consensus pattern (23 bp):
AAAATAATGAAAAAACAACAACA
Found at i:2469912 original size:29 final size:29
Alignment explanation
Indices: 2469865--2469931 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 29
2469855 TTTAAATTAA
2469865 TAAAAAT-A-AAATATTATTT-AGCTCTT
1 TAAAAATAATAAATATTATTTAAGCTCTT
* ** *
2469891 TAAAAATAATAAATTTTGATTTAATTTTTT
1 TAAAAATAATAAATATT-ATTTAAGCTCTT
2469921 TAAAAATAATA
1 TAAAAATAATA
2469932 TTTTTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 7 0.21
27 1 0.03
28 6 0.18
29 4 0.12
30 15 0.45
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (29 bp):
TAAAAATAATAAATATTATTTAAGCTCTT
Found at i:2471354 original size:17 final size:18
Alignment explanation
Indices: 2471327--2471362 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2471317 TAAATATTCC
2471327 AATAGTCAATTTTTGAAA
1 AATAGTCAATTTTTGAAA
*
2471345 AATA-TCAATTTTTTAAA
1 AATAGTCAATTTTTGAAA
2471362 A
1 A
2471363 TTAATAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (18 bp):
AATAGTCAATTTTTGAAA
Found at i:2478029 original size:59 final size:58
Alignment explanation
Indices: 2477829--2478029 Score: 171
Period size: 59 Copynumber: 3.4 Consensus size: 58
2477819 AATTTGGGCT
2477829 TTTAGGGGT-AAAATGGTAATTTTT-GTGAAATCGGGGCTAAAAATGGAATTTGGAAAG
1 TTTAGGGGTAAAAATGGTAATTTTTGGTGAAATCGGGG-TAAAAATGGAATTTGGAAAG
* * ** ** *
2477886 TTT-GGGGAATAAAATGGTAAATTTTGGCAAAAAT-AAGGTCAAAAATGAAATTTTGGAAAG
1 TTTAGGGGTA-AAAATGGTAATTTTTGG-TGAAATCGGGGT-AAAAATGGAA-TTTGGAAAG
* * * * * * *
2477946 -TTCGGAGG-CAAAACGGTAAGTTTTGGTGAAATCGGGGTTAAAATGGGATTTAGGGAAG
1 TTTAGG-GGTAAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAATGGAATTT-GGAAAG
2478004 TTTAGGGGTAAAAATGGTAATTTTTG
1 TTTAGGGGTAAAAATGGTAATTTTTG
2478030 AAAGTTTTGG
Statistics
Matches: 110, Mismatches: 22, Indels: 22
0.71 0.14 0.14
Matches are distributed among these distances:
56 4 0.04
57 6 0.05
58 33 0.30
59 50 0.45
60 15 0.14
61 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.30
Consensus pattern (58 bp):
TTTAGGGGTAAAAATGGTAATTTTTGGTGAAATCGGGGTAAAAATGGAATTTGGAAAG
Found at i:2478042 original size:30 final size:29
Alignment explanation
Indices: 2478001--2478238 Score: 226
Period size: 30 Copynumber: 8.0 Consensus size: 29
2477991 GGATTTAGGG
* *
2478001 AAGTTTAGGGGTAAAAATGGTAATTTTTGA
1 AAGTTTTGGGGTCAAAAT-GTAATTTTTGA
* *
2478031 AAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTTG-A
** * *
2478061 AAGTTTTGGCATCAAAACGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTTG-A
* * **
2478091 AATTTTTAGGGTCAAAATGTAATTTCCAGA
1 AAGTTTTGGGGTCAAAATGTAATTT-TTGA
*** *
2478121 AAGTTTCAAGGTCAAAATATAATTTTTAGA
1 AAGTTTTGGGGTCAAAATGTAATTTTT-GA
2478151 AAGTTTTGGGGTCAAAATGTAATTTTTAGA
1 AAGTTTTGGGGTCAAAATGTAATTTTT-GA
* *
2478181 AAGTTTCGAGGTCAAAATGTAA-TTTTGAAA
1 AAGTTTTGGGGTCAAAATGTAATTTTTG--A
*
2478211 AAGTTTTAGGGTCAAAATGTAATTTTTG
1 AAGTTTTGGGGTCAAAATGTAATTTTTG
2478239 GACAATTTAG
Statistics
Matches: 172, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
28 1 0.01
29 12 0.07
30 153 0.89
31 6 0.03
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (29 bp):
AAGTTTTGGGGTCAAAATGTAATTTTTGA
Found at i:2478237 original size:60 final size:60
Alignment explanation
Indices: 2478014--2478237 Score: 249
Period size: 60 Copynumber: 3.7 Consensus size: 60
2478004 TTTAGGGGTA
* * * * *
2478014 AAAATGGTAATTTTTG--AAAGTTTTGGGGTCAAAATATAA-TTTTGGAAAAGTTTTG-GCATC
1 AAAAT-GTAA-TTTTGAAAAAGTTTTAGGGTCAAAATGTAATTTTTAG-AAAGTTTCGAG-GTC
* * * ** *
2478074 AAAACGTAATTTTGGAAAATTTTTAGGGTCAAAATGTAATTTCCAGAAAGTTTCAAGGTC
1 AAAATGTAATTTTGAAAAAGTTTTAGGGTCAAAATGTAATTTTTAGAAAGTTTCGAGGTC
* * * *
2478134 AAAATATAATTTTTAGAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAGTTTCGAGGTC
1 AAAATGTAATTTTGAAAAAGTTTTAGGGTCAAAATGTAATTTTTAGAAAGTTTCGAGGTC
2478194 AAAATGTAATTTTGAAAAAGTTTTAGGGTCAAAATGTAATTTTT
1 AAAATGTAATTTTGAAAAAGTTTTAGGGTCAAAATGTAATTTTT
2478238 GGACAATTTA
Statistics
Matches: 136, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
58 5 0.04
59 4 0.03
60 123 0.90
61 4 0.03
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (60 bp):
AAAATGTAATTTTGAAAAAGTTTTAGGGTCAAAATGTAATTTTTAGAAAGTTTCGAGGTC
Found at i:2478237 original size:90 final size:90
Alignment explanation
Indices: 2478009--2478237 Score: 250
Period size: 90 Copynumber: 2.5 Consensus size: 90
2477999 GGAAGTTTAG
* * *
2478009 GGGTAAAAATGGTAATTTTTG-AAAGTTTTGGGGTCAAAATATAA-TTTTGGAAAAGTTTTGGCA
1 GGGTCAAAAT-GTAA-TTTTGAAAAGTTTTAGGGTCAAAATATAATTTTTAGAAAAGTTTTGGCA
* **
2478072 TCAAAACGTAATTTTGGAAAATTTTTA
64 TCAAAACGTAATTTTAGAAAATTTCGA
** * * **
2478099 GGGTCAAAATGTAATTTCCAGAAAGTTTCAAGGTCAAAATATAATTTTTAG-AAAGTTTTGGGGT
1 GGGTCAAAATGTAATTTTGA-AAAGTTTTAGGGTCAAAATATAATTTTTAGAAAAGTTTTGGCAT
* *
2478163 CAAAATGTAATTTTTAGAAAGTTTCGA
65 CAAAACGTAA-TTTTAGAAAATTTCGA
*
2478190 -GGTCAAAATGTAATTTTGAAAAAGTTTTAGGGTCAAAATGTAATTTTT
1 GGGTCAAAATGTAATTTTG-AAAAGTTTTAGGGTCAAAATATAATTTTT
2478238 GGACAATTTA
Statistics
Matches: 115, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
88 3 0.03
89 4 0.03
90 90 0.78
91 18 0.16
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (90 bp):
GGGTCAAAATGTAATTTTGAAAAGTTTTAGGGTCAAAATATAATTTTTAGAAAAGTTTTGGCATC
AAAACGTAATTTTAGAAAATTTCGA
Found at i:2479371 original size:3 final size:3
Alignment explanation
Indices: 2479363--2479395 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2479353 TTTTATTGCT
2479363 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2479396 ATGTTTCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2480116 original size:6 final size:6
Alignment explanation
Indices: 2480105--2480191 Score: 67
Period size: 6 Copynumber: 14.8 Consensus size: 6
2480095 TTTAATTTAA
* * *
2480105 TTAAAT TTAAAT TTAAA- ATAAAT TTAAAT AAGTGAAT TTAAAT TTAAGA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAA-AT
* *
2480154 -TAAAT TTAAAT TTAAAA TTAAA- TTAAAA TT-AAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
2480192 CTTTTAAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 16 0.25
6 43 0.66
7 1 0.02
8 4 0.06
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:2480128 original size:17 final size:17
Alignment explanation
Indices: 2480106--2480183 Score: 90
Period size: 17 Copynumber: 4.7 Consensus size: 17
2480096 TTAATTTAAT
2480106 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
2480123 TAAATTTAAA--T-AAG
1 TAAATTTAAATTTAAAA
* *
2480137 TGAATTTAAATTTAAGA
1 TAAATTTAAATTTAAAA
2480154 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
2480171 TTAAATTAAAATT
1 -TAAATTTAAATT
2480184 AATTTAAACT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
14 11 0.22
15 1 0.02
16 1 0.02
17 26 0.52
18 11 0.22
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:2480185 original size:17 final size:17
Alignment explanation
Indices: 2480098--2480185 Score: 70
Period size: 17 Copynumber: 5.0 Consensus size: 17
2480088 TGTTGTTTTT
*
2480098 AATTTAATTAAATTTAA
1 AATTAAATTAAATTTAA
* *
2480115 ATTTAAAATAAATTTAAA
1 AATTAAATTAAATTT-AA
* *
2480133 TAAGTGAATTTAAATTTAA
1 -AA-TTAAATTAAATTTAA
*
2480152 GA-TAAATTTAAATTTAA
1 AATTAAA-TTAAATTTAA
*
2480169 AATTAAATTAAAATTAA
1 AATTAAATTAAATTTAA
2480186 TTTAAACTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
16 2 0.04
17 32 0.59
18 7 0.13
19 3 0.06
20 10 0.19
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AATTAAATTAAATTTAA
Found at i:2480203 original size:23 final size:22
Alignment explanation
Indices: 2480123--2480205 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 22
2480113 AAATTTAAAA
* *
2480123 TAAATTTAAAT--AAGTGAATT
1 TAAATTTAAATAAAATTAAATT
*
2480143 TAAATTTAAGATAAATTTAAATT
1 TAAATTTAA-ATAAAATTAAATT
*
2480166 TAAAATTAAATTAAAATT-AATT
1 TAAATTTAAA-TAAAATTAAATT
2480188 TAAACTTTTAAATAAAAT
1 TAAA--TTTAAATAAAAT
2480206 CAAAAGCTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 9 0.18
21 2 0.04
22 9 0.18
23 26 0.51
24 5 0.10
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (22 bp):
TAAATTTAAATAAAATTAAATT
Found at i:2482933 original size:29 final size:29
Alignment explanation
Indices: 2482900--2482978 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 29
2482890 AGGTCCGCTA
2482900 ATATTAATTTTTATTTTTAAAAAAATATT
1 ATATTAATTTTTATTTTTAAAAAAATATT
* * ** *
2482929 ATATT-ATTTTAATATTTAAAAATTTTTT
1 ATATTAATTTTTATTTTTAAAAAAATATT
*
2482957 ATA-TATTTTTTATTTATTAAAA
1 ATATTAATTTTTATTT-TTAAAA
2482979 GTTTTTATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 1 0.03
28 28 0.70
29 11 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
ATATTAATTTTTATTTTTAAAAAAATATT
Found at i:2482970 original size:26 final size:28
Alignment explanation
Indices: 2482927--2482989 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
2482917 TAAAAAAATA
*
2482927 TTATATTATTTTAATATTTA-AAAATTTT
1 TTATA-TATTTTAATATTTATAAAAGTTT
*
2482955 TTATATATTTT-TTATTTATTAAAAGTTT
1 TTATATATTTTAATATTTA-TAAAAGTTT
2482983 TTATATA
1 TTATATA
2482990 GTCATCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 6 0.19
27 6 0.19
28 19 0.61
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TTATATATTTTAATATTTATAAAAGTTT
Found at i:2493939 original size:91 final size:92
Alignment explanation
Indices: 2493720--2493939 Score: 211
Period size: 89 Copynumber: 2.4 Consensus size: 92
2493710 AAAAGTTTTC
* *
2493720 AAATTTTTTTTAAAAAAGTAATTAAGT--TT-TTATTTTTTTTACACTCAATTGAATACTTAAAC
1 AAATTTTTTTTAAAAAAGCAATTAAGTCCTTATTAATTTTTTTACACTCAATTGAATACTTAAAC
*
2493782 TTTCAAAATACATAAAAAAAAATTCTT
66 TTTCAAAATACATAAAAAAAAACTCTT
* * * * * *** ** *
2493809 AAACTTTTTTAAAAAAAGCAATTAA-ACTCTTA-TACTTTTTTTGCACTCAATTTTGTGTTTGAA
1 AAATTTTTTTTAAAAAAGCAATTAAGTC-CTTATTAATTTTTTTACACTCAATTGAATACTTAAA
* * *
2493872 CTTTCAAAATGCAT-CAAAAAAGCTC-T
65 CTTTCAAAATACATAAAAAAAAACTCTT
*
2493898 CAATTTTTTTTAAAAAAGCAATTAAGTCCTTAATTAATTTTT
1 AAATTTTTTTTAAAAAAGCAATTAAGTCCTT-ATTAATTTTT
2493940 ACTTAATTAG
Statistics
Matches: 103, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
89 48 0.47
90 10 0.10
91 45 0.44
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (92 bp):
AAATTTTTTTTAAAAAAGCAATTAAGTCCTTATTAATTTTTTTACACTCAATTGAATACTTAAAC
TTTCAAAATACATAAAAAAAAACTCTT
Found at i:2493946 original size:15 final size:16
Alignment explanation
Indices: 2493926--2493956 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2493916 CAATTAAGTC
2493926 CTTAATTA-ATTTTTA
1 CTTAATTAGATTTTTA
2493941 CTTAATTAGATTTTTA
1 CTTAATTAGATTTTTA
2493957 AACTGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
CTTAATTAGATTTTTA
Found at i:2494112 original size:20 final size:20
Alignment explanation
Indices: 2494084--2494124 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2494074 ATGTAACAAA
*
2494084 AAACTAAAAAAATAAAAAAT
1 AAACAAAAAAAATAAAAAAT
**
2494104 AAACAAAAATTATAAAAAAT
1 AAACAAAAAAAATAAAAAAT
2494124 A
1 A
2494125 TTAAATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (20 bp):
AAACAAAAAAAATAAAAAAT
Found at i:2494142 original size:18 final size:17
Alignment explanation
Indices: 2494109--2494161 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
2494099 AAAATAAACA
*
2494109 AAAATTATAAAAAATAT
1 AAAATTTTAAAAAATAT
*
2494126 TAAATTTTAATAAAATAT
1 AAAATTTTAA-AAAATAT
2494144 AAAATTTATTAAAAAATA
1 AAAA-TT-TTAAAAAATA
2494162 GATTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 8 0.27
18 10 0.33
19 8 0.27
20 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTTTAAAAAATAT
Found at i:2494498 original size:29 final size:28
Alignment explanation
Indices: 2494466--2494546 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 28
2494456 CTTATGAGTA
2494466 TATAAAATTTTATAATTTTTCTATATTTC
1 TATAAAATTTTATAATTTTT-TATATTTC
* *
2494495 TAT-ATATTTTATAATTTTTT-TAATTTT
1 TATAAAATTTTATAATTTTTTAT-ATTTC
*
2494522 TATTAAAATTTAATAATTTTTTATA
1 TA-TAAAATTTTATAATTTTTTATA
2494547 ACTTTTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 1 0.02
27 7 0.16
28 16 0.36
29 19 0.43
30 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
TATAAAATTTTATAATTTTTTATATTTC
Found at i:2494499 original size:57 final size:57
Alignment explanation
Indices: 2494426--2494546 Score: 131
Period size: 57 Copynumber: 2.1 Consensus size: 57
2494416 TTTTTACGAA
* * *
2494426 TTTTATATTTTTTATAT-TTTCTGTAATTTTCTT-ATGAGTATATAAAATTTTATAATT
1 TTTTATATTTTCTATATATTT-TATAATTTTCTTAATGAGTAT-TAAAATTTAATAATT
* ***
2494483 TTTCTATA-TTTCTATATATTTTATAATTTTTTTAATTTTTATTAAAATTTAATAATT
1 TTT-TATATTTTCTATATATTTTATAATTTTCTTAATGAGTATTAAAATTTAATAATT
2494540 TTTTATA
1 TTTTATA
2494547 ACTTTTATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
56 4 0.07
57 38 0.70
58 12 0.22
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.63
Consensus pattern (57 bp):
TTTTATATTTTCTATATATTTTATAATTTTCTTAATGAGTATTAAAATTTAATAATT
Found at i:2494513 original size:9 final size:9
Alignment explanation
Indices: 2494473--2494554 Score: 58
Period size: 9 Copynumber: 8.7 Consensus size: 9
2494463 GTATATAAAA
2494473 TTTTATAAT
1 TTTTATAAT
*
2494482 TTTTCTATAT
1 TTTTATA-AT
*
2494492 TTCTAT-AT
1 TTTTATAAT
2494500 ATTTTATAAT
1 -TTTTATAAT
*
2494510 TTTTTTAAT
1 TTTTATAAT
*
2494519 TTTTATTAAAA
1 TTTTA-T-AAT
*
2494530 TTTAATAATT
1 TTTTATAA-T
*
2494540 TTTTATAAC
1 TTTTATAAT
2494549 TTTTAT
1 TTTTAT
2494555 TTTTTATTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
8 2 0.04
9 31 0.55
10 17 0.30
11 6 0.11
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2494533 original size:28 final size:28
Alignment explanation
Indices: 2494468--2494555 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 28
2494458 TATGAGTATA
* *
2494468 TAAAATTTTATAATTTTTCTATATTTCTA-
1 TAAAA-TTTATAATTTTTTTA-ATTTTTAT
* *
2494497 TATATTTTATAATTTTTTTAATTTTTAT
1 TAAAATTTATAATTTTTTTAATTTTTAT
*
2494525 TAAAATTTAATAATTTTTTATAACTTTTAT
1 TAAAATTT-ATAATTTTTT-TAATTTTTAT
2494555 T
1 T
2494556 TTTTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
27 6 0.12
28 20 0.41
29 13 0.27
30 10 0.20
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
TAAAATTTATAATTTTTTTAATTTTTAT
Found at i:2495679 original size:21 final size:19
Alignment explanation
Indices: 2495653--2495700 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
2495643 CAGGGGATTG
*
2495653 AATCAAATGAGAAACAATGCA
1 AATCAAA-GAG-AACAATGAA
*
2495674 AATCAACAGAGAGCAATGAA
1 AATCAA-AGAGAACAATGAA
2495694 AATCAAA
1 AATCAAA
2495701 ATGATTCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 13 0.54
21 9 0.38
22 1 0.04
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (19 bp):
AATCAAAGAGAACAATGAA
Found at i:2513458 original size:18 final size:18
Alignment explanation
Indices: 2513435--2513471 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2513425 ATGGTTCAAC
2513435 ATTACACAACCACCCACT
1 ATTACACAACCACCCACT
2513453 ATTACACAACCACCCACT
1 ATTACACAACCACCCACT
2513471 A
1 A
2513472 GTTGACATTC
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:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (18 bp):
ATTACACAACCACCCACT
Found at i:2518471 original size:23 final size:23
Alignment explanation
Indices: 2518445--2518498 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2518435 TATTTACTTT
2518445 GAATTT-AATATTTTTATTTTTAG
1 GAATTTAAAT-TTTTTATTTTTAG
*
2518468 GAATTTAAATTTTTTATTTTTTG
1 GAATTTAAATTTTTTATTTTTAG
2518491 G-ATTTAAA
1 GAATTTAAA
2518499 AAATTTCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 7 0.24
23 19 0.66
24 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (23 bp):
GAATTTAAATTTTTTATTTTTAG
Found at i:2519165 original size:2 final size:2
Alignment explanation
Indices: 2519160--2519186 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2519150 CTCTTCACTG
2519160 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2519187 TTTTTAGCTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2520103 original size:48 final size:48
Alignment explanation
Indices: 2520009--2520104 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
2519999 TTTTTTTTAT
*
2520009 CATTACAATATTGGTTTGAACTCGTGTTATGTAAGTACTAGATAGGAG
1 CATTACAATATTGGTTTGAACTCGTGTTATGTAAGTACCAGATAGGAG
* * * *
2520057 CATTACGATATTGGTTTGGACTCGTGTTATGTAAGTGCCAGGTAGGAG
1 CATTACAATATTGGTTTGAACTCGTGTTATGTAAGTACCAGATAGGAG
2520105 TTTTTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.34
Consensus pattern (48 bp):
CATTACAATATTGGTTTGAACTCGTGTTATGTAAGTACCAGATAGGAG
Found at i:2524532 original size:19 final size:20
Alignment explanation
Indices: 2524510--2524560 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
2524500 CTCATAATGA
2524510 TTTTAAAATAATTT-TAT-AT
1 TTTTAAAAT-ATTTCTATAAT
* *
2524529 TTTTATAATTTTTCTATAAT
1 TTTTAAAATATTTCTATAAT
2524549 TTTT-AAATATTT
1 TTTTAAAATATTT
2524561 ATCCACACCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 3 0.12
19 17 0.65
20 6 0.23
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAAAATATTTCTATAAT
Found at i:2525674 original size:2 final size:2
Alignment explanation
Indices: 2525669--2525708 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2525659 AGAGTACATT
2525669 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2525709 CCTTTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2533824 original size:17 final size:17
Alignment explanation
Indices: 2533802--2533835 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2533792 ATTGAAAGAT
2533802 TATTACAGATAATTAAC
1 TATTACAGATAATTAAC
2533819 TATTACAGATAATTAAC
1 TATTACAGATAATTAAC
2533836 CCAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (17 bp):
TATTACAGATAATTAAC
Found at i:2534150 original size:55 final size:55
Alignment explanation
Indices: 2534086--2534194 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
2534076 ATATTAAACC
2534086 AAAAGTTATTAATAAATAATAAATTGAATA-AGAAAAAATCTACTTATCAAGGGCA
1 AAAAGTTATTAATAAATAATAAATTGAATAGA-AAAAAATCTACTTATCAAGGGCA
*
2534141 AAAAGTTATTAATAAATAATAAATTGAATAGAAAAAAATTTACTTATCAAGGGC
1 AAAAGTTATTAATAAATAATAAATTGAATAGAAAAAAATCTACTTATCAAGGGC
2534195 GTAACTAAGG
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
55 51 0.98
56 1 0.02
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.28
Consensus pattern (55 bp):
AAAAGTTATTAATAAATAATAAATTGAATAGAAAAAAATCTACTTATCAAGGGCA
Found at i:2535284 original size:16 final size:16
Alignment explanation
Indices: 2535233--2535302 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
2535223 AATGTAATTA
*
2535233 AAAAATATTTAGCTAATT
1 AAAAATATTTA-AT-ATT
*
2535251 AAGAATAATTT-ATATT
1 AAAAAT-ATTTAATATT
* * *
2535267 AATATTATTTAATCTT
1 AAAAATATTTAATATT
2535283 AAAAATATTTAATATT
1 AAAAATATTTAATATT
2535299 AAAA
1 AAAA
2535303 TAATAAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 4 0.10
16 28 0.67
17 1 0.02
18 5 0.12
19 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (16 bp):
AAAAATATTTAATATT
Found at i:2541680 original size:24 final size:25
Alignment explanation
Indices: 2541640--2541692 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
2541630 TTAAAATGGA
*
2541640 GAATAATATACAGTTAAATGAGCTT
1 GAATAATATACACTTAAATGAGCTT
2541665 GAAT-ATATACACTTAAATGAGCTT
1 GAATAATATACACTTAAATGAGCTT
2541689 GAAT
1 GAAT
2541693 TCACCTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (25 bp):
GAATAATATACACTTAAATGAGCTT
Found at i:2550629 original size:31 final size:28
Alignment explanation
Indices: 2550594--2550663 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 28
2550584 TCAATAAAGG
*
2550594 TAAAATTATATTTTAATCTTTTTAGAAATAA
1 TAAAATTATAATTTAATC-TTTTA-AAA-AA
2550625 TAAAAATT-TAATTTAATCTTTTAAAAAA
1 T-AAAATTATAATTTAATCTTTTAAAAAA
*
2550653 AAAAATTATAA
1 TAAAATTATAA
2550664 AAATAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 6 0.17
28 5 0.14
29 3 0.09
30 5 0.14
31 10 0.29
32 6 0.17
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (28 bp):
TAAAATTATAATTTAATCTTTTAAAAAA
Found at i:2550676 original size:17 final size:15
Alignment explanation
Indices: 2550646--2550679 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
2550636 TTTAATCTTT
2550646 TAAAAAAAAAAATTA
1 TAAAAAAAAAAATTA
2550661 TAAAAATAATAAAATTA
1 TAAAAA-AA-AAAATTA
2550678 TA
1 TA
2550680 TTTTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 2 0.12
17 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAAAAAAAATTA
Found at i:2551428 original size:22 final size:22
Alignment explanation
Indices: 2551390--2551439 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2551380 CATTAATTTT
* *
2551390 ATTTTTATTTAATACTTAGTAA
1 ATTTTTATTCAATACTTAATAA
*
2551412 ATTTTTATATCAA-ACTTAATAT
1 ATTTTTAT-TCAATACTTAATAA
2551434 ATTTTT
1 ATTTTT
2551440 TAGTGTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTTTATTCAATACTTAATAA
Found at i:2576300 original size:15 final size:15
Alignment explanation
Indices: 2576280--2576324 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2576270 TAGACTTAGC
2576280 TTTCTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
* *
2576295 TTTCTTTTTCTTTAT
1 TTTCTTTTTTTTTTT
**
2576310 TAACTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
2576325 ATATTTATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCTTTTTTTTTTT
Found at i:2576331 original size:23 final size:24
Alignment explanation
Indices: 2576290--2576334 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2576280 TTTCTTTTTT
* *
2576290 TTTTTTTTCTTTTTCTTTATTAAC
1 TTTTTTTTCTTTATATTTATTAAC
2576314 TTTTTTTT-TTTATATTTATTA
1 TTTTTTTTCTTTATATTTATTA
2576335 TAAGGGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTTTTCTTTATATTTATTAAC
Found at i:2577276 original size:16 final size:17
Alignment explanation
Indices: 2577257--2577288 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2577247 TTTAACTATT
2577257 TAAAA-TTTTATAATTA
1 TAAAATTTTTATAATTA
2577273 TAAAATTTTTATAATT
1 TAAAATTTTTATAATT
2577289 TAATCTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAATTTTTATAATTA
Found at i:2581625 original size:25 final size:24
Alignment explanation
Indices: 2581597--2581645 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2581587 TTTAACATAG
2581597 TTTTTCTATTTTTTTTCATTTGTTA
1 TTTTTCTA-TTTTTTTCATTTGTTA
2581622 TTTTTCTATTTTTTTCATTTGTTA
1 TTTTTCTATTTTTTTCATTTGTTA
2581646 AACTGTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTTTCTATTTTTTTCATTTGTTA
Found at i:2581863 original size:20 final size:20
Alignment explanation
Indices: 2581821--2581864 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2581811 TTATTTTAAA
* *
2581821 TTTAAGAATTTATACTATTT
1 TTTAAGAATTTATAATATAT
2581841 TTTAA-AATTTATCAATATAT
1 TTTAAGAATTTAT-AATATAT
2581861 TTTA
1 TTTA
2581865 TTTTTAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTAAGAATTTATAATATAT
Found at i:2582321 original size:17 final size:18
Alignment explanation
Indices: 2582296--2582333 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2582286 AATATATTTT
* *
2582296 TATTTAACGTATTA-ATC
1 TATTAAACGTAATATATC
2582313 TATTAAACGTAATATATC
1 TATTAAACGTAATATATC
2582331 TAT
1 TAT
2582334 ATATTACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (18 bp):
TATTAAACGTAATATATC
Found at i:2583422 original size:2 final size:2
Alignment explanation
Indices: 2583415--2583472 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2583405 AATTTATTCA
2583415 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
2583457 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2583473 TACTCATTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2587415 original size:107 final size:107
Alignment explanation
Indices: 2587293--2587506 Score: 392
Period size: 107 Copynumber: 2.0 Consensus size: 107
2587283 AAAATTTGAG
2587293 GCATTACAACTCTCAATTCACTAATCCAATTTTTACTAACCCGATTTTTTGAATGTGACAGAGAT
1 GCATTACAACTCTCAATTCACTAATCCAATTTTTACTAACCCGATTTTTTGAATGTGACAGAGAT
*
2587358 GGTCTAACCAATCATGCCAAGTAATTAACACATTTGGACTTA
66 GGTCTAACCAATCATACCAAGTAATTAACACATTTGGACTTA
* * *
2587400 GCATTGCAACTCTCAATTCACTAATCCAATTTTTACTAACCCGATTTTTTTAATGTGGCAGAGAT
1 GCATTACAACTCTCAATTCACTAATCCAATTTTTACTAACCCGATTTTTTGAATGTGACAGAGAT
2587465 GGTCTAACCAATCATACCAAGTAATTAACACATTTGGACTTA
66 GGTCTAACCAATCATACCAAGTAATTAACACATTTGGACTTA
2587507 TAAACTTTCA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (107 bp):
GCATTACAACTCTCAATTCACTAATCCAATTTTTACTAACCCGATTTTTTGAATGTGACAGAGAT
GGTCTAACCAATCATACCAAGTAATTAACACATTTGGACTTA
Found at i:2594710 original size:12 final size:12
Alignment explanation
Indices: 2594690--2594719 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2594680 TACTTGCATT
*
2594690 AAAACAGAAAAA
1 AAAAAAGAAAAA
2594702 AAAAAAGAAAAA
1 AAAAAAGAAAAA
2594714 AAAAAA
1 AAAAAA
2594720 AAAGAGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:2604373 original size:2 final size:2
Alignment explanation
Indices: 2604366--2604413 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2604356 TGATAATTCG
2604366 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
2604408 A- AT AT A
1 AT AT AT A
2604414 ATTGATATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2606265 original size:26 final size:26
Alignment explanation
Indices: 2606228--2606288 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
2606218 CAGGGTATAA
2606228 TTGAGATATTGGTAAATAAGCTCGAAC
1 TTGAG-TATTGGTAAATAAGCTCGAAC
* * *
2606255 TTGAGTATTGGTAAATGAGTTCGAAT
1 TTGAGTATTGGTAAATAAGCTCGAAC
2606281 TTGAGTAT
1 TTGAGTAT
2606289 AAAAATTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 26 0.84
27 5 0.16
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TTGAGTATTGGTAAATAAGCTCGAAC
Found at i:2608283 original size:5 final size:5
Alignment explanation
Indices: 2608275--2608320 Score: 65
Period size: 5 Copynumber: 9.0 Consensus size: 5
2608265 GAGAAGAAAA
* *
2608275 GAGAC GAGAA GATAC GAAGAC GAGAC GAGAC GAGAC GAGAC GAGAC
1 GAGAC GAGAC GAGAC G-AGAC GAGAC GAGAC GAGAC GAGAC GAGAC
2608321 AAATACAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
5 32 0.89
6 4 0.11
ACGTcount: A:0.43, C:0.17, G:0.37, T:0.02
Consensus pattern (5 bp):
GAGAC
Found at i:2622520 original size:30 final size:27
Alignment explanation
Indices: 2622452--2622523 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 27
2622442 TATTTGCGAA
2622452 TTTAAAATTTAATCCTTATATTTTATT
1 TTTAAAATTTAATCCTTATATTTTATT
*
2622479 TTTAAGAATTTAGTCTCTCTA-ATTTTAATAT
1 TTTAA-AATTTAATC-CT-TATATTTT-AT-T
2622510 TTTAAAATTTAATC
1 TTTAAAATTTAATC
2622524 AAATTGTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 5 0.13
28 8 0.21
29 7 0.18
30 12 0.32
31 6 0.16
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (27 bp):
TTTAAAATTTAATCCTTATATTTTATT
Found at i:2622723 original size:23 final size:23
Alignment explanation
Indices: 2622680--2622723 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2622670 GAATTTTAAA
*
2622680 TTTTAAAAAATAAAGAGACAAAT
1 TTTTAAAAAATAAAAAGACAAAT
* *
2622703 TTTTTAAAAATAAAAATACAA
1 TTTTAAAAAATAAAAAGACAA
2622724 TAACTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (23 bp):
TTTTAAAAAATAAAAAGACAAAT
Found at i:2622913 original size:2 final size:2
Alignment explanation
Indices: 2622908--2622954 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2622898 ATATACAAAA
2622908 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
*
2622950 TT AT A
1 AT AT A
2622955 AACATAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.