Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 8 of 128
Found at i:2245663 original size:22 final size:23
Alignment explanation
Indices: 2245607--2245663 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
2245597 AGTTTAAAAT
2245607 AAAATATATAAAAGAAAGTCTTA
1 AAAATATATAAAAGAAAGTCTTA
*
2245630 AATAATA-A-AAAAGACAGT-TTA
1 AA-AATATATAAAAGAAAGTCTTA
2245651 AAAATATATAAAA
1 AAAATATATAAAA
2245664 ATAGTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 13 0.43
23 3 0.10
24 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAATATATAAAAGAAAGTCTTA
Found at i:2246392 original size:13 final size:13
Alignment explanation
Indices: 2246374--2246398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2246364 AAATGCGTAG
2246374 ATAAATAAATGAA
1 ATAAATAAATGAA
2246387 ATAAATAAATGA
1 ATAAATAAATGA
2246399 TAGATGATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATAAATAAATGAA
Found at i:2253935 original size:20 final size:20
Alignment explanation
Indices: 2253910--2253950 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2253900 GAAAGAGAAA
*
2253910 AAATAAAAGAAA-AATAAAAT
1 AAATAAAA-AAACAAAAAAAT
2253930 AAATAAAAAAACAAAAAAAT
1 AAATAAAAAAACAAAAAAAT
2253950 A
1 A
2253951 GAGAACTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (20 bp):
AAATAAAAAAACAAAAAAAT
Found at i:2253949 original size:16 final size:17
Alignment explanation
Indices: 2253909--2253950 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2253899 AGAAAGAGAA
* *
2253909 AAAATAAA-AGAAAAAT
1 AAAATAAATAAAAAAAC
2253925 AAAATAAATAAAAAAAC
1 AAAATAAATAAAAAAAC
2253942 AAAA-AAATA
1 AAAATAAATA
2253951 GAGAACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (17 bp):
AAAATAAATAAAAAAAC
Found at i:2261679 original size:26 final size:26
Alignment explanation
Indices: 2261644--2261698 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
2261634 TAATTCATGG
* *
2261644 TGGTGCTTGATATCGAGTGGTATCTA
1 TGGTGCTTGATATCAAGTGGCATCTA
*
2261670 TGGTGTTTGATATCAAGTGGCATCTA
1 TGGTGCTTGATATCAAGTGGCATCTA
2261696 TGG
1 TGG
2261699 GATATGTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.38
Consensus pattern (26 bp):
TGGTGCTTGATATCAAGTGGCATCTA
Found at i:2267720 original size:20 final size:20
Alignment explanation
Indices: 2267695--2267736 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2267685 TTGATCTCAA
2267695 AAATGATAAAAAATTTATTT
1 AAATGATAAAAAATTTATTT
*
2267715 AAATGATAAAAATTTTATTT
1 AAATGATAAAAAATTTATTT
2267735 AA
1 AA
2267737 TTATTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
AAATGATAAAAAATTTATTT
Found at i:2268290 original size:18 final size:18
Alignment explanation
Indices: 2268234--2268290 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
2268224 ACTTTGACGT
* * *
2268234 GCTCGCAACTTGAGTTGA
1 GCTCACAACTTTAGGTGA
* *
2268252 GCTCACATCTTTAGGTAA
1 GCTCACAACTTTAGGTGA
2268270 GCTCACAACTTT-GGATGA
1 GCTCACAACTTTAGG-TGA
2268288 GCT
1 GCT
2268291 TAGAAGTGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
17 2 0.06
18 29 0.94
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (18 bp):
GCTCACAACTTTAGGTGA
Found at i:2275502 original size:666 final size:664
Alignment explanation
Indices: 2274231--2275562 Score: 2197
Period size: 666 Copynumber: 2.0 Consensus size: 664
2274221 TTTAAGTACT
*
2274231 GAACCAAGAAATTCTAATTCAAATAATATATTAATAGGTTTACAAATTTCGGTGATAAAAAATCT
1 GAACCAAGAAAATCTAATTCAAATAATATATTAATAGGTTTACAAATTTCGGTGATAAAAAATCT
2274296 CAAGTTAGGTGACATAACTACAAATTTTCAAAAAGAAAAGGACCAAAAGTGTAATTTATTTAAAA
66 CAAGTTAGGTGACATAACTACAAATTTTCAAAAAGAAAAGGACCAAAAGTGTAATTTATTTAAAA
2274361 ACATGATTATTTAAATAGTATATATTACGTGTTTCCTTTTTATAGAATATAGCTTGTTCAAGTAA
131 ACATGATTATTTAAATAGTATATATTACGTGTTTCCTTTTTATAGAATATAGCTTGTTCAAGTAA
* * * * *
2274426 TAATTTAAAATATATTTTGATATATTATTTGAATTAGAATTTTTAATATTTTGATATATAAAATT
196 TAATTTAAAATATATTTTGATATATTA--TAAATTAGAATTTTCAATATTATGAAACATAAAATT
* *
2274491 CAAACATGTTTCAATATATATAAAACATGATTATTTAAATATTTCAAATTTCAAATTTTAATACA
259 CAAACATGTTTCAATATATATAAAACAGGATTATTTAAATATTTAAAATTTCAAATTTTAATACA
* ** *
2274556 AAATTTTTTTATATATTTTTAATTACATCAAAATATTCGAAATTTTAATAGTTTATATAATCTAA
324 AAATGTTTAAAAATATTTTTAATTACATCAAAATATTCGAAATTTTAATAGTTTATATAATCTAA
2274621 AAATGTAATTTCATTATTTTAATAGTTTACATTTTATAATTTTTGAAAGATTAAATTAAATTTTT
389 AAATGTAATTTCATTATTTTAATAGTTTACATTTTATAATTTTTGAAAGATTAAATTAAATTTTT
2274686 ATCAGTTTTAGAGAAGTCAAAATATAATTTTATTATTATTAATTTAAAATTTTATAAATTATAAA
454 ATCAGTTTTAGAGAAGTCAAAATATAATTTTATTATTATTAATTTAAAATTTTATAAATTATAAA
2274751 GGGTGTAAAATGAAAAATTTTTCATTTCACCACTAACAGGTGCAGTTAGTCAACAATGGCTAGAA
519 GGGTGTAAAATGAAAAATTTTTCATTTCACCACTAACAGGTGCAGTTAGTCAACAATGGCTAGAA
2274816 AAAAATAATAAAAAAAATAGTGACAGAAATTTCATGGAGATTATATAAATCATTGATCCTTTAAA
584 AAAAATAATAAAAAAAATAGTGACAGAAATTTCATGGAGATTATATAAATCATTGATCCTTTAAA
2274881 TTAAGTTTACAATAAG
649 TTAAGTTTACAATAAG
2274897 GAACCAA-AAAATCTAATTCAAATAATATATTAATAGGTTTACAAATTTCGGTGATAAAAAATCT
1 GAACCAAGAAAATCTAATTCAAATAATATATTAATAGGTTTACAAATTTCGGTGATAAAAAATCT
2274961 CAAGTTAGGTGACATAACTACAAATTTTCAAAAAGAAAAGGACCAAAAGTGTAATTTATTTAAAA
66 CAAGTTAGGTGACATAACTACAAATTTTCAAAAAGAAAAGGACCAAAAGTGTAATTTATTTAAAA
* *
2275026 ACATGATTATTTAAATAGTATATATTACGTGTTTCCTTTTTATAGAATATAGCTTGTTCACGTGA
131 ACATGATTATTTAAATAGTATATATTACGTGTTTCCTTTTTATAGAATATAGCTTGTTCAAGTAA
2275091 TAATTTAAAATATATTTTGATATA-TA-AAATTCA-AACGTGTTTCAATATATAT-ACAACATGA
196 TAATTTAAAATATATTTTGATATATTATAAATT-AGAA--T-TTTCAATAT-TATGA-AACAT-A
** * * * * *
2275152 TTATTTAAATAT-TTT-AAT-T-T-TAATAC-GGAATTTTTTATATA-TTAAAATATT-AAATAT
254 AAATTCAAACATGTTTCAATATATATAAAACAGG-ATTATTTAAATATTTAAAAT-TTCAAAT-T
**
2275209 ATTTTTA-AAAGGATAGTTTAAACAATTATTTTTAATTACATCAAAATATTCGAAATTTTAATAG
316 -TTAATACAAA--AT-GTTTAAA-AA-TATTTTTAATTACATCAAAATATTCGAAATTTTAATAG
2275273 TTTATATAATCTAAAAATGTAATTTCATTATTTTAATAGTTTACATTTTATAATTTTTGAAAGAT
375 TTTATATAATCTAAAAATGTAATTTCATTATTTTAATAGTTTACATTTTATAATTTTTGAAAGAT
2275338 TAAATTAAATTTTTATCAGTTTTAGAGAAGTCAAAATATAATTTTATTATTATTAATTTAAAATT
440 TAAATTAAATTTTTATCAGTTTTAGAGAAGTCAAAATATAATTTTATTATTATTAATTTAAAATT
2275403 TTATAAATTATAAAGGGTGTAAAATGAAAAATTTTTCATTTCACCACTAACAGGTGCAGTTAGTC
505 TTATAAATTATAAAGGGTGTAAAATGAAAAATTTTTCATTTCACCACTAACAGGTGCAGTTAGTC
2275468 AACAATGGCTAGAAAAAAATAATAAAAAAAATAGTGACAGAAATTTCATGGAGATTATATAAATC
570 AACAATGGCTAGAAAAAAATAATAAAAAAAATAGTGACAGAAATTTCATGGAGATTATATAAATC
2275533 ATTGATCCTTTAAATTAAGTTTACAATAAG
635 ATTGATCCTTTAAATTAAGTTTACAATAAG
2275563 CAATTGAATA
Statistics
Matches: 627, Mismatches: 23, Indels: 32
0.92 0.03 0.05
Matches are distributed among these distances:
660 11 0.02
661 27 0.04
662 6 0.01
663 4 0.01
664 18 0.03
665 217 0.35
666 344 0.55
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (664 bp):
GAACCAAGAAAATCTAATTCAAATAATATATTAATAGGTTTACAAATTTCGGTGATAAAAAATCT
CAAGTTAGGTGACATAACTACAAATTTTCAAAAAGAAAAGGACCAAAAGTGTAATTTATTTAAAA
ACATGATTATTTAAATAGTATATATTACGTGTTTCCTTTTTATAGAATATAGCTTGTTCAAGTAA
TAATTTAAAATATATTTTGATATATTATAAATTAGAATTTTCAATATTATGAAACATAAAATTCA
AACATGTTTCAATATATATAAAACAGGATTATTTAAATATTTAAAATTTCAAATTTTAATACAAA
ATGTTTAAAAATATTTTTAATTACATCAAAATATTCGAAATTTTAATAGTTTATATAATCTAAAA
ATGTAATTTCATTATTTTAATAGTTTACATTTTATAATTTTTGAAAGATTAAATTAAATTTTTAT
CAGTTTTAGAGAAGTCAAAATATAATTTTATTATTATTAATTTAAAATTTTATAAATTATAAAGG
GTGTAAAATGAAAAATTTTTCATTTCACCACTAACAGGTGCAGTTAGTCAACAATGGCTAGAAAA
AAATAATAAAAAAAATAGTGACAGAAATTTCATGGAGATTATATAAATCATTGATCCTTTAAATT
AAGTTTACAATAAG
Found at i:2276165 original size:14 final size:13
Alignment explanation
Indices: 2276138--2276176 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2276128 AAAATATCAA
*
2276138 TTTTTAAAAGATT
1 TTTTTAAAATATT
2276151 TTTTTATAAATATT
1 TTTTTA-AAATATT
2276165 TCTTTTAAAATA
1 T-TTTTAAAATA
2276177 ATATATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.26
14 12 0.52
15 5 0.22
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (13 bp):
TTTTTAAAATATT
Found at i:2281132 original size:7 final size:7
Alignment explanation
Indices: 2281120--2281163 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
2281110 AGGTACTATC
2281120 TTATTGA
1 TTATTGA
2281127 TTATTGA
1 TTATTGA
2281134 TTATTGA
1 TTATTGA
2281141 TTATT-A
1 TTATTGA
2281147 TTATTGA
1 TTATTGA
2281154 TTATTGA
1 TTATTGA
2281161 TTA
1 TTA
2281164 AATGACTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (7 bp):
TTATTGA
Found at i:2281151 original size:20 final size:21
Alignment explanation
Indices: 2281120--2281163 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
2281110 AGGTACTATC
2281120 TTATTGATTATTGATTATTGA
1 TTATTGATTATTGATTATTGA
2281141 TTATT-ATTATTGATTATTGA
1 TTATTGATTATTGATTATTGA
2281161 TTA
1 TTA
2281164 AATGACTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
TTATTGATTATTGATTATTGA
Found at i:2284540 original size:13 final size:13
Alignment explanation
Indices: 2284518--2284551 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2284508 AAATCCAAAC
*
2284518 ATTTTATTATGTT
1 ATTTTTTTATGTT
*
2284531 ATTTTTTTATTTT
1 ATTTTTTTATGTT
2284544 ATTTTTTT
1 ATTTTTTT
2284552 CAGGCACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
ATTTTTTTATGTT
Found at i:2290844 original size:26 final size:26
Alignment explanation
Indices: 2290809--2290863 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
2290799 TAATTCATGG
*
2290809 TGGTGCTTGATATCGAGTGGTATCTA
1 TGGTGCTTGATATCAAGTGGTATCTA
2290835 TGGTGCTTGATATCAAGTGGTATCTA
1 TGGTGCTTGATATCAAGTGGTATCTA
2290861 TGG
1 TGG
2290864 GATATGTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.38
Consensus pattern (26 bp):
TGGTGCTTGATATCAAGTGGTATCTA
Found at i:2292434 original size:28 final size:28
Alignment explanation
Indices: 2292403--2292458 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
2292393 ACTAAGGCAA
*
2292403 CAAGGCCGATCATATATTATTCAAGCGG
1 CAAGGCCGATCATATATCATTCAAGCGG
2292431 CAAGGCCGATCATATATCATTCAAGCGG
1 CAAGGCCGATCATATATCATTCAAGCGG
2292459 TAGAACCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (28 bp):
CAAGGCCGATCATATATCATTCAAGCGG
Found at i:2296662 original size:21 final size:21
Alignment explanation
Indices: 2296638--2296680 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2296628 GTACATTGAC
2296638 AACTTAGTTCAAATCAAACTA
1 AACTTAGTTCAAATCAAACTA
2296659 AACTTAGTTCAAATCAAACTA
1 AACTTAGTTCAAATCAAACTA
2296680 A
1 A
2296681 GTAACAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.28
Consensus pattern (21 bp):
AACTTAGTTCAAATCAAACTA
Found at i:2308037 original size:26 final size:27
Alignment explanation
Indices: 2308008--2308059 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2307998 TTTCGTACAT
*
2308008 TTAG-AATTTAA-TCTTTACACTTTTTA
1 TTAGAAATTTAATTCCTTA-ACTTTTTA
2308034 TTAGAAATTTAATTCCTTAACTTTTT
1 TTAGAAATTTAATTCCTTAACTTTTT
2308060 TAATTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 14 0.61
28 5 0.22
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.54
Consensus pattern (27 bp):
TTAGAAATTTAATTCCTTAACTTTTTA
Found at i:2319853 original size:31 final size:31
Alignment explanation
Indices: 2319811--2319870 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2319801 CTCAAGATTA
* *
2319811 TTTTTTGTTC-AATTAGGTATCTAAATTTGGT
1 TTTTTTATTCAAATT-GGTACCTAAATTTGGT
*
2319842 TTTTTTATTCAAATTGGTACCTGAATTTG
1 TTTTTTATTCAAATTGGTACCTAAATTTG
2319871 ATTTCATAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.53
Consensus pattern (31 bp):
TTTTTTATTCAAATTGGTACCTAAATTTGGT
Found at i:2321320 original size:10 final size:10
Alignment explanation
Indices: 2321305--2321330 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2321295 ACAATTCTTT
2321305 ATTTTCATTC
1 ATTTTCATTC
2321315 ATTTTCATTC
1 ATTTTCATTC
2321325 ATTTTC
1 ATTTTC
2321331 CTGCGTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTCATTC
Found at i:2326142 original size:34 final size:34
Alignment explanation
Indices: 2326104--2326218 Score: 131
Period size: 35 Copynumber: 3.3 Consensus size: 34
2326094 AACGTGCAAG
* * *
2326104 AATAAAAGCAATATGAAGACTTAAAATTTCCATT
1 AATAAAACCAAAATGAAGACCTAAAATTTCCATT
* ** *
2326138 AATAAAACCAAAATCAAAGAAGTAAAATTTCCATG
1 AATAAAACCAAAAT-GAAGACCTAAAATTTCCATT
*
2326173 AATAAAACCAAAAATGAAGACCTAAATTTTCCATT
1 AATAAAACC-AAAATGAAGACCTAAAATTTCCATT
*
2326208 AATAAAGCCAA
1 AATAAAACCAA
2326219 GTCAAGATTA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 14 0.21
35 48 0.72
36 5 0.07
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (34 bp):
AATAAAACCAAAATGAAGACCTAAAATTTCCATT
Found at i:2330639 original size:12 final size:12
Alignment explanation
Indices: 2330619--2330651 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2330609 TTGTTTCAGG
2330619 TTGTATTATTAA
1 TTGTATTATTAA
*
2330631 TTGTGTTATTAA
1 TTGTATTATTAA
2330643 TT-TATTATT
1 TTGTATTATT
2330652 TTAAATTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (12 bp):
TTGTATTATTAA
Found at i:2330966 original size:43 final size:43
Alignment explanation
Indices: 2330901--2331007 Score: 160
Period size: 43 Copynumber: 2.5 Consensus size: 43
2330891 GTTCTTTAGG
* * *
2330901 TCATGATCTTTAGTGGCATTTGTGACAAAAGCGCCGCTAAAGC
1 TCATGGTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGC
* * *
2330944 TCATGGTCTTTAGCGGCGTTTGTGACAGACGCGCCGCTAAAGG
1 TCATGGTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGC
2330987 TCATGGTCTTTAGCGGCGTTT
1 TCATGGTCTTTAGCGGCGTTT
2331008 TTTCGCATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (43 bp):
TCATGGTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGC
Found at i:2340487 original size:2 final size:2
Alignment explanation
Indices: 2340480--2340510 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2340470 TTTAATTTTC
2340480 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2340511 GTATGTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2340751 original size:2 final size:2
Alignment explanation
Indices: 2340744--2340772 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2340734 NNTATTTTTC
2340744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2340773 GTATGTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2349464 original size:31 final size:31
Alignment explanation
Indices: 2349424--2349486 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2349414 GATATAGTGT
*
2349424 AATTATACACATAAAACTTTT-ATTTTGATTC
1 AATTATACACATAAAA-TTTTAACTTTGATTC
* *
2349455 AATTGTACACATGAAATTTTAACTTTGATTC
1 AATTATACACATAAAATTTTAACTTTGATTC
2349486 A
1 A
2349487 GTTGCATGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (31 bp):
AATTATACACATAAAATTTTAACTTTGATTC
Found at i:2353578 original size:20 final size:20
Alignment explanation
Indices: 2353553--2353592 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2353543 TAATGTCTAG
2353553 GGAAAGTATTAATTGAGAAA
1 GGAAAGTATTAATTGAGAAA
2353573 GGAAAGTATTAATTGAGAAA
1 GGAAAGTATTAATTGAGAAA
2353593 ATTATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (20 bp):
GGAAAGTATTAATTGAGAAA
Found at i:2355028 original size:36 final size:36
Alignment explanation
Indices: 2354982--2355090 Score: 182
Period size: 36 Copynumber: 3.0 Consensus size: 36
2354972 GGTAGCTTTA
* *
2354982 GCTACACTTATCTGATCAAGTGAAAAAGTGATAATT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
2355018 GCTATACTTATCTGATCAAGTGAAAAGGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
2355054 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
2355090 G
1 G
2355091 GTAGCTTTAG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:2355111 original size:46 final size:46
Alignment explanation
Indices: 2355054--2355273 Score: 329
Period size: 46 Copynumber: 4.8 Consensus size: 46
2355044 GGTGATAAGT
* *
2355054 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
*
2355100 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
* *
2355146 GCTACACTTATTTGATCAAGTGAAAAAGTGATAAGTGGTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
* * *
2355192 GCTACACTTATCTGATCAAATAAAAAAAAGTGATAAGTGGTAGCC-TA
1 GCTACACTTATCTGATCAAGT--GACAAAGTGATAAGTGGTAGCCTTA
2355239 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
2355274 ATCATACGTA
Statistics
Matches: 160, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
43 12 0.08
44 1 0.01
46 105 0.66
47 21 0.13
48 21 0.13
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
Found at i:2358238 original size:19 final size:19
Alignment explanation
Indices: 2358186--2358238 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
2358176 ATTGGCGCAT
*
2358186 GAAGTGCATCCTGACACAC
1 GAAGTGCATCCTGGCACAC
*
2358205 GAAGTGCATCTTGGCACAC
1 GAAGTGCATCCTGGCACAC
2358224 GAAGTGCATCCTGGC
1 GAAGTGCATCCTGGC
2358239 GCATAAGCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (19 bp):
GAAGTGCATCCTGGCACAC
Found at i:2368789 original size:40 final size:40
Alignment explanation
Indices: 2368745--2368863 Score: 159
Period size: 39 Copynumber: 3.0 Consensus size: 40
2368735 AGTGAAAAGG
* *
2368745 TATATAGTTGCTAGTTTGTATTTTTGTACGATGCACGGGT
1 TATATAATTGCTAGTTTGTATTTTTATACGATGCACGGGT
* * * *
2368785 TATATAATTGCTAATTTGTATTTTTATGCGATGCA-TGAT
1 TATATAATTGCTAGTTTGTATTTTTATACGATGCACGGGT
**
2368824 TATATAATTATTAGTTTGTATTTTTATACGATGCACGGGT
1 TATATAATTGCTAGTTTGTATTTTTATACGATGCACGGGT
2368864 CATTTGTGTA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 33 0.50
40 33 0.50
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (40 bp):
TATATAATTGCTAGTTTGTATTTTTATACGATGCACGGGT
Found at i:2370833 original size:215 final size:209
Alignment explanation
Indices: 2370572--2371343 Score: 598
Period size: 215 Copynumber: 3.6 Consensus size: 209
2370562 AGGTTCTGGA
* * * *
2370572 AAAACGGTATTCAAATTGTATTACCAGGGAAAACAAAAGAATAAATAAACGTAGCTTGCCAACTA
1 AAAACGGTACTCAAATTATATTAACAGGGAAAACAAAAGAATAAATAAACATAGCTTGCCAACTA
* *
2370637 AATTTAACAATTTATTGATCAAGTTCATGGTTCAGAGTACGACATCGGTGCTTTAT-GTATTGAT
66 AATTTAACAATTTATTGATCAAGTTCATGGTTCAAAGTACGACATCGATGCTTTATCG----G--
* * * ** *
2370701 CTTGGTCCTTACTGATTTTAACAGCAGTTATGTGTTGATACGAGAGAGTGCATTGTTGAGATTAC
125 -TTAGTCCTTACTGAATTTAACAGCAGTTATGTGTTGATACGAGAGAATGCATCCTTAAGATTAC
2370766 CTGAGGCAATAAGGTTTAGGC
189 CTGAGGCAATAAGGTTTAGGC
* * * *
2370787 AAAATGGTACTCAAATTATATTAACAGGGAAAAGAGAAGAATAAATAAACATAGCTTGTCAACTA
1 AAAACGGTACTCAAATTATATTAACAGGGAAAACAAAAGAATAAATAAACATAGCTTGCCAACTA
* * * *
2370852 AATTTTACAATTTATTGATTAGGTTCATGGTTCAAAGTACTACATCGATGCTTTATCGGTTAGTC
66 AATTTAACAATTTATTGATCAAGTTCATGGTTCAAAGTACGACATCGATGCTTTATCGGTTAGTC
* *
2370917 CTTACTGAATTTAACAGCTGTTATGTGTTGATGCGAGAGAATGCATCCTTAAGATTACCTGGCGG
131 CTTACTGAATTTAACAGCAGTTATGTGTTGATACGAGAGAATGCATCCTTAAGATTACCT-----
2370982 GGGAGAG-AATTAA-GTTTAGGC
191 --GAG-GCAA-TAAGGTTTAGGC
* * ** * *
2371003 AAAATGATAC-CTGGATTGTATT-ACTAGGAAAAGAAAA-AAATAGAATAAATGAACATAGCTTG
1 AAAACGGTACTC-AAATTATATTAAC-AGG----GAAAACAAA-AGAATAAATAAACATAGCTTG
* *
2371065 CCAACTAAATTTTAACATTTTATTGA-CAAGTTCATGGTTCAAAGT-CTGACATCTATGCTTTAT
59 CCAACTAAA-TTTAACAATTTATTGATCAAGTTCATGGTTCAAAGTAC-GACATCGATGCTTTAT
* * ** * * * *
2371128 -GCGTT-GTTCATTACTGAACTTGGCAGCTGTTACGTGTTGATACGAGATAATGAATCCTTAAGA
122 CG-GTTAG-TCCTTACTGAATTTAACAGCAGTTATGTGTTGATACGAGAGAATGCATCCTTAAGA
*
2371191 TTACCTGGGAGGGAATTAAGTTTTAAGTTTAGGC
185 TTACCT--GAGGCAA-TAAG------GTTTAGGC
* * * * ** ** * * * * * **
2371225 AGAATGATACCCGGATTATATTTCCA-CGAAAAAAACAAGAATAAATAAGCTTA-CTTACTGACT
1 AAAACGGTACTCAAATTATATTAACAGGGAAAACAA-AAGAATAAATAAACATAGCTTGCCAACT
* *
2371288 GAATTGTAACATTTTATTGATCAAGTTCATGGTTCAAAGTTA-GACATCGATGCTTT
65 AAATT-TAACAATTTATTGATCAAGTTCATGGTTCAAAG-TACGACATCGATGCTTT
2371344 TTGTGTCGGT
Statistics
Matches: 465, Mismatches: 55, Indels: 71
0.79 0.09 0.12
Matches are distributed among these distances:
209 58 0.12
212 1 0.00
214 1 0.00
215 121 0.26
216 35 0.08
217 32 0.07
218 46 0.10
219 7 0.02
220 121 0.26
221 14 0.03
222 27 0.06
223 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (209 bp):
AAAACGGTACTCAAATTATATTAACAGGGAAAACAAAAGAATAAATAAACATAGCTTGCCAACTA
AATTTAACAATTTATTGATCAAGTTCATGGTTCAAAGTACGACATCGATGCTTTATCGGTTAGTC
CTTACTGAATTTAACAGCAGTTATGTGTTGATACGAGAGAATGCATCCTTAAGATTACCTGAGGC
AATAAGGTTTAGGC
Found at i:2371100 original size:220 final size:215
Alignment explanation
Indices: 2370600--2371360 Score: 691
Period size: 220 Copynumber: 3.5 Consensus size: 215
2370590 TATTACCAGG
*
2370600 GAAAACAAAAGAATAAATAAACGTAGCTTGCCAACTAAA-TTTAACAATTTATTGATCAAGTTCA
1 GAAAACAAAAGAATAAATAAACATAGCTTGCCAACTAAATTTTAACAATTTATTGATCAAGTTCA
* * * *
2370664 TGGTTCAGAGTACGACATCGGTGCTTTATGTATTGATCTTGGTCCTTACTGATTTTAACAGCAGT
66 TGGTTCAAAGTACGACATCGATGCTTTATG---TG---TT-GTCCTTACTGAATTTAACAGCTGT
* ** *
2370729 TATGTGTTGATACGAGAGAGTGCATTGTTGAGATTACCT-----GAG-GCAA-TAAGGTTTAGGC
124 TATGTGTTGATACGAGAGAATGCATCCTTAAGATTACCTGGGGGGAGAG-AATTAA-GTTTAGGC
* **
2370787 AAAATGGTA-CTCAAATTATATTAACAGG--
187 AAAATGATACCT-GGATTATATT-ACAGGAA
* * * * *
2370815 GAAAAGAGAAGAATAAATAAACATAGCTTGTCAACTAAATTTT-ACAATTTATTGATTAGGTTCA
1 GAAAACAAAAGAATAAATAAACATAGCTTGCCAACTAAATTTTAACAATTTATTGATCAAGTTCA
*
2370879 TGGTTCAAAGTACTACATCGATGCTTTATCG-GTTAGTCCTTACTGAATTTAACAGCTGTTATGT
66 TGGTTCAAAGTACGACATCGATGCTTTAT-GTGTT-GTCCTTACTGAATTTAACAGCTGTTATGT
*
2370943 GTTGATGCGAGAGAATGCATCCTTAAGATTACCTGGCGGGGGAGAGAATTAAGTTTAGGCAAAAT
129 GTTGATACGAGAGAATGCATCCTTAAGATTACCT-G-GGGGGAGAGAATTAAGTTTAGGCAAAAT
*
2371008 GATACCTGGATTGTATTACTAGGAAAA
192 GATACCTGGATTATATTAC-AGG--AA
* *
2371035 GAAAA-AAATAGAATAAATGAACATAGCTTGCCAACTAAATTTTAACATTTTATTGA-CAAGTTC
1 GAAAACAAA-AGAATAAATAAACATAGCTTGCCAACTAAATTTTAACAATTTATTGATCAAGTTC
* * * * ** *
2371098 ATGGTTCAAAGT-CTGACATCTATGCTTTATGCGTTGTTCATTACTGAACTTGGCAGCTGTTACG
65 ATGGTTCAAAGTAC-GACATCGATGCTTTATGTGTTG-TCCTTACTGAATTTAACAGCTGTTATG
* * *
2371162 TGTTGATACGAGATAATGAATCCTTAAGATTACCTGGGAGGGA-ATTAAGTTTTAAGTTTAGGCA
128 TGTTGATACGAGAGAATGCATCCTTAAGATTACCTGGG-GGGAGA-GAA---TTAAGTTTAGGCA
* * * *
2371226 GAATGATACCCGGATTATATTTCCACGAA
188 AAATGATACCTGGATTATA-TTACAGGAA
* * * * ** * * *
2371255 -AAAA-ACAAGAATAAATAAGCTTA-CTTACTGACTGAATTGTAACATTTTATTGATCAAGTTCA
1 GAAAACAAAAGAATAAATAAACATAGCTTGCCAACTAAATTTTAACAATTTATTGATCAAGTTCA
* *
2371317 TGGTTCAAAGTTA-GACATCGATGCTTTTTGTGTCGGTCCTTACT
66 TGGTTCAAAG-TACGACATCGATGCTTTATGTGT-TGTCCTTACT
2371361 TTGCCACTAT
Statistics
Matches: 457, Mismatches: 57, Indels: 61
0.79 0.10 0.11
Matches are distributed among these distances:
209 58 0.13
212 1 0.00
215 82 0.18
216 35 0.08
217 31 0.07
218 58 0.13
219 20 0.04
220 127 0.28
221 11 0.02
222 31 0.07
223 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (215 bp):
GAAAACAAAAGAATAAATAAACATAGCTTGCCAACTAAATTTTAACAATTTATTGATCAAGTTCA
TGGTTCAAAGTACGACATCGATGCTTTATGTGTTGTCCTTACTGAATTTAACAGCTGTTATGTGT
TGATACGAGAGAATGCATCCTTAAGATTACCTGGGGGGAGAGAATTAAGTTTAGGCAAAATGATA
CCTGGATTATATTACAGGAA
Found at i:2379633 original size:221 final size:221
Alignment explanation
Indices: 2379219--2379741 Score: 642
Period size: 221 Copynumber: 2.4 Consensus size: 221
2379209 AGGACCGACA
* * *
2379219 CATAAAGCATCA-ATGTCTGACTCTGAACCATGAACCTGATCAATAAAATGTTACAATTCAGTCA
1 CATAAAGCAT-AGATGTCAGACTCTGAACCATGAACCTGATCAATAAAATGTTAAAATTCAGTTA
* *
2379283 GTAAG-TATG--C--TTATT-TATTCTTGTTTTTTCCTGAAAATACAATCCGGGTATCATTTTGC
65 GCAAGCTATGTTCATTTATTCTATTCTTGTTTTTTCCTGAAAATACAATCCAGGTATCATTTTGC
* * *
2379342 CTAAACTTAAAACTTAATTCCCTCTCAGGTAATATTAAGGATTCACTCTCTCGTATCAACACATA
130 CTAAACTT-AAACTTAATTCCCCCTCAGGTAATATTAAGGATGCACTCTCTCGCATCAACACATA
*
2379407 ACAGCTGCCAAGTTCAATAAGGAAC-AAC
194 ACAGCTGCCAAATTCAATAAGG-ACTAAC
* * *
2379435 GCATAAAGCATAGATGTCAGACTCTGAACCATGAACCTG-TCTATAAACTGTTAAAATTCGGTTA
1 -CATAAAGCATAGATGTCAGACTCTGAACCATGAACCTGATCAATAAAATGTTAAAATTCAGTTA
* * **
2379499 GCAAGCTATGTTCATTTATTCTATTTTTTTTCTTTTCCTGGTAATACAATCCAGGTATCATTTTG
65 GCAAGCTATGTTCATTTATTCTATTCTTGTT-TTTTCCTGAAAATACAATCCAGGTATCATTTTG
* * *
2379564 CCTAAACTT-AA-TT-CTCTCCCCCGTCAGGTAATCTTAAGGATGCATTCTCTCGCATCAACACA
129 CCTAAACTTAAACTTAAT-TCCCCC-TCAGGTAATATTAAGGATGCACTCTCTCGCATCAACACA
**
2379626 TAACAGCTGTTAAATTCAATAAGGACTAAC
192 TAACAGCTGCCAAATTCAATAAGGACTAAC
* *
2379656 CAATAAAGCATTGATGT-AGTACTCTGAACCATGAACCTGATCAATAAATTG-TAAAATTCAGTT
1 C-ATAAAGCATAGATGTCAG-ACTCTGAACCATGAACCTGATCAATAAAATGTTAAAATTCAGTT
* *
2379719 GGCAAGCTATGTTTATTTATTCT
64 AGCAAGCTATGTTCATTTATTCT
2379742 TCTCTTTTCC
Statistics
Matches: 265, Mismatches: 27, Indels: 24
0.84 0.09 0.08
Matches are distributed among these distances:
216 25 0.09
217 39 0.15
219 2 0.01
220 12 0.05
221 131 0.49
222 17 0.06
223 39 0.15
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (221 bp):
CATAAAGCATAGATGTCAGACTCTGAACCATGAACCTGATCAATAAAATGTTAAAATTCAGTTAG
CAAGCTATGTTCATTTATTCTATTCTTGTTTTTTCCTGAAAATACAATCCAGGTATCATTTTGCC
TAAACTTAAACTTAATTCCCCCTCAGGTAATATTAAGGATGCACTCTCTCGCATCAACACATAAC
AGCTGCCAAATTCAATAAGGACTAAC
Found at i:2380787 original size:11 final size:11
Alignment explanation
Indices: 2380773--2380798 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2380763 TTTCTTCCTC
2380773 TTTTTTTCTTT
1 TTTTTTTCTTT
2380784 TTTTTTTCTTT
1 TTTTTTTCTTT
2380795 TTTT
1 TTTT
2380799 GTGTGTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:2393277 original size:504 final size:504
Alignment explanation
Indices: 2392330--2393337 Score: 2016
Period size: 504 Copynumber: 2.0 Consensus size: 504
2392320 ATCCTCAGCT
2392330 TTGGTTTGCTCATCATTTGCAGCTAATTCATTGGAAGAAGAAGAGATGGAAGAAGAGTTTGGCGT
1 TTGGTTTGCTCATCATTTGCAGCTAATTCATTGGAAGAAGAAGAGATGGAAGAAGAGTTTGGCGT
2392395 CGCGGGGTTGTTCAAGACCTCGGAAGATTCCGGCACGGTGGAAGCCGGCGACAAAAGACCAGCCT
66 CGCGGGGTTGTTCAAGACCTCGGAAGATTCCGGCACGGTGGAAGCCGGCGACAAAAGACCAGCCT
2392460 GATGATTGAGGTGCTGCTGCTTAGAGTCAGTGTGGGGTTCGTGTAATATATCATCATCATGGTGG
131 GATGATTGAGGTGCTGCTGCTTAGAGTCAGTGTGGGGTTCGTGTAATATATCATCATCATGGTGG
2392525 TGAAACACTGGTAATGGAGGTGAGGATGGTGGAAGAATCGAAGGCTGAAAAGAATCGAATAAAGA
196 TGAAACACTGGTAATGGAGGTGAGGATGGTGGAAGAATCGAAGGCTGAAAAGAATCGAATAAAGA
2392590 AGGAGCAACAAAATCTTGATGGATACCTAGCAAATCCATGAAACCCAATGACCCCCACTTATCTC
261 AGGAGCAACAAAATCTTGATGGATACCTAGCAAATCCATGAAACCCAATGACCCCCACTTATCTC
2392655 CACCACTGCCTTCACATGATGTTCCTGCCATGTCAAAGATGCTCCCACCACCACCACCACCAAAG
326 CACCACTGCCTTCACATGATGTTCCTGCCATGTCAAAGATGCTCCCACCACCACCACCACCAAAG
2392720 ACTGACGGAATCTCATCGGAAAATCTCATATTCGCCATGGGATTATTCTCGTTCTTCTTCTCCAT
391 ACTGACGGAATCTCATCGGAAAATCTCATATTCGCCATGGGATTATTCTCGTTCTTCTTCTCCAT
2392785 AAAACTATTCACATATTCTGTTTCCTTTTTTATTGAACAAAACTAGGGA
456 AAAACTATTCACATATTCTGTTTCCTTTTTTATTGAACAAAACTAGGGA
2392834 TTGGTTTGCTCATCATTTGCAGCTAATTCATTGGAAGAAGAAGAGATGGAAGAAGAGTTTGGCGT
1 TTGGTTTGCTCATCATTTGCAGCTAATTCATTGGAAGAAGAAGAGATGGAAGAAGAGTTTGGCGT
2392899 CGCGGGGTTGTTCAAGACCTCGGAAGATTCCGGCACGGTGGAAGCCGGCGACAAAAGACCAGCCT
66 CGCGGGGTTGTTCAAGACCTCGGAAGATTCCGGCACGGTGGAAGCCGGCGACAAAAGACCAGCCT
2392964 GATGATTGAGGTGCTGCTGCTTAGAGTCAGTGTGGGGTTCGTGTAATATATCATCATCATGGTGG
131 GATGATTGAGGTGCTGCTGCTTAGAGTCAGTGTGGGGTTCGTGTAATATATCATCATCATGGTGG
2393029 TGAAACACTGGTAATGGAGGTGAGGATGGTGGAAGAATCGAAGGCTGAAAAGAATCGAATAAAGA
196 TGAAACACTGGTAATGGAGGTGAGGATGGTGGAAGAATCGAAGGCTGAAAAGAATCGAATAAAGA
2393094 AGGAGCAACAAAATCTTGATGGATACCTAGCAAATCCATGAAACCCAATGACCCCCACTTATCTC
261 AGGAGCAACAAAATCTTGATGGATACCTAGCAAATCCATGAAACCCAATGACCCCCACTTATCTC
2393159 CACCACTGCCTTCACATGATGTTCCTGCCATGTCAAAGATGCTCCCACCACCACCACCACCAAAG
326 CACCACTGCCTTCACATGATGTTCCTGCCATGTCAAAGATGCTCCCACCACCACCACCACCAAAG
2393224 ACTGACGGAATCTCATCGGAAAATCTCATATTCGCCATGGGATTATTCTCGTTCTTCTTCTCCAT
391 ACTGACGGAATCTCATCGGAAAATCTCATATTCGCCATGGGATTATTCTCGTTCTTCTTCTCCAT
2393289 AAAACTATTCACATATTCTGTTTCCTTTTTTATTGAACAAAACTAGGGA
456 AAAACTATTCACATATTCTGTTTCCTTTTTTATTGAACAAAACTAGGGA
2393338 GGAAATGGTG
Statistics
Matches: 504, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
504 504 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (504 bp):
TTGGTTTGCTCATCATTTGCAGCTAATTCATTGGAAGAAGAAGAGATGGAAGAAGAGTTTGGCGT
CGCGGGGTTGTTCAAGACCTCGGAAGATTCCGGCACGGTGGAAGCCGGCGACAAAAGACCAGCCT
GATGATTGAGGTGCTGCTGCTTAGAGTCAGTGTGGGGTTCGTGTAATATATCATCATCATGGTGG
TGAAACACTGGTAATGGAGGTGAGGATGGTGGAAGAATCGAAGGCTGAAAAGAATCGAATAAAGA
AGGAGCAACAAAATCTTGATGGATACCTAGCAAATCCATGAAACCCAATGACCCCCACTTATCTC
CACCACTGCCTTCACATGATGTTCCTGCCATGTCAAAGATGCTCCCACCACCACCACCACCAAAG
ACTGACGGAATCTCATCGGAAAATCTCATATTCGCCATGGGATTATTCTCGTTCTTCTTCTCCAT
AAAACTATTCACATATTCTGTTTCCTTTTTTATTGAACAAAACTAGGGA
Found at i:2403135 original size:22 final size:23
Alignment explanation
Indices: 2403089--2403135 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2403079 GTTATGATAA
**
2403089 AAAAATCTTATATTGTAAATCCT
1 AAAAATCTTATATTGTAAAAACT
2403112 AAAAA-CTTATATTGTAAAAACT
1 AAAAATCTTATATTGTAAAAACT
2403134 AA
1 AA
2403136 TTTATCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (23 bp):
AAAAATCTTATATTGTAAAAACT
Found at i:2408652 original size:24 final size:24
Alignment explanation
Indices: 2408616--2408661 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2408606 GACACACAAT
*
2408616 AGCTCTTCTGAGCATTCTGTTATA
1 AGCTCTTCTGAGCATTCCGTTATA
*
2408640 AGCTC-TCTCGAGCTTTCCGTTA
1 AGCTCTTCT-GAGCATTCCGTTA
2408662 CATGGTTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.39
Consensus pattern (24 bp):
AGCTCTTCTGAGCATTCCGTTATA
Found at i:2412702 original size:15 final size:16
Alignment explanation
Indices: 2412682--2412716 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2412672 TGATCCCCAT
2412682 TTTTCAAAAAATA-AC
1 TTTTCAAAAAATACAC
*
2412697 TTTTCAAAAATTACAC
1 TTTTCAAAAAATACAC
2412713 TTTT
1 TTTT
2412717 ATCCCAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTTCAAAAAATACAC
Found at i:2414644 original size:19 final size:19
Alignment explanation
Indices: 2414620--2414657 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2414610 GGACAATATG
2414620 ATTGAATATGATTGGTTTT
1 ATTGAATATGATTGGTTTT
2414639 ATTGAATATGATTGGTTTT
1 ATTGAATATGATTGGTTTT
2414658 GGATATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (19 bp):
ATTGAATATGATTGGTTTT
Found at i:2416250 original size:14 final size:14
Alignment explanation
Indices: 2416231--2416270 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2416221 TTGATTGCCA
2416231 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
2416245 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
2416259 GGAAAATGTTTT
1 GTAAAATGTTTT
2416271 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:2416279 original size:20 final size:20
Alignment explanation
Indices: 2416254--2416293 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2416244 CGTAAAATGA
*
2416254 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
2416274 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
2416294 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:2416283 original size:34 final size:35
Alignment explanation
Indices: 2416239--2416305 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2416229 CAGTAAAATG
* *
2416239 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
2416273 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
2416306 CTGGTGTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:2419638 original size:24 final size:24
Alignment explanation
Indices: 2419611--2419668 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
2419601 GATGCTGCAA
*
2419611 TCGATAGGGTGAAGAGATGAGCTG
1 TCGAAAGGGTGAAGAGATGAGCTG
2419635 TCGAAAGGGTGAAGAGATGAGCTG
1 TCGAAAGGGTGAAGAGATGAGCTG
*
2419659 TGGAAAGGGT
1 TCGAAAGGGT
2419669 TTCAAAGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.31, C:0.07, G:0.43, T:0.19
Consensus pattern (24 bp):
TCGAAAGGGTGAAGAGATGAGCTG
Found at i:2423532 original size:21 final size:21
Alignment explanation
Indices: 2423481--2423526 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2423471 AAGAGTTAGA
*
2423481 ATTTAGGGTTTAAGGTTCAAG
1 ATTTAGGATTTAAGGTTCAAG
*
2423502 ATTTAGGATTTAAGGTTCATG
1 ATTTAGGATTTAAGGTTCAAG
2423523 ATTT
1 ATTT
2423527 TAGATTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.04, G:0.24, T:0.43
Consensus pattern (21 bp):
ATTTAGGATTTAAGGTTCAAG
Found at i:2429882 original size:7 final size:7
Alignment explanation
Indices: 2429872--2429901 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2429862 AAAATATAAA
2429872 ATTTTAT
1 ATTTTAT
2429879 ATTTTAT
1 ATTTTAT
2429886 ATTTTAT
1 ATTTTAT
*
2429893 ATTTAAT
1 ATTTTAT
2429900 AT
1 AT
2429902 AATAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
ATTTTAT
Found at i:2443491 original size:21 final size:21
Alignment explanation
Indices: 2443445--2443493 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
2443435 CTAATTTAAT
*
2443445 AAAAAAATCATATATAATTTTCA
1 AAAAAAATCATATATAA--TTGA
*
2443468 AAAAAATTCATATATAA-TGA
1 AAAAAAATCATATATAATTGA
2443488 AAAAAA
1 AAAAAA
2443494 CACCTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
23 16 0.67
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAAAATCATATATAATTGA
Found at i:2445846 original size:21 final size:21
Alignment explanation
Indices: 2445800--2445848 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
2445790 CTAATTTAAT
*
2445800 AAAAAAATCATATATAATTTTCA
1 AAAAAAATCATATATAA--TTGA
*
2445823 AAAAAATTCATATATAA-TGA
1 AAAAAAATCATATATAATTGA
2445843 AAAAAA
1 AAAAAA
2445849 CACCTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
23 16 0.67
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAAAATCATATATAATTGA
Found at i:2446922 original size:21 final size:21
Alignment explanation
Indices: 2446876--2446924 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
2446866 CTAATTTAAT
*
2446876 AAAAAAATCATATATAATTTTCA
1 AAAAAAATCATATATAA--TTGA
*
2446899 AAAAAATTCATATATAA-TGA
1 AAAAAAATCATATATAATTGA
2446919 AAAAAA
1 AAAAAA
2446925 CACCTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
23 16 0.67
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAAAATCATATATAATTGA
Found at i:2449655 original size:30 final size:31
Alignment explanation
Indices: 2449614--2449684 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
2449604 ATGATAAATG
* *
2449614 TAATAATATATTTTTAT-TTTTATTTGGTAT
1 TAATTATATATTTTTATATTTTACTTGGTAT
2449644 TAATTATATA-TTTTATATTTTACTTGGTAT
1 TAATTATATATTTTTATATTTTACTTGGTAT
2449674 TAATTAT-TATT
1 TAATTATATATT
2449685 GAAAAATCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (31 bp):
TAATTATATATTTTTATATTTTACTTGGTAT
Found at i:2450257 original size:14 final size:15
Alignment explanation
Indices: 2450240--2450272 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2450230 TAATTATATG
*
2450240 CATATT-TCTCCAAT
1 CATATTATCTCAAAT
2450254 CATATTATCTCAAAT
1 CATATTATCTCAAAT
2450269 CATA
1 CATA
2450273 CATTATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (15 bp):
CATATTATCTCAAAT
Found at i:2450334 original size:129 final size:129
Alignment explanation
Indices: 2450104--2450360 Score: 478
Period size: 129 Copynumber: 2.0 Consensus size: 129
2450094 CCATATAAAC
*
2450104 TTATATGCATATTTCTCCAATCATATTATCTCAAATAATACATTATCATATTCATAAATTATTCA
1 TTATATGCATATTTCTCCAATCATATTATCTCAAATAATACATTATCATATTCATAAATTATCCA
2450169 TTACTCAACCACATTAAACACAACAAACATATTAAGCCACACATACATATACATATCAAAATAA
66 TTACTCAACCACATTAAACACAACAAACATATTAAGCCACACATACATATACATATCAAAATAA
* *
2450233 TTATATGCATATTTCTCCAATCATATTATCTCAAATCATACATTATCATTTTCATAAATTATCCA
1 TTATATGCATATTTCTCCAATCATATTATCTCAAATAATACATTATCATATTCATAAATTATCCA
*
2450298 TTACTCAACCACATTAAACACAACAAACGTATTAAGCCACACATACATATACATATCAAAATA
66 TTACTCAACCACATTAAACACAACAAACATATTAAGCCACACATACATATACATATCAAAATA
2450361 TGTCTAACTC
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 124 1.00
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.33
Consensus pattern (129 bp):
TTATATGCATATTTCTCCAATCATATTATCTCAAATAATACATTATCATATTCATAAATTATCCA
TTACTCAACCACATTAAACACAACAAACATATTAAGCCACACATACATATACATATCAAAATAA
Found at i:2450981 original size:25 final size:25
Alignment explanation
Indices: 2450953--2451047 Score: 113
Period size: 24 Copynumber: 3.9 Consensus size: 25
2450943 AGCTCTTTCA
*
2450953 AGCCATATAAGGGGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGTG
* *
2450978 AGCCATGTAACGGAAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGTG
* *
2451003 AGCCA-ATATCGCGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGTG
* *
2451027 AGCCA-ATATCGAGAAGCTCAT
1 AGCCATATAACGGGAAGCTCAT
2451048 AAAAGAGCCT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
24 35 0.56
25 27 0.44
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATGTG
Found at i:2451118 original size:25 final size:25
Alignment explanation
Indices: 2451084--2451148 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
2451074 CGAAAAGCTA
2451084 TTAACAGGAAGCTCACAAGAACCAT
1 TTAACAGGAAGCTCACAAGAACCAT
*
2451109 TTAACGGGAAGCTCACAAGAACCAT
1 TTAACAGGAAGCTCACAAGAACCAT
2451134 TTAACAGGAAGCTCA
1 TTAACAGGAAGCTCA
2451149 TGAGAGCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (25 bp):
TTAACAGGAAGCTCACAAGAACCAT
Found at i:2452919 original size:20 final size:19
Alignment explanation
Indices: 2452868--2452920 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
2452858 CTTGTTTAAA
* *
2452868 AAACAATTTTAACATGATTG
1 AAAC-ATTTTAACTTAATTG
2452888 AAA-ATGTTTAACTTAATTG
1 AAACAT-TTTAACTTAATTG
2452907 AAACTATTTTAACT
1 AAAC-ATTTTAACT
2452921 AGATTTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 2 0.07
19 14 0.50
20 10 0.36
21 2 0.07
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (19 bp):
AAACATTTTAACTTAATTG
Found at i:2453793 original size:17 final size:19
Alignment explanation
Indices: 2453771--2453807 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
2453761 TATAAAGGGA
2453771 TAAAAATA-ATTTT-TTTT
1 TAAAAATATATTTTATTTT
2453788 TAAAAATATATTTTATTTT
1 TAAAAATATATTTTATTTT
2453807 T
1 T
2453808 TAGAGTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 5 0.28
19 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAAAAATATATTTTATTTT
Found at i:2454046 original size:26 final size:27
Alignment explanation
Indices: 2454002--2454056 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
2453992 TTTTAAAATG
** * *
2454002 TTTTTAAAATACTTGTTTTATTTTTTA
1 TTTTTAAAATAAATGTTTTAGTGTTTA
2454029 TTTTTAAAATAAAT-TTTTAGTGTTTA
1 TTTTTAAAATAAATGTTTTAGTGTTTA
2454055 TT
1 TT
2454057 AGGGTCGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (27 bp):
TTTTTAAAATAAATGTTTTAGTGTTTA
Found at i:2457129 original size:18 final size:18
Alignment explanation
Indices: 2457106--2457146 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2457096 AACAATTCTA
*
2457106 AAAAATTAAAAGA-ATCTT
1 AAAAATTAAAA-ATATATT
2457124 AAAAA-TAAAAATATATT
1 AAAAATTAAAAATATATT
2457141 AAAAAT
1 AAAAAT
2457147 GCATATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAATTAAAAATATATT
Found at i:2464219 original size:56 final size:56
Alignment explanation
Indices: 2464153--2464267 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
2464143 CTTTTCACTA
*
2464153 AAATTCAAATATCTAAAAGTATATAATTCTTTTGCTTACTCCACTTCTTTCATATG
1 AAATTCAAATATCTAAAAATATATAATTCTTTTGCTTACTCCACTTCTTTCATATG
2464209 AAATTCAAATATCTAAAAATATATAATTCTTTTGCTTACTCCACTTCTTTCATATG
1 AAATTCAAATATCTAAAAATATATAATTCTTTTGCTTACTCCACTTCTTTCATATG
2464265 AAA
1 AAA
2464268 GTAGACTCTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.42
Consensus pattern (56 bp):
AAATTCAAATATCTAAAAATATATAATTCTTTTGCTTACTCCACTTCTTTCATATG
Found at i:2465093 original size:46 final size:45
Alignment explanation
Indices: 2464987--2465110 Score: 189
Period size: 46 Copynumber: 2.8 Consensus size: 45
2464977 CATATGACCT
* *
2464987 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* *
2465030 CTTATCACTTTACCACTTGATAAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
2465076 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
2465111 CACTTATCAC
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
43 8 0.11
44 3 0.04
45 20 0.28
46 41 0.57
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (45 bp):
CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:2476933 original size:18 final size:19
Alignment explanation
Indices: 2476907--2476946 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2476897 ATTACTTCTC
*
2476907 AAAAGTATTTTT-AAGCTA
1 AAAAATATTTTTGAAGCTA
*
2476925 AAAAATATTTTTGAGGCTA
1 AAAAATATTTTTGAAGCTA
2476944 AAA
1 AAA
2476947 TTTTCTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.35
Consensus pattern (19 bp):
AAAAATATTTTTGAAGCTA
Found at i:2478806 original size:39 final size:40
Alignment explanation
Indices: 2478760--2478862 Score: 174
Period size: 38 Copynumber: 2.6 Consensus size: 40
2478750 AAACTAAAAT
*
2478760 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATT-A
1 AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATTAA
2478799 AAAAATT-AAAAAAGTATTTTAAAAAAATTTTAAAATTAA
1 AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATTAA
2478838 AAAAATTAAAAAAAAGTATTTTAAA
1 AAAAATT-AAAAAAAGTATTTTAAA
2478863 GTTAAAAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
38 29 0.48
39 15 0.25
41 16 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (40 bp):
AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATTAA
Found at i:2478859 original size:30 final size:28
Alignment explanation
Indices: 2478834--2478900 Score: 50
Period size: 28 Copynumber: 2.4 Consensus size: 28
2478824 AATTTTAAAA
*
2478834 TTAAAAAAATTAAAAAAAAGTATTTTAAAG
1 TTAAAAAAATTAAAAAAAA--ATTTTAAAA
**
2478864 TT-AAAAAA-TAAAAAATAAA-AATAAAA
1 TTAAAAAAATTAAAAAA-AAATTTTAAAA
*
2478890 ATAAAAAAATT
1 TTAAAAAAATT
2478901 TATTAGGCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
26 5 0.17
27 7 0.23
28 8 0.27
29 8 0.27
30 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (28 bp):
TTAAAAAAATTAAAAAAAAATTTTAAAA
Found at i:2478877 original size:7 final size:7
Alignment explanation
Indices: 2478865--2478897 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2478855 ATTTTAAAGT
2478865 TAAAAAA
1 TAAAAAA
2478872 TAAAAAA
1 TAAAAAA
2478879 T-AAAAA
1 TAAAAAA
2478885 T-AAAAA
1 TAAAAAA
2478891 TAAAAAA
1 TAAAAAA
2478898 ATTTATTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:2478883 original size:5 final size:6
Alignment explanation
Indices: 2478867--2478896 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
2478857 TTTAAAGTTA
2478867 AAAAAT AAAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT -AAAAAT AAAAAT AAAAAT AAAAA
2478897 AATTTATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:2488276 original size:21 final size:21
Alignment explanation
Indices: 2488250--2488305 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
2488240 AATAGTGGTG
*
2488250 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
2488271 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
2488292 GCGGTAAGATTAGA
1 GCGGTGAGATTAGA
2488306 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:2496892 original size:12 final size:12
Alignment explanation
Indices: 2496877--2496906 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2496867 AAAATTTAAT
*
2496877 ATTATTTTTAGG
1 ATTATTGTTAGG
2496889 ATTATTGTTAGG
1 ATTATTGTTAGG
2496901 ATTATT
1 ATTATT
2496907 ATGATATTGT
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:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (12 bp):
ATTATTGTTAGG
Found at i:2501910 original size:22 final size:23
Alignment explanation
Indices: 2501863--2501913 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
2501853 ATGAATGTTG
2501863 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTATCACATA-TATTAT
2501887 TTTAAATTTATCACATA-ATTAT
1 TTTAAATTTATCACATATATTAT
2501909 TTTAA
1 TTTAA
2501914 GTTTTCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 10 0.37
24 17 0.63
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAATTTATCACATATATTAT
Found at i:2508572 original size:22 final size:23
Alignment explanation
Indices: 2508547--2508593 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2508537 AATTCTCAAT
*
2508547 AATAATATTTGGTA-TTTATAAA
1 AATAATATTTAGTATTTTATAAA
*
2508569 AATAATATTTATTATTTTATAAA
1 AATAATATTTAGTATTTTATAAA
2508592 AA
1 AA
2508594 ATAGATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
AATAATATTTAGTATTTTATAAA
Found at i:2508601 original size:23 final size:23
Alignment explanation
Indices: 2508561--2508606 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2508551 ATATTTGGTA
*
2508561 TTTATAAAAATAATATTTATTAT
1 TTTATAAAAATAAGATTTATTAT
*
2508584 TTTATAAAAA-ATAGATTTTTTAT
1 TTTATAAAAATA-AGATTTATTAT
2508607 AATTTCTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTATAAAAATAAGATTTATTAT
Found at i:2508675 original size:104 final size:105
Alignment explanation
Indices: 2508545--2508758 Score: 403
Period size: 104 Copynumber: 2.0 Consensus size: 105
2508535 AAAATTCTCA
*
2508545 ATAATAATATTTGGTATTTATAAAAATAATATTTATTATTTTATAAAAAATAGATTTTTTATAAT
1 ATAATAATATAT-GTATTTATAAAAATAATATTTATTATTTTATAAAAAATAGATTTTTTATAAT
2508610 TTCTGAATTAATTTGAAATGCGTAAGCCTTTAGATACGTAG
65 TTCTGAATTAATTTGAAATGCGTAAGCCTTTAGATACGTAG
2508651 ATAATAATATAT-TATTTATAAAAATAATATTTATTATTTTATAAAAAATAGATTTTTTATAATT
1 ATAATAATATATGTATTTATAAAAATAATATTTATTATTTTATAAAAAATAGATTTTTTATAATT
2508715 TCTGAATTAATTTGAAATGCGTAAGCCTTTAGATACGTAG
66 TCTGAATTAATTTGAAATGCGTAAGCCTTTAGATACGTAG
2508755 ATAA
1 ATAA
2508759 GTCAAAGTTA
Statistics
Matches: 107, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
104 96 0.90
106 11 0.10
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (105 bp):
ATAATAATATATGTATTTATAAAAATAATATTTATTATTTTATAAAAAATAGATTTTTTATAATT
TCTGAATTAATTTGAAATGCGTAAGCCTTTAGATACGTAG
Found at i:2508688 original size:22 final size:24
Alignment explanation
Indices: 2508651--2508697 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2508641 AGATACGTAG
2508651 ATAATAATATATTA-TTTATAAAA
1 ATAATAATATATTATTTTATAAAA
*
2508674 ATAAT-ATTTATTATTTTATAAAA
1 ATAATAATATATTATTTTATAAAA
2508697 A
1 A
2508698 ATAGATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATAATAATATATTATTTTATAAAA
Found at i:2508705 original size:23 final size:23
Alignment explanation
Indices: 2508660--2508710 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2508650 GATAATAATA
*
2508660 TATTA-TTTATAAAAATAATATT
1 TATTATTTTATAAAAATAAGATT
2508682 TATTATTTTATAAAAA-ATAGATT
1 TATTATTTTATAAAAATA-AGATT
*
2508705 TTTTAT
1 TATTAT
2508711 AATTTCTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTATTTTATAAAAATAAGATT
Found at i:2510121 original size:16 final size:16
Alignment explanation
Indices: 2510092--2510135 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2510082 AAAAATATTA
2510092 TAAAA-ATATAAAAAC
1 TAAAATATATAAAAAC
* * *
2510107 TAAATTATATTAAAAT
1 TAAAATATATAAAAAC
2510123 TAAAATATATAAA
1 TAAAATATATAAA
2510136 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAATATATAAAAAC
Found at i:2510150 original size:14 final size:14
Alignment explanation
Indices: 2510094--2510156 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
2510084 AAATATTATA
*
2510094 AAAATATAAAAACT
1 AAAATATAAAAATT
*
2510108 AAATTATATTAAAATT
1 AAA--ATATAAAAATT
*
2510124 AAAATATATAAATT
1 AAAATATAAAAATT
* *
2510138 AAATTTTAAAAATTT
1 AAAATATAAAAA-TT
2510153 AAAA
1 AAAA
2510157 ACTATTATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 21 0.55
15 5 0.13
16 12 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:2511204 original size:3 final size:3
Alignment explanation
Indices: 2511198--2511224 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2511188 CATTTTTTTG
2511198 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
2511225 AAAAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2525669 original size:3 final size:3
Alignment explanation
Indices: 2525661--2525690 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2525651 CAAACACAGC
2525661 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2525691 CAAAGGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2526368 original size:18 final size:18
Alignment explanation
Indices: 2526345--2526379 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2526335 ATAATTTTTA
2526345 AAAGTAAAAACGAAAAAT
1 AAAGTAAAAACGAAAAAT
*
2526363 AAAGTAAAACCGAAAAA
1 AAAGTAAAAACGAAAAA
2526380 AGTGGGAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.09, G:0.11, T:0.09
Consensus pattern (18 bp):
AAAGTAAAAACGAAAAAT
Found at i:2526787 original size:22 final size:22
Alignment explanation
Indices: 2526762--2526815 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
2526752 TTAGGTTTTG
2526762 GGTTTTTAGGGTTAGGGTTTAA
1 GGTTTTTAGGGTTAGGGTTTAA
*
2526784 GGTTTTCAGGGTTAGGGTTTAA
1 GGTTTTTAGGGTTAGGGTTTAA
2526806 GGTTTTTAGG
1 GGTTTTTAGG
2526816 ATTTTAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.02, G:0.37, T:0.44
Consensus pattern (22 bp):
GGTTTTTAGGGTTAGGGTTTAA
Found at i:2527155 original size:123 final size:124
Alignment explanation
Indices: 2526881--2527185 Score: 470
Period size: 124 Copynumber: 2.5 Consensus size: 124
2526871 AGGGTTTAGA
*
2526881 ATGCTTTATCAGAAGAATTTTTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCT
1 ATGCTTTATCAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCT
2526946 GAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAACACTTCAAGCAGG
66 GAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAACACTTCAAGCAGG
* * * * *
2527005 ATGCTTTATCAGAAGAATTTCTAAAATCGTGCCCACGTGAACGCGTTTTTGCTACAGTTGGTCCT
1 ATGCTTTATCAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCT
** *
2527070 GAAAAAA-AATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAAAACGCTTCAAGCA-G
66 GAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTAT-AAAAACACTTCAAGCAGG
* * * *
2527128 ATGCTTTATCAAAAGAATTTATGAAATCGCACCCTCGTGGACGCACTTTTGCTACAGT
1 ATGCTTTATCAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
2527186 AGCATGTTTG
Statistics
Matches: 163, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
123 81 0.50
124 82 0.50
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (124 bp):
ATGCTTTATCAGAAGAATTTATGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCT
GAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAACACTTCAAGCAGG
Found at i:2529914 original size:50 final size:51
Alignment explanation
Indices: 2529849--2529947 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 51
2529839 TTTTAAAAAT
* *
2529849 AATTAAAATAGGGATTTAAGATAAATTTA-AGAGGAAATTGTGAGCAAATAA
1 AATTAAAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATAA
* * *
2529900 AATT-AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAAAT
1 AATTAAAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAAT
2529948 TGAGAGCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 37 0.88
51 5 0.12
ACGTcount: A:0.48, C:0.02, G:0.22, T:0.27
Consensus pattern (51 bp):
AATTAAAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATAA
Found at i:2529949 original size:11 final size:11
Alignment explanation
Indices: 2529933--2529963 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2529923 ATTTGGAAGG
2529933 AAATTGAGAGC
1 AAATTGAGAGC
2529944 AAATTGAGAGC
1 AAATTGAGAGC
2529955 AAATTGAGA
1 AAATTGAGA
2529964 AAATAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.06, G:0.26, T:0.19
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:2532260 original size:18 final size:18
Alignment explanation
Indices: 2532237--2532280 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
2532227 ATGTGTGTTA
*
2532237 CTATTATTGT-TGCTGCTG
1 CTATTATT-TCTGCTGCTC
2532255 CTATTATTTCTGCTGCTC
1 CTATTATTTCTGCTGCTC
2532273 CTATTATT
1 CTATTATT
2532281 ACAATTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.52
Consensus pattern (18 bp):
CTATTATTTCTGCTGCTC
Found at i:2539178 original size:11 final size:11
Alignment explanation
Indices: 2539157--2539181 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2539147 TAAACCGACC
2539157 TTTAACCGAAT
1 TTTAACCGAAT
2539168 TTTAACCGAAT
1 TTTAACCGAAT
2539179 TTT
1 TTT
2539182 GAACACCCCT
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTAACCGAAT
Found at i:2541737 original size:3 final size:3
Alignment explanation
Indices: 2541729--2541765 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2541719 AGATGAGTGT
2541729 ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2541766 TTATTATCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2541749 original size:17 final size:17
Alignment explanation
Indices: 2541729--2541761 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2541719 AGATGAGTGT
2541729 ATAATAATAATAATAAA
1 ATAATAATAATAATAAA
2541746 ATAATAATAATAATAA
1 ATAATAATAATAATAA
2541762 TAATTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATAATAATAATAAA
Found at i:2562258 original size:2 final size:2
Alignment explanation
Indices: 2562251--2562284 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2562241 TAAAGGAGCT
2562251 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2562285 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2565100 original size:14 final size:15
Alignment explanation
Indices: 2565069--2565099 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2565059 GCTAAACATT
2565069 AATTCATAGTAAAAA
1 AATTCATAGTAAAAA
2565084 AATTCATAGTAAAAA
1 AATTCATAGTAAAAA
2565099 A
1 A
2565100 TGCCAACACT
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:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AATTCATAGTAAAAA
Found at i:2572784 original size:12 final size:11
Alignment explanation
Indices: 2572766--2572816 Score: 59
Period size: 12 Copynumber: 4.4 Consensus size: 11
2572756 GTATAAAGAG
2572766 AAATAAAAATA
1 AAATAAAAATA
2572777 AGAATAAAAATA
1 A-AATAAAAATA
2572789 AAATAATAAATA
1 AAATAA-AAATA
2572801 ACAA-AAGAAATA
1 A-AATAA-AAATA
2572813 AAAT
1 AAAT
2572817 TATCAACTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 8 0.23
12 25 0.71
13 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:2572800 original size:18 final size:18
Alignment explanation
Indices: 2572766--2572815 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
2572756 GTATAAAGAG
*
2572766 AAATAAAAATAAGAATAA
1 AAATAAAAATAAAAATAA
2572784 AAAT-AAAATAATAAATAA
1 AAATAAAAATAA-AAATAA
*
2572802 CAAA-AGAAATAAAA
1 -AAATAAAAATAAAA
2572816 TTATCAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 7 0.26
18 11 0.41
19 9 0.33
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (18 bp):
AAATAAAAATAAAAATAA
Found at i:2572811 original size:24 final size:23
Alignment explanation
Indices: 2572766--2572816 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
2572756 GTATAAAGAG
*
2572766 AAATAAAAATAAGAATAAAAATA
1 AAATAAAAATAACAATAAAAATA
2572789 AAATAATAAATAACAA-AAGAAATA
1 AAATAA-AAATAACAATAA-AAATA
2572813 AAAT
1 AAAT
2572817 TATCAACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (23 bp):
AAATAAAAATAACAATAAAAATA
Found at i:2578262 original size:22 final size:21
Alignment explanation
Indices: 2578209--2578262 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
2578199 ATTAACTCAA
*
2578209 TCATATAACATTTCAATTCAT
1 TCATAAAACATTTCAATTCAT
** *
2578230 TCGATTCAACATTTCATTATCAT
1 TC-ATAAAACATTTCAAT-TCAT
2578253 TCATAAAACA
1 TCATAAAACA
2578263 AACAATCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.08
22 18 0.69
23 6 0.23
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (21 bp):
TCATAAAACATTTCAATTCAT
Found at i:2578631 original size:17 final size:17
Alignment explanation
Indices: 2578591--2578638 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2578581 ATTGCATATT
*
2578591 CCATTTCACATATTACTT
1 CCATTTCACATATTA-TG
2578609 CCATTTCACATCATT-TG
1 CCATTTCACAT-ATTATG
*
2578626 CCATTTCAAATAT
1 CCATTTCACATAT
2578639 CAAATATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 2 0.07
17 11 0.41
18 11 0.41
19 3 0.11
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.42
Consensus pattern (17 bp):
CCATTTCACATATTATG
Found at i:2579301 original size:22 final size:23
Alignment explanation
Indices: 2579253--2579301 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2579243 TACAAAATTG
*
2579253 TAAATAATTAAAATTTTAATTAA
1 TAAATAATTAAAATTATAATTAA
*
2579276 -AAATAATTACAATTATAA-TAA
1 TAAATAATTAAAATTATAATTAA
2579297 TAAAT
1 TAAAT
2579302 GCATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATAATTAAAATTATAATTAA
Found at i:2581799 original size:25 final size:25
Alignment explanation
Indices: 2581765--2581814 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2581755 ATTTTCCCTA
2581765 TCAGAGGCTACACAAACATATCTCC
1 TCAGAGGCTACACAAACATATCTCC
2581790 TCAGAGGCTACACAAACATATCTCC
1 TCAGAGGCTACACAAACATATCTCC
2581815 GCATCCTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (25 bp):
TCAGAGGCTACACAAACATATCTCC
Found at i:2583038 original size:28 final size:28
Alignment explanation
Indices: 2583006--2583063 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2582996 CGGATATTCT
2583006 CTTTGGTTGTTAAACTATCAAAAAGAGA
1 CTTTGGTTGTTAAACTATCAAAAAGAGA
2583034 CTTTGGTTGTTAAACTATCAAAAAGAGA
1 CTTTGGTTGTTAAACTATCAAAAAGAGA
2583062 CT
1 CT
2583064 AACTCTGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (28 bp):
CTTTGGTTGTTAAACTATCAAAAAGAGA
Found at i:2584552 original size:23 final size:24
Alignment explanation
Indices: 2584500--2584551 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
2584490 TCGGGAAATA
*
2584500 TATT-TATTTTAATATATTTGATG
1 TATTATATTTTAATAAATTTGATG
2584523 TATTATATTTT-ATAAATTT-ATG
1 TATTATATTTTAATAAATTTGATG
2584545 T-TTATAT
1 TATTATAT
2584552 AAAAATAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 6 0.22
22 4 0.15
23 11 0.41
24 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (24 bp):
TATTATATTTTAATAAATTTGATG
Found at i:2587224 original size:18 final size:19
Alignment explanation
Indices: 2587190--2587242 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
2587180 AATTTTCAAA
*
2587190 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTAT
*
2587209 AAAAATCCAAAT-ATTTAT
1 AAAAATCAAAATAATTTAT
*
2587227 AAAATTCTAAAATAAT
1 AAAAATC-AAAATAAT
2587243 AATTTTTGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 11 0.39
19 15 0.54
20 2 0.07
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:2587401 original size:22 final size:22
Alignment explanation
Indices: 2587376--2587421 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2587366 GATAACAAAA
*
2587376 TTTTAATTTAA-TATATATAATT
1 TTTTAATTTAACT-TAAATAATT
2587398 TTTTAATTTAACTTAAATAATT
1 TTTTAATTTAACTTAAATAATT
2587420 TT
1 TT
2587422 ATTCTATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAATTTAACTTAAATAATT
Found at i:2609172 original size:20 final size:21
Alignment explanation
Indices: 2609133--2609201 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 21
2609123 ATTATACCCG
* *
2609133 TATATTGATTTTAAAATAATAT
1 TATATT-ATATTATAATAATAT
2609155 TATATT-TA-TACTAATAATA-
1 TATATTATATTA-TAATAATAT
2609174 TATATTATATTATAATCAATTAT
1 TATATTATATTATAAT-AA-TAT
2609197 TATAT
1 TATAT
2609202 ATGGGTCTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
19 8 0.21
20 14 0.36
21 4 0.10
22 8 0.21
23 5 0.13
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (21 bp):
TATATTATATTATAATAATAT
Found at i:2609692 original size:36 final size:35
Alignment explanation
Indices: 2609647--2609723 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 35
2609637 TTGTGTGACT
* *
2609647 CAAATTCTAAAAGATTGCTTGCAAGT-TAAGTTAAAA
1 CAAAATCTAAAAGATTACTTGCAAGTCT-AGTT-AAA
*
2609683 CAAAATCTAAGAGATTACTTGCAAGTCTAGTTAAA
1 CAAAATCTAAAAGATTACTTGCAAGTCTAGTTAAA
2609718 CAAAAT
1 CAAAAT
2609724 ATATTTTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 9 0.24
36 27 0.73
37 1 0.03
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (35 bp):
CAAAATCTAAAAGATTACTTGCAAGTCTAGTTAAA
Found at i:2610573 original size:29 final size:29
Alignment explanation
Indices: 2610533--2610591 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2610523 GAATATAAAC
*
2610533 TATATTTTTTATTTTTAAAATACACCACA
1 TATATTTTTTATTTTTAAAAAACACCACA
*
2610562 TATATTTTTTATTTTTAAAAAACACTACA
1 TATATTTTTTATTTTTAAAAAACACCACA
2610591 T
1 T
2610592 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAAAACACCACA
Found at i:2612564 original size:19 final size:19
Alignment explanation
Indices: 2612523--2612565 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2612513 TATTATTTTT
*
2612523 GTTGTTTATTTGGAATCAT
1 GTTGTTTATTTGGAATCAC
* *
2612542 GTTGTTTATTTGGATTGAC
1 GTTGTTTATTTGGAATCAC
2612561 GTTGT
1 GTTGT
2612566 GTTACTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (19 bp):
GTTGTTTATTTGGAATCAC
Found at i:2613887 original size:15 final size:14
Alignment explanation
Indices: 2613867--2613894 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2613857 ATCTCCCCCA
2613867 TTTTTTTAGTTTTC
1 TTTTTTTAGTTTTC
2613881 TTTTTTTAGTTTTC
1 TTTTTTTAGTTTTC
2613895 AACACTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTTAGTTTTC
Found at i:2617553 original size:59 final size:59
Alignment explanation
Indices: 2617482--2617604 Score: 151
Period size: 59 Copynumber: 2.1 Consensus size: 59
2617472 GGTACCTTGA
* * * * * *
2617482 CTTTTTATGGTCCAATTTAGTACTTGAATTTGACA-TATTTTCCTAATTTGGTATTTAAT
1 CTTTTTATGGTCCAATTTAGTACATAAACTCGACACT-TTTTCCTAATTTGATATCTAAT
*
2617541 CTTTTT-TGGGTCCCATTTAGTACATAAACTCGACACTTTTTCCTAATTTGATATCTAAT
1 CTTTTTAT-GGTCCAATTTAGTACATAAACTCGACACTTTTTCCTAATTTGATATCTAAT
2617600 CTTTT
1 CTTTT
2617605 ATTTTTGCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 1 0.02
59 53 0.96
60 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (59 bp):
CTTTTTATGGTCCAATTTAGTACATAAACTCGACACTTTTTCCTAATTTGATATCTAAT
Found at i:2618302 original size:35 final size:35
Alignment explanation
Indices: 2618256--2618325 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
2618246 GAATTATATG
* *
2618256 GGGTTTAAAATATAGTTAGGATTCAAATCCAAACT
1 GGGTTTAAAATATAATTAAGATTCAAATCCAAACT
2618291 GGGTTTAAAATATAATTAAGATTCAAATCCAAACT
1 GGGTTTAAAATATAATTAAGATTCAAATCCAAACT
2618326 ATTTTTATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (35 bp):
GGGTTTAAAATATAATTAAGATTCAAATCCAAACT
Found at i:2632748 original size:50 final size:50
Alignment explanation
Indices: 2632672--2632814 Score: 187
Period size: 50 Copynumber: 2.8 Consensus size: 50
2632662 NNNNNNNNNN
* * *
2632672 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACATG
* * * *
2632722 AGAGGTCCCCTATAAGACCATATCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACATG
** *
2632772 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
2632815 TGTTATGATC
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 45 0.58
51 33 0.42
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACATG
Found at i:2634205 original size:4 final size:4
Alignment explanation
Indices: 2634191--2634224 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
2634181 CAAGCAACAT
*
2634191 TTTC CTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
2634225 ATTCGGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:2635127 original size:12 final size:12
Alignment explanation
Indices: 2635108--2635141 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2635098 GCAACCCCAG
*
2635108 TCATAATTATAA
1 TCATAATTAAAA
*
2635120 TTATAATTAAAA
1 TCATAATTAAAA
2635132 TCATAATTAA
1 TCATAATTAA
2635142 TATATTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (12 bp):
TCATAATTAAAA
Found at i:2637723 original size:20 final size:21
Alignment explanation
Indices: 2637684--2637723 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2637674 TTTTTAAATA
**
2637684 ATTTTTTAGTAATTTGTATAT
1 ATTTTTTACAAATTTGTATAT
2637705 ATTTTTTACAAATTT-TATA
1 ATTTTTTACAAATTTGTATA
2637724 ATTGTGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTTTTTACAAATTTGTATAT
Found at i:2638058 original size:72 final size:73
Alignment explanation
Indices: 2637965--2638111 Score: 287
Period size: 72 Copynumber: 2.0 Consensus size: 73
2637955 AGAGAGAAAA
2637965 ATAAAGTAAAAAATAAAAATATTAAAAATATTTTTTAAAGTTTATATGATGTGACAATCTATTAT
1 ATAAAGTAAAAAATAAAAATATTAAAAATATTTTTTAAAGTTTATATGATGTGACAATCTATTAT
2638030 TGGATGAC
66 TGGATGAC
2638038 ATAAAGTAAAAAA-AAAAATATTAAAAATATTTTTTAAAGTTTATATGATGTGACAATCTATTAT
1 ATAAAGTAAAAAATAAAAATATTAAAAATATTTTTTAAAGTTTATATGATGTGACAATCTATTAT
2638102 TGGATGAC
66 TGGATGAC
2638110 AT
1 AT
2638112 TTTTTTAATG
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 61 0.82
73 13 0.18
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (73 bp):
ATAAAGTAAAAAATAAAAATATTAAAAATATTTTTTAAAGTTTATATGATGTGACAATCTATTAT
TGGATGAC
Found at i:2642204 original size:9 final size:9
Alignment explanation
Indices: 2642190--2642238 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
2642180 TTTGGTTAAA
2642190 AATTAACCG
1 AATTAACCG
2642199 AATTAACCG
1 AATTAACCG
* *
2642208 AATTACCCA
1 AATTAACCG
*
2642217 AATTACCCG
1 AATTAACCG
*
2642226 AATTAACCA
1 AATTAACCG
2642235 AATT
1 AATT
2642239 GAATCACTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:2642220 original size:18 final size:18
Alignment explanation
Indices: 2642190--2642238 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
2642180 TTTGGTTAAA
*
2642190 AATTAACCGAATTAACCG
1 AATTAACCAAATTAACCG
* *
2642208 AATTACCCAAATTACCCG
1 AATTAACCAAATTAACCG
2642226 AATTAACCAAATT
1 AATTAACCAAATT
2642239 GAATCACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (18 bp):
AATTAACCAAATTAACCG
Found at i:2670585 original size:17 final size:17
Alignment explanation
Indices: 2670554--2670604 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
2670544 TAGTGTGATA
2670554 CAACTCCAA-CAAGCTTC
1 CAAC-CCAATCAAGCTTC
* *
2670571 CAACCCACTCGAGCTTC
1 CAACCCAATCAAGCTTC
2670588 CAACCCAATCAAGCTTC
1 CAACCCAATCAAGCTTC
2670605 TGATAATCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 3 0.10
17 26 0.90
ACGTcount: A:0.31, C:0.43, G:0.08, T:0.18
Consensus pattern (17 bp):
CAACCCAATCAAGCTTC
Found at i:2671492 original size:21 final size:21
Alignment explanation
Indices: 2671468--2671580 Score: 66
Period size: 21 Copynumber: 5.4 Consensus size: 21
2671458 CGTAAGGATC
2671468 GAACGGAAGCTCATAAGAGCT
1 GAACGGAAGCTCATAAGAGCT
* * *
2671489 GAACGGAAACCCATAAG-GGT
1 GAACGGAAGCTCATAAGAGCT
* ** * *
2671509 TAATTAGAAGCTCAAAATAGCT
1 GAA-CGGAAGCTCATAAGAGCT
* * * *
2671531 GAACGGAAACCCATAAGGGTT
1 GAACGGAAGCTCATAAGAGCT
* * *
2671552 AAACAGAAGCTCAAAAGAGCT
1 GAACGGAAGCTCATAAGAGCT
*
2671573 AAACGGAA
1 GAACGGAA
2671581 ACCCAATAGG
Statistics
Matches: 62, Mismatches: 28, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
20 4 0.06
21 54 0.87
22 4 0.06
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (21 bp):
GAACGGAAGCTCATAAGAGCT
Found at i:2671519 original size:42 final size:42
Alignment explanation
Indices: 2671473--2671598 Score: 191
Period size: 42 Copynumber: 3.0 Consensus size: 42
2671463 GGATCGAACG
* **
2671473 GAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTAATTA
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACA
*
2671515 GAAGCTCAAAATAGCTGAACGGAAACCCATAAGGGTTAAACA
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACA
*
2671557 GAAGCTCAAAAGAGCTAAACGGAAACCCA-ATAGGGTTAAACA
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATA-AGGGTTAAACA
2671599 AAAACTCATA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
41 1 0.01
42 76 0.99
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.15
Consensus pattern (42 bp):
GAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACA
Found at i:2671596 original size:21 final size:21
Alignment explanation
Indices: 2671532--2671597 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
2671522 AAAATAGCTG
2671532 AACGGAAACCC-ATAAGGGTTA
1 AACGGAAACCCAAT-AGGGTTA
* * * * * *
2671553 AACAGAAGCTCAAAAGAGCTA
1 AACGGAAACCCAATAGGGTTA
2671574 AACGGAAACCCAATAGGGTTA
1 AACGGAAACCCAATAGGGTTA
2671595 AAC
1 AAC
2671598 AAAAACTCAT
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (21 bp):
AACGGAAACCCAATAGGGTTA
Found at i:2672962 original size:24 final size:24
Alignment explanation
Indices: 2672935--2672981 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2672925 AATTTAAAAA
2672935 TATAAATTTAAACCCCTAATTATG
1 TATAAATTTAAACCCCTAATTATG
* *
2672959 TATATATTTAAGCCCCTAATTAT
1 TATAAATTTAAACCCCTAATTAT
2672982 TTTTTTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (24 bp):
TATAAATTTAAACCCCTAATTATG
Found at i:2678787 original size:3 final size:3
Alignment explanation
Indices: 2678779--2678826 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
2678769 ATCTACACTC
2678779 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A-A ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
2678826 A
1 A
2678827 TTTGTGAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:2681848 original size:43 final size:42
Alignment explanation
Indices: 2681801--2681914 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 42
2681791 CCAGACGTGA
* *
2681801 TCTTACATGAAATCAAATATCGATGCCACTATCCCCGACAGGG
1 TCTTACACGAAATCAAATATCGATGCCA-TATCCCAGACAGGG
* ** * *
2681844 TCTTACACGAACTCGTATA-CGATGCCTATGTCCCAGACATGG
1 TCTTACACGAAATCAAATATCGATGCC-ATATCCCAGACAGGG
2681886 TCTTACACGTAAATCACAA-ATCGATGCCA
1 TCTTACACG-AAATCA-AATATCGATGCCA
2681915 ACGTCCCAGT
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
42 27 0.47
43 22 0.39
44 8 0.14
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (42 bp):
TCTTACACGAAATCAAATATCGATGCCATATCCCAGACAGGG
Found at i:2689553 original size:159 final size:159
Alignment explanation
Indices: 2689252--2689586 Score: 636
Period size: 159 Copynumber: 2.1 Consensus size: 159
2689242 ATTTAATATT
2689252 ATAAATACGAGATAAATTTTAAAATTATATATAAATTTAAATTTAATGTGTAATTCGATACATAA
1 ATAAATACGAG-TAAATTTTAAAATTATATATAAATTTAAATTTAATGTGTAATTCGATACATAA
*
2689317 ACTTTGATTTTATGTAATCATACATGAAATTCTAATTGTGGTTCAAAGATATATGTAAAATTTTA
65 ACTTTGATTTTATGTAATCATACATGAAAATCTAATTGTGGTTCAAAGATATATGTAAAATTTTA
2689382 ATTTTGATTTAATTATATATATTTTAAGAA
130 ATTTTGATTTAATTATATATATTTTAAGAA
2689412 ATAAATACGAGTAAATTTTAAAATTATATATAAATTTAAATTTAATGTGTAATTCGATACATAAA
1 ATAAATACGAGTAAATTTTAAAATTATATATAAATTTAAATTTAATGTGTAATTCGATACATAAA
2689477 CTTTGATTTTATGTAATCATACATGAAAATCTAATTGTGGTTCAAAGATATATGTAAAATTTTAA
66 CTTTGATTTTATGTAATCATACATGAAAATCTAATTGTGGTTCAAAGATATATGTAAAATTTTAA
2689542 TTTTGATTTAATTATATATATTTTAAGAA
131 TTTTGATTTAATTATATATATTTTAAGAA
*
2689571 ATAAATAC-ATTAAATT
1 ATAAATACGAGTAAATT
2689587 ATTTTTATAA
Statistics
Matches: 173, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
158 7 0.04
159 155 0.90
160 11 0.06
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (159 bp):
ATAAATACGAGTAAATTTTAAAATTATATATAAATTTAAATTTAATGTGTAATTCGATACATAAA
CTTTGATTTTATGTAATCATACATGAAAATCTAATTGTGGTTCAAAGATATATGTAAAATTTTAA
TTTTGATTTAATTATATATATTTTAAGAA
Found at i:2689620 original size:25 final size:25
Alignment explanation
Indices: 2689570--2689620 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
2689560 TATTTTAAGA
* **
2689570 AATAAATACATTAAATTATTTTTAT
1 AATAAATAAATTAAATTATTCGTAT
2689595 AATAAATAAA-TATAATTATTCGTAT
1 AATAAATAAATTA-AATTATTCGTAT
2689620 A
1 A
2689621 TGTAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (25 bp):
AATAAATAAATTAAATTATTCGTAT
Done.