Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 14 of 27
Found at i:2247738 original size:23 final size:22
Alignment explanation
Indices: 2247707--2247750 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2247697 AATTATTAAA
2247707 TATAAATTATTTAAATATATTC
1 TATAAATTATTTAAATATATTC
**
2247729 TATAATATTATTTTTATATATT
1 TATAA-ATTATTTAAATATATT
2247751 TATCAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATAAATTATTTAAATATATTC
Found at i:2248154 original size:2 final size:2
Alignment explanation
Indices: 2248149--2248182 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2248139 GTGAAATCTT
2248149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2248183 AACTTGTTTT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2248406 original size:21 final size:22
Alignment explanation
Indices: 2248381--2248428 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2248371 TTATTAAAGA
2248381 ATATCTAAT-CATTCAAAAAAT
1 ATATCTAATCCATTCAAAAAAT
*
2248402 ATATC-AATCCATTTAAAAAAT
1 ATATCTAATCCATTCAAAAAAT
2248423 -TATCTA
1 ATATCTA
2248429 TTATTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATCTAATCCATTCAAAAAAT
Found at i:2248559 original size:18 final size:19
Alignment explanation
Indices: 2248538--2248577 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2248528 TTTTATTAAT
2248538 TTATGTAA-AAATAAAAAA
1 TTATGTAATAAATAAAAAA
*
2248556 TTATTTAATAAATAAAAAA
1 TTATGTAATAAATAAAAAA
2248575 TTA
1 TTA
2248578 ATATTTACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
TTATGTAATAAATAAAAAA
Found at i:2254517 original size:162 final size:162
Alignment explanation
Indices: 2254250--2254566 Score: 634
Period size: 162 Copynumber: 2.0 Consensus size: 162
2254240 GAATCAAACA
2254250 AAAATTAACCAGATCTGATGGGAAAACAAAGCATAACAGAAGAAATAATCAAACGTGAAAAATGA
1 AAAATTAACCAGATCTGATGGGAAAACAAAGCATAACAGAAGAAATAATCAAACGTGAAAAATGA
2254315 AGACCTATTATTCTCAGATCTAAAGGAAAATCAAACAAATGACTAAAAGATGCAATGAATCTAAG
66 AGACCTATTATTCTCAGATCTAAAGGAAAATCAAACAAATGACTAAAAGATGCAATGAATCTAAG
2254380 CAGATCATAGATATAAATATAAGATCTAAAGG
131 CAGATCATAGATATAAATATAAGATCTAAAGG
2254412 AAAATTAACCAGATCTGATGGGAAAACAAAGCATAACAGAAGAAATAATCAAACGTGAAAAATGA
1 AAAATTAACCAGATCTGATGGGAAAACAAAGCATAACAGAAGAAATAATCAAACGTGAAAAATGA
2254477 AGACCTATTATTCTCAGATCTAAAGGAAAATCAAACAAATGACTAAAAGATGCAATGAATCTAAG
66 AGACCTATTATTCTCAGATCTAAAGGAAAATCAAACAAATGACTAAAAGATGCAATGAATCTAAG
2254542 CAGATCATAGATATAAATATAAGAT
131 CAGATCATAGATATAAATATAAGAT
2254567 TGAAAGGTGA
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 155 1.00
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (162 bp):
AAAATTAACCAGATCTGATGGGAAAACAAAGCATAACAGAAGAAATAATCAAACGTGAAAAATGA
AGACCTATTATTCTCAGATCTAAAGGAAAATCAAACAAATGACTAAAAGATGCAATGAATCTAAG
CAGATCATAGATATAAATATAAGATCTAAAGG
Found at i:2255492 original size:27 final size:32
Alignment explanation
Indices: 2255428--2255493 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 32
2255418 ATATATTTGA
2255428 ATTTATATTTATAATATATTTTTAAAAATCAT
1 ATTTATATTTATAATATATTTTTAAAAATCAT
*
2255460 ACTTATA-TT-TAA-AT-TTTTTAAAAAT-AT
1 ATTTATATTTATAATATATTTTTAAAAATCAT
2255487 ATTTATA
1 ATTTATA
2255494 AAATTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 8 0.25
28 11 0.34
29 2 0.06
30 3 0.09
31 2 0.06
32 6 0.19
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (32 bp):
ATTTATATTTATAATATATTTTTAAAAATCAT
Found at i:2255508 original size:13 final size:13
Alignment explanation
Indices: 2255462--2255535 Score: 61
Period size: 12 Copynumber: 6.0 Consensus size: 13
2255452 AAAATCATAC
2255462 TTATATTT-AAAT
1 TTATATTTAAAAT
*
2255474 TT-T-TTAAAAAT
1 TTATATTTAAAAT
*
2255485 ATAT-TTATAAAAT
1 TTATATT-TAAAAT
2255498 TTATATTTAAAA-
1 TTATATTTAAAAT
*
2255510 TAATATTT-AAAT
1 TTATATTTAAAAT
2255522 TTATATTTCAAAAT
1 TTATATTT-AAAAT
2255536 AATATTAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
10 2 0.04
11 9 0.18
12 19 0.39
13 13 0.27
14 6 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (13 bp):
TTATATTTAAAAT
Found at i:2255517 original size:12 final size:12
Alignment explanation
Indices: 2255500--2255541 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
2255490 TATAAAATTT
2255500 ATATTTAAAATA
1 ATATTTAAAATA
* *
2255512 ATATTTAAATTT
1 ATATTTAAAATA
2255524 ATATTTCAAAATA
1 ATATTT-AAAATA
2255537 ATATT
1 ATATT
2255542 AATAAATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATTTAAAATA
Found at i:2255543 original size:24 final size:24
Alignment explanation
Indices: 2255464--2255541 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
2255454 AATCATACTT
*
2255464 ATATTTAAATTT-T-TTAAAAAT-
1 ATATTTAAATTTATATTTAAAATA
2255485 ATATTTATAAAATTTATATTTAAAATA
1 ATA-TT-T-AAATTTATATTTAAAATA
2255512 ATATTTAAATTTATATTTCAAAATA
1 ATATTTAAATTTATATTT-AAAATA
2255537 ATATT
1 ATATT
2255542 AATAAATCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
21 3 0.06
22 2 0.04
23 1 0.02
24 18 0.37
25 13 0.27
26 9 0.18
27 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATTTAAATTTATATTTAAAATA
Found at i:2255627 original size:16 final size:16
Alignment explanation
Indices: 2255606--2255636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2255596 AATAGTTTTC
*
2255606 ATAATAATATTTTAAT
1 ATAATAATATATTAAT
2255622 ATAATAATATATTAA
1 ATAATAATATATTAA
2255637 AAAATGTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATAATATATTAAT
Found at i:2256328 original size:29 final size:30
Alignment explanation
Indices: 2256289--2256352 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
2256279 TATCATAACT
*
2256289 ATTTTTAAAATATTAA-TTA-TTTATATAA
1 ATTTTTAAAATAATAATTTATTTTATATAA
2256317 ATTTTTATAAATAATAATTTATTTTATATAA
1 ATTTTTA-AAATAATAATTTATTTTATATAA
2256348 ATTTT
1 ATTTT
2256353 AATGTATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 3 0.09
31 14 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTTTAAAATAATAATTTATTTTATATAA
Found at i:2256348 original size:21 final size:21
Alignment explanation
Indices: 2256317--2256367 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2256307 ATTTATATAA
*
2256317 ATTTT-TATAAATAATAATTT
1 ATTTTATATAAATAATAATGT
**
2256337 ATTTTATATAAATTTTAATGT
1 ATTTTATATAAATAATAATGT
2256358 ATTTATATAT
1 ATTT-TATAT
2256368 TTATATTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 5 0.19
21 16 0.62
22 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTTATATAAATAATAATGT
Found at i:2263111 original size:17 final size:17
Alignment explanation
Indices: 2263086--2263118 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2263076 AATTTTTGTG
*
2263086 CTTTTTATTGAATATGT
1 CTTTCTATTGAATATGT
2263103 CTTTCTATTGAATATG
1 CTTTCTATTGAATATG
2263119 ATGCGAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (17 bp):
CTTTCTATTGAATATGT
Found at i:2267681 original size:105 final size:105
Alignment explanation
Indices: 2267499--2267705 Score: 369
Period size: 105 Copynumber: 2.0 Consensus size: 105
2267489 ATGTCTCCTC
* *
2267499 GGTTCTCACAGTTTTTACCAAACTAATGGAGTGGACTGTCAAAACTTTGTGTTGTTTGGGGTAAT
1 GGTTCTCACAGTTTTTACCAAACTAATGGAGTGAACTGTCAAAACTTTGTGTTGTTTGGAGTAAT
* *
2267564 TGATTTTTAAGAAGCTCTCTTCCAGGTCATATGGCTTCTT
66 TGATTTATAAGAAGCTCTCTTCCAGGTCATATAGCTTCTT
*
2267604 GGTTCTCACAGTTTTTACCAAACTAATGGAGTGAACTGTCAAAACTTTGTGTTGTTTGGAGTGAT
1 GGTTCTCACAGTTTTTACCAAACTAATGGAGTGAACTGTCAAAACTTTGTGTTGTTTGGAGTAAT
2267669 TGATTTATAAGAAGCTCTCTTCCAGGTCATATAGCTT
66 TGATTTATAAGAAGCTCTCTTCCAGGTCATATAGCTT
2267706 TTAATGGAGG
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 97 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (105 bp):
GGTTCTCACAGTTTTTACCAAACTAATGGAGTGAACTGTCAAAACTTTGTGTTGTTTGGAGTAAT
TGATTTATAAGAAGCTCTCTTCCAGGTCATATAGCTTCTT
Found at i:2268655 original size:12 final size:12
Alignment explanation
Indices: 2268625--2268654 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2268615 CTGATAGTTG
2268625 TCTTTTTCTTCT
1 TCTTTTTCTTCT
2268637 TCTTTTTCTTCT
1 TCTTTTTCTTCT
2268649 T-TTTTT
1 TCTTTTT
2268655 TTTTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTCT
Found at i:2269341 original size:17 final size:17
Alignment explanation
Indices: 2269310--2269343 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2269300 TTTTACCTTC
2269310 TGCAACTTTAGTTTATA
1 TGCAACTTTAGTTTATA
2269327 TGCATACTTTA-TTTATA
1 TGCA-ACTTTAGTTTATA
2269344 GACATGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (17 bp):
TGCAACTTTAGTTTATA
Found at i:2275941 original size:171 final size:171
Alignment explanation
Indices: 2275642--2275978 Score: 530
Period size: 171 Copynumber: 2.0 Consensus size: 171
2275632 AATCGAAGGT
* * * * *
2275642 ATGATATTTATTTGCATTTATATATGTTTGAAATGTTTCAACACTTGATTAGTGATTATTGCTGC
1 ATGATATTTATTTCCATTTATATATGTTTGAAATGGTTCAACACTTAATTAGTGATCATTACTGC
* *
2275707 TGCAGCATGCATCTACACCTAAATCAGATGGTAAAAACAAGCATAAAAGGCATAAGAGAGACCAT
66 TGCAGCATGCATCTACACCTAAATCAGATGGTAAAAACAAGCATAAAAGACAGAAGAGAGACCAT
*
2275772 CAGAATGGTTCACATAGAAATGTTGACCCTGAGGAGGTATG
131 CAGAATGGTTCACAGAGAAATGTTGACCCTGAGGAGGTATG
*
2275813 ATGATATTTATTTCCATTTATATATGTTTGAAATGGTTCAACCCTTAATTAGTGATCATTACTGC
1 ATGATATTTATTTCCATTTATATATGTTTGAAATGGTTCAACACTTAATTAGTGATCATTACTGC
* * * * *
2275878 TGCAGCATGCATCTACACCTGAATCAGATGGTAAAAAGAGGCATGAAAGACAGAAGGGAGACCAT
66 TGCAGCATGCATCTACACCTAAATCAGATGGTAAAAACAAGCATAAAAGACAGAAGAGAGACCAT
* *
2275943 CGGAATGGTTCACCGAGAAATGTTGACCCTGAGGAG
131 CAGAATGGTTCACAGAGAAATGTTGACCCTGAGGAG
2275979 CTTGAAGATG
Statistics
Matches: 150, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
171 150 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (171 bp):
ATGATATTTATTTCCATTTATATATGTTTGAAATGGTTCAACACTTAATTAGTGATCATTACTGC
TGCAGCATGCATCTACACCTAAATCAGATGGTAAAAACAAGCATAAAAGACAGAAGAGAGACCAT
CAGAATGGTTCACAGAGAAATGTTGACCCTGAGGAGGTATG
Found at i:2278711 original size:2 final size:2
Alignment explanation
Indices: 2278704--2278737 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2278694 TGTGGGATAC
2278704 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
2278738 TAGGCTGATA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2280634 original size:23 final size:22
Alignment explanation
Indices: 2280594--2280636 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2280584 TAAATATCGA
*
2280594 TTTAAAAAATATTTATTTTTAC
1 TTTAAAAAATATTAATTTTTAC
*
2280616 TTTAAAAATTATGTAATTTTT
1 TTTAAAAAATAT-TAATTTTT
2280637 TTAAAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAAAAATATTAATTTTTAC
Found at i:2281278 original size:3 final size:3
Alignment explanation
Indices: 2281224--2281262 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2281214 ATCATTTATT
2281224 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2281263 TATTAAATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2282951 original size:2 final size:2
Alignment explanation
Indices: 2282944--2282973 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2282934 GTTTTTATGA
*
2282944 AT AT AT AT AT AA 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
2282974 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2283990 original size:2 final size:2
Alignment explanation
Indices: 2283985--2284011 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2283975 TATATATATA
2283985 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
2284012 CTTACACTGT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2284436 original size:2 final size:2
Alignment explanation
Indices: 2284431--2284469 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2284421 TATATGTGTG
2284431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2284470 GAATTGGCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2286642 original size:15 final size:16
Alignment explanation
Indices: 2286610--2286643 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2286600 AAATTTAAAT
2286610 ATATTTATATCAATTAC
1 ATATTTATAT-AATTAC
2286627 ATATTTATAT-ATTAC
1 ATATTTATATAATTAC
2286642 AT
1 AT
2286644 TCTGTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTTATATAATTAC
Found at i:2287157 original size:23 final size:23
Alignment explanation
Indices: 2287130--2287177 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
2287120 TTCATTAATC
2287130 ATAATTAACCTATTAA-AATGCAT
1 ATAATTAACCTA-TAACAATGCAT
2287153 ATAATTAACCTATAACAATGCAT
1 ATAATTAACCTATAACAATGCAT
2287176 AT
1 AT
2287178 CAGGAACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (23 bp):
ATAATTAACCTATAACAATGCAT
Found at i:2288932 original size:35 final size:33
Alignment explanation
Indices: 2288859--2288933 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 33
2288849 ATAATATTTT
*
2288859 TTAATTAAAAATAAATTTGATATTATATTATAA
1 TTAATTAAAAATAAATTTCATATTATATTATAA
* * *
2288892 ATAATTATAAAATTAATTATCATATTTTAATT-TAA
1 TTAATTA-AAAATAAATT-TCATATTAT-ATTATAA
2288927 TTAATTA
1 TTAATTA
2288934 CGTTTTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
33 6 0.18
34 9 0.26
35 16 0.47
36 3 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (33 bp):
TTAATTAAAAATAAATTTCATATTATATTATAA
Found at i:2289286 original size:15 final size:15
Alignment explanation
Indices: 2289249--2289290 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2289239 AATAAATTAG
*
2289249 AATTAATTTATTTTA
1 AATTAAATTATTTTA
* *
2289264 CATAAAATTATTTTA
1 AATTAAATTATTTTA
2289279 AATTAAA-TATTT
1 AATTAAATTATTT
2289291 GGAAAGTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTAAATTATTTTA
Found at i:2290171 original size:21 final size:21
Alignment explanation
Indices: 2290121--2290190 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
2290111 ATAAAATTTT
*
2290121 TATTTAAAT-TTAATTATAAAA
1 TATTAAAATATTAA-TATAAAA
*
2290142 -AATATAAATATTAATATAAAA
1 TATTA-AAATATTAATATAAAA
* *
2290163 TATTAAAATAATAA-ATAAAT
1 TATTAAAATATTAATATAAAA
*
2290183 TTTTAAAA
1 TATTAAAA
2290191 CATGATAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
20 14 0.35
21 19 0.47
22 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTAAAATATTAATATAAAA
Found at i:2291669 original size:19 final size:19
Alignment explanation
Indices: 2291647--2291686 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2291637 TAAATAATAA
2291647 TTATGATATTATA-TTATAT
1 TTATGAT-TTATATTTATAT
*
2291666 TTATTATTTATATTTATAT
1 TTATGATTTATATTTATAT
2291685 TT
1 TT
2291687 TTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTATGATTTATATTTATAT
Found at i:2291676 original size:13 final size:13
Alignment explanation
Indices: 2291653--2291696 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
2291643 ATAATTATGA
2291653 TATTATATTATATT
1 TATTAT-TTATATT
2291667 TATTATTTATATT
1 TATTATTTATATT
*
2291680 TA-TATTTTTAATT
1 TATTATTTAT-ATT
2291693 TATT
1 TATT
2291697 TCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 6 0.22
13 14 0.52
14 7 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTTATATT
Found at i:2291679 original size:6 final size:6
Alignment explanation
Indices: 2291655--2291704 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
2291645 AATTATGATA
* * *
2291655 TTATA- TTATAT TTATTAT TTATAT TTATAT TTTTAA TT-TAT TTCTAT
1 TTATAT TTATAT TTA-TAT TTATAT TTATAT TTATAT TTATAT TTATAT
2291702 TTA
1 TTA
2291705 AAATATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
5 9 0.24
6 23 0.61
7 6 0.16
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:2291693 original size:19 final size:18
Alignment explanation
Indices: 2291655--2291704 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
2291645 AATTATGATA
2291655 TTATATTATATTTATTAT
1 TTATATTATATTTATTAT
2291673 TTATATTTATATTT-TTAAT
1 TTATA-TTATATTTATT-AT
*
2291692 TTAT-TTCTATTTA
1 TTATATTATATTTA
2291705 AAATATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 7 0.25
18 7 0.25
19 14 0.50
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATATTATATTTATTAT
Found at i:2293260 original size:13 final size:13
Alignment explanation
Indices: 2293242--2293297 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
2293232 AAAAATTAAA
2293242 AATATTTTATATT
1 AATATTTTATATT
2293255 AATA-TTTATA-T
1 AATATTTTATATT
*
2293266 -ATTTTTTATAATT
1 AATATTTTAT-ATT
2293279 -ATATTTTATTATT
1 AATATTTTA-TATT
2293292 AATATT
1 AATATT
2293298 AACTAAAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.17
12 7 0.19
13 15 0.42
14 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTTTATATT
Found at i:2294079 original size:18 final size:18
Alignment explanation
Indices: 2294053--2294090 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
2294043 GATTAAAGAA
2294053 TTAATAGTTAGTATAAAAT
1 TTAATAGTTAG-ATAAAAT
*
2294072 TTAA-AGTTAGATACAAT
1 TTAATAGTTAGATAAAAT
2294089 TT
1 TT
2294091 CAAAATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 6 0.33
19 4 0.22
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (18 bp):
TTAATAGTTAGATAAAAT
Found at i:2294294 original size:22 final size:22
Alignment explanation
Indices: 2294269--2294315 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2294259 GAAAGATTAG
* *
2294269 TTTATTATTAATATTTATAT-AT
1 TTTATAATTAA-ATTTAAATAAT
2294291 TTTATAATTAAATTTAAATAAT
1 TTTATAATTAAATTTAAATAAT
2294313 TTT
1 TTT
2294316 TTTTTAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTATAATTAAATTTAAATAAT
Found at i:2296656 original size:2 final size:2
Alignment explanation
Indices: 2296649--2296679 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2296639 TATAGCAATG
2296649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2296680 AACAATTTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2299276 original size:2 final size:2
Alignment explanation
Indices: 2299271--2299297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2299261 AAGCTGTCTT
2299271 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
2299298 GTACCTATAA
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:2300414 original size:11 final size:11
Alignment explanation
Indices: 2300400--2300457 Score: 70
Period size: 11 Copynumber: 5.6 Consensus size: 11
2300390 AGAATATGAA
2300400 ATATAAAAATT
1 ATATAAAAATT
*
2300411 ATAT-CAAA-T
1 ATATAAAAATT
2300420 ATATAAAAATT
1 ATATAAAAATT
*
2300431 ATATAAAAAAT
1 ATATAAAAATT
2300442 -TAT-AAAATT
1 ATATAAAAATT
2300451 ATATAAA
1 ATATAAA
2300458 CTATTTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 10 0.26
10 12 0.31
11 17 0.44
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
ATATAAAAATT
Found at i:2300423 original size:20 final size:20
Alignment explanation
Indices: 2300398--2300457 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
2300388 ATAGAATATG
*
2300398 AAATATAAAAATTATATCAA
1 AAATATAAAAATTATATAAA
*
2300418 ATATATAAAAATTATATAAA
1 AAATATAAAAATTATATAAA
2300438 AAAT-TATAAAATTATATAAA
1 AAATATA-AAAATTATATAAA
2300458 CTATTTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 2 0.06
20 34 0.94
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATAAAAATTATATAAA
Found at i:2300770 original size:20 final size:18
Alignment explanation
Indices: 2300721--2300771 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
2300711 TATTATATTT
2300721 AATATTAATTTAATAATAA
1 AATATT-ATTTAATAATAA
*
2300740 AAT-TATGTTTAATAATTTAA
1 AATAT-TATTTAATAA--TAA
2300760 AATATTATTTAA
1 AATATTATTTAA
2300772 ATGAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 9 0.35
19 4 0.15
20 12 0.46
21 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
AATATTATTTAATAATAA
Found at i:2300861 original size:2 final size:2
Alignment explanation
Indices: 2300856--2300887 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2300846 AACCTTTGTT
2300856 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2300888 GTGTCATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2303261 original size:123 final size:123
Alignment explanation
Indices: 2303122--2303368 Score: 467
Period size: 123 Copynumber: 2.0 Consensus size: 123
2303112 GTTTTGTTTG
2303122 TACGTTTATCAAATTAAATAATATAATTGTGAATTAAATACAATAATCGAATTGAATATGATTAA
1 TACGTTTATCAAATTAAATAATATAATTGTGAATTAAATACAATAATCGAATTGAATATGATTAA
2303187 TACTTAATATAGATAAAAATATATTATTTATTTATTTTTAATTAAATATTAATTTTAT
66 TACTTAATATAGATAAAAATATATTATTTATTTATTTTTAATTAAATATTAATTTTAT
* * *
2303245 TACGTTTATCAAATTAAATAATATAATTGTGAGTTAAATATAATAATCGAGTTGAATATGATTAA
1 TACGTTTATCAAATTAAATAATATAATTGTGAATTAAATACAATAATCGAATTGAATATGATTAA
2303310 TACTTAATATAGATAAAAATATATTATTTATTTATTTTTAATTAAATATTAATTTTAT
66 TACTTAATATAGATAAAAATATATTATTTATTTATTTTTAATTAAATATTAATTTTAT
2303368 T
1 T
2303369 GGTTGATTTG
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 121 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (123 bp):
TACGTTTATCAAATTAAATAATATAATTGTGAATTAAATACAATAATCGAATTGAATATGATTAA
TACTTAATATAGATAAAAATATATTATTTATTTATTTTTAATTAAATATTAATTTTAT
Found at i:2303644 original size:108 final size:108
Alignment explanation
Indices: 2303526--2303739 Score: 392
Period size: 108 Copynumber: 2.0 Consensus size: 108
2303516 TTAATTCGCC
* * *
2303526 TCTAGTATCCGTATGCATGTTGTCACCGGCTAAAAATTCAACCACTTAAGTTTTAGATTTGTCTT
1 TCTAGTATCCGTATGCATGTTGTCACCGGCTAAAAATTCAACCACCTAAGTCTTAGACTTGTCTT
2303591 GAAAAAATGGAGATGTTAATGGAGAATTTTAGGACATTAAAAT
66 GAAAAAATGGAGATGTTAATGGAGAATTTTAGGACATTAAAAT
*
2303634 TCTAGTATCCGTATGCATGTTGTCACCGGCTAAAAATTTAACCACCTAAGTCTTAGACTTGTCTT
1 TCTAGTATCCGTATGCATGTTGTCACCGGCTAAAAATTCAACCACCTAAGTCTTAGACTTGTCTT
2303699 GAAAAAATGGAGATGTTAATGGAGAATTTTAGGACATTAAA
66 GAAAAAATGGAGATGTTAATGGAGAATTTTAGGACATTAAA
2303740 GAAAGTTCTA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 102 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (108 bp):
TCTAGTATCCGTATGCATGTTGTCACCGGCTAAAAATTCAACCACCTAAGTCTTAGACTTGTCTT
GAAAAAATGGAGATGTTAATGGAGAATTTTAGGACATTAAAAT
Found at i:2303799 original size:20 final size:20
Alignment explanation
Indices: 2303776--2303894 Score: 82
Period size: 20 Copynumber: 6.0 Consensus size: 20
2303766 TCTAAAACAC
2303776 TTTGAAAAGTTCTAGAATAT
1 TTTGAAAAGTTCTAGAATAT
* *
2303796 TTTGGAATGTTCTAGAATAT
1 TTTGAAAAGTTCTAGAATAT
** * * *
2303816 CATGAAAGGCTCT-GAAAGAT
1 TTTGAAAAGTTCTAG-AATAT
*
2303836 TTT-AAAATGTTTTAGAATAT
1 TTTGAAAA-GTTCTAGAATAT
* * *
2303856 TGTGAAAAGTTCTGGAAGAT
1 TTTGAAAAGTTCTAGAATAT
*
2303876 TCT-AAAATGTTCTAGAATA
1 TTTGAAAA-GTTCTAGAATA
2303895 ATGTGGAAGG
Statistics
Matches: 73, Mismatches: 21, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
19 8 0.11
20 60 0.82
21 5 0.07
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (20 bp):
TTTGAAAAGTTCTAGAATAT
Found at i:2303822 original size:40 final size:39
Alignment explanation
Indices: 2303778--2303894 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 39
2303768 TAAAACACTT
* **
2303778 TGAAAAGTTCTAGAATATTTTGGAATGTTCTAGAATATCA
1 TGAAAAGTTCT-GAAGATTTTAAAATGTTCTAGAATATCA
* * * **
2303818 TGAAAGGCTCTGAAAGATTTTAAAATGTTTTAGAATATTG
1 TGAAAAGTTCTG-AAGATTTTAAAATGTTCTAGAATATCA
*
2303858 TGAAAAGTTCTGGAAGATTCTAAAATGTTCTAGAATA
1 TGAAAAGTTCT-GAAGATTTTAAAATGTTCTAGAATA
2303895 ATGTGGAAGG
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 61 0.97
41 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (39 bp):
TGAAAAGTTCTGAAGATTTTAAAATGTTCTAGAATATCA
Found at i:2303908 original size:40 final size:40
Alignment explanation
Indices: 2303801--2303908 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
2303791 AATATTTTGG
* * *
2303801 AATGTTCTAGAAT-ATCATGAAAGGCTCTGAAAGATTTTAA
1 AATGTTCTAGAATAAT-GTGAAAGGTTCTGAAAGATTCTAA
* * * *
2303841 AATGTTTTAGAATATTGTGAAAAGTTCTGGAAGATTCTAA
1 AATGTTCTAGAATAATGTGAAAGGTTCTGAAAGATTCTAA
*
2303881 AATGTTCTAGAATAATGTGGAAGGTTCT
1 AATGTTCTAGAATAATGTGAAAGGTTCT
2303909 AGAACTTTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 55 0.98
41 1 0.02
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.35
Consensus pattern (40 bp):
AATGTTCTAGAATAATGTGAAAGGTTCTGAAAGATTCTAA
Found at i:2304992 original size:2 final size:2
Alignment explanation
Indices: 2304985--2305016 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2304975 ATCTTGTCTG
2304985 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
2305017 GACGTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2305629 original size:2 final size:2
Alignment explanation
Indices: 2305624--2305664 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2305614 TTCTCTCTCC
*
2305624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2305665 CCATAAGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2306262 original size:19 final size:20
Alignment explanation
Indices: 2306230--2306268 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2306220 CGATCAAATT
2306230 TTTGATTTAAATTTA-AAAA
1 TTTGATTTAAATTTATAAAA
2306249 TTTG-TTTAATATTTATAAAA
1 TTTGATTTAA-ATTTATAAAA
2306269 ATTTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTGATTTAAATTTATAAAA
Found at i:2307123 original size:22 final size:23
Alignment explanation
Indices: 2307075--2307124 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
2307065 TGAATTTAAC
2307075 TAATTT-TATTATTTTAAAATAT
1 TAATTTATATTATTTTAAAATAT
* *
2307097 T-ATTTATATTTTTTTATAAT-T
1 TAATTTATATTATTTTAAAATAT
2307118 TAATTTA
1 TAATTTA
2307125 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TAATTTATATTATTTTAAAATAT
Found at i:2308893 original size:30 final size:30
Alignment explanation
Indices: 2308859--2308951 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
2308849 TATAATAAAA
2308859 ATATTAAATTAATTTATAAAATTATATTAC
1 ATATTAAATTAATTTATAAAATTATATTAC
* * * *
2308889 ATATTAAATAAAATTATAATATTAAATT--
1 ATATTAAATTAATTTATAAAATTATATTAC
* *
2308917 -TAAT-AATTAATTTATTAAA-TAT-TTATC
1 ATATTAAATTAATTTATAAAATTATATTA-C
2308944 ATATTAAA
1 ATATTAAA
2308952 ATTATATAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 11
0.68 0.16 0.16
Matches are distributed among these distances:
24 2 0.04
25 2 0.04
26 11 0.23
27 3 0.06
28 3 0.06
29 2 0.04
30 24 0.51
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
ATATTAAATTAATTTATAAAATTATATTAC
Found at i:2310788 original size:2 final size:2
Alignment explanation
Indices: 2310781--2310813 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2310771 AATCCAATTC
2310781 CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2310814 TCACCTTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:2310999 original size:21 final size:20
Alignment explanation
Indices: 2310973--2311027 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
2310963 CGATAAATTT
*
2310973 TTAAATAATTATGCATTATAA
1 TTAAATAATTAT-AATTATAA
2310994 TTAAATAAATATATAATTATAA
1 TTAAAT-AAT-TATAATTATAA
*
2311016 TATAAAAAATTA
1 T-TAAATAATTA
2311028 AGTGAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 8 0.28
22 14 0.48
23 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TTAAATAATTATAATTATAA
Found at i:2311120 original size:20 final size:20
Alignment explanation
Indices: 2311089--2311137 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2311079 ATTATTTTAA
*
2311089 AATAAA-AT-TTTTATAATT
1 AATAAATATATTTTACAATT
*
2311107 AATAAATATATTTTACCATT
1 AATAAATATATTTTACAATT
*
2311127 AATAACTATAT
1 AATAAATATAT
2311138 ACAAAAGGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 6 0.23
19 2 0.08
20 18 0.69
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAAATATATTTTACAATT
Found at i:2311452 original size:10 final size:10
Alignment explanation
Indices: 2311437--2311461 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2311427 GTTTTTTATG
2311437 TTATATCATA
1 TTATATCATA
2311447 TTATATCATA
1 TTATATCATA
2311457 TTATA
1 TTATA
2311462 ATTATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (10 bp):
TTATATCATA
Found at i:2311489 original size:17 final size:18
Alignment explanation
Indices: 2311469--2311529 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 18
2311459 ATAATTATTT
2311469 TTTAAATTT-TTTTATAA
1 TTTAAATTTATTTTATAA
*
2311486 TTT-AATTTATTTTATAT
1 TTTAAATTTATTTTATAA
*
2311503 TTTACATAATTTATTGTAATAA
1 TTT--A-AATTTATT-TTATAA
2311525 TTTAA
1 TTTAA
2311530 TTTTTACTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
16 5 0.14
17 13 0.37
19 1 0.03
20 1 0.03
21 8 0.23
22 7 0.20
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTAAATTTATTTTATAA
Found at i:2311628 original size:13 final size:13
Alignment explanation
Indices: 2311610--2311634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2311600 TAACTAAAAA
2311610 AATTTATTTTATT
1 AATTTATTTTATT
2311623 AATTTATTTTAT
1 AATTTATTTTAT
2311635 GATGTTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTTATTTTATT
Found at i:2315089 original size:18 final size:19
Alignment explanation
Indices: 2315068--2315117 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
2315058 TTTTAAAACT
2315068 TAATTAATATATTAT-TTA
1 TAATTAATATATTATATTA
2315086 TAA-TAATATTATTATATTA
1 TAATTAATA-TATTATATTA
2315105 -AATATAATA-ATTA
1 TAAT-TAATATATTA
2315118 ATAATTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 5 0.18
18 15 0.54
19 3 0.11
20 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATTAATATATTATATTA
Found at i:2315096 original size:23 final size:21
Alignment explanation
Indices: 2315068--2315142 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
2315058 TTTTAAAACT
2315068 TAATTAATATATTATTTATAA
1 TAATTAATATATTATTTATAA
* **
2315089 TAATATTATTATATTAAATATAA
1 T-A-ATTAATATATTATTTATAA
* *
2315112 TAATTAATAATTTTATTTATTA
1 TAATTAAT-ATATTATTTATAA
*
2315134 TTATTAATA
1 TAATTAATA
2315143 CCAGTTTGCT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
21 7 0.17
22 18 0.43
23 17 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATTAATATATTATTTATAA
Found at i:2323557 original size:42 final size:42
Alignment explanation
Indices: 2323498--2323583 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
2323488 AGAAATTAAA
2323498 GTAAGATGATTTACAGATGATAAAAGGAACTAGTCATTGGTT
1 GTAAGATGATTTACAGATGATAAAAGGAACTAGTCATTGGTT
2323540 GTAAGATGATTTACAGATGATAAAAGGAACTAGTCATTGGTT
1 GTAAGATGATTTACAGATGATAAAAGGAACTAGTCATTGGTT
2323582 GT
1 GT
2323584 CTCAATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.31
Consensus pattern (42 bp):
GTAAGATGATTTACAGATGATAAAAGGAACTAGTCATTGGTT
Found at i:2326652 original size:26 final size:27
Alignment explanation
Indices: 2326601--2326652 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
2326591 ATTCAACTCG
*
2326601 TATAAATTTAATTTTGATTAAAATTTT
1 TATAAATTTAATATTGATTAAAATTTT
*
2326628 TATAAATTTAA-ATTGATTAAGATTT
1 TATAAATTTAATATTGATTAAAATTT
2326653 GATGTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (27 bp):
TATAAATTTAATATTGATTAAAATTTT
Found at i:2326945 original size:2 final size:2
Alignment explanation
Indices: 2326938--2326981 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2326928 ACATTAAGCA
2326938 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
2326980 AT
1 AT
2326982 CATCTTCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2329958 original size:2 final size:2
Alignment explanation
Indices: 2329951--2329982 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2329941 TAATTTATCA
2329951 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
2329983 GCAAAGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2330467 original size:29 final size:28
Alignment explanation
Indices: 2330435--2330514 Score: 72
Period size: 31 Copynumber: 2.7 Consensus size: 28
2330425 TATTTTATTT
* *
2330435 AAAACAAAATTTTATTTAAGTATAAATCAA
1 AAAAAAAAATTTTATTTAAATAT-AAT-AA
*
2330465 AAATAAATAATTATTATTTAAATATAATAA
1 AAA-AAAAAATT-TTATTTAAATATAATAA
2330495 AAATATAAAAA-TTTATTTAA
1 AAA-A-AAAAATTTTATTTAA
2330515 TAAAATATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 8 0.19
30 11 0.26
31 13 0.30
32 11 0.26
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (28 bp):
AAAAAAAAATTTTATTTAAATATAATAA
Found at i:2330491 original size:32 final size:29
Alignment explanation
Indices: 2330442--2330514 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 29
2330432 TTTAAAACAA
*
2330442 AATTTTATTTAAGTATAAATCAAAAATAAAT
1 AATTTTATTTAAATAT-AAT-AAAAATAAAT
2330473 AATTATTATTTAAATATAATAAAAATATAA-
1 AATT-TTATTTAAATATAATAAAAATA-AAT
*
2330503 AAATTTATTTAA
1 AATTTTATTTAA
2330515 TAAAATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 8 0.21
30 10 0.26
31 9 0.24
32 11 0.29
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
AATTTTATTTAAATATAATAAAAATAAAT
Found at i:2330521 original size:28 final size:27
Alignment explanation
Indices: 2330440--2330521 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 27
2330430 TATTTAAAAC
2330440 AAAATTTTATTTAAGTATAAATCAAAAATA
1 AAAATTTTATTTAA-TA-AAAT-AAAAATA
*
2330470 AATAATTATTATTTAAATATAATAAAAATA
1 AA-AATT-TTATTT-AATAAAATAAAAATA
*
2330500 TAAAAATTTATTTAATAAAATA
1 -AAAATTTTATTTAATAAAATA
2330522 TAATTTAAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
28 8 0.18
29 6 0.13
30 12 0.27
31 9 0.20
32 8 0.18
33 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (27 bp):
AAAATTTTATTTAATAAAATAAAAATA
Found at i:2332316 original size:18 final size:19
Alignment explanation
Indices: 2332293--2332345 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
2332283 TTAAATATTC
*
2332293 ATTTAATTTTTTATTTTA-
1 ATTTAATTTTTTATTTGAT
*
2332311 ATTTAATTTTTAATTTGAT
1 ATTTAATTTTTTATTTGAT
*
2332330 ATATAATTCTTTTATT
1 ATTTAATT-TTTTATT
2332346 AATTTAGCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 16 0.55
19 7 0.24
20 6 0.21
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTAATTTTTTATTTGAT
Found at i:2332445 original size:15 final size:16
Alignment explanation
Indices: 2332415--2332447 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2332405 TAATGATGTG
2332415 ATATTTGTTATGTATT
1 ATATTTGTTATGTATT
*
2332431 ATATTT-TTATTTATT
1 ATATTTGTTATGTATT
2332446 AT
1 AT
2332448 TAATTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
ATATTTGTTATGTATT
Found at i:2332608 original size:26 final size:25
Alignment explanation
Indices: 2332579--2332628 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2332569 ATAAAAATAA
*
2332579 ATAAATATTTAATCTATTATTTTTTT
1 ATAAAT-TTGAATCTATTATTTTTTT
*
2332605 ATAAATTTGACTCTATTATTTTTT
1 ATAAATTTGAATCTATTATTTTTT
2332629 AATATGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (25 bp):
ATAAATTTGAATCTATTATTTTTTT
Found at i:2332676 original size:16 final size:17
Alignment explanation
Indices: 2332639--2332676 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2332629 AATATGTTTC
2332639 TAATAATTATTTATAAA
1 TAATAATTATTTATAAA
*
2332656 T-ATAATT-TTTATAAT
1 TAATAATTATTTATAAA
2332671 TAATAA
1 TAATAA
2332677 ATGAGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 10 0.53
17 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATAATTATTTATAAA
Found at i:2333960 original size:25 final size:26
Alignment explanation
Indices: 2333930--2333984 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
2333920 TTCTTTAATG
2333930 TTTTATTATAACT-ATAAATT-TTTAT
1 TTTTATTATAA-TAATAAATTATTTAT
*
2333955 TTTTATTTTAATAATAAATTATTTAT
1 TTTTATTATAATAATAAATTATTTAT
2333981 TTTT
1 TTTT
2333985 TACCTCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 1 0.04
25 17 0.63
26 9 0.33
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTTATTATAATAATAAATTATTTAT
Found at i:2334940 original size:30 final size:29
Alignment explanation
Indices: 2334906--2335047 Score: 103
Period size: 30 Copynumber: 4.7 Consensus size: 29
2334896 ACTATTAAAA
2334906 ATAATTAAAATATAATATTTTAAAAAATAT
1 ATAATTAAAATATAATATTTTAAAAAAT-T
* * **
2334936 ATAATATAAATATATTAATATATCAAAATTTAT
1 ATAAT-TAAA-ATA-TAATATTTTAAAAAAT-T
*
2334969 ATAATAAAAATTATAAATATTTT--AAAATT
1 ATAATTAAAA-TAT-AATATTTTAAAAAATT
* * *
2334998 ATTA-TAAATTTTAATATTTTAAATATAATT
1 ATAATTAAAATATAATATTTTAAA-A-AATT
2335028 ATAATTAAAA-ATAATATTTT
1 ATAATTAAAATATAATATTTT
2335048 TTTTTTTACT
Statistics
Matches: 86, Mismatches: 16, Indels: 20
0.70 0.13 0.16
Matches are distributed among these distances:
26 8 0.09
27 2 0.02
28 4 0.05
29 5 0.06
30 24 0.28
31 10 0.12
32 14 0.16
33 19 0.22
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (29 bp):
ATAATTAAAATATAATATTTTAAAAAATT
Found at i:2334954 original size:14 final size:14
Alignment explanation
Indices: 2334904--2334957 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
2334894 TAACTATTAA
*
2334904 AAATA-ATTAAAAT
1 AAATATATTAATAT
*
2334917 ATAATATTTTAA-A-
1 A-AATATATTAATAT
2334930 AAATATA-TAATAT
1 AAATATATTAATAT
2334943 AAATATATTAATAT
1 AAATATATTAATAT
2334957 A
1 A
2334958 TCAAAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
11 3 0.09
12 6 0.18
13 9 0.26
14 12 0.35
15 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATATTAATAT
Found at i:2334997 original size:17 final size:17
Alignment explanation
Indices: 2334975--2335023 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
2334965 TTATATAATA
2334975 AAAATTATAAATATTTT
1 AAAATTATAAATATTTT
2334992 AAAATTATTATAA-ATTTT
1 AAAATTA-TA-AATATTTT
* *
2335010 AATATTTTAAATAT
1 AAAATTATAAATAT
2335024 AATTATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 2 0.07
17 11 0.41
18 12 0.44
19 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATTATAAATATTTT
Found at i:2335004 original size:32 final size:32
Alignment explanation
Indices: 2334906--2335004 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 32
2334896 ACTATTAAAA
* *
2334906 ATAATTAAAA-TATAATATTTTAAAA-AATAT
1 ATAATAAAAATTATAATATTTTAAAATTATAT
* * *
2334936 ATAATATAAATATATTAATATATCAAAATT-TAT
1 ATAATAAAAAT-TA-TAATATTTTAAAATTATAT
2334969 ATAATAAAAATTATAAATATTTTAAAATTAT-T
1 ATAATAAAAATTAT-AATATTTTAAAATTATAT
2335001 ATAA
1 ATAA
2335005 ATTTTAATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 8 0.15
31 1 0.02
32 21 0.38
33 25 0.45
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
ATAATAAAAATTATAATATTTTAAAATTATAT
Found at i:2335028 original size:27 final size:28
Alignment explanation
Indices: 2334967--2335040 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 28
2334957 ATCAAAATTT
*
2334967 ATATAA-TAAAAATTATAAATATTTTAA
1 ATATAATTATAAATTATAAATATTTTAA
* *
2334994 A-ATTATTATAAATT-TTAATATTTTAA
1 ATATAATTATAAATTATAAATATTTTAA
*
2335020 ATATAATTAT-AATTAAAAATA
1 ATATAATTATAAATTATAAATA
2335041 ATATTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 19 0.50
27 19 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATAATTATAAATTATAAATATTTTAA
Found at i:2335519 original size:19 final size:19
Alignment explanation
Indices: 2335495--2335545 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2335485 ATATCTATAA
* *
2335495 ATATTATTAATTTTATTTT
1 ATATTATAAATTTAATTTT
2335514 ATATTATAAATTTAATTTT
1 ATATTATAAATTTAATTTT
2335533 -T-TTAATAAATTTA
1 ATATT-ATAAATTTA
2335546 TCAACTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 10 0.34
19 17 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTATAAATTTAATTTT
Found at i:2336798 original size:27 final size:27
Alignment explanation
Indices: 2336754--2336806 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
2336744 TCCCTCACAA
**
2336754 GGATATCCTCAGGGTTAT-CCACCTCAG
1 GGATATCCTCAGCCTTATGCC-CCTCAG
*
2336781 GGATATCCTCCGCCTTATGCCCCTCA
1 GGATATCCTCAGCCTTATGCCCCTCA
2336807 ATATGCTCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (27 bp):
GGATATCCTCAGCCTTATGCCCCTCAG
Found at i:2337166 original size:65 final size:66
Alignment explanation
Indices: 2337090--2337220 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 66
2337080 GTTTGTTGGC
*
2337090 TAAAGTCCCGAAAACACCCCTACTCCTTCTTTTCTGGCTTTTGGTT-ACTTTAGTTCTTTTTCAA
1 TAAAGTCCCGAAAACACCCCTACTCCTTCTTTTCTGGCTTTTCGTTAACTTTAGTTCTTTTTCAA
2337154 T
66 T
2337155 TAAAGTCCCGAAAACACCCCTACTCCTTCTTTTCTGGCTTTTCGTTAACTTTAGTTCTTTTTCAA
1 TAAAGTCCCGAAAACACCCCTACTCCTTCTTTTCTGGCTTTTCGTTAACTTTAGTTCTTTTTCAA
2337220 T
66 T
2337221 ACCACCAGCT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 45 0.70
66 19 0.30
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.43
Consensus pattern (66 bp):
TAAAGTCCCGAAAACACCCCTACTCCTTCTTTTCTGGCTTTTCGTTAACTTTAGTTCTTTTTCAA
T
Found at i:2338875 original size:15 final size:16
Alignment explanation
Indices: 2338857--2338893 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2338847 GTTAATAAAT
*
2338857 TTTATTA-TTATATTA
1 TTTATTATTTATAATA
2338872 TTTA-TATTTATAATA
1 TTTATTATTTATAATA
2338887 TTTATTA
1 TTTATTA
2338894 AAAATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.11
15 15 0.79
16 2 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTATTTATAATA
Found at i:2338962 original size:21 final size:21
Alignment explanation
Indices: 2338937--2338990 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
2338927 AATATTAATT
2338937 TAATTAATAAATTTATAAAAA
1 TAATTAATAAATTTATAAAAA
* *
2338958 TAATTAAATAAATTTATAATAT
1 TAATT-AATAAATTTATAAAAA
*
2338980 TAAGTAATAAA
1 TAATTAATAAA
2338991 ATTAGATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAATTAATAAATTTATAAAAA
Found at i:2338992 original size:22 final size:22
Alignment explanation
Indices: 2338932--2338993 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
2338922 CAAATAATAT
2338932 TAAT-TTAATTAAT-AAATTTA
1 TAATATTAATTAATAAAATTTA
* *
2338952 TAAAAATAATTAA-ATAAATTTA
1 TAATATTAATTAATA-AAATTTA
*
2338974 TAATATTAAGTAATAAAATT
1 TAATATTAATTAATAAAATT
2338994 AGATATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 3 0.09
21 7 0.21
22 22 0.67
23 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TAATATTAATTAATAAAATTTA
Found at i:2339304 original size:16 final size:16
Alignment explanation
Indices: 2339283--2339313 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2339273 ATTATATATA
2339283 AATAAATTTTTAATTG
1 AATAAATTTTTAATTG
2339299 AATAAATTTTTAATT
1 AATAAATTTTTAATT
2339314 TTTAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
AATAAATTTTTAATTG
Found at i:2343228 original size:21 final size:21
Alignment explanation
Indices: 2343204--2343250 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2343194 CTGCTGCTCG
*
2343204 TGCAGTCGCAGAAGCAGAAGC
1 TGCAGTAGCAGAAGCAGAAGC
* *
2343225 TGCAATAGCAGAAGCTGAAGC
1 TGCAGTAGCAGAAGCAGAAGC
*
2343246 AGCAG
1 TGCAG
2343251 CAAGAGAGGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.32, T:0.11
Consensus pattern (21 bp):
TGCAGTAGCAGAAGCAGAAGC
Found at i:2348556 original size:19 final size:20
Alignment explanation
Indices: 2348532--2348579 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2348522 TAAATCATTC
2348532 TAAATAATAAT-ATATATTT
1 TAAATAATAATAATATATTT
**
2348551 TAAAT-ATTTTAATATATTT
1 TAAATAATAATAATATATTT
*
2348570 AAAATAATAA
1 TAAATAATAA
2348580 ATGAGTTTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
18 3 0.14
19 17 0.77
20 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATAATAATAATATATTT
Found at i:2355030 original size:2 final size:2
Alignment explanation
Indices: 2355023--2355063 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2355013 CTGAGTTCTT
*
2355023 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2355064 TTCTTTTGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:2359889 original size:16 final size:17
Alignment explanation
Indices: 2359864--2359896 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2359854 ATTTTCATAA
2359864 TAATTAATA-TCAATTT
1 TAATTAATATTCAATTT
*
2359880 TAATTTATATTCAATTT
1 TAATTAATATTCAATTT
2359897 CAACTTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATTAATATTCAATTT
Found at i:2360490 original size:21 final size:22
Alignment explanation
Indices: 2360464--2360508 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
2360454 TTATTTAAAA
2360464 AATATTAAAAAATTTTAT-ATT
1 AATATTAAAAAATTTTATAATT
* * *
2360485 AATATTTATATATTTTATAATT
1 AATATTAAAAAATTTTATAATT
2360507 AA
1 AA
2360509 ATTTAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTAAAAAATTTTATAATT
Found at i:2360534 original size:21 final size:20
Alignment explanation
Indices: 2360510--2360553 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2360500 TATAATTAAA
2360510 TTTAAATAAAAAATATATTAT
1 TTTAAATAAAAAAT-TATTAT
*
2360531 TTT-AATTAAAAATTATTAT
1 TTTAAATAAAAAATTATTAT
2360550 TTTA
1 TTTA
2360554 TTTCGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 9 0.43
21 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAATAAAAAATTATTAT
Found at i:2361167 original size:33 final size:34
Alignment explanation
Indices: 2361104--2361176 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 34
2361094 AATTTATTTT
*
2361104 TTATTAATTATATAAATATAAATATAATAAA-AA
1 TTATTAAATATATAAATATAAATATAATAAATAA
* ** *
2361137 TTATTAAATATATTAATATATGTATTATAAATAA
1 TTATTAAATATATAAATATAAATATAATAAATAA
2361171 TATATT
1 T-TATT
2361177 TAAACATGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 26 0.79
34 3 0.09
35 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (34 bp):
TTATTAAATATATAAATATAAATATAATAAATAA
Found at i:2366202 original size:12 final size:12
Alignment explanation
Indices: 2366178--2366225 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
2366168 GATTTAATTC
2366178 ATATTTTA-A-A
1 ATATTTTATATA
2366188 ATATTTTATATA
1 ATATTTTATATA
*
2366200 ATAATTTATATA
1 ATATTTTATATA
*
2366212 TATATTTTACATA
1 -ATATTTTATATA
2366225 A
1 A
2366226 ATATAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 8 0.25
11 1 0.03
12 13 0.41
13 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATTTTATATA
Found at i:2366229 original size:13 final size:13
Alignment explanation
Indices: 2366186--2366229 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
2366176 TCATATTTTA
2366186 AAATATTTTATAT
1 AAATATTTTATAT
*
2366199 -AATAATTTATAT
1 AAATATTTTATAT
* *
2366211 ATATATTTTACAT
1 AAATATTTTATAT
2366224 AAATAT
1 AAATAT
2366230 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATTTTATAT
Found at i:2366776 original size:21 final size:21
Alignment explanation
Indices: 2366752--2366801 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2366742 AACTTACCAG
*
2366752 AAAACCATCCATTTATATTT-A
1 AAAACCACCCATTTAT-TTTGA
* *
2366773 AAAACTACCCTTTTATTTTGA
1 AAAACCACCCATTTATTTTGA
2366794 AAAACCAC
1 AAAACCAC
2366802 TAATGTTCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAACCACCCATTTATTTTGA
Found at i:2367963 original size:16 final size:16
Alignment explanation
Indices: 2367914--2367996 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
2367904 ATGATTTTTT
2367914 ATTTTAT-TTTATTATA
1 ATTTTATATTTA-TATA
*
2367930 A--TTATATTTA-AGA
1 ATTTTATATTTATATA
2367943 TATTTTATATTTATATA
1 -ATTTTATATTTATATA
*
2367960 ATTTTGATAGTTA-AT-
1 ATTTT-ATATTTATATA
*
2367975 AGTTTATA-TTATATA
1 ATTTTATATTTATATA
2367990 GATTTTA
1 -ATTTTA
2367997 AAAATATACT
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
13 5 0.09
14 10 0.19
15 8 0.15
16 22 0.42
17 8 0.15
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATTTTATATTTATATA
Found at i:2368374 original size:10 final size:10
Alignment explanation
Indices: 2368361--2368385 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2368351 TTATTAAATT
2368361 TAATTAATAA
1 TAATTAATAA
2368371 TAATTAATAA
1 TAATTAATAA
2368381 TAATT
1 TAATT
2368386 TATTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAATTAATAA
Found at i:2368412 original size:19 final size:20
Alignment explanation
Indices: 2368378--2368426 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2368368 TAATAATTAA
*
2368378 TAATAATTTATTATATATT-TT
1 TAAT-ATTTATTATAT-TTACT
2368399 TAATATTT-TTATATTTACT
1 TAATATTTATTATATTTACT
2368418 TAATATTTA
1 TAATATTTA
2368427 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 15 0.60
20 4 0.16
21 4 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATATTTATTATATTTACT
Found at i:2368423 original size:11 final size:10
Alignment explanation
Indices: 2368368--2368426 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
2368358 ATTTAATTAA
* *
2368368 TAATAATTAA
1 TAATATTTAT
2368378 TAATAATTTAT
1 TAAT-ATTTAT
2368389 TATATATTT-T
1 TA-ATATTTAT
2368399 TAATATTT-T
1 TAATATTTAT
2368408 T-ATATTTACT
1 TAATATTTA-T
2368418 TAATATTTA
1 TAATATTTA
2368427 AAAATTTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
8 6 0.14
9 8 0.19
10 9 0.21
11 17 0.40
12 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
TAATATTTAT
Found at i:2368462 original size:17 final size:17
Alignment explanation
Indices: 2368409--2368462 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
2368399 TAATATTTTT
*
2368409 ATATTTACTTAATATTTAA
1 ATATTTA-TAAAT-TTTAA
* *
2368428 AAATTT-TAAATATTAA
1 ATATTTATAAATTTTAA
2368444 ATATTTATAAATTTTAA
1 ATATTTATAAATTTTAA
2368461 AT
1 AT
2368463 TTATATTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 9 0.31
17 15 0.52
19 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTATAAATTTTAA
Found at i:2368464 original size:15 final size:16
Alignment explanation
Indices: 2368427--2368467 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2368417 TTAATATTTA
2368427 AAAATTT-TAAATATT
1 AAAATTTATAAATATT
2368442 AAATATTTATAAAT-TT
1 AAA-ATTTATAAATATT
*
2368458 TAAATTTATA
1 AAAATTTATA
2368468 TTTGTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 8 0.35
17 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAATTTATAAATATT
Found at i:2374624 original size:3 final size:3
Alignment explanation
Indices: 2374616--2374655 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
2374606 GACTATTCTT
2374616 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2374656 GCATTTGCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2375053 original size:2 final size:2
Alignment explanation
Indices: 2375046--2375076 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2375036 ACAATAATCA
2375046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2375077 GCAGTTTTAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2375224 original size:24 final size:24
Alignment explanation
Indices: 2375208--2375269 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 24
2375198 TTATTTTATA
2375208 TTTTTAT-AATTAAATTATATAAT
1 TTTTTATAAATTAAATTATATAAT
2375231 TTTTTATAAATTAAA-TA-ATAA-
1 TTTTTATAAATTAAATTATATAAT
*
2375252 TTTTAATTAAATTAAATT
1 TTTTTA-TAAATTAAATT
2375270 TATTAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 5 0.14
22 13 0.37
23 10 0.29
24 7 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTTATAAATTAAATTATATAAT
Found at i:2375578 original size:3 final size:3
Alignment explanation
Indices: 2375570--2375599 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2375560 TTTGTAAGGA
2375570 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2375600 CATAAATCAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2381749 original size:34 final size:34
Alignment explanation
Indices: 2381705--2381772 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
2381695 AACAAACCTA
* *
2381705 TCATGCTATGTTAACTTTTTAGTTAGAATTATAT
1 TCATGCTATGTCAACTTTTTAGTTAAAATTATAT
* * *
2381739 TCATGTTATGTCAATTTTTTTGTTAAAATTATAT
1 TCATGCTATGTCAACTTTTTAGTTAAAATTATAT
2381773 AAGAAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.53
Consensus pattern (34 bp):
TCATGCTATGTCAACTTTTTAGTTAAAATTATAT
Found at i:2382372 original size:24 final size:26
Alignment explanation
Indices: 2382318--2382375 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
2382308 TGGGTGGCTA
*
2382318 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
* *
2382344 ATCAACAAAAGTCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2382368 GTCAACAA
1 GTCAACAA
2382376 TGGTGGTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 14 0.50
25 2 0.07
26 12 0.43
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:2382421 original size:24 final size:24
Alignment explanation
Indices: 2382389--2382434 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2382379 TGGTTCCTTT
2382389 TTGTTTGTCAAAAATT-ATGGCTTG
1 TTGTTTGTC-AAAATTGATGGCTTG
2382413 TTGTTTGTCAAAATTGATGGCT
1 TTGTTTGTCAAAATTGATGGCT
2382435 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.46
Consensus pattern (24 bp):
TTGTTTGTCAAAATTGATGGCTTG
Found at i:2385008 original size:21 final size:22
Alignment explanation
Indices: 2384979--2385024 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2384969 TGTTCAGACA
** *
2384979 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2385001 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2385022 AGT
1 AGT
2385025 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2386939 original size:24 final size:26
Alignment explanation
Indices: 2386888--2386945 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
2386878 TGAGTGGCTA
*
2386888 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2386914 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2386938 GTCAACAA
1 GTCAACAA
2386946 TGGTGGTTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:2386991 original size:24 final size:24
Alignment explanation
Indices: 2386959--2387004 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2386949 TGGTTCCTTT
2386959 TTGTTTGTCAAAAATT-ATGGCTTG
1 TTGTTTGTC-AAAATTGATGGCTTG
2386983 TTGTTTGTCAAAATTGATGGCT
1 TTGTTTGTCAAAATTGATGGCT
2387005 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.46
Consensus pattern (24 bp):
TTGTTTGTCAAAATTGATGGCTTG
Found at i:2387566 original size:2 final size:2
Alignment explanation
Indices: 2387559--2387601 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2387549 AGAGTTTAAG
2387559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2387601 T
1 T
2387602 GTAAAATTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2387942 original size:16 final size:17
Alignment explanation
Indices: 2387914--2387946 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2387904 TTTTATTTTA
2387914 ATAATTATTTTTAAAAT
1 ATAATTATTTTTAAAAT
2387931 ATAATT-TTTTTAAAAT
1 ATAATTATTTTTAAAAT
2387947 TTATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAATTATTTTTAAAAT
Found at i:2391889 original size:3 final size:3
Alignment explanation
Indices: 2391881--2391939 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
2391871 AAGAACCACT
*
2391881 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2391929 ATA ATA ATA AT
1 ATA ATA ATA AT
2391940 CAAATATTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2392875 original size:2 final size:2
Alignment explanation
Indices: 2392870--2392904 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2392860 TTTTTTATTA
2392870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2392905 AGACTAGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2402082 original size:21 final size:20
Alignment explanation
Indices: 2402042--2402088 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
2402032 TGTATCATCA
*
2402042 TATAAA-ATAAAAATATAAT
1 TATAAATATAAAAATAAAAT
*
2402061 TATAAATATTAAAATTAAAAT
1 TATAAATA-TAAAAATAAAAT
*
2402082 TTTAAAT
1 TATAAAT
2402089 TTATTAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 16 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TATAAATATAAAAATAAAAT
Found at i:2402967 original size:19 final size:20
Alignment explanation
Indices: 2402943--2402988 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2402933 AGATGCAATC
2402943 AATTTTTTT-AAATAAATTT
1 AATTTTTTTCAAATAAATTT
**
2402962 AATTTTTTTCATCTAAATTT
1 AATTTTTTTCAAATAAATTT
2402982 -ATTTTTT
1 AATTTTTT
2402989 AAACTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
AATTTTTTTCAAATAAATTT
Found at i:2402998 original size:18 final size:20
Alignment explanation
Indices: 2402943--2402999 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
2402933 AGATGCAATC
2402943 AATTTTTTTAAA-TAAATTT
1 AATTTTTTTAAACTAAATTT
* *
2402962 AATTTTTTTCATCTAAATTT
1 AATTTTTTTAAACTAAATTT
*
2402982 -A-TTTTTTAAACTTAATTT
1 AATTTTTTTAAACTAAATTT
2403000 TAACCTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 14 0.44
19 11 0.34
20 7 0.22
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTTTTTTAAACTAAATTT
Found at i:2404657 original size:5 final size:5
Alignment explanation
Indices: 2404647--2404688 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
2404637 AAAAAATTAA
* *
2404647 AATAT AATAT AATAT AAAAT AATATT AATAT TATA- AATAT AA
1 AATAT AATAT AATAT AATAT AATA-T AATAT AATAT AATAT AA
2404689 AATATATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 3 0.10
5 23 0.74
6 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:2404706 original size:25 final size:25
Alignment explanation
Indices: 2404647--2404698 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
2404637 AAAAAATTAA
*
2404647 AATATAATATAATATAAAATAATATT
1 AATATTATA-AATATAAAATAATATT
2404673 AATATTATAAATATAAAAT-ATATT
1 AATATTATAAATATAAAATAATATT
2404697 AA
1 AA
2404699 ATTTTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.28
25 10 0.40
26 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AATATTATAAATATAAAATAATATT
Found at i:2404789 original size:82 final size:81
Alignment explanation
Indices: 2404639--2404791 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 81
2404629 AGAACAATAA
* *
2404639 AAAATTAAAATATAATATAATATAAAATAATATTAATATTATAAATATAAAATATATTAAATTTT
1 AAAATTAAAAAATAATATAATATAAAATAATATTAATATTAAAAATATAAAATATATTAAA--TT
2404704 ATATAAAAATTTAAAATT
64 ATATAAAAATTTAAAATT
*
2404722 AAAATTAAAAAAT-ATATAA-ACTATAATAAT-TTATATATTAAAAATATATAAATATAATTTAA
1 AAAATTAAAAAATAATATAATA-TAAAATAATATTA-ATATTAAAAATATA-AAATAT-A-TTAA
2404784 A-TATATAA
61 ATTATATAA
2404792 TTACTTGATT
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
81 4 0.06
82 34 0.55
83 18 0.29
84 1 0.02
85 5 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.39
Consensus pattern (81 bp):
AAAATTAAAAAATAATATAATATAAAATAATATTAATATTAAAAATATAAAATATATTAAATTAT
ATAAAAATTTAAAATT
Found at i:2404930 original size:18 final size:19
Alignment explanation
Indices: 2404909--2404947 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2404899 AAATAATATT
2404909 TTTAAAAAATAAAATA-AA
1 TTTAAAAAATAAAATATAA
* *
2404927 TTTATAATATAAAATATAA
1 TTTAAAAAATAAAATATAA
2404946 TT
1 TT
2404948 ATATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTAAAAAATAAAATATAA
Done.