Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 11 of 125
Found at i:3672215 original size:30 final size:28
Alignment explanation
Indices: 3672168--3672447 Score: 110
Period size: 30 Copynumber: 9.6 Consensus size: 28
3672158 TGACTTTCGA
3672168 GGGTAAAAATGTA-ATTTTTGGTGAAATCG
1 GGGT-AAAATG-AGATTTTTGGTGAAATCG
*
3672197 GGGTCGAAAATGAGA-TTTTAG-GAAATTCG
1 GGGT--AAAATGAGATTTTTGGTGAAA-TCG
*
3672226 AGGAGTAAAATG-GTAATTTTGGTGAAATCG
1 -GG-GTAAAATGAG-ATTTTTGGTGAAATCG
* *
3672256 GGGTTAAAAATGGGA-TTTT-G-GAAGTTCG
1 GGG-T-AAAATGAGATTTTTGGTGAA-ATCG
*
3672284 AGGGTAAAAATG-GTAATTTTTGGTGAAACCG
1 -GGGT-AAAATGAG--ATTTTTGGTGAAATCG
3672315 GGGTTAAAATG-G-TATTTT-G-GAAAGTTCG
1 GGG-TAAAATGAGAT-TTTTGGTGAAA--TCG
*
3672343 GGGTAAAATG-GTAATTTTTGGTGAAACCG
1 GGGTAAAATGAG--ATTTTTGGTGAAATCG
3672372 GGGTTAAAATG-G-TATTTT-G-GAAAGTTCG
1 GGG-TAAAATGAGAT-TTTTGGTGAAA--TCG
3672400 GGGTAAAATG-GTAATTTTTGGTGAAATCG
1 GGGTAAAATGAG--ATTTTTGGTGAAATCG
*
3672429 GGGTTAAAAATGGGATTTT
1 GGG-T-AAAATGAGATTTT
3672448 GGAAGTTTAG
Statistics
Matches: 203, Mismatches: 9, Indels: 77
0.70 0.03 0.27
Matches are distributed among these distances:
26 8 0.04
27 24 0.12
28 36 0.18
29 50 0.25
30 56 0.28
31 25 0.12
32 4 0.02
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (28 bp):
GGGTAAAATGAGATTTTTGGTGAAATCG
Found at i:3672370 original size:57 final size:58
Alignment explanation
Indices: 3672163--3672476 Score: 437
Period size: 57 Copynumber: 5.4 Consensus size: 58
3672153 ATTTTTGACT
* *
3672163 TTCGAGGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTCGAAAATGAGATTTTAGGAAA-
1 TTCGAGGGT-AAAATGGTAATTTTTGGTGAAATCGGGGT-TAAAATGGGATTTT-GGAAAG
3672222 TTCGAGGAGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGG-AAG
1 TTCGAGG-GTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGGATTTTGGAAAG
* *
3672280 TTCGAGGGTAAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAATGGTATTTTGGAAAG
1 TTCGAGGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAG
* *
3672339 TTCG-GGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAATGGTATTTTGGAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAG
3672396 TTCG-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGG-AAG
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGGATTTTGGAAAG
*
3672453 TT-TAGGGGTAAAATGGTAATTTTT
1 TTCGA-GGGTAAAATGGTAATTTTT
3672477 TGGATAGTCC
Statistics
Matches: 238, Mismatches: 7, Indels: 21
0.89 0.03 0.08
Matches are distributed among these distances:
57 95 0.40
58 70 0.29
59 67 0.28
60 6 0.03
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (58 bp):
TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGGATTTTGGAAAG
Found at i:3672476 original size:29 final size:28
Alignment explanation
Indices: 3672231--3672475 Score: 170
Period size: 29 Copynumber: 8.5 Consensus size: 28
3672221 ATTCGAGGAG
*
3672231 TAAAATGGTAATTTTGGTGAA-ATCGGGGT
1 TAAAATGGTAATTTT-G-GAAGTTCGGGGT
*
3672260 TAAAAATGG-GATTTTGGAAGTTCGAGGGT
1 T-AAAATGGTAATTTTGGAAGTTCG-GGGT
* **
3672289 AAAAATGGTAATTTTTGGTGAA-ACCGGGGT
1 TAAAATGGTAA-TTTT-G-GAAGTTCGGGGT
3672319 TAAAATGGT-ATTTTGGAAAGTTCGGGG-
1 TAAAATGGTAATTTTGG-AAGTTCGGGGT
**
3672346 TAAAATGGTAATTTTTGGTGAA-ACCGGGGT
1 TAAAATGGTAA-TTTT-G-GAAGTTCGGGGT
3672376 TAAAATGGT-ATTTTGGAAAGTTCGGGG-
1 TAAAATGGTAATTTTGG-AAGTTCGGGGT
*
3672403 TAAAATGGTAATTTTTGGTGAA-ATCGGGGT
1 TAAAATGGTAA-TTTT-G-GAAGTTCGGGGT
* *
3672433 TAAAAATGG-GATTTTGGAAGTTTAGGGG-
1 T-AAAATGGTAATTTTGGAAG-TTCGGGGT
3672461 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
3672476 TTGGATAGTC
Statistics
Matches: 173, Mismatches: 18, Indels: 51
0.71 0.07 0.21
Matches are distributed among these distances:
26 2 0.01
27 37 0.21
28 38 0.22
29 41 0.24
30 40 0.23
31 12 0.07
32 3 0.02
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (28 bp):
TAAAATGGTAATTTTGGAAGTTCGGGGT
Found at i:3673572 original size:3 final size:3
Alignment explanation
Indices: 3673564--3673597 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3673554 TAATGCTGTA
*
3673564 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3673598 ATGTCATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3673604 original size:15 final size:15
Alignment explanation
Indices: 3673573--3673606 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3673563 AATTATTATT
*
3673573 ATTATTATTATTATC
1 ATTATTATTAATATC
*
3673588 ATTATTATTAATGTC
1 ATTATTATTAATATC
3673603 ATTA
1 ATTA
3673607 AGGTTATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (15 bp):
ATTATTATTAATATC
Found at i:3674315 original size:14 final size:14
Alignment explanation
Indices: 3674296--3674322 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3674286 TTAAATTTAA
3674296 AGTAAATTTAAATG
1 AGTAAATTTAAATG
3674310 AGTAAATTTAAAT
1 AGTAAATTTAAAT
3674323 TTAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
AGTAAATTTAAATG
Found at i:3674324 original size:31 final size:31
Alignment explanation
Indices: 3674281--3674339 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3674271 TAAATTTGAT
*
3674281 TAAACTTAAATTTAAAGTAAATTTAAATGAG
1 TAAACTTAAATTTAAAATAAATTTAAATGAG
*
3674312 TAAATTTAAATTTAAAATAAATTTAAAT
1 TAAACTTAAATTTAAAATAAATTTAAAT
3674340 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (31 bp):
TAAACTTAAATTTAAAATAAATTTAAATGAG
Found at i:3674343 original size:7 final size:6
Alignment explanation
Indices: 3674280--3674356 Score: 61
Period size: 6 Copynumber: 12.8 Consensus size: 6
3674270 TTAAATTTGA
* * *
3674280 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT GAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
* *
3674328 ATAAAT TTAAATT TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAA-T TTAAAT TTAAAT TTAAA
3674357 ACCCATTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
5 12 0.21
6 33 0.59
7 6 0.11
8 5 0.09
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:3674345 original size:18 final size:17
Alignment explanation
Indices: 3674281--3674356 Score: 86
Period size: 17 Copynumber: 4.6 Consensus size: 17
3674271 TAAATTTGAT
* *
3674281 TAAACTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
* *
3674298 TAAATTTAAA--T-GAG
1 TAAATTTAAATTTAAAA
3674312 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
3674329 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
3674347 TAAATTTAAA
1 TAAATTTAAA
3674357 ACCCATTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
14 12 0.24
15 1 0.02
16 1 0.02
17 20 0.39
18 17 0.33
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:3674352 original size:12 final size:11
Alignment explanation
Indices: 3674318--3674357 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
3674308 TGAGTAAATT
3674318 TAAATTTAAAA
1 TAAATTTAAAA
3674329 TAAATTT-AAA
1 TAAATTTAAAA
3674339 T---TTTAAAA
1 TAAATTTAAAA
3674347 TAAATTTAAAA
1 TAAATTTAAAA
3674358 CCCATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
7 3 0.12
8 4 0.16
10 4 0.16
11 14 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:3680495 original size:15 final size:14
Alignment explanation
Indices: 3680475--3680530 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
3680465 TTAATTTAAT
3680475 TTAATTTTATCAAAA
1 TTAATTTT-TCAAAA
3680490 TTAATTTTTTCAAAA
1 TTAA-TTTTTCAAAA
* *
3680505 ATAA-CTTTCTAAAA
1 TTAATTTTTC-AAAA
3680519 TTAATTTTTCAA
1 TTAATTTTTCAA
3680531 GAAAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 4 0.12
14 9 0.26
15 17 0.50
16 4 0.12
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAATTTTTCAAAA
Found at i:3683315 original size:106 final size:107
Alignment explanation
Indices: 3683194--3683405 Score: 284
Period size: 107 Copynumber: 2.0 Consensus size: 107
3683184 TTGAATGTCA
* * * *** * * *
3683194 ATTTCTTATTTGCTTTCTTTAATAATTCT-ATTTTTGAATAAATTAAAAATTATC-GTTAGTAAT
1 ATTTATTATTTGCTTTCCTTAATAATTATAATTTCAAAAAAAACTAAAAATTA-CAATTAGTAAT
* * *
3683257 TGATTTTGTATAAGCTAAAGTTAAAATATTATATTCAAACTAG
65 CGATTTTGTATAAGCTAAAGTTAAAATATTAAATCCAAACTAG
3683300 ATTTATTATTTGCTTTCCTTAATAATTATAATTTCAAAAAAAACTAAAAATTACAATTAGTAATC
1 ATTTATTATTTGCTTTCCTTAATAATTATAATTTCAAAAAAAACTAAAAATTACAATTAGTAATC
*
3683365 GATTTTGTATAAGCTAAAGTTAAAATCTTAAATCCAAACTA
66 GATTTTGTATAAGCTAAAGTTAAAATATTAAATCCAAACTA
3683406 AATGTATAAG
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
106 27 0.30
107 64 0.70
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (107 bp):
ATTTATTATTTGCTTTCCTTAATAATTATAATTTCAAAAAAAACTAAAAATTACAATTAGTAATC
GATTTTGTATAAGCTAAAGTTAAAATATTAAATCCAAACTAG
Found at i:3694104 original size:24 final size:23
Alignment explanation
Indices: 3694073--3694133 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
3694063 AAATATACGT
3694073 AATAAAATTAAAATAT-ATTAAA
1 AATAAAATTAAAATATGATTAAA
*
3694095 ATATTAAAA-TAAAACTTTGATTAAA
1 A-A-TAAAATTAAAA-TATGATTAAA
*
3694120 AATAAATTTAAAAT
1 AATAAAATTAAAAT
3694134 TTTAATAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
22 1 0.03
23 11 0.34
24 13 0.41
25 7 0.22
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
AATAAAATTAAAATATGATTAAA
Found at i:3694293 original size:12 final size:12
Alignment explanation
Indices: 3694260--3694290 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3694250 CATAAAATTT
3694260 AATAAGAATAGG
1 AATAAGAATAGG
3694272 AATAAGAATAGG
1 AATAAGAATAGG
3694284 -ATAAGAA
1 AATAAGAA
3694291 ATATTGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (12 bp):
AATAAGAATAGG
Found at i:3694676 original size:26 final size:25
Alignment explanation
Indices: 3694637--3694705 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
3694627 ACCTCTCTTA
3694637 ATAAAAATTAAAAAAATTA-ATATTT
1 ATAAAAATT-AAAAAATTATATATTT
* *
3694662 ATAAAAATTCCAAAATTTATATATTT
1 ATAAAAATT-AAAAAATTATATATTT
* *
3694688 TTAAAAAATATAAAAATT
1 ATAAAAATTA-AAAAATT
3694706 CTAAAAATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
25 16 0.46
26 19 0.54
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAAAAATTAAAAAATTATATATTT
Found at i:3694745 original size:34 final size:36
Alignment explanation
Indices: 3694661--3694730 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
3694651 AATTAATATT
* * * *
3694661 TATAAAAATTC-CAAAATTTATATATTTTTAAAAAA
1 TATAAAAATTCTAAAAATATATATATATATAAAAAA
3694696 TATAAAAATTCTAAAAATATATATATATATAAAAA
1 TATAAAAATTCTAAAAATATATATATATATAAAAA
3694731 GTTAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (36 bp):
TATAAAAATTCTAAAAATATATATATATATAAAAAA
Found at i:3695202 original size:23 final size:23
Alignment explanation
Indices: 3695175--3695228 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
3695165 AAAATTGAAT
*
3695175 TTCGAGTTAA-TTGAATCGAGTTA
1 TTCGAGTTAACTTGAAT-GAGTAA
*
3695198 TTCGAGTCAACTTGAATGAGTAA
1 TTCGAGTTAACTTGAATGAGTAA
3695221 TTCGAGTT
1 TTCGAGTT
3695229 TCGAGATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (23 bp):
TTCGAGTTAACTTGAATGAGTAA
Found at i:3695439 original size:3 final size:3
Alignment explanation
Indices: 3695427--3695468 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
3695417 CATACTAAAA
3695427 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3695469 TTACTTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:3720264 original size:30 final size:29
Alignment explanation
Indices: 3720226--3720298 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 29
3720216 GTCAACAAAT
3720226 AATTTTAAAATTATTTTTTAAAAATATAA
1 AATTTTAAAATTATTTTTTAAAAATATAA
*
3720255 AATTATTAAAATTATTTTTTTAAAATATAA
1 AATT-TTAAAATTATTTTTTAAAAATATAA
3720285 AATTTTTAAAATTA
1 AA-TTTTAAAATTA
3720299 ATTAAAATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 4 0.10
30 35 0.85
31 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATTTTAAAATTATTTTTTAAAAATATAA
Found at i:3720279 original size:14 final size:14
Alignment explanation
Indices: 3720228--3720280 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
3720218 CAACAAATAA
3720228 TTTTAAAATTATTT
1 TTTTAAAATTATTT
* **
3720242 TTTAAAAATATAAAAT
1 TTTTAAAAT-T-ATTT
*
3720258 TATTAAAATTATTT
1 TTTTAAAATTATTT
3720272 TTTTAAAAT
1 TTTTAAAAT
3720281 ATAAAATTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
14 18 0.62
15 2 0.07
16 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAAAATTATTT
Found at i:3720295 original size:39 final size:39
Alignment explanation
Indices: 3720244--3720335 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
3720234 AATTATTTTT
*
3720244 TAAAAATA-TAAAATT-ATTAAAATTATTTTTTTAAAATA
1 TAAAATTATTAAAATTAATTAAAATTA-TTTTTTAAAATA
*
3720282 TAAAATTTTTAAAATTAATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTAATTAAAATTATTTTTTAAAATA
3720321 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
3720336 CATCATCATC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
38 6 0.12
39 33 0.67
40 10 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (39 bp):
TAAAATTATTAAAATTAATTAAAATTATTTTTTAAAATA
Found at i:3720317 original size:23 final size:20
Alignment explanation
Indices: 3720261--3720330 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
3720251 ATAAAATTAT
3720261 TAAAATTATTTTTTTAAAATA
1 TAAAATTA-TTTTTTAAAATA
3720282 T-AAA--A-TTTTTAAAATTAA
1 TAAAATTATTTTTTAAAA-T-A
3720300 TTAAAATTATTTTTTAAAATA
1 -TAAAATTATTTTTTAAAATA
3720321 TAAAATTATT
1 TAAAATTATT
3720331 AAAATCATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
16 9 0.21
17 1 0.02
18 2 0.05
19 1 0.02
20 16 0.38
21 2 0.05
22 2 0.05
23 9 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAAATTATTTTTTAAAATA
Found at i:3726533 original size:31 final size:31
Alignment explanation
Indices: 3726420--3726535 Score: 107
Period size: 31 Copynumber: 3.8 Consensus size: 31
3726410 TTAATATAAC
*
3726420 ATTTGGTATCTAAACTTGACA-TTTTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTTC-TA
** *
3726451 ATTTGGTACCTAAACTT---TTTTTTTGTCCA
1 ATTTGGTACCTAAACTTGACACTTTTT-TCTA
* *
3726480 ATTTGGTA-CTCAGACTTAACACTTTTTTCTA
1 ATTTGGTACCT-AAACTTGACACTTTTTTCTA
*
3726511 ATTTAGTACCTAAACTTGACACTTT
1 ATTTGGTACCTAAACTTGACACTTT
3726536 CTTTTAAGTA
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
28 2 0.03
29 19 0.28
30 2 0.03
31 38 0.56
32 7 0.10
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.47
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTTCTA
Found at i:3726875 original size:59 final size:59
Alignment explanation
Indices: 3726803--3726947 Score: 193
Period size: 59 Copynumber: 2.5 Consensus size: 59
3726793 ATCAACTAGG
* * * * * *
3726803 AAAAAACACCAAGTTTAGGTACCAAATT-GGATCCAAAAAATTTTATGTACCAAATTAGG
1 AAAAAATATCAAGTTTAGGTACCAAATTCGG-TCAAAAAAAATTTAAGTACCAAATTAGA
** *
3726862 AAAAGTTATCAAGTTCAGGTACCAAATTCGGTCAAAAAAAATTTAAGTACCAAATTAGA
1 AAAAAATATCAAGTTTAGGTACCAAATTCGGTCAAAAAAAATTTAAGTACCAAATTAGA
3726921 AAAAAATATCAAGTTTAGGTACCAAAT
1 AAAAAATATCAAGTTTAGGTACCAAAT
3726948 GTTATATTAA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 71 0.97
60 2 0.03
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.26
Consensus pattern (59 bp):
AAAAAATATCAAGTTTAGGTACCAAATTCGGTCAAAAAAAATTTAAGTACCAAATTAGA
Found at i:3726945 original size:31 final size:31
Alignment explanation
Indices: 3726844--3726947 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 31
3726834 TCCAAAAAAT
* * **
3726844 TTTATGTACCAAATTAGGAAAAGTTATCAAG
1 TTTAGGTACCAAATTAGAAAAAAATATCAAG
* * **
3726875 TTCAGGTACCAAATTCGGTCAAAAA-A--AA-
1 TTTAGGTACCAAATT-AGAAAAAAATATCAAG
*
3726903 TTTAAGTACCAAATTAGAAAAAAATATCAAG
1 TTTAGGTACCAAATTAGAAAAAAATATCAAG
3726934 TTTAGGTACCAAAT
1 TTTAGGTACCAAAT
3726948 GTTATATTAA
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
27 6 0.11
28 14 0.25
29 2 0.04
30 2 0.04
31 27 0.49
32 4 0.07
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.28
Consensus pattern (31 bp):
TTTAGGTACCAAATTAGAAAAAAATATCAAG
Found at i:3728027 original size:13 final size:13
Alignment explanation
Indices: 3728009--3728034 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3727999 GAATATAACT
3728009 TCAAATTATCGAC
1 TCAAATTATCGAC
3728022 TCAAATTATCGAC
1 TCAAATTATCGAC
3728035 CCACAATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
TCAAATTATCGAC
Found at i:3733349 original size:22 final size:21
Alignment explanation
Indices: 3733319--3733359 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3733309 TGTTTTTAAA
* *
3733319 ATAATAAAATTTATTAAAAACG
1 ATAAAAAAAATTA-TAAAAACG
3733341 ATAAAAAAAATTATAAAAA
1 ATAAAAAAAATTATAAAAA
3733360 TTATTAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAAAAAAAATTATAAAAACG
Found at i:3735268 original size:83 final size:83
Alignment explanation
Indices: 3735129--3735282 Score: 308
Period size: 83 Copynumber: 1.9 Consensus size: 83
3735119 CCACTATCAT
3735129 TAGAGGGCTAATGTGGGGATTCGGTGATCCAACGAACTGAAGCACTACCATTTTGGGAAATTGGA
1 TAGAGGGCTAATGTGGGGATTCGGTGATCCAACGAACTGAAGCACTACCATTTTGGGAAATTGGA
3735194 CGTAACCCTCTTCATTGG
66 CGTAACCCTCTTCATTGG
3735212 TAGAGGGCTAATGTGGGGATTCGGTGATCCAACGAACTGAAGCACTACCATTTTGGGAAATTGGA
1 TAGAGGGCTAATGTGGGGATTCGGTGATCCAACGAACTGAAGCACTACCATTTTGGGAAATTGGA
3735277 CGTAAC
66 CGTAAC
3735283 TACCATTTTG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (83 bp):
TAGAGGGCTAATGTGGGGATTCGGTGATCCAACGAACTGAAGCACTACCATTTTGGGAAATTGGA
CGTAACCCTCTTCATTGG
Found at i:3735291 original size:26 final size:26
Alignment explanation
Indices: 3735255--3735308 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
3735245 GAACTGAAGC
3735255 ACTACCATTTTGGGAAATTGGACGTA
1 ACTACCATTTTGGGAAATTGGACGTA
3735281 ACTACCATTTTGGGAAATTGGACGTA
1 ACTACCATTTTGGGAAATTGGACGTA
3735307 AC
1 AC
3735309 CCTCTTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (26 bp):
ACTACCATTTTGGGAAATTGGACGTA
Found at i:3735363 original size:109 final size:109
Alignment explanation
Indices: 3735172--3735391 Score: 431
Period size: 109 Copynumber: 2.0 Consensus size: 109
3735162 GAACTGAAGC
3735172 ACTACCATTTTGGGAAATTGGACGTAACCCTCTTCATTGGTAGAGGGCTAATGTGGGGATTCGGT
1 ACTACCATTTTGGGAAATTGGACGTAACCCTCTTCATTGGTAGAGGGCTAATGTGGGGATTCGGT
*
3735237 GATCCAACGAACTGAAGCACTACCATTTTGGGAAATTGGACGTA
66 GATCCAACGAACTGAAGCACCACCATTTTGGGAAATTGGACGTA
3735281 ACTACCATTTTGGGAAATTGGACGTAACCCTCTTCATTGGTAGAGGGCTAATGTGGGGATTCGGT
1 ACTACCATTTTGGGAAATTGGACGTAACCCTCTTCATTGGTAGAGGGCTAATGTGGGGATTCGGT
3735346 GATCCAACGAACTGAAGCACCACCATTTTGGGAAATTGGACGTA
66 GATCCAACGAACTGAAGCACCACCATTTTGGGAAATTGGACGTA
3735390 AC
1 AC
3735392 CCTCTTCATT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (109 bp):
ACTACCATTTTGGGAAATTGGACGTAACCCTCTTCATTGGTAGAGGGCTAATGTGGGGATTCGGT
GATCCAACGAACTGAAGCACCACCATTTTGGGAAATTGGACGTA
Found at i:3738571 original size:42 final size:39
Alignment explanation
Indices: 3738500--3738618 Score: 211
Period size: 42 Copynumber: 3.0 Consensus size: 39
3738490 TGGCTTCAAC
3738500 TTTCACAATCTCCTTCTTTTCTTCCTTACCCTCCATTGG
1 TTTCACAATCTCCTTCTTTTCTTCCTTACCCTCCATTGG
3738539 TTTCACAATCTCCTTCTTCTTTTCTTCCTTACCCTCCATTGG
1 TTTCACAATCT-C--CTTCTTTTCTTCCTTACCCTCCATTGG
3738581 TTTCACAATCTCCTTCTTTTCTTCCTTACCCTCCATTG
1 TTTCACAATCTCCTTCTTTTCTTCCTTACCCTCCATTG
3738619 TTTTTGAGCT
Statistics
Matches: 77, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
39 37 0.48
40 1 0.01
41 1 0.01
42 38 0.49
ACGTcount: A:0.13, C:0.36, G:0.04, T:0.47
Consensus pattern (39 bp):
TTTCACAATCTCCTTCTTTTCTTCCTTACCCTCCATTGG
Found at i:3740006 original size:22 final size:22
Alignment explanation
Indices: 3739981--3740064 Score: 53
Period size: 27 Copynumber: 3.5 Consensus size: 22
3739971 CAACTTTTTT
3739981 AATTTATAATAATTCTAAATTA
1 AATTTATAATAATTCTAAATTA
*
3740003 AATTCATCAACATATAATTCTAAATTA
1 AATT--T--ATA-ATAATTCTAAATTA
* * *
3740030 AATATTAT-ATTATTTTAAATTTT
1 AAT-TTATAATAATTCTAAA-TTA
3740053 AATTTAGTAATA
1 AATTTA-TAATA
3740065 TGTTAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
22 16 0.34
23 6 0.13
24 4 0.09
26 3 0.06
27 17 0.36
28 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (22 bp):
AATTTATAATAATTCTAAATTA
Found at i:3755617 original size:14 final size:13
Alignment explanation
Indices: 3755581--3755619 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
3755571 TCAAACAATA
3755581 AAAATATAATAGT
1 AAAATATAATAGT
*
3755594 AACAACATAATAGT
1 AA-AATATAATAGT
3755608 AAAATGATAATA
1 AAAAT-ATAATA
3755620 AAATAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (13 bp):
AAAATATAATAGT
Found at i:3755623 original size:11 final size:11
Alignment explanation
Indices: 3755577--3755649 Score: 65
Period size: 11 Copynumber: 6.6 Consensus size: 11
3755567 ATGTTCAAAC
* *
3755577 AATAAAAATAT
1 AATAATAATAA
* *
3755588 AATAGTAACAA
1 AATAATAATAA
* *
3755599 CATAATAGTAA
1 AATAATAATAA
*
3755610 AATGATAATAA
1 AATAATAATAA
*
3755621 AATAATAAGAA
1 AATAATAATAA
*
3755632 AACAATAATAA
1 AATAATAATAA
3755643 AATAATA
1 AATAATA
3755650 GCAAAACAGC
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 46 1.00
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.23
Consensus pattern (11 bp):
AATAATAATAA
Found at i:3755625 original size:22 final size:21
Alignment explanation
Indices: 3755600--3755657 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
3755590 TAGTAACAAC
**
3755600 ATAATAGTAAAATGATAATAAA
1 ATAATAG-AAAACAATAATAAA
3755622 ATAATAAGAAAACAATAATAAA
1 ATAAT-AGAAAACAATAATAAA
3755644 ATAATAGCAAAACA
1 ATAATAG-AAAACA
3755658 GCAAGAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (21 bp):
ATAATAGAAAACAATAATAAA
Found at i:3755666 original size:22 final size:22
Alignment explanation
Indices: 3755619--3755666 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
3755609 AAATGATAAT
* *
3755619 AAAATAATAAGAAAACAATAAT
1 AAAATAATAAGAAAACAACAAG
*
3755641 AAAATAAT-AGCAAAACAGCAAG
1 AAAATAATAAG-AAAACAACAAG
3755663 AAAA
1 AAAA
3755667 CAACAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.71, C:0.08, G:0.08, T:0.12
Consensus pattern (22 bp):
AAAATAATAAGAAAACAACAAG
Found at i:3757741 original size:15 final size:16
Alignment explanation
Indices: 3757716--3757745 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3757706 ATTAATAGAA
3757716 TGACATAATTTAACAG
1 TGACATAATTTAACAG
3757732 TGAC-TAATTTAACA
1 TGACATAATTTAACA
3757746 TTAAACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (16 bp):
TGACATAATTTAACAG
Found at i:3759413 original size:16 final size:16
Alignment explanation
Indices: 3759392--3759427 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3759382 GTTAATCGCT
3759392 CTAACCAGGGATGAAG
1 CTAACCAGGGATGAAG
3759408 CTAACCAGGGATGAAG
1 CTAACCAGGGATGAAG
3759424 CTAA
1 CTAA
3759428 GAAGGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (16 bp):
CTAACCAGGGATGAAG
Found at i:3761592 original size:20 final size:18
Alignment explanation
Indices: 3761541--3761592 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
3761531 GGGATATTTT
*
3761541 TATTTATTTAATATTAATA
1 TATTTTTTTAAT-TTAATA
*
3761560 TAATTTTTT-ATTTAATTA
1 TATTTTTTTAATTTAA-TA
3761578 TATTTTTTTCAATTT
1 TATTTTTTT-AATTT
3761593 TCTAATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.15
18 12 0.44
19 7 0.26
20 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTTTTTAATTTAATA
Found at i:3762276 original size:96 final size:96
Alignment explanation
Indices: 3762153--3762347 Score: 227
Period size: 96 Copynumber: 2.0 Consensus size: 96
3762143 AATTAAATAG
* * *
3762153 TAAGGACTTAAAATGAGAAATATATCATACTTC-AAAATAGATTAATTATAGAAGTCAAAAAATT
1 TAAGGACTCAAAATGAGAAATATATCATACTTCAAAAAT-GACTAATTATAAAAGT-AAAAAATT
*
3762217 -AATTAGACCTTAACATGTAATATCCCACAATTAT
64 GAATT-GACATTAACATGTAAT-TCCCACAATTAT
* * *
3762251 TAAGGAC-CAAAAT-AGAAATGTATCATACTTTAAAAATGCCTAATTATAAAAGTAAAAAATTGA
1 TAAGGACTCAAAATGAGAAATATATCATACTTCAAAAATGACTAATTATAAAAGTAAAAAATTGA
* * * *
3762314 ATTGATATTAACGTGTGATTTCCACAATTAT
66 ATTGACATTAACATGTAATTCCCACAATTAT
3762345 TAA
1 TAA
3762348 AATAAATTTG
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
94 14 0.17
95 20 0.24
96 33 0.39
97 10 0.12
98 7 0.08
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.31
Consensus pattern (96 bp):
TAAGGACTCAAAATGAGAAATATATCATACTTCAAAAATGACTAATTATAAAAGTAAAAAATTGA
ATTGACATTAACATGTAATTCCCACAATTAT
Found at i:3764474 original size:87 final size:91
Alignment explanation
Indices: 3764063--3764474 Score: 280
Period size: 92 Copynumber: 4.5 Consensus size: 91
3764053 TATTTTTCAA
* * * * * * *
3764063 AATAATTATATTAATCATTATTTATTTCATTTCATTTTCAAGGAACTTCG-GCTTGAGT-ATGTG
1 AATAACTATAATAATCACTATTTATTTCCTTTCA-TTTCGAGGCACTT-GAGCTTGAGTCATATG
* * * *
3764126 ATTGTAATGATT-TTTTTTAAATTTT-TGG
64 -CTGCAA-CATTATTTTTTTAATTTTCTGG
* * * ** * * *
3764154 GATAATTATAATAATCACTATTTTTTTTAATTTCACTTTCG-GTGCACTTGGGTTTAAGTC---T
1 AATAACTATAATAATCACTA-TTTATTTCCTTTCA-TTTCGAG-GCACTTGAGCTTGAGTCATAT
* * *
3764215 GGTGCTACATTTTTTTTTTTAATTTTCTAGG
63 GCTGCAACA-TTATTTTTTTAATTTTCT-GG
* ** *
3764246 AA-AACTATAAAAATCACTATTTATTT-CTCTTCATTTTTAGGTCACTTGAGCTTGAGTCTTATG
1 AATAACTATAATAATCACTATTTATTTCCT-TTCATTTCGAGG-CACTTGAGCTTGAGTCATATG
* *
3764309 CTGCAACATTTTTTTTTTAATTTTCGGG
64 CTGCAACATTATTTTTTTAATTTTCTGG
* * *
3764337 GATAACTATAATAATCACTATTTATTTCATTTCATTTGCGGGGCACTTGAGCTTG-GTCA-ATTG
1 AATAACTATAATAATCACTATTTATTTCCTTTCATTT-CGAGGCACTTGAGCTTGAGTCATA-TG
3764400 CTGC-A-A-TATTTTTTTAA-TTTCTGG
64 CTGCAACATTATTTTTTTAATTTTCTGG
* * *
3764424 AATAAGTATAATAATAACTATTTATTTCCTTTCATTCTCGAGGCATTTGAG
1 AATAACTATAATAATCACTATTTATTTCCTTTCATT-TCGAGGCACTTGAG
3764475 TTTAGGTCCA
Statistics
Matches: 259, Mismatches: 43, Indels: 42
0.75 0.12 0.12
Matches are distributed among these distances:
87 49 0.19
88 12 0.05
89 11 0.04
90 40 0.15
91 47 0.18
92 89 0.34
93 11 0.04
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.47
Consensus pattern (91 bp):
AATAACTATAATAATCACTATTTATTTCCTTTCATTTCGAGGCACTTGAGCTTGAGTCATATGCT
GCAACATTATTTTTTTAATTTTCTGG
Found at i:3776929 original size:60 final size:60
Alignment explanation
Indices: 3776832--3776953 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
3776822 ATATTACATG
*
3776832 TAATTTTATAATAAATAAAAATTTAACTAAACCATAAATTCTCTCTTGGATTTAATAACA
1 TAATTTTATAATAAATAAAAATTTAACTAAACCATAAATTCTATCTTGGATTTAATAACA
*
3776892 TAATTTTATAATAAATAAAAATTTAACTAAACTATAAATTCTATCTTGGATTTAATAACA
1 TAATTTTATAATAAATAAAAATTTAACTAAACCATAAATTCTATCTTGGATTTAATAACA
3776952 TA
1 TA
3776954 TGCAATGATA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (60 bp):
TAATTTTATAATAAATAAAAATTTAACTAAACCATAAATTCTATCTTGGATTTAATAACA
Found at i:3788566 original size:69 final size:70
Alignment explanation
Indices: 3788419--3788559 Score: 176
Period size: 69 Copynumber: 2.0 Consensus size: 70
3788409 TTAATAATGT
* **
3788419 TATAATGTAATTATAATAGTTTGAAGTTTGAGAACCAATTTAAAATTAAAATAATAATTTGGGAT
1 TATAAT-TAATTAGAATAGTTTGAAGTTTGAGAACCAATTTAAAATTAAAATAATAATTTGCAAT
**
3788484 GCTTAA
65 GCGGAA
* * * *
3788490 TATAATTAATTAGAATAG-TTGAAGTTTGAGAACTAATTTGAAATTAAAATTATAGTTTGCAATG
1 TATAATTAATTAGAATAGTTTGAAGTTTGAGAACCAATTTAAAATTAAAATAATAATTTGCAATG
3788554 TCGGAA
66 -CGGAA
3788560 GTAATTACCT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
69 40 0.67
70 14 0.23
71 6 0.10
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.38
Consensus pattern (70 bp):
TATAATTAATTAGAATAGTTTGAAGTTTGAGAACCAATTTAAAATTAAAATAATAATTTGCAATG
CGGAA
Found at i:3788702 original size:11 final size:11
Alignment explanation
Indices: 3788686--3788724 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
3788676 ACAGTAAAAT
3788686 TATTTTATTTA
1 TATTTTATTTA
3788697 TATTTTATTTA
1 TATTTTATTTA
*
3788708 TAATTTAATATTA
1 T-ATTTTAT-TTA
3788721 TATT
1 TATT
3788725 AATATTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 12 0.48
12 9 0.36
13 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTTATTTA
Found at i:3791404 original size:32 final size:30
Alignment explanation
Indices: 3791335--3791409 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
3791325 TGATACTTAA
* *
3791335 ATTTTTTGTCTAATTTAGTATCTAAATTTG
1 ATTTTTTTTTTAATTTAGTATCTAAATTTG
* *
3791365 ATATTTTTTTTAATTTGGTATCTAAATTTG
1 ATTTTTTTTTTAATTTAGTATCTAAATTTG
*
3791395 ACATTTTTTTCTTAA
1 --ATTTTTTTTTTAA
3791410 GTTAACACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 26 0.70
32 11 0.30
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.59
Consensus pattern (30 bp):
ATTTTTTTTTTAATTTAGTATCTAAATTTG
Found at i:3794014 original size:30 final size:31
Alignment explanation
Indices: 3793975--3794034 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3793965 CAAAACGGTC
*
3793975 TAAATTATTTG-AAGTTTTCATTTAAGTCAT
1 TAAACTATTTGAAAGTTTTCATTTAAGTCAT
*
3794005 TAAACTATTTGAAAGTTTTTATTTAAGTCA
1 TAAACTATTTGAAAGTTTTCATTTAAGTCA
3794035 CTAGATTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (31 bp):
TAAACTATTTGAAAGTTTTCATTTAAGTCAT
Found at i:3800735 original size:27 final size:27
Alignment explanation
Indices: 3800684--3800736 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3800674 ATCTAGTAAA
*
3800684 TTTTTAAAAATTTAAGGAGTTTAATTT
1 TTTTTAAAAATTTAAGGAGTCTAATTT
*
3800711 TTTTTAAAAATATTGAGG-GTCTAATT
1 TTTTTAAAAAT-TTAAGGAGTCTAATT
3800737 ACAATTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (27 bp):
TTTTTAAAAATTTAAGGAGTCTAATTT
Found at i:3809219 original size:23 final size:23
Alignment explanation
Indices: 3809192--3809244 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3809182 TAAATTTTTT
*
3809192 ATTTAATTAT-TTAAAAATTATA
1 ATTTAATTATCGTAAAAATTATA
* *
3809214 TTTTTATTATCGTAAAAATTATA
1 ATTTAATTATCGTAAAAATTATA
3809237 ATTTAATT
1 ATTTAATT
3809245 TCGACCCCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTAATTATCGTAAAAATTATA
Found at i:3810120 original size:3 final size:3
Alignment explanation
Indices: 3810112--3810136 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3810102 GTCGTTTACG
3810112 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
3810137 AAACAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:3820771 original size:8 final size:8
Alignment explanation
Indices: 3820758--3820789 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3820748 GATTTGGAAC
3820758 TATGATAT
1 TATGATAT
3820766 TATGATAT
1 TATGATAT
3820774 TATGATAT
1 TATGATAT
*
3820782 TACGATAT
1 TATGATAT
3820790 GGTGCATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (8 bp):
TATGATAT
Found at i:3823037 original size:20 final size:20
Alignment explanation
Indices: 3823002--3823039 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3822992 TAATTACTTC
3823002 GTAACAAAACGATAACATAA
1 GTAACAAAACGATAACATAA
3823022 GTAACTAAAACG-TAACAT
1 GTAAC-AAAACGATAACAT
3823040 TTTAAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (20 bp):
GTAACAAAACGATAACATAA
Found at i:3823526 original size:2 final size:2
Alignment explanation
Indices: 3823519--3823550 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3823509 TCATTATGAA
3823519 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
3823551 CACACACAAA
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:3823958 original size:8 final size:8
Alignment explanation
Indices: 3823945--3823971 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3823935 CCTAACCTTG
3823945 AACTCTAA
1 AACTCTAA
3823953 AACTCTAA
1 AACTCTAA
3823961 AACTCTAA
1 AACTCTAA
3823969 AAC
1 AAC
3823972 CTTAAACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (8 bp):
AACTCTAA
Found at i:3824221 original size:21 final size:21
Alignment explanation
Indices: 3824163--3824222 Score: 57
Period size: 25 Copynumber: 2.7 Consensus size: 21
3824153 TTTTTGAAAT
*
3824163 ATCATTAAATAATTGAAAGGA
1 ATCATAAAATAATTGAAAGGA
*
3824184 ATCATGGATAATGTAATTGAAAGGA
1 ATCAT--A-AA-ATAATTGAAAGGA
*
3824209 TTCATAAAATAATT
1 ATCATAAAATAATT
3824223 TCTCATGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
21 10 0.32
22 2 0.06
23 1 0.03
24 2 0.06
25 16 0.52
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.32
Consensus pattern (21 bp):
ATCATAAAATAATTGAAAGGA
Found at i:3826241 original size:35 final size:35
Alignment explanation
Indices: 3826202--3826277 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
3826192 AATTATGTTA
3826202 AAAATTAATGAATAAAGAATAGAGAGACCAAAAAT
1 AAAATTAATGAATAAAGAATAGAGAGACCAAAAAT
* * *
3826237 AAAATTAATGAATAGAGAATAGAGGGACCAAAAGT
1 AAAATTAATGAATAAAGAATAGAGAGACCAAAAAT
3826272 AAAATT
1 AAAATT
3826278 TAAACATTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.18
Consensus pattern (35 bp):
AAAATTAATGAATAAAGAATAGAGAGACCAAAAAT
Found at i:3826703 original size:22 final size:22
Alignment explanation
Indices: 3826656--3826707 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3826646 AAAATTTTCA
*
3826656 ATAAATA-AAAATATAAAAAAT
1 ATAAATATTAAATATAAAAAAT
*
3826677 TTAAATATTAAAT-TAAAATAAT
1 ATAAATATTAAATATAAAA-AAT
3826699 ATAAATATT
1 ATAAATATT
3826708 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAAATATTAAATATAAAAAAT
Found at i:3830993 original size:3 final size:3
Alignment explanation
Indices: 3830985--3831013 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3830975 TCTTGATTGA
3830985 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3831014 CAATAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3841809 original size:16 final size:17
Alignment explanation
Indices: 3841788--3841822 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3841778 ACATCAGGAG
3841788 TGGAG-TATCCCAATTT
1 TGGAGTTATCCCAATTT
3841804 TGGAGTTATCCCAATTT
1 TGGAGTTATCCCAATTT
3841821 TG
1 TG
3841823 AAGGATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (17 bp):
TGGAGTTATCCCAATTT
Found at i:3842369 original size:23 final size:21
Alignment explanation
Indices: 3842338--3842383 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3842328 AATAACTTCA
3842338 TTAACTCAAATAACTTGAATTAT
1 TTAACTC-AA-AACTTGAATTAT
* *
3842361 TTAATTCAAAATTTGAATTAT
1 TTAACTCAAAACTTGAATTAT
3842382 TT
1 TT
3842384 TTTAGCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 2 0.10
23 6 0.29
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAACTCAAAACTTGAATTAT
Found at i:3843613 original size:12 final size:12
Alignment explanation
Indices: 3843596--3843620 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3843586 CAAGGAGTGT
3843596 CTAGACCAATGC
1 CTAGACCAATGC
3843608 CTAGACCAATGC
1 CTAGACCAATGC
3843620 C
1 C
3843621 AACCGATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (12 bp):
CTAGACCAATGC
Found at i:3844669 original size:26 final size:26
Alignment explanation
Indices: 3844620--3844669 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
3844610 TATGTTTTAA
* * *
3844620 ATTATAAAAATTTAATTGACTTTTTC
1 ATTAAAAAAATCTAATTAACTTTTTC
3844646 ATTAAAAAAATCTAATTAA-TTTTT
1 ATTAAAAAAATCTAATTAACTTTTT
3844670 ACTTATCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (26 bp):
ATTAAAAAAATCTAATTAACTTTTTC
Found at i:3847132 original size:22 final size:22
Alignment explanation
Indices: 3847037--3847134 Score: 65
Period size: 22 Copynumber: 4.5 Consensus size: 22
3847027 AAAGCACCGT
* *
3847037 AGTGCTAAACATAGAGCAAAAA
1 AGTGCTAAACAAAGAGCACAAA
*
3847059 AGTGCT-AACAAGAGAGCACCAA
1 AGTGCTAAACAA-AGAGCACAAA
*** * * **
3847081 AGTGCTGGTCAGAGAGTACCGTA
1 AGTGCTAAACAAAGAGCA-CAAA
*
3847104 A-TACTAAACAAAGAGCACAAA
1 AGTGCTAAACAAAGAGCACAAA
3847125 AGTGCTAAAC
1 AGTGCTAAAC
3847135 TCGTACAAAC
Statistics
Matches: 54, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
21 7 0.13
22 42 0.78
23 5 0.09
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (22 bp):
AGTGCTAAACAAAGAGCACAAA
Found at i:3848569 original size:7 final size:7
Alignment explanation
Indices: 3848527--3848568 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
3848517 CCTGATTCTT
3848527 AAAATTA
1 AAAATTA
3848534 AAAATTA
1 AAAATTA
3848541 AAAATTA
1 AAAATTA
3848548 AAAATTA
1 AAAATTA
*
3848555 AAATATTT
1 AAA-ATTA
3848563 AAAATT
1 AAAATT
3848569 TTATTTTACG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
AAAATTA
Found at i:3872957 original size:18 final size:18
Alignment explanation
Indices: 3872934--3872968 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3872924 AAAATAAATT
3872934 AAAATAAATCAAAAGTCC
1 AAAATAAATCAAAAGTCC
*
3872952 AAAATAAATTAAAAGTC
1 AAAATAAATCAAAAGTC
3872969 TTTTAAATTA
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:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAATAAATCAAAAGTCC
Found at i:3874995 original size:21 final size:21
Alignment explanation
Indices: 3874971--3875011 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3874961 TAGTAGTTTT
3874971 CATACTTGTATCGGTAGAAAC
1 CATACTTGTATCGGTAGAAAC
* * *
3874992 CATATTTTTATTGGTAGAAA
1 CATACTTGTATCGGTAGAAA
3875012 ACTGCAGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (21 bp):
CATACTTGTATCGGTAGAAAC
Found at i:3876953 original size:15 final size:15
Alignment explanation
Indices: 3876933--3876961 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3876923 TGTATAAAAG
3876933 GTTAAAAAATTGTAT
1 GTTAAAAAATTGTAT
3876948 GTTAAAAAATTGTA
1 GTTAAAAAATTGTA
3876962 GAATCGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (15 bp):
GTTAAAAAATTGTAT
Found at i:3881042 original size:13 final size:13
Alignment explanation
Indices: 3881010--3881042 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3881000 AATTTGGACC
3881010 TTTAA-TTAAATT
1 TTTAATTTAAATT
3881022 TTTAAATTTAAATT
1 TTT-AATTTAAATT
3881036 TTTAATT
1 TTTAATT
3881043 CGAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 6 0.32
14 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAATTTAAATT
Found at i:3881811 original size:39 final size:39
Alignment explanation
Indices: 3881764--3881846 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
3881754 TGGCGGAAAG
* *
3881764 GATCAAATGACTGT-AATCTGCCCCTGGCTCGGGGTAAGA
1 GATCAAATG-CTGTCAATCTGCCCCTCGCTCGGGGCAAGA
* * * *
3881803 GATCAAATGGTTTCAATTTGCCCCTCGTTCGGGGCAAGA
1 GATCAAATGCTGTCAATCTGCCCCTCGCTCGGGGCAAGA
3881842 GATCA
1 GATCA
3881847 GAATCTTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 2 0.05
39 35 0.95
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
GATCAAATGCTGTCAATCTGCCCCTCGCTCGGGGCAAGA
Found at i:3882047 original size:76 final size:76
Alignment explanation
Indices: 3881918--3882831 Score: 1390
Period size: 76 Copynumber: 12.0 Consensus size: 76
3881908 ATCTCCACTA
** *
3881918 GCTCTTACTTCAATTTCAGAGGGACGAAGGCTTGATATCCAACTTTACTTCAATTTCAAGAGGAT
1 GCTCTTACTTCAATTTCAGA--GATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGAT
3881983 AGAAAATGATCTT
64 AGAAAATGATCTT
* *
3881996 GCTCTTACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTCAAGAGGATA-
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
3882060 AGAAATGATCTT
66 A-AAATGATCTT
* * *
3882072 ACTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
*
3882137 GAAATGATCTT
66 AAAATGATCTT
*
3882148 GCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAAC-TTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATA-
3882212 GAAAA-GATCTT
65 GAAAATGATCTT
* * *
3882223 GTTCTTACTTCAATTTCAGAGAGACGAAGGCTTGATATCCAACTTTACTTCAATTTCAAGAGGAT
1 GCTCTTACTTCAATTTCAGAGATA--AAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGAT
3882288 AGAAAATGATCTT
64 AGAAAATGATCTT
* * *
3882301 GCTCTTACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATTTTAAGAGGATA-
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
3882365 AGAAATGATCTT
66 A-AAATGATCTT
* * *
3882377 ACTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCATCTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
*
3882442 GAAATGATCTT
66 AAAATGATCTT
* * * * *
3882453 GCTCTTACTTCAATTTCAAAGATAAAGACTTGTTATCCAACTCTACTTCAATTACAAGAGGATCG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
*
3882518 GAAATGATCTT
66 AAAATGATCTT
*
3882529 GCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAAC-TTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATA-
3882593 GAAAA-GATCTT
65 GAAAATGATCTT
**
3882604 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGTTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
*
3882669 GAAATGATCTT
66 AAAATGATCTT
* * *
3882680 ACTCTTACTTCAATTTCAGAGATAAAAACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
*
3882745 GAAATGATCTT
66 AAAATGATCTT
*
3882756 GCTCTTACTTCAATTTCAGAGATAAAAACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
*
3882821 GAAATGATCTT
66 AAAATGATCTT
3882832 AGTGCTTCAT
Statistics
Matches: 770, Mismatches: 54, Indels: 26
0.91 0.06 0.03
Matches are distributed among these distances:
75 118 0.15
76 561 0.73
77 21 0.03
78 70 0.09
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (76 bp):
GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAG
AAAATGATCTT
Found at i:3882122 original size:152 final size:152
Alignment explanation
Indices: 3881919--3882999 Score: 1608
Period size: 152 Copynumber: 7.0 Consensus size: 152
3881909 TCTCCACTAG
** *
3881919 CTCTTACTTCAATTTCAGAGGGACGAAGGCTTGATATCCAACTTTACTTCAATTTCAAGAGGATA
1 CTCTTACTTCAATTTCAGAGATA-G-AGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATA
* * *
3881984 GAAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATT
64 GGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATT
*
3882049 TCAAGAGGATAAGAAATGATCTTA
129 TCAAGAGGATAGGAAATGATCTTA
*
3882073 CTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGG
*
3882138 AAATGATCTTGCTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAAC-TTACTTCAATTTC
66 AAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTC
* *
3882202 AAGAGGATAGGAAAAGATCTTG
131 AAGAGGATAGGAAATGATCTTA
* * *
3882224 TTCTTACTTCAATTTCAGAGAGACGAAGGCTTGATATCCAACTTTACTTCAATTTCAAGAGGATA
1 CTCTTACTTCAATTTCAGAGATA-G-AGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATA
* * *
3882289 GAAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACCTGATATCCAGCTTTACTTCAATT
64 GGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATT
* *
3882354 TTAAGAGGATAAGAAATGATCTTA
129 TCAAGAGGATAGGAAATGATCTTA
*
3882378 CTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCATCTTTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGG
* * * *
3882443 AAATGATCTTGCTCTTACTTCAATTTCAAAGATAAAGACTTGTTATCCAACTCTACTTCAATTAC
66 AAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTC
* *
3882508 AAGAGGATCGGAAATGATCTTG
131 AAGAGGATAGGAAATGATCTTA
* *
3882530 CTCTTACTTCAATTTCGGAGATAAAGACTTGATATCCAAC-TTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGG
* **
3882594 AAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGTTTTACTTCAATTTC
66 AAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTC
3882659 AAGAGGATAGGAAATGATCTTA
131 AAGAGGATAGGAAATGATCTTA
* * *
3882681 CTCTTACTTCAATTTCAGAGATAAAAACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGG
*
3882746 AAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAAACTTGATATCCAACTTTACTTCAATTTC
66 AAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTC
3882811 AAGAGGATAGGAAATGATCTTAGTGCTTCATCTTA
131 AAGAGGATAGG--A--A----A-TG----ATCTTA
* * * *
3882846 CTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAACTCTACTTCAATTTCAAGAGGATA
1 CTCTTACTTCAATTTCAG--AGATAGAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATA
* *
3882911 GGAAATGATATTACTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATT
64 GGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATT
3882976 TCAAGAGGATAGGAAATGATCTTA
129 TCAAGAGGATAGGAAATGATCTTA
3883000 GTGCTTCATC
Statistics
Matches: 843, Mismatches: 65, Indels: 38
0.89 0.07 0.04
Matches are distributed among these distances:
151 192 0.23
152 335 0.40
153 88 0.10
154 80 0.09
156 1 0.00
158 2 0.00
159 1 0.00
160 1 0.00
161 2 0.00
163 1 0.00
165 25 0.03
167 115 0.14
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (152 bp):
CTCTTACTTCAATTTCAGAGATAGAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGG
AAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTC
AAGAGGATAGGAAATGATCTTA
Found at i:3882904 original size:91 final size:89
Alignment explanation
Indices: 3882751--3882919 Score: 275
Period size: 91 Copynumber: 1.9 Consensus size: 89
3882741 ATAGGAAATG
* * *
3882751 ATCTTGCTCTTACTTCAATTTCAGAGATAAAAACTTGATATCCAACTTTACTTCAATTTCAAGAG
1 ATCTTACTCTTACTTCAATTTCAGAGACAAAAACTTGATATCCAACTCTACTTCAATTTCAAGAG
3882816 GATAGGAAATGATCTTAGTGCTTC
66 GATAGGAAATGATCTTAGTGCTTC
**
3882840 ATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAACTCTACTTCAATTTCAAG
1 ATCTTACTCTTACTTCAATTTCAG--AGACAAAAACTTGATATCCAACTCTACTTCAATTTCAAG
3882905 AGGATAGGAAATGAT
64 AGGATAGGAAATGAT
3882920 ATTACTCTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
89 23 0.32
91 50 0.68
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (89 bp):
ATCTTACTCTTACTTCAATTTCAGAGACAAAAACTTGATATCCAACTCTACTTCAATTTCAAGAG
GATAGGAAATGATCTTAGTGCTTC
Found at i:3882940 original size:38 final size:39
Alignment explanation
Indices: 3882877--3882995 Score: 140
Period size: 38 Copynumber: 3.1 Consensus size: 39
3882867 GACAAAGGCT
3882877 TGATATCCAACTC-TACTTCAATTTCAAGAGGATAGGAAA
1 TGATAT-CAACTCTTACTTCAATTTCAAGAGGATAGGAAA
* * **
3882916 TGATAT-TACTCTTACTTCAATTTC-AGA-GATAAAGACT
1 TGATATCAACTCTTACTTCAATTTCAAGAGGAT-AGGAAA
3882953 TGATATCCAACT-TTACTTCAATTTCAAGAGGATAGGAAA
1 TGATAT-CAACTCTTACTTCAATTTCAAGAGGATAGGAAA
3882992 TGAT
1 TGAT
3882996 CTTAGTGCTT
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
36 3 0.05
37 16 0.24
38 25 0.38
39 19 0.29
40 3 0.05
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (39 bp):
TGATATCAACTCTTACTTCAATTTCAAGAGGATAGGAAA
Found at i:3882956 original size:167 final size:167
Alignment explanation
Indices: 3882675--3883080 Score: 726
Period size: 167 Copynumber: 2.4 Consensus size: 167
3882665 ATAGGAAATG
* ** *
3882675 ATCTTACTCTTACTTCAATTTCAG--AGATAAAAACTTGATATCCAGCTTTACTTCAATTTCAAG
1 ATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAG
* *
3882738 AGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAAACTTGATATCCAACTTTACT
66 AGGATAGGAAATGATATTACTCTTACTTCAATTTCAGAGATAAAAACTTGATATCCAACTTTACT
3882803 TCAATTTCAAGAGGATAGGAAATGATCTTAGTGCTTC
131 TCAATTTCAAGAGGATAGGAAATGATCTTAGTGCTTC
*
3882840 ATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAACTCTACTTCAATTTCAAG
1 ATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAG
*
3882905 AGGATAGGAAATGATATTACTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACT
66 AGGATAGGAAATGATATTACTCTTACTTCAATTTCAGAGATAAAAACTTGATATCCAACTTTACT
3882970 TCAATTTCAAGAGGATAGGAAATGATCTTAGTGCTTC
131 TCAATTTCAAGAGGATAGGAAATGATCTTAGTGCTTC
3883007 ATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAG
1 ATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAG
3883072 AGGATAGGA
66 AGGATAGGA
3883081 CTTGTCATTT
Statistics
Matches: 230, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
165 24 0.10
167 206 0.90
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (167 bp):
ATCTTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAG
AGGATAGGAAATGATATTACTCTTACTTCAATTTCAGAGATAAAAACTTGATATCCAACTTTACT
TCAATTTCAAGAGGATAGGAAATGATCTTAGTGCTTC
Found at i:3882973 original size:76 final size:77
Alignment explanation
Indices: 3882843--3882995 Score: 263
Period size: 76 Copynumber: 2.0 Consensus size: 77
3882833 GTGCTTCATC
*
3882843 TTACTCTTACTTCAATTTCAGATAGACAAAGGCTTGATATCCAACTCTACTTCAATTTCAAGAGG
1 TTACTCTTACTTCAATTTCAGA-AGACAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGG
3882908 ATAGGAAATGATA
65 ATAGGAAATGATA
* *
3882921 TTACTCTTACTTCAATTTCAG-AGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGA
1 TTACTCTTACTTCAATTTCAGAAGACAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGA
3882985 TAGGAAATGAT
66 TAGGAAATGAT
3882996 CTTAGTGCTT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
76 51 0.71
78 21 0.29
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (77 bp):
TTACTCTTACTTCAATTTCAGAAGACAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGA
TAGGAAATGATA
Found at i:3883363 original size:51 final size:50
Alignment explanation
Indices: 3883259--3883379 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 50
3883249 TCATGTATCG
* * * *
3883259 CCGTTACGA-CTTAGATCTTTCTCGTCGTGTCTTCGTGGTACTAGATCTG
1 CCGTTGCGATCTTAGATCTTTCCCGTCGTATCTTCGTGGTACTAGATCTA
* * * *
3883308 CCGTTGCGATCTTAGATCTTTCCCTTCTGTATCTTTGTGGTACTGGATTTA
1 CCGTTGCGATCTTAGATCTTTCCCGTC-GTATCTTCGTGGTACTAGATCTA
*
3883359 CCGTTGCGGTCTTAGATCTTT
1 CCGTTGCGATCTTAGATCTTT
3883380 TCGGTCCATG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 8 0.13
50 15 0.25
51 38 0.62
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.42
Consensus pattern (50 bp):
CCGTTGCGATCTTAGATCTTTCCCGTCGTATCTTCGTGGTACTAGATCTA
Found at i:3883445 original size:50 final size:50
Alignment explanation
Indices: 3883391--3883594 Score: 122
Period size: 50 Copynumber: 4.1 Consensus size: 50
3883381 CGGTCCATGC
*
3883391 TTTTGAGGTACACGG-TCCGCAGTTGCGACTTAGACCTTTCCCTTTTCTGT
1 TTTTGAGGTACACGGATCCACAGTTGCGACTTAGACCTTT-CCTTTTCTGT
* ** * * *
3883441 TTTTGAAGTA-TTGGATCTGC-CA-TTGTGACTTAGACCTTTTCTTGT-TGT
1 TTTTGAGGTACACGGATC--CACAGTTGCGACTTAGACCTTTCCTTTTCTGT
* * * * * * *
3883489 GTTTT-ATGGTGC-TGGATCCACCGTTGCGGTCTTAGATCTTT--TTGGTCCATGC
1 -TTTTGA-GGTACACGGATCCACAGTTGC-GACTTAGACCTTTCCTT--TTC-TGT
3883541 TTTTGAGGTACACGG-TCCACAGTTGCGACTTAGACCTTTCCCTTTTCTGT
1 TTTTGAGGTACACGGATCCACAGTTGCGACTTAGACCTTT-CCTTTTCTGT
3883591 TTTT
1 TTTT
3883595 AAAGTACTGG
Statistics
Matches: 114, Mismatches: 22, Indels: 36
0.66 0.13 0.21
Matches are distributed among these distances:
47 1 0.01
48 7 0.06
49 21 0.18
50 55 0.48
51 22 0.19
52 6 0.05
53 2 0.02
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (50 bp):
TTTTGAGGTACACGGATCCACAGTTGCGACTTAGACCTTTCCTTTTCTGT
Found at i:3883537 original size:150 final size:150
Alignment explanation
Indices: 3883358--3883652 Score: 527
Period size: 150 Copynumber: 2.0 Consensus size: 150
3883348 TACTGGATTT
*
3883358 ACCGTTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCGCAGTTGCGACTTA
1 ACCGTTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCACAGTTGCGACTTA
* * *
3883423 GACCTTTCCCTTTTCTGTTTTTGAAGTATTGGATCTGCCATTGTGACTTAGACCTTTTCTTGTTG
66 GACCTTTCCCTTTTCTGTTTTTAAAGTACTGGATCTGCCATTATGACTTAGACCTTTTCTTGTTG
3883488 TGTTTTATGGTGCTGGATCC
131 TGTTTTATGGTGCTGGATCC
*
3883508 ACCGTTGCGGTCTTAGATCTTTTTGGTCCATGCTTTTGAGGTACACGGTCCACAGTTGCGACTTA
1 ACCGTTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCACAGTTGCGACTTA
*
3883573 GACCTTTCCCTTTTCTGTTTTTAAAGTACTGGATCTGCCATTATGACTTAGACTTTTTCTTGTTG
66 GACCTTTCCCTTTTCTGTTTTTAAAGTACTGGATCTGCCATTATGACTTAGACCTTTTCTTGTTG
*
3883638 TGTTTTGTGGTGCTG
131 TGTTTTATGGTGCTG
3883653 AGACCTATAA
Statistics
Matches: 138, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 138 1.00
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.42
Consensus pattern (150 bp):
ACCGTTGCGGTCTTAGATCTTTTCGGTCCATGCTTTTGAGGTACACGGTCCACAGTTGCGACTTA
GACCTTTCCCTTTTCTGTTTTTAAAGTACTGGATCTGCCATTATGACTTAGACCTTTTCTTGTTG
TGTTTTATGGTGCTGGATCC
Found at i:3891987 original size:13 final size:13
Alignment explanation
Indices: 3891955--3891987 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3891945 AATTTGGACC
3891955 TTTAA-TTAAATT
1 TTTAATTTAAATT
3891967 TTTAAATTTAAATT
1 TTT-AATTTAAATT
3891981 TTTAATT
1 TTTAATT
3891988 CGAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 6 0.32
14 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAATTTAAATT
Found at i:3897227 original size:18 final size:18
Alignment explanation
Indices: 3897204--3897244 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3897194 AATCTATGGG
3897204 TTGGATTTT-GATGGAATA
1 TTGGATTTTGGA-GGAATA
*
3897222 TTGGATTTTGGAGGAATC
1 TTGGATTTTGGAGGAATA
3897240 TTGGA
1 TTGGA
3897245 GGGAGCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.24, C:0.02, G:0.32, T:0.41
Consensus pattern (18 bp):
TTGGATTTTGGAGGAATA
Found at i:3897401 original size:60 final size:60
Alignment explanation
Indices: 3897308--3897428 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
3897298 ATCTACATTT
3897308 CTTTATTAATAGTCTAGAAGAAAAGGTGGAGTATACAACAAAGAGAGCATCTTACACGTA
1 CTTTATTAATAGTCTAGAAGAAAAGGTGGAGTATACAACAAAGAGAGCATCTTACACGTA
3897368 CTTTATTAATAGTCTAGAAGAAAAGGTGGAGTATACAACAAAGAGAGCATCTTACACGTA
1 CTTTATTAATAGTCTAGAAGAAAAGGTGGAGTATACAACAAAGAGAGCATCTTACACGTA
3897428 C
1 C
3897429 AAGGGAAACA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (60 bp):
CTTTATTAATAGTCTAGAAGAAAAGGTGGAGTATACAACAAAGAGAGCATCTTACACGTA
Found at i:3908140 original size:12 final size:12
Alignment explanation
Indices: 3908123--3908147 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3908113 AAAAAGAATC
3908123 AAAGATAAAGGA
1 AAAGATAAAGGA
3908135 AAAGATAAAGGA
1 AAAGATAAAGGA
3908147 A
1 A
3908148 TTTCGAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (12 bp):
AAAGATAAAGGA
Found at i:3913152 original size:2 final size:2
Alignment explanation
Indices: 3913097--3913137 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3913087 ATATGATGTG
3913097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3913138 AAATTTGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3913707 original size:37 final size:38
Alignment explanation
Indices: 3913657--3913759 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 38
3913647 TTCGAAGCAA
* *
3913657 TAAAGTGACACCCAGTGTCTCATCG-GTCTAGCCGAAG
1 TAAAGTGATACCCAGTGTCTCATCGAATCTAGCCGAAG
* ** *
3913694 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGATACCCAGTGTCTCATCGAATCTAGCCGAAG
* *
3913732 TAAAATAATGACACCAGTGTCTCATCGA
1 TAAAGTGAT-AC-CCAGTGTCTCATCGA
3913760 CTCATGGTCG
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
37 21 0.40
38 16 0.31
39 2 0.04
40 13 0.25
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (38 bp):
TAAAGTGATACCCAGTGTCTCATCGAATCTAGCCGAAG
Found at i:3914604 original size:2 final size:2
Alignment explanation
Indices: 3914597--3914633 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3914587 TCTTATTTCT
3914597 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 T
3914634 TAGTTAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3920109 original size:2 final size:2
Alignment explanation
Indices: 3920102--3920148 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3920092 TTAATTTACA
3920102 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
3920144 -T AT AT
1 AT AT AT
3920149 GCTTACATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3921308 original size:23 final size:23
Alignment explanation
Indices: 3921272--3921321 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3921262 TAATTTTTAA
*
3921272 ATTTTTAAAGATAAAATTATATTT
1 ATTTTTAAAGATAAAATT-TAATT
* *
3921296 ATTTTT-AATATAATATTTAATT
1 ATTTTTAAAGATAAAATTTAATT
3921318 ATTT
1 ATTT
3921322 ATATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 9 0.39
24 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTTTAAAGATAAAATTTAATT
Found at i:3923112 original size:21 final size:21
Alignment explanation
Indices: 3923086--3923128 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3923076 TTAATCCCAT
3923086 TTTATTATTAAA-ATCTATTTA
1 TTTATTATTAAATATC-ATTTA
*
3923107 TTTATTTTTAAATATCATTTA
1 TTTATTATTAAATATCATTTA
3923128 T
1 T
3923129 ATTTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATTATTAAATATCATTTA
Found at i:3929087 original size:29 final size:29
Alignment explanation
Indices: 3929055--3929116 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
3929045 AAACGGGACC
*
3929055 TTTGGA-TGCCCGGGGGT-GAAATGGTAATT
1 TTTGGACT-CCCGGGGGTAAAAAT-GTAATT
*
3929084 TTT-GACTTCCGGGGGTAAAAATGTAATT
1 TTTGGACTCCCGGGGGTAAAAATGTAATT
3929112 TTTGG
1 TTTGG
3929117 TGAAATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (29 bp):
TTTGGACTCCCGGGGGTAAAAATGTAATT
Found at i:3929160 original size:58 final size:58
Alignment explanation
Indices: 3929094--3929401 Score: 331
Period size: 58 Copynumber: 5.3 Consensus size: 58
3929084 TTTGACTTCC
* *
3929094 GGGGGTAAAAAT-GTAATTTTTGGTGAAATTAGAGTCAAAATGGAATTTTGAAAAGTTT
1 GGGGGT-AAAATGGTAATTTTTGGTGAAATTAGGGTAAAAATGGAATTTTGAAAAGTTT
* * * * * * * *
3929152 GCGAGTAAAACGATAATTTTTGGTGAAATT-GGAGCTAAAAAAGGGATTTTG-GAAGGTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGG-G-TAAAAATGGAATTTTGAAAAGTTT
* ** *
3929210 GAGGGGTAAAATAGTAATTTTTGGTGAAATCCGGGTAAAAAT-GAGATTTTGGAAAGTTT
1 G-GGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTAAAAATGGA-ATTTTGAAAAGTTT
** * *
3929269 GGGGGTAAAATGGT-ATTTTTTATGAAATTAGGGTTAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTAAAAATGGAATTTTGAAAAGTTT
* *
3929326 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAATGCAATTTT-AGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTAAAAATGGAATTTTGA-AAAGTTT
*
3929384 AGGGGTAAAATGGTAATT
1 GGGGGTAAAATGGTAATT
3929402 ATCTAAAAGT
Statistics
Matches: 209, Mismatches: 31, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
57 55 0.26
58 109 0.52
59 43 0.21
60 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTAAAAATGGAATTTTGAAAAGTTT
Found at i:3929274 original size:29 final size:29
Alignment explanation
Indices: 3929242--3929401 Score: 88
Period size: 29 Copynumber: 5.6 Consensus size: 29
3929232 GGTGAAATCC
3929242 GGGTAAAAAT-GAGATTTTGGAAAGTTTGG
1 GGGTAAAAATGGA-ATTTTGGAAAGTTTGG
* * *
3929271 GGGT-AAAATGGTATTTTTTATGAAA--TT-A
1 GGGTAAAAATGG-A-ATTTT-GGAAAGTTTGG
*
3929299 GGGTTAAAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAAATGGAATTTTGGAAAGTTTGG
*
3929328 GGGT-AAAATGGTAATTTTTGGTGAAA--TT-A
1 GGGTAAAAATGG-AA-TTTT-G-GAAAGTTTGG
* * * *
3929357 GGGTTAAAATGCAATTTTAGAAAGTTTAG
1 GGGTAAAAATGGAATTTTGGAAAGTTTGG
3929386 GGGT-AAAATGGTAATT
1 GGGTAAAAATGG-AATT
3929402 ATCTAAAAGT
Statistics
Matches: 103, Mismatches: 12, Indels: 32
0.70 0.08 0.22
Matches are distributed among these distances:
26 8 0.08
27 4 0.04
28 31 0.30
29 34 0.33
30 17 0.17
31 5 0.05
32 4 0.04
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTGGAAAGTTTGG
Found at i:3929278 original size:28 final size:28
Alignment explanation
Indices: 3929242--3929401 Score: 114
Period size: 28 Copynumber: 5.5 Consensus size: 28
3929232 GGTGAAATCC
3929242 GGGTAAAAAT-GAGATTTTGGAAAGTTTGG
1 GGGT-AAAATGGA-ATTTTGGAAAGTTTGG
* * *
3929271 GGGTAAAATGGTATTTTTTATGAAA--TTAG
1 GGGTAAAATGG-A-ATTTT-GGAAAGTTTGG
*
3929300 GGTTAAAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAATGGAATTTTGGAAAGTTTGG
*
3929328 GGGTAAAATGGTAATTTTTGGTGAAA--TTAG
1 GGGTAAAATGG-AA-TTTT-G-GAAAGTTTGG
* * * *
3929358 GGTTAAAATGCAATTTTAGAAAGTTTAG
1 GGGTAAAATGGAATTTTGGAAAGTTTGG
3929386 GGGTAAAATGGTAATT
1 GGGTAAAATGG-AATT
3929402 ATCTAAAAGT
Statistics
Matches: 104, Mismatches: 15, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
26 8 0.08
27 4 0.04
28 36 0.35
29 26 0.25
30 21 0.20
31 5 0.05
32 4 0.04
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.36
Consensus pattern (28 bp):
GGGTAAAATGGAATTTTGGAAAGTTTGG
Found at i:3929366 original size:115 final size:114
Alignment explanation
Indices: 3929094--3929398 Score: 339
Period size: 115 Copynumber: 2.6 Consensus size: 114
3929084 TTTGACTTCC
* * * * *
3929094 GGGGGTAAAAATGTAATTTTTGGTGAAATTAGAGTCAAAATG-GAATTTTGAAAAGTTTGCGAGT
1 GGGGGT-AAAATGTAATTTTTGGTGAAATTAGGGTAAAAATGAG-ATTTTGGAAAGTTTGGGGGT
* * * *
3929158 AAAACGATAATTTTTGGTGAAATTGGAGCTAAAAAAGGGATTTTGGAAGGTT
64 AAAATGGT-ATTTTTGATGAAATTGGAGCTAAAAAAGGAATTTTGGAAGGTT
**
3929210 GAGGGGTAAAATAGTAATTTTTGGTGAAATCCGGGTAAAAATGAGATTTTGGAAAGTTTGGGGGT
1 G-GGGGTAAAAT-GTAATTTTTGGTGAAATTAGGGTAAAAATGAGATTTTGGAAAGTTTGGGGGT
* * * *
3929275 AAAATGGTATTTTTTATGAAATTAGG-G-TTAAAATGGAATTTTGGAAAGTTT
64 AAAATGGTATTTTTGATGAAATT-GGAGCTAAAAAAGGAATTTTGG-AAGGTT
* * *
3929326 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAATGCA-ATTTTAGAAAGTTTAGGGGT
1 GGGGGTAAAAT-GTAATTTTTGGTGAAATTAGGGTAAAAATG-AGATTTTGGAAAGTTTGGGGGT
3929390 AAAATGGTA
64 AAAATGGTA
3929399 ATTATCTAAA
Statistics
Matches: 162, Mismatches: 21, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
115 78 0.48
116 27 0.17
117 56 0.35
118 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (114 bp):
GGGGGTAAAATGTAATTTTTGGTGAAATTAGGGTAAAAATGAGATTTTGGAAAGTTTGGGGGTAA
AATGGTATTTTTGATGAAATTGGAGCTAAAAAAGGAATTTTGGAAGGTT
Found at i:3929773 original size:32 final size:33
Alignment explanation
Indices: 3929709--3929778 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
3929699 AATTATCGGG
* *
3929709 CCAAATTAAAAATAATTAAAAGTATGAAAAGGA
1 CCAAATTAAAAATAATTAAAAATACGAAAAGGA
*
3929742 CCAAATT-AAAATAATTAAAAAATACG-GAAGGA
1 CCAAATTAAAAATAATT-AAAAATACGAAAAGGA
3929774 CCAAA
1 CCAAA
3929779 CGCGTAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 19 0.58
33 14 0.42
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (33 bp):
CCAAATTAAAAATAATTAAAAATACGAAAAGGA
Found at i:3931384 original size:17 final size:17
Alignment explanation
Indices: 3931364--3931425 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
3931354 ATTTAATTTA
*
3931364 AAATTTGAATTTATAAT
1 AAATTTAAATTTATAAT
*
3931381 AAATTTAAATTT-TATAC
1 AAATTTAAATTTATA-AT
*
3931398 AAATTTAAATTTAAAAT
1 AAATTTAAATTTATAAT
*
3931415 AAATCTAAATT
1 AAATTTAAATT
3931426 AAAACTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
16 2 0.05
17 35 0.92
18 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (17 bp):
AAATTTAAATTTATAAT
Found at i:3931388 original size:34 final size:35
Alignment explanation
Indices: 3931349--3931427 Score: 83
Period size: 34 Copynumber: 2.3 Consensus size: 35
3931339 GACATTGGAC
* * *
3931349 ATTTAATTTAATTTA-AAATTTGAATTTATAATAA
1 ATTTAATTTAATATACAAATTTAAATTTAAAATAA
3931383 ATTTAAATTT--TATACAAATTTAAATTTAAAATAA
1 ATTT-AATTTAATATACAAATTTAAATTTAAAATAA
* *
3931417 ATCTAAATTAA
1 ATTTAATTTAA
3931428 AACTAAATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
33 7 0.19
34 24 0.67
35 5 0.14
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46
Consensus pattern (35 bp):
ATTTAATTTAATATACAAATTTAAATTTAAAATAA
Found at i:3931434 original size:17 final size:17
Alignment explanation
Indices: 3931371--3931435 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
3931361 TTAAAATTTG
* *
3931371 AATTTATAATAAATTTA
1 AATTTAAAATAAATCTA
* * * *
3931388 AATTTTATACAAATTTA
1 AATTTAAAATAAATCTA
3931405 AATTTAAAATAAATCTA
1 AATTTAAAATAAATCTA
3931422 AA-TTAAAACTAAAT
1 AATTTAAAA-TAAAT
3931436 TCATTGGACC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
16 6 0.15
17 33 0.85
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTAAAATAAATCTA
Found at i:3931436 original size:34 final size:34
Alignment explanation
Indices: 3931364--3931436 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
3931354 ATTTAATTTA
* * * * *
3931364 AAATTTGAATTTATAATAAATTTAAATTTTATAC
1 AAATTTAAATTTAAAATAAATCTAAATTTAAAAC
3931398 AAATTTAAATTTAAAATAAATCTAAA-TTAAAAC
1 AAATTTAAATTTAAAATAAATCTAAATTTAAAAC
3931431 TAAATT
1 -AAATT
3931437 CATTGGACCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 5 0.15
34 28 0.85
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (34 bp):
AAATTTAAATTTAAAATAAATCTAAATTTAAAAC
Found at i:3934588 original size:14 final size:14
Alignment explanation
Indices: 3934556--3934582 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3934546 ATGTTATATT
3934556 ATTAAATATAAATA
1 ATTAAATATAAATA
3934570 ATTAAATATAAAT
1 ATTAAATATAAAT
3934583 GTTTAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTAAATATAAATA
Found at i:3948447 original size:2 final size:2
Alignment explanation
Indices: 3948442--3948477 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3948432 AAATGAGGGG
*
3948442 GA GA GA GA GA GA GA GA CA 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 GA
3948478 ATCAATTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3953523 original size:18 final size:18
Alignment explanation
Indices: 3953487--3953525 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3953477 TTTTAACTCA
* *
3953487 CTTTCATATAACAGGTTG
1 CTTTCATAAAACACGTTG
*
3953505 CTTTCATAAAACACTTTG
1 CTTTCATAAAACACGTTG
3953523 CTT
1 CTT
3953526 AAATGTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (18 bp):
CTTTCATAAAACACGTTG
Found at i:3962244 original size:22 final size:24
Alignment explanation
Indices: 3962218--3962273 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 24
3962208 GGTCATGATT
3962218 TTAAAAATTAAGAA-A-ATAT-AAA
1 TTAAAAATTAA-AAGATATATAAAA
3962240 TT-AAAATTAAAAGATATATAAAA
1 TTAAAAATTAAAAGATATATAAAA
3962263 TTCAAAAATTA
1 TT-AAAAATTA
3962274 TTAAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.07
21 9 0.31
22 6 0.21
23 5 0.17
25 7 0.24
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
TTAAAAATTAAAAGATATATAAAA
Found at i:3962269 original size:18 final size:16
Alignment explanation
Indices: 3962241--3962298 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
3962231 AAATATAAAT
3962241 TAAAATTAAAAGATATA
1 TAAAATTAAAA-ATATA
3962258 TAAAATTCAAAAAT-TA
1 TAAAATT-AAAAATATA
3962274 TTAAAATTAATAAAATATA
1 -TAAAATT-A-AAAATATA
3962293 TAAAAT
1 TAAAAT
3962299 ACTCAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 2 0.06
17 17 0.47
18 15 0.42
19 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
TAAAATTAAAAATATA
Found at i:3962528 original size:18 final size:18
Alignment explanation
Indices: 3962505--3962582 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 18
3962495 CCTTTTTTTA
*
3962505 TTTATAATTTTT-TAGTAT
1 TTTATAATTTTTATA-AAT
3962523 TTTATATATTTTTATAAAT
1 TTTATA-ATTTTTATAAAT
* *
3962542 TTTAATAATTTTT-GAATT
1 TTT-ATAATTTTTATAAAT
3962560 TTATATTAATTTTT-TAAAT
1 TT-TA-TAATTTTTATAAAT
3962579 TTTA
1 TTTA
3962583 ATTTATATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
18 14 0.28
19 31 0.62
20 5 0.10
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTATAATTTTTATAAAT
Found at i:3962535 original size:19 final size:19
Alignment explanation
Indices: 3962505--3962582 Score: 76
Period size: 20 Copynumber: 4.2 Consensus size: 19
3962495 CCTTTTTTTA
*
3962505 TTTATA-ATTTTTTAGTAT
1 TTTATATATTTTTTAGAAT
3962523 TTTATATATTTTTATA-AAT
1 TTTATATATTTTT-TAGAAT
*
3962542 TTTA-ATAATTTTT-GAAT
1 TTTATATATTTTTTAGAAT
3962559 TTTATATTAATTTTTTA-AAT
1 TTTATA-T-ATTTTTTAGAAT
3962579 TTTA
1 TTTA
3962583 ATTTATATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
17 8 0.16
18 14 0.28
19 13 0.26
20 15 0.30
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTATATATTTTTTAGAAT
Found at i:3962536 original size:10 final size:9
Alignment explanation
Indices: 3962505--3962582 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 9
3962495 CCTTTTTTTA
3962505 TTTATAATT
1 TTTATAATT
*
3962514 TTT-TAGTAT
1 TTTATAAT-T
3962523 TTTATATATT
1 TTTATA-ATT
3962533 TTTATAAATT
1 TTTAT-AATT
*
3962543 TTAATAATT
1 TTTATAATT
*
3962552 TTT-GAATT
1 TTTATAATT
3962560 TTATATTAATT
1 TT-TA-TAATT
*
3962571 TTT-TAAAT
1 TTTATAATT
3962579 TTTA
1 TTTA
3962583 ATTTATATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
8 16 0.30
9 14 0.26
10 16 0.30
11 8 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTATAATT
Found at i:3962593 original size:20 final size:20
Alignment explanation
Indices: 3962527--3962593 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
3962517 TAGTATTTTA
3962527 TATATTTTTATAAATTTTAA--
1 TATA-TTTT-TAAATTTTAATT
*
3962547 TA-ATTTTTGAATTTTATATT
1 TATATTTTTAAATTTTA-ATT
*
3962567 AAT-TTTTTAAATTTTAATT
1 TATATTTTTAAATTTTAATT
3962586 TATATTTT
1 TATATTTT
3962594 CTTAATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
17 8 0.21
18 5 0.13
19 6 0.16
20 19 0.50
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (20 bp):
TATATTTTTAAATTTTAATT
Found at i:3969485 original size:20 final size:21
Alignment explanation
Indices: 3969456--3969494 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3969446 ATTTTAACAT
3969456 TAATAATTTTAA-ATTTTAAG
1 TAATAATTTTAATATTTTAAG
*
3969476 TAATATTTTTAATATTTTA
1 TAATAATTTTAATATTTTA
3969495 TTTACAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TAATAATTTTAATATTTTAAG
Found at i:3969646 original size:15 final size:16
Alignment explanation
Indices: 3969626--3969658 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3969616 ACATAAAAAA
3969626 TAGAAA-ATATTTTAT
1 TAGAAATATATTTTAT
*
3969641 TAGAAATATTTTTTAT
1 TAGAAATATATTTTAT
3969657 TA
1 TA
3969659 TTATTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TAGAAATATATTTTAT
Found at i:3978198 original size:23 final size:23
Alignment explanation
Indices: 3978167--3978233 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
3978157 GAGTTAAGGT
3978167 TATTAATATTTGAGCATAAATCA
1 TATTAATATTTGAGCATAAATCA
* *
3978190 TATTGATATTTAAGCATAAATCA
1 TATTAATATTTGAGCATAAATCA
* *
3978213 CATTAATATTTGAACATAAAT
1 TATTAATATTTGAGCATAAAT
3978234 AGTTAAGAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (23 bp):
TATTAATATTTGAGCATAAATCA
Found at i:3981605 original size:30 final size:28
Alignment explanation
Indices: 3981540--3981924 Score: 253
Period size: 29 Copynumber: 13.2 Consensus size: 28
3981530 CAAAAATCAT
* *
3981540 ATTTTAACTCTCGAA-TTTATCTAAAATTAT
1 ATTTTAAC-CTCAAACTTT-TC-AAAATTAC
*
3981570 ATTTTAACCTCAAACTTCTTCAAAATTGC
1 ATTTTAACCTCAAACTT-TTCAAAATTAC
*
3981599 ATTTTTATCCT-AAACTTTTCTAAAATTAC
1 A-TTTTAACCTCAAACTTTTC-AAAATTAC
* *
3981628 ATTTTCACCTTAAACTTTTCCAAAATTAC
1 ATTTTAACCTCAAACTTTT-CAAAATTAC
* * *
3981657 ATTTTGACC-CTAAACCTTTCTAAAATCAC
1 ATTTTAACCTC-AAACTTTTC-AAAATTAC
* *
3981686 ATTTTAACCCTAAAACTTTTCTAAAATCAC
1 ATTTTAA-CCTCAAACTTTTC-AAAATTAC
* * *
3981716 ATTTTAACCCCCAAACTTTTCTAAAATCAT
1 ATTTTAA-CCTCAAACTTTTC-AAAATTAC
* * * *
3981746 ATTTTTATCC-CAAACTTCTCCAGAATCAC
1 A-TTTTAACCTCAAACTT-TTCAAAATTAC
* *
3981775 ATTTTAACCATCAAACCTTCTCAAAATCAC
1 ATTTTAACC-TCAAA-CTTTTCAAAATTAC
* *
3981805 ATTTTAACC-CTAAACTTCTCCAAAATTAT
1 ATTTTAACCTC-AAACTT-TTCAAAATTAC
* * *
3981834 ATTTTAACC-CTAAAGTTTCCCAAATTAC
1 ATTTTAACCTC-AAACTTTTCAAAATTAC
* *
3981862 ATTTTTACCCTTAAACTTTTCCAAAATTAC
1 A-TTTTAACCTCAAACTTTT-CAAAATTAC
* *
3981892 ATTTTAACCTCGAACTCTTCAAAACTT-C
1 ATTTTAACCTCAAACTTTTCAAAA-TTAC
3981920 ATTTT
1 ATTTT
3981925 TGGCACGTGG
Statistics
Matches: 293, Mismatches: 41, Indels: 44
0.78 0.11 0.12
Matches are distributed among these distances:
28 43 0.15
29 139 0.47
30 102 0.35
31 9 0.03
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (28 bp):
ATTTTAACCTCAAACTTTTCAAAATTAC
Found at i:3981643 original size:58 final size:58
Alignment explanation
Indices: 3981559--3981900 Score: 302
Period size: 58 Copynumber: 5.8 Consensus size: 58
3981549 CTCGAATTTA
* * * * * *
3981559 TCTAAAATTATATTTTAA-CCTCAAACTTCTTCAAAATTGCATTTTTATCCTAAACTTT
1 TCTAAAATCACATTTTAACCCTTAAACTT-TTCAAAATTACATTTTAACCCTAAACTTT
* * * *
3981617 TCTAAAATTACATTTTCA-CCTTAAACTTTTCCAAAATTACATTTTGACCCTAAACCTT
1 TCTAAAATCACATTTTAACCCTTAAACTTTT-CAAAATTACATTTTAACCCTAAACTTT
* * *
3981675 TCTAAAATCACATTTTAACCCTAAAACTTTTCTAAAATCACATTTTAACCCCCAAACTTT
1 TCTAAAATCACATTTTAACCCTTAAACTTTTC-AAAATTACATTTTAA-CCCTAAACTTT
* * * * * * *
3981735 TCTAAAATCATATTTTTATCCC--AAACTTCTCCAGAATCACATTTTAACCATCAAAC-CT
1 TCTAAAATCACA-TTTTAACCCTTAAACTT-TTCAAAATTACATTTTAACCCT-AAACTTT
* * *
3981793 TCTCAAAATCACATTTTAACCC-TAAACTTCTCCAAAATTATATTTTAACCCTAAA-GTT
1 TCT-AAAATCACATTTTAACCCTTAAACTT-TTCAAAATTACATTTTAACCCTAAACTTT
** * *
3981851 TCCCAAATTACATTTTTACCCTTAAACTTTTCCAAAATTACATTTTAACC
1 TCTAAAATCACATTTTAACCCTTAAACTTTT-CAAAATTACATTTTAACC
3981901 TCGAACTCTT
Statistics
Matches: 238, Mismatches: 34, Indels: 24
0.80 0.11 0.08
Matches are distributed among these distances:
57 18 0.08
58 109 0.46
59 81 0.34
60 22 0.09
61 8 0.03
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.38
Consensus pattern (58 bp):
TCTAAAATCACATTTTAACCCTTAAACTTTTCAAAATTACATTTTAACCCTAAACTTT
Found at i:3982000 original size:30 final size:30
Alignment explanation
Indices: 3981966--3982377 Score: 213
Period size: 30 Copynumber: 14.2 Consensus size: 30
3981956 GTTTTGGATT
*
3981966 AAAATGTAATTTT-GGAAATTTTTAAGGGTA
1 AAAATGTAATTTTAGGAAA-GTTTAAGGGTA
* * * *
3981996 AAAATGTCATTTTGGGAAAGTTT-GGGGTG
1 AAAATGTAATTTTAGGAAAGTTTAAGGGTA
*
3982025 AAAATGTAATTTT-GGAAAGTTTTAGGGGTA
1 AAAATGTAATTTTAGGAAAG-TTTAAGGGTA
*
3982055 AAAATGTCATTTTAGG-AAGTTTAAGGGTA
1 AAAATGTAATTTTAGGAAAGTTTAAGGGTA
* * * **
3982084 AAAATATGATTTTTGG--AGTTCGA-GG-A
1 AAAATGTAATTTTAGGAAAGTTTAAGGGTA
* **
3982110 AAAATGTAATTTTTGG-AAGTTTGGGGGTA
1 AAAATGTAATTTTAGGAAAGTTTAAGGGTA
* **
3982139 AAATATG--ATTTTTGG-AAGTTCGAGGG-A
1 AAA-ATGTAATTTTAGGAAAGTTTAAGGGTA
* *
3982166 AAAATGTAAATTTT--GAGAAGTTTAGGGGTT
1 AAAATGT-AATTTTAGGA-AAGTTTAAGGGTA
* * * *
3982196 AAAATGCAATTTTTGGAAAGTTTGAGAGTA
1 AAAATGTAATTTTAGGAAAGTTTAAGGGTA
* *
3982226 AAAATATGAATTTT-GG-AAG-TTATGCGGT-
1 AAAATGT-AATTTTAGGAAAGTTTAAG-GGTA
* *
3982254 AAAATGCAATTTT-TGAGAAGTTT-AGGAGTA
1 AAAATGTAATTTTAGGA-AAGTTTAAGG-GTA
* * * *
3982284 AAAATGTGATTTTTGG-AAGTTCATGGGTA
1 AAAATGTAATTTTAGGAAAGTTTAAGGGTA
* * *
3982313 AAAATGTAATTTTTA-AAAAGTTTAGGGGTT
1 AAAATGTAA-TTTTAGGAAAGTTTAAGGGTA
* * * * *
3982343 AAAATATGATTTTAGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTAGGAAAGTTTAAGGGTA
3982373 AAAAT
1 AAAAT
3982378 ATGATTTTTG
Statistics
Matches: 303, Mismatches: 51, Indels: 56
0.74 0.12 0.14
Matches are distributed among these distances:
26 18 0.06
27 19 0.06
28 39 0.13
29 96 0.32
30 115 0.38
31 16 0.05
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTAGGAAAGTTTAAGGGTA
Found at i:3982128 original size:55 final size:56
Alignment explanation
Indices: 3981990--3982400 Score: 241
Period size: 59 Copynumber: 7.1 Consensus size: 56
3981980 GAAATTTTTA
* * * * **
3981990 AGGGTAAAAATGTCATTTTGGGAAAGTTT-GGGGTGAAA-ATGTAATTTTGGAAAGTTTT
1 AGGG-AAAAATGTAATTTTTGG-AAGTTTAGGGGTAAAATATG-ATTTTTGG-AAGTTCG
* * *
3982048 AGGGGTAAAAATGTCATTTTAGGAAGTTTAAGGGTAAAAATATGATTTTTGG-AGTTCG
1 A-GGG-AAAAATGTAATTTTTGGAAGTTTAGGGGT-AAAATATGATTTTTGGAAGTTCG
*
3982106 A-GGAAAAATGTAATTTTTGGAAGTTTGGGGGTAAAATATGATTTTTGGAAGTTCG
1 AGGGAAAAATGTAATTTTTGGAAGTTTAGGGGTAAAATATGATTTTTGGAAGTTCG
* * *
3982161 AGGGAAAAATGTAAATTTTGAGAAGTTTAGGGGTTAAA-ATGCAATTTTTGGAAAGTTTG
1 AGGGAAAAATGTAATTTTTG-GAAGTTTAGGGGTAAAATATG--ATTTTTGG-AAGTTCG
* * * *** *
3982220 AGAGTAAAAATATGAA-TTTTGGAAG-TTATGCGGTAAAATGCAATTTTTGAGAAGTT-T
1 AG-GGAAAAATGT-AATTTTTGGAAGTTTA-GGGGTAAAATATGATTTTTG-GAAGTTCG
* * * ** *
3982277 AGGAGTAAAAATGTGATTTTTGGAAGTTCATGGGTAAAA-ATGTAATTTTTAAAAAGTT-T
1 AGG-G-AAAAATGTAATTTTTGGAAGTTTAGGGGTAAAATATG--ATTTTT-GGAAGTTCG
* * * * *
3982336 AGGGGTTAAAATATGATTTTAGAAAAGTTTAGGGGTCAAAATATGATTTTTGGACAGTTC-
1 A-GGG-AAAAATGTAATTTTTG-GAAGTTTAGGGGT-AAAATATGATTTTTGGA-AGTTCG
3982396 AGGGA
1 AGGGA
3982401 CCTTTTGGGT
Statistics
Matches: 283, Mismatches: 42, Indels: 56
0.74 0.11 0.15
Matches are distributed among these distances:
54 16 0.06
55 32 0.11
56 23 0.08
57 18 0.06
58 58 0.20
59 78 0.28
60 46 0.16
61 9 0.03
62 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.35
Consensus pattern (56 bp):
AGGGAAAAATGTAATTTTTGGAAGTTTAGGGGTAAAATATGATTTTTGGAAGTTCG
Found at i:3982257 original size:58 final size:58
Alignment explanation
Indices: 3981965--3982335 Score: 250
Period size: 59 Copynumber: 6.4 Consensus size: 58
3981955 AGTTTTGGAT
* * * * *
3981965 TAAAATGTAA-TTTTGGAAATTTTTAAGGGTAAAAATGT-CATTTTGGGAAAGTTT-GGGG
1 TAAAATGCAATTTTTGGAAA-GTTTGAGAGTAAAAATGTGAATTTT-GG-AAGTTTAGGGG
* * * * *
3982023 TGAAAATGTAA-TTTTGGAAAGTTTTAGGGGTAAAAATGT-CATTTTAGGAAGTTTAAGGG
1 T-AAAATGCAATTTTTGGAAAGTTTGA-GAGTAAAAATGTGAATTTT-GGAAGTTTAGGGG
*** * *
3982082 TAAAAATATGATTTTTGG--AGTTCGAG-G-AAAAATGT-AATTTTTGGAAGTTTGGGGG
1 T-AAAATGCAATTTTTGGAAAGTTTGAGAGTAAAAATGTGAA-TTTTGGAAGTTTAGGGG
*** * * *
3982137 TAAAATATGATTTTTGG-AAGTTCGAG-GGAAAAATGTAAATTTTGAGAAGTTTAGGGG
1 TAAAATGCAATTTTTGGAAAGTTTGAGAGTAAAAATGTGAATTTTG-GAAGTTTAGGGG
* *
3982194 TTAAAATGCAATTTTTGGAAAGTTTGAGAGTAAAAATATGAATTTTGGAAG-TTATGCGG
1 -TAAAATGCAATTTTTGGAAAGTTTGAGAGTAAAAATGTGAATTTTGGAAGTTTA-GGGG
* * *
3982253 TAAAATGCAATTTTT-GAGAAGTTT-AGGAGTAAAAATGTGATTTTTGGAAGTTCATGGG
1 TAAAATGCAATTTTTGGA-AAGTTTGA-GAGTAAAAATGTGAATTTTGGAAGTTTAGGGG
* **
3982311 TAAAAATGTAATTTTTAAAAAGTTT
1 T-AAAATGCAATTTTTGGAAAGTTT
3982336 AGGGGTTAAA
Statistics
Matches: 267, Mismatches: 28, Indels: 35
0.81 0.08 0.11
Matches are distributed among these distances:
54 16 0.06
55 30 0.11
56 18 0.07
57 17 0.06
58 79 0.30
59 85 0.32
60 22 0.08
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (58 bp):
TAAAATGCAATTTTTGGAAAGTTTGAGAGTAAAAATGTGAATTTTGGAAGTTTAGGGG
Found at i:3982378 original size:30 final size:29
Alignment explanation
Indices: 3982323--3982385 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 29
3982313 AAAATGTAAT
*
3982323 TTTTAAAAAGTTTAGGGGTTAAAATATGA
1 TTTTAAAAAGTTTAGGGGTCAAAATATGA
3982352 TTTTAGAAAAGTTTAGGGGTCAAAATATGA
1 TTTTA-AAAAGTTTAGGGGTCAAAATATGA
3982382 TTTT
1 TTTT
3982386 TGGACAGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.40
Consensus pattern (29 bp):
TTTTAAAAAGTTTAGGGGTCAAAATATGA
Found at i:3984119 original size:5 final size:6
Alignment explanation
Indices: 3984093--3984160 Score: 65
Period size: 6 Copynumber: 11.8 Consensus size: 6
3984083 ATTTGGACAT
* *
3984093 TTTAAA TTTAAA TTTGAA TTT-AA TTTAAA -ATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3984139 --T-AA TTTAAAA TTTAAAA TTTAA
1 TTTAAA TTT-AAA TTT-AAA TTTAA
3984161 GATTAAGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 10 0.19
6 28 0.53
7 12 0.23
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:3984128 original size:28 final size:26
Alignment explanation
Indices: 3984095--3984149 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 26
3984085 TTGGACATTT
*
3984095 TAAATTTAAATTTGAATTTAATTTAAAA
1 TAAATTTAAATTT-AA-ATAATTTAAAA
3984123 TAAATTTAAATTTAAATAATTTAAAA
1 TAAATTTAAATTTAAATAATTTAAAA
3984149 T
1 T
3984150 TTAAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 11 0.42
27 2 0.08
28 13 0.50
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
TAAATTTAAATTTAAATAATTTAAAA
Found at i:3984130 original size:16 final size:16
Alignment explanation
Indices: 3984093--3984156 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 16
3984083 ATTTGGACAT
*
3984093 TTTAAATTTAAATTTGAA
1 TTTAAATTTAAA-AT-AA
3984111 TTT-AATTTAAAATAAA
1 TTTAAATTTAAAAT-AA
3984127 TTTAAATTT-AAATAA
1 TTTAAATTTAAAATAA
3984142 TTTAAAATTTAAAAT
1 TTT-AAATTTAAAAT
3984157 TTAAGATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.12
16 16 0.39
17 17 0.41
18 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTAAATTTAAAATAA
Found at i:3984210 original size:2 final size:2
Alignment explanation
Indices: 3984203--3984227 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3984193 GAACTCCAAC
3984203 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 A
3984228 ATTATCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3984388 original size:32 final size:31
Alignment explanation
Indices: 3984351--3984426 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
3984341 AATCTTAATA
3984351 ATTTTATTTAATTAATAA-TTAAATATTATTTT
1 ATTTTA-TTAATTAATAATTTAAATATT-TTTT
* *
3984383 ATTTTAATATATTAATAATTTTATATATTTTTT
1 ATTTTATTA-ATTAATAA-TTTAAATATTTTTT
3984416 A-TTTATTAATT
1 ATTTTATTAATT
3984427 TTTTATATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
31 5 0.13
32 20 0.53
33 5 0.13
34 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTTTATTAATTAATAATTTAAATATTTTTT
Done.