Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008384.1 Hibiscus syriacus cultivar Beakdansim tig00111146_pilon, whole genome shotgun sequence
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: 473027
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:230420 original size:18 final size:17
Alignment explanation
Indices: 230273--230424 Score: 66
Period size: 18 Copynumber: 8.7 Consensus size: 17
230263 TAAAATATGG
230273 ATTGATTTATTT-TA-A
1 ATTGATTTATTTGTATA
*
230288 A-TAATTTATTTGTATGA
1 ATTGATTTATTTGTAT-A
*
230305 ATTGATTTATTTTAAAATATGA
1 ATTGATTTA-TTT---GTAT-A
*
230327 ATTGATTTATTT-TAAA
1 ATTGATTTATTTGTATA
* * *
230343 ATATGGATTAATTTATTTTA
1 AT-T-GATTTATTT-GTATA
* * *
230363 AATAATTTATTAGTATA
1 ATTGATTTATTTGTATA
230380 TATTGATTTATTT-TA-A
1 -ATTGATTTATTTGTATA
*
230396 A-TAATTTATTTGTATA
1 ATTGATTTATTTGTATA
230412 GATTGATTTATTT
1 -ATTGATTTATTT
230425 TAAAATATGG
Statistics
Matches: 102, Mismatches: 18, Indels: 31
0.68 0.12 0.21
Matches are distributed among these distances:
14 18 0.18
15 6 0.06
16 5 0.05
17 11 0.11
18 38 0.37
19 4 0.04
20 3 0.03
21 3 0.03
22 14 0.14
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
ATTGATTTATTTGTATA
Found at i:230459 original size:26 final size:26
Alignment explanation
Indices: 230430--230529 Score: 121
Period size: 26 Copynumber: 3.6 Consensus size: 26
230420 TATTTTAAAA
230430 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTATTGTAGTTG
*
230456 TATGGATTGATTTATTTTAAATAATTTA-TTAG
1 TATGGATTGATTTA--TT--AT--TGTAGTT-G
230488 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTATTGTAGTTG
230514 TATGGATTGATTTATT
1 TATGGATTGATTTATT
230530 TTAAATAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
26 34 0.53
27 2 0.03
28 4 0.06
30 4 0.06
31 2 0.03
32 18 0.28
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (26 bp):
TATGGATTGATTTATTATTGTAGTTG
Found at i:230494 original size:58 final size:58
Alignment explanation
Indices: 230430--230598 Score: 265
Period size: 58 Copynumber: 3.0 Consensus size: 58
230420 TATTTTAAAA
230430 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
230488 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
* *** *
230546 TATAGATTGATTTA-T-TT-TA-AAATATAGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
230599 TTGTAGTTGT
Statistics
Matches: 106, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
54 30 0.28
55 2 0.02
56 2 0.02
57 1 0.01
58 71 0.67
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (58 bp):
TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:230496 original size:32 final size:32
Alignment explanation
Indices: 230455--230566 Score: 148
Period size: 32 Copynumber: 3.7 Consensus size: 32
230445 TATTGTAGTT
230455 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
230487 GTATGGATTGATTTA--TT--AT--TGTAGTT-
1 GTATGGATTGATTTATTTTAAATAATTTA-TTA
230513 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
230545 GTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
230567 ATATAGATTG
Statistics
Matches: 69, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
26 18 0.26
27 2 0.03
28 4 0.06
30 4 0.06
31 2 0.03
32 39 0.57
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:230571 original size:22 final size:22
Alignment explanation
Indices: 230546--230588 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
230536 AATTTATTAG
230546 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
230568 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
230589 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:231289 original size:18 final size:18
Alignment explanation
Indices: 231266--231312 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 18
231256 ACTTTAATTA
231266 CTTAACTTTCAAATTACT
1 CTTAACTTTCAAATTACT
*
231284 CTTAAC-TT--AATCACT
1 CTTAACTTTCAAATTACT
231299 C-TAACTTTCAAATT
1 CTTAACTTTCAAATT
231313 TTTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
14 4 0.17
15 9 0.38
17 5 0.21
18 6 0.25
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (18 bp):
CTTAACTTTCAAATTACT
Found at i:231326 original size:32 final size:30
Alignment explanation
Indices: 231247--231318 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
231237 GTTAAAGTTT
* *
231247 AATTTTTTTACTTTAATTACTTAACTTTCA
1 AATTTTTTTAATTTAATCACTTAACTTTCA
* * *
231277 AATTACTCTTAACTTAATCACTCTAACTTTCA
1 AATT-TTTTTAATTTAATCACT-TAACTTTCA
231309 AATTTTTTTA
1 AATTTTTTTA
231319 TTTTTAATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 4 0.12
31 16 0.48
32 13 0.39
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (30 bp):
AATTTTTTTAATTTAATCACTTAACTTTCA
Found at i:231829 original size:2 final size:2
Alignment explanation
Indices: 231822--231937 Score: 123
Period size: 2 Copynumber: 57.5 Consensus size: 2
231812 GACAGGTGAG
231822 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
* * * *
231864 AT AT AT GA- AT TT CAT GT -T CA- AT GT CA- AA AT GAT 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
231905 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 A
231938 GAGAGAGAGA
Statistics
Matches: 99, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
1 4 0.04
2 91 0.92
3 4 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:231942 original size:2 final size:2
Alignment explanation
Indices: 231937--231974 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
231927 ATATATATAT
231937 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
231975 GGTTGTTGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:232507 original size:20 final size:20
Alignment explanation
Indices: 232484--232535 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
232474 AACGCGATCC
232484 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
232504 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
232524 CCAAAATCGCAA
1 CCAGAATCGCAA
232536 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:232616 original size:20 final size:20
Alignment explanation
Indices: 232591--232784 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
232581 GATTTTCCAT
* *
232591 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
232611 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
232631 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
232651 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
232671 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
232691 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
232711 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
232731 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
232752 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
232772 AATCGCAACGCGA
1 AATCGCAACGCGA
232785 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:232636 original size:40 final size:39
Alignment explanation
Indices: 232587--232784 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
232577 TTGCGATTTT
* ** *
232587 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
232625 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
232666 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
232706 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
232745 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
232785 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:232674 original size:60 final size:60
Alignment explanation
Indices: 232591--232783 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
232581 GATTTTCCAT
* ** * *
232591 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
232651 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
232711 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
232772 AATCGCAACGCG
1 AATCGCAACGCG
232784 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:233204 original size:33 final size:33
Alignment explanation
Indices: 233165--233235 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
233155 TTCACTTAGA
*
233165 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
233198 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
233231 TTTCA
1 TTTCA
233236 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:233375 original size:14 final size:14
Alignment explanation
Indices: 233356--233410 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
233346 AGAATGACTG
233356 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
233370 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
233389 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
233403 TCGCAACG
1 TCGCAACG
233411 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:233393 original size:33 final size:33
Alignment explanation
Indices: 233356--233426 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
233346 AGAATGACTG
**
233356 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
233389 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
233422 TCGCA
1 TCGCA
233427 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:233444 original size:19 final size:19
Alignment explanation
Indices: 233422--233519 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
233412 GAAACCAAAA
*
233422 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
233441 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
233455 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
233474 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
233488 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
233507 TCGCGTTGCGATT
1 TCGCGTTGCGATT
233520 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:233463 original size:14 final size:14
Alignment explanation
Indices: 233444--233533 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
233434 TTTCATTTCG
233444 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
233458 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
233477 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
233491 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
233508 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
233524 CGTTGCGATT
1 CGTTGCGATT
233534 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:233469 original size:33 final size:33
Alignment explanation
Indices: 233427--233541 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
233417 CAAAATCGCA
233427 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
233460 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
233493 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
233526 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
233542 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:235545 original size:93 final size:93
Alignment explanation
Indices: 235240--235700 Score: 804
Period size: 93 Copynumber: 5.1 Consensus size: 93
235230 TAGATTGCTT
*
235240 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
235305 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
235333 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
235397 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
235425 AGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
235490 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
235518 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC--TG---------ACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
235571 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
235599 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
235664 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
235692 AGTAAATTT
1 AGTAAATTT
235701 ATCCATTCAA
Statistics
Matches: 350, Mismatches: 5, Indels: 26
0.92 0.01 0.07
Matches are distributed among these distances:
81 66 0.19
82 13 0.04
83 2 0.01
91 2 0.01
92 103 0.29
93 164 0.47
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:235581 original size:81 final size:84
Alignment explanation
Indices: 235474--235700 Score: 352
Period size: 81 Copynumber: 2.6 Consensus size: 84
235464 GTATTCTTTA
235474 ACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTG
1 ACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTG
235539 CCAATTCTGCTAAAC-TG-
66 CCAATTCTGCTAAACGTGT
235556 ACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTG
1 ACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTG
235620 CCAATTCTGCTAAACTGTGTATTCTTT
66 CCAATTCTGCTAAAC-GTG-------T
235647 AACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
1 -ACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
235701 ATCCATTCAA
Statistics
Matches: 133, Mismatches: 0, Indels: 13
0.91 0.00 0.09
Matches are distributed among these distances:
81 66 0.50
82 13 0.10
83 2 0.02
92 13 0.10
93 39 0.29
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (84 bp):
ACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTG
CCAATTCTGCTAAACGTGT
Found at i:235606 original size:174 final size:174
Alignment explanation
Indices: 235382--235700 Score: 629
Period size: 174 Copynumber: 1.8 Consensus size: 174
235372 ATATTCTTTA
235382 ACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGC
1 ACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGC
235447 CAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTG
66 CAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTG
235512 GTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
131 GTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
235556 ACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGC
1 ACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGC
*
235621 CAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTG
66 CAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTG
235686 GTTGAAAGTAAATTT
131 GTTGAAAGTAAATTT
235701 ATCCATTCAA
Statistics
Matches: 144, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 144 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (174 bp):
ACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGC
CAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTG
GTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
Found at i:235784 original size:19 final size:19
Alignment explanation
Indices: 235744--235872 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
235734 TAGTTTACTT
* *
235744 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
235764 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
235783 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
235802 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
235816 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
235835 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
235849 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
235868 TCGCA
1 TCGCA
235873 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:235823 original size:33 final size:32
Alignment explanation
Indices: 235780--235872 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
235770 CGCGAAACCA
**
235780 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
235812 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
235845 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
235873 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:235870 original size:52 final size:52
Alignment explanation
Indices: 235744--235872 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
235734 TAGTTTACTT
**
235744 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
235796 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
235849 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
235873 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:235890 original size:19 final size:19
Alignment explanation
Indices: 235868--236002 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
235858 GAAACCAAAA
*
235868 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
235887 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
235903 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
235920 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
235936 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
235953 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
235972 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
235992 TCGTGTTGCGA
1 TCGCGTTGCGA
236003 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:235909 original size:14 final size:14
Alignment explanation
Indices: 235890--235946 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
235880 TTTCATTTCG
235890 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
235904 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
235921 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
235937 CGTTGCGATT
1 CGTTGCGATT
235947 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:235915 original size:33 final size:33
Alignment explanation
Indices: 235873--235965 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
235863 CAAAATCGCA
*
235873 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
235906 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
235939 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
235966 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:237923 original size:14 final size:14
Alignment explanation
Indices: 237904--237939 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
237894 ATTGTTTAAT
237904 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
237918 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
237932 TGATTTGT
1 TGATTTGT
237940 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:238062 original size:19 final size:19
Alignment explanation
Indices: 238046--238147 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
238036 AAAAATGACT
238046 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
238065 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
238084 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
238098 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
238117 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
238137 ATCGCAATGCG
1 ATCGCAATGCG
238148 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:238200 original size:19 final size:19
Alignment explanation
Indices: 238176--238468 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
238166 GATTATCTCG
238176 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
238195 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
238214 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
238228 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
238247 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
238266 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
238285 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
238304 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
238323 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
238342 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
238356 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
238375 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
238394 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
238408 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
238428 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
238442 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
238461 TTGCGATT
1 TTGCGATT
238469 GTATTTTCCG
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 29 0.12
16 24 0.10
17 20 0.08
18 3 0.01
19 157 0.64
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:238216 original size:52 final size:52
Alignment explanation
Indices: 238154--238468 Score: 330
Period size: 52 Copynumber: 5.9 Consensus size: 52
238144 TGCGTTTATA
*
238154 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
238206 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
238258 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
238315 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
238367 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
238419 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
238469 GTATTTTCCG
Statistics
Matches: 241, Mismatches: 9, Indels: 25
0.88 0.03 0.09
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 4 0.02
52 129 0.54
53 18 0.07
54 6 0.02
55 8 0.03
57 62 0.26
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:238324 original size:128 final size:122
Alignment explanation
Indices: 238176--238440 Score: 194
Period size: 128 Copynumber: 2.1 Consensus size: 122
238166 GATTATCTCG
*
238176 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
238238 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
238302 CA
121 CA
* * *
238304 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
238366 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
238426 CA
121 CA
238428 TTGCGATTTTCAT
1 TTGCGATTTTCAT
238441 GTTGGGATTT
Statistics
Matches: 125, Mismatches: 5, Indels: 18
0.84 0.03 0.12
Matches are distributed among these distances:
121 7 0.06
122 4 0.03
123 18 0.14
124 18 0.14
125 2 0.02
126 2 0.02
128 74 0.59
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:240768 original size:12 final size:12
Alignment explanation
Indices: 240751--240775 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
240741 TCTTCGGGGA
240751 CTTTTTCTTCTT
1 CTTTTTCTTCTT
240763 CTTTTTCTTCTT
1 CTTTTTCTTCTT
240775 C
1 C
240776 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:240984 original size:24 final size:24
Alignment explanation
Indices: 240950--240996 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
240940 CTGAAACATC
240950 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
240974 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
240997 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:241707 original size:20 final size:20
Alignment explanation
Indices: 241679--242047 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
241669 AAATTTAAGT
* * * *
241679 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
241699 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
241719 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
241739 GTTGCGATTTACTGATTA-TC
1 GTTGCGATTTACGGA-TACGC
241759 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
241779 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
241799 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
241819 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
241839 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
241859 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
241879 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
241899 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
241919 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
241939 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
241959 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
241979 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
241999 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
242019 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
242039 GTTGCGATT
1 GTTGCGATT
242048 ATGGAAAATC
Statistics
Matches: 308, Mismatches: 31, Indels: 20
0.86 0.09 0.06
Matches are distributed among these distances:
19 6 0.02
20 296 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:245959 original size:29 final size:29
Alignment explanation
Indices: 245922--246003 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
245912 AAACTAAATT
*
245922 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
* *
245951 GATGCCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
245980 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
246004 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:250724 original size:29 final size:29
Alignment explanation
Indices: 250689--250770 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
250679 AAACTAAATT
*
250689 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
250718 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
250747 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
250771 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:260160 original size:14 final size:15
Alignment explanation
Indices: 260121--260160 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
260111 ATTATAAATT
260121 AATAAAATATTTAGA
1 AATAAAATATTTAGA
* *
260136 AGTACAATATTTA-A
1 AATAAAATATTTAGA
260150 AATAAAATATT
1 AATAAAATATT
260161 AATTTAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (15 bp):
AATAAAATATTTAGA
Found at i:260205 original size:23 final size:23
Alignment explanation
Indices: 260166--260210 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
260156 ATATTAATTT
* *
260166 AATTATTTTACATATTTTTTAAC
1 AATTATTTTAAATATTTGTTAAC
260189 AATT-TTTTAAATAATTTGTTAA
1 AATTATTTTAAAT-ATTTGTTAA
260211 AGGTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
AATTATTTTAAATATTTGTTAAC
Found at i:261749 original size:37 final size:37
Alignment explanation
Indices: 261673--261749 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
261663 TTTTTATATT
*
261673 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
261710 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
261747 TTT
1 TTT
261750 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:263000 original size:21 final size:21
Alignment explanation
Indices: 262974--263018 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
262964 GGTATTGGTG
*
262974 CTGGAGGGATCAGTACTGATA
1 CTGGAGGGATCAGTACTGAGA
262995 CTGGAGGGATCAGTACTGAGA
1 CTGGAGGGATCAGTACTGAGA
263016 CTG
1 CTG
263019 TTCATGTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.36, T:0.22
Consensus pattern (21 bp):
CTGGAGGGATCAGTACTGAGA
Found at i:277918 original size:32 final size:33
Alignment explanation
Indices: 277854--277927 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 33
277844 TTGTTTTGAT
*
277854 TTTGTCCCCCTCATTTTCTATGGTTAATTATAC
1 TTTGTCCCCCTCATTTTCTATGATTAATTATAC
277887 TTTGTCCCCCT-A-TTTCTTATGATTAATTATAC
1 TTTGTCCCCCTCATTTTC-TATGATTAATTATAC
277919 TTTGTCCCC
1 TTTGTCCCC
277928 TTAAGTTGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 4 0.10
32 24 0.62
33 11 0.28
ACGTcount: A:0.18, C:0.26, G:0.08, T:0.49
Consensus pattern (33 bp):
TTTGTCCCCCTCATTTTCTATGATTAATTATAC
Found at i:282476 original size:29 final size:29
Alignment explanation
Indices: 282436--282506 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
282426 ATTAAAAAAA
* **
282436 AACATAAATTAAAAGGCATGAATGTAAAT
1 AACATAAATTAAAAGGAAAAAATGTAAAT
*
282465 AACA-AAACTTAAAGGGAAAAAATGTAAAT
1 AACATAAA-TTAAAAGGAAAAAATGTAAAT
* *
282494 AAAAGAAATTAAA
1 AACATAAATTAAA
282507 GTGCAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 3 0.09
29 29 0.83
30 3 0.09
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.20
Consensus pattern (29 bp):
AACATAAATTAAAAGGAAAAAATGTAAAT
Found at i:282507 original size:29 final size:28
Alignment explanation
Indices: 282456--282549 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
282446 AAAAGGCATG
*
282456 AATGTAAATAACAAAACTTAAAGGGAAAA
1 AATGTAAATAA-AAAAATTAAAGGGAAAA
* *
282485 AATGTAAATAAAAGAAATTAAAGTGCAAA
1 AATGTAAATAAAA-AAATTAAAGGGAAAA
* ** * *
282514 AATATAAATGGTAAAAATTAAAGGGTAGA
1 AATGTAAAT-AAAAAAATTAAAGGGAAAA
282543 AATGTAA
1 AATGTAA
282550 TTAGAGTTGG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 2 0.04
29 49 0.92
30 2 0.04
ACGTcount: A:0.60, C:0.03, G:0.16, T:0.21
Consensus pattern (28 bp):
AATGTAAATAAAAAAATTAAAGGGAAAA
Found at i:296625 original size:110 final size:112
Alignment explanation
Indices: 296469--296682 Score: 369
Period size: 110 Copynumber: 1.9 Consensus size: 112
296459 CCATGGAAGC
* *
296469 TTCAGAAATGAAAGGAACTGTCTTTATTTTTATGAGTCAACTTCGTGGGAACATCCATGGAAAAA
1 TTCAGAAATGAAAGCAACTGACTTTATTTTTATGAGTCAACTTCGTGGGAACATCCATGGAAAAA
*
296534 ACAAGATT-A-AAAGTGTGGGTGTTGATTCAACTTGTTTGTGGTTGA
66 ACAAGATTAACAAAGTATGGGTGTTGATTCAACTTGTTTGTGGTTGA
296579 TTCAGAAATGAAAGCAACTGACTTTATTTTTATGAGTCAACTTCGTGGGAACATCCATGGAAAAA
1 TTCAGAAATGAAAGCAACTGACTTTATTTTTATGAGTCAACTTCGTGGGAACATCCATGGAAAAA
*
296644 ACAAGATTAAACAAAGTATGGGTGTTGATTCAATTTGTT
66 ACAAGATT-AACAAAGTATGGGTGTTGATTCAACTTGTT
296683 GTTTAAAGCA
Statistics
Matches: 97, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
110 71 0.73
112 1 0.01
113 25 0.26
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (112 bp):
TTCAGAAATGAAAGCAACTGACTTTATTTTTATGAGTCAACTTCGTGGGAACATCCATGGAAAAA
ACAAGATTAACAAAGTATGGGTGTTGATTCAACTTGTTTGTGGTTGA
Found at i:307321 original size:13 final size:13
Alignment explanation
Indices: 307303--307336 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
307293 TCGGTCACAC
307303 ATTGGTGGCAACT
1 ATTGGTGGCAACT
307316 ATTGGTGGCAACT
1 ATTGGTGGCAACT
*
307329 ATCGGTGG
1 ATTGGTGG
307337 TAAAGAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.35, T:0.29
Consensus pattern (13 bp):
ATTGGTGGCAACT
Found at i:312493 original size:28 final size:29
Alignment explanation
Indices: 312420--312493 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
312410 AGGACTAAGT
* *
312420 CTAATCCCATGCAGAATCAAGACGGGGATA
1 CTAATCCCATACATAATCAAGAC-GGGATA
*
312450 -TAATCCCATACCTAATCAAGAC-GGATA
1 CTAATCCCATACATAATCAAGACGGGATA
*
312477 CTAAGCCCATACATAAT
1 CTAATCCCATACATAAT
312494 TAGGACGAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 5 0.13
28 14 0.37
29 19 0.50
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (29 bp):
CTAATCCCATACATAATCAAGACGGGATA
Found at i:315641 original size:153 final size:153
Alignment explanation
Indices: 315363--315790 Score: 675
Period size: 153 Copynumber: 2.8 Consensus size: 153
315353 ACTGAGGGAC
*
315363 TGCAATCTTTGTGAAGGAGATATTCCCAGTGATTTTTCTTGTCTATCCTCTTTGAAACGAGTTGA
1 TGCAATCTTTGTGAAGGAGATATTCCCAGTGATTTTTCTTGTCTATCCTCTTTGAAACGACTTGA
**
315428 TCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTTCTGAGCTTGAATAAC
66 TCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTTCCAAGCTTGAATAAC
315493 TTAGACTATCAAATTGTGGCATT
131 TTAGACTATCAAATTGTGGCATT
315516 TGCAATCTTTGTGAAGGAGATATTCCCAGTGATTTTTCTTGTCTATCCTCTTTGAAACGACTTGA
1 TGCAATCTTTGTGAAGGAGATATTCCCAGTGATTTTTCTTGTCTATCCTCTTTGAAACGACTTGA
*
315581 TCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTTCCAAGCTTGAATATC
66 TCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTTCCAAGCTTGAATAAC
*
315646 TTGGACTATCAAATTGTGGCATT
131 TTAGACTATCAAATTGTGGCATT
* * * ** * * *
315669 TGCAATCTTTGT---GGAGATATTCCTAGTAATATTTCTCATCTGTCATCTTTGACA-GATCTTG
1 TGCAATCTTTGTGAAGGAGATATTCCCAGTGATTTTTCTTGTCTATCCTCTTTGAAACGA-CTTG
* * *
315730 ATCTTAGTGGTAACAATTTCATTAGCATATCTCCGTCCCTTACTCGACTTACCAAGCTTGA
65 ATCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTTCCAAGCTTGA
315791 TTATCTTAAA
Statistics
Matches: 258, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
149 2 0.01
150 96 0.37
153 160 0.62
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (153 bp):
TGCAATCTTTGTGAAGGAGATATTCCCAGTGATTTTTCTTGTCTATCCTCTTTGAAACGACTTGA
TCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTTCCAAGCTTGAATAAC
TTAGACTATCAAATTGTGGCATT
Found at i:315850 original size:150 final size:150
Alignment explanation
Indices: 315424--315800 Score: 468
Period size: 150 Copynumber: 2.5 Consensus size: 150
315414 TTGAAACGAG
* **
315424 TTGATCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTTCTGAGCTTGAA
1 TTGATCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTACCAAGCTTGAA
* * * * * *** *
315489 TAACTTAGACTATCAAATTGTGGCATTTGCAATCTTTGTGAAGGAGATATTCCCAGTGATTTTTC
66 TATCTTAAACTATCAAATTGAGGCACTTGCAATCTTTGT---GGAGATATTCCTACAAATATTTC
** * * *
315554 TTGTCTATCCTCTTTGAAACGA-C
128 TCATCTGTCATCTTTGACA-GATC
*
315577 TTGATCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTTCCAAGCTTGAA
1 TTGATCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTACCAAGCTTGAA
** * * **
315642 TATCTTGGACTATCAAATTGTGGCATTTGCAATCTTTGTGGAGATATTCCTAGTAATATTTCTCA
66 TATCTTAAACTATCAAATTGAGGCACTTGCAATCTTTGTGGAGATATTCCTACAAATATTTCTCA
315707 TCTGTCATCTTTGACAGATC
131 TCTGTCATCTTTGACAGATC
* * *
315727 TTGATCTTAGTGGTAACAATTTCATTAGCATATCTCCGTCCCTTACTCGACTTACCAAGCTTGAT
1 TTGATCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTACCAAGCTTGAA
315792 TATCTTAAA
66 TATCTTAAA
315801 TTGTCGAATT
Statistics
Matches: 205, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
149 2 0.01
150 103 0.50
153 100 0.49
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (150 bp):
TTGATCTTAGTGGTAACAATTTCATCAGCATACCTCCGTCCCTTACTCGACTTACCAAGCTTGAA
TATCTTAAACTATCAAATTGAGGCACTTGCAATCTTTGTGGAGATATTCCTACAAATATTTCTCA
TCTGTCATCTTTGACAGATC
Found at i:316353 original size:22 final size:23
Alignment explanation
Indices: 316310--316355 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
316300 AAAATACGGT
*
316310 ATGAACAGTACCGTATGAACAATA
1 ATGAACAATACCG-ATGAACAATA
316334 ATGAACAATACCG-TGAACAATA
1 ATGAACAATACCGATGAACAATA
316356 CCCGAATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
24 12 0.57
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (23 bp):
ATGAACAATACCGATGAACAATA
Found at i:316413 original size:21 final size:21
Alignment explanation
Indices: 316388--316430 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
316378 AATGCTGGAG
316388 GGGTACCGATACCCTACTACA
1 GGGTACCGATACCCTACTACA
*
316409 GGGTACCGATACCCTGCTACA
1 GGGTACCGATACCCTACTACA
316430 G
1 G
316431 TACTGATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.19
Consensus pattern (21 bp):
GGGTACCGATACCCTACTACA
Found at i:317169 original size:31 final size:31
Alignment explanation
Indices: 317122--317215 Score: 111
Period size: 31 Copynumber: 3.0 Consensus size: 31
317112 AAACCTTGAC
* *
317122 AACTGTCCATAGGTTCCGAAGAACTTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* **
317153 AACTGTCTATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
317184 AACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
317215 A
1 A
317216 CCCTTGACTC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.06
31 50 0.94
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:321382 original size:103 final size:103
Alignment explanation
Indices: 321250--321765 Score: 1014
Period size: 103 Copynumber: 5.0 Consensus size: 103
321240 CTCCATAGCC
*
321250 AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACAAACAGCATGAATCA
1 AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACTAACAGCATGAATCA
321315 TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
66 TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
321353 AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACTAACAGCATGAATCA
1 AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACTAACAGCATGAATCA
321418 TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
66 TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
*
321456 AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACAAACAGCATGAATCA
1 AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACTAACAGCATGAATCA
321521 TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
66 TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
321559 AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACTAACAGCATGAATCA
1 AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACTAACAGCATGAATCA
321624 TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
66 TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
321662 AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACTAACAGCATGAATCA
1 AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACTAACAGCATGAATCA
321727 TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
66 TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
321765 A
1 A
321766 CTTTATCACT
Statistics
Matches: 410, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 410 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (103 bp):
AGGTTCTGAATGAGCACGAGGTGTCTTTGAAGATTTCGATCATCAACGACTAACAGCATGAATCA
TAGCACACTTCGAATTCAAGGGGGCGGTAGTACCCATA
Found at i:322175 original size:3 final size:3
Alignment explanation
Indices: 322167--322199 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
322157 CGTTTGAGTT
322167 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
322200 CCATCCTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:325049 original size:24 final size:24
Alignment explanation
Indices: 325022--325073 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
325012 TTTTATGCTT
**
325022 GTTCATTTATATTTGTTTACGTTC
1 GTTCATTTATATTAATTTACGTTC
* *
325046 GTTCGTTTATGTTAATTTACGTTC
1 GTTCATTTATATTAATTTACGTTC
325070 GTTC
1 GTTC
325074 GTGTTTGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (24 bp):
GTTCATTTATATTAATTTACGTTC
Found at i:325084 original size:20 final size:19
Alignment explanation
Indices: 325033--325084 Score: 50
Period size: 24 Copynumber: 2.4 Consensus size: 19
325023 TTCATTTATA
325033 TTTGTTTACGTTCGTTCGT
1 TTTGTTTACGTTCGTTCGT
325052 TTATGTTAATTTACGTTCGTTCGT
1 TT-TG----TTTACGTTCGTTCGT
325076 GTTTGTTTA
1 -TTTGTTTA
325085 TCATTTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 11
0.71 0.00 0.29
Matches are distributed among these distances:
19 2 0.07
20 6 0.22
24 17 0.63
25 2 0.07
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (19 bp):
TTTGTTTACGTTCGTTCGT
Found at i:330277 original size:30 final size:30
Alignment explanation
Indices: 330243--330311 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
330233 TTTTTTTAAG
* *
330243 GGTTTCCTTGAATTACTCCTATTTTTTTCT
1 GGTTTCCTTGAATTACTACTATTCTTTTCT
330273 GGTTTCCTTGAATTACTACTATTCTTTTCT
1 GGTTTCCTTGAATTACTACTATTCTTTTCT
330303 GGTTTCCTT
1 GGTTTCCTT
330312 ATAATTTTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.13, C:0.20, G:0.12, T:0.55
Consensus pattern (30 bp):
GGTTTCCTTGAATTACTACTATTCTTTTCT
Found at i:348521 original size:38 final size:38
Alignment explanation
Indices: 348447--348522 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
348437 GACTTTAACG
*
348447 CTATTTTACATATTAGTAATTAATGAATGTTTTTAATA
1 CTATTTTACATATCAGTAATTAATGAATGTTTTTAATA
* * *
348485 CTATTTTACATATCAGTAGTTGATGGATGTTTTTAATA
1 CTATTTTACATATCAGTAATTAATGAATGTTTTTAATA
348523 TTATAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.49
Consensus pattern (38 bp):
CTATTTTACATATCAGTAATTAATGAATGTTTTTAATA
Found at i:349910 original size:19 final size:19
Alignment explanation
Indices: 349869--349909 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
349859 GGATTAAGGA
349869 TTTTGGAATATTTTGAGAT
1 TTTTGGAATATTTTGAGAT
349888 TTTTGAGAA-ATTTTGA-AT
1 TTTTG-GAATATTTTGAGAT
349906 TTTT
1 TTTT
349910 TAAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 12 0.57
20 3 0.14
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (19 bp):
TTTTGGAATATTTTGAGAT
Found at i:350130 original size:20 final size:20
Alignment explanation
Indices: 350102--350147 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
350092 AGAAAAGAGA
*
350102 TATAGTTTGAAAAATATTTT
1 TATATTTTGAAAAATATTTT
350122 TATATTTTGAAAAATATTTT
1 TATATTTTGAAAAATATTTT
350142 TATATT
1 TATATT
350148 AAGTCTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
TATATTTTGAAAAATATTTT
Found at i:353703 original size:38 final size:38
Alignment explanation
Indices: 353661--353738 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 38
353651 CGTGATGAAC
* ***
353661 TTTAACGCTATTTTACATATTTGTAATTAATGAATGTT
1 TTTAACACTATTTTACATATCAATAATTAATGAATGTT
* *
353699 TTTAATACTATTTTACATATCAATAATTAATGGATGTT
1 TTTAACACTATTTTACATATCAATAATTAATGAATGTT
353737 TT
1 TT
353739 AATATTATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (38 bp):
TTTAACACTATTTTACATATCAATAATTAATGAATGTT
Found at i:353875 original size:3 final size:3
Alignment explanation
Indices: 353864--353924 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
353854 TTTTTTTCCG
** *
353864 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
353909 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
353925 CATATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:353930 original size:28 final size:28
Alignment explanation
Indices: 353870--353935 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
353860 TCCGTTATTT
* *
353870 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
353899 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
353927 TATTTTTTT
1 TATTATTTT
353936 TGCAGGCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:356451 original size:22 final size:22
Alignment explanation
Indices: 356426--356469 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
356416 TCAAACGATG
*
356426 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
356448 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
356470 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:358775 original size:15 final size:14
Alignment explanation
Indices: 358742--358778 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
358732 GGATCAATAT
358742 TTTTGCATC-TGCA
1 TTTTGCATCTTGCA
358755 -TTTGCATCTTTGCA
1 TTTTGCATC-TTGCA
358769 TTTTGCATCT
1 TTTTGCATCT
358779 GTATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.38
14 5 0.24
15 8 0.38
ACGTcount: A:0.14, C:0.22, G:0.14, T:0.51
Consensus pattern (14 bp):
TTTTGCATCTTGCA
Found at i:361280 original size:14 final size:14
Alignment explanation
Indices: 361261--361287 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
361251 AGAAAAGTAT
361261 ATACATACATACAC
1 ATACATACATACAC
361275 ATACATACATACA
1 ATACATACATACA
361288 TACCTGATAC
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:0.26, G:0.00, T:0.22
Consensus pattern (14 bp):
ATACATACATACAC
Found at i:361941 original size:105 final size:103
Alignment explanation
Indices: 361753--361987 Score: 273
Period size: 105 Copynumber: 2.3 Consensus size: 103
361743 TGAGAATTTT
** * *
361753 AAAACAAATTGCGTCTCGCTTGAGACATTTTTTCCTTTGAGATACAAATTGTGAATTTGATTCAC
1 AAAACAAATTTTGTCTCGCTTGAGACACTTTTCCCTTTGAGATACAAATTGTGAATTTGATTCAC
*
361818 TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 TTAAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * *
361859 AAAACAAATTTTGGCTCGCTTGAGAC-CTTTTCCCTTTGAGATCCAAATT-TCGAATTTGTTTCA
1 AAAACAAATTTTGTCTCGCTTGAGACACTTTTCCCTTTGAGATACAAATTGT-GAATTTGATTCA
* *
361922 CATT-AAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
65 C-TTAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
*
361961 AAAACAAACTTTGTCTCGCTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
361988 ATTTCTCTAA
Statistics
Matches: 112, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
101 2 0.02
102 24 0.21
103 4 0.04
104 5 0.04
105 52 0.46
106 25 0.22
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (103 bp):
AAAACAAATTTTGTCTCGCTTGAGACACTTTTCCCTTTGAGATACAAATTGTGAATTTGATTCAC
TTAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:361983 original size:36 final size:36
Alignment explanation
Indices: 361938--362057 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 36
361928 ACAAAGTTGA
**
361938 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
361974 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * *
362010 TCTCATTTGAGACTATATCT-T-AAAGCAAA-TTTCG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTT-G
*
362044 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
362058 TCATTTTCTC
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
33 3 0.04
34 19 0.27
35 8 0.11
36 40 0.57
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:362344 original size:28 final size:27
Alignment explanation
Indices: 362306--362430 Score: 121
Period size: 28 Copynumber: 4.5 Consensus size: 27
362296 AATTTCTTTT
*
362306 AAAAATATTTGAGTTTGTTTCTCTTGGA
1 AAAAATCTTTGAGTTTGTTTCT-TTGGA
*
362334 AAAAATCTTTGAGTTTG-TTCATTTTGAA
1 AAAAATCTTTGAGTTTGTTTC--TTTGGA
* * *
362362 TAAAAATCTTGGAGTTTGTTCCTTTTGA
1 -AAAAATCTTTGAGTTTGTTTCTTTGGA
*
362390 ATAAATATCTTTGAG-TTGTTTCTTTTG-
1 A-AAA-ATCTTTGAGTTTGTTTCTTTGGA
362417 AAAAATCTTTGAGT
1 AAAAATCTTTGAGT
362431 CTATTTATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
25 9 0.11
26 3 0.04
27 5 0.06
28 38 0.46
29 25 0.30
30 2 0.02
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (27 bp):
AAAAATCTTTGAGTTTGTTTCTTTGGA
Found at i:362376 original size:29 final size:28
Alignment explanation
Indices: 362305--362430 Score: 136
Period size: 29 Copynumber: 4.5 Consensus size: 28
362295 CAATTTCTTT
* * *
362305 TAAAAATATTTGAGTTTGTTTCTCTTGGA
1 TAAAAATCTTTGAGTTTG-TTCTTTTGAA
362334 -AAAAATCTTTGAGTTTGTTCATTTTGAA
1 TAAAAATCTTTGAGTTTGTTC-TTTTGAA
*
362362 TAAAAATCTTGGAGTTTGTTCCTTTTGAA
1 TAAAAATCTTTGAGTTTGTT-CTTTTGAA
*
362391 TAAATATCTTTGAG-TTGTTTCTTTTG--
1 TAAAAATCTTTGAGTTTG-TTCTTTTGAA
362417 -AAAAATCTTTGAGT
1 TAAAAATCTTTGAGT
362431 CTATTTATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
25 12 0.14
27 3 0.04
28 30 0.35
29 39 0.46
30 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.48
Consensus pattern (28 bp):
TAAAAATCTTTGAGTTTGTTCTTTTGAA
Found at i:362409 original size:57 final size:57
Alignment explanation
Indices: 362305--362418 Score: 144
Period size: 57 Copynumber: 2.0 Consensus size: 57
362295 CAATTTCTTT
* *
362305 TAAAAATATTTGAGTTTGTTTCTCTTGGAAAAAATCTTTGAGTTTG-TTCATTTTGAA
1 TAAAAATATTGGAGTTTGTTCCTCTTGGAAAAAATCTTTGAGTTTGTTTC-TTTTGAA
* *
362362 TAAAAATCTTGGAGTTTGTTCCT-TTTGAATAAATATCTTTGAG-TTGTTTCTTTTGAA
1 TAAAAATATTGGAGTTTGTTCCTCTTGGAA-AAA-ATCTTTGAGTTTGTTTCTTTTGAA
362419 AAATCTTTGA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
56 5 0.10
57 33 0.66
58 12 0.24
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (57 bp):
TAAAAATATTGGAGTTTGTTCCTCTTGGAAAAAATCTTTGAGTTTGTTTCTTTTGAA
Found at i:362445 original size:26 final size:25
Alignment explanation
Indices: 362334--362445 Score: 75
Period size: 29 Copynumber: 4.1 Consensus size: 25
362324 TTCTCTTGGA
362334 AAAAATCTTTGAGTT-TGTTCATTTTG
1 AAAAATCTTTGAGTTAT-TT-ATTTTG
* *
362360 AATAAAAATCTTGGAGTT-TGTTCCTTTTG
1 ---AAAAATCTTTGAGTTAT-TT-ATTTTG
* *
362389 AATAAATATCTTTGAGTTGTTTCTTTTG
1 -A-AAA-ATCTTTGAGTTATTTATTTTG
362417 AAAAATCTTTGAGTCTATTTATTTTG
1 AAAAATCTTTGAGT-TATTTATTTTG
362443 AAA
1 AAA
362446 CAAAGTTTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
25 10 0.14
26 15 0.21
27 2 0.03
28 9 0.12
29 36 0.49
30 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.48
Consensus pattern (25 bp):
AAAAATCTTTGAGTTATTTATTTTG
Found at i:362565 original size:141 final size:141
Alignment explanation
Indices: 362387--362756 Score: 600
Period size: 141 Copynumber: 2.6 Consensus size: 141
362377 TTGTTCCTTT
*
362387 TGAATAAATATCTTTGAG-TTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAG
1 TGAA-AAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAG
*
362451 TTTTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTCTGAAACAAAGTTTTGTCTCTCTT
65 TTTTGTCTCTCTTGAGACAATTTCGTGAAAAAGCCTTGAGTCTGAAACAAAGTTTTGTCTCTCTT
362516 GAGACAATTTTG
130 GAGACAATTTTG
362528 TGAAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGT
1 TGAAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGT
* * *
362593 TTTGTTTCTCTTGAGACAATTTCGTGAAAAATCCTTGAGTCTGAAACAAAGTTTTGTCTTTCTTG
66 TTTGTCTCTCTTGAGACAATTTCGTGAAAAAGCCTTGAGTCTGAAACAAAGTTTTGTCTCTCTTG
362658 AGACAATTTTG
131 AGACAATTTTG
* * * * *
362669 TGAAAAAAATCTTTGAGA-TGTTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAA
1 TGAAAAAAATCTTTGAGATTGTTTCTTTTG-AAAAATCTTTGAGTCTATTTATTTTGAAACAAAG
* *
362733 TTTTGTCTCTCTTAAGATAATTTC
65 TTTTGTCTCTCTTGAGACAATTTC
362757 TTTTGAAAAA
Statistics
Matches: 214, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
140 23 0.11
141 191 0.89
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (141 bp):
TGAAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGT
TTTGTCTCTCTTGAGACAATTTCGTGAAAAAGCCTTGAGTCTGAAACAAAGTTTTGTCTCTCTTG
AGACAATTTTG
Found at i:362582 original size:26 final size:26
Alignment explanation
Indices: 362532--362586 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
362522 ATTTTGTGAA
* *
362532 AAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAATCTTTGAGATTATTTATTTTG
362558 AAAAATCTTTGAG-TCTATTTATTTTG
1 AAAAATCTTTGAGAT-TATTTATTTTG
362584 AAA
1 AAA
362587 CAAAGTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (26 bp):
AAAAATCTTTGAGATTATTTATTTTG
Found at i:362701 original size:26 final size:27
Alignment explanation
Indices: 362672--362727 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
362662 AATTTTGTGA
*
362672 AAAAAATCTTTGAG-ATGTTTCTTTTG
1 AAAAAATCTTTGAGTATGTTTCTTTGG
*
362698 AAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAATCTTTGAGTATGTTTCTTTGG
362725 AAA
1 AAA
362728 CAAAATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (27 bp):
AAAAAATCTTTGAGTATGTTTCTTTGG
Found at i:362765 original size:64 final size:64
Alignment explanation
Indices: 362689--362983 Score: 500
Period size: 64 Copynumber: 4.5 Consensus size: 64
362679 CTTTGAGATG
362689 TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
362753 TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
362817 TTTCTTTTGAAACAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1 TTTCTTTTG----AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
362882 TAA
62 TAA
*
362885 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTGTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTG--A-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
362950 AA
63 AA
* *
362952 TTTCTTTTGAAAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCT
362984 CTTAAAATGA
Statistics
Matches: 222, Mismatches: 4, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
64 93 0.42
65 1 0.00
66 2 0.01
67 62 0.28
68 64 0.29
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (64 bp):
TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:362871 original size:68 final size:68
Alignment explanation
Indices: 362698--362963 Score: 488
Period size: 68 Copynumber: 4.0 Consensus size: 68
362688 GTTTCTTTTG
362698 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG-
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
362762 ---
66 AAC
362762 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
362827 AAC
66 AAC
362830 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
362895 AAC
66 AAC
*
362898 -AAAAATCTTTGAGTTTGTTTCTGTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
362962 AA
66 AA
362964 AAATCTTTGA
Statistics
Matches: 197, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
64 64 0.32
67 65 0.33
68 68 0.35
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (68 bp):
AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
AAC
Found at i:363516 original size:15 final size:15
Alignment explanation
Indices: 363495--363530 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
363485 GTTACAATTA
363495 AAAACATTTTCTCTT
1 AAAACATTTTCTCTT
*
363510 GAAACATTTTCTCTT
1 AAAACATTTTCTCTT
363525 AAAACA
1 AAAACA
363531 AGATCATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (15 bp):
AAAACATTTTCTCTT
Found at i:364109 original size:43 final size:42
Alignment explanation
Indices: 364007--364249 Score: 181
Period size: 43 Copynumber: 5.7 Consensus size: 42
363997 CTAAAGATGG
* * ** *
364007 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGATCA
1 CCAGCC-TCCTCATCACGTAGGAACCGTGTCAACCATAGATAA
* * *
364050 -GAG-CTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGCCTCCTCATCACGTAGGAACCGTGTCAACCATAGATAA
* * **
364090 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGCC-TCCTCATCACGTAGGAACCGTGTCA--ACC-ATAGATAA
* * * * * **
364136 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGAT--
1 CCAG-CCTCCTCATCACGTAGGAACCGTGTCA-ACCATAGATAA
* *
364178 -CAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAG-CCTCCTCATCACGTAGGAACCGTGTCAACCATAGATAA
364220 CCAGCCGTCCTCATCACGTAGGAACCGTGT
1 CCAGCC-TCCTCATCACGTAGGAACCGTGT
364250 TATCACCTTA
Statistics
Matches: 157, Mismatches: 32, Indels: 22
0.74 0.15 0.10
Matches are distributed among these distances:
40 35 0.22
41 31 0.20
42 4 0.03
43 47 0.30
44 4 0.03
45 5 0.03
46 30 0.19
47 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (42 bp):
CCAGCCTCCTCATCACGTAGGAACCGTGTCAACCATAGATAA
Found at i:364233 original size:130 final size:130
Alignment explanation
Indices: 364017--364338 Score: 495
Period size: 130 Copynumber: 2.5 Consensus size: 130
364007 CCAGCCGTCC
* * *
364017 TCATCATGTAGGAACCGTGTCATCCCCAGATCAGAGCTCTTCATCACGTAGGAGCCGTGTCAACC
1 TCATCATGTATGAGCCGTGTCATCCCCAGATCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
*
364082 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCT
* *
364146 TCATCACGTATGAGCCGTGTCATTCCCCAGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
1 TCATCATGTATGAGCCGTGTCA-TCCCCAGATCAGATCTCTTCATCACGTAGGAGCCGTGTCAAC
364211 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTC
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTC
364276 T
130 T
** * * * * *
364277 TCATCATGTATGAGTAGTGTCATCCTTC-GACCAGATGTCTTCATCACGTAGGAACCATGTCA
1 TCATCATGTATGAGCCGTGTCATCC-CCAGATCAGATCTCTTCATCACGTAGGAGCCGTGTCA
364339 TCCTTAGACG
Statistics
Matches: 175, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
129 19 0.11
130 128 0.73
131 28 0.16
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (130 bp):
TCATCATGTATGAGCCGTGTCATCCCCAGATCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCT
Found at i:364551 original size:3 final size:3
Alignment explanation
Indices: 364540--364600 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
364530 TTTTTTTCCG
** *
364540 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
364585 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
364601 CATATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:364606 original size:28 final size:28
Alignment explanation
Indices: 364546--364611 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
364536 TCCGTTATTT
* *
364546 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
364575 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
364603 TATTTTTTT
1 TATTATTTT
364612 TGCAGGCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:367128 original size:22 final size:22
Alignment explanation
Indices: 367103--367146 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
367093 TCAAACGATG
*
367103 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
367125 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
367147 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:368976 original size:20 final size:20
Alignment explanation
Indices: 368948--368993 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
368938 AGTAAAGAGA
*
368948 TATAATTTGAAAAATATTTT
1 TATATTTTGAAAAATATTTT
368968 TATATTTTGAAAAATATTTT
1 TATATTTTGAAAAATATTTT
368988 TATATT
1 TATATT
368994 AAGTCTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
TATATTTTGAAAAATATTTT
Found at i:370389 original size:27 final size:25
Alignment explanation
Indices: 370340--370396 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 25
370330 TAACCAACAT
370340 ATAAAATGTTTAAATTTGAATTTAA
1 ATAAAATGTTTAAATTTGAATTTAA
*
370365 ATAAAATGTTTTTTAATTTGAATTTAA
1 ATAAAATG--TTTAAATTTGAATTTAA
370392 ATAAA
1 ATAAA
370397 TTCTATCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 8 0.28
27 21 0.72
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (25 bp):
ATAAAATGTTTAAATTTGAATTTAA
Found at i:373201 original size:2 final size:2
Alignment explanation
Indices: 373194--373224 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
373184 GTCAATAACT
373194 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
373225 GAATATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:375006 original size:29 final size:29
Alignment explanation
Indices: 374973--375050 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
374963 TAAATTGATA
* *
374973 TCATTACTTACATCATTTAATTAAAGATG
1 TCATTGCTTACATCATTTAAGTAAAGATG
*
375002 TCATTGCTTACATCATTTAAGTAATGATG
1 TCATTGCTTACATCATTTAAGTAAAGATG
*
375031 TCTTTGCTTACATCAATTTA
1 TCATTGCTTACATC-ATTTA
375051 GTTAGGTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 39 0.89
30 5 0.11
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (29 bp):
TCATTGCTTACATCATTTAAGTAAAGATG
Found at i:379744 original size:29 final size:29
Alignment explanation
Indices: 379709--379790 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
379699 AAACTAAATT
* * *
379709 GATGTCATTACTGACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
379738 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
379767 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
379791 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:380854 original size:5 final size:5
Alignment explanation
Indices: 380844--381392 Score: 926
Period size: 5 Copynumber: 110.6 Consensus size: 5
380834 ATATGATTTA
380844 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
380894 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
380944 ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT ATAATAT ATAAT ATAAT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT
380994 ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
381042 ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT AAATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT --ATAAT
381093 ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT A-ATAT AATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT ATAAT ATAAT
381143 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
381191 ATAAT ATATAT ATAAT ATAATAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATA-AT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT
381239 AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
381285 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
381335 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
381385 ATAAT ATA
1 ATAAT ATA
381393 TACTTCTACT
Statistics
Matches: 522, Mismatches: 0, Indels: 44
0.92 0.00 0.08
Matches are distributed among these distances:
3 8 0.02
4 23 0.04
5 465 0.89
6 12 0.02
7 14 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:382190 original size:143 final size:143
Alignment explanation
Indices: 381927--382193 Score: 390
Period size: 143 Copynumber: 1.9 Consensus size: 143
381917 TCAAAAACTT
* * * *
381927 ATTATGAACACAATCAATGCACATATAGTATCATAGTACACATAGTACCACTCCAAGTACACAAA
1 ATTATGAACACAATCAATGCACACATAGTATCATAGAACACAAAGTACCACTCCAAATACACAAA
* * * *
381992 GTAATGGTACAATAACGCAATAATGCATTAAACAAAATCGATTGATAATCGCCTTATTCATGGTA
66 GTAATGGTACAATAACGCAATAATGAATTAAACAAAATCGATCGATAACCACCTTATTCATGGTA
382057 CTAACAAGTTCTC
131 CTAACAAGTTCTC
* * * * * *
382070 ATTATGAACACCATCATTGCACACATAGTGTTATAGAACACAAAGTACTACTCCAAATACACAAT
1 ATTATGAACACAATCAATGCACACATAGTATCATAGAACACAAAGTACCACTCCAAATACACAAA
* *
382135 GTACTGGTACAATAACGCAATAATGAATTAAACAAAATCGATCGGTAACCACCTTATTC
66 GTAATGGTACAATAACGCAATAATGAATTAAACAAAATCGATCGATAACCACCTTATTC
382194 TTACTATAGA
Statistics
Matches: 108, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
143 108 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.26
Consensus pattern (143 bp):
ATTATGAACACAATCAATGCACACATAGTATCATAGAACACAAAGTACCACTCCAAATACACAAA
GTAATGGTACAATAACGCAATAATGAATTAAACAAAATCGATCGATAACCACCTTATTCATGGTA
CTAACAAGTTCTC
Found at i:384085 original size:12 final size:10
Alignment explanation
Indices: 384056--384089 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
384046 TAGTTTCTCA
384056 TTGTTTTATT
1 TTGTTTTATT
384066 TTGTTTTATT
1 TTGTTTTATT
384076 TTACGTTTTATT
1 TT--GTTTTATT
384088 TT
1 TT
384090 TTATTTTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
12 10 0.45
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (10 bp):
TTGTTTTATT
Found at i:386582 original size:31 final size:31
Alignment explanation
Indices: 386520--386582 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
386510 TATCGCTTTA
* **
386520 TTTTTTTAGTTTATTTTATTTTATATTTACC
1 TTTTTTTAGTTTATTTTATTTGATAGATACC
*
386551 TTTTTTTAGTTTGATTTT-TTTGGTAGATACC
1 TTTTTTTAGTTT-ATTTTATTTGATAGATACC
386582 T
1 T
386583 ATTTCGAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.17, C:0.06, G:0.10, T:0.67
Consensus pattern (31 bp):
TTTTTTTAGTTTATTTTATTTGATAGATACC
Found at i:389300 original size:21 final size:21
Alignment explanation
Indices: 389258--389300 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
389248 TTTCTGGGCT
* *
389258 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
389279 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
389300 A
1 A
389301 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:389953 original size:13 final size:13
Alignment explanation
Indices: 389935--389999 Score: 57
Period size: 13 Copynumber: 5.1 Consensus size: 13
389925 ATATGATTTC
389935 ATAAGAATATGAA
1 ATAAGAATATGAA
389948 ATAAGAAGTATGAA
1 ATAAGAA-TATGAA
* *
389962 A-AGGACATA--AG
1 ATAAGA-ATATGAA
389973 A-AAGAATATGAA
1 ATAAGAATATGAA
389985 ATAAGAAGTATGAA
1 ATAAGAA-TATGAA
389999 A
1 A
390000 AGGACATAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 5 0.12
12 2 0.05
13 17 0.40
14 15 0.36
ACGTcount: A:0.60, C:0.02, G:0.20, T:0.18
Consensus pattern (13 bp):
ATAAGAATATGAA
Found at i:389973 original size:20 final size:20
Alignment explanation
Indices: 389948--390011 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
389938 AGAATATGAA
389948 ATAAGAAGTATGAAAAGGAC
1 ATAAGAAGTATGAAAAGGAC
* * *
389968 ATAAGAA--A-GAATATGAA
1 ATAAGAAGTATGAAAAGGAC
389985 ATAAGAAGTATGAAAAGGAC
1 ATAAGAAGTATGAAAAGGAC
390005 ATAAGAA
1 ATAAGAA
390012 AGAATATGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 13 0.37
18 1 0.03
19 1 0.03
20 20 0.57
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.16
Consensus pattern (20 bp):
ATAAGAAGTATGAAAAGGAC
Found at i:389983 original size:37 final size:37
Alignment explanation
Indices: 389937--390024 Score: 176
Period size: 37 Copynumber: 2.4 Consensus size: 37
389927 ATGATTTCAT
389937 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
1 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
389974 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
1 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
390011 AAGAATATGAAATA
1 AAGAATATGAAATA
390025 TACAGAATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.60, C:0.02, G:0.20, T:0.17
Consensus pattern (37 bp):
AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
Found at i:390349 original size:30 final size:30
Alignment explanation
Indices: 390308--390704 Score: 722
Period size: 30 Copynumber: 13.2 Consensus size: 30
390298 AAGGAACATA
390308 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
390338 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
390368 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
390398 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
390428 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
390458 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
390488 TGGATAGTTTCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
390518 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
390548 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
390578 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
390608 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
390638 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
390668 TGGATGGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
390698 TGGATAG
1 TGGATAG
390705 GTCCTTCGGA
Statistics
Matches: 353, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 353 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:394061 original size:21 final size:21
Alignment explanation
Indices: 394019--394061 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
394009 TTTCTGGGCT
* *
394019 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
394040 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
394061 A
1 A
394062 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:394709 original size:13 final size:12
Alignment explanation
Indices: 394693--394815 Score: 69
Period size: 13 Copynumber: 10.0 Consensus size: 12
394683 ATGATTTCAT
394693 AAGAATATGAAA
1 AAGAATATGAAA
394705 TAAGAAGTATGAAA
1 -AAGAA-TATGAAA
* *
394719 AGGACATA--AGA
1 AAGA-ATATGAAA
394730 AAGAATATGAAA
1 AAGAATATGAAA
394742 TAAGAAGTATGAAA
1 -AAGAA-TATGAAA
* *
394756 AGGACATA--AGA
1 AAGA-ATATGAAA
394767 AAGAATATGAAA
1 AAGAATATGAAA
394779 TAAGAAGTATGAAA
1 -AAGAA-TATGAAA
* *
394793 AGGACATA--AGA
1 AAGA-ATATGAAA
394804 AAGAATATGAAA
1 AAGAATATGAAA
394816 TATACAGAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 29
0.67 0.10 0.23
Matches are distributed among these distances:
10 9 0.11
11 15 0.18
12 6 0.07
13 30 0.36
14 24 0.29
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.16
Consensus pattern (12 bp):
AAGAATATGAAA
Found at i:394729 original size:20 final size:20
Alignment explanation
Indices: 394704--394804 Score: 106
Period size: 20 Copynumber: 5.3 Consensus size: 20
394694 AGAATATGAA
394704 ATAAGAAGTATGAAAAGGAC
1 ATAAGAAGTATGAAAAGGAC
* * *
394724 ATAAGAA--A-GAATATGAA
1 ATAAGAAGTATGAAAAGGAC
394741 ATAAGAAGTATGAAAAGGAC
1 ATAAGAAGTATGAAAAGGAC
* * *
394761 ATAAGAA--A-GAATATGAA
1 ATAAGAAGTATGAAAAGGAC
394778 ATAAGAAGTATGAAAAGGAC
1 ATAAGAAGTATGAAAAGGAC
394798 ATAAGAA
1 ATAAGAA
394805 AGAATATGAA
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
17 26 0.41
18 2 0.03
19 2 0.03
20 33 0.52
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.16
Consensus pattern (20 bp):
ATAAGAAGTATGAAAAGGAC
Found at i:394737 original size:37 final size:37
Alignment explanation
Indices: 394693--394817 Score: 250
Period size: 37 Copynumber: 3.4 Consensus size: 37
394683 ATGATTTCAT
394693 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
1 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
394730 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
1 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
394767 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
1 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
394804 AAGAATATGAAATA
1 AAGAATATGAAATA
394818 TACAGAATAT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 88 1.00
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.17
Consensus pattern (37 bp):
AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
Found at i:395142 original size:30 final size:30
Alignment explanation
Indices: 395101--395497 Score: 713
Period size: 30 Copynumber: 13.2 Consensus size: 30
395091 AAGGAAAATA
395101 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
395131 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
395161 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
395191 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
395221 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
395251 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
395281 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
395311 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
* *
395341 TGGACATTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
395371 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
* *
395401 TGGACAATTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
395431 TGGATAGTTACCGATGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
395461 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
395491 TGGATAG
1 TGGATAG
395498 GTCATTCGGA
Statistics
Matches: 351, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 351 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:408108 original size:33 final size:32
Alignment explanation
Indices: 408048--408148 Score: 91
Period size: 32 Copynumber: 3.1 Consensus size: 32
408038 GAGCCATCCT
* *
408048 AAGAGAATACCTTGGGGCCTTAA-AGCCTACCA
1 AAGAGAGTACTTTGGGG-CTTAAGAGCCTACCA
*
408080 AAGAGAGTACTTTAGGGGCTTAAGAGCCTACCC
1 AAGAGAGTACTTT-GGGGCTTAAGAGCCTACCA
* *
408113 AAG-GCAGTA-TCTCGGGGCCTAAGAGCCTACCCA
1 AAGAG-AGTACT-TTGGGGCTTAAGAGCCTA-CCA
408146 AAG
1 AAG
408149 GTCACCTTAG
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
32 33 0.57
33 25 0.43
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.18
Consensus pattern (32 bp):
AAGAGAGTACTTTGGGGCTTAAGAGCCTACCA
Found at i:409303 original size:22 final size:23
Alignment explanation
Indices: 409278--409320 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
409268 TATAAACTAT
409278 TTTTAATTTCATAA-TTTTTAAA
1 TTTTAATTTCATAAGTTTTTAAA
* *
409300 TTTTATTTTTATAAGTTTTTA
1 TTTTAATTTCATAAGTTTTTA
409321 TAAATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTAATTTCATAAGTTTTTAAA
Found at i:409531 original size:21 final size:22
Alignment explanation
Indices: 409475--409562 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 22
409465 GTAATAAAGT
409475 AATAATATATATTTTAATTTTTG
1 AATAAT-TATATTTTAATTTTTG
409498 AATAATT-TAATTTT-ATTTTTCG
1 AATAATTAT-ATTTTAATTTTT-G
*
409520 TAT-ATTATA-TTTAAGTTTTTG
1 AATAATTATATTTTAA-TTTTTG
*
409541 AATATTTTTATATTTTGAATTT
1 AATA--ATTATATTTT-AATTT
409563 AATTTTTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
20 3 0.06
21 15 0.29
22 15 0.29
23 6 0.12
24 5 0.10
25 6 0.12
26 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (22 bp):
AATAATTATATTTTAATTTTTG
Found at i:413153 original size:18 final size:18
Alignment explanation
Indices: 413127--413161 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
413117 TCGAAAGGAC
*
413127 TAAAGTAAATGATAAGAT
1 TAAAGTAAATAATAAGAT
*
413145 TAAATTAAATAATAAGA
1 TAAAGTAAATAATAAGA
413162 CCTGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
TAAAGTAAATAATAAGAT
Found at i:414312 original size:23 final size:23
Alignment explanation
Indices: 414286--414368 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
414276 TCCGACTTGA
* *
414286 ATTCTGTTATGATCCTGACCTGG
1 ATTCTGATATGATCATGACCTGG
* *
414309 ATTCTGATCTGAT-ATTGACATGG
1 ATTCTGATATGATCA-TGACCTGG
*
414332 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGAT-CATGACCTGG
414356 ATTCTGATATGAT
1 ATTCTGATATGAT
414369 ACTTGACTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
23 31 0.61
24 19 0.37
25 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTCTGATATGATCATGACCTGG
Found at i:414356 original size:24 final size:24
Alignment explanation
Indices: 414301--414375 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
414291 GTTATGATCC
414301 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* *
414324 TGACATGGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
414348 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
414372 TGAC
1 TGAC
414376 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:416863 original size:20 final size:20
Alignment explanation
Indices: 416838--416906 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
416828 TATATTCAAA
416838 AAAATAAATATAAAATTTCT
1 AAAATAAATATAAAATTTCT
416858 AAAATAAGA-AT-AAATTGT-T
1 AAAATAA-ATATAAAATT-TCT
* *
416877 AAAAATTAAATATAAAAATACT
1 -AAAA-TAAATATAAAATTTCT
416899 AAAATAAA
1 AAAATAAA
416907 AAATTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
19 6 0.15
20 19 0.47
21 10 0.25
22 5 0.12
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATAAATATAAAATTTCT
Found at i:421921 original size:15 final size:15
Alignment explanation
Indices: 421901--421932 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
421891 TGTAACATAT
421901 ATCAAATTATCTCAA
1 ATCAAATTATCTCAA
421916 ATCAAATTATCTCAA
1 ATCAAATTATCTCAA
421931 AT
1 AT
421933 TGGTCTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (15 bp):
ATCAAATTATCTCAA
Found at i:423785 original size:29 final size:29
Alignment explanation
Indices: 423743--423825 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 29
423733 CTCAAGATGC
* *
423743 TAATATAAATAAACTTGTCTACCACAATT
1 TAATATGAAGAAACTTGTCTACCACAATT
* *
423772 TAATGTGAAGAAACTTGTCTACCACAGTT
1 TAATATGAAGAAACTTGTCTACCACAATT
*
423801 TAATATGAAGAAACGTGTCTACCAC
1 TAATATGAAGAAACTTGTCTACCAC
423826 TTTGAGTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (29 bp):
TAATATGAAGAAACTTGTCTACCACAATT
Found at i:426034 original size:27 final size:25
Alignment explanation
Indices: 425985--426041 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 25
425975 TAACCAACAT
425985 ATAAAATGTTTAAATTTGAATTTAA
1 ATAAAATGTTTAAATTTGAATTTAA
*
426010 ATAAAATGTTTTTTAATTTGAATTTAA
1 ATAAAATG--TTTAAATTTGAATTTAA
426037 ATAAA
1 ATAAA
426042 TTTTATCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 8 0.28
27 21 0.72
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (25 bp):
ATAAAATGTTTAAATTTGAATTTAA
Found at i:431902 original size:27 final size:25
Alignment explanation
Indices: 431853--431908 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 25
431843 CAACCCACCT
431853 ATAAAATGTTTAAATTTGAATTTAA
1 ATAAAATGTTTAAATTTGAATTTAA
*
431878 ATAAAATGTTTTTTAATTTGAATTTAA
1 ATAAAATG--TTTAAATTTGAATTTAA
431905 ATAA
1 ATAA
431909 TATTATCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 8 0.29
27 20 0.71
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (25 bp):
ATAAAATGTTTAAATTTGAATTTAA
Found at i:433371 original size:29 final size:29
Alignment explanation
Indices: 433334--433416 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 29
433324 CTCAAGATGC
* *
433334 TAATATGAATAAAATTGTCTACCACAATT
1 TAATATGAAGAAACTTGTCTACCACAATT
* *
433363 TAATGTGAAGAAACTTGTCTACCACAGTT
1 TAATATGAAGAAACTTGTCTACCACAATT
*
433392 TAATATGAAGAAACGTGTCTACCAC
1 TAATATGAAGAAACTTGTCTACCAC
433417 TTTGAGTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (29 bp):
TAATATGAAGAAACTTGTCTACCACAATT
Found at i:434887 original size:156 final size:154
Alignment explanation
Indices: 434686--435197 Score: 658
Period size: 157 Copynumber: 3.3 Consensus size: 154
434676 CATGTGAAAT
* *
434686 TTGGTAAAAAAATGAACTTAAAA-AAATGACAAATTGAAGGAATAAGTAGATTATGAAAAATTGA
1 TTGGTAAAAAAA-G-ACTTAAAATAAATGA-GAATTGAAGAAATAAG-AGATTATGAAAAATTGA
* * **
434750 AGGACCAAATTGAAAAATAAATAATTTGTAAT-AAAAAGAGGAATTGAAAGTATGCATGTATTCT
62 AGGACTAAATTGAAAAATAAA-AATTTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATTCT
434814 ACTATGGTTTAGGAACATGTGGCTCAAAG
126 ACTATGGTTTAGGAACATGTGGCTCAAAG
434843 TTGGTAAAAAAAGACTTAAAATAAATGATGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAG
1 TTGGTAAAAAAAGACTTAAAATAAATGA-GAATTGAAGAAATAA-GAGATTATGAAAAATTGAAG
* * *
434908 GACTAAATTGAAAAATAAAAAATTTGTTATCAAAGAGAGGAATTGAAATTACACATGTATTCTAC
64 GACTAAATTGAAAAAT-AAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATTCTAC
* * *
434973 TATGGTTTA-GAAGCATGTGACTAAAAT
128 TATGGTTTAGGAA-CATGTGGCTCAAAG
* * *
435000 TTGGTAAAAAAGGACTTAAAATAAATTACAATTGAAGAAATAAAGAGATTATG-AAAATTGAAGG
1 TTGGTAAAAAAAGACTTAAAATAAATGAGAATTGAAGAAAT-AAGAGATTATGAAAAATTGAAGG
* *
435064 ACTAAATTG-AAAATAAAAAGTTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATTCTATTA
65 ACTAAATTGAAAAATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATTCTACTA
* *
435128 AGGTTTAGGAGCATGTGGCTC-AAG
130 TGGTTTAGGAACATGTGGCTCAAAG
** * *
435152 TTTGGTAAAAGACGGACTTAAAATAAAGGAGGAATTGAATAAATAA
1 -TTGGTAAAA-AAAGACTTAAAATAAATGA-GAATTGAAGAAATAA
435198 TGAAATCGGG
Statistics
Matches: 315, Mismatches: 30, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
152 2 0.01
153 68 0.22
154 25 0.08
155 39 0.12
156 87 0.28
157 94 0.30
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (154 bp):
TTGGTAAAAAAAGACTTAAAATAAATGAGAATTGAAGAAATAAGAGATTATGAAAAATTGAAGGA
CTAAATTGAAAAATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATTCTACTAT
GGTTTAGGAACATGTGGCTCAAAG
Found at i:438030 original size:20 final size:20
Alignment explanation
Indices: 438005--438045 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
437995 TGCTTAAGGT
438005 TTAGTTTCTGTTTATTTTAG
1 TTAGTTTCTGTTTATTTTAG
*
438025 TTAGTTTTTGTTTATTTTAG
1 TTAGTTTCTGTTTATTTTAG
438045 T
1 T
438046 ACCCGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.02, G:0.15, T:0.68
Consensus pattern (20 bp):
TTAGTTTCTGTTTATTTTAG
Found at i:444079 original size:15 final size:16
Alignment explanation
Indices: 444061--444093 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
444051 GTGGCAGATC
444061 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
444076 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
444092 AA
1 AA
444094 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:455373 original size:31 final size:31
Alignment explanation
Indices: 455312--455373 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
455302 TATCGCTTTA
* **
455312 TTTTTTAGTTTATTTTATTTTATATTTACCT
1 TTTTTTAGTTTATTTTATTTGATAGATACCT
*
455343 TTTTTTAGTTTGATTTT-TTTGGTAGATACCT
1 TTTTTTAGTTT-ATTTTATTTGATAGATACCT
455374 ATTTCGAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.18, C:0.06, G:0.10, T:0.66
Consensus pattern (31 bp):
TTTTTTAGTTTATTTTATTTGATAGATACCT
Found at i:461853 original size:4 final size:4
Alignment explanation
Indices: 461844--461881 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
461834 ACTAATTGAC
461844 AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AG
1 AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AG
461882 ATTGAAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (4 bp):
AGTT
Done.