Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007068.1 Hibiscus syriacus cultivar Beakdansim tig00018390_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: 617230
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:269464 original size:18 final size:19
Alignment explanation
Indices: 269426--269469 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
269416 AAAATCGCAA
*
269426 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
269445 TGCGTTTTTTATTTCG-GT
1 TGCGATTTTTATTTCGCGT
269463 TGCGATT
1 TGCGATT
269470 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.07, C:0.14, G:0.25, T:0.55
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:270086 original size:20 final size:20
Alignment explanation
Indices: 270061--270114 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
270051 GATTTTGTAT
270061 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
270081 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
270101 TATCGCATTGCGAT
1 TATCGCATTGCGAT
270115 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:270133 original size:61 final size:61
Alignment explanation
Indices: 270021--270135 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
270011 CGCTATGTAA
* * * ** *
270021 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
* *
270082 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
270136 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 43 0.96
62 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
Found at i:270816 original size:17 final size:17
Alignment explanation
Indices: 270789--270836 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
270779 AAAAGATTGT
270789 ATAAGATTTAAATTAA-A
1 ATAA-ATTTAAATTAAGA
*
270806 ATTAAATTTAAAATAAGA
1 A-TAAATTTAAATTAAGA
*
270824 ATAAATTAAAATT
1 ATAAATTTAAATT
270837 GATTGATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (17 bp):
ATAAATTTAAATTAAGA
Found at i:271081 original size:19 final size:21
Alignment explanation
Indices: 271038--271083 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
271028 GTCTGATTTT
* *
271038 AATAACACTGTTATTTTTTCC
1 AATAACACTGTTATTGTTTCA
271059 AATAACA-TGTTA-TGTTTCA
1 AATAACACTGTTATTGTTTCA
271078 AATAAC
1 AATAAC
271084 CTTGAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 5 0.22
21 7 0.30
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (21 bp):
AATAACACTGTTATTGTTTCA
Found at i:272502 original size:13 final size:13
Alignment explanation
Indices: 272470--272502 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
272460 TATTTTAAAT
272470 TTTAT-ATTTAGA
1 TTTATAATTTAGA
272482 TTATATAATTTAGA
1 TT-TATAATTTAGA
272496 TTTATAA
1 TTTATAA
272503 ATTTTATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 8 0.42
14 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (13 bp):
TTTATAATTTAGA
Found at i:281922 original size:31 final size:28
Alignment explanation
Indices: 281879--281960 Score: 76
Period size: 31 Copynumber: 2.8 Consensus size: 28
281869 ACTAAGTATC
*
281879 TAAAGTATTTTTTAATCAAAATAAATA-T
1 TAAATTATTTTTT-ATCAAAATAAATACT
* **
281907 ATAAACTTATCTTTTTGATAAAAATAGTTACT
1 -TAAA-TTAT-TTTTT-ATCAAAATAAATACT
281939 TAAATTATTTTTTATCAAAATA
1 TAAATTATTTTTTATCAAAATA
281961 GGTGCTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 8 0.18
29 9 0.20
30 7 0.16
31 19 0.43
32 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (28 bp):
TAAATTATTTTTTATCAAAATAAATACT
Found at i:281958 original size:28 final size:29
Alignment explanation
Indices: 281879--281975 Score: 81
Period size: 28 Copynumber: 3.3 Consensus size: 29
281869 ACTAAGTATC
*
281879 TAAAGTATTTTTTAATCAAAATAAATA-T
1 TAAAGTATTTTTTAATCAAAATAGATACT
* * * *
281907 ATAAACTTATCTTTTTGATAAAAATAGTTACT
1 -TAAA-GTAT-TTTTTAATCAAAATAGATACT
* * *
281939 TAAATTATTTTTT-ATCAAAATAGGTGCT
1 TAAAGTATTTTTTAATCAAAATAGATACT
281967 TAAAGTATT
1 TAAAGTATT
281976 CAATTTTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
28 20 0.36
29 9 0.16
30 7 0.12
31 19 0.34
32 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (29 bp):
TAAAGTATTTTTTAATCAAAATAGATACT
Found at i:291834 original size:20 final size:20
Alignment explanation
Indices: 291798--291845 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
291788 GCAATACAAA
*
291798 CGAACAAATACAAATCCTAC
1 CGAACAAATACAAATCCAAC
*
291818 CGAACTAAAT-CAGATCCAAC
1 CGAAC-AAATACAAATCCAAC
*
291838 CGACCAAA
1 CGAACAAA
291846 CATAGCAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 17 0.71
21 4 0.17
ACGTcount: A:0.48, C:0.31, G:0.08, T:0.12
Consensus pattern (20 bp):
CGAACAAATACAAATCCAAC
Found at i:292027 original size:15 final size:15
Alignment explanation
Indices: 292003--292037 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
291993 TGATAATCAT
*
292003 AAGAGGTATTTGGTG
1 AAGAGATATTTGGTG
292018 AAGAGATATTTGGTG
1 AAGAGATATTTGGTG
292033 AAGAG
1 AAGAG
292038 GCCGTTACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (15 bp):
AAGAGATATTTGGTG
Found at i:292400 original size:23 final size:23
Alignment explanation
Indices: 292358--292401 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
292348 AGACGCAATA
* * *
292358 AACAATGCATTGGTTTCCCACAG
1 AACAATGCAATGATTCCCCACAG
292381 AACAATGCAATGATTCCCCAC
1 AACAATGCAATGATTCCCCAC
292402 TAAACTCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.23
Consensus pattern (23 bp):
AACAATGCAATGATTCCCCACAG
Found at i:304060 original size:6 final size:6
Alignment explanation
Indices: 304047--304400 Score: 635
Period size: 6 Copynumber: 59.3 Consensus size: 6
304037 TACATATAGG
*
304047 ATGTAT ATGCAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
304095 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
304143 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
304191 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
304239 ATGTAT ATGTAT ATG--T ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
304285 ATGTAT ATGTAT ATGTAT ATGTAT ATG--T ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
* *
304331 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGCAT ATGCAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
304379 ATGCATAT ATGTAT ATGTAT AT
1 ATG--TAT ATGTAT ATGTAT AT
304401 ATACCTCTTT
Statistics
Matches: 338, Mismatches: 4, Indels: 12
0.95 0.01 0.03
Matches are distributed among these distances:
4 8 0.02
6 325 0.96
8 5 0.01
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.49
Consensus pattern (6 bp):
ATGTAT
Found at i:306409 original size:2 final size:2
Alignment explanation
Indices: 306402--306462 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
306392 TTTTTAAAAC
306402 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
306444 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
306463 CTCCCATCCC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:306656 original size:24 final size:24
Alignment explanation
Indices: 306627--306690 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
306617 GAGATATCAA
* *
306627 AAATCAAAACAGAATTCTGACCAG
1 AAATCAGAACAGAATTCAGACCAG
* * * *
306651 ATATCAGAACAAAATCCAGATCAG
1 AAATCAGAACAGAATTCAGACCAG
306675 AAATCAGAACAGAATT
1 AAATCAGAACAGAATT
306691 TAGGTAATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.52, C:0.19, G:0.12, T:0.17
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAGACCAG
Found at i:306670 original size:12 final size:12
Alignment explanation
Indices: 306627--306688 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
306617 GAGATATCAA
*
306627 AAATCAAAACAG
1 AAATCAGAACAG
* * *
306639 AATTCTGACCAG
1 AAATCAGAACAG
*
306651 ATATCAGAACA-
1 AAATCAGAACAG
*
306662 AAATCCAGATCAG
1 AAAT-CAGAACAG
306675 AAATCAGAACAG
1 AAATCAGAACAG
306687 AA
1 AA
306689 TTTAGGTAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
11 3 0.08
12 30 0.81
13 4 0.11
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.15
Consensus pattern (12 bp):
AAATCAGAACAG
Found at i:309217 original size:13 final size:13
Alignment explanation
Indices: 309199--309254 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
309189 GCCGGTCAAC
*
309199 GGTCAACGAGTTG
1 GGTCAACGGGTTG
*
309212 GGTCAACGGGTCG
1 GGTCAACGGGTTG
309225 GGTCAACGGGTTG
1 GGTCAACGGGTTG
* *
309238 AGTCAACGGGTCG
1 GGTCAACGGGTTG
309251 GGTC
1 GGTC
309255 GGGTTGTGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.18, C:0.20, G:0.43, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTTG
Found at i:309231 original size:26 final size:26
Alignment explanation
Indices: 309199--309254 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
309189 GCCGGTCAAC
*
309199 GGTCAACGAGTTGGGTCAACGGGTCG
1 GGTCAACGAGTTGAGTCAACGGGTCG
*
309225 GGTCAACGGGTTGAGTCAACGGGTCG
1 GGTCAACGAGTTGAGTCAACGGGTCG
309251 GGTC
1 GGTC
309255 GGGTTGTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.43, T:0.20
Consensus pattern (26 bp):
GGTCAACGAGTTGAGTCAACGGGTCG
Found at i:310554 original size:13 final size:13
Alignment explanation
Indices: 310536--310579 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
310526 AGTGGTCAAC
*
310536 GGTCAACGGGTTG
1 GGTCAACGGGTCG
310549 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
310562 AGTCAACGGGTCG
1 GGTCAACGGGTCG
310575 GGTCA
1 GGTCA
310580 GGTTGTGACC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:312251 original size:20 final size:20
Alignment explanation
Indices: 312226--312267 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
312216 GAATTTTTTA
312226 TTATATAATTTAAATAATTT
1 TTATATAATTTAAATAATTT
*
312246 TTATATAATTTATATAATTT
1 TTATATAATTTAAATAATTT
312266 TT
1 TT
312268 TATTTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATATAATTTAAATAATTT
Found at i:312253 original size:11 final size:9
Alignment explanation
Indices: 312226--312265 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
312216 GAATTTTTTA
312226 TTATATAAT
1 TTATATAAT
*
312235 TTAAATAATTT
1 TTATATAA--T
312246 TTATATAAT
1 TTATATAAT
312255 TTATATAAT
1 TTATATAAT
312264 TT
1 TT
312266 TTTATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTATATAAT
Found at i:317065 original size:29 final size:29
Alignment explanation
Indices: 317031--317089 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
317021 CCTAAATTAA
317031 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
317060 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
317089 T
1 T
317090 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:324525 original size:17 final size:17
Alignment explanation
Indices: 324503--324551 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
324493 AAATATTTAC
324503 TTATTAAATAATCTTAA
1 TTATTAAATAATCTTAA
324520 TTATTAAATAATCTTAA
1 TTATTAAATAATCTTAA
324537 TTATTAAATAATCTT
1 TTATTAAATAATCTT
324552 CGACCACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATTAAATAATCTTAA
Found at i:324816 original size:33 final size:33
Alignment explanation
Indices: 324779--324845 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
324769 CGCCGTGTAG
324779 AAAACACTCTCTCATCAAGTCATTGCCATGGAA
1 AAAACACTCTCTCATCAAGTCATTGCCATGGAA
*
324812 AAAACACTCTCTCATCAAGTCATTGCCGTGGAA
1 AAAACACTCTCTCATCAAGTCATTGCCATGGAA
324845 A
1 A
324846 GCAAGTCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (33 bp):
AAAACACTCTCTCATCAAGTCATTGCCATGGAA
Found at i:326749 original size:20 final size:21
Alignment explanation
Indices: 326724--326765 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
326714 TTTCGATTGG
326724 ACTCGAC-AAGAAAAAAATTA
1 ACTCGACTAAGAAAAAAATTA
**
326744 ACTCGACTTGGAAAAAAATTA
1 ACTCGACTAAGAAAAAAATTA
326765 A
1 A
326766 ATTCTAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.19
Consensus pattern (21 bp):
ACTCGACTAAGAAAAAAATTA
Found at i:328026 original size:16 final size:16
Alignment explanation
Indices: 328005--328045 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
327995 TGGGCTTATT
328005 GTTGGGCTTCCCACCG
1 GTTGGGCTTCCCACCG
328021 GTTGGGCTTCCCACCG
1 GTTGGGCTTCCCACCG
328037 GTTGGGCTT
1 GTTGGGCTT
328046 TATTGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.05, C:0.32, G:0.34, T:0.29
Consensus pattern (16 bp):
GTTGGGCTTCCCACCG
Found at i:328114 original size:3 final size:3
Alignment explanation
Indices: 328100--328172 Score: 53
Period size: 3 Copynumber: 24.3 Consensus size: 3
328090 AAAAAATGAA
* *
328100 AAT AAT ATT AAT AAT AAT -AT CAT -AT AAT -AT AAT AAAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT
* * *
328144 AAT AAA AAT ACT AAA AAT AAT ATAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT A
328173 TATATACTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
2 6 0.11
3 41 0.73
4 9 0.16
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:328172 original size:7 final size:7
Alignment explanation
Indices: 328121--328466 Score: 185
Period size: 7 Copynumber: 47.4 Consensus size: 7
328111 TAATAATATC
328121 ATATAAT
1 ATATAAT
328128 ATAATAAAT
1 AT-AT-AAT
328137 ATATAAT
1 ATATAAT
*
328144 A-ATAAAA
1 ATAT-AAT
328151 ATACTAA-
1 ATA-TAAT
*
328158 AAATAAT
1 ATATAAT
328165 ATATAAT
1 ATATAAT
328172 ATAT-AT
1 ATATAAT
*
328178 ACTATACAA
1 A-TATA-AT
328187 ATATATAT
1 ATATA-AT
*
328195 ACTTTAAT
1 A-TATAAT
328203 ATAATATAT
1 AT-ATA-AT
328212 ATACTAAT
1 ATA-TAAT
328220 ATAT-AT
1 ATATAAT
*
328226 GTATAAT
1 ATATAAT
*
328233 ATATTA-
1 ATATAAT
328239 ATATAAT
1 ATATAAT
328246 ATATAAT
1 ATATAAT
**
328253 ATACCAT
1 ATATAAT
328260 ATA-AAT
1 ATATAAT
328266 ATAT-AT
1 ATATAAT
328272 ATATAAT
1 ATATAAT
*
328279 AAAT-AT
1 ATATAAT
328285 ATACTAATAT
1 ATA-T-A-AT
*
328295 ATATAAC
1 ATATAAT
328302 ATATAAT
1 ATATAAT
328309 ATATAAT
1 ATATAAT
328316 ATAATATAT
1 AT-ATA-AT
328325 ATAATAAT
1 AT-ATAAT
* *
328333 AAATACT
1 ATATAAT
328340 ATATAAT
1 ATATAAT
328347 A-AT-AT
1 ATATAAT
*
328352 AACATAAT
1 -ATATAAT
328360 ATATAAT
1 ATATAAT
328367 ACTATATACT
1 A-TATA-A-T
328377 ATATAAAT
1 ATAT-AAT
328385 ATTATAAT
1 A-TATAAT
*
328393 ATATATGTT
1 ATATA--AT
*
328402 ATATAAC
1 ATATAAT
* **
328409 ACCATGCT
1 A-TATAAT
328417 ATATAAT
1 ATATAAT
*
328424 ATATATT
1 ATATAAT
*
328431 GTATAA-
1 ATATAAT
328437 A-ATAAT
1 ATATAAT
328443 ATATAAT
1 ATATAAT
*
328450 ATATTAT
1 ATATAAT
328457 ATATAAT
1 ATATAAT
328464 ATA
1 ATA
328467 GTATAATACT
Statistics
Matches: 263, Mismatches: 40, Indels: 72
0.70 0.11 0.19
Matches are distributed among these distances:
5 6 0.02
6 37 0.14
7 126 0.48
8 46 0.17
9 40 0.15
10 8 0.03
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (7 bp):
ATATAAT
Found at i:328175 original size:2 final size:2
Alignment explanation
Indices: 328163--328471 Score: 135
Period size: 2 Copynumber: 165.5 Consensus size: 2
328153 ACTAAAAATA
* * *
328163 AT AT AT A- AT AT AT AT ACT AT AC AA AT AT AT AT ACT TT A- AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT
*
328205 A- AT AT AT AT ACT A- AT AT AT AT GT AT A- AT AT AT -T A- AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
328243 A- AT AT AT A- AT AT ACC AT AT AA AT AT AT AT AT AT A- AT AA AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
328283 AT AT ACT A- AT AT AT AT A- AC AT AT A- AT AT AT A- AT AT A- AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
328321 AT AT AT A- AT A- AT AA AT ACT AT AT A- AT A- AT AT A- AC AT A-
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
328358 AT AT AT A- AT ACT AT AT ACT AT AT AA AT AT -T AT A- AT AT AT AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
328399 GT -T AT AT A- AC ACC AT GCT AT AT A- AT AT AT AT -T GT AT A- AA
1 AT AT AT AT AT AT A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
328438 AT A- AT AT AT A- AT AT AT -T AT AT AT A- AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
328472 ATACTATAGT
Statistics
Matches: 238, Mismatches: 25, Indels: 88
0.68 0.07 0.25
Matches are distributed among these distances:
1 33 0.14
2 186 0.78
3 19 0.08
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:328191 original size:17 final size:16
Alignment explanation
Indices: 328164--328395 Score: 99
Period size: 17 Copynumber: 14.2 Consensus size: 16
328154 CTAAAAATAA
*
328164 TATATAATATATATAC
1 TATAAAATATATATAC
328180 TATACAAATATATATAC
1 TATA-AAATATATATAC
* *
328197 TTTAATATA-ATATA-
1 TATAAAATATATATAC
* *
328211 TATACTAATATATAT-G
1 TATA-AAATATATATAC
*
328227 TAT--AATATAT-TAA
1 TATAAAATATATATAC
*
328240 TATAATATATAATATAC
1 TATAAAATAT-ATATAC
*
328257 CATATAAATATATATA-
1 TATA-AAATATATATAC
328273 TATAATAA-ATATATAC
1 TATAA-AATATATATAC
* * *
328289 TAATATATATAACATATAA
1 T-ATA-AAAT-ATATATAC
*
328308 TATATAATATAATATA-
1 TATAAAATAT-ATATAC
*
328324 TATAATAATAAATACTA-
1 TATAA-AATATATA-TAC
* *
328341 TATAATAATATAACATAA
1 TATAA-AATAT-ATATAC
*
328359 TATATAATACTATATAC
1 TATAAAATA-TATATAC
*
328376 TATATAAATAT-TATAA
1 TATA-AAATATATATAC
328392 TATA
1 TATA
328396 TATGTTATAT
Statistics
Matches: 166, Mismatches: 27, Indels: 46
0.69 0.11 0.19
Matches are distributed among these distances:
12 1 0.01
13 10 0.06
14 3 0.02
15 20 0.12
16 39 0.23
17 66 0.40
18 20 0.12
19 7 0.04
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAAAATATATATAC
Found at i:328212 original size:38 final size:36
Alignment explanation
Indices: 328121--328479 Score: 224
Period size: 38 Copynumber: 9.7 Consensus size: 36
328111 TAATAATATC
* * *
328121 ATATAATATAATAAATATATAATAATAAAAATACTAA-
1 ATATAATATAATATATATATACT-ATATAAATA-TAAT
* *
328158 AAATAATAT-ATAATATATATACTATACAAATATATAT
1 ATATAATATAAT-ATATATATACTATATAAATATA-AT
* * **
328195 ACTTTAATATAATATATATACTAATATATATGTATAAT
1 A-TATAATATAATATATATA-TACTATATAAATATAAT
*
328233 ATATTAATATAATATATAATATACCATATAAATATATAT
1 ATA-TAATATAATATAT-ATATACTATATAAATATA-AT
328272 ATATAATA-AATATATACTAATA-TATATAACATATAAT
1 ATATAATATAATATATA-T-ATACTATATAA-ATATAAT
* * *
328309 ATATAATATAATATATATAATAATAAATACTATATAAT
1 ATATAATATAATATATAT-ATACTATATA-AATATAAT
* *
328347 AATATAACATAATATATA-ATACTATATACTATATAA-
1 -ATATAATATAATATATATATACTATATA-AATATAAT
* * **
328383 ATAT--TATAATATATATGT--TATATAACACCATGCT
1 ATATAATATAATATATATATACTATATAA-A-TATAAT
* *
328417 ATATAATAT-ATAT-TGTATA--AAATAATATATAAT
1 ATATAATATAATATATATATACTATATAA-ATATAAT
328450 ATATTATATATAATATAGTATAATACTATA
1 ATA-TA-ATATAATATA-TAT-ATACTATA
328480 GTGTATAAAA
Statistics
Matches: 255, Mismatches: 36, Indels: 58
0.73 0.10 0.17
Matches are distributed among these distances:
32 7 0.03
33 18 0.07
34 16 0.06
35 14 0.05
36 19 0.07
37 64 0.25
38 75 0.29
39 40 0.16
41 2 0.01
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (36 bp):
ATATAATATAATATATATATACTATATAAATATAAT
Found at i:328308 original size:63 final size:59
Alignment explanation
Indices: 328110--328398 Score: 215
Period size: 61 Copynumber: 5.0 Consensus size: 59
328100 AATAATATTA
* *
328110 ATAATA-ATAT-CATATAATATA-ATA-A-ATATATAATAATAAAAATACTAA-AAATAATAT
1 ATAATATATATACATATAATATATATATACATATA-AAT-ATATATATA-TAATAAAT-ATAT
* * * *
328167 ATAATATATATAC-TATACAAATATATATAC-TTTAATATAATATATATACTAATATATATGT
1 ATAATATATATACATATA-ATATATATATACATATAA-AT-ATATATATA-TAATAAATATAT
328228 ATAATATAT-TA-ATATAATATATAATATACCATATAAATATATATATATAATAAATATAT
1 ATAATATATATACATATAATATAT-ATATA-CATATAAATATATATATATAATAAATATAT
*
328287 ACTAATATATATA-ACAT-ATA-ATATATA-ATAT-AATATATATA-ATAATAAATACTAT
1 A-TAATATATATACATATAATATATATATACATATAAATATATATATATAATAAATA-TAT
* * * *
328342 ATAATA-ATATA-ACATAATATATA-ATAC-TATATACTATATAAATATTAT-AATATAT
1 ATAATATATATACATATAATATATATATACATATA-AATATATATATATAATAAATATAT
328397 AT
1 AT
328399 GTTATATAAC
Statistics
Matches: 197, Mismatches: 14, Indels: 44
0.77 0.05 0.17
Matches are distributed among these distances:
53 9 0.05
54 24 0.12
55 22 0.11
56 16 0.08
57 10 0.05
58 13 0.07
59 23 0.12
60 35 0.18
61 38 0.19
62 7 0.04
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (59 bp):
ATAATATATATACATATAATATATATATACATATAAATATATATATATAATAAATATAT
Found at i:328380 original size:94 final size:92
Alignment explanation
Indices: 328108--328397 Score: 252
Period size: 97 Copynumber: 3.0 Consensus size: 92
328098 AAAATAATAT
* * * *
328108 TAATA-ATAATATCATATAATATAATAAATATATAATA-ATAAAAATACTAAAAATAATATATAA
1 TAATATATAATATAATAT-ATATAAT-AATAAATAATATATAATAATA-T-AACATAATATATAA
*
328171 TATATATACTATACA-AATATATAT-ACTTTAATA
62 TATATATACTATATACAATATATATAAC----ATA
* * * *
328204 TAATATAT-ATACTAATATATATGTATAATATATTAATATAATATATAATATACCATATAAATAT
1 TAATATATAATA-TAATATATAT-AATAATA-AATAATAT-ATA-ATAATATAACATA-ATATAT
*
328268 ATATATATAATAAATATATACTAATATATATAACATA
60 A-ATATAT-AT-ACTATATAC-AATATATATAACATA
*
328305 TAATATATAATATAATATATATAATAATAAATACTATATAATAATATAACATAATATATAATACT
1 TAATATATAATATAATATATATAATAATAAATAATATATAATAATATAACATAATATATAATA-T
*
328370 ATATACTATATA-AATAT-TATAATATA
65 ATATACTATATACAATATATATAACATA
328396 TA
1 TA
328398 TGTTATATAA
Statistics
Matches: 161, Mismatches: 17, Indels: 37
0.75 0.08 0.17
Matches are distributed among these distances:
91 10 0.06
92 5 0.03
94 7 0.04
95 5 0.03
96 25 0.16
97 26 0.16
98 7 0.04
99 16 0.10
100 17 0.11
101 23 0.14
102 9 0.06
104 9 0.06
105 2 0.01
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (92 bp):
TAATATATAATATAATATATATAATAATAAATAATATATAATAATATAACATAATATATAATATA
TATACTATATACAATATATATAACATA
Found at i:328444 original size:24 final size:24
Alignment explanation
Indices: 328417--328489 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 24
328407 ACACCATGCT
328417 ATATAATATATATTGTATAAAATA
1 ATATAATATATATTGTATAAAATA
*
328441 ATAT-ATAATATATTATATATAATATA
1 ATATAAT-ATATATTGTATA-AA-ATA
* *
328467 GTATAATACTATAGTGTATAAAA
1 ATATAATA-TATATTGTATAAAA
328490 AGAAATTCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
23 2 0.05
24 15 0.38
25 3 0.08
26 9 0.22
27 11 0.28
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.41
Consensus pattern (24 bp):
ATATAATATATATTGTATAAAATA
Found at i:329466 original size:15 final size:15
Alignment explanation
Indices: 329448--329476 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
329438 TTTCTCACCT
329448 TTCTTGTTCTTGTTC
1 TTCTTGTTCTTGTTC
329463 TTCTTGTTCTTGTT
1 TTCTTGTTCTTGTT
329477 TGGAGCTGGA
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:0.00, C:0.17, G:0.14, T:0.69
Consensus pattern (15 bp):
TTCTTGTTCTTGTTC
Found at i:343617 original size:18 final size:19
Alignment explanation
Indices: 343591--343628 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
343581 TATATTTTAC
* *
343591 ATTAGTAAATAATTTTAAA
1 ATTAGTAAAAAATATTAAA
343610 ATTA-TAAAAAATATTAAA
1 ATTAGTAAAAAATATTAAA
343628 A
1 A
343629 AACACAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
ATTAGTAAAAAATATTAAA
Found at i:343670 original size:12 final size:12
Alignment explanation
Indices: 343653--343678 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
343643 TAAAATAATG
343653 TAATTATTTTCT
1 TAATTATTTTCT
343665 TAATTATTTTCT
1 TAATTATTTTCT
343677 TA
1 TA
343679 TATGTTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (12 bp):
TAATTATTTTCT
Found at i:347533 original size:53 final size:54
Alignment explanation
Indices: 347433--347605 Score: 251
Period size: 54 Copynumber: 3.2 Consensus size: 54
347423 GGTTCTCGCA
* * *
347433 TAAGGTGTGGGCACGACTTATTCGTCCAT-AGCTATCGCAGAAGAAGTCATCAGT
1 TAAGGCGTGGGCACGACTTATTCATCC-TGAGCTATCGCAGAAGAAGTCTTCAGT
*
347487 TAAGGCGTGGGCACGGCTTA-TCATCCTGAGCTATCGCAGAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGACTTATTCATCCTGAGCTATCGCAGAAGAAGTCTTCAGT
* * * *
347540 TAAGGCGTGGGCACGACTTATTCATCCTGAGATATCACAGAAGAAATCTTCAAT
1 TAAGGCGTGGGCACGACTTATTCATCCTGAGCTATCGCAGAAGAAGTCTTCAGT
347594 TAAGGCGTGGGC
1 TAAGGCGTGGGC
347606 GCATCTTCAA
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
52 1 0.01
53 48 0.44
54 59 0.55
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.25
Consensus pattern (54 bp):
TAAGGCGTGGGCACGACTTATTCATCCTGAGCTATCGCAGAAGAAGTCTTCAGT
Found at i:348657 original size:13 final size:13
Alignment explanation
Indices: 348641--348666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
348631 TTATAAAATA
348641 AAAATTAAATTTT
1 AAAATTAAATTTT
348654 AAAATTAAATTTT
1 AAAATTAAATTTT
348667 TTTATTTTTA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATTAAATTTT
Found at i:363761 original size:21 final size:20
Alignment explanation
Indices: 363722--363762 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
363712 AAGTATTAGG
* *
363722 TCCAAAAAAAAACTGAAGCA
1 TCCAAAAAAAAAATCAAGCA
363742 TCCAAAAAAATAAATCAAGCA
1 TCCAAAAAAA-AAATCAAGCA
363763 GTAAACATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.61, C:0.20, G:0.07, T:0.12
Consensus pattern (20 bp):
TCCAAAAAAAAAATCAAGCA
Found at i:365552 original size:21 final size:21
Alignment explanation
Indices: 365503--365565 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
365493 TTAATAGTTG
365503 TATCTTT-TTGACACGTATTCTTC
1 TATCTTTATTG-CACGT-TT-TTC
365526 TATCTTTATTGCACGTTTTTC
1 TATCTTTATTGCACGTTTTTC
* * *
365547 TGTCTTTATGGCATGTTTT
1 TATCTTTATTGCACGTTTT
365566 CAGTTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 19 0.53
22 2 0.06
23 12 0.33
24 3 0.08
ACGTcount: A:0.14, C:0.17, G:0.13, T:0.56
Consensus pattern (21 bp):
TATCTTTATTGCACGTTTTTC
Found at i:366759 original size:17 final size:17
Alignment explanation
Indices: 366733--366766 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
366723 CGCCTAAAAT
* *
366733 ATTTACTTATTAAATAA
1 ATTTAATTATCAAATAA
366750 ATTTAATTATCAAATAA
1 ATTTAATTATCAAATAA
366767 TCTTCGACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAATTATCAAATAA
Found at i:367176 original size:31 final size:32
Alignment explanation
Indices: 367122--367194 Score: 121
Period size: 31 Copynumber: 2.3 Consensus size: 32
367112 TCTTCGCATA
*
367122 CCGTAGAAAAAACACTCTCTCATCAAGTCATTG
1 CCGTGGAAAAAACAC-CTCTCATCAAGTCATTG
367155 CCGTGGAAAAAACA-CTCTCATCAAGTCATTG
1 CCGTGGAAAAAACACCTCTCATCAAGTCATTG
367186 CCGTGGAAA
1 CCGTGGAAA
367195 GCAAGTCATA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 26 0.67
33 13 0.33
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (32 bp):
CCGTGGAAAAAACACCTCTCATCAAGTCATTG
Found at i:371988 original size:20 final size:20
Alignment explanation
Indices: 371950--371987 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
371940 ACTAATAAAA
*
371950 TTTCAGATATAAAAATATAT
1 TTTCAGATAGAAAAATATAT
371970 TTTCA-ATAG-AAAATATAT
1 TTTCAGATAGAAAAATATAT
371988 AAAAAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
TTTCAGATAGAAAAATATAT
Found at i:372982 original size:22 final size:23
Alignment explanation
Indices: 372930--372984 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
372920 AGTGATCATC
372930 AAATTTT-TATTGAAATGTTATA
1 AAATTTTATATTGAAATGTTATA
*
372952 AAA-TGTATATT-AAAT-TTATTA
1 AAATTTTATATTGAAATGTTA-TA
372973 AAATTTTATATT
1 AAATTTTATATT
372985 TATTATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 11 0.39
22 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
AAATTTTATATTGAAATGTTATA
Found at i:375768 original size:29 final size:29
Alignment explanation
Indices: 375732--375808 Score: 154
Period size: 29 Copynumber: 2.7 Consensus size: 29
375722 TGTGTTCCCG
375732 CTGCTCCCTCGTGCCATAGCTGCTCCCTC
1 CTGCTCCCTCGTGCCATAGCTGCTCCCTC
375761 CTGCTCCCTCGTGCCATAGCTGCTCCCTC
1 CTGCTCCCTCGTGCCATAGCTGCTCCCTC
375790 CTGCTCCCTCGTGCCATAG
1 CTGCTCCCTCGTGCCATAG
375809 TTGCCAGACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.08, C:0.47, G:0.18, T:0.27
Consensus pattern (29 bp):
CTGCTCCCTCGTGCCATAGCTGCTCCCTC
Found at i:386277 original size:17 final size:17
Alignment explanation
Indices: 386255--386288 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
386245 TGATTAAAAT
*
386255 ATTTAATTATTAAATAA
1 ATTTAATTATCAAATAA
386272 ATTTAATTATCAAATAA
1 ATTTAATTATCAAATAA
386289 TCTTCAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAATTATCAAATAA
Found at i:387329 original size:21 final size:23
Alignment explanation
Indices: 387303--387348 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
387293 TTATTATTTG
387303 TTCATTT-TG-GTCACTGCACTT
1 TTCATTTCTGAGTCACTGCACTT
* *
387324 TTCATTTCTGATTTACTGCACTT
1 TTCATTTCTGAGTCACTGCACTT
387347 TT
1 TT
387349 ATCATTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 2 0.10
23 12 0.57
ACGTcount: A:0.15, C:0.22, G:0.11, T:0.52
Consensus pattern (23 bp):
TTCATTTCTGAGTCACTGCACTT
Found at i:387628 original size:21 final size:21
Alignment explanation
Indices: 387589--387628 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
387579 TTATGCTTAT
*
387589 TTTAAGTTTTTTATTTATTGG
1 TTTAAGTTTTTTATCTATTGG
387610 TTTAATGTTTTTTA-CTATT
1 TTTAA-GTTTTTTATCTATT
387629 TTTTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.20, C:0.03, G:0.10, T:0.68
Consensus pattern (21 bp):
TTTAAGTTTTTTATCTATTGG
Found at i:389004 original size:12 final size:12
Alignment explanation
Indices: 388962--389009 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
388952 TTTCCTCTTT
*
388962 TAATAAAA-TAA
1 TAATAAAACAAA
388973 TAATAAAACAAA
1 TAATAAAACAAA
* *
388985 AAACAAAACAAA
1 TAATAAAACAAA
*
388997 TAATAAAAAAAA
1 TAATAAAACAAA
389009 T
1 T
389010 GGTGTTTACA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (12 bp):
TAATAAAACAAA
Found at i:392781 original size:13 final size:13
Alignment explanation
Indices: 392749--392781 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
392739 TATTTTAAAT
392749 TTTAT-ATTTAGA
1 TTTATAATTTAGA
392761 TTATATAATTTAGA
1 TT-TATAATTTAGA
392775 TTTATAA
1 TTTATAA
392782 ATTTTATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 8 0.42
14 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (13 bp):
TTTATAATTTAGA
Found at i:392883 original size:18 final size:18
Alignment explanation
Indices: 392842--392877 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
392832 TTTTATGTGG
* *
392842 ATTTTAAAATAATATAAA
1 ATTTAAAAATAAAATAAA
392860 ATTTAAAAATAAAATAAA
1 ATTTAAAAATAAAATAAA
392878 TATTAATTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTTAAAAATAAAATAAA
Found at i:398585 original size:30 final size:30
Alignment explanation
Indices: 398527--398655 Score: 176
Period size: 29 Copynumber: 4.4 Consensus size: 30
398517 ACCGGGTGAC
* *
398527 ATTTTGGGAA-TTAATTCGAAATAGGTGCT
1 ATTTTGGGAATTTAATTCAAAAAAGGTGCT
*
398556 ATTTTGTGAA-TTAATTCAAAAAAAGGTGCT
1 ATTTTGGGAATTTAATTC-AAAAAAGGTGCT
398586 ATTTTGGGAATTTAATTCAAAAAA-GTGCT
1 ATTTTGGGAATTTAATTCAAAAAAGGTGCT
*
398615 ATTTTGTGAATTTAATTC-AAAAAGGTGCT
1 ATTTTGGGAATTTAATTCAAAAAAGGTGCT
*
398644 ATTTTGGTAATT
1 ATTTTGGGAATT
398656 ATTTTAAAAA
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
28 5 0.06
29 53 0.59
30 25 0.28
31 7 0.08
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (30 bp):
ATTTTGGGAATTTAATTCAAAAAAGGTGCT
Found at i:398619 original size:59 final size:59
Alignment explanation
Indices: 398527--398655 Score: 192
Period size: 59 Copynumber: 2.2 Consensus size: 59
398517 ACCGGGTGAC
* *
398527 ATTTTGGGAA-TTAATTCGAAATAGGTGCTATTTTGTGAA-TTAATTCAAAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAAGTGCTATTTTGTGAATTTAATTC--AAAAAGGTGCT
398586 ATTTTGGGAATTTAATTC-AAAAAAGTGCTATTTTGTGAATTTAATTCAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAAAGTGCTATTTTGTGAATTTAATTCAAAAAGGTGCT
*
398644 ATTTTGGTAATT
1 ATTTTGGGAATT
398656 ATTTTAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
58 22 0.34
59 29 0.45
60 14 0.22
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (59 bp):
ATTTTGGGAATTTAATTCGAAAAAAGTGCTATTTTGTGAATTTAATTCAAAAAGGTGCT
Found at i:398665 original size:29 final size:29
Alignment explanation
Indices: 398549--398676 Score: 118
Period size: 29 Copynumber: 4.4 Consensus size: 29
398539 AATTCGAAAT
**
398549 AGGTGCTATTTTGTGAATTAATTCAAAAAA
1 AGGTGCTATTTTGTGAATT-ATTTTAAAAA
* * *
398579 AGGTGCTATTTTGGGAATTTAATTCAAAAA
1 AGGTGCTATTTTGTGAA-TTATTTTAAAAA
* *
398609 A-GTGCTATTTTGTGAATT-TAATTCAAAA
1 AGGTGCTATTTTGTGAATTAT-TTTAAAAA
398637 AGGTGCTATTTTG-GTAATTATTTTAAAAA
1 AGGTGCTATTTTGTG-AATTATTTTAAAAA
* *
398666 TGGTGATATTT
1 AGGTGCTATTT
398677 CTGTAAAATG
Statistics
Matches: 80, Mismatches: 13, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
28 9 0.11
29 44 0.55
30 25 0.31
31 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.41
Consensus pattern (29 bp):
AGGTGCTATTTTGTGAATTATTTTAAAAA
Found at i:398676 original size:58 final size:59
Alignment explanation
Indices: 398527--398676 Score: 184
Period size: 58 Copynumber: 2.6 Consensus size: 59
398517 ACCGGGTGAC
*
398527 ATTTTGGGAA-TTAATTC-GAAATAGGTGCTATTTTGTGAATTAATTCAAAAAAAGGTGCT
1 ATTTTGGGAATTTAATTCAAAAAT-GGTGCTATTTTGTGAATTAATTC-AAAAAAGGTGCT
*
398586 ATTTTGGGAATTTAATTCAAAAA-AGTGCTATTTTGTGAATTTAATTC-AAAAAGGTGCT
1 ATTTTGGGAATTTAATTCAAAAATGGTGCTATTTTGTGAA-TTAATTCAAAAAAGGTGCT
* * * *
398644 ATTTTGGTAA-TTATTTTAAAAATGGTGATATTT
1 ATTTTGGGAATTTAATTCAAAAATGGTGCTATTT
398677 CTGTAAAATG
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
57 10 0.12
58 28 0.35
59 25 0.31
60 14 0.17
61 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.41
Consensus pattern (59 bp):
ATTTTGGGAATTTAATTCAAAAATGGTGCTATTTTGTGAATTAATTCAAAAAAGGTGCT
Found at i:405773 original size:5 final size:5
Alignment explanation
Indices: 405765--405810 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
405755 CCCGATCGTT
* *
405765 GACCC GACCC GACCC GACCC GACCGTT GACCC GACCC AACCC GACC
1 GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
405811 GTTGACCCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 31 0.89
7 4 0.11
ACGTcount: A:0.22, C:0.54, G:0.20, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:405774 original size:22 final size:22
Alignment explanation
Indices: 405770--405819 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
405760 TCGTTGACCC
*
405770 GACCCGACCCGACCCGACCGTT
1 GACCCGACCCAACCCGACCGTT
405792 GACCCGACCCAACCCGACCGTT
1 GACCCGACCCAACCCGACCGTT
405814 GACCCG
1 GACCCG
405820 TTGACCGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.50, G:0.22, T:0.08
Consensus pattern (22 bp):
GACCCGACCCAACCCGACCGTT
Found at i:405784 original size:27 final size:27
Alignment explanation
Indices: 405746--405810 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
405736 CTGAACTGGT
* *
405746 CCGACCCTACCCGATCGTTGACCCGAC
1 CCGACCCGACCCGACCGTTGACCCGAC
405773 CCGACCCGACCCGACCGTTGACCCGAC
1 CCGACCCGACCCGACCGTTGACCCGAC
*
405800 CCAACCCGACC
1 CCGACCCGACC
405811 GTTGACCCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.20, C:0.52, G:0.18, T:0.09
Consensus pattern (27 bp):
CCGACCCGACCCGACCGTTGACCCGAC
Found at i:405868 original size:29 final size:28
Alignment explanation
Indices: 405833--405953 Score: 161
Period size: 29 Copynumber: 4.2 Consensus size: 28
405823 ACCGGGTGAC
*
405833 ATTTTGGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTCGAAA-AGGTGCT
*
405862 ATTTTGGGAATTAATTCGAAAAGGTACT
1 ATTTTGGGAATTAATTCGAAAAGGTGCT
* *
405890 ATTTTGGGAAATTAATTCGAAAAAGTGCC
1 ATTTTGGG-AATTAATTCGAAAAGGTGCT
* *
405919 ATTTTGTGAATTTAATTCAAAAAGGTGCT
1 ATTTTGGGAA-TTAATTCGAAAAGGTGCT
405948 ATTTTG
1 ATTTTG
405954 ATAATTATTT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
28 15 0.19
29 66 0.81
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (28 bp):
ATTTTGGGAATTAATTCGAAAAGGTGCT
Found at i:417876 original size:18 final size:19
Alignment explanation
Indices: 417853--417889 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
417843 GTGGATTTTT
*
417853 AAAATAATATAAA-ATTAA
1 AAAATAAAATAAATATTAA
417871 AAAATAAAATAAATATTAA
1 AAAATAAAATAAATATTAA
417890 TTAGGTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATAAAATAAATATTAA
Found at i:418225 original size:2 final size:2
Alignment explanation
Indices: 418218--418246 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
418208 AGGGATAGAA
418218 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 A
418247 GAAATAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:428983 original size:29 final size:29
Alignment explanation
Indices: 428949--429007 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
428939 CCTAAATTAA
428949 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
428978 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
429007 T
1 T
429008 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:433595 original size:29 final size:29
Alignment explanation
Indices: 433561--433619 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
433551 CCTAAATTAA
433561 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
433590 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
433619 T
1 T
433620 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:437203 original size:285 final size:284
Alignment explanation
Indices: 436666--437237 Score: 975
Period size: 285 Copynumber: 2.0 Consensus size: 284
436656 TTGAGTTGAA
* * *
436666 AAAAAATAAGATTTTTTAAATTTAAATATTTTAGAATGGATTTATATGAGTTTAATATTTATATG
1 AAAAAATAAGATATTTTAAATTTAAATATTTTAGAATGGATTTATATAAGTTTAATATTTAAATG
*
436731 ATTTATGTTTGAATACAAAAGGACACGTCAAATGACAAAAATTCTTATAACTAATTAATAAATAT
66 ATTTATGTTTGAATACAAAAGGACACATCAAATGACAAAAATTCTTATAACTAATTAATAAATAT
* * *
436796 ATAACAAAATAACAACAAAAAGAGGAAGTAAAATTATGTTATACCTGTCAAGTTGTTATTGGAAA
131 ATAACAAAATAACAACAAAAAGAGGAAGTAAAATTATATTATACCAGTCAAGTTGTTATTCGAAA
* *
436861 AATGAATAATCTCTAGAGAAATTATATTTTCGATAACCGATGGAATTGTACCTGAAATGTAAAAT
196 AATCAATAATCTCTAGAGAAATTATATTTCCGATAACCGATGGAATTGTACCTGAAATGTAAAAT
436926 TAAATTTGTCAAAATAATTTGACG
261 TAAATTTGTCAAAATAATTTGACG
*
436950 AAAAAATAAGATATTTTAAATTTAAATCATTTTAGAATGGATTTATCTAAGTTTAATATTTAAAT
1 AAAAAATAAGATATTTTAAATTTAAAT-ATTTTAGAATGGATTTATATAAGTTTAATATTTAAAT
* * *
437015 GATTTATGTTTGAATACAAAAGGCCACATCAAGTTACAAAAATTCTTATAACTAATTAATAAATA
65 GATTTATGTTTGAATACAAAAGGACACATCAAATGACAAAAATTCTTATAACTAATTAATAAATA
437080 TATAACAAAATAACAACAAAAAGAGGAAG-AAAAGTTATATTATACCAGTCAAGTTGTTATTCGA
130 TATAACAAAATAACAACAAAAAGAGGAAGTAAAA-TTATATTATACCAGTCAAGTTGTTATTCGA
* *
437144 AAAATCAATAATTTCTAGAGAAATTATATTTCCGATAGCCGATGGAATTGTACCTGAAATGTAAA
194 AAAATCAATAATCTCTAGAGAAATTATATTTCCGATAACCGATGGAATTGTACCTGAAATGTAAA
*
437209 ATTAAATTTGTCAAAATGATTTGACG
259 ATTAAATTTGTCAAAATAATTTGACG
437235 AAA
1 AAA
437238 TAAGAATATT
Statistics
Matches: 270, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
284 30 0.11
285 240 0.89
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (284 bp):
AAAAAATAAGATATTTTAAATTTAAATATTTTAGAATGGATTTATATAAGTTTAATATTTAAATG
ATTTATGTTTGAATACAAAAGGACACATCAAATGACAAAAATTCTTATAACTAATTAATAAATAT
ATAACAAAATAACAACAAAAAGAGGAAGTAAAATTATATTATACCAGTCAAGTTGTTATTCGAAA
AATCAATAATCTCTAGAGAAATTATATTTCCGATAACCGATGGAATTGTACCTGAAATGTAAAAT
TAAATTTGTCAAAATAATTTGACG
Found at i:441131 original size:54 final size:53
Alignment explanation
Indices: 441052--441301 Score: 189
Period size: 54 Copynumber: 4.6 Consensus size: 53
441042 GCGAAATATT
* * * *
441052 AAAATCTCCCACCTCATTCGTATTAACAAGATCTGAACCCTTATGCGAATTAAC
1 AAAAGCTCCCACCTCATGCGAATTAA-AAAATCTGAACCCTTATGCGAATTAAC
* * **
441106 AAAAGCTCCCACCTCATGCGCATTAAAAAATACTAAACCCTTATGCGAATTTTC
1 AAAAGCTCCCACCTCATGCGAATTAAAAAAT-CTGAACCCTTATGCGAATTAAC
* * ** * ** * * *
441160 TAACGCTCCCACCTCCGGCGCATTTAAAAGTTCTGAACCCTTTTGTGAATTATC
1 AAAAGCTCCCACCTCATGCG-AATTAAAAAATCTGAACCCTTATGCGAATTAAC
* * * * *
441214 AAAAGCTCCCACTTCATGTGAATTAACAAAAGCT--CCCACTTCATGTGAATTAAC
1 AAAAGCTCCCACCTCATGCGAATTAA-AAAATCTGAACC-CTT-ATGCGAATTAAC
* * *
441268 AAAAGTTCCCACCTCAAGCGAATTATTAAAATCT
1 AAAAGCTCCCACCTCATGCGAATTA-AAAAATCT
441302 CCCTCCACCT
Statistics
Matches: 152, Mismatches: 38, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
52 2 0.01
53 12 0.08
54 131 0.86
55 7 0.05
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (53 bp):
AAAAGCTCCCACCTCATGCGAATTAAAAAATCTGAACCCTTATGCGAATTAAC
Found at i:441304 original size:27 final size:27
Alignment explanation
Indices: 441203--441279 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
441193 TGAACCCTTT
*
441203 TGTGAATTATCAAAAGCTCCCACTTCA
1 TGTGAATTAACAAAAGCTCCCACTTCA
441230 TGTGAATTAACAAAAGCTCCCACTTCA
1 TGTGAATTAACAAAAGCTCCCACTTCA
*
441257 TGTGAATTAACAAAAGTTCCCAC
1 TGTGAATTAACAAAAGCTCCCAC
441280 CTCAAGCGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (27 bp):
TGTGAATTAACAAAAGCTCCCACTTCA
Found at i:441645 original size:29 final size:29
Alignment explanation
Indices: 441600--441682 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
441590 CTCACCTAAC
* *
441600 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGAGGTAAGCAATGACATCATTAAT
* *
441630 TAAATGAGGTCAGCAATGACATCTTTAAT
1 TAAATGAGGTAAGCAATGACATCATTAAT
* *
441659 TAAATGATGTAAGTAATGACATCA
1 TAAATGAGGTAAGCAATGACATCA
441683 ATTTAGTTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 41 0.91
30 4 0.09
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (29 bp):
TAAATGAGGTAAGCAATGACATCATTAAT
Found at i:445068 original size:15 final size:15
Alignment explanation
Indices: 445048--445077 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
445038 CTTTCTCATA
445048 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
445063 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
445078 CCAGCCTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:446402 original size:29 final size:29
Alignment explanation
Indices: 446355--446437 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
446345 CTCACCTAAC
*
446355 TAAATTGATGTAAGAAATGACATCATTACT
1 TAAA-TGATGTAAGAAATGACATCATTAAT
* * *
446385 TAAATGAGGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGAAATGACATCATTAAT
*
446414 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGAAATGACATCA
446438 ATTTAGTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 42 0.91
30 4 0.09
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGAAATGACATCATTAAT
Found at i:447811 original size:23 final size:22
Alignment explanation
Indices: 447785--447827 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
447775 CACGTATTCT
*
447785 TCTGCCTTTATGACATGTTTTTC
1 TCTGCCTCTATGACAT-TTTTTC
*
447808 TCTGCCTCTATGGCATTTTT
1 TCTGCCTCTATGACATTTTT
447828 CAATTGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.12, C:0.23, G:0.14, T:0.51
Consensus pattern (22 bp):
TCTGCCTCTATGACATTTTTTC
Found at i:453154 original size:30 final size:30
Alignment explanation
Indices: 453120--453207 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
453110 GTGTACAACT
* * *
453120 CTCTAGAAGCTTGTGGAAGA-GTGTGGAATC
1 CTCTAGAAGATTCTGG-AGACGTATGGAATC
*
453150 CTCTAGAATATTCTGGAGACGTATGGAATC
1 CTCTAGAAGATTCTGGAGACGTATGGAATC
* * * *
453180 CTCTAGAATATTATGGAGATGTGTGGAA
1 CTCTAGAAGATTCTGGAGACGTATGGAA
453208 CCTTATGGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 3 0.06
30 47 0.94
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (30 bp):
CTCTAGAAGATTCTGGAGACGTATGGAATC
Found at i:453213 original size:20 final size:19
Alignment explanation
Indices: 453189--453247 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
453179 CCTCTAGAAT
453189 ATTATGGAGATGTGTGGAAC
1 ATTATGGAGA-GTGTGGAAC
*
453209 CTTATGGAAGAGTGTGGAAC
1 ATTATGG-AGAGTGTGGAAC
*
453229 ATTATGGAAGAGTATGGAA
1 ATTATGG-AGAGTGTGGAA
453248 GAATATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 32 0.91
21 3 0.09
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.27
Consensus pattern (19 bp):
ATTATGGAGAGTGTGGAAC
Found at i:453226 original size:10 final size:10
Alignment explanation
Indices: 453211--453254 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
453201 TGTGGAACCT
453211 TATGGAAGAG
1 TATGGAAGAG
* * *
453221 TGTGGAACAT
1 TATGGAAGAG
453231 TATGGAAGAG
1 TATGGAAGAG
*
453241 TATGGAAGAA
1 TATGGAAGAG
453251 TATG
1 TATG
453255 AAAGGGAGTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.39, C:0.02, G:0.34, T:0.25
Consensus pattern (10 bp):
TATGGAAGAG
Found at i:453254 original size:20 final size:20
Alignment explanation
Indices: 453211--453254 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
453201 TGTGGAACCT
* *
453211 TATGGAAGAGTGTGGAACAT
1 TATGGAAGAGTATGGAACAA
*
453231 TATGGAAGAGTATGGAAGAA
1 TATGGAAGAGTATGGAACAA
453251 TATG
1 TATG
453255 AAAGGGAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.34, T:0.25
Consensus pattern (20 bp):
TATGGAAGAGTATGGAACAA
Found at i:453864 original size:13 final size:13
Alignment explanation
Indices: 453845--453887 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
453835 GTCACAACCC
453845 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
453858 TACCCGACCCATT
1 GACCCGACCCGTT
453871 GACCCGACCCGTT
1 GACCCGACCCGTT
453884 GACC
1 GACC
453888 GTTGACCGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:454414 original size:2 final size:2
Alignment explanation
Indices: 454409--454442 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
454399 ATGCTTTAAA
454409 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
454443 CTTTTTACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:456436 original size:29 final size:29
Alignment explanation
Indices: 456403--456488 Score: 163
Period size: 29 Copynumber: 3.0 Consensus size: 29
456393 CTAAATTAAT
456403 TTGATGTCATTGCTTACATCAATTTAGTA
1 TTGATGTCATTGCTTACATCAATTTAGTA
456432 TTGATGTCATTGCTTACATCAATTTAGTA
1 TTGATGTCATTGCTTACATCAATTTAGTA
*
456461 TTGATGTCATTTCTTACATCAATTTAGT
1 TTGATGTCATTGCTTACATCAATTTAGT
456489 TAGGTGAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.47
Consensus pattern (29 bp):
TTGATGTCATTGCTTACATCAATTTAGTA
Found at i:461152 original size:29 final size:29
Alignment explanation
Indices: 461119--461175 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
461109 CTAAATTAAT
461119 TTGATGTCATTGCTTACATCAATTTAGTA
1 TTGATGTCATTGCTTACATCAATTTAGTA
461148 TTGATGTCATTGCTTACATCAATTTAGT
1 TTGATGTCATTGCTTACATCAATTTAGT
461176 TAGGTGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
TTGATGTCATTGCTTACATCAATTTAGTA
Found at i:467951 original size:28 final size:30
Alignment explanation
Indices: 467868--467959 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 30
467858 AGTCGGGCGA
467868 TCATTTTGTAACTTTTAATAATCGAGGGAC
1 TCATTTTGTAACTTTTAATAATCGAGGGAC
** * ** *
467898 TCAACATAGTAACTCCCT-ATAGTCGA-GGAC
1 TC-ATTTTGTAACT-TTTAATAATCGAGGGAC
*
467928 -CATTTTGTAACTTTTAATAATCGATGGAC
1 TCATTTTGTAACTTTTAATAATCGAGGGAC
467957 TCA
1 TCA
467960 ATAAAATAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
27 1 0.02
28 15 0.33
29 5 0.11
30 8 0.18
31 15 0.33
32 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (30 bp):
TCATTTTGTAACTTTTAATAATCGAGGGAC
Found at i:471090 original size:35 final size:35
Alignment explanation
Indices: 471017--471090 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
471007 CGTCACGTCC
* **
471017 AGTAAGGCCCTGAGCACACAACCGAGGAACCGGTA
1 AGTAAGGCCCTAAGCACACAACCGAGGAACCGCCA
* * *
471052 AGTAAGGCCCTAAGCACACAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTAAGCACACAACCGAGGAACCGCCA
471087 AGTA
1 AGTA
471091 TACTTCCTCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.30, G:0.27, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTAAGCACACAACCGAGGAACCGCCA
Found at i:471197 original size:24 final size:24
Alignment explanation
Indices: 471170--471265 Score: 140
Period size: 24 Copynumber: 4.0 Consensus size: 24
471160 CATAATTAAT
* *
471170 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAA
471194 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
*
471218 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAA
*
471242 GTC-AGATATCAGATCAGAATCCAA
1 GTCAAG-TATCATATCAGAATCCAA
471266 ATCGAAAATC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 2 0.03
24 64 0.97
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:471276 original size:24 final size:23
Alignment explanation
Indices: 471170--471279 Score: 103
Period size: 24 Copynumber: 4.6 Consensus size: 23
471160 CATAATTAAT
* * *
471170 GTCAAGTATCATATCAAAATCCAG
1 GTCAA-TATCAGATCAGAATCCAA
*
471194 GTCAAGTATCATATCAGAATCCAA
1 GTCAA-TATCAGATCAGAATCCAA
* *
471218 GTCAAGTATCATATCAGAATCCAT
1 GTCAA-TATCAGATCAGAATCCAA
471242 GTCAGATATCAGATCAGAATCCAA
1 GTCA-ATATCAGATCAGAATCCAA
* *
471266 ATCGAAAATCAGAT
1 GTC-AATATCAGAT
471280 AAAATATTCA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
24 75 0.97
25 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAA
Found at i:477863 original size:12 final size:12
Alignment explanation
Indices: 477846--477871 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
477836 TAAAAGAATG
477846 TAATTATTTTCT
1 TAATTATTTTCT
477858 TAATTATTTTCT
1 TAATTATTTTCT
477870 TA
1 TA
477872 TATGTTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (12 bp):
TAATTATTTTCT
Found at i:478617 original size:60 final size:60
Alignment explanation
Indices: 478449--478633 Score: 343
Period size: 60 Copynumber: 3.1 Consensus size: 60
478439 CCGAATACTA
*
478449 AATCAATTTATCCCAAGGTACCCTTGCACCATGCTCACGAATAGCTTTTCATATATTTGC
1 AATCAATTTGTCCCAAGGTACCCTTGCACCATGCTCACGAATAGCTTTTCATATATTTGC
478509 AATCAATTTGTCCCAAAGGTACCCTTGCACCATGCTCACGAATAGCTTTTCATATATTTGC
1 AATCAATTTGTCCC-AAGGTACCCTTGCACCATGCTCACGAATAGCTTTTCATATATTTGC
*
478570 AATCAATTTGTCCCAAGGTACCCTCGCACCATGCTCACGAATAGCTTTTCATATATTTGC
1 AATCAATTTGTCCCAAGGTACCCTTGCACCATGCTCACGAATAGCTTTTCATATATTTGC
478630 AATC
1 AATC
478634 GACGTTGAAG
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
60 62 0.51
61 60 0.49
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.32
Consensus pattern (60 bp):
AATCAATTTGTCCCAAGGTACCCTTGCACCATGCTCACGAATAGCTTTTCATATATTTGC
Found at i:479360 original size:380 final size:377
Alignment explanation
Indices: 478638--479358 Score: 1171
Period size: 380 Copynumber: 1.9 Consensus size: 377
478628 GCAATCGACG
* *
478638 TTGAAGAACCCATCCACAATTTACTCATATTATTATTAGGATAAGCTTTATCAGTGATCACCCAA
1 TTGAAGAACCCATCCACAATTTACTCATATTATTATTAGGATAAGCTATATCAGTGACCACCCAA
* * * *
478703 CTATTGTGATCCCTTTTCATTTTGATCACTATTTTTGATTTTTTGTCAATTAGGTTAGCTAACTA
66 CTATTGTGATCCCTTTTCATTTTGATCACCATTTTTGAATTTTTGTCAATTAGGTCACCTAACTA
* *
478768 TTTAAATGATTCAATCGAGACACTTACCGTTAACCTTTAACGGAAGTGTTGACGTGGTAGTTAAT
131 TTTAAATGATTCAATCGAGACACTTACCGTTAACCTTTAACGGAAGTGCTGACATGGTAGTTAAT
478833 AAAATTGATATAATTACACATTTGATCTTCAATATTTATACATTATATCAATTTGGTCATAATTT
196 AAAATTGATATAATTACACATTTGATCTTCAATATTTATACATTATATCAATTTGGTCATAA---
* *
478898 TAATTTAATTTAATAAATTTAATCTTCAATTAAATGATGACACAAATCATTGCGTGGTTGGAGGA
258 TAATTTAATTTAATAAATTTAATATCCAATTAAATGATGACACAAATCATTGCGTGGTTGGAGGA
478963 TATTTTTTAAAATTTAATTTATCTAATTTAATATTTTATCCTCCAATTAAGTGGT
323 TATTTTTTAAAATTTAATTTATCTAATTTAATATTTTATCCTCCAATTAAGTGGT
* * * *
479018 TTGAGGAACCCGTCCACAATTTACTCTTATTATTATTAGGATAAGCTATA-CTAGTGACCACCTA
1 TTGAAGAACCCATCCACAATTTACTCATATTATTATTAGGATAAGCTATATC-AGTGACCACCCA
*
479082 ACTATTGTGATCCCTTTTCATTTTGATCACCATTTTTGAATTTTTGTTAATTAGGTCACCTAACT
65 ACTATTGTGATCCCTTTTCATTTTGATCACCATTTTTGAATTTTTGTCAATTAGGTCACCTAACT
*
479147 ATTTAAATGATTCAATCGAGTCACTTACCGTTAACCTTTAACGGAAGTGCTGACATGGTAGTTAA
130 ATTTAAATGATTCAATCGAGACACTTACCGTTAACCTTTAACGGAAGTGCTGACATGGTAGTTAA
** * *
479212 TAACTTTGGTATAGTTACACATTTGATCTTCAATATTTATACATTATATCAATTTGGTCAT-A-A
195 TAAAATTGATATAATTACACATTTGATCTTCAATATTTATACATTATATCAATTTGGTCATAATA
* *
479275 ATTTAATTTAATAAATTTAATATCCAATTAAATGGTGACACAAGTCATTGCAG-GGTTGGAGGAT
260 ATTTAATTTAATAAATTTAATATCCAATTAAATGATGACACAAATCATTGC-GTGGTTGGAGGAT
479339 ATTTTTTAAAATTTAATTTA
324 ATTTTTTAAAATTTAATTTA
479359 ATATTCTACC
Statistics
Matches: 317, Mismatches: 22, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
375 79 0.25
376 1 0.00
379 2 0.01
380 235 0.74
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (377 bp):
TTGAAGAACCCATCCACAATTTACTCATATTATTATTAGGATAAGCTATATCAGTGACCACCCAA
CTATTGTGATCCCTTTTCATTTTGATCACCATTTTTGAATTTTTGTCAATTAGGTCACCTAACTA
TTTAAATGATTCAATCGAGACACTTACCGTTAACCTTTAACGGAAGTGCTGACATGGTAGTTAAT
AAAATTGATATAATTACACATTTGATCTTCAATATTTATACATTATATCAATTTGGTCATAATAA
TTTAATTTAATAAATTTAATATCCAATTAAATGATGACACAAATCATTGCGTGGTTGGAGGATAT
TTTTTAAAATTTAATTTATCTAATTTAATATTTTATCCTCCAATTAAGTGGT
Found at i:484448 original size:5 final size:5
Alignment explanation
Indices: 484440--484491 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
484430 GAGGGAAGTG
484440 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
484490 AA
1 AA
484492 AACCCAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:497460 original size:285 final size:285
Alignment explanation
Indices: 497125--497682 Score: 899
Period size: 285 Copynumber: 2.0 Consensus size: 285
497115 GCATTTCGAG
497125 TTGAAAAAAAAAAGATATTTTAAATTTAGAAAATTTTAGAATGAATTTATCTGAGTTTAATATTT
1 TTGAAAAAAAAAAGATATTTTAAATTTAGAAAATTTTAGAATGAATTTATCTGAGTTTAATATTT
* *
497190 AAATGATTTATGTTTGAATACAAAAGGACACGTCAAATGACAAAAATTCTTATAACTAATTAATA
66 AAATGATTTATGTTTGAATACAAAAGGACACGTCAAATGAAAAAAATCCTTATAACTAATTAATA
* *
497255 AATATATAACAAAATAAC-AATA-AAAAGAGGAAAGAAAGTTATATTATATATGTCAAGTTGTTA
131 AATATATAACAAAATAACAAAAACAAAAGAGGAAAGAAAGTTATATTATACATGTCAAGTTGTTA
* *
497318 TTCGAAAAATCAATCATTTCTAGAGAAATTATATTTCCGATAA-TCGATGGGATTGTACCTGAAA
196 TTCGAAAAATCAATCATTTCTAGAGAAATTATATTTCCGATAACT-GACGGAATTGTACCTGAAA
497382 TGTAAAATTAAATTTGAAAAAATAAT
260 TGTAAAATTAAATTTGAAAAAATAAT
* * *
497408 TTGACAAAAAAATAATATATTTTAAATTTA-AATCATTTTAGAATGGATTTATCTGAGTTTAATA
1 TTGA-AAAAAAA-AAGATATTTTAAATTTAGAA-AATTTTAGAATGAATTTATCTGAGTTTAATA
* *
497472 TTTAAATGATTTATGTTTGTATACAAAAGGACATGTCAAATGAAAAAAATCCTTATAACTAATTA
63 TTTAAATGATTTATGTTTGAATACAAAAGGACACGTCAAATGAAAAAAATCCTTATAACTAATTA
* *
497537 ATAAATATATAACAAAATAACAAAAAACAAAAGAGGAAGGAAAGTTATATTATACCTGTCAAGTT
128 ATAAATATATAACAAAATAAC-AAAAACAAAAGAGGAAAGAAAGTTATATTATACATGTCAAGTT
* * *
497602 GTTATTCGAGAAATCAATCATTTTTAGAGAAATTATATTTCCGATAACTGACGGAATTGTACCTT
192 GTTATTCGAAAAATCAATCATTTCTAGAGAAATTATATTTCCGATAACTGACGGAATTGTACCTG
497667 AAATGTAAAATTAAAT
257 AAATGTAAAATTAAAT
497683 AATCAGTCCA
Statistics
Matches: 252, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
283 4 0.02
284 9 0.04
285 127 0.50
287 3 0.01
288 108 0.43
289 1 0.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (285 bp):
TTGAAAAAAAAAAGATATTTTAAATTTAGAAAATTTTAGAATGAATTTATCTGAGTTTAATATTT
AAATGATTTATGTTTGAATACAAAAGGACACGTCAAATGAAAAAAATCCTTATAACTAATTAATA
AATATATAACAAAATAACAAAAACAAAAGAGGAAAGAAAGTTATATTATACATGTCAAGTTGTTA
TTCGAAAAATCAATCATTTCTAGAGAAATTATATTTCCGATAACTGACGGAATTGTACCTGAAAT
GTAAAATTAAATTTGAAAAAATAAT
Found at i:499280 original size:72 final size:72
Alignment explanation
Indices: 499137--499286 Score: 210
Period size: 72 Copynumber: 2.1 Consensus size: 72
499127 TTAAATTTTC
* * * * ** *
499137 AAGTTTTGACAAATTGCCAAGAGTGGACGGGATAACACCAGTGATGTTGTTTCTGAACAAGTGTA
1 AAGTTTTGACAAATAGCCAAGAGTGGACGGGATAACACCAGTGAAGTTGTTCCAGAACAAAAGCA
499202 ACCTTTG
66 ACCTTTG
* *
499209 CAGTTTTGACATATAGCCAAGAGTGGACGGGATAACACCAGTGAAGTTGTTCCAGAACAAAAGCA
1 AAGTTTTGACAAATAGCCAAGAGTGGACGGGATAACACCAGTGAAGTTGTTCCAGAACAAAAGCA
*
499274 AGCTTTG
66 ACCTTTG
499281 AAGTTT
1 AAGTTT
499287 AGTGAAGGAA
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (72 bp):
AAGTTTTGACAAATAGCCAAGAGTGGACGGGATAACACCAGTGAAGTTGTTCCAGAACAAAAGCA
ACCTTTG
Found at i:501062 original size:33 final size:33
Alignment explanation
Indices: 500980--501055 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
500970 TTTGAAATCG
500980 AGTCATTGCCGTGGAAAAAACACTCTCTCATCA
1 AGTCATTGCCGTGGAAAAAACACTCTCTCATCA
501013 AGTCATTGCCGTGGAAAAAACACTCTCTCATCA
1 AGTCATTGCCGTGGAAAAAACACTCTCTCATCA
501046 AGTCATTGCC
1 AGTCATTGCC
501056 ACGGAAAGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (33 bp):
AGTCATTGCCGTGGAAAAAACACTCTCTCATCA
Found at i:501278 original size:26 final size:25
Alignment explanation
Indices: 501222--501279 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
501212 ACTAAAGTAT
*
501222 CCAAAATCATTCTTTTAATATAACT
1 CCAAAATCATTCTTTTAATATAACC
**
501247 ATAAAACTCATT-TTTGTAATATAACC
1 CCAAAA-TCATTCTTT-TAATATAACC
501273 CCAAAAT
1 CCAAAAT
501280 ATAGAGAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (25 bp):
CCAAAATCATTCTTTTAATATAACC
Found at i:501395 original size:17 final size:17
Alignment explanation
Indices: 501365--501408 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
501355 AATTATTACC
*
501365 TCAAATAAATATTTACTTA
1 TCAAAT-AA-ATTTAATTA
*
501384 TTAAATAAATTTAATTA
1 TCAAATAAATTTAATTA
501401 TCAAATAA
1 TCAAATAA
501409 TCATCGACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 15 0.68
18 2 0.09
19 5 0.23
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (17 bp):
TCAAATAAATTTAATTA
Found at i:506078 original size:59 final size:59
Alignment explanation
Indices: 505971--506093 Score: 151
Period size: 59 Copynumber: 2.1 Consensus size: 59
505961 GTTGTGCGAT
* * *
505971 CATTTTGTAACTTTTAATAATCGATGGACTCAACAGAGCAACTCCCTATAGTCGAGGAC
1 CATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAACAACTCCCTATAGTCGAGGAC
* * * *
506030 CATTTTGTAACTTTTAATAATC-AGGGGACTCAATAAAATAA-TATCCTATAGTCGATGAC
1 CATTTTGTAACTTTTAATAATCGA-GGGACTCAACAAAACAACT-CCCTATAGTCGAGGAC
506089 CATTT
1 CATTT
506094 ATGTTCTTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 2 0.04
59 53 0.96
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (59 bp):
CATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAACAACTCCCTATAGTCGAGGAC
Found at i:511609 original size:2 final size:2
Alignment explanation
Indices: 511602--511639 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
511592 ACGATAGAAC
511602 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
511640 TGACATTTAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:515116 original size:29 final size:30
Alignment explanation
Indices: 515070--515132 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
515060 CATATAATAT
*
515070 ATAATTTTTGCTAGGTGAT-TGCATATTAA
1 ATAATTTTTGCTAGGTGATATACATATTAA
*
515099 ATAATATTTTGC-ATGTGATAGTACATATTAA
1 ATAAT-TTTTGCTAGGTGATA-TACATATTAA
515130 ATA
1 ATA
515133 GTAGTTGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 11 0.38
30 6 0.21
31 12 0.41
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (30 bp):
ATAATTTTTGCTAGGTGATATACATATTAA
Found at i:515188 original size:17 final size:18
Alignment explanation
Indices: 515166--515203 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
515156 AGTTTCATAT
515166 TAAATA-ATTGCATATTA
1 TAAATAGATTGCATATTA
515183 TAAATAGTATTGCATATTA
1 TAAATAG-ATTGCATATTA
515202 TA
1 TA
515204 TTAGATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (18 bp):
TAAATAGATTGCATATTA
Found at i:515212 original size:19 final size:19
Alignment explanation
Indices: 515162--515212 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
515152 ATATAGTTTC
*
515162 ATATTAAATAATTGCATATT
1 ATATTAGAT-ATTGCATATT
*
515182 ATAAATAG-TATTGCATATT
1 AT-ATTAGATATTGCATATT
515201 ATATTAGATATT
1 ATATTAGATATT
515213 AAATCATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.15
19 16 0.62
20 3 0.12
21 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (19 bp):
ATATTAGATATTGCATATT
Found at i:516046 original size:37 final size:36
Alignment explanation
Indices: 515974--516047 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
515964 GTTGAAAAAT
*
515974 ATTTATATATATTTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATATTTTTAAAAAAATTAAAATCATAAA
* * *
516010 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATATTTTTAAAAAAATT-AAAATCATAAA
516047 A
1 A
516048 AATACTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 8 0.25
37 20 0.62
38 4 0.12
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (36 bp):
ATTTATATATATTTTTAAAAAAATTAAAATCATAAA
Found at i:521271 original size:18 final size:18
Alignment explanation
Indices: 521248--521305 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
521238 CAACAATTGG
*
521248 TAACAATAGATATCTTTT
1 TAACAATTGATATCTTTT
521266 TAACAATTGATATCATTTTGT
1 TAACAATTGATATC--TTT-T
*
521287 TAACAATTGGTATCTTTT
1 TAACAATTGATATCTTTT
521305 T
1 T
521306 CACTAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 15 0.43
19 3 0.09
20 3 0.09
21 14 0.40
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:521291 original size:21 final size:19
Alignment explanation
Indices: 521248--521305 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 19
521238 CAACAATTGG
*
521248 TAACAATAGATATC-TTTT
1 TAACAATTGATATCTTTTT
521266 TAACAATTGATATCATTTTGT
1 TAACAATTGATATC-TTTT-T
*
521287 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCTTTTT
521306 CACTAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 13 0.37
19 1 0.03
20 7 0.20
21 14 0.40
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (19 bp):
TAACAATTGATATCTTTTT
Found at i:521541 original size:20 final size:20
Alignment explanation
Indices: 521512--521553 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
521502 TTCCAGATTG
521512 CCCAGAGGGTACAGATACCC
1 CCCAGAGGGTACAGATACCC
* *
521532 CCCAGGGGGTACAGATTCCC
1 CCCAGAGGGTACAGATACCC
521552 CC
1 CC
521554 TGAATGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.38, G:0.26, T:0.12
Consensus pattern (20 bp):
CCCAGAGGGTACAGATACCC
Found at i:524359 original size:20 final size:20
Alignment explanation
Indices: 524312--524419 Score: 67
Period size: 20 Copynumber: 5.4 Consensus size: 20
524302 AAATAACTAA
*
524312 CGAATTCGCAACTCGAATTC
1 CGAATTCGCAACACGAATTC
524332 C-AATTTCGCAACAC-AGATTC
1 CGAA-TTCGCAACACGA-ATTC
* * * *
524352 CGAATTCGCGACGCTAATTT
1 CGAATTCGCAACACGAATTC
* * * *
524372 CGAATTCGCGACGCTAATTT
1 CGAATTCGCAACACGAATTC
* * * *
524392 CGAATTCGCGACGCTAATTT
1 CGAATTCGCAACACGAATTC
524412 CGAATTCG
1 CGAATTCG
524420 TGACGTTAAT
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.04
20 74 0.93
21 3 0.04
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (20 bp):
CGAATTCGCAACACGAATTC
Found at i:524380 original size:40 final size:40
Alignment explanation
Indices: 524336--524451 Score: 135
Period size: 40 Copynumber: 2.9 Consensus size: 40
524326 GAATTCCAAT
524336 TTCGCAACAC-AGATTCCGAATTCGCGACGCTAATTTCGAA
1 TTCGCAACACTA-ATTCCGAATTCGCGACGCTAATTTCGAA
* * *
524376 TTCGCGACGCTAATTTCGAATTCGCGACGCTAATTTCGAA
1 TTCGCAACACTAATTCCGAATTCGCGACGCTAATTTCGAA
** ** * *
524416 TTCGTGACGTTAATTTCGAATTTGCGACGCTAATTT
1 TTCGCAACACTAATTCCGAATTCGCGACGCTAATTT
524452 TAAATTATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
40 68 0.99
41 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (40 bp):
TTCGCAACACTAATTCCGAATTCGCGACGCTAATTTCGAA
Found at i:524457 original size:20 final size:20
Alignment explanation
Indices: 524352--524451 Score: 173
Period size: 20 Copynumber: 5.0 Consensus size: 20
524342 ACACAGATTC
524352 CGAATTCGCGACGCTAATTT
1 CGAATTCGCGACGCTAATTT
524372 CGAATTCGCGACGCTAATTT
1 CGAATTCGCGACGCTAATTT
524392 CGAATTCGCGACGCTAATTT
1 CGAATTCGCGACGCTAATTT
* *
524412 CGAATTCGTGACGTTAATTT
1 CGAATTCGCGACGCTAATTT
*
524432 CGAATTTGCGACGCTAATTT
1 CGAATTCGCGACGCTAATTT
524452 TAAATTATTT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (20 bp):
CGAATTCGCGACGCTAATTT
Found at i:524470 original size:6 final size:6
Alignment explanation
Indices: 524459--524503 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
524449 TTTTAAATTA
* *
524459 TTTATT TTTATT TTAATT ATTTATT TTTATT TTAATT ATTTATT T
1 TTTATT TTTATT TTTATT -TTTATT TTTATT TTTATT -TTTATT T
524504 AATAGTATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 23 0.70
7 10 0.30
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:524504 original size:23 final size:19
Alignment explanation
Indices: 524448--524503 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
524438 TGCGACGCTA
524448 ATTTTAAATTATTTATTTTT
1 ATTTT-AATTATTTATTTTT
524468 ATTTTAATTATTTATTTTT
1 ATTTTAATTATTTATTTTT
524487 ATTTTAATTATTTATTT
1 ATTTTAATTATTTATTT
524504 AATAGTATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 31 0.86
20 5 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTAATTATTTATTTTT
Found at i:525008 original size:20 final size:20
Alignment explanation
Indices: 524985--525048 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
524975 TAAAATAAAT
524985 AATTTGAAATTAGCGTCGCG
1 AATTTGAAATTAGCGTCGCG
*
525005 AATTTGAAATTAGCGTCGGG
1 AATTTGAAATTAGCGTCGCG
*
525025 AATTCGAAATTAGCGTCGCG
1 AATTTGAAATTAGCGTCGCG
525045 AATT
1 AATT
525049 CAAAATTCGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (20 bp):
AATTTGAAATTAGCGTCGCG
Found at i:525068 original size:40 final size:40
Alignment explanation
Indices: 524985--525068 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
524975 TAAAATAAAT
* ** * *
524985 AATTTGAAATTAGCGTCGCGAATTTGAAATTAGCGTCGGG
1 AATTCGAAATTAGCGTCGCGAATTCAAAATTAGCATCGCG
* *
525025 AATTCGAAATTAGCGTCGCGAATTCAAAATTCGCATTGCG
1 AATTCGAAATTAGCGTCGCGAATTCAAAATTAGCATCGCG
525065 AATT
1 AATT
525069 TAGAAACTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (40 bp):
AATTCGAAATTAGCGTCGCGAATTCAAAATTAGCATCGCG
Found at i:527221 original size:26 final size:24
Alignment explanation
Indices: 527191--527280 Score: 90
Period size: 26 Copynumber: 3.5 Consensus size: 24
527181 CACCTGAAAG
* *
527191 TTTATAAGTTCGTTTCTCTTTAAAAT
1 TTTATAAATTC-TTCCT-TTTAAAAT
*
527217 TTTATAAATTAACTACCTTTTAAAAT
1 TTTATAAATT--CTTCCTTTTAAAAT
527243 TTTATAAATTCATATCCTTTTTAAAAT
1 TTTATAAATTC-T-TCC-TTTTAAAAT
527270 TTTATAAATTC
1 TTTATAAATTC
527281 ATATTCCTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 1 0.02
25 1 0.02
26 29 0.53
27 23 0.42
28 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTATAAATTCTTCCTTTTAAAAT
Found at i:527272 original size:27 final size:26
Alignment explanation
Indices: 527209--527284 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 26
527199 TTCGTTTCTC
*
527209 TTTAAAATTTTATAAATTAACTA-CCT
1 TTTAAAATTTTATAAATTCA-TATCCT
527235 TTTAAAATTTTATAAATTCATATCCTT
1 TTTAAAATTTTATAAATTCATATCC-T
527262 TTTAAAATTTTATAAATTCATAT
1 TTTAAAATTTTATAAATTCATAT
527285 TCCTAATATA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 2 0.04
26 21 0.45
27 24 0.51
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTAAAATTTTATAAATTCATATCCT
Found at i:528260 original size:19 final size:19
Alignment explanation
Indices: 528236--528275 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
528226 AATAAATTTA
528236 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
528255 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
528274 AT
1 AT
528276 ATACCCGGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:535672 original size:2 final size:2
Alignment explanation
Indices: 535665--535740 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
535655 GCTTCAATGC
535665 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
535707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
535741 CACACACAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:539096 original size:20 final size:20
Alignment explanation
Indices: 539071--539121 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
539061 TCATATCTAT
539071 CCGTTGGGGATGTTTTGGAG
1 CCGTTGGGGATGTTTTGGAG
* *
539091 CCGTTGAGAATGTTTTGGAG
1 CCGTTGGGGATGTTTTGGAG
539111 CCGTTGGGGAT
1 CCGTTGGGGAT
539122 TAATTTTCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.41, T:0.33
Consensus pattern (20 bp):
CCGTTGGGGATGTTTTGGAG
Found at i:542674 original size:69 final size:69
Alignment explanation
Indices: 542588--542741 Score: 299
Period size: 69 Copynumber: 2.2 Consensus size: 69
542578 ATGGAAACGA
542588 CGATTATGCTACCATGCTAGAGAAACATCCTTTACCTCAAGGAAAAGAGCTACCAATTGACAGGC
1 CGATTATGCTACCATGCTAGAGAAACATCCTTTACCTCAAGGAAAAGAGCTACCAATTGACAGGC
542653 ATGG
66 ATGG
*
542657 CGATTATGCTACCATGCTAGAGAAACATCCTTTACCTCAAGGAAAAGAGCTACCGATTGACAGGC
1 CGATTATGCTACCATGCTAGAGAAACATCCTTTACCTCAAGGAAAAGAGCTACCAATTGACAGGC
542722 ATGG
66 ATGG
542726 CGATTATGCTACCATG
1 CGATTATGCTACCATG
542742 ATGAACGTCG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 84 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (69 bp):
CGATTATGCTACCATGCTAGAGAAACATCCTTTACCTCAAGGAAAAGAGCTACCAATTGACAGGC
ATGG
Found at i:543927 original size:2 final size:2
Alignment explanation
Indices: 543920--543968 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
543910 AGATCATTCA
543920 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
543962 AT AT AT A
1 AT AT AT A
543969 CCTTTAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:549062 original size:2 final size:2
Alignment explanation
Indices: 549055--549084 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
549045 AAGAATTATT
549055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
549085 AGTTCATGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:549935 original size:2 final size:2
Alignment explanation
Indices: 549928--550010 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
549918 CGAAGATTGT
549928 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
549970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
550011 GCATACATAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:551772 original size:60 final size:60
Alignment explanation
Indices: 551700--551817 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
551690 TGCATGTCCC
* * * * *
551700 GGTAAGATTTTATGGCTGCAGCACATCTCGTAGTCGTCCGGTGGGGTTGCGACTCTACGT
1 GGTAAGAGTTTATGGCTGCAGCACATCTCGAAGTCCTCCGATGGGGTCGCGACTCTACGT
*
551760 GGTAAGAGTTTATGGCTGCAGCACATCTCGAAGTCCTCCTATGGGGTCGCGACTCTAC
1 GGTAAGAGTTTATGGCTGCAGCACATCTCGAAGTCCTCCGATGGGGTCGCGACTCTAC
551818 TGTAAATGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.28
Consensus pattern (60 bp):
GGTAAGAGTTTATGGCTGCAGCACATCTCGAAGTCCTCCGATGGGGTCGCGACTCTACGT
Found at i:552294 original size:28 final size:28
Alignment explanation
Indices: 552263--552331 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
552253 TGTTTGTCTT
*
552263 CTTAGTGAACCTTATCTGCAAAGCTTCA
1 CTTAGTGATCCTTATCTGCAAAGCTTCA
552291 CTTAGTGATCCTTATCTGCAAAGCTTCA
1 CTTAGTGATCCTTATCTGCAAAGCTTCA
552319 CTTAGTGATCCTT
1 CTTAGTGATCCTT
552332 GCGGCTCGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (28 bp):
CTTAGTGATCCTTATCTGCAAAGCTTCA
Found at i:558557 original size:18 final size:18
Alignment explanation
Indices: 558536--558768 Score: 306
Period size: 18 Copynumber: 12.9 Consensus size: 18
558526 GTGCATCGAT
*
558536 CTTACTCAAA-CTGCCAAT
1 CTTACTCAAATC-GCCAAG
* *
558554 CTTACTCAACTCTCCAAG
1 CTTACTCAAATCGCCAAG
* *
558572 ATTACTCAAATCTCCAAG
1 CTTACTCAAATCGCCAAG
*
558590 TTTACTCAAATCGCCAAG
1 CTTACTCAAATCGCCAAG
* *
558608 CCTACTCAAATCACCAAG
1 CTTACTCAAATCGCCAAG
*
558626 TTTACTCAAATCGCCAAG
1 CTTACTCAAATCGCCAAG
*
558644 CCTACTCAAATCGCCAAG
1 CTTACTCAAATCGCCAAG
*
558662 CCTACTCAAATCGCCAAG
1 CTTACTCAAATCGCCAAG
*
558680 CCTACTCAAATCGCCAAG
1 CTTACTCAAATCGCCAAG
*
558698 CCTACTCAAATCGCCAAG
1 CTTACTCAAATCGCCAAG
*
558716 TTTACTCAAATCGCCAAG
1 CTTACTCAAATCGCCAAG
*
558734 CCTACTCAAATCGCCAAG
1 CTTACTCAAATCGCCAAG
*
558752 TTTACTCAAATCGCCAA
1 CTTACTCAAATCGCCAA
558769 CCTGCAATAA
Statistics
Matches: 193, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
18 192 0.99
19 1 0.01
ACGTcount: A:0.34, C:0.34, G:0.09, T:0.23
Consensus pattern (18 bp):
CTTACTCAAATCGCCAAG
Found at i:561796 original size:102 final size:102
Alignment explanation
Indices: 561390--561789 Score: 570
Period size: 102 Copynumber: 3.9 Consensus size: 102
561380 TAGCCACACC
* * *
561390 TTGGGCAGCTGAGATGGCATCGGATGAGAGCTGCTTGACGAAACCAGAGGCAGTGCCCAACAGTC
1 TTGGGCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGCCCAACAGTC
* * *
561455 CAGAAGGTTGACCCTGAGGAGACACACCCGGAGACAT
66 CAAAATGTTGACCCTGAGGAGACACTCCCGGAGACAT
* * * *
561492 TTGAGCAGCCGAGATGGCATCGGATGAGATCTGCTTGACGAATCCAGAGGCATTGCCCACCAGTC
1 TTGGGCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGCCCAACAGTC
* * *
561557 CAAAAAGTTGACCCTGAGGAGACCCTCCCGGGGACAT
66 CAAAATGTTGACCCTGAGGAGACACTCCCGGAGACAT
* *
561594 TTGGACGGCCGAGATGGCATCGGATGAGACCTGCTTGAC-AAGTCCAGAGGCAGTGCCCAACAGT
1 TTGGGCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAA-TCCAGAGGCAGTGCCCAACAGT
*
561658 CCAGAAAT-TTGGCCCTGAGGAGACACTCCCGGAGACAT
65 CCA-AAATGTTGACCCTGAGGAGACACTCCCGGAGACAT
* * * *
561696 TTGGGCAGCCGAGATGACATCGGATGAGACCTGCTTGACTAACCCAGAGGCAGTCCCCAACAGTC
1 TTGGGCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGCCCAACAGTC
* *
561761 CAAAATGCTGGCCCTGAGGAGACACTCCC
66 CAAAATGTTGACCCTGAGGAGACACTCCC
561790 CCAGACACTC
Statistics
Matches: 267, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
101 6 0.02
102 256 0.96
103 5 0.02
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.16
Consensus pattern (102 bp):
TTGGGCAGCCGAGATGGCATCGGATGAGACCTGCTTGACGAATCCAGAGGCAGTGCCCAACAGTC
CAAAATGTTGACCCTGAGGAGACACTCCCGGAGACAT
Done.