Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014199.1 Kokia drynarioides strain JFW-HI SEQ_129232, 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: 247569
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 92 characters in sequence are not A, C, G, or T
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--43 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 ATA
4 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
44 TAAGTTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76 original size:14 final size:14
Alignment explanation
Indices: 59--85 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49 TAAAATATTT
59 AAATAAAATAAAAA
1 AAATAAAATAAAAA
73 AAATAAAATAAAA
1 AAATAAAATAAAA
86 TTGAAGTTTA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAATAAAATAAAAA
Found at i:210 original size:21 final size:20
Alignment explanation
Indices: 186--230 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
176 TAGAACACGA
186 ATTAAT-TTTTTATAAAAAAGT
1 ATTAATATTTTTA-AAAAAA-T
207 ATTAATAATTTTTAAAAAAAT
1 ATTAAT-ATTTTTAAAAAAAT
228 ATT
1 ATT
231 TTCAGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 10 0.45
22 6 0.27
23 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTAATATTTTTAAAAAAAT
Found at i:305 original size:21 final size:21
Alignment explanation
Indices: 279--325 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
269 GAGACTTTGA
* *
279 GAGAATGTT-AGAAAGTGATTT
1 GAGAAT-TTGAGAAAATGATGT
300 GAGAATTTGAGAAAATGATGT
1 GAGAATTTGAGAAAATGATGT
321 GAGAA
1 GAGAA
326 AATGAGTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.28
Consensus pattern (21 bp):
GAGAATTTGAGAAAATGATGT
Found at i:331 original size:21 final size:21
Alignment explanation
Indices: 288--331 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
278 AGAGAATGTT
* * **
288 AGAAAGTGATTTGAGAATTTG
1 AGAAAATGATGTGAGAAAATG
309 AGAAAATGATGTGAGAAAATG
1 AGAAAATGATGTGAGAAAATG
330 AG
1 AG
332 TAGGGGTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (21 bp):
AGAAAATGATGTGAGAAAATG
Found at i:2469 original size:2 final size:2
Alignment explanation
Indices: 2462--2487 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2452 GCTGTTCCTC
2462 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
2488 ATGCATGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:8164 original size:21 final size:23
Alignment explanation
Indices: 8127--8173 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
8117 ATCGACCGAA
8127 TCGATCTAATTTGTTTAA-TCGG
1 TCGATCTAATTTGTTTAATTCGG
8149 TCGAT-TAA-TTGATTTAATTCGG
1 TCGATCTAATTTG-TTTAATTCGG
8171 TCG
1 TCG
8174 GAAGCCGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.13
21 8 0.35
22 12 0.52
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (23 bp):
TCGATCTAATTTGTTTAATTCGG
Found at i:14500 original size:50 final size:50
Alignment explanation
Indices: 14446--14546 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
14436 TTTAATTTTT
14446 CATTGTGTATCAAATAATCTCATATAGAAAGGTATTTTAATGCACTCGAA
1 CATTGTGTATCAAATAATCTCATATAGAAAGGTATTTTAATGCACTCGAA
14496 CATTGTGTATCAAATAATCTCATATAGAAAGGTATTTTAATGCACTCGAA
1 CATTGTGTATCAAATAATCTCATATAGAAAGGTATTTTAATGCACTCGAA
14546 C
1 C
14547 CCAATATTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (50 bp):
CATTGTGTATCAAATAATCTCATATAGAAAGGTATTTTAATGCACTCGAA
Found at i:23442 original size:6 final size:6
Alignment explanation
Indices: 23428--23480 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
23418 TTAAATTTGT
* * *
23428 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TTTAAA TTT-AT TTTCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
23475 TTTAAA
1 TTTAAA
23481 ATTATGTCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 7 0.18
6 27 0.71
7 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:23442 original size:17 final size:17
Alignment explanation
Indices: 23417--23460 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
23407 CTAAGTTTAT
*
23417 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
23434 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
23451 TTTAAATTTA
1 TTTAAATTTA
23461 AATTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:23454 original size:23 final size:24
Alignment explanation
Indices: 23428--23480 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
23418 TTAAATTTGT
*
23428 TTTAAATTTAGATTTATTTT-AAA
1 TTTAAATTTAAATTTATTTTCAAA
23451 TTTAAATTTAAATTTATTTTCAAA
1 TTTAAATTTAAATTTATTTTCAAA
23475 TTTAAA
1 TTTAAA
23481 ATTATGTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTAAATTTAAATTTATTTTCAAA
Found at i:24235 original size:15 final size:16
Alignment explanation
Indices: 24210--24243 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
24200 TTTTATAACC
24210 TAATAAATATTATTAA
1 TAATAAATATTATTAA
24226 TAAT-AATATTATTAA
1 TAATAAATATTATTAA
24241 TAA
1 TAA
24244 CAGAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAAATATTATTAA
Found at i:24272 original size:21 final size:20
Alignment explanation
Indices: 24223--24298 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 20
24213 TAAATATTAT
*
24223 TAATAATAATATTATTAATAA
1 TAATAATAATAAT-TTAATAA
*
24244 CAGA-AATAATGAATTTAATAA
1 TA-ATAATAAT-AATTTAATAA
24265 TAATAATAAATAAATATTTAATAA
1 TAATAAT-AAT--A-ATTTAATAA
24289 TAATTAATAA
1 TAA-TAATAA
24299 CAAAAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
20 1 0.02
21 18 0.41
22 6 0.14
23 1 0.02
24 14 0.32
25 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (20 bp):
TAATAATAATAATTTAATAA
Found at i:25405 original size:58 final size:58
Alignment explanation
Indices: 25343--25513 Score: 238
Period size: 58 Copynumber: 2.9 Consensus size: 58
25333 CCCAAACTTT
*
25343 CAAAAATTA-CATTTTTACCCTCAAACTTTCCAAAATTCCATTTTAACCTCGATTTCAC
1 CAAAAATTACCA-TTTTACCCTCGAACTTTCCAAAATTCCATTTTAACCTCGATTTCAC
* *
25401 CAAAAATTACCATTTTACCCTTGAACATTT-CAAAATTCCATTTTGACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCTCGAAC-TTTCCAAAATTCCATTTTAACCTCGATTTCAC
* * * *
25459 CAAAACTTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTCAACTTCGATT
1 CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTT-AACCTCGATT
25514 ATTTTTATTT
Statistics
Matches: 100, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
57 3 0.03
58 84 0.84
59 13 0.13
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.35
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTAACCTCGATTTCAC
Found at i:25406 original size:29 final size:30
Alignment explanation
Indices: 25374--25475 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 30
25364 CAAACTTTCC
25374 AAAATT-CCATTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTAACCTCGATTTCACCA
* *
25403 AAAATTACCATTTTACCCTTGAACATTT---C-
1 AAAATTACCATTTTAACCTCG---ATTTCACCA
*
25432 AAAATT-CCATTTTGACCTCGATTTCACCA
1 AAAATTACCATTTTAACCTCGATTTCACCA
*
25461 AAACTTACCATTTTA
1 AAAATTACCATTTTA
25476 CCCCCGAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
25 4 0.07
28 12 0.21
29 17 0.30
30 20 0.35
33 4 0.07
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTAACCTCGATTTCACCA
Found at i:25492 original size:30 final size:29
Alignment explanation
Indices: 25316--25502 Score: 133
Period size: 29 Copynumber: 6.5 Consensus size: 29
25306 GATTTTGCTA
* * * * *
25316 AAAATTATCGTTTTACCCCCAAACTTTCA
1 AAAATTACCATTTTACCCTCGAACTTTCC
*
25345 AAAATTA-CATTTTTACCCTCAAACTTTCC
1 AAAATTACCA-TTTTACCCTCGAACTTTCC
*
25374 AAAATT-CCATTTTAACCTCG-A-TTTCACC
1 AAAATTACCATTTTACCCTCGAACTTT--CC
*
25402 AAAAATTACCATTTTACCCTTGAACATTT-C
1 -AAAATTACCATTTTACCCTCGAAC-TTTCC
25432 AAAATT-CCATTTTGA-CCTCG-A-TTTCACC
1 AAAATTACCATTTT-ACCCTCGAACTTT--CC
*
25460 AAAACTTACCATTTTACCCCCGAACTTTCC
1 AAAA-TTACCATTTTACCCTCGAACTTTCC
*
25490 AAAA-TCCCATTTT
1 AAAATTACCATTTT
25503 CAACTTCGAT
Statistics
Matches: 130, Mismatches: 10, Indels: 37
0.73 0.06 0.21
Matches are distributed among these distances:
25 3 0.02
26 3 0.02
27 2 0.02
28 36 0.28
29 48 0.37
30 30 0.23
31 2 0.02
32 3 0.02
33 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAACTTTCC
Found at i:36635 original size:194 final size:194
Alignment explanation
Indices: 36306--37135 Score: 1063
Period size: 194 Copynumber: 4.2 Consensus size: 194
36296 CACAAACAGT
** * * *
36306 GAGGCGATTGTCTTCCTGATGAGGTACAGAGAAGTATACCAACTCAATACGAACAAATCTTTGAA
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
* * * *
36371 CCCCAACTTCATGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTAATGA
66 TCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGA
* * * * * ** *
36436 GACACTGAGAAGTTAATCAAATTCGTCTTCCTGATGAGGTACATAAAAGTAGATTGAATCAAAC
131 AACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAAC
* *
36500 GAGGCGATCCTCTTCCTGATGAGATACAGAGAAGTATACCAACTTAATGCGAACAAATCTTCGAA
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
* * *
36565 -CACCAGCTTCTTGATGAGATACTGAGAAGTAGTTCGAAGCAATAAAAAGGTTAGCTTCCTGATG
66 TC-CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATG
* * * * *
36629 AGACACTGAGAAGTGAACCAAATTTGTCTTCCTGATAAGATATAGAGAAGCGGATTGAAACAAAC
130 AAACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAAC
* * * * *
36694 GAGGCGGTCTTCTTCCTAATGAGATACAAAGAAGTATACCAACTCAATGTGAACAAATCTTCGAA
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
* * *
36759 TCCCAGCTTCCTGATGAGGTATTGAGAAGCAGGTCAAAGCAATAAAAAGGTTAGCTTCCTGATGA
66 TCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGA
* * *
36824 AACATTGAGAAGTGAACCAAATTCGTTTTCCTGATGAGGTACAGAGAAGCGGATTGAAATAAAC
131 AACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAAC
* * * *
36888 GGGGCGATTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGTGAGCAAAT
1 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCA-------ATGCGAACAAAT
*
36953 CTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTC
59 CTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTC
* * * * * *
37018 TTGATGAAATACTGAGAAGTAAACCAAATTCGTCTTTCTCATGAGGTGCAGAGAAGCGGATTGAA
124 CTGATGAAACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAA
*
37083 ACAAGC
189 ACAAAC
* * * *
37089 GATGC-AGTCATCTTCCTGATAAGATACTA-AGAAGTAAACCAAATCAA
1 GAGGCGA-TCATCTTCCTGATGAGATAC-AGAGAAGTATACCAACTCAA
37136 CAACACCAAA
Statistics
Matches: 556, Mismatches: 69, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
193 1 0.00
194 383 0.69
195 1 0.00
200 1 0.00
201 169 0.30
202 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (194 bp):
GAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAA
TCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGA
AACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAAC
Found at i:37463 original size:6 final size:6
Alignment explanation
Indices: 37449--37518 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
37439 TTAAATTTGT
* * **
37449 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TTTAAA TTT-AA TTTAGG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
37495 TTTAAA TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA
37519 ATTATGTCCC
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
5 12 0.24
6 34 0.68
7 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:37463 original size:17 final size:17
Alignment explanation
Indices: 37438--37523 Score: 73
Period size: 17 Copynumber: 4.6 Consensus size: 17
37428 CTAAGTTTAT
*
37438 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
37455 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
37472 TTTAAATTTAAATTTAATTTA
1 TTTAAATTT-ATTTTAA---A
37493 GGTTTAAATTTATTTTCAAA
1 --TTTAAATTTATTTT-AAA
*
37513 TTTAAAATTAT
1 TTTAAATTTAT
37524 GTCCCAATAC
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
17 23 0.41
18 16 0.29
20 1 0.02
21 1 0.02
22 4 0.07
23 11 0.20
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:37469 original size:11 final size:11
Alignment explanation
Indices: 37433--37517 Score: 57
Period size: 11 Copynumber: 7.5 Consensus size: 11
37423 CCCTTCTAAG
*
37433 TTTATTTTAAA
1 TTTAATTTAAA
**
37444 TTTGTTTTAAA
1 TTTAATTTAAA
*
37455 TTTAGATTT-AT
1 TTTA-ATTTAAA
37466 TTTAAATTTAAA
1 TTT-AATTTAAA
37478 TTTAAATTT-AA
1 TTT-AATTTAAA
*
37489 TTTAGGTTTAAA
1 TTTA-ATTTAAA
*
37501 TTTATTTTCAAA
1 TTTAATTT-AAA
37513 TTTAA
1 TTTAA
37518 AATTATGTCC
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
10 1 0.02
11 32 0.53
12 27 0.45
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:37475 original size:23 final size:23
Alignment explanation
Indices: 37449--37504 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
37439 TTAAATTTGT
* *
37449 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTAAATTTAATTTAAA
**
37472 TTTAAATTTAAATTTAATTTAGG
1 TTTAAATTTAAATTTAATTTAAA
37495 TTTAAATTTA
1 TTTAAATTTA
37505 TTTTCAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATTTAAA
Found at i:37498 original size:29 final size:27
Alignment explanation
Indices: 37433--37517 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 27
37423 CCCTTCTAAG
* **
37433 TTTATTTTAAATTTGTTTTAAATTTAGA
1 TTTAGTTTAAATTTAATTTAAATTTA-A
*
37461 TTTATTTTAAATTTAAATTTAAATTTAA
1 TTTAGTTTAAATTT-AATTTAAATTTAA
*
37489 TTTAGGTTTAAATTTATTTTCAAATTTAA
1 TTTA-GTTTAAATTTAATTT-AAATTTAA
37518 AATTATGTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
28 23 0.46
29 27 0.54
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (27 bp):
TTTAGTTTAAATTTAATTTAAATTTAA
Found at i:38274 original size:15 final size:16
Alignment explanation
Indices: 38249--38282 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
38239 TTTTATAACC
38249 TAATAAATATTAATAA
1 TAATAAATATTAATAA
*
38265 TAAT-AATATTATTAA
1 TAATAAATATTAATAA
38280 TAA
1 TAA
38283 CAGTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAAATATTAATAA
Found at i:38277 original size:18 final size:19
Alignment explanation
Indices: 38249--38309 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
38239 TTTTATAACC
*
38249 TAATAAATATTAATAATAA
1 TAATGAATATTAATAATAA
*
38268 TAAT-ATTATTAATAACAGTAA
1 TAATGAATATTAAT-A-A-TAA
38289 TAATGAAT-TTAATAATAA
1 TAATGAATATTAATAATAA
38307 TAA
1 TAA
38310 ATAACAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 14 0.39
19 6 0.17
20 2 0.06
21 12 0.33
22 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (19 bp):
TAATGAATATTAATAATAA
Found at i:39408 original size:28 final size:29
Alignment explanation
Indices: 39339--39410 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
39329 CAATTTCGCT
*
39339 AAAAATTACCA-TTTTACCCTCGAACTTTC
1 AAAAATT-CCATTTTTACCCTCAAACTTTC
**
39368 AAAAATTAGATTTTTACCCTCAAACTTTC
1 AAAAATTCCATTTTTACCCTCAAACTTTC
*
39397 -CAAATTCCATTTTT
1 AAAAATTCCATTTTT
39411 GACCTTGATT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 12 0.33
29 24 0.67
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCTCAAACTTTC
Found at i:39540 original size:57 final size:59
Alignment explanation
Indices: 39379--39641 Score: 347
Period size: 58 Copynumber: 4.5 Consensus size: 59
39369 AAAATTAGAT
* **
39379 TTTTACCCTCAAACTTTCC-AAATTCCATTTTTGACCTTGATTTCACCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCA
* *
39437 TTTTACCCCCTAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCA
* * * * * * *
39495 TTTTA-CCTCGAACATTCCAAAATTTCA-TTTTGACCTCGATTTCACCAAAAAATATCA
1 TTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCA
* *
39552 TTTTA-CCCCAAACTTTCCAAAATTTCATTTTTGACCCCGATTTCACCAAAACTTACCA
1 TTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCA
* *
39610 TTTTACCCCCGAACTTTCCAAAATCCCATTTT
1 TTTTACCCCCAAACTTTCCAAAATTCCATTTT
39642 CAACTTCTAT
Statistics
Matches: 179, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
57 68 0.38
58 80 0.45
59 31 0.17
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (59 bp):
TTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCA
Found at i:39554 original size:115 final size:117
Alignment explanation
Indices: 39379--39641 Score: 381
Period size: 115 Copynumber: 2.3 Consensus size: 117
39369 AAAATTAGAT
* * *
39379 TTTTACCCTCAAACTTTCC-AAATTCCATTTTTGACCTTGATTTCACCAAAAATTACCATTTTAC
1 TTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACCAAAAAATACCATTTTA-
*
39443 CCCCTAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACCAAAAATTACCA
65 CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* * *
39495 TTTTA-CCTCGAACATTCCAAAATTTCA-TTTTGACCTCGATTTCACCAAAAAATATCATTTTAC
1 TTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACCAAAAAATACCATTTTAC
* * *
39558 CCCAAACTTTCCAAAATTTCATTTTTGACCCCGATTTCACCAAAACTTACCA
66 CCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCA
* *
39610 TTTTACCCCCGAACTTTCCAAAATCCCATTTT
1 TTTTACCCTCGAACTTTCCAAAATTCCATTTT
39642 CAACTTCTAT
Statistics
Matches: 129, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
114 20 0.16
115 76 0.59
116 30 0.23
117 3 0.02
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (117 bp):
TTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACCAAAAAATACCATTTTAC
CCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCA
Found at i:46725 original size:40 final size:40
Alignment explanation
Indices: 46670--46755 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
46660 TTTGTTGATG
*
46670 ATGTAGTTGAATGTGAATAAAATACAAAATATGAGTGGCT
1 ATGTAATTGAATGTGAATAAAATACAAAATATGAGTGGCT
46710 ATGTAATTGAATGTGAATAAAATACAAAATATGAGTGGCT
1 ATGTAATTGAATGTGAATAAAATACAAAATATGAGTGGCT
46750 ATGTAA
1 ATGTAA
46756 ACGTTTGGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (40 bp):
ATGTAATTGAATGTGAATAAAATACAAAATATGAGTGGCT
Found at i:49685 original size:24 final size:25
Alignment explanation
Indices: 49620--49673 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
49610 AAATCTTCTT
*
49620 AAAAAAGTAATGTTTATAATAATTA
1 AAAAAAGTAATATTTATAATAATTA
49645 AAAAAAGTAATATTTATAATAATTA
1 AAAAAAGTAATATTTATAATAATTA
49670 AAAA
1 AAAA
49674 TATAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (25 bp):
AAAAAAGTAATATTTATAATAATTA
Found at i:53291 original size:18 final size:18
Alignment explanation
Indices: 53268--53310 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
53258 ATTCAAGGTG
53268 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
53286 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
53304 TAATTAA
1 TAATTAA
53311 AAATTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:57818 original size:3 final size:3
Alignment explanation
Indices: 57810--57844 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
57800 AGGCACGCAG
57810 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
57845 GGCCAAAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.34, G:0.34, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:58835 original size:122 final size:122
Alignment explanation
Indices: 58618--58862 Score: 472
Period size: 122 Copynumber: 2.0 Consensus size: 122
58608 GAATGAAAAA
58618 TTTTCGACTTAATCGAGTTTTCGAATCCTATTTCATCATCCTAACTCAATTTGAAATTTTTACGA
1 TTTTCGACTTAATCGAGTTTTCGAATCCTATTTCATCATCCTAACTCAATTTGAAATTTTTACGA
* *
58683 ATCGAGTCGAGTGAGATAGAATTTGAATCGAATCGAATTGAATATATTTGTTCAAAT
66 ATCGAGTCGAGTGAGACAGAATTTGAATCGAATCGAATCGAATATATTTGTTCAAAT
58740 TTTTCGACTTAATCGAGTTTTCGAATCCTATTTCATCATCCTAACTCAATTTGAAATTTTTACGA
1 TTTTCGACTTAATCGAGTTTTCGAATCCTATTTCATCATCCTAACTCAATTTGAAATTTTTACGA
58805 ATCGAGTCGAGTGAGACAGAATTTGAATCGAATCGAATCGAATATATTTGTTCAAAT
66 ATCGAGTCGAGTGAGACAGAATTTGAATCGAATCGAATCGAATATATTTGTTCAAAT
58862 T
1 T
58863 AAATTAAAAA
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 121 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (122 bp):
TTTTCGACTTAATCGAGTTTTCGAATCCTATTTCATCATCCTAACTCAATTTGAAATTTTTACGA
ATCGAGTCGAGTGAGACAGAATTTGAATCGAATCGAATCGAATATATTTGTTCAAAT
Found at i:59073 original size:19 final size:20
Alignment explanation
Indices: 59029--59073 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
59019 AAAAAAAATA
*
59029 AACAA-AAATTCAAGTAAAC
1 AACAATAAATCCAAGTAAAC
59048 AAC-ATAAATCCAAGT-AAC
1 AACAATAAATCCAAGTAAAC
59066 AACAATAA
1 AACAATAA
59074 CACAACAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.62, C:0.18, G:0.04, T:0.16
Consensus pattern (20 bp):
AACAATAAATCCAAGTAAAC
Found at i:59470 original size:58 final size:58
Alignment explanation
Indices: 59401--59520 Score: 186
Period size: 58 Copynumber: 2.1 Consensus size: 58
59391 AAAATGAGTT
* * *
59401 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAATATTTGATTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGGCTTAAAAATATTTGAGTTTA
* * *
59459 GTTTATGAGTGTTTTTTAAGAATAAAATTATATTTGGGCTTACAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGGCTTAAAAATATTTGAGTTTA
59517 GTTT
1 GTTT
59521 GTTGATGAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGGCTTAAAAATATTTGAGTTTA
Found at i:59776 original size:21 final size:21
Alignment explanation
Indices: 59747--59811 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
59737 TCAACTCGAT
*
59747 TCGTTTACGTGTAAGGAAAGC
1 TCGTATACGTGTAAGGAAAGC
****
59768 TCGTATACGTGTAA-G-CTTT
1 TCGTATACGTGTAAGGAAAGC
59787 TCGTATACGTGTAAGGAAAGC
1 TCGTATACGTGTAAGGAAAGC
59808 TCGT
1 TCGT
59812 CTAGCTAGAT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
19 14 0.42
20 2 0.06
21 17 0.52
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (21 bp):
TCGTATACGTGTAAGGAAAGC
Found at i:61911 original size:34 final size:34
Alignment explanation
Indices: 61873--61942 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
61863 CTATGAGAAA
61873 GTAAAAATGTTAAAAGATGCTAACCTGCATTTCG
1 GTAAAAATGTTAAAAGATGCTAACCTGCATTTCG
61907 GTAAAAATGTTAAAAGATGCTAACCTGCATTTCG
1 GTAAAAATGTTAAAAGATGCTAACCTGCATTTCG
61941 GT
1 GT
61943 GGAGAGCCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (34 bp):
GTAAAAATGTTAAAAGATGCTAACCTGCATTTCG
Found at i:66032 original size:19 final size:17
Alignment explanation
Indices: 66008--66058 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
65998 CATCACTTCA
66008 ATTTTTATTATAGTTTTAT
1 ATTTTT-TTATA-TTTTAT
*
66027 ATTTTTTTAGATTTTAT
1 ATTTTTTTATATTTTAT
66044 ATATTTTTT-TATTTT
1 AT-TTTTTTATATTTT
66059 TTTAATAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.45
18 10 0.34
19 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (17 bp):
ATTTTTTTATATTTTAT
Found at i:66051 original size:27 final size:28
Alignment explanation
Indices: 66010--66062 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
66000 TCACTTCAAT
66010 TTTTATTATAGTTTTATATTTTTTTAGA
1 TTTTATTATAGTTTTATATTTTTTTAGA
* *
66038 TTTTA-TATATTTTTTTATTTTTTTA
1 TTTTATTATAGTTTTATATTTTTTTA
66063 ATAATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (28 bp):
TTTTATTATAGTTTTATATTTTTTTAGA
Found at i:66057 original size:17 final size:18
Alignment explanation
Indices: 66024--66058 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
66014 ATTATAGTTT
66024 TATATTTTTTTAGATTTTA
1 TATATTTTTTTA-ATTTTA
66043 TATATTTTTTT-ATTTT
1 TATATTTTTTTAATTTT
66059 TTTAATAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
19 11 0.69
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TATATTTTTTTAATTTTA
Found at i:68203 original size:12 final size:12
Alignment explanation
Indices: 68176--68265 Score: 55
Period size: 12 Copynumber: 7.9 Consensus size: 12
68166 TTTTTTACTA
*
68176 TTTTGGTTGTTG
1 TTTTTGTTGTTG
*
68188 TTTTCG-TGTTG
1 TTTTTGTTGTTG
68199 TTTTTGTTGTTG
1 TTTTTGTTGTTG
**
68211 ---TTAATGTTG
1 TTTTTGTTGTTG
* *
68220 -TTTTGCTGTTA
1 TTTTTGTTGTTG
**
68231 TTTTTACTGTTG
1 TTTTTGTTGTTG
* *
68243 TTTTGGTTGTTA
1 TTTTTGTTGTTG
68255 TTTTTGTTGTT
1 TTTTTGTTGTT
68266 TGGATGTTAT
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
9 7 0.12
11 16 0.27
12 37 0.62
ACGTcount: A:0.06, C:0.03, G:0.23, T:0.68
Consensus pattern (12 bp):
TTTTTGTTGTTG
Found at i:68229 original size:23 final size:22
Alignment explanation
Indices: 68194--68299 Score: 71
Period size: 23 Copynumber: 4.9 Consensus size: 22
68184 GTTGTTTTCG
*
68194 TGTTGTTTT-TGTTGTTGTTAA
1 TGTTGTTTTGTGTTATTGTTAA
* *
68215 TGTTGTTTTGCTGTTATTTTTAC
1 TGTTGTTTTG-TGTTATTGTTAA
68238 TGTTGTTTTGGTTGTTATT-TT--
1 TGTTGTTTT-G-TGTTATTGTTAA
* * *
68259 TGTTGTTTGGATGTTATTTTTTA
1 TGTTGTTTTG-TGTTATTGTTAA
*
68282 TG-TGTTTT-TATTATTGTT
1 TGTTGTTTTGTGTTATTGTT
68300 TTACTGTCTT
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
20 16 0.23
21 19 0.27
22 5 0.07
23 22 0.31
24 8 0.11
ACGTcount: A:0.09, C:0.02, G:0.21, T:0.68
Consensus pattern (22 bp):
TGTTGTTTTGTGTTATTGTTAA
Found at i:68235 original size:32 final size:32
Alignment explanation
Indices: 68183--68244 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
68173 CTATTTTGGT
* **
68183 TGTTGTTTTCGTGTTGTTTTTGTTGTTGTTAA
1 TGTTGTTTTCGTGTTATTTTTACTGTTGTTAA
68215 TGTTGTTTT-GCTGTTATTTTTACTGTTGTT
1 TGTTGTTTTCG-TGTTATTTTTACTGTTGTT
68245 TTGGTTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.06, C:0.05, G:0.23, T:0.66
Consensus pattern (32 bp):
TGTTGTTTTCGTGTTATTTTTACTGTTGTTAA
Found at i:68242 original size:44 final size:44
Alignment explanation
Indices: 68194--68279 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
68184 GTTGTTTTCG
* * * *
68194 TGTTGTTTTTGTTGTTGTTAATGTTGTTTTGCTGTTATTTTTAC
1 TGTTGTTTTGGTTGTTATTAATGTTGTTTGGATGTTATTTTTAC
**
68238 TGTTGTTTTGGTTGTTATTTTTGTTGTTTGGATGTTATTTTT
1 TGTTGTTTTGGTTGTTATTAATGTTGTTTGGATGTTATTTTT
68280 TATGTGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.08, C:0.02, G:0.22, T:0.67
Consensus pattern (44 bp):
TGTTGTTTTGGTTGTTATTAATGTTGTTTGGATGTTATTTTTAC
Found at i:68273 original size:20 final size:20
Alignment explanation
Indices: 68215--68279 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
68205 TTGTTGTTAA
* *
68215 TGTTGTTTTGCTGTTATTTTT
1 TGTTGTTTGGATGTTA-TTTT
*
68236 ACTGTTGTTTTGGTTGTTATTTT
1 --TGTTG-TTTGGATGTTATTTT
68259 TGTTGTTTGGATGTTATTTT
1 TGTTGTTTGGATGTTATTTT
68279 T
1 T
68280 TATGTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
20 15 0.39
21 5 0.13
23 9 0.24
24 9 0.24
ACGTcount: A:0.08, C:0.03, G:0.22, T:0.68
Consensus pattern (20 bp):
TGTTGTTTGGATGTTATTTT
Found at i:68295 original size:20 final size:22
Alignment explanation
Indices: 68272--68312 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
68262 TGTTTGGATG
*
68272 TTATT-TTTTA-TGTGTTTTTA
1 TTATTGTTTTACTGTCTTTTTA
68292 TTATTGTTTTACTGTCTTTTT
1 TTATTGTTTTACTGTCTTTTT
68313 TAATATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.73
Consensus pattern (22 bp):
TTATTGTTTTACTGTCTTTTTA
Found at i:71204 original size:179 final size:179
Alignment explanation
Indices: 70904--71263 Score: 621
Period size: 179 Copynumber: 2.0 Consensus size: 179
70894 ATGAAAATGC
*
70904 AATGCAATCAATCAATATCATTATCAACATTTTATCTCATTGCAAGAATAGACAATTCATAAATC
1 AATGCAATCAATCAATATCATTATCAACATTCTATCTCATTGCAAGAATAGACAATTCATAAATC
*
70969 AATCATTAAAATATGTGAGACATTTATTCAACATGTATAGCATTAATAAATATATATAATCATTC
66 AATCATTAAAACATGTGAGACATTTATTCAACATGTATAGCATTAATAAATATATATAATCATTC
* *
71034 ACGAATTTAAACAAACAATCATAAGCAATTATAACATAATAGCAATCAT
131 ACGAATTTAAACAAACAATCATAAGCAACTATAACATAATAGCAACCAT
* * *
71083 AATGCAATCAATCAATATCATTATCGACATTCTATCTCATTGCAGGAATAGACAATTCATATATC
1 AATGCAATCAATCAATATCATTATCAACATTCTATCTCATTGCAAGAATAGACAATTCATAAATC
*
71148 AATCATTAAAACATGTGAGACATTTATTCGACATGTATAGCATTAATAAATATATATAATCATTC
66 AATCATTAAAACATGTGAGACATTTATTCAACATGTATAGCATTAATAAATATATATAATCATTC
** *
71213 ACGAATTTAAACAAACAATCATAAGTGACTATATCATAATAGCAACCAT
131 ACGAATTTAAACAAACAATCATAAGCAACTATAACATAATAGCAACCAT
71262 AA
1 AA
71264 AATCATTCAC
Statistics
Matches: 170, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
179 170 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (179 bp):
AATGCAATCAATCAATATCATTATCAACATTCTATCTCATTGCAAGAATAGACAATTCATAAATC
AATCATTAAAACATGTGAGACATTTATTCAACATGTATAGCATTAATAAATATATATAATCATTC
ACGAATTTAAACAAACAATCATAAGCAACTATAACATAATAGCAACCAT
Found at i:71685 original size:35 final size:34
Alignment explanation
Indices: 71572--71742 Score: 171
Period size: 34 Copynumber: 5.1 Consensus size: 34
71562 GTTTTATTTA
*
71572 CTTGATTGTTTA--ATATATGAATGAATTGAAAAT
1 CTTGATTGTTTATGATATATGAATGAATT-AAATT
*
71605 CTTTGATTGTTTATGATATATGAATGGATTAAA--
1 C-TTGATTGTTTATGATATATGAATGAATTAAATT
71638 -TT--TT-TTTATGATATATGAATGAATTAAAATT
1 CTTGATTGTTTATGATATATGAATGAATT-AAATT
* *
71669 -TGTGATTGTTTGTGATATATGAATAAATTAAATT
1 CT-TGATTGTTTATGATATATGAATGAATTAAATT
* * *
71703 CTTGATTGTTTATAATATATGGATGAATAGAAATT
1 CTTGATTGTTTATGATATATGAATGAAT-TAAATT
71738 CTTGA
1 CTTGA
71743 ATGATAGATA
Statistics
Matches: 117, Mismatches: 9, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
28 20 0.17
29 5 0.04
31 3 0.03
32 1 0.01
33 1 0.01
34 40 0.34
35 33 0.28
36 14 0.12
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.46
Consensus pattern (34 bp):
CTTGATTGTTTATGATATATGAATGAATTAAATT
Found at i:78342 original size:34 final size:35
Alignment explanation
Indices: 78283--78375 Score: 127
Period size: 34 Copynumber: 2.7 Consensus size: 35
78273 TTTTTATGAT
* *
78283 ATATGAATGAATTAAAATT-TGTGATTGTTTGTGAG
1 ATATGAATGAATTAAAATTCT-TGATTGTTTATAAG
*
78318 ATATGAATGAATT-AAATTCTTGATTGTTTATAAT
1 ATATGAATGAATTAAAATTCTTGATTGTTTATAAG
*
78352 ATATGAATGAATTGAAATTCTTGA
1 ATATGAATGAATTAAAATTCTTGA
78376 ACAGTAGATA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
34 29 0.55
35 24 0.45
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (35 bp):
ATATGAATGAATTAAAATTCTTGATTGTTTATAAG
Found at i:81421 original size:34 final size:34
Alignment explanation
Indices: 81314--81447 Score: 148
Period size: 34 Copynumber: 3.9 Consensus size: 34
81304 TATTCACTTG
*
81314 ATTGTTTA--ATATATGAATGAATTGAAAATATTTT
1 ATTGTTTATGATATATGAATGAATT-AAAAT-TTTA
* *
81348 ATTATTTATGATATATGAATGAATTAAAATTTGTG
1 ATTGTTTATGATATATGAATGAATTAAAATTT-TA
*
81383 ATTGTTTGTGATATATGAATGAATT-AAATTCTTA
1 ATTGTTTATGATATATGAATGAATTAAAATT-TTA
** *
81417 ATTGTTTAAAATATATGAATGAATTGAAATT
1 ATTGTTTATGATATATGAATGAATTAAAATT
81448 CTTGAACGGT
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
34 37 0.43
35 35 0.40
36 15 0.17
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.46
Consensus pattern (34 bp):
ATTGTTTATGATATATGAATGAATTAAAATTTTA
Found at i:89424 original size:26 final size:24
Alignment explanation
Indices: 89393--89440 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
89383 ATTTGTTTTA
*
89393 ATATTTTTAAATGTATTTGATATATC
1 ATATTTTAAAAT-TATTT-ATATATC
89419 ATATTTTAAAATTATTTATATA
1 ATATTTTAAAATTATTTATATA
89441 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATTTTAAAATTATTTATATATC
Found at i:96614 original size:17 final size:16
Alignment explanation
Indices: 96579--96611 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
96569 ATGAAAAATT
96579 ATTTTTTAAAATTTTA
1 ATTTTTTAAAATTTTA
*
96595 ATTTTTTTAAATTTTA
1 ATTTTTTAAAATTTTA
96611 A
1 A
96612 ATTAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTTAAAATTTTA
Found at i:96661 original size:32 final size:30
Alignment explanation
Indices: 96624--96687 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 30
96614 TAATAAATAT
* *
96624 AAAATTATATTTTAATCTCATTTAAAATCATA
1 AAAATTATAATTTAATAT--TTTAAAATCATA
* *
96656 AAAATTTTAATTTAATATTTTAAAATTATA
1 AAAATTATAATTTAATATTTTAAAATCATA
96686 AA
1 AA
96688 TATATAGACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 13 0.46
32 15 0.54
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (30 bp):
AAAATTATAATTTAATATTTTAAAATCATA
Found at i:97326 original size:23 final size:21
Alignment explanation
Indices: 97280--97332 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
97270 CAAACTTTAT
97280 ATTTTAAAAAGATATATAAAA
1 ATTTTAAAAAGATATATAAAA
*
97301 ATTTTAAAATATATATATTAAAA
1 ATTTTAAAA-AGATATA-TAAAA
*
97324 ATTCTAAAA
1 ATTTTAAAA
97333 GAATTCTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 9 0.32
22 6 0.21
23 13 0.46
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTTTAAAAAGATATATAAAA
Found at i:99711 original size:23 final size:23
Alignment explanation
Indices: 99678--99724 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
99668 TTACCAGTAC
*
99678 CTAACGTTGCTCACATGAGTTGT
1 CTAACGCTGCTCACATGAGTTGT
99701 CTAACGCTGCTCACATGAGTTGT
1 CTAACGCTGCTCACATGAGTTGT
99724 C
1 C
99725 GAGTACTCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (23 bp):
CTAACGCTGCTCACATGAGTTGT
Found at i:101850 original size:16 final size:16
Alignment explanation
Indices: 101829--101862 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
101819 ATTTATAATG
101829 ATTTTTCAAAGTTAGA
1 ATTTTTCAAAGTTAGA
101845 ATTTTTCAAAGTTAGA
1 ATTTTTCAAAGTTAGA
101861 AT
1 AT
101863 AGGGGAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
ATTTTTCAAAGTTAGA
Found at i:104703 original size:31 final size:32
Alignment explanation
Indices: 104668--104730 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
104658 TTAAGGGCAT
104668 ATTATTATTAA-ATTTTTAAATGTTAAAATAA
1 ATTATTATTAATATTTTTAAATGTTAAAATAA
*
104699 ATTATTATTAATTTTTTTAAATGTTAAAATAA
1 ATTATTATTAATATTTTTAAATGTTAAAATAA
104731 TATCATTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (32 bp):
ATTATTATTAATATTTTTAAATGTTAAAATAA
Found at i:113932 original size:507 final size:506
Alignment explanation
Indices: 112958--113973 Score: 1574
Period size: 507 Copynumber: 2.0 Consensus size: 506
112948 AATGTTTATA
* * *
112958 TATATATATATATATATATGGCTCATGACATATTATGCTTATATGTAATATTAATTATGATTTCT
1 TATATATATATATATATATGGCTCATGACATATCATGCTTATATGTAACATTAATTAAGATTTCT
* * * * * *
113023 TTAATTGCACACGTACTCTTATCAAGGTTATCCATTTGAGTGACAGTCATTCATTTATTTATATA
66 CTAAGTACACACATACTCTTATCAAGGTTATCCATTTGAGTGACAGTCACTAATTTATTTATATA
* * * * *
113088 TCGGTCTATAGAAATCGAAATGAAGATCTGCTTGTTGTGTTTGAAACTAGACTCAATGAGTTTTA
131 ACGATCTATAGAAATCGAAATGAAGATCCGCTTATTGTGTTTGAAACTAGACTCAATGAGCTTTA
* * * * *
113153 TATAATAAAAATTTCATAATTTTTGCTTAGGTCAATTAGTACAATTTTTTTTCTCTTCAAATCTT
196 TACAATAAAAATTTCATAATTTCTACTTAGGCCAATTAATACAATTTTTTTTCTCTTCAAATCTT
* * *
113218 TCTTTGTTCTGCTACTAGGTAGCTCTGACCCTTCTTCACTAAAAATTAAATATCTTTCAGTACAT
261 TCTCTGTTCTGCTACTAGGTAGCTCTAACCCTTCTTCACTAAAAATTAAATATCTTTCAATACAT
* * *
113283 GTCTTGTATTATGTTTCCCTTGAAAATAGACTCATTAAGATTTTAGGCATATAAATTTCATCTCC
326 GTCTCGTATTATGTTTCCCTTGAAAATAGACTCATTAAAATTTTAGGCATATAAATGTCATCTCC
*
113348 TAAACATTTTTTTTTTTTTACAATTTATAATGATTTTTCAAAGTTAAAATAGGGAACCTGAAATT
391 TAAACA-TTTTTTTTTTTTACAATTTATAATGATTTTTCAAAGTTAAAATAGGGAACCCGAAATT
113413 ATTTTGACCTTGTCTCACAAAACTTATCATGTCTCATAATCTACAATTCCAT
455 ATTTTGACCTTGTCTCACAAAACTTATCATGTCTCATAATCTACAATTCCAT
113465 TATATATATGA-AT-TAT-TGGCTCATGACATATCATGCTTATATGTAACATTAATTAAGATTTC
1 TATATATAT-ATATATATATGGCTCATGACATATCATGCTTATATGTAACATTAATTAAGATTTC
* *
113527 TCTAGGTACACACATACTCTTATCAAGGTTGTCCATTTGAGTGACAGTCACTAATTTATTTATAT
65 TCTAAGTACACACATACTCTTATCAAGGTTATCCATTTGAGTGACAGTCACTAATTTATTTATAT
* *
113592 AACGATCTATAGAAATTGAAATTAAGATCCGCTTATTGTGTTTGAAACTAGACTCAATGAGCTTT
130 AACGATCTATAGAAATCGAAATGAAGATCCGCTTATTGTGTTTGAAACTAGACTCAATGAGCTTT
* * * * *
113657 ATACCATAAGATTTTCATAATTTCTACTTAGGCCAATTAATGCAGTTTTTTTTTTCTCTTCAAAT
195 ATACAATAAAAATTTCATAATTTCTACTTAGGCCAATTAATACA--ATTTTTTTTCTCTTCAAAT
* *
113722 CTTTCTCTGTTCTGCTGCTAGGTAGCTTTAACCCTTCTTCACTAAAAATTAAATATCTTTCAATA
258 CTTTCTCTGTTCTGCTACTAGGTAGCTCTAACCCTTCTTCACTAAAAATTAAATATCTTTCAATA
113787 CATGTCTCGTATTATGTTTCCCTTGAAAATAGACTCATTAAAATTTTAGGCATATAAATGTCATC
323 CATGTCTCGTATTATGTTTCCCTTGAAAATAGACTCATTAAAATTTTAGGCATATAAATGTCATC
*
113852 TCCTAAAC-TTTTTTTTTTTTACAATTTTATAATGATTTTTCAAAGTTAGAATAGGAGAACCCGA
388 TCCTAAACATTTTTTTTTTTTACAA-TTTATAATGATTTTTCAAAGTTAAAATAGG-GAACCCGA
* *
113916 AA-TATTTCTGACCTTGTCTCACAAAATTTATTATGTCTCATAATCTACAATTCCAT
451 AATTATTT-TGACCTTGTCTCACAAAACTTATCATGTCTCATAATCTACAATTCCAT
113972 TA
1 TA
113974 CTAACACTGT
Statistics
Matches: 463, Mismatches: 40, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
505 209 0.45
506 37 0.08
507 216 0.47
508 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (506 bp):
TATATATATATATATATATGGCTCATGACATATCATGCTTATATGTAACATTAATTAAGATTTCT
CTAAGTACACACATACTCTTATCAAGGTTATCCATTTGAGTGACAGTCACTAATTTATTTATATA
ACGATCTATAGAAATCGAAATGAAGATCCGCTTATTGTGTTTGAAACTAGACTCAATGAGCTTTA
TACAATAAAAATTTCATAATTTCTACTTAGGCCAATTAATACAATTTTTTTTCTCTTCAAATCTT
TCTCTGTTCTGCTACTAGGTAGCTCTAACCCTTCTTCACTAAAAATTAAATATCTTTCAATACAT
GTCTCGTATTATGTTTCCCTTGAAAATAGACTCATTAAAATTTTAGGCATATAAATGTCATCTCC
TAAACATTTTTTTTTTTTACAATTTATAATGATTTTTCAAAGTTAAAATAGGGAACCCGAAATTA
TTTTGACCTTGTCTCACAAAACTTATCATGTCTCATAATCTACAATTCCAT
Found at i:114844 original size:24 final size:24
Alignment explanation
Indices: 114816--114877 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
114806 ACTTAGAGTC
* *
114816 TAACTGGAAAAATATAATAAAGTT
1 TAACTGGAAAAAGATAACAAAGTT
*
114840 TAACTGGAAAAAGATAACAGAGTT
1 TAACTGGAAAAAGATAACAAAGTT
*
114864 TAACTGGAAGAAGA
1 TAACTGGAAAAAGA
114878 AATCCGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (24 bp):
TAACTGGAAAAAGATAACAAAGTT
Found at i:136920 original size:16 final size:17
Alignment explanation
Indices: 136901--136933 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
136891 ACAATTTTAC
*
136901 TTTTACTAA-TTTAAAA
1 TTTTAATAAGTTTAAAA
136917 TTTTAATAAGTTTAAAA
1 TTTTAATAAGTTTAAAA
136934 AATTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTTAATAAGTTTAAAA
Found at i:138144 original size:29 final size:29
Alignment explanation
Indices: 138102--138162 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
138092 TTAATTTTAA
138102 TTGTTTAAATATTAAAGATAAATGATATT
1 TTGTTTAAATATTAAAGATAAATGATATT
138131 TTGTTTAAATATTAAAGATAAATGATATT
1 TTGTTTAAATATTAAAGATAAATGATATT
138160 TTG
1 TTG
138163 AACTATGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (29 bp):
TTGTTTAAATATTAAAGATAAATGATATT
Found at i:142325 original size:15 final size:15
Alignment explanation
Indices: 142307--142343 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
142297 AATAAAAAAT
142307 ATATAAAATTATTAA
1 ATATAAAATTATTAA
*
142322 ATATTAAA-TATTAA
1 ATATAAAATTATTAA
142336 A-ATAAAAT
1 ATATAAAAT
142344 AAATATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 5 0.26
14 7 0.37
15 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATAAAATTATTAA
Found at i:144326 original size:7 final size:7
Alignment explanation
Indices: 144316--144392 Score: 57
Period size: 7 Copynumber: 10.6 Consensus size: 7
144306 TTGTTGAACT
144316 TTGATCG
1 TTGATCG
*
144323 TTGACCCG
1 TTGA-TCG
*
144331 TTGACCG
1 TTGATCG
*
144338 TTGACTTG
1 TTGA-TCG
*
144346 TT-AGCCG
1 TTGATC-G
*
144353 TTGATCAA
1 TTGATC-G
*
144361 TTGACCG
1 TTGATCG
144368 TTGATCG
1 TTGATCG
144375 TTGATCG
1 TTGATCG
144382 TTGATCG
1 TTGATCG
144389 TTGA
1 TTGA
144393 CCTTTTGGGT
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
7 39 0.71
8 16 0.29
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (7 bp):
TTGATCG
Found at i:144341 original size:22 final size:22
Alignment explanation
Indices: 144316--144394 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
144306 TTGTTGAACT
144316 TTGATCGTTGACCCGTTGACCG
1 TTGATCGTTGACCCGTTGACCG
* * **
144338 TTGACTTGTT-AGCCGTTGATCAA
1 TTGA-TCGTTGACCCGTTGA-CCG
* * *
144361 TTGACCGTTGA-TCGTTGATCG
1 TTGATCGTTGACCCGTTGACCG
144382 TTGATCGTTGACC
1 TTGATCGTTGACC
144395 TTTTGGGTTA
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
21 10 0.24
22 21 0.51
23 10 0.24
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (22 bp):
TTGATCGTTGACCCGTTGACCG
Found at i:144383 original size:14 final size:14
Alignment explanation
Indices: 144329--144394 Score: 71
Period size: 15 Copynumber: 4.6 Consensus size: 14
144319 ATCGTTGACC
144329 CGTTGACCGTTGACT
1 CGTTGACCGTTGA-T
*
144344 TGTT-AGCCGTTGAT
1 CGTTGA-CCGTTGAT
*
144358 CAATTGACCGTTGAT
1 C-GTTGACCGTTGAT
*
144373 CGTTGATCGTTGAT
1 CGTTGACCGTTGAT
144387 CGTTGACC
1 CGTTGACC
144395 TTTTGGGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
14 20 0.48
15 21 0.50
16 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (14 bp):
CGTTGACCGTTGAT
Found at i:151448 original size:20 final size:20
Alignment explanation
Indices: 151419--151456 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
151409 CCCATTGATC
151419 GTTGACCGTTAACTTTTTGG
1 GTTGACCGTTAACTTTTTGG
* *
151439 GTTGATCGTTGACTTTTT
1 GTTGACCGTTAACTTTTT
151457 TTGAGACACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.24, T:0.50
Consensus pattern (20 bp):
GTTGACCGTTAACTTTTTGG
Found at i:156196 original size:18 final size:18
Alignment explanation
Indices: 156173--156208 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
156163 CACTTTAGTT
*
156173 ACCTCATACATCGGATGA
1 ACCTCATACATCCGATGA
156191 ACCTCATACATCCGATGA
1 ACCTCATACATCCGATGA
156209 TTGTGGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (18 bp):
ACCTCATACATCCGATGA
Found at i:158345 original size:20 final size:22
Alignment explanation
Indices: 158306--158346 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
158296 ATCGAAACTA
158306 TATTATATATTTTTAGATAATAT
1 TATTATATATTTTTA-ATAATAT
158329 TATT-TATATTTTT-ATAAT
1 TATTATATATTTTTAATAAT
158347 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TATTATATATTTTTAATAATAT
Found at i:158388 original size:28 final size:31
Alignment explanation
Indices: 158333--158408 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 31
158323 TAATATTATT
* * *
158333 TATATTTTTATAATT-TTTTAAAAATTAAAT
1 TATAATTTTATCATTATTTTAAAAATTAAAA
*
158363 TA-AATTTT-T-ATTATTTTAAGAATTAAAA
1 TATAATTTTATCATTATTTTAAAAATTAAAA
158391 TATAATTTTATCATTATT
1 TATAATTTTATCATTATT
158409 ATTTTAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 3 0.08
28 16 0.41
29 11 0.28
30 3 0.08
31 6 0.15
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (31 bp):
TATAATTTTATCATTATTTTAAAAATTAAAA
Found at i:158391 original size:29 final size:30
Alignment explanation
Indices: 158333--158408 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
158323 TAATATTATT
* *
158333 TATATTTTTATAATT-TTTTAAAAATTAAA
1 TATAATTTTATCATTATTTTAAAAATTAAA
*
158362 T-TAAATTTT-T-ATTATTTTAAGAATTAAAA
1 TAT-AATTTTATCATTATTTTAAAAATT-AAA
158391 TATAATTTTATCATTATT
1 TATAATTTTATCATTATT
158409 ATTTTAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 3 0.08
28 12 0.31
29 16 0.41
30 2 0.05
31 6 0.15
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (30 bp):
TATAATTTTATCATTATTTTAAAAATTAAA
Found at i:168193 original size:42 final size:42
Alignment explanation
Indices: 168115--168299 Score: 196
Period size: 42 Copynumber: 4.4 Consensus size: 42
168105 GAATCACTTG
* * * *
168115 ATGTATAAATGGAGGACTCATGTCTTGGGACAAGCATAAGATT
1 ATGTTTAAA-GGAAGACTCATGTCTCGGGATAAGCATAAGATT
* * * *
168158 ATATTTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCGGGATAAGCATAAGATT
* *
168200 ATGTTTAAAGGAAGACTCATGTCTCGGGATAAGAATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCGGGATAAGCATAAGATT
* * * *
168242 ATGTTAAAAGGAAGACTTATGACTC-GG-TAGAGCATAAAATT
1 ATGTTTAAAGGAAGACTCATGTCTCGGGATA-AGCATAAGATT
168283 -TGTTTGAAAGGAAGACT
1 ATGTTT-AAAGGAAGACT
168300 TATATGACTC
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
40 6 0.05
41 21 0.17
42 87 0.72
43 7 0.06
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTCATGTCTCGGGATAAGCATAAGATT
Found at i:169488 original size:22 final size:22
Alignment explanation
Indices: 169404--169481 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
169394 CTGCTGGGGA
*
169404 AACAGAAGCACACACAGTGTTG
1 AACAGAAGCACACACAGTGCTG
*
169426 AACAGAAGCACACACAATGCTG
1 AACAGAAGCACACACAGTGCTG
169448 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
169470 AACAGTAAGCAC
1 AACAG-AAGCAC
169482 GCTAGTGTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 46 0.88
23 6 0.12
ACGTcount: A:0.44, C:0.26, G:0.21, T:0.10
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:169580 original size:24 final size:26
Alignment explanation
Indices: 169542--169589 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
169532 TCTACATGGA
169542 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
169568 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
169590 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:171543 original size:9 final size:9
Alignment explanation
Indices: 171529--171580 Score: 77
Period size: 9 Copynumber: 5.8 Consensus size: 9
171519 ATTTTACAAT
171529 TCGAATAAC
1 TCGAATAAC
*
171538 TCGAATAAT
1 TCGAATAAC
171547 TCGAATAAC
1 TCGAATAAC
* *
171556 TCAAATAAT
1 TCGAATAAC
171565 TCGAATAAC
1 TCGAATAAC
171574 TCGAATA
1 TCGAATA
171581 TTTTAAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (9 bp):
TCGAATAAC
Found at i:171591 original size:18 final size:18
Alignment explanation
Indices: 171526--171580 Score: 101
Period size: 18 Copynumber: 3.1 Consensus size: 18
171516 TCAATTTTAC
171526 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
*
171544 AATTCGAATAACTCAAAT
1 AATTCGAATAACTCGAAT
171562 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
171580 A
1 A
171581 TTTTAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.27
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:171743 original size:10 final size:10
Alignment explanation
Indices: 171728--171785 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 10
171718 ATATTTTTTA
171728 AAAAAATTAT
1 AAAAAATTAT
171738 AAAAAATT-T
1 AAAAAATTAT
*
171747 AAAAAA-TCT
1 AAAAAATTAT
171756 AAAAAATATAT
1 AAAAAAT-TAT
171767 AAAGAAAGTTA-
1 AAA-AAA-TTAT
171778 AAAAAATT
1 AAAAAATT
171786 CTAGAACAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
8 1 0.02
9 16 0.38
10 11 0.26
11 8 0.19
12 5 0.12
13 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:177985 original size:28 final size:27
Alignment explanation
Indices: 177933--177992 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
177923 AATTAAGTCC
177933 ATTTTTTTATTTTTTATTAATTATTCTT
1 ATTTTTTTATTTTTTATTAATTATT-TT
*
177961 ATTTTTTT-TTCTTTTATGTTA-TATTTT
1 ATTTTTTTATT-TTTTAT-TAATTATTTT
177988 ATTTT
1 ATTTT
177993 ATCTATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 9 0.31
28 18 0.62
29 2 0.07
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (27 bp):
ATTTTTTTATTTTTTATTAATTATTTT
Found at i:177992 original size:17 final size:17
Alignment explanation
Indices: 177967--178022 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
177957 TCTTATTTTT
*
177967 TTTTCTTTTATGTTATA
1 TTTTATTTTATGTTATA
*
177984 TTTTATTTTAT-CTATTA
1 TTTTATTTTATGTTA-TA
* * *
178001 TTGTATGTTATGTTATT
1 TTTTATTTTATGTTATA
178018 TTTTA
1 TTTTA
178023 AATATTTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.70
Consensus pattern (17 bp):
TTTTATTTTATGTTATA
Found at i:182037 original size:2 final size:2
Alignment explanation
Indices: 182032--182056 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
182022 TTTTTTAATT
182032 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 T
182057 TTATGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:184721 original size:18 final size:19
Alignment explanation
Indices: 184686--184721 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
184676 TTTGAAACTT
184686 CAAACACCATACTATTTTC
1 CAAACACCATACTATTTTC
*
184705 CAAACACTATA-TATTTT
1 CAAACACCATACTATTTT
184722 AGAAGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (19 bp):
CAAACACCATACTATTTTC
Found at i:184768 original size:18 final size:18
Alignment explanation
Indices: 184745--184781 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
184735 AAAATATATG
184745 TTTGTCATTAATATTGGA
1 TTTGTCATTAATATTGGA
184763 TTTGTCATTAATATTGGA
1 TTTGTCATTAATATTGGA
184781 T
1 T
184782 ATATATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.51
Consensus pattern (18 bp):
TTTGTCATTAATATTGGA
Found at i:185170 original size:9 final size:9
Alignment explanation
Indices: 185156--185189 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
185146 CTAGACGTAG
185156 TTTAAAATA
1 TTTAAAATA
185165 TTTAAAATA
1 TTTAAAATA
*
185174 TTAAAAATA
1 TTTAAAATA
185183 -TTAAAAT
1 TTTAAAAT
185190 TTGTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TTTAAAATA
Found at i:187507 original size:37 final size:36
Alignment explanation
Indices: 187409--187510 Score: 107
Period size: 37 Copynumber: 2.8 Consensus size: 36
187399 TGGGCACACG
*
187409 CAAGTTAAGACATTCCACTGAACTTGTCCTCATGTTT
1 CAAGATAAGACATT-CACTGAACTTGTCCTCATGTTT
* * *
187446 CAAGATAAGGTA-ATCCATTAAACTTGTCCTCATGTTT
1 CAAGATAA-G-ACATTCACTGAACTTGTCCTCATGTTT
* *
187483 CAAGCTAAGACAGTTCGCTGAACTTGTC
1 CAAGATAAGACA-TTCACTGAACTTGTC
187511 TCCAAGTTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
35 1 0.02
36 2 0.04
37 45 0.87
38 3 0.06
39 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (36 bp):
CAAGATAAGACATTCACTGAACTTGTCCTCATGTTT
Found at i:187651 original size:14 final size:14
Alignment explanation
Indices: 187634--187678 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
187624 TACCTACATA
187634 TATGAATTTGTATC
1 TATGAATTTGTATC
* *
187648 TATGAATTTGAATA
1 TATGAATTTGTATC
187662 TATGAATTTGTATC
1 TATGAATTTGTATC
187676 TAT
1 TAT
187679 AAACCCGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (14 bp):
TATGAATTTGTATC
Found at i:187662 original size:28 final size:28
Alignment explanation
Indices: 187630--187774 Score: 150
Period size: 28 Copynumber: 5.2 Consensus size: 28
187620 TATGTACCTA
187630 CATATATGAATTTGTATCTATGAATTTG
1 CATATATGAATTTGTATCTATGAATTTG
* * ***
187658 AATATATGAATTTGTATCTATAAACCCG
1 CATATATGAATTTGTATCTATGAATTTG
* **
187686 CATATATGAATTCGTA-CTTATGAATCAG
1 CATATATGAATTTGTATC-TATGAATTTG
* *
187714 CATAAATG-ATTTTTCATCTATGAATTTG
1 CATATATGAATTTGT-ATCTATGAATTTG
* *
187742 CATATATGATTTTGTATCCATGAATTTG
1 CATATATGAATTTGTATCTATGAATTTG
187770 CATAT
1 CATAT
187775 TGATTCCTTA
Statistics
Matches: 94, Mismatches: 19, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
27 5 0.05
28 84 0.89
29 5 0.05
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (28 bp):
CATATATGAATTTGTATCTATGAATTTG
Found at i:187736 original size:14 final size:14
Alignment explanation
Indices: 187713--187779 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 14
187703 TTATGAATCA
*
187713 GCATAAATGATTTT
1 GCATATATGATTTT
* * *
187727 TCATCTATGAATTT
1 GCATATATGATTTT
187741 GCATATATGATTTT
1 GCATATATGATTTT
* ** *
187755 GTATCCATGAATTT
1 GCATATATGATTTT
187769 GCATAT-TGATT
1 GCATATATGATT
187780 CCTTATCTAT
Statistics
Matches: 38, Mismatches: 15, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
13 4 0.11
14 34 0.89
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.46
Consensus pattern (14 bp):
GCATATATGATTTT
Found at i:187786 original size:27 final size:28
Alignment explanation
Indices: 187630--187819 Score: 90
Period size: 28 Copynumber: 6.9 Consensus size: 28
187620 TATGTACCTA
*
187630 CATATATGAATT-TGTATCTATGAATTTG
1 CATATATG-ATTCTGTATCCATGAATTTG
* * * ***
187658 AATATATGAATT-TGTATCTATAAACCCG
1 CATATATG-ATTCTGTATCCATGAATTTG
* **
187686 CATATATGAATTC-GTA-CTTATGAATCAG
1 CATATATG-ATTCTGTATC-CATGAATTTG
* * *
187714 CATAAATGATT-TTTCATCTATGAATTTG
1 CATATATGATTCTGT-ATCCATGAATTTG
*
187742 CATATATGATTTTGTATCCATGAATTTG
1 CATATATGATTCTGTATCCATGAATTTG
* * * *
187770 CATAT-TGATTCCT-TATCTATGGATCTA
1 CATATATGATT-CTGTATCCATGAATTTG
* *
187797 CATATGTGATTCTGCAT-CATGAA
1 CATATATGATTCTGTATCCATGAA
187820 CCCGTATGAA
Statistics
Matches: 129, Mismatches: 24, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
27 31 0.24
28 95 0.74
29 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (28 bp):
CATATATGATTCTGTATCCATGAATTTG
Found at i:189730 original size:22 final size:22
Alignment explanation
Indices: 189690--189750 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
189680 CGATCTAAGG
*
189690 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
189711 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
189733 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
189751 GAAAGTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 11 0.31
22 24 0.67
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:189741 original size:15 final size:16
Alignment explanation
Indices: 189716--189745 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
189706 GAATTAAAAA
189716 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
189732 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
189746 AATAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:190574 original size:19 final size:19
Alignment explanation
Indices: 190550--190592 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
190540 AAACATAAAT
190550 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
190569 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
190588 TAAAT
1 TAAAT
190593 CTTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:195800 original size:19 final size:19
Alignment explanation
Indices: 195776--195818 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
195766 AAACATAAAT
195776 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
195795 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
195814 TAAAT
1 TAAAT
195819 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:196408 original size:3 final size:3
Alignment explanation
Indices: 196400--196439 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
196390 AATCTTGGAT
196400 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
196440 TTAAAACTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:199333 original size:19 final size:20
Alignment explanation
Indices: 199305--199362 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
199295 TGTTCAAAAA
*
199305 TTCAAAATAT-TTATAAATT
1 TTCAAAATATATTAAAAATT
*
199324 TTCAATATATATTAAAAA-T
1 TTCAAAATATATTAAAAATT
* *
199343 TTAAAGAATATATAAAAAAT
1 TTCAA-AATATATTAAAAAT
199363 AAAAAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (20 bp):
TTCAAAATATATTAAAAATT
Found at i:200364 original size:25 final size:26
Alignment explanation
Indices: 200334--200390 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
200324 AAATTTGAAA
*
200334 TTTAAACAGTAAA-ATA-GATTAAATT
1 TTTAAA-AGTAAATATAGGACTAAATT
200359 TTTAAAAGTAAATATAGGACTAAA-T
1 TTTAAAAGTAAATATAGGACTAAATT
200384 TTTAAAA
1 TTTAAAA
200391 TATATGAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 6 0.21
25 17 0.59
26 6 0.21
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (26 bp):
TTTAAAAGTAAATATAGGACTAAATT
Found at i:204916 original size:17 final size:18
Alignment explanation
Indices: 204877--204917 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
204867 TGTGTTATAA
* *
204877 AGAAGAAAAAAAAAGTGC
1 AGAAAAAAAAAAAAGTAC
204895 A-AAAAAAAAAAAAG-AC
1 AGAAAAAAAAAAAAGTAC
204911 AGAAAAA
1 AGAAAAA
204918 TAGGAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 17 0.85
18 1 0.05
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (18 bp):
AGAAAAAAAAAAAAGTAC
Found at i:222301 original size:20 final size:20
Alignment explanation
Indices: 222259--222302 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
222249 TTAATCTTTA
*
222259 TATTTTTATTTGATATGATT
1 TATTTTTATTTGATATAATT
*
222279 TATTTTTATTT-TTATAATAT
1 TATTTTTATTTGATATAAT-T
222299 TATT
1 TATT
222303 AATTAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TATTTTTATTTGATATAATT
Found at i:222495 original size:25 final size:24
Alignment explanation
Indices: 222460--222510 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
222450 AAGATGAAGT
* * *
222460 AGAAGATTAAACTTATTTTAAAAAA
1 AGAAGACTAAAC-TATATAAAAAAA
222485 AGAAGACTAAACTATATAAAAAAA
1 AGAAGACTAAACTATATAAAAAAA
222509 AG
1 AG
222511 GGGTCAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.24
Consensus pattern (24 bp):
AGAAGACTAAACTATATAAAAAAA
Found at i:223607 original size:6 final size:6
Alignment explanation
Indices: 223575--223604 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
223565 GTGGGAGAGG
*
223575 GGGGAA GGGGAA GGGGAA GGGGAA AGGGAA
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA
223605 AGGACAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:224984 original size:2 final size:2
Alignment explanation
Indices: 224977--225004 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
224967 CTTTTTGTGG
224977 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
225005 TAATTTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:240316 original size:31 final size:32
Alignment explanation
Indices: 240280--240351 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
240270 ATTTTGAATT
* *
240280 CCTTAAAAGTTGG-AGAAA-ATTTTTTTAGACC
1 CCTTAAAAGTTGGTA-AAACAATATTTTAGACC
*
240311 CCTTAAAATTTGGTAAAACAATATTTTAGACC
1 CCTTAAAAGTTGGTAAAACAATATTTTAGACC
240343 CCTTAAAAG
1 CCTTAAAAG
240352 CAGAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 15 0.43
32 20 0.57
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (32 bp):
CCTTAAAAGTTGGTAAAACAATATTTTAGACC
Found at i:240380 original size:30 final size:30
Alignment explanation
Indices: 240335--240391 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
240325 AAAACAATAT
*
240335 TTTAGACCCCTTAAAAGCAGAAAAAAAAAA
1 TTTAAACCCCTTAAAAGCAGAAAAAAAAAA
* *
240365 TTTAAACCTCTTAAAAGCTGAAAAAAA
1 TTTAAACCCCTTAAAAGCAGAAAAAAA
240392 TTGGACCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.54, C:0.16, G:0.09, T:0.21
Consensus pattern (30 bp):
TTTAAACCCCTTAAAAGCAGAAAAAAAAAA
Found at i:245018 original size:18 final size:18
Alignment explanation
Indices: 244995--245064 Score: 82
Period size: 18 Copynumber: 4.2 Consensus size: 18
244985 TTTCGGGTAA
244995 AATCGAATT-AATTCGGTT
1 AATCG-ATTGAATTCGGTT
245013 AATCGATTGAATTCGGTT
1 AATCGATTGAATTCGGTT
245031 AATC-----AA-TCGGTT
1 AATCGATTGAATTCGGTT
245043 AATCGATTGAATTCGGTT
1 AATCGATTGAATTCGGTT
245061 AATC
1 AATC
245065 AATCGGTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
12 10 0.22
13 2 0.04
17 5 0.11
18 28 0.62
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (18 bp):
AATCGATTGAATTCGGTT
Found at i:245041 original size:30 final size:30
Alignment explanation
Indices: 245007--245074 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
244997 TCGAATTAAT
245007 TCGGTTAATCGATTGAATTCGGTTAATCAA
1 TCGGTTAATCGATTGAATTCGGTTAATCAA
245037 TCGGTTAATCGATTGAATTCGGTTAATCAA
1 TCGGTTAATCGATTGAATTCGGTTAATCAA
245067 TCGGTTAA
1 TCGGTTAA
245075 ATGAATTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (30 bp):
TCGGTTAATCGATTGAATTCGGTTAATCAA
Found at i:246566 original size:31 final size:31
Alignment explanation
Indices: 246530--246590 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
246520 ATTTGATTAC
*
246530 TGAACTATTCGAAAGTTTTCATTTAAGTCAT
1 TGAACTATTCAAAAGTTTTCATTTAAGTCAT
*
246561 TGAACTATTCAAAAGTTTTTATTTAAGTCA
1 TGAACTATTCAAAAGTTTTCATTTAAGTCA
246591 CTAAGTTGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTCATTTAAGTCAT
Done.