Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 144 of 199
Found at i:43259834 original size:7 final size:7
Alignment explanation
Indices: 43259802--43259847 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
43259792 GATTTAAGGT
43259802 TTAGGGG
1 TTAGGGG
*
43259809 TTAAGGG
1 TTAGGGG
43259816 TTAGGGG
1 TTAGGGG
43259823 TTTAGGGG
1 -TTAGGGG
**
43259831 TTAGACG
1 TTAGGGG
43259838 TTAGGGG
1 TTAGGGG
43259845 TTA
1 TTA
43259848 ATAGTTATGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 25 0.78
8 7 0.22
ACGTcount: A:0.20, C:0.02, G:0.46, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:43260077 original size:7 final size:7
Alignment explanation
Indices: 43260054--43260101 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
43260044 GTTTAGGGAG
43260054 TATGGATT
1 TATGGA-T
*
43260062 TAGGGAT
1 TATGGAT
43260069 TATGGAT
1 TATGGAT
43260076 TA-GGAAT
1 TATGG-AT
43260083 TATGGAT
1 TATGGAT
*
43260090 TAGGGAT
1 TATGGAT
43260097 TATGG
1 TATGG
43260102 TTTAAGGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
6 2 0.06
7 25 0.74
8 7 0.21
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (7 bp):
TATGGAT
Found at i:43260084 original size:14 final size:14
Alignment explanation
Indices: 43260046--43260101 Score: 85
Period size: 14 Copynumber: 3.9 Consensus size: 14
43260036 ATTTTAAGGT
*
43260046 TTAGGGAGTATGGA
1 TTAGGGATTATGGA
43260060 TTTAGGGATTATGGA
1 -TTAGGGATTATGGA
*
43260075 TTAGGAATTATGGA
1 TTAGGGATTATGGA
43260089 TTAGGGATTATGG
1 TTAGGGATTATGG
43260102 TTTAAGGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.29, C:0.00, G:0.36, T:0.36
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:43260611 original size:21 final size:21
Alignment explanation
Indices: 43260585--43260624 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43260575 TTAAAATACA
43260585 AAAATAAAACAATTTTTGTTC
1 AAAATAAAACAATTTTTGTTC
* *
43260606 AAAATAAAATATTTTTTGT
1 AAAATAAAACAATTTTTGT
43260625 GACGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
AAAATAAAACAATTTTTGTTC
Found at i:43264297 original size:12 final size:12
Alignment explanation
Indices: 43264280--43264307 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
43264270 GCTAGCCATG
43264280 ATGTTACTATTA
1 ATGTTACTATTA
43264292 ATGTTACTATTA
1 ATGTTACTATTA
43264304 ATGT
1 ATGT
43264308 CCTTAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (12 bp):
ATGTTACTATTA
Found at i:43269487 original size:20 final size:19
Alignment explanation
Indices: 43269452--43269490 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
43269442 GATGACAAGG
43269452 ATGAGAAATGGAATATGAA
1 ATGAGAAATGGAATATGAA
43269471 ATGACGAAATAGG-ATATGAA
1 ATGA-GAAAT-GGAATATGAA
43269491 TATTGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 12 0.67
21 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.21
Consensus pattern (19 bp):
ATGAGAAATGGAATATGAA
Found at i:43282242 original size:3 final size:3
Alignment explanation
Indices: 43282234--43282296 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
43282224 CCTGAGCAGT
* *
43282234 AGA AGA AGA AG- AGA AAA AGA AGA ATA AG- AGA AGA A-A TAGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA
* *
43282277 AG- AGG AGA AGA AGA ATA AGA
1 AGA AGA AGA AGA AGA AGA AGA
43282297 GAAAATGGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
2 7 0.15
3 40 0.83
4 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (3 bp):
AGA
Found at i:43282256 original size:17 final size:17
Alignment explanation
Indices: 43282234--43282301 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
43282224 CCTGAGCAGT
43282234 AGAAGAAGAAGAGAAAA
1 AGAAGAAGAAGAGAAAA
*
43282251 AGAAGAATAAGAGAAGAA
1 AGAAGAAGAAGAGAA-AA
* * *
43282269 A-TAGAAGAAGAGGAGA
1 AGAAGAAGAAGAGAAAA
*
43282285 AGAAGAATAAGAGAAAA
1 AGAAGAAGAAGAGAAAA
43282302 TGGAAGGAGC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
16 2 0.05
17 35 0.88
18 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.04
Consensus pattern (17 bp):
AGAAGAAGAAGAGAAAA
Found at i:43282262 original size:20 final size:20
Alignment explanation
Indices: 43282234--43282288 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
43282224 CCTGAGCAGT
43282234 AGAAGAAGA-AGAGAAAAAGA
1 AGAAGAAGAGA-AGAAAAAGA
* *
43282254 AGAATAAGAGAAGAAATAGA
1 AGAAGAAGAGAAGAAAAAGA
*
43282274 AGAAGAGGAGAAGAA
1 AGAAGAAGAGAAGAA
43282289 GAATAAGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (20 bp):
AGAAGAAGAGAAGAAAAAGA
Found at i:43282298 original size:14 final size:14
Alignment explanation
Indices: 43282234--43282299 Score: 52
Period size: 14 Copynumber: 5.1 Consensus size: 14
43282224 CCTGAGCAGT
43282234 AGAAGAAGAAGAGA
1 AGAAGAAGAAGAGA
* *
43282248 AAAAGAAG-A-ATA
1 AGAAGAAGAAGAGA
*
43282260 AG-AGAAGAA-A-T
1 AGAAGAAGAAGAGA
*
43282271 AGAAGAAGAGGAGA
1 AGAAGAAGAAGAGA
*
43282285 AGAAGAATAAGAGA
1 AGAAGAAGAAGAGA
43282299 A
1 A
43282300 AATGGAAGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
11 7 0.17
12 11 0.28
13 2 0.05
14 20 0.50
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (14 bp):
AGAAGAAGAAGAGA
Found at i:43282299 original size:11 final size:12
Alignment explanation
Indices: 43282236--43282296 Score: 51
Period size: 11 Copynumber: 5.3 Consensus size: 12
43282226 TGAGCAGTAG
43282236 AAGAAGAAGAGA-
1 AAGAAGAAGA-AT
43282248 AA-AAGAAGAAT
1 AAGAAGAAGAAT
43282259 AAG-AGAAGAA-
1 AAGAAGAAGAAT
*
43282269 ATAGAAGAAG-AG
1 A-AGAAGAAGAAT
*
43282281 GAGAAGAAGAAT
1 AAGAAGAAGAAT
43282293 AAGA
1 AAGA
43282297 GAAAATGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
10 2 0.05
11 27 0.68
12 11 0.28
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.05
Consensus pattern (12 bp):
AAGAAGAAGAAT
Found at i:43292987 original size:16 final size:16
Alignment explanation
Indices: 43292962--43292998 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
43292952 TATGTTCACG
43292962 GTAATGGAATAGAGCT
1 GTAATGGAATAGAGCT
* *
43292978 GTAATTGAATAGAGTT
1 GTAATGGAATAGAGCT
43292994 GTAAT
1 GTAAT
43292999 CAGTAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (16 bp):
GTAATGGAATAGAGCT
Found at i:43293300 original size:22 final size:22
Alignment explanation
Indices: 43293264--43293306 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43293254 AACTAGATAA
* * *
43293264 ATATTATTTATTTTATTAATAC
1 ATATTATTAAATTTAATAATAC
43293286 ATATTATTAAATTTAATAATA
1 ATATTATTAAATTTAATAATA
43293307 AATAATAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTATTAAATTTAATAATAC
Found at i:43296342 original size:84 final size:84
Alignment explanation
Indices: 43296201--43296364 Score: 256
Period size: 84 Copynumber: 2.0 Consensus size: 84
43296191 CAGATGAATG
* * * *
43296201 AAATCCTCCCAACCACAAAAAACACCTCTCTGCAGGTGTTTTCCACATACCATATAGCATGTGAA
1 AAATCCTCCCAACCACAAAAAACACATATCTACAGGTGTTTTCCACATACCAGATAGCATGTGAA
43296266 ATACATATGCCTTGGAACA
66 ATACATATGCCTTGGAACA
* * *
43296285 AAATCCTCCCAACCACATAAAGCACATATCTATAGGTGTTTTCCACATACCAGATAGCATGTGAA
1 AAATCCTCCCAACCACAAAAAACACATATCTACAGGTGTTTTCCACATACCAGATAGCATGTGAA
*
43296350 ATACATCTGCCTTGG
66 ATACATATGCCTTGG
43296365 CACCAGTGTT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (84 bp):
AAATCCTCCCAACCACAAAAAACACATATCTACAGGTGTTTTCCACATACCAGATAGCATGTGAA
ATACATATGCCTTGGAACA
Found at i:43298339 original size:27 final size:27
Alignment explanation
Indices: 43298298--43298353 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
43298288 CTAAAAAAAG
*
43298298 AAATTTCCCATAGTCAAGTTCATACAT
1 AAATTTCCCACAGTCAAGTTCATACAT
43298325 AAATTTCCCACAGTCAAGTTCATACAT
1 AAATTTCCCACAGTCAAGTTCATACAT
43298352 AA
1 AA
43298354 TAAAACATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.30
Consensus pattern (27 bp):
AAATTTCCCACAGTCAAGTTCATACAT
Found at i:43299335 original size:10 final size:10
Alignment explanation
Indices: 43299303--43299345 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
43299293 AATCTAATTA
43299303 TATAATTTATT
1 TATAA-TTATT
*
43299314 TAT-ATGATT
1 TATAATTATT
43299323 TATAATTATT
1 TATAATTATT
*
43299333 TATAATAATT
1 TATAATTATT
43299343 TAT
1 TAT
43299346 TTATATTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 7 0.25
10 18 0.64
11 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
TATAATTATT
Found at i:43299343 original size:20 final size:20
Alignment explanation
Indices: 43299297--43299345 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
43299287 AATTTTAATC
43299297 TAATTATATAATTTATTTATA
1 TAATT-TATAATTTATTTATA
*
43299318 TGATTTATAA-TTATTTATAA
1 TAATTTATAATTTATTTAT-A
43299338 TAATTTAT
1 TAATTTAT
43299346 TTATATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.32
20 13 0.52
21 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TAATTTATAATTTATTTATA
Found at i:43302766 original size:28 final size:28
Alignment explanation
Indices: 43302494--43302779 Score: 263
Period size: 28 Copynumber: 10.2 Consensus size: 28
43302484 CAGCCTGTAT
* * ** *
43302494 GGACTATCTTTCAAGCAAAATTTTGTAG
1 GGACTATCTTTCAAGCAAGAGTCCGCAG
43302522 GGACTATCTTTCATA-CAAGAGTCCGCAG
1 GGACTATCTTTCA-AGCAAGAGTCCGCAG
* * **
43302550 GGACTATCTTTCATGCAAGATTTTGCAG
1 GGACTATCTTTCAAGCAAGAGTCCGCAG
* **
43302578 GGACTATCTTTCAAGCAAGAGCCCATAG
1 GGACTATCTTTCAAGCAAGAGTCCGCAG
* * * *
43302606 AGACTATCTTT-AATGCAAAAGTCCACAT
1 GGACTATCTTTCAA-GCAAGAGTCCGCAG
* ** *
43302634 GGATTATCTTTCAAGCAAGAGTCTACAA
1 GGACTATCTTTCAAGCAAGAGTCCGCAG
** * *
43302662 TAACTATCTTTCATGCAAGAGTCCGCAA
1 GGACTATCTTTCAAGCAAGAGTCCGCAG
* *
43302690 GGACTATCTTTCAAGTAAGAGTTCGCAG
1 GGACTATCTTTCAAGCAAGAGTCCGCAG
*
43302718 GGACTATCTTTCACA-CAAGAGTCCGTAG
1 GGACTATCTTTCA-AGCAAGAGTCCGCAG
*
43302746 GGACTATCTTTCAAGTAAGAGTCCGCAG
1 GGACTATCTTTCAAGCAAGAGTCCGCAG
*
43302774 GAACTA
1 GGACTA
43302780 ATTGTAAGTA
Statistics
Matches: 208, Mismatches: 44, Indels: 12
0.79 0.17 0.05
Matches are distributed among these distances:
27 3 0.01
28 201 0.97
29 4 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (28 bp):
GGACTATCTTTCAAGCAAGAGTCCGCAG
Found at i:43302811 original size:20 final size:20
Alignment explanation
Indices: 43302786--43302828 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
43302776 ACTAATTGTA
43302786 AGTATGAATCCTCATGTATG
1 AGTATGAATCCTCATGTATG
43302806 AGTATGAATCCTCATGTATG
1 AGTATGAATCCTCATGTATG
43302826 AGT
1 AGT
43302829 CCACTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
AGTATGAATCCTCATGTATG
Found at i:43302850 original size:29 final size:29
Alignment explanation
Indices: 43302806--43302982 Score: 264
Period size: 29 Copynumber: 6.1 Consensus size: 29
43302796 CTCATGTATG
* *
43302806 AGTATGAATCCTCATGTATGAGTCCACTA
1 AGTATGAATCCACATGTATGAGTCCACCA
* * *
43302835 ATTATGAATCTACATGTATTAGTCCACCA
1 AGTATGAATCCACATGTATGAGTCCACCA
43302864 AGTATGAATCCACATGTATGAGTCCACCA
1 AGTATGAATCCACATGTATGAGTCCACCA
*
43302893 GGTATGAATCCACATGTATGAGTCCACCA
1 AGTATGAATCCACATGTATGAGTCCACCA
* *
43302922 AGTATGAATCCACATGTATAAGTTCACCA
1 AGTATGAATCCACATGTATGAGTCCACCA
* *
43302951 GGTATGTATCCACATGTATGAGTCCACCA
1 AGTATGAATCCACATGTATGAGTCCACCA
43302980 AGT
1 AGT
43302983 TTTTGTGATA
Statistics
Matches: 131, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 131 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (29 bp):
AGTATGAATCCACATGTATGAGTCCACCA
Found at i:43308215 original size:68 final size:69
Alignment explanation
Indices: 43308116--43308303 Score: 272
Period size: 68 Copynumber: 2.8 Consensus size: 69
43308106 TTTATCTGAC
* * * **
43308116 TCCATAGCCCAACTAAGGTCATACATTTTATGAACCCATGTTTAATGTCCTGGCAAACTCCATAT
1 TCCATAGCCTAACTATGGTCTTACACATTATGAACCCATGTTTAATGTCCTGGCAAACTCCATAT
43308181 GTT-
66 GTTG
* ***
43308184 TCCATAGTCTAACTATGGTCTTACACATTATGAACCCATGTTTAATGTCCTGGTGGACTCCATAT
1 TCCATAGCCTAACTATGGTCTTACACATTATGAACCCATGTTTAATGTCCTGGCAAACTCCATAT
43308249 GTTG
66 GTTG
*
43308253 T-CACAGCCTAACTATGGTCTTACACATTATGAACCCATGTTTAATGTCCTG
1 TCCATAGCCTAACTATGGTCTTACACATTATGAACCCATGTTTAATGTCCTG
43308304 ACGGGCTCCA
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 107 0.99
69 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (69 bp):
TCCATAGCCTAACTATGGTCTTACACATTATGAACCCATGTTTAATGTCCTGGCAAACTCCATAT
GTTG
Found at i:43311537 original size:41 final size:40
Alignment explanation
Indices: 43311472--43311572 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 40
43311462 TGCGCACGTT
* *
43311472 TTAAAATTAAAAAAAGT-AAAAAAGTATTTTAAAAAAAAA
1 TTAAAATTTAAAAAATTAAAAAAAGTATTTTAAAAAAAAA
** **
43311511 TTAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAAGTATT
1 TTAAAATTTAAAAAA-TTAAAAAAAGTATTTTAAAAAAAAA
43311552 TTAAAATTT-AAAAATTAAAAA
1 TTAAAATTTAAAAAATTAAAAA
43311573 TAATAAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
39 21 0.39
40 6 0.11
41 27 0.50
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (40 bp):
TTAAAATTTAAAAAATTAAAAAAAGTATTTTAAAAAAAAA
Found at i:43311546 original size:11 final size:11
Alignment explanation
Indices: 43311532--43311557 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43311522 AAAATTTAAA
43311532 AAAAGTATTTT
1 AAAAGTATTTT
43311543 AAAAGTATTTT
1 AAAAGTATTTT
43311554 AAAA
1 AAAA
43311558 TTTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:43312771 original size:17 final size:18
Alignment explanation
Indices: 43312744--43312777 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
43312734 CCTTCATTTC
43312744 TTTCTTTTATTCTTTTAG
1 TTTCTTTTATTCTTTTAG
43312762 TTTC-TTTATTCTTTTA
1 TTTCTTTTATTCTTTTA
43312778 TGTTAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTCTTTTATTCTTTTAG
Found at i:43317434 original size:24 final size:23
Alignment explanation
Indices: 43317400--43317451 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 23
43317390 CTTATTTCTG
43317400 AAAT-ATTTTTTATTTTATTTTGAGA
1 AAATGATTTTTTA--TTATTTT-AGA
43317425 AAATGATTTTTTATTATTTTAGA
1 AAATGATTTTTTATTATTTTAGA
43317448 AAAT
1 AAAT
43317452 TGAAAAACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.27
24 7 0.27
25 4 0.15
26 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.56
Consensus pattern (23 bp):
AAATGATTTTTTATTATTTTAGA
Found at i:43318878 original size:19 final size:19
Alignment explanation
Indices: 43318851--43318890 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43318841 CCGGGCACAA
*
43318851 AAAATCCAATACCCAAA-AC
1 AAAACCCAA-ACCCAAATAC
43318870 AAAACCCAAACCCAAATAC
1 AAAACCCAAACCCAAATAC
43318889 AA
1 AA
43318891 TCCAAACCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.60, C:0.33, G:0.00, T:0.07
Consensus pattern (19 bp):
AAAACCCAAACCCAAATAC
Found at i:43320167 original size:2 final size:2
Alignment explanation
Indices: 43320160--43320189 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43320150 TCACATAAAC
43320160 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
43320190 TATCCCTATA
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):
AT
Found at i:43322360 original size:6 final size:6
Alignment explanation
Indices: 43322349--43322374 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43322339 ACTTGGATTT
43322349 TGAAAA TGAAAA TGAAAA TGAAAA TG
1 TGAAAA TGAAAA TGAAAA TGAAAA TG
43322375 GGAGTCGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAAAA
Found at i:43322833 original size:113 final size:108
Alignment explanation
Indices: 43322662--43322877 Score: 324
Period size: 113 Copynumber: 2.0 Consensus size: 108
43322652 AGATTTAGGA
*
43322662 GGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTTCTCGAA
1 GGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTTCTCGAA
* *
43322727 TTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAAG
66 TTTCCAAACGCAAAACATTACCTTATTTTAAAATTTTTTAAAG
* *
43322770 GGATATTTGGCTATTTAGTTGAACGAGAAAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTC
1 GGATATTTGGCTATTTAGTCGAACGAG-----AAATCGAAACCCAACACATTAGGGCACGTTTTC
* *
43322835 TCGAATTTCCAAACGTAAAATATTACCTTATTTTAAAATTTTT
61 TCGAATTTCCAAACGCAAAACATTACCTTATTTTAAAATTTTT
43322878 AAGAGGATAT
Statistics
Matches: 96, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
108 25 0.26
113 71 0.74
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (108 bp):
GGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTTCTCGAA
TTTCCAAACGCAAAACATTACCTTATTTTAAAATTTTTTAAAG
Found at i:43325447 original size:45 final size:44
Alignment explanation
Indices: 43325388--43325501 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 44
43325378 TTGACCCGTT
*
43325388 CCACTGCAACTTTAGGGAGATATGACTTAT-ATCTTCAAACTTGCC
1 CCACTGCAACTTTAGGGAGATAAGACTTATGAT-TTC-AACTTGCC
* * *
43325433 CCACTGCAACTTTAGGGGGAATAAGGCTTATGATTTCAACTTGCT
1 CCACTGCAACTTTAGGGAG-ATAAGACTTATGATTTCAACTTGCC
* * *
43325478 CTACTGCAACTTCAGAGAGATAAG
1 CCACTGCAACTTTAGGGAGATAAG
43325502 GTTTGATATG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
44 5 0.08
45 40 0.68
46 12 0.20
47 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (44 bp):
CCACTGCAACTTTAGGGAGATAAGACTTATGATTTCAACTTGCC
Found at i:43325787 original size:89 final size:89
Alignment explanation
Indices: 43325628--43325948 Score: 399
Period size: 89 Copynumber: 3.6 Consensus size: 89
43325618 CTGTCAACTA
* * * * *
43325628 TGGTGTCTTCGATCTGCTTCGCTGTTAATACGGGAAGGCGAGATCTGTTATCTTTAGTCTGCTCC
1 TGGTGTTTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTTAGTCTGCTCC
* *
43325693 ACTGCAAACTCAAGGAGGCGAGGC
66 GCTGCAAACTCAGGGAGGCGAGGC
* * * * *
43325717 TGGTGTTTTCGATCTGCTTTGTTGTCAGTTCAGGAAGGCAAGATCTGTTATCTTTAGTCTACTCT
1 TGGTGTTTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTTAGTCTGCTCC
*
43325782 GCTGCAAACTCAGGGAGACGAGGC
66 GCTGCAAACTCAGGGAGGCGAGGC
* ** * * * *
43325806 TGGTCTTTTCGATCTGCTTCATTGTCAGTACAAGAAGGCAAGATCTGTTATATTCAGTCTGTTCC
1 TGGTGTTTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTTAGTCTGCTCC
* *
43325871 GCTGTAAACACAGGGAGGCGAGGC
66 GCTGCAAACTCAGGGAGGCGAGGC
* * ** *
43325895 TGGTGTTTTCGATTTGTTTCGCTGTCAGTACAGGAAAACAAGATCTGCTATCTT
1 TGGTGTTTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTT
43325949 CACTAATCTG
Statistics
Matches: 196, Mismatches: 36, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
89 196 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (89 bp):
TGGTGTTTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTTAGTCTGCTCC
GCTGCAAACTCAGGGAGGCGAGGC
Found at i:43327459 original size:3 final size:3
Alignment explanation
Indices: 43327451--43327475 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43327441 TAGGGCGAAC
43327451 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
43327476 TTTGTGAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:43329558 original size:24 final size:25
Alignment explanation
Indices: 43329531--43329583 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
43329521 GGTTCTTTCG
*
43329531 TGAAATTTAATGCAAATG-ATGCAA
1 TGAAATGTAATGCAAATGCATGCAA
* *
43329555 TGAAATGTAATGCAGATGCATGGAA
1 TGAAATGTAATGCAAATGCATGCAA
43329580 TGAA
1 TGAA
43329584 TGCAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.26
Consensus pattern (25 bp):
TGAAATGTAATGCAAATGCATGCAA
Found at i:43331179 original size:112 final size:108
Alignment explanation
Indices: 43331006--43331220 Score: 340
Period size: 112 Copynumber: 2.0 Consensus size: 108
43330996 AGATTTAGGA
43331006 GGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAA
1 GGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAA
*** *
43331071 TTTCCAAACGCAAAACATTGTTTTATTTTGAACTTTTTTAAAG
66 TTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTTAAAG
* *
43331114 GGATATTTTGCTATTTGGTCGAACGAGAAAAAAATCGAAACCCAGCACATTAGGGCATGTTTTCT
1 GGATATTTGGCTATTTGGTCGAACGAG----AAATCGAAACCCAGCACATTAGGGCACGTTTTCT
43331179 CAAATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTT
62 CAAATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTT
43331221 AAGAGGATAT
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
108 26 0.27
112 71 0.73
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (108 bp):
GGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAAA
TTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTTAAAG
Found at i:43337653 original size:30 final size:29
Alignment explanation
Indices: 43337615--43337675 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
43337605 ACTTATCCAC
43337615 TTTTTCTT-AATTGATACTTAAAGTTTTTT
1 TTTTTCTTAAATTGATACTTAAA-TTTTTT
* *
43337644 TTTTATCTTAAATTGATATTTGAATTTTTT
1 TTTT-TCTTAAATTGATACTTAAATTTTTT
43337674 TT
1 TT
43337676 CCATCAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 4 0.14
30 12 0.43
31 12 0.43
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (29 bp):
TTTTTCTTAAATTGATACTTAAATTTTTT
Found at i:43347747 original size:24 final size:25
Alignment explanation
Indices: 43347694--43347748 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
43347684 AAAATGGCTT
43347694 AATTTTGTTTATGTTAGATTGATTG
1 AATTTTGTTTATGTTAGATTGATTG
*
43347719 CATTTT-TTTA-GCTTAGATT-ATTAG
1 AATTTTGTTTATG-TTAGATTGATT-G
43347743 AATTTT
1 AATTTT
43347749 ATTAATGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 4 0.15
24 17 0.65
25 5 0.19
ACGTcount: A:0.25, C:0.04, G:0.15, T:0.56
Consensus pattern (25 bp):
AATTTTGTTTATGTTAGATTGATTG
Found at i:43357556 original size:7 final size:7
Alignment explanation
Indices: 43357544--43357577 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
43357534 AGTAATATAA
43357544 TTAATAT
1 TTAATAT
43357551 TTAATAT
1 TTAATAT
43357558 TTAATAT
1 TTAATAT
43357565 TTAATAT
1 TTAATAT
43357572 TTAATA
1 TTAATA
43357578 AACTTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAATAT
Found at i:43357656 original size:26 final size:23
Alignment explanation
Indices: 43357625--43357678 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 23
43357615 AGGTAGATCT
*
43357625 AAATTTTGAAAATAAATAAATAAATA
1 AAATTTTAAAAAT-AA-AAATAAA-A
43357651 AAATTTTAAAAATAAAAATAAAA
1 AAATTTTAAAAATAAAAATAAAA
43357674 AAATT
1 AAATT
43357679 ACAAAAAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 7 0.26
25 2 0.07
26 12 0.44
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATTTTAAAAATAAAAATAAAA
Found at i:43361221 original size:146 final size:146
Alignment explanation
Indices: 43360957--43361251 Score: 581
Period size: 146 Copynumber: 2.0 Consensus size: 146
43360947 TTACATGTTC
43360957 AGATGCCAATAAGTATGTATTCTGGGACGCCTTCCACCCGACAGAGAAAACAAATGCCATTTTGG
1 AGATGCCAATAAGTATGTATTCTGGGACGCCTTCCACCCGACAGAGAAAACAAATGCCATTTTGG
43361022 CTGATTATGTGGTCAAAACTACCCTAGCCGAGTTCCAATAATTACTAAAAGTAAAAGAAAGCAGC
66 CTGATTATGTGGTCAAAACTACCCTAGCCGAGTTCCAATAATTACTAAAAGTAAAAGAAAGCAGC
43361087 ACTGCTTCATTGTTGT
131 ACTGCTTCATTGTTGT
*
43361103 AGATGCCAATAAGTATGTATTCTGGGATGCCTTCCACCCGACAGAGAAAACAAATGCCATTTTGG
1 AGATGCCAATAAGTATGTATTCTGGGACGCCTTCCACCCGACAGAGAAAACAAATGCCATTTTGG
43361168 CTGATTATGTGGTCAAAACTACCCTAGCCGAGTTCCAATAATTACTAAAAGTAAAAGAAAGCAGC
66 CTGATTATGTGGTCAAAACTACCCTAGCCGAGTTCCAATAATTACTAAAAGTAAAAGAAAGCAGC
43361233 ACTGCTTCATTGTTGT
131 ACTGCTTCATTGTTGT
43361249 AGA
1 AGA
43361252 ACTAGTATTA
Statistics
Matches: 148, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 148 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (146 bp):
AGATGCCAATAAGTATGTATTCTGGGACGCCTTCCACCCGACAGAGAAAACAAATGCCATTTTGG
CTGATTATGTGGTCAAAACTACCCTAGCCGAGTTCCAATAATTACTAAAAGTAAAAGAAAGCAGC
ACTGCTTCATTGTTGT
Found at i:43362987 original size:3 final size:3
Alignment explanation
Indices: 43362979--43363004 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43362969 CACTTAACAA
43362979 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
43363005 CAAATTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43365475 original size:20 final size:20
Alignment explanation
Indices: 43365450--43365515 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
43365440 ACTATTAACC
* *
43365450 ATAAAAATAGATTAAGAACA
1 ATAAAAATAAATAAAGAACA
*
43365470 ATAAAAATAAATAAACAACA
1 ATAAAAATAAATAAAGAACA
* *
43365490 AAAATAAATAAATAAAGAAAA
1 ATAA-AAATAAATAAAGAACA
43365511 ATAAA
1 ATAAA
43365516 CAAATTAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.17
Consensus pattern (20 bp):
ATAAAAATAAATAAAGAACA
Found at i:43365492 original size:17 final size:17
Alignment explanation
Indices: 43365466--43365515 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
43365456 ATAGATTAAG
*
43365466 AACAATAAAAATAAATA
1 AACAACAAAAATAAATA
43365483 AACAACAAAAATAAATA
1 AACAACAAAAATAAATA
* *
43365500 AATAAAGAAAAATAAA
1 AA-CAACAAAAATAAA
43365516 CAAATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 18 0.62
18 11 0.38
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (17 bp):
AACAACAAAAATAAATA
Found at i:43365510 original size:18 final size:18
Alignment explanation
Indices: 43365472--43365520 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
43365462 TAAGAACAAT
*
43365472 AAAAATAAATAAA-CAAC
1 AAAAATAAATAAATAAAC
*
43365489 AAAAATAAATAAATAAAG
1 AAAAATAAATAAATAAAC
*
43365507 AAAAATAAACAAAT
1 AAAAATAAATAAAT
43365521 TAATTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (18 bp):
AAAAATAAATAAATAAAC
Found at i:43376231 original size:48 final size:48
Alignment explanation
Indices: 43376174--43376267 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 48
43376164 ATTTTTTTTA
* *
43376174 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATATG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATCTTATATG
43376222 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATCTTATA
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATCTTATA
43376268 AATTATTGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.52
Consensus pattern (48 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATCTTATATG
Found at i:43386300 original size:16 final size:16
Alignment explanation
Indices: 43386279--43386309 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43386269 TAATATTAAC
*
43386279 GTATATCTAATTAATA
1 GTATATATAATTAATA
43386295 GTATATATAATTAAT
1 GTATATATAATTAAT
43386310 TTTTTATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (16 bp):
GTATATATAATTAATA
Found at i:43394201 original size:21 final size:20
Alignment explanation
Indices: 43394164--43394222 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
43394154 TTAACTTTAC
*
43394164 AAGTC-AAAAAAATATAAAA
1 AAGTCTAAAAATATATAAAA
43394183 AAGTCTAAAGAATATATAAAA
1 AAGTCTAAA-AATATATAAAA
* *
43394204 AATTTTAAAAATATA-AAAA
1 AAGTCTAAAAATATATAAAA
43394223 CCCCTAAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.26
20 9 0.26
21 17 0.49
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (20 bp):
AAGTCTAAAAATATATAAAA
Found at i:43395934 original size:22 final size:22
Alignment explanation
Indices: 43395904--43396005 Score: 132
Period size: 22 Copynumber: 4.6 Consensus size: 22
43395894 TTGTGTTTGA
*
43395904 AAGCTCTCATGTTTAACGAACT
1 AAGCTCTCATGTTTAACGTACT
* * **
43395926 AAACCCTCATGGCTAACGTACT
1 AAGCTCTCATGTTTAACGTACT
**
43395948 AAGCTCTCATGGCTAACGTACT
1 AAGCTCTCATGTTTAACGTACT
*
43395970 AAGCTCTCATGTTTCACGTACT
1 AAGCTCTCATGTTTAACGTACT
43395992 AAGCTCTCATGTTT
1 AAGCTCTCATGTTT
43396006 GAACAATAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (22 bp):
AAGCTCTCATGTTTAACGTACT
Found at i:43403579 original size:17 final size:17
Alignment explanation
Indices: 43403529--43403580 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 17
43403519 TTATCTATTC
43403529 AGTTTTT-ATTCAATTT
1 AGTTTTTCATTCAATTT
*
43403545 AGCTTTTCATT--A---
1 AGTTTTTCATTCAATTT
43403557 AGTTTTTCATTCAATTT
1 AGTTTTTCATTCAATTT
43403574 AGTTTTT
1 AGTTTTT
43403581 GTTTTATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
12 10 0.36
14 1 0.04
15 1 0.04
16 6 0.21
17 10 0.36
ACGTcount: A:0.23, C:0.10, G:0.08, T:0.60
Consensus pattern (17 bp):
AGTTTTTCATTCAATTT
Found at i:43406318 original size:32 final size:33
Alignment explanation
Indices: 43406161--43406320 Score: 121
Period size: 37 Copynumber: 4.7 Consensus size: 33
43406151 TTTTAATAGT
*
43406161 TTAATATTAAATTAATTTAATACTTATCTTA-A
1 TTAATATTAAATTAATTTAATATTTATCTTAGA
* * * **
43406193 -TAATATTTAA-TAATTTAATATTAAAGTGATTATC
1 TTAATATTAAATTAATTTAATATT-TA-T-CTTAGA
* *
43406227 TTAATATTAAATTTAATTTAATGTTTATCTACAAGA
1 TTAATATTAAA-TTAATTTAATATTTATCT--TAGA
*
43406263 TTTAATATTAAATTTAATCTAATATTTATCTTA-A
1 -TTAATATTAAA-TTAATTTAATATTTATCTTAGA
* *
43406297 TAAATATTATATTAATTTAATATT
1 TTAATATTAAATTAATTTAATATT
43406321 AAAGTGGTTA
Statistics
Matches: 100, Mismatches: 18, Indels: 20
0.72 0.13 0.14
Matches are distributed among these distances:
30 11 0.11
31 10 0.10
32 13 0.13
33 12 0.12
34 2 0.02
35 11 0.11
36 2 0.02
37 39 0.39
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (33 bp):
TTAATATTAAATTAATTTAATATTTATCTTAGA
Found at i:43406996 original size:30 final size:30
Alignment explanation
Indices: 43406941--43406998 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
43406931 TTGGGCTTTC
*
43406941 CCACACGGGCTGGACATAAGACCATGTGAG
1 CCACACGGGCTGGACACAAGACCATGTGAG
43406971 CCACACGGGCTGGACACACAG-CCATGTG
1 CCACACGGGCTGGACACA-AGACCATGTG
43406999 CCAGACTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.28, C:0.31, G:0.29, T:0.12
Consensus pattern (30 bp):
CCACACGGGCTGGACACAAGACCATGTGAG
Found at i:43409572 original size:43 final size:43
Alignment explanation
Indices: 43409524--43409832 Score: 385
Period size: 43 Copynumber: 7.3 Consensus size: 43
43409514 TTTTAGAAAT
*
43409524 AAACGCCGCTATAGATCATGACCTTTAACGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
* *
43409567 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTT-ACAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
43409609 AAACGTCGCTATAGATCAGGACCTTTAGCAGCGCTTTT-ACAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
* * **
43409651 AAACGCCGCTATAGATTA-GAACCTTTAGCGGC-TTTTTTACAC
1 AAACGCCGCTATAGATCATG-ACCTTTAGCGGCGCTTTTCCCAC
* *
43409693 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATCCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
43409736 AAACGCCACTATAGATCATGACTTTTAGTGGCG-TTTTCCCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTT-CCCAC
** * *
43409779 AAACATCGCTATAGATCATGACTTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
43409822 AAACGCCGCTA
1 AAACGCCGCTA
43409833 AAAACATATC
Statistics
Matches: 236, Mismatches: 24, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
41 5 0.02
42 106 0.45
43 121 0.51
44 4 0.02
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:43409689 original size:84 final size:84
Alignment explanation
Indices: 43409524--43409832 Score: 395
Period size: 84 Copynumber: 3.6 Consensus size: 84
43409514 TTTTAGAAAT
*
43409524 AAACGCCGCTATAGATCATGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCA-GAC
**
43409589 CTTTAGCGGCGCTTTTACAC
65 CTTTAGCGGCTTTTTTACAC
* * * * *
43409609 AAACGTCGCTATAGATCAGGACCTTTAGCAGCGCTTTT-ACACAAACGCCGCTATAGATTAGAAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAG-AC
43409673 CTTTAGCGGCTTTTTTACAC
65 CTTTAGCGGCTTTTTTACAC
* * *
43409693 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATCCCACAAACGCCACTATAGATCATGAC
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCA-GAC
* * ***
43409758 TTTTAGTGGCGTTTTCCCCAC
65 CTTTAGCGGC-TTTTTTACAC
** * *
43409779 AAACATCGCTATAGATCATGACTTTTAGTGGCGCTTTTCCCACAAACGCCGCTA
1 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
43409833 AAAACATATC
Statistics
Matches: 193, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
83 1 0.01
84 74 0.38
85 63 0.33
86 55 0.28
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (84 bp):
AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGACC
TTTAGCGGCTTTTTTACAC
Found at i:43411942 original size:122 final size:122
Alignment explanation
Indices: 43411718--43411961 Score: 373
Period size: 122 Copynumber: 2.0 Consensus size: 122
43411708 ATGCATGCTA
* * * **
43411718 TATGAGGTGCCACTTGATACTGTCATAATTTCTGAGCTTAGATTCCCAGTTTTCTAGTCAATGTT
1 TATGAGGTGCCACTTGATACTGTCACAATTTCTGAGCTTAAATTCCCAGTTTTCAAGTCAATACT
* *
43411783 GAATGCAGAAAGGTTCAAAGTGTATACAACATTGAATCCTAATGTTGCATGTCAGGG
66 GAATGCAGAAAGGTTCAAAGTGTATACAAAATAGAATCCTAATGTTGCATGTCAGGG
*
43411840 TATGAGGTGCCACTTGATCCAT-TCACAATTTCTGAGCTTAAATTCCCAGTTTTCAAGTCAATAC
1 TATGAGGTGCCACTTGATAC-TGTCACAATTTCTGAGCTTAAATTCCCAGTTTTCAAGTCAATAC
* * *
43411904 TGAATGTAGAAAGGTTCAAAGTGTATATAAAATAGAATCCTAATGTTGTATGTCAGGG
65 TGAATGCAGAAAGGTTCAAAGTGTATACAAAATAGAATCCTAATGTTGCATGTCAGGG
43411962 AAAGCAGTTG
Statistics
Matches: 110, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
122 109 0.99
123 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (122 bp):
TATGAGGTGCCACTTGATACTGTCACAATTTCTGAGCTTAAATTCCCAGTTTTCAAGTCAATACT
GAATGCAGAAAGGTTCAAAGTGTATACAAAATAGAATCCTAATGTTGCATGTCAGGG
Found at i:43413097 original size:253 final size:253
Alignment explanation
Indices: 43412649--43413199 Score: 881
Period size: 253 Copynumber: 2.2 Consensus size: 253
43412639 AAAGAACCTG
* * *
43412649 ATTTATGTTAAAAACGACGTCGTTTTCTATTTTAACATTTGCGGCGCTTACAAAAAAATGCCACT
1 ATTTATGTTAAAAACGGCGTCGTTTTCTATTTTAACATTTGCGGCACTTACAAAAAAACGCCACT
*
43412714 AGTTTCACAACTTTTACGGCGTTTTGATAAAAAACGCCACTAACATTTAACTCGTCAACGAAGCG
66 AGTTTCACAACTTTTACGGCGTTTTGATAAAAAACGCCACTAACATTTAACTCATCAACGAAGCG
*
43412779 GTGCCGTTTTGTTTAATTTTTAATATGTTATTTGCGGCGTTTTAAGAACAAACACCGCTAGTATT
131 GTGCCATTTTGTTTAATTTTTAATATGTTATTTGCGGCGTTTTAAGAACAAACACCGCTAGTATT
*
43412844 TAGATTTTGTGGCGTTTTACATCG-AATCGCTGCTACTGATTAACTTTCTATTAATATT
196 TAGATTTTGTGGCGTTTTACATCGAAAT-GCCGCTACTGATTAACTTTCTATTAATATT
* * * * *
43412902 ATTTATGCTAAAAACGGCATTGTTTTCTATTTCAACATTTGCGGCACTTACGAAAAAACGCCACT
1 ATTTATGTTAAAAACGGCGTCGTTTTCTATTTTAACATTTGCGGCACTTACAAAAAAACGCCACT
* * *
43412967 AGTTTCACAACTTTTGCGGCGTTTTGATAAGAAACGCCACTAACATTTAACTCATCAATGAAGCG
66 AGTTTCACAACTTTTACGGCGTTTTGATAAAAAACGCCACTAACATTTAACTCATCAACGAAGCG
* * *
43413032 GTGCCATTTTGTTTAATTTTTAATATGTTTTTTTCGGCGTTTTCTA-AACAAACACCGCTAGTAT
131 GTGCCATTTTGTTTAATTTTTAATATGTTATTTGCGGCGTTTT-AAGAACAAACACCGCTAGTAT
* *
43413096 TTAGATTTTGTGGCGTTTTACATGGAAATGCCGCTACTGATTAACTTTTTATTAATATT
195 TTAGATTTTGTGGCGTTTTACATCGAAATGCCGCTACTGATTAACTTTCTATTAATATT
* *
43413155 ATTTATGTTTAAAACGGCGTCATTTTCTATTTTAACATTTGCGGC
1 ATTTATGTTAAAAACGGCGTCGTTTTCTATTTTAACATTTGCGGC
43413200 GTTTTGACAA
Statistics
Matches: 271, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
253 267 0.99
254 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (253 bp):
ATTTATGTTAAAAACGGCGTCGTTTTCTATTTTAACATTTGCGGCACTTACAAAAAAACGCCACT
AGTTTCACAACTTTTACGGCGTTTTGATAAAAAACGCCACTAACATTTAACTCATCAACGAAGCG
GTGCCATTTTGTTTAATTTTTAATATGTTATTTGCGGCGTTTTAAGAACAAACACCGCTAGTATT
TAGATTTTGTGGCGTTTTACATCGAAATGCCGCTACTGATTAACTTTCTATTAATATT
Found at i:43413258 original size:213 final size:214
Alignment explanation
Indices: 43412979--43413374 Score: 650
Period size: 213 Copynumber: 1.9 Consensus size: 214
43412969 TTTCACAACT
* * *
43412979 TTTGCGGCGTTTTGATAAGAAACGCCACTAACATTTAACTCATCAATGAAGCGGTGCCATTTTGT
1 TTTGCGGCGTTTTGACAAAAAACACCACTAACATTTAACTCATCAATGAAGCGGTGCCATTTTGT
* *
43413044 TTAATTTTTAATATGTTTTTTTCGGCGTTTTCTAAACAAACACCGCTAGTATTTAGATTTTGTGG
66 TTAATTTTTAATATGTTTTTTGCGGCGTTTTCTAAACAAACACCGCTAATATTTAGATTTTGTGG
* *
43413109 CG-TTTTACATGGAAATGCCGCTACTGATTAACTTTTTATTAATATTATTTATGTTTAAAACGGC
131 CGTTTTTACATGGAAACGCCGCTACTAATTAACTTTTTATTAATATTATTTATGTTTAAAACGGC
43413173 GTCATTTTCTATTTTAACA
196 GTCATTTTCTATTTTAACA
* * *
43413192 TTTGCGGCGTTTTGACAAAAAACACCACTAATATTTAACTCGTCAATGAAGCGGTGCCGTTTTGT
1 TTTGCGGCGTTTTGACAAAAAACACCACTAACATTTAACTCATCAATGAAGCGGTGCCATTTTGT
* * * *
43413257 TTAATTTTTTATATGTTTTTTGCGGCGTTTTCTGAACAAACGCTGCTAATATTTAGATTTTGTGG
66 TTAATTTTTAATATGTTTTTTGCGGCGTTTTCTAAACAAACACCGCTAATATTTAGATTTTGTGG
*
43413322 CGTTTTTACATGGAAACGTCGCTACTAATTAACTTTTTATTAATATTATTTAT
131 CGTTTTTACATGGAAACGCCGCTACTAATTAACTTTTTATTAATATTATTTAT
43413375 AAATTTTCAA
Statistics
Matches: 167, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
213 120 0.72
214 47 0.28
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (214 bp):
TTTGCGGCGTTTTGACAAAAAACACCACTAACATTTAACTCATCAATGAAGCGGTGCCATTTTGT
TTAATTTTTAATATGTTTTTTGCGGCGTTTTCTAAACAAACACCGCTAATATTTAGATTTTGTGG
CGTTTTTACATGGAAACGCCGCTACTAATTAACTTTTTATTAATATTATTTATGTTTAAAACGGC
GTCATTTTCTATTTTAACA
Found at i:43413487 original size:13 final size:13
Alignment explanation
Indices: 43413454--43413484 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
43413444 TTAAAATGAC
43413454 ATTATTAATATAT
1 ATTATTAATATAT
43413467 ATTATTAATAT-T
1 ATTATTAATATAT
43413479 ATTATT
1 ATTATT
43413485 TAAAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTATTAATATAT
Found at i:43413924 original size:21 final size:21
Alignment explanation
Indices: 43413886--43413925 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43413876 ACCATGCATT
* **
43413886 GTAAACCTTAAATTATAAATA
1 GTAAACCGTAAACCATAAATA
43413907 GTAAACCGTAAACCATAAA
1 GTAAACCGTAAACCATAAA
43413926 CATCAAGCCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (21 bp):
GTAAACCGTAAACCATAAATA
Found at i:43414026 original size:14 final size:14
Alignment explanation
Indices: 43414007--43414038 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
43413997 CCTAAATCCC
43414007 ACCCCAAATCTTAA
1 ACCCCAAATCTTAA
43414021 ACCCCAAATCTTAA
1 ACCCCAAATCTTAA
43414035 ACCC
1 ACCC
43414039 TAAACCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.19
Consensus pattern (14 bp):
ACCCCAAATCTTAA
Found at i:43414213 original size:161 final size:158
Alignment explanation
Indices: 43414033--43414334 Score: 534
Period size: 161 Copynumber: 1.9 Consensus size: 158
43414023 CCCAAATCTT
43414033 AAACCCTAAACCAAAAACACTAAACCTACATCATAAACCTTAAACTCAAAACTCTAATCCCAAAA
1 AAACCCTAAACCAAAAACACTAAACCTACATCATAAACCTTAAACTCAAAACTCTAATCCCAAAA
*
43414098 TAATAAACATTATATAATGATTAACCCTAAAACCTTAAACCATATACGATAAACTTTAAATTATA
66 TAATAAACATTATATAATG---AACCCTAAAACCCTAAACCATATACGATAAACTTTAAATTATA
43414163 ATAATCA-CTAAACCTTAATCACCAAACTCCC
128 ATAA-CACCTAAACCTTAATCACCAAACTCCC
*
43414194 AAACCCTAAACCCAAAACACTAAACCTACATCATAAACCTTAAACTCAAAACTCTAATCCCAAAA
1 AAACCCTAAACCAAAAACACTAAACCTACATCATAAACCTTAAACTCAAAACTCTAATCCCAAAA
*
43414259 TAATAAACATTATATAATGAACCCTAAAACCCTAAACCATATATGATAAACTTTAAATTATAATA
66 TAATAAACATTATATAATGAACCCTAAAACCCTAAACCATATACGATAAACTTTAAATTATAATA
43414324 ACACCTAAACC
131 ACACCTAAACC
43414335 CTAAAATTAT
Statistics
Matches: 137, Mismatches: 3, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
157 2 0.01
158 52 0.38
161 83 0.61
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.24
Consensus pattern (158 bp):
AAACCCTAAACCAAAAACACTAAACCTACATCATAAACCTTAAACTCAAAACTCTAATCCCAAAA
TAATAAACATTATATAATGAACCCTAAAACCCTAAACCATATACGATAAACTTTAAATTATAATA
ACACCTAAACCTTAATCACCAAACTCCC
Found at i:43414522 original size:41 final size:41
Alignment explanation
Indices: 43414455--43414650 Score: 288
Period size: 41 Copynumber: 4.8 Consensus size: 41
43414445 ACAACTTTTT
* *
43414455 GCGGTGCTTTCTCAAAAACTCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
43414496 GCGGCGCTTACTCAAAAACGCCGCTAAATCCCTGAGCATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
43414537 GCAGCGCTTACTCAAAAACGCCGCTAAAGCCCTGAGAATTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
43414578 GCGGCGCTTTC-CTAAAAACGCCGCTAAAGCCCTGAGTATTA
1 GCGGCGCTTTCTC-AAAAACGCCGCTAAAGCCCTGAGCATTA
43414619 GCGGCGCTTTC-CTAAAAACGCCGCTAAAGCCC
1 GCGGCGCTTTCTC-AAAAACGCCGCTAAAGCCC
43414651 CGAAAGCTCA
Statistics
Matches: 144, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 1 0.01
41 143 0.99
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:43416605 original size:2 final size:2
Alignment explanation
Indices: 43416593--43416629 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
43416583 CCAGATGAGG
*
43416593 TC TC TC GC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
43416630 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
TC
Found at i:43417534 original size:20 final size:20
Alignment explanation
Indices: 43417509--43417548 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43417499 CGTAAAATAA
*
43417509 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
43417529 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
43417549 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:43417538 original size:34 final size:34
Alignment explanation
Indices: 43417495--43417560 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
43417485 AGTAAAATGT
*
43417495 TTTTCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCGTAAAATAATTTACTGGAAAATATTTTAC
*
43417528 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATAATTTACTGGAAAATATTTT
43417561 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 11 0.38
35 13 0.45
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (34 bp):
TTTTCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:43420149 original size:6 final size:6
Alignment explanation
Indices: 43420132--43420180 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
43420122 ATGTGAGGTA
* * * * *
43420132 AGTATT AATATT AGTATT AGTAAT AGTATT ATTATT ATTATT ATTATT
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT
43420180 A
1 A
43420181 AGATGAGTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (6 bp):
AGTATT
Found at i:43420149 original size:12 final size:12
Alignment explanation
Indices: 43420132--43420180 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
43420122 ATGTGAGGTA
*
43420132 AGTATTAATATT
1 AGTATTATTATT
* *
43420144 AGTATTAGTAAT
1 AGTATTATTATT
43420156 AGTATTATTATT
1 AGTATTATTATT
*
43420168 ATTATTATTATT
1 AGTATTATTATT
43420180 A
1 A
43420181 AGATGAGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (12 bp):
AGTATTATTATT
Found at i:43420368 original size:24 final size:27
Alignment explanation
Indices: 43420331--43420394 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
43420321 AATTGCGGAT
*
43420331 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
43420355 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
43420381 TTGTGATTGAATTG
1 TAATGATTGAATTG
43420395 GGATTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:43421715 original size:17 final size:17
Alignment explanation
Indices: 43421693--43421727 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
43421683 TATTGCTAAA
43421693 TAGCATAGTTGTCAAGT
1 TAGCATAGTTGTCAAGT
43421710 TAGCATAGTTGTCAAGT
1 TAGCATAGTTGTCAAGT
43421727 T
1 T
43421728 TTCTGAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (17 bp):
TAGCATAGTTGTCAAGT
Found at i:43423356 original size:21 final size:21
Alignment explanation
Indices: 43423327--43423367 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43423317 ACGGAAATTG
*
43423327 AAAAGGTAAGACATTTTCCCT
1 AAAAGGTAAGACAATTTCCCT
* *
43423348 AAAATGTAAGCCAATTTCCC
1 AAAAGGTAAGACAATTTCCC
43423368 GTGCTTTGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (21 bp):
AAAAGGTAAGACAATTTCCCT
Found at i:43429322 original size:31 final size:29
Alignment explanation
Indices: 43429258--43429326 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
43429248 ACGATAACGT
* *
43429258 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
43429287 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
43429318 AAGTGACTA
1 AAGTGACTA
43429327 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:43432754 original size:26 final size:26
Alignment explanation
Indices: 43432713--43432789 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 26
43432703 CCTCATCCCT
* * *
43432713 ATTTTATCCCCAGTAAAATTTTGACG
1 ATTTTAACCCTAGTAAAATTTTGACA
* * **
43432739 ATTTTACCCCTGGTAATTTTTTTGACA
1 ATTTTAACCCTAGTAA-AATTTTGACA
43432766 ATTTTAACCCTAGTAAAATTTTGA
1 ATTTTAACCCTAGTAAAATTTTGA
43432790 GAAAATAAGT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 19 0.47
27 21 0.52
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (26 bp):
ATTTTAACCCTAGTAAAATTTTGACA
Found at i:43435943 original size:2 final size:2
Alignment explanation
Indices: 43435936--43435963 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43435926 ATCAAGCCAT
43435936 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
43435964 GATCATTCAA
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):
TA
Found at i:43440469 original size:22 final size:22
Alignment explanation
Indices: 43440421--43440484 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
43440411 TTTTGAGCAA
* *
43440421 TTTAATTCTTTTCTTTTATGTTCT
1 TTTAATT-TTCTCTTTT-TTTTCT
43440445 TTTAATTTTCTCTTTTTTTTCT
1 TTTAATTTTCTCTTTTTTTTCT
*
43440467 TTTAATTTTC-ATTTTTTT
1 TTTAATTTTCTCTTTTTTT
43440485 CTACTTCTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.19
22 15 0.41
23 8 0.22
24 7 0.19
ACGTcount: A:0.12, C:0.11, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTAATTTTCTCTTTTTTTTCT
Found at i:43440475 original size:11 final size:10
Alignment explanation
Indices: 43440429--43440486 Score: 55
Period size: 11 Copynumber: 5.6 Consensus size: 10
43440419 AATTTAATTC
43440429 TTTTCTTTTA
1 TTTTCTTTTA
*
43440439 TGTTCTTTTAA
1 TTTTCTTTT-A
*
43440450 TTTTCTCTTTT
1 TTTTCT-TTTA
43440461 TTTTCTTTTAA
1 TTTTCTTTT-A
*
43440472 TTTTCATTT-
1 TTTTCTTTTA
43440481 TTTTCT
1 TTTTCT
43440487 ACTTCTCCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
9 5 0.13
10 11 0.28
11 20 0.51
12 3 0.08
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:43441711 original size:31 final size:30
Alignment explanation
Indices: 43441644--43441712 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
43441634 ACGATATCGT
**
43441644 AAGTGACTAAAATGTAACATTTTAAACATA
1 AAGTGACTAAAATGTAACATGATAAACATA
*
43441674 AA-TGACTAAAATGTAACCTGAGATAAACA-A
1 AAGTGACTAAAATGTAACAT--GATAAACATA
43441704 AAGTGACTA
1 AAGTGACTA
43441713 TTTTAGTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 16 0.48
30 5 0.15
31 12 0.36
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.25
Consensus pattern (30 bp):
AAGTGACTAAAATGTAACATGATAAACATA
Found at i:43441857 original size:16 final size:16
Alignment explanation
Indices: 43441836--43441868 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
43441826 AATTAGGATT
43441836 TAAATAAAAAATCTTA
1 TAAATAAAAAATCTTA
*
43441852 TAAATAAAAAATTTTA
1 TAAATAAAAAATCTTA
43441868 T
1 T
43441869 TTACAGCAAA
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:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATAAAAAATCTTA
Found at i:43442759 original size:21 final size:22
Alignment explanation
Indices: 43442735--43442775 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
43442725 TGTTTAGTAT
*
43442735 ATTACCATTCT-GGTTTCTTTG
1 ATTAACATTCTGGGTTTCTTTG
*
43442756 ATTAACATTTTGGGTTTCTT
1 ATTAACATTCTGGGTTTCTT
43442776 GGCAGGTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.54
Consensus pattern (22 bp):
ATTAACATTCTGGGTTTCTTTG
Found at i:43462175 original size:16 final size:16
Alignment explanation
Indices: 43462154--43462184 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
43462144 CGATTTCGTT
43462154 TTTCTTGAAATTTGTA
1 TTTCTTGAAATTTGTA
43462170 TTTCTTGAAATTTGT
1 TTTCTTGAAATTTGT
43462185 TGGAGTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (16 bp):
TTTCTTGAAATTTGTA
Found at i:43464883 original size:120 final size:120
Alignment explanation
Indices: 43464732--43465055 Score: 612
Period size: 120 Copynumber: 2.7 Consensus size: 120
43464722 TAAATTACTG
43464732 AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATT
1 AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATT
* * *
43464797 TAATAATAATTATTTTAAATTATATTTTATAGTATTATATGTTATGATTTTATTA
66 TAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTA
*
43464852 AATTCATATAAGAATATTTAATATTATGAATTTTATTAAATTATATATTTTTATTAAATTATATT
1 AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATT
43464917 TAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTA
66 TAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTA
43464972 AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATT
1 AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATT
43465037 TAATAATAATTATGTTAAA
66 TAATAATAATTATGTTAAA
43465056 ATATGATTAA
Statistics
Matches: 199, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 199 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATT
TAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTA
Found at i:43465866 original size:17 final size:19
Alignment explanation
Indices: 43465839--43465873 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
43465829 GTTAATTAAT
43465839 TTTTTTATAAATT-TTTTA
1 TTTTTTATAAATTCTTTTA
43465857 TTTTTT-TAAATTCTTTT
1 TTTTTTATAAATTCTTTT
43465874 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTATAAATTCTTTTA
Found at i:43467824 original size:298 final size:299
Alignment explanation
Indices: 43467289--43468113 Score: 816
Period size: 298 Copynumber: 2.8 Consensus size: 299
43467279 CTCATTAGAG
* * *
43467289 TATGCATAATATAATTAAAATGTAAATATTATATTAAATTAAAGTC-ATGGTTTAGTTGTAACAT
1 TATGCATAATATAATTAAAATGT-AATATTATATTAAAATAAA-TCTTTGG-TTAG-TGTAAAAT
* * * * * * * * * * * *
43467353 TGTTTAATTATTGTCAATAACTTGAG-TTAAATCCAATCATATATAATTTTCTATTTGTTTTTCA
62 TGTTTTATTAATGTAAATAGCATAAGTTTAAATCTAATCACATAAAATTTTTTATTGGTTTTTAA
* * * * * * * *
43467417 GAAATAGAAAGACAAAAATACTCTCGAATTATATAACTAATTTTAATTATGGAATGATATTTTTG
127 GAAATAAAAAGACTAAAATACTCTCAAATAATATAACTTATTTTAATTACGGAATAACATTTTTG
* *** *
43467482 AAATTTTCTTAACTGGGTTGGTGCTCGGTTGACTCGTAACACCAACTTAGTTAGGGGCTT-A-AA
192 AAATTTTCCTAACCAAGTTGGTGCTCGGTTGACTCATAACACCAACTTA---A-GGGCTTAATAA
* * *
43467545 TACTA-AT-ATA-A-ATA-A-ATATATAATTGATGGAGATTATAAAA
253 TACTATATAATATAGATAGAGATATACAATTGATAGAGATAATAAAA
*
43467586 TATGCATAATACAATTAAAATGTAGATATTATATTAAAATAAATCTTTGGTTCAGTGATAAAATT
1 TATGCATAATATAATTAAAATGTA-ATATTATATTAAAATAAATCTTTGGTT-AGTG-TAAAATT
* *
43467651 GTTTTATTAATGTAAATAGCATAAGTTTAAATCTAATCACATACAATTTTTTATTGGTTTTTAAA
63 GTTTTATTAATGTAAATAGCATAAGTTTAAATCTAATCACATAAAATTTTTTATTGGTTTTTAAG
* * * **
43467716 AAATAAAAAGACTAAAATATTCACAAATAATATAAGTTATTTTAATTACACAATAACATTTTTGA
128 AAATAAAAAGACTAAAATACTCTCAAATAATATAACTTATTTTAATTACGGAATAACATTTTTGA
* * * *
43467781 AATTTCCCTAACCAAGTTGGTGCCCGGTTGACTCATGACACCAACTTAAGGGCTTAAATAATAGT
193 AATTTTCCTAACCAAGTTGGTGCTCGGTTGACTCATAACACCAACTTAAGGGCTT-AATAATACT
*
43467846 ATATAGATATAGATAGAGATATACAATTGATAGAGATAATAAAG
257 ATATA-ATATAGATAGAGATATACAATTGATAGAGATAATAAAA
* * * *
43467890 TATGTATAATATAATTAAAAT-T--TA-AATATTAAAATAAAGCTTTAGATTAGTGGTAAAATTG
1 TATGCATAATATAATTAAAATGTAATATTATATTAAAATAAATCTTT-GGTTAGT-GTAAAATTG
* * * * * * * * *
43467951 TTTTATTAATATATATAGCAGAGGTTCAAATCTAGTTACATATAAATTTTTTATTGATTTTTTAG
64 TTTTATTAATGTAAATAGCATAAGTTTAAATCTAATCACATA-AAATTTTTTATTGGTTTTTAAG
* * * * *
43468016 AAATAAAAATACTAAAATACTCTCAAATAATTTAACATATTTTAATTACGGAA-AGACATTTATA
128 AAATAAAAAGACTAAAATACTCTCAAATAATATAACTTATTTTAATTACGGAATA-ACATTTTTG
* *
43468080 AAATTTTCCTAACCAAATTGGTGCTCGATTGACT
192 AAATTTTCCTAACCAAGTTGGTGCTCGGTTGACT
43468114 TGTGGCACTG
Statistics
Matches: 436, Mismatches: 73, Indels: 35
0.80 0.13 0.06
Matches are distributed among these distances:
294 6 0.01
295 1 0.00
296 8 0.02
297 75 0.17
298 126 0.29
299 64 0.15
300 109 0.25
301 1 0.00
302 3 0.01
303 2 0.00
304 41 0.09
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (299 bp):
TATGCATAATATAATTAAAATGTAATATTATATTAAAATAAATCTTTGGTTAGTGTAAAATTGTT
TTATTAATGTAAATAGCATAAGTTTAAATCTAATCACATAAAATTTTTTATTGGTTTTTAAGAAA
TAAAAAGACTAAAATACTCTCAAATAATATAACTTATTTTAATTACGGAATAACATTTTTGAAAT
TTTCCTAACCAAGTTGGTGCTCGGTTGACTCATAACACCAACTTAAGGGCTTAATAATACTATAT
AATATAGATAGAGATATACAATTGATAGAGATAATAAAA
Found at i:43468061 original size:300 final size:302
Alignment explanation
Indices: 43467560--43468113 Score: 713
Period size: 300 Copynumber: 1.8 Consensus size: 302
43467550 ATATAAATAA
* * * *
43467560 ATATATAATTGATGGAGATTATAAAATATGCATAATACAATTAAAATGTAGATATTATATTAAAA
1 ATATACAATTGATAGAGATAATAAAATATGCATAATACAATTAAAATGT--ATATAATATTAAAA
* * * * *
43467625 TAAATCTTTGGTTCAGTGATAAAATTGTTTTATTAATGTAAATAGCATAAGTTTAAATCTAATCA
64 TAAAGCTTTGATTCAGTGATAAAATTGTTTTATTAATATAAATAGCAGAAGTTCAAATCTAATCA
* * * **
43467690 CATACAATTTTTTATTGGTTTTTAAAAAATAAAAAGACTAAAATATTCACAAATAATATAAGTTA
129 CATAAAATTTTTTATTGATTTTTAAAAAATAAAAAGACTAAAATACTCACAAATAATATAACATA
* * * *
43467755 TTTTAATTACACAATA-ACATTTTTGAAATTTCCCTAACCAAGTTGGTGCCCGGTTGACTCATGA
194 TTTTAATTACACAA-AGACATTTATAAAATTTCCCTAACCAAATTGGTGCCCGATTGACTCATGA
43467819 CACCAACTTAAGGGCTTAAATAATAGTATATAGATATAGATAGAG
258 CACCAACTTAAGGGCTTAAATAATAGTATATAGATATAGATAGAG
* * *
43467864 ATATACAATTGATAGAGATAATAAAGTATGTATAATATAATTAAAAT-T-TA-AATATTAAAATA
1 ATATACAATTGATAGAGATAATAAAATATGCATAATACAATTAAAATGTATATAATATTAAAATA
* * * * *
43467926 AAGCTTTAGATT-AGTGGTAAAATTGTTTTATTAATATATATAGCAGAGGTTCAAATCTAGTTAC
66 AAGCTTT-GATTCAGTGATAAAATTGTTTTATTAATATAAATAGCAGAAGTTCAAATCTAATCAC
* * * * *
43467990 ATATAAATTTTTTATTGATTTTTTAGAAATAAAAATACTAAAATACTCTCAAATAATTTAACATA
130 ATA-AAATTTTTTATTGATTTTTAAAAAATAAAAAGACTAAAATACTCACAAATAATATAACATA
** * *
43468055 TTTTAATTACGGAAAGACATTTATAAAATTTTCCTAACCAAATTGGTGCTCGATTGACT
194 TTTTAATTACACAAAGACATTTATAAAATTTCCCTAACCAAATTGGTGCCCGATTGACT
43468114 TGTGGCACTG
Statistics
Matches: 212, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
299 65 0.31
300 105 0.50
303 1 0.00
304 41 0.19
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (302 bp):
ATATACAATTGATAGAGATAATAAAATATGCATAATACAATTAAAATGTATATAATATTAAAATA
AAGCTTTGATTCAGTGATAAAATTGTTTTATTAATATAAATAGCAGAAGTTCAAATCTAATCACA
TAAAATTTTTTATTGATTTTTAAAAAATAAAAAGACTAAAATACTCACAAATAATATAACATATT
TTAATTACACAAAGACATTTATAAAATTTCCCTAACCAAATTGGTGCCCGATTGACTCATGACAC
CAACTTAAGGGCTTAAATAATAGTATATAGATATAGATAGAG
Found at i:43474397 original size:18 final size:18
Alignment explanation
Indices: 43474374--43474411 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
43474364 TTTATTGTCT
43474374 AAATTAATAAATTTA-ATG
1 AAATT-ATAAATTTAGATG
*
43474392 AAATTATTAATTTAGATG
1 AAATTATAAATTTAGATG
43474410 AA
1 AA
43474412 GATCAGGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
AAATTATAAATTTAGATG
Found at i:43475378 original size:15 final size:16
Alignment explanation
Indices: 43475354--43475403 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
43475344 TACATGAAAT
43475354 TCATGAAAATGATGATA
1 TCATG-AAATGATGATA
43475371 -CATGAAAT-ATTGATA
1 TCATGAAATGA-TGATA
*
43475386 TAATGAAATGAATGATA
1 TCATGAAATG-ATGATA
43475403 T
1 T
43475404 ATGTTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 1 0.04
15 9 0.32
16 11 0.39
17 6 0.21
18 1 0.04
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (16 bp):
TCATGAAATGATGATA
Found at i:43475403 original size:17 final size:17
Alignment explanation
Indices: 43475361--43475404 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
43475351 AATTCATGAA
43475361 AATGATGATACATGAAAT
1 AATGAT-ATACATGAAAT
*
43475379 ATTGATATA-ATGAAAT
1 AATGATATACATGAAAT
43475395 GAATGATATA
1 -AATGATATA
43475405 TGTTTATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (17 bp):
AATGATATACATGAAAT
Found at i:43479490 original size:3 final size:3
Alignment explanation
Indices: 43479482--43479506 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43479472 CTCTATGGGA
43479482 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
43479507 TGGGATCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:43481047 original size:16 final size:15
Alignment explanation
Indices: 43481022--43481055 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
43481012 AAAGTTGATA
*
43481022 ATAATTAATATATATT
1 ATAATAAATATA-ATT
43481038 ATAATAAATATAATT
1 ATAATAAATATAATT
43481053 ATA
1 ATA
43481056 TACTTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:43482930 original size:18 final size:18
Alignment explanation
Indices: 43482909--43482945 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
43482899 CTCTTAAAGT
43482909 AGAAGTACCCATCGGATC
1 AGAAGTACCCATCGGATC
43482927 AGAAGTACCCATCGGATC
1 AGAAGTACCCATCGGATC
43482945 A
1 A
43482946 ATCTCGGCTT
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:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (18 bp):
AGAAGTACCCATCGGATC
Found at i:43485936 original size:47 final size:47
Alignment explanation
Indices: 43485878--43486264 Score: 497
Period size: 47 Copynumber: 8.2 Consensus size: 47
43485868 CAATAACATG
* * * * * *
43485878 CTCAAAA-TGGACAGCATTATACATCAAATTCGACAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* * * * * * * *
43485924 CCCAAAATTGGACAGCATTATCCATCAAATTAGACAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* * * * * * *
43485971 CTCACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* *
43486018 CTCACAATTGGACAGCATTATATATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
*
43486065 CTCAAAATTGGACAGCATATTATACATTACAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGC--ATTATACATTAAAATGGACAGCATCAATACA
*
43486114 CTCAAAATTGGACAGCATTATACATTAAAATGGGCAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
*
43486161 CTCAAAATTGGACAGCATTACACATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* *
43486208 CTCAAAATTGGACAGCATTACACATTAAAATGGGCAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
43486255 CTCAAAATTG
1 CTCAAAATTG
43486265 TAATACCCAA
Statistics
Matches: 317, Mismatches: 21, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
46 6 0.02
47 266 0.84
49 45 0.14
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (47 bp):
CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
Found at i:43486172 original size:190 final size:188
Alignment explanation
Indices: 43485878--43486264 Score: 499
Period size: 190 Copynumber: 2.1 Consensus size: 188
43485868 CAATAACATG
* *
43485878 CTCAAAA-TGGACAGCATTATACATCAAATTCGACAGCTTAAATATACCCAAAATTGGACAGCAT
1 CTCAAAATTGGACAGCATTATACATCAAATTCGACAGCATAAATACACCCAAAATTGGACAGCAT
* * * * * * *
43485942 TATCCATCAAATTAGACAGCTTAAATATACTCACAATTGGACAGCATTATACATCAAATTAGACA
66 TATACATCAAAATAGACAGCATAAATACACTCAAAATTGGACAGCATTACACATCAAAATAGACA
* * * * *
43486007 GCTTAAATATACTCACAATTGGACAGCATTATATATTAAAATGGACAGCATCAATACA
131 GCATAAATACACTCAAAATTGGACAGCATTACACATTAAAATGGACAGCATCAATACA
* * * *
43486065 CTCAAAATTGGACAGCATATTATACATTACAA-TGGACAGCATCAATACACTCAAAATTGGACAG
1 CTCAAAATTGGACAGC--ATTATACATCA-AATTCGACAGCATAAATACACCCAAAATTGGACAG
* * * * * *
43486129 CATTATACATTAAAATGGGCAGCATCAATACACTCAAAATTGGACAGCATTACACATTAAAATGG
63 CATTATACATCAAAATAGACAGCATAAATACACTCAAAATTGGACAGCATTACACATCAAAATAG
* *
43486194 ACAGCATCAATACACTCAAAATTGGACAGCATTACACATTAAAATGGGCAGCATCAATACA
128 ACAGCATAAATACACTCAAAATTGGACAGCATTACACATTAAAATGGACAGCATCAATACA
43486255 CTCAAAATTG
1 CTCAAAATTG
43486265 TAATACCCAA
Statistics
Matches: 170, Mismatches: 26, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
187 7 0.04
188 8 0.05
190 153 0.90
191 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (188 bp):
CTCAAAATTGGACAGCATTATACATCAAATTCGACAGCATAAATACACCCAAAATTGGACAGCAT
TATACATCAAAATAGACAGCATAAATACACTCAAAATTGGACAGCATTACACATCAAAATAGACA
GCATAAATACACTCAAAATTGGACAGCATTACACATTAAAATGGACAGCATCAATACA
Found at i:43486245 original size:22 final size:23
Alignment explanation
Indices: 43486023--43486247 Score: 162
Period size: 25 Copynumber: 9.6 Consensus size: 23
43486013 ATATACTCAC
* *
43486023 AATTGGACAGCATTATATATTAA
1 AATTGGACAGCATTACACATTAA
*
43486046 AA-TGGACAGCATCAATACAC-TCAA
1 AATTGGACAGCAT---TACACATTAA
* *
43486070 AATTGGACAGCATATTATACATTAC
1 AATTGGACAGC--ATTACACATTAA
*
43486095 AA-TGGACAGCATCAATACAC-TCAA
1 AATTGGACAGCAT---TACACATTAA
*
43486119 AATTGGACAGCATTATACATTAA
1 AATTGGACAGCATTACACATTAA
* *
43486142 AA-TGGGCAGCATCAATACAC-TCAA
1 AATTGGACAGCAT---TACACATTAA
43486166 AATTGGACAGCATTACACATTAA
1 AATTGGACAGCATTACACATTAA
*
43486189 AA-TGGACAGCATCAATACAC-TCAA
1 AATTGGACAGCAT---TACACATTAA
43486213 AATTGGACAGCATTACACATTAA
1 AATTGGACAGCATTACACATTAA
*
43486236 AA-TGGGCAGCAT
1 AATTGGACAGCAT
43486248 CAATACACTC
Statistics
Matches: 161, Mismatches: 19, Indels: 45
0.72 0.08 0.20
Matches are distributed among these distances:
22 54 0.34
23 17 0.11
24 31 0.19
25 57 0.35
27 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (23 bp):
AATTGGACAGCATTACACATTAA
Found at i:43487243 original size:28 final size:27
Alignment explanation
Indices: 43487211--43487309 Score: 103
Period size: 28 Copynumber: 3.6 Consensus size: 27
43487201 TTAATAAGTA
*
43487211 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT-ATAATTAAACT
* **
43487239 CGCACACTTAGTGCTT-TACCCTTATCCT
1 CGCACACTTAGTGCTTATA--ATTAAACT
43487267 CGCACACTTAGTGCATT-TCAATTAAACT
1 CGCACACTTAGTGC-TTAT-AATTAAACT
43487295 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43487310 AATCTCATTA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 53 0.88
29 3 0.05
30 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATTAAACT
Found at i:43495178 original size:21 final size:21
Alignment explanation
Indices: 43495152--43495191 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
43495142 TCGTTCTAGT
43495152 TTGAAAGACTAGTATACAAGA
1 TTGAAAGACTAGTATACAAGA
43495173 TTGAAAGACTAGTATACAA
1 TTGAAAGACTAGTATACAA
43495192 ATTCATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.25
Consensus pattern (21 bp):
TTGAAAGACTAGTATACAAGA
Found at i:43501275 original size:16 final size:16
Alignment explanation
Indices: 43501223--43501278 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
43501213 CGTTTGGTTC
43501223 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
43501239 GCAGTAATTGAATAGA
1 GCTGTAATGGAATAGA
43501255 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
43501271 ACTGTAAT
1 GCTGTAAT
43501279 AGTAATTCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:43501311 original size:45 final size:44
Alignment explanation
Indices: 43501260--43501352 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 44
43501250 ATAGAGCTGT
43501260 AATGGAATAGAACTGTAATAGTAATTCTAT-TGTTTGGTTAAATGG
1 AATGGAATAGAACTGTAATAGT-ATT-TATGTGTTTGGTTAAATGG
* *
43501305 AATGGAATAGAACTGTAATAGTATTTTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTTATGTGTTTGGTTAAATGG
43501349 AATG
1 AATG
43501353 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 2 0.04
44 21 0.47
45 22 0.49
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTTATGTGTTTGGTTAAATGG
Found at i:43501574 original size:56 final size:56
Alignment explanation
Indices: 43501459--43501587 Score: 136
Period size: 56 Copynumber: 2.3 Consensus size: 56
43501449 AATAAGATTA
* * *
43501459 TTAATATAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAAAATTTTAACAAAATTATTATT-AATATAAT
* * *
43501517 TTAATAAAA-AATATATAATTTAATAAAATTCTTAATAAAATTATTCTT-ATATGAAT
1 TTAATAAAATAATAAATAATTTAATAAAATT-TTAACAAAATTATTATTAATAT-AAT
* *
43501573 TTACTAAAATCATAA
1 TTAATAAAATAATAA
43501588 TATATAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
55 4 0.07
56 29 0.49
57 20 0.34
58 6 0.10
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (56 bp):
TTAATAAAATAATAAATAATTTAATAAAATTTTAACAAAATTATTATTAATATAAT
Found at i:43502953 original size:38 final size:39
Alignment explanation
Indices: 43502899--43502976 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
43502889 GGTTGAGAAA
*
43502899 AGGGAAAAAAACAGCAATTACTTTACCAAAATGGATCCC
1 AGGGAAAAAAACAGCAACTACTTTACCAAAATGGATCCC
*
43502938 AGGG-AAAAAAGAGCAACTACTTTACCAAAATGGATCCC
1 AGGGAAAAAAACAGCAACTACTTTACCAAAATGGATCCC
43502976 A
1 A
43502977 ATACAAGAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 33 0.89
39 4 0.11
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.17
Consensus pattern (39 bp):
AGGGAAAAAAACAGCAACTACTTTACCAAAATGGATCCC
Found at i:43504009 original size:19 final size:19
Alignment explanation
Indices: 43503969--43504009 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
43503959 CTTAGCCCAG
*
43503969 CAAAACCCAATATCCAAAA
1 CAAAACCCAATACCCAAAA
43503988 CAAAACCCAA-ACCCAAATA
1 CAAAACCCAATACCCAAA-A
43504007 CAA
1 CAA
43504010 CTAAACCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.59, C:0.34, G:0.00, T:0.07
Consensus pattern (19 bp):
CAAAACCCAATACCCAAAA
Found at i:43504523 original size:16 final size:17
Alignment explanation
Indices: 43504499--43504531 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43504489 TCCCCGATTG
*
43504499 TTTTTTTAT-TTTTTTA
1 TTTTATTATGTTTTTTA
43504515 TTTTATTATGTTTTTTA
1 TTTTATTATGTTTTTTA
43504532 ACACAAAAAT
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:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTATTATGTTTTTTA
Found at i:43507329 original size:19 final size:19
Alignment explanation
Indices: 43507305--43507349 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
43507295 TTTTTATTTT
43507305 TGCATT-CATTCCATACATA
1 TGCATTACATTCCAT-CATA
*
43507324 TGCATTACATTGCATCATA
1 TGCATTACATTCCATCATA
43507343 TGCATTA
1 TGCATTA
43507350 GATTTTCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (19 bp):
TGCATTACATTCCATCATA
Found at i:43510140 original size:10 final size:10
Alignment explanation
Indices: 43510099--43510141 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
43510089 CCAAAAACAC
43510099 AAAAACAAAA
1 AAAAACAAAA
43510109 AAAGAAC-AAA
1 AAA-AACAAAA
* *
43510119 AGAGACAAAA
1 AAAAACAAAA
43510129 AAAAACAAAA
1 AAAAACAAAA
43510139 AAA
1 AAA
43510142 CCTCTACTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
9 2 0.07
10 22 0.81
11 3 0.11
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:43511079 original size:97 final size:93
Alignment explanation
Indices: 43510949--43511130 Score: 258
Period size: 97 Copynumber: 1.9 Consensus size: 93
43510939 ATTCTCATTC
* *
43510949 TAGCAAAAAATTGTTATCTTGATTGATTCATTCATTTCAAGCTTTGTTCTCAATAAAATTTCACC
1 TAGCAAAAAATTGCTATCTTGATTAATTCATTCATTTCAAGCTTTGTTCTCAAT-AAATTT----
43511014 TTATCCATTGTGATAATCTTTTTCATCTTATCT
61 TTATCCATTGTGATAATCTTTTTCATCTTATCT
* * **
43511047 TAGC-AAAATTTGCTATCTTGATTAATTTATTCATTTCGGGCTTTGTTCTCAATAAATTTTTATC
1 TAGCAAAAAATTGCTATCTTGATTAATTCATTCATTTCAAGCTTTGTTCTCAATAAATTTTTATC
43511111 CATTGTGATAATCTTTTTCA
66 CATTGTGATAATCTTTTTCA
43511131 AGCATTTTTG
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
92 25 0.32
96 6 0.08
97 43 0.55
98 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.47
Consensus pattern (93 bp):
TAGCAAAAAATTGCTATCTTGATTAATTCATTCATTTCAAGCTTTGTTCTCAATAAATTTTTATC
CATTGTGATAATCTTTTTCATCTTATCT
Found at i:43511635 original size:24 final size:24
Alignment explanation
Indices: 43511603--43511660 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
43511593 ATGTCCCTAA
43511603 ATTATAGTGGACTGAACCTTGAAG
1 ATTATAGTGGACTGAACCTTGAAG
* *
43511627 ATTATAGTGGATTGAACTTTGAAG
1 ATTATAGTGGACTGAACCTTGAAG
*
43511651 ATTACAGTGG
1 ATTATAGTGG
43511661 GGCAGTCCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.33
Consensus pattern (24 bp):
ATTATAGTGGACTGAACCTTGAAG
Found at i:43512134 original size:100 final size:100
Alignment explanation
Indices: 43511940--43512806 Score: 1211
Period size: 100 Copynumber: 8.7 Consensus size: 100
43511930 ATGAAGTTAC
* * * * * *
43511940 CTTCCCTGGCAATGCAGTGGAGCAGATTGAAGCTACAACTACGAAACTTG-TTCCCCAACATTGC
1 CTTCCATGGCGATGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGC
* * *
43512004 AATTTAAAGGATTGAAGCCACAACGACGAATCTTA
66 AATTTAAAAGATTGAAGCCGCAACGGCGAATCTTA
* *
43512039 CTTCCCA-GGTGATGCAGTGGAACAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTG
1 CTT-CCATGGCGATGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTG
43512103 CAATTTAAAAGATTGAAGCCGCAACGGCGAATCTTA
65 CAATTTAAAAGATTGAAGCCGCAACGGCGAATCTTA
* ***
43512139 CTTCCATGGCGATGCAGTGGGGCAGATTAAAGCTACAAC-AGCGAATCTTGCTTCCTTTACATTG
1 CTTCCATGGCGATGCAGTGGAGCAGATTAAAGCTACAACGA-CGAATCTTGCTTCCCCGACATTG
* *
43512203 CAATTTAAAAGATTGAGGCCACAACGGCGAATCTTA
65 CAATTTAAAAGATTGAAGCCGCAACGGCGAATCTTA
* * * * * *
43512239 CTTCCATGGTGATGCAGTGGAACAGATTGAAGCTACAATGGCGAATCTTCCTTCCCCGACATTGC
1 CTTCCATGGCGATGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGC
*
43512304 AATTTAAAAGATTGAAGCCGCAACGGTGAATCTTA
66 AATTTAAAAGATTGAAGCCGCAACGGCGAATCTTA
* * * * * *
43512339 CTTCCATGGCAATGCAATAGG-GCAGATTAAAGTTACAACGGCGAATCTTGCTTCCTCAACATTG
1 CTTCCATGGCGATGCAGT-GGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTG
* *
43512403 CAATTTAAAAGATTGAGGCCGTAACGGCGAATCTTA
65 CAATTTAAAAGATTGAAGCCGCAACGGCGAATCTTA
*
43512439 CTTCCATGGCAATGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGC
1 CTTCCATGGCGATGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGC
* * *
43512504 AATTTAAAAGATTGAAGCCACAAAGGTGAATCTTA
66 AATTTAAAAGATTGAAGCCGCAACGGCGAATCTTA
* * * **
43512539 CTTCCATGGCAATGCAGTGGAGCAGATTGACGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
1 CTTCCATGGCGATGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGC
*
43512604 AATTTAAAAGATTGAAGCCGCAACAGCGAATCTTA
66 AATTTAAAAGATTGAAGCCGCAACGGCGAATCTTA
** *
43512639 CTTCCATGGCGATGCAGTGGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCTGACATTGC
1 CTTCCATGGCGATGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGC
*
43512704 AATTTAAAAGATTGAAGCCGCAACAGCGAATCTTA
66 AATTTAAAAGATTGAAGCCGCAACGGCGAATCTTA
* * * * **
43512739 CTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTATTTCCCCGACATTGC
1 CTTCCATGGCGATGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGC
43512804 AAT
66 AAT
43512807 CAATTTGAAA
Statistics
Matches: 685, Mismatches: 76, Indels: 13
0.89 0.10 0.02
Matches are distributed among these distances:
99 46 0.07
100 637 0.93
101 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (100 bp):
CTTCCATGGCGATGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGC
AATTTAAAAGATTGAAGCCGCAACGGCGAATCTTA
Found at i:43512948 original size:82 final size:82
Alignment explanation
Indices: 43512860--43513267 Score: 762
Period size: 82 Copynumber: 5.0 Consensus size: 82
43512850 AGTGGATTAA
* * *
43512860 AACCACATATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGCCTCAACTCTTATCTCCCTAAGC
1 AACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGC
*
43512925 AGTAGTGGAGCAGACAA
66 AGTAGTGGAGCAGACAG
43512942 AACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGC
1 AACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGC
43513007 AGTAGTGGAGCAGACAG
66 AGTAGTGGAGCAGACAG
* *
43513024 AACCACAAATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGCCTCAAGTCTTATCTCCCTAAGC
1 AACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGC
43513089 AGTAGTGGAGCAGACAG
66 AGTAGTGGAGCAGACAG
43513106 AACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGC
1 AACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGC
43513171 AGTAGTGGAGCAGACAG
66 AGTAGTGGAGCAGACAG
43513188 AACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGC
1 AACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGC
43513253 AGTAGTGGAGCAGAC
66 AGTAGTGGAGCAGAC
43513268 GAAATAAACC
Statistics
Matches: 318, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 318 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (82 bp):
AACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCCTCAAGTCTTATCTCCCTAAGC
AGTAGTGGAGCAGACAG
Found at i:43513638 original size:19 final size:19
Alignment explanation
Indices: 43513598--43513638 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
43513588 CTTAGCCCAG
*
43513598 CAAAACCCAATATCCAAAA
1 CAAAACCCAATACCCAAAA
43513617 CAAAACCCAA-ACCCAAATA
1 CAAAACCCAATACCCAAA-A
43513636 CAA
1 CAA
43513639 CTAAACCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.59, C:0.34, G:0.00, T:0.07
Consensus pattern (19 bp):
CAAAACCCAATACCCAAAA
Found at i:43518039 original size:43 final size:43
Alignment explanation
Indices: 43517987--43518235 Score: 322
Period size: 43 Copynumber: 5.8 Consensus size: 43
43517977 TTTTATAAAT
43517987 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAC
* * * *
43518030 AAACGCCGCTATAGATCAGGATCTTTAGCGGTGCTTTTT-TAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAC
* * * *
43518072 AAACGCCGCTATAGATCAAGACCATTAGCGGCGCTTATACCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAC
* * *
43518115 AAAGGCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTCAAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAC
* * * * *
43518158 AAATGCTGCTATAGATTACGACCTTTAGCGGCGTTTTTTC-AC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAC
* *
43518200 AAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
43518236 CTCGCAAAAA
Statistics
Matches: 173, Mismatches: 32, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
42 65 0.38
43 108 0.62
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAC
Found at i:43518141 original size:85 final size:86
Alignment explanation
Indices: 43517987--43518235 Score: 331
Period size: 85 Copynumber: 2.9 Consensus size: 86
43517977 TTTTATAAAT
* * * *
43517987 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAACAAACGCCGCTATAGATCAGGAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGCTCAAGAC
* * *
43518052 CTTTAGCGGTGCTTTTT-TAC
66 CTTTAGCGGCGCTTTTTCAAA
* * * *
43518072 AAACGCCGCTATAGATCAAGACCATTAGCGGCGCTTATACCACAAAGGCCGCTATAGCTCAAGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGCTCAAGAC
43518137 CTTTAGCGGCGCTTTTTCAAA
66 CTTTAGCGGCGCTTTTTCAAA
* * * * *
43518158 AAATGCTGCTATAGATTACGACCTTTAGCGGCG-TTTTTTCACAAACGCCGCTATAGCTCAAGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGCTCAAGAC
*
43518222 CTTTAGCGACGCTT
66 CTTTAGCGGCGCTT
43518236 CTCGCAAAAA
Statistics
Matches: 142, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
85 113 0.80
86 29 0.20
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (86 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGCTCAAGAC
CTTTAGCGGCGCTTTTTCAAA
Found at i:43518144 original size:128 final size:128
Alignment explanation
Indices: 43517991--43518235 Score: 375
Period size: 128 Copynumber: 1.9 Consensus size: 128
43517981 ATAAATAAAC
* * *
43517991 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAACAAACGCCGCTATAGATCAGGATCTTT
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAAAAACGCCGCTATAGATCACGACCTTT
* *
43518056 AGCGGTGCTTTTTT-ACAAACGCCGCTATAGATCAAGACCATTAGCGGCGCTTATACCACAAAG
66 AGCGGCG-TTTTTTCACAAACGCCGCTATAGATCAAGACCATTAGCGACGCTTATACCACAAAG
* * * *
43518119 GCCGCTATAGCTCAAGACCTTTAGCGGCGCTTTTTCAAAAAATGCTGCTATAGATTACGACCTTT
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAAAAACGCCGCTATAGATCACGACCTTT
* *
43518184 AGCGGCGTTTTTTCACAAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTT
66 AGCGGCGTTTTTTCACAAACGCCGCTATAGATCAAGACCATTAGCGACGCTT
43518236 CTCGCAAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
127 6 0.06
128 99 0.94
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (128 bp):
GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCAAAAAACGCCGCTATAGATCACGACCTTT
AGCGGCGTTTTTTCACAAACGCCGCTATAGATCAAGACCATTAGCGACGCTTATACCACAAAG
Found at i:43519504 original size:13 final size:13
Alignment explanation
Indices: 43519486--43519515 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
43519476 TAAACAATGC
43519486 ATAAACAAGGCAT
1 ATAAACAAGGCAT
43519499 ATAAACAAGGCAT
1 ATAAACAAGGCAT
43519512 ATAA
1 ATAA
43519516 TTAAGCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (13 bp):
ATAAACAAGGCAT
Found at i:43519549 original size:20 final size:20
Alignment explanation
Indices: 43519524--43519566 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
43519514 AATTAAGCCT
43519524 CAATAATTTATACTTGAACC
1 CAATAATTTATACTTGAACC
43519544 CAATAATTTATACTTGAACC
1 CAATAATTTATACTTGAACC
43519564 CAA
1 CAA
43519567 ACTTTGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.33
Consensus pattern (20 bp):
CAATAATTTATACTTGAACC
Found at i:43520445 original size:10 final size:9
Alignment explanation
Indices: 43520432--43520480 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
43520422 ATAATTTTAT
*
43520432 TTTTTATAA
1 TTTTTACAA
43520441 TTTTTACAA
1 TTTTTACAA
43520450 TTTTTTACAA
1 -TTTTTACAA
43520460 -TTTTACAA
1 TTTTTACAA
*
43520468 TTTTTATAA
1 TTTTTACAA
43520477 TTTT
1 TTTT
43520481 AAATTATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 8 0.22
9 19 0.53
10 9 0.25
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTACAA
Found at i:43520446 original size:9 final size:9
Alignment explanation
Indices: 43520420--43520480 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
43520410 TATATTCAAA
43520420 TTATAA-TT
1 TTATAATTT
43520428 TTAT--TTT
1 TTATAATTT
43520435 TTATAATTT
1 TTATAATTT
*
43520444 TTACAATTT
1 TTATAATTT
*
43520453 TT-TACAATT
1 TTATA-ATTT
*
43520462 TTACAATTT
1 TTATAATTT
43520471 TTATAATTT
1 TTATAATTT
43520480 T
1 T
43520481 AAATTATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
7 6 0.14
8 5 0.12
9 30 0.71
10 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (9 bp):
TTATAATTT
Found at i:43520740 original size:76 final size:76
Alignment explanation
Indices: 43520577--43520802 Score: 276
Period size: 76 Copynumber: 2.9 Consensus size: 76
43520567 TATAAATAAC
* * *
43520577 TTATTTAATATATAAATTAAAAAGTACTAATTAATTCAAATCTTAAACCCT-AACCTGACCCCAA
1 TTATTTAATATAAAAATTAAAAA--AC--ACTAATT--AATC-TAAACCCTAAACCAGACCCCAA
43520641 ATCCCTAACCCCTAAACT
59 ATCCCTAACCCCTAAACT
* * *
43520659 TTATTTATTATAAAAATTAAAAAACACTAATTAATCTAAACCTTAAACCCGACCCCAAATCCCTA
1 TTATTTAATATAAAAATTAAAAAACACTAATTAATCTAAACCCTAAACCAGACCCCAAATCCCTA
*
43520724 ACCCCTAAATT
66 ACCCCTAAACT
* * * *
43520735 TTATTTAATATATAACTTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCC-AATCCCTA
1 TTATTTAATATAAAAATTAAAAAACACTAATTAATCTAAACCCTAAACCAGACCCCAAATCCCTA
43520799 ACCC
66 ACCC
43520803 TTAACCCCTA
Statistics
Matches: 130, Mismatches: 13, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
75 19 0.15
76 82 0.63
78 6 0.05
80 2 0.02
82 21 0.16
ACGTcount: A:0.44, C:0.25, G:0.01, T:0.29
Consensus pattern (76 bp):
TTATTTAATATAAAAATTAAAAAACACTAATTAATCTAAACCCTAAACCAGACCCCAAATCCCTA
ACCCCTAAACT
Found at i:43520803 original size:6 final size:7
Alignment explanation
Indices: 43520794--43520827 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
43520784 ATAACCCAAT
43520794 CCCTAAC
1 CCCTAAC
*
43520801 CCTTAAC
1 CCCTAAC
43520808 CCCTAAC
1 CCCTAAC
*
43520815 CCCTAAT
1 CCCTAAC
43520822 CCCTAA
1 CCCTAA
43520828 ACCTTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAC
Found at i:43520813 original size:14 final size:14
Alignment explanation
Indices: 43520794--43520833 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
43520784 ATAACCCAAT
43520794 CCCTAACCCTTAAC
1 CCCTAACCCTTAAC
* *
43520808 CCCTAACCCCTAAT
1 CCCTAACCCTTAAC
*
43520822 CCCTAAACCTTA
1 CCCTAACCCTTA
43520834 TTTAATATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.47, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:43520997 original size:14 final size:14
Alignment explanation
Indices: 43520929--43520998 Score: 81
Period size: 14 Copynumber: 5.1 Consensus size: 14
43520919 TCTTAACATC
*
43520929 TAACCCATAA-CC-
1 TAACCCCTAACCCT
43520941 TAACCCCTAACCCT
1 TAACCCCTAACCCT
* **
43520955 GAATTCCTAACCCT
1 TAACCCCTAACCCT
43520969 TAACCCCTAACCCT
1 TAACCCCTAACCCT
*
43520983 TAACCCCTAAACCT
1 TAACCCCTAACCCT
43520997 TA
1 TA
43520999 TTCAATATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
12 9 0.19
13 2 0.04
14 37 0.77
ACGTcount: A:0.33, C:0.43, G:0.01, T:0.23
Consensus pattern (14 bp):
TAACCCCTAACCCT
Found at i:43521118 original size:164 final size:165
Alignment explanation
Indices: 43520795--43521118 Score: 551
Period size: 164 Copynumber: 2.0 Consensus size: 165
43520785 TAACCCAATC
* *
43520795 CCTAACCCTTAACCCCTAACCCCTAATCCCTAAACCTTATTTAATATATAATTAAAACACACTAA
1 CCTAACCCTTAACCCCTAACCCCTAACCCCTAAACCTTATTCAATATATAATTAAAACACACTAA
*
43520860 TTAATCTAAATCCCTAAACTCTAACCTAACACCGATTTTATAAACCCTAAATCCCTAACTCTTAA
66 TTAATCTAAATCCCTAAACTCTAACCTAACACCGAATTTATAAACCCTAAATCCCTAACTCTTAA
43520925 CATCTAACCCATAACCTAACCCCTAACCCTGAATT
131 CATCTAACCCATAACCTAACCCCTAACCCTGAATT
* *
43520960 CCTAACCCTTAACCCCTAACCCTTAACCCCTAAACCTTATTCAATATATAATTAAAATACACTAA
1 CCTAACCCTTAACCCCTAACCCCTAACCCCTAAACCTTATTCAATATATAATTAAAACACACTAA
* * *
43521025 TTAATCTAAA-CCCTAAACTGTAACTTAACACCGAATTTCTAAACCCTAAATCCCTAACTCTTAA
66 TTAATCTAAATCCCTAAACTCTAACCTAACACCGAATTTATAAACCCTAAATCCCTAACTCTTAA
* *
43521089 CATCTAACCCCTAACCTAACCCTTAACCCT
131 CATCTAACCCATAACCTAACCCCTAACCCT
43521119 TAACCCATAA
Statistics
Matches: 149, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
164 78 0.52
165 71 0.48
ACGTcount: A:0.38, C:0.33, G:0.01, T:0.28
Consensus pattern (165 bp):
CCTAACCCTTAACCCCTAACCCCTAACCCCTAAACCTTATTCAATATATAATTAAAACACACTAA
TTAATCTAAATCCCTAAACTCTAACCTAACACCGAATTTATAAACCCTAAATCCCTAACTCTTAA
CATCTAACCCATAACCTAACCCCTAACCCTGAATT
Found at i:43521177 original size:14 final size:15
Alignment explanation
Indices: 43521158--43521190 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
43521148 CTTAAACCAG
43521158 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
43521172 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
43521187 AATC
1 AATC
43521191 TATAAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:43522059 original size:114 final size:115
Alignment explanation
Indices: 43521923--43522294 Score: 508
Period size: 113 Copynumber: 3.3 Consensus size: 115
43521913 AGTTGATTTA
* * *
43521923 TTTTTTGCGGCG-TTTTTCCAAAAACGCCGCTAAAGCCCTGGGCATTAGTGGCGCTTTAC-CAAA
1 TTTTTTGCGGCGCTTTCT-CAAAAACGCCGCTAAAGCCCTGGGCATTAGCGGCGCTTTACTTAAA
* *
43521986 AACGCCGCTAAATCCCTGAAAGTTCAGAAAACGGCGTTGTTGGGCTTAGGT
65 AACGCCGCTAAATCCCCGAAAGTTCAGAAAACGGCGTCGTTGGGCTTAGGT
* * *
43522037 TTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTAGG-ATTAGCGGCGC-ATACTTAAAA
1 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGGGCATTAGCGGCGCTTTACTTAAAA
* *
43522100 ATGTCGCTAAATCCCCGAAAGCTT-A-AAAACGGCGTCGTTGGGCTTAGGT
66 ACGCCGCTAAATCCCCGAAAG-TTCAGAAAACGGCGTCGTTGGGCTTAGGT
* * * * **
43522149 TTTTTTGCGGCGCTTTCCCAAAAATGCCGCTAAAACCCCGAACATTAGCGGCGCTTT-CTTAAAA
1 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGGGCATTAGCGGCGCTTTACTTAAAA
* *
43522213 GCGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG-
66 ACGCCGCTAAATCCCCGAAAGTTCAGAAAACGGCGTCGTTGGGCTTAGGT
43522262 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
1 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
43522295 TGCTTTTTTA
Statistics
Matches: 227, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
112 61 0.27
113 101 0.44
114 61 0.27
115 4 0.02
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (115 bp):
TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGGGCATTAGCGGCGCTTTACTTAAAA
ACGCCGCTAAATCCCCGAAAGTTCAGAAAACGGCGTCGTTGGGCTTAGGT
Found at i:43522378 original size:12 final size:12
Alignment explanation
Indices: 43522361--43522386 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43522351 TTTTTTATCC
43522361 AAACGCCGCTAA
1 AAACGCCGCTAA
43522373 AAACGCCGCTAA
1 AAACGCCGCTAA
43522385 AA
1 AA
43522387 GCCTGTTTTG
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Done.