Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 76 of 135
Found at i:25361003 original size:18 final size:18
Alignment explanation
Indices: 25360980--25361014 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25360970 ATAATTATAG
25360980 ACTTATTATCTTATTTTA
1 ACTTATTATCTTATTTTA
*
25360998 ACTTATTATTTTATTTT
1 ACTTATTATCTTATTTT
25361015 TGCGTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
ACTTATTATCTTATTTTA
Found at i:25367329 original size:21 final size:21
Alignment explanation
Indices: 25367301--25367354 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
25367291 TGGGAAGGTT
25367301 CTACCGATACAAGTATGACTA
1 CTACCGATACAAGTATGACTA
* * * *
25367322 CTATCGATACAATTATTACTT
1 CTACCGATACAAGTATGACTA
25367343 CTACCGATACAA
1 CTACCGATACAA
25367355 CAAACTCCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (21 bp):
CTACCGATACAAGTATGACTA
Found at i:25368295 original size:94 final size:94
Alignment explanation
Indices: 25368122--25368434 Score: 371
Period size: 94 Copynumber: 3.4 Consensus size: 94
25368112 GTCATTTCTG
* * * * * **
25368122 TTACCAGTATATGATGTTGCTCACACTAAGCTGATGAGGACTCGCAACATATGCAGTGTCTCAGC
1 TTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGATTCGCAACATATGCGGTACCTCAGC
* ** * * *
25368187 CATCAATATTGTATCTGTACATATAATTG
66 CATCGATACGGTATCTGTGCATATAACTA
* * * **
25368216 TTACTAGTATACGATGCTGCTCACACTAAGCTGACGAAGATTCGCAACATATGTGGTACCTCAAT
1 TTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGATTCGCAACATATGCGGTACCTCAGC
*
25368281 CATCGATACGGTATCTATGCATATAACTA
66 CATCGATACGGTATCTGTGCATATAACTA
* * * *
25368310 TTACCAGTATATGATGCTGCTTACACTAAGCTAACGAGGATTCACAACATATGCGGTACCTCAGC
1 TTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGATTCGCAACATATGCGGTACCTCAGC
*
25368375 CATCGATACGGTATTTGTGCATATAACTA
66 CATCGATACGGTATCTGTGCATATAACTA
* *
25368404 TT-CC-CTA-ACGATGTTGCTCACACTAAGCTGA
1 TTACCAGTATACGATGCTGCTCACACTAAGCTGA
25368435 TGAGAATATG
Statistics
Matches: 184, Mismatches: 35, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
91 20 0.11
92 2 0.01
93 2 0.01
94 160 0.87
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (94 bp):
TTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGATTCGCAACATATGCGGTACCTCAGC
CATCGATACGGTATCTGTGCATATAACTA
Found at i:25372099 original size:98 final size:98
Alignment explanation
Indices: 25371930--25372127 Score: 396
Period size: 98 Copynumber: 2.0 Consensus size: 98
25371920 CCATAACTAA
25371930 AAGTCAGAACAATAATATAAAATCTTCCAATACCCATTTTCCTCAGTTTTGTTAGCAACCAAACA
1 AAGTCAGAACAATAATATAAAATCTTCCAATACCCATTTTCCTCAGTTTTGTTAGCAACCAAACA
25371995 AGGAATTCGTCAACCAAACAGCGAAAAAAATGT
66 AGGAATTCGTCAACCAAACAGCGAAAAAAATGT
25372028 AAGTCAGAACAATAATATAAAATCTTCCAATACCCATTTTCCTCAGTTTTGTTAGCAACCAAACA
1 AAGTCAGAACAATAATATAAAATCTTCCAATACCCATTTTCCTCAGTTTTGTTAGCAACCAAACA
25372093 AGGAATTCGTCAACCAAACAGCGAAAAAAATGT
66 AGGAATTCGTCAACCAAACAGCGAAAAAAATGT
25372126 AA
1 AA
25372128 TCTCAAAAAA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.24
Consensus pattern (98 bp):
AAGTCAGAACAATAATATAAAATCTTCCAATACCCATTTTCCTCAGTTTTGTTAGCAACCAAACA
AGGAATTCGTCAACCAAACAGCGAAAAAAATGT
Found at i:25375459 original size:17 final size:17
Alignment explanation
Indices: 25375437--25375533 Score: 62
Period size: 17 Copynumber: 5.7 Consensus size: 17
25375427 CTACAAGATA
25375437 AATATTAAATTAAATTT
1 AATATTAAATTAAATTT
25375454 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAA--A-TTT
*
25375474 AATATTAAATTAACA--A
1 AATATTAAATTAA-ATTT
* *
25375490 AATACT--ATTAAA-AT
1 AATATTAAATTAAATTT
25375504 AAGTATTAAATTAAATTT
1 AA-TATTAAATTAAATTT
*
25375522 ACTATTAAATTA
1 AATATTAAATTA
25375534 TTAAAATAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
13 1 0.02
14 7 0.11
15 3 0.05
16 5 0.08
17 27 0.42
18 3 0.05
19 4 0.06
20 14 0.22
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (17 bp):
AATATTAAATTAAATTT
Found at i:25375670 original size:20 final size:19
Alignment explanation
Indices: 25375636--25375674 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
25375626 TTTAATTAAT
*
25375636 TTGATTAATTTAATTTTTC
1 TTGATTAAATTAATTTTTC
25375655 TTGATCTAAATTAATTTTTC
1 TTGAT-TAAATTAATTTTTC
25375675 AAAAATCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (19 bp):
TTGATTAAATTAATTTTTC
Found at i:25377409 original size:20 final size:20
Alignment explanation
Indices: 25377384--25377426 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
25377374 GAGATTTAAT
25377384 TTGGAAATAGTGGGTTTTGA
1 TTGGAAATAGTGGGTTTTGA
25377404 TTGGAAATAGTGGGTTTTGA
1 TTGGAAATAGTGGGTTTTGA
25377424 TTG
1 TTG
25377427 AGCTAGTCAT
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:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (20 bp):
TTGGAAATAGTGGGTTTTGA
Found at i:25379146 original size:22 final size:22
Alignment explanation
Indices: 25379104--25379148 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
25379094 CCATGAAAAG
* *
25379104 GTCTAAGTAAATTTATCATTAT
1 GTCTAAGTAAATTAATAATTAT
25379126 GTCTAA-TAAATATAATAATTAT
1 GTCTAAGTAAAT-TAATAATTAT
25379148 G
1 G
25379149 GTAGCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (22 bp):
GTCTAAGTAAATTAATAATTAT
Found at i:25387911 original size:16 final size:18
Alignment explanation
Indices: 25387871--25387910 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
25387861 ATTCTTTCGG
25387871 AATTAAAATATTTCAATT
1 AATTAAAATATTTCAATT
25387889 --TTAAAATATTT-AATT
1 AATTAAAATATTTCAATT
25387904 AATTAAA
1 AATTAAA
25387911 TTTATTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.20
16 11 0.55
17 5 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAAAATATTTCAATT
Found at i:25389393 original size:21 final size:23
Alignment explanation
Indices: 25389368--25389413 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
25389358 GAATTTTTAT
*
25389368 AAATGGTGTTTTG-AAGA-AGAA
1 AAATGGTGTTTGGCAAGAGAGAA
25389389 AAATGGTGTTTGGCAAGAGAGAA
1 AAATGGTGTTTGGCAAGAGAGAA
25389412 AA
1 AA
25389414 TGAGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 4 0.18
23 6 0.27
ACGTcount: A:0.43, C:0.02, G:0.30, T:0.24
Consensus pattern (23 bp):
AAATGGTGTTTGGCAAGAGAGAA
Found at i:25389451 original size:16 final size:17
Alignment explanation
Indices: 25389430--25389462 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25389420 AAAAAAATGG
*
25389430 GGGAAGGAG-AGAAAGA
1 GGGAAGAAGAAGAAAGA
25389446 GGGAAGAAGAAGAAAGA
1 GGGAAGAAGAAGAAAGA
25389463 TGAAACAAGA
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:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (17 bp):
GGGAAGAAGAAGAAAGA
Found at i:25397461 original size:30 final size:30
Alignment explanation
Indices: 25397404--25397462 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
25397394 AGATTTTAGG
* * *
25397404 AGCCACACGGGCTGGACACATGGCCATGTA
1 AGCCACACAGGCTGGACACACGACCATGTA
* *
25397434 AGCCGCACAGGCTGGGCACACGACCATGT
1 AGCCACACAGGCTGGACACACGACCATGT
25397463 GTTAAATCGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.32, G:0.31, T:0.12
Consensus pattern (30 bp):
AGCCACACAGGCTGGACACACGACCATGTA
Found at i:25401413 original size:11 final size:11
Alignment explanation
Indices: 25401388--25401430 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
25401378 CTATTTTTTT
* *
25401388 AAAAGAAATGA
1 AAAAAAAATTA
* *
25401399 AAAAACAATTC
1 AAAAAAAATTA
25401410 AAAAAAAATTA
1 AAAAAAAATTA
25401421 AAAAAAAATT
1 AAAAAAAATT
25401431 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTA
Found at i:25401418 original size:22 final size:22
Alignment explanation
Indices: 25401388--25401430 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25401378 CTATTTTTTT
* *
25401388 AAAAGAAATGAAAAAACAATTC
1 AAAAAAAATGAAAAAAAAATTC
*
25401410 AAAAAAAATTAAAAAAAAATT
1 AAAAAAAATGAAAAAAAAATT
25401431 GAATTTTTTT
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:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (22 bp):
AAAAAAAATGAAAAAAAAATTC
Found at i:25401468 original size:6 final size:6
Alignment explanation
Indices: 25401457--25401520 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
25401447 AATTACTACA
* * * *
25401457 TTTATT TTTATT TTCATT TTCATT TTTCATT TTCATTT TTTATT TTCATT
1 TTTATT TTTATT TTTATT TTTATT TTT-ATT TTTA-TT TTTATT TTTATT
25401507 TTT-TAT TTTATT TT
1 TTTAT-T TTTATT TT
25401521 ATTATGCACT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 1 0.02
6 36 0.75
7 11 0.23
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:25401488 original size:19 final size:18
Alignment explanation
Indices: 25401457--25401520 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
25401447 AATTACTACA
25401457 TTTATTTTT-ATTTTCAT
1 TTTATTTTTCATTTTCAT
25401474 TTTCATTTTTCATTTTCAT
1 TTT-ATTTTTCATTTTCAT
* *
25401493 TTTTTATTTTCATTTTTTAT
1 TTTAT-TTTTCA-TTTTCAT
25401513 TTTATTTT
1 TTTATTTT
25401521 ATTATGCACT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 3 0.08
18 7 0.17
19 20 0.50
20 10 0.25
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTTTCATTTTCAT
Found at i:25401525 original size:13 final size:13
Alignment explanation
Indices: 25401457--25401525 Score: 88
Period size: 13 Copynumber: 5.4 Consensus size: 13
25401447 AATTACTACA
*
25401457 TTTATTTTTA-TT
1 TTTATTTTCATTT
*
25401469 TTCATTTTCATTT
1 TTTATTTTCATTT
*
25401482 TTCATTTTCATTT
1 TTTATTTTCATTT
25401495 TTTATTTTCATTT
1 TTTATTTTCATTT
25401508 TTTATTTT-ATTT
1 TTTATTTTCATTT
25401520 TATTAT
1 T-TTAT
25401526 GCACTATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
12 13 0.25
13 39 0.75
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTATTTTCATTT
Found at i:25403344 original size:30 final size:30
Alignment explanation
Indices: 25403309--25403365 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
25403299 TTTTAAGAGC
25403309 CACACGGGTTGGACACATGACCATGTGAGA
1 CACACGGGTTGGACACATGACCATGTGAGA
*
25403339 CACACGGGTTGGGCACATGACCATGTG
1 CACACGGGTTGGACACATGACCATGTG
25403366 CCAGACCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.32, T:0.18
Consensus pattern (30 bp):
CACACGGGTTGGACACATGACCATGTGAGA
Found at i:25405383 original size:3 final size:3
Alignment explanation
Indices: 25405375--25405401 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25405365 CTTTGTCTAC
25405375 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
25405402 CTATTCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:25406401 original size:9 final size:9
Alignment explanation
Indices: 25406384--25406416 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
25406374 TCGAGTTAAT
25406384 TCAAATAAC
1 TCAAATAAC
*
25406393 TCAATTAAC
1 TCAAATAAC
25406402 TCAAATAAC
1 TCAAATAAC
25406411 TCAAAT
1 TCAAAT
25406417 TATTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (9 bp):
TCAAATAAC
Found at i:25406405 original size:18 final size:18
Alignment explanation
Indices: 25406379--25406414 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
25406369 TTTATTCGAG
*
25406379 TTAATTCAAATAACTCAA
1 TTAACTCAAATAACTCAA
25406397 TTAACTCAAATAACTCAA
1 TTAACTCAAATAACTCAA
25406415 ATTATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAACTCAAATAACTCAA
Found at i:25406458 original size:21 final size:22
Alignment explanation
Indices: 25406411--25406458 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
25406401 CTCAAATAAC
25406411 TCAAATTATTTAATTAAAAATT
1 TCAAATTATTTAATTAAAAATT
* **
25406433 T-AAATT-TTTTATTAAATTTT
1 TCAAATTATTTAATTAAAAATT
25406453 TCAAAT
1 TCAAAT
25406459 CGAATCGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.55
21 9 0.41
22 1 0.05
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
TCAAATTATTTAATTAAAAATT
Found at i:25408307 original size:53 final size:53
Alignment explanation
Indices: 25408249--25408355 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
25408239 AAATTTAGTC
*
25408249 TATTTACTTTTATTTTTAAAAAATTAGTCCCTATACTATTCAGTTTCCAAAAT
1 TATTTACTTTTATTTTTAAAAAATTAGTCCCTATACTATTCAATTTCCAAAAT
* * * *
25408302 TATTTACTTTTATTTTTAGAAATTTAGTTCCTATACTATTCAATTTTCAAAAT
1 TATTTACTTTTATTTTTAAAAAATTAGTCCCTATACTATTCAATTTCCAAAAT
25408355 T
1 T
25408356 CAGGTCCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (53 bp):
TATTTACTTTTATTTTTAAAAAATTAGTCCCTATACTATTCAATTTCCAAAAT
Found at i:25409705 original size:21 final size:21
Alignment explanation
Indices: 25409681--25409720 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25409671 ACCTTTCCTA
**
25409681 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAAACAAAACTATT
25409702 AAGTTAAAAAACAAAACTA
1 AAGTTAAAAAACAAAACTA
25409721 CGTCGTTTTG
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:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAAACAAAACTATT
Found at i:25410226 original size:9 final size:9
Alignment explanation
Indices: 25410214--25410251 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
25410204 GATATTTGGT
25410214 TTATTCGAA
1 TTATTCGAA
*
25410223 TTATTCAAA
1 TTATTCGAA
*
25410232 TTATTCGAG
1 TTATTCGAA
25410241 TTATTCGAA
1 TTATTCGAA
25410250 TT
1 TT
25410252 CGAAAAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:25413323 original size:24 final size:24
Alignment explanation
Indices: 25413296--25413464 Score: 266
Period size: 24 Copynumber: 7.0 Consensus size: 24
25413286 AAGAGACCAA
*
25413296 AATGATTAACTCTTACGAGCCCAG
1 AATGATTAGCTCTTACGAGCCCAG
25413320 AATGATTAGCTCTTACGAGCCCAG
1 AATGATTAGCTCTTACGAGCCCAG
25413344 AATGATTAGCTCTTACGAGCCCAG
1 AATGATTAGCTCTTACGAGCCCAG
*
25413368 AATGATTAGCTCTTACGAGCCCAT
1 AATGATTAGCTCTTACGAGCCCAG
* * *
25413392 AGTAATTAGCTCTTACGAGCCCAA
1 AATGATTAGCTCTTACGAGCCCAG
* * *
25413416 AATAATTAGCTTTTACGAGCCCAA
1 AATGATTAGCTCTTACGAGCCCAG
25413440 AATGATTAGCTCTTACGAGCCCAG
1 AATGATTAGCTCTTACGAGCCCAG
25413464 A
1 A
25413465 TAGAGTTTAA
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 135 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (24 bp):
AATGATTAGCTCTTACGAGCCCAG
Found at i:25413673 original size:81 final size:82
Alignment explanation
Indices: 25413484--25413702 Score: 345
Period size: 81 Copynumber: 2.7 Consensus size: 82
25413474 ACTAGTATAA
* *
25413484 GATG-TGCTCACACAAGCTGATGAGAACCTGCAACATATGCGAAGACTTAGCCATCGATACGGTC
1 GATGCTGCTCACACAAGCTGATGAGAATCTGCAACATATGCGAAGACTCAGCCATCGATACGGTC
25413548 TAGAATTTCTCACTCTC
66 TAGAATTTCTCACTCTC
25413565 GATGCTAGC-CACACAAGCTGATGAGAATCTGCAACATATGCGAAGACTCAGCCATCGATAC-GT
1 GATGCT-GCTCACACAAGCTGATGAGAATCTGCAACATATGCGAAGACTCAGCCATCGATACGGT
25413628 CTAGAATTTCTCACTCTC
65 CTAGAATTTCTCACTCTC
*** * *
25413646 GATGCTGCTCACACAAGCTGATGAGAATCCATAACATATGCGAATACTCAACCATCG
1 GATGCTGCTCACACAAGCTGATGAGAATCTGCAACATATGCGAAGACTCAGCCATCG
25413703 GAGGAATCCA
Statistics
Matches: 128, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
80 2 0.02
81 73 0.57
82 51 0.40
83 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (82 bp):
GATGCTGCTCACACAAGCTGATGAGAATCTGCAACATATGCGAAGACTCAGCCATCGATACGGTC
TAGAATTTCTCACTCTC
Found at i:25422196 original size:5 final size:5
Alignment explanation
Indices: 25422186--25422210 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25422176 ATACTAAATC
25422186 GATTT GATTT GATTT GATTT GATTT
1 GATTT GATTT GATTT GATTT GATTT
25422211 CATTCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
GATTT
Found at i:25422368 original size:16 final size:15
Alignment explanation
Indices: 25422351--25422379 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25422341 TTTTTCTTTC
25422351 TCTCT-CAAAATTTT
1 TCTCTACAAAATTTT
25422365 TCTCTACAAAATTTT
1 TCTCTACAAAATTTT
25422380 CATACGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (15 bp):
TCTCTACAAAATTTT
Found at i:25424065 original size:29 final size:28
Alignment explanation
Indices: 25424023--25424134 Score: 152
Period size: 29 Copynumber: 3.9 Consensus size: 28
25424013 AGTCCTTTAC
*
25424023 AGAATCAGCCACAAAAGCTCACATTTAAT
1 AGAAT-AGCCACAAAGGCTCACATTTAAT
25424052 AGATATAGCCACAAAGGCTCACATTTAAT
1 AGA-ATAGCCACAAAGGCTCACATTTAAT
* * *
25424081 AGAATCGACCACAAAGGCTCGCATTTAAG
1 AGAATAG-CCACAAAGGCTCACATTTAAT
25424110 AGAATCAGCCACAAAGGCTCACATT
1 AGAAT-AGCCACAAAGGCTCACATT
25424135 AACATATTCA
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.04
29 68 0.92
30 3 0.04
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (28 bp):
AGAATAGCCACAAAGGCTCACATTTAAT
Found at i:25429268 original size:20 final size:20
Alignment explanation
Indices: 25429240--25429278 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25429230 CCATGGCTTT
*
25429240 CATTATTAAGTTTAATTAAC
1 CATTATTAACTTTAATTAAC
*
25429260 CATTTTTAACTTTAATTAA
1 CATTATTAACTTTAATTAA
25429279 ACCTATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (20 bp):
CATTATTAACTTTAATTAAC
Found at i:25429287 original size:20 final size:20
Alignment explanation
Indices: 25429245--25429288 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
25429235 GCTTTCATTA
* *
25429245 TTAAGTTTAATTAACCATTT
1 TTAACTTTAATTAACCATAT
25429265 TTAACTTTAATTAAACC-TAT
1 TTAACTTTAATT-AACCATAT
25429285 TTAA
1 TTAA
25429289 AAGTAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAACTTTAATTAACCATAT
Found at i:25437273 original size:15 final size:12
Alignment explanation
Indices: 25437241--25437274 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
25437231 AGGATGAAAA
25437241 AAAAGAAGAAGG
1 AAAAGAAGAAGG
25437253 AAAAGAAGAA-G
1 AAAAGAAGAAGG
25437264 AGAAAGAAGAA
1 A-AAAGAAGAA
25437275 ACAAAACCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.10
12 19 0.90
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAGG
Found at i:25440938 original size:146 final size:145
Alignment explanation
Indices: 25440617--25441143 Score: 702
Period size: 146 Copynumber: 3.6 Consensus size: 145
25440607 GATCTTGGGA
* * * * *
25440617 AAAGTTTTTACTTTTTAACAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAATGATTTTA
1 AAAGTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTT-
* *
25440682 TTTAAAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATA-TTTTTAGTCATTTTAATG-A
65 CTT---AAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTCATTTTAATGAA
25440745 AAAGTTTAAATTTTTAAAC
127 AAAGTTTAAATTTTTAAAC
*
25440764 AAAGTTTTGATTTCTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTC
1 AAAGTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTC
*
25440829 TTAAAAAATAGAAAGTTTAGATTTTTAAAAACAAAAATCTATTTTTTAGTCATTTTAATGAAAAA
66 TTAAAAAA-AGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTCATTTTAATGAAAAA
*
25440894 GTTTAAAATTTTAAAC
130 GTTTAAATTTTTAAAC
*
25440910 AAACTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTC
1 AAAGTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTC
* * * * * *
25440975 TTAAAAAAA-AAAGTTTAAATTTTCAAACATAAATATCTATTTTTTAGTCATTTTAAAGAAAAAA
66 TTAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTCATTTTAATGAAAAAG
** * *
25441039 TACAATTTTTTAAAT
131 TTTAAATTTTTAAAC
* * * *
25441054 AAAGTTTT-ATTTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAGTAGTGATTT
1 AAAGTTTTGA--TTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGA-TT
* **
25441118 TTTTTAAAAAGGGAAAGTTTAGATTT
63 TTCTTAAAAAAAGAAAGTTTAGATTT
25441144 CAAAAAAAAA
Statistics
Matches: 340, Mismatches: 33, Indels: 14
0.88 0.09 0.04
Matches are distributed among these distances:
143 7 0.02
144 95 0.28
145 65 0.19
146 103 0.30
147 70 0.21
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (145 bp):
AAAGTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGATTTTC
TTAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTCATTTTAATGAAAAAG
TTTAAATTTTTAAAC
Found at i:25440971 original size:50 final size:47
Alignment explanation
Indices: 25440628--25440978 Score: 148
Period size: 50 Copynumber: 7.1 Consensus size: 47
25440618 AAGTTTTTAC
* * *
25440628 TTTTTAACAATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAATAATGATT
1 TTTTTAACTATTT--AAATAAAAGTTTAGATTTTTAA-AAAAATAGTGA-T
** * * *
25440679 TTATTTAA--A-AAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAAT-AT
1 TT-TTTAACTATTTAAATA-AAAGTTTAGATTTTTAAAAA-AATAGTGAT
* * * * **
25440725 ATTTTT-AGTCATTTTAATGAAAAGTTTAAATTTTTAAACAAAGTTTTGAT
1 -TTTTTAACT-ATTTAAAT-AAAAGTTTAGATTTTTAAA-AAAATAGTGAT
* *
25440775 TTCTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGAT
1 TTTTTAACTATTT--AAATAAAAGTTTAGATTTTTAA-AAAAATAGTGAT
* * *
25440825 TTTCTTAA--A---AAATAGAAAGTTTAGATTTTTAAAAACAAAAATCTAT
1 TTT-TTAACTATTTAAATA-AAAGTTTAGATTTTTAAAAA-AATAGT-GAT
* * * * * **
25440871 TTTTT-AGTCATTTTAATGAAAAAGTTTAAAATTTTAAACAAACTTTTGAT
1 TTTTTAACT-ATTTAAAT--AAAAGTTTAGATTTTTAAA-AAAATAGTGAT
*
25440921 TTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGAAAAATAGTGAT
1 TTTTTAACTATTT--AAATAAAAGTTTAGATTTTTAA-AAAAATAGTGAT
25440971 TTTCTTAA
1 TTT-TTAA
25440979 AAAAAAAAGT
Statistics
Matches: 224, Mismatches: 43, Indels: 66
0.67 0.13 0.20
Matches are distributed among these distances:
44 9 0.04
45 23 0.10
46 9 0.04
47 11 0.05
48 22 0.10
49 30 0.13
50 74 0.33
51 35 0.16
52 11 0.05
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (47 bp):
TTTTTAACTATTTAAATAAAAGTTTAGATTTTTAAAAAAATAGTGAT
Found at i:25441737 original size:20 final size:21
Alignment explanation
Indices: 25441695--25441740 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
25441685 CAAAACTTTT
* *
25441695 TTTATTTATTCTTCTTTTATA
1 TTTATTTATTCTTCATATATA
*
25441716 TTTATTTA-TCTTCATATCTA
1 TTTATTTATTCTTCATATATA
25441736 TTTAT
1 TTTAT
25441741 ATTTATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATTTATTCTTCATATATA
Found at i:25458889 original size:26 final size:26
Alignment explanation
Indices: 25458860--25458933 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 26
25458850 TATCTGGGTG
25458860 CAATTCAGGACATGATCATGCAGTGA
1 CAATTCAGGACATGATCATGCAGTGA
*
25458886 CAATTCTA-GACATGTTCATGCAGTGA
1 CAATTC-AGGACATGATCATGCAGTGA
* **
25458912 CAATTCTGGACATTCTCATGCA
1 CAATTCAGGACATGATCATGCA
25458934 ACGACATTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 41 0.98
27 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (26 bp):
CAATTCAGGACATGATCATGCAGTGA
Found at i:25459998 original size:17 final size:18
Alignment explanation
Indices: 25459967--25460007 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
25459957 CTAAAATACC
*
25459967 ATGACAAATGGAAATGCA
1 ATGACAAATGCAAATGCA
25459985 ATGA-AAATGCAAATGCA
1 ATGACAAATGCAAATGCA
25460002 ATGACA
1 ATGACA
25460008 GTTAAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.51, C:0.12, G:0.20, T:0.17
Consensus pattern (18 bp):
ATGACAAATGCAAATGCA
Found at i:25466336 original size:21 final size:21
Alignment explanation
Indices: 25466270--25466337 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
25466260 CATTGAAGAT
* *
25466270 TGTTGTGGCTGCATCCGATTC
1 TGTTGTGGCTGCATCTGAGTC
* * *
25466291 TGGTATGGCTGCATCT-AGCTT
1 TGTTGTGGCTGCATCTGAG-TC
*
25466312 TGTTGTGGATGCATCTGAGTC
1 TGTTGTGGCTGCATCTGAGTC
25466333 TGTTG
1 TGTTG
25466338 ATTATAATTC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
20 1 0.03
21 33 0.92
22 2 0.06
ACGTcount: A:0.12, C:0.18, G:0.31, T:0.40
Consensus pattern (21 bp):
TGTTGTGGCTGCATCTGAGTC
Found at i:25478512 original size:42 final size:42
Alignment explanation
Indices: 25478455--25478602 Score: 219
Period size: 42 Copynumber: 3.5 Consensus size: 42
25478445 GAGCGTGATG
* *
25478455 ATAT-ATTTAAGGAAGACTGATGTCTCAAGATGAGAATGAGA
1 ATATGATTAAAGGAAGACTCATGTCTCAAGATGAGAATGAGA
* * *
25478496 ATATGATTAAAGGAAGACTCATGCCTTAGGATGAGAATGAG-
1 ATATGATTAAAGGAAGACTCATGTCTCAAGATGAGAATGAGA
*
25478537 ATAATGATGAAAGGAAGACTCATGTCTCAAGATGAGAATGAGA
1 AT-ATGATTAAAGGAAGACTCATGTCTCAAGATGAGAATGAGA
25478580 ATATGATTAAAGGAAGACTCATG
1 ATATGATTAAAGGAAGACTCATG
25478603 ACTCGGAATG
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
41 6 0.06
42 86 0.91
43 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.25, T:0.24
Consensus pattern (42 bp):
ATATGATTAAAGGAAGACTCATGTCTCAAGATGAGAATGAGA
Found at i:25478614 original size:42 final size:42
Alignment explanation
Indices: 25478424--25478658 Score: 194
Period size: 42 Copynumber: 5.6 Consensus size: 42
25478414 TTATATGAAT
* * ** *
25478424 GGAAGACTCGTGACTCGAAACGAGCGTGATG-ATAT-ATTTAA
1 GGAAGACTCATGACTCGAAATGAGAATGA-GAATATGATTAAA
* *
25478465 GGAAGACTGATGTCTC-AAGATGAGAATGAGAATATGATTAAA
1 GGAAGACTCATGACTCGAA-ATGAGAATGAGAATATGATTAAA
* * * *
25478507 GGAAGACTCATGCCT-TAGGATGAGAATGAG-ATAATGATGAAA
1 GGAAGACTCATGACTCGA-AATGAGAATGAGAAT-ATGATTAAA
*
25478549 GGAAGACTCATGTCTC-AAGATGAGAATGAGAATATGATTAAA
1 GGAAGACTCATGACTCGAA-ATGAGAATGAGAATATGATTAAA
* ** * * *
25478591 GGAAGACTCATGACTCGGAATGAGCGTGGGATTATGTTTAAAAA
1 GGAAGACTCATGACTCGAAATGAGAATGAGAATATGATT--AAA
*
25478635 GGAAGACTCATGACTCGGAATGAG
1 GGAAGACTCATGACTCGAAATGAG
25478659 CGTGGGATTA
Statistics
Matches: 161, Mismatches: 21, Indels: 21
0.79 0.10 0.10
Matches are distributed among these distances:
40 3 0.02
41 26 0.16
42 102 0.63
43 3 0.02
44 27 0.17
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.23
Consensus pattern (42 bp):
GGAAGACTCATGACTCGAAATGAGAATGAGAATATGATTAAA
Found at i:25478644 original size:44 final size:44
Alignment explanation
Indices: 25478588--25478696 Score: 200
Period size: 44 Copynumber: 2.5 Consensus size: 44
25478578 GAATATGATT
25478588 AAAGGAAGACTCATGACTCGGAATGAGCGTGGGATTATGTTTAA
1 AAAGGAAGACTCATGACTCGGAATGAGCGTGGGATTATGTTTAA
25478632 AAAGGAAGACTCATGACTCGGAATGAGCGTGGGATTATGTTTAA
1 AAAGGAAGACTCATGACTCGGAATGAGCGTGGGATTATGTTTAA
**
25478676 AAAGGAAGACTTTTGACTCGG
1 AAAGGAAGACTCATGACTCGG
25478697 TATAGCATAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (44 bp):
AAAGGAAGACTCATGACTCGGAATGAGCGTGGGATTATGTTTAA
Found at i:25481720 original size:43 final size:43
Alignment explanation
Indices: 25481659--25481740 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
25481649 GAATTAAGAT
*
25481659 TGATCCTAATAAAGTCAAGGCTATACAAGAGTTACCACCGTCG
1 TGATCCCAATAAAGTCAAGGCTATACAAGAGTTACCACCGTCG
25481702 TGATCCCAATAAAGTCAAGGCTATACAAGAGTTACCACC
1 TGATCCCAATAAAGTCAAGGCTATACAAGAGTTACCACC
25481741 ATTGTGTACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (43 bp):
TGATCCCAATAAAGTCAAGGCTATACAAGAGTTACCACCGTCG
Found at i:25485492 original size:15 final size:16
Alignment explanation
Indices: 25485467--25485505 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
25485457 CCTAGTTTCT
25485467 TTTTCTAATTAAA-TTA
1 TTTT-TAATTAAATTTA
25485483 TTTTTAATTAAATTTA
1 TTTTTAATTAAATTTA
25485499 TTTTTAA
1 TTTTTAA
25485506 GCTTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAATTAAATTTA
Found at i:25496228 original size:17 final size:17
Alignment explanation
Indices: 25496206--25496243 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
25496196 TTTTATCTAG
25496206 TTGTCA-TTACATTTTAA
1 TTGTCACTT-CATTTTAA
*
25496223 TTGTCACTTCATTTTAC
1 TTGTCACTTCATTTTAA
25496240 TTGT
1 TTGT
25496244 TCTCACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (17 bp):
TTGTCACTTCATTTTAA
Found at i:25498414 original size:23 final size:24
Alignment explanation
Indices: 25498387--25498435 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
25498377 AACAACAATT
* *
25498387 CATTTTCTATTA-ATTTGCTTTGA
1 CATTTTATATTATATTTGCATTGA
*
25498410 CATTTTATGTTATATTTGCATTGA
1 CATTTTATATTATATTTGCATTGA
25498434 CA
1 CA
25498436 GATTTAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (24 bp):
CATTTTATATTATATTTGCATTGA
Found at i:25517746 original size:22 final size:24
Alignment explanation
Indices: 25517721--25517765 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
25517711 CAATCGAGTA
*
25517721 CCCAAAGCTTC-ATGT-AATTTCT
1 CCCAAAACTTCAATGTAAATTTCT
25517743 CCCAAAACTTCAATGTAAATTTC
1 CCCAAAACTTCAATGTAAATTTC
25517766 GGATCCCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (24 bp):
CCCAAAACTTCAATGTAAATTTCT
Found at i:25522569 original size:22 final size:22
Alignment explanation
Indices: 25522542--25522604 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
25522532 CTAATGGACG
*
25522542 GAGAGCACTTAA-GTGCTATAC
1 GAGAGCACTTAATGTGCTAAAC
*
25522563 AGAGAGCA-TGAATGTGCTAAAC
1 -GAGAGCACTTAATGTGCTAAAC
25522585 GAAGAGCAC-TAATGTGCTAA
1 G-AGAGCACTTAATGTGCTAA
25522605 TAAATGGAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (22 bp):
GAGAGCACTTAATGTGCTAAAC
Found at i:25524018 original size:48 final size:51
Alignment explanation
Indices: 25523961--25524058 Score: 139
Period size: 48 Copynumber: 2.0 Consensus size: 51
25523951 AACATTTATA
* *
25523961 AAATTTAATTTAATAATTATC-TTA-AT-AGTATTTTATTAATTTAATATT
1 AAATTTAATTTAATAATTATCTTTAGATAAATATTCTATTAATTTAATATT
*
25524009 AAATTTAATTTAATATTTATCTTTTAGATAAATATTCTATTAATTTAATA
1 AAATTTAATTTAATAATTATC-TTTAGATAAATATTCTATTAATTTAATA
25524059 AGATTTAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 20 0.47
50 3 0.07
51 2 0.05
52 18 0.42
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (51 bp):
AAATTTAATTTAATAATTATCTTTAGATAAATATTCTATTAATTTAATATT
Found at i:25525005 original size:278 final size:278
Alignment explanation
Indices: 25524506--25525063 Score: 1026
Period size: 278 Copynumber: 2.0 Consensus size: 278
25524496 TAACACACCT
* * *
25524506 AGGACACACGCCCGTGTGTAGGCCGTGTGTGCTTAAAATGCCTAGAACTCAACTCAACCATCACA
1 AGGACACACGCCCGTGTGCAGGCCGTGTATGCCTAAAATGCCTAGAACTCAACTCAACCATCACA
* *
25524571 TATTTGACTAGGTATCTAAACTAATTCATACCTCAATGTTACCATGAATTAAAACACACCTAAGA
66 TATTTGACTAGGTATCTAAACCAATTCATACCTCAATGTTACCATGAATTAAAACACACCTAAAA
*
25524636 ACATCTAAAACATAATTCAATTATCCATTCAAGGCTACATACGATCACCTACGTATTGTCACATT
131 ACATCTAAAACATAATTCAATTATCCATTCAAGGCTACATACGATCACCTACGTATAGTCACATT
25524701 TCAAATAGCATATGAACATACCAAATCAACCAAGATTTACCCATTTCAATTTAACATATCTACAA
196 TCAAATAGCATATGAACATACCAAATCAACCAAGATTTACCCATTTCAATTTAACATATCTACAA
25524766 TTTCAAAAGATCATTTCA
261 TTTCAAAAGATCATTTCA
25524784 AGGACACACGCCCGTGTGCAGGCCGTGTATGCCTAAAATGCCTAGAACTCAACTCAACCATCACA
1 AGGACACACGCCCGTGTGCAGGCCGTGTATGCCTAAAATGCCTAGAACTCAACTCAACCATCACA
25524849 TATTTGACTAGGTATCTAAACCAATTCATACCTCAATGTTACCATGAATTAAAACACACCTAAAA
66 TATTTGACTAGGTATCTAAACCAATTCATACCTCAATGTTACCATGAATTAAAACACACCTAAAA
* *
25524914 AGATCTAAAACATAATTCAATTATCCATTCAAGGCTACATACGATCACTTACGTATAGTCACATT
131 ACATCTAAAACATAATTCAATTATCCATTCAAGGCTACATACGATCACCTACGTATAGTCACATT
*
25524979 TCAAATAGCATATGAACATTCCAAATCAACCAAGATTTACCCATTTCAATTTAACATATCTACAA
196 TCAAATAGCATATGAACATACCAAATCAACCAAGATTTACCCATTTCAATTTAACATATCTACAA
*
25525044 TTTTAAAAGATCATTTCA
261 TTTCAAAAGATCATTTCA
25525062 AG
1 AG
25525064 ACATCAACAC
Statistics
Matches: 270, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
278 270 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (278 bp):
AGGACACACGCCCGTGTGCAGGCCGTGTATGCCTAAAATGCCTAGAACTCAACTCAACCATCACA
TATTTGACTAGGTATCTAAACCAATTCATACCTCAATGTTACCATGAATTAAAACACACCTAAAA
ACATCTAAAACATAATTCAATTATCCATTCAAGGCTACATACGATCACCTACGTATAGTCACATT
TCAAATAGCATATGAACATACCAAATCAACCAAGATTTACCCATTTCAATTTAACATATCTACAA
TTTCAAAAGATCATTTCA
Found at i:25525637 original size:19 final size:15
Alignment explanation
Indices: 25525595--25525625 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
25525585 AATATTTCCT
25525595 TATTTCACTCTTAAG
1 TATTTCACTCTTAAG
25525610 TATTTCACTCTTAAG
1 TATTTCACTCTTAAG
25525625 T
1 T
25525626 GATTCATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (15 bp):
TATTTCACTCTTAAG
Found at i:25526961 original size:24 final size:25
Alignment explanation
Indices: 25526913--25526958 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
25526903 AGTTGTAAAG
25526913 AGAAAATTCTCTAAGAGATTATTTC
1 AGAAAATTCTCTAAGAGATTATTTC
25526938 AGAAAATT-TCT-AGAGA-TATTT
1 AGAAAATTCTCTAAGAGATTATTT
25526959 TTCTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 5 0.24
24 3 0.14
25 8 0.38
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (25 bp):
AGAAAATTCTCTAAGAGATTATTTC
Found at i:25530266 original size:27 final size:27
Alignment explanation
Indices: 25530236--25530289 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
25530226 ATAACTTTGG
25530236 GTTCTACCAATACAACCCAAACTTCAA
1 GTTCTACCAATACAACCCAAACTTCAA
*
25530263 GTTCTACCAGTACAACCCAAACTTCAA
1 GTTCTACCAATACAACCCAAACTTCAA
25530290 TCGATAGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.22
Consensus pattern (27 bp):
GTTCTACCAATACAACCCAAACTTCAA
Found at i:25532641 original size:102 final size:102
Alignment explanation
Indices: 25532352--25533139 Score: 853
Period size: 102 Copynumber: 7.7 Consensus size: 102
25532342 ACGACAACTA
* * * * * *
25532352 CTATATCCTTGAAGTTGTAATGGATCGGATTAAAACTAACAATAGTGA-ATCTCAATCTCCCTAA
1 CTATATCCCTGAAGTTCTAGTGGATC-GATTAAAACTAACAGTAGCGAGATCTCAATCTCCCTGA
*
25532416 AGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATC
65 AGTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATC
* * * * ** * *
25532454 TTATAACCCTGAA-TTGC-AATGTATCGGATTAAAACTAATTGTAG-TAGATCTCAATCTCCTTG
1 CTATATCCCTGAAGTT-CTAGTGGATC-GATTAAAACTAACAGTAGCGAGATCTCAATCTCCCTG
*
25532516 AAGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATC
64 AAGTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATC
* * * *
25532555 CTATATCCTTGAAGTTCTAGTGGATCAGATTAAAACTAATACTAGCGA-ATCTGAATCTCCCTGA
1 CTATATCCCTGAAGTTCTAGTGGATC-GATTAAAACTAACAGTAGCGAGATCTCAATCTCCCTGA
* * * *
25532619 AGTTGTAGTGGAATGAAATGAAGTTACAACACCAAATT
65 AGTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATC
* * * * * * *
25532657 CTATATCCTTGAATTTTTAGTGGATCGAACTAAACCTAACAGTA-CCAGATCTCAATCTCCCAGA
1 CTATATCCCTGAAGTTCTAGTGGATCG-ATTAAAACTAACAGTAGCGAGATCTCAATCTCCCTGA
*
25532721 AGTTGCAATGGAATGGAGTGAAGTTACAACACCAAATC
65 AGTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATC
* * * *
25532759 CCATATCCCTGAAGTTAC-AATGGATCGAATTAAAACTAATAGTAG-TAGATCTCAATCTCCCTG
1 CTATATCCCTGAAGTT-CTAGTGGATCG-ATTAAAACTAACAGTAGCGAGATCTCAATCTCCCTG
* * * *
25532822 AAGTTGCAATCGAATGGAGTGAAGTTAAAACACCAAATT
64 AAGTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATC
* *
25532861 CTATATCCCTGAAGTTACT-GTGGATTGAATTAAAACTAACAGTAGC-AGATCTCAATCTCCTTG
1 CTATATCCCTGAAGTT-CTAGTGGATCG-ATTAAAACTAACAGTAGCGAGATCTCAATCTCCCTG
* * * *
25532924 AAGTTGTAGTGGAATGGAGTGAAGCTACATCACAAAATC
64 AAGTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATC
* * * *
25532963 CTATATCCCAGAAGTTGTAGTGGATCAGATTAAAACTAATAGTAACG-GATCTCAATCTCCCTGA
1 CTATATCCCTGAAGTTCTAGTGGATC-GATTAAAACTAACAGTAGCGAGATCTCAATCTCCCTGA
* *
25533027 AGTTGTAGTGAAATGGAGTGAAGTTACAACACCAAATC
65 AGTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATC
* * * ** * * *
25533065 CTATATCCCTTATGTTGTAGTATATCGATTAAAACTAACAATAG-TAGATCTCAATCTCCCTAAA
1 CTATATCCCTGAAGTTCTAGTGGATCGATTAAAACTAACAGTAGCGAGATCTCAATCTCCCTGAA
*
25533129 GTTGTAGTGGA
66 GTTGCAGTGGA
25533140 TCGAATTAAA
Statistics
Matches: 583, Mismatches: 88, Indels: 31
0.83 0.13 0.04
Matches are distributed among these distances:
100 1 0.00
101 134 0.23
102 446 0.77
103 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (102 bp):
CTATATCCCTGAAGTTCTAGTGGATCGATTAAAACTAACAGTAGCGAGATCTCAATCTCCCTGAA
GTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATC
Found at i:25532920 original size:306 final size:305
Alignment explanation
Indices: 25532352--25533132 Score: 955
Period size: 306 Copynumber: 2.6 Consensus size: 305
25532342 ACGACAACTA
** * * * * **
25532352 CTATATCCTTGAAGTTGTAATGGATCGGATTAAAACTAACAAT-AGTGAATCTCAATCTCCCTA-
1 CTATATCCCAGAAGTTGTAGTGGATCAGACTAAAACTAACAGTAACAG-ATCTCAATCTCCC-AG
* * *
25532415 AAGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCTTATAACCCTGAA-TTGCAATGTATC
64 AAGTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGCAATGTATC
* * * * * *
25532479 GGATTAAAACTAATTGTAGTAGATCTCAATCTCCTTGAAGTTACAGTGGAATGGAGTGAAGTTAC
129 -GATTAAAACTAATAGTAGTAGATCTCAATCTCCCTGAAGTTGCAATCGAATGGAGTGAAGTTAA
* * *
25532544 AACACCAAATCCTATATCCTTGAAGTTCTAGTGGATCAGATTAAAACTAATACTAGCGAATCTGA
193 AACACCAAATCCTATATCCCTGAAGTTCTAGTGGATCAGATTAAAACTAACACTAGCGAATCTCA
* * *
25532609 ATCTCCCTGAAGTTGTAGTGGAATGAAATGAAGTTACAACACCAAATT
258 ATCTCCCTGAAGTTGTAGTGGAATGAAATGAAGCTACAACACAAAATC
** * * * *
25532657 CTATATCCTTGAATTTTTAGTGGATC-GAACTAAACCTAACAGTACCAGATCTCAATCTCCCAGA
1 CTATATCCCAGAAGTTGTAGTGGATCAG-ACTAAAACTAACAGTAACAGATCTCAATCTCCCAGA
* * * *
25532721 AGTTGCAATGGAATGGAGTGAAGTTACAACACCAAATCCCATATCCCTGAAGTTACAATGGATCG
65 AGTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGCAATGTATCG
25532786 AATTAAAACTAATAGTAGTAGATCTCAATCTCCCTGAAGTTGCAATCGAATGGAGTGAAGTTAAA
130 -ATTAAAACTAATAGTAGTAGATCTCAATCTCCCTGAAGTTGCAATCGAATGGAGTGAAGTTAAA
* * *
25532851 ACACCAAATTCTATATCCCTGAAGTTACT-GTGGAT-TGAATTAAAACTAACAGTAGC-AGATCT
194 ACACCAAATCCTATATCCCTGAAGTT-CTAGTGGATCAG-ATTAAAACTAACACTAGCGA-ATCT
* * * *
25532913 CAATCTCCTTGAAGTTGTAGTGGAATGGAGTGAAGCTACATCACAAAATC
256 CAATCTCCCTGAAGTTGTAGTGGAATGAAATGAAGCTACAACACAAAATC
* * * *
25532963 CTATATCCCAGAAGTTGTAGTGGATCAGATTAAAACTAATAGTAACGGATCTCAATCTCCCTGAA
1 CTATATCCCAGAAGTTGTAGTGGATCAGACTAAAACTAACAGTAACAGATCTCAATCTCCCAGAA
* * * * * * *
25533028 GTTGTAGTGAAATGGAGTGAAGTTACAACACCAAATCCTATATCCCTTATGTTGTAGTATATCGA
66 GTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGCAATGTATCGA
* * *
25533093 TTAAAACTAACAATAGTAGATCTCAATCTCCCTAAAGTTG
131 TTAAAACTAATAGTAGTAGATCTCAATCTCCCTGAAGTTG
25533133 TAGTGGATCG
Statistics
Matches: 408, Mismatches: 59, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
304 2 0.00
305 136 0.33
306 267 0.65
307 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (305 bp):
CTATATCCCAGAAGTTGTAGTGGATCAGACTAAAACTAACAGTAACAGATCTCAATCTCCCAGAA
GTTGCAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATATCCCTGAAGTTGCAATGTATCGA
TTAAAACTAATAGTAGTAGATCTCAATCTCCCTGAAGTTGCAATCGAATGGAGTGAAGTTAAAAC
ACCAAATCCTATATCCCTGAAGTTCTAGTGGATCAGATTAAAACTAACACTAGCGAATCTCAATC
TCCCTGAAGTTGTAGTGGAATGAAATGAAGCTACAACACAAAATC
Found at i:25533166 original size:52 final size:52
Alignment explanation
Indices: 25532880--25533183 Score: 189
Period size: 52 Copynumber: 5.9 Consensus size: 52
25532870 TGAAGTTACT
* * *
25532880 GTGGATTGAATTAAAACTAACAGTAGCAGATCTCAATCTCCTTGAAGTTGTA
1 GTGGATCGAATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAGTTGTA
* * * * * * *
25532932 GTGGAAT-GGAGTGAAGCT-ACA-TCA-CAAAATC-CTATATCCC-AGAAGTTGTA
1 GTGG-ATCGAATTAAAACTAACAGT-AGC-AGATCTCAATCTCCCTA-AAGTTGTA
* * * *
25532982 GTGGATC-AGATTAAAACTAATAGTAACGGATCTCAATCTCCCTGAAGTTGTA
1 GTGGATCGA-ATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAGTTGTA
* * * * * * ** * * * * * *
25533034 GTGAAAT-GGAGT-GAAGTTACAACACCAAATC-CTATATCCCTTATGTTGTA
1 GTG-GATCGAATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAGTTGTA
** * *
25533084 GTATATCG-ATTAAAACTAACAATAGTAGATCTCAATCTCCCTAAAGTTGTA
1 GTGGATCGAATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAGTTGTA
25533135 GTGGATCGAATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAGTT
1 GTGGATCGAATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAGTT
25533184 ACAGTGGAAT
Statistics
Matches: 182, Mismatches: 53, Indels: 34
0.68 0.20 0.13
Matches are distributed among these distances:
49 6 0.03
50 56 0.31
51 45 0.25
52 71 0.39
53 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
GTGGATCGAATTAAAACTAACAGTAGCAGATCTCAATCTCCCTAAAGTTGTA
Found at i:25534644 original size:15 final size:15
Alignment explanation
Indices: 25534626--25534655 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25534616 TATAGTTGTT
*
25534626 TATATTAATAATTTC
1 TATAATAATAATTTC
25534641 TATAATAATAATTTC
1 TATAATAATAATTTC
25534656 GAAAACTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATAATAATTTC
Found at i:25537266 original size:18 final size:18
Alignment explanation
Indices: 25537245--25537279 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25537235 AATTAAAAAC
*
25537245 AAATAAAGCAAGAAAAGT
1 AAATAAAGAAAGAAAAGT
*
25537263 AAATATAGAAAGAAAAG
1 AAATAAAGAAAGAAAAG
25537280 GAGTTTGAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.17, T:0.11
Consensus pattern (18 bp):
AAATAAAGAAAGAAAAGT
Found at i:25543687 original size:16 final size:16
Alignment explanation
Indices: 25543666--25543701 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
25543656 AAATAATCCC
*
25543666 AAAATTACAAGTCTCA
1 AAAATTAAAAGTCTCA
25543682 AAAATTAAAAGTCTCA
1 AAAATTAAAAGTCTCA
25543698 AAAA
1 AAAA
25543702 CTCTTTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (16 bp):
AAAATTAAAAGTCTCA
Found at i:25565272 original size:95 final size:95
Alignment explanation
Indices: 25565156--25565342 Score: 356
Period size: 95 Copynumber: 2.0 Consensus size: 95
25565146 CAGCACTCAA
* *
25565156 CACTCAATACTCAACACATTTGATTTACTTTCAGTACATTGAAATTTAGCACCTGACATTTAATT
1 CACTCAACACTCAACACATTTGATTTACTTTCAGTACATTGAAATTTAACACCTGACATTTAATT
25565221 CTAATTGTGTGCAAATCTGACATATTGTAG
66 CTAATTGTGTGCAAATCTGACATATTGTAG
25565251 CACTCAACACTCAACACATTTGATTTACTTTCAGTACATTGAAATTTAACACCTGACATTTAATT
1 CACTCAACACTCAACACATTTGATTTACTTTCAGTACATTGAAATTTAACACCTGACATTTAATT
25565316 CTAATTGTGTGCAAATCTGACATATTG
66 CTAATTGTGTGCAAATCTGACATATTG
25565343 CACTGACGTC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (95 bp):
CACTCAACACTCAACACATTTGATTTACTTTCAGTACATTGAAATTTAACACCTGACATTTAATT
CTAATTGTGTGCAAATCTGACATATTGTAG
Found at i:25569853 original size:25 final size:25
Alignment explanation
Indices: 25569825--25569877 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
25569815 TCTTTTCGTT
*
25569825 GACACACATGAAAGCACGATTTGTC
1 GACACACATGAAAGCACAATTTGTC
25569850 GACACACATGAAAGCACAATTTGTC
1 GACACACATGAAAGCACAATTTGTC
25569875 GAC
1 GAC
25569878 GCATCCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (25 bp):
GACACACATGAAAGCACAATTTGTC
Found at i:25571361 original size:15 final size:16
Alignment explanation
Indices: 25571336--25571365 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
25571326 ACAGGTGTTG
25571336 AAGAGGAAGAAGAGAT
1 AAGAGGAAGAAGAGAT
25571352 AAGA-GAAGAAGAGA
1 AAGAGGAAGAAGAGA
25571366 GGAAAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (16 bp):
AAGAGGAAGAAGAGAT
Found at i:25587472 original size:18 final size:18
Alignment explanation
Indices: 25587451--25587489 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25587441 TGGCTATTTA
*
25587451 TGAGCATGTGACTGCATC
1 TGAGCATATGACTGCATC
*
25587469 TGAGTATATGACTGCATC
1 TGAGCATATGACTGCATC
25587487 TGA
1 TGA
25587490 TCGTGATGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (18 bp):
TGAGCATATGACTGCATC
Found at i:25604911 original size:3 final size:3
Alignment explanation
Indices: 25604903--25604958 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
25604893 GAAAAAGCAA
* *
25604903 AAG AAG AAG GAG AA- AGAG AAG AAG AAG AAA AAG AAG -AG AAG AAAG
1 AAG AAG AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG -AAG
25604948 AAG AAG AAG AA
1 AAG AAG AAG AA
25604959 ATTGCCTCGA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 3 0.07
3 38 0.84
4 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:25604924 original size:15 final size:15
Alignment explanation
Indices: 25604904--25604958 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
25604894 AAAAAGCAAA
*
25604904 AGAAGAAGGAGAAAG
1 AGAAGAAGAAGAAAG
*
25604919 AGAAGAAGAAGAAAA
1 AGAAGAAGAAGAAAG
25604934 AGAAG-AGAAGAAAG
1 AGAAGAAGAAGAAAG
25604948 AAGAAGAAGAA
1 -AGAAGAAGAA
25604959 ATTGCCTCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
14 8 0.23
15 23 0.66
16 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAGAAAG
Found at i:25604949 original size:27 final size:27
Alignment explanation
Indices: 25604906--25604959 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
25604896 AAAGCAAAAG
*
25604906 AAGAAGGAGAAAGAGAAGAAGAAGAAA
1 AAGAAGGAGAAAAAGAAGAAGAAGAAA
25604933 AAGAA-GAGAAGAAAGAAGAAGAAGAAA
1 AAGAAGGAGAA-AAAGAAGAAGAAGAAA
25604960 TTGCCTCGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (27 bp):
AAGAAGGAGAAAAAGAAGAAGAAGAAA
Found at i:25605362 original size:17 final size:16
Alignment explanation
Indices: 25605339--25605375 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
25605329 CATGCATTTT
*
25605339 ATTTTTTTGTCATTGC
1 ATTTTTTTGTCACTGC
*
25605355 ATTTTTTTGTCCCTGC
1 ATTTTTTTGTCACTGC
25605371 ATTTT
1 ATTTT
25605376 ATTTTTTTTC
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:0.11, C:0.16, G:0.11, T:0.62
Consensus pattern (16 bp):
ATTTTTTTGTCACTGC
Found at i:25613397 original size:17 final size:18
Alignment explanation
Indices: 25613375--25613415 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
25613365 TTAGTTTTCA
25613375 TGCATTCTT-ATTGT-GCT
1 TGCATTCTTAATTGTCG-T
25613392 TGCATT-TTAATTGTCGT
1 TGCATTCTTAATTGTCGT
25613409 TGCATTC
1 TGCATTC
25613416 ATTTTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.10
17 18 0.86
18 1 0.05
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (18 bp):
TGCATTCTTAATTGTCGT
Found at i:25613577 original size:162 final size:161
Alignment explanation
Indices: 25613297--25613619 Score: 592
Period size: 162 Copynumber: 2.0 Consensus size: 161
25613287 ACCCGAAAAA
* *
25613297 GATGAAAAAGAAAACCAAAGCAACCTCTGCATCGACTGCTGCTGAATAATTTGGTACATTTTTTT
1 GATGAAAAAGAAAACCAAAGCAACCTCTGCATCGACTGCTGCTAAATAATTTGGTACATTGTTTT
25613362 TAGTTAGTTTTCATGCATTCTTATTGTGCTTGCATTTTAATTGTCGTTGCATTCATTTTAGTTTA
66 TAGTTAGTTTTCATGCATTCTTATTGTGCTTGCATTTTAATTGTCGTTGCATTCATTTTAGTTTA
25613427 GTACATTATAGCTGCATTTCCATTATATATG
131 GTACATTATAGCTGCATTTCCATTATATATG
*
25613458 GATGAAAAAGAAAACCAAAGCAACCTCTGCATCGGCTGCTGCTAAATAATTTGGTACATCTGTTT
1 GATGAAAAAGAAAACCAAAGCAACCTCTGCATCGACTGCTGCTAAATAATTTGGTACAT-TGTTT
*
25613523 TTAGTTAGTTTTCATGCATTCTTGTTGTGCTTGCATTTTAATTGTCGTTGCATTCATTTTAGTTT
65 TTAGTTAGTTTTCATGCATTCTTATTGTGCTTGCATTTTAATTGTCGTTGCATTCATTTTAGTTT
*
25613588 AGTACGTTATAGCTGCATTTCCATTATATATG
130 AGTACATTATAGCTGCATTTCCATTATATATG
25613620 TATATTGTCA
Statistics
Matches: 156, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
161 57 0.37
162 99 0.63
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (161 bp):
GATGAAAAAGAAAACCAAAGCAACCTCTGCATCGACTGCTGCTAAATAATTTGGTACATTGTTTT
TAGTTAGTTTTCATGCATTCTTATTGTGCTTGCATTTTAATTGTCGTTGCATTCATTTTAGTTTA
GTACATTATAGCTGCATTTCCATTATATATG
Found at i:25616167 original size:305 final size:306
Alignment explanation
Indices: 25615615--25616195 Score: 1110
Period size: 305 Copynumber: 1.9 Consensus size: 306
25615605 AGTTGCTATT
*
25615615 TTTAAGATTTAAAGCATGATGTTAGCATTATTGAAGTTGCTATTTTTACTATTCGTGCCTATAAA
1 TTTAAGATTTAAAGCATGATGTTAGCATTATTGAAGTTGCTATTTTTACTATTCGTGCCTAAAAA
25615680 TTGTCGGCGCAATACTTCAGCATATTATTATAATTTATACATTAGAATTTCAGAGAATATAAGTT
66 TTGTCGGCGCAATACTTCAGCATATTATTATAATTTATACATTAGAATTTCAGAGAATATAAGTT
*
25615745 ACTAGAATGATGAATATGGTGACGAAAATTTAGATATAATTTTGCTAGCTTTTATTTACTTGAGG
131 ACTAGAATGATGAATATGGTGACGAAAATTTAGATATAATTTTGCTAACTTTTATTTACTTGAGG
*
25615810 ACAAGTAAAAACTCAAGTTTGGGGGTGTGATAGCATTAGAAATGACACTCAATTTCTCCTTAAAT
196 ACAAGTAAAAACTCAAGTTTGGGGGTGTGATAGCATTAGAAATGACACTCAATTTCTCCCTAAAT
25615875 TAATGTGTAAATTGTTATACAATAAATGCTGTGTTGGTTAAGAAAA
261 TAATGTGTAAATTGTTATACAATAAATGCTGTGTTGGTTAAGAAAA
25615921 TTTAAGATTTAAAGCATGATGTTAGCATTATTGAAGTTGCTA-TTTTACTATTCGTGCCTAAAAA
1 TTTAAGATTTAAAGCATGATGTTAGCATTATTGAAGTTGCTATTTTTACTATTCGTGCCTAAAAA
25615985 TTGTCGGCGCAATACTTCAGCATATTATTATAATTTATACATTAGAATTTCAGAGAATATAAGTT
66 TTGTCGGCGCAATACTTCAGCATATTATTATAATTTATACATTAGAATTTCAGAGAATATAAGTT
* *
25616050 GCTAGAATGATGAATGTGGTGACGAAAATTTAGATATAATTTTGCTAACTTTTATTTACTTGAGG
131 ACTAGAATGATGAATATGGTGACGAAAATTTAGATATAATTTTGCTAACTTTTATTTACTTGAGG
25616115 ACAAGTAAAAACTCAAGTTTGGGGGTGTGATAGCATTAGAAATGACACTCAATTTCTCCCTAAAT
196 ACAAGTAAAAACTCAAGTTTGGGGGTGTGATAGCATTAGAAATGACACTCAATTTCTCCCTAAAT
25616180 TAATGTGTAAATTGTT
261 TAATGTGTAAATTGTT
25616196 CCTTTCATAC
Statistics
Matches: 270, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
305 228 0.84
306 42 0.16
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (306 bp):
TTTAAGATTTAAAGCATGATGTTAGCATTATTGAAGTTGCTATTTTTACTATTCGTGCCTAAAAA
TTGTCGGCGCAATACTTCAGCATATTATTATAATTTATACATTAGAATTTCAGAGAATATAAGTT
ACTAGAATGATGAATATGGTGACGAAAATTTAGATATAATTTTGCTAACTTTTATTTACTTGAGG
ACAAGTAAAAACTCAAGTTTGGGGGTGTGATAGCATTAGAAATGACACTCAATTTCTCCCTAAAT
TAATGTGTAAATTGTTATACAATAAATGCTGTGTTGGTTAAGAAAA
Found at i:25617454 original size:25 final size:24
Alignment explanation
Indices: 25617401--25617457 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
25617391 ACAATTCATT
*
25617401 CATTTTGTATTACAGTTGCACTGA
1 CATTTTTTATTACAGTTGCACTGA
25617425 CATTTTTTATTAC-GTTTGCACTGA
1 CATTTTTTATTACAG-TTGCACTGA
*
25617449 CAATTTTTA
1 CATTTTTTA
25617458 CTCTTAACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (24 bp):
CATTTTTTATTACAGTTGCACTGA
Found at i:25624660 original size:12 final size:13
Alignment explanation
Indices: 25624643--25624671 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25624633 GCATAAAAGA
25624643 AAATAAATAAAT-
1 AAATAAATAAATC
25624655 AAATAAATAAATC
1 AAATAAATAAATC
25624668 AAAT
1 AAAT
25624672 GAAAGAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAATAAATC
Found at i:25627568 original size:16 final size:16
Alignment explanation
Indices: 25627546--25627582 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
25627536 AATAAAGAAC
*
25627546 GAAAAAAATTTGG-AA
1 GAAAAAAACTTGGCAA
25627561 GAAAAAAACTTGGCAA
1 GAAAAAAACTTGGCAA
25627577 GAAAAA
1 GAAAAA
25627583 TTTGAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.62, C:0.05, G:0.19, T:0.14
Consensus pattern (16 bp):
GAAAAAAACTTGGCAA
Found at i:25639535 original size:15 final size:16
Alignment explanation
Indices: 25639502--25639544 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
25639492 GTCCAGCTAG
25639502 AATTGAAATAAATTTTT
1 AATT-AAATAAATTTTT
25639519 AATTAAATAAA-TTTT
1 AATTAAATAAATTTTT
*
25639534 AATTAATTAAA
1 AATTAAATAAA
25639545 ACTTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 7 0.28
17 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
AATTAAATAAATTTTT
Found at i:25640774 original size:31 final size:31
Alignment explanation
Indices: 25640733--25640799 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
25640723 AAAGTTGCTA
*
25640733 TTTAGGCACTATC-GTTATATACATTTATCAT
1 TTTAGACACTATCGGTT-TATACATTTATCAT
**
25640764 TTTAGACACTATCGGTTTATATTTTTATCAT
1 TTTAGACACTATCGGTTTATACATTTATCAT
25640795 TTTAG
1 TTTAG
25640800 TTATTCACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.49
Consensus pattern (31 bp):
TTTAGACACTATCGGTTTATACATTTATCAT
Found at i:25641797 original size:21 final size:21
Alignment explanation
Indices: 25641769--25641814 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
25641759 TTCTAGGAAT
25641769 AGTG-GGGTCAAGTCATGAAC
1 AGTGAGGGTCAAGTCATGAAC
* *
25641789 AGTGAGGGTCATGTCATGAAT
1 AGTGAGGGTCAAGTCATGAAC
25641810 AGTGA
1 AGTGA
25641815 TAGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.24
Consensus pattern (21 bp):
AGTGAGGGTCAAGTCATGAAC
Found at i:25664022 original size:16 final size:16
Alignment explanation
Indices: 25664001--25664031 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25663991 ATAATGTGAA
25664001 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
25664017 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
25664032 GTATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:25664883 original size:26 final size:26
Alignment explanation
Indices: 25664832--25664884 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
25664822 AATTTTGGGC
*
25664832 ACAATTCTGGACACGTTCATGCAGCG
1 ACAATTCTGGACACGTTCAAGCAGCG
* *
25664858 ACAATTCTGGACATGTTCAAGTAGCG
1 ACAATTCTGGACACGTTCAAGCAGCG
25664884 A
1 A
25664885 TATTCTTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (26 bp):
ACAATTCTGGACACGTTCAAGCAGCG
Found at i:25664921 original size:37 final size:38
Alignment explanation
Indices: 25664880--25664973 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 38
25664870 ATGTTCAAGT
25664880 AGCGATATTCTTGGGTGCAA-TTGAAGAAT-TCTTATGC
1 AGCGATATTCTTGGGTGCAATTTGAAGAATAT-TTATGC
* * *
25664917 AGCGATAGTTC-TAGATGCAATTTGAAGAATATTTATGT
1 AGCGATA-TTCTTGGGTGCAATTTGAAGAATATTTATGC
* *
25664955 AGCGACAGTCTTGGGTGCA
1 AGCGATATTCTTGGGTGCA
25664974 TTCCTAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
37 16 0.35
38 29 0.63
39 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (38 bp):
AGCGATATTCTTGGGTGCAATTTGAAGAATATTTATGC
Found at i:25666473 original size:37 final size:36
Alignment explanation
Indices: 25666431--25666540 Score: 100
Period size: 37 Copynumber: 2.9 Consensus size: 36
25666421 ATGATAAAAA
25666431 TTAAATTAAATTAAATATTAAAATAATCAT-TTTAATT
1 TTAAATTAAATTAAATATTAAAATAAT-ATATTTAA-T
* *
25666468 TTAAATGAATAAAAT-ACTATTAAAATAA-ATATTTAAT
1 TTAAAT---TAAATTAAATATTAAAATAATATATTTAAT
*
25666505 TTAATTTAATATTAAACTATTAAAATAATATTATTT
1 TTAAATTAA-ATTAAA-TATTAAAATAATA-TATTT
25666541 TTGGAATAGT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
34 3 0.05
35 2 0.03
36 1 0.02
37 25 0.42
38 6 0.10
39 17 0.29
40 5 0.08
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.45
Consensus pattern (36 bp):
TTAAATTAAATTAAATATTAAAATAATATATTTAAT
Found at i:25666490 original size:39 final size:38
Alignment explanation
Indices: 25666446--25666540 Score: 106
Period size: 37 Copynumber: 2.5 Consensus size: 38
25666436 TTAAATTAAA
25666446 TATTAAAATAATCAT-TTTAATTTTAAATGAATA-AAATAC
1 TATTAAAATAAT-ATATTTAA-TTTAAATGAATATAAA-AC
* * *
25666485 TATTAAAATAA-ATATTTAATTTAATTTAATATTAAAC
1 TATTAAAATAATATATTTAATTTAAATGAATATAAAAC
25666522 TATTAAAATAATATTATTT
1 TATTAAAATAATA-TATTT
25666541 TTGGAATAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
37 25 0.51
38 8 0.16
39 16 0.33
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (38 bp):
TATTAAAATAATATATTTAATTTAAATGAATATAAAAC
Found at i:25675468 original size:20 final size:21
Alignment explanation
Indices: 25675429--25675468 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25675419 AGTATTTGGA
* *
25675429 AGTGTTCATGGATGACTTTTC
1 AGTGTTCAAGGATCACTTTTC
25675450 AGTGTTCAAGGA-CACTTTT
1 AGTGTTCAAGGATCACTTTT
25675469 GATGATTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (21 bp):
AGTGTTCAAGGATCACTTTTC
Found at i:25676837 original size:44 final size:44
Alignment explanation
Indices: 25676774--25676862 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
25676764 TGGTCGACTA
* * *
25676774 CGTATTGAAATGGATTGAGGTCGAGG-CGTATCCGACAAATGATG
1 CGTATCGAAATAGATTGAGGTCGAGGTAG-ATCCGACAAATGATG
*
25676818 CGTATCGAAATAGATTGAGGTCGAGGTAGATCCGATAAATGATG
1 CGTATCGAAATAGATTGAGGTCGAGGTAGATCCGACAAATGATG
25676862 C
1 C
25676863 CAAGGTAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.25
Consensus pattern (44 bp):
CGTATCGAAATAGATTGAGGTCGAGGTAGATCCGACAAATGATG
Found at i:25683265 original size:126 final size:126
Alignment explanation
Indices: 25683040--25683271 Score: 392
Period size: 126 Copynumber: 1.8 Consensus size: 126
25683030 TTATTAAGAC
*
25683040 AGTGTTAAGGCCAGTGTGAACTTAATGAATAGCTAGGATACAAATGAAATGTCATTAGGGTTTCT
1 AGTGTTAAGGCCAGTGTGAACTTAATGAATAGCTAGGATACAAATGAAATGTCATTAGGGTTTAT
* ** **
25683105 ATTCAGCAGGTGCTTTGTATCGATGTTGGCTATGTGCCATTAACACTAATGACATGTCATT
66 ATTCAGCAAGAACTACGTATCGATGTTGGCTATGTGCCATTAACACTAATGACATGTCATT
* *
25683166 AGTGTTAAGGCCAGTGTGAACTTAGTGAATAGCTAGGATACAAATGACATGTCATTAGGGTTTAT
1 AGTGTTAAGGCCAGTGTGAACTTAATGAATAGCTAGGATACAAATGAAATGTCATTAGGGTTTAT
25683231 ATTCAGCAAGAACTACGTATCGATGTTGGCTATGTGCCATT
66 ATTCAGCAAGAACTACGTATCGATGTTGGCTATGTGCCATT
25683272 TATATTTAGC
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 98 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (126 bp):
AGTGTTAAGGCCAGTGTGAACTTAATGAATAGCTAGGATACAAATGAAATGTCATTAGGGTTTAT
ATTCAGCAAGAACTACGTATCGATGTTGGCTATGTGCCATTAACACTAATGACATGTCATT
Found at i:25684800 original size:62 final size:58
Alignment explanation
Indices: 25684710--25684842 Score: 187
Period size: 62 Copynumber: 2.2 Consensus size: 58
25684700 TACAAAAATA
*
25684710 ATATTATTTTAAT-AGTTTAATATAAAATTTAATTTAATGTTTATCTTGTAGATAAATATT
1 ATATTATTTTAATAAGTTTAATATAAAATTTAATTTAATATTTATC-T-T-GATAAATATT
* *
25684770 TTATTATTTTAATAAGATTTAATATTAAATTTAATTTAATATTTATCTTGATAAATATT
1 ATATTATTTTAATAAG-TTTAATATAAAATTTAATTTAATATTTATCTTGATAAATATT
*
25684829 ATATTAATTTAATA
1 ATATTATTTTAATA
25684843 TTAAAGTGAT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
59 22 0.33
60 13 0.20
61 3 0.05
62 28 0.42
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (58 bp):
ATATTATTTTAATAAGTTTAATATAAAATTTAATTTAATATTTATCTTGATAAATATT
Found at i:25692274 original size:3 final size:3
Alignment explanation
Indices: 25692266--25692305 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
25692256 CATGAAACCT
*
25692266 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
25692306 GATGATGATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:25692310 original size:3 final size:3
Alignment explanation
Indices: 25692304--25692341 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
25692294 AATAATAATA
25692304 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
25692342 AATTTACGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:25692829 original size:42 final size:42
Alignment explanation
Indices: 25692747--25693493 Score: 809
Period size: 42 Copynumber: 18.0 Consensus size: 42
25692737 ATACAATGAA
* * * * *
25692747 AAAAATAAATGGACCT-CACGCCTAGGCCTCTGAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTGGCCTCTAAATGCAATG
* * *
25692788 AAAAGTAAATGGGCCTCCACACCTAGGCTTCTAAATACAATG
1 AAAAGTAAATGGGCCTCCACACCTTGGCCTCTAAATGCAATG
* * * *
25692830 AAAAGTAAATAGACCTCCAC-GCTTGG-GTCTTAAAGTGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTGGCCTC-TAAA-TGCAATG
* * *
25692872 AAAAGTAAAT-GGCCTGCACA-CTAGGCCTTTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTGGCCTCTAAATGCAATG
* * * *
25692912 AAAAGTAAATGGGCTTACACA-ATTGGACCACTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTGG-CCTCTAAATGCAATG
* *
25692954 AAAAGCAAATGGGCCTCTACA-CTTGTGCCTCTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTG-GCCTCTAAATGCAATG
* * *
25692996 AAAAGCAAATGGGCCTCCACA-CTTGTGCCTCTAAATCCATTG
1 AAAAGTAAATGGGCCTCCACACCTTG-GCCTCTAAATGCAATG
* *
25693038 AAAAGTAAATGGACCTCCACACCTTGGCCTTTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTGGCCTCTAAATGCAATG
* * *
25693080 AAAAGTAAATGAGTCTCCACACC-TGCGCCTTTAAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTG-GCCTCT-AAATGCAATG
* * *
25693123 AAAAGTAAATGGGCCTCTACACCTTTGCCTCTAAATGCAATA
1 AAAAGTAAATGGGCCTCCACACCTTGGCCTCTAAATGCAATG
* * **
25693165 AAAATTAAATGGACCTCCACACCCGGGCCTCTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTGGCCTCTAAATGCAATG
* *
25693207 AAAAGTAAAAGGACCTCCACACCTTGGCCTCTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTGGCCTCTAAATGCAATG
** *
25693249 AAAAGTAAATGAACCTCTACACC-TGTGCCTCTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTG-GCCTCTAAATGCAATG
* *
25693291 AAAACTAAATGGACCTCCACACCTTGGCCTCTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTGGCCTCTAAATGCAATG
**
25693333 AAAAGTAAATGACCCTCCACA-CTTGGGCCTC----T---A--
1 AAAAGTAAATGGGCCTCCACACCTT-GGCCTCTAAATGCAATG
*
25693366 AAAAGTAAATGGGCCTCCACACCTAGGCCTCTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTGGCCTCTAAATGCAATG
*
25693408 AAAAGTAAATGAGCCTCCACA-CTTAGGCCTCTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTT-GGCCTCTAAATGCAATG
*
25693450 AAAAGTAAATGGACCTCCACA-CTTGTGCCTCTAAATGCAATG
1 AAAAGTAAATGGGCCTCCACACCTTG-GCCTCTAAATGCAATG
25693492 AA
1 AA
25693494 TGCTTTCCTT
Statistics
Matches: 606, Mismatches: 73, Indels: 53
0.83 0.10 0.07
Matches are distributed among these distances:
33 25 0.04
34 2 0.00
35 1 0.00
37 1 0.00
38 1 0.00
40 20 0.03
41 58 0.10
42 455 0.75
43 42 0.07
44 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (42 bp):
AAAAGTAAATGGGCCTCCACACCTTGGCCTCTAAATGCAATG
Found at i:25693375 original size:33 final size:33
Alignment explanation
Indices: 25693333--25693400 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
25693323 AAATGCAATG
* *
25693333 AAAAGTAAATGACCCTCCACACTTGGGCCTCTA
1 AAAAGTAAATGACCCTCCACACCTAGGCCTCTA
**
25693366 AAAAGTAAATGGGCCTCCACACCTAGGCCTCTA
1 AAAAGTAAATGACCCTCCACACCTAGGCCTCTA
25693399 AA
1 AA
25693401 TGCAATGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.19
Consensus pattern (33 bp):
AAAAGTAAATGACCCTCCACACCTAGGCCTCTA
Found at i:25693419 original size:75 final size:75
Alignment explanation
Indices: 25693291--25693442 Score: 259
Period size: 75 Copynumber: 2.0 Consensus size: 75
25693281 AAATGCAATG
*
25693291 AAAACTAAATGGACCTCCACACCTTGGCCTCTAAATGCAATGAAAAGTAAATGACCCTCCACACT
1 AAAACTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGACCCTCCACACT
*
25693356 TGGGCCTCTA
66 TAGGCCTCTA
* * *
25693366 AAAAGTAAATGGGCCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGAGCCTCCACACT
1 AAAACTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGACCCTCCACACT
25693431 TAGGCCTCTA
66 TAGGCCTCTA
25693441 AA
1 AA
25693443 TGCAATGAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (75 bp):
AAAACTAAATGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGACCCTCCACACT
TAGGCCTCTA
Found at i:25693455 original size:117 final size:117
Alignment explanation
Indices: 25693249--25693484 Score: 363
Period size: 117 Copynumber: 2.0 Consensus size: 117
25693239 AAATGCAATG
*
25693249 AAAAGTAAATGAACCTCTACACCTGTGCCTCTAAATGCAATGAAAACTAAATGGACCTCCACACC
1 AAAAGTAAATGAACCTCCACACCTGTGCCTCTAAATGCAATGAAAACTAAATGGACCTCCACACC
25693314 TTGGCCTCTAAATGCAATGAAAAGTAAAT-GACCCTCCACACTTGGGCCTCTA
66 TTGGCCTCTAAATGCAATGAAAAGTAAATGGA-CCTCCACACTTGGGCCTCTA
** *
25693366 AAAAGTAAATGGGCCTCCACACCTAG-GCCTCTAAATGCAATGAAAAGTAAAT-GAGCCTCCACA
1 AAAAGTAAATGAACCTCCACACCT-GTGCCTCTAAATGCAATGAAAACTAAATGGA-CCTCCACA
*
25693429 -CTTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTGTGCCTCTA
64 CCTT-GGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTA
25693483 AA
1 AA
25693485 TGCAATGAAT
Statistics
Matches: 110, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
116 5 0.05
117 102 0.93
118 3 0.03
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (117 bp):
AAAAGTAAATGAACCTCCACACCTGTGCCTCTAAATGCAATGAAAACTAAATGGACCTCCACACC
TTGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTA
Found at i:25698523 original size:18 final size:18
Alignment explanation
Indices: 25698502--25698536 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25698492 AAATTGGTAT
25698502 ATGAATGAAAA-TGATTAA
1 ATGAAT-AAAAGTGATTAA
25698520 ATGAATAAAAGTGATTA
1 ATGAATAAAAGTGATTA
25698537 GGGACATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
ATGAATAAAAGTGATTAA
Found at i:25704350 original size:21 final size:21
Alignment explanation
Indices: 25704326--25704365 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
25704316 TCGACATACG
25704326 CATTGACATACATATCAAACA
1 CATTGACATACATATCAAACA
25704347 CATTGACATACATATCAAA
1 CATTGACATACATATCAAA
25704366 ATAGGATAAG
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:0.23, G:0.05, T:0.25
Consensus pattern (21 bp):
CATTGACATACATATCAAACA
Found at i:25706836 original size:154 final size:150
Alignment explanation
Indices: 25706429--25706937 Score: 620
Period size: 153 Copynumber: 3.4 Consensus size: 150
25706419 TGATTAAAAC
* * * * * *
25706429 AAAATCACTACTTTACTT-CAAA-TCAAAATTTTTATTTCAAAATAGCTAAAACAATTCAAAGCT
1 AAAATCACTACTTTACTTAAAAATTC-AAACTTTTATTTCGAAATAGTTAAAA-AAATCAAAACT
* * * *
25706492 TTGTTTAAAAATTTTAAACTTTTTCTTTAAAATTATTAAAAAATATATTTTTATTTTTTTAAAAT
64 TTGTTTAAAAA-TTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTA-TTTTTAAAAAT
* *
25706557 CTAAACT-TTTTTTCTTTT-TAATG
127 ATAAACTATTTTTT-TTTTCTAAAG
25706580 AAAATCACTACTTTACTTAAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTT
1 AAAATCACTACTTTACTT-AAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTT
* * *
25706645 TGTTTAAAAATTTAAA-TTTTTCTTTAAAATGACTAAAAAATAGATTTTTATTTTTAAAAATGTA
65 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTATTTTTAAAAATATA
25706709 AACTTTATCTTTTTGTTTTCTAAAG
130 AAC--TAT-TTTTT-TTTTCTAAAG
* * * * *
25706734 AAAATCACTATTTTACTTAAAAA-TCTAAATTTTTATTTCGAAATTGTTAAAAAAATAAAAAATT
1 AAAATCACTACTTTACTTAAAAATTC-AAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTT
* * *
25706798 TGTTTAAAAATTTAAACTTTTTCTTTAAAACAACTAAAAAACAAATTTTTATTTTTGAAAATATA
65 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTATTTTTAAAAATATA
* *
25706863 AAC-ATTCTCTTTTTCTAAAG
130 AACTATTTTTTTTTTCTAAAG
*
25706883 AAAATCACTACTTCACTTAAAAATTCAAACTTTTATTTCGAAATTA-TTAAAAAAA
1 AAAATCACTACTTTACTTAAAAATTCAAACTTTTATTTCGAAA-TAGTTAAAAAAA
25706938 GACCAAAACT
Statistics
Matches: 316, Mismatches: 30, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
149 71 0.22
150 37 0.12
151 27 0.09
152 23 0.07
153 90 0.28
154 68 0.22
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (150 bp):
AAAATCACTACTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTATTTTTAAAAATATAA
ACTATTTTTTTTTTCTAAAG
Found at i:25717570 original size:12 final size:12
Alignment explanation
Indices: 25717553--25717593 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
25717543 ATTTGAGAAT
25717553 ATAAAATAAAAG
1 ATAAAATAAAAG
*
25717565 ATAAAATAAAAT
1 ATAAAATAAAAG
*
25717577 AGAAAATAAAAG
1 ATAAAATAAAAG
25717589 A-AAAA
1 ATAAAA
25717594 GTTTGAGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:25717575 original size:17 final size:17
Alignment explanation
Indices: 25717553--25717592 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
25717543 ATTTGAGAAT
25717553 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
25717570 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
*
25717587 AGAAAA
1 ATAAAA
25717593 AGTTTGAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:25731326 original size:14 final size:15
Alignment explanation
Indices: 25731307--25731350 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
25731297 CATTTTTCTA
25731307 TTTACTTTTATTT-T
1 TTTACTTTTATTTGT
25731321 TTTACTTTTATTTGT
1 TTTACTTTTATTTGT
* *
25731336 TTCACTTTTACTTGT
1 TTTACTTTTATTTGT
25731351 GTTGTTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (15 bp):
TTTACTTTTATTTGT
Found at i:25742811 original size:15 final size:15
Alignment explanation
Indices: 25742791--25742823 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
25742781 TTTTCCTGTA
25742791 AATTCAAATCCAACC
1 AATTCAAATCCAACC
25742806 AATTCAAATCCAACC
1 AATTCAAATCCAACC
25742821 AAT
1 AAT
25742824 AACTTCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (15 bp):
AATTCAAATCCAACC
Found at i:25743056 original size:21 final size:22
Alignment explanation
Indices: 25743031--25743081 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
25743021 CTTGTAGCCT
25743031 CTGCTTCCTT-CGCTTGCCTCG
1 CTGCTTCCTTCCGCTTGCCTCG
*
25743052 CTGC-TGCTTCCGCTTGCCTCG
1 CTGCTTCCTTCCGCTTGCCTCG
25743073 CTGCTTCCT
1 CTGCTTCCT
25743082 CCACTTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 19 0.73
22 3 0.12
ACGTcount: A:0.00, C:0.43, G:0.20, T:0.37
Consensus pattern (22 bp):
CTGCTTCCTTCCGCTTGCCTCG
Found at i:25743170 original size:64 final size:65
Alignment explanation
Indices: 25743069--25743223 Score: 258
Period size: 66 Copynumber: 2.4 Consensus size: 65
25743059 TTCCGCTTGC
** * *
25743069 CTCGCTGCTTCCTCCACTTTAAGTTGTAGGTTGAGTTCATCATA-TTTTTTGAGCCTCTGCTTCT
1 CTCGCTGCAGCCTCCTCTTTAAGTTGTAGGTGGAGTTCATCATATTTTTTTGAGCCTCTGCTTCT
25743133 CTCGCTGCAGCCTCCTCTTTAAGTTGTAGGTGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTC
1 CTCGCTGCAGCCTCCTCTTTAAGTTGTAGGTGGAGTTCATCATA-TTTTTTTGAGCCTCTGCTTC
25743198 T
65 T
25743199 CTCGCTGCAGCCTCCTCTTTAAGTT
1 CTCGCTGCAGCCTCCTCTTTAAGTT
25743224 CATCAAATTT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
64 40 0.47
66 45 0.53
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.42
Consensus pattern (65 bp):
CTCGCTGCAGCCTCCTCTTTAAGTTGTAGGTGGAGTTCATCATATTTTTTTGAGCCTCTGCTTCT
Found at i:25750892 original size:5 final size:5
Alignment explanation
Indices: 25750882--25750916 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
25750872 TGGCAATACA
*
25750882 TTTCT TTTCT TTTCT TTTCT TTTCT CTT-T TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
25750917 CTTCCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 3 0.11
5 24 0.89
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:25750925 original size:13 final size:14
Alignment explanation
Indices: 25750882--25750926 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
25750872 TGGCAATACA
*
25750882 TTTCTTTTCTTTTCT
1 TTTCTTTTCTCTT-T
25750897 TTTCTTTTCTCTTT
1 TTTCTTTTCTCTTT
25750911 TTTCTTCTTC-CTTT
1 TTTCTT-TTCTCTTT
25750925 TT
1 TT
25750927 GTGATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCTTTTCTCTTT
Found at i:25762496 original size:14 final size:15
Alignment explanation
Indices: 25762479--25762513 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
25762469 CCACAGAATT
*
25762479 TTTTTTTATTTTT-C
1 TTTTTTCATTTTTGC
25762493 TTTTTTCATTTTTGC
1 TTTTTTCATTTTTGC
25762508 TTTTTT
1 TTTTTT
25762514 ATCACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTTCATTTTTGC
Found at i:25762498 original size:15 final size:16
Alignment explanation
Indices: 25762478--25762523 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
25762468 CCCACAGAAT
*
25762478 TTTTTTTTATTTTT-C
1 TTTTTTTCATTTTTGC
25762493 -TTTTTTCATTTTTGC
1 TTTTTTTCATTTTTGC
25762508 TTTTTTATCACTTTTT
1 TTTTTT-TCA-TTTTT
25762524 TTTGGGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 12 0.46
15 1 0.04
16 5 0.19
17 3 0.12
18 5 0.19
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTTTCATTTTTGC
Found at i:25763925 original size:18 final size:18
Alignment explanation
Indices: 25763878--25763929 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
25763868 AAACTGCGAG
* *
25763878 AAATGATATTCAAATTTT
1 AAATGATATTCACATTTC
* *
25763896 AAATAATGTTCACATTTC
1 AAATGATATTCACATTTC
*
25763914 AAATGATTTTCACATT
1 AAATGATATTCACATT
25763930 GATGGAAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (18 bp):
AAATGATATTCACATTTC
Found at i:25767077 original size:19 final size:18
Alignment explanation
Indices: 25767055--25767098 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
25767045 TTTTCTCTCT
*
25767055 TTTTTTTCTTTTTTATCAA
1 TTTTTTTCCTTTTT-TCAA
*
25767074 TTTTTTTCCTTTTTTCGA
1 TTTTTTTCCTTTTTTCAA
25767092 TTTTTTT
1 TTTTTTT
25767099 ATTTAGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTTTCCTTTTTTCAA
Found at i:25768548 original size:12 final size:12
Alignment explanation
Indices: 25768531--25768564 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
25768521 AAATGTTACT
25768531 AAATTTTTTTTC
1 AAATTTTTTTTC
*
25768543 AAATTTTTTATC
1 AAATTTTTTTTC
*
25768555 AGATTTTTTT
1 AAATTTTTTT
25768565 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (12 bp):
AAATTTTTTTTC
Found at i:25788755 original size:8 final size:7
Alignment explanation
Indices: 25788730--25788766 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
25788720 ACCCAAATTC
25788730 ATTTTT-
1 ATTTTTA
25788736 ATTTTTA
1 ATTTTTA
25788743 ATTTTTA
1 ATTTTTA
25788750 ATTTTTA
1 ATTTTTA
*
25788757 A-GTTTA
1 ATTTTTA
25788763 ATTT
1 ATTT
25788767 CAGTTGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 11 0.41
7 16 0.59
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (7 bp):
ATTTTTA
Found at i:25794006 original size:52 final size:52
Alignment explanation
Indices: 25793928--25794269 Score: 438
Period size: 52 Copynumber: 6.6 Consensus size: 52
25793918 GTAAATAAAA
*
25793928 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
25793980 AGGTCCGATGACTACGTGCCATCGTGAGTATATGAATCCTTTACGAATTATA
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
25794032 AGGTCCGATGAATACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
25794084 AGGTTCGATAACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* ** * * *
25794136 AGGTCCGATGACTATGCATCATCATGAGTATAAGAATCCTTTATGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * ** * * *
25794188 AGGTCTGATAACTATTTGTCATCGTGAGTATATG-ATCCCTCTACGAATTA-A
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTATG
** *
25794239 AGGTCTTATGACT-CTATGTCATCGTGAGTAT
1 AGGTCCGATGACTAC-GTGTCATCGTGAGTAT
25794270 CAAATATGCA
Statistics
Matches: 254, Mismatches: 34, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
51 28 0.11
52 226 0.89
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (52 bp):
AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:25794961 original size:21 final size:21
Alignment explanation
Indices: 25794937--25795057 Score: 84
Period size: 21 Copynumber: 5.7 Consensus size: 21
25794927 AGAGCTTTTA
*
25794937 GTATCGGTAGAAGTAAGACTT
1 GTATCGGTAGAAGTAACACTT
* **
25794958 GTATTGGTAGAAAG-AGTTACTT
1 GTATCGGTAG-AAGTA-ACACTT
* * * *
25794980 GTATTGGTAGGACTATCACTT
1 GTATCGGTAGAAGTAACACTT
25795001 GTATCGGTAGAAAG-AATCACTT
1 GTATCGGTAG-AAGTAA-CACTT
* * * *
25795023 GTATTGGTAGGACTATCACTT
1 GTATCGGTAGAAGTAACACTT
25795044 GTATCGGTAGAAGT
1 GTATCGGTAGAAGT
25795058 TTGCACTATT
Statistics
Matches: 77, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
21 43 0.56
22 34 0.44
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGTAACACTT
Found at i:25794982 original size:22 final size:21
Alignment explanation
Indices: 25794954--25795055 Score: 105
Period size: 22 Copynumber: 4.8 Consensus size: 21
25794944 TAGAAGTAAG
*
25794954 ACTTGTATTGGTAGAAAGAGTT
1 ACTTGTATTGGTAGAAAGA-TC
* **
25794976 ACTTGTATTGGTAGGACTATC
1 ACTTGTATTGGTAGAAAGATC
*
25794997 ACTTGTATCGGTAGAAAGAATC
1 ACTTGTATTGGTAGAAAG-ATC
* **
25795019 ACTTGTATTGGTAGGACTATC
1 ACTTGTATTGGTAGAAAGATC
*
25795040 ACTTGTATCGGTAGAA
1 ACTTGTATTGGTAGAA
25795056 GTTTGCACTA
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
21 32 0.49
22 33 0.51
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (21 bp):
ACTTGTATTGGTAGAAAGATC
Found at i:25795003 original size:43 final size:43
Alignment explanation
Indices: 25794954--25795055 Score: 177
Period size: 43 Copynumber: 2.4 Consensus size: 43
25794944 TAGAAGTAAG
* * *
25794954 ACTTGTATTGGTAGAAAGAGTTACTTGTATTGGTAGGACTATC
1 ACTTGTATCGGTAGAAAGAATCACTTGTATTGGTAGGACTATC
25794997 ACTTGTATCGGTAGAAAGAATCACTTGTATTGGTAGGACTATC
1 ACTTGTATCGGTAGAAAGAATCACTTGTATTGGTAGGACTATC
25795040 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
25795056 GTTTGCACTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (43 bp):
ACTTGTATCGGTAGAAAGAATCACTTGTATTGGTAGGACTATC
Found at i:25796592 original size:3 final size:3
Alignment explanation
Indices: 25796584--25796622 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
25796574 ATGGAGAAAG
25796584 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
25796623 GAATCAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:25797211 original size:24 final size:23
Alignment explanation
Indices: 25797171--25797228 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
25797161 TATATATTCT
*
25797171 AATTAA-ATTTTATAAATAATTAA
1 AATTAATA-TTTAGAAATAATTAA
* *
25797194 TATTAATTATTTAGAAATATTTAA
1 AATTAA-TATTTAGAAATAATTAA
25797218 AATTAATATTT
1 AATTAATATTT
25797229 CCTATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 10 0.34
24 18 0.62
25 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAATATTTAGAAATAATTAA
Found at i:25797334 original size:19 final size:22
Alignment explanation
Indices: 25797312--25797354 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
25797302 CTAATTTGAA
25797312 TATTA-TTTA-AATAT-ATATT
1 TATTATTTTATAATATCATATT
25797331 TATTATTTTATAATATCATATT
1 TATTATTTTATAATATCATATT
25797353 TA
1 TA
25797355 AAATAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 5 0.24
22 7 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTATTTTATAATATCATATT
Found at i:25798075 original size:21 final size:22
Alignment explanation
Indices: 25798045--25798098 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
25798035 ATATACTTTG
* *
25798045 TTTTACTGTTTTATTGCT-GTT
1 TTTTATTGTTTTATTACTAGTT
* *
25798066 TTTTATTGTTTTGTTACTATTT
1 TTTTATTGTTTTATTACTAGTT
25798088 TTTTATTGTTT
1 TTTTATTGTTT
25798099 AAATATTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.11, C:0.06, G:0.11, T:0.72
Consensus pattern (22 bp):
TTTTATTGTTTTATTACTAGTT
Found at i:25799772 original size:14 final size:14
Alignment explanation
Indices: 25799741--25799771 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
25799731 TAATTTATTC
25799741 TTTTAATGTTTATA
1 TTTTAATGTTTATA
25799755 TTTTAAT-TTTATA
1 TTTTAATGTTTATA
25799768 TTTT
1 TTTT
25799772 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTTAATGTTTATA
Found at i:25800078 original size:14 final size:15
Alignment explanation
Indices: 25800053--25800081 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25800043 ATTAAAATTT
25800053 AAATTAAAAATATAA
1 AAATTAAAAATATAA
25800068 AAATT-AAAATATAA
1 AAATTAAAAATATAA
25800082 TTTACAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATTAAAAATATAA
Found at i:25800770 original size:22 final size:22
Alignment explanation
Indices: 25800745--25800794 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
25800735 TATTTTTTTA
25800745 TAAATATTTAT-AAAAAATATTT
1 TAAA-ATTTATCAAAAAATATTT
* *
25800767 TAAACTTTATCAAATAATATTT
1 TAAAATTTATCAAAAAATATTT
*
25800789 AAAAAT
1 TAAAAT
25800795 CATAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAATTTATCAAAAAATATTT
Found at i:25801823 original size:11 final size:12
Alignment explanation
Indices: 25801798--25801832 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
25801788 TTTTAAATAT
*
25801798 AAAAATTAAATAA
1 AAAAAGTAAA-AA
25801811 AAAAAGTAAAAA
1 AAAAAGTAAAAA
25801823 AAAAAGTAAA
1 AAAAAGTAAA
25801833 TGGAAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (12 bp):
AAAAAGTAAAAA
Done.