Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 42 of 187
Found at i:12891180 original size:24 final size:24
Alignment explanation
Indices: 12891153--12891204 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12891143 TTAGTAAGTC
*
12891153 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
12891177 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12891201 AAAT
1 AAAT
12891205 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:12893148 original size:24 final size:24
Alignment explanation
Indices: 12893121--12893172 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
12893111 TTAGTAAGTC
*
12893121 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
12893145 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12893169 AAAT
1 AAAT
12893173 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:12894481 original size:29 final size:29
Alignment explanation
Indices: 12894420--12894484 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
12894410 GTCTAATGTG
* * *
12894420 TAATTTTATATATGAAGTTTGATTTTGTT
1 TAATTTTATATATAAAATTTGATTTTGTC
12894449 TAATTTTATATATAAAATTTGA-TTTGATC
1 TAATTTTATATATAAAATTTGATTTTG-TC
12894478 TAATTTT
1 TAATTTT
12894485 CACAAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (29 bp):
TAATTTTATATATAAAATTTGATTTTGTC
Found at i:12894678 original size:26 final size:27
Alignment explanation
Indices: 12894598--12894668 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
12894588 ATTTATTTAA
* * *
12894598 ATATATAATTAAATCAAAATTAAAATT
1 ATATATATTTAAATTACAATTAAAATT
12894625 ATATATATTTAAATTACAATTAAAATT
1 ATATATATTTAAATTACAATTAAAATT
12894652 ATATATA-TTAAATTACA
1 ATATATATTTAAATTACA
12894669 TATCGAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 10 0.24
27 31 0.76
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATATATTTAAATTACAATTAAAATT
Found at i:12898377 original size:14 final size:14
Alignment explanation
Indices: 12898358--12898396 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
12898348 TTGTTTCACT
*
12898358 GAAAATGGCTTCCG
1 GAAAATGACTTCCG
* *
12898372 GAAAATGATTTCTG
1 GAAAATGACTTCCG
12898386 GAAAATGACTT
1 GAAAATGACTT
12898397 ACGTTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:12903537 original size:27 final size:27
Alignment explanation
Indices: 12903473--12903530 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
12903463 TACTAGTTGG
12903473 GTTTGCCAGTTGGTTTGGCGAACTGGT
1 GTTTGCCAGTTGGTTTGGCGAACTGGT
12903500 GTTTGCCAGTTGGTTTGGCGAACTGGT
1 GTTTGCCAGTTGGTTTGGCGAACTGGT
12903527 GTTT
1 GTTT
12903531 AGCAGTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.10, C:0.14, G:0.36, T:0.40
Consensus pattern (27 bp):
GTTTGCCAGTTGGTTTGGCGAACTGGT
Found at i:12903588 original size:26 final size:26
Alignment explanation
Indices: 12903518--12903588 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
12903508 GTTGGTTTGG
* *
12903518 CGAACTGGTGTTTAGCAGTTAAGTTA
1 CGAACTGGTGTTCACCAGTTAAGTTA
** *
12903544 CGAACTGGTGTTCGTCAGTTAAGTTG
1 CGAACTGGTGTTCACCAGTTAAGTTA
* *
12903570 TGAACTAGTGTTCACCAGT
1 CGAACTGGTGTTCACCAGT
12903589 CAAAGTTAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (26 bp):
CGAACTGGTGTTCACCAGTTAAGTTA
Found at i:12905195 original size:43 final size:43
Alignment explanation
Indices: 12905059--12905258 Score: 178
Period size: 43 Copynumber: 4.7 Consensus size: 43
12905049 TGTGATTTTG
**
12905059 TGTAAGACCACATCTGGGAC-GTTGGCATCG--ATTTGAGATTTACA
1 TGTAAGACCATGTCTGGGACAG-TGGCATCGTTATTT-A-A-TTACA
* * * * * *
12905103 TGTAAGACCAAGTCTGGGACATTAGCGTCG-TATATAATTACG
1 TGTAAGACCATGTCTGGGACAGTGGCATCGTTATTTAATTACA
* *
12905145 TGTAAGACCCTGTCTGGGACAGTGGCATCGTTATTTAATTACG
1 TGTAAGACCATGTCTGGGACAGTGGCATCGTTATTTAATTACA
* * * *
12905188 TGTAAGACTC-TGTCTGAGACAATGGCATCATTATTTGATTACA
1 TGTAAGAC-CATGTCTGGGACAGTGGCATCGTTATTTAATTACA
12905231 TGTAAGACCATGTCTGGGAC-GTTGGCAT
1 TGTAAGACCATGTCTGGGACAG-TGGCAT
12905259 GTATGAACTT
Statistics
Matches: 130, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
42 30 0.23
43 71 0.55
44 26 0.20
45 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGTTATTTAATTACA
Found at i:12910907 original size:15 final size:17
Alignment explanation
Indices: 12910889--12910920 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
12910879 TTATTTATTT
12910889 ATTAAA-AATAA-AAAA
1 ATTAAATAATAATAAAA
12910904 ATTAAATAATAATAAAA
1 ATTAAATAATAATAAAA
12910921 GTAGATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
ATTAAATAATAATAAAA
Found at i:12913215 original size:20 final size:20
Alignment explanation
Indices: 12913190--12913229 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12913180 CGTAAAATGA
*
12913190 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
12913210 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
12913230 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:12913219 original size:34 final size:35
Alignment explanation
Indices: 12913175--12913241 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
12913165 CAGTAAAATA
*
12913175 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
12913209 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
12913242 CCGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:12914056 original size:28 final size:27
Alignment explanation
Indices: 12913999--12914057 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
12913989 AAAAAGCCTT
12913999 TTTTTTAAATTTACCGAAATAGGCCGA
1 TTTTTTAAATTTACCGAAATAGGCCGA
* *
12914026 TTTTTTAATTATTTACCGGAATGGGCC-A
1 TTTTTTAA--ATTTACCGAAATAGGCCGA
12914054 TTTT
1 TTTT
12914058 CCCCGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 5 0.18
29 15 0.54
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (27 bp):
TTTTTTAAATTTACCGAAATAGGCCGA
Found at i:12914360 original size:52 final size:52
Alignment explanation
Indices: 12914282--12914438 Score: 269
Period size: 52 Copynumber: 3.0 Consensus size: 52
12914272 GGGTTTTAGG
* ** *
12914282 GTTTAGGGTGCAAGCTTTTTTAGGGTTTAGGGGTCCCCCAAAAAATTATTTT
1 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTC
*
12914334 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTGCCGAAAAAAATTATTTC
1 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTC
12914386 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTC
1 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTC
12914438 G
1 G
12914439 AGTTGACGTT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 99 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (52 bp):
GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTC
Found at i:12914585 original size:29 final size:28
Alignment explanation
Indices: 12914516--12914609 Score: 152
Period size: 28 Copynumber: 3.3 Consensus size: 28
12914506 TTTATAATTA
*
12914516 AATTAAATTATGTTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGTTAGGGTTTTT
12914544 AATTAAATTAGGTTAGGTTAGGGTTTTAT
1 AATTAAATTAGGTTAGGTTAGGGTTTT-T
*
12914573 AATTGAATTAGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGGTTA-GGTTAGGGTTTTT
12914602 AATTAAAT
1 AATTAAAT
12914610 CAAATAATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
28 26 0.43
29 23 0.38
30 12 0.20
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (28 bp):
AATTAAATTAGGTTAGGTTAGGGTTTTT
Found at i:12915788 original size:7 final size:7
Alignment explanation
Indices: 12915778--12915809 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
12915768 ATATATACAT
12915778 AATACTA
1 AATACTA
12915785 AATACTA
1 AATACTA
12915792 AATACTA
1 AATACTA
12915799 AATACTA
1 AATACTA
12915806 AATA
1 AATA
12915810 TCAATCCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:12916795 original size:25 final size:25
Alignment explanation
Indices: 12916745--12916801 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
12916735 CTTTTATAAC
*
12916745 AAAAAATAAATTAATATTTATCTAA
1 AAAAAATAAATTAATAATTATCTAA
12916770 AAAAACATAAA-TAA-AATTATCTTAA
1 AAAAA-ATAAATTAATAATTATC-TAA
*
12916795 ATAAAAT
1 AAAAAAT
12916802 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 8 0.29
25 15 0.54
26 5 0.18
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
AAAAAATAAATTAATAATTATCTAA
Found at i:12916962 original size:29 final size:29
Alignment explanation
Indices: 12916898--12916956 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
12916888 CAGAAAATAT
12916898 TAAAAA-TTTTAAAATTATTTTAAAAAAA
1 TAAAAATTTTTAAAATTATTTTAAAAAAA
*
12916926 TAAAAATTTTTAAAATTTTCTTTAAAAAAA
1 TAAAAATTTTTAAAATTAT-TTTAAAAAAA
12916956 T
1 T
12916957 GAAATTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 6 0.21
29 11 0.39
30 11 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAAAATTTTTAAAATTATTTTAAAAAAA
Found at i:12917065 original size:52 final size:51
Alignment explanation
Indices: 12916987--12917092 Score: 140
Period size: 52 Copynumber: 2.1 Consensus size: 51
12916977 ATTTAATATG
* * * *
12916987 GAGTTTAGAGATTTTTTGAAGGAAATTGTGAGGATTTTGGAAGGAATTCGA
1 GAGTTTAGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
* * *
12917038 GAGTTTAAGAGAATTTTGGAAGGAAATTGAGAGAATTTTTGAAGGACTTTGA
1 GAGTTT-AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
12917090 GAG
1 GAG
12917093 AATTTTTGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 6 0.13
52 41 0.87
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (51 bp):
GAGTTTAGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
Found at i:12917072 original size:22 final size:22
Alignment explanation
Indices: 12917045--12917113 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
12917035 CGAGAGTTTA
*
12917045 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
**
12917067 AGAGAATTTTTGAAGGACTTTG
1 AGAGAATTTTTGAAGGAAATTG
*
12917089 AGAGAATTTTTGAATGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
12917111 AGA
1 AGA
12917114 TAGGATTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.39, C:0.01, G:0.28, T:0.32
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGAAATTG
Found at i:12917442 original size:28 final size:29
Alignment explanation
Indices: 12917392--12917446 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
12917382 CGGGAAAAAT
12917392 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCGGTAAATAATTAAAAAACC
* * *
12917421 GGCCTATTTCGGTAAAT-TTTAAAAAA
1 GGCCCATTCCGGTAAATAATTAAAAAA
12917447 AAGGGCGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATAATTAAAAAACC
Found at i:12918459 original size:26 final size:25
Alignment explanation
Indices: 12918407--12918460 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
12918397 ATTTTTTTAA
* * **
12918407 TTTTAAAATAATTTTAAAATACTTT
1 TTTTAAAAAAATTTCAAAATAAATT
12918432 TTTTAAAAAAAATTTCAAAATAAATT
1 TTTT-AAAAAAATTTCAAAATAAATT
12918458 TTT
1 TTT
12918461 GGTGTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTAAAAAAATTTCAAAATAAATT
Found at i:12922481 original size:7 final size:7
Alignment explanation
Indices: 12922468--12922508 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
12922458 CGCAAAACCA
12922468 TTTCCAG
1 TTTCCAG
*
12922475 ATTCCAG
1 TTTCCAG
12922482 TTTCCAG
1 TTTCCAG
12922489 TTTCCAG
1 TTTCCAG
12922496 TTTCCAG
1 TTTCCAG
12922503 TTTCCA
1 TTTCCA
12922509 CACGCCTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.41
Consensus pattern (7 bp):
TTTCCAG
Found at i:12925048 original size:2 final size:2
Alignment explanation
Indices: 12925041--12925082 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
12925031 ATTCTGATAA
12925041 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12925083 GGCAATTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12927355 original size:22 final size:23
Alignment explanation
Indices: 12927322--12927397 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 23
12927312 AACTAATTCT
*
12927322 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCATCTCAATTTC
*
12927345 CTCT-AAATTTCATCTCAATTTG
1 CTCTCAAATTTCATCTCAATTTC
* *
12927367 CTCTCAAATTCCTTC-CAAATTT-
1 CTCTCAAATTTCATCTC-AATTTC
12927389 CTCTCAAAT
1 CTCTCAAAT
12927398 CCATATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 30 0.64
23 17 0.36
ACGTcount: A:0.26, C:0.30, G:0.01, T:0.42
Consensus pattern (23 bp):
CTCTCAAATTTCATCTCAATTTC
Found at i:12927371 original size:33 final size:33
Alignment explanation
Indices: 12927316--12927395 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
12927306 TTCACAAACT
* *
12927316 AATTCTCTCTCAAATTTCCTCTCAATTTCC-TCTA
1 AATT-TCTCTC-AATTTCCTCTCAAATTCCTTCCA
*
12927350 AATTTCATCTCAATTTGCTCTCAAATTCCTTCCA
1 AATTTC-TCTCAATTTCCTCTCAAATTCCTTCCA
12927384 AATTTCTCTCAA
1 AATTTCTCTCAA
12927396 ATCCATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.59
34 17 0.41
ACGTcount: A:0.26, C:0.30, G:0.01, T:0.42
Consensus pattern (33 bp):
AATTTCTCTCAATTTCCTCTCAAATTCCTTCCA
Found at i:12927396 original size:11 final size:11
Alignment explanation
Indices: 12927316--12927397 Score: 73
Period size: 11 Copynumber: 7.3 Consensus size: 11
12927306 TTCACAAACT
12927316 AATTCTCTCTCA
1 AATT-TCTCTCA
12927328 AATTTCCTCTC-
1 AATTT-CTCTCA
12927339 AATTTC-CTCTA
1 AATTTCTCTC-A
12927350 AATTTCATCTC-
1 AATTTC-TCTCA
12927361 AATTTGCTCTCA
1 AATTT-CTCTCA
*
12927373 AATTCCT-TCCA
1 AATTTCTCT-CA
12927384 AATTTCTCTCA
1 AATTTCTCTCA
12927395 AAT
1 AAT
12927398 CCATATTTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 19
0.74 0.03 0.24
Matches are distributed among these distances:
9 3 0.05
10 2 0.03
11 36 0.61
12 15 0.25
13 3 0.05
ACGTcount: A:0.27, C:0.29, G:0.01, T:0.43
Consensus pattern (11 bp):
AATTTCTCTCA
Found at i:12928637 original size:7 final size:7
Alignment explanation
Indices: 12928625--12928650 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12928615 TAGTCGATTG
12928625 GTATTTA
1 GTATTTA
12928632 GTATTTA
1 GTATTTA
12928639 GTATTTA
1 GTATTTA
12928646 GTATT
1 GTATT
12928651 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:12929328 original size:18 final size:18
Alignment explanation
Indices: 12929301--12929340 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
12929291 CAGGTGCATT
*
12929301 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
12929319 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
12929337 TCCT
1 TCCT
12929341 TTTCCAAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:12929620 original size:21 final size:21
Alignment explanation
Indices: 12929596--12929644 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
12929586 AGATGTCGTA
* * *
12929596 CCGGAAGAACCAGAATCCCCG
1 CCGGAAGAACAACAATCACCG
*
12929617 CCGGAGGAACAACAATCACCG
1 CCGGAAGAACAACAATCACCG
12929638 CCGGAAG
1 CCGGAAG
12929645 TTAGAGAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.27, T:0.04
Consensus pattern (21 bp):
CCGGAAGAACAACAATCACCG
Found at i:12931597 original size:24 final size:25
Alignment explanation
Indices: 12931568--12931636 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
12931558 CAAATAATAA
12931568 AATAATAATACAACATAACTTTTA-
1 AATAATAATACAACATAACTTTTAG
*
12931592 AGTAATAATACATA-ATAA-TTTTAG
1 AATAATAATACA-ACATAACTTTTAG
12931616 AATAATAATAC-ACGATAACTT
1 AATAATAATACAAC-ATAACTT
12931637 CAAAAATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 1 0.03
23 5 0.13
24 29 0.76
25 3 0.08
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (25 bp):
AATAATAATACAACATAACTTTTAG
Found at i:12932517 original size:13 final size:13
Alignment explanation
Indices: 12932499--12932523 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12932489 AAAAGAATCC
12932499 AAAGAAGAAAAAG
1 AAAGAAGAAAAAG
12932512 AAAGAAGAAAAA
1 AAAGAAGAAAAA
12932524 TCTGCAATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAG
Found at i:12933282 original size:44 final size:43
Alignment explanation
Indices: 12933234--12933478 Score: 134
Period size: 44 Copynumber: 5.6 Consensus size: 43
12933224 CGATGCAGGA
*
12933234 AGGCAAGACCTGCTATCTTCAACCTACTCCACTACAATCGAGGG
1 AGGCAAGACCTG-TATCTTCAACCTGCTCCACTACAATCGAGGG
* * * * * * *** *
12933278 AGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTTGAT-GTAGGA
1 AGGCAAGACCTGTATCTTCAACCTGCTCCACT-ACAATCG-AGGG
* * *
12933322 AGACAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG
1 AGGCAAGACCTG-TATCTTCAACCTGCTCCACTACAATCGAGGG
* * * * * * * * * *
12933366 AGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCGAT-GTAGGA
1 AGGCAAGACCTGTATCTTCAACCTGCTCCACT-ACAATCG-AGGG
* *
12933410 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG
1 AGGCAAGACCTG-TATCTTCAACCTGCTCCACTACAATCGAGGG
** * *
12933454 AGATAAGATCTGTAATTTTCAACCT
1 AGGCAAGACCTGT-ATCTTCAACCT
12933479 ACTCTACAGC
Statistics
Matches: 140, Mismatches: 52, Indels: 18
0.67 0.25 0.09
Matches are distributed among these distances:
43 33 0.24
44 74 0.53
45 33 0.24
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (43 bp):
AGGCAAGACCTGTATCTTCAACCTGCTCCACTACAATCGAGGG
Found at i:12933335 original size:88 final size:88
Alignment explanation
Indices: 12933205--12933455 Score: 430
Period size: 88 Copynumber: 2.9 Consensus size: 88
12933195 GGACCATTGG
* * * *
12933205 CTTCGATCTGCTTCACTATCGATGCAGGAAGGCAAGACCTGCTATCTTCAACCTACTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
*
12933270 ATCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* *
12933293 CTTCGATCTGCTTCACTGTTGATGTAGGAAGACAAGATCTGCTATCTTCAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
12933358 ACCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
*
12933381 CTTCGATCTGCTTCGCTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
12933446 ACCGAGGGAG
66 ACCGAGGGAG
12933456 ATAAGATCTG
Statistics
Matches: 153, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 153 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.26
Consensus pattern (88 bp):
CTTCGATCTGCTTCACTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
ACCGAGGGAGGCAAGGCTTGTGT
Found at i:12933498 original size:44 final size:43
Alignment explanation
Indices: 12933450--12933675 Score: 109
Period size: 44 Copynumber: 5.1 Consensus size: 43
12933440 ACTACAACCG
*
12933450 AGGGAGATAAGATCTGT-AATTTTCAACCTACTCTACAGCTGGTC
1 AGGGAGATAAGA-CT-TAAATCTTCAACCTACTCTACAGCTGGTC
* * * * *
12933494 AGGGAGCTAGGACTTACAATCTTCTACCTATTCTACTGCTGGTC
1 AGGGAGATAAGACTTA-AATCTTCAACCTACTCTACAGCTGGTC
* * ** * * * *
12933538 AGGGAGCTAGGACTTACAGCCTTCCACATATTCCACTA-CTGGTC
1 AGGGAGATAAGACTTA-AATCTTCAACCTACTCTAC-AGCTGGTC
* * * * * *
12933582 TA-GGAGCTAGGACTTACAATCTTCTACCTATTCCACTGCTGGTC
1 -AGGGAGATAAGACTTA-AATCTTCAACCTACTCTACAGCTGGTC
* * * * * *
12933626 AGGGAGCTAGGACTTACAGTCTTCCAA-CTATTCCACTGCTGGTC
1 AGGGAGATAAGACTTA-AATCTT-CAACCTACTCTACAGCTGGTC
12933670 AGGGAG
1 AGGGAG
12933676 CTAGGATATA
Statistics
Matches: 156, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
42 1 0.01
43 3 0.02
44 149 0.96
45 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (43 bp):
AGGGAGATAAGACTTAAATCTTCAACCTACTCTACAGCTGGTC
Found at i:12933676 original size:44 final size:44
Alignment explanation
Indices: 12933487--12933814 Score: 437
Period size: 44 Copynumber: 7.5 Consensus size: 44
12933477 CTACTCTACA
*
12933487 GCTGGTCAGGGAGCTAGGACTTACAATCTTCTACCTATTCTACT
1 GCTGGTCAGGGAGCTAGGACTTACAATCTTCTACCTATTCCACT
** * *
12933531 GCTGGTCAGGGAGCTAGGACTTACAGCCTTCCACATATTCCACT
1 GCTGGTCAGGGAGCTAGGACTTACAATCTTCTACCTATTCCACT
*
12933575 ACTGGTCTA-GGAGCTAGGACTTACAATCTTCTACCTATTCCACT
1 GCTGGTC-AGGGAGCTAGGACTTACAATCTTCTACCTATTCCACT
* * *
12933619 GCTGGTCAGGGAGCTAGGACTTACAGTCTTCCAACTATTCCACT
1 GCTGGTCAGGGAGCTAGGACTTACAATCTTCTACCTATTCCACT
* *
12933663 GCTGGTCAGGGAGCTAGGA-TATACAATCTT-TCGCCTATTCCAAT
1 GCTGGTCAGGGAGCTAGGACT-TACAATCTTCT-ACCTATTCCACT
* * * *
12933707 GCTGTTCAGGGAGCTAGGTCTTTCAGTCTTCTACCTATTCCACT
1 GCTGGTCAGGGAGCTAGGACTTACAATCTTCTACCTATTCCACT
* *
12933751 GTTGGTCAGGGAGCTAGGACTCACAATCTTCTACCTATTCCACT
1 GCTGGTCAGGGAGCTAGGACTTACAATCTTCTACCTATTCCACT
* *
12933795 GCTGTTCAGGGAGATAGGAC
1 GCTGGTCAGGGAGCTAGGAC
12933815 ATATAGTTTC
Statistics
Matches: 244, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
43 2 0.01
44 239 0.98
45 3 0.01
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.30
Consensus pattern (44 bp):
GCTGGTCAGGGAGCTAGGACTTACAATCTTCTACCTATTCCACT
Found at i:12935109 original size:15 final size:17
Alignment explanation
Indices: 12935085--12935118 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12935075 GGCCTCTCCA
12935085 TTTTACTTTTT-ATTTT
1 TTTTACTTTTTCATTTT
12935101 TTTTA-TTTTTCATTTT
1 TTTTACTTTTTCATTTT
12935117 TT
1 TT
12935119 GGACTCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTACTTTTTCATTTT
Found at i:12935174 original size:48 final size:51
Alignment explanation
Indices: 12935113--12935217 Score: 128
Period size: 48 Copynumber: 2.1 Consensus size: 51
12935103 TTATTTTTCA
* * * *
12935113 TTTTTT-GGACTCAAAGTGCCCTTTAAGGGTTTTTACTTTGAT-CTTT-T-
1 TTTTTTCGAACTCAAAGCGCCCTTTAAGGGTTTTCACCTTGATCCTTTCTC
**
12935160 TTTTTTCGAACTCAAAGCGCCCTTTGTGGGTTTTCACCTTGATCCTTTCTC
1 TTTTTTCGAACTCAAAGCGCCCTTTAAGGGTTTTCACCTTGATCCTTTCTC
12935211 TTTTTTC
1 TTTTTTC
12935218 AGGTGAAGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 6 0.12
48 30 0.62
49 4 0.08
50 1 0.02
51 7 0.15
ACGTcount: A:0.14, C:0.21, G:0.15, T:0.50
Consensus pattern (51 bp):
TTTTTTCGAACTCAAAGCGCCCTTTAAGGGTTTTCACCTTGATCCTTTCTC
Found at i:12939820 original size:24 final size:25
Alignment explanation
Indices: 12939791--12939859 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
12939781 CAAATAATAA
12939791 AATAATAATACAACATAACTTTTA-
1 AATAATAATACAACATAACTTTTAG
*
12939815 AGTAATAATACATA-ATAA-TTTTAG
1 AATAATAATACA-ACATAACTTTTAG
12939839 AATAATAATAC-ACGATAACTT
1 AATAATAATACAAC-ATAACTT
12939860 CAAAAATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 1 0.03
23 5 0.13
24 29 0.76
25 3 0.08
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (25 bp):
AATAATAATACAACATAACTTTTAG
Found at i:12940729 original size:13 final size:13
Alignment explanation
Indices: 12940711--12940735 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12940701 AAAAGAATCC
12940711 AAAGAAGAAAAAG
1 AAAGAAGAAAAAG
12940724 AAAGAAGAAAAA
1 AAAGAAGAAAAA
12940736 TCTGCAATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAG
Found at i:12943601 original size:125 final size:124
Alignment explanation
Indices: 12943359--12943728 Score: 508
Period size: 125 Copynumber: 3.0 Consensus size: 124
12943349 CATGTTACTG
* * *
12943359 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCAACTTGGTAGAAG
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTAACAAATTCTTCTCA-AAAGCATCCTGGTAGAAG
* *
12943424 TGATTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACTA
65 CGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACTA
* * * * * * *
12943484 TAGTAAAAACGCGTCCACGAGGGCGCGATTTTAGAAATTCTTCTCAAATAGCATCCTGCTTGAAG
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTAACAAATTCTTCTCAAA-AGCATCCTGGTAGAAG
* * * * ** *
12943549 CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATAATTT-TTTCAGGACGTACTG
65 CG-ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACTA
* *
12943609 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTAACAAATTCTTCTCTTAAAGCATCCTGGTAAAAG
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTAACAAATTCTTCTC-AAAAGCATCCTGGTAGAAG
12943674 CGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACC
65 CGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACC
12943729 TAAAAACCTT
Statistics
Matches: 209, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
124 41 0.20
125 128 0.61
126 40 0.19
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (124 bp):
TAGCAAAAGCGCGTCCACGTGGGCGCGATTTAACAAATTCTTCTCAAAAGCATCCTGGTAGAAGC
GATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACTA
Found at i:12946369 original size:3 final size:3
Alignment explanation
Indices: 12946357--12946398 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
12946347 CATGTATGTT
12946357 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12946399 AATCATAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:12948124 original size:44 final size:44
Alignment explanation
Indices: 12948069--12948653 Score: 275
Period size: 44 Copynumber: 13.3 Consensus size: 44
12948059 CTGTAACCTC
* **
12948069 AGGGAGGTAAGATCTGCCATCTTTGATCTACTCCACTACTGTCT
1 AGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGTCT
* ** * * * *
12948113 GGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGTCT
* * * * *
12948157 AGGGAGAT-AGAAT-TACTAGCTTCAATGTACTCCACTGTAAC-CTC-
1 AGGGAGATAAG-ATCTGCCATCTTCAATCTACTCCAC--T-ACTGTCT
* ** *
12948201 AGGGAGGTAAGATCTGCCATCTTTGATATACTCCACTACTGTCT
1 AGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGTCT
** * * * *
12948245 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGTCT
* *** * *
12948289 AGGGAGAT-AGAAT-TACTGGCTTCAATGTACTCCACTGTAAC-CTC-
1 AGGGAGATAAG-ATCTGCCATCTTCAATCTACTCCAC--T-ACTGTCT
* * *
12948333 AGGGAGGTAAAATCTGCCA-CATTCGATCTACTCCACTACTGTCT
1 AGGGAGATAAGATCTGCCATC-TTCAATCTACTCCACTACTGTCT
** * * * * *
12948377 AGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGTCT
* ** * * * ***
12948421 AGGGAGAT-AGAAT-TACCGGCTTCAATATACTCCGCTGCAACCT
1 AGGGAGATAAG-ATCTGCCATCTTCAATCTACTCCACTACTGTCT
* * * * * *
12948464 CAGGGAGGTAAAATCTGTCATCTTCGATCTGCTCCACTACTGTTT
1 -AGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGTCT
* ** * * * * *
12948509 AGGAAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGTCT
* ** *
12948553 AGGGAGAT-AGAAT-TACCGGCTTCAATGTACTCCACTGTAACT-TC-
1 AGGGAGATAAG-ATCTGCCATCTTCAATCTACTCCAC--T-ACTGTCT
* * *
12948597 AGGGAGGTAAAATCTGCCATCCTT-GATCTACTCCACTACTGTCT
1 AGGGAGATAAGATCTGCCAT-CTTCAATCTACTCCACTACTGTCT
12948641 AGGGAGATAAGAT
1 AGGGAGATAAGAT
12948654 TTGTTTTCTT
Statistics
Matches: 385, Mismatches: 125, Indels: 62
0.67 0.22 0.11
Matches are distributed among these distances:
42 7 0.02
43 80 0.21
44 219 0.57
45 72 0.19
46 7 0.02
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATCTGCCATCTTCAATCTACTCCACTACTGTCT
Found at i:12948190 original size:132 final size:132
Alignment explanation
Indices: 12948025--12948653 Score: 1044
Period size: 132 Copynumber: 4.8 Consensus size: 132
12948015 CACGCCAACT
* * *
12948025 AGGGAGATAGGATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAGATCTGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
* *
12948090 TTTGATCTACTCCACTACTGTCTGGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
66 TTTGATCTACTCCACTACTGTCTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGC
12948155 CC
131 CC
* *
12948157 AGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAGATCTGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
* *
12948222 TTTGATATACTCCACTACTGTCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
66 TTTGATCTACTCCACTACTGTCTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGC
12948287 CC
131 CC
12948289 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCA-C
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
*
12948353 ATTCGATCTACTCCACTACTGTCTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTG
66 -TTTGATCTACTCCACTACTGTCTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTG
12948418 CCC
130 CCC
* * * * *
12948421 AGGGAGATAGAATTACCGGCTTCAATATACTCCGCTGCAACCTCAGGGAGGTAAAATCTGTCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
* * * *
12948486 TTCGATCTGCTCCACTACTGTTTAGGAAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGC
66 TTTGATCTACTCCACTACTGTCTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGC
12948551 CC
131 CC
* *
12948553 AGGGAGATAGAATTACCGGCTTCAATGTACTCCACTGTAACTTCAGGGAGGTAAAATCTGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
*
12948618 CTTGATCTACTCCACTACTGTCTAGGGAGATAAGAT
66 TTTGATCTACTCCACTACTGTCTAGGGAGATAAGAT
12948654 TTGTTTTCTT
Statistics
Matches: 467, Mismatches: 28, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 465 1.00
133 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATC
TTTGATCTACTCCACTACTGTCTAGGGAGATAAGATCTGTAATATTCAATCTATTCCACTGCTGC
CC
Found at i:12950298 original size:50 final size:50
Alignment explanation
Indices: 12950229--12950372 Score: 198
Period size: 50 Copynumber: 2.9 Consensus size: 50
12950219 NNNNNNNGAC
* * *
12950229 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACAT
* * *
12950279 GAGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACAT
** *
12950329 GAGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12950373 TGTTATTATC
Statistics
Matches: 81, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 47 0.58
51 34 0.42
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACAT
Found at i:12952098 original size:13 final size:13
Alignment explanation
Indices: 12952080--12952104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12952070 AAATTGTCGA
12952080 GGATAACAAAGAT
1 GGATAACAAAGAT
12952093 GGATAACAAAGA
1 GGATAACAAAGA
12952105 AATTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:12952496 original size:20 final size:21
Alignment explanation
Indices: 12952473--12952520 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
12952463 TTAGCCTCTC
12952473 CATTTTT-ACTTTTCAT-TTTT
1 CATTTTTCA-TTTTCATCTTTT
12952493 CATTTTTCATTTTCATCTTTT
1 CATTTTTCATTTTCATCTTTT
12952514 CATTTTT
1 CATTTTT
12952521 TCACATCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (21 bp):
CATTTTTCATTTTCATCTTTT
Found at i:12952499 original size:14 final size:14
Alignment explanation
Indices: 12952473--12952520 Score: 64
Period size: 13 Copynumber: 3.5 Consensus size: 14
12952463 TTAGCCTCTC
*
12952473 CATTTTT-ACTTTT
1 CATTTTTCATTTTT
12952486 CATTTTTCATTTTT
1 CATTTTTCATTTTT
12952500 CA-TTTTCATCTTTT
1 CATTTTTCAT-TTTT
12952514 CATTTTT
1 CATTTTT
12952521 TCACATCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 14 0.45
14 13 0.42
15 4 0.13
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:12952523 original size:8 final size:7
Alignment explanation
Indices: 12952473--12952520 Score: 64
Period size: 7 Copynumber: 7.0 Consensus size: 7
12952463 TTAGCCTCTC
12952473 CATTTTT
1 CATTTTT
*
12952480 -ACTTTT
1 CATTTTT
12952486 CATTTTT
1 CATTTTT
12952493 CATTTTT
1 CATTTTT
12952500 CA-TTTT
1 CATTTTT
12952506 CATCTTTT
1 CAT-TTTT
12952514 CATTTTT
1 CATTTTT
12952521 TCACATCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 11 0.31
7 18 0.50
8 7 0.19
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:12953466 original size:14 final size:14
Alignment explanation
Indices: 12953449--12953477 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12953439 GAAAAAATCC
12953449 AAAAGAATGAAAGA
1 AAAAGAATGAAAGA
12953463 AAAAGAATGAAAGA
1 AAAAGAATGAAAGA
12953477 A
1 A
12953478 TATTTGCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (14 bp):
AAAAGAATGAAAGA
Found at i:12954404 original size:349 final size:348
Alignment explanation
Indices: 12953761--12954455 Score: 1345
Period size: 349 Copynumber: 2.0 Consensus size: 348
12953751 CATGATTGGG
12953761 AAACGGATTTTTTTGCACTAGATGAGTCATCAAGCTTAACAACACCCATGTTGATGAGTTTTTCA
1 AAACGGATTTTTTTGCACTAGATGAGTCATCAAGCTTAACAACACCCATGTTGATGAGTTTTTCA
12953826 ACTAGCTTTTTGAAGGTAATGCAATTCTCGATAGAGTGCCCCGTAATTCTTGCATGGTAGTCACA
66 ACTAGCTTTTTGAAGGTAATGCAATTCTCGATAGAGTGCCCCGTAATTCTTGCATGGTAGTCACA
12953891 TTGTGCGTTCGCATCATACCACTTGGGATACAGAGGTTGTGGGGGTTTTAAGTAGGAAGGGGAAA
131 TTGTGCGTTCGCATCATACCACTTGGGATACAGAGGTTGTGGGGGTTTTAAGTAGGAAGGGGAAA
12953956 CAACGTGTGCATCGAATAAGCTTTGGTACAGCTCCTTATACGACATCGAAATTGGCGTGAACTGG
196 CAACGTGTGCATCGAATAAGCTTTGGTACAGCTCCTTATACGACATCGAAATTGGCGTGAACTGG
*
12954021 AGCTTCTCAATACCTGGTTTCACTCCATATTCCTGTCTCATTGAACTTTGTTGACTAGCAACCCC
261 AGCTTCTCAATACCTGGTTTCACTCCAGATTCCTGTCTCATTGAACTTTGTTGACTAGCAACCCC
12954086 CTTTCCTGGATGACTTACAGCACC
326 CTTTCCT-GATGACTTACAGCACC
12954110 AAACGGATTTTTTTGCACTAGATGAGTCATCAAGCTTAACAACACCCATGTTGATGAGTTTTTCA
1 AAACGGATTTTTTTGCACTAGATGAGTCATCAAGCTTAACAACACCCATGTTGATGAGTTTTTCA
*
12954175 ACTAGCTTTTTGAAGGTAATGCAATTCTCGATTGAGTGCCCCGTAATTCTTGCATGGTAGTCACA
66 ACTAGCTTTTTGAAGGTAATGCAATTCTCGATAGAGTGCCCCGTAATTCTTGCATGGTAGTCACA
*
12954240 TTGTGCGTTCGCATCATACCACTTGGGATACGGAGGTTGTGGGGGTTTTAAGTAGGAAGGGGAAA
131 TTGTGCGTTCGCATCATACCACTTGGGATACAGAGGTTGTGGGGGTTTTAAGTAGGAAGGGGAAA
12954305 CAACGTGTGCATCGAATAAGCTTTGGTACAGCTCCTTATACGACATCGAAATTGGCGTGAACTGG
196 CAACGTGTGCATCGAATAAGCTTTGGTACAGCTCCTTATACGACATCGAAATTGGCGTGAACTGG
*
12954370 AGCTTCTCAGTACCTGGTTTCACTCCAGATTCCTGTCTCATTGAACTTTGTTGACTAGCAACCCC
261 AGCTTCTCAATACCTGGTTTCACTCCAGATTCCTGTCTCATTGAACTTTGTTGACTAGCAACCCC
12954435 CTTTCCTGATGACTTACAGCA
326 CTTTCCTGATGACTTACAGCA
12954456 ATTGATTTAG
Statistics
Matches: 342, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
348 14 0.04
349 328 0.96
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (348 bp):
AAACGGATTTTTTTGCACTAGATGAGTCATCAAGCTTAACAACACCCATGTTGATGAGTTTTTCA
ACTAGCTTTTTGAAGGTAATGCAATTCTCGATAGAGTGCCCCGTAATTCTTGCATGGTAGTCACA
TTGTGCGTTCGCATCATACCACTTGGGATACAGAGGTTGTGGGGGTTTTAAGTAGGAAGGGGAAA
CAACGTGTGCATCGAATAAGCTTTGGTACAGCTCCTTATACGACATCGAAATTGGCGTGAACTGG
AGCTTCTCAATACCTGGTTTCACTCCAGATTCCTGTCTCATTGAACTTTGTTGACTAGCAACCCC
CTTTCCTGATGACTTACAGCACC
Found at i:12955734 original size:19 final size:19
Alignment explanation
Indices: 12955694--12955735 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12955684 ATAATCTTTT
* *
12955694 ATGCATATGATGTAATGTA
1 ATGCAAATGATGAAATGTA
12955713 ATGCAAATGCATGAAATG-A
1 ATGCAAATG-ATGAAATGTA
12955732 ATGC
1 ATGC
12955736 GAAAAGAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (19 bp):
ATGCAAATGATGAAATGTA
Found at i:12955784 original size:13 final size:13
Alignment explanation
Indices: 12955766--12955791 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12955756 GTTCAATTTT
12955766 TTTACTAGAAAAC
1 TTTACTAGAAAAC
12955779 TTTACTAGAAAAC
1 TTTACTAGAAAAC
12955792 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:12964216 original size:22 final size:22
Alignment explanation
Indices: 12964162--12964218 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
12964152 TTATTCACAC
**
12964162 AGCTCTCATGGCTAACGTACTA
1 AGCTCTCATGTTTAACGTACTA
*
12964184 AGCTCTCATGTTTCACGTACTA
1 AGCTCTCATGTTTAACGTACTA
12964206 AGCTCTCATGTTT
1 AGCTCTCATGTTT
12964219 GAACAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (22 bp):
AGCTCTCATGTTTAACGTACTA
Found at i:12965255 original size:2 final size:2
Alignment explanation
Indices: 12965248--12965278 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12965238 GCACTAAAGT
*
12965248 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12965279 TTGGATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12965330 original size:171 final size:173
Alignment explanation
Indices: 12965037--12965385 Score: 567
Period size: 171 Copynumber: 2.0 Consensus size: 173
12965027 GAGCTTATAA
*
12965037 GAGCATAAACTATACCACATCAATATGCACTAAAGTAGAGAGAGAGGGAGAGAGAGAGAAAGAGA
1 GAGCATAAACTACACCACATCAATATGCACTAAAGTAGAGAGAGA-GGAGAGAGAGAG-AAGAGA
* *
12965102 CAGAGATTGGAATCATGAATGTAAAGTTGTTTTTAAGCTTGATTTATAAAAGAATCATGCTAGGA
64 AAGAGATTGGAATCATGAATGTAAAATTGTTTTTAAGCTTGATTTATAAAAGAATCATGCTAGGA
*
12965167 AAATACTGGGATTAGTAGTAAGTGAGGCTTTATTTAGGGCTATTT
129 AAATACTGGGATTAATAGTAAGTGAGGCTTTATTTAGGGCTATTT
12965212 GAGCATAAACTACACCACATCAATATGCACTAAAGTAGAGAGAGA-GAGAGAGAGAG-AGAGAAA
1 GAGCATAAACTACACCACATCAATATGCACTAAAGTAGAGAGAGAGGAGAGAGAGAGAAGAGAAA
* * * * *
12965275 GAGATTGGATTCATGAATGTAAAATTGTTTTTAAGCTTGATTTATGAAGGAATCATGTTGGGAAA
66 GAGATTGGAATCATGAATGTAAAATTGTTTTTAAGCTTGATTTATAAAAGAATCATGCTAGGAAA
* *
12965340 ATATTGGGTTTAATAGTAAGTGAGGCTTTATTTAGGGCTATTT
131 ATACTGGGATTAATAGTAAGTGAGGCTTTATTTAGGGCTATTT
12965383 GAG
1 GAG
12965386 TAACCATTGG
Statistics
Matches: 163, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
171 108 0.66
173 11 0.07
175 44 0.27
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (173 bp):
GAGCATAAACTACACCACATCAATATGCACTAAAGTAGAGAGAGAGGAGAGAGAGAGAAGAGAAA
GAGATTGGAATCATGAATGTAAAATTGTTTTTAAGCTTGATTTATAAAAGAATCATGCTAGGAAA
ATACTGGGATTAATAGTAAGTGAGGCTTTATTTAGGGCTATTT
Found at i:12981936 original size:13 final size:13
Alignment explanation
Indices: 12981918--12981942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12981908 ACTATTTCTA
12981918 AATAAGTATTTTT
1 AATAAGTATTTTT
12981931 AATAAGTATTTT
1 AATAAGTATTTT
12981943 ATTAGTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
AATAAGTATTTTT
Found at i:12994296 original size:6 final size:6
Alignment explanation
Indices: 12994270--12994311 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
12994260 GTAGTTCCGT
* * *
12994270 CTCTGC CTCCGG CTCTAG CTCTGG CTCTGG CTCTGG CTCTGG
1 CTCTGG CTCTGG CTCTGG CTCTGG CTCTGG CTCTGG CTCTGG
12994312 TGCATGATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.02, C:0.38, G:0.29, T:0.31
Consensus pattern (6 bp):
CTCTGG
Found at i:12996029 original size:7 final size:7
Alignment explanation
Indices: 12996019--12996044 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12996009 ACTAAACATA
12996019 AATAATT
1 AATAATT
12996026 AATAATT
1 AATAATT
12996033 AATAATT
1 AATAATT
12996040 AATAA
1 AATAA
12996045 CAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATAATT
Found at i:12996575 original size:19 final size:19
Alignment explanation
Indices: 12996519--12996576 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
12996509 ATATATATTT
12996519 AAATA-TTTTTAATA-AAA
1 AAATATTTTTTAATATAAA
* * *
12996536 AATTATATTTT-ATTTAAA
1 AAATATTTTTTAATATAAA
12996554 AAATATTTTTTAATATAAA
1 AAATATTTTTTAATATAAA
12996573 AAAT
1 AAAT
12996577 TAATTCGCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 6 0.19
18 16 0.50
19 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATATTTTTTAATATAAA
Found at i:12999294 original size:14 final size:13
Alignment explanation
Indices: 12999272--12999307 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
12999262 TAAATTTAGC
12999272 TTAAATTTTTTCAA
1 TTAAATTTTTT-AA
*
12999286 TTTAATTTTTTAA
1 TTAAATTTTTTAA
12999299 TTAAATTTT
1 TTAAATTTT
12999308 AATTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAAATTTTTTAA
Found at i:12999907 original size:2 final size:2
Alignment explanation
Indices: 12999900--12999934 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12999890 TTATGTTTTC
12999900 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12999935 ATGATTATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13002653 original size:26 final size:26
Alignment explanation
Indices: 13002604--13002654 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
13002594 ACAATTAATC
**
13002604 ATAATTTTTATGTCATGTTATTTTTT
1 ATAATTTTTATGTCATAATATTTTTT
13002630 ATAATTTTTATGCTCATAAT-TTTTT
1 ATAATTTTTATG-TCATAATATTTTT
13002655 ATTCACAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (26 bp):
ATAATTTTTATGTCATAATATTTTTT
Found at i:13003418 original size:23 final size:23
Alignment explanation
Indices: 13003371--13003418 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
13003361 AAAATTTATT
* **
13003371 TATTTATTCAATCAGTTTTTTAA
1 TATTTATTCAATAAGTTTTAAAA
*
13003394 TATTTATTTAATAAGTTTTAAAA
1 TATTTATTCAATAAGTTTTAAAA
13003417 TA
1 TA
13003419 ATTCAAGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
TATTTATTCAATAAGTTTTAAAA
Found at i:13007727 original size:42 final size:42
Alignment explanation
Indices: 13007657--13007796 Score: 133
Period size: 42 Copynumber: 3.3 Consensus size: 42
13007647 GCCCGAAGGC
* * *
13007657 TGAACAAAAGCAC-ATAAGCGCTAAACAGAAACCCATAAGGGT
1 TGAACAAAAGCTCAAT-AGAGCTGAACAGAAACCCATAAGGGT
** * * *
13007699 TGAACGGAAGCTTATTAGAGCTGAACAGAAACCTATAAGGGT
1 TGAACAAAAGCTCAATAGAGCTGAACAGAAACCCATAAGGGT
* **
13007741 TAAACAAAAGCTCAATAGAGCTGAATGGAAACCCATTAA-GGT
1 TGAACAAAAGCTCAATAGAGCTGAACAGAAACCCA-TAAGGGT
13007783 TGAACAGAAA-CTCA
1 TGAACA-AAAGCTCA
13007797 TATGAGTTAA
Statistics
Matches: 78, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
42 71 0.91
43 7 0.09
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (42 bp):
TGAACAAAAGCTCAATAGAGCTGAACAGAAACCCATAAGGGT
Found at i:13010055 original size:14 final size:14
Alignment explanation
Indices: 13010036--13010063 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13010026 GAGGCTGAAT
13010036 ATGACAGAGATTAA
1 ATGACAGAGATTAA
13010050 ATGACAGAGATTAA
1 ATGACAGAGATTAA
13010064 GTATAGCCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
ATGACAGAGATTAA
Found at i:13015931 original size:24 final size:25
Alignment explanation
Indices: 13015898--13015947 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
13015888 TGTAAATCAG
13015898 AAAAATATCTC-TAGA-AATTTTCT
1 AAAAATATCTCTTAGATAATTTTCT
13015921 AAAAATAATCTCTTTAGATAATTTTCT
1 AAAAAT-ATCTC-TTAGATAATTTTCT
13015948 CTCTACAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.26
24 5 0.22
26 4 0.17
27 8 0.35
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (25 bp):
AAAAATATCTCTTAGATAATTTTCT
Found at i:13018068 original size:28 final size:28
Alignment explanation
Indices: 13018029--13018186 Score: 167
Period size: 28 Copynumber: 5.7 Consensus size: 28
13018019 GTGTCCACTG
* * *
13018029 TTTTCAAATTTTATAGTTTTGCCCCTAT
1 TTTTCAGATTTTACAGTTTTACCCCTAT
* *
13018057 TTTTCAGATTTTATAGTTTTACCTCTAT
1 TTTTCAGATTTTACAGTTTTACCCCTAT
*
13018085 TTTTGAGATTTTACAGTTTTACCCCTAAT
1 TTTTCAGATTTTACAGTTTTACCCCT-AT
* * *
13018114 TTTT-AGATTTTCCAGTTTTGCCTCTAT
1 TTTTCAGATTTTACAGTTTTACCCCTAT
* *
13018141 TTTTCAGATTTTACAGTTTT-CCCTTGT
1 TTTTCAGATTTTACAGTTTTACCCCTAT
* * *
13018168 TATTCATATTTTATAGTTT
1 TTTTCAGATTTTACAGTTT
13018187 GGACCTAGAA
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
27 26 0.23
28 80 0.71
29 6 0.05
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (28 bp):
TTTTCAGATTTTACAGTTTTACCCCTAT
Found at i:13018104 original size:56 final size:55
Alignment explanation
Indices: 13018029--13018186 Score: 192
Period size: 56 Copynumber: 2.8 Consensus size: 55
13018019 GTGTCCACTG
* *
13018029 TTTTCAAATTTTATAGTTTTGCCCCTATTTTTCAGATTTTATAGTTTTACCTCTAT
1 TTTTCAGATTTTACAGTTTT-CCCCTATTTTTCAGATTTTATAGTTTTACCTCTAT
* ** *
13018085 TTTTGAGATTTTACAGTTTTACCCCTAATTTTT-AGATTTTCCAGTTTTGCCTCTAT
1 TTTTCAGATTTTACAGTTTT-CCCCT-ATTTTTCAGATTTTATAGTTTTACCTCTAT
* * * *
13018141 TTTTCAGATTTTACAGTTTTCCCTTGTTATTCATATTTTATAGTTT
1 TTTTCAGATTTTACAGTTTTCCCCTATTTTTCAGATTTTATAGTTT
13018187 GGACCTAGAA
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
54 4 0.05
55 15 0.17
56 61 0.71
57 6 0.07
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (55 bp):
TTTTCAGATTTTACAGTTTTCCCCTATTTTTCAGATTTTATAGTTTTACCTCTAT
Found at i:13018199 original size:84 final size:84
Alignment explanation
Indices: 13018043--13018200 Score: 192
Period size: 84 Copynumber: 1.9 Consensus size: 84
13018033 CAAATTTTAT
* * * *
13018043 AGTTTTGCCCCTATTTTTCAGATTTTATAGTTTTACCTCTATTTTTGAGATTTTACAGTTTTACC
1 AGTTTTGCCCCTATTTTTCAGATTTTACAGTTTTACCTCTATTATTCAGATTTTACAGTTTGACC
**
13018108 CCTAATTTTTAGATTTTCC
66 CAGAATTTTTAGATTTTCC
* * * * *
13018127 AGTTTTGCCTCTATTTTTCAGATTTTACAGTTTTCCCT-TGTTATTCATATTTTATAGTTTGGAC
1 AGTTTTGCCCCTATTTTTCAGATTTTACAGTTTTACCTCTATTATTCAGATTTTACAGTTT-GAC
*
13018191 CTAGAATTTT
65 CCAGAATTTT
13018201 ATGTTGTGAC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
83 17 0.28
84 44 0.72
ACGTcount: A:0.20, C:0.16, G:0.11, T:0.53
Consensus pattern (84 bp):
AGTTTTGCCCCTATTTTTCAGATTTTACAGTTTTACCTCTATTATTCAGATTTTACAGTTTGACC
CAGAATTTTTAGATTTTCC
Found at i:13018578 original size:69 final size:69
Alignment explanation
Indices: 13018496--13018633 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 69
13018486 TACATGTTAT
*
13018496 CAACATAATGAAACAGATAATATGTTAGTGTTAATATTGACACTACCCTATTGAAATACCTGTTA
1 CAACATAATGAAACAGATAATATGTTAGTGTTAATATTGACACTACCCTATTGAAATACATGTTA
13018561 AAGC
66 AAGC
*
13018565 CAACATAATGAAACATATAATATGTTAGTGTTAATATTGACACTACCCTATTGAAATACATGTTA
1 CAACATAATGAAACAGATAATATGTTAGTGTTAATATTGACACTACCCTATTGAAATACATGTTA
13018630 AAGC
66 AAGC
13018634 ATGTTAAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (69 bp):
CAACATAATGAAACAGATAATATGTTAGTGTTAATATTGACACTACCCTATTGAAATACATGTTA
AAGC
Found at i:13022147 original size:2 final size:2
Alignment explanation
Indices: 13022140--13022164 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13022130 TGAGATACTA
13022140 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13022165 GACTAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13027403 original size:2 final size:2
Alignment explanation
Indices: 13027396--13027435 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
13027386 TTTTATCATG
13027396 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
13027436 TATATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:13027982 original size:12 final size:13
Alignment explanation
Indices: 13027958--13027986 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
13027948 GTCCTCAATA
13027958 TATTTAGTTTATT
1 TATTTAGTTTATT
13027971 TATTTA-TTTATT
1 TATTTAGTTTATT
13027983 TATT
1 TATT
13027987 AAAAATAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TATTTAGTTTATT
Found at i:13032598 original size:23 final size:26
Alignment explanation
Indices: 13032544--13032600 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 26
13032534 TACAAGGACT
13032544 TATGACATATTTTAACCTAGTATAAAA
1 TATGA-ATATTTTAACCTAGTATAAAA
*
13032571 TATGAATATTTTAA-TTA-TAT-AAA
1 TATGAATATTTTAACCTAGTATAAAA
13032594 TATGAAT
1 TATGAAT
13032601 GTTTAGCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 10 0.34
24 3 0.10
25 2 0.07
26 9 0.31
27 5 0.17
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (26 bp):
TATGAATATTTTAACCTAGTATAAAA
Found at i:13049353 original size:13 final size:13
Alignment explanation
Indices: 13049335--13049360 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13049325 TTTCTCAAAG
13049335 ATTTTCTCTTTTA
1 ATTTTCTCTTTTA
13049348 ATTTTCTCTTTTA
1 ATTTTCTCTTTTA
13049361 GATGGTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTCTCTTTTA
Found at i:13050581 original size:15 final size:14
Alignment explanation
Indices: 13050560--13050595 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
13050550 ATAATCCTTA
*
13050560 ATAATTATCTTAAT
1 ATAATTATCCTAAT
13050574 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
13050589 ATAATTA
1 ATAATTA
13050596 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:13053040 original size:135 final size:136
Alignment explanation
Indices: 13052768--13053048 Score: 386
Period size: 135 Copynumber: 2.1 Consensus size: 136
13052758 CAGATTGAAT
* * *
13052768 TCATGTTTAATGTCCCGGCGGACTATTTATAATGCCATAGTCAAGCTATGGTCTTACACAATTGA
1 TCATATTTAATGTCCCGGCGGACTATTTATAATGCCATAGCCAAGCTATGATCTTACACAATTGA
* * *
13052833 ATGCCCGTGTTTACTATCCCGATGGACTACCTATGTTGCCAGGGTCAAGCCAAGGCCTTACACCT
66 ACGCCCGTGTTTACTATCCCGATGAACTACCTATGTTGCCAGGGCCAAGCCAAGGCCTTACACCT
13052898 AAGATC
131 AAGATC
** * *
13052904 TCATATTTAATGTCTTGGTGGACTCTTTATAATGCCATAGCCAAGCTATGATCTTACACAATT-A
1 TCATATTTAATGTCCCGGCGGACTATTTATAATGCCATAGCCAAGCTATGATCTTACACAATTGA
* * * * * * *
13052968 ACGCTCGTGTTTATTGTCCCGATGAACTACCTATGTTGCCATGGCCAAGCCAGGGTCTTACACTT
66 ACGCCCGTGTTTACTATCCCGATGAACTACCTATGTTGCCAGGGCCAAGCCAAGGCCTTACACCT
13053033 GAA-ATC
131 -AAGATC
13053039 TCATATTTAA
1 TCATATTTAA
13053049 GATCCCAGCG
Statistics
Matches: 127, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
135 69 0.54
136 58 0.46
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (136 bp):
TCATATTTAATGTCCCGGCGGACTATTTATAATGCCATAGCCAAGCTATGATCTTACACAATTGA
ACGCCCGTGTTTACTATCCCGATGAACTACCTATGTTGCCAGGGCCAAGCCAAGGCCTTACACCT
AAGATC
Found at i:13054218 original size:25 final size:25
Alignment explanation
Indices: 13054190--13054251 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
13054180 ATTAAGTTAG
13054190 TTAAATATATTTATAAT-ATATTATT
1 TTAAATATATTTATAATAATA-TATT
*
13054215 TTAAATATATATT-TTATAATATATT
1 TTAAATATAT-TTATAATAATATATT
13054240 TTAAATA-ATTTA
1 TTAAATATATTTA
13054252 GTTAATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 24 0.73
26 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAAATATATTTATAATAATATATT
Found at i:13054221 original size:14 final size:14
Alignment explanation
Indices: 13054165--13054239 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 14
13054155 AATATTTTTA
13054165 ATTATTTTAAATAT
1 ATTATTTTAAATAT
13054179 AATTAAGTTAGTTAAATAT
1 -ATT-A-TT--TTAAATAT
*
13054198 A-T-TTAT-AATAT
1 ATTATTTTAAATAT
13054209 ATTATTTTAAATAT
1 ATTATTTTAAATAT
13054223 A-TATTTTATAATAT
1 ATTATTTTA-AATAT
13054237 ATT
1 ATT
13054240 TTAAATAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
11 6 0.12
12 2 0.04
13 10 0.20
14 14 0.29
15 4 0.08
16 1 0.02
17 3 0.06
18 1 0.02
19 8 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTATTTTAAATAT
Found at i:13054247 original size:14 final size:14
Alignment explanation
Indices: 13054193--13054248 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
13054183 AAGTTAGTTA
13054193 AATATA-TTTATAAT
1 AATATATTTTA-AAT
13054207 -ATATTATTTTAAAT
1 AATA-TATTTTAAAT
13054221 -ATATATTTT--AT
1 AATATATTTTAAAT
13054232 AATATATTTTAAAT
1 AATATATTTTAAAT
13054246 AAT
1 AAT
13054249 TTAGTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.05
12 9 0.24
13 9 0.24
14 13 0.35
15 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATATTTTAAAT
Found at i:13054250 original size:10 final size:12
Alignment explanation
Indices: 13054193--13054250 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
13054183 AAGTTAGTTA
13054193 AATATA-TTTAT
1 AATATATTTTAT
*
13054204 AATATATTATTTTAA
1 -A-ATA-TATTTTAT
13054219 ATATATATTTTAT
1 A-ATATATTTTAT
13054232 AATATATTTTA-
1 AATATATTTTAT
13054243 AATA-ATTT
1 AATATATTT
13054251 AGTTAATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 4 0.10
11 4 0.10
12 11 0.27
13 11 0.27
14 7 0.17
15 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATATATTTTAT
Found at i:13069119 original size:20 final size:21
Alignment explanation
Indices: 13069090--13069214 Score: 89
Period size: 20 Copynumber: 5.9 Consensus size: 21
13069080 TTAATTAAAT
13069090 TTAATTTAATATTAAGA-TAA
1 TTAATTTAATATTAAGATTAA
*
13069110 TTACTTTAATATTAA-ATTAA
1 TTAATTTAATATTAAGATTAA
* * *
13069130 TAAAATAATATTAAGATAAACATTAAA
1 T----TAAT-TTAATATTAAGATT-AA
13069157 TTAAATTTAATATTAAGA-TAA
1 TT-AATTTAATATTAAGATTAA
*
13069178 TTACTTTAATATTAA-ATTAA
1 TTAATTTAATATTAAGATTAA
**
13069198 -TAAAATAATATTAAGAT
1 TTAATTTAATATTAAGAT
13069215 AAACATTAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
19 13 0.16
20 35 0.42
21 4 0.05
22 1 0.01
23 10 0.12
24 6 0.07
25 8 0.10
26 3 0.04
27 3 0.04
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (21 bp):
TTAATTTAATATTAAGATTAA
Found at i:13069155 original size:31 final size:31
Alignment explanation
Indices: 13069120--13069228 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 31
13069110 TTACTTTAAT
13069120 ATTAAATTAATAAAATAATATTAAGATAAAC
1 ATTAAATTAATAAAATAATATTAAGATAAAC
**
13069151 ATTAAATT-A-AATTTAATATTAAGATAATTAC
1 ATTAAATTAATAAAATAATATTAAGATAA--AC
13069182 TTTAATATTAAATTAATAAAATAATATTAAGATAAAC
1 ------ATTAAATTAATAAAATAATATTAAGATAAAC
13069219 ATTAAATTAA
1 ATTAAATTAA
13069229 ATTTAATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
29 16 0.25
30 1 0.02
31 20 0.31
37 10 0.16
38 1 0.02
39 16 0.25
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (31 bp):
ATTAAATTAATAAAATAATATTAAGATAAAC
Found at i:13069164 original size:68 final size:68
Alignment explanation
Indices: 13069083--13069240 Score: 307
Period size: 68 Copynumber: 2.3 Consensus size: 68
13069073 AATTTTATTA
*
13069083 ATTAAATTTAATTTAATATTAAGATAATTACTTTAATATTAAATTAATAAAATAATATTAAGATA
1 ATTAAATTAAATTTAATATTAAGATAATTACTTTAATATTAAATTAATAAAATAATATTAAGATA
13069148 AAC
66 AAC
13069151 ATTAAATTAAATTTAATATTAAGATAATTACTTTAATATTAAATTAATAAAATAATATTAAGATA
1 ATTAAATTAAATTTAATATTAAGATAATTACTTTAATATTAAATTAATAAAATAATATTAAGATA
13069216 AAC
66 AAC
13069219 ATTAAATTAAATTTAATATTAA
1 ATTAAATTAAATTTAATATTAA
13069241 ACTATTAAAA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 89 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (68 bp):
ATTAAATTAAATTTAATATTAAGATAATTACTTTAATATTAAATTAATAAAATAATATTAAGATA
AAC
Found at i:13069192 original size:37 final size:35
Alignment explanation
Indices: 13069082--13069255 Score: 128
Period size: 37 Copynumber: 4.9 Consensus size: 35
13069072 AAATTTTATT
*
13069082 AATTAAATTTAATTTAATATTAAGATAATTACTTTA
1 AATTAAATTAAATTTAATATTAAGATAA-TACTTTA
**
13069118 ATATTAAATTAATAAAATAATATTAAGATAA-AC----
1 A-ATTAAATT-A-AATTTAATATTAAGATAATACTTTA
13069151 -ATTAAATTAAATTTAATATTAAGATAATTACTTTA
1 AATTAAATTAAATTTAATATTAAGATAA-TACTTTA
** *
13069186 ATATTAAATTAATAAAATAATATTAAGATAA-ACATTA
1 A-ATTAAATT-A-AATTTAATATTAAGATAATACTTTA
* *
13069223 AATTAAATTTAATATTAAACTATTAAAATAATA
1 AATTAAA-TTAA-ATTTAA-TATTAAGATAATA
13069256 TTATTTTTGG
Statistics
Matches: 109, Mismatches: 12, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
29 16 0.15
30 1 0.01
31 10 0.09
35 1 0.01
36 11 0.10
37 36 0.33
38 2 0.02
39 32 0.29
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (35 bp):
AATTAAATTAAATTTAATATTAAGATAATACTTTA
Found at i:13070912 original size:41 final size:40
Alignment explanation
Indices: 13070866--13070963 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 40
13070856 CAGAACACCG
*
13070866 GCATTAAGCCTGCTAGACATATAGTCTGAAA-ATTTTTACC
1 GCATTAAGCCTGCTAGACATATAGTCCGAAATA-TTTTACC
*
13070906 GACATTAAGCCTGCTAGACGTATAGTCCGAAATATTTTACCC
1 G-CATTAAGCCTGCTAGACATATAGTCCGAAATATTTTA-CC
*
13070948 GCGTTAAGCCTGCTAG
1 GCATTAAGCCTGCTAG
13070964 GCACAAAGGC
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
40 1 0.02
41 47 0.90
42 4 0.08
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (40 bp):
GCATTAAGCCTGCTAGACATATAGTCCGAAATATTTTACC
Found at i:13071304 original size:37 final size:37
Alignment explanation
Indices: 13071185--13071304 Score: 111
Period size: 37 Copynumber: 3.2 Consensus size: 37
13071175 ATATAAGAAA
*
13071185 CATACTTTAATTTCCAACTCAATAACTTGATTAAATG
1 CATACATTAATTTCCAACTCAATAACTTGATTAAATG
* * * *
13071222 CATACA-TATATGTTCGAATCTCCCTATAA-TT-ATAAAATT
1 CATACATTA-AT-TTCCAA-CT--CAATAACTTGATTAAATG
* *
13071261 CATACATTAATTCCCAACTCAATAACTTGATTATATG
1 CATACATTAATTTCCAACTCAATAACTTGATTAAATG
13071298 CATACAT
1 CATACAT
13071305 ATTTATATTC
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
35 5 0.08
36 4 0.06
37 21 0.33
38 9 0.14
39 16 0.25
40 4 0.06
41 5 0.08
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (37 bp):
CATACATTAATTTCCAACTCAATAACTTGATTAAATG
Found at i:13074250 original size:9 final size:9
Alignment explanation
Indices: 13074236--13074272 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
13074226 TATAGTTTGA
13074236 TATTCGAAT
1 TATTCGAAT
13074245 TATTCGAAT
1 TATTCGAAT
*
13074254 TATTCGAGT
1 TATTCGAAT
13074263 TATTCGAAT
1 TATTCGAAT
13074272 T
1 T
13074273 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:13077515 original size:25 final size:25
Alignment explanation
Indices: 13077487--13077535 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
13077477 CACTTCACTT
* *
13077487 AACTTTTAG-TTTTTTTTCTTCAAAA
1 AACTCTTAGATTTTCTTT-TTCAAAA
13077512 AACTCTTAGATTTTCTTTTTCAAA
1 AACTCTTAGATTTTCTTTTTCAAA
13077536 CTTATCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (25 bp):
AACTCTTAGATTTTCTTTTTCAAAA
Found at i:13083084 original size:2 final size:2
Alignment explanation
Indices: 13083079--13083106 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13083069 ATGTATATGG
13083079 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
13083107 GTAGATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13083193 original size:2 final size:2
Alignment explanation
Indices: 13083186--13083219 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13083176 ACATACATAG
*
13083186 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13083220 GTACAACGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13083350 original size:3 final size:3
Alignment explanation
Indices: 13083342--13083370 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13083332 TAAATGAATA
13083342 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
13083371 ATTTGTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:13084068 original size:11 final size:12
Alignment explanation
Indices: 13084052--13084088 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
13084042 AGAAAACTCA
13084052 AAAAAT-AAAGT
1 AAAAATAAAAGT
*
13084063 AAAAATAAAAAT
1 AAAAATAAAAGT
13084075 AAAAATAAAAGT
1 AAAAATAAAAGT
13084087 AA
1 AA
13084089 GTAAATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAAATAAAAGT
Found at i:13084073 original size:6 final size:6
Alignment explanation
Indices: 13084052--13084084 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
13084042 AGAAAACTCA
*
13084052 AAAAAT -AAAGT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
13084085 GTAAGTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:13084106 original size:28 final size:23
Alignment explanation
Indices: 13084051--13084106 Score: 58
Period size: 27 Copynumber: 2.3 Consensus size: 23
13084041 AAGAAAACTC
13084051 AAAAAATAAAGTAAAAATAAAAA
1 AAAAAATAAAGTAAAAATAAAAA
*
13084074 TAAAAATAAAAGTAAGTAAATGAAAAA
1 AAAAAAT-AAAGTAA--AAAT-AAAAA
*
13084101 GAAAAA
1 AAAAAA
13084107 GAACTCAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 6 0.22
24 7 0.26
26 4 0.15
27 10 0.37
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (23 bp):
AAAAAATAAAGTAAAAATAAAAA
Found at i:13085073 original size:132 final size:132
Alignment explanation
Indices: 13084836--13085630 Score: 1292
Period size: 132 Copynumber: 6.0 Consensus size: 132
13084826 ATTGTTGATA
* * * * *
13084836 TGCTCTACTACTGCTTAGGGTGACAAAATCTACAATCTTCAACCTACTCCACTACTACTTAGGGT
1 TGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGT
* * * *
13084901 GATAGGACTAACGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAATATTTACCATATTCGA
66 GATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGA
13084966 TC
131 TC
* * * *
13084968 TGCTCTACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACCTATTCCACTACTGCTTAGGGT
1 TGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGT
*
13085033 GATAGGACTAATGGCTTAAATCTGCTTCTCCATTGTATTGGGAAGAT-AGATTCACCATCTTCGA
66 GATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGA
13085097 TC
131 TC
* *
13085099 TGCT-CACTACTGCTTA-GGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCTTAGGGT
1 TGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGT
*
13085162 GATCA-GACTAATGGCTTAAGTCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCG
66 GAT-AGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCG
13085226 ATC
130 ATC
* *
13085229 TGCTCCACTACTAATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCTTAGGGT
1 TGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGT
* * *
13085294 GATAGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGAAAGATAAGATTCACCATCTTTGA
66 GATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGA
13085359 TC
131 TC
* *
13085361 TGTTCCACTACTGATTAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGT
1 TGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGT
* *
13085426 GATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGAAAGATAAGATTCACCATCTTTGA
66 GATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGA
13085491 TC
131 TC
* *
13085493 TGTTCCACTACTGATTAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGT
1 TGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGT
*
13085558 GATAGGACTAATGGCTTAAATCTGTTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGA
66 GATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGA
13085623 TC
131 TC
13085625 TGCTCC
1 TGCTCC
13085631 GCTGCCAAAT
Statistics
Matches: 629, Mismatches: 29, Indels: 10
0.94 0.04 0.01
Matches are distributed among these distances:
129 89 0.14
130 35 0.06
131 31 0.05
132 474 0.75
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (132 bp):
TGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGT
GATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGA
TC
Found at i:13085665 original size:46 final size:46
Alignment explanation
Indices: 13085615--13085989 Score: 570
Period size: 46 Copynumber: 8.2 Consensus size: 46
13085605 AAGATTCACC
* *
13085615 ATCTTCGATCTGCTCCGCTGCCAAATACAGAAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * * *
13085661 ATCTTCGATCTCTTCCGCTACCAAATACAAGAAGAAAATATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
13085707 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
13085753 ATCTTCGATCTCTTCCGCTGCTAAATACAGGAAGACAAGATCTGTT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
13085799 ATCTTCGATCTCTTCCGCTGCCAAATACAGGAAGACAAGATCTGTT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
*
13085845 ATCTTCGATCTCCTCCGCTGCCAAATACAGAAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * * * * *
13085891 ATTTTTGATCTCCTTCGTTGCCAAATACAGGAAGATAAGATATGTT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
13085937 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
13085983 ATCTTCG
1 ATCTTCG
13085990 TTGATCTATT
Statistics
Matches: 295, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 295 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (46 bp):
ATCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCT
Found at i:13087225 original size:8 final size:8
Alignment explanation
Indices: 13087212--13087275 Score: 112
Period size: 8 Copynumber: 8.0 Consensus size: 8
13087202 CTTTTTTCTC
13087212 TTTCATTT
1 TTTCATTT
13087220 TTTCA-TT
1 TTTCATTT
13087227 TTTCATTT
1 TTTCATTT
13087235 TTTCATTT
1 TTTCATTT
13087243 TTTCATTT
1 TTTCATTT
13087251 TTTCATTT
1 TTTCATTT
13087259 TTTCATTTT
1 TTTCA-TTT
13087268 TTTCATTT
1 TTTCATTT
13087276 CATTTTTGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.13
8 39 0.72
9 8 0.15
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTCATTT
Found at i:13087236 original size:16 final size:15
Alignment explanation
Indices: 13087203--13087275 Score: 103
Period size: 16 Copynumber: 4.7 Consensus size: 15
13087193 TGGCCTCTCC
*
13087203 TTTTTTC-TCTTTCA
1 TTTTTTCATTTTTCA
13087217 TTTTTTCATTTTTCA
1 TTTTTTCATTTTTCA
13087232 TTTTTTCATTTTTTCA
1 TTTTTTCA-TTTTTCA
13087248 TTTTTTCATTTTTTCA
1 TTTTTTCA-TTTTTCA
13087264 TTTTTTTCATTT
1 -TTTTTTCATTT
13087276 CATTTTTGTT
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
14 7 0.13
15 14 0.25
16 26 0.47
17 8 0.15
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTTCATTTTTCA
Found at i:13087306 original size:11 final size:12
Alignment explanation
Indices: 13087278--13087305 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13087268 TTTCATTTCA
13087278 TTTTTGTTTTGT
1 TTTTTGTTTTGT
13087290 TTTTTGTTTTGT
1 TTTTTGTTTTGT
13087302 TTTT
1 TTTT
13087306 GACTCAAAGT
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:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (12 bp):
TTTTTGTTTTGT
Found at i:13088107 original size:7 final size:7
Alignment explanation
Indices: 13088095--13088128 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
13088085 TGACCTCTCC
13088095 TTTTTCT
1 TTTTTCT
13088102 TTTTTCT
1 TTTTTCT
*
13088109 TCTTT-T
1 TTTTTCT
13088115 TTTTTCT
1 TTTTTCT
13088122 TTTTTCT
1 TTTTTCT
13088129 CCTATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:13088113 original size:10 final size:10
Alignment explanation
Indices: 13088098--13088128 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
13088088 CCTCTCCTTT
13088098 TTCTTTTTTC
1 TTCTTTTTTC
*
13088108 TTCTTTTTTT
1 TTCTTTTTTC
13088118 TTCTTTTTTC
1 TTCTTTTTTC
13088128 T
1 T
13088129 CCTATTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:13088136 original size:20 final size:20
Alignment explanation
Indices: 13088095--13088137 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13088085 TGACCTCTCC
* *
13088095 TTTTTCTTTTTTCTTCTTTT
1 TTTTTCTTTTTTCTCCTATT
13088115 TTTTTCTTTTTTCTCCTATT
1 TTTTTCTTTTTTCTCCTATT
13088135 TTT
1 TTT
13088138 GACTTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTCTTTTTTCTCCTATT
Found at i:13088143 original size:20 final size:20
Alignment explanation
Indices: 13088100--13088143 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
13088090 TCTCCTTTTT
* * **
13088100 CTTTTTTCTTCTTTTTTTTT
1 CTTTTTTCTCCTATTTTTGA
13088120 CTTTTTTCTCCTATTTTTGA
1 CTTTTTTCTCCTATTTTTGA
13088140 CTTT
1 CTTT
13088144 GATTTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (20 bp):
CTTTTTTCTCCTATTTTTGA
Found at i:13088158 original size:14 final size:14
Alignment explanation
Indices: 13088141--13088167 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13088131 TATTTTTGAC
13088141 TTTGATTTTTTTTA
1 TTTGATTTTTTTTA
13088155 TTTGATTTTTTTT
1 TTTGATTTTTTTT
13088168 GAGTCTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTGATTTTTTTTA
Found at i:13093008 original size:2 final size:2
Alignment explanation
Indices: 13093003--13093042 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
13092993 ATGTATATGG
13093003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13093043 GTAGATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13093166 original size:2 final size:2
Alignment explanation
Indices: 13093122--13093157 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
13093112 ACATACATAG
*
13093122 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13093158 AAAATATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13097289 original size:46 final size:46
Alignment explanation
Indices: 13097186--13097337 Score: 256
Period size: 46 Copynumber: 3.4 Consensus size: 46
13097176 TACGTATGAT
* *
13097186 CACTTATCAC-TTGTCTC-TGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
13097229 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
13097275 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
13097321 CACTTATCACTTTGTCA
1 CACTTATCACTTTGTCA
13097338 TTTGTCACTG
Statistics
Matches: 103, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
43 10 0.10
44 6 0.06
45 19 0.18
46 68 0.66
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:13109508 original size:37 final size:37
Alignment explanation
Indices: 13109454--13109566 Score: 174
Period size: 37 Copynumber: 3.1 Consensus size: 37
13109444 TTATGTGTTA
13109454 ATTC-AAGACTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
* * *
13109490 ATTCAAAGACTTATGTAATATTTTTAGTCATGTAGTG
1 ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
* *
13109527 ATTCAAAGATTTACGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
13109564 ATT
1 ATT
13109567 TTATTCAGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
36 4 0.06
37 64 0.94
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
Found at i:13109598 original size:11 final size:10
Alignment explanation
Indices: 13109574--13109610 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
13109564 ATTTTATTCA
13109574 GGTAATTT-G
1 GGTAATTTCG
13109583 GGTAATTTTCG
1 GGTAA-TTTCG
13109594 GGTAA-TTCG
1 GGTAATTTCG
13109603 GGTAATTT
1 GGTAATTT
13109611 TTAACCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 14 0.56
10 5 0.20
11 6 0.24
ACGTcount: A:0.22, C:0.05, G:0.30, T:0.43
Consensus pattern (10 bp):
GGTAATTTCG
Found at i:13109599 original size:20 final size:20
Alignment explanation
Indices: 13109574--13109611 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13109564 ATTTTATTCA
*
13109574 GGTAATTTGGGTAATTTTCG
1 GGTAATTCGGGTAATTTTCG
13109594 GGTAATTCGGGTAATTTT
1 GGTAATTCGGGTAATTTT
13109612 TAACCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.29, T:0.45
Consensus pattern (20 bp):
GGTAATTCGGGTAATTTTCG
Found at i:13109746 original size:28 final size:27
Alignment explanation
Indices: 13109703--13109780 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 27
13109693 ATTATTTTAA
* *
13109703 AAAAAATTCGGTTCGGTTAACGGTTA-
1 AAAAATTTCGGGTCGGTTAACGGTTAT
*
13109729 AAAAATTTGGGAGGTCGGTTAATTCGGTTAT
1 AAAAATTT-CG-GGTCGGTTAA--CGGTTAT
*
13109760 AACAATTTCGGGTCGGTTAAC
1 AAAAATTTCGGGTCGGTTAAC
13109781 CGGTCGGTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
26 7 0.17
27 2 0.05
28 9 0.21
29 10 0.24
30 7 0.17
31 7 0.17
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.32
Consensus pattern (27 bp):
AAAAATTTCGGGTCGGTTAACGGTTAT
Found at i:13110761 original size:40 final size:42
Alignment explanation
Indices: 13110646--13110776 Score: 101
Period size: 37 Copynumber: 3.0 Consensus size: 42
13110636 CCACTGATCC
*
13110646 TAATAACTAACACAATAAAAATAATAATAGTTTTATACTCAAAATAA
1 TAATAACTAAC-C-ATAATAATAAT-ATAGTTTTATA-T-AAAATAA
* * **
13110693 TAGTAACTAACAATAATAAT--TAGGGTTTTAT-T-AAA-AA
1 TAATAACTAACCATAATAATAATATAGTTTTATATAAAATAA
*
13110730 TAATAACTAACCATAATAATAATACTAGTTTTTTACTAACAATAA
1 TAATAACTAACCATAATAATAATA-TAGTTTTATA-TAA-AATAA
13110775 TA
1 TA
13110777 CTACGTAACA
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
37 20 0.30
38 3 0.05
39 2 0.03
40 7 0.11
42 9 0.14
43 2 0.03
44 2 0.03
45 11 0.17
47 10 0.15
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.34
Consensus pattern (42 bp):
TAATAACTAACCATAATAATAATATAGTTTTATATAAAATAA
Found at i:13110764 original size:42 final size:42
Alignment explanation
Indices: 13110646--13110776 Score: 124
Period size: 42 Copynumber: 3.1 Consensus size: 42
13110636 CCACTGATCC
* *
13110646 TAATAACTAACACAATAAAAATAATAATAGTTTTATACTCAAAA
1 TAATAACTAAC-C-ATAAAAATAATAATAGTTTTTTACTAAAAA
* * ** *
13110690 TAAT-AGTAA-C-TAACAATAATAATTAGGGTTTTATTAAAAA
1 TAATAACTAACCATAAAAATAATAA-TAGTTTTTTACTAAAAA
* * *
13110730 TAATAACTAACCATAATAATAATACTAGTTTTTTACTAACAA
1 TAATAACTAACCATAAAAATAATAATAGTTTTTTACTAAAAA
13110772 TAATA
1 TAATA
13110777 CTACGTAACA
Statistics
Matches: 69, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
39 11 0.16
40 16 0.23
41 5 0.07
42 19 0.28
43 14 0.20
44 4 0.06
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.34
Consensus pattern (42 bp):
TAATAACTAACCATAAAAATAATAATAGTTTTTTACTAAAAA
Found at i:13111895 original size:25 final size:24
Alignment explanation
Indices: 13111867--13111926 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
13111857 TGCAATTGAG
13111867 ATATATCTATATATA-TAATATTCT
1 ATATATCTATATATACTAATA-TCT
13111891 CATAT-T-TATATAATACTAATATCT
1 -ATATATCTATAT-ATACTAATATCT
13111915 A-ATATCTA-ATAT
1 ATATATCTATATAT
13111927 CAAATGTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
22 4 0.13
23 9 0.29
24 9 0.29
25 9 0.29
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATATCTATATATACTAATATCT
Found at i:13125098 original size:4 final size:4
Alignment explanation
Indices: 13125091--13125119 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
13125081 ACAGAGAGAC
13125091 AGGG AGGG AGGG AGGG AGGG AGGG AGGG A
1 AGGG AGGG AGGG AGGG AGGG AGGG AGGG A
13125120 TGCATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.72, T:0.00
Consensus pattern (4 bp):
AGGG
Found at i:13126347 original size:2 final size:2
Alignment explanation
Indices: 13126340--13126401 Score: 115
Period size: 2 Copynumber: 30.5 Consensus size: 2
13126330 TAAAAGAGTA
13126340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13126382 AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT A-T AT A
13126402 CTAATAACGT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 57 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13132707 original size:25 final size:25
Alignment explanation
Indices: 13132659--13132707 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
13132649 TTGCAGTGGC
* *
13132659 TGATTTCTCTTTTGTTAGCTCTGAT
1 TGATTTCTCTTTTGTCAGCGCTGAT
13132684 TGATTTCTCTTTTG-CAGCGGCTGA
1 TGATTTCTCTTTTGTCAGC-GCTGA
13132708 CAATGCCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.49
Consensus pattern (25 bp):
TGATTTCTCTTTTGTCAGCGCTGAT
Found at i:13133294 original size:67 final size:67
Alignment explanation
Indices: 13133214--13133362 Score: 262
Period size: 67 Copynumber: 2.2 Consensus size: 67
13133204 AGAAAATTTT
* *
13133214 AACAATATGATAAACAATCTAAATAAAGGGTAATTGTATTATTATAAAAAATTTGTACAATATGA
1 AACAATATGATAAACAATCTAAATAAAGGGTAATTATAATATTATAAAAAATTTGTACAATATGA
13133279 TA
66 TA
* *
13133281 AACAATACGATAAACAATCTAAATAAAGGGTAATTATAATATTATAGAAAATTTGTACAATATGA
1 AACAATATGATAAACAATCTAAATAAAGGGTAATTATAATATTATAAAAAATTTGTACAATATGA
13133346 TA
66 TA
13133348 AACAATATGATAAAC
1 AACAATATGATAAAC
13133363 CTTGTATACA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 77 1.00
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.30
Consensus pattern (67 bp):
AACAATATGATAAACAATCTAAATAAAGGGTAATTATAATATTATAAAAAATTTGTACAATATGA
TA
Found at i:13133354 original size:12 final size:12
Alignment explanation
Indices: 13133337--13133362 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13133327 GAAAATTTGT
13133337 ACAATATGATAA
1 ACAATATGATAA
13133349 ACAATATGATAA
1 ACAATATGATAA
13133361 AC
1 AC
13133363 CTTGTATACA
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:0.58, C:0.12, G:0.08, T:0.23
Consensus pattern (12 bp):
ACAATATGATAA
Done.