Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 188 of 410
Found at i:57463627 original size:27 final size:27
Alignment explanation
Indices: 57463579--57463669 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 27
57463569 GGGCAAAATG
* * ** *
57463579 GTAATTTTACCCCACAAAGGTATCTCA
1 GTAATTCTACCCTACAGGGGTATTTCA
* *
57463606 GAAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCA
* * * *
57463633 GTATTTCTACCTTATAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCA
57463660 GTAATTCTAC
1 GTAATTCTAC
57463670 AACTTATCCA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCA
Found at i:57466358 original size:46 final size:46
Alignment explanation
Indices: 57466209--57466382 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 46
57466199 TGTAACCCGC
* * *
57466209 CCATAAGTGAACTCGGACTCAACTCAAC-AGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
* * *
57466254 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GATGCCTAGTTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACG-CTCG-CAT
*** * *
57466301 --ATCTCTCGAACTCGGACTCAACTTAACGAGTTCGGACGCTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
*
57466346 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
57466383 TGCCCAAATA
Statistics
Matches: 104, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
45 35 0.34
46 61 0.59
47 8 0.08
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
Found at i:57466373 original size:92 final size:92
Alignment explanation
Indices: 57466217--57466386 Score: 270
Period size: 92 Copynumber: 1.8 Consensus size: 92
57466207 GCCCATAAGT
* *
57466217 GAACTCGGACTCAACTCAACAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACAGCTCGGACGCTCACATCCATAAGTGAACTCGGACTCAACTCAAC
57466282 GAGCTC-GATGCCTAGTTATATCTCTC
66 GAGCTCGGATGCCTAGTTATATCTCTC
* * *
57466308 GAACTCGGACTCAACTTAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAC-AGCTCGGACGCTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
57466373 CGAGTTCGGATGCC
65 CGAGCTCGGATGCC
57466387 CAAATATCCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
91 19 0.27
92 46 0.65
93 6 0.08
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACAGCTCGGACGCTCACATCCATAAGTGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTATATCTCTC
Found at i:57466401 original size:46 final size:45
Alignment explanation
Indices: 57466259--57466401 Score: 114
Period size: 46 Copynumber: 3.1 Consensus size: 45
57466249 CACATCCATA
* * *
57466259 AGTGAACTCGGACTCAACTCAACGAGCTC-GATGCCTAGTTATATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---ATATCCC
* * * ** *
57466306 --TCGAACTCGGACTCAACTTAACGAGTTCGGACGCTC-GCATCCATA
1 AGT-GAACTCGGACTCAACTCAACGAGTTCGGATGCCCAATATCC--C
57466351 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AATATCCC
57466397 AGTGA
1 AGTGA
57466402 CATGTCACTT
Statistics
Matches: 73, Mismatches: 15, Indels: 17
0.70 0.14 0.16
Matches are distributed among these distances:
43 3 0.04
45 1 0.01
46 60 0.82
47 5 0.07
48 4 0.05
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAATATCCC
Found at i:57469505 original size:40 final size:39
Alignment explanation
Indices: 57469461--57469678 Score: 233
Period size: 40 Copynumber: 5.5 Consensus size: 39
57469451 GCTCGATTGT
* * *
57469461 CTTCGGGACATT-GCCCGGTTATAGTGATTCGCACAATTGC
1 CTTCGGGAC-TTAGCCCGGTT-TAGTAACTCGCACAAATGC
* *
57469501 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGC
* *
57469541 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGC
* * *
57469581 CTTCGGGACTTAACCCGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGTTTAGTAACTCGCACAAATGC
* * * *
57469620 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGG-TTTAGTAAC-TCGCACAAATGC
57469661 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
57469679 ACACCATTCG
Statistics
Matches: 153, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
39 37 0.24
40 88 0.58
41 27 0.18
42 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.27
Consensus pattern (39 bp):
CTTCGGGACTTAGCCCGGTTTAGTAACTCGCACAAATGC
Found at i:57469612 original size:39 final size:40
Alignment explanation
Indices: 57469489--57469679 Score: 240
Period size: 40 Copynumber: 4.8 Consensus size: 40
57469479 TTATAGTGAT
* * *
57469489 TCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* * *
57469529 TCGCACGAATGCCTTCGGGACTTAACCCGGTTTTGGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* *
57469569 TCGCACAAATGCCTTCGGGACTTAACCC-GTTTTGGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* * *
57469608 TCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTCAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* * *
57469648 TTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 -TCGCACAAATGCCTTCGGGACTTAACCCGGA
57469680 CACCATTCGA
Statistics
Matches: 132, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
39 37 0.28
40 69 0.52
41 26 0.20
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
Found at i:57470395 original size:2 final size:2
Alignment explanation
Indices: 57470388--57470413 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57470378 ATGTGCAAAC
57470388 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
57470414 GCTAGAGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57477599 original size:40 final size:38
Alignment explanation
Indices: 57477555--57477771 Score: 206
Period size: 40 Copynumber: 5.5 Consensus size: 38
57477545 GCTCGATTGT
* *
57477555 CTTCGGGACATT-GCCCGGTTATAGTGATTCGCACAATTGC
1 CTTCGGGAC-TTAGCCCGGTT-TAGTAACTCGCACAA-TGC
*
57477595 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCAC-AATGC
* *
57477635 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAATGC
1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCACAATGC
* *
57477674 CTTCGGGACTTA-ACCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCAC-AATGC
* * * *
57477713 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGG-TTTAGTAAC-TCGCAC-AATGC
57477754 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
57477772 ACACCATTCG
Statistics
Matches: 153, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
38 20 0.13
39 34 0.22
40 69 0.45
41 29 0.19
42 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (38 bp):
CTTCGGGACTTAGCCCGGTTTAGTAACTCGCACAATGC
Found at i:57477653 original size:80 final size:77
Alignment explanation
Indices: 57477541--57477772 Score: 232
Period size: 80 Copynumber: 2.9 Consensus size: 77
57477531 GGATATAGCG
* * * * * *
57477541 ACTCGCTCGATTGTCTTCGGGACATTGCCCGGTTATAGTGATTCGCACAATTGCCTTCGGGAATT
1 ACTCGCACGAATGCCTTCGGGAC-TTACCCGGTT-TAGTAATTCGCACAA-TGCCTTCGGGACTT
57477606 AGCCCGGATTTAGTA
63 AGCCCGGATTTAGTA
* *
57477621 ACTCGCACGAATGCCTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAATGCCTTCGGGACTTA
1 ACTCGCACGAATGCCTTCGGGACTT-ACCCGG-TTTAGTAATTCGCACAATGCCTTCGGGACTTA
* * *
57477686 -ACCGGTTTTGGTA
64 GCCCGGATTTAGTA
* * * * *
57477699 ACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACT
1 ACTCGCACGAATGCCTTCGGGACTT-ACCCGG-TTTAGT-AATTCGCAC-AATGCCTTCGGGACT
57477764 TAGCCCGGA
62 TAGCCCGGA
57477773 CACCATTCGA
Statistics
Matches: 125, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
78 44 0.35
79 22 0.18
80 53 0.42
81 6 0.05
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.27
Consensus pattern (77 bp):
ACTCGCACGAATGCCTTCGGGACTTACCCGGTTTAGTAATTCGCACAATGCCTTCGGGACTTAGC
CCGGATTTAGTA
Found at i:57477684 original size:39 final size:40
Alignment explanation
Indices: 57477583--57477772 Score: 231
Period size: 40 Copynumber: 4.8 Consensus size: 40
57477573 TTATAGTGAT
* * *
57477583 TCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* * *
57477623 TCGCACGAATGCCTTCGGGACTTAACCCGGTTTTGGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* *
57477663 TCGCAC-AATGCCTTCGGGACTTAA-CCGGTTTTGGTAAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* * *
57477701 TCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTCAC
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
* * *
57477741 TTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 -TCGCACAAATGCCTTCGGGACTTAACCCGGA
57477773 CACCATTCGA
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
38 20 0.15
39 34 0.26
40 51 0.39
41 26 0.20
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC
Found at i:57478488 original size:2 final size:2
Alignment explanation
Indices: 57478481--57478505 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57478471 ATGTGCAAAC
57478481 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
57478506 GCTAGAGCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57489284 original size:40 final size:40
Alignment explanation
Indices: 57489239--57489368 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
57489229 CGGAATACAA
57489239 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
57489279 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
57489319 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
57489359 CCGGATATAA
1 CCGGATATAA
57489369 TTTCCAGCAT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:57489383 original size:40 final size:40
Alignment explanation
Indices: 57489239--57489402 Score: 145
Period size: 40 Copynumber: 4.1 Consensus size: 40
57489229 CGGAATACAA
* **
57489239 CCGGATATAACCACGTGCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCACCAGCAC-AATTGCCTTCGGGTCTTAGC
* *
57489279 CCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC
* ** * *
57489319 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
** * * *
57489359 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
57489399 CCGG
1 CCGG
57489403 GTATCATTCA
Statistics
Matches: 100, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
39 2 0.02
40 98 0.98
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:57491169 original size:40 final size:39
Alignment explanation
Indices: 57491114--57491247 Score: 162
Period size: 40 Copynumber: 3.4 Consensus size: 39
57491104 GGCTGTCACA
*
57491114 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 TTATATCCGGGCTAAGACCCGAAGGCATT-GTGCAAGTTG
*
57491154 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTA
1 TTATATCCGGGCTAAGACCCGAAGGCA-TTGTGCAAGTTG
* * * ** *
57491194 TCAAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTGTGCAAGTTG
57491234 TTATATCC-GGCTAA
1 TTATATCCGGGCTAA
57491248 ATTCCGAAGA
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
39 5 0.06
40 72 0.90
41 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTGTGCAAGTTG
Found at i:57501973 original size:29 final size:29
Alignment explanation
Indices: 57501899--57501971 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
57501889 CACCTAGTTG
*
57501899 TTGGACCAAGTTGGGTGAATGACAGGTTC
1 TTGGACCGAGTTGGGTGAATGACAGGTTC
57501928 TTGGACCGAGTTGGGTGAATGACAGGTTC
1 TTGGACCGAGTTGGGTGAATGACAGGTTC
57501957 TTGGACCTGAGTTGG
1 TTGGACC-GAGTTGG
57501972 TGGCAGATAC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 35 0.83
30 7 0.17
ACGTcount: A:0.21, C:0.14, G:0.37, T:0.29
Consensus pattern (29 bp):
TTGGACCGAGTTGGGTGAATGACAGGTTC
Found at i:57504153 original size:27 final size:26
Alignment explanation
Indices: 57504101--57504160 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
57504091 ATATATATAT
*
57504101 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
57504127 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
57504154 ATATCTG
1 ATATCTG
57504161 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:57505009 original size:17 final size:17
Alignment explanation
Indices: 57504987--57505031 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
57504977 TTAATTTATG
57504987 AAATAAAAAATTAATTA
1 AAATAAAAAATTAATTA
57505004 AAATAAAAAATTAATTA
1 AAATAAAAAATTAATTA
*
57505021 AAATAAGAAAT
1 AAATAAAAAAT
57505032 GATAATAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAATAAAAAATTAATTA
Found at i:57505520 original size:16 final size:16
Alignment explanation
Indices: 57505499--57505530 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
57505489 TATAAGTTGG
57505499 ATTTAAGGTTGTTAAA
1 ATTTAAGGTTGTTAAA
57505515 ATTTAAGGTTGTTAAA
1 ATTTAAGGTTGTTAAA
57505531 TTGCCATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
ATTTAAGGTTGTTAAA
Found at i:57508684 original size:2 final size:2
Alignment explanation
Indices: 57508677--57508705 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57508667 TCATGACATG
57508677 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57508706 GACTAGTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57510374 original size:45 final size:44
Alignment explanation
Indices: 57510302--57510429 Score: 161
Period size: 45 Copynumber: 2.9 Consensus size: 44
57510292 GCACAGTACT
57510302 ATTCGGGTCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATACC
1 ATTCGGG-CTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATACC
* **
57510347 ACTT-GGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATATT
1 A-TTCGGG-CTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATACC
* * *
57510392 ATTCGGGCTTCGAGCCTAGCAGGCGA-AATGCTGGTGAA
1 ATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAA
57510430 TGAATTCGGA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
43 10 0.14
44 19 0.26
45 42 0.58
46 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (44 bp):
ATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAAATACC
Found at i:57510614 original size:35 final size:35
Alignment explanation
Indices: 57510567--57510645 Score: 149
Period size: 35 Copynumber: 2.2 Consensus size: 35
57510557 TTGTATTTAT
57510567 ATGTGAGTATGATTTGAATTGAATCATAAGTGTATA
1 ATGTGA-TATGATTTGAATTGAATCATAAGTGTATA
57510603 ATGTGATATGATTTGAATTGAATCATAAGTGTATA
1 ATGTGATATGATTTGAATTGAATCATAAGTGTATA
57510638 ATGTGATA
1 ATGTGATA
57510646 CATATGTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 37 0.86
36 6 0.14
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.39
Consensus pattern (35 bp):
ATGTGATATGATTTGAATTGAATCATAAGTGTATA
Found at i:57511580 original size:40 final size:39
Alignment explanation
Indices: 57511489--57511593 Score: 129
Period size: 40 Copynumber: 2.7 Consensus size: 39
57511479 ACAAAAGTGA
* * **
57511489 AAACAGGGGTACAGATGTGCATTTAGGGGTACCAAGTAC
1 AAACAGGGGCACTGATGTGCAAATAGGGGTACCAAGTAC
* * * *
57511528 AATCAGAGGCACTGATATGCAAATAGGGGTACCAAATTAC
1 AAACAGGGGCACTGATGTGCAAATAGGGGTACC-AAGTAC
57511568 AAACAGGGGCACTGATGTGCAAATAG
1 AAACAGGGGCACTGATGTGCAAATAG
57511594 ACACACTTCT
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
39 26 0.48
40 28 0.52
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (39 bp):
AAACAGGGGCACTGATGTGCAAATAGGGGTACCAAGTAC
Found at i:57512449 original size:13 final size:14
Alignment explanation
Indices: 57512433--57512464 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
57512423 ATTTTTTAAC
57512433 ATTTTATTTT-ATT
1 ATTTTATTTTAATT
57512446 A-TTTATTTTAATT
1 ATTTTATTTTAATT
57512459 ATTTTA
1 ATTTTA
57512465 ACATTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.47
13 5 0.29
14 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTATTTTAATT
Found at i:57525378 original size:47 final size:47
Alignment explanation
Indices: 57525320--57525441 Score: 226
Period size: 47 Copynumber: 2.6 Consensus size: 47
57525310 GCATTGGAAC
57525320 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
57525367 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
57525414 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
57525442 CCAAGGTATG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:57525454 original size:142 final size:140
Alignment explanation
Indices: 57525186--57525511 Score: 325
Period size: 142 Copynumber: 2.3 Consensus size: 140
57525176 ATTGACGGTT
** *
57525186 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGGTAAGGATCCCATGTAAGACCA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGACAAGGATACCATGTAAGACCA
* * * *
57525251 TGTCAAGACATGGCATCAGCATTGATTAAGGACTCTATGTAAGACCACATCAAGATGTGGCATTG
66 TGTCAAGACATGGCATCAGCATAGATTAAGGAATCTATGTAAGACCACACCAAGATATGGCATTG
57525316 GAACTAAGAC
131 GAACTAAGAC
***
57525326 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGACAAGGATACCATGTAAGAC
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGTAAGACAAGGATACCATGTAAGAC
*** ** * ** *
57525391 CATGTTTGGAACATGGCATTTG-GTAAGA-TAAGGATATC-ATGTAAGACCATGCCAAGGTATGG
64 CATGTCAAG-ACATGGCATCAGCAT-AGATTAAGGA-ATCTATGTAAGACCACACCAAGATATGG
* *
57525453 CATTGATAAGTTCTATAAGGC
126 CATTG-GAA---C--TAAGAC
* *
57525474 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTG
57525512 ATGAGTTACT
Statistics
Matches: 149, Mismatches: 26, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
140 24 0.16
141 8 0.05
142 62 0.42
143 16 0.11
146 4 0.03
147 8 0.05
148 27 0.18
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (140 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGACAAGGATACCATGTAAGACCA
TGTCAAGACATGGCATCAGCATAGATTAAGGAATCTATGTAAGACCACACCAAGATATGGCATTG
GAACTAAGAC
Found at i:57525561 original size:55 final size:55
Alignment explanation
Indices: 57525420--57525616 Score: 222
Period size: 55 Copynumber: 3.6 Consensus size: 55
57525410 TTGGTAAGAT
* * *
57525420 AAGGATATCATGTAAGACCATGCCAAGGTATGGCATTGATAAGTTCTATAAGGC-
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGCA
* *
57525474 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCA
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTT-CTATAAGGCA
** * * *
57525530 AAGG-TCTCATGTAAGATCATGCCAAGGCATGGAATTGGTGAGTTC-ATAAGGC-
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGCA
* * * * *
57525582 AAGGATACCACGTAAGACCATGTCAAGACATGGCA
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCA
57525617 ATGGTAAGTT
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
52 4 0.03
53 30 0.25
54 41 0.34
55 42 0.35
56 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (55 bp):
AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGCA
Found at i:57526999 original size:44 final size:45
Alignment explanation
Indices: 57526911--57526999 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 45
57526901 CAGAACGAAA
*
57526911 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGAT
1 TGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGGAT
*
57526957 TGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGA
1 TGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGA
57527000 ATAATTCATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 20 0.49
46 21 0.51
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (45 bp):
TGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAT
Found at i:57527014 original size:44 final size:45
Alignment explanation
Indices: 57526913--57527037 Score: 126
Period size: 44 Copynumber: 2.8 Consensus size: 45
57526903 GAACGAAATG
* * * *
57526913 AGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGATTG
1 AGCCATATAAGTCCATATTA-AAATATGGCATTGGAGACAGGAATA
* *
57526959 AGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGAATA
1 AGCCATATAAGTCCATATTAAAATATGGCATTGGAGACAGGAATA
** * * *
57527003 ATTCATATAAGTCCATGTCAAAGACATGGCATTGG
1 AGCCATATAAGTCCATATTAAA-ATATGGCATTGG
57527038 CAGGATATTG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 35 0.53
45 1 0.02
46 30 0.45
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
AGCCATATAAGTCCATATTAAAATATGGCATTGGAGACAGGAATA
Found at i:57531191 original size:49 final size:49
Alignment explanation
Indices: 57531114--57531301 Score: 205
Period size: 49 Copynumber: 3.8 Consensus size: 49
57531104 TAGCCGAAGC
*
57531114 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * *** *
57531163 AATCTGGTACACTTAGTAGCCTGTACTTAGTACTACACACATGATCACAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAT
* * **
57531214 TTTCGGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
** * * *
57531263 TATCCAGTACACGTAGTAGCCTGTACATAGTACTACACA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
57531302 CGTGACCTCA
Statistics
Matches: 110, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
49 71 0.65
50 2 0.02
51 37 0.34
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:57531236 original size:100 final size:100
Alignment explanation
Indices: 57531119--57531302 Score: 314
Period size: 100 Copynumber: 1.8 Consensus size: 100
57531109 GAAGCTATCT
** *
57531119 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACTTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACGTAGTAGCC
*
57531184 TGTACTTAGTACTACACACATGATCACAGTTTTCG
66 TGTACATAGTACTACACACATGATCACAGTTTTCG
* *
57531219 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACGTAGTAGCC
57531284 TGTACATAGTACTACACAC
66 TGTACATAGTACTACACAC
57531303 GTGACCTCAC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 78 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACGTAGTAGCC
TGTACATAGTACTACACACATGATCACAGTTTTCG
Found at i:57532805 original size:31 final size:31
Alignment explanation
Indices: 57532770--57532833 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
57532760 CCTTTGCATG
57532770 TTTCATATTCCATAACACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
* **
57532801 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
57532832 TT
1 TT
57532834 ACTATAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATATTCCATAACACTGGGCCGAAGCCT
Found at i:57533076 original size:24 final size:24
Alignment explanation
Indices: 57533025--57533191 Score: 257
Period size: 24 Copynumber: 7.0 Consensus size: 24
57533015 GCTTTATCAT
* *
57533025 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* **
57533050 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTG
57533074 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
57533097 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
57533121 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
57533145 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
57533169 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
57533192 TCACTTCCTC
Statistics
Matches: 135, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.17
24 100 0.74
25 12 0.09
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:57533125 original size:71 final size:71
Alignment explanation
Indices: 57533024--57533191 Score: 257
Period size: 71 Copynumber: 2.3 Consensus size: 71
57533014 TGCTTTATCA
*
57533024 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
57533088 AGCCCTTT
64 AGCCCTTT
* * **
57533096 TATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
57533161 CCCTTT
66 CCCTTT
57533167 TGATAACTGGGGCATAAGCCCTTTT
1 T-ATAACTGGGGCATAAGCCCTTTT
57533192 TCACTTCCTC
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
71 53 0.60
72 36 0.40
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (71 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
CCCTTT
Found at i:57533266 original size:20 final size:20
Alignment explanation
Indices: 57533241--57533301 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
57533231 TTATGATTAC
57533241 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
57533261 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
57533281 TTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
57533301 A
1 A
57533302 CCATATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:57533272 original size:11 final size:11
Alignment explanation
Indices: 57533241--57533296 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
57533231 TTATGATTAC
57533241 ATCATGTGCAT
1 ATCATGTGCAT
*
57533252 ATCA--TACAT
1 ATCATGTGCAT
57533261 ATCATGTGCAT
1 ATCATGTGCAT
*
57533272 ATCA--TACAT
1 ATCATGTGCAT
*
57533281 TTCATGTGCAT
1 ATCATGTGCAT
57533292 ATCAT
1 ATCAT
57533297 ACATACCATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:57533376 original size:25 final size:25
Alignment explanation
Indices: 57533344--57533391 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
57533334 ATACATAAAC
* * *
57533344 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
57533369 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
57533392 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:57534640 original size:27 final size:27
Alignment explanation
Indices: 57534549--57534632 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
57534539 GGGCATATTC
* *
57534549 GTCATTTTACCATACAAGGG-TATTACG
1 GTCACTTTACCCTACAAGGGCT-TTACG
57534576 GTCACTTTACCCTACAAGGGCTTTACG
1 GTCACTTTACCCTACAAGGGCTTTACG
*
57534603 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAAGGGCTTTACG
57534630 GTC
1 GTC
57534633 TTTTTACCTA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
27 52 0.98
28 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (27 bp):
GTCACTTTACCCTACAAGGGCTTTACG
Found at i:57534724 original size:27 final size:27
Alignment explanation
Indices: 57534694--57534745 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
57534684 GTAAATCAAC
57534694 AAACCAAAGGTATTT-TAGTAATTTTGT
1 AAACCAAAGGTATTTCTA-TAATTTTGT
*
57534721 AAACCAATGGTATTTCTATAATTTT
1 AAACCAAAGGTATTTCTATAATTTT
57534746 TAGAAGGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (27 bp):
AAACCAAAGGTATTTCTATAATTTTGT
Found at i:57534786 original size:21 final size:20
Alignment explanation
Indices: 57534740--57534777 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
57534730 GTATTTCTAT
57534740 AATTTTTAGAAGGTCAAGGG
1 AATTTTTAGAAGGTCAAGGG
57534760 AATTTTTAGAAGGTCAAG
1 AATTTTTAGAAGGTCAAG
57534778 TGTATTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (20 bp):
AATTTTTAGAAGGTCAAGGG
Found at i:57534817 original size:27 final size:27
Alignment explanation
Indices: 57534779--57534929 Score: 162
Period size: 27 Copynumber: 5.6 Consensus size: 27
57534769 AAGGTCAAGT
* * **
57534779 GTATTTTTGTAACTTTGTAAATCAGGG
1 GTATTTTGGTAATTTTACAAATCAGGG
*
57534806 GTATTTTGGTAATTTTACAAAT-TGAGG
1 GTATTTTGGTAATTTTACAAATCAG-GG
* * * *
57534833 GTATTTCGGTAATTTCACAAACCAAGG
1 GTATTTTGGTAATTTTACAAATCAGGG
57534860 GTATTTTGGTAATTTTACAAA-CTAGGG
1 GTATTTTGGTAATTTTACAAATC-AGGG
* *
57534887 GTATTTTGGTAATTTTACAAACCAAGG
1 GTATTTTGGTAATTTTACAAATCAGGG
*
57534914 GTATTTTAGTAATTTT
1 GTATTTTGGTAATTTT
57534930 GTAAATCGAG
Statistics
Matches: 105, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.02
27 102 0.97
28 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.42
Consensus pattern (27 bp):
GTATTTTGGTAATTTTACAAATCAGGG
Found at i:57534862 original size:54 final size:54
Alignment explanation
Indices: 57534804--57534943 Score: 201
Period size: 54 Copynumber: 2.6 Consensus size: 54
57534794 TGTAAATCAG
57534804 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
* * *
57534858 GGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTGA-GGGTATTTCGGTAATTTCACAAACCAA
* ** *
57534912 GGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTA
57534944 AAACAGTAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 1 0.01
54 74 0.97
55 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
Found at i:57534941 original size:27 final size:27
Alignment explanation
Indices: 57534779--57535024 Score: 109
Period size: 27 Copynumber: 9.1 Consensus size: 27
57534769 AAGGTCAAGT
* *
57534779 GTATTTTTGTAACTTTGTAAATC-AGGG
1 GTATTTTAGTAATTTTGTAAATCGA-GG
* ** *
57534806 GTATTTTGGTAATTTTACAAATTGAGG
1 GTATTTTAGTAATTTTGTAAATCGAGG
** *** * *
57534833 GTATTTCGGTAATTTCACAAACCAAGG
1 GTATTTTAGTAATTTTGTAAATCGAGG
* ** *
57534860 GTATTTTGGTAATTTTACAAA-CTAGGG
1 GTATTTTAGTAATTTTGTAAATCGA-GG
* ** * *
57534887 GTATTTTGGTAATTTTACAAACCAAGG
1 GTATTTTAGTAATTTTGTAAATCGAGG
57534914 GTATTTTAGTAATTTTGTAAATCGAGG
1 GTATTTTAGTAATTTTGTAAATCGAGG
**** * *
57534941 GTAAAACAGTAATTCTGTAAATCAAGG
1 GTATTTTAGTAATTTTGTAAATCGAGG
**** * *
57534968 GTAAAACAGTAATTCTGTAAATTGAGG
1 GTATTTTAGTAATTTTGTAAATCGAGG
**** *
57534995 GTAAAACAGTAATTCTGTAAATCGAGG
1 GTATTTTAGTAATTTTGTAAATCGAGG
57535022 GTA
1 GTA
57535025 AAACGGTAAT
Statistics
Matches: 188, Mismatches: 28, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
26 2 0.01
27 183 0.97
28 3 0.02
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (27 bp):
GTATTTTAGTAATTTTGTAAATCGAGG
Found at i:57535025 original size:27 final size:27
Alignment explanation
Indices: 57534921--57535342 Score: 537
Period size: 27 Copynumber: 15.6 Consensus size: 27
57534911 AGGGTATTTT
*
57534921 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
57534948 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
57534975 AGTAATTCTGTAAATTGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
57535002 AGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
57535029 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
57535056 -GATAATTCTATAAATCGAGGGTAAAAC
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* *
57535083 AGTAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
57535110 AATAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
* *
57535137 GGTAATTCTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
57535164 AGTAATTCTGTAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
57535191 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
57535218 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
57535245 GGTAATTCTATAAATCCAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * **
57535272 GGTAATTTTACAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
57535299 AGTAATTCTATAAA-CTGAGGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
*
57535326 GGTAATTCTGTAAATCG
1 AGTAATTCTGTAAATCG
57535343 GGAGTACTTT
Statistics
Matches: 350, Mismatches: 37, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
26 4 0.01
27 342 0.98
28 4 0.01
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.27
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:57538088 original size:15 final size:15
Alignment explanation
Indices: 57538030--57538094 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
57538020 TAAAGATAAC
*
57538030 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
57538044 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
** *
57538059 GAA-AAGCCCAAAATA
1 -AAGAAATCCAGAATA
57538074 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
57538089 AAGAAA
1 AAGAAA
57538095 CCCAAGATAC
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 11 0.28
15 26 0.65
16 3 0.08
ACGTcount: A:0.63, C:0.14, G:0.14, T:0.09
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:57538099 original size:30 final size:30
Alignment explanation
Indices: 57538040--57538099 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
57538030 AAGAAAACCG
*
57538040 AATAAAGAAATCCAAGATAGAAAAGCCCAA
1 AATAAAGAAATCCAAGATAGAAAAACCCAA
57538070 AATAAAGAAATCC-AGAATA-AAGAAACCCAA
1 AATAAAGAAATCCAAG-ATAGAA-AAACCCAA
57538100 GATACGATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.62, C:0.17, G:0.12, T:0.10
Consensus pattern (30 bp):
AATAAAGAAATCCAAGATAGAAAAACCCAA
Found at i:57539507 original size:32 final size:32
Alignment explanation
Indices: 57539471--57539531 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
57539461 AGCAAGTATA
57539471 GATATTTATCACAACATGACCTTTCATCTATG
1 GATATTTATCACAACATGACCTTTCATCTATG
57539503 GATATTTATCACAACATGACCTTTCATCT
1 GATATTTATCACAACATGACCTTTCATCT
57539532 CACGTGTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (32 bp):
GATATTTATCACAACATGACCTTTCATCTATG
Found at i:57542746 original size:49 final size:49
Alignment explanation
Indices: 57542678--57542800 Score: 219
Period size: 49 Copynumber: 2.5 Consensus size: 49
57542668 TACATATATG
*
57542678 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTACGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTACGTATA
*
57542727 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTACGTATA
*
57542776 TGTGATGAGGCCTAATGGCCAATGT
1 TGTGATGAGGCCTAATGGCCGATGT
57542801 AAAATATATG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.27, C:0.11, G:0.33, T:0.29
Consensus pattern (49 bp):
TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTACGTATA
Found at i:57542951 original size:37 final size:37
Alignment explanation
Indices: 57542903--57542980 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
57542893 GTTCCGGGCG
*
57542903 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
1 AGACCCAATGACTACGTGTGGAGATTATGACCGGGTA
57542940 AGACCCAATGACTACGTGTGGAGATTATGACCGGGTA
1 AGACCCAATGACTACGTGTGGAGATTATGACCGGGTA
57542977 AGAC
1 AGAC
57542981 TTCTTTTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (37 bp):
AGACCCAATGACTACGTGTGGAGATTATGACCGGGTA
Found at i:57545349 original size:49 final size:49
Alignment explanation
Indices: 57545277--57545459 Score: 231
Period size: 49 Copynumber: 3.7 Consensus size: 49
57545267 TCTGGTACGA
*
57545277 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACAC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACAC
* * * * * ** **
57545326 ATAGTAGCCTGTACTTAGTACTACACAAGTGATCACAGTTTTCGGGTATGC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAATTATCCAGTACAC
57545377 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACAC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACAC
* * *
57545426 GTAGTAGCCTGTACTTAGTACTACACATGTGACC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACC
57545460 CAACAATAGT
Statistics
Matches: 110, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
49 70 0.64
50 2 0.02
51 38 0.35
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (49 bp):
ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACAC
Found at i:57545393 original size:100 final size:100
Alignment explanation
Indices: 57545277--57545457 Score: 335
Period size: 100 Copynumber: 1.8 Consensus size: 100
57545267 TCTGGTACGA
57545277 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACATAGTAGCCTGTACTT
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACATAGTAGCCTGTACTT
57545342 AGTACTACACAAGTGATCACAGTTTTCGGGTATGC
66 AGTACTACACAAGTGATCACAGTTTTCGGGTATGC
* *
57545377 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGTAGCCTGTACTT
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACATAGTAGCCTGTACTT
*
57545442 AGTACTACACATGTGA
66 AGTACTACACAAGTGA
57545458 CCCAACAATA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 78 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (100 bp):
ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACATAGTAGCCTGTACTT
AGTACTACACAAGTGATCACAGTTTTCGGGTATGC
Found at i:57547699 original size:13 final size:13
Alignment explanation
Indices: 57547681--57547705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57547671 TTTAAATGTG
57547681 TTTAATGTGTTTT
1 TTTAATGTGTTTT
57547694 TTTAATGTGTTT
1 TTTAATGTGTTT
57547706 GTTTGTATCT
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:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (13 bp):
TTTAATGTGTTTT
Found at i:57547703 original size:22 final size:21
Alignment explanation
Indices: 57547662--57547705 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
57547652 TTATTAAGTC
57547662 TAATGTGTGTTTAAATGTGTT
1 TAATGTGTGTTTAAATGTGTT
* *
57547683 TAATGTGTTTTTTTAATGTGTT
1 TAATGTG-TGTTTAAATGTGTT
57547705 T
1 T
57547706 GTTTGTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.59
Consensus pattern (21 bp):
TAATGTGTGTTTAAATGTGTT
Found at i:57547840 original size:24 final size:23
Alignment explanation
Indices: 57547807--57547888 Score: 89
Period size: 24 Copynumber: 3.6 Consensus size: 23
57547797 AAAGGGCTGT
*
57547807 TACATTATTTAAAGCAGAGCATTA
1 TACATCATTTAAAG-AGAGCATTA
57547831 TACATCATTTAAAG-GAGC-TGT-
1 TACATCATTTAAAGAGAGCAT-TA
*
57547852 TACATCATTTAAAGGAGGGCATTA
1 TACATCATTTAAA-GAGAGCATTA
*
57547876 TACATCCTTTAAA
1 TACATCATTTAAA
57547889 TTAGGCAGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
21 14 0.28
22 6 0.12
23 4 0.08
24 26 0.52
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (23 bp):
TACATCATTTAAAGAGAGCATTA
Found at i:57547852 original size:45 final size:44
Alignment explanation
Indices: 57547797--57547888 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 44
57547787 AGTTACATAC
*
57547797 AAAGGGCTGTTACATTATTTAAAGCAGAGCATTATACATCATTT
1 AAAGGGCTGTTACATCATTTAAAGCAGAGCATTATACATCATTT
* * *
57547841 AAAGGAGCTGTTACATCATTTAAAGGAGGGCATTATACATCCTTT
1 AAAGG-GCTGTTACATCATTTAAAGCAGAGCATTATACATCATTT
57547886 AAA
1 AAA
57547889 TTAGGCAGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 5 0.12
45 38 0.88
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (44 bp):
AAAGGGCTGTTACATCATTTAAAGCAGAGCATTATACATCATTT
Found at i:57547857 original size:21 final size:21
Alignment explanation
Indices: 57547797--57547868 Score: 85
Period size: 21 Copynumber: 3.3 Consensus size: 21
57547787 AGTTACATAC
*
57547797 AAAGG-GCTGTTACATTATTT
1 AAAGGAGCTGTTACATCATTT
57547817 AAAGCAGAGCAT-TATACATCATTT
1 AAAG--GAGC-TGT-TACATCATTT
57547841 AAAGGAGCTGTTACATCATTT
1 AAAGGAGCTGTTACATCATTT
57547862 AAAGGAG
1 AAAGGAG
57547869 GGCATTATAC
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
20 4 0.09
21 18 0.40
22 6 0.13
23 3 0.07
24 14 0.31
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (21 bp):
AAAGGAGCTGTTACATCATTT
Found at i:57552332 original size:38 final size:38
Alignment explanation
Indices: 57552281--57552357 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
57552271 ACAGTACAGA
57552281 TATGCAATCAAGAGATCCTACCCAGCCAGCCTCTACAC
1 TATGCAATCAAGAGATCCTACCCAGCCAGCCTCTACAC
* *
57552319 TATGCAATCAAGAGATCCTATCCAGCCATCCTCTACAC
1 TATGCAATCAAGAGATCCTACCCAGCCAGCCTCTACAC
57552357 T
1 T
57552358 CTATCTCTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.22
Consensus pattern (38 bp):
TATGCAATCAAGAGATCCTACCCAGCCAGCCTCTACAC
Found at i:57559551 original size:28 final size:28
Alignment explanation
Indices: 57559519--57559587 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
57559509 GCGTAGATCA
57559519 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
57559547 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
57559575 CGATA-TACCCCTA
1 CGAAATTACCCCTA
57559588 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:57565886 original size:20 final size:20
Alignment explanation
Indices: 57565861--57565898 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57565851 GTTTATTCGC
*
57565861 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
57565881 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
57565899 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:57567557 original size:28 final size:28
Alignment explanation
Indices: 57567525--57567593 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
57567515 GCGTAGATCA
57567525 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
57567553 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
57567581 CGATA-TACCCCTA
1 CGAAATTACCCCTA
57567594 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:57569177 original size:37 final size:37
Alignment explanation
Indices: 57569124--57569214 Score: 146
Period size: 37 Copynumber: 2.4 Consensus size: 37
57569114 TTATTACGAA
*
57569124 GTCTTACCTGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
57569161 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
57569198 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
57569215 CTCCAAGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 45 0.92
38 4 0.08
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:57569404 original size:32 final size:32
Alignment explanation
Indices: 57569367--57569430 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
57569357 CGGCCATTAG
57569367 GCCTTATCACATATACATACACTTTCACATTC
1 GCCTTATCACATATACATACACTTTCACATTC
57569399 GCCTTATCACATATACATACACTTTCACATTC
1 GCCTTATCACATATACATACACTTTCACATTC
57569431 ACCACATCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.34
Consensus pattern (32 bp):
GCCTTATCACATATACATACACTTTCACATTC
Found at i:57569406 original size:81 final size:79
Alignment explanation
Indices: 57569318--57569477 Score: 293
Period size: 81 Copynumber: 2.0 Consensus size: 79
57569308 TAGCCATTAG
*
57569318 GCCTTATCACATATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATAC
1 GCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATAT--
57569383 ATACACTTTCACATTC
64 ATACACTTTCACATTC
57569399 GCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATAT
1 GCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATAT
57569464 ACACTTTCACATTC
66 ACACTTTCACATTC
57569478 ATCACATTGG
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
79 16 0.21
81 62 0.79
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.32
Consensus pattern (79 bp):
GCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATAT
ACACTTTCACATTC
Found at i:57569476 original size:47 final size:47
Alignment explanation
Indices: 57569399--57569511 Score: 172
Period size: 47 Copynumber: 2.4 Consensus size: 47
57569389 TTTCACATTC
57569399 GCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAG
1 GCCTTATCACATAT--ATACACTTTCACATTCACCACATCGGCCATTAG
* * *
57569448 GCCTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCG
1 GCCTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAG
*
57569495 GCCTTATCACACATATA
1 GCCTTATCACATATATA
57569512 TGTATATCAT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
47 46 0.77
49 14 0.23
ACGTcount: A:0.30, C:0.31, G:0.08, T:0.31
Consensus pattern (47 bp):
GCCTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAG
Found at i:57578512 original size:26 final size:25
Alignment explanation
Indices: 57578474--57578522 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
57578464 CATAGCACTT
*
57578474 AACATGATAAGCA-AAATTGAATTCA
1 AACATAATAAGCATAAA-TGAATTCA
57578499 AACATAATCAAGCATAAATGAATT
1 AACATAAT-AAGCATAAATGAATT
57578523 TATCATAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 11 0.52
27 3 0.14
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.24
Consensus pattern (25 bp):
AACATAATAAGCATAAATGAATTCA
Found at i:57584546 original size:34 final size:32
Alignment explanation
Indices: 57584492--57584569 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 32
57584482 TCTGTATTGT
* *
57584492 TACTGACACTGAAATAGGCTAAGGCCCACACTGA
1 TACTGA-ACTGTAATAGGCTAAGGCCCA-AATGA
*
57584526 TACTGATACTGTAATGGGCTAAGGCCCAAATGA
1 TACTGA-ACTGTAATAGGCTAAGGCCCAAATGA
*
57584559 AACTGAACTGT
1 TACTGAACTGT
57584570 TACTAATGCG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 5 0.13
33 9 0.23
34 25 0.64
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (32 bp):
TACTGAACTGTAATAGGCTAAGGCCCAAATGA
Found at i:57586164 original size:29 final size:29
Alignment explanation
Indices: 57586132--57586190 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
57586122 TTCCCGAGCC
57586132 TAGGGG-AAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGC-AAAGTT
* * *
57586161 TAGGGGCAAAATTGTAATTTTGCAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAGTT
57586190 T
1 T
57586191 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (29 bp):
TAGGGGCAAAAGTGTAAATATGCAAAGTT
Found at i:57586970 original size:68 final size:66
Alignment explanation
Indices: 57586898--57587047 Score: 169
Period size: 67 Copynumber: 2.2 Consensus size: 66
57586888 CATCATGTGT
* * * *
57586898 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
57586961 TGTAG
62 TGTAG
** * *
57586966 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
57587031 AG
65 AG
57587033 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
57587048 GATAAATTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 24 0.34
65 3 0.04
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:57587003 original size:64 final size:64
Alignment explanation
Indices: 57586922--57587101 Score: 186
Period size: 67 Copynumber: 2.8 Consensus size: 64
57586912 AGACATTATG
* * *
57586922 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
57586986 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
57587051 AA
63 AA
* * * *
57587053 AT-TGGCTAAGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGA
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGA
57587102 AAGCCGAACT
Statistics
Matches: 94, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 15 0.16
64 25 0.27
66 20 0.21
67 33 0.35
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:57589355 original size:44 final size:43
Alignment explanation
Indices: 57589284--57589499 Score: 183
Period size: 44 Copynumber: 5.0 Consensus size: 43
57589274 ACATAGGATC
*
57589284 CGATATATGTTTT-CATGTAAGACCACGTCTGGGACATTGGCAT
1 CGAT-TATGTTTTACGTGTAAGACCACGTCTGGGACATTGGCAT
* *
57589327 CGACTTATGTTTTACGTGTAAGACCACGTTTGGTACATTGGCAT
1 CGA-TTATGTTTTACGTGTAAGACCACGTCTGGGACATTGGCAT
* * **
57589371 CGACTTATGTTTCACGTGTAAGACCATGTCTGGGATGTTGGCAT
1 CGA-TTATGTTTTACGTGTAAGACCACGTCTGGGACATTGGCAT
* * * * ** *
57589415 CGTATT-TGATTT-CGTGTAAAACC-CTATCTAGGACAGCGACAT
1 CG-ATTATGTTTTACGTGTAAGACCAC-GTCTGGGACATTGGCAT
* *
57589457 CGA-TAT-TTGGTTACATGTAAGACCACGTCTAGGACATTGGCAT
1 CGATTATGTT--TTACGTGTAAGACCACGTCTGGGACATTGGCAT
57589500 TGTATAAGCT
Statistics
Matches: 137, Mismatches: 27, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 24 0.18
43 37 0.27
44 71 0.52
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (43 bp):
CGATTATGTTTTACGTGTAAGACCACGTCTGGGACATTGGCAT
Found at i:57589999 original size:25 final size:25
Alignment explanation
Indices: 57589971--57590045 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 25
57589961 AAAGTATGGC
57589971 ATGTATAGGCTAGAAGTGTGTGAAT
1 ATGTATAGGCTAGAAGTGTGTGAAT
* * * *
57589996 ATGTTTA-G-TA-ATGTGTATGGA-
1 ATGTATAGGCTAGAAGTGTGTGAAT
57590017 ATGTATAGGCTAGAAGTGTGTGAAT
1 ATGTATAGGCTAGAAGTGTGTGAAT
57590042 ATGT
1 ATGT
57590046 TTAGTAATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
21 6 0.16
22 9 0.24
23 4 0.11
24 9 0.24
25 10 0.26
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.36
Consensus pattern (25 bp):
ATGTATAGGCTAGAAGTGTGTGAAT
Found at i:57590031 original size:46 final size:46
Alignment explanation
Indices: 57589964--57590059 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
57589954 ATATATTAAA
*
57589964 GTATGGCATGTATAGGCTAGAAGTGTGTGAATATGTTTAGTAATGT
1 GTATGGAATGTATAGGCTAGAAGTGTGTGAATATGTTTAGTAATGT
57590010 GTATGGAATGTATAGGCTAGAAGTGTGTGAATATGTTTAGTAATGT
1 GTATGGAATGTATAGGCTAGAAGTGTGTGAATATGTTTAGTAATGT
57590056 GTAT
1 GTAT
57590060 ATTTAGCCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.29, C:0.03, G:0.30, T:0.38
Consensus pattern (46 bp):
GTATGGAATGTATAGGCTAGAAGTGTGTGAATATGTTTAGTAATGT
Found at i:57590622 original size:12 final size:12
Alignment explanation
Indices: 57590605--57590640 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
57590595 CTAGACACAC
57590605 GGGCGTGTGACT
1 GGGCGTGTGACT
57590617 GGGCGTGTGACT
1 GGGCGTGTGACT
57590629 -GGCTGTGTGACT
1 GGGC-GTGTGACT
57590641 CAAGTCAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 3 0.13
12 20 0.87
ACGTcount: A:0.08, C:0.17, G:0.47, T:0.28
Consensus pattern (12 bp):
GGGCGTGTGACT
Found at i:57592370 original size:46 final size:46
Alignment explanation
Indices: 57592320--57592495 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
57592310 TATTTGGGCA
57592320 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
57592366 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
57592413 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
57592459 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
57592496 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:57592475 original size:93 final size:93
Alignment explanation
Indices: 57592316--57592487 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
57592306 TGGATATTTG
* *
57592316 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
57592381 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
57592409 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
57592474 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
57592488 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:57595475 original size:15 final size:15
Alignment explanation
Indices: 57595455--57595523 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
57595445 GTATCTTGGG
57595455 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
57595470 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
57595485 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
57595500 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
57595515 TTTCTTTAT
1 TTTCTTTAT
57595524 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:57595524 original size:30 final size:30
Alignment explanation
Indices: 57595446--57595533 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
57595436 CATAGTATCG
* * * *
57595446 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
57595476 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
57595506 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
57595534 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:57597998 original size:20 final size:20
Alignment explanation
Indices: 57597933--57597998 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
57597923 TATTTGGGCA
57597933 TCCGAACTCGTTGAGTTGAG
1 TCCGAACTCGTTGAGTTGAG
** * *
57597953 TCCGAGTTCACTT-A-TGGAGCG
1 TCCGAACTC-GTTGAGTTGA--G
57597974 TCCGAACTCGTTGAGTTGAG
1 TCCGAACTCGTTGAGTTGAG
57597994 TCCGA
1 TCCGA
57597999 GTTCGTGAGA
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
19 3 0.09
20 16 0.48
21 11 0.33
22 3 0.09
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (20 bp):
TCCGAACTCGTTGAGTTGAG
Found at i:57598094 original size:46 final size:45
Alignment explanation
Indices: 57597934--57598103 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 45
57597924 ATTTGGGCAT
*
57597934 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA--G--CGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACGC
* * *
57597975 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAC---GC
57598020 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACGC
*
57598068 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
57598104 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
38 2 0.02
40 2 0.02
41 28 0.26
42 1 0.01
45 1 0.01
46 35 0.32
47 28 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACGC
Found at i:57601067 original size:15 final size:15
Alignment explanation
Indices: 57601047--57601115 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
57601037 GTATCTTGGG
57601047 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
57601062 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
57601077 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
57601092 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
57601107 TTTCTTTAT
1 TTTCTTTAT
57601116 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:57601116 original size:30 final size:30
Alignment explanation
Indices: 57601038--57601125 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
57601028 CATAGTATCG
* * * *
57601038 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
57601068 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
57601098 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
57601126 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:57603563 original size:46 final size:46
Alignment explanation
Indices: 57603510--57603685 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
57603500 TATTTGGGCA
57603510 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
57603556 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
57603603 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
57603649 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
57603686 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:57603665 original size:93 final size:93
Alignment explanation
Indices: 57603506--57603677 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
57603496 GGGATATTTG
* *
57603506 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
57603571 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
57603599 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
57603664 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
57603678 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:57612011 original size:16 final size:16
Alignment explanation
Indices: 57611992--57612023 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57611982 AATTGTTCTA
57611992 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
57612008 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
57612024 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:57612288 original size:50 final size:50
Alignment explanation
Indices: 57612223--57612561 Score: 346
Period size: 50 Copynumber: 6.7 Consensus size: 50
57612213 ACCGAAGCTC
* * *
57612223 TCTGGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGGCCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
** * * * *
57612273 TCTGGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* * * ** *
57612323 TTTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGATCAAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCTA-TCAA
* *
57612375 -CAGGTA-AGCATAATAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACA-CATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* **
57612424 TCTAGTACACATAGTAGCCTGCACTTAGTACTACACACATGATCGAAGT-T-AA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACT--ACACATG--CGACCTATCAA
* *
57612476 -CGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* * * *
57612525 TCTGGTACACGTAGTTGCCTGCATTTAATACTACACA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
57612562 CGTGACTCAC
Statistics
Matches: 234, Mismatches: 43, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
47 4 0.02
48 1 0.00
49 12 0.05
50 137 0.59
51 65 0.28
52 10 0.04
53 1 0.00
54 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
Found at i:57612419 original size:101 final size:101
Alignment explanation
Indices: 57612287--57612566 Score: 400
Period size: 101 Copynumber: 2.8 Consensus size: 101
57612277 GTACATGTAG
* * * * *
57612287 TAGCCTGCACTTAGTACTACACACGTGACCTAACCATTTGATACACATAGTAGCCTGCACTTAGT
1 TAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACATAGTAGCCTGCACTTAGT
*
57612352 ACTACACATGTGATCAAAGTTAACAGGTAAGCATAA
66 ACTACACACGTGATCAAAGTTAACAGGTAAGCATAA
57612388 TAGCCTGCACTTAGTACTACACATGCGACCTATCAATCT-AGTACACATAGTAGCCTGCACTTAG
1 TAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGA-TACACATAGTAGCCTGCACTTAG
* * * * *
57612452 TACTACACACATGATCGAAGTTAACGGGTACGCATAG
65 TACTACACACGTGATCAAAGTTAACAGGTAAGCATAA
* * * * *
57612489 TAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTTGCCTGCATTTAAT
1 TAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACATAGTAGCCTGCACTTAGT
57612554 ACTACACACGTGA
66 ACTACACACGTGA
57612567 CTCACAATGG
Statistics
Matches: 160, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
100 1 0.01
101 159 0.99
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (101 bp):
TAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGATACACATAGTAGCCTGCACTTAGT
ACTACACACGTGATCAAAGTTAACAGGTAAGCATAA
Found at i:57612491 original size:51 final size:51
Alignment explanation
Indices: 57612332--57612511 Score: 208
Period size: 51 Copynumber: 3.5 Consensus size: 51
57612322 ATTTGATACA
** * *
57612332 CATAGTAGCCTGCACTTAGTACTACACATGTGATCAAAGTTAACAGGTAAG
1 CATAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACAGGTACG
* ** *
57612383 CATAATAGCCTGCACTTAGTACT--ACACATG--CGACCTATCAATCTA-GTACA
1 CATAGTAGCCTGCACTTAGTACTACACACATGATCGAAGT-T-AA-C-AGGTACG
*
57612433 CATAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACAGGTACG
57612484 CATAGTAGCCTGCACTTAGTACTACACA
1 CATAGTAGCCTGCACTTAGTACTACACA
57612512 TGCGACCTAT
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
47 3 0.03
48 1 0.01
49 7 0.07
50 26 0.24
51 56 0.52
52 9 0.08
53 1 0.01
54 4 0.04
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (51 bp):
CATAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACAGGTACG
Found at i:57612545 original size:151 final size:152
Alignment explanation
Indices: 57612223--57612561 Score: 398
Period size: 151 Copynumber: 2.2 Consensus size: 152
57612213 ACCGAAGCTC
* * * * **
57612223 TCTGGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGGCCTATCAATCTGGTACATGTAGT
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACATAGT
* * ***
57612288 AGCCTGCACTTAGTACTACACACGTGACCTAACCATTTGATACACATAGTAGCCTGCACTTAGTA
66 AGCCTGCACTTAGTACTACACACATGACCGAACCAACGGATACACATAGTAGCCTGCACTTAGTA
* *
57612353 CTACACATGTGATCAAAGTTAA
131 CTACACATGCGATCAAAGTCAA
* *
57612375 -CAGGTA-AGCATAATAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACATAG
1 TCTGGTACA-CATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACATAG
* ** * *
57612438 TAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACGGGTACGCATAGTAGCCTGCACTTAG
65 TAGCCTGCACTTAGTACTACACACATGACCGAA-CCAACGGATACACATAGTAGCCTGCACTTAG
**
57612503 TACTACACATGCGA-CCTA-TCAA
129 TACTACACATGCGATCAAAGTCAA
* * * *
57612525 TCTGGTACACGTAGTTGCCTGCATTTAATACTACACA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
57612562 CGTGACTCAC
Statistics
Matches: 155, Mismatches: 28, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
150 3 0.02
151 114 0.74
152 38 0.25
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (152 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACATAGT
AGCCTGCACTTAGTACTACACACATGACCGAACCAACGGATACACATAGTAGCCTGCACTTAGTA
CTACACATGCGATCAAAGTCAA
Found at i:57617604 original size:16 final size:16
Alignment explanation
Indices: 57617585--57617616 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57617575 AATTGTTTTA
57617585 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
57617601 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
57617617 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:57617919 original size:50 final size:50
Alignment explanation
Indices: 57617825--57617952 Score: 148
Period size: 50 Copynumber: 2.6 Consensus size: 50
57617815 CTCTGGAATG
* * * * *
57617825 CATAGTAGCGTACACTTAGTTCTACACATGCAACCTATCAATCTGGTACA
1 CATAGTAGCCTACACTTAGTACTACACATACAACCTAACAATCTGATACA
* ** * * *
57617875 CGTAGTAGCCTACACTTAGTACTACACATATGACTTAACCATCTGATATA
1 CATAGTAGCCTACACTTAGTACTACACATACAACCTAACAATCTGATACA
*
57617925 CATAGTAGCCTGCACTTAGTACTACACA
1 CATAGTAGCCTACACTTAGTACTACACA
57617953 CGTGTTTGAA
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (50 bp):
CATAGTAGCCTACACTTAGTACTACACATACAACCTAACAATCTGATACA
Found at i:57618277 original size:19 final size:20
Alignment explanation
Indices: 57618255--57618304 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
57618245 ATTTACATAC
57618255 AAAC-TTATTCATTTCAAAG
1 AAACATTATTCATTTCAAAG
*
57618274 AAACATCATACTCATTTCAAAG
1 AAACAT--TATTCATTTCAAAG
57618296 AAACATTAT
1 AAACATTAT
57618305 ATTCCATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 3 0.12
22 19 0.73
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.32
Consensus pattern (20 bp):
AAACATTATTCATTTCAAAG
Found at i:57618460 original size:19 final size:20
Alignment explanation
Indices: 57618430--57618476 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
57618420 GAGAACATGT
57618430 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
*
57618451 TA-ATATCAAAATATTCACA
1 TATATATCAAAATAATCACA
57618470 TATATAT
1 TATATAT
57618477 ACTTACAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 16 0.67
20 6 0.25
21 2 0.08
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:57624297 original size:29 final size:29
Alignment explanation
Indices: 57624255--57624326 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
57624245 TATTCATAAG
* **
57624255 GCCCATTAGGCCCAAATTACCTGTATATA
1 GCCCATTAGGCCCAAATCAAATGTATATA
* *
57624284 GCCCATTAGGCCCAAATCAAATTTATATG
1 GCCCATTAGGCCCAAATCAAATGTATATA
57624313 GCCCATTAGGCCCA
1 GCCCATTAGGCCCA
57624327 GTCACATTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCAAATGTATATA
Found at i:57629625 original size:31 final size:32
Alignment explanation
Indices: 57629567--57629626 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
57629557 TAAAGAACCT
*
57629567 AAAAATGAAAACTAAATGATAAAGTAATGAAC
1 AAAAATGAAAACTAAATCATAAAGTAATGAAC
**
57629599 AAAAATGAAAACTAGTTCA-AAAGTAATG
1 AAAAATGAAAACTAAATCATAAAGTAATG
57629627 GAGATTATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (32 bp):
AAAAATGAAAACTAAATCATAAAGTAATGAAC
Found at i:57638240 original size:57 final size:58
Alignment explanation
Indices: 57638170--57638280 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
57638160 AAATTCACAT
* * *
57638170 ACCTGTATCTGGCCCATTAAG-CCC-ATTCATATTCATATGGCCCATTAGGCCCAAAAC
1 ACCTGTATATGGCCCATT-AGTCCCAAATCACATTCATATGGCCCATTAGGCCCAAAAC
* *
57638227 ACCTGTATATGGCCCATTAGTCCCAAATCACATTTATATGGCCCTTTAGGCCCA
1 ACCTGTATATGGCCCATTAGTCCCAAATCACATTCATATGGCCCATTAGGCCCA
57638281 GTCACATTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
56 2 0.04
57 20 0.43
58 25 0.53
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.28
Consensus pattern (58 bp):
ACCTGTATATGGCCCATTAGTCCCAAATCACATTCATATGGCCCATTAGGCCCAAAAC
Found at i:57638244 original size:29 final size:29
Alignment explanation
Indices: 57638204--57638280 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
57638194 ATTCATATTC
*
57638204 ATATGGCCCATTAGGCCCAAAACACCTGT
1 ATATGGCCCATTAGGCCCAAAACACATGT
* * *
57638233 ATATGGCCCATTAGTCCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAAACACATGT
*
57638262 ATATGGCCCTTTAGGCCCA
1 ATATGGCCCATTAGGCCCA
57638281 GTCACATTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.26
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAAACACATGT
Found at i:57638536 original size:11 final size:11
Alignment explanation
Indices: 57638516--57638546 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
57638506 TACAATTGAT
*
57638516 AGTGTGTGTGC
1 AGTGTATGTGC
57638527 AGTGTATGTGC
1 AGTGTATGTGC
57638538 AGTGTATGT
1 AGTGTATGT
57638547 ACACACCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.06, G:0.39, T:0.39
Consensus pattern (11 bp):
AGTGTATGTGC
Found at i:57639966 original size:13 final size:13
Alignment explanation
Indices: 57639948--57639972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57639938 TTTAAATGTG
57639948 TTTAATGTGTTTT
1 TTTAATGTGTTTT
57639961 TTTAATGTGTTT
1 TTTAATGTGTTT
57639973 GTTTGTAGGT
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:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (13 bp):
TTTAATGTGTTTT
Found at i:57643179 original size:29 final size:29
Alignment explanation
Indices: 57643121--57643189 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
57643111 ACTGTACTAG
**
57643121 GACATATTAAAAACATGTTTTAATTTTAA
1 GACATATTAAAAACATGTTTTAATGCTAA
* *
57643150 GAGATATTAATAACATGTATTTAA-GCTAA
1 GACATATTAAAAACATGT-TTTAATGCTAA
57643179 GACATATTAAA
1 GACATATTAAA
57643190 TGTAACAGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.36
Consensus pattern (29 bp):
GACATATTAAAAACATGTTTTAATGCTAA
Found at i:57644769 original size:26 final size:24
Alignment explanation
Indices: 57644710--57644796 Score: 156
Period size: 24 Copynumber: 3.6 Consensus size: 24
57644700 AATCTCAAAT
57644710 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
* *
57644734 GCACTATGTGTGCGATTTACTGTA
1 GCACTATGTGTGCGATTTACTATG
57644758 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
57644782 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
57644797 ACATAATAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:57644809 original size:48 final size:48
Alignment explanation
Indices: 57644710--57644818 Score: 166
Period size: 48 Copynumber: 2.3 Consensus size: 48
57644700 AATCTCAAAT
** * *
57644710 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGATTTACTGTA
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGACATAATGAA
57644758 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAAT-AA
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCG-ACATAATGAA
57644806 GCACTATGTGTGC
1 GCACTATGTGTGC
57644819 AACGTTTGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
48 52 0.93
49 4 0.07
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (48 bp):
GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGACATAATGAA
Found at i:57647763 original size:29 final size:28
Alignment explanation
Indices: 57647708--57647782 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
57647698 CATATTTTAT
* **
57647708 ACAAGTCT-TTAATGTGTCTTAGCTTAAA
1 ACAAG-CTATTAATATGTCTTAAATTAAA
*
57647736 TACATGCTATTAATATGTCTTAAATTAAA
1 -ACAAGCTATTAATATGTCTTAAATTAAA
* *
57647765 ACAAGTTTTTAATATGTC
1 ACAAGCTATTAATATGTC
57647783 CTAGTGTAGC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 17 0.45
29 21 0.55
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (28 bp):
ACAAGCTATTAATATGTCTTAAATTAAA
Found at i:57654331 original size:29 final size:30
Alignment explanation
Indices: 57654265--57654379 Score: 143
Period size: 29 Copynumber: 4.0 Consensus size: 30
57654255 TGCAAACATC
57654265 CATATGGCCCA-CTAGGCCCAA-TC-TCATT
1 CATATGGCCCATCTAGGCCCAATTCAT-ATT
*
57654293 CATATGGCCCATCT-GGCCCAGTTCATATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
* *
57654322 CTTATGGCCCA-CTAGGCCCAATTCACATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
*
57654351 CATATGGCCCAT-TAGGCCCAAATCATATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
57654380 ATACTCATGC
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
28 19 0.25
29 55 0.73
30 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (30 bp):
CATATGGCCCATCTAGGCCCAATTCATATT
Found at i:57654369 original size:58 final size:57
Alignment explanation
Indices: 57654267--57654379 Score: 174
Period size: 58 Copynumber: 2.0 Consensus size: 57
57654257 CAAACATCCA
* **
57654267 TATGGCCCACTAGGCCCAATCTCATTCATATGGCCCATCTGGCCCAGTTCATATTCT
1 TATGGCCCACTAGGCCCAATCACATTCATATGGCCCATCTGGCCCAAATCATATTCT
57654324 TATGGCCCACTAGGCCCAATTCACATTCATATGGCCCAT-TAGGCCCAAATCATATT
1 TATGGCCCACTAGGCCCAA-TCACATTCATATGGCCCATCT-GGCCCAAATCATATT
57654380 ATACTCATGC
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
57 20 0.39
58 31 0.61
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCACATTCATATGGCCCATCTGGCCCAAATCATATTCT
Found at i:57654466 original size:9 final size:9
Alignment explanation
Indices: 57654452--57654476 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
57654442 TGGGCCCAAC
57654452 AGCCCATCT
1 AGCCCATCT
57654461 AGCCCATCT
1 AGCCCATCT
57654470 AGCCCAT
1 AGCCCAT
57654477 TCCGACCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.44, G:0.12, T:0.20
Consensus pattern (9 bp):
AGCCCATCT
Found at i:57655802 original size:15 final size:16
Alignment explanation
Indices: 57655778--57655809 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
57655768 AAATTTGAAA
57655778 TTTCAGGATTTTGGGG
1 TTTCAGGATTTTGGGG
57655794 TTTCA-GATTTTGGGG
1 TTTCAGGATTTTGGGG
57655809 T
1 T
57655810 GTTACATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.12, C:0.06, G:0.34, T:0.47
Consensus pattern (16 bp):
TTTCAGGATTTTGGGG
Found at i:57656656 original size:21 final size:20
Alignment explanation
Indices: 57656626--57656666 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
57656616 TATTTTTCAA
57656626 TCTCAATCTCTTTTTGCTTTC
1 TCTCAATCTCTTTTT-CTTTC
*
57656647 TCTCACTCTCTTTTTCTTTC
1 TCTCAATCTCTTTTTCTTTC
57656667 ATTTCTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.07, C:0.32, G:0.02, T:0.59
Consensus pattern (20 bp):
TCTCAATCTCTTTTTCTTTC
Found at i:57660183 original size:9 final size:9
Alignment explanation
Indices: 57660171--57660209 Score: 69
Period size: 9 Copynumber: 4.2 Consensus size: 9
57660161 TTTAAATTAC
57660171 TTAATGTGT
1 TTAATGTGT
57660180 TTAATGTGT
1 TTAATGTGT
57660189 TTAATGTGTT
1 TTAATGTG-T
57660199 TTAATGTGT
1 TTAATGTGT
57660208 TT
1 TT
57660210 GTTAATGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (9 bp):
TTAATGTGT
Found at i:57660203 original size:19 final size:18
Alignment explanation
Indices: 57660171--57660209 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
57660161 TTTAAATTAC
57660171 TTAATGTGTTTAATGTGT
1 TTAATGTGTTTAATGTGT
57660189 TTAATGTGTTTTAATGTGT
1 TTAATGTG-TTTAATGTGT
57660208 TT
1 TT
57660210 GTTAATGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (18 bp):
TTAATGTGTTTAATGTGT
Found at i:57661327 original size:14 final size:13
Alignment explanation
Indices: 57661308--57661342 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
57661298 GTTACAAGTA
57661308 AAAAAAACATCATG
1 AAAAAAA-ATCATG
57661322 AAAAAAAATCATG
1 AAAAAAAATCATG
57661335 AAAAAAAA
1 AAAAAAAA
57661343 GAGAAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.11
Consensus pattern (13 bp):
AAAAAAAATCATG
Found at i:57661328 original size:16 final size:14
Alignment explanation
Indices: 57661307--57661342 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
57661297 TGTTACAAGT
57661307 AAAAAAAACATCATG
1 AAAAAAAA-ATCATG
57661322 -AAAAAAAATCATG
1 AAAAAAAAATCATG
57661335 AAAAAAAA
1 AAAAAAAA
57661343 GAGAAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.75, C:0.08, G:0.06, T:0.11
Consensus pattern (14 bp):
AAAAAAAAATCATG
Found at i:57665560 original size:43 final size:43
Alignment explanation
Indices: 57665438--57665719 Score: 306
Period size: 43 Copynumber: 6.6 Consensus size: 43
57665428 GCCCCAACTG
* * *
57665438 TGGTCTTATATGTAATCACATATCGATGCCACTGTCCCAGATA
1 TGGTCTTACACGTAATCACATATCGATGCCACTGTCCCAGACA
* * * * * **
57665481 GGGCCTCACACG-AATAAAATA-CGATGTTGA-TGTCCCAGACA
1 TGGTCTTACACGTAATCACATATCGATG-CCACTGTCCCAGACA
* * *
57665522 TAGTCTTACACGTAATCACGTATCGATGCCAAC-GTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCC-ACTGTCCCAGACA
* *
57665565 TGGTCTTACACGTAATCACGTATCGATGCCACTGTCCCAGATA
1 TGGTCTTACACGTAATCACATATCGATGCCACTGTCCCAGACA
* * *
57665608 -GGTCCTACATGTAATCACATATCGATGCCAAC-GTCCCAGGCA
1 TGGTCTTACACGTAATCACATATCGATGCC-ACTGTCCCAGACA
*
57665650 TGGTCTTACACATAATCACATATCGATGCCACTGTCCCAGACA
1 TGGTCTTACACGTAATCACATATCGATGCCACTGTCCCAGACA
* *
57665693 GGGTCTTACATGTAATCACATATCGAT
1 TGGTCTTACACGTAATCACATATCGAT
57665720 ATCACATATC
Statistics
Matches: 195, Mismatches: 35, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
41 23 0.12
42 52 0.27
43 120 0.62
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
TGGTCTTACACGTAATCACATATCGATGCCACTGTCCCAGACA
Found at i:57665636 original size:85 final size:85
Alignment explanation
Indices: 57665439--57665719 Score: 320
Period size: 85 Copynumber: 3.3 Consensus size: 85
57665429 CCCCAACTGT
* * * * * * * *
57665439 GGTCTTATATGTAATCACATATCGATGCC-ACTGTCCCAGATAGGGCCTCACAC-GAATAAAATA
1 GGTCTTACATGTAATCACATATCGATGCCAAC-GTCCCAGACATGGTCTTACACATAATCACATA
**
57665502 -CGATGTTGA-TGTCCCAGACATA
65 TCGATG-CCACTGTCCCAG--ATA
* * * * *
57665524 -GTCTTACACGTAATCACGTATCGATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACGTAT
1 GGTCTTACATGTAATCACATATCGATGCCAACGTCCCAGACATGGTCTTACACATAATCACATAT
57665588 CGATGCCACTGTCCCAGATA
66 CGATGCCACTGTCCCAGATA
* *
57665608 GGTCCTACATGTAATCACATATCGATGCCAACGTCCCAGGCATGGTCTTACACATAATCACATAT
1 GGTCTTACATGTAATCACATATCGATGCCAACGTCCCAGACATGGTCTTACACATAATCACATAT
*
57665673 CGATGCCACTGTCCCAGACA
66 CGATGCCACTGTCCCAGATA
57665693 GGGTCTTACATGTAATCACATATCGAT
1 -GGTCTTACATGTAATCACATATCGAT
57665720 ATCACATATC
Statistics
Matches: 167, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
84 44 0.26
85 85 0.51
86 38 0.23
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (85 bp):
GGTCTTACATGTAATCACATATCGATGCCAACGTCCCAGACATGGTCTTACACATAATCACATAT
CGATGCCACTGTCCCAGATA
Found at i:57665687 original size:128 final size:128
Alignment explanation
Indices: 57665423--57665719 Score: 379
Period size: 128 Copynumber: 2.3 Consensus size: 128
57665413 TCGTACAATA
* * *
57665423 CCAACGCCCCA-ACTGTGGTCTTATATGTAATCACATATCGATGCCACTGTCCCAGATAGGGCCT
1 CCAACGTCCCAGACAGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGATAGGGCCT
*** * * *
57665487 CACACGAATAAAATACGATGTTGATGTCCCAGACATAGTCTTACACGTAATCACGTATCGATG
66 CACACGAATAAAATACGATGCCAACGTCCCAGACATAGTCTTACACATAATCACATATCGATG
* * *
57665550 CCAACGTCCCAGAC-GTGGTCTTACACGTAATCACGTATCGATGCCACTGTCCCAGATAGGTCCT
1 CCAACGTCCCAGACAGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGATAGGGCCT
* * * * *
57665614 -ACATGTAATCACATATCGATGCCAACGTCCCAGGCATGGTCTTACACATAATCACATATCGATG
66 CACACG-AATAAAATA-CGATGCCAACGTCCCAGACATAGTCTTACACATAATCACATATCGATG
57665678 CC-ACTGTCCCAGACAG-GGTCTTACATGTAATCACATATCGAT
1 CCAAC-GTCCCAGACAGTGGTCTTACATGTAATCACATATCGAT
57665720 ATCACATATC
Statistics
Matches: 147, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
126 4 0.03
127 65 0.44
128 77 0.52
129 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (128 bp):
CCAACGTCCCAGACAGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGATAGGGCCT
CACACGAATAAAATACGATGCCAACGTCCCAGACATAGTCTTACACATAATCACATATCGATG
Found at i:57669820 original size:71 final size:71
Alignment explanation
Indices: 57669736--57669899 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
57669726 CGATTTGTCT
57669736 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
57669801 CTTTCA
66 CTTTCA
* *
57669807 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
57669872 CTTTCA
66 CTTTCA
57669878 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
57669900 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:57669937 original size:71 final size:70
Alignment explanation
Indices: 57669736--57669933 Score: 249
Period size: 71 Copynumber: 2.8 Consensus size: 70
57669726 CGATTTGTCT
* * * * *
57669736 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
57669801 CTTTCA
65 CTTTCA
* * * *
57669807 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
57669872 CTTTCA
65 CTTTCA
* *
57669878 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
57669934 TACAGGGTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 1 0.01
71 94 0.80
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:57673450 original size:9 final size:9
Alignment explanation
Indices: 57673436--57673460 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
57673426 ACAAGTTTTG
57673436 CAATTTATT
1 CAATTTATT
57673445 CAATTTATT
1 CAATTTATT
57673454 CAATTTA
1 CAATTTA
57673461 GTCCCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (9 bp):
CAATTTATT
Found at i:57677088 original size:13 final size:14
Alignment explanation
Indices: 57677070--57677102 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
57677060 AACCAAAAAC
*
57677070 AAACATATCAATA-
1 AAACATATAAATAT
57677083 AAACATATAAATAT
1 AAACATATAAATAT
57677097 AAACAT
1 AAACAT
57677103 GGTCGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACATATAAATAT
Found at i:57678530 original size:43 final size:43
Alignment explanation
Indices: 57678410--57678678 Score: 235
Period size: 43 Copynumber: 6.3 Consensus size: 43
57678400 TCCCGGACAT
* * * * *
57678410 GTAATCACATATCGGTGCCACTGTCCCAGATAG-GGTCTCACAT
1 GTAATCACATATCGATGCCAATGTCCCAAAT-GTGGTCTTACAC
* *** * **
57678453 G-AATCAAATAT-GATGCTGGTGTCCCAGACATGGTCTTACAC
1 GTAATCACATATCGATGCCAATGTCCCAAATGTGGTCTTACAC
*
57678494 GTAATCACATATCGATGCCAATGTTCCAAATGTGGTCTTACAC
1 GTAATCACATATCGATGCCAATGTCCCAAATGTGGTCTTACAC
* * * * ***
57678537 GTAATCACAAATCGATGCCACTATCCCAGACAAGGTCTTACAC
1 GTAATCACATATCGATGCCAATGTCCCAAATGTGGTCTTACAC
*
57678580 GTAATCACATATCG-TCGCCAATGTCCCAGATGTGGTCTTACAC
1 GTAATCACATATCGAT-GCCAATGTCCCAAATGTGGTCTTACAC
* * * *
57678623 ATAATCACATATTGATGCCACTGTCCCAGACA-G-GGTCTTAAAC
1 GTAATCACATATCGATGCCAATGTCCCA-A-ATGTGGTCTTACAC
57678666 GTAATCACATATC
1 GTAATCACATATC
57678679 AATATCACAT
Statistics
Matches: 181, Mismatches: 38, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
41 22 0.12
42 19 0.10
43 137 0.76
44 2 0.01
45 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (43 bp):
GTAATCACATATCGATGCCAATGTCCCAAATGTGGTCTTACAC
Found at i:57678579 original size:86 final size:86
Alignment explanation
Indices: 57678474--57678678 Score: 313
Period size: 86 Copynumber: 2.4 Consensus size: 86
57678464 GATGCTGGTG
* * *
57678474 TCCCAGACATGGTCTTACACGTAATCACATATCGAT-GCCAATGTTCCAAATGTGGTCTTACACG
1 TCCCAGACAAGGTCTTACACGTAATCACATATCG-TCGCCAATGTCCCAAATGTGGTCTTACACA
57678538 TAATCACAAATCGATGCCACTA
65 TAATCACAAATCGATGCCACTA
*
57678560 TCCCAGACAAGGTCTTACACGTAATCACATATCGTCGCCAATGTCCCAGATGTGGTCTTACACAT
1 TCCCAGACAAGGTCTTACACGTAATCACATATCGTCGCCAATGTCCCAAATGTGGTCTTACACAT
* * *
57678625 AATCACATATTGATGCCACTG
66 AATCACAAATCGATGCCACTA
* *
57678646 TCCCAGACAGGGTCTTAAACGTAATCACATATC
1 TCCCAGACAAGGTCTTACACGTAATCACATATC
57678679 AATATCACAT
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
85 1 0.01
86 108 0.99
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (86 bp):
TCCCAGACAAGGTCTTACACGTAATCACATATCGTCGCCAATGTCCCAAATGTGGTCTTACACAT
AATCACAAATCGATGCCACTA
Found at i:57678687 original size:13 final size:13
Alignment explanation
Indices: 57678669--57678693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57678659 CTTAAACGTA
57678669 ATCACATATCAAT
1 ATCACATATCAAT
57678682 ATCACATATCAA
1 ATCACATATCAA
57678694 ATAGTCAACT
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:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (13 bp):
ATCACATATCAAT
Done.