Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 175 of 193
Found at i:54522745 original size:20 final size:18
Alignment explanation
Indices: 54522691--54522769 Score: 56
Period size: 20 Copynumber: 4.3 Consensus size: 18
54522681 TTTATAAAAT
*
54522691 TTTAAT-TT-AATAATAA
1 TTTAATATTAAATATTAA
**
54522707 TCTTAATATTATTTTATTAA
1 T-TTAATATTA-AATATTAA
*
54522727 TTTAATATTAAAGTGATTAC
1 TTTAATATTAAA-T-ATTAA
*
54522747 CTTAATATTAAAT-TTAA
1 TTTAATATTAAATATTAA
54522764 TTTAAT
1 TTTAAT
54522770 GTTTATTTTG
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
16 1 0.02
17 13 0.27
18 2 0.04
19 11 0.23
20 21 0.44
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.52
Consensus pattern (18 bp):
TTTAATATTAAATATTAA
Found at i:54522863 original size:59 final size:62
Alignment explanation
Indices: 54522748--54522864 Score: 177
Period size: 62 Copynumber: 1.9 Consensus size: 62
54522738 AGTGATTACC
* * * *
54522748 TTAATATTAAATTTAATTTAATGTTTATTTTGTAGATAAATATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATTCTGTAGATAAATATTATATTAATTTAATAAGAT
54522810 TTAATATTAAATTTAATCTAATATTTA-TCT-T-GATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATTCTGTAGATAAATATTATATTAATTTAATA
54522865 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 23 0.45
60 1 0.02
61 2 0.04
62 25 0.49
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (62 bp):
TTAATATTAAATTTAATCTAATATTTATTCTGTAGATAAATATTATATTAATTTAATAAGAT
Found at i:54524954 original size:1 final size:1
Alignment explanation
Indices: 54524948--54524973 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
54524938 GGGTGACAAA
54524948 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
54524974 ATTTATTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:54526175 original size:22 final size:22
Alignment explanation
Indices: 54526139--54526184 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
54526129 AGTTATATTC
* *
54526139 TAGTCATTTATGTTTGAAATGT
1 TAGTCACTTAAGTTTGAAATGT
54526161 TAGTCACTTAAGTTTGAAATGT
1 TAGTCACTTAAGTTTGAAATGT
54526183 TA
1 TA
54526185 CGTGTTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (22 bp):
TAGTCACTTAAGTTTGAAATGT
Found at i:54530148 original size:17 final size:19
Alignment explanation
Indices: 54530126--54530165 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
54530116 AAACTTGAGA
54530126 TTTAATAT-ATATAAT-TT
1 TTTAATATAATATAATATT
*
54530143 TTTAATATAATTTAATATT
1 TTTAATATAATATAATATT
54530162 TTTA
1 TTTA
54530166 TTTTTATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 6 0.30
19 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATATAATATAATATT
Found at i:54530170 original size:27 final size:27
Alignment explanation
Indices: 54530125--54530177 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
54530115 GAAACTTGAG
*
54530125 ATTTAATATATATAATTTTTTAATATA
1 ATTTAATATATATAATTTTATAATATA
* * *
54530152 ATTTAATATTTTTATTTTTATAATAT
1 ATTTAATATATATAATTTTATAATAT
54530178 CATTAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTAATATATATAATTTTATAATATA
Found at i:54532787 original size:18 final size:18
Alignment explanation
Indices: 54532760--54532807 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
54532750 AATAAATAAT
*
54532760 ACACTAAATTAAAAAATA
1 ACACTTAATTAAAAAATA
54532778 ACACTTAATTTAAAAAAATA
1 ACACTTAA-TT-AAAAAATA
*
54532798 A-ACGTAATTA
1 ACACTTAATTA
54532808 TCTAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 9 0.35
19 7 0.27
20 9 0.35
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.27
Consensus pattern (18 bp):
ACACTTAATTAAAAAATA
Found at i:54538897 original size:1 final size:1
Alignment explanation
Indices: 54538861--54538889 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
54538851 CATTTTCTTG
54538861 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54538890 ATGTTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:54542134 original size:22 final size:24
Alignment explanation
Indices: 54542109--54542154 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
54542099 GAATAGAAAA
54542109 ACCAA-TA-TCGACATGCAATTGT
1 ACCAATTACTCGACATGCAATTGT
*
54542131 ACCAATTACTTTGACATGCAATTG
1 ACCAATTAC-TCGACATGCAATTG
54542155 AACTTACCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 2 0.10
25 13 0.65
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (24 bp):
ACCAATTACTCGACATGCAATTGT
Found at i:54542192 original size:22 final size:22
Alignment explanation
Indices: 54542164--54542213 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
54542154 GAACTTACCA
54542164 TTGTTGTAAGTGTGGTTTGCGT
1 TTGTTGTAAGTGTGGTTTGCGT
54542186 TTGTTGTAAGTGTGGTTTGCGT
1 TTGTTGTAAGTGTGGTTTGCGT
54542208 TTGTTG
1 TTGTTG
54542214 AAAGCAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.04, G:0.36, T:0.52
Consensus pattern (22 bp):
TTGTTGTAAGTGTGGTTTGCGT
Found at i:54547568 original size:20 final size:19
Alignment explanation
Indices: 54547543--54547699 Score: 66
Period size: 19 Copynumber: 8.5 Consensus size: 19
54547533 TGAATATATC
*
54547543 ATAAAATATTTTTAAAAATT
1 ATAAAA-ATTATTAAAAATT
* *
54547563 ATAAAAGTTATTGAAAATT
1 ATAAAAATTATTAAAAATT
* *
54547582 AT--AAATAATTAAAAGTT
1 ATAAAAATTATTAAAAATT
**
54547599 -TAAGAAATTA-TAGATTATT
1 ATAA-AAATTATTA-AAAATT
*
54547618 -TAAAAA-TATTAAAAAGTC
1 ATAAAAATTATTAAAAA-TT
54547636 ATAAAAATTA-T-AAAA-T
1 ATAAAAATTATTAAAAATT
* * *
54547652 A-GATAATATATTAAAAA-C
1 ATAAAAAT-TATTAAAAATT
*
54547670 ATAAAAATTATAAAGAAAATT
1 ATAAAAATTAT-TA-AAAATT
54547691 ATAAAAATT
1 ATAAAAATT
54547700 TGTAAAACCC
Statistics
Matches: 100, Mismatches: 22, Indels: 29
0.66 0.15 0.19
Matches are distributed among these distances:
15 4 0.04
16 4 0.04
17 16 0.16
18 20 0.20
19 35 0.35
20 12 0.12
21 9 0.09
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.34
Consensus pattern (19 bp):
ATAAAAATTATTAAAAATT
Found at i:54552362 original size:19 final size:19
Alignment explanation
Indices: 54552338--54552382 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
54552328 ATGTATCATT
54552338 TATAAAATT-TTATATGAAA
1 TATAAAATTATTATAT-AAA
*
54552357 TATAAATTTATTATATAAA
1 TATAAAATTATTATATAAA
54552376 -ATAAAAT
1 TATAAAAT
54552383 GTGATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 11 0.48
20 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TATAAAATTATTATATAAA
Found at i:54556417 original size:10 final size:9
Alignment explanation
Indices: 54556397--54556438 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
54556387 TATTTTTTAT
54556397 TTAAAATTA
1 TTAAAATTA
54556406 TTAAAATATA
1 TTAAAAT-TA
*
54556416 TTAAAATCA
1 TTAAAATTA
*
54556425 TAAAAATTA
1 TTAAAATTA
54556434 -TAAAA
1 TTAAAA
54556439 ACTCATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 4 0.14
9 15 0.54
10 9 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
TTAAAATTA
Found at i:54556430 original size:19 final size:18
Alignment explanation
Indices: 54556397--54556444 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
54556387 TATTTTTTAT
* *
54556397 TTAAAATTATTAAAATATA
1 TTAAAATCATAAAAAT-TA
54556416 TTAAAATCATAAAAATTA
1 TTAAAATCATAAAAATTA
*
54556434 TAAAAACTCAT
1 TTAAAA-TCAT
54556445 TAATTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAAATCATAAAAATTA
Found at i:54563831 original size:18 final size:16
Alignment explanation
Indices: 54563800--54563843 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
54563790 GGTCTAGGGT
*
54563800 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
54563817 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
54563831 TTAAAAATTTATT
1 TTAAAAATTTATT
54563844 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:54564170 original size:3 final size:3
Alignment explanation
Indices: 54564162--54564201 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
54564152 AGAAGGGAAT
54564162 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
54564202 AACTTCCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54566899 original size:29 final size:29
Alignment explanation
Indices: 54566864--54566925 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
54566854 TTGACGAATC
*
54566864 AATTATTTGAAATAAAAGCA-AAGAGATTA
1 AATTATTTGAAATAAAAGCACAAG-GACTA
*
54566893 AATTATTTGAAATAGAAGCACAAGGACTA
1 AATTATTTGAAATAAAAGCACAAGGACTA
54566922 AATT
1 AATT
54566926 CTAACATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (29 bp):
AATTATTTGAAATAAAAGCACAAGGACTA
Found at i:54567465 original size:19 final size:20
Alignment explanation
Indices: 54567443--54567483 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54567433 AAAGACATTT
54567443 AATA-ATTAAAAATAAATAA
1 AATATATTAAAAATAAATAA
* *
54567462 AATATTTTAAAATTAAATAA
1 AATATATTAAAAATAAATAA
54567482 AA
1 AA
54567484 AAAAGCATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATATATTAAAAATAAATAA
Found at i:54586640 original size:2 final size:2
Alignment explanation
Indices: 54586633--54586677 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
54586623 TTTTTAATAA
54586633 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
54586675 AT A
1 AT A
54586678 GTAGGACTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54587301 original size:23 final size:22
Alignment explanation
Indices: 54587250--54587293 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
54587240 ACCTTTAATC
*
54587250 ATTCTT-ACTTTTTTTAAAAAA
1 ATTCTTAATTTTTTTTAAAAAA
54587271 ATTCTTAATTTTTTTTAAAAAA
1 ATTCTTAATTTTTTTTAAAAAA
54587293 A
1 A
54587294 ATTGTTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTCTTAATTTTTTTTAAAAAA
Found at i:54588947 original size:26 final size:25
Alignment explanation
Indices: 54588881--54588959 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 25
54588871 GAAGTAATCA
* *
54588881 TTTAATAATTATTATTATGAAATTAAT
1 TTTAATAATTATTATT-T-AACTTTAT
* *
54588908 ATTAAGTAAATATTATTTAACTTTAT
1 TTTAA-TAATTATTATTTAACTTTAT
*
54588934 TTTAATTAATTATTATTTATCTTTAT
1 TTTAA-TAATTATTATTTAACTTTAT
54588960 GATAAATAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 28 0.65
27 5 0.12
28 10 0.23
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTAATAATTATTATTTAACTTTAT
Found at i:54592235 original size:18 final size:17
Alignment explanation
Indices: 54592191--54592259 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
54592181 TAAATAAGCG
*
54592191 ATATTATAGTAAAAATA
1 ATATTATAATAAAAATA
* *
54592208 ATGATAATAATAAAATTAA
1 AT-ATTATAATAAAAAT-A
54592227 ATATTATAATAATAATATA
1 ATATTATAATAA-AA-ATA
*
54592246 ATA-TAAAATAAAAA
1 ATATTATAATAAAAA
54592260 ATAAATTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
16 1 0.02
17 4 0.10
18 27 0.64
19 9 0.21
20 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATTATAATAAAAATA
Found at i:54594489 original size:16 final size:18
Alignment explanation
Indices: 54594461--54594495 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
54594451 TAATTAATTT
54594461 ATTAAATTAA-TTTCTCA
1 ATTAAATTAATTTTCTCA
54594478 ATTAAA-TAATTTTCTCA
1 ATTAAATTAATTTTCTCA
54594495 A
1 A
54594496 CTCAACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAAATTAATTTTCTCA
Found at i:54595445 original size:19 final size:19
Alignment explanation
Indices: 54595418--54595455 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54595408 ATATCACAAA
*
54595418 TGAATAAATCCATAAATAG
1 TGAACAAATCCATAAATAG
54595437 TGAACAAATCCATAAATAG
1 TGAACAAATCCATAAATAG
54595456 ATTTAGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.24
Consensus pattern (19 bp):
TGAACAAATCCATAAATAG
Found at i:54596756 original size:12 final size:13
Alignment explanation
Indices: 54596733--54596761 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
54596723 ACTTTTTTAA
54596733 AAAAAATAAAAAT
1 AAAAAATAAAAAT
54596746 AAAAAAT-AAAAT
1 AAAAAATAAAAAT
54596758 AAAA
1 AAAA
54596762 TTTATCATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:54602262 original size:28 final size:26
Alignment explanation
Indices: 54602231--54602282 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
54602221 AAAATAAATT
*
54602231 AATTTTGATTGATAAAATAAAATTCATG
1 AATTTT-ATTAATAAAA-AAAATTCATG
*
54602259 AATTTTATTAATTAAAAAAATTCA
1 AATTTTATTAATAAAAAAAATTCA
54602283 GTTTAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 8 0.36
28 6 0.27
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (26 bp):
AATTTTATTAATAAAAAAAATTCATG
Found at i:54603225 original size:56 final size:56
Alignment explanation
Indices: 54603139--54603251 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
54603129 CCTATACTGA
*
54603139 AAGTTGAAAATGTAATACGTACTCATGGTCCGAAGGGTTTGACTAGATTCTGGGCT
1 AAGTTGAAAATGTAATACGTACTCATGGTCCGAAGGGTTTGACTAGATTCAGGGCT
54603195 AAGTTGAAAATGTAATACGTACTCATGGTCCGAAGGGTTTGACTAGATTCAGGGCT
1 AAGTTGAAAATGTAATACGTACTCATGGTCCGAAGGGTTTGACTAGATTCAGGGCT
54603251 A
1 A
54603252 GTGGAATGAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (56 bp):
AAGTTGAAAATGTAATACGTACTCATGGTCCGAAGGGTTTGACTAGATTCAGGGCT
Found at i:54609584 original size:17 final size:17
Alignment explanation
Indices: 54609562--54609599 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
54609552 GGTGGAGAAT
* *
54609562 TTGTTCGTTGAGAGTTC
1 TTGTTCGTAGAGAATTC
54609579 TTGTTCGTAGAGAATTC
1 TTGTTCGTAGAGAATTC
54609596 TTGT
1 TTGT
54609600 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.26, T:0.47
Consensus pattern (17 bp):
TTGTTCGTAGAGAATTC
Found at i:54611653 original size:26 final size:28
Alignment explanation
Indices: 54611593--54611653 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
54611583 TTATAATGTG
* *
54611593 TAATATTATAAAAATACATATTTAATTAT
1 TAATATTATAAAAATA-ATAATAAATTAT
*
54611622 TTATATT-TAAAAAT-ATAATAAATTAT
1 TAATATTATAAAAATAATAATAAATTAT
54611648 TAATAT
1 TAATAT
54611654 AATCTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 15 0.54
28 7 0.25
29 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATATTATAAAAATAATAATAAATTAT
Found at i:54615109 original size:39 final size:40
Alignment explanation
Indices: 54615066--54615149 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 40
54615056 AATATTAAAT
54615066 TTTTTAAATAATATATTC-AATACAATAAAATATTCATTA
1 TTTTTAAATAATATATTCTAATACAATAAAATATTCATTA
* * * * *
54615105 TTTTT-ATTTATTTTTTCTAATACAATAAAATATTTATTA
1 TTTTTAAATAATATATTCTAATACAATAAAATATTCATTA
*
54615144 TATTTA
1 TTTTTA
54615150 TGATAGTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
38 8 0.22
39 29 0.78
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (40 bp):
TTTTTAAATAATATATTCTAATACAATAAAATATTCATTA
Found at i:54627560 original size:79 final size:80
Alignment explanation
Indices: 54627470--54627630 Score: 306
Period size: 79 Copynumber: 2.0 Consensus size: 80
54627460 TAACCATTTG
54627470 ACAATGCACACACATCTTGCACACAGGTGCTCGAACTCGAAACTCTTAAGATGAACAACA-TTTA
1 ACAATGCACACACATCTTGCACACAGGTGCTCGAACTCGAAACTCTTAAGATGAACAACATTTTA
54627534 TTTTTCATTGGAGCC
66 TTTTTCATTGGAGCC
*
54627549 ACAATGCACACACATCTTGCACACAGGTGCTCGAACTCGAAACTCTTAAGATGAACAACATTTTT
1 ACAATGCACACACATCTTGCACACAGGTGCTCGAACTCGAAACTCTTAAGATGAACAACATTTTA
54627614 TTTTTCATTGGAGCC
66 TTTTTCATTGGAGCC
54627629 AC
1 AC
54627631 TAGTTAGATT
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 60 0.75
80 20 0.25
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (80 bp):
ACAATGCACACACATCTTGCACACAGGTGCTCGAACTCGAAACTCTTAAGATGAACAACATTTTA
TTTTTCATTGGAGCC
Found at i:54637191 original size:17 final size:16
Alignment explanation
Indices: 54637169--54637269 Score: 94
Period size: 17 Copynumber: 6.0 Consensus size: 16
54637159 AGGCCCAAAC
54637169 TATTTTGAAATTAAATT
1 TATTTT-AAATTAAATT
*
54637186 TATTTTAATTTTAAATT
1 TATTTTAA-ATTAAATT
*
54637203 TATTTTAAATTTAATT
1 TATTTTAAATTAAATT
* *
54637219 TAATTTGAAATTGAATT
1 T-ATTTTAAATTAAATT
* *
54637236 TAATTTAAATTTAATAT
1 TATTTTAAATTAAAT-T
*
54637253 TATTATAAATTTAAATT
1 TATTTTAAA-TTAAATT
54637270 AAAAATATCC
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
16 20 0.29
17 44 0.64
18 5 0.07
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATTTTAAATTAAATT
Found at i:54637220 original size:28 final size:28
Alignment explanation
Indices: 54637173--54637250 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
54637163 CCAAACTATT
* * *
54637173 TTGAAATTAAATTTATTTTAATTTTAAA
1 TTGAATTTAAATTTAATTTAATTTGAAA
* *
54637201 TTTATTTTAAATTTAATTTAATTTGAAA
1 TTGAATTTAAATTTAATTTAATTTGAAA
54637229 TTGAATTT-AATTTAAATTTAAT
1 TTGAATTTAAATTT-AATTTAAT
54637251 ATTATTATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 5 0.12
28 37 0.88
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
TTGAATTTAAATTTAATTTAATTTGAAA
Found at i:54637248 original size:6 final size:6
Alignment explanation
Indices: 54637179--54637269 Score: 56
Period size: 6 Copynumber: 16.2 Consensus size: 6
54637169 TATTTTGAAA
* * *
54637179 TTAAAT TT-ATT TTAATT TTAAAT TT-ATT TTAAAT TT-AAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
54637223 TTGAAA- TTGAAT TT-AAT TTAAAT TT-AAT ATT--AT TATAAAT TTAAAT
1 TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT T-TAAAT TTAAAT
54637269 T
1 T
54637270 AAAAATATCC
Statistics
Matches: 70, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
4 1 0.01
5 31 0.44
6 33 0.47
7 5 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:54637249 original size:11 final size:11
Alignment explanation
Indices: 54637176--54637250 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 11
54637166 AACTATTTTG
*
54637176 AAATTAAATTT
1 AAATTTAATTT
*
54637187 -ATTTTAATTTT
1 AAATTTAA-TTT
*
54637198 AAATTTATTTT
1 AAATTTAATTT
54637209 AAATTTAATTT
1 AAATTTAATTT
*
54637220 -AATTTGAAATT
1 AAATTT-AATTT
*
54637231 GAATTTAATTT
1 AAATTTAATTT
54637242 AAATTTAAT
1 AAATTTAAT
54637251 ATTATTATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
10 10 0.19
11 32 0.62
12 10 0.19
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:54637249 original size:50 final size:50
Alignment explanation
Indices: 54637172--54637271 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 50
54637162 CCCAAACTAT
* * * *
54637172 TTTGAAATTAAATTTATTTTAATTTTAA-ATTTATTTTAAATTTAATTTAA
1 TTTGAAATTAAATTTAATTTAAATTTAATA-TTATTATAAATTTAAATTAA
*
54637222 TTTGAAATTGAATTTAATTTAAATTTAATATTATTATAAATTTAAATTAA
1 TTTGAAATTAAATTTAATTTAAATTTAATATTATTATAAATTTAAATTAA
54637272 AAATATCCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 43 0.98
51 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (50 bp):
TTTGAAATTAAATTTAATTTAAATTTAATATTATTATAAATTTAAATTAA
Found at i:54637263 original size:28 final size:26
Alignment explanation
Indices: 54637179--54637272 Score: 79
Period size: 28 Copynumber: 3.6 Consensus size: 26
54637169 TATTTTGAAA
* *
54637179 TTAAATTTATTTTAATTTTAAATTTATT
1 TTAAATTTAATTTAAATTTAAA-TTA-T
*
54637207 TTAAATTTAATTT-AATTTGAA--A-
1 TTAAATTTAATTTAAATTTAAATTAT
*
54637229 TTGAATTTAATTTAAATTTAATATTAT
1 TTAAATTTAATTTAAATTTAA-ATTAT
*
54637256 TATAAATTTAAATTAAA
1 T-TAAATTTAATTTAAA
54637273 AATATCCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
22 12 0.23
23 6 0.11
24 2 0.04
26 1 0.02
27 7 0.13
28 25 0.47
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TTAAATTTAATTTAAATTTAAATTAT
Found at i:54638064 original size:9 final size:9
Alignment explanation
Indices: 54638050--54638078 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
54638040 ATTAATGAGA
54638050 AATATTAAT
1 AATATTAAT
54638059 AATATTAAT
1 AATATTAAT
54638068 AATATTAAT
1 AATATTAAT
54638077 AA
1 AA
54638079 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AATATTAAT
Found at i:54638089 original size:18 final size:19
Alignment explanation
Indices: 54638049--54638089 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
54638039 TATTAATGAG
*
54638049 AAATATTAATAATATTAAT
1 AAATATTAATAATATAAAT
54638068 -AATATTAATAA-ATAAAT
1 AAATATTAATAATATAAAT
54638085 AAATA
1 AAATA
54638090 AATAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATTAATAATATAAAT
Found at i:54639179 original size:30 final size:30
Alignment explanation
Indices: 54639126--54639346 Score: 304
Period size: 30 Copynumber: 7.4 Consensus size: 30
54639116 AAACTGTCCA
*
54639126 AAAATTACATTTT-ACCC-AAAACTTTTCA
1 AAAATTACATTTTAACCCTAAAACTTTTCC
*
54639154 AAAATTACATTTTAACCCTAAAACTTCTCC
1 AAAATTACATTTTAACCCTAAAACTTTTCC
* *
54639184 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCTAAAACTTTTCC
* *
54639214 AAAATTACATTTTAACCCCCAAAAGTTTTCC
1 AAAATTACATTTTAA-CCCTAAAACTTTTCC
* *
54639245 AATATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTAACCCTAAAACTTTTCC
*
54639275 AATATTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTAACCCTAAAACTTTTCC
**
54639305 AAAATTACATTTTAACCCTTGAAC-TTTCC
1 AAAATTACATTTTAACCCTAAAACTTTTCC
*
54639334 AAAATTCCATTTT
1 AAAATTACATTTT
54639347 TGACCTCGGT
Statistics
Matches: 174, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
28 13 0.07
29 21 0.12
30 113 0.65
31 27 0.16
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTAAAACTTTTCC
Found at i:54639268 original size:91 final size:91
Alignment explanation
Indices: 54639126--54639322 Score: 301
Period size: 91 Copynumber: 2.2 Consensus size: 91
54639116 AAACTGTCCA
54639126 AAAATTACATTTT-A--CCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAACTTCTCCAAAA
1 AAAATTACATTTTAACCCCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAACTTCTCCAAAA
*
54639188 TTACATTTTGACCCCAAAACTTTTCC
66 TTACATTTTAACCCCAAAACTTTTCC
* * * * * *
54639214 AAAATTACATTTTAACCCCCAAAAGTTTTCCAATATTACATTTTGACCCTAAAACTTTTCCAATA
1 AAAATTACATTTTAACCCCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAACTTCTCCAAAA
*
54639279 TTACATTTTAACCCTAAAACTTTTCC
66 TTACATTTTAACCCCAAAACTTTTCC
54639305 AAAATTACATTTTAACCC
1 AAAATTACATTTTAACCC
54639323 TTGAACTTTC
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
88 13 0.13
89 1 0.01
91 84 0.86
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.36
Consensus pattern (91 bp):
AAAATTACATTTTAACCCCCAAAACTTTTCAAAAATTACATTTTAACCCTAAAACTTCTCCAAAA
TTACATTTTAACCCCAAAACTTTTCC
Found at i:54648008 original size:19 final size:19
Alignment explanation
Indices: 54647981--54648049 Score: 50
Period size: 19 Copynumber: 3.5 Consensus size: 19
54647971 TATTTTAAGT
*
54647981 TTTTTTTTTTGGAAATACG
1 TTTTATTTTTGGAAATACG
* * **
54648000 TTTTATTTTTAGTAATAAA
1 TTTTATTTTTGGAAATACG
*
54648019 TTTTCATTTTGTTGAAAATACG
1 TTTT-A-TTT-TTGGAAATACG
54648041 TTTT-TTTTT
1 TTTTATTTTT
54648050 TTTTTTGTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 7
0.69 0.19 0.13
Matches are distributed among these distances:
18 2 0.05
19 21 0.57
20 1 0.03
21 3 0.08
22 10 0.27
ACGTcount: A:0.25, C:0.04, G:0.10, T:0.61
Consensus pattern (19 bp):
TTTTATTTTTGGAAATACG
Found at i:54650722 original size:27 final size:28
Alignment explanation
Indices: 54650692--54650756 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
54650682 TTTTATTTAA
*
54650692 ATTTAAATTTATTT-TAAGTTTAAATTT
1 ATTTAAATTTATTTCTAAATTTAAATTT
54650719 ATTTAAATTT-TTTCTAAATTTAAATTT
1 ATTTAAATTTATTTCTAAATTTAAATTT
*
54650746 AATTAAATTTA
1 ATTTAAATTTA
54650757 AAATGATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 3 0.09
27 31 0.91
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
ATTTAAATTTATTTCTAAATTTAAATTT
Found at i:54650739 original size:17 final size:16
Alignment explanation
Indices: 54650669--54650758 Score: 73
Period size: 17 Copynumber: 5.8 Consensus size: 16
54650659 TTTATTTTAA
*
54650669 AATTAATTTTAAATTTT
1 AATTAAATTTAAA-TTT
*
54650686 ATTTAAATTTAAATTT
1 AATTAAATTTAAATTT
* *
54650702 ATTTTAAGTTTAAATTT
1 A-ATTAAATTTAAATTT
*
54650719 ATTTAAATTT---TTT
1 AATTAAATTTAAATTT
*
54650732 --CTAAATTTAAATTT
1 AATTAAATTTAAATTT
54650746 AATTAAATTTAAA
1 AATTAAATTTAAA
54650759 ATGATATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
11 7 0.11
13 3 0.05
14 3 0.05
16 22 0.36
17 26 0.43
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (16 bp):
AATTAAATTTAAATTT
Found at i:54650742 original size:6 final size:6
Alignment explanation
Indices: 54650664--54650758 Score: 71
Period size: 6 Copynumber: 17.0 Consensus size: 6
54650654 TTTTGTTTAT
* * * * *
54650664 TTTAAA ATTAAT TTTAAA TTT-TA TTTAAA TTTAAA TTT-AT TTTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
54650710 TTTAAA TTT--A TTTAAA TTT--T TTCTAAA TTTAAA TTT-AA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA
54650753 TTTAAA
1 TTTAAA
54650759 ATGATATTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
4 8 0.12
5 13 0.19
6 46 0.67
7 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:54650749 original size:11 final size:11
Alignment explanation
Indices: 54650659--54650758 Score: 73
Period size: 11 Copynumber: 9.0 Consensus size: 11
54650649 TTGGATTTTG
*
54650659 TTTATTTTAAA
1 TTTAATTTAAA
*
54650670 ATTAATTTTAAA
1 TTTAA-TTTAAA
*
54650682 TTTTATTTAAA
1 TTTAATTTAAA
*
54650693 TTTAAATTT-AT
1 TTT-AATTTAAA
54650704 TTTAAGTTTAAA
1 TTTAA-TTTAAA
54650716 TTT-ATTTAAA
1 TTTAATTTAAA
*
54650726 TTT-TTTCTAAA
1 TTTAATT-TAAA
54650737 TTTAAATTT-AA
1 TTT-AATTTAAA
*
54650748 TTAAATTTAAA
1 TTTAATTTAAA
54650759 ATGATATTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
10 18 0.25
11 33 0.46
12 18 0.25
13 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:54650767 original size:17 final size:16
Alignment explanation
Indices: 54650733--54650783 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
54650723 AAATTTTTTC
* *
54650733 TAAATTTAAATTTAAT
1 TAAATTTAAAATGAAT
54650749 TAAATTTAAAATGATAT
1 TAAATTTAAAATGA-AT
*
54650766 TAAAATT--AATGAAT
1 TAAATTTAAAATGAAT
54650780 TAAA
1 TAAA
54650784 GGTCCAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 6 0.19
15 5 0.16
16 12 0.39
17 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
TAAATTTAAAATGAAT
Found at i:54650769 original size:44 final size:44
Alignment explanation
Indices: 54650676--54650769 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 44
54650666 TAAAATTAAT
* * * *
54650676 TTTAAATTTTATTTAAATTTAAATTTATTTTAAGTTTAAATTTA
1 TTTAAATTTTATTTAAATTTAAATTTATATTAAATTTAAAATGA
54650720 TTTAAATTTT-TTCTAAATTTAAATTTA-ATTAAATTTAAAATGA
1 TTTAAATTTTATT-TAAATTTAAATTTATATTAAATTTAAAATGA
54650763 TATTAAA
1 T-TTAAA
54650770 ATTAATGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 15 0.34
44 29 0.66
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (44 bp):
TTTAAATTTTATTTAAATTTAAATTTATATTAAATTTAAAATGA
Found at i:54651486 original size:3 final size:3
Alignment explanation
Indices: 54651478--54651578 Score: 69
Period size: 3 Copynumber: 32.7 Consensus size: 3
54651468 ATAACTTTAT
* * *
54651478 ATA ATA ATA ATA ATA ATA ATA ATC ATA ATA ATA ATTA ATA TTTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA -ATA ATA
* * * * * * *
54651525 ATTA ATA TTA GTCA TTA ATA TTA ATA AT- ATC TTA ATA ATA GTA ATA
1 A-TA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54651571 ATA ATA AT
1 ATA ATA AT
54651579 GTTAAAGGAC
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
2 2 0.03
3 65 0.84
4 10 0.13
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:54651541 original size:13 final size:13
Alignment explanation
Indices: 54651509--54651552 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
54651499 ATCATAATAA
54651509 TAATTAATATTTAG
1 TAATTAATA-TTAG
54651523 TAATTAATATTAG
1 TAATTAATATTAG
* *
54651536 TCATTAATATTAA
1 TAATTAATATTAG
54651549 TAAT
1 TAAT
54651553 ATCTTAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (13 bp):
TAATTAATATTAG
Found at i:54652778 original size:58 final size:57
Alignment explanation
Indices: 54652602--54653024 Score: 542
Period size: 58 Copynumber: 7.2 Consensus size: 57
54652592 AAAATTTTAG
*
54652602 AAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCAATTTCACC
1 AAAATTACCATTTTACCCCCGAA-CTTCTAAAATTCCATTTTTAACCCCGATTTCACC
* * * *
54652660 GAAAATTATCATTTTACCCCCAAACATTCTAAAATACCATTTTTAACCCCGGTTTCACC
1 -AAAATTACCATTTTACCCCCGAAC-TTCTAAAATTCCATTTTTAACCCCGATTTCACC
* * * *
54652719 AAAACTTACCATTTTACCCCTGAACTTCTAAAATTCCATTTTTATCCCTGATTTGACC
1 AAAA-TTACCATTTTACCCCCGAACTTCTAAAATTCCATTTTTAACCCCGATTTCACC
*
54652777 AAAATTTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAA-TTACCATTTTACCCCCGAACTTCTAAAATTCCATTTTTAACCCCGATTTCACC
* *
54652835 AAAAATTACCATTTTACCCCCGAACTTCCAAAATTCAATTTTTAACCCCGATTTCACC
1 -AAAATTACCATTTTACCCCCGAACTTCTAAAATTCCATTTTTAACCCCGATTTCACC
* * * *
54652893 GAAGATTACCATTTTACCCTCAAACTTTCTAAAATACCA-TTTTAACCCCGATTTCACC
1 -AAAATTACCATTTTACCCCCGAAC-TTCTAAAATTCCATTTTTAACCCCGATTTCACC
* * * * *
54652951 AAAAATTACCGTTTTACCCCCAAACTCTCAAAAATTCTATTTTTTAACCCCGACTTCACC
1 -AAAATTACCATTTTACCCCCGAACT-TCTAAAATTCCA-TTTTTAACCCCGATTTCACC
*
54653011 ACAATTACCATTTT
1 AAAATTACCATTTT
54653025 GCCCTCTAGT
Statistics
Matches: 320, Mismatches: 37, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
57 1 0.00
58 207 0.65
59 94 0.29
60 18 0.06
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCCGAACTTCTAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:54652877 original size:28 final size:28
Alignment explanation
Indices: 54652602--54652885 Score: 163
Period size: 29 Copynumber: 9.8 Consensus size: 28
54652592 AAAATTTTAG
*
54652602 AAAATTACCA-TTTTACCCCCGAACCTTCT
1 AAAATT-CCATTTTTACCCCCGAA-CTTCC
* *
54652631 AAAATTCCATTTTTAACCCC-AATTTCACC
1 AAAATTCCATTTTTACCCCCGAACTT--CC
* * *
54652660 GAAAATTATCA-TTTTACCCCCAAACATTCT
1 -AAAATT-CCATTTTTACCCCCGAAC-TTCC
* * **
54652690 AAAATACCATTTTTAACCCCG-GTTTCACC
1 AAAATTCCATTTTTACCCCCGAACTT--CC
* *
54652719 AAAACTTACCA-TTTTACCCCTGAACTTCT
1 AAAA-TT-CCATTTTTACCCCCGAACTTCC
* * *
54652748 AAAATTCCATTTTTATCCCTG-ATTTGACC
1 AAAATTCCATTTTTACCCCCGAACTT--CC
54652777 AAAATTTACCA-TTTTACCCCCGAACTTCC
1 AAAA-TT-CCATTTTTACCCCCGAACTTCC
* *
54652806 AAAATTCCATTTTTAACCCCG-ATTTCACC
1 AAAATTCCATTTTTACCCCCGAACTT--CC
54652835 AAAAATTACCA-TTTTACCCCCGAACTTCC
1 -AAAATT-CCATTTTTACCCCCGAACTTCC
* *
54652864 AAAATTCAATTTTTAACCCCGA
1 AAAATTCCATTTTTACCCCCGA
54652886 TTTCACCGAA
Statistics
Matches: 197, Mismatches: 32, Indels: 53
0.70 0.11 0.19
Matches are distributed among these distances:
27 18 0.09
28 48 0.24
29 55 0.28
30 53 0.27
31 21 0.11
32 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCCGAACTTCC
Found at i:54652956 original size:29 final size:29
Alignment explanation
Indices: 54652690--54653024 Score: 124
Period size: 30 Copynumber: 11.4 Consensus size: 29
54652680 CAAACATTCT
*
54652690 AAAATACCATTTTTAACCCCGGTTTCACCA
1 AAAATACCA-TTTTAACCCCGATTTCACCA
* * *
54652720 AAACTTACCATTTT-ACCCCTGAACTT---CT
1 AAA-ATACCATTTTAACCCC-G-ATTTCACCA
* * * *
54652748 AAAATTCCATTTTTATCCCTGATTTGACCA
1 AAAATACCA-TTTTAACCCCGATTTCACCA
* * *
54652778 AAATTTACCATTTTACCCCCGAACTT--CC-
1 AAA-ATACCATTTTAACCCCG-ATTTCACCA
*
54652806 AAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATACCA-TTTTAACCCCGATTTCACCA
* *
54652836 AAAATTACCATTTTACCCCCGAACTT--CC-
1 AAAA-TACCATTTTAACCCCG-ATTTCACCA
* *
54652864 AAAATTCAATTTTTAACCCCGATTTCACCGA
1 AAAATACCA-TTTTAACCCCGATTTCACC-A
* * * *
54652895 AGATTACCATTTT-ACCCTCAAACTTT---CT
1 AAAATACCATTTTAACCC-C-GA-TTTCACCA
54652923 AAAATACCATTTTAACCCCGATTTCACCA
1 AAAATACCATTTTAACCCCGATTTCACCA
* * * ** *
54652952 AAAATTACCGTTTTACCCCCAAACTC-TCA
1 AAAA-TACCATTTTAACCCCGATTTCACCA
* * *
54652981 AAAATTCTATTTTTTAACCCCGACTTCACCA
1 AAAATACCA--TTTTAACCCCGATTTCACCA
* *
54653012 CAATTACCATTTT
1 AAAATACCATTTT
54653025 GCCCTCTAGT
Statistics
Matches: 219, Mismatches: 54, Indels: 65
0.65 0.16 0.19
Matches are distributed among these distances:
26 3 0.01
27 21 0.10
28 50 0.23
29 40 0.18
30 68 0.31
31 34 0.16
32 3 0.01
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAATACCATTTTAACCCCGATTTCACCA
Found at i:54654916 original size:2 final size:2
Alignment explanation
Indices: 54654909--54654933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54654899 TCTTTGTATT
54654909 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
54654934 GAATATAATT
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:54659127 original size:19 final size:19
Alignment explanation
Indices: 54659099--54659135 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54659089 CATATTTTAG
*
54659099 GTTTTCTTTTTGGAAATAC
1 GTTTTATTTTTGGAAATAC
*
54659118 GTTTTATTTTTGGTAATA
1 GTTTTATTTTTGGAAATA
54659136 AATTTGTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.05, G:0.16, T:0.57
Consensus pattern (19 bp):
GTTTTATTTTTGGAAATAC
Found at i:54659172 original size:16 final size:16
Alignment explanation
Indices: 54659124--54659175 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
54659114 ATACGTTTTA
54659124 TTTT-TGGTAATAAAT
1 TTTTATGGTAATAAAT
* * * *
54659139 TTGTAT-GCATTTAAT
1 TTTTATGGTAATAAAT
54659154 TTTTATGGTAATAAAT
1 TTTTATGGTAATAAAT
54659170 TTTTAT
1 TTTTAT
54659176 TTTGTTGAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.56
Consensus pattern (16 bp):
TTTTATGGTAATAAAT
Found at i:54659208 original size:20 final size:20
Alignment explanation
Indices: 54659153--54659213 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
54659143 ATGCATTTAA
* *
54659153 TTTTTATGGTAATAAATTTT
1 TTTTTTTGGTAATAAGTTTT
** *
54659173 TATTTTGTTGAAAATACGTTTT
1 T-TTTT-TTGGTAATAAGTTTT
54659195 TTTTTTTGGTAATAAGTTT
1 TTTTTTTGGTAATAAGTTT
54659214 GTAGGTATTT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 12 0.39
21 8 0.26
22 11 0.35
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.59
Consensus pattern (20 bp):
TTTTTTTGGTAATAAGTTTT
Found at i:54668470 original size:9 final size:9
Alignment explanation
Indices: 54668458--54668484 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
54668448 TAAATCCAAT
54668458 AAAATAAAA
1 AAAATAAAA
54668467 AAAATAAAA
1 AAAATAAAA
54668476 AAAATAAAA
1 AAAATAAAA
54668485 CAAGGTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAATAAAA
Found at i:54669218 original size:19 final size:18
Alignment explanation
Indices: 54669190--54669228 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
54669180 TTTTATCATT
* *
54669190 TATATATTATTTTTTAAA
1 TATATATTATATTCTAAA
54669208 TATATATTTATATTCTAAA
1 TATATA-TTATATTCTAAA
54669227 TA
1 TA
54669229 CGTGATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTATATTCTAAA
Found at i:54670268 original size:28 final size:29
Alignment explanation
Indices: 54670235--54670303 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
54670225 TCAATAGTTA
54670235 ATATTTTTATAATTTTTAAAGAATAAAAT
1 ATATTTTTATAATTTTTAAAGAATAAAAT
* **
54670264 -TATTTTTTATTATTTTTAAAGTTTAAAAT
1 ATA-TTTTTATAATTTTTAAAGAATAAAAT
*
54670293 ATAATTTTATA
1 ATATTTTTATA
54670304 TAAAATTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 2 0.06
29 29 0.88
30 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
ATATTTTTATAATTTTTAAAGAATAAAAT
Found at i:54672055 original size:30 final size:31
Alignment explanation
Indices: 54672021--54672078 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
54672011 ACAAAAAAAC
54672021 ATATTAAAATTAAT-AAAATTAAATTTTACA
1 ATATTAAAATTAATGAAAATTAAATTTTACA
* *
54672051 ATATTCAAATTAATGAAATTTAAATTTT
1 ATATTAAAATTAATGAAAATTAAATTTT
54672079 CGTATTATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (31 bp):
ATATTAAAATTAATGAAAATTAAATTTTACA
Found at i:54673222 original size:29 final size:30
Alignment explanation
Indices: 54673177--54673257 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
54673167 AAATTAAATC
* *
54673177 AAATAAAAATTTAATGTATAAAATTATACA-
1 AAATCAAAATTT-ATGTATAAAATTACACAT
* * * *
54673207 AAATCAAAGTTTATGTATGATATTGCACATT
1 AAATCAAAATTTATGTATAAAATTACACA-T
54673238 AAATCAAAATTTATGTATAA
1 AAATCAAAATTTATGTATAA
54673258 TTTAGATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 13 0.32
30 10 0.24
31 18 0.44
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.36
Consensus pattern (30 bp):
AAATCAAAATTTATGTATAAAATTACACAT
Found at i:54676811 original size:59 final size:58
Alignment explanation
Indices: 54676748--54676939 Score: 255
Period size: 59 Copynumber: 3.3 Consensus size: 58
54676738 TTCGGGGTTA
*
54676748 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTTAGGGG
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTTAGGGG
* *
54676806 CAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAACT-AGATTTTGGAAAGTCTAGGGG
1 -AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTTAGGGG
* * * * *
54676864 TAAATGGTAATTTTT-G-GAAGTTTTGGGGTTAAAAATGAAATTTTGAAAAGTTTAGGGG
1 AAAATGGTAATTTTTGGTGAA--ATCGGGGTTAAAAATGAGATTTTGGAAAGTTTAGGGG
54676922 TAAAATGGTAATTTTTGG
1 -AAAATGGTAATTTTTGG
54676940 AAGTTTCGGT
Statistics
Matches: 117, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
55 3 0.03
56 1 0.01
57 26 0.22
58 38 0.32
59 48 0.41
60 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTTAGGGG
Found at i:54676819 original size:29 final size:30
Alignment explanation
Indices: 54676788--54676945 Score: 122
Period size: 29 Copynumber: 5.4 Consensus size: 30
54676778 AAAAATGAGA
*
54676788 TTTTGGAAAGTTTAGGGGCAAAATGGTAAT
1 TTTTGGAAAGTTTAGGGGTAAAATGGTAAT
* *
54676818 TTTTGGTGAAA---TCGGGGTTAAAA--CTAGA-
1 TTTT-G-GAAAGTTTAGGGG-TAAAATGGTA-AT
*
54676846 TTTTGGAAAGTCTAGGGGT-AAATGGTAAT
1 TTTTGGAAAGTTTAGGGGTAAAATGGTAAT
* *
54676875 TTTTGG-AAGTTTTGGGGTTAAAAAT-G-AAA
1 TTTTGGAAAGTTTAGGGG-T-AAAATGGTAAT
*
54676904 TTTTGAAAAGTTTAGGGGTAAAATGGTAAT
1 TTTTGGAAAGTTTAGGGGTAAAATGGTAAT
54676934 TTTTGG-AAGTTT
1 TTTTGGAAAGTTT
54676946 CGGTGTCAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 33
0.69 0.08 0.23
Matches are distributed among these distances:
26 4 0.04
27 4 0.04
28 22 0.22
29 35 0.35
30 26 0.26
31 5 0.05
32 4 0.04
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (30 bp):
TTTTGGAAAGTTTAGGGGTAAAATGGTAAT
Found at i:54676957 original size:30 final size:28
Alignment explanation
Indices: 54676846--54676965 Score: 100
Period size: 29 Copynumber: 4.1 Consensus size: 28
54676836 TAAAACTAGA
*
54676846 TTTTGGAAAGTCTAGGGGT-AAATGGTAAT
1 TTTTGG-AAGTTTAGGGGTAAAAT-GTAAT
* *
54676875 TTTTGGAAGTTTTGGGGTTAAAAATG-AAA
1 TTTTGGAAGTTTAGGGG-T-AAAATGTAAT
*
54676904 TTTTGAAAAGTTTAGGGGTAAAATGGTAAT
1 TTTTG-GAAGTTTAGGGGTAAAAT-GTAAT
* * *
54676934 TTTTGGAAGTTTCGGTGTCAAAATATAAT
1 TTTTGGAAGTTTAGGGGT-AAAATGTAAT
54676963 TTT
1 TTT
54676966 CTAAAGTTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
28 14 0.19
29 33 0.45
30 23 0.31
31 4 0.05
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.39
Consensus pattern (28 bp):
TTTTGGAAGTTTAGGGGTAAAATGTAAT
Found at i:54676957 original size:58 final size:57
Alignment explanation
Indices: 54676777--54676974 Score: 204
Period size: 58 Copynumber: 3.4 Consensus size: 57
54676767 AAATCGAGGT
* * *
54676777 TAAAAATGAGATTTTGGAAAGTTTAGGGGCAAAATGGTAATTTTTGGTGAA--ATCGGGG
1 TAAAAAT-AAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT-G-GAAGTTTCGGGG
* * * *
54676835 TTAAAACTAGATTTTGGAAAGTCTAGGGGT-AAATGGTAATTTTTGGAAGTTTTGGGG
1 -TAAAAATAAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGG
* *
54676892 TTAAAAATGAAATTTTGAAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGTTTCGGTG
1 -TAAAAAT-AAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGG
* **
54676951 TCAAAATATAATTTTCTAAAGTTT
1 TAAAAATA-AATTTTGGAAAGTTT
54676975 TGGATCACAA
Statistics
Matches: 120, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
55 3 0.03
56 1 0.01
57 27 0.22
58 58 0.48
59 31 0.26
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (57 bp):
TAAAAATAAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGTTTCGGGG
Found at i:54678479 original size:26 final size:26
Alignment explanation
Indices: 54678462--54678526 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
54678452 AGATTGTAAC
*
54678462 TATGTATTGATTTCAAAGTGGGTTCG
1 TATGTATTGATTTCAAAGTGGGTACG
*
54678488 TATGTATTGATTTCAAAGTGGGTTCG
1 TATGTATTGATTTCAAAGTGGGTACG
54678514 TATGTATTGATTT
1 TATGTATTGATTT
54678527 TCAGAAAGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.23, C:0.06, G:0.25, T:0.46
Consensus pattern (26 bp):
TATGTATTGATTTCAAAGTGGGTACG
Found at i:54678986 original size:17 final size:17
Alignment explanation
Indices: 54678932--54679007 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
54678922 AATTTAATTT
* *
54678932 TAAATTTAAAATTATAA
1 TAAATTTAAATTTAAAA
* **
54678949 TAAATTTAAATTTTATG
1 TAAATTTAAATTTAAAA
*
54678966 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
54678983 TAAATCT-AATTTAAAA
1 TAAATTTAAATTTAAAA
54678999 CTAAATTTA
1 -TAAATTTA
54679008 TCTCATTGGG
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
16 8 0.18
17 37 0.82
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:54688371 original size:22 final size:21
Alignment explanation
Indices: 54688345--54688386 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
54688335 AATTTAACTT
*
54688345 TTTAATATTTACAAGATAAATC
1 TTTAAAATTTACAAG-TAAATC
*
54688367 TTTAAAATTTTCAAGTAAAT
1 TTTAAAATTTACAAGTAAAT
54688387 AAATATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (21 bp):
TTTAAAATTTACAAGTAAATC
Found at i:54697310 original size:17 final size:17
Alignment explanation
Indices: 54697290--54697348 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
54697280 CCCTAATCAG
54697290 TAAAAAACTCTAAACCA
1 TAAAAAACTCTAAACCA
* *
54697307 TAAAAAGCCCTAAATCCA
1 TAAAAAACTCTAAA-CCA
54697325 TAAAAAAACT-TAAAACC-
1 T-AAAAAACTCT-AAACCA
54697342 TAAAAAA
1 TAAAAAA
54697349 TATAAATCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 6 0.17
17 13 0.37
18 7 0.20
19 9 0.26
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.17
Consensus pattern (17 bp):
TAAAAAACTCTAAACCA
Found at i:54697338 original size:18 final size:17
Alignment explanation
Indices: 54697291--54697348 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
54697281 CCTAATCAGT
54697291 AAAAAACTCTAAACCATA
1 AAAAAACT-TAAACCATA
** *
54697309 AAAAGCCCTAAATCCATA
1 AAAAAACTTAAA-CCATA
54697327 AAAAAACTTAAAACC-TA
1 AAAAAACTT-AAACCATA
54697344 AAAAA
1 AAAAA
54697349 TATAAATCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 11 0.34
18 18 0.56
19 3 0.09
ACGTcount: A:0.62, C:0.21, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAAACTTAAACCATA
Found at i:54697379 original size:14 final size:15
Alignment explanation
Indices: 54697360--54697392 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
54697350 ATAAATCATC
*
54697360 AAAACCTTAAAATA-
1 AAAACCCTAAAATAT
54697374 AAAACCCTAAAATAT
1 AAAACCCTAAAATAT
54697389 AAAA
1 AAAA
54697393 AATATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAACCCTAAAATAT
Found at i:54698377 original size:18 final size:16
Alignment explanation
Indices: 54698346--54698389 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
54698336 TGTTTAGGGT
*
54698346 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
54698363 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
54698377 TTAAAAATTTATT
1 TTAAAAATTTATT
54698390 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:54704823 original size:17 final size:17
Alignment explanation
Indices: 54704803--54704861 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
54704793 CCCTAATCAG
54704803 TAAAAAACTCTAAACCA
1 TAAAAAACTCTAAACCA
* *
54704820 TAAAAAGCCCTAAATCCA
1 TAAAAAACTCTAAA-CCA
54704838 TAAAAAAACT-TAAAACC-
1 T-AAAAAACTCT-AAACCA
54704855 TAAAAAA
1 TAAAAAA
54704862 TATAAATCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 6 0.17
17 13 0.37
18 7 0.20
19 9 0.26
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.17
Consensus pattern (17 bp):
TAAAAAACTCTAAACCA
Found at i:54704851 original size:18 final size:17
Alignment explanation
Indices: 54704804--54704861 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
54704794 CCTAATCAGT
54704804 AAAAAACTCTAAACCATA
1 AAAAAACT-TAAACCATA
** *
54704822 AAAAGCCCTAAATCCATA
1 AAAAAACTTAAA-CCATA
54704840 AAAAAACTTAAAACC-TA
1 AAAAAACTT-AAACCATA
54704857 AAAAA
1 AAAAA
54704862 TATAAATCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 11 0.34
18 18 0.56
19 3 0.09
ACGTcount: A:0.62, C:0.21, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAAACTTAAACCATA
Found at i:54704892 original size:14 final size:15
Alignment explanation
Indices: 54704873--54704905 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
54704863 ATAAATCATC
*
54704873 AAAACCTTAAAATA-
1 AAAACCCTAAAATAT
54704887 AAAACCCTAAAATAT
1 AAAACCCTAAAATAT
54704902 AAAA
1 AAAA
54704906 AATATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAACCCTAAAATAT
Found at i:54705889 original size:18 final size:16
Alignment explanation
Indices: 54705858--54705901 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
54705848 TGTTTAGGGT
*
54705858 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
54705875 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
54705889 TTAAAAATTTATT
1 TTAAAAATTTATT
54705902 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:54713702 original size:24 final size:26
Alignment explanation
Indices: 54713655--54713702 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
54713645 AGTCGAGTGA
54713655 AATGAAATTCGATTCGAGTCAAATCG
1 AATGAAATTCGATTCGAGTCAAATCG
*
54713681 AATGAAATT-G-TTCGAGTTAAAT
1 AATGAAATTCGATTCGAGTCAAAT
54713703 TAAAAGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 1 0.05
26 9 0.43
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (26 bp):
AATGAAATTCGATTCGAGTCAAATCG
Found at i:54749173 original size:108 final size:108
Alignment explanation
Indices: 54748984--54749200 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
54748974 GCAGAGAGAG
54748984 AGAGATGGACTCTCATTGCGAATACTCTCTTTTAACATTACGAGAAACAATAAAGCTGAAACAAT
1 AGAGATGGACTCTCATTGCGAATACTCTCTTTTAACATTACGAGAAACAATAAAGCTGAAACAAT
54749049 GAGCTTCATTCCTGTTTAAGCTAAAGAGTTAAGGAGAAAGTGA
66 GAGCTTCATTCCTGTTTAAGCTAAAGAGTTAAGGAGAAAGTGA
54749092 AGAGATGGACTCTCATTGCGAATACTCTCTTTTAACATTACGAGAAACAATAAAGCTGAAACAAT
1 AGAGATGGACTCTCATTGCGAATACTCTCTTTTAACATTACGAGAAACAATAAAGCTGAAACAAT
54749157 GAGCTTCATTCCTGTTTAAGCTAAAGAGTTAAGGAGAAAGTGA
66 GAGCTTCATTCCTGTTTAAGCTAAAGAGTTAAGGAGAAAGTGA
54749200 A
1 A
54749201 ACACAAAGCA
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (108 bp):
AGAGATGGACTCTCATTGCGAATACTCTCTTTTAACATTACGAGAAACAATAAAGCTGAAACAAT
GAGCTTCATTCCTGTTTAAGCTAAAGAGTTAAGGAGAAAGTGA
Found at i:54765508 original size:3 final size:3
Alignment explanation
Indices: 54765500--54765547 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
54765490 ATGGAAACAC
* *
54765500 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
54765548 TCATAAAGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:54766807 original size:17 final size:17
Alignment explanation
Indices: 54766785--54766840 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
54766775 AATATTGCAA
54766785 TTTTATTTTAATAATAT
1 TTTTATTTTAATAATAT
**
54766802 TTTTATAATAATAAT-T
1 TTTTATTTTAATAATAT
* **
54766818 GTAAATTTTAAATAATAT
1 TTTTATTTT-AATAATAT
54766836 TTTTA
1 TTTTA
54766841 ATATATTATT
Statistics
Matches: 27, Mismatches: 10, Indels: 3
0.68 0.25 0.08
Matches are distributed among these distances:
16 5 0.19
17 19 0.70
18 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTTATTTTAATAATAT
Found at i:54770787 original size:86 final size:85
Alignment explanation
Indices: 54770631--54770788 Score: 210
Period size: 86 Copynumber: 1.8 Consensus size: 85
54770621 ATCGTGTTTG
* * *
54770631 TATTAAGCAAATATTTGAAAAAAAAAAGATTTACAACATGCATAATGCATTAATAATTATGCATG
1 TATTAAGCAAATATTTGAAAAAAAAAAGATTTACAACATACATAATGCACTAATAATGATGCATG
*
54770696 TATCTTATAGTAAACATTGA
66 CATCTTATAGTAAACATTGA
* * * * *
54770716 TATTAAGTAAATATTTGAAAAAAAAAA-AGTTTCGCAACATACGTAATGCACTGATAATGATGTA
1 TATTAAGCAAATATTTGAAAAAAAAAAGA-TTT-ACAACATACATAATGCACTAATAATGATGCA
54770780 TGCATCTTA
64 TGCATCTTA
54770789 CATTAAACTT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 1 0.02
85 29 0.47
86 32 0.52
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (85 bp):
TATTAAGCAAATATTTGAAAAAAAAAAGATTTACAACATACATAATGCACTAATAATGATGCATG
CATCTTATAGTAAACATTGA
Found at i:54775958 original size:14 final size:15
Alignment explanation
Indices: 54775941--54775973 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
54775931 TTGACTATAA
54775941 AAATTTA-ATAAGTC
1 AAATTTATATAAGTC
*
54775955 AAATTTATATAATTC
1 AAATTTATATAAGTC
54775970 AAAT
1 AAAT
54775974 CCGAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATTTATATAAGTC
Found at i:54777902 original size:35 final size:35
Alignment explanation
Indices: 54777863--54777933 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
54777853 TAAATTCTAG
54777863 AGAAAATAAGAATATAAAAAA-TTAGTTAAAATTTT
1 AGAAAATAA-AATATAAAAAATTTAGTTAAAATTTT
* *
54777898 AGAAAATAAAATCTAAAAAATTTTAGTTAAACTTTT
1 AGAAAATAAAATATAAAAAA-TTTAGTTAAAATTTT
54777934 TCAAAATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 10 0.31
35 9 0.28
36 13 0.41
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (35 bp):
AGAAAATAAAATATAAAAAATTTAGTTAAAATTTT
Found at i:54783165 original size:22 final size:22
Alignment explanation
Indices: 54783122--54783163 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
54783112 GTGAACGGGA
54783122 AAAAAAATAACAGAAAATAAAG
1 AAAAAAATAACAGAAAATAAAG
*
54783144 AAAAAAAT-ACAGAAATTAAA
1 AAAAAAATAACAGAAAATAAA
54783164 AGTTAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAAAAATAACAGAAAATAAAG
Found at i:54787115 original size:35 final size:37
Alignment explanation
Indices: 54787076--54787166 Score: 96
Period size: 39 Copynumber: 2.4 Consensus size: 37
54787066 ATAAAAATAA
* * *
54787076 TAAATAT-TTTAATTATATTTTT-GCATAATTATTAT
1 TAAATATATTTAATAACATTTTTAACATAATTATTAT
*
54787111 TAAATATAATTTAATAACATTTTTAATATAATTATTAT
1 TAAATAT-ATTTAATAACATTTTTAACATAATTATTAT
*
54787149 TAAAATATGAATTAATAA
1 T-AAATAT-ATTTAATAA
54787167 AAATCATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 7 0.15
37 13 0.28
38 12 0.26
39 14 0.30
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (37 bp):
TAAATATATTTAATAACATTTTTAACATAATTATTAT
Found at i:54787177 original size:39 final size:38
Alignment explanation
Indices: 54787100--54787179 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 38
54787090 ATATTTTTGC
* * **
54787100 ATAATTATTATTAAATATAATTTAATAACATTTTTAAT
1 ATAATTATTATTAAATATAATTTAATAAAAATCATAAT
54787138 ATAATTATTATTAAAATATGAA-TTAATAAAAATCATAAT
1 ATAATTATTATT-AAATAT-AATTTAATAAAAATCATAAT
54787177 ATA
1 ATA
54787180 TAATATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 12 0.33
39 22 0.61
40 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (38 bp):
ATAATTATTATTAAATATAATTTAATAAAAATCATAAT
Found at i:54793633 original size:20 final size:21
Alignment explanation
Indices: 54793608--54793651 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
54793598 AAATAAAATG
* *
54793608 AGTTTTTC-CGTAAAAATTCA
1 AGTTTTTCTCATAAAAACTCA
54793628 AGTTTTTCTCATAAAAACTCA
1 AGTTTTTCTCATAAAAACTCA
54793649 AGT
1 AGT
54793652 AATTTTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (21 bp):
AGTTTTTCTCATAAAAACTCA
Found at i:54793663 original size:21 final size:22
Alignment explanation
Indices: 54793638--54793694 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
54793628 AGTTTTTCTC
54793638 ATAAAAACTCAAGTAATT-TTT
1 ATAAAAACTCAAGTAATTCTTT
* * * *
54793659 GTAAAATCCCAAGCAATTCTTT
1 ATAAAAACTCAAGTAATTCTTT
*
54793681 ATAAAACCTCAAGT
1 ATAAAAACTCAAGT
54793695 TTTTTTAAGA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.32
Consensus pattern (22 bp):
ATAAAAACTCAAGTAATTCTTT
Found at i:54796072 original size:22 final size:22
Alignment explanation
Indices: 54796044--54796088 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
54796034 TAAAATCGAA
54796044 CTTGTGATGAATTCTTTCGCTT
1 CTTGTGATGAATTCTTTCGCTT
54796066 CTTGTGATGAATTCTTTCGCTT
1 CTTGTGATGAATTCTTTCGCTT
54796088 C
1 C
54796089 AACTCACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.49
Consensus pattern (22 bp):
CTTGTGATGAATTCTTTCGCTT
Found at i:54800175 original size:33 final size:33
Alignment explanation
Indices: 54800135--54800202 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
54800125 GTTTCCTAGG
54800135 AAAATATAAAAAAGCAAAGGAATTCTACAGAGA
1 AAAATATAAAAAAGCAAAGGAATTCTACAGAGA
54800168 AAAATATAAAAAAGCAAAGGAATTCTACAGAGA
1 AAAATATAAAAAAGCAAAGGAATTCTACAGAGA
54800201 AA
1 AA
54800203 GGAACACCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.62, C:0.09, G:0.15, T:0.15
Consensus pattern (33 bp):
AAAATATAAAAAAGCAAAGGAATTCTACAGAGA
Found at i:54801816 original size:29 final size:30
Alignment explanation
Indices: 54801760--54801817 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
54801750 ATTTAACAAT
* *
54801760 TTTATATTTTTAAATATTTTTAGTAATTTA
1 TTTATATTTTTAAATATTTATAGAAATTTA
54801790 TTTAT-TTTTTAACATATTTATA-AAATTT
1 TTTATATTTTTAA-ATATTTATAGAAATTT
54801818 TGGGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTATATTTTTAAATATTTATAGAAATTTA
Found at i:54803317 original size:28 final size:30
Alignment explanation
Indices: 54803277--54803340 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
54803267 TTAGTATTAT
54803277 TAAAA-TTATTTTTAAA-AAATATAAAATA
1 TAAAATTTATTTTTAAATAAATATAAAATA
** *
54803305 TAAAATTTA-TTTTAAATTTATTTAAAATA
1 TAAAATTTATTTTTAAATAAATATAAAATA
54803334 TAAAATT
1 TAAAATT
54803341 ATTAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAAAATTTATTTTTAAATAAATATAAAATA
Found at i:54803428 original size:13 final size:13
Alignment explanation
Indices: 54803394--54803438 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
54803384 TCTGTTACCC
*
54803394 TTCCCCTTCCCC-
1 TTCCCTTTCCCCT
54803406 TTCCCTTTCCCCT
1 TTCCCTTTCCCCT
*
54803419 TTCTCTTTCCCCT
1 TTCCCTTTCCCCT
*
54803432 TTTCCTT
1 TTCCCTT
54803439 CTGTTTAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (13 bp):
TTCCCTTTCCCCT
Found at i:54804073 original size:13 final size:13
Alignment explanation
Indices: 54804039--54804075 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
54804029 AGTCATCAAG
54804039 GAAGGGAAAGGGGA
1 GAAGGG-AAGGGGA
54804053 -AAGGGAAGGGGA
1 GAAGGGAAGGGGA
54804065 GAAGGGAAGGG
1 GAAGGGAAGGG
54804076 TACTAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (13 bp):
GAAGGGAAGGGGA
Found at i:54804136 original size:16 final size:16
Alignment explanation
Indices: 54804115--54804175 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
54804105 GAATGATAAT
54804115 TATTTTAATTATTTTA
1 TATTTTAATTATTTTA
*
54804131 TATTTTAATTTAATTTAAAA
1 TATTTTAA-TT-ATTT--TA
*
54804151 TAATTTTAATAATTTTA
1 T-ATTTTAATTATTTTA
54804168 TATTTTAA
1 TATTTTAA
54804176 AAAAATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 15 0.41
17 4 0.11
18 4 0.11
19 4 0.11
20 3 0.08
21 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTAATTATTTTA
Found at i:54804184 original size:21 final size:22
Alignment explanation
Indices: 54804158--54804199 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
54804148 AAATAATTTT
*
54804158 AATAATTTT-ATATTTTAAAAA
1 AATAATTTTAATAATTTAAAAA
54804179 AATAATTTTAATAATTTAAAA
1 AATAATTTTAATAATTTAAAA
54804200 TCATTTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTAATAATTTAAAAA
Found at i:54804193 original size:9 final size:9
Alignment explanation
Indices: 54804111--54804195 Score: 51
Period size: 9 Copynumber: 10.0 Consensus size: 9
54804101 CTTAGAATGA
*
54804111 TAATTATTT
1 TAATAATTT
*
54804120 TAATTATTT
1 TAATAATTT
54804129 T-AT-ATTT
1 TAATAATTT
54804136 TAATTTAATTT
1 TAA--TAATTT
*
54804147 AAAATAATTT
1 -TAATAATTT
54804157 TAATAATTT
1 TAATAATTT
54804166 T-AT-ATTT
1 TAATAATTT
54804173 TAA-AA---
1 TAATAATTT
*
54804178 AAATAATTT
1 TAATAATTT
54804187 TAATAATTT
1 TAATAATTT
54804196 AAAATCATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 10 0.16
8 7 0.11
9 27 0.44
10 7 0.11
11 4 0.07
12 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAATAATTT
Found at i:54804389 original size:31 final size:31
Alignment explanation
Indices: 54804351--54804409 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
54804341 CTAATTTGAC
*
54804351 CAAAAAAAACAAAAG-TTAGGGCCAAAGTGAG
1 CAAAAAAAA-AAAAGATAAGGGCCAAAGTGAG
*
54804382 CAAAAAAAAAAACGATAAGGGCCAAAGT
1 CAAAAAAAAAAAAGATAAGGGCCAAAGT
54804410 AACCAAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.58, C:0.14, G:0.20, T:0.08
Consensus pattern (31 bp):
CAAAAAAAAAAAAGATAAGGGCCAAAGTGAG
Found at i:54807278 original size:68 final size:70
Alignment explanation
Indices: 54807174--54807305 Score: 196
Period size: 68 Copynumber: 1.9 Consensus size: 70
54807164 GCTTGTTGAG
* *
54807174 AAGGTAGCAACAACTCAACTCTATGAGACTCCCAAACAAAC-T-ATAAGCTGAAGGAGGAGTTCT
1 AAGGTAGCAACAACTCAACCCTATAAGACTCCCAAACAAACTTGATAAGCTGAAGGAGGAGTTCT
54807237 AAGGT
66 AAGGT
* * *
54807242 AAGGTAGCAGCAACTCACCCCTATAAGACTCCCAAACAAGCTTGGATAAGCTGAAGGAGGAGTT
1 AAGGTAGCAACAACTCAACCCTATAAGACTCCCAAACAAACTT-GATAAGCTGAAGGAGGAGTT
54807306 GATGGAGCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
68 36 0.64
69 1 0.02
71 19 0.34
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (70 bp):
AAGGTAGCAACAACTCAACCCTATAAGACTCCCAAACAAACTTGATAAGCTGAAGGAGGAGTTCT
AAGGT
Found at i:54820672 original size:3 final size:3
Alignment explanation
Indices: 54820664--54820688 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54820654 ACAAAACAGG
54820664 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
54820689 CATACAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:54826453 original size:18 final size:19
Alignment explanation
Indices: 54826414--54826454 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54826404 TCATGTCAAT
*
54826414 AAATAATTTAAAATTTATA
1 AAATAATTTAAAATTTAAA
*
54826433 AAATATTTTAAAA-TTAAA
1 AAATAATTTAAAATTTAAA
54826451 AAAT
1 AAAT
54826455 TAATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATAATTTAAAATTTAAA
Found at i:54826496 original size:18 final size:18
Alignment explanation
Indices: 54826414--54826496 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
54826404 TCATGTCAAT
*
54826414 AAATAATTTAAAATTTATA
1 AAATAATATAAAATTTA-A
* * *
54826433 AAATATTTTAAAATTAAA
1 AAATAATATAAAATTTAA
* * *
54826451 AAATTA-ATAATATATAA
1 AAATAATATAAAATTTAA
*
54826468 AAAGTTA-ATAAAATTTAA
1 AAA-TAATATAAAATTTAA
54826486 AAATAATATAA
1 AAATAATATAA
54826497 GTATACGTGG
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
17 12 0.24
18 24 0.47
19 15 0.29
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (18 bp):
AAATAATATAAAATTTAA
Found at i:54840018 original size:4 final size:4
Alignment explanation
Indices: 54840003--54840041 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
54839993 GTGTAAGTGC
54840003 TAAA TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
54840042 ACATGTGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:54842139 original size:29 final size:29
Alignment explanation
Indices: 54842104--54842174 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
54842094 TTAAAATTTT
*
54842104 TAATAAAATTATACTTTAATCTTTAAAAA
1 TAATAAAATTATAATTTAATCTTTAAAAA
*
54842133 TAATAAAAATT-TAATTTAATCTTTAAAAT
1 TAAT-AAAATTATAATTTAATCTTTAAAAA
*
54842162 TTATAAAATTATA
1 TAATAAAATTATA
54842175 GACCATTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 6 0.16
29 25 0.68
30 6 0.16
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATAAAATTATAATTTAATCTTTAAAAA
Found at i:54848560 original size:47 final size:47
Alignment explanation
Indices: 54848491--54848580 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
54848481 CTTTGCAGAC
* * *
54848491 TCATCCTAACATTACTATTATTGGAGAAGAGGTATTTTATAAATCAT
1 TCATCCTAACATCACTATTATTGGAGAAGAGATATTCTATAAATCAT
* *
54848538 TCATCCTAGCATCACTCTTATTGGAGAAGAGATATTCTATAAA
1 TCATCCTAACATCACTATTATTGGAGAAGAGATATTCTATAAA
54848581 CCATCCTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (47 bp):
TCATCCTAACATCACTATTATTGGAGAAGAGATATTCTATAAATCAT
Found at i:54855407 original size:51 final size:52
Alignment explanation
Indices: 54855331--54855435 Score: 158
Period size: 51 Copynumber: 2.0 Consensus size: 52
54855321 TTTTAACGTC
* *
54855331 TATTTTGGTAAGTGTTTTACTATGTGGTTTATCTTGAACTTCTTTTC-CGGT
1 TATTTTGGTAAGTGTTTTACTATGTGATTTATCTTGAACTTCTTCTCTCGGT
* * *
54855382 TATTTTGGTAATTGTTTTATTATGTGATTTATCTTGAATTTCTTCTCTCGGT
1 TATTTTGGTAAGTGTTTTACTATGTGATTTATCTTGAACTTCTTCTCTCGGT
54855434 TA
1 TA
54855436 AAAGTAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 42 0.88
52 6 0.12
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.55
Consensus pattern (52 bp):
TATTTTGGTAAGTGTTTTACTATGTGATTTATCTTGAACTTCTTCTCTCGGT
Found at i:54856127 original size:132 final size:132
Alignment explanation
Indices: 54855951--54856218 Score: 509
Period size: 132 Copynumber: 2.0 Consensus size: 132
54855941 TGTTTATTGA
*
54855951 GTTACACTTGAATATCAATCTTTGAAATTAATTCCTTCCTGACTCCTATGTATATTTCAAAAAAA
1 GTTACACTTGAATATCAATCTTTGAAATTAATTCCTTCCTGACTCCTATGTATATTCCAAAAAAA
*
54856016 AAATCTTGAATCCTCGAATTTCAACATTATAAATTTAATTGTCAACGTGTTATAATATTCTATTA
66 AAATATTGAATCCTCGAATTTCAACATTATAAATTTAATTGTCAACGTGTTATAATATTCTATTA
54856081 AT
131 AT
54856083 GTTACACTTGAATATCAATCTTTGAAATTAATTCCTTCCTGACTCCTATGTATATTCCAAAAAAA
1 GTTACACTTGAATATCAATCTTTGAAATTAATTCCTTCCTGACTCCTATGTATATTCCAAAAAAA
*
54856148 AAATATTGAATCCTCGAATTTCAACATTATAAATTTAATTGTCAACGTGTTATAATATTCTATTG
66 AAATATTGAATCCTCGAATTTCAACATTATAAATTTAATTGTCAACGTGTTATAATATTCTATTA
54856213 AT
131 AT
54856215 GTTA
1 GTTA
54856219 AGGTTAAAGT
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (132 bp):
GTTACACTTGAATATCAATCTTTGAAATTAATTCCTTCCTGACTCCTATGTATATTCCAAAAAAA
AAATATTGAATCCTCGAATTTCAACATTATAAATTTAATTGTCAACGTGTTATAATATTCTATTA
AT
Found at i:54860561 original size:30 final size:30
Alignment explanation
Indices: 54860503--54860595 Score: 89
Period size: 30 Copynumber: 3.0 Consensus size: 30
54860493 TCCTTTTAAT
* *
54860503 AAAAAGACTCACACTTTTCTCAA-AAAAAAA
1 AAAAAGACTCACACTTTAC-CAATTAAAAAA
54860533 AAAAAGACTCACACTTTACCAATTAAAAAATA
1 AAAAAGACTCACACTTTACCAATT-AAAAA-A
* * * *
54860565 AAAATAAAATCACATTTTACTAATTAAAAAA
1 AAAA-AGACTCACACTTTACCAATTAAAAAA
54860596 GTAAATAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
29 3 0.06
30 18 0.34
31 6 0.11
32 10 0.19
33 16 0.30
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.24
Consensus pattern (30 bp):
AAAAAGACTCACACTTTACCAATTAAAAAA
Found at i:54860568 original size:33 final size:33
Alignment explanation
Indices: 54860503--54860606 Score: 101
Period size: 33 Copynumber: 3.2 Consensus size: 33
54860493 TCCTTTTAAT
*
54860503 AAAAAGACTCACACTTTTCTC-A--AAAAAA-AA
1 AAAAAGACTCACACTTTAC-CAATTAAAAAATAA
54860533 AAAAAGACTCACACTTTACCAATTAAAAAATAA
1 AAAAAGACTCACACTTTACCAATTAAAAAATAA
* * *
54860566 AAATAA-AATCACATTTTACTAATTAAAAAAGTAA
1 AAA-AAGACTCACACTTTACCAATTAAAAAA-TAA
*
54860600 ATAAAGA
1 AAAAAGA
54860607 TTATAGTAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
29 1 0.02
30 19 0.31
32 6 0.10
33 28 0.45
34 8 0.13
ACGTcount: A:0.59, C:0.14, G:0.04, T:0.23
Consensus pattern (33 bp):
AAAAAGACTCACACTTTACCAATTAAAAAATAA
Found at i:54860742 original size:14 final size:16
Alignment explanation
Indices: 54860723--54860756 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
54860713 GCATAATCGT
54860723 ATATATT-AAT-TAAA
1 ATATATTAAATATAAA
54860737 ATATATTAAATATAAA
1 ATATATTAAATATAAA
54860753 ATAT
1 ATAT
54860757 GAGTATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 3 0.17
16 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATTAAATATAAA
Found at i:54860806 original size:8 final size:8
Alignment explanation
Indices: 54860795--54860823 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
54860785 TTTATTATTT
54860795 TATATTAA
1 TATATTAA
54860803 TATATTAA
1 TATATTAA
54860811 TATATTAA
1 TATATTAA
54860819 -ATATT
1 TATATT
54860824 TTTTTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TATATTAA
Found at i:54860923 original size:14 final size:15
Alignment explanation
Indices: 54860903--54860936 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
54860893 CATGTATCTT
*
54860903 TAAATTAAATTTAAA
1 TAAATTAAAATTAAA
54860918 -AAATTAAAATTAAA
1 TAAATTAAAATTAAA
54860932 TAAAT
1 TAAAT
54860937 AAGACACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATTAAAATTAAA
Found at i:54861344 original size:18 final size:18
Alignment explanation
Indices: 54861323--54861371 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
54861313 AAAAAGAATC
*
54861323 AAAATATTTTTAAAATTA
1 AAAATATTTATAAAATTA
*
54861341 AAAATATTTATAAAATTTT
1 AAAATATTTATAAAA-TTA
*
54861360 AAAATTTTTATA
1 AAAATATTTATA
54861372 TTATAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATATTTATAAAATTA
Found at i:54861369 original size:19 final size:18
Alignment explanation
Indices: 54861323--54861371 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
54861313 AAAAAGAATC
54861323 AAAATATTTT-TAAAATTA
1 AAAAT-TTTTATAAAATTA
* *
54861341 AAAATATTTATAAAATTTT
1 AAAATTTTTATAAAA-TTA
54861360 AAAATTTTTATA
1 AAAATTTTTATA
54861372 TTATAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 10 0.38
19 13 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATTTTTATAAAATTA
Found at i:54871388 original size:20 final size:21
Alignment explanation
Indices: 54871327--54871388 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
54871317 AATGATTATA
* *
54871327 TTTAAATATTTAAAATATAA-
1 TTTAAATAATTAATATATAAT
* *
54871347 TTTATATAATCTAAT-TAAAAT
1 TTTAAATAAT-TAATATATAAT
54871368 TTTAAATAATTAATAT-TAAT
1 TTTAAATAATTAATATATAAT
54871388 T
1 T
54871389 ACTTAGAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
20 20 0.61
21 13 0.39
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAAATAATTAATATATAAT
Found at i:54871410 original size:30 final size:30
Alignment explanation
Indices: 54871330--54871431 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
54871320 GATTATATTT
54871330 AAATATTTAAAATATAATTTATATAATCTAATTA
1 AAATATTTAAAAT-TAA--TAT-TAATCTAATTA
*
54871364 AAAT-TTTAAATAATTAATATTAAT-TACTTA
1 AAATATTT-AA-AATTAATATTAATCTAATTA
54871394 GAAATATTTAAAATTAATATT--TCATATATTA
1 -AAATATTTAAAATTAATATTAATC-TA-ATTA
54871425 AAATATT
1 AAATATT
54871432 AACAGTAAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
28 1 0.02
30 24 0.41
31 13 0.22
32 6 0.10
33 3 0.05
34 9 0.15
35 3 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (30 bp):
AAATATTTAAAATTAATATTAATCTAATTA
Found at i:54878085 original size:20 final size:21
Alignment explanation
Indices: 54878062--54878108 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
54878052 AAAAATAAAA
*
54878062 TAAAATTCAATA-AAAATTAT
1 TAAAATTCAATAGAAAAGTAT
* *
54878082 TAAATTTTAATAGAAAAGTAT
1 TAAAATTCAATAGAAAAGTAT
*
54878103 AAAAAT
1 TAAAAT
54878109 ATTTAAAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (21 bp):
TAAAATTCAATAGAAAAGTAT
Found at i:54878127 original size:30 final size:30
Alignment explanation
Indices: 54878071--54878127 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
54878061 ATAAAATTCA
** *
54878071 ATAAAAATTATTAAATTTTAATAGAAAAGT
1 ATAAAAATTATTAAAAATTAAAAGAAAAGT
54878101 ATAAAAA-TATTTAAAAATTAAAAGAAA
1 ATAAAAATTA-TTAAAAATTAAAAGAAA
54878128 TCATAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (30 bp):
ATAAAAATTATTAAAAATTAAAAGAAAAGT
Found at i:54878495 original size:20 final size:20
Alignment explanation
Indices: 54878464--54878523 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
54878454 TTTTATAAAA
54878464 AAATATTTTTTAATAAATTTT
1 AAATA-TTTTTAATAAATTTT
* *
54878485 AAATATTTTTACTAAAATTT
1 AAATATTTTTAATAAATTTT
*
54878505 -AGTAATTTTT-ATAAATTTT
1 AAAT-ATTTTTAATAAATTTT
54878524 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 9 0.27
20 19 0.58
21 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
AAATATTTTTAATAAATTTT
Done.