Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 133 of 199
Found at i:40220488 original size:19 final size:19
Alignment explanation
Indices: 40220456--40220492 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
40220446 TTTTTAATAT
40220456 TTTCCCTCCAAACTATTTAC
1 TTTCCCTCCAAACT-TTTAC
40220476 TTTCCCT-CAAACTTTTA
1 TTTCCCTCCAAACTTTTA
40220493 TTCTCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTCCCTCCAAACTTTTAC
Found at i:40224078 original size:19 final size:19
Alignment explanation
Indices: 40224056--40224093 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40224046 TCATTATCAC
40224056 CCACTGTAATCAAATTTGT
1 CCACTGTAATCAAATTTGT
40224075 CCACTGTAATCAAATTTGT
1 CCACTGTAATCAAATTTGT
40224094 TATTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (19 bp):
CCACTGTAATCAAATTTGT
Found at i:40231339 original size:14 final size:15
Alignment explanation
Indices: 40231320--40231348 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40231310 AATGTTAAAT
40231320 TTTATTATT-TATTA
1 TTTATTATTGTATTA
40231334 TTTATTATTGTATTA
1 TTTATTATTGTATTA
40231349 ATACTATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTATTATTGTATTA
Found at i:40232130 original size:49 final size:50
Alignment explanation
Indices: 40232076--40232277 Score: 252
Period size: 49 Copynumber: 4.1 Consensus size: 50
40232066 GTGGAAGCAG
* *
40232076 TGGCAGTATATCTCCAAATCAGAT-GTGGCTTGTCTA-AACAATTTATCAG
1 TGGCAGTATATCTGCAAATCAGATGGTGGCTTGTCTACAA-AATTTATCAA
*
40232125 TGGCAGTATATCTGTAAATCA-ATGGTGGCTTGTCTACAAAATTTATCAA
1 TGGCAGTATATCTGCAAATCAGATGGTGGCTTGTCTACAAAATTTATCAA
* * * *
40232174 TGGTAATATATCTGCAAATCAG-TGGTGCCTTGTCCACAAAATTTATCAA
1 TGGCAGTATATCTGCAAATCAGATGGTGGCTTGTCTACAAAATTTATCAA
* * *
40232223 TGGCAGTATATCTGCATATCAG-TGGTGTCTTGTCCACAAAAGTGTTATCAA
1 TGGCAGTATATCTGCAAATCAGATGGTGGCTTGTCTACAAAA-T-TTATCAA
40232274 TGGC
1 TGGC
40232278 GTCTTGTCCA
Statistics
Matches: 136, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
48 2 0.01
49 120 0.88
50 3 0.02
51 11 0.08
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TGGCAGTATATCTGCAAATCAGATGGTGGCTTGTCTACAAAATTTATCAA
Found at i:40232281 original size:29 final size:29
Alignment explanation
Indices: 40232239--40232306 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
40232229 TATATCTGCA
* *
40232239 TATCAGTGGTGTCTTGTCCACAAAAGTGT
1 TATCAATGGCGTCTTGTCCACAAAAGTGT
40232268 TATCAATGGCGTCTTGTCCACAAAAGTGT
1 TATCAATGGCGTCTTGTCCACAAAAGTGT
40232297 TATCAATGGC
1 TATCAATGGC
40232307 AGTATCAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (29 bp):
TATCAATGGCGTCTTGTCCACAAAAGTGT
Found at i:40234326 original size:22 final size:23
Alignment explanation
Indices: 40234284--40234326 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
40234274 AGAGATAACT
40234284 TGTAATCTTAGAAGATATGATAA
1 TGTAATCTTAGAAGATATGATAA
*
40234307 TGTAATCTTAG-AGATTTGAT
1 TGTAATCTTAGAAGATATGAT
40234327 TTGTAGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATGATAA
Found at i:40245446 original size:23 final size:23
Alignment explanation
Indices: 40245415--40245465 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
40245405 ACCTACTTTC
*
40245415 TTACTGTAGTAATTTTCAGGG-TA
1 TTACAGTAGTAATTTTC-GGGATA
40245438 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
40245461 TTACA
1 TTACA
40245466 CTTAGAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:40246473 original size:18 final size:17
Alignment explanation
Indices: 40246450--40246483 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40246440 CAAGAACAGT
40246450 AAGCATCAAAATAGTTTC
1 AAGCAT-AAAATAGTTTC
*
40246468 AAGCATGAAATAGTTT
1 AAGCATAAAATAGTTT
40246484 AGCCCATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (17 bp):
AAGCATAAAATAGTTTC
Found at i:40248264 original size:10 final size:10
Alignment explanation
Indices: 40248234--40248266 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
40248224 GCCCAATACC
40248234 TTAAACCCAAA
1 TTAAACCC-AA
40248245 TT-AACCCAA
1 TTAAACCCAA
40248254 TTAAACCCAA
1 TTAAACCCAA
40248264 TTA
1 TTA
40248267 TAATGGCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.19
10 15 0.71
11 2 0.10
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (10 bp):
TTAAACCCAA
Found at i:40249255 original size:4 final size:4
Alignment explanation
Indices: 40249239--40249271 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
40249229 GTCTATTGTG
*
40249239 TATT TACT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
40249272 CTTTTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:40251064 original size:22 final size:22
Alignment explanation
Indices: 40251039--40251095 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
40251029 ATTAGTAAGT
40251039 ACCGAAGTGCAAAGCAATAGGC
1 ACCGAAGTGCAAAGCAATAGGC
* *
40251061 ACCGAAGTGCAGAGCAGTAGGC
1 ACCGAAGTGCAAAGCAATAGGC
* *
40251083 ACTGTAGTGCAAA
1 ACCGAAGTGCAAA
40251096 TTATGTACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.21, G:0.30, T:0.12
Consensus pattern (22 bp):
ACCGAAGTGCAAAGCAATAGGC
Found at i:40251510 original size:26 final size:27
Alignment explanation
Indices: 40251475--40251525 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
40251465 TATATGACAA
40251475 CTAAATTTTA-ATTTT-TACAATTTCC
1 CTAAATTTTACATTTTATACAATTTCC
*
40251500 CTAAAGTTTTACATTTTATTCAATTT
1 CTAAA-TTTTACATTTTATACAATTT
40251526 AGTCCCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 5 0.23
27 5 0.23
28 7 0.32
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.53
Consensus pattern (27 bp):
CTAAATTTTACATTTTATACAATTTCC
Found at i:40254126 original size:21 final size:22
Alignment explanation
Indices: 40254096--40254140 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
40254086 ATATTTTTAA
40254096 TATTGTAAAATTACTTAATTAT
1 TATTGTAAAATTACTTAATTAT
* *
40254118 TATT-TAAAATTATTTTATTAT
1 TATTGTAAAATTACTTAATTAT
40254139 TA
1 TA
40254141 ATATTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTGTAAAATTACTTAATTAT
Found at i:40254137 original size:18 final size:20
Alignment explanation
Indices: 40254090--40254139 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
40254080 AGATATATAT
*
40254090 TTTTAATATTGTAAAATTAC
1 TTTTATTATTGTAAAATTAC
40254110 TTAATTATTATT-TAAAATTA-
1 TT--TTATTATTGTAAAATTAC
40254130 TTTTATTATT
1 TTTTATTATT
40254140 AATATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.30
20 4 0.15
21 8 0.30
22 7 0.26
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTATTATTGTAAAATTAC
Found at i:40270097 original size:24 final size:24
Alignment explanation
Indices: 40270070--40270118 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
40270060 GCTGTTTATT
40270070 TGTAGTTATCTCCTGAACAACCTG
1 TGTAGTTATCTCCTGAACAACCTG
40270094 TGTAGTTATCTCCTGAACAACCTG
1 TGTAGTTATCTCCTGAACAACCTG
40270118 T
1 T
40270119 TTAAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (24 bp):
TGTAGTTATCTCCTGAACAACCTG
Found at i:40280464 original size:2 final size:2
Alignment explanation
Indices: 40280457--40280486 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40280447 TGCATAGTGA
40280457 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40280487 GAAAACCAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40286888 original size:42 final size:43
Alignment explanation
Indices: 40286827--40286941 Score: 135
Period size: 42 Copynumber: 2.7 Consensus size: 43
40286817 GATTTCAGAT
* *
40286827 TTACGTGTAAGGCCATGTCTGGGACATTGGCATCG-TATATGA
1 TTACGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGA
* * * *
40286869 TTATGTGTAAGACCCTGTCTGGGACAGTGACATCGTTATTTGA
1 TTACGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGA
* *
40286912 TTACATGTAAGACCAC-GTCTGGGACGTTGG
1 TTACGTGTAAGACC-CTGTCTGGGACATTGG
40286942 TATTTTACGA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 30 0.50
43 29 0.48
44 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (43 bp):
TTACGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGA
Found at i:40288877 original size:20 final size:21
Alignment explanation
Indices: 40288852--40288891 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40288842 CTTGTCAAAA
40288852 CCAATTC-ATTTCCAAATACT
1 CCAATTCAATTTCCAAATACT
*
40288872 CCAATTCAATTTCCACATAC
1 CCAATTCAATTTCCAAATAC
40288892 ACATCTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (21 bp):
CCAATTCAATTTCCAAATACT
Found at i:40289532 original size:30 final size:30
Alignment explanation
Indices: 40289491--40289639 Score: 199
Period size: 30 Copynumber: 5.0 Consensus size: 30
40289481 GTATTTTTAT
* *
40289491 AATTGCCCACACAAGTTGGCATTATAATTG
1 AATTGCTCACACAAGTTGACATTATAATTG
** *
40289521 AATTGCTCACACAAGCCGACATTATAATCG
1 AATTGCTCACACAAGTTGACATTATAATTG
* * * *
40289551 GATTGCTTAAACAAGCTGACATTATAATTG
1 AATTGCTCACACAAGTTGACATTATAATTG
*
40289581 AATTGCTCACATAAGTTGACATTATAATTG
1 AATTGCTCACACAAGTTGACATTATAATTG
*
40289611 AATTGTTCACACAAGTTGACATTATAATT
1 AATTGCTCACACAAGTTGACATTATAATT
40289640 ATGGTTCCCG
Statistics
Matches: 102, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 102 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (30 bp):
AATTGCTCACACAAGTTGACATTATAATTG
Found at i:40290048 original size:9 final size:9
Alignment explanation
Indices: 40290036--40290139 Score: 129
Period size: 9 Copynumber: 11.4 Consensus size: 9
40290026 AAATAAAAAA
*
40290036 AATTCAGGT
1 AATTCGGGT
40290045 AATTCGGGT
1 AATTCGGGT
* *
40290054 ATTTTTC-GAT
1 A--ATTCGGGT
*
40290064 AATTCGGTT
1 AATTCGGGT
*
40290073 AATTCGGTT
1 AATTCGGGT
40290082 AATTCGGGT
1 AATTCGGGT
*
40290091 AATTCGGTT
1 AATTCGGGT
40290100 AATTCGGGT
1 AATTCGGGT
40290109 AATTCGGGT
1 AATTCGGGT
40290118 AATTCGGGT
1 AATTCGGGT
40290127 AATTCGGGT
1 AATTCGGGT
40290136 AATT
1 AATT
40290140 TTTAACCAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
8 3 0.04
9 75 0.89
10 3 0.04
11 3 0.04
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (9 bp):
AATTCGGGT
Found at i:40290315 original size:12 final size:12
Alignment explanation
Indices: 40290298--40290323 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40290288 ATAGTAATTT
40290298 CGGTCGGTTAAC
1 CGGTCGGTTAAC
40290310 CGGTCGGTTAAC
1 CGGTCGGTTAAC
40290322 CG
1 CG
40290324 AATGAACACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.27, G:0.35, T:0.23
Consensus pattern (12 bp):
CGGTCGGTTAAC
Found at i:40296889 original size:20 final size:20
Alignment explanation
Indices: 40296839--40296889 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
40296829 CCCTATCAAG
*
40296839 GTATCGATACCCTTCTCAAA
1 GTATCGATACCCTTCACAAA
* * *
40296859 GTATC-AGTACCTTTGACATA
1 GTATCGA-TACCCTTCACAAA
40296879 GTATCGATACC
1 GTATCGATACC
40296890 ATTTCATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (20 bp):
GTATCGATACCCTTCACAAA
Found at i:40298107 original size:4 final size:4
Alignment explanation
Indices: 40298081--40298151 Score: 72
Period size: 4 Copynumber: 17.0 Consensus size: 4
40298071 TTCCTGATTG
* * *
40298081 ATTT ATTA ATTT AATTC ATTT ATTT ATTT TTCTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT -ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT
40298131 ATTT -TCGTT ATTT ATTT ATTT
1 ATTT AT--TT ATTT ATTT ATTT
40298152 TTATCTCATT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
3 1 0.02
4 46 0.82
5 8 0.14
6 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:40298126 original size:25 final size:25
Alignment explanation
Indices: 40298089--40298151 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
40298079 TGATTTATTA
*
40298089 ATTTAATTCATTTATTTATTTTTC-TT
1 ATTT-ATTTATTTATTTA-TTTTCGTT
40298115 ATTTATTTATTTATTTATTTTCGTT
1 ATTTATTTATTTATTTATTTTCGTT
40298140 ATTTATTTATTT
1 ATTTATTTATTT
40298152 TTATCTCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
24 5 0.14
25 26 0.74
26 4 0.11
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (25 bp):
ATTTATTTATTTATTTATTTTCGTT
Found at i:40298141 original size:21 final size:21
Alignment explanation
Indices: 40298098--40298153 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
40298088 AATTTAATTC
*
40298098 ATTTATTTATTTTTCTTATTT
1 ATTTATTTATTTTTCTTAGTT
*
40298119 ATTTATTTATTTATT-TTCGTT
1 ATTTATTTATTT-TTCTTAGTT
40298140 ATTTATTTATTTTT
1 ATTTATTTATTTTT
40298154 ATCTCATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (21 bp):
ATTTATTTATTTTTCTTAGTT
Found at i:40298549 original size:13 final size:13
Alignment explanation
Indices: 40298506--40298554 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
40298496 TATAGATATG
*
40298506 ATTTTCAATTTTT
1 ATTTTCTATTTTT
*
40298519 GTTATT-TATTTTT
1 ATT-TTCTATTTTT
40298532 A-TTTCTATTTTT
1 ATTTTCTATTTTT
40298544 ATTTTCT-TTTT
1 ATTTTCTATTTT
40298555 AGGTCGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
11 2 0.07
12 13 0.43
13 13 0.43
14 2 0.07
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (13 bp):
ATTTTCTATTTTT
Found at i:40302715 original size:2 final size:2
Alignment explanation
Indices: 40302708--40302736 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40302698 TTTAGTAGTT
40302708 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
40302737 TTGTGTGTTT
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:40305286 original size:18 final size:17
Alignment explanation
Indices: 40305253--40305291 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
40305243 TTTTATAAAT
40305253 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
40305271 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
40305288 TGTG
1 TGTG
40305292 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:40305546 original size:23 final size:23
Alignment explanation
Indices: 40305520--40305638 Score: 195
Period size: 23 Copynumber: 5.2 Consensus size: 23
40305510 GTTATTGATA
40305520 AGTGGTAGCTTCGGCTACA-ATTC
1 AGTGGTAGCTTCGGCTACATA-TC
*
40305543 AGTGGTAGCTACGGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
*
40305566 AGTGGTAGCTTCGGCTACATTTC
1 AGTGGTAGCTTCGGCTACATATC
*
40305589 AGTGGTAGCTACGGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
40305612 AGTGGTAGCTTCGGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
40305635 AGTG
1 AGTG
40305639 TGGCACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
23 88 0.99
24 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACATATC
Found at i:40306895 original size:21 final size:21
Alignment explanation
Indices: 40306871--40306912 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40306861 TAATCGATAG
40306871 GTTTATTCTTT-TAATTTATTT
1 GTTTATT-TTTCTAATTTATTT
*
40306892 GTTTATTTTTCTTATTTATTT
1 GTTTATTTTTCTAATTTATTT
40306913 ATTTTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (21 bp):
GTTTATTTTTCTAATTTATTT
Found at i:40306908 original size:17 final size:17
Alignment explanation
Indices: 40306886--40306918 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40306876 TTCTTTTAAT
*
40306886 TTATTTGTTTATTTTTC
1 TTATTTATTTATTTTTC
40306903 TTATTTATTTATTTTT
1 TTATTTATTTATTTTT
40306919 ATCTCATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (17 bp):
TTATTTATTTATTTTTC
Found at i:40307464 original size:31 final size:31
Alignment explanation
Indices: 40307429--40307489 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
40307419 CAAGCTCACA
40307429 AGAGCTTAGCAAGCGTATCAAAAATCATACG
1 AGAGCTTAGCAAGCGTATCAAAAATCATACG
*
40307460 AGAGCTTAGTAAGCGTATCAAAAATCATAC
1 AGAGCTTAGCAAGCGTATCAAAAATCATAC
40307490 CATGCAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (31 bp):
AGAGCTTAGCAAGCGTATCAAAAATCATACG
Found at i:40309958 original size:2 final size:2
Alignment explanation
Indices: 40309951--40310178 Score: 164
Period size: 2 Copynumber: 116.5 Consensus size: 2
40309941 ATTTTCACCT
* * * *
40309951 TC TC TC TC TT TT TC TC TC TC TC TC TC TC CC TC TC -C CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
40309992 CC CC TC AC TC TC TC TC TC TT TC TC CC TC TC TC TC TC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
40310034 TC -C CC TC TC CC CC TC CC TC TC TC TC TC TT TC TGC -C TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC
* * * *
40310075 TT TC TC CC TC TC CC TC TC TC TC TC CC TC TC TC TC TC TC -C ATC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC
* * * * *
40310117 TC TC TC CC TC -C T- TC CC TC TC CC TC TC TC CC TC TC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
40310157 CC TC -C TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
40310179 AGTTTCATCT
Statistics
Matches: 175, Mismatches: 42, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
1 7 0.04
2 166 0.95
3 2 0.01
ACGTcount: A:0.01, C:0.57, G:0.00, T:0.42
Consensus pattern (2 bp):
TC
Found at i:40315543 original size:242 final size:242
Alignment explanation
Indices: 40314868--40315837 Score: 1852
Period size: 242 Copynumber: 4.0 Consensus size: 242
40314858 TCATTTGACC
*
40314868 CAAGAGAACCGACTCGATTCAAATAATTGATGGAGAAGCCTGGGTGGCCCAATGATGCAGATATA
1 CAAGAGAACCGACTCGATTCAAAGAATTGATGGAGAAGCCTGGGTGGCCCAATGATGCAGATATA
40314933 GGAAGTTAGGCTACCTTGGTAAATAGGGAAACTAATTTTAAAAGATTGTGGGGAATCATATCTAA
66 GGAAGTTAGGCTACCTTGGTAAATAGGGAAACTAATTTTAAAAGATTGTGGGGAATCATATCTAA
*
40314998 TAATATTAGATTTAATTTGATTATGTAATCTTGTAAATTCCTTGATTTTAGGGATAGGCTTAATC
131 TAATATTAGATTTAATTTGATTATGTAATCTTGTAAATCCCTTGATTTTAGGGATAGGCTTAATC
40315063 TCATCCGTTGATGTAATTCGATCTATACCGTCAATTTGAAGGGAGCT
196 TCATCCGTTGATGTAATTCGATCTATACCGTCAATTTGAAGGGAGCT
40315110 CAAGAGAA-CGACTCGATTCAAAGAATTGATGGAGAAGCCTGGGTGGCCCAATGATGCAGATATA
1 CAAGAGAACCGACTCGATTCAAAGAATTGATGGAGAAGCCTGGGTGGCCCAATGATGCAGATATA
40315174 GGAAGTTAGGCTACCTTGGTAAATAGGGAAACTAATTTTAAAAGATTGTGGGGAATCATATCTAA
66 GGAAGTTAGGCTACCTTGGTAAATAGGGAAACTAATTTTAAAAGATTGTGGGGAATCATATCTAA
*
40315239 TAATATTAGATTTAATTTGATTATGTAATCTTGTAAATTCCTTGATTTTAGGGATAGGCTTAATC
131 TAATATTAGATTTAATTTGATTATGTAATCTTGTAAATCCCTTGATTTTAGGGATAGGCTTAATC
40315304 TCATCCGTTGATGTAATTCGATCTATACCGTCAATTTGAAGGGAGCT
196 TCATCCGTTGATGTAATTCGATCTATACCGTCAATTTGAAGGGAGCT
40315351 CAAGAGAACCGACTCGATTCAAAGAATTGATGGAGAAGCCTGGGTGGCCCAATGATGCAGATATA
1 CAAGAGAACCGACTCGATTCAAAGAATTGATGGAGAAGCCTGGGTGGCCCAATGATGCAGATATA
40315416 GGAAGTTAGGCTACCTTGGTAAATAGGGAAACTAATTTTAAAAGATTGTGGGGAATCATATCTAA
66 GGAAGTTAGGCTACCTTGGTAAATAGGGAAACTAATTTTAAAAGATTGTGGGGAATCATATCTAA
40315481 TAATATTAGATTTAATTTGATTATGTAATCTTGTAAATCCCTTGATTTTAGGGATAGGCTTAATC
131 TAATATTAGATTTAATTTGATTATGTAATCTTGTAAATCCCTTGATTTTAGGGATAGGCTTAATC
40315546 TCATCCGTTGATGTAATTCGATCTATACCGTCAATTTGAAGGGAGCT
196 TCATCCGTTGATGTAATTCGATCTATACCGTCAATTTGAAGGGAGCT
40315593 CAAGAGAACCGACTCGATTCAAAGAATTGATGGAGAAGCCTGGGTGGCCCAATGATGCAGATATA
1 CAAGAGAACCGACTCGATTCAAAGAATTGATGGAGAAGCCTGGGTGGCCCAATGATGCAGATATA
* * * * *
40315658 GGAAGTTAGGCTACCTTGGTAAATAGGGAAACTAATCTTAGAAGATTGCGGGGAATCATATATGA
66 GGAAGTTAGGCTACCTTGGTAAATAGGGAAACTAATTTTAAAAGATTGTGGGGAATCATATCTAA
40315723 TAATATTAGATTTAATTTGATTATGTAATCTTGTAAATCCCTTGATTTTAGGGATAGGCTTAATC
131 TAATATTAGATTTAATTTGATTATGTAATCTTGTAAATCCCTTGATTTTAGGGATAGGCTTAATC
*
40315788 TCATCCGTTGATGTAATTCGATCTATACCGTCAGTTTGAAGGGAGCT
196 TCATCCGTTGATGTAATTCGATCTATACCGTCAATTTGAAGGGAGCT
40315835 CAA
1 CAA
40315838 CTATAAATAG
Statistics
Matches: 719, Mismatches: 8, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
241 240 0.33
242 479 0.67
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (242 bp):
CAAGAGAACCGACTCGATTCAAAGAATTGATGGAGAAGCCTGGGTGGCCCAATGATGCAGATATA
GGAAGTTAGGCTACCTTGGTAAATAGGGAAACTAATTTTAAAAGATTGTGGGGAATCATATCTAA
TAATATTAGATTTAATTTGATTATGTAATCTTGTAAATCCCTTGATTTTAGGGATAGGCTTAATC
TCATCCGTTGATGTAATTCGATCTATACCGTCAATTTGAAGGGAGCT
Found at i:40325306 original size:114 final size:114
Alignment explanation
Indices: 40325106--40325448 Score: 643
Period size: 114 Copynumber: 3.0 Consensus size: 114
40325096 ATAATTCCAA
40325106 AGGACTTCCAGTAAGACCGGTAATGTGTAGATCTGGCATGCATTCATTTTTCCCTTTTAGTAAAT
1 AGGACTTCCAGTAAGACCGGTAATGTGTAGATCTGGCATGCATTCATTTTTCCCTTTTAGTAAAT
* *
40325171 AGTAGGTGCATCAGTGATGTAGAATAAGTAGGGAAAAGGAATTAAATAT
66 ACTTGGTGCATCAGTGATGTAGAATAAGTAGGGAAAAGGAATTAAATAT
40325220 AGGACTTCCAGTAAGACCGGTAATGTGTAGATCTGGCATGCATTCATTTTTCCCTTTTAGTAAAT
1 AGGACTTCCAGTAAGACCGGTAATGTGTAGATCTGGCATGCATTCATTTTTCCCTTTTAGTAAAT
40325285 ACTTGGTGCATCAGTGATGTAGAATAAGTAGGGAAAAGGAATTAAATAT
66 ACTTGGTGCATCAGTGATGTAGAATAAGTAGGGAAAAGGAATTAAATAT
*
40325334 AGGACTTCCAGTAAGACCGGTAATGTGTAGATCTGGCATGCATTCATTTTTCCCTTTTAGTAAGT
1 AGGACTTCCAGTAAGACCGGTAATGTGTAGATCTGGCATGCATTCATTTTTCCCTTTTAGTAAAT
*
40325399 ACTT-GTGCATCAGTGATGTAGAATAAGTAGGGAAAAGAAATTAAATAT
66 ACTTGGTGCATCAGTGATGTAGAATAAGTAGGGAAAAGGAATTAAATAT
40325447 AG
1 AG
40325449 AACAGAAATT
Statistics
Matches: 225, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
113 45 0.20
114 180 0.80
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (114 bp):
AGGACTTCCAGTAAGACCGGTAATGTGTAGATCTGGCATGCATTCATTTTTCCCTTTTAGTAAAT
ACTTGGTGCATCAGTGATGTAGAATAAGTAGGGAAAAGGAATTAAATAT
Found at i:40330842 original size:13 final size:12
Alignment explanation
Indices: 40330816--40330853 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
40330806 TTGATTCTTA
40330816 AAAATTAAAATTT
1 AAAA-TAAAATTT
40330829 AAAATAAAACTTT
1 AAAATAAAA-TTT
40330842 AAAATAAAATTT
1 AAAATAAAATTT
40330854 TTTTAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAATAAAATTT
Found at i:40336420 original size:98 final size:98
Alignment explanation
Indices: 40336289--40336484 Score: 311
Period size: 98 Copynumber: 2.0 Consensus size: 98
40336279 CAAAATAGAA
* *
40336289 GCAAGAGTGCATTTGACATATTAGACTTGTGTGACTCAATCCTGTTAGATTCAGCCTGAAAAGTT
1 GCAAGAGTGCATTTGACATATTAAACTTGTGTGACTCAATCCTGTTAGATCCAGCCTGAAAAGTT
** *
40336354 TGATGTGCACAAGTTGTATTCGTATAGGACTAT
66 CAATGTGCACAAATTGTATTCGTATAGGACTAT
* * * *
40336387 GCAAGAGTTCATTTGACATGTTAAACTTGTGTGACTCAATCTTGTTTGATCCAGCCTGAAAAGTT
1 GCAAGAGTGCATTTGACATATTAAACTTGTGTGACTCAATCCTGTTAGATCCAGCCTGAAAAGTT
40336452 CAATGTGCACAAATTGTATTCGTATAGGACTAT
66 CAATGTGCACAAATTGTATTCGTATAGGACTAT
40336485 ACTTCTTCTA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (98 bp):
GCAAGAGTGCATTTGACATATTAAACTTGTGTGACTCAATCCTGTTAGATCCAGCCTGAAAAGTT
CAATGTGCACAAATTGTATTCGTATAGGACTAT
Found at i:40340374 original size:29 final size:30
Alignment explanation
Indices: 40340332--40340407 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
40340322 AAACACATCA
*
40340332 AAATTTCATGTATAAAATCACACA-AAATC
1 AAATTTTATGTATAAAATCACACATAAATC
* * * *
40340361 AAATTTTATATATAATATTACACATTAGATC
1 AAATTTTATGTATAAAATCACACA-TAAATC
*
40340392 AAAATTTATGTATAAA
1 AAATTTTATGTATAAA
40340408 TTTAATATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 20 0.54
31 17 0.46
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.36
Consensus pattern (30 bp):
AAATTTTATGTATAAAATCACACATAAATC
Found at i:40340400 original size:31 final size:29
Alignment explanation
Indices: 40340328--40340407 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 29
40340318 ATTGAAACAC
40340328 ATCAAAATTTCATGTATAAAATCACACAAA
1 ATCAAAATTT-ATGTATAAAATCACACAAA
* * * * *
40340358 ATCAAATTTTATATATAATATTACACATTAG
1 ATCAAAATTTATGTATAAAATCACACA--AA
40340389 ATCAAAATTTATGTATAAA
1 ATCAAAATTTATGTATAAA
40340408 TTTAATATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 14 0.35
30 9 0.22
31 17 0.43
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.35
Consensus pattern (29 bp):
ATCAAAATTTATGTATAAAATCACACAAA
Found at i:40351077 original size:20 final size:20
Alignment explanation
Indices: 40351039--40351077 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40351029 GAAAATATAA
* **
40351039 AAAAAATTTAAAATTATTTT
1 AAAAAATATAAAAAAATTTT
40351059 AAAAAATATAAAAAAATTT
1 AAAAAATATAAAAAAATTT
40351078 GGGGGGGCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATATAAAAAAATTTT
Found at i:40351684 original size:29 final size:29
Alignment explanation
Indices: 40351642--40351710 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
40351632 AAATTCTACC
*
40351642 ATAAAGTAATATTCTACCTAGAATATTAG
1 ATAAACTAATATTCTACCTAGAATATTAG
40351671 ATAAACTAATATTCTACCTAGAATATTAG
1 ATAAACTAATATTCTACCTAGAATATTAG
40351700 ATAAACTAATA
1 ATAAACTAATA
40351711 AATAGGTCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (29 bp):
ATAAACTAATATTCTACCTAGAATATTAG
Found at i:40352281 original size:17 final size:17
Alignment explanation
Indices: 40352254--40352286 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
40352244 TGCTAAGAAT
40352254 TTAAAAATTAT-TAAAA
1 TTAAAAATTATATAAAA
40352270 TTAAAAATTTATATAAA
1 TTAAAAA-TTATATAAA
40352287 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATTATATAAAA
Found at i:40352294 original size:27 final size:26
Alignment explanation
Indices: 40352224--40352299 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 26
40352214 TTTCAAATAA
*
40352224 TTATAAAATTATTTAAAAATTGCTAAGAAT
1 TTATAAAATTATTT-AAAA-T--TAAAAAT
40352254 TTA-AAAATTA-TTAAAATTAAAAAT
1 TTATAAAATTATTTAAAATTAAAAAT
40352278 TTATATAAATTATTTAAAATTA
1 TTATA-AAATTATTTAAAATTA
40352300 CGATAAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
24 9 0.21
25 1 0.02
26 7 0.17
27 13 0.31
28 2 0.05
29 7 0.17
30 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (26 bp):
TTATAAAATTATTTAAAATTAAAAAT
Found at i:40362458 original size:13 final size:13
Alignment explanation
Indices: 40362440--40362473 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
40362430 ATTGTTCAAC
40362440 TAAAGAATTTGAT
1 TAAAGAATTTGAT
40362453 TAAAGAATTTGAT
1 TAAAGAATTTGAT
40362466 TAAA-AATT
1 TAAAGAATT
40362474 AATTTTGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (13 bp):
TAAAGAATTTGAT
Found at i:40363066 original size:12 final size:12
Alignment explanation
Indices: 40363049--40363082 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
40363039 AGTGATTATC
40363049 TTAATATTAAAT
1 TTAATATTAAAT
40363061 TTAATATTAAA-
1 TTAATATTAAAT
40363072 TTAA-ATTAAAT
1 TTAATATTAAAT
40363083 ATTTATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 4 0.19
12 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAATATTAAAT
Found at i:40363076 original size:17 final size:18
Alignment explanation
Indices: 40363049--40363085 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
40363039 AGTGATTATC
*
40363049 TTAATATTAAATTTAATA
1 TTAATATTAAATTAAATA
40363067 TTAA-ATTAAATTAAATA
1 TTAATATTAAATTAAATA
40363084 TT
1 TT
40363086 TATTTTGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATATTAAATTAAATA
Found at i:40365610 original size:11 final size:11
Alignment explanation
Indices: 40365594--40365736 Score: 68
Period size: 11 Copynumber: 12.7 Consensus size: 11
40365584 ATTAATCACT
40365594 TTAATATTAAA
1 TTAATATTAAA
40365605 TTAATA-TAATA
1 TTAATATTAA-A
* *
40365616 TTTATCTT-AA
1 TTAATATTAAA
* *
40365626 TAAATATTATA
1 TTAATATTAAA
40365637 TTAAT-TTAATA
1 TTAATATTAA-A
* *
40365648 TTAAGATAATCACA
1 TT-A-AT-ATTAAA
40365662 TTAATATTAAA
1 TTAATATTAAA
40365673 TTAATA--AAA
1 TTAATATTAAA
40365682 -TAATATTAAGA
1 TTAATATTAA-A
40365693 -TAAGTATTAAA
1 TTAA-TATTAAA
40365704 TTAA-ATTTAATA
1 TTAATA-TTAA-A
40365716 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
40365729 ATAATATT
1 TTAATATT
40365737 GTTTTTGGAA
Statistics
Matches: 101, Mismatches: 13, Indels: 36
0.67 0.09 0.24
Matches are distributed among these distances:
8 5 0.05
9 3 0.03
10 15 0.15
11 43 0.43
12 18 0.18
13 7 0.07
14 7 0.07
15 3 0.03
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:40365631 original size:21 final size:20
Alignment explanation
Indices: 40365607--40365647 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
40365597 ATATTAAATT
*
40365607 AATATAATATTTATCTTAATA
1 AATATAATATTAAT-TTAATA
*
40365628 AATATTATATTAATTTAATA
1 AATATAATATTAATTTAATA
40365648 TTAAGATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATAATATTAATTTAATA
Found at i:40365645 original size:5 final size:6
Alignment explanation
Indices: 40365594--40365719 Score: 67
Period size: 6 Copynumber: 21.7 Consensus size: 6
40365584 ATTAATCACT
* *
40365594 TTAATA TTAA-A TTAATA -TAATA TTTATC TTAATA --AATA TT-ATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
* *
40365637 TTAAT- TTAATA TTAAGA -TAATCACA TTAATA TTAA-A TTAATAAA ATAATA
1 TTAATA TTAATA TTAATA TTAAT---A TTAATA TTAATA TTAAT--A TTAATA
*
40365687 TTAAGA -TAAGTA TTAA-A TTAA-A TTTAATA TTAA
1 TTAATA TTAA-TA TTAATA TTAATA -TTAATA TTAA
40365720 ACTATTAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 34
0.68 0.07 0.25
Matches are distributed among these distances:
4 4 0.04
5 37 0.40
6 38 0.41
7 4 0.04
8 6 0.06
9 4 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
TTAATA
Found at i:40365658 original size:68 final size:68
Alignment explanation
Indices: 40365586--40365719 Score: 182
Period size: 68 Copynumber: 2.0 Consensus size: 68
40365576 CAAAAAAAAT
* * * * *
40365586 TAATCACTTTAATATTAAATTAATATAATATTTATCTTA-ATAAATATTATATT-AATTTAATAT
1 TAATCACATTAATATTAAATTAATAAAATA-ATAT-TAAGATAAATATTAAATTAAATTTAATAT
40365649 TAAGA
64 TAAGA
*
40365654 TAATCACATTAATATTAAATTAATAAAATAATATTAAGATAAGTATTAAATTAAATTTAATATTA
1 TAATCACATTAATATTAAATTAATAAAATAATATTAAGATAAATATTAAATTAAATTTAATATTA
40365719 A
66 A
40365720 ACTATTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
66 2 0.03
67 15 0.26
68 41 0.71
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (68 bp):
TAATCACATTAATATTAAATTAATAAAATAATATTAAGATAAATATTAAATTAAATTTAATATTA
AGA
Found at i:40365665 original size:20 final size:19
Alignment explanation
Indices: 40365642--40365695 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
40365632 TTATATTAAT
*
40365642 TTAATATTAAGATAATCACA
1 TTAATATTAAGATAAT-AAA
40365662 TTAATATTAA-ATTAATAAA
1 TTAATATTAAGA-TAATAAA
*
40365681 ATAATATTAAGATAA
1 TTAATATTAAGATAA
40365696 GTATTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (19 bp):
TTAATATTAAGATAATAAA
Found at i:40366223 original size:25 final size:25
Alignment explanation
Indices: 40366193--40366241 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
40366183 TTAGATTTTT
*
40366193 CAAGAAAATTCTTTAATCAAATTCA
1 CAAGAAAATTATTTAATCAAATTCA
40366218 CAAGAAAATTATTTAATCAAATTC
1 CAAGAAAATTATTTAATCAAATTC
40366242 TTTAGTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (25 bp):
CAAGAAAATTATTTAATCAAATTCA
Found at i:40367351 original size:16 final size:16
Alignment explanation
Indices: 40367330--40367363 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40367320 CTATGCATGA
* *
40367330 AAAGTATAAAATACAT
1 AAAGTAAAAAAGACAT
40367346 AAAGTAAAAAAGACAT
1 AAAGTAAAAAAGACAT
40367362 AA
1 AA
40367364 TAATGAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.09, T:0.18
Consensus pattern (16 bp):
AAAGTAAAAAAGACAT
Found at i:40378982 original size:16 final size:15
Alignment explanation
Indices: 40378943--40378984 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
40378933 TTCCAGGACT
*
40378943 AGAGAAGATTGGATC
1 AGAGAAGATGGGATC
*
40378958 TGA-AAGATGGGAATC
1 AGAGAAGATGGG-ATC
40378973 AGAGAAGATGGG
1 AGAGAAGATGGG
40378985 GAGACGAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 7 0.32
15 7 0.32
16 8 0.36
ACGTcount: A:0.40, C:0.05, G:0.38, T:0.17
Consensus pattern (15 bp):
AGAGAAGATGGGATC
Found at i:40384908 original size:2 final size:2
Alignment explanation
Indices: 40384903--40384960 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
40384893 TTAATACGGA
40384903 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
40384945 TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG
40384961 GAAACAGTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:40385178 original size:29 final size:29
Alignment explanation
Indices: 40385140--40385256 Score: 120
Period size: 29 Copynumber: 4.1 Consensus size: 29
40385130 GGACTATATA
40385140 AATCGATAATGATTGAAATACATCAAAAT
1 AATCGATAATGATTGAAATACATCAAAAT
40385169 AATCGATAATGATTGAAATACATCAAAAT
1 AATCGATAATGATTGAAATACATCAAAAT
* * * **
40385198 GAAAT-TAAAAT-ATTAAAATTTAT-ATAAAT
1 --AATCGATAATGATTGAAATACATCA-AAAT
40385227 -A--GATAATGATTGAAATACATCAAAAT
1 AATCGATAATGATTGAAATACATCAAAAT
40385253 AATC
1 AATC
40385257 TAAAAATATT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
25 4 0.06
26 14 0.20
27 2 0.03
28 1 0.01
29 42 0.60
30 4 0.06
31 3 0.04
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.30
Consensus pattern (29 bp):
AATCGATAATGATTGAAATACATCAAAAT
Found at i:40387548 original size:49 final size:49
Alignment explanation
Indices: 40387494--40387597 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
40387484 TCATGTGTTA
* * ** * *
40387494 TAATTTTATACAGTGTTGAGTTTTTTATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
*
40387543 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
40387592 TAATTT
1 TAATTT
40387598 GTTTTTTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:40389015 original size:25 final size:24
Alignment explanation
Indices: 40388972--40389019 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
40388962 AAGTAGATTA
40388972 TAAATTATATTTAAAAATAATTATT
1 TAAATTATATTTAAAAAT-ATTATT
* *
40388997 TAAATTATATTTTATAATATTAT
1 TAAATTATATTTAAAAATATTAT
40389020 ATATTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAATTATATTTAAAAATATTATT
Found at i:40389132 original size:110 final size:114
Alignment explanation
Indices: 40388968--40389216 Score: 323
Period size: 110 Copynumber: 2.2 Consensus size: 114
40388958 AATAAAGTAG
*
40388968 ATTA-TAAATTATATTTAAAAATAATTATTTAAATTATATTTTATAATATTATATATTATGA-TT
1 ATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAATATTATATATTATGATTT
* *
40389031 -TTAGTAAATTCATAT-AAGA-A-TAAGAATTTTATTAAATTATATATT
66 ATTAGTAAATCCATATAAAGATATTAACAATTTTATTAAATTATATATT
* * *
40389076 ATTATTAAACTATATTTAATAATAATTATTTTAAATTATATTTTATAGTCTTATATATTATGATT
1 ATTATTAAATTATATTTAATAATAATTA-TTTAAATTATATTTTATAATATTATATATTATGA-T
*
40389141 TTATTAGTAAATCCATATAAAAATATTTATTAACAATTTTATTAAATTATATATT
64 TTATTAGTAAATCCATAT--AAAGA--TATTAACAATTTTATTAAATTATATATT
*
40389196 -TTATTAAATTATATTTTATAA
1 ATTATTAAATTATATTTAATAA
40389217 CAGTTATGTT
Statistics
Matches: 120, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
108 4 0.03
109 21 0.17
110 32 0.27
112 2 0.02
113 14 0.12
116 3 0.03
119 20 0.17
120 24 0.20
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (114 bp):
ATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAATATTATATATTATGATTT
ATTAGTAAATCCATATAAAGATATTAACAATTTTATTAAATTATATATT
Found at i:40389214 original size:15 final size:17
Alignment explanation
Indices: 40389176--40389209 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40389166 TTTATTAACA
40389176 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
40389193 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
40389210 TTTATAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:40389459 original size:46 final size:44
Alignment explanation
Indices: 40389376--40389464 Score: 151
Period size: 46 Copynumber: 2.0 Consensus size: 44
40389366 TCTATTCCAT
*
40389376 TCAACCAAACACAAGAATACCATTACGCCTCTATTCCATTACAG
1 TCAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTACAG
40389420 TCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTACA
1 TCAACCAAACAAAAGAA-TACC-ATTACGCCTCTATTCCATTACA
40389465 ACGAACCAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 16 0.38
45 4 0.10
46 22 0.52
ACGTcount: A:0.39, C:0.30, G:0.06, T:0.25
Consensus pattern (44 bp):
TCAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTACAG
Found at i:40389472 original size:46 final size:43
Alignment explanation
Indices: 40389356--40389475 Score: 149
Period size: 46 Copynumber: 2.8 Consensus size: 43
40389346 TTTCCTTATG
* *
40389356 CTATTACACCTCTATTCCATT---CAACCAAACACAAGAATAC
1 CTATTACGCCTCTATTCCATTACACAACCAAACAAAAGAATAC
40389396 C-ATTACGCCTCTATTCCATTACAGTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATTCCATTACA--CAACCAAACAAAAGAA-TAC
40389441 CTATTACGCCTCTATTCCATTACAACGAACCAAAC
1 CTATTACGCCTCTATTCCATTAC-AC-AACCAAAC
40389476 GTGCTGTTAA
Statistics
Matches: 69, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
39 18 0.26
40 1 0.01
44 15 0.22
45 5 0.07
46 29 0.42
47 1 0.01
ACGTcount: A:0.38, C:0.32, G:0.05, T:0.25
Consensus pattern (43 bp):
CTATTACGCCTCTATTCCATTACACAACCAAACAAAAGAATAC
Found at i:40400121 original size:2 final size:2
Alignment explanation
Indices: 40400114--40400148 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40400104 AAGATTGAAC
40400114 TA TA TA 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 TA TA TA T
40400149 GTAGAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40400911 original size:29 final size:29
Alignment explanation
Indices: 40400817--40400921 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
40400807 TTCAGCGCTT
*
40400817 TCTGTTCTAATAATGCACTTTGGTGCCAC
1 TCTGTTCTAATAATGCACTTCGGTGCCAC
* * * ****
40400846 TCTGTTATGATAAAGCAGC-TCGGTGTTGT
1 TCTGTTCTAATAATGCA-CTTCGGTGCCAC
* *
40400875 TCTATTCTAATACTGCACTTCGGTGCCAC
1 TCTGTTCTAATAATGCACTTCGGTGCCAC
* *
40400904 TCTGTTCTATTATTGCAC
1 TCTGTTCTAATAATGCAC
40400922 CTAAGTGCAA
Statistics
Matches: 54, Mismatches: 20, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
28 1 0.02
29 52 0.96
30 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (29 bp):
TCTGTTCTAATAATGCACTTCGGTGCCAC
Found at i:40404030 original size:28 final size:28
Alignment explanation
Indices: 40403976--40404049 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
40403966 TACATGGCCA
* * *
40403976 CCCACACGGCTTGGACACGGTCGTGTGG
1 CCCACACGGCCTGGACACGATCATGTGG
* *
40404004 CCCACACGGCCTGGATACTATCATGTGG
1 CCCACACGGCCTGGACACGATCATGTGG
* *
40404032 CCCATACGACCTGGACAC
1 CCCACACGGCCTGGACAC
40404050 ACACCCGTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (28 bp):
CCCACACGGCCTGGACACGATCATGTGG
Found at i:40407394 original size:22 final size:22
Alignment explanation
Indices: 40407364--40407406 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40407354 AGGTGGGACG
*
40407364 CATACCAGTTCTGTGTTAAACA
1 CATACCAGTTATGTGTTAAACA
*
40407386 CATATCAGTTATGTGTTAAAC
1 CATACCAGTTATGTGTTAAAC
40407407 TCTTAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (22 bp):
CATACCAGTTATGTGTTAAACA
Found at i:40407486 original size:19 final size:19
Alignment explanation
Indices: 40407459--40407503 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
40407449 CTCGTTTATG
*
40407459 ATGTTTGATTAGTGGAACC
1 ATGTGTGATTAGTGGAACC
*
40407478 ATGTGTGATTAGTGGAATC
1 ATGTGTGATTAGTGGAACC
40407497 ATGTGTG
1 ATGTGTG
40407504 CCTGAAAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (19 bp):
ATGTGTGATTAGTGGAACC
Found at i:40417296 original size:5 final size:5
Alignment explanation
Indices: 40417286--40417311 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40417276 TGAGCATTCG
40417286 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
40417312 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:40418098 original size:31 final size:29
Alignment explanation
Indices: 40418063--40418121 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
40418053 GGAGGTGGGA
*
40418063 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTT-GGGGAAAAG
* *
40418094 TGGGAGGGAGTAAAAATTTTGGGGAAAA
1 TGGGAGAGAATAAAAATTTTGGGGAAAA
40418122 ATAAAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 13 0.52
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.20
Consensus pattern (29 bp):
TGGGAGAGAATAAAAATTTTGGGGAAAAG
Found at i:40418350 original size:9 final size:9
Alignment explanation
Indices: 40418336--40418372 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40418326 TATAGTTTGA
40418336 TATTCGAAT
1 TATTCGAAT
40418345 TATTCGAAT
1 TATTCGAAT
*
40418354 TATTCGAGT
1 TATTCGAAT
40418363 TATTCGAAT
1 TATTCGAAT
40418372 T
1 T
40418373 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40418442 original size:9 final size:9
Alignment explanation
Indices: 40418425--40418455 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40418415 TCGAGTTGAT
40418425 TCGAATAAC
1 TCGAATAAC
*
40418434 TCGATTAAC
1 TCGAATAAC
40418443 TCGAATAAC
1 TCGAATAAC
40418452 TCGA
1 TCGA
40418456 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:40426275 original size:24 final size:25
Alignment explanation
Indices: 40426229--40426275 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
40426219 AGAAGGTATC
* *
40426229 CTAATAAAAATAAGCTAAGATCTCT
1 CTAACAAAAATAAGCTAACATCTCT
*
40426254 CTAACAAAAATAA-TTAACATCT
1 CTAACAAAAATAAGCTAACATCT
40426276 TTAATGGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (25 bp):
CTAACAAAAATAAGCTAACATCTCT
Found at i:40427067 original size:2 final size:2
Alignment explanation
Indices: 40427060--40427087 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40427050 AACCTATTTC
40427060 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
40427088 TCTTTTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40429595 original size:51 final size:50
Alignment explanation
Indices: 40429501--40429597 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
40429491 GTTTACACGT
* *
40429501 TCTATCAATTTAGTATTGATTTAATAAATTTATCCTACGATATTTATGTAC
1 TCTATCAATTTAGTATTGATTTAACAAATTTATCATAC-ATATTTATGTAC
* *
40429552 TCTATCAATTTGGTCTTGATTTAACAAATTTAGCTCATA-ATATTTA
1 TCTATCAATTTAGTATTGATTTAACAAATTTA--TCATACATATTTA
40429598 CATATTTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
51 36 0.90
53 4 0.10
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (50 bp):
TCTATCAATTTAGTATTGATTTAACAAATTTATCATACATATTTATGTAC
Found at i:40438318 original size:2 final size:2
Alignment explanation
Indices: 40438311--40438349 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
40438301 NNNNTAATAC
*
40438311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40438350 GTGTGTATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40443084 original size:15 final size:16
Alignment explanation
Indices: 40443060--40443101 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
40443050 CCCCCCCCCC
*
40443060 CAAAA-AAAAAAAAAA
1 CAAAAGAAAAAAAAGA
40443075 CAAAAGAAAAAAAAGA
1 CAAAAGAAAAAAAAGA
40443091 -AAAAGAGAAAA
1 CAAAAGA-AAAA
40443102 CGGAAGAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (16 bp):
CAAAAGAAAAAAAAGA
Found at i:40443086 original size:17 final size:17
Alignment explanation
Indices: 40443063--40443101 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
40443053 CCCCCCCCAA
*
40443063 AAAAAAAAAAAACAAAAG
1 AAAAAAAAGAAA-AAAAG
*
40443081 AAAAAAAAGAAAAAGAG
1 AAAAAAAAGAAAAAAAG
40443098 AAAA
1 AAAA
40443102 CGGAAGAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAG
Found at i:40447022 original size:20 final size:19
Alignment explanation
Indices: 40446989--40447027 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
40446979 ATTTGAATGA
*
40446989 ATAGTTAAATTCAAGTAGT
1 ATAGTTAAAATCAAGTAGT
40447008 ATAGCTTAAAATCAAGTAGT
1 ATAG-TTAAAATCAAGTAGT
40447028 TTTAGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (19 bp):
ATAGTTAAAATCAAGTAGT
Found at i:40448405 original size:20 final size:20
Alignment explanation
Indices: 40448380--40448460 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
40448370 TTGTATGAGA
40448380 TTGCACTTCGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
* * * *
40448400 TTGCACTTTGCTGCTTCTGA
1 TTGCACTTCGGTGCCTCTGT
* *
40448420 TTGCACATT-TGTGCCTCTAT
1 TTGCAC-TTCGGTGCCTCTGT
* *
40448440 CTGCACTTCTGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
40448460 T
1 T
40448461 ACATATCTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
19 2 0.04
20 43 0.91
21 2 0.04
ACGTcount: A:0.09, C:0.28, G:0.20, T:0.43
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTGT
Found at i:40456165 original size:37 final size:38
Alignment explanation
Indices: 40456078--40456166 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 38
40456068 AACAGTAGAT
* * *
40456078 ATGCCTAACATGTATTCAGTTCAACACTAGCAGTGGAC
1 ATGCATAACATGTATTCAATTCAACACTAGCAATGGAC
* * * * *
40456116 ATGCTTAACATGTATTCAATTCAACATTGGTAAT-GTC
1 ATGCATAACATGTATTCAATTCAACACTAGCAATGGAC
40456153 ATGCATAACATGTA
1 ATGCATAACATGTA
40456167 CTCAGTAGGG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 15 0.35
38 28 0.65
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (38 bp):
ATGCATAACATGTATTCAATTCAACACTAGCAATGGAC
Found at i:40458298 original size:26 final size:26
Alignment explanation
Indices: 40458268--40458319 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
40458258 TTCTAGATGA
*
40458268 CTCACCACAAAGG-TTTCCAAGATAAT
1 CTCACCACAAAGGCTTCCCAA-ATAAT
*
40458294 CTCACCACTAAGGCTTCCCAAATAAT
1 CTCACCACAAAGGCTTCCCAAATAAT
40458320 ATGTCATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.37, C:0.31, G:0.10, T:0.23
Consensus pattern (26 bp):
CTCACCACAAAGGCTTCCCAAATAAT
Found at i:40469460 original size:29 final size:29
Alignment explanation
Indices: 40469415--40469479 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
40469405 GGCTTATTTC
**
40469415 CCTAATTAATT-TTAAAACAGACCTAAAGG
1 CCTAATTAATTAAAAAAACA-ACCTAAAGG
**
40469444 CCTAATTAATTAAAAAAACAACCTTTAGG
1 CCTAATTAATTAAAAAAACAACCTAAAGG
40469473 CCTAATT
1 CCTAATT
40469480 TAGCCAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (29 bp):
CCTAATTAATTAAAAAAACAACCTAAAGG
Found at i:40478520 original size:29 final size:29
Alignment explanation
Indices: 40478487--40478545 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
40478477 AAAGAAGTTA
40478487 GAATATAAGACTTTGCTAATTGTTTATTT
1 GAATATAAGACTTTGCTAATTGTTTATTT
* *
40478516 GAATATGAGACTTTGCTAATTGTTTCTTT
1 GAATATAAGACTTTGCTAATTGTTTATTT
40478545 G
1 G
40478546 TATGTAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.47
Consensus pattern (29 bp):
GAATATAAGACTTTGCTAATTGTTTATTT
Found at i:40483690 original size:51 final size:50
Alignment explanation
Indices: 40483462--40483952 Score: 498
Period size: 51 Copynumber: 9.7 Consensus size: 50
40483452 TATCATTTGA
* *
40483462 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AGTTTTACTG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTT-CGG
* *
40483511 TTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTT-CGG
*
40483561 CT-CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTACGG
1 -TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTT-CGG
*
40483611 CT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTTCGG
1 -TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TTTTCGG
* * * * * * * *
40483662 TACCCATTGTAGCCTTCACTTAGTACTACACATGTAACCATAGTTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTT-TCGG
* *
40483713 TACACGTAGTAGCATTCACACAGTACTACACACGTG-CTCAAAGCTTTTCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGAC-CAAAG-TTTTCGG
* * * * *
40483764 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTT-TCGG
*
40483815 TACACGTAGTAGCCTTCACACAGTACTACACACGTG-CTCAAAGCTTTTCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGAC-CAAAG-TTTTCGG
* * * * ** * *
40483866 TACACATAGTACCCTTCACTTAGTACTACACATGAAACCATTA-TTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTT-TCGG
*
40483917 TACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTG
40483953 TTCATCGACA
Statistics
Matches: 373, Mismatches: 52, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
49 38 0.10
50 107 0.29
51 214 0.57
52 14 0.04
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (50 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTTCGG
Found at i:40483748 original size:102 final size:102
Alignment explanation
Indices: 40483462--40483952 Score: 626
Period size: 102 Copynumber: 4.9 Consensus size: 102
40483452 TATCATTTGA
* * * * * * *
40483462 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGT-TTTA-CTG-TTCACGTAGTAGC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTAACCATTATTTATC-GATACACGTAGTAGC
* *
40483524 CTTCACATAGTACTACACACGTGATC-AAG-TTTTACGG
65 CTTCACACAGTACTACACACGTGCTCAAAGCTTTT-CGG
* * * * * * *
40483561 CT-CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTA-CGGCT-CACGTAGTA
1 -TACACATAGTAGCCTTCACTTAGTACTACACATGT-AACCATTATTTATC-GATACACGTAGTA
* *
40483622 GCCTTCACATAGTACTACATACGTGAC-CAAAGCTTTTCGG
63 GCCTTCACACAGTACTACACACGTG-CTCAAAGCTTTTCGG
* *
40483662 TACCCATTGTAGCCTTCACTTAGTACTACACATGTAACCA-TAGTTTATCGATACACGTAGTAGC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTAACCATTA-TTTATCGATACACGTAGTAGC
*
40483726 ATTCACACAGTACTACACACGTGCTCAAAGCTTTTCGG
65 CTTCACACAGTACTACACACGTGCTCAAAGCTTTTCGG
*
40483764 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCGATACACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTAACCATTATTTATCGATACACGTAGTAGCC
40483829 TTCACACAGTACTACACACGTGCTCAAAGCTTTTCGG
66 TTCACACAGTACTACACACGTGCTCAAAGCTTTTCGG
* *
40483866 TACACATAGTACCCTTCACTTAGTACTACACATGAAACCATTATTTATCGATACACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTAACCATTATTTATCGATACACGTAGTAGCC
40483931 TTCACACAGTACTACACACGTG
66 TTCACACAGTACTACACACGTG
40483953 TTCATCGACA
Statistics
Matches: 354, Mismatches: 25, Indels: 22
0.88 0.06 0.05
Matches are distributed among these distances:
99 34 0.10
100 48 0.14
101 42 0.12
102 228 0.64
103 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (102 bp):
TACACATAGTAGCCTTCACTTAGTACTACACATGTAACCATTATTTATCGATACACGTAGTAGCC
TTCACACAGTACTACACACGTGCTCAAAGCTTTTCGG
Found at i:40485989 original size:25 final size:25
Alignment explanation
Indices: 40485955--40486004 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40485945 AAATTCTTAG
40485955 TTATGATTATTACATAACATATAGA
1 TTATGATTATTACATAACATATAGA
40485980 TTATGATTATTACATAACATATAGA
1 TTATGATTATTACATAACATATAGA
40486005 AGAGAACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (25 bp):
TTATGATTATTACATAACATATAGA
Found at i:40505848 original size:134 final size:138
Alignment explanation
Indices: 40505704--40505962 Score: 316
Period size: 138 Copynumber: 1.9 Consensus size: 138
40505694 TTTTGAACAA
** *
40505704 ATCATATATA-T-TATTACAAGC-TCTAGAAAATTTTGTGTTCACATCT-TA-TTTT-TGTCATT
1 ATCATATATATTATATTACAAGCTTCTA-AAAAAATTGTGTTCAC-TCTGTATTTTTATGCCATT
*** * * **
40505763 TTTCATTTTAATATTTATTTCCCTTTTGAA-AATTTTCATGTATATATTTATTTTTTAAATTTAT
64 TGGAATTTTAATATCTATTTCCCTTTTGAAGAA-ATTCATGTATATATTTATTTCATAAATTTAT
40505827 TTTTAAATCAT
128 TTTTAAATCAT
* *
40505838 ATCATATATATTATATTACAAGCTTTTAAAAAAATTGTGTTCACTTTGTATTTTTATGCCATTTG
1 ATCATATATATTATATTACAAGCTTCTAAAAAAATTGTGTTCACTCTGTATTTTTATGCCATTTG
* *
40505903 GAATTTTAATATCTATTTCTCTTTTTAAGAAATTCATGTATATATTTATTTCATAAATTT
66 GAATTTTAATATCTATTTCCCTTTTGAAGAAATTCATGTATATATTTATTTCATAAATTT
40505963 TAAAAATTAA
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
134 10 0.10
135 3 0.03
136 26 0.25
137 7 0.07
138 56 0.54
139 2 0.02
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (138 bp):
ATCATATATATTATATTACAAGCTTCTAAAAAAATTGTGTTCACTCTGTATTTTTATGCCATTTG
GAATTTTAATATCTATTTCCCTTTTGAAGAAATTCATGTATATATTTATTTCATAAATTTATTTT
TAAATCAT
Found at i:40507882 original size:19 final size:19
Alignment explanation
Indices: 40507831--40507884 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
40507821 AATCATATCT
40507831 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* * *
40507850 TTTAAGAATACATATCATA
1 TCTAAGATTGCATATCATA
40507869 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
40507885 CTTGAAGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40508483 original size:45 final size:44
Alignment explanation
Indices: 40508396--40508775 Score: 217
Period size: 45 Copynumber: 8.7 Consensus size: 44
40508386 TTCTAATCCA
* * * * * *
40508396 CTCCACTACAACTTTAGGGAGATAGGATTTGTTTATTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTCTTGAGTCTG
* * *
40508440 CCCCACTGCAATTTTTAGGG-GATAAGACTTGATTTCTTGAGTCTG
1 CTCCACTGCAA-CTTCAGGGAGATAAGACTTG-TTTCTTGAGTCTG
* * * *
40508485 CTCCACTACAACTTCAGGAAGATAAGACTCGCTTTCTTGGGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TTTCTTGAGTCTG
** * * *
40508530 CTCCACTGCAACTTCAGGGAGATAAGACCCGATGC--GA-TTTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTCTTGAGTCTG
* * * * **
40508571 CT-CTCTGCAACTTCAGAGAGATAAGATTTGTGATT-TT-AATCCA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGT--TTCTTGAGTCTG
* * * * * *
40508614 TTCCACTGCAACTTCAGGGAGATAGGA-TTATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTT-TCTTGAGTCTG
** * * *
40508658 CTCCACTAAAACTTCAGGGAGATAAGA-TTCTCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGT--TTCTTGAGTCTG
* * * *
40508703 C-CTTACTACAACTTCA-GGAGGATAAGGCTTGCTTACTT-AGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTG-TTTCTTGAGTCTG
*
40508747 CTCCACTGTAACTTCAGGGAGATAAGACT
1 CTCCACTGCAACTTCAGGGAGATAAGACT
40508776 AGATACGATC
Statistics
Matches: 257, Mismatches: 59, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
40 23 0.09
41 6 0.02
42 3 0.01
43 7 0.03
44 105 0.41
45 110 0.43
46 2 0.01
47 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTCTTGAGTCTG
Found at i:40508627 original size:44 final size:44
Alignment explanation
Indices: 40508575--40508686 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
40508565 GATTTGCTCT
* * *
40508575 CTGCAACTTCAGAGAGATAAGATT-TGTGATTTTAATCCATTCCA
1 CTGCAACTTCAGGGAGATAAGATTAT-TGACTTTAATCCACTCCA
* * **
40508619 CTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATTATTGACTTTAATCCACTCCA
**
40508663 CTAAAACTTCAGGGAGATAAGATT
1 CTGCAACTTCAGGGAGATAAGATT
40508687 CTCCATCTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 56 0.98
45 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGATTATTGACTTTAATCCACTCCA
Found at i:40508822 original size:217 final size:218
Alignment explanation
Indices: 40508489--40508918 Score: 610
Period size: 217 Copynumber: 2.0 Consensus size: 218
40508479 AGTCTGCTCC
* *
40508489 ACTACAACTTCAGGAAGATAAGACTCGCTTTCTTGGGTCTGCTCCACTGCAACTTCAGGGAGATA
1 ACTACAACTTCAGGAAGATAAGACTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGGGAGATA
* * * * * * * *
40508554 AGACCCGATGCGATTTGCTCTCTGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCCATTCCA
66 AGACCAGATACGATCTGCCCTCTGCAACTTCAAAGAGATAAAATCTGTGATTTTAATCCACTCCA
* * *
40508619 CTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTAAAACTTCAGGGAGATAAG
131 CTGCAACTTCAGAGAGATAGGATTATTGGCTTCAATCTGCTCCACTAAAACTTCAAGGAGATAAG
* *
40508684 ATTCTCCATCTTCAGTCTGCCTT
196 ATTCGCCATATTCAGTCTGCCTT
* * * *
40508707 ACTACAACTTCAGGAGGATAAGGCTTGCTTACTT-AGTCTGCTCCACTGTAACTTCAGGGAGATA
1 ACTACAACTTCAGGAAGATAAGACTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGGGAGATA
* * *
40508771 AGACTAGATACGATCTGCCCTCTGGAACTTCAAAGAGATAAAATCTGTGATTTTAATCCGCTCCA
66 AGACCAGATACGATCTGCCCTCTGCAACTTCAAAGAGATAAAATCTGTGATTTTAATCCACTCCA
* * **
40508836 CTGCGACTTCAGAGAGATAGGATTATTGGCTTCAATCTTCTCCACTGCAACTTCAAGGAGATAAG
131 CTGCAACTTCAGAGAGATAGGATTATTGGCTTCAATCTGCTCCACTAAAACTTCAAGGAGATAAG
*
40508901 ATTCGCCTTATTCAGTCT
196 ATTCGCCATATTCAGTCT
40508919 TTTAAATTGC
Statistics
Matches: 185, Mismatches: 27, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
217 155 0.84
218 30 0.16
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (218 bp):
ACTACAACTTCAGGAAGATAAGACTCGCTTACTTGAGTCTGCTCCACTGCAACTTCAGGGAGATA
AGACCAGATACGATCTGCCCTCTGCAACTTCAAAGAGATAAAATCTGTGATTTTAATCCACTCCA
CTGCAACTTCAGAGAGATAGGATTATTGGCTTCAATCTGCTCCACTAAAACTTCAAGGAGATAAG
ATTCGCCATATTCAGTCTGCCTT
Found at i:40509315 original size:44 final size:43
Alignment explanation
Indices: 40509267--40509459 Score: 217
Period size: 44 Copynumber: 4.4 Consensus size: 43
40509257 ATCTGCTATT
* * *
40509267 TTCAACCTACTCCACTGTTGCTCAATGAGATAAGA-TTCACAATC
1 TTCAACCTATTCCACTGTTGC-CAAGGAGATAGGACTT-ACAATC
* *
40509311 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGTTG-CCAAGGAGATAGGACTTACAATC
**
40509355 TTCAACCTATTCCACTGCTAACCAAGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTG-TTGCCAAGGAGATAGGACTTACAATC
* * * * *
40509399 TTCAACCTATTCCACTGCTGACCAGGGAGATAGAACTTATAATT
1 TTCAACCTATTCCACTGTTG-CCAAGGAGATAGGACTTACAATC
*
40509443 TTCAACATATTCCACTG
1 TTCAACCTATTCCACTG
40509460 CTGACCTGGG
Statistics
Matches: 128, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
44 125 0.98
45 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (43 bp):
TTCAACCTATTCCACTGTTGCCAAGGAGATAGGACTTACAATC
Found at i:40509370 original size:88 final size:88
Alignment explanation
Indices: 40509267--40509475 Score: 278
Period size: 88 Copynumber: 2.4 Consensus size: 88
40509257 ATCTGCTATT
* ** *
40509267 TTCAACCTACTCCACTG-TTGCTCAATGAGATAAGA-TTCACAATCTTCAACCTATTCCACTGCT
1 TTCAACCTATTCCACTGCTAAC-CAAGGAGATAAGACTT-ACAATCTTCAACCTATTCCACTGCT
*
40509330 GACCAGGGAGATAGGACTTACAATC
64 GACCAGGGAGATAGAACTTACAATC
*
40509355 TTCAACCTATTCCACTGCTAACCAAGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGA
1 TTCAACCTATTCCACTGCTAACCAAGGAGATAAGACTTACAATCTTCAACCTATTCCACTGCTGA
* *
40509420 CCAGGGAGATAGAACTTATAATT
66 CCAGGGAGATAGAACTTACAATC
* * **
40509443 TTCAACATATTCCACTGCTGACCTGGGAGATAA
1 TTCAACCTATTCCACTGCTAACCAAGGAGATAA
40509476 AGCTTTGTGA
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
88 102 0.96
89 4 0.04
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (88 bp):
TTCAACCTATTCCACTGCTAACCAAGGAGATAAGACTTACAATCTTCAACCTATTCCACTGCTGA
CCAGGGAGATAGAACTTACAATC
Found at i:40509460 original size:44 final size:44
Alignment explanation
Indices: 40509305--40509474 Score: 277
Period size: 44 Copynumber: 3.9 Consensus size: 44
40509295 GATAAGATTC
40509305 ACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
1 ACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
* *
40509349 ACAATCTTCAACCTATTCCACTGCTAACCAAGGAGATAGGACTT
1 ACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
*
40509393 ACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGAACTT
1 ACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
* * * *
40509437 ATAATTTTCAACATATTCCACTGCTGACCTGGGAGATA
1 ACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATA
40509475 AAGCTTTGTG
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 117 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (44 bp):
ACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
Found at i:40510746 original size:6 final size:6
Alignment explanation
Indices: 40510721--40510798 Score: 122
Period size: 6 Copynumber: 12.8 Consensus size: 6
40510711 TGGCCTCTCC
40510721 TTTTCT TATTT-T TCTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT T-TTTCT T-TTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
*
40510770 TTTTCT TTTTCT TTTTCT TTTCCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
40510799 CATCATCATT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
6 62 0.93
7 5 0.07
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:40515632 original size:2 final size:2
Alignment explanation
Indices: 40515625--40515660 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
40515615 TTATAACAAA
*
40515625 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40515661 ACATATGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40515640 original size:12 final size:12
Alignment explanation
Indices: 40515625--40515666 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
40515615 TTATAACAAA
40515625 ATATATATATAC
1 ATATATATATAC
*
40515637 ATATATATATAT
1 ATATATATATAC
40515649 ATATATATTATAAC
1 ATATATA-TAT-AC
40515663 ATAT
1 ATAT
40515667 GTGTTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 18 0.69
13 3 0.12
14 5 0.19
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATATATATAC
Found at i:40515725 original size:2 final size:2
Alignment explanation
Indices: 40515720--40515750 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40515710 AGACATGTGC
40515720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40515751 AAAATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40515797 original size:23 final size:23
Alignment explanation
Indices: 40515771--40515816 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40515761 TATTCATTAG
* *
40515771 AAATAATATACAAATCAATAAAA
1 AAATAATACACAAATCAACAAAA
*
40515794 AAATTATACACAAATCAACAAAA
1 AAATAATACACAAATCAACAAAA
40515817 TAAGAACGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAATACACAAATCAACAAAA
Found at i:40516049 original size:24 final size:22
Alignment explanation
Indices: 40515994--40516056 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 22
40515984 AAATTAAATC
* *
40515994 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGC-ATATCATATCT
40516017 TCTAAGATTGCATATCATATCAT
1 TCTAAGATTGCATATCATATC-T
40516040 ATCTAAGATTGCATATC
1 -TCTAAGATTGCATATC
40516057 CTTGAAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 9 0.25
23 11 0.31
24 16 0.44
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (22 bp):
TCTAAGATTGCATATCATATCT
Found at i:40517180 original size:2 final size:2
Alignment explanation
Indices: 40517173--40517203 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40517163 ACCCATTGAT
40517173 TA 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 TA T
40517204 TAATTAGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40517537 original size:29 final size:30
Alignment explanation
Indices: 40517474--40517553 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
40517464 ATTCAAAAAC
* *
40517474 TATACACGAACTATGATTTAATGTGCAATTG
1 TATACATGAACTTTGATTT-ATGTGCAATTG
*
40517505 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTTTGATTTATGTGCAATTG
*
40517534 TATACATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
40517554 CATACAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 17 0.39
30 10 0.23
31 17 0.39
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.44
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTG
Found at i:40517562 original size:30 final size:29
Alignment explanation
Indices: 40517499--40517562 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
40517489 ATTTAATGTG
** *
40517499 CAATTGTATACATGAACTTTGATTTTGTG
1 CAATTGTATACATGAACTTTGATTTCATA
* *
40517528 CAATTTTATACATGAAATTTTGATTTCATA
1 CAATTGTATACATG-AACTTTGATTTCATA
40517558 CAATT
1 CAATT
40517563 CTTTTAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (29 bp):
CAATTGTATACATGAACTTTGATTTCATA
Found at i:40517740 original size:31 final size:30
Alignment explanation
Indices: 40517705--40517762 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
40517695 AAAATTAAGG
*
40517705 TTTCAAGTATATACTTGAACCACAATTAGAC
1 TTTCAAGTATATAATTGAACCA-AATTAGAC
* * *
40517736 TTTCATGTGTATAATTGCACCAAATTA
1 TTTCAAGTATATAATTGAACCAAATTA
40517763 AAGTTCATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 5 0.22
31 18 0.78
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (30 bp):
TTTCAAGTATATAATTGAACCAAATTAGAC
Found at i:40520884 original size:25 final size:25
Alignment explanation
Indices: 40520856--40520942 Score: 93
Period size: 25 Copynumber: 3.5 Consensus size: 25
40520846 TTACTTTCTT
* *
40520856 GAGCTTCCCAATAAATGGCTCGCAA
1 GAGCTTCCCATTATATGGCTCGCAA
* ** * *
40520881 GAGCTTCCCGTTATACAGCTCACAT
1 GAGCTTCCCATTATATGGCTCGCAA
* *
40520906 GAGCTTCCCGTTATATGGCTCGAAA
1 GAGCTTCCCATTATATGGCTCGCAA
40520931 GAGCTTCCCATT
1 GAGCTTCCCATT
40520943 TACATGTTTG
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (25 bp):
GAGCTTCCCATTATATGGCTCGCAA
Found at i:40522948 original size:18 final size:18
Alignment explanation
Indices: 40522921--40522955 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40522911 ACTTTGAAAT
* *
40522921 TCACTTCACTTCAATATA
1 TCACTACACTTAAATATA
40522939 TCACTACACTTAAATAT
1 TCACTACACTTAAATAT
40522956 GTTATTTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (18 bp):
TCACTACACTTAAATATA
Found at i:40523835 original size:11 final size:11
Alignment explanation
Indices: 40523819--40523858 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
40523809 TATATTAACT
40523819 TAAAATATTAA
1 TAAAATATTAA
40523830 TAAAATATTTAAA
1 TAAAATA-TT-AA
*
40523843 TAAAATATTAT
1 TAAAATATTAA
40523854 TAAAA
1 TAAAA
40523859 AATATTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 13 0.50
12 4 0.15
13 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAAATATTAA
Found at i:40523846 original size:24 final size:25
Alignment explanation
Indices: 40523810--40523870 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
40523800 CCTTCCTTTT
* *
40523810 ATATTAACTTAAAATATTAATAAAAT
1 ATATTAA-ATAAAATATTAATAAAAA
*
40523836 AT-TTAAATAAAATATTATTAAAAA
1 ATATTAAATAAAATATTAATAAAAA
40523860 ATATTAAATAA
1 ATATTAAATAA
40523871 TTTAACCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.55
25 12 0.39
26 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
ATATTAAATAAAATATTAATAAAAA
Found at i:40523860 original size:13 final size:14
Alignment explanation
Indices: 40523824--40523865 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
40523814 TAACTTAAAA
40523824 TATTAATAAAATAT
1 TATTAATAAAATAT
*
40523838 T-TAAATAAAATAT
1 TATTAATAAAATAT
40523851 TATTAA-AAAATAT
1 TATTAATAAAATAT
40523864 TA
1 TA
40523866 AATAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATTAATAAAATAT
Found at i:40524404 original size:18 final size:18
Alignment explanation
Indices: 40524372--40524413 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
40524362 GTTTAGCAAT
40524372 TATTTTTATCATAA-TAA
1 TATTTTTATCATAATTAA
40524389 TAATTTTTAT-AGTAATTAA
1 T-ATTTTTATCA-TAATTAA
40524408 TATTTT
1 TATTTT
40524414 AAAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 16 0.73
19 4 0.18
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TATTTTTATCATAATTAA
Found at i:40524758 original size:3 final size:3
Alignment explanation
Indices: 40524750--40524810 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
40524740 AGGTAAAGTC
40524750 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40524798 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
40524811 CCAATCACTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40526659 original size:25 final size:26
Alignment explanation
Indices: 40526609--40526668 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
40526599 AATTTTCTCG
*
40526609 AAATTTTATCGAGGGTAAAATCGTCA
1 AAATTTTATCCAGGGTAAAATCGTCA
* *
40526635 AAATTTTA-CCAGGGTAGAATTGTCA
1 AAATTTTATCCAGGGTAAAATCGTCA
40526660 AAATTTTAT
1 AAATTTTAT
40526669 TGGGGTGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 22 0.73
26 8 0.27
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (26 bp):
AAATTTTATCCAGGGTAAAATCGTCA
Found at i:40526674 original size:25 final size:25
Alignment explanation
Indices: 40526609--40526680 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
40526599 AATTTTCTCG
40526609 AAATTTTATCGAGGGTAAAATCGTCA
1 AAATTTTATCG-GGGTAAAATCGTCA
* * * *
40526635 AAATTTTACCAGGGTAGAATTGTCA
1 AAATTTTATCGGGGTAAAATCGTCA
*
40526660 AAATTTTATTGGGGTGAAAAT
1 AAATTTTATCGGGGT-AAAAT
40526681 GAAGTGAGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 24 0.65
26 13 0.35
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (25 bp):
AAATTTTATCGGGGTAAAATCGTCA
Found at i:40533253 original size:174 final size:174
Alignment explanation
Indices: 40532963--40533302 Score: 581
Period size: 174 Copynumber: 2.0 Consensus size: 174
40532953 GAAATCCTTA
* * ***
40532963 AGTAAGAAGGGGAAAGACAAGGTTGACGTCGAGTTGCTCGAAATATATGGTTTGTGTTTCTATAA
1 AGTAAGAAGGGGAAAGACAAGGTTGACATCGAGTAGCTCGAAATATACAATTTGTGTTTCTATAA
*
40533028 TCCAAACTAAATTATGAATTATTGCATATTGAATTGATTGTGTATGGTAAGTATTTGAGGTGAGA
66 TCCAAACTAAATTATGAATTATTGCATATTGAATTGATTGTGTATGGTAAGTATTTGAAGTGAGA
* *
40533093 ACTCTTGTACATTTGGACTGACTTGAATTTAATGATAATCCTCG
131 ACTCTTGTACATTTGGACTAAATTGAATTTAATGATAATCCTCG
*
40533137 AGTAAGAAGGGGAAAGACAAGGTTGACATCTAGTAGCTCGAAATATACAATTTGTGTTTCTATAA
1 AGTAAGAAGGGGAAAGACAAGGTTGACATCGAGTAGCTCGAAATATACAATTTGTGTTTCTATAA
40533202 TCCAAACTAAATTATGAATTATTGCATATTGAATTGATTGTGTATGGTAAGTATTTGAAGTGAGA
66 TCCAAACTAAATTATGAATTATTGCATATTGAATTGATTGTGTATGGTAAGTATTTGAAGTGAGA
* *
40533267 ACTCTTGTACATTTGGATTAAATTGAGTTTAATGAT
131 ACTCTTGTACATTTGGACTAAATTGAATTTAATGAT
40533303 GGTTGAAATG
Statistics
Matches: 155, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
174 155 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (174 bp):
AGTAAGAAGGGGAAAGACAAGGTTGACATCGAGTAGCTCGAAATATACAATTTGTGTTTCTATAA
TCCAAACTAAATTATGAATTATTGCATATTGAATTGATTGTGTATGGTAAGTATTTGAAGTGAGA
ACTCTTGTACATTTGGACTAAATTGAATTTAATGATAATCCTCG
Found at i:40533808 original size:18 final size:19
Alignment explanation
Indices: 40533782--40533818 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40533772 AATGACAAAG
40533782 GATGAGAAATGGAA-ATGA
1 GATGAGAAATGGAATATGA
*
40533800 GATGTGAAATGGAATATGA
1 GATGAGAAATGGAATATGA
40533819 AATGGTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (19 bp):
GATGAGAAATGGAATATGA
Found at i:40537714 original size:21 final size:22
Alignment explanation
Indices: 40537668--40537714 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
40537658 TCTTAACGAA
* * *
40537668 ATTCCAATTTCCCTATTTCTTC
1 ATTCCAATTCCCCCATTTCATC
40537690 -TTCC-ATTCCCCCATTTCATC
1 ATTCCAATTCCCCCATTTCATC
40537710 ATTCC
1 ATTCC
40537715 TAACCTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.17, C:0.38, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTCCAATTCCCCCATTTCATC
Found at i:40540740 original size:22 final size:23
Alignment explanation
Indices: 40540715--40540770 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
40540705 TTTAGCACAT
*
40540715 AAGCCA-CACTGATATGTAGCCG
1 AAGCCACCACTGAAATGTAGCCG
* *
40540737 AAGCTACCATTGAAATGTAGCCG
1 AAGCCACCACTGAAATGTAGCCG
*
40540760 AAGCTACCACT
1 AAGCCACCACT
40540771 AATCAATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
AAGCCACCACTGAAATGTAGCCG
Found at i:40545091 original size:27 final size:27
Alignment explanation
Indices: 40545053--40545118 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
40545043 GTATTCTTCG
* *
40545053 TGTTTACTGTCCTGACGGACTACCCTA
1 TGTTTACTGTCCTGACGAACTACCATA
40545080 TGTTTACTGTCCTGACGAACTACCATA
1 TGTTTACTGTCCTGACGAACTACCATA
40545107 TGTTTACTGTCC
1 TGTTTACTGTCC
40545119 CGACTAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (27 bp):
TGTTTACTGTCCTGACGAACTACCATA
Found at i:40546875 original size:19 final size:19
Alignment explanation
Indices: 40546834--40546882 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
40546824 TTCACATCCA
*
40546834 ATTTCACGATTTCATATTAC
1 ATTTCAC-ATCTCATATTAC
* *
40546854 ATTTCACATCTCATTTTCC
1 ATTTCACATCTCATATTAC
*
40546873 ATTTCTCATC
1 ATTTCACATC
40546883 CTTATCAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.47
Consensus pattern (19 bp):
ATTTCACATCTCATATTAC
Found at i:40548065 original size:3 final size:3
Alignment explanation
Indices: 40548057--40548105 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
40548047 TACCATTACC
40548057 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
40548103 TAT
1 TAT
40548106 ACATTTATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Done.