Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 126 of 206
Found at i:37879919 original size:12 final size:11
Alignment explanation
Indices: 37879898--37879930 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
37879888 TTAAACTAAG
37879898 TAAAAAATAAA
1 TAAAAAATAAA
37879909 TAAATAAATAAA
1 TAAA-AAATAAA
37879921 T-AAAAATAAA
1 TAAAAAATAAA
37879931 ACTTTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 6 0.29
12 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:37883575 original size:23 final size:23
Alignment explanation
Indices: 37883543--37883654 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
37883533 CTTTTTGAAC
* *
37883543 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
37883566 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
37883589 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
37883612 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
37883635 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
37883655 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:37883619 original size:46 final size:46
Alignment explanation
Indices: 37883543--37883654 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
37883533 CTTTTTGAAC
* *
37883543 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
37883589 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
37883635 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
37883655 CCCAAAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:37885954 original size:21 final size:21
Alignment explanation
Indices: 37885930--37885973 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
37885920 AAAGTTTGAC
37885930 AAGGTAAACCCTGACTTAGTG
1 AAGGTAAACCCTGACTTAGTG
37885951 AAGGTAAACCCTGACTTAGTG
1 AAGGTAAACCCTGACTTAGTG
37885972 AA
1 AA
37885974 TTCAGATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (21 bp):
AAGGTAAACCCTGACTTAGTG
Found at i:37887191 original size:15 final size:15
Alignment explanation
Indices: 37887167--37887205 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
37887157 ATCCTATTAT
37887167 GAAA-GAAGTTGTGA
1 GAAAGGAAGTTGTGA
*
37887181 GAAAGGAAGTTGTTA
1 GAAAGGAAGTTGTGA
*
37887196 GAAAGTAAGT
1 GAAAGGAAGT
37887206 GATCAAATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (15 bp):
GAAAGGAAGTTGTGA
Found at i:37899465 original size:54 final size:54
Alignment explanation
Indices: 37899406--37899521 Score: 178
Period size: 54 Copynumber: 2.1 Consensus size: 54
37899396 TTAACTAACT
* * * * *
37899406 AACTAGAACTGAATTAAATCTTTATTCCAGCAATTAAATTCTCAAGTTAAAGGA
1 AACTAGAACCGAATTAAATCCTTATTACAGCAATTAAATTCTCAAGCTAAAAGA
*
37899460 AACTAGAACCGAATTAATTCCTTATTACAGCAATTAAATTCTCAAGCTAAAAGA
1 AACTAGAACCGAATTAAATCCTTATTACAGCAATTAAATTCTCAAGCTAAAAGA
37899514 AACTAGAA
1 AACTAGAA
37899522 TTGGGCTCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.28
Consensus pattern (54 bp):
AACTAGAACCGAATTAAATCCTTATTACAGCAATTAAATTCTCAAGCTAAAAGA
Found at i:37903304 original size:10 final size:10
Alignment explanation
Indices: 37903289--37903350 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
37903279 TTTGAACCAT
*
37903289 TACCAATTCG
1 TACCAATTCA
*
37903299 TACCAAATACCA
1 TACC-AAT-TCA
*
37903311 TACCATTTCA
1 TACCAATTCA
37903321 TACCAATTCCA
1 TACCAATT-CA
* *
37903332 TACCATTTCG
1 TACCAATTCA
37903342 TACCAATTC
1 TACCAATTC
37903351 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:37903334 original size:21 final size:21
Alignment explanation
Indices: 37903289--37903351 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37903279 TTTGAACCAT
* *
37903289 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
37903311 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
37903332 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
37903352 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:37904813 original size:20 final size:20
Alignment explanation
Indices: 37904788--37904832 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
37904778 GCGAAAATAC
*
37904788 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
37904808 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
37904827 AAAAGA
1 AAAAGA
37904833 GAATGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:37904880 original size:14 final size:15
Alignment explanation
Indices: 37904851--37904880 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37904841 AGAGAGCGAG
37904851 AAAAGAAAAAGATGA
1 AAAAGAAAAAGATGA
37904866 AAAAGAAAAAG-TGA
1 AAAAGAAAAAGATGA
37904880 A
1 A
37904881 TGAAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAGATGA
Found at i:37909047 original size:10 final size:10
Alignment explanation
Indices: 37909032--37909093 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
37909022 TTTGAACCAT
*
37909032 TACCAATTCG
1 TACCAATTCA
*
37909042 TACCAAATACCA
1 TACC-AAT-TCA
*
37909054 TACCATTTCA
1 TACCAATTCA
37909064 TACCAATTCCA
1 TACCAATT-CA
* *
37909075 TACCATTTCG
1 TACCAATTCA
37909085 TACCAATTC
1 TACCAATTC
37909094 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:37909077 original size:21 final size:21
Alignment explanation
Indices: 37909032--37909094 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37909022 TTTGAACCAT
* *
37909032 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
37909054 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
37909075 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
37909095 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:37917964 original size:59 final size:63
Alignment explanation
Indices: 37917901--37918042 Score: 175
Period size: 70 Copynumber: 2.2 Consensus size: 63
37917891 ATTTAAAGGG
*
37917901 AAGCAAAGACATG-AATTAA-A-T-CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
1 AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
*
37917960 AAGCATAGACATGCATTTAAGGTGATGTTCAACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTA
1 AAGCATAGACATGCAATTAA---GA--TT--ACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTA
37918025 ATGTA
59 ATGTA
37918030 AAGCATAGACATG
1 AAGCATAGACATG
37918043 TATTTAAGGT
Statistics
Matches: 70, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
59 12 0.17
60 5 0.07
64 1 0.01
67 1 0.01
70 51 0.73
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (63 bp):
AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
Found at i:37918005 original size:70 final size:70
Alignment explanation
Indices: 37917922--37918058 Score: 256
Period size: 70 Copynumber: 2.0 Consensus size: 70
37917912 TGAATTAAAT
37917922 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
37917987 TTCAA
66 TTCAA
* *
37917992 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGTATTTAAGGTGCTG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
37918057 TT
66 TT
37918059 GGGCATGCAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.27
Consensus pattern (70 bp):
CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
TTCAA
Found at i:37926251 original size:20 final size:20
Alignment explanation
Indices: 37926226--37926272 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
37926216 AGCTCGTTTC
37926226 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * * *
37926246 CAGCTCATTCGAGTTGAATT
1 CAGCTCACTCGAGCTCAAGT
37926266 CAGCTCA
1 CAGCTCA
37926273 ACCTCAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:37928956 original size:18 final size:18
Alignment explanation
Indices: 37928930--37928988 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
37928920 AAATTGAAAG
* *
37928930 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* *
37928948 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
37928966 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
37928984 AAAAG
1 AAAAG
37928989 TGAGAGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:37928958 original size:6 final size:6
Alignment explanation
Indices: 37928926--37929018 Score: 62
Period size: 6 Copynumber: 15.3 Consensus size: 6
37928916 AAAGAAATTG
* * ** *
37928926 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * *
37928973 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AAGGAAGA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA
37929019 TTGAAAAGGA
Statistics
Matches: 63, Mismatches: 22, Indels: 5
0.70 0.24 0.06
Matches are distributed among these distances:
5 3 0.05
6 54 0.86
7 2 0.03
8 4 0.06
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:37929050 original size:17 final size:18
Alignment explanation
Indices: 37929018--37929051 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37929008 AGAAAAGAAA
*
37929018 ATTGAAAAGGAAATTGAT
1 ATTGAAAAGAAAATTGAT
37929036 ATTGAAAA-AAAATTGA
1 ATTGAAAAGAAAATTGA
37929052 AAAAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (18 bp):
ATTGAAAAGAAAATTGAT
Found at i:37929052 original size:29 final size:29
Alignment explanation
Indices: 37928913--37929073 Score: 89
Period size: 30 Copynumber: 5.6 Consensus size: 29
37928903 GAAAGAGATT
* * *
37928913 GAAAAAGAAATTGAAAGAAAA--CAAAAA
1 GAAAAAGATATTGAAAAAAAATTGAAAAA
* * ** *
37928940 GAAAACGAAAAAGAAAAAGAAATTGCAAAA
1 GAAAAAGATATTGAAAAA-AAATTGAAAAA
* * ** **
37928970 GAAAAAGAAATCGAAAAAGTGAGAGAAAAA
1 GAAAAAGATATTGAAAAA-AAATTGAAAAA
* *
37929000 GAAAAGGA-A--GAAAAGAAAATTGAAAAG
1 GAAAAAGATATTGAAAA-AAAATTGAAAAA
**
37929027 GAAATTGATATTGAAAAAAAATTGAAAAA
1 GAAAAAGATATTGAAAAAAAATTGAAAAA
*
37929056 GAAAAAGATGTTGAAAAA
1 GAAAAAGATATTGAAAAA
37929074 GAAACGAGAG
Statistics
Matches: 101, Mismatches: 26, Indels: 12
0.73 0.19 0.09
Matches are distributed among these distances:
27 31 0.31
28 5 0.05
29 27 0.27
30 38 0.38
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.11
Consensus pattern (29 bp):
GAAAAAGATATTGAAAAAAAATTGAAAAA
Found at i:37938816 original size:20 final size:20
Alignment explanation
Indices: 37938791--37938837 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
37938781 AGCTCGTTTC
37938791 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * * *
37938811 CAGCTCATTCGAGTTGAATT
1 CAGCTCACTCGAGCTCAAGT
37938831 CAGCTCA
1 CAGCTCA
37938838 ACCTCAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:37941970 original size:10 final size:10
Alignment explanation
Indices: 37941955--37942016 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
37941945 TTTGAACCAT
*
37941955 TACCAATTCG
1 TACCAATTCA
*
37941965 TACCAAATACCA
1 TACC-AAT-TCA
*
37941977 TACCATTTCA
1 TACCAATTCA
37941987 TACCAATTCCA
1 TACCAATT-CA
* *
37941998 TACCATTTCG
1 TACCAATTCA
37942008 TACCAATTC
1 TACCAATTC
37942017 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:37942000 original size:21 final size:21
Alignment explanation
Indices: 37941955--37942017 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37941945 TTTGAACCAT
* *
37941955 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
37941977 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
37941998 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
37942018 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:37946050 original size:29 final size:29
Alignment explanation
Indices: 37946013--37946085 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
37946003 TTAGATATTA
* *
37946013 TTAAATATGTCCTAATTAGTTTATGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
37946042 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
37946071 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
37946086 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:37959367 original size:21 final size:21
Alignment explanation
Indices: 37959341--37959403 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37959331 TTGGTATTTG
37959341 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
37959362 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
37959383 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
37959404 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:37960581 original size:30 final size:30
Alignment explanation
Indices: 37960523--37960581 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
37960513 TTGAAAAGGT
* *
37960523 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
37960553 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
37960582 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:37961618 original size:52 final size:53
Alignment explanation
Indices: 37961535--37961636 Score: 152
Period size: 52 Copynumber: 1.9 Consensus size: 53
37961525 TGATTTATGT
* * *
37961535 CTATTAAGTATGTTCTAATTCGAACATCATCAATGCATGTT-TTAAGTCACAC
1 CTATTAACTATGCTCTAATTCGAACAACATCAATGCATGTTATTAAGTCACAC
* *
37961587 CTATTAACTATGCTCTAGTTTGAACAACATCAATGCATGTTATTAAGTCA
1 CTATTAACTATGCTCTAATTCGAACAACATCAATGCATGTTATTAAGTCA
37961637 GACTTCTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 36 0.82
53 8 0.18
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (53 bp):
CTATTAACTATGCTCTAATTCGAACAACATCAATGCATGTTATTAAGTCACAC
Found at i:37964223 original size:23 final size:23
Alignment explanation
Indices: 37964195--37964298 Score: 111
Period size: 23 Copynumber: 4.5 Consensus size: 23
37964185 GGGTTTGTTA
**
37964195 CGAAATGGTAATGTGATTTGGTT
1 CGAAATGGTAATACGATTTGGTT
* *
37964218 CAAAATGGTAATACGATTTGGTA
1 CGAAATGGTAATACGATTTGGTT
* ***
37964241 CGAATTGGTAAGGTGATTTGGTT
1 CGAAATGGTAATACGATTTGGTT
37964264 CGAAATGGTAATACGATTTGGTAT
1 CGAAATGGTAATACGATTTGGT-T
*
37964288 -GAAATGTTAAT
1 CGAAATGGTAAT
37964299 GGTTCAAAAA
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
23 64 0.98
24 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.36
Consensus pattern (23 bp):
CGAAATGGTAATACGATTTGGTT
Found at i:37964250 original size:46 final size:46
Alignment explanation
Indices: 37964188--37964293 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
37964178 CGGTTTTGGG
* *
37964188 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
* *
37964234 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
*
37964280 TTTGGTATGAAATG
1 TTTGGTACGAAATG
37964294 TTAATGGTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
Found at i:37966161 original size:39 final size:38
Alignment explanation
Indices: 37966118--37966227 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 38
37966108 TAAAATATGC
* * * *
37966118 ATTAAAGATGTCCTAAACTATGACATAATTAAAACCCTT
1 ATTAATGATGTTC-AAATTATGACATAATTAAAACCCAT
* * * * *
37966157 ATTAATGTTATTCAGATTATGACAAAATTAAAAACTCAT
1 ATTAATGATGTTCAAATTATGACATAATT-AAAACCCAT
37966196 ATTAATGATGTTCAAATTATGACATAATTAAA
1 ATTAATGATGTTCAAATTATGACATAATTAAA
37966228 TACTCGAACT
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
38 16 0.28
39 41 0.72
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (38 bp):
ATTAATGATGTTCAAATTATGACATAATTAAAACCCAT
Found at i:37967599 original size:18 final size:19
Alignment explanation
Indices: 37967576--37967624 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
37967566 GTTGTAAAGT
*
37967576 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
37967594 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
37967613 TTTAATTTTTAT
1 TTT-ATTTTTAT
37967625 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:37967604 original size:22 final size:22
Alignment explanation
Indices: 37967575--37967624 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
37967565 AGTTGTAAAG
* *
37967575 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
37967596 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
37967619 TTTTAT
1 TTTTAT
37967625 GTAAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:37970364 original size:19 final size:20
Alignment explanation
Indices: 37970327--37970370 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
37970317 GTTCAAACCG
37970327 AATTAATTAGGCTTAG-TTT
1 AATTAATTAGGCTTAGTTTT
*
37970346 AATTAATTATGTCTT-GTTTT
1 AATTAATTA-GGCTTAGTTTT
37970366 AATTA
1 AATTA
37970371 TATGGATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (20 bp):
AATTAATTAGGCTTAGTTTT
Found at i:37971642 original size:20 final size:20
Alignment explanation
Indices: 37971605--37971644 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
37971595 AAAAATTTGA
**
37971605 AAAAAAAATCGAAAAAAAAG
1 AAAAAAAAGAGAAAAAAAAG
37971625 AAAAAAAAGAGAAGAAAAAA
1 AAAAAAAAGAGAA-AAAAAA
37971645 AATTGCATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (20 bp):
AAAAAAAAGAGAAAAAAAAG
Found at i:37973889 original size:7 final size:6
Alignment explanation
Indices: 37973846--37973958 Score: 52
Period size: 6 Copynumber: 17.3 Consensus size: 6
37973836 ATCAAATGAG
*
37973846 AGAAAA AGAAAA GAGCAAAA ATACAAA AG-AAA AGAAAA ATGAAAA A-AAGAA
1 AGAAAA AGAAAA -AG-AAAA AGA-AAA AGAAAA AGAAAA A-GAAAA AGAA-AA
* * * *
37973897 AGAAAA TTCAAAAAA AGAAAA TG-AAA AGAAAG CGACAAA AGAAAAA GATGAAAA
1 AGAAAA ---AGAAAA AGAAAA AGAAAA AGAAAA AGA-AAA AG-AAAA -A-GAAAA
37973951 AGAAAA AG
1 AGAAAA AG
37973959 TGAGTGAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
5 11 0.13
6 33 0.40
7 22 0.27
8 10 0.12
9 6 0.07
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.05
Consensus pattern (6 bp):
AGAAAA
Found at i:37973892 original size:19 final size:18
Alignment explanation
Indices: 37973848--37973923 Score: 55
Period size: 19 Copynumber: 3.8 Consensus size: 18
37973838 CAAATGAGAG
37973848 AAAAAGAAAAGAGCAAAAATA
1 AAAAAG-AAA-AG-AAAAATA
*
37973869 CAAAAGAAAAGAAAAATGA
1 AAAAAGAAAAGAAAAAT-A
*
37973888 AAAAA-AGAAAGAAAATTCAA
1 AAAAAGA-AAAGAAAAAT--A
37973908 AAAAAGAAAATGAAAA
1 AAAAAGAAAA-GAAAA
37973924 GAAAGCGACA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
18 7 0.15
19 16 0.35
20 12 0.26
21 11 0.24
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAATA
Found at i:37981226 original size:10 final size:10
Alignment explanation
Indices: 37981211--37981272 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
37981201 TTTGAACCAT
*
37981211 TACCAATTCG
1 TACCAATTCA
*
37981221 TACCAAATACCA
1 TACC-AAT-TCA
*
37981233 TACCATTTCA
1 TACCAATTCA
37981243 TACCAATTCCA
1 TACCAATT-CA
* *
37981254 TACCATTTCG
1 TACCAATTCA
37981264 TACCAATTC
1 TACCAATTC
37981273 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:37981256 original size:21 final size:21
Alignment explanation
Indices: 37981211--37981273 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37981201 TTTGAACCAT
* *
37981211 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
37981233 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
37981254 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
37981274 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:37983316 original size:10 final size:10
Alignment explanation
Indices: 37983301--37983383 Score: 67
Period size: 10 Copynumber: 7.9 Consensus size: 10
37983291 TTTGAACCAT
*
37983301 TACCAATTCG
1 TACCAATTCA
*
37983311 TACCAAATACCA
1 TACC-AAT-TCA
*
37983323 TACCATTTCA
1 TACCAATTCA
37983333 TACCAATTCCA
1 TACCAATT-CA
* *
37983344 TACCATTTCG
1 TACCAATTCA
37983354 TACCAATTCCA
1 TACCAATT-CA
* *
37983365 TACCATTTCG
1 TACCAATTCA
37983375 TACCAATTC
1 TACCAATTC
37983384 CCAAATACCA
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
10 30 0.53
11 22 0.39
12 5 0.09
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:37983346 original size:21 final size:21
Alignment explanation
Indices: 37983301--37983384 Score: 132
Period size: 21 Copynumber: 4.0 Consensus size: 21
37983291 TTTGAACCAT
* *
37983301 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
37983323 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
37983344 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
37983365 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
37983385 CAAATACCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 46 0.79
22 12 0.21
ACGTcount: A:0.32, C:0.33, G:0.04, T:0.31
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:37983379 original size:42 final size:43
Alignment explanation
Indices: 37983301--37983420 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 43
37983291 TTTGAACCAT
37983301 TACCAATTCGTACCAAATACCATACCATTTCATACCAATTCCA
1 TACCAATTCGTACCAAATACCATACCATTTCATACCAATTCCA
* * *
37983344 TACCATTTCGTACC-AATTCCATACCATTTCGTACCAATTCCCAAA
1 TACCAATTCGTACCAAATACCATACCATTTCATACCAATT-CC--A
**
37983389 TACCAAAACGTACCAAA-ACCAAATACCATTTC
1 TACCAATTCGTACCAAATACC--ATACCATTTC
37983421 TTAATTATCT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
42 23 0.36
43 15 0.23
45 14 0.22
46 2 0.03
47 10 0.16
ACGTcount: A:0.38, C:0.33, G:0.03, T:0.27
Consensus pattern (43 bp):
TACCAATTCGTACCAAATACCATACCATTTCATACCAATTCCA
Found at i:37983744 original size:17 final size:16
Alignment explanation
Indices: 37983724--37983763 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 16
37983714 AAACAAAAAC
37983724 AAAAAAAAATTCGAAAG
1 AAAAAAAAATT-GAAAG
37983741 AAAAAAAAATTGAAAG
1 AAAAAAAAATTGAAAG
37983757 AAAAAAA
1 AAAAAAA
37983764 TTGTATACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.78, C:0.03, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAAAAATTGAAAG
Found at i:37991889 original size:10 final size:10
Alignment explanation
Indices: 37991874--37991935 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
37991864 TTTGAACCAT
*
37991874 TACCAATTCG
1 TACCAATTCA
*
37991884 TACCAAATACCA
1 TACC-AAT-TCA
*
37991896 TACCATTTCA
1 TACCAATTCA
37991906 TACCAATTCCA
1 TACCAATT-CA
* *
37991917 TACCATTTCG
1 TACCAATTCA
37991927 TACCAATTC
1 TACCAATTC
37991936 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:37991919 original size:21 final size:21
Alignment explanation
Indices: 37991874--37991936 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
37991864 TTTGAACCAT
* *
37991874 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
37991896 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
37991917 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
37991937 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:37995112 original size:20 final size:20
Alignment explanation
Indices: 37995084--37995142 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
37995074 GAGAAAAACG
* *
37995084 AAGACGAGCTGAATGAGCTA
1 AAGATGAGCTGAATGAACTA
*
37995104 AAGATGAGCTCAATGAACTA
1 AAGATGAGCTGAATGAACTA
** *
37995124 TGGTTGAGCTGAATGAACT
1 AAGATGAGCTGAATGAACT
37995143 TGAAGTAGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (20 bp):
AAGATGAGCTGAATGAACTA
Found at i:38000869 original size:16 final size:16
Alignment explanation
Indices: 38000837--38000881 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
38000827 CTCACAAGAC
**
38000837 TTTTCACTTCTTTTTT
1 TTTTCACTTCAATTTT
*
38000853 TTTTATACTTCAATTTT
1 TTTT-CACTTCAATTTT
38000870 TTTTCACTTCAA
1 TTTTCACTTCAA
38000882 ATACAATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTCACTTCAATTTT
Found at i:38003078 original size:20 final size:20
Alignment explanation
Indices: 38003053--38003095 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
38003043 AAAAGAAAAG
38003053 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
38003073 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
38003093 AAA
1 AAA
38003096 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:38005363 original size:10 final size:11
Alignment explanation
Indices: 38005343--38005387 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
38005333 ATAGTAGTTT
38005343 CTCGAAAAAAA
1 CTCGAAAAAAA
38005354 CTCGAAAAAAAA
1 CTCG-AAAAAAA
* *
38005366 TTCAAAAAAAA
1 CTCGAAAAAAA
*
38005377 TTCGAAAAAAA
1 CTCGAAAAAAA
38005388 ACTAGTTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (11 bp):
CTCGAAAAAAA
Found at i:38005364 original size:12 final size:12
Alignment explanation
Indices: 38005343--38005390 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
38005333 ATAGTAGTTT
38005343 CTCG-AAAAAAA
1 CTCGAAAAAAAA
38005354 CTCGAAAAAAAA
1 CTCGAAAAAAAA
*
38005366 TTC-AAAAAAAA
1 CTCGAAAAAAAA
*
38005377 TTCGAAAAAAAA
1 CTCGAAAAAAAA
38005389 CT
1 CT
38005391 AGTTTCCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 15 0.45
12 18 0.55
ACGTcount: A:0.65, C:0.15, G:0.06, T:0.15
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:38005449 original size:12 final size:14
Alignment explanation
Indices: 38005426--38005465 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
38005416 GGATATCAAG
38005426 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
*
38005440 AT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
38005453 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
38005466 GAGAGCTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:38006414 original size:18 final size:17
Alignment explanation
Indices: 38006393--38006437 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
38006383 GAGTGACGAG
38006393 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
38006411 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
38006429 AGAGAAAAA
1 AGA-AAAAA
38006438 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:38006442 original size:18 final size:18
Alignment explanation
Indices: 38006391--38006442 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
38006381 AAGAGTGACG
*
38006391 AGAGAAAAAGAAACTGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
38006411 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
38006429 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
38006443 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:38024362 original size:10 final size:10
Alignment explanation
Indices: 38024347--38024408 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
38024337 TTTGAACCAT
*
38024347 TACCAATTCG
1 TACCAATTCA
*
38024357 TACCAAATACCA
1 TACC-AAT-TCA
*
38024369 TACCATTTCA
1 TACCAATTCA
38024379 TACCAATTCCA
1 TACCAATT-CA
* *
38024390 TACCATTTCG
1 TACCAATTCA
38024400 TACCAATTC
1 TACCAATTC
38024409 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:38024392 original size:21 final size:21
Alignment explanation
Indices: 38024347--38024409 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38024337 TTTGAACCAT
* *
38024347 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
38024369 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
38024390 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
38024410 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:38029688 original size:14 final size:14
Alignment explanation
Indices: 38029648--38029692 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
38029638 TTCGTTTCTT
*
38029648 TCCTTTTCTTTTCAC
1 TCCTTTTCTTTT-TC
*
38029663 TCCTTTTGTTTTTC
1 TCCTTTTCTTTTTC
*
38029677 TCTTTTTCTTTTTC
1 TCCTTTTCTTTTTC
38029691 TC
1 TC
38029693 GCTCAATAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (14 bp):
TCCTTTTCTTTTTC
Found at i:38040534 original size:10 final size:10
Alignment explanation
Indices: 38040519--38040580 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
38040509 TTTGAACCAT
*
38040519 TACCAATTCG
1 TACCAATTCA
*
38040529 TACCAAATACCA
1 TACC-AAT-TCA
*
38040541 TACCATTTCA
1 TACCAATTCA
38040551 TACCAATTCCA
1 TACCAATT-CA
* *
38040562 TACCATTTCG
1 TACCAATTCA
38040572 TACCAATTC
1 TACCAATTC
38040581 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:38040564 original size:21 final size:21
Alignment explanation
Indices: 38040519--38040581 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38040509 TTTGAACCAT
* *
38040519 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
38040541 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
38040562 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
38040582 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:38041413 original size:19 final size:19
Alignment explanation
Indices: 38041391--38041439 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
38041381 ATACAAAATA
*
38041391 AAAGAAAAATGAAAAAAAG
1 AAAGAAAAATCAAAAAAAG
*
38041410 AAAGAAAATTCAAAAAAAG
1 AAAGAAAAATCAAAAAAAG
38041429 AGAATGAAAAA
1 A-AA-GAAAAA
38041440 AAAATGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 18 0.72
20 2 0.08
21 5 0.20
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAGAAAAATCAAAAAAAG
Found at i:38043127 original size:11 final size:10
Alignment explanation
Indices: 38043104--38043163 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
38043094 ATTGGGTTAA
38043104 AATTGAGCTG
1 AATTGAGCTG
*
38043114 AATTGATCTCG
1 AATTGAGCT-G
38043125 AA-TGAGCTG
1 AATTGAGCTG
* *
38043134 ACTTGAGCTC
1 AATTGAGCTG
*
38043144 AAGTGAGCTGG
1 AATTGAGCT-G
*
38043155 AAATGAGCT
1 AATTGAGCT
38043164 AAACAGAGCT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 2 0.05
10 26 0.67
11 11 0.28
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (10 bp):
AATTGAGCTG
Found at i:38043130 original size:20 final size:20
Alignment explanation
Indices: 38043107--38043209 Score: 64
Period size: 20 Copynumber: 4.8 Consensus size: 20
38043097 GGGTTAAAAT
*
38043107 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
38043127 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
*
38043147 TGAGCTGGAAATGAGCTAAACAGAG
1 TGAGCT-GAATTGAGCT---CA-AG
* * *
38043172 CTCAACTGACTTGAGCTCAAG
1 -TGAGCTGAATTGAGCTCAAG
*
38043193 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
38043210 AAACAGAGCT
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
19 2 0.03
20 25 0.40
21 18 0.29
22 2 0.03
24 2 0.03
25 10 0.16
26 4 0.06
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.23
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:38043163 original size:21 final size:21
Alignment explanation
Indices: 38043137--38043209 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
38043127 TGAGCTGACT
38043137 TGAGCTCAAGTGAGCTGGAAA
1 TGAGCTCAAGTGAGCTGGAAA
* * **
38043158 TGAGCTAAACAGAGCTCAACT-GACT
1 TGAGCT---CA-AG-TGAGCTGGAAA
38043183 TGAGCTCAAGTGAGCTGGAAA
1 TGAGCTCAAGTGAGCTGGAAA
38043204 TGAGCT
1 TGAGCT
38043210 AAACAGAGCT
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
20 4 0.11
21 16 0.42
22 2 0.05
24 2 0.05
25 10 0.26
26 4 0.11
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.21
Consensus pattern (21 bp):
TGAGCTCAAGTGAGCTGGAAA
Found at i:38043183 original size:46 final size:46
Alignment explanation
Indices: 38043131--38043223 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
38043121 CTCGAATGAG
38043131 CTGACTTGAGCTCAAGTGAGCTGGAAATGAGCTAAACAGAGCTCAA
1 CTGACTTGAGCTCAAGTGAGCTGGAAATGAGCTAAACAGAGCTCAA
38043177 CTGACTTGAGCTCAAGTGAGCTGGAAATGAGCTAAACAGAGCTCAA
1 CTGACTTGAGCTCAAGTGAGCTGGAAATGAGCTAAACAGAGCTCAA
38043223 C
1 C
38043224 GAGAAGAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.19
Consensus pattern (46 bp):
CTGACTTGAGCTCAAGTGAGCTGGAAATGAGCTAAACAGAGCTCAA
Found at i:38043218 original size:21 final size:21
Alignment explanation
Indices: 38043148--38043219 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
38043138 GAGCTCAAGT
38043148 GAGCTGGAAATGAGCTAAACA
1 GAGCTGGAAATGAGCTAAACA
* * **
38043169 GAGCT-CAACTGACTTGAGCTCAAGT
1 GAGCTGGAA---A--TGAGCTAAACA
38043194 GAGCTGGAAATGAGCTAAACA
1 GAGCTGGAAATGAGCTAAACA
38043215 GAGCT
1 GAGCT
38043220 CAACGAGAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 2 0.05
21 18 0.49
23 2 0.05
25 13 0.35
26 2 0.05
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (21 bp):
GAGCTGGAAATGAGCTAAACA
Found at i:38045116 original size:26 final size:26
Alignment explanation
Indices: 38045057--38045106 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
38045047 GCGAACTCTT
38045057 TTTC-TTTTCCACTCGATTTCTTTTCAA
1 TTTCTTTTTCCACTC-ATTTCTTTTC-A
38045084 TTTCTTTTTCCACTC-TTTCTTTT
1 TTTCTTTTTCCACTCATTTCTTTT
38045107 TCTTCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 8 0.36
27 4 0.18
28 10 0.45
ACGTcount: A:0.10, C:0.26, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTCTTTTTCCACTCATTTCTTTTCA
Found at i:38045129 original size:12 final size:12
Alignment explanation
Indices: 38045072--38045140 Score: 56
Period size: 12 Copynumber: 5.8 Consensus size: 12
38045062 TTTCCACTCG
38045072 ATTTC-TTTTCA
1 ATTTCTTTTTCA
38045083 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
38045096 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
38045109 --TTCTCTTTCA
1 ATTTCTTTTTCA
38045119 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
38045131 ATCTCTTTTT
1 ATTTCTTTTT
38045141 GCTTTTCACT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
9 8 0.17
11 5 0.11
12 22 0.47
13 2 0.04
14 1 0.02
15 9 0.19
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:38045193 original size:15 final size:15
Alignment explanation
Indices: 38045170--38045216 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
38045160 TTTTGAAATC
38045170 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
38045185 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
38045200 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
38045216 T
1 T
38045217 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:38050037 original size:23 final size:23
Alignment explanation
Indices: 38050005--38050116 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
38049995 CTTTTTGAAC
* *
38050005 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
38050028 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
38050051 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
38050074 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
38050097 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
38050117 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:38050081 original size:46 final size:46
Alignment explanation
Indices: 38050005--38050116 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
38049995 CTTTTTGAAC
* *
38050005 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
38050051 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
38050097 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
38050117 CCCAAAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:38051771 original size:20 final size:20
Alignment explanation
Indices: 38051743--38051786 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
38051733 TCGTTTCCAT
38051743 CTCACTCGAGCTCAAGTCAG
1 CTCACTCGAGCTCAAGTCAG
* * * *
38051763 CTCATTCGAGTTGAATTCAG
1 CTCACTCGAGCTCAAGTCAG
38051783 CTCA
1 CTCA
38051787 ACCTCAACCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (20 bp):
CTCACTCGAGCTCAAGTCAG
Found at i:38058488 original size:27 final size:27
Alignment explanation
Indices: 38058450--38058511 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
38058440 CTTAATTTAA
38058450 ACACAATTTAATTTGTCTAAACATTAG
1 ACACAATTTAATTTGTCTAAACATTAG
*
38058477 ACACAATTTAATTTTTCTAAACATTAG
1 ACACAATTTAATTTGTCTAAACATTAG
38058504 ACACAATT
1 ACACAATT
38058512 ATGGTGTCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (27 bp):
ACACAATTTAATTTGTCTAAACATTAG
Found at i:38060162 original size:20 final size:19
Alignment explanation
Indices: 38060137--38060174 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
38060127 AACATTTTTG
38060137 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATT-GAGCTCA
38060157 ATTCAGCTCATTGAGCTC
1 ATTCAGCTCATTGAGCTC
38060175 GTTATTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (19 bp):
ATTCAGCTCATTGAGCTCA
Found at i:38060707 original size:59 final size:63
Alignment explanation
Indices: 38060644--38060785 Score: 166
Period size: 70 Copynumber: 2.2 Consensus size: 63
38060634 ATTTAAAGGG
*
38060644 AAGCAAAGACATG-AATTAA-A-T-CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
1 AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
* *
38060703 AAGCATAGACATGCATTTAAGGTGATGTTCAACAGTAGCAATAAAGGAGGTGTTGGCCGAATTTA
1 AAGCATAGACATGCAATTAA---GA--TT--ACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTA
38060768 ATGTA
59 ATGTA
38060773 AAGCATAGACATG
1 AAGCATAGACATG
38060786 TATTTAAGGT
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
59 12 0.17
60 5 0.07
64 1 0.01
67 1 0.01
70 50 0.72
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (63 bp):
AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
Found at i:38060782 original size:70 final size:70
Alignment explanation
Indices: 38060669--38060801 Score: 248
Period size: 70 Copynumber: 1.9 Consensus size: 70
38060659 TTAAATCAGC
38060669 AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTTCA
1 AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTTCA
38060734 ACAGT
66 ACAGT
* *
38060739 AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGTATTTAAGGTGTTGTT
1 AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTT
38060802 GGGCATGCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (70 bp):
AGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATGTTCA
ACAGT
Found at i:38069334 original size:11 final size:12
Alignment explanation
Indices: 38069318--38069348 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38069308 AGAGAGAAAG
38069318 AAAAAAATTGAA
1 AAAAAAATTGAA
38069330 AAAAAAATTGAA
1 AAAAAAATTGAA
38069342 AAAAAAA
1 AAAAAAA
38069349 GAGAAGAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:38075269 original size:21 final size:19
Alignment explanation
Indices: 38075238--38075284 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
38075228 GTATTGGATT
*
38075238 AAAAAAAGAAAGAAAA-TCG
1 AAAAAAAGAAAAAAAAGT-G
38075257 AAAAAAATTGAAAAAAAAGTG
1 AAAAAAA--GAAAAAAAAGTG
38075278 AAAAAAA
1 AAAAAAA
38075285 AATCGAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
21 16 0.67
22 1 0.04
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.09
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAGTG
Found at i:38079861 original size:23 final size:23
Alignment explanation
Indices: 38079829--38079940 Score: 116
Period size: 23 Copynumber: 4.9 Consensus size: 23
38079819 CTTTTTGAAC
* *
38079829 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
38079852 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * * *
38079875 CCTTACTAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
38079898 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
38079921 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
38079941 CCCAAAACCG
Statistics
Matches: 68, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:38079905 original size:46 final size:46
Alignment explanation
Indices: 38079829--38079940 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 46
38079819 CTTTTTGAAC
* *
38079829 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* * *
38079875 CCTTACTAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
38079921 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
38079941 CCCAAAACCG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:38085028 original size:31 final size:31
Alignment explanation
Indices: 38084992--38085061 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
38084982 ACCGTTTCTA
* *
38084992 TGTGTGAACTAAAGGAAA-TGATCAGGCCTT-G
1 TGTGTGAAC-AAACGAAATTGA-AAGGCCTTAG
*
38085023 TGTGTGAACACACGAAATTGAAAGGCCTTAG
1 TGTGTGAACAAACGAAATTGAAAGGCCTTAG
38085054 TGTGTGAA
1 TGTGTGAA
38085062 GGGAACATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (31 bp):
TGTGTGAACAAACGAAATTGAAAGGCCTTAG
Found at i:38089817 original size:18 final size:18
Alignment explanation
Indices: 38089786--38089820 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38089776 AGAAAAGAAA
**
38089786 ATTGAAAAGGAAATTGAG
1 ATTGAAAAAAAAATTGAG
38089804 ATTGAAAAAAAAATTGA
1 ATTGAAAAAAAAATTGA
38089821 AAAAGTAAAA
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:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAAAAAAAAATTGAG
Found at i:38091654 original size:20 final size:20
Alignment explanation
Indices: 38091626--38091669 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
38091616 TCGTTTCCAA
38091626 CTCACTCGAGCTCAAGTCAG
1 CTCACTCGAGCTCAAGTCAG
* * * *
38091646 CTCATTCGAGTTGAATTCAG
1 CTCACTCGAGCTCAAGTCAG
38091666 CTCA
1 CTCA
38091670 ACCTCAACCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (20 bp):
CTCACTCGAGCTCAAGTCAG
Found at i:38094007 original size:10 final size:10
Alignment explanation
Indices: 38093992--38094053 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
38093982 TTTGAACCAT
*
38093992 TACCAATTCG
1 TACCAATTCA
*
38094002 TACCAAATACCA
1 TACC-AAT-TCA
*
38094014 TACCATTTCA
1 TACCAATTCA
38094024 TACCAATTCCA
1 TACCAATT-CA
* *
38094035 TACCATTTCG
1 TACCAATTCA
38094045 TACCAATTC
1 TACCAATTC
38094054 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:38094037 original size:21 final size:21
Alignment explanation
Indices: 38093992--38094054 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38093982 TTTGAACCAT
* *
38093992 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
38094014 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
38094035 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
38094055 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:38107930 original size:23 final size:23
Alignment explanation
Indices: 38107898--38108009 Score: 116
Period size: 23 Copynumber: 4.9 Consensus size: 23
38107888 CTTTTTGAAC
* *
38107898 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
38107921 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * * *
38107944 CCTTACTAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
38107967 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
38107990 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
38108010 CCCAAAACCG
Statistics
Matches: 68, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:38107974 original size:46 final size:46
Alignment explanation
Indices: 38107898--38108009 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 46
38107888 CTTTTTGAAC
* *
38107898 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* * *
38107944 CCTTACTAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
38107990 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
38108010 CCCAAAACCG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:38113787 original size:59 final size:63
Alignment explanation
Indices: 38113724--38113865 Score: 166
Period size: 70 Copynumber: 2.2 Consensus size: 63
38113714 ATTTAAAGGG
* *
38113724 AAGCAAAGACATG-AATTAA-A-T-CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
1 AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTA
*
38113783 AAGCATAGACATGCATTTAAGGTGATGTTCAACAGCAGCAATAAAGGAGGTGTTGGCCGAAATTA
1 AAGCATAGACATGCAATTAA---GA--TT--ACAGCAGCAATAAAGGAGGTGTTGGCCGAAATTA
38113848 ATGTA
59 ATGTA
38113853 AAGCATAGACATG
1 AAGCATAGACATG
38113866 TATTTAAGGT
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
59 12 0.17
60 5 0.07
64 1 0.01
67 1 0.01
70 50 0.72
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.23
Consensus pattern (63 bp):
AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTA
Found at i:38113828 original size:70 final size:70
Alignment explanation
Indices: 38113745--38113881 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
38113735 TGAATTAAAT
*
38113745 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGCATTTAAGGTGATG
38113810 TTCAA
66 TTCAA
* *
38113815 CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGTATTTAAGGTGCTG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGCATTTAAGGTGATG
38113880 TT
66 TT
38113882 GGGCATGCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (70 bp):
CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGCATTTAAGGTGATG
TTCAA
Found at i:38119787 original size:64 final size:64
Alignment explanation
Indices: 38119668--38119792 Score: 139
Period size: 64 Copynumber: 1.9 Consensus size: 64
38119658 TTAAATAAAA
* * *
38119668 ATGCTTCTTAATTGATCTAGTTCCTAGGATTATTTATTGATGCATAACTTAAGTTC-TTTAAATT
1 ATGCTTCTTAATTAAACTAGTTCCTAGGAATATTTATTGAT-CATAACTTAAGTTCATTTAAATT
* * *
38119732 ATGCTTCTTTAATTAAACTAGTTGCT-GGAATATTTATTGCAT-ATAAGTTTTAGTTCATTTA
1 ATGCTTC-TTAATTAAACTAGTTCCTAGGAATATTTATTG-ATCATAA-CTTAAGTTCATTTA
38119793 TTTAAGTAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
63 4 0.08
64 26 0.51
65 21 0.41
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (64 bp):
ATGCTTCTTAATTAAACTAGTTCCTAGGAATATTTATTGATCATAACTTAAGTTCATTTAAATT
Found at i:38121756 original size:14 final size:14
Alignment explanation
Indices: 38121734--38121767 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
38121724 GGACTGAAAT
38121734 ATTAAAAAAATTTG
1 ATTAAAAAAATTTG
38121748 A-TAAAAAAATTTG
1 ATTAAAAAAATTTG
38121761 ATTAAAA
1 ATTAAAA
38121768 GAGAGAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (14 bp):
ATTAAAAAAATTTG
Found at i:38123366 original size:11 final size:10
Alignment explanation
Indices: 38123341--38123401 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
38123331 ACCAATAAAA
38123341 TAAA-TGAGC
1 TAAATTGAGC
*
38123350 TGAATTGTAGC
1 TAAATTG-AGC
38123361 TAAATTGAGC
1 TAAATTGAGC
**
38123371 TCGATTGAGC
1 TAAATTGAGC
38123381 TGAAA-TGAGC
1 T-AAATTGAGC
*
38123391 TCAATTGAGC
1 TAAATTGAGC
38123401 T
1 T
38123402 GGTCGGAGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:38123402 original size:20 final size:20
Alignment explanation
Indices: 38123342--38123402 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
38123332 CCAATAAAAT
*
38123342 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
38123362 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
38123383 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
38123403 GTCGGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:38123411 original size:30 final size:30
Alignment explanation
Indices: 38123346--38123422 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
38123336 TAAAATAAAT
* *
38123346 GAGCTGAATTGTAGCTAAATTGAGCTCGATT
1 GAGCTGAAATG-AGCTAAATTGAGCTCGATG
* *
38123377 GAGCTGAAATGAGCTCAATTGAGCT-GGTCG
1 GAGCTGAAATGAGCTAAATTGAGCTCGAT-G
*
38123407 GAGCTGAAACGAGCTA
1 GAGCTGAAATGAGCTA
38123423 GAAAAGCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 2 0.05
30 27 0.69
31 10 0.26
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (30 bp):
GAGCTGAAATGAGCTAAATTGAGCTCGATG
Found at i:38127044 original size:15 final size:13
Alignment explanation
Indices: 38127010--38127043 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38127000 TCGTGAATTA
*
38127010 AAAAAAATTGTGC
1 AAAAAAATCGTGC
38127023 AAAAAAATCGTGC
1 AAAAAAATCGTGC
38127036 ATAAAAAA
1 A-AAAAAA
38127044 AAAGAGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.18
Consensus pattern (13 bp):
AAAAAAATCGTGC
Found at i:38134458 original size:23 final size:23
Alignment explanation
Indices: 38134426--38134537 Score: 116
Period size: 23 Copynumber: 4.9 Consensus size: 23
38134416 CTTTTTGAAC
* *
38134426 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
38134449 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * * *
38134472 CCTTACAAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
38134495 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
38134518 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
38134538 CCCAAAACCG
Statistics
Matches: 68, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:38134502 original size:46 final size:46
Alignment explanation
Indices: 38134435--38134537 Score: 161
Period size: 46 Copynumber: 2.2 Consensus size: 46
38134425 CCATTAACAT
*
38134435 TTCGTACCAAATCGTATTACCATTTCGAACCAAATCACCTTACAAA
1 TTCGTACCAAATCGTATTACCATTTCGAACCAAATCACATTACAAA
* * *
38134481 TTCGTACCAAATCGTATTACCATTTTGAACCAAATCACATTACCAT
1 TTCGTACCAAATCGTATTACCATTTCGAACCAAATCACATTACAAA
*
38134527 TTCGTAACAAA
1 TTCGTACCAAA
38134538 CCCAAAACCG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (46 bp):
TTCGTACCAAATCGTATTACCATTTCGAACCAAATCACATTACAAA
Found at i:38160219 original size:52 final size:53
Alignment explanation
Indices: 38160136--38160237 Score: 152
Period size: 52 Copynumber: 1.9 Consensus size: 53
38160126 TGATTTATGT
* * *
38160136 CTATTAAGTATGTTCTAATTCGAACATCATCAATGCATGTT-TTAAGTCACAC
1 CTATTAACTATGCTCTAATTCGAACAACATCAATGCATGTTATTAAGTCACAC
* *
38160188 CTATTAACTATGCTCTAGTTTGAACAACATCAATGCATGTTATTAAGTCA
1 CTATTAACTATGCTCTAATTCGAACAACATCAATGCATGTTATTAAGTCA
38160238 GACTTCTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 36 0.82
53 8 0.18
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (53 bp):
CTATTAACTATGCTCTAATTCGAACAACATCAATGCATGTTATTAAGTCACAC
Found at i:38161654 original size:39 final size:38
Alignment explanation
Indices: 38161611--38161720 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 38
38161601 TAAAATATGC
* * * *
38161611 ATTAAAGATGTCCTAAACTATGACATAATTAAAACCCTT
1 ATTAATGATGTTC-AAATTATGACATAATTAAAACCCAT
* * * *
38161650 ATTAATGTTGTTCAGATTATGACAAAATTAAAAACTCAT
1 ATTAATGATGTTCAAATTATGACATAATT-AAAACCCAT
38161689 ATTAATGATGTTCAAATTATGACATAATTAAA
1 ATTAATGATGTTCAAATTATGACATAATTAAA
38161721 TACTCGAACT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
38 16 0.27
39 43 0.73
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (38 bp):
ATTAATGATGTTCAAATTATGACATAATTAAAACCCAT
Found at i:38166384 original size:22 final size:22
Alignment explanation
Indices: 38166353--38166416 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
38166343 CCTTTTTGAA
*
38166353 CCATTTCCATTTCGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
**
38166375 CCATTACCATTTCGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
*
38166397 CCCTTACCGA-TTCGTACCAA
1 CCATTACC-ATTTCGTACCAA
38166417 TTCCCAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.27, C:0.33, G:0.06, T:0.34
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:38171468 original size:29 final size:29
Alignment explanation
Indices: 38171431--38171503 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
38171421 TTAGATATTA
* *
38171431 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
38171460 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
38171489 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
38171504 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:38174270 original size:22 final size:22
Alignment explanation
Indices: 38174239--38174349 Score: 116
Period size: 22 Copynumber: 5.0 Consensus size: 22
38174229 CCTTTTTGAA
*
38174239 CCATTTCCATTTCGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
**
38174261 CCATTACCATTTCGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
*
38174283 CCCTTACCGA-TTCGTACCAAAT
1 CCATTACC-ATTTCGTACCAAAT
* * *
38174305 CGTATTACCATTTTGAACCAAAT
1 C-CATTACCATTTCGTACCAAAT
*
38174328 CACATTACCATTTCGTAACAAA
1 C-CATTACCATTTCGTACCAAA
38174350 CCCAAAACCG
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
22 38 0.54
23 33 0.46
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.33
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:38174370 original size:68 final size:67
Alignment explanation
Indices: 38174245--38174372 Score: 152
Period size: 68 Copynumber: 1.9 Consensus size: 67
38174235 TGAACCATTT
* ** ** *
38174245 CCATTTCGTACCAAATCCATTACCATTTCGTTTCAAATCCCTTACCGATTCGTACCAAATCGTAT
1 CCATTTCGAACCAAATCCATTACCATTTCGTAACAAATCCCAAACCGACTCGTACCAAATCGTAT
38174310 TA
66 TA
*
38174312 CCATTTTGAACCAAATCACATTACCATTTCGTAACAAA-CCCAAAACCGAACTCG-ACCAAAT
1 CCATTTCGAACCAAATC-CATTACCATTTCGTAACAAATCCC-AAACCG-ACTCGTACCAAAT
38174373 TCAAACCAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
67 18 0.35
68 29 0.57
69 4 0.08
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.28
Consensus pattern (67 bp):
CCATTTCGAACCAAATCCATTACCATTTCGTAACAAATCCCAAACCGACTCGTACCAAATCGTAT
TA
Found at i:38176058 original size:14 final size:14
Alignment explanation
Indices: 38176030--38176073 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
38176020 ACGAGATTGT
38176030 AAAAAAAATTC---
1 AAAAAAAATTCGAA
*
38176041 AAAAAAAATTTGAA
1 AAAAAAAATTCGAA
38176055 AAAAAAAATTCGAA
1 AAAAAAAATTCGAA
38176069 AAAAA
1 AAAAA
38176074 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
14 18 0.64
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (14 bp):
AAAAAAAATTCGAA
Found at i:38178182 original size:15 final size:14
Alignment explanation
Indices: 38178146--38178187 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
38178136 TCTATTGAGC
38178146 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
38178160 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
38178174 GAGTGAAAAGAAAA
1 GAG-AAAAAGAAAA
38178188 GGAAAGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:38183346 original size:52 final size:51
Alignment explanation
Indices: 38183217--38183348 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 51
38183207 ATGTGTTCTG
* * *
38183217 CATTTAATAAAGTCATGCATTATGTAACTCTCATGCTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGCTAGTTAAGTTTGCAT
* * * * * *
38183268 CA-CAAATTATGACATACATTATGTAACTCCCATGTTAGTTAAATTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGCTAGTT-AAGTTTGCAT
*
38183319 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTATGTAACTC
38183349 ATTTGTTCAT
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
50 30 0.46
51 13 0.20
52 22 0.34
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATGCTAGTTAAGTTTGCAT
Found at i:38192572 original size:8 final size:9
Alignment explanation
Indices: 38192554--38192580 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
38192544 CAATTCCTCC
38192554 TTTATTTTT
1 TTTATTTTT
38192563 TTTATTTTT
1 TTTATTTTT
38192572 TTTATTTTT
1 TTTATTTTT
38192581 GAATCTGATT
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:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTATTTTT
Found at i:38220407 original size:15 final size:14
Alignment explanation
Indices: 38220371--38220412 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
38220361 TCTATTGAGC
38220371 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
38220385 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
38220399 GAGTGAAAAGAAAA
1 GAG-AAAAAGAAAA
38220413 GGAAAGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:38227368 original size:10 final size:10
Alignment explanation
Indices: 38227353--38227385 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
38227343 TCAGATTCAC
38227353 TCTCTCTTTT
1 TCTCTCTTTT
38227363 TCTCTCTTTT
1 TCTCTCTTTT
38227373 TCT-TCTTGTT
1 TCTCTCTT-TT
38227383 TCT
1 TCT
38227386 GCAACTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (10 bp):
TCTCTCTTTT
Found at i:38228021 original size:25 final size:25
Alignment explanation
Indices: 38227987--38228038 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
38227977 CACTTTGCCA
38227987 TTAACAGTATTCTGTTCAGGGCTCT
1 TTAACAGTATTCTGTTCAGGGCTCT
38228012 TTAACAGTATTCTGTTCAGGGCTCT
1 TTAACAGTATTCTGTTCAGGGCTCT
38228037 TT
1 TT
38228039 GTCAATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (25 bp):
TTAACAGTATTCTGTTCAGGGCTCT
Found at i:38228492 original size:15 final size:15
Alignment explanation
Indices: 38228459--38228492 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38228449 ATACACCAAC
*
38228459 TTTTTTATATATTGA
1 TTTTTTATATATTCA
38228474 TTTTTTATATATTC-
1 TTTTTTATATATTCA
38228488 TTTTT
1 TTTTT
38228493 CTCGAGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTTATATATTCA
Found at i:38231034 original size:63 final size:59
Alignment explanation
Indices: 38230966--38231087 Score: 145
Period size: 63 Copynumber: 2.0 Consensus size: 59
38230956 TATTAATGCG
*
38230966 GTACAAACTAAGACACCATTAATAAACTTAGAACAACTAAACAATCAGACATGTAATAATGTT
1 GTACAAACTAAGACACAATTAATAAACTT--AACAA--AAACAATCAGACATGTAATAATGTT
* * * * * *
38231029 GTACAAAGTAGGACACAATTAATAGACTTAACTAAAATAATTAGACATGTAATAATGTT
1 GTACAAACTAAGACACAATTAATAAACTTAACAAAAACAATCAGACATGTAATAATGTT
38231088 ATATGAAATC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 23 0.44
61 4 0.08
63 25 0.48
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.26
Consensus pattern (59 bp):
GTACAAACTAAGACACAATTAATAAACTTAACAAAAACAATCAGACATGTAATAATGTT
Found at i:38234832 original size:10 final size:10
Alignment explanation
Indices: 38234817--38234878 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
38234807 TTTGAACCAT
*
38234817 TACCAATTCG
1 TACCAATTCA
*
38234827 TACCAAATACCA
1 TACC-AAT-TCA
*
38234839 TACCATTTCA
1 TACCAATTCA
38234849 TACCAATTCCA
1 TACCAATT-CA
* *
38234860 TACCATTTCG
1 TACCAATTCA
38234870 TACCAATTC
1 TACCAATTC
38234879 TCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:38234862 original size:21 final size:21
Alignment explanation
Indices: 38234817--38234878 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
38234807 TTTGAACCAT
* *
38234817 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
38234839 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
38234860 TACCATTTCGTACCAATTC
1 TACCATTTCGTACCAATTC
38234879 TCAAATACCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.67
22 12 0.33
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:38235210 original size:16 final size:16
Alignment explanation
Indices: 38235191--38235243 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
38235181 AAAAAGTTCG
38235191 AAAAAAAAATTTG---
1 AAAAAAAAATTTGAAA
38235204 AAAAAAAAATTTGAAA
1 AAAAAAAAATTTGAAA
*
38235220 GAAAAAAAATTTGAAA
1 AAAAAAAAATTTGAAA
38235236 GAAAAAAA
1 -AAAAAAA
38235244 TTGTATACGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 13 0.38
16 15 0.44
17 6 0.18
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (16 bp):
AAAAAAAAATTTGAAA
Found at i:38235240 original size:12 final size:13
Alignment explanation
Indices: 38235178--38235242 Score: 76
Period size: 13 Copynumber: 4.7 Consensus size: 13
38235168 ATAGGTACGT
* *
38235178 AAAAAAAAGTTCG
1 AAAAAAAAATTTG
38235191 AAAAAAAAATTTG
1 AAAAAAAAATTTG
38235204 AAAAAAAAATTTG
1 AAAAAAAAATTTG
38235217 AAAGAAAAAAAATTTG
1 --A-AAAAAAAATTTG
38235233 AAAGAAAAAA
1 AAA-AAAAAA
38235243 ATTGTATACG
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
13 26 0.57
14 7 0.15
15 1 0.02
16 12 0.26
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.17
Consensus pattern (13 bp):
AAAAAAAAATTTG
Found at i:38239977 original size:23 final size:23
Alignment explanation
Indices: 38239945--38240056 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
38239935 CTTTTTGAAC
* *
38239945 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
38239968 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
38239991 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
38240014 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
38240037 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
38240057 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:38240021 original size:46 final size:46
Alignment explanation
Indices: 38239945--38240056 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
38239935 CTTTTTGAAC
* *
38239945 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
38239991 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
38240037 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
38240057 CCCAAAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:38240371 original size:19 final size:19
Alignment explanation
Indices: 38240334--38240370 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
38240324 AAAAAAGAGT
38240334 TCGAAAAAAAAATTCAAAA
1 TCGAAAAAAAAATTCAAAA
38240353 TCGAAAAAAAAA-TCAAAA
1 TCGAAAAAAAAATTCAAAA
38240371 AAAATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.70, C:0.11, G:0.05, T:0.14
Consensus pattern (19 bp):
TCGAAAAAAAAATTCAAAA
Found at i:38252843 original size:20 final size:20
Alignment explanation
Indices: 38252818--38252862 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
38252808 GCGAAAATAC
*
38252818 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
38252838 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
38252857 AAAAGA
1 AAAAGA
38252863 GAATGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:38258440 original size:23 final size:23
Alignment explanation
Indices: 38258408--38258519 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
38258398 CTTTTTGAAC
* *
38258408 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
38258431 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
38258454 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
38258477 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
38258500 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
38258520 CCCAAAACTG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:38258484 original size:46 final size:46
Alignment explanation
Indices: 38258408--38258519 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
38258398 CTTTTTGAAC
* *
38258408 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
38258454 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
38258500 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
38258520 CCCAAAACTG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:38260311 original size:14 final size:14
Alignment explanation
Indices: 38260283--38260324 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
38260273 GTTTCTTTCC
*
38260283 TTTTCTTTTCACTCT
1 TTTTCTTTT-TCTCT
*
38260298 TTTTGTTTTTCTCT
1 TTTTCTTTTTCTCT
38260312 TTTTCTTTTTCTC
1 TTTTCTTTTTCTC
38260325 GCTCAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTTCTCT
Found at i:38262417 original size:14 final size:13
Alignment explanation
Indices: 38262397--38262428 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
38262387 TATATATATA
38262397 TTTTTTCGAATTT
1 TTTTTTCGAATTT
38262410 TATTTTTCGAATTT
1 T-TTTTTCGAATTT
38262424 TTTTT
1 TTTTT
38262429 ACAATCTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTTTTCGAATTT
Done.