Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 127 of 325
Found at i:39689442 original size:24 final size:24
Alignment explanation
Indices: 39689415--39689461 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
39689405 ATGTTTTTTT
39689415 TTGCTAAATTCTTTATATGACCGG
1 TTGCTAAATTCTTTATATGACCGG
*
39689439 TTGCTAAATTCTTTATGTGACCG
1 TTGCTAAATTCTTTATATGACCG
39689462 ATTAGCTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (24 bp):
TTGCTAAATTCTTTATATGACCGG
Found at i:39691403 original size:24 final size:25
Alignment explanation
Indices: 39691376--39691423 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39691366 ATTTAATTGA
* *
39691376 TTTAGGG-TTAGGGTTTTATAAAAG
1 TTTAGGGTTTAAGGTTTTAGAAAAG
39691400 TTTAGGGTTTAAGGTTTTAGAAAA
1 TTTAGGGTTTAAGGTTTTAGAAAA
39691424 AAAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (25 bp):
TTTAGGGTTTAAGGTTTTAGAAAAG
Found at i:39692099 original size:126 final size:126
Alignment explanation
Indices: 39691873--39692380 Score: 775
Period size: 126 Copynumber: 4.0 Consensus size: 126
39691863 TTTCTGCAAG
* * * *
39691873 AATAATTCTGAGCAGACGTTTCTGGAA-AAATAGTGTCGGAAAATGTTTCAAGCAGGATGCACTG
1 AATAATTCTGAGTAGACGTTTCT-GAACAAATAGTG-CCGAAAACGCTTCAAGCAGGATGCACTG
* * *
39691937 TCAGAAAAATTTCTGGAAAAAACTCCCACGTGGACGCTCTTTCGCTACAGTAGTTCGTGGAAA
64 TCAGAAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
* * *
39692000 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGCCTAAAACACTTCAAGCAGGATGCACTGTT
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
* *
39692065 GGAAAAATTTATGGAAAAAGCTCTCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
66 AGAAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
* * *
39692126 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAATGCTTCAAGCAGGATACACTGTC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
* * * *
39692191 AGCAAAATTTCTAGAAAAAGCTCCTACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
66 AGAAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
* *
39692252 AATAATTCTGAGTAGACGTTTTTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
* * *
39692317 AGCAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACTGTAGTTCGTAGAAA
66 AGAAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
39692378 AAT
1 AAT
39692381 GAGGCTATAA
Statistics
Matches: 348, Mismatches: 32, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
126 318 0.91
127 30 0.09
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (126 bp):
AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGCCGAAAACGCTTCAAGCAGGATGCACTGTC
AGAAAAATTTATGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTGGAAA
Found at i:39695891 original size:18 final size:18
Alignment explanation
Indices: 39695865--39695907 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
39695855 GACTAGGAAA
* *
39695865 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
39695883 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
39695901 AGGATAC
1 AGGATAC
39695908 TCACCTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:39697722 original size:15 final size:15
Alignment explanation
Indices: 39697699--39697730 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39697689 GGATTTTTTT
*
39697699 AATTTAAAAAAATTA
1 AATTAAAAAAAATTA
39697714 AATTAAAAAAAATTA
1 AATTAAAAAAAATTA
39697729 AA
1 AA
39697731 CAAAGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATTAAAAAAAATTA
Found at i:39699390 original size:18 final size:18
Alignment explanation
Indices: 39699367--39699453 Score: 120
Period size: 18 Copynumber: 4.8 Consensus size: 18
39699357 CCAGGTTCGT
39699367 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
***
39699385 ACTATTCACGTATACAAT
1 ACTATTCACGTATACGGC
*
39699403 ACTATTTACGTATACGGC
1 ACTATTCACGTATACGGC
*
39699421 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
*
39699439 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
39699454 AGTAGTTGGG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:39699414 original size:36 final size:36
Alignment explanation
Indices: 39699366--39699453 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
39699356 ACCAGGTTCG
39699366 TACTATTCACGTATACGGCACTATTCACGTATACAA
1 TACTATTCACGTATACGGCACTATTCACGTATACAA
* **
39699402 TACTATTTACGTATACGGCACTATTCACGTATACGG
1 TACTATTCACGTATACGGCACTATTCACGTATACAA
*
39699438 TACTGTTCACGTATAC
1 TACTATTCACGTATAC
39699454 AGTAGTTGGG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (36 bp):
TACTATTCACGTATACGGCACTATTCACGTATACAA
Found at i:39706307 original size:19 final size:20
Alignment explanation
Indices: 39706270--39706307 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39706260 CCTTTAAAAT
39706270 AATAAGATTATTAACAATAA
1 AATAAGATTATTAACAATAA
39706290 AATAAG-TT-TTATACAATA
1 AATAAGATTATTA-ACAATA
39706308 TCCAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 8 0.47
20 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
AATAAGATTATTAACAATAA
Found at i:39719112 original size:21 final size:21
Alignment explanation
Indices: 39719088--39719142 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
39719078 CTTACAAATT
39719088 TTTATTATATATACATTTTAC
1 TTTATTATATATACATTTTAC
**
39719109 TTTA-TATATTATTTATTTTAC
1 TTTATTATA-TATACATTTTAC
*
39719130 TATATTTATATAT
1 TTTA-TTATATAT
39719143 GTAAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 17 0.61
22 3 0.11
23 4 0.14
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTATATATACATTTTAC
Found at i:39719201 original size:24 final size:26
Alignment explanation
Indices: 39719121--39719201 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 26
39719111 TATATATTAT
*
39719121 TTATTTTACTATATTTATATATGTA-AA
1 TTATTATAC-ATATTTAT-TATGTATAA
* *
39719148 TTATTATACATTATTATATTAT-TTTTA
1 TTATTATACA-TATT-TATTATGTATAA
39719175 TTATTA-AC-TATTTATTATGTATAA
1 TTATTATACATATTTATTATGTATAA
39719199 TTA
1 TTA
39719202 ACATTTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
23 6 0.13
24 10 0.22
26 4 0.09
27 22 0.49
28 3 0.07
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (26 bp):
TTATTATACATATTTATTATGTATAA
Found at i:39731273 original size:44 final size:44
Alignment explanation
Indices: 39731210--39731794 Score: 762
Period size: 44 Copynumber: 13.3 Consensus size: 44
39731200 TAGATCACCA
* * * * *
39731210 ATAGCTGATTTGGCATCTCTATATTGTCAGAGAGCAAATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
39731254 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* **
39731298 AT-GACAGATTTGGCATCTCTGTATTGTTAGAGAGCAGATCGAAG
1 ATAG-CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* * * * *
39731342 ATAACAAATTTGGCATCTCTGTGTTGACAGAGAGCAGATCAAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* * *
39731386 ATAGCAGATTTGGCATCTCTGTATTGACAGAGAACAGATCAAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* * *
39731430 ATAGCAGATTTGGCATCTCTGTATTGACGGAGAGCAGATTGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* *
39731474 ATAGCAGATTTGGTGTCTCTGTATTGACGGAGAGCAGATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* * *
39731518 ATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* *
39731562 ATAGCAGATTTGGCGTCTCTGTATTGACGGAGAGCATATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* * *
39731606 ATAACAGATTTGGCGTCTCTGTATTGACGGAGAGCATATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* *
39731650 ATAGTAGATTTGGAGTCTCTGTATTGACAGAGAGCAGATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
* * * *
39731694 ATAGCAGATTTGGCGTCT-TAGTATTGATAAAGAGCAGATTGAAA
1 ATAGCAGATTTGGCGTCTCT-GTATTGACAGAGAGCAGATCGAAG
* * * *
39731738 ATAACAGATTTTGCGTCTCTGTGTTAGA-TGAGGAGCAGATCGAAG
1 ATAGCAGATTTGGCGTCTCTGTATT-GACAGA-GAGCAGATCGAAG
39731783 ATAGCAGATTTG
1 ATAGCAGATTTG
39731795 ACATTTGTAT
Statistics
Matches: 479, Mismatches: 56, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
43 2 0.00
44 453 0.95
45 24 0.05
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (44 bp):
ATAGCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAG
Found at i:39732958 original size:20 final size:20
Alignment explanation
Indices: 39732929--39732973 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
39732919 TGCAGTGGCT
*
39732929 GGAGGCCGGAGGTCTGGGCC
1 GGAGGCCGGAGGTCGGGGCC
*
39732949 GGAGGTCGGAGGTCGGGGCC
1 GGAGGCCGGAGGTCGGGGCC
39732969 GGAGG
1 GGAGG
39732974 GCTTCCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.20, G:0.60, T:0.09
Consensus pattern (20 bp):
GGAGGCCGGAGGTCGGGGCC
Found at i:39733516 original size:28 final size:28
Alignment explanation
Indices: 39733458--39733516 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
39733448 TTAGTCTTTT
*
39733458 TTATATGTATTTAATTTATTTTAAAATA
1 TTATATGTATTTAATTTATTTTAAAACA
39733486 TTATATGTA-TT-ATTTATTTTTATAAACA
1 TTATATGTATTTAATTTA-TTTTA-AAACA
39733514 TTA
1 TTA
39733517 GTTATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 5 0.18
27 7 0.25
28 16 0.57
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
TTATATGTATTTAATTTATTTTAAAACA
Found at i:39733556 original size:17 final size:15
Alignment explanation
Indices: 39733536--39733699 Score: 63
Period size: 13 Copynumber: 11.5 Consensus size: 15
39733526 AAAAATAATG
*
39733536 TATATTAGTTTTATTTA
1 TATATTA-TATTA-TTA
39733553 TATATTATATTATTA
1 TATATTATATTATTA
* *
39733568 TATA-TGT-TTCTTA
1 TATATTATATTATTA
*
39733581 TA-ATT-TTTTATTA
1 TATATTATATTATTA
*
39733594 TATA-TACATT-TTA
1 TATATTATATTATTA
*
39733607 CTTTA-TATATTATT-
1 -TATATTATATTATTA
*
39733621 TATTTTACTA-TATTTA
1 TATATTA-TATTA-TTA
*
39733637 TATATGTAAATTATTA
1 TATAT-TATATTATTA
39733653 TATA-T-TATTATT-
1 TATATTATATTATTA
*
39733665 TAT-TTTTATTATTA
1 TATATTATATTATTA
39733679 -ACTATT-TATTATGTA
1 TA-TATTATATTAT-TA
39733694 TA-ATTA
1 TATATTA
39733700 ACATTTTTTA
Statistics
Matches: 114, Mismatches: 13, Indels: 42
0.67 0.08 0.25
Matches are distributed among these distances:
12 6 0.05
13 35 0.31
14 28 0.25
15 17 0.15
16 17 0.15
17 11 0.10
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (15 bp):
TATATTATATTATTA
Found at i:39733705 original size:20 final size:20
Alignment explanation
Indices: 39733661--39733705 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
39733651 TATATATTAT
* *
39733661 TATTTATTTTTATTATTAAC
1 TATTTATTTGTATAATTAAC
39733681 TATTTATTATGTATAATTAAC
1 TATTTATT-TGTATAATTAAC
39733702 -ATTT
1 TATTT
39733706 TTTAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTTATTTGTATAATTAAC
Found at i:39735329 original size:13 final size:12
Alignment explanation
Indices: 39735311--39735353 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
39735301 TATTCTATAT
39735311 AAATAAAATAAA
1 AAATAAAATAAA
39735323 AATATAACAATAAA
1 AA-ATAA-AATAAA
*
39735337 AAATATTAATAAA
1 AAATA-AAATAAA
39735350 AAAT
1 AAAT
39735354 TATCACTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 2 0.07
13 17 0.63
14 8 0.30
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:39743985 original size:18 final size:18
Alignment explanation
Indices: 39743939--39743974 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39743929 TAATTTATTT
39743939 TATAAATTTTTCTACATA
1 TATAAATTTTTCTACATA
39743957 TATAAATTTTTCTACATA
1 TATAAATTTTTCTACATA
39743975 AGTCATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAATTTTTCTACATA
Found at i:39745851 original size:18 final size:18
Alignment explanation
Indices: 39745830--39745896 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
39745820 AATCGGTTAA
*
39745830 TCAGTAACAATCATTTAT
1 TCAGTAACAGTCATTTAT
* * *
39745848 TCAGTATCAGTCGTTTAG
1 TCAGTAACAGTCATTTAT
*
39745866 TCAGTAACAGTCAATTAT
1 TCAGTAACAGTCATTTAT
*
39745884 TCAGTAGCAGTCA
1 TCAGTAACAGTCA
39745897 GTTTTTAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (18 bp):
TCAGTAACAGTCATTTAT
Found at i:39745870 original size:36 final size:37
Alignment explanation
Indices: 39745830--39745900 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 37
39745820 AATCGGTTAA
* *
39745830 TCAGTAACAATCATTTATTCAGTATCAGTC-GTTTAG
1 TCAGTAACAATCAATTATTCAGTAGCAGTCAGTTTAG
*
39745866 TCAGTAACAGTCAATTATTCAGTAGCAGTCAGTTT
1 TCAGTAACAATCAATTATTCAGTAGCAGTCAGTTT
39745901 TTAATACTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (37 bp):
TCAGTAACAATCAATTATTCAGTAGCAGTCAGTTTAG
Found at i:39746036 original size:6 final size:6
Alignment explanation
Indices: 39746019--39746065 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
39746009 TACACTGTGT
* * *
39746019 CAGTAA CGGTAA CAGTAA CAGTAA TAGTAA CAGTAA TAGTAA CAGTA
1 CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
39746066 GCGGTACACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (6 bp):
CAGTAA
Found at i:39746431 original size:3 final size:3
Alignment explanation
Indices: 39746423--39746448 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39746413 ATTCAATACC
39746423 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
39746449 TACCATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:39752888 original size:20 final size:20
Alignment explanation
Indices: 39752863--39752912 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
39752853 GTAATAGCAG
39752863 TCGACACAAATAGTGTCTCA
1 TCGACACAAATAGTGTCTCA
39752883 TCGACACAAATAGTGTCTCA
1 TCGACACAAATAGTGTCTCA
39752903 TCGACACAAA
1 TCGACACAAA
39752913 GTCGGAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (20 bp):
TCGACACAAATAGTGTCTCA
Found at i:39762842 original size:43 final size:43
Alignment explanation
Indices: 39762793--39762883 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
39762783 TCACACATGT
*
39762793 GGTTCACACCTAGGGGTTCGCACATA-AGGGTTTGC-TCAAGTAA
1 GGTTCACACATA-GGGTTCGCACATATAGGGTTTGCAT-AAGTAA
* * *
39762836 GGTTCACACATAGGGTTTGCACATATAGGTTTTGCATAAGTAG
1 GGTTCACACATAGGGTTCGCACATATAGGGTTTGCATAAGTAA
39762879 GGTTC
1 GGTTC
39762884 GCCTATAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 12 0.29
43 29 0.69
44 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
GGTTCACACATAGGGTTCGCACATATAGGGTTTGCATAAGTAA
Found at i:39764050 original size:21 final size:21
Alignment explanation
Indices: 39763991--39764043 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
39763981 CACAGGCGCA
39763991 GTGTTGCAACATCAAAGGGCC
1 GTGTTGCAACATCAAAGGGCC
39764012 GTGTTGCAACATCAAAGGGCC
1 GTGTTGCAACATCAAAGGGCC
39764033 GTGTTGCAACA
1 GTGTTGCAACA
39764044 CAGAAGGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (21 bp):
GTGTTGCAACATCAAAGGGCC
Found at i:39764477 original size:23 final size:22
Alignment explanation
Indices: 39764441--39764562 Score: 68
Period size: 23 Copynumber: 5.4 Consensus size: 22
39764431 AGATTGCGCA
* *
39764441 ATAATAGTTCCTATAGGCTTCAC
1 ATAATATTTTCTATAGG-TTCAC
* *
39764464 ATGATATTTTCTATAGGGTTCGC
1 ATAATATTTTCTATA-GGTTCAC
* * * *
39764487 ATAACATTTACTATGGGATTCGC
1 ATAATATTTTCTATAGG-TTCAC
* *
39764510 ATAACA-GTTCTTATACGGTTCAC
1 ATAATATTTTC-TATA-GGTTCAC
* *
39764533 ATGATATTTCCTATAAGGTTCAC
1 ATAATATTTTCTAT-AGGTTCAC
39764556 AT-ATATT
1 ATAATATT
39764563 CACTAAGGGC
Statistics
Matches: 77, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
22 9 0.12
23 61 0.79
24 7 0.09
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (22 bp):
ATAATATTTTCTATAGGTTCAC
Found at i:39764843 original size:23 final size:23
Alignment explanation
Indices: 39764813--39764907 Score: 104
Period size: 23 Copynumber: 4.1 Consensus size: 23
39764803 GGTTTACACA
*
39764813 ATAACAGTTCCTATAGGGTTCGC
1 ATAACAGTTCCTATAGGGTTTGC
* *
39764836 ATAACAGTTACTATAAGGTTTGC
1 ATAACAGTTCCTATAGGGTTTGC
39764859 ATAAC-GATTCCTATA-GGTTTGGC
1 ATAACAG-TTCCTATAGGGTTT-GC
* * *
39764882 ATGATATTTCCTATAGGGTTTGC
1 ATAACAGTTCCTATAGGGTTTGC
39764905 ATA
1 ATA
39764908 TACTCATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
22 6 0.10
23 49 0.82
24 5 0.08
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (23 bp):
ATAACAGTTCCTATAGGGTTTGC
Found at i:39768285 original size:14 final size:14
Alignment explanation
Indices: 39768266--39768295 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39768256 AGCTTTTAAT
*
39768266 CTGCTCTACTGCAA
1 CTGCTCCACTGCAA
39768280 CTGCTCCACTGCAA
1 CTGCTCCACTGCAA
39768294 CT
1 CT
39768296 TCAAGGAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.13, T:0.27
Consensus pattern (14 bp):
CTGCTCCACTGCAA
Found at i:39768386 original size:44 final size:43
Alignment explanation
Indices: 39768339--39768670 Score: 242
Period size: 44 Copynumber: 7.5 Consensus size: 43
39768329 TGCTTTACAG
* *
39768339 CAACTTCAGATAGATAAGGATTGTGACTTTGATCTGCTCCACTG
1 CAACTTCAGAGAGATAA-GATTGTGACTTTGATCTGCTCCACTA
* *
39768383 CAACTTCAGAGAGATAAGATCTGCTAACTTT-AGTTTGCTCCACTA
1 CAACTTCAGAGAGATAAGAT-TG-TGACTTTGA-TCTGCTCCACTA
* * * * * *
39768428 CAACTTCAGGGAGATAAGACTTGGGTAATTTTATCTTGCTCTACTG
1 CAACTTCAGAGAGATAAGA-TTGTG-ACTTTGATC-TGCTCCACTA
* *
39768474 CAACTTCAGAGAGATAAGGATTAG-GGCTTCGATCTGCTCCACTA
1 CAACTTCAGAGAGATAA-GATT-GTGACTTTGATCTGCTCCACTA
* * * * *
39768518 CAACTTTAGGGAGATAAGATTTTCTA-TCTTCAGTCTGCTCCACTA
1 CAACTTCAGAGAGATAAGATTGT-GACT-TTGA-TCTGCTCCACTA
* * * * * *
39768563 CAACTTCAGGGAGATAAGACTT-TCTA-TTTCAACCCGCTCAACTA
1 CAACTTCAGAGAGATAAGA-TTGT-GACTTT-GATCTGCTCCACTA
* * *
39768607 CAACTTCAGAGAGATAAGGTTTGTGACTTCGATCTGCTCCACTG
1 CAACTTCAGAGAGATAA-GATTGTGACTTTGATCTGCTCCACTA
*
39768651 CAACTTCAGGGAGATAAGAT
1 CAACTTCAGAGAGATAAGAT
39768671 CTTCAATCTT
Statistics
Matches: 229, Mismatches: 41, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
43 10 0.04
44 99 0.43
45 86 0.38
46 31 0.14
47 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
CAACTTCAGAGAGATAAGATTGTGACTTTGATCTGCTCCACTA
Found at i:39768508 original size:135 final size:133
Alignment explanation
Indices: 39768321--39768686 Score: 484
Period size: 135 Copynumber: 2.7 Consensus size: 133
39768311 TCGTGTATTT
* * * *
39768321 TTTTATCCTGCTTTACAGCAACTTCAGATAGATAAGGATTGTGACTTTGATCTGCTCCACTGCAA
1 TTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAA
* *
39768386 CTTCAGAGAGATAAGATCTGCTAACTTTAGTTTGCTCCACTACAACTTCAGGGAGATAAGACTTG
66 CTTCAGGGAGATAAGATCTTCTAACTTTAGTTTGCTCCACTACAACTTCAGGGAGATAAGACTT-
*
39768451 GGTAA
130 GCT-A
* * *
39768456 TTTTATCTTGCTCTACTGCAACTTCAGAGAGATAAGGATTAG-GGCTTCGATCTGCTCCACTACA
1 TTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAGGATT-GTGACTTCGATCTGCTCCACTGCA
* * * * *
39768520 ACTTTAGGGAGATAAGATTTTCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTT
65 ACTTCAGGGAGATAAGATCTTCTAACTTTAGTTTGCTCCACTACAACTTCAGGGAGATAAGACTT
*
39768585 TCTA
130 GCTA
* * * * * *
39768589 TTTCAACCCGCTCAACTACAACTTCAGAGAGATAAGGTTTGTGACTTCGATCTGCTCCACTGCAA
1 TTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAA
39768654 CTTCAGGGAGATAAGATCTTC-AATCTTTAGTTT
66 CTTCAGGGAGATAAGATCTTCTAA-CTTTAGTTT
39768687 TCTTTCTTGC
Statistics
Matches: 198, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
132 2 0.01
133 81 0.41
134 1 0.01
135 113 0.57
136 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (133 bp):
TTTTATCCTGCTCTACTGCAACTTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAA
CTTCAGGGAGATAAGATCTTCTAACTTTAGTTTGCTCCACTACAACTTCAGGGAGATAAGACTTG
CTA
Found at i:39779423 original size:127 final size:127
Alignment explanation
Indices: 39779252--39779553 Score: 444
Period size: 127 Copynumber: 2.4 Consensus size: 127
39779242 CGTAACCTAG
* * * * * *
39779252 CACGATAGGGCACAATGCCTCGAATTTCCAAACATTGAACATTGCGTTGCTTTAGAATTTATAAA
1 CACGATAGGGCACGATTCCCCGAATTTCCAAACATTGAACATTGCCTTGCTTTAAAATTTAGAAA
* *
39779317 ACACGAGTGAAATTCTAAAGGAATATTCAATTATTTTGAACAAATCG-GAAATCGAAACCCAA
66 ACACAAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAA-CGAGAAATCGAAACCCAA
* * *
39779379 CACGATAGGGCACGATTTCCCGAATTTCCAAACATTGAACATTGCCTTGTTTTAAAATTTGGAAA
1 CACGATAGGGCACGATTCCCCGAATTTCCAAACATTGAACATTGCCTTGCTTTAAAATTTAGAAA
*
39779444 ACACAAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAACGAGAAATCGAAACCCAG
66 ACACAAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAACGAGAAATCGAAACCCAA
* * **
39779506 CACGATAGGACACGATTCCCCAAATTTCCAAACATCAAACATTGCCTT
1 CACGATAGGGCACGATTCCCCGAATTTCCAAACATTGAACATTGCCTT
39779554 CGTTTTAGGG
Statistics
Matches: 157, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
126 2 0.01
127 155 0.99
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (127 bp):
CACGATAGGGCACGATTCCCCGAATTTCCAAACATTGAACATTGCCTTGCTTTAAAATTTAGAAA
ACACAAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAACGAGAAATCGAAACCCAA
Found at i:39781842 original size:24 final size:24
Alignment explanation
Indices: 39781815--39781860 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39781805 TAGGTCTAGG
*
39781815 TTTTGGGCCATTGGGCT-ATGTATT
1 TTTTAGGCC-TTGGGCTGATGTATT
*
39781839 TTTTAGGTCTTGGGCTGATGTA
1 TTTTAGGCCTTGGGCTGATGTA
39781861 ATTGGATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.13, C:0.11, G:0.30, T:0.46
Consensus pattern (24 bp):
TTTTAGGCCTTGGGCTGATGTATT
Found at i:39785143 original size:35 final size:35
Alignment explanation
Indices: 39785097--39785172 Score: 152
Period size: 35 Copynumber: 2.2 Consensus size: 35
39785087 GTCCAATAAC
39785097 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
1 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
39785132 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
1 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
39785167 GATCAA
1 GATCAA
39785173 CTAGAATTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (35 bp):
GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
Found at i:39791164 original size:18 final size:18
Alignment explanation
Indices: 39791141--39791177 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39791131 TAGGGAACTC
39791141 TAAATCCTTCT-GGGATTT
1 TAAATCCTT-TAGGGATTT
39791159 TAAATCCTTTAGGGATTT
1 TAAATCCTTTAGGGATTT
39791177 T
1 T
39791178 TATATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (18 bp):
TAAATCCTTTAGGGATTT
Found at i:39794306 original size:15 final size:14
Alignment explanation
Indices: 39794282--39794313 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
39794272 CCACTATTGG
39794282 TTTCACTAACCCAA
1 TTTCACTAACCCAA
39794296 TTTCTACTAACCCAA
1 TTTC-ACTAACCCAA
39794311 TTT
1 TTT
39794314 TTGGGGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTCACTAACCCAA
Found at i:39811746 original size:20 final size:20
Alignment explanation
Indices: 39811721--39811765 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
39811711 TTTTTCACTA
*
39811721 AATAGAGAAAATTAAAGCAG
1 AATAGAGAAAATGAAAGCAG
39811741 AATAGAGAAAATGAAAGCAG
1 AATAGAGAAAATGAAAGCAG
39811761 AATAG
1 AATAG
39811766 GGTAAGGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.04, G:0.22, T:0.13
Consensus pattern (20 bp):
AATAGAGAAAATGAAAGCAG
Found at i:39813316 original size:7 final size:7
Alignment explanation
Indices: 39813304--39813329 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39813294 TAAAAATTTA
39813304 AATATTC
1 AATATTC
39813311 AATATTC
1 AATATTC
39813318 AATATTC
1 AATATTC
39813325 AATAT
1 AATAT
39813330 GAAATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:39814297 original size:42 final size:42
Alignment explanation
Indices: 39814250--39814333 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
39814240 TGCTAATATG
39814250 TATGAATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
1 TATGAATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
39814292 TATGAATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
1 TATGAATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
39814334 CATTAATATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (42 bp):
TATGAATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
Found at i:39815619 original size:13 final size:13
Alignment explanation
Indices: 39815603--39815632 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
39815593 CCAAAAGTAT
39815603 TTCCCCAATTTAC
1 TTCCCCAATTTAC
39815616 TTCCCCAATTTAC
1 TTCCCCAATTTAC
39815629 TTCC
1 TTCC
39815633 TATGCATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCCCCAATTTAC
Found at i:39815959 original size:11 final size:11
Alignment explanation
Indices: 39815943--39815986 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
39815933 TTGCAAGTTA
39815943 AATTTTATTTT
1 AATTTTATTTT
39815954 AATTTTATTTT
1 AATTTTATTTT
* * *
39815965 AATATTA-CTA
1 AATTTTATTTT
39815975 AATTTTATTTT
1 AATTTTATTTT
39815986 A
1 A
39815987 TTTACTTCTG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
AATTTTATTTT
Found at i:39832268 original size:43 final size:43
Alignment explanation
Indices: 39832212--39832375 Score: 188
Period size: 43 Copynumber: 3.8 Consensus size: 43
39832202 AGCTCATACA
* * * *
39832212 ATGCCAA-ATCCCAGATATGGTCTTACATGTTATCAT-ATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATAT-G
* * * *
39832254 ATGCCACTGTCCCAGAGAGGGTCTTACACGAAATCATAATATG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATATG
* * * *
39832297 ATGCCAATGTCCCAAACATGGTCTTACACGCAATCTTAATATA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATATG
*
39832340 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
39832376 CATCTTGGTA
Statistics
Matches: 102, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 6 0.06
43 92 0.90
44 4 0.04
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATATG
Found at i:39832842 original size:16 final size:16
Alignment explanation
Indices: 39832806--39832845 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
39832796 TTATCTATTA
39832806 TAACTATAATAACCATT
1 TAACTA-AATAACCATT
39832823 TAACTAAACTAACC-TT
1 TAACTAAA-TAACCATT
39832839 TAACTAA
1 TAACTAA
39832846 CATTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (16 bp):
TAACTAAATAACCATT
Found at i:39838547 original size:49 final size:49
Alignment explanation
Indices: 39838494--39838718 Score: 236
Period size: 49 Copynumber: 4.5 Consensus size: 49
39838484 TTGGTACGCA
*
39838494 TAGTAGCCTGCACTTAGTACTACAGATGCAACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACG
* * ** ** * * *
39838543 TAGTAGCCTACACTTAGTACTACACACGTGACCTAACCATCTGATATACG
1 TAGTAGCCTGCACTTAGTACTACACATGCAACC-AATTATCCGGTACACG
* *** * * *
39838593 TAGTAGCCTGCAATTAGTACTACACACGTG-ATTGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACA--TGCAACCAA-TTATCCGGTACACG
* *
39838644 TAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACG
39838693 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
39838719 CGTGACCTCA
Statistics
Matches: 139, Mismatches: 32, Indels: 10
0.77 0.18 0.06
Matches are distributed among these distances:
49 67 0.48
50 39 0.28
51 32 0.23
52 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACG
Found at i:39841131 original size:19 final size:19
Alignment explanation
Indices: 39841096--39841133 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
39841086 TTACAATTTA
*
39841096 AATTTTTATTTTCTTTTCT
1 AATTTTTATTTTATTTTCT
39841115 AATTTTTCA-TTTATTTTCT
1 AATTTTT-ATTTTATTTTCT
39841134 TCTGACAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTATTTTATTTTCT
Found at i:39849794 original size:48 final size:48
Alignment explanation
Indices: 39849723--39850147 Score: 423
Period size: 48 Copynumber: 8.9 Consensus size: 48
39849713 TAAATTGCCA
* * *
39849723 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * * * *
39849771 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * *
39849819 ATTCCATGTCCCAGACATAGTCTTACGCTAGCT-ATCATAAT-GAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCA-CAT-ATCGAGGCCG
* * * * * * *
39849867 ATGTCATGTCCCAGACATGGTCTTATACTAACACACATATCAACGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* *
39849915 ATGCCATGTCCCAGACATGGTCTTACACT-GACTCTCATAAT-GTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTCACAT-ATCGAGGCCG
* * *
39849963 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * *
39850011 ATGCCATGTCCCAGACATGGTCTTACATTAGCACACATATCTACGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * *
39850059 ATGCCATGTCCCATACATGGTCTTACACT-GAATCTCATAAT-GTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTCACAT-ATCGAGGCCG
* *
39850107 ATGCCATGTCCCA-AGCATGGTCTTACACTAGCACACCTATC
1 ATGCCATGTCCCAGA-CATGGTCTTACACTAGCTCACATATC
39850148 ACCCAAATGG
Statistics
Matches: 306, Mismatches: 58, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
47 8 0.03
48 290 0.95
49 8 0.03
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
Found at i:39849987 original size:144 final size:144
Alignment explanation
Indices: 39849723--39850148 Score: 533
Period size: 144 Copynumber: 3.0 Consensus size: 144
39849713 TAAATTGCCA
* * * * * *
39849723 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCTGATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCAGACA
* * * *
39849788 TGGTCTTACACT-AGCTCTCGTCTCAATGT---CGATTCCATGTCCCAGACATAGTCTTACGCTA
66 TGGTCTTACACTGA-CTCTC--AT-AATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTA
* * *
39849849 GCTA-TCATAAT-GAGGCTG
127 GC-ACACAT-ATCAAGGCCG
* * * *
39849867 ATGTCATGTCCCAGACATGGTCTTATACTAACACACATATCAACGTCGATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCAGACA
39849932 TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
66 TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
*
39849997 ACATATCAATGCCG
131 ACATATCAAGGCCG
* * *
39850011 ATGCCATGTCCCAGACATGGTCTTACATTAGCACACATATCTACGCCGATGCCATGTCCCATACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCAGACA
*
39850076 TGGTCTTACACTGAATCTCATAATGTGGCCGATGCCATGTCCCA-AGCATGGTCTTACACTAGCA
66 TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGA-CATGGTCTTACACTAGCA
*
39850140 CACCTATCA
130 CACATATCA
39850149 CCCAAATGGC
Statistics
Matches: 248, Mismatches: 27, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
141 5 0.02
142 1 0.00
143 4 0.02
144 237 0.96
145 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (144 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCAGACA
TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
ACATATCAAGGCCG
Found at i:39855684 original size:22 final size:21
Alignment explanation
Indices: 39855650--39855692 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
39855640 AAAGCCCTAA
39855650 CTTTTTCTCCTTT-TTCTTTCT
1 CTTTTTCTCCTTTCTT-TTTCT
*
39855671 CTTTTTCCTTCTTTCTTTTTCT
1 CTTTTT-CTCCTTTCTTTTTCT
39855693 TAAGTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 11 0.58
23 2 0.11
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
CTTTTTCTCCTTTCTTTTTCT
Found at i:39855685 original size:20 final size:20
Alignment explanation
Indices: 39855652--39855693 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
39855642 AGCCCTAACT
39855652 TTTTCTCCTTTTTCTTTCTC
1 TTTTCTCCTTTTTCTTTCTC
*
39855672 TTTT-TCCTTCTTTCTTTTTC
1 TTTTCTCCTT-TTTCTTTCTC
39855692 TT
1 TT
39855694 AAGTTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCTCCTTTTTCTTTCTC
Found at i:39855783 original size:5 final size:5
Alignment explanation
Indices: 39855773--39855806 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
39855763 AATTATTATA
*
39855773 ATAAT ATAAT ATGAT ATAAT ATAAT ATATAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATA
39855807 CTTAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:39855793 original size:15 final size:14
Alignment explanation
Indices: 39855760--39855804 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
39855750 CTTATTCTTT
*
39855760 TATAAT-TATTATA
1 TATAATATAATATA
39855773 -ATAATATAATATGA
1 TATAATATAATAT-A
39855787 TATAATATAATATA
1 TATAATATAATATA
39855801 TATA
1 TATA
39855805 TACTTAAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.18
13 5 0.18
14 6 0.21
15 12 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TATAATATAATATA
Found at i:39855852 original size:20 final size:19
Alignment explanation
Indices: 39855827--39855874 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
39855817 AAGTATTACA
*
39855827 TATATTATTATATACATATG
1 TATATTATT-TATACACATG
*
39855847 TATATTATTTTTACACATG
1 TATATTATTTATACACATG
39855866 TA-ATTATTT
1 TATATTATTT
39855875 TTACCATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 7 0.27
19 10 0.38
20 9 0.35
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (19 bp):
TATATTATTTATACACATG
Found at i:39855873 original size:18 final size:19
Alignment explanation
Indices: 39855827--39855878 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
39855817 AAGTATTACA
* *
39855827 TATATTATTATATACATATG
1 TATATTATT-TTTACACATG
39855847 TATATTATTTTTACACATG
1 TATATTATTTTTACACATG
39855866 TA-ATTATTTTTAC
1 TATATTATTTTTAC
39855879 CATACACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.37
19 10 0.33
20 9 0.30
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (19 bp):
TATATTATTTTTACACATG
Found at i:39856306 original size:30 final size:30
Alignment explanation
Indices: 39856271--39856333 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
39856261 ACTTTTTTTA
* * *
39856271 TTGTTATTTTTGTTATTATTTTAAAGATAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
*
39856301 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
39856331 TTG
1 TTG
39856334 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:39856433 original size:18 final size:18
Alignment explanation
Indices: 39856412--39856451 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
39856402 GAAATATTTA
*
39856412 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTAT-GTAT
39856430 TTTTGATGTATTATGTAT
1 TTTTGATGTATTATGTAT
39856448 TTTT
1 TTTT
39856452 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATGTAT
Found at i:39857052 original size:21 final size:22
Alignment explanation
Indices: 39857017--39857059 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
39857007 AATTGCTAAT
*
39857017 ACACAACAACCAACACTGTAGAC
1 ACACAACAA-CAACACCGTAGAC
39857040 ACACAACAA-AACACCGTAGA
1 ACACAACAACAACACCGTAGA
39857060 TGGAATCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.51, C:0.33, G:0.09, T:0.07
Consensus pattern (22 bp):
ACACAACAACAACACCGTAGAC
Found at i:39860025 original size:21 final size:23
Alignment explanation
Indices: 39859985--39860028 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
39859975 GGTTATCGTA
39859985 TTAATATTGTTTAATTTTAATGT
1 TTAATATTGTTTAATTTTAATGT
*
39860008 TTAATA-TG-TTATTTTTAATGT
1 TTAATATTGTTTAATTTTAATGT
39860029 AAATGGCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 2 0.10
23 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (23 bp):
TTAATATTGTTTAATTTTAATGT
Found at i:39861626 original size:13 final size:13
Alignment explanation
Indices: 39861591--39861632 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
39861581 AGTATGTATG
39861591 TATATGATTAG-T
1 TATATGATTAGAT
39861603 T-TATGATTAGAT
1 TATATGATTAGAT
*
39861615 TATATTATTAGAT
1 TATATGATTAGAT
*
39861628 GATAT
1 TATAT
39861633 TAAGTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 9 0.35
12 3 0.12
13 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TATATGATTAGAT
Found at i:39874183 original size:45 final size:45
Alignment explanation
Indices: 39874131--39874260 Score: 136
Period size: 45 Copynumber: 2.8 Consensus size: 45
39874121 CCTGAGCTGA
* * * *
39874131 TGAACAGTTAGCTCTAACAAGCTGAAATGGTAAGCTTTTTTCAGT
1 TGAACAGTAAGCTCTAACAAGCTGAAATGGTAAGCTCTATTAAGT
* * *
39874176 TGAACAGTAAGCTC-ATACGAGTTGAAACGGTAAGCTCTATTAAGT
1 TGAACAGTAAGCTCTA-ACAAGCTGAAATGGTAAGCTCTATTAAGT
**
39874221 TGAACAGTAAGCTCTTTCAAGCTGATATATCGGTAAGCTC
1 TGAACAGTAAGCTCTAACAAGCTGA-A-AT-GGTAAGCTC
39874261 ATACGAGCTG
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
44 1 0.01
45 56 0.82
46 1 0.01
47 1 0.01
48 9 0.13
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (45 bp):
TGAACAGTAAGCTCTAACAAGCTGAAATGGTAAGCTCTATTAAGT
Found at i:39874188 original size:22 final size:22
Alignment explanation
Indices: 39874160--39874233 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
39874150 AGCTGAAATG
*
39874160 GTAAGCTTTTTTCAGTTGAACA
1 GTAAGCTTTATTCAGTTGAACA
* * *
39874182 GTAAGC-TCATACGAGTTGAAACG
1 GTAAGCTTTATTC-AGTTG-AACA
* *
39874205 GTAAGCTCTATTAAGTTGAACA
1 GTAAGCTTTATTCAGTTGAACA
39874227 GTAAGCT
1 GTAAGCT
39874234 CTTTCAAGCT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
21 3 0.08
22 21 0.52
23 14 0.35
24 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (22 bp):
GTAAGCTTTATTCAGTTGAACA
Found at i:39874234 original size:22 final size:22
Alignment explanation
Indices: 39874172--39874235 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
39874162 AAGCTTTTTT
39874172 CAGTTGAACAGTAAGCTC-ATA
1 CAGTTGAACAGTAAGCTCTATA
*
39874193 CGAGTTGAAACGGTAAGCTCTATTA
1 C-AGTTG-AACAGTAAGCTCTA-TA
39874218 -AGTTGAACAGTAAGCTCT
1 CAGTTGAACAGTAAGCTCT
39874236 TTCAAGCTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
21 1 0.03
22 17 0.46
23 16 0.43
24 1 0.03
25 2 0.05
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (22 bp):
CAGTTGAACAGTAAGCTCTATA
Found at i:39880255 original size:36 final size:36
Alignment explanation
Indices: 39880208--39880277 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
39880198 TTAGAGTAAT
*
39880208 TCTAAATCCTCCAGAATCCTTTCCATCGACTCCAAG
1 TCTAAATCCTCCAAAATCCTTTCCATCGACTCCAAG
39880244 TCTAAATCCTCCAAAATCCTTTCCATCGACTCCA
1 TCTAAATCCTCCAAAATCCTTTCCATCGACTCCA
39880278 TCCAATATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.29, C:0.37, G:0.06, T:0.29
Consensus pattern (36 bp):
TCTAAATCCTCCAAAATCCTTTCCATCGACTCCAAG
Found at i:39881852 original size:22 final size:22
Alignment explanation
Indices: 39881827--39881871 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
39881817 ACATATTAGA
*
39881827 TTGTAGTTTAACCACCAATGGT
1 TTGTAGATTAACCACCAATGGT
**
39881849 TTGTAGATTAACTGCCAATGGT
1 TTGTAGATTAACCACCAATGGT
39881871 T
1 T
39881872 GTGGACAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (22 bp):
TTGTAGATTAACCACCAATGGT
Found at i:39886856 original size:41 final size:41
Alignment explanation
Indices: 39886799--39886883 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
39886789 ATTTGACCCG
39886799 ATTAAGCAGCGAACAAGTAAAATAGCGGGATAAATTGAAAA
1 ATTAAGCAGCGAACAAGTAAAATAGCGGGATAAATTGAAAA
39886840 ATTAAGCAGCGAACAAGTAAAATAGCGGGATAAATTGAAAA
1 ATTAAGCAGCGAACAAGTAAAATAGCGGGATAAATTGAAAA
39886881 ATT
1 ATT
39886884 GAACACACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (41 bp):
ATTAAGCAGCGAACAAGTAAAATAGCGGGATAAATTGAAAA
Found at i:39891695 original size:35 final size:35
Alignment explanation
Indices: 39891649--39891718 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
39891639 CTCCTCCTTT
**
39891649 AATGAGTCTAGTTGGACTAAAATTCATGTCCTATG
1 AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
39891684 AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
1 AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
39891719 TTAAACTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (35 bp):
AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
Found at i:39895995 original size:6 final size:6
Alignment explanation
Indices: 39895984--39896051 Score: 136
Period size: 6 Copynumber: 11.3 Consensus size: 6
39895974 AATTCATTAC
39895984 TGTAGA TGTAGA TGTAGA TGTAGA TGTAGA TGTAGA TGTAGA TGTAGA
1 TGTAGA TGTAGA TGTAGA TGTAGA TGTAGA TGTAGA TGTAGA TGTAGA
39896032 TGTAGA TGTAGA TGTAGA TG
1 TGTAGA TGTAGA TGTAGA TG
39896052 AATGTGATGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (6 bp):
TGTAGA
Found at i:39896062 original size:9 final size:10
Alignment explanation
Indices: 39895984--39896063 Score: 63
Period size: 12 Copynumber: 7.1 Consensus size: 10
39895974 AATTCATTAC
39895984 TGTAGATGTAGA
1 TGTAGATG-A-A
39895996 TGTAGATGTAGA
1 TGTAGATG-A-A
39896008 TGTAGATGTAGA
1 TGTAGATG-A-A
39896020 TGTAGATGTAGA
1 TGTAGATG-A-A
39896032 TGTAGATGTAGA
1 TGTAGATG-A-A
39896044 TGTAGATGAA
1 TGTAGATGAA
39896054 TGT-GATGAA
1 TGTAGATGAA
39896063 T
1 T
39896064 CCTTTGATCA
Statistics
Matches: 68, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.10
10 4 0.06
11 1 0.01
12 56 0.82
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.34
Consensus pattern (10 bp):
TGTAGATGAA
Found at i:39901012 original size:26 final size:26
Alignment explanation
Indices: 39900983--39901057 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 26
39900973 ATTCAACTGG
39900983 TCCATATCGGTTCTCAATCCAACCAA
1 TCCATATCGGTTCTCAATCCAACCAA
* * * ***
39901009 TCCATACCGGCTCTCAGTCCAATTGA
1 TCCATATCGGTTCTCAATCCAACCAA
** *
39901035 TCCATATATGTTCTCAACCCAAC
1 TCCATATCGGTTCTCAATCCAAC
39901058 TGGTCAATAA
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.28, C:0.35, G:0.09, T:0.28
Consensus pattern (26 bp):
TCCATATCGGTTCTCAATCCAACCAA
Found at i:39906736 original size:25 final size:25
Alignment explanation
Indices: 39906708--39906755 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
39906698 AGCTCCTCTA
* *
39906708 AGCTGAATAATGGGAAGCTCATAAG
1 AGCTAAATAACGGGAAGCTCATAAG
39906733 AGCTAAATAACGGGAAGCTCATA
1 AGCTAAATAACGGGAAGCTCATA
39906756 CAAGCTGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.19
Consensus pattern (25 bp):
AGCTAAATAACGGGAAGCTCATAAG
Found at i:39906761 original size:25 final size:24
Alignment explanation
Indices: 39906707--39906761 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
39906697 AAGCTCCTCT
* *
39906707 AAGCTGAATAATGGGAAGCTCATA
1 AAGCTAAATAACGGGAAGCTCATA
39906731 AGAGCTAAATAACGGGAAGCTCATA
1 A-AGCTAAATAACGGGAAGCTCATA
39906756 CAAGCT
1 -AAGCT
39906762 GTGGTGTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 1 0.04
25 25 0.93
26 1 0.04
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (24 bp):
AAGCTAAATAACGGGAAGCTCATA
Found at i:39910106 original size:20 final size:20
Alignment explanation
Indices: 39910081--39910132 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 20
39910071 TTAAGGTAGA
39910081 ATCAAGAAGAACTCATGAAC
1 ATCAAGAAGAACTCATGAAC
39910101 ATCAAGAAGAACTCATGAAC
1 ATCAAGAAGAACTCATGAAC
39910121 ATCAAGATAGAA
1 ATCAAGA-AGAA
39910133 GCAAACTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.15
Consensus pattern (20 bp):
ATCAAGAAGAACTCATGAAC
Found at i:39910370 original size:26 final size:26
Alignment explanation
Indices: 39910334--39910441 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
39910324 TGAAATGCCC
* *
39910334 ATCATGGAACATTTACCTAAACAATT
1 ATCATGGAACATTTACCTAACCCATT
39910360 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
39910386 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
39910412 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39910438 ATCA
1 ATCA
39910442 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39912423 original size:19 final size:20
Alignment explanation
Indices: 39912399--39912437 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
39912389 TATAATTAAA
39912399 AAAAATT-CTTCAATT-TTTT
1 AAAAATTACTT-AATTATTTT
39912418 AAAAATTACTTAATTATTTT
1 AAAAATTACTTAATTATTTT
39912438 TAATTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAAATTACTTAATTATTTT
Found at i:39912566 original size:7 final size:7
Alignment explanation
Indices: 39912554--39912578 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39912544 TAAATATTTA
39912554 AAATTAT
1 AAATTAT
39912561 AAATTAT
1 AAATTAT
39912568 AAATTAT
1 AAATTAT
39912575 AAAT
1 AAAT
39912579 ATCTTTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTAT
Found at i:39914601 original size:12 final size:12
Alignment explanation
Indices: 39914584--39914608 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39914574 TTGTGTGTTC
39914584 TTTATTTTATTT
1 TTTATTTTATTT
39914596 TTTATTTTATTT
1 TTTATTTTATTT
39914608 T
1 T
39914609 ATTTTCACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:39924538 original size:72 final size:69
Alignment explanation
Indices: 39924462--39924604 Score: 164
Period size: 72 Copynumber: 2.0 Consensus size: 69
39924452 GAAAGAAACG
* *
39924462 TTTGAAAAATCAAAGAACG-TTAGAAAAAGAAG-TATTTGAGAAACCAAAGAAGAGCATTTGAAA
1 TTTGAAAAAACAAAGAACGTTTA-AAAAAGAAGCT-TTTGAGAAACC---GAAGAGCATCTGAAA
39924525 GAAAAGCTT
61 GAAAAGCTT
* * * * *
39924534 TTTGAAAAAACAGAGAGCGTTTAAAAGAGAAGCTTTTGAGAAACCGAAGAGTATCTGAAAGACAA
1 TTTGAAAAAACAAAGAACGTTTAAAAAAGAAGCTTTTGAGAAACCGAAGAGCATCTGAAAGAAAA
39924599 GCTT
66 GCTT
39924603 TT
1 TT
39924605 GAGAGAAGTA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
69 23 0.37
72 35 0.56
73 4 0.06
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (69 bp):
TTTGAAAAAACAAAGAACGTTTAAAAAAGAAGCTTTTGAGAAACCGAAGAGCATCTGAAAGAAAA
GCTT
Found at i:39924551 original size:35 final size:35
Alignment explanation
Indices: 39924509--39924604 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 35
39924499 GAGAAACCAA
39924509 AGAAGAGCATTTGAAAGAAAAGCTTTTTGAAAAAAC
1 AGAAGAGCATTTGAAAGAAAAGCTTTTTG-AAAAAC
* * * *
39924545 AG-AGAGCGTTTAAAAGAGAAGC-TTTTGAGAAAC
1 AGAAGAGCATTTGAAAGAAAAGCTTTTTGAAAAAC
* * * *
39924578 CGAAGAGTATCTGAAAGACAAGCTTTT
1 AGAAGAGCATTTGAAAGAAAAGCTTTT
39924605 GAGAGAAGTA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
33 6 0.12
34 20 0.42
35 20 0.42
36 2 0.04
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (35 bp):
AGAAGAGCATTTGAAAGAAAAGCTTTTTGAAAAAC
Found at i:39928189 original size:96 final size:96
Alignment explanation
Indices: 39928025--39928206 Score: 262
Period size: 96 Copynumber: 1.9 Consensus size: 96
39928015 CTTCTTTTTG
* * *
39928025 CTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTTGTC
1 CTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCCTAGGCTCCTTATC
* *
39928090 TGCTTC-ATCGTTCCCTTCGATGATAGACTTA
66 TGC-TCGATCATTCCCATCGATGATAGACTTA
*
39928121 CTCCTCTTTGCCCTCTTGGCTTC-AGCTTTTCCCTTGCTCGAACCAAGCTTCCTAGGCT-CTGTA
1 CTCCTCTTTGCCCTCTTGGCTTCGA-CTTTACCCTTGCTCGAACCAAGCTTCCTAGGCTCCT-TA
39928184 TCTGCTCGATCATTCCCATCGAT
64 TCTGCTCGATCATTCCCATCGAT
39928207 AACAAACTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
95 5 0.06
96 72 0.94
ACGTcount: A:0.13, C:0.35, G:0.16, T:0.37
Consensus pattern (96 bp):
CTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCCTAGGCTCCTTATC
TGCTCGATCATTCCCATCGATGATAGACTTA
Found at i:39936085 original size:62 final size:60
Alignment explanation
Indices: 39935982--39936114 Score: 185
Period size: 62 Copynumber: 2.2 Consensus size: 60
39935972 AGCCGTATGA
* ** * *
39935982 GGTACACGGGCTAGCACACGGGCATGTGACCAGGCTGTGTGACTCATTGATTTGATAAATAG
1 GGTACACGGGTTAGCACACGGGCATGTGACCAGGCCATGTGACAC-TAG-TTTGATAAATAG
*
39936044 GGTACAAGGGTTAGCACACGGGCATGTGACCAGGCCATGTGACACTAGTTTGATAAATAG
1 GGTACACGGGTTAGCACACGGGCATGTGACCAGGCCATGTGACACTAGTTTGATAAATAG
*
39936104 GGCACACGGGT
1 GGTACACGGGT
39936115 GACCACACAG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 21 0.33
61 2 0.03
62 40 0.63
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (60 bp):
GGTACACGGGTTAGCACACGGGCATGTGACCAGGCCATGTGACACTAGTTTGATAAATAG
Found at i:39941687 original size:52 final size:52
Alignment explanation
Indices: 39941608--39941876 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
39941598 TACTTCTGAT
* *
39941608 CAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
39941661 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
* *
39941713 CAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
* * *
39941765 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
* *
39941817 C------AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
*
39941863 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
39941877 GCTACACTTA
Statistics
Matches: 198, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
46 43 0.22
52 143 0.72
53 12 0.06
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
Found at i:39941884 original size:37 final size:37
Alignment explanation
Indices: 39941840--39941948 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
39941830 GATAGCTTTA
39941840 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
39941877 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
39941914 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
39941949 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:39955607 original size:36 final size:36
Alignment explanation
Indices: 39955567--39955637 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
39955557 AGAGGTGAAA
* *
39955567 TATGATGCCTTAGAGGTAAGTATGAAAGAATAATGT
1 TATGATGCCTTAGAGGCAAGTATGAAAGAACAATGT
* * *
39955603 TATGATGCCTTGGAGGCGAGTATGGAAGAACAATG
1 TATGATGCCTTAGAGGCAAGTATGAAAGAACAATG
39955638 CTAATAGCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.30, T:0.27
Consensus pattern (36 bp):
TATGATGCCTTAGAGGCAAGTATGAAAGAACAATGT
Found at i:39955970 original size:60 final size:59
Alignment explanation
Indices: 39955866--39956003 Score: 136
Period size: 60 Copynumber: 2.3 Consensus size: 59
39955856 ACTCTACAAT
* * ** * * *
39955866 AGTAGATATATAATGAACTCTCCAATAATGTAGTTTACTTAAATGGGTGAACTCTGA-AAG
1 AGTAGATATATAATGAACTCTCCAATAAAG-AGTTCACGCAAATGAGTGAACAC-CATAAG
* *
39955926 TGTAGATATATAATGAACTCTCCGATGAAA-AGGTTCACGCAAATGAGTGAACACCATAAG
1 AGTAGATATATAATGAACTCTCCAAT-AAAGA-GTTCACGCAAATGAGTGAACACCATAAG
*
39955986 AGTAGACATATAATGAAC
1 AGTAGATATATAATGAAC
39956004 GGTTCGCCTG
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 2 0.03
60 60 0.94
61 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (59 bp):
AGTAGATATATAATGAACTCTCCAATAAAGAGTTCACGCAAATGAGTGAACACCATAAG
Found at i:39957968 original size:26 final size:26
Alignment explanation
Indices: 39957939--39957993 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
39957929 TGGAATCATT
*
39957939 CCACTAAAGTACAATGATTGGACATG
1 CCACTAAAGAACAATGATTGGACATG
39957965 CCACTAAAGAACAATGATTGGACATG
1 CCACTAAAGAACAATGATTGGACATG
39957991 CCA
1 CCA
39957994 TTGACTACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (26 bp):
CCACTAAAGAACAATGATTGGACATG
Found at i:39972662 original size:20 final size:20
Alignment explanation
Indices: 39972609--39972666 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
39972599 TGCGTAACAA
* *
39972609 AGGCACCAAAGTGAAAACAG
1 AGGCACCAAAGTGCAATCAG
39972629 AGGCA-CAAATGTGCAATCAG
1 AGGCACCAAA-GTGCAATCAG
*
39972649 AGGCACCGAAGTGCAATC
1 AGGCACCAAAGTGCAATC
39972667 CTGTACAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 4 0.12
20 26 0.79
21 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.26, T:0.10
Consensus pattern (20 bp):
AGGCACCAAAGTGCAATCAG
Found at i:39978179 original size:23 final size:24
Alignment explanation
Indices: 39978152--39978208 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
39978142 AATATTTACG
*
39978152 AAGTTAAGTG-AGTG-ATTAATTTA
1 AAGTTAA-TGAAGTGAATTAACTTA
39978175 AAGTTTAATGAAGTGAATTAACTTA
1 AAG-TTAATGAAGTGAATTAACTTA
39978200 AA-TTAATGA
1 AAGTTAATGA
39978209 TAGTTAGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 12 0.40
24 8 0.27
25 10 0.33
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.37
Consensus pattern (24 bp):
AAGTTAATGAAGTGAATTAACTTA
Found at i:39978194 original size:25 final size:22
Alignment explanation
Indices: 39978162--39978208 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 22
39978152 AAGTTAAGTG
*
39978162 AGTGATTAATTTAAAGTTTAATGA
1 AGTGATTAACTTAAA--TTAATGA
39978186 AGTGAATTAACTTAAATTAATGA
1 AGTG-ATTAACTTAAATTAATGA
39978209 TAGTTAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 4 0.19
25 10 0.48
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (22 bp):
AGTGATTAACTTAAATTAATGA
Found at i:39978617 original size:15 final size:14
Alignment explanation
Indices: 39978585--39978623 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
39978575 AAATAAAAAG
*
39978585 GAAATA-AAAGAAA
1 GAAATAGAATGAAA
39978598 GAAATAGAATGAAGA
1 GAAATAGAATGAA-A
39978613 GAAATAGAATG
1 GAAATAGAATG
39978624 TGGAACGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 5 0.22
15 12 0.52
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.13
Consensus pattern (14 bp):
GAAATAGAATGAAA
Found at i:39978668 original size:21 final size:19
Alignment explanation
Indices: 39978644--39978681 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
39978634 CAGGGAAAGG
39978644 AAGAAAG-A-AAAAGAGAA
1 AAGAAAGAAGAAAAGAGAA
39978661 AAGAAAGAAGAAAAGAGAA
1 AAGAAAGAAGAAAAGAGAA
39978680 AA
1 AA
39978682 TTAAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAGAAAGAAGAAAAGAGAA
Found at i:39979693 original size:51 final size:53
Alignment explanation
Indices: 39979624--39979723 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 53
39979614 TGACTGTTCC
* *
39979624 GGATTCGTTCCGAAGAGGTAC-TCCGTACCTC-ACTGTTACTGTTATTATTCT
1 GGATTCGTTCAGAAGAGGTACTTCCGTACCGCTACTGTTACTGTTATTATTCT
* * **
39979675 GGATTTGTTCAGATGAGGTACTTTGTGTACCGCTACTGTTACTGTTATT
1 GGATTCGTTCAGAAGAGGTAC-TTCCGTACCGCTACTGTTACTGTTATT
39979724 GTTACTGTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 18 0.45
53 7 0.17
54 15 0.38
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (53 bp):
GGATTCGTTCAGAAGAGGTACTTCCGTACCGCTACTGTTACTGTTATTATTCT
Found at i:39979909 original size:18 final size:18
Alignment explanation
Indices: 39979866--39979912 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
39979856 GACTGTCTGC
** *
39979866 TACTGAATAATTGACTGT
1 TACTGAATAAACGACTGA
39979884 TA-TAGAATAAACGACTGA
1 TACT-GAATAAACGACTGA
39979902 TACTGAATAAA
1 TACTGAATAAA
39979913 TGAATATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.30
Consensus pattern (18 bp):
TACTGAATAAACGACTGA
Found at i:39979923 original size:18 final size:19
Alignment explanation
Indices: 39979902--39979942 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
39979892 AAACGACTGA
39979902 TACTGAA-TAAATGAATAT
1 TACTGAATTAAATGAATAT
* *
39979920 TACT-AATTAACTGATTAT
1 TACTGAATTAAATGAATAT
39979938 TACTG
1 TACTG
39979943 TTGACTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
TACTGAATTAAATGAATAT
Found at i:39981512 original size:12 final size:13
Alignment explanation
Indices: 39981478--39981513 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
39981468 TTTCTTCCAT
39981478 GGAGATACTTTCA
1 GGAGATACTTTCA
39981491 GGAGATACTTTCA
1 GGAGATACTTTCA
39981504 GGA-ATACTTT
1 GGAGATACTTT
39981514 AGCACCAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (13 bp):
GGAGATACTTTCA
Found at i:39992986 original size:17 final size:18
Alignment explanation
Indices: 39992958--39992993 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
39992948 GGTAATAAAT
39992958 TTTTTTGAAATTTTTTTA
1 TTTTTTGAAATTTTTTTA
39992976 TTTTTTG-AATTTTTTTA
1 TTTTTTGAAATTTTTTTA
39992993 T
1 T
39992994 AATCTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTTTGAAATTTTTTTA
Found at i:39994238 original size:20 final size:23
Alignment explanation
Indices: 39994209--39994253 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 23
39994199 GACGAGGTAA
*
39994209 TATTATAAT-ATTTT-T-ATTTT
1 TATTAAAATAATTTTCTAATTTT
39994229 TATTAAAATAATTTTCTAATTTT
1 TATTAAAATAATTTTCTAATTTT
39994252 TA
1 TA
39994254 GTTTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 5 0.24
22 1 0.05
23 7 0.33
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTAAAATAATTTTCTAATTTT
Found at i:39996408 original size:46 final size:46
Alignment explanation
Indices: 39996330--39996484 Score: 147
Period size: 46 Copynumber: 3.4 Consensus size: 46
39996320 GCCATAGTGC
* * * *
39996330 CTTTTAACTATGGTCTTACTCACTTTCTGTCATGTTGTCATAATGT
1 CTTTCAACTATGGTCTTATTCATTTTCCGTCATGTTGTCATAATGT
* * *
39996376 CTTTCAACCATGGTCTTATTTATTTTCCGTCATGTT-TCCATAGTGT
1 CTTTCAACTATGGTCTTATTCATTTTCCGTCATGTTGT-CATAATGT
* * * * *
39996422 CTTGCAACTATGGCCTTATACGTTTT-CGAT-ATAG-TGCCATAATGT
1 CTTTCAACTATGGTCTTATTCATTTTCCG-TCAT-GTTGTCATAATGT
39996467 CTTTCAACTATGGTCTTA
1 CTTTCAACTATGGTCTTA
39996485 CACGTTTTTT
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
45 29 0.33
46 59 0.67
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (46 bp):
CTTTCAACTATGGTCTTATTCATTTTCCGTCATGTTGTCATAATGT
Found at i:39996475 original size:45 final size:45
Alignment explanation
Indices: 39996413--39996536 Score: 160
Period size: 45 Copynumber: 2.8 Consensus size: 45
39996403 CGTCATGTTT
* * * *
39996413 CCATAGTGTCTTGCAACTATGGCCTTATACGTTTTCGATATAGTG
1 CCATAGTGTCTTTCAACTATGGTCTTACACGTTTTCGATATAATG
* **
39996458 CCATAATGTCTTTCAACTATGGTCTTACACGTTTTTTATATAATG
1 CCATAGTGTCTTTCAACTATGGTCTTACACGTTTTCGATATAATG
*
39996503 CCATAGT-TCCTTTCAACTATGGTCTTACATGTTT
1 CCATAGTGT-CTTTCAACTATGGTCTTACACGTTT
39996537 GAATCGTGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.01
45 68 0.99
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (45 bp):
CCATAGTGTCTTTCAACTATGGTCTTACACGTTTTCGATATAATG
Found at i:39998973 original size:22 final size:22
Alignment explanation
Indices: 39998948--39998995 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
39998938 GATATCACGG
*
39998948 CATCCACTGACCGATGTCGTGA
1 CATCCACTGACCCATGTCGTGA
*
39998970 CATCCACTGGCCCATGTCGTGA
1 CATCCACTGACCCATGTCGTGA
39998992 CATC
1 CATC
39998996 ATCCTTAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (22 bp):
CATCCACTGACCCATGTCGTGA
Found at i:40002128 original size:25 final size:27
Alignment explanation
Indices: 40002091--40002143 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
40002081 TCAAACATGC
40002091 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
40002117 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
40002143 A
1 A
40002144 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:40003649 original size:26 final size:26
Alignment explanation
Indices: 40003618--40003725 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
40003608 ATGAAATTCC
*
40003618 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
40003644 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
40003670 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
40003696 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40003722 ATCA
1 ATCA
40003726 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40010259 original size:26 final size:26
Alignment explanation
Indices: 40010213--40010265 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
40010203 TCAAACATGC
*
40010213 ATTTAGGTCAATTTAACCCTATGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* *
40010239 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAAC-CCTAGGGGT
40010265 A
1 A
40010266 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:40011781 original size:26 final size:26
Alignment explanation
Indices: 40011750--40011909 Score: 266
Period size: 26 Copynumber: 6.2 Consensus size: 26
40011740 TGAAATTCCC
*
40011750 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
40011776 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
40011802 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
40011828 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
40011854 ATAATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
40011880 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40011906 ATCA
1 ATCA
40011910 ATTTGTATCA
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 123 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40011827 original size:52 final size:52
Alignment explanation
Indices: 40011750--40011909 Score: 293
Period size: 52 Copynumber: 3.1 Consensus size: 52
40011740 TGAAATTCCC
* *
40011750 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
40011802 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
*
40011854 ATAATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
40011906 ATCA
1 ATCA
40011910 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 104 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (52 bp):
ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
Found at i:40013674 original size:54 final size:55
Alignment explanation
Indices: 40013520--40013674 Score: 152
Period size: 55 Copynumber: 2.8 Consensus size: 55
40013510 TTTCCTTTTT
* * * *
40013520 AAACTTACC-ATTGCCATGCCTTGGCATGGTCTTGCATGGGATCTTTGCCTTATCG
1 AAACTTACCAATT-CCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATCA
* ** * * * * * *
40013575 TAGTTTACCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGT-A
1 AAACTTACCAATTCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATCA
* *
40013629 AAACTTACCAATTTCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AAACTTACCAATTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
40013675 AAACCCTAAT
Statistics
Matches: 76, Mismatches: 23, Indels: 3
0.75 0.23 0.03
Matches are distributed among these distances:
54 36 0.47
55 38 0.50
56 2 0.03
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (55 bp):
AAACTTACCAATTCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATCA
Found at i:40020972 original size:53 final size:53
Alignment explanation
Indices: 40020887--40021093 Score: 189
Period size: 53 Copynumber: 3.8 Consensus size: 53
40020877 TTCCTTTTTA
* * * *
40020887 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCATGCCTTATG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
* * * * *
40020940 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATTG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA-TG
** * * * * * * * * *
40020994 TAGTTTATCAATGCAATGTCTTGACATGGTCTTACATGATTTTCTTTCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G
* *
40021049 AACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
40021094 AAACCCTAAT
Statistics
Matches: 118, Mismatches: 33, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
53 44 0.37
54 38 0.32
55 36 0.31
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (53 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
Found at i:40022477 original size:86 final size:86
Alignment explanation
Indices: 40022373--40022546 Score: 321
Period size: 86 Copynumber: 2.0 Consensus size: 86
40022363 AAAGTTTTAC
40022373 ACAACTTTGAGTTATTGTTATTTTTCCCAAAAATAGCGAGAATTTATTTTCTAATTATAAATTAT
1 ACAACTTTGAGTTATTGTTATTTTTCCCAAAAATAGCGAGAATTTATTTTCTAATTATAAATTAT
40022438 ATTTTCTAGGATAACAATTCT
66 ATTTTCTAGGATAACAATTCT
* * *
40022459 ACAATTTTGAGTTATTGTTATTTTTCTCGAAAATAGCGAGAATTTATTTTCTAATTATAAATTAT
1 ACAACTTTGAGTTATTGTTATTTTTCCCAAAAATAGCGAGAATTTATTTTCTAATTATAAATTAT
40022524 ATTTTCTAGGATAACAATTCT
66 ATTTTCTAGGATAACAATTCT
40022545 AC
1 AC
40022547 CAGTTTTTAT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (86 bp):
ACAACTTTGAGTTATTGTTATTTTTCCCAAAAATAGCGAGAATTTATTTTCTAATTATAAATTAT
ATTTTCTAGGATAACAATTCT
Found at i:40024096 original size:60 final size:60
Alignment explanation
Indices: 40024026--40024140 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
40024016 TTTATACCTA
* * * *
40024026 CAATGTTTACACATTTTATCAATTTGATGCTAAATCT-AAAAATTCAACAAATTTAGTCTT
1 CAATGTTTACAAAATTAATC-ATTTAATGCTAAATCTAAAAAATTCAACAAATTTAGTCTT
** * *
40024086 CAATGTTTACAAAATTAATCATTTAATTTTAATTCTAAAAAATTCAATAAATTTA
1 CAATGTTTACAAAATTAATCATTTAATGCTAAATCTAAAAAATTCAACAAATTTA
40024141 ACCCTAAACG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 12 0.26
60 34 0.74
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (60 bp):
CAATGTTTACAAAATTAATCATTTAATGCTAAATCTAAAAAATTCAACAAATTTAGTCTT
Found at i:40030501 original size:3 final size:3
Alignment explanation
Indices: 40030493--40030517 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40030483 CTCGAAAAAC
40030493 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
40030518 GATCAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40031312 original size:11 final size:12
Alignment explanation
Indices: 40031291--40031320 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
40031281 AACGGAGCAT
40031291 CATATATTATTC
1 CATATATTATTC
40031303 CATA-ATTATTC
1 CATATATTATTC
40031314 CATATAT
1 CATATAT
40031321 ATATATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (12 bp):
CATATATTATTC
Found at i:40031675 original size:15 final size:15
Alignment explanation
Indices: 40031657--40031691 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
40031647 TTACTTATAT
40031657 TATATGTATTTATTA
1 TATATGTATTTATTA
40031672 TATATGTATTTATTA
1 TATATGTATTTATTA
40031687 TATAT
1 TATAT
40031692 TATAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (15 bp):
TATATGTATTTATTA
Found at i:40031700 original size:11 final size:11
Alignment explanation
Indices: 40031686--40031720 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
40031676 TGTATTTATT
*
40031686 ATATATTATAA
1 ATATATTAAAA
40031697 ATATATTAAAA
1 ATATATTAAAA
40031708 ATA-ATTAAAA
1 ATATATTAAAA
40031718 ATA
1 ATA
40031721 ATATATGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATATTAAAA
Found at i:40031703 original size:22 final size:24
Alignment explanation
Indices: 40031652--40031704 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
40031642 TTAACTTACT
* *
40031652 TATATTATATGTATTTATTATATA
1 TATATTATATGTATATATTATAAA
*
40031676 TGTATT-TAT-TATATATTATAAA
1 TATATTATATGTATATATTATAAA
40031698 TATATTA
1 TATATTA
40031705 AAAATAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 16 0.67
23 3 0.12
24 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TATATTATATGTATATATTATAAA
Found at i:40035602 original size:28 final size:28
Alignment explanation
Indices: 40035562--40035619 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
40035552 AAAGACAAGC
40035562 TAAAGTGGGGTGAGAGAATGGATTAACA
1 TAAAGTGGGGTGAGAGAATGGATTAACA
40035590 TAAAGTGGGGTGAGAGAATGGATTAACA
1 TAAAGTGGGGTGAGAGAATGGATTAACA
40035618 TA
1 TA
40035620 CACTTGCCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.34, T:0.22
Consensus pattern (28 bp):
TAAAGTGGGGTGAGAGAATGGATTAACA
Found at i:40035917 original size:19 final size:18
Alignment explanation
Indices: 40035877--40035917 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
40035867 AGGGCTATTA
*
40035877 TTTTTTTAGGGTTAGGGT
1 TTTTTTTAGGGTTAGGGG
*
40035895 TTTTGTTTAGGGTTTGGGG
1 TTTT-TTTAGGGTTAGGGG
40035914 TTTT
1 TTTT
40035918 AAGAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.07, C:0.00, G:0.34, T:0.59
Consensus pattern (18 bp):
TTTTTTTAGGGTTAGGGG
Found at i:40039090 original size:38 final size:38
Alignment explanation
Indices: 40039047--40039124 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
40039037 AAAAATTGGA
*
40039047 GTAAGGATGAGAGTTTTAATTTATTTAGTTATACAAGG
1 GTAAGGATAAGAGTTTTAATTTATTTAGTTATACAAGG
40039085 GTAAGGATAAGAGTTTTAATTTATTTAGTTATACAAGG
1 GTAAGGATAAGAGTTTTAATTTATTTAGTTATACAAGG
40039123 GT
1 GT
40039125 GATGCAATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.40
Consensus pattern (38 bp):
GTAAGGATAAGAGTTTTAATTTATTTAGTTATACAAGG
Found at i:40040110 original size:10 final size:10
Alignment explanation
Indices: 40040083--40040121 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
40040073 TTAAATTCTA
40040083 AAAGATAAAT
1 AAAGATAAAT
40040093 ACAA-ATAAAT
1 A-AAGATAAAT
*
40040103 AAAGATAATT
1 AAAGATAAAT
40040113 AAAGATAAA
1 AAAGATAAA
40040122 AAGCTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40040964 original size:99 final size:99
Alignment explanation
Indices: 40040788--40040989 Score: 280
Period size: 99 Copynumber: 2.0 Consensus size: 99
40040778 TTTAAATTTT
** * *
40040788 TTAAATTATTTATTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATAACAACCAA
1 TTAAATTATTTATTTTTGCTTAAGAATATACCGAACCTCTTGACACGAAGAGAGATAACAACCAA
*
40040853 GCACCCCACCCCGGTTACTCAGCCCAACATACTC
66 GCACCCCACCCCGGTTACTCAGCCCAACACACTC
* * * *
40040887 TTAATTTATTATATTTTT-CTTAAGAATATACCGAACCTCTTGACACGAAGAGAGATGATAGCCA
1 TTAAATTATT-TATTTTTGCTTAAGAATATACCGAACCTCTTGACACGAAGAGAGATAACAACCA
** *
40040951 AGCACCTTACCCCGGTTACTCAGCCCAACACATTC
65 AGCACCCCACCCCGGTTACTCAGCCCAACACACTC
40040986 TTAA
1 TTAA
40040990 GTATTTTAAC
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
99 83 0.92
100 7 0.08
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (99 bp):
TTAAATTATTTATTTTTGCTTAAGAATATACCGAACCTCTTGACACGAAGAGAGATAACAACCAA
GCACCCCACCCCGGTTACTCAGCCCAACACACTC
Found at i:40041844 original size:26 final size:26
Alignment explanation
Indices: 40041812--40041862 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
40041802 GGAAGAGTTT
40041812 CCTTAAGCTGGTTTTTTCATATTTTC
1 CCTTAAGCTGGTTTTTTCATATTTTC
40041838 CCTTAAGCTGGTTTTTTCATATTTT
1 CCTTAAGCTGGTTTTTTCATATTTT
40041863 TACTTCAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.55
Consensus pattern (26 bp):
CCTTAAGCTGGTTTTTTCATATTTTC
Found at i:40043394 original size:83 final size:83
Alignment explanation
Indices: 40043255--40043422 Score: 327
Period size: 83 Copynumber: 2.0 Consensus size: 83
40043245 CATCTCTTTG
40043255 GAATTTTATTCTAATATGTTGGAATGAAGCCGATGGTAAAAATAAATAAATAAATAAAAATATTC
1 GAATTTTATTCTAATATGTTGGAATGAAGCCGATGGTAAAAATAAATAAATAAATAAAAATATTC
40043320 GAGGTTCAACCGAATTGT
66 GAGGTTCAACCGAATTGT
*
40043338 GAATTTTATTCTAATATGTTGGAATGAAGTCGATGGTAAAAATAAATAAATAAATAAAAATATTC
1 GAATTTTATTCTAATATGTTGGAATGAAGCCGATGGTAAAAATAAATAAATAAATAAAAATATTC
40043403 GAGGTTCAACCGAATTGT
66 GAGGTTCAACCGAATTGT
40043421 GA
1 GA
40043423 TTCTGAGAAG
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (83 bp):
GAATTTTATTCTAATATGTTGGAATGAAGCCGATGGTAAAAATAAATAAATAAATAAAAATATTC
GAGGTTCAACCGAATTGT
Found at i:40045586 original size:50 final size:50
Alignment explanation
Indices: 40045505--40045634 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
40045495 GGACCATGAC
* *
40045505 AACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGT
1 AACAAGTGATAAGTG-TAGCTTCGGCTACACTTATCTGATCAAGGACAAAT
40045556 GAA-AA-TGATAAGTAGTAGCTTCGGCTACACTTATCTGATCAAGGACAAAT
1 -AACAAGTGATAAGT-GTAGCTTCGGCTACACTTATCTGATCAAGGACAAAT
*
40045606 AACAAGTGAAAAGTGGTAGCTTCGGCTAC
1 AACAAGTGATAAGT-GTAGCTTCGGCTAC
40045635 CTGATCAGTG
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
49 2 0.03
50 43 0.61
51 24 0.34
52 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (50 bp):
AACAAGTGATAAGTGTAGCTTCGGCTACACTTATCTGATCAAGGACAAAT
Found at i:40045648 original size:31 final size:31
Alignment explanation
Indices: 40045610--40045758 Score: 208
Period size: 31 Copynumber: 4.8 Consensus size: 31
40045600 ACAAATAACA
40045610 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
** * *
40045641 AGTGAAAAGTGGTAGCTTTTGTTACCTGGTC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
40045672 AGTGAAAAATGGTAGCTCCGACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
40045703 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
40045734 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
40045759 AAGTGACAAG
Statistics
Matches: 103, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 103 1.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:40045952 original size:49 final size:48
Alignment explanation
Indices: 40045776--40045949 Score: 194
Period size: 47 Copynumber: 3.7 Consensus size: 48
40045766 AAGTGACTTC
* * * *
40045776 CGTATAAGACCATATCTGGGATATGGCATCG-GTGTGATATATG-CTA
1 CGTATAAGACCATAGCTGGGATATGGCATCGAATGTGATATGTGATTA
* * *
40045822 CTGTATAAGACCATATCTGGGATATGGCATC-AGTGAGATATGTGATT-
1 C-GTATAAGACCATAGCTGGGATATGGCATCGAATGTGATATGTGATTA
* *
40045869 CGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTA
1 CGTATAAGACCATAGCTGGGATATGGCATCGA-ATGTGATATGTGATTA
* * *
40045918 CGCATAAGACCATAGCTGGGCTATGACATCGA
1 CGTATAAGACCATAGCTGGGATATGGCATCGA
40045950 TATATGAAGA
Statistics
Matches: 111, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
46 27 0.24
47 41 0.37
48 14 0.13
49 29 0.26
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (48 bp):
CGTATAAGACCATAGCTGGGATATGGCATCGAATGTGATATGTGATTA
Done.