Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 122 of 216
Found at i:38770295 original size:41 final size:41
Alignment explanation
Indices: 38770250--38770331 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
38770240 ATATTTCATT
* * *
38770250 TTATCTTTTAGTAGTTTATTAGAAT-AAGGAAATTATTTTCC
1 TTATCTTTTAGTAGTTTACTAAAATAAAAG-AATTATTTTCC
38770291 TTATCTTTTAGTAGTTTACTAAAATAAAAGAATTATTTTCC
1 TTATCTTTTAGTAGTTTACTAAAATAAAAGAATTATTTTCC
38770332 CAATTAGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 34 0.92
42 3 0.08
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTACTAAAATAAAAGAATTATTTTCC
Found at i:38772754 original size:19 final size:19
Alignment explanation
Indices: 38772730--38772770 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
38772720 TATTTTAAGG
38772730 TTATTT-AGATAGATAAATC
1 TTATTTAAG-TAGATAAATC
38772749 TTATTTAAGTAGATAAATC
1 TTATTTAAGTAGATAAATC
38772768 TTA
1 TTA
38772771 GAATAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (19 bp):
TTATTTAAGTAGATAAATC
Found at i:38772849 original size:37 final size:37
Alignment explanation
Indices: 38772808--38772878 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
38772798 ATATCTTATT
38772808 TTATCCTTTAGTAGTTTATTAGAATAAGGGAATTTCC
1 TTATCCTTTAGTAGTTTATTAGAATAAGGGAATTTCC
*
38772845 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATT
1 TTATCCTTTAGTAGTTTATTAGAATAAGGGAATT
38772879 ATTTTCCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (37 bp):
TTATCCTTTAGTAGTTTATTAGAATAAGGGAATTTCC
Found at i:38776346 original size:29 final size:30
Alignment explanation
Indices: 38776283--38776362 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 30
38776273 ATCCCAAAAC
*
38776283 TATACATGAACTTTGGTTTAATGTGCAATTG
1 TATACATGAACTTTGATTT-ATGTGCAATTG
*
38776314 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTTTGATTTATGTGCAATTG
*
38776343 TATACATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
38776363 GATTCAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.38
30 10 0.22
31 18 0.40
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTG
Found at i:38788961 original size:17 final size:17
Alignment explanation
Indices: 38788939--38788973 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
38788929 TTTCAAATGC
38788939 ACCACACGAGAACATAA
1 ACCACACGAGAACATAA
38788956 ACCACACGAGAACATAA
1 ACCACACGAGAACATAA
38788973 A
1 A
38788974 GGCTACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.29, G:0.11, T:0.06
Consensus pattern (17 bp):
ACCACACGAGAACATAA
Found at i:38807438 original size:14 final size:14
Alignment explanation
Indices: 38807419--38807450 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
38807409 AACATCTATC
38807419 ACAATGATCATACA
1 ACAATGATCATACA
38807433 ACAATGATCATACA
1 ACAATGATCATACA
38807447 ACAA
1 ACAA
38807451 AAGTTGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.22, G:0.06, T:0.19
Consensus pattern (14 bp):
ACAATGATCATACA
Found at i:38809079 original size:47 final size:47
Alignment explanation
Indices: 38809026--38809120 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
38809016 TGAGAACCAC
38809026 TACTTTCTTATTGATGATGGTGTTTGATTAATGAAATTTAATGGCTT
1 TACTTTCTTATTGATGATGGTGTTTGATTAATGAAATTTAATGGCTT
*
38809073 TACTTTCTTATTGATTATGGTGTTTGATTAATGAAATTTAATGGCTT
1 TACTTTCTTATTGATGATGGTGTTTGATTAATGAAATTTAATGGCTT
38809120 T
1 T
38809121 CTGAGCCTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.25, C:0.06, G:0.18, T:0.51
Consensus pattern (47 bp):
TACTTTCTTATTGATGATGGTGTTTGATTAATGAAATTTAATGGCTT
Found at i:38809498 original size:13 final size:13
Alignment explanation
Indices: 38809480--38809515 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
38809470 AAAAAAGAGA
38809480 TTGTTTTAAATTC
1 TTGTTTTAAATTC
38809493 TTGTTTTAAATTC
1 TTGTTTTAAATTC
38809506 TAT-TTTTAAA
1 T-TGTTTTAAA
38809516 ATATTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 21 0.95
14 1 0.05
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (13 bp):
TTGTTTTAAATTC
Found at i:38813585 original size:13 final size:13
Alignment explanation
Indices: 38813567--38813599 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
38813557 GAGTGTTAGA
38813567 ATATTATTATAGG
1 ATATTATTATAGG
*
38813580 ATATTATTATGGG
1 ATATTATTATAGG
38813593 ATATTAT
1 ATATTAT
38813600 CTCTTAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
ATATTATTATAGG
Found at i:38813893 original size:9 final size:9
Alignment explanation
Indices: 38813879--38813971 Score: 107
Period size: 9 Copynumber: 10.4 Consensus size: 9
38813869 TTTGGTTAAA
38813879 AATTAACCG
1 AATTAACCG
* *
38813888 AATTAAGCA
1 AATTAACCG
38813897 AATTAACCG
1 AATTAACCG
*
38813906 AATTACCCG
1 AATTAACCG
*
38813915 AATTACCCG
1 AATTAACCG
38813924 AATTAACCG
1 AATTAACCG
*
38813933 AA-TACCCG
1 AATTAACCG
*
38813941 AATTACCCG
1 AATTAACCG
38813950 AATTAACCG
1 AATTAACCG
* *
38813959 GATTAACCT
1 AATTAACCG
38813968 AATT
1 AATT
38813972 GAATCATACA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
8 7 0.10
9 65 0.90
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:38813945 original size:26 final size:27
Alignment explanation
Indices: 38813879--38813963 Score: 118
Period size: 27 Copynumber: 3.2 Consensus size: 27
38813869 TTTGGTTAAA
* ** *
38813879 AATTAACCGAATTAAGCAAATTAACCG
1 AATTACCCGAATTACCCGAATTAACCG
38813906 AATTACCCGAATTACCCGAATTAACCG
1 AATTACCCGAATTACCCGAATTAACCG
38813933 AA-TACCCGAATTACCCGAATTAACCG
1 AATTACCCGAATTACCCGAATTAACCG
*
38813959 GATTA
1 AATTA
38813964 ACCTAATTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
26 25 0.48
27 27 0.52
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (27 bp):
AATTACCCGAATTACCCGAATTAACCG
Found at i:38813949 original size:35 final size:36
Alignment explanation
Indices: 38813879--38813971 Score: 125
Period size: 35 Copynumber: 2.6 Consensus size: 36
38813869 TTTGGTTAAA
*
38813879 AATTAACCGAATTAAGCAAATTAACCGAATTACCCG
1 AATTAACCGAATTAACCAAATTAACCGAATTACCCG
* * *
38813915 AATTACCCGAATTAACCGAA-TACCCGAATTACCCG
1 AATTAACCGAATTAACCAAATTAACCGAATTACCCG
* *
38813950 AATTAACCGGATTAACCTAATT
1 AATTAACCGAATTAACCAAATT
38813972 GAATCATACA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
35 31 0.63
36 18 0.37
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.24
Consensus pattern (36 bp):
AATTAACCGAATTAACCAAATTAACCGAATTACCCG
Found at i:38826967 original size:23 final size:23
Alignment explanation
Indices: 38826938--38827059 Score: 163
Period size: 23 Copynumber: 5.3 Consensus size: 23
38826928 AGTGTTATTG
38826938 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
38826961 TTTAGTGGTGGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
38826984 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
38827007 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
38827030 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
38827053 ATCAGTG
1 ATCAGTG
38827060 TGGCACTTAT
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 82 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:38826990 original size:46 final size:46
Alignment explanation
Indices: 38826938--38827059 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
38826928 AGTGTTATTG
* * *
38826938 ATCAGTGGTAGCTTCGGCTACATTTTAGTGGTGGCTACGGCTACAT
1 ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
38826984 ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACAT
*
38827030 ATCAGTGGTAGCTTTGGCTACATATCAGTG
1 ATCAGTGGTAGCTTTGGCTACATTTCAGTG
38827060 TGGCACTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTTTGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:38830689 original size:98 final size:97
Alignment explanation
Indices: 38830513--38830706 Score: 271
Period size: 98 Copynumber: 2.0 Consensus size: 97
38830503 GAAATCAGGC
* * * * *
38830513 TTTTATTTGAATCAAAGTATACGAGTCACGCATACATAGTCCATTATCCACTTAGGATTAAGGTA
1 TTTTATTTGAATCAAAGTATACGAGCCACACATACATAGTCCATCATCCACTCAGAATTAAGGTA
*
38830578 TGACACACAATGAACGTCACAAGTGAATAAAA
66 TGACACACAATGAACGTCACAAATGAATAAAA
* * * *
38830610 TTTTCATTTGCATCATAGTATACGAGCCACACATACATAGTCTATCATCTACTCAGAATTAAGGT
1 TTTT-ATTTGAATCAAAGTATACGAGCCACACATACATAGTCCATCATCCACTCAGAATTAAGGT
* *
38830675 ATGACACACTATGAAGGTCACAAATGAATAAA
65 ATGACACACAATGAACGTCACAAATGAATAAA
38830707 TCTATAAATG
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
97 4 0.05
98 80 0.95
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (97 bp):
TTTTATTTGAATCAAAGTATACGAGCCACACATACATAGTCCATCATCCACTCAGAATTAAGGTA
TGACACACAATGAACGTCACAAATGAATAAAA
Found at i:38834046 original size:22 final size:22
Alignment explanation
Indices: 38834017--38834059 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
38834007 ACAGATACGC
*
38834017 GGATTCC-ACCCAAACACACCA
1 GGATTCCAACCAAAACACACCA
38834038 GGATATCCAACCAAAACACACC
1 GGAT-TCCAACCAAAACACACC
38834060 CGAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.42, C:0.40, G:0.09, T:0.09
Consensus pattern (22 bp):
GGATTCCAACCAAAACACACCA
Found at i:38837749 original size:11 final size:11
Alignment explanation
Indices: 38837729--38837760 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
38837719 TTAATTAGTT
38837729 TAATATAATAA
1 TAATATAATAA
*
38837740 TAATAAAATAA
1 TAATATAATAA
38837751 TAATATAATA
1 TAATATAATA
38837761 TTACTTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATATAATAA
Found at i:38837897 original size:14 final size:13
Alignment explanation
Indices: 38837871--38837921 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
38837861 GTTTATTTGA
38837871 AATATAATAATAT
1 AATATAATAATAT
38837884 AATATAATTAATAT
1 AATATAA-TAATAT
* *
38837898 AAT-TTACAATAT
1 AATATAATAATAT
*
38837910 AATAAAATAATA
1 AATATAATAATA
38837922 ATATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:38839490 original size:16 final size:16
Alignment explanation
Indices: 38839471--38839504 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
38839461 AACCAGAATG
38839471 TTGTAGGCAAAATACC
1 TTGTAGGCAAAATACC
38839487 TTGTAGGCAAAATACC
1 TTGTAGGCAAAATACC
38839503 TT
1 TT
38839505 ACACCGTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (16 bp):
TTGTAGGCAAAATACC
Found at i:38842097 original size:51 final size:51
Alignment explanation
Indices: 38842041--38842195 Score: 247
Period size: 51 Copynumber: 3.0 Consensus size: 51
38842031 CGTACAACAA
* * * *
38842041 CAACATTATCCAGTCCATTTAATGTTGAAAAATCACCAGCATATTCATCAG
1 CAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCATCAG
*
38842092 CAACATTATCCACTCCATCTGATGTTGCAAAATCACCAACATATTCATCAG
1 CAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCATCAG
* *
38842143 CAACATTATCCACTCTATCTGATGTTGCAAAATCACTAGCATATTCATCAG
1 CAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCATCAG
38842194 CA
1 CA
38842196 GCAACTTCAC
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 96 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.29
Consensus pattern (51 bp):
CAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCATCAG
Found at i:38842355 original size:33 final size:32
Alignment explanation
Indices: 38842299--38842441 Score: 97
Period size: 33 Copynumber: 4.3 Consensus size: 32
38842289 GTAGCAGACA
** * *
38842299 CACCCTCCCCATCAGCTTGTACCTCTCCTACAT
1 CACCCTCCCCATCAAATTCTACCCCTCC-ACAT
* ** *
38842332 CACCCTCCCCACCAAATTCTACCTATCCCAGAT
1 CACCCTCCCCATCAAATTCTACCCCT-CCACAT
* ** * *
38842365 CACCTTTACCATCATATTCTACCCCTTCATCAT
1 CACCCTCCCCATCAAATTCTACCCCTCCA-CAT
* * **
38842398 CACCCTCCCCATCAACTTCCACCCCTTGAACAT
1 CACCCTCCCCATCAAATTCTACCCC-TCCACAT
38842431 CACCCTCCCCA
1 CACCCTCCCCA
38842442 GTAGTCAAAA
Statistics
Matches: 84, Mismatches: 23, Indels: 6
0.74 0.20 0.05
Matches are distributed among these distances:
32 2 0.02
33 78 0.93
34 4 0.05
ACGTcount: A:0.23, C:0.49, G:0.03, T:0.25
Consensus pattern (32 bp):
CACCCTCCCCATCAAATTCTACCCCTCCACAT
Found at i:38843554 original size:8 final size:8
Alignment explanation
Indices: 38843532--38843567 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
38843522 AAAGTTTTGA
38843532 ATTTAGGGG
1 ATTT-GGGG
38843541 -TTTGGGG
1 ATTTGGGG
38843548 ATTTGGGG
1 ATTTGGGG
38843556 ATTTGGGG
1 ATTTGGGG
38843564 ATTT
1 ATTT
38843568 AAGGTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.15
8 22 0.85
ACGTcount: A:0.14, C:0.00, G:0.44, T:0.42
Consensus pattern (8 bp):
ATTTGGGG
Found at i:38848924 original size:22 final size:22
Alignment explanation
Indices: 38848896--38848972 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
38848886 TTTCTTTTAA
38848896 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
** * *
38848918 TTAGGAGATAATATTTTGGTTTAA--
1 TTAGGAGAT--TA-GAT-GCTAAAGT
38848942 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
38848964 TTAGGAGAT
1 TTAGGAGAT
38848973 AATATTTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 20 0.49
24 11 0.27
25 1 0.02
26 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (22 bp):
TTAGGAGATTAGATGCTAAAGT
Found at i:38848941 original size:46 final size:46
Alignment explanation
Indices: 38848891--38848985 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
38848881 TCTATTTTCT
38848891 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
38848937 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
38848983 TTT
1 TTT
38848986 CTATCTTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:38853462 original size:46 final size:46
Alignment explanation
Indices: 38853412--38853506 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
38853402 TCTATTTTCT
* *
38853412 TTTAATTATGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAATATTTTGG
38853458 TTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAATATTTTGG
38853504 TTT
1 TTT
38853507 TTATCTTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAATATTTTGG
Found at i:38854242 original size:171 final size:170
Alignment explanation
Indices: 38853957--38854293 Score: 444
Period size: 171 Copynumber: 2.0 Consensus size: 170
38853947 ACAATTCAGA
* * *
38853957 AACAAACTAAAAATGCATTAATTTGATCAAATTACTAAAATTTGCATCCTAATTGTGCCATCATC
1 AACAAACTAAAAATGCATTAACTTGATCAAATTACTAAAATTTACATCCTAATTATGCCATCATC
** * *
38854022 AAATCAACTTGATGATGAACACCAATCAACCAATAAACAACTGCCAAAAGTCCCAAG-AGACCCA
66 AAATCAACTTGACAATGAACACCAATCAACCAATAAACAACTCCCAAAAGGCCCAAGAAG-CCCA
* * *
38854086 TCATATCAAATGATGCACGAAAGATCAAGTCTTAGATGCAAG
130 TCATATC-AATGATGCACAAAAGATAAAATCTTAGATGCAAG
** ** *
38854128 AACAAACTAGCAATGCATTAACTTGATCAAATTA-TAGAAATTTACATTTTAGTTATGCCATCAT
1 AACAAACTAAAAATGCATTAACTTGATCAAATTACTA-AAATTTACATCCTAATTATGCCATCAT
* * * *
38854192 CAAATCAACTTGACAATGAATATCAATCAACTAATAAACAACTCCCAAAAGGCCCAAGAAGCCTA
65 CAAATCAACTTGACAATGAACACCAATCAACCAATAAACAACTCCCAAAAGGCCCAAGAAGCCCA
* *
38854257 TTATATCAATGATGCACAAAAGTTAAAATCTTAGATG
130 TCATATCAATGATGCACAAAAGATAAAATCTTAGATG
38854294 GACTTCCTCA
Statistics
Matches: 143, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
170 28 0.20
171 113 0.79
172 2 0.01
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (170 bp):
AACAAACTAAAAATGCATTAACTTGATCAAATTACTAAAATTTACATCCTAATTATGCCATCATC
AAATCAACTTGACAATGAACACCAATCAACCAATAAACAACTCCCAAAAGGCCCAAGAAGCCCAT
CATATCAATGATGCACAAAAGATAAAATCTTAGATGCAAG
Found at i:38861357 original size:16 final size:16
Alignment explanation
Indices: 38861336--38861395 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
38861326 TTTGGTTCGC
38861336 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
38861352 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
38861368 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
38861384 TGTATTAGATTA
1 TGTATTGGATTA
38861396 AATGTGTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:38861372 original size:32 final size:32
Alignment explanation
Indices: 38861336--38861403 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
38861326 TTTGGTTCGC
*
38861336 TGTATTGGATTAGAGGTGTATTGGATTAGAA-G
1 TGTATTGGATTAGAGGTGTATTAGATTA-AATG
38861368 TGTATTGGATTAGAGGTGTATTAGATTAAATG
1 TGTATTGGATTAGAGGTGTATTAGATTAAATG
38861400 TGTA
1 TGTA
38861404 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 2 0.06
32 32 0.94
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTAGATTAAATG
Found at i:38861402 original size:16 final size:16
Alignment explanation
Indices: 38861336--38861403 Score: 84
Period size: 16 Copynumber: 4.2 Consensus size: 16
38861326 TTTGGTTCGC
*
38861336 TGTATTGGATTAGAGG
1 TGTATTGGATTAAAGG
38861352 TGTATTGGATTAGAA-G
1 TGTATTGGATTA-AAGG
*
38861368 TGTATTGGATTAGAGG
1 TGTATTGGATTAAAGG
* *
38861384 TGTATTAGATTAAATG
1 TGTATTGGATTAAAGG
38861400 TGTA
1 TGTA
38861404 ATAGCAAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
15 1 0.02
16 43 0.96
17 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAAAGG
Found at i:38861727 original size:157 final size:157
Alignment explanation
Indices: 38861533--38861842 Score: 548
Period size: 157 Copynumber: 2.0 Consensus size: 157
38861523 CCCTTAGCAT
*
38861533 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
38861598 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
38861663 TTTAATAAAATTCTTAATAATTACCAA
131 TTTAATAAAATTCTTAATAATTACCAA
* * *
38861690 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTGATAAGATTATTAATATGAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
38861755 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
38861820 TTTAATAAAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
38861843 ATATTCTTAT
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTACCAA
Found at i:38861916 original size:157 final size:155
Alignment explanation
Indices: 38861579--38861900 Score: 349
Period size: 157 Copynumber: 2.0 Consensus size: 155
38861569 TTAAATTTTA
* * * *
38861579 ATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATA
1 ATAAGATTATGAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATA
* * * * ** *
38861644 TTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTACCAAAAATTTGTTTTGGTAAATT
66 TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACAAAAATATGATTTACTAAATC
* * * * *
38861709 ATTATTGTTATTGTTATTTAAATTTTG
131 ATAATTATTATTGATATATAAA--TAG
* *
38861736 ATAAGATTATTAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATA
1 ATAAGATTATGAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATA
* * ***
38861801 TTATACTTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCA
66 TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACA--AAAATATG-ATTTACT-A
38861866 AATCATAATATATTATATGATACTATAAA-AG
127 AATCATAAT-TATTAT-TGATA-TATAAATAG
38861897 ATAA
1 ATAA
38861901 TTTGAAATAA
Statistics
Matches: 137, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
157 102 0.74
159 4 0.03
160 4 0.03
161 13 0.09
162 5 0.04
163 4 0.03
164 5 0.04
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (155 bp):
ATAAGATTATGAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATA
TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACAAAAATATGATTTACTAAATC
ATAATTATTATTGATATATAAATAG
Found at i:38862737 original size:13 final size:13
Alignment explanation
Indices: 38862719--38862748 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
38862709 CAATCAGCTA
38862719 AATTCAGAAAAAC
1 AATTCAGAAAAAC
38862732 AATTCAGAAAAAC
1 AATTCAGAAAAAC
38862745 AATT
1 AATT
38862749 ACATGACAAT
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:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:38865970 original size:9 final size:9
Alignment explanation
Indices: 38865956--38865981 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
38865946 AGTTTGAGCT
38865956 TTAGTGGCA
1 TTAGTGGCA
38865965 TTAGTGGCA
1 TTAGTGGCA
38865974 TTAGTGGC
1 TTAGTGGC
38865982 GCTTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.35, T:0.35
Consensus pattern (9 bp):
TTAGTGGCA
Found at i:38866326 original size:55 final size:53
Alignment explanation
Indices: 38866220--38866335 Score: 146
Period size: 55 Copynumber: 2.2 Consensus size: 53
38866210 AATAATTAAT
* * * *
38866220 GTTTAGAGTTTAGTGTTTGGTTTAGGTTGTAGGTTTATAGTTTAGTATTTAGG
1 GTTTAGGGTTTAGTGTTTGGTTTAGGGTGTAGGGTTAAAGTTTAGTATTTAGG
38866273 GTTTAGGGTTTAGTGTTTAGGGTTTATGGGT-TAGGGTTAAAGTTTA-TAGTTTAGG
1 GTTTAGGGTTTAGTGTTT--GGTTTA-GGGTGTAGGGTTAAAGTTTAGTA-TTTAGG
38866328 GTTTAGGG
1 GTTTAGGG
38866336 GCTTAGGATT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
53 17 0.31
54 2 0.04
55 33 0.60
56 3 0.05
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (53 bp):
GTTTAGGGTTTAGTGTTTGGTTTAGGGTGTAGGGTTAAAGTTTAGTATTTAGG
Found at i:38866331 original size:7 final size:7
Alignment explanation
Indices: 38866220--38866363 Score: 75
Period size: 7 Copynumber: 21.0 Consensus size: 7
38866210 AATAATTAAT
*
38866220 GTTTAGA
1 GTTTAGG
*
38866227 GTTTAGT
1 GTTTAGG
38866234 GTTT--G
1 GTTTAGG
38866239 GTTTA-G
1 GTTTAGG
38866245 GTTGTA-G
1 GTT-TAGG
**
38866252 GTTTATA
1 GTTTAGG
*
38866259 GTTTAGT
1 GTTTAGG
*
38866266 ATTTAGG
1 GTTTAGG
38866273 GTTTAGG
1 GTTTAGG
*
38866280 GTTTAGT
1 GTTTAGG
38866287 GTTTAGG
1 GTTTAGG
38866294 GTTTATGG
1 GTTTA-GG
38866302 G-TTAGG
1 GTTTAGG
**
38866308 G-TTAAA
1 GTTTAGG
**
38866314 GTTTATA
1 GTTTAGG
38866321 GTTTAGG
1 GTTTAGG
38866328 GTTTAGGG
1 GTTTA-GG
*
38866336 GCTTAGG
1 GTTTAGG
* **
38866343 ATTTATA
1 GTTTAGG
*
38866350 GTTTAGT
1 GTTTAGG
38866357 GTTTAGG
1 GTTTAGG
38866364 ATTTTAAACA
Statistics
Matches: 107, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
5 4 0.04
6 13 0.12
7 81 0.76
8 9 0.08
ACGTcount: A:0.19, C:0.01, G:0.33, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:38867131 original size:39 final size:41
Alignment explanation
Indices: 38867075--38867162 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 41
38867065 AAAAATGCAG
* ** *
38867075 CAAAAAGTAAGCAAATAGT-AGTTTTTTTAAAAAAACGCCA
1 CAAAAAATAAGCAAATAGTGACATTTTTGAAAAAAACGCCA
**
38867115 CAAAAAATAAGC-AATAGTGACATTTTTGAAAAAAACGCTG
1 CAAAAAATAAGCAAATAGTGACATTTTTGAAAAAAACGCCA
38867155 CAAAAAAT
1 CAAAAAAT
38867163 CATAAACAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 6 0.15
40 35 0.85
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (41 bp):
CAAAAAATAAGCAAATAGTGACATTTTTGAAAAAAACGCCA
Found at i:38868857 original size:24 final size:24
Alignment explanation
Indices: 38868822--38868873 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
38868812 TTGTTTAAAC
*
38868822 ATTT-TTACCT-AATAAAACTAAT
1 ATTTCTTACCTAAAAAAAACTAAT
38868844 ATTTCTTACCCTAAAAAAAACTAAT
1 ATTTCTTA-CCTAAAAAAAACTAAT
38868869 ATTTC
1 ATTTC
38868874 AGTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 3 0.12
24 3 0.12
25 16 0.62
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.38
Consensus pattern (24 bp):
ATTTCTTACCTAAAAAAAACTAAT
Found at i:38869773 original size:220 final size:229
Alignment explanation
Indices: 38869384--38869842 Score: 684
Period size: 220 Copynumber: 2.0 Consensus size: 229
38869374 TGACGTTTCA
** * * *
38869384 ATTTGGGATCATTGTCGTTGGGACTATTTTATTACGGTACATTTTTCAAGTTTATTACTGTACAT
1 ATTTGGGATCATTGTAATTGGAACTATTTTATTACGGCACATTTTTCAAGTTTATTACTGTACAC
*
38869449 TTTGAAATTGTGCTTCTTTTTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAG
66 TTTGAAATTGTGCTAC---TTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAG
38869514 TTTTGATATTAACAATGTTTGATTTTAATA-TT-TAA-T-AAT-TTTTTAAAACTTATAAATATA
128 TTTTGATATTAACAATGTTTGATTTTAATATTTATAATTAAATGTTTTTAAAACTTATAAATATA
38869574 TTTTGTAAGAGAGTAATTTTGATCATTATTTAAATTT
193 TTTTGTAAGAGAGTAATTTTGATCATTATTTAAATTT
* *
38869611 ATTTGGGATCTTTGTAATTGGAACTATTTTATTACTGCACATTTTTCAAGTTTATTACTGTACAC
1 ATTTGGGATCATTGTAATTGGAACTATTTTATTACGGCACATTTTTCAAGTTTATTACTGTACAC
* *
38869676 TTTG-AATT-TG-TAC-TTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAATTAATTTT
66 TTTGAAATTGTGCTACTTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAGTTT
*
38869737 TGATATTAACAATGTTTGATTTTAATATTTAATAATTTTAAATGTTTTTAAAACTTATAAATATT
131 TGATATTAACAATGTTTGATTTTAATATTT-ATAA--TTAAATGTTTTTAAAACTTATAAATATA
**
38869802 TTTTGTGGGAGAGTAATTTTGATCATTATTTAAATTT
193 TTTTGTAAGAGAGTAATTTTGATCATTATTTAAATTT
38869839 ATTT
1 ATTT
38869843 TAATATAAAA
Statistics
Matches: 211, Mismatches: 13, Indels: 15
0.88 0.05 0.06
Matches are distributed among these distances:
220 73 0.35
221 2 0.01
223 3 0.01
224 2 0.01
225 2 0.01
226 5 0.02
227 65 0.31
228 59 0.28
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.51
Consensus pattern (229 bp):
ATTTGGGATCATTGTAATTGGAACTATTTTATTACGGCACATTTTTCAAGTTTATTACTGTACAC
TTTGAAATTGTGCTACTTTTTTTTTGATAATATTTTCAAGTATATATTTAATACTAAATAAGTTT
TGATATTAACAATGTTTGATTTTAATATTTATAATTAAATGTTTTTAAAACTTATAAATATATTT
TGTAAGAGAGTAATTTTGATCATTATTTAAATTT
Found at i:38869885 original size:19 final size:19
Alignment explanation
Indices: 38869861--38869918 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
38869851 AAATCAAAAC
38869861 TTACATAACTTTAAAGAAT
1 TTACATAACTTTAAAGAAT
* *
38869880 TTACATAAC-TTACATAAT
1 TTACATAACTTTAAAGAAT
38869898 TTACATAACTTTAAAGAAT
1 TTACATAACTTTAAAGAAT
38869917 TT
1 TT
38869919 TCGATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 16 0.47
19 18 0.53
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (19 bp):
TTACATAACTTTAAAGAAT
Found at i:38869997 original size:8 final size:9
Alignment explanation
Indices: 38869858--38870243 Score: 133
Period size: 9 Copynumber: 40.6 Consensus size: 9
38869848 TAAAAATCAA
38869858 AACTTACAT
1 AACTTACAT
* *
38869867 AACTTTAAAG
1 AAC-TTACAT
*
38869877 AATTTACAT
1 AACTTACAT
38869886 AACTTACAT
1 AACTTACAT
*
38869895 AATTTACAT
1 AACTTACAT
* *
38869904 AACTTTAAAG
1 AAC-TTACAT
* *
38869914 AATTTTCGATTTT
1 AACTTAC-A---T
38869927 AACTTA-AT
1 AACTTACAT
*
38869935 AACTTATAT
1 AACTTACAT
*
38869944 ATATGTATATCAT
1 A-A-CT-TA-CAT
38869957 AACTTACAT
1 AACTTACAT
*
38869966 AACTCACATAT
1 AACTTAC--AT
38869977 AACTTACAT
1 AACTTACAT
38869986 AACTTA-AT
1 AACTTACAT
38869994 AACTTACAT
1 AACTTACAT
*
38870003 ATATCATATCAT
1 A-A-CTTA-CAT
38870015 AA-TTCACAT
1 AACTT-ACAT
38870024 AACTTA-AT
1 AACTTACAT
*
38870032 AACTTATATAT
1 AAC-T-TACAT
*
38870043 ATATCATATCAT
1 A-A-CTTA-CAT
38870055 AACTTACAT
1 AACTTACAT
* *
38870064 AACTCACAA
1 AACTTACAT
*
38870073 AACATACAT
1 AACTTACAT
*
38870082 AACATA-AT
1 AACTTACAT
*
38870090 AACTTATATAT
1 AAC-T-TACAT
*
38870101 ATATCATATCAT
1 A-A-CTTA-CAT
38870113 AACTTACAT
1 AACTTACAT
* *
38870122 AACTCATAT
1 AACTTACAT
* *
38870131 AACATATAT
1 AACTTACAT
* *
38870140 CATTTA-AT
1 AACTTACAT
*
38870148 AACTTATAT
1 AACTTACAT
*
38870157 ATATCATATCAT
1 A-A-CTTA-CAT
*
38870169 AACTTACGT
1 AACTTACAT
38870178 AACTTACAT
1 AACTTACAT
*
38870187 AACTCACAT
1 AACTTACAT
38870196 AACTTACAT
1 AACTTACAT
38870205 AA--TACAT
1 AACTTACAT
* *
38870212 AA-ATATAT
1 AACTTACAT
* *
38870220 ATCATATCAT
1 AACTTA-CAT
38870230 AACTTACAT
1 AACTTACAT
38870239 AACTT
1 AACTT
38870244 GTTTATACTT
Statistics
Matches: 283, Mismatches: 56, Indels: 76
0.68 0.13 0.18
Matches are distributed among these distances:
7 7 0.02
8 36 0.13
9 142 0.50
10 40 0.14
11 31 0.11
12 18 0.06
13 9 0.03
ACGTcount: A:0.45, C:0.17, G:0.01, T:0.37
Consensus pattern (9 bp):
AACTTACAT
Found at i:38870056 original size:40 final size:38
Alignment explanation
Indices: 38869955--38870196 Score: 164
Period size: 40 Copynumber: 6.3 Consensus size: 38
38869945 TATGTATATC
*
38869955 ATAACTTACATA-ACTCACAT-ATAACTTACATAACTTA
1 ATAACTTACATATA-TCATATCATAACTTACATAACTTA
38869992 ATAACTTACATATATCATATCATAA-TTCACATAACTTA
1 ATAACTTACATATATCATATCATAACTT-ACATAACTTA
* *
38870030 ATAACTTATATATATATCATATCATAACTTACATAACTCA
1 ATAAC-T-TACATATATCATATCATAACTTACATAACTTA
* * * *
38870070 CAAAACATACATA-A-CATA--ATAACTTATATATATATCATATC
1 -ATAACTTACATATATCATATCATAAC-T-TACATA-A-C-T-TA
* * * *
38870111 ATAACTTACATA-A-C-TCAT-ATAACATATATCATTTA
1 ATAACTTACATATATCAT-ATCATAACTTACATAACTTA
* *
38870146 ATAACTTATATATATCATATCATAACTTACGTAACTTA
1 ATAACTTACATATATCATATCATAACTTACATAACTTA
*
38870184 CATAACTCACATA
1 -ATAACTTACATA
38870197 ACTTACATAA
Statistics
Matches: 162, Mismatches: 23, Indels: 38
0.73 0.10 0.17
Matches are distributed among these distances:
35 17 0.10
36 3 0.02
37 31 0.19
38 36 0.22
39 23 0.14
40 41 0.25
41 11 0.07
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (38 bp):
ATAACTTACATATATCATATCATAACTTACATAACTTA
Found at i:38870160 original size:21 final size:21
Alignment explanation
Indices: 38870134--38870174 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38870124 CTCATATAAC
*
38870134 ATATATCATTTAATAACTTAT
1 ATATATCATATAATAACTTAT
*
38870155 ATATATCATATCATAACTTA
1 ATATATCATATAATAACTTA
38870175 CGTAACTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATATCATATAATAACTTAT
Found at i:38870188 original size:65 final size:61
Alignment explanation
Indices: 38870052--38870243 Score: 193
Period size: 61 Copynumber: 3.1 Consensus size: 61
38870042 TATATCATAT
* * *
38870052 CATAACTTACATAACTCACAAAACATACATAACATA-ATAACTTATATAT-ATATCAT-A--T-
1 CATAACTTACATAACTCACATAACTTACAT-A-ATACATAA-ATATATATCATATCATAACTTA
* *
38870110 CATAACTTACATAACTCATATAACATATATCATTTAATA-ACT-TATATATATCATATCATAACT
1 CATAACTTACATAACTCACATAAC-T-TA-CA--TAATACA-TAAATATATATCATATCATAACT
38870173 TA
60 TA
*
38870175 CGTAACTTACATAACTCACATAACTTACATAATACATAAATATATATCATATCATAACTTA
1 CATAACTTACATAACTCACATAACTTACATAATACATAAATATATATCATATCATAACTTA
38870236 CATAACTT
1 CATAACTT
38870244 GTTTATACTT
Statistics
Matches: 112, Mismatches: 9, Indels: 23
0.78 0.06 0.16
Matches are distributed among these distances:
58 22 0.20
60 15 0.13
61 43 0.38
62 5 0.04
63 3 0.03
64 2 0.02
65 22 0.20
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (61 bp):
CATAACTTACATAACTCACATAACTTACATAATACATAAATATATATCATATCATAACTTA
Found at i:38870189 original size:56 final size:58
Alignment explanation
Indices: 38870020--38870242 Score: 299
Period size: 58 Copynumber: 3.8 Consensus size: 58
38870010 ATCATAATTC
*
38870020 ACATAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACAAAACAT
1 ACATAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACATAACAT
* *
38870078 ACATAACATAATAACTTATATATATATCATATCATAACTTACATAACTCATATAACAT
1 ACATAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACATAACAT
* * * * *
38870136 ATATCATTTAATAAC-T-TATATATATCATATCATAACTTACGTAACTTACATAAC-T
1 ACATAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACATAACAT
* *
38870191 CACATAACTTACATAATACATAAATATATATCATATCATAACTTACATAACT
1 -ACATAACTTA-AT-A-ACTTATATATATATCATATCATAACTTACATAACT
38870243 TGTTTATACT
Statistics
Matches: 144, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
55 1 0.01
56 42 0.29
57 3 0.02
58 67 0.47
59 2 0.01
60 1 0.01
61 28 0.19
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (58 bp):
ACATAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACATAACAT
Found at i:38870577 original size:12 final size:12
Alignment explanation
Indices: 38870560--38870595 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
38870550 AATATCAATG
38870560 GATGAATCTGAT
1 GATGAATCTGAT
38870572 GATGAATCTGAT
1 GATGAATCTGAT
38870584 GATGAATCTGAT
1 GATGAATCTGAT
38870596 AAAGATGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:38871951 original size:120 final size:120
Alignment explanation
Indices: 38871738--38872149 Score: 731
Period size: 120 Copynumber: 3.4 Consensus size: 120
38871728 ATCATATTTA
38871738 AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
38871803 TATTCTTATATGAATTTATTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTATTCAAATCATAATATATGATACTATAAAATATAAATT
38871858 AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
38871923 TATTCTTATATGAATTTATTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTATTCAAATCATAATATATGATACTATAAAATATAAATT
*
38871978 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
38872043 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT
66 TATTCTTATATGAATTTATTCAAATCATAATATATGATACTATAAAATATAAATT
* * *
38872098 GAA-ATAATTAA-TATTAAATATATT-TTATTTAAATATATGATTTAATAAAATT
1 -AACATAA-TAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
38872150 TAAAATAATT
Statistics
Matches: 283, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
119 25 0.09
120 254 0.90
121 4 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTATTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:38872023 original size:14 final size:15
Alignment explanation
Indices: 38871974--38872025 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
38871964 ATAAAATATA
38871974 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
38871989 TATTAAATATATTAT
1 AATTAAATATATTAT
38872004 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
38872017 AATTTAATA
1 AATTAAATA
38872026 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:38872200 original size:47 final size:46
Alignment explanation
Indices: 38872131--38872298 Score: 139
Period size: 47 Copynumber: 3.7 Consensus size: 46
38872121 TTTATTTAAA
*
38872131 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTATCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTATCT
* * * * * * *
38872178 TATATGAATTTGTATAATTTAAAATAGTTATTATTACATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
* * * *
38872223 TA-AT-AATAATATATAATTTCATAA-AATTATTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTA-TAATAATAAATTATCT
*
38872269 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
38872299 ATATTAAATA
Statistics
Matches: 92, Mismatches: 21, Indels: 16
0.71 0.16 0.12
Matches are distributed among these distances:
43 3 0.03
44 15 0.16
45 14 0.15
46 13 0.14
47 40 0.43
48 7 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
Found at i:38872241 original size:91 final size:91
Alignment explanation
Indices: 38872146--38872372 Score: 289
Period size: 91 Copynumber: 2.5 Consensus size: 91
38872136 GATTTAATAA
* * * *
38872146 AATTT-AAAATAATTA-TAACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAGTTAT
1 AATTTCAAAA-AATTATTAA-TAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAA
*
38872209 TATTACATATAATTTAATAATAATATAT
64 TATTAAATATAATTTAATAATAATATAT
* * *
38872237 AATTTCATAAAATTATTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATA
1 AATTTCAAAAAATTATTAATAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATA
*
38872302 TTAAATATAATTTAATAATGATATAT
66 TTAAATATAATTTAATAATAATATAT
* * *
38872328 AATTTCATAAATTTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 AATTTCAAAAAATTATTAATAAT-AAAT-TATCTTATATGAATTTA
38872373 CTAAAATCAA
Statistics
Matches: 120, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
91 95 0.79
92 24 0.20
93 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (91 bp):
AATTTCAAAAAATTATTAATAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATA
TTAAATATAATTTAATAATAATATAT
Found at i:38872253 original size:44 final size:43
Alignment explanation
Indices: 38872205--38872338 Score: 112
Period size: 44 Copynumber: 3.0 Consensus size: 43
38872195 TTTAAAATAG
38872205 TTATTATTACATATAATTTAATAATAATATATAATTTCATAAAA
1 TTATTATTA-ATATAATTTAATAATAATATATAATTTCATAAAA
** * *
38872249 TTATTGA-TAATA-AATTTTCTTATATGAATTTATACAATTT-AAAATAA
1 TTATT-ATTAATATAA-TTTAATA-AT-AA--TATATAATTTCATAA-AA
* *
38872296 TTAATATTAAATATAATTTAATAATGATATATAATTTCATAAA
1 TTATTATT-AATATAATTTAATAATAATATATAATTTCATAAA
38872339 TTTCTTAATA
Statistics
Matches: 69, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
42 2 0.03
43 8 0.12
44 19 0.28
45 6 0.09
46 5 0.07
47 18 0.26
48 9 0.13
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (43 bp):
TTATTATTAATATAATTTAATAATAATATATAATTTCATAAAA
Found at i:38875474 original size:33 final size:33
Alignment explanation
Indices: 38875435--38875510 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
38875425 ATTATAAAGC
*
38875435 ATGTATAATTGACCTAAAATTAATTGTTAGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTAGTAT
*
38875468 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTAGTAT
38875501 ATGTATAATT
1 ATGTATAATT
38875511 CAAGTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTAGTAT
Found at i:38875608 original size:37 final size:37
Alignment explanation
Indices: 38875553--38875639 Score: 147
Period size: 37 Copynumber: 2.4 Consensus size: 37
38875543 GTATAAATAT
* * *
38875553 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
38875590 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
38875627 ATTGATTAGTTTA
1 ATTGATTAGTTTA
38875640 TTTATTTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (37 bp):
ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
Found at i:38876916 original size:69 final size:69
Alignment explanation
Indices: 38876806--38876945 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 69
38876796 AATCAAGTTC
*
38876806 CAGTTTCATATTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAATTGCC
1 CAGTTTCATATTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAATTGCC
38876871 AGAA
66 AGAA
* * * * * *
38876875 CAGTTTCATCTTCTACTCACTAACAAATTAATAACATTTTCCAGCAGACTATCAAAACAATTTCC
1 CAGTTTCATATTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAATTGCC
38876940 AGAA
66 AGAA
38876944 CA
1 CA
38876946 AATCAACAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.26
Consensus pattern (69 bp):
CAGTTTCATATTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAATTGCC
AGAA
Found at i:38878387 original size:36 final size:37
Alignment explanation
Indices: 38878303--38878410 Score: 148
Period size: 36 Copynumber: 2.9 Consensus size: 37
38878293 GGCAGAAACT
38878303 GAGCAAATCGGTC-GAAAAAGAAAAGAAAAGAAACGGGGG
1 GAGCAAATCGG-CAG-AAAAGAAAAGAAAAGAAAC-GGGG
* *
38878342 GAGCAAATCGGCAGAAAAGAAAAGAAAATAAAC-TGG
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACGGGG
*
38878378 GAGCAAATCGGCAGAAAAGAAAAGCAAAGAAAC
1 GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAAC
38878411 AAGTAAGCAA
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
36 33 0.52
38 19 0.30
39 12 0.19
ACGTcount: A:0.55, C:0.12, G:0.28, T:0.06
Consensus pattern (37 bp):
GAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACGGGG
Found at i:38880511 original size:26 final size:26
Alignment explanation
Indices: 38880475--38880524 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
38880465 GTAGTAGAGG
*
38880475 TTTGCTTTAGA-GCTCTCGGATAATAA
1 TTTGCTTTAGATG-TCTCAGATAATAA
38880501 TTTGCTTTAGATGTCTCAGATAAT
1 TTTGCTTTAGATGTCTCAGATAAT
38880525 TTTGTCAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (26 bp):
TTTGCTTTAGATGTCTCAGATAATAA
Found at i:38881930 original size:43 final size:43
Alignment explanation
Indices: 38881883--38882024 Score: 164
Period size: 43 Copynumber: 3.3 Consensus size: 43
38881873 GAACGGTACT
* * *
38881883 TTTAGCGGTGTTTGTGAAAAAGGCTTCGCTAAATGTCTTGTTC
1 TTTAGCGGCGTTTGTGAAAAAGGCTTCGCTAAAGGTCATGTTC
* * *
38881926 TTTAGGGGCGTTTGTGAAAAAGG-TGCCGCTAAAGGTCATGTTT
1 TTTAGCGGCGTTTGTGAAAAAGGCT-TCGCTAAAGGTCATGTTC
*
38881969 TTTAGCGGCGTTTGTGATAAAAGTGC-T-GCTAAAGGTCACGTTC
1 TTTAGCGGCGTTTGTGA-AAAAG-GCTTCGCTAAAGGTCATGTTC
*
38882012 TTTAGTGGCGTTT
1 TTTAGCGGCGTTT
38882025 ATGTGAAAGA
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
42 1 0.01
43 77 0.92
44 5 0.06
45 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.37
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAAAAAGGCTTCGCTAAAGGTCATGTTC
Found at i:38884446 original size:15 final size:16
Alignment explanation
Indices: 38884414--38884447 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38884404 ATTTAATCTT
*
38884414 ATTTGCATTTAGGTTA
1 ATTTGCATCTAGGTTA
38884430 ATTTGCATCTA-GTTA
1 ATTTGCATCTAGGTTA
38884445 ATT
1 ATT
38884448 AATTTAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (16 bp):
ATTTGCATCTAGGTTA
Found at i:38886280 original size:19 final size:19
Alignment explanation
Indices: 38886205--38886281 Score: 91
Period size: 19 Copynumber: 4.0 Consensus size: 19
38886195 ATATGTCAAG
*
38886205 ATGCACTTTGTGTGCTAGAT
1 ATGCACTTTGTGTGCCAG-T
** * *
38886225 ATATACTTTCTGTGCCAAT
1 ATGCACTTTGTGTGCCAGT
38886244 ATGCACTTTGTGTGCCAGT
1 ATGCACTTTGTGTGCCAGT
*
38886263 ATGCACTTTATGTGCCAGT
1 ATGCACTTTGTGTGCCAGT
38886282 TTACCCTACT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 34 0.72
20 13 0.28
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (19 bp):
ATGCACTTTGTGTGCCAGT
Found at i:38887238 original size:28 final size:28
Alignment explanation
Indices: 38887207--38887289 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 28
38887197 TCCTATTCAA
* *
38887207 TTTCAACATAATAAGTGTAGACACTTAT
1 TTTCAACATAATAAATGAAGACACTTAT
* *
38887235 TTTCAACATAATAAAT-ACGGAAACTTAT
1 TTTCAACATAATAAATGA-AGACACTTAT
*
38887263 TTCCAACATAATAAATGAAGACACTTA
1 TTTCAACATAATAAATGAAGACACTTA
38887290 ATCAATCACA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 45 0.98
29 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (28 bp):
TTTCAACATAATAAATGAAGACACTTAT
Found at i:38890568 original size:55 final size:54
Alignment explanation
Indices: 38890404--38890569 Score: 176
Period size: 55 Copynumber: 3.0 Consensus size: 54
38890394 CGGATATTCT
* * * *
38890404 TATATATGTTAAACTATGACTTTGTAGAGGCTTGGGTCGGTTGTA-CAGAGATTTC
1 TATATATGTTAAATTATGACTTTGCAGAGGCTT-GGTAGGTTGTATGA-AGATTTC
* * * *
38890459 TATATATGTTAAATTATGGCTTTACAGAGGCTCAGGTAGGCTGT-TCAGAA-ATTTC
1 TATATATGTTAAATTATGACTTTGCAGAGGCT-TGGTAGGTTGTAT--GAAGATTTC
*
38890514 TATATATGTTAAATTATGACTTTGCAGAGGCTTGGTTGGGTTGTATGAAGATTTC
1 TATATATGTTAAATTATGACTTTGCAGAGGCTTGG-TAGGTTGTATGAAGATTTC
38890569 T
1 T
38890570 CAGTGTATTA
Statistics
Matches: 91, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
54 5 0.05
55 83 0.91
56 2 0.02
57 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (54 bp):
TATATATGTTAAATTATGACTTTGCAGAGGCTTGGTAGGTTGTATGAAGATTTC
Found at i:38890569 original size:110 final size:109
Alignment explanation
Indices: 38890353--38890558 Score: 272
Period size: 110 Copynumber: 1.9 Consensus size: 109
38890343 TAAAAGCATC
* * * * * *
38890353 ATATGTTAAATGTGGCTTTGCGGAGGTTCAGGTGGACTGTACGGATATTCTTATATATGTTAAAC
1 ATATGTTAAATATGGCTTTACAGAGGCTCAGGTGGACTGTACAGAAATTCTTATATATGTTAAAC
*
38890418 TATGACTTTGTAGAGGCTTGGGTCGGTTGTACAGAGATTTCTAT
66 TATGACTTTGCAGAGGCTTGGGTCGGTTGTACAGAGATTTCTAT
*
38890462 ATATGTTAAATTATGGCTTTACAGAGGCTCAGGTAGG-CTGTTCAGAAATT-TCTATATATGTTA
1 ATATGTTAAA-TATGGCTTTACAGAGGCTCAGGT-GGACTGTACAGAAATTCT-TATATATGTTA
* * *
38890525 AATTATGACTTTGCAGAGGCTTGGTTGGGTTGTA
63 AACTATGACTTTGCAGAGGCTTGGGTCGGTTGTA
38890559 TGAAGATTTC
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
109 11 0.13
110 70 0.84
111 2 0.02
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (109 bp):
ATATGTTAAATATGGCTTTACAGAGGCTCAGGTGGACTGTACAGAAATTCTTATATATGTTAAAC
TATGACTTTGCAGAGGCTTGGGTCGGTTGTACAGAGATTTCTAT
Found at i:38896392 original size:25 final size:26
Alignment explanation
Indices: 38896336--38896394 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
38896326 TAAACAACCT
*
38896336 AAAAAAATTAAAAATAAATGGAACAA
1 AAAAAAATTAAAAATAAATGAAACAA
* *
38896362 ATAAAAA-TAAAAATAAAT-AAATAA
1 AAAAAAATTAAAAATAAATGAAACAA
*
38896386 ACAAAAATT
1 AAAAAAATT
38896395 TTACTATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 10 0.36
25 12 0.43
26 6 0.21
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (26 bp):
AAAAAAATTAAAAATAAATGAAACAA
Found at i:38896496 original size:16 final size:16
Alignment explanation
Indices: 38896454--38896489 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
38896444 TAAACCCTGA
38896454 AACCAGAAAAATAAAG
1 AACCAGAAAAATAAAG
38896470 AACCAGAAAAATAAAG
1 AACCAGAAAAATAAAG
38896486 AACC
1 AACC
38896490 TTCAAAACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.67, C:0.17, G:0.11, T:0.06
Consensus pattern (16 bp):
AACCAGAAAAATAAAG
Found at i:38899641 original size:28 final size:28
Alignment explanation
Indices: 38899601--38899689 Score: 124
Period size: 28 Copynumber: 3.2 Consensus size: 28
38899591 TAGTAGTAGT
38899601 ACAGTGTGGGCCTTAGCCCAATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
* * **
38899629 ATAGTGTGAGCCTTAGCCCAATATTGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
* *
38899657 ACAGTGTGGGCCTTAGCCCAATATAGAA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
38899685 ACAGT
1 ACAGT
38899690 CTAGTGCAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAGTA
Found at i:38900096 original size:56 final size:56
Alignment explanation
Indices: 38900010--38900129 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
38900000 ACAAGGGATG
38900010 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
38900066 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
38900122 ATGGGCAA
1 ATGGGCAA
38900130 TAAACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:38902806 original size:22 final size:22
Alignment explanation
Indices: 38902778--38902899 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
38902768 TTCCACATCC
38902778 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
38902800 ATCACATATATACACTTTC-TCATT
1 ATCACAT-T-GGC-CATTCGGCCTT
38902824 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
38902847 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
38902871 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
38902894 ATCACA
1 ATCACA
38902900 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:38902813 original size:47 final size:47
Alignment explanation
Indices: 38902750--38903095 Score: 464
Period size: 47 Copynumber: 7.3 Consensus size: 47
38902740 CCCTTCGGGA
* * *
38902750 CTTATCACATTTATACACT-TCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
*
38902797 CTTATCACATATATACACT-TTCTCATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* *
38902844 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
38902891 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
38902938 CTTATCACACATACACATGTTCACATTCATCATATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
38902985 CTTATTACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
38903032 CTTATCACGCATATATATACT-TTCACATTCATCACATTCGCCACTCGGC
1 CTTATCA--CATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
*
38903081 CCTATCACATATATA
1 CTTATCACATATATA
38903096 TACTTGTACA
Statistics
Matches: 274, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.00
47 233 0.85
49 39 0.14
50 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:38906120 original size:40 final size:40
Alignment explanation
Indices: 38905889--38906113 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
38905879 TCGAATGATG
* * * *
38905889 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
38905929 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
38905969 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
38906008 TCCGGGTTAAGTCCCGAAGGAATTTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
38906048 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
38906089 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
38906114 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 34 0.21
40 117 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:38912625 original size:55 final size:55
Alignment explanation
Indices: 38912541--38912714 Score: 339
Period size: 55 Copynumber: 3.1 Consensus size: 55
38912531 ACAAGGGATG
38912541 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAATAAAATAAGAAGC
38912596 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAATAAAATAAGAAGC
38912651 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGG-AAAATAAAATAAGAAGC
38912707 ATGGGCAA
1 ATGGGCAA
38912715 TAAACTAATA
Statistics
Matches: 118, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
55 93 0.79
56 25 0.21
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.23
Consensus pattern (55 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAATAAAATAAGAAGC
Found at i:38914035 original size:78 final size:80
Alignment explanation
Indices: 38913894--38914117 Score: 269
Period size: 79 Copynumber: 2.8 Consensus size: 80
38913884 TCGAATGATG
* * * * * *
38913894 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
38913957 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
* *
38913974 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AATTC-GGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
38914036 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* * *
38914052 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
38914117 G
66 G
38914118 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
77 1 0.01
78 41 0.33
79 42 0.34
80 39 0.32
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:38914124 original size:40 final size:40
Alignment explanation
Indices: 38913894--38914117 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
38913884 TCGAATGATG
* * * *
38913894 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
38913934 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
38913974 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
38914013 TTC-GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
38914052 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
38914093 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
38914118 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 6 0.04
39 55 0.34
40 90 0.56
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:38915652 original size:26 final size:26
Alignment explanation
Indices: 38915579--38915665 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 26
38915569 CCAATATCGC
* * *
38915579 AGCAAAGCTGTCAGTAATAGCATTGC
1 AGCAAAGCTGCCAGTAATAGTATTGT
*
38915605 AGCAGAGCTGCCAGT-ATCAGTATTGT
1 AGCAAAGCTGCCAGTAAT-AGTATTGT
38915631 AGCAAAGCTGCCAGTAATAGTATATGT
1 AGCAAAGCTGCCAGTAATAGTAT-TGT
*
38915658 GGCAAAGC
1 AGCAAAGC
38915666 CACCAGTAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
25 2 0.04
26 38 0.73
27 12 0.23
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (26 bp):
AGCAAAGCTGCCAGTAATAGTATTGT
Found at i:38915671 original size:27 final size:27
Alignment explanation
Indices: 38915615--38915673 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
38915605 AGCAGAGCTG
**
38915615 CCAGT-ATCAGTATTGTAGCAAAGCTG
1 CCAGTAATCAGTATTGTAGCAAAGCCA
*
38915641 CCAGTAAT-AGTATATGTGGCAAAGCCA
1 CCAGTAATCAGTAT-TGTAGCAAAGCCA
38915668 CCAGTA
1 CCAGTA
38915674 GGTCTACAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
CCAGTAATCAGTATTGTAGCAAAGCCA
Found at i:38915999 original size:81 final size:82
Alignment explanation
Indices: 38915885--38916255 Score: 332
Period size: 81 Copynumber: 4.6 Consensus size: 82
38915875 AGGGGTATAA
* *
38915885 CAGTCATGTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCAGTCATGTTA
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCAGTCATTTTA
38915950 CCCTATG-A-GGGT-ATT
66 CCC-ATGTAGGGGTAATT
** ** * * *
38915965 TTGATCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGGGGGTATTTCGGTTATTTT
1 CAG-TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCAGTCATTTT
38916030 A-CCATGTAGGGGTAATT
65 ACCCATGTAGGGGTAATT
* * ** *
38916047 CAGTTATTTTACCCTATGGGGGTAATTCGGTCATTTTACCCTATAAAGGTAATTCAGTCATTTTA
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCAGTCATTTTA
* *
38916112 -CCTTGTGGGGGTAATT
66 CCCATGTAGGGGTAATT
* * * * * * * * * *
38916128 TAAT-AATTTCCCCTGTGAGGGTAATTCGGTCATTTTACCTTGT-GAGGGTAATTT-AGT-AATT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAG-GGGT-ATTTCAGTCATTT
* *
38916189 T-CCCTTGTGGGGGTAATT
64 TACCCATGTAGGGGTAATT
* * *
38916207 C-GATCATTTTACCCTGTGGGGGTAATTCGGTCATTTTATCCTATGAGGG
1 CAG-TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT-AGGG
38916256 TAATTCGATC
Statistics
Matches: 237, Mismatches: 43, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
79 24 0.10
80 76 0.32
81 132 0.56
82 5 0.02
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (82 bp):
CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCAGTCATTTTA
CCCATGTAGGGGTAATT
Found at i:38916125 original size:54 final size:54
Alignment explanation
Indices: 38915885--38916269 Score: 348
Period size: 54 Copynumber: 7.2 Consensus size: 54
38915875 AGGGGTATAA
* * * *
38915885 CAGTCATGTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATT
* * * * * *
38915939 CAGTCATGTTACCCTATGAGGGTATTTTGATCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATT
* * * * * *
38915993 TAGTCATTTTACCCTATGGGGGTATTTCGGTTATTTTACCATGTAGGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATT
* ***
38916047 CAGTTATTTTACCCTATGGGGGTAATTCGGTCATTTTACCCTATAAAGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATT
* * *** * * * *
38916101 CAGTCATTTTACCTTGTGGGGGTAATTTAAT-AATTTCCCCTGTGAGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATT
* * * * ** * *
38916154 CGGTCATTTTACCTTGTGAGGGTAATTTAGT-AATTT-CCCTTGTGGGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCC-TATGGGGGTAATT
* * *
38916207 C-GATCATTTTACCCTGTGGGGGTAATTCGGTCATTTTATCCTATGAGGGTAATT
1 CAG-TCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATT
38916261 C-GATCATTT
1 CAG-TCATTT
38916270 ATCGACCTCT
Statistics
Matches: 282, Mismatches: 45, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
52 4 0.01
53 87 0.31
54 189 0.67
55 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (54 bp):
CAGTCATTTTACCCTATGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATT
Found at i:38916166 original size:53 final size:53
Alignment explanation
Indices: 38916094--38916233 Score: 217
Period size: 53 Copynumber: 2.6 Consensus size: 53
38916084 ACCCTATAAA
*
38916094 GGTAATTCAGTCATTTTACCTTGTGGGGGTAATTTAATAATTTCCCCTGTGAG
1 GGTAATTCGGTCATTTTACCTTGTGGGGGTAATTTAATAATTTCCCCTGTGAG
* * * *
38916147 GGTAATTCGGTCATTTTACCTTGTGAGGGTAATTTAGTAATTTCCCTTGTGGG
1 GGTAATTCGGTCATTTTACCTTGTGGGGGTAATTTAATAATTTCCCCTGTGAG
* *
38916200 GGTAATTCGATCATTTTACCCTGTGGGGGTAATT
1 GGTAATTCGGTCATTTTACCTTGTGGGGGTAATT
38916234 CGGTCATTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 79 1.00
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.40
Consensus pattern (53 bp):
GGTAATTCGGTCATTTTACCTTGTGGGGGTAATTTAATAATTTCCCCTGTGAG
Found at i:38916258 original size:27 final size:27
Alignment explanation
Indices: 38915887--38916269 Score: 301
Period size: 27 Copynumber: 14.3 Consensus size: 27
38915877 GGGTATAACA
* * *
38915887 GTCATGTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTAATTCG
* *
38915914 GTCATTTTACCCTAT-AGGGGTATTTCA
1 GTCATTTTACCCTATGA-GGGTAATTCG
* * *
38915941 GTCATGTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTAATTCG
* * * **
38915968 ATCATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATGAGGGTAATTCG
* *
38915995 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTAATTCG
* *
38916022 GTTATTTTA-CC-ATGTAGGGGTAATTCA
1 GTCATTTTACCCTATG-A-GGGTAATTCG
* *
38916049 GTTATTTTACCCTATGGGGGTAATTCG
1 GTCATTTTACCCTATGAGGGTAATTCG
* * *
38916076 GTCATTTTACCCTATAAAGGTAATTCA
1 GTCATTTTACCCTATGAGGGTAATTCG
* * * **
38916103 GTCATTTTACCTTGTGGGGGTAATTTA
1 GTCATTTTACCCTATGAGGGTAATTCG
* * * *
38916130 AT-AATTTCCCCTGTGAGGGTAATTCG
1 GTCATTTTACCCTATGAGGGTAATTCG
* * **
38916156 GTCATTTTACCTTGTGAGGGTAATTTA
1 GTCATTTTACCCTATGAGGGTAATTCG
* * *
38916183 GT-AATTT-CCCTTGTGGGGGTAATTCG
1 GTCATTTTACCC-TATGAGGGTAATTCG
* * *
38916209 ATCATTTTACCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATGAGGGTAATTCG
*
38916236 GTCATTTTATCCTATGAGGGTAATTCG
1 GTCATTTTACCCTATGAGGGTAATTCG
*
38916263 ATCATTT
1 GTCATTT
38916270 ATCGACCTCT
Statistics
Matches: 291, Mismatches: 55, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
25 5 0.02
26 38 0.13
27 239 0.82
28 6 0.02
29 3 0.01
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTAATTCG
Found at i:38916498 original size:19 final size:19
Alignment explanation
Indices: 38916463--38916500 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
38916453 GTGTGGGGCC
*
38916463 CACGAGCCCATTGAGCCCA
1 CACGAGCCCATTCAGCCCA
38916482 CACG-GCCCATTTCAGCCCA
1 CACGAGCCCA-TTCAGCCCA
38916501 ACGTGGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.13
Consensus pattern (19 bp):
CACGAGCCCATTCAGCCCA
Found at i:38918488 original size:105 final size:100
Alignment explanation
Indices: 38918369--38918561 Score: 224
Period size: 105 Copynumber: 1.9 Consensus size: 100
38918359 TTTGTAGTGC
* * * * *
38918369 CATAACCCAATTATGATCTTATCATCATAATGTCATATCCCAACTATGGTCTTACACATGTATAT
1 CATAACCCAATTATGATCTTATCATCAAAATGCCATAACCCAACTATGGTATT--ACAT-T-TAA
* *
38918434 ATACTGCCATGGTCCAACCATGGTCTTACGTTCAAGGTCT
62 ACACTACCATGGTCCAA-CATGGTCTTACGTTCAAGGTCT
* * * * * *
38918474 CATAACCCAGTTATGGTCTTTTCATTAAAATGCCATAACCTAGCTATGGTATTACATTTAAACAC
1 CATAACCCAATTATGATCTTATCATCAAAATGCCATAACCCAACTATGGTATTACATTTAAACAC
38918539 TACCATGGTCCAACATGGTCTTA
66 TACCATGGTCCAACATGGTCTTA
38918562 TCCGCCAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
100 10 0.13
101 17 0.23
102 1 0.01
103 4 0.05
105 43 0.57
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (100 bp):
CATAACCCAATTATGATCTTATCATCAAAATGCCATAACCCAACTATGGTATTACATTTAAACAC
TACCATGGTCCAACATGGTCTTACGTTCAAGGTCT
Found at i:38921215 original size:5 final size:5
Alignment explanation
Indices: 38921181--38921214 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
38921171 CCCAGTCGTT
*
38921181 CCTCC CCTCC CCTCC CCTCC CCTCC CCTCT CCTC
1 CCTCC CCTCC CCTCC CCTCC CCTCC CCTCC CCTC
38921215 TTTTCTCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (5 bp):
CCTCC
Found at i:38925747 original size:18 final size:17
Alignment explanation
Indices: 38925718--38925781 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
38925708 AAGAAAACTT
38925718 TTTGAAATTGAATAACGA
1 TTTGAAA-TGAATAACGA
* *
38925736 TTTGTAAATGAATAATGT
1 TTTG-AAATGAATAACGA
*
38925754 TTTGGAAACGAATGACACGA
1 TTT-GAAATGAAT-A-ACGA
38925774 TTTGAAAT
1 TTTGAAAT
38925782 TAACATAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 22 0.61
19 9 0.25
20 5 0.14
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (17 bp):
TTTGAAATGAATAACGA
Found at i:38932712 original size:16 final size:16
Alignment explanation
Indices: 38932663--38932715 Score: 88
Period size: 16 Copynumber: 3.2 Consensus size: 16
38932653 TTTGGTTCGC
38932663 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
38932679 CGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
38932696 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
38932712 TGTA
1 TGTA
38932716 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 19 0.56
17 15 0.44
ACGTcount: A:0.25, C:0.02, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:38932969 original size:16 final size:16
Alignment explanation
Indices: 38932932--38932973 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
38932922 TTAATCATAT
*
38932932 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
38932948 TT-AAATATATTATAA
1 TTAAAATATATTATAA
38932963 TTAAAATATAT
1 TTAAAATATAT
38932974 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:38932980 original size:14 final size:15
Alignment explanation
Indices: 38932941--38932982 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38932931 TTTAAACATA
*
38932941 ATTATTATTAAATAT
1 ATTATAATTAAATAT
38932956 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
38932970 A-TATAATTTAATA
1 ATTATAATTAAATA
38932983 AAATTCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:38933091 original size:16 final size:16
Alignment explanation
Indices: 38933047--38933093 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
38933037 TACTATAAAA
*
38933047 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
38933063 TATTATT-AAATATAT
1 TATAATTAAAATATAT
38933078 TATAATTAAAATATAT
1 TATAATTAAAATATAT
38933094 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:38933154 original size:119 final size:120
Alignment explanation
Indices: 38932930--38933186 Score: 462
Period size: 119 Copynumber: 2.1 Consensus size: 120
38932920 ATTTAATCAT
*
38932930 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTTATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
38932995 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
38933051 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAAT-AAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
38933115 TTAATATTCTTATATGAATTTACTCAAATTATAATATATGATACTATAAAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
38933170 ATTTAACATAATTATTA
1 ATTTAACATAATTATTA
38933187 GACAACTGCC
Statistics
Matches: 132, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
119 81 0.61
120 47 0.36
121 4 0.03
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:38938314 original size:21 final size:21
Alignment explanation
Indices: 38938290--38938329 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
38938280 CGACATGGCC
38938290 GTGT-ATTTCAGCCACACGAGT
1 GTGTGATTT-AGCCACACGAGT
38938311 GTGTGATTTAGCCACACGA
1 GTGTGATTTAGCCACACGA
38938330 CCGTGTCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (21 bp):
GTGTGATTTAGCCACACGAGT
Found at i:38938335 original size:21 final size:21
Alignment explanation
Indices: 38938288--38938335 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
38938278 AACGACATGG
38938288 CCGTGTATTTCAGCCACACGA
1 CCGTGTATTTCAGCCACACGA
**
38938309 GTGTGTGATTT-AGCCACACGA
1 CCGTGT-ATTTCAGCCACACGA
38938330 CCGTGT
1 CCGTGT
38938336 CTACTCTGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (21 bp):
CCGTGTATTTCAGCCACACGA
Found at i:38938465 original size:21 final size:21
Alignment explanation
Indices: 38938441--38938493 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
38938431 GTCTCAGTCG
38938441 CACGGCCGTGTGCT-TCACTTA
1 CACGGCCGTGTG-TATCACTTA
* *
38938462 CACGGGCGTGTGTATCATTTA
1 CACGGCCGTGTGTATCACTTA
*
38938483 CACGGTCGTGT
1 CACGGCCGTGT
38938494 ACCTTTGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CACGGCCGTGTGTATCACTTA
Found at i:38941308 original size:30 final size:30
Alignment explanation
Indices: 38941274--38941422 Score: 203
Period size: 30 Copynumber: 5.0 Consensus size: 30
38941264 CTGAATTAAA
*
38941274 GCATGCATGTATTTAGGGAGTTGAATGGGG
1 GCATGCATGTATTTAGGGAGCTGAATGGGG
*
38941304 GCATGCATGTATTTAGGGAGTTGAATGGGG
1 GCATGCATGTATTTAGGGAGCTGAATGGGG
*
38941334 GCATGCATGTATTTAGGGAGCTGAAT-GGA
1 GCATGCATGTATTTAGGGAGCTGAATGGGG
* * *
38941363 GCATGCATGAATTTAGGGAGCTAAAT-GGA
1 GCATGCATGTATTTAGGGAGCTGAATGGGG
* *
38941392 GCATGCATGTAATTGAAGGAGCTGAATGGGG
1 GCATGCATGT-ATTTAGGGAGCTGAATGGGG
38941423 ATGCTAGATT
Statistics
Matches: 108, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
29 38 0.35
30 68 0.63
31 2 0.02
ACGTcount: A:0.28, C:0.09, G:0.37, T:0.27
Consensus pattern (30 bp):
GCATGCATGTATTTAGGGAGCTGAATGGGG
Found at i:38941376 original size:29 final size:29
Alignment explanation
Indices: 38941250--38941420 Score: 198
Period size: 30 Copynumber: 5.8 Consensus size: 29
38941240 GGTTCGGCCA
* * **
38941250 ATGTGTTTATGGAGCTGAATTAAAGCATGC
1 ATGTATTTAGGGAGCTGAA-TGGAGCATGC
* *
38941280 ATGTATTTAGGGAGTTGAATGGGGGCATGC
1 ATGTATTTAGGGAGCTGAAT-GGAGCATGC
* *
38941310 ATGTATTTAGGGAGTTGAATGGGGGCATGC
1 ATGTATTTAGGGAGCTGAAT-GGAGCATGC
38941340 ATGTATTTAGGGAGCTGAATGGAGCATGC
1 ATGTATTTAGGGAGCTGAATGGAGCATGC
* *
38941369 ATGAATTTAGGGAGCTAAATGGAGCATGC
1 ATGTATTTAGGGAGCTGAATGGAGCATGC
* *
38941398 ATGTAATTGAAGGAGCTGAATGG
1 ATGT-ATTTAGGGAGCTGAATGG
38941421 GGATGCTAGA
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
29 39 0.31
30 86 0.69
ACGTcount: A:0.29, C:0.08, G:0.35, T:0.29
Consensus pattern (29 bp):
ATGTATTTAGGGAGCTGAATGGAGCATGC
Found at i:38941413 original size:59 final size:59
Alignment explanation
Indices: 38941273--38941420 Score: 199
Period size: 59 Copynumber: 2.5 Consensus size: 59
38941263 GCTGAATTAA
* * * * *
38941273 AGCATGCATGTATTTAGGGAGTTGAATGGGGGCATGCATGTATTTAGGGAGTTGAATGGG
1 AGCATGCATGTATTTAGGGAGCTGAAT-GGAGCATGCATGAATTTAGGGAGCTAAATGGG
*
38941333 GGCATGCATGTATTTAGGGAGCTGAATGGAGCATGCATGAATTTAGGGAGCTAAAT-GG
1 AGCATGCATGTATTTAGGGAGCTGAATGGAGCATGCATGAATTTAGGGAGCTAAATGGG
* *
38941391 AGCATGCATGTAATTGAAGGAGCTGAATGG
1 AGCATGCATGT-ATTTAGGGAGCTGAATGG
38941421 GGATGCTAGA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
58 12 0.15
59 41 0.53
60 25 0.32
ACGTcount: A:0.28, C:0.09, G:0.36, T:0.27
Consensus pattern (59 bp):
AGCATGCATGTATTTAGGGAGCTGAATGGAGCATGCATGAATTTAGGGAGCTAAATGGG
Found at i:38943664 original size:21 final size:21
Alignment explanation
Indices: 38943637--38943683 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
38943627 GCTACATGGG
38943637 TGTGTGATTTAGCCACACAGGC
1 TGTGTGATTTAGCCACAC-GGC
38943659 -GTGTGATTTAGCCACACGGC
1 TGTGTGATTTAGCCACACGGC
38943679 TGTGT
1 TGTGT
38943684 CTACTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TGTGTGATTTAGCCACACGGC
Found at i:38958251 original size:44 final size:44
Alignment explanation
Indices: 38958188--38958329 Score: 212
Period size: 44 Copynumber: 3.2 Consensus size: 44
38958178 ATACCACACT
*
38958188 AGTAGGCACCGAAGTGCTGATTAGTAGGCACCATAGTGCAAATC
1 AGTAGGCACCGAAGTGCTGATTAGTAGGCACTATAGTGCAAATC
* * *
38958232 AGTAGGTACCGAAGTGCTGAGTAGTAGGCACTATAGTGCAAATT
1 AGTAGGCACCGAAGTGCTGATTAGTAGGCACTATAGTGCAAATC
* * * *
38958276 AGTACGCACTGTAGTGCTAATTAGTAGGCACTATAGTGCAAATC
1 AGTAGGCACCGAAGTGCTGATTAGTAGGCACTATAGTGCAAATC
38958320 AGTAGGCACC
1 AGTAGGCACC
38958330 ATAATGCTAA
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 85 1.00
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (44 bp):
AGTAGGCACCGAAGTGCTGATTAGTAGGCACTATAGTGCAAATC
Found at i:38958341 original size:22 final size:22
Alignment explanation
Indices: 38958188--38958341 Score: 125
Period size: 22 Copynumber: 7.0 Consensus size: 22
38958178 ATACCACACT
* *
38958188 AGTAGGCACCGA-AGTGCTGATT
1 AGTAGGCACC-ATAGTGCTAATC
*
38958210 AGTAGGCACCATAGTGCAAATC
1 AGTAGGCACCATAGTGCTAATC
* *
38958232 AGTAGGTACCGA-AGTGCTGAGT-
1 AGTAGGCACC-ATAGTGCT-AATC
* * *
38958254 AGTAGGCACTATAGTGCAAATT
1 AGTAGGCACCATAGTGCTAATC
* ** *
38958276 AGTACGCACTGTAGTGCTAATT
1 AGTAGGCACCATAGTGCTAATC
* *
38958298 AGTAGGCACTATAGTGCAAATC
1 AGTAGGCACCATAGTGCTAATC
*
38958320 AGTAGGCACCATAATGCTAATC
1 AGTAGGCACCATAGTGCTAATC
38958342 CTATACAATT
Statistics
Matches: 107, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
21 4 0.04
22 100 0.93
23 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (22 bp):
AGTAGGCACCATAGTGCTAATC
Found at i:38969742 original size:19 final size:20
Alignment explanation
Indices: 38969715--38969758 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
38969705 GTTGGTAAAT
*
38969715 ACATGTGTA-ATAATAATAA
1 ACATATGTATATAATAATAA
*
38969734 ACATATGTATTTAATAATAA
1 ACATATGTATATAATAATAA
38969754 A-ATAT
1 ACATAT
38969759 ATATTGCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (20 bp):
ACATATGTATATAATAATAA
Found at i:38969750 original size:20 final size:19
Alignment explanation
Indices: 38969725--38969763 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
38969715 ACATGTGTAA
*
38969725 TAATAATAAACATATGTATT
1 TAATAATAAA-ATATATATT
38969745 TAATAATAAAATATATATT
1 TAATAATAAAATATATATT
38969764 GCTTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (19 bp):
TAATAATAAAATATATATT
Found at i:38969797 original size:24 final size:26
Alignment explanation
Indices: 38969753--38969800 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
38969743 TTTAATAATA
*
38969753 AAATATATATTGCTTATTAATTAAGT
1 AAATATATATTGATTATTAATTAAGT
38969779 AAATATATATT-ATTA-TAATTAA
1 AAATATATATTGATTATTAATTAA
38969801 AACAAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
26 11 0.52
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (26 bp):
AAATATATATTGATTATTAATTAAGT
Found at i:38970892 original size:40 final size:40
Alignment explanation
Indices: 38970771--38970910 Score: 144
Period size: 40 Copynumber: 3.5 Consensus size: 40
38970761 AAGTTTGAGT
* *
38970771 CGATGAGACACTGGGTGTCAATTTATTACTTT-AGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTTGA-ATT-ATC
* * * ** *
38970812 CGATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
38970849 CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
* *
38970889 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
38970911 CTGGTGTGTT
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 17 0.22
38 11 0.14
39 2 0.03
40 33 0.42
41 16 0.20
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTTGAATTATC
Found at i:38976900 original size:40 final size:37
Alignment explanation
Indices: 38976818--38976906 Score: 117
Period size: 40 Copynumber: 2.3 Consensus size: 37
38976808 CAATTCAATA
*
38976818 ACAGT-TCAGTTCAGTTGGGCCTTAGCCCATTACAGT
1 ACAGTATCAGTTCAGTTAGGCCTTAGCCCATTACAGT
38976854 ATCAGTATCAGTATCAGTGTAGGCCTTAGCCCATTACAGT
1 A-CAGTATCAGT-TCAGT-TAGGCCTTAGCCCATTACAGT
*
38976894 GACAGTAACAGTT
1 -ACAGTATCAGTT
38976907 TAGACATGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
36 1 0.02
37 4 0.09
38 5 0.11
39 6 0.13
40 29 0.63
41 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (37 bp):
ACAGTATCAGTTCAGTTAGGCCTTAGCCCATTACAGT
Found at i:38977192 original size:25 final size:27
Alignment explanation
Indices: 38977164--38977216 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
38977154 ACAGTCATAC
38977164 ATAACATAAAG-CAT-ACAGTCATTTT
1 ATAACATAAAGCCATAACAGTCATTTT
**
38977189 ATAACATAGGGCCATAACAGTCATTTT
1 ATAACATAAAGCCATAACAGTCATTTT
38977216 A
1 A
38977217 CCACGTGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 3 0.12
27 12 0.50
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (27 bp):
ATAACATAAAGCCATAACAGTCATTTT
Found at i:38977212 original size:27 final size:27
Alignment explanation
Indices: 38977178--38977245 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
38977168 CATAAAGCAT
38977178 ACAGTCATTTTATAACATAGGGCCATA
1 ACAGTCATTTTATAACATAGGGCCATA
** * * *
38977205 ACAGTCATTTTACCACGTGGGGGCATA
1 ACAGTCATTTTATAACATAGGGCCATA
*
38977232 ACAATCATTTTATA
1 ACAGTCATTTTATA
38977246 TCAGTTTGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (27 bp):
ACAGTCATTTTATAACATAGGGCCATA
Found at i:38988021 original size:156 final size:156
Alignment explanation
Indices: 38987700--38988014 Score: 504
Period size: 156 Copynumber: 2.0 Consensus size: 156
38987690 TCAATCTTTC
* * ** * * *
38987700 TAGGATAAATTCAAATTGCCTCAACAGAAACCACGTGCCCTAGAAAAGTCACCTCTCGCAACCAG
1 TAGGATAAACTAAAATCACCTCAACAGAAACCACGTACCCCAGAAAAGTCACCTCTCACAACCAG
*
38987765 AACTCACACTTGCTCAACTTAGCGTAGAGTTGTTTCTCTCGAAATATCTGAAGCACTACTCTAAT
66 AACTCACACTTGCTCAACTTAGCGTAGAGTTGTTTCTCTCGAAATATCTGAAGCACTACTCTAAG
*
38987830 ATGTTCATCATGCTCATCCTCGGTCT
131 ATATTCATCATGCTCATCCTCGGTCT
* * *
38987856 TAGGATAAACTAAAATCACCTCAGCAGAAACTACGTACCCCAGAAAAGTCACCTCTCACAACTAG
1 TAGGATAAACTAAAATCACCTCAACAGAAACCACGTACCCCAGAAAAGTCACCTCTCACAACCAG
*
38987921 AACTCACACTTGCTCAACTTAGCGTAGAGTTGTTTCTCTCGAAGTATCTGAAGCACTACTCTAAG
66 AACTCACACTTGCTCAACTTAGCGTAGAGTTGTTTCTCTCGAAATATCTGAAGCACTACTCTAAG
*
38987986 ATATTCATCATGTTCATCCTCGGTCT
131 ATATTCATCATGCTCATCCTCGGTCT
38988012 TAG
1 TAG
38988015 AGTAAACCAA
Statistics
Matches: 145, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
156 145 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (156 bp):
TAGGATAAACTAAAATCACCTCAACAGAAACCACGTACCCCAGAAAAGTCACCTCTCACAACCAG
AACTCACACTTGCTCAACTTAGCGTAGAGTTGTTTCTCTCGAAATATCTGAAGCACTACTCTAAG
ATATTCATCATGCTCATCCTCGGTCT
Found at i:38992704 original size:16 final size:16
Alignment explanation
Indices: 38992683--38992738 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
38992673 CAGGGCATTA
*
38992683 CATTACAACTCTATTC
1 CATTACAGCTCTATTC
*
38992699 CATTACAGCTCTATTG
1 CATTACAGCTCTATTC
*
38992715 AATTACAGCTCTATTC
1 CATTACAGCTCTATTC
38992731 CATTACAG
1 CATTACAG
38992739 TAAACCAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (16 bp):
CATTACAGCTCTATTC
Found at i:39000398 original size:36 final size:36
Alignment explanation
Indices: 39000357--39000434 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
39000347 ATATGTTTAT
* *
39000357 TTTTTTATTAGTCCAAAAGATGACAATTATGTGCTT-A
1 TTTTTTATTACTCCAAAA-ATGACAATTATGCG-TTAA
* * *
39000394 TTTTTTATTACTCCTAAAATTATAATTATGCGTTAA
1 TTTTTTATTACTCCAAAAATGACAATTATGCGTTAA
39000430 TTTTT
1 TTTTT
39000435 ATTTAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
35 2 0.06
36 17 0.49
37 16 0.46
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (36 bp):
TTTTTTATTACTCCAAAAATGACAATTATGCGTTAA
Found at i:39003180 original size:44 final size:44
Alignment explanation
Indices: 39003112--39003202 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
39003102 GTAGGTCAAA
* *
39003112 TAATATTGAAATAACCTACACTAATAAGAGTTTAAGTG-GAAAAC
1 TAATATTAAAAAAACCTACACTAATAAGAGTTTAAGTGAG-AAAC
* *
39003156 TAATATTAAAAAAACCTACGCTAATCAGAGTTTAAGTGAGAAAC
1 TAATATTAAAAAAACCTACACTAATAAGAGTTTAAGTGAGAAAC
39003200 TAA
1 TAA
39003203 AAACATAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.26
Consensus pattern (44 bp):
TAATATTAAAAAAACCTACACTAATAAGAGTTTAAGTGAGAAAC
Found at i:39015706 original size:18 final size:19
Alignment explanation
Indices: 39015685--39015720 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39015675 ACATGTGTAA
39015685 TAATAA-ACAACATGTATT
1 TAATAATACAACATGTATT
*
39015703 TAATAATACAATATGTAT
1 TAATAATACAACATGTAT
39015721 GGCTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (19 bp):
TAATAATACAACATGTATT
Found at i:39016918 original size:23 final size:23
Alignment explanation
Indices: 39016892--39016946 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 23
39016882 AGACACTTTA
*
39016892 TGTGTCGTATTTTAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* *
39016915 TGTGTTGTA--TCAGGCACTTCG
1 TGTGTCGTATTTCAGGCACCTCG
39016936 TGTGTCGTATT
1 TGTGTCGTATT
39016947 AGGCAGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 18 0.69
23 8 0.31
ACGTcount: A:0.13, C:0.18, G:0.27, T:0.42
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:39016929 original size:21 final size:21
Alignment explanation
Indices: 39016905--39016951 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
39016895 GTCGTATTTT
*
39016905 AGGCACCTCGTGTGTTGTATC
1 AGGCACCTCGTGTGTCGTATC
* *
39016926 AGGCACTTCGTGTGTCGTATT
1 AGGCACCTCGTGTGTCGTATC
39016947 AGGCA
1 AGGCA
39016952 GTTATGTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.32
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTATC
Found at i:39028891 original size:26 final size:26
Alignment explanation
Indices: 39028840--39028901 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
39028830 TACCTATAGT
*
39028840 AGTTTCAAAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
39028866 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
39028892 AGTTTCAGAA
1 AGTTTCAGAA
39028902 CACTTACAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:39035733 original size:27 final size:27
Alignment explanation
Indices: 39035660--39035719 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
39035650 GCATCATAGT
** *
39035660 TAGTCTGACAGGACATTAAACACGAGA
1 TAGTCTGATGGGACAATAAACACGAGA
39035687 TAGTCTGATGGGACAATAAACACGAGA
1 TAGTCTGATGGGACAATAAACACGAGA
39035714 TAGTCT
1 TAGTCT
39035720 ATAGGGGCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (27 bp):
TAGTCTGATGGGACAATAAACACGAGA
Found at i:39037448 original size:536 final size:533
Alignment explanation
Indices: 39036146--39037727 Score: 2661
Period size: 536 Copynumber: 3.0 Consensus size: 533
39036136 CATCTTGAAG
* *
39036146 TATTCATGAACAATAACACACTAGTAGGTGCCTGGTGTATAGGCAAACAAAAGAAGGTTTATCCG
1 TATTCATGAACAATAACACACTAGTAGGTGCCTGGTGTATAGGTAAAAAAAAGAAGGTTTATCCG
* * *
39036211 AGGATCACAGATAAAGATCTACCAATAATAACCTCCAAAGGGTGCTCAGTGAAAACCTACATGTT
66 AGGATCACAGATAAAGATCCACCAATAAAAACCACCAAAGGGTGCTCAGTGAAAACCTACATGTT
39036276 AGAGATTGAGCATAAATACGACAGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGT
131 AGAGATTGAGCATAAATACGACAGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGT
* *
39036341 CAGAGTGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAATACTATTCCTCTTTA
196 CAGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTA
* * * *
39036406 AGGGGAATATGTTGCT-AAGTACTCACCAAATGGGTAGTTCCATGGGAACCAACATGTAAGAGGA
261 AGGGGATTATGTTG-TGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACATGTAAGCGGA
*
39036470 ATCGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAATCCATAGTTGATGGGCAT
325 ATCGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCAT
** * *
39036535 GTTATGTAT-A-AG-AGGTAACACATGTGAATTGGGTTACAAAGATGTAATCCCATCACTATGAA
390 GTTATGTATAAGAGTAGGTAACGTAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATTAA
* * *
39036597 ACCCAATTGCTATTTAGCTTGCCATAGTGGTATGGGATCTCATCAATTATTCCAATAAATGGTGT
455 ACCCAATTGCTATTTAGCTTGCCAGAGTGGTGTGGGATCTCATCAGTTATTCCAATAAATGGTGT
39036662 GGGATCTCATCAAT
520 GGGATCTCATCAAT
*
39036676 TATTCATGAACAATAACACGCTAGTAGGTGCCTGGTGTATAGGT-AAAAAAAGAAGGTTTATCCG
1 TATTCATGAACAATAACACACTAGTAGGTGCCTGGTGTATAGGTAAAAAAAAGAAGGTTTATCCG
* *
39036740 AGGATCACAGATAAAGATCCACCAATAAGAACCACCAAAAGGTGCTCAGTGAAAACCTACATGTT
66 AGGATCACAGATAAAGATCCACCAATAAAAACCACCAAAGGGTGCTCAGTGAAAACCTACATGTT
** * *
39036805 AGAGATTGAGCATAAATACGACAACTAGTCCATTGAATAAAGAGGTTTTAGCTAGAAGCCATAGT
131 AGAGATTGAGCATAAATACGACAGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGT
** *
39036870 TGGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTAA
196 CAGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTA
39036935 AGGGGATTATGTTGTGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACATGTAAGCGGAA
261 AGGGGATTATGTTGTGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACATGTAAGCGGAA
* *
39037000 TCGTGAACTTAAATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGTCATG
326 TCGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCATG
39037065 TTATGTATAAGAGTAAGGTAACGTAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATTAA
391 TTATGTATAAGAGT-AGGTAACGTAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATTAA
*
39037130 ACCCAATTTCTATTTAGCTTGCCAGAGTGGTGTGGGATCTCATCAGTTATTCCAATAAATGGTGT
455 ACCCAATTGCTATTTAGCTTGCCAGAGTGGTGTGGGATCTCATCAGTTATTCCAATAAATGGTGT
*
39037195 GGGATCTCATCAGT
520 GGGATCTCATCAAT
* *
39037209 TATTCAAGAACAATAAACACACTATTAGGTGCCTGGTGTATAGGTAAAAAAGAAGAAGGTTTATC
1 TATTCATGAACAAT-AACACACTAGTAGGTGCCTGGTGTATAGGTAAAAAA-AAGAAGGTTTATC
* * *
39037274 CGAGGATCACAGATAAAGATCCACGAATAAAAACCACTAAAGGGTGCTCAGTGAAAACCTGCATG
64 CGAGGATCACAGATAAAGATCCACCAATAAAAACCACCAAAGGGTGCTCAGTGAAAACCTACATG
*
39037339 TTAGAGATTGAGCATAAATACGACGGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATA
129 TTAGAGATTGAGCATAAATACGACAGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATA
* *
39037404 GTCAGAGAGAGTCACACAAAGGGATATATCAAGTGACAAATATGTCTGTTAAGACTATTCCTCTT
194 GTCAGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTT
* *
39037469 TAAGGGGATTATGTTGTGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACGTGTAAGCGA
259 TAAGGGGATTATGTTGTGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACATGTAAGCGG
*
39037534 AATCGTGAACTTAGATGACAATTATCTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCA
324 AATCGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCA
39037599 TGTTATGTATAAGAGTGAGGTAACGTAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATT
389 TGTTATGTATAAGAGT-AGGTAACGTAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATT
* * *
39037664 AAACCCAATTGCTATTTAGTTTGCCAGAGTGGTGTGAGATCTCATCAGTTATTCCAACAAATGG
453 AAACCCAATTGCTATTTAGCTTGCCAGAGTGGTGTGGGATCTCATCAGTTATTCCAATAAATGG
39037728 AATGTGAGTA
Statistics
Matches: 984, Mismatches: 60, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
528 1 0.00
529 330 0.34
530 43 0.04
531 2 0.00
533 133 0.14
534 28 0.03
535 5 0.01
536 442 0.45
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (533 bp):
TATTCATGAACAATAACACACTAGTAGGTGCCTGGTGTATAGGTAAAAAAAAGAAGGTTTATCCG
AGGATCACAGATAAAGATCCACCAATAAAAACCACCAAAGGGTGCTCAGTGAAAACCTACATGTT
AGAGATTGAGCATAAATACGACAGTTAGTCCATTGAGTAAAGAGGGTTTAGCTAGAAGCCATAGT
CAGAGAGAGTCACACAGAGGGATATATCGAGTGACAAATATGTCTGTTAAGACTATTCCTCTTTA
AGGGGATTATGTTGTGAAGTACTCGCCAAATGGGTAGTTCCATGGTAACCAACATGTAAGCGGAA
TCGTGAACTTAGATGACAATTATTTGAGTACAATAGGCCAAGATAGTCCATAGTTGATGGGCATG
TTATGTATAAGAGTAGGTAACGTAGGTGAATTGGGTTACAAAGATGTAATCCCATCACTATTAAA
CCCAATTGCTATTTAGCTTGCCAGAGTGGTGTGGGATCTCATCAGTTATTCCAATAAATGGTGTG
GGATCTCATCAAT
Found at i:39042238 original size:38 final size:38
Alignment explanation
Indices: 39042187--39042264 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
39042177 ATAAAACAAG
* *
39042187 TATGTTATTACAATCATCTCATGACTGGTCTTTGGGCA
1 TATGTTATTACAATCATCTCATGACTGGTCCTTGGCCA
39042225 TATGTTATTACAATCATCTCATGACTGGTCCTTGGCCA
1 TATGTTATTACAATCATCTCATGACTGGTCCTTGGCCA
39042263 TA
1 TA
39042265 CTCCATTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (38 bp):
TATGTTATTACAATCATCTCATGACTGGTCCTTGGCCA
Found at i:39057316 original size:39 final size:39
Alignment explanation
Indices: 39057260--39057347 Score: 167
Period size: 39 Copynumber: 2.3 Consensus size: 39
39057250 TAATGAAGTT
39057260 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
1 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
*
39057299 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGAG
1 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
39057338 GGTGAGGGTG
1 GGTGAGGGTG
39057348 AGGGTGGTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.18, C:0.02, G:0.52, T:0.27
Consensus pattern (39 bp):
GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
Found at i:39057345 original size:45 final size:44
Alignment explanation
Indices: 39057260--39057387 Score: 158
Period size: 45 Copynumber: 3.0 Consensus size: 44
39057250 TAATGAAGTT
*
39057260 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAA-T-GT---GGTGAG
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGTGGTGAGGGTGAG
39057299 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGAGGGTGAG
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAA-GTGGTGAGGGTGAG
* * * *
39057344 GGTGAGGGTGGTGAGGTTGCTGACAGTAGAGGTGGTGAGAGTGA
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTA-AAGTGGTGAGGGTGA
39057388 TAGAAGTGGT
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
39 29 0.38
41 1 0.01
42 2 0.03
45 44 0.57
46 1 0.01
ACGTcount: A:0.20, C:0.03, G:0.52, T:0.26
Consensus pattern (44 bp):
GGTGAGGGTGGTGAGGTTGTTGGCAGTAAAGTGGTGAGGGTGAG
Found at i:39057381 original size:39 final size:39
Alignment explanation
Indices: 39057260--39057387 Score: 139
Period size: 39 Copynumber: 3.1 Consensus size: 39
39057250 TAATGAAGTT
* * *
39057260 GGTGAGGGTGGTAAGGTTGTTGGCAGTAAATGTGGTGAG
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTAGAGGTGGTGAG
*
39057299 GGTGAGGGTGGTGAGGTTGTTGGCAGTAAATGTGGTGAGGGTGAG
1 GGTGAGGGTGGTGAGGTTGTTGGCAGT--A-GAGGT---GGTGAG
* *
39057344 GGTGAGGGTGGTGAGGTTGCTGACAGTAGAGGTGGTGAG
1 GGTGAGGGTGGTGAGGTTGTTGGCAGTAGAGGTGGTGAG
*
39057383 AGTGA
1 GGTGA
39057388 TAGAAGTGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
39 36 0.48
41 1 0.01
42 6 0.08
43 1 0.01
45 31 0.41
ACGTcount: A:0.20, C:0.03, G:0.52, T:0.26
Consensus pattern (39 bp):
GGTGAGGGTGGTGAGGTTGTTGGCAGTAGAGGTGGTGAG
Found at i:39060055 original size:82 final size:82
Alignment explanation
Indices: 39059927--39060129 Score: 334
Period size: 82 Copynumber: 2.5 Consensus size: 82
39059917 TTGAGATTGT
*
39059927 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACAACTTACTACTATA
1 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAATGATTGGTTAACAACTTACTACTATA
39059992 GGATCATTTTGTTAGCA
66 GGATCATTTTGTTAGCA
* * * * *
39060009 TAACATATTTTGTTTGTTTTTTTAAATGATTTGTTGAAATGATTGGTTAACATCTTATTGCTATA
1 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAATGATTGGTTAACAACTTACTACTATA
*
39060074 GGATCATTTTGTTAGTA
66 GGATCATTTTGTTAGCA
*
39060091 TAACATATTTTATTTGTTTTTTGGAATGATTTGTTGAAA
1 TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAA
39060130 GATGTATACC
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 111 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (82 bp):
TAACATATTTTATTTGTTTTTTGAAATGATTTGTTGAAATGATTGGTTAACAACTTACTACTATA
GGATCATTTTGTTAGCA
Found at i:39061625 original size:115 final size:112
Alignment explanation
Indices: 39061468--39061678 Score: 325
Period size: 115 Copynumber: 1.9 Consensus size: 112
39061458 TACTCTAATA
*
39061468 TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAATAAAAAAATAAAAAAAGAATC-CCCAA
1 TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAAT-AAAAAAT-AAAAAA-AATCACACAA
* *
39061532 TTTCTTATGAACCTTAAAATAAATCGGCTAAATATGCTTACCCGAATACAT
63 TTTCTTATGAACCCTAAAACAAAT-GGCTAAATATGCTTACCCGAATACAT
* * *
39061583 TTCATGCATGGGAAAGAAATGTTTCATTAATATCCAATTAAAAAATAAAAAAAATCACACAATTT
1 TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAATAAAAAATAAAAAAAATCACACAATTT
39061648 CTTATGAACCCTAAAACAAATGGCTAAATAT
66 CTTATGAACCCTAAAACAAATGGCTAAATAT
39061679 ACAGTGATTA
Statistics
Matches: 89, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
112 14 0.16
113 32 0.36
114 7 0.08
115 36 0.40
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (112 bp):
TTCAAGCATGGGAAAGAAATGTTTCATCAATATCCAAATAAAAAATAAAAAAAATCACACAATTT
CTTATGAACCCTAAAACAAATGGCTAAATATGCTTACCCGAATACAT
Found at i:39062172 original size:18 final size:18
Alignment explanation
Indices: 39062139--39062177 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
39062129 TTAAATATTT
*
39062139 TTTTTTAATTTTAATT-A
1 TTTTTTAATTTAAATTCA
39062156 TTTTTTAAGTTTAAATTCA
1 TTTTTTAA-TTTAAATTCA
39062175 TTT
1 TTT
39062178 GCTGATGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTTTAATTTAAATTCA
Found at i:39063224 original size:29 final size:31
Alignment explanation
Indices: 39063192--39063255 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
39063182 TCTAGAAAAA
*
39063192 AATAATCTAGTAACTTAAATA-AA-ATTTTT
1 AATAATCTACTAACTTAAATAGAATATTTTT
* *
39063221 AATAATTTACTAACTTAAATAGAATCTTTTT
1 AATAATCTACTAACTTAAATAGAATATTTTT
39063252 AATA
1 AATA
39063256 TTTGAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 19 0.63
30 2 0.07
31 9 0.30
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
AATAATCTACTAACTTAAATAGAATATTTTT
Done.