Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 128 of 325
Found at i:40047753 original size:5 final size:5
Alignment explanation
Indices: 40047743--40047808 Score: 55
Period size: 5 Copynumber: 12.6 Consensus size: 5
40047733 ATTAATATCC
*
40047743 AAATA AAATA AAGTA ATAATAA ATAATA AAATTA AAATTA AAATA AAA-A
1 AAATA AAATA AAATA A-AAT-A A-AATA AAA-TA AAA-TA AAATA AAATA
*
40047792 GAA-A AAATA AAATA AAA
1 AAATA AAATA AAATA AAA
40047809 ATTGGGTTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
4 6 0.11
5 26 0.49
6 15 0.28
7 6 0.11
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:40047791 original size:18 final size:18
Alignment explanation
Indices: 40047770--40047811 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40047760 AATAAATAAT
*
40047770 AAAATTAAAATTAAAATA
1 AAAATTAAAAATAAAATA
**
40047788 AAAAGAAAAAATAAAATA
1 AAAATTAAAAATAAAATA
40047806 AAAATT
1 AAAATT
40047812 GGGTTACCTC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAATTAAAAATAAAATA
Found at i:40058504 original size:10 final size:9
Alignment explanation
Indices: 40058473--40058511 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
40058463 TTGAATCATT
*
40058473 AAAATATTA
1 AAAATATAA
*
40058482 ATAATATAA
1 AAAATATAA
40058491 AAAATATGAA
1 AAAATAT-AA
40058501 AAAATATAA
1 AAAATATAA
40058510 AA
1 AA
40058512 CTAAAAGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (9 bp):
AAAATATAA
Found at i:40059271 original size:16 final size:15
Alignment explanation
Indices: 40059241--40059269 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40059231 ATGTCCCTTT
40059241 TTTTTAAAATATTTA
1 TTTTTAAAATATTTA
40059256 TTTTTAAAATATTT
1 TTTTTAAAATATTT
40059270 TACTATATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAAAATATTTA
Found at i:40063140 original size:42 final size:41
Alignment explanation
Indices: 40063083--40063284 Score: 140
Period size: 43 Copynumber: 4.9 Consensus size: 41
40063073 CGTTTGTTTG
*
40063083 AAAAAACGCCACTAAAGATCATGACTTTTAGCGGCTTTTTT
1 AAAAAACGCCGCTAAAGATCATGACTTTTAGCGGCTTTTTT
* * * * *
40063124 AAAAAAGCGCCGCTAAA-AGCCTG-GTCTTTAGTGGCACTGTTTT
1 AAAAAA-CGCCGCTAAAGATCATGACT-TTTAGCGG--CTTTTTT
* * * * * *
40063167 AGAAAACGCCGCTAAAGGTCCTGTC-TTTAGCGACATTTTT
1 AAAAAACGCCGCTAAAGATCATGACTTTTAGCGGCTTTTTT
* ** * * *
40063207 ATAAAACGCCATTAAAAACCAAGACTTTTAGCGGCATTTTTTT
1 AAAAAACGCCGCTAAAGATCATGACTTTTAGCGGC--TTTTTT
* * *
40063250 AAAAAACGCCGCTAAAGCTAATGACCTTTAGCGGC
1 AAAAAACGCCGCTAAAGATCATGACTTTTAGCGGC
40063285 GCTTTACCCA
Statistics
Matches: 118, Mismatches: 34, Indels: 16
0.70 0.20 0.10
Matches are distributed among these distances:
40 22 0.19
41 25 0.21
42 25 0.21
43 46 0.39
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGATCATGACTTTTAGCGGCTTTTTT
Found at i:40063458 original size:25 final size:25
Alignment explanation
Indices: 40063408--40063468 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
40063398 TATCCATGAT
* * *
40063408 ATAAATATAAAAATTTTCTATTAAA
1 ATAAAAATAAAAATTTTCAATCAAA
40063433 ATAAAAATAAAAATTTAT-AATCAAA
1 ATAAAAATAAAAATTT-TCAATCAAA
40063458 ACT-AAAATAAA
1 A-TAAAAATAAA
40063469 TAATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (25 bp):
ATAAAAATAAAAATTTTCAATCAAA
Found at i:40068471 original size:16 final size:16
Alignment explanation
Indices: 40068452--40068483 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40068442 GCTGAGATTA
40068452 TATTTTTTGAAATTTT
1 TATTTTTTGAAATTTT
*
40068468 TATTTTTTTAAATTTT
1 TATTTTTTGAAATTTT
40068484 AAATATTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TATTTTTTGAAATTTT
Found at i:40068545 original size:7 final size:7
Alignment explanation
Indices: 40068535--40068617 Score: 78
Period size: 7 Copynumber: 11.6 Consensus size: 7
40068525 AATATTAAAA
40068535 TTTTAAGT
1 TTTTAA-T
40068543 TTTTAAGT
1 TTTTAA-T
40068551 TTTTAA-
1 TTTTAAT
40068557 TTTTAAT
1 TTTTAAT
*
40068564 TTTTTAT
1 TTTTAAT
40068571 TTTTCAAT
1 TTTT-AAT
*
40068579 TTTCAAT
1 TTTTAAT
*
40068586 TTTCAAT
1 TTTTAAT
*
40068593 TTTCAAT
1 TTTTAAT
*
40068600 TTTCAAT
1 TTTTAAT
*
40068607 TTTCAAT
1 TTTTAAT
40068614 TTTT
1 TTTT
40068618 TTAAAGATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
6 6 0.09
7 44 0.64
8 19 0.28
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTTAAT
Found at i:40068562 original size:14 final size:14
Alignment explanation
Indices: 40068550--40068616 Score: 91
Period size: 14 Copynumber: 4.8 Consensus size: 14
40068540 AGTTTTTAAG
*
40068550 TTTTTAATTTT-AA
1 TTTTCAATTTTCAA
**
40068563 TTTTTTATTTTTCAA
1 TTTTCAAT-TTTCAA
40068578 TTTTCAATTTTCAA
1 TTTTCAATTTTCAA
40068592 TTTTCAATTTTCAA
1 TTTTCAATTTTCAA
40068606 TTTTCAATTTT
1 TTTTCAATTTT
40068617 TTTAAAGATT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
13 7 0.14
14 34 0.69
15 8 0.16
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTTCAA
Found at i:40068595 original size:21 final size:21
Alignment explanation
Indices: 40068571--40068616 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
40068561 AATTTTTTAT
40068571 TTTTCAATTTTCAATTTTCAA
1 TTTTCAATTTTCAATTTTCAA
40068592 TTTTCAATTTTCAATTTTCAA
1 TTTTCAATTTTCAATTTTCAA
40068613 TTTT
1 TTTT
40068617 TTTAAAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTCAATTTTCAATTTTCAA
Found at i:40069266 original size:6 final size:6
Alignment explanation
Indices: 40069257--40069299 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
40069247 TTTCAAAACC
* *
40069257 AAAGGG AAAGGG AAAGGG AAAGGG AAAAGG AAAGGG GAAGGG A
1 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG A
40069300 TCATATGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
AAAGGG
Found at i:40069981 original size:15 final size:15
Alignment explanation
Indices: 40069958--40069987 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40069948 CTACCCATGG
*
40069958 CCATTAAACCTTAAA
1 CCATAAAACCTTAAA
40069973 CCATAAAACCTTAAA
1 CCATAAAACCTTAAA
40069988 TTATAGACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (15 bp):
CCATAAAACCTTAAA
Found at i:40070188 original size:48 final size:46
Alignment explanation
Indices: 40070144--40070267 Score: 124
Period size: 48 Copynumber: 2.6 Consensus size: 46
40070134 TGTTTTTTAA
* * *
40070144 GGTTTAGGGTTTTAGGGGTTATAGATTAGTGTTTAA-AGTTTTTTTG
1 GGTTTAGGGTTTTAGGGGTTATAGACTAATGTCTAAGA-TTTTTTTG
* * *
40070190 GGTTTAGGGGTTTAGAGGTTATATAGACTAATGTCTATGATTTTTTTTGG
1 GGTTTAGGGTTTTAG-GGGT-TATAGACTAATGTCTAAGA-TTTTTTT-G
*
40070240 GGTTTAAGGTTTTAGGGGTTATATGACT
1 GGTTTAGGGTTTTAGGGGTTATA-GACT
40070268 TTTAGCGGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
46 14 0.22
47 3 0.05
48 17 0.27
49 15 0.24
50 14 0.22
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.47
Consensus pattern (46 bp):
GGTTTAGGGTTTTAGGGGTTATAGACTAATGTCTAAGATTTTTTTG
Found at i:40070314 original size:41 final size:41
Alignment explanation
Indices: 40070286--40070502 Score: 355
Period size: 41 Copynumber: 5.3 Consensus size: 41
40070276 CATTTTTGGT
40070286 AAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGCTTTGACC-
1 AAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGCTTTG-CCA
* * *
40070327 AAAACGCCGCTTTTACTCTGTTTTTTAGCTGCGCTTTGCCA
1 AAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGCTTTGCCA
*
40070368 AAAACGCCGCTATTGCTCTGTTTTTTAGCTGCGCTTTGCCA
1 AAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGCTTTGCCA
*
40070409 AAAACGCCGCTATTGCTCTGTTTTTTAGTGGCGCTTTGCCA
1 AAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGCTTTGCCA
* *
40070450 AAAACGCCGCTATTGCTCTGTTTTTTAGTGGCGCTTTGTCA
1 AAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGCTTTGCCA
40070491 AAAACGCCGCTA
1 AAAACGCCGCTA
40070503 ATGTATAATT
Statistics
Matches: 167, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 2 0.01
41 165 0.99
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.35
Consensus pattern (41 bp):
AAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGCTTTGCCA
Found at i:40070515 original size:82 final size:80
Alignment explanation
Indices: 40070286--40070542 Score: 306
Period size: 82 Copynumber: 3.1 Consensus size: 80
40070276 CATTTTTGGT
* * *
40070286 AAAACGCCGCTATTGCTCTGTTTTTTAGCGGCGCTTTGACCAAAACGCCGCT-TTTACTCTGTTT
1 AAAACGCCGCTATTGCTCTGTTTTTTAGTGGCGCTTTGACAAAAACGCCGCTATGTA---TGTTT
40070350 TTTAGCT-GCGCTTTGCCA
63 TTTAG-TGGCGCTTTGCCA
* *
40070368 AAAACGCCGCTATTGCTCTGTTTTTTAGCT-GCGCTTTGCCAAAAACGCCGCTATTGCTCTGTTT
1 AAAACGCCGCTATTGCTCTGTTTTTTAG-TGGCGCTTTGACAAAAACGCCGCTA-TG-TATGTTT
40070432 TTTAGTGGCGCTTTGCCA
63 TTTAGTGGCGCTTTGCCA
* **
40070450 AAAACGCCGCTATTGCTCTGTTTTTTAGTGGCGCTTTGTCAAAAACGCCGCTAATGTATAATTTT
1 AAAACGCCGCTATTGCTCTGTTTTTTAGTGGCGCTTTGACAAAAACGCCGCT-ATGTATGTTTTT
* **
40070515 T-GTGGCGTTTTTTCA
65 TAGTGGCGCTTTGCCA
40070530 TAAAACGCCGCTA
1 -AAAACGCCGCTA
40070543 AAGCCCTATT
Statistics
Matches: 155, Mismatches: 12, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
80 11 0.07
81 21 0.14
82 120 0.77
83 1 0.01
84 1 0.01
85 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (80 bp):
AAAACGCCGCTATTGCTCTGTTTTTTAGTGGCGCTTTGACAAAAACGCCGCTATGTATGTTTTTT
AGTGGCGCTTTGCCA
Found at i:40070554 original size:40 final size:40
Alignment explanation
Indices: 40070348--40070546 Score: 125
Period size: 41 Copynumber: 4.9 Consensus size: 40
40070338 TTTACTCTGT
* ** * **
40070348 TTTTTAGCT-GCGCTTTGCCAAAAACGCCGCTATTGCTCTGT
1 TTTTTAG-TGGCGCTTTGTCAAAAACGCCGCTAAAGC-ATAA
* ** * **
40070389 TTTTTAGCT-GCGCTTTGCCAAAAACGCCGCTATTGCTCTGT
1 TTTTTAG-TGGCGCTTTGTCAAAAACGCCGCTAAAGC-ATAA
* ** * **
40070430 TTTTTAGTGGCGCTTTGCCAAAAACGCCGCTATTGCTCTGT
1 TTTTTAGTGGCGCTTTGTCAAAAACGCCGCTAAAGC-ATAA
* *
40070471 TTTTTAGTGGCGCTTTGTCAAAAACGCCGCTAATGTATAA
1 TTTTTAGTGGCGCTTTGTCAAAAACGCCGCTAAAGCATAA
* *
40070511 TTTTT-GTGGCGTTTTTTCATAAAACGCCGCTAAAGC
1 TTTTTAGTGGCGCTTTGTCA-AAAACGCCGCTAAAGC
40070547 CCTATTTTCC
Statistics
Matches: 146, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 12 0.08
40 21 0.14
41 113 0.77
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (40 bp):
TTTTTAGTGGCGCTTTGTCAAAAACGCCGCTAAAGCATAA
Found at i:40075249 original size:62 final size:58
Alignment explanation
Indices: 40075165--40075297 Score: 151
Period size: 62 Copynumber: 2.2 Consensus size: 58
40075155 TCCAAAAATA
* * * *
40075165 ATATTATTTTAAT-ATTTTAATATTAGATTTAATTTAATGCTTATCTACAAGATAAATATT
1 ATATTATTTTAATAAATTTAATATTAAATTTAATCTAATACTTATCT--AA-ATAAATATT
* * *
40075225 TTATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAATATT
1 ATATTATTTTAATAA-ATTTAATATTAAATTTAATCTAATACTTATCTAAATAAATATT
*
40075284 ATATTAATTTAATA
1 ATATTATTTTAATA
40075298 TTAAAGTAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
59 21 0.34
60 13 0.21
61 1 0.02
62 27 0.44
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (58 bp):
ATATTATTTTAATAAATTTAATATTAAATTTAATCTAATACTTATCTAAATAAATATT
Found at i:40077555 original size:24 final size:24
Alignment explanation
Indices: 40077523--40077717 Score: 101
Period size: 25 Copynumber: 7.8 Consensus size: 24
40077513 AAATAATATA
*
40077523 AAAATAAATAATATAACAAGATTT
1 AAAATAAATAATATAAAAAGATTT
* ** *
40077547 AAAATAAATAATAGGTGAAACCAATT
1 AAAATAAATAATA--TAAAAAGATTT
* *
40077573 AAAGTAAAAAGATATAAAAAG-TTT
1 AAAATAAATA-ATATAAAAAGATTT
* *
40077597 AAAAATAAATAATATATAAAAAAATT
1 -AAAATAAATAATATA-AAAAGATTT
* *
40077623 AAAATAAATAATATATGAAATGATTC
1 AAAATAAATAATATA--AAAAGATTT
* *
40077649 AGAATAAACAATATATGAAAAAGATTT
1 AAAATAAA-TA-ATAT-AAAAAGATTT
* * *
40077676 GACATAAAT-ATA-AAACA-ATTT
1 AAAATAAATAATATAAAAAGATTT
*
40077697 AGAATAAAATAATATATAAAA
1 AAAAT-AAATAATATA-AAAA
40077718 CAATTTCAAA
Statistics
Matches: 124, Mismatches: 33, Indels: 27
0.67 0.18 0.15
Matches are distributed among these distances:
21 6 0.05
22 8 0.06
23 3 0.02
24 24 0.19
25 34 0.27
26 28 0.23
27 16 0.13
28 4 0.03
29 1 0.01
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.27
Consensus pattern (24 bp):
AAAATAAATAATATAAAAAGATTT
Found at i:40077624 original size:26 final size:25
Alignment explanation
Indices: 40077523--40077763 Score: 109
Period size: 26 Copynumber: 9.5 Consensus size: 25
40077513 AAATAATATA
* * *
40077523 AAAATAAATAATATA-ACAAGATTT
1 AAAATAAATAATATATAAAAAAATT
** **
40077547 AAAATAAATAATAGGTGAAACCAATT
1 AAAATAAATAATATAT-AAAAAAATT
* * **
40077573 AAAGTAAA-AAGATATAAAAAGTTT
1 AAAATAAATAATATATAAAAAAATT
40077597 AAAAATAAATAATATATAAAAAAATT
1 -AAAATAAATAATATATAAAAAAATT
* **
40077623 AAAATAAATAATATATGAAATGATT
1 AAAATAAATAATATATAAAAAAATT
* * *
40077648 CAGAATAAACAATATATGAAAAAGATT
1 -AAAATAAATAATATAT-AAAAAAATT
* *
40077675 ----TGACATAA-ATATAAAACAATTT
1 AAAAT-AAATAATATATAAAA-AAATT
* *
40077697 AGAATAAAATAATATATAAAACAATTT
1 AAAAT-AAATAATATATAAAA-AAATT
* * * *
40077724 CAAATACATAAATATATGTAATAAATT
1 AAAATAAAT-AATATAT-AAAAAAATT
*
40077751 AAAAGAAATAATA
1 AAAATAAATAATA
40077764 CACAAAGTAA
Statistics
Matches: 162, Mismatches: 40, Indels: 28
0.70 0.17 0.12
Matches are distributed among these distances:
21 4 0.02
22 8 0.05
23 4 0.02
24 18 0.11
25 33 0.20
26 52 0.32
27 41 0.25
28 2 0.01
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (25 bp):
AAAATAAATAATATATAAAAAAATT
Found at i:40077729 original size:27 final size:26
Alignment explanation
Indices: 40077679--40077739 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
40077669 AAGATTTGAC
40077679 ATAAATATAAAACAATTTAGAATAAA
1 ATAAATATAAAACAATTTAGAATAAA
*
40077705 ATAATATATAAAACAATTTCA-AAT-AC
1 ATAA-ATATAAAACAATTT-AGAATAAA
40077731 ATAAATATA
1 ATAAATATA
40077740 TGTAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 5 0.16
26 9 0.28
27 17 0.53
28 1 0.03
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (26 bp):
ATAAATATAAAACAATTTAGAATAAA
Found at i:40077840 original size:23 final size:23
Alignment explanation
Indices: 40077799--40077855 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
40077789 CTTTAAAAAC
*
40077799 ATATAAAAGAGTTTAAAATAAATA
1 ATATAAAA-ATTTTAAAATAAATA
*
40077823 ATATAAAAATTTTAAAATGAATA
1 ATATAAAAATTTTAAAATAAATA
* *
40077846 ACATATAAAT
1 ATATAAAAAT
40077856 CAACATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (23 bp):
ATATAAAAATTTTAAAATAAATA
Found at i:40077970 original size:27 final size:26
Alignment explanation
Indices: 40077909--40077971 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
40077899 TTAAACAGAT
* * *
40077909 AATAATATATAAAGTAGTTTAAAATA
1 AATAATATATAAAATACTTAAAAATA
* *
40077935 AAGAGTATATAAAAATACTTAAAAATA
1 AATAATATAT-AAAATACTTAAAAATA
40077962 AATAATATAT
1 AATAATATAT
40077972 GGAAAGTTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (26 bp):
AATAATATATAAAATACTTAAAAATA
Found at i:40078074 original size:24 final size:26
Alignment explanation
Indices: 40078036--40078089 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
40078026 ATAATATATC
*
40078036 TAAATAACATATAAAA-A-TTTTAAA
1 TAAATAACATATAAAATAGTTTAAAA
* *
40078060 TAAATAATATGTAAAATAGTTTAAAA
1 TAAATAACATATAAAATAGTTTAAAA
40078086 TAAA
1 TAAA
40078090 AGGTATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 1 0.04
26 10 0.40
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
TAAATAACATATAAAATAGTTTAAAA
Found at i:40079035 original size:19 final size:19
Alignment explanation
Indices: 40079011--40079049 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40079001 GAAAACTTAG
40079011 ATCCGAAAGAAAAGATTGA
1 ATCCGAAAGAAAAGATTGA
40079030 ATCCGAAAGAAAAGATTGA
1 ATCCGAAAGAAAAGATTGA
40079049 A
1 A
40079050 ATCCACTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.10, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCCGAAAGAAAAGATTGA
Found at i:40079825 original size:44 final size:45
Alignment explanation
Indices: 40079776--40079885 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 45
40079766 TCGATTCGCT
*
40079776 CCACTGCAACTTCAGGGAGAT-AGGACTCATAACTTTAAC-CTGCC
1 CCACTGCAACTTCAGGGAGATAAGG-CTCATAACTTTAACTCAGCC
* * *
40079820 CCACTGCAACTTCAAGGG-GATAAGGCTTATAGCTTTAACTCAGCT
1 CCACTGCAACTTC-AGGGAGATAAGGCTCATAACTTTAACTCAGCC
* * *
40079865 CTATTGCAATTTCAGGGAGAT
1 CCACTGCAACTTCAGGGAGAT
40079886 GAGGTTTGTG
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
44 32 0.58
45 23 0.42
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGGCTCATAACTTTAACTCAGCC
Found at i:40079831 original size:86 final size:86
Alignment explanation
Indices: 40079670--40079832 Score: 186
Period size: 86 Copynumber: 1.9 Consensus size: 86
40079660 TAGAATGAGA
* ** * * **
40079670 TTTACTATCTTTATTCTGCCCCACTGCAACTTCAAGGAGATAAGGCTGGTAGCTTCAATCTGCTT
1 TTTACTATCTTGATTCTGCCCCACTGCAACTTCAAGGAGATAAGGCTCATAACTTCAACCTGCCC
*
40079735 CGCTGAAACTTCGAGATAAGG
66 CACTGAAACTTCGAGATAAGG
* * *
40079756 TTTACTATCTTCGATTC-GCTCCACTGCAACTTCAGGGAGAT-AGGACTCATAACTTTAACCTGC
1 TTTACTATCTT-GATTCTGCCCCACTGCAACTTCAAGGAGATAAGG-CTCATAACTTCAACCTGC
*
40079819 CCCACTGCAACTTC
64 CCCACTGAAACTTC
40079833 AAGGGGATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
85 3 0.05
86 56 0.89
87 4 0.06
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (86 bp):
TTTACTATCTTGATTCTGCCCCACTGCAACTTCAAGGAGATAAGGCTCATAACTTCAACCTGCCC
CACTGAAACTTCGAGATAAGG
Found at i:40080034 original size:44 final size:45
Alignment explanation
Indices: 40079929--40080560 Score: 259
Period size: 44 Copynumber: 14.0 Consensus size: 45
40079919 TGTAGCTTGA
* * * * *
40079929 TCTGCTCCATTGCAACTTCAAGGAGATAAGATCTTCTATCTTC-AG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTTGTAACTTCAAC
* *
40079974 TGTGCTCCATTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
* * ** *
40080019 T-TGCCCCACTGCAACTTCAGGGGGATAAGGTTTGTAGCTTCAA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
* ** * * *
40080062 TCTACTCCACTATAACTTCAGGGAGATAAGA-TT-CACCATAGT-AAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAAC-T--TCAAC
* * * * * * * *
40080107 TTTGATCCAACCTGCTGCAACTTCA-GAAGTATAGGATTTATAGCTTTAA-
1 TCTGCTCC-A----CTGCAACTTCAGGGAG-ATAAGACTTGTAACTTCAAC
* * * * * * *
40080156 TTTGCTCTACTGCAACTTTAGAGAGATAAGATTTGCTATCTTC-AG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTCAAC
* * * *
40080201 TCTGTTCCACTGTAACTTCAGGTG-TATAAGACTCGTAACTTCAAC
1 TCTGCTCCACTGCAACTTCAGG-GAGATAAGACTTGTAACTTCAAC
* ** * ** *
40080246 -CTGCCCCACTGCAGAGATAAGGTTTG-T--GA-TCTGTAGCTTCAA-
1 TCTGCTCCACTGCA-ACTTCAGG-GAGATAAGACT-TGTAACTTCAAC
* * * ** *
40080288 TCTGCCCCACTGCAACTTCAGAGAGATAAGA-TTCACTATTTTC-AG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT--GTAACTTCAAC
* * *
40080333 TCTGCTCTACT-AAACTTCAGGGAGATAAGACTTGTAATTTCAAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
**
40080377 -CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGATCTGTAGCTTCAA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT-A-----A-CTTCAAC
* * * ** *
40080427 TCTGCCCCACTGCAACTTCAGGGAGATAAGATTTACTATTTTC-AG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTAACTTCAAC
* * * *
40080472 TCTGCTCTACTGCAGCTTCAGGGAGATAAGACTTTTAATTTCAAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
* * *
40080517 -CTGCTTCACTGCAACTTTAGGGAGATAAGA-TTTTAACTTCAAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
40080560 T
1 T
40080561 TGTTCCATTG
Statistics
Matches: 446, Mismatches: 96, Indels: 91
0.70 0.15 0.14
Matches are distributed among these distances:
41 1 0.00
42 8 0.02
43 56 0.13
44 181 0.41
45 127 0.28
46 2 0.00
48 1 0.00
49 10 0.02
50 17 0.04
51 40 0.09
52 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAAC
Found at i:40080432 original size:139 final size:140
Alignment explanation
Indices: 40080164--40080545 Score: 532
Period size: 139 Copynumber: 2.8 Consensus size: 140
40080154 AATTTGCTCT
* * * * * * *
40080164 ACTGCAACTTTAGAGAGATAAGATTTGCTATCTTCAGTCTGTTCCACTGTAACTTCAGGTG-TAT
1 ACTGCAACTTCAGAGAGATAAGATTTACTATTTTCAGTCTGCTCTACTGAAACTTCAGG-GAGAT
* * *
40080228 AAGACTCGTAACTTCAACCTG--CC-C--C-ACTGCA--GAGATAAGGTTTGTGATCTGTAGCTT
65 AAGACTTGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGATCTGTAGCTT
40080285 CAATCTGCCCC
130 CAATCTGCCCC
*
40080296 ACTGCAACTTCAGAGAGATAAGATTCACTATTTTCAGTCTGCTCTACT-AAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTACTATTTTCAGTCTGCTCTACTGAAACTTCAGGGAGATA
40080360 AGACTTGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGATCTGTAGCTTC
66 AGACTTGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGATCTGTAGCTTC
40080425 AATCTGCCCC
131 AATCTGCCCC
* * *
40080435 ACTGCAACTTCAGGGAGATAAGATTTACTATTTTCAGTCTGCTCTACTGCAGCTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTACTATTTTCAGTCTGCTCTACTGAAACTTCAGGGAGATA
* * *
40080500 AGACTTTTAATTTCAACCTGCTTCACTGCAACTTTAGGGAGATAAG
66 AGACTTGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG
40080546 ATTTTAACTT
Statistics
Matches: 222, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
130 1 0.00
131 30 0.14
132 42 0.19
133 2 0.01
134 1 0.00
136 1 0.00
137 5 0.02
139 83 0.37
140 57 0.26
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (140 bp):
ACTGCAACTTCAGAGAGATAAGATTTACTATTTTCAGTCTGCTCTACTGAAACTTCAGGGAGATA
AGACTTGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGATCTGTAGCTTC
AATCTGCCCC
Found at i:40080686 original size:88 final size:87
Alignment explanation
Indices: 40080607--40081029 Score: 395
Period size: 88 Copynumber: 4.8 Consensus size: 87
40080597 GCTTCAATAT
* * *
40080607 GCTCCAATATCATTTCAGGGAGAAGAGATCTGTAGCTTCGATCTACTCCATTGAAACTTCAAGGG
1 GCTCCAAT-TCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTGAAACTTCAAGGA
* *
40080672 GATACGGATCATGGCTTCAGGCC
65 GATACGAATCATGGCTTCAAGCC
* * * * * *
40080695 GTTCCAGTGCTATTTTAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTAAAACTTCAAGGA
1 GCTCCAATTC-ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTGAAACTTCAAGGA
* **
40080760 GATATGAATTGTGGCTTCAAGCC
65 GATACGAATCATGGCTTCAAGCC
* * *
40080783 GCTCCAACTTCATTTCAGGTAGAAGAGATTTGTAGCTTCGATCTACTTCACTGGAACTTCAAGGA
1 GCTCCAA-TTCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTGAAACTTCAAGGA
* ** * **
40080848 GATACAAATTGTAGCTTCGGGCC
65 GATACGAATCATGGCTTCAAGCC
* * * * ** * *
40080871 TCT-CAGTGCCATTTCAGGGAGAAGAGATTTATAGCTTCGATCTACTCTGCTGGAACTTTAAGGA
1 GCTCCAAT-TCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTGAAACTTCAAGGA
* * * *
40080935 GAT-CTG-CT-GTGGCTTCGAGCA
65 GATAC-GAATCATGGCTTCAAGCC
* * * * *
40080956 GCTCCAATGCCATGTCAGGGAGAAGAGATTTGTAGCCTCGATCTACTCCGCTGAAACTCCAAGGA
1 GCTCCAAT-TCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTGAAACTTCAAGGA
*
40081021 GATATGAAT
65 GATACGAAT
40081030 TGTTGATTTC
Statistics
Matches: 275, Mismatches: 53, Indels: 15
0.80 0.15 0.04
Matches are distributed among these distances:
85 12 0.04
86 60 0.22
87 56 0.20
88 145 0.53
89 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (87 bp):
GCTCCAATTCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTGAAACTTCAAGGAG
ATACGAATCATGGCTTCAAGCC
Found at i:40080798 original size:176 final size:173
Alignment explanation
Indices: 40080607--40081024 Score: 516
Period size: 176 Copynumber: 2.4 Consensus size: 173
40080597 GCTTCAATAT
* * *
40080607 GCTCCAATATCATTTCAGGGAGAAGAGATCTGTAGCTTCGATCTACTCCATTGAAACTTCAAGGG
1 GCTCCAATATCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTGAAACTTCAAGGA
** * * * *
40080672 GATACGGATCATGGCTTCAGGCCGT-TCCAGTGCTATTTTAGGGAGAAGAGATTTGTAGCTTCGA
66 GATACAAATCATAGCTTCAGGCC-TCT-CAGTGCCATTTCAGGGAGAAGAGATTTATAGCTTCGA
* *
40080736 TCTACTCCGCTAAAACTTCAAGGAGATATGAATTGTGGCTTCAAGCC
129 TCTACTCCGCTAAAACTTCAAGGAGATATG--CTGTGGCTTCAAGCA
* * *
40080783 GCTCCAACT-TCATTTCAGGTAGAAGAGATTTGTAGCTTCGATCTACTTCACTGGAACTTCAAGG
1 GCTCCAA-TATCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTGAAACTTCAAGG
** *
40080847 AGATACAAATTGTAGCTTCGGGCCTCTCAGTGCCATTTCAGGGAGAAGAGATTTATAGCTTCGAT
65 AGATACAAATCATAGCTTCAGGCCTCTCAGTGCCATTTCAGGGAGAAGAGATTTATAGCTTCGAT
* ** * * *
40080912 CTACTCTGCTGGAACTTTAAGGAGATCTGCTGTGGCTTCGAGCA
130 CTACTCCGCTAAAACTTCAAGGAGATATGCTGTGGCTTCAAGCA
** * * * *
40080956 GCTCCAATGCCATGTCAGGGAGAAGAGATTTGTAGCCTCGATCTACTCCGCTGAAACTCCAAGGA
1 GCTCCAATATCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTGAAACTTCAAGGA
40081021 GATA
66 GATA
40081025 TGAATTGTTG
Statistics
Matches: 208, Mismatches: 31, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
172 1 0.00
173 71 0.34
175 60 0.29
176 75 0.36
177 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (173 bp):
GCTCCAATATCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTGAAACTTCAAGGA
GATACAAATCATAGCTTCAGGCCTCTCAGTGCCATTTCAGGGAGAAGAGATTTATAGCTTCGATC
TACTCCGCTAAAACTTCAAGGAGATATGCTGTGGCTTCAAGCA
Found at i:40081317 original size:131 final size:131
Alignment explanation
Indices: 40081052--40081325 Score: 408
Period size: 131 Copynumber: 2.1 Consensus size: 131
40081042 CCTGCTCTAT
* * *
40081052 TACTGCTTAGAGAGATAGGATGGTGGCTTAAATCTGCTCCACTACGGTTTAGGGAGACAAGATTT
1 TACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACGGTTTAGGAAGACAAGATTC
** * *
40081117 GTTGTCTTCGATCTGTTCCACTGCAACTTCAAGGAGACAAGATCTACAATCTTCGGCCTACTCTG
66 GCCGTCTTCGATCTGTTCCACTGCAACTTCAAGGAGACAAGATCTACAATCTTCAGCCTACTCTC
40081182 C
131 C
*
40081183 TACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTATGGTTTAGGAAGACAAGATTC
1 TACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACGGTTTAGGAAGACAAGATTC
* * **
40081248 GCCGTCTTCGATCTGTTCTACTGTAACTTC-AGAGAGACAAGATCTACAATCTTCAGCCTGTTAC
66 GCCGTCTTCGATCTGTTCCACTGCAACTTCAAG-GAGACAAGATCTACAATCTTCAGCCTACT-C
40081312 -CC
129 TCC
40081314 TACTGCTTAGGG
1 TACTGCTTAGGG
40081326 GGTTAAGGTT
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
130 2 0.02
131 126 0.98
132 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (131 bp):
TACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTACGGTTTAGGAAGACAAGATTC
GCCGTCTTCGATCTGTTCCACTGCAACTTCAAGGAGACAAGATCTACAATCTTCAGCCTACTCTC
C
Found at i:40081362 original size:44 final size:43
Alignment explanation
Indices: 40081313--40081447 Score: 114
Period size: 44 Copynumber: 3.1 Consensus size: 43
40081303 GCCTGTTACC
40081313 CTACTGCTTAGGGGGTTAAGGTTCACCGTCTTTGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGG-TCACCGTCTTTGATCTGCTCCA
* * * ** * * *
40081357 CTACTGCTTAGGGAGATAAGGT--CTGTAATTCAGCCTGTTACC-
1 CTACTGCTTAGGGGGTTAAGGTCACCGTCTTTGA-TCTGCT-CCA
* * *
40081399 CTACTGCTCAAGGGGTTAAGCCTCACCGTCTTTGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAG-GTCACCGTCTTTGATCTGCTCCA
40081443 CTACT
1 CTACT
40081448 ATCTGTAATT
Statistics
Matches: 66, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
41 6 0.09
42 20 0.30
43 6 0.09
44 28 0.42
45 6 0.09
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (43 bp):
CTACTGCTTAGGGGGTTAAGGTCACCGTCTTTGATCTGCTCCA
Found at i:40081624 original size:64 final size:64
Alignment explanation
Indices: 40081523--40081646 Score: 221
Period size: 64 Copynumber: 1.9 Consensus size: 64
40081513 GTATCTATGT
* *
40081523 TTATGCCAAATGATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGTTGTGATGC
1 TTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGATGC
*
40081587 TTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 TTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
40081647 TTATGAATGA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (64 bp):
TTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGATGC
Found at i:40082813 original size:50 final size:50
Alignment explanation
Indices: 40082758--40082853 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
40082748 TCCCCTTTGG
* *
40082758 TCTCAAAGCGTCCTTTG-AGGGTTTTCGCCTTAGCCTCTCCCTTTTTTTTT
1 TCTCAAAGCGTCCTTTGCA-AGTTTTCACCTTAGCCTCTCCCTTTTTTTTT
* *
40082808 TCTCAAGGCGTCCTTTGCAAGTTTTCACCTTGGCCTCTCCCTTTTT
1 TCTCAAAGCGTCCTTTGCAAGTTTTCACCTTAGCCTCTCCCTTTTT
40082854 AGGTAGAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 40 0.98
51 1 0.02
ACGTcount: A:0.10, C:0.30, G:0.16, T:0.44
Consensus pattern (50 bp):
TCTCAAAGCGTCCTTTGCAAGTTTTCACCTTAGCCTCTCCCTTTTTTTTT
Found at i:40088017 original size:127 final size:127
Alignment explanation
Indices: 40087866--40088098 Score: 296
Period size: 127 Copynumber: 1.8 Consensus size: 127
40087856 ATATGGACGG
* ** *
40087866 AATTTTAAAGGAATGTTTGATTATTTGGATAAACAGAAA-ATCGAAACCC-ATCACATTAGGGTA
1 AATTTTAAAGGAATATTTGATTATTTAAATAAAC-GAAAGATCGAAACCCAAT-ACATTAGGGCA
* * *
40087929 CGATTTCC-CAAA-TTCTCAAACATCAATCATCGCTTTTGTTTTAAAGTTTAAAAAACGCAAACG
64 CGA-TCCCTCAAATTTCT-AAACATCAAACATCGCCTTTGTTTTAAAGTTTAAAAAACGCAAACG
40087992 A
127 A
* *
40087993 AATTTTAAAGGGAA-ATTTGATTATTTAAATAAACGAAAGATCGAAGCCCAATACGTTAGGGCAC
1 AATTTTAAA-GGAATATTTGATTATTTAAATAAACGAAAGATCGAAACCCAATACATTAGGGCAC
*
40088057 GATCCCTCGAATTTCTAAACATCAAACATCGCCTTTGTTTTA
65 GATCCCTCAAATTTCTAAACATCAAACATCGCCTTTGTTTTA
40088099 TAAAGTCTAC
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
126 7 0.08
127 74 0.81
128 10 0.11
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Consensus pattern (127 bp):
AATTTTAAAGGAATATTTGATTATTTAAATAAACGAAAGATCGAAACCCAATACATTAGGGCACG
ATCCCTCAAATTTCTAAACATCAAACATCGCCTTTGTTTTAAAGTTTAAAAAACGCAAACGA
Found at i:40088657 original size:26 final size:25
Alignment explanation
Indices: 40088556--40088703 Score: 93
Period size: 26 Copynumber: 5.9 Consensus size: 25
40088546 AAATAATATA
* ***
40088556 AAAATAAATAATATA-ACAAGGTTT
1 AAAATAAATAATATATAAAAAAATT
** **
40088580 AAAATAAATAATAGGTGAAACCAATT
1 AAAATAAATAATATAT-AAAAAAATT
* * **
40088606 AAAGTAAA-AAGATATAAAAAGTTT
1 AAAATAAATAATATATAAAAAAATT
40088630 AAAAATAAATAATATATAAAAAAATT
1 -AAAATAAATAATATATAAAAAAATT
* **
40088656 AAAATAAATAATATATGAAATGATT
1 AAAATAAATAATATATAAAAAAATT
* * *
40088681 CAGAATAAACAATATATGAAAAA
1 -AAAATAAATAATATATAAAAAA
40088704 GATTTGACAT
Statistics
Matches: 93, Mismatches: 26, Indels: 8
0.73 0.20 0.06
Matches are distributed among these distances:
24 18 0.19
25 33 0.35
26 42 0.45
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (25 bp):
AAAATAAATAATATATAAAAAAATT
Found at i:40088658 original size:50 final size:51
Alignment explanation
Indices: 40088556--40088663 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 51
40088546 AAATAATATA
* * * **
40088556 AAAATAAATA-ATATAACAAGGTTTAAAATAAATAATAGGTGAAACCAATT
1 AAAATAAAAAGATATAACAAAGTTTAAAATAAATAATAGATGAAAAAAATT
* *
40088606 AAAGTAAAAAGATATAA-AAAGTTTAAAAATAAATAATATAT-AAAAAAATT
1 AAAATAAAAAGATATAACAAAGTTT-AAAATAAATAATAGATGAAAAAAATT
40088656 AAAATAAA
1 AAAATAAA
40088664 TAATATATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
50 28 0.58
51 20 0.42
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (51 bp):
AAAATAAAAAGATATAACAAAGTTTAAAATAAATAATAGATGAAAAAAATT
Found at i:40088762 original size:27 final size:26
Alignment explanation
Indices: 40088712--40088772 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
40088702 AAGATTTGAC
**
40088712 ATAAATATAAAACAATTTGGAATAAA
1 ATAAATATAAAACAATTTCAAATAAA
* *
40088738 ATAATATATAAAATAATTTCAAAT-AC
1 ATAA-ATATAAAACAATTTCAAATAAA
40088764 ATAAATATA
1 ATAAATATA
40088773 TGTAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 9 0.30
27 16 0.53
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (26 bp):
ATAAATATAAAACAATTTCAAATAAA
Found at i:40088873 original size:23 final size:26
Alignment explanation
Indices: 40088825--40088888 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
40088815 TAAGACCCTT
40088825 TAAA-AACATATAAAAGAGTTTAAAA
1 TAAATAACATATAAAAGAGTTTAAAA
*
40088850 TAAAT-A-ATATAAAAG-TTTTAAAA
1 TAAATAACATATAAAAGAGTTTAAAA
*
40088873 TGAATAACATATAAAA
1 TAAATAACATATAAAA
40088889 CAACATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 11 0.32
24 10 0.29
25 13 0.38
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (26 bp):
TAAATAACATATAAAAGAGTTTAAAA
Found at i:40088895 original size:12 final size:12
Alignment explanation
Indices: 40088878--40088903 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40088868 TAAAATGAAT
40088878 AACATATAAAAC
1 AACATATAAAAC
40088890 AACATATAAAAC
1 AACATATAAAAC
40088902 AA
1 AA
40088904 TTTAAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (12 bp):
AACATATAAAAC
Found at i:40089003 original size:27 final size:26
Alignment explanation
Indices: 40088942--40089004 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
40088932 TTAAACAGAT
* * *
40088942 AATAATATATAAAGTAGTTTAAAATA
1 AATAATATATAAAATACTTAAAAATA
40088968 AA-AAGTATATAAAAATACTTAAAAATA
1 AATAA-TATAT-AAAATACTTAAAAATA
40088995 AATAATATAT
1 AATAATATAT
40089005 GGAAAGTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 2 0.06
26 7 0.23
27 20 0.65
28 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (26 bp):
AATAATATATAAAATACTTAAAAATA
Found at i:40089107 original size:24 final size:26
Alignment explanation
Indices: 40089069--40089122 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
40089059 ATAATATATC
*
40089069 TAAATAACATATAAAA-A-TTTTAAA
1 TAAATAACATATAAAATAGTTTAAAA
* *
40089093 TAAATAATATGTAAAATAGTTTAAAA
1 TAAATAACATATAAAATAGTTTAAAA
40089119 TAAA
1 TAAA
40089123 AGGTATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 1 0.04
26 10 0.40
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
TAAATAACATATAAAATAGTTTAAAA
Found at i:40090069 original size:19 final size:19
Alignment explanation
Indices: 40090042--40090085 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
40090032 GAAAACTTAG
40090042 ATCCAAAAGAAAAGATTGA
1 ATCCAAAAGAAAAGATTGA
*
40090061 ATCCGAAAGAAAAGATTGAA
1 ATCCAAAAGAAAAGATTG-A
40090081 ATCCA
1 ATCCA
40090086 CTTTCTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (19 bp):
ATCCAAAAGAAAAGATTGA
Found at i:40096802 original size:19 final size:19
Alignment explanation
Indices: 40096778--40096817 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
40096768 ATCAATTTTG
40096778 ATTAAGTAAAATT-AAATTA
1 ATTAAGT-AAATTAAAATTA
*
40096797 ATTAAGTCAATTAAAATTA
1 ATTAAGTAAATTAAAATTA
40096816 AT
1 AT
40096818 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (19 bp):
ATTAAGTAAATTAAAATTA
Found at i:40100947 original size:18 final size:19
Alignment explanation
Indices: 40100917--40100953 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
40100907 ATCACTGTCA
40100917 CCCACCGTAATCAAATTTG
1 CCCACCGTAATCAAATTTG
40100936 CCCACC-TAATCAAATTTG
1 CCCACCGTAATCAAATTTG
40100954 TTATTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.27
Consensus pattern (19 bp):
CCCACCGTAATCAAATTTG
Found at i:40101098 original size:18 final size:16
Alignment explanation
Indices: 40101066--40101100 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
40101056 ATGTATTTTG
40101066 AAATTAAAAAAATATT
1 AAATTAAAAAAATATT
40101082 AAATGTAAAAAATATATT
1 AAAT-TAAAAAA-ATATT
40101100 A
1 A
40101101 CTATTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 7 0.41
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAATTAAAAAAATATT
Found at i:40111330 original size:21 final size:21
Alignment explanation
Indices: 40111306--40111367 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
40111296 TGAATGAAAA
40111306 CTCATAAGAGTTAAACAGAAG
1 CTCATAAGAGTTAAACAGAAG
* *
40111327 CTCAAAAGAGTTAAACAAAAG
1 CTCATAAGAGTTAAACAGAAG
* * *
40111348 ATCATGAGAGCTAAACAGAA
1 CTCATAAGAGTTAAACAGAA
40111368 AGTAAACACA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.52, C:0.15, G:0.18, T:0.16
Consensus pattern (21 bp):
CTCATAAGAGTTAAACAGAAG
Found at i:40113729 original size:50 final size:48
Alignment explanation
Indices: 40113608--40113767 Score: 148
Period size: 49 Copynumber: 3.3 Consensus size: 48
40113598 TCTATCAAGT
* * *
40113608 CGATGCCATGTTCCAGATATGGTCTTACAC-AGACTATCA-AAATCGAGGC
1 CGATGCCATG-TCCAGATATGGTCTTACACTAG-CTCTCACATATCG-TGC
* *
40113657 CGATGCCATATCCCAGACATGGTCTTACACTAGCTCTCACATATCCGTGC
1 CGATGCCATGT-CCAGATATGGTCTTACACTAGCTCTCACATAT-CGTGC
* * *
40113707 CGATGCCATGTCCTAGATATGGTCTTACACTGGCAC-CTC-TATTCGTGC
1 CGATGCCATGTCC-AGATATGGTCTTACACTAGCTCTCACATA-TCGTGC
*
40113755 CGATGCAATGTCC
1 CGATGCCATGTCC
40113768 CAGACATGTT
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
48 20 0.21
49 36 0.38
50 36 0.38
51 2 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCAGATATGGTCTTACACTAGCTCTCACATATCGTGC
Found at i:40113766 original size:48 final size:50
Alignment explanation
Indices: 40113608--40113775 Score: 159
Period size: 50 Copynumber: 3.4 Consensus size: 50
40113598 TCTATCAAGT
* * * *
40113608 CGATGCCATGTTCCAGATATGGTCTTACAC-AG-ACT-ATCAAAAT-CGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCA-C-ATATCCG-TGC
* *
40113657 CGATGCCATATCCCAGACATGGTCTTACACTAGCTCTCACATATCCGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCACATATCCGTGC
* * * * *
40113707 CGATGCCATGTCCTAGATATGGTCTTACACTGGCAC-CTC-TATTCGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCACATATCCGTGC
*
40113755 CGATGCAATGTCCCAGACATG
1 CGATGCCATGTCCCAGACATG
40113776 TTTTACATTG
Statistics
Matches: 99, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
48 26 0.26
49 29 0.29
50 38 0.38
51 5 0.05
52 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (50 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCACATATCCGTGC
Found at i:40116970 original size:21 final size:22
Alignment explanation
Indices: 40116934--40116975 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
40116924 ATTGAGGAAA
40116934 AAATAAAAATAAAAAA-AACTG
1 AAATAAAAATAAAAAATAACTG
* *
40116955 AAATAAAATTATAAAATAACT
1 AAATAAAAATAAAAAATAACT
40116976 ACTACTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (22 bp):
AAATAAAAATAAAAAATAACTG
Found at i:40124743 original size:49 final size:48
Alignment explanation
Indices: 40124630--40125182 Score: 242
Period size: 49 Copynumber: 11.6 Consensus size: 48
40124620 TATAGTGCCA
* * * * *
40124630 ATGCCATGTCCCAGACATGATCTTACACTGGA-TCATC-CA-TCAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACT-GACT-ATCAAATTGAGGCCG
* * *
40124677 ATGCCATGTTCCGGACATGGTCTTACACTGACTATCGAAATTGAGGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTATC-AAATTGAGGCCG
* * * ** *
40124726 ACGCCATGTCCCAGACATGGTCTTACACT-AGCTTTCACATATCCGTGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CTATCAAAT-TGAG-GCCG
* *
40124776 ATGCCATG-CCCAGACATGGTCTTACACTGGCAC-CTC-TA-T-ACGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACT-G-ACTATCAAATTGA-G-GCCG
* * *
40124823 ATGCCATGTCCCATACATGGTCTTACATTGACTATCGAAATCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTATC-AAATTGAGGCCG
* * * * * *
40124872 ACGCCATATACCAGACATGCTCTTACACT-AGCTCTCACATATCTG-TGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CTATCA-A-AT-TGAGGCCG
* * *
40124922 ATGCCATGTCCCAGACATGGTCTTACACTGGCAC-CTC-TA-T-ACGTGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACT-G-ACTATCAAATTGA-G-GCCG
* ** * *
40124970 ATGCCATGTCCCAAACATGGTCTTACACTGAC-A-CATCTCGTA-GCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAATTG-AGGCCG
* * * * *
40125016 ATG-CATGTCCCAGACAT-GTCTTACATTG-GT-TTACATCTCAAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAAT-T-GAGGCCG
* * *** * * *
40125062 ATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCGTCTTAATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAATTGAGGCCG
* * * *
40125108 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAA-TGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTATCA-AATTGAGGCCG
* *
40125156 ATG-CATGTCCTAGGCAT-GTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
40125183 AGCATACAAA
Statistics
Matches: 390, Mismatches: 75, Indels: 83
0.71 0.14 0.15
Matches are distributed among these distances:
44 12 0.03
45 15 0.04
46 64 0.16
47 71 0.18
48 83 0.21
49 93 0.24
50 43 0.11
51 6 0.02
52 2 0.01
53 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAATTGAGGCCG
Found at i:40124988 original size:48 final size:48
Alignment explanation
Indices: 40124620--40125182 Score: 314
Period size: 48 Copynumber: 11.8 Consensus size: 48
40124610 AAACATATGG
* * *
40124620 TATA-GTGCCAATGCCATGTCCCAGACATGATCTTACACTGG-ATCATC
1 TATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCA-CCTC
* * * * *
40124667 CATCAAGT--CGATGCCATGTTCCGGACATGGTCTTACACT-G-ACTATC
1 TAT-ACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC-CTC
* * * * * * * ** *
40124713 GAAATTGAGGTCGACGCCATGTCCCAGACATGGTCTTACACTAGCTTTCAC
1 TATA-CG-TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-ACCTC
* *
40124764 ATATCCGTGCTGATGCCATG-CCCAGACATGGTCTTACACTGGCACCTC
1 -TATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTC
* * *
40124812 TATACGTGCCGATGCCATGTCCCATACATGGTCTTACA-TTG-ACTATC
1 TATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC-CTC
* * * * * * * * *
40124859 GAAATCGAGGCCGACGCCATATACCAGACATGCTCTTACACTAGC-TCTC
1 TATA-CG-TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTC
*
40124908 ACATATCTGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTC
1 -TATA-C-GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTC
* * * *
40124959 TATACGTGTCGATGCCATGTCCCAAACATGGTCTTACACTGACACATC
1 TATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTC
* * * *
40125007 --T-CGTAGCCAATG-CATGTCCCAGACAT-GTCTTACATTGGTTTACATC
1 TATACGT-GCCGATGCCATGTCCCAGACATGGTCTTACACTGG--CACCTC
*
40125053 TCA-A-G-GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCGTC
1 T-ATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC-C-TC
* * * *
40125099 T-TA-ATGCCAATGCCATGTCCCAAACATGGTCTTACACTGGC-TCTC
1 TATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTC
* * *
40125144 -ATAATGTGGCCGATG-CATGTCCTAGGCAT-GTCTTACACT
1 TAT-ACGT-GCCGATGCCATGTCCCAGACATGGTCTTACACT
40125183 AGCATACAAA
Statistics
Matches: 401, Mismatches: 78, Indels: 75
0.72 0.14 0.14
Matches are distributed among these distances:
44 11 0.03
45 22 0.05
46 72 0.18
47 77 0.19
48 81 0.20
49 81 0.20
50 50 0.12
51 6 0.01
52 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (48 bp):
TATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTC
Found at i:40124995 original size:147 final size:145
Alignment explanation
Indices: 40124623--40125185 Score: 584
Period size: 146 Copynumber: 3.9 Consensus size: 145
40124613 CATATGGTAT
* * * * * *
40124623 AGTGCCAATGCCATGTCCCAGACATGATCTTACACTGG-ATCATCCAT-CAAGTCGATGCCATGT
1 AGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCA-CCTCTATACATGCCGATGCCATGT
* ** * *
40124686 TCCGGACATGGTCTTACACTGACTATCGAAATTGAGGTCGACGCCATGTCCCAGACATGGTCTTA
65 CCCAAACATGGTCTTACACTGACTATCGAAATCGAGGCCGACGCCATGTCCCAGACAT-GTCTTA
40124751 CACTAGCTTTCACATATC
129 CACTAGC-TTCACATATC
* * *
40124769 CGTGCTGATGCCATG-CCCAGACATGGTCTTACACTGGCACCTCTATACGTGCCGATGCCATGTC
1 AGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTCTATACATGCCGATGCCATGTC
* * * *
40124833 CCATACATGGTCTTACATTGACTATCGAAATCGAGGCCGACGCCATATACCAGACATGCTCTTAC
66 CCAAACATGGTCTTACACTGACTATCGAAATCGAGGCCGACGCCATGTCCCAGACATG-TCTTAC
40124898 ACTAGCTCTCACATATC
130 ACTAGCT-TCACATATC
* * *
40124915 TGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTCTATACGTGTCGATGCCATGTC
1 AGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTCTATACATGCCGATGCCATGTC
** * *
40124980 CCAAACATGGTCTTACACTGAC-A-C-ATCTCGTA-GCCAATG-CATGTCCCAGACATGTCTTAC
66 CCAAACATGGTCTTACACTGACTATCGAAATCG-AGGCCGACGCCATGTCCCAGACATGTCTTAC
* * * *
40125040 A-TTGGTTTACATCTC
130 ACTAGCTTCACATATC
* *
40125055 AAG-GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCGTCT-TA-ATGCCAATGCCAT
1 -AGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC-C-TCTATACATGCCGATGCCAT
* * * * * *
40125115 GTCCCAAACATGGTCTTACACTGGCTCTC-ATAAT-GTGGCCGATG-CATGTCCTAGGCATGTCT
63 GTCCCAAACATGGTCTTACACTGACTATCGA-AATCGAGGCCGACGCCATGTCCCAGACATGTCT
40125177 TACACTAGC
127 TACACTAGC
40125186 ATACAAAGAA
Statistics
Matches: 356, Mismatches: 47, Indels: 33
0.82 0.11 0.08
Matches are distributed among these distances:
138 48 0.13
139 17 0.05
140 46 0.13
141 7 0.02
142 7 0.02
143 13 0.04
144 9 0.03
145 30 0.08
146 111 0.31
147 68 0.19
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (145 bp):
AGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACCTCTATACATGCCGATGCCATGTC
CCAAACATGGTCTTACACTGACTATCGAAATCGAGGCCGACGCCATGTCCCAGACATGTCTTACA
CTAGCTTCACATATC
Found at i:40133249 original size:16 final size:16
Alignment explanation
Indices: 40133230--40133260 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40133220 CTTCTTCACT
40133230 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
40133246 TACTTACTTACTTAA
1 TACTCACTTACTTAA
40133261 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:40133266 original size:20 final size:20
Alignment explanation
Indices: 40133227--40133266 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
40133217 AAACTTCTTC
* *
40133227 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
40133247 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
40133267 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:40133635 original size:55 final size:53
Alignment explanation
Indices: 40133521--40133707 Score: 139
Period size: 55 Copynumber: 3.5 Consensus size: 53
40133511 GTCATCTCTC
* *
40133521 GACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTT
1 GACATGGTCTTACATGGGATCCTTCCCTTATGAACTCACCAATGCCATGCCTT
* * * *
40133574 -AGCATGGTCTTACATGGGA-CCTTTCCCTTCTAGAAACTTATCAATGCCATGTCTT
1 GA-CATGGTCTTACATGGGATCC-TTCCCTTAT-G-AACTCACCAATGCCATGCCTT
* ** * * *
40133629 GACATGGTCTTA-AAGAATATCCTTGCCTTA-GAAACCTTACCAATTTCCATGCCTT
1 GACATGGTCTTACATG-GGATCCTTCCCTTATG-AA-CTCACCAA-TGCCATGCCTT
** *
40133684 GGTATGGTCTTACATGGTATCCTT
1 GACATGGTCTTACATGGGATCCTT
40133708 AAACCCTAAT
Statistics
Matches: 106, Mismatches: 18, Indels: 18
0.75 0.13 0.13
Matches are distributed among these distances:
52 3 0.03
53 27 0.25
54 10 0.09
55 61 0.58
56 5 0.05
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (53 bp):
GACATGGTCTTACATGGGATCCTTCCCTTATGAACTCACCAATGCCATGCCTT
Found at i:40138439 original size:331 final size:332
Alignment explanation
Indices: 40137831--40138491 Score: 1288
Period size: 331 Copynumber: 2.0 Consensus size: 332
40137821 GGTCCCCGGC
*
40137831 TCAACGTTAGCTACGGGAATCAAACAATTAAAATTTATCAATACACTACAATTTAACATTGAATA
1 TCAACGTTAGCTACGGGAATCAAACAATTAAAATCTATCAATACACTACAATTTAACATTGAATA
40137896 TTTCAATTTATACATAACTTTTGCCTAAATTCCAAATTAGTCCTTAAATCAAAACTAACTCTTTT
66 TTTCAATTTATACATAACTTTTGCCTAAATTCCAAATTAGTCCTTAAATCAAAACTAACTCTTTT
40137961 TTCTTCCAAACTAATTCCATATTTTCATTTAATTCCCATTTAAAACTAAATTTAACTCCCTAATT
131 TTCTTCCAAACTAATTCCATATTTTCATTTAATTCCCATTTAAAACTAAATTTAACTCCCTAATT
40138026 TCATCATAAATTCCTAATTTCGAAATTCTCTCAACCTAGTCCCTATTACTTAAATTTTATGATTT
196 TCATCATAAATTCCTAATTTCGAAATTCTCTCAACCTAGTCCCTATTACTTAAATTTTATGATTT
40138091 ATTTTACAATTCAATCCCTTTTTCACTAGTAACTTGAAATTCTATCAATTTAACGCCTAATTATT
261 ATTTTACAATTCAATCCCTTTTTCACTAGTAACTTGAAATTCTATCAATTTAACGCCTAATTATT
40138156 CAATTCT
326 CAATTCT
*
40138163 TCAATGTTAGCTACGGGAATCAAACAATTAAAATCTATCAATACACTACAATTTAACATTGAATA
1 TCAACGTTAGCTACGGGAATCAAACAATTAAAATCTATCAATACACTACAATTTAACATTGAATA
40138228 TTTCAATTTATACATAACTTTTGCCTAAATTCCAAATTAGTCCTTAAATCAAAAC-AACTCTTTT
66 TTTCAATTTATACATAACTTTTGCCTAAATTCCAAATTAGTCCTTAAATCAAAACTAACTCTTTT
40138292 TTCTTCCAAACTAATTCCATATTTTCATTTAATTCCCATTTAAAACTAAATTTAACTCCCTAATT
131 TTCTTCCAAACTAATTCCATATTTTCATTTAATTCCCATTTAAAACTAAATTTAACTCCCTAATT
40138357 TCATCATAAATTCCTAATTTCGAAATTCTCTCAACCTAGTCCCTATTACTTAAATTTTATGATTT
196 TCATCATAAATTCCTAATTTCGAAATTCTCTCAACCTAGTCCCTATTACTTAAATTTTATGATTT
*
40138422 ATTTTACAATTCAATCCCTTTTTCACTAGTAACTTGAAATTCTATCAATTTAACGCCTAATTCTT
261 ATTTTACAATTCAATCCCTTTTTCACTAGTAACTTGAAATTCTATCAATTTAACGCCTAATTATT
40138487 CAATT
326 CAATT
40138492 TATTCAACAT
Statistics
Matches: 326, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
331 208 0.64
332 118 0.36
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (332 bp):
TCAACGTTAGCTACGGGAATCAAACAATTAAAATCTATCAATACACTACAATTTAACATTGAATA
TTTCAATTTATACATAACTTTTGCCTAAATTCCAAATTAGTCCTTAAATCAAAACTAACTCTTTT
TTCTTCCAAACTAATTCCATATTTTCATTTAATTCCCATTTAAAACTAAATTTAACTCCCTAATT
TCATCATAAATTCCTAATTTCGAAATTCTCTCAACCTAGTCCCTATTACTTAAATTTTATGATTT
ATTTTACAATTCAATCCCTTTTTCACTAGTAACTTGAAATTCTATCAATTTAACGCCTAATTATT
CAATTCT
Found at i:40138800 original size:34 final size:33
Alignment explanation
Indices: 40138730--40138799 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
40138720 TTTCTTTTAT
40138730 TTATTTGTTTTAATTATAATAATATAATATAATA
1 TTATTTGTTTTAA-TATAATAATATAATATAATA
40138764 TTATTT-TTTTAA-ATAATAAGTA-AATAT-ATA
1 TTATTTGTTTTAATATAATAA-TATAATATAATA
40138794 TGTATT
1 T-TATT
40138800 ACAAATGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
30 4 0.12
31 16 0.47
32 2 0.06
33 6 0.18
34 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (33 bp):
TTATTTGTTTTAATATAATAATATAATATAATA
Found at i:40138979 original size:97 final size:98
Alignment explanation
Indices: 40138862--40139052 Score: 375
Period size: 97 Copynumber: 2.0 Consensus size: 98
40138852 CAATTGTTAA
40138862 AATTTGGTTTTATTTATTTATTTAGTCCCTTGAATTTTCTCTATTCTATATTTAAGCTTTCACAC
1 AATTTGGTTTTATTTATTTATTTAGTCCCTTGAATTTTCTCTATTCTATATTTAAGCTTTCACAC
40138927 TTTATTCAATTTTCTTAATTCACGGAAATTTAC
66 TTTATTCAATTTTCTTAATTCACGGAAATTTAC
40138960 AATTTGG-TTTATTTATTTATTTAGTCCCTTGAATTTTCTCTATTCTATATTTAAGCTTTCACAC
1 AATTTGGTTTTATTTATTTATTTAGTCCCTTGAATTTTCTCTATTCTATATTTAAGCTTTCACAC
40139024 TTTATTCAATTTTCTTAATTCACGGAAAT
66 TTTATTCAATTTTCTTAATTCACGGAAAT
40139053 AGTGACCCGA
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 86 0.92
98 7 0.08
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (98 bp):
AATTTGGTTTTATTTATTTATTTAGTCCCTTGAATTTTCTCTATTCTATATTTAAGCTTTCACAC
TTTATTCAATTTTCTTAATTCACGGAAATTTAC
Found at i:40143638 original size:46 final size:47
Alignment explanation
Indices: 40143502--40143656 Score: 149
Period size: 47 Copynumber: 3.3 Consensus size: 47
40143492 TGGGTAAGGT
* * * *
40143502 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAA
1 GCCGATGCCATGTCCCAGACATAGTCTTACACTGGCTTACATCTCTA
* * **
40143549 GTCGATGCCATGTCCCA-AGCATAGTCTTATACTAAC-TATCATCTCGTA
1 GCCGATGCCATGTCCCAGA-CATAGTCTTACACTGGCTTA-CATCTC-TA
* *
40143597 GCCGATG-CATGTCACAGACAT-GTCTTACACTGGCTTACATCTTTA
1 GCCGATGCCATGTCCCAGACATAGTCTTACACTGGCTTACATCTCTA
40143642 GGCCGATG-CATGTCC
1 -GCCGATGCCATGTCC
40143657 TAGATGTAAT
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
45 2 0.02
46 30 0.34
47 47 0.54
48 8 0.09
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATAGTCTTACACTGGCTTACATCTCTA
Found at i:40144365 original size:27 final size:28
Alignment explanation
Indices: 40144335--40144391 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
40144325 ATTTTTGATG
40144335 AAATGAGCTATTTG-GG-CTAATTTGTGA
1 AAATGAGCT-TTTGAGGACTAATTTGTGA
*
40144362 AAATGAGGTTTTGAAGGACTAATTTGTGA
1 AAATGAGCTTTTG-AGGACTAATTTGTGA
40144391 A
1 A
40144392 TTTAACATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
27 8 0.31
28 2 0.08
29 12 0.46
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
AAATGAGCTTTTGAGGACTAATTTGTGA
Found at i:40151581 original size:27 final size:28
Alignment explanation
Indices: 40151551--40151607 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
40151541 ATTTTTGATG
40151551 AAATGAGCTATTTG-GG-CTAATTTGTGA
1 AAATGAGCT-TTTGAGGACTAATTTGTGA
*
40151578 AAATGAGGTTTTGAAGGACTAATTTGTGA
1 AAATGAGCTTTTG-AGGACTAATTTGTGA
40151607 A
1 A
40151608 TTTAACATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 4 0.15
27 8 0.31
28 2 0.08
29 12 0.46
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
AAATGAGCTTTTGAGGACTAATTTGTGA
Found at i:40153786 original size:30 final size:30
Alignment explanation
Indices: 40153729--40153786 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40153719 AAATTTACAT
* *
40153729 CCTTAGTAAAATGACCATTTTGGCCCTATA
1 CCTTAGCAAAATGACCATTTTGACCCTATA
*
40153759 CCTTAGCAAAATGACCATTTTTACCCTA
1 CCTTAGCAAAATGACCATTTTGACCCTA
40153787 GGCTCGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (30 bp):
CCTTAGCAAAATGACCATTTTGACCCTATA
Found at i:40154124 original size:12 final size:12
Alignment explanation
Indices: 40154107--40154131 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40154097 AAAAAATGTA
40154107 AAAATCATCAAG
1 AAAATCATCAAG
40154119 AAAATCATCAAG
1 AAAATCATCAAG
40154131 A
1 A
40154132 TCACTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:40165075 original size:43 final size:42
Alignment explanation
Indices: 40164864--40165075 Score: 160
Period size: 43 Copynumber: 5.0 Consensus size: 42
40164854 CACATAAGCT
* * * * * *
40164864 CATACAATGCC-ATATCCCGGATATGGTCTTACATGTTATCA
1 CATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCG
* * * * * * *
40164905 CATATCGATGCCACTGTCCTAAACAGGGTCTTACACGAAATCA
1 CATA-CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCG
* * * * * *
40164948 TATAACGATGCCAATGTCCTAAACATGGTCTTACACATAATAG
1 CAT-ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCG
*
40164991 CATA-ATGATGCCAATG-CCCTAGACATGGTCTTACACATAATCG
1 CATACA--ATGCCAATGTCCC-AGACATGGTCTTACACGTAATCG
*
40165034 CAATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATC
1 C-ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATC
40165076 TCATCTTGGT
Statistics
Matches: 137, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
41 4 0.03
42 9 0.07
43 116 0.85
44 7 0.05
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (42 bp):
CATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCG
Found at i:40170813 original size:21 final size:21
Alignment explanation
Indices: 40170789--40170833 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40170779 CTCATGTGAC
*
40170789 AATTAACATATACTTCATAAA
1 AATTAACAAATACTTCATAAA
* *
40170810 AATTCAGAAATACTTCATAAA
1 AATTAACAAATACTTCATAAA
40170831 AAT
1 AAT
40170834 ATTTTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (21 bp):
AATTAACAAATACTTCATAAA
Found at i:40175596 original size:2 final size:2
Alignment explanation
Indices: 40175591--40175617 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40175581 TATATATATA
40175591 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
40175618 TTGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:40176337 original size:2 final size:2
Alignment explanation
Indices: 40176330--40176354 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40176320 AATTCATGTT
40176330 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
40176355 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40182770 original size:90 final size:91
Alignment explanation
Indices: 40182664--40182848 Score: 345
Period size: 91 Copynumber: 2.0 Consensus size: 91
40182654 TTGGGTCACT
40182664 ATTTTACATCCACTTGAATTTAAGAGAAAGTTGTAAAG-AAAAAATCCTCTGAAGAGATTATTTC
1 ATTTTACATCCACTTGAATTTAAGAGAAAGTTGTAAAGAAAAAAATCCTCTGAAGAGATTATTTC
*
40182728 AGAAAATTTCTAAAGATATTTTTCTA
66 AGAAAATTTCTAAAAATATTTTTCTA
40182754 ATTTTACATCCACTTGAATTTAAGAGAAAGTTGTAAAGAAAAAAATCCTCTGAAGAGATTATTTC
1 ATTTTACATCCACTTGAATTTAAGAGAAAGTTGTAAAGAAAAAAATCCTCTGAAGAGATTATTTC
*
40182819 AGAAAATTTCTAAAAATATTTTTTTA
66 AGAAAATTTCTAAAAATATTTTTCTA
40182845 ATTT
1 ATTT
40182849 ACAACTTGAC
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
90 38 0.41
91 54 0.59
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (91 bp):
ATTTTACATCCACTTGAATTTAAGAGAAAGTTGTAAAGAAAAAAATCCTCTGAAGAGATTATTTC
AGAAAATTTCTAAAAATATTTTTCTA
Found at i:40188196 original size:78 final size:78
Alignment explanation
Indices: 40188113--40188268 Score: 231
Period size: 78 Copynumber: 2.0 Consensus size: 78
40188103 ACCTTTCATT
* ** *
40188113 TTTTTTAAAGTCTTTTTAATTTTTTGTCTTTTTAATCCATACATTTGTATTATTTGTTAAATTAC
1 TTTTTTAAAATCTTTTTAATTTTTCATCTTTTTAATCCATACATTTGTATTATTTGTTAAATCAC
*
40188178 TTGAAATGAATGA
66 TCGAAATGAATGA
* * * *
40188191 TTTTTTAAAATTTTTTTAATTTTTCATTTTTTTAATCTATATATTTGTATTATTTGTTAAATCAC
1 TTTTTTAAAATCTTTTTAATTTTTCATCTTTTTAATCCATACATTTGTATTATTTGTTAAATCAC
40188256 TCGAAATGAATGA
66 TCGAAATGAATGA
40188269 AAAAATTAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.56
Consensus pattern (78 bp):
TTTTTTAAAATCTTTTTAATTTTTCATCTTTTTAATCCATACATTTGTATTATTTGTTAAATCAC
TCGAAATGAATGA
Found at i:40189688 original size:16 final size:16
Alignment explanation
Indices: 40189669--40189704 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
40189659 TATTATTTTT
40189669 TATTAGTATT-AGTATG
1 TATTAGTATTGA-TATG
40189685 TATTAGTATTGATATG
1 TATTAGTATTGATATG
40189701 TATT
1 TATT
40189705 GATATCGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.53
Consensus pattern (16 bp):
TATTAGTATTGATATG
Found at i:40191593 original size:41 final size:41
Alignment explanation
Indices: 40191536--40191736 Score: 294
Period size: 41 Copynumber: 4.9 Consensus size: 41
40191526 GGCGTTTTAG
*
40191536 AGAGCATTAGCAGCGCTTTTGGTAAAACGCCGCTAAAGACC
1 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGACC
40191577 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGACC
1 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGACC
* *
40191618 AGAGCACTAGCGGCGCTTTTGTTAAAACGCCGCTAAAGACC
1 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGACC
* * * * **
40191659 AAAGCATCAACAGCGCTTTTATTAAAACGCCGCTAAAGACC
1 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGACC
* * *
40191700 AGAGAATTAGCGGCGCTCTTGGTAAAACGCCACTAAA
1 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAA
40191737 AGTCATATAA
Statistics
Matches: 142, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 142 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (41 bp):
AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAGACC
Found at i:40191961 original size:14 final size:14
Alignment explanation
Indices: 40191939--40191977 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
40191929 TAGGATTTAT
* *
40191939 GATTTAGGGTTTTG
1 GATTTAGGGGTTGG
40191953 GATTTAGGGGTTGG
1 GATTTAGGGGTTGG
*
40191967 GGTTTAGGGGT
1 GATTTAGGGGT
40191978 AAATATAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.46, T:0.41
Consensus pattern (14 bp):
GATTTAGGGGTTGG
Found at i:40193152 original size:22 final size:22
Alignment explanation
Indices: 40193124--40193166 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
40193114 ACATTCCTGC
40193124 GAATCCTGCTGTTAACGTTAAG
1 GAATCCTGCTGTTAACGTTAAG
40193146 GAATCCTGCTGTTAACGTTAA
1 GAATCCTGCTGTTAACGTTAA
40193167 AGATGATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (22 bp):
GAATCCTGCTGTTAACGTTAAG
Found at i:40199852 original size:43 final size:43
Alignment explanation
Indices: 40199788--40199881 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
40199778 TACAAAATTT
40199788 CGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGATCTTTAG
1 CGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGATCTTTAG
* * * *
40199831 CGGCGTTTGTGGGAAAGGCGCCGTTAATGGTCATGATCTTTAG
1 CGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGATCTTTAG
40199874 CGGCGTTT
1 CGGCGTTT
40199882 TTCCAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (43 bp):
CGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGATCTTTAG
Found at i:40206152 original size:28 final size:27
Alignment explanation
Indices: 40206115--40206168 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
40206105 GAAATTTTAA
*
40206115 AAAAAAATAAAATATTATAAAAATCATG
1 AAAAAAATAAAAAATT-TAAAAATCATG
* *
40206143 AAAAATATAAAAAATTTAAAATTCAT
1 AAAAAAATAAAAAATTTAAAAATCAT
40206169 TATCAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAAAAATAAAAAATTTAAAAATCATG
Found at i:40209901 original size:24 final size:24
Alignment explanation
Indices: 40209873--40209921 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
40209863 CCAAAATAAC
40209873 AATTAATTTTTATATAAACTTTTA
1 AATTAATTTTTATATAAACTTTTA
*
40209897 AATTAATTTTTGTATAAACTTTTA
1 AATTAATTTTTATATAAACTTTTA
40209921 A
1 A
40209922 TAAATATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (24 bp):
AATTAATTTTTATATAAACTTTTA
Found at i:40210547 original size:41 final size:41
Alignment explanation
Indices: 40210502--40210818 Score: 411
Period size: 41 Copynumber: 7.7 Consensus size: 41
40210492 TTATATGACT
* * *
40210502 TTTAGTGGCGTTTTACCAAAAGCGCCACGAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* *
40210543 TTTAGCGGCGTTTTACCAAAAGCGTCGCTAATGGTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* *
40210584 TTTAGCGGCGTTTTTCTAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* *
40210625 TTTAGCGGCGTTTTGCCAAAAGCGCCGTTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* *
40210666 TTTAGCGGCGTTTTGCCAAAAGTGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* * * *
40210707 TTTAGCGGCATTTTGCCAAAAACGCCGTTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* * * * * *
40210748 TTTAGCGGCGTTTTAACAAAAAACGCCGCTATTACTC-AGTT
1 TTTAGCGGCGTTTT-ACCAAAAGCGCCGCTAATGCTCTGGTC
* *
40210789 TTTAGCGGCGTTTTAGCAAAAACGCCGCTA
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTA
40210819 TTTCTCTGTG
Statistics
Matches: 247, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
40 14 0.06
41 216 0.87
42 17 0.07
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
Found at i:40216855 original size:20 final size:22
Alignment explanation
Indices: 40216830--40216869 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40216820 GCAAGCCACC
*
40216830 ATTGAT-GA-ATTAGGCTTAAA
1 ATTGATAGATATTAAGCTTAAA
40216850 ATTGATAGATATTAAGCTTA
1 ATTGATAGATATTAAGCTTA
40216870 GATTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (22 bp):
ATTGATAGATATTAAGCTTAAA
Found at i:40221038 original size:12 final size:12
Alignment explanation
Indices: 40221005--40221038 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
40220995 TAGAAATTAC
40221005 TTAACTT-GTAA
1 TTAACTTGGTAA
40221016 TTAAC-TGGTAA
1 TTAACTTGGTAA
40221027 TTAACTTGGTAA
1 TTAACTTGGTAA
40221039 ACACAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (12 bp):
TTAACTTGGTAA
Found at i:40230293 original size:25 final size:25
Alignment explanation
Indices: 40230263--40230319 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
40230253 TCTCACATCC
40230263 ATTTATAAATTAATTCATATGTGAT
1 ATTTATAAATTAATTCATATGTGAT
40230288 ATTTATAAATTAATTCATATGTGAT
1 ATTTATAAATTAATTCATATGTGAT
40230313 ATTTATA
1 ATTTATA
40230320 GTGTGATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (25 bp):
ATTTATAAATTAATTCATATGTGAT
Found at i:40231021 original size:3 final size:3
Alignment explanation
Indices: 40231013--40231078 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
40231003 TGAAGGTGAG
* * * * *
40231013 AGA AGA AGA A-A GAGG AGG AGA AGA A-A GAGA AGG AGA AGG AGA AGG
1 AGA AGA AGA AGA -AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA
40231058 AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA
40231079 TGATGATGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 48 0.94
4 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:40231036 original size:15 final size:15
Alignment explanation
Indices: 40231016--40231078 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
40231006 AGGTGAGAGA
*
40231016 AGAAGAAAGAGGAGG
1 AGAAGAAAGAGAAGG
40231031 AGAAGAAAGAGAAGG
1 AGAAGAAAGAGAAGG
40231046 AGAAG---GAGAAGG
1 AGAAGAAAGAGAAGG
*
40231058 AGAAG-AAGAAGAAGA
1 AGAAGAAAG-AGAAGG
40231073 AGAAGA
1 AGAAGA
40231079 TGATGATGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 12 0.29
14 1 0.02
15 29 0.69
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (15 bp):
AGAAGAAAGAGAAGG
Found at i:40231065 original size:21 final size:21
Alignment explanation
Indices: 40230984--40231077 Score: 66
Period size: 21 Copynumber: 4.4 Consensus size: 21
40230974 CCCTCAATGA
* *
40230984 AAGGAGAAGGAATAAG-AGGTG
1 AAGGAGAAGG-AGAAGAAGGAG
* * *
40231005 AAGGTGAGAGAAGAAGAAAGAG
1 AAGGAGA-AGGAGAAGAAGGAG
* *
40231027 GAGGAGAA-GAAAGAGAAGGAG
1 AAGGAGAAGGAGA-AGAAGGAG
*
40231048 AAGGAGAAGGAGAAGAAGAAG
1 AAGGAGAAGGAGAAGAAGGAG
*
40231069 AAGAAGAAG
1 AAGGAGAAG
40231078 ATGATGATGA
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
20 2 0.04
21 40 0.73
22 13 0.24
ACGTcount: A:0.54, C:0.00, G:0.43, T:0.03
Consensus pattern (21 bp):
AAGGAGAAGGAGAAGAAGGAG
Found at i:40231083 original size:3 final size:3
Alignment explanation
Indices: 40231077--40231129 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
40231067 AGAAGAAGAA
40231077 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
40231125 GAT GA
1 GAT GA
40231130 AGAAAGGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:40233058 original size:3 final size:3
Alignment explanation
Indices: 40233052--40233085 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
40233042 AAATAGAAAA
40233052 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
40233086 AAGCTAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40241018 original size:15 final size:15
Alignment explanation
Indices: 40240998--40241027 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40240988 TCTTGTTAGT
40240998 CGTTGGAAAAGTTAC
1 CGTTGGAAAAGTTAC
*
40241013 CGTTGGAATAGTTAC
1 CGTTGGAAAAGTTAC
40241028 TATTGAAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (15 bp):
CGTTGGAAAAGTTAC
Found at i:40243319 original size:17 final size:18
Alignment explanation
Indices: 40243289--40243325 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
40243279 AATTAAAATA
*
40243289 AATTTAATTGATTTTCTT
1 AATTAAATTGATTTTCTT
40243307 AATTAAATT-ATTTTCTT
1 AATTAAATTGATTTTCTT
40243324 AA
1 AA
40243326 CCCAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (18 bp):
AATTAAATTGATTTTCTT
Found at i:40243972 original size:42 final size:43
Alignment explanation
Indices: 40243906--40243993 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 43
40243896 AGCCAAACTA
* * **
40243906 TGTACAATTCAAAATGAGGGTCACACGGCCATGTCGCAACCCG
1 TGTACAAATCAAAATGAAGGTCACACAACCATGTCGCAACCCG
* * *
40243949 TGTACAAATCGAAAT-AAGGTCACACAACCATGTTGCAAGCCG
1 TGTACAAATCAAAATGAAGGTCACACAACCATGTCGCAACCCG
40243991 TGT
1 TGT
40243994 CCCAAACCGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 25 0.66
43 13 0.34
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (43 bp):
TGTACAAATCAAAATGAAGGTCACACAACCATGTCGCAACCCG
Found at i:40247018 original size:33 final size:33
Alignment explanation
Indices: 40246941--40247018 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
40246931 ATATGTATAC
* * *
40246941 GTGTAAGACCATAGCTGGGCTATGTCATCCTGA
1 GTGTAAGACCATAACTGGGCTATGGCATCATGA
* * *
40246974 -TGATAAAACCATAACTGGGTTATGGCATTATGA
1 GTG-TAAGACCATAACTGGGCTATGGCATCATGA
40247007 GTGTAAGACCAT
1 GTGTAAGACCAT
40247019 GGCAAGGCCA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
32 2 0.06
33 32 0.89
34 2 0.06
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (33 bp):
GTGTAAGACCATAACTGGGCTATGGCATCATGA
Found at i:40248874 original size:17 final size:17
Alignment explanation
Indices: 40248848--40248893 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
40248838 ATGCTAAAAC
*
40248848 AATTATAAAAACATAAA
1 AATTACAAAAACATAAA
*
40248865 AATTACAAAAATATAAA
1 AATTACAAAAACATAAA
*
40248882 ACTTACTAAAAA
1 AATTAC-AAAAA
40248894 ACGGAACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (17 bp):
AATTACAAAAACATAAA
Found at i:40253021 original size:10 final size:10
Alignment explanation
Indices: 40253006--40253030 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40252996 TGCATAATTA
40253006 TATATATATG
1 TATATATATG
40253016 TATATATATG
1 TATATATATG
40253026 TATAT
1 TATAT
40253031 CTCGTGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:40259207 original size:52 final size:49
Alignment explanation
Indices: 40259122--40259488 Score: 449
Period size: 46 Copynumber: 7.6 Consensus size: 49
40259112 TTTGAGTACT
* **
40259122 TCTGATCAAGTG---ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
40259168 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
40259220 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
40259266 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
40259312 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
40259364 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
40259416 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
40259462 TCTGATCAAGTGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
40259489 GCTACACTTA
Statistics
Matches: 291, Mismatches: 16, Indels: 28
0.87 0.05 0.08
Matches are distributed among these distances:
46 154 0.53
48 1 0.00
49 2 0.01
50 1 0.00
52 133 0.46
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:40259242 original size:98 final size:97
Alignment explanation
Indices: 40259122--40259488 Score: 510
Period size: 98 Copynumber: 3.7 Consensus size: 97
40259112 TTTGAGTACT
* *
40259122 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
40259187 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
40259220 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
40259280 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
40259312 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
40259377 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * *
40259416 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
40259481 GATAAGTG
65 GA-AAGTG
40259489 GCTACACTTA
Statistics
Matches: 241, Mismatches: 14, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 1 0.00
98 146 0.61
99 10 0.04
101 1 0.00
104 41 0.17
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:40259470 original size:196 final size:196
Alignment explanation
Indices: 40259136--40259488 Score: 616
Period size: 196 Copynumber: 1.8 Consensus size: 196
40259126 ATCAAGTGAT
* * *
40259136 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * *
40259201 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
40259266 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
40259331 G
196 G
* * *
40259332 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
40259397 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
40259462 TCTGATCAAGTGACAAAGTGATAAGTG
131 TCTGATCAAGTGACAAAGTGATAAGTG
40259489 GCTACACTTA
Statistics
Matches: 147, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
196 147 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:40259496 original size:37 final size:37
Alignment explanation
Indices: 40259452--40259597 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
40259442 GATAGCTTTA
**
40259452 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40259489 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
40259526 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
40259563 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40259598 ATCATACGTA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 88 0.85
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:40259525 original size:150 final size:149
Alignment explanation
Indices: 40259122--40259477 Score: 476
Period size: 150 Copynumber: 2.4 Consensus size: 149
40259112 TTTGAGTACT
* * * *
40259122 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * * *
40259187 GAAAGTGATAAGTAATAGCTTC-G---GCTATACTTATC---TGATCAAGTGATAAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGCAAACTAAACTGATCAAGTGA-CAAGTGATAAAGTGATAAG
40259245 TGATAGCTTCGGCTACACTTA
129 TGATAGCTTCGGCTACACTTA
*
40259266 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * * * *
40259331 GAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTGA-AAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAG
*
40259395 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTACACTTA
*
40259416 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAA
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
40259478 AGTGATAAGT
Statistics
Matches: 192, Mismatches: 12, Indels: 10
0.90 0.06 0.05
Matches are distributed among these distances:
144 83 0.43
145 1 0.01
149 7 0.04
150 91 0.47
151 7 0.04
152 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (149 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAACTATAGCTTCAGCAAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAGTG
ATAGCTTCGGCTACACTTA
Found at i:40260914 original size:49 final size:49
Alignment explanation
Indices: 40260853--40260996 Score: 225
Period size: 49 Copynumber: 2.9 Consensus size: 49
40260843 ATGTGAACAT
*
40260853 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
40260903 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * *
40260952 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
40260997 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 84 0.95
50 4 0.05
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:40264208 original size:52 final size:49
Alignment explanation
Indices: 40264123--40264489 Score: 449
Period size: 46 Copynumber: 7.6 Consensus size: 49
40264113 TTTGAGTACT
* **
40264123 TCTGATCAAGTG---ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
40264169 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
40264221 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
40264267 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
40264313 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
40264365 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
40264417 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
40264463 TCTGATCAAGTGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
40264490 GCTACACTTA
Statistics
Matches: 291, Mismatches: 16, Indels: 28
0.87 0.05 0.08
Matches are distributed among these distances:
46 154 0.53
48 1 0.00
49 2 0.01
50 1 0.00
52 133 0.46
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:40264243 original size:98 final size:97
Alignment explanation
Indices: 40264123--40264489 Score: 510
Period size: 98 Copynumber: 3.7 Consensus size: 97
40264113 TTTGAGTACT
* *
40264123 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
40264188 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
40264221 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
40264281 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
40264313 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
40264378 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * *
40264417 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
40264482 GATAAGTG
65 GA-AAGTG
40264490 GCTACACTTA
Statistics
Matches: 241, Mismatches: 14, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 1 0.00
98 146 0.61
99 10 0.04
101 1 0.00
104 41 0.17
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:40264471 original size:196 final size:196
Alignment explanation
Indices: 40264137--40264489 Score: 616
Period size: 196 Copynumber: 1.8 Consensus size: 196
40264127 ATCAAGTGAT
* * *
40264137 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * *
40264202 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
40264267 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
40264332 G
196 G
* *
40264333 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
40264398 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
40264463 TCTGATCAAGTGACAAAGTGATAAGTG
131 TCTGATCAAGTGACAAAGTGATAAGTG
40264490 GCTACACTTA
Statistics
Matches: 147, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
196 147 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:40264497 original size:37 final size:37
Alignment explanation
Indices: 40264453--40264598 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
40264443 GATAGCTTTA
**
40264453 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40264490 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
40264527 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
40264564 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40264599 ATCATACGTA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 88 0.85
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:40264526 original size:150 final size:149
Alignment explanation
Indices: 40264123--40264478 Score: 485
Period size: 150 Copynumber: 2.4 Consensus size: 149
40264113 TTTGAGTACT
* * * *
40264123 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * * *
40264188 GAAAGTGATAAGTAATAGCTTC-G---GCTATACTTATC---TGATCAAGTGATAAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGCAAACTAAACTGATCAAGTGA-CAAGTGATAAAGTGATAAG
40264246 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
*
40264267 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * * * *
40264332 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA-AAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAG
40264396 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
*
40264417 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAA
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
40264479 AGTGATAAGT
Statistics
Matches: 193, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
144 83 0.43
145 1 0.01
149 7 0.04
150 92 0.48
151 7 0.04
152 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (149 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAACTATAGCTTCAGCAAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAGTG
ATAGCTTCGGCTATACTTA
Found at i:40273852 original size:76 final size:76
Alignment explanation
Indices: 40273753--40274611 Score: 783
Period size: 76 Copynumber: 10.9 Consensus size: 76
40273743 GATGTTTTTA
* *
40273753 TTTCAAAATTCAATTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
40273818 TTTTTTATATG
66 TTTTTTATATG
** *
40273829 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACATGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
** *
40273894 TTTCTGTCCT-TC
66 TTT-T-TTATATG
**** *
40273906 AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC-A
*
40273971 TTGATGTTTTTTCAATTTACG
65 ---A--TTTTTT--A--TATG
* *
40273992 ATTTTCAAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCGGGGA-ACGCTGAGGTATTTT
1 --TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTATTTT
40274056 CAA----TTA-ATG
63 CAATTTTTTATATG
* * * **
40274065 CTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGCGCCTCGGGTCACATGCCAAGGTATTT
1 --TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCTGAGGTATTT
*
40274130 TCAAAATCTATTTTGCAAATTCTG
62 TC--AAT-T-TTTT----A-TATG
* *
40274154 TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
1 -TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTT
* **
40274219 CAATTTCTGCT-TG
63 CAATTTTTTATATG
* *
40274232 --TC-AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
40274294 TTTTTTATATG
66 TTTTTTATATG
* *
40274305 TTTCAAAAATCAACTCATATT-CGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGGTATTGTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
40274369 TTTTTTATATG
66 TTTTTTATATG
* *
40274380 TTTCAAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
** *
40274445 TTTCTGTCCT-TC
66 TTT-T-TTATATG
**** * * *
40274457 AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTGAGCTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC-A
*
40274522 TTGATGTTTTTTCAATTTACG
65 ---A--TTTTTT--A--TATG
* * *
40274543 CTTTTCAAAAATCAACTCATATTACGATAGGTGAGTTGAGCCTCGGGGA-ACGCTGAAGTATTTT
1 --TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTATTTT
40274607 CAATT
63 CAATT
40274612 AATATTTTTT
Statistics
Matches: 647, Mismatches: 80, Indels: 106
0.78 0.10 0.13
Matches are distributed among these distances:
72 64 0.10
73 45 0.07
74 1 0.00
75 90 0.14
76 122 0.19
77 119 0.18
78 10 0.02
79 1 0.00
81 4 0.01
82 4 0.01
83 8 0.01
84 4 0.01
85 3 0.00
86 3 0.00
87 3 0.00
88 120 0.19
89 8 0.01
90 38 0.06
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (76 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
TTTTTTATATG
Found at i:40273945 original size:77 final size:76
Alignment explanation
Indices: 40273757--40274788 Score: 692
Period size: 88 Copynumber: 12.8 Consensus size: 76
40273747 TTTTTATTTC
* * *
40273757 AAAATTCAATTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
* * ***
40273822 -TTATATGTTTC
66 GTCAT-TCTAAA
* *
40273833 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACATGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT-
* *
40273898 TGTCCTTCAAAA
65 TGTCATTCTAAA
40273910 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC-A---A
* *
40273975 TGTTTTTTCAATT-TACGATTTTC
62 --TTTTGTC-ATTCTA--A----A
* * *
40273998 AAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCGGGGA-ACGCTGAGGTATTTTCAATTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATT-
* **
40274062 ATG-C-TT-T-TC
64 TTGTCATTCTAAA
* * * * **
40274071 AAAAATCAACTCATATTACGAGAGGTGAGTTGCGCCTCGGGTCACATGCCAAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTC--AA
* *
40274136 TCTATTTTGCAAATTCTGTTTTCAA
62 T-T-TTGT-C--ATTC-----TAAA
*
40274161 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT-
*
40274226 TG-C-TTGT---
65 TGTCATTCTAAA
* * * *
40274233 CAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
* * ***
40274298 -TTATATGTTTC
66 GTCAT-TCTAAA
** *
40274309 AAAAATCAACTCATATT-CGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGGTATTGTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
* * ***
40274373 -TTATATGTTTC
66 GTCAT-TCTAAA
*
40274384 AAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT-
* *
40274449 TGTCCTTCAAAA
65 TGTCATTCTAAA
* *
40274461 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTGAGCTATTTTCAATTGA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC-A---A
* ***
40274526 TGTTTTTTCAATTTACGCTTTTC
62 --TTTTGTC-A-TT---C-TAAA
* * * *
40274549 AAAAATCAACTCATATTACGATAGGTGAGTTGAGCCTCGGGGA-ACGCTGAAGTATTTTCAATTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTC-----
* ***
40274613 ATATTTTTTCAATTTATGCTTTTC
60 A-ATTTTGTC-A--T-T-C-TAAA
* * *
40274637 AAAAATTAACTCATATTACGAGAGGTGAGTTGAGTCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT-
40274702 TGTTTTTCAATTTCTATCCTAAA
65 TG----TC-A----T-T-CTAAA
40274725 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
40274789 GATGTTTTTT
Statistics
Matches: 791, Mismatches: 92, Indels: 133
0.78 0.09 0.13
Matches are distributed among these distances:
71 1 0.00
72 63 0.08
73 40 0.05
74 1 0.00
75 87 0.11
76 117 0.15
77 120 0.15
78 9 0.01
80 6 0.01
81 2 0.00
82 14 0.02
83 14 0.02
84 5 0.01
85 2 0.00
86 3 0.00
87 9 0.01
88 185 0.23
89 71 0.09
90 40 0.05
92 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (76 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTT
GTCATTCTAAA
Found at i:40274194 original size:163 final size:155
Alignment explanation
Indices: 40273753--40274852 Score: 861
Period size: 165 Copynumber: 6.8 Consensus size: 155
40273743 GATGTTTTTA
* *
40273753 TTTCAAAATTCAATTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC--
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
*
40273816 AATTTTTT---A-TATG-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGAC
66 AATTTTTTCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGAC
* **
40273876 ATGCTGAGGTATTTTCAATTTCTGT
131 ACGCTGAGGTATTTTCAATTAATGT
* *
40273901 CCTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT
1 -TTTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
* * * *
40273966 TTCAATTGATGTTTTTTCAATTTAC-GATTTTCAAAAATCAACTCATATTACAAGAGGTGAGTTG
61 TTCAA---A-ATTTTTTCAAATT-CTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
**
40274030 AGCCTCGGGGA-ACGCTGAGGTATTTTCAATTAATGCT
120 AGCCT-TAGGACACGCTGAGGTATTTTCAATTAATG-T
* * * **
40274067 TTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGCGCCTCGGGTCACATGCCAAGGTATTTTC
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCTGAGGTATTTTC
40274132 AAAATCTATTTTGCAAATTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
64 AAAAT-T-TTTT-CAAATTCTGTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* * **
40274197 TCAGGACACGCTGAGGTAATTTCAATTTCTGCT
124 TTAGGACACGCTGAGGTATTTTCAATTAATG-T
* * *
40274230 TGTC-AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTC--
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
* *
40274292 AATTTTTT---A-TATG-TTTCAAAAATCAACTCATATT-CGAGAGGTGAGTTGAGCCTTGGGAC
66 AATTTTTTCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGAC
*
40274351 ACGCTGAGGTATTGTCAATTTTTTATATG-
131 ACGCTGAGGTATTTTCAA----TTA-ATGT
* *
40274380 TTTCAAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC--
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
* * **** *
40274443 AATTTCTGTC--CTTC---AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
66 AATTT-TTTCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGA
* *
40274503 CGCGCTGAGCTATTTTCAATTGATGTTTTTTCAATTTACGCT
130 CACGCTGAGGTATTTTC-A---A------TT-AA--T--G-T
* * *
40274545 TTTCAAAAATCAACTCATATTACGATAGGTGAGTTGAGCCTCGGGGA-ACGCTGAAGTATTTTCA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTATTTTC-
* * * * *
40274609 ATTAATATTTTTTCAATTTATGCTTTTCAAAAATTAACTCATATTACGAGAGGTGAGTTGAGTCT
64 A--AA-ATTTTTTCAAATTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
*
40274674 CAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAT-T
125 TAGGACACGCTGAGGTATTTTCAA---------TT-AATGT
*
40274714 TCTATCCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
1 T-T-T-C-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT
* * * *
40274779 ATTTTCAATTGATGTTTTTTCAATTTATGCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAG
58 ATTTTCAA---A-ATTTTTTCAAATTCTGTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAG
40274844 TTGAGCCTT
117 TTGAGCCTT
40274853 GGCTCACGTG
Statistics
Matches: 778, Mismatches: 92, Indels: 133
0.78 0.09 0.13
Matches are distributed among these distances:
147 39 0.05
148 17 0.02
149 3 0.00
150 7 0.01
151 64 0.08
152 22 0.03
153 92 0.12
154 2 0.00
156 4 0.01
157 2 0.00
158 4 0.01
159 14 0.02
160 17 0.02
161 49 0.06
162 46 0.06
163 81 0.10
165 117 0.15
166 7 0.01
169 2 0.00
170 5 0.01
171 5 0.01
172 4 0.01
173 1 0.00
174 1 0.00
175 9 0.01
176 62 0.08
177 68 0.09
178 34 0.04
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (155 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
AATTTTTTCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGAC
ACGCTGAGGTATTTTCAATTAATGT
Found at i:40274597 original size:88 final size:88
Alignment explanation
Indices: 40274461--40274851 Score: 529
Period size: 88 Copynumber: 4.4 Consensus size: 88
40274451 TCCTTCAAAA
* *
40274461 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTGAGCTATTTTCAATTGA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGA
40274526 TGTTTTTTCAATTTACGCTTTTC
66 TGTTTTTTCAATTTACGCTTTTC
* * * * *
40274549 AAAAATCAACTCATATTACGATAGGTGAGTTGAGCCTCGGGGA-ACGCTGAAGTATTTTCAATTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTG
* *
40274613 ATATTTTTTCAATTTATGCTTTTC
65 ATGTTTTTTCAATTTACGCTTTTC
* * * **
40274637 AAAAATTAACTCATATTACGAGAGGTGAGTTGAGTCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGA
****
40274702 TG-TTTTTCAATTTCTATC-CTAAAA
66 TGTTTTTTCAA-TT-TA-CGCTTTTC
40274726 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGA
*
40274791 TGTTTTTTCAATTTATGC-TTTC
66 TGTTTTTTCAATTTACGCTTTTC
40274813 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
40274852 TGGCTCACGT
Statistics
Matches: 262, Mismatches: 32, Indels: 17
0.84 0.10 0.05
Matches are distributed among these distances:
87 11 0.04
88 135 0.52
89 108 0.41
90 8 0.03
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (88 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGA
TGTTTTTTCAATTTACGCTTTTC
Found at i:40274650 original size:476 final size:474
Alignment explanation
Indices: 40273755--40275155 Score: 1407
Period size: 476 Copynumber: 2.9 Consensus size: 474
40273745 TGTTTTTATT
*
40273755 TCAAAATTCAATTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATT
1 TCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATT
* *
40273820 TTTTATATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACATGCTGAGG
65 TTTTATATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGG
** **** *
40273885 TATTTTCAATTTCTGTCCTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
130 TA-TTTCAATTT-T-TTATTGTTTAAAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCAG
*
40273950 GACACGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTACGATTTTCAAAAATCAACTCATATT
192 GACACGCTGAGGTATTTTCAATTGCTG--TTTTCAA---A--A-----AAAAATCAACTCATATT
* * *
40274015 ACAAGAGGTGAGTTGAGCCTCGGGGA-ACGCTGAGGTATTTTC-A--A-----TT-AA--T-GCT
245 GCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTATGTTTTTCAATTTAGCT
* * * *
40274067 TTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGCGCCTCGGGTCACATGC-CAAGGTATTTT
309 TTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG-GA-ACGCTGAA-GTATTTT
* * * * *
40274131 CAA--AATCTATTTTGCAAATTCTG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
371 CAATTAATAT-TTTTTCAATTTATGCTTTTC--AAAAATCAACTCATATTACGAGAGGTGAGTTG
*
40274193 AGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-C-T-TG
433 AGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTCATCTA
* *
40274232 TCAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTCAATTT
1 TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT
40274297 TTTATATGTTTCAAAAATCAACTCATATT-CGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGGT
66 TTTATATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGGT
*
40274361 ATTGTCAATTTTTTATATGTTTCAAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCAGGA
131 ATT-TCAATTTTTTAT-TGTTTAAAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCAGGA
* *
40274426 CACGCTGAGGTATTTTCAATTTCTGTCCTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGT
194 CACGCTGAGGTATTTTCAATTGCTGT-TTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGT
* *
40274491 TGAGCCTCAGGACGCGCTGAGCTATTTTCAATTGATGTTTTTTCAATTTACGCTTTTCAAAAATC
258 TGAGCCTCAGGACACGCTGAGGTATTTTCAATT-ATG-TTTTTCAATTTA-GCTTTTCAAAAATC
*
40274556 AACTCATATTACGATAGGTGAGTTGAGCCTCGGGGAACGCTGAAGTATTTTCAATTAATATTTTT
320 AACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGAACGCTGAAGTATTTTCAATTAATATTTTT
* *
40274621 TCAATTTATGCTTTTCAAAAATTAACTCATATTACGAGAGGTGAGTTGAGTCTCAGGACACGCTG
385 TCAATTTATGCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
40274686 AGGTATTTTCAATTTCTGTTTTTCAATTTCTA
450 AGGTAATTTCAATTTCTG----TC-A--TCTA
*
40274718 TCCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTT
1 T-C------AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTT
40274783 TCAATTGATGTTTTTTCAATTTATGCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
59 TC-A---A--TTTTTT--A--TATG-TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
** * ***
40274848 GCCTTGGCTCACG-TGTTGAGTCACTTTCAATTTCTATTTTTATGTCTGTTTTTTTTAAATCAAC
111 GCCTTGGGACACGCTG-AG-GT-A-TTTCAA----T-TTTTTA--T-TG--TTTAAAAAATCAAC
* * * *
40274912 TCATATTGCGGGAGGCGAGTTGAGCCTCGGGGCGCGCTGAGGTATTTTCAATTGCTGTTTGTC--
162 TCATATTGCGGGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGCTGTTT-TCAA
* * *
40274975 --AAAAATCAACTCATACTGCGAGAGGAGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCAATT
226 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA-T
* *
40275038 TCTGTTTTTCAATTTATG-TTTTCAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTCGGC
290 TATGTTTTTCAATTTA-GCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGG-
* * * * * *
40275102 TCGCACGCTGAGGTATTTTTAATTTTTATTTTTTTTCAATTTATGCTTTTCAAA
353 -GGAACGCTGAAGTATTTTCAA--TTAATATTTTTTCAATTTATGCTTTTCAAA
40275156 TTCTGCTTTT
Statistics
Matches: 785, Mismatches: 66, Indels: 107
0.82 0.07 0.11
Matches are distributed among these distances:
462 3 0.00
463 50 0.06
464 1 0.00
467 1 0.00
468 1 0.00
470 1 0.00
472 1 0.00
473 9 0.01
474 70 0.09
475 41 0.05
476 162 0.21
477 20 0.03
478 55 0.07
481 1 0.00
485 1 0.00
486 2 0.00
487 1 0.00
493 55 0.07
494 1 0.00
497 1 0.00
499 6 0.01
501 1 0.00
503 4 0.01
504 4 0.01
506 19 0.02
507 27 0.03
508 2 0.00
509 5 0.01
510 2 0.00
512 43 0.05
513 14 0.02
514 81 0.10
515 2 0.00
516 31 0.04
517 1 0.00
518 66 0.08
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (474 bp):
TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT
TTTATATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGGT
ATTTCAATTTTTTATTGTTTAAAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTATTTTCAATTGCTGTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
GCCTCAGGACACGCTGAGGTATTTTCAATTATGTTTTTCAATTTAGCTTTTCAAAAATCAACTCA
TATTACGAGAGGTGAGTTGAGCCTCGGGGAACGCTGAAGTATTTTCAATTAATATTTTTTCAATT
TATGCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA
TTTCAATTTCTGTCATCTA
Found at i:40274815 original size:176 final size:174
Alignment explanation
Indices: 40274461--40275155 Score: 689
Period size: 176 Copynumber: 4.0 Consensus size: 174
40274451 TCCTTCAAAA
* * **
40274461 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTGAGCTATTTTCAATTGA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
40274526 TGTTTTTTCAATTTACGCTTTTCAAAAATCAACTCATATTACGATAGGTGAGTTGAGCCTCGGGG
66 TG-TTTTTCAATTTA-TCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC-GGG
* * *
40274591 A-ACGCTGAAGTATTTTCAATTAATATTTTTTCAATTTATGCTTTTC
128 ACACGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGCTTTTC
* * *
40274637 AAAAATTAACTCATATTACGAGAGGTGAGTTGAGTCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
**** * *
40274702 TGTTTTTCAATTTCTATCCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
66 TGTTTTTCAA-TT-TAT-CTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG
40274767 ACACGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGC-TTTC
128 ACACGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGCTTTTC
* * * *
40274813 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACG-TGTTGAGTCACTTTC
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTG-AG-GT-ATTTTC
* * *** * * *
40274876 AATTTCTATTTTT--ATGTCTGT-TTTTTTTAAATCAACTCATATTGCGGGAGGCGAGTTGAGCC
60 AATTTCTGTTTTTCAAT-T-TATCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCC
* * *
40274938 TCGGGGCGCGCTGAGGTATTTTCAATTGCTG----------TT-TG----TC
123 TCGGGACACGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGCTTTTC
* * *
40274975 AAAAATCAACTCATACTGCGAGAGGAGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
40275040 TGTTTTTCAATTTATGTTTTCAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTCGGCTCG
66 TGTTTTTCAATTTATCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGG---G
* * *
40275105 -CACGCTGAGGTATTTTTAATTTTTATTTTTTTTCAATTTATGCTTTTC
128 ACACGCTGAGGTATTTTCAA--TTGATGTTTTTTCAATTTATGCTTTTC
40275153 AAA
1 AAA
40275156 TTCTGCTTTT
Statistics
Matches: 423, Mismatches: 60, Indels: 70
0.76 0.11 0.13
Matches are distributed among these distances:
158 19 0.04
159 41 0.10
160 41 0.10
161 21 0.05
162 3 0.01
163 3 0.01
165 2 0.00
166 2 0.00
173 2 0.00
174 2 0.00
175 8 0.02
176 129 0.30
177 82 0.19
178 49 0.12
179 2 0.00
180 17 0.04
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (174 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTTTTCAATTTATCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACA
CGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGCTTTTC
Found at i:40274934 original size:265 final size:262
Alignment explanation
Indices: 40274438--40275155 Score: 790
Period size: 265 Copynumber: 2.8 Consensus size: 262
40274428 CGCTGAGGTA
40274438 TTTTCAATTTCTGTCCTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
1 TTTTCAATTTCTGTCC-T-AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
* * *
40274503 CGCGCTGAGCTATTTTCAATTGATGTTTTTTCAATTTACGCTTTTCAAAAATCAACTCATATTAC
64 CACGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGC-TTTCAAAAATCAACTCATATTAC
* *** * *
40274568 GATAGGTGAGTTGAGCCTCGGGGAACGCTGAAGTATTTTCAATTAATATTTTTTCAATTTATGCT
128 GAGAGGTGAGTTGAGCCTCGGCTCACGCTGAAGTACTTTCAATTAATATTTTTT-AATGTATGCT
* * *
40274633 TTTCAAAAATTAACTCATATTACGAGAGGTGAGTTGAGTCTCAGGACACGCTGAGGTATTTTCAA
192 TTTCAAAAATCAACTCATATTACGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
*
40274698 TTTCTG
257 TTGCTG
*
40274704 TTTTTCAATTTCTATCCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 -TTTTCAATTTCTGTCCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
*
40274769 ACGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGCTTTCAAAAAAATCAACTCATATTGC
65 ACGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGCTTTC--AAAAATCAACTCATATTAC
* * ** *
40274834 GAGAGGTGAGTTGAGCCTTGGCTCACG-TGTTGAGTCACTTTCAATTTCTA-TTTTT-ATGTCTG
128 GAGAGGTGAGTTGAGCCTCGGCTCACGCTG--AAGT-ACTTTCAATTAATATTTTTTAATGTATG
* *** * * * * *
40274896 TTTTTTTTAAATCAACTCATATTGCGGGAGGCGAGTTGAGCCTCGGGGCGCGCTGAGGTATTTTC
190 CTTTTCAAAAATCAACTCATATTACGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
40274961 AATTGCTG
255 AATTGCTG
* *
40274969 --------TT-TGT-C-----AAAAATCAACTCATACTGCGAGAGGAGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTCCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* ** * *
40275019 TGCTGAGGTATTTTCAATTTCTG-TTTTTCAATTTATGTTTTCAAAAATCAACTCATATTATGAG
66 CGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGCTTTCAAAAATCAACTCATATTACGAG
* * * * * *
40275083 AGGTGAGTTGAGCCTCGGCTCGCACGCTGAGGTATTTTTAATTTTTATTTTTTTTCAATTTATGC
131 AGGTGAGTTGAGCCTCGGCT--CACGCTGAAGTACTTTCAA--TTAATATTTTTT-AATGTATGC
40275148 TTTTCAAA
191 TTTTCAAA
40275156 TTCTGCTTTT
Statistics
Matches: 387, Mismatches: 51, Indels: 42
0.81 0.11 0.09
Matches are distributed among these distances:
246 45 0.12
247 2 0.01
248 26 0.07
249 69 0.18
251 10 0.03
254 1 0.00
255 2 0.01
256 2 0.01
264 4 0.01
265 151 0.39
266 41 0.11
267 23 0.06
268 11 0.03
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (262 bp):
TTTTCAATTTCTGTCCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGCTTTCAAAAATCAACTCATATTACGAG
AGGTGAGTTGAGCCTCGGCTCACGCTGAAGTACTTTCAATTAATATTTTTTAATGTATGCTTTTC
AAAAATCAACTCATATTACGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGC
TG
Found at i:40274983 original size:73 final size:73
Alignment explanation
Indices: 40274904--40275049 Score: 211
Period size: 73 Copynumber: 2.0 Consensus size: 73
40274894 TGTTTTTTTT
* * * * * *
40274904 AAATCAACTCATATTGCGGGAGGCGAGTTGAGCCTCGGGGCGCGCTGAGGTATTTTCAATTGCTG
1 AAATCAACTCATACTGCGAGAGGAGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGCTG
40274969 TTTGTCAA
66 TTTGTCAA
* *
40274977 AAATCAACTCATACTGCGAGAGGAGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCAATTTCTG
1 AAATCAACTCATACTGCGAGAGGAGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGCTG
*
40275042 TTTTTCAA
66 TTTGTCAA
40275050 TTTATGTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (73 bp):
AAATCAACTCATACTGCGAGAGGAGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGCTG
TTTGTCAA
Found at i:40275062 original size:13 final size:14
Alignment explanation
Indices: 40275029--40275059 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40275019 TGCTGAGGTA
*
40275029 TTTTCAATTTCTGT
1 TTTTCAATTTATGT
40275043 TTTTCAATTTATGT
1 TTTTCAATTTATGT
40275057 TTT
1 TTT
40275060 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTCAATTTATGT
Found at i:40277254 original size:10 final size:10
Alignment explanation
Indices: 40277239--40277263 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40277229 ATTGCATAAT
40277239 TATATATATG
1 TATATATATG
40277249 TATATATATG
1 TATATATATG
40277259 TATAT
1 TATAT
40277264 CTCGTGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:40279851 original size:26 final size:26
Alignment explanation
Indices: 40279822--40279873 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
40279812 TATAATATAA
*
40279822 GATTGAGCCTTAATTTGATTAGTATC
1 GATTGAACCTTAATTTGATTAGTATC
40279848 GATTGAACCTTAATTTGATTAGTATC
1 GATTGAACCTTAATTTGATTAGTATC
40279874 TTTTCTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (26 bp):
GATTGAACCTTAATTTGATTAGTATC
Found at i:40287334 original size:18 final size:20
Alignment explanation
Indices: 40287298--40287338 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
40287288 AAAAAAACTT
40287298 AAATTTCTTAAAGATAATTA
1 AAATTTCTTAAAGATAATTA
40287318 AAATTTC-TAAA-ATAATTA
1 AAATTTCTTAAAGATAATTA
40287336 AAA
1 AAA
40287339 CAATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
19 4 0.19
20 7 0.33
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATTTCTTAAAGATAATTA
Found at i:40287611 original size:19 final size:20
Alignment explanation
Indices: 40287584--40287628 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
40287574 TTTTTAAGCC
*
40287584 AATGTTAAATATT-ATTTAT
1 AATGATAAATATTAATTTAT
*
40287603 AATGATAAATTTTAATTTAT
1 AATGATAAATATTAATTTAT
40287623 ATATGA
1 A-ATGA
40287629 ATGTAGCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 7 0.32
21 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
AATGATAAATATTAATTTAT
Found at i:40288726 original size:31 final size:31
Alignment explanation
Indices: 40288684--40288750 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
40288674 TTAAATCTCA
* *
40288684 AATACTATTATTTTGATAAATAAATAGGATT
1 AATATTATTATTTTGATAAACAAATAGGATT
40288715 AATATTATTATTTTGATAAACAAATAGGATT
1 AATATTATTATTTTGATAAACAAATAGGATT
40288746 AATAT
1 AATAT
40288751 AGAGAGGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (31 bp):
AATATTATTATTTTGATAAACAAATAGGATT
Found at i:40289357 original size:21 final size:22
Alignment explanation
Indices: 40289316--40289357 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40289306 AAATGCAAAC
*
40289316 ACAGACAATTGAATACAAAAAT
1 ACAGACAATCGAATACAAAAAT
*
40289338 ACAGAGAATCGAAT-CAAAAA
1 ACAGACAATCGAATACAAAAA
40289358 AGGAAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (22 bp):
ACAGACAATCGAATACAAAAAT
Found at i:40290316 original size:3 final size:3
Alignment explanation
Indices: 40290295--40290331 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
40290285 CTATTCTTTG
* *
40290295 TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40290332 TTAAACCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:40291350 original size:13 final size:13
Alignment explanation
Indices: 40291332--40291371 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
40291322 GAAGATATCG
40291332 CACACGGGCGTGT
1 CACACGGGCGTGT
40291345 CACACGGGCGTGT
1 CACACGGGCGTGT
*
40291358 CACACGGACGTGT
1 CACACGGGCGTGT
40291371 C
1 C
40291372 CCTGCTGAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.17, C:0.33, G:0.35, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Done.