Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 123 of 320
Found at i:40027346 original size:30 final size:30
Alignment explanation
Indices: 40027312--40027408 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
40027302 TAAACTAAAA
40027312 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
40027342 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
40027372 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
40027402 TGAGCTA
1 TGAGCTA
40027409 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:40030696 original size:11 final size:10
Alignment explanation
Indices: 40030678--40030709 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
40030668 GTATCTATCT
40030678 TTAAAAAAAA
1 TTAAAAAAAA
40030688 TTAAAAAAAA
1 TTAAAAAAAA
*
40030698 TTGAAAAAAA
1 TTAAAAAAAA
40030708 TT
1 TT
40030710 TTGTGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (10 bp):
TTAAAAAAAA
Found at i:40032115 original size:30 final size:30
Alignment explanation
Indices: 40032043--40032124 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
40032033 ACTCACGAGC
* *
40032043 TAAACCTTAGCTCAACTTCAGCTTAGGAGT
1 TAAACCTTAGCTCAACTTTAGCTAAGGAGT
* *
40032073 TTAACCTCAGCTCAACTTTAGCTCAAGG-GT
1 TAAACCTTAGCTCAACTTTAGCT-AAGGAGT
* *
40032103 TAAAGCTTAGCTC-ATTTTAGCT
1 TAAACCTTAGCTCAACTTTAGCT
40032125 TAAACCCGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 32 0.74
31 3 0.07
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (30 bp):
TAAACCTTAGCTCAACTTTAGCTAAGGAGT
Found at i:40039724 original size:20 final size:21
Alignment explanation
Indices: 40039699--40039746 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
40039689 TCAGTTCCCA
*
40039699 TTAGCTCACTTGAGCTTG-TT
1 TTAGCTCACTTGAGCTTGAAT
**
40039719 TTAGCTCGTTTGAGCTTGAAT
1 TTAGCTCACTTGAGCTTGAAT
40039740 TTAGCTC
1 TTAGCTC
40039747 GTTTCATCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.44
Consensus pattern (21 bp):
TTAGCTCACTTGAGCTTGAAT
Found at i:40039744 original size:21 final size:20
Alignment explanation
Indices: 40039708--40039750 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
40039698 ATTAGCTCAC
*
40039708 TTGAGCTTGTTTTAGCTCGT
1 TTGAGCTTGATTTAGCTCGT
40039728 TTGAGCTTGAATTTAGCTCGT
1 TTGAGCTTG-ATTTAGCTCGT
40039749 TT
1 TT
40039751 CATCTCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (20 bp):
TTGAGCTTGATTTAGCTCGT
Found at i:40039998 original size:13 final size:13
Alignment explanation
Indices: 40039980--40040004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40039970 AATAGTTGTG
40039980 TGTTATTTAATTA
1 TGTTATTTAATTA
40039993 TGTTATTTAATT
1 TGTTATTTAATT
40040005 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:40042908 original size:20 final size:20
Alignment explanation
Indices: 40042885--40042931 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40042875 GGGTTAAGAT
*
40042885 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
40042905 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
40042925 TGAGCTG
1 TGAGCTG
40042932 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40044654 original size:48 final size:48
Alignment explanation
Indices: 40044599--40044704 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
40044589 TTGTCTTTTC
*
40044599 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
40044647 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
40044695 TTTCTTTTTC
1 TTTCTTTTTC
40044705 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:40047321 original size:20 final size:20
Alignment explanation
Indices: 40047298--40047344 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40047288 GGGTTAAGAT
*
40047298 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
40047318 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
40047338 TGAGCTG
1 TGAGCTG
40047345 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40049066 original size:48 final size:48
Alignment explanation
Indices: 40049014--40049119 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
40049004 TTGTCTTTTC
*
40049014 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
40049062 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
40049110 TTTCTTTTTC
1 TTTCTTTTTC
40049120 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:40051741 original size:20 final size:20
Alignment explanation
Indices: 40051718--40051764 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40051708 GGGTTAAGAT
*
40051718 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
40051738 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
40051758 TGAGCTG
1 TGAGCTG
40051765 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40054447 original size:4 final size:4
Alignment explanation
Indices: 40054438--40054471 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
40054428 AAGTTTTATT
40054438 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
40054472 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:40054479 original size:22 final size:22
Alignment explanation
Indices: 40054421--40054480 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
40054411 AAGTGGCCCA
*
40054421 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
40054445 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
40054466 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
40054481 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:40057005 original size:4 final size:4
Alignment explanation
Indices: 40056987--40057025 Score: 51
Period size: 4 Copynumber: 9.0 Consensus size: 4
40056977 TATAAAAATT
40056987 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA T-AAA TAAA
40057026 ACTTTACAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 20 0.62
5 12 0.38
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:40057491 original size:21 final size:21
Alignment explanation
Indices: 40057452--40057491 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40057442 TTGAGCTCGT
*
40057452 TTTAGCTCGTTTGAGCTCAAA
1 TTTAGCTCGTTTCAGCTCAAA
*
40057473 TTTAGCTCGTTTCATCTCA
1 TTTAGCTCGTTTCAGCTCA
40057492 TTCCTTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (21 bp):
TTTAGCTCGTTTCAGCTCAAA
Found at i:40057733 original size:13 final size:13
Alignment explanation
Indices: 40057715--40057739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40057705 AATAGTTGTG
40057715 TGTTATTTAATTA
1 TGTTATTTAATTA
40057728 TGTTATTTAATT
1 TGTTATTTAATT
40057740 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:40060556 original size:20 final size:20
Alignment explanation
Indices: 40060533--40060578 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
40060523 CCAGCTCGAA
*
40060533 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
40060553 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
40060573 TTAGCT
1 TTAGCT
40060579 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:40060560 original size:30 final size:30
Alignment explanation
Indices: 40060525--40060598 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
40060515 AGTTTTTCCC
40060525 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
40060555 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
40060585 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
40060599 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:40062310 original size:20 final size:20
Alignment explanation
Indices: 40062287--40062333 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
40062277 AGGTTAAGAT
*
40062287 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
40062307 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
40062327 TGAGCTG
1 TGAGCTG
40062334 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:40065144 original size:14 final size:14
Alignment explanation
Indices: 40065122--40065169 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
40065112 ACCTAAACCG
* *
40065122 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
40065136 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
40065150 ACC-TTTTCGTTCCT
1 ACCATTTT-GTTCCT
40065164 ACCATT
1 ACCATT
40065170 CCATTCGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 4 0.13
14 24 0.80
15 2 0.07
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:40066977 original size:12 final size:11
Alignment explanation
Indices: 40066960--40067013 Score: 72
Period size: 11 Copynumber: 4.7 Consensus size: 11
40066950 TTGTAGATTC
40066960 AAAAAAAAGTCG
1 AAAAAAAA-TCG
40066972 AAAAAAAATCG
1 AAAAAAAATCG
*
40066983 AAAAAAAATTG
1 AAAAAAAATCG
*
40066994 AAAAAAAATTTG
1 AAAAAAAA-TCG
40067006 AAAAAAAA
1 AAAAAAAA
40067014 ATTTGCATAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
11 21 0.52
12 19 0.47
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:40073627 original size:10 final size:10
Alignment explanation
Indices: 40073614--40073648 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
40073604 AAGCTCGGTT
40073614 GAGCTCAAAC
1 GAGCTCAAAC
*
40073624 GAGCTGAAAC
1 GAGCTCAAAC
*
40073634 GAGCTCAAAT
1 GAGCTCAAAC
40073644 GAGCT
1 GAGCT
40073649 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:40073657 original size:20 final size:20
Alignment explanation
Indices: 40073611--40073658 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40073601 AGTAAGCTCG
40073611 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
40073631 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
40073651 GTTGAGCT
1 GTTGAGCT
40073659 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:40075262 original size:18 final size:18
Alignment explanation
Indices: 40075241--40075289 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
40075231 AAACTCTTTT
40075241 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
40075259 TCATTTTC-TTTTCACTC
1 TCATTCTCTTTTTCAATC
*
40075276 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
40075290 TTTTCTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:40075345 original size:21 final size:20
Alignment explanation
Indices: 40075321--40075386 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
40075311 CTTTTCTCGA
40075321 TTTCATTCAAGATTCTCTCAT
1 TTTCATTCAA-ATTCTCTCAT
* **** *
40075342 TTTCTTTGTTTCTTCTCTCAA
1 TTTCATT-CAAATTCTCTCAT
*
40075363 TTTCATTCAAATCCTCTCAT
1 TTTCATTCAAATTCTCTCAT
40075383 TTTC
1 TTTC
40075387 TCTCATAATC
Statistics
Matches: 31, Mismatches: 13, Indels: 3
0.66 0.28 0.06
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.18, C:0.26, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTCATTCAAATTCTCTCAT
Found at i:40075380 original size:41 final size:42
Alignment explanation
Indices: 40075300--40075387 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
40075290 TTTTCTTTCA
* * *
40075300 TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGATTCTCTCAT
1 TTTCTTTGTTTCTTCTCTCAATTTCATTCAAGATCCTCTCAT
40075342 TTTCTTTGTTTCTTCTCTCAATTTCATTCAA-ATCCTCTCAT
1 TTTCTTTGTTTCTTCTCTCAATTTCATTCAAGATCCTCTCAT
40075383 TTTCT
1 TTTCT
40075388 CTCATAATCT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
41 14 0.33
42 29 0.67
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.57
Consensus pattern (42 bp):
TTTCTTTGTTTCTTCTCTCAATTTCATTCAAGATCCTCTCAT
Found at i:40078669 original size:29 final size:28
Alignment explanation
Indices: 40078631--40078686 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
40078621 ATAACCAAAC
*
40078631 CTACAAAACTTTATATCCATAAACCCAA
1 CTACAAAACTTCATATCCATAAACCCAA
40078659 CTACATAAACTTCATATCCATAAACCCA
1 CTACA-AAACTTCATATCCATAAACCCA
40078687 TCTTTGAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (28 bp):
CTACAAAACTTCATATCCATAAACCCAA
Found at i:40078921 original size:11 final size:11
Alignment explanation
Indices: 40078905--40078942 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
40078895 AGTAAGTTTC
40078905 AAAAAAAAACG
1 AAAAAAAAACG
*
40078916 --AAAAAAATG
1 AAAAAAAAACG
40078925 AAAAAAAAACG
1 AAAAAAAAACG
40078936 AAAAAAA
1 AAAAAAA
40078943 TTTCAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.84, C:0.05, G:0.08, T:0.03
Consensus pattern (11 bp):
AAAAAAAAACG
Found at i:40078930 original size:20 final size:20
Alignment explanation
Indices: 40078905--40078943 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40078895 AGTAAGTTTC
40078905 AAAAAAAAACGAAAAAAATG
1 AAAAAAAAACGAAAAAAATG
40078925 AAAAAAAAACGAAAAAAAT
1 AAAAAAAAACGAAAAAAAT
40078944 TTCAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (20 bp):
AAAAAAAAACGAAAAAAATG
Found at i:40082105 original size:28 final size:28
Alignment explanation
Indices: 40082000--40082177 Score: 179
Period size: 27 Copynumber: 6.5 Consensus size: 28
40081990 ATATTGAGTC
* * *
40082000 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAGTCAAACT
*
40082027 CGCACACTTAGTGCTACATAATCAAA-T
1 CGCACACTTAGTGCTACATAGTCAAACT
40082054 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
* ** * *
40082082 CTCACACTTAGTGCCGCATGGTC-AATT
1 CGCACACTTAGTGCTACATAGTCAAACT
* **
40082109 CGCACACTTAGTGC-ATCATATTC-ATTT
1 CGCACACTTAGTGCTA-CATAGTCAAACT
*
40082136 CGCACACTTAGTGCAACATAGTCAAA-T
1 CGCACACTTAGTGCTACATAGTCAAACT
*
40082163 CACACACTTAGTGCT
1 CGCACACTTAGTGCT
40082178 GTACAATTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAGTCAAACT
Found at i:40082139 original size:82 final size:81
Alignment explanation
Indices: 40082021--40082176 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40082011 TGCTATATAA
* *
40082021 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCTCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCACA
40082086 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40082103 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCACA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCACA
40082167 CACTTAGTGC
65 CACTTAGTGC
40082177 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.78
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCACAC
ACTTAGTGCCGCATGG
Found at i:40082676 original size:12 final size:12
Alignment explanation
Indices: 40082659--40082684 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40082649 ATGGCATACT
40082659 TATGTATATATA
1 TATGTATATATA
40082671 TATGTATATATA
1 TATGTATATATA
40082683 TA
1 TA
40082685 CTTCGGAATG
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:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:40088502 original size:13 final size:13
Alignment explanation
Indices: 40088484--40088508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40088474 TGGTCATCAT
40088484 GGTGTGAACACAA
1 GGTGTGAACACAA
40088497 GGTGTGAACACA
1 GGTGTGAACACA
40088509 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:40091768 original size:1 final size:1
Alignment explanation
Indices: 40091762--40091794 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
40091752 TTCCAGACTC
40091762 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40091795 ACGGATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40091861 original size:16 final size:15
Alignment explanation
Indices: 40091835--40091865 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40091825 CTAGACCGTA
40091835 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
40091850 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
40091865 T
1 T
40091866 CCTTCTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.74
Consensus pattern (15 bp):
TGCAATTTTTTTTTT
Found at i:40091891 original size:15 final size:14
Alignment explanation
Indices: 40091839--40091926 Score: 63
Period size: 15 Copynumber: 6.1 Consensus size: 14
40091829 ACCGTATGCA
*
40091839 ATTTTTTTTTTTGCA
1 ATTTTTTTTTTT-CG
40091854 ATTTTTTTTTTTC-
1 ATTTTTTTTTTTCG
*
40091867 CTTCTCTTTTTTTTCGG
1 ATT-T-TTTTTTTTC-G
40091884 ATTTTTTTTTTTCG
1 ATTTTTTTTTTTCG
*** *
40091898 AAACTTTTTTTT-A
1 ATTTTTTTTTTTCG
40091911 ACTTTTTTTTTTTCG
1 A-TTTTTTTTTTTCG
40091926 A
1 A
40091927 AGCTACGATT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
13 3 0.05
14 20 0.35
15 31 0.54
16 1 0.02
17 2 0.04
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (14 bp):
ATTTTTTTTTTTCG
Found at i:40092788 original size:13 final size:13
Alignment explanation
Indices: 40092770--40092794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40092760 TGGTCATCAT
40092770 GGTGTGAACACAA
1 GGTGTGAACACAA
40092783 GGTGTGAACACA
1 GGTGTGAACACA
40092795 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:40094910 original size:27 final size:27
Alignment explanation
Indices: 40094880--40095057 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
40094870 ATATTGAGTC
* * * *
40094880 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
40094907 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40094934 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40094962 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40094989 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40095016 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40095043 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40095058 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40095019 original size:82 final size:81
Alignment explanation
Indices: 40094901--40095056 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
40094891 TGCTATATAA
*
40094901 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40094966 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40094983 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40095047 CACTTAGTGC
65 CACTTAGTGC
40095057 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40095556 original size:12 final size:12
Alignment explanation
Indices: 40095539--40095564 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40095529 ATGGCATACT
40095539 TATGTATATATA
1 TATGTATATATA
40095551 TATGTATATATA
1 TATGTATATATA
40095563 TA
1 TA
40095565 CTTCGGAATG
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:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:40101177 original size:20 final size:20
Alignment explanation
Indices: 40101130--40101177 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
40101120 AGTAAGCTCG
40101130 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
40101150 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
40101170 GTTGAGCT
1 GTTGAGCT
40101178 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:40102848 original size:11 final size:12
Alignment explanation
Indices: 40102818--40102849 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
40102808 TTTCACTCTT
40102818 CTCTTTTTCAAA
1 CTCTTTTTCAAA
40102830 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
40102842 TTCTTTTT
1 CTCTTTTT
40102850 TCGCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:40102861 original size:27 final size:27
Alignment explanation
Indices: 40102831--40102892 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
40102821 TTTTTCAAAC
*
40102831 TCTTTTTCAAATTCTT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
40102858 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
40102885 TCTTTTTC
1 TCTTTTTC
40102893 TCTCACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:40102864 original size:6 final size:6
Alignment explanation
Indices: 40102853--40102942 Score: 58
Period size: 6 Copynumber: 14.7 Consensus size: 6
40102843 TCTTTTTTCG
* * * **
40102853 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * *
40102904 -TGATTT CTTTTT CTTTTT CGTTTT CTTTTT -GTTTT CTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
40102943 CAATTTCTCT
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
5 5 0.08
6 44 0.71
7 10 0.16
8 3 0.05
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:40102884 original size:14 final size:14
Alignment explanation
Indices: 40102833--40102891 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
40102823 TTTCAAACTC
*
40102833 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
40102846 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
40102859 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
40102874 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
40102888 TTTT
1 TTTT
40102892 CTCTCACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:40104034 original size:10 final size:10
Alignment explanation
Indices: 40104019--40104045 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
40104009 CTTCAAAATT
40104019 TTTTTTTGAA
1 TTTTTTTGAA
40104029 TTTTTTTGAA
1 TTTTTTTGAA
40104039 TTTTTTT
1 TTTTTTT
40104046 TTCAAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:40105596 original size:20 final size:20
Alignment explanation
Indices: 40105549--40105596 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
40105539 AGTAAGCTCG
40105549 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
40105569 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
40105589 GTTGAGCT
1 GTTGAGCT
40105597 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:40107454 original size:24 final size:23
Alignment explanation
Indices: 40107400--40107477 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
40107390 GGATAATTAA
**
40107400 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
40107423 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
40107447 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
40107468 GAAATAGTAT
1 GAAATGGTAT
40107478 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:40107462 original size:21 final size:21
Alignment explanation
Indices: 40107436--40107502 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
40107426 TTGGTATTTG
40107436 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40107457 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40107478 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
40107501 GG
1 GG
40107503 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:40111761 original size:17 final size:17
Alignment explanation
Indices: 40111736--40111791 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
40111726 TCTCTTTTCA
*
40111736 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
40111753 TTCTTTTTTTTT-ATCATTT
1 TTCTTTTTTTTTGA--A-TT
* *
40111772 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
40111789 TTC
1 TTC
40111792 GCTCTTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 16 0.50
18 2 0.06
19 13 0.41
ACGTcount: A:0.09, C:0.12, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:40114028 original size:13 final size:13
Alignment explanation
Indices: 40114010--40114042 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
40114000 CCGTATGCAA
40114010 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
40114023 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
40114036 TTTTTTT
1 TTTTTTT
40114043 ACGCACCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:40114359 original size:24 final size:23
Alignment explanation
Indices: 40114305--40114382 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
40114295 GGATAATTAA
**
40114305 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
40114328 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
40114352 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
40114373 GAAATAGTAT
1 GAAATGGTAT
40114383 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:40114367 original size:21 final size:21
Alignment explanation
Indices: 40114341--40114407 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
40114331 TTGGTATTTG
40114341 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40114362 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40114383 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
40114406 GG
1 GG
40114408 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:40123819 original size:21 final size:20
Alignment explanation
Indices: 40123780--40123819 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40123770 TTTGTTCTTC
*
40123780 TTTTCTTATTTCAATTAATA
1 TTTTCTTATTTCAAATAATA
*
40123800 TTTTTTTATTTCAAAATAAT
1 TTTTCTTATTTC-AAATAAT
40123820 GCAAATTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTCTTATTTCAAATAATA
Found at i:40130380 original size:39 final size:39
Alignment explanation
Indices: 40130337--40130491 Score: 274
Period size: 39 Copynumber: 4.0 Consensus size: 39
40130327 CCGAACATAT
* * *
40130337 TTCCAGCACGTAGCCTACGGACCTTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
40130376 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
40130415 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
*
40130454 TTCCAGCACATAGCCTGCGGACCCTCAGTCCGGATATA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATA
40130492 CATCACTGAA
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 112 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
Found at i:40133993 original size:31 final size:29
Alignment explanation
Indices: 40133957--40134014 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
40133947 AGTCGAAAAA
* *
40133957 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTTT
40133988 GAAAAAGAGAGTGAGCAAAAAGAAAGT
1 GAAAAAGAGAGTGAGCAAAAAGAAAGT
40134015 GTGGAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 4 0.16
31 16 0.64
ACGTcount: A:0.52, C:0.03, G:0.29, T:0.16
Consensus pattern (29 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTTT
Found at i:40138040 original size:20 final size:20
Alignment explanation
Indices: 40137995--40138040 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
40137985 GCTCGTTTCT
* *
40137995 AGCTTACTCGAGCTCAAGTC
1 AGCTCACTCAAGCTCAAGTC
* *
40138015 AACTCACTCAAGCTCAATTC
1 AGCTCACTCAAGCTCAAGTC
40138035 AGCTCA
1 AGCTCA
40138041 ATCTTAACCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.24
Consensus pattern (20 bp):
AGCTCACTCAAGCTCAAGTC
Found at i:40139720 original size:30 final size:30
Alignment explanation
Indices: 40139686--40139782 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
40139676 AGCTCACTCC
40139686 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
40139716 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
40139746 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
40139776 TAGCTCA
1 TAGCTCA
40139783 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:40141503 original size:19 final size:19
Alignment explanation
Indices: 40141479--40141532 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
40141469 TGGATTTAAA
* *
40141479 AAAAAAAGAGAAGAAATTC
1 AAAAAAAGAGAAAAAAATC
* *
40141498 AAAAAAAAATAAAAAAATC
1 AAAAAAAGAGAAAAAAATC
40141517 AAAAAAAG-GAAAAAAA
1 AAAAAAAGAGAAAAAAA
40141533 AGTGAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.80, C:0.04, G:0.09, T:0.07
Consensus pattern (19 bp):
AAAAAAAGAGAAAAAAATC
Found at i:40141503 original size:20 final size:19
Alignment explanation
Indices: 40141477--40141532 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
40141467 ATTGGATTTA
*
40141477 AAAAAAAAAGAGAAGAAATTC
1 AAAAAAAAAGA-AA-AAAATC
*
40141498 AAAAAAAAATAAAAAAATC
1 AAAAAAAAAGAAAAAAATC
*
40141517 -AAAAAAAGGAAAAAAA
1 AAAAAAAAAGAAAAAAA
40141533 AGTGAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 14 0.45
19 5 0.16
20 2 0.06
21 10 0.32
ACGTcount: A:0.80, C:0.04, G:0.09, T:0.07
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAAATC
Found at i:40142479 original size:5 final size:5
Alignment explanation
Indices: 40142459--40142530 Score: 60
Period size: 5 Copynumber: 14.0 Consensus size: 5
40142449 ACATTCTTGT
* *
40142459 AAAGA AAA-A CAAAGA AAAGA AAAGAA AAAGA AAA-A GCAAGA GAAGAA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAG-A
40142506 AAAGA AAAGA AATA-A AAAGA AAAGA
1 AAAGA AAAGA AA-AGA AAAGA AAAGA
40142531 GAGGCAAGAG
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
4 3 0.05
5 41 0.73
6 12 0.21
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (5 bp):
AAAGA
Found at i:40142499 original size:21 final size:19
Alignment explanation
Indices: 40142459--40142528 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 19
40142449 ACATTCTTGT
*
40142459 AAAGAAAAACAAAGAAAAGA
1 AAAGAAAAAGAAA-AAAAGA
40142479 AAAGAAAAAGAAAAAGCAAGA
1 AAAGAAAAAGAAAAA--AAGA
* *
40142500 GAAGAAAAAGAAAAGAAATAA
1 AAAGAAAAAGAAAA-AAA-GA
40142521 AAAGAAAA
1 AAAGAAAA
40142529 GAGAGGCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 2 0.05
20 14 0.33
21 25 0.60
22 1 0.02
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (19 bp):
AAAGAAAAAGAAAAAAAGA
Found at i:40142499 original size:26 final size:25
Alignment explanation
Indices: 40142459--40142530 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 25
40142449 ACATTCTTGT
40142459 AAAGAAAAACAAAGAAAAG-AAAAGAA
1 AAAGAAAAAC-AAGAAAAGAAAAAG-A
*
40142485 AAAGAAAAAGCAAGAGAAGAAAAAGA
1 AAAGAAAAA-CAAGAAAAGAAAAAGA
*
40142511 AAAGAAATAAAAAGAAAAGA
1 AAAGAAA-AACAAGAAAAGA
40142531 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 32 0.80
27 8 0.20
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (25 bp):
AAAGAAAAACAAGAAAAGAAAAAGA
Found at i:40142528 original size:6 final size:6
Alignment explanation
Indices: 40142469--40142517 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
40142459 AAAGAAAAAC
40142469 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAG-A AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
40142517 A
1 A
40142518 TAAAAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
5 14 0.36
6 16 0.41
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:40142610 original size:11 final size:12
Alignment explanation
Indices: 40142578--40142608 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
40142568 TTGAGAGAAC
40142578 TTGAAAAAGCCT
1 TTGAAAAAGCCT
40142590 TTGAAAAAGCCT
1 TTGAAAAAGCCT
40142602 TTGAAAA
1 TTGAAAA
40142609 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:40144821 original size:30 final size:30
Alignment explanation
Indices: 40144787--40144883 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
40144777 AGCTCACTCC
40144787 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
40144817 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
40144847 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
40144877 TAGCTCA
1 TAGCTCA
40144884 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:40149811 original size:20 final size:20
Alignment explanation
Indices: 40149788--40149841 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40149778 AGTTTTTCCC
*
40149788 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
40149808 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
40149828 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
40149842 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:40149823 original size:30 final size:30
Alignment explanation
Indices: 40149788--40149861 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
40149778 AGTTTTTCCC
40149788 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
40149818 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
40149848 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
40149862 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:40149851 original size:20 final size:20
Alignment explanation
Indices: 40149788--40149852 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
40149778 AGTTTTTCCC
* * * *
40149788 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
40149808 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
40149827 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
40149848 AGCTC
1 AGCTC
40149853 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:40151401 original size:13 final size:12
Alignment explanation
Indices: 40151371--40151445 Score: 71
Period size: 12 Copynumber: 6.0 Consensus size: 12
40151361 GTTCGAAACG
40151371 TGAAAGAAAAAA-
1 TGAAA-AAAAAAT
*
40151383 TCAAAAAAAAATT
1 TGAAAAAAAAA-T
40151396 TGAAAAAAAAAT
1 TGAAAAAAAAAT
*
40151408 TGATTGAAAAAAAT
1 TGA--AAAAAAAAT
* *
40151422 TCAAAAAAAAAG
1 TGAAAAAAAAAT
40151434 TGAAAAAAAAAT
1 TGAAAAAAAAAT
40151446 CGAGCAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
11 6 0.12
12 25 0.49
13 10 0.20
14 10 0.20
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (12 bp):
TGAAAAAAAAAT
Found at i:40151456 original size:38 final size:38
Alignment explanation
Indices: 40151377--40151458 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 38
40151367 AACGTGAAAG
* *
40151377 AAAAAATCAAAAAAAAATTTGAAAAAAAAATTGATTG-AA
1 AAAAAATCAAAAAAAAATGTGAAAAAAAAATCGA--GCAA
*
40151416 AAAAATTCAAAAAAAAA-GTGAAAAAAAAATCGAGCAA
1 AAAAAATCAAAAAAAAATGTGAAAAAAAAATCGAGCAA
40151453 AAAAAA
1 AAAAAA
40151459 AAAGGTGACC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 1 0.03
37 7 0.18
38 14 0.37
39 16 0.42
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.15
Consensus pattern (38 bp):
AAAAAATCAAAAAAAAATGTGAAAAAAAAATCGAGCAA
Found at i:40151487 original size:31 final size:29
Alignment explanation
Indices: 40151424--40151497 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
40151414 AAAAAAATTC
*
40151424 AAAAAAAAAGTGAAAAAAAAATCGAGCAA
1 AAAAAAAAAGTGAAAAAAAAATCAAGCAA
* *
40151453 AAAAAAAAAGGTGACCAAAAAAATCAAG--T
1 AAAAAAAAA-GTGA-AAAAAAAATCAAGCAA
*
40151482 TAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
40151498 GTCTTGCGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.05
28 4 0.11
29 17 0.45
30 4 0.11
31 11 0.29
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (29 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGCAA
Found at i:40152425 original size:15 final size:16
Alignment explanation
Indices: 40152405--40152436 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40152395 AGAAAATGAA
40152405 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
40152420 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
40152436 A
1 A
40152437 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:40152551 original size:17 final size:18
Alignment explanation
Indices: 40152519--40152552 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40152509 AAAAGAGAGT
*
40152519 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
40152537 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
40152553 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:40153840 original size:20 final size:20
Alignment explanation
Indices: 40153817--40153870 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40153807 AGTTTTTCCC
*
40153817 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
40153837 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
40153857 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
40153871 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:40153852 original size:30 final size:30
Alignment explanation
Indices: 40153817--40153890 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
40153807 AGTTTTTCCC
40153817 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
40153847 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
40153877 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
40153891 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:40153880 original size:20 final size:20
Alignment explanation
Indices: 40153817--40153881 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
40153807 AGTTTTTCCC
* * * *
40153817 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
40153837 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
40153856 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
40153877 AGCTC
1 AGCTC
40153882 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:40155431 original size:13 final size:12
Alignment explanation
Indices: 40155401--40155477 Score: 66
Period size: 13 Copynumber: 6.0 Consensus size: 12
40155391 GTTCGAAACG
40155401 TGAAAGAAAAAA-
1 TGAAA-AAAAAAT
*
40155413 TCAAAAAAAAATT
1 TGAAAAAAAAA-T
40155426 TGAAAAAAAAAT
1 TGAAAAAAAAAT
40155438 TGATTGAAAAAAAAT
1 TGA---AAAAAAAAT
* *
40155453 TCAAAAAAAAAAG
1 T-GAAAAAAAAAT
40155466 TGAAAAAAAAAT
1 TGAAAAAAAAAT
40155478 CGAGCAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
11 6 0.11
12 17 0.32
13 19 0.36
15 10 0.19
16 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (12 bp):
TGAAAAAAAAAT
Found at i:40155457 original size:40 final size:41
Alignment explanation
Indices: 40155401--40155477 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
40155391 GTTCGAAACG
**
40155401 TGAAAGAAAAAATCAAAAAAAAATTTGAAAAAAAAATTGAT
1 TGAAAGAAAAAATCAAAAAAAAAAGTGAAAAAAAAATTGAT
*
40155442 TGAAA-AAAAATTCAAAAAAAAAAGTGAAAAAAAAAT
1 TGAAAGAAAAAATCAAAAAAAAAAGTGAAAAAAAAAT
40155478 CGAGCAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 28 0.85
41 5 0.15
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (41 bp):
TGAAAGAAAAAATCAAAAAAAAAAGTGAAAAAAAAATTGAT
Found at i:40155488 original size:40 final size:39
Alignment explanation
Indices: 40155407--40155491 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 39
40155397 AACGTGAAAG
** *
40155407 AAAAAATCAAAAAAAAATTTGAAAAAAAAATTGATTG-AAA
1 AAAAAATCAAAAAAAAAAGTGAAAAAAAAATCGA--GCAAA
*
40155447 AAAAATTCAAAAAAAAAAGTGAAAAAAAAATCGAGCAAA
1 AAAAAATCAAAAAAAAAAGTGAAAAAAAAATCGAGCAAA
40155486 AAAAAA
1 AAAAAA
40155492 AAGGTGACCA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 1 0.03
39 8 0.21
40 30 0.77
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.14
Consensus pattern (39 bp):
AAAAAATCAAAAAAAAAAGTGAAAAAAAAATCGAGCAAA
Found at i:40155520 original size:32 final size:29
Alignment explanation
Indices: 40155455--40155530 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
40155445 AAAAAAATTC
*
40155455 AAAAAAAAAAGTGAAAAAAAAATCGAGCA
1 AAAAAAAAAAGTGAAAAAAAAATCAAGCA
40155484 AAAAAAAAAAGGTGACCAAAAAAAATCAAG--
1 AAAAAAAAAA-GTGA--AAAAAAAATCAAGCA
**
40155514 TTAAAAAAAAGTGAAAA
1 AAAAAAAAAAGTGAAAA
40155531 GTCTTGCGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 3 0.07
29 14 0.34
30 12 0.29
32 12 0.29
ACGTcount: A:0.71, C:0.07, G:0.13, T:0.09
Consensus pattern (29 bp):
AAAAAAAAAAGTGAAAAAAAAATCAAGCA
Found at i:40156456 original size:15 final size:16
Alignment explanation
Indices: 40156436--40156467 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40156426 AGAAAATGAA
40156436 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
40156451 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
40156467 A
1 A
40156468 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:40156582 original size:17 final size:18
Alignment explanation
Indices: 40156550--40156583 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40156540 AAAAGAGAGT
*
40156550 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
40156568 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
40156584 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:40157869 original size:20 final size:20
Alignment explanation
Indices: 40157846--40157899 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
40157836 AGTTTTTCCC
*
40157846 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
40157866 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
40157886 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
40157900 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:40157881 original size:30 final size:30
Alignment explanation
Indices: 40157846--40157919 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
40157836 AGTTTTTCCC
40157846 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
40157876 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
40157906 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
40157920 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:40157909 original size:20 final size:20
Alignment explanation
Indices: 40157846--40157910 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
40157836 AGTTTTTCCC
* * * *
40157846 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
40157866 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
40157885 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
40157906 AGCTC
1 AGCTC
40157911 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:40169011 original size:27 final size:28
Alignment explanation
Indices: 40168927--40169024 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
40168917 CATGAGATTG
* * * *
40168927 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
40168956 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40168984 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40169011 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
40169025 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:40169035 original size:27 final size:27
Alignment explanation
Indices: 40168955--40169037 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
40168945 TAAATTGTAC
* *
40168955 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
40168983 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
40169010 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
40169037 A
1 A
40169038 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:40170985 original size:17 final size:18
Alignment explanation
Indices: 40170963--40170999 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40170953 TGGAATAAAC
40170963 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
40170980 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
40170998 TT
1 TT
40171000 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:40174278 original size:11 final size:11
Alignment explanation
Indices: 40174262--40174289 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40174252 AGGAAATTTG
40174262 AAAAAAAATTC
1 AAAAAAAATTC
40174273 AAAAAAAATTC
1 AAAAAAAATTC
40174284 AAAAAA
1 AAAAAA
40174290 TTTTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:40175276 original size:17 final size:18
Alignment explanation
Indices: 40175239--40175279 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40175229 AAATCAAAAG
* *
40175239 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAGAATCA
40175257 AAAAGAAAAAGA-AATCA
1 AAAAGAAAAAGAGAATCA
40175274 AAAAGA
1 AAAAGA
40175280 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAGAATCA
Found at i:40177103 original size:17 final size:18
Alignment explanation
Indices: 40177081--40177117 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40177071 TGGAATAAAC
40177081 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
40177098 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
40177116 TT
1 TT
40177118 CAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:40189550 original size:27 final size:27
Alignment explanation
Indices: 40189520--40189697 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
40189510 ATATCGAGTC
* * * *
40189520 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
40189547 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40189574 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40189602 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40189629 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40189656 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40189683 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40189698 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40189659 original size:82 final size:81
Alignment explanation
Indices: 40189541--40189696 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
40189531 TGCTATATAA
*
40189541 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40189606 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40189623 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40189687 CACTTAGTGC
65 CACTTAGTGC
40189697 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40197600 original size:27 final size:27
Alignment explanation
Indices: 40197570--40197747 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
40197560 ATATCGAGTC
* * * *
40197570 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
40197597 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40197624 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40197652 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40197679 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40197706 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40197733 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40197748 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40197709 original size:82 final size:81
Alignment explanation
Indices: 40197591--40197746 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
40197581 TGCTATATAA
*
40197591 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40197656 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40197673 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40197737 CACTTAGTGC
65 CACTTAGTGC
40197747 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40228245 original size:44 final size:44
Alignment explanation
Indices: 40228197--40228286 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
40228187 GAGCAAGATA
* * * *
40228197 AAGCTACAAAACTTATATCCCTGAAATTGTAGTGGATCAGATTG
1 AAGCTACAAAACATATACCCCTGAAATTGCAGTGGATCAGAATG
** * *
40228241 AAGCTACAATTCATATACCCCTGAAGTTGCAGTGGGTCAGAATG
1 AAGCTACAAAACATATACCCCTGAAATTGCAGTGGATCAGAATG
40228285 AA
1 AA
40228287 ACTATGAGGG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (44 bp):
AAGCTACAAAACATATACCCCTGAAATTGCAGTGGATCAGAATG
Found at i:40228313 original size:94 final size:94
Alignment explanation
Indices: 40228203--40228743 Score: 541
Period size: 94 Copynumber: 5.8 Consensus size: 94
40228193 GATAAAGCTA
* * * * *
40228203 CAAAACTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCTACAATTCATATACCCCTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT
* **
40228268 TGCAGTGGGTCAGAATGAAACTATGAGGG
66 TGCAGTGGGTCAGAATGAAACTACGATAG
* ** * *
40228297 TAAATCTTATCTCCCTGATGTTGCAGTGGAGCAAGA-TGAAGCTACAAATCTTATACCCCTAAAG
1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGC-AGATTGAAGCTACAAATCTTATACCCCTGAAG
* ** *
40228361 TTACAGTGGGTTGGAATAAAACTACGATAG
65 TTGCAGTGGGTCAGAATGAAACTACGATAG
** * *
40228391 CAAATCTTATCTCCCT-AAAGTTGTAGTAAAGTAAGA-TGAAGCTACAAATCCTATACCCCTGAA
1 CAAATCTTATCTCCCTGAAA-TTGTAGTGGAG-CAGATTGAAGCTACAAATCTTATACCCCTGAA
* * * * *
40228454 GTTGTAGTGAGTCAGATTGAATCTACCATAG
64 GTTGCAGTGGGTCAGAATGAAACTACGATAG
* * *
40228485 CAAATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCCCCCTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT
* ** * * *
40228550 TGCAGTAGGTTGGATTGAATCTACTATAG
66 TGCAGTGGGTCAGAATGAAACTACGATAG
* ** **
40228579 CAAATCTTATCTCCCTGAAATTGTAGTAGAGCAGATTGAAATTACAAATCTTATACATCTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT
** **
40228644 TGCAGTGGGTCA-AATTGATTCTAATATAG
66 TGCAGTGGGTCAGAA-TGAAACTACGATAG
* * * * * * * * *
40228673 CAAACCTTATCTCCTTGAAGTTGCAATGGAGCAAATTAAACCTACAAATCTTATACCCTTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT
40228738 TGCAGT
66 TGCAGT
40228744 AGATTAGATG
Statistics
Matches: 366, Mismatches: 75, Indels: 12
0.81 0.17 0.03
Matches are distributed among these distances:
93 5 0.01
94 356 0.97
95 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (94 bp):
CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT
TGCAGTGGGTCAGAATGAAACTACGATAG
Found at i:40228368 original size:44 final size:43
Alignment explanation
Indices: 40228298--40228555 Score: 103
Period size: 44 Copynumber: 5.6 Consensus size: 43
40228288 CTATGAGGGT
* *
40228298 AAATCTTAT-CTCCCTGATGTTGCAGTGGAGCAAGATGAAGCTAC
1 AAATCTTATAC-CCCTAAAGTTGCAGTGGAGC-AGATGAAGCTAC
* ** * *
40228342 AAATCTTATACCCCTAAAGTTACAGTGG-GTTGGAATAAAACTACGATAGC
1 AAATCTTATACCCCTAAAGTTGCAGTGGAG-CAG-AT--GA--A-GCTA-C
* ** *
40228392 AAATCTTAT-CTCCCTAAAGTTGTAGTAAAGTAAGATGAAGCTAC
1 AAATCTTATAC-CCCTAAAGTTGCAGTGGAG-CAGATGAAGCTAC
* * * *
40228436 AAATCCTATACCCCTGAAGTTGTAGT-GAGTCAGATTGAATCTACCATAGC
1 AAATCTTATACCCCTAAAGTTGCAGTGGAG-CAGA-TG-A---AGC-TA-C
* * *
40228486 AAATCTTAT-CTCCTTGAAGTTGTAGTGGAGCAGATTGAAGCTAC
1 AAATCTTATAC-CCCTAAAGTTGCAGTGGAGCAGA-TGAAGCTAC
* *
40228530 AAATCTTATCCCCCTGAAGTTGCAGT
1 AAATCTTATACCCCTAAAGTTGCAGT
40228556 AGGTTGGATT
Statistics
Matches: 167, Mismatches: 25, Indels: 44
0.71 0.11 0.19
Matches are distributed among these distances:
43 8 0.05
44 73 0.44
45 9 0.05
46 4 0.02
48 4 0.02
49 8 0.05
50 55 0.33
51 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (43 bp):
AAATCTTATACCCCTAAAGTTGCAGTGGAGCAGATGAAGCTAC
Found at i:40228369 original size:138 final size:138
Alignment explanation
Indices: 40228116--40228369 Score: 341
Period size: 138 Copynumber: 1.8 Consensus size: 138
40228106 AAACAAATCC
* * * * * * *
40228116 TATACCCTTGAAGTTGCAGTGGGTCGGATTGAACCTACTATGGCGAATCTTATCTCCTTGAAGTT
1 TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACTAGGGCAAATCTTATCTCCCTGAAGTT
* * **
40228181 TCAGTGGAGCAAGATAAAGCTACAAAACTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCT
66 GCAGTGGAGCAAGATAAAGCTACAAAACTTATACCCCTGAAATTACAGTGGATCAGATTGAAGCT
40228246 ACAATTCA
131 ACAATTCA
* *
40228254 TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTA-TGAGGGTAAATCTTATCTCCCTGATGT
1 TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACT-AGGGCAAATCTTATCTCCCTGAAGT
* *
40228318 TGCAGTGGAGCAAGATGAAGCTACAAATCTTATACCCCT-AAAGTTACAGTGG
65 TGCAGTGGAGCAAGATAAAGCTACAAAACTTATACCCCTGAAA-TTACAGTGG
40228370 GTTGGAATAA
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
137 4 0.04
138 95 0.96
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (138 bp):
TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACTAGGGCAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAAGATAAAGCTACAAAACTTATACCCCTGAAATTACAGTGGATCAGATTGAAGCT
ACAATTCA
Found at i:40228492 original size:188 final size:189
Alignment explanation
Indices: 40228203--40228745 Score: 619
Period size: 188 Copynumber: 2.9 Consensus size: 189
40228193 GATAAAGCTA
* * ** ** *
40228203 CAAAACTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCTACAATTCATATACCCCTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTAAAGAAGATTGAAGCTACAAATCATATACCCCTGAAGT
* * ** ** * * *
40228268 TGCAGTGGGTCAGAATGAAACTATGAGGGTAAATCTTATCTCCCTGATGTTGCAGTGGAGCAAGA
66 TGCAGTGGGTCAGATTGAATCTAACATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGA
*
40228333 -TGAAGCTACAAATCTTATACCCCTAAAGTTACAGTGGGTTGGAATAAAACTACGATAG
131 TTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAGGTTGGAATAAAACTACGATAG
*
40228391 CAAATCTTATCTCCCT-AAAGTTGTAGTAAAGTAAGA-TGAAGCTACAAATCCTATACCCCTGAA
1 CAAATCTTATCTCCCTGAAA-TTGTAGTAAAG-AAGATTGAAGCTACAAATCATATACCCCTGAA
* * * *
40228454 GTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCTCCTTGAAGTTGTAGTGGAGC-A
64 GTTGCAGTGGGTCAGATTGAATCTAACATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAA
* * * * * * *
40228518 GATTGAAGCTACAAATCTTATCCCCCTGAAGTTGCAGTAGGTTGGATTGAATCTACTATAG
129 GATTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAGGTTGGAATAAAACTACGATAG
* * ** * **
40228579 CAAATCTTATCTCCCTGAAATTGTAGTAGAGCAGATTGAAATTACAAATCTTATACATCTGAAGT
1 CAAATCTTATCTCCCTGAAATTGTAGTAAAGAAGATTGAAGCTACAAATCATATACCCCTGAAGT
* * * * *
40228644 TGCAGTGGGTCAAATTGATTCTAATATAGCAAACCTTATCTCCTTGAAGTTGCAATGGAGCAA-A
66 TGCAGTGGGTCAGATTGAATCTAACATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGA
* * * * *
40228708 TTAAACCTACAAATCTTATACCCTTGAAGTTGCAGTAG
131 TTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAG
40228746 ATTAGATGCA
Statistics
Matches: 301, Mismatches: 48, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
187 9 0.03
188 285 0.95
189 7 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (189 bp):
CAAATCTTATCTCCCTGAAATTGTAGTAAAGAAGATTGAAGCTACAAATCATATACCCCTGAAGT
TGCAGTGGGTCAGATTGAATCTAACATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGA
TTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAGGTTGGAATAAAACTACGATAG
Found at i:40228510 original size:50 final size:50
Alignment explanation
Indices: 40228447--40228618 Score: 182
Period size: 50 Copynumber: 3.6 Consensus size: 50
40228437 AATCCTATAC
40228447 CCCTGAAGTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCT
1 CCCTGAAGTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCT
* * *
40228497 CCTTGAAGTTGTAGTGGAG-CAGATTG-A---AGC-TA-CAAATCTTATCC
1 CCCTGAAGTTGTAGT-GAGTCAGATTGAATCTACCATAGCAAATCTTATCT
* ** *
40228541 CCCTGAAGTTGCAGT-AGGTTGGATTGAATCTACTATAGCAAATCTTATCT
1 CCCTGAAGTTGTAGTGA-GTCAGATTGAATCTACCATAGCAAATCTTATCT
*
40228591 CCCTGAAATTGTAGTAGAG-CAGATTGAA
1 CCCTGAAGTTGTAGT-GAGTCAGATTGAA
40228619 ATTACAAATC
Statistics
Matches: 97, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 29 0.30
45 3 0.03
46 2 0.02
48 1 0.01
49 3 0.03
50 52 0.54
51 4 0.04
52 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (50 bp):
CCCTGAAGTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCT
Found at i:40228730 original size:282 final size:282
Alignment explanation
Indices: 40228203--40228739 Score: 605
Period size: 282 Copynumber: 1.9 Consensus size: 282
40228193 GATAAAGCTA
* *
40228203 CAAAACTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCTACAATTCATATACCCCTGAAGT
1 CAAAACTTATATCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCATATACCCCTGAAGT
* * * ** *
40228268 TGCAGTGGGTCAGAATGAAACTATGAGGGTAAATCTTATCTCCCTGATGTTGCAGTGGAGCAAGA
66 TGCAGTAGGTCAGAATGAAACTATGAGAGCAAATCTTATCTCCCTGAAATTGCAGTAGAGCAAGA
* * ** * *
40228333 TGAAGCTACAAATCTTATACCCCTAAAGTTACAGTGGGTTGGAATAAAACTACGATAGCAAATCT
131 TGAAACTACAAATCTTATACACCTAAAGTTACAGTGGGTTCAAATAAAACTAAGATAGCAAACCT
* * * * *
40228398 TATCTCCCTAAAGTTGTAGTAAAGTAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTG
196 TATCTCCCTAAAGTTGCAATAAAGCAAGATAAACCTACAAATCCTATACCCCTGAAGTTGTAGTG
40228463 AGTCAGATTGAATCTACCATAG
261 AGTCAGATTGAATCTACCATAG
* * * * * *
40228485 CAAATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCCCCCTGAAGT
1 CAAAACTTATATCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCATATACCCCTGAAGT
** * * * *
40228550 TGCAGTAGGTTGGATTGAATCTACT-ATAGCAAATCTTATCTCCCTGAAATTGTAGTAGAGC-AG
66 TGCAGTAGGTCAGAATGAAACTA-TGAGAGCAAATCTTATCTCCCTGAAATTGCAGTAGAGCAAG
* * * * * ** *
40228613 ATTGAAATTACAAATCTTATACATCTGAAGTTGCAGTGGG-TCAAATTGATTCTAATATAGCAAA
130 A-TGAAACTACAAATCTTATACACCTAAAGTTACAGTGGGTTCAAA-TAAAACTAAGATAGCAAA
* * ** * *
40228677 CCTTATCTCCTTGAAGTTGCAATGGAGCAA-ATTAAACCTACAAATCTTATACCCTTGAAGTTG
193 CCTTATCTCCCTAAAGTTGCAATAAAGCAAGA-TAAACCTACAAATCCTATACCCCTGAAGTTG
40228740 CAGTAGATTA
Statistics
Matches: 206, Mismatches: 45, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
281 7 0.03
282 198 0.96
283 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (282 bp):
CAAAACTTATATCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCATATACCCCTGAAGT
TGCAGTAGGTCAGAATGAAACTATGAGAGCAAATCTTATCTCCCTGAAATTGCAGTAGAGCAAGA
TGAAACTACAAATCTTATACACCTAAAGTTACAGTGGGTTCAAATAAAACTAAGATAGCAAACCT
TATCTCCCTAAAGTTGCAATAAAGCAAGATAAACCTACAAATCCTATACCCCTGAAGTTGTAGTG
AGTCAGATTGAATCTACCATAG
Found at i:40231205 original size:40 final size:40
Alignment explanation
Indices: 40231125--40231343 Score: 345
Period size: 40 Copynumber: 5.5 Consensus size: 40
40231115 TTCGGATGAC
*
40231125 ATCCGGGCTAAGTCCCGAAGGCA-TGGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
40231164 ATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
40231204 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
40231244 ATTCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
* *
40231284 ATCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTAT
*
40231324 ATCC-GGCTAAATCCCGAAGG
1 ATCCGGGCTAAGTCCCGAAGG
40231344 TACTTGGGTT
Statistics
Matches: 168, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
39 38 0.23
40 128 0.76
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
Found at i:40235725 original size:14 final size:14
Alignment explanation
Indices: 40235706--40235732 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40235696 AATTTTTATA
40235706 AAAAATTATTTTCT
1 AAAAATTATTTTCT
40235720 AAAAATTATTTTC
1 AAAAATTATTTTC
40235733 AATAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAAATTATTTTCT
Found at i:40235739 original size:15 final size:14
Alignment explanation
Indices: 40235705--40235739 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
40235695 CAATTTTTAT
40235705 AAAAAATTATTTTC
1 AAAAAATTATTTTC
*
40235719 TAAAAATTATTTTC
1 AAAAAATTATTTTC
40235733 AATAAAA
1 AA-AAAA
40235740 CAATCACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAAATTATTTTC
Found at i:40244854 original size:14 final size:14
Alignment explanation
Indices: 40244835--40244870 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
40244825 GCTTTGAATG
40244835 CCAAAATTTATGAA
1 CCAAAATTTATGAA
40244849 CCAAAATTTATGAA
1 CCAAAATTTATGAA
40244863 CCAAAATT
1 CCAAAATT
40244871 CAAACGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (14 bp):
CCAAAATTTATGAA
Found at i:40251931 original size:90 final size:93
Alignment explanation
Indices: 40251818--40251985 Score: 256
Period size: 90 Copynumber: 1.8 Consensus size: 93
40251808 GGATGGTTGA
* *
40251818 GCATCCGAACTCGTTGAGTTGAGT-CGAGTTCA-TTAT-GGATGCAAATG-TCCGAGCTCGTTGA
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCATTTATGGGATGC-AACGCT-CGAGCTCGTTGA
40251879 -TTGAGTCCGAGTTCGTGAGATGTAACTAG
64 GTTGAGTCCGAGTTCGTGAGATGTAACTAG
*
40251908 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCATTTATGGGATGCGACGCTCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCATTTATGGGATGCAACGCTCGAGCTCGTTGAGT
40251973 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40251986 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
90 23 0.33
91 8 0.11
92 18 0.26
93 21 0.30
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCATTTATGGGATGCAACGCTCGAGCTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40252541 original size:28 final size:27
Alignment explanation
Indices: 40252497--40252549 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
40252487 TGTGTAAATA
40252497 ATTTTATGATATGACCATGTTTGGTTG
1 ATTTTATGATATGACCATGTTTGGTTG
40252524 ATTTTATGAATATGACCATGTTTGGT
1 ATTTTATG-ATATGACCATGTTTGGT
40252550 GAGAAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.47
Consensus pattern (27 bp):
ATTTTATGATATGACCATGTTTGGTTG
Found at i:40279107 original size:46 final size:47
Alignment explanation
Indices: 40278938--40279153 Score: 164
Period size: 46 Copynumber: 4.6 Consensus size: 47
40278928 TATGAGAGCA
** * *
40278938 AGTGTAAGACCATGTCTGGGACATGGCATC-GAAATTGAGACG-AGTGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-CGAGATGTAGT-C
* *
40278985 TAGTGTAAGA-CATGTCTGGGACAT-GCATTGGCCT-CGAGATGTAAGCC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGG-CTACGAGATGT-AGTC
* * *
40279032 AGTATAAGA-TATATCTGGGA-AT-GCATCGGCTACGAGATGT-GTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACGAGATGTAGTC
* * **
40279075 AGTGTAAGACCCTGTCTGGGACATGGCATCGGC-ACAGATATGCTAGAG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTAC-GAGATG-TAGTC
40279123 ATTGTGTAAGACCATGTCTGGGACATGGCAT
1 A--GTGTAAGACCATGTCTGGGACATGGCAT
40279154 TGGCACCTGC
Statistics
Matches: 136, Mismatches: 19, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
43 10 0.07
44 10 0.07
45 20 0.15
46 39 0.29
47 17 0.12
48 13 0.10
50 27 0.20
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACGAGATGTAGTC
Found at i:40283493 original size:53 final size:53
Alignment explanation
Indices: 40283389--40283493 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
40283379 TTCCTTTTTA
* * ** *
40283389 AACTTACCATTGCCATGTCTTGACATGGTCTTATGTGGTATCCTTGCCTTATG
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * *
40283442 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGTCTTAT
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTAT
40283494 AGTAGTTTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (53 bp):
AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:40283527 original size:55 final size:53
Alignment explanation
Indices: 40283389--40283527 Score: 134
Period size: 53 Copynumber: 2.6 Consensus size: 53
40283379 TTCCTTTTTA
* * ** *
40283389 AACTTACCATTGCCATGTCTTGACATGGTCTTATGTGGTATCCTTGCCTTATG
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * * * *
40283442 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGTCTTATAG
1 AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTAT-G
** * *
40283496 TAGTTTATCAATGCCATGTCTTGACATGGTCT
1 -AACTCACCAATGCCATGTCTTGACATGGTCT
40283528 GTAATATCCT
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
53 44 0.64
54 1 0.01
55 24 0.35
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.38
Consensus pattern (53 bp):
AACTCACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:40284780 original size:26 final size:26
Alignment explanation
Indices: 40284747--40284801 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
40284737 CAAAGATGTG
40284747 GATATCCCGTTTGAACCTTAGGAATA
1 GATATCCCGTTTGAACCTTAGGAATA
40284773 GATATCCCGTTTGAACCTTAGGAATA
1 GATATCCCGTTTGAACCTTAGGAATA
40284799 GAT
1 GAT
40284802 TAGGATACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (26 bp):
GATATCCCGTTTGAACCTTAGGAATA
Found at i:40287923 original size:15 final size:15
Alignment explanation
Indices: 40287884--40287963 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
40287874 ATATCTTGGG
* *
40287884 TTTCTTTATCCTAGA
1 TTTCTTTATTCTGGA
*
40287899 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
40287914 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
40287929 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
40287944 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
40287958 TTTCTT
1 TTTCTT
40287964 GTTATCTTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
14 10 0.19
15 42 0.78
16 2 0.04
ACGTcount: A:0.11, C:0.17, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:40287944 original size:30 final size:30
Alignment explanation
Indices: 40287875--40287962 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
40287865 CATAGTATCA
* * * * *
40287875 TATCTTGGGTTTCTTTATCCTAGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
40287905 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
40287935 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
40287963 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
29 8 0.16
30 40 0.82
31 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:40296258 original size:47 final size:47
Alignment explanation
Indices: 40296207--40296452 Score: 325
Period size: 47 Copynumber: 5.1 Consensus size: 47
40296197 TTAGGATTTT
* * *
40296207 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCTGAGTGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
40296254 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
40296301 ATGTGATGAATGTGAGCATGCATATATGTGATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGC----A--T-ATATGTGATAAGGCCGAATGGCCA
*
40296355 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
40296402 ATGTGGTGAATATGAACATGC--ATATGTGGTAAAGCCGAATGGTCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
40296447 ATGTGA
1 ATGTGA
40296453 AATATATATA
Statistics
Matches: 180, Mismatches: 12, Indels: 16
0.87 0.06 0.08
Matches are distributed among these distances:
45 25 0.14
47 106 0.59
48 1 0.01
50 1 0.01
51 1 0.01
53 1 0.01
54 45 0.25
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:40296282 original size:25 final size:25
Alignment explanation
Indices: 40296206--40296332 Score: 94
Period size: 25 Copynumber: 5.3 Consensus size: 25
40296196 TTTAGGATTT
*
40296206 TATGTGATGAATGTGAACATGCATA
1 TATGTGATGAATGTGAGCATGCATA
* *
40296231 TATGTGAT-AAGGCTGAG--TGGC-CA
1 TATGTGATGAATG-TGAGCAT-GCATA
40296254 -ATGTGATGAATGTGAGCATGCATA
1 TATGTGATGAATGTGAGCATGCATA
* * *
40296278 TATGTGAT-AA-G-GCCGAATGGC-CA
1 TATGTGATGAATGTG-AGCAT-GCATA
40296301 -ATGTGATGAATGTGAGCATGCATA
1 TATGTGATGAATGTGAGCATGCATA
40296325 TATGTGAT
1 TATGTGAT
40296333 ATGTGATAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 28
0.66 0.09 0.24
Matches are distributed among these distances:
22 19 0.25
23 16 0.21
24 16 0.21
25 26 0.34
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.29
Consensus pattern (25 bp):
TATGTGATGAATGTGAGCATGCATA
Found at i:40296361 original size:101 final size:101
Alignment explanation
Indices: 40296230--40296426 Score: 340
Period size: 101 Copynumber: 2.0 Consensus size: 101
40296220 GAACATGCAT
* *
40296230 ATATGTGATAAGGCTGAGTGGCCAATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAA
1 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAA
* *
40296295 TGGCCAATGTGATGAATGTGAGCATGCATATATGTG
66 TGGCCAATGTGATGAATATGAACATGCATATATGTG
*
40296331 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAA
1 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAA
*
40296396 TGGCCAATGTGGTGAATATGAACATGCATAT
66 TGGCCAATGTGATGAATATGAACATGCATAT
40296427 GTGGTAAAGC
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 90 1.00
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.27
Consensus pattern (101 bp):
ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAA
TGGCCAATGTGATGAATATGAACATGCATATATGTG
Found at i:40296410 original size:25 final size:25
Alignment explanation
Indices: 40296335--40296410 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
40296325 TATGTGATAT
40296335 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
40296360 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
40296382 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
40296407 GTGA
1 GTGA
40296411 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:40296484 original size:50 final size:50
Alignment explanation
Indices: 40296411--40296557 Score: 244
Period size: 50 Copynumber: 3.0 Consensus size: 50
40296401 AATGTGGTGA
*
40296411 ATATGA-ACATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
40296460 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
* *
40296510 ATATGAGATATGTATATGTGGTAAAGCCGAATGG-CTAGTGTGAAATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTC-AATGTGAAATAT
40296558 GTAGGCGATG
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
49 7 0.08
50 86 0.92
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.30
Consensus pattern (50 bp):
ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
Done.