Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 140 of 343
Found at i:46622606 original size:6 final size:6
Alignment explanation
Indices: 46622590--46622639 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
46622580 TTTCTTTTTA
*
46622590 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
46622639 T
1 T
46622640 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:46622622 original size:37 final size:37
Alignment explanation
Indices: 46622579--46622649 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
46622569 CTTGCCTCTC
46622579 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
46622616 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
46622650 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:46622650 original size:16 final size:16
Alignment explanation
Indices: 46622575--46622635 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
46622565 GCCTCTTGCC
*
46622575 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
46622591 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
46622607 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
46622623 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
46622636 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:46623570 original size:11 final size:11
Alignment explanation
Indices: 46623554--46623595 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
46623544 TATACTTCGA
46623554 TTTTTTTTAAT
1 TTTTTTTTAAT
**
46623565 TTTTTTTCGAT
1 TTTTTTTTAAT
46623576 TTTTTTTTAAAT
1 TTTTTTTT-AAT
46623588 TTTTTTTT
1 TTTTTTTT
46623596 CGAATTTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:46623571 original size:12 final size:12
Alignment explanation
Indices: 46623554--46623595 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
46623544 TATACTTCGA
46623554 TTTTTTTT-AA-
1 TTTTTTTTAAAT
**
46623564 TTTTTTTTCGAT
1 TTTTTTTTAAAT
46623576 TTTTTTTTAAAT
1 TTTTTTTTAAAT
46623588 TTTTTTTT
1 TTTTTTTT
46623596 CGAATTTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 8 0.30
11 1 0.04
12 18 0.67
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTTTTAAAT
Found at i:46623573 original size:21 final size:23
Alignment explanation
Indices: 46623549--46623594 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
46623539 TTTTATATAC
46623549 TTCGA-TTTTTTTT-AATTTTTT
1 TTCGATTTTTTTTTAAATTTTTT
46623570 TTCGATTTTTTTTTAAATTTTTT
1 TTCGATTTTTTTTTAAATTTTTT
46623593 TT
1 TT
46623595 TCGAATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 5 0.22
22 8 0.35
23 10 0.43
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.76
Consensus pattern (23 bp):
TTCGATTTTTTTTTAAATTTTTT
Found at i:46623601 original size:13 final size:13
Alignment explanation
Indices: 46623564--46623602 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
46623554 TTTTTTTTAA
46623564 TTTTTTTTCG-AT
1 TTTTTTTTCGAAT
*
46623576 TTTTTTTT-AAAT
1 TTTTTTTTCGAAT
46623588 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
46623601 TT
1 TT
46623603 CTCTTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:46625321 original size:30 final size:30
Alignment explanation
Indices: 46625287--46625383 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
46625277 AAAACTAAAA
46625287 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
46625317 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
46625347 TGAGCTAAGCTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
46625376 ATGAGCTA
1 -TGAGCTA
46625384 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 4 0.08
30 45 0.87
31 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:46628660 original size:20 final size:20
Alignment explanation
Indices: 46628637--46628683 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46628627 GGGTTAAGAT
*
46628637 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
46628657 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
46628677 TGAGCTG
1 TGAGCTG
46628684 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:46630444 original size:48 final size:46
Alignment explanation
Indices: 46630349--46630453 Score: 140
Period size: 48 Copynumber: 2.2 Consensus size: 46
46630339 TTGTCTTTTC
*
46630349 TTTCTTTTTCAATTTTCTCTTTTTCCTCACACTTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTTCTCTTTTT-CTCACACCTTTTTCAATCTCAA
* *
46630396 TTTCTTTTTCGATTTCTTTCTCTTTT-TCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTT-TCTCT-TTTTCTCACA-CCTTTTTCAATCTCAA
46630444 TTTCTTTTTC
1 TTTCTTTTTC
46630454 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
47 19 0.37
48 29 0.56
49 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.01, T:0.60
Consensus pattern (46 bp):
TTTCTTTTTCAATTTTCTCTTTTTCTCACACCTTTTTCAATCTCAA
Found at i:46630546 original size:21 final size:21
Alignment explanation
Indices: 46630517--46630572 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
46630507 CAAGCTCTCT
*
46630517 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
46630538 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
46630559 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
46630573 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:46630552 original size:13 final size:12
Alignment explanation
Indices: 46630536--46630655 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
46630526 TTTTTTCGCT
46630536 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
46630549 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
46630563 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
46630574 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
46630588 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
46630598 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
* *
46630611 TTTTCTTCTTCG
1 TTTTCTTTTTCA
*
46630623 TTTTCTTTTT-G
1 TTTTCTTTTTCA
46630634 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
46630644 ATTTCTTTTTCA
1 TTTTCTTTTTCA
46630656 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 10 0.12
12 42 0.51
13 12 0.14
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:46630565 original size:14 final size:14
Alignment explanation
Indices: 46630516--46630572 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
46630506 TCAAGCTCTC
46630516 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
46630529 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
46630543 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
46630557 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
46630571 TT
1 TT
46630573 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:46630600 original size:18 final size:18
Alignment explanation
Indices: 46630579--46630637 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
46630569 TTTTCTCTCA
46630579 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
46630597 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
46630615 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
46630633 GTTTT
1 CTTTT
46630638 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:46630654 original size:6 final size:6
Alignment explanation
Indices: 46630534--46630641 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
46630524 TCTTTTTTCG
* * * **
46630534 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
46630585 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
46630633 -GTTTT CTTT
1 CTTTTT CTTT
46630642 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:46631736 original size:30 final size:28
Alignment explanation
Indices: 46631678--46631741 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
46631668 TTAAACTTGA
*
46631678 TTTTTTTTTGCTCACCTTTTTTTTCTTTT
1 TTTTTTTTTGCTCA-CTTTTTTTACTTTT
46631707 CTTTTTTTTTGCTCGA-TTTTTTTCACTTTT
1 -TTTTTTTTTGCTC-ACTTTTTTT-ACTTTT
46631737 TTTTT
1 TTTTT
46631742 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 12 0.39
30 18 0.58
31 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTTTTTTTGCTCACTTTTTTTACTTTT
Found at i:46631738 original size:12 final size:12
Alignment explanation
Indices: 46631723--46631792 Score: 61
Period size: 12 Copynumber: 5.5 Consensus size: 12
46631713 TTTTGCTCGA
*
46631723 TTTTTTTCACTT
1 TTTTTTTCAATT
*
46631735 TTTTTTTGAATT
1 TTTTTTTCAATT
46631747 TTTTTTTCAATTAATT
1 TTTTTTTC----AATT
46631763 TTTTTTTCGAATT
1 TTTTTTTC-AATT
*
46631776 TTTTTTT-GATT
1 TTTTTTTCAATT
46631787 TTTTTT
1 TTTTTT
46631793 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
11 9 0.18
12 17 0.35
13 11 0.22
16 12 0.24
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:46631762 original size:16 final size:17
Alignment explanation
Indices: 46631743--46631775 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
46631733 TTTTTTTTTG
46631743 AATTTTTTTTTC-AATT
1 AATTTTTTTTTCGAATT
46631759 AATTTTTTTTTCGAATT
1 AATTTTTTTTTCGAATT
46631776 TTTTTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (17 bp):
AATTTTTTTTTCGAATT
Found at i:46633290 original size:20 final size:20
Alignment explanation
Indices: 46633267--46633313 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
46633257 GGGTTAAGAT
*
46633267 TGAGCTGAATTGAGCTTAAG
1 TGAGCTGAATTGAGCTCAAG
* * *
46633287 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCAAG
46633307 TGAGCTG
1 TGAGCTG
46633314 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):
TGAGCTGAATTGAGCTCAAG
Found at i:46634941 original size:19 final size:20
Alignment explanation
Indices: 46634919--46634988 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
46634909 AACTATTCAT
46634919 ATAATTATAATTTA-AAATA
1 ATAATTATAATTTAGAAATA
* * **
46634938 ATAACTAAATAATTTATAAGCA
1 ATAA-T-TATAATTTAGAAATA
*
46634960 ATAATTA-AATTTAGATATA
1 ATAATTATAATTTAGAAATA
46634979 ATAATTATAA
1 ATAATTATAA
46634989 GTCAACTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 19 0.49
20 4 0.10
21 9 0.23
22 7 0.18
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
ATAATTATAATTTAGAAATA
Found at i:46635168 original size:10 final size:10
Alignment explanation
Indices: 46635155--46635189 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
46635145 AAGCTCGGTT
46635155 GAGCTCAAAC
1 GAGCTCAAAC
*
46635165 GAGCTGAAAC
1 GAGCTCAAAC
*
46635175 GAGCTCAAAT
1 GAGCTCAAAC
46635185 GAGCT
1 GAGCT
46635190 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:46635198 original size:20 final size:20
Alignment explanation
Indices: 46635152--46635199 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
46635142 AGTAAGCTCG
46635152 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
46635172 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
46635192 GTTGAGCT
1 GTTGAGCT
46635200 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:46635636 original size:30 final size:30
Alignment explanation
Indices: 46635541--46635637 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
46635531 AGCTCACTCC
* *
46635541 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
46635571 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
* *
46635601 CAGCTCAACTTTAGCTCATGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
46635631 TAGCTCA
1 TAGCTCA
46635638 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:46636521 original size:22 final size:20
Alignment explanation
Indices: 46636489--46636537 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
46636479 GCCGAATTTA
46636489 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
46636512 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
46636532 TGAACA
1 TGAACA
46636538 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:46638536 original size:18 final size:18
Alignment explanation
Indices: 46638515--46638564 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
46638505 AAACTCTCTT
*
46638515 TCATTCTCTTTTTCAATC
1 TCATTATCTTTTTCAATC
* *
46638533 TCATTTTCTTTTTCACTC
1 TCATTATCTTTTTCAATC
*
46638551 TCAATATCTTTTTC
1 TCATTATCTTTTTC
46638565 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTATCTTTTTCAATC
Found at i:46638621 original size:21 final size:21
Alignment explanation
Indices: 46638597--46638663 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
46638587 CTTTTCTCGA
*
46638597 TTTCATTCAAGATTCTCTCAT
1 TTTCATTCAAAATTCTCTCAT
* ***** *
46638618 TTTCTTTGTTTCTTCTCTCAA
1 TTTCATTCAAAATTCTCTCAT
*
46638639 TTTCATTCAAAATCCTCTCAT
1 TTTCATTCAAAATTCTCTCAT
46638660 TTTC
1 TTTC
46638664 TCTCATAATC
Statistics
Matches: 31, Mismatches: 15, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.03, T:0.52
Consensus pattern (21 bp):
TTTCATTCAAAATTCTCTCAT
Found at i:46638623 original size:42 final size:42
Alignment explanation
Indices: 46638568--46638664 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
46638558 CTTTTTCTTT
* * * *
46638568 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCAATTTCATTCAAAA
46638609 TTCTCTCATTTTCTTTGTTTCTTCTCTCAATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCAATTTCATTCAAAA
*
46638651 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
46638665 CTCATAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.15, C:0.24, G:0.04, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCAATTTCATTCAAAA
Found at i:46640844 original size:19 final size:19
Alignment explanation
Indices: 46640822--46640891 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
46640812 AACTATTCAT
46640822 ATAATTATAATTTAAAATA
1 ATAATTATAATTTAAAATA
* *
46640841 ATAAATAAATAATTTAAAAGCA
1 AT-AAT-TATAATTTAAAA-TA
*
46640863 ATAATTA-AATTTAGATATA
1 ATAATTATAATTTA-AAATA
46640882 ATAATTATAA
1 ATAATTATAA
46640892 GTCAACTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 16 0.39
20 8 0.20
21 14 0.34
22 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (19 bp):
ATAATTATAATTTAAAATA
Found at i:46640871 original size:22 final size:21
Alignment explanation
Indices: 46640828--46640872 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
46640818 TCATATAATT
*
46640828 ATAATTTAAAATAATAAATAA
1 ATAATTTAAAACAATAAATAA
*
46640849 ATAATTTAAAAGCAATAATTAA
1 ATAATTTAAAA-CAATAAATAA
46640871 AT
1 AT
46640873 TTAGATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAATTTAAAACAATAAATAA
Found at i:46641131 original size:20 final size:20
Alignment explanation
Indices: 46641084--46641132 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
46641074 AAACAAGCTC
46641084 AAATGAGCTGAGTTGAGCTGG
1 AAATGAGCTGAG-TGAGCTGG
*
46641105 ACA-GAGCTCGAG-GAGCTGG
1 AAATGAGCT-GAGTGAGCTGG
46641124 AAATGAGCT
1 AAATGAGCT
46641133 AGGATCAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.31, C:0.14, G:0.37, T:0.18
Consensus pattern (20 bp):
AAATGAGCTGAGTGAGCTGG
Found at i:46651667 original size:23 final size:24
Alignment explanation
Indices: 46651623--46651665 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
46651613 CATTTTCTCT
46651623 TCTTTCTTCAATTTCTCTTTTTGC
1 TCTTTCTTCAATTTCTCTTTTTGC
46651647 TCTTT-TTC-A-TTCTCTTTTT
1 TCTTTCTTCAATTTCTCTTTTT
46651666 TTTTTTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 3 0.16
24 5 0.26
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.67
Consensus pattern (24 bp):
TCTTTCTTCAATTTCTCTTTTTGC
Found at i:46657423 original size:4 final size:4
Alignment explanation
Indices: 46657414--46657441 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
46657404 AAGTTTTATT
46657414 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
46657442 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:46658386 original size:10 final size:10
Alignment explanation
Indices: 46658373--46658416 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
46658363 AGCTCAACTC
46658373 AGCTCATTTG
1 AGCTCATTTG
*
46658383 AGCTCATTTC
1 AGCTCATTTG
*
46658393 AGCTCGTTTG
1 AGCTCATTTG
*
46658403 AGCTCAATTG
1 AGCTCATTTG
46658413 AGCT
1 AGCT
46658417 TACTTTCAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (10 bp):
AGCTCATTTG
Found at i:46658416 original size:20 final size:20
Alignment explanation
Indices: 46658363--46658416 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
46658353 ACTCATTTCC
*
46658363 AGCTCAACTCAGCTCATTTG
1 AGCTCAATTCAGCTCATTTG
* *
46658383 AGCTCATTTCAGCTCGTTTG
1 AGCTCAATTCAGCTCATTTG
*
46658403 AGCTCAATTGAGCT
1 AGCTCAATTCAGCT
46658417 TACTTTCAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAATTCAGCTCATTTG
Found at i:46660743 original size:14 final size:14
Alignment explanation
Indices: 46660721--46660765 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
46660711 TTAAAGAAGC
46660721 AACTCATTAAATTA
1 AACTCATTAAATTA
*
46660735 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
46660748 AACTCATTTAATTA
1 AACTCATTAAATTA
46660762 AACT
1 AACT
46660766 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:46662569 original size:10 final size:10
Alignment explanation
Indices: 46662554--46662614 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
46662544 TTTGAACCGT
*
46662554 TACCAATTCG
1 TACCAATTCA
*
46662564 TACCAAATACCA
1 TACC-AAT-TCA
*
46662576 TACCATTTCA
1 TACCAATTCA
46662586 TACCAATTCCA
1 TACCAATT-CA
* *
46662597 TACCATTTCG
1 TACCAATTCA
46662607 TACCAATT
1 TACCAATT
46662615 TCCAAATACC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
10 21 0.52
11 14 0.35
12 5 0.12
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:46662599 original size:21 final size:21
Alignment explanation
Indices: 46662554--46662614 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
46662544 TTTGAACCGT
* *
46662554 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
46662576 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
46662597 TACCATTTCGTACCAATT
1 TACCATTTCGTACCAATT
46662615 TCCAAATACC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 23 0.66
22 12 0.34
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:46662615 original size:11 final size:11
Alignment explanation
Indices: 46662574--46662616 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
46662564 TACCAAATAC
46662574 CATACC-ATTT
1 CATACCAATTT
*
46662584 CATACCAATTC
1 CATACCAATTT
46662595 CATACC-ATTT
1 CATACCAATTT
*
46662605 CGTACCAATTT
1 CATACCAATTT
46662616 C
1 C
46662617 CAAATACCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 14 0.50
11 14 0.50
ACGTcount: A:0.30, C:0.33, G:0.02, T:0.35
Consensus pattern (11 bp):
CATACCAATTT
Found at i:46668581 original size:28 final size:28
Alignment explanation
Indices: 46668520--46668671 Score: 252
Period size: 28 Copynumber: 5.5 Consensus size: 28
46668510 ATTAAGTCCA
* *
46668520 CACACTCAGTGCTATATAATC-AACTCG
1 CACACTTAGTGCTACATAATCAAACTCG
*
46668547 CACACTTAGTGCTATATAATCAAACTCG
1 CACACTTAGTGCTACATAATCAAACTCG
*
46668575 CACACTTAGTGCTACATAATCAAGCTCG
1 CACACTTAGTGCTACATAATCAAACTCG
46668603 CACACTTAGTGCTACATAATCAAACTCG
1 CACACTTAGTGCTACATAATCAAACTCG
46668631 CACACTTAGTGCTACATAATCAAACTCG
1 CACACTTAGTGCTACATAATCAAACTCG
*
46668659 TACACTTAGTGCT
1 CACACTTAGTGCT
46668672 GTACAATTTA
Statistics
Matches: 119, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 20 0.17
28 99 0.83
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CACACTTAGTGCTACATAATCAAACTCG
Found at i:46668610 original size:56 final size:55
Alignment explanation
Indices: 46668520--46668701 Score: 256
Period size: 56 Copynumber: 3.3 Consensus size: 55
46668510 ATTAAGTCCA
* *
46668520 CACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTATATAATCAAACTCG
1 CACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTATATAATCAAACTCG
*
46668575 CACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCTACATAATCAAACTCG
1 CACACTTAGTGCTACATAATCAA-CTCGCACACTTAGTGCTATATAATCAAACTCG
* * * * *
46668631 CACACTTAGTGCTACATAATCAAACTCGTACACTTAGTGCTGTACAATTTAAACCCG
1 CACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTATATAA-TCAAACTCG
*
46668688 CACACTTAGCGCTA
1 CACACTTAGTGCTA
46668702 AAATTTGAAA
Statistics
Matches: 114, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
55 21 0.18
56 71 0.62
57 22 0.19
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (55 bp):
CACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTATATAATCAAACTCG
Found at i:46671096 original size:16 final size:16
Alignment explanation
Indices: 46671075--46671106 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46671065 CATTCTACAT
46671075 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
46671091 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
46671107 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:46672555 original size:30 final size:30
Alignment explanation
Indices: 46672521--46672617 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
46672511 TAAACTAAAA
46672521 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
46672551 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
46672581 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
46672611 TGAGCTA
1 TGAGCTA
46672618 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:46675296 original size:14 final size:14
Alignment explanation
Indices: 46675274--46675318 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
46675264 TTAAAGAAGC
46675274 AACTCATTAAATTA
1 AACTCATTAAATTA
*
46675288 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
46675301 AACTCATTTAATTA
1 AACTCATTAAATTA
46675315 AACT
1 AACT
46675319 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:46677505 original size:12 final size:12
Alignment explanation
Indices: 46677488--46677543 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
46677478 CTCTCTCAAA
46677488 CTCTTTTTCATT
1 CTCTTTTTCATT
46677500 CTCTTTTTCAATT
1 CTCTTTTTC-ATT
*
46677513 -TCTTTTTCAAT
1 CTCTTTTTCATT
* *
46677524 CTCATTTTCACT
1 CTCTTTTTCATT
46677536 CTCTTTTT
1 CTCTTTTT
46677544 TTCTTTCTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 2 0.05
12 33 0.87
13 3 0.08
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (12 bp):
CTCTTTTTCATT
Found at i:46677516 original size:24 final size:24
Alignment explanation
Indices: 46677483--46677543 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
46677473 TTTTTCTCTC
* * *
46677483 TCAAACTCTTTTTCATTCTCTTTT
1 TCAATCTCTTTTTCAATCTCATTT
*
46677507 TCAATTTCTTTTTCAATCTCATTT
1 TCAATCTCTTTTTCAATCTCATTT
*
46677531 TCACTCTCTTTTT
1 TCAATCTCTTTTT
46677544 TTCTTTCTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.59
Consensus pattern (24 bp):
TCAATCTCTTTTTCAATCTCATTT
Found at i:46678174 original size:20 final size:20
Alignment explanation
Indices: 46678122--46678178 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
46678112 GCTCGCCCAA
* *
46678122 CTCACAACCAGCTCAGCAAG
1 CTCACATCCAGCTCAACAAG
** *
46678142 CTCAGTTCTAGCTCAACAAG
1 CTCACATCCAGCTCAACAAG
*
46678162 TTCACATCCAGCTCAAC
1 CTCACATCCAGCTCAAC
46678179 TCCAGCTTAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.37, G:0.12, T:0.19
Consensus pattern (20 bp):
CTCACATCCAGCTCAACAAG
Found at i:46680321 original size:46 final size:46
Alignment explanation
Indices: 46680217--46680431 Score: 168
Period size: 46 Copynumber: 4.7 Consensus size: 46
46680207 AGATTTGTGT
* * ** * *
46680217 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTACAGATGAGA
* *
46680265 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCC-ACAGTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTACAG-ATGAGA
* * ** **
46680311 GCCAGTGTAAGACATGTTTGGGACATGCATCGGCCTTGAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTACAGATGAGA
* * * * *
46680357 GCCAGTGTTAGACATGTCTGGGACATGCGT-TGGCTACGAGAT-A-T
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTAC-AGATGAGA
* * *
46680401 GCTAATGTAAGACATGTTTGGGACATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
46680432 GACACGGTTA
Statistics
Matches: 133, Mismatches: 30, Indels: 11
0.76 0.17 0.06
Matches are distributed among these distances:
44 25 0.19
45 5 0.04
46 77 0.58
47 15 0.11
48 11 0.08
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTACAGATGAGA
Found at i:46680351 original size:92 final size:90
Alignment explanation
Indices: 46680217--46680432 Score: 236
Period size: 92 Copynumber: 2.4 Consensus size: 90
46680207 AGATTTGTGT
* * *
46680217 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGT
1 GCCAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCATTGAGACGAGAGCCAGTGTAAGACATGT
46680282 CTAGGACATGCATCAGCCAC-AGTATGAGA
64 CTAGGACATGCATCAGCCACGAG-AT-A-A
* * ** *
46680311 GCCAGTGTAAGACATGTTTGGGACATGCATCGGCCTTGAGATGTTAGCCAGTGTTAGACATGTCT
1 GCCAGTGTAAGACATGTTTGGGACATGCATCGGCATTGAGACGAGAGCCAGTGTAAGACATGTCT
* * ** * *
46680376 GGGACATGCGTTGGCTACGAGATAT
66 AGGACATGCATCAGCCACGAGATAA
* *
46680401 GCTAATGTAAGACATGTTTGGGACATGCATCG
1 GCCAGTGTAAGACATGTTTGGGACATGCATCG
46680433 ACACGGTTAC
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
90 30 0.29
91 1 0.01
92 47 0.45
93 15 0.14
94 12 0.11
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (90 bp):
GCCAGTGTAAGACATGTTTGGGACATGCATCGGCATTGAGACGAGAGCCAGTGTAAGACATGTCT
AGGACATGCATCAGCCACGAGATAA
Found at i:46684708 original size:21 final size:22
Alignment explanation
Indices: 46684669--46684712 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
46684659 ATGCATACTC
46684669 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
46684691 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
46684712 C
1 C
46684713 GAGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:46692715 original size:9 final size:9
Alignment explanation
Indices: 46692701--46692727 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
46692691 AGAAAGTGAA
46692701 TCTTGATTT
1 TCTTGATTT
46692710 TCTTGATTT
1 TCTTGATTT
46692719 TCTTGATTT
1 TCTTGATTT
46692728 GAGCCCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (9 bp):
TCTTGATTT
Found at i:46692996 original size:21 final size:22
Alignment explanation
Indices: 46692957--46693000 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
46692947 ATGCATACTC
46692957 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
46692979 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
46693000 C
1 C
46693001 GAGCTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:46696526 original size:21 final size:20
Alignment explanation
Indices: 46696496--46696548 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
46696486 AAAAAGAGTT
*
46696496 TGAAAGAAAGCAAAAA-GAAAG
1 TGAAA-AAAG-AAAAACGAAAC
46696517 TGAGAAAAAGAAAAACGAAAC
1 TGA-AAAAAGAAAAACGAAAC
46696538 TG-AAAAAGAAA
1 TGAAAAAAGAAA
46696549 GTGAAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 9 0.31
20 5 0.17
21 13 0.45
22 2 0.07
ACGTcount: A:0.68, C:0.06, G:0.21, T:0.06
Consensus pattern (20 bp):
TGAAAAAAGAAAAACGAAAC
Found at i:46696530 original size:6 final size:6
Alignment explanation
Indices: 46696519--46696582 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
46696509 AAAGAAAGTG
* * * * *
46696519 AGAAAA AGAAAA ACGAAAC TGAAAA AGAAAG TGAAAA AGAAAA AGAGAA
1 AGAAAA AGAAAA A-GAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
*
46696568 GGAAAA AGAAAA AGA
1 AGAAAA AGAAAA AGA
46696583 GATCGAGAGT
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
6 41 0.91
7 4 0.09
ACGTcount: A:0.72, C:0.03, G:0.22, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:46696554 original size:18 final size:18
Alignment explanation
Indices: 46696539--46696584 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
46696529 AAACGAAACT
46696539 GAAAAAGA-AAGTGAAAAA
1 GAAAAAGAGAAG-GAAAAA
46696557 GAAAAAGAGAAGGAAAAA
1 GAAAAAGAGAAGGAAAAA
46696575 GAAAAAGAGA
1 GAAAAAGAGA
46696585 TCGAGAGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (18 bp):
GAAAAAGAGAAGGAAAAA
Found at i:46698412 original size:21 final size:20
Alignment explanation
Indices: 46698373--46698412 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
46698363 ATCAGCTCAC
* *
46698373 TTGAGCTTGATTCAGCTCGT
1 TTGAGCTAGATTCAACTCGT
46698393 TTGAGCTAGAATTCAACTCG
1 TTGAGCTAG-ATTCAACTCG
46698413 ATCTAGCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
TTGAGCTAGATTCAACTCGT
Found at i:46701413 original size:30 final size:30
Alignment explanation
Indices: 46701379--46701475 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
46701369 TAAACTAAAA
*
46701379 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * * *
46701409 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* *
46701439 TGAGCTAAGGTTTAGCTCGTAAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAGCT-AAAGT
46701469 TGAGCTA
1 TGAGCTA
46701476 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:46702409 original size:15 final size:15
Alignment explanation
Indices: 46702389--46702436 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
46702379 TCAAAGATGG
46702389 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
46702404 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
46702419 -TTTATGGATATAAA
1 GTTTATGGATATGAA
46702433 GTTT
1 GTTT
46702437 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:46702416 original size:29 final size:29
Alignment explanation
Indices: 46702383--46702442 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
46702373 AAGGATTCAA
* *
46702383 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
46702412 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
46702441 AG
1 AG
46702443 GTTTGGTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:46703450 original size:14 final size:14
Alignment explanation
Indices: 46703428--46703472 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
46703418 TTAAAGAAGC
46703428 AACTCATTAAATTA
1 AACTCATTAAATTA
*
46703442 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
46703455 AACTCATTTAATTA
1 AACTCATTAAATTA
46703469 AACT
1 AACT
46703473 AAGATGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:46703947 original size:14 final size:14
Alignment explanation
Indices: 46703928--46703972 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
46703918 AACTCATCTT
*
46703928 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
46703942 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
46703955 AATTTAATTTAATG
1 AGTTTAATTTAATG
46703969 AGTT
1 AGTT
46703973 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:46704203 original size:30 final size:30
Alignment explanation
Indices: 46704168--46704241 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
46704158 AGTTTTTCCC
*
46704168 AGCTCGAATT-AGCTCACA-TGAGCTTATTTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTACTTT
* *
46704198 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTACTTT
*
46704228 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
46704242 TGCCTTAAGT
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:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTACTTT
Found at i:46707603 original size:10 final size:10
Alignment explanation
Indices: 46707590--46707627 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
46707580 TTGTAGCTAA
46707590 ATTGAGCTCG
1 ATTGAGCTCG
46707600 ATTGAGCT-G
1 ATTGAGCTCG
46707609 ACTTGAGCTCG
1 A-TTGAGCTCG
*
46707620 AGTGAGCT
1 ATTGAGCT
46707628 GGAATCGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:46707607 original size:20 final size:20
Alignment explanation
Indices: 46707567--46707627 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
46707557 ACCAATAAAA
46707567 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
46707587 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
46707607 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
46707627 T
1 T
46707628 GGAATCGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:46707628 original size:20 final size:20
Alignment explanation
Indices: 46707591--46707628 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
46707581 TGTAGCTAAA
*
46707591 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
46707611 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
46707629 GAATCGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:46710371 original size:1 final size:1
Alignment explanation
Indices: 46710365--46710393 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
46710355 CTCCAGACTC
46710365 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46710394 ACGGATCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:46710454 original size:13 final size:13
Alignment explanation
Indices: 46710436--46710484 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
46710426 AAACCGTATG
46710436 CAATTTTTTTTTT
1 CAATTTTTTTTTT
46710449 CAATTTTTTTTTT
1 CAATTTTTTTTTT
46710462 -AATTTTTTTTTTT
1 CAA-TTTTTTTTTT
*
46710475 TAATTTTTTT
1 CAATTTTTTT
46710485 ACGCACCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.06
13 30 0.88
14 2 0.06
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:46710457 original size:12 final size:12
Alignment explanation
Indices: 46710440--46710472 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
46710430 CGTATGCAAT
46710440 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
46710452 TTTTTTTTTTAA
1 TTTTTTTTTCAA
46710464 TTTTTTTTT
1 TTTTTTTTT
46710473 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:46710458 original size:14 final size:13
Alignment explanation
Indices: 46710437--46710484 Score: 71
Period size: 14 Copynumber: 3.7 Consensus size: 13
46710427 AACCGTATGC
*
46710437 AATTTTTTTTTTC
1 AATTTTTTTTTTT
46710450 AA-TTTTTTTTTT
1 AATTTTTTTTTTT
46710462 AATTTTTTTTTTTT
1 AA-TTTTTTTTTTT
46710476 AATTTTTTT
1 AATTTTTTT
46710485 ACGCACCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 11 0.34
13 9 0.28
14 12 0.38
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (13 bp):
AATTTTTTTTTTT
Found at i:46711807 original size:10 final size:10
Alignment explanation
Indices: 46711794--46711831 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
46711784 TTGTAGCTAA
46711794 ATTGAGCTCG
1 ATTGAGCTCG
46711804 ATTGAGCT-G
1 ATTGAGCTCG
46711813 ACTTGAGCTCG
1 A-TTGAGCTCG
*
46711824 AGTGAGCT
1 ATTGAGCT
46711832 GGAATCGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:46711811 original size:20 final size:20
Alignment explanation
Indices: 46711771--46711831 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
46711761 ACCAATAAAA
46711771 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
46711791 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
46711811 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
46711831 T
1 T
46711832 GGAATCGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:46711832 original size:20 final size:20
Alignment explanation
Indices: 46711795--46711832 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
46711785 TGTAGCTAAA
*
46711795 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
46711815 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
46711833 GAATCGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:46712541 original size:17 final size:17
Alignment explanation
Indices: 46712516--46712562 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
46712506 AAATTGAAAG
*
46712516 AAAACAAAAGAAAACGA
1 AAAAGAAAAGAAAACGA
** *
46712533 AAAAGAAAAGAAATTGC
1 AAAAGAAAAGAAAACGA
46712550 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
46712563 TCAAAAAGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.04
Consensus pattern (17 bp):
AAAAGAAAAGAAAACGA
Found at i:46712664 original size:31 final size:31
Alignment explanation
Indices: 46712624--46712688 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
46712614 GCGGAAAAAA
*
46712624 GAAATGAAAGAGAG-CTGAAAAGAAATCAAGT
1 GAAAAGAAAGAGAGTCTGAAAAGAAA-CAAGT
* *
46712655 GAAAAGAAAGAGAGTCTGTAAAGAAACGAGT
1 GAAAAGAAAGAGAGTCTGAAAAGAAACAAGT
46712686 GAA
1 GAA
46712689 GTGAGTAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.54, C:0.06, G:0.28, T:0.12
Consensus pattern (31 bp):
GAAAAGAAAGAGAGTCTGAAAAGAAACAAGT
Found at i:46713629 original size:11 final size:11
Alignment explanation
Indices: 46713613--46713682 Score: 65
Period size: 10 Copynumber: 6.5 Consensus size: 11
46713603 TTGGTACGTT
46713613 TTGGTATGGAA
1 TTGGTATGGAA
*
46713624 TTGGTA-CGAA
1 TTGGTATGGAA
*
46713634 ATGGTATGGAA
1 TTGGTATGGAA
46713645 TTGGTAT-GAA
1 TTGGTATGGAA
* *
46713655 ATGGTATGGTAT
1 TTGGTATGG-AA
*
46713667 TTGGTA-CGAA
1 TTGGTATGGAA
46713677 TTGGTA
1 TTGGTA
46713683 ACGGTTCAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
10 24 0.51
11 17 0.36
12 6 0.13
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.36
Consensus pattern (11 bp):
TTGGTATGGAA
Found at i:46713629 original size:21 final size:21
Alignment explanation
Indices: 46713614--46713682 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
46713604 TGGTACGTTT
46713614 TGGTATGGAATTGGTACGAAA
1 TGGTATGGAATTGGTACGAAA
*
46713635 TGGTATGGAATTGGTATGAAA
1 TGGTATGGAATTGGTACGAAA
* *
46713656 TGGTATGGTATTTGGTACGAAT
1 TGGTATGG-AATTGGTACGAAA
46713678 TGGTA
1 TGGTA
46713683 ACGGTTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
21 28 0.65
22 15 0.35
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.35
Consensus pattern (21 bp):
TGGTATGGAATTGGTACGAAA
Found at i:46716106 original size:20 final size:20
Alignment explanation
Indices: 46716081--46716126 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
46716071 CCCAGCTCGA
*
46716081 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
46716101 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
46716121 TTAGCT
1 TTAGCT
46716127 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:46716117 original size:30 final size:30
Alignment explanation
Indices: 46716074--46716146 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
46716064 AGTTTTTCCC
*
46716074 AGCTCGATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCGTTTGAGCTCA-ATTGAGCTTAATTT
* *
46716103 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
46716133 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
46716147 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.23
30 30 0.77
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:46717777 original size:20 final size:20
Alignment explanation
Indices: 46717754--46717800 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46717744 GGGTTAAGAT
*
46717754 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
46717774 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
46717794 TGAGCTG
1 TGAGCTG
46717801 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:46724014 original size:40 final size:40
Alignment explanation
Indices: 46723959--46724221 Score: 465
Period size: 40 Copynumber: 6.6 Consensus size: 40
46723949 AACATTGGAT
46723959 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
46723999 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
*
46724039 CATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
46724079 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* * *
46724119 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
46724159 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
* *
46724199 TATGTCCGGGTTAAGA-CCGAAGG
1 TATATCCGGGCTAAGACCCGAAGG
46724222 AAATGTGTTT
Statistics
Matches: 213, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
39 7 0.03
40 206 0.97
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
Found at i:46729378 original size:10 final size:11
Alignment explanation
Indices: 46729356--46729380 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
46729346 AAAAAAATCG
46729356 AAATTCAAAAA
1 AAATTCAAAAA
46729367 AAATTCAAAAA
1 AAATTCAAAAA
46729378 AAA
1 AAA
46729381 AGTGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:46729403 original size:15 final size:15
Alignment explanation
Indices: 46729385--46729452 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
46729375 AAAAAAAGTG
*
46729385 AAAAAAAATCGAGCA
1 AAAAAAAATCAAGCA
**
46729400 AAAAAAAAGAAAG-A
1 AAAAAAAATCAAGCA
*
46729414 AAAAAAAAGT-GAGCA
1 AAAAAAAA-TCAAGCA
*
46729429 AAAAAAAATCAAGTTA
1 AAAAAAAATCAAG-CA
46729445 AAAAAAAA
1 AAAAAAAA
46729453 GTGAAAAGTC
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
14 12 0.29
15 21 0.50
16 9 0.21
ACGTcount: A:0.75, C:0.06, G:0.12, T:0.07
Consensus pattern (15 bp):
AAAAAAAATCAAGCA
Found at i:46729405 original size:29 final size:30
Alignment explanation
Indices: 46729373--46729456 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 30
46729363 AAAAAAATTC
*
46729373 AAAAAA-AAAGTGAAAAAAAA-TCGAGCAAA
1 AAAAAAGAAAGTAAAAAAAAAGT-GAGCAAA
46729402 AAAAAAGAAAG-AAAAAAAAAGTGAGCAAA
1 AAAAAAGAAAGTAAAAAAAAAGTGAGCAAA
**
46729431 AAAAAATCAAGTTAAAAAAAAAGTGA
1 AAAAAAGAAAG-TAAAAAAAAAGTGA
46729457 AAAGTCTTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 30 0.62
30 5 0.10
31 13 0.27
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.08
Consensus pattern (30 bp):
AAAAAAGAAAGTAAAAAAAAAGTGAGCAAA
Found at i:46729416 original size:14 final size:15
Alignment explanation
Indices: 46729396--46729436 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
46729386 AAAAAAATCG
46729396 AGCAAAAAAAAAGAA
1 AGCAAAAAAAAAGAA
**
46729411 AG-AAAAAAAAAGTG
1 AGCAAAAAAAAAGAA
46729425 AGCAAAAAAAAA
1 AGCAAAAAAAAA
46729437 TCAAGTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (15 bp):
AGCAAAAAAAAAGAA
Found at i:46730462 original size:12 final size:12
Alignment explanation
Indices: 46730445--46730574 Score: 56
Period size: 12 Copynumber: 10.8 Consensus size: 12
46730435 GCGAGAAAAG
*
46730445 GAAAAAGAGATT
1 GAAAAAGAAATT
46730457 GAAAAAGAAATT
1 GAAAAAGAAATT
*
46730469 G--AAAGAAA-A
1 GAAAAAGAAATT
* *
46730478 CAAAAAGAAAAT
1 GAAAAAGAAATT
46730490 GAAAAAGAAA--
1 GAAAAAGAAATT
* *
46730500 AAAAAATTGCAAA-A
1 GAAAAA--G-AAATT
*
46730514 GAAAAAGAAATC
1 GAAAAAGAAATT
** **
46730526 GAAAAAGTGAGA
1 GAAAAAGAAATT
*
46730538 GAAAAAGAAAAT
1 GAAAAAGAAATT
46730550 GAAGAAAAGAAAATT
1 G-A-AAAAG-AAATT
46730565 GAAAAAGAAA
1 GAAAAAGAAA
46730575 AAGCGAAAAA
Statistics
Matches: 90, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
10 12 0.13
11 10 0.11
12 43 0.48
13 9 0.10
14 11 0.12
15 5 0.06
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.09
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:46730466 original size:18 final size:18
Alignment explanation
Indices: 46730439--46730577 Score: 95
Period size: 18 Copynumber: 7.7 Consensus size: 18
46730429 CATTGAGCGA
* *
46730439 GAAAAGGAAAAAGAGATT
1 GAAAAAGAAAAAGAAATT
**
46730457 GAAAAAGAAATTGAAA--
1 GAAAAAGAAAAAGAAATT
* *
46730473 G-AAAACAAAAAGAAAAT
1 GAAAAAGAAAAAGAAATT
*
46730490 GAAAAAGAAAAAAAAATT
1 GAAAAAGAAAAAGAAATT
* *
46730508 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATT
** * **
46730526 GAAAAAGTGAGAGAAAAA
1 GAAAAAGAAAAAGAAATT
*
46730544 GAAAATGAAGAAAAGAAAATT
1 GAAAAAG-A-AAAAG-AAATT
46730565 GAAAAAGAAAAAG
1 GAAAAAGAAAAAG
46730578 CGAAAAAAGA
Statistics
Matches: 89, Mismatches: 26, Indels: 11
0.71 0.21 0.09
Matches are distributed among these distances:
15 11 0.12
16 1 0.01
17 1 0.01
18 58 0.65
19 5 0.06
20 4 0.04
21 9 0.10
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:46730517 original size:24 final size:23
Alignment explanation
Indices: 46730458--46730575 Score: 75
Period size: 24 Copynumber: 5.0 Consensus size: 23
46730448 AAAGAGATTG
*
46730458 AAAAAGAAATTG--AAAGAAAAC
1 AAAAAGAAAATGAAAAAGAAAAC
46730479 AAAAAGAAAATGAAAAAGAAAA-
1 AAAAAGAAAATGAAAAAGAAAAC
*
46730501 AAAAATTGCAAAA-GAAAAAGAAATC
1 AAAAA--G-AAAATGAAAAAGAAAAC
* * *
46730526 GAAAAAGTGAGA-GAAAAAGAAAATGA
1 -AAAAAG-AAAATGAAAAAGAAAA--C
46730552 AGAAAAGAAAATTGAAAAAGAAAA
1 A-AAAAGAAAA-TGAAAAAGAAAA
46730576 AGCGAAAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
21 11 0.14
22 5 0.07
23 8 0.11
24 24 0.32
25 7 0.09
26 10 0.13
27 11 0.14
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.08
Consensus pattern (23 bp):
AAAAAGAAAATGAAAAAGAAAAC
Found at i:46730518 original size:57 final size:55
Alignment explanation
Indices: 46730457--46730577 Score: 138
Period size: 57 Copynumber: 2.1 Consensus size: 55
46730447 AAAAGAGATT
* *
46730457 GAAAAAGAAATTGAAAGAA-A-ACAAAAAGAAAATGAAAAAGAAAAAAAAATTGCAAAA
1 GAAAAAGAAATCGAAA-AAGAGACAAAAAGAAAATG---AAGAAAAAAAAATTGAAAAA
* *
46730514 GAAAAAGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAA
1 GAAAAAGAAATCGAAAAA--GAGACAAAAAGAAAATGAAGAAAAAAAAATTGAAAAA
46730571 GAAAAAG
1 GAAAAAG
46730578 CGAAAAAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
56 2 0.04
57 40 0.71
59 1 0.02
60 13 0.23
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.08
Consensus pattern (55 bp):
GAAAAAGAAATCGAAAAAGAGACAAAAAGAAAATGAAGAAAAAAAAATTGAAAAA
Found at i:46730523 original size:81 final size:83
Alignment explanation
Indices: 46730438--46730592 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 83
46730428 CCATTGAGCG
* ** * *
46730438 AGAAAAGGAAAAAGAGATTGAAAAAGAAATTGAAAGAAAACAAAA-AGAAAATGAAAAA-GAAAA
1 AGAAAACGAAAAAGAGAGAGAAAAAGAAAATG-AAGAAAACAAAATAGAAAAAGAAAAACGAAAA
46730501 AA-AAATTGCAAAAGAAAA
65 AAGAAATTGCAAAAGAAAA
* * * *
46730519 AGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAAGAAAAAGCGAAAA
1 AGAAAACGAAAAAGAGAGAGAAAAAGAAAATGAAGAAAACAAAATAGAAAAAGAAAAA-CGAAAA
46730584 AAGAAATTG
65 AAGAAATTG
46730593 AAAGAGAGCT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
80 11 0.18
81 37 0.61
83 7 0.11
84 6 0.10
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09
Consensus pattern (83 bp):
AGAAAACGAAAAAGAGAGAGAAAAAGAAAATGAAGAAAACAAAATAGAAAAAGAAAAACGAAAAA
AGAAATTGCAAAAGAAAA
Found at i:46730559 original size:14 final size:13
Alignment explanation
Indices: 46730538--46730575 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
46730528 AAAAGTGAGA
46730538 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
46730550 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
46730565 GAAAAAGAAAA
1 GAAAAAGAAAA
46730576 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:46730589 original size:21 final size:21
Alignment explanation
Indices: 46730539--46730589 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
46730529 AAAGTGAGAG
*
46730539 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
46730560 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
46730581 AAAAAGAAA
1 AAAAAGAAA
46730590 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:46730629 original size:33 final size:33
Alignment explanation
Indices: 46730592--46730654 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
46730582 AAAAGAAATT
46730592 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
46730625 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
46730655 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:46734935 original size:12 final size:12
Alignment explanation
Indices: 46734918--46734965 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
46734908 GAGGAAATTC
46734918 AAAAAAAATCG-
1 AAAAAAAATCGA
*
46734929 -AAAAAAATTGA
1 AAAAAAAATCGA
*
46734940 AAAAAAAATTGA
1 AAAAAAAATCGA
46734952 AAAAAAAATTCGA
1 AAAAAAAA-TCGA
46734965 A
1 A
46734966 GTATTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 9 0.28
12 19 0.59
13 4 0.12
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:46734954 original size:10 final size:10
Alignment explanation
Indices: 46734919--46734957 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
46734909 AGGAAATTCA
*
46734919 AAAAAAATCG
1 AAAAAAATTG
46734929 AAAAAAATTG
1 AAAAAAATTG
46734939 AAAAAAAAATTG
1 --AAAAAAATTG
46734951 AAAAAAA
1 AAAAAAA
46734958 AATTCGAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 16 0.62
12 10 0.38
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:46742747 original size:12 final size:13
Alignment explanation
Indices: 46742730--46742764 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
46742720 CATAAATCAC
46742730 TTTTTTTTTC-GA
1 TTTTTTTTTCGGA
46742742 TTTTTTTTTCGGA
1 TTTTTTTTTCGGA
*
46742755 ATTTTTTTTC
1 TTTTTTTTTC
46742765 AAACTTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTCGGA
Found at i:46742748 original size:13 final size:14
Alignment explanation
Indices: 46742730--46742763 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
46742720 CATAAATCAC
46742730 TTTTTTTTTC-G-A
1 TTTTTTTTTCGGAA
46742742 TTTTTTTTTCGGAA
1 TTTTTTTTTCGGAA
46742756 TTTTTTTT
1 TTTTTTTT
46742764 CAAACTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 1 0.05
14 9 0.45
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTCGGAA
Found at i:46747723 original size:33 final size:33
Alignment explanation
Indices: 46747685--46747747 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
46747675 GATTACTCAC
46747685 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
46747718 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
46747748 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:46747814 original size:18 final size:17
Alignment explanation
Indices: 46747793--46747886 Score: 84
Period size: 18 Copynumber: 5.4 Consensus size: 17
46747783 TTTTCTCTCA
46747793 CTTTTTCGATTTCTTTTT
1 CTTTTTC-ATTTCTTTTT
*
46747811 CTTTTGCAATTTCTTTTT
1 CTTTTTC-ATTTCTTTTT
46747829 CTTTTTCATTTTCTTTTT
1 CTTTTTCA-TTTCTTTTT
* **
46747847 -GTTTTC-TTTCAATTT
1 CTTTTTCATTTCTTTTT
*
46747862 CTTTTTCAATCTCTTTTT
1 CTTTTTC-ATTTCTTTTT
*
46747880 CCTTTTC
1 CTTTTTC
46747887 TCGCTCAATG
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
15 7 0.11
16 5 0.08
17 6 0.10
18 43 0.70
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.69
Consensus pattern (17 bp):
CTTTTTCATTTCTTTTT
Found at i:46747851 original size:11 final size:12
Alignment explanation
Indices: 46747764--46747887 Score: 80
Period size: 12 Copynumber: 10.5 Consensus size: 12
46747754 TTTTTTCGCT
46747764 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
46747777 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
46747788 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
46747802 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
46747812 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
46747825 TTTTCTTTTTCA
1 TTTTCTTTTTCA
*
46747837 TTTTCTTTTT-G
1 TTTTCTTTTTCA
46747848 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
46747858 ATTTCTTTTTCA
1 TTTTCTTTTTCA
* * *
46747870 ATCTCTTTTTCC
1 TTTTCTTTTTCA
46747882 TTTTCT
1 TTTTCT
46747888 CGCTCAATGG
Statistics
Matches: 86, Mismatches: 16, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
9 3 0.03
10 4 0.05
11 9 0.10
12 55 0.64
13 15 0.17
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:46747868 original size:6 final size:6
Alignment explanation
Indices: 46747762--46747855 Score: 73
Period size: 6 Copynumber: 15.7 Consensus size: 6
46747752 TCTTTTTTCG
* * ** **
46747762 CTTTTT CTTTTT CAATTTT CTTTTT CTCTCA CTTTTT CGATTT CTTTTT
1 CTTTTT CTTTTT C-TTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
* ** * *
46747811 CTTTTG CAATTT CTTTTT CTTTTT CATTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
46747856 CAATTTCTTT
Statistics
Matches: 64, Mismatches: 22, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
5 4 0.06
6 55 0.86
7 5 0.08
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:46753101 original size:13 final size:13
Alignment explanation
Indices: 46753083--46753113 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
46753073 CGGCAGGGAA
46753083 ACGCCTGTGGCAC
1 ACGCCTGTGGCAC
46753096 ACGCCTGTGGCAC
1 ACGCCTGTGGCAC
46753109 ACGCC
1 ACGCC
46753114 CGTGTTCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.42, G:0.29, T:0.13
Consensus pattern (13 bp):
ACGCCTGTGGCAC
Found at i:46754615 original size:11 final size:11
Alignment explanation
Indices: 46754601--46754635 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
46754591 ATTTAAAAAT
46754601 TATTTTATGTG
1 TATTTTATGTG
46754612 TATTTTATGTG
1 TATTTTATGTG
*
46754623 AATTTGTATGTG
1 TATTT-TATGTG
46754635 T
1 T
46754636 GAAATTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (11 bp):
TATTTTATGTG
Found at i:46779660 original size:42 final size:42
Alignment explanation
Indices: 46779601--46779706 Score: 194
Period size: 42 Copynumber: 2.5 Consensus size: 42
46779591 CATTTAAGCC
46779601 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
*
46779643 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATATAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
46779685 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
46779707 TATTTAATGA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 52 0.84
43 10 0.16
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:46779708 original size:14 final size:14
Alignment explanation
Indices: 46779689--46779733 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
46779679 AACTCATCTT
*
46779689 AGTTTAATTAAATG
1 AGTTTAATTTAATG
46779703 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
46779716 AATTTAATTTAATG
1 AGTTTAATTTAATG
46779730 AGTT
1 AGTT
46779734 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:46780750 original size:29 final size:29
Alignment explanation
Indices: 46780705--46780764 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
46780695 ATAACCAAAC
* *
46780705 CTACAAAAACTTTATATCCGTAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
46780734 CTACATAAAA-TTCATATCCATAAACCTAT
1 CTACA-AAAACTTCATATCCATAAACCCAT
46780763 CT
1 CT
46780765 TTGAATCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:46781044 original size:17 final size:19
Alignment explanation
Indices: 46781012--46781046 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
46781002 AAAAAATTTC
46781012 AAACAAAAATTCTGAAAAA
1 AAACAAAAATTCTGAAAAA
46781031 AAAC-AAAA-TCTGAAAA
1 AAACAAAAATTCTGAAAA
46781047 TTTGAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (19 bp):
AAACAAAAATTCTGAAAAA
Found at i:46782114 original size:18 final size:18
Alignment explanation
Indices: 46782091--46782143 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
46782081 GAAAGAAAAA
46782091 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGATTGAGAGT
* * *
46782109 GAAAAAGAAAATGAGATT
1 GAAAAAGAGATTGAGAGT
*
46782127 GAAAAAGAGTTTGAGAG
1 GAAAAAGAGATTGAGAG
46782144 AGAGAAAGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (18 bp):
GAAAAAGAGATTGAGAGT
Found at i:46784617 original size:42 final size:42
Alignment explanation
Indices: 46784558--46784663 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
46784548 CATTTAAGCC
46784558 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
46784600 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
46784642 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
46784664 TATTTAATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 53 0.84
43 10 0.16
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:46784665 original size:14 final size:14
Alignment explanation
Indices: 46784646--46784690 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
46784636 AACTCATCTT
*
46784646 AGTTTAATTAAATG
1 AGTTTAATTTAATG
46784660 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
46784673 AATTTAATTTAATG
1 AGTTTAATTTAATG
46784687 AGTT
1 AGTT
46784691 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:46785694 original size:29 final size:29
Alignment explanation
Indices: 46785661--46785720 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
46785651 ATAACCAAAC
*
46785661 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
46785690 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
46785719 CT
1 CT
46785721 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:46785713 original size:15 final size:15
Alignment explanation
Indices: 46785667--46785714 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
46785657 AAACCTACAA
*
46785667 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
46785682 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
46785696 AAACTTCATATCCAT
1 AAACTTCATATCCAT
46785711 AAAC
1 AAAC
46785715 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:46786441 original size:14 final size:14
Alignment explanation
Indices: 46786394--46786441 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
46786384 GTACGAATGG
*
46786394 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
46786408 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
46786422 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
46786436 ATTGGT
1 AATGGT
46786442 CAGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:46794750 original size:40 final size:40
Alignment explanation
Indices: 46794528--46794742 Score: 378
Period size: 40 Copynumber: 5.4 Consensus size: 40
46794518 ATAGCAACTC
* *
46794528 GCACGAATGCCTTCGGGACTTAGCCCGGACATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
*
46794568 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
*
46794608 GCACAAATGCCTTCGAGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
46794648 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
46794688 GCACAAATGCCTTC-GGATCTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGA-CTTAGCCCGGATATAATCACTA
46794728 GCACAAATGCCTTCG
1 GCACAAATGCCTTCG
46794743 AATCTTAGTC
Statistics
Matches: 167, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
39 3 0.02
40 164 0.98
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
Found at i:46797634 original size:27 final size:27
Alignment explanation
Indices: 46797604--46797853 Score: 292
Period size: 27 Copynumber: 9.3 Consensus size: 27
46797594 GGGGCAAAAT
* * *
46797604 GGTAATTTTATCCC-ACGAGGGTATCTC
1 GGTAATTCTA-CCCTACAAGGGTATTTC
46797631 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
46797658 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
46797685 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
46797712 GGTAATTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
46797739 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
46797766 GGTAATTCTA-CCTA-ACAGAGGTATTTT
1 GGTAATTCTACCCTACA-AG-GGTATTTC
* *
46797793 AGTAATTCTACCTTAC-AGAGGTATTTC
1 GGTAATTCTACCCTACAAG-GGTATTTC
* * *
46797820 AGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
46797847 AGTAATT
1 GGTAATT
46797854 TTACAAATCA
Statistics
Matches: 197, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
25 1 0.01
26 9 0.05
27 183 0.93
28 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:46797741 original size:81 final size:80
Alignment explanation
Indices: 46797622--46797880 Score: 342
Period size: 81 Copynumber: 3.2 Consensus size: 80
46797612 TATCCCACGA
* * *
46797622 GGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGA
1 GGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGA
46797687 TAATTCTACCCTACAG
66 TAATTCTA-CCTACAG
*
46797703 GGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGG
1 GGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGA
46797768 TAATTCTACCTAACAG
66 TAATTCTACCT-ACAG
* ** * *
46797784 AGGTATTTTAGTAATTCTACCTTAC-AGAGGTATTTCAGTAATTCTACCTTACAGGGGTATTTC-
1 GGGTATTTCGGTAATTCTACCTTACAAG-GGTATTTCAGTAATTCTACCCTACAAGGGTATTTCG
* **
46797847 AGTAATTTTACAAATCAG
65 A-TAATTCTACCTA-CAG
*
46797865 GGGTATTTGGGTAATT
1 GGGTATTTCGGTAATT
46797881 TTACAAACCA
Statistics
Matches: 158, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
80 6 0.04
81 152 0.96
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (80 bp):
GGGTATTTCGGTAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGA
TAATTCTACCTACAG
Found at i:46797865 original size:27 final size:27
Alignment explanation
Indices: 46797812--46797926 Score: 108
Period size: 27 Copynumber: 4.3 Consensus size: 27
46797802 ACCTTACAGA
* **
46797812 GGTATTTCAGTAATTCTAC-CTTACAGG
1 GGTATTTCAGTAATTTTACAAAT-CAGG
46797839 GGTATTTCAGTAATTTTACAAATCAGG
1 GGTATTTCAGTAATTTTACAAATCAGG
** *
46797866 GGTATTTGGGTAATTTTACAAACCAGG
1 GGTATTTCAGTAATTTTACAAATCAGG
** * *
46797893 GGTATTTTGGTAATTTTGCTAATC-GAG
1 GGTATTTCAGTAATTTTACAAATCAG-G
46797920 GGTATTT
1 GGTATTT
46797927 TTATAATTTG
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 74 0.97
28 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (27 bp):
GGTATTTCAGTAATTTTACAAATCAGG
Found at i:46797879 original size:54 final size:54
Alignment explanation
Indices: 46797622--46797880 Score: 297
Period size: 54 Copynumber: 4.8 Consensus size: 54
46797612 TATCCCACGA
* * * * * * * *
46797622 GGGTATCTCGGTAATTCTACCCTACAAGGGTATTTCAGTATTTCTACCCTACAA
1 GGGTATTTCAGTAATTCTACCATACAGGGGTATTTCGGTAATTCTACCTTACAG
* *
46797676 GGGTATTTC-GATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAA
1 GGGTATTTCAG-TAATTCTACCATACAGGGGTATTTCGGTAATTCTACCTTACAG
* * *
46797730 GGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCTAACAG
1 GGGTATTTCAGTAATTCTACCATACAGGGGTATTTCGGTAATTCTACCTTACAG
* * * * *
46797784 AGGTATTTTAGTAATTCTACCTTACAGAGGTATTTCAGTAATTCTACCTTACAG
1 GGGTATTTCAGTAATTCTACCATACAGGGGTATTTCGGTAATTCTACCTTACAG
* * *
46797838 GGGTATTTCAGTAATTTTA-CAAATCAGGGGTATTTGGGTAATT
1 GGGTATTTCAGTAATTCTACCATA-CAGGGGTATTTCGGTAATT
46797881 TTACAAACCA
Statistics
Matches: 179, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
53 3 0.02
54 175 0.98
55 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (54 bp):
GGGTATTTCAGTAATTCTACCATACAGGGGTATTTCGGTAATTCTACCTTACAG
Found at i:46800790 original size:27 final size:27
Alignment explanation
Indices: 46800760--46800964 Score: 277
Period size: 27 Copynumber: 7.6 Consensus size: 27
46800750 TATCCCACGA
* * *
46800760 GGGTATCTCGGTAATTCTACCCTATAG
1 GGGTATTTCAGTAATTCTACCCTACAG
* *
46800787 GGGTATTTCAGTATTTCTACCCTACAA
1 GGGTATTTCAGTAATTCTACCCTACAG
*
46800814 GGGTATTTC-GATAATTCTACCTTACAG
1 GGGTATTTCAG-TAATTCTACCCTACAG
46800841 GGGTATTTCAGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
** *
46800868 GGGTATTTTGGTAATTCTACCTTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
* *
46800895 GGGTATTTTAGTAATTCTACCCTATAG
1 GGGTATTTCAGTAATTCTACCCTACAG
* *
46800922 GGGTATTTCAGTAATTCTACCTTATAG
1 GGGTATTTCAGTAATTCTACCCTACAG
46800949 GGGTATTTCAGTAATT
1 GGGTATTTCAGTAATT
46800965 TTACAAATTA
Statistics
Matches: 159, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
26 1 0.01
27 157 0.99
28 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.38
Consensus pattern (27 bp):
GGGTATTTCAGTAATTCTACCCTACAG
Found at i:46800980 original size:27 final size:27
Alignment explanation
Indices: 46800893--46801020 Score: 107
Period size: 27 Copynumber: 4.7 Consensus size: 27
46800883 TCTACCTTAC
* * **
46800893 AGGGGTATTTTAGTAATTCTAC-CCTAT
1 AGGGGTATTTCAGTAATTTTACAAAT-T
* **
46800920 AGGGGTATTTCAGTAATTCTAC-CTTAT
1 AGGGGTATTTCAGTAATTTTACAAAT-T
46800947 AGGGGTATTTCAGTAATTTTACAAATT
1 AGGGGTATTTCAGTAATTTTACAAATT
* ** *
46800974 AGAGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTCAGTAATTTTACAAATT
**
46801001 AGGGGTATTTTGGTAATTTT
1 AGGGGTATTTCAGTAATTTT
46801021 GCTAATCGAG
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
27 89 0.99
28 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (27 bp):
AGGGGTATTTCAGTAATTTTACAAATT
Found at i:46800981 original size:54 final size:54
Alignment explanation
Indices: 46800760--46800991 Score: 277
Period size: 54 Copynumber: 4.3 Consensus size: 54
46800750 TATCCCACGA
* * * * * * *
46800760 GGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCAGTATTTCTACCCTACAA
1 GGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCATATAG
* * *
46800814 GGGTATTTCGATAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCCTACAG
1 GGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCATATAG
* * *
46800868 GGGTATTTTGGTAATTCTACCTTACAGGGGTATTTTAGTAATTCTACCCTATAG
1 GGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCATATAG
* * * *
46800922 GGGTATTTCAGTAATTCTACCTTATAGGGGTATTTCAGTAATTTTA-CAAATTAG
1 GGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCATA-TAG
* *
46800976 AGGTATTTTGGTAATT
1 GGGTATTTCGGTAATT
46800992 TTACAAACTA
Statistics
Matches: 157, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 2 0.01
54 155 0.99
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (54 bp):
GGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCATATAG
Found at i:46801004 original size:81 final size:79
Alignment explanation
Indices: 46800760--46801010 Score: 231
Period size: 81 Copynumber: 3.1 Consensus size: 79
46800750 TATCCCACGA
* * ** *
46800760 GGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCAGT-ATTTCTACCCTACAAGGGTATTTCG
1 GGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCAGTAATTT-TA--C-ATTAGGGTATTTTG
* *
46800824 ATAATTCTACCTTAC-AG
62 GTAATTCTACCATACTAG
* ** * * *
46800841 GGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCTTACAGGGGTATTTTAG
1 GGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCAGTAATTTTACATT--A-GGGTATTTTGG
*
46800906 TAATTCTACCCTA-TAG
63 TAATTCTACCATACTAG
*
46800922 GGGTATTTCAGTAATTCTACCTTATAGGGGTATTTCAGTAATTTTACAAATTAGAGGTATTTTGG
1 GGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCAGTAATTTTAC--ATTAG-GGTATTTTGG
* *
46800987 TAATTTTA-CAAACTAG
63 TAATTCTACCATACTAG
46801003 GGGTATTT
1 GGGTATTT
46801011 TGGTAATTTT
Statistics
Matches: 138, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
79 1 0.01
80 4 0.03
81 128 0.93
82 3 0.02
83 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (79 bp):
GGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCAGTAATTTTACATTAGGGTATTTTGGTAA
TTCTACCATACTAG
Done.