Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 117 of 259
Found at i:38179524 original size:37 final size:37
Alignment explanation
Indices: 38179482--38179552 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
38179472 CTTGCCTCTC
38179482 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTACT
1 TTTTCTTTTTCATTTC-TTTTCTTTATT-TTCTCTTACT
*
38179519 TTTTCTTTTTCTTTTCTTTTCTTTATTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTATTTTCTCTT
38179553 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:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTATTTTCTCTTACT
Found at i:38180515 original size:13 final size:13
Alignment explanation
Indices: 38180489--38180526 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
38180479 TTTTTTTTCC
38180489 TTTTTTTC-G-AT
1 TTTTTTTCTGAAT
38180500 TTTTTTT-TGAAT
1 TTTTTTTCTGAAT
38180512 TTTTTTTCTGAAT
1 TTTTTTTCTGAAT
38180525 TT
1 TT
38180527 CTTCTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 9 0.38
13 7 0.29
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (13 bp):
TTTTTTTCTGAAT
Found at i:38182285 original size:30 final size:30
Alignment explanation
Indices: 38182251--38182338 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
38182241 TAAACTAAAA
*
38182251 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
38182281 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
38182311 TGAGCTAAGGTTTAGCTCGTGAGCTAAA
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAA
38182339 TATAAGCTAG
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:38184572 original size:21 final size:22
Alignment explanation
Indices: 38184546--38184604 Score: 57
Period size: 27 Copynumber: 2.5 Consensus size: 22
38184536 CTCTTGCCTC
38184546 TCTTTTCTTTTTA-TTTCATTT
1 TCTTTTCTTTTTATTTTCATTT
*
38184567 TCTTTTTCTTCTCTTACTTTTTCTTTT
1 TC-TTTTCTT-T-TTA--TTTTCATTT
38184594 TCTTTTCTTTT
1 TCTTTTCTTTT
38184605 CTTTATTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
21 2 0.06
22 7 0.23
23 1 0.03
24 4 0.13
25 1 0.03
26 7 0.23
27 9 0.29
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (22 bp):
TCTTTTCTTTTTATTTTCATTT
Found at i:38184575 original size:6 final size:6
Alignment explanation
Indices: 38184559--38184608 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
38184549 TTTCTTTTTA
*
38184559 TTTCAT TTTCTT TTTCTT CTCTTACTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
38184608 T
1 T
38184609 ATTTTCTCTT
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:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:38184590 original size:37 final size:37
Alignment explanation
Indices: 38184548--38184618 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
38184538 CTTGCCTCTC
38184548 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTACT
1 TTTTCTTTTTCATTTC-TTTTCTTTATT-TTCTCTTACT
*
38184585 TTTTCTTTTTCTTTTCTTTTCTTTATTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTATTTTCTCTT
38184619 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:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTATTTTCTCTTACT
Found at i:38187354 original size:30 final size:30
Alignment explanation
Indices: 38187320--38187407 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
38187310 TAAACTAAAA
*
38187320 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * *
38187350 TGAGCTAAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
38187380 TGAGCTAAGGTTTAGCTCGTGAGCTAAA
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAA
38187408 TATAAGCTAG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:38189474 original size:12 final size:12
Alignment explanation
Indices: 38189457--38189500 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
38189447 ACGGTATTGT
38189457 AAAAAAAATAT-A
1 AAAAAAAAT-TCA
* *
38189469 AAAAAAATTTGA
1 AAAAAAAATTCA
38189481 AAAAAAAATTCA
1 AAAAAAAATTCA
38189493 AAAAAAAA
1 AAAAAAAA
38189501 GTTTGTATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 1 0.04
12 27 0.96
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:38189584 original size:26 final size:27
Alignment explanation
Indices: 38189547--38189609 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
38189537 TATTGAAGGA
* **
38189547 AAAAAAAGAAGAAAAAAATTCGGAATT-
1 AAAAAAA-AAGAAAAAAAATCAAAATTG
38189574 AAAAAAAAAGAAAAAAAATCAAAATTG
1 AAAAAAAAAGAAAAAAAATCAAAATTG
38189601 AAAAAAAAA
1 AAAAAAAAA
38189610 AAGAGTGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 16 0.50
27 16 0.50
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.11
Consensus pattern (27 bp):
AAAAAAAAAGAAAAAAAATCAAAATTG
Found at i:38189588 original size:27 final size:29
Alignment explanation
Indices: 38189546--38189613 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
38189536 GTATTGAAGG
**
38189546 AAAAAAAAGAAGAAAAAAATTCGGAATT-A
1 AAAAAAAAGAAGAAAAAAA-TCAAAATTGA
38189575 AAAAAAAAG-A-AAAAAAATCAAAATTGA
1 AAAAAAAAGAAGAAAAAAATCAAAATTGA
38189602 AAAAAAAA-AAGA
1 AAAAAAAAGAAGA
38189614 GTGATTGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 6 0.18
27 17 0.50
28 2 0.06
29 9 0.26
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (29 bp):
AAAAAAAAGAAGAAAAAAATCAAAATTGA
Found at i:38191478 original size:15 final size:15
Alignment explanation
Indices: 38191458--38191494 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
38191448 GCAATTTTGA
38191458 CTTTCGAGATTATGT
1 CTTTCGAGATTATGT
38191473 CTTTCGAGATTATGT
1 CTTTCGAGATTATGT
38191488 CTTTCGA
1 CTTTCGA
38191495 CTGTTTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.46
Consensus pattern (15 bp):
CTTTCGAGATTATGT
Found at i:38197692 original size:20 final size:20
Alignment explanation
Indices: 38197669--38197715 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
38197659 GGGTTAAGAT
*
38197669 TGAGCTGAATTGAGCTTGAC
1 TGAGCTGAATTGAGCTCGAC
* * *
38197689 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAC
38197709 TGAGCTG
1 TGAGCTG
38197716 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:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAC
Found at i:38200942 original size:48 final size:48
Alignment explanation
Indices: 38200887--38200992 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
38200877 TTGTCTTTTC
*
38200887 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
38200935 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
38200983 TTTCTTTTTC
1 TTTCTTTTTC
38200993 TATGACACTC
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:38203639 original size:20 final size:20
Alignment explanation
Indices: 38203616--38203662 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
38203606 GGGTTAAGAT
*
38203616 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
38203636 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
38203656 TGAGCTG
1 TGAGCTG
38203663 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:38206667 original size:20 final size:19
Alignment explanation
Indices: 38206644--38206701 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
38206634 AGCTCAAACG
38206644 AGCTAAAGTAAGCTAAATTA
1 AGCTAAAGT-AGCTAAATTA
38206664 AGCTCAAACG-AGCTAAATTA
1 AGCT-AAA-GTAGCTAAATTA
* *
38206684 AGCTCATGTGAGCTAAAT
1 AGCTAAAGT-AGCTAAAT
38206702 CGAGCTGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 26 0.81
21 3 0.09
22 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (19 bp):
AGCTAAAGTAGCTAAATTA
Found at i:38208523 original size:33 final size:33
Alignment explanation
Indices: 38208485--38208547 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
38208475 GATTACTCAC
38208485 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
38208518 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
38208548 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:38208574 original size:21 final size:21
Alignment explanation
Indices: 38208545--38208600 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
38208535 CAAGCTCTCT
*
38208545 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
38208566 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
38208587 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
38208601 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:38208593 original size:14 final size:13
Alignment explanation
Indices: 38208544--38208600 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
38208534 TCAAGCTCTC
*
38208544 TTTCAATTTCTTT
1 TTTCATTTTCTTT
*
38208557 TTTCGCTTTT-TCTT
1 TTTC-ATTTTCT-TT
38208571 TTTCAATTTTCTTT
1 TTTC-ATTTTCTTT
38208585 TCTTCATTTTCTTT
1 T-TTCATTTTCTTT
38208599 TT
1 TT
38208601 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 (13 bp):
TTTCATTTTCTTT
Found at i:38208628 original size:18 final size:18
Alignment explanation
Indices: 38208607--38208682 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 18
38208597 TTTTCTCTCA
38208607 CTTTTTTTATTTCTTTTT
1 CTTTTTTTATTTCTTTTT
***
38208625 CTTTTGCAATTTCTTTTT
1 CTTTTTTTATTTCTTTTT
*
38208643 CTTTTTCGT-TTTCTTTTT
1 CTTTTT-TTATTTCTTTTT
*
38208661 GTTTTCTTTCAATTTCTTTTT
1 CTTTT-TTT--ATTTCTTTTT
38208682 C
1 C
38208683 AATCTCTTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
18 34 0.77
19 1 0.02
21 9 0.20
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.74
Consensus pattern (18 bp):
CTTTTTTTATTTCTTTTT
Found at i:38208682 original size:6 final size:6
Alignment explanation
Indices: 38208562--38208669 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
38208552 TCTTTTTTCG
* * * **
38208562 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* ** *
38208613 -TTATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTT-TTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
38208661 -GTTTT CTTT
1 CTTTTT CTTT
38208670 CAATTTCTTT
Statistics
Matches: 76, Mismatches: 21, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
5 6 0.08
6 56 0.74
7 11 0.14
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:38209749 original size:19 final size:20
Alignment explanation
Indices: 38209727--38209781 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
38209717 TGTCACTTCT
38209727 TTTTTTTTCTTTTTTTCG-A
1 TTTTTTTTCTTTTTTTCGAA
** *
38209746 TTTTTTTAATTTTTTTTGAA
1 TTTTTTTTCTTTTTTTCGAA
* *
38209766 TTTCTTCTCTTTTTTT
1 TTTTTTTTCTTTTTTT
38209782 TAAATCCAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTTTTTCTTTTTTTCGAA
Found at i:38210309 original size:48 final size:48
Alignment explanation
Indices: 38210254--38210359 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
38210244 TTGTCTTTTC
*
38210254 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
38210302 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
38210350 TTTCTTTTTC
1 TTTCTTTTTC
38210360 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:38213010 original size:20 final size:20
Alignment explanation
Indices: 38212987--38213035 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
38212977 GGGTTAAGAT
*
38212987 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
38213007 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
38213027 TGAGCTGAA
1 TGAGCTGAA
38213036 AACGAGCTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.29
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:38216229 original size:21 final size:21
Alignment explanation
Indices: 38216184--38216246 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
38216174 TTTGAACCAT
* *
38216184 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
38216206 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
38216227 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
38216247 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:38217663 original size:27 final size:28
Alignment explanation
Indices: 38217600--38217666 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 28
38217590 CCTTTCCACG
*
38217600 TCTTTTTC-TTTTGTTTCTTTTTCACTC
1 TCTTTTTCTTTTTGTCTCTTTTTCACTC
** * *
38217627 TCAATCTCTTTTTG-CTCTTTTTCATTC
1 TCTTTTTCTTTTTGTCTCTTTTTCACTC
38217654 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
38217667 CCTCACTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.06, C:0.22, G:0.03, T:0.69
Consensus pattern (28 bp):
TCTTTTTCTTTTTGTCTCTTTTTCACTC
Found at i:38223368 original size:20 final size:20
Alignment explanation
Indices: 38223345--38223391 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
38223335 GGGTTAAAAT
*
38223345 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
38223365 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
38223385 TGAGCTG
1 TGAGCTG
38223392 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:38225103 original size:21 final size:21
Alignment explanation
Indices: 38225063--38225103 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38225053 TCAAGTGAAA
*
38225063 GAAAAAGAAAAGAATGAGAAT
1 GAAAAAGAAAAGAATAAGAAT
38225084 GAAAAAGAAAAAGAA-AAGAA
1 GAAAAAG-AAAAGAATAAGAA
38225104 AGTTGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (21 bp):
GAAAAAGAAAAGAATAAGAAT
Found at i:38225180 original size:9 final size:9
Alignment explanation
Indices: 38225162--38225191 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
38225152 AGAAAGTGGG
38225162 AGAAGAAAA
1 AGAAGAAAA
*
38225171 AGATGAAAA
1 AGAAGAAAA
38225180 AGAAGAAAA
1 AGAAGAAAA
38225189 AGA
1 AGA
38225192 GATAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.03
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:38229961 original size:23 final size:22
Alignment explanation
Indices: 38229910--38229961 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
38229900 CCTCGTCTTT
*
38229910 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
38229932 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
38229955 TTCTTTT
1 TTCTTTT
38229962 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:38234243 original size:18 final size:19
Alignment explanation
Indices: 38234220--38234258 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
38234210 TTTATCTCAA
*
38234220 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
38234238 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
38234257 TT
1 TT
38234259 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:38234274 original size:48 final size:49
Alignment explanation
Indices: 38234222--38234325 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 49
38234212 TATCTCAATT
* * *
38234222 TCTTTTTCCACTCT-TTTTTC-TTGTTCACATTCTTTTTCTCTCTCAAAC
1 TCTTTTTCCACTCTCTTTTTCAAT-CTCACATTCTTTTTCACTCTCAAAC
* ** *
38234270 TCTTTTT-CATTCTCTTTTTCAATCTCATTTTCTTTTTCACTCTCAATC
1 TCTTTTTCCACTCTCTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
38234318 TCTTTTTC
1 TCTTTTTC
38234326 TTTTTCTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
47 5 0.11
48 40 0.87
49 1 0.02
ACGTcount: A:0.12, C:0.28, G:0.01, T:0.59
Consensus pattern (49 bp):
TCTTTTTCCACTCTCTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
Found at i:38234297 original size:18 final size:18
Alignment explanation
Indices: 38234276--38234325 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
38234266 AAACTCTTTT
38234276 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
38234294 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
38234312 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
38234326 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:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:38234315 original size:24 final size:24
Alignment explanation
Indices: 38234251--38234332 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
38234241 CTTGTTCACA
*
38234251 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
* * * * *
38234275 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTCTTT
*
38234299 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
38234323 TTCTTTTTCT
1 TTCTTTTTCT
38234333 TTCATTTCTT
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (24 bp):
TTCTTTTTCTCTCTCAATCTCTTT
Found at i:38234360 original size:21 final size:20
Alignment explanation
Indices: 38234336--38234403 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 20
38234326 TTTTTCTTTC
38234336 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTC-TTTCTCG
*
38234357 ATTTCATTTAAGATTC--TCTC-
1 ATTTC-TTT--GTTTCTTTCTCG
38234377 ATTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTT-TCTCG
38234399 ATTTC
1 ATTTC
38234404 ATTCAAAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
18 4 0.11
20 4 0.11
21 21 0.57
22 4 0.11
24 4 0.11
ACGTcount: A:0.12, C:0.21, G:0.07, T:0.60
Consensus pattern (20 bp):
ATTTCTTTGTTTCTTTCTCG
Found at i:38234384 original size:42 final size:42
Alignment explanation
Indices: 38234329--38234425 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
38234319 CTTTTTCTTT
* * * *
38234329 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTTAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
38234370 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
38234412 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
38234426 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:0.14, C:0.23, G:0.05, T:0.58
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:38237771 original size:13 final size:14
Alignment explanation
Indices: 38237753--38237817 Score: 64
Period size: 14 Copynumber: 4.6 Consensus size: 14
38237743 CGTAGCTTCG
38237753 AAAAAAAAAGTT--
1 AAAAAAAAAGTTCA
38237765 AAAAAAAAAGTTTCGA
1 AAAAAAAAAG-TTC-A
* *
38237781 AAAAAAAAAATTCG
1 AAAAAAAAAGTTCA
38237795 AAAAAAAAA-TTGCA
1 AAAAAAAAAGTT-CA
38237809 AAAAAAAAA
1 AAAAAAAAA
38237818 TTGCATACGG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
12 10 0.22
13 4 0.09
14 19 0.42
15 3 0.07
16 9 0.20
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAGTTCA
Found at i:38237783 original size:15 final size:15
Alignment explanation
Indices: 38237749--38237816 Score: 74
Period size: 15 Copynumber: 4.9 Consensus size: 15
38237739 AAATCGTAGC
38237749 TTCGAAAAAAAAAG-
1 TTCGAAAAAAAAAGT
38237763 TT--AAAAAAAAAGT
1 TTCGAAAAAAAAAGT
**
38237776 TTCGAAAAAAAAAAA
1 TTCGAAAAAAAAAGT
38237791 TTCGAAAAAAAAA-T
1 TTCGAAAAAAAAAGT
*
38237805 TGC-AAAAAAAAA
1 TTCGAAAAAAAAA
38237817 ATTGCATACG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
12 10 0.21
13 11 0.23
14 4 0.09
15 22 0.47
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.16
Consensus pattern (15 bp):
TTCGAAAAAAAAAGT
Found at i:38237784 original size:16 final size:15
Alignment explanation
Indices: 38237749--38237819 Score: 64
Period size: 13 Copynumber: 5.1 Consensus size: 15
38237739 AAATCGTAGC
*
38237749 TTCG-AAAAAAAAAG
1 TTCGAAAAAAAAAAA
**
38237763 TT--AAAAAAAAAGT
1 TTCGAAAAAAAAAAA
38237776 TTCGAAAAAAAAAAA
1 TTCGAAAAAAAAAAA
38237791 TTCG--AAAAAAAAA
1 TTCGAAAAAAAAAAA
*
38237804 TT-GCAAAAAAAAAA
1 TTCGAAAAAAAAAAA
38237818 TT
1 TT
38237820 GCATACGGTC
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
12 1 0.02
13 21 0.44
14 13 0.27
15 13 0.27
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.18
Consensus pattern (15 bp):
TTCGAAAAAAAAAAA
Found at i:38237817 original size:15 final size:14
Alignment explanation
Indices: 38237781--38237822 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
38237771 AAAGTTTCGA
38237781 AAAAAAAAAATT-C
1 AAAAAAAAAATTGC
*
38237794 GAAAAAAAAATTGC
1 AAAAAAAAAATTGC
38237808 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
38237822 A
1 A
38237823 TACGGTCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Found at i:38240097 original size:24 final size:25
Alignment explanation
Indices: 38240070--38240123 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
38240060 ATGAGTGATA
*
38240070 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
38240094 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
38240118 AAAAAA
1 AAAAAA
38240124 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:38248392 original size:20 final size:20
Alignment explanation
Indices: 38248369--38248415 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
38248359 AGCTCCAGTC
38248369 AGCTCAAATCAGCTCGTTTG
1 AGCTCAAATCAGCTCGTTTG
* **
38248389 AGCTTATTTCAGCTCGTTTG
1 AGCTCAAATCAGCTCGTTTG
*
38248409 AGTTCAA
1 AGCTCAA
38248416 TTTAGCTACT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (20 bp):
AGCTCAAATCAGCTCGTTTG
Found at i:38250549 original size:17 final size:18
Alignment explanation
Indices: 38250513--38250551 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
38250503 AAGCAATCAA
38250513 AATTAATGTGTCTAAATT
1 AATTAATGTGTCTAAATT
*
38250531 AATTAATGTG-CTGAATT
1 AATTAATGTGTCTAAATT
38250548 AATT
1 AATT
38250552 TGTGTGTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (18 bp):
AATTAATGTGTCTAAATT
Found at i:38255774 original size:50 final size:51
Alignment explanation
Indices: 38255694--38255926 Score: 200
Period size: 50 Copynumber: 4.7 Consensus size: 51
38255684 AATCTTACAC
* * * * * **
38255694 ATCGATGCCGATGTCATATCCTAGATATGGTCTTACACCGA-CTCTCATAA
1 ATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACCGAGCTCTCATCT
* * *
38255744 ATCGAGGCCTATGCCATGTCCCAGACATGGTCTTATA-CTAGCTCTCATCT
1 ATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACCGAGCTCTCATCT
* * * *
38255794 GTCG-GTGACGATGCCATGTCCCAGACATGGTCTCACA-CTAGCTCTCATCT
1 ATCGAG-GCCGATGCCATGTCCCAGACATGGTCTTACACCGAGCTCTCATCT
* * * * *
38255844 GTCGATGCCGATGCCATGTCCCAAACATGGTCTTACACTGA-CACAT-AT-T
1 ATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACCGAGCTC-TCATCT
38255893 A---A-GCCGATGCCATGTCCCAGACATGGTCTTACAC
1 ATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACAC
38255927 TGGCTCACAT
Statistics
Matches: 154, Mismatches: 24, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
45 31 0.20
46 1 0.01
49 4 0.03
50 116 0.75
51 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (51 bp):
ATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACCGAGCTCTCATCT
Found at i:38259293 original size:20 final size:20
Alignment explanation
Indices: 38259268--38259318 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
38259258 TGCAAGATGA
38259268 AGCTCATTTCAGCT-CAA-TC
1 AGCTCATTT-AGCTACAATTC
38259287 GAGCTCAATTTAGCTACAATTC
1 -AGCTC-ATTTAGCTACAATTC
38259309 AGCTCATTTA
1 AGCTCATTTA
38259319 TTTTATTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 14 0.50
21 12 0.43
22 2 0.07
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (20 bp):
AGCTCATTTAGCTACAATTC
Found at i:38259312 original size:11 final size:10
Alignment explanation
Indices: 38259268--38259314 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
38259258 TGCAAGATGA
*
38259268 AGCTCATTTC
1 AGCTCAATTC
38259278 AGCTCAA-TC
1 AGCTCAATTC
*
38259287 GAGCTCAATTT
1 -AGCTCAATTC
38259298 AGCTACAATTC
1 AGCT-CAATTC
38259309 AGCTCA
1 AGCTCA
38259315 TTTATTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.06
10 19 0.61
11 10 0.32
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:38260041 original size:20 final size:20
Alignment explanation
Indices: 38259995--38260041 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
38259985 AGCTCGTTTC
*
38259995 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
38260015 CAACTCACTCAAGCTTAATT
1 CAGCTCACTCAAGCTCAAGT
38260035 CAGCTCA
1 CAGCTCA
38260042 ATCTTAACCC
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:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:38262737 original size:47 final size:46
Alignment explanation
Indices: 38262659--38262762 Score: 131
Period size: 47 Copynumber: 2.2 Consensus size: 46
38262649 GAGTGTCATG
*
38262659 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAA-AGAAA-AAATC
* *
38262706 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAGAAAAAATC
38262753 GAAAAAGAAA
1 GAAAAAGAAA
38262763 GAAAAGACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
47 40 0.78
48 8 0.16
49 3 0.06
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (46 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAGAAAAAATC
Found at i:38265146 original size:30 final size:30
Alignment explanation
Indices: 38265112--38265208 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
38265102 TAAACTAAAA
*
38265112 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
38265142 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
38265172 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
38265201 ATGAGCTA
1 -TGAGCTA
38265209 GGAGTGAGCT
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:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:38267384 original size:12 final size:12
Alignment explanation
Indices: 38267369--38267399 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
38267359 TTCTTTTTGC
*
38267369 TTTTCAAAGGTT
1 TTTTCAAAGGCT
38267381 TTTTCAAAGGCT
1 TTTTCAAAGGCT
38267393 TTTTCAA
1 TTTTCAA
38267400 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:38267476 original size:6 final size:6
Alignment explanation
Indices: 38267460--38267509 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
38267450 TTTCTTTTTA
*
38267460 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
38267509 T
1 T
38267510 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:38267492 original size:37 final size:37
Alignment explanation
Indices: 38267449--38267519 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
38267439 CTTGCCTCTC
38267449 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
38267486 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
38267520 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:38267520 original size:16 final size:16
Alignment explanation
Indices: 38267445--38267505 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
38267435 GCCTCTTGCC
*
38267445 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
38267461 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
38267477 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
38267493 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
38267506 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:38268461 original size:10 final size:11
Alignment explanation
Indices: 38268437--38268487 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
38268427 TTTAACTCAA
38268437 TTTTTTTGTCAC
1 TTTTTTT-TCAC
38268449 TTTTTTTTC-C
1 TTTTTTTTCAC
38268459 TTTTTTTTCGA-
1 TTTTTTTTC-AC
* *
38268470 TTTTTTTTGAA
1 TTTTTTTTCAC
38268481 TTTTTTT
1 TTTTTTT
38268488 CTGAATTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
10 11 0.31
11 17 0.49
12 7 0.20
ACGTcount: A:0.08, C:0.10, G:0.06, T:0.76
Consensus pattern (11 bp):
TTTTTTTTCAC
Found at i:38268473 original size:11 final size:10
Alignment explanation
Indices: 38268436--38268488 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
38268426 TTTTAACTCA
38268436 ATTTTTTTGTC
1 ATTTTTTT-TC
38268447 ACTTTTTTTTC
1 A-TTTTTTTTC
*
38268458 CTTTTTTTTC
1 ATTTTTTTTC
*
38268468 GATTTTTTTTG
1 -ATTTTTTTTC
*
38268479 AATTTTTTTC
1 ATTTTTTTTC
38268489 TGAATTTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 17 0.49
11 11 0.31
12 7 0.20
ACGTcount: A:0.09, C:0.11, G:0.06, T:0.74
Consensus pattern (10 bp):
ATTTTTTTTC
Found at i:38268485 original size:12 final size:12
Alignment explanation
Indices: 38268460--38268495 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
38268450 TTTTTTTCCT
38268460 TTTTTTTC-G-A
1 TTTTTTTCTGAA
38268470 TTTTTTT-TGAA
1 TTTTTTTCTGAA
38268481 TTTTTTTCTGAA
1 TTTTTTTCTGAA
38268493 TTT
1 TTT
38268496 CTTCTCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.35
11 8 0.35
12 7 0.30
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (12 bp):
TTTTTTTCTGAA
Found at i:38268592 original size:11 final size:11
Alignment explanation
Indices: 38268576--38268604 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
38268566 CAACTCAAAA
38268576 TTTTTTTTGA-
1 TTTTTTTTGAC
38268586 TTTTTTTTGAC
1 TTTTTTTTGAC
38268597 TTTTTTTT
1 TTTTTTTT
38268605 TTCGTTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:38272885 original size:20 final size:20
Alignment explanation
Indices: 38272839--38272885 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
38272829 AGCTCGTTTC
*
38272839 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
38272859 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
38272879 CAGCTCA
1 CAGCTCA
38272886 ATCTTAACCC
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:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:38275483 original size:13 final size:13
Alignment explanation
Indices: 38275467--38275498 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
38275457 AAAGAGTTCG
38275467 AAAAAAATTGAAA
1 AAAAAAATTGAAA
38275480 AAAAAAATTGAAA
1 AAAAAAATTGAAA
38275493 AAAAAA
1 AAAAAA
38275499 GAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAAAAATTGAAA
Found at i:38276592 original size:18 final size:18
Alignment explanation
Indices: 38276554--38276595 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38276544 AAATCGAAAG
* **
38276554 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
38276572 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
38276590 AAAAGA
1 AAAAGA
38276596 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:38282050 original size:18 final size:18
Alignment explanation
Indices: 38282028--38282071 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
38282018 AAAAAGTGAG
*
38282028 AGAAAAAGAAATTGAGAA
1 AGAAAAAGAAATTGAAAA
* *
38282046 TGAAAAAAAAATTGAAAA
1 AGAAAAAGAAATTGAAAA
38282064 AGAAAAAG
1 AGAAAAAG
38282072 CGAAAAAAGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.11
Consensus pattern (18 bp):
AGAAAAAGAAATTGAAAA
Found at i:38282123 original size:33 final size:33
Alignment explanation
Indices: 38282086--38282148 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
38282076 AAAAGAAATT
38282086 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
38282119 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
38282149 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:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:38283593 original size:20 final size:20
Alignment explanation
Indices: 38283570--38283623 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
38283560 AGTTTTTCCC
*
38283570 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
38283590 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
38283610 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
38283624 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:38283605 original size:30 final size:30
Alignment explanation
Indices: 38283570--38283643 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
38283560 AGTTTTTCCC
38283570 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
38283600 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
38283630 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
38283644 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:38283633 original size:20 final size:20
Alignment explanation
Indices: 38283570--38283634 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
38283560 AGTTTTTCCC
* * * *
38283570 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
38283590 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
38283609 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
38283630 AGCTC
1 AGCTC
38283635 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:38285562 original size:20 final size:21
Alignment explanation
Indices: 38285529--38285567 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
38285519 TGCAAGATGA
38285529 AGCTCATTTAAGCT-CAATCG
1 AGCTCATTTAAGCTACAATCG
38285549 AGCTCAATTT-AGCTACAAT
1 AGCTC-ATTTAAGCTACAAT
38285568 TCAACTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (21 bp):
AGCTCATTTAAGCTACAATCG
Found at i:38286938 original size:13 final size:13
Alignment explanation
Indices: 38286922--38286980 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
38286912 CAAAAAAATC
38286922 AAAAAAAATTCGA
1 AAAAAAAATTCGA
*
38286935 AAAAAAAATTTGA
1 AAAAAAAATTCGA
38286948 TTGAAAAAAAA-TC-A
1 ---AAAAAAAATTCGA
*
38286962 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
38286974 AAAAAAA
1 AAAAAAA
38286981 TCGAGCAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
11 8 0.21
12 9 0.23
13 12 0.31
14 1 0.03
15 1 0.03
16 8 0.21
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:38288108 original size:12 final size:12
Alignment explanation
Indices: 38288038--38288136 Score: 50
Period size: 12 Copynumber: 8.6 Consensus size: 12
38288028 AGAAAAGGAG
*
38288038 AAAGAGATTGAA
1 AAAGAAATTGAA
* *
38288050 AATGAAATCGAA
1 AAAGAAATTGAA
** **
38288062 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
38288074 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
38288088 AAAGAAAATTGAA
1 AAAG-AAATTGAA
38288101 AAAGAAATTG--
1 AAAGAAATTGAA
38288111 --AG-AA-TGAA
1 AAAGAAATTGAA
38288119 AAA-AAATTGAA
1 AAAGAAATTGAA
38288130 AAAGAAA
1 AAAGAAA
38288137 AAGCGAAAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 20
0.66 0.13 0.21
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 2 0.03
10 3 0.05
11 7 0.11
12 31 0.48
13 6 0.09
14 6 0.09
15 5 0.08
ACGTcount: A:0.66, C:0.01, G:0.20, T:0.13
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:38288125 original size:17 final size:18
Alignment explanation
Indices: 38288091--38288139 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
38288081 ATGAAGAAAA
38288091 GAAAATTGAAAAAGAAATT
1 GAAAA-TGAAAAAGAAATT
*
38288110 GAGAATGAAAAA-AAATT
1 GAAAATGAAAAAGAAATT
*
38288127 GAAAAAGAAAAAG
1 GAAAATGAAAAAG
38288140 CGAAAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 15 0.58
18 7 0.27
19 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.14
Consensus pattern (18 bp):
GAAAATGAAAAAGAAATT
Found at i:38288134 original size:29 final size:27
Alignment explanation
Indices: 38288071--38288137 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 27
38288061 AAAAGTGAGA
38288071 GAAAAAGAAAATGAAGAAAAGAAAATT
1 GAAAAAGAAAATGAAGAAAAGAAAATT
*
38288098 GAAAAAGAAATTGAGAATGAAAA-AAAATT
1 GAAAAAGAAAAT--GAA-GAAAAGAAAATT
38288127 GAAAAAGAAAA
1 GAAAAAGAAAA
38288138 AGCGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 11 0.31
29 19 0.54
30 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (27 bp):
GAAAAAGAAAATGAAGAAAAGAAAATT
Found at i:38288191 original size:33 final size:33
Alignment explanation
Indices: 38288154--38288216 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
38288144 AAAAGAAATT
38288154 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
38288187 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
38288217 GTGAGTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 17 0.61
34 10 0.36
35 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:38288847 original size:29 final size:29
Alignment explanation
Indices: 38288813--38288883 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
38288803 GGCCTAATGA
* *
38288813 GCCATATGAATGTGAATTGGGCTTAG-TGG
1 GCCATATGAATGTGAACTGGGC-CAGATGG
* *
38288842 GCCATAAGAATATGAACTGGGCCAGATGG
1 GCCATATGAATGTGAACTGGGCCAGATGG
*
38288871 GCCATATGCATGT
1 GCCATATGAATGT
38288884 ATGTAGGGGT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 2 0.06
29 32 0.94
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.25
Consensus pattern (29 bp):
GCCATATGAATGTGAACTGGGCCAGATGG
Found at i:38292831 original size:14 final size:14
Alignment explanation
Indices: 38292814--38292854 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
38292804 CGAATGGAAT
*
38292814 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
38292828 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
38292842 GATATGAACAAAA
1 GGTAGGAACAAAA
38292855 TGGTCGGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.51, C:0.07, G:0.32, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:38294699 original size:8 final size:8
Alignment explanation
Indices: 38294672--38294701 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
38294662 ATGAATAGGC
38294672 AAAAGCCA
1 AAAAGCCA
*
38294680 AAATGCCA
1 AAAAGCCA
38294688 AAAAGCCA
1 AAAAGCCA
38294696 AAAAGC
1 AAAAGC
38294702 TGAAATACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.23, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAGCCA
Found at i:38296206 original size:34 final size:33
Alignment explanation
Indices: 38296142--38296207 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
38296132 TTAAAGATGT
* *
38296142 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
38296175 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
38296208 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:38297242 original size:11 final size:10
Alignment explanation
Indices: 38297226--38297255 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
38297216 GTTCGTAACG
38297226 AAAAAAAAGTC
1 AAAAAAAA-TC
38297237 AAAAAAAATC
1 AAAAAAAATC
38297247 AAAAAAAAT
1 AAAAAAAAT
38297256 TTGAGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:38297356 original size:11 final size:11
Alignment explanation
Indices: 38297340--38297365 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38297330 AGGAAATTTG
38297340 AAAAAAAATTC
1 AAAAAAAATTC
38297351 AAAAAAAATTC
1 AAAAAAAATTC
38297362 AAAA
1 AAAA
38297366 TTTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:38300590 original size:34 final size:33
Alignment explanation
Indices: 38300526--38300591 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
38300516 TTAAAGATGT
* *
38300526 TGTTCTACATGCATGGAACGGTAATTAATGAGA
1 TGTTCCACATGCATGGAACGATAATTAATGAGA
*
38300559 TGTTCCACATGCAATGG-ACGATATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGATAATT-AATGAG
38300592 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGATAATTAATGAGA
Found at i:38303003 original size:11 final size:13
Alignment explanation
Indices: 38302987--38303018 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
38302977 AGCTTCGAAA
38302987 AAAAAAAAG-TT-
1 AAAAAAAAGTTTC
38302998 AAAAAAAAGTTTC
1 AAAAAAAAGTTTC
38303011 AAAAAAAA
1 AAAAAAAA
38303019 AATACGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (13 bp):
AAAAAAAAGTTTC
Found at i:38304879 original size:34 final size:33
Alignment explanation
Indices: 38304815--38304880 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
38304805 TTAAAGATGT
* *
38304815 TGTTCTACATGCATGGAACGGTAATTAATGAGA
1 TGTTCCACATGCATGGAACGATAATTAATGAGA
*
38304848 TGTTCCACATGCAATGG-ACGATATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGATAATT-AATGAG
38304881 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGATAATTAATGAGA
Found at i:38308087 original size:15 final size:15
Alignment explanation
Indices: 38308055--38308088 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38308045 GTTCAACGAA
*
38308055 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
38308070 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
38308085 GAGG
1 GAGG
38308089 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:38312486 original size:30 final size:30
Alignment explanation
Indices: 38312452--38312608 Score: 163
Period size: 30 Copynumber: 5.2 Consensus size: 30
38312442 AGCTCACTCC
38312452 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
38312482 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* *
38312512 CAGCTCAACTTTAGCTCACGAGCTAAACCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * * *
38312542 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
38312572 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
38312602 TAGCTCA
1 TAGCTCA
38312609 TTTTAGTTTA
Statistics
Matches: 99, Mismatches: 27, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
29 1 0.01
30 98 0.99
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:38312517 original size:60 final size:60
Alignment explanation
Indices: 38312464--38312608 Score: 281
Period size: 60 Copynumber: 2.4 Consensus size: 60
38312454 GCTCATATTC
38312464 AGCTCACGAGCTAAACCTTAGCTCAACTTCAGCTTAGGAGTTTAATCTCAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTCAGCTTAGGAGTTTAATCTCAGCTCAACTTT
38312524 AGCTCACGAGCTAAACCTTAGCTCAACTTCAGCTTAGGAGTTTAATCTCAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTCAGCTTAGGAGTTTAATCTCAGCTCAACTTT
*
38312584 AGCTCACGAGCTAAAGCTTAGCTCA
1 AGCTCACGAGCTAAACCTTAGCTCA
38312609 TTTTAGTTTA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 84 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (60 bp):
AGCTCACGAGCTAAACCTTAGCTCAACTTCAGCTTAGGAGTTTAATCTCAGCTCAACTTT
Found at i:38315362 original size:20 final size:20
Alignment explanation
Indices: 38315337--38315390 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
38315327 TGTGGTTCAA
*
38315337 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
38315357 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
38315377 CTCATTCAAGCTCA
1 CTCATTCGAGCTCA
38315391 GTTTAACTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:38315742 original size:45 final size:45
Alignment explanation
Indices: 38315678--38315896 Score: 366
Period size: 45 Copynumber: 4.9 Consensus size: 45
38315668 AAGAGGTGGA
*
38315678 CAACATCATGCATAATTCATGAAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
38315723 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
38315768 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* *
38315813 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* * * *
38315858 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCA
38315897 CCATGGCCGA
Statistics
Matches: 164, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 164 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:38319622 original size:93 final size:93
Alignment explanation
Indices: 38319510--38319681 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
38319500 GCCCATAAGT
*
38319510 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
38319574 ATGAGCTCAGATGCCTAGTTACATCTCTC
65 ACGAGCTCAGATGCCTAGTTACATCTCTC
*
38319603 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
38319668 CGAGTTCGGATGCC
66 CGAGCTCAGATGCC
38319682 CAAATATCCC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCAGATGCCTAGTTACATCTCTC
Found at i:38319672 original size:46 final size:46
Alignment explanation
Indices: 38319502--38319677 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 46
38319492 TGTAACCCGC
*
38319502 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGACGCTCGCAT
* * * * *
38319548 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCAGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACG-CTCGCAT
* *** *
38319594 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
*
38319641 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
38319678 TGCCCAAATA
Statistics
Matches: 106, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
45 1 0.01
46 71 0.67
47 34 0.32
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
Found at i:38322133 original size:15 final size:15
Alignment explanation
Indices: 38322059--38322138 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
38322049 CAAAGATAAC
*
38322059 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
38322073 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* * *
38322088 GAGAAACCCGGAATA
1 AAGAAATCCAGAATA
38322103 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* * *
38322118 AAGAGATGCAGGATA
1 AAGAAATCCAGAATA
38322133 AAGAAA
1 AAGAAA
38322139 CCCAAGATAC
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
14 9 0.17
15 42 0.81
16 1 0.02
ACGTcount: A:0.57, C:0.12, G:0.20, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:38322147 original size:15 final size:15
Alignment explanation
Indices: 38322070--38322147 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
38322060 AGAAAACCGA
38322070 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
38322085 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
38322099 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* * *
38322114 AATAAAGAGATGCAGG
1 -ATAAAGAAATCCAAG
*
38322130 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
38322145 ATA
1 ATA
38322148 CGATACTATG
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
14 3 0.06
15 42 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.14, G:0.19, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:38324611 original size:13 final size:13
Alignment explanation
Indices: 38324593--38324617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38324583 TGGTCATCAT
38324593 GGTGTGAACACAA
1 GGTGTGAACACAA
38324606 GGTGTGAACACA
1 GGTGTGAACACA
38324618 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:38325136 original size:10 final size:10
Alignment explanation
Indices: 38325123--38325160 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
38325113 TTGTAGCTAA
38325123 ATTGAGCTCG
1 ATTGAGCTCG
38325133 ATTGAGCT-G
1 ATTGAGCTCG
38325142 ACTTGAGCTCG
1 A-TTGAGCTCG
*
38325153 AGTGAGCT
1 ATTGAGCT
38325161 GGAAACGAGC
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:38325140 original size:20 final size:20
Alignment explanation
Indices: 38325100--38325160 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
38325090 ACCAATAAAA
38325100 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
38325120 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
38325140 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
38325160 T
1 T
38325161 GGAAACGAGC
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:38325161 original size:20 final size:20
Alignment explanation
Indices: 38325124--38325161 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38325114 TGTAGCTAAA
*
38325124 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
38325144 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
38325162 GAAACGAGCT
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:38327966 original size:15 final size:15
Alignment explanation
Indices: 38327946--38327985 Score: 66
Period size: 13 Copynumber: 2.8 Consensus size: 15
38327936 AAACCGTATG
38327946 CAATTTTTTTTTTTT
1 CAATTTTTTTTTTTT
38327961 CAA--TTTTTTTTTT
1 CAATTTTTTTTTTTT
38327974 CAATTTTTTTTT
1 CAATTTTTTTTT
38327986 CGAACTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.57
15 10 0.43
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (15 bp):
CAATTTTTTTTTTTT
Found at i:38327969 original size:13 final size:13
Alignment explanation
Indices: 38327951--38327999 Score: 73
Period size: 13 Copynumber: 3.7 Consensus size: 13
38327941 GTATGCAATT
38327951 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
38327964 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
38327977 -TTTTTTTTTCGAA
1 TTTTTTTTTTC-AA
38327990 CTTTTTTTTT
1 -TTTTTTTTT
38328000 ACGCACCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.30
13 15 0.45
15 8 0.24
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:38328975 original size:13 final size:13
Alignment explanation
Indices: 38328957--38328981 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38328947 TGGTCATCAT
38328957 GGTGTGAACACAA
1 GGTGTGAACACAA
38328970 GGTGTGAACACA
1 GGTGTGAACACA
38328982 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:38329500 original size:10 final size:10
Alignment explanation
Indices: 38329487--38329524 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
38329477 TTGTAGCTAA
38329487 ATTGAGCTCG
1 ATTGAGCTCG
38329497 ATTGAGCT-G
1 ATTGAGCTCG
38329506 ACTTGAGCTCG
1 A-TTGAGCTCG
*
38329517 AGTGAGCT
1 ATTGAGCT
38329525 GGAAACGAGC
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:38329504 original size:20 final size:20
Alignment explanation
Indices: 38329464--38329524 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
38329454 ACCAATAAAA
38329464 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
38329484 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
38329504 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
38329524 T
1 T
38329525 GGAAACGAGC
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:38329525 original size:20 final size:20
Alignment explanation
Indices: 38329488--38329525 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38329478 TGTAGCTAAA
*
38329488 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
38329508 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
38329526 GAAACGAGCT
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:38329880 original size:20 final size:20
Alignment explanation
Indices: 38329834--38329880 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
38329824 AGCTTGTTTC
*
38329834 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
38329854 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
38329874 CAGCTCA
1 CAGCTCA
38329881 ATCTTAACCC
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:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:38331608 original size:15 final size:14
Alignment explanation
Indices: 38331580--38331607 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38331570 TCGAAACGTG
38331580 AAAAAAAAAATTTT
1 AAAAAAAAAATTTT
38331594 AAAAAAAAAATTTT
1 AAAAAAAAAATTTT
38331608 TGTTGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAAAAAAAATTTT
Found at i:38331694 original size:16 final size:17
Alignment explanation
Indices: 38331673--38331714 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
38331663 CAAAAAAAAT
38331673 AAAAAAAAAAT-TCGAA
1 AAAAAAAAAATATCGAA
38331689 AAAAAAAAAATGATCGAA
1 AAAAAAAAAAT-ATCGAA
38331707 AAAAAAAA
1 AAAAAAAA
38331715 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
18 13 0.54
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.10
Consensus pattern (17 bp):
AAAAAAAAAATATCGAA
Found at i:38331695 original size:19 final size:18
Alignment explanation
Indices: 38331667--38331714 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
38331657 GAGTAACAAA
38331667 AAAAATAAAAAAAAAATTCG
1 AAAAA-AAAAAAAAAA-TCG
**
38331687 AAAAAAAAAAAATGATCG
1 AAAAAAAAAAAAAAATCG
38331705 AAAAAAAAAA
1 AAAAAAAAAA
38331715 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 13 0.50
19 8 0.31
20 5 0.19
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.10
Consensus pattern (18 bp):
AAAAAAAAAAAAAAATCG
Found at i:38331751 original size:17 final size:18
Alignment explanation
Indices: 38331729--38331768 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
38331719 AAAAAAAGTG
*
38331729 AAAAAAAA-CTGAGCAAA
1 AAAAAAAAGCTGACCAAA
*
38331746 AAAAAAAAGGTGACCAAA
1 AAAAAAAAGCTGACCAAA
38331764 AAAAA
1 AAAAA
38331769 TCAAGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.72, C:0.10, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAAAAAAGCTGACCAAA
Found at i:38332731 original size:15 final size:16
Alignment explanation
Indices: 38332711--38332742 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
38332701 AGAAAATGAA
38332711 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
38332726 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
38332742 A
1 A
38332743 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:38332857 original size:17 final size:18
Alignment explanation
Indices: 38332825--38332858 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38332815 AAAAGAGAGT
*
38332825 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
38332843 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
38332859 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:38334147 original size:20 final size:20
Alignment explanation
Indices: 38334124--38334177 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
38334114 AGTTTTTCCC
*
38334124 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
38334144 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
38334164 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
38334178 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:38334159 original size:30 final size:30
Alignment explanation
Indices: 38334124--38334197 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
38334114 AGTTTTTCCC
38334124 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
38334154 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
38334184 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
38334198 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:38334187 original size:20 final size:20
Alignment explanation
Indices: 38334124--38334188 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
38334114 AGTTTTTCCC
* * * *
38334124 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
38334144 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
38334163 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
38334184 AGCTC
1 AGCTC
38334189 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:38337343 original size:48 final size:47
Alignment explanation
Indices: 38337264--38337369 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 47
38337254 GAGTGTCATG
* *
38337264 GAAAAAGAAATTGAGATTGATAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGACAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
38337312 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTG-ACAAAAGATGTGA-GAAAAAGAAAAAATC
38337360 GAAAAAGAAA
1 GAAAAAGAAA
38337370 GAAAAGACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
48 38 0.75
49 9 0.18
50 4 0.08
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGACAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:38340706 original size:20 final size:20
Alignment explanation
Indices: 38340660--38340706 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
38340650 AGCTCGTTTC
*
38340660 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
38340680 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
38340700 CAGCTCA
1 CAGCTCA
38340707 ATCTTAACCC
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:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:38343456 original size:93 final size:93
Alignment explanation
Indices: 38343348--38343519 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 93
38343338 GCCCATAAGT
* * * *
38343348 AAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTTAGACTCAACTCAA
1 AAACTCAGACTCAACTCAACGAGCTCGGACGCTCACATCCATAAGTGAACTCAGACTCAACTCAA
*
38343413 TGAGCTT-GGATGCCTAGTTACATCTCTC
66 CGAG-TTCGGATGCCTAGTTACATCTCTC
* * *
38343441 AAACTCAGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 AAACTCAGACTCAACTCAACGAGCTCGGACGCTCACATCCATAAGTGAACTCAGACTCAACTCAA
38343506 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
38343520 CAAATATCCC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
92 2 0.03
93 68 0.97
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
AAACTCAGACTCAACTCAACGAGCTCGGACGCTCACATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCTC
Found at i:38343515 original size:46 final size:46
Alignment explanation
Indices: 38343340--38343515 Score: 158
Period size: 46 Copynumber: 3.8 Consensus size: 46
38343330 TGTAACCCGC
* * * * *
38343340 CCATAAGTAAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGTAAACTCAGACTCAACTCAACGAGTTCGGACGCTCGCAT
* * * * * *
38343386 CCATAAGTGAACTTAGACTCAACTCAATGAGCTT-GGATGCCTAG-TT
1 CCATAAGTAAACTCAGACTCAACTCAACGAG-TTCGGACG-CTCGCAT
* ***
38343432 ACATCTCTCAAACTCAGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGT-AAACTCAGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
38343479 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTAAACTCAGACTCAACTCAACGAGTTCGGA
38343516 TGCCCAAATA
Statistics
Matches: 98, Mismatches: 27, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
46 67 0.68
47 31 0.32
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTAAACTCAGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:38350910 original size:13 final size:13
Alignment explanation
Indices: 38350892--38350916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38350882 GTATTGATCA
38350892 TGTGTTCACACCT
1 TGTGTTCACACCT
38350905 TGTGTTCACACC
1 TGTGTTCACACC
38350917 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:38352234 original size:30 final size:29
Alignment explanation
Indices: 38352200--38352263 Score: 119
Period size: 30 Copynumber: 2.2 Consensus size: 29
38352190 ATGAATCAGA
38352200 AGCTTTGGCACTAAGTGTGCGATTTAAACT
1 AGCTTTGGCACTAAGTGTGCGATTT-AACT
38352230 AGCTTTGGCACTAAGTGTGCGATTTAACT
1 AGCTTTGGCACTAAGTGTGCGATTTAACT
38352259 AGCTT
1 AGCTT
38352264 CGGCTACTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (29 bp):
AGCTTTGGCACTAAGTGTGCGATTTAACT
Found at i:38353752 original size:27 final size:27
Alignment explanation
Indices: 38353714--38353960 Score: 121
Period size: 27 Copynumber: 9.1 Consensus size: 27
38353704 CAAAACAGTT
* * * *
38353714 ATTTTACCCTACAGGGGTATGTCGGTC
1 ATTTTACACTACAAGGGTATTTCGGTA
**
38353741 ATTTTACACTACAAGGGTATTTAAGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
*
38353768 ATTTTACACTATAAGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGGTA
* * * *
38353795 ATTTTACA-AATCAGGGGTGTTTCAGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * * *
38353822 ATTTTACA-AATCGAGGGTGTTTCAGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * * *
38353849 ATTTTACA-AATCGA-GGTCGTTTCGATA
1 ATTTTACACTA-CAAGGGT-ATTTCGGTA
* * * *
38353876 ATTTCACA-AATCGAGGGTATTTTGGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* **
38353903 ATTTTACAC-ATCGAGGGTATTTCATTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
* * *
38353930 ATTTTACA-AATCGAGGGTGTTTCGGTA
1 ATTTTACACTA-CAAGGGTATTTCGGTA
38353957 ATTT
1 ATTT
38353961 CTCTTTACTA
Statistics
Matches: 186, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
26 4 0.02
27 179 0.96
28 3 0.02
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGGTA
Found at i:38353772 original size:54 final size:54
Alignment explanation
Indices: 38353714--38353860 Score: 136
Period size: 54 Copynumber: 2.7 Consensus size: 54
38353704 CAAAACAGTT
* * * *
38353714 ATTTTACCCTACAGGGGTATGTCGGTCATTTTAC-ACTACAAGGGTATTTAAGTA
1 ATTTTACACTACAAGGGTATGTCGGTAATTTTACAAAT-CAAGGGTATTTAAGTA
* * * * *
38353768 ATTTTACACTATAAGGGTATTTCGGTAATTTTACAAATCAGGGGTGTTTCAGTA
1 ATTTTACACTACAAGGGTATGTCGGTAATTTTACAAATCAAGGGTATTTAAGTA
* * * * *
38353822 ATTTTACA-AATCGAGGGTGTTTCAGTAATTTTACAAATC
1 ATTTTACACTA-CAAGGGTATGTCGGTAATTTTACAAATC
38353861 GAGGTCGTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 74 0.96
55 2 0.03
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (54 bp):
ATTTTACACTACAAGGGTATGTCGGTAATTTTACAAATCAAGGGTATTTAAGTA
Found at i:38353839 original size:81 final size:79
Alignment explanation
Indices: 38353754--38353961 Score: 238
Period size: 81 Copynumber: 2.6 Consensus size: 79
38353744 TTACACTACA
* * * * *
38353754 AGGGTATTTAAGTAATTTTACACTATAAGGGTATTTCGGTAATTTTACAAATC-AGGGGTGTTTC
1 AGGGTATTTCAGTAATTTTACA-AAT-AGGGTGTTTCGGTAATTTCACAAATCGA-GGGTATTTC
38353818 AGTAATTTTACAAATCG
63 AGTAATTTTACAAATCG
* * * **
38353835 AGGGTGTTTCAGTAATTTTACAAATCGAGGTCGTTTCGATAATTTCACAAATCGAGGGTATTTTG
1 AGGGTATTTCAGTAATTTTACAAATAG-GGT-GTTTCGGTAATTTCACAAATCGAGGGTATTTCA
*
38353900 GTAATTTTACACATCG
64 GTAATTTTACAAATCG
*
38353916 AGGGTATTTCATTAATTTTACAAATCGAGGGTGTTTCGGTAATTTC
1 AGGGTATTTCAGTAATTTTACAAAT--AGGGTGTTTCGGTAATTTC
38353962 TCTTTACTAT
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
79 1 0.01
80 5 0.05
81 96 0.90
82 4 0.04
83 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (79 bp):
AGGGTATTTCAGTAATTTTACAAATAGGGTGTTTCGGTAATTTCACAAATCGAGGGTATTTCAGT
AATTTTACAAATCG
Found at i:38353871 original size:54 final size:53
Alignment explanation
Indices: 38353764--38353960 Score: 236
Period size: 54 Copynumber: 3.7 Consensus size: 53
38353754 AGGGTATTTA
* * *
38353764 AGTAATTTTACACTAT-AAGGGTATTTCGGTAATTTTACAAATCAGGGGTGTTTC
1 AGTAATTTTACA-AATCGAGGGTATTTCGGTAATTTTACAAATC-GAGGTGTTTC
* *
38353818 AGTAATTTTACAAATCGAGGGTGTTTCAGTAATTTTACAAATCGAGGTCGTTTC
1 AGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCGAGGT-GTTTC
* * * *
38353872 -GATAATTTCACAAATCGAGGGTATTTTGGTAATTTTACACATCGAGGGTATTTC
1 AG-TAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCGA-GGTGTTTC
* *
38353926 ATTAATTTTACAAATCGAGGGTGTTTCGGTAATTT
1 AGTAATTTTACAAATCGAGGGTATTTCGGTAATTT
38353961 CTCTTTACTA
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
53 7 0.06
54 113 0.92
55 3 0.02
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (53 bp):
AGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAATCGAGGTGTTTC
Found at i:38356771 original size:30 final size:30
Alignment explanation
Indices: 38356749--38356833 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
38356739 GCTCATATTC
38356749 AGCTCACGAGCTAAACCTTAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
* * * * * *
38356779 AGCTTAGGAGTTTAGCCTCAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
*
38356809 AGCTCACGAGCTAAAGCTTAGCTCA
1 AGCTCACGAGCTAAACCTTAGCTCA
38356834 TTTTTAGTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (30 bp):
AGCTCACGAGCTAAACCTTAGCTCAACTTT
Found at i:38358254 original size:21 final size:21
Alignment explanation
Indices: 38358228--38358290 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38358218 TTGGTATTTG
38358228 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
38358249 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
38358270 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
38358291 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Done.