Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 1 of 255
Found at i:2710 original size:14 final size:14
Alignment explanation
Indices: 2691--2724 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2681 ATTTCATTTT
**
2691 ATATTAATTGTATA
1 ATATTAATTAAATA
2705 ATATTAATTAAATA
1 ATATTAATTAAATA
2719 ATATTA
1 ATATTA
2725 TAATTGCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
ATATTAATTAAATA
Found at i:4814 original size:21 final size:21
Alignment explanation
Indices: 4782--4822 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4772 TCCTGCAGCA
4782 TAAAAAATCTGAACCGGACAC
1 TAAAAAATCTGAACCGGACAC
4803 TAAAAGAA-CTGAACCGGACA
1 TAAAA-AATCTGAACCGGACA
4823 GGGGAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (21 bp):
TAAAAAATCTGAACCGGACAC
Found at i:5753 original size:40 final size:40
Alignment explanation
Indices: 5698--5781 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
5688 CTACGTGCGT
5698 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
5738 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
5778 CACA
1 CACA
5782 GATGCAGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (40 bp):
CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
Found at i:7091 original size:15 final size:15
Alignment explanation
Indices: 7068--7103 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
7058 CTTTTATTCC
*
7068 TTTCCTTACACTGTA
1 TTTCTTTACACTGTA
7083 TTTCTTTACACTGTA
1 TTTCTTTACACTGTA
7098 TTTCTT
1 TTTCTT
7104 CCTCCTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.06, T:0.56
Consensus pattern (15 bp):
TTTCTTTACACTGTA
Found at i:10215 original size:22 final size:23
Alignment explanation
Indices: 10189--10231 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
10179 ATTTAGAATT
*
10189 TAAAC-TAAAATGATAAATTTTG
1 TAAACATAAAAGGATAAATTTTG
*
10211 TAAACATTAAAGGATAAATTT
1 TAAACATAAAAGGATAAATTT
10232 GTTGAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (23 bp):
TAAACATAAAAGGATAAATTTTG
Found at i:10730 original size:35 final size:35
Alignment explanation
Indices: 10681--10820 Score: 235
Period size: 35 Copynumber: 4.0 Consensus size: 35
10671 ACTCAACCTT
**
10681 TGCAATCGACAGTCAGTCGCGCGGCTCGCAAGCAG
1 TGCAATCGGTAGTCAGTCGCGCGGCTCGCAAGCAG
10716 TGCAATCGGTAGTCAGTCGCGCGGCTCGCAAGCAG
1 TGCAATCGGTAGTCAGTCGCGCGGCTCGCAAGCAG
*
10751 TGCAATCGGTAGTCAGTCGCGCGGATCGCAAGCAG
1 TGCAATCGGTAGTCAGTCGCGCGGCTCGCAAGCAG
* *
10786 TGCAATCGGTAGTCAGTTGCGCAGCTCGCAAGCAG
1 TGCAATCGGTAGTCAGTCGCGCGGCTCGCAAGCAG
10821 CAAGCTCGTC
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 99 1.00
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.17
Consensus pattern (35 bp):
TGCAATCGGTAGTCAGTCGCGCGGCTCGCAAGCAG
Found at i:17409 original size:4 final size:4
Alignment explanation
Indices: 17400--17459 Score: 120
Period size: 4 Copynumber: 15.0 Consensus size: 4
17390 ATCTCCCTCA
17400 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
17448 GTAT GTAT GTAT
1 GTAT GTAT GTAT
17460 AACTGGATTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:20477 original size:35 final size:35
Alignment explanation
Indices: 20431--20535 Score: 165
Period size: 35 Copynumber: 3.0 Consensus size: 35
20421 GACGAGCTTG
* *
20431 CTGCTTGCGAGCTGCGCAACTGACTATCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
*
20466 CTGCTTGCGAGCCGCGCGACTGACTACCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
* *
20501 CTGCTTGCGAGTTGCGCGACTGACTGCCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
20536 AGGGTTGAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (35 bp):
CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
Found at i:20534 original size:19 final size:19
Alignment explanation
Indices: 20479--20534 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
20469 CTTGCGAGCC
*
20479 GCGCGACTGACTACCGATT
1 GCGCGACTGACTGCCGATT
20498 --GC-ACTG-CTTG-CGAGTT
1 GCGCGACTGAC-TGCCGA-TT
20514 GCGCGACTGACTGCCGATT
1 GCGCGACTGACTGCCGATT
20533 GC
1 GC
20535 AAGGGTTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
15 4 0.14
16 7 0.24
17 2 0.07
18 2 0.07
19 10 0.34
20 4 0.14
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (19 bp):
GCGCGACTGACTGCCGATT
Found at i:20553 original size:33 final size:34
Alignment explanation
Indices: 20449--20553 Score: 86
Period size: 35 Copynumber: 3.1 Consensus size: 34
20439 GAGCTGCGCA
* ** ** *
20449 ACTGACTATCGATTGCACTGCTTGCGAGCCGCGCG
1 ACTGACTACCGATTGCAAGGCTT-CGAGTTGAGCG
** *
20484 ACTGACTACCGATTGCACTGCTTGCGAGTTGCGCG
1 ACTGACTACCGATTGCAAGGCTT-CGAGTTGAGCG
* *
20519 ACTGACTGCCGATTGCAAGGGTT-GAGTTGAGCG
1 ACTGACTACCGATTGCAAGGCTTCGAGTTGAGCG
20552 AC
1 AC
20554 GGAAAGAGGC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 11 0.18
35 51 0.82
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.24
Consensus pattern (34 bp):
ACTGACTACCGATTGCAAGGCTTCGAGTTGAGCG
Found at i:22603 original size:39 final size:39
Alignment explanation
Indices: 22523--22605 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
22513 GAGATTGACG
* **
22523 GGTGAACCGATGGTGACTACCTGACTGATGAACGATGAT
1 GGTGGACCGATGGTGACTACCTGACTGATGAACGACAAT
* * *
22562 GGTGGACCGGTGGTGACTGCCTGACTCG-TGAACGGCAAT
1 GGTGGACCGATGGTGACTACCTGACT-GATGAACGACAAT
22601 GGTGG
1 GGTGG
22606 TGGCCGTAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 36 0.97
40 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (39 bp):
GGTGGACCGATGGTGACTACCTGACTGATGAACGACAAT
Found at i:23900 original size:19 final size:19
Alignment explanation
Indices: 23872--23911 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
23862 AGGCTGAAGA
23872 AAACGAACAGCTTTCTCCT
1 AAACGAACAGCTTTCTCCT
*
23891 AAACGGACAGCTTTCTCCT
1 AAACGAACAGCTTTCTCCT
23910 AA
1 AA
23912 GAGATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (19 bp):
AAACGAACAGCTTTCTCCT
Found at i:42399 original size:7 final size:8
Alignment explanation
Indices: 42387--42436 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 8
42377 TTTCTTCCAC
42387 TATTAT-T
1 TATTATAT
42394 TATTATACT
1 TATTATA-T
42403 TATTATAT
1 TATTATAT
42411 CATATTAT-T
1 --TATTATAT
42420 TATTATACT
1 TATTATA-T
42429 TATTATAT
1 TATTATAT
42437 CATTTTCGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
7 12 0.32
8 2 0.05
9 17 0.46
10 6 0.16
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:42407 original size:9 final size:9
Alignment explanation
Indices: 42393--42435 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
42383 CCACTATTAT
42393 TTATTATAC
1 TTATTATAC
42402 TTATTATATC
1 TTATTATA-C
*
42412 ATATTAT--
1 TTATTATAC
42419 TTATTATAC
1 TTATTATAC
42428 TTATTATA
1 TTATTATA
42436 TCATTTTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 6 0.21
9 16 0.55
10 7 0.24
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATTATAC
Found at i:42418 original size:26 final size:26
Alignment explanation
Indices: 42387--42439 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
42377 TTTCTTCCAC
42387 TATTATTTATTATACTTATTATATCA
1 TATTATTTATTATACTTATTATATCA
42413 TATTATTTATTATACTTATTATATCA
1 TATTATTTATTATACTTATTATATCA
42439 T
1 T
42440 TTTCGTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTATTTATTATACTTATTATATCA
Found at i:42448 original size:26 final size:26
Alignment explanation
Indices: 42387--42449 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
42377 TTTCTTCCAC
*
42387 TATTATTTATTATACTTATTATATCA
1 TATTAGTTATTATACTTATTATATCA
*
42413 TATTATTTATTATACTTATTATATCA
1 TATTAGTTATTATACTTATTATATCA
* *
42439 TTTTCGTTATT
1 TATTAGTTATT
42450 TTTATCTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTAGTTATTATACTTATTATATCA
Found at i:42676 original size:22 final size:22
Alignment explanation
Indices: 42651--42703 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
42641 TTTTATTTCC
*
42651 TTTTATATATATTTTATAATAA
1 TTTTATATATAGTTTATAATAA
* * *
42673 TTTTAAATATAGTTTATTATAC
1 TTTTATATATAGTTTATAATAA
42695 TTATTATAT
1 TT-TTATAT
42704 TTTATTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTATATATAGTTTATAATAA
Found at i:42712 original size:14 final size:14
Alignment explanation
Indices: 42695--42727 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
42685 TTTATTATAC
42695 TTATTATATTTTAT
1 TTATTATATTTTAT
42709 TTATTATATTTTAT
1 TTATTATATTTTAT
42723 TTATT
1 TTATT
42728 TTTTCCTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTATATTTTAT
Found at i:42712 original size:23 final size:23
Alignment explanation
Indices: 42685--42729 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42675 TTAAATATAG
42685 TTTATTATA-CTTATTATATTTTA
1 TTTATTATATCTTATT-TATTTTA
*
42708 TTTATTATATTTTATTTATTTT
1 TTTATTATATCTTATTTATTTT
42730 TTCCTACCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTATTATATCTTATTTATTTTA
Found at i:42731 original size:11 final size:10
Alignment explanation
Indices: 42651--42724 Score: 53
Period size: 9 Copynumber: 7.3 Consensus size: 10
42641 TTTTATTTCC
42651 TTTTATATATA
1 TTTTAT-TATA
*
42662 TTTTATAATAA
1 TTTTATTAT-A
*
42673 TTTTAAATATA
1 TTTT-ATTATA
*
42684 GTTTATTATA
1 TTTTATTATA
*
42694 -CTTATTATA
1 TTTTATTATA
42703 TTTTATT-TA
1 TTTTATTATA
* *
42712 TTATATTTTA
1 TTTTATTATA
42722 TTT
1 TTT
42725 ATTTTTTCCT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
9 16 0.32
10 16 0.32
11 15 0.30
12 3 0.06
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATTATA
Found at i:50528 original size:15 final size:15
Alignment explanation
Indices: 50508--50539 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
50498 TAAATGCAAT
50508 ATTCTTTTATTTTAC
1 ATTCTTTTATTTTAC
50523 ATTCTTTTATTTTAC
1 ATTCTTTTATTTTAC
50538 AT
1 AT
50540 GCCTGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTCTTTTATTTTAC
Found at i:53336 original size:45 final size:45
Alignment explanation
Indices: 53151--53492 Score: 163
Period size: 45 Copynumber: 7.6 Consensus size: 45
53141 TATCATCAGC
53151 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA-A-ACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGAT
* * * * * *** **
53194 CTTATCTTCACTGTGTAGGAGTGAAGCAGATCGAATTTTGATGA-AT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAG-GCTAAACAT-ACCAGAT
* * * * * * *
53240 CTTATCTCCAC-GTACCGACGA-TGGAGCAGATTCCAATCAT--CAG-C
1 CTTATCTTCACTG-AGC-AGGAGTGGAGCAG--GCTAAACATACCAGAT
53284 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGAT
* * ** **
53329 CTTATCTTCACTGAGCAGGAGTGAAGCA-GATCAAATTTTGGCA-AGT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAA-CATACCAGA-T
* * * * ** * * * *
53375 CTTATCTCCA-TGTATC-GGCAATAGAGCAGATTTCAGC-CACCAG-C
1 CTTATCTTCACTG-AGCAGG-AGTGGAGCAG-GCTAAACATACCAGAT
*
53419 CTTATCTTCACTGAGCAGGAGTGGAACAGGCTAAACATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGAT
*
53464 CTTATCTTCACTGAGCAGGAGTGAAGCAG
1 CTTATCTTCACTGAGCAGGAGTGGAGCAG
53493 ATCAAATTTT
Statistics
Matches: 213, Mismatches: 61, Indels: 48
0.66 0.19 0.15
Matches are distributed among these distances:
42 6 0.03
43 32 0.15
44 52 0.24
45 70 0.33
46 40 0.19
47 12 0.06
48 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (45 bp):
CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGAT
Found at i:53382 original size:135 final size:135
Alignment explanation
Indices: 53147--53634 Score: 736
Period size: 135 Copynumber: 3.6 Consensus size: 135
53137 CAGATATCAT
* *
53147 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA-A-ACCAGATCTTATCTTCACTGTGT
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
* * * * * *
53210 AGGAGTGAAGCAGATCGAATTTTGATG-AA-TCTTATCTCCACGTACCGACGATGGAGCAGATTC
66 AGGAGTGAAGCAGATCAAATTTTG--GCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTT
* *
53273 CAATCAT
129 CAACCAC
53280 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
*
53345 AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATAGAGCAGATTTCA
66 AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCA
*
53410 GCCAC
131 ACCAC
*
53415 CAGCCTTATCTTCACTGAGCAGGAGTGGAACAGGCTAAACATACCAGATCTTATCTTCACTGAGC
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
*
53480 AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTTA
66 AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCA
*
53545 GCCAC
131 ACCAC
* * **
53550 CAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAACATA-CAGATCTTATCTTCGCTGATT
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
53614 AGGAGT-AGAGCAGATCAAATT
66 AGGAGTGA-AGCAGATCAAATT
53635 ACAGCAGACC
Statistics
Matches: 330, Mismatches: 20, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
133 41 0.12
134 40 0.12
135 249 0.75
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (135 bp):
CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTCA
ACCAC
Found at i:54972 original size:7 final size:8
Alignment explanation
Indices: 54960--55009 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 8
54950 TTTCTTCCAC
54960 TATTAT-T
1 TATTATAT
54967 TATTATACT
1 TATTATA-T
54976 TATTATAT
1 TATTATAT
54984 CATATTAT-T
1 --TATTATAT
54993 TATTATACT
1 TATTATA-T
55002 TATTATAT
1 TATTATAT
55010 CATTTTCGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
7 12 0.32
8 2 0.05
9 17 0.46
10 6 0.16
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:54980 original size:9 final size:9
Alignment explanation
Indices: 54966--55008 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
54956 CCACTATTAT
54966 TTATTATAC
1 TTATTATAC
54975 TTATTATATC
1 TTATTATA-C
*
54985 ATATTAT--
1 TTATTATAC
54992 TTATTATAC
1 TTATTATAC
55001 TTATTATA
1 TTATTATA
55009 TCATTTTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 6 0.21
9 16 0.55
10 7 0.24
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATTATAC
Found at i:54991 original size:26 final size:26
Alignment explanation
Indices: 54960--55012 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
54950 TTTCTTCCAC
54960 TATTATTTATTATACTTATTATATCA
1 TATTATTTATTATACTTATTATATCA
54986 TATTATTTATTATACTTATTATATCA
1 TATTATTTATTATACTTATTATATCA
55012 T
1 T
55013 TTTCGTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTATTTATTATACTTATTATATCA
Found at i:55021 original size:26 final size:26
Alignment explanation
Indices: 54960--55022 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
54950 TTTCTTCCAC
*
54960 TATTATTTATTATACTTATTATATCA
1 TATTAGTTATTATACTTATTATATCA
*
54986 TATTATTTATTATACTTATTATATCA
1 TATTAGTTATTATACTTATTATATCA
* *
55012 TTTTCGTTATT
1 TATTAGTTATT
55023 TTTATCTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTAGTTATTATACTTATTATATCA
Found at i:55249 original size:22 final size:22
Alignment explanation
Indices: 55224--55276 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
55214 TTTTATTTCC
*
55224 TTTTATATATATTTTATAATAA
1 TTTTATATATAGTTTATAATAA
* * *
55246 TTTTAAATATAGTTTATTATAC
1 TTTTATATATAGTTTATAATAA
55268 TTATTATAT
1 TT-TTATAT
55277 TTTATTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTATATATAGTTTATAATAA
Found at i:55286 original size:9 final size:10
Alignment explanation
Indices: 55224--55288 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
55214 TTTTATTTCC
55224 TTTTATATATA
1 TTTTAT-TATA
*
55235 TTTTATAATAA
1 TTTTATTAT-A
*
55246 TTTTAAATATA
1 TTTT-ATTATA
*
55257 GTTTATTATA
1 TTTTATTATA
*
55267 -CTTATTATA
1 TTTTATTATA
55276 TTTTATT-TA
1 TTTTATTATA
55285 TTTT
1 TTTT
55289 TTCCTACCGT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
9 14 0.32
10 12 0.27
11 15 0.34
12 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTATTATA
Found at i:56257 original size:17 final size:18
Alignment explanation
Indices: 56235--56272 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
56225 TTTCATGAAT
56235 TAATAATAAT-TAAAAAA
1 TAATAATAATATAAAAAA
*
56252 TAATAATGATATAAAAAA
1 TAATAATAATATAAAAAA
56270 TAA
1 TAA
56273 AAAAATGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
TAATAATAATATAAAAAA
Found at i:56854 original size:21 final size:19
Alignment explanation
Indices: 56829--56872 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
56819 TTATGTTATA
56829 AAAATAAAAAAAATTATATTT
1 AAAATAAAAAAAA-TA-ATTT
**
56850 AAAATAGTAAAAATAATTT
1 AAAATAAAAAAAATAATTT
56869 AAAA
1 AAAA
56873 GTTCTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATAAAAAAAATAATTT
Found at i:59908 original size:25 final size:25
Alignment explanation
Indices: 59875--59925 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
59865 TGTTTCCACC
59875 AATAATTTCCT-ATAAAGTTATTCAT
1 AATAATTT-CTAATAAAGTTATTCAT
* **
59900 AATAGTTTCTAATAATTTTATTCAT
1 AATAATTTCTAATAAAGTTATTCAT
59925 A
1 A
59926 TAACTCAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (25 bp):
AATAATTTCTAATAAAGTTATTCAT
Found at i:61594 original size:7 final size:7
Alignment explanation
Indices: 61578--61616 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
61568 ATTTTTTTAC
61578 TTTCTAAA
1 TTTC-AAA
*
61586 TTTTAAA
1 TTTCAAA
61593 TTTCAAA
1 TTTCAAA
61600 TTTCAAA
1 TTTCAAA
61607 TTTCAAA
1 TTTCAAA
61614 TTT
1 TTT
61617 AACCATCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 26 0.90
8 3 0.10
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (7 bp):
TTTCAAA
Found at i:62185 original size:16 final size:16
Alignment explanation
Indices: 62164--62196 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
62154 AAAATAGAGA
62164 ATAATTTTATATTAAG
1 ATAATTTTATATTAAG
62180 ATAATTTTATATTAAG
1 ATAATTTTATATTAAG
62196 A
1 A
62197 ATATATAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
ATAATTTTATATTAAG
Found at i:62800 original size:17 final size:16
Alignment explanation
Indices: 62769--62802 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
62759 ATTTATTCTC
*
62769 TTAAAAATAATATATA
1 TTAAAAATAAAATATA
62785 TTAAATAATAAAATATA
1 TTAAA-AATAAAATATA
62802 T
1 T
62803 GATTTGAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAAATAAAATATA
Found at i:63871 original size:28 final size:28
Alignment explanation
Indices: 63831--63886 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
63821 ATTTTTGGAA
63831 GTTAAAATATCTATTTTAGATATGATGT
1 GTTAAAATATCTATTTTAGATATGATGT
63859 GTTAAAATATCTATTTTAGATATGATGT
1 GTTAAAATATCTATTTTAGATATGATGT
63887 TGCAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (28 bp):
GTTAAAATATCTATTTTAGATATGATGT
Found at i:63893 original size:28 final size:28
Alignment explanation
Indices: 63834--63895 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
63824 TTTGGAAGTT
*
63834 AAAATATCTATTTTAGATATGATGTGTT
1 AAAATATCTATTTTAGATATGATGTGTC
63862 AAAATATCTATTTTAGATATGATGT-TGC
1 AAAATATCTATTTTAGATATGATGTGT-C
63890 AAAATA
1 AAAATA
63896 AAAGATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (28 bp):
AAAATATCTATTTTAGATATGATGTGTC
Found at i:71101 original size:5 final size:6
Alignment explanation
Indices: 71079--71108 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
71069 AGGTTCCGTT
71079 TTTTGTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTT-TA TTTTTA TTTTTA TTTTTA TTTTT
71109 GAGATAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:73275 original size:22 final size:20
Alignment explanation
Indices: 73256--73294 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
73246 TGGTAAAATT
*
73256 GTTATTCTCAGAAAATAAAA
1 GTTATACTCAGAAAATAAAA
*
73276 GTTATACTTAGAAAATAAA
1 GTTATACTCAGAAAATAAA
73295 TTCTCATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (20 bp):
GTTATACTCAGAAAATAAAA
Found at i:84638 original size:21 final size:21
Alignment explanation
Indices: 84614--84673 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
84604 ACAAACTGTG
*
84614 GCTAAGGTCGCGACATTAGAA
1 GCTAAGGTCGCAACATTAGAA
* * *
84635 GCTAGGAGTCACAACATTGGAA
1 GCTAAG-GTCGCAACATTAGAA
* *
84657 GCTAAAGTCGCAGCATT
1 GCTAAGGTCGCAACATT
84674 CAACACTTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (21 bp):
GCTAAGGTCGCAACATTAGAA
Found at i:88932 original size:33 final size:34
Alignment explanation
Indices: 88890--88959 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
88880 CTTCTTTGAC
*
88890 TATTTATCACTA-TTTTTATTTAATATATTTGGG
1 TATTTATCACTATTTTTTAGTTAATATATTTGGG
88923 TATTTATCACTATTTTTTAGTTAATATATTTGGG
1 TATTTATCACTATTTTTTAGTTAATATATTTGGG
88957 TAT
1 TAT
88960 ACTAGTATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 12 0.34
34 23 0.66
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.57
Consensus pattern (34 bp):
TATTTATCACTATTTTTTAGTTAATATATTTGGG
Found at i:91255 original size:35 final size:35
Alignment explanation
Indices: 91215--91285 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
91205 TATGAGAAAG
*
91215 AACTTTAACAAGAAAAATATAAATCCTTCTATGAC
1 AACTTTAACAAGAAAAAGATAAATCCTTCTATGAC
91250 AACTTTAACAAGAAAAAGATAAATCCTTCTATGAC
1 AACTTTAACAAGAAAAAGATAAATCCTTCTATGAC
91285 A
1 A
91286 TCACAGGTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (35 bp):
AACTTTAACAAGAAAAAGATAAATCCTTCTATGAC
Found at i:96643 original size:39 final size:39
Alignment explanation
Indices: 96554--96659 Score: 113
Period size: 39 Copynumber: 2.7 Consensus size: 39
96544 TGAGATACTG
* * * *
96554 ATTCTATTGGAAGTATGCTCAATCTAACCATACCCACTG
1 ATTCTATTGAAAGTATGCTCAATCGAGCCATACCCACTA
* * * *
96593 GTTTTATTGAAAGTATGCTCAATCGAGTCATACCCATTA
1 ATTCTATTGAAAGTATGCTCAATCGAGCCATACCCACTA
* * *
96632 ATTCTACTGAAAGTATACTCAAACGAGC
1 ATTCTATTGAAAGTATGCTCAATCGAGC
96660 AATATCTATT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (39 bp):
ATTCTATTGAAAGTATGCTCAATCGAGCCATACCCACTA
Found at i:97051 original size:2 final size:2
Alignment explanation
Indices: 97044--97107 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
97034 TGTGGTATCT
97044 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
97086 TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC
97108 AAGTGCCTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:106270 original size:21 final size:21
Alignment explanation
Indices: 106244--106284 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
106234 ATCTGCTCAA
* *
106244 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
106265 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
106285 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:107130 original size:20 final size:20
Alignment explanation
Indices: 107107--107148 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
107097 TGCACCTTTC
107107 AACAATCCTTGCTTTGCCAG
1 AACAATCCTTGCTTTGCCAG
107127 AACAATCCTTGCTTTGCCAG
1 AACAATCCTTGCTTTGCCAG
107147 AA
1 AA
107149 TTTGCAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (20 bp):
AACAATCCTTGCTTTGCCAG
Found at i:126521 original size:4 final size:4
Alignment explanation
Indices: 126512--126542 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
126502 TCTAAATTTC
126512 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
126543 TTTGCTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:129701 original size:38 final size:38
Alignment explanation
Indices: 129650--129730 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
129640 CTTTACATTC
* * *
129650 TTTCATTAGGGACCCTATACTTCCTATTTGTAACATAA
1 TTTCATTAAGGACCCTATACTTCCTATCTATAACATAA
129688 TTTCATTAAGGACCCTATACTTCCTATCTATAACATAA
1 TTTCATTAAGGACCCTATACTTCCTATCTATAACATAA
129726 TTTCA
1 TTTCA
129731 CAATAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (38 bp):
TTTCATTAAGGACCCTATACTTCCTATCTATAACATAA
Found at i:130553 original size:20 final size:19
Alignment explanation
Indices: 130528--130565 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
130518 AGAAATCACA
130528 ATTCTTAGAAAATAGAATTT
1 ATTCTTAGAAAATA-AATTT
130548 ATTCTTAGAAAATAAATT
1 ATTCTTAGAAAATAAATT
130566 ATCACTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (19 bp):
ATTCTTAGAAAATAAATTT
Found at i:130959 original size:16 final size:18
Alignment explanation
Indices: 130935--130968 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
130925 TTAAATTAAA
130935 TTAATTAATTTCC-CAAT
1 TTAATTAATTTCCTCAAT
130952 TTAA-TAATTTCCTCAAT
1 TTAATTAATTTCCTCAAT
130969 CCAATTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAATTTCCTCAAT
Found at i:132364 original size:12 final size:12
Alignment explanation
Indices: 132347--132371 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
132337 TCATTTTTAA
132347 ATATTTATAAAT
1 ATATTTATAAAT
132359 ATATTTATAAAT
1 ATATTTATAAAT
132371 A
1 A
132372 AAAATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATTTATAAAT
Found at i:137722 original size:5 final size:5
Alignment explanation
Indices: 137712--137739 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
137702 AGAGATTGGC
137712 AGATG AGATG AGATG AGATG AGATG AGA
1 AGATG AGATG AGATG AGATG AGATG AGA
137740 ATGGGTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.18
Consensus pattern (5 bp):
AGATG
Found at i:138650 original size:22 final size:23
Alignment explanation
Indices: 138606--138650 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
138596 ATATCTAGAA
* *
138606 AAAACTAAATTATTCATTCATAT
1 AAAACTAAATTATTCAATAATAT
*
138629 AAAA-TAAATTATTGAATAATAT
1 AAAACTAAATTATTCAATAATAT
138651 TTTTAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAACTAAATTATTCAATAATAT
Found at i:142398 original size:18 final size:16
Alignment explanation
Indices: 142353--142398 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 16
142343 TAGAAAACTG
142353 TTAAACAATTATTTATT
1 TTAAACAA-TATTTATT
142370 TT-AA-AATATTTATT
1 TTAAACAATATTTATT
142384 TTAATACAATGATTT
1 TTAA-ACAAT-ATTT
142399 TAAATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 3 0.12
17 5 0.20
18 4 0.16
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
TTAAACAATATTTATT
Found at i:144062 original size:214 final size:214
Alignment explanation
Indices: 143693--144121 Score: 858
Period size: 214 Copynumber: 2.0 Consensus size: 214
143683 TTTCTAAATT
143693 ATCCCTATAATTTTTTGTACTACTTAAAATACCCCTGTTAACTCCTACGACTCCCTTAGGAGTTG
1 ATCCCTATAATTTTTTGTACTACTTAAAATACCCCTGTTAACTCCTACGACTCCCTTAGGAGTTG
143758 GTTTTATATAATATATAGATTTAAAGGATGGAGAAGTTAACACTAAAATTCGAACATGAACTTTA
66 GTTTTATATAATATATAGATTTAAAGGATGGAGAAGTTAACACTAAAATTCGAACATGAACTTTA
143823 AAATGTCAATAGAAAACTTTAACCACTTTTTTCTTTGAGTTACTCGCCTTCTCTATGTAATCATT
131 AAATGTCAATAGAAAACTTTAACCACTTTTTTCTTTGAGTTACTCGCCTTCTCTATGTAATCATT
143888 GAACTCAATTCATCGAGGC
196 GAACTCAATTCATCGAGGC
143907 ATCCCTATAATTTTTTGTACTACTTAAAATACCCCTGTTAACTCCTACGACTCCCTTAGGAGTTG
1 ATCCCTATAATTTTTTGTACTACTTAAAATACCCCTGTTAACTCCTACGACTCCCTTAGGAGTTG
143972 GTTTTATATAATATATAGATTTAAAGGATGGAGAAGTTAACACTAAAATTCGAACATGAACTTTA
66 GTTTTATATAATATATAGATTTAAAGGATGGAGAAGTTAACACTAAAATTCGAACATGAACTTTA
144037 AAATGTCAATAGAAAACTTTAACCACTTTTTTCTTTGAGTTACTCGCCTTCTCTATGTAATCATT
131 AAATGTCAATAGAAAACTTTAACCACTTTTTTCTTTGAGTTACTCGCCTTCTCTATGTAATCATT
144102 GAACTCAATTCATCGAGGC
196 GAACTCAATTCATCGAGGC
144121 A
1 A
144122 AAAAGTAAAT
Statistics
Matches: 215, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 215 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (214 bp):
ATCCCTATAATTTTTTGTACTACTTAAAATACCCCTGTTAACTCCTACGACTCCCTTAGGAGTTG
GTTTTATATAATATATAGATTTAAAGGATGGAGAAGTTAACACTAAAATTCGAACATGAACTTTA
AAATGTCAATAGAAAACTTTAACCACTTTTTTCTTTGAGTTACTCGCCTTCTCTATGTAATCATT
GAACTCAATTCATCGAGGC
Found at i:145551 original size:2 final size:2
Alignment explanation
Indices: 145544--145593 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
145534 CCCTCTAATT
145544 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
145586 TC TC -C TC T
1 TC TC TC TC T
145594 ACTTGTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:149267 original size:24 final size:24
Alignment explanation
Indices: 149239--149286 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
149229 TTTTGGTTCT
149239 CTTCGAGTTGATTGTATGTTTTAG
1 CTTCGAGTTGATTGTATGTTTTAG
149263 CTTCGAGTTGATTGTATGTTTTAG
1 CTTCGAGTTGATTGTATGTTTTAG
149287 TTTCAATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.08, G:0.25, T:0.50
Consensus pattern (24 bp):
CTTCGAGTTGATTGTATGTTTTAG
Found at i:174156 original size:16 final size:16
Alignment explanation
Indices: 174135--174172 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
174125 AATTTATCAT
174135 ATATATACATACATAC
1 ATATATACATACATAC
174151 ATATATACATACATAC
1 ATATATACATACATAC
*
174167 AAATAT
1 ATATAT
174173 TAAATTATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (16 bp):
ATATATACATACATAC
Found at i:175963 original size:16 final size:16
Alignment explanation
Indices: 175938--175968 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
175928 AAAATTTTTT
*
175938 TAACTTGAACTCAAAC
1 TAACTCGAACTCAAAC
175954 TAACTCGAACTCAAA
1 TAACTCGAACTCAAA
175969 ATAATGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (16 bp):
TAACTCGAACTCAAAC
Found at i:178944 original size:20 final size:21
Alignment explanation
Indices: 178910--178963 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
178900 TGATGATATT
*
178910 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
178931 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
178951 TTTTATTATTTTA
1 TTATATTATTTTA
178964 TTATTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:181159 original size:46 final size:46
Alignment explanation
Indices: 181108--181339 Score: 313
Period size: 46 Copynumber: 5.0 Consensus size: 46
181098 GTGTGCTCTC
* *
181108 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
181154 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATAGTAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
181200 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
181246 TGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
181292 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
181338 TG
1 TG
181340 TCAAAGATAA
Statistics
Matches: 168, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 167 0.99
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:184531 original size:9 final size:10
Alignment explanation
Indices: 184512--184549 Score: 55
Period size: 9 Copynumber: 4.1 Consensus size: 10
184502 TGTAAGAATG
184512 AGAGAGAAAA
1 AGAGAGAAAA
184522 AGAG-GAAAA
1 AGAGAGAAAA
184531 AGAG-GAAAA
1 AGAGAGAAAA
184540 A-AGAGAAAA
1 AGAGAGAAAA
184549 A
1 A
184550 CTAATTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 2 0.07
9 21 0.78
10 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AGAGAGAAAA
Found at i:193255 original size:126 final size:126
Alignment explanation
Indices: 193113--193346 Score: 330
Period size: 126 Copynumber: 1.9 Consensus size: 126
193103 TATTTAAAAT
**
193113 TAATAATAACACATATGTAATTTGTATGAAATTAAAATTAA-AAAATAGTTTAAA-TAGTAAGTA
1 TAATAATAACACATATGTAATACGTATGAAATTAAAA-TAATAAAATAGTTTAAATTA-TAAGTA
* *
193176 AAAT-GAATTTTAAATAGGTAAATACATTAAATAAAGAATATTAAACGTAAGGTTTGGAACTAA
64 AAATAGAA-TTTAAATAGGTAAAAACATCAAATAAAGAATATTAAACGTAAGGTTTGGAACTAA
* *
193239 TAATAATAACATATATGTAATACGTATGAAATTAAAATAATAAAATAGTTTAAATTATGAGTAAA
1 TAATAATAACACATATGTAATACGTATGAAATTAAAATAATAAAATAGTTTAAATTATAAGTAAA
* * * *
193304 ATAGAATTTAAATATGTAAAAATATCATATGAAGAATATTAAA
66 ATAGAATTTAAATAGGTAAAAACATCAAATAAAGAATATTAAA
193347 TGCACTTTGA
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
125 3 0.03
126 87 0.92
127 5 0.05
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (126 bp):
TAATAATAACACATATGTAATACGTATGAAATTAAAATAATAAAATAGTTTAAATTATAAGTAAA
ATAGAATTTAAATAGGTAAAAACATCAAATAAAGAATATTAAACGTAAGGTTTGGAACTAA
Found at i:193993 original size:48 final size:48
Alignment explanation
Indices: 193940--194036 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
193930 AGGGAATAAA
193940 TTAATTTGAAC-TTATTAGCAAGTACTTATAGCTCTAATTAATAAAATC
1 TTAA-TTGAACTTTATTAGCAAGTACTTATAGCTCTAATTAATAAAATC
* * * *
193988 TTAATTGTACTTTATTAGTAAGTATTTATAGCTTTAATTAATAAAATC
1 TTAATTGAACTTTATTAGCAAGTACTTATAGCTCTAATTAATAAAATC
194036 T
1 T
194037 ATTCAAGATG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 5 0.11
48 39 0.89
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.44
Consensus pattern (48 bp):
TTAATTGAACTTTATTAGCAAGTACTTATAGCTCTAATTAATAAAATC
Found at i:194547 original size:23 final size:24
Alignment explanation
Indices: 194512--194561 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
194502 TTAAACTATG
194512 TTTTACATAATTTT-ATAAAAATTA
1 TTTTACATAATTTTGA-AAAAATTA
*
194536 TTTT-CATAATTTTGAATAAATTA
1 TTTTACATAATTTTGAAAAAATTA
194559 TTT
1 TTT
194562 GACTAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTACATAATTTTGAAAAAATTA
Found at i:200761 original size:13 final size:13
Alignment explanation
Indices: 200743--200767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
200733 TATTTAAAAA
200743 TAATTAAAAATAT
1 TAATTAAAAATAT
200756 TAATTAAAAATA
1 TAATTAAAAATA
200768 ATTAGAATTT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATTAAAAATAT
Found at i:204869 original size:17 final size:18
Alignment explanation
Indices: 204843--204877 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
204833 GGGACTCTTC
204843 AACAAAAAAAAA-AAAAA
1 AACAAAAAAAAAGAAAAA
*
204860 AACAAGAAAAAAGAAAAA
1 AACAAAAAAAAAGAAAAA
204878 GAAAGAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (18 bp):
AACAAAAAAAAAGAAAAA
Found at i:204884 original size:17 final size:18
Alignment explanation
Indices: 204843--204877 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
204833 GGGACTCTTC
204843 AACAA-AAAAAAAAAAAA
1 AACAAGAAAAAAAAAAAA
204860 AACAAGAAAAAAGAAAAA
1 AACAAGAAAAAA-AAAAA
204878 GAAAGAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (18 bp):
AACAAGAAAAAAAAAAAA
Found at i:204886 original size:23 final size:20
Alignment explanation
Indices: 204846--204887 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 20
204836 ACTCTTCAAC
204846 AAAAAAAAAAAAAAAACAAG
1 AAAAAAAAAAAAAAAACAAG
204866 AAAAAAGAAAAAGAAAGAACAA
1 AAAAAA-AAAAA-AAA-AACAA
204888 ATGTGCATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 3 0.16
23 5 0.26
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAACAAG
Found at i:213228 original size:21 final size:22
Alignment explanation
Indices: 213204--213256 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
213194 ATTATTACTA
*
213204 TTTTTATTATCAT-TTTTTATTT
1 TTTTTATT-TAATATTTTTATTT
213226 TTTTTATTTAATATTTTTA-TT
1 TTTTTATTTAATATTTTTATTT
*
213247 CTTTTATTTA
1 TTTTTATTTA
213257 TTTGCTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTATTTAATATTTTTATTT
Found at i:213232 original size:22 final size:22
Alignment explanation
Indices: 213204--213256 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
213194 ATTATTACTA
* *
213204 TTTTTATTATCAT-TTTTTATTT
1 TTTTTATT-TAATATTTTTATTC
213226 TTTTTATTTAATATTTTTATTC
1 TTTTTATTTAATATTTTTATTC
213248 -TTTTATTTA
1 TTTTTATTTA
213257 TTTGCTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTATTTAATATTTTTATTC
Found at i:214980 original size:92 final size:95
Alignment explanation
Indices: 214813--214988 Score: 218
Period size: 92 Copynumber: 1.9 Consensus size: 95
214803 AGAAGGCATG
* * ***
214813 AAAGTTTAAAGGATTATTTGGATGTAAAAGAAAAAGTATGAGAGGTATTTTTTCAATAAAATGAA
1 AAAGTTTAAAGGATTATTTAGATGTAAAAGAAAAAGTATAAGAGGTATTTTAAAAATAAAATGAA
214878 AAAGTTTAAGGACTTATTTGAGTACCAATT
66 AAAGTTTAAGGACTTATTTGAGTACCAATT
* *
214908 AAAGTTTAAGGGATTATTTAGATG-AAAA-AAAAAGTATAAG-GGCT-TTTTAAAAATAAAGT-A
1 AAAGTTTAAAGGATTATTTAGATGTAAAAGAAAAAGTATAAGAGG-TATTTTAAAAATAAAATGA
* *
214968 ACAAATTTTAAGGGCTTATTT
65 A-AAAGTTTAAGGACTTATTT
214989 AATGTATTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
91 2 0.03
92 30 0.43
93 12 0.17
94 4 0.06
95 22 0.31
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (95 bp):
AAAGTTTAAAGGATTATTTAGATGTAAAAGAAAAAGTATAAGAGGTATTTTAAAAATAAAATGAA
AAAGTTTAAGGACTTATTTGAGTACCAATT
Found at i:218181 original size:14 final size:15
Alignment explanation
Indices: 218154--218186 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
218144 TTAGATTTAC
218154 AAATAAAATTTTAAAA
1 AAATAAAA-TTTAAAA
218170 AAATAAAA-TTAAAA
1 AAATAAAATTTAAAA
218184 AAA
1 AAA
218187 AAGTGTACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAATTTAAAA
Found at i:218185 original size:16 final size:16
Alignment explanation
Indices: 218154--218188 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
218144 TTAGATTTAC
**
218154 AAATAAAATTTTAAAA
1 AAATAAAATTAAAAAA
218170 AAATAAAATTAAAAAA
1 AAATAAAATTAAAAAA
218186 AAA
1 AAA
218189 GTGTACGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAATTAAAAAA
Found at i:218186 original size:15 final size:16
Alignment explanation
Indices: 218154--218187 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
218144 TTAGATTTAC
*
218154 AAATAAAATTTTAAAA
1 AAATAAAATTTAAAAA
218170 AAATAAAA-TTAAAAA
1 AAATAAAATTTAAAAA
218185 AAA
1 AAA
218188 AGTGTACGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAAATTTAAAAA
Found at i:221132 original size:14 final size:14
Alignment explanation
Indices: 221113--221143 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
221103 TAATTGATTT
221113 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
221127 TTTAATTAATTAAA
1 TTTAATTAAATAAA
221141 TTT
1 TTT
221144 TCTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:236302 original size:197 final size:195
Alignment explanation
Indices: 235949--236339 Score: 739
Period size: 197 Copynumber: 2.0 Consensus size: 195
235939 TGGCTTTTTT
235949 CTTATCACTTGTTGAAAGAACATAAGAAGACTTCATGTAAGCTAGGAACAATAAAGAGAGAGGCA
1 CTTATCACTTGTTGAAAGAACATAAGAAGACTTCATGTAAGCTAGGAACAATAAAGAGAGAGGCA
236014 GATGAACAGTATCAAGCACTGCAGATTTCAGGATATCAAGGGAAAGACCAAAAGAAAACAACTCA
66 GATGAACAGTATCAAGCACTGCAGATTTCAGGATATCAAGGGAAAGACCAAAAGAAAACAACTCA
236079 CCTCATGGATTATTTGCTTCACCGACTTTTTAAAGGGAACAACTAAATCCACATGTTGTTCTTTG
131 CCTCATGGATTATTTGCTTCACCGACTTTTTAAAGGGAACAACTAAATCCACATGTTGTTCTTTG
236144 CTTATCACTTGTTGAAAGAACATAAGAAGACTTCATGTAAGCTAGGAACAATAAAGAGTA-AGGC
1 CTTATCACTTGTTGAAAGAACATAAGAAGACTTCATGTAAGCTAGGAACAATAAAGAG-AGAGGC
*
236208 AGCTGAACAGTATCAAGCAATCTGCAGATTTCAGGATATCAAGGGAAAGACCAAAAGAAAACAAC
65 AGATGAACAGTATCAAGC-A-CTGCAGATTTCAGGATATCAAGGGAAAGACCAAAAGAAAACAAC
236273 TCACCTCATGGATTATTTGCTTCACCGACTTTTTAAAGGGAACAACTAAATCCACATGTTGTTCT
128 TCACCTCATGGATTATTTGCTTCACCGACTTTTTAAAGGGAACAACTAAATCCACATGTTGTTCT
236338 TT
193 TT
236340 AGTGTCCTGC
Statistics
Matches: 192, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
195 79 0.41
196 2 0.01
197 111 0.58
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (195 bp):
CTTATCACTTGTTGAAAGAACATAAGAAGACTTCATGTAAGCTAGGAACAATAAAGAGAGAGGCA
GATGAACAGTATCAAGCACTGCAGATTTCAGGATATCAAGGGAAAGACCAAAAGAAAACAACTCA
CCTCATGGATTATTTGCTTCACCGACTTTTTAAAGGGAACAACTAAATCCACATGTTGTTCTTTG
Found at i:242147 original size:32 final size:31
Alignment explanation
Indices: 242111--242175 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 31
242101 AAAAAGTAAT
*
242111 TTAAAAAATATAAAATATT-TAGAAATTAAAAA
1 TTAAAAAATA-AAAACATTATA-AAATTAAAAA
242143 TTAAAAAATAAAAACATTCATAAAATTAAAAA
1 TTAAAAAATAAAAACATT-ATAAAATTAAAAA
242175 T
1 T
242176 ATATATAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.23
32 21 0.70
33 2 0.07
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (31 bp):
TTAAAAAATAAAAACATTATAAAATTAAAAA
Found at i:247945 original size:7 final size:7
Alignment explanation
Indices: 247933--247957 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
247923 TAAATGTAAG
247933 TAAAATT
1 TAAAATT
247940 TAAAATT
1 TAAAATT
247947 TAAAATT
1 TAAAATT
247954 TAAA
1 TAAA
247958 TCGAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAAATT
Found at i:249054 original size:82 final size:81
Alignment explanation
Indices: 248953--249112 Score: 257
Period size: 82 Copynumber: 2.0 Consensus size: 81
248943 TGTTAACCCG
* * *
248953 ATGATAAAGAGTGTTCATCGATTCAAATGATTTAAATTTGAGGTCATGCTATTTATTTTTATAAT
1 ATGATAAAGAGTGTTCATCGATTCAAATGATTTAAATTTGA-GTCATGATAATTATTCTTATAAT
249018 TCACTAAAAATATTCTA
65 TCACTAAAAATATTCTA
* * *
249035 ATGATAAAGGGTGTTCATCGTTTCAAATGATTTAAATTTGAGTTATGATAATTATTCTTATAATT
1 ATGATAAAGAGTGTTCATCGATTCAAATGATTTAAATTTGAGTCATGATAATTATTCTTATAATT
249100 CACTAAAAATATT
66 CACTAAAAATATT
249113 ATACATTTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 33 0.46
82 39 0.54
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (81 bp):
ATGATAAAGAGTGTTCATCGATTCAAATGATTTAAATTTGAGTCATGATAATTATTCTTATAATT
CACTAAAAATATTCTA
Found at i:258062 original size:21 final size:22
Alignment explanation
Indices: 258033--258079 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
258023 CAGAAGGAGT
*
258033 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
258055 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
258076 GAGT
1 GAGT
258080 TTGAGCAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:261852 original size:28 final size:29
Alignment explanation
Indices: 261820--261880 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
261810 ACTTATGCGA
** *
261820 CAAACATATCATAACCCGAA-CAAAAAAT
1 CAAACATAAAATAACCCAAATCAAAAAAT
*
261848 CAAACTTAAAATAACCCAAATTCAAAAAAT
1 CAAACATAAAATAACCCAAA-TCAAAAAAT
261878 CAA
1 CAA
261881 TTTTATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 16 0.59
30 11 0.41
ACGTcount: A:0.59, C:0.23, G:0.02, T:0.16
Consensus pattern (29 bp):
CAAACATAAAATAACCCAAATCAAAAAAT
Found at i:265074 original size:12 final size:12
Alignment explanation
Indices: 265057--265086 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
265047 TATTGCATTT
265057 ATACATATATAC
1 ATACATATATAC
*
265069 ATACATATATAT
1 ATACATATATAC
265081 ATACAT
1 ATACAT
265087 GAACATGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (12 bp):
ATACATATATAC
Found at i:267557 original size:23 final size:25
Alignment explanation
Indices: 267527--267577 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
267517 AGCTTGAATC
267527 TTTTTTTTAT-T-TGTATAATACGA
1 TTTTTTTTATATGTGTATAATACGA
*
267550 TTTTTTTTATATGTGTATAATATGA
1 TTTTTTTTATATGTGTATAATACGA
267575 TTT
1 TTT
267578 ATGTTCAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 10 0.40
24 1 0.04
25 14 0.56
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (25 bp):
TTTTTTTTATATGTGTATAATACGA
Found at i:267650 original size:15 final size:15
Alignment explanation
Indices: 267630--267660 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
267620 ATAACACAAA
*
267630 TTTTTTTATTTTAAT
1 TTTTTTTAATTTAAT
267645 TTTTTTTAATTTAAT
1 TTTTTTTAATTTAAT
267660 T
1 T
267661 ATAAAGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTAATTTAAT
Found at i:272056 original size:12 final size:12
Alignment explanation
Indices: 272039--272064 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
272029 TTTACCTCCG
272039 ATTAGGGTAGAA
1 ATTAGGGTAGAA
272051 ATTAGGGTAGAA
1 ATTAGGGTAGAA
272063 AT
1 AT
272065 AATAGTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (12 bp):
ATTAGGGTAGAA
Found at i:275486 original size:2 final size:2
Alignment explanation
Indices: 275479--275511 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
275469 GGTTTATGCC
*
275479 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
275512 TAACGAGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:276151 original size:13 final size:13
Alignment explanation
Indices: 276129--276158 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
276119 CGCCAAATTA
*
276129 AAATTTATATATT
1 AAATTGATATATT
276142 AAATTGATATATT
1 AAATTGATATATT
276155 AAAT
1 AAAT
276159 CAAAGTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AAATTGATATATT
Found at i:278648 original size:15 final size:15
Alignment explanation
Indices: 278603--278654 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
278593 AGAATTAATC
*
278603 TTTATATTTTAATTTG
1 TTTA-ATTTTAATTTT
*
278619 GTTAATTTTAATTTT
1 TTTAATTTTAATTTT
278634 TTTAATTTT--TTTT
1 TTTAATTTTAATTTT
*
278647 TTAAATTT
1 TTTAATTT
278655 CAATCATCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.34
15 18 0.56
16 3 0.09
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (15 bp):
TTTAATTTTAATTTT
Found at i:282632 original size:7 final size:7
Alignment explanation
Indices: 282620--282648 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
282610 CACATACGAT
282620 GTAAGAG
1 GTAAGAG
282627 GTAAGAG
1 GTAAGAG
282634 GTAAGAG
1 GTAAGAG
282641 GTAAGAG
1 GTAAGAG
282648 G
1 G
282649 ATGACTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.45, T:0.14
Consensus pattern (7 bp):
GTAAGAG
Found at i:283747 original size:17 final size:18
Alignment explanation
Indices: 283725--283759 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
283715 ATGATATTGA
*
283725 ATTTTT-GAATGTTTTTT
1 ATTTTTGGAATATTTTTT
283742 ATTTTTGGAATATTTTTT
1 ATTTTTGGAATATTTTTT
283760 TATCACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (18 bp):
ATTTTTGGAATATTTTTT
Found at i:284936 original size:16 final size:15
Alignment explanation
Indices: 284915--284944 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
284905 AATCTCTTTC
284915 TAAAATTTTATATTAT
1 TAAAATTTTA-ATTAT
284931 TAAAATTTTAATTA
1 TAAAATTTTAATTA
284945 GAGAATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAAATTTTAATTAT
Found at i:289435 original size:26 final size:26
Alignment explanation
Indices: 289398--289481 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
289388 TGATACAAAT
*
289398 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
289424 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
289450 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
289476 TGATAA
1 TGATAA
289482 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:291142 original size:27 final size:26
Alignment explanation
Indices: 291102--291213 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
291092 AGGAAGCGTC
*
291102 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
291129 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
291156 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
291184 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
291210 CTGG
1 CTGG
291214 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 7 0.09
27 52 0.68
28 17 0.22
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:291206 original size:54 final size:54
Alignment explanation
Indices: 291102--291213 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 54
291092 AGGAAGCGTC
*
291102 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACGATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* *
291156 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACGATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
291210 CTGG
1 CTGG
291214 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (54 bp):
CTGGTGGCTATGCCACGATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:291299 original size:19 final size:22
Alignment explanation
Indices: 291275--291314 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
291265 CTCCCCACAC
291275 GGTGTA-A-GGTTGG-TATGGG
1 GGTGTATACGGTTGGATATGGG
291294 GGTGTATACGGTTGGATATGG
1 GGTGTATACGGTTGGATATGG
291315 TTGGGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTGTATACGGTTGGATATGGG
Found at i:292586 original size:24 final size:24
Alignment explanation
Indices: 292557--292610 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
292547 TAGAAAATGG
292557 TTTAAACTAC-ATGATATATGAA-AA
1 TTTAAACT-CTATGATATAT-AAGAA
*
292581 TTTAAAGTCTATGATATATAAGAA
1 TTTAAACTCTATGATATATAAGAA
292605 TTTAAA
1 TTTAAA
292611 ATAAATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (24 bp):
TTTAAACTCTATGATATATAAGAA
Found at i:292752 original size:24 final size:24
Alignment explanation
Indices: 292720--292765 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
292710 CTAAAATAAT
292720 ATACAATAAAACAATTTGAAATGA
1 ATACAATAAAACAATTTGAAATGA
* * *
292744 ATACTATAAATCAATTTTAAAT
1 ATACAATAAAACAATTTGAAAT
292766 AAATGATGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (24 bp):
ATACAATAAAACAATTTGAAATGA
Found at i:295739 original size:93 final size:93
Alignment explanation
Indices: 295632--295802 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
295622 GCCCCTAAGT
* * * *
295632 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCATAAGTGAACTC-AGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGA-ACTCAACTCA
295696 ACGAGTTCGGATGCCTAGTTACGTTTCAC
65 ACGAGTTCGGATGCCTAGTTACGTTTCAC
* *
295725 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAATGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGAACTCAACTCAA
295790 CGAGTTCGGATGC
66 CGAGTTCGGATGC
295803 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 70 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGAACTCAACTCAA
CGAGTTCGGATGCCTAGTTACGTTTCAC
Found at i:296175 original size:30 final size:30
Alignment explanation
Indices: 296141--296200 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
296131 ATTTAATACG
296141 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
296171 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
296201 GGCACGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:308789 original size:46 final size:46
Alignment explanation
Indices: 308722--308847 Score: 225
Period size: 46 Copynumber: 2.7 Consensus size: 46
308712 AACCCGCCCC
* * *
308722 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
308768 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
308814 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
308848 TGCTCAACCA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:308866 original size:46 final size:45
Alignment explanation
Indices: 308724--308866 Score: 146
Period size: 46 Copynumber: 3.1 Consensus size: 45
308714 CCCGCCCCTA
* ** * *
308724 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
*** *
308769 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
308815 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCT
308862 AGTGA
1 AGTGA
308867 CATGTCACTT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
46 82 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCT
Found at i:309296 original size:30 final size:29
Alignment explanation
Indices: 309262--309320 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
309252 ATTTAATACG
309262 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTT-GAAAAATTACACTTTTGCCCCTA
** *
309292 AACTTTTCATAATTACACTTTTGCCCCTA
1 AACTTTGAAAAATTACACTTTTGCCCCTA
309321 GGCTCGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (29 bp):
AACTTTGAAAAATTACACTTTTGCCCCTA
Found at i:316300 original size:46 final size:46
Alignment explanation
Indices: 316233--316358 Score: 234
Period size: 46 Copynumber: 2.7 Consensus size: 46
316223 AACCCGCCCC
* *
316233 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
316279 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
316325 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
316359 TGCTCAACCA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:316802 original size:30 final size:30
Alignment explanation
Indices: 316768--316827 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
316758 ATTTAATACG
316768 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
316798 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
316828 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:321812 original size:31 final size:30
Alignment explanation
Indices: 321775--321869 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 30
321765 AGCTTAGGTG
321775 CCAAATTAGGAAAAAAAATCAAGTTTAGATA
1 CCAAATT-GGAAAAAAAATCAAGTTTAGATA
* *
321806 CCAAATTGGACAAAAAA--AA-TTTAGGTA
1 CCAAATTGGAAAAAAAATCAAGTTTAGATA
* * * *
321833 TCAAATTTGAAAAAAGTATCAAGTCTAGATA
1 CCAAATTGGAAAAAA-AATCAAGTTTAGATA
*
321864 CGAAAT
1 CCAAAT
321870 ATTATATTAC
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
27 19 0.38
28 3 0.06
30 11 0.22
31 17 0.34
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.24
Consensus pattern (30 bp):
CCAAATTGGAAAAAAAATCAAGTTTAGATA
Found at i:324446 original size:12 final size:12
Alignment explanation
Indices: 324421--324469 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
324411 GCGGGGTATA
*
324421 TTTTTCATCATCT
1 TTTTTC-TCTTCT
324434 TTTTTCTCTTCT
1 TTTTTCTCTTCT
*
324446 TTCTTCTCTTCT
1 TTTTTCTCTTCT
324458 TTTATT-TCTTCT
1 TTT-TTCTCTTCT
324470 ATGGTCAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 24 0.75
13 8 0.25
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTCTCTTCT
Found at i:326372 original size:23 final size:23
Alignment explanation
Indices: 326342--326389 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
326332 GATTTCATAC
326342 TTAAGCTTTATTCACCAAAGTAT
1 TTAAGCTTTATTCACCAAAGTAT
326365 TTAAGCTTTATTCACCAAAGTAT
1 TTAAGCTTTATTCACCAAAGTAT
326388 TT
1 TT
326390 GAAATATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (23 bp):
TTAAGCTTTATTCACCAAAGTAT
Found at i:327097 original size:42 final size:42
Alignment explanation
Indices: 327034--327145 Score: 154
Period size: 42 Copynumber: 2.7 Consensus size: 42
327024 CTTCGTTTTC
** * *
327034 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCAGATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGAT-A
*
327077 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATA
*
327118 TCGATGCCATAGCCCAGATATGGTCTTA
1 TCGATGCCATAGCCCAGCTATGGTCTTA
327146 TACGTAAATC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
41 2 0.03
42 59 0.95
43 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATA
Found at i:327202 original size:31 final size:31
Alignment explanation
Indices: 327167--327315 Score: 255
Period size: 31 Copynumber: 4.8 Consensus size: 31
327157 CTTGTCACTT
*
327167 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
327198 GTAGCC-AGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
327229 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
327260 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
327291 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
327316 TGTTATTTGT
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
30 1 0.01
31 110 0.99
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:327397 original size:50 final size:50
Alignment explanation
Indices: 327291--327467 Score: 282
Period size: 50 Copynumber: 3.5 Consensus size: 50
327281 CACTGATCAG
* * * *
327291 GTAGCCGAAGCTACCACTTTTCACTTGTTATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* *
327342 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGGTAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
327392 GTAGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
327442 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
327468 GTTGCCATGG
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 92 0.79
51 24 0.21
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:327849 original size:27 final size:27
Alignment explanation
Indices: 327811--327865 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
327801 TGTATATTTT
327811 TCCTCCTCCTCCTCTCCATCCACATCC
1 TCCTCCTCCTCCTCTCCATCCACATCC
327838 TCCTCCTCCTCCTCTCCATCCACATCC
1 TCCTCCTCCTCCTCTCCATCCACATCC
327865 T
1 T
327866 TAGTATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.11, C:0.58, G:0.00, T:0.31
Consensus pattern (27 bp):
TCCTCCTCCTCCTCTCCATCCACATCC
Found at i:330516 original size:2 final size:2
Alignment explanation
Indices: 330509--330533 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
330499 TCATTCACCA
330509 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
330534 AATAAACATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:331786 original size:19 final size:18
Alignment explanation
Indices: 331762--331860 Score: 65
Period size: 19 Copynumber: 5.3 Consensus size: 18
331752 TTTTAAAATT
331762 TTTTTTGAAATTTTTATAA
1 TTTTTT-AAATTTTTATAA
***
331781 TTTTTTAAA-AAATATAA
1 TTTTTTAAATTTTTATAA
**
331798 AATTTTAAATTTTTATAAA
1 TTTTTTAAATTTTTAT-AA
* * *
331817 TATTTTAAATTTTAAAAA
1 TTTTTTAAATTTTTATAA
*
331835 TTATTTTGAATTATTTTATAA
1 TT-TTTT-AAAT-TTTTATAA
331856 TTTTT
1 TTTTT
331861 ATTGAGAGAG
Statistics
Matches: 60, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
17 12 0.20
18 9 0.15
19 25 0.42
20 6 0.10
21 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTTTAAATTTTTATAA
Found at i:331793 original size:21 final size:21
Alignment explanation
Indices: 331750--331793 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
331740 CTTTATATAG
***
331750 ATTTTTAAAATTTTTTTTGAA
1 ATTTTTAAAATTTTTTAAAAA
*
331771 ATTTTTATAATTTTTTAAAAA
1 ATTTTTAAAATTTTTTAAAAA
331792 AT
1 AT
331794 ATAAAATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTTAAAATTTTTTAAAAA
Found at i:331814 original size:18 final size:19
Alignment explanation
Indices: 331793--331829 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
331783 TTTTAAAAAA
331793 TATAAA-ATTTTAAATTTT
1 TATAAATATTTTAAATTTT
331811 TATAAATATTTTAAATTTT
1 TATAAATATTTTAAATTTT
331830 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:338355 original size:9 final size:9
Alignment explanation
Indices: 338326--338360 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
338316 CCAATTTGTG
338326 AAAA-AAAT
1 AAAATAAAT
338334 AAAATAGAAT
1 AAAATA-AAT
338344 AAAATAAAT
1 AAAATAAAT
338353 AAAATAAA
1 AAAATAAA
338361 GAACACACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 4 0.16
9 12 0.48
10 9 0.36
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (9 bp):
AAAATAAAT
Found at i:342256 original size:18 final size:18
Alignment explanation
Indices: 342233--342271 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
342223 ACATGTGGGG
342233 CATCTTGGAAAGCTTGGT
1 CATCTTGGAAAGCTTGGT
342251 CATCTTGGAAAGCTTGGT
1 CATCTTGGAAAGCTTGGT
342269 CAT
1 CAT
342272 TGTAATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (18 bp):
CATCTTGGAAAGCTTGGT
Found at i:343040 original size:21 final size:22
Alignment explanation
Indices: 343011--343056 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
343001 ATATTTTTAA
343011 TTTTAAAAATTATTTTA-AATT
1 TTTTAAAAATTATTTTATAATT
*
343032 TTTTGAAAATTATTTTATAATT
1 TTTTAAAAATTATTTTATAATT
343054 TTT
1 TTT
343057 GTTGAGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTAAAAATTATTTTATAATT
Found at i:343057 original size:21 final size:21
Alignment explanation
Indices: 343002--343057 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
342992 TTTGTATAAA
*
343002 TATTTT-TAA-TTTTAAAAAT
1 TATTTTATAATTTTTGAAAAT
343021 TATTTTA-AATTTTTTGAAAAT
1 TATTTTATAA-TTTTTGAAAAT
343042 TATTTTATAATTTTTG
1 TATTTTATAATTTTTG
343058 TTGAGAGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.25
21 22 0.69
22 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
TATTTTATAATTTTTGAAAAT
Done.