Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 15 of 190
Found at i:4382148 original size:16 final size:16
Alignment explanation
Indices: 4382080--4382149 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
4382070 AAATTTTTAC
* * *
4382080 TTTTTAATATATATAT
1 TTTTTAACAAATATTT
* *
4382096 TTTTAAATAAAT-TTAT
1 TTTTTAACAAATATT-T
4382112 TTTTTAACAAATAAATCTT
1 TTTTTAACAAAT--AT-TT
4382131 TTTTTAACAAATATTT
1 TTTTTAACAAATATTT
4382147 TTT
1 TTT
4382150 ATTTTTTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.02
16 26 0.59
17 2 0.05
19 14 0.32
20 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTTAACAAATATTT
Found at i:4382482 original size:20 final size:21
Alignment explanation
Indices: 4382459--4382599 Score: 80
Period size: 20 Copynumber: 6.8 Consensus size: 21
4382449 ATAAAAAAAT
4382459 AAATAATATTTAAAATATT-A
1 AAATAATATTTAAAATATTAA
* *
4382479 AAATAATAATAATAAAT-TTGAA
1 AAATAATATTTA-AAATATT-AA
** * *
4382501 AGGTCATATCTTTAAAATATT-T
1 AAAT-A-ATATTTAAAATATTAA
* *
4382523 AAAT-AT-TTTATATTATTAA
1 AAATAATATTTAAAATATTAA
* *
4382542 AAATATATATTTAATATTTTAA
1 AAATA-ATATTTAAAATATTAA
*
4382564 AAATAATATTCAAAAT-TTAA
1 AAATAATATTTAAAATATTAA
*
4382584 AAATAAT-TTAAAAATA
1 AAATAATATTTAAAATA
4382600 ATAGTTAAAA
Statistics
Matches: 90, Mismatches: 20, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
18 9 0.10
19 13 0.14
20 23 0.26
21 15 0.17
22 19 0.21
23 5 0.06
24 6 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AAATAATATTTAAAATATTAA
Found at i:4382492 original size:29 final size:28
Alignment explanation
Indices: 4382436--4382497 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
4382426 TAAAAATCAT
4382436 AATTTAAAATATTATAAAAAAATAAATA
1 AATTTAAAATATTATAAAAAAATAAATA
4382464 ATATTTAAAATATTA-AAATAATAAT-AATA
1 A-ATTTAAAATATTATAAA-AA-AATAAATA
4382493 AATTT
1 AATTT
4382498 GAAAGGTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
28 8 0.26
29 20 0.65
30 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AATTTAAAATATTATAAAAAAATAAATA
Found at i:4382558 original size:23 final size:21
Alignment explanation
Indices: 4382524--4382590 Score: 82
Period size: 20 Copynumber: 3.1 Consensus size: 21
4382514 AAAATATTTA
*
4382524 AATATTTTATATTATTAAAAAT
1 AATATTTAATATT-TTAAAAAT
4382546 ATATATTTAATATTTTAAAAAT
1 A-ATATTTAATATTTTAAAAAT
* *
4382568 AATATTCAA-AATTTAAAAAT
1 AATATTTAATATTTTAAAAAT
4382588 AAT
1 AAT
4382591 TTAAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
20 13 0.32
21 7 0.17
22 10 0.24
23 11 0.27
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (21 bp):
AATATTTAATATTTTAAAAAT
Found at i:4382595 original size:31 final size:32
Alignment explanation
Indices: 4382554--4382618 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
4382544 ATATATATTT
*
4382554 AATATTTTAAAAATAATA-TTCAAAA-TTTAAA
1 AATAATTTAAAAATAATAGTT-AAAATTTTAAA
4382585 AATAATTTAAAAATAATAGTTAAAATTTTAAA
1 AATAATTTAAAAATAATAGTTAAAATTTTAAA
4382617 AA
1 AA
4382619 ATATATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (32 bp):
AATAATTTAAAAATAATAGTTAAAATTTTAAA
Found at i:4382600 original size:11 final size:11
Alignment explanation
Indices: 4382577--4382601 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4382567 TAATATTCAA
4382577 AATTTAAAAAT
1 AATTTAAAAAT
4382588 AATTTAAAAAT
1 AATTTAAAAAT
4382599 AAT
1 AAT
4382602 AGTTAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTTAAAAAT
Found at i:4382688 original size:9 final size:9
Alignment explanation
Indices: 4382662--4382705 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
4382652 CAATTTTTTA
*
4382662 AAAATTAAT
1 AAAATAAAT
4382671 AACAATAAAT
1 AA-AATAAAT
4382681 AAAATAAAT
1 AAAATAAAT
*
4382690 -AAATAAAC
1 AAAATAAAT
4382698 AAAATAAA
1 AAAATAAA
4382706 ATAAGAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.23
9 16 0.52
10 8 0.26
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:4382747 original size:19 final size:19
Alignment explanation
Indices: 4382720--4382783 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
4382710 GAGAAAATAT
*
4382720 AAAACTTAAAAAAAAGAAA
1 AAAATTTAAAAAAAAGAAA
*
4382739 AAAATTTAAATAAAAAG-AC
1 AAAATTTAAA-AAAAAGAAA
*
4382758 AAAAGTTAATAAAAAAGTAAA
1 AAAATTTAA-AAAAAAG-AAA
4382779 AAAAT
1 AAAAT
4382784 AAAAAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 24 0.67
20 7 0.19
21 5 0.14
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAATTTAAAAAAAAGAAA
Found at i:4382786 original size:16 final size:15
Alignment explanation
Indices: 4382674--4382794 Score: 57
Period size: 17 Copynumber: 7.5 Consensus size: 15
4382664 AATTAATAAC
4382674 AATAAATAAAATAAATA
1 AATAAA-AAAATAAA-A
4382691 AATAAACAAAATAAAA
1 AATAAA-AAAATAAAA
* *
4382707 TAAGAGAAAATATAAAA
1 -AATA-AAAAAATAAAA
**
4382724 CTTAAAAAAA-AGAAA
1 AATAAAAAAATA-AAA
**
4382739 AA-AATTTAAATAAAA
1 AATAA-AAAAATAAAA
* *
4382754 AGACAAAAGTTAATAAAA
1 A-ATAAAA--AAATAAAA
4382772 AAGTAAAAAAATAAAA
1 AA-TAAAAAAATAAAA
4382788 AATAAAA
1 AATAAAA
4382795 TAAGGGTGTC
Statistics
Matches: 78, Mismatches: 16, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
14 3 0.04
15 20 0.26
16 13 0.17
17 28 0.36
18 14 0.18
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.17
Consensus pattern (15 bp):
AATAAAAAAATAAAA
Found at i:4383814 original size:7 final size:7
Alignment explanation
Indices: 4383804--4383858 Score: 58
Period size: 7 Copynumber: 7.4 Consensus size: 7
4383794 AAAAAAGGAA
4383804 AAAGAAC
1 AAAGAAC
4383811 AAAGAAC
1 AAAGAAC
*
4383818 AAAGAAG
1 AAAGAAC
4383825 ATAACGGGAA-
1 A-AA---GAAC
4383835 AAAGAAC
1 AAAGAAC
4383842 AAAGAAC
1 AAAGAAC
4383849 AAAGAAC
1 AAAGAAC
4383856 AAA
1 AAA
4383859 AAAGAGGAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
6 3 0.07
7 31 0.74
8 2 0.05
9 2 0.05
10 1 0.02
11 3 0.07
ACGTcount: A:0.69, C:0.11, G:0.18, T:0.02
Consensus pattern (7 bp):
AAAGAAC
Found at i:4384495 original size:17 final size:18
Alignment explanation
Indices: 4384473--4384506 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
4384463 CGACCGCGAC
4384473 AAACGCGAC-GCGACCGA
1 AAACGCGACTGCGACCGA
4384490 AAACGCGACTGCGACCG
1 AAACGCGACTGCGACCG
4384507 CAATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.35, G:0.29, T:0.03
Consensus pattern (18 bp):
AAACGCGACTGCGACCGA
Found at i:4384966 original size:25 final size:27
Alignment explanation
Indices: 4384911--4384966 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
4384901 AACGTCCACT
*
4384911 ACCTATCGACCACTTAATGCCCGCAAT
1 ACCTATCGACCACTTAATGCCCGCAAA
*
4384938 ACCTATCGACCACTT-A-GCCCGTAAA
1 ACCTATCGACCACTTAATGCCCGCAAA
4384963 ACCT
1 ACCT
4384967 GAACCCACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 11 0.41
26 1 0.04
27 15 0.56
ACGTcount: A:0.30, C:0.38, G:0.11, T:0.21
Consensus pattern (27 bp):
ACCTATCGACCACTTAATGCCCGCAAA
Found at i:4387099 original size:2 final size:2
Alignment explanation
Indices: 4387092--4387129 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4387082 AACCATTTTC
4387092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4387130 ATCACTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4387690 original size:2 final size:2
Alignment explanation
Indices: 4387633--4387670 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4387623 AACTAATAAT
4387633 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4387671 CGAAATGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4388226 original size:41 final size:41
Alignment explanation
Indices: 4388181--4388287 Score: 101
Period size: 41 Copynumber: 2.6 Consensus size: 41
4388171 CCTGATTCAA
* * *
4388181 TTCACCAGCAATT-AGCCTGCTAGACTTAAAGTCTGAATTAT
1 TTCACCAGC-ATTAAGCATGCTAGACATAAAGTCCGAATTAT
* * *
4388222 TTCACCGGCATTAAGCATGCTGGACATAAAGTCCGAATTAC
1 TTCACCAGCATTAAGCATGCTAGACATAAAGTCCGAATTAT
* * *
4388263 ATCACC-GACCTTAAGCCTGCTAGAC
1 TTCACCAG-CATTAAGCATGCTAGAC
4388288 TTTAAGCCTG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
40 4 0.07
41 50 0.93
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (41 bp):
TTCACCAGCATTAAGCATGCTAGACATAAAGTCCGAATTAT
Found at i:4388847 original size:22 final size:22
Alignment explanation
Indices: 4388822--4388864 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4388812 AAACAATGTA
4388822 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
4388844 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
4388865 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:4389956 original size:13 final size:13
Alignment explanation
Indices: 4389938--4389962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4389928 TCAAACGATC
4389938 AAATTTTCACACG
1 AAATTTTCACACG
4389951 AAATTTTCACAC
1 AAATTTTCACAC
4389963 ATATAACTTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:4393243 original size:2 final size:2
Alignment explanation
Indices: 4393238--4393269 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4393228 ATATAACATG
4393238 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4393270 AGTCTTGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4395770 original size:2 final size:2
Alignment explanation
Indices: 4395763--4395804 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4395753 TATTTGCTCC
4395763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4395805 GGGAAGTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4396254 original size:2 final size:2
Alignment explanation
Indices: 4396249--4396275 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4396239 TACGATATGT
4396249 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4396276 TTTGCAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4397401 original size:26 final size:26
Alignment explanation
Indices: 4397351--4397404 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
4397341 TTGAATTTTT
* *
4397351 TTCGAATCGAGTCGAGTGAAATGAAA
1 TTCGAATCGAGTCGAATCAAATGAAA
* *
4397377 TTCGAGTCGAGTCGAATCAAGTGAAA
1 TTCGAATCGAGTCGAATCAAATGAAA
4397403 TT
1 TT
4397405 GTTCGAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (26 bp):
TTCGAATCGAGTCGAATCAAATGAAA
Found at i:4397622 original size:9 final size:10
Alignment explanation
Indices: 4397610--4397666 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
4397600 GAACATTTTT
4397610 AATTTTTTA-
1 AATTTTTTAG
*
4397619 AA-TTTTTAT
1 AATTTTTTAG
*
4397628 ATTTTTTTAG
1 AATTTTTTAG
4397638 AATTTTTTTAG
1 AA-TTTTTTAG
*
4397649 AA-TTTTTAT
1 AATTTTTTAG
4397658 AATTTTTTA
1 AATTTTTTA
4397667 AAAATATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 6 0.15
9 11 0.28
10 13 0.32
11 10 0.25
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (10 bp):
AATTTTTTAG
Found at i:4397665 original size:11 final size:11
Alignment explanation
Indices: 4397628--4397655 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4397618 AAATTTTTAT
4397628 ATTTTTTTAGA
1 ATTTTTTTAGA
4397639 ATTTTTTTAGA
1 ATTTTTTTAGA
4397650 ATTTTT
1 ATTTTT
4397656 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (11 bp):
ATTTTTTTAGA
Found at i:4397740 original size:21 final size:20
Alignment explanation
Indices: 4397661--4397749 Score: 74
Period size: 20 Copynumber: 4.3 Consensus size: 20
4397651 TTTTTATAAT
*
4397661 TTTTTAAAAATATAAATTTTGGGA
1 TTTTTAAAAAT-T--ATTTT-GAA
*
4397685 TTTTTATAAA-TATTTT-AA
1 TTTTTAAAAATTATTTTGAA
*
4397703 ATTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
* *
4397723 TTTTTGAAAATTATTTTTTAA
1 TTTTTAAAAATTA-TTTTGAA
4397744 TTTTTA
1 TTTTTA
4397750 TTGAGAGAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
18 9 0.17
19 6 0.11
20 18 0.33
21 11 0.20
22 1 0.02
24 9 0.17
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:4404577 original size:54 final size:54
Alignment explanation
Indices: 4404460--4404581 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 54
4404450 GTGTTTCAAG
* * *
4404460 TCAGTGAGTTACACGGCCTATCACCTGGCTCGGCACACGGGCGTCTGTGGCAAT
1 TCAGTGAGTTACACGACCTAGCACCTGGCTCGGCACACGGGCGTCTGTGGCAAC
* * * *
4404514 TGAGAGAGTTACACGACCTAGCACAC-GGC-CTGGCACACGGGCGTGT-TGGGTAAC
1 TCAGTGAGTTACACGACCTAGCAC-CTGGCTC-GGCACACGGGCGTCTGT-GGCAAC
4404568 TCAGTGAGTTACAC
1 TCAGTGAGTTACAC
4404582 AGGTGAGGAC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
53 2 0.04
54 53 0.95
55 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.30, T:0.20
Consensus pattern (54 bp):
TCAGTGAGTTACACGACCTAGCACCTGGCTCGGCACACGGGCGTCTGTGGCAAC
Found at i:4407361 original size:23 final size:23
Alignment explanation
Indices: 4407343--4407389 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4407333 ACTCTTGTGT
*
4407343 TAGAAAATTACATTTTCTTCGTA
1 TAGAAAACTACATTTTCTTCGTA
*
4407366 TAGAAAACTGCATTTTCTTCGTA
1 TAGAAAACTACATTTTCTTCGTA
4407389 T
1 T
4407390 TTATAGTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (23 bp):
TAGAAAACTACATTTTCTTCGTA
Found at i:4429226 original size:24 final size:24
Alignment explanation
Indices: 4429196--4429249 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
4429186 CTGTGGAGAT
* *
4429196 TGATGATGCTT-TGGTGATTGAAGA
1 TGATGATACTTCTGATGA-TGAAGA
*
4429220 TGATGATATTTCTGATGATGAAGA
1 TGATGATACTTCTGATGATGAAGA
4429244 TGATGA
1 TGATGA
4429250 ACATGAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.37
Consensus pattern (24 bp):
TGATGATACTTCTGATGATGAAGA
Found at i:4434343 original size:16 final size:17
Alignment explanation
Indices: 4434318--4434351 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4434308 TTAGAAATTG
*
4434318 TAAAAGATTATA-AAAA
1 TAAAAAATTATATAAAA
4434334 TAAAAAATTATATAAAA
1 TAAAAAATTATATAAAA
4434351 T
1 T
4434352 GATTAAAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAAAAATTATATAAAA
Found at i:4434377 original size:18 final size:18
Alignment explanation
Indices: 4434327--4434377 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
4434317 GTAAAAGATT
*
4434327 ATAAAAATAA-AAAA-TT
1 ATAAAAATAATAAAAGTG
* *
4434343 ATATAAAATGATTAAAGTG
1 ATA-AAAATAATAAAAGTG
4434362 ATAAAAATAATAAAAG
1 ATAAAAATAATAAAAG
4434378 ATGTAGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 3 0.11
17 6 0.22
18 14 0.52
19 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (18 bp):
ATAAAAATAATAAAAGTG
Found at i:4434527 original size:17 final size:17
Alignment explanation
Indices: 4434505--4434539 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4434495 TTTATACAAT
4434505 ATTTTAATATTTTATAA
1 ATTTTAATATTTTATAA
* *
4434522 ATTTTAATTTTTTTTAA
1 ATTTTAATATTTTATAA
4434539 A
1 A
4434540 ATTATACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTAATATTTTATAA
Found at i:4434550 original size:18 final size:19
Alignment explanation
Indices: 4434514--4434551 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4434504 TATTTTAATA
*
4434514 TTTTATAAATTTTAATTTT
1 TTTTATAAATTATAATTTT
*
4434533 TTTTA-AAATTATACTTTT
1 TTTTATAAATTATAATTTT
4434551 T
1 T
4434552 GTTTTCCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATAAATTATAATTTT
Found at i:4435837 original size:17 final size:18
Alignment explanation
Indices: 4435810--4435843 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4435800 ATTTACAAAA
*
4435810 TATGTATATATATATAAG
1 TATGTATATATAAATAAG
4435828 TATG-ATATATAAATAA
1 TATGTATATATAAATAA
4435844 ATTTTGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
TATGTATATATAAATAAG
Found at i:4436049 original size:26 final size:27
Alignment explanation
Indices: 4435982--4436050 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 27
4435972 TAGAAAATGC
* *
4435982 ATGTATATGCATGGATTATAAAATATGGA
1 ATGTATAT--ATGTATTATAAAATATGAA
* *
4436011 ATATATATATGTATTATAAAATGT-AA
1 ATGTATATATGTATTATAAAATATGAA
4436037 ATGTATATATGTAT
1 ATGTATATATGTAT
4436051 ACATGTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 14 0.40
27 14 0.40
29 7 0.20
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.41
Consensus pattern (27 bp):
ATGTATATATGTATTATAAAATATGAA
Found at i:4436238 original size:3 final size:3
Alignment explanation
Indices: 4436230--4436271 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
4436220 AAAACGTAAC
4436230 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4436272 GCAATATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4438032 original size:10 final size:10
Alignment explanation
Indices: 4438017--4438076 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
4438007 TAATAAATTA
4438017 ATAATATTTT
1 ATAATATTTT
4438027 ATAATA---T
1 ATAATATTTT
4438034 ATAATATTTT
1 ATAATATTTT
*
4438044 ATATTATTTTT
1 ATAATA-TTTT
4438055 ATAATATTTCT
1 ATAATATTT-T
4438066 A-AAT-TTTT
1 ATAATATTTT
4438074 ATA
1 ATA
4438077 CAATTTTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
7 7 0.17
8 2 0.05
9 4 0.10
10 18 0.43
11 11 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
ATAATATTTT
Found at i:4438058 original size:21 final size:19
Alignment explanation
Indices: 4438033--4438093 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 19
4438023 TTTTATAATA
4438033 TATAATATTTTATATTATTTT
1 TATAATATTTTA-A-TATTTT
4438054 TATAATATTTCTAA-ATTTT
1 TATAATATTT-TAATATTTT
4438073 TATACA-ATTTTAATATTTT
1 TATA-ATATTTTAATATTTT
4438092 TA
1 TA
4438094 GAATTAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
18 3 0.08
19 20 0.54
20 1 0.03
21 11 0.30
22 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TATAATATTTTAATATTTT
Found at i:4440163 original size:19 final size:21
Alignment explanation
Indices: 4440112--4440164 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 21
4440102 TTTTTTTTGC
*
4440112 AAAATC-AAATTTTTCTTTAA
1 AAAATCAAAACTTTTCTTTAA
**
4440132 AAAATCATTACTTTTC-TT-A
1 AAAATCAAAACTTTTCTTTAA
4440151 AAAATCAAAACTTT
1 AAAATCAAAACTTT
4440165 ATTTAGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 13 0.48
20 8 0.30
21 6 0.22
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATCAAAACTTTTCTTTAA
Found at i:4440213 original size:23 final size:23
Alignment explanation
Indices: 4440177--4440228 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
4440167 TTAGAAATAG
**
4440177 TTAAAAAAGATCAAAATTTTGTT
1 TTAAAAAAGATCAAAATTTTCCT
*
4440200 TTAAAAAA-ATTCAAACTTTTCCT
1 TTAAAAAAGA-TCAAAATTTTCCT
4440223 TTAAAA
1 TTAAAA
4440229 TGACTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (23 bp):
TTAAAAAAGATCAAAATTTTCCT
Found at i:4440361 original size:22 final size:21
Alignment explanation
Indices: 4440327--4440373 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
4440317 GAAATAGAAA
4440327 AAAAAAATCAAAACTTTAT-TTT
1 AAAAAAATCAAAA-TTT-TCTTT
* *
4440349 AAAAAATTTAAAATTTTCTTT
1 AAAAAAATCAAAATTTTCTTT
4440370 AAAA
1 AAAA
4440374 TGACTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 10 0.45
22 11 0.50
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAAATCAAAATTTTCTTT
Found at i:4440366 original size:146 final size:146
Alignment explanation
Indices: 4440112--4440582 Score: 580
Period size: 149 Copynumber: 3.2 Consensus size: 146
4440102 TTTTTTTTGC
* * * * * *
4440112 AAAATC-AAA-TTTTTCTTTAAAAAATCATTACTTTTCTTAAAAATCAAAAC-TTTATTTAGAAA
1 AAAATCTAAACTTTCTCTTTAAAAAAACACTATTTTTCTTAAAGATCAAAACTTTTATTTTGAAA
** * * * *
4440174 TAGTTAAAAAAGATCAAAATTTTGTTTTAAAAAAATTCAAACTTTTCCTTTAAAATGACTAAAAA
66 TAGAAAAAAAAAATCAAAACTTTGTTTT-AAAAAATTTAAAATTTTCCTTTAAAATGACTAAAAA
*
4440239 ACA-A-ATTTTTATTTTA
130 A-ATAGATTTTTATTTTT
4440255 AAAATCTAAACTTTCTCTTTAAGAAAAACACTATTTTTCTTAAAGATCAAAACTTTTATTTTGAA
1 AAAATCTAAACTTTCTCTTTAA-AAAAACACTATTTTTCTTAAAGATCAAAACTTTTATTTTGAA
*
4440320 ATAGAAAAAAAAAATCAAAACTTTATTTTAAAAAATTTAAAATTTT-CTTTAAAATGACTAAAAA
65 ATAGAAAAAAAAAATCAAAACTTTGTTTTAAAAAATTTAAAATTTTCCTTTAAAATGACTAAAAA
4440384 AATAGATTTTTATTTTTT
130 AATAGATTTTTA-TTTTT
* * * *
4440402 AAAATCTAAAATTTGTCCTTTTAAAAAAAACGCTATTTTTCTTAAAGATCAAAGCTTTTATTTTG
1 AAAATCTAAACTTTCT-C-TTT-AAAAAAACACTATTTTTCTTAAAGATCAAAACTTTTATTTTG
* *
4440467 AAATAGTTGAAAAAAAAATCAAAACTTTGTTTT-AAAAATTT-AAACTTTCCTTTAAAATGACTA
63 AAATAG--AAAAAAAAAATCAAAACTTTGTTTTAAAAAATTTAAAATTTTCCTTTAAAATGACT-
4440530 AAAAAAAATAGATTTTTAATTTTT
125 -AAAAAAATAGATTTTT-ATTTTT
4440554 AAAATCTAAACTTTCTCTTTTTAAAAAAA
1 AAAATCTAAACTTTCTC--TTTAAAAAAA
4440583 ATCTAAACTT
Statistics
Matches: 288, Mismatches: 23, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
143 6 0.02
144 4 0.01
145 30 0.10
146 48 0.17
147 52 0.18
148 1 0.00
149 53 0.18
150 23 0.08
151 31 0.11
152 39 0.14
153 1 0.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (146 bp):
AAAATCTAAACTTTCTCTTTAAAAAAACACTATTTTTCTTAAAGATCAAAACTTTTATTTTGAAA
TAGAAAAAAAAAATCAAAACTTTGTTTTAAAAAATTTAAAATTTTCCTTTAAAATGACTAAAAAA
ATAGATTTTTATTTTT
Found at i:4440467 original size:149 final size:148
Alignment explanation
Indices: 4440143--4440583 Score: 597
Period size: 147 Copynumber: 3.0 Consensus size: 148
4440133 AAATCATTAC
* * ** * *
4440143 TTTTCTTAAAAATCAAAAC-TTTATTTAGAAATAGTTAAAAAAGATCAAAATTTTGTTTTAAAAA
1 TTTTCTTAAAGATCAAAACTTTTATTTTGAAATAGAAAAAAAAAATCAAAACTTTGTTTT-AAAA
* *
4440207 AATTCAAACTTTTCCTTTAAAATGACTAAAAAACA-A-ATTTTTATTTTAAAAATCTAAACTTTC
65 AATTTAAACTTTT-CTTTAAAATGACTAAAAAA-ATAGATTTTTATTTTTAAAATCTAAACTTTC
*
4440270 T-C-TTTAAGAAAAACACTAT
128 TCCTTTTAAAAAAAACACTAT
*
4440289 TTTTCTTAAAGATCAAAACTTTTATTTTGAAATAGAAAAAAAAAATCAAAACTTTATTTTAAAAA
1 TTTTCTTAAAGATCAAAACTTTTATTTTGAAATAGAAAAAAAAAATCAAAACTTTGTTTTAAAAA
* * *
4440354 ATTTAAAATTTTCTTTAAAATGACTAAAAAAATAGATTTTTATTTTTTAAAATCTAAAATTTGTC
66 ATTTAAACTTTTCTTTAAAATGACTAAAAAAATAGATTTTTA-TTTTTAAAATCTAAACTTTCTC
*
4440419 CTTTTAAAAAAAACGCTAT
130 CTTTTAAAAAAAACACTAT
* *
4440438 TTTTCTTAAAGATCAAAGCTTTTATTTTGAAATAGTTGAAAAAAAAATCAAAACTTTGTTTT-AA
1 TTTTCTTAAAGATCAAAACTTTTATTTTGAAATAG--AAAAAAAAAATCAAAACTTTGTTTTAAA
*
4440502 AAATTTAAACTTTCCTTTAAAATGACTAAAAAAAAATAGATTTTTAATTTTTAAAATCTAAACTT
64 AAATTTAAACTTTTCTTTAAAATGACT--AAAAAAATAGATTTTT-ATTTTTAAAATCTAAACTT
*
4440567 TCTCTTTTTAAAAAAAA
126 TCTCCTTTTAAAAAAAA
4440584 TCTAAACTTT
Statistics
Matches: 262, Mismatches: 22, Indels: 16
0.87 0.07 0.05
Matches are distributed among these distances:
144 1 0.00
145 20 0.08
146 40 0.15
147 52 0.20
148 1 0.00
149 49 0.19
150 27 0.10
151 23 0.09
152 48 0.18
153 1 0.00
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (148 bp):
TTTTCTTAAAGATCAAAACTTTTATTTTGAAATAGAAAAAAAAAATCAAAACTTTGTTTTAAAAA
ATTTAAACTTTTCTTTAAAATGACTAAAAAAATAGATTTTTATTTTTAAAATCTAAACTTTCTCC
TTTTAAAAAAAACACTAT
Found at i:4441324 original size:16 final size:16
Alignment explanation
Indices: 4441303--4441334 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4441293 AAACCTATTA
4441303 GGCTTAATTGAGATTT
1 GGCTTAATTGAGATTT
4441319 GGCTTAATTGAGATTT
1 GGCTTAATTGAGATTT
4441335 TGAAAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (16 bp):
GGCTTAATTGAGATTT
Found at i:4442424 original size:21 final size:20
Alignment explanation
Indices: 4442400--4442439 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4442390 AATTGGATTG
4442400 AATTGAATATGAAATTTATTA
1 AATTG-ATATGAAATTTATTA
* *
4442421 AATTGATGTTAAATTTATT
1 AATTGATATGAAATTTATT
4442440 TATATAGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (20 bp):
AATTGATATGAAATTTATTA
Found at i:4442757 original size:23 final size:23
Alignment explanation
Indices: 4442723--4442776 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
4442713 CGAACACACC
* * *
4442723 ATAGCTCGCATGAGCGTCTCGAT
1 ATAGCTCACATGAGCATCCCGAT
4442746 ATAGCTCACATGAGCATCCCGAT
1 ATAGCTCACATGAGCATCCCGAT
4442769 ATAAGCTC
1 AT-AGCTC
4442777 TTTTGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (23 bp):
ATAGCTCACATGAGCATCCCGAT
Found at i:4443069 original size:24 final size:24
Alignment explanation
Indices: 4442982--4443071 Score: 69
Period size: 24 Copynumber: 3.7 Consensus size: 24
4442972 GTTAAACTCG
*
4442982 CATGAGCTTTCTGATT-TAAGCTCT
1 CATGAGCTTTCTG-TTATAAGCTCA
* * *
4443006 TATGAGCTTCCTGTTATTAAGCCCGA
1 CATGAGCTTTCTGTTA-TAAGCTC-A
* *
4443032 -ATAAGC-TTCTTGTTACAAGCTCA
1 CATGAGCTTTC-TGTTATAAGCTCA
4443055 CATGAGCTTTCTGTTAT
1 CATGAGCTTTCTGTTAT
4443072 TTGGCTTGGA
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
23 3 0.06
24 28 0.56
25 19 0.38
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (24 bp):
CATGAGCTTTCTGTTATAAGCTCA
Found at i:4449324 original size:19 final size:19
Alignment explanation
Indices: 4449277--4449323 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4449267 AACAAGCAAC
4449277 TTTCATTTTTCTTCTTTTCT
1 TTTC-TTTTTCTTCTTTTCT
* *
4449297 TTTCTTTTTGTTCTTTTGT
1 TTTCTTTTTCTTCTTTTCT
4449316 TTT-TTTTT
1 TTTCTTTTT
4449324 TTTTTTTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.20
19 16 0.64
20 4 0.16
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (19 bp):
TTTCTTTTTCTTCTTTTCT
Found at i:4453997 original size:20 final size:20
Alignment explanation
Indices: 4453933--4454017 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
4453923 ATTTTATATT
* *
4453933 TTTTTAAAATATAATTTTTTAA
1 TTTTTAAAAT-TTA-TTTTGAA
4453955 TTTTTATAAA--TATTTTGAA
1 TTTTTA-AAATTTATTTTGAA
*
4453974 -TTTTAAAATTTATTTTTAA
1 TTTTTAAAATTTATTTTGAA
*
4453993 TTTTTAAAAATTATTTTGAA
1 TTTTTAAAATTTATTTTGAA
4454013 TTTTT
1 TTTTT
4454018 GTAATTTTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
17 3 0.06
18 5 0.09
19 14 0.26
20 23 0.43
22 6 0.11
23 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTTAAAATTTATTTTGAA
Found at i:4454008 original size:39 final size:40
Alignment explanation
Indices: 4453934--4454016 Score: 125
Period size: 38 Copynumber: 2.1 Consensus size: 40
4453924 TTTTATATTT
*
4453934 TTTTAAAATATAATTTTTTAATTTTTATAAATATTTTGAA
1 TTTTAAAATATAATTTTTTAATTTTTAAAAATATTTTGAA
*
4453974 TTTTAAAAT-TTA-TTTTTAATTTTTAAAAATTATTTTGAA
1 TTTTAAAATATAATTTTTTAATTTTTAAAAA-TATTTTGAA
4454013 TTTT
1 TTTT
4454017 TGTAATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 16 0.40
39 15 0.38
40 9 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (40 bp):
TTTTAAAATATAATTTTTTAATTTTTAAAAATATTTTGAA
Found at i:4454614 original size:16 final size:16
Alignment explanation
Indices: 4454593--4454623 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4454583 GTTTATTTAA
*
4454593 TATTTTTATATATTTT
1 TATTTTTAAATATTTT
4454609 TATTTTTAAATATTT
1 TATTTTTAAATATTT
4454624 AAAAAATTAA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTAAATATTTT
Found at i:4458027 original size:37 final size:37
Alignment explanation
Indices: 4457986--4458061 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
4457976 TTTTGAGTTT
4457986 AAAAAAGGGGTGAATTGTATGTTATTTCTTCTATTTC
1 AAAAAAGGGGTGAATTGTATGTTATTTCTTCTATTTC
4458023 AAAAAAGGGGTGAATTGTATGTTATTTCTTCTATTTC
1 AAAAAAGGGGTGAATTGTATGTTATTTCTTCTATTTC
4458060 AA
1 AA
4458062 TGGAAAATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (37 bp):
AAAAAAGGGGTGAATTGTATGTTATTTCTTCTATTTC
Found at i:4459558 original size:13 final size:13
Alignment explanation
Indices: 4459540--4459564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4459530 AAATCTGTTT
4459540 TGAGTGCTGCTCA
1 TGAGTGCTGCTCA
4459553 TGAGTGCTGCTC
1 TGAGTGCTGCTC
4459565 TTGTTAAGGC
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:0.12, C:0.24, G:0.32, T:0.32
Consensus pattern (13 bp):
TGAGTGCTGCTCA
Found at i:4460046 original size:16 final size:16
Alignment explanation
Indices: 4460025--4460066 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
4460015 TTATTAAATT
*
4460025 ATATATTTTAATTATA
1 ATATATTTTAATAATA
4460041 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
4460056 AT-TATGTTTAA
1 ATATAT-TTTAA
4460067 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:4460051 original size:15 final size:15
Alignment explanation
Indices: 4460016--4460057 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4460006 TTAAGAATTT
*
4460016 TATTAAATTAT-ATA
1 TATTTAATTATAATA
4460030 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
4460044 TATTTAATAATAAT
1 TATTTAATTATAAT
4460058 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:4460197 original size:18 final size:17
Alignment explanation
Indices: 4460169--4460203 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4460159 ATTATTAAGA
*
4460169 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
4460186 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
4460204 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:4460202 original size:157 final size:157
Alignment explanation
Indices: 4460000--4460316 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
4459990 ATAAGAATAT
*
4460000 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
4460065 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAAATTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
*
4460130 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
4460157 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
4460222 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
*
4460287 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
4460314 TAA
1 TAA
4460317 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:4460449 original size:45 final size:43
Alignment explanation
Indices: 4460349--4460458 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
4460339 TTTTCCATTA
4460349 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
4460388 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
4460433 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
4460459 CCTCTAATCT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:4460460 original size:16 final size:16
Alignment explanation
Indices: 4460439--4460506 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
4460429 GATTTGCTAT
*
4460439 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
* *
4460455 TACACCTCTAATCTAT
1 TACACCTCTAATCCAA
4460471 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
4460487 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
4460503 TACA
1 TACA
4460507 GCGAACCAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.35, C:0.34, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:4460471 original size:32 final size:32
Alignment explanation
Indices: 4460435--4460506 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
4460425 AGTTGATTTG
*
4460435 CTATTACACCTCTATTCCAATACACCTCTAAT
1 CTATTACACCTCTAATCCAATACACCTCTAAT
4460467 CTATTACACCTCTAATCCAATACACCTCTAAT
1 CTATTACACCTCTAATCCAATACACCTCTAAT
*
4460499 CTAATACA
1 CTATTACA
4460507 GCGAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.32
Consensus pattern (32 bp):
CTATTACACCTCTAATCCAATACACCTCTAAT
Found at i:4464583 original size:34 final size:34
Alignment explanation
Indices: 4464540--4464608 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
4464530 TGCATGTAAG
*
4464540 TCCATTCTAAACCCATTTTTAGTAATTTTTATGT
1 TCCATTCTAAACCCATTTTTAGTAATTTTCATGT
* ***
4464574 TCCATTCTAAGCTTGTTTTTAGTAATTTTCATGT
1 TCCATTCTAAACCCATTTTTAGTAATTTTCATGT
4464608 T
1 T
4464609 TTTGAGATCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (34 bp):
TCCATTCTAAACCCATTTTTAGTAATTTTCATGT
Found at i:4471104 original size:3 final size:3
Alignment explanation
Indices: 4471096--4471122 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4471086 AAAATAATCC
4471096 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
4471123 CCTTCCCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4489245 original size:22 final size:22
Alignment explanation
Indices: 4489172--4489245 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
4489162 AAGTTACTAT
4489172 AGGAGATATGCTGAGAAAAACC
1 AGGAGATATGCTGAGAAAAACC
*
4489194 AGGAGA-AT--TGCA-AATAACTCC
1 AGGAGATATGCTG-AGAA-AA-ACC
4489215 AAAAGGAGATATGCTGAGAAAAACC
1 ---AGGAGATATGCTGAGAAAAACC
4489240 AGGAGA
1 AGGAGA
4489246 ATTAAAGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 20
0.65 0.03 0.32
Matches are distributed among these distances:
19 4 0.10
20 3 0.08
21 4 0.10
22 12 0.30
24 6 0.15
25 4 0.10
26 3 0.08
27 4 0.10
ACGTcount: A:0.47, C:0.14, G:0.26, T:0.14
Consensus pattern (22 bp):
AGGAGATATGCTGAGAAAAACC
Found at i:4496857 original size:19 final size:18
Alignment explanation
Indices: 4496829--4496864 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4496819 ACCTTGTCAC
4496829 CTTGCTTTCTCACACTTT
1 CTTGCTTTCTCACACTTT
*
4496847 CTTGACTTTCTCTCACTT
1 CTTG-CTTTCTCACACTT
4496865 CCAGCCATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.11, C:0.33, G:0.06, T:0.50
Consensus pattern (18 bp):
CTTGCTTTCTCACACTTT
Found at i:4512021 original size:4 final size:4
Alignment explanation
Indices: 4512012--4512036 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4512002 TATCGTTCAC
4512012 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
4512037 TTCTAGGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:4513792 original size:27 final size:26
Alignment explanation
Indices: 4513762--4513819 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
4513752 CATTAGACTG
* *
4513762 GTTGATTCATGAGCCGATACAAAACTA
1 GTTGATCCACGAGCCGATAC-AAACTA
* *
4513789 GTTGATCCGCGAGTCGATACAAACTA
1 GTTGATCCACGAGCCGATACAAACTA
4513815 GTTGA
1 GTTGA
4513820 ATAGGATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (26 bp):
GTTGATCCACGAGCCGATACAAACTA
Found at i:4523758 original size:287 final size:287
Alignment explanation
Indices: 4523226--4523801 Score: 931
Period size: 287 Copynumber: 2.0 Consensus size: 287
4523216 ATCGCGGTCT
* * *
4523226 TCATCGGCGATATTCTGGTTTACTTTAAGACCGAGGATGAGCATGATGAACAACTAAGAGTAGTG
1 TCATCGACAATATTCTAGTTTACTTTAAGACCGAGGATGAGCATGATGAACAACTAAGAGTAGTG
* * * *
4523291 CTTCAGATACTCTAAGAGAAGCAGCTCTATGCTAAGTTTAGCAAGTGTGAGTTCTGGTTGCGTGA
66 CTTCAGATACTCCAAGAGAAGCAACTCTATGCTAAGTTGAGCAAGTGTGAGCTCTGGTTGCGTGA
*
4523356 GGTAACTTTTCTGGGTCATGTGGTTTCCACTGAGGGGATTCAAGTTGATCTAAAGAAGATTGAAG
131 GGTAACTTTTCTGGGTCATATGGTTTCCACTGAGGGGATTCAAGTTGATCTAAAGAAGATTGAAG
** *
4523421 TTGCGTTTGATTGGAAGCAACCTAAGAATATATCTGAGATTCGTAGTTTTCTGGGTCTTGCGGGG
196 TTGCACTTGATTGGAAGCAACCTAAGAATATATCTGAGATTCGCAGTTTTCTGGGTCTTGCGGGG
*
4523486 TATTATCGGTGTTTTGTTGAGGGGTTC
261 TATTATCAGTGTTTTGTTGAGGGGTTC
4523513 TCATCGACAATATTCTAGTTTACTTTAAGACCGAGGATGAGCATGATGAACAACTAAGAGTAGTG
1 TCATCGACAATATTCTAGTTTACTTTAAGACCGAGGATGAGCATGATGAACAACTAAGAGTAGTG
* * *
4523578 CTTCAGATACTCCGAGGGAAGCAACTCTATGTTAAGTTGAGCAAGTGTGAGCTCTGGTTGCGTGA
66 CTTCAGATACTCCAAGAGAAGCAACTCTATGCTAAGTTGAGCAAGTGTGAGCTCTGGTTGCGTGA
** * *
4523643 GGTAACTTTTCTGGGTCATATGGTTTCTGCTGAGGGGATTCGAGTTGATCTGAAGAAGATTG-AG
131 GGTAACTTTTCTGGGTCATATGGTTTCCACTGAGGGGATTCAAGTTGATCTAAAGAAGATTGAAG
*
4523707 ATTGCACTTGATTGGAAGCAGA-CTAAGAATGTATCTGAGATTCGCAGTTTTCTGGGTCTTGCGG
196 -TTGCACTTGATTGGAAGCA-ACCTAAGAATATATCTGAGATTCGCAGTTTTCTGGGTCTTGCGG
*
4523771 GGTATTATCAGTGTTTTTTTGAGGGGTTC
259 GGTATTATCAGTGTTTTGTTGAGGGGTTC
4523800 TC
1 TC
4523802 TTTGATTGCA
Statistics
Matches: 266, Mismatches: 21, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
286 2 0.01
287 263 0.99
288 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (287 bp):
TCATCGACAATATTCTAGTTTACTTTAAGACCGAGGATGAGCATGATGAACAACTAAGAGTAGTG
CTTCAGATACTCCAAGAGAAGCAACTCTATGCTAAGTTGAGCAAGTGTGAGCTCTGGTTGCGTGA
GGTAACTTTTCTGGGTCATATGGTTTCCACTGAGGGGATTCAAGTTGATCTAAAGAAGATTGAAG
TTGCACTTGATTGGAAGCAACCTAAGAATATATCTGAGATTCGCAGTTTTCTGGGTCTTGCGGGG
TATTATCAGTGTTTTGTTGAGGGGTTC
Found at i:4527501 original size:26 final size:24
Alignment explanation
Indices: 4527466--4527514 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
4527456 TTTTATGAAC
* *
4527466 TTTTTATATTCTTTTTATTTTTTAT
1 TTTTTATATT-TTTATAATTTTTAT
4527491 TTTTGTATATTTTTATAATTTTTA
1 TTTT-TATATTTTTATAATTTTTA
4527515 AATTATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTTTATATTTTTATAATTTTTAT
Found at i:4528123 original size:29 final size:30
Alignment explanation
Indices: 4528091--4528151 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
4528081 TCAATTTTTA
*
4528091 ATGTATAAAATTGCACA-AAATTAAAGTTC
1 ATGTATAAAATTGCACATAAACTAAAGTTC
*
4528120 ATGTATAACATTGCACATTAAACTAAAGTTC
1 ATGTATAAAATTGCACA-TAAACTAAAGTTC
4528151 A
1 A
4528152 ATTATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 16 0.57
31 12 0.43
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (30 bp):
ATGTATAAAATTGCACATAAACTAAAGTTC
Found at i:4528778 original size:83 final size:82
Alignment explanation
Indices: 4528624--4528779 Score: 199
Period size: 83 Copynumber: 1.9 Consensus size: 82
4528614 TTGAACATAC
* *
4528624 ATCAATATTAATAATAAACGAATTAATTCGATTATATTTTAAGTAGAAATCGAATATCATTTTAA
1 ATCAATATTAATAATAAACGAATTAATTCGATTATATTATAAGTAGAAATCGAATAT-ATTTAAA
*
4528689 GAAAAAAAAGTCAACTTT
65 AAAAAAAAAGTCAACTTT
* * * * *
4528707 ATCAATTTTAATAATAAACGAATTTATTCTATTAT-TTATAAGTAGAAATGGAATAT-TTTCCAA
1 ATCAATATTAATAATAAACGAATTAATTCGATTATATTATAAGTAGAAATCGAATATATTT-AAA
*
4528770 AAATAAAAAG
65 AAAAAAAAAG
4528780 CTTCACGATT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 3 0.05
81 10 0.16
82 19 0.30
83 32 0.50
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (82 bp):
ATCAATATTAATAATAAACGAATTAATTCGATTATATTATAAGTAGAAATCGAATATATTTAAAA
AAAAAAAAGTCAACTTT
Found at i:4529252 original size:26 final size:25
Alignment explanation
Indices: 4529213--4529262 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
4529203 ATTTTTAGAA
4529213 TTTTTAAAAAATTTAAAATTTGAAT
1 TTTTTAAAAAATTTAAAATTTGAAT
* **
4529238 TTTTTATAAATATTTTGAATTTGAA
1 TTTTTA-AAAAATTTAAAATTTGAA
4529263 ATTTATTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (25 bp):
TTTTTAAAAAATTTAAAATTTGAAT
Found at i:4530185 original size:18 final size:18
Alignment explanation
Indices: 4530150--4530185 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4530140 TTATAAAAAG
4530150 TTACAAATTTTTATTTTT
1 TTACAAATTTTTATTTTT
*
4530168 TTACAATTTTTCTATTTT
1 TTACAAATTTT-TATTTT
4530186 CAATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TTACAAATTTTTATTTTT
Found at i:4530654 original size:29 final size:29
Alignment explanation
Indices: 4530620--4530676 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
4530610 ACACCTTTTT
*
4530620 ACTTTC-CCCAAATACTTTTACTTCCCCTC
1 ACTTTCTCCCAAA-ACTTTTACTACCCCTC
4530649 ACTTTCTCCCAAAACTTTTACTACCCCT
1 ACTTTCTCCCAAAACTTTTACTACCCCT
4530677 GTCATCCCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37
Consensus pattern (29 bp):
ACTTTCTCCCAAAACTTTTACTACCCCTC
Found at i:4539525 original size:21 final size:21
Alignment explanation
Indices: 4539501--4539552 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
4539491 GTTTAACTTA
* *
4539501 TATGAGTTTCCGTTCAGCTCT
1 TATGAGTTTCCGTTCAACCCT
*
4539522 TATGAGCTTCCGTTCAACCCT
1 TATGAGTTTCCGTTCAACCCT
*
4539543 TATGGGTTTC
1 TATGAGTTTC
4539553 TGTTATCACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.40
Consensus pattern (21 bp):
TATGAGTTTCCGTTCAACCCT
Found at i:4541653 original size:12 final size:12
Alignment explanation
Indices: 4541636--4541660 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4541626 GGTGTTCATT
4541636 CGGTTAACTGAC
1 CGGTTAACTGAC
4541648 CGGTTAACTGAC
1 CGGTTAACTGAC
4541660 C
1 C
4541661 CGAAATTACT
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:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (12 bp):
CGGTTAACTGAC
Found at i:4541832 original size:9 final size:9
Alignment explanation
Indices: 4541818--4541898 Score: 101
Period size: 9 Copynumber: 8.9 Consensus size: 9
4541808 TTTGGTTAAA
4541818 AATTACCCG
1 AATTACCCG
4541827 AATTACCCG
1 AATTACCCG
4541836 AATTACCCG
1 AATTACCCG
4541845 AATTACCCG
1 AATTACCCG
*
4541854 AATTAACCG
1 AATTACCCG
* *
4541863 AATTAACCA
1 AATTACCCG
4541872 AATTA-CCG
1 AATTACCCG
*
4541880 AAAAATACCCG
1 --AATTACCCG
4541891 AATTACCC
1 AATTACCC
4541899 AAAATTTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
8 2 0.03
9 55 0.86
10 4 0.06
11 3 0.05
ACGTcount: A:0.41, C:0.30, G:0.09, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:4542062 original size:13 final size:13
Alignment explanation
Indices: 4542044--4542073 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4542034 TTTTAGTTTT
4542044 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
4542057 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
4542070 ATTG
1 ATTG
4542074 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:4547027 original size:21 final size:21
Alignment explanation
Indices: 4546995--4547052 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
4546985 GCTTCTGTTT
*
4546995 AACTCATATGAGTTTCCATTC
1 AACTCTTATGAGTTTCCATTC
* * *
4547016 AGCTCTTATGAGCTTCCGTTC
1 AACTCTTATGAGTTTCCATTC
*
4547037 AACTCTTATGGGTTTC
1 AACTCTTATGAGTTTC
4547053 TGTTTAGCAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.40
Consensus pattern (21 bp):
AACTCTTATGAGTTTCCATTC
Found at i:4547066 original size:42 final size:42
Alignment explanation
Indices: 4546965--4547067 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 42
4546955 TTATGTTTAC
* * * *
4546965 TTTCTATTTAGCTCTCACGAGCTTCTGTTTAACTCATATGAG
1 TTTCTATTTAGCTCTTATGAGCTTCCGTTCAACTCATATGAG
* * * *
4547007 TTTCCATTCAGCTCTTATGAGCTTCCGTTCAACTCTTATGGG
1 TTTCTATTTAGCTCTTATGAGCTTCCGTTCAACTCATATGAG
* *
4547049 TTTCTGTTTAGCACTTATG
1 TTTCTATTTAGCTCTTATG
4547068 TCCTTCTATT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (42 bp):
TTTCTATTTAGCTCTTATGAGCTTCCGTTCAACTCATATGAG
Found at i:4559668 original size:90 final size:90
Alignment explanation
Indices: 4559515--4559680 Score: 332
Period size: 90 Copynumber: 1.8 Consensus size: 90
4559505 CGGCGGATTC
4559515 ATTTCTAATCTGTTGTCTAATAACATTCGCTAACACTTACGCTTTTCTTTTCCTTCATCTACAAG
1 ATTTCTAATCTGTTGTCTAATAACATTCGCTAACACTTACGCTTTTCTTTTCCTTCATCTACAAG
4559580 ATTTTAGTGTCCCGGTGGACCATCA
66 ATTTTAGTGTCCCGGTGGACCATCA
4559605 ATTTCTAATCTGTTGTCTAATAACATTCGCTAACACTTACGCTTTTCTTTTCCTTCATCTACAAG
1 ATTTCTAATCTGTTGTCTAATAACATTCGCTAACACTTACGCTTTTCTTTTCCTTCATCTACAAG
4559670 ATTTTAGTGTC
66 ATTTTAGTGTC
4559681 TAATAACATT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.42
Consensus pattern (90 bp):
ATTTCTAATCTGTTGTCTAATAACATTCGCTAACACTTACGCTTTTCTTTTCCTTCATCTACAAG
ATTTTAGTGTCCCGGTGGACCATCA
Found at i:4560636 original size:21 final size:23
Alignment explanation
Indices: 4560611--4560656 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
4560601 AAAAACACAC
*
4560611 AAAACCCTTAA-ATTG-GTTCTA
1 AAAACCATTAACATTGTGTTCTA
*
4560632 AAAACCATTAACTTTGTGTTCTA
1 AAAACCATTAACATTGTGTTCTA
4560655 AA
1 AA
4560657 TCTTACACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 3 0.14
23 8 0.38
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (23 bp):
AAAACCATTAACATTGTGTTCTA
Found at i:4565262 original size:28 final size:26
Alignment explanation
Indices: 4565222--4565274 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
4565212 CTTTTCAATT
*
4565222 AATAAATTCTCTTTGAGTTTTTCTTTTC
1 AATAAATTCTC-TTAAG-TTTTCTTTTC
* *
4565250 AATAATTTTTCTTAAGTTTTCTTTT
1 AATAAATTCTCTTAAGTTTTCTTTT
4565275 AGAAGAGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 9 0.41
27 4 0.18
28 9 0.41
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (26 bp):
AATAAATTCTCTTAAGTTTTCTTTTC
Found at i:4569200 original size:10 final size:10
Alignment explanation
Indices: 4569185--4569209 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4569175 TATAACTTAC
4569185 AAATATGTAT
1 AAATATGTAT
4569195 AAATATGTAT
1 AAATATGTAT
4569205 AAATA
1 AAATA
4569210 CATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (10 bp):
AAATATGTAT
Found at i:4569381 original size:30 final size:28
Alignment explanation
Indices: 4569347--4569408 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
4569337 TAAAAGCCCT
4569347 TTTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTT-AAAATTTACCGAAATGGGCC-A
** *
4569377 TTTTTTTATTATTTACCGGAATGGGCCA
1 TTTTTTTAAAATTTACCGAAATGGGCCA
4569405 TTTT
1 TTTT
4569409 CCGCGAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 17 0.59
30 7 0.24
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (28 bp):
TTTTTTTAAAATTTACCGAAATGGGCCA
Found at i:4572681 original size:17 final size:17
Alignment explanation
Indices: 4572641--4572682 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
4572631 CCCTATATAC
*
4572641 AATTATATTATTATAAT
1 AATTATATTTTTATAAT
*
4572658 -A-TATATTTTTATATT
1 AATTATATTTTTATAAT
4572673 AATTATATTT
1 AATTATATTT
4572683 AAGCTTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTATATTTTTATAAT
Found at i:4572859 original size:20 final size:20
Alignment explanation
Indices: 4572825--4572866 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
4572815 AACTATTTAA
** *
4572825 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
4572845 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
4572865 AT
1 AT
4572867 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:4574915 original size:15 final size:16
Alignment explanation
Indices: 4574890--4574923 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4574880 AAGATGAAGC
*
4574890 GTTTGATAAATTTAAA
1 GTTTGATAAATCTAAA
4574906 GTTT-ATAAATCTAAA
1 GTTTGATAAATCTAAA
4574921 GTT
1 GTT
4574924 GAACTTCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (16 bp):
GTTTGATAAATCTAAA
Found at i:4578350 original size:21 final size:21
Alignment explanation
Indices: 4578326--4578365 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4578316 TGTACATTTC
4578326 CATAATAATTCATCTCAAATT
1 CATAATAATTCATCTCAAATT
* * *
4578347 CATATTATTTCATGTCAAA
1 CATAATAATTCATCTCAAA
4578366 ACTTTTCCCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (21 bp):
CATAATAATTCATCTCAAATT
Found at i:4578744 original size:26 final size:26
Alignment explanation
Indices: 4578679--4578749 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 26
4578669 AGTCATATCG
*
4578679 GGAAACTCTTG-AGAGCCATTAATCA
1 GGAAACTCTTGAAGAGCCATTAAACA
*** *
4578704 GGAAACTCACAAAGAGCCTTTAAACA
1 GGAAACTCTTGAAGAGCCATTAAACA
*
4578730 GGAAGCTCTTGAAGAGCCAT
1 GGAAACTCTTGAAGAGCCAT
4578750 ATAACGAGAC
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
25 8 0.23
26 27 0.77
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (26 bp):
GGAAACTCTTGAAGAGCCATTAAACA
Found at i:4580956 original size:20 final size:20
Alignment explanation
Indices: 4580933--4580974 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4580923 AACTATTTAA
* *
4580933 ATAATATTAATTGAATAGTT
1 ATAATATTAAATGAATAATT
4580953 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
4580973 AT
1 AT
4580975 GTGTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:4583889 original size:21 final size:21
Alignment explanation
Indices: 4583865--4583927 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
4583855 CATAGAAGCA
* *
4583865 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTGAACAGAAACC
* * * *
4583886 CATAAGGGTTGAACAGAAGCT
1 CATAAGAGCTGAACAGAAACC
*
4583907 CATAAGAGCTGAACGGAAACC
1 CATAAGAGCTGAACAGAAACC
4583928 TAAAAGGGTT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.14
Consensus pattern (21 bp):
CATAAGAGCTGAACAGAAACC
Found at i:4583926 original size:42 final size:42
Alignment explanation
Indices: 4583859--4584049 Score: 206
Period size: 42 Copynumber: 4.6 Consensus size: 42
4583849 AGGCTGCATA
* * * * * *
4583859 GAAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGAACA
1 GAAGCTCATAAGAGCTGAACTGAAACCCATAAGGGTTAAACT
* * *
4583901 GAAGCTCATAAGAGCTGAACGGAAACCTAAAAGGGTTAAACT
1 GAAGCTCATAAGAGCTGAACTGAAACCCATAAGGGTTAAACT
* * * *
4583943 GAAGCTTAAAATAGCTGAACTGAAACCCATTAGGGTTAAACT
1 GAAGCTCATAAGAGCTGAACTGAAACCCATAAGGGTTAAACT
*
4583985 GAAGCTCGA-AAGAGCTGAACTGAAACCCATTAGGGTTAAACT
1 GAAGCTC-ATAAGAGCTGAACTGAAACCCATAAGGGTTAAACT
* * *
4584027 GAAACTCATATGAG-TTAACTGAA
1 GAAGCTCATAAGAGCTGAACTGAA
4584050 GCTTATAAGA
Statistics
Matches: 127, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
41 9 0.07
42 117 0.92
43 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.19
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTGAACTGAAACCCATAAGGGTTAAACT
Found at i:4583984 original size:21 final size:21
Alignment explanation
Indices: 4583960--4584031 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
4583950 AAAATAGCTG
4583960 AACTGAAACCCATTAGGGTTA
1 AACTGAAACCCATTAGGGTTA
* * * * * *
4583981 AACTGAAGCTCGA-AAGAGCTG
1 AACTGAAAC-CCATTAGGGTTA
4584002 AACTGAAACCCATTAGGGTTA
1 AACTGAAACCCATTAGGGTTA
4584023 AACTGAAAC
1 AACTGAAAC
4584032 TCATATGAGT
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
20 2 0.05
21 33 0.89
22 2 0.05
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (21 bp):
AACTGAAACCCATTAGGGTTA
Found at i:4584043 original size:21 final size:21
Alignment explanation
Indices: 4584002--4584071 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
4583992 GAAAGAGCTG
* *
4584002 AACTGAAACCCAT-TAGGGTTA
1 AACTGAAACTCATAT-GAGTTA
4584023 AACTGAAACTCATATGAGTT-
1 AACTGAAACTCATATGAGTTA
* * * *
4584043 AACTGAAGCTTATAAGAGCTA
1 AACTGAAACTCATATGAGTTA
4584064 AACTGAAA
1 AACTGAAA
4584072 GCAAACATGG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 16 0.40
21 23 0.57
22 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (21 bp):
AACTGAAACTCATATGAGTTA
Found at i:4600022 original size:2 final size:2
Alignment explanation
Indices: 4600015--4600041 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4600005 CATGTGCATA
4600015 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
4600042 ACACACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4600835 original size:22 final size:22
Alignment explanation
Indices: 4600810--4600859 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
4600800 AATCCAAAAG
*
4600810 CATTTCTAAACATTCATT-TAA
1 CATTTCTAAACATCCATTCTAA
4600831 CCATTTCTAAACATCCATTCTAA
1 -CATTTCTAAACATCCATTCTAA
4600854 CATTTC
1 CATTTC
4600860 CACAATTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
CATTTCTAAACATCCATTCTAA
Found at i:4601704 original size:20 final size:20
Alignment explanation
Indices: 4601679--4601716 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4601669 TGTTGTACAG
4601679 AGGCACCAAAGTGCAAACAA
1 AGGCACCAAAGTGCAAACAA
*
4601699 AGGCACCGAAGTGCAAAC
1 AGGCACCAAAGTGCAAAC
4601717 CTATACAAGT
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:0.45, C:0.26, G:0.24, T:0.05
Consensus pattern (20 bp):
AGGCACCAAAGTGCAAACAA
Found at i:4607929 original size:12 final size:11
Alignment explanation
Indices: 4607914--4607944 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
4607904 TTTTTATTGT
4607914 TTATTATTATAA
1 TTATTATTAT-A
4607926 TTATTATTATA
1 TTATTATTATA
4607937 TTATTATT
1 TTATTATT
4607945 GTATGTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTATTATA
Found at i:4611556 original size:138 final size:138
Alignment explanation
Indices: 4611386--4611662 Score: 446
Period size: 138 Copynumber: 2.0 Consensus size: 138
4611376 TAGATAAAAC
* **
4611386 TAATATATAAATTTGATTCATACAAATTATTAATTATATATATTTTACCAAATTTATTAATATAA
1 TAATATATAAATATGATTCATACAAAAAATTAATTATATATATTTTACCAAATTTATTAATATAA
* * *
4611451 ACAATTATATTAATTAATTTCGGTCAAAATATAAAATATATGGAAATTAATATTCTTTTGGAAAG
66 ACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGAAAAG
4611516 AATATAAT
131 AATATAAT
* *
4611524 TAATATATGAATATGATTCATACAAAAAATTAATTGTATATATTTTACCAAATTTATTAATATAA
1 TAATATATAAATATGATTCATACAAAAAATTAATTATATATATTTTACCAAATTTATTAATATAA
* * * *
4611589 ACAGTTCTATTAATTAATTTCGGTTAAAATATAAAAGACATGGAATTTAATATTCTTTTGAAAAG
66 ACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGAAAAG
4611654 AATATAAT
131 AATATAAT
4611662 T
1 T
4611663 CATTTTTTTC
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 127 1.00
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (138 bp):
TAATATATAAATATGATTCATACAAAAAATTAATTATATATATTTTACCAAATTTATTAATATAA
ACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGAAAAG
AATATAAT
Found at i:4611774 original size:75 final size:76
Alignment explanation
Indices: 4611638--4611789 Score: 225
Period size: 75 Copynumber: 2.0 Consensus size: 76
4611628 ATGGAATTTA
* * * *
4611638 ATATTCTTTTGAAAAGAATATAATTCATTTTTTTCTAAATTTTCATTTGTCTTCTCTATTAATAC
1 ATATTCTTTCGAAAAGAATATAATTCA-TTTTTTCTAAATTTCCATTTGCCTTCTCTATTAATAA
4611703 GAGAATAATCTT
65 GAGAATAATCTT
* *
4611715 ATATTCTTTCGGAAAGAATATAATTC-TTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAG
1 ATATTCTTTCGAAAAGAATATAATTCATTTTTTCTAAATTTCCATTTGCCTTCTCTATTAATAAG
*
4611779 GGAATAATCTT
66 AGAATAATCTT
4611790 GGTTTTCCTT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 44 0.65
77 24 0.35
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (76 bp):
ATATTCTTTCGAAAAGAATATAATTCATTTTTTCTAAATTTCCATTTGCCTTCTCTATTAATAAG
AGAATAATCTT
Found at i:4615875 original size:29 final size:29
Alignment explanation
Indices: 4615833--4615893 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
4615823 TTCTCCATGT
4615833 AAGAATGTTGTTTTCACATATAACTACTC
1 AAGAATGTTGTTTTCACATATAACTACTC
4615862 AAGAATGTTGTTTTCACATATAACTACTC
1 AAGAATGTTGTTTTCACATATAACTACTC
4615891 AAG
1 AAG
4615894 CTCTAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (29 bp):
AAGAATGTTGTTTTCACATATAACTACTC
Found at i:4620982 original size:19 final size:18
Alignment explanation
Indices: 4620954--4621033 Score: 58
Period size: 20 Copynumber: 4.2 Consensus size: 18
4620944 AAATTACAAA
4620954 AAAAAT-TATACAGAATTAT
1 AAAAATATA-ACA-AATTAT
4620973 GAAAAATATAACAAATTAT
1 -AAAAATATAACAAATTAT
4620992 AAAAATTATTTAA-AAATTAT
1 AAAAA-TA--TAACAAATTAT
* *
4621012 AAATATATTAA-AAATTAC
1 AAAAATA-TAACAAATTAT
4621030 AAAA
1 AAAA
4621034 TATTATAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
18 18 0.34
19 10 0.19
20 20 0.38
21 5 0.09
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAATATAACAAATTAT
Found at i:4620997 original size:18 final size:18
Alignment explanation
Indices: 4620967--4621043 Score: 77
Period size: 18 Copynumber: 4.1 Consensus size: 18
4620957 AATTATACAG
4620967 AATTATGAAAAATA-TAACA
1 AATTAT-AAAAATATTAA-A
4620986 AATTATAAAAATTATTTAAA
1 AATTATAAAAA-TA-TTAAA
*
4621006 AATTATAAATATATTAAA
1 AATTATAAAAATATTAAA
*
4621024 AATTA-CAAAATATTATAA
1 AATTATAAAAATATTA-AA
4621042 AA
1 AA
4621044 ACAAATTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
17 8 0.16
18 19 0.37
19 10 0.20
20 11 0.22
21 3 0.06
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (18 bp):
AATTATAAAAATATTAAA
Found at i:4621042 original size:19 final size:19
Alignment explanation
Indices: 4620932--4621044 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 19
4620922 AAATTTATTT
4620932 AAATATTATAGAAAATTACAAA
1 AAATATTATA-AAAATTAC--A
* * *
4620954 AAAAATTATACAGAATTATGA
1 AAATATTATA-AAAATTA-CA
*
4620975 AAA-A-TATAACAAATTATA
1 AAATATTATAA-AAATTACA
*
4620993 AAA-ATTATTTAAAAATTA-T
1 AAATATTA--TAAAAATTACA
4621012 AAATA-TATTAAAAATTACA
1 AAATATTA-TAAAAATTACA
4621031 AAATATTATAAAAA
1 AAATATTATAAAAA
4621045 CAAATTAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 19
0.74 0.08 0.19
Matches are distributed among these distances:
18 16 0.21
19 27 0.36
20 10 0.13
21 7 0.09
22 15 0.20
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATATTATAAAAATTACA
Found at i:4629151 original size:23 final size:24
Alignment explanation
Indices: 4629095--4629157 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
4629085 TTATTAACAT
*
4629095 TGTTTGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTATA
* **
4629119 TGTTCATGAACATGTTCGTTTA-A
1 TGTTCGTGAACATGTTCAATTATA
4629142 TGTTCGTGAACATGTT
1 TGTTCGTGAACATGTT
4629158 TGATTAAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 16 0.47
24 18 0.53
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.44
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCAATTATA
Found at i:4629164 original size:23 final size:23
Alignment explanation
Indices: 4629095--4629164 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
4629085 TTATTAACAT
* *
4629095 TGTTTGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
4629119 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
4629142 TGTTCGTGAACATGTTTGATTAA
1 TGTTCGTGAACATGTTCGATTAA
4629165 GTTAAATGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 21 0.54
24 18 0.46
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:4630027 original size:24 final size:24
Alignment explanation
Indices: 4630000--4630052 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
4629990 TATCTCTATC
* *
4630000 TTTTATTTTTTGTATATTTTTAAA
1 TTTTATTTGTTATATATTTTTAAA
*
4630024 TTTTATTTGTTATATATTTTTAGA
1 TTTTATTTGTTATATATTTTTAAA
4630048 TTTTA
1 TTTTA
4630053 AAATTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.70
Consensus pattern (24 bp):
TTTTATTTGTTATATATTTTTAAA
Found at i:4630204 original size:17 final size:17
Alignment explanation
Indices: 4630173--4630219 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
4630163 TTATCTCTTA
4630173 CAAATTTTTTGAATTTTTT
1 CAAA-TTTTT-AATTTTTT
4630192 CAAATTTTTAATTTTTT
1 CAAATTTTTAATTTTTT
**
4630209 TTAATTTTTAA
1 CAAATTTTTAA
4630220 GAATGACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 17 0.65
18 5 0.19
19 4 0.15
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (17 bp):
CAAATTTTTAATTTTTT
Found at i:4636307 original size:18 final size:18
Alignment explanation
Indices: 4636286--4636323 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4636276 AATTTGGAAT
*
4636286 TTTTATAAA-TATTTTTAA
1 TTTTA-AAACTATTTTGAA
4636304 TTTTAAAACTATTTTGAA
1 TTTTAAAACTATTTTGAA
4636322 TT
1 TT
4636324 ATTTTGTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTAAAACTATTTTGAA
Found at i:4641285 original size:3 final size:3
Alignment explanation
Indices: 4641279--4641320 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
4641269 CATAATAAAA
4641279 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4641321 TTAGCATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4642037 original size:13 final size:14
Alignment explanation
Indices: 4642019--4642047 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4642009 AAGAGAATTT
4642019 TTTATAATTA-TAA
1 TTTATAATTATTAA
4642032 TTTATAATTATTAA
1 TTTATAATTATTAA
4642046 TT
1 TT
4642048 AAAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATAATTATTAA
Found at i:4642197 original size:42 final size:42
Alignment explanation
Indices: 4642150--4642229 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
4642140 ATGACTTAAT
4642150 TAGTATTAGAGTTAT-T-TGCTAATTAAAATTTAACTTTATAAA
1 TAGTATTAGAGTTATATAT-C-AATTAAAATTTAACTTTATAAA
4642192 TAGTATTAGAGTTATATATCAATTAAAATTTAACTTTA
1 TAGTATTAGAGTTATATATCAATTAAAATTTAACTTTA
4642230 ACTTAGCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
42 33 0.92
43 2 0.06
44 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (42 bp):
TAGTATTAGAGTTATATATCAATTAAAATTTAACTTTATAAA
Found at i:4642333 original size:2 final size:2
Alignment explanation
Indices: 4642326--4642363 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4642316 AAGTTAGGAT
4642326 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4642364 AAAGAATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4642808 original size:29 final size:29
Alignment explanation
Indices: 4642776--4642831 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
4642766 AAAAAGCCCA
4642776 TTTTTTAAAAAATTACCGAAATGGGCCGG
1 TTTTTTAAAAAATTACCGAAATGGGCCGG
** * *
4642805 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAAAAAATTACCGAAATGGGCC
4642832 ATTTTCCGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.38
Consensus pattern (29 bp):
TTTTTTAAAAAATTACCGAAATGGGCCGG
Found at i:4642836 original size:28 final size:28
Alignment explanation
Indices: 4642773--4642836 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
4642763 CAAAAAAAGC
4642773 CCATTTTTTAAAAAATTACCGAAATGGG
1 CCATTTTTTAAAAAATTACCGAAATGGG
* ** * *
4642801 CCGGTTTTTTAATTATTTACCGGAATGGG
1 CC-ATTTTTTAAAAAATTACCGAAATGGG
4642830 CCATTTT
1 CCATTTT
4642837 CCGCGAAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (28 bp):
CCATTTTTTAAAAAATTACCGAAATGGG
Found at i:4643132 original size:22 final size:21
Alignment explanation
Indices: 4643107--4643176 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 21
4643097 AAATTCAATA
4643107 TCAATTTCCTTCAAAAATTCTC
1 TCAA-TTCCTTCAAAAATTCTC
4643129 TCAATTCCATTCAAAAATTCTC
1 TCAATTCC-TTCAAAAATTCTC
** *
4643151 TCAAATTCCTTCTCAAATTCCC
1 TC-AATTCCTTCAAAAATTCTC
4643173 TCAA
1 TCAA
4643177 ACTCTCAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.14
22 31 0.72
23 6 0.14
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (21 bp):
TCAATTCCTTCAAAAATTCTC
Found at i:4643164 original size:12 final size:11
Alignment explanation
Indices: 4643143--4643217 Score: 65
Period size: 11 Copynumber: 7.3 Consensus size: 11
4643133 TTCCATTCAA
4643143 AAATT-CTCTC
1 AAATTCCTCTC
4643153 AAATTCCTTCTC
1 AAATTCC-TCTC
4643165 AAATTCC-CTC
1 AAATTCCTCTC
4643175 AAA---CTCTC
1 AAATTCCTCTC
4643183 AAATTCCT-TCC
1 AAATTCCTCT-C
*
4643194 AAAATCCTCTC
1 AAATTCCTCTC
*
4643205 AATTTCCT-TC
1 AAATTCCTCTC
4643215 AAA
1 AAA
4643218 AAATCTCCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
7 1 0.02
8 6 0.11
10 16 0.30
11 18 0.34
12 12 0.23
ACGTcount: A:0.32, C:0.33, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATTCCTCTC
Found at i:4643177 original size:22 final size:22
Alignment explanation
Indices: 4643107--4643217 Score: 63
Period size: 22 Copynumber: 5.2 Consensus size: 22
4643097 AAATTCAATA
* ** *
4643107 TCAATTTCCTTCAAAAATTCTC
1 TCAAATTCCTTCTCAAATTCCC
** *
4643129 TC-AATTCCATTCAAAAATTCTC
1 TCAAATTCC-TTCTCAAATTCCC
4643151 TCAAATTCCTTCTCAAATTCCC
1 TCAAATTCCTTCTCAAATTCCC
*
4643173 TCAAA---C-TCTCAAATTCCT
1 TCAAATTCCTTCTCAAATTCCC
* * *
4643191 TCCAAAATCC-TCTCAATTTCCT
1 T-CAAATTCCTTCTCAAATTCCC
4643213 TCAAA
1 TCAAA
4643218 AAATCTCCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
18 12 0.16
19 5 0.06
21 9 0.12
22 45 0.58
23 6 0.08
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (22 bp):
TCAAATTCCTTCTCAAATTCCC
Found at i:4643183 original size:30 final size:30
Alignment explanation
Indices: 4643148--4643206 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4643138 TTCAAAAATT
*
4643148 CTCTCAAATTCCTTCTCAAATTCC-CTCAAA
1 CTCTCAAATTCCTTC-CAAAATCCTCTCAAA
4643178 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
4643207 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.32
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:4643326 original size:29 final size:29
Alignment explanation
Indices: 4643263--4643326 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
4643253 TAAATTTCAT
* *
4643263 TATTTTAAGAAAATTTTAAAATTTTTTAT
1 TATTTTAAAAAAATTTTAAAATTTTTTAA
*
4643292 TTTTTTAAAAATAATTTTAAAA-TTTTTAA
1 TATTTTAAAAA-AATTTTAAAATTTTTTAA
4643321 TATTTT
1 TATTTT
4643327 CAACAATGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
TATTTTAAAAAAATTTTAAAATTTTTTAA
Found at i:4643446 original size:14 final size:15
Alignment explanation
Indices: 4643417--4643450 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4643407 AAATTTTAAA
4643417 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
4643432 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
4643446 TTTTA
1 TTTTA
4643451 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:4645654 original size:28 final size:28
Alignment explanation
Indices: 4645596--4645897 Score: 259
Period size: 23 Copynumber: 11.4 Consensus size: 28
4645586 TTTTGACATT
* *
4645596 ATTTGATTAAAAACCCTAACCCTAGCCTA
1 ATTTAATTAAAAACCCTAA-CCTAACCTA
4645625 ATTTAATTAAAAACCCTAACCTAA-C--
1 ATTTAATTAAAAACCCTAACCTAACCTA
**
4645650 --TTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
4645676 ATTTAATTAAAAACCCTAA-CT----TA
1 ATTTAATTAAAAACCCTAACCTAACCTA
* **
4645699 ACTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
* **
4645727 ATTTAATTAAAAACCCTAACCCAATTTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
4645755 ATCTAATTAAAAA--C---CCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
4645778 ATTTAGTTAAAAACCCTAACCT-A--T-
1 ATTTAATTAAAAACCCTAACCTAACCTA
4645802 -TTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACCTA
* *
4645830 TTTTACA-TGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAAACCCTAA-CCTAACCTA
* * *
4645859 TTTTAATTAAAATCTCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACCTA
4645888 ATTTAATTAA
1 ATTTAATTAA
4645898 TGTAAAAACC
Statistics
Matches: 232, Mismatches: 18, Indels: 46
0.78 0.06 0.16
Matches are distributed among these distances:
23 76 0.33
24 5 0.02
25 3 0.01
26 1 0.00
27 5 0.02
28 65 0.28
29 76 0.33
30 1 0.00
ACGTcount: A:0.44, C:0.23, G:0.01, T:0.32
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACCTA
Done.