Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1772
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: 62101
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:911 original size:10 final size:10
Alignment explanation
Indices: 896--922 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
886 TGCTAACTAA
896 GTTTTTGTTT
1 GTTTTTGTTT
906 GTTTTTGTTT
1 GTTTTTGTTT
916 GTTTTTG
1 GTTTTTG
923 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:10613 original size:1 final size:1
Alignment explanation
Indices: 10607--10692 Score: 55
Period size: 1 Copynumber: 86.0 Consensus size: 1
10597 GGCGTCCTCC
** ** ** * * * *
10607 AAAAAAAAAAAATGAAAAAAATGAAAAACCAAAAAAAAAACAAAAAAAAAACAAAAACAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
10672 AAACAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAA
10693 GGGGTCCGGA
Statistics
Matches: 63, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.85, C:0.09, G:0.02, T:0.03
Consensus pattern (1 bp):
A
Found at i:10645 original size:12 final size:11
Alignment explanation
Indices: 10630--10690 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
10620 GAAAAAAATG
*
10630 AAAAACCAAAA
1 AAAAAACAAAA
10641 AAAAAACAAAA
1 AAAAAACAAAA
10652 AAAAAACAAAA
1 AAAAAACAAAA
* *
10663 ACAATA-AAAA
1 AAAAAACAAAA
*
10673 AACAAACAAAA
1 AAAAAACAAAA
10684 ACAAAAA
1 A-AAAAA
10691 AAGGGGTCCG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
10 7 0.17
11 30 0.73
12 4 0.10
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:10651 original size:17 final size:16
Alignment explanation
Indices: 10637--10690 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
10627 ATGAAAAACC
10637 AAAAAA-AAAACAAAA
1 AAAAAACAAAACAAAA
*
10652 AAAAAACAAAAACAATA
1 AAAAAAC-AAAACAAAA
10669 AAAAAAC-AAACAAAA
1 AAAAAACAAAACAAAA
10684 ACAAAAA
1 A-AAAAA
10691 AAGGGGTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 14 0.41
16 5 0.15
17 15 0.44
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (16 bp):
AAAAAACAAAACAAAA
Found at i:10662 original size:28 final size:28
Alignment explanation
Indices: 10605--10689 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 28
10595 ACGGCGTCCT
10605 CCAAAAAAAAAA-AATGAAAAAAATGA-AAAA
1 CCAAAAAAAAAACAA--AAAAAAA--ACAAAA
10635 CCAAAAAAAAAACAAAAAAAAAACAAAA
1 CCAAAAAAAAAACAAAAAAAAAACAAAA
* * *
10663 ACAATAAAAAAAC-AAACAAAAACAAAA
1 CCAAAAAAAAAACAAAAAAAAAACAAAA
10690 AAAGGGGTCC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 14 0.28
28 15 0.30
29 7 0.14
30 12 0.24
31 2 0.04
ACGTcount: A:0.82, C:0.12, G:0.02, T:0.04
Consensus pattern (28 bp):
CCAAAAAAAAAACAAAAAAAAAACAAAA
Found at i:10673 original size:39 final size:38
Alignment explanation
Indices: 10609--10692 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
10599 CGTCCTCCAA
* * *
10609 AAAAAAAAAATGAAAAAAATGAAAAACCAAAAAAAAAAC
1 AAAAAAAAAATCAAAAAAATAAAAAAAC-AAAAAAAAAC
*
10648 AAAAAAAAAA-CAAAAACAATAAAAAAACAAACAAAAAC
1 AAAAAAAAAATCAAAAA-AATAAAAAAACAAAAAAAAAC
10686 AAAAAAA
1 AAAAAAA
10693 GGGGTCCGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 21 0.52
39 19 0.47
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.04
Consensus pattern (38 bp):
AAAAAAAAAATCAAAAAAATAAAAAAACAAAAAAAAAC
Found at i:10679 original size:21 final size:18
Alignment explanation
Indices: 10609--10692 Score: 71
Period size: 21 Copynumber: 4.4 Consensus size: 18
10599 CGTCCTCCAA
*
10609 AAAAAAAAAATGAAAAAAATG
1 AAAAAAAAAA--AAAAAAA-C
**
10630 AAAAACCAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAC
*
10648 -AAAAAAAAAACAAAAAC
1 AAAAAAAAAAAAAAAAAC
10665 AATAAAAAAACAAACAAAAAC
1 AA-AAAAAAA-AAA-AAAAAC
10686 AAAAAAA
1 AAAAAAA
10693 GGGGTCCGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
17 14 0.27
18 1 0.02
19 14 0.27
20 7 0.13
21 16 0.31
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.04
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAC
Found at i:12168 original size:30 final size:30
Alignment explanation
Indices: 12132--12428 Score: 202
Period size: 30 Copynumber: 10.1 Consensus size: 30
12122 CATCAACCTT
*
12132 CAAAGCCCACAAATCAGTGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* * *
12162 CGAAGCCCACAAGTCGGTGGCA-TCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* * * *
12191 CAAAGTCCACAACTCCGTGGCACTCTTTTTC
1 CAAAGCCCACAAGTCAGTGGCAC-CCTTTTC
** * * * *
12222 TTTTGTAAGCTCACAACTCTA-TAGCACTCTTTT-
1 ----CAAAGCCCACAAGTC-AGTGGCACCCTTTTC
* *
12255 --TAGCCCACAAGTTAGTGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* ***
12283 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* *
12313 AAAAGCCCACAAGTCAGTGGCAACC-TTT-
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* *
12341 AAAAGCCCACAAGTCAGTGGCAACC--TT-
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
*
12368 CAAAGCCCACAAATCAGTGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* * * *
12398 CGAAGACCACAAATCGGTGGCA-CCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
12427 CA
1 CA
12429 TCTTTAAGTC
Statistics
Matches: 214, Mismatches: 39, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.00
27 43 0.20
28 25 0.12
29 37 0.17
30 83 0.39
31 5 0.02
34 4 0.02
35 16 0.07
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (30 bp):
CAAAGCCCACAAGTCAGTGGCACCCTTTTC
Found at i:12408 original size:85 final size:86
Alignment explanation
Indices: 12256--12424 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 86
12246 CACTCTTTTT
* * * * * *
12256 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTCAGTGGCAACC-TTTCAAAAGCCCACAAATCAGTGGCACACTTTTCAAAAGACC
*
12321 ACAAGTCAGTGGCAACCTTTAAA
65 ACAAATCAGTGGC-ACCTTTAAA
* **
12344 AGCCCACAAGTCAGTGGCAACC-TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGACCA
1 AGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAATCAGTGGCACACTTTTCAAAAGACCA
*
12407 CAAATCGGTGGCACCTTT
66 CAAATCAGTGGCACCTTT
12425 TCCATCTTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
84 6 0.09
85 41 0.59
86 3 0.04
88 20 0.29
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (86 bp):
AGCCCACAAGTCAGTGGCAACCTTTCAAAAGCCCACAAATCAGTGGCACACTTTTCAAAAGACCA
CAAATCAGTGGCACCTTTAAA
Found at i:12472 original size:52 final size:52
Alignment explanation
Indices: 12415--12626 Score: 190
Period size: 52 Copynumber: 4.2 Consensus size: 52
12405 CACAAATCGG
* *
12415 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCCGACCTTGAATCAGCACAT
1 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
* *
12467 TGGCA-------C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
1 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
*
12510 TGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACAT
1 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
* * * * * * * * * *
12562 TGACATCTTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATAT
1 TGGCA-C-CTTTTC-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
*
12617 TGGCATCTTT
1 TGGCACCTTT
12627 ATCACTTTTC
Statistics
Matches: 127, Mismatches: 21, Indels: 23
0.74 0.12 0.13
Matches are distributed among these distances:
43 38 0.30
45 1 0.01
50 1 0.01
52 43 0.34
53 4 0.03
54 5 0.04
55 35 0.28
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (52 bp):
TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
Found at i:12498 original size:43 final size:43
Alignment explanation
Indices: 12430--12519 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
12420 CCTTTTCCAT
*
12430 CTTTAAGTCCAATGTAGCCGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
* * *
12473 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
12516 CTTT
1 CTTT
12520 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
Found at i:12609 original size:55 final size:54
Alignment explanation
Indices: 12473--12626 Score: 186
Period size: 55 Copynumber: 2.9 Consensus size: 54
12463 ACATTGGCAC
* *
12473 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-CTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCCAG
* * * *
12525 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCTCAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTC-CAG
* * * * *
12580 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTT
12627 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
52 38 0.45
53 1 0.01
54 5 0.06
55 40 0.48
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCCAG
Found at i:13562 original size:13 final size:13
Alignment explanation
Indices: 13544--13568 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13534 ATCACTTAAA
13544 TGTATCGATACAT
1 TGTATCGATACAT
13557 TGTATCGATACA
1 TGTATCGATACA
13569 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13621 original size:52 final size:51
Alignment explanation
Indices: 13557--13705 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
13547 ATCGATACAT
**
13557 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAAA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAAA
* *
13609 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAAA
13661 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
13706 TCATATTTCG
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.97
53 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAAA
Found at i:23630 original size:33 final size:32
Alignment explanation
Indices: 23593--23656 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
23583 ACAAGTTATA
*
23593 TATCGATACAATTCAT-TATGTATCGATACAATG
1 TATCGATAC-ATT-ATACATGTATCGATACAATG
23626 TATCGATACATTATACCATGTATCGATACAA
1 TATCGATACATTATA-CATGTATCGATACAA
23657 ACAGTGGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 2 0.07
32 3 0.11
33 23 0.82
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (32 bp):
TATCGATACATTATACATGTATCGATACAATG
Found at i:23641 original size:20 final size:20
Alignment explanation
Indices: 23618--23655 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23608 TTATGTATCG
23618 ATACAATGTATCGATACATT
1 ATACAATGTATCGATACATT
*
23638 ATACCATGTATCGATACA
1 ATACAATGTATCGATACA
23656 AACAGTGGAA
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:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCGATACATT
Found at i:23654 original size:13 final size:13
Alignment explanation
Indices: 23610--23635 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23600 ACAATTCATT
23610 ATGTATCGATACA
1 ATGTATCGATACA
23623 ATGTATCGATACA
1 ATGTATCGATACA
23636 TTATACCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:23729 original size:19 final size:19
Alignment explanation
Indices: 23685--23742 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
23675 CTGCCAATCT
*
23685 CATGTATCGATACAACTGTC
1 CATGTATCGATACAA-TGTA
23705 CATGTATCGATACAAT-TAA
1 CATGTATCGATACAATGT-A
23724 CATGTATCGATACAATGTA
1 CATGTATCGATACAATGTA
23743 TCGATATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.51
20 16 0.46
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGTA
Found at i:24020 original size:19 final size:20
Alignment explanation
Indices: 23983--24021 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
23973 TTTGAGTGAA
23983 TAAAACTTGTTTACGATTTT
1 TAAAACTTGTTTACGATTTT
24003 TAAAACATT-TTT-CGATTTT
1 TAAAAC-TTGTTTACGATTTT
24022 ATTCAATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 9 0.50
21 2 0.11
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (20 bp):
TAAAACTTGTTTACGATTTT
Found at i:26082 original size:20 final size:23
Alignment explanation
Indices: 26057--26103 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
26047 TTTTGTTGAT
26057 GATTTTG-A-TGAAAAA-TGAAA
1 GATTTTGAAGTGAAAAAGTGAAA
26077 GATTTTGAAGTGAAAAAGTGAAA
1 GATTTTGAAGTGAAAAAGTGAAA
26100 -ATTT
1 GATTT
26104 GCGAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.29
21 1 0.04
22 11 0.46
23 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (23 bp):
GATTTTGAAGTGAAAAAGTGAAA
Found at i:29408 original size:259 final size:259
Alignment explanation
Indices: 28949--29470 Score: 1008
Period size: 259 Copynumber: 2.0 Consensus size: 259
28939 AAGGAGTAAC
* *
28949 CTTTTTCATTTTTGAACAATTTTACAAAAAGTGATTAATTTTTCTAAAGCTTCATCTTTAGTGCT
1 CTTTTTCATTTTTGAACAATTTTACAAAAAGTGATGAATTTTTCTAAAGCTTCATCTTTAGTACT
29014 TAAAAATAAAACCCAAGTATATCTTGAATAATCATCCACAATGACAAATCCATATCTCTTACCAC
66 TAAAAATAAAACCCAAGTATATCTTGAATAATCATCCACAATGACAAATCCATATCTCTTACCAC
29079 CTAGACTTTGCGTTCTAGTTGGACCAAAAAGATCGATGTGAACTAGTTGCAAGACTCTAGATGTC
131 CTAGACTTTGCGTTCTAGTTGGACCAAAAAGATCGATGTGAACTAGTTGCAAGACTCTAGATGTC
29144 GTGACAATGTTTATAGGTTTAAAGGTATTTCTTTTATGCTTACCCTTAATACATGCATCACAAA
196 GTGACAATGTTTATAGGTTTAAAGGTATTTCTTTTATGCTTACCCTTAATACATGCATCACAAA
29208 CTTTTTCATTTTTGAACAATTTTACAAAAAGTGATGAATTTTTCTAAAGCTTCATCTTTAGTACT
1 CTTTTTCATTTTTGAACAATTTTACAAAAAGTGATGAATTTTTCTAAAGCTTCATCTTTAGTACT
*
29273 TAAAAATAAAACCTAAGTATATCTTGAATAATCATCCACAATGACAAATCCATATCTCTTACCAC
66 TAAAAATAAAACCCAAGTATATCTTGAATAATCATCCACAATGACAAATCCATATCTCTTACCAC
29338 CTAGACTTTGCGTTCTAGTTGGACCAAAAAGATCGATGTGAACTAGTTGCAAGACTCTAGATGTC
131 CTAGACTTTGCGTTCTAGTTGGACCAAAAAGATCGATGTGAACTAGTTGCAAGACTCTAGATGTC
*
29403 GTGACAATGTTTATAGGTTTAAAGGTATTTCTTTTATGCTTACCCTTAATACATGTATCACAAA
196 GTGACAATGTTTATAGGTTTAAAGGTATTTCTTTTATGCTTACCCTTAATACATGCATCACAAA
29467 CTTT
1 CTTT
29471 ATCACAATCA
Statistics
Matches: 259, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
259 259 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (259 bp):
CTTTTTCATTTTTGAACAATTTTACAAAAAGTGATGAATTTTTCTAAAGCTTCATCTTTAGTACT
TAAAAATAAAACCCAAGTATATCTTGAATAATCATCCACAATGACAAATCCATATCTCTTACCAC
CTAGACTTTGCGTTCTAGTTGGACCAAAAAGATCGATGTGAACTAGTTGCAAGACTCTAGATGTC
GTGACAATGTTTATAGGTTTAAAGGTATTTCTTTTATGCTTACCCTTAATACATGCATCACAAA
Found at i:31409 original size:19 final size:18
Alignment explanation
Indices: 31384--31448 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
31374 ATTTCAACGA
31384 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
31402 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
31418 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
31434 TTTTGTATCGATACA
1 -TTTGTATCGATACA
31449 ATGTAAGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:31422 original size:32 final size:32
Alignment explanation
Indices: 31386--31453 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
31376 TTCAACGATT
31386 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
31418 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
31450 TGTA
1 TGTA
31454 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:31423 original size:13 final size:13
Alignment explanation
Indices: 31405--31429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31395 ACATAAGTGT
31405 TGTATCGATACAA
1 TGTATCGATACAA
31418 TGTATCGATACA
1 TGTATCGATACA
31430 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:31568 original size:52 final size:52
Alignment explanation
Indices: 31524--31652 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
31514 CACTGATCTT
*
31524 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
31576 TGTATCGATACATGCAGGCAAATTTGCCCAGATTTATCAATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
31628 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
31653 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:36274 original size:32 final size:33
Alignment explanation
Indices: 36233--36295 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
36223 GTTACAAGCT
*
36233 ATGTATCGATACAATTG-ATCA-GTATCGATATA
1 ATGTATCGATAC-ATTGTACCATGTATCGATATA
36265 ATGTATCGATACATTGTACCATGTATCGATA
1 ATGTATCGATACATTGTACCATGTATCGATA
36296 CAAATAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 15 0.54
33 9 0.32
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATATA
Found at i:36371 original size:19 final size:20
Alignment explanation
Indices: 36327--36381 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
36317 CTGCCAATCT
**
36327 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
36347 CATGTATCGATACAATT-AA
1 CATGTATCGATACAATTGAA
36366 CATGTATCGATACAAT
1 CATGTATCGATACAAT
36382 GTATCGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:36385 original size:13 final size:13
Alignment explanation
Indices: 36367--36393 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
36357 TACAATTAAC
36367 ATGTATCGATACA
1 ATGTATCGATACA
36380 ATGTATCGATACA
1 ATGTATCGATACA
36393 A
1 A
36394 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:38113 original size:14 final size:14
Alignment explanation
Indices: 38090--38120 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38080 GATTTTTATC
38090 GATACATGAATAGT
1 GATACATGAATAGT
*
38104 GATACGTGAATAGT
1 GATACATGAATAGT
38118 GAT
1 GAT
38121 GAATAGTGAT
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:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (14 bp):
GATACATGAATAGT
Found at i:38125 original size:10 final size:10
Alignment explanation
Indices: 38110--38198 Score: 67
Period size: 10 Copynumber: 9.0 Consensus size: 10
38100 TAGTGATACG
38110 TGAATAGTGA
1 TGAATAGTGA
38120 TGAATAGTGA
1 TGAATAGTGA
38130 TG-A-A-TGA
1 TGAATAGTGA
*
38137 TGAACAGTGA
1 TGAATAGTGA
* * *
38147 TGAACAATAA
1 TGAATAGTGA
* * *
38157 TGTATCGATACA
1 TGAATAG-T-GA
38169 TGAATAGTGA
1 TGAATAGTGA
38179 TGAATAGTGA
1 TGAATAGTGA
*
38189 TGAACAGTGA
1 TGAATAGTGA
38199 AAATGAGATT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
7 5 0.08
8 2 0.03
9 2 0.03
10 46 0.73
11 2 0.03
12 6 0.10
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.27
Consensus pattern (10 bp):
TGAATAGTGA
Found at i:38137 original size:17 final size:17
Alignment explanation
Indices: 38117--38150 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38107 ACGTGAATAG
*
38117 TGATGAATAGTGATGAA
1 TGATGAACAGTGATGAA
38134 TGATGAACAGTGATGAA
1 TGATGAACAGTGATGAA
38151 CAATAATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.29, T:0.26
Consensus pattern (17 bp):
TGATGAACAGTGATGAA
Found at i:38245 original size:19 final size:19
Alignment explanation
Indices: 38221--38257 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
38211 GCTACTACCA
*
38221 ATGTATCGATACATATTTT
1 ATGTATCGATACAAATTTT
38240 ATGTATCGATACAAATTT
1 ATGTATCGATACAAATTT
38258 GGCTACTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACAAATTTT
Found at i:38286 original size:53 final size:53
Alignment explanation
Indices: 38222--38358 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
38212 CTACTACCAA
*
38222 TGTATCGATACATATTTTATGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
38275 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
38328 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
38359 TATGCAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:38391 original size:20 final size:20
Alignment explanation
Indices: 38328--38398 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
38318 GCCAATGTCC
**
38328 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
38348 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
38368 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
38388 TGTATCGATAC
1 TGTATCGATAC
38399 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:38463 original size:21 final size:21
Alignment explanation
Indices: 38437--38477 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38427 GTCAACCTTG
38437 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
38458 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
38478 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:39966 original size:16 final size:17
Alignment explanation
Indices: 39923--39966 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
39913 TTTAAAAAGT
39923 AATTTTAATATTAAATA
1 AATTTTAATATTAAATA
39940 AATTTTAA-A-TATAATA
1 AATTTTAATATTA-AATA
39956 AATATTTAATA
1 AAT-TTTAATA
39967 AAAATACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.08
16 8 0.33
17 13 0.54
18 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTTAATATTAAATA
Found at i:40786 original size:2 final size:2
Alignment explanation
Indices: 40779--40808 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40769 TACTTCTATG
40779 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
40809 TTACTAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44379 original size:30 final size:30
Alignment explanation
Indices: 44343--44400 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
44333 TATAGATTGT
44343 GTATTCATTGGATATGCAAACAACAGTGGC
1 GTATTCATTGGATATGCAAACAACAGTGGC
*
44373 GTATTCATTGGATATGCAAACAATAGTG
1 GTATTCATTGGATATGCAAACAACAGTG
44401 TAATAATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (30 bp):
GTATTCATTGGATATGCAAACAACAGTGGC
Found at i:44411 original size:30 final size:30
Alignment explanation
Indices: 44347--44411 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
44337 GATTGTGTAT
** *
44347 TCATTGGATATGCAAACAACAGTGGCGTAT
1 TCATTGGATATGCAAACAACAGTGGAATAA
* *
44377 TCATTGGATATGCAAACAATAGTGTAATAA
1 TCATTGGATATGCAAACAACAGTGGAATAA
44407 TCATT
1 TCATT
44412 TTTTTGTGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (30 bp):
TCATTGGATATGCAAACAACAGTGGAATAA
Found at i:46970 original size:2 final size:2
Alignment explanation
Indices: 46963--46989 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46953 TTACTTCTAT
46963 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
46990 TTACCAAGTA
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:47261 original size:3 final size:3
Alignment explanation
Indices: 47253--47295 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
47243 CAAAATTTAA
47253 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
47296 TCTTGATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:50146 original size:20 final size:22
Alignment explanation
Indices: 50121--50160 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
50111 TATTTTTATT
50121 TAAA-TTTAAT-TAAAAATATA
1 TAAATTTTAATATAAAAATATA
50141 TAAATTTTAATATAAAAATA
1 TAAATTTTAATATAAAAATA
50161 AATTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTTAATATAAAAATATA
Found at i:50169 original size:27 final size:27
Alignment explanation
Indices: 50139--50190 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
50129 ATTAAAAATA
50139 TATAAATTTTA-ATATAAAAATAAATTT
1 TATAAATTTTATA-ATAAAAATAAATTT
* *
50166 TATATATTTTTTAATAAAAATAAAT
1 TATAAATTTTATAATAAAAATAAAT
50191 AATAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TATAAATTTTATAATAAAAATAAATTT
Found at i:50735 original size:21 final size:21
Alignment explanation
Indices: 50709--50748 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
50699 TTTACTAACG
50709 TGACTTTTGACTATTTTGACA
1 TGACTTTTGACTATTTTGACA
50730 TGACTTTTGACTATTTTGA
1 TGACTTTTGACTATTTTGA
50749 TGTAACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (21 bp):
TGACTTTTGACTATTTTGACA
Found at i:50756 original size:21 final size:21
Alignment explanation
Indices: 50711--50758 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
50701 TACTAACGTG
*
50711 ACTTTTGACTATTTTGACATG
1 ACTTTTGACTATTTTGACATA
**
50732 ACTTTTGACTATTTTGATGTA
1 ACTTTTGACTATTTTGACATA
50753 ACTTTT
1 ACTTTT
50759 AATTATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.52
Consensus pattern (21 bp):
ACTTTTGACTATTTTGACATA
Found at i:52907 original size:79 final size:79
Alignment explanation
Indices: 52754--52930 Score: 221
Period size: 79 Copynumber: 2.2 Consensus size: 79
52744 GAGATAATAA
* * * * ** **
52754 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTGGATTGTGAACGATCGATGA
1 CGGGGTTGGAGTATCCCCTAGAAAATAACAGGGTTGGAGTATCCTCGACTACGAAAAATCGATGA
* *
52819 TTTATAAATAAAAT
66 TTTAGAAATAAAAC
* *
52833 CGGGATTGGAGTATCCCCTAGAAAATAACAGGGTTGGAGTAT-CTCCGACTACGAAAAATTGATG
1 CGGGGTTGGAGTATCCCCTAGAAAATAACAGGGTTGGAGTATCCT-CGACTACGAAAAATCGATG
*
52897 TTTTAGAAATAAAAC
65 ATTTAGAAATAAAAC
52912 CGGGGTTGGAGTATCCCCT
1 CGGGGTTGGAGTATCCCCT
52931 CGAGATGAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 2 0.02
79 81 0.98
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTAGAAAATAACAGGGTTGGAGTATCCTCGACTACGAAAAATCGATGA
TTTAGAAATAAAAC
Found at i:54056 original size:20 final size:20
Alignment explanation
Indices: 54031--54076 Score: 78
Period size: 18 Copynumber: 2.4 Consensus size: 20
54021 AAATCTACTT
54031 TTGGCACACAAATAAGCATC
1 TTGGCACACAAATAAGCATC
54051 TTGG--CACAAATAAGCATC
1 TTGGCACACAAATAAGCATC
54069 TTGGCACA
1 TTGGCACA
54077 AACAACATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 18 0.75
20 6 0.25
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (20 bp):
TTGGCACACAAATAAGCATC
Found at i:54060 original size:18 final size:18
Alignment explanation
Indices: 54037--54078 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
54027 ACTTTTGGCA
54037 CACAAATAAGCATCTTGG
1 CACAAATAAGCATCTTGG
54055 CACAAATAAGCATCTTGG
1 CACAAATAAGCATCTTGG
54073 CACAAA
1 CACAAA
54079 CAACATGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (18 bp):
CACAAATAAGCATCTTGG
Found at i:55274 original size:20 final size:20
Alignment explanation
Indices: 55249--55342 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
55239 AAAATGCCTG
* * *
55249 AATGTATCGATATATTGTGA
1 AATGTATCGATACAATGAGA
*
55269 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
* *
55289 AATGTATCGATACAAGGAGC
1 AATGTATCGATACAATGAGA
*
55309 AATATATCGATACAATGCA-A
1 AATGTATCGATACAATG-AGA
55329 AATGTATCGATACA
1 AATGTATCGATACA
55343 TCTGAGTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 63 0.98
21 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:55711 original size:15 final size:14
Alignment explanation
Indices: 55678--55716 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
55668 TGTATTAACA
55678 AAAATATAAAAATT
1 AAAATATAAAAATT
*
55692 CAAATATAATAAATT
1 AAAATATAA-AAATT
*
55707 AAAATCTAAA
1 AAAATATAAA
55717 TTTAACTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:56959 original size:22 final size:22
Alignment explanation
Indices: 56916--56956 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
56906 TAAATTTAAA
*
56916 TTAGCTTAATTAAAATTATTAT
1 TTAGCTTAATAAAAATTATTAT
56938 TTAG-TTAATAAAAATTATT
1 TTAGCTTAATAAAAATTATT
56957 TATATGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
TTAGCTTAATAAAAATTATTAT
Found at i:57831 original size:9 final size:10
Alignment explanation
Indices: 57816--57859 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 10
57806 TAGCTTAATT
57816 AATATTTAAA
1 AATATTTAAA
57826 AA-ATTTAAA
1 AATATTTAAA
57835 ATATATTTAATA
1 A-ATATTTAA-A
57847 AACTATTTAAA
1 AA-TATTTAAA
57858 AA
1 AA
57860 CTCATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.27
10 3 0.10
11 10 0.33
12 9 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
AATATTTAAA
Found at i:57854 original size:23 final size:20
Alignment explanation
Indices: 57817--57858 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 20
57807 AGCTTAATTA
57817 ATATTTAAAAAATTTAAAAT
1 ATATTTAAAAAATTTAAAAT
57837 ATATTTAATAAACTATTTAAAA
1 ATATTTAA-AAA--ATTTAAAA
57859 ACTCATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
23 8 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATTTAAAAAATTTAAAAT
Found at i:60862 original size:1 final size:1
Alignment explanation
Indices: 60858--60888 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
60848 TTTTTTTTTT
60858 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
60889 TCTTTTATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Done.