Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018086.1 Corchorus olitorius cultivar O-4 contig18119, whole genome shotgun sequence
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: 59625
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:407 original size:2 final size:2
Alignment explanation
Indices: 400--471 Score: 90
Period size: 2 Copynumber: 33.0 Consensus size: 2
390 ATTGTTATCA
400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT
444 AT GAT AT GAT AT AT GAT AT AT GAT AT AT
1 AT -AT AT -AT AT AT -AT AT AT -AT AT AT
472 GATACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
2 52 0.81
3 12 0.19
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (2 bp):
AT
Found at i:475 original size:7 final size:6
Alignment explanation
Indices: 400--471 Score: 90
Period size: 7 Copynumber: 11.0 Consensus size: 6
390 ATTGTTATCA
400 ATATAT ATATAT ATATAT ATATAT ATATGAT ATATAT GATATAT ATGATAT
1 ATATAT ATATAT ATATAT ATATAT ATAT-AT ATATAT -ATATAT AT-ATAT
451 GATATAT GATATAT GATATAT
1 -ATATAT -ATATAT -ATATAT
472 GATACTAATA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
6 26 0.42
7 34 0.55
8 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (6 bp):
ATATAT
Found at i:475 original size:14 final size:13
Alignment explanation
Indices: 400--471 Score: 103
Period size: 14 Copynumber: 5.5 Consensus size: 13
390 ATTGTTATCA
400 ATATATATATAT-
1 ATATATATATATG
412 ATATATATATAT-
1 ATATATATATATG
424 ATATGATATATATG
1 ATAT-ATATATATG
438 ATATATATGATATG
1 ATATATAT-ATATG
452 ATATATGATATATG
1 ATATAT-ATATATG
466 ATATAT
1 ATATAT
472 GATACTAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
12 16 0.29
13 12 0.21
14 26 0.46
15 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
ATATATATATATG
Found at i:6747 original size:2 final size:2
Alignment explanation
Indices: 6740--6846 Score: 81
Period size: 2 Copynumber: 48.5 Consensus size: 2
6730 TTGTTATCAT
6740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA TA
* * *
6784 TGA TA TGA TA TT TA GA CA -A GTA TA TA TGA TA TA TGA TA TA TGA
1 T-A TA T-A TA TA TA TA TA TA -TA TA TA T-A TA TA T-A TA TA T-A
6827 TA TGA TA TA TGA TA TGA TA T
1 TA T-A TA TA T-A TA T-A TA T
6847 TTAGACAAGT
Statistics
Matches: 89, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
1 1 0.01
2 67 0.75
3 21 0.24
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (2 bp):
TA
Found at i:6757 original size:12 final size:13
Alignment explanation
Indices: 6740--6846 Score: 107
Period size: 12 Copynumber: 8.2 Consensus size: 13
6730 TTGTTATCAT
6740 TATATAT-ATATA
1 TATATATGATATA
6752 TATATAT-ATATA
1 TATATATGATATA
6764 TATATATGATATA
1 TATATATGATATA
6777 TGATATATGATATGA
1 T-ATATATGATAT-A
* *
6792 TATTTA-GACA-A
1 TATATATGATATA
6803 GTATATATGATATA
1 -TATATATGATATA
6817 TGATATATGATAT-
1 T-ATATATGATATA
*
6830 GATATATGATATGA
1 TATATATGATAT-A
6844 TAT
1 TAT
6847 TTAGACAAGT
Statistics
Matches: 80, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
11 1 0.01
12 35 0.44
13 13 0.16
14 29 0.36
15 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (13 bp):
TATATATGATATA
Found at i:6784 original size:40 final size:43
Alignment explanation
Indices: 6740--6846 Score: 136
Period size: 40 Copynumber: 2.6 Consensus size: 43
6730 TTGTTATCAT
6740 TATAT-ATAT-ATATATATATATATA-TATATATGATATATGA
1 TATATGATATGATATATATATATATAGTATATATGATATATGA
* *
6780 TATATGATATGATAT-T-TAGACA-AGTATATATGATATATGA
1 TATATGATATGATATATATATATATAGTATATATGATATATGA
6820 TATATGATATGATATATGATATGATAT
1 TATATGATATGATATAT-ATAT-ATAT
6847 TTAGACAAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
39 1 0.02
40 40 0.73
41 6 0.11
42 4 0.07
43 2 0.04
44 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (43 bp):
TATATGATATGATATATATATATATAGTATATATGATATATGA
Found at i:6808 original size:52 final size:52
Alignment explanation
Indices: 6752--6858 Score: 182
Period size: 52 Copynumber: 2.1 Consensus size: 52
6742 TATATATATA
6752 TATATAT-ATATAT-ATATATGATATATGATATATGATATGATATTTAGACAAG
1 TATATATGATATATGATATATG--ATATGATATATGATATGATATTTAGACAAG
6804 TATATATGATATATGATATATGATATGATATATGATATGATATTTAGACAAG
1 TATATATGATATATGATATATGATATGATATATGATATGATATTTAGACAAG
6856 TAT
1 TAT
6859 GTAAAACCAC
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
52 40 0.75
53 6 0.11
54 7 0.13
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.42
Consensus pattern (52 bp):
TATATATGATATATGATATATGATATGATATATGATATGATATTTAGACAAG
Found at i:7740 original size:23 final size:24
Alignment explanation
Indices: 7714--7760 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
7704 AACCCAATCC
*
7714 AACCGAACTATAAA-CCGAAAATT
1 AACCGAACCATAAACCCGAAAATT
*
7737 AACCGGACCATAAACCCGAAAATT
1 AACCGAACCATAAACCCGAAAATT
7761 CATTAACCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.49, C:0.26, G:0.11, T:0.15
Consensus pattern (24 bp):
AACCGAACCATAAACCCGAAAATT
Found at i:8126 original size:5 final size:5
Alignment explanation
Indices: 8094--8125 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
8084 TGTGAGAACT
8094 TTTTG TTTTG TTTTG TTTTG TTTT- TTTT- TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
8126 TATGAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (5 bp):
TTTTG
Found at i:8692 original size:16 final size:16
Alignment explanation
Indices: 8665--8703 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
8655 TCCTTAATTT
8665 ATTACT-ATAATTATA
1 ATTACTCATAATTATA
8680 ATTACTCATAATTATA
1 ATTACTCATAATTATA
*
8696 ATCACTCA
1 ATTACTCA
8704 ACGATTTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTACTCATAATTATA
Found at i:11027 original size:26 final size:25
Alignment explanation
Indices: 10973--11027 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
10963 AGTACTTTAT
**
10973 TATGCATCAATAATGGTTTCTTGTT
1 TATGCATCAATAATGGTTTCTTGAA
* *
10998 TATGCATTTAATAATGGTTTTTTGAA
1 TATGCA-TCAATAATGGTTTCTTGAA
11024 TATG
1 TATG
11028 GACAAGCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.49
Consensus pattern (25 bp):
TATGCATCAATAATGGTTTCTTGAA
Found at i:11442 original size:74 final size:77
Alignment explanation
Indices: 11317--11507 Score: 264
Period size: 74 Copynumber: 2.5 Consensus size: 77
11307 GTATAGGGTG
* *
11317 ATCCAAAATTTTGTTTCACTGCACATAGTTTACAAATTTGTTCTGTAACAAAT-AAGA-AGAC-T
1 ATCCAAAATTTTATTTCACTGCACATAGTTTACAAATTTGTTCTGTAACAAATAAAAAGAGACTT
11379 GTTTTCTGTACA
66 GTTTTCTGTACA
* * *
11391 ATCCAAAATTTTATTTCACTGCACATAGTTAATAAATTTGTTGTGCT-ACAAATAAAAAGAGACT
1 ATCCAAAATTTTATTTCACTGCACATAGTTTACAAATTTGTTCTG-TAACAAATAAAAAGAGAC-
* *
11455 TTGTTTTTTTTACA
64 TTGTTTTCTGTACA
*
11469 ATCCAAAATTTTATTTCACTGCAAATAGTTTACAAATTT
1 ATCCAAAATTTTATTTCACTGCACATAGTTTACAAATTT
11508 TGTTTTTTCT
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
74 47 0.46
75 4 0.04
76 4 0.04
78 47 0.46
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (77 bp):
ATCCAAAATTTTATTTCACTGCACATAGTTTACAAATTTGTTCTGTAACAAATAAAAAGAGACTT
GTTTTCTGTACA
Found at i:13092 original size:35 final size:37
Alignment explanation
Indices: 13017--13107 Score: 123
Period size: 35 Copynumber: 2.5 Consensus size: 37
13007 AAAAAAGAAT
* **
13017 AACAATAGTTAAAATATAGTACTATAACTCTTTATCA
1 AACAATAGTTAAAAAATAGTACTATAACTCTAAATCA
* *
13054 AACAATAGTTAAAAGATAGTA-T-TAACTCTAAATTA
1 AACAATAGTTAAAAAATAGTACTATAACTCTAAATCA
13089 AACAATAGTTAAAAAATAG
1 AACAATAGTTAAAAAATAG
13108 AAAAAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
35 28 0.57
36 1 0.02
37 20 0.41
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.31
Consensus pattern (37 bp):
AACAATAGTTAAAAAATAGTACTATAACTCTAAATCA
Found at i:14474 original size:45 final size:45
Alignment explanation
Indices: 14418--14507 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
14408 AACCAAAGAC
* *
14418 TAGCATTTGAGACAAAAATAAATAAAGTCTAACTATTAACTACTT
1 TAGCATTTGAGACAAAAAGAAATAAAGTCAAACTATTAACTACTT
*
14463 TAGCGTTTGAGACAAAAAGAAATAAAGTCAAACTATTAACTACTT
1 TAGCATTTGAGACAAAAAGAAATAAAGTCAAACTATTAACTACTT
14508 CAGCCAGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (45 bp):
TAGCATTTGAGACAAAAAGAAATAAAGTCAAACTATTAACTACTT
Found at i:20562 original size:21 final size:21
Alignment explanation
Indices: 20522--20562 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20512 GTCTGTTAAG
*
20522 TCCTTGATTTTAGATGCTGCC
1 TCCTTGATTTTAGATACTGCC
20543 TCCTTGATTTTA-ACTACTGC
1 TCCTTGATTTTAGA-TACTGC
20563 GTTAATATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.44
Consensus pattern (21 bp):
TCCTTGATTTTAGATACTGCC
Found at i:24851 original size:35 final size:35
Alignment explanation
Indices: 24809--24875 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
24799 GAAACCCAAT
* *
24809 AAAAAATGCGTTGTTTTTAGCTAATTTGACTGATA
1 AAAAAATGCATTGTTTTTAGCTAATTTAACTGATA
24844 AAAAAATGCATTGTTTTTAGCTAATTTAACTG
1 AAAAAATGCATTGTTTTTAGCTAATTTAACTG
24876 CCTATCTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (35 bp):
AAAAAATGCATTGTTTTTAGCTAATTTAACTGATA
Found at i:25532 original size:12 final size:12
Alignment explanation
Indices: 25515--25539 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25505 GACACATCAT
25515 GAGGGTCAAGTA
1 GAGGGTCAAGTA
25527 GAGGGTCAAGTA
1 GAGGGTCAAGTA
25539 G
1 G
25540 CAAAACTCCT
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:0.32, C:0.08, G:0.44, T:0.16
Consensus pattern (12 bp):
GAGGGTCAAGTA
Found at i:31330 original size:28 final size:28
Alignment explanation
Indices: 31290--31344 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
31280 GGGGGGAATC
31290 TGCTTACCACCTCAATCAACAAATGAGA
1 TGCTTACCACCTCAATCAACAAATGAGA
31318 TGCTTACCACCTCAATCAACAAATGAG
1 TGCTTACCACCTCAATCAACAAATGAG
31345 GTATCAGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (28 bp):
TGCTTACCACCTCAATCAACAAATGAGA
Found at i:31714 original size:14 final size:14
Alignment explanation
Indices: 31695--31721 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31685 GTTAAAATAC
31695 TCTTTCTTTTTTTT
1 TCTTTCTTTTTTTT
31709 TCTTTCTTTTTTT
1 TCTTTCTTTTTTT
31722 AATTTAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TCTTTCTTTTTTTT
Found at i:33114 original size:13 final size:13
Alignment explanation
Indices: 33096--33140 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
33086 TAAAAGATAA
33096 TTTTATTTTTTTC
1 TTTTATTTTTTTC
33109 TTTTATTTTTTTC
1 TTTTATTTTTTTC
* *
33122 CTTTACTTTGTTTTA
1 TTTTA-TTT-TTTTC
33137 TTTT
1 TTTT
33141 TATTAGTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 17 0.63
14 3 0.11
15 7 0.26
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTATTTTTTTC
Found at i:33301 original size:31 final size:29
Alignment explanation
Indices: 33256--33329 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
33246 CTAAATATCT
* * *
33256 AAAAAAATCCCTTATATTTTGCTTTTGGGAC
1 AAAATAATCACTTATATTTT--TTTCGGGAC
* *
33287 AAAATAATCTCTTATGTTTTTTTCGGGAC
1 AAAATAATCACTTATATTTTTTTCGGGAC
*
33316 AAATTAATCACTTA
1 AAAATAATCACTTA
33330 CGTTTCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 20 0.54
31 17 0.46
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
AAAATAATCACTTATATTTTTTTCGGGAC
Found at i:33309 original size:28 final size:29
Alignment explanation
Indices: 33278--33334 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
33268 TATATTTTGC
* *
33278 TTTT-GGGACAAAATAATCTCTTATGTTT
1 TTTTCGGGACAAAATAATCACTTACGTTT
*
33306 TTTTCGGGACAAATTAATCACTTACGTTT
1 TTTTCGGGACAAAATAATCACTTACGTTT
33335 CAAAAATAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (29 bp):
TTTTCGGGACAAAATAATCACTTACGTTT
Found at i:33520 original size:31 final size:31
Alignment explanation
Indices: 33478--33538 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
33468 AAGAGACTGA
33478 TTTGTCCCAAAAGAAAAACATAAGGGATTTG
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTG
* *
33509 TTTGTCTCAAAAGAAAAATATAAGGGATTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTT
33539 TTTTTAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.30
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTG
Found at i:45179 original size:30 final size:30
Alignment explanation
Indices: 45138--45215 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
45128 CGGATGTTTT
* *
45138 ATTGCTGCAGGATTTACAAACTA-ATGTTCC
1 ATTGCCGCAGGATGTACAAAC-AGATGTTCC
*
45168 -TCTGCCTCAGGATGTACAAACAGATGTTCC
1 AT-TGCCGCAGGATGTACAAACAGATGTTCC
45198 ATTGCCGCAGGATGTACA
1 ATTGCCGCAGGATGTACA
45216 GCTGGCTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.05
30 38 0.93
31 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (30 bp):
ATTGCCGCAGGATGTACAAACAGATGTTCC
Found at i:46821 original size:2 final size:2
Alignment explanation
Indices: 46764--46804 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
46754 AGTTACAATG
46764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46805 AGTTACAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49251 original size:15 final size:15
Alignment explanation
Indices: 49231--49260 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
49221 TCCTTTACCA
49231 CAATCATAAGTTGAC
1 CAATCATAAGTTGAC
49246 CAATCATAAGTTGAC
1 CAATCATAAGTTGAC
49261 GCTATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
CAATCATAAGTTGAC
Found at i:49683 original size:23 final size:23
Alignment explanation
Indices: 49640--49684 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
49630 TTAACTTCAT
*
49640 GTACAAATTTAAAGTCTGATTAA
1 GTACAAATTTAAAGTCAGATTAA
*
49663 GTAC-AATTTAAGGTCAAGATTA
1 GTACAAATTTAAAGTC-AGATTA
49685 GGTCCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (23 bp):
GTACAAATTTAAAGTCAGATTAA
Found at i:55486 original size:33 final size:32
Alignment explanation
Indices: 55444--55759 Score: 429
Period size: 33 Copynumber: 9.6 Consensus size: 32
55434 TTGAACACTC
55444 CTCCAGTCACCCCTTGGGCGCCTTTGAGCGCTT
1 CTCCAGTCACCCCTTGGGC-CCTTTGAGCGCTT
*
55477 CTCCAGTCACCTCTTGGGTCCCTTTGAGCGCTT
1 CTCCAGTCACCCCTTGGG-CCCTTTGAGCGCTT
*
55510 CTCCAGTCACCCCTTGGGCGCCTTTGAACGCTT
1 CTCCAGTCACCCCTTGGGC-CCTTTGAGCGCTT
* *
55543 CTCGAGTCACCCCTTCGGTG-CCTTTGAGAGCTT
1 CTCCAGTCACCCCTT-GG-GCCCTTTGAGCGCTT
55576 CTCCAGTCACCCCTTGGGTCCCTTTGAGCGCTT
1 CTCCAGTCACCCCTTGGG-CCCTTTGAGCGCTT
*
55609 CTCCAGTCACCCCTTGGGCCTCTTTGAGCACTT
1 CTCCAGTCACCCCTTGGGCC-CTTTGAGCGCTT
* *
55642 CT-CTGATAACCCCTTGGGTCCCTTTGAGCGCTT
1 CTCCAG-TCACCCCTTGGG-CCCTTTGAGCGCTT
* *
55675 CTCCAGTAACCCCTTGGGCGCCTTTGAGTGCTT
1 CTCCAGTCACCCCTTGGGC-CCTTTGAGCGCTT
55708 CTCCAGTCACCCCTTGGGCTCCTTTGAGCGCTT
1 CTCCAGTCACCCCTTGGGC-CCTTTGAGCGCTT
*
55741 CTTCAGTCACCCCTTGGGC
1 CTCCAGTCACCCCTTGGGC
55760 TCCGTCAAGC
Statistics
Matches: 254, Mismatches: 18, Indels: 22
0.86 0.06 0.07
Matches are distributed among these distances:
31 1 0.00
32 8 0.03
33 237 0.93
34 7 0.03
35 1 0.00
ACGTcount: A:0.11, C:0.37, G:0.22, T:0.30
Consensus pattern (32 bp):
CTCCAGTCACCCCTTGGGCCCTTTGAGCGCTT
Found at i:58094 original size:2 final size:2
Alignment explanation
Indices: 58087--58125 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
58077 TTTTGCAAAA
58087 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58126 ATAGTAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58492 original size:27 final size:27
Alignment explanation
Indices: 58440--58504 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 27
58430 TACCCTTTTT
58440 TTAAATATATATTTCTAAATTGCCATTA
1 TTAAATA-ATATTTCTAAATTGCCATTA
58468 TTAAATAATATTT-TAATTATT-CCATTA
1 TTAAATAATATTTCTAA--ATTGCCATTA
58495 TTAAAATAAT
1 TT-AAATAAT
58505 GGAAATTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 3 0.09
27 14 0.41
28 17 0.50
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAAATAATATTTCTAAATTGCCATTA
Found at i:58883 original size:22 final size:21
Alignment explanation
Indices: 58825--59119 Score: 127
Period size: 22 Copynumber: 13.5 Consensus size: 21
58815 TGTGCTTCCA
* *
58825 GTTAACAAAATTTTATAAGGAA
1 GTTATCAAAATTTTAT-AGGAG
* *
58847 GTTAT-AGAAAATTTATAGGTAT
1 GTTATCA-AAATTTTATAGG-AG
*
58869 GTTATCAAAATTTTATAAGATG
1 GTTATCAAAATTTTATAGGA-G
* *
58891 GATATCAAAATTTCAT--GAG
1 GTTATCAAAATTTTATAGGAG
* *
58910 GTTATCAAAATTTCAAATGGAG
1 GTTATCAAAATTTTATA-GGAG
58932 GTTATCAAAATTTTATAAGGAG
1 GTTATCAAAATTTTAT-AGGAG
*
58954 GTTTAT-AAAATTTTCACAGTGAG
1 G-TTATCAAAATTTT-ATAG-GAG
* *
58977 G-TATCACAATTTCCTGATA--TG
1 GTTATCAAAATTT--T-ATAGGAG
* *
58998 GTTATCAAAATTTTATAATGTG
1 GTTATCAAAATTTTAT-AGGAG
* * * *
59020 ATTACCAATATTTTATCGGAAG
1 GTTATCAAAATTTTATAGG-AG
* * *
59042 GTTATCAAAATTTCATAATGTAT
1 GTTATCAAAATTTTAT-A-GGAG
* * * * *
59065 GCTACCAACATTTCATTGGGAG
1 GTTATCAAAATTTTA-TAGGAG
* *
59087 GTTATCAAAATTTCATAGGGTG
1 GTTATCAAAATTTTATA-GGAG
59109 GTTATCAAAAT
1 GTTATCAAAAT
59120 GAAATTTAAA
Statistics
Matches: 208, Mismatches: 42, Indels: 46
0.70 0.14 0.16
Matches are distributed among these distances:
19 17 0.08
20 4 0.02
21 12 0.06
22 146 0.70
23 24 0.12
24 5 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
GTTATCAAAATTTTATAGGAG
Found at i:59090 original size:45 final size:44
Alignment explanation
Indices: 58997--59103 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 44
58987 TTCCTGATAT
* * *
58997 GGTTATCAAAATTTTATAATGTGATTACCAATATTTTATCGGAA
1 GGTTATCAAAATTTCATAATGTGATTACCAACATTTCATCGGAA
* *
59041 GGTTATCAAAATTTCATAATGT-ATGCTACCAACATTTCATTGGGA
1 GGTTATCAAAATTTCATAATGTGAT--TACCAACATTTCATCGGAA
59086 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
59104 GGGTGGTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
43 2 0.04
44 21 0.38
45 33 0.59
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATGTGATTACCAACATTTCATCGGAA
Found at i:59278 original size:20 final size:20
Alignment explanation
Indices: 59214--59280 Score: 80
Period size: 22 Copynumber: 3.1 Consensus size: 20
59204 TATCGTCATA
*
59214 AAAATTTTATTATGTAATTATC
1 AAAATTTTA-TA-GTGATTATC
*
59236 AAAATTTTATATTGAGGTTATC
1 AAAATTTTATAGTGA--TTATC
59258 AAAATTTTATAGTGATTATC
1 AAAATTTTATAGTGATTATC
59278 AAA
1 AAA
59281 TTTCATAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.25
21 2 0.05
22 28 0.70
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (20 bp):
AAAATTTTATAGTGATTATC
Found at i:59553 original size:12 final size:12
Alignment explanation
Indices: 59536--59562 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
59526 AAATAGAAAA
59536 TAATTATAAATT
1 TAATTATAAATT
59548 TAATTATAAATT
1 TAATTATAAATT
59560 TAA
1 TAA
59563 AGTCTTGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATTATAAATT
Done.