Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012539.1 Corchorus olitorius cultivar O-4 contig12572, 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: 101355
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1230 original size:20 final size:20
Alignment explanation
Indices: 1198--1237 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1188 AATTCATTTT
*
1198 GACTATAGTGGGAGGAGAGA
1 GACTATAGTGGGAAGAGAGA
1218 GACT-TAGTGGGGAAGAGAGA
1 GACTATAGT-GGGAAGAGAGA
1238 AGAAGGGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.35, C:0.05, G:0.45, T:0.15
Consensus pattern (20 bp):
GACTATAGTGGGAAGAGAGA
Found at i:1236 original size:18 final size:20
Alignment explanation
Indices: 1198--1237 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1188 AATTCATTTT
*
1198 GACTATAGTGGGAGGAGAGA
1 GACTATAGTGGGAGAAGAGA
1218 GACT-TAGTGGG-GAAGAGA
1 GACTATAGTGGGAGAAGAGA
1236 GA
1 GA
1238 AGAAGGGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.35, C:0.05, G:0.45, T:0.15
Consensus pattern (20 bp):
GACTATAGTGGGAGAAGAGA
Found at i:2157 original size:35 final size:35
Alignment explanation
Indices: 2106--2176 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
2096 CATGATTGGG
*
2106 AACCCAACATTCCAAAACCAATTTAATTTAGAGCA
1 AACCAAACATTCCAAAACCAATTTAATTTAGAGCA
2141 AACCAAACATTCCAAAACCAATTTAATTTAGAGCA
1 AACCAAACATTCCAAAACCAATTTAATTTAGAGCA
2176 A
1 A
2177 TCCGTTAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.23
Consensus pattern (35 bp):
AACCAAACATTCCAAAACCAATTTAATTTAGAGCA
Found at i:2398 original size:20 final size:20
Alignment explanation
Indices: 2375--2418 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2365 CATTTTTTAA
*
2375 TTCACATTAAAATTTGTTTT
1 TTCACATCAAAATTTGTTTT
* * *
2395 TTCACGTCAAGATTTTTTTT
1 TTCACATCAAAATTTGTTTT
2415 TTCA
1 TTCA
2419 ATTTGGAGGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.55
Consensus pattern (20 bp):
TTCACATCAAAATTTGTTTT
Found at i:3465 original size:2 final size:2
Alignment explanation
Indices: 3460--3517 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
3450 ATTGTGTGTG
* * * *
3460 TA TA TA TA TA TA TA TA TA TA TA TA CA CA CA TA TA TA CA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3500 TG TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3518 TTGTAAAACT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:5882 original size:30 final size:30
Alignment explanation
Indices: 5848--5909 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
5838 ATTTTTATCT
5848 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
*
5878 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
5908 TG
1 TG
5910 GCTTATTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:10864 original size:19 final size:18
Alignment explanation
Indices: 10836--10877 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
10826 AATTAATTGT
10836 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
10854 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
*
10873 CTTAA
1 TTTAA
10878 AAATTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:18716 original size:20 final size:21
Alignment explanation
Indices: 18693--18731 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
18683 AAATTAATTC
18693 AATTCATTAT-TAAATAATCA
1 AATTCATTATCTAAATAATCA
* *
18713 AATTGATTTTCTAAATAAT
1 AATTCATTATCTAAATAAT
18732 AAGGATGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (21 bp):
AATTCATTATCTAAATAATCA
Found at i:18825 original size:20 final size:20
Alignment explanation
Indices: 18788--18825 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18778 GAATTGATTT
*
18788 TGATAATTAATAATTAATAA
1 TGATAATTAATAAATAATAA
18808 TGATAA-TAATTAAATAAT
1 TGATAATTAA-TAAATAAT
18826 TCCATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
TGATAATTAATAAATAATAA
Found at i:20245 original size:34 final size:32
Alignment explanation
Indices: 20207--20272 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 32
20197 TTGACACCTT
*
20207 ACACACTCTAGCTCACTCACGCTCACACACTACA
1 ACACACTCTAGCTCACTC-CACT-ACACACTACA
20241 ACACACTCTAGCTCACTCCACTACACACTACA
1 ACACACTCTAGCTCACTCCACTACACACTACA
20273 CTAATTGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 10 0.32
33 3 0.10
34 18 0.58
ACGTcount: A:0.33, C:0.44, G:0.05, T:0.18
Consensus pattern (32 bp):
ACACACTCTAGCTCACTCCACTACACACTACA
Found at i:22651 original size:12 final size:13
Alignment explanation
Indices: 22622--22651 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22612 TAACAAGTGA
*
22622 AAAAAAGCAAATT
1 AAAAAAGAAAATT
22635 AAAAAAGAAAATT
1 AAAAAAGAAAATT
22648 AAAA
1 AAAA
22652 GACATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAAAAGAAAATT
Found at i:25006 original size:25 final size:25
Alignment explanation
Indices: 24978--25026 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
24968 GATGGATTTG
24978 TAGAGACCGAGCGAGAGTGATCAAA
1 TAGAGACCGAGCGAGAGTGATCAAA
*
25003 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGATCAA
25027 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGATCAAA
Found at i:25623 original size:16 final size:16
Alignment explanation
Indices: 25596--25654 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
25586 TTTGGTTGGG
25596 AGGAAA-GAAATAGGA
1 AGGAAAGGAAATAGGA
*
25611 AGGAAAGGAAATAGCA
1 AGGAAAGGAAATAGGA
*
25627 AGAGAAAGGAAATAGGG
1 AG-GAAAGGAAATAGGA
*
25644 AGGAAGGGAAA
1 AGGAAAGGAAA
25655 GGAAGTCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 6 0.16
16 18 0.47
17 14 0.37
ACGTcount: A:0.56, C:0.02, G:0.37, T:0.05
Consensus pattern (16 bp):
AGGAAAGGAAATAGGA
Found at i:25635 original size:17 final size:16
Alignment explanation
Indices: 25596--25641 Score: 67
Period size: 17 Copynumber: 2.9 Consensus size: 16
25586 TTTGGTTGGG
*
25596 AGGAAA-GAAATAGGA
1 AGGAAAGGAAATAGCA
25611 AGGAAAGGAAATAGCA
1 AGGAAAGGAAATAGCA
25627 AGAGAAAGGAAATAG
1 AG-GAAAGGAAATAG
25642 GGAGGAAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 6 0.21
16 10 0.36
17 12 0.43
ACGTcount: A:0.59, C:0.02, G:0.33, T:0.07
Consensus pattern (16 bp):
AGGAAAGGAAATAGCA
Found at i:27464 original size:20 final size:20
Alignment explanation
Indices: 27441--27486 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
27431 ATAGAATGTT
*
27441 GAATTCTTAAATAATGGTCA
1 GAATTCTTAAATAATGGCCA
27461 GAATTCTTAAATAATGGCCA
1 GAATTCTTAAATAATGGCCA
27481 GAATTC
1 GAATTC
27487 AAACCTAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
GAATTCTTAAATAATGGCCA
Found at i:27948 original size:25 final size:26
Alignment explanation
Indices: 27896--27948 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
27886 ATTACCTGTA
* *
27896 ATATAAAATCAAGATAAAATAAGTCT
1 ATATAAAAACAAGATAAAATAAGACT
27922 ATATAAAAACAA-ATAAAATTAA-ACT
1 ATATAAAAACAAGATAAAA-TAAGACT
27947 AT
1 AT
27949 TTTATATGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (26 bp):
ATATAAAAACAAGATAAAATAAGACT
Found at i:30870 original size:22 final size:22
Alignment explanation
Indices: 30839--30882 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30829 GCCTCTCATT
30839 ATCTTAAATCATAATTTTCGAG
1 ATCTTAAATCATAATTTTCGAG
*
30861 ATCTTGAATCATAATTTTCGAG
1 ATCTTAAATCATAATTTTCGAG
30883 TGATAGAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (22 bp):
ATCTTAAATCATAATTTTCGAG
Found at i:34959 original size:82 final size:82
Alignment explanation
Indices: 34822--34985 Score: 292
Period size: 82 Copynumber: 2.0 Consensus size: 82
34812 TAGCGAGTTG
* *
34822 CTTTCTATGCTTCTGGCTTTCATTTGTCATAGACTTGCACAGTTCAAATTTTACCCATGAGTTTT
1 CTTTCTATGCTTCTGGCTTTCATTTCTCATAGACTTGCACAGTTCAAATTTTACCCATGAATTTT
34887 GAGCTCATCATTTGTTT
66 GAGCTCATCATTTGTTT
* *
34904 CTTTCTATGCTTCTGTCTTTCATTTCTCATAGACTTGCACAGTTTAAATTTTACCCATGAATTTT
1 CTTTCTATGCTTCTGGCTTTCATTTCTCATAGACTTGCACAGTTCAAATTTTACCCATGAATTTT
34969 GAGCTCATCATTTGTTT
66 GAGCTCATCATTTGTTT
34986 TAAGAAGCAT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.46
Consensus pattern (82 bp):
CTTTCTATGCTTCTGGCTTTCATTTCTCATAGACTTGCACAGTTCAAATTTTACCCATGAATTTT
GAGCTCATCATTTGTTT
Found at i:39980 original size:58 final size:58
Alignment explanation
Indices: 39911--40092 Score: 355
Period size: 58 Copynumber: 3.1 Consensus size: 58
39901 GGAGAATACC
39911 TGCTGATTGGGTTATTTAGCTGATTTACAATGAATCGTTGAGGTCAGCTTTGCAGTAA
1 TGCTGATTGGGTTATTTAGCTGATTTACAATGAATCGTTGAGGTCAGCTTTGCAGTAA
39969 TGCTGATTGGGTTATTTAGCTGATTTACAATGAATCGTTGAGGTCAGCTTTGCAGTAA
1 TGCTGATTGGGTTATTTAGCTGATTTACAATGAATCGTTGAGGTCAGCTTTGCAGTAA
*
40027 TGCTGATTGGGTTATTTAGCTGATTTACAATGAATCATTGAGGTCAGCTTTGCAGTAA
1 TGCTGATTGGGTTATTTAGCTGATTTACAATGAATCGTTGAGGTCAGCTTTGCAGTAA
40085 TGCTGATT
1 TGCTGATT
40093 TACAATTAAT
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 123 1.00
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.38
Consensus pattern (58 bp):
TGCTGATTGGGTTATTTAGCTGATTTACAATGAATCGTTGAGGTCAGCTTTGCAGTAA
Found at i:40104 original size:41 final size:41
Alignment explanation
Indices: 40045--40122 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
40035 GGGTTATTTA
*
40045 GCTGATTTACAATGAATCATTGAGGTCAGCTTTGCAGTAAT
1 GCTGATTTACAATGAATCATGGAGGTCAGCTTTGCAGTAAT
* *
40086 GCTGATTTACAATTAATCATGGAGGTGAGCTTTGCAG
1 GCTGATTTACAATGAATCATGGAGGTCAGCTTTGCAG
40123 GTTTTGATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (41 bp):
GCTGATTTACAATGAATCATGGAGGTCAGCTTTGCAGTAAT
Found at i:41149 original size:58 final size:58
Alignment explanation
Indices: 41027--41149 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 58
41017 GCATAAAATG
* * *
41027 TTGTATTTGTACTCTTGTACGGTGCATACTCCCTGAATCATTAGGCCTTAGATTCAAA
1 TTGTATTTGTACTCTTATACGGTGCATACTCCCTGAATCATAAGGCCTCAGATTCAAA
* * * * * *
41085 TCGTATTTGTACTTTTATATGGTGCATACTCCCTGAATCATAAGGTCTCAGGTTGAAA
1 TTGTATTTGTACTCTTATACGGTGCATACTCCCTGAATCATAAGGCCTCAGATTCAAA
41143 TTGTATT
1 TTGTATT
41150 GGTAGTCATT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (58 bp):
TTGTATTTGTACTCTTATACGGTGCATACTCCCTGAATCATAAGGCCTCAGATTCAAA
Found at i:44715 original size:4 final size:4
Alignment explanation
Indices: 44706--44744 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
44696 AAACCTCAGC
*
44706 AAAT AAAT AAAT AAAT AAAT AATAT AAA- AAAT AATT AAA
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAA
44745 GTCGGTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.77
5 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:47103 original size:20 final size:20
Alignment explanation
Indices: 47078--47126 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
47068 ACCCCCAGAG
*
47078 GGATGGCTGAAGTTGAACAC
1 GGATGGCAGAAGTTGAACAC
47098 GGATGGCAGAAGTTGAACAC
1 GGATGGCAGAAGTTGAACAC
47118 GGATGGCAG
1 GGATGGCAG
47127 TTGGAACCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.14, G:0.39, T:0.16
Consensus pattern (20 bp):
GGATGGCAGAAGTTGAACAC
Found at i:47614 original size:12 final size:12
Alignment explanation
Indices: 47597--47621 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47587 AAAAAACATT
47597 ACAGAAACTCCA
1 ACAGAAACTCCA
47609 ACAGAAACTCCA
1 ACAGAAACTCCA
47621 A
1 A
47622 ATTTCATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.08, T:0.08
Consensus pattern (12 bp):
ACAGAAACTCCA
Found at i:48959 original size:14 final size:14
Alignment explanation
Indices: 48940--48969 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
48930 TTCACGAAAG
48940 TTAGAAGAAAGAAT
1 TTAGAAGAAAGAAT
48954 TTAGAAGAAAGAAT
1 TTAGAAGAAAGAAT
48968 TT
1 TT
48970 CACAAAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (14 bp):
TTAGAAGAAAGAAT
Found at i:49485 original size:18 final size:18
Alignment explanation
Indices: 49462--49499 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
49452 CAATGATGCA
49462 ATCGAGATGAAGAAGAAG
1 ATCGAGATGAAGAAGAAG
49480 ATCGAGATGAAGAAGAAG
1 ATCGAGATGAAGAAGAAG
49498 AT
1 AT
49500 AAAATTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.32, T:0.13
Consensus pattern (18 bp):
ATCGAGATGAAGAAGAAG
Found at i:51093 original size:7 final size:7
Alignment explanation
Indices: 51066--51121 Score: 55
Period size: 7 Copynumber: 8.4 Consensus size: 7
51056 TCAAAATATA
51066 TATATTC
1 TATATTC
*
51073 TAT-TTA
1 TATATTC
*
51079 TTTATTC
1 TATATTC
51086 TATATTC
1 TATATTC
*
51093 TTTATTC
1 TATATTC
*
51100 TATAAT-
1 TATATTC
51106 TATATT-
1 TATATTC
51112 TATATTC
1 TATATTC
51119 TAT
1 TAT
51122 TATATAGAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
6 15 0.38
7 24 0.62
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (7 bp):
TATATTC
Found at i:51098 original size:27 final size:27
Alignment explanation
Indices: 51068--51124 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
51058 AAAATATATA
*
51068 TATTCTATTTATT-TATTCTATATTCT-T
1 TATTCTA-TAATTATATT-TATATTCTAT
51095 TATTCTATAATTATATTTATATTCTAT
1 TATTCTATAATTATATTTATATTCTAT
51122 TAT
1 TAT
51125 ATAGAGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTCTATAATTATATTTATATTCTAT
Found at i:51550 original size:15 final size:15
Alignment explanation
Indices: 51530--51560 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51520 ATTTCATGTA
51530 TTTAATTAATTATAC
1 TTTAATTAATTATAC
*
51545 TTTAATTAGTTATAC
1 TTTAATTAATTATAC
51560 T
1 T
51561 ACATAATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTAATTAATTATAC
Found at i:51688 original size:3 final size:3
Alignment explanation
Indices: 51682--51728 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
51672 ATATTCATAT
51682 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
51729 TTATTTAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:53026 original size:3 final size:3
Alignment explanation
Indices: 53018--53059 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
53008 ACAGAGTGAG
53018 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53060 AAAATTAATG
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):
TAT
Found at i:57276 original size:46 final size:45
Alignment explanation
Indices: 57175--57302 Score: 220
Period size: 46 Copynumber: 2.8 Consensus size: 45
57165 AATTCTACTT
57175 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
* *
57220 CATCTTTAGGTAATTCATCAAAATAAAGCTAAATATTCTACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCT-AATATTATACTCCTC
*
57266 CATCTCTAGGTAATTCATCAAAATAAACCTAATATTA
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
57303 ATTGTTGCTT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 35 0.45
46 42 0.55
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (45 bp):
CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
Found at i:58463 original size:29 final size:28
Alignment explanation
Indices: 58375--58478 Score: 124
Period size: 29 Copynumber: 3.8 Consensus size: 28
58365 TGTTTGCACC
*
58375 TCCAGGGGTATTTTGGTCATTTTGCATG
1 TCCAGGGGCATTTTGGTCATTTTGCATG
* * **
58403 T---TGGGCGTTTTGGTCATTTTGCAAA
1 TCCAGGGGCATTTTGGTCATTTTGCATG
58428 TCCAGGGGCATTTTGGTCATTCTTGCATG
1 TCCAGGGGCATTTTGGTCATT-TTGCATG
*
58457 TCCAGGGGCATTTTAGTCATTT
1 TCCAGGGGCATTTTGGTCATTT
58479 CAAGTATCTT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
25 20 0.32
28 17 0.27
29 25 0.40
ACGTcount: A:0.15, C:0.16, G:0.27, T:0.41
Consensus pattern (28 bp):
TCCAGGGGCATTTTGGTCATTTTGCATG
Found at i:61656 original size:2 final size:2
Alignment explanation
Indices: 61649--61683 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
61639 TATTACTAGC
61649 TA TA TA TA 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 TA TA TA TA T
61684 TCTTTTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65313 original size:26 final size:26
Alignment explanation
Indices: 65284--65361 Score: 61
Period size: 27 Copynumber: 2.9 Consensus size: 26
65274 TCACTTGAGT
65284 TGAAAACCCGAAAAGGGCGGCTCAAG
1 TGAAAACCCGAAAAGGGCGGCTCAAG
* ** **
65310 TGAAGGA-TGGAAAAGGAG-GAGCTTGAG
1 TGAA-AACCCGAAAAGG-GCG-GCTCAAG
65337 TCGAAAACCCGAAAAGGGCGGCTCA
1 T-GAAAACCCGAAAAGGGCGGCTCA
65362 GGTAAAAGAT
Statistics
Matches: 36, Mismatches: 10, Indels: 11
0.63 0.18 0.19
Matches are distributed among these distances:
26 12 0.33
27 13 0.36
28 11 0.31
ACGTcount: A:0.37, C:0.18, G:0.35, T:0.10
Consensus pattern (26 bp):
TGAAAACCCGAAAAGGGCGGCTCAAG
Found at i:65575 original size:2 final size:2
Alignment explanation
Indices: 65568--65596 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
65558 CTGGTACTCC
65568 TA 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 TA T
65597 TAAAATTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66345 original size:51 final size:51
Alignment explanation
Indices: 66282--66525 Score: 438
Period size: 51 Copynumber: 4.8 Consensus size: 51
66272 TCCAGAAAAG
*
66282 TGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTATT-TAAGAT
1 TGAATTGAAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCT-TTATAAGAT
66333 TGAATTGAAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTATAAGAT
1 TGAATTGAAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTATAAGAT
*
66384 TGAATTGAAAGACAGTTCAAAGGATAAGCGGAAGACGGTTCTTTATAAGAT
1 TGAATTGAAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTATAAGAT
66435 TGAATTGAAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTT-TAAGAT
1 TGAATTGAAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTATAAGAT
*
66485 TGAATTGAAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
1 TGAATTGAAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
66526 CTTTCATGTT
Statistics
Matches: 188, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
50 48 0.26
51 140 0.74
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (51 bp):
TGAATTGAAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTATAAGAT
Found at i:66424 original size:23 final size:23
Alignment explanation
Indices: 66392--66470 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 23
66382 ATTGAATTGA
66392 AAGACAGTTCAAAGGATAAGCGG
1 AAGACAGTTCAAAGGATAAGCGG
* ** *
66415 AAGACGGTTCTTTATAA-GATTGAATTGA
1 AAGACAGTTC---A-AAGGA-T-AAGCGG
66443 AAGACAGTTCAAAGGATAAGCGG
1 AAGACAGTTCAAAGGATAAGCGG
66466 AAGAC
1 AAGAC
66471 GGTCCTTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
23 17 0.41
24 3 0.07
25 3 0.07
26 3 0.07
27 3 0.07
28 12 0.29
ACGTcount: A:0.42, C:0.11, G:0.27, T:0.20
Consensus pattern (23 bp):
AAGACAGTTCAAAGGATAAGCGG
Found at i:66912 original size:29 final size:28
Alignment explanation
Indices: 66840--66926 Score: 111
Period size: 28 Copynumber: 3.1 Consensus size: 28
66830 ATTTTAGTTG
* *
66840 TTTGCACCTCCAGGGGTATTTTGGTCAT
1 TTTGCACATCCAGGGGCATTTTGGTCAT
** *
66868 TTTGCATGTCCGGGGGCATTTTGGTCAT
1 TTTGCACATCCAGGGGCATTTTGGTCAT
*
66896 TCTTGCACATCCAGGGGCATTTTAGTCAT
1 T-TTGCACATCCAGGGGCATTTTGGTCAT
66925 TT
1 TT
66927 CAAGTCCCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
28 26 0.52
29 24 0.48
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (28 bp):
TTTGCACATCCAGGGGCATTTTGGTCAT
Found at i:75826 original size:21 final size:22
Alignment explanation
Indices: 75781--75828 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
75771 TTGGAATCAT
*
75781 TGGTG-TGTGGATGGCCGGTGG
1 TGGTGCTGTGGATGGCCGGTGC
75802 TGGTGCTGT-GATGGCACGG-GC
1 TGGTGCTGTGGATGGC-CGGTGC
75823 TGGTGC
1 TGGTGC
75829 GGTAGTGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.06, C:0.15, G:0.52, T:0.27
Consensus pattern (22 bp):
TGGTGCTGTGGATGGCCGGTGC
Found at i:78595 original size:35 final size:35
Alignment explanation
Indices: 78548--78614 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
78538 AATGTAATTG
*
78548 TTTTTATTAGTAAATCTCTTTCGTAGACTCTTTGTA
1 TTTTTATTAGTAAATCTCTTT-GTAAACTCTTTGTA
78584 TTTTT-TTAGTAAATCTCTTTGTAAACTCTTT
1 TTTTTATTAGTAAATCTCTTTGTAAACTCTTT
78615 ATTTATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 10 0.33
35 15 0.50
36 5 0.17
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.55
Consensus pattern (35 bp):
TTTTTATTAGTAAATCTCTTTGTAAACTCTTTGTA
Found at i:85257 original size:41 final size:40
Alignment explanation
Indices: 85156--85260 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 40
85146 TAAGGTGACA
* * * * **
85156 ACTTCTGGTATCAACAGTAATTATAATTTACCAGAGCTAC
1 ACTTCTGATGTCAATAGTAATTTTAATTTACCAGAAATAC
* *
85196 ACTTCTGGTGTCTATAGTAATTTTAATTTACC-GAAATGAC
1 ACTTCTGATGTCAATAGTAATTTTAATTTACCAGAAAT-AC
*
85236 AGCTTCTGATGTCAATGGTAATTTT
1 A-CTTCTGATGTCAATAGTAATTTT
85261 TAAATAATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
39 3 0.06
40 31 0.57
41 20 0.37
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (40 bp):
ACTTCTGATGTCAATAGTAATTTTAATTTACCAGAAATAC
Found at i:87101 original size:15 final size:17
Alignment explanation
Indices: 87081--87113 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
87071 CGCTCAAACG
87081 TCGGGTC-A-TTTGGGT
1 TCGGGTCAATTTTGGGT
87096 TCGGGTCAATTTTGGGT
1 TCGGGTCAATTTTGGGT
87113 T
1 T
87114 TGGTCGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.09, C:0.12, G:0.36, T:0.42
Consensus pattern (17 bp):
TCGGGTCAATTTTGGGT
Found at i:88912 original size:16 final size:16
Alignment explanation
Indices: 88891--88922 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
88881 ATAAGGTTAC
88891 TTTCTTTTCCATTTCG
1 TTTCTTTTCCATTTCG
88907 TTTCTTTTCCATTTCG
1 TTTCTTTTCCATTTCG
88923 GACCAGTTGC
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:0.06, C:0.25, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTCTTTTCCATTTCG
Found at i:89395 original size:16 final size:16
Alignment explanation
Indices: 89376--89425 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
89366 TCCCAAAATA
89376 TAGCTTTCCCTTGGCT
1 TAGCTTTCCCTTGGCT
89392 TAGCTTT--CTTGATGACT
1 TAGCTTTCCCTTG--G-CT
*
89409 TAGCTCTCCCTTGGCT
1 TAGCTTTCCCTTGGCT
89425 T
1 T
89426 GATGACTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
14 4 0.14
16 11 0.39
17 9 0.32
19 4 0.14
ACGTcount: A:0.10, C:0.28, G:0.18, T:0.44
Consensus pattern (16 bp):
TAGCTTTCCCTTGGCT
Found at i:89431 original size:24 final size:24
Alignment explanation
Indices: 89399--89462 Score: 128
Period size: 24 Copynumber: 2.7 Consensus size: 24
89389 GCTTAGCTTT
89399 CTTGATGACTTAGCTCTCCCTTGG
1 CTTGATGACTTAGCTCTCCCTTGG
89423 CTTGATGACTTAGCTCTCCCTTGG
1 CTTGATGACTTAGCTCTCCCTTGG
89447 CTTGATGACTTAGCTC
1 CTTGATGACTTAGCTC
89463 GGCATGCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.14, C:0.28, G:0.20, T:0.38
Consensus pattern (24 bp):
CTTGATGACTTAGCTCTCCCTTGG
Found at i:91431 original size:14 final size:14
Alignment explanation
Indices: 91412--91440 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
91402 TAGGGTTCTT
91412 ATACAGAGACAAAA
1 ATACAGAGACAAAA
91426 ATACAGAGACAAAA
1 ATACAGAGACAAAA
91440 A
1 A
91441 AAAAAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.14, G:0.14, T:0.07
Consensus pattern (14 bp):
ATACAGAGACAAAA
Found at i:93072 original size:24 final size:24
Alignment explanation
Indices: 93045--93100 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
93035 GAAATTTGGT
93045 AAGTAGAA-GGAAATTTGGTAACTA
1 AAGTAGAATGG-AATTTGGTAACTA
* *
93069 AAGTTA-AATGGTATTTGGTAATTA
1 AAG-TAGAATGGAATTTGGTAACTA
93093 AAGTAGAA
1 AAGTAGAA
93101 AGAGTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.07
24 21 0.78
25 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (24 bp):
AAGTAGAATGGAATTTGGTAACTA
Found at i:93077 original size:19 final size:19
Alignment explanation
Indices: 93030--93077 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
93020 GTAAACAGAA
*
93030 AAAGTGAAATTTGGTAAGT
1 AAAGTGAAATTTGGTAACT
93049 AGAAG-GAAATTTGGTAACT
1 A-AAGTGAAATTTGGTAACT
*
93068 AAAGTTAAAT
1 AAAGTGAAAT
93078 GGTATTTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.12
19 19 0.76
20 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.29
Consensus pattern (19 bp):
AAAGTGAAATTTGGTAACT
Found at i:93114 original size:33 final size:33
Alignment explanation
Indices: 93073--93334 Score: 169
Period size: 33 Copynumber: 7.9 Consensus size: 33
93063 TAACTAAAGT
*
93073 TAAA-TGGTATTTGGTAATTAAAGTAGAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
*
93105 TAAATTGGTATTTGGTAATCAAAGTAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
* * ** * *
93138 AAAAAAATGAAATTCGGTAATTAAAATAAAAAAGAG
1 --TAAATTGGTATTTGGTAATTAAAGT-AAAAAGAG
****
93174 T-AATATGGTAAAAAG-AGATTAAAGTAAAAAGAG
1 TAAAT-TGGTATTTGGTA-ATTAAAGTAAAAAGAG
* ** * ** *
93207 TAAAATGGTAAAAT-GAAATT-TGGTAACTAAAG-T
1 TAAATTGGT-ATTTGGTAATTAAAGTAA--AAAGAG
* *
93240 TAAA-TGGTATTCGGTAATTAAAATAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
* * *
93272 TAAATTGGTATTTGGAAAATATAGTAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
*
93305 TAAAATTGGTATTTGATAATTAAAGTAAAA
1 T-AAATTGGTATTTGGTAATTAAAGTAAAA
93335 TTGGTAAAAA
Statistics
Matches: 174, Mismatches: 40, Indels: 30
0.71 0.16 0.12
Matches are distributed among these distances:
31 5 0.03
32 21 0.12
33 77 0.44
34 45 0.26
35 18 0.10
36 8 0.05
ACGTcount: A:0.51, C:0.02, G:0.19, T:0.28
Consensus pattern (33 bp):
TAAATTGGTATTTGGTAATTAAAGTAAAAAGAG
Found at i:93219 original size:16 final size:17
Alignment explanation
Indices: 93166--93219 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
93156 AATTAAAATA
*
93166 AAAAAGAGTAATATGGT
1 AAAAAGAGTAAAATGGT
*
93183 AAAAAGAGATTAAA--GT
1 AAAAAGAG-TAAAATGGT
93199 AAAAAGAGTAAAATGGT
1 AAAAAGAGTAAAATGGT
93216 AAAA
1 AAAA
93220 TGAAATTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 14 0.45
18 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.19
Consensus pattern (17 bp):
AAAAAGAGTAAAATGGT
Found at i:100080 original size:11 final size:11
Alignment explanation
Indices: 100061--100090 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
100051 TTTTCACCCT
*
100061 GTTCATCACTC
1 GTTCTTCACTC
100072 GTTCTTCACTC
1 GTTCTTCACTC
100083 GTTCTTCA
1 GTTCTTCA
100091 TATTTTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.33, G:0.10, T:0.43
Consensus pattern (11 bp):
GTTCTTCACTC
Found at i:100194 original size:51 final size:50
Alignment explanation
Indices: 100093--100194 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 50
100083 GTTCTTCATA
* *
100093 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTCAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
100143 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
100194 T
1 T
100195 CTTCATTCAG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
50 8 0.17
51 37 0.80
52 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Done.