Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007761.1 Corchorus capsularis cultivar CVL-1 contig07782, 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: 94538
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:39 original size:14 final size:14
Alignment explanation
Indices: 18--56 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
8 AATAAAAACT
18 AAAAAGAATGAAAA
1 AAAAAGAATGAAAA
* *
32 ATAAAGAAAGAAAA
1 AAAAAGAATGAAAA
*
46 AAAAAAAATGA
1 AAAAAGAATGA
57 CACGTCAGGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (14 bp):
AAAAAGAATGAAAA
Found at i:138 original size:2 final size:2
Alignment explanation
Indices: 131--169 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
121 AAACCTATTA
131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
170 GCTAATTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:486 original size:128 final size:128
Alignment explanation
Indices: 289--537 Score: 324
Period size: 128 Copynumber: 1.9 Consensus size: 128
279 ATTAAAAAGA
* *
289 CCCTCAATTAGTTTCTCACCATTCCCTTCTCCTCCATACCTTTTTTTTTATAATTACAAGGGGTT
1 CCCTCAATTAGTTTCTCAACATTCCCTTCTCCTCCA-ACC-TTTTTATTATAATTACAAGGGGTT
* * *
354 TTAACCAGTTAAATGTGAAA-GCATTTATTGACCATAAAATCATGTATTATTTATTTACTAAGAA
64 TTAACCACTTAAATGT-AAACACATTTATTGACCATAAAATCATGTACTA-TTATTTACTAAGAA
418 GG
127 GG
* * * * **
420 CCCTCAATTAGTTTCTCAACATTTCCTTTTTCCTCC-GCC-TTTTATTGTAATTACAAGGTTTTT
1 CCCTCAATTAGTTTCTCAACA-TTCCCTTCTCCTCCAACCTTTTTATTATAATTACAAGGGGTTT
*
483 TAACCACTTCAATGTAAACACATTTATTGACCATAAAATCATGTACTATTATTTA
65 TAACCACTTAAATGTAAACACATTTATTGACCATAAAATCATGTACTATTATTTA
538 TTCACTTTAT
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
127 10 0.10
128 60 0.58
130 2 0.02
131 20 0.19
132 12 0.12
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (128 bp):
CCCTCAATTAGTTTCTCAACATTCCCTTCTCCTCCAACCTTTTTATTATAATTACAAGGGGTTTT
AACCACTTAAATGTAAACACATTTATTGACCATAAAATCATGTACTATTATTTACTAAGAAGG
Found at i:590 original size:1 final size:1
Alignment explanation
Indices: 586--621 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
576 CTAAATCTGG
586 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
622 GGAGGTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2481 original size:16 final size:16
Alignment explanation
Indices: 2454--2515 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
2444 TCTCGGATTC
2454 AGATTTTATCGGGTTTT
1 AGATTTT-TCGGGTTTT
2471 AGATTTTTCGGGTTTT
1 AGATTTTTCGGGTTTT
* * *
2487 -GGTTTTTTGGGTTTG
1 AGATTTTTCGGGTTTT
* *
2502 AGTTTTTTGGGGTT
1 AGATTTTTCGGGTT
2516 CGGATTCGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
15 12 0.31
16 20 0.51
17 7 0.18
ACGTcount: A:0.10, C:0.03, G:0.31, T:0.56
Consensus pattern (16 bp):
AGATTTTTCGGGTTTT
Found at i:2501 original size:14 final size:16
Alignment explanation
Indices: 2464--2512 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
2454 AGATTTTATC
*
2464 GGGTTTT-AGATTTTTC
1 GGGTTTTGAG-TTTTTT
2480 GGGTTTTG-GTTTTTT
1 GGGTTTTGAGTTTTTT
2495 GGG-TTTGAGTTTTTT
1 GGGTTTTGAGTTTTTT
2510 GGG
1 GGG
2513 GTTCGGATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.13
15 18 0.60
16 8 0.27
ACGTcount: A:0.06, C:0.02, G:0.35, T:0.57
Consensus pattern (16 bp):
GGGTTTTGAGTTTTTT
Found at i:3694 original size:2 final size:2
Alignment explanation
Indices: 3687--3716 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3677 AAAATAGTAC
3687 TA TA TA TA TA T- 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 T
3717 GTCAAATAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3957 original size:19 final size:19
Alignment explanation
Indices: 3933--3971 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3923 AGTTTGCCAC
3933 GAATGATAATTCAGGTGCT
1 GAATGATAATTCAGGTGCT
3952 GAATGATAATTCAGGTGCT
1 GAATGATAATTCAGGTGCT
3971 G
1 G
3972 TCATTAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (19 bp):
GAATGATAATTCAGGTGCT
Found at i:6486 original size:30 final size:31
Alignment explanation
Indices: 6439--6500 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
6429 TAATCTACAC
6439 CTATATATCTAAATCTAATGCCATACAGCTT
1 CTATATATCTAAATCTAATGCCATACAGCTT
6470 CTATATATCT-AATCTAATGCCATACAGCTT
1 CTATATATCTAAATCTAATGCCATACAGCTT
6500 C
1 C
6501 AAGAAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.35
Consensus pattern (31 bp):
CTATATATCTAAATCTAATGCCATACAGCTT
Found at i:16776 original size:18 final size:18
Alignment explanation
Indices: 16755--16810 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
16745 TGCAAAACCC
16755 GTGGCAAATTGAAAAGTT
1 GTGGCAAATTGAAAAGTT
*
16773 GTGGCAAA--G----GTC
1 GTGGCAAATTGAAAAGTT
16785 GTGGCAAATTGAAAAGTT
1 GTGGCAAATTGAAAAGTT
16803 GTGGCAAA
1 GTGGCAAA
16811 GGCCGTGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 10 0.33
14 1 0.03
16 1 0.03
18 18 0.60
ACGTcount: A:0.36, C:0.09, G:0.32, T:0.23
Consensus pattern (18 bp):
GTGGCAAATTGAAAAGTT
Found at i:16788 original size:30 final size:30
Alignment explanation
Indices: 16753--16823 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
16743 GCTGCAAAAC
16753 CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
1 CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
*
16783 TCGTGGCAAATTGAAAAGTTGTGGCAAAGG
1 CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
*
16813 CCGTGCCAAAT
1 CCGTGGCAAAT
16824 AGCCACGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.21
Consensus pattern (30 bp):
CCGTGGCAAATTGAAAAGTTGTGGCAAAGG
Found at i:19694 original size:18 final size:18
Alignment explanation
Indices: 19661--19695 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19651 GAATACTTCT
*
19661 TATTATTAATATATATAC
1 TATTATTAATACATATAC
*
19679 TATTATTACTACATATA
1 TATTATTAATACATATA
19696 TAAAAGGTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTATTAATACATATAC
Found at i:20046 original size:34 final size:34
Alignment explanation
Indices: 20000--20065 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
19990 TACTCCATCT
*
20000 CTAGGTAGTTCATCAAAATAAAGCTAATATTAAC
1 CTAGGTAATTCATCAAAATAAAGCTAATATTAAC
*
20034 CTAGGTAATTCATCAAAATAAAGTTAATATTA
1 CTAGGTAATTCATCAAAATAAAGCTAATATTA
20066 TCCGTTGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (34 bp):
CTAGGTAATTCATCAAAATAAAGCTAATATTAAC
Found at i:23447 original size:15 final size:15
Alignment explanation
Indices: 23347--23449 Score: 58
Period size: 15 Copynumber: 7.1 Consensus size: 15
23337 TAACTGACCT
*
23347 AACCAAAATGA-CCG
1 AACCCAAATGACCCG
23361 AACCC-AA--ACCC-
1 AACCCAAATGACCCG
* *
23372 AACCCAAAATTATCCG
1 AACCC-AAATGACCCG
*
23388 AA-CCATATGACCCG
1 AACCCAAATGACCCG
* **
23402 AAGCCGAAACAACCC-
1 AA-CCCAAATGACCCG
23417 AACCCAGAATTGACCCG
1 AACCCA-AA-TGACCCG
23434 AACCCAAATGACCCG
1 AACCCAAATGACCCG
23449 A
1 A
23450 CATTTGAACG
Statistics
Matches: 66, Mismatches: 12, Indels: 21
0.67 0.12 0.21
Matches are distributed among these distances:
11 6 0.09
12 2 0.03
13 4 0.06
14 16 0.24
15 17 0.26
16 15 0.23
17 6 0.09
ACGTcount: A:0.43, C:0.37, G:0.12, T:0.09
Consensus pattern (15 bp):
AACCCAAATGACCCG
Found at i:23522 original size:192 final size:192
Alignment explanation
Indices: 23190--23557 Score: 558
Period size: 192 Copynumber: 1.9 Consensus size: 192
23180 AACCTGAAAG
* *
23190 TATCCGAACCATATGAACCGAAAACGAAAACGACCCAACCCAGAATTGCCCCGAACCCAAATGAC
1 TATCCGAACCATATGAACCGAAAACGAAAACAACCCAACCCAGAATTGACCCGAACCCAAATGAC
* ** *
23255 CTGACATTTGAATTATCCAAACCCAACCCAACCCAAAACCAAAATTAACTGAACCCGAATGACCC
66 CCGACATTTGAACGATCCAAACCCAACCCAACCCAAAACCAAAATTAACCGAACCCGAATGACCC
* *
23320 GAAATTTCCTTATCCCGTAACTGACCTAACCAAAATGACCGAACCCAAACCCAACCCAAAAT
131 GAAATTTCCTTATCCCGAAACTGACCCAACCAAAATGACCGAACCCAAACCCAACCCAAAAT
* **
23382 TATCCGAACCATATGACCCGAAGCCG-AAACAACCCAACCCAGAATTGACCCGAACCCAAATGAC
1 TATCCGAACCATATGAACCGAAAACGAAAACAACCCAACCCAGAATTGACCCGAACCCAAATGAC
* * * * * *
23446 CCGACATTTGAACGATCCGAACCTAACCTAACCCGAAACCGAAAATTAACCGAACCTGTATGACC
66 CCGACATTTGAACGATCCAAACCCAACCCAACCCAAAACC-AAAATTAACCGAACCCGAATGACC
*
23511 CGAAATTTCCTTATCCCGAAACTGACCCAACCCAAATGACCGAACCC
130 CGAAATTTCCTTATCCCGAAACTGACCCAACCAAAATGACCGAACCC
23558 GACCTGCCCA
Statistics
Matches: 157, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
191 69 0.44
192 88 0.56
ACGTcount: A:0.39, C:0.35, G:0.11, T:0.15
Consensus pattern (192 bp):
TATCCGAACCATATGAACCGAAAACGAAAACAACCCAACCCAGAATTGACCCGAACCCAAATGAC
CCGACATTTGAACGATCCAAACCCAACCCAACCCAAAACCAAAATTAACCGAACCCGAATGACCC
GAAATTTCCTTATCCCGAAACTGACCCAACCAAAATGACCGAACCCAAACCCAACCCAAAAT
Found at i:24031 original size:14 final size:14
Alignment explanation
Indices: 23990--24024 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
23980 TCGGTGTCGG
*
23990 TCGGTGTCGGTTTTT
1 TCGGT-TCGATTTTT
24005 TCGGTTCGATTTTT
1 TCGGTTCGATTTTT
24019 TCGGTT
1 TCGGTT
24025 TTATTTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.03, C:0.14, G:0.29, T:0.54
Consensus pattern (14 bp):
TCGGTTCGATTTTT
Found at i:26373 original size:21 final size:22
Alignment explanation
Indices: 26348--26388 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
26338 GATTAATTCC
*
26348 AATAATAATTCTT-ATTAACTA
1 AATAATAATTATTCATTAACTA
26369 AATAATAATTATTCATTAAC
1 AATAATAATTATTCATTAAC
26389 ACCAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAATAATTATTCATTAACTA
Found at i:29993 original size:20 final size:18
Alignment explanation
Indices: 29970--30022 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
29960 CTTTTTTTAA
* *
29970 TTTTCCTTTTCTTTCTTCT
1 TTTTTCTTTTCTTT-TCCT
29989 TTTTTCTCTTTCTTTTCCT
1 TTTTTCT-TTTCTTTTCCT
30008 TTTTT-TCTTTCTTTT
1 TTTTTCT-TTTCTTTT
30023 TTTCCTCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 10 0.32
19 14 0.45
20 7 0.23
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTCCT
Found at i:30024 original size:20 final size:20
Alignment explanation
Indices: 29977--30024 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
29967 TAATTTTCCT
*
29977 TTTCTTTCTTCTTTTTTCTC
1 TTTCTTTTTTCTTTTTTCTC
*
29997 TTTC-TTTTCCTTTTTT-TC
1 TTTCTTTTTTCTTTTTTCTC
30015 TTTCTTTTTT
1 TTTCTTTTTT
30025 TCCTCTTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.25
19 14 0.58
20 4 0.17
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTTCTC
Found at i:30025 original size:21 final size:20
Alignment explanation
Indices: 29988--30028 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
29978 TTCTTTCTTC
29988 TTTTTTCTCTTTCTTTTCCT
1 TTTTTTCTCTTTCTTTTCCT
30008 TTTTTTCTTTCTTT-TTTTCCT
1 TTTTTTC--TCTTTCTTTTCCT
30029 CTTCTACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTCTCTTTCTTTTCCT
Found at i:33066 original size:69 final size:71
Alignment explanation
Indices: 32943--33097 Score: 183
Period size: 70 Copynumber: 2.2 Consensus size: 71
32933 TAATTAAAAT
* * * * *
32943 AGTAAAATGGTAAAATATAATAGTTATAAGAGATATTAGATTTAATTATATAAAAA-AGAGTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAGAGATATTAGATTTAATTAAATAAAAATAGAATTTT
33007 TAGTT-
66 TAGTTG
** * *
33012 ATGTAAAATAGTAAAATAAAATAATTATAA-TTATATTATATTTAATTAAATAAAAATATAATTT
1 A-GTAAAATAGTAAAATAAAATAATTATAAGAGATATTAGATTTAATTAAATAAAAATAGAATTT
33076 TTAGTTG
65 TTAGTTG
33083 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
33098 AGCTAAACAA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
69 23 0.32
70 47 0.64
71 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.38
Consensus pattern (71 bp):
AGTAAAATAGTAAAATAAAATAATTATAAGAGATATTAGATTTAATTAAATAAAAATAGAATTTT
TAGTTG
Found at i:36627 original size:2 final size:2
Alignment explanation
Indices: 36620--36647 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36610 AAACTCTACT
36620 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
36648 AATTATAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37005 original size:49 final size:51
Alignment explanation
Indices: 36931--37029 Score: 166
Period size: 49 Copynumber: 2.0 Consensus size: 51
36921 GCAATAAAAT
*
36931 TAAAAGAAAAAAGAAAAGAAAAATCAACCAATAAGGAGGAGGCCATTTGTA
1 TAAAAGAAAAAAGAAAAGAAAAATCAACCAATAAGAAGGAGGCCATTTGTA
*
36982 TAAAA-AAAAAA-AGAAGAAAAATCAACCAATAAGAAGGAGGCCATTTGT
1 TAAAAGAAAAAAGAAAAGAAAAATCAACCAATAAGAAGGAGGCCATTTGT
37030 CAAAAGTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 35 0.76
50 6 0.13
51 5 0.11
ACGTcount: A:0.58, C:0.10, G:0.18, T:0.14
Consensus pattern (51 bp):
TAAAAGAAAAAAGAAAAGAAAAATCAACCAATAAGAAGGAGGCCATTTGTA
Found at i:39648 original size:12 final size:12
Alignment explanation
Indices: 39633--39657 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39623 TACTTTGGAG
39633 ACAGAAATCCCC
1 ACAGAAATCCCC
39645 ACAGAAATCCCC
1 ACAGAAATCCCC
39657 A
1 A
39658 GCATTGAATA
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:0.44, C:0.40, G:0.08, T:0.08
Consensus pattern (12 bp):
ACAGAAATCCCC
Found at i:41952 original size:3 final size:3
Alignment explanation
Indices: 41946--41984 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
41936 AACGAGGAAG
41946 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
41985 TTGCCTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:46360 original size:26 final size:26
Alignment explanation
Indices: 46331--46385 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
46321 AAAACTAAGG
*
46331 AAATAATTTAGAAAACAATCAATTAA
1 AAATAATTTAGAAAACAATAAATTAA
46357 AAATAATTTAGAAAACAATAAATTAA
1 AAATAATTTAGAAAACAATAAATTAA
46383 AAA
1 AAA
46386 GCATACTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.25
Consensus pattern (26 bp):
AAATAATTTAGAAAACAATAAATTAA
Found at i:58826 original size:50 final size:50
Alignment explanation
Indices: 58751--58894 Score: 245
Period size: 50 Copynumber: 2.9 Consensus size: 50
58741 ATCTCTTTGA
58751 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAGGT
1 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAGGT
*
58801 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGAGAAAGCTTAGGT
1 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAGGT
* * *
58851 TTGTGATAAGTGCGGGGAGCACTTGTT-TGAGCTTGGGGAAAGCT
1 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGGAAAGCT
58895 CGGTGTTGTC
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
49 15 0.17
50 74 0.83
ACGTcount: A:0.22, C:0.13, G:0.35, T:0.30
Consensus pattern (50 bp):
TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAGGT
Found at i:70701 original size:99 final size:99
Alignment explanation
Indices: 70525--70705 Score: 229
Period size: 99 Copynumber: 1.8 Consensus size: 99
70515 AAACCAATGT
* * * * * **
70525 TCAAATGTCGTGTCTCAGAATAAGTAGAACTTATTGAAAAGTGTGCTCGCTAAACAAAAGTTTTT
1 TCAAATATCGTGTCTCAAAATAAGTAGAACTTATTGAAAAGTGTACTCGCTAAACAAAACTCTAA
* *
70590 GAAGTTTGAAACCTCAATTTTGCAAAATCATCAC
66 GAAGTCTAAAACCTCAATTTTGCAAAATCATCAC
* * * *
70624 TCAAATATTGTGTCTCAAAATGAGTAGAACTTATTGGAAAGTG-ACTCGCTAAATAAAACTCCTA
1 TCAAATATCGTGTCTCAAAATAAGTAGAACTTATTGAAAAGTGTACTCGCTAAACAAAACT-CTA
70688 AGAAGTCTAAAACCTCAA
65 AGAAGTCTAAAACCTCAA
70706 CTTCTCGTAT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
98 14 0.21
99 54 0.79
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (99 bp):
TCAAATATCGTGTCTCAAAATAAGTAGAACTTATTGAAAAGTGTACTCGCTAAACAAAACTCTAA
GAAGTCTAAAACCTCAATTTTGCAAAATCATCAC
Found at i:72684 original size:2 final size:2
Alignment explanation
Indices: 72677--72707 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
72667 TACTAGTGTC
72677 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 T
72708 TGCTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78649 original size:2 final size:2
Alignment explanation
Indices: 78642--78669 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
78632 CTAGAGTCAA
78642 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
78670 CTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92521 original size:13 final size:12
Alignment explanation
Indices: 92502--92543 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
92492 TCTTACAGCT
92502 TATATAATATAA
1 TATATAATATAA
92514 TAATATAATAT-A
1 T-ATATAATATAA
92526 TA-ATAATAATAA
1 TATATAAT-ATAA
92538 TATATA
1 TATATA
92544 CTAGAACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 5 0.19
11 3 0.12
12 6 0.23
13 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TATATAATATAA
Found at i:92972 original size:11 final size:11
Alignment explanation
Indices: 92958--92995 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
92948 ATTCATAACA
92958 AATTTATAATT
1 AATTTATAATT
92969 AATTTATAATT
1 AATTTATAATT
92980 -ATTTGATAATT
1 AATTT-ATAATT
*
92991 TATTT
1 AATTT
92996 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:93195 original size:10 final size:10
Alignment explanation
Indices: 93182--93275 Score: 52
Period size: 11 Copynumber: 8.9 Consensus size: 10
93172 TATAAATGGA
*
93182 AATATTAATT
1 AATAATAATT
93192 AATAATAATT
1 AATAATAATT
93202 AATTAATAAATGT
1 AA-TAAT-AAT-T
*
93215 CAA-AAAAATT
1 -AATAATAATT
93225 -AT--TAATT
1 AATAATAATT
93232 AATAATAATT
1 AATAATAATT
93242 AAATATATATATAT
1 -AATA-ATA-AT-T
*
93256 AATAATAATA
1 AATAATAATT
93266 ATATAATAAT
1 A-ATAATAAT
93276 GAAAATTCCA
Statistics
Matches: 67, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
7 4 0.06
8 3 0.04
10 18 0.27
11 21 0.31
12 11 0.16
13 7 0.10
14 3 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (10 bp):
AATAATAATT
Found at i:93204 original size:14 final size:14
Alignment explanation
Indices: 93185--93272 Score: 55
Period size: 14 Copynumber: 6.4 Consensus size: 14
93175 AAATGGAAAT
93185 ATTAATTAATAATA
1 ATTAATTAATAATA
93199 ATTAATTAAT-A-A
1 ATTAATTAATAATA
* *
93211 ATGTCAA--AAAAATT
1 AT-T-AATTAATAATA
93225 ATTAATTAATAATA
1 ATTAATTAATAATA
*
93239 ATTAAAT-AT-ATA
1 ATTAATTAATAATA
93251 TATATAA-TAATAATA
1 -AT-TAATTAATAATA
93266 ATATAAT
1 AT-TAAT
93273 AATGAAAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 21
0.69 0.06 0.25
Matches are distributed among these distances:
12 10 0.17
13 9 0.16
14 36 0.62
15 3 0.05
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (14 bp):
ATTAATTAATAATA
Found at i:93204 original size:40 final size:39
Alignment explanation
Indices: 93160--93257 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 39
93150 TAGGTTTAAT
*
93160 TTAATAATATAATATAAATGGAAA-TATTAATTAATAATAA
1 TTAATAATATAATATAAA--AAAATTATTAATTAATAATAA
*
93200 TTAATTAATA-AATGTCAAAAAAATTATTAATTAATAATAA
1 TTAA-TAATATAATAT-AAAAAAATTATTAATTAATAATAA
93240 TTAA-ATATATATATATAA
1 TTAATA-ATATA-ATATAA
93258 TAATAATAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
38 1 0.02
39 6 0.12
40 31 0.63
41 11 0.22
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (39 bp):
TTAATAATATAATATAAAAAAATTATTAATTAATAATAA
Done.