Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020354.1 Corchorus olitorius cultivar O-4 contig20387, 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: 111319
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1100 original size:2 final size:2
Alignment explanation
Indices: 1093--1122 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1083 TCAATCACTC
1093 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1123 GTGGGGGGGT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1234 original size:20 final size:20
Alignment explanation
Indices: 1209--1249 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1199 TTATACCAGC
1209 TGCAGAACCTTCAATAGTTA
1 TGCAGAACCTTCAATAGTTA
1229 TGCAGAACCTTCAATAGTTA
1 TGCAGAACCTTCAATAGTTA
1249 T
1 T
1250 CTCTGAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (20 bp):
TGCAGAACCTTCAATAGTTA
Found at i:4893 original size:21 final size:21
Alignment explanation
Indices: 4833--4897 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 21
4823 TGAGATGATA
*
4833 TAATATTCCAACAAACAATTG
1 TAATATTCCATCAAACAATTG
*
4854 TAATACACAATTTCATCAAACAATTG
1 TAAT-----ATTCCATCAAACAATTG
4880 TAATATTCCATCAAACAA
1 TAATATTCCATCAAACAA
4898 GTGAAACCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
21 17 0.47
26 19 0.53
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.29
Consensus pattern (21 bp):
TAATATTCCATCAAACAATTG
Found at i:9507 original size:42 final size:44
Alignment explanation
Indices: 9456--9549 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
9446 AGTGCATTAC
* * *
9456 CTAA-ATTCTACT-C-CATCTTTAGGTAGTTCATCAAAATAAAG
1 CTAATATTCTACTCCGCATCTCTAGATAATTCATCAAAATAAAG
9497 CTAATATTCTACTCCTGCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCC-GCATCTCTAGATAATTCATCAAAATAAAG
9542 CTAATATT
1 CTAATATT
9550 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
43 1 0.02
45 33 0.72
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCCGCATCTCTAGATAATTCATCAAAATAAAG
Found at i:11553 original size:26 final size:28
Alignment explanation
Indices: 11510--11564 Score: 96
Period size: 26 Copynumber: 2.0 Consensus size: 28
11500 TTTTGAGATG
11510 ACATAATATTCCATCAAACAATTGTAAT
1 ACATAATATTCCATCAAACAATTGTAAT
11538 ACATAAT-TT-CATCAAACAATTGTAAT
1 ACATAATATTCCATCAAACAATTGTAAT
11564 A
1 A
11565 TTCAATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 18 0.67
27 2 0.07
28 7 0.26
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (28 bp):
ACATAATATTCCATCAAACAATTGTAAT
Found at i:12046 original size:9 final size:9
Alignment explanation
Indices: 12014--12058 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
12004 TTCCTTGAAA
12014 TTCTTTTTC
1 TTCTTTTTC
12023 TT-TTTTT-
1 TTCTTTTTC
*
12030 TTC-CTTTC
1 TTCTTTTTC
12038 TTCTTTTTC
1 TTCTTTTTC
*
12047 TTCTTCTTC
1 TTCTTTTTC
12056 TTC
1 TTC
12059 AAGATGCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
7 5 0.17
8 8 0.27
9 17 0.57
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:13674 original size:28 final size:28
Alignment explanation
Indices: 13640--13699 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
13630 TTACTACAAC
*
13640 AATTAAAAA-GATTGATTAATTGATTGCA
1 AATTAAAAATGATTAATTAATTGATT-CA
13668 AATTAAAAATGATTAATTAATTGATTCA
1 AATTAAAAATGATTAATTAATTGATTCA
13696 AATT
1 AATT
13700 GGAGTACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (28 bp):
AATTAAAAATGATTAATTAATTGATTCA
Found at i:14044 original size:109 final size:109
Alignment explanation
Indices: 13922--14139 Score: 384
Period size: 109 Copynumber: 2.0 Consensus size: 109
13912 CTATTATATA
13922 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATCAAATAAGCACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATCAAATAAGCACACATACCAAACAATA
13987 CAAAA-TGCAATAAACTATTGGATTTAAAGAAAAATACAAGCACC
66 -AAAAGTGCAATAAACTATTGGATTTAAAGAAAAATACAAGCACC
* * *
14031 TATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATCCCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATCAAATAAGCACACATACCAAACAATA
*
14096 AAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 AAAAGTGCAATAAACTATTGGATTTAAAGAAAAATACAAGCACC
14140 AAAATGACTA
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
108 4 0.04
109 100 0.96
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (109 bp):
TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATCAAATAAGCACACATACCAAACAATA
AAAAGTGCAATAAACTATTGGATTTAAAGAAAAATACAAGCACC
Found at i:16500 original size:67 final size:68
Alignment explanation
Indices: 16410--16548 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 68
16400 CTGCATAATG
16410 AAATTCGGCCATTACTTCC-AAAAAAAAAATTTGTTATATGCGTTCTCACCTTAATTGTAAGGAT
1 AAATTCGGCCATTACTTCCAAAAAAAAAAATTTGTTATATGCGTTCTCACCTTAATTGTAAGGAT
16474 GGA
66 GGA
16477 AAATTCGGCCATTACTTCCAAAAAAAAAAAATTTGTTATATGCGTTCTCACCTTAATTGTAAGGA
1 AAATTCGGCCATTACTTCC-AAAAAAAAAAATTTGTTATATGCGTTCTCACCTTAATTGTAAGGA
16542 TGGA
65 TGGA
16546 AAA
1 AAA
16549 ATTGCAGTTG
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
67 19 0.27
69 51 0.73
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (68 bp):
AAATTCGGCCATTACTTCCAAAAAAAAAAATTTGTTATATGCGTTCTCACCTTAATTGTAAGGAT
GGA
Found at i:23610 original size:65 final size:67
Alignment explanation
Indices: 23511--23642 Score: 178
Period size: 67 Copynumber: 2.0 Consensus size: 67
23501 TTTAGCCATC
* * * * *
23511 CACCATAGATCACATAGAGTTCAAAGAGAGTAAAGTATC-TATATATCTGAAAATATAAAGCATA
1 CACCAGAGATCACATAGAGATCAAAGAAAGTAAAGTATCATATATATCTAAAAATATAAAACATA
23575 TT
66 TT
* *
23577 CACCAGAGATTACATAGAGAT-AAAGAAATTAAAGTATCTATATATATCTAAAAATATAAAACAT
1 CACCAGAGATCACATAGAGATCAAAGAAAGTAAAGTATC-ATATATATCTAAAAATATAAAACAT
23641 AT
65 AT
23643 GATTAAGTAG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
65 15 0.26
66 18 0.32
67 24 0.42
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.27
Consensus pattern (67 bp):
CACCAGAGATCACATAGAGATCAAAGAAAGTAAAGTATCATATATATCTAAAAATATAAAACATA
TT
Found at i:23998 original size:15 final size:16
Alignment explanation
Indices: 23967--24043 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 16
23957 TCAAAGGAAG
23967 TATTATATATATATATAT
1 TATTATA-AT-TATATAT
23985 ATATTATAATTATA-AT
1 -TATTATAATTATATAT
*
24001 TATTATTATTAT-TAT
1 TATTATAATTATATAT
*
24016 TATTATTATTATTATAT
1 TATTATAATTA-TATAT
24033 ATATATATAAT
1 -TAT-TATAAT
24044 ATAATTTAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
15 24 0.47
16 3 0.06
17 7 0.14
18 5 0.10
19 12 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATAATTATATAT
Found at i:24005 original size:9 final size:9
Alignment explanation
Indices: 23993--24049 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
23983 ATATATTATA
23993 ATTATAATT
1 ATTATAATT
*
24002 ATTATTATT
1 ATTATAATT
*
24011 ATTATTATT
1 ATTATAATT
*
24020 ATTATTATT
1 ATTATAATT
24029 ATATATATATAT
1 AT-TATA-AT-T
*
24041 AATATAATT
1 ATTATAATT
24050 TAGGATCATC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 29 0.69
10 5 0.12
11 6 0.14
12 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTATAATT
Found at i:24518 original size:71 final size:74
Alignment explanation
Indices: 24427--24574 Score: 196
Period size: 71 Copynumber: 2.0 Consensus size: 74
24417 GTAAAAAAAT
* *
24427 TGACACTGTTCCAGTTTAGGTGATCG-AGAA-GAATAGAAATTTATCAA-TAATCAACTTTCCAC
1 TGACACTGTTCCAGTTTAGGTGATCGAAGAAGGAACAGAAATTTATCAATTAATCAACTCTCCAC
24489 AAAAGGAAA
66 AAAAGGAAA
* *
24498 TGACACTGTTCCA-TTATAGGTGATTGAAGAAGTTGGAACAGAAATTTATCAATTACTCAACTCT
1 TGACACTGTTCCAGTT-TAGGTGATCGAAGAA---GGAACAGAAATTTATCAATTAATCAACTCT
24562 CCACAAAAGGAAA
62 CCACAAAAGGAAA
24575 AATTAAATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
70 2 0.03
71 22 0.33
72 4 0.06
76 16 0.24
77 22 0.33
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (74 bp):
TGACACTGTTCCAGTTTAGGTGATCGAAGAAGGAACAGAAATTTATCAATTAATCAACTCTCCAC
AAAAGGAAA
Found at i:42751 original size:22 final size:24
Alignment explanation
Indices: 42693--42750 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
42683 GTTTAACAAT
* *
42693 TATATATATTATTATATATATCTAA
1 TATATA-ATAATTATATACATCTAA
42718 TATATAATAATTATATACATCTAA
1 TATATAATAATTATATACATCTAA
*
42742 AATTATAAT
1 TA-TATAAT
42751 TGTTAAGCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (24 bp):
TATATAATAATTATATACATCTAA
Found at i:42792 original size:9 final size:9
Alignment explanation
Indices: 42780--42813 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
42770 TTTAATAATT
42780 ATATATATA
1 ATATATATA
*
42789 ATAT-TATT
1 ATATATATA
42797 ATATATATA
1 ATATATATA
42806 ATATATAT
1 ATATATAT
42814 TTAATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
ATATATATA
Found at i:42799 original size:15 final size:15
Alignment explanation
Indices: 42772--42829 Score: 65
Period size: 14 Copynumber: 4.2 Consensus size: 15
42762 TTAGACCGTT
42772 TAATAATTATATATA
1 TAATAATTATATATA
42787 TAAT-ATTAT-TATA
1 TAATAATTATATATA
42800 TATATAA-TATATAT-
1 TA-ATAATTATATATA
42814 T--TAATTATATATA
1 TAATAATTATATATA
42827 TAA
1 TAA
42830 CTAAACGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
11 3 0.08
12 7 0.19
13 7 0.19
14 11 0.31
15 8 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATAATTATATATA
Found at i:42799 original size:17 final size:18
Alignment explanation
Indices: 42777--42814 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
42767 CCGTTTAATA
42777 ATTATATATATAATAT-T
1 ATTATATATATAATATAT
42794 ATTATATATATAATATAT
1 ATTATATATATAATATAT
42812 ATT
1 ATT
42815 TAATTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATATATATAATATAT
Found at i:42803 original size:19 final size:22
Alignment explanation
Indices: 42770--42828 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
42760 GTTTAGACCG
*
42770 TTTAATAAT-TATATATATA-A
1 TTTAATTATATATATATATATA
42790 TATT-ATTATATATATAATATATA
1 T-TTAATTATATATAT-ATATATA
42813 TTTAATTATATATATA
1 TTTAATTATATATATA
42829 ACTAAACGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 5 0.15
21 7 0.21
22 8 0.24
23 13 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAATTATATATATATATATA
Found at i:42805 original size:21 final size:23
Alignment explanation
Indices: 42779--42829 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
42769 GTTTAATAAT
42779 TATATAT-ATA-ATA-TT-ATTA
1 TATATATAATATATATTTAATTA
42798 TATATATAATATATATTTAATTA
1 TATATATAATATATATTTAATTA
42821 TATATATAA
1 TATATATAA
42830 CTAAACGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.25
20 3 0.11
21 3 0.11
22 2 0.07
23 13 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATATAATATATATTTAATTA
Found at i:43864 original size:2 final size:2
Alignment explanation
Indices: 43857--43898 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
43847 TAAAAGGACT
* *
43857 TA TA TA TA TA TA TA TA TA T- TA GA TA TA TC TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
43899 AAAGTACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:44595 original size:26 final size:26
Alignment explanation
Indices: 44549--44598 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
44539 ATATATTAGA
* *
44549 ATTTTTAAAATATATTCTTTTACAAT
1 ATTTTTAAAATAAACTCTTTTACAAT
44575 ATTTTTAGAAATAAACT-TTTTACA
1 ATTTTTA-AAATAAACTCTTTTACA
44599 TGTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTTTTAAAATAAACTCTTTTACAAT
Found at i:46366 original size:57 final size:57
Alignment explanation
Indices: 46295--46411 Score: 207
Period size: 57 Copynumber: 2.1 Consensus size: 57
46285 CAAATTTGTA
46295 ATATATGAACAAATTAGTCTTTGAACTTCCAATCTTTTCAATTGCACACTTAAACTT
1 ATATATGAACAAATTAGTCTTTGAACTTCCAATCTTTTCAATTGCACACTTAAACTT
* * *
46352 ATATATGAATAAATTAGTCTTTGAATTTCCAATCTTTTCAATTGCACACTTAAATTT
1 ATATATGAACAAATTAGTCTTTGAACTTCCAATCTTTTCAATTGCACACTTAAACTT
46409 ATA
1 ATA
46412 AAAAAAGATA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (57 bp):
ATATATGAACAAATTAGTCTTTGAACTTCCAATCTTTTCAATTGCACACTTAAACTT
Found at i:47282 original size:10 final size:10
Alignment explanation
Indices: 47267--47292 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
47257 TCTTAACATG
47267 TAATCAAGTT
1 TAATCAAGTT
47277 TAATCAAGTT
1 TAATCAAGTT
47287 TAATCA
1 TAATCA
47293 GTAATCACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (10 bp):
TAATCAAGTT
Found at i:47539 original size:16 final size:17
Alignment explanation
Indices: 47507--47540 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47497 TTTTATTTTT
*
47507 TATTTGTTAATATATAA
1 TATTTATTAATATATAA
47524 TATTTATTAA-ATATAA
1 TATTTATTAATATATAA
47540 T
1 T
47541 TTATACGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTATTAATATATAA
Found at i:48873 original size:13 final size:13
Alignment explanation
Indices: 48855--48879 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48845 TATACCTTAG
48855 AAAAGAAAAAGGA
1 AAAAGAAAAAGGA
48868 AAAAGAAAAAGG
1 AAAAGAAAAAGG
48880 CTATCAAGTC
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGGA
Found at i:56552 original size:21 final size:21
Alignment explanation
Indices: 56526--56567 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
56516 AAAATAGGAA
56526 ATTGCTTAAAACTCATGTACT
1 ATTGCTTAAAACTCATGTACT
*
56547 ATTGCTTAAAACTTATGTACT
1 ATTGCTTAAAACTCATGTACT
56568 CTGTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (21 bp):
ATTGCTTAAAACTCATGTACT
Found at i:58676 original size:58 final size:58
Alignment explanation
Indices: 58611--58727 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
58601 AACGGTAATA
* * * *
58611 TATTCTTTTTAATGAATTATATTTATGAAACTTCTATTTTTTTGTAGATTAAGTTGTC
1 TATTCTTTATAATGAATTATATTCATGAAACTTCTATTCTTTCGTAGATTAAGTTGTC
58669 TATTCTTTATAATGAATTATATTCATGAAACTTCTATTCTTTCGTAGATTAAGTTGTC
1 TATTCTTTATAATGAATTATATTCATGAAACTTCTATTCTTTCGTAGATTAAGTTGTC
58727 T
1 T
58728 TATAACCTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.52
Consensus pattern (58 bp):
TATTCTTTATAATGAATTATATTCATGAAACTTCTATTCTTTCGTAGATTAAGTTGTC
Found at i:62485 original size:16 final size:15
Alignment explanation
Indices: 62454--62484 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
62444 GTGGCATTCC
62454 ATTTTCTTAAAAAAA
1 ATTTTCTTAAAAAAA
62469 ATTTTCTTAAAAAAA
1 ATTTTCTTAAAAAAA
62484 A
1 A
62485 AAGAAACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTTTCTTAAAAAAA
Found at i:76845 original size:42 final size:43
Alignment explanation
Indices: 76793--76886 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
76783 CGCGCATTAC
* *
76793 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAGAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
* *
76834 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCTAATTAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
76879 CTAATATT
1 CTAATATT
76887 AATCGTTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 35 0.78
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:78800 original size:29 final size:29
Alignment explanation
Indices: 78758--78815 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
78748 TTTAATACTA
78758 AATTGAGCAAACTATTAAAGTTGAGGCCG
1 AATTGAGCAAACTATTAAAGTTGAGGCCG
78787 AATTGAGCAAACTATTAAAGTTGAGGCCG
1 AATTGAGCAAACTATTAAAGTTGAGGCCG
78816 CATTTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
AATTGAGCAAACTATTAAAGTTGAGGCCG
Found at i:90031 original size:1 final size:1
Alignment explanation
Indices: 90025--90060 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
90015 CCAATTATCC
*
90025 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
90061 GAAGAAGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:91887 original size:19 final size:21
Alignment explanation
Indices: 91863--91903 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
91853 TATGGGTAAT
91863 ATTAAATTCTT-CA-ATTAAA
1 ATTAAATTCTTACAGATTAAA
91882 ATTAAATTCTTACAGATTAAA
1 ATTAAATTCTTACAGATTAAA
91903 A
1 A
91904 GATTAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
20 2 0.10
21 7 0.35
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTAAATTCTTACAGATTAAA
Found at i:98174 original size:81 final size:80
Alignment explanation
Indices: 98097--98616 Score: 456
Period size: 81 Copynumber: 6.4 Consensus size: 80
98087 GTCTGAAGTG
* * *
98097 AAGGACTCT-AATGCGAAGCCTCAGTCATTGGAAGTTACTCCAACAATCAAAAATAGTGATGAAG
1 AAGGACTCTCAA-GCGAAGCCTCAGTCATTAGAAGTTACACCAACAA-CAAAAATAGTGAAGAAG
* * ***
98161 CTGCAAAAGCTGAATTG
64 CTACAAAAACTGAAACC
** * * * * * **
98178 AAGGGTTCTGATGCGAAG-CTACAGTCATTAGAAGTTGCACCAACAAACGAAGATAGCAAAGAAG
1 AAGGACTCTCAAGCGAAGCCT-CAGTCATTAGAAGTTACACCAAC-AACAAAAATAGTGAAGAAG
98242 CTACAAAAACTGAAACC
64 CTACAAAAACTGAAACC
* * * * * *
98259 AACGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGACAAAGATAGTGAAGAAGC
1 AAGGACTCTCAAGCGAAGCCTCAGTCATTAGAAGTTACACCAACA-ACAAAAATAGTGAAGAAGC
98324 TACAAAAACTGAAACC
65 TACAAAAACTGAAACC
* * * *
98340 AATGACAT-TCAAGC-AAGGCCTCAGTCATTGGAAGTTACTCCAACAAGCAAAAATAGTGATGAA
1 AAGGAC-TCTCAAGCGAA-GCCTCAGTCATTAGAAGTTACACCAACAA-CAAAAATAGTGAAGAA
* * * *
98403 GCTGCAAAAGCTGAATCA
63 GCTACAAAAACTGAAACC
** * * * * * * **
98421 AAGGGTTCTGATGCAAAG-CTGCAGTCATTAGAAGTTGCACCAACAAACGAAGATAGCAAAGAAG
1 AAGGACTCTCAAGCGAAGCCT-CAGTCATTAGAAGTTACACCAAC-AACAAAAATAGTGAAGAAG
98485 CTACAAAAACTGAAACC
64 CTACAAAAACTGAAACC
* * * * *
98502 AATGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGACAAAAATAGTGAAGAAGC
1 AAGGACTCTCAAGCGAAGCCTCAGTCATTAGAAGTTACACCAACA-ACAAAAATAGTGAAGAAGC
*
98567 TACAAAAACTGAAAAC
65 TACAAAAACTGAAACC
* * *
98583 AATGACACTCAAGCAAAGCCTCAGTCATTAGAAG
1 AAGGACTCTCAAGCGAAGCCTCAGTCATTAGAAG
98617 ATGCCGCAAA
Statistics
Matches: 356, Mismatches: 69, Indels: 28
0.79 0.15 0.06
Matches are distributed among these distances:
80 10 0.03
81 335 0.94
82 11 0.03
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.17
Consensus pattern (80 bp):
AAGGACTCTCAAGCGAAGCCTCAGTCATTAGAAGTTACACCAACAACAAAAATAGTGAAGAAGCT
ACAAAAACTGAAACC
Found at i:98454 original size:243 final size:243
Alignment explanation
Indices: 98112--98616 Score: 911
Period size: 243 Copynumber: 2.1 Consensus size: 243
98102 CTCTAATGCG
* *
98112 AAGCCTCAGTCATTGGAAGTTACTCCAACAATCAAAAATAGTGATGAAGCTGCAAAAGCTGAATT
1 AAGCCTCAGTCATTGGAAGTTACTCCAACAAGCAAAAATAGTGATGAAGCTGCAAAAGCTGAATC
* *
98177 GAAGGGTTCTGATGCGAAGCTACAGTCATTAGAAGTTGCACCAACAAACGAAGATAGCAAAGAAG
66 AAAGGGTTCTGATGCAAAGCTACAGTCATTAGAAGTTGCACCAACAAACGAAGATAGCAAAGAAG
98242 CTACAAAAACTGAAACCAACGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGAC
131 CTACAAAAACTGAAACCAACGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGAC
* * *
98307 AAAGATAGTGAAGAAGCTACAAAAACTGAAACCAATGACATTCAAGCA
196 AAAAATAGTGAAGAAGCTACAAAAACTGAAAACAATGACACTCAAGCA
*
98355 AGGCCTCAGTCATTGGAAGTTACTCCAACAAGCAAAAATAGTGATGAAGCTGCAAAAGCTGAATC
1 AAGCCTCAGTCATTGGAAGTTACTCCAACAAGCAAAAATAGTGATGAAGCTGCAAAAGCTGAATC
*
98420 AAAGGGTTCTGATGCAAAGCTGCAGTCATTAGAAGTTGCACCAACAAACGAAGATAGCAAAGAAG
66 AAAGGGTTCTGATGCAAAGCTACAGTCATTAGAAGTTGCACCAACAAACGAAGATAGCAAAGAAG
*
98485 CTACAAAAACTGAAACCAATGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGAC
131 CTACAAAAACTGAAACCAACGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGAC
98550 AAAAATAGTGAAGAAGCTACAAAAACTGAAAACAATGACACTCAAGCA
196 AAAAATAGTGAAGAAGCTACAAAAACTGAAAACAATGACACTCAAGCA
*
98598 AAGCCTCAGTCATTAGAAG
1 AAGCCTCAGTCATTGGAAG
98617 ATGCCGCAAA
Statistics
Matches: 250, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
243 250 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (243 bp):
AAGCCTCAGTCATTGGAAGTTACTCCAACAAGCAAAAATAGTGATGAAGCTGCAAAAGCTGAATC
AAAGGGTTCTGATGCAAAGCTACAGTCATTAGAAGTTGCACCAACAAACGAAGATAGCAAAGAAG
CTACAAAAACTGAAACCAACGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGAC
AAAAATAGTGAAGAAGCTACAAAAACTGAAAACAATGACACTCAAGCA
Found at i:98631 original size:81 final size:81
Alignment explanation
Indices: 98199--98642 Score: 529
Period size: 81 Copynumber: 5.5 Consensus size: 81
98189 TGCGAAGCTA
* ** *
98199 CAGTCATTAGAAGTTGCACCAACAA-ACGAAGATAGCAAAGAAGCTACAAAAACTGAAACCAACG
1 CAGTCATTAGAAGTTGCACCAA-AAGACAAAGATAGTGAAGAAGCTACAAAAACTGAAACCAATG
98263 ACACTCAAGCAAAGCCT
65 ACACTCAAGCAAAGCCT
* *
98280 CGGTCATTAGAAGTTGCACCAACAGACAAAGATAGTGAAGAAGCTACAAAAACTGAAACCAATGA
1 CAGTCATTAGAAGTTGCACCAAAAGACAAAGATAGTGAAGAAGCTACAAAAACTGAAACCAATGA
* *
98345 CATTCAAGCAAGGCCT
66 CACTCAAGCAAAGCCT
* * * * * * * * * *
98361 CAGTCATTGGAAGTTACTCCAACAAG-CAAAAATAGTGATGAAGCTGCAAAAGCTGAATCAAAGG
1 CAGTCATTAGAAGTTGCACCAA-AAGACAAAGATAGTGAAGAAGCTACAAAAACTGAAACCAATG
*** * *
98425 GTTCTGATGCAAAG-CT
65 ACACTCAAGCAAAGCCT
* **
98441 GCAGTCATTAGAAGTTGCACCAACAA-ACGAAGATAGCAAAGAAGCTACAAAAACTGAAACCAAT
1 -CAGTCATTAGAAGTTGCACCAA-AAGACAAAGATAGTGAAGAAGCTACAAAAACTGAAACCAAT
98505 GACACTCAAGCAAAGCCT
64 GACACTCAAGCAAAGCCT
* * * *
98523 CGGTCATTAGAAGTTGCACCAACAGACAAAAATAGTGAAGAAGCTACAAAAACTGAAAACAATGA
1 CAGTCATTAGAAGTTGCACCAAAAGACAAAGATAGTGAAGAAGCTACAAAAACTGAAACCAATGA
98588 CACTCAAGCAAAGCCT
66 CACTCAAGCAAAGCCT
*
98604 CAGTCATTAGAAGATGC-CGCAAAAGACAAAGATAGTGAA
1 CAGTCATTAGAAGTTGCAC-CAAAAGACAAAGATAGTGAA
98643 AGGGCTCCGA
Statistics
Matches: 300, Mismatches: 56, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
80 5 0.02
81 291 0.97
82 4 0.01
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.16
Consensus pattern (81 bp):
CAGTCATTAGAAGTTGCACCAAAAGACAAAGATAGTGAAGAAGCTACAAAAACTGAAACCAATGA
CACTCAAGCAAAGCCT
Found at i:98728 original size:243 final size:241
Alignment explanation
Indices: 98112--98701 Score: 735
Period size: 243 Copynumber: 2.4 Consensus size: 241
98102 CTCTAATGCG
* * * * *
98112 AAGCCTCAGTCATTGGAAGTTACTCCAACAATCAAAAATAGTGATGAAGCTGCAAAAGCTGAATT
1 AAGCCTCAGTCATTAGAAGATACTCCAACAAGCAAAAATAGTGA-GAAGCTCCAAAAGC-GAATC
* ** * * * * *
98177 GAAGGGTTCTGATGCGAAGCTACAGTCATTAGAAGTTGCACCAACAAACGAAGATAGCAAAGAAG
64 AAAGGGTTCTGAAACAAAGCTCCAGTCAGTAGAAGTTACACCAACAAACAAAGATAGCAAAGAAG
98242 CTACAAAAACTGAAACCAACGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGAC
129 CTACAAAAACTGAAACCAACGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGAC
* * *
98307 AAAGATAGTGAAGAAGCTACAAAAACTGAAACCAATGACATTCAAGCA
194 AAAAATAGTGAAGAAGCTACAAAAACTGAAAACAATGACACTCAAGCA
* * * *
98355 AGGCCTCAGTCATTGGAAGTTACTCCAACAAGCAAAAATAGTGATGAAGCTGCAAAAGCTGAATC
1 AAGCCTCAGTCATTAGAAGATACTCCAACAAGCAAAAATAGTGA-GAAGCTCCAAAAGC-GAATC
** * * * *
98420 AAAGGGTTCTGATGCAAAGCTGCAGTCATTAGAAGTTGCACCAACAAACGAAGATAGCAAAGAAG
64 AAAGGGTTCTGAAACAAAGCTCCAGTCAGTAGAAGTTACACCAACAAACAAAGATAGCAAAGAAG
*
98485 CTACAAAAACTGAAACCAATGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGAC
129 CTACAAAAACTGAAACCAACGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGAC
98550 AAAAATAGTGAAGAAGCTACAAAAACTGAAAACAATGACACTCAAGCA
194 AAAAATAGTGAAGAAGCTACAAAAACTGAAAACAATGACACTCAAGCA
* *
98598 AAGCCTCAGTCATTAGAAGATGC-CGCAA-AAGACAAAGATAGTGA-AAGGGCTCCGAAAA-C-A
1 AAGCCTCAGTCATTAGAAGATACTC-CAACAAG-CAAAAATAGTGAGAA--GCTCC-AAAAGCGA
* *
98658 AT-AGTGAATGGTTCTGAAACAAGGCCTCCA-TCAGTAGAAGTTAC
61 ATCA---AAGGGTTCTGAAACAAAG-CTCCAGTCAGTAGAAGTTAC
98702 TTTAACTGAC
Statistics
Matches: 315, Mismatches: 23, Indels: 18
0.88 0.06 0.05
Matches are distributed among these distances:
240 1 0.00
241 5 0.02
242 4 0.01
243 297 0.94
244 8 0.03
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (241 bp):
AAGCCTCAGTCATTAGAAGATACTCCAACAAGCAAAAATAGTGAGAAGCTCCAAAAGCGAATCAA
AGGGTTCTGAAACAAAGCTCCAGTCAGTAGAAGTTACACCAACAAACAAAGATAGCAAAGAAGCT
ACAAAAACTGAAACCAACGACACTCAAGCAAAGCCTCGGTCATTAGAAGTTGCACCAACAGACAA
AAATAGTGAAGAAGCTACAAAAACTGAAAACAATGACACTCAAGCA
Found at i:102638 original size:55 final size:55
Alignment explanation
Indices: 102554--102665 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
102544 GAACAGAATA
102554 TATCTAATGAGAAAAATCAGGCTACTAGAAAATTGCCATAAGTCAGTCCCATGGC
1 TATCTAATGAGAAAAATCAGGCTACTAGAAAATTGCCATAAGTCAGTCCCATGGC
102609 TATCTAATGAGAAAAATCAGGCTACTAGAAAATTGCCATAAGTCAGTCCCATGGC
1 TATCTAATGAGAAAAATCAGGCTACTAGAAAATTGCCATAAGTCAGTCCCATGGC
102664 TA
1 TA
102666 ATCACATCCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (55 bp):
TATCTAATGAGAAAAATCAGGCTACTAGAAAATTGCCATAAGTCAGTCCCATGGC
Found at i:107133 original size:29 final size:31
Alignment explanation
Indices: 107101--107168 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
107091 ATGCAACTTG
107101 GGATATAACGTTA-C-AAAACAAGCAATTAA
1 GGATATAACGTTACCAAAAACAAGCAATTAA
* *
107130 GGATATAATGTTACCAAAAAACGAGCAATTAA
1 GGATATAACGTTACC-AAAAACAAGCAATTAA
107162 GGATATA
1 GGATATA
107169 GTCCGTTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 12 0.35
30 1 0.03
32 21 0.62
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (31 bp):
GGATATAACGTTACCAAAAACAAGCAATTAA
Found at i:107367 original size:32 final size:31
Alignment explanation
Indices: 107298--107378 Score: 126
Period size: 32 Copynumber: 2.6 Consensus size: 31
107288 CCCTAACTGA
**
107298 TTATATCCTTAATTGCTTAAAATCGAAAACG
1 TTATATCCTTAATTGCTTAAAATAAAAAACG
*
107329 TCATATCCTTAATTGCTTAAAATAAAAAAACG
1 TTATATCCTTAATTGCTTAAAAT-AAAAAACG
107361 TTATATCCTTAATTGCTT
1 TTATATCCTTAATTGCTT
107379 GTTTTATAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 22 0.49
32 23 0.51
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.38
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTAAAATAAAAAACG
Found at i:109395 original size:13 final size:14
Alignment explanation
Indices: 109364--109398 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
109354 ACTATAAAAG
*
109364 TTTAAACAATATCA
1 TTTAAAAAATATCA
109378 TTTAAAAAATAT-A
1 TTTAAAAAATATCA
109391 TTTAAAAA
1 TTTAAAAA
109399 GTTCCAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTAAAAAATATCA
Found at i:109776 original size:32 final size:31
Alignment explanation
Indices: 109706--109816 Score: 118
Period size: 31 Copynumber: 3.6 Consensus size: 31
109696 TTTGTTGCCA
* ***
109706 CAAGCAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
* **
109735 CAAGCAATTAAGGATGTAACGTTTTTTTATTT
1 CAAGCAATTAAGGATATAACG-TTTTCGATTT
* *
109767 CAAGCAATTAAGGATATGATGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
109798 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
109817 TCAGTTAGGG
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 20 0.30
31 28 0.42
32 19 0.28
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Found at i:110019 original size:28 final size:31
Alignment explanation
Indices: 109946--110011 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
109936 CCTATCGGAC
109946 TATATCCTTAATTGCTCGTTTTTCGTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
*
109977 TATATCCTTAATTGCTTG-TTTT-GTAAC-T
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
110005 TATATCC
1 TATATCC
110012 CAAATTGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 8 0.24
29 5 0.15
30 4 0.12
31 17 0.50
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGTTTTTCGTAACGT
Done.