Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013209.1 Corchorus olitorius cultivar O-4 contig13242, 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: 83949
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1123 original size:52 final size:52
Alignment explanation
Indices: 1062--1165 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
1052 TTGAATTGCT
*
1062 CGATCCTAGATCTACCATCACACCCTAATGTTTTTCTCATCCATTTAAAATC
1 CGATCCTAGATCTACCATCAAACCCTAATGTTTTTCTCATCCATTTAAAATC
1114 CGATCCTAGATCTACCATCAAACCCTAATGTTTTTCTCATCCATTTAAAATC
1 CGATCCTAGATCTACCATCAAACCCTAATGTTTTTCTCATCCATTTAAAATC
1166 TGAATCAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.35
Consensus pattern (52 bp):
CGATCCTAGATCTACCATCAAACCCTAATGTTTTTCTCATCCATTTAAAATC
Found at i:7079 original size:19 final size:19
Alignment explanation
Indices: 7055--7116 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
7045 CATCTCTAGG
7055 TAATTCATCAATGATATTC
1 TAATTCATCAATGATATTC
* * * **
7074 TAATTC-TCCAT-CTCTAGG
1 TAATTCATCAATGATAT-TC
7092 TAATTCATCAATGATATTC
1 TAATTCATCAATGATATTC
7111 TAATTC
1 TAATTC
7117 TCCATCTCTA
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
17 2 0.07
18 10 0.33
19 16 0.53
20 2 0.07
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (19 bp):
TAATTCATCAATGATATTC
Found at i:7151 original size:37 final size:37
Alignment explanation
Indices: 7045--7139 Score: 181
Period size: 37 Copynumber: 2.6 Consensus size: 37
7035 AATTCTACTT
7045 CATCTCTAGGTAATTCATCAATGATATTCTAATTCTC
1 CATCTCTAGGTAATTCATCAATGATATTCTAATTCTC
7082 CATCTCTAGGTAATTCATCAATGATATTCTAATTCTC
1 CATCTCTAGGTAATTCATCAATGATATTCTAATTCTC
*
7119 CATCTCTAGATAATTCATCAA
1 CATCTCTAGGTAATTCATCAA
7140 AATAAAACTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (37 bp):
CATCTCTAGGTAATTCATCAATGATATTCTAATTCTC
Found at i:8598 original size:14 final size:13
Alignment explanation
Indices: 8567--8612 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
8557 GTCGGATTTT
8567 AGTCAGTTTGTTG
1 AGTCAGTTTGTTG
*
8580 AGTCAGTTTTTTCG
1 AGTCAGTTTGTT-G
8594 AGTCAGTTAGTGTTG
1 AGTCAGTT--TGTTG
8609 AGTC
1 AGTC
8613 TGAGTCTGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.43
Consensus pattern (13 bp):
AGTCAGTTTGTTG
Found at i:9971 original size:439 final size:437
Alignment explanation
Indices: 9138--10125 Score: 1349
Period size: 439 Copynumber: 2.2 Consensus size: 437
9128 TGGGTCCCGC
* *
9138 TCTCAATAAACAAATCATTTTTTTAGTGGATTATTTATCAAATGATCCCTATACTTTTATGTTTT
1 TCTCTATAAACAAAT-ATTTTTTT-GTGGATTATTTATCAAATGATCCTTATACTTTTATG-TTT
* * * * ** *
9203 ATGTTATTTAATCCTTCACAAATTCTGGGTTGGACGATTGAACGTTTCGGCTTTAATTCTTTTAT
63 ATGCTATTTAATCCTTTA-AAATTATGGGTTGGACGATTTAACGCGTCGGCTTTAATTCTTGTAT
* * *
9268 TTTTTGTTTTACTTGTCCGATCAAAGTGATTCAAGTGTCTATTAAAAGATAATTTCATGATCTAC
127 TTTCTGTTCTACTTGTCCGATCAAAGTGATTCAAGTGTCTATTAAAAGATAATCTCATGATCTAC
** *
9333 AACTTTCATGAAGGACTGCAAACCAATTTTCATGTTTCGATTCTAAAAAAATGCTTCTTAAATTT
192 AACTTTCATGAAAAACTGCAAACCAATTTTAATGTTTCGATTCTAAAAAAATGCTTCTTAAATTT
* * *
9398 TATGGTCTCGATTGTCGGTCTATCTAATATTGTATAATTTTCGATCCACTTGTCCGATTGAGGTT
257 TATGGTCTCGATTGCCGGTCTATCTAATATCGTATAATTTTCGATCCACTTGTCCGATTGAAGTT
* * * *
9463 GTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACTTTCGTCAAGGACCTGAAAGCTAAA
322 GTTCAAGTGTCGGTTAAAAGGTTATTGTATGATCTACGACTTTCATCAAGGACATGAAAGCTAAA
* *
9528 TTTGATTAATGAGTTTCGTGGAGGGA-TCGAGAGAGA-ATTTTTATGTTTGG
387 TTTGATTAATAAGTTTCGTGGA-GGATTCAAGAGAGATATTTTTATGTTTGG
9578 TCTCTATAAACAAATATATTTTTTGCTGGATTATTTATCAAATGATCCTTATACTTTTATGCTTT
1 TCTCTATAAACAAATAT-TTTTTTG-TGGATTATTTATCAAATGATCCTTATACTTTTATG-TTT
* *
9643 ATGCTATTTAATCCTTTATAATTATGGGTTGGATGATTTAACGCGTCGGCTTTTAATT-TTGTAT
63 ATGCTATTTAATCCTTTAAAATTATGGGTTGGACGATTTAACGCGTCGGC-TTTAATTCTTGTAT
* * * *
9707 TTTCTGTTCTATTTGTCCGATCAAGGTGATTTAAGTGTCTATTAAAAGGTAATCTCATGATCTAC
127 TTTCTGTTCTACTTGTCCGATCAAAGTGATTCAAGTGTCTATTAAAAGATAATCTCATGATCTAC
* * *
9772 AACTTTCATGAAAAACT-CAGAAGCCAATTTTAATGTTTTGATTCT-AAAAAGTGTTTCTTAAAT
192 AACTTTCATGAAAAACTGCA-AA-CCAATTTTAATGTTTCGATTCTAAAAAAATGCTTCTTAAAT
* * * *
9835 TTTGTGGTTTCGATTGCCGGTCTATTTAATATCGTATAATTTTCGGTCCACTTGTCCGATTGAAG
255 TTTATGGTCTCGATTGCCGGTCTATCTAATATCGTATAATTTTCGATCCACTTGTCCGATTGAAG
* * * *
9900 TTGTTCAAGTGTCGGTTAAAAGGTTATTGTATGATCTACGACTTTCATTAAGGGCATGAAAGTTG
320 TTGTTCAAGTGTCGGTTAAAAGGTTATTGTATGATCTACGACTTTCATCAAGGACATGAAAGCTA
* * *
9965 AATTTGATTAATAAGTTTCGTGGAGGATTCAAGAGGGATTTTTTTATGTTTTG
385 AATTTGATTAATAAGTTTCGTGGAGGATTCAAGAGAGATATTTTTATGTTTGG
* * * *
10018 TCT-TCATAAACTAATATTTTTTTGTTGGATTATTTATCTAATGACCCTCATACTTTTATGTTTC
1 TCTCT-ATAAACAAATATTTTTTTG-TGGATTATTTATCAAATGATCCTTATACTTTTATGTTT-
* * *
10082 ATGCTATTGAATCCTTTACAATTATAGGTTGGACGATTTAACGC
63 ATGCTATTTAATCCTTTAAAATTATGGGTTGGACGATTTAACGC
10126 TTTGACTTTT
Statistics
Matches: 485, Mismatches: 54, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
438 8 0.02
439 351 0.72
440 126 0.26
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.42
Consensus pattern (437 bp):
TCTCTATAAACAAATATTTTTTTGTGGATTATTTATCAAATGATCCTTATACTTTTATGTTTATG
CTATTTAATCCTTTAAAATTATGGGTTGGACGATTTAACGCGTCGGCTTTAATTCTTGTATTTTC
TGTTCTACTTGTCCGATCAAAGTGATTCAAGTGTCTATTAAAAGATAATCTCATGATCTACAACT
TTCATGAAAAACTGCAAACCAATTTTAATGTTTCGATTCTAAAAAAATGCTTCTTAAATTTTATG
GTCTCGATTGCCGGTCTATCTAATATCGTATAATTTTCGATCCACTTGTCCGATTGAAGTTGTTC
AAGTGTCGGTTAAAAGGTTATTGTATGATCTACGACTTTCATCAAGGACATGAAAGCTAAATTTG
ATTAATAAGTTTCGTGGAGGATTCAAGAGAGATATTTTTATGTTTGG
Found at i:11291 original size:21 final size:20
Alignment explanation
Indices: 11263--11328 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
11253 GCTAAGTCTT
11263 GAAAATTCTCTGTAAATTAA
1 GAAAATTCTCTGTAAATTAA
* * *
11283 GAAATATTCAACT-CAAATCATA
1 GAAA-ATTC-TCTGTAAATTA-A
*
11305 GAAAATTCTTTGTAAATTAA
1 GAAAATTCTCTGTAAATTAA
11325 GAAA
1 GAAA
11329 TACTCAATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
20 10 0.29
21 18 0.51
22 7 0.20
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (20 bp):
GAAAATTCTCTGTAAATTAA
Found at i:11322 original size:42 final size:42
Alignment explanation
Indices: 11263--11343 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
11253 GCTAAGTCTT
*
11263 GAAAATTCTCTGTAAATTAAGAAATATTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
* *
11305 GAAAATTCTTTGTAAATTAAGAAATACTCAATTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
11344 CTGATCCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:11481 original size:56 final size:56
Alignment explanation
Indices: 11409--11522 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
11399 TTTATTTTGT
11409 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
11465 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
11521 AG
1 AG
11523 GAAACGGATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
Found at i:12328 original size:87 final size:88
Alignment explanation
Indices: 12230--12392 Score: 256
Period size: 87 Copynumber: 1.9 Consensus size: 88
12220 TTATTTAAAA
* *
12230 TTTTATAGTTTTACTCAACTAAAAATTCTATTTTTAT-TAATTAAGTCTAATATCCTTATAGCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAGCTA
12294 TTTTATTTTTAACAGTTTACTAT
66 TTTTATTTTTAACAGTTTACTAT
* * ** *
12317 TTTTATAGTTTTACTCAATTAAAAACTCTATTTTTATCTTATTAAATCTAATATTTTTATATCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAGCTA
12382 TTTTATTTTTA
66 TTTTATTTTTA
12393 CCATTTTTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
87 35 0.51
88 33 0.49
ACGTcount: A:0.32, C:0.10, G:0.03, T:0.55
Consensus pattern (88 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTATAGCTA
TTTTATTTTTAACAGTTTACTAT
Found at i:26753 original size:20 final size:20
Alignment explanation
Indices: 26728--26775 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
26718 AAAAGAAACT
26728 GGAGAAAGGAAGAACCAGGA
1 GGAGAAAGGAAGAACCAGGA
26748 GGAGAAAGGAAGAACCAGGA
1 GGAGAAAGGAAGAACCAGGA
26768 GGAGAAAG
1 GGAGAAAG
26776 AGGTTCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (20 bp):
GGAGAAAGGAAGAACCAGGA
Found at i:29501 original size:21 final size:21
Alignment explanation
Indices: 29475--29514 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29465 ATCCATAGAC
29475 CATAT-CTTAAGCCATAGCAGG
1 CATATCCTTAAGCCA-AGCAGG
*
29496 CATATCCTTGAGCCAAGCA
1 CATATCCTTAAGCCAAGCA
29515 TCGAGCAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (21 bp):
CATATCCTTAAGCCAAGCAGG
Found at i:37924 original size:19 final size:20
Alignment explanation
Indices: 37894--37957 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
37884 TTGACACTGT
37894 TTAGCAACTGTACAGATAAGA
1 TTAGC-ACTGTACAGATAAGA
*
37915 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATAAGA
* *
37934 TTAGGTACTGTACAGATGAGA
1 TTA-GCACTGTACAGATAAGA
37955 TTA
1 TTA
37958 TTAGAGCAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 17 0.45
20 1 0.03
21 20 0.53
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
TTAGCACTGTACAGATAAGA
Found at i:38024 original size:11 final size:11
Alignment explanation
Indices: 38008--38044 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
37998 TTTGGTTCCA
38008 AAACGGTGATG
1 AAACGGTGATG
38019 AAACGGT--T-
1 AAACGGTGATG
38027 AAACGGTGATG
1 AAACGGTGATG
38038 AAACGGT
1 AAACGGT
38045 TACAGATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.30
9 1 0.04
10 1 0.04
11 14 0.61
ACGTcount: A:0.38, C:0.11, G:0.32, T:0.19
Consensus pattern (11 bp):
AAACGGTGATG
Found at i:38032 original size:19 final size:19
Alignment explanation
Indices: 38008--38046 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
37998 TTTGGTTCCA
38008 AAACGGTGATGAAACGGTT
1 AAACGGTGATGAAACGGTT
38027 AAACGGTGATGAAACGGTT
1 AAACGGTGATGAAACGGTT
38046 A
1 A
38047 CAGATAAGAA
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:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (19 bp):
AAACGGTGATGAAACGGTT
Found at i:38646 original size:34 final size:30
Alignment explanation
Indices: 38576--38637 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
38566 TCATTGATTT
38576 ATTTATTTGTTATTTTGTTTTTCCGTGTAG
1 ATTTATTTGTTATTTTGTTTTTCCGTGTAG
38606 ATTTATTTGTTATTTTGTTTTTCCGTGTAG
1 ATTTATTTGTTATTTTGTTTTTCCGTGTAG
38636 AT
1 AT
38638 AGTATTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.15, C:0.06, G:0.16, T:0.63
Consensus pattern (30 bp):
ATTTATTTGTTATTTTGTTTTTCCGTGTAG
Found at i:40204 original size:13 final size:13
Alignment explanation
Indices: 40186--40211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40176 GGTTGTGGTC
40186 ATGTTAGGAAAGT
1 ATGTTAGGAAAGT
40199 ATGTTAGGAAAGT
1 ATGTTAGGAAAGT
40212 TAACATTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
ATGTTAGGAAAGT
Found at i:50534 original size:2 final size:2
Alignment explanation
Indices: 50527--50562 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
50517 TTGGCCTTTT
50527 TA TA TA TA 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 TA TA TA TA
50563 CTTCTCATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50679 original size:7 final size:7
Alignment explanation
Indices: 50663--50695 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
50653 CTTACTTTCA
*
50663 TCATAAT
1 TCATAGT
50670 TCATAGT
1 TCATAGT
50677 TCATAGT
1 TCATAGT
50684 TCATAGT
1 TCATAGT
50691 TCATA
1 TCATA
50696 CGGATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (7 bp):
TCATAGT
Found at i:61403 original size:20 final size:19
Alignment explanation
Indices: 61363--61400 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
61353 TTAAATGAAA
*
61363 AAAATAGCCACGTGGCATT
1 AAAATAGCCACGTGGAATT
61382 AAAATAGCCACGTGGAATT
1 AAAATAGCCACGTGGAATT
61401 TAATTAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAATAGCCACGTGGAATT
Found at i:63296 original size:18 final size:18
Alignment explanation
Indices: 63273--63309 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
63263 ACACCGTTAC
63273 ATGATTCTTAAAAGGGGG
1 ATGATTCTTAAAAGGGGG
63291 ATGATTCTTAAAAGGGGG
1 ATGATTCTTAAAAGGGGG
63309 A
1 A
63310 AAAGGACGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.32, T:0.27
Consensus pattern (18 bp):
ATGATTCTTAAAAGGGGG
Found at i:69435 original size:2 final size:2
Alignment explanation
Indices: 69417--69452 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
69407 ACATTTCATT
* *
69417 TA TA TT TA TA AA 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 TA TA TA TA
69453 GATTCGAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71623 original size:15 final size:16
Alignment explanation
Indices: 71603--71648 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
71593 TGATTTAAAA
*
71603 AATATATATAT-CTAT
1 AATATATATATAATAT
71618 AATATATAATATAATAT
1 AATATAT-ATATAATAT
71635 AATATAATATATAA
1 AATAT-ATATATAA
71649 AAAGAGAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 7 0.26
16 4 0.15
17 14 0.52
18 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATATATATAATAT
Found at i:71629 original size:5 final size:5
Alignment explanation
Indices: 71621--71645 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
71611 TATCTATAAT
71621 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
71646 TAAAAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:72011 original size:28 final size:28
Alignment explanation
Indices: 71971--72052 Score: 164
Period size: 28 Copynumber: 2.9 Consensus size: 28
71961 TTATCCGATC
71971 AAGGTGATTCAAGTGTCTATTAAAAGAT
1 AAGGTGATTCAAGTGTCTATTAAAAGAT
71999 AAGGTGATTCAAGTGTCTATTAAAAGAT
1 AAGGTGATTCAAGTGTCTATTAAAAGAT
72027 AAGGTGATTCAAGTGTCTATTAAAAG
1 AAGGTGATTCAAGTGTCTATTAAAAG
72053 GTAATTTCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (28 bp):
AAGGTGATTCAAGTGTCTATTAAAAGAT
Found at i:74757 original size:28 final size:28
Alignment explanation
Indices: 74725--74778 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
74715 AATTTAGTCA
*
74725 ACCAAGGGTAAA-ATGGTAATTTTAACCG
1 ACCAAGGGTAAATA-CGTAATTTTAACCG
74753 ACCAAGGGTAAATACGTAATTTTAAC
1 ACCAAGGGTAAATACGTAATTTTAAC
74779 ATCCTAAGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (28 bp):
ACCAAGGGTAAATACGTAATTTTAACCG
Found at i:75552 original size:16 final size:16
Alignment explanation
Indices: 75533--75566 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
75523 TATTTCTCTC
* *
75533 TCTTTTTTTTTCCTTT
1 TCTTTTCTTTTCCCTT
75549 TCTTTTCTTTTCCCTT
1 TCTTTTCTTTTCCCTT
75565 TC
1 TC
75567 CCTTTTTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TCTTTTCTTTTCCCTT
Found at i:76372 original size:11 final size:11
Alignment explanation
Indices: 76356--76390 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
76346 TTGACAGCGC
76356 AACAAAAACAA
1 AACAAAAACAA
*
76367 AACAAAAACGA
1 AACAAAAACAA
76378 AACAAAAACAA
1 AACAAAAACAA
76389 AA
1 AA
76391 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:80718 original size:13 final size:13
Alignment explanation
Indices: 80700--80732 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
80690 GATAAATAGG
80700 AAAATAAGTTAAA
1 AAAATAAGTTAAA
*
80713 AAAATAATTTAAA
1 AAAATAAGTTAAA
80726 AAAATAA
1 AAAATAA
80733 ATAGGTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AAAATAAGTTAAA
Found at i:80815 original size:19 final size:19
Alignment explanation
Indices: 80782--81032 Score: 138
Period size: 19 Copynumber: 13.4 Consensus size: 19
80772 AATAGGTAGT
80782 TAAA-AAATA-ATAATAAA
1 TAAATAAATAGATAATAAA
*
80799 TAAATAAATAGATAATAAC
1 TAAATAAATAGATAATAAA
* * *
80818 TAAATTAATAAATAAAAAGA
1 TAAATAAATAGATAATAA-A
*
80838 TAAATAGTAAATAAATAGAT-AA
1 T-AA-A-TAAATAGATA-ATAAA
*
80860 TAATTAAA-A-ATAAATAAA
1 TAAATAAATAGAT-AATAAA
*
80878 AAAGATAAATAG-TAAATAAA
1 TAA-ATAAATAGAT-AATAAA
*
80898 -AAGAT-AATAGTTAA-AAA
1 TAA-ATAAATAGATAATAAA
80915 TAAATAAATAG-TAAATAAA
1 TAAATAAATAGAT-AATAAA
* *
80934 TAGAT-AATAGTTAA-AAA
1 TAAATAAATAGATAATAAA
**
80951 TAAATAAATAGATAA-ATGG
1 TAAATAAATAGATAATA-AA
80970 TAAATAAATAGATAATAAA
1 TAAATAAATAGATAATAAA
*
80989 -AAAAAAATAG-TAAATAAA
1 TAAATAAATAGAT-AATAAA
*
81007 TAGATAAATAG-TGAATAAA
1 TAAATAAATAGAT-AATAAA
*
81026 TAGATAA
1 TAAATAA
81033 TAGTTAAAAA
Statistics
Matches: 190, Mismatches: 21, Indels: 44
0.75 0.08 0.17
Matches are distributed among these distances:
17 22 0.12
18 58 0.31
19 81 0.43
20 11 0.06
21 4 0.02
22 3 0.02
23 10 0.05
24 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (19 bp):
TAAATAAATAGATAATAAA
Found at i:80848 original size:27 final size:27
Alignment explanation
Indices: 80793--80859 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
80783 AAAAAATAAT
*
80793 AATAAATAAATAAATAGATAATAACTA
1 AATAAATAAATAAAAAGATAATAACTA
* *
80820 AATTAATAAATAAAAAGATAA-ATAGTA
1 AATAAATAAATAAAAAGATAATA-ACTA
*
80847 AATAAATAGATAA
1 AATAAATAAATAA
80860 TAATTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.25
Consensus pattern (27 bp):
AATAAATAAATAAAAAGATAATAACTA
Found at i:80934 original size:81 final size:74
Alignment explanation
Indices: 80828--81013 Score: 257
Period size: 81 Copynumber: 2.4 Consensus size: 74
80818 TAAATTAATA
*
80828 AATAAAAAGATAAATAGTAAATAAATAGATAATAATTAAAAATAAATAAAAAAGATAAATAGTAA
1 AATAAAAAAATAAATAGTAAATAAATAGATAATAATTAAAAATAAAT-AAAAAGATAAATAGTAA
80893 ATAAAAAGAT
65 ATAAAAAGAT
* *
80903 AATAGTTAAAAATAAATAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGATAAAT
1 -A-A--T-AAAA-AAATAAATAGTAAATAAATAGATAATAATTAAAAATAAATAAAAAGATAAAT
* *
80968 GGTAAATAAATAGAT
60 AGTAAATAAAAAGAT
80983 AATAAAAAAA-AAATAGTAAATAAATAGATAA
1 AATAAAAAAATAAATAGTAAATAAATAGATAA
81014 ATAGTGAATA
Statistics
Matches: 100, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
73 21 0.21
74 3 0.03
75 4 0.04
76 2 0.02
77 1 0.01
78 1 0.01
79 2 0.02
80 28 0.28
81 38 0.38
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (74 bp):
AATAAAAAAATAAATAGTAAATAAATAGATAATAATTAAAAATAAATAAAAAGATAAATAGTAAA
TAAAAAGAT
Found at i:81027 original size:4 final size:4
Alignment explanation
Indices: 80782--81016 Score: 110
Period size: 4 Copynumber: 61.5 Consensus size: 4
80772 AATAGGTAGT
* * *
80782 TAAA -AAA T-AA T-AA TAAA TAAA TAAA TAGA T-AA TAAC TAAA TTAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
80826 TAAA TAAA -AAGA TAAA T-AG TAAA TAAA TAGA T-AA T-AA TTAA -AAA
1 TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
80870 TAAA TAAA AAAGA TAAA T-AG TAAA TAAA -AAGA TAATA GTTAA -AAA
1 TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAA-A TAA-A -TAAA TAAA
* * * *
80915 TAAA TAAA T-AG TAAA TAAA TAGA TAATA GTTAA -AAA TAAA TAAA TAGA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA TAAA
** * * *
80963 TAAA T-GG TAAA TAAA TAGA T-AA TAAA -AAA AAAA T-AG TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
*
81007 TAGA TAAA TA
1 TAAA TAAA TA
81017 GTGAATAAAT
Statistics
Matches: 172, Mismatches: 37, Indels: 44
0.68 0.15 0.17
Matches are distributed among these distances:
3 40 0.23
4 117 0.68
5 11 0.06
6 4 0.02
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:81077 original size:11 final size:11
Alignment explanation
Indices: 80782--81082 Score: 127
Period size: 11 Copynumber: 27.8 Consensus size: 11
80772 AATAGGTAGT
80782 TAAA-AAATAA
1 TAAATAAATAA
80792 T-AATAAATAAA
1 TAAATAAAT-AA
*
80803 TAAATAGATAA
1 TAAATAAATAA
*
80814 TAACTAAATTAA
1 TAAATAAA-TAA
*
80826 TAAATAAAAAGA
1 TAAATAAATA-A
*
80838 TAAAT-AGTAAA
1 TAAATAAAT-AA
*
80849 TAAATAGATAA
1 TAAATAAATAA
*
80860 TAATTAAA-AA
1 TAAATAAATAA
80870 TAAATAAA-AA
1 TAAATAAATAA
* *
80880 -AGATAAATAG
1 TAAATAAATAA
*
80890 TAAATAAAAAGA
1 TAAATAAATA-A
80902 TAATAGTTAAA-AA
1 TAA-A--TAAATAA
*
80915 TAAATAAATAG
1 TAAATAAATAA
80926 TAAATAAATAGA
1 TAAATAAATA-A
**
80938 T-AATAGTTAA
1 TAAATAAATAA
80948 -AAATAAATAAA
1 TAAATAAAT-AA
* **
80959 TAGATAAATGG
1 TAAATAAATAA
80970 TAAATAAATAGA
1 TAAATAAATA-A
80982 T-AAT-AA-AA
1 TAAATAAATAA
*
80990 -AAA-AAATAG
1 TAAATAAATAA
80999 TAAATAAATAGA
1 TAAATAAATA-A
*
81011 TAAAT-AGTGAA
1 TAAATAAAT-AA
*
81022 TAAATAGATAA
1 TAAATAAATAA
**
81033 TAGTTAAA-AA
1 TAAATAAATAA
* *
81043 TGTAA-AAAGAA
1 T-AAATAAATAA
*
81054 -AAA-AAATAG
1 TAAATAAATAA
81063 TAAATAAATAA
1 TAAATAAATAA
*
81074 TAAAAAAAT
1 TAAATAAAT
81083 CTTTTTGGTC
Statistics
Matches: 215, Mismatches: 45, Indels: 61
0.67 0.14 0.19
Matches are distributed among these distances:
8 5 0.02
9 16 0.07
10 41 0.19
11 99 0.46
12 44 0.20
13 5 0.02
14 1 0.00
15 4 0.02
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:82727 original size:35 final size:35
Alignment explanation
Indices: 82681--83033 Score: 396
Period size: 35 Copynumber: 10.0 Consensus size: 35
82671 ATCAATGTGA
* *
82681 AGATCAACTCTGCTCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
82716 AGATCAACTCTGATCATAAAAAAAATCTTCTTGAAAGG
1 AGATCAACTCTGATCAT--CAAAAA-CTTCTTGAAATG
* *
82754 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATC--ATCAAAAACTTCTTGAAATG
* *
82791 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATC--ATCAAAAACTTCTTGAAATG
* *
82828 AGATCAACTCTGATCAACAAAAAC-TCTTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTC-TTGAAATG
*
82863 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
82898 AGATCAA--C---TCAT-AAAAACATCTTGAAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTG-AAATG
* * *
82928 AGATCAACTCTGATCATAAAAAACTTCCTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
82963 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
82998 AGATCAACTCTGATCATCGAAAACTTCTTGGAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
83033 A
1 A
83034 CCGCACTGGA
Statistics
Matches: 278, Mismatches: 26, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
29 10 0.04
30 16 0.06
32 1 0.00
33 1 0.00
34 2 0.01
35 137 0.49
36 12 0.04
37 66 0.24
38 31 0.11
40 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (35 bp):
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
Found at i:82960 original size:100 final size:99
Alignment explanation
Indices: 82811--83007 Score: 308
Period size: 100 Copynumber: 2.0 Consensus size: 99
82801 TGACCATATA
* *
82811 AAAAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACTCTTTGAAACGAGATCAACTCTGA
1 AAAAACATCTTGAAATGAGATCAACTCTGATCAACAAAAACTCTCTGAAACGAGATCAACTCTGA
* *
82876 TCATCGAAAACTTCTTGAAATGAGATCAACTCAT
66 TCACCGAAAACTTCTTGAAACGAGATCAACTCAT
*
82910 AAAAACATCTTGAAAATGAGATCAACTCTGATCATA-AAAAACT-TCCTGAAAGGAGATCAACTC
1 AAAAACATCTTG-AAATGAGATCAACTCTGATCA-ACAAAAACTCT-CTGAAACGAGATCAACTC
82973 TGATCACCGAAAACTTCTTGAAACGAGATCAACTC
63 TGATCACCGAAAACTTCTTGAAACGAGATCAACTC
83008 TGATCATCGA
Statistics
Matches: 90, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
99 12 0.13
100 77 0.86
101 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (99 bp):
AAAAACATCTTGAAATGAGATCAACTCTGATCAACAAAAACTCTCTGAAACGAGATCAACTCTGA
TCACCGAAAACTTCTTGAAACGAGATCAACTCAT
Found at i:82974 original size:135 final size:139
Alignment explanation
Indices: 82681--83033 Score: 457
Period size: 135 Copynumber: 2.5 Consensus size: 139
82671 ATCAATGTGA
* * * **
82681 AGATCAACTCTGCTCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAAAATCTTC
1 AGATCAACTCTGATCAACGAAAACTTCTTGAAACGAGATCAACTCTGATCAT--CGAAAA-CTTC
* *
82746 TTGAAAGGAGATCAACTCTGACCATATAAAAAACTTCTTGAAATGAGATCAACTCTGACCATATA
63 TTGAAATGAGATCAAC-CT-A-CA-ATAAAAAACATCTTGAAATGAGATCAACTCTGACCA-ATA
* *
82811 AAAAACTTCTTGAAATG
123 AAAAACTTCCTGAAAGG
*
82828 AGATCAACTCTGATCAACAAAAAC-TCTTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTT
1 AGATCAACTCTGATCAACGAAAACTTC-TTGAAACGAGATCAACTCTGATCATCGAAAACTTCTT
*
82892 GAAATGAGATCAA-CT-C-AT-AAAAACATCTTGAAAATGAGATCAACTCTGATC-ATAAAAAAC
65 GAAATGAGATCAACCTACAATAAAAAACATCTTG-AAATGAGATCAACTCTGACCAATAAAAAAC
82952 TTCCTGAAAGG
129 TTCCTGAAAGG
*
82963 AGATCAACTCTGATCACCGAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTG
1 AGATCAACTCTGATCAACGAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTG
*
83028 GAATGA
66 AAATGA
83034 CCGCACTGGA
Statistics
Matches: 189, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
135 83 0.44
136 13 0.07
137 21 0.11
139 1 0.01
142 2 0.01
144 18 0.10
145 4 0.02
146 2 0.01
147 45 0.24
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (139 bp):
AGATCAACTCTGATCAACGAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTG
AAATGAGATCAACCTACAATAAAAAACATCTTGAAATGAGATCAACTCTGACCAATAAAAAACTT
CCTGAAAGG
Found at i:83080 original size:54 final size:54
Alignment explanation
Indices: 82998--83106 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
82988 TCTTGAAACG
*
82998 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
*
83052 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
83106 A
1 A
83107 CACCTGTTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (54 bp):
AGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
Done.