Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017339.1 Corchorus olitorius cultivar O-4 contig17372, 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: 124035
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7120 original size:13 final size:13
Alignment explanation
Indices: 7099--7141 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
7089 TAAAATTTTG
7099 TTTTAATTTTTAT
1 TTTTAATTTTTAT
*
7112 TTTTTATTTTTAT
1 TTTTAATTTTTAT
7125 TTTTAGGATTTTTAT
1 TTTTA--ATTTTTAT
7140 TT
1 TT
7142 GATGCACTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 16 0.62
15 10 0.38
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTAATTTTTAT
Found at i:18149 original size:17 final size:17
Alignment explanation
Indices: 18127--18177 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
18117 TTTGAAGAGG
*
18127 AAAACATTACTAGTCAT
1 AAAACATTAATAGTCAT
* *
18144 AAAACATGAAT-GATAAT
1 AAAACATTAATAG-TCAT
*
18161 AAAACATTATTAGTCAT
1 AAAACATTAATAGTCAT
18178 GGTATGGGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.29
Consensus pattern (17 bp):
AAAACATTAATAGTCAT
Found at i:19216 original size:84 final size:84
Alignment explanation
Indices: 19075--19242 Score: 318
Period size: 84 Copynumber: 2.0 Consensus size: 84
19065 GGTTTTAGCT
19075 TTATTGAGTTTGTGGAGTTTGAGATTAACCTGCCTATCATAAGCAAGTTACTAATACCACTTCTT
1 TTATTGAGTTTGTGGAGTTTGAGATTAACCTGCCTATCATAAGCAAGTTACTAATACCACTTCTT
*
19140 TTTTTACTTTAATCTATCC
66 TTTTGACTTTAATCTATCC
*
19159 TTATTGAGTTTGTGGAGTTTGAGATTAGCCTGCCTATCATAAGCAAGTTACTAATACCACTTCTT
1 TTATTGAGTTTGTGGAGTTTGAGATTAACCTGCCTATCATAAGCAAGTTACTAATACCACTTCTT
19224 TTTTGACTTTAATCTATCC
66 TTTTGACTTTAATCTATCC
19243 ATCAACTCTA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (84 bp):
TTATTGAGTTTGTGGAGTTTGAGATTAACCTGCCTATCATAAGCAAGTTACTAATACCACTTCTT
TTTTGACTTTAATCTATCC
Found at i:22295 original size:38 final size:39
Alignment explanation
Indices: 22251--22350 Score: 116
Period size: 39 Copynumber: 2.6 Consensus size: 39
22241 TTTCTCTTGG
*
22251 TTTTGCGTTTTTAATTAAAAAAAAATT-TCTCTCTTTT-T
1 TTTTGCGTTTTTAATTAAAAAAAAATTCTCT-TATTTTGT
* *
22289 TTTTGCGTTTTTTATTTTAAAAAAAATTCTCTTATTTTGT
1 TTTTGCG-TTTTTAATTAAAAAAAAATTCTCTTATTTTGT
*
22329 TTTCTGCGTTATTAA-TAAAAAA
1 TTT-TGCGTTTTTAATTAAAAAA
22351 TTTCTTATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
38 7 0.13
39 29 0.56
40 12 0.23
41 4 0.08
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (39 bp):
TTTTGCGTTTTTAATTAAAAAAAAATTCTCTTATTTTGT
Found at i:25440 original size:21 final size:21
Alignment explanation
Indices: 25407--25446 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25397 TCATGCTAGG
*
25407 ACCGGCCATCGCCACGCCACC
1 ACCGGCCACCGCCACGCCACC
* *
25428 ACCGGCTACCGCCATGCCA
1 ACCGGCCACCGCCACGCCA
25447 AGACCGGTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.53, G:0.20, T:0.07
Consensus pattern (21 bp):
ACCGGCCACCGCCACGCCACC
Found at i:37209 original size:1 final size:1
Alignment explanation
Indices: 37203--37280 Score: 57
Period size: 1 Copynumber: 78.0 Consensus size: 1
37193 GATAAAATGG
* * * * * * * * * *
37203 AAAAAAAACAAAAAAAAACAAACAAAAAAACAAACAAAAAAAACAAACAAAAAAAACAAACAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
37268 AAAAACAAAAAAA
1 AAAAAAAAAAAAA
37281 TAAACAAACA
Statistics
Matches: 55, Mismatches: 22, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:37229 original size:13 final size:13
Alignment explanation
Indices: 37203--37292 Score: 132
Period size: 13 Copynumber: 7.0 Consensus size: 13
37193 GATAAAATGG
37203 AAAAA-AAACAAAA
1 AAAAACAAAC-AAA
37216 AAAAACAAAC-AA
1 AAAAACAAACAAA
37228 AAAAACAAACAAA
1 AAAAACAAACAAA
37241 AAAAACAAACAAA
1 AAAAACAAACAAA
37254 AAAAACAAACAAA
1 AAAAACAAACAAA
37267 CAAAAACAAA-AAA
1 -AAAAACAAACAAA
*
37280 ATAAACAAACAAA
1 AAAAACAAACAAA
37293 GTTGTGCTCA
Statistics
Matches: 72, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
12 20 0.28
13 39 0.54
14 13 0.18
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.01
Consensus pattern (13 bp):
AAAAACAAACAAA
Found at i:37232 original size:22 final size:21
Alignment explanation
Indices: 37204--37292 Score: 108
Period size: 22 Copynumber: 4.1 Consensus size: 21
37194 ATAAAATGGA
37204 AAAAAAACAAAAAAAAACAAAC
1 AAAAAAA-AAAAAAAAACAAAC
*
37226 AAAAAAACAAACAAAAA-AAAC
1 AAAAAAA-AAAAAAAAACAAAC
* *
37247 AAACAAAAAAAACAAACAAAC
1 AAAAAAAAAAAAAAAACAAAC
*
37268 AAAAACAAAAAAATAAACAAAC
1 AAAAA-AAAAAAAAAAACAAAC
37290 AAA
1 AAA
37293 GTTGTGCTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
20 7 0.12
21 18 0.31
22 34 0.58
ACGTcount: A:0.84, C:0.15, G:0.00, T:0.01
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAACAAAC
Found at i:37289 original size:4 final size:4
Alignment explanation
Indices: 37208--37292 Score: 79
Period size: 4 Copynumber: 21.8 Consensus size: 4
37198 AATGGAAAAA
* * *
37208 AAAC AAA- AAA- AAAC AAAC AAAA AAAC AAAC AAAAA AAAC AAAC AAAAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC -AAAC AAAC AAAC -AAAC
* *
37256 AAAC AAAC AAAC -AA- AAAC AAAA AAAT AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
37293 GTTGTGCTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
3 10 0.15
4 51 0.76
5 6 0.09
ACGTcount: A:0.84, C:0.15, G:0.00, T:0.01
Consensus pattern (4 bp):
AAAC
Found at i:54328 original size:13 final size:13
Alignment explanation
Indices: 54310--54334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54300 AAAAATCACA
54310 AAACAAAGATAAT
1 AAACAAAGATAAT
54323 AAACAAAGATAA
1 AAACAAAGATAA
54335 AAATGAAAAA
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:0.72, C:0.08, G:0.08, T:0.12
Consensus pattern (13 bp):
AAACAAAGATAAT
Found at i:55338 original size:21 final size:18
Alignment explanation
Indices: 55294--55348 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
55284 AGGGTAAGAC
*
55294 TATATTATATATAATAAT
1 TATATTACATATAATAAT
55312 TA-ATTACATATATATAAT
1 TATATTACATATA-ATAAT
*
55330 TACATATTACTTATAATAA
1 T--ATATTACATATAATAA
55349 ATCAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 9 0.29
18 8 0.26
20 5 0.16
21 9 0.29
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TATATTACATATAATAAT
Found at i:57137 original size:33 final size:33
Alignment explanation
Indices: 57088--57151 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
57078 CTTAAATTAA
* *
57088 GTTATAGAATTGTGTAAAACAAATTTGTTTACG
1 GTTATAAAATTATGTAAAACAAATTTGTTTACG
57121 GTTATAAAATTATGTAAAACAAATTTGTTTA
1 GTTATAAAATTATGTAAAACAAATTTGTTTA
57152 TACTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (33 bp):
GTTATAAAATTATGTAAAACAAATTTGTTTACG
Found at i:61074 original size:2 final size:2
Alignment explanation
Indices: 61067--61098 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
61057 ACATACATAC
61067 AT AT 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 AT AT
61099 GAATTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 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):
AT
Found at i:61234 original size:22 final size:22
Alignment explanation
Indices: 61207--61436 Score: 107
Period size: 22 Copynumber: 10.5 Consensus size: 22
61197 ATTACACTAT
*
61207 TTTTGATCACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
*
61229 TTTTGATAACCTTCCTATGCAA
1 TTTTGATAACCTTCCTATGAAA
** * *
61251 TTTT-AGTAACGATACTATGGAA
1 TTTTGA-TAACCTTCCTATGAAA
* * * **
61273 CTTCGAGAACCTTTTTAT--AA
1 TTTTGATAACCTTCCTATGAAA
** *
61293 TTTTTTTAACCTTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* * * *
61315 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCCTATGAAA
*
61337 TTTTGA-AGACC-TCACTATAAAA
1 TTTTGATA-ACCTTC-CTATGAAA
*
61359 TTTTGATAA-CTTCCCAATGAAA
1 TTTTGATAACCTT-CCTATGAAA
** *
61381 TTTTGATAACCAACACTATGAGA
1 TTTTGATAACCTTC-CTATGAAA
* *
61404 TGTTGATAACC-TCCATATGATA
1 TTTTGATAACCTTCC-TATGAAA
*
61426 TGTTGATAACC
1 TTTTGATAACC
61437 ACGTTATGAA
Statistics
Matches: 157, Mismatches: 38, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
20 14 0.09
21 5 0.03
22 115 0.73
23 23 0.15
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.38
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:61783 original size:30 final size:31
Alignment explanation
Indices: 61720--61796 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
61710 AAAAAGTGAG
*
61720 TCAGGGACCCAATTGCTCAATTAACTCCACT
1 TCAGGGACCCAATTGCTCAACTAACTCCACT
* * *
61751 TCAGGGACTCAATTGCTC-ACTAAGTTCACT
1 TCAGGGACCCAATTGCTCAACTAACTCCACT
*
61781 TCAGGGACCCATTTGC
1 TCAGGGACCCAATTGC
61797 ATATTTCCCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 23 0.57
31 17 0.43
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (31 bp):
TCAGGGACCCAATTGCTCAACTAACTCCACT
Found at i:62499 original size:30 final size:30
Alignment explanation
Indices: 62465--62521 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
62455 TTTTTTTTAA
*
62465 TTTTTTCAAAAAAAGAAAAGAAGAAAATTG
1 TTTTTTCAAAAAAAGAAAAAAAGAAAATTG
** *
62495 TTTTTTTTAAAACAGAAAAAAAGAAAA
1 TTTTTTCAAAAAAAGAAAAAAAGAAAA
62522 AAATGAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.28
Consensus pattern (30 bp):
TTTTTTCAAAAAAAGAAAAAAAGAAAATTG
Found at i:62533 original size:33 final size:32
Alignment explanation
Indices: 62463--62534 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 32
62453 CTTTTTTTTT
* *
62463 AATTTTTTCAAAAAAAGAAAAGAAGAAAATTG
1 AATTTTTTCAAAAAAAAAAAAGAAGAAAAATG
* *
62495 -TTTTTTTTAAAACAGAAAAAAAGAA-AAAAATG
1 AATTTTTTCAAAA-A-AAAAAAAGAAGAAAAATG
62527 AATTTTTT
1 AATTTTTT
62535 ATTTTATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
31 10 0.31
32 7 0.22
33 15 0.47
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.32
Consensus pattern (32 bp):
AATTTTTTCAAAAAAAAAAAAGAAGAAAAATG
Found at i:62936 original size:22 final size:22
Alignment explanation
Indices: 62911--63149 Score: 109
Period size: 22 Copynumber: 11.1 Consensus size: 22
62901 GAATTGTTAG
*
62911 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
62933 TAATCACACTATCAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
62955 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * * *
62977 TAAACCTCCCTATAAAATTTTGC
1 T-AATCACACTATGAAATTTTGA
* * *
63000 TAATCTTC-TTATGAAATCTTG-
1 TAATC-ACACTATGAAATTTTGA
*
63021 --GT-A-ACTA-GAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * **
63038 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
63060 TAATCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
63082 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
63104 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
63126 -AAACTAAACTATTAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
63148 TA
1 TA
63150 TCCTCCCTGA
Statistics
Matches: 162, Mismatches: 42, Indels: 25
0.71 0.18 0.11
Matches are distributed among these distances:
16 8 0.05
17 2 0.01
19 1 0.01
21 5 0.03
22 124 0.77
23 22 0.14
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:63058 original size:83 final size:82
Alignment explanation
Indices: 62946--63098 Score: 198
Period size: 82 Copynumber: 1.9 Consensus size: 82
62936 TCACACTATC
* * * *
62946 AAATTGTGATAACCTCGCTATGAAATTTTGATAAACCTCCCTATAAAATTTTGCTAATCTTCTTA
1 AAATTGTGATAACCTCCCTATGAAATTTTGAT-AACCTCACTATAAAATTTTGCTAATCTCCCTA
63011 TGAAATCTTGGTAACTAG
65 TGAAATCTTGGTAACTAG
* ** * * * *
63029 AAATTTTGATAACCTCCCTATGATTTTTTGATAATCTCATTATGAAATTTTGTTAATCTCCCTAT
1 AAATTGTGATAACCTCCCTATGAAATTTTGATAACCTCACTATAAAATTTTGCTAATCTCCCTAT
63094 GAAAT
66 GAAAT
63099 TTTGATCTAC
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
82 31 0.53
83 28 0.47
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (82 bp):
AAATTGTGATAACCTCCCTATGAAATTTTGATAACCTCACTATAAAATTTTGCTAATCTCCCTAT
GAAATCTTGGTAACTAG
Found at i:63299 original size:22 final size:22
Alignment explanation
Indices: 63250--63438 Score: 131
Period size: 22 Copynumber: 8.7 Consensus size: 22
63240 AAAATACCAC
* * *
63250 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCTC-TT
*
63273 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
63294 TATGAAATTTTGATAACCTC--
1 TATGAAATTTTGATAACCTCTT
* * * * *
63314 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTCTT
* * *
63336 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAACCTCTT
* *
63358 TATGTAATTTTGATAACCTCACT
1 TATGAAATTTTGATAACCTC-TT
** **
63381 T-TGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCTCTT
63402 TATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAACCTCTT
63422 CCTAT-AAATTTTGATAA
1 --TATGAAATTTTGATAA
63439 TCCGATCTCC
Statistics
Matches: 131, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
20 17 0.13
21 16 0.12
22 95 0.73
23 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:63300 original size:44 final size:43
Alignment explanation
Indices: 63250--63438 Score: 158
Period size: 44 Copynumber: 4.4 Consensus size: 43
63240 AAAATACCAC
* *
63250 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAA-CACATTATGAAAATTTGATAACCTCTT
* * * *
63294 TATGAAATTTTGATAAC-C-TCTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACACAT-TATGAAAA-TTTGATAACCTCTT
* * *
63336 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCACT
1 TATGAAATTTTGATAA-CACATTATGAAAATTTGATAACCTC-TT
* *
63381 T-TGAAATTTTGATAACAACACTATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAAC-ACATTATGAAAATTTGATAACCTCTT
63422 CCTAT-AAATTTTGATAA
1 --TATGAAATTTTGATAA
63439 TCCGATCTCC
Statistics
Matches: 118, Mismatches: 16, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
41 6 0.05
42 31 0.26
43 16 0.14
44 61 0.52
45 4 0.03
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (43 bp):
TATGAAATTTTGATAACACATTATGAAAATTTGATAACCTCTT
Found at i:63594 original size:23 final size:23
Alignment explanation
Indices: 63538--63600 Score: 101
Period size: 22 Copynumber: 2.8 Consensus size: 23
63528 ATAAACTTCA
*
63538 TATGAAATTTTGATAACCACACT
1 TATGAAATTTTGATAACCACACC
*
63561 TA-AAAATTTTGATAACCACACC
1 TATGAAATTTTGATAACCACACC
63583 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
63601 TCCCCATGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.33
Consensus pattern (23 bp):
TATGAAATTTTGATAACCACACC
Found at i:63742 original size:22 final size:22
Alignment explanation
Indices: 63717--63767 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
63707 TAAAATTGTG
*
63717 ATAACC-ACACTATGAAATTTCA
1 ATAACCTAC-CTAAGAAATTTCA
* *
63739 ATAACCTTCCTAAGAAATTTTA
1 ATAACCTACCTAAGAAATTTCA
63761 ATAACCT
1 ATAACCT
63768 GATCCTTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (22 bp):
ATAACCTACCTAAGAAATTTCA
Found at i:63816 original size:22 final size:22
Alignment explanation
Indices: 63789--63914 Score: 98
Period size: 22 Copynumber: 5.7 Consensus size: 22
63779 ACCACACTAA
63789 GAAATTTTGATAACCTTCTCAT
1 GAAATTTTGATAACCTTCTCAT
*
63811 GCAATTTTGATAA-CTTC-CATAT
1 GAAATTTTGATAACCTTCTC--AT
* *
63833 GAAATTTTGGTAACAAC-ACT-AT
1 GAAATTTTGATAAC--CTTCTCAT
*
63855 GGAATTTTTGATAACCTTCTCAT
1 -GAAATTTTGATAACCTTCTCAT
* * * *
63878 GAAATTATAATAACCATCTTAT
1 GAAATTTTGATAACCTTCTCAT
*
63900 GAAATTTTGAGAACC
1 GAAATTTTGATAACC
63915 ACACAGAGAC
Statistics
Matches: 80, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
20 1 0.01
21 5 0.06
22 58 0.73
23 14 0.17
24 1 0.01
25 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
GAAATTTTGATAACCTTCTCAT
Found at i:63891 original size:67 final size:66
Alignment explanation
Indices: 63773--63908 Score: 175
Period size: 67 Copynumber: 2.0 Consensus size: 66
63763 AACCTGATCC
* * * * *
63773 TTGGTAACCACACTAAGAAATTTTGATAACCTTCTCATGCAATTTTGATAA-CTTCCATATGAAA
1 TTGGTAACAACACTAAGAAATTTTGATAACCTTCTCATGAAATTATAATAACCAT-CATATGAAA
63837 TT
65 TT
* * *
63839 TTGGTAACAACACTATGGAATTTTTGATAACCTTCTCATGAAATTATAATAACCATCTTATGAAA
1 TTGGTAACAACACTA-AGAAATTTTGATAACCTTCTCATGAAATTATAATAACCATCATATGAAA
63904 TT
65 TT
63906 TTG
1 TTG
63909 AGAACCACAC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
66 14 0.23
67 44 0.73
68 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (66 bp):
TTGGTAACAACACTAAGAAATTTTGATAACCTTCTCATGAAATTATAATAACCATCATATGAAAT
T
Found at i:66604 original size:28 final size:28
Alignment explanation
Indices: 66552--66610 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
66542 AGATTTTGTT
* * **
66552 AAATAAAAATAGAGTTTTTTTTTGAGAA
1 AAATAAAAATAAAATTTTTAATTGAGAA
*
66580 AAATAAAAATAAAATTTTTAATTGAGTA
1 AAATAAAAATAAAATTTTTAATTGAGAA
66608 AAA
1 AAA
66611 CTATAAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (28 bp):
AAATAAAAATAAAATTTTTAATTGAGAA
Found at i:67464 original size:10 final size:10
Alignment explanation
Indices: 67449--67508 Score: 88
Period size: 10 Copynumber: 6.1 Consensus size: 10
67439 TCATTATTAA
67449 AATTTTGTAT
1 AATTTTGTAT
*
67459 AA-TTT-TAA
1 AATTTTGTAT
67467 AATTTTGTAT
1 AATTTTGTAT
67477 AATTTTGTAT
1 AATTTTGTAT
67487 AATTTTGTAT
1 AATTTTGTAT
67497 AATTTTAGTAT
1 AATTTT-GTAT
67508 A
1 A
67509 TATATATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
8 4 0.09
9 6 0.13
10 30 0.67
11 5 0.11
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (10 bp):
AATTTTGTAT
Found at i:67468 original size:18 final size:18
Alignment explanation
Indices: 67445--67503 Score: 91
Period size: 18 Copynumber: 3.2 Consensus size: 18
67435 ATTGTCATTA
67445 TTAAAATTTTGTATAATT
1 TTAAAATTTTGTATAATT
67463 TTAAAATTTTGTATAATTT
1 TTAAAATTTTGTATAA-TT
*
67482 TGTATAATTTTGTATAATT
1 T-TAAAATTTTGTATAATT
67501 TTA
1 TTA
67504 GTATATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
18 18 0.47
19 6 0.16
20 14 0.37
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (18 bp):
TTAAAATTTTGTATAATT
Found at i:69928 original size:41 final size:41
Alignment explanation
Indices: 69871--69963 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
69861 TCATCATAAT
69871 ATATCCTTCAAAAATAAATCCTTTAAAAAACACATTCTTAA
1 ATATCCTTCAAAAATAAATCCTTTAAAAAACACATTCTTAA
* * * * *
69912 ATATCCTTTAAGAATAAGTCCTTTAAAAAATATATTCTTAA
1 ATATCCTTCAAAAATAAATCCTTTAAAAAACACATTCTTAA
69953 ATATCCTTCAA
1 ATATCCTTCAA
69964 CAATGGAGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.35
Consensus pattern (41 bp):
ATATCCTTCAAAAATAAATCCTTTAAAAAACACATTCTTAA
Found at i:73829 original size:19 final size:18
Alignment explanation
Indices: 73791--73829 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
73781 GGTTCTTGTT
* *
73791 TTTGTGCAATTGAGCTAA
1 TTTGTGCAATTAACCTAA
73809 TTTGTGCAATTAACCCTAA
1 TTTGTGCAATTAA-CCTAA
73828 TT
1 TT
73830 GGAGATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (18 bp):
TTTGTGCAATTAACCTAA
Found at i:84767 original size:2 final size:2
Alignment explanation
Indices: 84760--84790 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
84750 TAATTACCCA
84760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
84791 AGAGGTTGCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85934 original size:16 final size:18
Alignment explanation
Indices: 85915--85953 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
85905 TTTTTATTTG
85915 AGTTTG-TTTTT-GAGTC
1 AGTTTGTTTTTTCGAGTC
85931 AGTTTGTTTTTTCGAGTC
1 AGTTTGTTTTTTCGAGTC
85949 AGTTT
1 AGTTT
85954 CGAATCTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.29
17 5 0.24
18 10 0.48
ACGTcount: A:0.13, C:0.08, G:0.23, T:0.56
Consensus pattern (18 bp):
AGTTTGTTTTTTCGAGTC
Found at i:86646 original size:17 final size:16
Alignment explanation
Indices: 86626--86673 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
86616 TTTTATTTTG
86626 AAAAAAAAAAGAGAAAA
1 AAAAAAAAAAG-GAAAA
86643 AAAAAGAAAGAAGGAAAA
1 AAAAA-AAA-AAGGAAAA
* *
86661 AGAAGAAAAAGGA
1 AAAAAAAAAAGGA
86674 CTTAAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 8 0.30
18 11 0.41
19 3 0.11
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGGAAAA
Found at i:86654 original size:14 final size:14
Alignment explanation
Indices: 86625--86670 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
86615 ATTTTATTTT
*
86625 GAAAAAAAAA-AGA
1 GAAAAAAAAAGAAA
86638 GAAAAAAAAAGAAA
1 GAAAAAAAAAGAAA
**
86652 GAAGGAAAAAG-AA
1 GAAAAAAAAAGAAA
86665 GAAAAA
1 GAAAAA
86671 GGACTTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAGAAA
Found at i:86660 original size:16 final size:16
Alignment explanation
Indices: 86640--86673 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
86630 AAAAAAGAGA
*
86640 AAAAAAAAGAAAGAAGG
1 AAAAAGAAGAAA-AAGG
86657 AAAAAGAAGAAAAAGG
1 AAAAAGAAGAAAAAGG
86673 A
1 A
86674 CTTAAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGAAAAAGG
Found at i:101158 original size:11 final size:11
Alignment explanation
Indices: 101128--101245 Score: 84
Period size: 11 Copynumber: 11.2 Consensus size: 11
101118 TGCTATTTAA
101128 ATAAAATATAT
1 ATAAAATATAT
* **
101139 TTATGATATAT
1 ATAAAATATAT
101150 ATAAAATATAT
1 ATAAAATATAT
101161 A-AAAA-ATAT
1 ATAAAATATAT
**
101170 ATTTAAT-TAT
1 ATAAAATATAT
* **
101180 TTATTATATAT
1 ATAAAATATAT
101191 ATAAAATATAT
1 ATAAAATATAT
*
101202 GT-AAA-ATAT
1 ATAAAATATAT
*
101211 ATAAATTATAT
1 ATAAAATATAT
* **
101222 TTATGATATAT
1 ATAAAATATAT
101233 ATAAAATATAT
1 ATAAAATATAT
101244 AT
1 AT
101246 GATAAATTAT
Statistics
Matches: 78, Mismatches: 24, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
9 10 0.13
10 18 0.23
11 50 0.64
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
ATAAAATATAT
Found at i:104545 original size:18 final size:18
Alignment explanation
Indices: 104522--104581 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
104512 CCAACCTGTT
*
104522 AACACATTCCCAGCACCG
1 AACACAGTCCCAGCACCG
*
104540 AACACAGTCCCAGCACCA
1 AACACAGTCCCAGCACCG
*
104558 AACACAGTCCCAGCATCG
1 AACACAGTCCCAGCACCG
104576 AACACA
1 AACACA
104582 AATTTTGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.38, C:0.42, G:0.12, T:0.08
Consensus pattern (18 bp):
AACACAGTCCCAGCACCG
Found at i:107061 original size:17 final size:17
Alignment explanation
Indices: 107039--107075 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
107029 TTAACTCAAC
107039 TTGTAGATGTATGATGT
1 TTGTAGATGTATGATGT
107056 TTGTAGATGTATGATGT
1 TTGTAGATGTATGATGT
107073 TTG
1 TTG
107076 GATATATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.49
Consensus pattern (17 bp):
TTGTAGATGTATGATGT
Found at i:107388 original size:12 final size:13
Alignment explanation
Indices: 107353--107398 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
107343 ATCTATACCT
107353 TTATATT-TATATA
1 TTATATTATAT-TA
*
107366 TTATA-TATATTT
1 TTATATTATATTA
107378 TTA-ATTATATTA
1 TTATATTATATTA
107390 TTATATTAT
1 TTATATTAT
107399 TATACCTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 1 0.04
12 14 0.50
13 13 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATATTATATTA
Found at i:107400 original size:16 final size:17
Alignment explanation
Indices: 107354--107402 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
107344 TCTATACCTT
107354 TATAT-TTATA-TATTA
1 TATATATTATATTATTA
107369 TATATATT-T-TTAATTA
1 TATATATTATATT-ATTA
107385 TAT-TATTATATTATTA
1 TATATATTATATTATTA
107401 TA
1 TA
107403 CCTACTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 11 0.38
16 16 0.55
17 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATATTATATTATTA
Found at i:109417 original size:41 final size:41
Alignment explanation
Indices: 109372--109449 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
109362 AGCAAGAGAT
* *
109372 TTTCTTAAATAAATTTTCTTAAAAGCACTTATAAAATTCCA
1 TTTCTTAAATAAATTTTCTTAAAAGAACTCATAAAATTCCA
* *
109413 TTTCTTAACTGAATTTTCTTAAAAGAACTCATAAAAT
1 TTTCTTAAATAAATTTTCTTAAAAGAACTCATAAAAT
109450 AAAATAGCCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (41 bp):
TTTCTTAAATAAATTTTCTTAAAAGAACTCATAAAATTCCA
Found at i:109784 original size:33 final size:33
Alignment explanation
Indices: 109746--109811 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
109736 TTTGCGCGGT
* *
109746 TATTGAAAAAAAAAATTTTGACGCGAATGCGTA
1 TATTGAAAAAAAAAAATCTGACGCGAATGCGTA
109779 TATTGAAAAAAAAAAATCTGACGCGAATGCGTA
1 TATTGAAAAAAAAAAATCTGACGCGAATGCGTA
109812 GGGATATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (33 bp):
TATTGAAAAAAAAAAATCTGACGCGAATGCGTA
Found at i:110006 original size:4 final size:4
Alignment explanation
Indices: 109997--110158 Score: 317
Period size: 4 Copynumber: 40.8 Consensus size: 4
109987 ATAGTAAGGT
109997 ATAG ATAG ATAG AT-G ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
110044 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
110092 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
110140 ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATA
110159 ATAAAAGCCA
Statistics
Matches: 157, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
3 3 0.02
4 154 0.98
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:111329 original size:29 final size:30
Alignment explanation
Indices: 111271--111331 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
111261 GTTCTAATTA
* *
111271 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
111301 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
111330 AT
1 AT
111332 ATTATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:112347 original size:25 final size:24
Alignment explanation
Indices: 112297--112347 Score: 79
Period size: 22 Copynumber: 2.2 Consensus size: 24
112287 TATCTTAGAT
112297 ATAATATATATTATTAAATAAATA
1 ATAATATATATTATTAAATAAATA
*
112321 ATAA-ATATATT-TTAAATAATTA
1 ATAATATATATTATTAAATAAATA
112343 ATAAT
1 ATAAT
112348 GAGTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 14 0.56
23 7 0.28
24 4 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATATATATTATTAAATAAATA
Found at i:118054 original size:6 final size:6
Alignment explanation
Indices: 118035--118064 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
118025 GCAAAGGCAG
118035 AAAAAT ATAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT A-AAAAT AAAAAT AAAAAT AAAAA
118065 GGAAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Done.