Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007891.1 Corchorus capsularis cultivar CVL-1 contig07912, 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: 66843
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:455 original size:2 final size:2
Alignment explanation
Indices: 448--476 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
438 TAGTCCTAAT
448 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
477 GTAAGATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1625 original size:47 final size:47
Alignment explanation
Indices: 1556--1663 Score: 207
Period size: 47 Copynumber: 2.3 Consensus size: 47
1546 ATAACTGAAT
*
1556 ATCACGACTTTCGGTGGCAGAATTAGTGAAGAATCCTAAGGCTAATC
1 ATCACGACTTTCGGTGGCAGAATTAGTGAAGAATCCTAAGGCTAACC
1603 ATCACGACTTTCGGTGGCAGAATTAGTGAAGAATCCTAAGGCTAACC
1 ATCACGACTTTCGGTGGCAGAATTAGTGAAGAATCCTAAGGCTAACC
1650 ATCACGACTTTCGG
1 ATCACGACTTTCGG
1664 GTGCAAAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (47 bp):
ATCACGACTTTCGGTGGCAGAATTAGTGAAGAATCCTAAGGCTAACC
Found at i:3682 original size:47 final size:46
Alignment explanation
Indices: 3581--4683 Score: 324
Period size: 47 Copynumber: 23.4 Consensus size: 46
3571 AAATCCGAAA
* * * * *
3581 GCTAACAATCACAACTATCCAGGGG-AAAAATGACCGAAAA--ATGAG
1 GCTAACCATCACGACT-TTCAGGGGCAAAATTGACCGAAAATCA-AAG
* **
3626 GCTAACCATCACGACTTTTAGGGGCAAAATTTTCCGAAAAGTCAAAG
1 GCTAACCATCACGACTTTCAGGGGCAAAATTGACCGAAAA-TCAAAG
* * * * * * *
3673 GCTAACCATCACGACTTT-TGGGACCCAAATTGGCTGAAAAGCCAAAA
1 GCTAACCATCACGACTTTCAGGG-GCAAAATTGACCGAAAA-TCAAAG
* * * * **
3720 GCTATCCTTCACGA-TTTCAGAGGCCAACATTGACCGAAAATCCAGTG
1 GCTAACCATCACGACTTTCAG-GGGCAAAATTGACCGAAAAT-CAAAG
* * * *
3767 GCTAACCATCTCGACTTTCAGGTGCCAAAATT-ATTCGAAAATTCAAAT
1 GCTAACCATCACGACTTTCAGG-GGCAAAATTGA-CCGAAAA-TCAAAG
* ** * * * *
3815 GCAAAATATCACGACTAT-AGGAGGCCAAAAATGACCTAAAATCCAAG
1 GCTAACCATCACGACTTTCAGG-GG-CAAAATTGACCGAAAATCAAAG
* * * * * *
3862 GCTAAGCATTACGACTTTCGGGGGCCAAATTGGA-CGAAAAGGCAAAT
1 GCTAACCATCACGACTTTCAGGGGCAAAATT-GACCGAAAA-TCAAAG
* * * * *
3909 GCTAAGCATCACAATTTTC-GGGGCGGAAATTGGCCGAAAATCCAAAG
1 GCTAACCATCACGACTTTCAGGGGC-AAAATTGACCGAAAAT-CAAAG
* * * * * * * *
3956 GCTAACCATCACAATTTTTCATGGTC-AAGTTTACAGAAAAGGGC-AAG
1 GCTAACCATCACGA-CTTTCAGGGGCAAAATTGACCGAAAA--TCAAAG
*
4003 GCTAACCATCATGACTTTCAGGGGGCAAAAATTGACCGAAAATCCAAAG
1 GCTAACCATCACGACTTTCA-GGGGC-AAAATTGACCGAAAAT-CAAAG
* * *
4052 GC-AAGCCATCACGACTTTCGGGTGGCAAAATTGTCCAAAAATTCAAAG
1 GCTAA-CCATCACGACTTTCAGG-GGCAAAATTGACCGAAAA-TCAAAG
* * * *
4100 GCTAACAATCATGACTTTCAGAGGCGAAAAATG---GATTAAATCGAAAG
1 GCTAACCATCACGACTTTCAGGGGC-AAAATTGACCGA--AAATC-AAAG
* * ** * *
4147 ACTAACCATCAC-AATTTTTGGAGGCTACAAA-TAACTGAAAATCCAAAG
1 GCTAACCATCACGACTTTCAGG-GGC-A-AAATTGACCGAAAAT-CAAAG
* * * * *
4195 ACTAACAATCACGACTTTC-GGGTGCCAATATTGTCCAAAAATTCAAAG
1 GCTAACCATCACGACTTTCAGGG-G-CAAAATTGACCGAAAA-TCAAAG
* * *
4243 GCTAACAATCACGACTTT-TGGAGGCGAAAAATG---GATTAAATCCAAAG
1 GCTAACCATCACGACTTTCAGG-GGC-AAAATTGACCGA--AAAT-CAAAG
* * * ** * * *
4290 ACTAACCATCACAATTTTTGGAGGGTACAAA-TAACTGAAAATCCAAAG
1 GCTAACCATCACGACTTTCAG-GGGCA-AAATTGACCGAAAAT-CAAAG
* * *
4338 GCTAACAATCACGACTTTCAGCAGGCGAAAA-TGACCTAAAATCCAAAG
1 GCTAACCATCACGACTTTCAG-GGGC-AAAATTGACCGAAAAT-CAAAG
* * * * ** * * *
4386 GCCAACTATCACGATTTTC-GAGG-AAAAAAGTCTGAAAAGCCAAAG
1 GCTAACCATCACGACTTTCAGGGGCAAAATTGACCGAAAA-TCAAAG
* * * * * *
4431 GCTAACTATAACGACTTT-AGGGGGCCAAATTGGCAGAAAAGTTAAAG
1 GCTAACCATCACGACTTTCA-GGGGCAAAATTGACCGAAAA-TCAAAG
* * * * * * * * * *
4478 GTTAAGCATCATGAGTTT-TGAGTGCCAAATTGGCCGAAAAGGCAGAG
1 GCTAACCATCACGACTTTCAG-GGGCAAAATTGACCGAAAA-TCAAAG
* ** *
4525 GCTAAACATCACGACTTTC-GATCGCGAAAATTGACCGAAAACCAAAG
1 GCTAACCATCACGACTTTCAG-GGGC-AAAATTGACCGAAAATCAAAG
** ** * * * *
4572 GCTAACCATCACGACTTTTTGTGTCCAGATTTG-CTGAAAATGATAAG
1 GCTAACCATCACGACTTTCAG-GGGCAAAATTGACCGAAAATCA-AAG
*** **
4619 GCTAACCATCACGACTTTCGAGGAAAAAAATT-ACCGAAAAGGAAAAG
1 GCTAACCATCACGACTTTC-AGGGGCAAAATTGACCGAAAA-TCAAAG
*
4666 GCTAAGCATCACGACTTT
1 GCTAACCATCACGACTTT
4684 TGGTGTTCAA
Statistics
Matches: 788, Mismatches: 196, Indels: 146
0.70 0.17 0.13
Matches are distributed among these distances:
44 10 0.01
45 54 0.07
46 49 0.06
47 375 0.48
48 246 0.31
49 50 0.06
50 4 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (46 bp):
GCTAACCATCACGACTTTCAGGGGCAAAATTGACCGAAAATCAAAG
Found at i:4101 original size:48 final size:49
Alignment explanation
Indices: 4000--4396 Score: 158
Period size: 48 Copynumber: 8.3 Consensus size: 49
3990 AGAAAAGGGC
*
4000 AAGGCTAACCATCATGACTTTCAGGGGGCAAAAATTGACCGAAAATCCA
1 AAGGCTAACCATCATGACTTTCAGGGGGCAAAAATTGACCAAAAATCCA
* * *
4049 AAGGC-AAGCCATCACGACTTTC-GGGTGGC-AAAATTGTCCAAAAATTCA
1 AAGGCTAA-CCATCATGACTTTCAGGG-GGCAAAAATTGACCAAAAATCCA
* * * ** *
4097 AAGGCTAACAATCATGACTTTCA-GAGGCGAAAAATGGA--TTAAATCGA
1 AAGGCTAACCATCATGACTTTCAGGGGGC-AAAAATTGACCAAAAATCCA
* * * ** * * * **
4144 AAGACTAACCATCA-CAATTTTTGGAGGCTACAAA-TAACTGAAAATCCA
1 AAGGCTAACCATCATGACTTTCAGGGGGC-AAAAATTGACCAAAAATCCA
* * * * * * * *
4192 AAGACTAACAATCACGACTTTC-GGGTGCCAATATTGTCCAAAAATTCA
1 AAGGCTAACCATCATGACTTTCAGGGGGCAAAAATTGACCAAAAATCCA
* * * * * **
4240 AAGGCTAACAATCACGACTTT-TGGAGGCGAAAAATGGA--TTAAATCCA
1 AAGGCTAACCATCATGACTTTCAGGGGGC-AAAAATTGACCAAAAATCCA
* * * ** * * * **
4287 AAGACTAACCATCA-CAATTTTTGGAGGGTACAAA-TAACTGAAAATCCA
1 AAGGCTAACCATCATGACTTTCAGG-GGGCAAAAATTGACCAAAAATCCA
* * ** * *
4335 AAGGCTAACAATCACGACTTTCAGCAGGCGAAAA-TGACCTAAAATCCA
1 AAGGCTAACCATCATGACTTTCAGGGGGCAAAAATTGACCAAAAATCCA
* *
4383 AAGGCCAACTATCA
1 AAGGCTAACCATCA
4397 CGATTTTCGA
Statistics
Matches: 253, Mismatches: 77, Indels: 37
0.69 0.21 0.10
Matches are distributed among these distances:
46 10 0.04
47 56 0.22
48 144 0.57
49 43 0.17
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (49 bp):
AAGGCTAACCATCATGACTTTCAGGGGGCAAAAATTGACCAAAAATCCA
Found at i:4209 original size:143 final size:143
Alignment explanation
Indices: 4040--4356 Score: 537
Period size: 143 Copynumber: 2.2 Consensus size: 143
4030 AAAATTGACC
* *
4040 GAAAATCCAAAGGC-AAGCCATCACGACTTTCGGGTGGCAAAATTGTCCAAAAATTCAAAGGCTA
1 GAAAATCCAAAGGCTAA-CAATCACGACTTTCGGGTGCCAAAATTGTCCAAAAATTCAAAGGCTA
* *
4104 ACAATCATGACTTTCAGAGGCGAAAAATGGATTAAATCGAAAGACTAACCATCACAATTTTTGGA
65 ACAATCACGACTTTCAGAGGCGAAAAATGGATTAAATCCAAAGACTAACCATCACAATTTTTGGA
4169 GGCTACAAATAACT
130 GGCTACAAATAACT
* *
4183 GAAAATCCAAAGACTAACAATCACGACTTTCGGGTGCCAATATTGTCCAAAAATTCAAAGGCTAA
1 GAAAATCCAAAGGCTAACAATCACGACTTTCGGGTGCCAAAATTGTCCAAAAATTCAAAGGCTAA
**
4248 CAATCACGACTTTTGGAGGCGAAAAATGGATTAAATCCAAAGACTAACCATCACAATTTTTGGAG
66 CAATCACGACTTTCAGAGGCGAAAAATGGATTAAATCCAAAGACTAACCATCACAATTTTTGGAG
*
4313 GGTACAAATAACT
131 GCTACAAATAACT
4326 GAAAATCCAAAGGCTAACAATCACGACTTTC
1 GAAAATCCAAAGGCTAACAATCACGACTTTC
4357 AGCAGGCGAA
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
143 161 0.99
144 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (143 bp):
GAAAATCCAAAGGCTAACAATCACGACTTTCGGGTGCCAAAATTGTCCAAAAATTCAAAGGCTAA
CAATCACGACTTTCAGAGGCGAAAAATGGATTAAATCCAAAGACTAACCATCACAATTTTTGGAG
GCTACAAATAACT
Found at i:4379 original size:143 final size:140
Alignment explanation
Indices: 4040--4408 Score: 490
Period size: 143 Copynumber: 2.6 Consensus size: 140
4030 AAAATTGACC
* *
4040 GAAAATCCAAAGGC-AAGCCATCACGACTTTCGGGTGGCAAAATTGTCCAAAAATTCAAAGGCTA
1 GAAAATCCAAAGGCTAA-CAATCACGACTTTC--GAGGCAAAA-TGTCCAAAAATTCAAAGGCTA
* * *
4104 ACAATCATGACTTTCAGAGGCGAAAAATGGATTAAATCGAAAGACTAACCATCACAATTTTTGGA
62 ACAATCACGACTTTTAGAGGCGAAAAATGGATTAAATCCAAAGACTAACCATCACAATTTTTGGA
4169 GGCTACAAATAACT
127 GGCTACAAATAACT
* * *
4183 GAAAATCCAAAGACTAACAATCACGACTTTCGGGTGCCAATATTGTCCAAAAATTCAAAGGCTAA
1 GAAAATCCAAAGGCTAACAATCACGACTTTCGAG-G-CAA-AATGTCCAAAAATTCAAAGGCTAA
*
4248 CAATCACGACTTTTGGAGGCGAAAAATGGATTAAATCCAAAGACTAACCATCACAATTTTTGGAG
63 CAATCACGACTTTTAGAGGCGAAAAATGGATTAAATCCAAAGACTAACCATCACAATTTTTGGAG
*
4313 GGTACAAATAACT
128 GCTACAAATAACT
* * * *
4326 GAAAATCCAAAGGCTAACAATCACGACTTTCAGCAGGCGAAAATGACCTAAAATCCAAAGGCCAA
1 GAAAATCCAAAGGCTAACAATCACGACTTTC-G-AGGC-AAAATGTCCAAAAATTCAAAGGCTAA
* *
4391 CTATCACGA-TTTTCGAGG
63 CAATCACGACTTTTAGAGG
4409 AAAAAAGTCT
Statistics
Matches: 201, Mismatches: 18, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
141 2 0.01
142 9 0.04
143 182 0.91
144 7 0.03
145 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (140 bp):
GAAAATCCAAAGGCTAACAATCACGACTTTCGAGGCAAAATGTCCAAAAATTCAAAGGCTAACAA
TCACGACTTTTAGAGGCGAAAAATGGATTAAATCCAAAGACTAACCATCACAATTTTTGGAGGCT
ACAAATAACT
Found at i:4438 original size:45 final size:49
Alignment explanation
Indices: 4324--4448 Score: 143
Period size: 45 Copynumber: 2.7 Consensus size: 49
4314 GTACAAATAA
* * *
4324 CTGAAAATCCAAAGGCTAACAATCACGACTTTCAGCAGGCGAAAATGAC
1 CTGAAAATCCAAAGGCTAACTATCACGACTTTCAGCAGGCAAAAAAGAC
* * *
4373 CT-AAAATCCAAAGGCCAACTATCACGATTTTC-G-AGG-AAAAAAG-T
1 CTGAAAATCCAAAGGCTAACTATCACGACTTTCAGCAGGCAAAAAAGAC
* *
4417 CTGAAAAGCCAAAGGCTAACTATAACGACTTT
1 CTGAAAATCCAAAGGCTAACTATCACGACTTT
4449 AGGGGGCCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
44 2 0.03
45 30 0.46
46 3 0.05
47 1 0.02
48 27 0.42
49 2 0.03
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (49 bp):
CTGAAAATCCAAAGGCTAACTATCACGACTTTCAGCAGGCAAAAAAGAC
Found at i:4582 original size:94 final size:94
Alignment explanation
Indices: 4474--4735 Score: 282
Period size: 94 Copynumber: 2.8 Consensus size: 94
4464 CAGAAAAGTT
* * * * *
4474 AAAGGTTAAGCATCATGAGTTTTGAGTG-CCAAATTGGCCGAAAAGGCAGAGGCTAAACATCACG
1 AAAGGCTAAGCATCACGACTTTTG-GTGTCCAAATTGGCCGAAAAGGCAAAGGCTAACCATCACG
** *
4538 ACTTTCGATCG-CGAAAATTGACCGAAAA-CC
65 ACTTTCGA-CGAAAAAAATT-ACCGAAAAGCA
* * * * * *
4568 AAAGGCTAACCATCACGACTTTTTGTGTCCAGATTTGCTGAAAATG-ATAAGGCTAACCATCACG
1 AAAGGCTAAGCATCACGACTTTTGGTGTCCAAATTGGCCGAAAAGGCA-AAGGCTAACCATCACG
* *
4632 ACTTTCGAGGAAAAAAATTACCGAAAAGGA
65 ACTTTCGACGAAAAAAATTACCGAAAAGCA
* *
4662 AAAGGCTAAGCATCACGACTTTTGGTGTTCAAATTGGCC-ATAAAGGCAAAGGTTAACCATCACG
1 AAAGGCTAAGCATCACGACTTTTGGTGTCCAAATTGGCCGA-AAAGGCAAAGGCTAACCATCACG
4726 ACTTTCGACG
65 ACTTTCGACG
4736 GCAGAATCAA
Statistics
Matches: 137, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
93 14 0.10
94 122 0.89
95 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (94 bp):
AAAGGCTAAGCATCACGACTTTTGGTGTCCAAATTGGCCGAAAAGGCAAAGGCTAACCATCACGA
CTTTCGACGAAAAAAATTACCGAAAAGCA
Found at i:6630 original size:4 final size:4
Alignment explanation
Indices: 6621--6650 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
6611 TAAAAAACTT
6621 TTAA TTAA TTAA TTAA TTAA TTAA -TAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
6651 GATAATAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:8289 original size:31 final size:31
Alignment explanation
Indices: 8246--8345 Score: 128
Period size: 31 Copynumber: 3.2 Consensus size: 31
8236 ATCCTTTTGT
*
8246 ACACGTGGCATGCCACGTGTCACTTTTTGAA
1 ACACGTGACATGCCACGTGTCACTTTTTGAA
* **
8277 ACATGTGACATGCCACGTGTCACTTTTTGGT
1 ACACGTGACATGCCACGTGTCACTTTTTGAA
* * **
8308 ACACGTGACATGACATGTGTCACTTTTTGGT
1 ACACGTGACATGCCACGTGTCACTTTTTGAA
8339 ACACGTG
1 ACACGTG
8346 GTGTGCAACA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (31 bp):
ACACGTGACATGCCACGTGTCACTTTTTGAA
Found at i:8360 original size:62 final size:61
Alignment explanation
Indices: 8240--8366 Score: 137
Period size: 62 Copynumber: 2.1 Consensus size: 61
8230 GCACGTATCC
* * * * * *
8240 TTTTGTACACGTGGCATGCCACGTGTCACTTTTTGAAACATGTGACATGCCACGTGTCACT
1 TTTTGTACACGTGACATGACACGTGTCACTTTTTGAAACACGTGACATGCAACATGTCAAT
* ** ***
8301 TTTTGGTACACGTGACATGACATGTGTCACTTTTTGGTACACGTGGTGTGCAACATGTCAAT
1 TTTT-GTACACGTGACATGACACGTGTCACTTTTTGAAACACGTGACATGCAACATGTCAAT
8363 TTTT
1 TTTT
8367 ATCCATGTGG
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
61 4 0.08
62 49 0.92
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (61 bp):
TTTTGTACACGTGACATGACACGTGTCACTTTTTGAAACACGTGACATGCAACATGTCAAT
Found at i:11013 original size:2 final size:2
Alignment explanation
Indices: 11006--11032 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10996 TTAAGAAGTC
11006 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 T
11033 GGTACTCCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12881 original size:16 final size:16
Alignment explanation
Indices: 12830--12886 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
12820 TTGGTAGGGA
*
12830 GAAAAGAATTAGGAAG
1 GAAAGGAATTAGGAAG
* *
12846 GAAAGGAAATAGCAAGG
1 GAAAGGAATTAGGAA-G
*
12863 GAAAGGAATTAGGGAG
1 GAAAGGAATTAGGAAG
*
12879 GAAGGGAA
1 GAAAGGAA
12887 AGGAAGTCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
16 20 0.61
17 13 0.39
ACGTcount: A:0.51, C:0.02, G:0.39, T:0.09
Consensus pattern (16 bp):
GAAAGGAATTAGGAAG
Found at i:13359 original size:25 final size:24
Alignment explanation
Indices: 13316--13406 Score: 96
Period size: 26 Copynumber: 3.7 Consensus size: 24
13306 TCACACAAAC
13316 AAAAA-AAA-TAGCAGCCCATTTCA
1 AAAAATAAAGTAGCAGCCCATTT-A
*
13339 AAAAATAAAGTAGCAGGCCATTTGAA
1 AAAAATAAAGTAGCAGCCCATTT--A
*
13365 AAAAATATAGTAGCAGCCCATTTA
1 AAAAATAAAGTAGCAGCCCATTTA
*
13389 ACCAAAAAAAAGTAGCAG
1 A--AAAATAAAGTAGCAG
13407 TACAAGTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
23 5 0.09
24 5 0.09
25 12 0.21
26 35 0.61
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (24 bp):
AAAAATAAAGTAGCAGCCCATTTA
Found at i:13679 original size:15 final size:15
Alignment explanation
Indices: 13656--13708 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
13646 AAAGAACTAT
*
13656 TTTCCTTCCTTCCCA
1 TTTCTTTCCTTCCCA
* *
13671 TTTCTTTCC-CCCCG
1 TTTCTTTCCTTCCCA
13685 TCTTCTTTCCTTCCCA
1 T-TTCTTTCCTTCCCA
13701 TTTCTTTC
1 TTTCTTTC
13709 GTACCAAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 4 0.13
15 23 0.74
16 4 0.13
ACGTcount: A:0.04, C:0.43, G:0.02, T:0.51
Consensus pattern (15 bp):
TTTCTTTCCTTCCCA
Found at i:18416 original size:2 final size:2
Alignment explanation
Indices: 18409--18446 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
18399 CCAATTTCCC
18409 AT AT AT 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 AT AT AT
18447 CTCCTCTACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19545 original size:24 final size:24
Alignment explanation
Indices: 19513--19568 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
19503 ACACGTGACA
*
19513 CGTGTCACCTTTTGGAACACATGG
1 CGTGCCACCTTTTGGAACACATGG
* * *
19537 CTTGCCACCTTTTGGTACACGTGG
1 CGTGCCACCTTTTGGAACACATGG
19561 CGTGCCAC
1 CGTGCCAC
19569 ATGTCATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.16, C:0.30, G:0.25, T:0.29
Consensus pattern (24 bp):
CGTGCCACCTTTTGGAACACATGG
Found at i:25130 original size:86 final size:86
Alignment explanation
Indices: 24985--25163 Score: 342
Period size: 86 Copynumber: 2.1 Consensus size: 86
24975 GTGGAAGTAA
24985 CTCAATGCCCATTAAGTGAGCTCTTGGATTTGAATCTAGTGAATACCACCGAAATAGGTGTTGGG
1 CTCAATGCCCATTAAGTGAGCTCTTGGATTTGAATCTAGTGAATACCACCGAAATAGGTGTTGGG
25050 AGAACTTTTCCCATGAAGCAT
66 AGAACTTTTCCCATGAAGCAT
*
25071 CTCAATGCCCATTAAGTGAGCTCTTGGATTTGAATCTAGTGAATGCCACCGAAATAGGTGTTGGG
1 CTCAATGCCCATTAAGTGAGCTCTTGGATTTGAATCTAGTGAATACCACCGAAATAGGTGTTGGG
25136 AGAACTTTTCCCATGAAGCAT
66 AGAACTTTTCCCATGAAGCAT
25157 C-CAATGC
1 CTCAATGC
25164 GGCTTTGTTG
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 6 0.07
86 86 0.93
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (86 bp):
CTCAATGCCCATTAAGTGAGCTCTTGGATTTGAATCTAGTGAATACCACCGAAATAGGTGTTGGG
AGAACTTTTCCCATGAAGCAT
Found at i:40953 original size:22 final size:23
Alignment explanation
Indices: 40928--40973 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40918 TTAATGGTTA
40928 GAAC-TAGTAAAAAATTTGTTGT
1 GAACATAGTAAAAAATTTGTTGT
* * *
40950 GAACATGGTAAATACTTTGTTGT
1 GAACATAGTAAAAAATTTGTTGT
40973 G
1 G
40974 TTTAGATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.37
Consensus pattern (23 bp):
GAACATAGTAAAAAATTTGTTGT
Found at i:43522 original size:21 final size:21
Alignment explanation
Indices: 43498--43537 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43488 TTTTTTTTTC
*
43498 TCATTTTCCACTATTTCTTCT
1 TCATTATCCACTATTTCTTCT
* *
43519 TCATTATCCCCTGTTTCTT
1 TCATTATCCACTATTTCTT
43538 AACTATGGGT
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:0.12, C:0.30, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTATCCACTATTTCTTCT
Found at i:58542 original size:108 final size:108
Alignment explanation
Indices: 58427--58637 Score: 379
Period size: 108 Copynumber: 2.0 Consensus size: 108
58417 TTATAAATAT
* *
58427 AAAAAAAAAGAGTCAACATTTCTTGAGCCACTTATGTCTTAACAGGGGAAATTGTCCCCATTTTG
1 AAAAAAAAAGAGTCAACATTTCTTGAGCCACTTATGACTTAACAGGGGAAATTGACCCCATTTTG
58492 ATAGTTGAGGG-GATGAAAGTTCCAAATTAAAAAAGTTCAATTC
66 ATAGTTGAGGGAG-TGAAAGTTCCAAATTAAAAAAGTTCAATTC
*
58535 AAAAAAAATGAGTCAACATTTCTTGAGCCACTTATGACTTAACAGGGGAAATTGACCCCATTTTG
1 AAAAAAAAAGAGTCAACATTTCTTGAGCCACTTATGACTTAACAGGGGAAATTGACCCCATTTTG
58600 ATAGTTGAGGGAGTGAAAGTTCCAAATTAAAAAAGTTC
66 ATAGTTGAGGGAGTGAAAGTTCCAAATTAAAAAAGTTC
58638 GATAGGGAAT
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
108 98 0.99
109 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (108 bp):
AAAAAAAAAGAGTCAACATTTCTTGAGCCACTTATGACTTAACAGGGGAAATTGACCCCATTTTG
ATAGTTGAGGGAGTGAAAGTTCCAAATTAAAAAAGTTCAATTC
Found at i:61589 original size:14 final size:14
Alignment explanation
Indices: 61570--61618 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
61560 CTGCTATGGC
61570 CAGTAAGCATCTTA
1 CAGTAAGCATCTTA
* * *
61584 CAGTAACCAACTTCG
1 CAGTAAGCATCTT-A
*
61599 CAATAAGCATCTTA
1 CAGTAAGCATCTTA
61613 CAGTAA
1 CAGTAA
61619 CCAACTTCGC
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (14 bp):
CAGTAAGCATCTTA
Found at i:61615 original size:29 final size:29
Alignment explanation
Indices: 61573--61630 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
61563 CTATGGCCAG
61573 TAAGCATCTTACAGTAACCAACTTCGCAA
1 TAAGCATCTTACAGTAACCAACTTCGCAA
61602 TAAGCATCTTACAGTAACCAACTTCGCAA
1 TAAGCATCTTACAGTAACCAACTTCGCAA
61631 CAGGGGCAAA
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:0.28, G:0.10, T:0.24
Consensus pattern (29 bp):
TAAGCATCTTACAGTAACCAACTTCGCAA
Done.