Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007313.1 Corchorus capsularis cultivar CVL-1 contig07334, 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: 29652
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3704 original size:25 final size:25
Alignment explanation
Indices: 3676--3791 Score: 198
Period size: 25 Copynumber: 4.6 Consensus size: 25
3666 CACTCATGTT
*
3676 CTTGCGTTTGGCAAACGAGCCT-TCG
1 CTTGCGTTTAGCAAACGAGCCTGT-G
*
3701 CTTGCGTTTAGCAAACGATCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTGTG
3726 CTTGCGTTTAGCAAACGAGCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTGTG
3751 CTTGCGTTTAGCAAACGAGCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTGTG
3776 CTTGCGTTTAGCAAAC
1 CTTGCGTTTAGCAAAC
3792 ACATAGGCTG
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
25 86 0.99
26 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (25 bp):
CTTGCGTTTAGCAAACGAGCCTGTG
Found at i:5434 original size:22 final size:20
Alignment explanation
Indices: 5409--5462 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
5399 TAATAATAAG
*
5409 ATTACTATTACTATTGTTATAT
1 ATTACTATTA-TATT-ATATAT
5431 ATTACTATTATATTATATAT
1 ATTACTATTATATTATATAT
5451 ATTA-TATTATAT
1 ATTACTATTATAT
5463 AATGTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 8 0.26
20 9 0.29
21 4 0.13
22 10 0.32
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTACTATTATATTATATAT
Found at i:5446 original size:5 final size:5
Alignment explanation
Indices: 5428--5462 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
5418 ACTATTGTTA
5428 TATAT TACTAT TATAT TATA- TATAT TATAT TATAT
1 TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT
5463 AATGTAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:5447 original size:16 final size:16
Alignment explanation
Indices: 5409--5462 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
5399 TAATAATAAG
*
5409 ATTACTATTACTATTGT
1 ATTA-TATTACTATTAT
5426 -TATATATTACTATTAT
1 AT-TATATTACTATTAT
5442 ATTATA-TA-TATTAT
1 ATTATATTACTATTAT
5456 ATTATAT
1 ATTATAT
5463 AATGTAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 12 0.36
15 2 0.06
16 16 0.48
17 3 0.09
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTATATTACTATTAT
Found at i:5455 original size:14 final size:14
Alignment explanation
Indices: 5436--5463 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5426 TATATATTAC
5436 TATTATATTATATA
1 TATTATATTATATA
5450 TATTATATTATATA
1 TATTATATTATATA
5464 ATGTAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTATATTATATA
Found at i:8108 original size:124 final size:124
Alignment explanation
Indices: 7925--8398 Score: 673
Period size: 124 Copynumber: 3.8 Consensus size: 124
7915 TGTGGGACTG
* * * *
7925 CCTTGCTGACGTGTCACTCTGTCGAGGAGGATGTTTCGCTGCTGGAAAGTGTTGTTGGGCACTTT
1 CCTTGCTGACGTGTCACTCTGCCGAGGAGGAGGTTTCGCTGCTGGAAAGTGCTGCTGGGCACTTT
* *
7990 CACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAGCAACATTGCTAACCTAGTGTAA
66 CACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAGCAACATTGCTAACCTGGTGCAA
* * *
8049 CCTTGCTCACGTGTCACTCTGCCGAGGAGGAGG-TTCTGCTGCTGGGAAGTGATGCTGGGCACTT
1 CCTTGCTGACGTGTCACTCTGCCGAGGAGGAGGTTTC-GCTGCTGGAAAGTGCTGCTGGGCACTT
* *
8113 TCACCAAAGTCTTATCCTTCATCAACAAAGGAGATCAGCAACATTACTAACCTGGTGCAA
65 TCACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAGCAACATTGCTAACCTGGTGCAA
* * *
8173 CCTTGCTGACGTGTCACTCTACTGAGGAGGAGGTTCCGCTGCTGGAAAGTGCTGCTGGGCACTTT
1 CCTTGCTGACGTGTCACTCTGCCGAGGAGGAGGTTTCGCTGCTGGAAAGTGCTGCTGGGCACTTT
* *
8238 CACCAAAGTCTTATCCTTCATCAATAAAGGAGGTCAGCAGCATTGCTAACCTGGTGCAA
66 CACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAGCAACATTGCTAACCTGGTGCAA
* * * * * * * *
8297 CATCGCTGACGAGTCGCTCTGCCGAGGAGAAGGTTTCGTTGCTGGAAAGTGCTGCTTGGCAC-AT
1 CCTTGCTGACGTGTCACTCTGCCGAGGAGGAGGTTTCGCTGCTGGAAAGTGCTGCTGGGCACTTT
* * *
8361 CAACCGAAGTCTTGTCCTTCATGAACAAAGGAGGTCAG
66 C-ACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAG
8399 TAGTGCGGCT
Statistics
Matches: 312, Mismatches: 35, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
123 5 0.02
124 305 0.98
125 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (124 bp):
CCTTGCTGACGTGTCACTCTGCCGAGGAGGAGGTTTCGCTGCTGGAAAGTGCTGCTGGGCACTTT
CACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCAGCAACATTGCTAACCTGGTGCAA
Found at i:8479 original size:248 final size:246
Alignment explanation
Indices: 7961--8456 Score: 550
Period size: 248 Copynumber: 2.0 Consensus size: 246
7951 GAGGATGTTT
* * *
7961 CGCTGCTGGAAAGTGTTGTTGGGCACTTTCACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCA
1 CGCTGCTGGAAAGCGCTGCTGGGCACTTTCACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCA
* * * * *
8026 GCAACATTGCTAACCTAGTGTAACCTTGCTCACGTGTCACTCTGCCGAGGAGGAGGTTCTGCTGC
66 GCAACATTGCTAACCTAGTGCAACATCGCTCACGAGTCACTCTGCCGAGGAGAAGGTTCTGCTGC
* *
8091 TGGGAAGTGATGCTGGGCACTTTCACCAAAGTCTTATCCTTCATCAACAAAGGAGATCAGCAACA
131 TGGAAAGTGATGCTGGGCACTATCACCAAAGTCTTATCCTTCATCAACAAAGGAGATCAGCAACA
* * * ** * **
8156 TTACTAACCTGGTGCAACCTTGCTGACGTGTCACTCTACTGAGGAGGAGGTTC
196 CTACTAA-C-GGTACAACCTTGCTGACGTGTCACTCCACAAAAGAGGAGGCAC
* *
8209 CGCTGCTGGAAAGTGCTGCTGGGCACTTTCACCAAAGTCTTATCCTTCATCAATAAAGGAGGTCA
1 CGCTGCTGGAAAGCGCTGCTGGGCACTTTCACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCA
* * * * *
8274 GCAGCATTGCTAACCTGGTGCAACATCGCTGACGAGTCGCTCTGCCGAGGAGAAGGTT-TCGTTG
66 GCAACATTGCTAACCTAGTGCAACATCGCTCACGAGTCACTCTGCCGAGGAGAAGGTTCT-GCTG
* * * * * * *
8338 CTGGAAAGTGCTGCTTGGCAC-ATCAACCGAAGTCTTGTCCTTCATGAACAAAGGAGGTCAGTAG
130 CTGGAAAGTGATGCTGGGCACTATC-ACCAAAGTCTTATCCTTCATCAACAAAGGAGATCAGCA-
* * * * * *
8402 TGCGGCTACTAA-GGTATAACTTTGTTGACGTGTCATTCCACCAAAAG-GGAGGCAC
193 -AC-ACTACTAACGGTACAACCTTGCTGACGTGTCACTCCA-CAAAAGAGGAGGCAC
8457 TTCTGTTGAG
Statistics
Matches: 206, Mismatches: 36, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
247 3 0.01
248 193 0.94
249 3 0.01
250 1 0.00
251 6 0.03
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (246 bp):
CGCTGCTGGAAAGCGCTGCTGGGCACTTTCACCAAAGTCTTATCCTTCATCAACAAAGGAGGTCA
GCAACATTGCTAACCTAGTGCAACATCGCTCACGAGTCACTCTGCCGAGGAGAAGGTTCTGCTGC
TGGAAAGTGATGCTGGGCACTATCACCAAAGTCTTATCCTTCATCAACAAAGGAGATCAGCAACA
CTACTAACGGTACAACCTTGCTGACGTGTCACTCCACAAAAGAGGAGGCAC
Found at i:8582 original size:137 final size:136
Alignment explanation
Indices: 8336--8680 Score: 447
Period size: 137 Copynumber: 2.5 Consensus size: 136
8326 AAGGTTTCGT
* * * * *
8336 TGCTGGAAAGTGCTGCTTGGCACATCAACCGAAGTCTTGTCCTTCATGAACAAAGGAGGTCAGTA
1 TGCTGGGAAGTGCTGC-TGGCACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGGTCAGTA
* * ** * *
8401 GTGCGGCTACTAAGGTATAACTTTGTTGACGTGTCATTCCACCAAAAGGGAGGCACTTCTGTTGA
65 GCGCGGCTACTAAGGTACAACACTGTTGACGTGTCATTCCACCAAAAGGGAAGCACTTCTGTCGA
8466 GACACGC
130 GACACGC
* * *
8473 TGCTGGGAAGTGCTGCTGGTCACTTCAACCGAGGTCCTGTTCTTCATCAACAAAGGATGTCAGTG
1 TGCTGGGAAGTGCTGCTGG-CACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGGTCAGTA
* * ** *
8538 GCGTGGCTATTGTGGTACAACACTGTTGACGTGTCATTCCACCAAGAGGGAAGCACTTCTGTCGA
65 GCGCGGCTACTAAGGTACAACACTGTTGACGTGTCATTCCACCAAAAGGGAAGCACTTCTGTCGA
8603 GACACGC
130 GACACGC
* * * * *
8610 TGCTGGGAAGTGCTGTTGGGCACTTCGATCGAAGTCCTTTTCTTCATCAACAAGGGAGGTCAGTA
1 TGCTGGGAAGTGCTGCT-GGCACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGGTCAGTA
8675 GCGCGG
65 GCGCGG
8681 TTCCCGAGGT
Statistics
Matches: 178, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
136 3 0.02
137 173 0.97
138 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (136 bp):
TGCTGGGAAGTGCTGCTGGCACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGGTCAGTAG
CGCGGCTACTAAGGTACAACACTGTTGACGTGTCATTCCACCAAAAGGGAAGCACTTCTGTCGAG
ACACGC
Found at i:8729 original size:137 final size:137
Alignment explanation
Indices: 8336--8735 Score: 415
Period size: 137 Copynumber: 2.9 Consensus size: 137
8326 AAGGTTTCGT
* * * * * *
8336 TGCTGGAAAGTGCTGCTTGGCACATCAACCGAAGTCTTGTCCTTCATGAACAAAGGAGGTCAGTA
1 TGCTGGGAAGTGCTGCTGGGCACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGGTCAGTA
* ** * ** * * * *
8401 GTGCGGCTACTAAGGTATAACTTTGTTGACGTGTCATTCCACCAA-AAGGGAGGCACTTCTGTTG
66 GCGCGGCTACCGAGGTACAACACTGCTGACGTGTCATTCCACCAAGAA-GAAAGCACTTCTGTCG
8465 AGACACGC
130 AGACACGC
* * * *
8473 TGCTGGGAAGTGCTGCTGGTCACTTCAACCGAGGTCCTGTTCTTCATCAACAAAGGATGTCAGTG
1 TGCTGGGAAGTGCTGCTGGGCACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGGTCAGTA
* ** * * * *
8538 GCGTGGCTATTGTGGTACAACACTGTTGACGTGTCATTCCACCAAGAGGGAAGCACTTCTGTCGA
66 GCGCGGCTACCGAGGTACAACACTGCTGACGTGTCATTCCACCAAGAAGAAAGCACTTCTGTCGA
8603 GACACGC
131 GACACGC
* * * * *
8610 TGCTGGGAAGTGCTGTTGGGCACTTCGATCGAAGTCCTTTTCTTCATCAACAAGGGAGGTCAGTA
1 TGCTGGGAAGTGCTGCTGGGCACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGGTCAGTA
* * * * * ** * *
8675 GCGCGGTTCCCGAGGTACAACGCTGCTGAGGTGTCGTTCTGCCGAGAAGAAAGCATTTCTG
66 GCGCGGCTACCGAGGTACAACACTGCTGACGTGTCATTCCACCAAGAAGAAAGCACTTCTG
8736 CCTAGAGTTG
Statistics
Matches: 216, Mismatches: 46, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
137 215 1.00
138 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (137 bp):
TGCTGGGAAGTGCTGCTGGGCACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGGTCAGTA
GCGCGGCTACCGAGGTACAACACTGCTGACGTGTCATTCCACCAAGAAGAAAGCACTTCTGTCGA
GACACGC
Found at i:10138 original size:2 final size:2
Alignment explanation
Indices: 10133--10157 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10123 TCTCTCTCTC
10133 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 T
10158 TAGCTTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10321 original size:44 final size:44
Alignment explanation
Indices: 10223--10323 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
10213 AAATTGTGAA
* ** * * ** *
10223 CTATAAAATTATGATAATTACATTATTAAATTTTTATAACCTCT
1 CTATAAAATTTTGATAACGACAATATGAAATTTCGAGAACCTCT
*
10267 CTATAAAATTTTGATAACGACAATATGAAATTTCGAGAACCTTT
1 CTATAAAATTTTGATAACGACAATATGAAATTTCGAGAACCTCT
10311 CTATAAAATTTTG
1 CTATAAAATTTTG
10324 TTTACCTTCC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (44 bp):
CTATAAAATTTTGATAACGACAATATGAAATTTCGAGAACCTCT
Found at i:10345 original size:23 final size:24
Alignment explanation
Indices: 10304--10360 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
10294 AAATTTCGAG
*
10304 AACCTTTCTA-TAAAATTTT-GTT
1 AACCTTCCTATTAAAATTTTAGTT
* *
10326 TACCTTCCTATTAAATTTTTAGTT
1 AACCTTCCTATTAAAATTTTAGTT
*
10350 AACCTCCCTAT
1 AACCTTCCTAT
10361 GGAATTTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 8 0.29
23 8 0.29
24 12 0.43
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.47
Consensus pattern (24 bp):
AACCTTCCTATTAAAATTTTAGTT
Found at i:10487 original size:44 final size:44
Alignment explanation
Indices: 10380--10523 Score: 123
Period size: 44 Copynumber: 3.2 Consensus size: 44
10370 AAGACTTCAT
* * *
10380 TATGAAATTTTGACAACTTCCCA-ATGAAATTTTGATAA-CTAACAC
1 TATGAAATTTTGAAAACCT-CCATATGAAATGTTGATAAGC--ACAC
** * * *
10425 TACAAAATTTTGATAACCTCCATGTGAAATGTTGATAAGCACAT
1 TATGAAATTTTGAAAACCTCCATATGAAATGTTGATAAGCACAC
* *
10469 TATGAAATTTTGAAAACCTTCATATAAAATGTT-AGTAATGACACAC
1 TATGAAATTTTGAAAACCTCCATATGAAATGTTGA-TAA-G-CACAC
10515 TATGAAATT
1 TATGAAATT
10524 GTGATAATCT
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
43 1 0.01
44 36 0.45
45 29 0.36
46 14 0.17
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (44 bp):
TATGAAATTTTGAAAACCTCCATATGAAATGTTGATAAGCACAC
Found at i:10780 original size:21 final size:21
Alignment explanation
Indices: 10754--10794 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10744 TTATCAAAAT
10754 TTTGATAACCTT-CATATGAAG
1 TTTGAT-ACCTTCCATATGAAG
*
10775 TTTGATATCTTCCATATGAA
1 TTTGATACCTTCCATATGAA
10795 ATTTAGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (21 bp):
TTTGATACCTTCCATATGAAG
Found at i:10866 original size:22 final size:22
Alignment explanation
Indices: 10243--10886 Score: 111
Period size: 22 Copynumber: 29.8 Consensus size: 22
10233 ATGATAATTA
* *
10243 CATTATTAAATTTTTATAACCT
1 CATTATGAAATTTTGATAACCT
* **
10265 C-TCTATAAAATTTTGATAACGA
1 CAT-TATGAAATTTTGATAACCT
* * *
10287 CAATATGAAATTTCGAGAACCT
1 CATTATGAAATTTTGATAACCT
* * * *
10309 -TTCTATAAAATTTTGTTTACCTT
1 CAT-TATGAAATTTTGATAACC-T
* * *
10332 C-CTATTAAATTTTTAGTTAACCT
1 CATTATGAAA-TTTT-GATAACCT
** * *
10355 CCCTATGGAATTTTGA-AGACTT
1 CATTATGAAATTTTGATA-ACCT
* *
10377 CATTATGAAATTTTGACAACTT
1 CATTATGAAATTTTGATAACCT
***
10399 CCCAATGAAATTTTGATAA-CT
1 CATTATGAAATTTTGATAACCT
* **
10420 AACACTACAAAATTTTGATAACCT
1 --CATTATGAAATTTTGATAACCT
* * * *
10444 CCA-TGTGAAATGTTGATAAGCA
1 -CATTATGAAATTTTGATAACCT
*
10466 CATTATGAAATTTTGAAAACCTT
1 CATTATGAAATTTTGATAACC-T
* * * *
10489 CA-TATAAAATGTT-AGTAATGACA
1 CATTATGAAATTTTGA-TAA--CCT
* * *
10512 CACTATGAAATTGTGATAATCT
1 CATTATGAAATTTTGATAACCT
*
10534 CGTTATGAAAGTTTT--T----T
1 CATTATGAAA-TTTTGATAACCT
* * **
10551 -TTTATAAAATTTTGATAAATAT
1 CATTATGAAATTTTGAT-AACCT
* * *
10573 CCCTT-TAAAATTTTCATAACCTT
1 -CATTATGAAATTTTGATAACC-T
10596 C-TTATGAAATTTTGATAA-C-
1 CATTATGAAATTTTGATAACCT
*
10615 C---A-CAAATTTTGATAACCT
1 CATTATGAAATTTTGATAACCT
**
10633 CCATT-TGATTTTTTTGATAACCT
1 -CATTATGA-AATTTTGATAACCT
* * * *
10656 TATTACGAAATTGTGTTAACCT
1 CATTATGAAATTTTGATAACCT
** *
10678 CCCTATGAAATTTTG--AACCA
1 CATTATGAAATTTTGATAACCT
* *
10698 CACTATGAAATTTTGA-AAACT
1 CATTATGAAATTTTGATAACCT
* * *
10719 AAACTATGAAATTTTGATAACTT
1 -CATTATGAAATTTTGATAACCT
* *
10742 CCTTATCAAAATTTTGATAACCTT
1 CATTAT-GAAATTTTGATAACC-T
* * *
10766 CA-TATG-AAGTTTGATATCTT
1 CATTATGAAATTTTGATAACCT
* *
10786 CCA-TATGAAATTTAGATTA-CT
1 -CATTATGAAATTTTGATAACCT
* * *
10807 GCATAATAAAATTTTAATAA-C-
1 -CATTATGAAATTTTGATAACCT
** * *
10828 C-TT-CCAAA-TTTGGTAACCG
1 CATTATGAAATTTTGATAACCT
10847 CATTATGAAATTTTGATAACCT
1 CATTATGAAATTTTGATAACCT
*
10869 C-TCTATGAAATTTCGATA
1 CAT-TATGAAATTTTGATA
10887 TGGAATTTTA
Statistics
Matches: 445, Mismatches: 122, Indels: 110
0.66 0.18 0.16
Matches are distributed among these distances:
15 4 0.01
16 19 0.04
17 10 0.02
18 4 0.01
19 4 0.01
20 22 0.05
21 36 0.08
22 234 0.53
23 81 0.18
24 30 0.07
25 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
CATTATGAAATTTTGATAACCT
Found at i:10903 original size:35 final size:35
Alignment explanation
Indices: 10850--10916 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
10840 GTAACCGCAT
* * *
10850 TATGAAATTTTGATAACCTCTCTATGAAATTTCGA
1 TATGAAATTTTAAAAACCTCGCTATGAAATTTCGA
* *
10885 TATGGAATTTTAAAAACCTCGCTTTGAAATTT
1 TATGAAATTTTAAAAACCTCGCTATGAAATTT
10917 TGAATAACCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (35 bp):
TATGAAATTTTAAAAACCTCGCTATGAAATTTCGA
Found at i:10954 original size:22 final size:23
Alignment explanation
Indices: 10909--11000 Score: 93
Period size: 22 Copynumber: 4.0 Consensus size: 23
10899 AACCTCGCTT
*
10909 TGAAATTTTGAATAACCTTC-CTA
1 TGAAATTTTG-ATAACCTACACTA
10932 TGAAATTTTGATAA-CTACACTA
1 TGAAATTTTGATAACCTACACTA
*
10954 T-AAAGTTTTGATAATCTGATCACTA
1 TGAAA-TTTTGATAACCT-A-CACTA
*
10979 TTAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTACACTA
11001 CAAAAATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.10
22 22 0.36
23 13 0.21
24 1 0.02
25 16 0.26
26 3 0.05
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (23 bp):
TGAAATTTTGATAACCTACACTA
Found at i:15520 original size:19 final size:18
Alignment explanation
Indices: 15496--15532 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
15486 TTGAAGATTT
15496 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
15515 CTTGAAGATTATTGAAGA
1 CTTGAAGATAATTGAAGA
15533 ATTTTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:29016 original size:17 final size:18
Alignment explanation
Indices: 28996--29032 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
28986 GCAACCTATC
28996 ACCTCATACTACCT-GGT
1 ACCTCATACTACCTAGGT
29013 ACCTCATACTACCTAGGT
1 ACCTCATACTACCTAGGT
29031 AC
1 AC
29033 TATGGGGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (18 bp):
ACCTCATACTACCTAGGT
Done.