Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016579.1 Corchorus olitorius cultivar O-4 contig16612, 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: 100557
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:133 original size:22 final size:22
Alignment explanation
Indices: 77--137 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
67 TGAATATTTT
* ** *
77 TATGAAATTTTGATAATTACCC
1 TATGTAATTTTGATAACCACAC
*
99 TATTTAAATTTTGATAACCACAC
1 TATGT-AATTTTGATAACCACAC
122 TATGTAATTTTGATAA
1 TATGTAATTTTGATAA
138 TTTACCTATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (22 bp):
TATGTAATTTTGATAACCACAC
Found at i:146 original size:22 final size:21
Alignment explanation
Indices: 77--222 Score: 89
Period size: 22 Copynumber: 6.6 Consensus size: 21
67 TGAATATTTT
77 TATGAAATTTTGATAATTACCC
1 TATGAAATTTTGATAATTA-CC
* **
99 TATTTAAATTTTGATAACCACAC
1 TA-TGAAATTTTGATAATTAC-C
*
122 TATGTAATTTTGATAATTTACC
1 TATGAAATTTTGATAA-TTACC
** *
144 TATGAAATTGCGATAAACT-CC
1 TATGAAATTTTGAT-AATTACC
* * *
165 ATATGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAA-TTACC
*
188 TATGAAATTTTAATAAACCTT-CC
1 TATGAAATTTTGAT-AA--TTACC
211 TATGAAATTTTG
1 TATGAAATTTTG
223 TAACCTTCCT
Statistics
Matches: 95, Mismatches: 20, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
21 4 0.04
22 53 0.56
23 36 0.38
24 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAATTACC
Found at i:213 original size:23 final size:21
Alignment explanation
Indices: 166--263 Score: 88
Period size: 21 Copynumber: 4.5 Consensus size: 21
156 ATAAACTCCA
* **
166 TATGAAACTTTGATAACCTAAC
1 TATGAAA-TTTTATAACCTTCC
188 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTT-AT-AACCTTCC
*
211 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTATAACCTTCC
** *
232 TATGATTTTTTATAACCTCCC
1 TATGAAATTTTATAACCTTCC
* *
253 TGTGAGATTTT
1 TATGAAATTTT
264 GTTAATCTCC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
21 36 0.57
22 10 0.16
23 17 0.27
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTATAACCTTCC
Found at i:263 original size:42 final size:43
Alignment explanation
Indices: 156--285 Score: 109
Period size: 43 Copynumber: 3.0 Consensus size: 43
146 TGAAATTGCG
* * * * ** * *
156 ATAAACTCCATATGAAACTTTGATAACCTAACTATGAAATTTTA
1 ATAACCTCCCTATGAAATTTTGTTAACCTCCCTAT-AATTTTTT
* * *
200 ATAAACCTTCCTATGAAATTTTG-TAACCTTCCTATGATTTTTT
1 AT-AACCTCCCTATGAAATTTTGTTAACCTCCCTATAATTTTTT
* * *
243 ATAACCTCCCTGTGAGATTTTGTTAATCTCCCTATAATTTTTT
1 ATAACCTCCCTATGAAATTTTGTTAACCTCCCTATAATTTTTT
286 GATACTATAG
Statistics
Matches: 69, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
42 17 0.25
43 24 0.35
44 12 0.17
45 16 0.23
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (43 bp):
ATAACCTCCCTATGAAATTTTGTTAACCTCCCTATAATTTTTT
Found at i:890 original size:29 final size:29
Alignment explanation
Indices: 857--932 Score: 145
Period size: 28 Copynumber: 2.7 Consensus size: 29
847 GGTCATTTAG
857 GGGGCATTTTGGTCATTTTTGCATGTTCA
1 GGGGCATTTTGGTCATTTTTGCATGTTCA
886 GGGGCATTTTGGTCA-TTTTGCATGTTCA
1 GGGGCATTTTGGTCATTTTTGCATGTTCA
914 GGGGCATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
933 AAGTTCACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 28 0.61
29 18 0.39
ACGTcount: A:0.13, C:0.13, G:0.29, T:0.45
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTTGCATGTTCA
Found at i:1803 original size:46 final size:46
Alignment explanation
Indices: 1736--1827 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
1726 GAATGAGCAA
1736 GGGTCATCAGGGCGTGCTAGCTTTACAAGCAAAAGTAATACAAGAC
1 GGGTCATCAGGGCGTGCTAGCTTTACAAGCAAAAGTAATACAAGAC
1782 GGGTCATCAGGGCGTGCTAGCTTTACAAGCAAAAGTAATACAAGAC
1 GGGTCATCAGGGCGTGCTAGCTTTACAAGCAAAAGTAATACAAGAC
1828 AAGGATGGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (46 bp):
GGGTCATCAGGGCGTGCTAGCTTTACAAGCAAAAGTAATACAAGAC
Found at i:7319 original size:695 final size:697
Alignment explanation
Indices: 5988--7369 Score: 2714
Period size: 695 Copynumber: 2.0 Consensus size: 697
5978 TGGAAAAAGA
5988 AAAATTCAAACTCTTTTCATGGCCACTGTACCGTATGGACATACGTTTAAGAAAAATGATATCAA
1 AAAATTCAAACTCTTTTCATGGCCACTGTACCGTATGGACATACGTTTAAGAAAAATGATATCAA
*
6053 AATTATAAATGCAACAATCATTTATTTATTATCATCATTATTTTTTGCTATATATTTATTATCAT
66 AATTACAAATGCAACAATCATTTATTTATTATCATCATTATTTTTTGCTATATATTTATTATCAT
6118 CGTTAATAATTTGGATAAGTAGTTTGAAATATATATATATATATATATAAAATAGTTTGAGTAAG
131 CGTTAATAATTTGGATAAGTAGTTTGAAATATATATATATATATATATAAAATAGTTTGAGTAAG
6183 ATTTAAACTTAAAATTAAATCATAAATAAATAATAATATATATAGTAGAAATTGGATTGGCCAAT
196 ATTTAAACTTAAAATTAAATCATAAATAAATAATAATATATATAGTAGAAATTGGATTGGCCAAT
6248 AATAATATATATAACATAATTTTAAGTAATGGCAATTTAAAATAAAAAAAGTAATGACAATTTAG
261 AATAATATATATAACATAATTTTAAGTAATGGCAATTTAAAATAAAAAAAGTAATGACAATTTAG
6313 AAATATTTTTTTAAAAAAGGTACAATCGGAAAACATAAAATTTCCATTATTCGTACTTTTATATA
326 AAATATTTTTTTAAAAAAGGTACAATCGGAAAACATAAAATTTCCATTATTCGTACTTTTATATA
*
6378 TAGTATAGATTTGGAGAAACTATTGATTTTGTCTCATTTCGGCCCAGTAGGCCCATTAGGTCCGT
391 TAGTATAGATTTGGAGAAACTAATGATTTTGTCTCATTTCGGCCCAGTAGGCCCATTAGGTCCGT
6443 TTGAGTCCATGAAGCCCAAATTGCCACGTCAAATATCTTGAAGTCTAAATCTAATATTCATAGGC
456 TTGAGTCCATGAAGCCCAAATTGCCACGTCAAATATCTTGAAGTCTAAATCTAATATTCATAGGC
6508 CCGATTCGTTAATATAGAGCGCAAAGAAAGAGTCCAAATCCAATTAGTAATTATGATGCAGTAAT
521 CCGATTCGTTAATATAGAGCGCAAAGAAAGAGTCCAAATCCAATTAGTAATTATGATGCAGTAAT
6573 GATTCAACCTTAATGCAACATTGTAAAATCCTATTTAAAGGCCGACCAAAAGAAAATCCTATATA
586 GATTCAACCTTAATGCAACATTGTAAAATCCTATTTAAAGGCCGACCAAAAGAAAATCCTATATA
6638 AAAAGGAGTACTTCAGAAGAGCAGTTTTGGAAGAAAACTGCTCTTCC
651 AAAAGGAGTACTTCAGAAGAGCAGTTTTGGAAGAAAACTGCTCTTCC
6685 AAAATTCAAACTCTTTTCATGGCCACTGTACCGTATGGACATACGTTTAAGAAAAATGATATCAA
1 AAAATTCAAACTCTTTTCATGGCCACTGTACCGTATGGACATACGTTTAAGAAAAATGATATCAA
*
6750 AATTACAAATGCAACAATCATTTATTTATTATCATCGTTATTTTTTGCTATATATTTATTATCAT
66 AATTACAAATGCAACAATCATTTATTTATTATCATCATTATTTTTTGCTATATATTTATTATCAT
6815 CGTTAATAATTTGGATAAGTAGTTTG-AA-ATATATATATATATATATAAAATAGTTTGAGTAAG
131 CGTTAATAATTTGGATAAGTAGTTTGAAATATATATATATATATATATAAAATAGTTTGAGTAAG
6878 ATTTAAACTTAAAATTAAATCATAAATAAATAATAATATATATAGTAGAAATTGGATTGGCCAAT
196 ATTTAAACTTAAAATTAAATCATAAATAAATAATAATATATATAGTAGAAATTGGATTGGCCAAT
6943 AATAATATATATAACATAATTTTAAGTAATGGCAATTTAAAATAAAAAAAGTAATGACAATTTAG
261 AATAATATATATAACATAATTTTAAGTAATGGCAATTTAAAATAAAAAAAGTAATGACAATTTAG
7008 AAATATTTTTTTAAAAAAGGTACAATCGGAAAACATAAAATTTCCATTATTCGTACTTTTATATA
326 AAATATTTTTTTAAAAAAGGTACAATCGGAAAACATAAAATTTCCATTATTCGTACTTTTATATA
*
7073 TAGTATAGATTTGGAGAAATTAATGATTTTGTCTCATTTCGGCCCAGTAGGCCCATTAGGTCCGT
391 TAGTATAGATTTGGAGAAACTAATGATTTTGTCTCATTTCGGCCCAGTAGGCCCATTAGGTCCGT
7138 TTGAGTCCATGAAGCCCAAATTGCCACGTCAAATATCTTGAAGTCTAAATCTAATATTCATAGGC
456 TTGAGTCCATGAAGCCCAAATTGCCACGTCAAATATCTTGAAGTCTAAATCTAATATTCATAGGC
7203 CCGATTCGTTAATATAGAGCGCAAAGAAAGAGTCCAAATCCAATTAGTAATTATGATGCAGTAAT
521 CCGATTCGTTAATATAGAGCGCAAAGAAAGAGTCCAAATCCAATTAGTAATTATGATGCAGTAAT
7268 GATTCAACCTTAATGCAACATTGTAAAATCCTATTTAAAGGCCGACCAAAAGAAAATCCTATATA
586 GATTCAACCTTAATGCAACATTGTAAAATCCTATTTAAAGGCCGACCAAAAGAAAATCCTATATA
7333 AAAAGGAGTACTTCAGAAGAGCAGTTTTGGAAGAAAA
651 AAAAGGAGTACTTCAGAAGAGCAGTTTTGGAAGAAAA
7370 GTCATAACTT
Statistics
Matches: 681, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
695 525 0.77
696 2 0.00
697 154 0.23
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (697 bp):
AAAATTCAAACTCTTTTCATGGCCACTGTACCGTATGGACATACGTTTAAGAAAAATGATATCAA
AATTACAAATGCAACAATCATTTATTTATTATCATCATTATTTTTTGCTATATATTTATTATCAT
CGTTAATAATTTGGATAAGTAGTTTGAAATATATATATATATATATATAAAATAGTTTGAGTAAG
ATTTAAACTTAAAATTAAATCATAAATAAATAATAATATATATAGTAGAAATTGGATTGGCCAAT
AATAATATATATAACATAATTTTAAGTAATGGCAATTTAAAATAAAAAAAGTAATGACAATTTAG
AAATATTTTTTTAAAAAAGGTACAATCGGAAAACATAAAATTTCCATTATTCGTACTTTTATATA
TAGTATAGATTTGGAGAAACTAATGATTTTGTCTCATTTCGGCCCAGTAGGCCCATTAGGTCCGT
TTGAGTCCATGAAGCCCAAATTGCCACGTCAAATATCTTGAAGTCTAAATCTAATATTCATAGGC
CCGATTCGTTAATATAGAGCGCAAAGAAAGAGTCCAAATCCAATTAGTAATTATGATGCAGTAAT
GATTCAACCTTAATGCAACATTGTAAAATCCTATTTAAAGGCCGACCAAAAGAAAATCCTATATA
AAAAGGAGTACTTCAGAAGAGCAGTTTTGGAAGAAAACTGCTCTTCC
Found at i:7694 original size:27 final size:26
Alignment explanation
Indices: 7645--7696 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
7635 TTTCCAATAT
7645 TTTAATAATGGAATAATTAAAATATTA
1 TTTAATAATGGAAT-ATTAAAATATTA
7672 TTTAATAATGGTAAT-TTAGAAATAT
1 TTTAATAATGG-AATATTA-AAATAT
7697 GTTTGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 3 0.13
27 17 0.74
28 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (26 bp):
TTTAATAATGGAATATTAAAATATTA
Found at i:8810 original size:2 final size:2
Alignment explanation
Indices: 8768--8794 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8758 CACATAATAC
8768 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 A
8795 GTAATATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17967 original size:3 final size:3
Alignment explanation
Indices: 17959--17990 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17949 GGGAAAGGAC
17959 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17991 ATGTTTAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19037 original size:3 final size:3
Alignment explanation
Indices: 19031--19079 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
19021 AACATACATT
**
19031 TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19079 T
1 T
19080 TTTATTGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:21442 original size:43 final size:43
Alignment explanation
Indices: 21383--21668 Score: 404
Period size: 43 Copynumber: 6.8 Consensus size: 43
21373 CCAATAACCA
*
21383 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
* ** *
21426 AAAGTCCTCAAACACATATATAACACAGAAGCATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
* *
21467 AAAATCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
* * *
21510 AAAGTCCTCAAACACATATATAACACAGCGGCATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
* *
21551 AAAATCCCCAAACACATATATAACACAGGGGCA--ACTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
21592 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
* *
21635 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAT
21669 TTCTCCTTAT
Statistics
Matches: 213, Mismatches: 24, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
39 2 0.01
40 1 0.00
41 98 0.46
42 3 0.01
43 109 0.51
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
Found at i:21463 original size:41 final size:41
Alignment explanation
Indices: 21383--21668 Score: 387
Period size: 41 Copynumber: 6.8 Consensus size: 41
21373 CCAATAACCA
*
21383 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCA--TCTATTAC
* **
21426 AAAGTCCTCAAACACATATATAACACAGAAGCATCTA-TATC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTATTA-C
*
21467 AAAATCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCA--TCTATTAC
* *
21510 AAAGTCCTCAAACACATATATAACACAGCGGCATCTA-TATC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTATTA-C
* *
21551 AAAATCCCCAAACACATATATAACACAGGGGCAACTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTATTAC
21592 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGGCA--TCTATTAC
* *
21635 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAT
21669 TTCTCCTTAT
Statistics
Matches: 216, Mismatches: 19, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
40 3 0.01
41 106 0.49
42 2 0.01
43 103 0.48
44 2 0.01
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTATTAC
Found at i:21484 original size:84 final size:84
Alignment explanation
Indices: 21381--21668 Score: 436
Period size: 84 Copynumber: 3.4 Consensus size: 84
21371 ACCCAATAAC
*
21381 CAAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAGTCCTCAAACACATATA
1 CAAAA-TCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATA
*
21446 TAACACAGAAGCATCTATAT
65 TAACACAGAGGCATCTATAT
*
21466 CAAAATCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATAT
1 CAAAATCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATAT
*
21531 AACACAGCGGCATCTATAT
66 AACACAGAGGCATCTATAT
* *
21550 CAAAATCCCCAAACACATATATAACACAGGGGCA--ACTATTACAAAGTCCCCAAACACATATAT
1 CAAAATCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATAT
* *
21613 AACACAGGGGCATCTCTATT
66 AACACAGAGGCATCTATA-T
* * *
21633 ACAAAGTCCTCAAACACATATATAACACAGAGGCAT
1 -CAAAATCCCCAAACACATATATAACACAGGGGCAT
21669 TTCTCCTTAT
Statistics
Matches: 189, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
82 43 0.23
83 1 0.01
84 140 0.74
85 5 0.03
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (84 bp):
CAAAATCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATAT
AACACAGAGGCATCTATAT
Found at i:24612 original size:503 final size:503
Alignment explanation
Indices: 23661--24671 Score: 1574
Period size: 503 Copynumber: 2.0 Consensus size: 503
23651 CATTCTCATT
*
23661 AATT-AGGATCCAACATGGCCAATAGGAATGCTCCACATCATCTGTAGTATCTAAATTTCGCCCA
1 AATTGAGGATCCAACATGGCCAATAGGAATGCTCCACATCATCTGTAGTATATAAATTTCGCCCA
* * * *
23725 AAACATTCTCCAAGTTAGTTTAGGAGAAGATCAATTCTGTCCATAAATTTCAAGGGCAAAATTGT
66 AAACATTCTCCAAGTCAGTTAAGGAGAAGATCAATTCAGTCCATAAATTTCAAGGGCAAAATCGT
* * *
23790 CCATTGGAACGGTAGAATTAGGTCTTGAGGCAAACATAAAAGTTGTAGATCTTGGAATCCTCTTT
131 CCACTGGAACGGCAGAATTAGGTCTTGAGGCAAACATAAAAGTTGTAGACCTTGGAATCCTCTTT
* * *
23855 CCAACAGTACCTCATTTGCATTTTTCTAAGCTCTAAATCAAAAGTTATGAATTTTCTTCCAAAAC
196 CCAACAGTACCTCATTTGAATTTTTCTAAACTCTAAATCAAAAATTATGAATTTTCTTCCAAAAC
* *
23920 TACTCTTGTGAAGTCCTCCTATAAATATGATTTAACAATGCTGCATCAGGGCTGAATCATTACTG
261 TACTCTTATGAAGTCCTCCTATAAATAGGATTTAACAATGCTGCATCAGGGCTGAATCATTACTG
* * * **
23985 CATCATAATTACTGATTGGACTTTGACTCCTTCTTTGGGCTTCCATATTAACGAGTTGAGTCTAA
326 CATCATAATTACTGATTGGACTTGGACTCCTTCTTTGGGCTTCCATAATAACGAATTGACCCTAA
* * * *
24050 GAATATCAGATTTAGCTTTCAGGACATCTAGCTTGGCAATTTGCGTTTCATAGACTCAAACGGGC
391 GAATATCAGATTTAGCTTTAAGAACATCTAACTTGGCAATTTGCGTTTCATAGACTCAAACAGGC
*
24115 TTAATGGGCCTACTAGGCCGAAATGAGACAAAATCAGTAGTTTCTCCA
456 CTAATGGGCCTACTAGGCCGAAATGAGACAAAATCAGTAGTTTCTCCA
* * ** * *
24163 AATTGAGGATCCAACGTGGCCAATAGGAATGTTGTACATCATCTGTAGTATATGAATTTCGTCCA
1 AATTGAGGATCCAACATGGCCAATAGGAATGCTCCACATCATCTGTAGTATATAAATTTCGCCCA
* **
24228 AAACATTCTCCAAGTCGGTTAAGGAGAAGATCAATTCAGTCCATAGCTTTCAAGGGCAAAATCGT
66 AAACATTCTCCAAGTCAGTTAAGGAGAAGATCAATTCAGTCCATAAATTTCAAGGGCAAAATCGT
* * *
24293 TCACTGGAACGGCAGAATTAGGTTTTGAGGTAAACATAAAAGTTGTAGACCTTGGAATCCTCTTT
131 CCACTGGAACGGCAGAATTAGGTCTTGAGGCAAACATAAAAGTTGTAGACCTTGGAATCCTCTTT
* * * * *
24358 CCAACGGTACCTTATTTGAATTTTTCTAAATTCTACATCAAAAATTATGAATTTTCTTCCAAAAT
196 CCAACAGTACCTCATTTGAATTTTTCTAAACTCTAAATCAAAAATTATGAATTTTCTTCCAAAAC
* * * *
24423 TGCTCTTATGAAGTCCTCCTTTGAATAGGATTTAACAATGCTGCATCATGGCTGAATCATTACTG
261 TACTCTTATGAAGTCCTCCTATAAATAGGATTTAACAATGCTGCATCAGGGCTGAATCATTACTG
* *
24488 CATCATAATTACTGATTGGACTTGGACTCTTTCTTTGGGCTTCCATAATAACGAATTGTCCCTAA
326 CATCATAATTACTGATTGGACTTGGACTCCTTCTTTGGGCTTCCATAATAACGAATTGACCCTAA
* * *
24553 GAATATCAGATTTAGGTTTAAGAACATCTAACTTGGCAATTTGGGTTTCATGGACTCAAACAGGC
391 GAATATCAGATTTAGCTTTAAGAACATCTAACTTGGCAATTTGCGTTTCATAGACTCAAACAGGC
24618 CTAATGGGCCTACTAGGCCGAAATGAGACAAAATCAGTAGTTTCTCCA
456 CTAATGGGCCTACTAGGCCGAAATGAGACAAAATCAGTAGTTTCTCCA
24666 AATTGA
1 AATTGA
24672 TCCAAATGGA
Statistics
Matches: 459, Mismatches: 49, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
502 4 0.01
503 455 0.99
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (503 bp):
AATTGAGGATCCAACATGGCCAATAGGAATGCTCCACATCATCTGTAGTATATAAATTTCGCCCA
AAACATTCTCCAAGTCAGTTAAGGAGAAGATCAATTCAGTCCATAAATTTCAAGGGCAAAATCGT
CCACTGGAACGGCAGAATTAGGTCTTGAGGCAAACATAAAAGTTGTAGACCTTGGAATCCTCTTT
CCAACAGTACCTCATTTGAATTTTTCTAAACTCTAAATCAAAAATTATGAATTTTCTTCCAAAAC
TACTCTTATGAAGTCCTCCTATAAATAGGATTTAACAATGCTGCATCAGGGCTGAATCATTACTG
CATCATAATTACTGATTGGACTTGGACTCCTTCTTTGGGCTTCCATAATAACGAATTGACCCTAA
GAATATCAGATTTAGCTTTAAGAACATCTAACTTGGCAATTTGCGTTTCATAGACTCAAACAGGC
CTAATGGGCCTACTAGGCCGAAATGAGACAAAATCAGTAGTTTCTCCA
Found at i:26840 original size:30 final size:30
Alignment explanation
Indices: 26804--26895 Score: 175
Period size: 30 Copynumber: 3.1 Consensus size: 30
26794 CATTCTTCAC
*
26804 CAGAAAACTCGTCAATACAGCTTGAAATGG
1 CAGAAAACTCGTCAACACAGCTTGAAATGG
26834 CAGAAAACTCGTCAACACAGCTTGAAATGG
1 CAGAAAACTCGTCAACACAGCTTGAAATGG
26864 CAGAAAACTCGTCAACACAGCTTGAAATGG
1 CAGAAAACTCGTCAACACAGCTTGAAATGG
26894 CA
1 CA
26896 TCTCTTAGTA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (30 bp):
CAGAAAACTCGTCAACACAGCTTGAAATGG
Found at i:30333 original size:31 final size:31
Alignment explanation
Indices: 30298--30357 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
30288 AAAAAATTGA
* * *
30298 TCAATTTAGTTCTTTTACTCACAAGATTCAG
1 TCAATTTAGTCCCTCTACTCACAAGATTCAG
30329 TCAATTTAGTCCCTCTACTCACAAGATTC
1 TCAATTTAGTCCCTCTACTCACAAGATTC
30358 GATTAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (31 bp):
TCAATTTAGTCCCTCTACTCACAAGATTCAG
Found at i:30371 original size:31 final size:31
Alignment explanation
Indices: 30313--30371 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
30303 TTAGTTCTTT
*
30313 TACTCACAAGATTCAGTCAATTTAGTCCCTC
1 TACTCACAAGATTCAGTCAATTGAGTCCCTC
*
30344 TACTCACAAGATTC-GATTAATTGAGTCC
1 TACTCACAAGATTCAG-TCAATTGAGTCC
30372 AATCAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (31 bp):
TACTCACAAGATTCAGTCAATTGAGTCCCTC
Found at i:37351 original size:26 final size:26
Alignment explanation
Indices: 37322--37382 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
37312 ACAAATTATT
**
37322 CAAACAGCATTACGGAGTGACCAATA
1 CAAACAGCATTAAAGAGTGACCAATA
37348 CAAACAGCATTAAAGAGTGACCAATA
1 CAAACAGCATTAAAGAGTGACCAATA
37374 CAAA-AGCAT
1 CAAACAGCAT
37383 ACATTTCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
25 5 0.15
26 28 0.85
ACGTcount: A:0.48, C:0.21, G:0.16, T:0.15
Consensus pattern (26 bp):
CAAACAGCATTAAAGAGTGACCAATA
Found at i:38749 original size:8 final size:8
Alignment explanation
Indices: 38732--38760 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
38722 AAATGCGAGC
38732 AGAG-GTG
1 AGAGAGTG
38739 AGAGAGTG
1 AGAGAGTG
38747 AGAGAGTG
1 AGAGAGTG
38755 AGAGAG
1 AGAGAG
38761 AGGGTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.52, T:0.10
Consensus pattern (8 bp):
AGAGAGTG
Found at i:46070 original size:24 final size:24
Alignment explanation
Indices: 46013--46071 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
46003 AAGTAATAAC
* **
46013 AATAAGGAAAATACATTATTTCAA
1 AATAAAGAAAATACATTAACTCAA
*
46037 AATAAGGAAAATACATTAAACTCAA
1 AATAAAGAAAATACATT-AACTCAA
46062 AA-AAAGAAAA
1 AATAAAGAAAA
46072 CTTATTTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.20
Consensus pattern (24 bp):
AATAAAGAAAATACATTAACTCAA
Found at i:61077 original size:45 final size:45
Alignment explanation
Indices: 61028--61168 Score: 202
Period size: 45 Copynumber: 3.2 Consensus size: 45
61018 AGCAACAATT
61028 AATATTAGGTTTTTTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGGTTTTTTTTGATGAATTACCTAGAGATGGAGGAGTAG
* * * *
61073 AATATTAGCTTTATTTTGATGAATTACTTAGAGATGGAGGAGTAT
1 AATATTAGGTTTTTTTTGATGAATTACCTAGAGATGGAGGAGTAG
61118 AATATTA-GTTTTATTTTGATGAATTACCTAGAGAT-GA--AGTAG
1 AATATTAGGTTTT-TTTTGATGAATTACCTAGAGATGGAGGAGTAG
61160 AAT-TTAGGT
1 AATATTAGGT
61169 AATACTCTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
41 3 0.03
42 9 0.10
44 5 0.06
45 69 0.80
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (45 bp):
AATATTAGGTTTTTTTTGATGAATTACCTAGAGATGGAGGAGTAG
Found at i:61611 original size:2 final size:2
Alignment explanation
Indices: 61604--61672 Score: 96
Period size: 2 Copynumber: 37.5 Consensus size: 2
61594 TAACTTTTTC
61604 AT AT AT AT AT AT AT AT -T AT AT -T AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61643 AT A- AT AT AT A- AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61673 GATTCTAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
1 6 0.10
2 55 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61632 original size:9 final size:9
Alignment explanation
Indices: 61604--61671 Score: 88
Period size: 9 Copynumber: 7.9 Consensus size: 9
61594 TAACTTTTTC
61604 ATATATA-T
1 ATATATATT
61612 ATATATATT
1 ATATATATT
61621 ATAT-TA-T
1 ATATATATT
*
61628 ATATATATA
1 ATATATATT
*
61637 ATATATATA
1 ATATATATT
*
61646 ATATATAAT
1 ATATATATT
61655 ATATATATT
1 ATATATATT
61664 ATATATAT
1 ATATATAT
61672 AGATTCTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
7 5 0.09
8 11 0.21
9 37 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
ATATATATT
Found at i:70805 original size:24 final size:24
Alignment explanation
Indices: 70773--70818 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
70763 CAATTAAGGA
70773 TATAACGTTACAAAACAAGTAAAT
1 TATAACGTTACAAAACAAGTAAAT
* *
70797 TATAACGTTACAGAACGAGTAA
1 TATAACGTTACAAAACAAGTAA
70819 TTAAGGATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (24 bp):
TATAACGTTACAAAACAAGTAAAT
Found at i:75598 original size:16 final size:14
Alignment explanation
Indices: 75566--75599 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
75556 ACAAACTTAG
75566 ATATGAATTATGAA
1 ATATGAATTATGAA
75580 ATATGTAATTATGGAA
1 ATATG-AATTAT-GAA
75596 ATAT
1 ATAT
75600 TATCAACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 6 0.33
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (14 bp):
ATATGAATTATGAA
Found at i:76516 original size:16 final size:16
Alignment explanation
Indices: 76495--76526 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
76485 GAAAATCTTG
76495 TGGGGAGAATAGAGTA
1 TGGGGAGAATAGAGTA
76511 TGGGGAGAATAGAGTA
1 TGGGGAGAATAGAGTA
76527 GAGAAGGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.44, T:0.19
Consensus pattern (16 bp):
TGGGGAGAATAGAGTA
Found at i:81397 original size:19 final size:20
Alignment explanation
Indices: 81349--81409 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
81339 ATCGCTGCTC
81349 TAATAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
*
81369 TACATAATCTAATCTGTACAG
1 TA-ATAATCTCATCTGTACAG
* *
81390 T-GTAATCTCATATGTACAG
1 TAATAATCTCATCTGTACAG
81409 T
1 T
81410 TGCCAAACAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 16 0.44
20 2 0.06
21 18 0.50
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
TAATAATCTCATCTGTACAG
Found at i:83794 original size:330 final size:329
Alignment explanation
Indices: 82843--84018 Score: 1354
Period size: 336 Copynumber: 3.6 Consensus size: 329
82833 TCCTTTGTTA
* *
82843 CCAAAAACCGTGATGG-TA-TACACGATTTCAGTTAAAATTTTGCAAAAATTTACCCGAAAGAAT
1 CCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAA-AA-
* * * *
82906 TTTCCTAAATTTTTTTGCCATGATACTCATAAAAAACTATATAATTCAACGCCAAAAAGATTGAA
64 TTTCCTCAA-TTTTTGGCCACGATACTCATAAAAAA-TATATAACTCAACGCCAAAAAGATTGAA
** *
82971 AG-----G-GTTT-TAAATATCGGTTTTACTATTTTTTCCAAATTAATTTCTAATTAAATCGAAA
127 AGCTTTCGCGTTTCTAAATATCCTTTTTACTATTTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * *
83029 CATGATTCAGATGCTCATAAAAACAAATCCTTAAATCCAATATGGTTGAGATTTGGTTAGATGGA
192 CATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGGA
* * *
83094 TATAGATATTTCAATGAGACTTGGCGCCAAAAATTATACAAAACAGAGCCGGGACTAC-GAATCG
257 TATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGACGGGACTACGGAA-CG
83158 CGTTTTTAG
321 CGTTTTTAG
* * * * *
83167 TCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACACGAAACATT
1 CCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAAATT
** * * ** *
83232 TCTCGTCAATTTCCGGCCACCATATTCATAAAAAATATATAACTCAACGTTAAAAAGATTGAAGG
66 TC-C-TCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAA-A
* * ** *
83297 GCTTCTCACGCTTCTAATATTATTATTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCG
128 GCTT-TCGCGTTTCTAA-A-TA-TCCTTTTTACTATTTTTTCCGAATTAATTTCTAATTAAATCG
** * ** **
83362 AAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTACCTGAGATTTCATTAGAT
189 AAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGAT
** * * * *
83427 AAATATAGATATTTCAATGAGTCTTGACGCAAAAAATCATGCAAAACTGAGACGGGACTACGGAA
254 GGATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGACGGGACTACGGAA
*
83492 CGTGTTTTTAG
319 CGCGTTTTTAG
* * *
83503 CCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGAAT
1 CCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAA-AAT
* * * *
83568 TACCTCAATTTTTGGCCACGATACTCATAAAAAATATAAAATTCAACACCAAAAAGATTGAAAGA
65 TTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAAG-
* * * *
83633 CTATTCGCGTTTCTAAA-ATCCTTTTTCCTA-TTTTTCCGAATTAATTCCCAATTGAATCGAAAC
129 CT-TTCGCGTTTCTAAATATCCTTTTTACTATTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * *
83696 ATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTAAGATTTGGTTAGATGGAT
193 ATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGGAT
* * * * *
83761 ATACATATTTCAATGAGACTTGGCGCCAAAAATCGTGCAAAACAGAGGCAGGG-CTCCGGAATGC
258 ATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGAC-GGGACTACGGAACGC
83825 GTTTTTAG
322 GTTTTTAG
* *
83833 TCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAGAAATT
1 CCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGA-AAAAT
* * * ** *
83898 TCTCCTCAATTTTGGGCCACAATACTAATAAAAAATATATAACTCAACGCCAAAAAGACGGAAGG
65 T-TCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAA-A
* * * * * *
83963 GTTTCTCACGCTTCT-AATATCGTTTTTCCTACCTTTTTCCGAATTAATTTCTAATT
128 GCTT-TCGCGTTTCTAAATATCCTTTTTACTA-TTTTTTCCGAATTAATTTCTAATT
84019 TAGAAATATA
Statistics
Matches: 711, Mismatches: 113, Indels: 47
0.82 0.13 0.05
Matches are distributed among these distances:
324 43 0.06
325 25 0.04
326 40 0.06
330 202 0.28
331 87 0.12
332 5 0.01
333 24 0.03
334 3 0.00
335 63 0.09
336 212 0.30
337 7 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (329 bp):
CCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAAATT
TCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAAGCT
TTCGCGTTTCTAAATATCCTTTTTACTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATG
ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGGATATA
GATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGACGGGACTACGGAACGCGTTT
TTAG
Found at i:84207 original size:95 final size:98
Alignment explanation
Indices: 84045--84230 Score: 279
Period size: 95 Copynumber: 1.9 Consensus size: 98
84035 AAAAGTATAC
* * ** *
84045 AAAATTATATTTTAATAATGGCATAGTTAAAATATATTTTAATCTTGACAATTTAAAAATATGTT
1 AAAATTATATTTTAATAATGACATAATTAAAATATATTTTAATAATGACAATTTAAAAATATATT
84110 TGAAAAAAAT-AGTACAATCGGAAAAAATACAT
66 TGAAAAAAATGAGTACAATCGGAAAAAATACAT
*
84142 AAAATTATATTTTAATAATGACATAATT-AAA-ATATTTTAATAATGACAATTTAGAAATATATT
1 AAAATTATATTTTAATAATGACATAATTAAAATATATTTTAATAATGACAATTTAAAAATATATT
* *
84205 TGAAAAAAATGGGTATAATCGGAAAA
66 TGAAAAAAATGAGTACAATCGGAAAA
84231 CATAAAGTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
95 38 0.47
96 16 0.20
97 26 0.32
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.35
Consensus pattern (98 bp):
AAAATTATATTTTAATAATGACATAATTAAAATATATTTTAATAATGACAATTTAAAAATATATT
TGAAAAAAATGAGTACAATCGGAAAAAATACAT
Found at i:84438 original size:16 final size:15
Alignment explanation
Indices: 84410--84450 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
84400 CGTTTTCGTT
84410 TTTCTGTTTTTTT-G
1 TTTCTGTTTTTTTCG
84424 TTTCTGTTTCGTTTTCG
1 TTTCTGTTT--TTTTCG
84441 -TTCTGTTTTT
1 TTTCTGTTTTT
84451 GTTGCGCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 11 0.46
16 12 0.50
17 1 0.04
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (15 bp):
TTTCTGTTTTTTTCG
Found at i:85962 original size:11 final size:11
Alignment explanation
Indices: 85933--85963 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
85923 TTTTCAAGAC
*
85933 TCAAGTTCCTT
1 TCAAGTTTCTT
85944 TCAAGTTTCTT
1 TCAAGTTTCTT
85955 TCAAGTTTC
1 TCAAGTTTC
85964 AACATTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (11 bp):
TCAAGTTTCTT
Found at i:86172 original size:3 final size:3
Alignment explanation
Indices: 86164--86197 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
86154 AGTATTTACC
*
86164 CAA CAA CAA CAA CAAA CAA CAA CGA CAA CAA CAA
1 CAA CAA CAA CAA C-AA CAA CAA CAA CAA CAA CAA
86198 ATTCCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.32, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:86185 original size:16 final size:16
Alignment explanation
Indices: 86164--86194 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
86154 AGTATTTACC
86164 CAACAACAACAACAAA
1 CAACAACAACAACAAA
*
86180 CAACAACGACAACAA
1 CAACAACAACAACAA
86195 CAAATTCCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.32, G:0.03, T:0.00
Consensus pattern (16 bp):
CAACAACAACAACAAA
Found at i:89040 original size:30 final size:30
Alignment explanation
Indices: 88986--89044 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
88976 TTTTTCTAAA
* * **
88986 TTATTGACGAGTTTATTGCCAAAAAAAAAG
1 TTATTGACGAGTTGACTGAAAAAAAAAAAG
89016 TTATTGACGAGTTGACTGAAAAAAAAAAA
1 TTATTGACGAGTTGACTGAAAAAAAAAAA
89045 TCGTAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.27
Consensus pattern (30 bp):
TTATTGACGAGTTGACTGAAAAAAAAAAAG
Found at i:90796 original size:13 final size:13
Alignment explanation
Indices: 90775--90888 Score: 65
Period size: 13 Copynumber: 8.5 Consensus size: 13
90765 CTAAGAACGG
*
90775 CAAATATTACTTA
1 CAAAAATTACTTA
*
90788 CAAAAATTACATA
1 CAAAAATTACTTA
*
90801 CAATAATAATTAACATA
1 C-A-AA-AATT-ACTTA
90818 -AAAAATTACTTA
1 CAAAAATTACTTA
90830 CAAAAATTA-TATA
1 CAAAAATTACT-TA
* *
90843 CAATAA-TAATTA
1 CAAAAATTACTTA
*
90855 CAAACATATTTCTGT-
1 CAAA-A-ATTACT-TA
*
90870 CAAATATTACTTA
1 CAAAAATTACTTA
90883 CAAAAA
1 CAAAAA
90889 AATATTTTGG
Statistics
Matches: 79, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
12 13 0.16
13 43 0.54
14 4 0.05
15 9 0.11
16 5 0.06
17 5 0.06
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (13 bp):
CAAAAATTACTTA
Found at i:91080 original size:32 final size:32
Alignment explanation
Indices: 91043--91104 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
91033 CACCACGGGG
* * *
91043 CGTGCCGTCCTCAGGGGATGGCAAGCCATGAT
1 CGTGCCATCCTCAAGGGACGGCAAGCCATGAT
*
91075 CGTGCCATCCTCAAGGGACGGCACGCCATG
1 CGTGCCATCCTCAAGGGACGGCAAGCCATG
91105 GGCATGGCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.16
Consensus pattern (32 bp):
CGTGCCATCCTCAAGGGACGGCAAGCCATGAT
Found at i:91786 original size:23 final size:22
Alignment explanation
Indices: 91753--91795 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
91743 CACATATCAC
91753 AATTAAATATAATTTTTAGTGA
1 AATTAAATATAATTTTTAGTGA
*
91775 AATTATAATATATTTTTTAGT
1 AATTA-AATATAATTTTTAGT
91796 AAAGTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
AATTAAATATAATTTTTAGTGA
Found at i:92782 original size:33 final size:33
Alignment explanation
Indices: 92710--92794 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
92700 AATGGTCGGT
* * *
92710 GCCGCCCTGCTAGGGCGGCATGGACTTGGCCAT
1 GCCGCCCTGCTAGGGCGGCATGGACATAGCCAC
* * * *
92743 GGCGCCCTCCTTGGGCGGCATGGTCATAGCCAC
1 GCCGCCCTGCTAGGGCGGCATGGACATAGCCAC
92776 GCCGCCCTGCTAGGGCGGC
1 GCCGCCCTGCTAGGGCGGC
92795 GCCGACCAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.11, C:0.36, G:0.36, T:0.16
Consensus pattern (33 bp):
GCCGCCCTGCTAGGGCGGCATGGACATAGCCAC
Found at i:93105 original size:29 final size:28
Alignment explanation
Indices: 93066--93121 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
93056 GTTATTCCAC
*
93066 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
93095 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
93122 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:100211 original size:39 final size:40
Alignment explanation
Indices: 100155--100235 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
100145 TTTAATTCCT
100155 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
100195 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
100234 AT
1 AT
100236 TCTTAGGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Done.