Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006006.1 Corchorus capsularis cultivar CVL-1 contig06024, 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: 20600
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:774 original size:50 final size:51
Alignment explanation
Indices: 695--1022 Score: 269
Period size: 50 Copynumber: 6.7 Consensus size: 51
685 GATATTTGGC
* *
695 TAAAAGATGTAACCTTTG-GATAAAAGATTGAATTTTTA-AGCAATTAGTAAA
1 TAAAA-ATGTCACCTTTGAG-TAAAAGATTGAATTTTTAGAGTAATTAGTAAA
* * *
746 TAAAAATGTTATCTTT-AGGTAAAAGATTGAA-TTTTAGGGTAATTAGTAAA
1 TAAAAATGTCACCTTTGA-GTAAAAGATTGAATTTTTAGAGTAATTAGTAAA
* * * *
796 TAAAGATGTGACCTTTGAGTAGAAGTTTG---TTTT----T--TT--TAAA
1 TAAAAATGTCACCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAA
* * *
836 TAAAAATATCATCTTT-AGGTAAAAGATTGAA-TTTTAGGGTAATTAGTAAA
1 TAAAAATGTCACCTTTGA-GTAAAAGATTGAATTTTTAGAGTAATTAGTAAA
* * * ** *
886 TAAAGATGTGACCTTTGAGTAGAAGATTGTTTTTTTTA-AGTAATTAATAAA
1 TAAAAATGTCACCTTTGAGTAAAAGATTG-AATTTTTAGAGTAATTAGTAAA
* *
937 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAA
1 TAAAAATGTCACCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAA
* * * *
988 TAAAGATTTAACCTTTGAATAAAAGATTGAATTTT
1 TAAAAATGTCACCTTTGAGTAAAAGATTGAATTTT
1023 CAAGTAAATA
Statistics
Matches: 220, Mismatches: 38, Indels: 38
0.74 0.13 0.13
Matches are distributed among these distances:
39 1 0.00
40 25 0.11
42 6 0.03
44 1 0.00
46 1 0.00
48 6 0.03
49 5 0.02
50 86 0.39
51 84 0.38
52 5 0.02
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.38
Consensus pattern (51 bp):
TAAAAATGTCACCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAA
Found at i:895 original size:90 final size:90
Alignment explanation
Indices: 742--1016 Score: 361
Period size: 90 Copynumber: 2.9 Consensus size: 90
732 AAGCAATTAG
* *
742 TAAATAAAAATGTTATCTTTAGGTAAAAGATTGAATTTTAGGGTAATTAGTAAATAAAGATGTGA
1 TAAATAAAAATATCATCTTTAGGTAAAAGATTGAATTTTAGGGTAATTAGTAAATAAAGATGTGA
*
807 CCTTTGAGTAGAAGTTTGTTTTTTT
66 CCTTTGAGTAGAAGATTGTTTTTTT
832 TAAATAAAAATATCATCTTTAGGTAAAAGATTGAATTTTAGGGTAATTAGTAAATAAAGATGTGA
1 TAAATAAAAATATCATCTTTAGGTAAAAGATTGAATTTTAGGGTAATTAGTAAATAAAGATGTGA
897 CCTTTGAGTAGAAGATTGTTTTTTT
66 CCTTTGAGTAGAAGATTGTTTTTTT
* *
922 TAAGTAATTAATAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAA
1 T-A--AA-TAA-AAAT----A--TCATCTTTAGGTAAAAGATTGAA-TTTTAGGGTAATTAGTAA
* * * *
987 ATAAAGATTTAACCTTTGAATAAAAGATTG
54 ATAAAGATGTGACCTTTGAGTAGAAGATTG
1017 AATTTTCAAG
Statistics
Matches: 164, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
90 88 0.54
91 1 0.01
93 2 0.01
94 3 0.02
95 4 0.02
99 1 0.01
101 22 0.13
102 43 0.26
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.39
Consensus pattern (90 bp):
TAAATAAAAATATCATCTTTAGGTAAAAGATTGAATTTTAGGGTAATTAGTAAATAAAGATGTGA
CCTTTGAGTAGAAGATTGTTTTTTT
Found at i:939 original size:51 final size:51
Alignment explanation
Indices: 854--1022 Score: 207
Period size: 51 Copynumber: 3.3 Consensus size: 51
844 TCATCTTTAG
* *
854 GTAAAAGATTGAA-TTTTAGGGTAATTAGTAAATAAAGATGTGACCTTTGA
1 GTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATGTAACCTTTGA
* ** * * * * *
904 GTAGAAGATTGTTTTTTTTA-AGTAATTAATAAATAAAAATGTCATCTTTGG
1 GTAAAAGATTG-AATTTTTAGAGTAATTAGTAAATAAAGATGTAACCTTTGA
*
955 GTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGA
1 GTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATGTAACCTTTGA
*
1006 ATAAAAGATTGAATTTT
1 GTAAAAGATTGAATTTT
1023 CAAGTAAATA
Statistics
Matches: 97, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
50 16 0.16
51 76 0.78
52 5 0.05
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.38
Consensus pattern (51 bp):
GTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATGTAACCTTTGA
Found at i:972 original size:140 final size:140
Alignment explanation
Indices: 715--973 Score: 292
Period size: 140 Copynumber: 1.9 Consensus size: 140
705 AACCTTTGGA
* *
715 TAAAAGATTGAATTTTTAAGCAATTAGTAAATAAAAATGTTATCTTTAGGTAAAAGATTGAATTT
1 TAAAAGATTGAATTTTTAAGCAATTAGTAAATAAAAATGTGACCTTTAGGTAAAAGATTGAATTT
* * * * * * **
780 TAGGGTAATTAGTAAATAAAGATGTGACCTTTGAGTAGAAGTTTGTTTTTTTTAAATAAAAATAT
66 TAGAGTAATTAATAAATAAAAATGTCACCTTTGAGTAAAAGATTGTAATTTTTAAATAAAAATAT
845 CATCTTTAGG
131 CATCTTTAGG
* * * * *
855 TAAAAGATTGAA-TTTTAGGGTAATTAGTAAATAAAGATGTGACCTTT-GAGTAGAAGATTGTTT
1 TAAAAGATTGAATTTTTA-AGCAATTAGTAAATAAAAATGTGACCTTTAG-GTAAAAGATTG--A
* * *
918 TTTTTA-AGTAATTAATAAATAAAAATGTCATCTTTGGGTAAAAGATTG-AATTTTTA
62 ATTTTAGAGTAATTAATAAATAAAAATGTCACCTTTGAGTAAAAGATTGTAATTTTTA
974 GAGTAATTAG
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
139 6 0.06
140 52 0.54
141 34 0.35
142 5 0.05
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.39
Consensus pattern (140 bp):
TAAAAGATTGAATTTTTAAGCAATTAGTAAATAAAAATGTGACCTTTAGGTAAAAGATTGAATTT
TAGAGTAATTAATAAATAAAAATGTCACCTTTGAGTAAAAGATTGTAATTTTTAAATAAAAATAT
CATCTTTAGG
Found at i:1014 original size:102 final size:101
Alignment explanation
Indices: 832--1016 Score: 298
Period size: 102 Copynumber: 1.8 Consensus size: 101
822 TTGTTTTTTT
* *
832 TAAATAAAAATATCATCTTTAGGTAAAAGATTGAATTTTAGGGTAATTAGTAAATAAAGATGTGA
1 TAAATAAAAATATCATCTTTAGGTAAAAGATTGAATTTTAGAGTAATTAGTAAATAAAGATGTAA
* *
897 CCTTTGAGTAGAAGATTGTTTTTTTTAAGTAATTAA
66 CCTTTGAATAAAAGATTGTTTTTTTTAAGTAATTAA
* * *
933 TAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTA
1 TAAATAAAAATATCATCTTTAGGTAAAAGATTGAA-TTTTAGAGTAATTAGTAAATAAAGATGTA
998 ACCTTTGAATAAAAGATTG
65 ACCTTTGAATAAAAGATTG
1017 AATTTTCAAG
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
101 33 0.43
102 43 0.57
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.37
Consensus pattern (101 bp):
TAAATAAAAATATCATCTTTAGGTAAAAGATTGAATTTTAGAGTAATTAGTAAATAAAGATGTAA
CCTTTGAATAAAAGATTGTTTTTTTTAAGTAATTAA
Found at i:1028 original size:101 final size:101
Alignment explanation
Indices: 832--1029 Score: 290
Period size: 101 Copynumber: 2.0 Consensus size: 101
822 TTGTTTTTTT
* *
832 TAAATAAAAATATCATCTTTAGGTAAAAGATTGAATTTTAGGGTAATTAGTAAATAAAGATGTGA
1 TAAATAAAAATATCATCTTTAGGTAAAAGATTGAATTTTAGAGTAATTAGTAAATAAAGATGTAA
* * ** *
897 CCTTTGAGTAGAAGATTGTTTTTTTTAAGTAATTAA
66 CCTTTGAATAAAAGATTGTAATTTTCAAGTAATTAA
* * *
933 TAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTA
1 TAAATAAAAATATCATCTTTAGGTAAAAGATTGAA-TTTTAGAGTAATTAGTAAATAAAGATGTA
998 ACCTTTGAATAAAAGATTG-AATTTTCAAGTAA
65 ACCTTTGAATAAAAGATTGTAATTTTCAAGTAA
1030 ATAAAATGTC
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 43 0.50
102 43 0.50
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (101 bp):
TAAATAAAAATATCATCTTTAGGTAAAAGATTGAATTTTAGAGTAATTAGTAAATAAAGATGTAA
CCTTTGAATAAAAGATTGTAATTTTCAAGTAATTAA
Found at i:1905 original size:55 final size:54
Alignment explanation
Indices: 1840--2036 Score: 279
Period size: 55 Copynumber: 3.6 Consensus size: 54
1830 TAAAAAGGGG
* *
1840 CAATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAGGCAATGGAAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAGGTAAT-GTAATCAGT
* * *
1895 CAATCTGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGATAATGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAGGTAATGTAATCAGT
1949 CAATCAGTAAATCAGTAAAAAGAGATTAATCAAGAGTCAAGGTAATAGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAA-AGTCAAGGTAAT-GTAATCAGT
* * *
2005 AAATCAGT-AATCAAGTAAAAAGATAGTAATCA
1 CAATCAGTAAATC-AGTAAAAAGAGATTAATCA
2037 GTAAATTGAT
Statistics
Matches: 128, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
54 39 0.30
55 56 0.44
56 33 0.26
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (54 bp):
CAATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAGGTAATGTAATCAGT
Found at i:2055 original size:71 final size:71
Alignment explanation
Indices: 1975--2130 Score: 176
Period size: 71 Copynumber: 2.2 Consensus size: 71
1965 AAAAAGAGAT
* * * *
1975 TAATCAAGAGTCAAGGTAATAG-T-AATCAGTAAATCAGTAATCAA-GTAAAAAGATAGTAATCA
1 TAATTAAGAGTCAAGATAAGAGATCAATCAGTAAATAAG-AATCAAGGT-AAAA-ATAGTAATCA
*
2037 GTAAAT-TG
63 GTAAATCAG
* *
2045 ATAATTAAGAGTCAAGATAAGAGATCAATCAGTAATTAAGAGTCAAGGTAAAAATAGTAATCAGT
1 -TAATTAAGAGTCAAGATAAGAGATCAATCAGTAAATAAGAATCAAGGTAAAAATAGTAATCAGT
2110 AAATCAG
65 AAATCAG
*
2117 TAATTAAAAGTCAA
1 TAATTAAGAGTCAA
2131 TGGATTAGTC
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
71 48 0.66
72 11 0.15
73 14 0.19
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (71 bp):
TAATTAAGAGTCAAGATAAGAGATCAATCAGTAAATAAGAATCAAGGTAAAAATAGTAATCAGTA
AATCAG
Found at i:2286 original size:14 final size:14
Alignment explanation
Indices: 2249--2288 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2239 AATGGTAAAG
*
2249 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
* *
2263 AGTAAGGAGTAATT
1 AGTAAAGAGTAATC
2277 AGTAAAGAGTAA
1 AGTAAAGAGTAA
2289 AATGATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.23
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:2342 original size:35 final size:35
Alignment explanation
Indices: 2263--2390 Score: 157
Period size: 35 Copynumber: 3.6 Consensus size: 35
2253 AAGAATAATC
* * * *
2263 AGTAAGGAGTAATTAGTAAAGAGTAAAATGATAAAAA
1 AGTAAAGAGTAATCAGTAAA-AGAAAAATGGT-AAAA
*
2300 AGTAAAGAGTAACCAGTAAAAGAAAAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAAGAAAAATGGTAAAA
* * *
2335 AGTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAAGAAAAATGGTAAAA
*
2370 AGTAAAGGGTAATCAGTAAAA
1 AGTAAAGAGTAATCAGTAAAA
2391 AGTAAAAAGA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
35 54 0.68
36 9 0.11
37 17 0.21
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.18
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAAGAAAAATGGTAAAA
Found at i:2453 original size:20 final size:20
Alignment explanation
Indices: 2428--2466 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2418 AATAGTAAAA
2428 GATAATCAATAAAAAGTAAT
1 GATAATCAATAAAAAGTAAT
* *
2448 GATAATCAGTAAAAGGTAA
1 GATAATCAATAAAAAGTAA
2467 AATAGTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.23
Consensus pattern (20 bp):
GATAATCAATAAAAAGTAAT
Found at i:2478 original size:22 final size:21
Alignment explanation
Indices: 2421--2574 Score: 118
Period size: 22 Copynumber: 7.2 Consensus size: 21
2411 AGAATGAAAT
* *
2421 AGTAAAA-GATAATCAATAAAA
1 AGTAAAATGGTAATCAGT-AAA
*
2442 AGT--AATGATAATCAGTAAA
1 AGTAAAATGGTAATCAGTAAA
* *
2461 AGGTAAAATAGTAATCAGTAAG
1 A-GTAAAATGGTAATCAGTAAA
* * * *
2483 AGCAAAATGGTAATCAATGAG
1 AGTAAAATGGTAATCAGTAAA
*
2504 AGCAAAATGGTAATCAGTAAA
1 AGTAAAATGGTAATCAGTAAA
*
2525 GAGTAAAATGGTAATCATTAAAA
1 -AGTAAAATGGTAATCAGT-AAA
*
2548 AGTAAGAA-GGTAACCAGTAAA
1 AGTAA-AATGGTAATCAGTAAA
2569 GAGTAA
1 -AGTAA
2575 GATGATATAG
Statistics
Matches: 110, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.05
20 11 0.10
21 40 0.36
22 48 0.44
23 5 0.05
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTAAAATGGTAATCAGTAAA
Found at i:2495 original size:21 final size:21
Alignment explanation
Indices: 2445--2541 Score: 113
Period size: 21 Copynumber: 4.5 Consensus size: 21
2435 AATAAAAAGT
* * *
2445 AATGATAATCAGTAAAAGGTAA
1 AATGGTAATCAGTAAGA-GCAA
*
2467 AATAGTAATCAGTAAGAGCAA
1 AATGGTAATCAGTAAGAGCAA
* *
2488 AATGGTAATCAATGAGAGCAA
1 AATGGTAATCAGTAAGAGCAA
*
2509 AATGGTAATCAGTAAAGAGTAA
1 AATGGTAATCAGT-AAGAGCAA
2531 AATGGTAATCA
1 AATGGTAATCA
2542 TTAAAAAGTA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 33 0.52
22 31 0.48
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.22
Consensus pattern (21 bp):
AATGGTAATCAGTAAGAGCAA
Found at i:2591 original size:44 final size:45
Alignment explanation
Indices: 2512--2597 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 45
2502 AGAGCAAAAT
* * *
2512 GGTAATCAGTAAAGAGTAAAATGGTAATCATTAAAA-AGTAAGAA
1 GGTAACCAGTAAAGAGTAAAATGATAATCAGTAAAATAGTAAGAA
* *
2556 GGTAACCAGTAAAGAGTAAGATGAT-ATAGAGTAAAATAGTAA
1 GGTAACCAGTAAAGAGTAAAATGATAAT-CAGTAAAATAGTAA
2598 TCAGTAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
43 2 0.06
44 28 0.80
45 5 0.14
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (45 bp):
GGTAACCAGTAAAGAGTAAAATGATAATCAGTAAAATAGTAAGAA
Found at i:2614 original size:14 final size:15
Alignment explanation
Indices: 2585--2625 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
2575 GATGATATAG
*
2585 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
2600 AGTAAAAGA-TAATC
1 AGTAAAAGAGTAATC
*
2614 AG-CAAAGAGTAA
1 AGTAAAAGAGTAA
2626 AATAATGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 5 0.22
14 10 0.43
15 8 0.35
ACGTcount: A:0.56, C:0.07, G:0.17, T:0.20
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:2705 original size:29 final size:28
Alignment explanation
Indices: 2683--2742 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
2673 AAAAGTGGTC
2683 ATAAATAAAAGAGAGTAAGAAAAGAGTA
1 ATAAATAAAAGAGAGTAAGAAAAGAGTA
* * *
2711 ATTAGTAAAA-AGAGTAAGAAAGGAGTA
1 ATAAATAAAAGAGAGTAAGAAAAGAGTA
2738 A-AAAT
1 ATAAAT
2743 GATAAAAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 2 0.07
27 17 0.63
28 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.17
Consensus pattern (28 bp):
ATAAATAAAAGAGAGTAAGAAAAGAGTA
Found at i:3209 original size:26 final size:26
Alignment explanation
Indices: 3173--3222 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3163 GTTCGGTACC
*
3173 CCCCGGACCCGGACGTTGCGACAGTT
1 CCCCGGACCCGAACGTTGCGACAGTT
*
3199 CCCCGGACCCGAACGTTTCGACAG
1 CCCCGGACCCGAACGTTGCGACAG
3223 AATTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.14
Consensus pattern (26 bp):
CCCCGGACCCGAACGTTGCGACAGTT
Found at i:3564 original size:17 final size:16
Alignment explanation
Indices: 3532--3563 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3522 TTTTCCCGAT
3532 GATTATTTTTTGAAAA
1 GATTATTTTTTGAAAA
3548 GATTATTTTTTGAAAA
1 GATTATTTTTTGAAAA
3564 ATCTGTACCT
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:0.12, T:0.50
Consensus pattern (16 bp):
GATTATTTTTTGAAAA
Found at i:4879 original size:30 final size:31
Alignment explanation
Indices: 4843--4909 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
4833 GAACCTCAAA
4843 TGGAACTTGAACA-TAGTTC-ACAAATTGTTG
1 TGGAACTTGAACATTA-TTCGACAAATTGTTG
*
4873 TGGAACTTGAACATTATTCGACAAGTTGTTG
1 TGGAACTTGAACATTATTCGACAAATTGTTG
*
4904 AGGAAC
1 TGGAAC
4910 AAGATACTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (31 bp):
TGGAACTTGAACATTATTCGACAAATTGTTG
Found at i:18794 original size:62 final size:62
Alignment explanation
Indices: 18696--18813 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 62
18686 ATAAAAGAAA
* * * * * *
18696 TTAAATGGTTCTTGGTCATACTACTTCTAAGGCATCAGCTGCAAGCAGCGATGTGAGTCACC
1 TTAAATGGTTCTTGGCCAGACTACTTCCAAGGCATCAACTACAAGCAACGATGTGAGTCACC
*
18758 TTAAATGGTTCTTGGCCAGACTACTTCCAAGTCATCAACTACAAGCAACGATGTGA
1 TTAAATGGTTCTTGGCCAGACTACTTCCAAGGCATCAACTACAAGCAACGATGTGA
18814 ACGCAGGTGG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (62 bp):
TTAAATGGTTCTTGGCCAGACTACTTCCAAGGCATCAACTACAAGCAACGATGTGAGTCACC
Found at i:19339 original size:12 final size:12
Alignment explanation
Indices: 19324--19365 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
19314 ATATGTATAT
19324 ATATAACATAAC
1 ATATAACATAAC
*
19336 ATATATCATAAC
1 ATATAACATAAC
*
19348 ATATAACAAAAAC
1 ATATAAC-ATAAC
19361 ATATA
1 ATATA
19366 TTAAAGTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (12 bp):
ATATAACATAAC
Done.