Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013089.1 Corchorus capsularis cultivar CVL-1 contig13110, 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: 12807
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:548 original size:71 final size:71
Alignment explanation
Indices: 432--659 Score: 375
Period size: 71 Copynumber: 3.2 Consensus size: 71
422 GATTAAAAAG
* *
432 AATTAAGAAAAGAAAATACAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAGTAAAGTCTTAATT
1 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAGTAAAGTCTTAATT
497 CAGGGT
66 CAGGGT
*
503 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGGGTAAAGTCTTAATT
1 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAGTAAAGTCTTAATT
568 CAGGGT
66 CAGGGT
* *
574 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGACAATTAAGAAGAGTAAGAGAACTTAA
1 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAGTAA-AG-TCTTAA
*
639 TTCTGGGT
64 TTCAGGGT
647 AATTAAGTAAAAG
1 AATTAAG-AAAAG
660 CAGGTAAAGA
Statistics
Matches: 147, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
71 121 0.82
72 2 0.01
73 19 0.13
74 5 0.03
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.25
Consensus pattern (71 bp):
AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAGTAAAGTCTTAATT
CAGGGT
Found at i:732 original size:142 final size:135
Alignment explanation
Indices: 441--733 Score: 297
Period size: 142 Copynumber: 2.1 Consensus size: 135
431 GAATTAAGAA
* *
441 AAGAAAA-TACAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAGTAAAGTCTTAATTCAGGGTAA
1 AAGAAAAGTACAGTCAAGGTCCTAAGTTGGACAATTAAGAAGAGTAAAGACTTAATTCAGGGTAA
* ** *
505 TTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGGGTAAAGTCTTAATTCA
66 TTAAGAAAAGAAAGTAAAG-CAA-G-CCTAAGTTGGGCAATTAAGAACAGTAAAATCTTAATTCA
*
570 GGGTAATT
128 GGGCAATT
* *
578 AAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGACAATTAAGAAGAGTAAGAGAACTTAATTCT
1 AAG---A-AAAGTACAGTCAAGGTCCTAAGTTGGACAATTAAGAAGAGTAA-AG-ACTTAATTCA
* * *
643 GGGTAATTAAGTAAAAGCAGGTAAAG-AA-CTTAA-TTCAGGGCAATTAAGTAAAAACAGTCAAA
60 GGGTAATTAAG-AAAAGAAAGTAAAGCAAGCCTAAGTT--GGGCAATTAAG----AACAGT-AAA
705 ATCTTAATTCAGGGCAATT
117 ATCTTAATTCAGGGCAATT
724 AAGAAAAGTA
1 AAGAAAAGTA
734 AACATAGTCA
Statistics
Matches: 129, Mismatches: 12, Indels: 25
0.78 0.07 0.15
Matches are distributed among these distances:
137 3 0.02
139 2 0.02
140 5 0.04
141 14 0.11
142 43 0.33
143 5 0.04
144 19 0.15
145 15 0.12
146 23 0.18
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (135 bp):
AAGAAAAGTACAGTCAAGGTCCTAAGTTGGACAATTAAGAAGAGTAAAGACTTAATTCAGGGTAA
TTAAGAAAAGAAAGTAAAGCAAGCCTAAGTTGGGCAATTAAGAACAGTAAAATCTTAATTCAGGG
CAATT
Found at i:890 original size:38 final size:38
Alignment explanation
Indices: 630--898 Score: 187
Period size: 37 Copynumber: 7.0 Consensus size: 38
620 GAAGAGTAAG
* *
630 AGAACTTAATTCTGGGTAATTAAGT-AAAAGCAGGTAA
1 AGAACTTAATTCAGGGTAATTAAGTAAAAAGCAGTTAA
* *
667 AGAACTTAATTCAGGGCAATTAAGTAAAAA-CAGTCAA
1 AGAACTTAATTCAGGGTAATTAAGTAAAAAGCAGTTAA
* * *
704 A-ATCTTAATTCAGGGCAATTAAGAAAAGTAAACATAGTCAGTCAA
1 AGAACTTAATTCAGGGTAATT-----AAGTAAA-A-AG-CAGTTAA
* * * * * *
749 A-ATCTTCATTCAAGG-AAATAAGGT-AAAAGTAGTCAA
1 AGAACTTAATTCAGGGTAATTAA-GTAAAAAGCAGTTAA
* * * *
785 AGGAGCTTAATTCAGGGAAATTAAGTAAACATG--GTCAA
1 A-GAACTTAATTCAGGGTAATTAAGTAAA-AAGCAGTTAA
* * *
823 ATAACTTAATTCAGGATAATTAAGTAAAAAGCAGTTGA
1 AGAACTTAATTCAGGGTAATTAAGTAAAAAGCAGTTAA
*
861 AGGACTTAATTCAGGGTAATTAAGTAAAAA-CAGTTAA
1 AGAACTTAATTCAGGGTAATTAAGTAAAAAGCAGTTAA
898 A
1 A
899 AGGTAAGGAT
Statistics
Matches: 189, Mismatches: 25, Indels: 36
0.76 0.10 0.14
Matches are distributed among these distances:
36 27 0.14
37 61 0.32
38 54 0.29
39 11 0.06
40 4 0.02
41 7 0.04
42 1 0.01
43 1 0.01
44 3 0.02
45 20 0.11
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (38 bp):
AGAACTTAATTCAGGGTAATTAAGTAAAAAGCAGTTAA
Found at i:1039 original size:76 final size:76
Alignment explanation
Indices: 911--1269 Score: 675
Period size: 76 Copynumber: 4.7 Consensus size: 76
901 GTAAGGATAG
* *
911 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAACATAGACTTAATTAAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
976 AAGTAAAGTAA
66 AAGTAAAGTAA
*
987 GTACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1052 AAGTAAAGTAA
66 AAGTAAAGTAA
1063 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1128 AAGTAAAGTAA
66 AAGTAAAGTAA
1139 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1204 AAGTAAAGTAA
66 AAGTAAAGTAA
1215 GCACAGACTTAATTTC-AGTGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATT
1 GCACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAAGACAAGCATAGACTTAATT
1270 TCAAGGAAGG
Statistics
Matches: 278, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
75 2 0.01
76 276 0.99
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (76 bp):
GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
AAGTAAAGTAA
Found at i:1377 original size:228 final size:227
Alignment explanation
Indices: 915--1379 Score: 613
Period size: 228 Copynumber: 2.0 Consensus size: 227
905 GGATAGGCAC
915 AGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAACATAGACTTAATTAAGGGTAATTAAGT
1 AGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAACATAGACTTAATTAAGGGTAATTAAGT
*
980 AAAGTAAGTACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAG
66 AAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAG
* * * *
1045 GGTAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAG
131 GGAAATTAAGTAAAGCAAGCACAGACTTAATTTCAAGG-AGGAAATTAAGTAAAGACAAGCAAAG
* * *
1110 ACTTAATTCAGGGTAATTAAGTAAAGTAAGCAC
195 ACTTAATTCAGAGTAATTAAGTAAAATAAGCAA
* *
1143 AGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATTAAGT
1 AGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAACATAGACTTAATTAAGGGTAATTAAGT
1208 AAAGTAAGCACAGACTTAATTTC-AGTGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTTC
66 AAAGTAAGCACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAAGACAAGCATAGACTTAA-TTC
* * * **
1272 AAGGAAGGAAATTAGGTAAAGACAAGCACATACTTAA-TTC-A-G-GGTAATTAAGT-AA-ATTA
129 -A-G--GGAAATTAAGTAAAG-CAAGCACAGACTTAATTTCAAGGAGGAAATTAAGTAAAGACAA
* * * *
1331 GCAAAGACTTGATTTCATTAG-AATTAAGTAAAATCATCAA
189 GCAAAGACTT-AATTCA-GAGTAATTAAGTAAAATAAGCAA
1371 AGACTTAAT
1 AGACTTAAT
1380 CCAAAGATGA
Statistics
Matches: 209, Mismatches: 19, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
227 13 0.06
228 150 0.72
229 13 0.06
230 1 0.00
231 2 0.01
232 1 0.00
233 16 0.08
234 13 0.06
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (227 bp):
AGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAACATAGACTTAATTAAGGGTAATTAAGT
AAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAG
GGAAATTAAGTAAAGCAAGCACAGACTTAATTTCAAGGAGGAAATTAAGTAAAGACAAGCAAAGA
CTTAATTCAGAGTAATTAAGTAAAATAAGCAA
Found at i:1379 original size:152 final size:151
Alignment explanation
Indices: 911--1310 Score: 577
Period size: 152 Copynumber: 2.6 Consensus size: 151
901 GTAAGGATAG
* * *
911 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAACATAGACTTAATTAAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGAAATT
* * * *
976 AAGTAAAGTAAGTACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAAT
66 AAGTAAAGCAAGCACAGACTTAATTTCAAGG-AGGAAATTAAGTAAAGACAAGCAAAGACTTAAT
*
1041 TCAGGGTAATTAAGTAAAGTAA
130 TCAGAGTAATTAAGTAAAGTAA
*
1063 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGAAATT
* * *
1128 AAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAAT
66 AAGTAAAGCAAGCACAGACTTAATTTCAAGG-AGGAAATTAAGTAAAGACAAGCAAAGACTTAAT
*
1193 TCAGGGTAATTAAGTAAAGTAA
130 TCAGAGTAATTAAGTAAAGTAA
1215 GCACAGACTTAATTTC-AGTGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTTCAAGGAAG
1 GCACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAAGACAAGCATAGACTTAA-TTC-A-G--G
* *
1279 GAAATTAGGTAAAGACAAGCACATACTTAATT
60 GAAATTAAGTAAAG-CAAGCACAGACTTAATT
1311 CAGGGTAATT
Statistics
Matches: 234, Mismatches: 7, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
151 2 0.01
152 199 0.85
153 3 0.01
154 1 0.00
155 1 0.00
157 13 0.06
158 15 0.06
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.24
Consensus pattern (151 bp):
GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGAAATT
AAGTAAAGCAAGCACAGACTTAATTTCAAGGAGGAAATTAAGTAAAGACAAGCAAAGACTTAATT
CAGAGTAATTAAGTAAAGTAA
Found at i:1478 original size:37 final size:37
Alignment explanation
Indices: 1437--1653 Score: 362
Period size: 37 Copynumber: 5.9 Consensus size: 37
1427 TAATTAAAGA
* *
1437 AAAGGACTTGGTTCCAAGGAAGGGAATTAAGTAGAGC
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1474 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1511 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
*
1548 AAGGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
*
1585 AGAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
* * * *
1622 TAAGGACTTAATTTCAAGGAAGGAAATTAAGT
1 AAAGGACTTGATTCCAAGGAAGGGAATTAAGT
1654 CAAGTTAGGG
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 170 1.00
ACGTcount: A:0.40, C:0.08, G:0.30, T:0.22
Consensus pattern (37 bp):
AAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGT
Found at i:1572 original size:19 final size:19
Alignment explanation
Indices: 1477--1572 Score: 65
Period size: 19 Copynumber: 5.2 Consensus size: 19
1467 GTAGAGCAAA
1477 GGACTTGATTCCAAGGAAG
1 GGACTTGATTCCAAGGAAG
* * * * *
1496 GGAATTAAGT--AGAGTAAA
1 GGACTTGATTCCA-AGGAAG
1514 GGACTTGATTCCAAGGAAG
1 GGACTTGATTCCAAGGAAG
* * * *
1533 GGAATTAAGT--AGAGTAAG
1 GGACTTGATTCCA-AGGAAG
1551 GGACTTGATTCCAAGGAAG
1 GGACTTGATTCCAAGGAAG
1570 GGA
1 GGA
1573 ATTAAGTAGA
Statistics
Matches: 53, Mismatches: 18, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 2 0.04
18 23 0.43
19 26 0.49
20 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (19 bp):
GGACTTGATTCCAAGGAAG
Found at i:1704 original size:111 final size:109
Alignment explanation
Indices: 1448--1687 Score: 326
Period size: 111 Copynumber: 2.2 Consensus size: 109
1438 AAGGACTTGG
*
1448 TTCCAAGGAAGGGAATTAAGTAGAGCAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTAA
1 TTCC-AGG-AGGGAATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTAA
* * *
1513 AGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTAAGGGACTTGA
64 AGGACTTAATTCCAAGGAAGGAAATTAAGTAGAGTAAGGGACTTAA
* *
1559 TTCCAAGGAAGGGAATTAAGTAGAGTAGAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTTA
1 TTCC-AGG-AGGGAATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTAA
* *
1624 AGGACTTAATTTCAAGGAAGGAAATTAAGTCA-AGTTAGGGACTTAA
64 AGGACTTAATTCCAAGGAAGGAAATTAAGT-AGAGTAAGGGACTTAA
*
1670 TT-C-GG-GGTAATTAAGTAG
1 TTCCAGGAGGGAATTAAGTAG
1688 CGTCGATAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
106 12 0.10
108 2 0.02
110 1 0.01
111 103 0.87
112 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.30, T:0.23
Consensus pattern (109 bp):
TTCCAGGAGGGAATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTAAAG
GACTTAATTCCAAGGAAGGAAATTAAGTAGAGTAAGGGACTTAA
Found at i:1750 original size:36 final size:36
Alignment explanation
Indices: 1665--1815 Score: 196
Period size: 36 Copynumber: 4.2 Consensus size: 36
1655 AAGTTAGGGA
* * *
1665 CTTAATTCGGGGTAATTAAGTAGCGTCGATAAAGGG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
*
1701 ACTTAATTTAGGGTAATTAAGTAGCGTCAATAAAAGG
1 -CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
* *
1738 TTTAATTCAGGGTAATTAAGTAACGTCAATAAAAGG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
* * *
1774 CTTAATTCAGGATAATTAAGTGGAGTCAAT-AAAGAG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAG-G
1810 CTTAAT
1 CTTAAT
1816 CTAAGAAGAG
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
35 4 0.04
36 65 0.64
37 32 0.32
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (36 bp):
CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
Found at i:1756 original size:73 final size:72
Alignment explanation
Indices: 1666--1806 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 72
1656 AGTTAGGGAC
* * * * * * *
1666 TTAATTCGGGGTAATTAAGTAGCGTCGATAAAGGGACTTAATTTAGGGTAATTAAGTAGCGTCAA
1 TTAATTCAGGGTAATTAAGTAACGTCAATAAAAGG-CTTAATTCAGGATAATTAAGTAGAGTCAA
1731 TAAAAGGT
65 TAAAAGGT
*
1739 TTAATTCAGGGTAATTAAGTAACGTCAATAAAAGGCTTAATTCAGGATAATTAAGTGGAGTCAAT
1 TTAATTCAGGGTAATTAAGTAACGTCAATAAAAGGCTTAATTCAGGATAATTAAGTAGAGTCAAT
1804 AAA
66 AAA
1807 GAGCTTAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 29 0.48
73 31 0.52
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (72 bp):
TTAATTCAGGGTAATTAAGTAACGTCAATAAAAGGCTTAATTCAGGATAATTAAGTAGAGTCAAT
AAAAGGT
Found at i:4518 original size:7 final size:7
Alignment explanation
Indices: 4506--4545 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
4496 CATTTGCATT
4506 AAAAGGA
1 AAAAGGA
4513 AAAAGGA
1 AAAAGGA
4520 AAAAGGA
1 AAAAGGA
*
4527 AAAAGTA
1 AAAAGGA
*
4534 AAAAGTA
1 AAAAGGA
4541 AAAAG
1 AAAAG
4546 AAAGGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (7 bp):
AAAAGGA
Found at i:9882 original size:22 final size:22
Alignment explanation
Indices: 9854--10141 Score: 344
Period size: 22 Copynumber: 13.1 Consensus size: 22
9844 AGTATCAAAA
*
9854 CAGACTTTCAAACGTCTCAGGG
1 CAGACTTTCAAGCGTCTCAGGG
9876 CAGACTTTCAAGCGTCTCAGGG
1 CAGACTTTCAAGCGTCTCAGGG
*
9898 CAGACTTTCAGGCGTCTCAGGG
1 CAGACTTTCAAGCGTCTCAGGG
*
9920 CAGACTTTCAAGCGTCTTAGGG
1 CAGACTTTCAAGCGTCTCAGGG
* * *
9942 TAGACTTTCAAGTGTATCAGGG
1 CAGACTTTCAAGCGTCTCAGGG
*
9964 CAGACTTTCAAGCGTATCAGGG
1 CAGACTTTCAAGCGTCTCAGGG
* * *
9986 TAGACTTTCAAGCGTTTCATGG
1 CAGACTTTCAAGCGTCTCAGGG
* *
10008 TAGACTTTCAAGCGTCTCCGGG
1 CAGACTTTCAAGCGTCTCAGGG
* * *
10030 AAGACTTTCAAGTGTCTCAAGG
1 CAGACTTTCAAGCGTCTCAGGG
*
10052 CAGACTTTCAAGCGTCTTAGGG
1 CAGACTTTCAAGCGTCTCAGGG
*
10074 CAGACTTTCAAGCGTCTCAGGA
1 CAGACTTTCAAGCGTCTCAGGG
* * *
10096 CAGAC-CTCTAAGTGTCTCAAGG
1 CAGACTTTC-AAGCGTCTCAGGG
* * **
10118 AAAACTTTTTAGCGTCTCAGGG
1 CAGACTTTCAAGCGTCTCAGGG
10140 CA
1 CA
10142 AAATCTCAGT
Statistics
Matches: 226, Mismatches: 38, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
21 2 0.01
22 223 0.99
23 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (22 bp):
CAGACTTTCAAGCGTCTCAGGG
Found at i:10755 original size:13 final size:13
Alignment explanation
Indices: 10727--10770 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
10717 TGATTCTTTC
10727 AAAAAAGAAAAA-
1 AAAAAAGAAAAAG
* *
10739 AAAAAAGAGAGAG
1 AAAAAAGAAAAAG
*
10752 AAAACAGAAAAAG
1 AAAAAAGAAAAAG
10765 AAAAAA
1 AAAAAA
10771 AAGTTTATAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Done.