Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016394.1 Corchorus capsularis cultivar CVL-1 contig16415, 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: 4655
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Found at i:844 original size:55 final size:55
Alignment explanation
Indices: 784--1089 Score: 488
Period size: 55 Copynumber: 5.6 Consensus size: 55
774 AAAAAGGGGC
*
784 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* * *
839 AATCAGTAGTTAAGTAAGAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAATA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* *
894 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* *
949 AATCAGTAGTTAAGTAAGAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* *
1004 AATCAGTAATTAAGT-AAAAGAGATTAAACAGAGTCAATGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* * *
1058 AATCAGTAATCAAGTAAAAAGATAGTAATCAG
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAG
1090 TAAATTGATA
Statistics
Matches: 229, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
54 50 0.22
55 179 0.78
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
Found at i:1136 original size:31 final size:32
Alignment explanation
Indices: 1098--1163 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
1088 AGTAAATTGA
* * *
1098 TAATTAAGAGTCAAGGTAAGAG-ATTAATCAG
1 TAATTAAGAGTCAAGATAAAAGTAGTAATCAG
1129 TAATTAAGAGTCAAGATAAAAGTAGTAATCAG
1 TAATTAAGAGTCAAGATAAAAGTAGTAATCAG
1161 TAA
1 TAA
1164 ATCAGTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 20 0.65
32 11 0.35
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (32 bp):
TAATTAAGAGTCAAGATAAAAGTAGTAATCAG
Found at i:1369 original size:51 final size:49
Alignment explanation
Indices: 1274--1372 Score: 144
Period size: 51 Copynumber: 2.0 Consensus size: 49
1264 AAATTCAAGA
* *
1274 GAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAG
1 GAGTAATCAGTAAAGGAAAAATGATAAAAAGTAAAGAATAATCAGTAAG
* *
1323 GAGTAATTAGTAAAGGGAAAAATGATAAAAAAGTAAAGAGTAATCAGTAA
1 GAGTAATCAGTAAA-GGAAAAATGAT-AAAAAGTAAAGAATAATCAGTAA
1373 AAGAAGAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 13 0.30
50 10 0.23
51 21 0.48
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.19
Consensus pattern (49 bp):
GAGTAATCAGTAAAGGAAAAATGATAAAAAGTAAAGAATAATCAGTAAG
Found at i:1396 original size:35 final size:35
Alignment explanation
Indices: 1317--1444 Score: 166
Period size: 35 Copynumber: 3.6 Consensus size: 35
1307 AAGAATAATC
* * * * *
1317 AGTAAGGAGTAATTAGTAAAGGGAAAAATGATAAAAA
1 AGTAAAGAGTAATCAGTAAA-AGAAGAATGGT-AAAA
1354 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
* *
1389 AGTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
*
1424 AGTAAAGGGTAATCAGTAAAA
1 AGTAAAGAGTAATCAGTAAAA
1445 AGTAAAAAGA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
35 56 0.68
36 8 0.10
37 18 0.22
ACGTcount: A:0.55, C:0.02, G:0.25, T:0.18
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
Found at i:1479 original size:121 final size:120
Alignment explanation
Indices: 1273--1544 Score: 286
Period size: 121 Copynumber: 2.2 Consensus size: 120
1263 TAAATTCAAG
** **
1273 AGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAAAG
1 AGAGTAATCAGTAAAGG-AAAATGGTAAAGAGTAAAGAATAATCAGTAAAAAGTAAAAAGTAAAG
* *
1338 GGAAAAATGATAAAAAAGT-AAAGAGTAATCAGTAAAAGAAG-AAT-GGTAAAAAGT-AA
65 GGAAAAATG--AAAAAAGTAAAAG-GTAATCAATAAAA-AAGTAATCAGTAAAAAGTAAA
**
1394 AGAGTAATCAGTAAAGGAAGAATGGTAAAGAGTAAAGGGTAATCAGTAAAAAGTAAAAAGATAAT
1 AGAGTAATCAGTAAAGGAA-AATGGTAAAGAGTAAAGAATAATCAGTAAAAAGTAAAAAG-TAA-
* * *
1459 CA-GTAAAGAATG-AAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAGGTAAA
63 -AGGGAAA-AATGAAAAAAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAAGTAAA
* *
1517 ATAGTAATCAGTAAGAGCAAAATGGTAA
1 AGAGTAATCAGTAA-AGGAAAATGGTAA
1545 TCAATGAGAG
Statistics
Matches: 128, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
120 5 0.04
121 72 0.56
122 15 0.12
123 27 0.21
124 9 0.07
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.19
Consensus pattern (120 bp):
AGAGTAATCAGTAAAGGAAAATGGTAAAGAGTAAAGAATAATCAGTAAAAAGTAAAAAGTAAAGG
GAAAAATGAAAAAAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAAGTAAA
Found at i:1512 original size:29 final size:29
Alignment explanation
Indices: 1449--1515 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1439 GTAAAAAGTA
* * *
1449 AAAAGATAATCAGTAAAGAATGAAATAGT
1 AAAAGGTAATCAATAAAGAAAGAAATAGT
*
1478 AAAAGGTAATCAATAAA-AAAGTAATCAGT
1 AAAAGGTAATCAATAAAGAAAGAAAT-AGT
1507 AAAAGGTAA
1 AAAAGGTAA
1516 AATAGTAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.60, C:0.04, G:0.16, T:0.19
Consensus pattern (29 bp):
AAAAGGTAATCAATAAAGAAAGAAATAGT
Found at i:1530 original size:15 final size:14
Alignment explanation
Indices: 1445--1515 Score: 63
Period size: 15 Copynumber: 4.9 Consensus size: 14
1435 ATCAGTAAAA
1445 AGTAAAAAGATAATC
1 AGTAAAAAG-TAATC
*
1460 AGTAAAGAATGAAAT-
1 AGTAAA-AA-GTAATC
*
1475 AGTAAAAGGTAATC
1 AGTAAAAAGTAATC
*
1489 AATAAAAAAGTAATC
1 AGT-AAAAAGTAATC
*
1504 AGTAAAAGGTAA
1 AGTAAAAAGTAA
1516 AATAGTAATC
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.09
14 11 0.24
15 24 0.53
16 5 0.11
17 1 0.02
ACGTcount: A:0.59, C:0.04, G:0.17, T:0.20
Consensus pattern (14 bp):
AGTAAAAAGTAATC
Found at i:1567 original size:108 final size:108
Alignment explanation
Indices: 1455--1782 Score: 419
Period size: 108 Copynumber: 3.1 Consensus size: 108
1445 AGTAAAAAGA
1455 TAATCAGTAAAGAATGAAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAGGTAAAATA
1 TAATCAGTAAAGAATGAAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAGGTAAAATA
1520 GTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATGG
66 GTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATGG
* * * * * * *
1563 TAATCAGTAAAGAGTAAAATAGTAATCA-TTAA-AAAGTAAGAAGGTAATCAGT-AAAGAGT-AA
1 TAATCAGTAAAGAATGAAATAGTAA-AAGGTAATCAA-TAAAAAAGTAATCAGTAAAAG-GTAAA
* * * * * *
1624 ATAGTAATC------AGCAAAA-GGTAAT-AGTAAAAAGTAAAAAGA
63 ATAGTAATCAGTAAGAGCAAAATGGTAATCAAT-GAGAGCAAAATGG
1663 TAATCAGTAAAGAATGAAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAGGTAAAATA
1 TAATCAGTAAAGAATGAAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAGGTAAAATA
1728 GTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATGG
66 GTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATGG
1771 TAATCAGTAAAG
1 TAATCAGTAAAG
1783 TAAAATAGTA
Statistics
Matches: 178, Mismatches: 26, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
99 3 0.02
100 56 0.31
101 24 0.13
107 24 0.13
108 68 0.38
109 3 0.02
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (108 bp):
TAATCAGTAAAGAATGAAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAGGTAAAATA
GTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATGG
Found at i:1624 original size:29 final size:28
Alignment explanation
Indices: 1592--1723 Score: 81
Period size: 29 Copynumber: 4.6 Consensus size: 28
1582 TAGTAATCAT
1592 TAAAAAGTAAGAAGGTAATCAGTAAAGAG
1 TAAAAAGTAA-AAGGTAATCAGTAAAGAG
* * * * *
1621 TAAATAGTAATCA-GCAA-AAGGT-AATAG
1 TAAAAAGTAA-AAGGTAATCA-GTAAAGAG
* *
1648 TAAAAAGTAAAAAGATAATCAGTAAAGAA
1 TAAAAAGT-AAAAGGTAATCAGTAAAGAG
* * *
1677 TGAAATAGTAAAAGGTAATCAATAAAAAAG
1 T-AAAAAGTAAAAGGTAATCAGT-AAAGAG
**
1707 TAATCAGTAAAAGGTAA
1 TAAAAAGTAAAAGGTAA
1724 AATAGTAATC
Statistics
Matches: 76, Mismatches: 20, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
27 13 0.17
28 11 0.14
29 41 0.54
30 11 0.14
ACGTcount: A:0.58, C:0.05, G:0.18, T:0.20
Consensus pattern (28 bp):
TAAAAAGTAAAAGGTAATCAGTAAAGAG
Found at i:1644 original size:21 final size:21
Alignment explanation
Indices: 1497--1851 Score: 132
Period size: 21 Copynumber: 16.9 Consensus size: 21
1487 TCAATAAAAA
1497 AGTAATCAGTAAAAGGTAAAAT
1 AGTAATCAGTAAAAGGT-AAAT
* **
1519 AGTAATCAGTAAGAGCAAAAT
1 AGTAATCAGTAAAAGGTAAAT
* * * * **
1540 GGTAATCAATGAGAGCAAAAT
1 AGTAATCAGTAAAAGGTAAAT
*
1561 GGTAATCAGT-AAAGAGTAAAAT
1 AGTAATCAGTAAAAG-GT-AAAT
* *
1583 AGTAATCATTAAAAAGTAAGA-
1 AGTAATCAGTAAAAGGTAA-AT
1604 AGGTAATCAGT-AAAGAGTAAAT
1 A-GTAATCAGTAAAAG-GTAAAT
*
1626 AGTAATCAGCAAAAGGT-AAT
1 AGTAATCAGTAAAAGGTAAAT
** *
1646 AGTAAAAAGTAAAAAG-ATAAT
1 AGTAATCAGTAAAAGGTA-AAT
** *
1667 CAGTAAAGAATGAAATA-GTAAA-
1 -AGTAATCAGT-AAA-AGGTAAAT
*
1689 AGGTAATCA--ATAA---AAA-
1 A-GTAATCAGTAAAAGGTAAAT
1705 AGTAATCAGTAAAAGGTAAAAT
1 AGTAATCAGTAAAAGGT-AAAT
* **
1727 AGTAATCAGTAAGAGCAAAAT
1 AGTAATCAGTAAAAGGTAAAT
* * * * **
1748 GGTAATCAATGAGAGCAAAAT
1 AGTAATCAGTAAAAGGTAAAT
*
1769 GGTAATCAGT-AAA-GTAAAAT
1 AGTAATCAGTAAAAGGT-AAAT
* *
1789 AGTAATCATTAAAAAGTAAGA-
1 AGTAATCAGTAAAAGGTAA-AT
1810 AGGTAATCAGT-AAAGAGTAAAAT
1 A-GTAATCAGTAAAAG-GT-AAAT
* *
1833 GGTAATCAGCAAAAGGTAA
1 AGTAATCAGTAAAAGGTAA
1852 TCAGTAAGAG
Statistics
Matches: 260, Mismatches: 42, Indels: 63
0.71 0.12 0.17
Matches are distributed among these distances:
15 7 0.03
16 4 0.02
17 3 0.01
18 1 0.00
19 2 0.01
20 32 0.12
21 97 0.37
22 97 0.37
23 15 0.06
24 2 0.01
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTAATCAGTAAAAGGTAAAT
Found at i:1650 original size:71 final size:71
Alignment explanation
Indices: 1575--1929 Score: 208
Period size: 71 Copynumber: 5.1 Consensus size: 71
1565 ATCAGTAAAG
*
1575 AGTAAAATAGTAATCATTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAATAGTAATCAGCAAAA
1 AGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAATAGTAATCAGCAAAA
1640 GGTAAT
66 GGTAAT
** ** * * * **
1646 AGTAAAA-AGTAAAAAGATAATCAGTAAAGAATGAAAT-AGTAAA-AGGT-AATCAATAAAAAAG
1 AGTAAAATAGTAATCAG-TAAAAAGT-AAGAAGGTAATCAGTAAAGA-GTAAAT-AGT-AATCAG
* * *
1707 TAATCA-GTAAA
61 CAA-AAGGTAAT
* * * * * *
1718 AGGTAAAATAGTAATCAGT-AAGAGCAA-AATGGTAATCAAT-GAGAGCAAAATGGTAAT---C-
1 A-GTAAAATAGTAATCAGTAAAAAGTAAGAA-GGTAATCAGTAAAGAG-TAAATAGTAATCAGCA
1776 --A-GTAA-
63 AAAGGTAAT
* *
1781 AGTAAAATAGTAATCATTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATGGTAATCAGCAAA
1 AGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGT-AAATAGTAATCAGCAAA
1846 AGGTAAT
65 AGGTAAT
* * ** *
1853 CAGTAAGAGTA-AAAT-AGTAATCAGT-AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTA
1 -AGTAA-AATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGT-AAATAGTAATCAGCA
*
1915 AAAGATAAT
63 AAAGGTAAT
1924 CAGTAA
1 -AGTAA
1930 GAGTAAAACA
Statistics
Matches: 216, Mismatches: 41, Indels: 54
0.69 0.13 0.17
Matches are distributed among these distances:
62 16 0.07
63 16 0.07
64 21 0.10
67 1 0.00
70 13 0.06
71 86 0.40
72 34 0.16
73 19 0.09
74 10 0.05
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (71 bp):
AGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAATAGTAATCAGCAAAA
GGTAAT
Found at i:1659 original size:208 final size:209
Alignment explanation
Indices: 1384--2001 Score: 864
Period size: 208 Copynumber: 3.0 Consensus size: 209
1374 AGAAGAATGG
* ** * *
1384 TAAAAAGT-A-AAGAGTAATCAGTAAAG-GAAGAATGGTAAAGAGTAAAGGGTAATCAGTAAAAA
1 TAAAAAGTAAGAAG-GTAATCAGTAAAGAGTA-AATGGTAATCAGCAAAAGGTAATCAGTAAAAA
1446 GTAAAAAGATAATCAGTAAAGAATGAAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAA
64 GTAAAAAGATAATCAGTAAAGAATGAAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAA
1511 GGTAAAATAGTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATGGTAATCAGTAAAGA
129 GGTAAAATAGTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATGGTAATCAGTAAAGA
1576 GTAAAATAGTAATCAT
194 GTAAAATAGTAATCAT
*
1592 TAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAATAGTAATCAGCAAAAGGTAAT-AGTAAAAAGT
1 TAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAATGGTAATCAGCAAAAGGTAATCAGTAAAAAGT
1656 AAAAAGATAATCAGTAAAGAATGAAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAGG
66 AAAAAGATAATCAGTAAAGAATGAAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAGG
1721 TAAAATAGTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATGGTAATCAGT-AA-AGT
131 TAAAATAGTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATGGTAATCAGTAAAGAGT
1784 AAAATAGTAATCAT
196 AAAATAGTAATCAT
*
1798 TAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATGGTAATCAGCAAAAGGTAATCAGT-AAGAG
1 TAAAAAGTAAGAAGGTAATCAGTAAAGAGT-AAATGGTAATCAGCAAAAGGTAATCAGTAAAAAG
* * * *
1862 TAAAATAG-TAATCAGTAGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGA-TAATC
65 TAAAA-AGATAATCAGTA-AA-G-AAT--G-AAATAGTAAAA-GGTAATCAATAAAAAAGTAATC
* * * * * * * *
1925 AGTAAGA-GTAAAACAGTAA-CTAGTAAGAGTAAAGTGGTAATTAGTAAGAGTC-AAATAGTAAT
122 AGTAAAAGGTAAAATAGTAATC-AGTAAGAGCAAAATGGTAATCAATGAGAG-CAAAATGGTAAT
1987 CAGTAAAGAGTAAAA
185 CAGTAAAGAGTAAAA
2002 AATGATCAGT
Statistics
Matches: 373, Mismatches: 20, Indels: 28
0.89 0.05 0.07
Matches are distributed among these distances:
206 47 0.13
207 43 0.12
208 148 0.40
209 33 0.09
210 8 0.02
211 1 0.00
212 49 0.13
213 24 0.06
214 20 0.05
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.21
Consensus pattern (209 bp):
TAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAATGGTAATCAGCAAAAGGTAATCAGTAAAAAGT
AAAAAGATAATCAGTAAAGAATGAAATAGTAAAAGGTAATCAATAAAAAAGTAATCAGTAAAAGG
TAAAATAGTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATGGTAATCAGTAAAGAGT
AAAATAGTAATCAT
Found at i:1738 original size:15 final size:14
Alignment explanation
Indices: 1653--1723 Score: 63
Period size: 15 Copynumber: 4.9 Consensus size: 14
1643 AATAGTAAAA
1653 AGTAAAAAGATAATC
1 AGTAAAAAG-TAATC
*
1668 AGTAAAGAATGAAAT-
1 AGTAAA-AA-GTAATC
*
1683 AGTAAAAGGTAATC
1 AGTAAAAAGTAATC
*
1697 AATAAAAAAGTAATC
1 AGT-AAAAAGTAATC
*
1712 AGTAAAAGGTAA
1 AGTAAAAAGTAA
1724 AATAGTAATC
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.09
14 11 0.24
15 24 0.53
16 5 0.11
17 1 0.02
ACGTcount: A:0.59, C:0.04, G:0.17, T:0.20
Consensus pattern (14 bp):
AGTAAAAAGTAATC
Found at i:1807 original size:22 final size:21
Alignment explanation
Indices: 1418--1847 Score: 165
Period size: 22 Copynumber: 20.3 Consensus size: 21
1408 AGGAAGAATG
*
1418 GTAAAGAGT-AAAGGGTAATCA
1 GTAAA-AGTAAAATGGTAATCA
* *
1439 GTAAAAAGTAAAAAGATAATCA
1 GT-AAAAGTAAAATGGTAATCA
* * * *
1461 GTAAAGAATGAAATAGTAA-AA
1 GTAAA-AGTAAAATGGTAATCA
* * **
1482 GGTAATCAATAAAAAAGTAATCA
1 -GTAA-AAGTAAAATGGTAATCA
*
1505 GTAAAAGGTAAAATAGTAATCA
1 GTAAAA-GTAAAATGGTAATCA
* *
1527 GTAAGAGCAAAATGGTAATCA
1 GTAAAAGTAAAATGGTAATCA
* * * *
1548 ATGAGAGCAAAATGGTAATCA
1 GTAAAAGTAAAATGGTAATCA
*
1569 GTAAAGAGTAAAATAGTAATCA
1 GTAAA-AGTAAAATGGTAATCA
*
1591 TTAAAAAGTAAGAA-GGTAATCA
1 GT-AAAAGTAA-AATGGTAATCA
*
1613 GTAAAGAGT-AAATAGTAATCA
1 GTAAA-AGTAAAATGGTAATCA
* * **
1634 GCAAAAGGT--AATAGTAAAAA
1 GTAAAA-GTAAAATGGTAATCA
* * **
1654 GTAAAAAG-ATAATCAGTAAAGA
1 GT-AAAAGTAAAAT-GGTAATCA
*
1676 ATGAAATAGTAAAA-GGTAATCA
1 GT-AAA-AGTAAAATGGTAATCA
* * *
1698 ATAAAA--AAGTAAT--CAGT-A
1 GTAAAAGTAA--AATGGTAATCA
* *
1716 --AAAGGTAAAATAGTAATCA
1 GTAAAAGTAAAATGGTAATCA
* *
1735 GTAAGAGCAAAATGGTAATCA
1 GTAAAAGTAAAATGGTAATCA
* * * *
1756 ATGAGAGCAAAATGGTAATCA
1 GTAAAAGTAAAATGGTAATCA
*
1777 GT-AAAGTAAAATAGTAATCA
1 GTAAAAGTAAAATGGTAATCA
*
1797 TTAAAAAGTAAGAA-GGTAATCA
1 GT-AAAAGTAA-AATGGTAATCA
1819 GTAAAGAGTAAAATGGTAATCA
1 GTAAA-AGTAAAATGGTAATCA
*
1841 GCAAAAG
1 GTAAAAG
1848 GTAATCAGTA
Statistics
Matches: 316, Mismatches: 59, Indels: 68
0.71 0.13 0.15
Matches are distributed among these distances:
16 6 0.02
18 7 0.02
19 3 0.01
20 33 0.10
21 113 0.36
22 141 0.45
23 10 0.03
24 3 0.01
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.20
Consensus pattern (21 bp):
GTAAAAGTAAAATGGTAATCA
Found at i:1832 original size:64 final size:64
Alignment explanation
Indices: 1706--1851 Score: 181
Period size: 64 Copynumber: 2.3 Consensus size: 64
1696 CAATAAAAAA
* *
1706 GTAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGCAAAATGGTAATCAATGAGAGCAAAATG
1 GTAATCAGTAAAAGGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCAATAAGAGCAAAATG
* * * *
1770 GTAATCAGT-AAA-GTAAAATAGTAATCATTAAAAAGTAAGAA-GGTAATCAGTAAAGAGTAAAA
1 GTAATCAGTAAAAGGTAAAATAGTAATCAGT-AAAAGCAA-AATGGTAATCAAT-AAGAGCAAAA
1832 TG
63 TG
*
1834 GTAATCAGCAAAAGGTAA
1 GTAATCAGTAAAAGGTAA
1852 TCAGTAAGAG
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
62 16 0.23
63 18 0.26
64 29 0.41
65 3 0.04
66 4 0.06
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.21
Consensus pattern (64 bp):
GTAATCAGTAAAAGGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCAATAAGAGCAAAATG
Found at i:1872 original size:21 final size:21
Alignment explanation
Indices: 1848--2001 Score: 90
Period size: 21 Copynumber: 7.9 Consensus size: 21
1838 TCAGCAAAAG
1848 GTAATCAGTAAGAGTAAAATA
1 GTAATCAGTAAGAGTAAAATA
1869 GTAATCAGT-AGAAGGT--AATCA
1 GTAATCAGTAAG-A-GTAAAAT-A
1890 GT-A--A---AGAGTAAAATA
1 GTAATCAGTAAGAGTAAAATA
*
1905 GTAATCAGT-A-A--AAGATA
1 GTAATCAGTAAGAGTAAAATA
*
1922 --A-TCAGTAAGAGTAAAACA
1 GTAATCAGTAAGAGTAAAATA
* *
1940 GTAA-CTAGTAAGAGTAAAGTG
1 GTAATC-AGTAAGAGTAAAATA
* *
1961 GTAATTAGTAAGAGTCAAATA
1 GTAATCAGTAAGAGTAAAATA
1982 GTAATCAGTAAAGAGTAAAA
1 GTAATCAGT-AAGAGTAAAA
2002 AATGATCAGT
Statistics
Matches: 101, Mismatches: 12, Indels: 39
0.66 0.08 0.26
Matches are distributed among these distances:
14 7 0.07
15 6 0.06
16 7 0.07
17 5 0.05
18 6 0.06
19 1 0.01
20 9 0.09
21 49 0.49
22 11 0.11
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.23
Consensus pattern (21 bp):
GTAATCAGTAAGAGTAAAATA
Found at i:1900 original size:14 final size:15
Alignment explanation
Indices: 1868--1900 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1858 AGAGTAAAAT
1868 AGTAATCAGTAGAAG
1 AGTAATCAGTAGAAG
1883 -GTAATCAGTA-AAG
1 AGTAATCAGTAGAAG
1896 AGTAA
1 AGTAA
1901 AATAGTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.21
Consensus pattern (15 bp):
AGTAATCAGTAGAAG
Found at i:1925 original size:14 final size:15
Alignment explanation
Indices: 1896--1929 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1886 ATCAGTAAAG
*
1896 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
1911 AGTAAAAGA-TAATC
1 AGTAAAAGAGTAATC
1925 AGTAA
1 AGTAA
1930 GAGTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:1949 original size:42 final size:40
Alignment explanation
Indices: 1901--2013 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 40
1891 TAAAGAGTAA
*
1901 AATAGTAATCAGTAAAAGATAATCAGTAAGAGTAAAACAGT
1 AATAGTAA-GAGTAAAAGATAATCAGTAAGAGTAAAACAGT
* * * * *
1942 AACTAGTAAGAGTAAAGTGGTAATTAGTAAGAGTCAAATAGT
1 AA-TAGTAAGAGTAAA-AGATAATCAGTAAGAGTAAAACAGT
* *
1984 AATCAGTAAAGAGTAAAAAATGATCAGTAA
1 AAT-AGT-AAGAGTAAAAGATAATCAGTAA
2014 TTCAAAGAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
41 9 0.16
42 39 0.68
43 9 0.16
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.23
Consensus pattern (40 bp):
AATAGTAAGAGTAAAAGATAATCAGTAAGAGTAAAACAGT
Found at i:1950 original size:35 final size:36
Alignment explanation
Indices: 1803--1943 Score: 214
Period size: 35 Copynumber: 3.9 Consensus size: 36
1793 ATCATTAAAA
*
1803 AGTAAGAAGGTAATCAGTAAAGAGTAAAATGGTAATC
1 AGTAA-AAGGTAATCAGTAAAGAGTAAAATAGTAATC
*
1840 AGCAAAAGGTAATCAGT-AAGAGTAAAATAGTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
*
1875 AGTAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
* *
1911 AGTAAAAGATAATCAGT-AAGAGTAAAACAGTAA
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAA
1944 CTAGTAAGAG
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
35 47 0.49
36 45 0.47
37 4 0.04
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (36 bp):
AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
Found at i:1971 original size:71 final size:71
Alignment explanation
Indices: 1807--1943 Score: 238
Period size: 71 Copynumber: 1.9 Consensus size: 71
1797 TTAAAAAGTA
* * *
1807 AGAAGGTAATCAGTAAAGAGTAAAATGGTAATCAGCAAAAGGTAATCAGTAAGAGTAAAATAGTA
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGATAATCAGTAAGAGTAAAACAGTA
1872 ATCAGT
66 ATCAGT
*
1878 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAGATAATCAGTAAGAGTAAAACAGTA
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGATAATCAGTAAGAGTAAAACAGTA
1943 A
66 A
1944 CTAGTAAGAG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.20
Consensus pattern (71 bp):
AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGATAATCAGTAAGAGTAAAACAGTA
ATCAGT
Found at i:2090 original size:13 final size:13
Alignment explanation
Indices: 2074--2120 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2064 GGTAATAAAT
2074 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
2087 AAAAGAGTAATTAG
1 AAAAGAG-AGTAAG
2101 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
2114 AAAAGAG
1 AAAAGAG
2121 TAAAAATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Found at i:2090 original size:29 final size:28
Alignment explanation
Indices: 2065--2127 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
2055 GTAAAAAGTG
2065 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
* *
2093 GTAATTAGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
2120 GTAA-AAAT
1 GTAATAAAT
2128 GATAAAAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.06
27 18 0.58
28 11 0.35
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:2802 original size:22 final size:22
Alignment explanation
Indices: 2776--2828 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2766 TTGAGTGTTA
2776 TTAAAATAAAA-AAGGGTTTTAT
1 TTAAAA-AAAAGAAGGGTTTTAT
* *
2798 TTAAAAAAAAGAAGTGTTTTAAG
1 TTAAAAAAAAGAAGGGTTTT-AT
2821 TTAAAAAA
1 TTAAAAAA
2829 TAATAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 4 0.15
22 14 0.52
23 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (22 bp):
TTAAAAAAAAGAAGGGTTTTAT
Found at i:3408 original size:19 final size:18
Alignment explanation
Indices: 3384--3419 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3374 TGAAGATTTC
3384 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
3403 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
3420 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.