Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006025.1 Corchorus capsularis cultivar CVL-1 contig06043, 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: 32550
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:797 original size:8 final size:8
Alignment explanation
Indices: 773--1075 Score: 75
Period size: 8 Copynumber: 40.6 Consensus size: 8
763 CATTTGGAAT
*
773 TTGAAGGA
1 TTGAAGTA
781 TTGAA--A
1 TTGAAGTA
787 TTGAAGTA
1 TTGAAGTA
**
795 TTGAAAAA
1 TTGAAGTA
*
803 TGGAA--A
1 TTGAAGTA
809 TTGAAGTA
1 TTGAAGTA
*
817 TTGAAGAA
1 TTGAAGTA
*
825 TCGAA--A
1 TTGAAGTA
831 TTGAA-TCA
1 TTGAAGT-A
*
839 TTGAAGAA
1 TTGAAGTA
847 TTG-AG-A
1 TTGAAGTA
853 TTGAAGTA
1 TTGAAGTA
* *
861 TCGAAATA
1 TTGAAGTA
869 TTGAA--A
1 TTGAAGTA
**
875 TTGAAACA
1 TTGAAGTA
*
883 TTGAAGAA
1 TTGAAGTA
891 TTGAA-T-
1 TTGAAGTA
* *
897 TTGGAGGA
1 TTGAAGTA
905 TTGAA--A
1 TTGAAGTA
***
911 TTGAACCG
1 TTGAAGTA
*
919 TTGAACTA
1 TTGAAGTA
927 TTTGAA--A
1 -TTGAAGTA
*
934 TTGAAGCA
1 TTGAAGTA
*
942 TTTGAAGAA
1 -TTGAAGTA
* *
951 TTAAAATA
1 TTGAAGTA
959 TTGAAGTA
1 TTGAAGTA
* *
967 TTGAAATT
1 TTGAAGTA
*
975 TTGAAGCA
1 TTGAAGTA
983 TTGACA-T-
1 TTGA-AGTA
990 TTGGAA-T-
1 TT-GAAGTA
*
997 TTGAAGAA
1 TTGAAGTA
1005 TTG-AG-A
1 TTGAAGTA
**
1011 TTGAAACA
1 TTGAAGTA
*
1019 TTGAAATA
1 TTGAAGTA
1027 TTGAA--A
1 TTGAAGTA
* *
1033 TCGAAGCA
1 TTGAAGTA
1041 TTGAAGTA
1 TTGAAGTA
1049 TTGAA--A
1 TTGAAGTA
*
1055 TTGAAGAA
1 TTGAAGTA
*
1063 TTGAAATA
1 TTGAAGTA
1071 TTGAA
1 TTGAA
1076 ATTGAAACAT
Statistics
Matches: 226, Mismatches: 40, Indels: 58
0.70 0.12 0.18
Matches are distributed among these distances:
6 59 0.26
7 14 0.06
8 140 0.62
9 13 0.06
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (8 bp):
TTGAAGTA
Found at i:798 original size:22 final size:22
Alignment explanation
Indices: 773--909 Score: 143
Period size: 22 Copynumber: 6.2 Consensus size: 22
763 CATTTGGAAT
*
773 TTGAAGGATTGAAATTGAAGTA
1 TTGAAGAATTGAAATTGAAGTA
* *
795 TTGAAAAATGGAAATTGAAGTA
1 TTGAAGAATTGAAATTGAAGTA
*
817 TTGAAGAATCGAAATTGAA-TCA
1 TTGAAGAATTGAAATTGAAGT-A
*
839 TTGAAGAATTGAGATTGAAGTA
1 TTGAAGAATTGAAATTGAAGTA
* **
861 TCGAA-ATATTGAAATTGAAACA
1 TTGAAGA-ATTGAAATTGAAGTA
* * *
883 TTGAAGAATTGAATTTGGAGGA
1 TTGAAGAATTGAAATTGAAGTA
905 TTGAA
1 TTGAA
910 ATTGAACCGT
Statistics
Matches: 95, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
21 2 0.02
22 91 0.96
23 2 0.02
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAGTA
Found at i:909 original size:66 final size:64
Alignment explanation
Indices: 731--901 Score: 173
Period size: 66 Copynumber: 2.6 Consensus size: 64
721 AACATTAAAA
* * *
731 AAAAATGAAGAAA-TGAAATATCGAAGCATTGACATTTGGAATTTGAAGGATTGAAATTGAAGTA
1 AAAAATG--GAAATTGAAATATTGAAGAATTGA-ATTTGGAA-TTGAAGAATTGAAATTGAAGTA
*
795 TTG
62 TCG
* * * * *
798 AAAAATGGAAATTGAAGTATTGAAGAATCGAAATTGAATCATTGAAGAATTGAGATTGAAGTATC
1 AAAAATGGAAATTGAAATATTGAAGAATTGAATTTGGA--ATTGAAGAATTGAAATTGAAGTATC
863 G
64 G
* * *
864 AAATATTGAAATTGAAACATTGAAGAATTGAATTTGGA
1 AAAAATGGAAATTGAAATATTGAAGAATTGAATTTGGA
902 GGATTGAAAT
Statistics
Matches: 85, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
65 9 0.11
66 68 0.80
67 8 0.09
ACGTcount: A:0.46, C:0.04, G:0.22, T:0.29
Consensus pattern (64 bp):
AAAAATGGAAATTGAAATATTGAAGAATTGAATTTGGAATTGAAGAATTGAAATTGAAGTATCG
Found at i:911 original size:44 final size:43
Alignment explanation
Indices: 780--1081 Score: 142
Period size: 44 Copynumber: 6.8 Consensus size: 43
770 AATTTGAAGG
** * *
780 ATTGAAATTGAAGTATTGAAAAATGGAAATTGAAGTATTGAAGA-
1 ATTGAAATTGAAACATTGAAGAATTG-AATTGAAGTATTGAA-AT
* * *
824 ATCGAAATTGAATCATTGAAGAATTGAGATTGAAGTATCGAAAT
1 ATTGAAATTGAAACATTGAAGAATTGA-ATTGAAGTATTGAAAT
* *
868 ATTGAAATTGAAACATTGAAGAATTGAATTTGGAGGATTG-AA-
1 ATTGAAATTGAAACATTGAAGAATTGAA-TTGAAGTATTGAAAT
* * *
910 ATTGAACCGTTG-AACTATTTG-A-AATTGAAGCATTTGAAGAATTAAAAT
1 ATTGAA--ATTGAAAC-A-TTGAAGAATTG-A--A-TTGAAGTATTGAAAT
** *
958 ATTGAAGTATTGAAATTTTGAAGCATTGACATTTGGAA-T-TTGAAGA-
1 ATTGAA--ATTGAAACATTGAAGAATTGA-A-TT-GAAGTATTGAA-AT
* * * *
1004 ATTGAGATTGAAACATTGAA-ATATTGAAATCGAAGCATTGAAGT
1 ATTGAAATTGAAACATTGAAGA-ATTG-AATTGAAGTATTGAAAT
1048 ATTGAAATTGAAGA-ATTGAA-ATATTGAAATTGAA
1 ATTGAAATTGAA-ACATTGAAGA-ATTG-AATTGAA
1082 ACATAGAAGG
Statistics
Matches: 203, Mismatches: 32, Indels: 46
0.72 0.11 0.16
Matches are distributed among these distances:
42 9 0.04
43 14 0.07
44 125 0.62
45 5 0.02
46 19 0.09
47 11 0.05
48 14 0.07
49 6 0.03
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (43 bp):
ATTGAAATTGAAACATTGAAGAATTGAATTGAAGTATTGAAAT
Found at i:1022 original size:22 final size:23
Alignment explanation
Indices: 997--1090 Score: 108
Period size: 22 Copynumber: 4.3 Consensus size: 23
987 CATTTGGAAT
*
997 TTGAAGA-ATTGAGATTGAAACA
1 TTGAAGATATTGAAATTGAAACA
* *
1019 TTGAA-ATATTGAAATCGAAGCA
1 TTGAAGATATTGAAATTGAAACA
1041 TTGAAG-TATTGAAATTGAAGA-A
1 TTGAAGATATTGAAATTGAA-ACA
1063 TTGAA-ATATTGAAATTGAAACA
1 TTGAAGATATTGAAATTGAAACA
*
1085 TAGAAG
1 TTGAAG
1091 GACTGAACAT
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.03
22 58 0.97
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (23 bp):
TTGAAGATATTGAAATTGAAACA
Found at i:1078 original size:14 final size:14
Alignment explanation
Indices: 1018--1082 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
1008 AGATTGAAAC
1018 ATTGAAATATTGAA
1 ATTGAAATATTGAA
* **
1032 ATCGAAGCATTGAA
1 ATTGAAATATTGAA
1046 GTATTG-AA-ATTGAAGA
1 --ATTGAAATATTG-A-A
1062 ATTGAAATATTGAA
1 ATTGAAATATTGAA
1076 ATTGAAA
1 ATTGAAA
1083 CATAGAAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
14 27 0.68
15 5 0.12
16 8 0.20
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.31
Consensus pattern (14 bp):
ATTGAAATATTGAA
Found at i:1104 original size:44 final size:44
Alignment explanation
Indices: 1010--1113 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 44
1000 AAGAATTGAG
* * * *
1010 ATTGAA-ACATTGAAATATTGAAATCGAAGCATTGAAGTATTGAA
1 ATTGAAGA-ATTGAAATATTGAAATCGAAACATAGAAGGACTGAA
*
1054 ATTGAAGAATTGAAATATTGAAATTGAAACATAGAAGGACTGAA
1 ATTGAAGAATTGAAATATTGAAATCGAAACATAGAAGGACTGAA
*
1098 CA-TGAAGAATTTAAAT
1 -ATTGAAGAATTGAAAT
1114 CGGATCATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 50 0.96
45 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (44 bp):
ATTGAAGAATTGAAATATTGAAATCGAAACATAGAAGGACTGAA
Found at i:1269 original size:58 final size:57
Alignment explanation
Indices: 1199--1329 Score: 140
Period size: 58 Copynumber: 2.3 Consensus size: 57
1189 GGAGATTTGG
* * *
1199 AATTG-AGACATTGAATAATT-AGGGAATGGAAGAAAGACCATCATGTATCATTGAAGCC
1 AATTGAAG-CATTGAATAATTAAGGG-A-CGAAGAAAGACCACCATGGATCATTGAAGCC
* * **
1257 AATTGAAGCATTGAATAATTGAAGGGACGAAGAAAGACCACCCTGGGTCATTGAAGTG
1 AATTGAAGCATTGAATAATT-AAGGGACGAAGAAAGACCACCATGGATCATTGAAGCC
*
1315 AATTGAAGAATTGAA
1 AATTGAAGCATTGAA
1330 GCATTGGGTA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
58 55 0.89
59 3 0.05
60 4 0.06
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.23
Consensus pattern (57 bp):
AATTGAAGCATTGAATAATTAAGGGACGAAGAAAGACCACCATGGATCATTGAAGCC
Found at i:1364 original size:24 final size:24
Alignment explanation
Indices: 1310--1384 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
1300 TGGGTCATTG
*
1310 AAGTGAATTGAAGAATTGAAGCATT
1 AAGT-AATTGAAGAATTGAAGCAAT
** *
1335 GGGTAATTGAATAATTGAAGCAAT
1 AAGTAATTGAAGAATTGAAGCAAT
** * *
1359 AAGTAATCAAAGAATCGAAGAAAT
1 AAGTAATTGAAGAATTGAAGCAAT
1383 AA
1 AA
1385 TTGAAATATT
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
24 37 0.95
25 2 0.05
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.24
Consensus pattern (24 bp):
AAGTAATTGAAGAATTGAAGCAAT
Found at i:1460 original size:22 final size:22
Alignment explanation
Indices: 1432--1520 Score: 103
Period size: 22 Copynumber: 4.1 Consensus size: 22
1422 TCATTGAAGT
1432 AAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* *
1454 AATTTGAAGAATTG-A-AATTG
1 AAATTGAAGCATTGAAGAATTG
*
1474 AAATTGAGGCATTGAAGAA-TG
1 AAATTGAAGCATTGAAGAATTG
* *
1495 AGAATTGAAACATTGAAGAACTG
1 A-AATTGAAGCATTGAAGAATTG
1518 AAA
1 AAA
1521 AAGAGATCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
20 16 0.29
21 5 0.09
22 32 0.57
23 3 0.05
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.26
Consensus pattern (22 bp):
AAATTGAAGCATTGAAGAATTG
Found at i:1462 original size:14 final size:14
Alignment explanation
Indices: 1442--1475 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1432 AAATTGAAGC
1442 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
*
1456 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
1470 ATTGAA
1 ATTGAA
1476 ATTGAGGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:1503 original size:42 final size:42
Alignment explanation
Indices: 1432--1511 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
1422 TCATTGAAGT
*
1432 AAATTGAAGCATTGAAGAATTGAATTTGAAGA-ATTGAAATTG
1 AAATTGAAGCATTGAAGAATTGAAATTGAA-ACATTGAAATTG
*
1474 AAATTGAGGCATTGAAGAA-TGAGAATTGAAACATTGAA
1 AAATTGAAGCATTGAAGAATTGA-AATTGAAACATTGAA
1512 GAACTGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 4 0.12
42 30 0.88
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.28
Consensus pattern (42 bp):
AAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAATTG
Found at i:1562 original size:16 final size:16
Alignment explanation
Indices: 1541--1571 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1531 CTTGAAATAA
*
1541 ATTGAAGTATTGAAGG
1 ATTGAAGAATTGAAGG
1557 ATTGAAGAATTGAAG
1 ATTGAAGAATTGAAG
1572 CTAATTGAAC
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:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (16 bp):
ATTGAAGAATTGAAGG
Found at i:2527 original size:8 final size:8
Alignment explanation
Indices: 2509--2549 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
2499 CTCTTTTCCA
2509 TTCATTTTT
1 TTCA-TTTT
2518 TTCATTTT
1 TTCATTTT
2526 TTCATTTT
1 TTCATTTT
2534 TT-A-TTT
1 TTCATTTT
2540 TTCATTTT
1 TTCATTTT
2548 TT
1 TT
2550 TTCATTGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.17
7 2 0.07
8 19 0.63
9 4 0.13
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (8 bp):
TTCATTTT
Found at i:2527 original size:22 final size:22
Alignment explanation
Indices: 2502--2549 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2492 CCTAGAGCTC
*
2502 TTTTCCATTCATT-TTTTTCAT
1 TTTTTCATTCATTATTTTTCAT
**
2523 TTTTTCATTTTTTATTTTTCAT
1 TTTTTCATTCATTATTTTTCAT
2545 TTTTT
1 TTTTT
2550 TTCATTGCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTCATTCATTATTTTTCAT
Found at i:2531 original size:17 final size:17
Alignment explanation
Indices: 2509--2555 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
2499 CTCTTTTCCA
2509 TTCATTTTTTTCATTTT
1 TTCATTTTTTTCATTTT
2526 TTCA-TTTTTT-A-TTT
1 TTCATTTTTTTCATTTT
2540 TTCATTTTTTTTCATT
1 TTCA-TTTTTTTCATT
2556 GCACTTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 7 0.27
15 1 0.04
16 12 0.46
17 5 0.19
18 1 0.04
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCATTTTTTTCATTTT
Found at i:2533 original size:7 final size:7
Alignment explanation
Indices: 2515--2548 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
2505 TCCATTCATT
2515 TTTTTCA
1 TTTTTCA
2522 TTTTTTCA
1 -TTTTTCA
*
2530 TTTTTTA
1 TTTTTCA
2537 TTTTTCA
1 TTTTTCA
2544 TTTTT
1 TTTTT
2549 TTTCATTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTCA
Found at i:2878 original size:6 final size:6
Alignment explanation
Indices: 2869--2896 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2859 TCACTTTCAC
2869 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
2897 TTTCTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:3256 original size:14 final size:14
Alignment explanation
Indices: 3224--3257 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3214 CAAAAATTAT
3224 TTTTTG-AAAAACA
1 TTTTTGAAAAAACA
3237 TTTTTGAAAAAACA
1 TTTTTGAAAAAACA
3251 TTTTTGA
1 TTTTTGA
3258 GAATCATGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (14 bp):
TTTTTGAAAAAACA
Found at i:3342 original size:11 final size:11
Alignment explanation
Indices: 3326--3352 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3316 CCTTTATTTA
3326 TTTTTCATCAT
1 TTTTTCATCAT
3337 TTTTTCATCAT
1 TTTTTCATCAT
3348 TTTTT
1 TTTTT
3353 TTGGACTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTCATCAT
Found at i:5220 original size:19 final size:18
Alignment explanation
Indices: 5187--5222 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5177 TTGAAATAAT
5187 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
5205 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
5223 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:11700 original size:14 final size:14
Alignment explanation
Indices: 11681--11710 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11671 TCTGACTATC
11681 TGACTATAAAGCCT
1 TGACTATAAAGCCT
11695 TGACTATAAAGCCT
1 TGACTATAAAGCCT
11709 TG
1 TG
11711 TAATTGCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (14 bp):
TGACTATAAAGCCT
Found at i:12399 original size:22 final size:22
Alignment explanation
Indices: 12374--12447 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
12364 CATATTAAAA
12374 TTTGATAACCACACTGTGAAAT
1 TTTGATAACCACACTGTGAAAT
* * *
12396 TTTGGTAACCAAACTATGAAAT
1 TTTGATAACCACACTGTGAAAT
* * * *
12418 TTCGATAATCTCAGTGTGAAAT
1 TTTGATAACCACACTGTGAAAT
12440 TTTGATAA
1 TTTGATAA
12448 TCTGCCTAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (22 bp):
TTTGATAACCACACTGTGAAAT
Found at i:12478 original size:22 final size:22
Alignment explanation
Indices: 12436--12479 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12426 TCTCAGTGTG
* *
12436 AAATTTTGATAATCTGCCTAAA
1 AAATTTTAATAATCTACCTAAA
12458 AAATTTTAATAATC-ACACTAAA
1 AAATTTTAATAATCTAC-CTAAA
12480 TAAAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (22 bp):
AAATTTTAATAATCTACCTAAA
Found at i:12627 original size:22 final size:21
Alignment explanation
Indices: 12595--12654 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
12585 CTCTCTATGT
12595 ATTTTCAATAACCTCTCTATAAA
1 ATTTTC-ATAACCTC-CTATAAA
12618 ATTTTCATAACCTACCTATAAA
1 ATTTTCATAACCT-CCTATAAA
**
12640 ATTTTGTTAACCTCC
1 ATTTTCATAACCTCC
12655 CTAGGAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.06
22 25 0.74
23 7 0.21
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTTCATAACCTCCTATAAA
Found at i:12657 original size:22 final size:22
Alignment explanation
Indices: 12602--12671 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
12592 TGTATTTTCA
* *
12602 ATAACCTCTCTATAAAATTTTC
1 ATAACCTCCCTATAAAATTTTG
*
12624 ATAACCTACCTATAAAATTTTG
1 ATAACCTCCCTATAAAATTTTG
* **
12646 TTAACCTCCCTAGGAAATTTTG
1 ATAACCTCCCTATAAAATTTTG
12668 ATAA
1 ATAA
12672 GCACAAATTC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (22 bp):
ATAACCTCCCTATAAAATTTTG
Found at i:12726 original size:22 final size:22
Alignment explanation
Indices: 12698--12885 Score: 93
Period size: 22 Copynumber: 8.5 Consensus size: 22
12688 CCTCCCTCGT
*
12698 TATGAAATTTTGTTAACTTTCA
1 TATGAAATTTTGATAACTTTCA
* * *
12720 TATGAAATTTT-ATTAACATCCC
1 TATGAAATTTTGA-TAACTTTCA
* * * *
12742 TAAGAAGTTTTGGTAAGCTTT-T
1 TATGAAATTTTGATAA-CTTTCA
* * *
12764 TATGAAATTTTGGTAAC-CTCTG
1 TATGAAATTTTGATAACTTTC-A
* *
12786 TATGAAATTTTGATAA-ATACA
1 TATGAAATTTTGATAACTTTCA
* *
12807 CTATGAAGTTTTGATAAC-CTCTA
1 -TATGAAATTTTGATAACTTTC-A
* **
12830 TATGAAATTTTGGTAACCAT-A
1 TATGAAATTTTGATAACTTTCA
12851 CTATGAAATTTTGATAATCTTTC-
1 -TATGAAATTTTGATAA-CTTTCA
*
12874 TATGTAATTTTG
1 TATGAAATTTTG
12886 GTTTGATTGT
Statistics
Matches: 125, Mismatches: 28, Indels: 26
0.70 0.16 0.15
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 116 0.93
23 6 0.05
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACTTTCA
Found at i:12797 original size:44 final size:43
Alignment explanation
Indices: 12698--12887 Score: 157
Period size: 44 Copynumber: 4.3 Consensus size: 43
12688 CCTCCCTCGT
* * * *
12698 TATGAAATTTTGTTAACTTTCATATGAAATTTT-ATTAACATCCC
1 TATGAAATTTTGGTAACTTAC-TATGAAATTTTGA-TAACCTCTC
* * ** * *
12742 TAAGAAGTTTTGGTAAGCTTTTTATGAAATTTTGGTAACCTCTG
1 TATGAAATTTTGGTAA-CTTACTATGAAATTTTGATAACCTCTC
* * * * *
12786 TATGAAATTTTGATAAATACACTATGAAGTTTTGATAACCTCTA
1 TATGAAATTTTGGTAACT-TACTATGAAATTTTGATAACCTCTC
* * *
12830 TATGAAATTTTGGTAACCATACTATGAAATTTTGATAATCTTTC
1 TATGAAATTTTGGTAA-CTTACTATGAAATTTTGATAACCTCTC
*
12874 TATGTAATTTTGGT
1 TATGAAATTTTGGT
12888 TTGATTGTCA
Statistics
Matches: 115, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
43 1 0.01
44 110 0.96
45 4 0.03
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.44
Consensus pattern (43 bp):
TATGAAATTTTGGTAACTTACTATGAAATTTTGATAACCTCTC
Found at i:12877 original size:66 final size:65
Alignment explanation
Indices: 12698--12867 Score: 184
Period size: 66 Copynumber: 2.6 Consensus size: 65
12688 CCTCCCTCGT
* * * * * * *
12698 TATGAAATTTTGTTAACTTTCATATGAAATTTT-ATTAACAT-CCCTAAGAAGTTTTGGTAAGCT
1 TATGAAATTTTGGTAAC-CTCGTATGAAATTTTGA-TAA-ATACACTATGAAGTTTTGATAACCT
* *
12761 TTT
63 CTA
12764 TATGAAATTTTGGTAACCTCTGTATGAAATTTTGATAAATACACTATGAAGTTTTGATAACCTCT
1 TATGAAATTTTGGTAACCTC-GTATGAAATTTTGATAAATACACTATGAAGTTTTGATAACCTCT
12829 A
65 A
12830 TATGAAATTTTGGTAACCATAC-TATGAAATTTTGATAA
1 TATGAAATTTTGGTAACC-T-CGTATGAAATTTTGATAA
12868 TCTTTCTATG
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
65 4 0.04
66 83 0.92
67 2 0.02
68 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (65 bp):
TATGAAATTTTGGTAACCTCGTATGAAATTTTGATAAATACACTATGAAGTTTTGATAACCTCTA
Found at i:14126 original size:67 final size:68
Alignment explanation
Indices: 13998--14134 Score: 213
Period size: 67 Copynumber: 2.0 Consensus size: 68
13988 ATTACTGATA
* * *
13998 AGTCTCTCAATTAGTTTCTTACACTTTCTTTCCCTCAGCCCTATTTTGGTAATAAATAGTGTCAT
1 AGTCCCTCAATTAGTTTCTTACACTTTC-TTCCCCCAGCCCTATTTTGGTAATAAACAGTGTCAT
14063 TAAT
65 TAAT
* *
14067 AGTCCCTCAATTAGTTTTTTACACTTTC-TCCCCCTGCCCTATTTTGGTAATAAACAGTGTCATT
1 AGTCCCTCAATTAGTTTCTTACACTTTCTTCCCCCAGCCCTATTTTGGTAATAAACAGTGTCATT
14131 AAT
66 AAT
14134 A
1 A
14135 TTCATTAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 37 0.59
69 26 0.41
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (68 bp):
AGTCCCTCAATTAGTTTCTTACACTTTCTTCCCCCAGCCCTATTTTGGTAATAAACAGTGTCATT
AAT
Found at i:16168 original size:11 final size:10
Alignment explanation
Indices: 16129--16170 Score: 52
Period size: 9 Copynumber: 4.2 Consensus size: 10
16119 GTTAATAAAT
16129 TATAAAAT-A
1 TATAAAATAA
16138 TATAAAA-AA
1 TATAAAATAA
16147 TATTAAAATAA
1 TA-TAAAATAA
16158 TATAAATATAA
1 TATAAA-ATAA
16169 TA
1 TA
16171 AATGATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 10 0.34
10 9 0.31
11 10 0.34
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TATAAAATAA
Found at i:16172 original size:19 final size:19
Alignment explanation
Indices: 16125--16172 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
16115 GTATGTTAAT
*
16125 AAATTATAAAATATATAAA
1 AAATAATAAAATATATAAA
*
16144 AAATATTAAAATA-ATATAA
1 AAATAATAAAATATATA-AA
*
16163 ATATAATAAA
1 AAATAATAAA
16173 TGATATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAATAAAATATATAAA
Found at i:16194 original size:29 final size:29
Alignment explanation
Indices: 16154--16260 Score: 78
Period size: 29 Copynumber: 3.7 Consensus size: 29
16144 AAATATTAAA
*
16154 ATAATATA-AATATAATAAATGATATATT
1 ATAATTTATAATATAATAAATGATATATT
* *
16182 ATAATTTGTAATATATATAAGATGA-ATAAT
1 ATAATTTATAATATA-ATAA-ATGATATATT
* * * *
16212 -TAATTTTTATATATAAAAAATAATAATTTT
1 ATAATTTATA-ATATAATAAATGAT-ATATT
*
16242 ATAAATTAT-ATATAATAAA
1 ATAATTTATAATATAATAAA
16261 AATCCAAATT
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
28 9 0.15
29 26 0.43
30 16 0.26
31 10 0.16
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (29 bp):
ATAATTTATAATATAATAAATGATATATT
Found at i:20538 original size:29 final size:29
Alignment explanation
Indices: 20469--20545 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
20459 GGCCTAATGT
* **
20469 CCAAATTGGGTCTAAACCTTTCCAAACTTG
1 CCAAATTGAGTCTAAACCTTT-CAAACAGG
*
20499 CTCAATTTGAGTCTAAACCTTT-AAACAGG
1 C-CAAATTGAGTCTAAACCTTTCAAACAGG
20528 ACCAAATTGAGTCTAAAC
1 -CCAAATTGAGTCTAAAC
20546 GTTAGCAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 20 0.50
30 2 0.05
31 18 0.45
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (29 bp):
CCAAATTGAGTCTAAACCTTTCAAACAGG
Found at i:23001 original size:17 final size:17
Alignment explanation
Indices: 22979--23013 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
22969 AAATTTTAAA
22979 ATTAAAGAGGGTATTTT
1 ATTAAAGAGGGTATTTT
22996 ATTAAAGAGGGTATTTT
1 ATTAAAGAGGGTATTTT
23013 A
1 A
23014 GATATTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (17 bp):
ATTAAAGAGGGTATTTT
Found at i:26785 original size:21 final size:21
Alignment explanation
Indices: 26761--26811 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
26751 TTGTAAACAC
26761 CTTGTATCAATCCTAACCTAT
1 CTTGTATCAATCCTAACCTAT
* *
26782 CTTGTACCGATCCTAACCTAT
1 CTTGTATCAATCCTAACCTAT
26803 CTTTGTATC
1 C-TTGTATC
26812 TCTATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.24, C:0.29, G:0.08, T:0.39
Consensus pattern (21 bp):
CTTGTATCAATCCTAACCTAT
Done.