Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000544.1 Corchorus capsularis cultivar CVL-1 contig00544, 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, 807
Length: 1346
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.22
Found at i:263 original size:40 final size:38
Alignment explanation
Indices: 172--267 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 38
162 AGTGAAAAGA
* *
172 AAAAGTAGTAATCAGTCAATTAGTAACTAAGAGGAAGT
1 AAAAGTAGTAATCAGTAAATTAGTAACCAAGAGGAAGT
* *
210 AAAAGGATTAATCAGTAAATT-GATAACCAAGAGAAGAAGT
1 AAAAGTAGTAATCAGTAAATTAG-TAACCAAGAG--GAAGT
*
250 AAAAGTAGCAATCAGTAA
1 AAAAGTAGTAATCAGTAA
268 GTAAGGGTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 1 0.02
38 27 0.56
40 20 0.42
ACGTcount: A:0.51, C:0.08, G:0.20, T:0.21
Consensus pattern (38 bp):
AAAAGTAGTAATCAGTAAATTAGTAACCAAGAGGAAGT
Found at i:329 original size:32 final size:31
Alignment explanation
Indices: 259--331 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
249 TAAAAGTAGC
*
259 AATCAGTAAGTAAGGGTCAAAGTAAAAGGGT
1 AATCAGTAAGTAAGAGTCAAAGTAAAAGGGT
* * * *
290 AAGTCAGTAATTAAGAGTCAAGGTAGAAGGATT
1 AA-TCAGTAAGTAAGAGTCAAAGTAAAAGG-GT
323 AATCAGTAA
1 AATCAGTAA
332 ATTGATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 2 0.06
32 30 0.86
33 3 0.09
ACGTcount: A:0.45, C:0.07, G:0.26, T:0.22
Consensus pattern (31 bp):
AATCAGTAAGTAAGAGTCAAAGTAAAAGGGT
Found at i:479 original size:32 final size:32
Alignment explanation
Indices: 404--513 Score: 136
Period size: 32 Copynumber: 3.5 Consensus size: 32
394 ATTAAAAAAA
* *
404 AAAAGAAGTAATCAGTAGAAAGAAAT-AAA--
1 AAAAGAAGTAATCAGTAGAATGAAGTGAAAGT
* * *
433 AGAGGAAGTGATCAGTAGAATGAAGTGAAAGT
1 AAAAGAAGTAATCAGTAGAATGAAGTGAAAGT
* *
465 AAAAGAAGTAATCAGTAAAATGGAGTGAAAGT
1 AAAAGAAGTAATCAGTAGAATGAAGTGAAAGT
497 AAAAGAAGTAATCAGTA
1 AAAAGAAGTAATCAGTA
514 AGTTGGTAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 21 0.31
30 3 0.04
32 44 0.65
ACGTcount: A:0.55, C:0.04, G:0.25, T:0.17
Consensus pattern (32 bp):
AAAAGAAGTAATCAGTAGAATGAAGTGAAAGT
Found at i:537 original size:40 final size:40
Alignment explanation
Indices: 492--634 Score: 259
Period size: 40 Copynumber: 3.6 Consensus size: 40
482 AAATGGAGTG
492 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
1 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
532 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
1 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
** *
572 AAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAAGAGTA
1 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
612 AAAGTAAAAGAAGTAATCAGTAA
1 AAAGTAAAAGAAGTAATCAGTAA
635 ATCGGTAAAG
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 100 1.00
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.23
Consensus pattern (40 bp):
AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAAGAATA
Found at i:659 original size:16 final size:17
Alignment explanation
Indices: 633--666 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
623 AGTAATCAGT
*
633 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
650 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAAAGTAA
666 A
1 A
667 GAGTAATCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.21, T:0.18
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:659 original size:40 final size:39
Alignment explanation
Indices: 492--688 Score: 153
Period size: 40 Copynumber: 5.0 Consensus size: 39
482 AAATGGAGTG
* *
492 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTA-AG-AATA
1 AAAGTAAAAGAAGTAATCAGTAAATCGGTAA--AGAGTAA-A
* *
532 AAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTA-AG-AATA
1 AAAGTAAAAGAAGTAATCAGTAAATCGGTAA--AGAGTAA-A
572 AAAGTAAAAGAAGTAATCAGTAAAAT-GGTAATTAAGAGT--A
1 AAAGTAAAAGAAGTAATCAGT-AAATCGGT-A--AAGAGTAAA
612 AAAGTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAA
1 AAAGTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAA
* ** *
651 AATGGT-AAA-AAGTAAAGAGT-AATCAGTAAAGAGTAAA
1 AA-AGTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAA
688 A
1 A
689 TGGTAAAATG
Statistics
Matches: 142, Mismatches: 5, Indels: 23
0.84 0.03 0.14
Matches are distributed among these distances:
37 23 0.16
38 9 0.06
39 11 0.08
40 91 0.64
41 5 0.04
42 2 0.01
43 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.22
Consensus pattern (39 bp):
AAAGTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAA
Found at i:720 original size:33 final size:32
Alignment explanation
Indices: 678--786 Score: 115
Period size: 32 Copynumber: 3.5 Consensus size: 32
668 AGTAATCAGT
678 AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAAT-GTAAAATGGTAATTAAATTC
*
711 AAAGAGTAAAATG-ACAAATGGTGATTAAATTC
1 AAAGAGTAAAATGTA-AAATGGTAATTAAATTC
*
743 AAAGAG-----TG-AAAATAGTAATTAAATTC
1 AAAGAGTAAAATGTAAAATGGTAATTAAATTC
769 AAGAGAGTAAAATAGTAA
1 AA-AGAGTAAAAT-GTAA
787 TCAGTAAAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
26 17 0.27
27 7 0.11
31 1 0.02
32 24 0.38
33 13 0.20
34 2 0.03
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.25
Consensus pattern (32 bp):
AAAGAGTAAAATGTAAAATGGTAATTAAATTC
Found at i:738 original size:32 final size:33
Alignment explanation
Indices: 678--760 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
668 AGTAATCAGT
678 AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
*
711 AAAGAGTAAAAT-G-ACAAATGGTGATTAAATTC
1 AAAGAGTAAAATGGTA-AAATGGTAATTAAATTC
*
743 AAAGAGTGAAAATAGTAA
1 AAAGAGT-AAAATGGTAA
761 TTAAATTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 1 0.02
32 24 0.53
33 17 0.38
34 2 0.04
35 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.24
Consensus pattern (33 bp):
AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
Found at i:763 original size:26 final size:26
Alignment explanation
Indices: 693--787 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 26
683 GTAAAATGGT
*
693 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATAGTAATTAAATTCAAAGAG-----TG
* *
724 ACAAATGGTGATTAAATTCAAAGAGTG
1 A-AAATAGTAATTAAATTCAAAGAGTG
751 AAAATAGTAATTAAATTCAAGAGAGT-
1 AAAATAGTAATTAAATTCAA-AGAGTG
777 AAAATAGTAAT
1 AAAATAGTAAT
788 CAGTAAAGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
26 28 0.47
27 8 0.14
31 1 0.02
32 22 0.37
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (26 bp):
AAAATAGTAATTAAATTCAAAGAGTG
Found at i:812 original size:7 final size:7
Alignment explanation
Indices: 789--912 Score: 92
Period size: 7 Copynumber: 17.9 Consensus size: 7
779 AATAGTAATC
789 AGTAAAG
1 AGTAAAG
*
796 AGAAAAG
1 AGTAAAG
803 AGTAAAG
1 AGTAAAG
**
810 AGTAATC
1 AGTAAAG
817 AGT-AAG
1 AGTAAAG
*
823 AGTAAAAT
1 AGT-AAAG
**
831 AGTAATC
1 AGTAAAG
838 AGTAAAG
1 AGTAAAG
*
845 AGAAAAG
1 AGTAAAG
852 AGTAAAG
1 AGTAAAG
**
859 AGTAATC
1 AGTAAAG
866 AGT-AAG
1 AGTAAAG
*
872 AGTAAAA
1 AGTAAAG
*
879 AGGTAAAA
1 A-GTAAAG
887 AGTAAAG
1 AGTAAAG
**
894 AGTAATC
1 AGTAAAG
901 AGTAAA-
1 AGTAAAG
907 AGTAAA
1 AGTAAA
913 AGAATAAATT
Statistics
Matches: 91, Mismatches: 22, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
6 14 0.15
7 65 0.71
8 12 0.13
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (7 bp):
AGTAAAG
Found at i:821 original size:28 final size:27
Alignment explanation
Indices: 772--891 Score: 119
Period size: 28 Copynumber: 4.5 Consensus size: 27
762 TAAATTCAAG
*
772 AGAGTAAAATAGTAATCAGTAAAGAGAAA
1 AGAGT-AAAGAGTAATCAGT-AAGAGAAA
*
801 AGAGTAAAGAGTAATCAGTAAGAGTAA
1 AGAGTAAAGAGTAATCAGTAAGAGAAA
828 A-A-T----AGTAATCAGTAAAGAGAAA
1 AGAGTAAAGAGTAATCAGT-AAGAGAAA
850 AGAGTAAAGAGTAATCAGTAAGAGTAAA
1 AGAGTAAAGAGTAATCAGTAAGAG-AAA
*
878 A-AGGTAAAAAGTAA
1 AGA-GTAAAGAGTAA
892 AGAGTAATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 19
0.77 0.04 0.19
Matches are distributed among these distances:
21 10 0.13
22 8 0.10
23 1 0.01
24 1 0.01
25 1 0.01
26 1 0.01
27 14 0.18
28 37 0.47
29 5 0.06
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (27 bp):
AGAGTAAAGAGTAATCAGTAAGAGAAA
Found at i:870 original size:35 final size:35
Alignment explanation
Indices: 831--913 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
821 AGAGTAAAAT
*
831 AGTAATCAGTAAAGA-G-AAAAGAGTAAAGAGTAATC
1 AGTAA-CAGTAAAAAGGTAAAA-AGTAAAGAGTAATC
*
866 AGTAAGAGTAAAAAGGTAAAAAGTAAAGAGTAATC
1 AGTAACAGTAAAAAGGTAAAAAGTAAAGAGTAATC
*
901 AGTAAAAGTAAAA
1 AGTAACAGTAAAA
914 GAATAAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 7 0.16
35 32 0.74
36 4 0.09
ACGTcount: A:0.58, C:0.04, G:0.22, T:0.17
Consensus pattern (35 bp):
AGTAACAGTAAAAAGGTAAAAAGTAAAGAGTAATC
Found at i:906 original size:49 final size:49
Alignment explanation
Indices: 772--895 Score: 214
Period size: 49 Copynumber: 2.5 Consensus size: 49
762 TAAATTCAAG
772 AGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTA
1 AGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTA
821 AGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTA
1 AGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTA
**
870 AGAGTAAAA-AGGTAAAAAGTAAAGAG
1 AGAGTAAAATA-GTAATCAGTAAAGAG
896 TAATCAGTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
48 1 0.01
49 71 0.99
ACGTcount: A:0.56, C:0.03, G:0.23, T:0.17
Consensus pattern (49 bp):
AGAGTAAAATAGTAATCAGTAAAGAGAAAAGAGTAAAGAGTAATCAGTA
Found at i:908 original size:28 final size:29
Alignment explanation
Indices: 772--920 Score: 107
Period size: 28 Copynumber: 5.3 Consensus size: 29
762 TAAATTCAAG
*
772 AGAGTAAAATAGTAATCAGT-AAAGAG-AAA
1 AGAGT-AAACAGTAATCAGTAAAAG-GTAAA
* *
801 AGAGTAAAGAGTAATCAGTAAGA-GTAAA
1 AGAGTAAACAGTAATCAGTAAAAGGTAAA
* * **
829 ATAGTAATCAGTAAAGAG-AAAAGAGT-AA
1 AGAGTAAACAGTAATCAGTAAAAG-GTAAA
* *
857 AGAGTAATCAGTAA-GAGTAAAAAGGTAAA
1 AGAGTAAACAGTAATCAGT-AAAAGGTAAA
*
886 A-AGTAAAGAGTAATCAGTAAAA-GTAAA
1 AGAGTAAACAGTAATCAGTAAAAGGTAAA
*
913 AGAATAAA
1 AGAGTAAA
921 TTAAAAAAAA
Statistics
Matches: 98, Mismatches: 13, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
27 13 0.13
28 65 0.66
29 20 0.20
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.17
Consensus pattern (29 bp):
AGAGTAAACAGTAATCAGTAAAAGGTAAA
Found at i:954 original size:29 final size:29
Alignment explanation
Indices: 922--1006 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
912 AAGAATAAAT
*
922 TAAAAAAAAAAGTAATCAGTAGAAAGAAA
1 TAAAAAAAGAAGTAATCAGTAGAAAGAAA
* * * * * *
951 TAAAAGAGGAAGTGATCAGTAGAACGGAG
1 TAAAAAAAGAAGTAATCAGTAGAAAGAAA
980 TGAAAGTAAAAGAAGTAATCAGTAGAA
1 T-AAA--AAAAGAAGTAATCAGTAGAA
1007 GTAATCAGTA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 23 0.53
30 3 0.07
32 17 0.40
ACGTcount: A:0.56, C:0.05, G:0.24, T:0.15
Consensus pattern (29 bp):
TAAAAAAAGAAGTAATCAGTAGAAAGAAA
Found at i:1008 original size:13 final size:13
Alignment explanation
Indices: 990--1016 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
980 TGAAAGTAAA
990 AGAAGTAATCAGT
1 AGAAGTAATCAGT
1003 AGAAGTAATCAGT
1 AGAAGTAATCAGT
1016 A
1 A
1017 AGTTGGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (13 bp):
AGAAGTAATCAGT
Found at i:1048 original size:40 final size:40
Alignment explanation
Indices: 1003--1178 Score: 316
Period size: 40 Copynumber: 4.4 Consensus size: 40
993 AGTAATCAGT
**
1003 AGAAGTAATCAGTAAGTTGGTAATTAAGAGTAAAAGTAAA
1 AGAAGTAATCAGTAAAATGGTAATTAAGAGTAAAAGTAAA
1043 AGAAGTAATCAGTAAAATGGTAATTAAGAGTAAAAGTAAA
1 AGAAGTAATCAGTAAAATGGTAATTAAGAGTAAAAGTAAA
**
1083 AGAAGTAATCAGTAAGTTGGTAATTAAGAGTAAAAGTAAA
1 AGAAGTAATCAGTAAAATGGTAATTAAGAGTAAAAGTAAA
1123 AGAAGTAATCAGTAAAATGGTAATTAAGAGTAAAAGTAAA
1 AGAAGTAATCAGTAAAATGGTAATTAAGAGTAAAAGTAAA
1163 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
1179 TCGGTAAAGA
Statistics
Matches: 130, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 130 1.00
ACGTcount: A:0.53, C:0.03, G:0.21, T:0.23
Consensus pattern (40 bp):
AGAAGTAATCAGTAAAATGGTAATTAAGAGTAAAAGTAAA
Found at i:1185 original size:80 final size:80
Alignment explanation
Indices: 1003--1177 Score: 350
Period size: 80 Copynumber: 2.2 Consensus size: 80
993 AGTAATCAGT
1003 AGAAGTAATCAGTAAGTTGGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATT
1 AGAAGTAATCAGTAAGTTGGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATT
1068 AAGAGTAAAAGTAAA
66 AAGAGTAAAAGTAAA
1083 AGAAGTAATCAGTAAGTTGGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATT
1 AGAAGTAATCAGTAAGTTGGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATT
1148 AAGAGTAAAAGTAAA
66 AAGAGTAAAAGTAAA
1163 AGAAGTAATCAGTAA
1 AGAAGTAATCAGTAA
1178 ATCGGTAAAG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 95 1.00
ACGTcount: A:0.53, C:0.03, G:0.21, T:0.23
Consensus pattern (80 bp):
AGAAGTAATCAGTAAGTTGGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATT
AAGAGTAAAAGTAAA
Found at i:1202 original size:16 final size:17
Alignment explanation
Indices: 1176--1209 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1166 AGTAATCAGT
*
1176 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
1193 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAAAGTAA
1209 A
1 A
1210 GAAGTAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.21, T:0.18
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:1266 original size:33 final size:31
Alignment explanation
Indices: 1224--1329 Score: 112
Period size: 33 Copynumber: 3.4 Consensus size: 31
1214 TAATACCGTA
1224 AAAGAGTAAAATGGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAAT-G-AAAATGGTAATTAAATTC
*
1257 AAAGAGTAAAATGACAAATGGTGATTAAAATTC
1 AAAGAGTAAAATGA-AAATGGTAATT-AAATTC
* *
1290 AAA-AG---AGTGAAAATAGTAATTAAATTC
1 AAAGAGTAAAATGAAAATGGTAATTAAATTC
1317 AAGAGAGTAAAAT
1 AA-AGAGTAAAAT
1330 AGTAATCAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
27 8 0.13
28 10 0.16
29 6 0.10
31 1 0.02
32 15 0.25
33 21 0.34
ACGTcount: A:0.54, C:0.04, G:0.18, T:0.25
Consensus pattern (31 bp):
AAAGAGTAAAATGAAAATGGTAATTAAATTC
Found at i:1323 original size:27 final size:27
Alignment explanation
Indices: 1239--1335 Score: 88
Period size: 32 Copynumber: 3.4 Consensus size: 27
1229 GTAAAATGGT
* *
1239 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATAGTAATTAAATTC-AAGAG---AGTG
* * *
1270 ACAAATGGTGATTAAAATTCAAAAGAGTG
1 A-AAATAGTAATT-AAATTCAAGAGAGTG
1299 AAAATAGTAATTAAATTCAAGAGAGT-
1 AAAATAGTAATTAAATTCAAGAGAGTG
1325 AAAATAGTAAT
1 AAAATAGTAAT
1336 CAGTAAAGAG
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
26 11 0.19
27 13 0.22
28 9 0.16
29 4 0.07
31 1 0.02
32 14 0.24
33 6 0.10
ACGTcount: A:0.54, C:0.04, G:0.16, T:0.26
Consensus pattern (27 bp):
AAAATAGTAATTAAATTCAAGAGAGTG
Found at i:1335 original size:26 final size:27
Alignment explanation
Indices: 1239--1335 Score: 88
Period size: 27 Copynumber: 3.4 Consensus size: 27
1229 GTAAAATGGT
* *
1239 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATAGTAATTAAATTCAAA-AG---AGTG
* *
1270 ACAAATGGTGATTAAAATTCAAAAGAGTG
1 A-AAATAGTAATT-AAATTCAAAAGAGTG
*
1299 AAAATAGTAATTAAATTCAAGAGAGT-
1 AAAATAGTAATTAAATTCAAAAGAGTG
1325 AAAATAGTAAT
1 AAAATAGTAAT
1336 CAGTAAAGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
26 11 0.19
27 13 0.22
28 9 0.15
29 4 0.07
31 1 0.02
32 12 0.20
33 9 0.15
ACGTcount: A:0.54, C:0.04, G:0.16, T:0.26
Consensus pattern (27 bp):
AAAATAGTAATTAAATTCAAAAGAGTG
Done.