Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000959.1 Corchorus capsularis cultivar CVL-1 contig00959, 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: 1792
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.24
Found at i:401 original size:27 final size:26
Alignment explanation
Indices: 363--463 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 26
353 GTAATCAGTA
363 ATCAGTAAAAAGAGTAAGAAAAGAGCC
1 ATCAGTAAAAAGAGTAAGAAAAGAG-C
* *
390 ATCAGTAAAAAGAGTAAG-AAACAGT
1 ATCAGTAAAAAGAGTAAGAAAAGAGC
* * *
415 ATTCAGTGAAAAGAATGAGAAAAGAGTC
1 A-TCAGTAAAAAGAGTAAGAAAAGAG-C
* *
443 ATTAGTAAAAAGAGTAGGAAA
1 ATCAGTAAAAAGAGTAAGAAA
464 TAATTTTTAG
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
25 1 0.02
26 19 0.32
27 38 0.64
28 1 0.02
ACGTcount: A:0.54, C:0.07, G:0.23, T:0.16
Consensus pattern (26 bp):
ATCAGTAAAAAGAGTAAGAAAAGAGC
Found at i:420 original size:26 final size:26
Alignment explanation
Indices: 358--489 Score: 97
Period size: 26 Copynumber: 5.0 Consensus size: 26
348 AATTAGTAAT
*
358 CAGTAATCAGTAAAAAGAGTAAGAAAA
1 CAGTATTCAGTAAAAAGAGTAAG-AAA
* *
385 GAGCCA-TCAGTAAAAAGAGTAAGAAA
1 CAG-TATTCAGTAAAAAGAGTAAGAAA
* * *
411 CAGTATTCAGTGAAAAGAATGAGAAAA
1 CAGTATTCAGTAAAAAGAGTAAG-AAA
* *
438 GAGTCATT-AGTAAAAAGAGTAGGAAA
1 CAGT-ATTCAGTAAAAAGAGTAAGAAA
* * * * *
464 TAATTTTTAGTAAAAAGTGTAAGAAA
1 CAGTATTCAGTAAAAAGAGTAAGAAA
490 AGTGCGATAG
Statistics
Matches: 83, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
25 3 0.04
26 40 0.48
27 36 0.43
28 4 0.05
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.20
Consensus pattern (26 bp):
CAGTATTCAGTAAAAAGAGTAAGAAA
Found at i:421 original size:53 final size:53
Alignment explanation
Indices: 358--491 Score: 160
Period size: 53 Copynumber: 2.5 Consensus size: 53
348 AATTAGTAAT
*
358 CAGTAATCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAAGAAA
1 CAGTATTCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAAGAAA
* * * * * *
411 CAGTATTCAGTGAAAAGAATGAGAAAAGAGTCATTAGTAAAAAGAGTAGGAAA
1 CAGTATTCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAAGAAA
* * * * *
464 TAATTTTTAGTAAAAAGTGTAAGAAAAG
1 CAGTATTCAGTAAAAAGAGTAAGAAAAG
492 TGCGATAGTA
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
53 66 1.00
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.19
Consensus pattern (53 bp):
CAGTATTCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAAGAAA
Found at i:697 original size:69 final size:68
Alignment explanation
Indices: 565--719 Score: 181
Period size: 69 Copynumber: 2.2 Consensus size: 68
555 TTGAAAAGGC
565 AATCAGTAAAGAGTAAAATGGTAAAAACTAATGGTAATCAGTAAACATTAAAATAATAAAGAGTA
1 AATCAGTAAAGAG--AAATGGTAAAAACTAATGGTAATCAGTAAACA-TAAAATAATAAAGAGTA
630 AAAAGT
63 AAAAGT
** * **
636 AATCAGTAAAGAGAAATGGTAAGGAGTAATAGAGTAATCAGTGAAA-A-AAAATGGTAAAGAGTA
1 AATCAGTAAAGAGAAATGGTAAAAACTAAT-G-GTAATCAGT-AAACATAAAATAATAAAGAGTA
*
699 AAGAGT
63 AAAAGT
705 AATCAGTAAAG-GAAA
1 AATCAGTAAAGAGAAA
720 AATGATAAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
68 4 0.05
69 44 0.59
70 1 0.01
71 23 0.31
72 3 0.04
ACGTcount: A:0.55, C:0.05, G:0.21, T:0.20
Consensus pattern (68 bp):
AATCAGTAAAGAGAAATGGTAAAAACTAATGGTAATCAGTAAACATAAAATAATAAAGAGTAAAA
AGT
Found at i:802 original size:40 final size:40
Alignment explanation
Indices: 758--850 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 40
748 AAATGGTAGA
*
758 GTAAAGAGTAAAGTAAAGAG-AGATCAGTAAA-AAGAAAATG
1 GTAAAGAGTAAAGTAAAAAGTA-ATCAGTAAAGAA-AAAATG
*
798 GTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAAAATATG
1 GTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAAAAAATG
**
838 GTAATCAGTAAAG
1 GTAAAGAGTAAAG
851 AGTAATAGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 44 0.94
41 3 0.06
ACGTcount: A:0.56, C:0.03, G:0.23, T:0.18
Consensus pattern (40 bp):
GTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAAAAAATG
Found at i:809 original size:35 final size:35
Alignment explanation
Indices: 565--856 Score: 170
Period size: 35 Copynumber: 8.1 Consensus size: 35
555 TTGAAAAGGC
* * * *
565 AATCAGTAAAGAGTAAAATGGTAAAAACTAATG-GT
1 AATCAGTAAAAAG-AAAATGGTAAAGAGTAAAGAGT
** ** *
600 AATCAGTAAACATTAAAATAATAAAGAGTAAAAAGT
1 AATCAGTAAA-AAGAAAATGGTAAAGAGTAAAGAGT
* *
636 AATCAGTAAAGAG-AAATGGTAAGGAGTAATAGAGT
1 AATCAGTAAAAAGAAAATGGTAAAGAGTAA-AGAGT
*
671 AATCAGTGAAAA-AAAATGGTAAAGAGTAAAGAGT
1 AATCAGTAAAAAGAAAATGGTAAAGAGTAAAGAGT
* * * *
705 AATCAGT-AAAGGAAAAATGATAAAGAATGAAGAGT
1 AATCAGTAAAAAG-AAAATGGTAAAGAGTAAAGAGT
* *
740 AATTAGCAAAATGGTAGAGTAAA-GAGT-AA-AGTAAAGAG-
1 AATCAGTAAAA----AGA--AAATG-GTAAAGAGTAAAGAGT
778 AGATCAGTAAAAAGAAAATGGTAAAGAGTAAAGTAAAAAGT
1 A-ATCAGTAAAAAGAAAATGGTAAAGAGTAAAG-----AGT
* **
819 AATCAGTAAAGAA-AATATGGTAATCAGTAAAGAGT
1 AATCAGTAAA-AAGAAAATGGTAAAGAGTAAAGAGT
854 AAT
1 AAT
857 AGTGATCAGT
Statistics
Matches: 198, Mismatches: 34, Indels: 50
0.70 0.12 0.18
Matches are distributed among these distances:
33 8 0.04
34 28 0.14
35 92 0.46
36 15 0.08
38 1 0.01
39 16 0.08
40 31 0.16
41 7 0.04
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.20
Consensus pattern (35 bp):
AATCAGTAAAAAGAAAATGGTAAAGAGTAAAGAGT
Found at i:913 original size:22 final size:22
Alignment explanation
Indices: 780--1045 Score: 215
Period size: 20 Copynumber: 12.7 Consensus size: 22
770 GTAAAGAGAG
780 ATCAGTAAAAAG-AAAATGGTA
1 ATCAGTAAAAAGTAAAATGGTA
** *
801 AAGAGT--AAAGTAAAA-AGTA
1 ATCAGTAAAAAGTAAAATGGTA
*
820 ATCAGTAAAGAA--AATATGGTA
1 ATCAGTAAA-AAGTAAAATGGTA
* * *
841 ATCAGTAAAGAGT--AATAGTG
1 ATCAGTAAAAAGTAAAATGGTA
* *
861 ATCAGTAAGAAGT--AATGGCA
1 ATCAGTAAAAAGTAAAATGGTA
*
881 ATCAGTAAAAAGTAAAAAGGTA
1 ATCAGTAAAAAGTAAAATGGTA
* *
903 ATTAATAAAAAGTAAAATGGTA
1 ATCAGTAAAAAGTAAAATGGTA
925 ATCAGTAAAAAGT-AAA-GGTA
1 ATCAGTAAAAAGTAAAATGGTA
*
945 ATCAGTGAAAAGTAAAATGGTA
1 ATCAGTAAAAAGTAAAATGGTA
* * *
967 ATTA-AAAAAGAGTAAAAGGGTA
1 ATCAGTAAAA-AGTAAAATGGTA
*
989 ATCAGT--AAAGCAAAATGGTA
1 ATCAGTAAAAAGTAAAATGGTA
*
1009 ATTAGTAAAAAGT-AAA-GAGTA
1 ATCAGTAAAAAGTAAAATG-GTA
*
1030 ATCAGTAAAGAGTAAA
1 ATCAGTAAAAAGTAAA
1046 GAGTAAAAAG
Statistics
Matches: 191, Mismatches: 37, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
19 11 0.06
20 71 0.37
21 45 0.24
22 64 0.34
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (22 bp):
ATCAGTAAAAAGTAAAATGGTA
Found at i:938 original size:64 final size:64
Alignment explanation
Indices: 861--1024 Score: 217
Period size: 64 Copynumber: 2.6 Consensus size: 64
851 AGTAATAGTG
* * *
861 ATCAGTAAGAAGTAATGGCAATCAGTAAAAAGTAAAAAGGTAATTAATAAAA-AGTAAAATGGTA
1 ATCAGTAAAAAGTAATGGTAATCAGTAAAAAGTAAAAAGGTAATTAA-AAAAGAGTAAAAGGGTA
* * *
925 ATCAGTAAAAAGTAAAGGTAATCAGTGAAAAGTAAAATGGTAATTAAAAAAGAGTAAAAGGGTA
1 ATCAGTAAAAAGTAATGGTAATCAGTAAAAAGTAAAAAGGTAATTAAAAAAGAGTAAAAGGGTA
*
989 ATCAGTAAAGCAA--AATGGTAATTAGTAAAAAGTAAA
1 ATCAGTAAA--AAGTAATGGTAATCAGTAAAAAGTAAA
1025 GAGTAATCAG
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 4 0.05
64 82 0.93
66 2 0.02
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (64 bp):
ATCAGTAAAAAGTAATGGTAATCAGTAAAAAGTAAAAAGGTAATTAAAAAAGAGTAAAAGGGTA
Found at i:942 original size:42 final size:42
Alignment explanation
Indices: 767--1045 Score: 231
Period size: 42 Copynumber: 6.7 Consensus size: 42
757 AGTAAAGAGT
**
767 AAAGTAAAGAG-AGATCAGTAAAAAG-AAAATGGTAAAGAGT--
1 AAAGTAAAG-GTA-ATCAGTAAAAAGTAAAATGGTAATCAGTAA
* *
807 AAAGTAAAAAGTAATCAGTAAAGAA--AATATGGTAATCAGTAA
1 AAAGT-AAAGGTAATCAGTAAA-AAGTAAAATGGTAATCAGTAA
* * * *
849 AGAGTAATA-GTGATCAGTAAGAAGT--AATGGCAATCAGTAA
1 AAAGTAA-AGGTAATCAGTAAAAAGTAAAATGGTAATCAGTAA
* *
889 AAAGTAAAAAGGTAATTAATAAAAAGTAAAATGGTAATCAGTAA
1 AAAGT--AAAGGTAATCAGTAAAAAGTAAAATGGTAATCAGTAA
* * *
933 AAAGTAAAGGTAATCAGTGAAAAGTAAAATGGTAATTA-AAA
1 AAAGTAAAGGTAATCAGTAAAAAGTAAAATGGTAATCAGTAA
* *
974 AAGAGTAAAAGGGTAATCAGT--AAAGCAAAATGGTAATTAGTAA
1 AA-AGT-AAA-GGTAATCAGTAAAAAGTAAAATGGTAATCAGTAA
*
1017 AAAGTAAAGAGTAATCAGTAAAGAGTAAA
1 AAAGTAAAG-GTAATCAGTAAAAAGTAAA
1046 GAGTAAAAAG
Statistics
Matches: 195, Mismatches: 24, Indels: 37
0.76 0.09 0.14
Matches are distributed among these distances:
40 47 0.24
41 35 0.18
42 71 0.36
43 13 0.07
44 29 0.15
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.20
Consensus pattern (42 bp):
AAAGTAAAGGTAATCAGTAAAAAGTAAAATGGTAATCAGTAA
Found at i:1022 original size:7 final size:7
Alignment explanation
Indices: 1012--1068 Score: 60
Period size: 7 Copynumber: 8.1 Consensus size: 7
1002 AATGGTAATT
*
1012 AGTAAAA
1 AGTAAAG
1019 AGTAAAG
1 AGTAAAG
**
1026 AGTAATC
1 AGTAAAG
1033 AGTAAAG
1 AGTAAAG
1040 AGTAAAG
1 AGTAAAG
*
1047 AGTAAAA
1 AGTAAAG
**
1054 AGTAATC
1 AGTAAAG
1061 AGTAAAG
1 AGTAAAG
1068 A
1 A
1069 AAAAATAGTA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.58, C:0.04, G:0.21, T:0.18
Consensus pattern (7 bp):
AGTAAAG
Found at i:1029 original size:14 final size:14
Alignment explanation
Indices: 1012--1068 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
1002 AATGGTAATT
*
1012 AGTAAAAAGTAAAG
1 AGTAAACAGTAAAG
*
1026 AGTAATCAGTAAAG
1 AGTAAACAGTAAAG
* *
1040 AGTAAAGAGTAAAA
1 AGTAAACAGTAAAG
*
1054 AGTAATCAGTAAAG
1 AGTAAACAGTAAAG
1068 A
1 A
1069 AAAAATAGTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.58, C:0.04, G:0.21, T:0.18
Consensus pattern (14 bp):
AGTAAACAGTAAAG
Found at i:1058 original size:42 final size:42
Alignment explanation
Indices: 755--1249 Score: 126
Period size: 42 Copynumber: 11.8 Consensus size: 42
745 GCAAAATGGT
* * *
755 AGAGTAAAGAGT--AAAGTAAAGAG-AGATCAGTAAAAAGAAA
1 AGAGTAAACAGTAAAAAGTAAAGAGTA-ATCAGTAAAGAGTAA
* *
795 ATG-GTAAAGAGT--AAAGTAAAAAGTAATCAGTAAAGA--AA
1 A-GAGTAAACAGTAAAAAGTAAAGAGTAATCAGTAAAGAGTAA
* * * * *
833 ATATGGTAATCAGTAAAGAGT-AATAGTGATCAGT-AAGAAGTAA
1 AGA--GTAAACAGTAAAAAGTAAAGAGTAATCAGTAAAG-AGTAA
* * * * * * *
876 TG-GCAATCAGTAAAAAGTAAAAAGGTAATTAATAAAAAGTAA
1 AGAGTAAACAGTAAAAAGTAAAGA-GTAATCAGTAAAGAGTAA
*
918 A-ATGGTAATCAGTAAAAAGTAAAG-GTAATCAGTGAAA-AGTAA
1 AGA--GTAAACAGTAAAAAGTAAAGAGTAATCAGT-AAAGAGTAA
** * *
960 A-ATGGTAATTA-AAAAAGAGTAAAAGGGTAATCAGTAAAGCA--AA
1 AGA--GTAAACAGTAAAA-AGT-AAAGAGTAATCAGTAAAG-AGTAA
**
1003 ATG-GTAATTAGTAAAAAGTAAAGAGTAATCAGTAAAGAGTAA
1 A-GAGTAAACAGTAAAAAGTAAAGAGTAATCAGTAAAGAGTAA
* ** **
1045 AGAGTAAAAAGTAATCAGTAAAGAAAAAAT-AGT-AAGAAGT-A
1 AGAGTAAACAGTAAAAAGTAAAG-AGTAATCAGTAAAG-AGTAA
* ** **
1086 AGAAG-AAATCAGTAAAATGGTAAAG-GATAAAGAGTAATCAGTAA
1 AG-AGTAAA-CAGTAAAA-AGTAAAGAG-TAATCAGTAAAGAGTAA
* ** * * * * *
1130 AG-GAAAATGGTAGAGAGTAAAATATTAATCAGTAAAAAGTAA
1 AGAGTAAACAGTAAAAAGT-AAAGAGTAATCAGTAAAGAGTAA
* * * * *
1172 AG-GCAATCAGTAAAGAA-TAAAATATTAATCAGTAAAGAGTAG
1 AGAGTAAACAGTAAA-AAGT-AAAGAGTAATCAGTAAAGAGTAA
* * *
1214 AGAGTAATCAGTAAAGAGTAAAATAGTAATCAGTAA
1 AGAGTAAACAGTAAAAAGT-AAAGAGTAATCAGTAA
1250 GTGGTGATTA
Statistics
Matches: 349, Mismatches: 63, Indels: 83
0.71 0.13 0.17
Matches are distributed among these distances:
38 3 0.01
40 55 0.16
41 50 0.14
42 140 0.40
43 69 0.20
44 31 0.09
45 1 0.00
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.20
Consensus pattern (42 bp):
AGAGTAAACAGTAAAAAGTAAAGAGTAATCAGTAAAGAGTAA
Found at i:1078 original size:28 final size:27
Alignment explanation
Indices: 1015--1086 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
1005 GGTAATTAGT
* *
1015 AAAAAGTAAAGAGTAATCAGTAAAGAGT
1 AAAAAGTAAAAAGTAATCAGTAAAGA-A
*
1043 AAAGAGTAAAAAGTAATCAGTAAAGAA
1 AAAAAGTAAAAAGTAATCAGTAAAGAA
*
1070 AAAATAGTAAGAAGTAA
1 AAAA-AGTAAAAAGTAA
1087 GAAGAAATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 3 0.08
28 35 0.92
ACGTcount: A:0.61, C:0.03, G:0.19, T:0.17
Consensus pattern (27 bp):
AAAAAGTAAAAAGTAATCAGTAAAGAA
Found at i:1160 original size:64 final size:65
Alignment explanation
Indices: 1011--1174 Score: 166
Period size: 64 Copynumber: 2.6 Consensus size: 65
1001 AAATGGTAAT
*
1011 TAGTAAAAAGT-A-AAGAGTAATCAGT-AAAGAGTAAA-GAGTAAAAAGTAATCAGTAAAGAAAA
1 TAGTAAGAAGTAAGAAGA-TAATCAGTAAAAG-GTAAAGGAGTAAAAAGTAATCAGTAAAGAAAA
1072 AA
64 AA
* *
1074 TAGTAAGAAGTAAGAAGA-AATCAGTAAAATGGTAAAGGA-TAAAGAGTAATCAGTAAAG-GAAA
1 TAGTAAGAAGTAAGAAGATAATCAGTAAAA-GGTAAAGGAGTAAAAAGTAATCAGTAAAGAAAAA
1136 A
65 A
* * *
1137 TGGT-AGAGAGTAA-AATATTAATCAGTAAAAAGTAAAGG
1 TAGTAAGA-AGTAAGAAGA-TAATCAGTAAAAGGTAAAGG
1175 CAATCAGTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
62 6 0.07
63 36 0.41
64 38 0.44
65 7 0.08
ACGTcount: A:0.56, C:0.03, G:0.22, T:0.19
Consensus pattern (65 bp):
TAGTAAGAAGTAAGAAGATAATCAGTAAAAGGTAAAGGAGTAAAAAGTAATCAGTAAAGAAAAAA
Found at i:1204 original size:22 final size:22
Alignment explanation
Indices: 1147--1249 Score: 97
Period size: 22 Copynumber: 4.8 Consensus size: 22
1137 TGGTAGAGAG
*
1147 TAAAATATTAATCAGTAAA-AA
1 TAAAATAGTAATCAGTAAAGAA
* *
1168 GT-AAA-GGCAATCAGTAAAGAA
1 -TAAAATAGTAATCAGTAAAGAA
* *
1189 TAAAATATTAATCAGTAAAGAG
1 TAAAATAGTAATCAGTAAAGAA
* * *
1211 T-AGAGAGTAATCAGTAAAGAG
1 TAAAATAGTAATCAGTAAAGAA
1232 TAAAATAGTAATCAGTAA
1 TAAAATAGTAATCAGTAA
1250 GTGGTGATTA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
20 11 0.17
21 26 0.40
22 28 0.43
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (22 bp):
TAAAATAGTAATCAGTAAAGAA
Found at i:1237 original size:43 final size:42
Alignment explanation
Indices: 1143--1249 Score: 160
Period size: 43 Copynumber: 2.5 Consensus size: 42
1133 AAAATGGTAG
1143 AGAGTAAAATATTAATCAGTAAAAAGTAAAGGCAATCAGTAA
1 AGAGTAAAATATTAATCAGTAAAAAGTAAAGGCAATCAGTAA
* * * *
1185 AGAATAAAATATTAATCAGTAAAGAGTAGAGAGTAATCAGTAA
1 AGAGTAAAATATTAATCAGTAAAAAGTAAAG-GCAATCAGTAA
*
1228 AGAGTAAAATAGTAATCAGTAA
1 AGAGTAAAATATTAATCAGTAA
1250 GTGGTGATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 28 0.48
43 30 0.52
ACGTcount: A:0.54, C:0.06, G:0.18, T:0.22
Consensus pattern (42 bp):
AGAGTAAAATATTAATCAGTAAAAAGTAAAGGCAATCAGTAA
Found at i:1437 original size:24 final size:25
Alignment explanation
Indices: 1406--1452 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1396 AGAGTAAGAA
1406 AAAAGTAAAAATGATAA-AAGTAGC
1 AAAAGTAAAAATGATAATAAGTAGC
* *
1430 AAAAGTAAGAATGGTAATAAGTA
1 AAAAGTAAAAATGATAATAAGTA
1453 AGAAGAGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (25 bp):
AAAAGTAAAAATGATAATAAGTAGC
Done.