Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013547.1 Corchorus capsularis cultivar CVL-1 contig13568, 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: 40641
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:931 original size:15 final size:14
Alignment explanation
Indices: 882--947 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 14
872 AAAGAATCAA
882 AGTAAAAGAAGTAATC
1 AGTAAAAG--GTAATC
* **
898 AGTAAAATAGTAAAA
1 AGTAAAA-GGTAATC
913 AGTAAGAAGGTAATC
1 AGTAA-AAGGTAATC
928 AGT-AAAGAGTAATC
1 AGTAAAAG-GTAATC
942 AGTAAA
1 AGTAAA
948 GGAAGAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 3 0.08
14 10 0.25
15 18 0.45
16 9 0.22
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.20
Consensus pattern (14 bp):
AGTAAAAGGTAATC
Found at i:994 original size:22 final size:22
Alignment explanation
Indices: 957--1052 Score: 99
Period size: 22 Copynumber: 4.4 Consensus size: 22
947 AGGAAGAATG
* *
957 ATCAGT-AAGAGCAAAATGGTA
1 ATCAGTAAAGAGTAAAATAGTA
*
978 ATCAGTAAAGAGTAAAATAGAA
1 ATCAGTAAAGAGTAAAATAGTA
* *
1000 ACCAGTAAA-AGGTAAGAA-GGTA
1 ATCAGTAAAGA-GTAA-AATAGTA
*
1022 ATCAGTAAAAAGTAAAATAGTA
1 ATCAGTAAAGAGTAAAATAGTA
1044 ATCAGTAAA
1 ATCAGTAAA
1053 AGGTAATCAG
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
21 9 0.15
22 50 0.81
23 3 0.05
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (22 bp):
ATCAGTAAAGAGTAAAATAGTA
Found at i:1028 original size:44 final size:44
Alignment explanation
Indices: 974--1058 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
964 AGAGCAAAAT
*
974 GGTAATCAGTAAAGAGTAAAATAGAAACCAGTAAAAGGTAAGAA
1 GGTAATCAGTAAAAAGTAAAATAGAAACCAGTAAAAGGTAAGAA
* *
1018 GGTAATCAGTAAAAAGTAAAATAGTAATCAGTAAAAGGTAA
1 GGTAATCAGTAAAAAGTAAAATAGAAACCAGTAAAAGGTAA
1059 TCAGTAAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (44 bp):
GGTAATCAGTAAAAAGTAAAATAGAAACCAGTAAAAGGTAAGAA
Found at i:1078 original size:35 final size:37
Alignment explanation
Indices: 1011--1088 Score: 133
Period size: 35 Copynumber: 2.2 Consensus size: 37
1001 CCAGTAAAAG
1011 GTAAGAAGGTAATCAGTAAAAAGTAAAATAGTAATCA
1 GTAAGAAGGTAATCAGTAAAAAGTAAAATAGTAATCA
*
1048 GTAA-AAGGTAATCAGT-AAGAGTAAAATAGTAATCA
1 GTAAGAAGGTAATCAGTAAAAAGTAAAATAGTAATCA
1083 GTAAGA
1 GTAAGA
1089 GCAAAATGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 22 0.56
36 13 0.33
37 4 0.10
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.22
Consensus pattern (37 bp):
GTAAGAAGGTAATCAGTAAAAAGTAAAATAGTAATCA
Found at i:1087 original size:21 final size:22
Alignment explanation
Indices: 1066--1114 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1056 TAATCAGTAA
1066 GAGTAAAATAGTAATCAGT-AA
1 GAGTAAAATAGTAATCAGTAAA
* * *
1087 GAGCAAAATGGTAATTAGTAAA
1 GAGTAAAATAGTAATCAGTAAA
1109 GAGTAA
1 GAGTAA
1115 TCAGTAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.22
Consensus pattern (22 bp):
GAGTAAAATAGTAATCAGTAAA
Found at i:1114 original size:14 final size:14
Alignment explanation
Indices: 1097--1128 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1087 GAGCAAAATG
*
1097 GTAATTAGTAAAGA
1 GTAATCAGTAAAGA
1111 GTAATCAGTAAAGA
1 GTAATCAGTAAAGA
1125 GTAA
1 GTAA
1129 CAGGTGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (14 bp):
GTAATCAGTAAAGA
Found at i:1121 original size:21 final size:21
Alignment explanation
Indices: 1097--1144 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1087 GAGCAAAATG
1097 GTAATTAGTAA-AGAGTAATCA
1 GTAATTAGTAACAG-GTAATCA
** *
1118 GTAAAGAGTAACAGGTGATCA
1 GTAATTAGTAACAGGTAATCA
1139 GTAATT
1 GTAATT
1145 CAAAGAATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (21 bp):
GTAATTAGTAACAGGTAATCA
Found at i:5333 original size:3 final size:3
Alignment explanation
Indices: 5325--5355 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5315 ATTTGAAAAA
5325 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5356 TTGCCATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6788 original size:16 final size:17
Alignment explanation
Indices: 6747--6788 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
6737 AAATTGCATA
6747 GAAAAGAAATAGCGAAG
1 GAAAAGAAATAGCGAAG
* *
6764 GAAATGAAATAG-GAGG
1 GAAAAGAAATAGCGAAG
6780 GAAAAGAAA
1 GAAAAGAAA
6789 AGAAAGTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.60, C:0.02, G:0.31, T:0.07
Consensus pattern (17 bp):
GAAAAGAAATAGCGAAG
Found at i:8503 original size:2 final size:2
Alignment explanation
Indices: 8492--8524 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
8482 ACACAAACAA
*
8492 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8525 GTTATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12806 original size:17 final size:17
Alignment explanation
Indices: 12781--12814 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12771 CCAAAAAAAA
*
12781 TTTGCGGATTGGGGTTT
1 TTTGCGGATTAGGGTTT
*
12798 TTTGGGGATTAGGGTTT
1 TTTGCGGATTAGGGTTT
12815 GCAATTTGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.03, G:0.41, T:0.47
Consensus pattern (17 bp):
TTTGCGGATTAGGGTTT
Found at i:14591 original size:19 final size:18
Alignment explanation
Indices: 14567--14602 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14557 TGAAGATTTC
14567 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
14586 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
14603 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
Found at i:22969 original size:22 final size:23
Alignment explanation
Indices: 22939--22981 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
22929 GGTTTAGCTA
22939 TTTAGTTTATG-CTTTATTTTTC
1 TTTAGTTTATGTCTTTATTTTTC
*
22961 TTTATTTTATGTCTTTATTTT
1 TTTAGTTTATGTCTTTATTTT
22982 CAAGTTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (23 bp):
TTTAGTTTATGTCTTTATTTTTC
Found at i:23464 original size:96 final size:96
Alignment explanation
Indices: 23356--23532 Score: 345
Period size: 96 Copynumber: 1.8 Consensus size: 96
23346 AAAATTTTGA
23356 TGATTTTTCAAGCATATATTGAATGATTGATTTGATTATGATTGATGAATGTTTAGAATTTTTAA
1 TGATTTTTCAAGCATATATTGAATGATTGATTTGATTATGATTGATGAATGTTTAGAATTTTTAA
23421 TAATACTTTATACTTTATTTTTCAAACTCTT
66 TAATACTTTATACTTTATTTTTCAAACTCTT
23452 TGATTTTTCAAGCATATATTGAATGATTGATTTGATTATGATTGATGAATGTTTAGAATTTTTAA
1 TGATTTTTCAAGCATATATTGAATGATTGATTTGATTATGATTGATGAATGTTTAGAATTTTTAA
*
23517 TAATACTTTATTCTTT
66 TAATACTTTATACTTT
23533 GATTAATTTA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 80 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (96 bp):
TGATTTTTCAAGCATATATTGAATGATTGATTTGATTATGATTGATGAATGTTTAGAATTTTTAA
TAATACTTTATACTTTATTTTTCAAACTCTT
Found at i:24608 original size:19 final size:18
Alignment explanation
Indices: 24584--24620 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
24574 TTGAAGATTT
24584 TTTGAAGATAATTTGAAGA
1 TTTGAAGATAA-TTGAAGA
*
24603 TTTGAAGATCATTGAAGA
1 TTTGAAGATAATTGAAGA
24621 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (18 bp):
TTTGAAGATAATTGAAGA
Found at i:25913 original size:13 final size:14
Alignment explanation
Indices: 25895--25924 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
25885 TCTTGATTGC
25895 TTACTTAGTTA-AT
1 TTACTTAGTTAGAT
25908 TTACTTAGTTAGAT
1 TTACTTAGTTAGAT
25922 TTA
1 TTA
25925 ATTTTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (14 bp):
TTACTTAGTTAGAT
Found at i:33396 original size:12 final size:12
Alignment explanation
Indices: 33379--33404 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33369 GTTCTTTTTC
33379 TTTTTTTCATTT
1 TTTTTTTCATTT
33391 TTTTTTTCATTT
1 TTTTTTTCATTT
33403 TT
1 TT
33405 CAGAGGGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTCATTT
Found at i:38182 original size:45 final size:45
Alignment explanation
Indices: 38118--38206 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
38108 TAATAGAGTA
38118 GTGGAATTACTAAAAGATCCCTACCCCGAATGAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATGAATGATGAGCTGG
* *
38163 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATGAATGATGAGCTG
38207 CAGAAGTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATGAATGATGAGCTGG
Found at i:38618 original size:30 final size:30
Alignment explanation
Indices: 38594--38657 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
38584 AGTCCTCAAG
*
38594 CACAAGGGCATCC-ATACTAAAGTCCCTAAA
1 CACAAAGGCA-CCTATACTAAAGTCCCTAAA
38624 CACAAAGGCACCTATACTAAAGTCCCTAAA
1 CACAAAGGCACCTATACTAAAGTCCCTAAA
38654 CACA
1 CACA
38658 TATAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.42, C:0.31, G:0.11, T:0.16
Consensus pattern (30 bp):
CACAAAGGCACCTATACTAAAGTCCCTAAA
Found at i:40030 original size:47 final size:48
Alignment explanation
Indices: 39913--40604 Score: 556
Period size: 47 Copynumber: 14.4 Consensus size: 48
39903 TTGTTATAAC
*
39913 CCGACCGGGAAGGGGCATTTTGGGAATA-AGAAAGGAAAACTGTGACCTT
1 CCGACCAGGAAGGGGCATTTTGGGAA-ACAGAAA-GAAAACTGTGACCTT
** * ** * *
39962 CCGACTGGGAATGGGTTTTTTGGGAAACA-AAAGAAAACTGTTACCAT
1 CCGACCAGGAAGGGGCATTTTGGGAAACAGAAAGAAAACTGTGACCTT
*
40009 CCGACCAGGAAGGGACATTTTGGGAAACA-AAAGAAAACTGTGACCTT
1 CCGACCAGGAAGGGGCATTTTGGGAAACAGAAAGAAAACTGTGACCTT
* * * * ** *
40056 CCGACTAGGAA-GGGC-TTTT-AGAAACAAATAAAGAGAAC-AAGAGCTT
1 CCGACCAGGAAGGGGCATTTTGGGAAAC--AGAAAGAAAACTGTGACCTT
*
40102 CCGACCAGGAAGGGGCATTTTGGGAAATAAGAAAGGAAAACTGTGACCTT
1 CCGACCAGGAAGGGGCATTTTGGGAAA-CAGAAA-GAAAACTGTGACCTT
** * ** *
40152 CCGACTGGGAATGGGTTTTTTGGGAAACA-AAAG-AAACTGTGACCAT
1 CCGACCAGGAAGGGGCATTTTGGGAAACAGAAAGAAAACTGTGACCTT
* * *
40198 CTGACCAAGAAGGGGCATTTTGGGAAACA-AAAGAGAACTGTGACCTT
1 CCGACCAGGAAGGGGCATTTTGGGAAACAGAAAGAAAACTGTGACCTT
* * * * *
40245 CCGACTAGGAA-GGGC-TTTTTGGAAACAAATAAAGAAAACAGGGACCTT
1 CCGACCAGGAAGGGGCATTTTGGGAAAC--AGAAAGAAAACTGTGACCTT
* *
40293 CTGACC-GAGAAGGGGCATTTTGGGAAATAAGAAAGGAAAACTGTGACCTT
1 CCGACCAG-GAAGGGGCATTTTGGGAAA-CAGAAA-GAAAACTGTGACCTT
* ** * * * * *
40343 CTGACTGGGAAGTGGC-TTTT-TGAAACAAATAAAGAAAACAGGGACCTT
1 CCGACCAGGAAGGGGCATTTTGGGAAAC--AGAAAGAAAACTGTGACCTT
* * * * *
40391 CCGACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAGAACAGGGACCTT
1 CCGACCAGGAAGGGGCATTTTGGGAAAC--AGAAAGAAAACTGTGACCTT
*
40441 CCGACCTGGAAGGGGCATTTTGGGAATA-AGAAAGGAAAACTGTGACCTT
1 CCGACCAGGAAGGGGCATTTTGGGAA-ACAGAAA-GAAAACTGTGACCTT
* ** * ** * * *
40490 TCGACTGGGAATGGGTTTTTTTGGAAACA-AAAGGAAACTGTGACCTA
1 CCGACCAGGAAGGGGCATTTTGGGAAACAGAAAGAAAACTGTGACCTT
* *
40537 CCGACCAAGAAGGGGCATTTTAGGAAACA-AAAGAAAACTGTGACCTT
1 CCGACCAGGAAGGGGCATTTTGGGAAACAGAAAGAAAACTGTGACCTT
* * *
40584 CCGACTAGGAAAGGGCTTTTT
1 CCGACCAGGAAGGGGCATTTT
40605 AGAAACAAAT
Statistics
Matches: 517, Mismatches: 99, Indels: 56
0.77 0.15 0.08
Matches are distributed among these distances:
44 5 0.01
45 14 0.03
46 61 0.12
47 163 0.32
48 75 0.15
49 85 0.16
50 112 0.22
51 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (48 bp):
CCGACCAGGAAGGGGCATTTTGGGAAACAGAAAGAAAACTGTGACCTT
Found at i:40240 original size:189 final size:191
Alignment explanation
Indices: 39913--40613 Score: 780
Period size: 189 Copynumber: 3.7 Consensus size: 191
39903 TTGTTATAAC
39913 CCGACCGGGAAGGGGCATTTTGGG-AATAAGAAAGGAAAACTGTGACCTTCCGACTGGGAATGGG
1 CCGACC-GGAAGGGGCATTTTGGGAAATAAGAAAGGAAAACTGTGACCTTCCGACTGGGAATGGG
* *
39977 TTTTTTGGGAAACAAAAGAAAACTGTTACCATCCGACCAGGAAGGGACATTTTGGGAAACAAAAG
65 TTTTTTGGGAAACAAAAGAAAACTGTGACCATCCGACCAGGAAGGGGCATTTTGGGAAACAAAAG
* * *
40042 AAAACTGTGACCTTCCGACTAGGAAGGGC-TTTTAGAAACAAATAAAGAGAACA-AGAGCTT
130 AGAACTGTGACCTTCCGACTAGGAAGGGCTTTTTAGAAACAAATAAAGAAAACAGAGACCTT
40102 CCGACCAGGAAGGGGCATTTTGGGAAATAAGAAAGGAAAACTGTGACCTTCCGACTGGGAATGGG
1 CCGACC-GGAAGGGGCATTTTGGGAAATAAGAAAGGAAAACTGTGACCTTCCGACTGGGAATGGG
* *
40167 TTTTTTGGGAAACAAAAG-AAACTGTGACCATCTGACCAAGAAGGGGCATTTTGGGAAACAAAAG
65 TTTTTTGGGAAACAAAAGAAAACTGTGACCATCCGACCAGGAAGGGGCATTTTGGGAAACAAAAG
* *
40231 AGAACTGTGACCTTCCGACTAGGAAGGGCTTTTTGGAAACAAATAAAGAAAACAGGGACCTT
130 AGAACTGTGACCTTCCGACTAGGAAGGGCTTTTTAGAAACAAATAAAGAAAACAGAGACCTT
* *
40293 CTGACCGAGAAGGGGCATTTTGGGAAATAAGAAAGGAAAACTGTGACCTTCTGACTGGGAA-GTG
1 CCGACCG-GAAGGGGCATTTTGGGAAATAAGAAAGGAAAACTGTGACCTTCCGACTGGGAATG-G
* * * * *
40357 GCTTTTT--GAAACAAATAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACA
64 GTTTTTTGGGAAAC--A-AAAGAAAACTGTGACCATCCGACCAGGAAGGGGCATTTTGGGAAAC-
* * * * * * * *
40420 AATAAAGAGAACAGGGACCTTCCGACCT-GGAAGGGGCATTTTGGGAATAAGA-AAGGAAAACTG
125 -A-AAAGAGAACTGTGACCTTCCGA-CTAGGAA-GGGCTTTTTAGAAACAA-ATAAAGAAAACAG
*
40483 TGACCTT
185 AGACCTT
* * * ** * * * *** *
40490 TCGACTGGGAATGGGTTTTTTTGGAAA-CA-AAAGG-AAACTGTGACCTACCGACCAAGAAGGGG
1 CCGAC-CGGAAGGGGCATTTTGGGAAATAAGAAAGGAAAACTGTGACCTTCCGACTGGGAATGGG
** * * * * **
40552 CATTTTAGGAAACAAAAGAAAACTGTGACCTTCCGACTAGGAAAGGGC-TTTTTAGAAACAAA
65 TTTTTTGGGAAACAAAAGAAAACTGTGACCATCCGACCAGGAAGGGGCATTTTGGGAAACAAA
40614 TAAAGAGAAC
Statistics
Matches: 445, Mismatches: 48, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
189 100 0.22
190 83 0.19
191 70 0.16
192 13 0.03
193 64 0.14
194 27 0.06
195 7 0.02
196 30 0.07
197 49 0.11
198 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (191 bp):
CCGACCGGAAGGGGCATTTTGGGAAATAAGAAAGGAAAACTGTGACCTTCCGACTGGGAATGGGT
TTTTTGGGAAACAAAAGAAAACTGTGACCATCCGACCAGGAAGGGGCATTTTGGGAAACAAAAGA
GAACTGTGACCTTCCGACTAGGAAGGGCTTTTTAGAAACAAATAAAGAAAACAGAGACCTT
Found at i:40616 original size:147 final size:145
Alignment explanation
Indices: 40041--40604 Score: 410
Period size: 146 Copynumber: 3.9 Consensus size: 145
40031 GGAAACAAAA
* * * * * * *
40041 GAAAACTGTGACCTTCCGACTAGGAAG-GGCTTTTAGAAACAAATAAAGAGAACA-AGAGCTTCC
1 GAAAACTGTGACCTTCTGACTGGGAAGTGGCTTTTTGAAAC-AATAAAGAAAACAGGGACCTACC
* * * * * * * *
40104 GACCAGGAAGGGGCATTTTGGGAAATAAGAAAGGAAAACTGTGACCTTCCGA-CTGGGAATGGGT
65 GACCAAGAAGGGGCATTTTAGGAAACAATAAA-GAAAACAGGGACCTTCCGACCT-GGAAAGGGC
* * *
40168 TTTTTGGGAAA-CA-AAA-
128 ATTTT-GCAAATAAGAAAG
* *** * * * * * *
40184 G-AAACTGTGACCATCTGACCAAGAAGGGGCATTTTGGGAAAC-A-AAAGAGAACTGTGACCTTC
1 GAAAACTGTGACCTTCTGACTGGGAAGTGGC-TTTT-TGAAACAATAAAGAAAACAGGGACCTAC
* * * * *
40246 CGACTAGGAA-GGGC-TTTTTGGAAACAAATAAAGAAAACAGGGACCTTCTGACC-GAGAAGGGG
64 CGACCAAGAAGGGGCATTTTAGGAAAC-AATAAAGAAAACAGGGACCTTCCGACCTG-GAAAGGG
*
40308 CATTTTGGGAAATAAGAAAG
127 CATTTT-GCAAATAAGAAAG
*
40328 GAAAACTGTGACCTTCTGACTGGGAAGTGGCTTTTTGAAACAAATAAAGAAAACAGGGACCTTCC
1 GAAAACTGTGACCTTCTGACTGGGAAGTGGCTTTTTGAAAC-AATAAAGAAAACAGGGACCTACC
** * * *
40393 GACCGGGAAGGGGCATTTTGGGAAACAAATAAAGAGAACAGGGACCTTCCGACCTGGAAGGGGCA
65 GACCAAGAAGGGGCATTTTAGGAAAC-AATAAAGAAAACAGGGACCTTCCGACCTGGAAAGGGCA
**
40458 TTTTGGGAATAAGAAAG
129 TTTTGCAAATAAGAAAG
* * * *
40475 GAAAACTGTGACCTT-TCGACTGGGAA-TGGGTTTTTTTGGAAAC-A-AAAGGAAACTGTGACCT
1 GAAAACTGTGACCTTCT-GACTGGGAAGT-GG-CTTTTT-GAAACAATAAAGAAAACAGGGACCT
* *
40536 ACCGACCAAGAAGGGGCATTTTAGGAAAC-A-AAAGAAAACTGTGACCTTCCGA-CTAGGAAAGG
62 ACCGACCAAGAAGGGGCATTTTAGGAAACAATAAAGAAAACAGGGACCTTCCGACCT-GGAAAGG
*
40598 GCTTTTT
126 GCATTTT
40605 AGAAACAAAT
Statistics
Matches: 352, Mismatches: 47, Indels: 44
0.79 0.11 0.10
Matches are distributed among these distances:
140 1 0.00
141 41 0.12
142 43 0.12
143 59 0.17
144 10 0.03
145 30 0.09
146 65 0.18
147 43 0.12
148 54 0.15
149 6 0.02
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.20
Consensus pattern (145 bp):
GAAAACTGTGACCTTCTGACTGGGAAGTGGCTTTTTGAAACAATAAAGAAAACAGGGACCTACCG
ACCAAGAAGGGGCATTTTAGGAAACAATAAAGAAAACAGGGACCTTCCGACCTGGAAAGGGCATT
TTGCAAATAAGAAAG
Done.