Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022613.1 Corchorus olitorius cultivar O-4 contig22646, 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: 19019
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:1313 original size:13 final size:13
Alignment explanation
Indices: 1295--1326 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1285 AGTTAATCCA
1295 TTCAAGCATAATG
1 TTCAAGCATAATG
1308 TTCAAGCATAATG
1 TTCAAGCATAATG
1321 TTCAAG
1 TTCAAG
1327 ATTTAAGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (13 bp):
TTCAAGCATAATG
Found at i:2169 original size:13 final size:13
Alignment explanation
Indices: 2151--2175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2141 AGAGTCATGA
2151 CAAAACAGAGGCG
1 CAAAACAGAGGCG
2164 CAAAACAGAGGC
1 CAAAACAGAGGC
2176 CTCAAGCATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.24, G:0.28, T:0.00
Consensus pattern (13 bp):
CAAAACAGAGGCG
Found at i:7068 original size:33 final size:33
Alignment explanation
Indices: 7031--7458 Score: 204
Period size: 33 Copynumber: 13.5 Consensus size: 33
7021 GGTAATAATA
7031 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* * ** * **
7064 ATTTGGTAATCAAGGTAAAAAGAAAAAAAATGAA
1 ATTTGGTAATTAAAGTAAAAAG-AGTAAATTGGT
*
7098 ATTTGGT-ATCT-AAG------G-TTAAA-TGGT
1 ATTTGGTAAT-TAAAGTAAAAAGAGTAAATTGGT
* *
7122 ATTTGGTAATTAAAGTCAAAAGAGTAAACTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* * * * * **
7155 ATTTGGTAATCAAGGTTAAAAGA-AAAAATGAA
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
*
7187 ATTTGGTAACTAAAGT--------TAAA-TGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
7211 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* * ** * **
7244 ATTTGGTAATCAAGGTAAAAAGAAAAAAATGAA
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* *
7277 ATTTGGCAATTAAAATAAAAAGAGT-AATATGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAT-TGGT
**** *
7310 AAAAAG-AGATTAAAGTAAAAAGAGTAAAATGGT
1 ATTTGGTA-ATTAAAGTAAAAAGAGTAAATTGGT
**** * ** *
7343 AAAACGAAATT-TGGTAACTAAAG-TTAAA-TGGT
1 ATTTGGTAATTAAAGTAA--AAAGAGTAAATTGGT
* *
7375 ATTCGGTAATTAAAATAAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* * *
7408 ATTTGGTAAATATAGTAAAAACAGTAAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGT-AAATTGGT
*
7442 ATTTGATAATTAAAGTA
1 ATTTGGTAATTAAAGTA
7459 GAAATTGGTA
Statistics
Matches: 293, Mismatches: 71, Indels: 61
0.69 0.17 0.14
Matches are distributed among these distances:
24 27 0.09
25 11 0.04
27 1 0.00
31 5 0.02
32 47 0.16
33 160 0.55
34 42 0.14
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.29
Consensus pattern (33 bp):
ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
Found at i:7205 original size:32 final size:32
Alignment explanation
Indices: 7122--7206 Score: 82
Period size: 32 Copynumber: 2.6 Consensus size: 32
7112 GTTAAATGGT
* * * **
7122 ATTTGGTAATTAAAGTCAAAAGAGTAAACTGGT
1 ATTTGGTAA-TAAAGTTAAAAGAGAAAAATGAA
*
7155 ATTTGGTAATCAAGGTTAAAAGA-AAAAATGAA
1 ATTTGGTAAT-AAAGTTAAAAGAGAAAAATGAA
7187 ATTTGGTAACTAAAGTTAAA
1 ATTTGGTAA-TAAAGTTAAA
7207 TGGTATTTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
32 23 0.53
33 20 0.47
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (32 bp):
ATTTGGTAATAAAGTTAAAAGAGAAAAATGAA
Found at i:7207 original size:24 final size:24
Alignment explanation
Indices: 7180--7226 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
7170 TTAAAAGAAA
7180 AAATGAAATTTGGTAACTAAAGTT
1 AAATGAAATTTGGTAACTAAAGTT
** *
7204 AAATGGTATTTGGTAATTAAAGT
1 AAATGAAATTTGGTAACTAAAGT
7227 AAAAAGAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (24 bp):
AAATGAAATTTGGTAACTAAAGTT
Found at i:7232 original size:89 final size:90
Alignment explanation
Indices: 7031--7282 Score: 443
Period size: 89 Copynumber: 2.8 Consensus size: 90
7021 GGTAATAATA
7031 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAAATG
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAG-AAAAAAATG
* *
7096 AAATTTGGTATCTAAGGTTAAATGGT
65 AAATTTGGTAACTAAAGTTAAATGGT
* * *
7122 ATTTGGTAATTAAAGTCAAAAGAGTAAACTGGTATTTGGTAATCAAGGTTAAAAG-AAAAAATGA
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAATGA
7186 AATTTGGTAACTAAAGTTAAATGGT
66 AATTTGGTAACTAAAGTTAAATGGT
7211 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAATGA
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAATGA
7276 AATTTGG
66 AATTTGG
7283 CAATTAAAAT
Statistics
Matches: 152, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
89 84 0.55
90 16 0.11
91 52 0.34
ACGTcount: A:0.46, C:0.03, G:0.21, T:0.30
Consensus pattern (90 bp):
ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAATGA
AATTTGGTAACTAAAGTTAAATGGT
Found at i:7327 original size:16 final size:17
Alignment explanation
Indices: 7285--7335 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
7275 AAATTTGGCA
*
7285 ATTAAAATAAAAAGAGT
1 ATTAAAGTAAAAAGAGT
* **
7302 AATATGGTAAAAAGAG-
1 ATTAAAGTAAAAAGAGT
7318 ATTAAAGTAAAAAGAGT
1 ATTAAAGTAAAAAGAGT
7335 A
1 A
7336 AAATGGTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.22
Consensus pattern (17 bp):
ATTAAAGTAAAAAGAGT
Found at i:7346 original size:16 final size:17
Alignment explanation
Indices: 7292--7346 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
7282 GCAATTAAAA
*
7292 TAAAAAGAGTAATATGG
1 TAAAAAGAGTAAAATGG
*
7309 TAAAAAGAGATTAAA--G
1 TAAAAAGAG-TAAAATGG
7325 TAAAAAGAGTAAAATGG
1 TAAAAAGAGTAAAATGG
7342 TAAAA
1 TAAAA
7347 CGAAATTTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 4 0.12
16 10 0.31
17 15 0.47
18 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (17 bp):
TAAAAAGAGTAAAATGG
Found at i:9925 original size:48 final size:48
Alignment explanation
Indices: 9812--9959 Score: 228
Period size: 47 Copynumber: 3.1 Consensus size: 48
9802 GGTTTGAATG
* * *
9812 AGATAAACAAAATTCTTTTGAATAAACAATCGTGTTTTGAA-TAAAAA
1 AGATAAACAAGATTCTTTTGAATAAACAATTGTGTTTTGAACAAAAAA
*
9859 AGATAAACAAGATTCTTTTGAATAATCAATTGTGTTTTGAACAAAAAA
1 AGATAAACAAGATTCTTTTGAATAAACAATTGTGTTTTGAACAAAAAA
* *
9907 AGGTAAACAAGATCCTTTTGAATAAACAATTGTGTTTTGAAC-AAAAA
1 AGATAAACAAGATTCTTTTGAATAAACAATTGTGTTTTGAACAAAAAA
9954 AGATAA
1 AGATAA
9960 GATAAGATCA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
47 48 0.52
48 44 0.48
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (48 bp):
AGATAAACAAGATTCTTTTGAATAAACAATTGTGTTTTGAACAAAAAA
Found at i:9967 original size:48 final size:47
Alignment explanation
Indices: 9812--9968 Score: 224
Period size: 48 Copynumber: 3.3 Consensus size: 47
9802 GGTTTGAATG
* * * *
9812 AGATAAACAAAATTCTTTTGAATAAACAATCGTGTTTTGAATAAAAA
1 AGATAAACAAGATCCTTTTGAATAAACAATTGTGTTTTGAACAAAAA
* *
9859 AGATAAACAAGATTCTTTTGAATAATCAATTGTGTTTTGAACAAAAAA
1 AGATAAACAAGATCCTTTTGAATAAACAATTGTGTTTTGAAC-AAAAA
*
9907 AGGTAAACAAGATCCTTTTGAATAAACAATTGTGTTTTGAACAAAAA
1 AGATAAACAAGATCCTTTTGAATAAACAATTGTGTTTTGAACAAAAA
*
9954 AGATAAGATAAGATC
1 AGATAA-ACAAGATC
9969 AAAACTGGAA
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
47 48 0.48
48 51 0.52
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (47 bp):
AGATAAACAAGATCCTTTTGAATAAACAATTGTGTTTTGAACAAAAA
Found at i:11126 original size:12 final size:13
Alignment explanation
Indices: 11103--11158 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
11093 TCGAAAGAAA
11103 AAAAAAGTTTTTC
1 AAAAAAGTTTTTC
*
11116 AAAAAAGTTTTTT
1 AAAAAAGTTTTTC
*
11129 AGAGAAAATTGTTTTC
1 A-A-AAAAGT-TTTTC
11145 --AAAAGTTTTTC
1 AAAAAAGTTTTTC
11156 AAA
1 AAA
11159 TGCAGGTGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 14 0.41
14 1 0.03
15 5 0.15
16 4 0.12
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (13 bp):
AAAAAAGTTTTTC
Found at i:11202 original size:21 final size:21
Alignment explanation
Indices: 11178--11235 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
11168 ATGGTGAGGT
11178 AAAATAAAAAAAAAGGAGAAA
1 AAAATAAAAAAAAAGGAGAAA
*
11199 AAAATAAAAGAGAAAAAGAGAAA
1 AAAATAAAA-A-AAAAGGAGAAA
* *
11222 TAAA-AAAGAAAAAG
1 AAAATAAAAAAAAAG
11236 AATAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.13
21 10 0.32
22 4 0.13
23 13 0.42
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (21 bp):
AAAATAAAAAAAAAGGAGAAA
Found at i:11222 original size:19 final size:19
Alignment explanation
Indices: 11200--11251 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 19
11190 AAGGAGAAAA
11200 AAATAAAAGAGAAAAAGAG
1 AAATAAAAGAGAAAAAGAG
*
11219 AAATAAAAAAG-AAAA-AG
1 AAATAAAAGAGAAAAAGAG
11236 -AATAAAAGA-AAAAAGA
1 AAATAAAAGAGAAAAAGA
11252 AGGATACGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 12 0.41
17 3 0.10
18 4 0.14
19 10 0.34
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (19 bp):
AAATAAAAGAGAAAAAGAG
Found at i:11242 original size:14 final size:13
Alignment explanation
Indices: 11194--11248 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 13
11184 AAAAAAAAGG
11194 AGAAAAAA-ATAAA
1 AGAAAAAAGA-AAA
*
11207 AGAGAAAAAGAGAA
1 AGA-AAAAAGAAAA
*
11221 ATAAAAAAGAAAA
1 AGAAAAAAGAAAA
11234 AGAATAAAAGAAAA
1 AGAA-AAAAGAAAA
11248 A
1 A
11249 AGAAGGATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 15 0.43
14 19 0.54
15 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:12423 original size:35 final size:33
Alignment explanation
Indices: 12384--12672 Score: 209
Period size: 35 Copynumber: 8.5 Consensus size: 33
12374 AAGTTCACCT
* * *
12384 AGGGCGGTCTCTCTTCAATTAGTTTCAATTGATCC
1 AGGGCGATCT-TCTTCATTTA-CTTCAATTGATCC
*
12419 AGGGCGATCATTCTTCAGTTTACTTCAATCGATCC
1 AGGGCGATC-TTCTTCA-TTTACTTCAATTGATCC
* * *
12454 AGAGCGATCTTGCTTC----A----AGTTGACCC
1 AGGGCGATCTT-CTTCATTTACTTCAATTGATCC
*
12480 AGGGCGGTCTTTCTTCAGTTTACTTCAATTGATCC
1 AGGGCGATC-TTCTTCA-TTTACTTCAATTGATCC
* * * *
12515 AGGGCGATCCTTCTTCAGTTAATTTCGAGTTGACCC
1 AGGGCGAT-CTTCTTCA-TTTACTTC-AATTGATCC
*
12551 GGGGC-AGTCTTTCTTCAGTTTACTTCAATTGATCC
1 AGGGCGA-TC-TTCTTCA-TTTACTTCAATTGATCC
* *
12586 AGGGCGATCTCTCTTCATTTAGTTGCAATAGATCC
1 AGGGCGATCT-TCTTCATTTACTT-CAATTGATCC
12621 AGGGCGATCATTCTTCAGTTTACTTCAATTGATCC
1 AGGGCGATC-TTCTTCA-TTTACTTCAATTGATCC
*
12656 AGAGCGATCTTTCTTCA
1 AGGGCGATC-TTCTTCA
12673 AGTTGACCCA
Statistics
Matches: 203, Mismatches: 29, Indels: 44
0.74 0.11 0.16
Matches are distributed among these distances:
26 17 0.08
27 2 0.01
30 1 0.00
31 1 0.00
34 9 0.04
35 134 0.66
36 39 0.19
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (33 bp):
AGGGCGATCTTCTTCATTTACTTCAATTGATCC
Found at i:12482 original size:61 final size:60
Alignment explanation
Indices: 12407--12709 Score: 268
Period size: 61 Copynumber: 4.7 Consensus size: 60
12397 TTCAATTAGT
* * *
12407 TTCAA-TTGATCCAGGGCGATCATTCTTCAGTTTACTTCAATCGATCCAGAGCGATCTTGC
1 TTCAAGTTGACCCAGGGCGATCTTTCTTCAGTTTACTTCAATTGATCCAGAGCGATCTT-C
* *
12467 TTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAATTGATCCAGGGCGATCCTTC
1 TTCAAGTTGACCCAGGGCGATCTTTCTTCAGTTTACTTCAATTGATCCAGAGCGAT-CTTC
* *
12528 TTCAGTTAATTTCGAGTTGACCCGGGGC-AGTCTTTCTTCAGTTTACTTCAATTGATCCAGGGCG
1 TTC-----A-----AGTTGACCCAGGGCGA-TCTTTCTTCAGTTTACTTCAATTGATCCAGAGCG
12592 ATCTCTC
55 ATCT-TC
* *
12599 TTCATTTAGTTGCAATAGATCCAGGGCGATCATTCTTCAGTTTACTTCAATTGATCCAGAGCGAT
1 TTCA---AG-T----T-GACCCAGGGCGATCTTTCTTCAGTTTACTTCAATTGATCCAGAGCGAT
12664 CTTTC
57 C-TTC
* * *
12669 TTCAAGTTGACCCAGGGTGGTCTTTCTTCAATTTACTTCAA
1 TTCAAGTTGACCCAGGGCGATCTTTCTTCAGTTTACTTCAA
12710 CAATCCAGGG
Statistics
Matches: 203, Mismatches: 18, Indels: 43
0.77 0.07 0.16
Matches are distributed among these distances:
60 5 0.02
61 77 0.38
62 4 0.02
64 3 0.01
65 1 0.00
66 3 0.01
67 2 0.01
69 1 0.00
70 51 0.25
71 56 0.28
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (60 bp):
TTCAAGTTGACCCAGGGCGATCTTTCTTCAGTTTACTTCAATTGATCCAGAGCGATCTTC
Found at i:12507 original size:96 final size:95
Alignment explanation
Indices: 12340--12709 Score: 400
Period size: 96 Copynumber: 3.7 Consensus size: 95
12330 TTGATTCGGG
* * *
12340 GTTTACTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTCACCTAGGGCGGTCTCTCTTCAATTA
1 GTTTACTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTGACCCAGGGCGGTCTCTCTTCATTTA
*
12405 GTTTCAATTGATCCAGGGCGATCATTCTTCA
66 -CTTCAATTGATCCAGGGCGATCATTCTTCA
*
12436 GTTTACTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTT
1 GTTTACTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTGACCCAGGGCGGTCTCTCTTCA-TTT
*
12501 ACTTCAATTGATCCAGGGCGATCCTTCTTCA
65 ACTTCAATTGATCCAGGGCGATCATTCTTCA
* * * * * * ** * *
12532 GTTAATTTCGAGTTGACCCGGGGCAGTCTTTCTTCAGTTTACTTCAA-TTGATCCAGGGCGATCT
1 GTTTACTTC-AATCGATCC--AG-AG-CGATCTT--G----CTTCAAGTTGACCCAGGGCGGTCT
* *
12596 CTCTTCATTTAGTTGCAATAGATCCAGGGCGATCATTCTTCA
55 CTCTTCATTTACTT-CAATTGATCCAGGGCGATCATTCTTCA
* * * *
12638 GTTTACTTCAATTGATCCAGAGCGATCTTTCTTCAAGTTGACCCAGGGTGGTCTTTCTTCAATTT
1 GTTTACTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTGACCCAGGGCGGTCTCTCTTC-ATTT
12703 ACTTCAA
65 ACTTCAA
12710 CAATCCAGGG
Statistics
Matches: 226, Mismatches: 33, Indels: 30
0.78 0.11 0.10
Matches are distributed among these distances:
95 6 0.03
96 115 0.51
97 16 0.07
99 1 0.00
100 2 0.01
101 10 0.04
102 2 0.01
103 2 0.01
105 13 0.06
106 53 0.23
107 6 0.03
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (95 bp):
GTTTACTTCAATCGATCCAGAGCGATCTTGCTTCAAGTTGACCCAGGGCGGTCTCTCTTCATTTA
CTTCAATTGATCCAGGGCGATCATTCTTCA
Found at i:12561 original size:71 final size:69
Alignment explanation
Indices: 12471--12672 Score: 262
Period size: 71 Copynumber: 2.9 Consensus size: 69
12461 TCTTGCTTCA
12471 AGTTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAATTGATCCAGGGCGATCCTTCTTCAGTTA
1 AGTTGACCCAGGGC-GTCTTTCTTCAGTTTACTTCAATTGATCCAGGGCGATCCTTCTTCAGTTA
*
12536 ATTTC
65 ATTGC
* *
12541 GAGTTGACCCGGGGCAGTCTTTCTTCAGTTTACTTCAATTGATCCAGGGCGAT-CTCTCTTCATT
1 -AGTTGACCCAGGGC-GTCTTTCTTCAGTTTACTTCAATTGATCCAGGGCGATCCT-TCTTCAGT
*
12605 TAGTTGC
63 TAATTGC
* * * * * *
12612 AATAGATCCAGGGCGATCATTCTTCAGTTTACTTCAATTGATCCAGAGCGATCTTTCTTCA
1 AGTTGACCCAGGGCG-TCTTTCTTCAGTTTACTTCAATTGATCCAGGGCGATCCTTCTTCA
12673 AGTTGACCCA
Statistics
Matches: 116, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
69 1 0.01
70 52 0.45
71 63 0.54
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (69 bp):
AGTTGACCCAGGGCGTCTTTCTTCAGTTTACTTCAATTGATCCAGGGCGATCCTTCTTCAGTTAA
TTGC
Found at i:12683 original size:26 final size:25
Alignment explanation
Indices: 12643--12701 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
12633 CTTCAGTTTA
*
12643 CTTCAATTGATCCAGAGCGATCTTT
1 CTTCAATTGACCCAGAGCGATCTTT
* * *
12668 CTTCAAGTTGACCCAGGGTGGTCTTT
1 CTTCAA-TTGACCCAGAGCGATCTTT
12694 CTTCAATT
1 CTTCAATT
12702 TACTTCAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (25 bp):
CTTCAATTGACCCAGAGCGATCTTT
Found at i:12815 original size:61 final size:61
Alignment explanation
Indices: 12750--12907 Score: 228
Period size: 61 Copynumber: 2.6 Consensus size: 61
12740 TTATTCAATA
* * *
12750 CTTCAGTTTACTGGTCCAGGGTGGTCTTTCTTCAATTCCTCAATCCTTCAATTA-TCCAACG
1 CTTCAATTTACTGATCCAGGGTGGTCTTTCTTCAATTCCTCAATCATTCAATTATTCC-ACG
* * *
12811 CTTCAATTTACTGATCCAGGGTGGTCTTTCTTCAATTCTTCAATTATTCAATTATTCCATG
1 CTTCAATTTACTGATCCAGGGTGGTCTTTCTTCAATTCCTCAATCATTCAATTATTCCACG
*
12872 CTTCAATTTACTGATCCCAGGGCGGTCTTTCTTCAA
1 CTTCAATTTACTGAT-CCAGGGTGGTCTTTCTTCAA
12908 CTCTTCCATT
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
61 66 0.75
62 22 0.25
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (61 bp):
CTTCAATTTACTGATCCAGGGTGGTCTTTCTTCAATTCCTCAATCATTCAATTATTCCACG
Done.