Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_29 ID=scaffold_29-JGI_221_v2.0
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: 50975
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:1076 original size:10 final size:10
Alignment explanation
Indices: 1061--1218 Score: 56
Period size: 10 Copynumber: 16.5 Consensus size: 10
1051 ATGTTTCCCA
1061 TAAAAATTAT
1 TAAAAATTAT
*
1071 TAAAAAATCA-
1 T-AAAAATTAT
1081 TAAAAATTA-
1 TAAAAATTAT
1090 T-AAAA-TAT
1 TAAAAATTAT
*
1098 TAAAAATGA-
1 TAAAAATTAT
1107 TATAAAATTAT
1 TA-AAAATTAT
*
1118 T-AAAATT-G
1 TAAAAATTAT
1126 T-AAAA-TA-
1 TAAAAATTAT
1133 TAAAATATAATAAT
1 TAAAA-AT--T-AT
*
1147 TAAAAAATAT
1 TAAAAATTAT
**
1157 TAAAACCTAT
1 TAAAAATTAT
*
1167 TTAAAATTA-
1 TAAAAATTAT
*
1176 -AAAAACATAT
1 TAAAAA-TTAT
*
1186 T-AAAATTTT
1 TAAAAATTAT
*
1195 TAAAAA-TAA
1 TAAAAATTAT
*
1204 TAAAAAATAT
1 TAAAAATTAT
1214 TAAAA
1 TAAAA
1219 TTGATATAAA
Statistics
Matches: 111, Mismatches: 18, Indels: 38
0.66 0.11 0.23
Matches are distributed among these distances:
7 4 0.04
8 17 0.15
9 33 0.30
10 40 0.36
11 9 0.08
12 1 0.01
13 2 0.02
14 5 0.05
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:1094 original size:17 final size:16
Alignment explanation
Indices: 1069--1137 Score: 66
Period size: 17 Copynumber: 4.0 Consensus size: 16
1059 CATAAAAATT
*
1069 ATTAAAAAATCATAAAA
1 ATTATAAAAT-ATAAAA
1086 ATTATAAAATATTAAAA
1 ATTATAAAATA-TAAAA
*
1103 ATGATATAAAATTATTAAA
1 AT--TATAAAA-TATAAAA
*
1122 ATTGTAAAATATAAAA
1 ATTATAAAATATAAAA
1138 TATAATAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 7 0.16
17 22 0.50
19 13 0.30
20 2 0.05
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (16 bp):
ATTATAAAATATAAAA
Found at i:1103 original size:9 final size:9
Alignment explanation
Indices: 1061--1218 Score: 66
Period size: 9 Copynumber: 17.6 Consensus size: 9
1051 ATGTTTCCCA
1061 TAAAAATTAT
1 TAAAAA-TAT
1071 TAAAAA-AT
1 TAAAAATAT
*
1079 CATAAAA-AT
1 TA-AAAATAT
1088 TATAAAATAT
1 TA-AAAATAT
1098 TAAAAATGAT
1 TAAAAAT-AT
*
1108 ATAAAATTAT
1 -TAAAAATAT
1118 T-AAAAT-T
1 TAAAAATAT
1125 GT-AAAATA-
1 -TAAAAATAT
1133 T-AAAATA-
1 TAAAAATAT
*
1140 TAATAAT-T
1 TAAAAATAT
*
1148 AAAAAATAT
1 TAAAAATAT
*
1157 TAAAACCTAT
1 TAAAA-ATAT
*
1167 TTAAAAT-T
1 TAAAAATAT
*
1175 AAAAAACATAT
1 -TAAAA-ATAT
* *
1186 TAAAATTTT
1 TAAAAATAT
1195 TAAAAATAAT
1 TAAAAAT-AT
*
1205 AAAAAATAT
1 TAAAAATAT
1214 TAAAA
1 TAAAA
1219 TTGATATAAA
Statistics
Matches: 114, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
7 9 0.08
8 23 0.20
9 41 0.36
10 34 0.30
11 7 0.06
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (9 bp):
TAAAAATAT
Found at i:1216 original size:19 final size:19
Alignment explanation
Indices: 1061--1218 Score: 51
Period size: 19 Copynumber: 8.3 Consensus size: 19
1051 ATGTTTCCCA
*
1061 TAAAAATTATTAAAAAATCA-
1 TAAAAA-TAATAAAAAAT-AT
*
1081 TAAAAAT--TATAAAATAT
1 TAAAAATAATAAAAAATAT
* *
1098 TAAAAATGATATAAAATTAT
1 TAAAAATAATA-AAAAATAT
** *
1118 T-AAAATTGTAAAATATA-
1 TAAAAATAATAAAAAATAT
*
1135 AAATATAATAATTAAAAAATAT
1 TAA-A-AATAA-TAAAAAATAT
* **
1157 TAAAACCT-ATTTAAAAT-T
1 TAAAA-ATAATAAAAAATAT
* * * * *
1175 AAAAAACATATTAAAATTTT
1 TAAAAATA-ATAAAAAATAT
1195 TAAAAATAATAAAAAATAT
1 TAAAAATAATAAAAAATAT
1214 TAAAA
1 TAAAA
1219 TTGATATAAA
Statistics
Matches: 100, Mismatches: 25, Indels: 27
0.66 0.16 0.18
Matches are distributed among these distances:
16 1 0.01
17 14 0.14
18 11 0.11
19 37 0.37
20 25 0.25
21 10 0.10
22 2 0.02
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (19 bp):
TAAAAATAATAAAAAATAT
Found at i:1237 original size:28 final size:27
Alignment explanation
Indices: 1063--1239 Score: 104
Period size: 28 Copynumber: 6.5 Consensus size: 27
1053 GTTTCCCATA
*
1063 AAAATTATTAAAAA-ATCATAAAAAT-TAT
1 AAAATTA-TAAAAATAT--TAAAATTATAT
1091 AAAA-TATTAAAAATGATATAAAATTAT-T
1 AAAATTA-TAAAAAT-AT-TAAAATTATAT
*
1119 AAAATTGT-AAAATA-TAAAA-TATA-
1 AAAATTATAAAAATATTAAAATTATAT
* * *
1142 ATAATTA-AAAAATATTAAAACCTATTT
1 AAAATTATAAAAATATTAAAA-TTATAT
* *
1169 AAAATTAAAAAACATATTAAAATT-TTT
1 AAAATTATAAAA-ATATTAAAATTATAT
*
1196 AAAAATAATAAAAAATATTAAAATTGATAT
1 -AAAATTAT-AAAAATATTAAAATT-ATAT
*
1226 AAACTTATAAAAAT
1 AAAATTATAAAAAT
1240 TACAAAAATA
Statistics
Matches: 121, Mismatches: 12, Indels: 32
0.73 0.07 0.19
Matches are distributed among these distances:
23 14 0.12
24 10 0.08
26 4 0.03
27 23 0.19
28 45 0.37
29 23 0.19
30 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (27 bp):
AAAATTATAAAAATATTAAAATTATAT
Found at i:1593 original size:11 final size:10
Alignment explanation
Indices: 1570--1736 Score: 86
Period size: 10 Copynumber: 17.2 Consensus size: 10
1560 AGTTCTTACG
1570 ATTTTTTATA
1 ATTTTTTATA
1580 ATTTTTTATCA
1 ATTTTTTAT-A
*
1591 A-TTTTAATA
1 ATTTTTTATA
*
1600 CTTTTTTATA
1 ATTTTTTATA
* *
1610 TTATTTTTATG
1 AT-TTTTTATA
1621 A--TTTTAT-
1 ATTTTTTATA
**
1628 ACGTTTTATA
1 ATTTTTTATA
**
1638 AAATTTTA-A
1 ATTTTTTATA
1647 ATATGTTTTATTA
1 AT-T-TTTTA-TA
* *
1660 ATATTATATA
1 ATTTTTTATA
*
1670 TTTTTTTATA
1 ATTTTTTATA
*
1680 ATTTCTTAT-
1 ATTTTTTATA
1689 ATTTTTTAT-
1 ATTTTTTATA
1698 ATTTTTTGA-A
1 ATTTTTT-ATA
*
1708 A-TATTTATA
1 ATTTTTTATA
1717 ATTTTTTA-A
1 ATTTTTTATA
1726 ATTTTTT-TA
1 ATTTTTTATA
1735 AT
1 AT
1737 AGAAAAACTA
Statistics
Matches: 122, Mismatches: 20, Indels: 31
0.71 0.12 0.18
Matches are distributed among these distances:
7 1 0.01
8 7 0.06
9 41 0.34
10 52 0.43
11 18 0.15
13 3 0.02
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:1734 original size:20 final size:20
Alignment explanation
Indices: 1631--1734 Score: 72
Period size: 19 Copynumber: 5.2 Consensus size: 20
1621 ATTTTATACG
** *
1631 TTTTATAAAATTTTAAATATG
1 TTTTATAATTTTTTAAAT-TT
* * *
1652 TTTTATTAATATTATATATTT
1 TTTTA-TAATTTTTTAAATTT
* *
1673 TTTTATAATTTCTTATA-TT
1 TTTTATAATTTTTTAAATTT
1692 TTTTAT-ATTTTTTGAAA--T
1 TTTTATAATTTTTT-AAATTT
*
1710 ATTTATAATTTTTTAAATTT
1 TTTTATAATTTTTTAAATTT
1730 TTTTA
1 TTTTA
1735 ATAGAAAAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
18 15 0.22
19 17 0.25
20 14 0.21
21 11 0.16
22 10 0.15
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTATAATTTTTTAAATTT
Found at i:1736 original size:18 final size:18
Alignment explanation
Indices: 1671--1736 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
1661 TATTATATAT
* *
1671 TTTTTTATAATTTCTTATA
1 TTTTTT-TAATTTTTTAAA
1690 -TTTTTTATATTTTTTGAAA
1 TTTTTTTA-ATTTTTT-AAA
* *
1709 TATTTATAATTTTTTAAA
1 TTTTTTTAATTTTTTAAA
1727 TTTTTTTAAT
1 TTTTTTTAAT
1737 AGAAAAACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
17 2 0.05
18 22 0.58
19 9 0.24
20 5 0.13
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTTTTAATTTTTTAAA
Found at i:5344 original size:101 final size:100
Alignment explanation
Indices: 5223--5407 Score: 309
Period size: 101 Copynumber: 1.8 Consensus size: 100
5213 AAAGTGATGC
*
5223 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-ATGGGTCGCATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGAAT-GGTCACATGTGTAGTA
5287 CTATGTGCAGGCTACTATGCATACCGAATAGCTTCGA
64 CTATGTGCAGGCTACTATGCATACCGAATAGCTTCGA
*
5324 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATG--AATGGTCACATGTGTAGTA
5389 CTATGTGCAGGCTACTATG
64 CTATGTGCAGGCTACTATG
5408 TGAACCGGGT
Statistics
Matches: 79, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
100 3 0.04
101 40 0.51
102 34 0.43
103 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAATGGTCACATGTGTAGTACT
ATGTGCAGGCTACTATGCATACCGAATAGCTTCGA
Found at i:5353 original size:51 final size:49
Alignment explanation
Indices: 5218--5414 Score: 207
Period size: 51 Copynumber: 3.9 Consensus size: 49
5208 AAGTGAAAGT
* *
5218 GATGCTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAT-
1 GATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAATA
* * **
5267 GATGGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCATACCGAATA
1 GAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATA
* * * * *
5317 GCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAA
1 G-AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT--A
* * *
5370 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 GATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
5415 GGTATCATTG
Statistics
Matches: 120, Mismatches: 23, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
49 7 0.06
50 36 0.30
51 75 0.62
52 1 0.01
53 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (49 bp):
GATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATA
Found at i:5409 original size:26 final size:26
Alignment explanation
Indices: 5329--5409 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
5319 TTCGATCACG
5329 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * ***
5355 CGTGTA-T-CGGATGAAAATGG-TCAC-A
1 TGTGTAGTAC-TATGTGCA-GGCT-ACTA
5380 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
5406 TGTG
1 TGTG
5410 AACCGGGTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
24 1 0.03
25 16 0.42
26 20 0.53
27 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:5478 original size:33 final size:33
Alignment explanation
Indices: 5435--5594 Score: 98
Period size: 33 Copynumber: 4.7 Consensus size: 33
5425 ACTATTAGGG
*
5435 GGTTGTTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * *
5468 GGTTGCTAAGTGCTGATTCCACCATATCTTGAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-GA-C-T-CAT-T---GGT
* *
5510 GGTTGCTAAGTGCTGATT-CCC--C-CA--AGA
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * *
5537 GGTTGCTAAGTGATGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
*
5570 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
5595 TAACGGTTAA
Statistics
Matches: 98, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
27 18 0.18
28 3 0.03
31 2 0.02
33 39 0.40
34 6 0.06
35 1 0.01
36 2 0.02
37 1 0.01
38 2 0.02
39 1 0.01
40 2 0.02
41 1 0.01
42 20 0.20
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
Found at i:9340 original size:19 final size:19
Alignment explanation
Indices: 9316--9352 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9306 AATTTCGGAA
*
9316 CATTATTTTTATTGATTTT
1 CATTATATTTATTGATTTT
*
9335 CATTATATTTATTTATTT
1 CATTATATTTATTGATTT
9353 ATTTATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (19 bp):
CATTATATTTATTGATTTT
Found at i:10869 original size:19 final size:20
Alignment explanation
Indices: 10839--10879 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
10829 AAAATATTGA
10839 TTTTCTATTTTTTTTACCTT
1 TTTTCTATTTTTTTTACCTT
10859 TTTTCTA-TTTTTTTACCTT
1 TTTTCTATTTTTTTTACCTT
10878 TT
1 TT
10880 ATGTTTCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCTATTTTTTTTACCTT
Found at i:11659 original size:25 final size:25
Alignment explanation
Indices: 11628--11701 Score: 103
Period size: 25 Copynumber: 2.8 Consensus size: 25
11618 CCCATTTTTA
11628 TTTAAAATTTAAAATTAAAAAGTAT
1 TTTAAAATTTAAAATTAAAAAGTAT
*
11653 TTTAAAATTAAAAATTAAAAAAGTAT
1 TTTAAAATTTAAAATT-AAAAAGTAT
*
11679 TTAAAATATTTTAAAATTAAAAA
1 TTTAAA-A-TTTAAAATTAAAAA
11702 TTAAAAAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 15 0.35
26 14 0.33
27 6 0.14
28 8 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (25 bp):
TTTAAAATTTAAAATTAAAAAGTAT
Found at i:11718 original size:36 final size:35
Alignment explanation
Indices: 11645--11766 Score: 159
Period size: 35 Copynumber: 3.6 Consensus size: 35
11635 TTTAAAATTA
11645 AAAAGTATTTTAAAATTAAAAATTAAAAAAGTATTT
1 AAAA-TATTTTAAAATTAAAAATTAAAAAAGTATTT
11681 AAAATATTTTAAAATTAAAAATTAAAAAAGTATTTT
1 AAAATATTTTAAAATTAAAAATTAAAAAAGTA-TTT
*
11717 AAAATATTTT--AA-T--AAATT-AAAAAGTATGT
1 AAAATATTTTAAAATTAAAAATTAAAAAAGTATTT
*
11746 AAAATA-TTTAAATTTAAAAAT
1 AAAATATTTTAAAATTAAAAAT
11767 AAATATATTA
Statistics
Matches: 78, Mismatches: 2, Indels: 15
0.82 0.02 0.16
Matches are distributed among these distances:
28 3 0.04
29 8 0.10
30 9 0.12
31 6 0.08
33 5 0.06
34 2 0.03
35 28 0.36
36 17 0.22
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (35 bp):
AAAATATTTTAAAATTAAAAATTAAAAAAGTATTT
Found at i:11741 original size:30 final size:29
Alignment explanation
Indices: 11695--11754 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
11685 TATTTTAAAA
*
11695 TTAAAAATTAAAAAAGTATTTTAAAATATT
1 TTAAAAATTAAAAAAGTA-TGTAAAATATT
11725 TTAATAAATT-AAAAAGTATGTAAAATATT
1 TTAA-AAATTAAAAAAGTATGTAAAATATT
11754 T
1 T
11755 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (29 bp):
TTAAAAATTAAAAAAGTATGTAAAATATT
Found at i:20241 original size:46 final size:46
Alignment explanation
Indices: 20188--20418 Score: 374
Period size: 46 Copynumber: 5.0 Consensus size: 46
20178 CATGGCAAAG
* * *
20188 TGTGAAAAGTAGGTATGGTGTTTTGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACCGAGT
20234 TGTGAAAAGTAGGTATGGTATTTTC-GTGAAGAAAACCATACCGAGT
1 TGTGAAAAGTAGGTATGGTA-TTTCGGTGAAGAAAACCATACCGAGT
**
20280 TGTGAAAAGTAGGTATGACATTTCGGTGAAGAAAACCATACCGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACCGAGT
*
20326 TGTAAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACCGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACCGAGT
* *
20372 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACCGAGT
20418 T
1 T
20419 ATAGCATTGT
Statistics
Matches: 172, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
45 4 0.02
46 165 0.96
47 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCGGTGAAGAAAACCATACCGAGT
Found at i:29767 original size:17 final size:17
Alignment explanation
Indices: 29742--29775 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29732 CTTGTTAGCC
* *
29742 ATTAGATTATATAATTA
1 ATTAAATTAAATAATTA
29759 ATTAAATTAAATAATTA
1 ATTAAATTAAATAATTA
29776 TAAAAATATA
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:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTAAATTAAATAATTA
Found at i:31550 original size:17 final size:17
Alignment explanation
Indices: 31528--31600 Score: 74
Period size: 17 Copynumber: 4.0 Consensus size: 17
31518 AAAATATTTT
31528 TTTTAAAATTTTTTAAA
1 TTTTAAAATTTTTTAAA
31545 TTTTAAAATTTTTTTAAATA
1 TTTTAAAA-TTTTTT-AA-A
** *
31565 CTTTTTTAATTTTTTTAA
1 -TTTTAAAATTTTTTAAA
31583 TTTTAAAATATTTTTAAA
1 TTTTAAAAT-TTTTTAAA
31601 ATACTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
17 15 0.33
18 14 0.31
19 3 0.07
20 7 0.16
21 6 0.13
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAATTTTTTAAA
Found at i:31579 original size:8 final size:9
Alignment explanation
Indices: 31525--31586 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
31515 TTTAAAATAT
31525 TTTTTTTAAA
1 TTTTTTT-AA
*
31535 ATTTTTTAA
1 TTTTTTTAA
* **
31544 ATTTTAAAA
1 TTTTTTTAA
31553 TTTTTTTAAA
1 TTTTTTT-AA
31563 TACTTTTTTAA
1 T--TTTTTTAA
31574 TTTTTTTAA
1 TTTTTTTAA
31583 TTTT
1 TTTT
31587 AAAATATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
9 25 0.58
10 9 0.21
11 3 0.07
12 6 0.14
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:31629 original size:20 final size:20
Alignment explanation
Indices: 31592--31630 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31582 ATTTTAAAAT
**
31592 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
31612 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
31631 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:32155 original size:21 final size:21
Alignment explanation
Indices: 32108--32155 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
32098 GTCCGAAATG
*
32108 AATTTTTAGATTTTCTTTTAT
1 AATTTTTAGATTATCTTTTAT
**
32129 TTTTTTTAGAATTATCTTTTA-
1 AATTTTTAG-ATTATCTTTTAT
32150 AATTTT
1 AATTTT
32156 ATTTTATCTA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
AATTTTTAGATTATCTTTTAT
Found at i:32155 original size:22 final size:21
Alignment explanation
Indices: 32110--32155 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
32100 CCGAAATGAA
* **
32110 TTTTTAGATTTTCTTTTATTT
1 TTTTTAGATTATCTTTTAAAT
32131 TTTTTAGAATTATCTTTTAAAT
1 TTTTTAG-ATTATCTTTTAAAT
32153 TTT
1 TTT
32156 ATTTTATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTAGATTATCTTTTAAAT
Found at i:33170 original size:26 final size:26
Alignment explanation
Indices: 33132--33184 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
33122 ACTTTTATAA
*
33132 AAAATATAT-AAAATTTTTAAAGAATT
1 AAAATATATAAAAATTTATAAA-AATT
33158 AAAAT-TATCAAAAATTTATAAAAATT
1 AAAATATAT-AAAAATTTATAAAAATT
33184 A
1 A
33185 GACAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 10 0.42
27 11 0.46
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAATATATAAAAATTTATAAAAATT
Found at i:40680 original size:19 final size:21
Alignment explanation
Indices: 40656--40697 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
40646 TCATTTTCAA
40656 AAGCA-CGAAG-GCTAAACAG
1 AAGCACCGAAGTGCTAAACAG
*
40675 AAGCACCTAAGTGCTAAACAG
1 AAGCACCGAAGTGCTAAACAG
40696 AA
1 AA
40698 ACCGGTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (21 bp):
AAGCACCGAAGTGCTAAACAG
Found at i:43273 original size:23 final size:25
Alignment explanation
Indices: 43247--43295 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
43237 TTTACATTTT
* *
43247 TACATTT-TTAAATTGAAA-AAAAA
1 TACATTTGATAAATAGAAATAAAAA
43270 TACATTTGATAAATAGAAATAAAAA
1 TACATTTGATAAATAGAAATAAAAA
43295 T
1 T
43296 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 9 0.41
25 6 0.27
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
TACATTTGATAAATAGAAATAAAAA
Found at i:46603 original size:90 final size:91
Alignment explanation
Indices: 46496--46668 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 91
46486 CATTAAAAGC
* *
46496 TTAATTGTAATATATAACAATAAGTGAATACCAACTTCATTTTTATATAAATTTTGAC-ATAGCA
1 TTAATTGTAATACATAACAATAAGTGAATACCAACTTCATTTTTATATAAATTTTAACAATAGCA
46560 TGTTATTTTTTATATTAAAAGCTTAA
66 TGTTATTTTTTATATTAAAAGCTTAA
*
46586 TTAATTGTAATACATAACAATAAGTGTATACCAACTTCATTTTTATATAAATTTTAACATATATA
1 TTAATTGTAATACATAACAATAAGTGAATACCAACTTCATTTTTATATAAATTTTAAC--A-ATA
46651 GCATGTTATTTTTTATAT
63 GCATGTTATTTTTTATAT
46669 GGGTTTATAT
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
90 55 0.72
94 21 0.28
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (91 bp):
TTAATTGTAATACATAACAATAAGTGAATACCAACTTCATTTTTATATAAATTTTAACAATAGCA
TGTTATTTTTTATATTAAAAGCTTAA
Done.