Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017931.1 Corchorus olitorius cultivar O-4 contig17964, 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: 75874
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:167 original size:32 final size:31
Alignment explanation
Indices: 120--181 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 31
110 GCACTAGTTA
*
120 TATGGTATGGTGTAAAAACCCATTTTGATTG
1 TATGCTATGGTGTAAAAACCCATTTTGATTG
*
151 TATGCTATGGTTGTAAAAACTCATTTTGATT
1 TATGCTATGG-TGTAAAAACCCATTTTGATT
182 ATTAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (31 bp):
TATGCTATGGTGTAAAAACCCATTTTGATTG
Found at i:4007 original size:101 final size:100
Alignment explanation
Indices: 3795--3988 Score: 255
Period size: 101 Copynumber: 1.9 Consensus size: 100
3785 AACTCATCAG
* * * * *
3795 AAAATTAATTCCCT-ATTCAACATATTTACATAATTGTAGAAATGCAACAAAAGTAACGGTTTAG
1 AAAATTACTTCCCTAAATCAACACA-TCACATAATTGTAGAAATGCAACAAAAGTAAAGGTTTAG
* *
3859 GTATTTGAAAATTCCTTTGACAGGATGGAGGTCTCAC
65 GTACTTGAAAATACCTTTGACAGGATGGAGG-CTCAC
* * *
3896 AAAATTACTTCCCTAAATCAACACATCACATAATTGTGGAAATGCAACAAAAGTAAAAGTTTTTG
1 AAAATTACTTCCCTAAATCAACACATCACATAATTGTAGAAATGCAACAAAAGT-AAAGGTTTAG
*
3961 GTACTTGAAACTACCTTTGACAGGATGG
65 GTACTTGAAAATACCTTTGACAGGATGG
3989 GAGGTCAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
101 40 0.50
102 40 0.50
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (100 bp):
AAAATTACTTCCCTAAATCAACACATCACATAATTGTAGAAATGCAACAAAAGTAAAGGTTTAGG
TACTTGAAAATACCTTTGACAGGATGGAGGCTCAC
Found at i:4697 original size:103 final size:104
Alignment explanation
Indices: 4579--4765 Score: 340
Period size: 103 Copynumber: 1.8 Consensus size: 104
4569 TTTCTTATTT
*
4579 GAATTTACTAAAAAAACTACAGGGCTATTAAGAACGAAGTTAAACATTAATCAA-TAAGAAGGTT
1 GAATTTACTAAAAAAACTACAGGGCTATTAAGAACAAAGTTAAACATTAATCAATTAAGAAGGTT
*
4643 ATCGATCTCTGATGCAAGAAGAAGAAGAAGAAGAAGAAA
66 ATCGATCTCTGATGAAAGAAGAAGAAGAAGAAGAAGAAA
*
4682 GAATTTACTAAAAAAACTACAGGGCTATTAAGAACAAAGTTAAATATTAATCAATTAAGAAGGTT
1 GAATTTACTAAAAAAACTACAGGGCTATTAAGAACAAAGTTAAACATTAATCAATTAAGAAGGTT
4747 ATCGATCTCTGATGAAAGA
66 ATCGATCTCTGATGAAAGA
4766 TGATTATCAA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
103 52 0.65
104 28 0.35
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.24
Consensus pattern (104 bp):
GAATTTACTAAAAAAACTACAGGGCTATTAAGAACAAAGTTAAACATTAATCAATTAAGAAGGTT
ATCGATCTCTGATGAAAGAAGAAGAAGAAGAAGAAGAAA
Found at i:6700 original size:179 final size:179
Alignment explanation
Indices: 6393--6737 Score: 609
Period size: 179 Copynumber: 1.9 Consensus size: 179
6383 AAAAGTTATG
6393 AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
1 AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
* *
6458 TGATCAATAATGAAAGTTGCCAATTTAATTACTTAAGTAATCTACTATAAAAGCTAAAAAAGTTA
66 TGATCAATAATGAAAGTTACCAATTTAATTACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTA
6523 TTAAAATTGTATTTACCAATCCTTACATTCTTAATATTTTTTTTGCCGA
131 TTAAAATTGTATTTACCAATCCTTACATTCTTAATATTTTTTTTGCCGA
* *
6572 AAAACATTATAGTACTATCTAGATTCAAGTAATCTTACATCCTTATTAATTTTAGTAACTTTTTA
1 AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
* * * *
6637 TGATTAATAATGAAAGTTACCAATTTAATTACTTGAGTAATCTACTAAAAAAGCTATAAAAGTTT
66 TGATCAATAATGAAAGTTACCAATTTAATTACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTA
*
6702 TTTAAATTGTATTTACCAATCCTTACATTCTTAATA
131 TTAAAATTGTATTTACCAATCCTTACATTCTTAATA
6738 ACATTAGTTA
Statistics
Matches: 157, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
179 157 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.41
Consensus pattern (179 bp):
AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
TGATCAATAATGAAAGTTACCAATTTAATTACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTA
TTAAAATTGTATTTACCAATCCTTACATTCTTAATATTTTTTTTGCCGA
Found at i:7240 original size:36 final size:36
Alignment explanation
Indices: 7193--7262 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
7183 TTCAATAACC
*
7193 TTACATCTTTTGTAATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
7229 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
7263 CCAAAATCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:8103 original size:45 final size:42
Alignment explanation
Indices: 8039--8127 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 42
8029 ATATCTAAGA
8039 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATA-TA-TA-TATTAC
* *
8084 ATTTAATTAATGTACGTATTTTAGTTATTATATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATATTAC
8126 AT
1 AT
8128 AGGAATTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
42 8 0.19
43 2 0.05
44 2 0.05
45 30 0.71
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (42 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATATTAC
Found at i:11049 original size:37 final size:37
Alignment explanation
Indices: 11005--11186 Score: 201
Period size: 37 Copynumber: 4.8 Consensus size: 37
10995 GGAATTTGAG
11005 TTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTAT
1 TTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTAT
11042 TTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTAT
1 TTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTAT
* ** * * * * *
11079 GGTATAATT-TCTAGTTTGGT-TGTAATGAG-AGGTCTA-TGAG
1 --TTTGTTTGTTTA-TTTGGTAAGT-A-G-GTA-GTTTATTTAT
11119 TTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTAT
1 TTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTAT
11156 TTTGTTTGTTTATTTGGTAAGTAGGTAGTTT
1 TTTGTTTGTTTATTTGGTAAGTAGGTAGTTT
11187 TATGGTATAG
Statistics
Matches: 118, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
36 5 0.04
37 72 0.61
38 16 0.14
39 16 0.14
40 4 0.03
41 5 0.04
ACGTcount: A:0.20, C:0.01, G:0.24, T:0.55
Consensus pattern (37 bp):
TTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTAT
Found at i:11142 original size:114 final size:111
Alignment explanation
Indices: 11001--11222 Score: 408
Period size: 114 Copynumber: 2.0 Consensus size: 111
10991 TCACGGAATT
11001 TGAGTTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTATTTTGTTTGTTTATTTGGTAAGTAG
1 TGAGTTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTATTTTGTTTGTTTATTTGGTAAGTAG
11066 GTAGTTTATTTATGGTATAATTTCTAGTTTGGTTGTAATGAGAGGTCTA
66 GTAG--T-TTTATGGTATAATTTCTAGTTTGGTTGTAATGAGAGGTCTA
11115 TGAGTTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTATTTTGTTTGTTTATTTGGTAAGTAG
1 TGAGTTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTATTTTGTTTGTTTATTTGGTAAGTAG
*
11180 GTAGTTTTATGGTATAGTTTCTAGTTTGGTTGTAATGAGAGGT
66 GTAGTTTTATGGTATAATTTCTAGTTTGGTTGTAATGAGAGGT
11223 AATGTAAACC
Statistics
Matches: 107, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
111 37 0.35
112 1 0.01
114 69 0.64
ACGTcount: A:0.20, C:0.01, G:0.26, T:0.53
Consensus pattern (111 bp):
TGAGTTTGTTTGTTTATTTGGTAAGTAGGTAGTTTATTTATTTTGTTTGTTTATTTGGTAAGTAG
GTAGTTTTATGGTATAATTTCTAGTTTGGTTGTAATGAGAGGTCTA
Found at i:11437 original size:57 final size:57
Alignment explanation
Indices: 11267--11438 Score: 235
Period size: 57 Copynumber: 3.1 Consensus size: 57
11257 CGGGATGTGA
*
11267 GTTTGTTTGTTTATTTGGTAGATAGGTAGTTTATTTATGGTATAGTTTCTAGTTTGG
1 GTTTGTTTGTTTATTTGGTAGGTAGGTAGTTTATTTATGGTATAGTTTCTAGTTTGG
* * * * *
11324 GTTTGTTTGTTTATTT-GAATTGTA-ATGAGATT-TGT-TGGTATAGTTTCTAGTTTGG
1 GTTTGTTTGTTTATTTGGTA-GGTAGGT-AGTTTATTTATGGTATAGTTTCTAGTTTGG
*
11379 GTTTATTTGTTTATTTGGTAGGTAGGTAGTTTATTTATGGTATAGTTTCTAGTTTGG
1 GTTTGTTTGTTTATTTGGTAGGTAGGTAGTTTATTTATGGTATAGTTTCTAGTTTGG
11436 GTT
1 GTT
11439 GAATTCTCGT
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
55 42 0.43
56 10 0.10
57 45 0.46
ACGTcount: A:0.17, C:0.02, G:0.26, T:0.55
Consensus pattern (57 bp):
GTTTGTTTGTTTATTTGGTAGGTAGGTAGTTTATTTATGGTATAGTTTCTAGTTTGG
Found at i:11643 original size:30 final size:30
Alignment explanation
Indices: 11607--11674 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
11597 CGGCCGGAAA
**
11607 AAAAAAAAAAACAACACTTCTCTTTTTGCC
1 AAAAAAAAAAACAACACTTCTCTTGGTGCC
11637 AAAAAAAAAAACAACACTTCTCTTGGTGCC
1 AAAAAAAAAAACAACACTTCTCTTGGTGCC
11667 AAAAAAAA
1 AAAAAAAA
11675 TAATAATAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.53, C:0.21, G:0.06, T:0.21
Consensus pattern (30 bp):
AAAAAAAAAAACAACACTTCTCTTGGTGCC
Found at i:12053 original size:18 final size:18
Alignment explanation
Indices: 12032--12075 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
12022 TAGACTCGAA
*
12032 ACTGACTTGAAAAAACTG
1 ACTGACTCGAAAAAACTG
12050 ACTGACTCGAAAAAACTG
1 ACTGACTCGAAAAAACTG
12068 ACTGACTC
1 ACTGACTC
12076 AAACTGACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (18 bp):
ACTGACTCGAAAAAACTG
Found at i:14844 original size:161 final size:164
Alignment explanation
Indices: 14669--14999 Score: 497
Period size: 161 Copynumber: 2.0 Consensus size: 164
14659 AAATGAAAGA
*
14669 TTGAGTACAAAACAAATCCAGAATTACTGGTTCAAAAACACAGTGTCCCACTGTCCACGACCAAG
1 TTGAGTACAAAACAAATCCAGAATTACTGGTTCAAAAACACAGTGTCCCACTGTCCACCACCAAG
* *
14734 AATGCCTAGATAT-CA-AGATGATCCATAAGCTTGCTAACAAATCTAAAAAGTACACATATCAAT
66 AATGCCTAGATATACACAGATGATCCATAAGCATGCTAACAAATCTAAAAAGCACACATATCAAT
14797 AGATCTAATTC-ATCTAAAGTATACAATTACTGG
131 AGATCTAATTCAATCTAAAGTATACAATTACTGG
*
14830 TTGAGTACAAAACAAATCCAGAATTACTGGTTCATAAACACAGTGTCCCACTGTCCACCACCAAG
1 TTGAGTACAAAACAAATCCAGAATTACTGGTTCAAAAACACAGTGTCCCACTGTCCACCACCAAG
* **
14895 AATGCCTAGATATCAGCAGACAGCAGATGATCTATAAGCATGCTAACAAATCTAAAAAGCACATG
66 AATGCCTAGATAT------ACA-CAGATGATCCATAAGCATGCTAACAAATCTAAAAAGCACACA
14960 TATCAATAGATCTAATTCATAATCTAAAGTATACAATTAC
124 TATCAATAGATCTAATTC--AATCTAAAGTATACAATTAC
15000 CACTGCAAAA
Statistics
Matches: 151, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
161 76 0.50
168 2 0.01
170 54 0.36
173 19 0.13
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.24
Consensus pattern (164 bp):
TTGAGTACAAAACAAATCCAGAATTACTGGTTCAAAAACACAGTGTCCCACTGTCCACCACCAAG
AATGCCTAGATATACACAGATGATCCATAAGCATGCTAACAAATCTAAAAAGCACACATATCAAT
AGATCTAATTCAATCTAAAGTATACAATTACTGG
Found at i:21936 original size:13 final size:13
Alignment explanation
Indices: 21918--21943 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21908 AATATTTCTC
21918 GTGGGGGGGGGGG
1 GTGGGGGGGGGGG
21931 GTGGGGGGGGGGG
1 GTGGGGGGGGGGG
21944 TTTCAAGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.92, T:0.08
Consensus pattern (13 bp):
GTGGGGGGGGGGG
Found at i:29700 original size:3 final size:3
Alignment explanation
Indices: 29692--29742 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
29682 TGTTCATTAG
29692 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29740 TAA
1 TAA
29743 ACCTTAGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31135 original size:2 final size:2
Alignment explanation
Indices: 31128--31156 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31118 AGATTTCCTA
31128 AT 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 A
31157 CCAAATCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37721 original size:19 final size:18
Alignment explanation
Indices: 37688--37723 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
37678 TTGAAATTAT
37688 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
37706 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
37724 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:40627 original size:6 final size:6
Alignment explanation
Indices: 40616--40680 Score: 77
Period size: 5 Copynumber: 11.5 Consensus size: 6
40606 GTAGTAGTTG
40616 TTGTTT TTGTTT TTGTTT TTG-TT TTG-TT TTG-TT TTG-TT TTGTTT
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT
*
40660 TTTTGTT TTGTTT TT-TTT TTG
1 TTGT-TT TTGTTT TTGTTT TTG
40681 CAATAGTGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
5 25 0.46
6 24 0.44
7 5 0.09
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTGTTT
Found at i:40648 original size:28 final size:29
Alignment explanation
Indices: 40616--40680 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
40606 GTAGTAGTTG
40616 TTGTTTTTGTTTT-TGTTTTTGTTTTGTT
1 TTGTTTTTGTTTTGTGTTTTTGTTTTGTT
*
40644 TTG-TTTTGTTTTGTTTTTTTGTTTTGTT
1 TTGTTTTTGTTTTGTGTTTTTGTTTTGTT
*
40672 TTTTTTTTG
1 TTGTTTTTG
40681 CAATAGTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 9 0.27
28 19 0.58
29 5 0.15
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (29 bp):
TTGTTTTTGTTTTGTGTTTTTGTTTTGTT
Found at i:41405 original size:22 final size:23
Alignment explanation
Indices: 41369--41412 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
41359 GGGCATAATC
* *
41369 TTTCTATTTGTTTTTATTTTGAA
1 TTTCTATTTCTTTTTATATTGAA
41392 TTTCT-TTTCTTTTTATATTGA
1 TTTCTATTTCTTTTTATATTGA
41413 TTTTAAATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.70
Consensus pattern (23 bp):
TTTCTATTTCTTTTTATATTGAA
Found at i:44199 original size:23 final size:24
Alignment explanation
Indices: 44173--44218 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
44163 GTAAAGAAAA
* *
44173 ATTTCGGTGAAAATTGG-ATGAGG
1 ATTTCAGTGAAAATCGGTATGAGG
44196 ATTTCAGTGAAAATCGGTATGAG
1 ATTTCAGTGAAAATCGGTATGAG
44219 CTCTACTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (24 bp):
ATTTCAGTGAAAATCGGTATGAGG
Found at i:48820 original size:36 final size:36
Alignment explanation
Indices: 48739--49053 Score: 533
Period size: 36 Copynumber: 8.8 Consensus size: 36
48729 AAATTATCAG
* *
48739 GAATTCAGATGACTCGGTGTAGCATCTT-CAAAGAT
1 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
* *
48774 GAATTCAGATGACTCGGTGTAGCATCTTCAAAAGTT
1 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
48810 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
1 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
48846 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
1 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
* *
48882 GAATTCAGATGACTCGATGTAGCATCTTCCAAAGTT
1 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
* *
48918 GAATTCAGATGACTCGGTGTAGCATCCTCCAAAGTT
1 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
48954 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
1 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
*
48990 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTC
1 GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
*
49026 GAATTTAGATGACTCAGTGTAGCATCTT
1 GAATTTAGATGACTCGGTGTAGCATCTT
49054 TAAAGGTTGG
Statistics
Matches: 267, Mismatches: 12, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
35 28 0.10
36 239 0.90
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (36 bp):
GAATTTAGATGACTCGGTGTAGCATCTTCCAAAGTT
Found at i:49493 original size:28 final size:28
Alignment explanation
Indices: 49453--49543 Score: 146
Period size: 28 Copynumber: 3.2 Consensus size: 28
49443 TTTACTTCTT
*
49453 ATTTTGATCATTTTGCATGTCCAGGGGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
*
49481 ATTTTGGTCATTTTGCATGTCTAGGGGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
* *
49509 ATTTTGGTCATTTTGCATATCCAGGCGC
1 ATTTTGGTCATTTTGCATGTCCAGGGGC
49537 ATTTTGG
1 ATTTTGG
49544 GTCACTTCAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.42
Consensus pattern (28 bp):
ATTTTGGTCATTTTGCATGTCCAGGGGC
Found at i:51716 original size:30 final size:30
Alignment explanation
Indices: 51682--51750 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
51672 CCAAGAAAAC
51682 CTCTCCCATTTC-AAAAAAGCC-GAAAATTTT
1 CTCTCCCATTTCGAAAAAA-CCAGAAAA-TTT
*
51712 CTCTCCCA-TTCGAGAAAACCAGAAAATTT
1 CTCTCCCATTTCGAAAAAACCAGAAAATTT
51741 CTCT-CCATTT
1 CTCTCCCATTT
51751 TTCTTCACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
28 3 0.09
29 14 0.40
30 18 0.51
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.30
Consensus pattern (30 bp):
CTCTCCCATTTCGAAAAAACCAGAAAATTT
Found at i:55533 original size:118 final size:123
Alignment explanation
Indices: 55320--55558 Score: 301
Period size: 118 Copynumber: 2.0 Consensus size: 123
55310 TTCAAACTCA
* * * * **
55320 TCAAATTCAATTAATGATTTACTTGAATTTTACAAGAATTATGAAAGCTTCTTAAAGGGTTTATT
1 TCAAATTCAATTAAAGATTGACTTAAATCTTACAAGAATTATGAAAGCTTCCCAAA-GGTTTATT
* *
55385 AACTAAAGGTGTTAATTACTCAATTAAACCTTAAG-TTTTAGGTTACTTAACCTTGGTT
65 AACTAAAGGTGTTAATTACTCAATTAAACCTAAAGCTTTAAGGTTACTTAACCTTGGTT
* * *
55443 TCAAATTCAATTAAAGATTGACTTAAATCTTA-ATGAATTATGAAA-C-TCCCAAA-TTTTATTG
1 TCAAATTCAATTAAAGATTGACTTAAATCTTACAAGAATTATGAAAGCTTCCCAAAGGTTTATTA
* *
55504 ACTATAGGT-TGTAATTACTTAATTAAACCTAAAGCTTTAAGGTTACTTAACCTTG
66 ACTAAAGGTGT-TAATTACTCAATTAAACCTAAAGCTTTAAGGTTACTTAACCTTG
55559 ATTGCCAATT
Statistics
Matches: 101, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
117 1 0.01
118 35 0.35
119 19 0.19
120 5 0.05
121 1 0.01
122 12 0.12
123 28 0.28
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (123 bp):
TCAAATTCAATTAAAGATTGACTTAAATCTTACAAGAATTATGAAAGCTTCCCAAAGGTTTATTA
ACTAAAGGTGTTAATTACTCAATTAAACCTAAAGCTTTAAGGTTACTTAACCTTGGTT
Found at i:56356 original size:121 final size:120
Alignment explanation
Indices: 56142--56533 Score: 642
Period size: 121 Copynumber: 3.2 Consensus size: 120
56132 AAACGTGCTG
* * *
56142 TTAAATCTTAATGAATTTTGAAACTTACCAAAAGCTTTTAAAACGAAGGTCTTAATTACTTAATT
1 TTAAATCTTAATGAATTGTGAAA-TTACCAAAAGCTTTTAAAACAAAGGTTTTAATTACTTAATT
*
56207 AAACCTAAGGTTTTAAGGTCACTTAACCTTGGCTTCAAATTCGATTAAGGATTCAC
65 AAACCTAAAGTTTTAAGGTCACTTAACCTTGGCTTCAAATTCGATTAAGGATTCAC
*
56263 TTAAATCATAATGAATTGTGAAATTGACCAAAAGCTTTTAAAACAAAGGTTTTAATTACTTAATT
1 TTAAATCTTAATGAATTGTGAAATT-ACCAAAAGCTTTTAAAACAAAGGTTTTAATTACTTAATT
*
56328 AAACCTAAAGTTTTAAGGTCACTTAACCTTGGCTTCAAGTTCGATTAAGGATTCAC
65 AAACCTAAAGTTTTAAGGTCACTTAACCTTGGCTTCAAATTCGATTAAGGATTCAC
*
56384 TTAAATCTTAATGAATTGTGAAATTTACCAAAAGCTTTTAAATCAAAGGTTTTAATTACTTAATT
1 TTAAATCTTAATGAATTGTGAAA-TTACCAAAAGCTTTTAAAACAAAGGTTTTAATTACTTAATT
* * * *
56449 AAACCTAGAGTTTTAAGGTCACTTAACCTTGACTTCAAATTCGATCAAGAATTCAC
65 AAACCTAAAGTTTTAAGGTCACTTAACCTTGGCTTCAAATTCGATTAAGGATTCAC
*
56505 TTAAATCTTAATGAATTG-GGAATTACCAA
1 TTAAATCTTAATGAATTGTGAAATTACCAA
56534 GAATGATTAG
Statistics
Matches: 255, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
119 7 0.03
120 5 0.02
121 241 0.95
122 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (120 bp):
TTAAATCTTAATGAATTGTGAAATTACCAAAAGCTTTTAAAACAAAGGTTTTAATTACTTAATTA
AACCTAAAGTTTTAAGGTCACTTAACCTTGGCTTCAAATTCGATTAAGGATTCAC
Found at i:59868 original size:146 final size:146
Alignment explanation
Indices: 59604--59891 Score: 549
Period size: 146 Copynumber: 2.0 Consensus size: 146
59594 GAAGAGCCTA
59604 TGTCACGCCCCGACCCGGAAGTCGAGCACGGACAACCGCCATGTTACCTCGAAACACGTGCCGGC
1 TGTCACGCCCCGACCCGGAAGTCGAGCACGGACAACCGCCATGTTACCTCGAAACACGTGCCGGC
59669 CGGTCACGCGCACCGAGGTTCCACGAAGCGTCAATACCAGATAAAATAATACCAAAAACATGAAC
66 CGGTCACGCGCACCGAGGTTCCACGAAGCGTCAATACCAGATAAAATAATACCAAAAACATGAAC
59734 TGAGTAATAAATAAGT
131 TGAGTAATAAATAAGT
*
59750 TGTCACGCCTCGACCCGGAAGTCGAGCACGGACAACCGCCATGTTACCTCGAAACACGTGCCGGC
1 TGTCACGCCCCGACCCGGAAGTCGAGCACGGACAACCGCCATGTTACCTCGAAACACGTGCCGGC
* *
59815 CGGTCACGCGCACCGAGGTTCCATGAAGCGTCAATACCAGATAAAATAATACCAAAAATATGAAC
66 CGGTCACGCGCACCGAGGTTCCACGAAGCGTCAATACCAGATAAAATAATACCAAAAACATGAAC
59880 TGAGTAATAAAT
131 TGAGTAATAAAT
59892 CTGAAATACT
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
146 139 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (146 bp):
TGTCACGCCCCGACCCGGAAGTCGAGCACGGACAACCGCCATGTTACCTCGAAACACGTGCCGGC
CGGTCACGCGCACCGAGGTTCCACGAAGCGTCAATACCAGATAAAATAATACCAAAAACATGAAC
TGAGTAATAAATAAGT
Found at i:61252 original size:27 final size:28
Alignment explanation
Indices: 61222--61289 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
61212 ATTTAAAGGC
* *
61222 AAAACTGTAATTTAATC-AACCAGGGGT
1 AAAACTGTAATTTAAGCTAACCAAGGGT
* *
61249 AAAA-TGGTAATTTTAGCTGACCAAGGGT
1 AAAACT-GTAATTTAAGCTAACCAAGGGT
*
61277 AAAACAGTAATTT
1 AAAACTGTAATTT
61290 TGACATCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
26 1 0.03
27 13 0.39
28 19 0.58
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (28 bp):
AAAACTGTAATTTAAGCTAACCAAGGGT
Found at i:74731 original size:28 final size:27
Alignment explanation
Indices: 74698--74796 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
74688 GTCACTCAAG
74698 GGGCATTTTGGTCATTTTTCACATTCA
1 GGGCATTTTGGTCATTTTTCACATTCA
* * *
74725 GTGGCATTATGGTCATTTTT-ACACTAA
1 G-GGCATTTTGGTCATTTTTCACATTCA
* *
74752 GGGCATTTTGGTCA-TTTGCATATTCA
1 GGGCATTTTGGTCATTTTTCACATTCA
*
74778 GGGGCATGTTGGTCATTTT
1 -GGGCATTTTGGTCATTTT
74797 GAGTCCACTT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
25 3 0.05
26 16 0.27
27 20 0.34
28 20 0.34
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTTCACATTCA
Found at i:75535 original size:40 final size:40
Alignment explanation
Indices: 75472--75874 Score: 605
Period size: 40 Copynumber: 10.1 Consensus size: 40
75462 GTCTTGTCTA
* * *
75472 GTTTAAATACTCAGTCTGCCCTTCCCCATCGGAAGGTGTT
1 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
*
75512 GTTTAAATACCCAGTTTGTCCTTCCCCACCGGAAGGTGTT
1 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
*
75552 GTTTAAATACCCAGTTTGCCCTTCCCCACCAGAAGGTGTT
1 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
* *
75592 GTTTAAATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTT
1 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
* *
75632 GTTTAAATTCCCAGTTTGCTCTTCCCCACCGGAAGGTGTT
1 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
* * * * *
75672 GTTTAAATTCCCAATTTGCTCTT-CCCACCGCAGGAGTGTT
1 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAG-GTGTT
75712 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
1 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
* **
75752 GTTTAAATACCCAGTTTGCCTTTCCCCGTCGGAAGGTGTT
1 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
75792 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
1 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
*
75832 G-TTAAAT-CCCAATTTGCCCTTCCCCACCGGAAGGTGTT
1 GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
*
75870 ATTTA
1 GTTTA
Statistics
Matches: 333, Mismatches: 27, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
38 30 0.09
39 18 0.05
40 276 0.83
41 9 0.03
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (40 bp):
GTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
Done.