Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014828.1 Corchorus olitorius cultivar O-4 contig14861, 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: 142383
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6312 original size:37 final size:37
Alignment explanation
Indices: 6262--6333 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
6252 GCCGCACATG
6262 TTCGGTTCTTACGTGGACCAATCATAATAAAGCTATA
1 TTCGGTTCTTACGTGGACCAATCATAATAAAGCTATA
*
6299 TTCGGTTCTTACGTGGACCAATCATAATGAAGCTA
1 TTCGGTTCTTACGTGGACCAATCATAATAAAGCTA
6334 AGTGGCTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (37 bp):
TTCGGTTCTTACGTGGACCAATCATAATAAAGCTATA
Found at i:13968 original size:6 final size:6
Alignment explanation
Indices: 13957--14005 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
13947 CCTCAAAATC
* *
13957 AACCAA ACCCAA AACCCCCAA ATCCAA AACCAA AACCAA AACCAA AACC
1 AACCAA AACCAA AA--CC-AA AACCAA AACCAA AACCAA AACCAA AACC
14006 CCATTGCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 29 0.81
7 2 0.06
8 2 0.06
9 3 0.08
ACGTcount: A:0.57, C:0.41, G:0.00, T:0.02
Consensus pattern (6 bp):
AACCAA
Found at i:14163 original size:21 final size:21
Alignment explanation
Indices: 14139--14185 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
14129 TACTCTTCTC
*
14139 CCTCTTCATCTTCTTCCTCAT
1 CCTCTTCATCTGCTTCCTCAT
* * *
14160 CCTCTTCCTCTGCTTCTTCTT
1 CCTCTTCATCTGCTTCCTCAT
14181 CCTCT
1 CCTCT
14186 GCTTCCTCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.45, G:0.02, T:0.49
Consensus pattern (21 bp):
CCTCTTCATCTGCTTCCTCAT
Found at i:14180 original size:15 final size:14
Alignment explanation
Indices: 14161--14201 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
14151 CTTCCTCATC
14161 CTCTTCCTCTGCTT
1 CTCTTCCTCTGCTT
14175 CTTCTTCCTCTGCTT
1 C-TCTTCCTCTGCTT
14190 C-C-TCCTCTGCTT
1 CTCTTCCTCTGCTT
14202 TGTCTCTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 10 0.38
13 1 0.04
14 1 0.04
15 14 0.54
ACGTcount: A:0.00, C:0.44, G:0.07, T:0.49
Consensus pattern (14 bp):
CTCTTCCTCTGCTT
Found at i:14217 original size:27 final size:27
Alignment explanation
Indices: 14147--14201 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
14137 TCCCTCTTCA
* *
14147 TCTTCTTCCTCAT-CCTCTTCCTCTGCT
1 TCTTCTTCCTC-TGCTTCCTCCTCTGCT
14174 TCTTCTTCCTCTGCTTCCTCCTCTGCT
1 TCTTCTTCCTCTGCTTCCTCCTCTGCT
14201 T
1 T
14202 TGTCTCTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.02, C:0.44, G:0.05, T:0.49
Consensus pattern (27 bp):
TCTTCTTCCTCTGCTTCCTCCTCTGCT
Found at i:17279 original size:135 final size:135
Alignment explanation
Indices: 17037--17451 Score: 776
Period size: 135 Copynumber: 3.1 Consensus size: 135
17027 AGATAATCTC
17037 AAGAAAATGAACAGAAATTTAAAATTTAACTGCAATCTGAACACTCAACCAAAAAGCCTGAAATA
1 AAGAAAATGAACAGAAATTTAAAATTTAACTGCAATCTGAACACTCAACCAAAAAGCCTGAAATA
17102 GCAAACTCTTTCTGTTCTTATTATTGATGCTATGCACTATTATTTCAGGCCAAACTCAGAAATTA
66 GCAAACTCTTTCTGTTCTTATTATTGATGCTATGCACTATTATTTCAGGCCAAACTCAGAAATTA
17167 AGGCA
131 AGGCA
* * * *
17172 AAGAATATGAGCAGAAATTTAAAATTTAACTGCTATCTTAACACTCAACCAAAAAGCCTGAAATA
1 AAGAAAATGAACAGAAATTTAAAATTTAACTGCAATCTGAACACTCAACCAAAAAGCCTGAAATA
17237 GCAAACTCTTTCTGTTCTTATTATTGATGCTATGCACTATTATTTCAGGCCAAACTCAGAAATTA
66 GCAAACTCTTTCTGTTCTTATTATTGATGCTATGCACTATTATTTCAGGCCAAACTCAGAAATTA
17302 AGGCA
131 AGGCA
*
17307 AAGAAAATTAACAGAAATTTAAAATTTAACTGCAATCTGAACACTCAACCAAAAAGCCTGAAATA
1 AAGAAAATGAACAGAAATTTAAAATTTAACTGCAATCTGAACACTCAACCAAAAAGCCTGAAATA
17372 GCAAACTCTTTCTGTTCTTATTATTGATGCTATGCACTATTATTTCAGGCCAAACTCAGAAATTA
66 GCAAACTCTTTCTGTTCTTATTATTGATGCTATGCACTATTATTTCAGGCCAAACTCAGAAATTA
17437 AGGCA
131 AGGCA
*
17442 AAGAATATGA
1 AAGAAAATGA
17452 GACCGCATGC
Statistics
Matches: 269, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 269 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (135 bp):
AAGAAAATGAACAGAAATTTAAAATTTAACTGCAATCTGAACACTCAACCAAAAAGCCTGAAATA
GCAAACTCTTTCTGTTCTTATTATTGATGCTATGCACTATTATTTCAGGCCAAACTCAGAAATTA
AGGCA
Found at i:23615 original size:8 final size:8
Alignment explanation
Indices: 23602--23631 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
23592 TCGCTTCTTC
23602 TTTTTTCT
1 TTTTTTCT
23610 TTTTTTCT
1 TTTTTTCT
23618 TTTTTTCT
1 TTTTTTCT
23626 TTTTTT
1 TTTTTT
23632 TTCACTTGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTCT
Found at i:23633 original size:18 final size:18
Alignment explanation
Indices: 23596--23631 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
23586 AATTCCTCGC
23596 TTCTTCTTTTTTCTTTTT
1 TTCTTCTTTTTTCTTTTT
23614 TTC-T-TTTTTTCTTTTT
1 TTCTTCTTTTTTCTTTTT
23630 TT
1 TT
23632 TTCACTTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 1 0.06
18 3 0.17
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
TTCTTCTTTTTTCTTTTT
Found at i:23634 original size:18 final size:18
Alignment explanation
Indices: 23596--23634 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23586 AATTCCTCGC
23596 TTCTTCTTTT-TTCTTTTT
1 TTCTTCTTTTCTT-TTTTT
*
23614 TTCTTTTTTTCTTTTTTT
1 TTCTTCTTTTCTTTTTTT
23632 TTC
1 TTC
23635 ACTTGGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (18 bp):
TTCTTCTTTTCTTTTTTT
Found at i:23894 original size:36 final size:36
Alignment explanation
Indices: 23847--23919 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
23837 GGATAATAGT
*
23847 TCACCATTGTTGAGGCTTTGTCGGGAGAGGAAGGAA
1 TCACCATTGTTGAGGCTTTGTCGAGAGAGGAAGGAA
23883 TCACCATTGTTGAGGCTTTGTCGAGAGAGGAAGGAA
1 TCACCATTGTTGAGGCTTTGTCGAGAGAGGAAGGAA
23919 T
1 T
23920 TGATTGAGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.26
Consensus pattern (36 bp):
TCACCATTGTTGAGGCTTTGTCGAGAGAGGAAGGAA
Found at i:24760 original size:6 final size:6
Alignment explanation
Indices: 24749--24779 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
24739 CTGAGGATGG
24749 TGAAAC TGAAAC TGAAAC TGAAAC TGAAAC T
1 TGAAAC TGAAAC TGAAAC TGAAAC TGAAAC T
24780 TCAAGCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
TGAAAC
Found at i:33005 original size:12 final size:12
Alignment explanation
Indices: 32988--33012 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32978 AGATCATTCC
32988 TCTTTTTTTTTT
1 TCTTTTTTTTTT
33000 TCTTTTTTTTTT
1 TCTTTTTTTTTT
33012 T
1 T
33013 TCCTTGAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:33008 original size:13 final size:13
Alignment explanation
Indices: 32990--33014 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32980 ATCATTCCTC
32990 TTTTTTTTTTTCT
1 TTTTTTTTTTTCT
33003 TTTTTTTTTTTC
1 TTTTTTTTTTTC
33015 CTTGAGGGTT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTTCT
Found at i:58361 original size:43 final size:43
Alignment explanation
Indices: 58300--58385 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
58290 GAGTGGGCTG
58300 ATCTTGAGGTGATTTTTGGAATTGAGTAAAAGAATAATTTTGT
1 ATCTTGAGGTGATTTTTGGAATTGAGTAAAAGAATAATTTTGT
58343 ATCTTGAGGTGATTTTTGGAATTGAGTAAAAGAATAATTTTGT
1 ATCTTGAGGTGATTTTTGGAATTGAGTAAAAGAATAATTTTGT
58386 TTACTTTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (43 bp):
ATCTTGAGGTGATTTTTGGAATTGAGTAAAAGAATAATTTTGT
Found at i:58595 original size:86 final size:86
Alignment explanation
Indices: 58445--58612 Score: 300
Period size: 86 Copynumber: 2.0 Consensus size: 86
58435 CATGAGTATG
* * *
58445 TATGTTTTGAAGTGGTCCATTGTCATTTGTGAATTTGCAATTGTGGAGAACTACTTTAGAGTTTC
1 TATGGTTTGAAGTAGTCCATTGTCATCTGTGAATTTGCAATTGTGGAGAACTACTTTAGAGTTTC
58510 TCTTATTAACAGTAGAAAATA
66 TCTTATTAACAGTAGAAAATA
*
58531 TATGGTTTGAAGTAGTCCATTGTCATCTGTGAATTTGCAATTGTGGAGAACTACTTTAGGGTTTC
1 TATGGTTTGAAGTAGTCCATTGTCATCTGTGAATTTGCAATTGTGGAGAACTACTTTAGAGTTTC
58596 TCTTATTAACAGTAGAA
66 TCTTATTAACAGTAGAA
58613 CTAGGAAGCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 78 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (86 bp):
TATGGTTTGAAGTAGTCCATTGTCATCTGTGAATTTGCAATTGTGGAGAACTACTTTAGAGTTTC
TCTTATTAACAGTAGAAAATA
Found at i:70288 original size:22 final size:22
Alignment explanation
Indices: 70260--70303 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
70250 CACATCAAAC
*
70260 CCACTATAAAGTTTCAAACCAA
1 CCACTATAAAATTTCAAACCAA
*
70282 CCACTATAAAATTTCAGACCAA
1 CCACTATAAAATTTCAAACCAA
70304 TCCAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (22 bp):
CCACTATAAAATTTCAAACCAA
Found at i:70312 original size:22 final size:22
Alignment explanation
Indices: 70260--70314 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
70250 CACATCAAAC
* *
70260 CCACTATAAAGTTTCAAACCAA
1 CCACAATAAAATTTCAAACCAA
* *
70282 CCACTATAAAATTTCAGACCAA
1 CCACAATAAAATTTCAAACCAA
70304 TCCA-AATAAAA
1 -CCACAATAAAA
70315 GATGATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.49, C:0.25, G:0.04, T:0.22
Consensus pattern (22 bp):
CCACAATAAAATTTCAAACCAA
Found at i:71515 original size:25 final size:24
Alignment explanation
Indices: 71464--71520 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
71454 GTCAGTCTTG
*
71464 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
71487 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
71512 AATTTATTT
1 AATTTATTT
71521 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:86158 original size:1 final size:1
Alignment explanation
Indices: 86152--86178 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
86142 CACCTATGGA
86152 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
86179 TTTGGGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:88474 original size:218 final size:218
Alignment explanation
Indices: 88093--88533 Score: 873
Period size: 218 Copynumber: 2.0 Consensus size: 218
88083 CTAACAATAG
88093 ACTGATAAAGTGCTCAATGATGATTACTGCTTTTTTCTCCCATCCGCAGTTCACCACCCTATTCA
1 ACTGATAAAGTGCTCAATGATGATTACTGCTTTTTTCTCCCATCCGCAGTTCACCACCCTATTCA
88158 ACTTTGGAGTTAGGCCTCATTAGCCGGAAAAATTTAAGGATTCCTACTTGCTCCAAAGATCCAAA
66 ACTTTGGAGTTAGGCCTCATTAGCCGGAAAAATTTAAGGATTCCTACTTGCTCCAAAGATCCAAA
88223 AGATAGAAACTTGAATAGTGTACATTAATAAGACCACCAAACTAGAAAAAAGCGGTTGCCTATCA
131 AGATAGAAACTTGAATAGTGTACATTAATAAGACCACCAAACTAGAAAAAAGCGGTTGCCTATCA
88288 TCAGTGTATTAATGGGTTAATGC
196 TCAGTGTATTAATGGGTTAATGC
88311 ACTGATAAAGTGCTCAATGATGATTACTGCTTTTTTCTCCCATCCGCAGTTCACCACCCTATTCA
1 ACTGATAAAGTGCTCAATGATGATTACTGCTTTTTTCTCCCATCCGCAGTTCACCACCCTATTCA
88376 ACTTTGGAGTTAGGCCTCATTAGCCGGAAAAATTTAAGGATTCCTACTTGCTCCAAAGATCCAAA
66 ACTTTGGAGTTAGGCCTCATTAGCCGGAAAAATTTAAGGATTCCTACTTGCTCCAAAGATCCAAA
*
88441 AGATAGAAACTTGAATAGTGTACATTTATAAGACCACCAAACTAGAAAAAAGCGGTTGCCTATCA
131 AGATAGAAACTTGAATAGTGTACATTAATAAGACCACCAAACTAGAAAAAAGCGGTTGCCTATCA
88506 TCAGTGTATTAATGGGTTAATGC
196 TCAGTGTATTAATGGGTTAATGC
88529 ACTGA
1 ACTGA
88534 CAGTCTAACA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
218 222 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (218 bp):
ACTGATAAAGTGCTCAATGATGATTACTGCTTTTTTCTCCCATCCGCAGTTCACCACCCTATTCA
ACTTTGGAGTTAGGCCTCATTAGCCGGAAAAATTTAAGGATTCCTACTTGCTCCAAAGATCCAAA
AGATAGAAACTTGAATAGTGTACATTAATAAGACCACCAAACTAGAAAAAAGCGGTTGCCTATCA
TCAGTGTATTAATGGGTTAATGC
Found at i:91142 original size:21 final size:20
Alignment explanation
Indices: 91096--91142 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
91086 CTTCCTCAAC
91096 TTCTCCTCCTCTTCCCTTTT
1 TTCTCCTCCTCTTCCCTTTT
*
91116 TT-TCCT-CTCTTCTGCTTCTT
1 TTCTCCTCCTCTTC-CCTT-TT
91136 TTCTCCT
1 TTCTCCT
91143 AGCAAGTGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 6 0.26
19 7 0.30
20 6 0.26
21 4 0.17
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.57
Consensus pattern (20 bp):
TTCTCCTCCTCTTCCCTTTT
Found at i:91323 original size:12 final size:12
Alignment explanation
Indices: 91293--91334 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
91283 CTGCTGCTGC
*
91293 CTTCTTCTCCTT
1 CTTCTTTTCCTT
91305 -TTCCTTTTCCTT
1 CTT-CTTTTCCTT
*
91317 CTTCTTTTTCTT
1 CTTCTTTTCCTT
91329 CTTCTT
1 CTTCTT
91335 CGCTGCAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
CTTCTTTTCCTT
Found at i:92110 original size:150 final size:152
Alignment explanation
Indices: 91924--92347 Score: 601
Period size: 150 Copynumber: 2.8 Consensus size: 152
91914 ATCCTCCTTG
* * *
91924 TCACCTGCCTCATCATCAAGCTCATCAAGTGCAACTGCCGCAAACAAGTTTCCACCCTTCTTTCC
1 TCACCTGCTTCATCATCAAGCTCATCAAGTGCAACTGCTGCAAACGAGTTTCCACCCTTCTTTCC
* * *
91989 CCCCTTTGACTTCTTCTTTTTCCCCGTCAGAGCTTTGACAACCATATCATCATCGTCGTCT-A-T
66 CCCCTTGGACTTCTT-TTTTTCCCTGTCAAAGCTTTGACAACCATATCATCATCGTCGTCTAATT
*
92052 -ATTCTCTTCCTCAACCAACTCT
130 GACTCTCTTCCTCAACCAACTCT
*
92074 TCACCTGCTTCATCATCAAGCTCATCAAGTGAAACTGCTGCAAACGAGTTTCCACCCTTCTTTCC
1 TCACCTGCTTCATCATCAAGCTCATCAAGTGCAACTGCTGCAAACGAGTTTCCACCCTTCTTTCC
* * * * *
92139 TCCCTTGGACTTCTTTTTTTTACATGTGAAAGCTTTGGCAACCATATCATCATC-T--TCTAATT
66 CCCCTTGGACTTC-TTTTTTTCCCTGTCAAAGCTTTGACAACCATATCATCATCGTCGTCTAATT
*
92201 GACTCTCTTCCTCAACCACCTCT
130 GACTCTCTTCCTCAACCAACTCT
* *
92224 TCACCTGCTTCATCATCAAGCTCATCAAGTGCAACTGCTGCAAACGAGTTTCCTCCTTTCTTTCC
1 TCACCTGCTTCATCATCAAGCTCATCAAGTGCAACTGCTGCAAACGAGTTTCCACCCTTCTTTCC
* **
92289 CCCCTTGGACTTCTTTTTTTCCCTTTCAAAGCTTT-AGTGACCATATCATCATCGTCGTC
66 CCCCTTGGACTTCTTTTTTTCCCTGTCAAAGCTTTGA-CAACCATATCATCATCGTCGTC
92348 ATCATCCACT
Statistics
Matches: 241, Mismatches: 25, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
147 3 0.01
148 1 0.00
149 34 0.14
150 199 0.83
151 2 0.01
152 2 0.01
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.35
Consensus pattern (152 bp):
TCACCTGCTTCATCATCAAGCTCATCAAGTGCAACTGCTGCAAACGAGTTTCCACCCTTCTTTCC
CCCCTTGGACTTCTTTTTTTCCCTGTCAAAGCTTTGACAACCATATCATCATCGTCGTCTAATTG
ACTCTCTTCCTCAACCAACTCT
Found at i:93913 original size:28 final size:30
Alignment explanation
Indices: 93871--93962 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 30
93861 TTTTTATTTG
*
93871 AGTTTG-TTTTT-GAGTCGGTTT-GAGTC-
1 AGTTTGTTTTTTCGAGTCAGTTTCGAGTCT
93897 AGTTTGTTTTTTCGAGTCAGTTTCGAGTCT
1 AGTTTGTTTTTTCGAGTCAGTTTCGAGTCT
*
93927 AGTCTCTGTTCTTTTCGAATCTGAGTTATCGAGTCT
1 AGT-T-TGTT-TTTTCGAGTC--AGTT-TCGAGTCT
93963 GAATTTTATG
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
26 6 0.11
27 5 0.09
28 9 0.17
29 5 0.09
30 3 0.06
31 1 0.02
32 4 0.07
33 9 0.17
35 4 0.07
36 8 0.15
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.48
Consensus pattern (30 bp):
AGTTTGTTTTTTCGAGTCAGTTTCGAGTCT
Found at i:95135 original size:23 final size:22
Alignment explanation
Indices: 95096--95156 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
95086 TGAATATTTT
*
95096 TATGAAATTTTGATAACTATAC
1 TATGAAATTTTGATAACCATAC
* * *
95118 TATTAAATTTTTACTAACCATGC
1 TATGAAATTTTGA-TAACCATAC
*
95141 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
95157 TTTACCAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATAC
Found at i:95233 original size:23 final size:22
Alignment explanation
Indices: 95096--95253 Score: 90
Period size: 22 Copynumber: 7.1 Consensus size: 22
95086 TGAATATTTT
* *
95096 TATGAAATTTTGATAA-CTATAC
1 TATGAAATTTTAATAACCT-TCC
* * * *
95118 TATTAAATTTTTACTAACCATGC
1 TATGAAA-TTTTAATAACCTTCC
*
95141 TATGAAATTTTAATAA-TTTACC
1 TATGAAATTTTAATAACCTT-CC
* * * * *
95163 AATAAAATTGTGATAA-ATTCC
1 TATGAAATTTTAATAACCTTCC
* ***
95184 ATATGAAACTTTAATAACCTAAT
1 -TATGAAATTTTAATAACCTTCC
95207 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTAAT-AACCTTCC
*
95230 TATGAAATTTT-GTAACCTTCC
1 TATGAAATTTTAATAACCTTCC
95251 TAT
1 TAT
95254 ATATGATTTT
Statistics
Matches: 101, Mismatches: 29, Indels: 13
0.71 0.20 0.09
Matches are distributed among these distances:
21 14 0.14
22 54 0.53
23 32 0.32
24 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTAATAACCTTCC
Found at i:95248 original size:21 final size:23
Alignment explanation
Indices: 95180--95253 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
95170 TTGTGATAAA
*
95180 TTCCATATGAAACTTTAAT-AACC
1 TTCC-TATGAAATTTTAATAAACC
***
95203 TAATTATGAAATTTTAATAAACC
1 TTCCTATGAAATTTTAATAAACC
*
95226 TTCCTATGAAATTTT-GT-AACC
1 TTCCTATGAAATTTTAATAAACC
95247 TTCCTAT
1 TTCCTAT
95254 ATATGATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 11 0.26
22 14 0.33
23 17 0.40
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (23 bp):
TTCCTATGAAATTTTAATAAACC
Found at i:95623 original size:49 final size:47
Alignment explanation
Indices: 95522--95663 Score: 169
Period size: 49 Copynumber: 3.0 Consensus size: 47
95512 GAGCGTGCCA
* * * *
95522 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
95569 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
95618 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
95664 GGATTGCTTG
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
47 12 0.15
48 28 0.34
49 42 0.51
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:96960 original size:9 final size:9
Alignment explanation
Indices: 96940--96968 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
96930 TTAATTCATT
96940 TAATTTCC-
1 TAATTTCCA
96948 TAATTTCCA
1 TAATTTCCA
96957 TAATTTCCA
1 TAATTTCCA
96966 TAA
1 TAA
96969 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:114794 original size:38 final size:38
Alignment explanation
Indices: 114741--114818 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
114731 CATAATGTCA
*
114741 CATACTAGAAGATAATGAGATATCATATACATTGCCCT
1 CATACTAGAAAATAATGAGATATCATATACATTGCCCT
114779 CATACTAGAAAATAATGAGATATCATATACATTGCCCT
1 CATACTAGAAAATAATGAGATATCATATACATTGCCCT
114817 CA
1 CA
114819 AAATTGAGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (38 bp):
CATACTAGAAAATAATGAGATATCATATACATTGCCCT
Found at i:122789 original size:92 final size:92
Alignment explanation
Indices: 122622--122799 Score: 250
Period size: 92 Copynumber: 1.9 Consensus size: 92
122612 AACATATAAA
* * **
122622 TATTGAGTCAAAGTTACTAAATATTCCTTAAATAAGGTCTTAGATTGTTTCAGATTCGAGTCTGT
1 TATTGAGTAAAAGTTACCAAATATTCCTTAAATAAGGTCTTAGATTGCCTCAGATTCGAGTCTGT
* *
122687 GCGAATAAAGAAAATAGATGTAGGTCG
66 GCGAACAAAGAAAATAAATGTAGGTCG
* * *
122714 TATTGAGTAAAAGTTACCCAATATTCCTTTAAATAAGGTCTTAGATTGCCTCGGATTTGAGTC-G
1 TATTGAGTAAAAGTTACCAAATATTCC-TTAAATAAGGTCTTAGATTGCCTCAGATTCGAGTCTG
*
122778 TGTGAACAAAGAAAATAAATGT
65 TGCGAACAAAGAAAATAAATGT
122800 TTGTAGAGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
92 44 0.59
93 31 0.41
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (92 bp):
TATTGAGTAAAAGTTACCAAATATTCCTTAAATAAGGTCTTAGATTGCCTCAGATTCGAGTCTGT
GCGAACAAAGAAAATAAATGTAGGTCG
Found at i:125053 original size:318 final size:314
Alignment explanation
Indices: 124228--125053 Score: 1034
Period size: 318 Copynumber: 2.6 Consensus size: 314
124218 ACTGGTTGGC
* * *
124228 AGAGGTTTCACCTCATTCTCCACAGGTTGCTTCTTACCCCCTTCCTTGATCTGTACTCCTCCCTT
1 AGAGGTTTCACCTCATTCTCTACAGGTTGCTTCTTACCCCCTTCCTTGAACTGCACTCCTCCCTT
* * * * * * *
124293 CCTTTCCAAAGGCTTTGCTCCTTTACAATGCTTCTTACCCTTTGATTTACCCAGATCATCTTTAA
66 CCCTTCCAAAAGCTTTGCTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGTAA
* * * * * * ***
124358 ACGGCCTCTTCTCTGTTTGACTACTTTCATGATGACCAAGCTGAGTTTTAGTTTGATGTACCATT
131 A-AGCCTCTTCTTTGTTTGACTACTTTCATGATGAACAAGCTGAGTTTTACTTTGATTTTCTGGT
* * * *
124423 CCTAGATTTTCTGTTAACTCTGTCTTTATTTCATTAGAATTATTCGGAACAGAAACCTTAGTTGT
195 CCTAGATGTTCTGTTAACTCTGTCTTTATTTCATCAGAATTATTCGGAACAGAAACATTAGTGGT
** *
124488 AATTTTAACATGATTGGTAGCAACACTATCCCCAATAGTATCCCTACTAATTGGC
260 AATTTTAACATGATTGGTAGCAACACTATCCCCAATAGTATCCCTACTAATCAGA
* *
124543 AGAGGTTTTACCTCATTCTCTACAGGTTGCTTATTACCCCCTTCCTTGAACTGCACTCCTCCCTT
1 AGAGGTTTCACCTCATTCTCTACAGGTTGCTTCTTACCCCCTTCCTTGAACTGCACTCCTCCCTT
*
124608 CCCTTCCACATAG-TTTGCTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGTA
66 CCCTTCCA-AAAGCTTTGCTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGTA
* ***
124672 AAAGGCCTCTTCTTTGTTTGACTACTTCCATGATGAACAAGCTGACCATTACTTTGATTTTCTGG
130 AAA-GCCTCTTCTTTGTTTGACTACTTTCATGATGAACAAGCTGAGTTTTACTTTGATTTTCTGG
* * *
124737 TCCTAGATGTTCTGTTAACTTTGTCTTATTTTTTTCATCAGATTTATT-GGAAACAG-AACTATT
194 TCCTAGATGTTCTGTTAACTCTGTC---TTTATTTCATCAGAATTATTCGG-AACAGAAAC-ATT
* * * * * *
124800 AGTGGTAGTTTTAACCA-GA-TGTGTAGCAATATTA-CTTCCTATAGTGTCCCTACTAATCAGA
254 AGTGGTAATTTTAA-CATGATTG-GTAGCAACACTATC-CCCAATAGTATCCCTACTAATCAGA
* *
124861 AGAGGTTTCACCTCATTCTCTACAGGTTGCTTCCTACCCACTTCCTTGAACTGCACTCCTCCCTT
1 AGAGGTTTCACCTCATTCTCTACAGGTTGCTTCTTACCCCCTTCCTTGAACTGCACTCCTCCCTT
* ** *
124926 CCCTTCCAAAAGCGTCACTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGCAA
66 CCCTTCCAAAAGCTTTGCTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGTAA
* * * *
124991 AAACTCTCTTCTTTGTTTGACTACTTTCATTATGAACAAGCTGGGTTTTACTTTGCTTTTCTG
131 AAGC-CTCTTCTTTGTTTGACTACTTTCATGATGAACAAGCTGAGTTTTACTTTGATTTTCTG
125054 TTAACTTCAT
Statistics
Matches: 440, Mismatches: 59, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
315 187 0.43
316 2 0.00
317 12 0.03
318 237 0.54
319 2 0.00
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.40
Consensus pattern (314 bp):
AGAGGTTTCACCTCATTCTCTACAGGTTGCTTCTTACCCCCTTCCTTGAACTGCACTCCTCCCTT
CCCTTCCAAAAGCTTTGCTCCTTTACATTGCTTTTTACCCTTTGATTTATCCAGATCTTCTGTAA
AAGCCTCTTCTTTGTTTGACTACTTTCATGATGAACAAGCTGAGTTTTACTTTGATTTTCTGGTC
CTAGATGTTCTGTTAACTCTGTCTTTATTTCATCAGAATTATTCGGAACAGAAACATTAGTGGTA
ATTTTAACATGATTGGTAGCAACACTATCCCCAATAGTATCCCTACTAATCAGA
Found at i:133751 original size:15 final size:15
Alignment explanation
Indices: 133731--133763 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
133721 AGTACATCAA
133731 AAAAAAGAAAAGGGT
1 AAAAAAGAAAAGGGT
133746 AAAAAAGAAAAGGGT
1 AAAAAAGAAAAGGGT
133761 AAA
1 AAA
133764 GAATGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (15 bp):
AAAAAAGAAAAGGGT
Found at i:134114 original size:33 final size:33
Alignment explanation
Indices: 134077--134182 Score: 144
Period size: 33 Copynumber: 3.2 Consensus size: 33
134067 GCGCTCCGGC
* *
134077 GGGGCGCCGTCTTTATTTCGGTGGCGCCCCCTG
1 GGGGCGCCGTCTTCATATCGGTGGCGCCCCCTG
134110 GGGGCGCCGTCTTCATATCGGTGGCGCCCCCTG
1 GGGGCGCCGTCTTCATATCGGTGGCGCCCCCTG
** *
134143 GGGGCGCCGTCGGCATGGT-GGTGGCGCCCCCT-
1 GGGGCGCCGTCTTCAT-ATCGGTGGCGCCCCCTG
134175 GGGGCGCC
1 GGGGCGCC
134183 ACAGCCGGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
32 8 0.12
33 58 0.87
34 1 0.01
ACGTcount: A:0.04, C:0.35, G:0.42, T:0.20
Consensus pattern (33 bp):
GGGGCGCCGTCTTCATATCGGTGGCGCCCCCTG
Found at i:134316 original size:19 final size:18
Alignment explanation
Indices: 134292--134342 Score: 84
Period size: 19 Copynumber: 2.8 Consensus size: 18
134282 TGTAATTAGT
134292 TAATTAGTTTATTAATTG
1 TAATTAGTTTATTAATTG
134310 ATAATTAGTTTATTAATTG
1 -TAATTAGTTTATTAATTG
*
134329 TAATTAGTTAATTA
1 TAATTAGTTTATTA
134343 GTTTATGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (18 bp):
TAATTAGTTTATTAATTG
Found at i:134318 original size:27 final size:26
Alignment explanation
Indices: 134271--134324 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
134261 AAAATAAATG
**
134271 AGTTTATTTTTTGTAATTAGTTAATT
1 AGTTTATTAATTGTAATTAGTTAATT
*
134297 AGTTTATTAATTGATAATTAGTTTATT
1 AGTTTATTAATTG-TAATTAGTTAATT
134324 A
1 A
134325 ATTGTAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (26 bp):
AGTTTATTAATTGTAATTAGTTAATT
Found at i:134358 original size:26 final size:26
Alignment explanation
Indices: 134303--134360 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
134293 AATTAGTTTA
*
134303 TTAATT-GATAATTAGTTTAT-TAAT
1 TTAATTAGATAATTAGTTTATGAAAT
*
134327 TGTAATTAGTTAATTAGTTTATGAAAT
1 T-TAATTAGATAATTAGTTTATGAAAT
134354 TTAATTA
1 TTAATTA
134361 AAATTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 1 0.03
25 5 0.17
26 19 0.66
27 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (26 bp):
TTAATTAGATAATTAGTTTATGAAAT
Found at i:134683 original size:27 final size:27
Alignment explanation
Indices: 134620--134687 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
134610 AAGAGATAAA
*
134620 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
*
134647 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
134674 GAGAG-GGAGGCTGC
1 GAG-GCGGAGGCTGC
134688 CGCTGGTGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.15, G:0.47, T:0.19
Consensus pattern (27 bp):
GAGGCGGAGGCTGCTCGGATGTATAGG
Found at i:134686 original size:33 final size:27
Alignment explanation
Indices: 134620--134676 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
134610 AAGAGATAAA
134620 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
134647 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
134674 GAG
1 GAG
134677 AGGGAGGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.14, G:0.46, T:0.21
Consensus pattern (27 bp):
GAGGCTGAGGCTGCTCGGATGTATAGG
Found at i:136732 original size:10 final size:10
Alignment explanation
Indices: 136714--136754 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
136704 TTATATTTTG
136714 GGATTTTTAT
1 GGATTTTTAT
*
136724 GGATGTTTAT
1 GGATTTTTAT
**
136734 GTCTTTTTAT
1 GGATTTTTAT
136744 GGATTTTTAT
1 GGATTTTTAT
136754 G
1 G
136755 TATATTGGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.17, C:0.02, G:0.22, T:0.59
Consensus pattern (10 bp):
GGATTTTTAT
Found at i:136742 original size:20 final size:20
Alignment explanation
Indices: 136717--136755 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
136707 TATTTTGGGA
136717 TTTTTATGGATGTTTATGTC
1 TTTTTATGGATGTTTATGTC
*
136737 TTTTTATGGATTTTTATGT
1 TTTTTATGGATGTTTATGT
136756 ATATTGGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.03, G:0.18, T:0.64
Consensus pattern (20 bp):
TTTTTATGGATGTTTATGTC
Done.