Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016319.1 Corchorus olitorius cultivar O-4 contig16352, 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: 139484
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:280 original size:86 final size:84
Alignment explanation
Indices: 90--288 Score: 226
Period size: 86 Copynumber: 2.3 Consensus size: 84
80 TTAGGGTTTC
* *
90 ATATTAAATAATAAT-TTATAATATAAAGATTAAATAATAATGAGATTATTTTCTAAATCTTGCC
1 ATATTAAATAA-AATAATA-AATATAAAGATTAAATAATAATGAGAATATTTTCTAAATCTTGCC
* *
154 AAATTATGGAAGGTTTAGGAG
64 AAATTATGGAAGATTTAGGAA
* *
175 ATATTTTAA-GAAATAAATAAATTATAAAGATTAAATAATAATGAGAATATTTTCTAAATCTTGC
1 ATA-TTAAATAAAAT-AATAAA-TATAAAGATTAAATAATAATGAGAATATTTTCTAAATCTTGC
* *
239 CAAAATTGTGGGAGATTT-GGAAA
63 C-AAATTATGGAAGATTTAGG-AA
*
262 ATATTAAATAAAATAAT-AATAAAAAGA
1 ATATTAAATAAAATAATAAATATAAAGA
289 AGTTAAGATA
Statistics
Matches: 96, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
84 10 0.10
85 8 0.08
86 57 0.59
87 21 0.22
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (84 bp):
ATATTAAATAAAATAATAAATATAAAGATTAAATAATAATGAGAATATTTTCTAAATCTTGCCAA
ATTATGGAAGATTTAGGAA
Found at i:1146 original size:21 final size:21
Alignment explanation
Indices: 1120--1211 Score: 139
Period size: 21 Copynumber: 4.4 Consensus size: 21
1110 GTTTAACGTG
*
1120 TTGACTATCAAAATTTTGGGT
1 TTGACTATCAAAATTTGGGGT
*
1141 TTGACTATCAAACTTTGGGGT
1 TTGACTATCAAAATTTGGGGT
* * *
1162 TTGACTTTCAAACTATGGGGT
1 TTGACTATCAAAATTTGGGGT
1183 TTGACTATCAAAATTTGGGGT
1 TTGACTATCAAAATTTGGGGT
1204 TTGACTAT
1 TTGACTAT
1212 GTATGTACAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (21 bp):
TTGACTATCAAAATTTGGGGT
Found at i:3161 original size:113 final size:113
Alignment explanation
Indices: 2958--3161 Score: 336
Period size: 113 Copynumber: 1.8 Consensus size: 113
2948 GAGTATGACA
** * * *
2958 CAATTGCCTGGCGCTCGATTAGCTGACGAAAGGTGTCGATCGCCAGAAACCATCTCAGAAGGACC
1 CAATTGCCTGGCGCTCGACAAGCTGACAAAAGGTGTCGACCGCCAGAAACCACCTCAGAAGGACC
3023 AGAGACCATTAAGTCATCTGACCCAATCAACTCCAAGGCCTAAGAGCC
66 AGAGACCATTAAGTCATCTGACCCAATCAACTCCAAGGCCTAAGAGCC
* *
3071 CAATTGCCTGGCGCTCGACAAGTTGACAAAAGGTGTCGACCGCCAGAAACCACCTCGGAAGGACC
1 CAATTGCCTGGCGCTCGACAAGCTGACAAAAGGTGTCGACCGCCAGAAACCACCTCAGAAGGACC
*
3136 AGAGACCATTAAGTCATCTGGCCCAA
66 AGAGACCATTAAGTCATCTGACCCAA
3162 GCACAATCAA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
113 83 1.00
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (113 bp):
CAATTGCCTGGCGCTCGACAAGCTGACAAAAGGTGTCGACCGCCAGAAACCACCTCAGAAGGACC
AGAGACCATTAAGTCATCTGACCCAATCAACTCCAAGGCCTAAGAGCC
Found at i:5861 original size:33 final size:33
Alignment explanation
Indices: 5818--5920 Score: 197
Period size: 33 Copynumber: 3.1 Consensus size: 33
5808 GACACAGCTC
5818 TTTCTCCTTCTTTGCTTCCACTTGCCATTTTCT
1 TTTCTCCTTCTTTGCTTCCACTTGCCATTTTCT
*
5851 TTTCTGCTTCTTTGCTTCCACTTGCCATTTTCT
1 TTTCTCCTTCTTTGCTTCCACTTGCCATTTTCT
5884 TTTCTCCTTCTTTGCTTCCACTTGCCATTTTCT
1 TTTCTCCTTCTTTGCTTCCACTTGCCATTTTCT
5917 TTTC
1 TTTC
5921 AACACTTACA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.06, C:0.32, G:0.07, T:0.55
Consensus pattern (33 bp):
TTTCTCCTTCTTTGCTTCCACTTGCCATTTTCT
Found at i:6935 original size:30 final size:30
Alignment explanation
Indices: 6899--6955 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
6889 ACTAAGCAAT
6899 AAAGAAGATGTGAGGAAAAAACAAACCGCG
1 AAAGAAGATGTGAGGAAAAAACAAACCGCG
*
6929 AAAGAAGATTTGAGGAAAAAACAAACC
1 AAAGAAGATGTGAGGAAAAAACAAACC
6956 TCTTCCTGCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.56, C:0.12, G:0.23, T:0.09
Consensus pattern (30 bp):
AAAGAAGATGTGAGGAAAAAACAAACCGCG
Found at i:16073 original size:12 final size:11
Alignment explanation
Indices: 16051--16084 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
16041 AAGTCTATCA
16051 CAAAGAAAAAATT
1 CAAA-AAAAAA-T
16064 CAAAAAAAAAT
1 CAAAAAAAAAT
16075 CAAAAAAAAA
1 CAAAAAAAAA
16085 AGAGATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 6 0.29
13 4 0.19
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (11 bp):
CAAAAAAAAAT
Found at i:16881 original size:29 final size:29
Alignment explanation
Indices: 16827--16882 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
16817 CACGTGTGCC
* * *
16827 CAAAAATGACACGTGGCACGCCACGTGAA
1 CAAAAAGGACACGTGGCACACAACGTGAA
16856 CAAAAAGGACACGTGGCACACAACGTG
1 CAAAAAGGACACGTGGCACACAACGTG
16883 TTAAATGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.27, G:0.25, T:0.09
Consensus pattern (29 bp):
CAAAAAGGACACGTGGCACACAACGTGAA
Found at i:17486 original size:132 final size:136
Alignment explanation
Indices: 17263--17539 Score: 384
Period size: 132 Copynumber: 2.0 Consensus size: 136
17253 TCAGGTTTTT
*
17263 TTTTTTATTTCCGCACAAAAAAATTTAATTTTAAGAAGGAAATCATAGGCCTATGCATAAGGGGT
1 TTTTTTATTTCCGCACAAAAAAATTTAATTTTAAGAAGGAAAGCATA-G-C---GCATAAGGGGT
17328 TTTAATTTGAAATAAGAGAAAACCTTGAATAAAC-AAAGAGA-ACTATTAATTCAAGTGAAAATA
61 TTTAATTTGAAATAAGAGAAAACCTTGAATAAACAAAAGAGACACTATTAATTCAAGTGAAAA-A
*
17391 TTAATTGTAATA
125 TCAATTGTAATA
* *
17403 TTTTTTATTTCTGCA-AAAAAAATTTAATTTTAAGAAGGAAAGCAT-G-GCATAAGGGTTTTTAA
1 TTTTTTATTTCCGCACAAAAAAATTTAATTTTAAGAAGGAAAGCATAGCGCATAAGGGGTTTTAA
* * *
17465 TTTGAAATGAGAGAAAACCTTGAATAAACAAAAGAGAGCTGCTATTAATTCAAGTGACAAATCAA
66 TTTGAAATAAGAGAAAACCTTGAATAAACAAAAGAGA-C-ACTATTAATTCAAGTGAAAAATCAA
17530 TTGTAATA
129 TTGTAATA
17538 TT
1 TT
17540 ATCTCAATGT
Statistics
Matches: 126, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
132 43 0.34
133 7 0.06
135 14 0.11
136 18 0.14
137 1 0.01
139 29 0.23
140 14 0.11
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (136 bp):
TTTTTTATTTCCGCACAAAAAAATTTAATTTTAAGAAGGAAAGCATAGCGCATAAGGGGTTTTAA
TTTGAAATAAGAGAAAACCTTGAATAAACAAAAGAGACACTATTAATTCAAGTGAAAAATCAATT
GTAATA
Found at i:23484 original size:119 final size:118
Alignment explanation
Indices: 23319--23667 Score: 418
Period size: 118 Copynumber: 3.0 Consensus size: 118
23309 GCGGTCGGGT
* ** * * *
23319 TGGAGAGCCGAGTTTTCCCATATCTATTAATGGATCTAAAAATTATGTATTTACAAATTTGATCT
1 TGGAGAGCCGAGTTTTACCAGCTCTACTAATGGACCTAAAAGTTATGTATTTACAAATTT-ATCT
*** ******* * *
23384 ATCCTTTTTTTTTTGGATTGAAATGGATAAAATACATTAAAAAGATTATTGGGC
65 ATCCTAAATCAAACAAATTGAAACGAATAAAATACATTAAAAAGATTATTGGGC
*
23438 TGGAGAGCCGAGTTTTACCAGCTCTACTAATGGACCTAAAAGTTATGTATTCACAAAATTTATCT
1 TGGAGAGCCGAGTTTTACCAGCTCTACTAATGGACCTAAAAGTTATGTATTTAC-AAATTTATCT
* *
23503 AT-CTAAATCAAACAAATTGAAACGAATAAAATCCATTAAAAAGATTATTGGGT
65 ATCCTAAATCAAACAAATTGAAACGAATAAAATACATTAAAAAGATTATTGGGC
* *
23556 TGGAGAGCCGAGTTTTACCAGCTCTACTAAGGGACCTAAAAGTTATATATTTA-AAATTTTATCT
1 TGGAGAGCCGAGTTTTACCAGCTCTACTAATGGACCTAAAAGTTATGTATTTACAAA-TTTATCT
* *
23620 AT-CTAAATCAAACAAATTGAAACGAATAAAATCCATTACAAA-ATTATT
65 ATCCTAAATCAAACAAATTGAAACGAATAAAATACATTAAAAAGATTATT
23668 TTTGAGGCTT
Statistics
Matches: 203, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
116 9 0.04
117 48 0.24
118 87 0.43
119 53 0.26
120 6 0.03
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (118 bp):
TGGAGAGCCGAGTTTTACCAGCTCTACTAATGGACCTAAAAGTTATGTATTTACAAATTTATCTA
TCCTAAATCAAACAAATTGAAACGAATAAAATACATTAAAAAGATTATTGGGC
Found at i:23572 original size:118 final size:117
Alignment explanation
Indices: 23400--23667 Score: 439
Period size: 118 Copynumber: 2.3 Consensus size: 117
23390 TTTTTTTTGG
* * *
23400 ATTGAAATGGATAAAATACATTAAAAAGATTATTGGGCTGGAGAGCCGAGTTTTACCAGCTCTAC
1 ATTGAAACGAATAAAATCCATTAAAAAGATTATTGGGCTGGAGAGCCGAGTTTTACCAGCTCTAC
* *
23465 TAATGGACCTAAAAGTTATGTATTCACAAAATTTATCTATCTAAATCAAACAA
66 TAAGGGACCTAAAAGTTATATATTCA-AAAATTTATCTATCTAAATCAAACAA
*
23518 ATTGAAACGAATAAAATCCATTAAAAAGATTATTGGGTTGGAGAGCCGAGTTTTACCAGCTCTAC
1 ATTGAAACGAATAAAATCCATTAAAAAGATTATTGGGCTGGAGAGCCGAGTTTTACCAGCTCTAC
* *
23583 TAAGGGACCTAAAAGTTATATATTTAAAATTTTATCTATCTAAATCAAACAA
66 TAAGGGACCTAAAAGTTATATATTCAAAAATTTATCTATCTAAATCAAACAA
*
23635 ATTGAAACGAATAAAATCCATTACAAA-ATTATT
1 ATTGAAACGAATAAAATCCATTAAAAAGATTATT
23668 TTTGAGGCTT
Statistics
Matches: 141, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
116 6 0.04
117 51 0.36
118 84 0.60
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (117 bp):
ATTGAAACGAATAAAATCCATTAAAAAGATTATTGGGCTGGAGAGCCGAGTTTTACCAGCTCTAC
TAAGGGACCTAAAAGTTATATATTCAAAAATTTATCTATCTAAATCAAACAA
Found at i:23967 original size:120 final size:127
Alignment explanation
Indices: 23826--24077 Score: 383
Period size: 120 Copynumber: 2.0 Consensus size: 127
23816 CATTGTTTAA
* *
23826 ACTTTTATAGTTTTCCTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-T
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACT
* *
23888 A-ATTTTTACCATTTTACTATTTTAATTAAAAAAC-T-TATATATT-GAATTTTTTAAATAT
66 ATATTTTTACCATTTTACCATTTTAATTAAAAAACTTATATATATTAGAAATTTTTAAATAT
23946 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA-C
24011 TATTTTATTTTTACCATTTTACCATTTTAATTAAAAAACTTATATATATTAGAAATTTTTAAATA
65 TA---TATTTTTACCATTTTACCATTTTAATTAAAAAACTTATATATATTAGAAATTTTTAAATA
24076 T
127 T
24077 A
1 A
24078 TTTCTTAAAT
Statistics
Matches: 117, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
120 54 0.46
121 3 0.03
122 2 0.02
124 2 0.02
128 32 0.27
129 1 0.01
130 8 0.07
131 15 0.13
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (127 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACT
ATATTTTTACCATTTTACCATTTTAATTAAAAAACTTATATATATTAGAAATTTTTAAATAT
Found at i:24427 original size:15 final size:16
Alignment explanation
Indices: 24398--24427 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24388 TTTTGGAGCG
24398 TGTATTGGTAGTTTAA
1 TGTATTGGTAGTTTAA
24414 TGTATTGG-AGTTTA
1 TGTATTGGTAGTTTA
24428 TAATAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (16 bp):
TGTATTGGTAGTTTAA
Found at i:24612 original size:33 final size:34
Alignment explanation
Indices: 24563--24698 Score: 256
Period size: 34 Copynumber: 4.0 Consensus size: 34
24553 TTTGAGGCTT
24563 AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGG
1 AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGG
24597 AGGGAAGCTTA-GCATTTTAGTTCTAAAAATTGG
1 AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGG
24630 AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGG
1 AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGG
*
24664 AGGGAAGATTAGGCATTTTAGTTCTAAAAATTGG
1 AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGG
24698 A
1 A
24699 AGAAAATAAT
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
33 33 0.33
34 67 0.67
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (34 bp):
AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGG
Found at i:24642 original size:67 final size:68
Alignment explanation
Indices: 24563--24698 Score: 256
Period size: 67 Copynumber: 2.0 Consensus size: 68
24553 TTTGAGGCTT
*
24563 AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGGAGGGAAGCTTA-GCATTTTAGTTCTAAAAAT
1 AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGGAGGGAAGATTAGGCATTTTAGTTCTAAAAAT
24627 TGG
66 TGG
24630 AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGGAGGGAAGATTAGGCATTTTAGTTCTAAAAAT
1 AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGGAGGGAAGATTAGGCATTTTAGTTCTAAAAAT
24695 TGG
66 TGG
24698 A
1 A
24699 AGAAAATAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
67 44 0.66
68 23 0.34
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (68 bp):
AGGGAAGCTTAGGCATTTTAGTTCTAAAAATTGGAGGGAAGATTAGGCATTTTAGTTCTAAAAAT
TGG
Found at i:30002 original size:58 final size:60
Alignment explanation
Indices: 29891--30015 Score: 182
Period size: 58 Copynumber: 2.1 Consensus size: 60
29881 TCAAATTTTC
* * * *
29891 TTCTGTTGATGAAGTTTTCCTTCTTTTTTTTTTAAACGAAAGGGGAAATTAAAAACCCTAA
1 TTCTATTGATGAAGTTTTCC-TCTTTTTTTTTCAAACAAAAGGGGAAACTAAAAACCCTAA
*
29952 TTCTATTGATGAAGTTTT-C-CTTTTTTTTTCGAACAAAAGGGGAAACTAAAAACCCTAA
1 TTCTATTGATGAAGTTTTCCTCTTTTTTTTTCAAACAAAAGGGGAAACTAAAAACCCTAA
30010 TTCTAT
1 TTCTAT
30016 CAATCTATCA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
58 41 0.69
60 1 0.02
61 17 0.29
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (60 bp):
TTCTATTGATGAAGTTTTCCTCTTTTTTTTTCAAACAAAAGGGGAAACTAAAAACCCTAA
Found at i:31455 original size:2 final size:2
Alignment explanation
Indices: 31448--31479 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
31438 CTGCTGTGTC
31448 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31480 CTAAATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31491 original size:19 final size:19
Alignment explanation
Indices: 31448--31491 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31438 CTGCTGTGTC
*
31448 ATATA-TATATATATATAT
1 ATATATTATATATATAAAT
31466 ATATATTATATATACTAAAT
1 ATATATTATATATA-TAAAT
31486 AT-TATT
1 ATATATT
31492 TGAAACACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 12 0.52
20 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATTATATATATAAAT
Found at i:35557 original size:13 final size:12
Alignment explanation
Indices: 35536--35583 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
35526 ACAGGGATAT
*
35536 CAAGTTCATGGAC
1 CAAGGTCATGG-C
35549 CAAGGTCATGGC
1 CAAGGTCATGGC
* *
35561 CATGGTCATGGT
1 CAAGGTCATGGC
*
35573 CATGGTCATGG
1 CAAGGTCATGG
35584 TCATCACTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 22 0.69
13 10 0.31
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (12 bp):
CAAGGTCATGGC
Found at i:35569 original size:12 final size:12
Alignment explanation
Indices: 35541--35583 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
35531 GATATCAAGT
*
35541 TCATGGACCAAGG
1 TCATGG-CCATGG
35554 TCATGGCCATGG
1 TCATGGCCATGG
*
35566 TCATGGTCATGG
1 TCATGGCCATGG
35578 TCATGG
1 TCATGG
35584 TCATCACTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 22 0.79
13 6 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (12 bp):
TCATGGCCATGG
Found at i:35570 original size:6 final size:6
Alignment explanation
Indices: 35552--35587 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
35542 CATGGACCAA
*
35552 GGTCAT GGCCAT GGTCAT GGTCAT GGTCAT GGTCAT
1 GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT
35588 CACTTGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (6 bp):
GGTCAT
Found at i:39162 original size:20 final size:20
Alignment explanation
Indices: 39118--39156 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
39108 TAAAAAGTTC
39118 ATTTTCAAAGGAACAGAGTA
1 ATTTTCAAAGGAACAGAGTA
39138 ATTTTCAAAGGAACAGAGT
1 ATTTTCAAAGGAACAGAGT
39157 TTTTTTGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (20 bp):
ATTTTCAAAGGAACAGAGTA
Found at i:42531 original size:6 final size:6
Alignment explanation
Indices: 42520--42553 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
42510 GATATCAAGT
*
42520 TCATGG TCATGG TCATGG TCATGA TCATGG TCAT
1 TCATGG TCATGG TCATGG TCATGG TCATGG TCAT
42554 CACTTGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (6 bp):
TCATGG
Found at i:51270 original size:34 final size:34
Alignment explanation
Indices: 51227--51294 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
51217 CATCTACAGT
51227 GCATCAATTCACCTCAATAGGAATATAAGTTGGC
1 GCATCAATTCACCTCAATAGGAATATAAGTTGGC
51261 GCATCAATTCACCTCAATAGGAATATAAGTTGGC
1 GCATCAATTCACCTCAATAGGAATATAAGTTGGC
51295 CGCTTTGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (34 bp):
GCATCAATTCACCTCAATAGGAATATAAGTTGGC
Found at i:55172 original size:3 final size:3
Alignment explanation
Indices: 55164--55190 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55154 AAGGTCAAGG
55164 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
55191 CTTGTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:72224 original size:166 final size:167
Alignment explanation
Indices: 71896--72233 Score: 563
Period size: 166 Copynumber: 2.0 Consensus size: 167
71886 ATTCCATATT
* * *
71896 CTTCTGACTCTCTTCATCCTCCCTAATCTTCTCAACCACAAGTTACCTTGTGTCTATCTTCCTAT
1 CTTCTGAATCTCTTCATCCTCCCCAATCTTCTCAACCACAAGTTACCTTGTGTCTACCTTCCTAT
* * *
71961 GTTTCAATTTTCTCTTCTCTGCCTCCTCAACAGCTCGTTCTTCTGCTTCCAACCATTCACATTTA
66 GTTCCAATTTTCTC-TCTCTGCCTCCTCAACAGCTCATTCTTCTGCTTCCAACCATTCACATTCA
72026 GCTATCGTATCTCTCTCAGACTAGGGATCATAAACCGC
130 GCTATCGTATCTCTCTCAGACTAGGGATCATAAACCGC
*
72064 CTTCTGAATCTCTTCATCCTCCCCAATCTTCTCAACCACAAGTTGCCTTGTGTCTACCTTCCTAT
1 CTTCTGAATCTCTTCATCCTCCCCAATCTTCTCAACCACAAGTTACCTTGTGTCTACCTTCCTAT
**
72129 GTTCCAATTTTCTC-CTCTGCCTCCTCAACAGCTCATTCTTCTGCTTCCAACCATTCAGGTTCAG
66 GTTCCAATTTTCTCTCTCTGCCTCCTCAACAGCTCATTCTTCTGCTTCCAACCATTCACATTCAG
72193 CTATCGTATCTCT-TGCAGACTAGGGATCATAAACCGC
131 CTATCGTATCTCTCT-CAGACTAGGGATCATAAACCGC
72230 CTTC
1 CTTC
72234 ACCATTGGAA
Statistics
Matches: 160, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
165 1 0.01
166 85 0.53
168 74 0.46
ACGTcount: A:0.20, C:0.34, G:0.10, T:0.36
Consensus pattern (167 bp):
CTTCTGAATCTCTTCATCCTCCCCAATCTTCTCAACCACAAGTTACCTTGTGTCTACCTTCCTAT
GTTCCAATTTTCTCTCTCTGCCTCCTCAACAGCTCATTCTTCTGCTTCCAACCATTCACATTCAG
CTATCGTATCTCTCTCAGACTAGGGATCATAAACCGC
Found at i:72407 original size:18 final size:19
Alignment explanation
Indices: 72372--72409 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
72362 TCTTCTAGGG
**
72372 CACCCTCATCCTTTTCCTC
1 CACCCTCATCCTCCTCCTC
72391 CACCCTC-TCCTCCTCCTC
1 CACCCTCATCCTCCTCCTC
72409 C
1 C
72410 TCTGTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.08, C:0.61, G:0.00, T:0.32
Consensus pattern (19 bp):
CACCCTCATCCTCCTCCTC
Found at i:78469 original size:3 final size:3
Alignment explanation
Indices: 78461--78501 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
78451 TCTCTGTCTT
78461 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
78502 CATATTCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:82492 original size:8 final size:8
Alignment explanation
Indices: 82479--82506 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
82469 TGGCGATGTT
82479 TGAAATTG
1 TGAAATTG
82487 TGAAATTG
1 TGAAATTG
82495 TGAAATTG
1 TGAAATTG
82503 TGAA
1 TGAA
82507 TACCAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (8 bp):
TGAAATTG
Found at i:86103 original size:12 final size:12
Alignment explanation
Indices: 86086--86110 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
86076 TATTTCCTGT
86086 TATGACAATGAC
1 TATGACAATGAC
86098 TATGACAATGAC
1 TATGACAATGAC
86110 T
1 T
86111 GAGATAAATG
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TATGACAATGAC
Found at i:89427 original size:17 final size:17
Alignment explanation
Indices: 89405--89455 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
89395 CTTAGATGGC
89405 TTGGGCCTGTTTTCATT
1 TTGGGCCTGTTTTCATT
89422 TTGGGCCTGTCTTT--TT
1 TTGGGCCTGT-TTTCATT
89438 TTGGG-CT-TTTTCAGTT
1 TTGGGCCTGTTTTCA-TT
89454 TT
1 TT
89456 CATTTGTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 1 0.03
15 2 0.07
16 11 0.37
17 10 0.33
18 3 0.10
ACGTcount: A:0.04, C:0.16, G:0.24, T:0.57
Consensus pattern (17 bp):
TTGGGCCTGTTTTCATT
Found at i:89441 original size:16 final size:16
Alignment explanation
Indices: 89405--89443 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
89395 CTTAGATGGC
89405 TTGGGCCTGTTTTCATT
1 TTGGGCCTGTTTT-ATT
89422 TTGGGCCTGTCTTT-TT
1 TTGGGCCTGT-TTTATT
89438 TTGGGC
1 TTGGGC
89444 TTTTTCAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 10 0.48
18 3 0.14
ACGTcount: A:0.03, C:0.18, G:0.28, T:0.51
Consensus pattern (16 bp):
TTGGGCCTGTTTTATT
Found at i:92641 original size:21 final size:21
Alignment explanation
Indices: 92617--92658 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
92607 CTCGTGCTTT
92617 TATTTATTACTAGTACTTTGC
1 TATTTATTACTAGTACTTTGC
92638 TATTTATTACTAGTACTTTGC
1 TATTTATTACTAGTACTTTGC
92659 CATGTGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (21 bp):
TATTTATTACTAGTACTTTGC
Found at i:94335 original size:2 final size:2
Alignment explanation
Indices: 94328--94354 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
94318 TAGTATTTAG
94328 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
94355 TTGTTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94434 original size:20 final size:21
Alignment explanation
Indices: 94409--94449 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
94399 TGGATCTGAA
94409 TTAGGTAGAAATT-AAAATTT
1 TTAGGTAGAAATTGAAAATTT
**
94429 TTAGGTTTAAATTGAAAATTT
1 TTAGGTAGAAATTGAAAATTT
94450 AGTTATACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (21 bp):
TTAGGTAGAAATTGAAAATTT
Found at i:95740 original size:12 final size:12
Alignment explanation
Indices: 95723--95747 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
95713 AGAAGAAAAG
95723 TATACATGACGA
1 TATACATGACGA
95735 TATACATGACGA
1 TATACATGACGA
95747 T
1 T
95748 GTGAGAAAAA
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TATACATGACGA
Found at i:99327 original size:56 final size:56
Alignment explanation
Indices: 99241--99352 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
99231 TACTGTTCAG
99241 AGTCAGAATCATACTCTGTAGTCATTGCTGCACAAAGACAATTAGCAAAATAAATA
1 AGTCAGAATCATACTCTGTAGTCATTGCTGCACAAAGACAATTAGCAAAATAAATA
99297 AGTCAGAATCATACTCTGTAGTCATTGCTGCACAAAGACAATTAGCAAAATAAATA
1 AGTCAGAATCATACTCTGTAGTCATTGCTGCACAAAGACAATTAGCAAAATAAATA
99353 CGGAATTAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (56 bp):
AGTCAGAATCATACTCTGTAGTCATTGCTGCACAAAGACAATTAGCAAAATAAATA
Found at i:110039 original size:26 final size:26
Alignment explanation
Indices: 110003--110062 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
109993 TCACTTTCAT
110003 GCAGGGGCGGGATCTAGAAATGTTAA
1 GCAGGGGCGGGATCTAGAAATGTTAA
110029 GCAGGGGCGGGATCTAGAAATGTTAA
1 GCAGGGGCGGGATCTAGAAATGTTAA
110055 GCAGGGGC
1 GCAGGGGC
110063 ACAATAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.28, C:0.13, G:0.42, T:0.17
Consensus pattern (26 bp):
GCAGGGGCGGGATCTAGAAATGTTAA
Found at i:122392 original size:70 final size:70
Alignment explanation
Indices: 122311--122446 Score: 247
Period size: 70 Copynumber: 1.9 Consensus size: 70
122301 ACCGAAACAC
122311 TAATCTATGAGCCAACAAACCCCTCCCCCAACAAACAAACCCAGTG-AAATCTCATTACAATTCA
1 TAATCTATGAGCCAACAAA-CCCTCCCCCAACAAACAAACCCAGTGAAAATCTCATTACAATTCA
122375 ATACGG
65 ATACGG
*
122381 TAATCTATGAGCCAACAAACCCTTCCCCAACAAACAAACCCAGTGAAAATCTCATTACAATTCAA
1 TAATCTATGAGCCAACAAACCCTCCCCCAACAAACAAACCCAGTGAAAATCTCATTACAATTCAA
122446 T
66 T
122447 TCAAACAAAC
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 25 0.39
70 39 0.61
ACGTcount: A:0.41, C:0.32, G:0.07, T:0.20
Consensus pattern (70 bp):
TAATCTATGAGCCAACAAACCCTCCCCCAACAAACAAACCCAGTGAAAATCTCATTACAATTCAA
TACGG
Found at i:122478 original size:56 final size:56
Alignment explanation
Indices: 122394--122507 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
122384 TCTATGAGCC
122394 AACAAACCCTTCCCCAACAAACAAACCCAGTGAAAATCTCATTACAATTCAATTCA
1 AACAAACCCTTCCCCAACAAACAAACCCAGTGAAAATCTCATTACAATTCAATTCA
*
122450 AACAAACCCTTCCCCAACAGACAAACCCAGTGAAAATCTCATTACAATTCAATTCA
1 AACAAACCCTTCCCCAACAAACAAACCCAGTGAAAATCTCATTACAATTCAATTCA
122506 AA
1 AA
122508 TAAATCTCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.45, C:0.32, G:0.04, T:0.19
Consensus pattern (56 bp):
AACAAACCCTTCCCCAACAAACAAACCCAGTGAAAATCTCATTACAATTCAATTCA
Found at i:128066 original size:16 final size:16
Alignment explanation
Indices: 128045--128086 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 16
128035 TATCTGATAT
128045 TGGAGTCATGATTTAG
1 TGGAGTCATGATTTAG
*
128061 TGGAGTCTTG--TTAG
1 TGGAGTCATGATTTAG
128075 TGGAGTCATGAT
1 TGGAGTCATGAT
128087 CTGATTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.21, C:0.07, G:0.33, T:0.38
Consensus pattern (16 bp):
TGGAGTCATGATTTAG
Found at i:138510 original size:79 final size:78
Alignment explanation
Indices: 138340--138512 Score: 310
Period size: 79 Copynumber: 2.2 Consensus size: 78
138330 GTGTCACAAA
* *
138340 AATGCCACGTGGCATTGCCATGTCAGTGGTTTTGTCCGACGTGGCAAGGCCACGTGGGCCGAATT
1 AATGCCACGTGGCATTGCCACGTCAGCGGTTTTGTCCGACGTGGCAAGGCCACGTGGGCCGAATT
138405 GGTCTGACATGGC
66 GGTCTGACATGGC
138418 AATGCCACGTGGCATTGCCACGTCAGCGGTTTTGTCCGACGTGGCAAAGGCCACGTGGGCCGAAT
1 AATGCCACGTGGCATTGCCACGTCAGCGGTTTTGTCCGACGTGGC-AAGGCCACGTGGGCCGAAT
138483 TGGTCTGACATGGC
65 TGGTCTGACATGGC
*
138497 AATGCCACATGGCATT
1 AATGCCACGTGGCATT
138513 TTTGTGCCAC
Statistics
Matches: 91, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
78 43 0.47
79 48 0.53
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (78 bp):
AATGCCACGTGGCATTGCCACGTCAGCGGTTTTGTCCGACGTGGCAAGGCCACGTGGGCCGAATT
GGTCTGACATGGC
Found at i:138640 original size:29 final size:29
Alignment explanation
Indices: 138567--138642 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
138557 TTAGTCTAAA
*
138567 GGGGCAAAACGTCCCAAAATTGAAGTTTAG
1 GGGGCAAAACGT-CCAAAATTGAAGTTCAG
* **
138597 GGGGTAAAATATCCAAAATTGAAGTTCAG
1 GGGGCAAAACGTCCAAAATTGAAGTTCAG
138626 GGGGCAAAACGTCCAAA
1 GGGGCAAAACGTCCAAA
138643 CGCTACAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 30 0.77
30 9 0.23
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.18
Consensus pattern (29 bp):
GGGGCAAAACGTCCAAAATTGAAGTTCAG
Done.