Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015534.1 Corchorus olitorius cultivar O-4 contig15567, 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: 114703
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1581 original size:96 final size:99
Alignment explanation
Indices: 1416--1614 Score: 271
Period size: 96 Copynumber: 2.0 Consensus size: 99
1406 GAACAAACAC
** * * *
1416 TTTAAGTTTAGGTTATACCCTTAAATTAATTTTTTTAATTTAGGGGTAAACCTTATTAATTTGGG
1 TTTAAGTTTAGGACATACCCTTAAAATAATTTTTTTAATTTAGGGGTAAACCTTATTAATTAGGA
1481 CTA-TTTTTT-TCT-AAACCCTAGAAATAAATAT
66 CTATTTTTTTATCTAAAACCCTAGAAATAAATAT
* *
1512 TTTAAGTTTAGGACATACCCTTAAAATCA-TTTTTTAATTTAGGGTTAAACCTTATTAACTTAGG
1 TTTAAGTTTAGGACATACCCTTAAAATAATTTTTTTAATTTAGGGGTAAACCTTATTAA-TTAGG
* *
1576 ACTATTTTTTTTATCTAAAACTCTATAAATAAATAT
65 ACTA-TTTTTTTATCTAAAACCCTAGAAATAAATAT
1612 TTT
1 TTT
1615 CACTCTAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
95 28 0.31
96 32 0.36
98 6 0.07
99 3 0.03
100 20 0.22
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.46
Consensus pattern (99 bp):
TTTAAGTTTAGGACATACCCTTAAAATAATTTTTTTAATTTAGGGGTAAACCTTATTAATTAGGA
CTATTTTTTTATCTAAAACCCTAGAAATAAATAT
Found at i:8675 original size:339 final size:331
Alignment explanation
Indices: 8256--8908 Score: 1099
Period size: 337 Copynumber: 1.9 Consensus size: 331
8246 AATTAAGAAA
* *
8256 GGGTCAATATTCATATCTTGAACGTATCATAAAGTAAAATTCTTTTTTTTTATCAAATGTTAATC
1 GGGTCAATATTCATATCTTGAACATATCATAAAGAAAAATTCTTTTTTTTTATCAAATGTTAATC
*
8321 CCATTAGGGTTAATATTCTTAATATCTTGAAGATATCATAAGGTAAAATTCTTTTCCTCTTATTT
66 CCATTAGGGTTAATATTCTTAATACCTTGAAGATATCATAAGGTAAAATTCTTTTCCTCTTATTT
*
8386 ACCCATTCTTAAAATGTGGAATTTCTGAAAAGTTTAAAAGAAAGAAGAAAAATGAAGTTATACTT
131 ACCCATTCTTAAAATGTGGAAATTCTGAAAAG--TAAAAGAAAGAAGAAAAATGAAGTTATACTT
* *
8451 TCAACTAAACCTATTCAAAGGATGAGCCATCCGTTCAAGTTATACTTTATATCCCATGCATGTTC
194 TCAACTAAACCTATCCAAAGGATGAGCCATCCGTTCAAGTTATACTTTATATCCCATGCAAGTTC
*
8516 CTGTCTTTCTATTTACTCATGACAAAGTTAGCATGGATTAAGAAAGGGTCAATATTGACTTAAAA
259 CTGTATTTCTATTTACTCATGACAAAGTTAGCATGGATTAAGAAAGGGTCAATATTGACTTAAAA
8581 AAAAAAAG
324 AAAAAAAG
8589 GGGTCAATATTCATATCTTGAACATATCATAAAGAAAAAATTCGTTTTCTTTTTTTTATCAAATG
1 GGGTCAATATTCATATCTTGAACATATCATAAAG-AAAAATTC----T-TTTTTTTTATCAAATG
*
8654 TTAATCTCATTAGGGTTAATATTCTTAATACCTTGAAGATATCATAAGGTAAAATTCTTTTCCTC
60 TTAATCCCATTAGGGTTAATATTCTTAATACCTTGAAGATATCATAAGGTAAAATTCTTTTCCTC
*
8719 TTGTTTACCCATTCTTAAAATGTGGAAATTCTGAAAAGTAAAAGAAAGAAGAAAAATGAAGTTAT
125 TTATTTACCCATTCTTAAAATGTGGAAATTCTGAAAAGTAAAAGAAAGAAGAAAAATGAAGTTAT
* * * *
8784 ATTTTCAACTAAACTTGTCCAAAGGATGGGCCATCCGTTCAAGTTATACTTTATATCCCATGCAA
190 ACTTTCAACTAAACCTATCCAAAGGATGAGCCATCCGTTCAAGTTATACTTTATATCCCATGCAA
* *
8849 GTTCCTTTATTTCTATTTACTCATGACAAAGTTAGCATGGATTAAGAAAGGGTCAGTATT
255 GTTCCTGTATTTCTATTTACTCATGACAAAGTTAGCATGGATTAAGAAAGGGTCAATATT
8909 CATATCTTGA
Statistics
Matches: 299, Mismatches: 15, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
333 33 0.11
334 7 0.02
337 143 0.48
338 1 0.00
339 115 0.38
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (331 bp):
GGGTCAATATTCATATCTTGAACATATCATAAAGAAAAATTCTTTTTTTTTATCAAATGTTAATC
CCATTAGGGTTAATATTCTTAATACCTTGAAGATATCATAAGGTAAAATTCTTTTCCTCTTATTT
ACCCATTCTTAAAATGTGGAAATTCTGAAAAGTAAAAGAAAGAAGAAAAATGAAGTTATACTTTC
AACTAAACCTATCCAAAGGATGAGCCATCCGTTCAAGTTATACTTTATATCCCATGCAAGTTCCT
GTATTTCTATTTACTCATGACAAAGTTAGCATGGATTAAGAAAGGGTCAATATTGACTTAAAAAA
AAAAAG
Found at i:9360 original size:299 final size:298
Alignment explanation
Indices: 8589--9723 Score: 1828
Period size: 299 Copynumber: 3.8 Consensus size: 298
8579 AAAAAAAAAG
*
8589 GGGTCAATATTCATATCTTGAACATATCATAAAGAAAAAATTCGTTTTCTTTTTTTTATCAAATG
1 GGGTCAATATTCATATCTTGAACATATCATAAAG-TAAAATTC---TT-TTTTTTTT-TCAAATG
* *
8654 TTAATCTCATTAGGGTTAATATTCTTAATACCTTGAAGATATCATAAGGTAAAATTCTTTTCCTC
60 TCAATCTCATTAGGGTTAATATTCTTAATATCTTGAAGATATCATAAGGTAAAATTCTTTTCCTC
* *
8719 TTGTTTACCCATTCTTAAAATGTGGAAATTCTGAAAAGTAAAAGAAAGAAGAAAAATGAAGTTAT
125 TTCTTTACTCATTCTTAAAATGTGGAAATTCTGAAAAGTAAAAGAAAGAAGAAAAATGAAGTTAT
* * * *
8784 ATTTTCAACTAAACTTGTCCAAAGGATGGGCCATCCGTTCAAGTTATACTTTATATCCCATGCAA
190 ACTTTCAACTAAACCTGTCCAAAGGATGGGCCATCCGTTCAAGTTATAC-TT-TAT---ATGTAT
* *
8849 GTTCCTTTATTTCTATTTACTCATGACAAAGTTAGCATGGA-TTAAGAAA
250 GTTCCTTTCTTTCCATTTACTCATGACAAAGTTAGCAT-GATTTAAGAAA
* ** *
8898 GGGTCAGTATTCATATCTTGAACATATCATAAAGTAAAATTCTTTTTTTTAATCAAATGTTAATC
1 GGGTCAATATTCATATCTTGAACATATCATAAAGTAAAATTCTTTTTTTTTTTCAAATGTCAATC
*
8963 TCATTAGGATTAATATTCTTAATATCTTGAA-ATTATCATAAGGTAAAATTCTTTTCCTCTTCTT
66 TCATTAGGGTTAATATTCTTAATATCTTGAAGA-TATCATAAGGTAAAATTCTTTTCCTCTTCTT
*
9027 TACTCATTCTTAAAATGTGGAAATTCTGAAATGTAAAAGAAAGAAGAAAAATGAAGTTATACTTT
130 TACTCATTCTTAAAATGTGGAAATTCTGAAAAGTAAAAGAAAGAAGAAAAATGAAGTTATACTTT
* *
9092 CAACTAAACCTGTCCAAAGGATGGGCTATCCATTCAAGTTATACTTTATATGTATGTTCCTTTCT
195 CAACTAAACCTGTCCAAAGGATGGGCCATCCGTTCAAGTTATACTTTATATGTATGTTCCTTTCT
9157 TTCCATTTACTCATGACAAAGTTAGCATGATTTAAGAAA
260 TTCCATTTACTCATGACAAAGTTAGCATGATTTAAGAAA
*
9196 GGGTTAATATTCATATCTTGAACATATCATAAAGTAAAATTCTTTTTGTTTTTTCAAATGTCAAT
1 GGGTCAATATTCATATCTTGAACATATCATAAAGTAAAATTCTTTTT-TTTTTTCAAATGTCAAT
* * *
9261 CTCATTAGGGTTAATATTCTTAATATCTTGAAGATGTCGTAAGGTAAGATTCTTTTCCTCTTCTT
65 CTCATTAGGGTTAATATTCTTAATATCTTGAAGATATCATAAGGTAAAATTCTTTTCCTCTTCTT
*
9326 TACTCATTCTTAAAATGTGGAAATTCTGAAATGTAAAAGAAAGAAGAAAAATGAAGTTATACTTT
130 TACTCATTCTTAAAATGTGGAAATTCTGAAAAGTAAAAGAAAGAAGAAAAATGAAGTTATACTTT
*
9391 CAACTAAACCTGTCCAAATGATGGGCCATCCGTTCAAGTTATACTTTATATGTATGTTCCTTTCT
195 CAACTAAACCTGTCCAAAGGATGGGCCATCCGTTCAAGTTATACTTTATATGTATGTTCCTTTCT
*
9456 TTCCATTTACTTATGACAAAGTTAGCATGATTTAAGAAA
260 TTCCATTTACTCATGACAAAGTTAGCATGATTTAAGAAA
9495 GGGTCAATATTCATATCTTGAACATATCATAAAGTAAAATTCTTTTTTTTTTTCAAATGTCAATC
1 GGGTCAATATTCATATCTTGAACATATCATAAAGTAAAATTCTTTTTTTTTTTCAAATGTCAATC
* *
9560 TCATTAGGGTTAATATTCTTAATATCTTGAAGATATCGTAAGGTAAGATTCTTTTCCTCTTCTTT
66 TCATTAGGGTTAATATTCTTAATATCTTGAAGATATCATAAGGTAAAATTCTTTTCCTCTTCTTT
*
9625 ACTCATTCTTAAAATGTGGAAATTCTGAAAAGTAAAAGAAAGAAGAAAAATGAAGTTATACTTTT
131 ACTCATTCTTAAAATGTGGAAATTCTGAAAAGTAAAAGAAAGAAGAAAAATGAAGTTATACTTTC
* * *
9690 AACT-GACCTGTCC-AAGGATGAGCTATCCGTTCAA
196 AACTAAACCTGTCCAAAGGATGGGCCATCCGTTCAA
9724 TCTGAAGGCA
Statistics
Matches: 784, Mismatches: 38, Indels: 21
0.93 0.05 0.02
Matches are distributed among these distances:
296 18 0.02
297 10 0.01
298 242 0.31
299 284 0.36
300 1 0.00
301 3 0.00
302 3 0.00
303 175 0.22
304 6 0.01
305 2 0.00
308 7 0.01
309 33 0.04
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (298 bp):
GGGTCAATATTCATATCTTGAACATATCATAAAGTAAAATTCTTTTTTTTTTTCAAATGTCAATC
TCATTAGGGTTAATATTCTTAATATCTTGAAGATATCATAAGGTAAAATTCTTTTCCTCTTCTTT
ACTCATTCTTAAAATGTGGAAATTCTGAAAAGTAAAAGAAAGAAGAAAAATGAAGTTATACTTTC
AACTAAACCTGTCCAAAGGATGGGCCATCCGTTCAAGTTATACTTTATATGTATGTTCCTTTCTT
TCCATTTACTCATGACAAAGTTAGCATGATTTAAGAAA
Found at i:12821 original size:18 final size:18
Alignment explanation
Indices: 12773--12825 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
12763 TACAACAGCG
12773 GCAAGTAATGAAGCACCT
1 GCAAGTAATGAAGCACCT
* *
12791 ACAATTGAA-GAAGCACCT
1 GCAAGT-AATGAAGCACCT
12809 GCAAGTAATGAAGCACC
1 GCAAGTAATGAAGCACC
12826 ACCTACTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 25 0.86
19 2 0.07
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.15
Consensus pattern (18 bp):
GCAAGTAATGAAGCACCT
Found at i:12966 original size:198 final size:198
Alignment explanation
Indices: 12609--12991 Score: 640
Period size: 198 Copynumber: 1.9 Consensus size: 198
12599 GCACCTGCAG
* ** * *
12609 CTGCATGTAATGAAGCATTACCTACCACTGGTGATGAAGCTGATAATGGTGGTAATTCAAATGTC
1 CTGCAAGTAATGAAGCACCACCTACCACAGGTGACGAAGCTGATAATGGTGGTAATTCAAATGTC
12674 AGCAGTGGCAAGATGAGGAGAAGAACATGCTACGAGTGTGGACAAAAGGGCCACTTGTCGTCTGC
66 AGCAGTGGCAAGATGAGGAGAAGAACATGCTACGAGTGTGGACAAAAGGGCCACTTGTCGTCTGC
* * *
12739 TTGTCCAAATACGAATACTGCAAATACAACAGCGGCAAGTAATGAAGCACCTACAATTGAAGAAG
131 TTGTCCAAATAAGAAAACTGCAAATACAACACCGGCAAGTAATGAAGCACCTACAATTGAAGAAG
12804 CAC
196 CAC
* * * *
12807 CTGCAAGTAATGAAGCACCACCTACTACAGTTGACGAAGCTGATAATGGTGGTCATTCGAATGTC
1 CTGCAAGTAATGAAGCACCACCTACCACAGGTGACGAAGCTGATAATGGTGGTAATTCAAATGTC
*
12872 AGCAGTGGCAAGATGAGGAGAAGAACATGCTACGAGTGTGGACAAAAGGGCCATTTGTCGTCTGC
66 AGCAGTGGCAAGATGAGGAGAAGAACATGCTACGAGTGTGGACAAAAGGGCCACTTGTCGTCTGC
*
12937 TTGTCCAAATAAGAAAACTGCAGATACAACACCGGCAAGTAATGAAGCACCTACA
131 TTGTCCAAATAAGAAAACTGCAAATACAACACCGGCAAGTAATGAAGCACCTACA
12992 GCTAATGAAG
Statistics
Matches: 171, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
198 171 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.21
Consensus pattern (198 bp):
CTGCAAGTAATGAAGCACCACCTACCACAGGTGACGAAGCTGATAATGGTGGTAATTCAAATGTC
AGCAGTGGCAAGATGAGGAGAAGAACATGCTACGAGTGTGGACAAAAGGGCCACTTGTCGTCTGC
TTGTCCAAATAAGAAAACTGCAAATACAACACCGGCAAGTAATGAAGCACCTACAATTGAAGAAG
CAC
Found at i:13123 original size:180 final size:180
Alignment explanation
Indices: 12800--13147 Score: 495
Period size: 180 Copynumber: 1.9 Consensus size: 180
12790 TACAATTGAA
*
12800 GAAGCACCTGCAAGTAATGAAGCACCACCTACTACAGTTGACGAAGCTGATAATGGTGGTCATTC
1 GAAGCACCTACAAGTAATGAAGCACCACCTACTACAGTTGACGAAGCTGATAATGGTGGTCATTC
* * * *
12865 GAATGTCAGCAGTGGCAAGATGAGGAGAAGAACATGCTACGAGTGTGGACAAAAGGGCCATTTGT
66 AAATATCAGCAGCGGCAAGATGAGGAGAAGAACATGCTACGAGTGTGGACAAAAGGGACATTTGT
* *
12930 CGTCTGCTTGTCCAAATAAGAAAACTGCAGATACAACACCGGCAAGTAAT
131 CGTCTGATTGTCCAAATAAGAAAACTGCAGACACAACACCGGCAAGTAAT
**
12980 GAAGCACCTAC-AGCTAATGAAGCACCACCTACTACAGTT-AGCGAAGCTGATAATGGTGGTGGT
1 GAAGCACCTACAAG-TAATGAAGCACCACCTACTACAGTTGA-CGAAGCTGATAATGGTGGTCAT
* * * * *
13043 TCAAATATCAGCAGCGGTAAGTTGAGGAGGAGGACTTGCTACGAGTGTGGACAAAAGGGACATCT
64 TCAAATATCAGCAGCGGCAAGATGAGGAGAAGAACATGCTACGAGTGTGGACAAAAGGGACAT-T
* * *
13108 T-TCTTCTGATTGTCCAAATAAGAAAGCTTCAGACACAACA
128 TGTCGTCTGATTGTCCAAATAAGAAAACTGCAGACACAACA
13148 AATACAAACA
Statistics
Matches: 148, Mismatches: 17, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
179 3 0.02
180 143 0.97
181 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (180 bp):
GAAGCACCTACAAGTAATGAAGCACCACCTACTACAGTTGACGAAGCTGATAATGGTGGTCATTC
AAATATCAGCAGCGGCAAGATGAGGAGAAGAACATGCTACGAGTGTGGACAAAAGGGACATTTGT
CGTCTGATTGTCCAAATAAGAAAACTGCAGACACAACACCGGCAAGTAAT
Found at i:15069 original size:5 final size:5
Alignment explanation
Indices: 15061--15086 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
15051 CATGACAAAG
15061 TTGAT TTGAT TTGAT TTGAT TTGAT T
1 TTGAT TTGAT TTGAT TTGAT TTGAT T
15087 CATTTCAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (5 bp):
TTGAT
Found at i:16200 original size:7 final size:7
Alignment explanation
Indices: 16190--16224 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
16180 TGGTTGGTGT
16190 CTGCTGC
1 CTGCTGC
16197 CTGCTGC
1 CTGCTGC
16204 CTGCTGC
1 CTGCTGC
16211 CTGCTGC
1 CTGCTGC
16218 CTGCTGC
1 CTGCTGC
16225 TGAGCACTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.00, C:0.43, G:0.29, T:0.29
Consensus pattern (7 bp):
CTGCTGC
Found at i:17218 original size:12 final size:13
Alignment explanation
Indices: 17193--17221 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
17183 ACCCAAACCG
17193 AAAGCCAGAAGCC
1 AAAGCCAGAAGCC
17206 AAAGCCA-AAGCC
1 AAAGCCAGAAGCC
17218 AAAG
1 AAAG
17222 GACAAAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.52, C:0.28, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGCCAGAAGCC
Found at i:29482 original size:7 final size:7
Alignment explanation
Indices: 29470--29495 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29460 TGGAACTCTG
29470 TTTTTCT
1 TTTTTCT
29477 TTTTTCT
1 TTTTTCT
29484 TTTTTCT
1 TTTTTCT
29491 TTTTT
1 TTTTT
29496 TTTCTAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:35132 original size:19 final size:19
Alignment explanation
Indices: 35104--35145 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
35094 CTACAAACTT
35104 GCTCGCGC-AAAAAACTAA
1 GCTCGCGCAAAAAAACTAA
35122 GCTCGGCGCAAAAAAACTAA
1 GCTC-GCGCAAAAAAACTAA
35142 GCTC
1 GCTC
35146 CACGCTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (19 bp):
GCTCGCGCAAAAAAACTAA
Found at i:36099 original size:29 final size:29
Alignment explanation
Indices: 36066--36126 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
36056 TAGGGCTCCT
* **
36066 AAATAAAACTTTAGGGGGTAAAATGTCCA
1 AAATAAAACTTTAGGGGGGAAAACATCCA
**
36095 AAATAATTCTTTAGGGGGGAAAACATCCA
1 AAATAAAACTTTAGGGGGGAAAACATCCA
36124 AAA
1 AAA
36127 CGCCATAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (29 bp):
AAATAAAACTTTAGGGGGGAAAACATCCA
Found at i:36549 original size:189 final size:189
Alignment explanation
Indices: 36303--36681 Score: 632
Period size: 189 Copynumber: 2.0 Consensus size: 189
36293 TAATAAAATT
* * *
36303 AGGGTAATTATTTGATACACCGGCGATGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGAC
1 AGGGTAATTATTTGATACACCGGCGATGTAAATTTTGAACTCCACAAGCGAGTTGTGGAGTTAAC
* * *
36368 ACATGTCCATTTTCTAAATTGATTAAATTTTAAATATTTCAATCTAGTCCCTAGGGGACACTTGT
66 ACATGTCCATTTTCTAAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGGAGACACATGT
* * * *
36433 CACCCTTCAAGACCCGCTTGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATATA
131 CACCATTCAAGACCCACTTATGCAGTCTGCTAAACTCCACTGACAGTGTATTATATATA
* *
36492 AGGGTAATTATTTGATACACCGGCGGTGTAAATTTTGAACTCCACACGCGAGTTGTGGAGTTAAC
1 AGGGTAATTATTTGATACACCGGCGATGTAAATTTTGAACTCCACAAGCGAGTTGTGGAGTTAAC
*
36557 ACATGTTCATTTTCTAAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGGAGACACATGT
66 ACATGTCCATTTTCTAAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGGAGACACATGT
*
36622 CATCATTCAAGACCCACTTATGCAGTCTGCTAAACTCCACTGACAGTGTATTATATATA
131 CACCATTCAAGACCCACTTATGCAGTCTGCTAAACTCCACTGACAGTGTATTATATATA
36681 A
1 A
36682 ACCCATAAAA
Statistics
Matches: 176, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
189 176 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (189 bp):
AGGGTAATTATTTGATACACCGGCGATGTAAATTTTGAACTCCACAAGCGAGTTGTGGAGTTAAC
ACATGTCCATTTTCTAAATTAATTAAATTTTAAATATTTCAATCTAGTCCCTAGGAGACACATGT
CACCATTCAAGACCCACTTATGCAGTCTGCTAAACTCCACTGACAGTGTATTATATATA
Found at i:37251 original size:2 final size:2
Alignment explanation
Indices: 37244--37275 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
37234 ACGACCGGTA
37244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37276 CTTTAATGAA
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:42124 original size:2 final size:2
Alignment explanation
Indices: 42117--42142 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42107 TCAATCCTTA
42117 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42143 GGTAATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47277 original size:2 final size:2
Alignment explanation
Indices: 47270--47298 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47260 ATGATGCTAC
47270 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
47299 ACTTCATGAT
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:48283 original size:6 final size:6
Alignment explanation
Indices: 48266--48305 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
48256 AAACTATCAT
* * *
48266 TTTTTA TATTTA TTTTTA TATTTA TCTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
48306 AAAAAAGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:48283 original size:12 final size:12
Alignment explanation
Indices: 48266--48305 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
48256 AAACTATCAT
48266 TTTTTATATTTA
1 TTTTTATATTTA
48278 TTTTTATATTTA
1 TTTTTATATTTA
* *
48290 TCTTTATTTTTA
1 TTTTTATATTTA
48302 TTTT
1 TTTT
48306 AAAAAAGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTATATTTA
Found at i:48295 original size:18 final size:17
Alignment explanation
Indices: 48267--48306 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
48257 AACTATCATT
48267 TTTTATATTTATTTTTA
1 TTTTATATTTATTTTTA
*
48284 TATTTATCTTTATTTTTA
1 T-TTTATATTTATTTTTA
48302 TTTTA
1 TTTTA
48307 AAAAAGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATATTTATTTTTA
Found at i:49071 original size:41 final size:41
Alignment explanation
Indices: 49014--49091 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
49004 CGACTGTTTT
* *
49014 ATTTTATGAGTTTTTTTAAGAAAATTCAGTTAAGAAATGGA
1 ATTTTATAAGTGTTTTTAAGAAAATTCAGTTAAGAAATGGA
* *
49055 ATTTTATAAGTGTTTTTAAGACAATTTAGTTAAGAAA
1 ATTTTATAAGTGTTTTTAAGAAAATTCAGTTAAGAAA
49092 AGAAAGTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (41 bp):
ATTTTATAAGTGTTTTTAAGAAAATTCAGTTAAGAAATGGA
Found at i:59904 original size:14 final size:14
Alignment explanation
Indices: 59885--59912 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59875 CATACTTTCG
59885 TCATGAGCTAGAAT
1 TCATGAGCTAGAAT
59899 TCATGAGCTAGAAT
1 TCATGAGCTAGAAT
59913 ACGAAGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
TCATGAGCTAGAAT
Found at i:66887 original size:21 final size:19
Alignment explanation
Indices: 66837--66890 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
66827 AAAATTAACC
66837 TTAGTCTAGTTAATAGTTAG
1 TTAGT-TAGTTAATAGTTAG
*
66857 TTATGCTTAGTTAAGTAAGTTTG
1 TTA-G-TTAGTTAA-T-AGTTAG
66880 TTAGTTAGTTA
1 TTAGTTAGTTA
66891 CCTTAAGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 3 0.10
21 15 0.52
22 3 0.10
23 8 0.28
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (19 bp):
TTAGTTAGTTAATAGTTAG
Found at i:69966 original size:15 final size:16
Alignment explanation
Indices: 69936--69973 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
69926 CAGAATTTTG
*
69936 TCAATCCTGTTGATCT
1 TCAATCCTGCTGATCT
69952 TCAATCCT-CTGATCT
1 TCAATCCTGCTGATCT
69967 TC-ATCCT
1 TCAATCCT
69974 TCGATCCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
16 8 0.38
ACGTcount: A:0.18, C:0.32, G:0.08, T:0.42
Consensus pattern (16 bp):
TCAATCCTGCTGATCT
Found at i:71804 original size:21 final size:21
Alignment explanation
Indices: 71772--71825 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 21
71762 AAAATTAACC
71772 TTAGTCTAGTTAA-TAA-TTAG
1 TTAGT-TAGTTAAGTAAGTTAG
71792 TTATGCTTAGTTAAGTAAGTTAG
1 TTA-G-TTAGTTAAGTAAGTTAG
71815 TTAGTTAGTTA
1 TTAGTTAGTTA
71826 CCCTTAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 3 0.10
21 15 0.50
22 5 0.17
23 7 0.23
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (21 bp):
TTAGTTAGTTAAGTAAGTTAG
Found at i:72308 original size:21 final size:21
Alignment explanation
Indices: 72284--72324 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
72274 GAGGACTTGT
*
72284 ATATTAGT-ATATATTAATATC
1 ATATAAGTAATATA-TAATATC
72305 ATATAAGTAATATATAATAT
1 ATATAAGTAATATATAATAT
72325 TTTGAGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
ATATAAGTAATATATAATATC
Found at i:78787 original size:27 final size:27
Alignment explanation
Indices: 78730--78787 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
78720 TTCATCAGTT
*
78730 ACTTGTTTTCTAAGTTAAGATAGAGTT
1 ACTTGTTTTCTAAGTTAAGATAGAGTC
78757 ACTTGTTTTCTAAGTTAAGGA-AGAGTC
1 ACTTGTTTTCTAAGTTAA-GATAGAGTC
78784 ACTT
1 ACTT
78788 AAACCAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (27 bp):
ACTTGTTTTCTAAGTTAAGATAGAGTC
Found at i:89239 original size:24 final size:25
Alignment explanation
Indices: 89196--89251 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
89186 TTTATTTATT
* * *
89196 TATGATGAAAATAAATACTTGAAAA
1 TATGTTGAAAAAAAAAACTTGAAAA
89221 TA-GTTGAAAAAAAAAACTTGAAAA
1 TATGTTGAAAAAAAAAACTTGAAAA
89245 TATGTTG
1 TATGTTG
89252 TGATTTCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.54, C:0.04, G:0.14, T:0.29
Consensus pattern (25 bp):
TATGTTGAAAAAAAAAACTTGAAAA
Found at i:90969 original size:17 final size:18
Alignment explanation
Indices: 90947--90980 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
90937 CTTAGAAATG
90947 AAAA-GGTTTGACAAAAC
1 AAAAGGGTTTGACAAAAC
*
90964 AAAAGGGTTTGTCAAAA
1 AAAAGGGTTTGACAAAA
90981 ATCATAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.21
Consensus pattern (18 bp):
AAAAGGGTTTGACAAAAC
Found at i:93194 original size:16 final size:17
Alignment explanation
Indices: 93175--93207 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
93165 CTGAGTAATG
93175 AAAAAAA-AAAAGAAAA
1 AAAAAAAGAAAAGAAAA
*
93191 AAAAAAAGAAAGGAAAA
1 AAAAAAAGAAAAGAAAA
93208 TTATGCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAGAAAA
Found at i:93207 original size:12 final size:12
Alignment explanation
Indices: 93174--93201 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
93164 ACTGAGTAAT
93174 GAAAAAAAAAAA
1 GAAAAAAAAAAA
93186 GAAAAAAAAAAA
1 GAAAAAAAAAAA
93198 GAAA
1 GAAA
93202 GGAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:97429 original size:63 final size:63
Alignment explanation
Indices: 97243--97432 Score: 308
Period size: 63 Copynumber: 3.0 Consensus size: 63
97233 TTCCACCAGG
* * *
97243 CCGCGAACTCTCACCTGGTCCAAGTGCAACAACCAAACCATCAGAGCAAGAGGAGAATCGATT
1 CCGCGAACCCTCACCTGGTCCAAGTGCAACAACCTAACCATCAGAGCAAGAGGAGAATCGGTT
*
97306 CCGTGAACCCTCACCTGGTCCAAGTGCAACAACCTAACCATCAGAGCAAGAGGAGAATCGGTT
1 CCGCGAACCCTCACCTGGTCCAAGTGCAACAACCTAACCATCAGAGCAAGAGGAGAATCGGTT
* * **
97369 CCGCAAACCCTCACCCGGTCCAAGTGCAACAACCTAACCATTGGAGCAAGAGGAGAATCGGTT
1 CCGCGAACCCTCACCTGGTCCAAGTGCAACAACCTAACCATCAGAGCAAGAGGAGAATCGGTT
97432 C
1 C
97433 TTAGCCACCA
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 118 1.00
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.15
Consensus pattern (63 bp):
CCGCGAACCCTCACCTGGTCCAAGTGCAACAACCTAACCATCAGAGCAAGAGGAGAATCGGTT
Found at i:103365 original size:1 final size:1
Alignment explanation
Indices: 103361--103400 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
103351 CCAAAAAGAG
103361 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
103401 CTAAGCCTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:105615 original size:21 final size:20
Alignment explanation
Indices: 105575--105625 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
105565 TCGTTTAGTA
*
105575 ATATT-TATA-ATTAAATAT
1 ATATTATATATATAAAATAT
105593 ATATTATATATATAAAATA-
1 ATATTATATATATAAAATAT
*
105612 ATATTAGATATATA
1 ATATTATATATATA
105626 TAATTACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.17
19 17 0.59
20 7 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATTATATATATAAAATAT
Found at i:105631 original size:14 final size:13
Alignment explanation
Indices: 105573--105655 Score: 55
Period size: 11 Copynumber: 7.2 Consensus size: 13
105563 GGTCGTTTAG
*
105573 TAATATTTATAAT
1 TAATATATATAAT
105586 TAA-ATATAT-AT
1 TAATATATATAAT
105597 T-ATATATAT-A-
1 TAATATATATAAT
105607 -AA-ATA-AT-AT
1 TAATATATATAAT
105616 TAGATATATATAAT
1 TA-ATATATATAAT
105630 TACATATA-A-AA-
1 TA-ATATATATAAT
105641 TAATATATATAAT
1 TAATATATATAAT
105654 TA
1 TA
105656 TTAAACGGTC
Statistics
Matches: 57, Mismatches: 2, Indels: 22
0.70 0.02 0.27
Matches are distributed among these distances:
8 3 0.05
9 3 0.05
10 8 0.14
11 14 0.25
12 12 0.21
13 8 0.14
14 9 0.16
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (13 bp):
TAATATATATAAT
Found at i:107770 original size:73 final size:73
Alignment explanation
Indices: 107651--107792 Score: 275
Period size: 73 Copynumber: 1.9 Consensus size: 73
107641 CGTCGGGAGG
107651 AATAGTCCCACACCACACGATTATCCAGCTCAATCTTAGCTAGAGAATATGCTAATAACATTGGC
1 AATAGTCCCACACCACACGATTATCCAGCTCAATCTTAGCTAGAGAATATGCTAATAACATTGGC
107716 TTCCCTAT
66 TTCCCTAT
*
107724 AATAGTCCCACACCACACGATTATCCAGCTCAATCTTAGCTAGAGAATATGCTAATAACATTGGT
1 AATAGTCCCACACCACACGATTATCCAGCTCAATCTTAGCTAGAGAATATGCTAATAACATTGGC
107789 TTCC
66 TTCC
107793 TTATTTACAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (73 bp):
AATAGTCCCACACCACACGATTATCCAGCTCAATCTTAGCTAGAGAATATGCTAATAACATTGGC
TTCCCTAT
Found at i:108772 original size:1 final size:1
Alignment explanation
Indices: 108766--108791 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
108756 ATTCCTTTTG
108766 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
108792 CTAATCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:111741 original size:2 final size:2
Alignment explanation
Indices: 111736--111761 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
111726 TACTAGTGTG
111736 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
111762 CCAACAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:114419 original size:2 final size:2
Alignment explanation
Indices: 114414--114452 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
114404 GAAGAGAGGC
114414 AT AT AT AT AT 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 AT AT AT AT AT A
114453 ATGAGATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.