Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021126.1 Corchorus olitorius cultivar O-4 contig21159, 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: 140527
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3056 original size:19 final size:20
Alignment explanation
Indices: 3032--3089 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
3022 CTGTTTGATA
3032 ACTGTACAAATGAGATTA-C
1 ACTGTACAAATGAGATTAGC
* * *
3051 ACTGTACATATTAGATTATGT
1 ACTGTACAAATGAGATTA-GC
*
3072 ACTGTACAGATGAGATTA
1 ACTGTACAAATGAGATTA
3090 TTAGAGCATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (20 bp):
ACTGTACAAATGAGATTAGC
Found at i:3077 original size:21 final size:21
Alignment explanation
Indices: 3032--3090 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
3022 CTGTTTGATA
* *
3032 ACTGTACAAATGAGATTA--C
1 ACTGTACAGATGAGATTATGT
* *
3051 ACTGTACATATTAGATTATGT
1 ACTGTACAGATGAGATTATGT
3072 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
3091 TAGAGCATCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (21 bp):
ACTGTACAGATGAGATTATGT
Found at i:8092 original size:15 final size:16
Alignment explanation
Indices: 8061--8094 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8051 TATAAGCATC
*
8061 AAATATATTTCTTTTA
1 AAATACATTTCTTTTA
8077 AAATACATTT-TTTTA
1 AAATACATTTCTTTTA
8092 AAA
1 AAA
8095 CCTCCATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATACATTTCTTTTA
Found at i:18404 original size:31 final size:31
Alignment explanation
Indices: 18369--18430 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
18359 CACAAGAGAA
* *
18369 CTCTTGATTCATGAATATTTACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
18400 CTCTTGATTCATGAATAATCACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
18431 TAATAACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (31 bp):
CTCTTGATTCATGAATAATCACAATATTCAT
Found at i:21297 original size:110 final size:110
Alignment explanation
Indices: 21096--21315 Score: 395
Period size: 110 Copynumber: 2.0 Consensus size: 110
21086 CATATATATA
* * *
21096 CTAAATATTATTTGAAAGATTCAGGAAATTTACCAAAGGCCCATTTTGAGAATCGATGAGGAGAC
1 CTAAATATTATTCGAAAGACTCAGGAAATTTACCAAAGACCCATTTTGAGAATCGATGAGGAGAC
21161 TCCATTTGAATTTTTTTATCCTTTTTTGTCTTTTCTCACTTGCCT
66 TCCATTTGAATTTTTTTATCCTTTTTTGTCTTTTCTCACTTGCCT
*
21206 CTAAATATTATTCGAAAGACTCAGGAAATTTACCAAAGACCCATTTTGAGAATCGATGAGGAGAT
1 CTAAATATTATTCGAAAGACTCAGGAAATTTACCAAAGACCCATTTTGAGAATCGATGAGGAGAC
21271 TCCATTTGAACTTTTTTTATCCTTTTTTGTCTTTTCTCACTTGCC
66 TCCATTTGAA-TTTTTTTATCCTTTTTTGTCTTTTCTCACTTGCC
21316 AAATTACTAA
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 71 0.68
111 34 0.32
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (110 bp):
CTAAATATTATTCGAAAGACTCAGGAAATTTACCAAAGACCCATTTTGAGAATCGATGAGGAGAC
TCCATTTGAATTTTTTTATCCTTTTTTGTCTTTTCTCACTTGCCT
Found at i:27169 original size:15 final size:15
Alignment explanation
Indices: 27145--27209 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
27135 CAAGGATGCT
* *
27145 TATCCACCACCGGGA
1 TATCCTCCACAGGGA
*
27160 TATCCTCCACAAGGA
1 TATCCTCCACAGGGA
*
27175 TATCCT---CAGGGT
1 TATCCTCCACAGGGA
*
27187 TATCCTCCTCAGGGA
1 TATCCTCCACAGGGA
27202 TATCCTCC
1 TATCCTCC
27210 GCAGTACGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
12 10 0.24
15 31 0.76
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (15 bp):
TATCCTCCACAGGGA
Found at i:28197 original size:19 final size:19
Alignment explanation
Indices: 28173--28209 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28163 CTTATCTGTA
*
28173 ACCGTTTCATCACCGTTTG
1 ACCGTTTCACCACCGTTTG
28192 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
28210 TAGGACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.35, G:0.14, T:0.35
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:28356 original size:33 final size:33
Alignment explanation
Indices: 28319--28386 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
28309 TTGTACAGTT
*
28319 GCCAAACAGTGTCAATCGCACCGTTACAACGAA
1 GCCAAACAGTGTCAATCGCACCGCTACAACGAA
28352 GCCAAACAGTGTCAATCGCACCGCTACAACGAA
1 GCCAAACAGTGTCAATCGCACCGCTACAACGAA
28385 GC
1 GC
28387 GTAAATCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.32, G:0.19, T:0.13
Consensus pattern (33 bp):
GCCAAACAGTGTCAATCGCACCGCTACAACGAA
Found at i:28483 original size:59 final size:59
Alignment explanation
Indices: 28391--28508 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
28381 CGAAGCGTAA
28391 ATCTTTATTTAAAATTTAAAGGTTAGCAAAAATTGCACAGCTATTACATTTGGAAGTTT
1 ATCTTTATTTAAAATTTAAAGGTTAGCAAAAATTGCACAGCTATTACATTTGGAAGTTT
28450 ATCTTTATTTAAAATTTAAAGGTTAGCAAAAATTGCACAGCTATTACATTTGGAAGTTT
1 ATCTTTATTTAAAATTTAAAGGTTAGCAAAAATTGCACAGCTATTACATTTGGAAGTTT
28509 TTGCGCTTTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (59 bp):
ATCTTTATTTAAAATTTAAAGGTTAGCAAAAATTGCACAGCTATTACATTTGGAAGTTT
Found at i:30550 original size:2 final size:2
Alignment explanation
Indices: 30545--30574 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30535 AGTATAATTA
30545 AT AT 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 AT AT
30575 TGGTATACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31810 original size:132 final size:131
Alignment explanation
Indices: 31674--31938 Score: 390
Period size: 131 Copynumber: 2.0 Consensus size: 131
31664 GTCATTTAAG
* * * * *
31674 AAATATATTTTAAAATTTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
1 AAATATATTTAAAAAATTCTAATATATATAAG-TTTTTAATTAAAATAGTAAAATGATAAAAATA
31739 AAATA-TGTATAAGGATATTAGATTTAATTAAATAAAAAAA-AGAGTTTTTAGTTGAGTAAAACT
65 AAATAGT-TATAAGGATATTAGATTTAATTAAATAAAAAAAGAG-GTTTTTAGTTGAGTAAAACT
31802 ATAA
128 ATAA
* *
31806 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTAATTAAAATAGTAAAATGGTAAAAATTA
1 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTAATTAAAATAGTAAAATGATAAAAATAA
* * * *
31871 AATAGTTATGAGGATATTATATTTAATTAAATAAAGATAGAGGTTTTTAGTTGAGTAAAACTATA
66 AATAGTTATAAGGATATTAGATTTAATTAAATAAAAAAAGAGGTTTTTAGTTGAGTAAAACTATA
31936 A
131 A
31937 AA
1 AA
31939 GTCTAATGGC
Statistics
Matches: 120, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
131 88 0.73
132 32 0.27
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.38
Consensus pattern (131 bp):
AAATATATTTAAAAAATTCTAATATATATAAGTTTTTAATTAAAATAGTAAAATGATAAAAATAA
AATAGTTATAAGGATATTAGATTTAATTAAATAAAAAAAGAGGTTTTTAGTTGAGTAAAACTATA
A
Found at i:35456 original size:1 final size:1
Alignment explanation
Indices: 35450--35482 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
35440 CAATTTTATG
35450 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35483 AAATTTACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:36380 original size:2 final size:2
Alignment explanation
Indices: 36368--36404 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
36358 CCAGGTTGGC
*
36368 GA GA CA GA GA GA GA GA -A GA GA GA GA GA -A GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
36405 CCGTTTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:36389 original size:9 final size:8
Alignment explanation
Indices: 36368--36404 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
36358 CCAGGTTGGC
*
36368 GAGACAGA
1 GAGAGAGA
36376 GAGAGAGA
1 GAGAGAGA
36384 -AGAGAGA
1 GAGAGAGA
36391 GAGA-AGA
1 GAGAGAGA
36398 GAGAGAG
1 GAGAGAG
36405 CCGTTTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
7 14 0.54
8 12 0.46
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (8 bp):
GAGAGAGA
Found at i:36391 original size:13 final size:11
Alignment explanation
Indices: 36368--36404 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
36358 CCAGGTTGGC
36368 GAGACAGAGAGA
1 GAGA-AGAGAGA
36380 GAGAAGAGAGA
1 GAGAAGAGAGA
36391 GAGAAGAGAGA
1 GAGAAGAGAGA
36402 GAG
1 GAG
36405 CCGTTTGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 21 0.84
12 4 0.16
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (11 bp):
GAGAAGAGAGA
Found at i:48791 original size:134 final size:134
Alignment explanation
Indices: 48551--48813 Score: 447
Period size: 134 Copynumber: 2.0 Consensus size: 134
48541 ATCCCCTGTT
*
48551 TCTTTTTTGTTCTCTATATCACAATTCCAAATAAATTATGAGAGAATATGGCCATTAAGTCAACA
1 TCTTTTTTGTTCTCTATATAACAATTCCAAATAAATTATGAGAGAATATGGCCATTAAGTCAACA
* * *
48616 TAAAAAAGTACAATAAATAAAACCTTTCTAACTTCAGATCTACTTGCTTTCTTAAAAGATTCCTC
66 TAAAAAAGAACAATAAATAAAACCTTCCTAAATTCAGATCTACTTGCTTTCTTAAAAGATTCCTC
48681 CAAC
131 CAAC
*
48685 TCTTTTTTGTTCTCTATATAACAATTCCAAATGAATTATGAGAGAATATGGCCATTAAGTCAACA
1 TCTTTTTTGTTCTCTATATAACAATTCCAAATAAATTATGAGAGAATATGGCCATTAAGTCAACA
* *
48750 TAAAAAGGCAAC-ATAAATAAAACCTTCCTAAATTCAGATCTACTTGCTTTCTTACAAGATTCCT
66 TAAAAAAG-AACAATAAATAAAACCTTCCTAAATTCAGATCTACTTGCTTTCTTAAAAGATTCCT
48814 GTGCGGTGAG
Statistics
Matches: 121, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
134 119 0.98
135 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (134 bp):
TCTTTTTTGTTCTCTATATAACAATTCCAAATAAATTATGAGAGAATATGGCCATTAAGTCAACA
TAAAAAAGAACAATAAATAAAACCTTCCTAAATTCAGATCTACTTGCTTTCTTAAAAGATTCCTC
CAAC
Found at i:52436 original size:22 final size:22
Alignment explanation
Indices: 52411--52455 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
52401 CGGGAGTCCT
52411 AGTAAATGTTAAATAAATAGTG
1 AGTAAATGTTAAATAAATAGTG
52433 AGTAAATGTTAAATAAATAGTG
1 AGTAAATGTTAAATAAATAGTG
52455 A
1 A
52456 ACATGATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (22 bp):
AGTAAATGTTAAATAAATAGTG
Found at i:52580 original size:36 final size:36
Alignment explanation
Indices: 52540--52611 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
52530 AATTCTCGGA
52540 ATGCCCCAGCCCCTGTTTCCCTTTTGTTCTCTATAT
1 ATGCCCCAGCCCCTGTTTCCCTTTTGTTCTCTATAT
**
52576 ATGCCCCAGCCCCTGTTTCTTTTTTGTTCTCTATAT
1 ATGCCCCAGCCCCTGTTTCCCTTTTGTTCTCTATAT
52612 CACAATTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.11, C:0.33, G:0.11, T:0.44
Consensus pattern (36 bp):
ATGCCCCAGCCCCTGTTTCCCTTTTGTTCTCTATAT
Found at i:52825 original size:134 final size:134
Alignment explanation
Indices: 52585--52854 Score: 459
Period size: 134 Copynumber: 2.0 Consensus size: 134
52575 TATGCCCCAG
* * *
52585 CCCCTGTTTCTTTTTTGTTCTCTATATCACAATTCCAATTAAATTATGAGAGAATATGGCCATTA
1 CCCCTGTTTCTTTTTTCTTCTCTATATCACAATTCCAAATAAATTATGAGAGAATATGGCCACTA
* * *
52650 AGTCAACATAAAAAGGTACAATAAATAAAACCTTTCTAACTTCAGATCTACTTGAATTCTTACAA
66 AGTCAACATAAAAAGGTAAAATAAATAAAACCTTCCCAACTTCAGATCTACTTGAATTCTTACAA
52715 GATT
131 GATT
*
52719 CCCCTGTTTCTTTTTTCTTCTCTATATCACAATTCCAAATGAATTATGAGAGAATATGGCCACTA
1 CCCCTGTTTCTTTTTTCTTCTCTATATCACAATTCCAAATAAATTATGAGAGAATATGGCCACTA
**
52784 AGTCAACATAAAAAGGTAAAATAAATAAAACCTTCCCAACTTCAGATCTACTTGCTTTCTTACAA
66 AGTCAACATAAAAAGGTAAAATAAATAAAACCTTCCCAACTTCAGATCTACTTGAATTCTTACAA
52849 GATT
131 GATT
52853 CC
1 CC
52855 TGTGCGGTGA
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
134 127 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (134 bp):
CCCCTGTTTCTTTTTTCTTCTCTATATCACAATTCCAAATAAATTATGAGAGAATATGGCCACTA
AGTCAACATAAAAAGGTAAAATAAATAAAACCTTCCCAACTTCAGATCTACTTGAATTCTTACAA
GATT
Found at i:77679 original size:73 final size:73
Alignment explanation
Indices: 77560--77715 Score: 269
Period size: 73 Copynumber: 2.1 Consensus size: 73
77550 CAAATTAACT
* *
77560 ATTGA-ACTTCTAAAATTGTCAATTGTAGACCTGAACTTGTAAAAAATGGACAAATTAGCTTCTT
1 ATTGATAC-TCTAAAATTGTCAATTGTAGACCCGAACTAGTAAAAAATGGACAAATTAGCTTCTT
77624 TGGACGGGA
65 TGGACGGGA
*
77633 ATTGATACTCTAAAATTGTCAATTGTAGACCCGAACTAGTAAAAAATGGACAAATTAGCTTTTTT
1 ATTGATACTCTAAAATTGTCAATTGTAGACCCGAACTAGTAAAAAATGGACAAATTAGCTTCTTT
77698 GGACGGGA
66 GGACGGGA
77706 ATTGATACTC
1 ATTGATACTC
77716 CTTGATTAAA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
73 77 0.97
74 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (73 bp):
ATTGATACTCTAAAATTGTCAATTGTAGACCCGAACTAGTAAAAAATGGACAAATTAGCTTCTTT
GGACGGGA
Found at i:78997 original size:60 final size:60
Alignment explanation
Indices: 78919--79063 Score: 236
Period size: 60 Copynumber: 2.4 Consensus size: 60
78909 TCCAAAAATA
* * *
78919 CTAACTTGTCAGTTTTTTACAAGTTCAGGAGTGCAAGTAGCAATTTTGGAAATTCAAGTG
1 CTAATTTGTCAGATTTTTACAAGTTCAGGAGTGCAAGTAGCAACTTTGGAAATTCAAGTG
*
78979 CTAATTTGTCAGATTTTTACAAGTTCAGGAGTGCAATTAGCAACTTTGGAAATTCAAGTG
1 CTAATTTGTCAGATTTTTACAAGTTCAGGAGTGCAAGTAGCAACTTTGGAAATTCAAGTG
* *
79039 CTAATTTGTCATATTTTTAAAAGTT
1 CTAATTTGTCAGATTTTTACAAGTT
79064 TAGGGGGCCG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 79 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (60 bp):
CTAATTTGTCAGATTTTTACAAGTTCAGGAGTGCAAGTAGCAACTTTGGAAATTCAAGTG
Found at i:81279 original size:27 final size:27
Alignment explanation
Indices: 81230--81284 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
81220 ACGATAAGTA
* *
81230 AATCCGAACAATTTGTAAATTCAATAG
1 AATCCGAACAAGTTATAAATTCAATAG
*
81257 AATCCGAACAAGTTATAACTTCAATAG
1 AATCCGAACAAGTTATAAATTCAATAG
81284 A
1 A
81285 TTAGTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (27 bp):
AATCCGAACAAGTTATAAATTCAATAG
Found at i:81298 original size:17 final size:17
Alignment explanation
Indices: 81276--81312 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
81266 AAGTTATAAC
81276 TTCAATAGATTAGTAAA
1 TTCAATAGATTAGTAAA
*
81293 TTCAATAGATTTGTAAA
1 TTCAATAGATTAGTAAA
81310 TTC
1 TTC
81313 TCCAGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (17 bp):
TTCAATAGATTAGTAAA
Found at i:109295 original size:28 final size:28
Alignment explanation
Indices: 109255--109329 Score: 150
Period size: 28 Copynumber: 2.7 Consensus size: 28
109245 GATTGTTGTG
109255 AAATTTAACATTTTTTTGTCCACCAAAA
1 AAATTTAACATTTTTTTGTCCACCAAAA
109283 AAATTTAACATTTTTTTGTCCACCAAAA
1 AAATTTAACATTTTTTTGTCCACCAAAA
109311 AAATTTAACATTTTTTTGT
1 AAATTTAACATTTTTTTGT
109330 GTTTTTTCCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (28 bp):
AAATTTAACATTTTTTTGTCCACCAAAA
Found at i:109449 original size:2 final size:2
Alignment explanation
Indices: 109442--109467 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
109432 CAACTATTAA
109442 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
109468 TATGAAAGTT
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:109721 original size:21 final size:21
Alignment explanation
Indices: 109696--109739 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
109686 CACACTTTCA
*
109696 AATTCAATAGAAACAAACTTT
1 AATTCAATAGAAACAAACGTT
109717 AATTCAATAGAAACAAACGTT
1 AATTCAATAGAAACAAACGTT
109738 AA
1 AA
109740 AACGATGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.25
Consensus pattern (21 bp):
AATTCAATAGAAACAAACGTT
Found at i:109768 original size:25 final size:25
Alignment explanation
Indices: 109740--109788 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
109730 CAAACGTTAA
*
109740 AACGATGAGAATCCAAATTCAGGAC
1 AACGATAAGAATCCAAATTCAGGAC
109765 AACGATAAGAATCCAAATTCAGGA
1 AACGATAAGAATCCAAATTCAGGA
109789 TATTTATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.16
Consensus pattern (25 bp):
AACGATAAGAATCCAAATTCAGGAC
Found at i:111230 original size:21 final size:21
Alignment explanation
Indices: 111205--111248 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
111195 CACACTTTCA
*
111205 AATTCAATAGAAACAAACTTT
1 AATTCAATAGAAACAAACGTT
111226 AATTCAATAGAAACAAACGTT
1 AATTCAATAGAAACAAACGTT
111247 AA
1 AA
111249 AACGATGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.25
Consensus pattern (21 bp):
AATTCAATAGAAACAAACGTT
Found at i:111277 original size:25 final size:25
Alignment explanation
Indices: 111249--111297 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
111239 CAAACGTTAA
*
111249 AACGATGAGAATCCAAATTCAGGAC
1 AACGATAAGAATCCAAATTCAGGAC
*
111274 AACGATAAGAATCTAAATTCAGGA
1 AACGATAAGAATCCAAATTCAGGA
111298 TATTTATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.18
Consensus pattern (25 bp):
AACGATAAGAATCCAAATTCAGGAC
Found at i:115190 original size:3 final size:3
Alignment explanation
Indices: 115182--115219 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
115172 GAAGAGTGTG
115182 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
115220 TGATGATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:116322 original size:29 final size:29
Alignment explanation
Indices: 116277--116336 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
116267 AAAACCTAGT
116277 TTCTGTTGTTATCAAGGTTTAATGTTTGA
1 TTCTGTTGTTATCAAGGTTTAATGTTTGA
* *
116306 TTCTGTTTTTATGAAGGTTTAATGTTTGA
1 TTCTGTTGTTATCAAGGTTTAATGTTTGA
116335 TT
1 TT
116337 GTAGATATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (29 bp):
TTCTGTTGTTATCAAGGTTTAATGTTTGA
Found at i:117302 original size:28 final size:30
Alignment explanation
Indices: 117262--117326 Score: 116
Period size: 28 Copynumber: 2.2 Consensus size: 30
117252 TTATTAGCCT
117262 TTTTGCCCCTGAACTT-CAAA-TCAGGACA
1 TTTTGCCCCTGAACTTCCAAATTCAGGACA
117290 TTTTGCCCCTGAACTTCCAAATTCAGGACA
1 TTTTGCCCCTGAACTTCCAAATTCAGGACA
117320 TTTTGCC
1 TTTTGCC
117327 GGTAAAATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 16 0.46
29 4 0.11
30 15 0.43
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (30 bp):
TTTTGCCCCTGAACTTCCAAATTCAGGACA
Found at i:130207 original size:17 final size:17
Alignment explanation
Indices: 130187--130219 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
130177 TCTTTAGTTT
130187 TTTTTTTTCTTTTTGAA
1 TTTTTTTTCTTTTTGAA
*
130204 TTTTTTTTTTTTTTGA
1 TTTTTTTTCTTTTTGA
130220 GAAATGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTTTTCTTTTTGAA
Found at i:130209 original size:18 final size:17
Alignment explanation
Indices: 130186--130219 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
130176 ATCTTTAGTT
130186 TTTTTTTTTCTTTTTGAA
1 TTTTTTTTT-TTTTTGAA
130204 TTTTTTTTTTTTTTGA
1 TTTTTTTTTTTTTTGA
130220 GAAATGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTTTTTGAA
Found at i:137496 original size:35 final size:35
Alignment explanation
Indices: 137456--137530 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
137446 AGTTCGTTTA
*
137456 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
137491 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
137526 TGTTC
1 TGTTC
137531 GTTTATATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (35 bp):
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
Found at i:138146 original size:59 final size:58
Alignment explanation
Indices: 137976--138207 Score: 412
Period size: 58 Copynumber: 4.0 Consensus size: 58
137966 GATTTGGCAC
137976 CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATCAAAAAAG
1 CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATCAAAAAAG
138034 CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATCAAAAAAG
1 CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATCAAAAAAG
*
138092 CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAAACCATCAAAAAAC
1 CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTG-AAAAAACCATCAAAAAAG
* *
138151 CAGATATCCGGAGGTGTGGAAAGAGCT-CATGTTAAAAGTGAAAAAACCATAAAAAAA
1 CAGATATCCGGAGGTGTGGAAAGAGCTGC-TGTGAAAAGTGAAAAAACCATCAAAAAA
138208 AGTTTATTTC
Statistics
Matches: 169, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
58 115 0.68
59 54 0.32
ACGTcount: A:0.44, C:0.14, G:0.26, T:0.16
Consensus pattern (58 bp):
CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATCAAAAAAG
Found at i:138190 original size:117 final size:116
Alignment explanation
Indices: 137976--138207 Score: 412
Period size: 117 Copynumber: 2.0 Consensus size: 116
137966 GATTTGGCAC
*
137976 CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATCAAAAAAGCAGATAT
1 CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATCAAAAAACCAGATAT
*
138041 CCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATCAAAAAAG
66 CCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATAAAAAAAG
138092 CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAAACCATCAAAAAACCAGATA
1 CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTG-AAAAAACCATCAAAAAACCAGATA
*
138157 TCCGGAGGTGTGGAAAGAGCT-CATGTTAAAAGTGAAAAAACCATAAAAAAA
65 TCCGGAGGTGTGGAAAGAGCTGC-TGTGAAAAGTGAAAAAACCATAAAAAAA
138208 AGTTTATTTC
Statistics
Matches: 111, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
116 41 0.37
117 70 0.63
ACGTcount: A:0.44, C:0.14, G:0.26, T:0.16
Consensus pattern (116 bp):
CAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATCAAAAAACCAGATAT
CCGGAGGTGTGGAAAGAGCTGCTGTGAAAAGTGAAAAAACCATAAAAAAAG
Done.