Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007770.1 Corchorus capsularis cultivar CVL-1 contig07791, 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: 99915
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:1585 original size:78 final size:78
Alignment explanation
Indices: 1456--1610 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 78
1446 AAAGGAGAGG
* *
1456 ACTAACTCCTATTGTGTAGTCAATTTCCGCAATATCATTTGGTGAGTGCAGCGCTAACCATGCCT
1 ACTAACTCCTATTGTGTAGTCAATTTCCGCAACATCATTTGGTGAGTGCAGCGCCAACCATGCCT
1521 GAAGTGAACTAGA
66 GAAGTGAACTAGA
*
1534 ACTAACTCCTATTGTGTAGTCAATTTCCGCAACATCATTTGGTGAGTGCAGCGCCAACCCTGCCT
1 ACTAACTCCTATTGTGTAGTCAATTTCCGCAACATCATTTGGTGAGTGCAGCGCCAACCATGCCT
1599 GAAGTGAACTAG
66 GAAGTGAACTAG
1611 GACACGATTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (78 bp):
ACTAACTCCTATTGTGTAGTCAATTTCCGCAACATCATTTGGTGAGTGCAGCGCCAACCATGCCT
GAAGTGAACTAGA
Found at i:6002 original size:11 final size:11
Alignment explanation
Indices: 5959--5996 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5949 TTCCTATATA
*
5959 AAATAAATTAT
1 AAATTAATTAT
5970 CAAA-TAATTAT
1 -AAATTAATTAT
5981 AAATTAATTAT
1 AAATTAATTAT
5992 AAATT
1 AAATT
5997 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:26189 original size:22 final size:22
Alignment explanation
Indices: 26161--26202 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
26151 ACATGTGGCA
26161 TGCCACATGTACCAAAAAGTCG
1 TGCCACATGTACCAAAAAGTCG
26183 TGCCACATGTACCAAAAAGT
1 TGCCACATGTACCAAAAAGT
26203 GACACATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (22 bp):
TGCCACATGTACCAAAAAGTCG
Found at i:26210 original size:19 final size:20
Alignment explanation
Indices: 26164--26211 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
26154 TGTGGCATGC
*
26164 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
26186 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
26205 CACATGT
1 CACATGT
26212 CACGCCGCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:26261 original size:31 final size:31
Alignment explanation
Indices: 26183--26281 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
26173 CAAAAAGTCG
* *
26183 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* * *
26214 CGCCGCGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** * *
26245 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
26276 TGCCAC
1 TGCCAC
26282 GTGCACAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:45803 original size:14 final size:14
Alignment explanation
Indices: 45784--45810 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45774 TAATCTCATT
45784 GTTTGTTTTCTTAA
1 GTTTGTTTTCTTAA
45798 GTTTGTTTTCTTA
1 GTTTGTTTTCTTA
45811 CATATCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.07, G:0.15, T:0.67
Consensus pattern (14 bp):
GTTTGTTTTCTTAA
Found at i:56509 original size:61 final size:60
Alignment explanation
Indices: 56400--56520 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 60
56390 ATAGCTAGGT
*
56400 TATAACATTTCCATTACATGTCACATCTCTGTGAGAAAATGGTAGTATGTGATTTCTACAA
1 TATAACATTTCCATTACATGTCACATCTCTGTAAGAAAAT-GTAGTATGTGATTTCTACAA
* *
56461 TATAACATTTCCATTATTGCATGTCACATCTCTGTAAG-GAAT-TGGTATGTGATTTCTACA
1 TATAACATTTCCATTA---CATGTCACATCTCTGTAAGAAAATGTAGTATGTGATTTCTACA
56521 GCTGATCTAC
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
61 33 0.61
63 3 0.06
64 18 0.33
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (60 bp):
TATAACATTTCCATTACATGTCACATCTCTGTAAGAAAATGTAGTATGTGATTTCTACAA
Found at i:58057 original size:10 final size:9
Alignment explanation
Indices: 58035--58084 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 9
58025 TATCTTTTTC
58035 TTTTTTC-T
1 TTTTTTCTT
*
58043 GTTTTTCTGT
1 TTTTTTCT-T
58053 TTTTTTC-T
1 TTTTTTCTT
58061 TTTTTTCTTT
1 TTTTTTC-TT
58071 TTTTTTCTT
1 TTTTTTCTT
58080 TTTTT
1 TTTTT
58085 ATGCCCTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
8 14 0.39
9 7 0.19
10 15 0.42
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.86
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:58063 original size:8 final size:8
Alignment explanation
Indices: 58029--58084 Score: 60
Period size: 8 Copynumber: 6.6 Consensus size: 8
58019 CCAGGTTATC
58029 TTTTTC-T
1 TTTTTCTT
58036 TTTTTCTGT
1 TTTTTCT-T
*
58045 TTTTCTGTT
1 TTTT-TCTT
58054 TTTTTCTT
1 TTTTTCTT
58062 TTTTTCTTTT
1 TTTTTC--TT
58072 TTTTTCTT
1 TTTTTCTT
58080 TTTTT
1 TTTTT
58085 ATGCCCTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 6 0.14
8 16 0.38
9 10 0.24
10 10 0.24
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:58084 original size:18 final size:18
Alignment explanation
Indices: 58035--58084 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
58025 TATCTTTTTC
*
58035 TTTTTTCTGTTTTTCTGT
1 TTTTTTCTTTTTTTCTGT
*
58053 TTTTTTCTTTTTTTCTTT
1 TTTTTTCTTTTTTTCTGT
58071 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
58085 ATGCCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.86
Consensus pattern (18 bp):
TTTTTTCTTTTTTTCTGT
Found at i:59729 original size:30 final size:29
Alignment explanation
Indices: 59633--59733 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
59623 TAATCTACCA
** * *
59633 TTTTGCCCCCTGAACTTGTAGCGTTTAGACG
1 TTTTGCCCCCTGAACTTCAATC--TTGGACG
* *
59664 TTTTGCCCCCCGAACTTCAATCTTGGACA
1 TTTTGCCCCCTGAACTTCAATCTTGGACG
*
59693 TTTTGCCCCCTGAACTTCAATTTTGGGACG
1 TTTTGCCCCCTGAACTTCAATCTT-GGACG
59723 TTTTGCCCCCT
1 TTTTGCCCCCT
59734 CAACCTAACG
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
29 27 0.45
30 15 0.25
31 18 0.30
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.36
Consensus pattern (29 bp):
TTTTGCCCCCTGAACTTCAATCTTGGACG
Found at i:59848 original size:29 final size:30
Alignment explanation
Indices: 59785--59864 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
59775 CGGAGCCATT
59785 AAGTTCAGAGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGAGGGCAAAACGTCCCAAAATTG
* *
59815 AAGTTCA-ATGGGCAAAATGT-CCAAGATTG
1 AAGTTCAGA-GGGCAAAACGTCCCAAAATTG
* *
59844 AAGTTCGGGGGGCAAAACGTC
1 AAGTTCAGAGGGCAAAACGTC
59865 TAAACGTTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
29 25 0.60
30 17 0.40
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (30 bp):
AAGTTCAGAGGGCAAAACGTCCCAAAATTG
Found at i:60346 original size:15 final size:14
Alignment explanation
Indices: 60326--60362 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
60316 GTTGTTGTTG
60326 TTTGTTTTTTTTTGT
1 TTTGTTTTTTTTT-T
60341 TTTGTTTTTTTTTT
1 TTTGTTTTTTTTTT
60355 TTT-TTTTT
1 TTTGTTTTT
60363 AATTTGGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 4 0.18
15 13 0.59
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (14 bp):
TTTGTTTTTTTTTT
Found at i:60362 original size:19 final size:19
Alignment explanation
Indices: 60317--60360 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
60307 GAATCTTGAG
60317 TTGTTGTTGTTTGTTTTTTT
1 TTGTT-TTGTTTGTTTTTTT
60337 TTGTTTTGTTT-TTTTTTT
1 TTGTTTTGTTTGTTTTTTT
60355 TT-TTTT
1 TTGTTTT
60361 TTAATTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 9 0.38
19 6 0.25
20 5 0.21
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (19 bp):
TTGTTTTGTTTGTTTTTTT
Found at i:93069 original size:322 final size:320
Alignment explanation
Indices: 92472--93072 Score: 723
Period size: 322 Copynumber: 1.9 Consensus size: 320
92462 AGAAAATTGT
* *
92472 GATGGTTACTACACGATTTCGCCAAAACTGAACCGAATTTTTTTTTCTTAATTTTTGGCCACAAT
1 GATGGTTACAACACGATTTCGCCAAAACTGAACCGAATTTTTTTTTCTTAAATTTTGGCCACAAT
* * *
92537 ACTCGTAAAAAATATATAATTCAGCGCCAAAAAGATTTGAGGGCTTTTCTGCTTCTAATATAATT
66 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTTGAGGGCTTTTCAGCTTCTAATATAATT
*** * ** *
92602 TTTCCTTGTTTTTTTTTTTCAGAATCAATTTCTATTTAAATCGAAACCGGTTTCTGATGCTTGTA
131 TTTCC-----TTTTTTTTTCAGAATCAATTTCTAAAAAAATCGAAACAGGAATATGATGCTTGTA
* *
92667 GAAATAAATCCTTAAATCAAATGTGGTTGAGATTTGGTTAGATAAATATAGATATTTAATGGAGT
191 GAAATAAATCCTTAAATCAAATGTGGTTGAGATTTGGTTAGATAAATATAAATATTTAATGGAGC
* *
92732 ATTGCTTCAAAAAATCATGTGAAACTGAGTCGGGGCCTCGATACACTTTTTTTACCAAAAACCGA
256 ATTGATGCAAAAAATCATGTGAAACTGAGTCGGGGCCTCGATACACTTTTTTTACCAAAAACCGA
***
92797 GATGGTTACAACACGATTTCGCCAAAACTGATTGGAAAATTTTTTTTTCTCTCAAATTTTGGCCA
1 GATGGTTACAACACGATTTCGCCAAAACTGAACCG--AATTTTTTTTTCT-T-AAATTTTGGCCA
* * * * *
92862 TAATACTCATAAAAAATATATAATTCAATGCCAGAAGGA-TTGAAGGGCTTTTCAGCTTCTAATG
62 CAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTTG-AGGGCTTTTCAGCTTCTAATA
* *
92926 TCA-TTTTCC-TTTTTTTTCAGAATTAATTT-TCAAAAAAATCGAAACAGGAATATGATGCTTGT
126 TAATTTTTCCTTTTTTTTTCAGAATCAATTTCT-AAAAAAATCGAAACAGGAATATGATGCTTGT
* * * *
92988 A-AAATCAAATCTTTAAATCCATTGT-GTCTGAGATTCT-GTTAGATGAATATAAATATTTCAA-
190 AGAAAT-AAATCCTTAAATCAAATGTGGT-TGAGATT-TGGTTAGATAAATATAAATATTT-AAT
* *
93049 GGAGCCTTGATGCTAAAAATCATG
251 GGAGCATTGATGCAAAAAATCATG
93073 CAAAACTAGG
Statistics
Matches: 234, Mismatches: 32, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
321 7 0.03
322 105 0.45
323 3 0.01
325 31 0.13
327 13 0.06
328 10 0.04
329 65 0.28
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (320 bp):
GATGGTTACAACACGATTTCGCCAAAACTGAACCGAATTTTTTTTTCTTAAATTTTGGCCACAAT
ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTTGAGGGCTTTTCAGCTTCTAATATAATT
TTTCCTTTTTTTTTCAGAATCAATTTCTAAAAAAATCGAAACAGGAATATGATGCTTGTAGAAAT
AAATCCTTAAATCAAATGTGGTTGAGATTTGGTTAGATAAATATAAATATTTAATGGAGCATTGA
TGCAAAAAATCATGTGAAACTGAGTCGGGGCCTCGATACACTTTTTTTACCAAAAACCGA
Found at i:94341 original size:328 final size:325
Alignment explanation
Indices: 93159--94400 Score: 1522
Period size: 328 Copynumber: 3.8 Consensus size: 325
93149 CCTGAAAAAA
** *
93159 TTTGGCCACAATACAT-TATAAAAATATATAATTCAAC-TTAAAAAAAATTGAAGTGCATTTTAC
1 TTTGGCCACAATAC-TCTATAAAAATATATAATTCAACGCCAAAAAAAATTGAAGTGCATTTCAC
* * * * *
93222 ACATTCAATATCATTTTTCCATTTTTTTTTCAAAATTAATTTCTAATTAAATCGTAACGAGTTTC
65 GCTTTCAATATCATTTTTCCA--TTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAGTTTC
* *
93287 TTAAACTCGTAGAAACAAATCCATAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATA
128 TAAAACTCGTAGAAACAAATCCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATA
* * * * * **
93352 TTTTAATGAGTCTTGGCGCCGAAAATCATGCAAAATTGAGTCGGGTCCCCGGAACGTATTTTTAC
193 TTTCAACGAGTCTTGGCGCCGAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAC
* * * * *
93417 CCAAAAATCAT-G-ACACGATTTCGGCTAAAATTTCGCAAAAACTGACCTGAAAAACTTTTCCTC
258 CAAAAAACCGTGGTACACGATTTCGGCTAAAATTTCGAAAAAACTGACC-GAAAAAATTTTCCTC
93480 AATT
322 AATT
* * * *
93484 TTTGGCCACAATAATCTATAAAAATAAATAATTCAGCACC-AAAAAAA-TGAAGTGCATTTCACG
1 TTTGGCCACAATACTCTATAAAAATATATAATTCAACGCCAAAAAAAATTGAAGTGCATTTCACG
* * *
93547 CTTTCAATATCAGTTTTCCATTTTTTTCCAAATTAATTTCTGATGAAATCGAAACCAGTTTCTAA
66 CTTTCAATATCATTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAGTTTCTAA
** *
93612 AACTCGTAG---CAAATCCTTAAATCCAATGTATTTGAATTTTGTTTAGAT--A-ATAGATATTT
131 AACTCGTAGAAACAAATCCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATATTT
* * * * * *
93671 TAACGAGTCTTGCCGCCGAAAATCATGCAAAACAGAGCCGGTGCCTCGGAACGCGTTTTTAGCAA
196 CAACGAGTCTTGGCGCCGAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTACCAA
* * * *
93736 AAAACATGATGATTAGTACACGATTT-TGATAAAAATTTTGCAAAAAACTGACACGAAAAAATTT
261 AAAAC-CG-TG----GTACACGATTTCGGCT-AAAATTTCG-AAAAAACTGAC-CGAAAAAATTT
93800 TCCTCAATT
317 TCCTCAATT
* *
93809 TTTGGCCACAATACTCTATAAAAATATATAATTCAATGCTAAAAAAAATTGAAGTGCATTTCACG
1 TTTGGCCACAATACTCTATAAAAATATATAATTCAACGCCAAAAAAAATTGAAGTGCATTTCACG
* * * *
93874 CTTTTAATATCGTTTTTCCA-TTTTTTCCAAATTAATTTCTAATTAAATCGAAACCCGTTTCAAA
66 CTTTCAATATCATTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAGTTTCTAA
* * *
93938 AACTCCTAGAAACAAATCCTTAAATCCAATGTGGTTGAAATTTGTTTAGATGAATATAGATATAT
131 AACTCGTAGAAACAAATCCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATATTT
* *
94003 CAACGAGTCTTGACGCCGAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAACAA
196 CAACGAGTCTTGGCGCCGAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTACCAA
* * * * ** *
94068 AAAACCGTGCCGTACATGATTTCGGCTAAAATTTCGTAATAACTGACCCAAAATTTTTTTTCTCA
261 AAAACCGTG--GTACACGATTTCGGCTAAAATTTCGAAAAAACTGACCGAAAA-AATTTTCCTCA
94133 ATT
323 ATT
* *
94136 TTTGGCTACAATACTCTATAAAAATATATAATTCAGCGCCAAAAAAAATTGAAGTGCATTTCACG
1 TTTGGCCACAATACTCTATAAAAATATATAATTCAACGCCAAAAAAAATTGAAGTGCATTTCACG
* * * ** * *
94201 CTTTTATTATCATTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAAACGAAAAGAGTTTTTGA
66 CTTTCAATATCATTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAGTTTCTAA
* * *
94266 AACTCGTAGAAACAAATCCTTAAATCCAGTGTGCTTGAAATTTGTTCAGATAAATATAGATATTT
131 AACTCGTAGAAACAAATCCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATATTT
** * ** * *
94331 CAGTGAGTCTTGGCACCGAAAATCATTAAAAAATGAGTCGGGGCCCCGGAACGCGTTTTTAGCCA
196 CAACGAGTCTTGGCGCCGAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTA-CCA
94396 AAAAA
260 AAAAA
94401 TCATGATCGT
Statistics
Matches: 788, Mismatches: 104, Indels: 46
0.84 0.11 0.05
Matches are distributed among these distances:
316 67 0.09
317 1 0.00
318 1 0.00
319 35 0.04
322 48 0.06
323 3 0.00
324 50 0.06
325 101 0.13
326 61 0.08
327 132 0.17
328 167 0.21
329 45 0.06
330 2 0.00
331 2 0.00
332 73 0.09
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (325 bp):
TTTGGCCACAATACTCTATAAAAATATATAATTCAACGCCAAAAAAAATTGAAGTGCATTTCACG
CTTTCAATATCATTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAGTTTCTAA
AACTCGTAGAAACAAATCCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATATTT
CAACGAGTCTTGGCGCCGAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTACCAA
AAAACCGTGGTACACGATTTCGGCTAAAATTTCGAAAAAACTGACCGAAAAAATTTTCCTCAATT
Found at i:95349 original size:18 final size:17
Alignment explanation
Indices: 95326--95361 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
95316 CTCAACCTAA
95326 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
95344 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
95361 A
1 A
95362 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:95990 original size:19 final size:18
Alignment explanation
Indices: 95956--95993 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
95946 CTTGAAATAT
95956 TTCTTCAATGATCTTCAA
1 TTCTTCAATGATCTTCAA
*
95974 TTCTTCAAATTATCTTCAA
1 TTCTTC-AATGATCTTCAA
95993 T
1 T
95994 AAATCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (18 bp):
TTCTTCAATGATCTTCAA
Found at i:97592 original size:21 final size:21
Alignment explanation
Indices: 97567--97607 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
97557 CAATCAAGCA
97567 AATCA-AGCAATTCAAAGCATC
1 AATCATAGC-ATTCAAAGCATC
*
97588 AATCATAGCATTCATAGCAT
1 AATCATAGCATTCAAAGCAT
97608 ATGAATCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (21 bp):
AATCATAGCATTCAAAGCATC
Done.