Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010245.1 Corchorus capsularis cultivar CVL-1 contig10266, 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: 41741
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3094 original size:61 final size:61
Alignment explanation
Indices: 3026--3153 Score: 220
Period size: 61 Copynumber: 2.1 Consensus size: 61
3016 ATTTTTACCT
* *
3026 AAAAACCATGATGCCAAAAATGACCCGAAACATTTTTCCTCAATTTTTGGAAAAAATACTC
1 AAAAACCATGATGCCAAAAATGACCCGAAACATGTTTCCTCAATTTTTAGAAAAAATACTC
*
3087 AAAAACCATGATGCCAAAAATGACCCGAAAGATGTTTCCTCAATTTTTAGAAAAAATACTC
1 AAAAACCATGATGCCAAAAATGACCCGAAACATGTTTCCTCAATTTTTAGAAAAAATACTC
3148 ATAAAA
1 A-AAAA
3154 TATATATAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
61 59 0.94
62 4 0.06
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (61 bp):
AAAAACCATGATGCCAAAAATGACCCGAAACATGTTTCCTCAATTTTTAGAAAAAATACTC
Found at i:5323 original size:305 final size:305
Alignment explanation
Indices: 4789--5357 Score: 677
Period size: 305 Copynumber: 1.9 Consensus size: 305
4779 AATCAACGCC
* * * *
4789 AAAAAGATTGAAGGGCCTTTAACGCTTTTAATATCGTTTTTCATATTTTTATGATTTAATTTTTA
1 AAAAAGATTGAAGGGCCTTTAACACTTTTAATATCGTTTTTCATATTTTTATAAATTAATTTCTA
* * * * *
4854 ATTAAATCGAAACAAGAATCAGATGCTCGTAAAAACAAATCCTTAAACGCAATGTGGTTAAAATT
66 ATTAAATCAAAACAAGAATCAGAAGCTCGTAAAAACAAATCATTAAACGCAATGTAGCTAAAATT
* * * * * * * *
4919 TTATTAGATGAATATAGATATTTTAAGGAGTTTCAGTTCCAAAAATTATGCAAAACTGAGTCGGG
131 TGATTAGATAAATATAGATATCTCAAGGAGTTTCAGTTCAAAAAATCATGCAAAACTAAGCCGGG
* *
4984 CCCCGAAACACGTTTTTAGCCAAAAATCGTGATGGTTAGTACATAATATT-GGCTCAAATTTTGC
196 CCCCGAAACACGTTTTTAGCCAAAAATCGTGATGGTTAGTACACAAT-TTCGGCTAAAATTTTGC
5048 AAAAATTTATGATAAAATACTCATAAAAAATATATAATTTAATTCA
260 AAAAATTTATGATAAAATACTCATAAAAAATATATAATTTAATTCA
* * * * * *
5094 AAAAATATTGGAGGGCTTTTCACACTTTTAATATTG-TTTTCATATTTTTTCTAAATTAATTTCT
1 AAAAAGATTGAAGGGCCTTTAACACTTTTAATATCGTTTTTCATA-TTTTTATAAATTAATTTCT
* * * * * *
5158 AATTAAATCAAAACAAGATTCAGAAGTTCGT-AAAACAAATTATTAAGTC-CAATGTAGCTGAGA
65 AATTAAATCAAAACAAGAATCAGAAGCTCGTAAAAACAAATCATTAA-ACGCAATGTAGCTAAAA
5221 TTTGATTAGATAAATATAGATATCTCAAGGAGTCTTGGC-G-T-AAAAAATCATGCAAAACTAAG
129 TTTGATTAGATAAATATAGATATCTCAAGGAGT-TT--CAGTTCAAAAAATCATGCAAAACTAAG
* * * * *
5283 CCGGGGCCCCGAAACGCTTTTTTAGCC-AAAACCTGTGATGGTTATTACACGATTTCGGCTAAAA
191 CC-GGGCCCCGAAACACGTTTTTAGCCAAAAATC-GTGATGGTTAGTACACAATTTCGGCTAAAA
*
5347 TTTTGTAAAAA
254 TTTTGCAAAAA
5358 ATTGACCCAA
Statistics
Matches: 219, Mismatches: 37, Indels: 16
0.81 0.14 0.06
Matches are distributed among these distances:
304 86 0.39
305 131 0.60
306 1 0.00
307 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (305 bp):
AAAAAGATTGAAGGGCCTTTAACACTTTTAATATCGTTTTTCATATTTTTATAAATTAATTTCTA
ATTAAATCAAAACAAGAATCAGAAGCTCGTAAAAACAAATCATTAAACGCAATGTAGCTAAAATT
TGATTAGATAAATATAGATATCTCAAGGAGTTTCAGTTCAAAAAATCATGCAAAACTAAGCCGGG
CCCCGAAACACGTTTTTAGCCAAAAATCGTGATGGTTAGTACACAATTTCGGCTAAAATTTTGCA
AAAATTTATGATAAAATACTCATAAAAAATATATAATTTAATTCA
Found at i:5884 original size:333 final size:330
Alignment explanation
Indices: 5060--5897 Score: 1004
Period size: 333 Copynumber: 2.5 Consensus size: 330
5050 AAATTTATGA
* * * *
5060 TAAAATACTCATAAAAAATATATAATTTAATTCAAAAAATATTGGAGGGCTTTTCACACTTTTAA
1 TAAAATACTCAT-AAAAATATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACACTTTTAA
* * *
5125 TATTGTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCAAAACAAGATTCAGAAGTTCGT-
65 TA-TGTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCATA
*
5189 AAAACAAATTATTAAGTCCAATGTAGCTGAGATTTGATTAGATAAATATAGATATCTCAAGGAGT
129 AAAACAAATTATTAAGTCCAATGTAGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGT
* ** * ** * *
5254 CTTGGCGTAAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACGCTTTTTTAGCCAAAACCTGT
194 CTGGGCCAAAAAAATCATGCAAAACTAAGCCGAGGAACCGAAACGCGTTTTTAGCCAAAACCTAT
* *
5319 GATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAAATTGACCCAAAAGATATTTCCTCAAT
259 GATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAAATTGACACAAAAGATATTTCCTCAAT
5384 TTTTGGC
324 TTTTGGC
* * * * * * *
5391 TAAAATACTCATTAAAATATATAATTCAACGCCAAAAAGATTGAAGTGCTCTTGACATTTTTAAT
1 TAAAATACTCATAAAAATATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACACTTTTAAT
* * * ** *
5456 ATATTTTTCCTAGTTTTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCAGAA
66 AT-GTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCATAA
** * ** * * *
5521 AAACAAATCCTCAAGTCCAATGCGGCTGAGATTTGATTAGATGAATATATATATTTCAAGTAGTC
130 AAACAAATTATTAAGTCCAATGTAGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTC
* * * * *
5586 TCGGAGCCAAAAAAATCATGCACAACTGAGTCGAGTAACCGGAACGCGTTTTTAGCCAAAAACC-
195 T-GG-GCCAAAAAAATCATGCAAAACTAAGCCGAGGAACCGAAACGCGTTTTTAGCC-AAAACCT
* * * *
5650 ATGATGGTTAGTACACGATTTCTGCTAAAACTTTT-T-AAAAATTGACACGATATAT-TTCTCCT
257 ATGATGGTTAGTACACGATTTCGGCTAAAA-TTTTGTAAAAAATTGACACAAAAGATATT-TCCT
5712 CAATTTTTGGC
320 CAATTTTTGGC
* *
5723 TAAAATACTCATAAAAATATATAATTCAATGCCAAAAAGATTGGAGGGATTTTCACGCTTTTAAT
1 TAAAATACTCATAAAAATATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACACTTTTAAT
* * * *
5788 ATCGTATTTCTTATTTTTTCTAAATTAATTTCTTATTAAATCAAAATAAAATTCAGATGCTCATA
66 AT-GT-TTTCATATTTTTTCTAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCATA
* * * * *
5853 AAAATAAATTTTTAAATCTAATGTTGCTGAGATTT-AGTTAGATGA
129 AAAACAAATTATTAAGTCCAATGTAGCTGAGATTTGA-TTAGATGA
5898 TGTAAAGTAT
Statistics
Matches: 423, Mismatches: 75, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
329 1 0.00
330 94 0.22
331 72 0.17
332 91 0.22
333 155 0.37
334 10 0.02
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (330 bp):
TAAAATACTCATAAAAATATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACACTTTTAAT
ATGTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCATAAA
AACAAATTATTAAGTCCAATGTAGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCT
GGGCCAAAAAAATCATGCAAAACTAAGCCGAGGAACCGAAACGCGTTTTTAGCCAAAACCTATGA
TGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAAATTGACACAAAAGATATTTCCTCAATTT
TTGGC
Found at i:10213 original size:2 final size:2
Alignment explanation
Indices: 10208--10243 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
10198 AAAAAAAAAG
*
10208 AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
10244 AAAGTACGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10303 original size:31 final size:31
Alignment explanation
Indices: 10265--10323 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
10255 TTTGTAAAAC
* * *
10265 TTTTGAAACGTCTATTATGCCCTTATTTAAT
1 TTTTGAAACGCCAATTATACCCTTATTTAAT
*
10296 TTTTGAAACGCCAATTATATCCTTATTT
1 TTTTGAAACGCCAATTATACCCTTATTT
10324 GTCTAACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.47
Consensus pattern (31 bp):
TTTTGAAACGCCAATTATACCCTTATTTAAT
Found at i:10416 original size:14 final size:16
Alignment explanation
Indices: 10387--10418 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
10377 AATCTAATAT
10387 TTTTATACCTATTTTA
1 TTTTATACCTATTTTA
10403 TTTT-TACC-ATTTTA
1 TTTTATACCTATTTTA
10417 TT
1 TT
10419 AATTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATACCTATTTTA
Found at i:13282 original size:107 final size:107
Alignment explanation
Indices: 13093--13316 Score: 369
Period size: 107 Copynumber: 2.1 Consensus size: 107
13083 TTTTGTCTTC
*
13093 ATTTGATCAATTATTTATCGTTGTAGGCTCCAATCAATTACTAGTATAAATAGGTAGGGTATGAC
1 ATTTGATCAATTATTTATCGTTGTAGGCTCCAATCAATTACTACTATAAATAGGTAGGGTATGAC
* *
13158 TACTATTAATATTAGGGCATGTACAAAATGCAACACCTAGCT
66 TACTATAAATATCAGGGCATGTACAAAATGCAACACCTAGCT
* *
13200 ATTTGATCAATTATTTATTGTT-TCAGGCTCCAATCAATTACTACTATAAATAGGTAGGGTATTA
1 ATTTGATCAATTATTTATCGTTGT-AGGCTCCAATCAATTACTACTATAAATAGGTAGGGTATGA
*
13264 CTACTATAAATATCAGGGCATGTACAAAATGCAACACCTAGGT
65 CTACTATAAATATCAGGGCATGTACAAAATGCAACACCTAGCT
*
13307 AGTTGATCAA
1 ATTTGATCAA
13317 ATGAAAGACA
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
106 1 0.01
107 108 0.99
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (107 bp):
ATTTGATCAATTATTTATCGTTGTAGGCTCCAATCAATTACTACTATAAATAGGTAGGGTATGAC
TACTATAAATATCAGGGCATGTACAAAATGCAACACCTAGCT
Found at i:14259 original size:31 final size:31
Alignment explanation
Indices: 14211--14328 Score: 177
Period size: 31 Copynumber: 3.9 Consensus size: 31
14201 ACACGTGACA
* * *
14211 CACG-CACGTATAACAAAAGGTGACACGTGG
1 CACGCCACGTGTACCAAAAGGTGACACATGG
*
14241 CACGTCACGTGTACCAAAAGGTGACACATGG
1 CACGCCACGTGTACCAAAAGGTGACACATGG
14272 CACGCCACGTGTACCAAAAGGTGACACATGG
1 CACGCCACGTGTACCAAAAGGTGACACATGG
*
14303 CACGCCACATGTACCAAAA-GTGACAC
1 CACGCCACGTGTACCAAAAGGTGACAC
14329 GTGTCACGTG
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
30 11 0.13
31 71 0.87
ACGTcount: A:0.35, C:0.28, G:0.24, T:0.14
Consensus pattern (31 bp):
CACGCCACGTGTACCAAAAGGTGACACATGG
Found at i:17204 original size:336 final size:327
Alignment explanation
Indices: 16507--17576 Score: 1034
Period size: 325 Copynumber: 3.2 Consensus size: 327
16497 TAATTCAATG
* * * * *
16507 CCAAAAAGATTG-AAAGACTTTTCATGCTT-TAAATACCGGTTTTCCTATTTTTTTCCGAATTAA
1 CCAAAAAGATTGAAAAG-CTATTCACGCTTCTAAA-ATCGTTTTTCCTA-TTTTTTCTGAATTAA
* * * * * *
16570 ATTCTAATTAAATCGAAATATGATTCAGATGCTCGTAAAAACAAAT-TTTAAATCCAATGTGGTT
63 TTTCTAATTAAATCGAAACACGATT-AGATGCTCG-AAAAACAAATCCTTAAATCTAATGTGGCT
* * * *
16634 GAGATTTGGTTAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAAGATCATGTAAAACAGA
126 GAGATTT-TTTAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGA
* * *
16699 GTCGGGACCCAGAAACGCGTTTTTAGTCAAAAACTGTGATGGTTAGTACACGATTTCGACTAAAA
190 GCCGGGACCCAG-AACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* * *
16764 TTTTGTAAAAATTGACACGAAACATTTCTCCTTAATTTTCGGCCACCATATTCATAAAAAATATA
254 TTTTGTAAAAATTGACACGAAA-ATTTCTCCTCAATTTTCGGCCACAATACTCATAAAAAATATA
*
16829 TAACTCAACG
318 TAACTCAACA
** * * * *
16839 CCAAAAAGATTGAAGGGTTTTTCACGCTTCTAAAATTGGTTTTTTTTTCTATTTTTTCTGAATTA
1 CCAAAAAGATTGAAAAGCTATTCACGCTTCTAAAA-TCG---TTTTTCCTATTTTTTCTGAATTA
* *
16904 ATTTCTAATTAAATTGAAAC-CAGGTTGAGATGCTCGAAAAAACAAATCCTTAAATCTAATGTGG
62 ATTTCTAATTAAATCGAAACAC-GATT-AGATGCTCG-AAAAACAAATCCTTAAATCTAATGTGG
** * * **
16968 CTGAGATTTCTTTAGATAAAAATAGATATTTCAATGAGTCTTGGCGTTAAAAATCATGCAAAACT
124 CTGAGATTT-TTTAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACT
* * * * * *
17033 GAGCCGAAGTCCCAGAACGCGTTTTTA-TGCAAAAACCGTGATAGTTAATATACGATTTTGGCTA
188 GAGCCG-GGACCCAGAACGCGTTTTTAGT-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
* *
17097 AAATTTTGTAAAAAATTGACTCGAAAGGATTT-TCCTCAATTTTTGGCCACAATACTCATAAAAA
251 AAATTTTGT-AAAAATTGACACGAAA--ATTTCTCCTCAATTTTCGGCCACAATACTCATAAAAA
*
17161 ATATATAATTCAACA
313 ATATATAACTCAACA
* * * *
17176 CCAAAAATATTGAAAAGCTATT-ACGCTTCTAATATCGTTTTTCCTATTTTTTCTAAATTAATTC
1 CCAAAAAGATTGAAAAGCTATTCACGCTTCTAAAATCGTTTTTCCTATTTTTTCTGAATTAATTT
* * * * *
17240 CTAATTTAATCG-AACACGATT-CAT-AT-G-AAAACAAATCCTTAAAT-TCAATGTGGGTAAGA
66 CTAATTAAATCGAAACACGATTAGATGCTCGAAAAACAAATCCTTAAATCT-AATGTGGCTGAGA
* * * * *
17299 TTTTGTTAGATGGATATAAATATTTCAACGAGGCTTGGCGCCAAAAATCTTACAAAACTGAGCCG
130 TTTT-TTAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCG
* * * * *
17364 GGCCTCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTGGTACACGATTTCAGTTAAAATTTT
194 GGAC-CCAGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTT
* * * * * *
17429 GCAAAATTTGACCCGAGAAATTTCTTCTCAATTTTGGGCCACAATACTAATAAATAATATATATA
258 GTAAAAATTGACACGA-AAATTTCTCCTCAATTTTCGGCCACAATACTCATAAA-AA-ATATATA
**
17494 ACTCAATG
320 ACTCAACA
* * * * * * * * * * *
17502 CCAAAAAGACTG-AAGGGTTTCTCACGCTTCTAATACCGCTTTCCCTACCTTTTTCCGAATTAAG
1 CCAAAAAGATTGAAAAGCTAT-TCACGCTTCTAAAATCGTTTTTCCTA-TTTTTTCTGAATTAAT
17566 TTCTAATTAAA
64 TTCTAATTAAA
17577 AAAATTATAT
Statistics
Matches: 607, Mismatches: 107, Indels: 52
0.79 0.14 0.07
Matches are distributed among these distances:
323 4 0.01
324 43 0.07
325 141 0.23
326 24 0.04
327 22 0.04
328 22 0.04
329 2 0.00
331 6 0.01
332 58 0.10
333 7 0.01
335 55 0.09
336 140 0.23
337 79 0.13
338 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (327 bp):
CCAAAAAGATTGAAAAGCTATTCACGCTTCTAAAATCGTTTTTCCTATTTTTTCTGAATTAATTT
CTAATTAAATCGAAACACGATTAGATGCTCGAAAAACAAATCCTTAAATCTAATGTGGCTGAGAT
TTTTTAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGG
ACCCAGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTA
AAAATTGACACGAAAATTTCTCCTCAATTTTCGGCCACAATACTCATAAAAAATATATAACTCAA
CA
Found at i:17357 original size:325 final size:330
Alignment explanation
Indices: 16546--17515 Score: 991
Period size: 336 Copynumber: 2.9 Consensus size: 330
16536 TAAATACCGG
** * * *
16546 TTTTCCTATTTTTTTCCGAATTAAATT-CTAATTAAATCGAAA-TATGATTCAGATGCTCGTAAA
1 TTTTCCTA-TTTTTTCTAAATT-AATTCCTAATTAAATCGAAACCA-GATT-ACATGATCG-AAA
* * * *
16609 AACAAAT-TTTAAATCCAATGTGGTTGAGATTTGGTTAGATGGATATAGATATTTCAATGAGACT
61 AACAAATCCTTAAATTCAATGTGGCTGAGATTTTGTTAGATGGATATAGATATTTCAATGAGACT
* * * * *
16673 TGGCGCCAAAGATCATGTAAAACAGAGTCGGGACCCAGAAACGCGTTTTTAGTCAAAAACTGTGA
126 TGGCGCCAAAAATCATGCAAAACTGAGCCGGGACCCAG-AACGCGTTTTTAGTCAAAAACCGTGA
* *
16738 TGGTTAGTACACGATTTCGACTAAAATTTTGTAAAAATTGACACGAAACATTTCTCCTTAATTTT
190 TGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAAA-ATTTCTCCTCAATTTT
* * * ** * *
16803 CGGCCACCATATTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTT
254 CGGCCACAATACTCATAAAAAATATATAACTCAACACCAAAAAGATTGAAAAGCTATTCACGCTT
*
16868 CTAAAATTGGTTTT
319 CTAAAATTCG--TT
* * * * * * *
16882 TTTTTCTATTTTTTCTGAATTAATTTCTAATTAAATTGAAACCAGGTTGAGATGCTCGAAAAAAC
1 TTTTCCTATTTTTTCTAAATTAATTCCTAATTAAATCGAAACCAGATT-ACATGATCG-AAAAAC
** * *
16947 AAATCCTTAAA-TCTAATGTGGCTGAGATTTCT-TTAGATAAAAATAGATATTTCAATGAGTCTT
64 AAATCCTTAAATTC-AATGTGGCTGAGATTT-TGTTAGATGGATATAGATATTTCAATGAGACTT
** * *
17010 GGCGTTAAAAATCATGCAAAACTGAGCCGAAGTCCCAGAACGCGTTTTTA-TGCAAAAACCGTGA
127 GGCGCCAAAAATCATGCAAAACTGAGCCG-GGACCCAGAACGCGTTTTTAGT-CAAAAACCGTGA
* * * * *
17074 TAGTTAATATACGATTTTGGCTAAAATTTTGTAAAAAATTGACTCGAAAGGATTT-TCCTCAATT
190 TGGTTAGTACACGATTTCGGCTAAAATTTTGT-AAAAATTGACACGAAA--ATTTCTCCTCAATT
* * *
17138 TTTGGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAATATTGAAAAGCTATT-ACGC
252 TTCGGCCACAATACTCATAAAAAATATATAACTCAACACCAAAAAGATTGAAAAGCTATTCACGC
*
17202 TTCTAATA-TCG-T
317 TTCTAAAATTCGTT
*
17214 TTTTCCTATTTTTTCTAAATTAATTCCTAATTTAATCG-AA-CACGATT-CAT-AT-G-AAAACA
1 TTTTCCTATTTTTTCTAAATTAATTCCTAATTAAATCGAAACCA-GATTACATGATCGAAAAACA
* * * * *
17273 AATCCTTAAATTCAATGTGGGTAAGATTTTGTTAGATGGATATAAATATTTCAACGAGGCTTGGC
65 AATCCTTAAATTCAATGTGGCTGAGATTTTGTTAGATGGATATAGATATTTCAATGAGACTTGGC
* * * *
17338 GCCAAAAATCTTACAAAACTGAGCCGGGCCTCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGT
130 GCCAAAAATCATGCAAAACTGAGCCGGGAC-CCAGAACGCGTTTTTAGTCAAAAACCGTGATGGT
* * * * * * * *
17403 TGGTACACGATTTCAGTTAAAATTTTGCAAAATTTGACCCGAGAAATTTCTTCTCAATTTTGGGC
194 TAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACACGA-AAATTTCTCCTCAATTTTCGGC
* ** *
17468 CACAATACTAATAAATAATATATATAACTCAATGCCAAAAAGACTGAA
258 CACAATACTCATAAA-AA-ATATATAACTCAACACCAAAAAGATTGAA
17516 GGGTTTCTCA
Statistics
Matches: 531, Mismatches: 85, Indels: 46
0.80 0.13 0.07
Matches are distributed among these distances:
323 4 0.01
324 42 0.08
325 135 0.25
326 27 0.05
327 1 0.00
328 1 0.00
329 2 0.00
330 2 0.00
331 5 0.01
332 34 0.06
334 4 0.01
335 52 0.10
336 139 0.26
337 79 0.15
338 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (330 bp):
TTTTCCTATTTTTTCTAAATTAATTCCTAATTAAATCGAAACCAGATTACATGATCGAAAAACAA
ATCCTTAAATTCAATGTGGCTGAGATTTTGTTAGATGGATATAGATATTTCAATGAGACTTGGCG
CCAAAAATCATGCAAAACTGAGCCGGGACCCAGAACGCGTTTTTAGTCAAAAACCGTGATGGTTA
GTACACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAAAATTTCTCCTCAATTTTCGGCCAC
AATACTCATAAAAAATATATAACTCAACACCAAAAAGATTGAAAAGCTATTCACGCTTCTAAAAT
TCGTT
Found at i:17776 original size:2 final size:2
Alignment explanation
Indices: 17764--17798 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
17754 TATAGATAGC
*
17764 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17799 CTCTATAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:19840 original size:2 final size:2
Alignment explanation
Indices: 19833--19861 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19823 ATCAACCACC
19833 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
19862 GTACAAAGCA
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:20818 original size:48 final size:48
Alignment explanation
Indices: 20747--20842 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
20737 CACTAAGATC
20747 GATTAACATATACACATAGAATAAGATAATAAAATTAAACTCCTAATT
1 GATTAACATATACACATAGAATAAGATAATAAAATTAAACTCCTAATT
*
20795 GATTAACATATACATATAGAATAAGATAATAAAATTAAACTCCTAATT
1 GATTAACATATACACATAGAATAAGATAATAAAATTAAACTCCTAATT
20843 CTATATACAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.30
Consensus pattern (48 bp):
GATTAACATATACACATAGAATAAGATAATAAAATTAAACTCCTAATT
Found at i:21240 original size:2 final size:2
Alignment explanation
Indices: 21229--21258 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21219 ATTAGTTTGG
21229 TA TA TA -A 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 TA TA T
21259 CAACTTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21288 original size:3 final size:3
Alignment explanation
Indices: 21280--21339 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
21270 AATTTAGTAC
21280 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21328 ATT ATT ATT ATT
1 ATT ATT ATT ATT
21340 TCAGAATAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23211 original size:2 final size:2
Alignment explanation
Indices: 23204--23237 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
23194 TAAATTTACA
* *
23204 AT AT AT AT AT AT AT AT AT AT AT TT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23238 TCTTAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:27450 original size:37 final size:37
Alignment explanation
Indices: 27408--27478 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
27398 ACATGATTAT
* *
27408 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATGTGAAAAGACATGTATTGA
27445 TCATAAAGTTATGTCTATGTGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATGTGAAAAGACATGTAT
27479 ATTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATGTGAAAAGACATGTATTGA
Found at i:29888 original size:37 final size:37
Alignment explanation
Indices: 29846--29916 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
29836 ACATGATTAT
* * *
29846 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGCCTATATGAAAAGACATGTATTGA
29883 TCATAAAGTTATGCCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGCCTATATGAAAAGACATGTAT
29917 GTTGATCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (37 bp):
TCATAAAGTTATGCCTATATGAAAAGACATGTATTGA
Found at i:36494 original size:27 final size:27
Alignment explanation
Indices: 36454--36505 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
36444 CTTATTTGAG
*
36454 TTTGTTTTTAAGTT-GTTTTGAGTCAA
1 TTTGTTTTTAAGTTAGTTTCGAGTCAA
*
36480 TTTGTTTTTTGAGTTAGTTTCGAGTC
1 TTTG-TTTTTAAGTTAGTTTCGAGTC
36506 TAGTCTCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 9 0.41
28 9 0.41
ACGTcount: A:0.15, C:0.06, G:0.21, T:0.58
Consensus pattern (27 bp):
TTTGTTTTTAAGTTAGTTTCGAGTCAA
Found at i:39452 original size:14 final size:14
Alignment explanation
Indices: 39433--39459 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39423 ATATTAGTGT
39433 TATGTATGTATATG
1 TATGTATGTATATG
39447 TATGTATGTATAT
1 TATGTATGTATAT
39460 ATATATTTGA
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:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (14 bp):
TATGTATGTATATG
Done.