Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006228.1 Corchorus capsularis cultivar CVL-1 contig06247, 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: 50483
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:3176 original size:51 final size:51
Alignment explanation
Indices: 3120--3221 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
3110 CAGGAAAGTC
3120 CCTAAATTTAGGACATTAATCTGCTGAGGTTAGAAATTTCTAGGAAAAAAT
1 CCTAAATTTAGGACATTAATCTGCTGAGGTTAGAAATTTCTAGGAAAAAAT
*
3171 CCTAAATTTAGGACATTAATCTGCTGGGGTTAGAAATTTCTAGGAAAAAAT
1 CCTAAATTTAGGACATTAATCTGCTGAGGTTAGAAATTTCTAGGAAAAAAT
3222 ATGACTTGTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (51 bp):
CCTAAATTTAGGACATTAATCTGCTGAGGTTAGAAATTTCTAGGAAAAAAT
Found at i:4990 original size:330 final size:329
Alignment explanation
Indices: 3841--5412 Score: 1458
Period size: 330 Copynumber: 4.8 Consensus size: 329
3831 AACTATGATG
* * *
3841 GTAAAAA-TGACCCGAGAGATTTTCTTCAATTTTTTGCAAAAATACTCATAAAATATATATAATT
1 GTAAAAATTGACCCGAAAGATTTTCCTCAA-TTTTTGCTAAAATACTCATAAAATATATATAATT
* * * * *
3905 CAACGCAAAAAAGATTGGAGAACTTTTCACGCTTT-TAATATTGTTTTTCATATTTTTTCTGAAT
65 CAACGCCAAAAATATTGAAGGACTTTTCACG-TTTCTAATATAGTTTTTCAT-TTTTTTCTGAAT
* * *
3969 TAATTTCTTATTACATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * ** * *
4034 GCTGAGATTTG---AGACGAATAAAGATGTCTCAAGGAGTCTCAGCGTCAAAAATTATGCAAAA-
193 GCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAT
* * * * * *
4095 CAGAGTCGTGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTGGTTGGTTCATGATTTC
258 TA-AGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACC---AT-GATGGTTAGTACATGATTTC
4160 GGCTAAAATTTT
318 GGCTAAAATTTT
** *
4172 ACAAAAAATT-ACCCGAAAGATATTTCCTC-ATTTTTGGGCTAAAATACTCATTAAAA-GTATAT
1 -GTAAAAATTGACCCGAAAGAT-TTTCCTCAATTTTT--GCTAAAATACTCA-TAAAATATATAT
** ** * *
4234 AATTTGACATCAAAAATATTGAAGGGCTTTTAACGTTTCTAATATA-----T-A-TTTTTTCTGA
61 AATTCAACGCCAAAAATATTGAAGGACTTTTCACGTTTCTAATATAGTTTTTCATTTTTTTCTGA
* *
4292 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * ** * * * *
4357 TGGCT-ACGTTTTTATTAGATCTATATAGATATTTCAAGGATTCTCGGCGCCAAAAATCATGCAC
191 TGGCTGA-GATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAA
* * * * * * * * * *
4421 AATTGAGGCAGGACCCAGAAACGCGTTTTTAGCCAAAAACCGTGATTGTTAGTACATGGTTTTGA
255 AATTAAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACATGATTTCGG
4486 CTAAAATTTT
320 CTAAAATTTT
* * * * * * *
4496 GGAAAAAATGATCCGAAAAATTATTCTTAAATTTTT--T----T--TGATAAAATATATATAATT
1 GTAAAAATTGACCCGAAAGATT-TTCCTCAATTTTTGCTAAAATACTCATAAAATATATATAATT
* * * ** * * *
4553 TAACGTCAAAAAAATTGGTGGACTTTTCACACTTT-TAATATTGTTTTTCATAATTTTTCTGAAT
65 CAACGCCAAAAATATTGAAGGACTTTTCAC-GTTTCTAATATAGTTTTTCAT-TTTTTTCTGAAT
* *
4617 TAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAAATCCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * *
4682 GCTGAGATTTGATTAAATGAATATGGATATCTCAAGCAGTCTTGGCGCCAAAAATCATGCAAAAT
193 GCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAT
* * * * * *
4747 TAAGTCGGGGCCCCGCAATG-ATTTTATAGCC-AAAACTATGATGGTTATTACATGATTTCGGTT
258 TAAGTCGGGGCCCCGAAACGCGTTTT-TAGCCAAAAACCATGATGGTTAGTACATGATTTCGGCT
4810 AAAATTTT
322 AAAATTTT
4818 GTAAAAATTGATCCC-AAAGATATTTCCTCAATTTCTTGCTAAAATACTCATAGAAA-ATAT-TA
1 GTAAAAATTGA-CCCGAAAGAT-TTTCCTCAATTT-TTGCTAAAATACTCATA-AAATATATATA
** * * *
4880 ATTCAACGCCAAAAATATTGAAGGGTTTTTGACGTTTCTAATATAGTTTTTTCCTTTTTTTCTAA
62 ATTCAACGCCAAAAATATTGAAGGACTTTTCACGTTTCTAATATAG-TTTTTCATTTTTTTCTGA
* * *
4945 ATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTTGTAAAAACAAATCCTTAAATCCCATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * * * * * ** *
5010 TGACTAAGATTTGGTTAGATGAATATAGATATTTCAAGCAGACTTGGAACCAAAAATCTTGCAAA
191 TGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAA
* * * * * *
5075 ACTGAAGT--GGGCTCCGAAATGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACATGATATCGG
256 A-TTAAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACATGATTTCGG
5138 -TCAAAATTTT
320 CT-AAAATTTT
* *
5148 GCT-AAAATTGACCACGAAAGATTTTTCCTCAATTTCTAG-TGAAAATACTCATAAAAGATATAT
1 G-TAAAAATTGACC-CGAAAGA-TTTTCCTCAATTT-TTGCT-AAAATACTCATAAAATATATAT
* * * * *
5211 AATTCAATGCCAAAAAT-TTGAAAGTCTTTTTCACGCTTCTAATATCATTTTTTCTATTTTATTT
61 AATTCAACGCCAAAAATATTGAAGGAC-TTTTCACGTTTCTAATAT-AGTTTTTC-ATTTT-TTT
** * * * * *
5275 CCAAATTAATTTGTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAATCCCTAAATAC
122 CTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* * * *
5340 AATGTGACTGAGATTTGGTTAGATGATTATAGATATATCTTAAGGAGTCTTGGTCG--AAAAATC
187 AATGTGGCTGAGATTTGATTAGATGAATATAG--ATATCTCAAGGAGTCTTGG-CGCCAAAAATC
5403 ATGCAAAATT
249 ATGCAAAATT
5413 GCCTCAATTT
Statistics
Matches: 1010, Mismatches: 172, Indels: 114
0.78 0.13 0.09
Matches are distributed among these distances:
314 5 0.00
315 40 0.04
316 3 0.00
317 1 0.00
320 1 0.00
321 2 0.00
322 59 0.06
323 154 0.15
324 40 0.04
325 87 0.09
327 1 0.00
328 70 0.07
329 23 0.02
330 210 0.21
331 68 0.07
332 62 0.06
333 60 0.06
334 95 0.09
335 14 0.01
336 15 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (329 bp):
GTAAAAATTGACCCGAAAGATTTTCCTCAATTTTTGCTAAAATACTCATAAAATATATATAATTC
AACGCCAAAAATATTGAAGGACTTTTCACGTTTCTAATATAGTTTTTCATTTTTTTCTGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
GAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAATTAA
GTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACATGATTTCGGCTAAAA
TTTT
Found at i:5265 original size:653 final size:641
Alignment explanation
Indices: 3885--5412 Score: 1428
Period size: 653 Copynumber: 2.3 Consensus size: 641
3875 TGCAAAAATA
* * * *
3885 CTCATAAAATATATATAATTCAACG-CAAAAAAGATTG-GAGAACTTTTCACGCTTTTAATATTG
1 CTCATAAAAGATATATAATTCAACGTCAAAAAA-ATTGAAAG-ACTTTTCACACTTCTAATA---
* * * *
3948 TTTTTCATATTTTTTCTGAATTAATTTCTTATTACATCGAAACAAGATTCAGATGCACGTAAAAA
61 ---TTC--ATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA
* ** * **
4013 CAAATCCTTAAATCCAATGTGGCTGAGATTTG--AGACGAATAAAGATGTCTCAAGGAGTCTCAG
121 CAAATCCTTAAATCCAATGTGGCTGAGATTTGTTAGATGAATATGGATATCTCAAGGAGTCTTGG
* * * * *
4076 CGTCAAAAATTATGCAAAA-CAGAGTCGTGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
186 CG-CAAAAATCATGCAAAATTAGAGTCGGGGCCCCGCAACGCATTTTTAGCCAAAAACCGTGATG
* *
4140 GTTGGTTGGTTCATGATTTCGGCTAAAATTTTACAAAAAATTACCCGAAAGATATTTCCTCATTT
250 GATGGTTGATTCATGATTTCGGCTAAAATTTTACAAAAAATTACCCGAAAGATATTTCCTCATTT
* ** *
4205 TTGGGCTAAAATACTCATTAAAAGTATATAATTTGACATCAAAAATATTGAAGGGCTTTTAACGT
315 TT-GGCTAAAATACTCATTAAAAATATATAATTCAACACCAAAAATATTGAAGGGCTTTTAACGT
* *
4270 TTCTAATATATATTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
379 TTCTAATATATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * * * * * **
4335 AAACAAATCCTTAAATGCAATGTGGCTACGTTTTTATTAGATCTATATAGATATTTCAAGGATTC
444 AAACAAATCCTTAAATCCAATGTGACTAAGATTTGATTAGATCAATATAGATATTTCAAGCAGAC
** * * *
4400 TCGGCGCCAAAAATCATGCACAATTGAGGCAGGACCCAGAAACGCGTTTTTAGCCAAAAACCGTG
509 TCGGAACCAAAAATCATGCAAAACTGAAGCAGGACCCAGAAACGCGTTTTTAGCCAAAAACCGTG
* * ** * * *
4465 ATTGTTAGTACATGGTTTTGACTAAAATTTTGGAAAAAATGATCCGAAAAATTATTCTTAAATTT
574 ATGGTTAGTACATGATTCGGACTAAAATTTTGCAAAAAATGACCCGAAAAATTATTCCTAAATTT
4530 TTT
639 TTT
* * * * *** *
4533 TTGATAAAATATATATAATTTAACGTCAAAAAAATTGGTGGACTTTTCACACTTTTAATATTGTT
1 CTCATAAAAGATATATAATTCAACGTCAAAAAAATTGAAAGACTTTTCACACTTCTAATA-----
4598 TTTCATAATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACA
61 -TTCAT--TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACA
* * *
4663 AATTCTTAAATCCAATGTGGCTGAGATTTGATTAAATGAATATGGATATCTCAAGCAGTCTTGGC
123 AATCCTTAAATCCAATGTGGCTGAGATTTG-TTAGATGAATATGGATATCTCAAGGAGTCTTGGC
*
4728 GCCAAAAATCATGCAAAATTA-AGTCGGGGCCCCGCAATG-ATTTTATAGCC-AAAA-C-T-AT-
187 G-CAAAAATCATGCAAAATTAGAGTCGGGGCCCCGCAACGCATTTT-TAGCCAAAAACCGTGATG
* **
4786 GATGGTT-ATTACATGATTTCGGTTAAAATTTT-GTAAAAATTGATCCC-AAAGATATTTCCTCA
250 GATGGTTGATT-CATGATTTCGGCTAAAATTTTACAAAAAATT-A-CCCGAAAGATATTTCCTC-
* *
4848 ATTTCTT-GCTAAAATACTCA-TAGAAAATAT-TAATTCAACGCCAAAAATATTGAAGGGTTTTT
311 ATTT-TTGGCTAAAATACTCATTA-AAAATATATAATTCAACACCAAAAATATTGAAGGGCTTTT
* * *
4910 GACGTTTCTAATATAGTTTTTTCCTTTTTTTCTAAATTAATTTCTAATTAAATCGAAATAAGATT
374 AACGTTTCTAATATA------T--ATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATT
* * * *
4975 CAGATGCTTGTAAAAACAAATCCTTAAATCCCATGTGACTAAGATTTGGTTAGATGAATATAGAT
431 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTAAGATTTGATTAGATCAATATAGAT
* * * * *
5040 ATTTCAAGCAGACTTGGAACCAAAAATCTTGCAAAACTGAAG-TGGGCTCC-GAAATGCGTTTTT
496 ATTTCAAGCAGACTCGGAACCAAAAATCATGCAAAACTGAAGCAGGAC-CCAGAAACGCGTTTTT
* * * *
5103 AGCCGAAAACCGTGATGGTTAGTACATGATATCGGTC-AAAATTTTGCTAAAATTGACCACGAAA
560 AGCCAAAAACCGTGATGGTTAGTACATGAT-TCGGACTAAAATTTTGCAAAAAATGACC-CGAAA
* * *
5167 GATTTTTCCTCAATTTCTAGTGAAAAT
623 AATTATTCCTAAATTT-T--T-----T
* * * * *
5194 ACTCATAAAAGATATATAATTCAATG-CCAAAAATTTGAAAGTCTTTTTCACGCTTCTAATATCA
1 -CTCATAAAAGATATATAATTCAACGTCAAAAAAATTGAAAGAC-TTTTCACACTTCT-A-AT-A
** * *
5258 TTTTTTCTATTTTATTTCCAAATTAATTTGTAATTAAATCGAAACAAGATTTAGATACTCGTAAA
61 ----TTC-A-TTT-TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAA
* * * * * *
5323 AACAAATCCCTAAATACAATGTGACTGAGATTTGGTTAGATGATTATAGATATATCTTAAGGAGT
119 AACAAATCCTTAAATCCAATGTGGCTGAGATTT-GTTAGATGAATAT-G-GATATCTCAAGGAGT
5388 CTTGGTCG-AAAAATCATGCAAAATT
181 CTTGG-CGCAAAAATCATGCAAAATT
5413 GCCTCAATTT
Statistics
Matches: 728, Mismatches: 106, Indels: 75
0.80 0.12 0.08
Matches are distributed among these distances:
645 52 0.07
646 62 0.09
647 9 0.01
648 138 0.19
649 9 0.01
650 8 0.01
651 61 0.08
652 60 0.08
653 146 0.20
654 1 0.00
656 1 0.00
661 12 0.02
662 31 0.04
663 9 0.01
664 89 0.12
665 21 0.03
666 17 0.02
667 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (641 bp):
CTCATAAAAGATATATAATTCAACGTCAAAAAAATTGAAAGACTTTTCACACTTCTAATATTCAT
TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTA
AATCCAATGTGGCTGAGATTTGTTAGATGAATATGGATATCTCAAGGAGTCTTGGCGCAAAAATC
ATGCAAAATTAGAGTCGGGGCCCCGCAACGCATTTTTAGCCAAAAACCGTGATGGATGGTTGATT
CATGATTTCGGCTAAAATTTTACAAAAAATTACCCGAAAGATATTTCCTCATTTTTGGCTAAAAT
ACTCATTAAAAATATATAATTCAACACCAAAAATATTGAAGGGCTTTTAACGTTTCTAATATATA
TTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
AAATCCAATGTGACTAAGATTTGATTAGATCAATATAGATATTTCAAGCAGACTCGGAACCAAAA
ATCATGCAAAACTGAAGCAGGACCCAGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
TGATTCGGACTAAAATTTTGCAAAAAATGACCCGAAAAATTATTCCTAAATTTTTT
Found at i:7696 original size:78 final size:78
Alignment explanation
Indices: 7534--7696 Score: 179
Period size: 78 Copynumber: 2.1 Consensus size: 78
7524 TCTTTGCGCC
* * * ** * *
7534 CAAAATCATGCAAAATTGAGTCGGGGCCCCAGAATGCTTTTTTAGCCAAAACCTGTGATGGTTAT
1 CAAAATCATGCAAAACTGAGTCGAGGCCCCAAAACACGTTTTTAGCCAAAACCTATGATGGTTAT
*
7599 TACACAATTTCGA
66 TACACAATATCGA
7612 CTAAAATCATGCAAAACTGAGTC-AGGCCCCAAAACACGTTTTTAGCCGAAAACC-ATGATGGTT
1 C-AAAATCATGCAAAACTGAGTCGAGGCCCCAAAACACGTTTTTAGCC-AAAACCTATGATGGTT
**
7675 -TGTACATGATATCGA
64 AT-TACACAATATCGA
7690 TCAAAAT
1 -CAAAAT
7697 TTTGCTAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
77 1 0.01
78 43 0.61
79 27 0.38
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (78 bp):
CAAAATCATGCAAAACTGAGTCGAGGCCCCAAAACACGTTTTTAGCCAAAACCTATGATGGTTAT
TACACAATATCGA
Found at i:10672 original size:328 final size:324
Alignment explanation
Indices: 9950--10677 Score: 761
Period size: 328 Copynumber: 2.2 Consensus size: 324
9940 AATTTCAGTT
* * * * **
9950 AAAATTTTGTAAAAATTGATCCAAAAGATATTTCCTCAATTTTTGGCTAAAATTTTCATAAAAAT
1 AAAATTTTGT-AAAATTGACCCGAAAGAT-TTTTCTCAATTTTTAGCTAAAATACTCATAAAAAT
* * * * * *
10015 ATATAGTTCAACGCCAAAAATATTGAACGACTGTTGACGTTTGTAATATTGTTTTTTCCTATTTT
64 ATATAATTCAACGCCAAAAATATTGAAAGACTGTTCACGCTTCTAATATTGTTTTTTCATATTTT
* * * *
10080 TCCGAATGAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCATAAAAACAAATCCTTAAATC
129 TCCAAATGAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCCTTAAATA
* ****
10145 CAATATGACTGAGATTTGGTTAGATAAATATACATATATTTAACTTTTTCTTGACACCAAAAATC
194 CAATATGACTGAGATTTGATTAGATAAATATACATATATTTAACGGAGTCTTGACACCAAAAATC
* *
10210 ATGGAAAATTGAGCCGAGCCCGAAACGCATTTTTAGCCGAAAACTGTGACGTACATGATATCGGT
259 ATGGAAAACTGAGCCGAGCCCGAAACGCATTTTTAGCCAAAAACTGTGACGTACATGATATCGGT
10275 C
324 C
* * *
10276 AAAATTTTGTTAAAATTGACTACGAAAGATTTTTCCTCAATTTCTAGCGAAAATACTCATAAAAA
1 AAAATTTTG-TAAAATTGAC-CCGAAAGATTTTT-CTCAATTTTTAGCTAAAATACTCAT-AAAA
* * *
10341 ATATATAATTCAACGCCAAAAA-ATTGAAAG-CTTTTTTCACGCTTCTAATATT-TTTTTTTATT
62 ATATATAATTCAACGCCAAAAATATTGAAAGAC--TGTTCACGCTTCTAATATTGTTTTTTCATA
** * * * * **
10403 TTATTTCCAAATTCATTTCTGATTAAATCGCAACAAGATTTAGATACTCGTAAAAACAAATTTTT
125 TT-TTTCCAAATGAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCCTT
* * * * **
10468 AAATACAATGTGACTGAGATTTGATTAGATGAATATAGATATATTTTAA-GGAGTCTTGGCGTCA
189 AAATACAATATGACTGAGATTTGATTAGATAAATATACATATA-TTTAACGGAGTCTTGACACCA
* ** *
10532 AAAATCAT-GCAAACTG-GCCCGAGGCCCGGGACGCGA-TTTTAGCCCAAAAAAACTGTGATGGT
253 AAAATCATGGAAAACTGAG-CCGA-GCCCGAAACGC-ATTTTTAG-CC--AAAAACTGTGA-CGT
*
10594 ACATGATTTCGG-C
311 ACATGATATCGGTC
* * *
10607 TTAAATTTTGTAAATATTGACCCGAAATATTTTTCTCAATTTTTAGCTACAATACTCATAAAATA
1 -AAAATTTTGTAAA-ATTGACCCGAAAGATTTTTCTCAATTTTTAGCTAAAATACTCATAAAA-A
10672 TATATA
63 TATATA
10678 TATATATATA
Statistics
Matches: 330, Mismatches: 54, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
326 22 0.07
327 54 0.16
328 160 0.48
329 12 0.04
330 29 0.09
331 26 0.08
332 27 0.08
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (324 bp):
AAAATTTTGTAAAATTGACCCGAAAGATTTTTCTCAATTTTTAGCTAAAATACTCATAAAAATAT
ATAATTCAACGCCAAAAATATTGAAAGACTGTTCACGCTTCTAATATTGTTTTTTCATATTTTTC
CAAATGAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCCTTAAATACA
ATATGACTGAGATTTGATTAGATAAATATACATATATTTAACGGAGTCTTGACACCAAAAATCAT
GGAAAACTGAGCCGAGCCCGAAACGCATTTTTAGCCAAAAACTGTGACGTACATGATATCGGTC
Found at i:14154 original size:2 final size:2
Alignment explanation
Indices: 14142--14182 Score: 57
Period size: 2 Copynumber: 20.0 Consensus size: 2
14132 TTGTAACTAT
14142 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA T- TA TA GTA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
14183 AAACTAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 31 0.86
3 4 0.11
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14793 original size:3 final size:3
Alignment explanation
Indices: 14785--14817 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
14775 TAACTGACAC
14785 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14818 ATGTATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:21074 original size:12 final size:12
Alignment explanation
Indices: 21057--21081 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21047 CCTGTTAAAA
21057 AAACTGGGCCCC
1 AAACTGGGCCCC
21069 AAACTGGGCCCC
1 AAACTGGGCCCC
21081 A
1 A
21082 CTTTTAGTGG
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:0.28, C:0.40, G:0.24, T:0.08
Consensus pattern (12 bp):
AAACTGGGCCCC
Found at i:25713 original size:12 final size:12
Alignment explanation
Indices: 25680--25719 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
25670 TTAATACAGG
25680 TATCGACGGATA
1 TATCGACGGATA
*
25692 TATCAAACGGATA
1 TATC-GACGGATA
25705 TATCGACGGATA
1 TATCGACGGATA
25717 TAT
1 TAT
25720 TGAGGTATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:27148 original size:10 final size:10
Alignment explanation
Indices: 27133--27168 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
27123 AATTTAATAT
27133 GGATATTTAC
1 GGATATTTAC
27143 GGATATTTAC
1 GGATATTTAC
27153 GGATATTTAC
1 GGATATTTAC
27163 GGATAT
1 GGATAT
27169 ATCGAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (10 bp):
GGATATTTAC
Found at i:35761 original size:12 final size:12
Alignment explanation
Indices: 35744--35768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35734 AATTTTTAAT
35744 TTTAATTACTAC
1 TTTAATTACTAC
35756 TTTAATTACTAC
1 TTTAATTACTAC
35768 T
1 T
35769 ATATAAGTAT
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAATTACTAC
Found at i:36837 original size:2 final size:2
Alignment explanation
Indices: 36830--36855 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36820 TGATTAATAC
36830 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
36856 GAAAATTAAA
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:45943 original size:2 final size:2
Alignment explanation
Indices: 45936--45960 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45926 CTAAAGATAG
45936 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 A
45961 ATAAGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47024 original size:31 final size:31
Alignment explanation
Indices: 46986--47050 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
46976 AACTGAACTA
46986 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
47017 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
47048 ACT
1 ACT
47051 GATAACCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTGGAG
Found at i:47461 original size:3 final size:3
Alignment explanation
Indices: 47447--47495 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
47437 TTTTTTATAG
47447 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47493 TAA
1 TAA
47496 AAAAGGACTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:49602 original size:4 final size:5
Alignment explanation
Indices: 49576--49604 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
49566 AAAAACACTC
49576 GAAAA GAAAA GAAAA GAAAA G-AAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
49605 AGCCAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:49606 original size:15 final size:15
Alignment explanation
Indices: 49576--49604 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
49566 AAAAACACTC
49576 GAAAAGAAAAGAAAA
1 GAAAAGAAAAGAAAA
49591 GAAAAG-AAAGAAAA
1 GAAAAGAAAAGAAAA
49605 AGCCAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAAAGAAAAGAAAA
Done.