Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005384.1 Hibiscus syriacus cultivar Beakdansim tig00012323_pilon, 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: 242709
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:180533 original size:21 final size:21
Alignment explanation
Indices: 180509--180552 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
180499 TTAAATTATA
180509 GACGGAGAGAGGCATTACATT
1 GACGGAGAGAGGCATTACATT
180530 GACGGAGAGAGGCATTACATT
1 GACGGAGAGAGGCATTACATT
180551 GA
1 GA
180553 TAGAGGCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.18
Consensus pattern (21 bp):
GACGGAGAGAGGCATTACATT
Found at i:188419 original size:178 final size:180
Alignment explanation
Indices: 188113--188435 Score: 442
Period size: 178 Copynumber: 1.8 Consensus size: 180
188103 TAGTGACATG
* *
188113 TTTTGTAACTATAAGCTATAATTATTATTACAAAAAAAGTTATCACTACAAATAATGAGATTCAA
1 TTTTGTAACTATAAGCTATAATAATTATTACAAAAAAAGTTATCACTAAAAATAATGAGATTCAA
* * * *
188178 GTTTTTAGTAAAAAACAGTATTTGTCGTTATATATTTTAATTATAGTGATAAAATATATTGTCAA
66 GATTTTAGTAAAAAACAGTATTTGTAGTTATAAATTTTAACTATAGTGATAAAATATATTGTCAA
188243 AAATATTTTTCTCCATATTTTTTTCGCAAAAAAAGTCATATGATGACAAA
131 AAATATTTTTCTCCATATTTTTTTCGCAAAAAAAGTCATATGATGACAAA
*
188293 TTTTGTAACTATAAATG-T-TAATAATTATTACAAAAAACA-TTATCAC-AAAAATAATGATATT
1 TTTTGTAACTAT-AA-GCTATAATAATTATTACAAAAAA-AGTTATCACTAAAAATAATGAGATT
* ** **
188354 CACGATTTT-GTAACAAATTA-TATTTGTAGTTATAAATTTTAACTATAGTGATAGCATATATTG
63 CAAGATTTTAGTAA-AAAACAGTATTTGTAGTTATAAATTTTAACTATAGTGATAAAATATATTG
* *
188417 TCATAATTATTTTTCTCCA
127 TCAAAAATATTTTTCTCCA
188436 CTTTTTTGTT
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
178 59 0.47
179 24 0.19
180 37 0.30
181 4 0.03
182 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (180 bp):
TTTTGTAACTATAAGCTATAATAATTATTACAAAAAAAGTTATCACTAAAAATAATGAGATTCAA
GATTTTAGTAAAAAACAGTATTTGTAGTTATAAATTTTAACTATAGTGATAAAATATATTGTCAA
AAATATTTTTCTCCATATTTTTTTCGCAAAAAAAGTCATATGATGACAAA
Found at i:189003 original size:418 final size:415
Alignment explanation
Indices: 188219--189035 Score: 1203
Period size: 418 Copynumber: 2.0 Consensus size: 415
188209 ATATTTTAAT
* * * *
188219 TATAGTGATAAAATATATTGTCAAAAATATTTTTCTCCATATTTTTTTCGCAAAAAAAGTCATAT
1 TATAGTAACAAAATATATTGTCAAAAAGATTTTTCTCCATATTTTTTTCGCAAAAAAAATCATAT
* * *
188284 GATGACAAATTTTGTAACTATAAATGTTAATAATTATTACAAAAAACATTATCACAAAAATAATG
66 CATAACAAATTTTGTAACTACAAATGTTAATAATTATTACAAAAAACATTATCACAAAAATAATG
*
188349 ATATTCACGATTTTGTAACAAATTATATTTGTAGTTATAAATTTTAACTATAGTGATAGCATATA
131 ATATTCACGATTTTGTAACAAATTATACTTGTAGTTATAAATTTTAACTATAGTGATAGCATATA
* * * * * *
188414 TTGTCATAATTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGACAATTTTTATACTTCTA
196 TTGTCATAAATATTTTTCTCCACTTTTTTGTTTCAAAAGTGACATTGACAAGTTTTATAATTATA
* *
188479 ATTTATAGTTATTTTTATAAAAAAAAATAATCACATCAAATAATAAAATTCAAGATTTTTGTAAT
261 ATTTATAGTTATTGTTATAAAAAAAAATAATCACATCAAATAATAAAATTAAAGATTTTTGTAAT
*
188544 AAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAGAATCATTTCTTC
326 AAATTATTTTTGTACTTATATATTTTAATAATTATGAAAAATTATACTATCAGAATCATTTCTTC
188609 ATATTTTTTAGTGTAAAAAATGTTA
391 ATATTTTTTAGTGTAAAAAATGTTA
** *
188634 TATAGTAACAAAATATATTGTCTTAAAGATTTTTCTTCATATTTTTTTGCGCAAAAAAAATCATA
1 TATAGTAACAAAATATATTGTCAAAAAGATTTTTCTCCATATTTTTTT-CGCAAAAAAAATCATA
* * *
188699 -CATAA-ACAATTGTTGTAACTACAAGTGTTTATAATTATTACAAAAAACATTGTCACAAAAAAT
65 TCATAACA-AATT-TTGTAACTACAAATGTTAATAATTATTACAAAAAACATTATCAC-AAAAAT
* * *
188762 AATGGTATTCAC-ATTATTGTGACAAATTATACTTGTAGTTATAAATTTTAATTATAGTGAT-GA
127 AATGATATTCACGATT-TTGTAACAAATTATACTTGTAGTTATAAATTTTAACTATAGTGATAG-
* * *
188825 CATATATTGTTATAAATATTTTTCTCCACTTTTTTTGTTTCAAAAAGTGACATTGATAAGTTTTG
190 CATATATTGTCATAAATATTTTTCTCCAC-TTTTTTGTTTC-AAAAGTGACATTGACAAGTTTTA
* * * *
188890 TAATTATAATTTATAGTTATTGTTAT-AGAAAAAATGATCACATCAGATAATAAAATTAAAGTTT
253 TAATTATAATTTATAGTTATTGTTATAAAAAAAAATAATCACATCAAATAATAAAATTAAAGATT
* *
188954 TTTGTAATCAATTATTTTTGTAGTTATATATTTTAATAATTATGAAAAATTATACTATCAGAATC
318 TTTGTAATAAATTATTTTTGTACTTATATATTTTAATAATTATGAAAAATTATACTATCAGAATC
*
189019 ATTTCTTCCTATTTTTT
383 ATTTCTTCATATTTTTT
189036 TGGTTCCAAA
Statistics
Matches: 358, Mismatches: 36, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
414 1 0.00
415 49 0.14
416 59 0.16
417 86 0.24
418 122 0.34
419 41 0.11
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.43
Consensus pattern (415 bp):
TATAGTAACAAAATATATTGTCAAAAAGATTTTTCTCCATATTTTTTTCGCAAAAAAAATCATAT
CATAACAAATTTTGTAACTACAAATGTTAATAATTATTACAAAAAACATTATCACAAAAATAATG
ATATTCACGATTTTGTAACAAATTATACTTGTAGTTATAAATTTTAACTATAGTGATAGCATATA
TTGTCATAAATATTTTTCTCCACTTTTTTGTTTCAAAAGTGACATTGACAAGTTTTATAATTATA
ATTTATAGTTATTGTTATAAAAAAAAATAATCACATCAAATAATAAAATTAAAGATTTTTGTAAT
AAATTATTTTTGTACTTATATATTTTAATAATTATGAAAAATTATACTATCAGAATCATTTCTTC
ATATTTTTTAGTGTAAAAAATGTTA
Found at i:190455 original size:78 final size:78
Alignment explanation
Indices: 190234--190504 Score: 398
Period size: 78 Copynumber: 3.5 Consensus size: 78
190224 AGGTTGTTCT
* * * * *
190234 TCAGCTTTGTCTTCCTTCTGTCGTTCCGAAACATTTACAGTCTCTTTTTGTTTTGCCTCGTTTCC
1 TCAGCATTGTCTTCTTTTTGTCGTTCCGAAACATTTGCAGTCTCTTTTTGTTTTGCCTCGTTTCT
190299 TTTCCCTTGATCC
66 TTTCCCTTGATCC
* * **
190312 TCAACATTGTCTTCTTTTTTTTCGTTTAGAAACATTTGCAGTCTCTTTTTGTTTTGCCTCGTTTC
1 TCAGCATTGTCTTC-TTTTTGTCGTTCCGAAACATTTGCAGTCTCTTTTTGTTTTGCCTCGTTTC
*
190377 TTTTCCCTTGATCT
65 TTTTCCCTTGATCC
* * * *
190391 TCAGCATTGTCTTCTTTTTGTCGCTCCGAAACACTTGCAGCCTCTTTTTGTTTTGCCTTGTTTCT
1 TCAGCATTGTCTTCTTTTTGTCGTTCCGAAACATTTGCAGTCTCTTTTTGTTTTGCCTCGTTTCT
190456 TTTCCCTTGATCC
66 TTTCCCTTGATCC
*
190469 TCAGCATTGTCTTCTTTTTGTTGTTCCGAAACATTT
1 TCAGCATTGTCTTCTTTTTGTCGTTCCGAAACATTT
190505 TTGTATCCCC
Statistics
Matches: 170, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
78 101 0.59
79 69 0.41
ACGTcount: A:0.12, C:0.25, G:0.13, T:0.50
Consensus pattern (78 bp):
TCAGCATTGTCTTCTTTTTGTCGTTCCGAAACATTTGCAGTCTCTTTTTGTTTTGCCTCGTTTCT
TTTCCCTTGATCC
Found at i:191703 original size:31 final size:31
Alignment explanation
Indices: 191629--191717 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
191619 ATTTCTCATT
* **
191629 ATAAAAAATTGTGACAAATGATATTTTTTTCACA
1 ATAAAAAATTGTAACAAA--ATA-TTTAATCACA
*
191663 ATAACAAATTGTAACAAAATATTTAATCACA
1 ATAAAAAATTGTAACAAAATATTTAATCACA
* *
191694 GTAAAAAATTATAA-AAAATATTTA
1 ATAAAAAATTGTAACAAAATATTTA
191718 GTGATGAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 10 0.21
31 19 0.40
32 3 0.06
34 16 0.33
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.34
Consensus pattern (31 bp):
ATAAAAAATTGTAACAAAATATTTAATCACA
Found at i:191714 original size:30 final size:31
Alignment explanation
Indices: 191584--191717 Score: 87
Period size: 34 Copynumber: 4.2 Consensus size: 31
191574 TTGAAAAATT
*
191584 TATTTAATCAAAAT-AAAAATGTATAAC-AAA
1 TATTTAATCACAATAAAAAAT-TATAACAAAA
* * *
191614 TA-TTAATTTCTCATTATAAAAAATTGTGACAAATGA
1 TATTTAA--TCACA--ATAAAAAATTATAACAAA--A
** * *
191650 TATTTTTTTCACAATAACAAATTGTAACAAAA
1 TA-TTTAATCACAATAAAAAATTATAACAAAA
*
191682 TATTTAATCACAGTAAAAAATTATAA-AAAA
1 TATTTAATCACAATAAAAAATTATAACAAAA
191712 TATTTA
1 TATTTA
191718 GTGATGAAAT
Statistics
Matches: 80, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
29 4 0.05
30 12 0.15
31 22 0.28
32 3 0.04
33 6 0.08
34 24 0.30
36 7 0.09
38 2 0.03
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.36
Consensus pattern (31 bp):
TATTTAATCACAATAAAAAATTATAACAAAA
Found at i:193678 original size:3 final size:3
Alignment explanation
Indices: 193658--193734 Score: 77
Period size: 3 Copynumber: 25.7 Consensus size: 3
193648 AACATGTAAA
* * * *
193658 AAT AAT AA- AAG AAA AAT AAT AAT AAT AAT AAT AAT AGT GAT AAT AATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
*
193706 AA- AAT AAT AAT GAT AAT AATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
193735 ACAATTGAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 4 0.06
3 52 0.84
4 6 0.10
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:193702 original size:21 final size:22
Alignment explanation
Indices: 193676--193734 Score: 95
Period size: 21 Copynumber: 2.8 Consensus size: 22
193666 AAGAAAAATA
*
193676 ATAATAA-TAATAATAATAGTG
1 ATAATAATTAATAATAATAATG
193697 ATAATAATTAA-AATAATAATG
1 ATAATAATTAATAATAATAATG
193718 ATAATAATTAATAATAA
1 ATAATAATTAATAATAA
193735 ACAATTGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 27 0.77
22 8 0.23
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (22 bp):
ATAATAATTAATAATAATAATG
Found at i:204343 original size:20 final size:21
Alignment explanation
Indices: 204320--204360 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
204310 TATTATATGT
**
204320 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
204340 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
204361 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:205752 original size:3 final size:3
Alignment explanation
Indices: 205744--205823 Score: 133
Period size: 3 Copynumber: 26.7 Consensus size: 3
205734 AATATATATT
*
205744 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
205792 TAG TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
205824 TTGATAAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:206389 original size:113 final size:112
Alignment explanation
Indices: 206142--206583 Score: 661
Period size: 113 Copynumber: 3.9 Consensus size: 112
206132 AGAATTATGC
* * * *
206142 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * *
206207 TATGAACT-TCTCCAGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTCT-TCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
206254 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * *
206319 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
66 TATGAACTC-TTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
206367 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
206432 TATGAACTTTCTCTGGAAAAGATGATCCATCAATTGACGAATTCATGT
66 TATGAACTCT-TCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
*
206480 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
206545 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATG
66 TATGAAC-TCTTCTGGAAAAGATGATCCATCAAATGATG
206584 GATTTGAATC
Statistics
Matches: 301, Mismatches: 25, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
112 69 0.23
113 229 0.76
114 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (112 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
Found at i:206516 original size:226 final size:225
Alignment explanation
Indices: 206142--206587 Score: 730
Period size: 226 Copynumber: 2.0 Consensus size: 225
206132 AGAATTATGC
* * *
206142 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
206207 TATGAACTTCTCCAGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAATTC
66 TATGAACTTCTCCAGAAAAGATAATCCATCAATTGACGAATTCAGGTAAAAGGTTGAACAAATTC
206272 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAA
206337 AAGATGATCCACCAAATGATGGATTCAGGT
196 AAGATGATCCACCAAATGATGGATTCAGGT
*
206367 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * * *
206432 TATGAACTTTCTCTGGAAAAGATGATCCATCAATTGACGAATTCATGTAAAAGGTTGAACAAGTT
66 TATGAAC-TTCTCCAGAAAAGATAATCCATCAATTGACGAATTCAGGTAAAAGGTTGAACAAATT
****
206497 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGA
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
* * *
206562 AAAGCTGATCCATCAGATGATGGATT
195 AAAGATGATCCACCAAATGATGGATT
206588 TGAATCTTTG
Statistics
Matches: 203, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
225 68 0.33
226 135 0.67
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (225 bp):
AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTCTCCAGAAAAGATAATCCATCAATTGACGAATTCAGGTAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAA
AAGATGATCCACCAAATGATGGATTCAGGT
Found at i:208179 original size:16 final size:16
Alignment explanation
Indices: 208158--208194 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
208148 GAATTTTCAA
208158 AAATAAATTGAATCTT-
1 AAATAAATTGAA-CTTG
208174 AAATAAATTGAACTTG
1 AAATAAATTGAACTTG
208190 AAATA
1 AAATA
208195 TATAGAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (16 bp):
AAATAAATTGAACTTG
Found at i:208526 original size:1 final size:1
Alignment explanation
Indices: 208522--208575 Score: 63
Period size: 1 Copynumber: 54.0 Consensus size: 1
208512 TTTTTTCCTC
* * * * *
208522 TTTTTTTTTCTTTTTTTCTTTTTTTTTTCTTTTTTTTCTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
208576 CTCTTCAAGC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:208535 original size:9 final size:9
Alignment explanation
Indices: 208523--208577 Score: 85
Period size: 9 Copynumber: 6.1 Consensus size: 9
208513 TTTTTCCTCT
208523 TTTTTTTTC
1 TTTTTTTTC
*
208532 TTTTTTTCTT
1 TTTTTTT-TC
208542 TTTTTTTTC
1 TTTTTTTTC
208551 TTTTTTTTC
1 TTTTTTTTC
208560 -TTTTTTTC
1 TTTTTTTTC
208568 TTTTTTTTC
1 TTTTTTTTC
208577 T
1 T
208578 CTTCAAGCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.19
9 26 0.62
10 8 0.19
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:208535 original size:19 final size:19
Alignment explanation
Indices: 208511--208580 Score: 90
Period size: 19 Copynumber: 3.6 Consensus size: 19
208501 CTTGACCCCC
208511 CTTTTTTCCTCTTTTTTTTT
1 CTTTTTT-CTCTTTTTTTTT
208531 CTTTTTT-TCTTTTTTTTTT
1 CTTTTTTCTC-TTTTTTTTT
*
208550 CTTTTTTTTCTTTTTTTCTT
1 CTTTTTTCTCTTTTTTT-TT
208570 -TTTTTTCTCTT
1 CTTTTTTCTCTT
208581 CAAGCATAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
18 2 0.04
19 33 0.72
20 11 0.24
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
CTTTTTTCTCTTTTTTTTT
Found at i:208542 original size:28 final size:28
Alignment explanation
Indices: 208511--208580 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
208501 CTTGACCCCC
208511 CTTTTTTC-CTCTTTTTTTTTCTTTTTTT
1 CTTTTTTCTCTC-TTTTTTTTCTTTTTTT
* *
208539 CTTTTTTTTTTCTTTTTTTTCTTTTTTT
1 CTTTTTTCTCTCTTTTTTTTCTTTTTTT
*
208567 CTTTTTTTTCTCTT
1 CTTTTTTCTCTCTT
208581 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (28 bp):
CTTTTTTCTCTCTTTTTTTTCTTTTTTT
Found at i:221368 original size:3 final size:3
Alignment explanation
Indices: 221360--221442 Score: 139
Period size: 3 Copynumber: 27.7 Consensus size: 3
221350 AATATATATT
*
221360 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
221408 TAA TAG TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
221443 TGGATAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:229532 original size:2 final size:2
Alignment explanation
Indices: 229525--229572 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
229515 ACTGCACTTT
229525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
229566 TA TA TA T
1 TA TA TA T
229573 CATAGATAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:231025 original size:18 final size:17
Alignment explanation
Indices: 230986--231030 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
230976 TTATATACTA
230986 TAAA-TATAA-ATTAAT
1 TAAATTATAATATTAAT
231001 T-AATTATAATATTAATT
1 TAAATTATAATATTAA-T
231018 TAAATTATAATAT
1 TAAATTATAATAT
231031 ATAAATGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.08
15 6 0.23
16 5 0.19
17 2 0.08
18 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTATAATATTAAT
Found at i:239917 original size:90 final size:89
Alignment explanation
Indices: 239795--239971 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 89
239785 TAATCCCGAA
* * * * * *
239795 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCACTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAAAAAAAAC-CTAATATAAT
239860 TAGGGTAACTTAGACATAAAAGGAT
65 TAGGGTAACTTAGACATAAAAGGAT
239885 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAAAAAAAACCTAATATAATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAAAAAAAACCTAATATAATT
* *
239950 AGGGTAACTTGGATATAAAAGG
66 AGGGTAACTTAGACATAAAAGG
239972 GTGTGTTGGG
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 30 0.38
90 49 0.62
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.36
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAAAAAAAACCTAATATAATT
AGGGTAACTTAGACATAAAAGGAT
Done.