Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013725.1 Kokia drynarioides strain JFW-HI SEQ_128753, 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: 43574
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:194 original size:9 final size:9
Alignment explanation
Indices: 180--224 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
170 AAACATATTA
180 CCTTCTTCC
1 CCTTCTTCC
*
189 CCTTCTTCT
1 CCTTCTTCC
198 CCTTCTTCC
1 CCTTCTTCC
*
207 CCTTCTTCT
1 CCTTCTTCC
216 CCTTCTTCC
1 CCTTCTTCC
225 TTCTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (9 bp):
CCTTCTTCC
Found at i:203 original size:18 final size:18
Alignment explanation
Indices: 180--224 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
170 AAACATATTA
180 CCTTCTTCCCCTTCTTCT
1 CCTTCTTCCCCTTCTTCT
198 CCTTCTTCCCCTTCTTCT
1 CCTTCTTCCCCTTCTTCT
216 CCTTCTTCC
1 CCTTCTTCC
225 TTCTTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (18 bp):
CCTTCTTCCCCTTCTTCT
Found at i:232 original size:4 final size:4
Alignment explanation
Indices: 225--266 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
215 TCCTTCTTCC
* *
225 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TTTT TTCT T
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT T
267 CATTTTTCGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 30 0.91
5 3 0.09
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTCT
Found at i:258 original size:21 final size:22
Alignment explanation
Indices: 209--274 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
199 CTTCTTCCCC
* *
209 TTCTTCTCCTTCTTCCTTCTTTCT
1 TTCTT-TCTTTCTTCATT-TTTCT
*
233 TTCTTTCTTTC-TCTTTTTTCT
1 TTCTTTCTTTCTTCATTTTTCT
*
254 TTCTTTTTTTCTTCATTTTTC
1 TTCTTTCTTTCTTCATTTTTC
275 GTTGGTCTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.41
22 12 0.32
23 5 0.14
24 5 0.14
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (22 bp):
TTCTTTCTTTCTTCATTTTTCT
Found at i:273 original size:12 final size:12
Alignment explanation
Indices: 225--266 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
215 TCCTTCTTCC
*
225 TTCTTTCTTTCT
1 TTCTTTCTTTTT
237 TTCTTTCTCTTTT
1 TTCTTTCT-TTTT
250 TTCTTTCTTTTT
1 TTCTTTCTTTTT
262 TTCTT
1 TTCTT
267 CATTTTTCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTCTTTCTTTTT
Found at i:356 original size:15 final size:15
Alignment explanation
Indices: 336--370 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
326 ATTTTTATCA
*
336 CCAACAAAAAAATTT
1 CCAACAAAAAAAATT
351 CCAACAAAAAAAATT
1 CCAACAAAAAAAATT
366 CCAAC
1 CCAAC
371 CACTCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.60, C:0.26, G:0.00, T:0.14
Consensus pattern (15 bp):
CCAACAAAAAAAATT
Found at i:3515 original size:16 final size:17
Alignment explanation
Indices: 3482--3516 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3472 ACCGATTTTC
*
3482 TTTATTTTTTAAACATT
1 TTTATTTTATAAACATT
3499 TTTATTTTATAAA-ATT
1 TTTATTTTATAAACATT
3515 TT
1 TT
3517 AATCATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATTTTATAAACATT
Found at i:4642 original size:29 final size:29
Alignment explanation
Indices: 4604--4671 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
4594 TAGGGAAGAG
* *
4604 ATCAAATTAATTC-TTTTATTATTAAATAA
1 ATCAAATTAA-TCATTGTATTATTAAAAAA
*
4633 ATCAATTTAATCATTGTATTATTAAAAAA
1 ATCAAATTAATCATTGTATTATTAAAAAA
*
4662 ATTAAATTAA
1 ATCAAATTAA
4672 ATTAAATTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 2 0.06
29 31 0.94
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (29 bp):
ATCAAATTAATCATTGTATTATTAAAAAA
Found at i:9066 original size:4 final size:4
Alignment explanation
Indices: 9059--9085 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
9049 TTAAAAATTA
9059 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
9086 ATGGGGTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:10191 original size:7 final size:6
Alignment explanation
Indices: 10174--10203 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
10164 TAGAATTCTA
*
10174 ATTTTT ATTTTT ATTTTT ATTTTT AATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
10204 GATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:10191 original size:12 final size:13
Alignment explanation
Indices: 10172--10203 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
10162 AATAGAATTC
10172 TAATTTTTATTTT
1 TAATTTTTATTTT
10185 T-ATTTTTATTTT
1 TAATTTTTATTTT
10197 TAATTTT
1 TAATTTT
10204 GATAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TAATTTTTATTTT
Found at i:11026 original size:22 final size:22
Alignment explanation
Indices: 10999--11046 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
10989 AAAAATATAT
10999 TTTTTTAGTGTTTGAATTTGAA
1 TTTTTTAGTGTTTGAATTTGAA
11021 TTTTTTAGTGTTTGAATTTGAA
1 TTTTTTAGTGTTTGAATTTGAA
11043 TTTT
1 TTTT
11047 CTCTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (22 bp):
TTTTTTAGTGTTTGAATTTGAA
Found at i:19632 original size:19 final size:20
Alignment explanation
Indices: 19608--19660 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
19598 AATATTTTTC
19608 TTATAAAAA-TAATTAAAAT
1 TTATAAAAACTAATTAAAAT
*
19627 TTATAAAAACTCATTAAAAGT
1 TTATAAAAACTAATTAAAA-T
* *
19648 GTAAAAAAACTAA
1 TTATAAAAACTAA
19661 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 9 0.32
20 8 0.29
21 11 0.39
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (20 bp):
TTATAAAAACTAATTAAAAT
Found at i:19635 original size:20 final size:19
Alignment explanation
Indices: 19608--19645 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
19598 AATATTTTTC
19608 TTATAAAAATAATTAAAAT
1 TTATAAAAATAATTAAAAT
*
19627 TTATAAAAACTCATTAAAA
1 TTATAAAAA-TAATTAAAA
19646 GTGTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
TTATAAAAATAATTAAAAT
Found at i:19740 original size:19 final size:18
Alignment explanation
Indices: 19718--19865 Score: 68
Period size: 19 Copynumber: 7.9 Consensus size: 18
19708 TATAAACTTA
*
19718 AAAAAATTATGCAAAATAT
1 AAAAAATTAT-AAAAATAT
*
19737 AAAATATTATAAAAATAT
1 AAAAAATTATAAAAATAT
* *
19755 -AAAAGTTCTAATAAATTAT
1 AAAAAATTATAA-AAA-TAT
***
19774 AAATTTTTATAAAAATAAT
1 AAAAAATTATAAAAAT-AT
**
19793 AAAACATATT-TAAATTTTAT
1 AAAA-A-ATTATAAA-AATAT
* *
19813 AAAAACATTTTAAAATTAT
1 AAAAA-ATTATAAAAATAT
*
19832 ATAAAAATCATAAAAATAT
1 A-AAAAATTATAAAAATAT
* *
19851 -TAAAATTATTAAAAT
1 AAAAAATTATAAAAAT
19866 TATTAAAAGT
Statistics
Matches: 98, Mismatches: 22, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
17 20 0.20
18 11 0.11
19 39 0.40
20 25 0.26
21 3 0.03
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (18 bp):
AAAAAATTATAAAAATAT
Found at i:19814 original size:20 final size:20
Alignment explanation
Indices: 19791--19873 Score: 61
Period size: 21 Copynumber: 4.3 Consensus size: 20
19781 TATAAAAATA
*
19791 ATAAAACATATTT-AAATTTT
1 ATAAAACAT-TTTAAAATTAT
19811 ATAAAAACATTTTAAAATTAT
1 AT-AAAACATTTTAAAATTAT
**
19832 ATAAAA-ATCATAAAA--AT
1 ATAAAACATTTTAAAATTAT
*
19849 ATTAAA-ATTATTAAAATTAT
1 ATAAAACATT-TTAAAATTAT
19869 -TAAAA
1 ATAAAA
19874 GTATTAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
17 9 0.18
18 5 0.10
19 11 0.22
20 11 0.22
21 15 0.29
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAAACATTTTAAAATTAT
Found at i:19819 original size:21 final size:22
Alignment explanation
Indices: 19793--19843 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
19783 TAAAAATAAT
*
19793 AAAACATATTT-AAATTTTATA
1 AAAACATATTTAAAATTATATA
19814 AAAACAT-TTTAAAATTATATA
1 AAAACATATTTAAAATTATATA
19835 AAAATCATA
1 AAAA-CATA
19844 AAAATATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 20 0.77
22 3 0.12
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAACATATTTAAAATTATATA
Found at i:19911 original size:9 final size:9
Alignment explanation
Indices: 19682--19911 Score: 90
Period size: 9 Copynumber: 24.7 Consensus size: 9
19672 GTATTAATAT
19682 TAAAAA-TA
1 TAAAAATTA
* *
19690 TAAAAAATC
1 TAAAAATTA
* *
19699 GAAAATTTA
1 TAAAAATTA
*
19708 TATAAACTTA
1 TA-AAAATTA
*
19718 AAAAAATTA
1 TAAAAATTA
*
19727 TGCAAAA-TA
1 T-AAAAATTA
19736 TAAAATATTA
1 TAAAA-ATTA
19746 TAAAAA-TA
1 TAAAAATTA
* *
19754 TAAAAGTTC
1 TAAAAATTA
19763 TAATAAATTA
1 TAA-AAATTA
**
19773 TAAATTTTTA
1 TAAA-AATTA
*
19783 TAAAAATAA
1 TAAAAATTA
*
19792 TAAAACATATT
1 TAAAA-AT-TA
**
19803 TAAATTTTA
1 TAAAAATTA
*
19812 TAAAAACATTT
1 T-AAAA-ATTA
*
19823 TAAAATTATA
1 TAAAAAT-TA
*
19833 TAAAAATCA
1 TAAAAATTA
19842 TAAAAA-TA
1 TAAAAATTA
*
19850 TTAAAATTA
1 TAAAAATTA
*
19859 TTAAAATTA
1 TAAAAATTA
* *
19868 TTAAAAGTA
1 TAAAAATTA
*
19877 TTAAAATTGA
1 TAAAAATT-A
* * *
19887 TATCAACTTG
1 TA-AAAATTA
19897 TAAAAATTA
1 TAAAAATTA
19906 TAAAAA
1 TAAAAA
19912 AAAATCACTA
Statistics
Matches: 162, Mismatches: 44, Indels: 31
0.68 0.19 0.13
Matches are distributed among these distances:
8 22 0.14
9 76 0.47
10 53 0.33
11 11 0.07
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:20389 original size:10 final size:10
Alignment explanation
Indices: 20367--20518 Score: 69
Period size: 10 Copynumber: 16.0 Consensus size: 10
20357 TTTATATCAA
20367 TTTTAAT-AT
1 TTTTAATAAT
20376 TTTTAATAATT
1 TTTTAATAA-T
* *
20387 TTTTTACAAT
1 TTTTAATAAT
* *
20397 TTTTTATTAT
1 TTTTAATAAT
* *
20407 TTTAAAGAA-
1 TTTTAATAAT
*
20416 TTCTAAT-AT
1 TTTTAATAAT
20425 GTTTT--TCAA-
1 -TTTTAAT-AAT
*
20434 TTTAAATA-T
1 TTTTAATAAT
*
20443 TTTAAATAAT
1 TTTTAATAAT
20453 TTTT-ATAAT
1 TTTTAATAAT
20462 TTATT-ATAA-
1 TT-TTAATAAT
20471 TTTTAATAA-
1 TTTTAATAAT
*
20480 GTTTATATAA-
1 TTTTA-ATAAT
20490 TTTTAAT-AT
1 TTTTAATAAT
*
20499 TTTTAATAAA
1 TTTTAATAAT
20509 TTTTAATAAT
1 TTTTAATAAT
20519 AACTAATATT
Statistics
Matches: 110, Mismatches: 18, Indels: 29
0.70 0.11 0.18
Matches are distributed among these distances:
8 8 0.07
9 46 0.42
10 48 0.44
11 8 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:20389 original size:19 final size:19
Alignment explanation
Indices: 20367--20518 Score: 84
Period size: 19 Copynumber: 8.0 Consensus size: 19
20357 TTTATATCAA
*
20367 TTTTAATATTTTTAATAATT
1 TTTTAATAATTTTAATAA-T
* * * *
20387 TTTTTACAATTTTTTATTAT
1 TTTTAATAA-TTTTAATAAT
* * *
20407 TTTAAAGAATTCTAAT-AT
1 TTTTAATAATTTTAATAAT
*
20425 GTTTT--TCAATTTAAAT-AT
1 -TTTTAAT-AATTTTAATAAT
* *
20443 TTTAAATAATTTTTATAAT
1 TTTTAATAATTTTAATAAT
20462 TTATT-ATAATTTTAATAA-
1 TT-TTAATAATTTTAATAAT
*
20480 GTTTATATAATTTTAAT-AT
1 TTTTA-ATAATTTTAATAAT
20499 TTTTAATAAATTTTAATAAT
1 TTTTAAT-AATTTTAATAAT
20519 AACTAATATT
Statistics
Matches: 99, Mismatches: 21, Indels: 24
0.69 0.15 0.17
Matches are distributed among these distances:
17 5 0.05
18 22 0.22
19 49 0.49
20 16 0.16
21 7 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTAATAATTTTAATAAT
Found at i:20490 original size:38 final size:38
Alignment explanation
Indices: 20443--20517 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
20433 ATTTAAATAT
*
20443 TTTAAATAATTTTTATAATTTATT-AT-AATTTTAATAAG
1 TTTAAATAATTTTAAT-ATTT-TTAATAAATTTTAATAAG
*
20481 TTTATATAATTTTAATATTTTTAATAAATTTTAATAA
1 TTTAAATAATTTTAATATTTTTAATAAATTTTAATAA
20518 TAACTAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 2 0.06
37 6 0.18
38 25 0.76
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (38 bp):
TTTAAATAATTTTAATATTTTTAATAAATTTTAATAAG
Found at i:20502 original size:28 final size:27
Alignment explanation
Indices: 20432--20507 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
20422 TATGTTTTTC
* * *
20432 AATTTAAATATTTTAAATAATTTTTAT
1 AATTTTAATATTTTTAATAATTTATAT
* *
20459 AATTTATTATAATTTTAATAAGTTTATAT
1 AATTT-TAATATTTTTAATAA-TTTATAT
20488 AATTTTAATATTTTTAATAA
1 AATTTTAATATTTTTAATAA
20508 ATTTTAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 5 0.12
28 24 0.60
29 11 0.28
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
AATTTTAATATTTTTAATAATTTATAT
Found at i:20561 original size:10 final size:10
Alignment explanation
Indices: 20538--20580 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
20528 TAATTTTTTA
* *
20538 TTTTTATAAG
1 TTTTTATGAT
20548 TTTTT-TGAT
1 TTTTTATGAT
*
20557 TTTTTATCAT
1 TTTTTATGAT
20567 TTTTTATGAT
1 TTTTTATGAT
20577 TTTT
1 TTTT
20581 AATCATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (10 bp):
TTTTTATGAT
Found at i:20571 original size:20 final size:20
Alignment explanation
Indices: 20548--20589 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
20538 TTTTTATAAG
*
20548 TTTTT-TGATTTTTTATCAT
1 TTTTTATGATTTTTAATCAT
20567 TTTTTATGATTTTTAATCAT
1 TTTTTATGATTTTTAATCAT
20587 TTT
1 TTT
20590 ATGGTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTTATGATTTTTAATCAT
Found at i:20581 original size:19 final size:18
Alignment explanation
Indices: 20531--20589 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
20521 CTAATATTAA
* *
20531 TTTTTT-ATTTTTATAAG
1 TTTTTTGATTTTTATCAT
20548 TTTTTTGATTTTTTATCAT
1 TTTTTTGA-TTTTTATCAT
20567 TTTTTATGATTTTTAATCAT
1 TTTTT-TGATTTTT-ATCAT
20587 TTT
1 TTT
20590 ATGGTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
17 6 0.17
18 1 0.03
19 18 0.50
20 11 0.31
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTTTGATTTTTATCAT
Found at i:20588 original size:10 final size:10
Alignment explanation
Indices: 20555--20589 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
20545 AAGTTTTTTG
20555 ATTTTTTATC
1 ATTTTTTATC
*
20565 ATTTTTTATG
1 ATTTTTTATC
*
20575 ATTTTTAATC
1 ATTTTTTATC
20585 ATTTT
1 ATTTT
20590 ATGGTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.69
Consensus pattern (10 bp):
ATTTTTTATC
Found at i:24675 original size:58 final size:57
Alignment explanation
Indices: 24602--24761 Score: 182
Period size: 58 Copynumber: 2.8 Consensus size: 57
24592 ATTATATATA
* *
24602 TTATGATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAAAT-GTT-ATTAAATT
1 TTAT-ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAAATAATTAAAT-AATT
* * *
24660 TTATATTATTTATTAAATTGTATTTAATAATAATTATGGTAAAAAATAATTAAATAATT
1 TTATATT-TTTATTAAATTATATTTAATAATAATTAT-ATTAAAAATAATTAAATAATT
* *
24719 TTTTATTTTTATTAAATTATATTTAATAATAATTTTATTAAAA
1 TTATATTTTTATTAAATTATATTTAATAATAATTATATTAAAA
24762 TTTAATAGCA
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
57 23 0.26
58 46 0.53
59 16 0.18
60 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (57 bp):
TTATATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATAATTAAATAATT
Found at i:25680 original size:31 final size:31
Alignment explanation
Indices: 25634--25695 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
25624 AAATTTTAAA
*
25634 TTAATAAAAATAAAATTATATTTTAATTTTT
1 TTAATAAAAATAAAATTATAATTTAATTTTT
25665 TTAA-AAATAATAAAATTATAATTTAATTTTT
1 TTAATAAA-AATAAAATTATAATTTAATTTTT
25696 AAAAATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TTAATAAAAATAAAATTATAATTTAATTTTT
Found at i:25701 original size:21 final size:21
Alignment explanation
Indices: 25676--25738 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
25666 TAAAAATAAT
25676 AAAATTATAATTTAATTTTTA
1 AAAATTATAATTTAATTTTTA
* * **
25697 AAAATTATATTTTTACTATGATA
1 AAAATTATA-ATTTAAT-TTTTA
25720 AAAATTATAATTTAATTTT
1 AAAATTATAATTTAATTTT
25739 CACCTATTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
21 10 0.31
22 10 0.31
23 12 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
AAAATTATAATTTAATTTTTA
Found at i:33247 original size:64 final size:60
Alignment explanation
Indices: 33085--33253 Score: 144
Period size: 64 Copynumber: 2.7 Consensus size: 60
33075 ATATTTGATA
* * * * **
33085 TTTTTTAATTTGGTATTTAAACTTTTTTTTA-TTCAATTTGATATTTGAACTTAACATTTT
1 TTTTTTAATTTGATATCT-AACTTTTTTTAAGTTCAATTTGGTACCTGAACTTAACATTTT
* * ** ** *
33145 TTTCTTAATTTGATA-CTTAAATTTTTATTGGGCCCAATTTGGTACCTGAACTTATCATGTTTTT
1 TTTTTTAATTTGATATC-TAACTTTTT-TTAAGTTCAATTTGGTACCTGAACTTAACA---TTTT
33209 TTTTTTAATTTGATATCTAAGCTTTTTTTAAGTTCAATTTGGTAC
1 TTTTTTAATTTGATATCTAA-CTTTTTTTAAGTTCAATTTGGTAC
33254 ATAAATTTAT
Statistics
Matches: 83, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
59 7 0.08
60 16 0.19
61 19 0.23
64 35 0.42
65 6 0.07
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (60 bp):
TTTTTTAATTTGATATCTAACTTTTTTTAAGTTCAATTTGGTACCTGAACTTAACATTTT
Found at i:34254 original size:44 final size:43
Alignment explanation
Indices: 34203--34289 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
34193 TAAAATCAAA
*
34203 TAATTAATTCAAAC-ATCATTATTATTTTTATATGTAAAATATTT
1 TAATTAATT-AAACGAT-ATCATTATTTTTATATGTAAAATATTT
** *
34247 TAATTAATTATTCGATATCATTATTTTTATATGTGAAATATTT
1 TAATTAATTAAACGATATCATTATTTTTATATGTAAAATATTT
34290 CAAATACAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 27 0.71
44 11 0.29
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (43 bp):
TAATTAATTAAACGATATCATTATTTTTATATGTAAAATATTT
Found at i:34494 original size:18 final size:20
Alignment explanation
Indices: 34459--34495 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
34449 GAAAAAACAA
34459 TGATATTTAAAATGATTATT
1 TGATATTTAAAATGATTATT
*
34479 TGAT-TTTATAAT-ATTAT
1 TGATATTTAAAATGATTAT
34496 AAATCACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 7 0.44
20 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TGATATTTAAAATGATTATT
Found at i:34716 original size:95 final size:92
Alignment explanation
Indices: 34601--34784 Score: 251
Period size: 93 Copynumber: 2.0 Consensus size: 92
34591 AAAATATATA
* * * *
34601 TTTAATATAATGATAAATATAAAAAATATATTTTCATTATATAATCACATATTTATTAATTTATT
1 TTTAACATAATCATAAATAT--AAAATACATTTTCATTATATAATCACAAATTTATTAATTTATT
*
34666 TATATAAATAAACGAATTATTAATTAATTT
64 TATATAAATAAA-AAATTATTAATTAATTT
* * * * *
34696 TTTAACATAATCATATATATAAAATGCATTTTTATTATATAATTACAAATTTATTATTTTATTTA
1 TTTAACATAATCATAAATATAAAATACATTTTCATTATATAATCACAAATTTATTAATTTATTTA
34761 TATAAATAAAAAATTATTAATTAA
66 TATAAATAAAAAATTATTAATTAA
34785 AATAAAAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
92 13 0.16
93 49 0.62
95 17 0.22
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (92 bp):
TTTAACATAATCATAAATATAAAATACATTTTCATTATATAATCACAAATTTATTAATTTATTTA
TATAAATAAAAAATTATTAATTAATTT
Found at i:34761 original size:28 final size:27
Alignment explanation
Indices: 34725--34779 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
34715 TAAAATGCAT
* * *
34725 TTTTATTATATAATTACAAATTTATTA
1 TTTTATTATATAAATAAAAAATTATTA
34752 TTTTATTTATATAAATAAAAAATTATTA
1 TTTTA-TTATATAAATAAAAAATTATTA
34780 ATTAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTTATTATATAAATAAAAAATTATTA
Done.