Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000702.1 Hibiscus syriacus cultivar Beakdansim tig00001365_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: 135243
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8305 original size:18 final size:19
Alignment explanation
Indices: 8275--8311 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
8265 TTCATGACAA
8275 TATATATTAAAATA-AAAT
1 TATATATTAAAATATAAAT
8293 TATATA-TACAAATATAAAT
1 TATATATTA-AAATATAAAT
8312 AAAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.12
18 11 0.65
19 4 0.24
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TATATATTAAAATATAAAT
Found at i:12202 original size:19 final size:21
Alignment explanation
Indices: 12166--12214 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
12156 TACAGTCCAC
12166 AAATAAATGAATCCA-TTTACA
1 AAATAAAT-AATCCATTTTACA
12187 AAATAAATAA-CCATTTTACA
1 AAATAAATAATCCATTTTACA
12207 AAA-AAATA
1 AAATAAATA
12215 TACAAGATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.30
20 11 0.41
21 8 0.30
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAAATAATCCATTTTACA
Found at i:12807 original size:10 final size:11
Alignment explanation
Indices: 12792--12820 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12782 TACACTCAAG
12792 AAAATAAG-GA
1 AAAATAAGTGA
12802 AAAATAAGTGA
1 AAAATAAGTGA
12813 AAAATAAG
1 AAAATAAG
12821 AAAGATACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (11 bp):
AAAATAAGTGA
Found at i:13731 original size:65 final size:65
Alignment explanation
Indices: 13650--13772 Score: 210
Period size: 65 Copynumber: 1.9 Consensus size: 65
13640 TTTCTAATCC
*
13650 TCCTATTTTAATCACTTGTTTAATTATACGCTAAAGCCTTTAGATTTTAGGTTCTTTAGTTTTCT
1 TCCTATTTTAATCACTTGTTTAATTATACACTAAAGCCTTTAGATTTTAGGTTCTTTAGTTTTCT
* * *
13715 TCCTATTTTAATCACTTGTTTAATTATATACTAAATCCTTTAGATTTTATGTTCTTTA
1 TCCTATTTTAATCACTTGTTTAATTATACACTAAAGCCTTTAGATTTTAGGTTCTTTA
13773 ATTTCAGTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (65 bp):
TCCTATTTTAATCACTTGTTTAATTATACACTAAAGCCTTTAGATTTTAGGTTCTTTAGTTTTCT
Found at i:15639 original size:26 final size:26
Alignment explanation
Indices: 15603--15664 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
15593 ATTGTTACTA
15603 TTGTTTATTTCTCTCTACTAACTTGG
1 TTGTTTATTTCTCTCTACTAACTTGG
*
15629 TTGTTTATTTCTCTTTACTAACTTGG
1 TTGTTTATTTCTCTCTACTAACTTGG
15655 TTGTTTATTT
1 TTGTTTATTT
15665 TCTTGATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.60
Consensus pattern (26 bp):
TTGTTTATTTCTCTCTACTAACTTGG
Found at i:19688 original size:22 final size:22
Alignment explanation
Indices: 19663--19736 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
19653 GGGTATATTA
19663 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
19685 GTCCTTCGAGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
19707 GTCCTTTGGGAC--AT--AGTG
1 GTCCTTCGGGACGTATCCAGTG
19725 GTCCTTCGGGAC
1 GTCCTTCGGGAC
19737 AAATACTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.31
20 2 0.04
22 31 0.65
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:19726 original size:18 final size:18
Alignment explanation
Indices: 19703--19737 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19693 AGACGTATCC
*
19703 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
19721 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
19738 AATACTGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:28558 original size:5 final size:5
Alignment explanation
Indices: 28532--28579 Score: 69
Period size: 5 Copynumber: 9.6 Consensus size: 5
28522 CTGGACTGGT
* * *
28532 CCGAG CTGAG TCGAG CCAAG CCGAG CCGAG CCGAG CCGAG CCGAG CCG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCG
28580 TTGACTGTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.21, C:0.38, G:0.38, T:0.04
Consensus pattern (5 bp):
CCGAG
Found at i:30551 original size:12 final size:12
Alignment explanation
Indices: 30534--30597 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
30524 CATGAATGTT
30534 TTATCTGATTTC
1 TTATCTGATTTC
*
30546 TTATCTGAATTC
1 TTATCTGATTTC
30558 TGT-TCTGATTTC
1 T-TATCTGATTTC
*
30570 TAATCTGGA-TTC
1 TTATCT-GATTTC
*
30582 TGT-TCTGATATC
1 T-TATCTGATTTC
30594 TTAT
1 TTAT
30598 ATAAATTCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
11 3 0.07
12 35 0.85
13 3 0.07
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (12 bp):
TTATCTGATTTC
Found at i:30565 original size:24 final size:24
Alignment explanation
Indices: 30537--30618 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
30527 GAATGTTTTA
30537 TCTGATTTCTTATCTGAATTCTGT
1 TCTGATTTCTTATCTGAATTCTGT
* *
30561 TCTGATTTCTAATCTGGATTCTGT
1 TCTGATTTCTTATCTGAATTCTGT
* * * *
30585 TCTGATATCTTATATAAATTCTAT
1 TCTGATTTCTTATCTGAATTCTGT
*
30609 TTTGATTTCT
1 TCTGATTTCT
30619 GATATCTCCG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.54
Consensus pattern (24 bp):
TCTGATTTCTTATCTGAATTCTGT
Found at i:30623 original size:24 final size:24
Alignment explanation
Indices: 30578--30623 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
30568 TCTAATCTGG
* *
30578 ATTCTGTTCTGATATCTTATATAA
1 ATTCTATTCTGATATCTGATATAA
* *
30602 ATTCTATTTTGATTTCTGATAT
1 ATTCTATTCTGATATCTGATAT
30624 CTCCGTTCAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (24 bp):
ATTCTATTCTGATATCTGATATAA
Found at i:30761 original size:44 final size:44
Alignment explanation
Indices: 30698--31042 Score: 299
Period size: 44 Copynumber: 8.1 Consensus size: 44
30688 TTTTTAACTT
*
30698 GTAAGACCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
* * *
30742 GTAAGTCCTTACCGTTACCGCAAGCTCCTCTTCTATGTGCAAGA
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
* * *
30786 GTAAGTCCTTACCGTTACCGTAAGCTACTCTGCTATGTGCAAGG
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
* * *
30830 GTATGTCCTTACCGTTATCGCATGCTCCTCTGCTATGTGCAAGG
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
* * ** * * *
30874 GTATGTCCTTACCATTTTC-CAGGCTCCTATG-TAAGGTGCAAGA
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCT-ATGTGCAAGG
* * **
30917 GTAAGTCCTTACTGTGT-CC-AAGGCTCCTCTATTATGTGCAAGG
1 GTAAGTCCTTACCGT-TACCGCAGGCTCCTCTGCTATGTGCAAGG
* * *
30960 ATAAG-----ACC-TTACTGCAGGCTCCTCTGCTTTGTGCACAGG
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCA-AGG
* * *
30999 ATAAG-----ACC-TTACCTCAGGCTCCTCTGCTTTGTGCACAGG
1 GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCA-AGG
31038 GTAAG
1 GTAAG
31043 CCCCTTTAGT
Statistics
Matches: 257, Mismatches: 38, Indels: 17
0.82 0.12 0.05
Matches are distributed among these distances:
36 1 0.00
37 2 0.01
38 19 0.07
39 44 0.17
42 1 0.00
43 52 0.20
44 138 0.54
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (44 bp):
GTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGG
Found at i:31017 original size:39 final size:39
Alignment explanation
Indices: 30937--31042 Score: 155
Period size: 39 Copynumber: 2.7 Consensus size: 39
30927 ACTGTGTCCA
*
30937 AGGCTCCTCT-ATTATGTGCA-AGGATAAGACCTTACTGC
1 AGGCTCCTCTGCTT-TGTGCACAGGATAAGACCTTACTGC
30975 AGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTACCT-C
1 AGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTA-CTGC
*
31014 AGGCTCCTCTGCTTTGTGCACAGGGTAAG
1 AGGCTCCTCTGCTTTGTGCACAGGATAAG
31043 CCCCTTTAGT
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
38 16 0.25
39 45 0.71
40 2 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (39 bp):
AGGCTCCTCTGCTTTGTGCACAGGATAAGACCTTACTGC
Found at i:38575 original size:22 final size:21
Alignment explanation
Indices: 38533--38572 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38523 GAGTTTGTTT
*
38533 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
38554 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
38573 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:45265 original size:37 final size:37
Alignment explanation
Indices: 45161--45270 Score: 132
Period size: 37 Copynumber: 3.0 Consensus size: 37
45151 TAAAATGTAT
* * * ** *
45161 TTGCTTCACTATTCTTTCCTGAAGGCTTATA-AATGAT
1 TTGCTTCACAACTCTTTCGTGAAGGCTTA-AGTTTGAA
* *
45198 TTGCTTCACCACTCTTCCGTGAAGGCTTAAGTTTGAA
1 TTGCTTCACAACTCTTTCGTGAAGGCTTAAGTTTGAA
45235 TTGCTTCACAACTCTTTCGTGAAGGCTTAAGTTTGA
1 TTGCTTCACAACTCTTTCGTGAAGGCTTAAGTTTGA
45271 CTTGTTTCGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 1 0.02
37 62 0.98
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (37 bp):
TTGCTTCACAACTCTTTCGTGAAGGCTTAAGTTTGAA
Found at i:58995 original size:2 final size:2
Alignment explanation
Indices: 58983--59023 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
58973 CATTTGGTTT
* *
58983 TA TA AA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59024 GTTCTTTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:60668 original size:30 final size:31
Alignment explanation
Indices: 60629--60696 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 31
60619 AGGGAGGGAA
*
60629 AAATATTTTGGATGAAAATGATCCTTGTCCT
1 AAATATTTTGGATGAAAATGAACCTTGTCCT
60660 AAAT-TTTTGGATGAAAATGAACCTTGTCCT
1 AAATATTTTGGATGAAAATGAACCTTGTCCT
60690 AAA-ATTT
1 AAATATTT
60697 AGGCTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (31 bp):
AAATATTTTGGATGAAAATGAACCTTGTCCT
Found at i:67485 original size:34 final size:34
Alignment explanation
Indices: 67437--67506 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
67427 CATAATTCAC
*
67437 ATATTCTTTTACTATACACTTCTTTTGAGATTGA
1 ATATCCTTTTACTATACACTTCTTTTGAGATTGA
67471 ATATCCTTTTACTATACACTTCTTTTGAGATTGA
1 ATATCCTTTTACTATACACTTCTTTTGAGATTGA
67505 AT
1 AT
67507 TTTATTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.49
Consensus pattern (34 bp):
ATATCCTTTTACTATACACTTCTTTTGAGATTGA
Found at i:69520 original size:34 final size:33
Alignment explanation
Indices: 69472--69538 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
69462 ACGATTAATC
* *
69472 TACTGATTGCAGAGAAAACTTTTCACTTAGTCAA
1 TACTGATGGCAGAGAAAAC-TTTCACTCAGTCAA
* * *
69506 TACTGATGGTAGAGAGAGCTTTCACTCAGTCAA
1 TACTGATGGCAGAGAAAACTTTCACTCAGTCAA
69539 ATAACAGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (33 bp):
TACTGATGGCAGAGAAAACTTTCACTCAGTCAA
Found at i:71658 original size:21 final size:21
Alignment explanation
Indices: 71634--71673 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
71624 TATTCAGTGT
71634 AAAAAAATTAATTATATACTC
1 AAAAAAATTAATTATATACTC
* *
71655 AAAAAAGTTATTTATATAC
1 AAAAAAATTAATTATATAC
71674 AAACTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAAAAATTAATTATATACTC
Found at i:72676 original size:12 final size:13
Alignment explanation
Indices: 72659--72688 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
72649 TTAAAACTTG
72659 ATAGAATG-ATAA
1 ATAGAATGAATAA
72671 ATAGAATGAATAA
1 ATAGAATGAATAA
72684 ATAGA
1 ATAGA
72689 GTGTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (13 bp):
ATAGAATGAATAA
Found at i:73674 original size:20 final size:21
Alignment explanation
Indices: 73643--73682 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
73633 AGCCGTTAGG
73643 GCCTTATGGTATCGATACTAT
1 GCCTTATGGTATCGATACTAT
73664 GCCTT-TGGTATCGATACTA
1 GCCTTATGGTATCGATACTA
73683 CTATACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (21 bp):
GCCTTATGGTATCGATACTAT
Found at i:74652 original size:201 final size:201
Alignment explanation
Indices: 74307--74709 Score: 797
Period size: 201 Copynumber: 2.0 Consensus size: 201
74297 ATACAAATAG
74307 TTGAAATTAAGTACAAATGCATAAAGCTTTAATTTTAGGTCAAAAATTTTAAAATTTGTAAAATC
1 TTGAAATTAAGTACAAATGCATAAAGCTTTAATTTTAGGTCAAAAATTTTAAAATTTGTAAAATC
*
74372 AAGCATTTTAAATGTTGATATCAATTGTTAGAGAGATATCGTTTGCATTAAAATCAATTTTGACC
66 AAGCATTTGAAATGTTGATATCAATTGTTAGAGAGATATCGTTTGCATTAAAATCAATTTTGACC
74437 AAAATTCATTATGATGAACAAAAAAATAATGAAAATATTAAAACTTTAAAATGTTCAACATAACA
131 AAAATTCATTATGATGAACAAAAAAATAATGAAAATATTAAAACTTTAAAATGTTCAACATAACA
74502 TCTTTT
196 TCTTTT
74508 TTGAAATTAAGTACAAATGCATAAAGCTTTAATTTTAGGTCAAAAATTTTAAAATTTGTAAAATC
1 TTGAAATTAAGTACAAATGCATAAAGCTTTAATTTTAGGTCAAAAATTTTAAAATTTGTAAAATC
74573 AAGCATTTGAAATGTTGATATCAATTGTTAGAGAGATATCGTTTGCATTAAAATCAATTTTGACC
66 AAGCATTTGAAATGTTGATATCAATTGTTAGAGAGATATCGTTTGCATTAAAATCAATTTTGACC
74638 AAAATTCATTATGATGAACAAAAAAATAATGAAAATATTAAAACTTTAAAATGTTCAACATAACA
131 AAAATTCATTATGATGAACAAAAAAATAATGAAAATATTAAAACTTTAAAATGTTCAACATAACA
74703 TCTTTT
196 TCTTTT
74709 T
1 T
74710 AACATACATG
Statistics
Matches: 201, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 201 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (201 bp):
TTGAAATTAAGTACAAATGCATAAAGCTTTAATTTTAGGTCAAAAATTTTAAAATTTGTAAAATC
AAGCATTTGAAATGTTGATATCAATTGTTAGAGAGATATCGTTTGCATTAAAATCAATTTTGACC
AAAATTCATTATGATGAACAAAAAAATAATGAAAATATTAAAACTTTAAAATGTTCAACATAACA
TCTTTT
Found at i:77130 original size:20 final size:21
Alignment explanation
Indices: 77096--77135 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
77086 AGCCGTTGGG
*
77096 GCCTTATGGTGTCGATACTAT
1 GCCTTATGGTATCGATACTAT
77117 GCCTT-TGGTATCGATACTA
1 GCCTTATGGTATCGATACTA
77136 CTATACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (21 bp):
GCCTTATGGTATCGATACTAT
Found at i:77447 original size:12 final size:11
Alignment explanation
Indices: 77421--77452 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
77411 TCTAAAGGTC
77421 GAAAAAATTCT
1 GAAAAAATTCT
77432 GAAAAAATTCT
1 GAAAAAATTCT
*
77443 GGAAAAATTC
1 GAAAAAATTC
77453 CTACGTACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (11 bp):
GAAAAAATTCT
Found at i:88920 original size:15 final size:16
Alignment explanation
Indices: 88892--88921 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88882 AGGAATGTAA
88892 GATTACTAGGGAATAG
1 GATTACTAGGGAATAG
88908 GATTACT-GGGAATA
1 GATTACTAGGGAATA
88922 TTGTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.27
Consensus pattern (16 bp):
GATTACTAGGGAATAG
Found at i:90281 original size:3 final size:3
Alignment explanation
Indices: 90273--90335 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
90263 TTATAAAATG
* * *
90273 TAA TAA TAA TAA TAA TAT TAG TAA TAA AAA TAA T-A TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
90318 TAA TAA T-A TAA TTAA TAA
1 TAA TAA TAA TAA -TAA TAA
90336 CCTTTTTTCG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.08
3 41 0.80
4 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:90296 original size:21 final size:22
Alignment explanation
Indices: 90272--90329 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
90262 CTTATAAAAT
90272 GTAATAATAATAATAAT-ATTA
1 GTAATAATAATAATAATAATTA
*
90293 GTAATAAAAATAAT-ATAATTA
1 GTAATAATAATAATAATAATTA
*
90314 ATAATAATAAT-ATAAT
1 GTAATAATAATAATAAT
90330 TAATAACCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (22 bp):
GTAATAATAATAATAATAATTA
Found at i:90299 original size:18 final size:18
Alignment explanation
Indices: 90276--90335 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
90266 TAAAATGTAA
*
90276 TAATAATAATAATATTAG
1 TAATAATAATAATATAAG
* *
90294 TAATAAAAATAATATAAT
1 TAATAATAATAATATAAG
*
90312 TAATAATAATAATATAAT
1 TAATAATAATAATATAAG
90330 TAATAA
1 TAATAA
90336 CCTTTTTTCG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
TAATAATAATAATATAAG
Found at i:90806 original size:131 final size:130
Alignment explanation
Indices: 90541--90880 Score: 371
Period size: 131 Copynumber: 2.6 Consensus size: 130
90531 AGTGGCATGA
* * * ** * * * *
90541 CTCCTACATGATGAGGAGATCTGGTCAGTAGATGACACTGTTCCTACACGATGAGGACGA-ATGA
1 CTCCTACGTGATGAGAAGGTCTGGTCAGGGGATGACACGGTTCCTACGCGATGAGGAAGACA-GG
* *
90605 CCATCTTTAGGAAGGGAGATAACATGGTTCCTATGCGATGAGAACGACTGATTATCTAAGGGTGA
65 CCATCTTT----AGGGAGATAACATAGTTCCTACGCGATGAGAACGACTGATTATCTAAGGGTGA
90670 CACGG
126 CACGG
* * * * ***
90675 CTCCTACGTGAT-A-AAGAGTTCTGGTCGGGGGATGACATGGTTCCTACGTGTTGAGGACTTCAG
1 CTCCTACGTGATGAGAAG-G-TCTGGTCAGGGGATGACACGGTTCCTACGCGATGAGGAAGACAG
* * * *
90738 GCCATCTTTAGGGATGATAACATAGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGACA
64 GCCATCTTTAGGGA-GATAACATAGTTCCTACGCGATGAGAACGACTGATTATCTAAGGGTGACA
90803 CGG
128 CGG
* *
90806 CTCCTACGTGATGAGAAGGTCTGGTCAGTGGATGACACGGTTCCTACGCGATGAGGAAGACATGC
1 CTCCTACGTGATGAGAAGGTCTGGTCAGGGGATGACACGGTTCCTACGCGATGAGGAAGACAGGC
90871 CATCTTTAGG
66 CATCTTTAGG
90881 TATTTGTTTC
Statistics
Matches: 171, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
130 5 0.03
131 106 0.62
132 4 0.02
133 4 0.02
134 51 0.30
135 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (130 bp):
CTCCTACGTGATGAGAAGGTCTGGTCAGGGGATGACACGGTTCCTACGCGATGAGGAAGACAGGC
CATCTTTAGGGAGATAACATAGTTCCTACGCGATGAGAACGACTGATTATCTAAGGGTGACACGG
Found at i:90989 original size:66 final size:64
Alignment explanation
Indices: 90883--91038 Score: 167
Period size: 66 Copynumber: 2.4 Consensus size: 64
90873 TCTTTAGGTA
* *
90883 TTTGTTTCAAGGGAAACAAACTCAAAGATGATCATTCAAGAGAAGA-TATCTTAAGAAAGACAAA
1 TTTGTTTCAAGAGAAACAAACTCAAAGATGATCATTCAAGAGAA-ACTATCTCAAG--AGACAAA
90947 AT
63 AT
* **
90949 TTTGTTTTAAGAGAAA-AAGACTCAAAGATTG-TGTTTCAAGAGAAACTATCTCAAGAGACAAAA
1 TTTGTTTCAAGAGAAACAA-ACTCAAAGA-TGATCATTCAAGAGAAACTATCTCAAGAGACAAAA
91012 -
64 T
* * *
91012 TTCGTTTCAAGATAAACAATCTCAAAG
1 TTTGTTTCAAGAGAAACAAACTCAAAG
91039 TTTGCCAATT
Statistics
Matches: 77, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
63 20 0.26
64 10 0.13
65 3 0.04
66 42 0.55
67 2 0.03
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (64 bp):
TTTGTTTCAAGAGAAACAAACTCAAAGATGATCATTCAAGAGAAACTATCTCAAGAGACAAAAT
Found at i:91314 original size:37 final size:37
Alignment explanation
Indices: 91183--91302 Score: 163
Period size: 36 Copynumber: 3.3 Consensus size: 37
91173 GTATTCCGAT
* * *
91183 AGAAACTGTCTCAAGTGAGACAAAATTTG-TTTTGAA
1 AGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAA
* * *
91219 AGAAATTGTTTCAAGCGAAACAAAATTTGTTTTTAAG
1 AGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAA
*
91256 A-AAATTGTCTCCAGCGAGACAAAATTTGTTTTTAAA
1 AGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAA
91292 AGAAATTGTCT
1 AGAAATTGTCT
91303 AAAAGGTGAC
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
36 57 0.79
37 15 0.21
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (37 bp):
AGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAA
Found at i:97207 original size:243 final size:240
Alignment explanation
Indices: 96752--97239 Score: 843
Period size: 243 Copynumber: 2.0 Consensus size: 240
96742 GTGAGTGGCT
* *
96752 AATGGGGATTGGAAATAAATACCTCTCAAGAAATGGCCCGGGCATATCTCATATTTTTTGCGGAT
1 AATGGGGATTGAAAATAAATACCTCTCAAGAAATGGCCCGGACATATCTCATATTTTTTGCGGAT
96817 AATTTGGTCATGTTTTCCGAGGTTTTCATGGATCAAGTTGTTGTGATAAAAGATATTATTGAACA
66 AATTTGGTCATGTTTTCCGAGGTTTTCATGGATCAA--TGTTGTGATAAAAGATATTATTGAACA
96882 TTCTTGTGCTTGTTCTGTTCATCGATTCATTATATCCAAGACTCAGATTTATTTTTCAAAAAATT
129 TTCTTGTGCTTGTTCTGTTCATCGATTCATTATATCCAAGACTCAGATTTATTTTTCAAAAAATT
* *
96947 GTGAGGCTGATTGATATGTGCTTAATTTAGTTAATATTTTGCTTTTA
194 GTGAGGCTGACTGATATGTGCTTAATTTAGTTAATATTTTACTTTTA
* *
96994 AATGGGGTTTGAAAATAAATACCCCTCTCAAGAAATGGCCCTGACATATCTCATATATTTTTTGC
1 AATGGGGATTGAAAATAAATA--CCTCTCAAGAAATGGCCCGGACATATCTC--ATATTTTTTGC
97059 GGATAATTTGGTCATGTTTTCCGAGGTTTTCATGGATCAA-GTTGTGATAAAAGATATTATTGAA
62 GGATAATTTGGTCATGTTTTCCGAGGTTTTCATGGATCAATGTTGTGATAAAAGATATTATTGAA
* *
97123 CATTCTTGTGCTTGTTCTGTTCATTGATTCATTATATCCAAGACTCATATTTATTTTTCAAAAAA
127 CATTCTTGTGCTTGTTCTGTTCATCGATTCATTATATCCAAGACTCAGATTTATTTTTCAAAAAA
97188 TTGTGAGGCTGACTGATATGTGCTTAATTTAGTTAATATTTTACTTTTA
192 TTGTGAGGCTGACTGATATGTGCTTAATTTAGTTAATATTTTACTTTTA
97237 AAT
1 AAT
97240 TACTCCTTAA
Statistics
Matches: 234, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
242 19 0.08
243 137 0.59
244 27 0.12
246 51 0.22
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (240 bp):
AATGGGGATTGAAAATAAATACCTCTCAAGAAATGGCCCGGACATATCTCATATTTTTTGCGGAT
AATTTGGTCATGTTTTCCGAGGTTTTCATGGATCAATGTTGTGATAAAAGATATTATTGAACATT
CTTGTGCTTGTTCTGTTCATCGATTCATTATATCCAAGACTCAGATTTATTTTTCAAAAAATTGT
GAGGCTGACTGATATGTGCTTAATTTAGTTAATATTTTACTTTTA
Found at i:97567 original size:16 final size:16
Alignment explanation
Indices: 97546--97579 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
97536 ATTTTATCTT
97546 TATATTTTAGTTTAAA
1 TATATTTTAGTTTAAA
97562 TATATTTTAGTTTAAA
1 TATATTTTAGTTTAAA
97578 TA
1 TA
97580 GATGTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TATATTTTAGTTTAAA
Found at i:101184 original size:28 final size:28
Alignment explanation
Indices: 101126--101184 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
101116 ACATATTTAA
* *
101126 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAATATAGTACC
** *
101154 AAGTAAACAATAAAACATGTATATTACC
1 AAGTAAACAATAAAACAAATATAGTACC
101182 AAG
1 AAG
101185 GAAAGATACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAGTACC
Found at i:101245 original size:14 final size:14
Alignment explanation
Indices: 101226--101255 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
101216 TATGTTGTTG
101226 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
101240 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
101254 AC
1 AC
101256 AATCAACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.30, G:0.07, T:0.53
Consensus pattern (14 bp):
ACTTGTTCTTTCTC
Found at i:103123 original size:260 final size:255
Alignment explanation
Indices: 102662--103179 Score: 991
Period size: 260 Copynumber: 2.0 Consensus size: 255
102652 GCCTTTGATT
102662 GGACGGGGCTCCTTACTTGGTGGCGCACCTACACATGCCAAAATTTCTAGATGCTCTTCACTTCA
1 GGACGGGGCTCCTTACTTGGTGGCGCACCTACACATGCCAAAATTTCTAGATGCTCTTCACTTCA
102727 ATTTGGGTGGATTCAATCCATCCAAAAATGATATATATATACGACCATGATACTTTTTATATGGG
66 ATTTGGGTGGATTCAATCCATCCAAAAATGATATATATATACGACCATGATACTTTTTATATGGG
102792 TAAACTATTGGATTGCTTTTTTTTTTATAATATTTTTACAATTTTTTCGTTAAATTCAAAATTTT
131 TAAACTATTGGATTGCTTTTTTTTTTATAATATTTTTACAATTTTTTCGTTAAATTCAAAATTTT
102857 ATGTTTTGATAATTTATGTTATCAATTATTACATTTTAGTCATTGACTTTTTTTTACAAG
196 ATGTTTTGATAATTTATGTTATCAATTATTACATTTTAGTCATTGACTTTTTTTTACAAG
102917 GGACGGGGCTCCTTACTTGGTGGCGCACCTACACATGCCAAAATTTCTAGATGCTCTTCACTTTC
1 GGACGGGGCTCCTTACTTGGTGGCGCACCTACACATGCCAAAATTTCTAGATGCTCTTCAC-TTC
102982 AATTTGGGTGGATTCAATCCATCCAAAAATGATATATATATAATCGACCATGATACTTTTTATAT
65 AATTTGGGTGGATTCAATCCATCCAAAAATGATATATATAT-A-CGACCATGATACTTTTTATA-
103047 TGGGTAAACTATTGGATTGCTTTTTTTTTTTATAATATTTTTACAATTTTTTCGTTAAATTCAAA
127 TGGGTAAACTATTGGATTGC-TTTTTTTTTTATAATATTTTTACAATTTTTTCGTTAAATTCAAA
103112 ATTTTATGTTTTGATAATTTATGTTATCAATTATTACATTTTAGTCATTGACTTTTTTTTACAAG
191 ATTTTATGTTTTGATAATTTATGTTATCAATTATTACATTTTAGTCATTGACTTTTTTTTACAAG
103177 GGA
1 GGA
103180 AAAAAGAACT
Statistics
Matches: 258, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
255 61 0.24
256 44 0.17
257 1 0.00
258 20 0.08
259 20 0.08
260 112 0.43
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (255 bp):
GGACGGGGCTCCTTACTTGGTGGCGCACCTACACATGCCAAAATTTCTAGATGCTCTTCACTTCA
ATTTGGGTGGATTCAATCCATCCAAAAATGATATATATATACGACCATGATACTTTTTATATGGG
TAAACTATTGGATTGCTTTTTTTTTTATAATATTTTTACAATTTTTTCGTTAAATTCAAAATTTT
ATGTTTTGATAATTTATGTTATCAATTATTACATTTTAGTCATTGACTTTTTTTTACAAG
Found at i:105096 original size:33 final size:35
Alignment explanation
Indices: 105028--105108 Score: 121
Period size: 33 Copynumber: 2.4 Consensus size: 35
105018 GGGTTTGGTT
* * *
105028 TTTCAAGAGAAACATTTTCAAAGGTTTTTTTTGTG
1 TTTCAAGAGAAACAATTCCAAAGGTATTTTTTGTG
105063 TTTCAAGAGAAACAATTCCAAA-G-ATTTTTTGTG
1 TTTCAAGAGAAACAATTCCAAAGGTATTTTTTGTG
105096 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
105109 TGTATTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 22 0.51
34 1 0.02
35 20 0.47
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (35 bp):
TTTCAAGAGAAACAATTCCAAAGGTATTTTTTGTG
Found at i:105119 original size:34 final size:33
Alignment explanation
Indices: 105028--105122 Score: 113
Period size: 33 Copynumber: 2.8 Consensus size: 33
105018 GGGTTTGGTT
*
105028 TTTCAAGAGAAACATT-TTCAAAGGTTTTTTTTGTG
1 TTTCAAGAGAAAC-TTATTCAAA-G-ATTTTTTGTG
*
105063 TTTCAAGAGAAAC-AATTCCAAAGATTTTTTGTG
1 TTTCAAGAGAAACTTATT-CAAAGATTTTTTGTG
105096 TTTCAAGAGAAACTGTATTCAAAGATT
1 TTTCAAGAGAAACT-TATTCAAAGATT
105123 GAAGTTTCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
33 22 0.42
34 11 0.21
35 20 0.38
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (33 bp):
TTTCAAGAGAAACTTATTCAAAGATTTTTTGTG
Found at i:105175 original size:36 final size:36
Alignment explanation
Indices: 105126--105235 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 36
105116 AAAGATTGAA
*
105126 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
*
105162 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--A
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * * *
105196 CTTCCAAAAGAAACTGTCTCAAGGGAGACGAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
105232 GTTT
1 GTTT
105236 AACGTAAAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
34 27 0.44
36 34 0.56
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:105208 original size:34 final size:35
Alignment explanation
Indices: 105135--105224 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 35
105125 AGTTTCAAGG
** * *
105135 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAA
105171 GAAACTGTCTCAAGAGAGACAAAA-ACTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
*
105205 GAAACTGTCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
105225 GAGATTTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 25 0.51
36 24 0.49
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:105340 original size:36 final size:36
Alignment explanation
Indices: 105293--105477 Score: 127
Period size: 36 Copynumber: 5.3 Consensus size: 36
105283 AAGTTTATGC
* *
105293 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * **
105329 TTCAAGGGAAACTATCTCATGAGTGACAAAATTCAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * *
105365 TTCAAGGG-AATTGTTTTC-A-A-TG-----TTTATGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT-TGT
* *
105394 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* * **
105431 TTCAAGGGAACCTATCTCAAGAGAGACAAAATTCAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
105467 TTCAAGGGAAA
1 TTCAAGGGAAA
105478 TGTTTTTAAT
Statistics
Matches: 110, Mismatches: 27, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
28 2 0.02
29 11 0.10
30 5 0.05
32 1 0.01
33 2 0.02
34 1 0.01
35 3 0.03
36 53 0.48
37 30 0.27
38 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (36 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:105449 original size:37 final size:36
Alignment explanation
Indices: 105391--105477 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 36
105381 TCAATGTTTA
* * *
105391 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
*
105428 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
**
105464 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
105478 TGTTTTTAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:105465 original size:102 final size:101
Alignment explanation
Indices: 105262--105644 Score: 428
Period size: 102 Copynumber: 3.8 Consensus size: 101
105252 AAATATTTTG
* * *
105262 TTTCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
105327 GTTTCAAGGGAAACTATCTCATGAGTGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
105364 TTTCAAGGGAATTGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
*
105429 GTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * * * * *
105466 TTTCAAGGGAAATGTTTTTAATGTTTATGTTTTAAGAGAAACTATCTCAAGAGAAACAAAACTTA
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* ** * * * * **
105531 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTG
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * * * * **
105568 TTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAACTATCTTAAGAAAGACAAAATT
1 TTTCAAGGGAAA-TGTTTTCAATG-TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
**
105631 CATTTCAAGGGAAA
64 TGTTTCAAGGGAAA
105645 TGTTTTCAAT
Statistics
Matches: 240, Mismatches: 38, Indels: 7
0.84 0.13 0.02
Matches are distributed among these distances:
101 58 0.24
102 178 0.74
103 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:105597 original size:167 final size:166
Alignment explanation
Indices: 105420--105741 Score: 527
Period size: 167 Copynumber: 1.9 Consensus size: 166
105410 TCAAGGGAGA
* * * *
105420 CAAAATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTT
1 CAAAATTTTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATTCATTTCAAGGGAAATGTTTTC
* *
105485 AATGTTTATGTTTTAAGAGAAACTATCTCAAGAGAAACAAAACTTAGTTCCAAAAGAAAATGTCT
66 AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACTTAGTTACAAAAGAAAATGTCT
105550 CAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
131 CAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
*
105586 CAAAGATTTTGTTTCAAGAGAAACTATCTTAAGAAAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAA-ATTTTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATTCATTTCAAGGGAAATGTTTT
* * * *
105651 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAACTTAGTTATAAAAGAAAATGTC
65 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACTTAGTTACAAAAGAAAATGTC
*
105716 TCGAGGGAGACGAAATTTGTTTCAAG
130 TCAAGGGAGACGAAATTTGTTTCAAG
105742 AGAGACAAAA
Statistics
Matches: 143, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
166 4 0.03
167 139 0.97
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (166 bp):
CAAAATTTTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATTCATTTCAAGGGAAATGTTTTC
AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAACAAAACTTAGTTACAAAAGAAAATGTCT
CAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
Found at i:105644 original size:65 final size:65
Alignment explanation
Indices: 105568--105689 Score: 158
Period size: 65 Copynumber: 1.9 Consensus size: 65
105558 ACGAAATTTG
*
105568 TTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAACTATCTTAAGAAAGACAAAATT
1 TTTCAAGGGAAA-AGTATTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATT
105631 CA
64 CA
* * * * *
105633 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAAAGAC
105690 GAAACTTAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
64 4 0.08
65 45 0.92
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (65 bp):
TTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATTCA
Found at i:105752 original size:21 final size:21
Alignment explanation
Indices: 105722--105770 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
105712 TGTCTCGAGG
*
105722 GAGACGAAATTTGTTTCAAGA
1 GAGACAAAATTTGTTTCAAGA
105743 GAGACAAAATTTGTTTCAAGA
1 GAGACAAAATTTGTTTCAAGA
*
105764 GAAACAA
1 GAGACAA
105771 TCTTGACTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.24
Consensus pattern (21 bp):
GAGACAAAATTTGTTTCAAGA
Found at i:105997 original size:72 final size:72
Alignment explanation
Indices: 105737--105989 Score: 285
Period size: 72 Copynumber: 3.5 Consensus size: 72
105727 GAAATTTGTT
* * * * * * *
105737 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTTGACTGAAATAAATCTTCTTTCGAGTGA
1 TCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTCTTTCGA-TTA
**
105802 AAATGGTC
65 AAACAGTC
* * * * *
105810 CCAAGAGAGACAAA-TCTGGTTTTAAGAAAAATAATCTTGAGTGGAATAAATCTTCTTTCGAGTA
1 TCAAGTGAGACAAAGTCT-GTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTCTTTCGATTA
105874 AAACAGTC
65 AAACAGTC
* * * *
105882 TC-AGTTGAGACAAAGTCTGTTTTAAGCAAAGCAAACTTGAGTGAAATAAATCTTATTTCGATTA
1 TCAAG-TGAGACAAAGTCTGTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTCTTTCGATTA
105946 AAACAGTC
65 AAACAGTC
* *
105954 TCAAGTGAGACAAAGTATGCTTTAAGAAAAACAATC
1 TCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATC
105990 ACAAGTGAGA
Statistics
Matches: 151, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
71 2 0.01
72 93 0.62
73 56 0.37
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (72 bp):
TCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTCTTTCGATTAA
AACAGTC
Found at i:107452 original size:183 final size:183
Alignment explanation
Indices: 107138--107491 Score: 645
Period size: 183 Copynumber: 1.9 Consensus size: 183
107128 ACCAAGTTTA
* *
107138 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTTGCCTGACAAAAGCAGTGGAGCAAACACCAAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCAAATT
* *
107203 GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 ACCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTAGAGTT
107268 TCCTCTATAACCAATTGCCTTAGTGGAATAACTCAGCTTTAAAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAACTCAGCTTTAAAGGGACAAATC
*
107321 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCAAATT
107386 ACCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTAGAGTT
66 ACCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTAGAGTT
* *
107451 TCCTCTATAACCAATTTCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAACTCAGCTTTA
107492 CGGATTTAAT
Statistics
Matches: 164, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 164 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCAAATT
ACCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTAGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAACTCAGCTTTAAAGGGACAAATC
Found at i:111360 original size:30 final size:25
Alignment explanation
Indices: 111324--111397 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 25
111314 ATAAAAACTA
*
111324 ACAAAATAGAAAACTGATGAAATAGAGAAG
1 ACAAAAT--AAAACTAAT-AAA-AGA-AAG
111354 ACAAAATAAAACTAATAAAAGAAAG
1 ACAAAATAAAACTAATAAAAGAAAG
* *
111379 ACAAAGAAAAAAATAATAA
1 ACAAA-ATAAAACTAATAA
111398 TAAATTAACG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.20
26 14 0.35
27 3 0.08
28 8 0.20
30 7 0.17
ACGTcount: A:0.69, C:0.07, G:0.12, T:0.12
Consensus pattern (25 bp):
ACAAAATAAAACTAATAAAAGAAAG
Found at i:111724 original size:38 final size:36
Alignment explanation
Indices: 111644--111728 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 36
111634 GATAATATGT
111644 ATATATATAAAATAAATAAAAACATAAAAAAATAGTAA
1 ATATATAT-AAATAAATAAAAACATAAAAAAATA-TAA
*
111682 ATATATATAAATTAAT-AAAACATATAATGAAAAT-TAA
1 ATATATATAAATAAATAAAAACATA-AA--AAAATATAA
111719 CATATATATA
1 -ATATATATA
111729 TGTGTGTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
36 8 0.19
37 12 0.29
38 17 0.40
39 5 0.12
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (36 bp):
ATATATATAAATAAATAAAAACATAAAAAAATATAA
Found at i:112161 original size:23 final size:23
Alignment explanation
Indices: 112125--112169 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
112115 CATTGCTCCG
* * *
112125 TTGTTGCACGTTTGTTGGTGTGA
1 TTGTTACACATTTGTTAGTGTGA
112148 TTGTTACACATTTGTTAGTGTG
1 TTGTTACACATTTGTTAGTGTG
112170 TGATAACTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.13, C:0.09, G:0.29, T:0.49
Consensus pattern (23 bp):
TTGTTACACATTTGTTAGTGTGA
Found at i:119991 original size:13 final size:13
Alignment explanation
Indices: 119970--120004 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
119960 CCCACTTACT
119970 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
119983 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
119996 TTTCACTTT
1 TTTCACTTT
120005 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:126217 original size:15 final size:17
Alignment explanation
Indices: 126197--126229 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
126187 TCAAGAACTT
126197 GAAAAG-AAC-TCAAAG
1 GAAAAGAAACTTCAAAG
126212 GAAAAGAAACTTCAAAG
1 GAAAAGAAACTTCAAAG
126229 G
1 G
126230 CACAAGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.58, C:0.12, G:0.21, T:0.09
Consensus pattern (17 bp):
GAAAAGAAACTTCAAAG
Found at i:128295 original size:45 final size:42
Alignment explanation
Indices: 128198--128304 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 42
128188 CGGTGCACTA
* * *
128198 AGAGTGCAACGATGCATGAAGTGCATTCGATGTTTGAAAAAT
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAAT
* *
128240 AGCCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAAT
1 AG---AGTGCATCGATGCATCAAATGCATTCGATGTTTGAA--AAAT
128287 CAGAGTGCATCGATGCAT
1 -AGAGTGCATCGATGCAT
128305 GGAGAGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.04
45 45 0.85
47 4 0.08
48 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (42 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAAT
Found at i:128312 original size:19 final size:19
Alignment explanation
Indices: 128288--128338 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
128278 TAATTAAATC
128288 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
128307 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
128326 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
128339 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:128376 original size:21 final size:21
Alignment explanation
Indices: 128352--128391 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
128342 CAATTTATTC
128352 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
128373 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
128392 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:131006 original size:24 final size:23
Alignment explanation
Indices: 130935--131014 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
130925 CATGGTCTTG
*
130935 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
130958 TGCATCGGTGCATCATGC-A--GA
1 TGCATCGATGCA-CATTCAAGGGA
130979 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
131003 TGCATCGATGCA
1 TGCATCGATGCA
131015 TTGTTAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.26
22 1 0.02
23 12 0.26
24 18 0.38
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:131027 original size:44 final size:42
Alignment explanation
Indices: 130912--131034 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 42
130902 AAAACCCGAC
* *
130912 GGATGCATCGATGCATGGTCTTGTGCATCGATGCACATTCAAG
1 GGATGCATCGATGCATCGT-TAGTGCATCGATGCACATTCAAG
* * * *
130955 GCATGCATCGGTGCATCATGCAGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCATCGT-TAG-TGCATCGATGCACATTC-AAG
* *
131000 GGATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GGATGCATCGATGCATCGTT-AGTGCATCGATGCA
131035 TTAAGCACAA
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
43 16 0.25
44 28 0.44
45 20 0.31
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (42 bp):
GGATGCATCGATGCATCGTTAGTGCATCGATGCACATTCAAG
Found at i:133047 original size:12 final size:12
Alignment explanation
Indices: 133030--133061 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
133020 ATGATTCTCC
133030 AACGTCATGTCT
1 AACGTCATGTCT
133042 AACGTCATGTCT
1 AACGTCATGTCT
133054 AACGTCAT
1 AACGTCAT
133062 TTGTATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (12 bp):
AACGTCATGTCT
Done.