Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002994.1 Hibiscus syriacus cultivar Beakdansim tig00006190_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: 83010
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:24312 original size:24 final size:23
Alignment explanation
Indices: 24285--24341 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
24275 AAATGAATGC
24285 TAAACGAACACATTAGCGAACAT
1 TAAACGAACACATTAGCGAACAT
* *
24308 ATAAACGAACACGTTCGCGAACAT
1 -TAAACGAACACATTAGCGAACAT
*
24332 TAAATGAACA
1 TAAACGAACA
24342 TGTTCGTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.18
Consensus pattern (23 bp):
TAAACGAACACATTAGCGAACAT
Found at i:24340 original size:23 final size:23
Alignment explanation
Indices: 24285--24359 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
24275 AAATGAATGC
* *
24285 TAAACGAACACATTAGCGAACAT
1 TAAACGAACACGTTCGCGAACAT
24308 ATAAACGAACACGTTCGCGAACAT
1 -TAAACGAACACGTTCGCGAACAT
* * * *
24332 TAAATGAACATGTTCGTGAACAA
1 TAAACGAACACGTTCGCGAACAT
24355 TAAAC
1 TAAAC
24360 TAACGAACAC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 23 0.52
24 21 0.48
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (23 bp):
TAAACGAACACGTTCGCGAACAT
Found at i:24742 original size:17 final size:17
Alignment explanation
Indices: 24717--24750 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24707 AATGAGATAA
*
24717 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
24734 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
24751 TGAGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:25419 original size:18 final size:19
Alignment explanation
Indices: 25374--25419 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
25364 ATAATATTCT
25374 AAAT-CCTAATTAAAATAC
1 AAATACCTAATTAAAATAC
*
25392 TAAA-ACCTAATTAAACTA-
1 -AAATACCTAATTAAAATAC
25410 AAATACCTAA
1 AAATACCTAA
25420 AACAAAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 3 0.12
18 6 0.25
19 15 0.62
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATACCTAATTAAAATAC
Found at i:25452 original size:32 final size:32
Alignment explanation
Indices: 25411--25506 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 32
25401 ATTAAACTAA
25411 AATACCTAAAACAAAGATAAAATATAAAA-AT
1 AATACCTAAAACAAAGATAAAATATAAAACAT
** *
25442 AATATCCTAAAACTTAGTTAAAATACTAAAACAT
1 AATA-CCTAAAACAAAGATAAAATA-TAAAACAT
* *
25476 ATTTAAACTAAAATACAAAGATAAAATATAA
1 A-AT-ACCT-AAA-ACAAAGATAAAATATAA
25507 TGTTTAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
31 4 0.08
32 17 0.34
33 5 0.10
34 3 0.06
35 3 0.06
36 7 0.14
37 11 0.22
ACGTcount: A:0.61, C:0.10, G:0.03, T:0.25
Consensus pattern (32 bp):
AATACCTAAAACAAAGATAAAATATAAAACAT
Found at i:27234 original size:29 final size:30
Alignment explanation
Indices: 27132--27235 Score: 77
Period size: 29 Copynumber: 3.4 Consensus size: 30
27122 TTGTTCGAAC
*
27132 TTTTCTGCA-TAGTTCGAACCAAATCTTTT
1 TTTTCTGCACTAGTTCGAACCAAATCTGTT
* * * ** *
27161 TTTTCTACACTGCATTGATCGAATCTGATGTGTAT
1 TTTTCTGCACT--A--GTTCGAACCAAATCTGT-T
*
27196 TTTCCTGCACTA-TTCGAACCAAATCTGTT
1 TTTTCTGCACTAGTTCGAACCAAATCTGTT
27225 TTTTCTGCACT
1 TTTTCTGCACT
27236 GCTCTATTCG
Statistics
Matches: 54, Mismatches: 15, Indels: 12
0.67 0.19 0.15
Matches are distributed among these distances:
29 19 0.35
30 12 0.22
32 1 0.02
33 1 0.02
34 11 0.20
35 10 0.19
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (30 bp):
TTTTCTGCACTAGTTCGAACCAAATCTGTT
Found at i:27357 original size:5 final size:5
Alignment explanation
Indices: 27335--27421 Score: 59
Period size: 5 Copynumber: 16.8 Consensus size: 5
27325 TTCAGAGAAA
* * * ** *
27335 AAAAT AAAAT TAATT AAAAT AAAAT -AAAT AGAAT GAAAAT AAAAAT TTACT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT
* *
27386 AAAAAT AAAAT AAAAAT AAAAT GAAAT GAAAT AAAA
1 -AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
27422 AATAGAACGA
Statistics
Matches: 63, Mismatches: 15, Indels: 8
0.73 0.17 0.09
Matches are distributed among these distances:
4 4 0.06
5 43 0.68
6 16 0.25
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:27399 original size:11 final size:11
Alignment explanation
Indices: 27334--27422 Score: 62
Period size: 11 Copynumber: 8.5 Consensus size: 11
27324 GTTCAGAGAA
27334 AAAAATAAAAT
1 AAAAATAAAAT
* *
27345 -TAATTAAAAT
1 AAAAATAAAAT
27355 -AAAAT-AAAT
1 AAAAATAAAAT
*
27364 -AGAATGAAAAT
1 AAAAAT-AAAAT
** *
27375 AAAAATTTACT
1 AAAAATAAAAT
27386 AAAAATAAAAT
1 AAAAATAAAAT
27397 AAAAATAAAAT
1 AAAAATAAAAT
* *
27408 -GAAATGAAAT
1 AAAAATAAAAT
27418 AAAAA
1 AAAAA
27423 ATAGAACGAA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
9 8 0.14
10 19 0.32
11 28 0.47
12 4 0.07
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:27422 original size:22 final size:21
Alignment explanation
Indices: 27388--27435 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
27378 AATTTACTAA
* *
27388 AAATAAAATAAAAATAAAATG
1 AAATGAAATAAAAATAAAACG
*
27409 AAATGAAATAAAAAATAGAACG
1 AAATGAAAT-AAAAATAAAACG
27431 AAATG
1 AAATG
27436 GGTTGCCTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (21 bp):
AAATGAAATAAAAATAAAACG
Found at i:29523 original size:4 final size:4
Alignment explanation
Indices: 29514--29543 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
29504 AGATAAAAAT
29514 TAAA TAAA TAAA TAAA TAAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA T-AAA TAAA TAAA T
29544 TGAGATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:29535 original size:17 final size:17
Alignment explanation
Indices: 29510--29543 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29500 AAGGAGATAA
*
29510 AAATTAAATAAATAAAT
1 AAATAAAATAAATAAAT
29527 AAATAAAATAAATAAAT
1 AAATAAAATAAATAAAT
29544 TGAGATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAAATAAATAAAT
Found at i:30321 original size:76 final size:75
Alignment explanation
Indices: 30141--30333 Score: 202
Period size: 76 Copynumber: 2.6 Consensus size: 75
30131 TAAAACACTT
* * *
30141 ACTAAAATACCTAAAA-AATA-AT-A-TTTAAAATAATATTCTAAATCCTAATTAAAATACGAAA
1 ACTAAAATACCTAAAATAAAATATAATTTTAAAATAATATCCTAAAACCTAATTAAAATACGAAA
30202 AACTATTTAA
66 AACTATTTAA
* * * * *
30212 ACTAAAATACCTAAAACAAAGATGA-AATATAAAAATAATATCCTAAAACTTAATTAAAATACTA
1 ACTAAAATACCTAAAATAAA-AT-ATAATTTTAAAATAATATCCTAAAACCTAATTAAAATACGA
* *
30276 AAACCTATTTTA
64 AAAACTATTTAA
*
30288 ACTAAAATA-C-AAAGATAAAATATAATGTTTAAAATATTATCCTAAA
1 ACTAAAATACCTAAA-ATAAAATATAAT-TTTAAAATAATATCCTAAA
30334 CTTGAGTTTA
Statistics
Matches: 100, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
71 16 0.16
72 2 0.02
73 2 0.02
74 8 0.08
75 23 0.23
76 49 0.49
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (75 bp):
ACTAAAATACCTAAAATAAAATATAATTTTAAAATAATATCCTAAAACCTAATTAAAATACGAAA
AACTATTTAA
Found at i:37649 original size:24 final size:25
Alignment explanation
Indices: 37611--37659 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
37601 TATAATAATA
*
37611 ATAATAATTTATTTTAAATTTATTT
1 ATAATAATATATTTTAAATTTATTT
**
37636 ATAAT-ATATATTTTATTTTTATTT
1 ATAATAATATATTTTAAATTTATTT
37660 TTTAATGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATAATAATATATTTTAAATTTATTT
Found at i:37659 original size:28 final size:27
Alignment explanation
Indices: 37608--37663 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
37598 CTATATAATA
37608 ATAATAATAATTTATTTTAAATTTATTT
1 ATAATAATAATTTATTTTAAATTT-TTT
* *
37636 ATAATATATATTTTATTTT-TATTTTTT
1 ATAATA-ATAATTTATTTTAAATTTTTT
37663 A
1 A
37664 ATGGTTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 10 0.40
29 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
ATAATAATAATTTATTTTAAATTTTTT
Found at i:41715 original size:34 final size:34
Alignment explanation
Indices: 41671--41736 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 34
41661 AATAGAAATT
41671 ACAACTTCTCTCGAT-ATAACAAGGAGAAAACAATA
1 ACAACTTCTCTC-ATGATAA-AAGGAGAAAACAATA
*
41706 ACAA-TTCTCTCTTGATAAAAGGAGAAAACAA
1 ACAACTTCTCTCATGATAAAAGGAGAAAACAA
41737 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 14 0.48
34 11 0.38
35 4 0.14
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCATGATAAAAGGAGAAAACAATA
Found at i:50409 original size:16 final size:18
Alignment explanation
Indices: 50385--50417 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
50375 TTTAAATTTA
50385 ATTTCATTTAA-TAAATT
1 ATTTCATTTAATTAAATT
50402 ATTT-ATTTAATTAAAT
1 ATTTCATTTAATTAAAT
50418 AATGACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTCATTTAATTAAATT
Found at i:52761 original size:21 final size:21
Alignment explanation
Indices: 52735--52782 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
52725 CTGGACCAGT
*
52735 CTGAGTTGATCGAGCCATTGA
1 CTGAGTTGACCGAGCCATTGA
52756 CTGAGTTGACCGAGCCATTGA
1 CTGAGTTGACCGAGCCATTGA
*
52777 TTGAGT
1 CTGAGT
52783 CGTTGACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
CTGAGTTGACCGAGCCATTGA
Found at i:52816 original size:12 final size:12
Alignment explanation
Indices: 52746--52817 Score: 57
Period size: 12 Copynumber: 6.5 Consensus size: 12
52736 TGAGTTGATC
52746 GAGCCATTGACT
1 GAGCCATTGACT
*
52758 GAG---TTGACC
1 GAGCCATTGACT
*
52767 GAGCCATTGATT
1 GAGCCATTGACT
* *
52779 GAGTCGTTGACT
1 GAGCCATTGACT
*
52791 CAGCCATT---T
1 GAGCCATTGACT
52800 GAGCCATTGACT
1 GAGCCATTGACT
52812 GAGCCA
1 GAGCCA
52818 AGTTGAGTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
9 16 0.36
12 28 0.64
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (12 bp):
GAGCCATTGACT
Found at i:59503 original size:21 final size:21
Alignment explanation
Indices: 59479--59520 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
59469 TTTTTTTGTT
*
59479 ATATAAT-TAAATATAAAATAA
1 ATATAATCT-AATAAAAAATAA
59500 ATATAATCTAATAAAAAATAA
1 ATATAATCTAATAAAAAATAA
59521 TTTTACATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
ATATAATCTAATAAAAAATAA
Found at i:59576 original size:13 final size:13
Alignment explanation
Indices: 59558--59584 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59548 TCTATTTAGC
59558 TTGATAGAAGAAA
1 TTGATAGAAGAAA
59571 TTGATAGAAGAAA
1 TTGATAGAAGAAA
59584 T
1 T
59585 AATGTGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (13 bp):
TTGATAGAAGAAA
Found at i:63959 original size:21 final size:23
Alignment explanation
Indices: 63934--63984 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
63924 AGTTGTGGGG
63934 ATATTTTTAG-T-TTTTTATTAA
1 ATATTTTTAGATATTTTTATTAA
*
63955 ATATTTTT-GATATTTTTATTTA
1 ATATTTTTAGATATTTTTATTAA
63977 AT-TTTTTA
1 ATATTTTTA
63985 AATAATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 14 0.54
22 11 0.42
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (23 bp):
ATATTTTTAGATATTTTTATTAA
Found at i:64069 original size:26 final size:26
Alignment explanation
Indices: 64040--64096 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
64030 CGACTGATTG
*
64040 AACCAGTAAACCGGTCCGATTCTGAA
1 AACCAATAAACCGGTCCGATTCTGAA
*
64066 AACCAATGAACCGGTCCGATTCTGAA
1 AACCAATAAACCGGTCCGATTCTGAA
64092 AACCA
1 AACCA
64097 TGTATTTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.18
Consensus pattern (26 bp):
AACCAATAAACCGGTCCGATTCTGAA
Found at i:64315 original size:36 final size:37
Alignment explanation
Indices: 64257--64327 Score: 135
Period size: 36 Copynumber: 1.9 Consensus size: 37
64247 GAGAAAGCAT
64257 GTGATCATGTCTCCCTTTTATTTATCATTCATTGAGC
1 GTGATCATGTCTCCCTTTTATTTATCATTCATTGAGC
64294 GTGATCATGTC-CCCTTTTATTTATCATTCATTGA
1 GTGATCATGTCTCCCTTTTATTTATCATTCATTGA
64328 ACGATTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 23 0.68
37 11 0.32
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.46
Consensus pattern (37 bp):
GTGATCATGTCTCCCTTTTATTTATCATTCATTGAGC
Found at i:65646 original size:28 final size:30
Alignment explanation
Indices: 65581--65647 Score: 93
Period size: 33 Copynumber: 2.2 Consensus size: 30
65571 CGTTCGATGT
65581 TTATATTTTATTTATGATTATCCTGGATCAATG
1 TTATATTTTATTTATGATTATCCTGG---AATG
65614 TTATATTTTATTTATGATTATCCTGG-ATG
1 TTATATTTTATTTATGATTATCCTGGAATG
65643 -TATAT
1 TTATAT
65648 CCAATATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 5 0.15
29 3 0.09
33 26 0.76
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (30 bp):
TTATATTTTATTTATGATTATCCTGGAATG
Found at i:70859 original size:42 final size:42
Alignment explanation
Indices: 70803--70914 Score: 188
Period size: 42 Copynumber: 2.7 Consensus size: 42
70793 AAATCTCTTG
*
70803 TTTATTTCATGTAATTCGTTTTTCGGAAAATATTTTCCCGTA
1 TTTATTTCACGTAATTCGTTTTTCGGAAAATATTTTCCCGTA
* *
70845 TTTGTTTCACGTAATTCGTTTTTCGGAAAATATTTTCCCGTG
1 TTTATTTCACGTAATTCGTTTTTCGGAAAATATTTTCCCGTA
*
70887 TTTATTTCACGTAATTCGTTTTCCGGAA
1 TTTATTTCACGTAATTCGTTTTTCGGAA
70915 CGTAATTCAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.48
Consensus pattern (42 bp):
TTTATTTCACGTAATTCGTTTTTCGGAAAATATTTTCCCGTA
Found at i:71140 original size:24 final size:23
Alignment explanation
Indices: 71051--71142 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 23
71041 TTTTATGAAT
*
71051 TTAATATTAATAAAATAT-TTTAA
1 TTAATATTTATAAAATATATTT-A
*
71074 TATAAT-TTTCATCAAAATATTAATTA
1 T-TAATATTT-AT-AAAATA-TATTTA
*
71100 TTAAAATATT-TAAAATATATTTA
1 TTAATAT-TTATAAAATATATTTA
71123 TTAATATTTATAATAATATA
1 TTAATATTTATAA-AATATA
71143 ATATTATATT
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
22 2 0.04
23 17 0.31
24 18 0.33
25 10 0.18
26 4 0.07
27 4 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAATATTTATAAAATATATTTA
Found at i:71146 original size:29 final size:28
Alignment explanation
Indices: 71113--71280 Score: 90
Period size: 29 Copynumber: 6.0 Consensus size: 28
71103 AAATATTTAA
71113 AATATATTTATTAATATTTATAATAATAT
1 AATATATTTATT-ATATTTATAATAATAT
* *
71142 AATATTATATTTTTA-ATATTAT-ATAAAAT
1 AATA-TAT-TTATTATAT-TTATAATAATAT
* * *
71171 AATCA-ATTATATTATAATAAT-ATAAGAT
1 AAT-ATATT-TATTATATTTATAATAATAT
*
71199 ATTATATTT-TTAT-TTTAATAAT-ATAT
1 AATATATTTATTATATTT-ATAATAATAT
71225 AATA-ATGTT-TTATATATT-TAATAATGAAT
1 AATATAT-TTATTATAT-TTATAATAAT--AT
71254 AATATTATTTA-TATATTTA-AATAATAT
1 AATA-TATTTATTATATTTATAATAATAT
71281 TTTAATAAAG
Statistics
Matches: 109, Mismatches: 11, Indels: 40
0.68 0.07 0.25
Matches are distributed among these distances:
25 3 0.03
26 22 0.20
27 10 0.09
28 22 0.20
29 30 0.28
30 16 0.15
31 6 0.06
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (28 bp):
AATATATTTATTATATTTATAATAATAT
Found at i:71149 original size:26 final size:26
Alignment explanation
Indices: 71096--71280 Score: 68
Period size: 28 Copynumber: 6.9 Consensus size: 26
71086 CAAAATATTA
*
71096 ATTATTAAAATATT-TAA-AATAT-AT
1 ATTATTAATAT-TTATAATAATATAAT
71120 -TTATTAATATTTATAATAATATAAT
1 ATTATTAATATTTATAATAATATAAT
*
71145 ATTA-T-AT-TTT-TAATATTATATAAA
1 ATTATTAATATTTATAATA--ATATAAT
* * *
71169 ATAATCAATTATATTATAATAATATAAG
1 ATTATTAA-TAT-TTATAATAATATAAT
*
71197 A-TATTATATTTTTATTTTAATAATATATAAT
1 ATTATTA-ATATTTA---TAAT-A-ATATAAT
* *
71228 AATGTTTTATATATTTAATAATGA-ATAAT
1 -AT-TATTA-ATATTT-ATAATAATATAAT
71257 ATTATTTATATATTTA-AATAATAT
1 ATTA-TTA-ATATTTATAATAATAT
71281 TTTAATAAAG
Statistics
Matches: 123, Mismatches: 14, Indels: 45
0.68 0.08 0.25
Matches are distributed among these distances:
22 7 0.06
23 15 0.12
24 16 0.13
25 3 0.02
26 11 0.09
27 10 0.08
28 21 0.17
29 11 0.09
30 7 0.06
31 6 0.05
32 5 0.04
34 10 0.08
35 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTATTAATATTTATAATAATATAAT
Found at i:71151 original size:22 final size:23
Alignment explanation
Indices: 71104--71164 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
71094 TAATTATTAA
* *
71104 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
71125 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
71148 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
71165 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:71180 original size:31 final size:32
Alignment explanation
Indices: 71115--71193 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
71105 ATATTTAAAA
71115 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAATATAATAT
*
71147 TATATTT-TTAATA-TTAT-ATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAATATAAT--AT
*
71178 TATATTATAATAATAT
1 TATATT-TATTAATAT
71194 AAGATATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 9 0.22
30 4 0.10
31 14 0.35
32 8 0.20
33 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATATAATAT
Found at i:71258 original size:19 final size:19
Alignment explanation
Indices: 71215--71288 Score: 55
Period size: 19 Copynumber: 3.9 Consensus size: 19
71205 TTTTTATTTT
71215 AATAATATA--TAATAATG
1 AATAATATATTTAATAATG
** *
71232 TTTTATATATTTAATAATG
1 AATAATATATTTAATAATG
* *
71251 AATAATATTATTTATATATTTA
1 AATAATA-TATTTA-ATA-ATG
71273 AATAATAT-TTTAATAA
1 AATAATATATTTAATAA
71289 AGATATTTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
17 6 0.14
19 15 0.35
20 10 0.23
21 4 0.09
22 8 0.19
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AATAATATATTTAATAATG
Found at i:71309 original size:23 final size:23
Alignment explanation
Indices: 71283--71327 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
71273 AATAATATTT
71283 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
71306 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
71328 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:71408 original size:90 final size:86
Alignment explanation
Indices: 71296--71465 Score: 200
Period size: 90 Copynumber: 1.9 Consensus size: 86
71286 TAAAGATATT
* * * * * *
71296 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAACACTATTACTTTAATAAATAATTAA
1 TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATA-TTTAAT-AATAAATAA
71359 TATAATTTATAATATTTTATTTCAC
64 -ATAATTT-TAATATTTTATTTCAC
*
71384 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TAAAATATA-CAA-ATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAA
*
71449 ATTATTTTAATATTTTA
64 ATAATTTTAATATTTTA
71466 AAATAATAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 19 0.27
89 8 0.11
90 21 0.30
91 12 0.17
92 10 0.14
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAAT
AATTTTAATATTTTATTTCAC
Done.