Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004553.1 Hibiscus syriacus cultivar Beakdansim tig00010112_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: 66910
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2239 original size:64 final size:63
Alignment explanation
Indices: 2153--2311 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 63
2143 GGCACTAAGA
* * * * * * *
2153 GTGCATTGATGCATGAAGTGCATTTGATGTTTCA-AACAAGCCCGAGTGCCTCGATACATGGTCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCATAA-AA-CCCGAGCGCATCGATACATGGTAT
* * * *
2217 TTGCATCGATGCATAAAATGCATTCAATGTTTTCATAAAACCTGAGCGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAACCCGAGCGCATCGATACATGGTAT
2281 GTGCATCGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
2312 CAATTTTATT
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
63 2 0.03
64 69 0.86
65 7 0.09
66 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAACCCGAGCGCATCGATACATGGTAT
Found at i:5529 original size:17 final size:16
Alignment explanation
Indices: 5494--5550 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
5484 CTAGCATACC
5494 TATTTTCCTCTATAT-TT
1 TATTTTCCT-TAT-TCTT
5511 TATTTTCCTTATCTCTT
1 TATTTTCCTTAT-TCTT
*
5528 TA--TTCATTATTCTT
1 TATTTTCCTTATTCTT
5542 TATTTTCCT
1 TATTTTCCT
5551 GTTAAAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 6 0.18
15 7 0.21
16 8 0.24
17 13 0.38
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTCCTTATTCTT
Found at i:6356 original size:45 final size:45
Alignment explanation
Indices: 6261--6649 Score: 540
Period size: 45 Copynumber: 8.7 Consensus size: 45
6251 AGTTATGGCA
** * *
6261 TTCATGCCT-TAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCT
1 TTCATGCCTATAATGCA-CCCAT-ATGCATTATTA-TTTTGGCATCCT
* *
6308 TTCATGCCTATAATGCACTCATATGCATTATTATTTTGGCATCAT
1 TTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCT
*
6353 TTCATGCCTATAATGCACCCATATGAATTATTATTTTGGCATCCT
1 TTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCT
* *
6398 TTTATGCCTATAATGCACCCATATGCATTATTATTTTTGCATCCT
1 TTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCT
* * *
6443 TTCATGCCTATAATACACCCATATGCATTATTATTTTGACATCTT
1 TTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCT
* *
6488 TTCATGCCTGTAATGCACCCATATGCATTATTATTTTGGAATCCT
1 TTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCT
* * *
6533 TTCATGCCTATAATGCGCCCATATGCATTATTTTTTTTGCA-CCTT
1 TTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCC-T
6578 TTCATGCCTATAATG----C-TATGCATTATTATTTTGGCATCCT
1 TTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCT
6618 TTCATGCCTATAATGCACCCATATGCATTATT
1 TTCATGCCTATAATGCACCCATATGCATTATT
6650 TGTTTTGTTC
Statistics
Matches: 305, Mismatches: 29, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
40 34 0.11
41 3 0.01
44 3 0.01
45 237 0.78
46 10 0.03
47 11 0.04
48 7 0.02
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.42
Consensus pattern (45 bp):
TTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCT
Found at i:7431 original size:29 final size:31
Alignment explanation
Indices: 7394--7451 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
7384 TAACTAATCA
*
7394 TTTCAACTAAC-TTG-GTTCTTTTTGTCTTG
1 TTTCAACTAACATTGAGTTCTTTTAGTCTTG
* *
7423 TTTCTACTAACATTGATTTCTTTTAGTCT
1 TTTCAACTAACATTGAGTTCTTTTAGTCT
7452 GATCTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.42
30 3 0.12
31 11 0.46
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.55
Consensus pattern (31 bp):
TTTCAACTAACATTGAGTTCTTTTAGTCTTG
Found at i:9480 original size:8 final size:8
Alignment explanation
Indices: 9469--9544 Score: 55
Period size: 8 Copynumber: 9.0 Consensus size: 8
9459 GAAAAAAGGG
9469 GAAAAAAA
1 GAAAAAAA
*
9477 GAAAAAAG
1 GAAAAAAA
9485 GAAAAAAA
1 GAAAAAAA
9493 GATGAAAAAA
1 GA--AAAAAA
*
9503 -AGAAAAA
1 GAAAAAAA
* **
9510 TAATGAAA
1 GAAAAAAA
9518 GAAAAAATA
1 GAAAAAA-A
9527 GAAAAGAAA
1 GAAAA-AAA
9536 GAACAAAAA
1 GAA-AAAAA
9545 AAGATAAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.09
8 24 0.45
9 14 0.26
10 10 0.19
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.05
Consensus pattern (8 bp):
GAAAAAAA
Found at i:9481 original size:27 final size:28
Alignment explanation
Indices: 9450--9517 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
9440 GAAAAGACAT
*
9450 AAAAATAGTGAAAAAAGGGGAAAAAAAG
1 AAAAATAGTGAAAAAAGAGGAAAAAAAG
*
9478 AAAAA-AG-GAAAAAAAGATGAAAAAAAG
1 AAAAATAGTG-AAAAAAGAGGAAAAAAAG
*
9505 AAAAATAATGAAA
1 AAAAATAGTGAAA
9518 GAAAAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 1 0.03
27 23 0.68
28 9 0.26
29 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (28 bp):
AAAAATAGTGAAAAAAGAGGAAAAAAAG
Found at i:9482 original size:18 final size:16
Alignment explanation
Indices: 9468--9560 Score: 55
Period size: 18 Copynumber: 5.4 Consensus size: 16
9458 TGAAAAAAGG
9468 GGAAAAAAAGAAAAAA
1 GGAAAAAAAGAAAAAA
9484 GGAAAAAAAGATGAAAAAA
1 GG-AAAAAA-A-GAAAAAA
*
9503 AGAAAAATAATGAAAGAAA
1 GGAAAAA-AA-GAAA-AAA
* *
9522 -AAATAGAAAAGAAAGAA
1 GGAA-A-AAAAGAAAAAA
*
9539 -CAAAAAAAGATAAAAA
1 GGAAAAAAAGA-AAAAA
9555 GGAAAA
1 GGAAAA
9561 GAGATACGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
15 6 0.10
16 7 0.11
17 14 0.23
18 18 0.29
19 15 0.24
20 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.05
Consensus pattern (16 bp):
GGAAAAAAAGAAAAAA
Found at i:9553 original size:22 final size:20
Alignment explanation
Indices: 9478--9553 Score: 55
Period size: 22 Copynumber: 3.6 Consensus size: 20
9468 GGAAAAAAAG
* *
9478 AAAAAAGGAAAA-AAAGATGA
1 AAAAAAGAAAAAGAAAGA-AA
* *
9498 AAAAAAGAAAAATAATGAAA
1 AAAAAAGAAAAAGAAAGAAA
*
9518 GAAAAAATAGAAAAGAAAGAACA
1 -AAAAAAGA-AAAAGAAAGAA-A
9541 AAAAAAGATAAAA
1 AAAAAAGA-AAAA
9554 AGGAAAAGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 12 0.27
21 11 0.25
22 20 0.45
23 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.07
Consensus pattern (20 bp):
AAAAAAGAAAAAGAAAGAAA
Found at i:9562 original size:43 final size:42
Alignment explanation
Indices: 9473--9562 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 42
9463 AAAGGGGAAA
* ** *
9473 AAAAGAAAAAAGGAAAAAAAGATGAAAAAAAGAAAAATAATG
1 AAAAGAAAAAAAGAAAAAAAGAACAAAAAAAGAAAAATAAGG
*
9515 -AAAGAAAAAATAGAAAAGAAAGAACAAAAAAAGATAAA-AAGG
1 AAAAGAAAAAA-AGAAAA-AAAGAACAAAAAAAGAAAAATAAGG
9557 AAAAGA
1 AAAAGA
9563 GATACGAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 10 0.25
42 8 0.20
43 22 0.55
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.06
Consensus pattern (42 bp):
AAAAGAAAAAAAGAAAAAAAGAACAAAAAAAGAAAAATAAGG
Found at i:11084 original size:36 final size:36
Alignment explanation
Indices: 10978--11088 Score: 114
Period size: 36 Copynumber: 3.1 Consensus size: 36
10968 GCAAATATCA
* *
10978 AAAATTTATCTCACTTGAGAGTGTTTTTCTTAAAAC
1 AAAATTTATCTCACTTGAGAATGTTTTTCTCAAAAC
** * * * ** *
11014 AACTTTTACCTCACTAGAGACATATTTCCCTCAAAAT
1 AAAATTTATCTCACTTGAGA-ATGTTTTTCTCAAAAC
*
11051 AAAATTTATCTCACTTGAGATTGTTTTTCTCAAAAC
1 AAAATTTATCTCACTTGAGAATGTTTTTCTCAAAAC
11087 AA
1 AA
11089 GTTTCGTCTC
Statistics
Matches: 55, Mismatches: 19, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
36 29 0.53
37 26 0.47
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (36 bp):
AAAATTTATCTCACTTGAGAATGTTTTTCTCAAAAC
Found at i:11411 original size:36 final size:36
Alignment explanation
Indices: 11149--11412 Score: 133
Period size: 36 Copynumber: 7.2 Consensus size: 36
11139 TTGGATATGT
* * *
11149 TTTTTCTTAAAAACCAGTTTCGTCTCACTAGAGACAG
1 TTTTTCTT-AAAACCAATTTCGTCTCACTTGAGATAG
** * ** * *
11186 TTTCCCTTAAAACAAGAAATTTTATCTCACTCGAGATGG
1 TTTTTCTTAAAAC---CAATTTCGTCTCACTTGAGATAG
* *
11225 TTTTTCTTAAAACCTAA-TTCGTCTCGCTTGAGACAG
1 TTTTTCTTAAAACC-AATTTCGTCTCACTTGAGATAG
* * * * * * *
11261 TTTTCCCTTGAAACAAAATGT-ATCTCACTTAAGATGG
1 TTTT-TCTTAAAAC-CAATTTCGTCTCACTTGAGATAG
* * *
11298 TTTTTATTAAAACCAACTTCGTCTCGCTTGAGATAG
1 TTTTTCTTAAAACCAATTTCGTCTCACTTGAGATAG
** * * * *
11334 TTTCCCTTGAAACAAAATTT-ATC-CAACTCGAGAT-G
1 TTTTTCTTAAAAC-CAATTTCGTCTC-ACTTGAGATAG
*
11369 TTTTTTTCTTAAAACCAATTTCGTCTCGCTTGAGATAG
1 --TTTTTCTTAAAACCAATTTCGTCTCACTTGAGATAG
11407 TTTTTC
1 TTTTTC
11413 CTCGAAAAAA
Statistics
Matches: 159, Mismatches: 53, Indels: 31
0.65 0.22 0.13
Matches are distributed among these distances:
35 5 0.03
36 69 0.43
37 55 0.35
38 3 0.02
39 27 0.17
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
TTTTTCTTAAAACCAATTTCGTCTCACTTGAGATAG
Found at i:11456 original size:73 final size:72
Alignment explanation
Indices: 10977--11440 Score: 382
Period size: 73 Copynumber: 6.3 Consensus size: 72
10967 AGCAAATATC
* * *** * * *
10977 AAAAATTTATCTCACTTGAGA-GTGTTTTTCTTAAAA-CAACTTTTACCTCACTAGAGACATATT
1 AAAAATTTATCTCAATCGAGATG-GTTTTTCTTAAAACCAA-TTTCGTCTCGCTTGAGACA-GTT
*
11040 TCCC-TCAAA
63 TCCCTTGAAA
* * * * * * *
11049 ATAAAATTTATCTCACTTGAGATTGTTTTTCTCAAAA-CAAGTTTCGTCTCACTGGAGACAATTT
1 A-AAAATTTATCTCAATCGAGATGGTTTTTCTTAAAACCAA-TTTCGTCTCGCTTGAGACAGTTT
11113 CCCTTGAAA
64 CCCTTGAAA
* * * * * * * *
11122 CAAGAAATTTTATCTTATTGGATATGTTTTTTCTTAAAAACCAGTTTCGTCTCACTAGAGACAGT
1 -AA-AAA-TTTATCTCAATCGAGATGGTTTTTCTT-AAAACCAATTTCGTCTCGCTTGAGACAGT
*
11187 TTCCCTTAAAA
62 TTCCCTTGAAA
*
11198 CAAGAAATTTTATCTCACTCGAGATGGTTTTTCTTAAAACCTAA-TTCGTCTCGCTTGAGACAGT
1 -AA-AAA-TTTATCTCAATCGAGATGGTTTTTCTTAAAACC-AATTTCGTCTCGCTTGAGACAG-
11262 TTTCCCTTGAAA
61 TTTCCCTTGAAA
* * * ** * * *
11274 CAAAATGTATCTCACTTAAGATGGTTTTTATTAAAACCAACTTCGTCTCGCTTGAGATAGTTTCC
1 AAAAATTTATCTCAATCGAGATGGTTTTTCTTAAAACCAATTTCGTCTCGCTTGAGACAGTTTCC
11339 CTTGAAA
66 CTTGAAA
* * *
11346 CAAAATTTATC-CAACTCGAGATGTTTTTTTCTTAAAACCAATTTCGTCTCGCTTGAGATAGTTT
1 AAAAATTTATCTCAA-TCGAGATG-GTTTTTCTTAAAACCAATTTCGTCTCGCTTGAGACAG-TT
* *
11410 TTCCTCGAAA
63 TCCCTTGAAA
11420 AAAAATTTATCTCAATCGAGA
1 AAAAATTTATCTCAATCGAGA
11441 GAGCTTCTCT
Statistics
Matches: 333, Mismatches: 44, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
71 2 0.01
72 38 0.11
73 136 0.41
74 33 0.10
75 47 0.14
76 75 0.23
77 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (72 bp):
AAAAATTTATCTCAATCGAGATGGTTTTTCTTAAAACCAATTTCGTCTCGCTTGAGACAGTTTCC
CTTGAAA
Found at i:11921 original size:117 final size:118
Alignment explanation
Indices: 11714--12105 Score: 527
Period size: 117 Copynumber: 3.3 Consensus size: 118
11704 AAGATAAACC
* * *
11714 GATCAACATTTCTAATGGATAGTTCATAATGAGAAGAACTTATCCGACAGAGGGACAAAAAGTTC
1 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGACAAAAAGTTC
* *
11779 ATAATGAGAAGAACTTGTTCAACCTTGGATCGATTCCATCACAGAAGGAGGTG
66 ATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGAAGGTG
* * *
11832 GATCAACATTTCCAATGGAGAGTTCATAAGGAGAAGAACTCATCTGA-AGAGGGAGAAAAAGTTC
1 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGACAAAAAGTTC
* * *
11896 ATAATGAGAAGAATTTGTTCAACCTTGGTTCAATTCCATCACAGAAGAAGATG
66 ATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGAAGGTG
* * * ** *
11949 GATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATA-AGATATAAAAAGTTC
1 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGACAAAAAGTTC
* ** * * * *
12013 ATAATGAGAAGAACTGGTTCAGTCTTTGTTTGATTGCATCACAGAAAAAGGTG
66 ATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGAAGGTG
* * *
12066 GATCATCATTCCCAATAGAGAGTTCATAATGAGAAGAACT
1 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACT
12106 TGTTAAACCT
Statistics
Matches: 240, Mismatches: 33, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
117 197 0.82
118 43 0.18
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (118 bp):
GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGACAAAAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAAGAAGGTG
Found at i:13695 original size:16 final size:15
Alignment explanation
Indices: 13660--13691 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
13650 TTATTTGTAA
13660 TTTA-TGTTATTTAT
1 TTTACTGTTATTTAT
13674 TTTACTGTTATTTAT
1 TTTACTGTTATTTAT
13689 TTT
1 TTT
13692 TACTTGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (15 bp):
TTTACTGTTATTTAT
Found at i:15995 original size:31 final size:30
Alignment explanation
Indices: 15956--16021 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
15946 TTAAATATAA
* *
15956 AATAACGT-ATAATATACTATATTACATAGT
1 AATAACGTAATAATATA-TATAATACATACT
*
15986 AATATACGTAATAATGTATATAATACATACT
1 AATA-ACGTAATAATATATATAATACATACT
16017 AATAA
1 AATAA
16022 TATTAATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 19 0.61
32 7 0.23
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (30 bp):
AATAACGTAATAATATATATAATACATACT
Found at i:16037 original size:16 final size:16
Alignment explanation
Indices: 16012--16054 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
16002 TATATAATAC
16012 ATACTAATAATAT-TA
1 ATACTAATAATATGTA
*
16027 ATACATAATAAAATGTA
1 ATAC-TAATAATATGTA
16044 ATACTAATAAT
1 ATACTAATAAT
16055 GTGCAGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 14 0.58
17 6 0.25
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (16 bp):
ATACTAATAATATGTA
Found at i:16367 original size:21 final size:21
Alignment explanation
Indices: 16338--16396 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
16328 TACAAAATAT
* *
16338 ATGTAATATATAATATATGAC
1 ATGTGATATATAATATATAAC
* *
16359 ATGTGATATATGATATTTAAC
1 ATGTGATATATAATATATAAC
16380 ATG-G-TATATAATATATA
1 ATGTGATATATAATATATA
16397 TATATATACA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 11 0.34
20 1 0.03
21 20 0.62
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTGATATATAATATATAAC
Found at i:16545 original size:14 final size:14
Alignment explanation
Indices: 16457--16574 Score: 60
Period size: 13 Copynumber: 8.9 Consensus size: 14
16447 TAATTATAAT
16457 ATATAAT-ATATATA
1 ATATAATAATAT-TA
*
16471 A-ATAATACTATGT-
1 ATATAATAATAT-TA
16484 A-ATAATAATATTTA
1 ATATAATAATA-TTA
* *
16498 A-AAAATAATGTTA
1 ATATAATAATATTA
16511 A-ATAATAA-A-TA
1 ATATAATAATATTA
16522 ATA-AGA-AATATTA
1 ATATA-ATAATATTA
16535 ATATAATAATATTA
1 ATATAATAATATTA
* * *
16549 ATACACTAATACT-
1 ATATAATAATATTA
16562 ATATAATATATAT
1 ATATAATA-ATAT
16575 AGTATAAACA
Statistics
Matches: 81, Mismatches: 13, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
11 6 0.07
12 3 0.04
13 37 0.46
14 35 0.43
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (14 bp):
ATATAATAATATTA
Found at i:17102 original size:117 final size:117
Alignment explanation
Indices: 16928--17151 Score: 290
Period size: 117 Copynumber: 1.9 Consensus size: 117
16918 TCCATGGACA
16928 AGTTCTTCTCAGTTTGAACTCCCCAATAAAATGTTAATCCACCTCATTCTATAATGGACTTGAGA
1 AGTTCTTCTCAGTTTGAACTCCCCAATAAAATGTTAATCCACCTCATTCTATAATGGACTTGAGA
16993 AAAAAGTCAAACAAGTTCTTATCATTATGAACTTCTTCTCCCACTGTGAACG
66 AAAAAGTCAAACAAGTTCTTATCATTATGAACTTCTTCTCCCACTGTGAACG
* * * * * * *
17045 AGTTCTTCTC-GTTATGATCT-CCTAATTAAAATGTTAATTCACCTCTTTCTGTTATGGATTTGA
1 AGTTCTTCTCAGTT-TGAACTCCCCAA-TAAAATGTTAATCCACCTCATTCTATAATGGACTTGA
** * ** * *
17108 GTGAAATGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCC
64 GAAAAAAGTCAAACAAGTTCTTATCATTATGAACTTCTTCTCCC
17152 CCCCCCCGTG
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
116 7 0.08
117 84 0.92
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (117 bp):
AGTTCTTCTCAGTTTGAACTCCCCAATAAAATGTTAATCCACCTCATTCTATAATGGACTTGAGA
AAAAAGTCAAACAAGTTCTTATCATTATGAACTTCTTCTCCCACTGTGAACG
Found at i:19396 original size:90 final size:90
Alignment explanation
Indices: 19275--19452 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
19265 TAATCCCGAA
* * *
19275 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
19340 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
19365 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATTAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
19430 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
19453 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:25102 original size:90 final size:89
Alignment explanation
Indices: 24981--25155 Score: 287
Period size: 90 Copynumber: 2.0 Consensus size: 89
24971 TCCCAAATAT
* * * * *
24981 TTAATTTCAATTTATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTAA
25046 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
25070 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTA
*
25135 AGGTAACTTGGCTATAAAAGG
65 AGGTAACTTGGATATAAAAGG
25156 GTGTGTTATG
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGATTAA
GGTAACTTGGATATAAAAGGATTA
Found at i:30909 original size:16 final size:16
Alignment explanation
Indices: 30875--30910 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30865 TAAACCCTCG
*
30875 TTTTATTTATTTTCCT
1 TTTTATTTATTTTCAT
*
30891 TTTTATTTATTTTTAT
1 TTTTATTTATTTTCAT
30907 TTTT
1 TTTT
30911 TCCTTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTATTTATTTTCAT
Found at i:39967 original size:13 final size:13
Alignment explanation
Indices: 39949--40003 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
39939 TGTGTCATGA
*
39949 ATTTATGACGTGC
1 ATTTATGACGCGC
*
39962 ATTTATGACACGC
1 ATTTATGACGCGC
*
39975 ATTTATGACGCGT
1 ATTTATGACGCGC
*
39988 ATTTATGACGCTC
1 ATTTATGACGCGC
40001 ATT
1 ATT
40004 GCGCGTCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:40129 original size:85 final size:84
Alignment explanation
Indices: 39975--40140 Score: 192
Period size: 85 Copynumber: 2.0 Consensus size: 84
39965 TATGACACGC
* * * * *
39975 ATTTATGACGCGTATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCATCATAAATGAAGACGA
1 ATTTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCACACACCATAAA-GAAGACGA
*
40040 CACACATTTGTGTGTCATAA
65 CACACATTCGTGTGTCATAA
* * *
40060 ATTTATGACACGCATTTATGAC-TTACATTGCGTGTCATTGAAGCACACACCATTAGAA-AAGAT
1 ATTTATGACACGCATTTATGACGCT-CATTGCGCGTCATTGAAGCACACACCA-TA-AAGAAGAC
*
40123 GGCACACATTCGTGTGTC
63 GACACACATTCGTGTGTC
40141 GTGATTGTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
84 1 0.01
85 63 0.93
86 2 0.03
87 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (84 bp):
ATTTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCACACACCATAAAGAAGACGAC
ACACATTCGTGTGTCATAA
Found at i:40167 original size:2 final size:2
Alignment explanation
Indices: 40160--40184 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40150 TGTCGTAAAT
40160 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40185 TGTAGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60516 original size:61 final size:61
Alignment explanation
Indices: 60406--60565 Score: 196
Period size: 61 Copynumber: 2.6 Consensus size: 61
60396 TAAGGACACT
*
60406 TAGTGCAAGTGGTGGGCACGACCTTATGTCTCATATAC-GGATCAACACTAGAGTGTAAACC
1 TAGTGCAAGTGGTGGGCACGACCTTATGTGTCATA-ACAGGATCAACACTAGAGTGTAAACC
* * * * * * *
60467 TGGTGCAGGTGGTGGGCACAACTTTATGTGTCATAACAGGATTAGCACTAGAGTGTAAACT
1 TAGTGCAAGTGGTGGGCACGACCTTATGTGTCATAACAGGATCAACACTAGAGTGTAAACC
* * * *
60528 TACTGCATGCGGTGGGCACGACCTTATGTGTCACAACA
1 TAGTGCAAGTGGTGGGCACGACCTTATGTGTCATAACA
60566 CTACGGTGCA
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 2 0.02
61 81 0.98
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (61 bp):
TAGTGCAAGTGGTGGGCACGACCTTATGTGTCATAACAGGATCAACACTAGAGTGTAAACC
Found at i:65015 original size:19 final size:17
Alignment explanation
Indices: 64982--65019 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
64972 ATCCTAGCCT
64982 TTCTTCCCTCTTCTTTC
1 TTCTTCCCTCTTCTTTC
64999 TTCTTCCACTCCTTCTTTC
1 TTCTTCC-CT-CTTCTTTC
65018 TT
1 TT
65020 TGCTAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (17 bp):
TTCTTCCCTCTTCTTTC
Done.