Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003862.1 Hibiscus syriacus cultivar Beakdansim tig00008300_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: 56895
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Found at i:211 original size:32 final size:33
Alignment explanation
Indices: 175--324 Score: 157
Period size: 32 Copynumber: 4.7 Consensus size: 33
165 CACTCTTGCT
* * *
175 CATTATCTGAATGCAACACTGACCT-TACTGTG
1 CATTATATGAATGTAACACTGACCTCTACTATG
* * * *
207 CATTATCTGAATGCAACAATGACCT-TA-TGTG
1 CATTATATGAATGTAACACTGACCTCTACTATG
* *
238 CATTATATGAATGTTACACTGA-CTCTATTATG
1 CATTATATGAATGTAACACTGACCTCTACTATG
* *
270 CATTATATGAATGTAACACT-AACTCTGCTATG
1 CATTATATGAATGTAACACTGACCTCTACTATG
*
302 CTTTATATGAATGTAACACTGAC
1 CATTATATGAATGTAACACTGAC
325 ACTATGCAAC
Statistics
Matches: 103, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
30 2 0.02
31 25 0.24
32 75 0.73
33 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (33 bp):
CATTATATGAATGTAACACTGACCTCTACTATG
Found at i:257 original size:63 final size:65
Alignment explanation
Indices: 175--324 Score: 162
Period size: 63 Copynumber: 2.4 Consensus size: 65
165 CACTCTTGCT
* * * * * * *
175 CATTATCTGAATGCAACACTGACCT-TACTGTGCATTATCTGAATGCAACAATGAC-CTTATGTG
1 CATTATATGAATGTAACACTGACCTCTACTATGCATTATATGAATGCAACAATAACTCTGATATG
* * * * *
238 CATTATATGAATGTTACACTGA-CTCTATTATGCATTATATGAATGTAACACTAACTCTGCTATG
1 CATTATATGAATGTAACACTGACCTCTACTATGCATTATATGAATGCAACAATAACTCTGATATG
*
302 CTTTATATGAATGTAACACTGAC
1 CATTATATGAATGTAACACTGAC
325 ACTATGCAAC
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
62 2 0.03
63 43 0.61
64 25 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (65 bp):
CATTATATGAATGTAACACTGACCTCTACTATGCATTATATGAATGCAACAATAACTCTGATATG
Found at i:1630 original size:45 final size:44
Alignment explanation
Indices: 1530--1702 Score: 197
Period size: 45 Copynumber: 3.9 Consensus size: 44
1520 TGAAATGATG
* *
1530 CTATAGTTGAAATGTATATGGGTACATTCTCAACAGAAAGTA-A
1 CTATAGTTGAAATGTATATGGGTACATTATCAACATAAAGTATA
* **
1573 GC-ACTGGTTGAAATGTATAAAGGTACATTATCAACAATAAAGTATA
1 -CTA-TAGTTGAAATGTATATGGGTACATTATCAAC-ATAAAGTATA
* *
1619 CTATAGTTGAAATGTATATGGGTACATTATCAACAAAAAAGTATG
1 CTATAGTTGAAATGTATATGGGTACATTATCAAC-ATAAAGTATA
* * * *
1664 TTATTGTTGAAATGCATATGGGTGCATTATCAACATAAA
1 CTATAGTTGAAATGTATATGGGTACATTATCAACATAAA
1703 AATATTATGA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.01
44 32 0.29
45 75 0.68
46 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (44 bp):
CTATAGTTGAAATGTATATGGGTACATTATCAACATAAAGTATA
Found at i:1702 original size:89 final size:88
Alignment explanation
Indices: 1494--1702 Score: 242
Period size: 89 Copynumber: 2.3 Consensus size: 88
1484 TGAAAAATTA
* * * * *
1494 AAATGAATACAGGTGCATTATCAGCATGAAATGATGCTATAGTTGAAATGTATATGGGTACATTC
1 AAATGCATAAAGGTGCATTATCAACAT-AAATGATACTATAGTTGAAATGTATATGGGTACATTA
*
1559 TCAACAGAAAGTAAGCACTGGTTG
65 TCAACAAAAAGTAAGCACTGGTTG
* *
1583 AAATGTATAAAGGTACATTATCAACAATAAA-GTATACTATAGTTGAAATGTATATGGGTACATT
1 AAATGCATAAAGGTGCATTATCAAC-ATAAATG-ATACTATAGTTGAAATGTATATGGGTACATT
* * *
1647 ATCAACAAAAAAGTATGTTA-TTGTTG
64 ATCAAC-AAAAAGTAAG-CACTGGTTG
**
1673 AAATGCATATGGGTGCATTATCAACATAAA
1 AAATGCATAAAGGTGCATTATCAACATAAA
1703 AATATTATGA
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
88 1 0.01
89 64 0.63
90 36 0.35
91 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (88 bp):
AAATGCATAAAGGTGCATTATCAACATAAATGATACTATAGTTGAAATGTATATGGGTACATTAT
CAACAAAAAGTAAGCACTGGTTG
Found at i:8436 original size:45 final size:45
Alignment explanation
Indices: 8339--8560 Score: 256
Period size: 45 Copynumber: 5.0 Consensus size: 45
8329 GAAAAGATGT
* * *
8339 TATAGTTG-AATGCATATGGGCACATTATTAA-AGAAAAGTA-AGC
1 TATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATA-C
*
8382 -ACTAGTTGAAATGTATATGGGTACATTATCAACAGTAAAGTATAC
1 TA-TAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATAC
* *
8427 TATAGTTGAAATGTATATGGGTACATTATCAATAGAAAAGTATGC
1 TATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATAC
* *
8472 TATAGTTGAAATGTATATGGGTACATAATCAACCA-AAAAGTATGC
1 TATAGTTGAAATGTATATGGGTACATTATCAA-CAGAAAAGTATAC
* * * * * *
8517 TATTGTAGAAATGCATATGGGTGCATTATCAACATAAAAATATA
1 TATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATA
8561 TTATGACTGA
Statistics
Matches: 156, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
42 1 0.01
43 6 0.04
44 22 0.14
45 124 0.79
46 3 0.02
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.31
Consensus pattern (45 bp):
TATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATAC
Found at i:8482 original size:90 final size:89
Alignment explanation
Indices: 8339--8548 Score: 282
Period size: 90 Copynumber: 2.4 Consensus size: 89
8329 GAAAAGATGT
* *
8339 TATAGTTG-AATGCATATGGGCACATTATTAAAGAAAAGTAAGCACTAGTTGAAATGTATATGGG
1 TATAGTTGAAATGCATATGGGTACATTATCAAAGAAAAGTAAGCACTAGTTGAAATGTATATGGG
* *
8403 TACATTATCAA-CAGTAAAGTATAC
66 TACATAATCAACCA-AAAAGTATAC
* *
8427 TATAGTTGAAATGTATATGGGTACATTATCAATAGAAAAGTATGCTA-TAGTTGAAATGTATATG
1 TATAGTTGAAATGCATATGGGTACATTATCAA-AGAAAAGTAAGC-ACTAGTTGAAATGTATATG
*
8491 GGTACATAATCAACCAAAAAGTATGC
64 GGTACATAATCAACCAAAAAGTATAC
* * *
8517 TATTGTAGAAATGCATATGGGTGCATTATCAA
1 TATAGTTGAAATGCATATGGGTACATTATCAA
8549 CATAAAAATA
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
88 8 0.07
89 20 0.19
90 76 0.71
91 3 0.03
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.31
Consensus pattern (89 bp):
TATAGTTGAAATGCATATGGGTACATTATCAAAGAAAAGTAAGCACTAGTTGAAATGTATATGGG
TACATAATCAACCAAAAAGTATAC
Found at i:8581 original size:135 final size:133
Alignment explanation
Indices: 8317--8590 Score: 290
Period size: 135 Copynumber: 2.0 Consensus size: 133
8307 CATACAGGTG
* * * *
8317 CATTATCAGTATGAAAAGATGTTATAGTTGAATGCATATGGGCACATTATTAAAGAAAAGTAAGC
1 CATTATCAATATGAAAAGATGCTATAGTTGAATGCATATGGGCACATAATCAAAGAAAAGTAAGC
* * * *
8382 ACTAGTTGAAATGTATATGGGTACATTATCAACAGTAAAGTATACTATAGTTGAAATGTATATGG
66 ACTAGTAGAAATGCATATGGGTACATTATCAACAGTAAAATATACTATAGCTGAAATGTATATGG
8447 GTA
131 GTA
* *
8450 CATTATCAATA-GAAAAGTATGCTATAGTTGAAATGTATATGGGTACATAATCAACCA-AAAAGT
1 CATTATCAATATGAAAAG-ATGCTATAGTTG-AATGCATATGGGCACATAATCAA--AGAAAAGT
* * * * *
8513 ATGCTA-TTGTAGAAATGCATATGGGTGCATTATCAACA-TAAAAATATATTAT-GACTGAATTG
62 AAGC-ACTAGTAGAAATGCATATGGGTACATTATCAACAGT-AAAATATACTATAG-CTGAAATG
*
8575 CT-TATGGGTG
124 -TATATGGGTA
8585 CATTAT
1 CATTAT
8591 TAACATAAAG
Statistics
Matches: 117, Mismatches: 16, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
132 6 0.05
133 21 0.18
134 21 0.18
135 66 0.56
136 3 0.03
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.32
Consensus pattern (133 bp):
CATTATCAATATGAAAAGATGCTATAGTTGAATGCATATGGGCACATAATCAAAGAAAAGTAAGC
ACTAGTAGAAATGCATATGGGTACATTATCAACAGTAAAATATACTATAGCTGAAATGTATATGG
GTA
Found at i:11420 original size:16 final size:16
Alignment explanation
Indices: 11403--11432 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11393 AAAAAAAATA
11403 AAAAAATA-ATATAAT
1 AAAAAATATATATAAT
11418 AAAAAATATATATAA
1 AAAAAATATATATAA
11433 AAGTATCGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAATATATATAAT
Found at i:11425 original size:12 final size:12
Alignment explanation
Indices: 11392--11434 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
11382 ATATTTTTAT
*
11392 TAAAAAAAATAA
1 TAAAAAATATAA
*
11404 AAAAATAATATAA
1 TAAAA-AATATAA
11417 TAAAAAATATATA
1 TAAAAAATATA-A
11430 TAAAA
1 TAAAA
11435 GTATCGATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
TAAAAAATATAA
Found at i:11840 original size:3 final size:3
Alignment explanation
Indices: 11834--11858 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11824 GTAGCTCCAC
11834 CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG C
11859 TCCGGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:13824 original size:25 final size:26
Alignment explanation
Indices: 13784--13833 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
13774 GAGAGTATTT
13784 TTAATTTAGATATTTAAATATTTTTTG
1 TTAATTTAGATATTTAAAT-TTTTTTG
13811 TTAA-TTAGAT-TTTAAATTTTTTT
1 TTAATTTAGATATTTAAATTTTTTT
13834 AACATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 7 0.30
26 6 0.26
27 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (26 bp):
TTAATTTAGATATTTAAATTTTTTTG
Found at i:14595 original size:25 final size:24
Alignment explanation
Indices: 14566--14631 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
14556 ATTATAAAAA
14566 TTATAAAAGT-ATTATAAGAAT-ATAT
1 TTATAAAA-TAATT-TAA-AATAATAT
14591 TTATAAAATAATTTAAAATAATAT
1 TTATAAAATAATTTAAAATAATAT
14615 TTGAT-AAATAATATTAA
1 TT-ATAAAATAAT-TTAA
14632 TTATTATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
23 3 0.08
24 17 0.46
25 17 0.46
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (24 bp):
TTATAAAATAATTTAAAATAATAT
Found at i:14639 original size:58 final size:56
Alignment explanation
Indices: 14575--14709 Score: 157
Period size: 58 Copynumber: 2.4 Consensus size: 56
14565 ATTATAAAAG
*
14575 TATTATAAGAATATATTTATAAAATAATTTAAAATAAT-ATTTGATAAATAATATTAAT
1 TATTATAATAATATATTTATAAAATAATTTAAAAT-ATCATTT-A-AAATAATATTAAT
* * * * *
14633 TATTATAATAATATATTCTTTTAATATTATTTAAAATATCATTTAAAATATTATTTAT
1 TATTATAATAATATA-T-TTATAAAATAATTTAAAATATCATTTAAAATAATATTAAT
14691 TATTATAATAATAT-TTTAT
1 TATTATAATAATATATTTAT
14710 TTAGGTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
55 3 0.04
56 1 0.01
58 39 0.58
59 4 0.06
60 20 0.30
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (56 bp):
TATTATAATAATATATTTATAAAATAATTTAAAATATCATTTAAAATAATATTAAT
Found at i:14676 original size:12 final size:12
Alignment explanation
Indices: 14655--14689 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
14645 ATATTCTTTT
14655 AATATTATTTAA
1 AATATTATTTAA
*
14667 AATATCATTTAA
1 AATATTATTTAA
14679 AATATTATTTA
1 AATATTATTTA
14690 TTATTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (12 bp):
AATATTATTTAA
Found at i:14944 original size:2 final size:2
Alignment explanation
Indices: 14937--14976 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
14927 TCCTCTTGTA
14937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14977 TGAGGAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18086 original size:2 final size:2
Alignment explanation
Indices: 18081--18171 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
18071 ACACACACAC
18081 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18165 AT AT AT A
1 AT AT AT A
18172 CTTATTCTTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18389 original size:31 final size:32
Alignment explanation
Indices: 18345--18404 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
18335 GTTTTGGGGG
*
18345 AAAAATGAAAGTTTAGGTACTAAA-GCATACC
1 AAAAATGAAAGTTTAGGCACTAAACGCATACC
* *
18376 AAAATTGATAGTTTAGGCACTAAACGCAT
1 AAAAATGAAAGTTTAGGCACTAAACGCAT
18405 TAAGTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (32 bp):
AAAAATGAAAGTTTAGGCACTAAACGCATACC
Found at i:23807 original size:30 final size:29
Alignment explanation
Indices: 23773--23832 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
23763 AAATAGATTT
* *
23773 AGTTTAGTGACCAAATTATAAGATTTTGAA
1 AGTTTAGTGACCAAAGTATAA-ATCTTGAA
*
23803 AGTTTGGTGACCAAAGTATAAATCTTGAA
1 AGTTTAGTGACCAAAGTATAAATCTTGAA
23832 A
1 A
23833 AAGTTTAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (29 bp):
AGTTTAGTGACCAAAGTATAAATCTTGAA
Found at i:26044 original size:33 final size:33
Alignment explanation
Indices: 26002--26171 Score: 277
Period size: 33 Copynumber: 5.2 Consensus size: 33
25992 GAGTTATATG
* *
26002 ACAAAGATCTATGAGATCATACAAGAATGATAC
1 ACAAGGATCTATGAGATCATACAAGAATGTTAC
*
26035 ACAAGGATCTATGAGATCATACAAGAATGATAC
1 ACAAGGATCTATGAGATCATACAAGAATGTTAC
26068 ACAAGGATCTATGAGATCATACAAGAATGTTAC
1 ACAAGGATCTATGAGATCATACAAGAATGTTAC
*
26101 ACAATGATCTATGAGATCATACAAGAATGTTAC
1 ACAAGGATCTATGAGATCATACAAGAATGTTAC
* * *
26134 ACAATGATCTATGAGATCACACAAGAATGTTAT
1 ACAAGGATCTATGAGATCATACAAGAATGTTAC
26167 ACAAG
1 ACAAG
26172 CTACATGATA
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 131 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (33 bp):
ACAAGGATCTATGAGATCATACAAGAATGTTAC
Found at i:26475 original size:42 final size:42
Alignment explanation
Indices: 26406--26510 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
26396 CTTAAGGAGT
* * *
26406 GGTCATTCAGGACATACAAGTGGTCCTTCGAGATATATACAA
1 GGTCCTTCAGGACATACAAGTCGTCCTTCGAGACATATACAA
* * * * **
26448 GGTCCTTCATGACATACATGTCGTCCTTTGGGACATATATGA
1 GGTCCTTCAGGACATACAAGTCGTCCTTCGAGACATATACAA
*
26490 GGTCCTTCGGGACATACAAGT
1 GGTCCTTCAGGACATACAAGT
26511 TGTACTCTAT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (42 bp):
GGTCCTTCAGGACATACAAGTCGTCCTTCGAGACATATACAA
Found at i:26482 original size:21 final size:21
Alignment explanation
Indices: 26449--26507 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
26439 TATATACAAG
** *
26449 GTCCTTCATGACATACATGTC
1 GTCCTTCGGGACATACATGAC
* * *
26470 GTCCTTTGGGACATATATGAG
1 GTCCTTCGGGACATACATGAC
26491 GTCCTTCGGGACATACA
1 GTCCTTCGGGACATACA
26508 AGTTGTACTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (21 bp):
GTCCTTCGGGACATACATGAC
Found at i:26810 original size:28 final size:28
Alignment explanation
Indices: 26723--26810 Score: 115
Period size: 28 Copynumber: 3.1 Consensus size: 28
26713 ATGATTCTAT
*
26723 ATGTTACAAATGTTAATTACAAGATGAC
1 ATGTTACAAATGTTAAGTACAAGATGAC
* *
26751 ATATTACAAATGTTAAGTGCAAGATGAC
1 ATGTTACAAATGTTAAGTACAAGATGAC
* *
26779 ATGTTACAAA-GATTAAGCACAAGATGAT
1 ATGTTACAAATG-TTAAGTACAAGATGAC
26807 ATGT
1 ATGT
26811 CTTTAATGGT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
27 1 0.02
28 51 0.98
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (28 bp):
ATGTTACAAATGTTAAGTACAAGATGAC
Found at i:32355 original size:30 final size:30
Alignment explanation
Indices: 32311--32378 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
32301 ACATGCCTTA
* * * *
32311 GAAAAATTGGGGACCATTTTG-TAATTTTT
1 GAAAAGTTGGGGACCAATTCGATAATTTTG
32340 GAAAAGTTGGGGGACCAATTCGATAATTTTG
1 GAAAAGTT-GGGGACCAATTCGATAATTTTG
32371 GAAAAGTT
1 GAAAAGTT
32379 ATGAATGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 7 0.21
30 11 0.33
31 15 0.45
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.34
Consensus pattern (30 bp):
GAAAAGTTGGGGACCAATTCGATAATTTTG
Found at i:34049 original size:33 final size:33
Alignment explanation
Indices: 34008--34143 Score: 236
Period size: 33 Copynumber: 4.1 Consensus size: 33
33998 GGGTTATATG
*
34008 ACAAAGATCTATGTGATCATACAAGAATGTTAC
1 ACAAAGATCTATGAGATCATACAAGAATGTTAC
34041 ACAAAGATCTATGAGATCATACAAGAATGTTAC
1 ACAAAGATCTATGAGATCATACAAGAATGTTAC
*
34074 ACAATGATCTATGAGATCATACAAGAATGTTAC
1 ACAAAGATCTATGAGATCATACAAGAATGTTAC
* *
34107 ACAATGATCTATGAGATCATACAAGAATGTTAT
1 ACAAAGATCTATGAGATCATACAAGAATGTTAC
34140 ACAA
1 ACAA
34144 GCTACATGAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 100 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (33 bp):
ACAAAGATCTATGAGATCATACAAGAATGTTAC
Found at i:34468 original size:21 final size:21
Alignment explanation
Indices: 34444--34505 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
34434 ATACATGTCA
*
34444 TCCTTTGGGACATATACGAGG
1 TCCTTCGGGACATATACGAGG
* * **
34465 TCCTTCGGGACATACAAGTTG
1 TCCTTCGGGACATATACGAGG
*
34486 TCATTCGGGACATATACGAG
1 TCCTTCGGGACATATACGAG
34506 ATTGTCCAGG
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (21 bp):
TCCTTCGGGACATATACGAGG
Found at i:34496 original size:42 final size:42
Alignment explanation
Indices: 34382--34505 Score: 140
Period size: 42 Copynumber: 3.0 Consensus size: 42
34372 AAGGAGTGGA
* * * * *
34382 CCTTCGGGACATTCAAGTGGTTATTCGAGACATATACAAGGT
1 CCTTCGGGACATACAAGTCGTCATTCGGGACATATACGAGGT
* * * * * *
34424 CATTCGGAACATACATGTCATCCTTTGGGACATATACGAGGT
1 CCTTCGGGACATACAAGTCGTCATTCGGGACATATACGAGGT
*
34466 CCTTCGGGACATACAAGTTGTCATTCGGGACATATACGAG
1 CCTTCGGGACATACAAGTCGTCATTCGGGACATATACGAG
34506 ATTGTCCAGG
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (42 bp):
CCTTCGGGACATACAAGTCGTCATTCGGGACATATACGAGGT
Found at i:34717 original size:13 final size:13
Alignment explanation
Indices: 34699--34740 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
34689 GATTCTATAT
34699 ATTACAAATGTTA
1 ATTACAAATGTTA
34712 ATTACAAGATGACTT-
1 ATTACAA-ATG--TTA
34727 ATTACAAATGTTA
1 ATTACAAATGTTA
34740 A
1 A
34741 GTGCAAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 2 0.08
13 8 0.32
14 6 0.24
15 7 0.28
16 2 0.08
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (13 bp):
ATTACAAATGTTA
Found at i:34729 original size:28 final size:28
Alignment explanation
Indices: 34697--34779 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 28
34687 ATGATTCTAT
*
34697 ATATTACAAATGTTAATTACAAGATGAC
1 ATATTACAAATGTTAAGTACAAGATGAC
* *
34725 TTATTACAAATGTTAAGTGCAAGATGAC
1 ATATTACAAATGTTAAGTACAAGATGAC
* *
34753 ATGTTACAAA-GATGAAGTACAAGATGA
1 ATATTACAAATG-TTAAGTACAAGATGA
34780 TATGTCTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.02
28 46 0.98
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (28 bp):
ATATTACAAATGTTAAGTACAAGATGAC
Found at i:35692 original size:24 final size:24
Alignment explanation
Indices: 35656--35715 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
35646 ATATATCTTA
35656 ATCATCATCATCATCACCATCACC
1 ATCATCATCATCATCACCATCACC
**
35680 ATCATCAAT-ATCATCACTGTCACC
1 ATCATC-ATCATCATCACCATCACC
*
35704 ATCACCATCATC
1 ATCATCATCATC
35716 GTCATCTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 2 0.06
24 27 0.87
25 2 0.06
ACGTcount: A:0.33, C:0.38, G:0.02, T:0.27
Consensus pattern (24 bp):
ATCATCATCATCATCACCATCACC
Found at i:35695 original size:30 final size:30
Alignment explanation
Indices: 35659--35715 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
35649 TATCTTAATC
35659 ATCATCA-TCATCACCATCACCATCATCAAT
1 ATCATCACT-ATCACCATCACCATCATCAAT
*
35689 ATCATCACTGTCACCATCACCATCATC
1 ATCATCACTATCACCATCACCATCATC
35716 GTCATCTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.33, C:0.39, G:0.02, T:0.26
Consensus pattern (30 bp):
ATCATCACTATCACCATCACCATCATCAAT
Found at i:37218 original size:25 final size:26
Alignment explanation
Indices: 37157--37220 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
37147 GCAAAATAAA
**
37157 AAAATTATCATAAATAAAATAAAATTTC
1 AAAA-TAT-ATAAATAAAATAAAAAATC
*
37185 AATAT-TATAAAT-AAATAAAAAATC
1 AAAATATATAAATAAAATAAAAAATC
37209 AAAATATATAAA
1 AAAATATATAAA
37221 CATAAATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 14 0.45
25 12 0.39
26 1 0.03
27 1 0.03
28 3 0.10
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (26 bp):
AAAATATATAAATAAAATAAAAAATC
Found at i:39994 original size:17 final size:18
Alignment explanation
Indices: 39972--40006 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
39962 TATTATTGAA
39972 AATAACTTTTAT-AATTT
1 AATAACTTTTATCAATTT
39989 AATAACTTTTATCAATTT
1 AATAACTTTTATCAATTT
40007 TAATTTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
AATAACTTTTATCAATTT
Found at i:43028 original size:14 final size:14
Alignment explanation
Indices: 43013--43053 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
43003 CCTTATTGTT
43013 TTTTA-TTA-ATTA
1 TTTTATTTATATTA
43025 TTTTATTTATATTA
1 TTTTATTTATATTA
*
43039 TTTTGAATTATATTA
1 TTTT-ATTTATATTA
43054 GTTAACTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 5 0.20
13 3 0.12
14 8 0.32
15 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTTATTTATATTA
Found at i:49592 original size:23 final size:23
Alignment explanation
Indices: 49543--49640 Score: 78
Period size: 23 Copynumber: 4.4 Consensus size: 23
49533 TAAGCTACTA
* * *
49543 AAAGACAGATA-AAAGCATGCCAC
1 AAAGGCAGATATAAA-CATGTCAT
*
49566 AAAGGCAGATATAAACGTGTCAT
1 AAAGGCAGATATAAACATGTCAT
* * * *
49589 AAAGGTAG--A-GAACATGCCAC
1 AAAGGCAGATATAAACATGTCAT
*
49609 AAAGGCAGATATAGACATGTCAT
1 AAAGGCAGATATAAACATGTCAT
49632 AAAGGCAGA
1 AAAGGCAGA
49641 GAACATGTCA
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
20 14 0.25
21 1 0.02
22 1 0.02
23 38 0.67
24 3 0.05
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.14
Consensus pattern (23 bp):
AAAGGCAGATATAAACATGTCAT
Found at i:49619 original size:43 final size:43
Alignment explanation
Indices: 49558--49655 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
49548 CAGATAAAAG
* *
49558 CATGCCACAAAGGCAGATATAAACGTGTCATAAAGGTAGAGAA
1 CATGCCACAAAGGCAGATATAAACATGTCATAAAGGCAGAGAA
*
49601 CATGCCACAAAGGCAGATATAGACATGTCATAAAGGCAGAGAA
1 CATGCCACAAAGGCAGATATAAACATGTCATAAAGGCAGAGAA
*
49644 CATGTCACAAAG
1 CATGCCACAAAG
49656 ACATAATTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.15
Consensus pattern (43 bp):
CATGCCACAAAGGCAGATATAAACATGTCATAAAGGCAGAGAA
Found at i:49648 original size:20 final size:20
Alignment explanation
Indices: 49583--49655 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
49573 GATATAAACG
* *
49583 TGTCATAAAGGTAGAGAACA
1 TGTCACAAAGGCAGAGAACA
* *
49603 TGCCACAAAGGCAGATATAGACA
1 TGTCACAAAGGCAG--AGA-ACA
*
49626 TGTCATAAAGGCAGAGAACA
1 TGTCACAAAGGCAGAGAACA
49646 TGTCACAAAG
1 TGTCACAAAG
49656 ACATAATTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 23 0.55
21 2 0.05
22 2 0.05
23 15 0.36
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.16
Consensus pattern (20 bp):
TGTCACAAAGGCAGAGAACA
Done.