Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007038.1 Hibiscus syriacus cultivar Beakdansim tig00018241_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: 65388
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1457 original size:20 final size:19
Alignment explanation
Indices: 1428--1466 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1418 AATGCTCGGA
1428 GGGAACCGATTCCCCCCAG
1 GGGAACCGATTCCCCCCAG
1447 GGGATACCGATTCCCCCCAG
1 GGGA-ACCGATTCCCCCCAG
1467 TTTAACGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.21, C:0.41, G:0.26, T:0.13
Consensus pattern (19 bp):
GGGAACCGATTCCCCCCAG
Found at i:1864 original size:14 final size:14
Alignment explanation
Indices: 1842--1875 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1832 AAACAACCTA
*
1842 CCTTATGAGGATTT
1 CCTTGTGAGGATTT
1856 CCTTGTGAGGATTT
1 CCTTGTGAGGATTT
1870 CCTTGT
1 CCTTGT
1876 AAGTTTGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.44
Consensus pattern (14 bp):
CCTTGTGAGGATTT
Found at i:5154 original size:83 final size:83
Alignment explanation
Indices: 4907--5209 Score: 426
Period size: 83 Copynumber: 3.6 Consensus size: 83
4897 ATAGAATCTG
* * * *
4907 ACTCGAAGGTTTGATGACAGATAACTCTTCTCGCCTTTGAGTTATGCTGTAAATTTGATATGCCC
1 ACTCGAAGGTTTGTTGACAGATAACCCTTCTCGCC-TTGAGCTATGCTATAAATTTGATATGCCC
4972 TTGAGCTGAATGTAATCAA
65 TTGAGCTGAATGTAATCAA
* * * * *
4991 ACTCGAAGGTTTTTATTAACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATGTGCC
1 ACTCGAAGG--TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCC
*
5056 CTTGAGCTGAATGTAATCGA
64 CTTGAGCTGAATGTAATCAA
* * * * * *
5076 ACTCGAAGGTTTGTTGACATATAGCCCTTATTGCCTTGAGCTATACTATAAATTTGATATGTCCT
1 ACTCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCCT
*
5141 TGAGCTGAGTGTAATCAA
66 TGAGCTGAATGTAATCAA
5159 ACTCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTATAA
1 ACTCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTATAA
5210 TAGGCTGGGA
Statistics
Matches: 193, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
83 107 0.55
84 9 0.05
85 55 0.28
86 22 0.11
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (83 bp):
ACTCGAAGGTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTATAAATTTGATATGCCCT
TGAGCTGAATGTAATCAA
Found at i:12193 original size:3 final size:3
Alignment explanation
Indices: 12181--12216 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
12171 TAAAGTGTTC
12181 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12217 AATGTCTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:12294 original size:18 final size:17
Alignment explanation
Indices: 12277--12343 Score: 59
Period size: 18 Copynumber: 4.0 Consensus size: 17
12267 TCCAAAAAAG
12277 CAAAATAACAAAATAAA
1 CAAAATAACAAAATAAA
* *
12294 GCAAACTAAAAAAAT-AA
1 -CAAAATAACAAAATAAA
* *
12311 TAAAA-AATAAAATAAA
1 CAAAATAACAAAATAAA
12327 C-AAATAACATAAATAAA
1 CAAAATAACA-AAATAAA
12344 ATAAACAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
15 10 0.26
16 8 0.21
17 9 0.23
18 12 0.31
ACGTcount: A:0.75, C:0.09, G:0.01, T:0.15
Consensus pattern (17 bp):
CAAAATAACAAAATAAA
Found at i:12322 original size:15 final size:14
Alignment explanation
Indices: 12304--12377 Score: 62
Period size: 14 Copynumber: 5.2 Consensus size: 14
12294 GCAAACTAAA
12304 AAAATAATAAAAAAT
1 AAAATAA-AAAAAAT
*
12319 AAAAT-AAACAAAT
1 AAAATAAAAAAAAT
* *
12332 AACATAAATAAAAT
1 AAAATAAAAAAAAT
**
12346 AAACA-AAACCAAAT
1 AAA-ATAAAAAAAAT
12360 AAAATAAAAAGAAAT
1 AAAATAAAAA-AAAT
12375 AAA
1 AAA
12378 CAAATAAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
13 11 0.24
14 22 0.48
15 13 0.28
ACGTcount: A:0.77, C:0.07, G:0.01, T:0.15
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:12327 original size:28 final size:26
Alignment explanation
Indices: 12312--12377 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 26
12302 AAAAAATAAT
*
12312 AAAAAATAAAATAAACAAATAACATAA
1 AAAAAATAAAA-AAACAAATAAAATAA
*
12339 ATAAAATAAACAAAACCAAATAAAATAA
1 AAAAAATAAA-AAAA-CAAATAAAATAA
12367 AAAGAAATAAA
1 AAA-AAATAAA
12378 CAAATAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 12 0.36
28 14 0.42
29 7 0.21
ACGTcount: A:0.77, C:0.08, G:0.02, T:0.14
Consensus pattern (26 bp):
AAAAAATAAAAAAACAAATAAAATAA
Found at i:12342 original size:9 final size:9
Alignment explanation
Indices: 12300--12377 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
12290 TAAAGCAAAC
12300 TAAA-AAAA
1 TAAATAAAA
*
12308 TAATAAAAAA
1 TAA-ATAAAA
12318 TAAA-ATAAA
1 TAAATA-AAA
* *
12327 CAAATAACA
1 TAAATAAAA
12336 TAAATAAAA
1 TAAATAAAA
*
12345 TAAACAAAA
1 TAAATAAAA
*
12354 CCAAATAAAA
1 -TAAATAAAA
*
12364 TAAAAAGAAA
1 TAAATA-AAA
12374 TAAA
1 TAAA
12378 CAAATAAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
8 4 0.07
9 29 0.53
10 22 0.40
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.15
Consensus pattern (9 bp):
TAAATAAAA
Found at i:12343 original size:22 final size:19
Alignment explanation
Indices: 12315--12367 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 19
12305 AAATAATAAA
*
12315 AAATAAAATAAACAAATAACAT
1 AAATAAAATAAAC-AA-AAC-C
12337 AAATAAAATAAACAAAACC
1 AAATAAAATAAACAAAACC
12356 AAATAAAATAAA
1 AAATAAAATAAA
12368 AAGAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.40
20 3 0.10
21 2 0.07
22 13 0.43
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.15
Consensus pattern (19 bp):
AAATAAAATAAACAAAACC
Found at i:12378 original size:51 final size:49
Alignment explanation
Indices: 12279--12392 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 49
12269 CAAAAAAGCA
*
12279 AAATAACAAAATAAAGCAAACTAAAAAAATAATAAAAAATAAAATAAAC
1 AAATAACAAAATAAAACAAACTAAAAAAATAATAAAAAATAAAATAAAC
*
12328 AAATAACATAAATAAAATAAAC-AAAACCAAATAA-AATAAAA-AGAAATAAAC
1 AAATAACA-AAATAAAACAAACTAAAA--AAATAATAA-AAAATA-AAATAAAC
*
12379 AAATAA-AAAGTAAA
1 AAATAACAAAATAAA
12393 TACCTGAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
49 18 0.32
50 15 0.26
51 24 0.42
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (49 bp):
AAATAACAAAATAAAACAAACTAAAAAAATAATAAAAAATAAAATAAAC
Found at i:12599 original size:5 final size:5
Alignment explanation
Indices: 12591--12653 Score: 53
Period size: 5 Copynumber: 13.2 Consensus size: 5
12581 AAAAATAGTA
* *
12591 AAAAT AAAAT AAAA- AATAAT AAAAT -AAAT AGAAT -AAAG AAAAT AAAAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
12639 AATA- AAAAT ATAAT A
1 AAAAT AAAAT AAAAT A
12654 TATAATAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 11 0.24
5 33 0.72
6 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:12599 original size:20 final size:19
Alignment explanation
Indices: 12576--12623 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
12566 AGGAAACTAA
*
12576 AAAAGAAAAATAGTAAAAAT
1 AAAAGAAAAATAAT-AAAAT
*
12596 AAAATAAAAAATAATAAAAT
1 AAAA-GAAAAATAATAAAAT
12616 AAATAGAA
1 AAA-AGAA
12624 TAAAGAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAAGAAAAATAATAAAAT
Found at i:12627 original size:14 final size:13
Alignment explanation
Indices: 12601--12653 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
12591 AAAATAAAAT
12601 AAAAA-ATAATAA
1 AAAAATATAATAA
*
12613 AATAAATAGAATAA
1 AA-AAATATAATAA
*
12627 AGAAAATAAAATAA
1 A-AAAATATAATAA
12641 TAAAAATATAATA
1 -AAAAATATAATA
12654 TATAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 2 0.06
13 3 0.09
14 27 0.79
15 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (13 bp):
AAAAATATAATAA
Found at i:14543 original size:12 final size:13
Alignment explanation
Indices: 14526--14601 Score: 75
Period size: 15 Copynumber: 5.5 Consensus size: 13
14516 TTTATAAATT
14526 AAAATAA-AATAA
1 AAAATAATAATAA
14538 AAAATAAATAGATAA
1 AAAAT-AATA-ATAA
*
14553 AAAATAAGAATAA
1 AAAATAATAATAA
14566 TAAAATAAATAGATAA
1 -AAAAT-AATA-ATAA
14582 AAAATAA-AATAA
1 AAAATAATAATAA
14594 TAAAATAA
1 -AAAATAA
14602 ATAAAATAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
12 9 0.16
13 14 0.25
14 11 0.20
15 17 0.31
16 4 0.07
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:14552 original size:15 final size:14
Alignment explanation
Indices: 14533--14598 Score: 80
Period size: 15 Copynumber: 4.5 Consensus size: 14
14523 ATTAAAATAA
14533 AATAAAAAATAAAT
1 AATAAAAAATAAAT
*
14547 AGATAAAAAAT-AAG
1 A-ATAAAAAATAAAT
14561 AATAATAAAATAAAT
1 AATAA-AAAATAAAT
14576 AGATAAAAAATAAAAT
1 A-ATAAAAAAT-AAAT
14592 AATAAAA
1 AATAAAA
14599 TAAATAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 4 0.09
14 9 0.20
15 23 0.51
16 9 0.20
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (14 bp):
AATAAAAAATAAAT
Found at i:14554 original size:20 final size:19
Alignment explanation
Indices: 14528--14605 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 19
14518 TATAAATTAA
14528 AATAAAATAAAAAATAAAT
1 AATAAAATAAAAAATAAAT
* *
14547 AGAT-AAA-AAATAA-GAAT
1 A-ATAAAATAAAAAATAAAT
* *
14564 AATAAAATAAATAGATAAAA
1 AATAAAATAAA-AAATAAAT
14584 AATAAAATAATAAAATAAAT
1 AATAAAATAA-AAAATAAAT
14604 AA
1 AA
14606 AATAGAGGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
16 2 0.04
17 7 0.16
18 8 0.18
19 5 0.11
20 22 0.49
21 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.21
Consensus pattern (19 bp):
AATAAAATAAAAAATAAAT
Found at i:14573 original size:29 final size:28
Alignment explanation
Indices: 14526--14604 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 28
14516 TTTATAAATT
14526 AAAATAAAATAA-AAAATAAATAGATAA
1 AAAATAAAATAATAAAATAAATAGATAA
14553 AAAATAAGAATAATAAAATAAATAGATAA
1 AAAATAA-AATAATAAAATAAATAGATAA
14582 AAAATAAAATAATAAAATAAATA
1 AAAATAAAATAATAAAATAAATA
14605 AAATAGAGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
27 7 0.14
28 21 0.42
29 22 0.44
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (28 bp):
AAAATAAAATAATAAAATAAATAGATAA
Found at i:14815 original size:25 final size:25
Alignment explanation
Indices: 14783--14870 Score: 158
Period size: 25 Copynumber: 3.5 Consensus size: 25
14773 CGACTAAAAT
14783 GTAATCATAACAAAATCTAAAGCTC
1 GTAATCATAACAAAATCTAAAGCTC
14808 GTAATCATAACAAAATCTAAAGCTC
1 GTAATCATAACAAAATCTAAAGCTC
14833 GTAATCATAACAAAATCTAAAGCTC
1 GTAATCATAACAAAATCTAAAGCTC
* *
14858 GAAATCAAAACAA
1 GTAATCATAACAA
14871 TTAAAAATCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.22
Consensus pattern (25 bp):
GTAATCATAACAAAATCTAAAGCTC
Found at i:16925 original size:22 final size:22
Alignment explanation
Indices: 16897--16957 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
16887 TTGGGAGCGT
*
16897 AGGTGTATTGGTACACTATCAA
1 AGGTGTATCGGTACACTATCAA
16919 AGGTGTATCGGTACACTATCAA
1 AGGTGTATCGGTACACTATCAA
16941 AGGTGTATCGGTACACT
1 AGGTGTATCGGTACACT
16958 CAAGTGTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (22 bp):
AGGTGTATCGGTACACTATCAA
Found at i:17020 original size:17 final size:17
Alignment explanation
Indices: 16998--17045 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
16988 AGTTGACCGA
16998 GTGTATCGGTACACCAG
1 GTGTATCGGTACACCAG
17015 GTGTATCGGTACACCAG
1 GTGTATCGGTACACCAG
*
17032 GTGTATCGATACAC
1 GTGTATCGGTACAC
17046 TAATTACATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (17 bp):
GTGTATCGGTACACCAG
Found at i:17501 original size:21 final size:21
Alignment explanation
Indices: 17475--17515 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
17465 TTTTTGAAAT
17475 CAATTTCGAAAATTACTCCCC
1 CAATTTCGAAAATTACTCCCC
*
17496 CAATTTTGAAAATTACTCCC
1 CAATTTCGAAAATTACTCCC
17516 TCCCCTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (21 bp):
CAATTTCGAAAATTACTCCCC
Found at i:19254 original size:12 final size:13
Alignment explanation
Indices: 19237--19269 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
19227 TGGGCAATAA
*
19237 TTTGAAAACTAT-
1 TTTGAAAACAATG
19249 TTTGAAAACAATG
1 TTTGAAAACAATG
19262 TTTGAAAA
1 TTTGAAAA
19270 ATCATAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:19648 original size:21 final size:21
Alignment explanation
Indices: 19597--19654 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
19587 GTTGAAGAAG
*
19597 AGTGTATCAATACACATTCAA
1 AGTGTATCGATACACATTCAA
* *
19618 AGAATGTATCGGTACACATTCAT
1 AG--TGTATCGATACACATTCAA
19641 AGTGTATCGATACA
1 AGTGTATCGATACA
19655 TAGCGAGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 13 0.42
23 18 0.58
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (21 bp):
AGTGTATCGATACACATTCAA
Found at i:28579 original size:18 final size:17
Alignment explanation
Indices: 28547--28580 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28537 ACGTGCAACA
*
28547 ACAACAAAAACAAAAAT
1 ACAAAAAAAACAAAAAT
28564 ACAAAAAAATACAAAAA
1 ACAAAAAAA-ACAAAAA
28581 GAAGTGACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.06
Consensus pattern (17 bp):
ACAAAAAAAACAAAAAT
Found at i:32000 original size:10 final size:10
Alignment explanation
Indices: 31985--32009 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31975 CAACAAAAAC
31985 AAAAATACAA
1 AAAAATACAA
31995 AAAAATACAA
1 AAAAATACAA
32005 AAAAA
1 AAAAA
32010 GTGACATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAATACAA
Found at i:32006 original size:18 final size:17
Alignment explanation
Indices: 31974--32007 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31964 GCAACGTGCA
*
31974 ACAACAAAAACAAAAAT
1 ACAAAAAAAACAAAAAT
31991 ACAAAAAAATACAAAAA
1 ACAAAAAAA-ACAAAAA
32008 AAGTGACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.06
Consensus pattern (17 bp):
ACAAAAAAAACAAAAAT
Found at i:37142 original size:19 final size:19
Alignment explanation
Indices: 37088--37158 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
37078 GCTGCTGGAA
* *
37088 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
*
37108 AACCGGTTTAACCGGTTCG
1 AACCGGTTTGACCGGTTCG
*
37127 AACCGGTTTGAGCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
37146 AACCGGGTTGACC
1 AACCGGTTTGACC
37159 CGACCCGACT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 2 0.05
19 29 0.67
20 12 0.28
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:37177 original size:7 final size:7
Alignment explanation
Indices: 37169--37222 Score: 83
Period size: 7 Copynumber: 7.9 Consensus size: 7
37159 CGACCCGACT
*
37169 GTTGACT
1 GTTGACC
37176 GTTGACC
1 GTTGACC
37183 GTTGACC
1 GTTGACC
37190 GTTGACC
1 GTTGACC
37197 GTTGACC
1 GTTGACC
37204 G-TGACC
1 GTTGACC
*
37210 GTTGATC
1 GTTGACC
37217 GTTGAC
1 GTTGAC
37223 TTTCTTTGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
6 6 0.14
7 37 0.86
ACGTcount: A:0.15, C:0.24, G:0.30, T:0.31
Consensus pattern (7 bp):
GTTGACC
Found at i:37210 original size:27 final size:28
Alignment explanation
Indices: 37169--37222 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
37159 CGACCCGACT
*
37169 GTTGACTGTTGACCGTTGACCGTTGACC
1 GTTGACCGTTGACCGTTGACCGTTGACC
*
37197 GTTGACCG-TGACCGTTGATCGTTGAC
1 GTTGACCGTTGACCGTTGACCGTTGAC
37223 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.15, C:0.24, G:0.30, T:0.31
Consensus pattern (28 bp):
GTTGACCGTTGACCGTTGACCGTTGACC
Found at i:38794 original size:21 final size:21
Alignment explanation
Indices: 38768--38814 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
38758 AATTTGTTTT
38768 CTACTAACCAATCTTTTCTTC
1 CTACTAACCAATCTTTTCTTC
38789 CTACTAACCAATCTTTTCTTC
1 CTACTAACCAATCTTTTCTTC
38810 CTACT
1 CTACT
38815 CATCCTCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (21 bp):
CTACTAACCAATCTTTTCTTC
Found at i:41210 original size:18 final size:17
Alignment explanation
Indices: 41178--41211 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41168 ACGTGCAACA
*
41178 ACAACAAAAACAAAAAT
1 ACAAAAAAAACAAAAAT
41195 ACAAAAAAATACAAAAA
1 ACAAAAAAA-ACAAAAA
41212 GAAGTGACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.06
Consensus pattern (17 bp):
ACAAAAAAAACAAAAAT
Found at i:42419 original size:19 final size:19
Alignment explanation
Indices: 42395--42431 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42385 TTAATATTTG
**
42395 TATTATATTTATATTAAAA
1 TATTATATCGATATTAAAA
42414 TATTATATCGATATTAAA
1 TATTATATCGATATTAAA
42432 TACATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
TATTATATCGATATTAAAA
Found at i:42713 original size:18 final size:19
Alignment explanation
Indices: 42661--42714 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
42651 CCATAATATT
42661 TTAATTAAA--AATTAAAAA
1 TTAATTAAATTAA-TAAAAA
*
42679 TTAAATTTAATTAATAAAAA
1 TT-AATTAAATTAATAAAAA
*
42699 TT-ATTAAATTGATAAA
1 TTAATTAAATTAATAAA
42715 GATAAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 14 0.47
19 6 0.20
20 8 0.27
21 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TTAATTAAATTAATAAAAA
Found at i:44673 original size:59 final size:60
Alignment explanation
Indices: 44530--44675 Score: 152
Period size: 59 Copynumber: 2.5 Consensus size: 60
44520 ACAAAGCACA
* * * ** *
44530 GATCATGAAGTGCACCTTCGAG-GGTTCTGTCCGAGCTGGTGTCACGGTGGAAAGGTACG
1 GATCAAGAAGCGCGCCTTCGAGAGGTTCTGTCCGAGCTGACGCCACGGTGGAAAGGTACG
* * * * * *
44589 GATCAAGAGGTGCGCCTCCGTGAGGTTCTGTCCGAGCTGACGCCACGTTGG-AAGGTGCG
1 GATCAAGAAGCGCGCCTTCGAGAGGTTCTGTCCGAGCTGACGCCACGGTGGAAAGGTACG
* *
44648 GATCAAGAAGCGTGCCTTCGCGAGGTTC
1 GATCAAGAAGCGCGCCTTCGAGAGGTTC
44676 CGTCATGATC
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
59 47 0.66
60 24 0.34
ACGTcount: A:0.19, C:0.23, G:0.36, T:0.22
Consensus pattern (60 bp):
GATCAAGAAGCGCGCCTTCGAGAGGTTCTGTCCGAGCTGACGCCACGGTGGAAAGGTACG
Found at i:52012 original size:86 final size:87
Alignment explanation
Indices: 51843--52012 Score: 234
Period size: 86 Copynumber: 2.0 Consensus size: 87
51833 CTACATATCA
* **
51843 GACCGTACTAAAAAGATACCTAGTGTGGGTCAGTACTAAAGGATACCTAGTGCTGATGGTGGGCA
1 GACCGTACTAAAAAGATACCTAGTGCGGGTCAGTACTAAAGGATACCTAGTGCTGATGGTGGAAA
* *
51908 CGACCTTATGTGTCATATTCGT
66 CGACCTCACGTGTCATATTCGT
* * *
51930 GACCGTACT-AAAGGATACCTAGTGCGGGTTAGTACTAAAGGATACCTAGTGTTGATGGTGGAAA
1 GACCGTACTAAAAAGATACCTAGTGCGGGTCAGTACTAAAGGATACCTAGTGCTGATGGTGGAAA
* * *
51994 TGACCTCCCGTGTGATATT
66 CGACCTCACGTGTCATATT
52013 GGTTTAGCAC
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
86 63 0.88
87 9 0.12
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (87 bp):
GACCGTACTAAAAAGATACCTAGTGCGGGTCAGTACTAAAGGATACCTAGTGCTGATGGTGGAAA
CGACCTCACGTGTCATATTCGT
Found at i:58090 original size:40 final size:40
Alignment explanation
Indices: 58025--58105 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
58015 GTTTTTTGAG
58025 GTTGCATATTCATTCTAAGTTTGTTTGATGATT-AAACAT
1 GTTGCATATTCATTCTAAGTTTGTTTGATGATTAAAACAT
58064 GTTGCATATTCATTTCTAAGTTTGTTTGATGATTAAAACAT
1 GTTGCATATTCA-TTCTAAGTTTGTTTGATGATTAAAACAT
58105 G
1 G
58106 CTCAACCCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 12 0.30
40 21 0.52
41 7 0.17
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (40 bp):
GTTGCATATTCATTCTAAGTTTGTTTGATGATTAAAACAT
Found at i:60642 original size:37 final size:37
Alignment explanation
Indices: 60600--60671 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
60590 GTTTCTATTA
60600 TTTAATTATTTGA-ATTGTAAAGTTTGTATTTAATTGT
1 TTTAATTATTT-ACATTGTAAAGTTTGTATTTAATTGT
* * *
60637 TTTAATTATTTACTTTGTAATGTTTTTATTTAATT
1 TTTAATTATTTACATTGTAAAGTTTGTATTTAATT
60672 TTCACTCGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 1 0.03
37 30 0.97
ACGTcount: A:0.28, C:0.01, G:0.10, T:0.61
Consensus pattern (37 bp):
TTTAATTATTTACATTGTAAAGTTTGTATTTAATTGT
Done.