Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003523.1 Hibiscus syriacus cultivar Beakdansim tig00007444_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: 70657
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Found at i:18180 original size:16 final size:16
Alignment explanation
Indices: 18138--18180 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
18128 GGTGTTTAAA
18138 TTCGAGTACCCGGGTT
1 TTCGAGTACCCGGGTT
**
18154 TTCGAAAACCCGGGTT
1 TTCGAGTACCCGGGTT
*
18170 TTCGGGTACCC
1 TTCGAGTACCC
18181 AAAGTACCAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (16 bp):
TTCGAGTACCCGGGTT
Found at i:18511 original size:24 final size:24
Alignment explanation
Indices: 18484--18530 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
18474 TTTATTAGTT
*
18484 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTATTAA
*
18508 TAATTAAATATATAATATTATTA
1 TAATTAAATATATAAAATTATTA
18531 TATATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATTAAATATATAAAATTATTAA
Found at i:18911 original size:20 final size:20
Alignment explanation
Indices: 18860--18961 Score: 111
Period size: 20 Copynumber: 5.2 Consensus size: 20
18850 TTTCGAATTT
* * *
18860 GCAATGCGATTATGACAATC
1 GCAACGCGATTCTGACTATC
*
18880 GCAATGCGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
* *
18900 ACAACGCGATTCTGATTATC
1 GCAACGCGATTCTGACTATC
*
18920 GCAACGAGATTCTGACTATC
1 GCAACGCGATTCTGACTATC
*
18940 G---CGCGATTCTGACTGTC
1 GCAACGCGATTCTGACTATC
18957 GCAAC
1 GCAAC
18962 ACTGAATTTC
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
17 15 0.22
20 54 0.78
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (20 bp):
GCAACGCGATTCTGACTATC
Found at i:19811 original size:24 final size:24
Alignment explanation
Indices: 19784--19837 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
19774 GTATTCGAAA
19784 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
19808 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
19832 TTTGAT
1 TTTGAT
19838 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:22122 original size:18 final size:18
Alignment explanation
Indices: 22099--22133 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22089 AGAAAAAGGC
*
22099 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
*
22117 AATCAAAGTCCCAATCA
1 AATCAAAATCCCAATCA
22134 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.26, G:0.06, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:22329 original size:20 final size:20
Alignment explanation
Indices: 22304--22523 Score: 178
Period size: 20 Copynumber: 11.7 Consensus size: 20
22294 TTACACATTC
* *
22304 ATTTGAATATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
22324 ATTTGACTATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
22344 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
22364 ATTTGACTATCGCAA--C-A
1 ATTTGACTATCGCAACGCGA
* **
22381 A---AAAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
22398 ATTTAACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
22418 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * * *
22438 ATTTGATTATCACAACGGGT
1 ATTTGACTATCGCAACGCGA
* *
22458 ATTCGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
22478 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
22492 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
22512 A-TTGACTTTCGC
1 ATTTGACTATCGC
22524 GTTGCGATTT
Statistics
Matches: 160, Mismatches: 28, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
14 18 0.11
16 2 0.01
17 4 0.03
18 2 0.01
19 9 0.06
20 125 0.78
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:22433 original size:74 final size:74
Alignment explanation
Indices: 22312--22453 Score: 221
Period size: 74 Copynumber: 1.9 Consensus size: 74
22302 TCATTTGAAT
* * * * *
22312 ATCGCAATGCGAATTTGACTATCGTAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
1 ATCGCAACGCGAATTTAACTATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGACTATCAC
22377 AACAAAAAA
66 AACAAAAAA
* *
22386 ATCGCAACGCGAATTTAACTATCGCAACGAGAATTTGACTATCGCAACGTGAATTTGATTATCAC
1 ATCGCAACGCGAATTTAACTATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGACTATCAC
22451 AAC
66 AAC
22454 GGGTATTCGA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (74 bp):
ATCGCAACGCGAATTTAACTATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGACTATCAC
AACAAAAAA
Found at i:22472 original size:94 final size:94
Alignment explanation
Indices: 22311--22523 Score: 277
Period size: 94 Copynumber: 2.3 Consensus size: 94
22301 TTCATTTGAA
* * * *
22311 TATCGCAATGCGAATTTGACTATCGTAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCG
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTCGACTATCG
*
22376 CAACAAAAAAATCGCAACGCGAATTTA-AC
66 CAACAAAAAAATCGCAAAGCGAA-TTAGAC
* * * * *
22405 TATCGCAACGAGAATTTGACTATCGCAACGTGAATTTGATTATCACAACGGGTATTCGACTATCG
1 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTCGACTATCG
* * *
22470 CAACGAGAAAATCGCAAAGCGTATTAGAC
66 CAACAAAAAAATCGCAAAGCGAATTAGAC
*
22499 TATCGCAACGCGAA-TTGACTTTCGC
1 TATCGCAACGCGAATTTGACTATCGC
22524 GTTGCGATTT
Statistics
Matches: 103, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
93 13 0.13
94 90 0.87
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (94 bp):
TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTCGACTATCG
CAACAAAAAAATCGCAAAGCGAATTAGAC
Found at i:22542 original size:20 final size:21
Alignment explanation
Indices: 22513--22570 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
22503 GCAACGCGAA
22513 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
22533 TTG-GCTTTCGCATTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
22553 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
22571 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.43
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:22708 original size:29 final size:28
Alignment explanation
Indices: 22674--22728 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
22664 ATAAGAATTA
*
22674 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAAT-TTAAACAAATCAACT
**
22703 TTTACAAATCAATTTTTACAAATCAA
1 TTTACAAATCAATTTAAACAAATCAA
22729 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (28 bp):
TTTACAAATCAATTTAAACAAATCAACT
Found at i:22729 original size:14 final size:14
Alignment explanation
Indices: 22669--22730 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
22659 CACAAATAAG
*
22669 AATTATTTACACATC
1 AATT-TTTACAAATC
**
22684 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
22699 AACTTTTACAAATC
1 AATTTTTACAAATC
22713 AATTTTTACAAATC
1 AATTTTTACAAATC
22727 AATT
1 AATT
22731 AAACAAGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 12 0.31
16 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:24165 original size:21 final size:21
Alignment explanation
Indices: 24136--24235 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 21
24126 GGGAGGGACA
* *
24136 TCTTCAACGATGACAGTGGCC
1 TCTTGAACGATGACAGAGGCC
* ** *
24157 TCTTGAACGGTGGGAGAGGAC
1 TCTTGAACGATGACAGAGGCC
** * *
24178 TCTTGAGGGATGATAGGGGCC
1 TCTTGAACGATGACAGAGGCC
* **
24199 TCTTGAATGAT-AGGGGAGGCC
1 TCTTGAACGATGA-CAGAGGCC
24220 TCTTGAACGATGACAG
1 TCTTGAACGATGACAG
24236 GTGAGTCGGG
Statistics
Matches: 56, Mismatches: 21, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 1 0.02
21 54 0.96
22 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (21 bp):
TCTTGAACGATGACAGAGGCC
Found at i:24223 original size:42 final size:42
Alignment explanation
Indices: 24144--24236 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
24134 CATCTTCAAC
* *
24144 GATGACAGTGGCCTCTTGAACGGTGGGAGAGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * * **
24186 GATGATAGGGGCCTCTTGAATGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
24228 GATGACAGG
1 GATGACAGG
24237 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.24, C:0.16, G:0.39, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:24745 original size:18 final size:19
Alignment explanation
Indices: 24722--24767 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
24712 GAAACTTAAA
24722 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
24740 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
*
24760 ATCTCAAC
1 ATCGCAAC
24768 GAGAGAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.42
20 14 0.58
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.17
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:26755 original size:19 final size:20
Alignment explanation
Indices: 26652--26747 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
26642 TTTGAAACTT
*
26652 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
26672 AAAATCACAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
26692 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
** *
26712 ACTATCGTAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
26731 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
26748 CTAAAATCAC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
19 14 0.23
20 48 0.77
ACGTcount: A:0.47, C:0.22, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:27158 original size:20 final size:21
Alignment explanation
Indices: 27133--27189 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
27123 TCTGAGAGAT
27133 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* * *
27153 GGAGATGGGACTGATTTCGTC
1 GGAGATGAGACGGATTTCGCC
*
27174 GGAGATGGGGACGGAT
1 GGAGAT-GAGACGGAT
27190 GTTGCCTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.19
21 17 0.55
22 8 0.26
ACGTcount: A:0.23, C:0.14, G:0.42, T:0.21
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:27431 original size:20 final size:20
Alignment explanation
Indices: 27359--27494 Score: 105
Period size: 20 Copynumber: 6.8 Consensus size: 20
27349 TGGCGCTTTG
27359 AAAATCGCATTGCGATAGTC
1 AAAATCGCATTGCGATAGTC
** * * *
27379 AGCATCTCGTTACGATAGTC
1 AAAATCGCATTGCGATAGTC
* *
27399 AGAATCGCGTTGCGATAGTC
1 AAAATCGCATTGCGATAGTC
* *
27419 ATAATCGCATTGCGAT-TTAC
1 AAAATCGCATTGCGATAGT-C
* * *
27439 ATATTCGCATTGCGAT-TTC
1 AAAATCGCATTGCGATAGTC
*
27458 AGAAAATCGCAATGCGATAGTC
1 --AAAATCGCATTGCGATAGTC
*
27480 AAAATCGCGTTGCGA
1 AAAATCGCATTGCGA
27495 ATCTGGAAAC
Statistics
Matches: 94, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.02
20 77 0.82
21 13 0.14
22 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (20 bp):
AAAATCGCATTGCGATAGTC
Found at i:28290 original size:14 final size:13
Alignment explanation
Indices: 28257--28298 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
28247 AACCACTAAG
28257 ATTTTATTATAAT
1 ATTTTATTATAAT
28270 ATTTTATATATAA-
1 ATTTTAT-TATAAT
28283 ATTGTTATTACTAAT
1 ATT-TTATTA-TAAT
28298 A
1 A
28299 GCAGAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 12 0.48
14 12 0.48
15 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
ATTTTATTATAAT
Found at i:28494 original size:20 final size:20
Alignment explanation
Indices: 28469--28518 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
28459 TAAAAAGTAA
28469 AAATTATATTTTATATTTTT
1 AAATTATATTTTATATTTTT
28489 AAATTATATTTTATATTTTT
1 AAATTATATTTTATATTTTT
28509 AAATTATATT
1 AAATTATATT
28519 GAGTCCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AAATTATATTTTATATTTTT
Found at i:29592 original size:6 final size:6
Alignment explanation
Indices: 29576--29612 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
29566 TAGGAGCACT
29576 CTTCTCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC
1 CTTC-CC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC
29613 TCCATATAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CTTCCC
Found at i:35587 original size:42 final size:42
Alignment explanation
Indices: 35513--35621 Score: 186
Period size: 42 Copynumber: 2.6 Consensus size: 42
35503 TTACTCATAA
*
35513 TTGTGACGA-AAATATTTTT-TCACTAGTCTTAGTTGGTGAT
1 TTGTGACGACAATTATTTTTGTCACTAGTCTTAGTTGGTGAT
35553 TTGTGACGACAATTATTTTTGTCACTAGTCTTAGTTGGTGAT
1 TTGTGACGACAATTATTTTTGTCACTAGTCTTAGTTGGTGAT
*
35595 TTGTGATGACAATTATTTTTGTCACTA
1 TTGTGACGACAATTATTTTTGTCACTA
35622 TTGAAGTGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 9 0.14
41 9 0.14
42 47 0.72
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (42 bp):
TTGTGACGACAATTATTTTTGTCACTAGTCTTAGTTGGTGAT
Found at i:36540 original size:23 final size:23
Alignment explanation
Indices: 36514--36574 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
36504 CACCACAGCT
*
36514 CGTATAAATGCACCGAAGTACCA
1 CGTAAAAATGCACCGAAGTACCA
* * *
36537 CGTAGAATTGCACCGAAGTACCG
1 CGTAAAAATGCACCGAAGTACCA
*
36560 CATAAAAATGCACCG
1 CGTAAAAATGCACCG
36575 TAGTGCCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (23 bp):
CGTAAAAATGCACCGAAGTACCA
Found at i:39956 original size:12 final size:12
Alignment explanation
Indices: 39938--39968 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39928 CCACTCCTCC
39938 ATCTTCATATCT
1 ATCTTCATATCT
*
39950 TTCTTCATATCT
1 ATCTTCATATCT
39962 ATCTTCA
1 ATCTTCA
39969 ACTCCTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.52
Consensus pattern (12 bp):
ATCTTCATATCT
Found at i:41640 original size:23 final size:23
Alignment explanation
Indices: 41572--41641 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
41562 GTCACCATAA
* *
41572 CTCGTATAAATGCACCGAAGTGA
1 CTCGTAGAAATGCACCGAAGTGC
* *
41595 CACGTAGAATTGCACCGAAGTGC
1 CTCGTAGAAATGCACCGAAGTGC
*
41618 CTCGTAGAAATGCACCGTAGTGC
1 CTCGTAGAAATGCACCGAAGTGC
41641 C
1 C
41642 ATATAAGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
CTCGTAGAAATGCACCGAAGTGC
Found at i:42112 original size:12 final size:12
Alignment explanation
Indices: 42095--42121 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42085 ATTAACTTAG
42095 ATCATATCATAT
1 ATCATATCATAT
42107 ATCATATCATAT
1 ATCATATCATAT
42119 ATC
1 ATC
42122 TCATGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (12 bp):
ATCATATCATAT
Found at i:44363 original size:24 final size:24
Alignment explanation
Indices: 44335--44386 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
44325 TATTGATGAC
44335 ATATAAAGTGATCAATAGTATTTG
1 ATATAAAGTGATCAATAGTATTTG
44359 ATATAAAGTGATCAATAGTATTTG
1 ATATAAAGTGATCAATAGTATTTG
44383 ATAT
1 ATAT
44387 TTGTTATGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.38
Consensus pattern (24 bp):
ATATAAAGTGATCAATAGTATTTG
Found at i:50100 original size:24 final size:25
Alignment explanation
Indices: 50052--50100 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
50042 AAAATTATAT
* * *
50052 TAAAATTTTAGGGGGTGCGATATTA
1 TAAAATCTTAGGGGGTGCAAAATTA
50077 TAAAATCTTA-GGGGTGCAAAATTA
1 TAAAATCTTAGGGGGTGCAAAATTA
50101 AATAATTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (25 bp):
TAAAATCTTAGGGGGTGCAAAATTA
Found at i:52659 original size:14 final size:14
Alignment explanation
Indices: 52640--52666 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52630 TTTTAATTTT
52640 GAGTTATTTGAGTC
1 GAGTTATTTGAGTC
52654 GAGTTATTTGAGT
1 GAGTTATTTGAGT
52667 TAACTTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.30, T:0.44
Consensus pattern (14 bp):
GAGTTATTTGAGTC
Found at i:53032 original size:160 final size:159
Alignment explanation
Indices: 52788--53346 Score: 680
Period size: 160 Copynumber: 3.5 Consensus size: 159
52778 TAGTCATTGC
* * * * *
52788 TTTCATTATTTC-TTCAATTCATCATTTATTTTAAG-TCTGTTTTTT-CCAAATTTG-ATCTACA
1 TTTCCTTATTTCTTTCAATTCTTCCTTTATTTTAAGTTCTTTTTTTTACCAAATTTGAAAC-ACA
* *
52849 TGCTCTTAAACCATTATAGAATACATATGTACTTTCAATTCCACTTTTTGATAAC-AATTTTCTA
65 TGCTCCTAAACCATCATAGAATACATATGTACTTTCAATTCCA-TTTTTGATAACAAATTTTCTA
*
52913 TTTTTCAATTTAGCCCCTCAATTTTTTATAA
129 TTTTTCAATTTAGTCCCTCAATTTTTTATAA
*
52944 TTTCCTTATTTTTTTCAATTCTTCCTTTATTTTAAGTCTCTTTTTTTTACCAAATTTGAAACACA
1 TTTCCTTATTTCTTTCAATTCTTCCTTTATTTTAAGT-TCTTTTTTTTACCAAATTTGAAACACA
* * *
53009 TGCTCCTAAACCATCGA-AGAATACATATGTACTTTCCATTCCTTTTTTGATAACAAATTTTATA
65 TGCTCCTAAACCATC-ATAGAATACATATGTACTTTCAATTCCATTTTTGATAACAAATTTTCTA
53073 TTTTTCAATTTAGTCCCTCAATTTTTTATAA
129 TTTTTCAATTTAGTCCCTCAATTTTTTATAA
* * * * *
53104 TTTCTTTGTTTCTTT-AATT-TATCCTATATTTTAAGTATGTTTTTTTTTACCAAATTTGAACCA
1 TTTCCTTATTTCTTTCAATTCT-TCCTTTATTTTAAGT-T-CTTTTTTTTACCAAATTTGAAACA
*
53167 CATGCTCCTAAATCATCATAGAATACATATGTACTTTCAATTCCTATTTTTGATAACAAATTTTC
63 CATGCTCCTAAACCATCATAGAATACATATGTACTTTCAATTCC-ATTTTTGATAACAAATTTTC
*
53232 TATTTTTTTAATTTAGTCCCTCAATTTTTTATAA
127 TA-TTTTTCAATTTAGTCCCTCAATTTTTTATAA
* * **
53266 TTTCCTTATTTC-TTCACTTCATT-C-TTATTTTAA----ATTTTTTTACCAAATTTGAGTCACA
1 TTTCCTTATTTCTTTCAATTC-TTCCTTTATTTTAAGTTCTTTTTTTTACCAAATTTGAAACACA
* * * *
53324 TTCTCATATACCATAATAGAATA
65 TGCTCCTAAACCATCATAGAATA
53347 TCCATGTAAC
Statistics
Matches: 352, Mismatches: 36, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
155 40 0.11
156 10 0.03
157 21 0.06
158 1 0.00
159 40 0.11
160 161 0.46
161 33 0.09
162 44 0.12
163 1 0.00
164 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (159 bp):
TTTCCTTATTTCTTTCAATTCTTCCTTTATTTTAAGTTCTTTTTTTTACCAAATTTGAAACACAT
GCTCCTAAACCATCATAGAATACATATGTACTTTCAATTCCATTTTTGATAACAAATTTTCTATT
TTTCAATTTAGTCCCTCAATTTTTTATAA
Found at i:54806 original size:24 final size:24
Alignment explanation
Indices: 54758--54806 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
54748 TTTAAAAATG
*
54758 ATTAACCGGTATTGGTTAACCGTT
1 ATTAACCGGTATTGGTTAACAGTT
54782 ATTAA-CGGT-TTGGTTACACAAGTT
1 ATTAACCGGTATTGGTTA-AC-AGTT
54806 A
1 A
54807 ACCTGTAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTAACCGGTATTGGTTAACAGTT
Found at i:54986 original size:16 final size:17
Alignment explanation
Indices: 54958--54991 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
54948 AAATACATAA
54958 TTAATCATATTATAAAT
1 TTAATCATATTATAAAT
*
54975 TTAATCAT-TTATCAAT
1 TTAATCATATTATAAAT
54991 T
1 T
54992 AACAATAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATCATATTATAAAT
Found at i:55050 original size:17 final size:17
Alignment explanation
Indices: 55028--55063 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
55018 TTTCAAAGAT
55028 AATCTTTAATAAACATA
1 AATCTTTAATAAACATA
*
55045 AATCTTTAGTAAACATA
1 AATCTTTAATAAACATA
55062 AA
1 AA
55064 ATAAACTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (17 bp):
AATCTTTAATAAACATA
Found at i:57410 original size:46 final size:46
Alignment explanation
Indices: 57358--57737 Score: 580
Period size: 46 Copynumber: 8.3 Consensus size: 46
57348 TTACTCATTA
* * * *
57358 ATTTCATTTATGGCATACTTTCATACCTTAATGCATCATTTCATAC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
57404 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
* ** *
57450 ATTTTATTTATCTCATCCTTTCATGCCTTAATGCATCATTTTATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
*
57496 ATTTCATATATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
*
57542 ATTTCATTTATGACATCCTTTCATGCTTTAATGCATCATTTCATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
** * * *
57588 ATTTCATTTATGGTATCATTTCATGCCTTAATACATCCTTTCATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
*
57634 ATTTCATTTATGACATCCTTTCACGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
57680 ATTTTATTTATGACATCCTTTCATGCCTTAATGCATCATTTCACGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
57726 ATTTCATTTATG
1 ATTTCATTTATG
57738 GATTCATTTT
Statistics
Matches: 302, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 302 1.00
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.45
Consensus pattern (46 bp):
ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:57543 original size:12 final size:12
Alignment explanation
Indices: 57526--57613 Score: 53
Period size: 12 Copynumber: 7.3 Consensus size: 12
57516 TCATGCCTTA
57526 ATGCATCATTTC
1 ATGCATCATTTC
57538 ATGCATTTCATTT-
1 ATGCA--TCATTTC
*
57551 ATGACATCCTTTC
1 ATG-CATCATTTC
*
57564 ATG---C-TTTA
1 ATGCATCATTTC
57572 ATGCATCATTTC
1 ATGCATCATTTC
57584 ATGCATTTCATTT-
1 ATGCA--TCATTTC
*
57597 ATGGTATCATTTC
1 AT-GCATCATTTC
57610 ATGC
1 ATGC
57614 CTTAATACAT
Statistics
Matches: 59, Mismatches: 5, Indels: 24
0.67 0.06 0.27
Matches are distributed among these distances:
8 6 0.10
9 1 0.02
11 1 0.02
12 25 0.42
13 10 0.17
14 16 0.27
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.45
Consensus pattern (12 bp):
ATGCATCATTTC
Found at i:66264 original size:20 final size:20
Alignment explanation
Indices: 66241--66283 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
66231 ATTCCACCAC
**
66241 ATGCAACTATATTCTCCTAA
1 ATGCAACTATATGATCCTAA
*
66261 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
66281 ATG
1 ATG
66284 GGCTATTAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:66417 original size:46 final size:46
Alignment explanation
Indices: 66350--66546 Score: 297
Period size: 46 Copynumber: 4.3 Consensus size: 46
66340 GAGTTACCGA
*
66350 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGG
1 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
*
66396 CATCCTTTCATTCCTTAATGCATCATTTCATGCATTTCATTTATGG
1 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
* * **
66442 CATCC-ATCTATGCCTTAATGCATCCTTTCATGCATTTCATTTATAA
1 CATCCTTTC-ATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
* * *
66488 CATTCTTTCATGCCTTAATGCATTATTTCATGCATTTCATTTATGT
1 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
66534 CATCCTTTCATGC
1 CATCCTTTCATGC
66547 ATTTCATTTA
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
45 2 0.01
46 131 0.97
47 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.45
Consensus pattern (46 bp):
CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGG
Found at i:66474 original size:20 final size:20
Alignment explanation
Indices: 66350--66474 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
66340 GAGTTACCGA
66350 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
66370 CATCATTTCATGCATTTTATTTATGG
1 CATCCTTTCATGC--CTTA---AT-G
*
66396 CATCCTTTCATTCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
66416 CATCATTTCATGCATTTCATTTATGG
1 CATCCTTTCATGC----C-TTAAT-G
*
66442 CATCC-ATCTATGCCTTAATG
1 CATCCTTTC-ATGCCTTAATG
66462 CATCCTTTCATGC
1 CATCCTTTCATGC
66475 ATTTCATTTA
Statistics
Matches: 79, Mismatches: 12, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
20 34 0.43
21 8 0.10
22 4 0.05
24 4 0.05
25 8 0.10
26 21 0.27
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.43
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:66543 original size:72 final size:73
Alignment explanation
Indices: 66462--66618 Score: 239
Period size: 72 Copynumber: 2.2 Consensus size: 73
66452 TGCCTTAATG
* *
66462 CATCCTTTCATGCATTTCATTTATAACATTCTTTCATGCCTTAATGCATTA-TTTCATGCATTTC
1 CATCCTTTCATGCATTTCATTTATAACATCCTTTCATACCTTAATGCA-TACTTTCATGCATTTC
66526 ATTTAT-GT
65 ATTTATGGT
**
66534 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATACCTTAATGCATACTTTCATGCATTTCA
1 CATCCTTTCATGCATTTCATTTATAACATCCTTTCATACCTTAATGCATACTTTCATGCATTTCA
66599 TTTATGGT
66 TTTATGGT
*
66607 -ATCATTTCATGC
1 CATCCTTTCATGC
66619 CATAATGCAT
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
71 2 0.03
72 74 0.95
73 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.08, T:0.46
Consensus pattern (73 bp):
CATCCTTTCATGCATTTCATTTATAACATCCTTTCATACCTTAATGCATACTTTCATGCATTTCA
TTTATGGT
Found at i:66554 original size:118 final size:118
Alignment explanation
Indices: 66416--66650 Score: 348
Period size: 118 Copynumber: 2.0 Consensus size: 118
66406 TTCCTTAATG
* *
66416 CATCATTTCATGCATTTCATTTATGGCATCCATCT-ATGCCTTAATGCATCCTTTCATGCATTTC
1 CATCATTTCATGCATTTCATTTATGGCATCC-TCTCATACCTTAATGCATACTTTCATGCATTTC
* *
66480 ATTTATAACATTC-TTTCATGCCTTAATGCATTATTTCATGCATTTCATTTATGT
65 ATTTATAACA-TCATTTCATGCCATAATGCATCATTTCATGCATTTCATTTATGT
* *
66534 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATACCTTAATGCATACTTTCATGCATTTCA
1 CATCATTTCATGCATTTCATTTATGGCATCCTCTCATACCTTAATGCATACTTTCATGCATTTCA
*** *
66599 TTTATGGTATCATTTCATGCCATAATGCATCCTTTCATGCATTTCATTTATG
66 TTTATAACATCATTTCATGCCATAATGCATCATTTCATGCATTTCATTTATG
66651 GATTCGTTTT
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
117 4 0.04
118 101 0.96
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (118 bp):
CATCATTTCATGCATTTCATTTATGGCATCCTCTCATACCTTAATGCATACTTTCATGCATTTCA
TTTATAACATCATTTCATGCCATAATGCATCATTTCATGCATTTCATTTATGT
Found at i:66588 original size:46 final size:46
Alignment explanation
Indices: 66538--66651 Score: 183
Period size: 46 Copynumber: 2.5 Consensus size: 46
66528 TTATGTCATC
* *
66538 CTTTCATGCATTTCATTTATGGCATCCTTTCATACCTTAATGCATA
1 CTTTCATGCATTTCATTTATGGCATCATTTCATACCATAATGCATA
* * *
66584 CTTTCATGCATTTCATTTATGGTATCATTTCATGCCATAATGCATC
1 CTTTCATGCATTTCATTTATGGCATCATTTCATACCATAATGCATA
66630 CTTTCATGCATTTCATTTATGG
1 CTTTCATGCATTTCATTTATGG
66652 ATTCGTTTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.45
Consensus pattern (46 bp):
CTTTCATGCATTTCATTTATGGCATCATTTCATACCATAATGCATA
Found at i:69129 original size:28 final size:29
Alignment explanation
Indices: 69076--69133 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
69066 TTTCATTTTA
*
69076 TTTACTGAAATGTGGTGGATTCTTTAATT
1 TTTACTGAAATGTGGTGGATTATTTAATT
*
69105 TTTACTGGAAA-G-GGTTGATTATTTAATT
1 TTTACT-GAAATGTGGTGGATTATTTAATT
69133 T
1 T
69134 GAGATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 15 0.58
29 7 0.27
30 4 0.15
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.48
Consensus pattern (29 bp):
TTTACTGAAATGTGGTGGATTATTTAATT
Done.