Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002232.1 Hibiscus syriacus cultivar Beakdansim tig00004539_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: 49799
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8660 original size:23 final size:23
Alignment explanation
Indices: 8617--8702 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
8607 CTCAAGACTC
* *
8617 GAGCTCGATT-GAGACTTGATTTT
1 GAGCTCGATTCAAG-CTCGATTTT
8640 GAGCTCGATTCAAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGATTTT
8663 GA----GATTCAAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGATTTT
* *
8682 GAGCTAGATTCAAGCTTGATT
1 GAGCTCGATTCAAGCTCGATT
8703 CAAGCTCGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
19 19 0.35
23 34 0.62
24 2 0.04
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGATTTT
Found at i:8670 original size:19 final size:19
Alignment explanation
Indices: 8646--8684 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
8636 TTTTGAGCTC
8646 GATTCAAGCTCGATTTTGA
1 GATTCAAGCTCGATTTTGA
8665 GATTCAAGCTCGATTTTGA
1 GATTCAAGCTCGATTTTGA
8684 G
1 G
8685 CTAGATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (19 bp):
GATTCAAGCTCGATTTTGA
Found at i:8863 original size:10 final size:10
Alignment explanation
Indices: 8848--8872 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
8838 AAGTTTCTGG
8848 AACAATGGCT
1 AACAATGGCT
8858 AACAATGGCT
1 AACAATGGCT
8868 AACAA
1 AACAA
8873 CTTTTGAAAC
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:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (10 bp):
AACAATGGCT
Found at i:10474 original size:11 final size:11
Alignment explanation
Indices: 10458--10520 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
10448 GTATTATAGA
10458 ATTTTTAATAT
1 ATTTTTAATAT
10469 ATTTTTAA-A-
1 ATTTTTAATAT
10478 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
10489 ATCAATAGTGT
1 ATTTTTAATAT
10500 ATTTTTAATAT
1 ATTTTTAATAT
10511 ATTTTTAATA
1 ATTTTTAATA
10521 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:10714 original size:27 final size:23
Alignment explanation
Indices: 10653--10711 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
10643 AACTCGAGTC
10653 CATTCGATTCGAGTATTTATCAAG
1 CATT-GATTCGAGTATTTATCAAG
*
10677 CATTGATTCGAGTATTTATCGAG
1 CATTGATTCGAGTATTTATCAAG
10700 CATTGATT-GAGT
1 CATTGATTCGAGT
10712 CGATCTCAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 4 0.12
23 26 0.76
24 4 0.12
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (23 bp):
CATTGATTCGAGTATTTATCAAG
Found at i:11419 original size:17 final size:18
Alignment explanation
Indices: 11385--11418 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11375 TGTGCACTCG
11385 ATATTTATAATTAATTTT
1 ATATTTATAATTAATTTT
11403 ATATTT-TAATT-ATTTT
1 ATATTTATAATTAATTTT
11419 TCATAGTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTTATAATTAATTTT
Found at i:14503 original size:21 final size:21
Alignment explanation
Indices: 14461--14527 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
14451 AATATGTAAA
**
14461 TCGCATTGCGATTTTAGGAAT
1 TCGCATTGCGATTTTACAAAT
* *
14482 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* ** *
14503 TTGCAACGCGATTTT-CAAAA
1 TCGCATTGCGATTTTACAAAT
14523 TCGCA
1 TCGCA
14528 ACGCGAATCT
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 8 0.22
21 28 0.78
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:14528 original size:20 final size:21
Alignment explanation
Indices: 14489--14533 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
14479 AATTCGCGTT
* *
14489 GCGATTTTCCAAATTTGCAAC
1 GCGATTTTCCAAAATCGCAAC
14510 GCGATTTT-CAAAATCGCAAC
1 GCGATTTTCCAAAATCGCAAC
14530 GCGA
1 GCGA
14534 ATCTGTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (21 bp):
GCGATTTTCCAAAATCGCAAC
Found at i:14968 original size:19 final size:20
Alignment explanation
Indices: 14930--14975 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
14920 TAACTATTCA
*
14930 CGATTTTCATTTTCGTGTTG
1 CGATTTTCATTTTCGCGTTG
14950 CGATTTTCA-TTTCGCGTTG
1 CGATTTTCATTTTCGCGTTG
14969 CGATTTT
1 CGATTTT
14976 AAGTTTCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.11, C:0.17, G:0.20, T:0.52
Consensus pattern (20 bp):
CGATTTTCATTTTCGCGTTG
Found at i:17556 original size:11 final size:11
Alignment explanation
Indices: 17540--17572 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
17530 CACGTGAGGA
17540 TTATTTTATTT
1 TTATTTTATTT
17551 TTATTTTATTT
1 TTATTTTATTT
17562 TCTA-TTTATTT
1 T-TATTTTATTT
17573 ACTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 19 0.90
12 2 0.10
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:20279 original size:15 final size:15
Alignment explanation
Indices: 20255--20297 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
20245 TGAGTGTTTG
20255 TTTG-TTTATTTTTA
1 TTTGTTTTATTTTTA
20269 TTTGTTTTATTTTT-
1 TTTGTTTTATTTTTA
* *
20283 TTAGTTTTAATTTTA
1 TTTGTTTTATTTTTA
20298 ATATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTGTTTTATTTTTA
Found at i:22640 original size:24 final size:24
Alignment explanation
Indices: 22595--22644 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
22585 TGGTGGTTGG
*
22595 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
22619 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
22643 TT
1 TT
22645 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:24296 original size:42 final size:42
Alignment explanation
Indices: 24249--24341 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
24239 ACCTGTCATT
24249 GTTCAAGAGGCCTCTC-CTATCATTCAAGAGGCCCCTCCCACC
1 GTTCAAGAGGCCTCTCTC-ATCATTCAAGAGGCCCCTCCCACC
* * * * *
24291 GTTCAAGGGGCCTCTGTCATCGTTCAAGAGGTCTCTCCCACC
1 GTTCAAGAGGCCTCTCTCATCATTCAAGAGGCCCCTCCCACC
*
24333 GTTCGAGAG
1 GTTCAAGAG
24342 CCAAATTCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 42 0.98
43 1 0.02
ACGTcount: A:0.19, C:0.34, G:0.23, T:0.24
Consensus pattern (42 bp):
GTTCAAGAGGCCTCTCTCATCATTCAAGAGGCCCCTCCCACC
Found at i:24335 original size:21 final size:21
Alignment explanation
Indices: 24249--24341 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
24239 ACCTGTCATT
* *
24249 GTTCAAGAGGCCTCTCCTATC
1 GTTCAAGAGGCCTCTCCCACC
* *
24270 ATTCAAGAGGCCCCTCCCACC
1 GTTCAAGAGGCCTCTCCCACC
* ** *
24291 GTTCAAGGGGCCTCTGTCATC
1 GTTCAAGAGGCCTCTCCCACC
*
24312 GTTCAAGAGGTCTCTCCCACC
1 GTTCAAGAGGCCTCTCCCACC
*
24333 GTTCGAGAG
1 GTTCAAGAG
24342 CCAAATTCAC
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.19, C:0.34, G:0.23, T:0.24
Consensus pattern (21 bp):
GTTCAAGAGGCCTCTCCCACC
Found at i:25716 original size:13 final size:14
Alignment explanation
Indices: 25691--25723 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
25681 AAATTGATGT
*
25691 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTA
25705 ATTTGT-AAAGTTA
1 ATTTGTAAAAGTTA
25718 ATTTGT
1 ATTTGT
25724 TTAATTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTA
Found at i:25780 original size:64 final size:63
Alignment explanation
Indices: 25702--25837 Score: 191
Period size: 64 Copynumber: 2.1 Consensus size: 63
25692 TTTGTAAAAG
*
25702 TTGATTTGTAAAGTTAATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTACTTGTTTAA
1 TTGATTTGTAAAGTTAATTTGTTTAATTGATGAGGAAATAAGAATTAGTTTTTACTTGTTTAA
* * * *** *
25765 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTAGTTTTTGCTTGTTTAA
1 TTGATTTGT-AAAGTTAATTTGTTTAATTGATGAGGAAATAAGAATTAGTTTTTACTTGTTTAA
25829 TTGATTTGT
1 TTGATTTGT
25838 TGTTTTAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
63 9 0.14
64 55 0.86
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (63 bp):
TTGATTTGTAAAGTTAATTTGTTTAATTGATGAGGAAATAAGAATTAGTTTTTACTTGTTTAA
Found at i:25816 original size:27 final size:27
Alignment explanation
Indices: 25759--25816 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
25749 TTTTTTACTT
* * *
25759 GTTTAATTGATTTGTAAAAGTTGATTT
1 GTTTAATTGATGTGTAAAAATTGATTA
*
25786 GTTTAATTGATGTGTAAATAATT-CTTA
1 GTTTAATTGATGTGTAAA-AATTGATTA
25813 GTTT
1 GTTT
25817 TTGCTTGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (27 bp):
GTTTAATTGATGTGTAAAAATTGATTA
Found at i:25971 original size:13 final size:14
Alignment explanation
Indices: 25937--25971 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
25927 GAAAGTCAAA
25937 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
*
25951 TTCACGTTGCGA-T
1 TTCGCGTTGCGATT
25964 TTCGCGTT
1 TTCGCGTT
25972 TCGAATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.09, C:0.23, G:0.26, T:0.43
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:25979 original size:14 final size:14
Alignment explanation
Indices: 25937--25979 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
25927 GAAAGTCAAA
*
25937 TTCGCGTTGCGATT
1 TTCGCGTTGCGAAT
*
25951 TTCACGTTGCG-AT
1 TTCGCGTTGCGAAT
*
25964 TTCGCGTTTCGAAT
1 TTCGCGTTGCGAAT
25978 TT
1 TT
25980 GACTTTCGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (14 bp):
TTCGCGTTGCGAAT
Found at i:26005 original size:29 final size:29
Alignment explanation
Indices: 25973--26028 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
25963 TTTCGCGTTT
*
25973 CGAATTTGACTTTCGCAATAATCGCAATG
1 CGAATTTGACTTTCGCAACAATCGCAATG
26002 CGAATTTGACTTTCGCAACAATCGCAA
1 CGAATTTGACTTTCGCAACAATCGCAA
26029 CAAAAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (29 bp):
CGAATTTGACTTTCGCAACAATCGCAATG
Found at i:27416 original size:18 final size:18
Alignment explanation
Indices: 27393--27429 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27383 CGAAATTTAT
27393 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
27411 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
27429 A
1 A
27430 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:27843 original size:25 final size:25
Alignment explanation
Indices: 27815--27864 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
27805 CATTATTTTC
* *
27815 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCAACAACAATGTT
27840 CAAATAATGTACCAACAACAATGTT
1 CAAATAATGTACCAACAACAATGTT
27865 TTATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.20, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCAACAACAATGTT
Found at i:28214 original size:18 final size:18
Alignment explanation
Indices: 28191--28226 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28181 AAGCCGGTTG
28191 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
28209 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
28227 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:30529 original size:24 final size:24
Alignment explanation
Indices: 30495--30548 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
30485 CTGAAACATC
30495 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
30519 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
30543 ATCAAA
1 ATCAAA
30549 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:31339 original size:14 final size:15
Alignment explanation
Indices: 31302--31340 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
31292 AGAAATCATT
31302 AAAAAATTATATAGA
1 AAAAAATTATATAGA
*
31317 AATAAAATTATGTA-A
1 AA-AAAATTATATAGA
31332 AAAAAATTA
1 AAAAAATTA
31341 GAGACGGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 10 0.45
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAAATTATATAGA
Found at i:31521 original size:20 final size:19
Alignment explanation
Indices: 31478--31565 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 19
31468 AAAACATTTA
* *
31478 TGTTGCGAAAATAAAA-CC
1 TGTTGCGAAATTAAAATCG
31496 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAA-TCG
31516 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATT--AAAATCG
* * *
31536 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATT-AAAATC-G
31557 TGTTGCGAA
1 TGTTGCGAA
31566 TTTGTAAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
18 15 0.26
19 4 0.07
20 23 0.40
21 16 0.28
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (19 bp):
TGTTGCGAAATTAAAATCG
Found at i:31575 original size:41 final size:41
Alignment explanation
Indices: 31497--31615 Score: 143
Period size: 41 Copynumber: 2.9 Consensus size: 41
31487 AATAAAACCT
* * *
31497 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCG-A
1 GTTGCGAATTTGAAATTCGTGTTGCGAATTTGAAAATCGCA
*
31537 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGTAAATCGCA
1 GTTGCGAATTTGAAATTC-GTGTTGCGAATTTGAAAATCGCA
** *
31579 -TTGCGAATTTGACTTTTGTGTTGCGAATTTGGAAAAT
1 GTTGCGAATTTGAAATTCGTGTTGCGAATTT-GAAAAT
31616 TGCAACGCGA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
40 29 0.43
41 38 0.56
42 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (41 bp):
GTTGCGAATTTGAAATTCGTGTTGCGAATTTGAAAATCGCA
Found at i:31584 original size:20 final size:18
Alignment explanation
Indices: 31518--31590 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 18
31508 AAAATTCGTG
*
31518 TTGCGAATTCGAAAATCGA
1 TTGCGAATTTG-AAATCGA
*
31537 GTTGCGAATTTGAAATTCAGTG
1 -TTGCGAATTTGAAA-TC-G-A
31559 TTGCGAATTTGTAAATCGCA
1 TTGCGAATTTG-AAATCG-A
31579 TTGCGAATTTGA
1 TTGCGAATTTGA
31591 CTTTTGTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
19 4 0.09
20 24 0.53
21 14 0.31
22 3 0.07
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.34
Consensus pattern (18 bp):
TTGCGAATTTGAAATCGA
Found at i:31627 original size:21 final size:21
Alignment explanation
Indices: 31601--31657 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
31591 CTTTTGTGTT
*
31601 GCGAATTTGGAAAATTGCAAC
1 GCGAATTCGGAAAATTGCAAC
31622 GCGAATTCGGAAAATTGCAAC
1 GCGAATTCGGAAAATTGCAAC
*
31643 GCGAATTCGTAAAAT
1 GCGAATTCGGAAAAT
31658 CGCTATGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (21 bp):
GCGAATTCGGAAAATTGCAAC
Found at i:37264 original size:3 final size:3
Alignment explanation
Indices: 37256--37332 Score: 77
Period size: 3 Copynumber: 25.0 Consensus size: 3
37246 CCGGTCTTAC
*
37256 TTA TTA TTA TTA TTA -TA TATA TATA TAA TTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA T-TA TTA TTA TTA TTA
* *
37303 TTA TTA -TA TATG TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
37333 AATATTACAA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
2 4 0.06
3 47 0.75
4 12 0.19
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:37288 original size:16 final size:15
Alignment explanation
Indices: 37257--37339 Score: 62
Period size: 16 Copynumber: 5.3 Consensus size: 15
37247 CGGTCTTACT
*
37257 TATTATTATTATTATA
1 TATTA-TATAATTATA
37273 TATATATATAATTATA
1 TAT-TATATAATTATA
*
37289 TATTATTATTATTAT-
1 TATTA-TATAATTATA
*
37304 TATTATATATGTTAT-
1 TATTATATA-ATTATA
* *
37319 TATTAATATTATTAAA
1 TATT-ATATAATTATA
37335 TATTA
1 TATTA
37340 CAAAACCCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 3 0.05
15 19 0.35
16 31 0.56
17 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (15 bp):
TATTATATAATTATA
Found at i:47673 original size:16 final size:14
Alignment explanation
Indices: 47652--47690 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
47642 TTTTTTATTA
47652 TTTTATTAATTAATAT
1 TTTTATTAA-TAA-AT
47668 TTTTATTCAATAAAT
1 TTTTATT-AATAAAT
47683 TTTTATTA
1 TTTTATTA
47691 TTTTTGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.05
15 9 0.41
16 10 0.45
17 2 0.09
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTATTAATAAAT
Found at i:47692 original size:24 final size:24
Alignment explanation
Indices: 47665--47710 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
47655 TATTAATTAA
47665 TATTTTTATTCAATAAATTTTTAT
1 TATTTTTATTCAATAAATTTTTAT
* * *
47689 TATTTTTGTTTAATTAATTTTT
1 TATTTTTATTCAATAAATTTTT
47711 GTATTCAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
TATTTTTATTCAATAAATTTTTAT
Found at i:47708 original size:15 final size:16
Alignment explanation
Indices: 47690--47726 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
47680 AATTTTTATT
47690 ATTTTTGT-TT-AATTA
1 ATTTTTGTATTCAA-TA
47705 ATTTTTGTATTCAATA
1 ATTTTTGTATTCAATA
47721 ATTTTT
1 ATTTTT
47727 TATGTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 10 0.50
17 2 0.10
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (16 bp):
ATTTTTGTATTCAATA
Found at i:47716 original size:41 final size:40
Alignment explanation
Indices: 47643--47739 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 40
47633 CCTTCCCCAT
47643 TTTTTATTA-TTTTATTAATTAATATTTTTATTCAATAAA
1 TTTTTATTATTTTTATTAATTAATATTTTTATTCAATAAA
* *
47682 TTTTTATTATTTTTGTTTAATTAAT-TTTTGTATTCAATAAT
1 TTTTTATTATTTTT-ATTAATTAATATTTT-TATTCAATAAA
47723 TTTTTATGTATTATTTA
1 TTTTTAT-TATT-TTTA
47740 ATTATAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
39 9 0.18
40 8 0.16
41 26 0.52
42 4 0.08
43 3 0.06
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (40 bp):
TTTTTATTATTTTTATTAATTAATATTTTTATTCAATAAA
Done.