Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015648.1 Corchorus olitorius cultivar O-4 contig15681, 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: 79329
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Found at i:1953 original size:51 final size:50
Alignment explanation
Indices: 1852--1953 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
1842 ATTCTTCATA
* **
1852 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCATACAGTGT
*
1902 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-ATACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCATACA-GTGT
1953 T
1 T
1954 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCATACAGTGT
Found at i:18689 original size:43 final size:41
Alignment explanation
Indices: 18641--18841 Score: 244
Period size: 41 Copynumber: 4.8 Consensus size: 41
18631 GCAATAACTA
** * *
18641 AAAGTCCAAAAACACAATTATAACACAGGGGCACCTCTATTCC
1 AAAGTCCTCAAACACATTTATAACACAGGGGCA--TCTATACC
* * *
18684 AAAGTCCTCAAACACATTTATAACACAGAGGCATCCATACT
1 AAAGTCCTCAAACACATTTATAACACAGGGGCATCTATACC
*
18725 AAAGTCC-CTAAACACATTTATAACACAGGGGCACCTCTATTCC
1 AAAGTCCTC-AAACACATTTATAACACAGGGGCA--TCTATACC
*
18768 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATACC
1 AAAGTCCTCAAACACATTTATAACACAGGGGCATCTATACC
*
18809 AAAGTGCC-CAAACACAATTATAACACAGGGGCA
1 AAAGT-CCTCAAACACATTTATAACACAGGGGCA
18842 ATTCTCTTTA
Statistics
Matches: 138, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.01
41 70 0.51
42 2 0.01
43 64 0.46
44 1 0.01
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (41 bp):
AAAGTCCTCAAACACATTTATAACACAGGGGCATCTATACC
Found at i:18782 original size:84 final size:83
Alignment explanation
Indices: 18641--18841 Score: 339
Period size: 84 Copynumber: 2.4 Consensus size: 83
18631 GCAATAACTA
*
18641 AAAGTCCAAAAACACAATTATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTATA
1 AAAGTCC-CAAACACAATTATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTATA
*
18706 ACACAGAGGCATCCATACT
65 ACACAGAGGCATCCATACC
*
18725 AAAGTCCCTAAACACATTTATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTATA
1 AAAGTCCC-AAACACAATTATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTATA
*
18790 ACACAGAGGCATCTATACC
65 ACACAGAGGCATCCATACC
18809 AAAGTGCCCAAACACAATTATAACACAGGGGCA
1 AAAGT-CCCAAACACAATTATAACACAGGGGCA
18842 ATTCTCTTTA
Statistics
Matches: 110, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
84 107 0.97
85 3 0.03
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (83 bp):
AAAGTCCCAAACACAATTATAACACAGGGGCACCTCTATTCCAAAGTCCTCAAACACATTTATAA
CACAGAGGCATCCATACC
Found at i:24927 original size:12 final size:12
Alignment explanation
Indices: 24910--24940 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
24900 TCTATTCATC
24910 TTTCATCAACTT
1 TTTCATCAACTT
24922 TTTCATCAACTT
1 TTTCATCAACTT
24934 TTTCATC
1 TTTCATC
24941 CATCAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTCATCAACTT
Found at i:31543 original size:15 final size:16
Alignment explanation
Indices: 31510--31549 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
31500 TTGCTTTGTT
31510 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
31526 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
31541 TTGTTTTCT
1 TTGTTTTCT
31550 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:31943 original size:52 final size:50
Alignment explanation
Indices: 31846--31948 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 50
31836 AATTTCCGTT
** *
31846 TTTAATTTTGAGTCTTGCGTTTTTTTAAAAAAAAATTTTGATTTTTGCGTC
1 TTTAATTTTGAGTCTTGCGTTTTTGAAAAAAAAAACTTT-ATTTTTGCGTC
*
31897 TTTAATTTCTTAGTCTTGCGTTTTTGAAAAAAAAAGGACTTT-TTTTTGCGTC
1 TTTAATTT-TGAGTCTTGCGTTTTTGAAAAAAAAA--ACTTTATTTTTGCGTC
31949 ATAAAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 8 0.18
52 33 0.73
54 4 0.09
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (50 bp):
TTTAATTTTGAGTCTTGCGTTTTTGAAAAAAAAAACTTTATTTTTGCGTC
Found at i:35084 original size:12 final size:12
Alignment explanation
Indices: 35067--35100 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
35057 TTTTTACCAA
35067 GCCATCCACCGT
1 GCCATCCACCGT
35079 GCCATCCACCGT
1 GCCATCCACCGT
35091 GCCA-CCACCG
1 GCCATCCACCG
35101 GTTAATCCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.18, C:0.53, G:0.18, T:0.12
Consensus pattern (12 bp):
GCCATCCACCGT
Found at i:35700 original size:22 final size:22
Alignment explanation
Indices: 35672--35715 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
35662 AGAGTCTGCA
35672 TGCATCATCATCTTAAAATATG
1 TGCATCATCATCTTAAAATATG
35694 TGCATCATCATCTTAAAATATG
1 TGCATCATCATCTTAAAATATG
35716 CCATAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TGCATCATCATCTTAAAATATG
Found at i:38056 original size:15 final size:16
Alignment explanation
Indices: 38023--38062 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
38013 TTGCTTTGTT
38023 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
38039 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
38054 TTGTTTTCT
1 TTGTTTTCT
38063 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:42366 original size:58 final size:55
Alignment explanation
Indices: 42222--42434 Score: 298
Period size: 58 Copynumber: 3.9 Consensus size: 55
42212 GTTAGGCTAA
* *
42222 TAAGTAAGGTAGTCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTAATT-AAG
1 TAAGTAAGGTAATCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAAG
42276 -AAGTAAGGTAATCA-TCAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAAG
1 TAAGTAAGGTAATCAGT-AAAATTGGCTTAATTAAAGTTAATTAAGTTGATT-A-AAG
*
42332 TAAAGTAAGGTAATCAGTAAAATTGACTTAATTAAAGTTAATTAAGTTGATTAAAG
1 T-AAGTAAGGTAATCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAAG
*
42388 T---T--GGTAATTAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTA
1 TAAGTAAGGTAATCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTA
42435 GTAAAATTGA
Statistics
Matches: 147, Mismatches: 5, Indels: 18
0.86 0.03 0.11
Matches are distributed among these distances:
50 43 0.29
52 2 0.01
53 46 0.31
56 7 0.05
57 1 0.01
58 47 0.32
59 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (55 bp):
TAAGTAAGGTAATCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAAG
Found at i:42401 original size:50 final size:50
Alignment explanation
Indices: 42340--42434 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
42330 AGTAAAGTAA
* *
42340 GGTAATCAGTAAAATTGACTTAATTAAAGTTAATTAAGTTGATTAAAGTT
1 GGTAATTAGTAAAATTGACTTAATTAAAGTTAATTAAGTTGATTAAAATT
*
42390 GGTAATTAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTA
1 GGTAATTAGTAAAATTGACTTAATTAAAGTTAATTAAGTTGATTA
42435 GTAAAATTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (50 bp):
GGTAATTAGTAAAATTGACTTAATTAAAGTTAATTAAGTTGATTAAAATT
Found at i:42449 original size:37 final size:37
Alignment explanation
Indices: 42394--42508 Score: 203
Period size: 37 Copynumber: 3.1 Consensus size: 37
42384 AAAGTTGGTA
42394 ATTAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTG
1 ATTAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTG
*
42431 ATTAGTAAAATTGACTTAATTAAAGTTAATTAAGTTG
1 ATTAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTG
* *
42468 ATTAGAAAAATTGGCTTAATTAAAATTAATTAAGTTG
1 ATTAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTG
42505 ATTA
1 ATTA
42509 AAGTTGGTAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (37 bp):
ATTAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTG
Found at i:42452 original size:18 final size:18
Alignment explanation
Indices: 42392--42452 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
42382 TTAAAGTTGG
*
42392 TAATTAGTAAAATTGGCT
1 TAATTAGTAAAATTGACT
* * *
42410 TAATTAAAGT-TAATTAAGT
1 TAATT--AGTAAAATTGACT
*
42429 TGATTAGTAAAATTGACT
1 TAATTAGTAAAATTGACT
42447 TAATTA
1 TAATTA
42453 AAGTTAATTA
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
17 3 0.10
18 16 0.52
19 9 0.29
20 3 0.10
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (18 bp):
TAATTAGTAAAATTGACT
Found at i:42532 original size:50 final size:50
Alignment explanation
Indices: 42468--42656 Score: 279
Period size: 50 Copynumber: 3.8 Consensus size: 50
42458 AATTAAGTTG
* * *
42468 ATTAGAAAAATTGGCTTAATTAAAATTAATTAAGTTGATTAAAGTTGGTA
1 ATTAGTAAAATTGACTTAATTAAAATTAATTAAGTTGATTAAAATTGGTA
*
42518 ATTAGTAAAATTGGCTTAATTAAAATTAATTAAGTTGATTAAAATTGGTA
1 ATTAGTAAAATTGACTTAATTAAAATTAATTAAGTTGATTAAAATTGGTA
* * * *
42568 ATTAGTAAAATTGACTTATTTAAAGTTTATTAGGTTGATTAAAATTGGTA
1 ATTAGTAAAATTGACTTAATTAAAATTAATTAAGTTGATTAAAATTGGTA
* * *
42618 ATCACTAAAATTGACTTAATTAAAGTTAATTAAGTTGAT
1 ATTAGTAAAATTGACTTAATTAAAATTAATTAAGTTGAT
42657 GAAGAGGAAA
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 127 1.00
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.40
Consensus pattern (50 bp):
ATTAGTAAAATTGACTTAATTAAAATTAATTAAGTTGATTAAAATTGGTA
Found at i:43568 original size:19 final size:19
Alignment explanation
Indices: 43528--43564 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43518 AATTTTTAAG
43528 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
43547 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
43565 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:45602 original size:42 final size:43
Alignment explanation
Indices: 45551--45644 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
45541 AAACCATTAT
*
45551 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
45592 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
45637 CTAATATT
1 CTAATATT
45645 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:46523 original size:19 final size:18
Alignment explanation
Indices: 46458--46525 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
46448 GCCACTAAAA
* *
46458 ATAATATATAGTATATATT
1 ATAATATATATTAAATA-T
*
46477 ATAA-ATATATCAGAAATAT
1 ATAATATATAT--TAAATAT
46496 ATAATATATATTAAATATT
1 ATAATATATATTAAATA-T
*
46515 ATTATATATAT
1 ATAATATATAT
46526 AATAAGTGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 10 0.25
19 20 0.50
20 10 0.25
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (18 bp):
ATAATATATATTAAATAT
Found at i:52785 original size:43 final size:43
Alignment explanation
Indices: 52660--52989 Score: 501
Period size: 43 Copynumber: 7.8 Consensus size: 43
52650 CCAATAACCA
* * *
52660 AAAGTCCCCAAATACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
52703 AAAAGTCCTCAAACACATATATAACACAGAGGCA--TCTATTAC
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
52745 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAG
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
52788 AAAGTCCTCAAACACATATATAACACAGAGGCA--TCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
52829 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
52872 AAAGTCCTCAAACACATATATAACACAGAGGCA--TCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
52913 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
52956 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
52990 TTCTCCTTAT
Statistics
Matches: 262, Mismatches: 18, Indels: 13
0.89 0.06 0.04
Matches are distributed among these distances:
41 108 0.41
42 7 0.03
43 117 0.45
44 30 0.11
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:53018 original size:84 final size:84
Alignment explanation
Indices: 52660--52989 Score: 615
Period size: 84 Copynumber: 3.9 Consensus size: 84
52650 CCAATAACCA
* *
52660 AAAGTCCCCAAATACATATATAACACAGGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC-AAAGTCCTCAAACACATATAT
52725 AACACAGAGGCATCTATTAC
65 AACACAGAGGCATCTATTAC
*
52745 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAGAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
52810 ACACAGAGGCATCTATTAC
66 ACACAGAGGCATCTATTAC
*
52829 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
52894 ACACAGAGGCATCTATTAC
66 ACACAGAGGCATCTATTAC
52913 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
52978 ACACAGAGGCAT
66 ACACAGAGGCAT
52990 TTCTCCTTAT
Statistics
Matches: 239, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
84 199 0.83
85 40 0.17
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATTAC
Found at i:53106 original size:2 final size:2
Alignment explanation
Indices: 53099--53143 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
53089 ACCAAATTCC
*
53099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53141 TA T
1 TA T
53144 GTGACAAAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:67979 original size:28 final size:28
Alignment explanation
Indices: 67906--67982 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
67896 CCCGTAGATG
67906 TGTAAAATGACCAAAATGCCCTCGGACA
1 TGTAAAATGACCAAAATGCCCTCGGACA
* * * *
67934 TGCAGACTGACCAAAATGCCCTTGGACA
1 TGTAAAATGACCAAAATGCCCTCGGACA
* *
67962 TGTAAAATGATCAGAATGCCC
1 TGTAAAATGACCAAAATGCCC
67983 CCTTAAGTGA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (28 bp):
TGTAAAATGACCAAAATGCCCTCGGACA
Found at i:68280 original size:35 final size:35
Alignment explanation
Indices: 68239--68550 Score: 335
Period size: 35 Copynumber: 8.9 Consensus size: 35
68229 CGAGTTCATA
* *
68239 TTGAAGATGCTACATCGAGTCACCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
68274 TTGAAGATGCTACACCGAGTCATCT-AAGTTTATCT
1 TTGAAGATGCTACACCGAGTCATCTGAA-TTCATCT
68309 TTGAAGATGCTACACCGAGTCATCTGAGA-TCA-CTT
1 TTGAAGATGCTACACCGAGTCATCTGA-ATTCATC-T
* * **
68344 TTGAAGATGCTACACCGAGTCGTTTGAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* **
68379 TTGAAGATGCTACACCGAGTTATCTGAGCTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT
* **
68414 TTGAAGATGCTACACCGAGTCATCCGAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*** *
68449 TTGAAGATGCTACACCGAGTCATCTGTGCTCATTTT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCA-TCT
* ** **
68485 TTGAAGATGCTACATCGAGTCATCCAAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* *
68520 TTGAAGATGCTACATCGAGTCATCCGAATTC
1 TTGAAGATGCTACACCGAGTCATCTGAATTC
68551 CTGAGAATTT
Statistics
Matches: 229, Mismatches: 39, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
34 5 0.02
35 194 0.85
36 29 0.13
37 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
Found at i:68313 original size:70 final size:69
Alignment explanation
Indices: 68239--68543 Score: 382
Period size: 70 Copynumber: 4.3 Consensus size: 69
68229 CGAGTTCATA
* * *
68239 TTGAAGATGCTACATCGAGTCACCTGAATTCATCTTTGAAGATGCTACACCGAGTCATCTAAGTT
1 TTGAAGATGCTACACCGAGTCATCTGAACTCATCTTTGAAGATGCTACACCGAGTCATCTAA-TT
*
68304 TATCT
65 TGTCT
* *
68309 TTGAAGATGCTACACCGAGTCATCTGAGA-TCA-CTTTTGAAGATGCTACACCGAGTCGTTTGAA
1 TTGAAGATGCTACACCGAGTCATCTGA-ACTCATC-TTTGAAGATGCTACACCGAGTCATCT-AA
68372 TTTGTCT
63 TTTGTCT
* * *
68379 TTGAAGATGCTACACCGAGTTATCTGAGCTCAAT-TTTGAAGATGCTACACCGAGTCATCCGAAT
1 TTGAAGATGCTACACCGAGTCATCTGAACTC-ATCTTTGAAGATGCTACACCGAGTCAT-CTAAT
68443 TTGTCT
64 TTGTCT
** * * *
68449 TTGAAGATGCTACACCGAGTCATCTGTGCTCATTTTTTGAAGATGCTACATCGAGTCATCCAAAT
1 TTGAAGATGCTACACCGAGTCATCTGAACTCA-TCTTTGAAGATGCTACACCGAGTCAT-CTAAT
68514 TTGTCT
64 TTGTCT
*
68520 TTGAAGATGCTACATCGAGTCATC
1 TTGAAGATGCTACACCGAGTCATC
68544 CGAATTCCTG
Statistics
Matches: 211, Mismatches: 15, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
69 2 0.01
70 148 0.70
71 61 0.29
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (69 bp):
TTGAAGATGCTACACCGAGTCATCTGAACTCATCTTTGAAGATGCTACACCGAGTCATCTAATTT
GTCT
Done.