Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007380.1 Corchorus capsularis cultivar CVL-1 contig07401, 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: 22320
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:2961 original size:13 final size:14
Alignment explanation
Indices: 2943--2972 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2933 TAAATAGTTG
2943 TTTTCCTTTTTA-T
1 TTTTCCTTTTTACT
2956 TTTTCCTTTTTACT
1 TTTTCCTTTTTACT
2970 TTT
1 TTT
2973 ACACTTGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCCTTTTTACT
Found at i:7465 original size:2 final size:2
Alignment explanation
Indices: 7429--7455 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7419 TTTAATTTAT
7429 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7456 TCCCATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15207 original size:12 final size:13
Alignment explanation
Indices: 15182--15215 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
15172 ATAATTATTG
15182 TTTGCTTTATTAA
1 TTTGCTTTATTAA
15195 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
15207 TCTGCTTTA
1 TTTGCTTTA
15216 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:15223 original size:6 final size:6
Alignment explanation
Indices: 15212--15238 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15202 TATAATCTGC
15212 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
15239 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:17797 original size:14 final size:14
Alignment explanation
Indices: 17760--17796 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
17750 AGAGTCATGA
17760 TTTTCAAAAATGTT
1 TTTTCAAAAATGTT
17774 TTTTCAAAAATG-T
1 TTTTCAAAAATGTT
17787 TTTTCAAAAA
1 TTTTCAAAAA
17797 AAAAAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (14 bp):
TTTTCAAAAATGTT
Found at i:18123 original size:6 final size:6
Alignment explanation
Indices: 18114--18141 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18104 GTGCAAAAAA
18114 AAAATC AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAA
18142 GCGAAAGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATC
Found at i:18128 original size:18 final size:18
Alignment explanation
Indices: 18107--18141 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18097 AATAAAAGTG
18107 CAAAAAAAAAATCAAAAT
1 CAAAAAAAAAATCAAAAT
**
18125 CAAAATCAAAATCAAAA
1 CAAAAAAAAAATCAAAA
18142 GCGAAAGTGA
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:0.74, C:0.14, G:0.00, T:0.11
Consensus pattern (18 bp):
CAAAAAAAAAATCAAAAT
Found at i:18483 original size:17 final size:17
Alignment explanation
Indices: 18461--18502 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
18451 AAGTGCAATG
18461 AAAAAAA-AAATAAAAAT
1 AAAAAAATAAA-AAAAAT
18478 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
18495 AAAAAAAT
1 AAAAAAAT
18503 GAGAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAATAAAAAAAAT
Found at i:18509 original size:17 final size:17
Alignment explanation
Indices: 18472--18521 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
18462 AAAAAAAAAT
*
18472 AAAAATAAAAAAATAAA
1 AAAAATAAAAAAATGAA
18489 AAAAATAAAAAAATG-A
1 AAAAATAAAAAAATGAA
* *
18505 GAAAATGAAAAAATGAA
1 AAAAATAAAAAAATGAA
18522 TGGAAAAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (17 bp):
AAAAATAAAAAAATGAA
Found at i:18521 original size:8 final size:8
Alignment explanation
Indices: 18461--18518 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
18451 AAGTGCAATG
*
18461 AAAAAAAA
1 AAAAAAAT
18469 AATAAAAAT
1 AA-AAAAAT
18478 AAAAAAAT
1 AAAAAAAT
18486 AAAAAAAAT
1 -AAAAAAAT
18495 AAAAAAAT
1 AAAAAAAT
* *
18503 GAGAAAAT
1 AAAAAAAT
*
18511 GAAAAAAT
1 AAAAAAAT
18519 GAATGGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
8 29 0.66
9 15 0.34
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:19510 original size:24 final size:24
Alignment explanation
Indices: 19473--19634 Score: 101
Period size: 24 Copynumber: 6.3 Consensus size: 24
19463 GCTAATCTTG
*
19473 TTCAATTCGCTTCAATTATTCAATCC
1 TTCAATT--CTTCAATTATTCAATAC
* * *
19499 TTCAATGCTTCAATTTTTTTCAAAATAA
1 TTCAATTCTTCAA--TTATTC--AATAC
* *
19527 TCTC-TTTCTTCAATTATTCAATGC
1 T-TCAATTCTTCAATTATTCAATAC
* *
19551 TTCAATTCTTCCATTATTCAATTC
1 TTCAATTCTTCAATTATTCAATAC
*
19575 TTCAATTCTTCAATGATTCAATTCATCTC
1 TTCAATTCTTCAATTATTCAA-T-A---C
* * *
19604 TTCGACTCTTTAATTATTCAATAC
1 TTCAATTCTTCAATTATTCAATAC
19628 TTCAATT
1 TTCAATT
19635 TATTTCTTCA
Statistics
Matches: 104, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
23 2 0.02
24 52 0.50
25 1 0.01
26 16 0.15
27 1 0.01
28 12 0.12
29 20 0.19
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (24 bp):
TTCAATTCTTCAATTATTCAATAC
Found at i:19548 original size:8 final size:8
Alignment explanation
Indices: 19532--20199 Score: 133
Period size: 8 Copynumber: 88.2 Consensus size: 8
19522 AATAATCTCT
19532 TTCTTCAA
1 TTCTTCAA
*
19540 TTATTCAA
1 TTCTTCAA
*
19548 TGCTTCAA
1 TTCTTCAA
*
19556 TTCTTCCA
1 TTCTTCAA
*
19564 TTATTCAA
1 TTCTTCAA
19572 TTCTTCAA
1 TTCTTCAA
19580 TTCTTCAA
1 TTCTTCAA
**
19588 TGATTCAA
1 TTCTTCAA
*
19596 TTCATC--
1 TTCTTCAA
*
19602 -TCTTCGA
1 TTCTTCAA
* *
19609 CTCTTTAA
1 TTCTTCAA
*
19617 TTATTCAA
1 TTCTTCAA
*
19625 TACTTCAA
1 TTCTTCAA
*
19633 -T-TT-AT
1 TTCTTCAA
19638 TTCTTCAA
1 TTCTTCAA
*
19646 TTCTTCGA
1 TTCTTCAA
*
19654 TCACTT--A
1 T-TCTTCAA
*
19661 TTGCTTAAA
1 TT-CTTCAA
19670 TTCTTCAA
1 TTCTTCAA
19678 TTAC-TCAA
1 TT-CTTCAA
*
19686 TGT-TTCGA
1 T-TCTTCAA
19694 TTCTTCAA
1 TTCTTCAA
19702 TTTACTTCAA
1 -TT-CTTCAA
* * *
19712 TGAC-CCAGG
1 T-TCTTCA-A
* ** *
19721 GTGGTC-T
1 TTCTTCAA
19728 TTCTTCAA
1 TTCTTCAA
*
19736 TTCTTTAA
1 TTCTTCAA
*
19744 TTATTCAA
1 TTCTTCAA
*
19752 TGCTTCAA
1 TTCTTCAA
*
19760 -T-TT-AT
1 TTCTTCAA
19765 TTCTGGTC-A
1 TTCT--TCAA
*
19774 TTCTTCGA
1 TTCTTCAA
19782 TTC--CAA
1 TTCTTCAA
19788 TTCTTCAA
1 TTCTTCAA
19796 -T-TTCAA
1 TTCTTCAA
19802 TTCTTCAA
1 TTCTTCAA
*
19810 TGCTTCAA
1 TTCTTCAA
19818 -T-TTCAA
1 TTCTTCAA
19824 TTCTTCAA
1 TTCTTCAA
*
19832 TTTTTCAA
1 TTCTTCAA
19840 TGT-TTCAA
1 T-TCTTCAA
19848 -T-TTCAA
1 TTCTTCAA
*
19854 TAT-TCCAA
1 T-TCTTCAA
*
19862 TGCTT-AA
1 TTCTTCAA
19869 TGT-TTCAA
1 T-TCTTCAA
19877 -T-TTCAA
1 TTCTTCAA
*
19883 TAT-TCCAA
1 T-TCTTCAA
*
19891 TGCTTCAA
1 TTCTTCAA
19899 -T-TTCAA
1 TTCTTCAA
19905 TTCTTCAA
1 TTCTTCAA
19913 TGT-TTCAA
1 T-TCTTCAA
*
19921 -T-TGCAA
1 TTCTTCAA
19927 TTCTTCAA
1 TTCTTCAA
** *
19935 TGATTTAA
1 TTCTTCAA
*
19943 -T-TTCAG
1 TTCTTCAA
19949 TAT-TTCAA
1 T-TCTTCAA
19957 TGT-TTCAA
1 T-TCTTCAA
19965 TTCTTCAA
1 TTCTTCAA
*
19973 TTGTTCAA
1 TTCTTCAA
*
19981 -T-TTCCA
1 TTCTTCAA
19987 TTCTTCAA
1 TTCTTCAA
** *
19995 TGATACAA
1 TTCTTCAA
*
20003 -T-TTCCA
1 TTCTTCAA
20009 TTCTTCAA
1 TTCTTCAA
* *
20017 TTCCTCCA
1 TTCTTCAA
**
20025 TTAATCAA
1 TTCTTCAA
*
20033 TGCTTCAA
1 TTCTTCAA
20041 -T-TTCAA
1 TTCTTCAA
20047 TT-TT-AA
1 TTCTTCAA
*
20053 GTCTTCAAA
1 TTCTTC-AA
20062 TTC--CAA
1 TTCTTCAA
* *
20068 AT-GTCAA
1 TTCTTCAA
*
20075 TGCTTCAA
1 TTCTTCAA
* *
20083 TTTTTCAG
1 TTCTTCAA
20091 TTCTTCAA
1 TTCTTCAA
20099 TT-TT-AA
1 TTCTTCAA
*
20105 TTTTTCAA
1 TTCTTCAA
*
20113 TGCTTCAA
1 TTCTTCAA
*
20121 AT-TTCAA
1 TTCTTCAA
20128 TTCTTCAAA
1 TTCTTC-AA
20137 TTC--CAA
1 TTCTTCAA
* *
20143 AT-GTCAA
1 TTCTTCAA
*
20150 TGCTTCGATA
1 TTCTTC-A-A
20160 TT-TT-AA
1 TTCTTCAA
*
20166 TACTTCAA
1 TTCTTCAA
20174 -TCTTTCAA
1 TTC-TTCAA
*
20182 TTGTTCAA
1 TTCTTCAA
20190 TTCTTCAA
1 TTCTTCAA
20198 TT
1 TT
20200 TACGTCAATG
Statistics
Matches: 471, Mismatches: 116, Indels: 146
0.64 0.16 0.20
Matches are distributed among these distances:
5 6 0.01
6 73 0.15
7 55 0.12
8 296 0.63
9 33 0.07
10 8 0.02
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (8 bp):
TTCTTCAA
Found at i:19632 original size:37 final size:37
Alignment explanation
Indices: 19533--19643 Score: 98
Period size: 37 Copynumber: 2.9 Consensus size: 37
19523 ATAATCTCTT
* * * * *
19533 TCTTCAATTATTCAATGCTTCAATTCTTCCATTATTCAAT
1 TCTTCAATTATTCAATGATTCAATTCAT-C--TCTTCGAC
*
19573 TCTTCAATTCTTCAATGATTCAATTCATCTCTTCGAC
1 TCTTCAATTATTCAATGATTCAATTCATCTCTTCGAC
* * *
19610 TCTTTAATTATTCAAT-ACTTCAATTTATTTCTTC
1 TCTTCAATTATTCAATGA-TTCAATTCATCTCTTC
19644 AATTCTTCGA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
36 1 0.02
37 33 0.55
39 1 0.02
40 25 0.42
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (37 bp):
TCTTCAATTATTCAATGATTCAATTCATCTCTTCGAC
Found at i:19636 original size:21 final size:21
Alignment explanation
Indices: 19612--19651 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19602 TCTTCGACTC
19612 TTTAATTATTCAATACTTCAA
1 TTTAATTATTCAATACTTCAA
* * *
19633 TTTATTTCTTCAATTCTTC
1 TTTAATTATTCAATACTTC
19652 GATCACTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATTATTCAATACTTCAA
Found at i:19792 original size:14 final size:14
Alignment explanation
Indices: 19773--19810 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
19763 ATTTCTGGTC
*
19773 ATTCTTCGATTCCA
1 ATTCTTCAATTCCA
*
19787 ATTCTTCAATTTCA
1 ATTCTTCAATTCCA
19801 ATTCTTCAAT
1 ATTCTTCAAT
19811 GCTTCAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (14 bp):
ATTCTTCAATTCCA
Found at i:19810 original size:22 final size:22
Alignment explanation
Indices: 19785--20199 Score: 107
Period size: 22 Copynumber: 18.2 Consensus size: 22
19775 TCTTCGATTC
19785 CAATTCTTCAATTTCAATTCTT
1 CAATTCTTCAATTTCAATTCTT
*
19807 CAATGCTTCAATTTCAATTCTT
1 CAATTCTTCAATTTCAATTCTT
*
19829 CAATTTTTCAATGTTTCAA-T-TT
1 CAATTCTTCAA--TTTCAATTCTT
*
19851 CAATAT-TCCAATGCTT-AATGT-TT
1 CAAT-TCTTCAAT--TTCAAT-TCTT
*
19874 CAA-T-TTCAATATTCCAATGCTT
1 CAATTCTTCAAT-TT-CAATTCTT
19896 CAA-T-TTCAATTCTTCAATGTTTCAATT
1 CAATTCTTCAA-T-TTCAA---TTC--TT
*
19923 GCAATTCTTCAATGATTTAA-T-TT
1 -CAATTCTTCAAT--TTCAATTCTT
*
19946 CAGTAT-TTCAATGTTTCAATTCTT
1 CAAT-TCTTCAA--TTTCAATTCTT
* *
19970 CAATTGTTCAATTTCCATTCTT
1 CAATTCTTCAATTTCAATTCTT
** * *
19992 CAATGATACAATTTCCATTCTT
1 CAATTCTTCAATTTCAATTCTT
* * *
20014 CAATTCCTCCATTAATCAATGCTT
1 CAATTCTTCAATT--TCAATTCTT
* *
20038 CAA-T-TTCAATTTTAAGTCTT
1 CAATTCTTCAATTTCAATTCTT
* *
20058 CAAATTC--CAAATGTCAATGCTT
1 C-AATTCTTC-AATTTCAATTCTT
* *
20080 CAATTTTTCAGTTCTTCAATT-TT
1 CAATTCTTCA-AT-TTCAATTCTT
* *
20103 -AATTTTTCAATGCTTCAAAT-TT
1 CAATTCTTCAAT--TTCAATTCTT
* * *
20125 CAATTCTTCAAATTCCAAAT-GT
1 CAATTCTTC-AATTTCAATTCTT
* * *
20147 CAATGCTTCGATATTTTAATACTT
1 CAATTCTTC-A-ATTTCAATTCTT
20171 CAA-TCTTTCAATTGTTCAATTCTT
1 CAATTC-TTCAA-T-TTCAATTCTT
20195 CAATT
1 CAATT
20200 TACGTCAATG
Statistics
Matches: 295, Mismatches: 53, Indels: 87
0.68 0.12 0.20
Matches are distributed among these distances:
20 10 0.03
21 16 0.05
22 160 0.54
23 36 0.12
24 53 0.18
25 3 0.01
26 1 0.00
27 2 0.01
28 3 0.01
29 2 0.01
30 9 0.03
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (22 bp):
CAATTCTTCAATTTCAATTCTT
Found at i:19822 original size:14 final size:14
Alignment explanation
Indices: 19805--19913 Score: 65
Period size: 14 Copynumber: 8.0 Consensus size: 14
19795 ATTTCAATTC
19805 TTCAATGCTTCAAT
1 TTCAATGCTTCAAT
*
19819 TTCAATTCTTCAATTT
1 TTCAATGCTTCAA--T
*
19835 TTCAATGTTTCAAT
1 TTCAATGCTTCAAT
19849 TTCAA----T--AT
1 TTCAATGCTTCAAT
*
19857 TCCAATGCTT-AATGT
1 TTCAATGCTTCAA--T
19872 TTCAAT--TTCAAT
1 TTCAATGCTTCAAT
19884 ATTCCAATGCTTCAAT
1 -TT-CAATGCTTCAAT
*
19900 TTCAATTCTTCAAT
1 TTCAATGCTTCAAT
19914 GTTTCAATTG
Statistics
Matches: 75, Mismatches: 6, Indels: 28
0.69 0.06 0.26
Matches are distributed among these distances:
8 6 0.08
10 1 0.01
12 2 0.03
13 5 0.07
14 35 0.47
15 8 0.11
16 18 0.24
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.47
Consensus pattern (14 bp):
TTCAATGCTTCAAT
Found at i:19878 original size:29 final size:29
Alignment explanation
Indices: 19791--19906 Score: 132
Period size: 30 Copynumber: 4.0 Consensus size: 29
19781 ATTCCAATTC
* *
19791 TTCAATTT-CAATTCTTCAATGCTTCAAT
1 TTCAATTTCCAATGCTTCAATGTTTCAAT
* **
19819 TTCAATTCTTCAATTTTTCAATGTTTCAAT
1 TTCAATT-TCCAATGCTTCAATGTTTCAAT
19849 TTCAATATTCCAATGCTT-AATGTTTCAAT
1 TTCAAT-TTCCAATGCTTCAATGTTTCAAT
19878 TTCAATATTCCAATGCTTCAA--TTTCAAT
1 TTCAAT-TTCCAATGCTTCAATGTTTCAAT
19906 T
1 T
19907 CTTCAATGTT
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
28 15 0.19
29 30 0.38
30 33 0.42
31 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.47
Consensus pattern (29 bp):
TTCAATTTCCAATGCTTCAATGTTTCAAT
Found at i:19934 original size:30 final size:29
Alignment explanation
Indices: 19786--20129 Score: 111
Period size: 30 Copynumber: 11.4 Consensus size: 29
19776 CTTCGATTCC
*
19786 AATTCTTCAATTTCAATTCTTCAATGCTTC
1 AATT-TTCAATTTCAATTCTTCAATTCTTC
*
19816 AA-TTTCAATTCTTCAATTTTTCAATGT-TTC
1 AATTTTCAA-T-TTCAATTCTTCAAT-TCTTC
*
19846 AA-TTTCAATATTCCAATGCTT-AATGT-TTC
1 AATTTTCAAT-TT-CAATTCTTCAAT-TCTTC
*
19875 AA-TTTCAATATTCCAATGCTTCAA-T-TTC
1 AATTTTCAAT-TT-CAATTCTTCAATTCTTC
*
19903 AATTCTTCAATGTTTCAA-T-TGCAATTCTTC
1 AATT-TTCAA--TTTCAATTCTTCAATTCTTC
19933 AATGATTT-AATTTCAGTATTTCAATGTTTCAATTCTTC
1 AAT--TTTCAATTTCA--A-TTC-----TTCAATTCTTC
* ** *
19971 AATTGTTCAATTTCCATTCTTCAATGATAC
1 AATT-TTCAATTTCAATTCTTCAATTCTTC
* * * * **
20001 AATTTCCATTCTTCAATTCCTCCATTAATC
1 AATTTTCAAT-TTCAATTCTTCAATTCTTC
* *
20031 AATGCTTCAATTTCAATT-TT-AAGTCTTC
1 AAT-TTTCAATTTCAATTCTTCAATTCTTC
* * * * *
20059 AAATTCCAAATGTCAATGCTTCAATTTTTC
1 AATTTTC-AATTTCAATTCTTCAATTCTTC
* * * *
20089 AGTTCTTCAATTTTAATTTTTCAATGCTTC
1 AATT-TTCAATTTCAATTCTTCAATTCTTC
*
20119 AAATTTCAATT
1 AATTTTCAATT
20130 CTTCAAATTC
Statistics
Matches: 237, Mismatches: 46, Indels: 63
0.68 0.13 0.18
Matches are distributed among these distances:
27 2 0.01
28 34 0.14
29 50 0.21
30 112 0.47
31 10 0.04
32 3 0.01
35 3 0.01
36 2 0.01
37 2 0.01
38 19 0.08
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.47
Consensus pattern (29 bp):
AATTTTCAATTTCAATTCTTCAATTCTTC
Found at i:20127 original size:15 final size:15
Alignment explanation
Indices: 20107--20138 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20097 AATTTTAATT
20107 TTTCAATGCTTCAAA
1 TTTCAATGCTTCAAA
*
20122 TTTCAATTCTTCAAA
1 TTTCAATGCTTCAAA
20137 TT
1 TT
20139 CCAAATGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (15 bp):
TTTCAATGCTTCAAA
Found at i:20147 original size:75 final size:77
Alignment explanation
Indices: 20045--20197 Score: 213
Period size: 75 Copynumber: 2.0 Consensus size: 77
20035 CTTCAATTTC
* * *
20045 AATTTTAAGTCTTCAAATTCCAAATGTCAATGCTTCAAT-TTTTCAGTTCTTCAAT-TTT-AATT
1 AATTTCAAGTCTTCAAATTCCAAATGTCAATGCTTCAATATTTT-AATACTTCAATCTTTCAATT
*
20107 TTTCAATGCTTCA
65 GTTCAATGCTTCA
* *
20120 AATTTCAATTCTTCAAATTCCAAATGTCAATGCTTCGATATTTTAATACTTCAATCTTTCAATTG
1 AATTTCAAGTCTTCAAATTCCAAATGTCAATGCTTCAATATTTTAATACTTCAATCTTTCAATTG
*
20185 TTCAATTCTTCA
66 TTCAATGCTTCA
20197 A
1 A
20198 TTTACGTCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 45 0.66
76 7 0.10
77 16 0.24
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (77 bp):
AATTTCAAGTCTTCAAATTCCAAATGTCAATGCTTCAATATTTTAATACTTCAATCTTTCAATTG
TTCAATGCTTCA
Found at i:20735 original size:2 final size:2
Alignment explanation
Indices: 20699--20725 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20689 TCCTTTAATT
20699 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20726 TCCCATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.