Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009881.1 Corchorus capsularis cultivar CVL-1 contig09902, 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: 28220
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5697 original size:2 final size:2
Alignment explanation
Indices: 5690--5714 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5680 TAAAACTTGA
5690 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5715 GTAGGGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10127 original size:107 final size:108
Alignment explanation
Indices: 9957--10216 Score: 423
Period size: 107 Copynumber: 2.4 Consensus size: 108
9947 ACTATTATAG
*
9957 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTA-AAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
*
10022 TATTTTTACCAAAAAATTTGGATATACT-AAAATTTTTCTAATATACAA
60 TATTTTTACCAAAAAAATTGGATATACTAAAAATTTTTCTAATATACAA
10070 TTTTATTCTACTAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTTT
1 TTTTATTCTACTAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTTT
*
10135 TACCAAAAAAATTGGATATATTAAAAATTTTTCTAATATACAA
66 TACCAAAAAAATTGGATATACTAAAAATTTTTCTAATATACAA
10178 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT
1 TTTTATTCTACT-AAAACTCTATTTTCATTTAATTAAAT
10217 TCAATATTAT
Statistics
Matches: 142, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
107 58 0.41
108 35 0.25
109 28 0.20
112 8 0.06
113 13 0.09
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.48
Consensus pattern (108 bp):
TTTTATTCTACTAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTTT
TACCAAAAAAATTGGATATACTAAAAATTTTTCTAATATACAA
Found at i:16186 original size:15 final size:15
Alignment explanation
Indices: 16166--16195 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16156 CAATAATATG
16166 TTCTTTTCTCTTTTT
1 TTCTTTTCTCTTTTT
*
16181 TTCTTTTTTCTTTTT
1 TTCTTTTCTCTTTTT
16196 CCTTTTTGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTCTTTTCTCTTTTT
Found at i:22618 original size:22 final size:21
Alignment explanation
Indices: 22567--22620 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
22557 ATGATCCCAT
* *
22567 TATGAAATTTTGATAACTTCC
1 TATGAAATTTTGATAACGTAC
22588 TATGAAATTTTGATAACGGTAC
1 TATGAAATTTTGATAAC-GTAC
*
22610 TATGGAATTTT
1 TATGAAATTTT
22621 AAGAATCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (21 bp):
TATGAAATTTTGATAACGTAC
Found at i:22755 original size:45 final size:45
Alignment explanation
Indices: 22697--22782 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
22687 AAGACTTCAA
* * *
22697 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACAC
* *
22742 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
22783 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:22776 original size:22 final size:22
Alignment explanation
Indices: 22567--23190 Score: 191
Period size: 22 Copynumber: 29.0 Consensus size: 22
22557 ATGATCCCAT
*
22567 TATGAAATTTTGATAACTTCC-
1 TATGAAATTTTGATAACCTCCA
* *
22588 TATGAAATTTTGATAACGGTAC-
1 TATGAAATTTTGATAAC-CTCCA
* * * **
22610 TATGGAATTTTAAGAATCCT-TT
1 TATGAAATTTTGATAA-CCTCCA
* * * * *
22632 TAT-AAATTTTTAAAACTTTCT
1 TATGAAATTTTGATAACCTCCA
* *
22653 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCCA
* * * *
22675 TAAGGAATTTTGA-AGACTTCAA
1 TATGAAATTTTGATA-ACCTCCA
*
22697 TATGAAATTTTGATAACTTCCCA
1 TATGAAATTTTGATAACCT-CCA
**
22720 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
22741 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * * **
22764 TATGATATATTGATAACCACTT
1 TATGAAATTTTGATAACCTCCA
* * * *
22786 TATAAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
22808 TATG-AATTATT-AGTAA--TCACA
1 TATGAAATT-TTGA-TAACCTC-CA
* *
22829 CTTTAAAATTTTGATAA--TCACA
1 -TATGAAATTTTGATAACCTC-CA
*
22851 CTATGAAATTGTGATAACCTCGC-
1 -TATGAAATTTTGATAACCTC-CA
* * *
22874 TATGAAATTTTTATAAATCTTTC-
1 TATGAAATTTTGAT-AA-CCTCCA
* *
22897 TATAAAATTTTAATAAACCTCC-
1 TATGAAATTTTGAT-AACCTCCA
* * * *
22919 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTCCA
* *
22941 TATAAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTCCA
* * *
22958 TA-CAAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCTCCA
**
22979 TATGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* * *
23000 TTATGAAATTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTCCA
* * *
23023 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
* *
23045 TATGAAATTTTGAT-ACCCCTCT
1 TATGAAATTTTGATAACCTC-CA
* **
23067 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
* *
23088 CTATGAAAATTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTCCA
*
23111 TATGAAATTTTGATATCCT-CA
1 TATGAAATTTTGATAACCTCCA
* *
23132 -CTG-AATTTTGATATCCTCC-
1 TATGAAATTTTGATAACCTCCA
* * *
23151 -CTG-AATTTTGGTATCCTCC-
1 TATGAAATTTTGATAACCTCCA
*
23170 T-TGAAATTTTGATTA-CTCCA
1 TATGAAATTTTGATAACCTCCA
23190 T
1 T
23191 CATAAAAGTT
Statistics
Matches: 459, Mismatches: 105, Indels: 79
0.71 0.16 0.12
Matches are distributed among these distances:
16 11 0.02
17 2 0.00
18 1 0.00
19 38 0.08
20 19 0.04
21 50 0.11
22 280 0.61
23 53 0.12
24 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:23188 original size:19 final size:18
Alignment explanation
Indices: 23116--23182 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 18
23106 CTTCATATGA
23116 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTC-CTG
23135 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCT-CCTG
*
23154 AATTTTGGTATCCTCCTTG
1 AATTTTGATATCCTCC-TG
23173 AAATTTTGAT
1 -AATTTTGAT
23183 TACTCCATCA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
18 2 0.05
19 32 0.74
20 9 0.21
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (18 bp):
AATTTTGATATCCTCCTG
Found at i:23321 original size:22 final size:22
Alignment explanation
Indices: 23294--23503 Score: 142
Period size: 22 Copynumber: 9.5 Consensus size: 22
23284 ATTTTAAAAA
23294 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* *
23316 TTTGATAACATCTTTATAAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * *
23338 TTTGTTGACCCCTCTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * *
23360 TTTGATAATCACATTATGTAAT
1 TTTGATAACCTCTTTATGAAAT
*
23382 TTTGATAACCTCGCTT-TGAAAT
1 TTTGATAACCTC-TTTATGAAAT
** **
23404 TTTGATAACAACACTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
23426 TTTGATAA--TCTTCATAT-AAAT
1 TTTGATAACCTCTT--TATGAAAT
**
23447 TTTGATAATTATATCTTTATGAAAT
1 TTTGAT-A--ACCTCTTTATGAAAT
* * * *
23472 TTTGATAATCACTCTATGAGA-
1 TTTGATAACCTCTTTATGAAAT
23493 TTTGATAACCT
1 TTTGATAACCT
23504 TCTATCAGAT
Statistics
Matches: 146, Mismatches: 32, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 20 0.14
22 104 0.71
23 2 0.01
24 5 0.03
25 10 0.07
26 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (22 bp):
TTTGATAACCTCTTTATGAAAT
Found at i:23336 original size:44 final size:43
Alignment explanation
Indices: 23264--23454 Score: 158
Period size: 44 Copynumber: 4.4 Consensus size: 43
23254 AAAATACCAC
* * *
23264 TATGAAATTTTTG-TAATCAGATTTTAAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAA-CACATTATAAAATTTTGATAACCTCTT
* * * * *
23308 TATGAAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACA-CATTATAAAATTTTGATAACCTCTT
** *
23352 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAA-CACATTATAAAATTTTGATAACCTC-TT
* *
23397 T-TGAAATTTTGATAACAACACTATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAAC-ACATTATAAAATTTTGATAACCTCTT
23438 CATAT-AAATTTTGATAA
1 --TATGAAATTTTGATAA
23455 TTATATCTTT
Statistics
Matches: 120, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 21 0.17
44 93 0.77
45 3 0.03
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (43 bp):
TATGAAATTTTGATAACACATTATAAAATTTTGATAACCTCTT
Found at i:23377 original size:66 final size:67
Alignment explanation
Indices: 23294--23454 Score: 170
Period size: 66 Copynumber: 2.5 Consensus size: 67
23284 ATTTTAAAAA
* * * * * ** *
23294 TTTGATAACCT-CTTTATGAAATTTTGATAACATC-TTTATAAAATTTTGTTGACCCCTCTATGA
1 TTTGATAATCTACATTATGAAATTTTGATAACATCGCTT-TAAAATTTTGATAACAACACTATGA
23357 AAT
65 AAT
* * *
23360 TTTGATAATC-ACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTATGAA
1 TTTGATAATCTACATTATGAAATTTTGATAACATCGCTTTAAAATTTTGATAACAACACTATGAA
23424 AT
66 AT
*
23426 TTTGATAATCTTCA-TAT-AAATTTTGATAA
1 TTTGATAATCTACATTATGAAATTTTGATAA
23455 TTATATCTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
65 11 0.14
66 64 0.81
67 4 0.05
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (67 bp):
TTTGATAATCTACATTATGAAATTTTGATAACATCGCTTTAAAATTTTGATAACAACACTATGAA
AT
Found at i:23426 original size:88 final size:88
Alignment explanation
Indices: 23263--23429 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
23253 AAAAATACCA
* * * *
23263 CTATGAAATTTTTGTAATCAGATTTTAAAAATTTGATAACCTCTTTATGAAATTTTGATAACATC
1 CTATGAAATTTTTGTAATCACATTATAAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
23328 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
** *
23351 CTATGAAA-TTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTTTG-TAATCACATTATAAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
23414 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
23430 ATAATCTTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 5 0.07
88 60 0.90
89 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (88 bp):
CTATGAAATTTTTGTAATCACATTATAAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:23472 original size:25 final size:23
Alignment explanation
Indices: 23418--23480 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
23408 ATAACAACAC
*
23418 TATGAAATTTTGATAA-TCTTCA
1 TATGAAATTTTGATAATTATTCA
*
23440 TAT-AAATTTTGATAATTATATCTT
1 TATGAAATTTTGATAATTAT-TC-A
23464 TATGAAATTTTGATAAT
1 TATGAAATTTTGATAAT
23481 CACTCTATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 12 0.34
22 5 0.14
23 2 0.06
24 3 0.09
25 13 0.37
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (23 bp):
TATGAAATTTTGATAATTATTCA
Found at i:23517 original size:21 final size:22
Alignment explanation
Indices: 23470--23517 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
23460 TCTTTATGAA
*
23470 ATTTTGATAATCACTCTATGAG
1 ATTTTGATAATCACTCTATCAG
23492 A-TTTGATAA-C-CTTCTATCAG
1 ATTTTGATAATCAC-TCTATCAG
23512 ATTTTG
1 ATTTTG
23518 GTACTCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 9 0.39
21 12 0.52
22 1 0.04
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (22 bp):
ATTTTGATAATCACTCTATCAG
Found at i:23569 original size:22 final size:22
Alignment explanation
Indices: 23294--23650 Score: 120
Period size: 22 Copynumber: 16.0 Consensus size: 22
23284 ATTTTAAAAA
*
23294 TTTGATAACC-TCTTTATGAAAT
1 TTTGATAACCTTC-ATATGAAAT
*
23316 TTTGATAACATCTT--TATAAAAT
1 TTTGATAAC--CTTCATATGAAAT
* * *
23338 TTTGTTGACCCCTC-TATGAAAT
1 TTTGAT-AACCTTCATATGAAAT
* * *
23360 TTTGATAATC-ACATTATGTAAT
1 TTTGATAACCTTCA-TATGAAAT
* *
23382 TTTGATAACC-TCGCTTTGAAAT
1 TTTGATAACCTTC-ATATGAAAT
**
23404 TTTGATAA-CAACACTATGAAAT
1 TTTGATAACCTTCA-TATGAAAT
*
23426 TTTGATAATCTTCATAT-AAAT
1 TTTGATAACCTTCATATGAAAT
** *
23447 TTTGATAATTATATCTTTATGAAAT
1 TTTGATAA-CCT-TC-ATATGAAAT
*
23472 TTTGATAATCAC-TC-TATGAGA-
1 TTTGATAA-C-CTTCATATGAAAT
* *
23493 TTTGATAACCTTC-TATCAGAT
1 TTTGATAACCTTCATATGAAAT
* * *
23514 TTTGGTACTCCTT-ATGAAATTGAGACT
1 TTTGATA-ACCTTCAT---A-TGA-AAT
23541 TTT-ATAACCTTCATATGAAAT
1 TTTGATAACCTTCATATGAAAT
* *
23562 TTTGATAACC-ACACTATAAAAT
1 TTTGATAACCTTCA-TATGAAAT
* **
23584 TTTGATAACCTCCCGATGAAAT
1 TTTGATAACCTTCATATGAAAT
*
23606 ATT-AGTAACCTT-ATAATGAAAT
1 TTTGA-TAACCTTCAT-ATGAAAT
* *
23628 TTTGTTAACCAT-ACTATGAAAT
1 TTTGATAACCTTCA-TATGAAAT
23650 T
1 T
23651 CGTATAACCT
Statistics
Matches: 255, Mismatches: 47, Indels: 66
0.69 0.13 0.18
Matches are distributed among these distances:
19 1 0.00
20 10 0.04
21 39 0.15
22 160 0.63
23 10 0.04
24 6 0.02
25 19 0.07
26 6 0.02
27 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TTTGATAACCTTCATATGAAAT
Found at i:23775 original size:24 final size:22
Alignment explanation
Indices: 23714--23876 Score: 100
Period size: 22 Copynumber: 7.3 Consensus size: 22
23704 TTGTGATAAT
* *
23714 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
23736 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
23758 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
23782 TAACC-ACTCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* **
23804 TAA-CTACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
**
23826 TAACC-ACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* * *
23848 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
23870 TAACCAA
1 TAACCAA
23877 AGTAAAATAT
Statistics
Matches: 119, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
21 4 0.03
22 96 0.81
23 1 0.01
24 18 0.15
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:23786 original size:46 final size:43
Alignment explanation
Indices: 23721--23845 Score: 135
Period size: 44 Copynumber: 2.8 Consensus size: 43
23711 AATTAACCAC
*** *
23721 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGA
1 CCTATGAAATTTTGGTAACCACA-CTATGAAATTTTAATAA-CT-A
* **
23766 TCCTATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTA
1 -CCTATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTA
23810 CACTATGAAATTTTGGTAACCACACTATGAAATTTT
1 C-CTATGAAATTTTGGTAACCACACTATGAAATTTT
23846 GGTAACCTCC
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 1 0.01
44 34 0.49
45 2 0.03
46 32 0.46
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (43 bp):
CCTATGAAATTTTGGTAACCACACTATGAAATTTTAATAACTA
Found at i:23825 original size:44 final size:44
Alignment explanation
Indices: 23768--23851 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
23758 TAACCTGATC
*
23768 CTATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACTACA
23812 CTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAAC
1 CTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAAC
23852 CTCCTCATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (44 bp):
CTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACTACA
Found at i:23874 original size:44 final size:44
Alignment explanation
Indices: 23768--23875 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 44
23758 TAACCTGATC
* ** *
23768 CTATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTACA
1 CTATGAAATTATAATAACCACACTATGAAATTTTGGTAACTACA
* **
23812 CTATGAAATTTTGGTAACCACACTATGAAATTTTGGTAACCT-C-
1 CTATGAAATTATAATAACCACACTATGAAATTTTGGTAA-CTACA
*
23855 CTCATGGAATTATAATAACCA
1 CT-ATGAAATTATAATAACCA
23876 AAGTAAAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
43 2 0.04
44 53 0.93
45 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (44 bp):
CTATGAAATTATAATAACCACACTATGAAATTTTGGTAACTACA
Found at i:23997 original size:30 final size:31
Alignment explanation
Indices: 23962--24025 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
23952 GACAATTTAA
*
23962 AAATATGTTTTAAAAA-AAAAGTACAATTGG
1 AAATATGTTTTAAAAATAAAAGTACAATCGG
**
23992 AAATATGTTTTAAAAATAAGGGTACAATCGG
1 AAATATGTTTTAAAAATAAAAGTACAATCGG
24023 AAA
1 AAA
24026 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.28
Consensus pattern (31 bp):
AAATATGTTTTAAAAATAAAAGTACAATCGG
Found at i:26927 original size:28 final size:28
Alignment explanation
Indices: 26856--26927 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
26846 CACAAATTAC
* *
26856 ATACCGTTGAATTTTTTTTTGGCACCAC
1 ATACCGTTGAATTTTTTTTTGGCACAAA
* *
26884 ATACTGTTGAACTTTTTTTTTGGTTA-AAA
1 ATACCGTTGAA-TTTTTTTTTGG-CACAAA
26913 ATACCGTTGAATTTT
1 ATACCGTTGAATTTT
26928 AGATACAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 14 0.38
29 22 0.59
30 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (28 bp):
ATACCGTTGAATTTTTTTTTGGCACAAA
Done.