Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013644.1 Corchorus capsularis cultivar CVL-1 contig13665, 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: 26548
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:641 original size:70 final size:70
Alignment explanation
Indices: 518--742 Score: 306
Period size: 70 Copynumber: 3.1 Consensus size: 70
508 TAATTAAAAT
* * *
518 AGTAAAATATTAAAATATAATAGTTATAAGGTTAATAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
583 AGTTG
66 AGTTG
*
588 AGTACAATAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
*
653 AGTTT
66 AGTTG
* * *
658 AGTAAAATAGTAAAATGATAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATA
1 AGTAAAATAGT-AAA--AT---AT--AATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
723 GAGTTTTTAGTTG
58 GAGTTTTTAGTTG
736 AGTAAAA
1 AGTAAAA
743 CTATAGAAAC
Statistics
Matches: 137, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
70 75 0.55
71 3 0.02
73 2 0.01
76 2 0.01
78 55 0.40
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.38
Consensus pattern (70 bp):
AGTAAAATAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:680 original size:78 final size:78
Alignment explanation
Indices: 598--742 Score: 245
Period size: 78 Copynumber: 1.9 Consensus size: 78
588 AGTACAATAG
* * * *
598 TAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAGTTTAGTAA
1 TAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
663 AATAGTAAAATGA
66 AATAGTAAAATGA
*
676 TAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
1 TAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
741 AA
66 AA
743 CTATAGAAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (78 bp):
TAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
AATAGTAAAATGA
Found at i:856 original size:6 final size:6
Alignment explanation
Indices: 838--871 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
828 GTACTTTTTA
838 ATATAG TATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATA
872 AGTATTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:1246 original size:31 final size:32
Alignment explanation
Indices: 1209--1274 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
1199 CTAAGGATTT
*
1209 ATTTGAGTTGATTTTGCAATATTAGGGAC-TG
1 ATTTGAGCTGATTTTGCAATATTAGGGACTTG
* * *
1240 ATTTGAGCTGATTTTGCCATGTTTGGGACTTG
1 ATTTGAGCTGATTTTGCAATATTAGGGACTTG
1272 ATT
1 ATT
1275 AATCAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (32 bp):
ATTTGAGCTGATTTTGCAATATTAGGGACTTG
Found at i:2250 original size:2 final size:2
Alignment explanation
Indices: 2243--2267 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2233 AGATTCAAGC
2243 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
2268 CACACACATT
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:2325 original size:3 final size:3
Alignment explanation
Indices: 2317--2356 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2307 AGAACTATTC
2317 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
2357 TCAGTCTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:8640 original size:6 final size:6
Alignment explanation
Indices: 8629--8653 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8619 ATACTACATC
8629 TGAAAA TGAAAA TGAAAA TGAAAA T
1 TGAAAA TGAAAA TGAAAA TGAAAA T
8654 AACTTGGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (6 bp):
TGAAAA
Found at i:15940 original size:24 final size:24
Alignment explanation
Indices: 15908--15960 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
15898 ATTACCAAGA
15908 AAACAGGAAACAACGAAATATACC
1 AAACAGGAAACAACGAAATATACC
15932 AAACAGGAAACAACGAAATATACC
1 AAACAGGAAACAACGAAATATACC
15956 AAACA
1 AAACA
15961 AACCTGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.60, C:0.21, G:0.11, T:0.08
Consensus pattern (24 bp):
AAACAGGAAACAACGAAATATACC
Found at i:15963 original size:28 final size:28
Alignment explanation
Indices: 15900--15963 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 28
15890 GTCATATAAT
15900 TACCAAGA-AAACAGGAAACAACGAAATA
1 TACCAA-ACAAACAGGAAACAACGAAATA
15928 TA-C---CAAACAGGAAACAACGAAATA
1 TACCAAACAAACAGGAAACAACGAAATA
15952 TACCAAACAAAC
1 TACCAAACAAAC
15964 CTGAGATTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
24 22 0.71
25 1 0.03
27 1 0.03
28 7 0.23
ACGTcount: A:0.59, C:0.22, G:0.11, T:0.08
Consensus pattern (28 bp):
TACCAAACAAACAGGAAACAACGAAATA
Found at i:19473 original size:22 final size:22
Alignment explanation
Indices: 19448--19499 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
19438 CTCCCTAGGG
19448 AATTTTGAAGACCT-CAATATGA
1 AATTTTGAAGACCTCCAA-ATGA
* * *
19470 AATTTTGATGACTTCCCAATGA
1 AATTTTGAAGACCTCCAAATGA
19492 AATTTTGA
1 AATTTTGA
19500 TAACCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
AATTTTGAAGACCTCCAAATGA
Found at i:19614 original size:22 final size:22
Alignment explanation
Indices: 19589--19873 Score: 90
Period size: 22 Copynumber: 13.1 Consensus size: 22
19579 GAATTGTTAG
*
19589 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
19611 TAATCACATTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
19633 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
19655 TAAATCTTC-CTATAAAATTTTGA
1 T-AATC-ACACTATGAAATTTTGA
* * * *
19678 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
** * *
19701 TAATTTTC-TTATGAAATCTTG-
1 TAA-TCACACTATGAAATTTTGA
*
19722 --AT-A-ACTA-CAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * **
19739 TAACCTC-CTTATGATTTTTTGA
1 TAATCACAC-TATGAAATTTTGA
* * ** *
19761 TAACCTCGTTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
19783 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
19805 T-CTACATACGATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
19827 TAA-CCCTCTTGTGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* *
19849 -AAACTAAACTATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
19871 TAA
1 TAA
19874 CTTTCGTATG
Statistics
Matches: 196, Mismatches: 48, Indels: 37
0.70 0.17 0.13
Matches are distributed among these distances:
16 7 0.04
17 2 0.01
18 1 0.01
19 2 0.01
20 1 0.01
21 7 0.04
22 133 0.68
23 41 0.21
24 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:19672 original size:23 final size:23
Alignment explanation
Indices: 19641--19725 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
19631 GATAACCTCG
*
19641 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
19664 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
19687 CTATAAAATTTTGAT-AATTTTC
1 CTATAAAATTTTGATAAATCTTC
* * *
19709 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
19726 CTACAAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.31
23 36 0.69
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:19724 original size:45 final size:44
Alignment explanation
Indices: 19602--19725 Score: 126
Period size: 45 Copynumber: 2.8 Consensus size: 44
19592 TCACACTCTG
** * *
19602 AAATTTTGATAA-TCACATTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAATTTTC-TTATGAAATT-TGATAAACCTCCCTATA
* * *
19646 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AATTTTCTTATGAAA-TTTGATAAACCTCCCTATA
19692 AAATTTTGATAATTTTCTTATGAAATCTTGATAA
1 AAATTTTGATAATTTTCTTATGAAAT-TTGATAA
19726 CTACAAATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
44 11 0.17
45 31 0.48
46 23 0.35
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (44 bp):
AAATTTTGATAATTTTCTTATGAAATTTGATAAACCTCCCTATA
Found at i:19825 original size:66 final size:65
Alignment explanation
Indices: 19600--19899 Score: 179
Period size: 66 Copynumber: 4.6 Consensus size: 65
19590 AATCACACTC
* * * * *
19600 TGAAATTTTGATAATCACA-TTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAATCT-T
1 TGAAATTTTGATAA-CATACGTATGAAATTTTGATAACCTC-TTATGAAATTTTGA-AAA-CTAA
*
19663 CCTA
62 ACTA
* * * * * ** *
19667 TAAAATTTTGATAAACCTCCCTATAAAATTTTGATAATTTTCTTATGAAATCTTG---A-T-AAC
1 TGAAATTTTGAT-AACATACGTATGAAATTTTGATAA-CCTCTTATGAAATTTTGAAAACTAAAC
19727 TA
64 TA
* * * * ** * * **
19729 -CAAATTTTGATAACCTCCTTATGATTTTTTGATAACCTCGTTATGAAATTTTGTTAATCT-CCC
1 TGAAATTTTGATAACATACGTATGAAATTTTGATAACCTC-TTATGAAATTTTG-AAAACTAAAC
19792 TA
64 TA
* *
19794 TGAAATTTTGATCTACATACG-ATGAAATTTTGATAACCCTCTTGTGAAATTTTGAAAACTAAAC
1 TGAAATTTTGAT-AACATACGTATGAAATTTTGATAA-CCTCTTATGAAATTTTGAAAACTAAAC
19858 TA
64 TA
* * *
19860 TGAAATTTTGATAACTTTCGTATGAAATTTTGATATCCTC
1 TGAAATTTTGATAACATACGTATGAAATTTTGATAACCTC
19900 CCTAAATTTT
Statistics
Matches: 179, Mismatches: 40, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
59 2 0.01
60 32 0.18
61 10 0.06
62 4 0.02
64 1 0.01
65 17 0.09
66 64 0.36
67 20 0.11
68 27 0.15
69 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (65 bp):
TGAAATTTTGATAACATACGTATGAAATTTTGATAACCTCTTATGAAATTTTGAAAACTAAACTA
Found at i:19842 original size:44 final size:42
Alignment explanation
Indices: 19771--19893 Score: 115
Period size: 44 Copynumber: 2.8 Consensus size: 42
19761 TAACCTCGTT
*
19771 ATGAAATTTTGTTAATCTCC-C-TATGAAATTTTGATCTACATACG
1 ATGAAATTTTGATAA-C-CCTCGTATGAAATTTTGATCTA-A-ACG
* * * *
19815 ATGAAATTTTGATAACCCTCTTGTGAAATTTTGAAAACTAAACT
1 ATGAAATTTTGATAACCCTCGTATGAAATTTTG--ATCTAAACG
**
19859 ATGAAATTTTGATAACTTTCGTATGAAATTTTGAT
1 ATGAAATTTTGATAACCCTCGTATGAAATTTTGAT
19894 ATCCTCCCTA
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
42 3 0.05
43 2 0.03
44 56 0.85
45 1 0.02
46 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (42 bp):
ATGAAATTTTGATAACCCTCGTATGAAATTTTGATCTAAACG
Found at i:19875 original size:22 final size:22
Alignment explanation
Indices: 19791--19894 Score: 72
Period size: 22 Copynumber: 4.7 Consensus size: 22
19781 GTTAATCTCC
19791 CTATGAAATTTTGAT--CTACATA
1 CTATGAAATTTTGATAACTA-A-A
* ***
19813 CGATGAAATTTTGATAAC-CCT
1 CTATGAAATTTTGATAACTAAA
* *
19834 CTTGTGAAATTTTGAAAACTAAA
1 C-TATGAAATTTTGATAACTAAA
**
19857 CTATGAAATTTTGATAACT-TT
1 CTATGAAATTTTGATAACTAAA
19878 CGTATGAAATTTTGATA
1 C-TATGAAATTTTGATA
19895 TCCTCCCTAA
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
21 2 0.03
22 59 0.94
23 1 0.02
24 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAACTAAA
Found at i:19928 original size:20 final size:20
Alignment explanation
Indices: 19882--19929 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
19872 AACTTTCGTA
*
19882 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCAC
*
19902 T-AAATTTTGATATCCTCAT
1 TGAAATTTTGATATCCTCAC
19921 TGAAATTTT
1 TGAAATTTT
19930 CATTACTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCAC
Found at i:20239 original size:22 final size:22
Alignment explanation
Indices: 20013--20250 Score: 146
Period size: 22 Copynumber: 10.8 Consensus size: 22
20003 AGAAATACCA
20013 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
20036 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * *
20057 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * * *
20079 TTTTAAAATTTTGTTGATCCCT
1 CTATGAAATTTTGATAATCACT
*
20101 CTATGAAATTCTGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
* * * *
20124 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* *
20145 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
* **
20167 CTATGGAATTTTGATAATCTTT
1 CTATGAAATTTTGATAATCACT
20189 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAAT-C-A-CT
*
20213 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
20235 CTATGAGA-TTTGATAA
1 CTATGAAATTTTGATAA
20251 ATTTCTATCA
Statistics
Matches: 166, Mismatches: 39, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
21 25 0.15
22 120 0.72
23 3 0.02
24 6 0.04
25 12 0.07
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:20319 original size:22 final size:20
Alignment explanation
Indices: 20290--20345 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 20
20280 AAATTGAGAC
20290 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TC-TATGAAA
* *
20311 TTTTGATAACCACACTATAAAA
1 TTTTGATAA-C-CTCTATGAAA
20333 TTTTGATAACCTC
1 TTTTGATAACCTC
20346 CCCATGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 2 0.07
21 5 0.17
22 19 0.66
23 2 0.07
24 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (20 bp):
TTTTGATAACCTCTATGAAA
Found at i:20355 original size:22 final size:22
Alignment explanation
Indices: 20305--20355 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
20295 TAACCTTCAT
*
20305 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
20327 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
20349 ATGAAAT
1 ATGAAAT
20356 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:20486 original size:26 final size:26
Alignment explanation
Indices: 20457--20523 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 26
20447 GTGATAATTA
20457 ACCATCCTATGAAATTTCAATAACCT
1 ACCATCCTATGAAATTTCAATAACCT
* * * *
20483 ACCAACCTAAGAGATTTTAATAACCT
1 ACCATCCTATGAAATTTCAATAACCT
*
20509 --GATCCTATGAAATTT
1 ACCATCCTATGAAATTT
20524 TGGTAACTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
24 11 0.33
26 22 0.67
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.31
Consensus pattern (26 bp):
ACCATCCTATGAAATTTCAATAACCT
Found at i:20680 original size:19 final size:20
Alignment explanation
Indices: 20649--20691 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
20639 TATTGACATT
20649 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTAAAAAG
20668 TAAAATATT-AAATTCAAAAAG
1 TAAAA-ATTGAAATT-AAAAAG
20689 TAA
1 TAA
20692 TATTAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (20 bp):
TAAAAATTGAAATTAAAAAG
Found at i:21032 original size:31 final size:31
Alignment explanation
Indices: 20992--21062 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
20982 AGTAATGGCA
*
20992 AATTAGAAATATGTTTTAAAGAA-AAGGGTAC
1 AATTGGAAATATGTTTTAAA-AATAAGGGTAC
21023 AATTGGAAATATGTTTTAAAAATAAGGGTAC
1 AATTGGAAATATGTTTTAAAAATAAGGGTAC
21054 -ATTCGGAAA
1 AATT-GGAAA
21063 ACATAAAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
30 5 0.14
31 32 0.86
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (31 bp):
AATTGGAAATATGTTTTAAAAATAAGGGTAC
Found at i:21811 original size:3 final size:3
Alignment explanation
Indices: 21803--21863 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
21793 GGTAATTTGC
*
21803 TCT TCT TCT TCT CCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
21851 TCT TCT TCT TCT T
1 TCT TCT TCT TCT T
21864 TTTTTTTAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Done.