Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014995.1 Corchorus capsularis cultivar CVL-1 contig15016, 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: 140408
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1070 original size:30 final size:30
Alignment explanation
Indices: 1036--1095 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1026 AATATTAAAC
*
1036 GTTTACAGGAAACTGCCCTCTCCAAACTCA
1 GTTTAAAGGAAACTGCCCTCTCCAAACTCA
1066 GTTTAAAGGAAACTGCCCTCTCCAAACTCA
1 GTTTAAAGGAAACTGCCCTCTCCAAACTCA
1096 AATCTGAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.32, G:0.13, T:0.23
Consensus pattern (30 bp):
GTTTAAAGGAAACTGCCCTCTCCAAACTCA
Found at i:13373 original size:13 final size:13
Alignment explanation
Indices: 13355--13380 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13345 ACTCCTTATG
13355 TTATTAATTATTA
1 TTATTAATTATTA
13368 TTATTAATTATTA
1 TTATTAATTATTA
13381 ATAATAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTAATTATTA
Found at i:15193 original size:57 final size:57
Alignment explanation
Indices: 15099--15212 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
15089 TGTTTTCTCA
*
15099 CATAAACTCTTGCTTGTTTATGATCTACTCTTAGCACGCCCCACTAGTTCCCGCAGG
1 CATAAACTCTTGCTTGTTTATGATCCACTCTTAGCACGCCCCACTAGTTCCCGCAGG
* * *
15156 CATAGACTCTTGCTTGTTTATGATCCACTTTTGGCACGCCCCACTAGTTCCCGCAGG
1 CATAAACTCTTGCTTGTTTATGATCCACTCTTAGCACGCCCCACTAGTTCCCGCAGG
15213 TATACCCTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.19, C:0.32, G:0.18, T:0.32
Consensus pattern (57 bp):
CATAAACTCTTGCTTGTTTATGATCCACTCTTAGCACGCCCCACTAGTTCCCGCAGG
Found at i:15693 original size:20 final size:20
Alignment explanation
Indices: 15664--15705 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
15654 ACAATTTTAC
*
15664 TGGTTCCCAAACACTACCTT
1 TGGTTACCAAACACTACCTT
15684 TGGTTACCAAACACTACCTT
1 TGGTTACCAAACACTACCTT
15704 TG
1 TG
15706 TTTGAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (20 bp):
TGGTTACCAAACACTACCTT
Found at i:16797 original size:3 final size:3
Alignment explanation
Indices: 16789--16831 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
16779 CTGTGTCTTG
16789 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
16832 CACAACTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:18811 original size:36 final size:36
Alignment explanation
Indices: 18749--18817 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
18739 CTTTAACTTT
*
18749 TTTTTTTTTTCAATTCAAATACCCTTCCTTCCCACA
1 TTTTTTTTTTCAATTCAAATACCCTTCATTCCCACA
*
18785 TTTTTTTTTTC-ATTCTAAA-ATTCCTTCATTCCC
1 TTTTTTTTTTCAATTC-AAATA-CCCTTCATTCCC
18818 TCTTAATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 5 0.17
36 24 0.83
ACGTcount: A:0.20, C:0.28, G:0.00, T:0.52
Consensus pattern (36 bp):
TTTTTTTTTTCAATTCAAATACCCTTCATTCCCACA
Found at i:19189 original size:19 final size:20
Alignment explanation
Indices: 19143--19190 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
19133 TGTGGTACGC
*
19143 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
19165 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
19184 CACATGT
1 CACATGT
19191 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:19196 original size:53 final size:53
Alignment explanation
Indices: 19110--19212 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 53
19100 GACGTGGCAC
* **
19110 GCCACGTGTACCAAAAAGTGACATGTGGTACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGTACGCCACATGTACCAAAAAGTCGT
*
19163 GCCACATGTACCAAAAAGTGACACAT-GTCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGT-ACGCCACATGTACCAAAAAGT
19213 GACACGTGGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 2 0.04
53 43 0.96
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGTACGCCACATGTACCAAAAAGTCGT
Found at i:19240 original size:31 final size:31
Alignment explanation
Indices: 19162--19261 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 31
19152 CAAAAAGTCG
* * *
19162 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACGTGTACCAAAAAGTGACACGTGGCA
*
19193 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACGTGTACCAAAAAGTGACACGTGGCA
* * * *
19224 TGCCA-GATGTTTCAAAAAAATGGCACGTGGCA
1 TGCCACG-TG-TACCAAAAAGTGACACGTGGCA
19256 TGCCAC
1 TGCCAC
19262 ATGCACAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 1 0.02
31 33 0.58
32 23 0.40
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (31 bp):
TGCCACGTGTACCAAAAAGTGACACGTGGCA
Found at i:22258 original size:23 final size:23
Alignment explanation
Indices: 22232--22277 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
22222 GGTTCGGTGC
22232 GGCTCAACTCCGAAATTAATCGG
1 GGCTCAACTCCGAAATTAATCGG
22255 GGCTCAACTCCGAAATTAATCGG
1 GGCTCAACTCCGAAATTAATCGG
22278 AGCCCAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
GGCTCAACTCCGAAATTAATCGG
Found at i:31512 original size:16 final size:16
Alignment explanation
Indices: 31479--31512 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31469 CCCTAGAGAG
*
31479 ATTATGTTCTACCCTA
1 ATTATGTTCTACCATA
*
31495 ATTATGTTCTATCATA
1 ATTATGTTCTACCATA
31511 AT
1 AT
31513 CTTAAACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTATGTTCTACCATA
Found at i:34399 original size:18 final size:18
Alignment explanation
Indices: 34376--34412 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
34366 GCCACGTGTC
*
34376 TTCTATTTTTTTTCTTTT
1 TTCTATTTTTATTCTTTT
34394 TTCTATTTTTATTCTTTT
1 TTCTATTTTTATTCTTTT
34412 T
1 T
34413 AGTAAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (18 bp):
TTCTATTTTTATTCTTTT
Found at i:34439 original size:21 final size:21
Alignment explanation
Indices: 34415--34468 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
34405 TTCTTTTTAG
34415 TAAGTTTAGCCCTAATTTCAC
1 TAAGTTTAGCCCTAATTTCAC
*
34436 TAAGTTTAACCCTAATTTCAC
1 TAAGTTTAGCCCTAATTTCAC
34457 TAAGTTTAGCCC
1 TAAGTTTAGCCC
34469 CAAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (21 bp):
TAAGTTTAGCCCTAATTTCAC
Found at i:38584 original size:14 final size:14
Alignment explanation
Indices: 38565--38611 Score: 76
Period size: 14 Copynumber: 3.2 Consensus size: 14
38555 TAACTCATAC
38565 ACCTACAACTTCTA
1 ACCTACAACTTCTA
38579 ACCTACAACTTCATA
1 ACCTACAACTTC-TA
38594 CACCTACAACTTCTA
1 -ACCTACAACTTCTA
38609 ACC
1 ACC
38612 ATTATGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 15 0.48
15 4 0.13
16 12 0.39
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (14 bp):
ACCTACAACTTCTA
Found at i:38600 original size:16 final size:16
Alignment explanation
Indices: 38559--38606 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
38549 CTGTCATAAC
38559 TCATACACCTACAACT
1 TCATACACCTACAACT
38575 TC-TA-ACCTACAACT
1 TCATACACCTACAACT
38589 TCATACACCTACAACT
1 TCATACACCTACAACT
38605 TC
1 TC
38607 TAACCATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 12 0.40
15 4 0.13
16 14 0.47
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.27
Consensus pattern (16 bp):
TCATACACCTACAACT
Found at i:38934 original size:27 final size:27
Alignment explanation
Indices: 38904--38985 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
38894 CATTTGACTT
38904 ACAATTTATGAAAGATCTCATTGGCTA
1 ACAATTTATGAAAGATCTCATTGGCTA
** * ** *
38931 ACAA-CCACT-ATA-AT-TCATTGAATC
1 ACAATTTA-TGAAAGATCTCATTGGCTA
38955 ACAATTTATGAAAGATCTCATTGGCTA
1 ACAATTTATGAAAGATCTCATTGGCTA
38982 ACAA
1 ACAA
38986 CCACTATAAT
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
24 12 0.32
25 5 0.13
26 5 0.13
27 16 0.42
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.30
Consensus pattern (27 bp):
ACAATTTATGAAAGATCTCATTGGCTA
Found at i:38948 original size:24 final size:24
Alignment explanation
Indices: 38921--39001 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
38911 ATGAAAGATC
38921 TCATTGGCTAACAACCACTATAAT
1 TCATTGGCTAACAACCACTATAAT
** * ** *
38945 TCATTGAATCACAATTTA-TGAAAGAT
1 TCATTGGCTAACAA-CCACT-ATA-AT
38971 CTCATTGGCTAACAACCACTATAAT
1 -TCATTGGCTAACAACCACTATAAT
38996 TCATTG
1 TCATTG
39002 AATCATTGCC
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
24 18 0.45
25 5 0.12
26 5 0.12
27 12 0.30
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (24 bp):
TCATTGGCTAACAACCACTATAAT
Found at i:38980 original size:51 final size:51
Alignment explanation
Indices: 38904--39006 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
38894 CATTTGACTT
38904 ACAATTTATGAAAGATCTCATTGGCTAACAACCACTATAATTCATTGAATC
1 ACAATTTATGAAAGATCTCATTGGCTAACAACCACTATAATTCATTGAATC
38955 ACAATTTATGAAAGATCTCATTGGCTAACAACCACTATAATTCATTGAATC
1 ACAATTTATGAAAGATCTCATTGGCTAACAACCACTATAATTCATTGAATC
39006 A
1 A
39007 TTGCCTAAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (51 bp):
ACAATTTATGAAAGATCTCATTGGCTAACAACCACTATAATTCATTGAATC
Found at i:43698 original size:31 final size:31
Alignment explanation
Indices: 43654--43827 Score: 163
Period size: 31 Copynumber: 5.5 Consensus size: 31
43644 GACGTGATAT
*
43654 GCCACATGTACCAAAAAGTGACATGTGGCAC
1 GCCACGTGTACCAAAAAGTGACATGTGGCAC
* *
43685 GCTACGTGTACCAAAAAAGTGACACATGTAATGCA-
1 GCCACGTGTACC-AAAAAGTG--ACATGT--GGCAC
* * *
43720 GCCATGTGTACAAAAAAGTGACATGTGACAC
1 GCCACGTGTACCAAAAAGTGACATGTGGCAC
* *
43751 GCCACGTGTACCAAAAAGTGACACGTGGCAT
1 GCCACGTGTACCAAAAAGTGACATGTGGCAC
* ** * *
43782 GCCACATGTTTCAAAAAGTGACACGTGGCAT
1 GCCACGTGTACCAAAAAGTGACATGTGGCAC
*
43813 GCCACATGTA-CAAAA
1 GCCACGTGTACCAAAA
43828 GGATACGTGT
Statistics
Matches: 120, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
30 7 0.06
31 73 0.61
32 14 0.12
34 14 0.12
35 9 0.08
36 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (31 bp):
GCCACGTGTACCAAAAAGTGACATGTGGCAC
Found at i:56203 original size:26 final size:26
Alignment explanation
Indices: 56174--56263 Score: 153
Period size: 26 Copynumber: 3.5 Consensus size: 26
56164 GTTGTATAAC
*
56174 CAAGTTGCTGCATGGACGATGATCTT
1 CAAGTTGCTGCATGGATGATGATCTT
*
56200 CAAGTTGCTGCATGGATGTTGATCTT
1 CAAGTTGCTGCATGGATGATGATCTT
*
56226 CAAGTTGCTACATGGATGATGATCTT
1 CAAGTTGCTGCATGGATGATGATCTT
56252 CAAGTTGCTGCA
1 CAAGTTGCTGCA
56264 AGTGCATGGC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (26 bp):
CAAGTTGCTGCATGGATGATGATCTT
Found at i:64783 original size:15 final size:15
Alignment explanation
Indices: 64735--64784 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
64725 GCTTTTCACC
64735 TTTTTCTTGTTTATA
1 TTTTTCTTGTTTATA
*
64750 TTTTT-TT-TTGAGGTAA
1 TTTTTCTTGTTTA--T-A
64766 TTTTTCTTGTTTATA
1 TTTTTCTTGTTTATA
64781 TTTT
1 TTTT
64785 AATTTTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.11
14 2 0.07
15 11 0.39
16 7 0.25
17 2 0.07
18 3 0.11
ACGTcount: A:0.14, C:0.04, G:0.10, T:0.72
Consensus pattern (15 bp):
TTTTTCTTGTTTATA
Found at i:66471 original size:2 final size:2
Alignment explanation
Indices: 66466--66495 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
66456 TGACAATTAC
66466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66496 TACTTGAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78626 original size:25 final size:26
Alignment explanation
Indices: 78572--78627 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
78562 GCCCGCACAT
*
78572 ATTT-AATTTTTAAAATAAAATGATA
1 ATTTAAATTTTTAAAATAAAATGAAA
78597 A-TTAAATTTTTAATAA-AAAAT-AAA
1 ATTTAAATTTTTAA-AATAAAATGAAA
78621 ATTTAAA
1 ATTTAAA
78628 CATTAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 5 0.19
25 20 0.74
26 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
ATTTAAATTTTTAAAATAAAATGAAA
Found at i:78774 original size:24 final size:24
Alignment explanation
Indices: 78729--78775 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
78719 AATGTATACA
* *
78729 TATAAATTATTTAATTTTATTATG
1 TATAAATTAATTAATTTAATTATG
78753 TATAAATATAATTAA-TTAATTAT
1 TATAAAT-TAATTAATTTAATTAT
78776 ATTATACTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TATAAATTAATTAATTTAATTATG
Found at i:78778 original size:29 final size:30
Alignment explanation
Indices: 78720--78780 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
78710 GTTCTAATTA
* * *
78720 ATGTATACATATAAATTATTTAATTTTATT
1 ATGTATAAATATAAATTAATTAATTATATT
78750 ATGTATAAATAT-AATTAATTAATTATATT
1 ATGTATAAATATAAATTAATTAATTATATT
78779 AT
1 AT
78781 ACTCCATCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTAATTAATTATATT
Found at i:92470 original size:38 final size:38
Alignment explanation
Indices: 92427--92499 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
92417 AAACATAAAT
92427 AACAAGAGTATTGTTACATGACCCTCCAACTTGTCAGG
1 AACAAGAGTATTGTTACATGACCCTCCAACTTGTCAGG
*
92465 AACAAGAGTATTGTTACATGACCGTCCAACTTGTC
1 AACAAGAGTATTGTTACATGACCCTCCAACTTGTC
92500 CCTCTTGACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (38 bp):
AACAAGAGTATTGTTACATGACCCTCCAACTTGTCAGG
Found at i:92735 original size:16 final size:16
Alignment explanation
Indices: 92714--92747 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
92704 GAATTATCCA
92714 AATAACAAAGGTCACT
1 AATAACAAAGGTCACT
92730 AATAACAAAGGTCACT
1 AATAACAAAGGTCACT
92746 AA
1 AA
92748 ACTTTTCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (16 bp):
AATAACAAAGGTCACT
Found at i:93225 original size:12 final size:12
Alignment explanation
Indices: 93208--93238 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
93198 GTTATATGAG
93208 TAAATTTTCAAA
1 TAAATTTTCAAA
93220 TAAATTTTCAAA
1 TAAATTTTCAAA
*
93232 GAAATTT
1 TAAATTT
93239 CAGTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (12 bp):
TAAATTTTCAAA
Found at i:93447 original size:2 final size:2
Alignment explanation
Indices: 93440--93466 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
93430 GGGATAAATG
93440 AT 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 AT A
93467 AATCTAACTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94733 original size:19 final size:20
Alignment explanation
Indices: 94687--94734 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
94677 TGTGGCACGC
*
94687 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
94709 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
94728 CACATGT
1 CACATGT
94735 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:94739 original size:53 final size:53
Alignment explanation
Indices: 94654--94756 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
94644 GAGGTGGCAC
* **
94654 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* *
94707 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
94757 GACACGTGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:94828 original size:31 final size:31
Alignment explanation
Indices: 94706--94830 Score: 133
Period size: 31 Copynumber: 4.0 Consensus size: 31
94696 CAAAAAGTCG
** * * *
94706 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTTTCAAAAAATGACACGTGGCA
* * ** * *
94737 CGCCACGTGTACCAAAAAGTGACACGTGGTA
1 TGCCACATGTTTCAAAAAATGACACGTGGCA
*
94768 TGCCACATGTTTCAAAAAATGTCACGTGGCA
1 TGCCACATGTTTCAAAAAATGACACGTGGCA
*
94799 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTTTCAAAAAATGACACGTGGCA
94830 T
1 T
94831 CCATGTGCAC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 81 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (31 bp):
TGCCACATGTTTCAAAAAATGACACGTGGCA
Found at i:96917 original size:2 final size:2
Alignment explanation
Indices: 96910--96948 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
96900 TGCTTATTAT
96910 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
96949 GTAGGACGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:101142 original size:24 final size:24
Alignment explanation
Indices: 101110--101158 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
101100 CTCCCCATTC
*
101110 ATCATAATCCCTCTCA-AATCTCGG
1 ATCATAATCCCTAT-AGAATCTCGG
101134 ATCATAATCCCTATAGAATCTCGG
1 ATCATAATCCCTATAGAATCTCGG
101158 A
1 A
101159 CACGGTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.29
Consensus pattern (24 bp):
ATCATAATCCCTATAGAATCTCGG
Found at i:104553 original size:39 final size:39
Alignment explanation
Indices: 104497--104574 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
104487 TATCGTTAAG
104497 ATTTTCCAGACCATGTTTCTTCATGATCTAAATCCCAAA
1 ATTTTCCAGACCATGTTTCTTCATGATCTAAATCCCAAA
* *
104536 ATTTTCCATACCTTGTTTCTTCATGATCTAAATCCCAAA
1 ATTTTCCAGACCATGTTTCTTCATGATCTAAATCCCAAA
104575 TGCAAATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (39 bp):
ATTTTCCAGACCATGTTTCTTCATGATCTAAATCCCAAA
Found at i:104673 original size:27 final size:27
Alignment explanation
Indices: 104641--104693 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
104631 TGGACGTAGT
*
104641 TTGTATATGCGATTTCTTATTGAATTG
1 TTGTATATGCGATTTCTTATTCAATTG
* *
104668 TTGTATTTGTGATTTCTTATTCAATT
1 TTGTATATGCGATTTCTTATTCAATT
104694 ATTTTGAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.57
Consensus pattern (27 bp):
TTGTATATGCGATTTCTTATTCAATTG
Found at i:106258 original size:13 final size:13
Alignment explanation
Indices: 106240--106267 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
106230 ATTTTCAGTA
106240 ATTAATATGTTAT
1 ATTAATATGTTAT
106253 ATTAATATGTTAT
1 ATTAATATGTTAT
106266 AT
1 AT
106268 AATCTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (13 bp):
ATTAATATGTTAT
Found at i:106316 original size:28 final size:26
Alignment explanation
Indices: 106285--106346 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 26
106275 TTATTTTAGA
*
106285 CAAACTCTTAACCATTTTTAATCTCAAC
1 CAAACTCTT--CCAATTTTAATCTCAAC
106313 CAAACTC--CCAATTTTAATCTCAAC
1 CAAACTCTTCCAATTTTAATCTCAAC
*
106337 CAATCTCTTC
1 CAAACTCTTC
106347 AAGATTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 22 0.73
26 1 0.03
28 7 0.23
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (26 bp):
CAAACTCTTCCAATTTTAATCTCAAC
Found at i:106553 original size:24 final size:24
Alignment explanation
Indices: 106525--106573 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
106515 TTGATTAATT
106525 ATATACAAAACGGATTAAATTTTA
1 ATATACAAAACGGATTAAATTTTA
106549 ATATACAAAACGGATTAAATTTTA
1 ATATACAAAACGGATTAAATTTTA
106573 A
1 A
106574 ATTTGAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (24 bp):
ATATACAAAACGGATTAAATTTTA
Found at i:106671 original size:24 final size:24
Alignment explanation
Indices: 106644--106696 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
106634 TTTGATAATT
106644 ATATACAAAACAGATTAAATTTTA
1 ATATACAAAACAGATTAAATTTTA
*
106668 ATATACAAAACGGATTAAATTTTA
1 ATATACAAAACAGATTAAATTTTA
106692 ATATA
1 ATATA
106697 GATAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.34
Consensus pattern (24 bp):
ATATACAAAACAGATTAAATTTTA
Found at i:107844 original size:2 final size:2
Alignment explanation
Indices: 107833--107879 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
107823 ACACACACAC
*
107833 AT AT AC AT AT AT A- AT AT -T AT -T AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
107871 AT AT AT AT A
1 AT AT AT AT A
107880 ATGTGGTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:107859 original size:15 final size:17
Alignment explanation
Indices: 107833--107877 Score: 67
Period size: 15 Copynumber: 2.8 Consensus size: 17
107823 ACACACACAC
*
107833 ATATACATATATAATAT
1 ATATATATATATAATAT
107850 -TAT-TATATATAATAT
1 ATATATATATATAATAT
107865 ATATATATATATA
1 ATATATATATATA
107878 TAATGTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 11 0.44
16 6 0.24
17 8 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATAATAT
Found at i:107969 original size:17 final size:17
Alignment explanation
Indices: 107947--107980 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
107937 TCAAAGGACC
107947 ATGTTAATTAAGGGGAG
1 ATGTTAATTAAGGGGAG
107964 ATGTTAATTAAGGGGAG
1 ATGTTAATTAAGGGGAG
107981 GAGGAGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (17 bp):
ATGTTAATTAAGGGGAG
Found at i:109380 original size:126 final size:125
Alignment explanation
Indices: 109156--109413 Score: 446
Period size: 126 Copynumber: 2.1 Consensus size: 125
109146 TCTACCGTCA
*
109156 GTGGAGTTTAACAGATTGCACTTGAGGTCTAGAAGGGTGACATGTCTCCTCTTACGGACTAGATT
1 GTGGAGTTTAACAGACTGCACTTGAGGTCTAGAAGGGTGACATGTCTCCTCTTACGGACTAGATT
*
109221 GAAATATTACAAATCTAATCAATTCTGAAATGAGGTATCTGTCAACATTTTAATCC-ATCT
66 GAAATATTACAAATCTAATCAATTCTGAAATGAGATATCTGTCAACATTTTAA-CCAATCT
* *
109281 GTGGAGTTTAACAGACTGCACTTGAGGGTTTAGAAGGGTGACATGTCTCCTCTTAGGGACTAGAT
1 GTGGAGTTTAACAGACTGCACTTGA-GGTCTAGAAGGGTGACATGTCTCCTCTTACGGACTAGAT
*
109346 TGAAATATTACAAATCTAATCAATTCTGAAATGAGATATTTGTCAACATTTTAACCAATCT
65 TGAAATATTACAAATCTAATCAATTCTGAAATGAGATATCTGTCAACATTTTAACCAATCT
109407 GTGGAGT
1 GTGGAGT
109414 CCAAAAACTC
Statistics
Matches: 126, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
125 26 0.21
126 100 0.79
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33
Consensus pattern (125 bp):
GTGGAGTTTAACAGACTGCACTTGAGGTCTAGAAGGGTGACATGTCTCCTCTTACGGACTAGATT
GAAATATTACAAATCTAATCAATTCTGAAATGAGATATCTGTCAACATTTTAACCAATCT
Found at i:112235 original size:15 final size:16
Alignment explanation
Indices: 112190--112242 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
112180 GATAGTTTCA
112190 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
112206 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
*
112222 T-GGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
112237 TCGGGT
1 TCGGGT
112243 TTTCGGTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 13 0.39
16 20 0.61
ACGTcount: A:0.06, C:0.15, G:0.40, T:0.40
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:112241 original size:38 final size:38
Alignment explanation
Indices: 112198--112281 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
112188 CATCGGGTCA
* * *
112198 TTCGGGTTTCGGGTCATCTGGGTTT-GGGTTATTCGGGT
1 TTCGGGTTTC-GGTCATATGGGTTTCGAGTCATTCGGGT
112236 TTCGGGTTTTCGGTCATATGGGTTTCGAGTCATTCGGGT
1 TTCGGG-TTTCGGTCATATGGGTTTCGAGTCATTCGGGT
*
112275 CTCGGGT
1 TTCGGGT
112282 CTACCGGGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
38 20 0.50
39 20 0.50
ACGTcount: A:0.07, C:0.15, G:0.37, T:0.40
Consensus pattern (38 bp):
TTCGGGTTTCGGTCATATGGGTTTCGAGTCATTCGGGT
Found at i:112247 original size:15 final size:15
Alignment explanation
Indices: 112198--112248 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
112188 CATCGGGTCA
*
112198 TTCGGGTTTCGGGTC
1 TTCGGGTTTCGGGTT
*
112213 ATCTGGGTTT-GGGTT
1 TTC-GGGTTTCGGGTT
112228 ATTCGGGTTTCGGGTT
1 -TTCGGGTTTCGGGTT
112244 TTCGG
1 TTCGG
112249 TCATATGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.04, C:0.14, G:0.39, T:0.43
Consensus pattern (15 bp):
TTCGGGTTTCGGGTT
Found at i:112271 original size:39 final size:39
Alignment explanation
Indices: 112198--112281 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
112188 CATCGGGTCA
* * *
112198 TTCGGG-TTTCGGGTCATCTGGGTTTGGGTTATTCGGGT
1 TTCGGGTTTTCGGGTCATATGGGTTTGAGTCATTCGGGT
112236 TTCGGGTTTTC-GGTCATATGGGTTTCGAGTCATTCGGGT
1 TTCGGGTTTTCGGGTCATATGGGTTT-GAGTCATTCGGGT
*
112275 CTCGGGT
1 TTCGGGT
112282 CTACCGGGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 19 0.47
39 21 0.52
ACGTcount: A:0.07, C:0.15, G:0.37, T:0.40
Consensus pattern (39 bp):
TTCGGGTTTTCGGGTCATATGGGTTTGAGTCATTCGGGT
Found at i:112570 original size:42 final size:42
Alignment explanation
Indices: 112523--112604 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
112513 TAGATATTAA
*
112523 TTTTGAATATTAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
*
112565 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
112605 TGTGTCAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:113167 original size:16 final size:16
Alignment explanation
Indices: 113148--113192 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
113138 ATTGGCCATT
113148 CGGATCTCGGGTCATC
1 CGGATCTCGGGTCATC
113164 CGGAT-TGCGGGTCATC
1 CGGATCT-CGGGTCATC
*
113180 CGGGTCTCGGGTC
1 CGGATCTCGGGTC
113193 GGACAGGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (16 bp):
CGGATCTCGGGTCATC
Found at i:114923 original size:6 final size:6
Alignment explanation
Indices: 114912--114936 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
114902 GACATTGTTG
114912 GGGAGA GGGAGA GGGAGA GGGAGA G
1 GGGAGA GGGAGA GGGAGA GGGAGA G
114937 TCTTGTAGTT
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:116705 original size:44 final size:44
Alignment explanation
Indices: 116642--116727 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
116632 GTCATGAGTC
116642 TTGTTTCATCTATCTATAATCTATAAATATTATACTAGTTTATA
1 TTGTTTCATCTATCTATAATCTATAAATATTATACTAGTTTATA
116686 TTGTTTCATCTATCTATAATCTATAAATATTATACTAGTTTA
1 TTGTTTCATCTATCTATAATCTATAAATATTATACTAGTTTA
116728 AACTTTATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.50
Consensus pattern (44 bp):
TTGTTTCATCTATCTATAATCTATAAATATTATACTAGTTTATA
Found at i:116936 original size:20 final size:20
Alignment explanation
Indices: 116911--116948 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
116901 CAAATTTTAT
116911 TCTTCAATGCTATCTACAAA
1 TCTTCAATGCTATCTACAAA
116931 TCTTCAATGCTATCTACA
1 TCTTCAATGCTATCTACA
116949 CCTTAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (20 bp):
TCTTCAATGCTATCTACAAA
Found at i:119159 original size:11 final size:11
Alignment explanation
Indices: 119145--119182 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
119135 ATTCATAACA
119145 AATTTATAATT
1 AATTTATAATT
119156 AATTTATAATT
1 AATTTATAATT
119167 -ATTTGATAATT
1 AATTT-ATAATT
*
119178 TATTT
1 AATTT
119183 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:119679 original size:6 final size:6
Alignment explanation
Indices: 119629--119677 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
119619 TGATCTAATT
*
119629 TATCTA TATCTA TATCTA TGAATCTATA TATCTA TATCTA TATTTA TAT
1 TATCTA TATCTA TATCTA T--ATC--TA TATCTA TATCTA TATCTA TAT
119678 TTTGAATCGA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
6 29 0.76
8 6 0.16
10 3 0.08
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (6 bp):
TATCTA
Found at i:122366 original size:34 final size:34
Alignment explanation
Indices: 122324--122422 Score: 135
Period size: 34 Copynumber: 2.9 Consensus size: 34
122314 ACAAAAATTA
* * *
122324 TGACAACTTCTAGTGTCAAAATAATAATTTAATG
1 TGACAACTTCTGGTGTTAAAGTAATAATTTAATG
* * **
122358 TGATAACTTCTGGTATTAGGGTAATAATTTAATG
1 TGACAACTTCTGGTGTTAAAGTAATAATTTAATG
122392 TGACAACTTCTGGTGTTAAAGTAATAATTTA
1 TGACAACTTCTGGTGTTAAAGTAATAATTTA
122423 CTTAGAAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (34 bp):
TGACAACTTCTGGTGTTAAAGTAATAATTTAATG
Found at i:125403 original size:2 final size:2
Alignment explanation
Indices: 125396--125430 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
125386 CCTTACTGTG
125396 TA TA TA TA 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 TA TA TA TA T
125431 GATAAGATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:127255 original size:21 final size:22
Alignment explanation
Indices: 127229--127273 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
127219 ATATACTGAA
127229 TTGCTAAAT-ACCGTCCC-CTTT
1 TTGCT-AATCACCGTCCCACTTT
*
127250 TTGCTATTCACCGTCCCACTTT
1 TTGCTAATCACCGTCCCACTTT
127272 TT
1 TT
127274 ACACTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 13 0.62
22 6 0.29
ACGTcount: A:0.16, C:0.33, G:0.09, T:0.42
Consensus pattern (22 bp):
TTGCTAATCACCGTCCCACTTT
Found at i:138014 original size:16 final size:17
Alignment explanation
Indices: 137988--138021 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
137978 TGACTCATCT
*
137988 TGCTCTTCAAATTAAAA
1 TGCTCTTCAAATGAAAA
138005 TGCT-TTCAAATGAAAA
1 TGCTCTTCAAATGAAAA
138021 T
1 T
138022 ATGTTTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (17 bp):
TGCTCTTCAAATGAAAA
Done.