Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012497.1 Corchorus capsularis cultivar CVL-1 contig12518, 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: 78888
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4770 original size:30 final size:32
Alignment explanation
Indices: 4725--4790 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
4715 TGGTAATTTA
* *
4725 GAAATATGTTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGATTTTAAAAATAAGGGTACAATCG
4756 GAAATAT-ATTTTAAAAATAAGGGTACAATCG
1 GAAATATGATTTTAAAAATAAGGGTACAATCG
4787 GAAA
1 GAAA
4791 ACATAAAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (32 bp):
GAAATATGATTTTAAAAATAAGGGTACAATCG
Found at i:5017 original size:25 final size:22
Alignment explanation
Indices: 4981--5045 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
4971 CTCATACAGT
*
4981 AATTATCGAAATTTCATAGAGATCA
1 AATTATCAAAATTTCATAG-GA--A
5006 AATTATCAAAATTT-ATAGGAA
1 AATTATCAAAATTTCATAGGAA
* *
5027 GATTATCACAATTTCATAG
1 AATTATCAAAATTTCATAG
5046 TGTTGTTATC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 13 0.36
22 4 0.11
23 2 0.06
24 4 0.11
25 13 0.36
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (22 bp):
AATTATCAAAATTTCATAGGAA
Found at i:5031 original size:21 final size:23
Alignment explanation
Indices: 4982--5111 Score: 90
Period size: 22 Copynumber: 5.8 Consensus size: 23
4972 TCATACAGTA
* * *
4982 ATTATCGAAATTTCATAGAGATCAA
1 ATTATCAAAATTTCATAGTGA--AG
5007 ATTATCAAAATTT-ATAG-GAAG
1 ATTATCAAAATTTCATAGTGAAG
* **
5028 ATTATCACAATTTCATAGTGTTG
1 ATTATCAAAATTTCATAGTGAAG
* *
5051 -TTATCAAAATTTCAAAGCG-AG
1 ATTATCAAAATTTCATAGTGAAG
* * * *
5072 GTTATCAAAATTACATAATG-TG
1 ATTATCAAAATTTCATAGTGAAG
*
5094 ATTATCAGAATTTCATAG
1 ATTATCAAAATTTCATAG
5112 AGGGGTCAAC
Statistics
Matches: 84, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
21 14 0.17
22 50 0.60
23 4 0.05
24 4 0.05
25 12 0.14
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (23 bp):
ATTATCAAAATTTCATAGTGAAG
Found at i:5054 original size:22 final size:21
Alignment explanation
Indices: 5008--5201 Score: 92
Period size: 22 Copynumber: 8.9 Consensus size: 21
4998 AGAGATCAAA
*
5008 TTATCAAAATTT-ATAG-GAAG
1 TTATCAAAATTTCATAGTG-TG
*
5028 ATTATCACAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAGTG-TG
* * *
5051 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTG-TG
* *
5073 TTATCAAAATTACATAATGTG
1 TTATCAAAATTTCATAGTGTG
* * *
5094 ATTATCAGAATTTCATAGAGGGG
1 -TTATCAAAATTTCATAG-TGTG
* * *
5117 TCAACAAAATTTTATAAAGTG-G
1 TTATCAAAATTTCAT--AGTGTG
*
5139 TTATCAAAATTTCATAAAGAG-G
1 TTATCAAAATTTCAT--AGTGTG
* * *
5161 TTATCAAATTTTCAAAATGTG
1 TTATCAAAATTTCATAGTGTG
5182 ATTA-CAAAAATTTCATAGTG
1 -TTATC-AAAATTTCATAGTG
5202 GTATATCTGG
Statistics
Matches: 130, Mismatches: 34, Indels: 17
0.72 0.19 0.09
Matches are distributed among these distances:
20 2 0.02
21 14 0.11
22 107 0.82
23 5 0.04
24 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGTGTG
Found at i:5100 original size:44 final size:44
Alignment explanation
Indices: 5007--5196 Score: 165
Period size: 44 Copynumber: 4.3 Consensus size: 44
4997 TAGAGATCAA
* * * *
5007 ATTATCAAAATTT-ATAG-GAAGATTATCACAATTTCATAGTGTTG
1 ATTATCAAAATTTCAAAGAG-AGGTTATCAAAATTTCATAATG-TG
* *
5051 -TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTG
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
* * * * * * *
5094 ATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGTG
1 ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
* * *
5138 GTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTG
1 ATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGTG
5182 ATTA-CAAAAATTTCA
1 ATTATC-AAAATTTCA
5197 TAGTGGTATA
Statistics
Matches: 116, Mismatches: 25, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
43 15 0.13
44 99 0.85
45 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (44 bp):
ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGTG
Found at i:5125 original size:66 final size:66
Alignment explanation
Indices: 5027--5155 Score: 152
Period size: 66 Copynumber: 2.0 Consensus size: 66
5017 TTTATAGGAA
* ** * * *
5027 GATTATCACAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAAT
1 GATTATCACAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAAT
5091 GT
65 GT
* * * *
5093 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGTGGTTATCAAAATTTCATAA
1 GATTATCACAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAA
5156 AGAGGTTATC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (66 bp):
GATTATCACAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
T
Found at i:5353 original size:22 final size:22
Alignment explanation
Indices: 5298--5416 Score: 75
Period size: 22 Copynumber: 5.4 Consensus size: 22
5288 TCAGGGACAA
* ***
5298 TATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAATAGGGT
*
5320 TTTCAAAAATTTCATAATAGGGT
1 TATC-AAAATTTCATAATAGGGT
* *
5343 TATCAAAATTTCATAGTA-TGT
1 TATCAAAATTTCATAATAGGGT
* *
5364 AGATCAAAATTTCAT-A-GGGAGAT
1 -TATCAAAATTTCATAATAGG-G-T
*
5387 TAACAAAATTTCATAAT-GAGGT
1 TATCAAAATTTCATAATAG-GGT
5409 TATCAAAA
1 TATCAAAA
5417 AATCATAAGG
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
21 2 0.03
22 50 0.68
23 21 0.28
24 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAATAGGGT
Found at i:5822 original size:41 final size:41
Alignment explanation
Indices: 5771--5886 Score: 106
Period size: 50 Copynumber: 2.6 Consensus size: 41
5761 TGATAATTGT
5771 CATAATTATCTTTAAAGATAATATGACTAATAAATATAATC
1 CATAATTATCTTTAAAGATAATATGACTAATAAATATAATC
**
5812 CATAATTATCTCTAATATTTATGTAGATAATATGGTTAATAAATATAATC
1 CATAATTATCT-T--TA---A---AGATAATATGACTAATAAATATAATC
* **
5862 CATAATTATCTCTATGGATAATATG
1 CATAATTATCTTTAAAGATAATATG
5887 GTAAATTATA
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
41 20 0.33
42 1 0.02
44 2 0.03
47 3 0.05
50 35 0.57
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (41 bp):
CATAATTATCTTTAAAGATAATATGACTAATAAATATAATC
Found at i:6575 original size:17 final size:17
Alignment explanation
Indices: 6553--6610 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
6543 TCAACAACAT
6553 GTATTACCAGTCAAAAG
1 GTATTACCAGTCAAAAG
* * *
6570 GTATTACCA-ACAACAT
1 GTATTACCAGTCAAAAG
* * *
6586 GTATTACCAGTTACAGG
1 GTATTACCAGTCAAAAG
6603 GTATTACC
1 GTATTACC
6611 TATAACATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 13 0.42
17 18 0.58
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (17 bp):
GTATTACCAGTCAAAAG
Found at i:6591 original size:16 final size:16
Alignment explanation
Indices: 6538--6594 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
6528 GTTCATAGGA
*
6538 TATTATCAACAACATG
1 TATTACCAACAACATG
* * *
6554 TATTACCAGTCAAAAGG
1 TATTACCA-ACAACATG
6571 TATTACCAACAACATG
1 TATTACCAACAACATG
6587 TATTACCA
1 TATTACCA
6595 GTTACAGGGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
16 20 0.61
17 13 0.39
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (16 bp):
TATTACCAACAACATG
Found at i:6618 original size:33 final size:33
Alignment explanation
Indices: 6538--6610 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
6528 GTTCATAGGA
*
6538 TATTATCAACAACATGTATTACCAGTCAAAAGG
1 TATTACCAACAACATGTATTACCAGTCAAAAGG
* * *
6571 TATTACCAACAACATGTATTACCAGTTACAGGG
1 TATTACCAACAACATGTATTACCAGTCAAAAGG
6604 TATTACC
1 TATTACC
6611 TATAACATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (33 bp):
TATTACCAACAACATGTATTACCAGTCAAAAGG
Found at i:6668 original size:30 final size:31
Alignment explanation
Indices: 6601--6674 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
6591 ACCAGTTACA
*
6601 GGGTATTACCTATAACATATGTAACCAAGTG
1 GGGTATTACCTGTAACATATGTAACCAAGTG
* * *
6632 GGGTATTACCTGTAACGTGTGTAACCACGT-
1 GGGTATTACCTGTAACATATGTAACCAAGTG
6662 GGGTATTACCTGT
1 GGGTATTACCTGT
6675 TGCAGGGTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 13 0.33
31 26 0.67
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (31 bp):
GGGTATTACCTGTAACATATGTAACCAAGTG
Found at i:8813 original size:41 final size:41
Alignment explanation
Indices: 8762--8904 Score: 126
Period size: 50 Copynumber: 3.2 Consensus size: 41
8752 TGATAATGGT
*
8762 CATAATTATCTTTAAAGATAATATGACTAATAAATATAATC
1 CATAATTATCTTTAAAGATAATATGATTAATAAATATAATC
*
8803 CATAATTATCTCTAATATTTATGTAGATAATATGGTTAATAAATATAATC
1 CATAATTATCT-T--TA---A---AGATAATATGATTAATAAATATAATC
* ** *
8853 CATAATTATCTCTATGGATAATATGATTAAT-TATATAATCAC
1 CATAATTATCTTTAAAGATAATATGATTAATAAATATAAT--C
8895 CATAATTATC
1 CATAATTATC
8905 CCATAAATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
40 7 0.08
41 25 0.30
42 12 0.14
44 2 0.02
47 3 0.04
50 35 0.42
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.40
Consensus pattern (41 bp):
CATAATTATCTTTAAAGATAATATGATTAATAAATATAATC
Found at i:9415 original size:23 final size:22
Alignment explanation
Indices: 9367--9570 Score: 90
Period size: 22 Copynumber: 9.2 Consensus size: 22
9357 TCAATATATA
* * *
9367 TCATAAGGAGGTTATCAACATC
1 TCATAGGGAGGTTATCAAAATT
**
9389 TCATAGTGTTGGTTATCAAAATT
1 TCATAG-GGAGGTTATCAAAATT
* *
9412 TCATTGGGAAGTTATCAAAATT
1 TCATAGGGAGGTTATCAAAATT
** *
9434 TCATATTGAGGTCT-TGAAAATT
1 TCATAGGGAGGT-TATCAAAATT
* * *
9456 CCTTAGGGAGGTTAACAAAATT
1 TCATAGGGAGGTTATCAAAATT
* * ** *
9478 TCATAAGAAGGTTAAAAAAAAT
1 TCATAGGGAGGTTATCAAAATT
* *** *
9500 TAATAAAAAGGTTCT-AGAAATT
1 TCATAGGGAGGTTATCA-AAATT
* * ** *
9522 CCATA-GTATCATTATTAAAATT
1 TCATAGGGA-GGTTATCAAAATT
*
9544 TCATAGGAAGGTTATCAAAATT
1 TCATAGGGAGGTTATCAAAATT
9566 TCATA
1 TCATA
9571 ATGGAGTCAT
Statistics
Matches: 132, Mismatches: 43, Indels: 14
0.70 0.23 0.07
Matches are distributed among these distances:
21 3 0.02
22 108 0.82
23 21 0.16
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATAGGGAGGTTATCAAAATT
Found at i:10730 original size:67 final size:67
Alignment explanation
Indices: 10570--10970 Score: 348
Period size: 68 Copynumber: 6.0 Consensus size: 67
10560 AAATTGCCAG
* * * * * * * * *
10570 TAAACTCAAATGCGAAAATGAAGAAACTGACCCTTTC-ACTGAAGGGGCATTTTTTGAAGA-TAA
1 TAAACTTAAATGC-AAAAAGAAGAAAATGACCC-TTCGACCGAAAGGGTATTTTTGGAAAACAAA
10633 A-AC
64 ATAC
* * * * * **
10636 TAAACTTTAGATGCAAAAAGACA-AAAATAACCCTTCGATCGGAAGGTTATTTTTGGAAATGAAA
1 TAAAC-TTAAATGCAAAAAGA-AGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAACAAA
*
10700 ATGC
64 ATAC
* * * * * *
10704 TAAATTTAAATGCGAAAAGAAGAAAATGACCCTTTGACCGAAAGGGGTA-TTCTAGAAAAGAAAA
1 TAAACTTAAATGCAAAAAGAAGAAAATGACCCTTCGACCGAAA-GGGTATTTTTGGAAAACAAAA
10768 TAC
65 TAC
* * *
10771 TAAAATTAAATGCAAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGGAAAACAAAA
1 TAAACTTAAATGCAAAAAGAAGAAAATGACCCTTCGACCGAAAGGGTATTTTT-GGAAAACAAAA
10836 TAC
65 TAC
** * * ** *
10839 TAAACCAAAACGCAGAAAGGCGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAACAAAA
1 TAAACTTAAATGCAAAAAGAAGAAAATGACCCTTCGACCGAAAGGGTATTTTTGG-AAAACAAAA
*
10904 TGC
65 TAC
* *
10907 TAAACTTAAATGCGGAAAA-AAGAAAATGACCCTTTGACCGAAAGGGGTATTTTTGGAAAA-AAA
1 TAAACTTAAATGC-AAAAAGAAGAAAATGACCCTTCGACCGAAA-GGGTATTTTTGGAAAACAAA
10970 A
64 A
10971 CAAAATTAAA
Statistics
Matches: 271, Mismatches: 52, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
65 3 0.01
66 39 0.14
67 101 0.37
68 113 0.42
69 15 0.06
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (67 bp):
TAAACTTAAATGCAAAAAGAAGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAACAAAAT
AC
Found at i:10786 original size:134 final size:134
Alignment explanation
Indices: 10577--10825 Score: 308
Period size: 134 Copynumber: 1.9 Consensus size: 134
10567 CAGTAAACTC
* * * * *
10577 AAATGCGAAAATGAAGAAACTGACCCTTTCACTGAAGGGGCATTTTTTGAAGATAAAACTAAACT
1 AAATGCGAAAATGAAGAAAATGACCCTTTCACCGAAGGGGCATTTCTAGAAGATAAAACTAAACA
* * * * *
10642 TTAGATGCAAAAAGACAAAAATAACCCTTCGATCGGAAGGTTATTTTTGGAAATGAAAATGCTAA
66 TTAAATGCAAAAAGACAAAAATAACCCTTCCACCGAAAGGGTATTTTTGGAAATGAAAATGCTAA
10707 ATTT
131 ATTT
* *
10711 AAATGCGAAAA-GAAGAAAATGACCCTTTGACCGAAAGGGGTA-TTCTAGAAAAGA-AAATACTA
1 AAATGCGAAAATGAAGAAAATGACCCTTTCACCG-AAGGGGCATTTCTAG--AAGATAAA-ACTA
* *
10773 AA-ATTAAATGCAAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGG
62 AACATTAAATGCAAAAAGACAAAAATAACCCTTCCACCGAAAGGGTATTTTTGG
10826 GAAAACAAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
133 23 0.24
134 64 0.66
135 10 0.10
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (134 bp):
AAATGCGAAAATGAAGAAAATGACCCTTTCACCGAAGGGGCATTTCTAGAAGATAAAACTAAACA
TTAAATGCAAAAAGACAAAAATAACCCTTCCACCGAAAGGGTATTTTTGGAAATGAAAATGCTAA
ATTT
Found at i:10965 original size:136 final size:134
Alignment explanation
Indices: 10646--10970 Score: 329
Period size: 135 Copynumber: 2.4 Consensus size: 134
10636 TAAACTTTAG
* * * * * * * * **
10646 ATGCAAAAAGACAAAAATAACCCTTCGATCGGAAGGTTATTTTT-GGAAATGAAAATGCTAAATT
1 ATGCAAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGGAAA-AAAAATACTAAACC
* * ** ** *
10710 TAAATGC-GAAAAGAAGAAAATGACCCTTTGACCGAAAGGGGTATTCTAGAAAAGAAAATACTAA
65 AAAACGCAG-AAAGGCGAAAATGACCCTTCCACCGAAAGGGGTATTCTAGAAAACAAAATACTAA
10774 AATTAA
129 AATTAA
10780 ATGCAAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGGAAAACAAAATACTAAACC
1 ATGCAAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGGAAAA-AAAATACTAAACC
* * *
10845 AAAACGCAGAAAGGCGAAAATGACCCTTCCACCGAAA-GGGTATTTTTGGAAAAACAAAATGCTA
65 AAAACGCAGAAAGGCGAAAATGACCCTTCCACCGAAAGGGGTA-TTCTAG-AAAACAAAATACTA
*
10909 AACTTAA
128 AAATTAA
**
10916 ATGCGGAAAAA-A-GAAAATGACCCTTTGACCGAAAGGGGTATTTTT-GGAAAAAAAA
1 ATGC--AAAAAGACGAAAATGACCCTTCCACCGAAA-GGGTATTTTTGGGAAAAAAAA
10971 CAAAATTAAA
Statistics
Matches: 160, Mismatches: 23, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
134 43 0.27
135 52 0.32
136 49 0.31
137 11 0.07
138 5 0.03
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.21
Consensus pattern (134 bp):
ATGCAAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGGAAAAAAAATACTAAACCA
AAACGCAGAAAGGCGAAAATGACCCTTCCACCGAAAGGGGTATTCTAGAAAACAAAATACTAAAA
TTAA
Found at i:16280 original size:20 final size:17
Alignment explanation
Indices: 16239--16270 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16229 AACGAAAAAG
16239 ATTTTTATTTATTTTAA
1 ATTTTTATTTATTTTAA
16256 A-TTTTATTTATTTTA
1 ATTTTTATTTATTTTA
16271 TTGAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 14 0.93
17 1 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTATTTATTTTAA
Found at i:17581 original size:23 final size:22
Alignment explanation
Indices: 17542--17586 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
17532 AATGAAAATG
*
17542 ATTCTTTCTAAAAAAAATTAGT
1 ATTCTTTCTAAAAAAAAATAGT
17564 ATTCTTTCTAAAAAAAAAATAGT
1 ATTCTTTCT-AAAAAAAAATAGT
17587 CAAATCATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (22 bp):
ATTCTTTCTAAAAAAAAATAGT
Found at i:18084 original size:17 final size:17
Alignment explanation
Indices: 18062--18096 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
18052 TATTTTCAGA
*
18062 TTCAGGTTCGGGTTTTT
1 TTCAGGTTCGGATTTTT
18079 TTCAGGTTCGGATTTTT
1 TTCAGGTTCGGATTTTT
18096 T
1 T
18097 CGGATTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.09, C:0.11, G:0.26, T:0.54
Consensus pattern (17 bp):
TTCAGGTTCGGATTTTT
Found at i:18096 original size:16 final size:17
Alignment explanation
Indices: 18062--18097 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
18052 TATTTTCAGA
*
18062 TTCAGGTTCGGGTTTTT
1 TTCAGGTTCGGGATTTT
18079 TTCAGGTTC-GGATTTT
1 TTCAGGTTCGGGATTTT
18095 TTC
1 TTC
18098 GGATTTGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.08, C:0.14, G:0.25, T:0.53
Consensus pattern (17 bp):
TTCAGGTTCGGGATTTT
Found at i:23906 original size:19 final size:19
Alignment explanation
Indices: 23882--23926 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
23872 TAAAATTTAG
23882 AACATACCTAGAAAATCTA
1 AACATACCTAGAAAATCTA
** * *
23901 AACATATTTTGTAAATCTA
1 AACATACCTAGAAAATCTA
23920 AACATAC
1 AACATAC
23927 ATTGTATATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (19 bp):
AACATACCTAGAAAATCTA
Found at i:23931 original size:19 final size:19
Alignment explanation
Indices: 23894--23937 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
23884 CATACCTAGA
**
23894 AAATCTAAACATATTTTGT
1 AAATCTAAACATACATTGT
23913 AAATCTAAACATACATTGT
1 AAATCTAAACATACATTGT
*
23932 ATATCT
1 AAATCT
23938 CTTATCATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (19 bp):
AAATCTAAACATACATTGT
Found at i:29221 original size:37 final size:37
Alignment explanation
Indices: 29165--29305 Score: 161
Period size: 37 Copynumber: 3.9 Consensus size: 37
29155 AAAAAGAGAT
*
29165 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAG
1 TAATCAGTAAATAGATAATTAAGAGTCAAGGTAATAG
* *
29202 TAATCAGTAAATCAG-TAATT-A-AGTAAAAG-AGAT--
1 TAATCAGTAAAT-AGATAATTAAGAGTCAAGGTA-ATAG
*
29235 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAG
1 TAATCAGTAAATAGATAATTAAGAGTCAAGGTAATAG
*
29272 TGATCAGTAAATCAG-TAATTAAGAGTCAAGGTAA
1 TAATCAGTAAAT-AGATAATTAAGAGTCAAGGTAA
29306 AGGGATTAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
32 1 0.01
33 17 0.20
34 2 0.02
35 16 0.18
36 2 0.02
37 47 0.54
38 2 0.02
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.28
Consensus pattern (37 bp):
TAATCAGTAAATAGATAATTAAGAGTCAAGGTAATAG
Found at i:29242 original size:70 final size:70
Alignment explanation
Indices: 29046--29294 Score: 386
Period size: 70 Copynumber: 3.6 Consensus size: 70
29036 TACCCCAATA
** *
29046 AATTAAGAGTCAAAATAATAGTAATCAGTAAATCAGTAATTCAGTAAAAAGAGATTAATCAGTAA
1 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATCAGTAA
*
29111 ATTGGT
65 ATTGAT
29117 AATTAAGAGTCAAGGTAATCAGTAATCAGTAAATCAG----T-A--AAAAGAGATTAATCAGTAA
1 AATTAAGAGTCAAGGTAAT-AGTAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGTAA
29175 ATTGAT
65 ATTGAT
29181 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGTAAA
1 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGTAAA
29246 TTGAT
66 TTGAT
*
29251 AATTAAGAGTCAAGGTAATAGTGATCAGTAAATCAGTAATTAAG
1 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAG
29295 AGTCAAGGTA
Statistics
Matches: 166, Mismatches: 4, Indels: 17
0.89 0.02 0.09
Matches are distributed among these distances:
63 17 0.10
64 43 0.26
67 2 0.01
68 2 0.01
70 68 0.41
71 17 0.10
72 17 0.10
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (70 bp):
AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAGAGATTAATCAGTAAA
TTGAT
Found at i:29296 original size:134 final size:135
Alignment explanation
Indices: 29046--29289 Score: 429
Period size: 134 Copynumber: 1.8 Consensus size: 135
29036 TACCCCAATA
*
29046 AATTAAGAGTCAAAATAATAGTAATCAGTAAATCAGTAATTCAGTAAAAAGAGATTAATCAGTAA
1 AATTAAGAGTCAAAATAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAA
*
29111 ATTGGTAATTAAGAGTCAAGGTAATCAGTAATCAGTAAATCAGTAAAAAGAGATTAATCAGTAAA
66 ATTGATAATTAAGAGTCAAGGTAATCAGTAATCAGTAAATCAGTAAAAAGAGATTAATCAGTAAA
29176 TTGAT
131 TTGAT
**
29181 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATCAGTAA
1 AATTAAGAGTCAAAATAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAA
*
29245 ATTGATAATTAAGAGTCAAGGTAAT-AGTGATCAGTAAATCAGTAA
66 ATTGATAATTAAGAGTCAAGGTAATCAGTAATCAGTAAATCAGTAA
29290 TTAAGAGTCA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
133 19 0.18
134 43 0.41
135 42 0.40
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.27
Consensus pattern (135 bp):
AATTAAGAGTCAAAATAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAA
ATTGATAATTAAGAGTCAAGGTAATCAGTAATCAGTAAATCAGTAAAAAGAGATTAATCAGTAAA
TTGAT
Found at i:29331 original size:40 final size:39
Alignment explanation
Indices: 29165--29416 Score: 164
Period size: 40 Copynumber: 6.6 Consensus size: 39
29155 AAAAAGAGAT
*
29165 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATA--G-
1 TAATCAGTAAATTCATAATTAAGAGTCAAGGTAA-AGGGA
*
29202 TAATCAGTAAA-TCAGTAATT-A-AGT--A---AAAGAGA
1 TAATCAGTAAATTCA-TAATTAAGAGTCAAGGTAAAGGGA
*
29234 TTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATA--G-
1 -TAATCAGTAAATTCATAATTAAGAGTCAAGGTAA-AGGGA
*
29272 TGATCAGTAAA-TCAGTAATTAAGAGTCAAGGTAAAGGGA
1 TAATCAGTAAATTCA-TAATTAAGAGTCAAGGTAAAGGGA
* * *
29311 TTAATCAGTAAATTCATAATTAAAAGAG-GAA-GTAAAAGTA
1 -TAATCAGTAAATTCATAATT--AAGAGTCAAGGTAAAGGGA
* * *
29351 GTAATCAGTAGA-CCAGTAATTAAGAGT-TAGAGTAAAGGGA
1 -TAATCAGTAAATTCA-TAATTAAGAGTCAAG-GTAAAGGGA
*
29391 TAGATCAGTAAATTGATAATTAAGAG
1 TA-ATCAGTAAATTCATAATTAAGAG
29417 AGAAAGTAAA
Statistics
Matches: 170, Mismatches: 17, Indels: 53
0.71 0.07 0.22
Matches are distributed among these distances:
29 1 0.01
30 2 0.01
31 1 0.01
33 17 0.10
34 3 0.02
35 6 0.04
36 6 0.04
37 46 0.27
38 7 0.04
39 5 0.03
40 64 0.38
41 7 0.04
42 5 0.03
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (39 bp):
TAATCAGTAAATTCATAATTAAGAGTCAAGGTAAAGGGA
Found at i:29386 original size:80 final size:79
Alignment explanation
Indices: 29227--29441 Score: 258
Period size: 80 Copynumber: 2.7 Consensus size: 79
29217 TAATTAAGTA
* * ** * * *
29227 AAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGT--AATAGTGATCAGTAAATCAGTAA
1 AAAGGGATTAATCAGTAAATTGATAATTAAAAGAGAAAGTAAAATAGTAATCAGTAAACCAGTAA
29290 TTAAGAGTCAAGGT
66 TTAAGAGTCAAGGT
* * *
29304 AAAGGGATTAATCAGTAAATTCATAATTAAAAGAGGAAGTAAAAGTAGTAATCAGTAGACCAGTA
1 AAAGGGATTAATCAGTAAATTGATAATTAAAAGAGAAAGTAAAA-TAGTAATCAGTAAACCAGTA
*
29369 ATTAAGAGT-TAGAGT
65 ATTAAGAGTCAAG-GT
*
29384 AAAGGGA-TAGATCAGTAAATTGATAATTAAGAGAGAAAGTAAAATTAGTAATCAGTAA
1 AAAGGGATTA-ATCAGTAAATTGATAATTAAAAGAGAAAGTAAAA-TAGTAATCAGTAA
29442 TTAAGAAAGG
Statistics
Matches: 117, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
77 33 0.28
79 6 0.05
80 78 0.67
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.26
Consensus pattern (79 bp):
AAAGGGATTAATCAGTAAATTGATAATTAAAAGAGAAAGTAAAATAGTAATCAGTAAACCAGTAA
TTAAGAGTCAAGGT
Found at i:29425 original size:40 final size:40
Alignment explanation
Indices: 29235--29441 Score: 147
Period size: 40 Copynumber: 5.2 Consensus size: 40
29225 TAAAAGAGAT
* * *
29235 TAATCAGTAAATTGATAATTAAGAGTCAAGGT-AA--TAG
1 TAATCAGTAAATTCATAATTAAGAGTCAAAGTAAAGGGAG
* * *
29272 TGATCAGTAAA-TCAGTAATTAAGAGTCAAGGTAAAGGGAT
1 TAATCAGTAAATTCA-TAATTAAGAGTCAAAGTAAAGGGAG
* *** * *
29312 TAATCAGTAAATTCATAATTAAAAGAGGAAGTAAAAGTAG
1 TAATCAGTAAATTCATAATTAAGAGTCAAAGTAAAGGGAG
* * * *
29352 TAATCAGTAGA-CCAGTAATTAAGAGTTAGAGTAAAGGGA-
1 TAATCAGTAAATTCA-TAATTAAGAGTCAAAGTAAAGGGAG
* ** ***
29391 TAGATCAGTAAATTGATAATTAAGAGAGAAAGTAAAATTAG
1 TA-ATCAGTAAATTCATAATTAAGAGTCAAAGTAAAGGGAG
29432 TAATCAGTAA
1 TAATCAGTAA
29442 TTAAGAAAGG
Statistics
Matches: 130, Mismatches: 31, Indels: 15
0.74 0.18 0.09
Matches are distributed among these distances:
36 2 0.02
37 27 0.21
38 2 0.02
39 4 0.03
40 89 0.68
41 6 0.05
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (40 bp):
TAATCAGTAAATTCATAATTAAGAGTCAAAGTAAAGGGAG
Found at i:29701 original size:35 final size:35
Alignment explanation
Indices: 29619--29866 Score: 227
Period size: 35 Copynumber: 6.9 Consensus size: 35
29609 AATTAAAAGT
*
29619 AAAATGGTAAGGAGTAAAAGAGTAATCAGTAAAGAGG
1 AAAATGGTAAAGAGT-AAAGAGTAATCAGTAAAGA-G
*
29656 AAAATGGTAAAGAGTATAGAGTAATCAGTAAAGAG
1 AAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAG
* *
29691 AAAA-GAGTAAAAAGTAAATAGTAATCAGTAAAGAG
1 AAAATG-GTAAAGAGTAAAGAGTAATCAGTAAAGAG
* * ** *
29726 AAAATGGTAAA-ATGGTAATTAAATTCAAGAGAGTAAAATAG
1 AAAATGGTAAAGA--GTAA--AGAGT-AA-TCAGT-AAAGAG
* * *
29767 TAATTAGTAAAGAGTAAAGAGTAATCAGT-AAGA-
1 AAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAG
*
29800 AAAATGGTAAAAAGTAAAGAGTAATCAGTAAAG-G
1 AAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAG
* *
29834 AAGAATGGCAAAGAGTAAAGGGTAATCAGTAAA
1 AA-AATGGTAAAGAGTAAAGAGTAATCAGTAAA
29867 ATGATAATCA
Statistics
Matches: 173, Mismatches: 25, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
33 25 0.14
34 10 0.06
35 67 0.39
36 26 0.15
37 16 0.09
38 6 0.03
39 2 0.01
40 7 0.04
41 13 0.08
42 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (35 bp):
AAAATGGTAAAGAGTAAAGAGTAATCAGTAAAGAG
Found at i:29713 original size:7 final size:7
Alignment explanation
Indices: 29625--29725 Score: 60
Period size: 7 Copynumber: 14.1 Consensus size: 7
29615 AAGTAAAATG
*
29625 GTAAGGA
1 GTAAAGA
29632 GTAAAAGA
1 GT-AAAGA
**
29640 GTAATCA
1 GTAAAGA
29647 GTAAAGA
1 GTAAAGA
*
29654 GGAAA-A
1 GTAAAGA
29660 TGGTAAAGA
1 --GTAAAGA
*
29669 GTATAGA
1 GTAAAGA
**
29676 GTAATCA
1 GTAAAGA
29683 GTAAAGA
1 GTAAAGA
*
29690 GAAAAGA
1 GTAAAGA
*
29697 GTAAAAA
1 GTAAAGA
*
29704 GTAAATA
1 GTAAAGA
**
29711 GTAATCA
1 GTAAAGA
29718 GTAAAGA
1 GTAAAGA
29725 G
1 G
29726 AAAATGGTAA
Statistics
Matches: 69, Mismatches: 21, Indels: 8
0.70 0.21 0.08
Matches are distributed among these distances:
6 1 0.01
7 57 0.83
8 10 0.14
9 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.26, T:0.18
Consensus pattern (7 bp):
GTAAAGA
Found at i:29730 original size:21 final size:21
Alignment explanation
Indices: 29696--29735 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29686 AAGAGAAAAG
*
29696 AGTAAAAAGTAAATAGTAATC
1 AGTAAAAAGAAAATAGTAATC
* *
29717 AGTAAAGAGAAAATGGTAA
1 AGTAAAAAGAAAATAGTAA
29736 AATGGTAATT
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:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTAAAAAGAAAATAGTAATC
Found at i:29789 original size:21 final size:21
Alignment explanation
Indices: 29755--29797 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29745 TAAATTCAAG
* *
29755 AGAGTAAAATAGTAATTAGTAA
1 AGAGT-AAAGAGTAATCAGTAA
29777 AGAGTAAAGAGTAATCAGTAA
1 AGAGTAAAGAGTAATCAGTAA
29798 GAAAAATGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.53, C:0.02, G:0.21, T:0.23
Consensus pattern (21 bp):
AGAGTAAAGAGTAATCAGTAA
Found at i:29946 original size:21 final size:22
Alignment explanation
Indices: 29922--29992 Score: 83
Period size: 21 Copynumber: 3.3 Consensus size: 22
29912 AAAAATAATA
*
29922 AAAATGGTAATTAGT-AAGAGT
1 AAAATGGTAATCAGTAAAGAGT
* *
29943 AAAATAGTAATCAATAAAGAGT
1 AAAATGGTAATCAGTAAAGAGT
*
29965 AAAA-GGTGATCAGTAAAGAGT
1 AAAATGGTAATCAGTAAAGAGT
*
29986 CAAATGG
1 AAAATGG
29993 CATGAATATA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 29 0.71
22 12 0.29
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.23
Consensus pattern (22 bp):
AAAATGGTAATCAGTAAAGAGT
Found at i:31490 original size:31 final size:31
Alignment explanation
Indices: 31448--31518 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
31438 GGGGAAACTT
31448 TATATTTTCCAATTGCACCCTTATT-TTTAAAA
1 TATA-TTTCCAATTGCACCCTT-TTCTTTAAAA
*
31480 TATATTTCCAATTGTACCCTTTTCTTTAAAA
1 TATATTTCCAATTGCACCCTTTTCTTTAAAA
*
31511 CATATTTC
1 TATATTTC
31519 TAAATTGCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 2 0.06
31 30 0.83
32 4 0.11
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.48
Consensus pattern (31 bp):
TATATTTCCAATTGCACCCTTTTCTTTAAAA
Found at i:31685 original size:38 final size:35
Alignment explanation
Indices: 31623--31697 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 35
31613 ATTTGACTTC
31623 TTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTCT
1 TTGTTTCCAACGTCCTATTTAATTTTG-C-TTTGTCT
**
31660 TTGTTTCCAATCGTTGTATTTAATTTTGCTTTGTCT
1 TTGTTTCCAA-CGTCCTATTTAATTTTGCTTTGTCT
31696 TT
1 TT
31698 AGTCTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 9 0.26
37 11 0.31
38 15 0.43
ACGTcount: A:0.13, C:0.17, G:0.12, T:0.57
Consensus pattern (35 bp):
TTGTTTCCAACGTCCTATTTAATTTTGCTTTGTCT
Found at i:31862 original size:19 final size:21
Alignment explanation
Indices: 31830--31872 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
31820 ATCTTTACTA
31830 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
31851 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
31870 TTA
1 TTA
31873 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:32118 original size:22 final size:23
Alignment explanation
Indices: 32031--32117 Score: 83
Period size: 22 Copynumber: 3.9 Consensus size: 23
32021 CTTGTCTCTA
32031 TGTGGTTATCAAAATTTCATAAG
1 TGTGGTTATCAAAATTTCATAAG
* * *
32054 ATGT--TTATTATAATTTCATGAG
1 -TGTGGTTATCAAAATTTCATAAG
* *
32076 -GAGGTTATCAAAATTCCAT-AG
1 TGTGGTTATCAAAATTTCATAAG
*
32097 TGTGGTTACCAAAATTTCATA
1 TGTGGTTATCAAAATTTCATA
32118 GGATCAGGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 43 0.88
24 3 0.06
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (23 bp):
TGTGGTTATCAAAATTTCATAAG
Found at i:36107 original size:26 final size:26
Alignment explanation
Indices: 36078--36145 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
36068 TTCCCTCATT
36078 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
36104 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
36130 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
36146 AAACTAAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:36145 original size:15 final size:15
Alignment explanation
Indices: 36078--36149 Score: 63
Period size: 11 Copynumber: 5.4 Consensus size: 15
36068 TTCCCTCATT
*
36078 TTAATCATAAACTAA
1 TTAAACATAAACTAA
36093 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
*
36104 TTAATCATAAACTAA
1 TTAAACATAAACTAA
36119 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
36130 TTAAACATAAACTAA
1 TTAAACATAAACTAA
36145 -TAAAC
1 TTAAAC
36150 TAAGTAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
11 14 0.30
12 3 0.07
13 8 0.17
14 7 0.15
15 14 0.30
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAACATAAACTAA
Found at i:38637 original size:494 final size:492
Alignment explanation
Indices: 37378--38842 Score: 2475
Period size: 494 Copynumber: 3.0 Consensus size: 492
37368 ATAAAAGAAT
* * *
37378 GCCTAGAGGAAACAAAAAAAATGACATGGCATGGAAACTAATATGTAGTTTGTCTAAGTTGCCTA
1 GCCTAAAGGAAACAAAAAAAATGACATGGCATGGAATCTAATATGTAGTTTGTCTAAGTTGGCTA
37443 CTAAACCAAACTAAAATTAAGCATGTAGTTCTACCCTAATCCAATAAAACCAAGTACTAATTAAG
66 CTAAACCAAAC-AAAATTAAGCATGTAGTTCTACCCTAATCCAATAAAACCAAGTACTAATTAAG
* *
37508 TATGCTAAAAAACTAAACCAACTTCTATAAATACTATGGGAGACAAAAATGACATGACATGAAAT
130 TATGCTAAAAAATTAAACCAACTTCTATAAATACTATAGGAGACAAAAATGACATGACATGAAAT
* * *
37573 CTAAACCCTAATCATGACATGACAAACCCTAAGTGAGATGAAGCATTGTCCCCATCTCATGAAAG
195 CTAAACCCTAAACATGACATGACAAACCCTAAGTGAGATGAACCATTGTCCCCATGTCATGAAAG
*
37638 CCAAACCCTAACAAATAATATAAACCCTAAGTGAGATAAAAGAAACCCTCAAAAAACACATTAAA
260 CCAAACCCT---AAACAATATAAACCCTAAGTGAGATAAAAGAAACCCTCAAAAAACACATTAAA
37703 CCCTAGGTGAGATAAAAAGAAAAAACATGAACAACCATATTCACCCTTACCAACTACACCAAATT
322 CCCTAGGTGAGATAAAAAGAAAAAACATGAACAACCATATTCACCCTTACCAACTACACCAAATT
37768 ACATGAAAACCAATGGTGGAGGGCAAAAAACAAAAAAATTTGAAATAACAAAAAAAATGGTGGAA
387 ACATGAAAACCAATGGTGGAGGGCAAAAAAC-AAAAAATTTGAAATAACAAAAAAAATGGTGGAA
* *
37833 AAATCATTATTTCAAAAGTTGTGACATGAAAGTCAAACCCTA
451 AAGTCACTATTTCAAAAGTTGTGACATGAAAGTCAAACCCTA
*
37875 GCTTAAAGGAAACAAAAAAAAATGACATGGCATGGAATCTAATATGTAGTTTGTCTAAGTTGGCT
1 GCCTAAAGGAAAC-AAAAAAAATGACATGGCATGGAATCTAATATGTAGTTTGTCTAAGTTGGCT
*
37940 ACT------------A--AA-CATGTAGTTCTATCCTAATCCAATAAAACCAAGTACTAATTAAG
65 ACTAAACCAAACAAAATTAAGCATGTAGTTCTACCCTAATCCAATAAAACCAAGTACTAATTAAG
37990 TATGCTAAAAAATTAAACCAACTTCTATAAATACTATAGGAGACAAAAATGACATGACATGAAAT
130 TATGCTAAAAAATTAAACCAACTTCTATAAATACTATAGGAGACAAAAATGACATGACATGAAAT
*
38055 CTAAACCCTAAACATGACACGACAAACCCTAAGTGAGATGAACCATTGTCCCCATGTCATGAAAG
195 CTAAACCCTAAACATGACATGACAAACCCTAAGTGAGATGAACCATTGTCCCCATGTCATGAAAG
* * ** *
38120 CCAAACCCTAAACAATATAAACCCTAAGTGAGATAAAAGCAGCTTTCAAAAAACACATTGAACCC
260 CCAAACCCTAAACAATATAAACCCTAAGTGAGATAAAAGAAACCCTCAAAAAACACATTAAACCC
* *
38185 TAGGTGAGATAAAAAGAAAAAACATTAACAACCATATTCACCCTTACCAACTAAACCAAATTACA
325 TAGGTGAGATAAAAAGAAAAAACATGAACAACCATATTCACCCTTACCAACTACACCAAATTACA
* *
38250 TGAAAACCAATGGTAGAGGGCAAAAAACAAAAAATTTGAAATAACAAAAAAAAATGGTGGAATAG
390 TGAAAACCAATGGTGGAGGGCAAAAAACAAAAAATTTGAAATAAC-AAAAAAAATGGTGGAAAAG
*
38315 TCACTATTTCAAAAGTTGTGACATGAAAGCCAAACCCTA
454 TCACTATTTCAAAAGTTGTGACATGAAAGTCAAACCCTA
*
38354 GCCTAAAGGAAACAAAAAAAATGACATGGCATGGAATCTAATATGTAGTTTATCTAAGTTGGCTA
1 GCCTAAAGGAAACAAAAAAAATGACATGGCATGGAATCTAATATGTAGTTTGTCTAAGTTGGCTA
38419 CTAAACCAAACCAAAATTAAGCATGTAGTTCTACCCTAATCCAATAAAACCAAGTACTAATTAAG
66 CTAAACCAAA-CAAAATTAAGCATGTAGTTCTACCCTAATCCAATAAAACCAAGTACTAATTAAG
38484 TATGCTAAAAAATTAAACCAACTTCTATAAATACTATAGGAGACAAAAATGACATGACATGAAAT
130 TATGCTAAAAAATTAAACCAACTTCTATAAATACTATAGGAGACAAAAATGACATGACATGAAAT
*
38549 CTAAACCCTAAACATGACATGACAAACCCTAAGTGAGAAGAACCATTGTCCCCATGTCATGAAAG
195 CTAAACCCTAAACATGACATGACAAACCCTAAGTGAGATGAACCATTGTCCCCATGTCATGAAAG
38614 CCAAACCCTAAACAATATAAACCCTAAGTGAGATAAAAGAAACCCTCAAAAAACACATTAAACCC
260 CCAAACCCTAAACAATATAAACCCTAAGTGAGATAAAAGAAACCCTCAAAAAACACATTAAACCC
38679 TAGGTGAGATAAAAAGAAAAAACATGAACAACCATATTCACCCTTACCAACTACACCAAATTACA
325 TAGGTGAGATAAAAAGAAAAAACATGAACAACCATATTCACCCTTACCAACTACACCAAATTACA
*
38744 TGAAAACCAATGGTGGAGGGC----AA-AAAAAATTGGAAATAACAAAAAAAATGGTGGAAAAGT
390 TGAAAACCAATGGTGGAGGGCAAAAAACAAAAAATTTGAAATAACAAAAAAAATGGTGGAAAAGT
38804 CACTATTTCAAAAGTTGTGACATGAAAGTCAAACCCTA
455 CACTATTTCAAAAGTTGTGACATGAAAGTCAAACCCTA
38842 G
1 G
38843 GGGCAAAAAA
Statistics
Matches: 910, Mismatches: 40, Indels: 45
0.91 0.04 0.05
Matches are distributed among these distances:
478 70 0.08
479 206 0.23
482 176 0.19
483 2 0.00
485 1 0.00
488 57 0.06
489 16 0.02
490 2 0.00
491 1 0.00
493 2 0.00
494 314 0.35
497 11 0.01
498 52 0.06
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (492 bp):
GCCTAAAGGAAACAAAAAAAATGACATGGCATGGAATCTAATATGTAGTTTGTCTAAGTTGGCTA
CTAAACCAAACAAAATTAAGCATGTAGTTCTACCCTAATCCAATAAAACCAAGTACTAATTAAGT
ATGCTAAAAAATTAAACCAACTTCTATAAATACTATAGGAGACAAAAATGACATGACATGAAATC
TAAACCCTAAACATGACATGACAAACCCTAAGTGAGATGAACCATTGTCCCCATGTCATGAAAGC
CAAACCCTAAACAATATAAACCCTAAGTGAGATAAAAGAAACCCTCAAAAAACACATTAAACCCT
AGGTGAGATAAAAAGAAAAAACATGAACAACCATATTCACCCTTACCAACTACACCAAATTACAT
GAAAACCAATGGTGGAGGGCAAAAAACAAAAAATTTGAAATAACAAAAAAAATGGTGGAAAAGTC
ACTATTTCAAAAGTTGTGACATGAAAGTCAAACCCTA
Found at i:40417 original size:39 final size:38
Alignment explanation
Indices: 40372--40475 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 38
40362 AAATTGTTCT
* *
40372 TGTGTTATATGTGTTTAGGGATTTTAGTATAGA-TG-CCTC
1 TGTGTTATATGTGTTTAGGGACTTT-G-AAAGAGTGTCC-C
40411 TGTGTTATATGTGTTT-GAGGACTTTGAAAGAGTTGTCCC
1 TGTGTTATATGTGTTTAG-GGACTTTGAAAGAG-TGTCCC
40450 TGTGTTATATGTGTTTAGGGACTTTG
1 TGTGTTATATGTGTTTAGGGACTTTG
40476 GGGAGAGAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
37 4 0.07
38 2 0.03
39 49 0.84
40 3 0.05
ACGTcount: A:0.19, C:0.08, G:0.28, T:0.45
Consensus pattern (38 bp):
TGTGTTATATGTGTTTAGGGACTTTGAAAGAGTGTCCC
Found at i:41639 original size:5 final size:5
Alignment explanation
Indices: 41629--41679 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
41619 CATATAATAG
* * * *
41629 TAAGA TAAGA TAAGA TAAGA CAAGA CAAGA CATGA TAAGA T-AG- TAAGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
41677 TAA
1 TAA
41680 TAATAATAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
3 1 0.03
4 4 0.10
5 35 0.88
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.18
Consensus pattern (5 bp):
TAAGA
Found at i:43611 original size:33 final size:32
Alignment explanation
Indices: 43574--43665 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 32
43564 CCGAGTCATG
*
43574 TGGCCGGGTG-TGGCCGGGCATGTCCATGTCGCA
1 TGGCC-GGTGATGGCCGGGCATCTCCA-GTCGCA
*
43607 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCA
*
43640 TGGCCGGTGATGGTCGGGCATCTCCA
1 TGGCCGGTGATGGCCGGGCATCTCCA
43666 AGACGCCTAG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
32 5 0.09
33 48 0.89
34 1 0.02
ACGTcount: A:0.10, C:0.28, G:0.41, T:0.21
Consensus pattern (32 bp):
TGGCCGGTGATGGCCGGGCATCTCCAGTCGCA
Found at i:48648 original size:6 final size:5
Alignment explanation
Indices: 48621--48650 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
48611 ATCACAAATT
48621 TTTTA TTTTA TTTTA TTTTA TTTATA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTT-TA TTTT
48651 TCGATATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:49736 original size:33 final size:32
Alignment explanation
Indices: 49693--49788 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 32
49683 CCGAGTCATG
* *
49693 TGGCTGGGCATGTCCATGTCGCGTGGCCGGTGA
1 TGGCCGGGCATCTCCA-GTCGCGTGGCCGGTGA
*
49726 TGGCCGGGCATCTCCGAGTCGCGTGGCCGATGA
1 TGGCCGGGCATCTCC-AGTCGCGTGGCCGGTGA
* *
49759 TGGTCGGGCATTTCCAAGTCGCGTGGCCGG
1 TGGCCGGGCATCTCC-AGTCGCGTGGCCGG
49789 ATCTCCAAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.10, C:0.27, G:0.41, T:0.22
Consensus pattern (32 bp):
TGGCCGGGCATCTCCAGTCGCGTGGCCGGTGA
Found at i:50673 original size:132 final size:131
Alignment explanation
Indices: 50350--50718 Score: 580
Period size: 131 Copynumber: 2.8 Consensus size: 131
50340 CTGACTCATT
* * * *
50350 TAATTTTTTAATTAAATTAATAAAATTGT-AAAATCAAAATAGGTATAAGAATATTAGATTTAAT
1 TAATTTTTTAATTAAAATAGTAAAATGGTAAAAAT-AAAATAGGTATAAGGATATTAGATTTAAT
* * *
50414 TAAATAAAAAATAGAGTTTTTAGTTGAGTAAAAGTATAAAAGTATATTTAAAAAGTTGTAATATA
65 TAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTAGAAAAGTATATTTAAAAAGTTCTAATATA
50479 TA
130 TA
* *
50481 TAAATTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAGGGATATTAGATTTAATT
1 TAATTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATT
*
50546 AAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTAGAAATGTATATTTAAAAAGTTCTAATATAT
66 AAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTAGAAAAGTATATTTAAAAAGTTCTAATATAT
50611 A
131 A
* *
50612 TAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGCTATAAGGATATTAGATTTAAT
1 TAA-TTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAAT
* *
50677 GAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
65 TAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTAGAAAAGT
50719 TTAAATAATG
Statistics
Matches: 219, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
131 153 0.70
132 66 0.30
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (131 bp):
TAATTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATT
AAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTAGAAAAGTATATTTAAAAAGTTCTAATATAT
A
Found at i:57304 original size:30 final size:31
Alignment explanation
Indices: 57252--57322 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 31
57242 TGAAAGCAAA
*
57252 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGA--ATAGCATTGAAAATAAT
57285 TCTGTTTTGGTTG-ATAGCATTGAAAATAAT
1 TCTGTTTTGGTTGAATAGCATTGAAAATAAT
57315 TCTGTTTT
1 TCTGTTTT
57323 AGGTGAAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 24 0.65
33 13 0.35
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.46
Consensus pattern (31 bp):
TCTGTTTTGGTTGAATAGCATTGAAAATAAT
Found at i:59491 original size:21 final size:21
Alignment explanation
Indices: 59428--59480 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
59418 AGGACTTTCT
59428 GGGGTCACCCGGGATCGGGCA
1 GGGGTCACCCGGGATCGGGCA
59449 GGGGTCACCCGGGATCGGGCA
1 GGGGTCACCCGGGATCGGGCA
59470 GGGGTCACCCG
1 GGGGTCACCCG
59481 CTAGCGGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.13, C:0.30, G:0.47, T:0.09
Consensus pattern (21 bp):
GGGGTCACCCGGGATCGGGCA
Found at i:61593 original size:58 final size:58
Alignment explanation
Indices: 61500--61610 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 58
61490 GAGGTCTTGG
* *
61500 GTTCTAGTCTCACAGAATGTGAGATTTTTTGTAATTTATTTGTTTGTGTATTTGGTAA
1 GTTCTAGTCTCACAGAATGTGAGATTTTTTATAATTTATTTATTTGTGTATTTGGTAA
61558 GTTCTAGTCTCAC-GAAATGTGAG-TTTATTTATAATTTATTTATTTGTGTATTT
1 GTTCTAGTCTCACAG-AATGTGAGATTT-TTTATAATTTATTTATTTGTGTATTT
61611 TTGTATGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
57 4 0.08
58 45 0.92
ACGTcount: A:0.23, C:0.07, G:0.18, T:0.51
Consensus pattern (58 bp):
GTTCTAGTCTCACAGAATGTGAGATTTTTTATAATTTATTTATTTGTGTATTTGGTAA
Found at i:61772 original size:120 final size:120
Alignment explanation
Indices: 61559--61799 Score: 482
Period size: 120 Copynumber: 2.0 Consensus size: 120
61549 ATTTGGTAAG
61559 TTCTAGTCTCACGAAATGTGAGTTTATTTATAATTTATTTATTTGTGTATTTTTGTATGTTTGGT
1 TTCTAGTCTCACGAAATGTGAGTTTATTTATAATTTATTTATTTGTGTATTTTTGTATGTTTGGT
61624 AATTATAGATGAAATTAGAGATTTGGCTTTGCACATTCTCTAGCTAAGATTGAGC
66 AATTATAGATGAAATTAGAGATTTGGCTTTGCACATTCTCTAGCTAAGATTGAGC
61679 TTCTAGTCTCACGAAATGTGAGTTTATTTATAATTTATTTATTTGTGTATTTTTGTATGTTTGGT
1 TTCTAGTCTCACGAAATGTGAGTTTATTTATAATTTATTTATTTGTGTATTTTTGTATGTTTGGT
61744 AATTATAGATGAAATTAGAGATTTGGCTTTGCACATTCTCTAGCTAAGATTGAGC
66 AATTATAGATGAAATTAGAGATTTGGCTTTGCACATTCTCTAGCTAAGATTGAGC
61799 T
1 T
61800 GGATAATCGT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (120 bp):
TTCTAGTCTCACGAAATGTGAGTTTATTTATAATTTATTTATTTGTGTATTTTTGTATGTTTGGT
AATTATAGATGAAATTAGAGATTTGGCTTTGCACATTCTCTAGCTAAGATTGAGC
Found at i:62241 original size:67 final size:67
Alignment explanation
Indices: 62169--62301 Score: 239
Period size: 67 Copynumber: 2.0 Consensus size: 67
62159 ATTACGTTTA
* *
62169 ATTGCATTGTTCTTTGTAATTTTTTTATAAGTGGTACATTAACTTGATTTAATTAATTGATTTTT
1 ATTGCATTGTTCTTTGAAATTTTTTTATAAGTAGTACATTAACTTGATTTAATTAATTGATTTTT
62234 TC
66 TC
*
62236 ATTGCATTGTTCTTTGAAATTTTTTTATAATTAGTACATTAACTTGATTTAATTAATTGATTTTT
1 ATTGCATTGTTCTTTGAAATTTTTTTATAAGTAGTACATTAACTTGATTTAATTAATTGATTTTT
62301 T
66 T
62302 TCTAAAGGAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.56
Consensus pattern (67 bp):
ATTGCATTGTTCTTTGAAATTTTTTTATAAGTAGTACATTAACTTGATTTAATTAATTGATTTTT
TC
Found at i:62894 original size:21 final size:21
Alignment explanation
Indices: 62850--62894 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
62840 AATTCACCAA
* **
62850 GAAGATGCCATTTGATCCTTT
1 GAAGATGCCATTAGATCCGAT
62871 GAAGATGCCATTAGATCCGAT
1 GAAGATGCCATTAGATCCGAT
62892 GAA
1 GAA
62895 AAGAGCAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (21 bp):
GAAGATGCCATTAGATCCGAT
Found at i:63949 original size:68 final size:68
Alignment explanation
Indices: 63870--64005 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 68
63860 ATTACGTTTA
*
63870 ATTGCATTGTTCTTTGTAATTTTTTTATAAGTGGTACATTAACTTGATTTAATTAATTGATTTTT
1 ATTGCATTGTTCTTTGTAATTTTTTTATAAGTAGTACATTAACTTGATTTAATTAATTGATTTTT
63935 TTC
66 TTC
*
63938 ATTGCATTGTTCTTTGTAATTTTTTTATAATTAGTACATTAACTTGATTTAATTAATTGATTTTT
1 ATTGCATTGTTCTTTGTAATTTTTTTATAAGTAGTACATTAACTTGATTTAATTAATTGATTTTT
64003 TTC
66 TTC
64006 TTAAGGATTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (68 bp):
ATTGCATTGTTCTTTGTAATTTTTTTATAAGTAGTACATTAACTTGATTTAATTAATTGATTTTT
TTC
Found at i:64023 original size:38 final size:38
Alignment explanation
Indices: 63978--64054 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
63968 TTAGTACATT
63978 AACTTGATTTAATTAATTGATTTTTTTCTTAAGGATTG
1 AACTTGATTTAATTAATTGATTTTTTTCTTAAGGATTG
64016 AACTTGATTTAATTAATTGATTTTTTTCTTAAGGATTG
1 AACTTGATTTAATTAATTGATTTTTTTCTTAAGGATTG
64054 A
1 A
64055 GGGATTAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.52
Consensus pattern (38 bp):
AACTTGATTTAATTAATTGATTTTTTTCTTAAGGATTG
Found at i:64053 original size:19 final size:19
Alignment explanation
Indices: 63993--64054 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
63983 GATTTAATTA
63993 ATTGATTTTTTTCTTAAGG
1 ATTGATTTTTTTCTTAAGG
** ** **
64012 ATTGAACTTGAT-TTAATTA
1 ATTGATTTTTTTCTTAA-GG
64031 ATTGATTTTTTTCTTAAGG
1 ATTGATTTTTTTCTTAAGG
64050 ATTGA
1 ATTGA
64055 GGGATTAAGA
Statistics
Matches: 29, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
18 4 0.14
19 21 0.72
20 4 0.14
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.53
Consensus pattern (19 bp):
ATTGATTTTTTTCTTAAGG
Found at i:70534 original size:34 final size:34
Alignment explanation
Indices: 70491--70560 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
70481 AGAAAAATAG
70491 ATGTTGCATCCAATGATTAAAATTTAATGGGTGC
1 ATGTTGCATCCAATGATTAAAATTTAATGGGTGC
*
70525 ATGTTGCATCTAATGATTAAAATTTAATGGGTGC
1 ATGTTGCATCCAATGATTAAAATTTAATGGGTGC
70559 AT
1 AT
70561 CACAACGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (34 bp):
ATGTTGCATCCAATGATTAAAATTTAATGGGTGC
Done.