Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002974.1 Hibiscus syriacus cultivar Beakdansim tig00006150_pilon, 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: 73722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3148 original size:57 final size:57
Alignment explanation
Indices: 3077--3190 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
3067 TTAGCAAAGG
* *
3077 TGATTAAACAAGGAATCTGATTATCTTTGATTTGTCTAGGTCCTAAAACAAAAGCTT
1 TGATTAAACAAGGAATCTGATCATCTTTGATTTGTCTAGATCCTAAAACAAAAGCTT
*
3134 TGATTAAACAAGGAATCTGGTCATCTTTGATTTGTCTAGATCCTAAAACAAAAGCTT
1 TGATTAAACAAGGAATCTGATCATCTTTGATTTGTCTAGATCCTAAAACAAAAGCTT
3191 GGTTGCACAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (57 bp):
TGATTAAACAAGGAATCTGATCATCTTTGATTTGTCTAGATCCTAAAACAAAAGCTT
Found at i:6419 original size:34 final size:35
Alignment explanation
Indices: 6347--6420 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 35
6337 AACTGAGAAA
6347 ATTT-AAGAAAATTTAAATTTAAAGTTTCCATCTT
1 ATTTAAAGAAAATTTAAATTTAAAGTTTCCATCTT
* *
6381 -TTTAAAGAAAATTTAAATTTAAA-TTTTCATTTT
1 ATTTAAAGAAAATTTAAATTTAAAGTTTCCATCTT
6414 ATTTAAA
1 ATTTAAA
6421 TAAATTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
33 11 0.31
34 25 0.69
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (35 bp):
ATTTAAAGAAAATTTAAATTTAAAGTTTCCATCTT
Found at i:6426 original size:21 final size:22
Alignment explanation
Indices: 6391--6434 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
6381 TTTAAAGAAA
6391 ATTTAAATTTAAATTTTCATTTT
1 ATTTAAA-TTAAATTTTCATTTT
6414 ATTTAAA-TAAATTTTCATTTT
1 ATTTAAATTAAATTTTCATTTT
6435 CTATTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.67
23 7 0.33
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTAAATTAAATTTTCATTTT
Found at i:9784 original size:28 final size:28
Alignment explanation
Indices: 9737--9808 Score: 67
Period size: 31 Copynumber: 2.4 Consensus size: 28
9727 TTTAAATAGT
9737 TATTATATTTTATATTAAT-ATA-TATAAA
1 TATTAT-TTTT-TATTAATAATATTATAAA
*
9765 TATTATTTTTTATTAAAATAATATTTATAAT
1 TATTATTTTTTATT--AATAATA-TTATAAA
9796 TATTATTTATTTA
1 TATTATTT-TTTA
9809 GAATTATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
26 4 0.11
27 4 0.11
28 9 0.24
29 3 0.08
31 13 0.35
32 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTATTTTTTATTAATAATATTATAAA
Found at i:9808 original size:17 final size:17
Alignment explanation
Indices: 9786--9824 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
9776 ATTAAAATAA
* *
9786 TATTTATAATTATTATT
1 TATTTAGAATTATTAAT
9803 TATTTAGAATTATTAAT
1 TATTTAGAATTATTAAT
9820 TATTT
1 TATTT
9825 TTTTATGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTTAGAATTATTAAT
Found at i:9973 original size:17 final size:16
Alignment explanation
Indices: 9951--10004 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
9941 TAATGTTAAT
9951 ATTTAAATTTATTTTTA
1 ATTTAAA-TTATTTTTA
* *
9968 ATTTAAAGTTATTATGA
1 ATTTAAA-TTATTTTTA
* *
9985 ATTTATATTAATTTTA
1 ATTTAAATTATTTTTA
10001 ATTT
1 ATTT
10005 TTTATAATGT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTTAAATTATTTTTA
Found at i:19524 original size:2 final size:2
Alignment explanation
Indices: 19517--19613 Score: 81
Period size: 2 Copynumber: 54.0 Consensus size: 2
19507 ACGCCCCGAT
*
19517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
19557 TA TA TA T- TT TA TA T- TA -A T- TA TA TA TA TA T- TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
19594 T- TT TA TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
19614 AAATATTTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
1 11 0.14
2 69 0.86
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:19586 original size:31 final size:31
Alignment explanation
Indices: 19515--19613 Score: 136
Period size: 31 Copynumber: 3.3 Consensus size: 31
19505 ACACGCCCCG
* *
19515 ATTATATATATA-TATATATA-TATATA-T-
1 ATTATATATATATTTTATATATTTTATATTA
19542 A-TATATATAATATTTTATATATTTTATATTA
1 ATTATATAT-ATATTTTATATATTTTATATTA
19573 ATTATATATATATTTTATATATTTTATATTA
1 ATTATATATATATTTTATATATTTTATATTA
19604 ATTATATATA
1 ATTATATATA
19614 AAATATTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
26 7 0.11
27 4 0.06
28 7 0.11
29 5 0.08
30 1 0.02
31 33 0.52
32 7 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTATATATATATTTTATATATTTTATATTA
Found at i:19608 original size:9 final size:11
Alignment explanation
Indices: 19517--19613 Score: 102
Period size: 10 Copynumber: 9.5 Consensus size: 11
19507 ACGCCCCGAT
19517 TATATATA-TA
1 TATATATATTA
19527 TATATATA-TA
1 TATATATATTA
19537 TATATATA-TA
1 TATATATATTA
*
19547 TATA-ATATTT
1 TATATATATTA
*
19557 TATATATTTTA
1 TATATATATTA
19568 TAT-TA-ATTA
1 TATATATATTA
*
19577 TATATATATTT
1 TATATATATTA
*
19588 TATATATTTTA
1 TATATATATTA
19599 TAT-TA-ATTA
1 TATATATATTA
19608 TATATA
1 TATATA
19614 AAATATTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 15 0.20
10 37 0.50
11 22 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATATATTA
Found at i:23750 original size:7 final size:7
Alignment explanation
Indices: 23738--23766 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
23728 GCACTTTGGC
23738 TCTGATT
1 TCTGATT
23745 TCTGATT
1 TCTGATT
23752 TCTGATT
1 TCTGATT
23759 TCTGATT
1 TCTGATT
23766 T
1 T
23767 ACAAAGTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (7 bp):
TCTGATT
Found at i:25708 original size:38 final size:39
Alignment explanation
Indices: 25657--25745 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 39
25647 ATTTAAGGGG
* * *
25657 GAATTTTATAGTCTCTTGGGAGTTA-AATGTTTTATTGT
1 GAATTTAAGAGTCTCTTGGGAGTTAGAATGTTTTATTCT
*
25695 GAATTTAAGAGTCTCTTGGGAGTTAGAGTGTTTTATTCT
1 GAATTTAAGAGTCTCTTGGGAGTTAGAATGTTTTATTCT
25734 GAATTTAAGAGT
1 GAATTTAAGAGT
25746 TTTTAGAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 23 0.50
39 23 0.50
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.45
Consensus pattern (39 bp):
GAATTTAAGAGTCTCTTGGGAGTTAGAATGTTTTATTCT
Found at i:26625 original size:22 final size:22
Alignment explanation
Indices: 26599--26672 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 22
26589 TATTTTTAAT
26599 TATATTTTATTTATTTAT-TTA
1 TATATTTTATTTATTTATATTA
*
26620 CTATATTCCTTTTTTATTTATATTA
1 -TATATT--TTATTTATTTATATTA
* *
26645 TATTATTTTTATTATATATATCTTA
1 TA-TA-TTTTATT-TATTTATATTA
26670 TAT
1 TAT
26673 CATTATGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 6 0.14
24 18 0.43
25 16 0.38
26 2 0.05
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TATATTTTATTTATTTATATTA
Found at i:26652 original size:14 final size:14
Alignment explanation
Indices: 26633--26672 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
26623 TATTCCTTTT
26633 TTATTTATATTATA
1 TTATTTATATTATA
*
26647 TTATTTTTATTATA
1 TTATTTATATTATA
26661 TATATCTTATAT
1 T-TAT-TTATAT
26673 CATTATGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:26670 original size:20 final size:20
Alignment explanation
Indices: 26583--26663 Score: 62
Period size: 20 Copynumber: 4.0 Consensus size: 20
26573 TCATCCCCTA
*
26583 TATATATATTTTTAATTATAT
1 TATAT-TATTTTTATTTATAT
* *
26604 TTTATT-TATTTATTTACTA-
1 TATATTATTTTTATTTA-TAT
26623 TAT-TCCT-TTTTTATTTATAT
1 TATAT--TATTTTTATTTATAT
26643 TATATTATTTTTATTATATAT
1 TATATTATTTTTATT-TATAT
26664 ATCTTATATC
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
18 1 0.02
19 13 0.27
20 24 0.50
21 10 0.21
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TATATTATTTTTATTTATAT
Found at i:26689 original size:2 final size:2
Alignment explanation
Indices: 26682--26715 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
26672 TCATTATGTG
*
26682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26716 AATGTATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27024 original size:17 final size:18
Alignment explanation
Indices: 26992--27026 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
26982 ATTTTCATTT
26992 CTTTTTAATTTCTTTTAC
1 CTTTTTAATTTCTTTTAC
*
27010 CTTTTTTATTT-TTTTAC
1 CTTTTTAATTTCTTTTAC
27027 TCCATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTTTAATTTCTTTTAC
Found at i:31792 original size:69 final size:69
Alignment explanation
Indices: 31710--31847 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
31700 GATTCAAACT
*
31710 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAAAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAAAGCA
31775 TCAA
66 TCAA
* *
31779 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCGCTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAAAGCA
31844 TCAA
66 TCAA
31848 GAGAGACACA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAAAGCA
TCAA
Found at i:33476 original size:106 final size:106
Alignment explanation
Indices: 33351--33674 Score: 441
Period size: 106 Copynumber: 3.1 Consensus size: 106
33341 ATATCGTGCC
*
33351 ACTCGAGACAACATAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCTC
33416 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
33457 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTTAACAAAAAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCTC
* * *
33522 AATTTTAGAGCCAATTTCAACTTCACAACGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * ** * * *
33563 ACTCGAGACAGCACAAGCTCAACTTCACAGCAAAGGGGCGGTTGGCTGTCAATAAACAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCTC
* * * * * *
33628 AGTTCCAGAGCCAATTTTAACTTCACGGCGGATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
33669 ACTCGA
1 ACTCGA
33675 AATAATACAA
Statistics
Matches: 189, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
106 189 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCTC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:34023 original size:65 final size:65
Alignment explanation
Indices: 33902--34059 Score: 192
Period size: 65 Copynumber: 2.4 Consensus size: 65
33892 TTTTGGAACT
*
33902 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAC
* * * * **** *
33967 GAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTGAATTTGTTTCCTTTGAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAACATTTCCCTTGAAA
34031 C
65 C
* *
34032 AAATTTCGTCTCCCTTGAGACATTTTCT
1 AAATTTTGTCTCCCTTGAGACAGTTTCT
34060 TTTGGAACTA
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 3 0.04
65 74 0.96
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (65 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAC
Found at i:34088 original size:167 final size:167
Alignment explanation
Indices: 33821--34341 Score: 898
Period size: 167 Copynumber: 3.1 Consensus size: 167
33811 ACAGTTTCCA
* * * *
33821 AGTTTCCCTTGAAACAAAATATTTAAATTTGTTTTCATTGAAACTAATTTCGTCTCCCTTGAGAC
1 AGTTTCCCTTGAAACAAAATCTTTGAATTTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGAC
* * *
33886 ATTTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
66 ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAA
33951 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
131 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
* *
33988 AGTTTCTCTTGAAACAAAATCTTTGAATTTGTTTCCTTTGAAACAAATTTCGTCTCCCTTGAGAC
1 AGTTTCCCTTGAAACAAAATCTTTGAATTTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGAC
*
34053 ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATCGAAA
66 ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAA
34118 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
131 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
* * *
34155 AGTTTCTCTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGAC
1 AGTTTCCCTTGAAACAAAATCTTTGAATTTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGAC
*
34220 ATTTTCTTTTGGAAATAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAA
66 ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAA
*
34285 ACATTTCCCTTGAGATGAATTTTGTCTCTCTTGAGAT
131 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
*
34322 AGGTTCCCTTGAAACAAAAT
1 AGTTTCCCTTGAAACAAAAT
34342 TTTTTCTCCT
Statistics
Matches: 337, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
167 337 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (167 bp):
AGTTTCCCTTGAAACAAAATCTTTGAATTTGTTTCCATTGAAACAAATTTCGTCTCCCTTGAGAC
ATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAA
ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
Found at i:34151 original size:102 final size:102
Alignment explanation
Indices: 33970--34153 Score: 253
Period size: 102 Copynumber: 1.8 Consensus size: 102
33960 TTGAAATGAA
* * **** *
33970 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTTTGAATTTGTTTCCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCATCGAAAACATTTCCCTTGAAACAAA
34035 TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
66 TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
**
34072 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAA-CATCGAAAACATTTCCCTTGAAATGA
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCATCGAAAACATTTCCCTTGAAACAA
* *
34136 ATTTTGTCTCTCTTGAGA
65 ATTTCGTCTCCCTTGAGA
34154 TAGTTTCTCT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
102 67 0.96
103 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (102 bp):
TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCATCGAAAACATTTCCCTTGAAACAAA
TTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
Found at i:34190 original size:65 final size:65
Alignment explanation
Indices: 34072--34218 Score: 190
Period size: 65 Copynumber: 2.3 Consensus size: 65
34062 TGGAACTAAG
**
34072 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATCGAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATCGAAAACATTTCCCTTGAAACAAA
* * * *
34137 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTG-AATCTGTTTCCCTTGAAACA
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAA-CATCGAAAAC-ATTTCCCTTGAAACA
34200 AA
64 AA
* *
34202 TTTCGTCTCCCTTGAGA
1 TTTTGTCTCTCTTGAGA
34219 CATTTTCTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
64 6 0.08
65 66 0.92
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATCGAAAACATTTCCCTTGAAACAAA
Found at i:34306 original size:102 final size:101
Alignment explanation
Indices: 34121--34503 Score: 439
Period size: 102 Copynumber: 3.8 Consensus size: 101
34111 ATCGAAAACA
* * * *
34121 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTG-AATC
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAAC
* ** * * * *
34184 TGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAT
65 -ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
** * *
34222 TTTCTTTTGGAAATAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
*
34287 ATTTCCCTTGAGATGAATTTTGTCTCTCTTGAGATAG
65 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
* * *
34324 GTTCCCTTGAAACAAAATTTTTTCTC-CTTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
1 TTTCCCTTGAAA-TAAATTTTGTCTCTC-TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
* * *
34388 CATTTCCCTTGAAATGAATTTTGTCACTCATAAGATAG
64 CATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
* * * * *
34426 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACATTTTCTCTTGAAGCATAAACTTTGAAAACA
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
34491 GTTTCCTTTGAAA
66 -TTTCCCTTGAAA
34504 CAAAATCTTT
Statistics
Matches: 243, Mismatches: 32, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
101 57 0.23
102 180 0.74
103 6 0.02
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (101 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
Found at i:34356 original size:37 final size:37
Alignment explanation
Indices: 34302--34374 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
34292 CCTTGAGATG
*
34302 AATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAA
1 AATTTTGTCTCTCTTGAGACAGGTTCCCTTGAAACAA
* * *
34339 AATTTTTTCTC-CTTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCTC-TTGAGACAGGTTCCCTTGAAACA
34375 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.03
37 30 0.97
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (37 bp):
AATTTTGTCTCTCTTGAGACAGGTTCCCTTGAAACAA
Found at i:34412 original size:167 final size:166
Alignment explanation
Indices: 33876--34439 Score: 590
Period size: 167 Copynumber: 3.4 Consensus size: 166
33866 AATTTCGTCT
* * * *
33876 CCCTTGAGACATTTTCTTTTGGAACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA
1 CCCTTGAGACATTTTCTTTTGGAAATAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATA
33941 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
66 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
** *
34006 ATCTTTGAATTTGTTTCCTTTGAAACAAATT-TC--G--TC-T--
131 A----T---TTT-TTTCCTTTG-AACAGTTTCTCTTGAAACATAA
*
34043 CCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATA
1 CCCTTGAGACATTTTCTTTTGGAAATAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATA
*
34108 AACATCGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
66 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
* *
34173 A------T-CTTTGAATCTGTTTCCCTTGAAACA-AA
131 ATTTTTTTCCTTTGAA-CAGTTTCTCTTGAAACATAA
34202 TTTCGTCTCCCTTGAGACATTTTCTTTTGGAAATAAGTTTTGTCTCTCTTGAGATAGTTTCTCTT
1 --------CCCTTGAGACATTTTCTTTTGGAAATAAGTTTTGTCTCTCTTGAGATAGTTTCTCTT
* * *
34267 GAAACATAAACATTGAAAACATTTCCCTTGAGATGAATTTTGTCTCTCTTGAGATAGGTTCCCTT
58 GAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTT
34332 GAAACAAAATTTTTTCTCCTTTGAGACAGTTTCTCTTGAAACATAA
123 GAAACAAAATTTTTT-TCCTTTGA-ACAGTTTCTCTTGAAACATAA
* * * ** * * * *
34378 ACATTGAAAACA-TTTCCCTT-GAAATGAA-TTTTGTCACTCATAAGATAGTTTCCCTTGAAACA
1 CCCTTG-AGACATTTTCTTTTGGAAAT-AAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
34440 AATTTTGTCT
Statistics
Matches: 343, Mismatches: 25, Indels: 58
0.81 0.06 0.14
Matches are distributed among these distances:
151 2 0.01
152 8 0.02
153 2 0.01
155 1 0.00
157 1 0.00
167 288 0.84
168 12 0.03
169 4 0.01
174 1 0.00
175 21 0.06
176 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (166 bp):
CCCTTGAGACATTTTCTTTTGGAAATAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATA
AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
ATTTTTTTCCTTTGAACAGTTTCTCTTGAAACATAA
Found at i:34617 original size:36 final size:36
Alignment explanation
Indices: 34541--34638 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 36
34531 AACAAATCTC
* * * *
34541 GTCTCCCTTGAGACAGTTTCTTTTG--GAAGTTTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAAAAATTTTT
34575 GTCTCTCTTGAGACAGTTTCTCTTGAAAAAATTTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAAAAATTTTT
* *
34611 GTCTCTCTTGAGACAATTTCCCTTGAAA
1 GTCTCTCTTGAGACAGTTTCTCTTGAAA
34639 CTTCAATCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
34 23 0.41
36 33 0.59
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.43
Consensus pattern (36 bp):
GTCTCTCTTGAGACAGTTTCTCTTGAAAAAATTTTT
Found at i:34698 original size:33 final size:34
Alignment explanation
Indices: 34658--34740 Score: 141
Period size: 35 Copynumber: 2.4 Consensus size: 34
34648 TTGAATACAT
*
34658 TTTCTCTTGAAACAC-AAAAAACCTTTGAAATTG
1 TTTCTCTTGAAACACAAAAAAACCTTTGAAAATG
34691 TTTCTCTTGAAACACAAAAAAAACCTTTGAAAATG
1 TTTCTCTTGAAACAC-AAAAAAACCTTTGAAAATG
34726 TTTCTCTTGAAACAC
1 TTTCTCTTGAAACAC
34741 CAAACCCTCG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 15 0.32
35 32 0.68
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (34 bp):
TTTCTCTTGAAACACAAAAAAACCTTTGAAAATG
Found at i:34884 original size:84 final size:85
Alignment explanation
Indices: 34748--34905 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 85
34738 CACCAAACCC
* * * *
34748 TCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAACTCAAGGTTAA-AAGGG
1 TCGAGTTCGACTACACTCAGCTCTGAAGGCACATCATTTACAGCATAACTCAAGG-CAATAAGGG
*
34812 TTATTTGTCACCAAAAGACCT
65 TTATCTGTCACCAAAAGACCT
** * *
34833 TCGAGTTCGACTATGCTCAGCTCT-AAGGCACATCATTTACAGTATAGCTCAAGGCAATAAGGGT
1 TCGAGTTCGACTACACTCAGCTCTGAAGGCACATCATTTACAGCATAACTCAAGGCAATAAGGGT
34897 TATCTGTCA
66 TATCTGTCA
34906 ATAAAATTGT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
83 2 0.03
84 41 0.65
85 20 0.32
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (85 bp):
TCGAGTTCGACTACACTCAGCTCTGAAGGCACATCATTTACAGCATAACTCAAGGCAATAAGGGT
TATCTGTCACCAAAAGACCT
Found at i:35985 original size:22 final size:22
Alignment explanation
Indices: 35959--36060 Score: 62
Period size: 25 Copynumber: 4.2 Consensus size: 22
35949 TATTTTTAAT
35959 TATATTTTATTTATTTAT-TTA
1 TATATTTTATTTATTTATATTA
*
35980 CTATATTCCTTTTTTATTTATATTA
1 -TATATT--TTATTTATTTATATTA
* *
36005 TATTAATTTTATTATATATATCTTA
1 TA-T-ATTTTATT-TATTTATATTA
* *
36030 TATCATTATGTATATATATATATATA
1 TAT-ATT-T-TATTTATTTATAT-TA
36056 TATAT
1 TATAT
36061 ATATATATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
22 6 0.09
24 21 0.33
25 26 0.41
26 11 0.17
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (22 bp):
TATATTTTATTTATTTATATTA
Found at i:36024 original size:2 final size:2
Alignment explanation
Indices: 36017--36081 Score: 80
Period size: 2 Copynumber: 33.0 Consensus size: 2
36007 TTAATTTTAT
* *
36017 TA TA TA TA TC T- TA TA TCA T- TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
*
36058 TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
36082 GATGTATTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
1 2 0.04
2 51 0.93
3 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36030 original size:14 final size:15
Alignment explanation
Indices: 35998--36081 Score: 70
Period size: 16 Copynumber: 5.6 Consensus size: 15
35988 CTTTTTTATT
35998 TATATTATAT-TA-A
1 TATATTATATATATA
36011 T-T-TTAT-TATATA
1 TATATTATATATATA
* *
36023 TATCTTATATCATTATG
1 TATATTATAT-A-TATA
36040 TATATATATATATATA
1 TATAT-TATATATATA
36056 TATATATATATATATA
1 TATAT-TATATATATA
36072 TATATGTATA
1 TATAT-TATA
36082 GATGTATTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
10 1 0.02
11 6 0.10
12 3 0.05
13 2 0.03
14 4 0.07
15 1 0.02
16 29 0.49
17 8 0.14
18 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:36164 original size:39 final size:36
Alignment explanation
Indices: 36111--36188 Score: 111
Period size: 39 Copynumber: 2.1 Consensus size: 36
36101 ATTTACTATG
*
36111 TATATATATTTTTTCTTAATATTATATCTTATATGTTTT
1 TATATATATATTTTCTTAATATTATAT-TT-T-TGTTTT
*
36150 TATATATATATTTTCTTAATATTCTATTTTTGTTTT
1 TATATATATATTTTCTTAATATTATATTTTTGTTTT
36186 TAT
1 TAT
36189 TTATTTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 9 0.24
37 1 0.03
38 2 0.05
39 25 0.68
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (36 bp):
TATATATATATTTTCTTAATATTATATTTTTGTTTT
Found at i:36235 original size:17 final size:17
Alignment explanation
Indices: 36186--36236 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
36176 TTTTTGTTTT
*
36186 TATTTATTTATATATATTA
1 TATTT-TTTCTAT-TATTA
*
36205 TATTTTTACT-TTATTA
1 TATTTTTTCTATTATTA
36221 TATTTTTTCTATTATT
1 TATTTTTTCTATTATT
36237 TTTTCTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 14 0.50
17 6 0.21
18 3 0.11
19 5 0.18
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTTTCTATTATTA
Found at i:36369 original size:18 final size:17
Alignment explanation
Indices: 36337--36381 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
36327 TGTACACATT
36337 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
36354 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
36372 ATTTTTTTAC
1 ATTTTTTTAC
36382 TCCATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:36379 original size:17 final size:17
Alignment explanation
Indices: 36335--36381 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
36325 TATGTACACA
36335 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
36352 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
36370 TTATTTTTTTAC
1 TTATTTTTTTAC
36382 TCCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:37397 original size:52 final size:53
Alignment explanation
Indices: 37313--37414 Score: 147
Period size: 52 Copynumber: 1.9 Consensus size: 53
37303 TTTGATGTTT
*
37313 ATAAAAACACATTTTTTGTCAAAATTATCAACAATCATAA-AAA-AAATCAAC
1 ATAAAAACACATTTTTTGACAAAATTATCAACAATCATAATAAACAAATCAAC
*
37364 ATAAAAACACATTTTTTAAGAC-AAATTATCAACATTCATAATAAACAAATC
1 ATAAAAACACATTTTTT--GACAAAATTATCAACAATCATAATAAACAAATC
37415 TACTAACATG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
51 17 0.38
52 18 0.40
53 5 0.11
54 5 0.11
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (53 bp):
ATAAAAACACATTTTTTGACAAAATTATCAACAATCATAATAAACAAATCAAC
Found at i:39000 original size:18 final size:18
Alignment explanation
Indices: 38962--39038 Score: 109
Period size: 18 Copynumber: 4.2 Consensus size: 18
38952 AAAACATAAC
38962 AAAGTATTTCTAATCATCAA
1 AAAGTATTTCTAATC--CAA
38982 AAAGTATTTCTAATCCAA
1 AAAGTATTTCTAATCCAA
* *
39000 AAACTTTTTCTAATCCAA
1 AAAGTATTTCTAATCCAA
*
39018 AGAGTATTTCTAATCCAA
1 AAAGTATTTCTAATCCAA
39036 AAA
1 AAA
39039 AACACATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
18 36 0.71
20 15 0.29
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (18 bp):
AAAGTATTTCTAATCCAA
Found at i:40551 original size:18 final size:18
Alignment explanation
Indices: 40509--40566 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
40499 TCTCTACGGT
*
40509 GGATGAATCGACCGAAGGA
1 GGATGAA-CAACCGAAGGA
*
40528 GG-TGAACAACCGAAGAA
1 GGATGAACAACCGAAGGA
40545 GGATGAACAACCGAAGGA
1 GGATGAACAACCGAAGGA
40563 GGAT
1 GGAT
40567 AAATCGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 11 0.31
18 22 0.63
19 2 0.06
ACGTcount: A:0.41, C:0.16, G:0.34, T:0.09
Consensus pattern (18 bp):
GGATGAACAACCGAAGGA
Found at i:43629 original size:60 final size:61
Alignment explanation
Indices: 43560--43692 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 61
43550 TTTTAAATGA
* * * *
43560 TTCAATTTCATCCCTAAAA-TATGAC-TATCATTTTAAATTAATCCTCAAAC-TTTTGAACAT
1 TTCAATTTCAT-CCGAAAACTATAACAT-TCATTCTAAATTAATCCCCAAACTTTTTGAACAT
* **
43620 TTCATTTTCATCCGAAAACTATAACATTCATTCTAAATTGGTCCCCAAACTTTTTGAACA-
1 TTCAATTTCATCCGAAAACTATAACATTCATTCTAAATTAATCCCCAAACTTTTTGAACAT
43680 TTCTAATTTCATC
1 TTC-AATTTCATC
43693 TCAAACTATA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 6 0.10
60 37 0.61
61 18 0.30
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.40
Consensus pattern (61 bp):
TTCAATTTCATCCGAAAACTATAACATTCATTCTAAATTAATCCCCAAACTTTTTGAACAT
Found at i:43928 original size:60 final size:60
Alignment explanation
Indices: 43836--44007 Score: 179
Period size: 60 Copynumber: 2.9 Consensus size: 60
43826 ATGGGCATGA
* * ** * *
43836 AATTGGAATATTCAAAAGCTTGGGTATTAATTTAGAAAGAGGGTCATAGTTTAGGGAT-G
1 AATTGAAATATTCAAAAGTTTAAGAACTAATTTAGAAAGAGGGTCATAGTTTAGGGATCG
* * * * *
43895 AAATT-AGAATGTTTAAAAGTTTAAGGACTAATTTAGAATGAGTGTCATAGTTTAGGGATCG
1 -AATTGA-AATATTCAAAAGTTTAAGAACTAATTTAGAAAGAGGGTCATAGTTTAGGGATCG
* *
43956 AATTGAAATATTCAAAAGTTTAAGAACTAATTTA-AAATGAGGCTTATAGTTT
1 AATTGAAATATTCAAAAGTTTAAGAACTAATTTAGAAA-GAGGGTCATAGTTT
44008 GAGGACATAT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
59 2 0.02
60 87 0.96
61 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (60 bp):
AATTGAAATATTCAAAAGTTTAAGAACTAATTTAGAAAGAGGGTCATAGTTTAGGGATCG
Found at i:45012 original size:46 final size:46
Alignment explanation
Indices: 44944--45054 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
44934 AATAAGGTTG
* *
44944 TGTTTGCTTTCTTT-TATTTCTTTTTTAAGCAGTTCTTGTTTAGTTCA
1 TGTTTG-TTTCTTTAT-TTTCTTTTTGAAGCAGTTCGTGTTTAGTTCA
44991 TGTTTGTTTCTTTATTTTCTTTTTGAAGCAGTTCGTGTTTAGTTCA
1 TGTTTGTTTCTTTATTTTCTTTTTGAAGCAGTTCGTGTTTAGTTCA
45037 TGTTTGTTTCTTTATTTT
1 TGTTTGTTTCTTTATTTT
45055 TTAAATTGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
46 54 0.89
47 7 0.11
ACGTcount: A:0.12, C:0.11, G:0.14, T:0.63
Consensus pattern (46 bp):
TGTTTGTTTCTTTATTTTCTTTTTGAAGCAGTTCGTGTTTAGTTCA
Found at i:57039 original size:24 final size:24
Alignment explanation
Indices: 57012--57077 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
57002 GTTATTTAAA
57012 CGGGTATTGGGCCGGGTATTGAGT
1 CGGGTATTGGGCCGGGTATTGAGT
* *
57036 CGGGTATTGGGTC-GGTATTGGGT
1 CGGGTATTGGGCCGGGTATTGAGT
* * *
57059 CAGGAATCGGGCCGGGTAT
1 CGGGTATTGGGCCGGGTAT
57078 ATATATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.14, C:0.14, G:0.45, T:0.27
Consensus pattern (24 bp):
CGGGTATTGGGCCGGGTATTGAGT
Found at i:57054 original size:11 final size:12
Alignment explanation
Indices: 57012--57059 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
57002 GTTATTTAAA
*
57012 CGGGTATTGGGC
1 CGGGTATTGGGT
*
57024 CGGGTATTGAGT
1 CGGGTATTGGGT
57036 CGGGTATTGGGT
1 CGGGTATTGGGT
57048 C-GGTATTGGGT
1 CGGGTATTGGGT
57059 C
1 C
57060 AGGAATCGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 11 0.33
12 22 0.67
ACGTcount: A:0.10, C:0.12, G:0.46, T:0.31
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:57139 original size:24 final size:25
Alignment explanation
Indices: 57075--57139 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
57065 TCGGGCCGGG
57075 TATATATATATATATATTTAAATTAAA
1 TATATAT-TATAT-TATTTAAATTAAA
*
57102 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
57126 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
57140 ATATATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.56
25 2 0.06
26 1 0.03
27 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:57188 original size:13 final size:13
Alignment explanation
Indices: 57169--57213 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
57159 TTTAATATTT
*
57169 ATCGGGTTGGGT-
1 ATCGGGGTGGGTA
57181 ATCGGGGTGGGTA
1 ATCGGGGTGGGTA
*
57194 ATCGGGGCGGGTA
1 ATCGGGGTGGGTA
57207 ATCGGGG
1 ATCGGGG
57214 CGGGGATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.13, C:0.11, G:0.53, T:0.22
Consensus pattern (13 bp):
ATCGGGGTGGGTA
Found at i:57214 original size:13 final size:13
Alignment explanation
Indices: 57177--57217 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
57167 TTATCGGGTT
*
57177 GGGT-ATCGGGGT
1 GGGTAATCGGGGC
57189 GGGTAATCGGGGC
1 GGGTAATCGGGGC
57202 GGGTAATCGGGGC
1 GGGTAATCGGGGC
57215 GGG
1 GGG
57218 GATTACCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 4 0.15
13 23 0.85
ACGTcount: A:0.12, C:0.12, G:0.59, T:0.17
Consensus pattern (13 bp):
GGGTAATCGGGGC
Found at i:58507 original size:42 final size:42
Alignment explanation
Indices: 58421--58527 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
58411 AAATTTTGTA
* * * *
58421 TTTGTTTCATGTAATTTGTTTTTTGAAAAATATTTTTTTATG
1 TTTGTTTCACGTAATTCGTTTTTCGAAAAATATTTTTTCATG
* * *
58463 TTTTTTTTACGTAATTCGTTTTTCGAAAAATATTTTTTCGTG
1 TTTGTTTCACGTAATTCGTTTTTCGAAAAATATTTTTTCATG
* *
58505 TTTGTTTCATGTAATTCATTTTT
1 TTTGTTTCACGTAATTCGTTTTT
58528 TAGAATGTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.21, C:0.07, G:0.11, T:0.61
Consensus pattern (42 bp):
TTTGTTTCACGTAATTCGTTTTTCGAAAAATATTTTTTCATG
Found at i:58730 original size:14 final size:15
Alignment explanation
Indices: 58704--58734 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
58694 CATTTTCATC
58704 AAAATATTATTTATT
1 AAAATATTATTTATT
58719 AAAATA-TATTTATT
1 AAAATATTATTTATT
58733 AA
1 AA
58735 TATTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATATTATTTATT
Found at i:58759 original size:22 final size:24
Alignment explanation
Indices: 58711--58774 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 24
58701 ATCAAAATAT
*
58711 TATTTATTAA-AATATATTTATTAA
1 TATTTA-TAATAATATATATATTAA
58735 TATTTATAATAATATA-ATATT-A
1 TATTTATAATAATATATATATTAA
* *
58757 TATTTTTAATATTATATA
1 TATTTATAATAATATATA
58775 AAATAATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 15 0.43
23 8 0.23
24 12 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTTATAATAATATATATATTAA
Found at i:58807 original size:33 final size:32
Alignment explanation
Indices: 58763--58837 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
58753 ATTATATTTT
*
58763 TAATATTATATAAAATAATCA-ATTATATTATAA
1 TAATATAATATAAAAT-ATCATATT-TATTATAA
* * *
58796 TAATATAATATAAGATATTATATTTATTTTAA
1 TAATATAATATAAAATATCATATTTATTATAA
58828 T-ATATAATAT
1 TAATATAATAT
58838 TTTTTATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 9 0.24
32 11 0.30
33 17 0.46
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (32 bp):
TAATATAATATAAAATATCATATTTATTATAA
Found at i:58837 original size:24 final size:25
Alignment explanation
Indices: 58801--58878 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 25
58791 TATAATAATA
58801 TAATATA-AGATATTATATTTAT-TT
1 TAATATATA-ATATTATATTTATATT
58825 TAATATATAATATT-T-TTTATATT
1 TAATATATAATATTATATTTATATT
58848 TAATAATGAATAATATTAT-TTATATATT
1 TAAT-AT--ATAATATTATATT-TATATT
58876 TAA
1 TAA
58879 ATAATATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
22 5 0.11
23 7 0.15
24 14 0.30
25 1 0.02
26 8 0.17
27 3 0.06
28 9 0.19
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (25 bp):
TAATATATAATATTATATTTATATT
Found at i:58854 original size:26 final size:29
Alignment explanation
Indices: 58825--58891 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 29
58815 ATATTTATTT
58825 TAATATATAATATT-TTT-TATATTT-AA
1 TAATATATAATATTATTTATATATTTAAA
58851 TAATGA-ATAATATTATTTATATATTTAAA
1 TAAT-ATATAATATTATTTATATATTTAAA
*
58880 TAATATTTAATA
1 TAATATATAATA
58892 AAGATATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
26 12 0.34
27 4 0.11
28 8 0.23
29 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
TAATATATAATATTATTTATATATTTAAA
Found at i:59251 original size:20 final size:21
Alignment explanation
Indices: 59216--59264 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
59206 TCAGATGTTT
59216 TCCAGAAATGTGTAATTCATTC
1 TCCAGAAA-GTGTAATTCATTC
*
59238 TCCAGAAA-TGTAATTCATTT
1 TCCAGAAAGTGTAATTCATTC
59258 TCCAGAA
1 TCCAGAA
59265 TTCAAATTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 18 0.69
22 8 0.31
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (21 bp):
TCCAGAAAGTGTAATTCATTC
Found at i:59272 original size:20 final size:20
Alignment explanation
Indices: 59229--59273 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
59219 AGAAATGTGT
**
59229 AATTCATTCTCCAGAAATGT
1 AATTCATTCTCCAGAAATCA
* *
59249 AATTCATTTTCCAGAATTCA
1 AATTCATTCTCCAGAAATCA
59269 AATTC
1 AATTC
59274 CGGTAATTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (20 bp):
AATTCATTCTCCAGAAATCA
Found at i:59283 original size:15 final size:15
Alignment explanation
Indices: 59247--59313 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
59237 CTCCAGAAAT
**
59247 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
59262 G-AATTCAAATTCCG
1 GTAATTCAAATTCCA
**
59276 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
59291 GTAATTCAAATTGCA
1 GTAATTCAAATTCCA
59306 GTAATTCA
1 GTAATTCA
59314 TTTTCCGGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 11 0.26
15 31 0.74
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:59289 original size:29 final size:30
Alignment explanation
Indices: 59247--59319 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
59237 CTCCAGAAAT
*
59247 GTAATTCATTTTCCAG-AATTCAAATTCCG
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
59276 GTAATTCATTTTCCAGTAATTCAAATTGCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
59306 GTAATTCATTTTCC
1 GTAATTCATTTTCC
59320 GGAAAACCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:71077 original size:20 final size:21
Alignment explanation
Indices: 71035--71079 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
71025 TTAATTAAAA
*
71035 TTTATTTAAAATATTATTATT
1 TTTATTTAAAACATTATTATT
71056 TTTATTTAAAACATTA-TATT
1 TTTATTTAAAACATTATTATT
71076 TTTA
1 TTTA
71080 ATATTTCTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATTTAAAACATTATTATT
Found at i:73345 original size:19 final size:19
Alignment explanation
Indices: 73321--73363 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
73311 GATGTGGGTT
*
73321 TTTAATTTTAAAATAAT-AA
1 TTTAATTTCAAAA-AATAAA
73340 TTTAA-TTCAAAAAATAAA
1 TTTAATTTCAAAAAATAAA
73358 TTTAAT
1 TTTAAT
73364 GTGATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.14
18 13 0.62
19 5 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAATTTCAAAAAATAAA
Found at i:73436 original size:18 final size:18
Alignment explanation
Indices: 73413--73447 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
73403 AGATATTGAC
73413 GTGATAATTTATGATGAT
1 GTGATAATTTATGATGAT
73431 GTGATAATTTATGATGA
1 GTGATAATTTATGATGA
73448 CTAATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (18 bp):
GTGATAATTTATGATGAT
Done.