Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 20 of 135
Found at i:8431197 original size:18 final size:16
Alignment explanation
Indices: 8431168--8431220 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
8431158 AAATATGTAC
8431168 TTATATAATAAAAATA
1 TTATATAATAAAAATA
*
8431184 TTATATACAT-TAAA-A
1 TTATATA-ATAAAAATA
*
8431199 GTATAT-ATAAAAATA
1 TTATATAATAAAAATA
8431214 TTATATA
1 TTATATA
8431221 TCATTATGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 12 0.41
16 10 0.34
17 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TTATATAATAAAAATA
Found at i:8434775 original size:3 final size:3
Alignment explanation
Indices: 8434767--8434817 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
8434757 TTAAGGAACA
8434767 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
8434815 AAT
1 AAT
8434818 GCTTCACATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:8437414 original size:20 final size:22
Alignment explanation
Indices: 8437375--8437422 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
8437365 TTATTTTCAG
*
8437375 CAAAAAAAAAAATCTGTTTGCT
1 CAAAAAAAAAAATCTATTTGCT
*
8437397 -AAAATAAAAAAT-TATTTGCT
1 CAAAAAAAAAAATCTATTTGCT
8437417 CAAAAA
1 CAAAAA
8437423 TTAAATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.27
Consensus pattern (22 bp):
CAAAAAAAAAAATCTATTTGCT
Found at i:8439170 original size:3 final size:3
Alignment explanation
Indices: 8439162--8439194 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
8439152 GGGAGGGAGA
8439162 CTT CTT CTT CTT CTT CTT CTT CTCT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT CT
8439195 CTGGACCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:8440777 original size:2 final size:2
Alignment explanation
Indices: 8440770--8440800 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8440760 AAAATAATCA
8440770 AT AT 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 AT AT A
8440801 GTGTTGGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8457885 original size:15 final size:14
Alignment explanation
Indices: 8457864--8457902 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
8457854 GTAGTTTACC
8457864 GTATTTTATATTAT
1 GTATTTTATATTAT
8457878 GTTATTTTATATATTAT
1 G-TA-TTT-TATATTAT
8457895 GTATTTTA
1 GTATTTTA
8457903 AAACACATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.14
15 5 0.23
16 5 0.23
17 9 0.41
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (14 bp):
GTATTTTATATTAT
Found at i:8457892 original size:17 final size:16
Alignment explanation
Indices: 8457870--8457902 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
8457860 TACCGTATTT
8457870 TATATTATGTTATTTTA
1 TATATTATG-TATTTTA
8457887 TATATTATGTATTTTA
1 TATATTATGTATTTTA
8457903 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TATATTATGTATTTTA
Found at i:8459035 original size:39 final size:41
Alignment explanation
Indices: 8458966--8459056 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 41
8458956 AATAATTATA
* * * *
8458966 TTTAATACAATAAAATCTCTATTGTTTTTAT-TTGTG-TTT
1 TTTAATATAATAAAATCTCTATTATATTTATATAGTGTTTT
*
8459005 TTTAATATAATAAAA-CATTTATTATATTTATGATAGTGTTTT
1 TTTAATATAATAAAATC-TCTATTATATTTAT-ATAGTGTTTT
8459047 TTTAATATAA
1 TTTAATATAA
8459057 ATATTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 1 0.02
39 25 0.58
41 4 0.09
42 13 0.30
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (41 bp):
TTTAATATAATAAAATCTCTATTATATTTATATAGTGTTTT
Found at i:8460729 original size:2 final size:2
Alignment explanation
Indices: 8460722--8460760 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8460712 GATGGATGCA
8460722 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
8460761 GAAAAGTTAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8462457 original size:23 final size:23
Alignment explanation
Indices: 8462431--8462475 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
8462421 AATTTCGAAT
**
8462431 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
8462454 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
8462476 GAATTGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:8468349 original size:28 final size:28
Alignment explanation
Indices: 8468310--8468528 Score: 110
Period size: 29 Copynumber: 7.5 Consensus size: 28
8468300 CCCGAGGGTG
*
8468310 AAATGGTAATTTTTGACTTTCGGGGGTAA
1 AAATGGTAATTTTTGAATTT-GGGGGTAA
* *
8468339 AAATGG-AATTTTGGTGAAATTGGGGTTAA
1 AAATGGTAATTTT--TGAATTTGGGGGTAA
* *
8468368 AAATGG-GATTTTGGAAAGTTTGGGGGT-A
1 AAATGGTAATTTTTG-AA-TTTGGGGGTAA
* ** *
8468396 AAATGGTAATTTTTGGTGAAATCAGGGTTAA
1 AAATGGTAA-TTTT--TGAATTTGGGGGTAA
* *
8468427 AAATGG-AATTTTGGAAAGTTTAGGGGT-A
1 AAATGGTAATTTTTG-AA-TTTGGGGGTAA
* * **
8468455 AAATGGTAATTTTTGGTGAAATCGGGATTAA
1 AAATGGTAA-TTTT--TGAATTTGGGGGTAA
*
8468486 AAATGG-AATTTTGGAAAGTTTGGGGGT-A
1 AAATGGTAATTTTTG-AA-TTTGGGGGTAA
8468514 AAATGGTAATTTTTG
1 AAATGGTAATTTTTG
8468529 GTGAAATTGG
Statistics
Matches: 142, Mismatches: 29, Indels: 38
0.68 0.14 0.18
Matches are distributed among these distances:
27 3 0.02
28 33 0.23
29 60 0.42
30 26 0.18
31 18 0.13
32 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (28 bp):
AAATGGTAATTTTTGAATTTGGGGGTAA
Found at i:8468429 original size:59 final size:59
Alignment explanation
Indices: 8468331--8468645 Score: 467
Period size: 59 Copynumber: 5.4 Consensus size: 59
8468321 TTTGACTTTC
** *
8468331 GGGGGTAAAAATGG-AA-TTTTGGTGAAATTGGGGTTAAAAATGGGATTTTGGAAAGTTT
1 GGGGGT-AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTT
8468389 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTT
*
8468448 AGGGGTAAAATGGTAATTTTTGGTGAAATC-GGGATTAAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGG-TTAAAAATGGAATTTTGGAAAGTTT
* * *
8468507 GGGGGTAAAATGGTAATTTTTGGTGAAAT-TGGGTCAAAAATGGAATTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTT
* * * * *
8468565 AGGGGTAAAATGGTAATTTTTGGTAAAACCAGGGTTAAAAATGGAATTTTAGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTT
*
8468624 GAGGGTAAAATGGTAATTTTTG
1 GGGGGTAAAATGGTAATTTTTG
8468646 AACAATTTAA
Statistics
Matches: 237, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
57 7 0.03
58 60 0.25
59 170 0.72
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTT
Found at i:8468583 original size:117 final size:117
Alignment explanation
Indices: 8468332--8468645 Score: 481
Period size: 117 Copynumber: 2.7 Consensus size: 117
8468322 TTGACTTTCG
* *
8468332 GGGGTAAAAATGG-AA-TTTTGGTGAAATTGGGGTTAAAAATGGGATTTTGGAAAGTTTGGGGGT
1 GGGGT-AAAATGGTAATTTTTGGTGAAA-TCGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
* *
8468395 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTA
64 AAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTCA
8468449 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTTGGAAAGTTTGGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGG-TTAAAAATGGAATTTTGGAAAGTTTGGGGGTA
*
8468514 AAATGGTAATTTTTGGTGAAAT-TGGGTCAAAAATGGAATTTTGGAAAGTTCA
65 AAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTCA
* * * * *
8468566 GGGGTAAAATGGTAATTTTTGGTAAAACCAGGGTTAAAAATGGAATTTTAGAAAGTTCGAGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATC-GGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTA
8468631 AAATGGTAATTTTTG
65 AAATGGTAATTTTTG
8468646 AACAATTTAA
Statistics
Matches: 183, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
116 7 0.04
117 109 0.60
118 67 0.37
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (117 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAA
AATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTCA
Found at i:8469871 original size:12 final size:11
Alignment explanation
Indices: 8469813--8469882 Score: 50
Period size: 13 Copynumber: 5.6 Consensus size: 11
8469803 TTATTAATAT
8469813 TAATATTAATTA
1 TAATATT-ATTA
8469825 TAAATATTTATTA
1 T-AATA-TTATTA
*
8469838 CTATTATTTATTA
1 -TAATA-TTATTA
*
8469851 TCATGATTATTA
1 TAAT-ATTATTA
8469863 CTAATATTATTAA
1 -TAATATTATT-A
8469876 TAATATT
1 TAATATT
8469883 TAAAAGGTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
12 22 0.46
13 23 0.48
14 3 0.06
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (11 bp):
TAATATTATTA
Found at i:8470621 original size:17 final size:17
Alignment explanation
Indices: 8470587--8470628 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
8470577 TTTAAATGTA
*
8470587 TTTAAATTTAAATTAAT
1 TTTAAATTTAAATAAAT
*
8470604 TTTAAATTTGAATAAAT
1 TTTAAATTTAAATAAAT
*
8470621 TTAAAATT
1 TTTAAATT
8470629 AATTCAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TTTAAATTTAAATAAAT
Found at i:8472733 original size:17 final size:16
Alignment explanation
Indices: 8472702--8472735 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
8472692 ATGTTAAAAA
8472702 TTATATAAAAATATAT
1 TTATATAAAAATATAT
*
8472718 TTATAGTAAAATTATAT
1 TTATA-TAAAAATATAT
8472735 T
1 T
8472736 AGAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTATATAAAAATATAT
Found at i:8473809 original size:22 final size:22
Alignment explanation
Indices: 8473784--8473827 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8473774 AAACATTAAC
* *
8473784 AATAAAATAGTAGCAAAATAAT
1 AATAAAATAGAAACAAAATAAT
*
8473806 AATAAAATGGAAACAAAATAAT
1 AATAAAATAGAAACAAAATAAT
8473828 GACAAAAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (22 bp):
AATAAAATAGAAACAAAATAAT
Found at i:8478612 original size:2 final size:2
Alignment explanation
Indices: 8478599--8478632 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
8478589 TTGTTACCAA
* *
8478599 AT AT AT AC AT AT AT AC 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 AT AT
8478633 TTGCAGGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:8478923 original size:16 final size:16
Alignment explanation
Indices: 8478899--8478930 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8478889 TACCGCTCGA
*
8478899 ATTTGGATTTTTTCGG
1 ATTTAGATTTTTTCGG
8478915 ATTTAGATTTTTTCGG
1 ATTTAGATTTTTTCGG
8478931 GCTTGGATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.22, T:0.56
Consensus pattern (16 bp):
ATTTAGATTTTTTCGG
Found at i:8485339 original size:29 final size:30
Alignment explanation
Indices: 8485307--8485376 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
8485297 AAATTAAAAT
*
8485307 TTCATGTATAAAATTGTACA-AAATCAAAG
1 TTCATGTATAAAATTGCACATAAATCAAAG
* * *
8485336 TTCATGCATACAATTGCACATTAAATCATAG
1 TTCATGTATAAAATTGCACA-TAAATCAAAG
8485367 TTCATGTATA
1 TTCATGTATA
8485377 GATTTGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (30 bp):
TTCATGTATAAAATTGCACATAAATCAAAG
Found at i:8495358 original size:19 final size:19
Alignment explanation
Indices: 8495330--8495366 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8495320 TGCTATCAGC
* *
8495330 AACACTATCACTTGCACCA
1 AACACCATCACATGCACCA
8495349 AACACCATCACATGCACC
1 AACACCATCACATGCACC
8495367 TTAGTTGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.41, G:0.05, T:0.16
Consensus pattern (19 bp):
AACACCATCACATGCACCA
Found at i:8498024 original size:15 final size:16
Alignment explanation
Indices: 8498004--8498033 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8497994 AAAATTGAAC
8498004 TTAATATTT-AATTAT
1 TTAATATTTCAATTAT
8498019 TTAATATTTCAATTA
1 TTAATATTTCAATTA
8498034 AAAAGTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATATTTCAATTAT
Found at i:8502209 original size:15 final size:15
Alignment explanation
Indices: 8502189--8502226 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
8502179 ATATAATGAT
8502189 ATATATGTGAGAAAA
1 ATATATGTGAGAAAA
* *
8502204 ATATATGTGTGAAAT
1 ATATATGTGAGAAAA
8502219 AT-TATGTG
1 ATATATGTG
8502227 GTTAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (15 bp):
ATATATGTGAGAAAA
Found at i:8502361 original size:6 final size:6
Alignment explanation
Indices: 8502350--8502400 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
8502340 TGATCATATT
* * *
8502350 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
8502398 TGA
1 TGA
8502401 TATGAATTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:8503497 original size:40 final size:41
Alignment explanation
Indices: 8503436--8503512 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
8503426 AAAAAGCGCC
*
8503436 GCTAAAGGTCAAAGCATTAGCGGCGCTTTCCCATAAATGCT
1 GCTAAAGGTCAAAGCAATAGCGGCGCTTTCCCATAAATGCT
* *
8503477 GCTAAAGGT-TAAGCAATAGCGGCGTTTTCCCATAAA
1 GCTAAAGGTCAAAGCAATAGCGGCGCTTTCCCATAAA
8503513 CGTCGCTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 24 0.73
41 9 0.27
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (41 bp):
GCTAAAGGTCAAAGCAATAGCGGCGCTTTCCCATAAATGCT
Found at i:8503521 original size:40 final size:40
Alignment explanation
Indices: 8503435--8503521 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 40
8503425 GAAAAAGCGC
* *
8503435 CGCTAAAGGTCAAAGCATTAGCGGCGCTTTCCCATAAATG
1 CGCTAAAGGTCAAAGCAATAGCGGCGCTTTCCCATAAACG
* *
8503475 CTGCTAAAGGT-TAAGCAATAGCGGCGTTTTCCCATAAACG
1 C-GCTAAAGGTCAAAGCAATAGCGGCGCTTTCCCATAAACG
8503515 TCGCTAA
1 -CGCTAA
8503522 TTTATTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 31 0.76
41 10 0.24
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (40 bp):
CGCTAAAGGTCAAAGCAATAGCGGCGCTTTCCCATAAACG
Found at i:8504158 original size:2 final size:2
Alignment explanation
Indices: 8504146--8504177 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8504136 TTTACTGCAA
*
8504146 AT AT TT 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 AT
8504178 GGTAAATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:8510768 original size:13 final size:13
Alignment explanation
Indices: 8510744--8510768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8510734 GAGAATTACA
8510744 TAAAAAAATTATT
1 TAAAAAAATTATT
8510757 TAAAAAAATTAT
1 TAAAAAAATTAT
8510769 ATGATTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAAAATTATT
Found at i:8511226 original size:2 final size:2
Alignment explanation
Indices: 8511219--8511249 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8511209 TTCCACATAA
8511219 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
8511250 TTTCTAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:8511830 original size:5 final size:5
Alignment explanation
Indices: 8511822--8511852 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
8511812 TTAGAATGAA
8511822 CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT C
1 CCAAT CCAAT CCAAT CCAAT CCAAT CCAAT C
8511853 TCCAAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (5 bp):
CCAAT
Found at i:8512396 original size:50 final size:50
Alignment explanation
Indices: 8512337--8512441 Score: 174
Period size: 50 Copynumber: 2.1 Consensus size: 50
8512327 ATATTCAGAC
*
8512337 TCAACTCGGCTTAATTACACCCTTGACATCCAAATACTTTTTCATATTTT
1 TCAAGTCGGCTTAATTACACCCTTGACATCCAAATACTTTTTCATATTTT
* * *
8512387 TCAAGTCGGCTTAATTACACCCTTGACGTTCAAATGCTTTTTCATATTTT
1 TCAAGTCGGCTTAATTACACCCTTGACATCCAAATACTTTTTCATATTTT
8512437 TCAAG
1 TCAAG
8512442 AATGACTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.40
Consensus pattern (50 bp):
TCAAGTCGGCTTAATTACACCCTTGACATCCAAATACTTTTTCATATTTT
Found at i:8520964 original size:7 final size:7
Alignment explanation
Indices: 8520949--8520988 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
8520939 ATTATATTTG
8520949 AAAAATT
1 AAAAATT
*
8520956 AAAACTT
1 AAAAATT
8520963 AAAAATT
1 AAAAATT
*
8520970 AAAATTT
1 AAAAATT
8520977 AAAAATT
1 AAAAATT
8520984 AAAAA
1 AAAAA
8520989 AATCATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAAATT
Found at i:8520966 original size:14 final size:14
Alignment explanation
Indices: 8520949--8520987 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
8520939 ATTATATTTG
8520949 AAAAATTAAAACTT
1 AAAAATTAAAACTT
*
8520963 AAAAATTAAAATTT
1 AAAAATTAAAACTT
8520977 AAAAATTAAAA
1 AAAAATTAAAA
8520988 AAATCATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATTAAAACTT
Found at i:8527951 original size:6 final size:6
Alignment explanation
Indices: 8527918--8527949 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
8527908 CGCGTGATCC
*
8527918 GCGTCG GCGTCG GCGTCG GCGTCG GCTTCG GC
1 GCGTCG GCGTCG GCGTCG GCGTCG GCGTCG GC
8527950 TTGTTTACGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.34, G:0.47, T:0.19
Consensus pattern (6 bp):
GCGTCG
Found at i:8533795 original size:24 final size:24
Alignment explanation
Indices: 8533763--8533810 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
8533753 ATGGATATTC
8533763 AACCTTTCATCTCTCTTAACCTTT
1 AACCTTTCATCTCTCTTAACCTTT
* *
8533787 AACCTTTCATCTTTTTTAACCTTT
1 AACCTTTCATCTCTCTTAACCTTT
8533811 CATATTCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (24 bp):
AACCTTTCATCTCTCTTAACCTTT
Found at i:8539839 original size:3 final size:3
Alignment explanation
Indices: 8539831--8539859 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
8539821 ATGTTGGAAA
8539831 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
8539860 GAAATTCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:8542355 original size:16 final size:17
Alignment explanation
Indices: 8542336--8542381 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
8542326 GTTATTAATG
8542336 TTATTGATTATA-TTAT
1 TTATTGATTATATTTAT
*
8542352 TTATT-TTTATATTTAT
1 TTATTGATTATATTTAT
8542368 TTATTG-TTA-ATTTA
1 TTATTGATTATATTTA
8542382 GGGAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (17 bp):
TTATTGATTATATTTAT
Found at i:8547780 original size:18 final size:19
Alignment explanation
Indices: 8547757--8547794 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
8547747 TGAGACTATG
*
8547757 ATAAAATTAA-AATTTTGT
1 ATAAAAATAATAATTTTGT
*
8547775 ATAAAAATAATTATTTTGT
1 ATAAAAATAATAATTTTGT
8547794 A
1 A
8547795 CACGATTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATAAAAATAATAATTTTGT
Found at i:8566050 original size:183 final size:180
Alignment explanation
Indices: 8565672--8566230 Score: 682
Period size: 183 Copynumber: 3.0 Consensus size: 180
8565662 AGCATGGAAA
* * * *
8565672 TGGAAGACGACTCTGCTTTACTTTTTAATGCCTTCGATTTTCTGGTAGCTCTTCAGTTCCCCCTC
1 TGGAAGACGACGCTGCATTACTTTTTAATGCCTT-GATTTT-TGGTGGCTCTTCAGTTCCCTCTC
* * * *
8565737 AATGCTGAAAGTGATGTTGATAATAACCCTACTACGAGTCTACGATTCCCGAAA-TTTCACACGA
64 AATGCTGAAAGTGATGATGA-CAT----C-ACTACTA--CTACGATTCCC-AAACTTTCACATGA
* * * *
8565801 TCATCATACCTTGTCCATGCTCCATATTTTCAGTGTAGACAGCTTGATATATGTTGAGGAAT
120 TCATCATACCTAGTCCATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTGA-GAAT
*
8565863 TGGAAGACGACGCCGCATTACTTTTTAATGCCTTGGAGTTTTTGGTGGCTCTTCAGTTCCCTCTC
1 TGGAAGACGACGCTGCATTACTTTTTAATGCCTT-GA-TTTTTGGTGGCTCTTCAGTTCCCTCTC
*
8565928 AATGCTGAAAGTGATGATGACATCACTCCTACTACGATTCCCAAACTTTCACATGATCATCATAC
64 AATGCTGAAAGTGATGATGACATCACTACTACTACGATTCCCAAACTTTCACATGATCATCATAC
8565993 CTAGTCCATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTGAGATAT
129 CTAGTCCATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTGAGA-AT
* * *
8566046 TGGAAGACGAAGTTGCATTACTTTTTAATGCCTCTGATTTTTTGGAGGCTCTTCA-----CTCTC
1 TGGAAGACGACGCTGCATTACTTTTTAATGCCT-TGA-TTTTTGGTGGCTCTTCAGTTCCCTCTC
* * **
8566106 AATGCTGAAACTGATGATGACATCACTTCTACTACGATTCCCAGTCTTTCACATGATCATCATAC
64 AATGCTGAAAGTGATGATGACATCACTACTACTACGATTCCCAAACTTTCACATGATCATCATAC
* * *
8566171 CTCA-TCTATGCTCCATATTTTCGCTGAAGATAGCTTGATATATGTTGCGGAAT
129 CT-AGTCCATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTG-AGAAT
8566224 TGGAAGA
1 TGGAAGA
8566231 TGATGCCCCT
Statistics
Matches: 335, Mismatches: 27, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
178 118 0.35
179 3 0.01
182 5 0.01
183 123 0.37
184 1 0.00
185 5 0.01
186 1 0.00
190 2 0.01
191 73 0.22
192 4 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (180 bp):
TGGAAGACGACGCTGCATTACTTTTTAATGCCTTGATTTTTGGTGGCTCTTCAGTTCCCTCTCAA
TGCTGAAAGTGATGATGACATCACTACTACTACGATTCCCAAACTTTCACATGATCATCATACCT
AGTCCATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTGAGAAT
Found at i:8581420 original size:23 final size:22
Alignment explanation
Indices: 8581369--8581422 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
8581359 TTATTTAATT
8581369 TATTTAA-AAATAATAAAATCA
1 TATTTAACAAATAATAAAATCA
* * *
8581390 TAAATTAACACATAGTAAAATCTA
1 T-ATTTAACAAATAATAAAATC-A
8581414 TATTTAACA
1 TATTTAACA
8581423 TCTCAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 5 0.19
23 18 0.69
24 2 0.08
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (22 bp):
TATTTAACAAATAATAAAATCA
Found at i:8583945 original size:24 final size:23
Alignment explanation
Indices: 8583908--8583963 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
8583898 ACTCTTTTTT
* *
8583908 TAAAAAACTGAAAATAAAATTTA
1 TAAAAAAATAAAAATAAAATTTA
*
8583931 GCTAAAAAAATAAAAATCAAATTTA
1 --TAAAAAAATAAAAATAAAATTTA
8583956 TAAAAAAA
1 TAAAAAAA
8583964 ATATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 8 0.29
25 20 0.71
ACGTcount: A:0.68, C:0.05, G:0.04, T:0.23
Consensus pattern (23 bp):
TAAAAAAATAAAAATAAAATTTA
Found at i:8590324 original size:22 final size:21
Alignment explanation
Indices: 8590282--8590324 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
8590272 TAAAATAACA
*
8590282 AATTATATTAAATATATTAAT
1 AATTATATTAAATATAGTAAT
8590303 AATT-TATTATAATATAAGTAAT
1 AATTATATTA-AATAT-AGTAAT
8590325 TAAACATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AATTATATTAAATATAGTAAT
Found at i:8594959 original size:2 final size:2
Alignment explanation
Indices: 8594952--8594992 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
8594942 CATCGACAAA
8594952 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
8594993 AGAAATCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8598595 original size:22 final size:22
Alignment explanation
Indices: 8598560--8598604 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
8598550 GGATTAGATT
8598560 GATATAATATTAATAG-TTTGAA
1 GATATAATATTAAT-GTTTTGAA
8598582 GATATAAT-TATAATGTTTTGAA
1 GATATAATAT-TAATGTTTTGAA
8598604 G
1 G
8598605 TTTAGGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (22 bp):
GATATAATATTAATGTTTTGAA
Found at i:8612283 original size:21 final size:21
Alignment explanation
Indices: 8612243--8612284 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8612233 CAACAAATAA
* * *
8612243 TTTAAAAATTATAAATATATT
1 TTTAAAAATAAAAAAAATATT
8612264 TTTAAAAATAAAAAAAATATT
1 TTTAAAAATAAAAAAAATATT
8612285 AAAAAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAAAAATAAAAAAAATATT
Found at i:8620521 original size:35 final size:35
Alignment explanation
Indices: 8620475--8620544 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
8620465 TGTTTGGGAC
8620475 AAGAAAGGTACTTTCAGAGTTTAATGGTATTGCTT
1 AAGAAAGGTACTTTCAGAGTTTAATGGTATTGCTT
8620510 AAGAAAGGTACTTTCAGAGTTTAATGGTATTGCTT
1 AAGAAAGGTACTTTCAGAGTTTAATGGTATTGCTT
8620545 CCTATTGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (35 bp):
AAGAAAGGTACTTTCAGAGTTTAATGGTATTGCTT
Found at i:8623735 original size:28 final size:28
Alignment explanation
Indices: 8623704--8623777 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
8623694 GTGTTGAAAA
* ** *
8623704 GAAAGTGAGAGGAAAAATTTGTTTGGAG
1 GAAAGTGAGAAGAAAAAGATGTTGGGAG
*
8623732 GAAATGGGAGAAGAAAAAGATGTTGGGAG
1 GAAA-GTGAGAAGAAAAAGATGTTGGGAG
*
8623761 AAATAGTGAGAAGAAAA
1 GAA-AGTGAGAAGAAAA
8623778 TGGTAGTCCA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 4 0.11
29 32 0.86
30 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.18
Consensus pattern (28 bp):
GAAAGTGAGAAGAAAAAGATGTTGGGAG
Found at i:8628976 original size:9 final size:8
Alignment explanation
Indices: 8628962--8628999 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
8628952 AAAAATATTA
8628962 TTTTATCAT
1 TTTTAT-AT
8628971 TTTTATA-
1 TTTTATAT
8628978 TTTTATAT
1 TTTTATAT
8628986 TTTTATAAT
1 TTTTAT-AT
8628995 TTTTA
1 TTTTA
8629000 AAATGTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.26
8 7 0.26
9 13 0.48
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTATAT
Found at i:8628981 original size:16 final size:15
Alignment explanation
Indices: 8628960--8628997 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
8628950 ATAAAAATAT
8628960 TATTTTATCATTTTTA
1 TATTTTAT-ATTTTTA
8628976 TATTTTATATTTTTA
1 TATTTTATATTTTTA
8628991 TAATTTT
1 T-ATTTT
8628998 TAAAATGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTATATTTTTA
Found at i:8630062 original size:24 final size:23
Alignment explanation
Indices: 8630035--8630082 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
8630025 TTAACATTGT
8630035 TCATAAAAATGTTCAATTATATGC
1 TCATAAAAATGTTCAATTA-ATGC
* * *
8630059 TCATGAACATGTTCATTTAATGC
1 TCATAAAAATGTTCAATTAATGC
8630082 T
1 T
8630083 GGTGCACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (23 bp):
TCATAAAAATGTTCAATTAATGC
Found at i:8631663 original size:38 final size:38
Alignment explanation
Indices: 8631612--8631688 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
8631602 GTGACAAAAG
8631612 ATAGACTGATTAGTACCTTTCAGAGATGATTCTCAATA
1 ATAGACTGATTAGTACCTTTCAGAGATGATTCTCAATA
8631650 ATAGACTGATTAGTACCTTTCAGAGATGATTCTCAATA
1 ATAGACTGATTAGTACCTTTCAGAGATGATTCTCAATA
8631688 A
1 A
8631689 GACGAAGCTA
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:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (38 bp):
ATAGACTGATTAGTACCTTTCAGAGATGATTCTCAATA
Found at i:8634269 original size:27 final size:29
Alignment explanation
Indices: 8634205--8634272 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
8634195 CCAAAACATC
*
8634205 TTATTAAACATAGATATTATAATATTCGATA
1 TTATTAAACATACATATTATAATATT--ATA
8634236 TTATTAAACATACATATT-TAATTATT-T-
1 TTATTAAACATACATATTATAA-TATTATA
8634263 TTATTAAACA
1 TTATTAAACA
8634273 ATATAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 10 0.29
28 1 0.03
30 3 0.09
31 21 0.60
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (29 bp):
TTATTAAACATACATATTATAATATTATA
Found at i:8634355 original size:18 final size:18
Alignment explanation
Indices: 8634332--8634366 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
8634322 ATGTTCTTAA
8634332 TATATTATTAA-AAATATT
1 TATATT-TTAATAAATATT
8634350 TATATTTTAATAAATAT
1 TATATTTTAATAAATAT
8634367 ATTACAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATTTTAATAAATATT
Found at i:8634386 original size:28 final size:28
Alignment explanation
Indices: 8634328--8634390 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
8634318 AATAATGTTC
* **
8634328 TTAATATATTATTAAAAATATTTATATT
1 TTAATAAATTATTAAAAATATAAATATT
*
8634356 TTAATAAATATATTACAAATATAAATA-T
1 TTAATAAAT-TATTAAAAATATAAATATT
8634384 TTAATAA
1 TTAATAA
8634391 TGACTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
TTAATAAATTATTAAAAATATAAATATT
Found at i:8636761 original size:24 final size:24
Alignment explanation
Indices: 8636728--8636798 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
8636718 CACAACACCG
* *
8636728 ACAACTCCGACTACAGGGACTCCA
1 ACAACACCGACCACAGGGACTCCA
*
8636752 ACAACACCGACCACAGGAACTCCA
1 ACAACACCGACCACAGGGACTCCA
*
8636776 ACAACACCCACCACAGGGACTCC
1 ACAACACCGACCACAGGGACTCC
8636799 TACCATAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.37, C:0.42, G:0.14, T:0.07
Consensus pattern (24 bp):
ACAACACCGACCACAGGGACTCCA
Found at i:8641919 original size:22 final size:21
Alignment explanation
Indices: 8641875--8641924 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
8641865 TTGGTTATCA
** *
8641875 AATTATTAATTTTTTCTATTT
1 AATTATTAAACTTTTCTAATT
8641896 AATTATTAAACTTTTCGTAATT
1 AATTATTAAACTTTTC-TAATT
*
8641918 AAGTATT
1 AATTATT
8641925 TTAGTCACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (21 bp):
AATTATTAAACTTTTCTAATT
Found at i:8642096 original size:62 final size:60
Alignment explanation
Indices: 8642022--8642150 Score: 161
Period size: 62 Copynumber: 2.1 Consensus size: 60
8642012 AATAAATATA
* * * * * * *
8642022 AAAAATTCAATAAATTT-AGCCCTCAATGTTTATAATATTTGTCATTTTAGTTCTAATTCAAT
1 AAAAATTCAATAAATTTGA-CCCTCAATATTTACAAAAGTTGTCAATTTAATCCTAATTC--T
8642084 AAAAATTCAATAAATTTGACCCTCAATATTTACAAAAGTTGTCAATTTAATCCTAATTCT
1 AAAAATTCAATAAATTTGACCCTCAATATTTACAAAAGTTGTCAATTTAATCCTAATTCT
8642144 AAAAATT
1 AAAAATT
8642151 AAAAAATATT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 8 0.14
62 50 0.85
63 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (60 bp):
AAAAATTCAATAAATTTGACCCTCAATATTTACAAAAGTTGTCAATTTAATCCTAATTCT
Found at i:8653062 original size:116 final size:117
Alignment explanation
Indices: 8652919--8653146 Score: 413
Period size: 116 Copynumber: 2.0 Consensus size: 117
8652909 AACATAATAT
*
8652919 TTATAATTAATTTGGGTTGGAATTAGTTTATTCTTTAATAAACGGATCACTTGAA-TTGCAAAAG
1 TTATAATTAATTTGGGTTGGAAATAGTTTATTCTTTAATAAACGGATCACTTGAATTTGCAAAAG
* *
8652983 TAAAAGTGCTTTTGTATCATACAGTTTTCTGCATACTCAAAATGAATGATAG
66 TAAAAATGCTTTTGTATCATACAGTTTTCTGAATACTCAAAATGAATGATAG
8653035 TTATAATTAATTTGGGTTGGAAATAGTTTATTCTTTAATAAACGGATCACTTGAATTTGCAAAAG
1 TTATAATTAATTTGGGTTGGAAATAGTTTATTCTTTAATAAACGGATCACTTGAATTTGCAAAAG
*
8653100 TAAAAATGCTTTTGTATCATACAGTTTTTTGAATACTCAAAATGAAT
66 TAAAAATGCTTTTGTATCATACAGTTTTCTGAATACTCAAAATGAAT
8653147 TATAATAATT
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
116 54 0.50
117 53 0.50
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (117 bp):
TTATAATTAATTTGGGTTGGAAATAGTTTATTCTTTAATAAACGGATCACTTGAATTTGCAAAAG
TAAAAATGCTTTTGTATCATACAGTTTTCTGAATACTCAAAATGAATGATAG
Found at i:8660482 original size:69 final size:68
Alignment explanation
Indices: 8660350--8660484 Score: 157
Period size: 69 Copynumber: 2.0 Consensus size: 68
8660340 AAAAAATAGA
* * * *
8660350 AGTGTAATTAAAACTTTGGAAAAAAAATAGAGGGACTAAATAGAATTGGGAGGAAAAATAAATAG
1 AGTGTAATTAAAAATTTGGAAAAAAAATA-AGGGACTAAATAGAAATGAGAGAAAAAATAAATAG
8660415 ATGG
65 ATGG
* * *
8660419 AGTGTAATTAAAAAATTTGG-GAAAAAAT-AGTGACTAAATTGAAATGAGAGAATAAAATAAAAT
1 AGTGTAATT-AAAAATTTGGAAAAAAAATAAGGGACTAAATAGAAATGAGAGAA-AAAAT-AAAT
8660482 AGA
63 AGA
8660485 AGGACTAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
67 19 0.34
68 5 0.09
69 23 0.41
70 9 0.16
ACGTcount: A:0.53, C:0.02, G:0.21, T:0.23
Consensus pattern (68 bp):
AGTGTAATTAAAAATTTGGAAAAAAAATAAGGGACTAAATAGAAATGAGAGAAAAAATAAATAGA
TGG
Found at i:8660614 original size:6 final size:6
Alignment explanation
Indices: 8660596--8660657 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
8660586 TTAAATTGAT
*
8660596 TTTAAA TTT--A TTTAAA TTTAAA TCT--A TCTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
8660640 -TTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TT-TAAA
8660658 ACAAATTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
4 8 0.17
5 5 0.11
6 27 0.59
7 6 0.13
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:8660617 original size:16 final size:16
Alignment explanation
Indices: 8660596--8660652 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
8660586 TTAAATTGAT
8660596 TTTAAATTTATTTAAA
1 TTTAAATTTATTTAAA
*
8660612 TTTAAATCTATCTTAAA
1 TTTAAATTTAT-TTAAA
*
8660629 TTTAAATTTAATTAAA
1 TTTAAATTTATTTAAA
8660645 TTTAAATT
1 TTTAAATT
8660653 ATAAAACAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 23 0.62
17 14 0.38
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:8660641 original size:11 final size:11
Alignment explanation
Indices: 8660586--8660649 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 11
8660576 AATTTAAAGG
* *
8660586 TTAAATTGATT
1 TTAAATTTAAT
8660597 TTAAATTT-AT
1 TTAAATTTAAT
8660607 TTAAATTTAAAT
1 TTAAATTT-AAT
* ** *
8660619 CTATCTTAAAT
1 TTAAATTTAAT
8660630 TTAAATTTAA-
1 TTAAATTTAAT
8660640 TTAAATTTAA
1 TTAAATTTAA
8660650 ATTATAAAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
10 19 0.46
11 16 0.39
12 6 0.15
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:8662330 original size:16 final size:15
Alignment explanation
Indices: 8662308--8662349 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
8662298 TTATTTCTGC
8662308 ATTTAATCCTTTTTA
1 ATTTAATCCTTTTTA
*
8662323 TTTTTAAT-CTGTTTTA
1 -ATTTAATCCT-TTTTA
8662339 ATTTAATCCTT
1 ATTTAATCCTT
8662350 AAATCGACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.62
Consensus pattern (15 bp):
ATTTAATCCTTTTTA
Found at i:8662425 original size:163 final size:162
Alignment explanation
Indices: 8662243--8662554 Score: 534
Period size: 163 Copynumber: 1.9 Consensus size: 162
8662233 GCTTTTCAAT
8662243 CTAGTCCTTTGACTGTTTGACCGCACTAGAGGCTGCCACGTGTCATCTCCTTGGATTATTTCTGC
1 CTAGTCCTTTGACTGTTTGACCGCACTAGAGGCTGCCACGTGTCATCTCCTTGGATTATTTCTGC
* *
8662308 ATTTAATCCTTTTTATTTTTAATCTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACG
66 ATTTAATCCCTTTTATTTTTAATCTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACA
8662373 AAATTGGCCCAATAATTTTTCAAGGTTTATGAA
131 AAATTGGCCCAA-AATTTTTCAAGGTTTATGAA
* ** *
8662406 CTAGTCCTTTGACTGTTTGACTGCACTAGAGGCTGCCACGTGTCATCTTTTTGGGTTATTTCTGC
1 CTAGTCCTTTGACTGTTTGACCGCACTAGAGGCTGCCACGTGTCATCTCCTTGGATTATTTCTGC
* *
8662471 ATTTAGTCCCTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACA
66 ATTTAATCCCTTTTATTTTTAATCTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACA
*
8662536 AAATTGGTCCAAAATTTTT
131 AAATTGGCCCAAAATTTTT
8662555 TGAGATTTTC
Statistics
Matches: 140, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
162 7 0.05
163 133 0.95
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (162 bp):
CTAGTCCTTTGACTGTTTGACCGCACTAGAGGCTGCCACGTGTCATCTCCTTGGATTATTTCTGC
ATTTAATCCCTTTTATTTTTAATCTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACA
AAATTGGCCCAAAATTTTTCAAGGTTTATGAA
Found at i:8662622 original size:163 final size:163
Alignment explanation
Indices: 8662243--8662611 Score: 451
Period size: 163 Copynumber: 2.3 Consensus size: 163
8662233 GCTTTTCAAT
* * * ** **
8662243 CTAGTCCTTTGACTGTTTGACCGCACTAGAGGCTGCCACGTGTCATCTCCTTGGATTATTTCTGC
1 CTAGTCCCTTGACTGCTGGACTACACTAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTCTGC
* *
8662308 ATTTAATCCTTTTTATTTTTAATCTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACG
66 ATTTAATCCCTTTTATTTTTAATCTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACA
* *
8662373 AAATTGGCCCAATAATTTTTCAAGGTTTATGAA
131 AAATTGGCCCAATAATTTTTCAAGATTTATAAA
* * * * *
8662406 CTAGTCCTTTGACTGTTTGACTGCACTAGAGGCTGCCACGTGTCATCTTTTTGGGTTATTTCTGC
1 CTAGTCCCTTGACTGCTGGACTACACTAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTCTGC
* *
8662471 ATTTAGTCCCTTTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACA
66 ATTTAATCCCTTTTATTTTTAATCTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACA
* **
8662536 AAATTGGTCCAA-AATTTTTTGAGATTT-TCAAA
131 AAATTGGCCCAATAATTTTTCAAGATTTAT-AAA
* * * *
8662568 TTGGTCCCTTGACCT-CTGGA-TAC-CTGTGGGGCTGCCACGTGTCA
1 CTAGTCCCTTGA-CTGCTGGACTACACT-AGAGGCTGCCACGTGTCA
8662612 CCTGTTTTTG
Statistics
Matches: 182, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
160 2 0.01
161 19 0.10
162 26 0.14
163 135 0.74
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (163 bp):
CTAGTCCCTTGACTGCTGGACTACACTAGAGGCTGCCACGTGTCATCTTTTTGGATTATTTCTGC
ATTTAATCCCTTTTATTTTTAATCTGTTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACA
AAATTGGCCCAATAATTTTTCAAGATTTATAAA
Found at i:8662691 original size:30 final size:30
Alignment explanation
Indices: 8662655--8662733 Score: 131
Period size: 30 Copynumber: 2.6 Consensus size: 30
8662645 AAATTGTCCA
* *
8662655 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTACC
8662685 AAAATTACATTTTGACCCCAAAACTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTACC
*
8662715 AAATTTACATTTTGACCCC
1 AAAATTACATTTTGACCCC
8662734 GATTTCACCG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTACC
Found at i:8662921 original size:58 final size:58
Alignment explanation
Indices: 8662722--8662997 Score: 356
Period size: 59 Copynumber: 4.7 Consensus size: 58
8662712 ACCAAATTTA
* * *
8662722 CATTTTGACCCCGATTTCACCGAAAATTACCATTTTACCTCTGAAGCTTCTAAAATTC
1 CATTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTC
* * * *
8662780 CGTTTTTAATCCCGATTTCACCAAAAATTACTATTTTACCCCCGAAGCTTCTAAAATTC
1 C-ATTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTC
* * * * * *
8662839 CGTTTTTAATCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAATTTT
1 C-ATTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTC
* * * *
8662898 CATTTTAACCCCTATTTCACCGAAAATTACCATTTTACCCCCAAATCTTCCAAAATTC
1 CATTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTC
* *
8662956 CATTTTAACCCCGATTTTACC-AAAATTACCATTTTGCCCCCG
1 CATTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCG
8662998 GGTATCCATA
Statistics
Matches: 192, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
57 19 0.10
58 69 0.36
59 104 0.54
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.36
Consensus pattern (58 bp):
CATTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTC
Found at i:8662937 original size:29 final size:29
Alignment explanation
Indices: 8662898--8662990 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
8662888 TTTAAATTTT
*
8662898 CATTTTAACCCCTATTTCACCGAAAATTAC
1 CATTTTAACCCCCATTTCACC-AAAATTAC
** *
8662928 CATTTT-ACCCCCAAATCTTCCAAAATT-C
1 CATTTTAACCCCCATTTC-ACCAAAATTAC
* *
8662956 CATTTTAACCCCGATTTTACCAAAATTAC
1 CATTTTAACCCCCATTTCACCAAAATTAC
8662985 CATTTT
1 CATTTT
8662991 GCCCCCGGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
28 15 0.29
29 28 0.55
30 8 0.16
ACGTcount: A:0.32, C:0.30, G:0.02, T:0.35
Consensus pattern (29 bp):
CATTTTAACCCCCATTTCACCAAAATTAC
Found at i:8662997 original size:29 final size:29
Alignment explanation
Indices: 8662679--8662997 Score: 133
Period size: 30 Copynumber: 11.0 Consensus size: 29
8662669 ACCCTAAAAC
**
8662679 TTTT-CCAAAATTA-CATTTTGACCCCAAAA
1 TTTTACCAAAATTACCATTTT-ACCCC-CGA
* *
8662708 CTTTACCAAATTTA-CATTTTGA-CCCCGA
1 TTTTACCAAAATTACCATTTT-ACCCCCGA
* * *
8662736 TTTCACCGAAAATTACCATTTTACCTCTGAA
1 TTTTACC-AAAATTACCATTTTACCCCCG-A
** * * **
8662767 GCTT-CTAAAATT-CCGTTTTTAATCCCGA
1 TTTTACCAAAATTACC-ATTTTACCCCCGA
* *
8662795 TTTCACCAAAAATTACTATTTTACCCCCGAA
1 TTTTACC-AAAATTACCATTTTACCCCCG-A
** * * **
8662826 GCTT-CTAAAATT-CCGTTTTTAATCCCGA
1 TTTTACCAAAATTACC-ATTTTACCCCCGA
*
8662854 TTTCACCGAAAATTACCATTTTACCCCCGAA
1 TTTTACC-AAAATTACCATTTTACCCCCG-A
* ** * *
8662885 TCTTT---TAAATTTTCATTTTAACCCCTA
1 T-TTTACCAAAATTACCATTTTACCCCCGA
* *
8662912 TTTCACCGAAAATTACCATTTTACCCCCAAA
1 TTTTACC-AAAATTACCATTTTACCCCC-GA
* *
8662943 TCTT-CCAAAATT-CCATTTTAACCCCGA
1 TTTTACCAAAATTACCATTTTACCCCCGA
*
8662970 TTTTACCAAAATTACCATTTTGCCCCCG
1 TTTTACCAAAATTACCATTTTACCCCCG
8662998 GGTATCCATA
Statistics
Matches: 207, Mismatches: 60, Indels: 46
0.66 0.19 0.15
Matches are distributed among these distances:
26 2 0.01
27 6 0.03
28 49 0.24
29 61 0.29
30 75 0.36
31 12 0.06
32 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
TTTTACCAAAATTACCATTTTACCCCCGA
Found at i:8672259 original size:52 final size:52
Alignment explanation
Indices: 8672181--8672282 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 52
8672171 TTTACCCTAA
*
8672181 CCTTTTTTCTATAAGACCAGAACCTATAGTATCACAAAGATACACTTGGCCT
1 CCTTTTTTCTATAAGACCAGAACCTATAGTATCACAAAGACACACTTGGCCT
* * *
8672233 CCTTTTTTCTGTAAGACCAGAACCTATATTATCACAAAGACACATTTGGC
1 CCTTTTTTCTATAAGACCAGAACCTATAGTATCACAAAGACACACTTGGC
8672283 TTTATCGGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (52 bp):
CCTTTTTTCTATAAGACCAGAACCTATAGTATCACAAAGACACACTTGGCCT
Found at i:8674859 original size:21 final size:20
Alignment explanation
Indices: 8674829--8674877 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
8674819 TGGTTCCACC
* *
8674829 TTTTATAATTGATTGATTGTTA
1 TTTT-TAATTAATTGATT-TAA
*
8674851 TTTTTAATTAATTTATTTAA
1 TTTTTAATTAATTGATTTAA
8674871 TTTTTAA
1 TTTTTAA
8674878 ACATTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.38
21 11 0.46
22 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (20 bp):
TTTTTAATTAATTGATTTAA
Found at i:8682582 original size:18 final size:18
Alignment explanation
Indices: 8682555--8682593 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
8682545 CGTTGAAGTG
*
8682555 ATATATATATAAACACAC
1 ATATACATATAAACACAC
* *
8682573 ATATACATATACATACAC
1 ATATACATATAAACACAC
8682591 ATA
1 ATA
8682594 CACACACACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (18 bp):
ATATACATATAAACACAC
Found at i:8684580 original size:19 final size:20
Alignment explanation
Indices: 8684540--8684583 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
8684530 AATATTCTTT
*
8684540 TTTTATTATGAATGATTTGA
1 TTTTATGATGAATGATTTGA
8684560 TTTTATGAT-AATG-TTTAGA
1 TTTTATGATGAATGATTT-GA
8684579 TTTTA
1 TTTTA
8684584 AAATTGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 11 0.50
20 8 0.36
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (20 bp):
TTTTATGATGAATGATTTGA
Found at i:8694384 original size:19 final size:21
Alignment explanation
Indices: 8694360--8694404 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
8694350 AAAGAAATAT
*
8694360 TTTTTAAAAT-ATTTTTAT-A
1 TTTTTAAAATAATTTTAATGA
8694379 TTTTT-AAATAATTTTAATGA
1 TTTTTAAAATAATTTTAATGA
8694399 TTTTTA
1 TTTTTA
8694405 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 12 0.55
20 6 0.27
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTTAAAATAATTTTAATGA
Found at i:8696363 original size:16 final size:17
Alignment explanation
Indices: 8696329--8696366 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
8696319 AGAAATTACA
8696329 AGTTTAAACTTTAAATTG
1 AGTTTAAAC-TTAAATTG
*
8696347 AGTTTAAA-TTAATTTG
1 AGTTTAAACTTAAATTG
8696363 AGTT
1 AGTT
8696367 AAGTTTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (17 bp):
AGTTTAAACTTAAATTG
Found at i:8703860 original size:28 final size:28
Alignment explanation
Indices: 8703820--8703886 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
8703810 ATTATAAAAA
* *
8703820 TAATCATTTAATTA-TATTTTTTTTATTT
1 TAATCACTTAATTATTAATTTTTTTA-TT
*
8703848 TAATTACTTAATTATTAATTTTTTTATT
1 TAATCACTTAATTATTAATTTTTTTATT
8703876 TAATCACTTAA
1 TAATCACTTAA
8703887 ATTTTCGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 24 0.71
29 10 0.29
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (28 bp):
TAATCACTTAATTATTAATTTTTTTATT
Found at i:8705234 original size:111 final size:112
Alignment explanation
Indices: 8705085--8705291 Score: 371
Period size: 111 Copynumber: 1.9 Consensus size: 112
8705075 ATACATAATC
* *
8705085 TTAAGGGTGAGTATTTGGTACACGTGTTATTTTTTAACTCCACGTGTCTT-AATTTTTTAATTTT
1 TTAAGGGTGAGTATTTGGTACACGTGTAATTTTTTAACTCCACATGTCTTAAATTTTTTAATTTT
8705149 TTACTATACTCTATATTCATTTATTATCAACTCAATCTTACTTGTGG
66 TTACTATACTCTATATTCATTTATTATCAACTCAATCTTACTTGTGG
8705196 TTAAGGGTGAGTATTTGGTACACGTGTAATTTTTTAACTCCACATGTCTTAAATTTTTTAATTTT
1 TTAAGGGTGAGTATTTGGTACACGTGTAATTTTTTAACTCCACATGTCTTAAATTTTTTAATTTT
**
8705261 TTTGTATACTCTATATTCATTTATTATCAAC
66 TTACTATACTCTATATTCATTTATTATCAAC
8705292 ATTAATTTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
111 48 0.53
112 43 0.47
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (112 bp):
TTAAGGGTGAGTATTTGGTACACGTGTAATTTTTTAACTCCACATGTCTTAAATTTTTTAATTTT
TTACTATACTCTATATTCATTTATTATCAACTCAATCTTACTTGTGG
Found at i:8705328 original size:20 final size:19
Alignment explanation
Indices: 8705265--8705328 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 19
8705255 AATTTTTTTG
8705265 TATACTCTATATTCATTTAT
1 TATACT-TATATTCATTTAT
* *
8705285 TATCAACATTA-ATT-TTTTAC
1 TAT--AC-TTATATTCATTTAT
8705305 TATACTGTATATTCATTTAT
1 TATACT-TATATTCATTTAT
8705325 TATA
1 TATA
8705329 ACTAACTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
17 1 0.03
18 4 0.12
19 3 0.09
20 18 0.53
21 3 0.09
22 4 0.12
23 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (19 bp):
TATACTTATATTCATTTAT
Found at i:8717832 original size:16 final size:16
Alignment explanation
Indices: 8717811--8717845 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
8717801 TATGATATTG
8717811 TATAATACTCCATTTA
1 TATAATACTCCATTTA
*
8717827 TATAATACTCTATTTA
1 TATAATACTCCATTTA
8717843 TAT
1 TAT
8717846 TTATTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (16 bp):
TATAATACTCCATTTA
Found at i:8734378 original size:5 final size:5
Alignment explanation
Indices: 8734368--8734406 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
8734358 GAAAGGATAG
* *
8734368 AGGGA AGGGA AGGGC AGGGC AGGGC AGGGC AGGGC AGGG
1 AGGGC AGGGC AGGGC AGGGC AGGGC AGGGC AGGGC AGGG
8734407 GTTTTAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.26, C:0.13, G:0.62, T:0.00
Consensus pattern (5 bp):
AGGGC
Found at i:8736677 original size:16 final size:16
Alignment explanation
Indices: 8736658--8736727 Score: 77
Period size: 16 Copynumber: 4.3 Consensus size: 16
8736648 ATTTAAAAAG
*
8736658 TATTTAATTTTTTTTA
1 TATTTAATATTTTTTA
* *
8736674 TATTTTATATTTTATA
1 TATTTAATATTTTTTA
*
8736690 TTTTTAATATTTTTTA
1 TATTTAATATTTTTTA
**
8736706 TATTTTTTAATTTTTTA
1 TATTTAAT-ATTTTTTA
8736723 TATTT
1 TATTT
8736728 GAAAAATATT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
16 31 0.70
17 13 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTAATATTTTTTA
Found at i:8736684 original size:23 final size:23
Alignment explanation
Indices: 8736658--8736727 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
8736648 ATTTAAAAAG
* *
8736658 TATTTAATTTTTTTTATATTTTA
1 TATTTAATATTTTTAATATTTTA
*
8736681 TATTTTATATTTTTAATATTTT-
1 TATTTAATATTTTTAATATTTTA
* *
8736703 T-TAT-AT-TTTTTAATTTTTTA
1 TATTTAATATTTTTAATATTTTA
8736723 TATTT
1 TATTT
8736728 GAAAAATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.31
20 3 0.08
21 4 0.10
22 1 0.03
23 19 0.49
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TATTTAATATTTTTAATATTTTA
Found at i:8736692 original size:25 final size:25
Alignment explanation
Indices: 8736660--8736727 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
8736650 TTAAAAAGTA
8736660 TTTA-ATTTTTTTTATATTTTATAT
1 TTTATATTTTTTTTATATTTTATAT
** *
8736684 TTTATATTTTTAATATTTTTTATAT
1 TTTATATTTTTTTTATATTTTATAT
* *
8736709 TTTTTA-ATTTTTTATATTT
1 TTTATATTTTTTTTATATTT
8736728 GAAAAATATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 13 0.37
25 22 0.63
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTATATTTTTTTTATATTTTATAT
Found at i:8736701 original size:9 final size:8
Alignment explanation
Indices: 8736668--8736727 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 8
8736658 TATTTAATTT
8736668 TTTTTATA
1 TTTTTATA
8736676 -TTTTATA
1 TTTTTATA
8736683 -TTTTATA
1 TTTTTATA
8736690 TTTTTAATA
1 TTTTT-ATA
8736699 TTTTTTATA
1 -TTTTTATA
8736708 TTTTT-TAA
1 TTTTTAT-A
8736716 TTTTTTATA
1 -TTTTTATA
8736725 TTT
1 TTT
8736728 GAAAAATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
7 15 0.33
8 13 0.28
9 12 0.26
10 6 0.13
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTATA
Found at i:8745013 original size:20 final size:21
Alignment explanation
Indices: 8744977--8745029 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
8744967 ATATGAAATT
8744977 TATCATAAAAACCAAAATAAA
1 TATCATAAAAACCAAAATAAA
* *
8744998 TATCATAAAAA-TAAAATGAA
1 TATCATAAAAACCAAAATAAA
8745018 TATCATAAAAAC
1 TATCATAAAAAC
8745030 AATCGGTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.23
Consensus pattern (21 bp):
TATCATAAAAACCAAAATAAA
Found at i:8750455 original size:25 final size:23
Alignment explanation
Indices: 8750377--8750506 Score: 131
Period size: 23 Copynumber: 5.6 Consensus size: 23
8750367 TATACGGAAC
* *
8750377 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
8750399 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
8750420 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
8750446 AAACAGAGAGCACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
8750469 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
8750492 AATAACAGAGAGCAC
1 -A-AACAGAGAGCAC
8750507 GAGACGTGCT
Statistics
Matches: 89, Mismatches: 11, Indels: 13
0.79 0.10 0.12
Matches are distributed among these distances:
21 17 0.19
23 41 0.46
24 1 0.01
25 24 0.27
26 6 0.07
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:8750499 original size:71 final size:69
Alignment explanation
Indices: 8750377--8750527 Score: 189
Period size: 71 Copynumber: 2.2 Consensus size: 69
8750367 TATACGGAAC
* * **
8750377 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCAC-ACACA
1 AAACAGAGAGCACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAACAGAGAGCACGACAC-
8750441 GTGCT
65 GTGCT
* *
8750446 AAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATAACAGAGAGCACGAG
1 AAACAGAGAGCAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAACAACAGAGAGCACGAC
8750510 ACGTGCT
63 ACGTGCT
*
8750517 AAATAGAGAGC
1 AAACAGAGAGC
8750528 GCGCTAGTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
69 12 0.17
70 11 0.15
71 38 0.54
72 10 0.14
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (69 bp):
AAACAGAGAGCACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAACAGAGAGCACGACACG
TGCT
Found at i:8755942 original size:65 final size:65
Alignment explanation
Indices: 8755838--8755969 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
8755828 ATTTAGCCTT
8755838 TCAATATTTACAAATATTATCAATTTGGTCTTAATTTTAAAAATTTTAATAAACTTAACCCTTAA
1 TCAATATTTACAAATATTATCAATTTGGTCTTAATTTTAAAAATTTTAATAAACTTAACCCTTAA
8755903 TCAATATTTACAAATATTATCAATTTGGTCTTAATTTTAAAAATTTTAATAAACTTAACCCTTAA
1 TCAATATTTACAAATATTATCAATTTGGTCTTAATTTTAAAAATTTTAATAAACTTAACCCTTAA
8755968 TC
1 TC
8755970 TTACATATTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.43
Consensus pattern (65 bp):
TCAATATTTACAAATATTATCAATTTGGTCTTAATTTTAAAAATTTTAATAAACTTAACCCTTAA
Found at i:8756105 original size:21 final size:21
Alignment explanation
Indices: 8756069--8756128 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
8756059 TAATTTTTCG
* *
8756069 ATAAAAATATAT-TAAATTTT
1 ATAAAAATACATATAAATATT
8756089 ATAAAAATACATATAAA-ATT
1 ATAAAAATACATATAAATATT
8756109 ATAAAAAATACATATAAATA
1 AT-AAAAATACATATAAATA
8756129 AATGAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.43
21 19 0.54
22 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAAATACATATAAATATT
Found at i:8756127 original size:20 final size:21
Alignment explanation
Indices: 8756069--8756127 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
8756059 TAATTTTTCG
* *
8756069 ATAAAAATATAT-TAAATTTT
1 ATAAAAATACATATAAATTAT
8756089 ATAAAAATACATATAAAATTAT
1 ATAAAAATACATAT-AAATTAT
8756111 A-AAAAATACATATAAAT
1 ATAAAAATACATATAAAT
8756128 AAATGAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.43
21 13 0.37
22 7 0.20
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAAAATACATATAAATTAT
Found at i:8757342 original size:22 final size:21
Alignment explanation
Indices: 8757317--8757367 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
8757307 TCCAAATAAA
8757317 AAATCAAC-TGAATAAATCAATT
1 AAATCAACATG-A-AAATCAATT
*
8757339 AAATCAAACATGAAAATTAATT
1 AAATC-AACATGAAAATCAATT
8757361 AAATCAA
1 AAATCAA
8757368 AAAAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.08
22 18 0.69
23 4 0.15
24 2 0.08
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (21 bp):
AAATCAACATGAAAATCAATT
Found at i:8757382 original size:22 final size:22
Alignment explanation
Indices: 8757330--8757382 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
8757320 TCAACTGAAT
* * *
8757330 AAATCAATTAAATCAAACATGA
1 AAATAAATTAAATCAAAAAAGA
*
8757352 AAATTAATTAAATCAAAAAAAGA
1 AAATAAATTAAATC-AAAAAAGA
8757375 AAA-AAATT
1 AAATAAATT
8757383 CTATTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.66, C:0.08, G:0.04, T:0.23
Consensus pattern (22 bp):
AAATAAATTAAATCAAAAAAGA
Found at i:8757694 original size:23 final size:23
Alignment explanation
Indices: 8757650--8757712 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
8757640 TACTGAAAAA
*
8757650 TAAAAGTTTTAAATAATTTTTATTTT
1 TAAAA-TTTT-AA-AATTTTTAGTTT
8757676 TAAAATTTTAAAATTTTTAGTTT
1 TAAAATTTTAAAATTTTTAGTTT
* *
8757699 TAAATTTTTTAAAT
1 TAAAATTTTAAAAT
8757713 AAAGACTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 23 0.68
24 2 0.06
25 4 0.12
26 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (23 bp):
TAAAATTTTAAAATTTTTAGTTT
Found at i:8758591 original size:100 final size:100
Alignment explanation
Indices: 8758465--8758897 Score: 740
Period size: 100 Copynumber: 4.3 Consensus size: 100
8758455 AGAGTAGCCA
*
8758465 ACTTAAGTTTCCTTGGTTGTGTAGATAGAGGAGTTGCACGTTTAAACAAGGGAGAACCATGGAAG
1 ACTT-AGTTTCCTTGGTTGTGTAGATAGAGCAGTTGCACGTTTAAACAAGGGAGAACCATGGAAG
* *
8758530 GGTACCTAGCTTATTTGCTACTTTTCTTTCTTCTTT
65 AGTACCTAGCTTATTTGCTACTTTTCTTACTTCTTT
*
8758566 ACTTAGTTTCCTTGGTTGTGTAGATAGAGCAGTTGCACGTTTAAATAAGGGAGAACCATGGAAGA
1 ACTTAGTTTCCTTGGTTGTGTAGATAGAGCAGTTGCACGTTTAAACAAGGGAGAACCATGGAAGA
*
8758631 GTACCTAGCTTATTTGCTACTTTTCTTAGTTCTTT
66 GTACCTAGCTTATTTGCTACTTTTCTTACTTCTTT
8758666 ACTTAGTTTCCTTGGTTGTGTAGATAGAGCAGTTGCACGTTTAAACAAGGGAGAACCATGGAAGA
1 ACTTAGTTTCCTTGGTTGTGTAGATAGAGCAGTTGCACGTTTAAACAAGGGAGAACCATGGAAGA
*
8758731 GTACCTAGCTTATTTGCTACTTTTCTTACTTATTT
66 GTACCTAGCTTATTTGCTACTTTTCTTACTTCTTT
* **
8758766 ACTTAGTTTCCTTGGTTGTGTAGATAGAGCAGTTACACGTTTAAACAAGGGAGAATTATGGAAGA
1 ACTTAGTTTCCTTGGTTGTGTAGATAGAGCAGTTGCACGTTTAAACAAGGGAGAACCATGGAAGA
* *
8758831 GTAGCTAGCTTATTTGCTACTTTTCTTACTTGTTT
66 GTACCTAGCTTATTTGCTACTTTTCTTACTTCTTT
* *
8758866 ACTAAGTTTTCTTGGTTGTGTAGATAGAGCAG
1 ACTTAGTTTCCTTGGTTGTGTAGATAGAGCAG
8758898 CAGCTGGCCG
Statistics
Matches: 317, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
100 313 0.99
101 4 0.01
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (100 bp):
ACTTAGTTTCCTTGGTTGTGTAGATAGAGCAGTTGCACGTTTAAACAAGGGAGAACCATGGAAGA
GTACCTAGCTTATTTGCTACTTTTCTTACTTCTTT
Found at i:8770212 original size:20 final size:21
Alignment explanation
Indices: 8770189--8770228 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
8770179 TTTATGATTT
8770189 AGGATTC-AAGTTTAAGGTTC
1 AGGATTCAAAGTTTAAGGTTC
*
8770209 AGGATTCAAAGTTTGAGGTT
1 AGGATTCAAAGTTTAAGGTT
8770229 TGGGGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (21 bp):
AGGATTCAAAGTTTAAGGTTC
Found at i:8778630 original size:2 final size:2
Alignment explanation
Indices: 8778623--8778670 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
8778613 AATCCCTCTT
8778623 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
8778665 TA TA TA
1 TA TA TA
8778671 ATGTAAAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8780111 original size:25 final size:24
Alignment explanation
Indices: 8780082--8780133 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
8780072 TGCTAATATC
*
8780082 ATATAAATTA-TTACATAAATATTAA
1 ATATAAATTAGTTA-ATAAA-AATAA
*
8780107 ATATAGATTAGTTAATAAAAATAA
1 ATATAAATTAGTTAATAAAAATAA
8780131 ATA
1 ATA
8780134 AATAACAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 14 0.58
26 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
ATATAAATTAGTTAATAAAAATAA
Found at i:8781590 original size:18 final size:18
Alignment explanation
Indices: 8781563--8781611 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
8781553 CTCTTTTTTT
8781563 TTAT-TTATAAAATATTA
1 TTATATTATAAAATATTA
8781580 TTATATTAT--AATATTA
1 TTATATTATAAAATATTA
*
8781596 TTA-ATAATTAAAATAT
1 TTATATTA-TAAAATAT
8781612 CTTTTGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 4 0.15
18 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATATTATAAAATATTA
Found at i:8782616 original size:22 final size:23
Alignment explanation
Indices: 8782585--8782628 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
8782575 TTTTTCTGCT
*
8782585 CTCTTTTATTTCCTT-CCTTTTC
1 CTCTTCTATTTCCTTCCCTTTTC
*
8782607 CTCTTCTATTTTCTTCCCTTTT
1 CTCTTCTATTTCCTTCCCTTTT
8782629 TCCATTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.64
Consensus pattern (23 bp):
CTCTTCTATTTCCTTCCCTTTTC
Found at i:8782637 original size:18 final size:18
Alignment explanation
Indices: 8782614--8782648 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8782604 TTCCTCTTCT
*
8782614 ATTTTCTTCCCTTTTTCC
1 ATTTTCTTCCCTATTTCC
8782632 ATTTTCTTCCCTATTTC
1 ATTTTCTTCCCTATTTC
8782649 TTGTTTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.31, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTCTTCCCTATTTCC
Found at i:8793142 original size:20 final size:20
Alignment explanation
Indices: 8793117--8793155 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
8793107 TTTTTGTCTT
8793117 TCCTCAATTT-ACTTCTTTTG
1 TCCTC-ATTTCACTTCTTTTG
*
8793137 TCCTCATTTCATTTCTTTT
1 TCCTCATTTCACTTCTTTT
8793156 TATCATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.59
Consensus pattern (20 bp):
TCCTCATTTCACTTCTTTTG
Found at i:8811106 original size:23 final size:21
Alignment explanation
Indices: 8811080--8811122 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8811070 GAAAAGAGAA
8811080 TTAATATTTACATTATAATATAT
1 TTAAT-TTTACA-TATAATATAT
*
8811103 TTAATTTTTCATATAATATA
1 TTAATTTTACATATAATATA
8811123 AATTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATTTTACATATAATATAT
Found at i:8811117 original size:21 final size:23
Alignment explanation
Indices: 8811093--8811140 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
8811083 ATATTTACAT
* *
8811093 TATAATAT-ATTTA-ATTTTTCA
1 TATAATATAAATTATATTATTCA
8811114 TATAATATAAATTATATTATTCA
1 TATAATATAAATTATATTATTCA
8811137 TATA
1 TATA
8811141 TCGTAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
23 11 0.48
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
TATAATATAAATTATATTATTCA
Found at i:8820229 original size:63 final size:63
Alignment explanation
Indices: 8820130--8820257 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
8820120 TTTAATAATT
8820130 TTATTATAAATTTCGATCATATATATTCTCTCTTAGATAATACTTAAAATTATTTATAGTCCC
1 TTATTATAAATTTCGATCATATATATTCTCTCTTAGATAATACTTAAAATTATTTATAGTCCC
8820193 TTATTATAAATTTCGATCATATATATTCTCTCTTAGATAATACTTAAAATTATTTATAGTCCC
1 TTATTATAAATTTCGATCATATATATTCTCTCTTAGATAATACTTAAAATTATTTATAGTCCC
8820256 TT
1 TT
8820258 CTCAACCTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (63 bp):
TTATTATAAATTTCGATCATATATATTCTCTCTTAGATAATACTTAAAATTATTTATAGTCCC
Found at i:8825098 original size:18 final size:19
Alignment explanation
Indices: 8825075--8825110 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8825065 AAAAACTCAA
8825075 ATAAATA-TATAAAAATAC
1 ATAAATATTATAAAAATAC
*
8825093 ATAAATATTTTAAAAATA
1 ATAAATATTATAAAAATA
8825111 TAATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAATATTATAAAAATAC
Found at i:8826470 original size:16 final size:16
Alignment explanation
Indices: 8826449--8826483 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
8826439 TGGATGAAAT
8826449 AAAATATTTT-TTGTTA
1 AAAATATTTTCTT-TTA
8826465 AAAATATTTTCTTTTA
1 AAAATATTTTCTTTTA
8826481 AAA
1 AAA
8826484 TTTATTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (16 bp):
AAAATATTTTCTTTTA
Found at i:8835418 original size:22 final size:22
Alignment explanation
Indices: 8835390--8835452 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
8835380 CAAAAAAATA
* *
8835390 ATAAAATTTTAATTTAATCTTTT
1 ATAAAATTATAATTTAA-CTATT
* *
8835413 A-AAAATTATATTTTTACTATT
1 ATAAAATTATAATTTAACTATT
8835434 ATAAAATTATAATTTAACT
1 ATAAAATTATAATTTAACT
8835453 TCTACTTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.15
22 27 0.82
23 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAAAATTATAATTTAACTATT
Found at i:8836819 original size:15 final size:15
Alignment explanation
Indices: 8836785--8836828 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
8836775 CAACAAAGTC
**
8836785 ATTTTTAATTTTATTT
1 ATTTTTAATTTT-TGA
8836801 ATTTTTAATTTTTGA
1 ATTTTTAATTTTTGA
*
8836816 ATTTGTAATTTTT
1 ATTTTTAATTTTT
8836829 TTCAAATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (15 bp):
ATTTTTAATTTTTGA
Found at i:8837666 original size:23 final size:23
Alignment explanation
Indices: 8837639--8837692 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
8837629 TTATTATACC
*
8837639 AATTA-AAATCATGTACGTAATTG
1 AATTATAAAT-ATCTACGTAATTG
* *
8837662 AATTATAGATATCTATGTAATTG
1 AATTATAAATATCTACGTAATTG
8837685 AATTATAA
1 AATTATAA
8837693 TTGATAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (23 bp):
AATTATAAATATCTACGTAATTG
Found at i:8843678 original size:18 final size:17
Alignment explanation
Indices: 8843636--8843678 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
8843626 ATTTTAAGTT
*
8843636 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
8843653 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
8843671 TATAATTT
1 TATAATTT
8843679 AAAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:8849096 original size:20 final size:21
Alignment explanation
Indices: 8849053--8849096 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
8849043 ACTTTCTTCA
*
8849053 TTAAGCTTTAATTAAACATTT
1 TTAAGCTTTAATTAAACATAT
* *
8849074 TTAA-CTTTTATTAAACCTAT
1 TTAAGCTTTAATTAAACATAT
8849094 TTA
1 TTA
8849097 TAATCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.50
Consensus pattern (21 bp):
TTAAGCTTTAATTAAACATAT
Found at i:8849810 original size:3 final size:3
Alignment explanation
Indices: 8849758--8849791 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
8849748 CTTTTGTATA
8849758 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
8849792 TGCATGCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:8856826 original size:36 final size:36
Alignment explanation
Indices: 8856777--8856847 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
8856767 ACTTCTAATA
*
8856777 AAATAATAACCTGATCAAATAATTAATTGTGGACTT
1 AAATAATAACCTGATCAAATAATTAATTGAGGACTT
* *
8856813 AAATAATATCCTGATCTAATAATTAATTGAGGACT
1 AAATAATAACCTGATCAAATAATTAATTGAGGACT
8856848 AACACCTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (36 bp):
AAATAATAACCTGATCAAATAATTAATTGAGGACTT
Found at i:8867723 original size:3 final size:3
Alignment explanation
Indices: 8867715--8867747 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
8867705 AAATATAATA
8867715 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
8867748 ATAAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:8889080 original size:26 final size:26
Alignment explanation
Indices: 8889044--8889098 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
8889034 GGCCATGTCG
8889044 GTTCAGTTGTTTTAGCAATTCATTAT
1 GTTCAGTTGTTTTAGCAATTCATTAT
8889070 GTTCAGTTGTTTTAGCAATTCATTAT
1 GTTCAGTTGTTTTAGCAATTCATTAT
8889096 GTT
1 GTT
8889099 AGCGATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.51
Consensus pattern (26 bp):
GTTCAGTTGTTTTAGCAATTCATTAT
Found at i:8893367 original size:2 final size:2
Alignment explanation
Indices: 8893360--8893390 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8893350 AAATCTTCTA
8893360 AT AT 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 AT AT A
8893391 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8901285 original size:132 final size:131
Alignment explanation
Indices: 8901038--8901300 Score: 348
Period size: 132 Copynumber: 2.0 Consensus size: 131
8901028 GCATTACAAG
* *
8901038 AGTTTAGGGTATTGTACAACTCTGGAGGTTTCACTGTAGGTATTTTGAGGAAATATGTATATGTC
1 AGTTTAGGGTATTGTACAACTCTGGAGGTTTCACTGTAGATATTTTGAGGAAATATGCATATGTC
* * * * * *
8901103 TAGCTCTGAGTAGATATTACTTATGATAAATAAAATGTCAGTCACAGCATGTGTTTGATTTTGTA
66 TAGCTCTAAGTAGATATCACTTATGACAAACAAAATGTCAGTCACAGCATGCGTTTGATATTGTA
8901168 T
131 T
* * * *
8901169 AGTTTAAGGGTATTTTACAATTCTGGAGGTTTCACTGTAGATGTTTTGA-GAAATTATGCATGTG
1 AGTTT-AGGGTATTGTACAACTCTGGAGGTTTCACTGTAGATATTTTGAGGAAA-TATGCATATG
* * ** *
8901233 TCTAGCTCTAAGTAGATATCACTTATGACAAACAATATTTTTGTCACTGCATGCGTTTGATATTG
64 TCTAGCTCTAAGTAGATATCACTTATGACAAACAAAATGTCAGTCACAGCATGCGTTTGATATTG
8901298 TAT
129 TAT
8901301 TCATGTCTGA
Statistics
Matches: 113, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
131 9 0.08
132 104 0.92
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.40
Consensus pattern (131 bp):
AGTTTAGGGTATTGTACAACTCTGGAGGTTTCACTGTAGATATTTTGAGGAAATATGCATATGTC
TAGCTCTAAGTAGATATCACTTATGACAAACAAAATGTCAGTCACAGCATGCGTTTGATATTGTA
T
Found at i:8908859 original size:29 final size:29
Alignment explanation
Indices: 8908826--8908885 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
8908816 GTAAATTATT
*
8908826 TGGCGCACAGTCCAAAGTGTAAGCCAAAG
1 TGGCGCACAGTCCAAAGTGCAAGCCAAAG
* ** *
8908855 TGGCGGACAGTCTGAAGTGCAAGCTAAAG
1 TGGCGCACAGTCCAAAGTGCAAGCCAAAG
8908884 TG
1 TG
8908886 ACAGGCAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.17
Consensus pattern (29 bp):
TGGCGCACAGTCCAAAGTGCAAGCCAAAG
Found at i:8911033 original size:20 final size:21
Alignment explanation
Indices: 8911008--8911052 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
8910998 TCAACTTAGT
8911008 TTTTAAATAAAAAAATAAT-C
1 TTTTAAATAAAAAAATAATAC
*
8911028 TTTT-AATAAAAAAATTATAC
1 TTTTAAATAAAAAAATAATAC
8911048 TTTTA
1 TTTTA
8911053 CAATTATGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTTAAATAAAAAAATAATAC
Found at i:8935783 original size:50 final size:50
Alignment explanation
Indices: 8935696--8935791 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
8935686 AATTCAGTCA
*
8935696 TGATCGATGCCCGCATCCTCATGGGAACGGATGACATTGAATTAAATGAC
1 TGATCGATGCCCGCATCCTCATGGGAACGGATGACATTGAAATAAATGAC
* * * * * *
8935746 TGATTGATGCCTGCGTCTTCATGGGAATGGATTACATTGAAATAAA
1 TGATCGATGCCCGCATCCTCATGGGAACGGATGACATTGAAATAAA
8935792 AAGGAAGGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (50 bp):
TGATCGATGCCCGCATCCTCATGGGAACGGATGACATTGAAATAAATGAC
Done.