Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002152.1 Kokia drynarioides strain JFW-HI SEQ_114101, 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: 98006
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 97 characters in sequence are not A, C, G, or T
Found at i:1094 original size:55 final size:55
Alignment explanation
Indices: 1001--1166 Score: 172
Period size: 55 Copynumber: 3.0 Consensus size: 55
991 TTGTACTATG
* * ** * *
1001 TGACAATCGATTTAAACATATAAATATTTTATTAAAAAGAAACATTATTCTAACA
1 TGACAATCGATTTAAACATATAAAAAATCGATTAAAAAGAAGCAATATTCTAACA
* * * * *
1056 TGATAATGGATTTAAACATATAAACAATCGATTTAAAAGAAGTAATATT-TCAACA
1 TGACAATCGATTTAAACATATAAAAAATCGATTAAAAAGAAGCAATATTCT-AACA
* * * *
1111 TGACAATCGATTTGAACATATAAAAATATCGATTCAAAAGAAGCAGTATTCCAACA
1 TGACAATCGATTTAAACATATAAAAA-ATCGATTAAAAAGAAGCAATATTCTAACA
1167 ATTAAGAAGA
Statistics
Matches: 90, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
54 1 0.01
55 65 0.72
56 24 0.27
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (55 bp):
TGACAATCGATTTAAACATATAAAAAATCGATTAAAAAGAAGCAATATTCTAACA
Found at i:2339 original size:25 final size:24
Alignment explanation
Indices: 2293--2340 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2283 TTTAGTTTCT
*
2293 TCAAGAAAATTTTCTTTGTTTTAA
1 TCAAGAAAATTTTCTTTATTTTAA
2317 TCAAGAATAATTTT-TTTAATTTTA
1 TCAAGAA-AATTTTCTTT-ATTTTA
2341 CTTTTAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (24 bp):
TCAAGAAAATTTTCTTTATTTTAA
Found at i:9810 original size:66 final size:66
Alignment explanation
Indices: 9728--9859 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
9718 CTTCTGCCTT
* * *
9728 AAACCTTTCTCCTGCTTAGTAAACCTAGTCCCTTATTATCTCCTTTAATTCCTTTAATCCTTCAC
1 AAACCTTTCTCCTGCTTAGTAAACCTAATCCCTTACTATCTCCTTTAATTCCTTTAACCCTTCAC
9793 A
66 A
9794 AAACCTTTCTCCTGCTTAGTAAACCTAATCCCTTACTATCTCCTTTAATTCCTTTAACCCTTCAC
1 AAACCTTTCTCCTGCTTAGTAAACCTAATCCCTTACTATCTCCTTTAATTCCTTTAACCCTTCAC
9859 A
66 A
9860 GGTGAACCGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.25, C:0.32, G:0.04, T:0.39
Consensus pattern (66 bp):
AAACCTTTCTCCTGCTTAGTAAACCTAATCCCTTACTATCTCCTTTAATTCCTTTAACCCTTCAC
A
Found at i:20132 original size:31 final size:31
Alignment explanation
Indices: 20064--20132 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
20054 TTAAAAATCT
* *
20064 AGTGACTTAAATGAAAACTTTCAAATAGTTT
1 AGTGACTTAAATGAAAACTTTCAAATAATTC
* * **
20095 AATGACTTAATTGAAAACTTTTGAATAATTC
1 AGTGACTTAAATGAAAACTTTCAAATAATTC
20126 AGTGACT
1 AGTGACT
20133 ATTTTATAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (31 bp):
AGTGACTTAAATGAAAACTTTCAAATAATTC
Found at i:22538 original size:52 final size:52
Alignment explanation
Indices: 22086--22527 Score: 634
Period size: 52 Copynumber: 8.5 Consensus size: 52
22076 ATATCATTTC
* *
22086 ATTCATATACTCACGATGACACATAGCCACCGGACCTCATAATCCGTAAAAG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* * * *
22138 ATTCATATACTCACAATGACAAATAGCCATCGGACCTTATAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* *
22190 ATTAATATACTCAAGATGACACATAGCCATC-GAGCCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGA-CCTCATAATCCGTAAAGG
* *
22242 ATTCATATACTCACGATGACACATAACCATCGGACCTCATAATCTGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
*
22294 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* * * * *
22346 ATTAATATATTCACGATGACACATAGTCATCGGACCTGATAATCCGTAAATG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* * * * * *
22398 ATTCATAAACTAATGATGACACATAGTCATCGAACCTCATAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* * *
22450 ATTCATATACTCACGATGACACATAACCATCTGACCTCATAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
*
22502 ATTCATATACTTACGATGACACATAG
1 ATTCATATACTCACGATGACACATAG
22528 TTATCTGACC
Statistics
Matches: 347, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
51 2 0.01
52 343 0.99
53 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
Found at i:29090 original size:125 final size:125
Alignment explanation
Indices: 28953--29197 Score: 490
Period size: 125 Copynumber: 2.0 Consensus size: 125
28943 AACATTAATA
28953 TCAAGTATTTGGATAATAATATTAATAGTAAGCGATACTCTTGTTGTAGCAATCAAACATTAACA
1 TCAAGTATTTGGATAATAATATTAATAGTAAGCGATACTCTTGTTGTAGCAATCAAACATTAACA
29018 ATAAATTATGTCAAATAATGAATCAATCTTTTAACCAACTTATTGCTCATATAAATTATG
66 ATAAATTATGTCAAATAATGAATCAATCTTTTAACCAACTTATTGCTCATATAAATTATG
29078 TCAAGTATTTGGATAATAATATTAATAGTAAGCGATACTCTTGTTGTAGCAATCAAACATTAACA
1 TCAAGTATTTGGATAATAATATTAATAGTAAGCGATACTCTTGTTGTAGCAATCAAACATTAACA
29143 ATAAATTATGTCAAATAATGAATCAATCTTTTAACCAACTTATTGCTCATATAAA
66 ATAAATTATGTCAAATAATGAATCAATCTTTTAACCAACTTATTGCTCATATAAA
29198 GTACCTTTTA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (125 bp):
TCAAGTATTTGGATAATAATATTAATAGTAAGCGATACTCTTGTTGTAGCAATCAAACATTAACA
ATAAATTATGTCAAATAATGAATCAATCTTTTAACCAACTTATTGCTCATATAAATTATG
Found at i:31078 original size:53 final size:52
Alignment explanation
Indices: 31020--31124 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 52
31010 GATGTCGATA
*
31020 TTGATTGTGATTTTTGATTTAAGGTT-TCTTTGATTTTAATTTGGATTTTGATT
1 TTGATTGTGATTTTTGATTTAAGGTTAT-TTTGATTTTAA-TTAGATTTTGATT
* *
31073 TTGATTTTGATTTTTGATTTAAGGTTATTTTGATTTTGATTAGATTTTGATT
1 TTGATTGTGATTTTTGATTTAAGGTTATTTTGATTTTAATTAGATTTTGATT
31125 GCTACTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
52 12 0.25
53 35 0.73
54 1 0.02
ACGTcount: A:0.20, C:0.01, G:0.18, T:0.61
Consensus pattern (52 bp):
TTGATTGTGATTTTTGATTTAAGGTTATTTTGATTTTAATTAGATTTTGATT
Found at i:31087 original size:7 final size:6
Alignment explanation
Indices: 31048--31124 Score: 70
Period size: 6 Copynumber: 13.2 Consensus size: 6
31038 TTAAGGTTTC
* * * *
31048 TTTGAT TTTAAT TTGGAT TTTGAT TTTGAT TTTGATT TTTGA- TTTAAG
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGA-T TTTGAT TTTGAT
* *
31096 GTT-AT TTTGAT TTTGA- TTAGAT TTTGAT T
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT T
31125 GCTACTGTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
5 11 0.19
6 40 0.70
7 6 0.11
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (6 bp):
TTTGAT
Found at i:31103 original size:47 final size:47
Alignment explanation
Indices: 30998--31125 Score: 116
Period size: 53 Copynumber: 2.6 Consensus size: 47
30988 TATTTTGTGC
* * * *
30998 TTATTTGAATTTGATGTCGATATTGATTGTGATTTTTGATTTAAGGTTTCT
1 TTATTTTAATTTGATTTAGATTTTGATTGTGATTTTTGATTTAAGG----T
* *
31049 TTGATTTTAATTTGGATTTTGATTTTGATTTTGATTTTTGATTTAAGG-
1 TT-ATTTTAATTT-GATTTAGATTTTGATTGTGATTTTTGATTTAAGGT
*
31097 TTATTTTGATTTTGA-TTAGATTTTGATTG
1 TTATTTT-AATTTGATTTAGATTTTGATTG
31126 CTACTGTTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
46 12 0.18
47 7 0.11
48 6 0.09
51 2 0.03
52 9 0.14
53 30 0.45
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.59
Consensus pattern (47 bp):
TTATTTTAATTTGATTTAGATTTTGATTGTGATTTTTGATTTAAGGT
Found at i:31628 original size:11 final size:10
Alignment explanation
Indices: 31590--31624 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
31580 TCAGAATATA
31590 AAATAAAAAT
1 AAATAAAAAT
31600 AAAGTAAAAAT
1 AAA-TAAAAAT
*
31611 AAATAAAATT
1 AAATAAAAAT
31621 AAAT
1 AAAT
31625 TAAATAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:33153 original size:9 final size:9
Alignment explanation
Indices: 33139--33170 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
33129 ACTTCAAACT
33139 AATCATTCC
1 AATCATTCC
33148 AATCATTCC
1 AATCATTCC
33157 AATCATTCC
1 AATCATTCC
33166 AATCA
1 AATCA
33171 ATAAGTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (9 bp):
AATCATTCC
Found at i:34850 original size:23 final size:23
Alignment explanation
Indices: 34802--34852 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
34792 GATATATATA
*
34802 TATATATATAGTTGGATGTGTGG
1 TATATATATAGTTGGATGTGTAG
34825 TATATATATAGTTGGATGCTG-AG
1 TATATATATAGTTGGATG-TGTAG
34848 TATAT
1 TATAT
34853 GATGATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.43
Consensus pattern (23 bp):
TATATATATAGTTGGATGTGTAG
Found at i:35201 original size:44 final size:43
Alignment explanation
Indices: 35093--35245 Score: 209
Period size: 44 Copynumber: 3.5 Consensus size: 43
35083 GTCATTAAGG
** *
35093 TTTATATTCAATAGGTACTATGTACCGGTGTTGGCTATGTGCCA
1 TTTATATTCAGCAGGTACTATGTATC-GTGTTGGCTATGTGCCA
* *
35137 -ATATATTTAGCAGGTACTATGTATCTGTGTTGGCTATGTGCCA
1 TTTATATTCAGCAGGTACTATGTATC-GTGTTGGCTATGTGCCA
35180 TTTATATTCAGCAGGTACTATGTATCGATGTTGGCTATGTGCCA
1 TTTATATTCAGCAGGTACTATGTATCG-TGTTGGCTATGTGCCA
* *
35224 TTTATATTTAGCTGGTACTATG
1 TTTATATTCAGCAGGTACTATG
35246 ACCGATGTTA
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
43 38 0.39
44 59 0.61
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (43 bp):
TTTATATTCAGCAGGTACTATGTATCGTGTTGGCTATGTGCCA
Found at i:35260 original size:87 final size:87
Alignment explanation
Indices: 35093--35260 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 87
35083 GTCATTAAGG
* *
35093 TTTATATTCAATAGGTACTATGTACCGGTGTTGGCTATGTGCCAATATATTTAGCAGGTACTATG
1 TTTATATTCAACAGGTACTATGTACCGATGTTGGCTATGTGCCAATATATTTAGCAGGTACTATG
* *
35158 TATCTGTGTTGGCTATGTGCCA
66 TATCCGTGTTAGCTATGTGCCA
* * * *
35180 TTTATATTCAGCAGGTACTATGTATCGATGTTGGCTATGTGCCATTTATATTTAGCTGGTACTAT
1 TTTATATTCAACAGGTACTATGTACCGATGTTGGCTATGTGCCA-ATATATTTAGCAGGTACTAT
35245 G-A-CCGATGTTAGCTAT
65 GTATCCG-TGTTAGCTAT
35261 TACACCATTT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
86 2 0.03
87 50 0.70
88 19 0.27
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (87 bp):
TTTATATTCAACAGGTACTATGTACCGATGTTGGCTATGTGCCAATATATTTAGCAGGTACTATG
TATCCGTGTTAGCTATGTGCCA
Found at i:35269 original size:44 final size:44
Alignment explanation
Indices: 35093--35297 Score: 184
Period size: 44 Copynumber: 4.7 Consensus size: 44
35083 GTCATTAAGG
** * * *
35093 TTTATATTCAATAGGTACTATGTACCGGTGTTGGCTATGTGCCA
1 TTTATATTCAGCAGGTACTATGTACCGATGTTAGCTATGTACCA
* * * * *
35137 -ATATATTTAGCAGGTACTATGTATCTG-TGTTGGCTATGTGCCA
1 TTTATATTCAGCAGGTACTATGTA-CCGATGTTAGCTATGTACCA
* * *
35180 TTTATATTCAGCAGGTACTATGTATCGATGTTGGCTATGTGCCA
1 TTTATATTCAGCAGGTACTATGTACCGATGTTAGCTATGTACCA
* *
35224 TTTATATTTAGCTGGTACTATG-ACCGATGTTAGCTAT-TACACCA
1 TTTATATTCAGCAGGTACTATGTACCGATGTTAGCTATGT--ACCA
* * * *
35268 TTTTTATACAGCAAGTACTTTGTACCGATG
1 TTTATATTCAGCAGGTACTATGTACCGATG
35298 ACGAATGTTT
Statistics
Matches: 135, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
42 1 0.01
43 49 0.36
44 78 0.58
45 7 0.05
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.39
Consensus pattern (44 bp):
TTTATATTCAGCAGGTACTATGTACCGATGTTAGCTATGTACCA
Found at i:35286 original size:88 final size:87
Alignment explanation
Indices: 35107--35297 Score: 226
Period size: 88 Copynumber: 2.2 Consensus size: 87
35097 TATTCAATAG
* * *
35107 GTACTATGTACCGGTGTTGGCTATGTGCCAATATATTTAGCAGGTACTATGTATCTGTGTTGGCT
1 GTACTATGTACCGATGTTGGCTATGTGCCAATATATTTAGCAGGTACTATGTATCCGTGTTAGCT
* * *
35172 ATGTGCCATTTATATTCAGCAG
66 ATGTACCATTTATATACAGCAA
* * *
35194 GTACTATGTATCGATGTTGGCTATGTGCCATTTATATTTAGCTGGTACTATG-A-CCGATGTTAG
1 GTACTATGTACCGATGTTGGCTATGTGCCA-ATATATTTAGCAGGTACTATGTATCCG-TGTTAG
*
35257 CTAT-TACACCATTTTTATACAGCAA
64 CTATGT--ACCATTTATATACAGCAA
*
35282 GTACTTTGTACCGATG
1 GTACTATGTACCGATG
35298 ACGAATGTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
86 3 0.03
87 38 0.43
88 47 0.53
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (87 bp):
GTACTATGTACCGATGTTGGCTATGTGCCAATATATTTAGCAGGTACTATGTATCCGTGTTAGCT
ATGTACCATTTATATACAGCAA
Found at i:41735 original size:28 final size:28
Alignment explanation
Indices: 41703--41771 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
41693 AAATGAAGAG
41703 TCCAAGCACCATAGGCTATGGCTTCTAA
1 TCCAAGCACCATAGGCTATGGCTTCTAA
41731 TCCAAGCACCATAGGCTATGGCTTCTAA
1 TCCAAGCACCATAGGCTATGGCTTCTAA
41759 TCCAAGCACCATA
1 TCCAAGCACCATA
41772 TACTCATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (28 bp):
TCCAAGCACCATAGGCTATGGCTTCTAA
Found at i:44097 original size:43 final size:43
Alignment explanation
Indices: 44050--44135 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
44040 AGTGGTGCAG
* * *
44050 TTCATGGTAATCAATTGTTGTACTTAATAGGGTATCAGTGGAA
1 TTCATGGTAATCAACTATTGCACTTAATAGGGTATCAGTGGAA
*
44093 TTCATGGTACTCAACTATTGCACTTAATAGGGTATCAGTGGAA
1 TTCATGGTAATCAACTATTGCACTTAATAGGGTATCAGTGGAA
44136 ACCATATTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (43 bp):
TTCATGGTAATCAACTATTGCACTTAATAGGGTATCAGTGGAA
Found at i:49937 original size:6 final size:6
Alignment explanation
Indices: 49926--49957 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
49916 TGATAAACCT
49926 CCATTC CCATTC CCATTC CCATTC CCATTC CC
1 CCATTC CCATTC CCATTC CCATTC CCATTC CC
49958 TACAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.53, G:0.00, T:0.31
Consensus pattern (6 bp):
CCATTC
Found at i:51233 original size:5 final size:5
Alignment explanation
Indices: 51223--51247 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
51213 ACAAATTCAC
51223 CCTTT CCTTT CCTTT CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT
51248 TTGCTCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CCTTT
Found at i:52984 original size:58 final size:57
Alignment explanation
Indices: 52830--53000 Score: 171
Period size: 60 Copynumber: 2.9 Consensus size: 57
52820 AATTGAATCT
* * *
52830 AAAAAAAACTTAGGTACCAAATTAGGAAAAAATGGCAAGTTCAAATACCAAATTGGGTC
1 AAAAAAAA-TTAGGTACCAAATTA-AAAAAAATGTCAACTTCAAATACCAAATTGGGTC
* * * ** *
52889 AAAAAAAGTTTTAGGTATCAAATTAAGAAAAATTGTCAACTTCAGGTTCCAAATTGGGTC
1 AAAAAAA--ATTAGGTACCAAATTAA-AAAAAATGTCAACTTCAAATACCAAATTGGGTC
* * * *
52949 AAAAAAAATTAGATACCAAATTAAAAATAAATGTCAAGTTTAAGTACCAAAT
1 AAAAAAAATTAGGTACCAAATTAAAAA-AAATGTCAACTTCAAATACCAAAT
53001 ATTATATTAA
Statistics
Matches: 91, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
57 3 0.03
58 33 0.36
59 7 0.08
60 48 0.53
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (57 bp):
AAAAAAAATTAGGTACCAAATTAAAAAAAATGTCAACTTCAAATACCAAATTGGGTC
Found at i:53187 original size:20 final size:19
Alignment explanation
Indices: 53137--53187 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
53127 AATAAATTTA
**
53137 ATTATTATTTTTATTTTAT
1 ATTATTATTTTTAGATTAT
*
53156 AATATT-TCTTTTAAGATTAT
1 ATTATTAT-TTTT-AGATTAT
53176 ATTATTATTTTT
1 ATTATTATTTTT
53188 TATTAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 1 0.04
19 9 0.36
20 14 0.56
21 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTATTATTTTTAGATTAT
Found at i:60494 original size:19 final size:19
Alignment explanation
Indices: 60472--60508 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
60462 GTGTTTCAAA
* *
60472 AATTTGATATTATTTAAAT
1 AATTTCATATTAATTAAAT
60491 AATTTCATATTAATTAAA
1 AATTTCATATTAATTAAA
60509 ATTATTGAAA
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:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
AATTTCATATTAATTAAAT
Found at i:61059 original size:26 final size:25
Alignment explanation
Indices: 61030--61092 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
61020 CATTAAGAGA
61030 AATAATATTTATCTTTATGATAAT-TC
1 AATAATATTTAT-TTT-TGATAATATC
* *
61056 AATAATATTTATTTTTTATAATATT
1 AATAATATTTATTTTTGATAATATC
*
61081 AATTATATTTAT
1 AATAATATTTAT
61093 GGTAAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.18
25 15 0.45
26 12 0.36
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (25 bp):
AATAATATTTATTTTTGATAATATC
Found at i:64972 original size:28 final size:27
Alignment explanation
Indices: 64941--65040 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 27
64931 ACCCCGGGGC
*
64941 AAAATGGCAATTTTAGGCAATCGAGGGT
1 AAAATGGTAATTTTAGG-AATCGAGGGT
*
64969 AAAATGGTAATTTT-GGAAAAATCGAGGTT
1 AAAATGGTAATTTTAGG---AATCGAGGGT
64998 AAAAATGG-AATTTTAGGAAGTTCGAGGGT
1 -AAAATGGTAATTTTAGGAA--TCGAGGGT
65027 AAAATGGTAATTTT
1 AAAATGGTAATTTT
65041 TGGTGAAGTC
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
27 4 0.07
28 20 0.33
29 28 0.46
30 9 0.15
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (27 bp):
AAAATGGTAATTTTAGGAATCGAGGGT
Found at i:65005 original size:30 final size:29
Alignment explanation
Indices: 64959--65248 Score: 141
Period size: 29 Copynumber: 9.8 Consensus size: 29
64949 AATTTTAGGC
64959 AATCGAGGGT-AAAATGGTAATTTTGGAAA
1 AATCGAGGGTAAAAATGG-AATTTTGGAAA
*
64988 AATCGAGGTTAAAAATGGAATTTTAGG-AA
1 AATCGAGGGTAAAAATGGAATTTT-GGAAA
** **
65017 GTTCGAGGGT-AAAATGGTAATTTTTGGTGA
1 AATCGAGGGTAAAAATGG-AA-TTTTGGAAA
* * *
65047 AGTC-AGGATCAAAAATGGAATTTTGGGAA
1 AATCGAGGGT-AAAAATGGAATTTTGGAAA
** * *
65076 GTTCGGGGGTAAAAATGTAATTTTTGGTAAA
1 AATCGAGGGTAAAAATGGAA-TTTTGG-AAA
65107 AATCG-GGGTAAAAATGGAATTTT-GAAA
1 AATCGAGGGTAAAAATGGAATTTTGGAAA
* * * **
65134 AGTTTG-GTGGTAAAAATGTAATTTTTGGTGA
1 A-ATCGAG-GGTAAAAATGGAA-TTTTGGAAA
*
65165 AAT-TAGGGTCAAAAAAAT-GAATTTTGGAAA
1 AATCGAGGGT---AAAAATGGAATTTTGGAAA
** * * *
65195 GTTTAGGGGGTAAAAATGTAATTTTTGGAAA
1 -AATCGAGGGTAAAAATGGAA-TTTTGGAAA
* * *
65226 AAT-TAGGGTTAAAATGAAATTTT
1 AATCGAGGGTAAAAATGGAATTTT
65249 AAAAAGTTTT
Statistics
Matches: 199, Mismatches: 40, Indels: 45
0.70 0.14 0.16
Matches are distributed among these distances:
27 4 0.02
28 15 0.08
29 87 0.44
30 56 0.28
31 27 0.14
32 10 0.05
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.32
Consensus pattern (29 bp):
AATCGAGGGTAAAAATGGAATTTTGGAAA
Found at i:65076 original size:59 final size:59
Alignment explanation
Indices: 64961--65279 Score: 278
Period size: 59 Copynumber: 5.4 Consensus size: 59
64951 TTTTAGGCAA
* *
64961 TCGAGGGT-AAAATGGTAA-TTTTGGAAAAATC-GAGGTTAAAAATGGAATTTTAGG-AAGT
1 TCGAGGGTAAAAAT-GTAATTTTTGGTAAAATCAG-GGTCAAAAATGGAATTTT-GGAAAGT
* * * *
65019 TCGAGGGT-AAAATGGTAATTTTTGGTGAAGTCAGGATCAAAAATGGAATTTTGGGAAGT
1 TCGAGGGTAAAAAT-GTAATTTTTGGTAAAATCAGGGTCAAAAATGGAATTTTGGAAAGT
* * *
65078 TCGGGGGTAAAAATGTAATTTTTGGTAAAAATCGGGGT-AAAAATGGAATTTTGAAAAGT
1 TCGAGGGTAAAAATGTAATTTTTGGT-AAAATCAGGGTCAAAAATGGAATTTTGGAAAGT
* * *
65137 TTG-GTGGTAAAAATGTAATTTTTGGTGAAATTAGGGTCAAAAAAAT-GAATTTTGGAAAGTT
1 TCGAG-GGTAAAAATGTAATTTTTGGTAAAATCAGGGTC--AAAAATGGAATTTTGGAAAG-T
* * * * * * **
65198 TAGGGGGTAAAAATGTAATTTTTGGAAAAATTAGGGT-TAAAATGAAATTTTAAAAAGT
1 TCGAGGGTAAAAATGTAATTTTTGGTAAAATCAGGGTCAAAAATGGAATTTTGGAAAGT
** *
65256 TTTAGGGATATAAATGTAATTTTT
1 TCGAGGG-TAAAAATGTAATTTTT
65280 AAAAAGTTTA
Statistics
Matches: 220, Mismatches: 28, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
58 39 0.18
59 116 0.53
60 25 0.11
61 39 0.18
62 1 0.00
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.33
Consensus pattern (59 bp):
TCGAGGGTAAAAATGTAATTTTTGGTAAAATCAGGGTCAAAAATGGAATTTTGGAAAGT
Found at i:65277 original size:30 final size:28
Alignment explanation
Indices: 65228--65337 Score: 103
Period size: 30 Copynumber: 3.7 Consensus size: 28
65218 TTTGGAAAAA
*
65228 TTAGGGTTAAAATGAAATTTTAAAAAGTT
1 TTAGGG-TAAAATGTAATTTTAAAAAGTT
65257 TTAGGGATATAAATGTAATTTTTAAAAAGTT
1 TTAGGG-TA-AAATGTAA-TTTTAAAAAGTT
* *
65288 TAAGGGTCAAAATATAATTTTAAAGAAGTT
1 TTAGGGT-AAAATGTAATTTTAAA-AAGTT
** *
65318 TGGGGGTTAAAATATAATTT
1 TTAGGG-TAAAATGTAATTT
65338 CTAAGTAGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
29 15 0.21
30 36 0.51
31 19 0.27
ACGTcount: A:0.43, C:0.01, G:0.18, T:0.38
Consensus pattern (28 bp):
TTAGGGTAAAATGTAATTTTAAAAAGTT
Found at i:65336 original size:60 final size:57
Alignment explanation
Indices: 65074--65337 Score: 210
Period size: 59 Copynumber: 4.4 Consensus size: 57
65064 GAATTTTGGG
* * ** * * *
65074 AAGTTCGGGGGTAAAAATGTAATTTTTGGTAAAAATCGGGGTAAAAATGGAATTTTGAA
1 AAGTTTGGGGGTTAAAATGTAATTTTT-G-AAAAATTAGGGTCAAAATGAAATTTTAAA
* * ** **
65133 AAGTTTGGTGGTAAAAATGTAATTTTTGGTGAAATTAGGGTCAAAAAAATG-AATTTTGGA
1 AAGTTTGGGGGTTAAAATGTAATTTTT-GAAAAATTAGGGTC---AAAATGAAATTTTAAA
* *
65193 AAGTTTAGGGGGTAAAAATGTAATTTTTGGAAAAATTAGGGTTAAAATGAAATTTTAAA
1 AAGTTT-GGGGGTTAAAATGTAATTTTT-GAAAAATTAGGGTCAAAATGAAATTTTAAA
** *
65252 AAGTTTTAGGGATATAAATGTAATTTTT-AAAAAGTTTAAGGGTCAAAAT-ATAATTTTAAA
1 AAGTTTGGGGGTTA-AAATGTAATTTTTGAAAAA--TT-AGGGTCAAAATGA-AATTTTAAA
*
65312 GAAGTTTGGGGGTTAAAATATAATTT
1 -AAGTTTGGGGGTTAAAATGTAATTT
65338 CTAAGTAGTT
Statistics
Matches: 171, Mismatches: 23, Indels: 21
0.80 0.11 0.10
Matches are distributed among these distances:
57 5 0.03
58 18 0.11
59 56 0.33
60 43 0.25
61 49 0.29
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.35
Consensus pattern (57 bp):
AAGTTTGGGGGTTAAAATGTAATTTTTGAAAAATTAGGGTCAAAATGAAATTTTAAA
Found at i:67985 original size:193 final size:193
Alignment explanation
Indices: 67591--68151 Score: 830
Period size: 193 Copynumber: 2.9 Consensus size: 193
67581 TGATTTAGTC
* * *
67591 TACTTCT-TAGTATCTTAT-AAGGAAGATGATCGCATCGCTTATTTCAATCCGCTTCTCTGTACC
1 TACTTCTCT-GTATCTTATCAA-GAAGATGATCGCCTCACTTGTTTCAATCCGCTTCTCTGTACC
* * * * *
67654 TTATCAGGAAGACAAATTTGGTCTACTTTTCAGTATTTCATTAGGAAACTAACCATTTTATTGCT
64 TTATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCT
* * * *
67719 TCGACTTGCTTCTCAGTATCTCGTCAAGAAGCTGGAGTTCGAATATTTGTTCGCATTGAGTTGGT
129 TCGCCCTGCTTCTCAGTATCTCATCAAGAAGCTGG-GTTCGAAGATTTGTTCGCATTGAGTTGGT
67784 A
193 A
*
67785 TACTTCTCTGTATCTTATCAAGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTT
1 TACTTCTCTGTATCTTATCAAGAAGATGATCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTT
*
67850 ATTAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTC
66 ATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
67914 GCCCTGCTTCTCAGTATCTCATCAAGAAGCTAGGGTTCGAAGATTTGTTCGCATTGAGTTGGTA
131 GCCCTGCTTCTCAGTATCTCATCAAGAAGCT-GGGTTCGAAGATTTGTTCGCATTGAGTTGGTA
* *
67978 TACTTCTCTGTATCTCATC-AGAAAGATAATCGCCTCACTTGTTTCAATCCGCTTCTCTG---CT
1 TACTTCTCTGTATCTTATCAAG-AAGATGATCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCT
* * *
68039 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTT
65 TATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* *
68104 CGCCCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTG
130 CGCCCTGCTTCTCAGTATCTCATCAAGAAGCT-GGGTTCGAAGATTTG
68152 CTCGTATTAA
Statistics
Matches: 339, Mismatches: 23, Indels: 13
0.90 0.06 0.03
Matches are distributed among these distances:
190 52 0.15
191 56 0.17
192 2 0.01
193 122 0.36
194 104 0.31
195 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (193 bp):
TACTTCTCTGTATCTTATCAAGAAGATGATCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTT
ATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
GCCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGTTCGAAGATTTGTTCGCATTGAGTTGGTA
Found at i:80157 original size:28 final size:29
Alignment explanation
Indices: 80125--80198 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
80115 TTAGGCACTC
80125 GAGGGTAAAATGGTAAGTTTAGAAAAATT
1 GAGGGTAAAATGGTAAGTTTAGAAAAATT
* * **
80154 -AGGGTAAAAAATGG-AATTTTAGGAAGTTT
1 GAGGGT--AAAATGGTAAGTTTAGAAAAATT
80183 GAGGGTAAAATGGTAA
1 GAGGGTAAAATGGTAA
80199 TTTTTGGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 12 0.32
29 13 0.35
30 12 0.32
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (29 bp):
GAGGGTAAAATGGTAAGTTTAGAAAAATT
Found at i:80192 original size:29 final size:29
Alignment explanation
Indices: 80103--80281 Score: 120
Period size: 30 Copynumber: 6.1 Consensus size: 29
80093 ACCTTGGGGC
* *
80103 AAAATGGTAATTTTAGGCACTCGAGGGT-
1 AAAATGGTAATTTTAGGAAATCGAGGGTA
* * *
80131 AAAATGGTAAGTTTAGAAAAAT-TAGGGTAA
1 AAAATGGTAATTTTAG-GAAATCGAGGGT-A
* *
80161 AAAATGG-AATTTTAGGAAGTTTGAGGGT-
1 AAAATGGTAATTTTAGGAA-ATCGAGGGTA
*
80189 AAAATGGTAATTTTTGGTGAAATCG-GGGTCA
1 AAAATGGTAA-TTTTAG-GAAATCGAGGGT-A
* *
80220 AAAATGG-AATTTTGGGAAGTTCGAGGGTA
1 AAAATGGTAATTTTAGGAA-ATCGAGGGTA
* *
80249 AAAAT-GTAATTTTTGATGAAATCGAGGTTA
1 AAAATGGTAA-TTTT-AGGAAATCGAGGGTA
80279 AAA
1 AAA
80282 TGAAATTTTT
Statistics
Matches: 119, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
28 33 0.28
29 33 0.28
30 40 0.34
31 13 0.11
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.30
Consensus pattern (29 bp):
AAAATGGTAATTTTAGGAAATCGAGGGTA
Found at i:80238 original size:59 final size:58
Alignment explanation
Indices: 80155--80439 Score: 299
Period size: 59 Copynumber: 4.9 Consensus size: 58
80145 AGAAAAATTA
*
80155 GGGTAAAAAATGGAATTTTAGG-AAGTTTGAGGGTAAAATGGTAATTTTTGGTGAAATCG
1 GGGTCAAAAATGGAATTTT-GGAAAGTTTGAGGGTAAAAT-GTAATTTTTGGTGAAATCG
* * *
80214 GGGTCAAAAATGGAATTTTGGGAAGTTCGAGGGTAAAAATGTAATTTTTGATGAAATCG
1 GGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGT-AAAATGTAATTTTTGGTGAAATCG
* * * *
80273 AGGT-TAAAATGAAATTTTTGAAAGTTT-AGGGATAAAATGTAATTTTTGGTGAAATCG
1 GGGTCAAAAATGGAATTTTGGAAAGTTTGAGGG-TAAAATGTAATTTTTGGTGAAATCG
* * ** ** *
80330 GGGTCAAAAATGGAATTTTGTAAAATTCGTGA-GCAAAAATGTAATTTTTGGAAAAATCA
1 GGGTCAAAAATGGAATTTTGGAAAGTT--TGAGGGTAAAATGTAATTTTTGGTGAAATCG
* * * * *
80389 AGTTCAAAAATGGAATTTTGGAAAGTTCGAGGGCAAAAATGTAAATTTTGG
1 GGGTCAAAAATGGAATTTTGGAAAGTTTGAGGG-TAAAATGTAATTTTTGG
80440 AAAGTTTAGG
Statistics
Matches: 189, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
57 32 0.17
58 39 0.21
59 110 0.58
60 7 0.04
61 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (58 bp):
GGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGTAATTTTTGGTGAAATCG
Found at i:80343 original size:116 final size:116
Alignment explanation
Indices: 80160--80439 Score: 343
Period size: 116 Copynumber: 2.4 Consensus size: 116
80150 AATTAGGGTA
*
80160 AAAAATGGAATTTTAGGAAGTTTGAGGG-TAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAA
1 AAAAATGGAATTTTAGAAAGTTT-AGGGATAAAAT-GTAATTTTTGGTGAAATCGGGGTCAAAAA
* * * * * *
80224 TGGAATTTTGGGAAGTTCGAGGGTAAAAATGTAATTTTT-GATGAAATCGAGGTT
64 TGGAATTTTGGAAAATTCGAGAGCAAAAATGTAATTTTTGGA-AAAATC-AAGTT
* *
80278 -AAAATGAAATTTTTGAAAGTTTAGGGATAAAATGTAATTTTTGGTGAAATCGGGGTCAAAAATG
1 AAAAATGGAATTTTAGAAAGTTTAGGGATAAAATGTAATTTTTGGTGAAATCGGGGTCAAAAATG
* *
80342 GAATTTTGTAAAATTCGTGAGCAAAAATGTAATTTTTGGAAAAATCAAGTT
66 GAATTTTGGAAAATTCGAGAGCAAAAATGTAATTTTTGGAAAAATCAAGTT
* * *
80393 CAAAAATGGAATTTTGGAAAGTTCGAGGGCA-AAAATGTAAATTTTGG
1 -AAAAATGGAATTTTAGAAAGTT-TAGGG-ATAAAATGTAATTTTTGG
80440 AAAGTTTAGG
Statistics
Matches: 141, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
115 4 0.03
116 71 0.50
117 46 0.33
118 19 0.13
119 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (116 bp):
AAAAATGGAATTTTAGAAAGTTTAGGGATAAAATGTAATTTTTGGTGAAATCGGGGTCAAAAATG
GAATTTTGGAAAATTCGAGAGCAAAAATGTAATTTTTGGAAAAATCAAGTT
Found at i:80425 original size:29 final size:29
Alignment explanation
Indices: 80160--80445 Score: 139
Period size: 29 Copynumber: 9.8 Consensus size: 29
80150 AATTAGGGTA
*
80160 AAAAATGGAATTTTAGG-AAGTTTGAGGG-
1 AAAAATGGAATTTT-GGAAAGTTCGAGGGC
*
80188 TAAAATGGTAATTTTTGGTGAAA--TCG-GGGTC
1 AAAAATGG-AA-TTTT-G-GAAAGTTCGAGGG-C
* *
80219 AAAAATGGAATTTTGGGAAGTTCGAGGGT
1 AAAAATGGAATTTTGGAAAGTTCGAGGGC
* *
80248 AAAAATGTAATTTTTGATGAAA--TCGA-GGT
1 AAAAATGGAA-TTTTG--GAAAGTTCGAGGGC
* * * *
80277 TAAAATGAAATTTTTGAAAGTT-TAGGG-
1 AAAAATGGAATTTTGGAAAGTTCGAGGGC
*
80304 ATAAAATGTAATTTTTGGTGAAA--TCG-GGGTC
1 A-AAAATGGAA-TTTT-G-GAAAGTTCGAGGG-C
* * * *
80335 AAAAATGGAATTTTGTAAAATTCGTGAGC
1 AAAAATGGAATTTTGGAAAGTTCGAGGGC
* ** * **
80364 AAAAATGTAATTTTTGGAAAAATCAAGTTC
1 AAAAATGGAA-TTTTGGAAAGTTCGAGGGC
80394 AAAAATGGAATTTTGGAAAGTTCGAGGGC
1 AAAAATGGAATTTTGGAAAGTTCGAGGGC
*
80423 AAAAATGTAAATTTTGGAAAGTT
1 AAAAATG-GAATTTTGGAAAGTT
80446 TAGGGGTTAA
Statistics
Matches: 198, Mismatches: 33, Indels: 52
0.70 0.12 0.18
Matches are distributed among these distances:
26 4 0.02
27 7 0.04
28 24 0.12
29 78 0.39
30 67 0.34
31 13 0.07
32 5 0.03
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAAGTTCGAGGGC
Found at i:80442 original size:59 final size:58
Alignment explanation
Indices: 80123--80440 Score: 288
Period size: 59 Copynumber: 5.4 Consensus size: 58
80113 TTTTAGGCAC
* * * * * *
80123 TCGAGGGTAAAATGGTAA-GTTTAGAAAAATTAGGGTAAAAAATGGAATTTTAGG-AAGT
1 TCGAGGGAAAAAT-GTAATTTTTGGAGAAATCAGGGTCAAAAATGGAATTTT-GGAAAGT
* * * * *
80181 TTGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGGAAGT
1 TCGAGGGAAAAAT-GTAATTTTTGGAGAAATCAGGGTCAAAAATGGAATTTTGGAAAGT
* * *
80240 TCGAGGGTAAAAATGTAATTTTT-GATGAAATC-GAGGT-TAAAATGAAATTTTTGAAAGT
1 TCGAGGG-AAAAATGTAATTTTTGGA-GAAATCAG-GGTCAAAAATGGAATTTTGGAAAGT
* * * * *
80298 T-TAGGGATAAAATGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGTAAAAT
1 TCGAGGGA-AAAATGTAATTTTTGGAGAAATCAGGGTCAAAAATGGAATTTTGGAAAGT
* * * * *
80356 TCGTGAGCAAAAATGTAATTTTTGGAAAAATCAAGTTCAAAAATGGAATTTTGGAAAGT
1 TCGAG-GGAAAAATGTAATTTTTGGAGAAATCAGGGTCAAAAATGGAATTTTGGAAAGT
*
80415 TCGAGGGCAAAAATGTAAATTTTGGA
1 TCGAGGG-AAAAATGTAATTTTTGGA
80441 AAGTTTAGGG
Statistics
Matches: 213, Mismatches: 35, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.00
57 27 0.13
58 59 0.28
59 119 0.56
60 7 0.03
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.31
Consensus pattern (58 bp):
TCGAGGGAAAAATGTAATTTTTGGAGAAATCAGGGTCAAAAATGGAATTTTGGAAAGT
Found at i:80458 original size:30 final size:29
Alignment explanation
Indices: 80393--80480 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 29
80383 AAATCAAGTT
** *
80393 CAAAAATGGAATTTTGGAAAG-TTCGAGGG
1 CAAAAATATAATTTTGGAAAGTTTAG-GGG
*
80422 CAAAAATGTAAATTTTGGAAAGTTTAGGGG
1 CAAAAATAT-AATTTTGGAAAGTTTAGGGG
** *
80452 TTAAAATATAATTTTAGAGAAGTTTAGGG
1 CAAAAATATAATTTTGGA-AAGTTTAGGG
80481 ACCTTTAAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 16 0.32
30 31 0.62
31 3 0.06
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (29 bp):
CAAAAATATAATTTTGGAAAGTTTAGGGG
Found at i:81639 original size:3 final size:3
Alignment explanation
Indices: 81590--81625 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
81580 GTTGTTGTTG
81590 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
81626 AAAAAGTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:87313 original size:14 final size:15
Alignment explanation
Indices: 87294--87328 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
87284 AGAAAAAAAG
87294 AGAAAAAGAAGAA-A
1 AGAAAAAGAAGAAGA
87308 AGAAAAAGAAGAAGA
1 AGAAAAAGAAGAAGA
87323 AGAAAA
1 AGAAAA
87329 TAGAGATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAGAAGA
Found at i:87322 original size:20 final size:19
Alignment explanation
Indices: 87280--87328 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
87270 TTTAGGGTTT
*
87280 AAGAAGAAAAAAAGAGAAA
1 AAGAAGAAAAAAAAAGAAA
*
87299 AAGAAGAAAAGAAAAAGAAG
1 AAGAAGAAAA-AAAAAGAAA
87319 AAGAAGAAAA
1 AAGAAGAAAA
87329 TAGAGATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (19 bp):
AAGAAGAAAAAAAAAGAAA
Found at i:88516 original size:21 final size:21
Alignment explanation
Indices: 88492--88541 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
88482 CCATTTGCAA
*
88492 CTGAGTTGTGTTGCTCACTTG
1 CTGAGTTGTGCTGCTCACTTG
*
88513 CTGAGATGTGCTGCTCACTTG
1 CTGAGTTGTGCTGCTCACTTG
88534 CTGAGTTG
1 CTGAGTTG
88542 GGGTCCTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.20, G:0.30, T:0.38
Consensus pattern (21 bp):
CTGAGTTGTGCTGCTCACTTG
Found at i:88550 original size:21 final size:21
Alignment explanation
Indices: 88505--88551 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
88495 AGTTGTGTTG
* *
88505 CTCACTTGCTGAGATGTGCTG
1 CTCACTTGCTGAGATGGGCTC
* *
88526 CTCACTTGCTGAGTTGGGGTC
1 CTCACTTGCTGAGATGGGCTC
88547 CTCAC
1 CTCAC
88552 ATGAATATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.32
Consensus pattern (21 bp):
CTCACTTGCTGAGATGGGCTC
Found at i:89251 original size:22 final size:22
Alignment explanation
Indices: 89226--89271 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
89216 CATCCAATAT
89226 AAAGCCAACATAAAGCAAACAA
1 AAAGCCAACATAAAGCAAACAA
* ** *
89248 AAAGTCATTATAAAGCCAACAA
1 AAAGCCAACATAAAGCAAACAA
89270 AA
1 AA
89272 CACAACATAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.61, C:0.20, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAGCCAACATAAAGCAAACAA
Found at i:89324 original size:12 final size:12
Alignment explanation
Indices: 89307--89346 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
89297 TAGGGTATTA
89307 AAAACAACATAC
1 AAAACAACATAC
*
89319 AAAACAAAATA-
1 AAAACAACATAC
89330 AAGAACAACATAC
1 AA-AACAACATAC
89343 AAAA
1 AAAA
89347 TAATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.72, C:0.17, G:0.03, T:0.07
Consensus pattern (12 bp):
AAAACAACATAC
Found at i:90955 original size:52 final size:52
Alignment explanation
Indices: 90819--91170 Score: 424
Period size: 52 Copynumber: 6.8 Consensus size: 52
90809 ATTTCACTTC
* * * * *
90819 ATTCATATACTCACGATGACACATAGCCATCGAACCT-TATAATCCGCAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCT-TAATCCGTAAAGG
* * * *
90871 ATTCATATATACTCATGATAAGA-TAGAGTCATCGGACCTCTTAATCCGTAAAGG
1 ATTC--ATATACTCACGATGACACT-TAGTCATCGGACCTCTTAATCCGTAAAGG
*** *
90925 ATTCATATACTCACGATGACACTTAGTCATCATCCCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGG
* * * * * *
90977 ATTGATATACTTACGATGACACTCAATAATCGGACCTCTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGG
* *
91029 ATTCATATACTCACGATG--ACTTAGTCATCAGACCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGG
*
91079 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGG
**
91131 ATTCATATACTCATAATGACACTTAGTCATCGGACCTCTT
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTT
91171 CGTTTATGGC
Statistics
Matches: 253, Mismatches: 40, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
50 44 0.17
52 167 0.66
53 1 0.00
54 40 0.16
55 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGG
Found at i:91095 original size:102 final size:103
Alignment explanation
Indices: 90819--91167 Score: 418
Period size: 102 Copynumber: 3.3 Consensus size: 103
90809 ATTTCACTTC
* * * * *
90819 ATTCATATACTCACGATGACACATAGCCATC-GAACCTTATAATCCGCAAGGGATTCATATATAC
1 ATTCATATACTCACGATGA-ACTTAGTCATCAG-ACCTTTTAATCCGTAAAGGATTC--ATATAC
* * * * *
90883 TCATGATAAGA-T-AGAGTCATCGGACCTCTTAATCCGTAAAGG
62 TCACGATGACACTCA-A-TAATCGGACCTCTTAATCCATAAAGG
** * *
90925 ATTCATATACTCACGATGACACTTAGTCATCATCCCTTTTAATCCGTAAAGGATTGATATACTTA
1 ATTCATATACTCACGATGA-ACTTAGTCATCAGACCTTTTAATCCGTAAAGGATTCATATACTCA
90990 CGATGACACTCAATAATCGGACCTCTTAATCCATAAAGG
65 CGATGACACTCAATAATCGGACCTCTTAATCCATAAAGG
91029 ATTCATATACTCACGATG-ACTTAGTCATCAGACCTTTTAATCCGTAAAGGATTCATATACTCAC
1 ATTCATATACTCACGATGAACTTAGTCATCAGACCTTTTAATCCGTAAAGGATTCATATACTCAC
* * *
91093 GATGACACTTAGTCATCGGACCTCTTAATCCATAAAGG
66 GATGACACTCAATAATCGGACCTCTTAATCCATAAAGG
** *
91131 ATTCATATACTCATAATGACACTTAGTCATCGGACCT
1 ATTCATATACTCACGATGA-ACTTAGTCATCAGACCT
91168 CTTCGTTTAT
Statistics
Matches: 214, Mismatches: 24, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
102 93 0.43
104 71 0.33
105 2 0.01
106 48 0.22
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (103 bp):
ATTCATATACTCACGATGAACTTAGTCATCAGACCTTTTAATCCGTAAAGGATTCATATACTCAC
GATGACACTCAATAATCGGACCTCTTAATCCATAAAGG
Found at i:93829 original size:31 final size:32
Alignment explanation
Indices: 93752--93830 Score: 76
Period size: 31 Copynumber: 2.5 Consensus size: 32
93742 CTAAATCTCA
* *
93752 AACA-ATGTTAACCAAAATTGAATACTAAGTCT
1 AACATATGTTAA-CAAAATTGAATACTAAGACC
**
93784 AA-ATCATAAT-ACAAAATTGAATACTAA-ACC
1 AACAT-ATGTTAACAAAATTGAATACTAAGACC
93814 AACATATGTTAACAAAA
1 AACATATGTTAACAAAA
93831 ACATGTGAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
30 6 0.16
31 25 0.68
32 3 0.08
33 3 0.08
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.25
Consensus pattern (32 bp):
AACATATGTTAACAAAATTGAATACTAAGACC
Found at i:95882 original size:37 final size:37
Alignment explanation
Indices: 95829--95901 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
95819 GGATCACTGG
*
95829 CATAAAGCCTATTAGGCACAAAGCCTGATAACACCGA
1 CATAAAGCCTACTAGGCACAAAGCCTGATAACACCGA
95866 CATAAAGCCTACTAGGCACAAAGCCTGATAACACCG
1 CATAAAGCCTACTAGGCACAAAGCCTGATAACACCG
95902 GAACAAAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.29, G:0.16, T:0.15
Consensus pattern (37 bp):
CATAAAGCCTACTAGGCACAAAGCCTGATAACACCGA
Found at i:95910 original size:37 final size:37
Alignment explanation
Indices: 95832--95912 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
95822 TCACTGGCAT
* *
95832 AAAGCCTATTAGGCACAAAGCCTGATAACACCGACAT
1 AAAGCCTACTAGGCACAAAGCCTGATAACACCGACAC
95869 AAAGCCTACTAGGCACAAAGCCTGATAACACCGGA-AC
1 AAAGCCTACTAGGCACAAAGCCTGATAACACC-GACAC
95906 AAAGCCT
1 AAAGCCT
95913 GAATTTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 39 0.95
38 2 0.05
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.14
Consensus pattern (37 bp):
AAAGCCTACTAGGCACAAAGCCTGATAACACCGACAC
Found at i:96848 original size:19 final size:19
Alignment explanation
Indices: 96807--96849 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
96797 TTATGAGTGT
* *
96807 AATTTACTCAATAAAATTT
1 AATTTACTAAATAAAATTA
**
96826 AATTTACTAAATGTAATTA
1 AATTTACTAAATAAAATTA
96845 AATTT
1 AATTT
96850 TAAAATCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (19 bp):
AATTTACTAAATAAAATTA
Done.