Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010357.1 Kokia drynarioides strain JFW-HI SEQ_125228, 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: 237765
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7214 original size:19 final size:19
Alignment explanation
Indices: 7192--7228 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7182 TCGCACATCG
*
7192 CCGTTGTCACTGTCGCATA
1 CCGTCGTCACTGTCGCATA
*
7211 CCGTCGTTACTGTCGCAT
1 CCGTCGTCACTGTCGCAT
7229 GCTATTGTTA
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:0.14, C:0.32, G:0.22, T:0.32
Consensus pattern (19 bp):
CCGTCGTCACTGTCGCATA
Found at i:10456 original size:23 final size:22
Alignment explanation
Indices: 10430--10473 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
10420 AAAATATTTC
*
10430 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
10453 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
10474 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:17433 original size:90 final size:90
Alignment explanation
Indices: 16782--17427 Score: 710
Period size: 90 Copynumber: 7.2 Consensus size: 90
16772 TTACCAGTAC
* * * *
16782 ACGATACTGCTCACACGAGCTATCGAGGACTCGCAACATATGCAGTACCTCAACCATCGATACGA
1 ACGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCAGTACCCCAGCCATCGATACGG
16847 TATCTGTGCATATAA-TGGTTCCCTA
66 TATCTGTGCATATAACT-GTTCCCTA
* ** * *
16872 ACGATACTGCTCACGTGAGCTATTGAGGACTCGCAACATATGCAGTA-CCCAGCCATTGATACGG
1 ACGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCAGTACCCCAGCCATCGATACGG
16936 TATCTGTGCATATAA-TGTTCCCTA
66 TATCTGTGCATATAACTGTTCCCTA
* * * * ** *
16960 ACGATGCTGCTCATACGAGCTATCCAGGACTTGTAACATATGTGGTACCCCAGCCATCAATACGG
1 ACGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCAGTACCCCAGCCATCGATACGG
17025 TATCTGTGCATATAACTGTTCCCTA
66 TATCTGTGCATATAACTGTTCCCTA
* ** ** * * * * *
17050 ACGATGCTACTTGCACGATTTGTCGAGGACTCGTAACATATGC-GATACTCCAACCATTGATACG
1 ACGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCAG-TACCCCAGCCATCGATACG
*
17114 GTATCTGTGCATATAACTGTACCCTA
65 GTATCTGTGCATATAACTGTTCCCTA
* * * * * *
17140 ACGATGTTGCTCATACGAGCTGTCGAGGACTCACAACATAGGCTA-TACCCCAGCCATCAATACG
1 ACGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGC-AGTACCCCAGCCATCGATACG
* * * *
17204 GTATCTATGTATATAATTGTTCTCTA
65 GTATCTGTGCATATAACTGTTCCCTA
* * * * *
17230 ACGATGCTGCTCACACGATCTATCGAGGACTCACAACATAGGC-GATTCCCCAGCCATCGATATG
1 ACGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCAG-TACCCCAGCCATCGATACG
* * *
17294 GTATCTATGCATATAACTATTCTCTA
65 GTATCTGTGCATATAACTGTTCCCTA
* * * * * * *
17320 ATGATGTTGCTCACACGATCTGTCGAGGACTCGTAATATATGCAGTACCCCAGCCATCAATACGG
1 ACGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCAGTACCCCAGCCATCGATACGG
*
17385 TATCTGTGCATATAATTGTTCCCTA
66 TATCTGTGCATATAACTGTTCCCTA
* * *
17410 ACAATGCTACTTACACGA
1 ACGATGCTGCTCACACGA
17428 ACTGTCAAAA
Statistics
Matches: 466, Mismatches: 82, Indels: 16
0.83 0.15 0.03
Matches are distributed among these distances:
88 45 0.10
89 60 0.13
90 360 0.77
91 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (90 bp):
ACGATGCTGCTCACACGAGCTATCGAGGACTCGCAACATATGCAGTACCCCAGCCATCGATACGG
TATCTGTGCATATAACTGTTCCCTA
Found at i:23549 original size:24 final size:24
Alignment explanation
Indices: 23519--23569 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
23509 ACAAACAACA
* *
23519 TTAGCTCTCATGAGCCTAGAATGG
1 TTAGCTCTCACGAGCCCAGAATGG
*
23543 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCTCTCACGAGCCCAGAATGG
23567 TTA
1 TTA
23570 ACCAGTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (24 bp):
TTAGCTCTCACGAGCCCAGAATGG
Found at i:28189 original size:24 final size:24
Alignment explanation
Indices: 28159--28233 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
28149 ACATACAACA
* *
28159 TTAGCTCTCATGAGCCCAAGATGG
1 TTAGCTCTTACGAGCCCAAGATGG
28183 TTAGCTCTTACGAGCCCAAGATGG
1 TTAGCTCTTACGAGCCCAAGATGG
28207 TTAGCTCTTACGAGCCC-AGAATGG
1 TTAGCTCTTACGAGCCCAAG-ATGG
28231 TTA
1 TTA
28234 ACCAATATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 2 0.04
24 46 0.96
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAAGATGG
Found at i:42278 original size:17 final size:15
Alignment explanation
Indices: 42223--42275 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
42213 TGTATGTTTC
42223 TTATTAAATTAATTTT
1 TTATT-AATTAATTTT
42239 TTGATTAATT--TTTT
1 TT-ATTAATTAATTTT
*
42253 TTGTTAATTGAATTTT
1 TTATTAATT-AATTTT
42269 TTATTAA
1 TTATTAA
42276 ATTAGGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 6 0.19
14 6 0.19
16 16 0.52
17 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (15 bp):
TTATTAATTAATTTT
Found at i:42309 original size:28 final size:28
Alignment explanation
Indices: 42277--42332 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
42267 TTTTATTAAA
42277 TTAGGTTAAAAGGAAAAGGTATGTTTAT
1 TTAGGTTAAAAGGAAAAGGTATGTTTAT
42305 TTAGGTTAAAAGGAAAAGGTATGTTTAT
1 TTAGGTTAAAAGGAAAAGGTATGTTTAT
42333 CTTTTTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (28 bp):
TTAGGTTAAAAGGAAAAGGTATGTTTAT
Found at i:52575 original size:18 final size:19
Alignment explanation
Indices: 52538--52575 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
52528 CAAGGACAAG
* *
52538 AAAAGAAAGAGAAAGGACA
1 AAAAGAAAAAGAAAGCACA
52557 AAAAGAAAAAG-AAGCACA
1 AAAAGAAAAAGAAAGCACA
52575 A
1 A
52576 TGAAGAACGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAGAAAGCACA
Found at i:52717 original size:17 final size:18
Alignment explanation
Indices: 52678--52719 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52668 ATGCATCTCA
*
52678 TTTAGTTGTCAATGCATT
1 TTTATTTGTCAATGCATT
*
52696 TTTATTTGTCACTGCA-T
1 TTTATTTGTCAATGCATT
52713 TTTATTT
1 TTTATTT
52720 ATTAGTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.57
Consensus pattern (18 bp):
TTTATTTGTCAATGCATT
Found at i:67251 original size:126 final size:126
Alignment explanation
Indices: 67023--67251 Score: 300
Period size: 126 Copynumber: 1.8 Consensus size: 126
67013 TTGCCAACTC
* * * * *
67023 TTATTTAAGTGTTGCCTTAGGCATGCATATCTCAACCCTTATACAAAGAGTTGGCCAAAACGTCT
1 TTATTTAAGCGTTGCCTTAGGCATGAATATCTCAACCCTTATACAAAGAGTTGACCAAAACATAT
** * *
67088 GTCGGCAAGTCTATTTCAACACTTAGGAAATTTTCGGCATAGTGTTGGACAAAGCCGACTA
66 GTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCATAGTGTTGGACAAAGCCGACTA
* * * * *
67149 TTATTTAAGCGTTGTCTTAGGCATGAATAT-TCCAGCTCTTGTACAAAGAGTTGACCAAAGCATA
1 TTATTTAAGCGTTGCCTTAGGCATGAATATCT-CAACCCTTATACAAAGAGTTGACCAAAACATA
67213 TGTCGGCAAGT-TGATCCCAACACTTAGGAAAGTGTCGGC
65 TGTCGGCAAGTCT-ATCCCAACACTTAGGAAAGTGTCGGC
67252 CGAAAAGTGT
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
125 2 0.02
126 85 0.98
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (126 bp):
TTATTTAAGCGTTGCCTTAGGCATGAATATCTCAACCCTTATACAAAGAGTTGACCAAAACATAT
GTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGGCATAGTGTTGGACAAAGCCGACTA
Found at i:67481 original size:145 final size:139
Alignment explanation
Indices: 67122--67541 Score: 382
Period size: 139 Copynumber: 3.0 Consensus size: 139
67112 AGGAAATTTT
* * * * *
67122 CGGCATAGTGTTGGACAAAGCCGACTATTATTTAAGCGTTGTCTTAGGCATGAATATTCCAGCTC
1 CGGCATAGTGTTGGACAAAACCGACTCTTATTTAAGCGTTGTCTTAGGCATGAATA-TCTAACCC
* ** * ** *
67187 TTGTACAAAGAGTTGACCAAAGCATATGTCGGC-AAGTTGATCCCAACACTTAGGAAAGTGTCGG
65 TTATACAAAGAGTTGACCAAAGTGTATGTCAGCAAAACT-ATCCCAACACTTAGGAAAGTGTCGA
* *
67251 CCGAAAAGTGT
129 CCCAAAAGTGG
* * * * * *
67262 CGGTATAATGTTGGAC-AAACCGACTCTTATTTAAGCATTG-CTTTTGGCAAGCATATCCTAACC
1 CGGCATAGTGTTGGACAAAACCGACTCTTATTTAAGCGTTGTC-TTAGGCATGAATAT-CTAACC
* *
67325 CTTATAGAAAGAGTTGATCAAAGTGTATGTCAGCAAAACTATCCCAACACTTGAGAAAGAAAAGT
64 CTTATACAAAGAGTTGACCAAAGTGTATGTCAGCAAAACTATCCCAACACTT-AG---G-AAAGT
*
67390 GTCTACCCAAAAGTGG
124 GTCGACCCAAAAGTGG
* * * * *
67406 CGGCATAGTGTTGGACAAAACCAACTCTTGTTTAAGCGTTGTCTTAAGTATGAATATCATAATCC
1 CGGCATAGTGTTGGACAAAACCGACTCTTATTTAAGCGTTGTCTTAGGCATGAATATC-TAACCC
* ** ** *
67471 TTATACAAAGAGTTGACCAAGACGTGTAT-TTA-CAAGTCTATCCCAACACTTAAAAAAGTGTAG
65 TTATACAAAGAGTTGACCAA-A-GTGTATGTCAGCAAAACTATCCCAACACTTAGGAAAGTGTCG
*
67534 GCCCAAAA
128 ACCCAAAA
67542 ATATCGTCTT
Statistics
Matches: 223, Mismatches: 44, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
138 2 0.01
139 74 0.33
140 33 0.15
143 1 0.00
144 33 0.15
145 70 0.31
146 4 0.02
147 6 0.03
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (139 bp):
CGGCATAGTGTTGGACAAAACCGACTCTTATTTAAGCGTTGTCTTAGGCATGAATATCTAACCCT
TATACAAAGAGTTGACCAAAGTGTATGTCAGCAAAACTATCCCAACACTTAGGAAAGTGTCGACC
CAAAAGTGG
Found at i:69547 original size:6 final size:6
Alignment explanation
Indices: 69536--69565 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
69526 AAAGTAAACC
*
69536 CATGGG CATGGG CATGGG CATGGC CATGGG
1 CATGGG CATGGG CATGGG CATGGG CATGGG
69566 GGAACACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.47, T:0.17
Consensus pattern (6 bp):
CATGGG
Found at i:73921 original size:27 final size:27
Alignment explanation
Indices: 73891--73951 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
73881 GACTTCTCTG
*
73891 TGTTTAACATCCCGTTGGATTATCCCA
1 TGTTTAACATCCCGTTGGACTATCCCA
** * *
73918 TGTTTAATGTCTCGTTTGACTATCCCA
1 TGTTTAACATCCCGTTGGACTATCCCA
73945 TGTTTAA
1 TGTTTAA
73952 TGTCCTATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (27 bp):
TGTTTAACATCCCGTTGGACTATCCCA
Found at i:73965 original size:27 final size:27
Alignment explanation
Indices: 73903--73977 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
73893 TTTAACATCC
*
73903 CGTTGGATTATCCCATGTTTAATGTCT
1 CGTTGGACTATCCCATGTTTAATGTCT
*
73930 CGTTTGACTATCCCATGTTTAATGTC-
1 CGTTGGACTATCCCATGTTTAATGTCT
*
73956 C-TATCGGACTATCCCGTGTTTA
1 CGT-T-GGACTATCCCATGTTTA
73978 TCGTCCAGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.02
26 2 0.05
27 39 0.93
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (27 bp):
CGTTGGACTATCCCATGTTTAATGTCT
Found at i:74226 original size:45 final size:45
Alignment explanation
Indices: 74177--74300 Score: 185
Period size: 45 Copynumber: 2.8 Consensus size: 45
74167 CATTATTACC
* * * *
74177 ATGATGTCATAGCATCTTTCATCTATGGTCTTACATATCAGTTTG
1 ATGATATCATAACATCTTTCATCTATGGTCTTACACATCAATTTG
* *
74222 ATGATATCATAACACCTTTAATCTATGGTCTTACACATCAATTTG
1 ATGATATCATAACATCTTTCATCTATGGTCTTACACATCAATTTG
*
74267 GTGATATCATAACATCTTTCATCTATGGTCTTAC
1 ATGATATCATAACATCTTTCATCTATGGTCTTAC
74301 TCATTTTTAG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (45 bp):
ATGATATCATAACATCTTTCATCTATGGTCTTACACATCAATTTG
Found at i:76019 original size:6 final size:6
Alignment explanation
Indices: 76008--76034 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
75998 TTAAGAGGAC
76008 CCCCCA CCCCCA CCCCCA CCCCCA CCC
1 CCCCCA CCCCCA CCCCCA CCCCCA CCC
76035 TTCCATTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.85, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCCCA
Found at i:76182 original size:2 final size:2
Alignment explanation
Indices: 76175--76199 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
76165 TTGCACCCAA
76175 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 T
76200 ATCAGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:85451 original size:27 final size:27
Alignment explanation
Indices: 85421--85475 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
85411 TGCCTAATAT
85421 ATGCATGTATTTAAGAATTCGGGATAA
1 ATGCATGTATTTAAGAATTCGGGATAA
*
85448 ATGCATGTATTTGAGAATTCGGGATAA
1 ATGCATGTATTTAAGAATTCGGGATAA
85475 A
1 A
85476 AATCAAGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (27 bp):
ATGCATGTATTTAAGAATTCGGGATAA
Found at i:85594 original size:2 final size:2
Alignment explanation
Indices: 85587--85617 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
85577 ATTACATCAA
85587 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
85618 AGTCAAGATG
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:87931 original size:18 final size:18
Alignment explanation
Indices: 87904--87941 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
87894 TGAGTTTAGC
87904 ATTTTAA-TTTCCTTTGTT
1 ATTTTAATTTTCCTTT-TT
*
87922 ATTTTCATTTTCCTTTTT
1 ATTTTAATTTTCCTTTTT
87940 AT
1 AT
87942 GGAGACGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTAATTTTCCTTTTT
Found at i:96369 original size:23 final size:22
Alignment explanation
Indices: 96338--96381 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
96328 AAAGAAATAA
*
96338 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
96360 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
96382 GAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:103728 original size:80 final size:80
Alignment explanation
Indices: 103595--103747 Score: 218
Period size: 80 Copynumber: 1.9 Consensus size: 80
103585 AGCCGCAAAC
* * * *
103595 CGTTGGTTAATCCAACTAGAGCTGAGCTCATTTATTGCGATTTGTCCGCTAGGCATTGGGTGCCA
1 CGTTGGTTAATCCAACTAGAGCTGAGCTCACTTATTGCGATCTATCCGCTAGGCACTGGGTGCCA
*
103660 TGAATTGATGAAATT
66 AGAATTGATGAAATT
* * *
103675 CGTTGGTTAATCCAACTAGAGCTGGGC-CTACTTATTGTGGTCTATCCGCTAGGCACTGGGTGCC
1 CGTTGGTTAATCCAACTAGAGCTGAGCTC-ACTTATTGCGATCTATCCGCTAGGCACTGGGTGCC
103739 AAGAATTGA
65 AAGAATTGA
103748 CGGATTTGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
79 1 0.02
80 63 0.98
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (80 bp):
CGTTGGTTAATCCAACTAGAGCTGAGCTCACTTATTGCGATCTATCCGCTAGGCACTGGGTGCCA
AGAATTGATGAAATT
Found at i:110877 original size:80 final size:80
Alignment explanation
Indices: 110744--110900 Score: 208
Period size: 80 Copynumber: 2.0 Consensus size: 80
110734 GGGCGCAAAC
* * * * * *
110744 CGTTGGTTAATCCAACTAGAGCTAAGCTCATTTATTGTGGTTTGTCCACTAGGCACTGGGTGCCA
1 CGTTGGTTAATCCAACTAGAGCTAAGCTCACTCATTGCGGTCTATCCACTAGGCACTGGGAGCCA
*
110809 TGAATTGATGAAATT
66 GGAATTGATGAAATT
* *
110824 CGTTGGTTAATCCAACTAGAGCT-AGACTTACTCATTGCGGTCTATCCGCTAGGCACTGGGAGCC
1 CGTTGGTTAATCCAACTAGAGCTAAG-CTCACTCATTGCGGTCTATCCACTAGGCACTGGGAGCC
*
110888 CGGAATTGATGAA
65 AGGAATTGATGAA
110901 TTTGGTTGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
79 2 0.03
80 64 0.97
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (80 bp):
CGTTGGTTAATCCAACTAGAGCTAAGCTCACTCATTGCGGTCTATCCACTAGGCACTGGGAGCCA
GGAATTGATGAAATT
Found at i:124033 original size:4 final size:4
Alignment explanation
Indices: 124024--124049 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
124014 TAAAATTTTA
124024 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
124050 ATAATTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:128516 original size:21 final size:21
Alignment explanation
Indices: 128492--128532 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
128482 TCAAAATGAC
128492 ATGATTTT-ACCTTTTAACTTA
1 ATGATTTTGA-CTTTTAACTTA
128513 ATGATTTTGACTTTTAACTT
1 ATGATTTTGACTTTTAACTT
128533 TAGAAAGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (21 bp):
ATGATTTTGACTTTTAACTTA
Found at i:129254 original size:37 final size:37
Alignment explanation
Indices: 129204--129277 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
129194 TTTCAGTGTG
129204 TTTGAGGTCATTCCCTGCAAAGACAAAGAAGAATGTC
1 TTTGAGGTCATTCCCTGCAAAGACAAAGAAGAATGTC
129241 TTTGAGGTCATTCCCTGCAAAGACAAAGAAGAATGTC
1 TTTGAGGTCATTCCCTGCAAAGACAAAGAAGAATGTC
129278 ACTACATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (37 bp):
TTTGAGGTCATTCCCTGCAAAGACAAAGAAGAATGTC
Found at i:133753 original size:17 final size:16
Alignment explanation
Indices: 133733--133793 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
133723 CACATTCCCT
*
133733 TTGTCTTTGCATTTCAA
1 TTGTCATTGCATTTC-A
* *
133750 TTGTCACTGCATGTGCA
1 TTGTCATTGCAT-TTCA
133767 TTGTCATTGCATTTCCA
1 TTGTCATTGCATTT-CA
133784 TGTGTCATTG
1 T-TGTCATTG
133794 TAAATTAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.03
17 25 0.69
18 10 0.28
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (16 bp):
TTGTCATTGCATTTCA
Found at i:150084 original size:28 final size:27
Alignment explanation
Indices: 150052--150117 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
150042 ATTATCGTAA
*
150052 ATGTGGAAGTCTGTTAGGACTGTCTTAT
1 ATGTGGAAGTCT-TCAGGACTGTCTTAT
* * *
150080 ATGTGGAAGCCCTTCAGTATTGTCTTAT
1 ATGTGGAAG-TCTTCAGGACTGTCTTAT
150108 ATGTGGAAGT
1 ATGTGGAAGT
150118 TGTAAACTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (27 bp):
ATGTGGAAGTCTTCAGGACTGTCTTAT
Found at i:150886 original size:10 final size:8
Alignment explanation
Indices: 150862--150895 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
150852 CTCATCACTA
150862 CATTCTCT
1 CATTCTCT
150870 CATTCTCT
1 CATTCTCT
150878 CATTCTCT
1 CATTCTCT
*
150886 CATCCTCT
1 CATTCTCT
150894 CA
1 CA
150896 AGTTCTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.15, C:0.41, G:0.00, T:0.44
Consensus pattern (8 bp):
CATTCTCT
Found at i:152103 original size:13 final size:13
Alignment explanation
Indices: 152085--152121 Score: 65
Period size: 14 Copynumber: 2.8 Consensus size: 13
152075 ATTTGAAAGA
152085 CATGACTATCCGT
1 CATGACTATCCGT
152098 CATGACTAATCCGT
1 CATGACT-ATCCGT
152112 CATGACTATC
1 CATGACTATC
152122 TCATATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.30
Consensus pattern (13 bp):
CATGACTATCCGT
Found at i:156029 original size:12 final size:12
Alignment explanation
Indices: 155999--156034 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
155989 ATGACCAGCT
155999 GAAGGAA-AAG-
1 GAAGGAAGAAGA
156009 GAA-GAAGAAGA
1 GAAGGAAGAAGA
156020 GAAGGAAGAAGA
1 GAAGGAAGAAGA
156032 GAA
1 GAA
156035 TGAAAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 6 0.26
11 3 0.13
12 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
GAAGGAAGAAGA
Found at i:157105 original size:16 final size:16
Alignment explanation
Indices: 157084--157114 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
157074 AAAAAAATTG
*
157084 AGAAAAAGGAAGAAAA
1 AGAAAAAGAAAGAAAA
157100 AGAAAAAGAAAGAAA
1 AGAAAAAGAAAGAAA
157115 TTTTTGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAGAAAA
Found at i:157903 original size:7 final size:7
Alignment explanation
Indices: 157891--157917 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
157881 GCTATAAATA
157891 GAAGAAT
1 GAAGAAT
157898 GAAGAAT
1 GAAGAAT
157905 GAAGAAT
1 GAAGAAT
157912 GAAGAA
1 GAAGAA
157918 ATCATCAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (7 bp):
GAAGAAT
Found at i:159937 original size:12 final size:13
Alignment explanation
Indices: 159906--159938 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
159896 TATTTTAACG
*
159906 AAATTATTAAAAT
1 AAATAATTAAAAT
159919 AAATAATTAAAAT
1 AAATAATTAAAAT
159932 -AATAATT
1 AAATAATT
159939 TTAGTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATAATTAAAAT
Found at i:164208 original size:26 final size:26
Alignment explanation
Indices: 164149--164217 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
164139 CTTCCAGAAA
** *
164149 TTTAGCTCAAACGAGCCCAGACAGAG
1 TTTAGCTCTTACGAGCCCAAACAGAG
164175 TTTAGCTCTTACGAGCCCAAACA-AG
1 TTTAGCTCTTACGAGCCCAAACAGAG
* *
164200 TTATCGCTCTTTCGAGCC
1 TT-TAGCTCTTACGAGCC
164218 AGACAGAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 4 0.11
26 33 0.89
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (26 bp):
TTTAGCTCTTACGAGCCCAAACAGAG
Found at i:164236 original size:25 final size:25
Alignment explanation
Indices: 164201--164320 Score: 105
Period size: 25 Copynumber: 4.8 Consensus size: 25
164191 CCAAACAAGT
*
164201 TATCGCTCTTTCGAGCCAGACAGAA
1 TATCGCTCTTTCGAGCCAGACAAAA
** *
164226 TATTTCTCTTTCGAGCCAAACAAAA
1 TATCGCTCTTTCGAGCCAGACAAAA
* * * * *
164251 TAACGCTCTTTTGAGCTAGATAGAA
1 TATCGCTCTTTCGAGCCAGACAAAA
* *
164276 TATCGCTATTTTGAGCCAGACAAAA
1 TATCGCTCTTTCGAGCCAGACAAAA
* * * *
164301 TAACACTCTTACGAACCAGA
1 TATCGCTCTTTCGAGCCAGA
164321 ATCCAGAGTA
Statistics
Matches: 72, Mismatches: 23, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 72 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (25 bp):
TATCGCTCTTTCGAGCCAGACAAAA
Found at i:164276 original size:50 final size:50
Alignment explanation
Indices: 164160--164320 Score: 142
Period size: 50 Copynumber: 3.2 Consensus size: 50
164150 TTAGCTCAAA
* * * * ** *
164160 CGAGCCCAGACAGAGTTTAGCTCTTACGAGCCCAAACAAGTTATCGCTCTTT
1 CGAG-CCAGACAGAATATCGCTCTTTCGAG-CCAAACAAAATAACGCTCTTT
**
164212 CGAGCCAGACAGAATATTTCTCTTTCGAGCCAAACAAAATAACGCTCTTT
1 CGAGCCAGACAGAATATCGCTCTTTCGAGCCAAACAAAATAACGCTCTTT
* * * * * * * *
164262 TGAGCTAGATAGAATATCGCTATTTTGAGCCAGACAAAATAACACTCTTA
1 CGAGCCAGACAGAATATCGCTCTTTCGAGCCAAACAAAATAACGCTCTTT
*
164312 CGAACCAGA
1 CGAGCCAGA
164321 ATCCAGAGTA
Statistics
Matches: 88, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
50 64 0.73
51 20 0.23
52 4 0.05
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (50 bp):
CGAGCCAGACAGAATATCGCTCTTTCGAGCCAAACAAAATAACGCTCTTT
Found at i:167518 original size:3 final size:3
Alignment explanation
Indices: 167510--167537 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
167500 GCATGAAAGT
167510 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
167538 TGAAGTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:167825 original size:77 final size:77
Alignment explanation
Indices: 167698--167853 Score: 276
Period size: 77 Copynumber: 2.0 Consensus size: 77
167688 ATTTGTTTTT
* *
167698 GCTCTACAATTTTCTATGTAAGAACTCCACATGGATGAAGCACAACAATTTCAAACTTCTAGCGA
1 GCTCTACAATTTTCTATGTAAGAACTCCACATGGACGAAGCACAACAATTTCAAACTTCTAGCAA
167763 TATAAGGAGAAG
66 TATAAGGAGAAG
* *
167775 GCTCTACAATTTTCTATGTAAGAACTCCAGATGGACGAAGCACAACAATTTCGAACTTCTAGCAA
1 GCTCTACAATTTTCTATGTAAGAACTCCACATGGACGAAGCACAACAATTTCAAACTTCTAGCAA
167840 TATAAGGAGAAG
66 TATAAGGAGAAG
167852 GC
1 GC
167854 ACCTACTAGT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (77 bp):
GCTCTACAATTTTCTATGTAAGAACTCCACATGGACGAAGCACAACAATTTCAAACTTCTAGCAA
TATAAGGAGAAG
Found at i:172792 original size:9 final size:9
Alignment explanation
Indices: 172778--172822 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
172768 CTTTCAGACC
172778 CCTCTTCGT
1 CCTCTTCGT
*
172787 CCTCTTTGT
1 CCTCTTCGT
172796 CCTCTTCGT
1 CCTCTTCGT
*
172805 TCTCTT-GT
1 CCTCTTCGT
172813 CCCTCTTCGT
1 -CCTCTTCGT
172823 TATCAATAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 2 0.07
9 26 0.87
10 2 0.07
ACGTcount: A:0.00, C:0.40, G:0.11, T:0.49
Consensus pattern (9 bp):
CCTCTTCGT
Found at i:172823 original size:18 final size:19
Alignment explanation
Indices: 172777--172823 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
172767 TCTTTCAGAC
*
172777 CCCTCTTCGTCCTCTTTGT
1 CCCTCTTCGTTCTCTTTGT
172796 -CCTCTTCGTTCTC-TTGT
1 CCCTCTTCGTTCTCTTTGT
172813 CCCTCTTCGTT
1 CCCTCTTCGTT
172824 ATCAATAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.00, C:0.40, G:0.11, T:0.49
Consensus pattern (19 bp):
CCCTCTTCGTTCTCTTTGT
Found at i:180011 original size:15 final size:17
Alignment explanation
Indices: 179991--180026 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
179981 GAATAAAGTG
179991 TTTTT-GAGACTT-TAA
1 TTTTTGGAGACTTGTAA
180006 TTTTTGGAGACTTGTAA
1 TTTTTGGAGACTTGTAA
180023 TTTT
1 TTTT
180027 GAATTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 7 0.37
17 7 0.37
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (17 bp):
TTTTTGGAGACTTGTAA
Found at i:203645 original size:18 final size:19
Alignment explanation
Indices: 203618--203653 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
203608 AATTTAACTT
203618 TTTTTAACATCAAAATTTA
1 TTTTTAACATCAAAATTTA
*
203637 TTTTT-ACATCACAATTT
1 TTTTTAACATCAAAATTT
203654 GGATTGGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTTAACATCAAAATTTA
Found at i:222683 original size:37 final size:37
Alignment explanation
Indices: 222642--222715 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
222632 TAATTTTTAA
*
222642 AGGATTAAATCAATTTTTTATCATTTTTAAAAAGGGT
1 AGGATTAAATCAAATTTTTATCATTTTTAAAAAGGGT
222679 AGGATTAAATCAAATTTTTATCATTTTTAAAAAGGGT
1 AGGATTAAATCAAATTTTTATCATTTTTAAAAAGGGT
222716 TAAAGTGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (37 bp):
AGGATTAAATCAAATTTTTATCATTTTTAAAAAGGGT
Found at i:223487 original size:24 final size:23
Alignment explanation
Indices: 223460--223546 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
223450 TCATTAACAT
223460 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* * *
223484 TGTTCATGAACATGGTCATTTAA
1 TGTTCGTGAACATGTTCAATTAA
* *
223507 TATTCGTGAACATATTCAATTAA
1 TGTTCGTGAACATGTTCAATTAA
**
223530 -GTTAAATGAACATGTTC
1 TGTT-CGTGAACATGTTC
223547 GTGAACATTA
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 2 0.04
23 29 0.58
24 19 0.38
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:223928 original size:2 final size:2
Alignment explanation
Indices: 223921--223951 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
223911 TATGATTTAA
223921 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
223952 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:223994 original size:21 final size:21
Alignment explanation
Indices: 223970--224010 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
223960 TTATTATTAG
223970 TTTTTAAAATTTTGATAATTT
1 TTTTTAAAATTTTGATAATTT
* *
223991 TTTTTATAATTTTTATAATT
1 TTTTTAAAATTTTGATAATT
224011 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTTAAAATTTTGATAATTT
Found at i:224021 original size:20 final size:20
Alignment explanation
Indices: 223996--224053 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
223986 AATTTTTTTT
223996 ATAATTTTTATAATTATTAA
1 ATAATTTTTATAATTATTAA
**
224016 ATAATTTTCTATAA-TATTGT
1 ATAATTTT-TATAATTATTAA
* *
224036 ATAAGTTCTATAATTATT
1 ATAATTTTTATAATTATT
224054 TAACAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.16
20 22 0.69
21 5 0.16
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
ATAATTTTTATAATTATTAA
Found at i:226500 original size:6 final size:6
Alignment explanation
Indices: 226489--226526 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
226479 ATCTGACTCG
* *
226489 CTTTCT CTTTCT CTTTCT CTTTCT CTTCCT TTTTCT CT
1 CTTTCT CTTTCT CTTTCT CTTTCT CTTTCT CTTTCT CT
226527 GGCTCTGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (6 bp):
CTTTCT
Found at i:228574 original size:14 final size:13
Alignment explanation
Indices: 228551--228585 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
228541 AGCAACAGCC
228551 AAAAAAAAAAAGAG
1 AAAAAAAAAAA-AG
228565 AAAGAAAAAAAAAG
1 AAA-AAAAAAAAAG
228579 AAAAAAA
1 AAAAAAA
228586 TTACATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 8 0.40
15 8 0.40
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:232191 original size:20 final size:20
Alignment explanation
Indices: 232166--232205 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
232156 AGTCTTCAAG
* *
232166 GTATCGGTATAAGTGGAGTT
1 GTATCGATAGAAGTGGAGTT
232186 GTATCGATAGAAGTGGAGTT
1 GTATCGATAGAAGTGGAGTT
232206 CTACCGGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.33
Consensus pattern (20 bp):
GTATCGATAGAAGTGGAGTT
Found at i:232369 original size:3 final size:3
Alignment explanation
Indices: 232361--232425 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
232351 TTTGTATTCA
*
232361 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
232409 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
232426 GAGTCTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:233679 original size:37 final size:37
Alignment explanation
Indices: 233638--233714 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
233628 GTTTTTATAA
* * *
233638 ATTAAAAAGATTAAAATA-TCTTCGAATAAAATAATTT
1 ATTAAAAAAATTAAAATACTC-TCAAATAAAATAACTT
*
233675 ATTAAAAAAATTAAAATACTCTCAAATAATATAACTT
1 ATTAAAAAAATTAAAATACTCTCAAATAAAATAACTT
233712 ATT
1 ATT
233715 TTAATTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 33 0.94
38 2 0.06
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.35
Consensus pattern (37 bp):
ATTAAAAAAATTAAAATACTCTCAAATAAAATAACTT
Done.