Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009783.1 Kokia drynarioides strain JFW-HI SEQ_124504, 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: 103762
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 445 characters in sequence are not A, C, G, or T
Found at i:102 original size:2 final size:2
Alignment explanation
Indices: 95--129 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
85 AAGGTTTAAT
95 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
130 TAAAGTTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4698 original size:65 final size:64
Alignment explanation
Indices: 4586--4711 Score: 146
Period size: 65 Copynumber: 2.0 Consensus size: 64
4576 TATCAAAATA
* * *
4586 ATATATAATTTAATTGACAAACTAAAAATTAGACTATAAATAAATATGTGTAAATTATTTAAATG
1 ATATATAATTTAATTAACAAACTAAAAATTAAACTATAAATAAATATGAG-AAA-TATTTAAATG
4651 T
64 T
* * *** *
4652 ATATATAATTT-ATTAAGAAACTAAAAATTAAACTTTTTGTATATATGAGAAATATTTAAA
1 ATATATAATTTAATTAACAAACTAAAAATTAAACTATAAATAAATATGAGAAATATTTAAA
4712 AATATCGATA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 8 0.16
64 3 0.06
65 29 0.57
66 11 0.22
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (64 bp):
ATATATAATTTAATTAACAAACTAAAAATTAAACTATAAATAAATATGAGAAATATTTAAATGT
Found at i:12662 original size:17 final size:15
Alignment explanation
Indices: 12637--12686 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
12627 TCAATTTTCA
12637 TTTGATTTGGATTAAT
1 TTTGATTTGGATT-AT
*
12653 TTTAGATTTGGAGTAT
1 TTT-GATTTGGATTAT
12669 TTTGAGTTTGGATT-T
1 TTTGA-TTTGGATTAT
12684 TTT
1 TTT
12687 TAGGTTGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 6 0.20
16 15 0.50
17 9 0.30
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.58
Consensus pattern (15 bp):
TTTGATTTGGATTAT
Found at i:14387 original size:31 final size:30
Alignment explanation
Indices: 14311--14388 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
14301 TTGAATCCAA
*
14311 TAAAAATTTCATGTACAAAATTATACAAAAT
1 TAAAAA-TTCATGTATAAAATTATACAAAAT
* *
14342 T-AAAATTCACGTATAAAATTATACATTAAT
1 TAAAAATTCATGTATAAAATTATACA-AAAT
14372 TAAAAATTCATGTATAA
1 TAAAAATTCATGTATAA
14389 TTTTAAGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 18 0.44
30 8 0.20
31 15 0.37
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (30 bp):
TAAAAATTCATGTATAAAATTATACAAAAT
Found at i:35173 original size:60 final size:60
Alignment explanation
Indices: 35075--35187 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
35065 AATAGTGGGA
*** *
35075 TGATCATTTTATAACTTTTCATAATTGTGTAACCAAAAAAG-AATTTCACTAATTGTTTAG
1 TGATCATTTTATAACTTTTCATAATTAACTAACAAAAAAAGAAATTT-ACTAATTGTTTAG
* *
35135 TGATCATTTTGTAACTTTTCATAGTTAACTAACAAAAAAAGAAATTTACTAAT
1 TGATCATTTTATAACTTTTCATAATTAACTAACAAAAAAAGAAATTTACTAAT
35188 AATTGGATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 41 0.89
61 5 0.11
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (60 bp):
TGATCATTTTATAACTTTTCATAATTAACTAACAAAAAAAGAAATTTACTAATTGTTTAG
Found at i:35773 original size:29 final size:29
Alignment explanation
Indices: 35739--35805 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
35729 AAAGTAAAGA
* * * *
35739 GACTAAATTTTTAGAAATAGATATGTAGG
1 GACTAAATTCTTAGAAATACAAATATAGG
*
35768 GACTAAATTCTTAGAAATACAAATATATG
1 GACTAAATTCTTAGAAATACAAATATAGG
35797 GACTAAATT
1 GACTAAATT
35806 AGTACTTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (29 bp):
GACTAAATTCTTAGAAATACAAATATAGG
Found at i:41060 original size:15 final size:17
Alignment explanation
Indices: 41040--41079 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
41030 AATTTTTTTA
41040 AAATTATAAAGAT-AT-
1 AAATTATAAAGATGATG
*
41055 AAATTATTAAGATGATG
1 AAATTATAAAGATGATG
41072 AAATTATA
1 AAATTATA
41080 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (17 bp):
AAATTATAAAGATGATG
Found at i:42779 original size:85 final size:86
Alignment explanation
Indices: 42568--42927 Score: 523
Period size: 85 Copynumber: 4.2 Consensus size: 86
42558 GGTTTTATTC
* * * *
42568 GTCTTTCTTAGGTATAGGTTGCTCTATCAAGGTTCCTTTTGTTATTGGTTGTATACTGTCCGGGT
1 GTCTTTCTTAAGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTGTCCGGGT
* *
42633 TTAGTCGTCCTATTGATGTTA
66 TTAATCGTCCTATTGATGTTT
*
42654 GTCTTTCTTAAGTGTAGGTTGCTCTATCAAGGTTCCTTTTGTTATTGGTTCTATACTGTCCGGG-
1 GTCTTTCTTAAGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTGTCCGGGT
42718 TTAATCGTCCTATTGATGTTT
66 TTAATCGTCCTATTGATGTTT
* * *
42739 GTCCTTCTTAAGTGTAGGTTGCTCTATCAAGGTTCTTTTTGCTATTGGTTCTATATTGTCCGGGT
1 GTCTTTCTTAAGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTGTCCGGGT
42804 TTAATCGTCCTATTGATGTTT
66 TTAATCGTCCTATTGATGTTT
* * *
42825 GTCTTTCTT-AGATGTAGGTTGCTCTATCAA-GTT-CTTTTAGCTATTGGTTCTATGCTATCTGG
1 GTCTTTCTTAAG-TGTAGGTTGCTCTATCAAGGTTCCTTTT-GCTATTGGTTCTATACTGTCCGG
*
42887 GTTTAATCGTCCTATTGATGTTC
64 GTTTAATCGTCCTATTGATGTTT
*
42910 GTATTTCTT-AGATGTAGG
1 GTCTTTCTTAAG-TGTAGG
42928 GTACTCCATC
Statistics
Matches: 254, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
84 4 0.02
85 142 0.56
86 108 0.43
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.47
Consensus pattern (86 bp):
GTCTTTCTTAAGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTGTCCGGGT
TTAATCGTCCTATTGATGTTT
Found at i:42895 original size:171 final size:171
Alignment explanation
Indices: 42572--42908 Score: 518
Period size: 171 Copynumber: 2.0 Consensus size: 171
42562 TTATTCGTCT
* * * *
42572 TTCTTAGGTATAGGTTGCTCTATCAAGGTTCCTTTTGTTATTGGTTGTATACTGTCCGGGTTTAG
1 TTCTTAAGTATAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTGTCCGGGTTTAA
*
42637 TCGTCCTATTGATGTTAGTCTTTCTTAAGTGTAGGTTGCTCTATCAAGGTTCCTTTTGTTATTGG
66 TCGTCCTATTGATGTTAGTCTTTCTTAAGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGG
*
42702 TTCTATACTGTCCGGGTTAATCGTCCTATTGATGTTTGTCC
131 TTCTATACTATCCGGGTTAATCGTCCTATTGATGTTTGTCC
* * *
42743 TTCTTAAGTGTAGGTTGCTCTATCAAGGTTCTTTTTGCTATTGGTTCTATATTGTCCGGGTTTAA
1 TTCTTAAGTATAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTGTCCGGGTTTAA
*
42808 TCGTCCTATTGATGTTTGTCTTTCTT-AGATGTAGGTTGCTCTATCAA-GTT-CTTTTAGCTATT
66 TCGTCCTATTGATGTTAGTCTTTCTTAAG-TGTAGGTTGCTCTATCAAGGTTCCTTTT-GCTATT
* *
42870 GGTTCTATGCTATCTGGGTTTAATCGTCCTATTGATGTT
129 GGTTCTATACTATCCGGG-TTAATCGTCCTATTGATGTT
42909 CGTATTTCTT
Statistics
Matches: 151, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
169 5 0.03
170 25 0.17
171 121 0.80
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (171 bp):
TTCTTAAGTATAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGGTTCTATACTGTCCGGGTTTAA
TCGTCCTATTGATGTTAGTCTTTCTTAAGTGTAGGTTGCTCTATCAAGGTTCCTTTTGCTATTGG
TTCTATACTATCCGGGTTAATCGTCCTATTGATGTTTGTCC
Found at i:56509 original size:17 final size:19
Alignment explanation
Indices: 56489--56525 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
56479 TTCATATAAC
56489 AAAAATA-AAAATAT-ATT
1 AAAAATATAAAATATGATT
56506 -AAAATATAAAATATGATT
1 AAAAATATAAAATATGATT
56524 AA
1 AA
56526 GCTCGCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.35
17 7 0.41
18 3 0.18
19 1 0.06
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAAATATAAAATATGATT
Found at i:60327 original size:42 final size:41
Alignment explanation
Indices: 60268--60347 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 41
60258 GTTATGGCCG
*
60268 CTCCTCTTTAACGGCTAGCTTTTCTATCAAATGGGTCCTTCT
1 CTCCTCCTTAACGGCTAGCTTTTCTATC-AATGGGTCCTTCT
60310 CTCCTCCTTAACGGCTAGCTTTTCTATCAATGGGTCCT
1 CTCCTCCTTAACGGCTAGCTTTTCTATCAATGGGTCCT
60348 ACTATACACA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 10 0.27
42 27 0.73
ACGTcount: A:0.16, C:0.30, G:0.15, T:0.39
Consensus pattern (41 bp):
CTCCTCCTTAACGGCTAGCTTTTCTATCAATGGGTCCTTCT
Found at i:61658 original size:5 final size:5
Alignment explanation
Indices: 61648--61673 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
61638 TTAGTGGTGC
61648 ATGAA ATGAA ATGAA ATGAA ATGAA A
1 ATGAA ATGAA ATGAA ATGAA ATGAA A
61674 GGGAAATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (5 bp):
ATGAA
Found at i:69118 original size:13 final size:13
Alignment explanation
Indices: 69100--69124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69090 TTTTAAACTC
69100 AAAAGTGGTTTTG
1 AAAAGTGGTTTTG
69113 AAAAGTGGTTTT
1 AAAAGTGGTTTT
69125 AAACCCAAAA
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:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (13 bp):
AAAAGTGGTTTTG
Found at i:69367 original size:21 final size:23
Alignment explanation
Indices: 69327--69368 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
69317 CTAATATTAA
69327 ATATTTACAAATATTTAAAATTT
1 ATATTTACAAATATTTAAAATTT
*
69350 ATATTT-CATATA-TTAAAAT
1 ATATTTACAAATATTTAAAAT
69369 ATTAATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTTACAAATATTTAAAATTT
Found at i:71529 original size:21 final size:21
Alignment explanation
Indices: 71505--71546 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
71495 ATCATCCAAT
71505 TTAAAAAATT-TAAATAGTTAA
1 TTAAAAAATTATAAATA-TTAA
*
71526 TTAAAAATTTATAAATATTAA
1 TTAAAAAATTATAAATATTAA
71547 GAAATAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAAAAAATTATAAATATTAA
Found at i:72286 original size:28 final size:28
Alignment explanation
Indices: 72248--72332 Score: 152
Period size: 28 Copynumber: 3.0 Consensus size: 28
72238 AGGCAACGTA
*
72248 TTTTTAAAGGCTGAAACTTCGGGAACTT
1 TTTTTAAAGGCTGAAACTTTGGGAACTT
72276 TTTTTAAAGGCTGAAACTTTGGGAACTT
1 TTTTTAAAGGCTGAAACTTTGGGAACTT
*
72304 CTTTTAAAGGCTGAAACTTTGGGAACTT
1 TTTTTAAAGGCTGAAACTTTGGGAACTT
72332 T
1 T
72333 GTCCCAAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (28 bp):
TTTTTAAAGGCTGAAACTTTGGGAACTT
Found at i:75322 original size:45 final size:47
Alignment explanation
Indices: 75273--75372 Score: 141
Period size: 47 Copynumber: 2.2 Consensus size: 47
75263 ATGTCTTGAT
* * * * *
75273 GTGGAAAATGACCATACC-AAACAAAGATAA-TGAGCATGTCCTAAG
1 GTGGAAAATGACCATACCAAAAAAAAAAAAAGAGAGCACGTCCTAAG
75318 GTGGAAAATGACCATACCAAAAAAAAAAAAAGAGAGCACGTCCTAAG
1 GTGGAAAATGACCATACCAAAAAAAAAAAAAGAGAGCACGTCCTAAG
75365 GTGGAAAA
1 GTGGAAAA
75373 CAACCATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 18 0.38
46 9 0.19
47 21 0.44
ACGTcount: A:0.49, C:0.16, G:0.21, T:0.14
Consensus pattern (47 bp):
GTGGAAAATGACCATACCAAAAAAAAAAAAAGAGAGCACGTCCTAAG
Found at i:80915 original size:61 final size:60
Alignment explanation
Indices: 80836--80953 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 60
80826 TTTATTCTCG
* *
80836 ATTCTAAACAATTCACTCAAAATCCGATTTAACCTTTTTGTTTAAATCAATAAATCAACTT
1 ATTCTAAACAATTAACTCAAAATCCGATTTAACC-CTTTGTTTAAATCAATAAATCAACTT
** ** *
80897 ATTCTAAATGATTAACTCAAAATTTGATTTAACCCTTTGTTTAAATCGATAAATCAA
1 ATTCTAAACAATTAACTCAAAATCCGATTTAACCCTTTGTTTAAATCAATAAATCAA
80954 TTAATTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 21 0.42
61 29 0.58
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (60 bp):
ATTCTAAACAATTAACTCAAAATCCGATTTAACCCTTTGTTTAAATCAATAAATCAACTT
Found at i:95190 original size:17 final size:17
Alignment explanation
Indices: 95164--95222 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
95154 TCGGGCCCCT
*
95164 TTTAATTTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
95181 TTTAGATTTAATCTAAA
1 TTTAAATTTATTTTAAA
95198 TTTAAATTTATTTTCAAAA
1 TTTAAATTTATTTT--AAA
95217 TTTAAA
1 TTTAAA
95223 AGATTATTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
17 24 0.73
19 9 0.27
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:97038 original size:29 final size:29
Alignment explanation
Indices: 97005--97316 Score: 200
Period size: 29 Copynumber: 10.6 Consensus size: 29
96995 AAACTGATCG
97005 AAAATTACA-TTTTACCCCCCAAACTTCCA
1 AAAATTACATTTTTA-CCCCCAAACTTCCA
* ** *
97034 AAAATTCCATTTTTGACATCCGAACTTCCA
1 AAAATTACATTTTT-ACCCCCAAACTTCCA
*** ***
97064 AAAATT-CTATTTTTACCCTTGAACTTTTG
1 AAAATTAC-ATTTTTACCCCCAAACTTCCA
* * * *
97093 AAAATTATATTTTTACCCCCCAATTTTCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* * * * *
97122 AAAATTCCATTTTGGACCCCGACACTTTCA
1 AAAATTACATTTT-TACCCCCAAACTTCCA
* * *
97152 AAAATTATATTTTTACTCCCGAACTTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* **** ***
97181 AAAATTCCATTTTTGACAATGAAACTTTTG
1 AAAATTACATTTTT-ACCCCCAAACTTCCA
*
97211 AAAATTACATTTTTACCCTCAAACTTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* * *
97240 AAAATTACATTTTTACCCTCGAACCTCCA
1 AAAATTACATTTTTACCCCCAAACTTCCA
* *
97269 AAAATT-CTATTTTTGACCCCAAAACTTTCA
1 AAAATTAC-ATTTTT-ACCCCCAAACTTCCA
97299 AAAATTACCA-TTTTACCC
1 AAAATTA-CATTTTTACCC
97317 TCGAATATCA
Statistics
Matches: 216, Mismatches: 57, Indels: 20
0.74 0.19 0.07
Matches are distributed among these distances:
28 1 0.00
29 123 0.57
30 89 0.41
31 2 0.01
32 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCCAAACTTCCA
Found at i:97097 original size:59 final size:57
Alignment explanation
Indices: 97034--97321 Score: 233
Period size: 59 Copynumber: 4.9 Consensus size: 57
97024 CAAACTTCCA
* * * *
97034 AAAATTCCATTTTTGACATCCGAACTTCCAAAAATTCTATTTTTACCCTTGAACTTTTG
1 AAAATTACATTTTT-AC-CCCGAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTTG
* * * * * **
97093 AAAATTATATTTTTACCCCCCAATTTTCAAAAATTCCATTTTGGACCC-CGACACTTTCA
1 AAAATTACATTTTTA-CCCCGAACTTCCAAAAATTCCATTTT-TACCCTCGA-ACTTTTG
* **
97152 AAAATTATATTTTTACTCCCGAACTTCCAAAAATTCCATTTTTGACAAT-GAAACTTTTG
1 AAAATTACATTTTTAC-CCCGAACTTCCAAAAATTCCATTTTT-ACCCTCG-AACTTTTG
* * * ***
97211 AAAATTACATTTTTACCCTCAAACTTCCAAAAATTACATTTTTACCCTCGAACCTCCA
1 AAAATTACATTTTTACCC-CGAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTTG
* *
97269 AAAATT-CTATTTTTGACCCCAAAACTTTCAAAAATTACCA-TTTTACCCTCGAA
1 AAAATTAC-ATTTTT-ACCCC-GAACTTCCAAAAATT-CCATTTTTACCCTCGAA
97322 TATCAAAAAA
Statistics
Matches: 186, Mismatches: 30, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
57 1 0.01
58 46 0.25
59 136 0.73
60 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.36
Consensus pattern (57 bp):
AAAATTACATTTTTACCCCGAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTTG
Found at i:97185 original size:88 final size:87
Alignment explanation
Indices: 97005--97341 Score: 292
Period size: 88 Copynumber: 3.8 Consensus size: 87
96995 AAACTGATCG
* *
97005 AAAATTACA-TTTT-ACCCCCCAAACTTCCAAAAATTCCATTTTTGACATCCGAACTTCCAAAAA
1 AAAATTACATTTTTGA-CCCCCAAACTTTCAAAAATTCCA-TTTTGAC-CCCGAACTTCCAAAAA
* * ***
97068 TTCTATTTTTACCCTTGAACTTTTG
63 TTATATTTTTACCCTCGAACTTCCA
* * * *
97093 AAAATTATATTTTT-ACCCCCCAATTTTCAAAAATTCCATTTTGGACCCCGACACTTTCAAAAAT
1 AAAATTACATTTTTGACCCCCAAACTTTCAAAAATTCCATTTT-GACCCCGA-ACTTCCAAAAAT
97157 TATATTTTTACTCC-CGAACTTCCA
64 TATATTTTTAC-CCTCGAACTTCCA
* **** ** * * *
97181 AAAATTCCATTTTTGACAATGAAACTTTTGAAAATTACATTTTTACCCTCAAACTTCCAAAAATT
1 AAAATTACATTTTTGACCCCCAAACTTTCAAAAATTCCATTTTGACCC-CGAACTTCCAAAAATT
* *
97246 ACATTTTTACCCTCGAACCTCCA
65 ATATTTTTACCCTCGAACTTCCA
* *
97269 AAAATT-CTATTTTTGACCCCAAAACTTTCAAAAATTACCATTTT-ACCCTCGAA-TATCAAAAA
1 AAAATTAC-ATTTTTGACCCCCAAACTTTCAAAAATT-CCATTTTGACCC-CGAACT-TCCAAAA
*
97331 ATTCTATTTTT
62 ATTATATTTTT
97342 GATCCTGATT
Statistics
Matches: 201, Mismatches: 38, Indels: 20
0.78 0.15 0.08
Matches are distributed among these distances:
87 12 0.06
88 155 0.77
89 34 0.17
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (87 bp):
AAAATTACATTTTTGACCCCCAAACTTTCAAAAATTCCATTTTGACCCCGAACTTCCAAAAATTA
TATTTTTACCCTCGAACTTCCA
Found at i:97331 original size:59 final size:59
Alignment explanation
Indices: 97005--97343 Score: 182
Period size: 59 Copynumber: 5.8 Consensus size: 59
96995 AAACTGATCG
* * * * * * *
97005 AAAATTACA-TTTTACCCCCCAAACTTCCAAAAATTCCATTTTTGA-CATCCGAACTTCCA
1 AAAATTACATTTTTA-CCCTCGAACATCAAAAAATTCTATTTTTGACCCT-CAAACTTCCA
* * *** * * * * *
97064 AAAATT-CTATTTTTACCCTTGAACTTTTGAAAATTATATTTTT-ACCCCCCAATTTTCA
1 AAAATTAC-ATTTTTACCCTCGAACATCAAAAAATTCTATTTTTGACCCTCAAACTTCCA
* * * * *
97122 AAAATTCCATTTTGGACCC-CGACACTTTC-AAAAATTATATTTTT-ACTCC-CGAACTTCCA
1 AAAATTACATTTT-TACCCTCGA-AC-ATCAAAAAATTCTATTTTTGAC-CCTCAAACTTCCA
* ** * ***
97181 AAAATTCCATTTTTGACAAT-GAAACTTTTGAAAATTAC-ATTTTT-ACCCTCAAACTTCCA
1 AAAATTACATTTTT-ACCCTCG-AACATCAAAAAATT-CTATTTTTGACCCTCAAACTTCCA
* * *
97240 AAAATTACATTTTTACCCTCGAACCTCCAAAAATTCTATTTTTGACCC-CAAAACTTTCA
1 AAAATTACATTTTTACCCTCGAACATCAAAAAATTCTATTTTTGACCCTC-AAACTTCCA
*
97299 AAAATTACCA-TTTTACCCTCGAATATCAAAAAATTCTATTTTTGA
1 AAAATTA-CATTTTTACCCTCGAACATCAAAAAATTCTATTTTTGA
97344 TCCTGATTTT
Statistics
Matches: 223, Mismatches: 38, Indels: 38
0.75 0.13 0.13
Matches are distributed among these distances:
57 1 0.00
58 46 0.21
59 164 0.74
60 12 0.05
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAATTACATTTTTACCCTCGAACATCAAAAAATTCTATTTTTGACCCTCAAACTTCCA
Found at i:97472 original size:28 final size:29
Alignment explanation
Indices: 97417--97477 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
97407 GAACTTTCCA
*
97417 AAAATTACCATTTTTCCCCCGATAATCC-
1 AAAATTACCATTTTGCCCCCGATAATCCG
*
97445 AAAATTACCATTTTGCCCTCGAGT-ATCCG
1 AAAATTACCATTTTGCCCCCGA-TAATCCG
97474 AAAA
1 AAAA
97478 GTCTCATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.30
Consensus pattern (29 bp):
AAAATTACCATTTTGCCCCCGATAATCCG
Done.