Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015277.1 Kokia drynarioides strain JFW-HI SEQ_130322, 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: 544247
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 933 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:435827 original size:19 final size:19
Alignment explanation
Indices: 435803--435867 Score: 78
Period size: 19 Copynumber: 3.3 Consensus size: 19
435793 AAATTACACA
435803 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
*
435822 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TT
435841 AAAATTCAAAATTTATATTTTT
1 AAAATTCAAAA--TA-ATTTTT
435863 AAAAT
1 AAAAT
435868 AATTTTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.10
19 24 0.62
21 1 0.03
22 6 0.15
23 4 0.10
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:437854 original size:31 final size:32
Alignment explanation
Indices: 437818--437878 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
437808 TTTTCAGCTA
* * *
437818 AATTTGACCCTCAACCT-TTTAAAAAGAGTAG
1 AATTTGACCATCAACATCTTGAAAAAGAGTAG
*
437849 AATTTGATCATCAACATCTTGAAAAAGAGT
1 AATTTGACCATCAACATCTTGAAAAAGAGT
437879 TGAAATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (32 bp):
AATTTGACCATCAACATCTTGAAAAAGAGTAG
Found at i:438958 original size:29 final size:27
Alignment explanation
Indices: 438909--438967 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
438899 GGACTAAATT
438909 TTTAAATAAAAAAGTACAGGGGCTTAATA
1 TTTAAATAAAAAAGTACAGGGG-TTAA-A
* **
438938 TTTAAATATAAAAGTTTAGGGGTTAAA
1 TTTAAATAAAAAAGTACAGGGGTTAAA
438965 TTT
1 TTT
438968 TCAATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 4 0.15
28 4 0.15
29 19 0.70
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (27 bp):
TTTAAATAAAAAAGTACAGGGGTTAAA
Found at i:443073 original size:16 final size:16
Alignment explanation
Indices: 443049--443098 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
443039 AAGTTTATCA
*
443049 TTATTAATTTAAAATT
1 TTATAAATTTAAAATT
**
443065 TTATAAATTATAAAAAA
1 TTATAAATT-TAAAATT
443082 TT-TAAA-TTAAAATT
1 TTATAAATTTAAAATT
443096 TTA
1 TTA
443099 CCATTTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 7 0.26
15 1 0.04
16 12 0.44
17 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATAAATTTAAAATT
Found at i:444191 original size:2 final size:2
Alignment explanation
Indices: 444184--444215 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
444174 CTATTTCAGG
444184 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
444216 TGCGTGTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:459171 original size:9 final size:9
Alignment explanation
Indices: 459159--459212 Score: 58
Period size: 10 Copynumber: 5.9 Consensus size: 9
459149 TTTTTTTACA
459159 AATTTTAAT
1 AATTTTAAT
*
459168 AATTTTTAAC
1 AA-TTTTAAT
459178 AATTTGTAAT
1 AATTT-TAAT
459188 AATTTTAA-
1 AATTTTAAT
459196 AATTTTTAAT
1 AA-TTTTAAT
459206 -ATTTTAA
1 AATTTTAA
459213 ATAAAATTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 8 0.21
9 15 0.38
10 16 0.41
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (9 bp):
AATTTTAAT
Found at i:459174 original size:10 final size:10
Alignment explanation
Indices: 459161--459216 Score: 64
Period size: 9 Copynumber: 5.9 Consensus size: 10
459151 TTTTTACAAA
459161 TTTTAATAAT
1 TTTTAATAAT
*
459171 TTTTAACAAT
1 TTTTAATAAT
*
459181 TTGTAATAA-
1 TTTTAATAAT
459190 TTTTAA-AAT
1 TTTTAATAAT
459199 TTTTAAT-AT
1 TTTTAATAAT
*
459208 TTTAAATAA
1 TTTTAATAA
459217 AATTTGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 2 0.05
9 19 0.50
10 17 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:459179 original size:20 final size:20
Alignment explanation
Indices: 459150--459210 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 20
459140 AATAATATTT
*
459150 TTTTTTACAAATTTTAATAA
1 TTTTTAACAAATTTTAATAA
459170 TTTTTAAC-AATTTGTAATAA
1 TTTTTAACAAATTT-TAATAA
*
459190 -TTTTAA-AATTTTTAAT-A
1 TTTTTAACAAATTTTAATAA
459207 TTTT
1 TTTT
459211 AAATAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 15 0.42
20 13 0.36
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTTAACAAATTTTAATAA
Found at i:459220 original size:29 final size:26
Alignment explanation
Indices: 459158--459238 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 26
459148 TTTTTTTTAC
459158 AAATTTTAATAATTTTTAACAATTTGTAAT
1 AAATTTTAA-AATTTTT-A-AATTT-TAAT
459188 -AATTTTAAAATTTTTAATATTTTAAAT
1 AAATTTTAAAATTTTTAA-ATTTT-AAT
* *
459215 AAAATTTGAAATTTTCTAAATTTT
1 AAATTTTAAAATTTT-TAAATTTT
459239 TTTTATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
26 2 0.04
27 8 0.18
28 24 0.53
29 11 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
AAATTTTAAAATTTTTAAATTTTAAT
Found at i:459234 original size:21 final size:21
Alignment explanation
Indices: 459193--459235 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
459183 GTAATAATTT
**
459193 TAAAATTTTTAATATTTTAAA
1 TAAAATTTGAAATATTTTAAA
459214 TAAAATTTGAAAT-TTTCTAAA
1 TAAAATTTGAAATATTT-TAAA
459235 T
1 T
459236 TTTTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAAATTTGAAATATTTTAAA
Found at i:464672 original size:21 final size:21
Alignment explanation
Indices: 464648--464697 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
464638 TCCTTAATCG
464648 TAAACCC-AAAATATAAAACCT
1 TAAACCCTAAAAT-TAAAACCT
* *
464669 TAAACCCTAAACTTAAAACCC
1 TAAACCCTAAAATTAAAACCT
*
464690 CAAACCCT
1 TAAACCCT
464698 TGAATCTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (21 bp):
TAAACCCTAAAATTAAAACCT
Found at i:464940 original size:16 final size:17
Alignment explanation
Indices: 464919--464952 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
464909 TTTGTTTATA
464919 ATTTAAA-AAATTAATT
1 ATTTAAATAAATTAATT
*
464935 ATTTAAATAATTTAATT
1 ATTTAAATAAATTAATT
464952 A
1 A
464953 AAATTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTAAATAAATTAATT
Found at i:466352 original size:2 final size:2
Alignment explanation
Indices: 466345--466387 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
466335 ATTAAATTTA
*
466345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
466387 A
1 A
466388 CATACACAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:466392 original size:10 final size:10
Alignment explanation
Indices: 466345--466393 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
466335 ATTAAATTTA
*
466345 ATATATATAT
1 ATATATACAT
*
466355 ATATATATAT
1 ATATATACAT
*
466365 ATATATATAT
1 ATATATACAT
466375 ATATATACAT
1 ATATATACAT
*
466385 ATACATACA
1 ATATATACA
466394 CAGAGAGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATACAT
Found at i:466400 original size:2 final size:2
Alignment explanation
Indices: 466395--466424 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
466385 ATACATACAC
*
466395 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
466425 GGTGGTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:472976 original size:96 final size:96
Alignment explanation
Indices: 472812--473003 Score: 357
Period size: 96 Copynumber: 2.0 Consensus size: 96
472802 TTCAATTTTA
* *
472812 CTTTATTTTTAATGTTTATTTTAAATTGTGTCATATTAAATTTTGTATTATTTAATAGTTACATA
1 CTTTATTTTCAATGTTTATTTTAAATTGTGTCATATTAAATTTTGTATTATTTAATAGTTAAATA
*
472877 ATATTTTTAATAAAGAAAAGATTTGATTGAT
66 ATATTTTTAATAAAAAAAAGATTTGATTGAT
472908 CTTTATTTTCAATGTTTATTTTAAATTGTGTCATATTAAATTTTGTATTATTTAATAGTTAAATA
1 CTTTATTTTCAATGTTTATTTTAAATTGTGTCATATTAAATTTTGTATTATTTAATAGTTAAATA
472973 ATATTTTTAATAAAAAAAAGATTTGATTGAT
66 ATATTTTTAATAAAAAAAAGATTTGATTGAT
473004 ATATCAACGA
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (96 bp):
CTTTATTTTCAATGTTTATTTTAAATTGTGTCATATTAAATTTTGTATTATTTAATAGTTAAATA
ATATTTTTAATAAAAAAAAGATTTGATTGAT
Found at i:483269 original size:32 final size:32
Alignment explanation
Indices: 483230--483295 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
483220 ACTACTGCAT
*
483230 TTTATTTTTGTTTTATTTTGTAGCTTGGGGTC
1 TTTATTTTTGTTTTACTTTGTAGCTTGGGGTC
483262 TTTATTTTTGTTTTACTTTGTAGCTTGGGGTC
1 TTTATTTTTGTTTTACTTTGTAGCTTGGGGTC
483294 TT
1 TT
483296 ACTTGACAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.09, C:0.08, G:0.21, T:0.62
Consensus pattern (32 bp):
TTTATTTTTGTTTTACTTTGTAGCTTGGGGTC
Found at i:494531 original size:22 final size:23
Alignment explanation
Indices: 494506--494564 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
494496 GAATCTGGAT
494506 ATAAAAA-AAGTAACAAAATTA-A
1 ATAAAAACAAGTAACAAAA-TAGA
*
494528 ATAAAAACAA-AAACAAAATAGA
1 ATAAAAACAAGTAACAAAATAGA
*
494550 ATTAAAAATAAGTAA
1 A-TAAAAACAAGTAA
494565 AATGAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 2 0.07
22 16 0.53
23 10 0.33
24 2 0.07
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (23 bp):
ATAAAAACAAGTAACAAAATAGA
Found at i:495389 original size:23 final size:21
Alignment explanation
Indices: 495321--495389 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
495311 ACCTACATAG
* *
495321 AAATTAATCAATTAAATGTAA
1 AAATTAATAAAATAAATGTAA
** *
495342 AAATTAATAAAATTTATGTCCA
1 AAATTAATAAAATAAATGT-AA
495364 AAATTAATTAAAATAAATGATAA
1 AAATTAA-TAAAATAAATG-TAA
495387 AAA
1 AAA
495390 ATACGACAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 15 0.41
22 8 0.22
23 13 0.35
24 1 0.03
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (21 bp):
AAATTAATAAAATAAATGTAA
Found at i:496085 original size:23 final size:23
Alignment explanation
Indices: 496023--496074 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
496013 TATAAGTTAA
496023 ATTTATAACTCTTAAATTTTTTC
1 ATTTATAACTCTTAAATTTTTTC
496046 ATTTATAACTCTTAAATTTTTTC
1 ATTTATAACTCTTAAATTTTTTC
496069 ATTTAT
1 ATTTAT
496075 TTTACCTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTATAACTCTTAAATTTTTTC
Found at i:496701 original size:31 final size:31
Alignment explanation
Indices: 496666--496726 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
496656 AAGAGTTAAA
* *
496666 TTTCAATATGAAAATATTTATCAAATTCAAG
1 TTTCAACATGAAAATATTGATCAAATTCAAG
* *
496697 TTTCAACGTGAAAATATTGGTCAAATTCAA
1 TTTCAACATGAAAATATTGATCAAATTCAA
496727 AATCTAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (31 bp):
TTTCAACATGAAAATATTGATCAAATTCAAG
Found at i:501529 original size:43 final size:43
Alignment explanation
Indices: 501468--501553 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
501458 CTTAGAGGCC
* *
501468 TTAGTCTGTTGTAGTCTTCCTGGCCTGAAAGAAATTATACTAT
1 TTAGTCTATTGTAGTCTTCCTGACCTGAAAGAAATTATACTAT
501511 TTAGTCTATTGTAGTCTTCCTGACCTGAAAGAAATTATACTAT
1 TTAGTCTATTGTAGTCTTCCTGACCTGAAAGAAATTATACTAT
501554 CAACACTAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (43 bp):
TTAGTCTATTGTAGTCTTCCTGACCTGAAAGAAATTATACTAT
Found at i:512133 original size:18 final size:19
Alignment explanation
Indices: 512096--512134 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
512086 ATTACAAAAT
*
512096 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
512115 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
512133 AA
1 AA
512135 AAATTCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:512437 original size:21 final size:20
Alignment explanation
Indices: 512413--512452 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
512403 AACTCGAATA
*
512413 ATTTTACTCGATTCTAATTTC
1 ATTTCACTCGATT-TAATTTC
*
512434 ATTTCACTCTATTTAATTT
1 ATTTCACTCGATTTAATTT
512453 TAAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTCACTCGATTTAATTTC
Found at i:514427 original size:122 final size:122
Alignment explanation
Indices: 514210--514454 Score: 481
Period size: 122 Copynumber: 2.0 Consensus size: 122
514200 TTTGTTGTTG
514210 TAGATTTTGGATGAATTTATTCTTACAAAATGGTTTTATTATACTATTACTGCAAGTATGCTTAG
1 TAGATTTTGGATGAATTTATTCTTACAAAATGGTTTTATTATACTATTACTGCAAGTATGCTTAG
*
514275 GTAACAAAGCTGATGGTATTGTTGCCTTATCACTTATCACCCTAATATTGTAGGATC
66 GTAACAAAGCTGATGGTATTGTTGCCTTATCACTTATCACCCTAATACTGTAGGATC
514332 TAGATTTTGGATGAATTTATTCTTACAAAATGGTTTTATTATACTATTACTGCAAGTATGCTTAG
1 TAGATTTTGGATGAATTTATTCTTACAAAATGGTTTTATTATACTATTACTGCAAGTATGCTTAG
514397 GTAACAAAGCTGATGGTATTGTTGCCTTATCACTTATCACCCTAATACTGTAGGATC
66 GTAACAAAGCTGATGGTATTGTTGCCTTATCACTTATCACCCTAATACTGTAGGATC
514454 T
1 T
514455 GATAGAGAAC
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (122 bp):
TAGATTTTGGATGAATTTATTCTTACAAAATGGTTTTATTATACTATTACTGCAAGTATGCTTAG
GTAACAAAGCTGATGGTATTGTTGCCTTATCACTTATCACCCTAATACTGTAGGATC
Found at i:522226 original size:135 final size:135
Alignment explanation
Indices: 521984--522252 Score: 493
Period size: 135 Copynumber: 2.0 Consensus size: 135
521974 CTCTTTAAAA
521984 TGATAATTTTAAGCTGTTGCCTTGTTGAATGCATCTTAAAAATCCAACCATGCAGCAAAAGAAAA
1 TGATAATTTTAAGCTGTTGCCTTGTTGAATGCATCTTAAAAATCCAACCATGCAGCAAAAGAAAA
*
522049 TCAAGAAGACCCAAGTTTGGAAGCTAAAAATTTGATATTTCATAATTGCAATGAATATTTCCAAG
66 TCAAGAAGACCCAAGTCTGGAAGCTAAAAATTTGATATTTCATAATTGCAATGAATATTTCCAAG
522114 AAATT
131 AAATT
* *
522119 TGATAATTTTAAGCTGTTGCCTTGTTGAATGCATCTTAAAAATCCAACCATGGAGTAAAAGAAAA
1 TGATAATTTTAAGCTGTTGCCTTGTTGAATGCATCTTAAAAATCCAACCATGCAGCAAAAGAAAA
**
522184 TCAAGAAGATGCAAGTCTGGAAGCTAAAAATTTGATATTTCATAATTGCAATGAATATTTCCAAG
66 TCAAGAAGACCCAAGTCTGGAAGCTAAAAATTTGATATTTCATAATTGCAATGAATATTTCCAAG
522249 AAAT
131 AAAT
522253 AACAATAATA
Statistics
Matches: 129, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 129 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (135 bp):
TGATAATTTTAAGCTGTTGCCTTGTTGAATGCATCTTAAAAATCCAACCATGCAGCAAAAGAAAA
TCAAGAAGACCCAAGTCTGGAAGCTAAAAATTTGATATTTCATAATTGCAATGAATATTTCCAAG
AAATT
Found at i:529787 original size:16 final size:15
Alignment explanation
Indices: 529766--529801 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
529756 TTTCTGTTTC
529766 TTTTTTTAATTTTTAA
1 TTTTTTTAATTTTT-A
529782 TTTTTTTAATTTTTA
1 TTTTTTTAATTTTTA
529797 TTTTT
1 TTTTT
529802 GAATTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTAATTTTTA
Found at i:533131 original size:22 final size:20
Alignment explanation
Indices: 533084--533131 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
533074 ATTAATTTTA
* *
533084 AATTTTAAAATTTTTTAATT
1 AATTTTAAAATTTATCAATT
533104 ATATTTTCAAAATTATATCAATT
1 A-ATTTT-AAAATT-TATCAATT
533127 AATTT
1 AATTT
533132 CTATTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 5 0.22
22 10 0.43
23 7 0.30
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTTTAAAATTTATCAATT
Found at i:533262 original size:12 final size:12
Alignment explanation
Indices: 533240--533275 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
533230 GTATAATTTT
533240 TAAAAATTAAAA
1 TAAAAATTAAAA
533252 CTAAAAA-TAAAA
1 -TAAAAATTAAAA
533264 TAAAAATTAAAA
1 TAAAAATTAAAA
533276 AAGAGAGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 10 0.45
13 6 0.27
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (12 bp):
TAAAAATTAAAA
Found at i:533269 original size:18 final size:18
Alignment explanation
Indices: 533242--533276 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
533232 ATAATTTTTA
*
533242 AAAATTAAAACTAAAAAT
1 AAAATAAAAACTAAAAAT
*
533260 AAAATAAAAATTAAAAA
1 AAAATAAAAACTAAAAA
533277 AGAGAGGGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAAAAACTAAAAAT
Found at i:537715 original size:23 final size:23
Alignment explanation
Indices: 537689--537779 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
537679 GTTCTCAGTT
537689 ATTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
* * * *
537712 ATTAGCACTTTGTGTGCTATTTA
1 ATTAGCACTGTGTGTGCTCTCTG
* * *
537735 ATTAGTACTTTGTGTACTCTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
* * *
537758 TTTAGTACTGTATGTGCTCTCT
1 ATTAGCACTGTGTGTGCTCTCT
537780 ATTGCCCAGC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.46
Consensus pattern (23 bp):
ATTAGCACTGTGTGTGCTCTCTG
Found at i:537814 original size:21 final size:20
Alignment explanation
Indices: 537736--537828 Score: 60
Period size: 25 Copynumber: 4.1 Consensus size: 20
537726 TGCTATTTAA
537736 TTAGTACTTTGTGTACTCTCTG
1 TTAGTACTTTGTG--CTCTCTG
*
537758 TTTAGTACTGTATGTGCTCTCTA
1 -TTAGTACT-T-TGTGCTCTCTG
*
537781 TTGCCCAGCACTTATGTGCTCTCTG
1 TT----AGTACTT-TGTGCTCTCTG
*
537806 TTAGTACTTTGGTACTCTCTG
1 TTAGTACTTT-GTGCTCTCTG
537827 TT
1 TT
537829 TGTTCCGTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
20 1 0.02
21 17 0.29
22 2 0.03
23 14 0.24
24 1 0.02
25 18 0.31
26 5 0.09
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (20 bp):
TTAGTACTTTGTGCTCTCTG
Found at i:538485 original size:4 final size:4
Alignment explanation
Indices: 538476--538500 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
538466 GTTTTTCAAA
538476 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
538501 GAAGTTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:539854 original size:36 final size:35
Alignment explanation
Indices: 539787--539855 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
539777 AAAATAATAG
* *
539787 CAAAATTAACAATAAAATAAGTATTATATAATATC
1 CAAAATTAACAATAAAATAAGTATAACATAATATC
*
539822 CAAATATTAATAATAAAATAA-TAGTAACATAATA
1 CAAA-ATTAACAATAAAATAAGTA-TAACATAATA
539856 GTGAAATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 6 0.21
36 23 0.79
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.30
Consensus pattern (35 bp):
CAAAATTAACAATAAAATAAGTATAACATAATATC
Found at i:541559 original size:2 final size:2
Alignment explanation
Indices: 541552--541579 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
541542 ATATGAAGAC
541552 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
541580 GAGATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:542515 original size:2 final size:2
Alignment explanation
Indices: 542508--542533 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
542498 CCAAATACTA
542508 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
542534 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.