Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168091.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_338, 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: 33812
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
File 2 of 2
Found at i:28392 original size:15 final size:15
Alignment explanation
Indices: 28369--28423 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
28359 ACATGTATAT
*
28369 TATATTATATTTAAA
1 TATAATATATTTAAA
*
28384 TATAATATATTTTAAT
1 TATAATATA-TTTAAA
*
28400 TATAAT-TAAATTAAA
1 TATAATAT-ATTTAAA
28415 -ATAATATAT
1 TATAATATAT
28424 ATTATTACTA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.19
15 14 0.44
16 12 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATAATATATTTAAA
Found at i:28403 original size:16 final size:15
Alignment explanation
Indices: 28367--28405 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
28357 TGACATGTAT
*
28367 ATTATATTATATTTA
1 ATTATAATATATTTA
*
28382 AATATAATATATTTTA
1 ATTATAATATA-TTTA
28398 ATTATAAT
1 ATTATAAT
28406 TAAATTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTATAATATATTTA
Found at i:28424 original size:32 final size:31
Alignment explanation
Indices: 28367--28426 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
28357 TGACATGTAT
* *
28367 ATTATATTATATTTAAATATAATATATTTTA
1 ATTATATTAAATTAAAATATAATATATTTTA
28398 ATTATAATTAAATTAAAATA-ATATATATT
1 ATTAT-ATTAAATTAAAATATA-ATATATT
28427 ATTACTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
ATTATATTAAATTAAAATATAATATATTTTA
Found at i:28436 original size:32 final size:31
Alignment explanation
Indices: 28379--28438 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
28369 TATATTATAT
*
28379 TTAAATATAATATATTTTAATTATAATTAAA
1 TTAAATATAATATATTTTAACTATAATTAAA
*
28410 TTAAA-ATAATATATATTATTACTATAATT
1 TTAAATATAATATAT-TT-TAACTATAATT
28439 GTTTTAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 7 0.28
32 9 0.36
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
TTAAATATAATATATTTTAACTATAATTAAA
Found at i:28559 original size:6 final size:6
Alignment explanation
Indices: 28543--28586 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
28533 TATTAGTTTT
* *
28543 ATTATTA ATTATA ATTATA ATTATA ATTATA TTTATA TTTATA A
1 ATTA-TA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA A
28587 ACTATTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 31 0.89
7 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
ATTATA
Found at i:29497 original size:177 final size:179
Alignment explanation
Indices: 29223--30021 Score: 686
Period size: 177 Copynumber: 4.5 Consensus size: 179
29213 AATCATAATG
* * * * *
29223 ATTTGAAATAAATAATTGCTT-AAATAGTC-T--TAATTTGAACCAATTTGATAAACAGATTTAT
1 ATTTGAAATAGATAATT-ATTCAAATAGTCATAATTATTTGAACTAGTTTGATAAACAGATTTAT
* * *
29284 TTTTTAAA-AT-TT--TTATTAATTTTTGAAATATTAATAAATTAGTATTATTTTATTTCGAACA
65 TTCTTAAATCTCTTACTTATTAATTTTTGAAATATTAATAAATTA-TATTATTTTATTTCGAATA
* *
29345 AACTTATATGAACAAAAACATTAGTTTTATGACAAAACAATAGGTCATAACA
129 AACTTATATGAACAAAAACATT-GTTTTATGACAAAACAAAAGGTTATAACA
* * * *
29397 ATTTGAAATAGATAATTGTTCAAATAGTCATAATTATTTGAACTAGTTAGGTAAACAGAATTATT
1 ATTTGAAATAGATAATTATTCAAATAGTCATAATTATTTGAACTAGTTTGATAAACAGATTTATT
* * *
29462 TCTT-AAT-TC-T-CTTATTAATTTTTGAAATTTTAATAAATTTATTTTATTTTA-TTCTAAATA
66 TCTTAAATCTCTTACTTATTAATTTTTGAAATATTAATAAA-TTATATTATTTTATTTC-GAATA
* ** * **
29522 AGC-TAGTATGAATTGAAAATATTGTTTTATGACAAAACAAAAGGTTATAATG
129 AACTTA-TATGAA-CAAAAACATTGTTTTATGACAAAACAAAAGGTTATAACA
* ** * * *
29574 ATTTGAAATAGATAATTATTCATATAGTTTTAACTATTTGAACTAGTTCGACAAACA-ATTTTAT
1 ATTTGAAATAGATAATTATTCAAATAGTCATAATTATTTGAACTAGTTTGATAAACAGA-TTTAT
* * * * * *
29638 TTTTTAAATCTCTTAATTATTAATTTTT-AGAATATTATTAGATTACTTTTATTTTATTTCAAAT
65 TTCTTAAATCTCTTACTTATTAATTTTTGA-AATATTAATAAATTA-TATTATTTTATTTCGAAT
* * * *
29702 AAGCTTGTATGAACAGAAATA-ATTATTTTATGATAAAACAAAAGGTTATAACA
128 AAACTTATATGAACA-AAA-ACATTGTTTTATGACAAAACAAAAGGTTATAACA
* * * * * * * *
29755 ATTT-AAAGTATACAACTACTCTAATAGTCATAACTATTTGAAATTGGTTTTG-TAAACAGATTT
1 ATTTGAAA-TAGATAATTATTCAAATAGTCATAATTATTTG-AACTAG-TTTGATAAACAGATTT
* *
29818 ATTTCTTAAATCTCTTACTTATTAATTTTTGAAAGATTAATAAATTAATATTATTTTATTCCGAA
63 ATTTCTTAAATCTCTTACTTATTAATTTTTGAAATATTAATAAATT-ATATTATTTTATTTCGAA
* * * * ** * * *
29883 TAAGCTTGTATGATCCAAAACAATTGTCATATGACCAAACAAAAGGTAAGAACA
127 TAAACTTATATGAACAAAAAC-ATTGTTTTATGACAAAACAAAAGGTTATAACA
* * * * ** *
29937 ATTTGAAATAGATAATTATTGAAATGGCCATAATTATTTGAACT-GATTTGGTAAACTTATTCAC
1 ATTTGAAATAGATAATTATTCAAATAGTCATAATTATTTGAACTAG-TTTGATAAACAGATTTA-
*
30001 TTT-TTAAATCACTTACTTATT
64 TTTCTTAAATCTCTTACTTATT
30022 TGAATTTGTT
Statistics
Matches: 506, Mismatches: 86, Indels: 59
0.78 0.13 0.09
Matches are distributed among these distances:
173 2 0.00
174 24 0.05
175 1 0.00
176 10 0.02
177 156 0.31
178 13 0.03
179 2 0.00
180 14 0.03
181 136 0.27
182 139 0.27
183 9 0.02
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (179 bp):
ATTTGAAATAGATAATTATTCAAATAGTCATAATTATTTGAACTAGTTTGATAAACAGATTTATT
TCTTAAATCTCTTACTTATTAATTTTTGAAATATTAATAAATTATATTATTTTATTTCGAATAAA
CTTATATGAACAAAAACATTGTTTTATGACAAAACAAAAGGTTATAACA
Found at i:30007 original size:363 final size:357
Alignment explanation
Indices: 28902--30021 Score: 819
Period size: 363 Copynumber: 3.1 Consensus size: 357
28892 ATTTAACATG
* * * * * *
28902 ACTATTTGAACTTGTTCGATAAGCATATTTATTTTTTAAATCTCTTAATTATTAA-TTTTAAAAT
1 ACTATTTGAACTAGTTCGACAAACAT-TTTACTTTTTAAATCACTTAATTATTAATTTTTGAAAT
* * * * * * *
28966 ATTAATAACTTAATATTATTTTATTTCAAATAAGCTTATATGAATTGAAATA-ATT-TTTTTATG
65 ATTAATAAATTACTATTATTTTATTTCAAACAAACTTATATGAA--CAAAAACATTAGTTTTATG
* * * * * * * * * **
29029 ACAGAAGAAAAGATCATAACGATTTGAAATAGATAACTATTCAAATAGTCATGATTGTTTGATTT
128 ACAAAACAAAAGGTCATAACAATTTGAAATAGACAACTACTCAAATAGTCATAACTATTTGAACT
* * * * * * ** * * *
29094 AGTTCA-GTGAACATATTTAATT-TT--TTAT-TTATTAATTGTCAAAACATTAATAAATTTACA
193 AGTT-AGGTAAACAGAATTATTTCTTAATTCTCTTATTAATTTTTGAAAGATTAATAAATTAATA
* ** * * * ** ** * * * * * ** * *
29154 TTATTTTAATCTGAATAAGCTTGAATAAATAGAAACTATTATCTTATAATAGAACAAAAAATCAT
257 TTATTTTATTCCAAATAAGCTAGTATGAATCCAAAAAATTGTCATATGACAAAACAAAAGGTAAG
** * * * *
29219 AATGATTTGAAATAAATAATTGCTT-AAATAGTC-TT
322 AACAATTTGAAATAGATAATT-ATTCAAATAGCCATA
* * * * * * *
29254 A--ATTTGAACCAATTTGATAAACAGATTTATTTTTTAAA--A-TT-TTTATTAATTTTTGAAAT
1 ACTATTTGAACTAGTTCGACAAACA-TTTTACTTTTTAAATCACTTAATTATTAATTTTTGAAAT
* *
29313 ATTAATAAATTAGTATTATTTTATTTCGAACAAACTTATATGAACAAAAACATTAGTTTTATGAC
65 ATTAATAAATTACTATTATTTTATTTCAAACAAACTTATATGAACAAAAACATTAGTTTTATGAC
* * * ** *
29378 AAAACAATAGGTCATAACAATTTGAAATAGATAATTGTTCAAATAGTCATAATTATTTGAACTAG
130 AAAACAAAAGGTCATAACAATTTGAAATAGACAACTACTCAAATAGTCATAACTATTTGAACTAG
** * *
29443 TTAGGTAAACAGAATTATTTCTTAATTCTCTTATTAATTTTTGAAATTTTAATAAATTTATTTTA
195 TTAGGTAAACAGAATTATTTCTTAATTCTCTTATTAATTTTTGAAAGATTAATAAATTAATATTA
* ** * ** * * *
29508 TTTTATTCTAAATAAGCTAGTATGAATTGAAAATATTGTTTTATGACAAAACAAAAGGTTATAAT
260 TTTTATTCCAAATAAGCTAGTATGAATCCAAAAAATTGTCATATGACAAAACAAAAGGTAAGAAC
* * ***
29573 GATTTGAAATAGATAATTATTCATATAGTTTTA
325 AATTTGAAATAGATAATTATTCAAATAGCCATA
* *
29606 ACTATTTGAACTAGTTCGACAAACAATTTTATTTTTTAAATCTCTTAATTATTAATTTTT-AGAA
1 ACTATTTGAACTAGTTCGACAAAC-ATTTTACTTTTTAAATCACTTAATTATTAATTTTTGA-AA
* * * * * *
29670 TATTATTAGATTACTTTTATTTTATTTCAAATAAGCTTGTATGAACAGAAATA-ATTA-TTTTAT
64 TATTAATAAATTACTATTATTTTATTTCAAACAAACTTATATGAACA-AAA-ACATTAGTTTTAT
* * * *
29733 GATAAAACAAAAGGTTATAACAATTT-AAAGTATACAACTACTCTAATAGTCATAACTATTTGAA
127 GACAAAACAAAAGGTCATAACAATTTGAAA-TAGACAACTACTCAAATAGTCATAACTATTTG-A
* * ** *
29797 ATTGGTTTTGTAAACAGATTTATTTCTTAAATCTCTTACTTATTAATTTTTGAAAGATTAATAAA
190 ACTAGTTAGGTAAACAGAATTATTTCTT-AAT-TC-T-CTTATTAATTTTTGAAAGATTAATAAA
* * *
29862 TTAATATTATTTTATTCCGAATAAGCTTGTATG-ATCCAAAACAATTGTCATATGACCAAACAAA
251 TTAATATTATTTTATTCCAAATAAGCTAGTATGAATCCAAAA-AATTGTCATATGACAAAACAAA
* *
29926 AGGTAAGAACAATTTGAAATAGATAATTATTGAAATGGCCATA
315 AGGTAAGAACAATTTGAAATAGATAATTATTCAAATAGCCATA
* * ** *
29969 ATTATTTGAACT-GATTTGGTAAAC-TTATTCACTTTTTAAATCACTTACTTATT
1 ACTATTTGAACTAG-TTCGACAAACATT-TT-ACTTTTTAAATCACTTAATTATT
30022 TGAATTTGTT
Statistics
Matches: 617, Mismatches: 120, Indels: 51
0.78 0.15 0.06
Matches are distributed among these distances:
345 4 0.01
346 11 0.02
347 126 0.20
348 2 0.00
350 35 0.06
351 101 0.16
352 3 0.00
354 30 0.05
355 1 0.00
357 6 0.01
358 107 0.17
359 31 0.05
360 4 0.01
361 4 0.01
362 10 0.02
363 142 0.23
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (357 bp):
ACTATTTGAACTAGTTCGACAAACATTTTACTTTTTAAATCACTTAATTATTAATTTTTGAAATA
TTAATAAATTACTATTATTTTATTTCAAACAAACTTATATGAACAAAAACATTAGTTTTATGACA
AAACAAAAGGTCATAACAATTTGAAATAGACAACTACTCAAATAGTCATAACTATTTGAACTAGT
TAGGTAAACAGAATTATTTCTTAATTCTCTTATTAATTTTTGAAAGATTAATAAATTAATATTAT
TTTATTCCAAATAAGCTAGTATGAATCCAAAAAATTGTCATATGACAAAACAAAAGGTAAGAACA
ATTTGAAATAGATAATTATTCAAATAGCCATA
Found at i:30214 original size:229 final size:228
Alignment explanation
Indices: 29807--30250 Score: 505
Period size: 229 Copynumber: 1.9 Consensus size: 228
29797 ATTGGTTTTG
* * * * *
29807 TAAACAGATTTATTTCTTAAATCTCTTACTTATTAATTTTTGAAAGATTAATAAATTAATATTAT
1 TAAACAAATTTATTTCTTAAATCTATTACATATTAATTTTTCAAAGATTAATAAATTAATATTAA
* * *
29872 TTTATTCCGAATAAGCTTGTATGATCCAAAACAATTGTCATATGACCAAACAAAAGGTAAGAACA
66 TTTATTCCGAATAAGCTTGTATGAACCAAAACAATTATCATATGACCAAACAAAAGATAAGAACA
* * ** ** * **
29937 ATTTGAAATAGATAATTATTGAAATGGCCATAATTATTTGAACTGATTTGGTAAACTTATTCACT
131 ATATGAAATAGATAATTATTCAAATAACCATAACCATTTGAACTGATTTAGTAAACAAATTCACT
30002 TTTTAAATCACTTACTTATTTGAATTTGTTCGA
196 TTTTAAATCACTTACTTATTTGAATTTGTTCGA
* * *
30035 TAAACAAATTTATTTTTTAAAATCTATTTCATATTAATTTTTCAAATG-TTAATAAATTAGTATT
1 TAAACAAATTTATTTCTT-AAATCTATTACATATTAATTTTTCAAA-GATTAATAAATTAATATT
** * * ** *
30099 AATTTATTTTGAATAAGCTTGTATGAACTAAAATAATTATTTTATGACTAAACAAAAGATCAA-A
64 AATTTATTCCGAATAAGCTTGTATGAACCAAAACAATTATCATATGACCAAACAAAAGAT-AAGA
** * * *** * *
30163 ATGATATGTAATAGATAATTATTCTAATAATTTTAACCATTTGATCTGATTTAGTAAACAAATTT
128 ACAATATGAAATAGATAATTATTCAAATAACCATAACCATTTGAACTGATTTAGTAAACAAATTC
* *
30228 ATTTTTTAAATCTCTTACTTATT
193 ACTTTTTAAATCACTTACTTATT
30251 AATTTTCAAA
Statistics
Matches: 175, Mismatches: 38, Indels: 5
0.80 0.17 0.02
Matches are distributed among these distances:
228 16 0.09
229 156 0.89
230 3 0.02
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (228 bp):
TAAACAAATTTATTTCTTAAATCTATTACATATTAATTTTTCAAAGATTAATAAATTAATATTAA
TTTATTCCGAATAAGCTTGTATGAACCAAAACAATTATCATATGACCAAACAAAAGATAAGAACA
ATATGAAATAGATAATTATTCAAATAACCATAACCATTTGAACTGATTTAGTAAACAAATTCACT
TTTTAAATCACTTACTTATTTGAATTTGTTCGA
Found at i:30626 original size:181 final size:180
Alignment explanation
Indices: 30224--30657 Score: 433
Period size: 181 Copynumber: 2.4 Consensus size: 180
30214 TAGTAAACAA
*
30224 ATTTATTTTTTAAATCTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTAATC
1 ATTTATTTTTTAAATCTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTATTC
* ** * *
30289 CAAATAAGCTTGTACAAACAAAACAATTGTTTTACATTAAAAGAAAAGGTCATAACAATTTGAAA
66 TAAATAAAATAGTACAAACAAAACAATTGTTTGACATTAAAAGAAAAGGTCATAACAATTTGAAA
* * ** * * *
30354 TAGATAATCATCCATAGAGTCTTAACTATATGAACTGGTTCGACAATTAG
131 TAAATAATCATCCAAAGAGTCAAAACTATATGAAATGATTCGACAAGTAG
* * ** *
30404 ATTTATTTTTTAATTTTCTTGGTTATTAAGTTTCAAAATATTATTAAATTAGTATTATTTTATTC
1 ATTTATTTTTTAAATCTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTATTC
** * * * * * * *
30469 TAAATAAAATAGTATGAATAGAACCGATTGTTTGATGA-TAAAATAAAAGGTTATAACGATTTGA
66 TAAATAAAATAGTACAAACA-AAACAATTGTTTGA-CATTAAAAGAAAAGGTCATAACAATTTGA
* ** * * **
30533 AATAAATAATTATTGAAAGAGTCAAAACTATTTGAAATGATTTGGTAAGTAG
129 AATAAATAATCATCCAAAGAGTCAAAACTATATGAAATGATTCGACAAGTAG
** * * * ** *
30585 ATTT-TCTTTTTAAATCTCTTACAAATTTATTTTCTAAATATTAATAAAACAATATTATTTTATT
1 ATTTAT-TTTTTAAATCTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTATT
30649 -TCAAATAAA
65 CT-AAATAAA
30658 CTTATATTAA
Statistics
Matches: 203, Mismatches: 47, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
180 74 0.36
181 128 0.63
182 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.41
Consensus pattern (180 bp):
ATTTATTTTTTAAATCTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTATTC
TAAATAAAATAGTACAAACAAAACAATTGTTTGACATTAAAAGAAAAGGTCATAACAATTTGAAA
TAAATAATCATCCAAAGAGTCAAAACTATATGAAATGATTCGACAAGTAG
Found at i:30880 original size:10 final size:10
Alignment explanation
Indices: 30843--30898 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
30833 AATTCGAATG
30843 ATTATCAATT
1 ATTATCAATT
30853 A--ATCAA--
1 ATTATCAATT
30859 ATTA-CAAGTT
1 ATTATCAA-TT
30869 ATTATCAATT
1 ATTATCAATT
30879 ATTATCAATT
1 ATTATCAATT
*
30889 ATTATTAATT
1 ATTATCAATT
30899 TATATTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
6 1 0.03
7 3 0.08
8 6 0.15
10 26 0.67
11 3 0.08
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (10 bp):
ATTATCAATT
Found at i:30942 original size:18 final size:16
Alignment explanation
Indices: 30919--31018 Score: 75
Period size: 18 Copynumber: 6.3 Consensus size: 16
30909 GTTATTAATG
30919 ATATTTATATTCATTTAT
1 ATATTTATATT-A-TTAT
30937 ATATTTATATTATTAT
1 ATATTTATATTATTAT
* *
30953 AT-TTTAAAAT-TTAT
1 ATATTTATATTATTAT
*
30967 A-ATTTAT-TTATTTT
1 ATATTTATATTATTAT
*
30981 AATATTATATCTTATTAT
1 -ATATT-TATATTATTAT
* *
30999 -TATATCTATTATTAT
1 ATATTTATATTATTAT
31014 ATATT
1 ATATT
31019 AGTATTCATA
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
13 1 0.02
14 12 0.18
15 16 0.25
16 15 0.23
17 4 0.06
18 17 0.26
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTATATTATTAT
Found at i:30944 original size:8 final size:8
Alignment explanation
Indices: 30896--30979 Score: 52
Period size: 8 Copynumber: 10.5 Consensus size: 8
30886 ATTATTATTA
30896 ATTTATATT
1 ATTTATA-T
*
30905 ATTTGT-T
1 ATTTATAT
*
30912 ATTAATGAT
1 ATTTAT-AT
30921 ATTTATATT
1 ATTTATA-T
30930 CATTTATAT
1 -ATTTATAT
30939 ATTTATAT
1 ATTTATAT
30947 -TATTATAT
1 AT-TTATAT
*
30955 -TTTA-AA
1 ATTTATAT
30961 ATTTATA-
1 ATTTATAT
*
30968 ATTTATTT
1 ATTTATAT
30976 ATTT
1 ATTT
30980 TAATATTATA
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
6 1 0.02
7 19 0.31
8 21 0.34
9 13 0.21
10 7 0.11
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (8 bp):
ATTTATAT
Found at i:30964 original size:22 final size:22
Alignment explanation
Indices: 30939--30998 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
30929 TCATTTATAT
30939 ATTTATATTATTATATTTTAAA
1 ATTTATATTATTATATTTTAAA
*
30961 ATTTATAATTTATT-TATTTTAAT
1 ATTTAT-A-TTATTATATTTTAAA
*
30984 ATTATATCTTATTAT
1 ATT-TATATTATTAT
30999 TATATCTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 11 0.34
23 13 0.41
24 8 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTATATTATTATATTTTAAA
Found at i:31010 original size:12 final size:13
Alignment explanation
Indices: 30970--31029 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
30960 AATTTATAAT
*
30970 TTATT-TATTTTA
1 TTATTATATCTTA
*
30982 ATATTATATCTTA
1 TTATTATATCTTA
30995 TTATTATATC-TA
1 TTATTATATCTTA
*
31007 TTATTATATATTA
1 TTATTATATCTTA
*
31020 GTATTCATAT
1 TTATT-ATAT
31030 ATTTAGTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
12 15 0.38
13 21 0.52
14 4 0.10
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (13 bp):
TTATTATATCTTA
Found at i:31037 original size:15 final size:15
Alignment explanation
Indices: 31008--31047 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
30998 TTATATCTAT
31008 TATT-ATATA-TTAG
1 TATTCATATATTTAG
31021 TATTCATATATTTAG
1 TATTCATATATTTAG
31036 TATTCATATATT
1 TATTCATATATT
31048 AAACAATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 4 0.16
14 5 0.20
15 16 0.64
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (15 bp):
TATTCATATATTTAG
Found at i:31531 original size:11 final size:10
Alignment explanation
Indices: 31497--31546 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
31487 TTTATTAATA
31497 ATAATTA-AT
1 ATAATTATAT
*
31506 ATTAATTGTATT
1 A-TAATTATA-T
31518 ATAATTATTAT
1 ATAATTA-TAT
31529 ATAATTA-AT
1 ATAATTATAT
31538 ATAATTATA
1 ATAATTATA
31547 ATAGTATAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 10 0.29
10 6 0.18
11 14 0.41
12 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (10 bp):
ATAATTATAT
Found at i:32251 original size:22 final size:22
Alignment explanation
Indices: 32215--32258 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
32205 TTTATTAAAA
**
32215 TATAAATATTTATAAACTATAT
1 TATAAATATAGATAAACTATAT
*
32237 TATAAATATAGATAATCTATAT
1 TATAAATATAGATAAACTATAT
32259 ACAATTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
TATAAATATAGATAAACTATAT
Found at i:33153 original size:172 final size:173
Alignment explanation
Indices: 32722--33393 Score: 535
Period size: 172 Copynumber: 3.8 Consensus size: 173
32712 TTTAAAATTT
* * * * * *
32722 TTATTAATTTTTGAAATATTAATAGATTAATTTTATTTTATTTCGAACAAACTTATATGAACA-A
1 TTATTAATTTTTG-AA-ATTATTAGATT-ATTTTATTTTATTTCAAATAAGC-TGTATGAATAGA
* **
32786 AAACATTAGTTTTATGACAAAACAAAAGGTCATAACAATTTGAAATAGATAATTGTTCAAATAGT
62 AAACATT-GTTTTATGACAAAACAAAAGGTTATAACAATTTGAAATAGATAATCATTCAAATAGT
* * * * *
32851 CATAATTATTTGAATTGGTTAGGTAAACAGAATTATTTTTAATTCTCTTAA
126 CATAACTATTTGAACTAGTTAGGCAAACAGAATTATTTTTAAATCTC---A
* *
32902 TTATTAATTTTTGAAATT-TTAATAATTTATTTTATTTTA-TTCTAAATAAGCTAGTATG-ATTG
1 TTATTAATTTTTGAAATTATT-A-GA-TTATTTTATTTTATTTC-AAATAAGCT-GTATGAATAG
* ** *
32964 AAAATATTGTTTTATGACAAAACAAAAGGTTATAATGATTTGAAATAGATAATCATTCATATAGT
61 AAAACATTGTTTTATGACAAAACAAAAGGTTATAACAATTTGAAATAGATAATCATTCAAATAGT
** *
33029 TTTAACTATTTGAACTAGTT-GGCAAAC--AATTTTATTTTAAATCTC-
126 CATAACTATTTGAACTAGTTAGGCAAACAGAATTAT-TTTTAAATCTCA
33074 TTATTAATTTTTAGAAATTATTAGATTAGTTTTATTTTATTTCAAATAAGCTGTATGAATAGAAA
1 TTATTAATTTTT-GAAATTATTAGATTA-TTTTATTTTATTTCAAATAAGCTGTATGAATAGAAA
* *
33139 TA-ATTGTTTTATGACAAAACAAAAGGTTATAACAATTTGAAGT--ATACAGCTATT-ATAATAG
64 -ACATTGTTTTATGACAAAACAAAAGGTTATAACAATTTGAAATAGATA-ATC-ATTCA-AATAG
* * ** * * *
33200 TCATAACTATTTGAATTGGTTTTGTAAATAGATTTATTTTTTAAATCTC-
125 TCATAACTATTTGAACTAGTTAGGCAAACAGAATTA-TTTTTAAATCTCA
* * * * * ** * *
33249 TTATTAATTTTGGAAAGATTAATAAATGAGTATTATTTTATTTTGAGTAAGCTTGTATG-ATAAA
1 TTATTAATTTTTG-AA-ATTATTAGATTA-TTTTATTTTATTTCAAATAAGC-TGTATGAATAGA
* ** * * * * * * * *
33313 AAACAATAGTCATATGACCAAACAAATGGTAAGAACAATTTGAAATAGATAATTATTGAAATGGC
62 AAAC-ATTGTTTTATGACAAAACAAAAGGTTATAACAATTTGAAATAGATAATCATTCAAATAGT
*
33378 CATAATTATTTGAACT
126 CATAACTATTTGAACT
33394 GATTTGGTAA
Statistics
Matches: 402, Mismatches: 62, Indels: 59
0.77 0.12 0.11
Matches are distributed among these distances:
170 3 0.01
171 11 0.03
172 100 0.25
173 15 0.04
174 3 0.01
175 33 0.08
176 45 0.11
177 67 0.17
178 77 0.19
179 33 0.08
180 15 0.04
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (173 bp):
TTATTAATTTTTGAAATTATTAGATTATTTTATTTTATTTCAAATAAGCTGTATGAATAGAAAAC
ATTGTTTTATGACAAAACAAAAGGTTATAACAATTTGAAATAGATAATCATTCAAATAGTCATAA
CTATTTGAACTAGTTAGGCAAACAGAATTATTTTTAAATCTCA
Found at i:33390 original size:177 final size:177
Alignment explanation
Indices: 32320--33430 Score: 738
Period size: 177 Copynumber: 6.3 Consensus size: 177
32310 ATTTAACATG
* * * **
32320 ACTATTTGAACTTGTTTGGTAAACAAATTCATTTTTTAAATCTCTTAATTATTAATTTTAAAAAT
1 ACTATTTGAACTGGTTTGGTAAACAGATTTATTTTTTAAATCTC----TTATTAATTTTTGAAAT
* * * * * *** *
32385 ATTAATAACTTAATATTATTTTATTTCGAATAAGCTTATATGAATTGAAATAAT--TTTTGATGA
62 ATTAATAAATTAGTTTTATTTTATTTCAAATAAGCTTGTATGAACAAAAACAATAGTTTT-ATGA
* * * * * *
32448 TAGAAGAAAAGGTTATAACGATTTGAAATAGATAACTATTCAAATAGTCCATG
126 CAAAACAAAAGGTTATAACAATTTGAAATAGATAATTATTCAAATAGT-CATA
* * ** * * ** * * **
32501 ACTGTTT-AATCTAGTTCAGTAAACATATTTAATTTTTCATTTTTTACTTATTAATTGTCAAAAT
1 ACTATTTGAA-CTGGTTTGGTAAACAGATTT-ATTTTTTA-AATCT-CTTATTAATTTTTGAAAT
* * * * * * * * * * *
32565 ATTAATAAATTTGTATTA-TTTA-ATCCAATAAGCTTGAAATAAATAGAAACTATTA-TCTTATA
62 ATTAATAAATTAGTTTTATTTTATTTCAAATAAGCTTG-TATGAACAAAAAC-AATAGTTTTATG
* * * ** * * *
32627 ACATAACAAAAAGTCATAATGATTTGAAATAAATAATTGGCTT-AAATAGTC-TT
125 ACAAAACAAAAGGTTATAACAATTTGAAATAGATAATT--ATTCAAATAGTCATA
* ** * * *
32680 A--ATTTGTACCAGTTTGATAAATAGATTTATTTTTTAAAAT-TTTTATTAATTTTTGAAATATT
1 ACTATTTGAACTGGTTTGGTAAACAGATTTATTTTTT-AAATCTCTTATTAATTTTTGAAATATT
* * * * * * *
32742 AATAGATTAATTTTATTTTATTTCGAACAAACTTATATGAACAAAAACATTAGTTTTATGACAAA
65 AATAAATTAGTTTTATTTTATTTCAAATAAGCTTGTATGAACAAAAACAATAGTTTTATGACAAA
* *
32807 ACAAAAGGTCATAACAATTTGAAATAGATAATTGTTCAAATAGTCATA
130 ACAAAAGGTTATAACAATTTGAAATAGATAATTATTCAAATAGTCATA
* * * * *
32855 ATTATTTGAATTGGTTAGGTAAACAGAATTA-TTTTTAATTCTCTTAATTATTAATTTTTGAAAT
1 ACTATTTGAACTGGTTTGGTAAACAGATTTATTTTTTAAATCTC----TTATTAATTTTTGAAAT
* * * *** * *
32919 TTTAATAATTTA-TTTTATTTTA-TTCTAAATAAGCTAGTATGATTGAAAA-TATTGTTTTATGA
62 ATTAATAAATTAGTTTTATTTTATTTC-AAATAAGCTTGTATGAACAAAAACAATAGTTTTATGA
** * * **
32981 CAAAACAAAAGGTTATAATGATTTGAAATAGATAATCATTCATATAGTTTTA
126 CAAAACAAAAGGTTATAACAATTTGAAATAGATAATTATTCAAATAGTCATA
* * *
33033 ACTATTTGAACTAG-TTGGCAAACA-ATTT-TATTTTAAATCTCTTATTAATTTTT-AGAA-ATT
1 ACTATTTGAACTGGTTTGGTAAACAGATTTATTTTTTAAATCTCTTATTAATTTTTGA-AATATT
* * * * * *
33093 ATTAGATTAGTTTTATTTTATTTCAAATAAGC-TGTATGAATAGAAATAATTGTTTTATGACAAA
65 AATAAATTAGTTTTATTTTATTTCAAATAAGCTTGTATGAACAAAAACAATAGTTTTATGACAAA
* * * **
33157 ACAAAAGGTTATAACAATTTGAAGTATACAGCTATT-ATAATAGTCATA
130 ACAAAAGGTTATAACAATTTGAAATAGATAATTATTCA-AATAGTCATA
* * * * *
33205 ACTATTTGAATTGGTTTTGTAAATAGATTTATTTTTTAAATCTCTTATTAATTTTGGAAAGATTA
1 ACTATTTGAACTGGTTTGGTAAACAGATTTATTTTTTAAATCTCTTATTAATTTTTGAAATATTA
* * ** * ** *
33270 ATAAATGAGTATTATTTTATTTTGAGTAAGCTTGTATGATA-AAAAACAATAGTCATATGACCAA
66 ATAAATTAGTTTTATTTTATTTCAAATAAGCTTGTATGA-ACAAAAACAATAGTTTTATGACAAA
* * * * * *
33334 ACAAATGGTAAGAACAATTTGAAATAGATAATTATTGAAATGGCCATA
130 ACAAAAGGTTATAACAATTTGAAATAGATAATTATTCAAATAGTCATA
* * * * * *
33382 ATTATTTGAACTGATTTGGTAAACATATTCAGTTTTTAAATCACTTATT
1 ACTATTTGAACTGGTTTGGTAAACAGATTTATTTTTTAAATCTCTTATT
33431 TGAATTTGTT
Statistics
Matches: 721, Mismatches: 171, Indels: 80
0.74 0.18 0.08
Matches are distributed among these distances:
171 20 0.03
172 95 0.13
173 12 0.02
174 44 0.06
175 82 0.11
176 64 0.09
177 146 0.20
178 82 0.11
179 40 0.06
180 93 0.13
181 31 0.04
182 9 0.01
183 2 0.00
184 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.42
Consensus pattern (177 bp):
ACTATTTGAACTGGTTTGGTAAACAGATTTATTTTTTAAATCTCTTATTAATTTTTGAAATATTA
ATAAATTAGTTTTATTTTATTTCAAATAAGCTTGTATGAACAAAAACAATAGTTTTATGACAAAA
CAAAAGGTTATAACAATTTGAAATAGATAATTATTCAAATAGTCATA
Done.