Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167984.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_241, 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: 44576
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
File 2 of 2
Found at i:31535 original size:21 final size:22
Alignment explanation
Indices: 31486--31540 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
31476 ATAGCATAAT
31486 ATATTAATAATTATACAATATA
1 ATATTAATAATTATACAATATA
* *
31508 TTATTAATAATTA-ATAATATA
1 ATATTAATAATTATACAATATA
31529 A-ATTTAATAATT
1 ATA-TTAATAATT
31541 GTTTATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 16 0.55
22 12 0.41
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTAATAATTATACAATATA
Found at i:33144 original size:46 final size:45
Alignment explanation
Indices: 33083--33208 Score: 152
Period size: 41 Copynumber: 2.9 Consensus size: 45
33073 TGACACAAAA
* *
33083 CTCCTCTAAGCAGAGGTTCAACAACTTTGAAAAAATAAATAAAAGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTG-AAAAATAAATAAAAGG
* *
33129 CTCCTCTAAATAGAGGCTCAACGACTTTG---AA-AAATAAAAGG
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAAAGG
* * *
33170 CTCATCTAAACAGAGGCACCACAACTTTGAAAAATAAAT
1 CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAAT
33209 GCTCTTCTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
41 34 0.51
42 2 0.03
44 2 0.03
45 4 0.06
46 25 0.37
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.21
Consensus pattern (45 bp):
CTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAAAAGG
Found at i:33236 original size:40 final size:41
Alignment explanation
Indices: 33119--33255 Score: 179
Period size: 40 Copynumber: 3.4 Consensus size: 41
33109 TTGAAAAAAT
* * *
33119 AAATAAAAGGCTCCTCTAAATAGAGGCTCAACGACTTTGAA
1 AAATAAAAGGCTCATCTAAATAGAGGCACAACAACTTTGAA
* *
33160 AAATAAAAGGCTCATCTAAACAGAGGCACCACAACTTTGAA
1 AAATAAAAGGCTCATCTAAATAGAGGCACAACAACTTTGAA
* * * *
33201 AAAT-AAATGCTCTTCTAAATAGAGGCACAATAACTTTGAC
1 AAATAAAAGGCTCATCTAAATAGAGGCACAACAACTTTGAA
33241 AAAT-AAAGGCTCATC
1 AAATAAAAGGCTCATC
33256 GATTTTAATT
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 43 0.52
41 40 0.48
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.22
Consensus pattern (41 bp):
AAATAAAAGGCTCATCTAAATAGAGGCACAACAACTTTGAA
Found at i:33606 original size:9 final size:9
Alignment explanation
Indices: 33592--33645 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
33582 ATACAATTTA
33592 TTATATAAT
1 TTATATAAT
*
33601 TTATATAAA
1 TTATATAAT
33610 TTATAT-AT
1 TTATATAAT
33618 TT-TATAAT
1 TTATATAAT
33626 TGTCATATAAT
1 T-T-ATATAAT
*
33637 ATAT-TAAT
1 TTATATAAT
33645 T
1 T
33646 ATGTGATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
7 3 0.08
8 10 0.27
9 17 0.46
10 1 0.03
11 6 0.16
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (9 bp):
TTATATAAT
Found at i:37499 original size:12 final size:11
Alignment explanation
Indices: 37481--37522 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 11
37471 TATTTCAATT
37481 AAATATATATA
1 AAATATATATA
37492 ATAATATATATA
1 A-AATATATATA
37504 AATATAATATATA
1 AA-AT-ATATATA
37517 AAATAT
1 AAATAT
37523 TAGCTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.14
12 15 0.54
13 9 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATATATATA
Found at i:37505 original size:22 final size:22
Alignment explanation
Indices: 37480--37522 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
37470 ATATTTCAAT
*
37480 TAAATAT-ATATAATAATATATA
1 TAAATATAATAT-ATAAAATATA
37502 TAAATATAATATATAAAATAT
1 TAAATATAATATATAAAATAT
37523 TAGCTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATAATATATAAAATATA
Found at i:38120 original size:26 final size:29
Alignment explanation
Indices: 38078--38134 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 29
38068 TTATTTTATT
*
38078 TAAATTATTAAATTTA-TA-ATTA-ATAA
1 TAAATTATGAAATTTATTATATTATATAA
38104 TAAATTATGACAA-TTATTATATTATATAA
1 TAAATTATGA-AATTTATTATATTATATAA
38133 TA
1 TA
38135 TTATATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 12 0.46
27 4 0.15
28 4 0.15
29 6 0.23
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
TAAATTATGAAATTTATTATATTATATAA
Found at i:38162 original size:17 final size:17
Alignment explanation
Indices: 38116--38170 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
38106 AATTATGACA
*
38116 ATTATTATATTATATAAT
1 ATTAATATATT-TATAAT
38134 ATT-ATATA-TTATAAT
1 ATTAATATATTTATAAT
* *
38149 ATTAATTTATTTATATT
1 ATTAATATATTTATAAT
38166 ATTAA
1 ATTAA
38171 ATAATTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.28
16 5 0.16
17 15 0.47
18 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAATATATTTATAAT
Found at i:38506 original size:18 final size:17
Alignment explanation
Indices: 38483--38516 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
38473 TTTAATAGAT
38483 AAAATTAAATTATAATTA
1 AAAATTAAATT-TAATTA
*
38501 AAAATTTAATTTAATT
1 AAAATTAAATTTAATT
38517 TATGGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTAAATTTAATTA
Found at i:39284 original size:20 final size:20
Alignment explanation
Indices: 39261--39320 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
39251 ACAATTATTA
39261 AATATTAATTATTTTAATAT
1 AATATTAATTATTTTAATAT
39281 AATATTAATTATTATT-ATAT
1 AATATTAATTATT-TTAATAT
*
39301 AAT-TT-ATTAATTTAAGTAT
1 AATATTAATTATTTTAA-TAT
39320 A
1 A
39321 TGATTTATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 2 0.06
18 6 0.17
19 6 0.17
20 20 0.56
21 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AATATTAATTATTTTAATAT
Found at i:39662 original size:180 final size:180
Alignment explanation
Indices: 39446--39923 Score: 608
Period size: 179 Copynumber: 2.7 Consensus size: 180
39436 TATGATTATC
* * * *
39446 TGAACAATTATCTATTTCAAAACATTATGACCTTTTGTTTTGTCATAAAATAATTGATTCTAATC
1 TGAACAATTATCTATTTCAAATCGTTATGACCTTTTGTTTTGTCATAAAATAATTGTTTCTATTC
* * * *
39511 ATGCAAGCTTATTTCGAATAAAATAATA-TAAATTTATTAATATTCTAGAAATTAAAAATTAAAA
66 ATACAATCTTATTTAGAATAAAATAATACT-AATTTATTAATATTCTA-AAATTAAAAAGTAAAA
* *
39575 -ATTTTAAAAATAAATATGTTT-TCTGA-ACATGTTCAAATAGTTATAACTATA
129 GATTTAAAAAATAAATATGTTTAAC-GAGACA-GTTCAAATAGTTATAACTATA
* * * *
39626 TGAATAATTATCTATTTCAAATCGTTATGACCTTTTGTTTTGTCATAAACTAATTGTTTATGTTC
1 TGAACAATTATCTATTTCAAATCGTTATGACCTTTTGTTTTGTCATAAAATAATTGTTTCTATTC
* * * *
39691 ATATAATCTTATTTGGAATAAAATAATACTAATTTATT--TATTCCAAAAATTAATAAGTAAAAG
66 ATACAATCTTATTTAGAATAAAATAATACTAATTTATTAATATT-CTAAAATTAAAAAGTAAAAG
** * *
39754 ATTTAAAAAATAAATATGTTTAACGAGTGAGTTCAAATAGTTATGACTATT
130 ATTTAAAAAATAAATATGTTTAACGAGACAGTTCAAATAGTTATAACTATA
* * ** *
39805 TGAACAATTATTTATTTCAAATTGTTATGATATTTTGTTTGGTCATAAAATAATTGTTTCTATTC
1 TGAACAATTATCTATTTCAAATCGTTATGACCTTTTGTTTTGTCATAAAATAATTGTTTCTATTC
* *
39870 ATACAATTTTATTTAGAATAAAATAATACTAATTTATTAATATTATAAAATTAA
66 ATACAATCTTATTTAGAATAAAATAATACTAATTTATTAATATTCTAAAATTAA
39924 TGAGATGAAA
Statistics
Matches: 256, Mismatches: 35, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
178 18 0.07
179 134 0.52
180 99 0.39
181 5 0.02
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (180 bp):
TGAACAATTATCTATTTCAAATCGTTATGACCTTTTGTTTTGTCATAAAATAATTGTTTCTATTC
ATACAATCTTATTTAGAATAAAATAATACTAATTTATTAATATTCTAAAATTAAAAAGTAAAAGA
TTTAAAAAATAAATATGTTTAACGAGACAGTTCAAATAGTTATAACTATA
Found at i:40352 original size:176 final size:177
Alignment explanation
Indices: 39981--40438 Score: 489
Period size: 177 Copynumber: 2.6 Consensus size: 177
39971 ACTATTATCT
* * * **
39981 ATTTCAAATTGTTATGACATTTTGTTTTGTCGTAAAATAATTGTTTTTGTTCATACAAAATTATT
1 ATTTCAAATCGTTATGACCTTTTGTTTTGTCGTAAAATAATTG-TTTTGTTCATATAAGTTTATT
* * * *
40046 CATAATAAAATAATACTAATTTATTGATATTTCAAAAATTAATAAGGTATTTAAAAACTAAATAT
65 TAGAATAAAATAATACTAATTTATTAATATTTCAAAAATCAATAAGGTATTTAAAAACTAAATAT
* * * * * *
40111 GTTTATCGATCTAGCTTTAAATAGTTATAAATATATGAATAATTATTT
130 ATTTACCCAACTAGCTTCAAATAGTTATAAATATATGAATAATTATTC
* * *
40159 ATTTCAAATCGTTATGACCTTTTGTTTTGTCGTAAAACAAATGTTTTGTTCATATAAGTTTGTTT
1 ATTTCAAATCGTTATGACCTTTTGTTTTGTCGTAAAATAATTGTTTTGTTCATATAAGTTTATTT
* * * * ** *
40224 AGAATATAATAGTATTAATTGATTAATATTTTGAAAATCAATAAGAG-ATTTGAAAAA-TAAATC
66 AGAATAAAATAATACTAATTTATTAATATTTCAAAAATCAATAAG-GTATTT-AAAAACTAAATA
* *
40287 TATTTACCCAACTAG-TTCAATTAGTTATAACA-ATTTGAA-AAGTTATTC
129 TATTTACCCAACTAGCTTCAAATAGTTATAA-ATATATGAATAA-TTATTC
* * * * * *
40335 ATTTCAAATCATTATGACCATCTGTTTTGTCATAAAATAATTGTTTCTATTGATAT-AGTCTTAT
1 ATTTCAAATCGTTATGACCTTTTGTTTTGTCGTAAAATAATTGTTT-TGTTCATATAAGT-TTAT
*
40399 TTAGAATAAAATAATGCTAATTTATTAATA-TTCTAAAAAT
64 TTAGAATAAAATAATACTAATTTATTAATATTTC-AAAAAT
40439 TAATGTGTAA
Statistics
Matches: 230, Mismatches: 43, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
175 2 0.01
176 69 0.30
177 114 0.50
178 45 0.20
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.43
Consensus pattern (177 bp):
ATTTCAAATCGTTATGACCTTTTGTTTTGTCGTAAAATAATTGTTTTGTTCATATAAGTTTATTT
AGAATAAAATAATACTAATTTATTAATATTTCAAAAATCAATAAGGTATTTAAAAACTAAATATA
TTTACCCAACTAGCTTCAAATAGTTATAAATATATGAATAATTATTC
Found at i:40430 original size:517 final size:518
Alignment explanation
Indices: 39446--40443 Score: 1209
Period size: 517 Copynumber: 1.9 Consensus size: 518
39436 TATGATTATC
*
39446 TGAACAATTATCTATTTCAAAACATTATGACCTTTTGTTTTGTCATAAAATAATTGATTCTAATC
1 TGAACAATTATCTATTTCAAAACATTATGACATTTTGTTTTGTCATAAAATAATTGATTCTAATC
* ** *
39511 ATGCAAGCTTATTTCGAATAAAATAATATAAATTTATTAATATTCTAGAAATTAAAAATTAAAAA
66 ATACAAAATTATTTCGAATAAAATAATATAAATTTATTAATATTCTAAAAATT--AAATTAAAAA
*
39576 TTTTAAAAATAAATATGTTTTCTGAACATGTTCAAATAGTTATAACTATATGAATAATTATCTAT
129 TTTTAAAAATAAATATGTTTTCTGAACATGTTCAAATAGTTATAAATATATGAATAATTATCTAT
* *
39641 TTCAAATCGTTATGACCTTTTGTTTTGTCATAAACTAATTGTTTATGTTCATATAATCTTATTTG
194 TTCAAATCGTTATGACCTTTTGTTTTGTCATAAACTAAATGTTTATGTTCATATAATCTTATTTA
* *
39706 GAATAAAATAATACTAATTTATTTATTCCAAAAATTAATAAGTAAAAGATTTAAAAAATAAATAT
259 GAATAAAATAATACTAATTGATTTATTCCAAAAATCAATAAG---AAGATTTAAAAAATAAATAT
* * * * * * ** *
39771 GTTTAACGAGTGAGTTCAAATAGTTATGACTATTTGAACAATTATTTATTTCAAATTGTTATGAT
321 ATTTAACAACTGAGTTCAAATAGTTATAACAATTTGAACAATTATTCATTTCAAATCATTATGAC
* *
39836 ATTTTGTTTGGTCATAAAATAATTGTTTCTATTCATACAATTTTATTTAGAATAAAATAATACTA
386 ATTCTGTTTGGTCATAAAATAATTGTTTCTATTCATACAATCTTATTTAGAATAAAATAATACTA
39901 ATTTATTAATATTAT-AAAATTAATGAGATGAAAATTTACTAAACAGGTTCAAATACTTATGTCT
451 ATTTATTAATATTATAAAAATTAATGAGATGAAAATTTACTAAACAGGTTCAAATACTTATGTCT
39965 ATT
516 ATT
* *** * * * **
39968 TGAACTATTATCTATTTCAAATTGTTATGACATTTTGTTTTGTCGTAAAATAATTGTTTTTGTTC
1 TGAACAATTATCTATTTCAAAACATTATGACATTTTGTTTTGTCATAAAATAATTGATTCTAATC
* * *
40033 ATACAAAATTA-TTCATAATAAAATAATACT-AATTTATTGATATT-TCAAAAATT-AA-T-AAG
66 ATACAAAATTATTTC-GAATAAAATAATA-TAAATTTATTAATATTCT-AAAAATTAAATTAAAA
* * *
40092 GTATTTAAAAACTAAATATGTTTATC-GATC-TAGCTTTAAATAGTTATAAATATATGAATAATT
128 AT-TTTAAAAA-TAAATATGTTT-TCTGAACAT-G-TTCAAATAGTTATAAATATATGAATAATT
* *
40155 ATTTATTTCAAATCGTTATGACCTTTTGTTTTGTCGTAAAAC-AAATGTTT-TGTTCATATAAGT
188 ATCTATTTCAAATCGTTATGACCTTTTGTTTTGTCAT-AAACTAAATGTTTATGTTCATATAA-T
* * * * *** *
40218 -TTGTTTAGAATATAATAGTATTAATTGATTAATATTTTGAAAATCAATAAG-AGATTTGAAAAA
251 CTTATTTAGAATAAAATAATACTAATTGATT--TATTCCAAAAATCAATAAGAAGATTTAAAAAA
* * *
40281 TAAATCTATTTACCCAACT-AGTTCAATTAGTTATAACAATTTGAA-AAGTTATTCATTTCAAAT
314 TAAATATATTTA-ACAACTGAGTTCAAATAGTTATAACAATTTGAACAA-TTATTCATTTCAAAT
* * * *
40344 CATTATGACCA-TCTGTTTTGTCATAAAATAATTGTTTCTATTGATATAGTCTTATTTAGAATAA
377 CATTATGA-CATTCTGTTTGGTCATAAAATAATTGTTTCTATTCATACAATCTTATTTAGAATAA
* *
40408 AATAATGCTAATTTATTAATATTCTAAAAATTAATG
441 AATAATACTAATTTATTAATATTATAAAAATTAATG
40444 TGTAATGGAT
Statistics
Matches: 405, Mismatches: 55, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
516 2 0.00
517 137 0.34
518 24 0.06
519 52 0.13
520 72 0.18
521 23 0.06
522 94 0.23
523 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (518 bp):
TGAACAATTATCTATTTCAAAACATTATGACATTTTGTTTTGTCATAAAATAATTGATTCTAATC
ATACAAAATTATTTCGAATAAAATAATATAAATTTATTAATATTCTAAAAATTAAATTAAAAATT
TTAAAAATAAATATGTTTTCTGAACATGTTCAAATAGTTATAAATATATGAATAATTATCTATTT
CAAATCGTTATGACCTTTTGTTTTGTCATAAACTAAATGTTTATGTTCATATAATCTTATTTAGA
ATAAAATAATACTAATTGATTTATTCCAAAAATCAATAAGAAGATTTAAAAAATAAATATATTTA
ACAACTGAGTTCAAATAGTTATAACAATTTGAACAATTATTCATTTCAAATCATTATGACATTCT
GTTTGGTCATAAAATAATTGTTTCTATTCATACAATCTTATTTAGAATAAAATAATACTAATTTA
TTAATATTATAAAAATTAATGAGATGAAAATTTACTAAACAGGTTCAAATACTTATGTCTATT
Found at i:40672 original size:181 final size:180
Alignment explanation
Indices: 40485--40891 Score: 448
Period size: 181 Copynumber: 2.3 Consensus size: 180
40475 CTGACCAGTG
* * *
40485 CAAATAGTTATGACTATTTGAATAATTATCTATTTTAAATTGTTATAACCCTTTATTTTGTCACA
1 CAAATAGTTATGACTATTTAAATAATTATCTATTTCAAATCGTTATAACCCTTTATTTTGTCACA
* * * * ***
40550 AAAAAATTATTTT-TGTTCGTACAAGCTTACTAGGAA-TAACATAATTTTAATTTATTAATATTC
66 AAAAAATT-TTTTCTATTCATACAAGCTTA-TAGCAATTAAAATAATAAAAATTTATTAATATT-
* *
40613 CA-AAAATTAATAAGTAAGAGATCTA-AAAACTGAA-TCTGTTTATCAAATAAGTT
128 CAGAAAATTAATAAGTAA-AGATCTACAAAA-T-AACTCTGATTACCAAATAAGTT
* * * * * * * *
40666 CAAATAGTTATGACTATTTCAACAATTACCTATATCAAATCGCTATAACCTTTTGTTTTGTCATA
1 CAAATAGTTATGACTATTTAAATAATTATCTATTTCAAATCGTTATAACCCTTTATTTTGTCACA
* **
40731 AAATAATTTTTTCTATTCATACAAGCTTATTTCAATTAAAATAATAAAAATTTATTAATATTCAG
66 AAAAAATTTTTTCTATTCATACAAGCTTATAGCAATTAAAATAATAAAAATTTATTAATATTCAG
* * *
40796 ACAATTAATAAGTAAAGATTTACAAAATAACTTTGATTACCAAATAAGTT
131 AAAATTAATAAGTAAAGATCTACAAAATAACTCTGATTACCAAATAAGTT
* * *
40846 CTAATCA-TTATGACTATTTAAATAGTTATTTATTTCAAATCGTTAT
1 CAAAT-AGTTATGACTATTTAAATAATTATCTATTTCAAATCGTTAT
40892 GACTTTTTTT
Statistics
Matches: 187, Mismatches: 33, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
179 2 0.01
180 68 0.36
181 117 0.63
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (180 bp):
CAAATAGTTATGACTATTTAAATAATTATCTATTTCAAATCGTTATAACCCTTTATTTTGTCACA
AAAAAATTTTTTCTATTCATACAAGCTTATAGCAATTAAAATAATAAAAATTTATTAATATTCAG
AAAATTAATAAGTAAAGATCTACAAAATAACTCTGATTACCAAATAAGTT
Found at i:42633 original size:534 final size:532
Alignment explanation
Indices: 41673--42654 Score: 1223
Period size: 534 Copynumber: 1.8 Consensus size: 532
41663 AATTATCTTC
* *
41673 TTTAAATTGTTATGACCTTTTGTTTTGTCATAAAATAATTGTTACTATTCATGTAAAATTATTCA
1 TTTAAATTGTTATGACCTTTTATTTTGTCATAAAACAATTGTTACTATTCA-GTAAAATTATTCA
41738 AAATAAAATAATACTAATCTATCAATATCTTGAAAATTAACAAGAGATTTAAAAACTAAATCCGT
65 AAATAAAATAATACTAATCTATCAATATCTTGAAAATTAACAAGAGATTT----ACTAAATCCGT
* * * * * *
41803 TTTCTGAAATAGTTTAAATAATTATGACTATTTGAATAATTATCTATCTCAAATCATTATGATCT
126 TTTCTCAAATAGTTCAAATAATTATGACTATTTAAACAAATATCAATCTCAAATCATTATGATCT
* * * * ** * * **
41868 TTATTTTGTCATAGAACAATTGTTTTTTTCTCATTAAAGCTTATTTGAATTAAAATAACACTAAT
191 TTATTTTCTCATAAAACAATTCTTTCTAACTCATCAAAGCTTATTCGAACAAAAATAACACTAAT
* * *
41933 TTAATAAAATTCCAAAAAATAATAAGAGATTTAAAAAATAAATATGTTTGTCGAAGCAGTTCAAA
256 TTAATAAAATCCCAAAAAATAACAAGAGATTTAAAAAATAAATATGTTTGCCGAAGCAGTTCAAA
* * *
41998 TAGTTAAGACTATTAGAACAATTATCTATTTCAAATTGTTCTGACATTTTGTTTAGTCATAAAAC
321 TAGCTAAGACTATTAGAACAATTATCAATTTCAAATCGTTCTGACATTTTGTTTAGTCATAAAAC
* * *
42063 ACTTATTTCGATTAATACAAGTCTATCCAGAATAAAATAATACTAATTTATTAACATTCAAAAAA
386 ACTTATTTAGATTAATAAAAGTCTATCCAAAATAAAATAATACTAATTTATTAACATTCAAAAAA
42128 TTAATGAGCAAGAGATTTAAAACAAATTTATTTACCAAACAAGTTCAAATAGATTTAACTATTTG
451 TTAATGAGCAAGAGATTTAAAACAAATTTATTTACCAAACAAGTTCAAATAGATTTAACTATTTG
42193 AACAATCATTCTAACTA
516 AACAATCATTCTAACTA
* *
42210 TTTAAAGTTGTTATGACCTTTTATTTTGTCATAAAGCAATTGTT-TTAGTTCA-TAAAGATTTAT
1 TTTAAA-TTGTTATGACCTTTTATTTTGTCATAAAACAATTGTTACTA-TTCAGTAAA-A-TTAT
* * *
42273 TCGAAATAAAATAATACTACTTTATCAATAT-TTAGAAAATTAGTAAGCAAGAGATTT-C-AAA-
62 TCAAAATAAAATAATACTAATCTATCAATATCTT-GAAAA-T--TAA-CAAGAGATTTACTAAAT
* * *
42334 CTGTTTTC-CAAATTAGTTCAAATAGTTATGATTATTTAAACAAATATCAATCTCAAATCATTAT
122 CCGTTTTCTCAAA-TAGTTCAAATAATTATGACTATTTAAACAAATATCAATCTCAAATCATTAT
* * * *
42398 GATCTTTCTTTTCTCATAAAACAATTCTTTCTAAC-CATCCAAGCTTATTCGGACAAAAATAATA
186 GATCTTTATTTTCTCATAAAACAATTCTTTCTAACTCATCAAAGCTTATTCGAACAAAAATAACA
* * * *
42462 CTAATTTAATAATATCCCAAAAATTAACAAGAGATTTAAAATATAAATGTGTTTGCCGAA-CTAG
251 CTAATTTAATAAAATCCCAAAAAATAACAAGAGATTTAAAAAATAAATATGTTTGCCGAAGC-AG
* * * *
42526 TTCAAATAGCTAAGACTATTAGAATAATTATCAATTTTAAATCGTTTTGACCTTTTGTTTAG-CT
315 TTCAAATAGCTAAGACTATTAGAACAATTATCAATTTCAAATCGTTCTGACATTTTGTTTAGTC-
* * * * * * *
42590 ATATAATAGTTGTTTTAG-TTGATAAAAG-CTTATTCAAAATAAAATAATATTAATTTATTAACA
379 ATAAAACACTT-ATTTAGATTAATAAAAGTC-TATCCAAAATAAAATAATACTAATTTATTAACA
42653 TT
442 TT
42655 TATTTATTTC
Statistics
Matches: 377, Mismatches: 54, Indels: 31
0.82 0.12 0.07
Matches are distributed among these distances:
533 3 0.01
534 183 0.49
535 83 0.22
536 7 0.02
537 12 0.03
538 75 0.20
539 1 0.00
541 3 0.01
542 10 0.03
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.39
Consensus pattern (532 bp):
TTTAAATTGTTATGACCTTTTATTTTGTCATAAAACAATTGTTACTATTCAGTAAAATTATTCAA
AATAAAATAATACTAATCTATCAATATCTTGAAAATTAACAAGAGATTTACTAAATCCGTTTTCT
CAAATAGTTCAAATAATTATGACTATTTAAACAAATATCAATCTCAAATCATTATGATCTTTATT
TTCTCATAAAACAATTCTTTCTAACTCATCAAAGCTTATTCGAACAAAAATAACACTAATTTAAT
AAAATCCCAAAAAATAACAAGAGATTTAAAAAATAAATATGTTTGCCGAAGCAGTTCAAATAGCT
AAGACTATTAGAACAATTATCAATTTCAAATCGTTCTGACATTTTGTTTAGTCATAAAACACTTA
TTTAGATTAATAAAAGTCTATCCAAAATAAAATAATACTAATTTATTAACATTCAAAAAATTAAT
GAGCAAGAGATTTAAAACAAATTTATTTACCAAACAAGTTCAAATAGATTTAACTATTTGAACAA
TCATTCTAACTA
Found at i:43698 original size:27 final size:27
Alignment explanation
Indices: 43681--43735 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
43671 TTAATTTTCT
43681 ATTATAATTAATAAATATTAATAATTA
1 ATTATAATTAATAAATATTAATAATTA
**
43708 ATTATAATTAATAAGGATT-ATAATTA
1 ATTATAATTAATAAATATTAATAATTA
43734 AT
1 AT
43736 GACAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (27 bp):
ATTATAATTAATAAATATTAATAATTA
Done.