Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168241.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_473, 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: 25706
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:419 original size:9 final size:10
Alignment explanation
Indices: 407--460 Score: 53
Period size: 9 Copynumber: 5.5 Consensus size: 10
397 TCTTTTCTTT
407 TGTATT-TTA
1 TGTATTATTA
416 TGTATT-TTA
1 TGTATTATTA
425 T-TATTTATTA
1 TGTA-TTATTA
435 T-TATTATTA
1 TGTATTATTA
444 TGTATTAATATA
1 TGTATT-AT-TA
456 TGTAT
1 TGTAT
461 ATCTTTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.05
9 19 0.47
10 10 0.25
11 2 0.05
12 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (10 bp):
TGTATTATTA
Found at i:431 original size:16 final size:16
Alignment explanation
Indices: 412--536 Score: 57
Period size: 16 Copynumber: 7.6 Consensus size: 16
402 TCTTTTGTAT
412 TTTATGTATT-TTATTA
1 TTTAT-TATTATTATTA
428 TTTATTATTATTATTA
1 TTTATTATTATTATTA
* *
444 TGTATTAATATATGTATATCT
1 TTTATT-AT-TAT-TAT-T-A
* * *
465 TTTATTTTTTTTGTTA
1 TTTATTATTATTATTA
481 TATT-TATATGTATT-TTA
1 T-TTAT-TAT-TATTATTA
498 TTTA-TA-TAGTTATATA
1 TTTATTATTA-TTAT-TA
514 TTTATTATTATTA-TA
1 TTTATTATTATTATTA
529 -TTATTATT
1 TTTATTATT
537 TTTTTTGTGT
Statistics
Matches: 85, Mismatches: 9, Indels: 32
0.67 0.07 0.25
Matches are distributed among these distances:
13 2 0.02
14 10 0.12
15 9 0.11
16 26 0.31
17 16 0.19
18 10 0.12
19 5 0.06
20 2 0.02
21 5 0.06
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.66
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:1604 original size:17 final size:16
Alignment explanation
Indices: 1584--1642 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
1574 TTTATCTTAT
1584 TTTTATTTTTGTTTTAC
1 TTTTATTTTT-TTTTAC
*
1601 TTTTCTTTATTTTTTA-
1 TTTTATTT-TTTTTTAC
* *
1617 TCTTTATTTATTTTCAC
1 T-TTTATTTTTTTTTAC
1634 TTTTATTTT
1 TTTTATTTT
1643 GTTCTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 13 0.38
17 19 0.56
18 2 0.06
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTATTTTTTTTTAC
Found at i:1650 original size:22 final size:22
Alignment explanation
Indices: 1612--1653 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1602 TTTCTTTATT
1612 TTTTATCTTTATTTATTTTCAC
1 TTTTATCTTTATTTATTTTCAC
*
1634 TTTTAT-TTTGTTCTATTTTC
1 TTTTATCTTTATT-TATTTTC
1654 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATCTTTATTTATTTTCAC
Found at i:1728 original size:58 final size:58
Alignment explanation
Indices: 1657--2008 Score: 340
Period size: 58 Copynumber: 5.9 Consensus size: 58
1647 TATTTTCTTT
*
1657 AAATAAAAATAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
1 AAATAAAATTAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
*
1715 AAATAAAATTAAAAAAAAA-AGGTTTTTGAGGAAAAGTTGAAAGTATCAA-TTTCCTTGA
1 AAATAAAATTAAAAAAAAATA--TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
**** *
1773 AAATCAAAATTTCCGAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
1 AAAT-AAAATTAAAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAA
* * * *
1832 AGATAAATTTTTCAAAAAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTCCTTGA
1 AAATAAA--ATT-----AAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
** * * *
1896 AAATCAAAATTTTCAAAAAACTA-TTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAA
1 AAAT-AAAA-TTAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
*** *
1955 AAAT-AAATTTTCAAAAAAGATTTTTG-GGAAAAAAGTTGAAAGTATCAATTTTCC
1 AAATAAAATTAAAAAAAAATATTTTTGAGG--AAAAGTTGAAAGTATCAATTTTCC
2009 CTACACAAGA
Statistics
Matches: 242, Mismatches: 32, Indels: 40
0.77 0.10 0.13
Matches are distributed among these distances:
56 11 0.05
57 9 0.04
58 106 0.44
59 66 0.27
60 3 0.01
64 12 0.05
65 34 0.14
66 1 0.00
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.32
Consensus pattern (58 bp):
AAATAAAATTAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA
Found at i:1906 original size:123 final size:122
Alignment explanation
Indices: 1670--1972 Score: 458
Period size: 123 Copynumber: 2.5 Consensus size: 122
1660 TAAAAATAAA
*
1670 AAAAAATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-ATT----AAAA
1 AAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAA
*
1729 AAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTCCTTGAAAATCAAAATTTCC
65 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTCCTTGAAAATCAAAATTTCC
* * *
1787 GAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAGATAAATTTTTCAAAAAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTTCAAAAAAA
*
1852 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTCCTTGAAAATCAAAATTTTC
65 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTCCTTGAAAATCAAAATTTCC
* *
1910 AAAAAACTA-TTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAA
1 AAAAAA-TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA
1973 GATTTTTGGG
Statistics
Matches: 167, Mismatches: 11, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
117 47 0.28
118 1 0.01
119 2 0.01
122 11 0.07
123 104 0.62
124 2 0.01
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (122 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAA
AAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTCCTTGAAAATCAAAATTTCC
Found at i:1991 original size:181 final size:182
Alignment explanation
Indices: 1662--2008 Score: 490
Period size: 181 Copynumber: 1.9 Consensus size: 182
1652 TCTTTAAATA
*
1662 AAAATAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTAA
1 AAAATAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTAA
* * * *
1727 AAAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTCCTTGAAAATCAAAATTTCCGAAAA
66 AAAAAAAAGCTTTTTAAGGAAAAGTTGAAAGTATCAATTTCCTTAAAAAT-AAAATTTCCAAAAA
*
1792 ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAGATAAATTTTTC
130 AGATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAGATAAATTTTTC
*
1845 AAAA-AAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTCCTTGAAAATCAAAATT-
1 AAAATAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTA
*** * *
1907 TTCAAAAAA-CTATTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAATTTTCAAA
65 AAAAAAAAAGCT-TTTTAAGGAAAAGTTGAAAGTATCAA-TTTCCTTAAAAATAAAATTTCCAAA
1970 AAAGATTTTT-GGGAAAAAAGTTGAAAGTATCAATTTTCC
128 AAAGATTTTTAGGG--AAAAGTTGAAAGTATCAATTTTCC
2009 CTACACAAGA
Statistics
Matches: 147, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
179 3 0.02
180 19 0.13
181 67 0.46
182 54 0.37
183 4 0.03
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.33
Consensus pattern (182 bp):
AAAATAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTAA
AAAAAAAAGCTTTTTAAGGAAAAGTTGAAAGTATCAATTTCCTTAAAAATAAAATTTCCAAAAAA
GATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAGATAAATTTTTC
Found at i:4282 original size:30 final size:30
Alignment explanation
Indices: 4248--4310 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
4238 CAGTGAGCCT
*
4248 AAAGCATTTCAGAGGATGAATGAGATGATC
1 AAAGCATTTCAGAGGATGAATGAGATAATC
4278 AAAGCATTTCAGAGGATGAATGAGATAATC
1 AAAGCATTTCAGAGGATGAATGAGATAATC
4308 AAA
1 AAA
4311 TTTGATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (30 bp):
AAAGCATTTCAGAGGATGAATGAGATAATC
Found at i:4966 original size:2 final size:2
Alignment explanation
Indices: 4959--4989 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4949 CAAATCGGTT
4959 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 T
4990 TGATTAAAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6352 original size:10 final size:9
Alignment explanation
Indices: 6323--6381 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
6313 CTGCATCATA
6323 ATTAAAATT
1 ATTAAAATT
**
6332 -TTTTAATT
1 ATTAAAATT
6340 ATTAAAATAT
1 ATTAAAAT-T
6350 ATTAAAAATT
1 ATT-AAAATT
*
6360 -TTATAATT
1 ATTAAAATT
6368 ATTTAAAATT
1 A-TTAAAATT
6378 ATTA
1 ATTA
6382 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
8 11 0.28
9 10 0.26
10 13 0.33
11 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATTAAAATT
Found at i:6366 original size:28 final size:28
Alignment explanation
Indices: 6326--6381 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
6316 CATCATAATT
*
6326 AAAATTTTTTAATTA-TTAAAATATATTA
1 AAAATTTTATAATTATTTAAAAT-TATTA
6354 AAAATTTTATAATTATTTAAAATTATTA
1 AAAATTTTATAATTATTTAAAATTATTA
6382 TTTTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
AAAATTTTATAATTATTTAAAATTATTA
Found at i:6382 original size:19 final size:20
Alignment explanation
Indices: 6336--6382 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
6326 AAAATTTTTT
*
6336 AATTATTAAAATATATTAAA
1 AATTATTATAATATATTAAA
*
6356 AATT-TTATAAT-TATTTAA
1 AATTATTATAATATATTAAA
6374 AATTATTAT
1 AATTATTAT
6383 TTTATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.42
19 10 0.42
20 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTATTATAATATATTAAA
Found at i:6557 original size:19 final size:19
Alignment explanation
Indices: 6535--6571 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6525 TTTATATATA
*
6535 ATAGTTTAGTATGAAAAAT
1 ATAGTTTAATATGAAAAAT
*
6554 ATAGTTTAATATTAAAAA
1 ATAGTTTAATATGAAAAA
6572 GATTACAAGT
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:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATAGTTTAATATGAAAAAT
Found at i:8706 original size:21 final size:21
Alignment explanation
Indices: 8682--8737 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
8672 TACATTTTAA
*
8682 AAAATAATA-ATAAATGAAAAT
1 AAAA-AATAGATAAATCAAAAT
8703 AAAAAATAGATAAATCAAAAT
1 AAAAAATAGATAAATCAAAAT
**
8724 AATCAATAGATAAA
1 AAAAAATAGATAAA
8738 AAAAGAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAAAATAGATAAATCAAAAT
Found at i:9444 original size:24 final size:24
Alignment explanation
Indices: 9395--9441 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
9385 GTTTACCCAA
9395 ATGAAATCATAAAATATTATTTTT
1 ATGAAATCATAAAATATTATTTTT
9419 ATGAAATCAT-AAATATTATTTTT
1 ATGAAATCATAAAATATTATTTTT
9442 TATTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
ATGAAATCATAAAATATTATTTTT
Found at i:9453 original size:22 final size:23
Alignment explanation
Indices: 9395--9444 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
9385 GTTTACCCAA
9395 ATGAAATCATAAAATATTA-TTTTT
1 ATGAAAT-AT-AAATATTATTTTTT
9419 ATGAAATCATAAATATTATTTTTT
1 ATGAAAT-ATAAATATTATTTTTT
9443 AT
1 AT
9445 TTAATTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
ATGAAATATAAATATTATTTTTT
Found at i:11827 original size:54 final size:54
Alignment explanation
Indices: 11767--11874 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
11757 AACAACTCAA
* * * *
11767 CTTAAATTTTTATATTTTGTAAT-TGGATATTGATTTAACAAAAATAATTTTTAC
1 CTTAAATTTTTATA-TTTGCAATGTGGACATTAATTTAACAAAAATAATTATTAC
* *
11821 CTTAAATTTTTATATTTGCAATGTGGACATTAATTTAATAAAGATAATTATTAC
1 CTTAAATTTTTATATTTGCAATGTGGACATTAATTTAACAAAAATAATTATTAC
11875 TATTGATGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 7 0.15
54 40 0.85
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.47
Consensus pattern (54 bp):
CTTAAATTTTTATATTTGCAATGTGGACATTAATTTAACAAAAATAATTATTAC
Found at i:15954 original size:61 final size:58
Alignment explanation
Indices: 15793--15975 Score: 161
Period size: 60 Copynumber: 3.1 Consensus size: 58
15783 TTGTACAAGG
* * * * * *
15793 AAATTAATACTTTCAACTTTTCCCCCAAAATGTTTTTTCTTGAAATTTTAATTTCGAGGA
1 AAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAA-TTT-ATTTCAAAGA
* * * ** * *
15853 AAATTTATACTTTCAACTTTTCCTAAAAAAAAAAACTTTTTTAGAAAATTATTTTCAAAGA
1 AAATTAATACTTTCAACTTTTCCT--CAAAAATATTTTTTTTTGAAATTTA-TTTCAAAGA
* * *
15914 AAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTTTTTGAATTTTATTT-AAAGA
1 AAATTAATACTTTCAACTTTTCCTCAAAAA-TATTTTTTTTTGAAATTTATTTCAAAGA
15972 AAAT
1 AAAT
15976 CATATAAAAA
Statistics
Matches: 97, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
58 9 0.09
59 8 0.08
60 35 0.36
61 32 0.33
62 13 0.13
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (58 bp):
AAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTGAAATTTATTTCAAAGA
Found at i:16054 original size:21 final size:22
Alignment explanation
Indices: 16008--16060 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
15998 TAAGGAATAC
** *
16008 TAAATAATTCTAATATAATCAA
1 TAAATAATAATAATATAATAAA
16030 TAAATAATAATAATA-AATAAA
1 TAAATAATAATAATATAATAAA
16051 TAAATAATAA
1 TAAATAATAA
16061 ACCTTTGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATAATAATAATATAATAAA
Found at i:16061 original size:7 final size:7
Alignment explanation
Indices: 16018--16061 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
16008 TAAATAATTC
16018 TAATATAA
1 TAATA-AA
16026 TCAATAAA
1 T-AATAAA
16034 TAAT-AA
1 TAATAAA
16040 TAATAAA
1 TAATAAA
16047 TAAATAAA
1 T-AATAAA
16055 TAATAAA
1 TAATAAA
16062 CCTTTGGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
6 6 0.18
7 12 0.36
8 11 0.33
9 4 0.12
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (7 bp):
TAATAAA
Found at i:16825 original size:24 final size:24
Alignment explanation
Indices: 16808--16919 Score: 77
Period size: 24 Copynumber: 4.4 Consensus size: 24
16798 ATATACATTG
16808 ATAATAAAAA-ATATATATTAATAA
1 ATAATAAAAACATATATA-TAATAA
*
16832 ATAATAAAAACATATATATATTAATAG
1 ATAATAAAAAC--ATATATA-TAATAA
* *
16859 ATAAATAAAAAAAGAT-TAATAGATAA
1 AT-AATAAAAACATATAT-ATA-ATAA
* *
16885 ATAATAATAA-ATATATATTTATAA
1 ATAATAAAAACATATATA-TAATAA
16909 ATAGATAAAAA
1 ATA-ATAAAAA
16920 TAAAAAATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
24 21 0.30
25 18 0.25
26 9 0.13
27 15 0.21
28 8 0.11
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (24 bp):
ATAATAAAAACATATATATAATAA
Found at i:16931 original size:5 final size:6
Alignment explanation
Indices: 16913--16942 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
16903 TTATAAATAG
16913 ATAAAA ATAAAAA ATAAAA ATAAAA ATAAA
1 ATAAAA AT-AAAA ATAAAA ATAAAA ATAAA
16943 CAAATGGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:18399 original size:17 final size:17
Alignment explanation
Indices: 18357--18399 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
18347 ATTTAGTTAT
*
18357 TAATTTTTATATAATAA
1 TAATTTTTATAAAATAA
**
18374 TAAAATTTATAAAATAA
1 TAATTTTTATAAAATAA
*
18391 TCATTTTTA
1 TAATTTTTA
18400 ATTCATAATA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTTTTATAAAATAA
Found at i:18407 original size:22 final size:22
Alignment explanation
Indices: 18377--18419 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18367 ATAATAATAA
* *
18377 AATTTATAAAATAATCATTTTT
1 AATTCATAAAATAATAATTTTT
*
18399 AATTCATAATATAATAATTTT
1 AATTCATAAAATAATAATTTT
18420 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTCATAAAATAATAATTTTT
Found at i:20608 original size:23 final size:23
Alignment explanation
Indices: 20582--20628 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
20572 TAGGTGATCA
*
20582 GAGGGGTGGGGGTAGGGCATGGT
1 GAGGGATGGGGGTAGGGCATGGT
*
20605 GAGGGATGGGTGTAGGGCATGGT
1 GAGGGATGGGGGTAGGGCATGGT
20628 G
1 G
20629 GTAGTGGTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.04, G:0.62, T:0.19
Consensus pattern (23 bp):
GAGGGATGGGGGTAGGGCATGGT
Found at i:20694 original size:21 final size:21
Alignment explanation
Indices: 20671--20740 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
20661 CTTGATTTTT
20671 TTTTTGTTCTTATTTTTGTAT-
1 TTTTTGTT-TTATTTTTGTATA
* *
20692 TTTTTGTTTTATATTTTTTATG
1 TTTTTGTTTTAT-TTTTGTATA
* *
20714 TATTTTGTATTATTTTGGTATA
1 T-TTTTGTTTTATTTTTGTATA
20736 TTTTT
1 TTTTT
20741 TTGTGTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
20 4 0.10
21 19 0.46
22 8 0.20
23 10 0.24
ACGTcount: A:0.14, C:0.01, G:0.10, T:0.74
Consensus pattern (21 bp):
TTTTTGTTTTATTTTTGTATA
Found at i:20723 original size:32 final size:31
Alignment explanation
Indices: 20684--20758 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
20674 TTGTTCTTAT
* *
20684 TTTTGTATTTTTTGTTTTATATTTTTTATGTA
1 TTTTGTATTTTTTGGTATAT-TTTTTTATGTA
*
20716 TTTTGTATTATTTTGGTATATTTTTTTGTGTA
1 TTTTGTATT-TTTTGGTATATTTTTTTATGTA
*
20748 TTTCGTATTTT
1 TTTTGTATTTT
20759 GTATTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 2 0.05
32 27 0.71
33 9 0.24
ACGTcount: A:0.15, C:0.01, G:0.12, T:0.72
Consensus pattern (31 bp):
TTTTGTATTTTTTGGTATATTTTTTTATGTA
Found at i:21289 original size:3 final size:3
Alignment explanation
Indices: 21283--21332 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
21273 CCAGTTTTTT
* *
21283 TTA TTA TTTA TTTA TTTA TTA TTA TTA TTG TTA TTA TTG TTA TTA TTA
1 TTA TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21331 TT
1 TT
21333 TATTGATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 31 0.74
4 11 0.26
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:21373 original size:5 final size:5
Alignment explanation
Indices: 21363--21406 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
21353 GTTTAATACT
*
21363 TTTTA TTTTA TTTTA TTTTTA TTTTA TTTT- TTTAA TTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
21407 CTTTAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 3 0.09
5 27 0.77
6 5 0.14
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:21382 original size:11 final size:11
Alignment explanation
Indices: 21363--21393 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
21353 GTTTAATACT
21363 TTTTA-TTTTA
1 TTTTATTTTTA
21373 TTTTATTTTTA
1 TTTTATTTTTA
21384 TTTTATTTTT
1 TTTTATTTTT
21394 TTAATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:21406 original size:11 final size:11
Alignment explanation
Indices: 21362--21406 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
21352 TGTTTAATAC
*
21362 TTTTTATTTTA
1 TTTTAATTTTA
*
21373 TTTTATTTTTA
1 TTTTAATTTTA
21384 TTTT-A-TTT-
1 TTTTAATTTTA
21392 TTTTAATTTTA
1 TTTTAATTTTA
21403 TTTT
1 TTTT
21407 CTTTAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
8 4 0.14
9 4 0.14
10 3 0.11
11 17 0.61
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTAATTTTA
Found at i:21595 original size:30 final size:29
Alignment explanation
Indices: 21505--21595 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 29
21495 TTTTGAGGAA
*
21505 AAGTTGAAAGTATCAATTTTTCTTAAAAAT
1 AAGTTGAAAATATCAA-TTTTCTTAAAAAT
* * *
21535 AAGTTTCTAAAATAT--A-TTT-TGAAGAA-
1 AAG-TT-GAAAATATCAATTTTCTTAAAAAT
21561 AAGTTGAAAATATCAATTTTCCTTAAAAAT
1 AAGTTGAAAATATCAATTTT-CTTAAAAAT
21591 AAGTT
1 AAGTT
21596 TCAAAAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
24 7 0.15
25 2 0.04
26 4 0.09
27 8 0.17
28 3 0.07
29 5 0.11
30 9 0.20
31 2 0.04
32 6 0.13
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (29 bp):
AAGTTGAAAATATCAATTTTCTTAAAAAT
Found at i:21637 original size:56 final size:56
Alignment explanation
Indices: 21433--21640 Score: 290
Period size: 56 Copynumber: 3.6 Consensus size: 56
21423 AAATATATAT
* *
21433 TTTTGAAGAAAAGTTGAAAGTATCAATTTTTCCTTGAAAATAAGTTTTTCAAAAAAAAATA
1 TTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTAAAAATAAG--TTTC--AAAAAAATA
* * *
21494 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTCTAAAATATA
1 -TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTCAAAAAAATA
* *
21551 TTTTGAAGAAAAGTTGAAAATATCAATTTTCCTTAAAAATAAGTTTCAAAAAAATA
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTCAAAAAAATA
*
21607 TTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
21641 GTAACAAAAG
Statistics
Matches: 133, Mismatches: 13, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
56 82 0.62
57 7 0.05
59 4 0.03
61 15 0.11
62 25 0.19
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (56 bp):
TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTCAAAAAAATA
Done.