Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167920.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_184, 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: 56251
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Found at i:1651 original size:483 final size:474
Alignment explanation
Indices: 745--2438 Score: 1986
Period size: 483 Copynumber: 3.5 Consensus size: 474
735 AAGTAAGTTT
* * * * * * *
745 AAAATCATTCATAACTTATATTTTACACTATAAAAAATTAAAACCAATGCAAATTATCATATTTC
1 AAAATCCTTCATAACTTACACTTAACACTATGAAAAATTAAAACCAATGCAAGTTATCATGTTTC
* * * * * * *
810 TATATTTGAGCAAGTTTAAAACTTTAGATTCAAGATATTCATTTCCATTTAAAAACTTGTTAGAA
66 TGTGTTTGAGCAAGTTTAAAACATTGGATTCAAGATATTCATTTCCACTTAAAAACTTGCTAAAA
* * * * * * * *
875 TAACATTTCATACTTCTAATGCTCAACTCCCA-CAGAAATGGTTTTCAATGCAAAACATAAAAGC
131 CAATATTTCATACTTTTAAAGCTCAACT-CCAGCAAAAATGATTTTCAAAGCAAAACATAAAAGA
* * * *
939 TT-AAAAACCATTGAGCTTTGAGTTTGTACATAATATGTAAAAACAAGTTAGTACACAATCGCAT
195 TTCAAAAA-CATTGAGCTTTGAGTTTGTGCATAATATATAAAAACAAGTTAGCACACAATCACAT
* * *
1003 CAAGCACCAATAACGATTTGACAAATGTCATCCAAATATCAACACCA-T-TC-CACAAATTCCCT
259 CAAGCACCAATAACGATTTCACAAATGACATCCAAATATC-ACA-TAGTATCTCACAAATTCCCT
* *
1065 AGAGCATTCATTAATCATCCTAAAAATGCATCTAAAGCAAATGAGTATGAAAAATTAAAATCATG
322 -GAGCATTCATGAATCCTCCTAAAAATGCATCTAAAGCAAATGAGTATGAAAAATTAAAATCATG
* * * * * * *
1130 CAAACGGGTTTTATATCGCAATTTGAAAATGTGCATATGGTTTTGAAGCCCATAATTATTCAAAA
386 CAAA-TGTTTTTATATCACAATTTGAAATTGTGCATATGATTTTGATGCCCATAATTATTCAGAA
*
1195 ATGAAATTTTGATATTTTAAGCTCC
450 ACGAAATTTTGATATTTTAAGCTCC
*
1220 AAAATCCTTCATAACTTACACTTAATACTATGAAAAATTAAAACCAATGCAAGTTATCATGTTTC
1 AAAATCCTTCATAACTTACACTTAACACTATGAAAAATTAAAACCAATGCAAGTTATCATGTTTC
* * * * *
1285 TGTGTTTCAGCAAATTTAAAACATTGGATTTAAGATATTCATTTTCACGTAAAAACTTGCTAAAA
66 TGTGTTTGAGCAAGTTTAAAACATTGGATTCAAGATATTCATTTCCACTTAAAAACTTGCTAAAA
* * *
1350 CAATATTTTGATGCTTTTAAAGCTCGACTCCAGCAAAAATGATTTTCAAAGCAAAACATAAAAGA
131 CAATA-TTTCATACTTTTAAAGCTCAACTCCAGCAAAAATGATTTTCAAAGCAAAACATAAAAGA
*
1415 TTCAAAAACATTGATCTTTGAGTTTGTGCATAATATATAAAAACAAGTTAGCACACAATTATTCA
195 TTCAAAAACATTGAGCTTTGAGTTTGTGCATAATATATAAAAACAAGTTAGCACAC-A--A-TCA
*
1480 CATCAAACACCAATAACGATCTT-ACAAATGACAT-CAAACTATCAGCAGTAGTATCTCACAAAT
256 CATCAAGCACCAATAACGAT-TTCACAAATGACATCCAAA-TATCA-CA-TAGTATCTCACAAAT
* * * *
1543 TTCTTGGAGCATTGATGAATCCTCCTAAAAATTCATCTAAAGCAAATGAGTATGAAAAATTAAAA
317 TCCCT-GAGCATTCATGAATCCTCCTAAAAATGCATCTAAAGCAAATGAGTATGAAAAATTAAAA
* * * *
1608 TTGA-GCAAATAGTTTTTATATCACAATTTGAAATTGCGCATATGATTTTTG-TGCTCATAATTG
381 -TCATGCAAAT-GTTTTTATATCACAATTTGAAATTGTGCATATGA-TTTTGATGCCCATAATTA
*
1671 TTTAGAAACGAAATTTTGATATTTTAAGCTCC
443 TTCAGAAACGAAATTTTGATATTTTAAGCTCC
* * * *
1703 AAAATCTTTCATAACTTACACTTAACA-T-TGTAAAATATAAAAACCAATACAAGTTGTCATGTT
1 AAAATCCTTCATAACTTACACTTAACACTATG-AAAA-ATTAAAACCAATGCAAGTTATCATGTT
* * *
1766 TCTGTGTTTGAGCAAGTTTAAAACATTGGATTCAAAATATTCATTTTC-TTCTAAAAACTTGCTA
64 TCTGTGTTTGAGCAAGTTTAAAACATTGGATTCAAGATATTCATTTCCACT-TAAAAACTTGCTA
* * * ** * *
1830 AAATAATATTTCATACTTTTAAAACTTAACTTTAGCAAAAATGGTTTTCAAAGCTAAACATAAAA
128 AAACAATATTTCATACTTTTAAAGCTCAACTCCAGCAAAAATGATTTTCAAAGCAAAACATAAAA
* * *
1895 GCTTCAAAAGCATTGAGCTTTGAGTTTGTGCATAATATATAAAAAATTAAGTTAG----CAATCA
193 GATTCAAAAACATTGAGCTTTGAGTTTGTGCATAATATAT-AAAAA-CAAGTTAGCACACAATCA
* * * *
1956 CATCAAGCACCAATAAAGATTTCATAAATGGCATCCAAATATCAC-TAGCATCTCACAAATTCCC
256 CATCAAGCACCAATAACGATTTCACAAATGACATCCAAATATCACATAGTATCTCACAAATTCCC
* * * * *
2020 TAACGCATTCATGAATTCTCCTAAAAATGCATCTAAAGCAAATAAGGATAAAAAATTAAAATCAT
321 TGA-GCATTCATGAATCCTCCTAAAAATGCATCTAAAGCAAATGAGTATGAAAAATTAAAATCAT
* * * * *
2085 GCAAATGATTTTTA-ATCACTATTTGAAGTTGTGCAGATGATTTTTATGCCCGTAATTATTCAGA
385 GCAAATG-TTTTTATATCACAATTTGAAATTGTGCATATGATTTTGATGCCCATAATTATTCAGA
*
2149 AACGAAATTTTGATATTTTAAGCTCA
449 AACGAAATTTTGATATTTTAAGCTCC
* * * *
2175 AAAATTCTTCATAACTTACACTTAACACTGTGAAAAATTAAAATCAATGTAAGTTATCATGTTTT
1 AAAATCCTTCATAACTTACACTTAACACTATGAAAAATTAAAACCAATGCAAGTTATCATG---T
* * *
2240 TATCATGTTTTTGTGTTTAAACAAGTTTAAAACATTGGATTCAAGATATTCATTTCCATTTAAAA
63 T-TC-------TGTGTTTGAGCAAGTTTAAAACATTGGATTCAAGATATTCATTTCCACTTAAAA
* * * *
2305 TCTTGCTAAAACAATATTTCATACTTTTAAAGCTCGACTCCAGCAGAAATGATTTTTAAAGCAAA
120 ACTTGCTAAAACAATATTTCATACTTTTAAAGCTCAACTCCAGCAAAAATGATTTTCAAAGCAAA
*
2370 ACATAAAA-ACTTCAAAAATATTGAGCTTTGAGTTTGTGCATAATATATAAAAACAAGTTAGCAC
185 ACATAAAAGA-TTCAAAAACATTGAGCTTTGAGTTTGTGCATAATATATAAAAACAAGTTAGCAC
2434 ACAAT
249 ACAAT
2439 TATACAATAC
Statistics
Matches: 1037, Mismatches: 136, Indels: 82
0.83 0.11 0.07
Matches are distributed among these distances:
471 4 0.00
472 110 0.11
473 85 0.08
474 2 0.00
475 121 0.12
476 129 0.12
477 11 0.01
479 7 0.01
480 39 0.04
481 12 0.01
482 97 0.09
483 400 0.39
484 16 0.02
485 4 0.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (474 bp):
AAAATCCTTCATAACTTACACTTAACACTATGAAAAATTAAAACCAATGCAAGTTATCATGTTTC
TGTGTTTGAGCAAGTTTAAAACATTGGATTCAAGATATTCATTTCCACTTAAAAACTTGCTAAAA
CAATATTTCATACTTTTAAAGCTCAACTCCAGCAAAAATGATTTTCAAAGCAAAACATAAAAGAT
TCAAAAACATTGAGCTTTGAGTTTGTGCATAATATATAAAAACAAGTTAGCACACAATCACATCA
AGCACCAATAACGATTTCACAAATGACATCCAAATATCACATAGTATCTCACAAATTCCCTGAGC
ATTCATGAATCCTCCTAAAAATGCATCTAAAGCAAATGAGTATGAAAAATTAAAATCATGCAAAT
GTTTTTATATCACAATTTGAAATTGTGCATATGATTTTGATGCCCATAATTATTCAGAAACGAAA
TTTTGATATTTTAAGCTCC
Found at i:3314 original size:31 final size:28
Alignment explanation
Indices: 3279--3335 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
3269 GAGCTGAGTT
*
3279 TCGAGCCTTGAATTTTGAATCGAGCTCAAGC
1 TCGAG-CTTG-ATATTGAATCG-GCTCAAGC
*
3310 TCGAGCTTGATATTGTATCGGCTCAA
1 TCGAGCTTGATATTGAATCGGCTCAA
3336 ATTCGACCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.25
29 9 0.38
30 4 0.17
31 5 0.21
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (28 bp):
TCGAGCTTGATATTGAATCGGCTCAAGC
Found at i:3341 original size:28 final size:31
Alignment explanation
Indices: 3278--3341 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 31
3268 CGAGCTGAGT
* *
3278 TTCGAGCCTTGAATTTTGAATCGAGCTCAAG
1 TTCGAGCCTTGAATATTGAATCGAGCTCAAA
* *
3309 CTCGAG-CTTG-ATATTGTATCG-GCTCAAA
1 TTCGAGCCTTGAATATTGAATCGAGCTCAAA
3337 TTCGA
1 TTCGA
3342 CCGATTACAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 10 0.36
29 9 0.32
30 4 0.14
31 5 0.18
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (31 bp):
TTCGAGCCTTGAATATTGAATCGAGCTCAAA
Found at i:6584 original size:16 final size:16
Alignment explanation
Indices: 6565--6597 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6555 AACTGTAAAT
6565 AAAAAAACTCACAAAG
1 AAAAAAACTCACAAAG
*
6581 AAAACAACTCACAAAG
1 AAAAAAACTCACAAAG
6597 A
1 A
6598 TTTGAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.21, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAAAAACTCACAAAG
Found at i:8480 original size:2 final size:2
Alignment explanation
Indices: 8473--8503 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
8463 TAGAAATGAG
*
8473 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8504 AACTTAAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:9404 original size:14 final size:14
Alignment explanation
Indices: 9374--9417 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
9364 AAAAATTTTA
*
9374 AAAAATCAAA-ATC
1 AAAAGTCAAAGATC
*
9387 AAAAGTCAAAGATT
1 AAAAGTCAAAGATC
*
9401 AAAAGTCAAAGGTC
1 AAAAGTCAAAGATC
9415 AAA
1 AAA
9418 GGGATTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.16
Consensus pattern (14 bp):
AAAAGTCAAAGATC
Found at i:31040 original size:12 final size:12
Alignment explanation
Indices: 31008--31042 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
30998 ACATAATATT
31008 ATTATATAATTAA
1 ATTATATAA-TAA
31021 ATTA-ATAATAA
1 ATTATATAATAA
31032 ATTATATAATA
1 ATTATATAATA
31043 TTTATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.33
12 10 0.48
13 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTATATAATAA
Found at i:31058 original size:17 final size:17
Alignment explanation
Indices: 31036--31079 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
31026 TAATAAATTA
*
31036 TATAATATTTA-TTATAT
1 TATAATATATATTTA-AT
*
31053 TATAATAAATATTTAAT
1 TATAATATATATTTAAT
31070 TATAATATAT
1 TATAATATAT
31080 CATATAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAATATATATTTAAT
Found at i:31109 original size:24 final size:26
Alignment explanation
Indices: 31048--31113 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
31038 TAATATTTAT
31048 TATATTATAAT-AAATATTTAATTATAA
1 TATATTATAATGAAATA--TAATTATAA
31075 TATATCATATAATGAAATA-AATTA-AA
1 TATAT--TATAATGAAATATAATTATAA
31101 TATATTATAATGA
1 TATATTATAATGA
31114 TAAACATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
24 8 0.22
26 7 0.19
27 10 0.28
29 6 0.17
30 5 0.14
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (26 bp):
TATATTATAATGAAATATAATTATAA
Found at i:31990 original size:17 final size:18
Alignment explanation
Indices: 31968--32008 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
31958 TTAATTAAAC
*
31968 TAATATTATTTAT-TTAT
1 TAATATTATTAATCTTAT
31985 TAATATTATTAATCCTTAT
1 TAATATTATTAAT-CTTAT
32004 TAATA
1 TAATA
32009 ATGATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
19 9 0.43
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATATTATTAATCTTAT
Found at i:32055 original size:16 final size:17
Alignment explanation
Indices: 32034--32065 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
32024 TAATCAATTG
32034 TTATATATAT-ACATAA
1 TTATATATATAACATAA
32050 TTATATATATAACATA
1 TTATATATATAACATA
32066 TGCTTCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATATATATAACATAA
Found at i:32542 original size:15 final size:14
Alignment explanation
Indices: 32492--32561 Score: 70
Period size: 15 Copynumber: 4.8 Consensus size: 14
32482 ATTAAACTAA
*
32492 TATATAAATATAAT
1 TATATATATATAAT
*
32506 TA-ATATACTATAGT
1 TATATATA-TATAAT
32520 TATAATATATATAAT
1 TAT-ATATATATAAT
*
32535 TAATATATATATAAC
1 T-ATATATATATAAT
32550 TATATATGATAT
1 TATATAT-ATAT
32562 TACAATGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
13 4 0.09
14 15 0.32
15 21 0.45
16 7 0.15
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (14 bp):
TATATATATATAAT
Found at i:32556 original size:29 final size:30
Alignment explanation
Indices: 32489--32561 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
32479 TGTATTAAAC
*
32489 TAATATATAAATATAATTAATATACTATAG
1 TAATATATATATATAATTAATATACTATAG
*
32519 TTATA-ATATATATAATTAATATA-TATA-
1 TAATATATATATATAATTAATATACTATAG
32546 TAACTATATATGATAT
1 TAA-TATATAT-ATAT
32562 TACAATGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 2 0.05
28 6 0.16
29 21 0.57
30 8 0.22
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (30 bp):
TAATATATATATATAATTAATATACTATAG
Found at i:32681 original size:6 final size:6
Alignment explanation
Indices: 32658--32695 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
32648 GTTTAAATCA
*
32658 TAATAT TAATAA TAATAT TAATAT TAGAT-T TAATAT TA
1 TAATAT TAATAT TAATAT TAATAT TA-ATAT TAATAT TA
32696 TTTAAACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 2 0.07
6 24 0.86
7 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
TAATAT
Found at i:32981 original size:20 final size:20
Alignment explanation
Indices: 32950--33006 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 20
32940 TATTCTATTA
32950 AATA-AATT-ATTATAATAT
1 AATATAATTAATTATAATAT
32968 AATATAATTAATTA-AAT-T
1 AATATAATTAATTATAATAT
*
32986 -ATTTAA-TAATTAATAATAT
1 AATATAATTAATT-ATAATAT
33005 AA
1 AA
33007 CATTTTTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 5 0.16
17 6 0.19
18 8 0.25
19 8 0.25
20 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATAATTAATTATAATAT
Found at i:33080 original size:19 final size:20
Alignment explanation
Indices: 33044--33086 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
33034 TACTAATAGC
33044 ATTTTAAATTAATAACAATT
1 ATTTTAAATTAATAACAATT
*
33064 ATTTTAAA-TATTAACAATT
1 ATTTTAAATTAATAACAATT
33083 ATTT
1 ATTT
33087 ATATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTAAATTAATAACAATT
Found at i:33304 original size:27 final size:28
Alignment explanation
Indices: 33248--33365 Score: 81
Period size: 27 Copynumber: 4.3 Consensus size: 28
33238 ATTCAGCCAT
* * *
33248 TATTATTAATAT-TAATAAT-TCAATAT
1 TATTATTAAAATATAATAATATTAATAA
33274 TATTATTAAAATATAATAATATTAA-AA
1 TATTATTAAAATATAATAATATTAATAA
*
33301 TATTAAGTT-AAATA-ATTAATAATTAAT--
1 TATT-A-TTAAAATATAATAAT-ATTAATAA
*
33328 TATT-TTAATTAATAAAATAATATTAAATAA
1 TATTATTAA--AATATAATAATATT-AATAA
33358 TATTATTA
1 TATTATTA
33366 GTAATATTAA
Statistics
Matches: 73, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
24 2 0.03
25 1 0.01
26 11 0.15
27 28 0.38
28 22 0.30
29 2 0.03
30 4 0.05
31 3 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TATTATTAAAATATAATAATATTAATAA
Found at i:33313 original size:28 final size:26
Alignment explanation
Indices: 33274--33354 Score: 67
Period size: 28 Copynumber: 3.0 Consensus size: 26
33264 AATTCAATAT
33274 TATT-ATTAAAATATAATAATATTAAAA
1 TATTAATT-AAATA-AATAATATTAAAA
* *
33301 TATTAAGTTAAATAATTAATAATTAATTA
1 TATTAA-TTAAATAAATAAT-ATTAA-AA
*
33330 TTTTAATT-AATAAAATAATATTAAA
1 TATTAATTAAAT-AAATAATATTAAA
33355 TAATATTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
27 17 0.39
28 19 0.43
29 8 0.18
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (26 bp):
TATTAATTAAATAAATAATATTAAAA
Found at i:33600 original size:26 final size:24
Alignment explanation
Indices: 33551--33607 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
33541 TTACCAAACC
33551 ATTATAATATAATTCATAATTTATT
1 ATTATAATATAATTCATAATTTA-T
33576 ATTTATAATATAATAT-ATAGA-TTAT
1 A-TTATAATATAAT-TCATA-ATTTAT
33601 ATTATAA
1 ATTATAA
33608 ATCACAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 6 0.21
25 3 0.10
26 18 0.62
27 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTATAATATAATTCATAATTTAT
Found at i:33833 original size:22 final size:22
Alignment explanation
Indices: 33803--33847 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
33793 ATAGATTAAC
* **
33803 TAAATTATATTTTTAAATATAA
1 TAAAATATATTTAAAAATATAA
33825 TAAAATATATTTAAAAATATAA
1 TAAAATATATTTAAAAATATAA
33847 T
1 T
33848 TATTATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAAATATATTTAAAAATATAA
Found at i:33862 original size:50 final size:47
Alignment explanation
Indices: 33797--33922 Score: 123
Period size: 50 Copynumber: 2.6 Consensus size: 47
33787 ACTATAATAG
*
33797 ATTAACTAAATTATATTTTTAAATATAATAAAATATATTTAAAAATATA
1 ATTAA-TAAAATATATTTTTAAATATAATAAAATAT-TTTAAAAATATA
* * * **
33846 ATTATTATAAAATATATTTTTATAATTTACTAATATATTTTAATTATATA
1 ATTA--ATAAAATATATTTTTA-AATATAATAAAATATTTTAAAAATATA
*
33896 ATTAAT-AAATA-ATTTATAAATA-AATAA
1 ATTAATAAAATATATTTTTAAATATAATAA
33923 TTTTTATTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
44 4 0.06
45 3 0.05
46 6 0.09
47 5 0.08
48 2 0.03
49 4 0.06
50 28 0.43
51 13 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (47 bp):
ATTAATAAAATATATTTTTAAATATAATAAAATATTTTAAAAATATA
Found at i:33870 original size:15 final size:15
Alignment explanation
Indices: 33824--33870 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
33814 TTTAAATATA
33824 ATAAAATATA--TTT
1 ATAAAATATATTTTT
*
33837 A-AAAATATAATTATT
1 ATAAAATAT-ATTTTT
33852 ATAAAATATATTTTT
1 ATAAAATATATTTTT
33867 ATAA
1 ATAA
33871 TTTACTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 7 0.25
13 2 0.07
15 12 0.43
16 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAAATATATTTTT
Found at i:34001 original size:21 final size:23
Alignment explanation
Indices: 33956--34008 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
33946 AATGATTAAC
*
33956 TTATAATTATATATAATACTATA
1 TTATAATTATATATAATAATATA
*
33979 TTATAATTATA-ATATTAAT-TA
1 TTATAATTATATATAATAATATA
*
34000 TTGTAATTA
1 TTATAATTA
34009 ATAAAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATAATTATATATAATAATATA
Found at i:34108 original size:37 final size:36
Alignment explanation
Indices: 34067--34148 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 36
34057 TGTTATAGGT
* *
34067 TATATATTAATA-TAATTATATT-AGATAATATAATTTA
1 TATATATTAAAATTAATTA-ATTCA-AT-ATATAATTAA
34104 TATATATTTAAAATTAATTAATTCAATATATAATTAA
1 TATATA-TTAAAATTAATTAATTCAATATATAATTAA
34141 TAT-TATTA
1 TATATATTA
34149 TAACTAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
35 3 0.08
36 2 0.05
37 18 0.45
38 10 0.25
39 7 0.17
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (36 bp):
TATATATTAAAATTAATTAATTCAATATATAATTAA
Found at i:34121 original size:26 final size:27
Alignment explanation
Indices: 34092--34151 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
34082 TTATATTAGA
* *
34092 TAATATAATT-TATATATATTTAAAAT
1 TAATATAATTCAATATATAATTAAAAT
*
34118 TAAT-TAATTCAATATATAATTAATAT
1 TAATATAATTCAATATATAATTAAAAT
*
34144 TATTATAA
1 TAATATAA
34152 CTAAATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 5 0.18
26 20 0.71
27 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
TAATATAATTCAATATATAATTAAAAT
Found at i:34365 original size:16 final size:16
Alignment explanation
Indices: 34346--34380 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34336 TAAATGTTCA
34346 AATAATAATATTA-TTT
1 AATAATAAT-TTAGTTT
34362 AATAATAATTTAGTTT
1 AATAATAATTTAGTTT
34378 AAT
1 AAT
34381 TATTATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
AATAATAATTTAGTTT
Found at i:35190 original size:16 final size:16
Alignment explanation
Indices: 35139--35197 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
35129 AAATTATTTT
35139 AATATTTAA-AATATTA
1 AATATTTAATAATA-TA
*
35155 AATATGTTATTAATAT-
1 AATAT-TTAATAATATA
35171 AATATTTAATAATATA
1 AATATTTAATAATATA
*
35187 AATAGTTAATA
1 AATATTTAATA
35198 TATTAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 9 0.24
16 20 0.54
17 4 0.11
18 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AATATTTAATAATATA
Found at i:35204 original size:16 final size:16
Alignment explanation
Indices: 35139--35205 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
35129 AAATTATTTT
* *
35139 AATATTTAAAATATTA
1 AATAGTTAATATATTA
*
35155 AATATGTT-AT-TAATA
1 AATA-GTTAATATATTA
*
35170 TAATATTTAATA-ATATA
1 -AATAGTTAATATAT-TA
35187 AATAGTTAATATATTA
1 AATAGTTAATATATTA
35203 AAT
1 AAT
35206 TTCAATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
15 6 0.15
16 27 0.69
17 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AATAGTTAATATATTA
Found at i:35639 original size:24 final size:24
Alignment explanation
Indices: 35599--35656 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
35589 ATTAGCTATT
*
35599 TTATTATATAATTTAATCAAA-TTA
1 TTATTAT-TAATTTAATAAAATTTA
*
35623 TTATTATTAGTTATAATAAAATTTA
1 TTATTATTAATT-TAATAAAATTTA
35648 TTATATATT
1 TTAT-TATT
35657 TTTCAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.14
24 14 0.48
25 7 0.24
26 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTATTATTAATTTAATAAAATTTA
Found at i:35769 original size:22 final size:22
Alignment explanation
Indices: 35743--35809 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 22
35733 AGAATATAAT
*
35743 TAATTATTAATTATTAATAAAA
1 TAATTATTAATAATTAATAAAA
35765 TAATTAATTGAAATAATT-ATAAAA
1 TAATT-ATT--AATAATTAATAAAA
35789 TAA-TATTTAATAAATTAATAA
1 TAATTA-TTAAT-AATTAATAA
35810 CAATTATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 3 0.08
22 10 0.26
23 10 0.26
24 9 0.24
25 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (22 bp):
TAATTATTAATAATTAATAAAA
Found at i:36313 original size:19 final size:17
Alignment explanation
Indices: 36291--36342 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 17
36281 ATTAAATTAT
36291 TTATTATTAATTAGTATAA
1 TTATTATTAATTA--ATAA
*
36310 TTATAATTAATTAATAA
1 TTATTATTAATTAATAA
*
36327 ATA-TATTAATT-ATAA
1 TTATTATTAATTAATAA
36342 T
1 T
36343 ATACTTTAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.14
16 7 0.24
17 6 0.21
19 12 0.41
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TTATTATTAATTAATAA
Found at i:36575 original size:25 final size:24
Alignment explanation
Indices: 36546--36617 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
36536 TTAACTTGTT
36546 TATTTATTATAATATAATA-ACTAGA
1 TATTTATTATAA-ATAATATACTA-A
*
36571 TATTT-TATATAACATAATATATTAA
1 TATTTAT-TATAA-ATAATATACTAA
*
36596 TATATATTATAAATAATTATAC
1 TATTTATTATAAATAA-TATAC
36618 AATTGTCACT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 5 0.13
25 30 0.77
26 4 0.10
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (24 bp):
TATTTATTATAAATAATATACTAA
Done.