Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168113.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_358, 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: 31741
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:150 original size:42 final size:42
Alignment explanation
Indices: 1--352 Score: 563
Period size: 40 Copynumber: 8.7 Consensus size: 42
1 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CA
1 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
42 AAGTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
1 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
82 AAGTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
1 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
*
122 AAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTT-CA
1 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
163 AAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
1 AAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
204 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-C-
1 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
244 AAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
1 AAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
285 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCCAA
1 AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCC-A
327 AAGTCGTGGTG--TCTGTTTAGAGGAGC
1 AAGTCGTGGTGCCTCTGTTTAGAGGAGC
353 TTTATCAAAC
Statistics
Matches: 296, Mismatches: 2, Indels: 27
0.91 0.01 0.08
Matches are distributed among these distances:
39 60 0.20
40 105 0.35
41 30 0.10
42 101 0.34
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCA
Found at i:295 original size:81 final size:82
Alignment explanation
Indices: 10--352 Score: 581
Period size: 82 Copynumber: 4.2 Consensus size: 82
1 AAGTCGTGG
10 TGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGT--TGCCTCTGTTTAGAGGAGCAATT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATT
72 TACTTTTCCAAAG-TCGT
66 TACTTTT-CAAAGTTCGT
*
89 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATT
154 TACTTTTCAAAGTTCGT
66 TACTTTTCAAAGTTCGT
171 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATT
236 TACTTTTC-AAGTTCGT
66 TACTTTTCAAAGTTCGT
252 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATT
1 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATT
*
317 TACTTTCCAAAAG-TCGT
66 TACTTTTC-AAAGTTCGT
* **
334 GGTGTCTGTTTAGAGGAGC
1 TGCCTCTGTTTAGAGGAGC
353 TTTATCAAAC
Statistics
Matches: 252, Mismatches: 6, Indels: 9
0.94 0.02 0.03
Matches are distributed among these distances:
79 30 0.12
80 9 0.04
81 85 0.34
82 125 0.50
83 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (82 bp):
TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATT
TACTTTTCAAAGTTCGT
Found at i:369 original size:6 final size:6
Alignment explanation
Indices: 359--408 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
349 GAGCTTTATC
* * *
359 AAACAC AAACAA AAAAAA AAACAA AAACAA AAA-AA CAAA-AA AACCAA
1 AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA -AAACAA AAACAA
406 AAA
1 AAA
409 ATGTTGAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:386 original size:18 final size:18
Alignment explanation
Indices: 359--409 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
349 GAGCTTTATC
*
359 AAACACAAACAAAAAAAA
1 AAACAAAAACAAAAAAAA
*
377 AAACAAAAACAAAAAAAC
1 AAACAAAAACAAAAAAAA
*
395 AAA-AAAACCAAAAAA
1 AAACAAAAACAAAAAA
410 TGTTGAGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 11 0.37
18 19 0.63
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (18 bp):
AAACAAAAACAAAAAAAA
Found at i:390 original size:16 final size:17
Alignment explanation
Indices: 368--409 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
358 CAAACACAAA
* *
368 CAAAAAAAAAAACAAAAA
1 CAAAAAAACAAA-AAAAC
386 CAAAAAAACAAAAAAAC
1 CAAAAAAACAAAAAAAC
403 CAAAAAA
1 CAAAAAA
410 TGTTGAGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (17 bp):
CAAAAAAACAAAAAAAC
Found at i:392 original size:8 final size:8
Alignment explanation
Indices: 363--409 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
353 TTTATCAAAC
363 ACAAACAAA
1 ACAAA-AAA
372 A-AAAAAA
1 ACAAAAAA
379 AC--AAAA
1 ACAAAAAA
385 ACAAAAAA
1 ACAAAAAA
393 ACAAAAAA
1 ACAAAAAA
*
401 ACCAAAAA
1 ACAAAAAA
409 A
1 A
410 TGTTGAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
6 6 0.18
7 4 0.12
8 23 0.68
9 1 0.03
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (8 bp):
ACAAAAAA
Found at i:621 original size:16 final size:19
Alignment explanation
Indices: 600--648 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
590 TTTTATGTAT
600 TGTATTATTTATT-AT-TA
1 TGTATTATTTATTAATATA
*
617 T-TATTATGTATTAATATA
1 TGTATTATTTATTAATATA
635 TGTATATATTTATT
1 TGTAT-TATTTATT
649 TATTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.38
17 3 0.12
18 3 0.12
19 3 0.12
20 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TGTATTATTTATTAATATA
Found at i:684 original size:68 final size:63
Alignment explanation
Indices: 604--798 Score: 166
Period size: 69 Copynumber: 2.9 Consensus size: 63
594 ATGTATTGTA
604 TTATTTA--TTATTATTATTATGTATTAATATATGTATATATTTATTTATTTTTTTTTTGTTATA
1 TTATTTATTTTATTATTATTAT-TATTAATATATGTATATATTTATTTATTTTTTTTTT-TTAT-
667 T
63 T
* *
668 TTATGTGTATTTTATTATTTATGTATTATTACTAATATGTATATATATA-TTATTTTTATCTTTT
1 TTAT-T-TATTTTATTA-TTAT-TATTATTAAT-ATATGTATATATTTATTTATTTTT-T-TTTT
732 TTATT
59 TTATT
* * * *
737 TTATTTATTTT-TGTATT-TTACTTATCTAATTATATATATGATATTTTTTTATTATTATTTTT
1 TTATTTATTTTAT-TATTATTA-TTAT-TAA-TATATGTAT-ATATTTATTTATTTTTTTTTTT
799 ATCCTATAAT
Statistics
Matches: 108, Mismatches: 8, Indels: 28
0.75 0.06 0.19
Matches are distributed among these distances:
64 6 0.06
65 6 0.06
66 19 0.18
67 14 0.13
68 14 0.13
69 23 0.21
70 22 0.20
71 4 0.04
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (63 bp):
TTATTTATTTTATTATTATTATTATTAATATATGTATATATTTATTTATTTTTTTTTTTTATT
Found at i:694 original size:16 final size:16
Alignment explanation
Indices: 591--694 Score: 51
Period size: 16 Copynumber: 6.6 Consensus size: 16
581 TCTTTTGTAT
*
591 TTTATGTATTGTATTA
1 TTTATGTATTTTATTA
607 TTTAT-TA--TTATTA
1 TTTATGTATTTTATTA
*
620 -TTATGTA-TTAATATA
1 TTTATGTATTTTAT-TA
* *
635 TGTATATA-TTTATTTA
1 TTTATGTATTTTA-TTA
* * *
651 TTTTTTTTTTGTTA-TA
1 TTTATGTATT-TTATTA
667 TTTATGTGTATTTTATTA
1 TTTA--TGTATTTTATTA
685 TTTATGTATT
1 TTTATGTATT
695 ATTACTAATA
Statistics
Matches: 66, Mismatches: 12, Indels: 20
0.67 0.12 0.20
Matches are distributed among these distances:
12 4 0.06
13 7 0.11
14 3 0.05
15 4 0.06
16 30 0.45
17 5 0.08
18 13 0.20
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (16 bp):
TTTATGTATTTTATTA
Found at i:753 original size:17 final size:18
Alignment explanation
Indices: 722--763 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
712 ATATATTATT
*
722 TTTATCTTTTTTATTTTA
1 TTTATCTTTTGTATTTTA
740 TTTAT-TTTTGTATTTTA
1 TTTATCTTTTGTATTTTA
*
757 CTTATCT
1 TTTATCT
764 AATTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTATCTTTTGTATTTTA
Found at i:1280 original size:19 final size:20
Alignment explanation
Indices: 1256--1297 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1246 GGCCAATTTT
*
1256 CGGTGA-AATTTCCAGATTC
1 CGGTGACAATTTCCAGAATC
*
1275 CGGTGACATTTTCCAGAATC
1 CGGTGACAATTTCCAGAATC
1295 CGG
1 CGG
1298 CACCGGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (20 bp):
CGGTGACAATTTCCAGAATC
Found at i:1664 original size:12 final size:11
Alignment explanation
Indices: 1642--1688 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
1632 TTTCTTTGAA
1642 TTTTT-TTTAT
1 TTTTTATTTAT
*
1652 TTCTTTGTTTAT
1 TT-TTTATTTAT
1664 TTGTTTATTTTAT
1 TT-TTTA-TTTAT
1677 TTTTTATTTAT
1 TTTTTATTTAT
1688 T
1 T
1689 AGATTAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 2 0.06
11 9 0.28
12 14 0.44
13 7 0.22
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.81
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:1846 original size:59 final size:58
Alignment explanation
Indices: 1756--2106 Score: 442
Period size: 59 Copynumber: 5.9 Consensus size: 58
1746 TAAAAATAAA
* *
1756 AAATTTCAAAAAAAATATTTTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAAT
1 AAATTTCAAAAAAAATA--TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1816 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAAT
1 AAATTTC-AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AAT
1875 AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT
1 AAATTT-CAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAAT
* * *
1939 AAATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAAT
1 AAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
***
1997 AAATTTTCAAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAAT
1 AAA-TTTCAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT
*
2056 CGAAATTTTC--AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 --AAA-TTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
2107 CTACAAAAAA
Statistics
Matches: 263, Mismatches: 13, Indels: 31
0.86 0.04 0.10
Matches are distributed among these distances:
58 10 0.04
59 170 0.65
60 11 0.04
61 18 0.07
62 1 0.00
63 43 0.16
64 9 0.03
65 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.34
Consensus pattern (58 bp):
AAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:1972 original size:122 final size:117
Alignment explanation
Indices: 1756--2106 Score: 469
Period size: 122 Copynumber: 2.9 Consensus size: 117
1746 TAAAAATAAA
* *
1756 AAATTTCAAAAAAAATATTTTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCAG-AAATAAAT
1 AAATTTCAAAAAAAATA--TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAAT
* *
1820 TTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAAT
64 TTC-CAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AAT
1875 AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATA
1 AAATTT-CAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG-AAAATA
*
1940 AATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAAT
61 AATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
***
1997 AAATTTTCAAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAA
1 AAA-TTTCAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAAT--AA
*
2060 ATTTTC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
62 ATTTCCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
2107 CTACAAAAAA
Statistics
Matches: 211, Mismatches: 10, Indels: 23
0.86 0.04 0.09
Matches are distributed among these distances:
117 5 0.02
118 74 0.35
119 13 0.06
120 11 0.05
121 3 0.01
122 90 0.43
123 15 0.07
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.34
Consensus pattern (117 bp):
AAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATTT
CCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:1982 original size:181 final size:180
Alignment explanation
Indices: 1747--2122 Score: 539
Period size: 181 Copynumber: 2.1 Consensus size: 180
1737 TTCTTTAAAT
1747 AAAAATAAAAAATTTCAAAAAAAATATTTTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCAG
1 AAAAA-AAAAAATTTCAAAAAAAATA-TTTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCAG
*
1812 AAATAAA-TTTCAAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAGAA
64 AAATAAATTTTCAAAAAAAAGAT-TTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTGAA-AA
*
1874 T-AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-
126 TCAAATTTCC--AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAC
* * *
1929 AAAGAAAAATAAATTTCCAAAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAG
1 AAA-AAAAA-AAATTTCAAAAAAAATATTTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCAG
* *
1993 AAATAAATTTTCAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCG
64 AAATAAATTTTCAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-
* *
2058 AAATTTTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTAC
128 AAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAC
2111 AAAAAAAAAAAT
1 AAAAAAAAAAAT
2123 CATTCTTTCC
Statistics
Matches: 177, Mismatches: 9, Indels: 18
0.87 0.04 0.09
Matches are distributed among these distances:
180 4 0.02
181 120 0.68
182 27 0.15
183 26 0.15
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (180 bp):
AAAAAAAAAAATTTCAAAAAAAATATTTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCAGAA
ATAAATTTTCAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAA
TTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCCTAC
Found at i:3172 original size:21 final size:23
Alignment explanation
Indices: 3125--3174 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
3115 TTCTTTTTTA
*
3125 GAAATTTTATTTATTGTTTTATT
1 GAAATTTTATTTATTGTTTAATT
3148 --AATTTT-TTTATT-TTTAATT
1 GAAATTTTATTTATTGTTTAATT
3167 GAAATTTT
1 GAAATTTT
3175 GAAGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
21 12 0.50
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (23 bp):
GAAATTTTATTTATTGTTTAATT
Found at i:3396 original size:18 final size:21
Alignment explanation
Indices: 3356--3396 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3346 TTTTTAATAA
*
3356 ATTAATAAATTTTTATTTATT
1 ATTAACAAATTTTTATTTATT
*
3377 ATTAACAAATTTTTTTTTAT
1 ATTAACAAATTTTTATTTAT
3397 AAATACTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTAACAAATTTTTATTTATT
Found at i:3724 original size:21 final size:21
Alignment explanation
Indices: 3677--3732 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
3667 TTAACATGTA
* *
3677 ATAATATCAAGAATAATAATT
1 ATAATAACAAAAATAATAATT
*
3698 AAAATAACAAAAATAAT-ATAT
1 ATAATAACAAAAATAATAAT-T
3719 ATAATATA-AAAAAT
1 ATAATA-ACAAAAAT
3733 TTTTTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
ATAATAACAAAAATAATAATT
Found at i:4705 original size:17 final size:15
Alignment explanation
Indices: 4672--4723 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
4662 GAAAGAAGAA
4672 AATAAATAAAAATAT
1 AATAAATAAAAATAT
*
4687 AATATAATAATAATGAT
1 AATA-AATAAAAAT-AT
*
4704 AATAAA-AAAAATAA
1 AATAAATAAAAATAT
4718 AATAAA
1 AATAAA
4724 AATAGTGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 7 0.22
15 9 0.28
16 10 0.31
17 6 0.19
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (15 bp):
AATAAATAAAAATAT
Found at i:4938 original size:50 final size:50
Alignment explanation
Indices: 4880--5081 Score: 191
Period size: 50 Copynumber: 4.1 Consensus size: 50
4870 TTGAAAATTT
* **
4880 AAAAAGCTCCTCTGAGCAGCGGCTCAACAACTTTAAAAAAAT-TCATCTT-A
1 AAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTT--AAAAATCTCATCTTGA
* * *
4930 AAAAAGCTCCTCTAAGTAAAAGCTCAATAACTTT-AAAATCTCATCTTGAA
1 AAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTTAAAAATCTCATCTTG-A
* * * *
4980 AAAAAAC-CCTCTCAA-TAGAGGTTCAACAACTTTAAAAATCTCATCTTGA
1 AAAAAGCTCCTCT-AAGCAGAAGCTCAACAACTTTAAAAATCTCATCTTGA
* * * * *
5029 AAAAGGCTCATCTTAGCAGAAGCTCAATAACTTTAAAAATCT-ATCTTTA
1 AAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTTAAAAATCTCATCTTGA
5078 AAAA
1 AAAA
5082 TTTATCTTAA
Statistics
Matches: 125, Mismatches: 20, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
47 5 0.04
48 7 0.06
49 36 0.29
50 77 0.62
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (50 bp):
AAAAAGCTCCTCTAAGCAGAAGCTCAACAACTTTAAAAATCTCATCTTGA
Found at i:5006 original size:99 final size:99
Alignment explanation
Indices: 4903--5081 Score: 256
Period size: 99 Copynumber: 1.8 Consensus size: 99
4893 GAGCAGCGGC
* *
4903 TCAACAACTTTAAAAAAAT-TCATCTT-AAAAAAGCTCCTCTAAGTAAAAGCTCAATAACTTT-A
1 TCAACAACTTT--AAAAATCTCATCTTGAAAAAAGCTCATCTAAGCAAAAGCTCAATAACTTTAA
4965 AAATCTCATCTTGAAAAAAAACCCTCTCAATAGAGGT
64 AAATCT-ATCTTGAAAAAAAACCCTCTCAATAGAGGT
* * *
5002 TCAACAACTTTAAAAATCTCATCTTGAAAAAGGCTCATCTTAGCAGAAGCTCAATAACTTTAAAA
1 TCAACAACTTTAAAAATCTCATCTTGAAAAAAGCTCATCTAAGCAAAAGCTCAATAACTTTAAAA
*
5067 ATCTATCTTTAAAAA
66 ATCTATCTTGAAAAA
5082 TTTATCTTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
97 6 0.08
98 7 0.10
99 51 0.72
100 7 0.10
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.28
Consensus pattern (99 bp):
TCAACAACTTTAAAAATCTCATCTTGAAAAAAGCTCATCTAAGCAAAAGCTCAATAACTTTAAAA
ATCTATCTTGAAAAAAAACCCTCTCAATAGAGGT
Found at i:5091 original size:13 final size:14
Alignment explanation
Indices: 5059--5094 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5049 AGCTCAATAA
5059 CTTTAAAAATCTAT
1 CTTTAAAAATCTAT
*
5073 CTTTAAAAATTTAT
1 CTTTAAAAATCTAT
5087 C-TTAAAAA
1 CTTTAAAAA
5095 AGGTTCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (14 bp):
CTTTAAAAATCTAT
Found at i:5307 original size:97 final size:96
Alignment explanation
Indices: 5073--5391 Score: 356
Period size: 97 Copynumber: 3.2 Consensus size: 96
5063 AAAAATCTAT
* * *
5073 CTTTAAAAATTTATCTTAAAAAAGGTTCATATCAGCAAAGATTTAACAACTTTAAAAATCCATAT
1 CTTTAAAAATTTATCTTAAAAAAGCTT-ATATCAGCAGAGATTCAACAACTTTAAAAATCCATAT
* * *
5138 TGAACAAGGCTC-TTCTCAGTAGAGACTTAACAA
65 TGAA-AAAGCTCATT-TCAGCAGAGGCTTAACAA
* * *
5171 CTTTAAAAAAATTTATCTTAAAAAAGCTCATCTCAGCAGAGATTCAATAACTTTAAAAATCTCAT
1 CTTT--AAAAATTTATCTTAAAAAAGCTTATATCAGCAGAGATTCAACAACTTTAAAAATC-CAT
*
5236 TTTGAAAAAGCTCATTTCAGCAGAGGCTTAAC-A
63 ATTGAAAAAGCTCATTTCAGCAGAGGCTTAACAA
* * *
5269 CTTTAAAAATCTTATCTTGAAAAAGCTTATATCAGCAGATG-CTCAACAACTTTAAAAATCCATC
1 CTTTAAAAAT-TTATCTTAAAAAAGCTTATATCAGCAGA-GATTCAACAACTTTAAAAATCCATA
* * * *
5333 TTGAAAAAGGCTCATCTCAACAAAGGCTCAACAA
64 TTGAAAAA-GCTCATTTCAGCAGAGGCTTAACAA
* *
5367 CTTTAAAAATCTCATCTTGAAAAAG
1 CTTTAAAAAT-TTATCTTAAAAAAG
5392 GTTCATCTTA
Statistics
Matches: 192, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
96 17 0.09
97 61 0.32
98 35 0.18
99 48 0.25
100 31 0.16
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (96 bp):
CTTTAAAAATTTATCTTAAAAAAGCTTATATCAGCAGAGATTCAACAACTTTAAAAATCCATATT
GAAAAAGCTCATTTCAGCAGAGGCTTAACAA
Found at i:5408 original size:50 final size:50
Alignment explanation
Indices: 5073--5434 Score: 346
Period size: 49 Copynumber: 7.4 Consensus size: 50
5063 AAAAATCTAT
* * * * * **
5073 CTTTAAAAAT-TTATCTTAAAAAAGGTTCATATCAGCAAAGATTTAACAA
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATCTCAGCAGAGGCTTAACAA
* * * * *
5122 CTTTAAAAATC-CATATTGAACAAGGCTCTTCTCAGTAGAGACTTAACAA
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATCTCAGCAGAGGCTTAACAA
* * * *
5171 CTTTAAAAAAAT-TTATCTT-AAAAAAGCTCATCTCAGCAGA-GATTCAATAA
1 CTTT--AAAAATCTCATCTTGAAAAAGGCTCATCTCAGCAGAGGCTT-AACAA
* *
5221 CTTTAAAAATCTCATTTTGAAAAA-GCTCATTTCAGCAGAGGCTTAAC-A
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATCTCAGCAGAGGCTTAACAA
* * * * *
5269 CTTTAAAAATCTTATCTTGAAAAA-GCTTATATCAGCAGATGCTCAACAA
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATCTCAGCAGAGGCTTAACAA
* * *
5318 CTTTAAAAATC-CATCTTGAAAAAGGCTCATCTCAACAAAGGCTCAACAA
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATCTCAGCAGAGGCTTAACAA
* * * * *
5367 CTTTAAAAATCTCATCTTGAAAAAGGTTCATCTTAGTAAAGGCTTAATAA
1 CTTTAAAAATCTCATCTTGAAAAAGGCTCATCTCAGCAGAGGCTTAACAA
*
5417 CTTTAAAAATCTTATCTT
1 CTTTAAAAATCTCATCTT
5435 TTCTCGAAAC
Statistics
Matches: 259, Mismatches: 43, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
48 59 0.23
49 108 0.42
50 82 0.32
51 10 0.04
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (50 bp):
CTTTAAAAATCTCATCTTGAAAAAGGCTCATCTCAGCAGAGGCTTAACAA
Found at i:5418 original size:196 final size:194
Alignment explanation
Indices: 5073--5428 Score: 450
Period size: 196 Copynumber: 1.8 Consensus size: 194
5063 AAAAATCTAT
* *
5073 CTTTAAAAATTTATCTTAAAAAAGGTTCATATCAGCAAAGATTTAACAACTTTAAAAATCCATAT
1 CTTTAAAAATTTATCTTAAAAAAGCTTCATATCAGC-AAGATTCAACAACTTTAAAAATCCATAT
* * ** * * *
5138 TGAACAAGGCTCTTCTCAGTAGAGACTTAACAACTTTAAAAAAATTTATCTTAAAAAAGCTCATC
65 TGAAAAAGGCTCATCTCAACAAAGACTCAACAACTTT-AAAAAATTCATCTTAAAAAAGCTCATC
*
5203 TCAGCAGAGATTCAATAACTTTAAAAATCTCATTTTGAAAAAGCTCATTTCAGCAGAGGCTTAAC
129 TCAGCAAAGATTCAATAACTTTAAAAATCTCATTTTGAAAAAGCTCATTTCAGCAGAGGCTTAAC
5268 A
194 A
*
5269 CTTTAAAAATCTTATCTTGAAAAAGCTT-ATATCAGC-AGATGCTCAACAACTTTAAAAATCCAT
1 CTTTAAAAAT-TTATCTTAAAAAAGCTTCATATCAGCAAGAT--TCAACAACTTTAAAAATCCAT
* * * *
5332 CTTGAAAAAGGCTCATCTCAACAAAGGCTCAACAACTTT-AAAAATCTCATCTTGAAAAAGGTTC
63 ATTGAAAAAGGCTCATCTCAACAAAGACTCAACAACTTTAAAAAAT-TCATCTT-AAAAAAGCTC
* * *
5396 ATCTTAGTAAAGGCTT-AATAACTTTAAAAATCT
126 ATCTCAGCAAA-GATTCAATAACTTTAAAAATCT
5429 TATCTTTTCT
Statistics
Matches: 136, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
194 10 0.07
195 6 0.04
196 102 0.75
197 18 0.13
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (194 bp):
CTTTAAAAATTTATCTTAAAAAAGCTTCATATCAGCAAGATTCAACAACTTTAAAAATCCATATT
GAAAAAGGCTCATCTCAACAAAGACTCAACAACTTTAAAAAATTCATCTTAAAAAAGCTCATCTC
AGCAAAGATTCAATAACTTTAAAAATCTCATTTTGAAAAAGCTCATTTCAGCAGAGGCTTAACA
Found at i:9596 original size:13 final size:12
Alignment explanation
Indices: 9574--9607 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
9564 CAATGCTTAA
9574 AAAAACAAAAAAT
1 AAAAA-AAAAAAT
9587 AAAAGAAAAAAAT
1 AAAA-AAAAAAAT
9600 AAAAAAAA
1 AAAAAAAA
9608 GACTTAGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 15 0.75
14 1 0.05
ACGTcount: A:0.88, C:0.03, G:0.03, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:10665 original size:43 final size:42
Alignment explanation
Indices: 10585--10703 Score: 109
Period size: 43 Copynumber: 2.8 Consensus size: 42
10575 TCAAAGAGCC
* * *
10585 TTTATTTTTCAAAGTTGTTGAGCTTCTGA-TTAAAGGAGCCATA
1 TTTATTTTTCAAAGTTGTTTACCTT-T-ACTTAGAGGAGCCATA
**
10628 TTTATTTTTCAAAGTTGTTATACCTTTACTTAGAGGAGCTTTA
1 TTTATTTTTCAAAGTTGTT-TACCTTTACTTAGAGGAGCCATA
* *
10671 TTTATTTCTT--AAGTTGTTGTGCCTTTGCTTAGA
1 TTTATTT-TTCAAAGTTGTT-TACCTTTACTTAGA
10704 AAAGCTTTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
42 21 0.32
43 38 0.58
44 6 0.09
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.48
Consensus pattern (42 bp):
TTTATTTTTCAAAGTTGTTTACCTTTACTTAGAGGAGCCATA
Found at i:10732 original size:45 final size:43
Alignment explanation
Indices: 10626--10742 Score: 128
Period size: 42 Copynumber: 2.7 Consensus size: 43
10616 AAAGGAGCCA
* * * **
10626 TATTTATTTTTCAAAGTTGTTATACCTTTACTTAGAGGAGCTT
1 TATTTATTTTCCAAAGTTGTTGTGCCTTTACTTAGAAAAGCTT
** *
10669 TATTTA-TTTCTTAAGTTGTTGTGCCTTTGCTTAGAAAAGCTTT
1 TATTTATTTTCCAAAGTTGTTGTGCCTTTACTTAGAAAAGC-TT
*
10712 TATTTACTTTTCCAAAGTTGTTGAGCCTTTA
1 TATTTA-TTTTCCAAAGTTGTTGTGCCTTTA
10743 TTTACTTATC
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 26 0.44
43 14 0.24
45 19 0.32
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (43 bp):
TATTTATTTTCCAAAGTTGTTGTGCCTTTACTTAGAAAAGCTT
Found at i:10775 original size:29 final size:29
Alignment explanation
Indices: 10705--10775 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
10695 TTGCTTAGAA
* * **
10705 AAGCTTTTATTTACTTTTCCAAAGTTGTT
1 AAGCTTTTATTTACTTATCCAAAATCATT
* *
10734 GAGCCTTTATTTACTTATCCAAAATCATT
1 AAGCTTTTATTTACTTATCCAAAATCATT
*
10763 AAGCTTTTGTTTA
1 AAGCTTTTATTTA
10776 AAGGAGCTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (29 bp):
AAGCTTTTATTTACTTATCCAAAATCATT
Found at i:11058 original size:5 final size:5
Alignment explanation
Indices: 11048--11106 Score: 56
Period size: 5 Copynumber: 12.4 Consensus size: 5
11038 AAATTATTTA
*
11048 TTATT TTA-T TTA-T TTA-T TTA-T TTATTT TTATT TT-TT TAGATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTA-TT TTATT TTATT T-TATT TTATT
11095 TTATT TTATT TT
1 TTATT TTATT TT
11107 GATGATTATC
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
4 19 0.40
5 22 0.46
6 7 0.15
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:11059 original size:4 final size:4
Alignment explanation
Indices: 11041--11074 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
11031 TAAGCCCAAA
11041 TTAT TTA- TTATT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT TT
11075 TTATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
4 22 0.79
5 3 0.11
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:11066 original size:20 final size:20
Alignment explanation
Indices: 11041--11105 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
11031 TAAGCCCAAA
11041 TTATTTATTATTTTATTTAT
1 TTATTTATTATTTTATTTAT
*
11061 TTATTTATTTATTTTTATTTTT
1 TTATTTA-TTA-TTTTATTTAT
*
11083 TTAGATT-TTATTTTATTTTAT
1 TTA-TTTATTATTTTA-TTTAT
11104 TT
1 TT
11106 TGATGATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 12 0.32
21 12 0.32
22 12 0.32
23 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.77
Consensus pattern (20 bp):
TTATTTATTATTTTATTTAT
Found at i:12126 original size:8 final size:8
Alignment explanation
Indices: 12113--12139 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
12103 GAAATTTGGG
12113 AAAAAATA
1 AAAAAATA
12121 AAAAAATA
1 AAAAAATA
12129 AAAAAATA
1 AAAAAATA
12137 AAA
1 AAA
12140 TATTTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:15959 original size:50 final size:50
Alignment explanation
Indices: 15889--16042 Score: 164
Period size: 55 Copynumber: 2.9 Consensus size: 50
15879 ACTTTAATAC
15889 CTCATATCATAATTACAAAAATATCATTTTCTTAAATTGACTATTATGCT
1 CTCATATCATAATTACAAAAATATCATTTTCTTAAATTGACTATTATGCT
* * * * *
15939 CTCATATCATAATTATAAAAATACTTATTTTCTTATAATTATTTACTATAATTCT
1 CTCATATCATAATTACAAAAATA-TCATTTTC-T-TAA--ATTGACTATTATGCT
* ** *
15994 CTCATATCATAATTACAGAAATATCCCGTCTCTTAAATTGACCTATTAT
1 CTCATATCATAATTACAAAAATAT-CATTTTCTTAAATTGA-CTATTAT
16043 ACATTTACAC
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
50 22 0.26
51 11 0.13
52 7 0.08
53 6 0.07
54 2 0.02
55 36 0.43
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (50 bp):
CTCATATCATAATTACAAAAATATCATTTTCTTAAATTGACTATTATGCT
Found at i:15981 original size:104 final size:104
Alignment explanation
Indices: 15863--16113 Score: 296
Period size: 106 Copynumber: 2.4 Consensus size: 104
15853 AAAATATCAC
* * * *
15863 TTTCTTATACTTATTTACTTTAATACCTCATATCATAATTACAAAAATAT-CATTTTCTTAAATT
1 TTTCTTATAATTATTTACTATAATACCTCATATCATAATTACAAAAATATCCAGTCTCTTAAATT
* *
15927 GA-CTATTATGC-TCTCATA-TCATAATTATA-AAAATACTTAT
66 GACCTATTATACAT-TCACACT-ATAA-TA-AGAAAATACTT-T
* * *
15967 TTTCTTATAATTATTTACTATAATTCTCTCATATCATAATTACAGAAATATCCCGTCTCTTAAAT
1 TTTCTTATAATTATTTACTATAATAC-CTCATATCATAATTACAAAAATATCCAGTCTCTTAAAT
*
16032 TGACCTATTATACATTTACACTATAATAAGAAAATACTTT
65 TGACCTATTATACATTCACACTATAATAAGAAAATACTTT
*
16072 TTCTCTTATAATTATTTACTATATTACCCTCATATCATAATT
1 TT-TCTTATAATTATTTACTATAATA-CCTCATATCATAATT
16114 TGTGAAAACT
Statistics
Matches: 127, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
104 23 0.18
105 27 0.21
106 59 0.46
107 16 0.13
108 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.02, T:0.45
Consensus pattern (104 bp):
TTTCTTATAATTATTTACTATAATACCTCATATCATAATTACAAAAATATCCAGTCTCTTAAATT
GACCTATTATACATTCACACTATAATAAGAAAATACTTT
Found at i:15998 original size:55 final size:54
Alignment explanation
Indices: 15853--16018 Score: 198
Period size: 55 Copynumber: 3.1 Consensus size: 54
15843 CATAATTGTG
* * *
15853 AAAATATCACTTTCTTATACTTATTTACTTTAATAC-CTCATATCATAATTACA
1 AAAATATCATTTTCTTATAATTATTTACTATAATACTCTCATATCATAATTACA
* * * *
15906 AAAATATCATTTTC-T-TAA--ATTGACTATTATGCTCTCATATCATAATTATA
1 AAAATATCATTTTCTTATAATTATTTACTATAATACTCTCATATCATAATTACA
* *
15956 AAAATACTTATTTTCTTATAATTATTTACTATAATTCTCTCATATCATAATTACA
1 AAAATA-TCATTTTCTTATAATTATTTACTATAATACTCTCATATCATAATTACA
*
16011 GAAATATC
1 AAAATATC
16019 CCGTCTCTTA
Statistics
Matches: 93, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
49 10 0.11
50 22 0.24
51 9 0.10
52 2 0.02
53 16 0.17
54 1 0.01
55 33 0.35
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.44
Consensus pattern (54 bp):
AAAATATCATTTTCTTATAATTATTTACTATAATACTCTCATATCATAATTACA
Found at i:21176 original size:21 final size:20
Alignment explanation
Indices: 21152--21190 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21142 TATTTAATAA
* *
21152 TAAATAAAATAAATAAAAAGT
1 TAAA-AAAACAAAAAAAAAGT
21173 TAAAAAAACAAAAAAAAA
1 TAAAAAAACAAAAAAAAA
21191 AAATTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (20 bp):
TAAAAAAACAAAAAAAAAGT
Found at i:22051 original size:13 final size:14
Alignment explanation
Indices: 22035--22063 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22025 TTTATTTAAT
22035 AATAAAT-AAAATA
1 AATAAATAAAAATA
22048 AATAAATAAAAATA
1 AATAAATAAAAATA
22062 AA
1 AA
22064 AAAAGCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAATAAAAATA
Found at i:24265 original size:2 final size:2
Alignment explanation
Indices: 24258--24302 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
24248 TTGAACTTAC
*
24258 AT AT AT AT GT AT AT 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 AT AT AT AT AT AT AT
24300 AT A
1 AT A
24303 GACACACACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24463 original size:8 final size:8
Alignment explanation
Indices: 24450--24484 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
24440 TTATAAGCGT
24450 TATATAAA
1 TATATAAA
24458 TATATAAA
1 TATATAAA
24466 TATATAAA
1 TATATAAA
*
24474 TATATATA
1 TATATAAA
24482 TAT
1 TAT
24485 GTAGACTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TATATAAA
Found at i:25154 original size:52 final size:51
Alignment explanation
Indices: 25051--25194 Score: 152
Period size: 52 Copynumber: 2.8 Consensus size: 51
25041 AAACTTGCTC
* * * *
25051 ATTAAGAATCCTCTCTT--CTTAGAATTCTTTTCCTG-TAGTCAAACTTGCCT
1 ATTAAGAAT-CTCT-TTCCCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
25101 ATTAAGAATC-CATTTCCCTTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
1 ATTAAGAATCTC-TTTCCC-TTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
* * *
25153 ATTAAGAATCTTCTTTCTCTTAGAATTCTTCTTTTACAAGTC
1 ATTAAGAATC-TCTTTCCCTTAGAATTCTTCTCTTGCAAGTC
25195 TTCTTGTCCA
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
48 3 0.04
49 2 0.03
50 10 0.12
51 15 0.19
52 44 0.55
53 5 0.06
54 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.42
Consensus pattern (51 bp):
ATTAAGAATCTCTTTCCCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCT
Found at i:25247 original size:11 final size:11
Alignment explanation
Indices: 25231--25263 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
25221 AAAATCCTAA
25231 AACAAATCTCT
1 AACAAATCTCT
*
25242 AACAAATCTCA
1 AACAAATCTCT
25253 AACAAATCTCT
1 AACAAATCTCT
25264 TATGAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (11 bp):
AACAAATCTCT
Found at i:25536 original size:25 final size:25
Alignment explanation
Indices: 25508--25555 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25498 TCTTTTCATA
*
25508 TCTCGAACCGTCAACTCTTCCCATG
1 TCTCGAACCATCAACTCTTCCCATG
**
25533 TCTCGAACCATCGGCTCTTCCCA
1 TCTCGAACCATCAACTCTTCCCA
25556 CATCTTGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.19, C:0.42, G:0.12, T:0.27
Consensus pattern (25 bp):
TCTCGAACCATCAACTCTTCCCATG
Found at i:28967 original size:21 final size:21
Alignment explanation
Indices: 28922--28976 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
28912 GTTGATGCAC
*
28922 AAATTTTATTT-TTTTTTTAA
1 AAATTTTATTTATTGTTTTAA
*
28942 AAATTTTATTTATTGTTTTAT
1 AAATTTTATTTATTGTTTTAA
*
28963 TAATTTTATTTATT
1 AAATTTTATTTATT
28977 TTTAATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
AAATTTTATTTATTGTTTTAA
Found at i:29546 original size:21 final size:21
Alignment explanation
Indices: 29499--29555 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
29489 TTAACATGTA
* *
29499 ATAATATCAAGAATAATAATT
1 ATAATAACAAAAATAATAATT
*
29520 AAAATAACAAAAATAAT-ATAT
1 ATAATAACAAAAATAATAAT-T
*
29541 ATAATATAAAAAAAT
1 ATAATA-ACAAAAAT
29556 TTAAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (21 bp):
ATAATAACAAAAATAATAATT
Found at i:30338 original size:23 final size:23
Alignment explanation
Indices: 30302--30346 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
30292 TATTTATAGA
30302 ATTTTTTGAGATTCAAATCTCAG
1 ATTTTTTGAGATTCAAATCTCAG
*
30325 ATTTTTT-AGAATTCGAATCTCA
1 ATTTTTTGAG-ATTCAAATCTCA
30347 TTTTTTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (23 bp):
ATTTTTTGAGATTCAAATCTCAG
Found at i:30352 original size:23 final size:22
Alignment explanation
Indices: 30303--30352 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
30293 ATTTATAGAA
30303 TTTTTTGAGATTCAAATCTCAG
1 TTTTTTGAGATTCAAATCTCAG
*
30325 ATTTTTT-AGAATTCGAATCTCA-
1 -TTTTTTGAG-ATTCAAATCTCAG
30347 TTTTTT
1 TTTTTT
30353 CAACCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 6 0.24
22 2 0.08
23 17 0.68
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (22 bp):
TTTTTTGAGATTCAAATCTCAG
Found at i:30497 original size:20 final size:22
Alignment explanation
Indices: 30472--30511 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
30462 TGAATCGGAT
30472 AAGAAAG-AAG-AAGAAAAAAA
1 AAGAAAGAAAGAAAGAAAAAAA
30492 AAGAAAGAAAGAAAGAAAAA
1 AAGAAAGAAAGAAAGAAAAA
30512 TAAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (22 bp):
AAGAAAGAAAGAAAGAAAAAAA
Found at i:30778 original size:48 final size:49
Alignment explanation
Indices: 30725--31266 Score: 224
Period size: 48 Copynumber: 11.0 Consensus size: 49
30715 TTTTTGAAAA
* *
30725 TTTAAAAGGCTCCTCTGAGCAGAGGCTCAACAACTTTAAAAAAT-TCAT-
1 TTTAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAAATCTCATC
* * * *
30773 TTTAAAAAAGCTCCTCTAAGTAAAGGCTCAATAACTTT-AAAATCTCATC
1 TTT-AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATC
* ** **
30822 TTGAAAAAAATCCTCTCAATAGAGGCTCAACAACTTTAAAAATCTCATC
1 TTTAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATC
* * *
30871 TTAAAAAAGGCTCATCTCAGCAGAGGCTCAATAACTTT-AAAATCT-ATC
1 TTTAAAAA-GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATC
* * * ** * * * * *
30919 TTTAAAAA-TTCATCTTAAAAAAGGCTCATATCAGC---AAAGACTCAACAAC
1 TTTAAAAAGCTCCTCTCAGCAGAGGCTCA-A-CAACTTTAAA-AATC-TCATC
* * * * * * * * * **
30968 TTT-AAAA--TCCATAT-TGAAAAAGGCTCTTCTCAGTAGAGAC-TCAACAACTTTAAAAA
1 TTTAAAAAGCTCC-TCTCAG-CAGAGG-----CTCA--ACA-ACTTTAA-AAATCT-CATC
* * * * *
31024 TTCAAAAAAGCTCATATCAGCAGAGACTTAA-AACTTTAAAAATCTCAT-
1 TT-TAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATC
* * * *
31072 TTTGAAAAAGCTCATTTCAGCAGAGGCTTAAC-ACTTTAAAAATCTTATC
1 TTT-AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATC
* * * * *
31121 TTGAAAAAGCTCATATCAGCAGATGTTCAACAACTTTAAAAATCT-ATC
1 TTTAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATC
* * *
31169 TTGAAAAAGGCTCATCTCAACAGAGGCTCAACAACTTTAAAAATCTCAT-
1 TTTAAAAA-GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATC
* * * *
31218 TTTGAAAAAGGCTCATCTTAGTAGAGGCT-AATAACTTTAAAAATCTCAT
1 TTT-AAAAA-GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCAT
31267 TTTTCTCGAA
Statistics
Matches: 387, Mismatches: 70, Indels: 73
0.73 0.13 0.14
Matches are distributed among these distances:
46 17 0.04
47 11 0.03
48 136 0.35
49 131 0.34
50 53 0.14
51 4 0.01
52 1 0.00
53 5 0.01
54 6 0.02
56 9 0.02
57 1 0.00
58 4 0.01
59 6 0.02
60 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (49 bp):
TTTAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATC
Found at i:30788 original size:49 final size:49
Alignment explanation
Indices: 30728--30926 Score: 210
Period size: 49 Copynumber: 4.1 Consensus size: 49
30718 TTGAAAATTT
* *
30728 AAAAGGCTCCTCTGAGCAGAGGCTCAACAACTTTAAAAAAT-TCATTTTA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAAATCTCATTTTA
* * * * *
30777 AAAAAGCTCCTCTAAGTAAAGGCTCAATAACTTT-AAAATCTCATCTTGA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCAT-TTTA
* ** *
30826 AAAAA-ATCCTCTCAATAGAGGCTCAACAACTTTAAAAATCTCATCTTA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTTA
* *
30874 AAAAAGGCTCATCTCAGCAGAGGCTCAATAACTTT-AAAATCT-ATCTTTA
1 AAAAA-GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCAT-TTTA
30923 AAAA
1 AAAA
30927 TTCATCTTAA
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
47 5 0.04
48 36 0.29
49 61 0.49
50 23 0.18
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.27
Consensus pattern (49 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTTA
Found at i:30859 original size:97 final size:97
Alignment explanation
Indices: 30745--30926 Score: 278
Period size: 97 Copynumber: 1.9 Consensus size: 97
30735 TCCTCTGAGC
* * *
30745 AGAGGCTCAACAACTTTAAAAAAT-TCATTTTAAAAAA-GCTCCTCTAAGTAAAGGCTCAATAAC
1 AGAGGCTCAACAACTTT-AAAAATCTCATCTTAAAAAAGGCTCATCTAAGCAAAGGCTCAATAAC
30808 TTTAAAATCTCATCTTGAAAAAAATCCTCTCAAT
65 TTTAAAATCT-ATCTTGAAAAAAATCCTCTCAAT
* *
30842 AGAGGCTCAACAACTTTAAAAATCTCATCTTAAAAAAGGCTCATCTCAGCAGAGGCTCAATAACT
1 AGAGGCTCAACAACTTTAAAAATCTCATCTTAAAAAAGGCTCATCTAAGCAAAGGCTCAATAACT
*
30907 TTAAAATCTATCTTTAAAAA
66 TTAAAATCTATCTTGAAAAA
30927 TTCATCTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
96 6 0.08
97 39 0.51
98 32 0.42
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (97 bp):
AGAGGCTCAACAACTTTAAAAATCTCATCTTAAAAAAGGCTCATCTAAGCAAAGGCTCAATAACT
TTAAAATCTATCTTGAAAAAAATCCTCTCAAT
Found at i:30932 original size:62 final size:63
Alignment explanation
Indices: 30855--30976 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 63
30845 GGCTCAACAA
* * * *
30855 CTTTAAAAATCTCATCTTAAAAAAGGCTCATCTCAGCAGAGGCTCAATAACTTTAAAATCTAT
1 CTTTAAAAATCTCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAATCTAT
30918 CTTTAAAAAT-TCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAATC
1 CTTTAAAAATCTCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAATC
30977 CATATTGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
62 45 0.82
63 10 0.18
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (63 bp):
CTTTAAAAATCTCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTTAAAATCTAT
Found at i:30972 original size:49 final size:49
Alignment explanation
Indices: 30918--31266 Score: 339
Period size: 48 Copynumber: 7.3 Consensus size: 49
30908 TAAAATCTAT
* *
30918 CTTTAAAAATTCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAA
1 CTTTAAAAATTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
* * * * *
30967 CTTT-AAAATCCATATTGAAAAAGGCTCTTCTCAGTAGAGACTCAACAA
1 CTTTAAAAATTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
*
31015 CTTTAAAAATTCA-----AAAAA-GCTCATATCAGCAGAGACTTAA-AA
1 CTTTAAAAATTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
* * * *
31057 CTTTAAAAATCTCATTTTGAAAAA-GCTCATTTCAGCAGAGGCTTAAC-A
1 CTTTAAAAAT-TCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
* *
31105 CTTTAAAAATCTTATCTTGAAAAA-GCTCATATCAGCAGATG-TTCAACAA
1 CTTTAAAAAT-TCATCTTGAAAAAGGCTCATATCAGCAGA-GACTCAACAA
* * *
31154 CTTTAAAAA-TCTATCTTGAAAAAGGCTCATCTCAACAGAGGCTCAACAA
1 CTTTAAAAATTC-ATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
* * * * * *
31203 CTTTAAAAATCTCATTTTGAAAAAGGCTCATCTTAGTAGAGGCT-AATAA
1 CTTTAAAAAT-TCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
31252 CTTTAAAAATCTCAT
1 CTTTAAAAAT-TCAT
31267 TTTTCTCGAA
Statistics
Matches: 257, Mismatches: 28, Indels: 30
0.82 0.09 0.10
Matches are distributed among these distances:
42 12 0.05
43 21 0.08
44 5 0.02
47 1 0.00
48 119 0.46
49 70 0.27
50 27 0.11
51 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (49 bp):
CTTTAAAAATTCATCTTGAAAAAGGCTCATATCAGCAGAGACTCAACAA
Found at i:31092 original size:139 final size:144
Alignment explanation
Indices: 30918--31233 Score: 362
Period size: 139 Copynumber: 2.2 Consensus size: 144
30908 TAAAATCTAT
* *
30918 CTTTAAAAAT-TCATCTTAAAAAAGGCTCATATCAGCAAAGACTCAACAACTTT-AAAATC-CAT
1 CTTTAAAAATCTCATTTTGAAAAAGGCTCATATCAGCAAAGACTCAAC-ACTTTAAAAATCTCAT
* * *
30980 ATTGAAAAAGGCTCTTCTCAGTAGA-GACTCAACAACTTTAAAAA-T-TC-AAAAAAGCTCATAT
65 ATTGAAAAA-GCTCATATCAGCAGATG-CTCAACAACTTTAAAAACTATCTAAAAAAGCTCATAT
* *
31041 CAGCAGAGACTTAA-AA
128 CAACAGAGACTCAACAA
* * * * * *
31057 CTTTAAAAATCTCATTTTGAAAAA-GCTCATTTCAGCAGAGGCTTAACACTTTAAAAATCTTATC
1 CTTTAAAAATCTCATTTTGAAAAAGGCTCATATCAGCAAAGACTCAACACTTTAAAAATCTCATA
* * *
31121 TTGAAAAAGCTCATATCAGCAGATGTTCAACAACTTTAAAAATCTATCTTGAAAAAGGCTCATCT
66 TTGAAAAAGCTCATATCAGCAGATGCTCAACAACTTTAAAAA-CTATC-T-AAAAAAGCTCATAT
*
31186 CAACAGAGGCTCAACAA
128 CAACAGAGACTCAACAA
31203 CTTTAAAAATCTCATTTTGAAAAAGGCTCAT
1 CTTTAAAAATCTCATTTTGAAAAAGGCTCAT
31234 CTTAGTAGAG
Statistics
Matches: 148, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
138 5 0.03
139 63 0.43
140 22 0.15
141 1 0.01
142 2 0.01
145 23 0.16
146 26 0.18
147 6 0.04
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (144 bp):
CTTTAAAAATCTCATTTTGAAAAAGGCTCATATCAGCAAAGACTCAACACTTTAAAAATCTCATA
TTGAAAAAGCTCATATCAGCAGATGCTCAACAACTTTAAAAACTATCTAAAAAAGCTCATATCAA
CAGAGACTCAACAA
Done.