Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 6 of 133
Found at i:1326009 original size:29 final size:29
Alignment explanation
Indices: 1325963--1326019 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1325953 ATAATCAATT
1325963 ATAATGAACTCAAACCTGCACTTGAAATG
1 ATAATGAACTCAAACCTGCACTTGAAATG
*
1325992 ATAATGAACTCAAGCCTGCACTTGAAAT
1 ATAATGAACTCAAACCTGCACTTGAAAT
1326020 CAAATTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (29 bp):
ATAATGAACTCAAACCTGCACTTGAAATG
Found at i:1330167 original size:30 final size:30
Alignment explanation
Indices: 1330131--1330189 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1330121 TCGAAATTAA
* * *
1330131 TAAAAATATTATTTTTTAAATATAAATATT
1 TAAAAATATCATTATATAAATATAAATATT
*
1330161 TAAAAATATCATTATATAAATATATATAT
1 TAAAAATATCATTATATAAATATAAATAT
1330190 AAATATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
TAAAAATATCATTATATAAATATAAATATT
Found at i:1331880 original size:39 final size:39
Alignment explanation
Indices: 1331812--1331896 Score: 113
Period size: 38 Copynumber: 2.2 Consensus size: 39
1331802 AAAAAATATT
*
1331812 TAAAAATAAAAATAAAAATCTGATAATTTAAAA-TTTGA
1 TAAAAATAAAAATAAAAATCTGATAATTTAAAATTTTAA
1331850 TAAAAAT-AAAATATAAAAT-TGATATGATTTAAAATTTTAA
1 TAAAAATAAAAATA-AAAATCTGATA--ATTTAAAATTTTAA
1331890 TAAAAAT
1 TAAAAAT
1331897 TATATATGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
37 11 0.26
38 12 0.29
39 8 0.19
40 11 0.26
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (39 bp):
TAAAAATAAAAATAAAAATCTGATAATTTAAAATTTTAA
Found at i:1331993 original size:31 final size:31
Alignment explanation
Indices: 1331936--1332008 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
1331926 ATATTTTATT
* *
1331936 TTTTTATATTAAGATAAATTATAATATGTAA
1 TTTTTATATTAAAATAAATTATAATATATAA
1331967 TTTTTATA-TAAAATATAA-TATAAATATATAAA
1 TTTTTATATTAAAATA-AATTAT-AATATAT-AA
*
1331999 TTTTAATATT
1 TTTTTATATT
1332009 TTATATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
30 9 0.26
31 16 0.46
32 9 0.26
33 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (31 bp):
TTTTTATATTAAAATAAATTATAATATATAA
Found at i:1333285 original size:24 final size:25
Alignment explanation
Indices: 1333257--1333318 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
1333247 TTTAAAATAA
*
1333257 AATATAATA-AAAAAATATAAATAT
1 AATATAATATAAAAAATATAAAAAT
* *
1333281 GATATAA-ATATAAAATATAAAAAT
1 AATATAATATAAAAAATATAAAAAT
*
1333305 AATATAATTTAAAA
1 AATATAATATAAAA
1333319 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.03
24 25 0.83
25 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
AATATAATATAAAAAATATAAAAAT
Found at i:1333300 original size:13 final size:13
Alignment explanation
Indices: 1333249--1333306 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
1333239 CAGGATAATT
1333249 TAAA-ATAAAATA
1 TAAATATAAAATA
*
1333261 T-AATAAAAAAATA
1 TAAAT-ATAAAATA
*
1333274 TAAATAT--GATA
1 TAAATATAAAATA
1333285 TAAATATAAAATA
1 TAAATATAAAATA
*
1333298 TAAAAATAA
1 TAAATATAA
1333307 TATAATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
11 12 0.33
12 1 0.03
13 20 0.56
14 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
TAAATATAAAATA
Found at i:1333329 original size:24 final size:22
Alignment explanation
Indices: 1333293--1333353 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
1333283 TATAAATATA
* *
1333293 AAATATAAAAATAA-TATAATTT
1 AAATTTAATAATAATTAT-ATTT
1333315 AAAATTTTAATAATAATTATATTT
1 -AAA-TTTAATAATAATTATATTT
1333339 AAATTTAATAA-AATT
1 AAATTTAATAATAATT
1333354 TTAAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.12
22 8 0.24
23 6 0.18
24 13 0.38
25 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTTAATAATAATTATATTT
Found at i:1333437 original size:32 final size:31
Alignment explanation
Indices: 1333394--1333475 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 31
1333384 TATAAATTAT
1333394 AATATATAATTTTTATATAAAATATAATAAA
1 AATATATAATTTTTATATAAAATATAATAAA
* ** *
1333425 AATATATAAATTTTAATATTTAATATAATATA
1 AATATAT-AATTTTTATATAAAATATAATAAA
*
1333457 AATATACTAATTATTATAT
1 AATATA-TAATTTTTATAT
1333476 TTATTTAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
31 7 0.16
32 35 0.81
33 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (31 bp):
AATATATAATTTTTATATAAAATATAATAAA
Found at i:1334009 original size:26 final size:25
Alignment explanation
Indices: 1333980--1334040 Score: 63
Period size: 29 Copynumber: 2.3 Consensus size: 25
1333970 TAATTTATTC
1333980 ATTTATTT-TTAAAAT-ATTAATATTT
1 ATTTATTTGTTAAAATAATT-AT-TTT
1334005 GATTTATGTTTGTTAAAATAATTATTTT
1 -ATTTA--TTTGTTAAAATAATTATTTT
1334033 ATTTATTT
1 ATTTATTT
1334041 AAATTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
25 3 0.10
26 5 0.16
27 5 0.16
28 6 0.19
29 9 0.29
30 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (25 bp):
ATTTATTTGTTAAAATAATTATTTT
Found at i:1334234 original size:10 final size:10
Alignment explanation
Indices: 1334190--1334271 Score: 51
Period size: 10 Copynumber: 8.0 Consensus size: 10
1334180 CATAATCAAA
1334190 TAAATTAAA-T
1 TAAA-TAAATT
*
1334200 TAAACAAATCT
1 TAAATAAAT-T
* **
1334211 TAAATGAACA
1 TAAATAAATT
*
1334221 TAAATGAATT
1 TAAATAAATT
*
1334231 TAAATAAATA
1 TAAATAAATT
1334241 TAAATAAATTT
1 TAAATAAA-TT
*
1334252 TAAAATAAAAT
1 T-AAATAAATT
1334263 TAAA-AAATT
1 TAAATAAATT
1334272 AAAAATATAA
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
9 7 0.12
10 31 0.55
11 11 0.20
12 7 0.12
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (10 bp):
TAAATAAATT
Found at i:1334235 original size:20 final size:20
Alignment explanation
Indices: 1334200--1334251 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1334190 TAAATTAAAT
* *
1334200 TAAACAAATCTTAAATGAACA
1 TAAATAAAT-TTAAATAAACA
* *
1334221 TAAATGAATTTAAATAAATA
1 TAAATAAATTTAAATAAACA
1334241 TAAATAAATTT
1 TAAATAAATTT
1334252 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.33
Consensus pattern (20 bp):
TAAATAAATTTAAATAAACA
Found at i:1335358 original size:19 final size:20
Alignment explanation
Indices: 1335321--1335358 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1335311 ATCATTTAAG
1335321 TTTTCTTCTTAATTCCCCCA
1 TTTTCTTCTTAATTCCCCCA
1335341 TTTT-TTCTGTAATTCCCC
1 TTTTCTTCT-TAATTCCCC
1335359 GCTTCTCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.13, C:0.32, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTCTTCTTAATTCCCCCA
Found at i:1335788 original size:3 final size:3
Alignment explanation
Indices: 1335775--1335832 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
1335765 TCTACCTCTC
* * * *
1335775 CTT CAT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CAT CTT ATC CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
1335823 CTC CTT CTT C
1 CTT CTT CTT C
1335833 CCAAACTTCC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.05, C:0.36, G:0.00, T:0.59
Consensus pattern (3 bp):
CTT
Found at i:1335793 original size:15 final size:15
Alignment explanation
Indices: 1335760--1335808 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1335750 ATGAAAAGTG
* * *
1335760 CTTCATCTACCTCTC
1 CTTCATCTTCTTCTT
1335775 CTTCATCTTCTTCTT
1 CTTCATCTTCTTCTT
*
1335790 CTTCTTCTTCTTCTT
1 CTTCATCTTCTTCTT
1335805 CTTC
1 CTTC
1335809 TTCATCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTCATCTTCTTCTT
Found at i:1336068 original size:3 final size:3
Alignment explanation
Indices: 1336062--1336096 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1336052 CTATCAACAA
*
1336062 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
1336097 ACTTGTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.34, G:0.29, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1344663 original size:6 final size:6
Alignment explanation
Indices: 1344652--1344743 Score: 59
Period size: 6 Copynumber: 15.2 Consensus size: 6
1344642 AATATATCAT
* * *
1344652 TTATAA TTATAA TTATTA TTATTA -TGTAA TTAATCAA TTATAA TT-TAA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TT-AT-AA TTATAA TTATAA
*
1344700 TT-TAA TT-TAA TTATATA TTATGA TTGATTAA TTACT-A TTATAA T
1 TTATAA TTATAA TTATA-A TTATAA TT-A-TAA TTA-TAA TTATAA T
1344744 AAAAAAAATT
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
5 19 0.27
6 33 0.46
7 11 0.15
8 8 0.11
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
TTATAA
Found at i:1344700 original size:19 final size:18
Alignment explanation
Indices: 1344646--1344701 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
1344636 TTGGAGAATA
*
1344646 TATCATTTATAATTATAAT
1 TATCAATTATAATT-TAAT
* * *
1344665 TAT-TATTATTATGTAAT
1 TATCAATTATAATTTAAT
1344682 TAATCAATTATAATTTAAT
1 T-ATCAATTATAATTTAAT
1344701 T
1 T
1344702 TAATTTAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
17 5 0.18
18 8 0.29
19 15 0.54
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (18 bp):
TATCAATTATAATTTAAT
Found at i:1345871 original size:40 final size:40
Alignment explanation
Indices: 1345816--1345895 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
1345806 TGTTATTTAT
*
1345816 ATATAACTATAAAGTGCAAGCTAAGATTACAAAAGGAATC
1 ATATAACTATAAAGTGCAAACTAAGATTACAAAAGGAATC
* *
1345856 ATATAACTATAAAGTGCAAACTAAGATTGCACAAGGAATC
1 ATATAACTATAAAGTGCAAACTAAGATTACAAAAGGAATC
1345896 CTAAGTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.23
Consensus pattern (40 bp):
ATATAACTATAAAGTGCAAACTAAGATTACAAAAGGAATC
Found at i:1348130 original size:21 final size:21
Alignment explanation
Indices: 1348105--1348145 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1348095 ATATAATTTT
1348105 ATAAA-AAGATAATTTTAATTA
1 ATAAATAA-ATAATTTTAATTA
*
1348126 ATAAATAAATTATTTTAATT
1 ATAAATAAATAATTTTAATT
1348146 TTAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAAATAAATAATTTTAATTA
Found at i:1355664 original size:35 final size:35
Alignment explanation
Indices: 1355625--1355693 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
1355615 CTTAAAAATG
1355625 TTCAAGTTTGATTCATATTT-AGTAAGAAAATTATA
1 TTCAAGTTTGATTCATATTTGA-TAAGAAAATTATA
* *
1355660 TTCAAGTTTGGTTCATATTTGATAATAAAATTAT
1 TTCAAGTTTGATTCATATTTGATAAGAAAATTAT
1355694 TCTATTCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.45
Consensus pattern (35 bp):
TTCAAGTTTGATTCATATTTGATAAGAAAATTATA
Found at i:1355910 original size:22 final size:22
Alignment explanation
Indices: 1355875--1355916 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1355865 ATATTATTAT
*
1355875 AAATGAACAGTAAACAAATATC
1 AAATGAACAATAAACAAATATC
* *
1355897 AAATGAATAATAAATAAATA
1 AAATGAACAATAAACAAATA
1355917 AATTTTAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (22 bp):
AAATGAACAATAAACAAATATC
Found at i:1356719 original size:3 final size:3
Alignment explanation
Indices: 1356711--1356747 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1356701 TTCTGTAAAA
* *
1356711 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAA TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1356748 TTTCCTTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1356892 original size:22 final size:21
Alignment explanation
Indices: 1356862--1356923 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
1356852 TTCAAAATTT
1356862 ATTATTTAAAATTTATTTAAA
1 ATTATTTAAAATTTATTTAAA
**
1356883 ATTGATTTAAAATAAATATT-AA
1 ATT-ATTTAAAATTTAT-TTAAA
1356905 ATTATTT-AAATTTATTTAA
1 ATTATTTAAAATTTATTTAA
1356924 TTTAAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 2 0.06
20 7 0.21
21 7 0.21
22 16 0.47
23 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTATTTAAAATTTATTTAAA
Found at i:1356921 original size:10 final size:11
Alignment explanation
Indices: 1356863--1356923 Score: 65
Period size: 11 Copynumber: 5.7 Consensus size: 11
1356853 TCAAAATTTA
1356863 TTATTTAAAAT
1 TTATTTAAAAT
1356874 TTATTTAAAAT
1 TTATTTAAAAT
*
1356885 TGATTTAAAAT
1 TTATTTAAAAT
**
1356896 AAATATT-AAA-
1 TTAT-TTAAAAT
1356906 TTATTT-AAAT
1 TTATTTAAAAT
1356916 TTATTTAA
1 TTATTTAA
1356924 TTTAAATTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 27 0.64
12 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
TTATTTAAAAT
Found at i:1356956 original size:20 final size:21
Alignment explanation
Indices: 1356908--1356957 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1356898 ATATTAAATT
1356908 ATTTAAATTTATTTAATTTAA
1 ATTTAAATTTATTTAATTTAA
*
1356929 A-TTCAATTT-TTGT-ATTTAA
1 ATTTAAATTTATT-TAATTTAA
1356948 ATTTAAATTT
1 ATTTAAATTT
1356958 GAATTGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 9 0.36
20 15 0.60
21 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTAAATTTATTTAATTTAA
Found at i:1360487 original size:21 final size:21
Alignment explanation
Indices: 1360461--1360504 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1360451 CTGCATGTAT
1360461 TTCATTTAAGTTATTGCTTTG
1 TTCATTTAAGTTATTGCTTTG
1360482 TTCATTTAAGTTATTGCTTTG
1 TTCATTTAAGTTATTGCTTTG
1360503 TT
1 TT
1360505 TTTGTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.14, T:0.59
Consensus pattern (21 bp):
TTCATTTAAGTTATTGCTTTG
Found at i:1360646 original size:2 final size:2
Alignment explanation
Indices: 1360639--1360678 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
1360629 GTAAATACAT
*
1360639 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
1360679 TATTAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1366116 original size:2 final size:2
Alignment explanation
Indices: 1366109--1366147 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1366099 ACACATATAA
1366109 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1366148 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1368393 original size:15 final size:16
Alignment explanation
Indices: 1368360--1368399 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
1368350 CAATCCGTAC
1368360 AAAAAAATATTTTCAAT
1 AAAAAAATATTTT-AAT
*
1368377 AAAAAAATCTTTT-AT
1 AAAAAAATATTTTAAT
1368392 AAAAAAAT
1 AAAAAAAT
1368400 TCAAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
17 12 0.55
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAAATATTTTAAT
Found at i:1368919 original size:28 final size:28
Alignment explanation
Indices: 1368888--1368944 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
1368878 AATTAATTTT
1368888 TAAAAATTAAAA-AATTTAATTTGATTAA
1 TAAAAA-TAAAATAATTTAATTTGATTAA
1368916 TAAAAATAAAATAATTTAATTTGATTAA
1 TAAAAATAAAATAATTTAATTTGATTAA
1368944 T
1 T
1368945 TTAATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (28 bp):
TAAAAATAAAATAATTTAATTTGATTAA
Found at i:1377956 original size:20 final size:20
Alignment explanation
Indices: 1377931--1377969 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1377921 AAAAAAAAAA
1377931 AGTTATATTTAA-ACACATAC
1 AGTTATA-TTAACACACATAC
1377951 AGTTATATTAACACACATA
1 AGTTATATTAACACACATA
1377970 AATTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (20 bp):
AGTTATATTAACACACATAC
Found at i:1378139 original size:43 final size:43
Alignment explanation
Indices: 1378091--1378172 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
1378081 CACAAAAGCA
*
1378091 TCAAATAAGGCGTTT-CTTTGAACAAACGCCTTATTTGATCCAT
1 TCAAATAAGGCGTTTCCTTT-AACAAACACCTTATTTGATCCAT
*
1378134 TCAAATAAGGCGTTTCCTTTTACAAACACCTTATTTGAT
1 TCAAATAAGGCGTTTCCTTTAACAAACACCTTATTTGAT
1378173 AGATGATCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 32 0.89
44 4 0.11
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (43 bp):
TCAAATAAGGCGTTTCCTTTAACAAACACCTTATTTGATCCAT
Found at i:1378291 original size:69 final size:71
Alignment explanation
Indices: 1378130--1378336 Score: 230
Period size: 69 Copynumber: 3.0 Consensus size: 71
1378120 CTTATTTGAT
* * *
1378130 CCATTCAAATAAGGCGTTTCC-TTTTACAAACACCTTATTTGATAGATGATCTTCTAAAATCTTT
1 CCATTCAAATAAGGCGTTTCCATTTTACAAACGCCTTATTTGATAGAT-ATCTTCCAAAATATTT
1378194 ACAAAAG
65 ACAAAAG
* * * *
1378201 -CA-TCAAATAAGGCGTTT-CATTTTACAAACGCCTTATTTTAT-GCT-TTTTCCAACATATTTA
1 CCATTCAAATAAGGCGTTTCCATTTTACAAACGCCTTATTTGATAGATATCTTCCAAAATATTTA
1378261 C-AAAG
66 CAAAAG
* * * * *
1378266 CCCATTCAAATAAAGCATTTCCATTTTACAAACGCCTTATTTGATAGACGATCTTCCAGAATCTT
1 -CCATTCAAATAAGGCGTTTCCATTTTACAAACGCCTTATTTGATAGA-TATCTTCCAAAATATT
1378331 TACAAA
64 TACAAA
1378337 TTCAAATAAG
Statistics
Matches: 111, Mismatches: 16, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
65 4 0.04
66 13 0.12
67 2 0.02
68 16 0.14
69 58 0.52
70 3 0.03
72 13 0.12
73 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.35
Consensus pattern (71 bp):
CCATTCAAATAAGGCGTTTCCATTTTACAAACGCCTTATTTGATAGATATCTTCCAAAATATTTA
CAAAAG
Found at i:1378426 original size:138 final size:137
Alignment explanation
Indices: 1378134--1378407 Score: 340
Period size: 136 Copynumber: 2.0 Consensus size: 137
1378124 TTTGATCCAT
* * * *
1378134 TCAAATAAGGCGTTTCC-TTTTACAAACACCTTATTTGATAGATGATCTTCTAAAATCTTTACAA
1 TCAAATAAAGCATTTCCATTTTACAAACACCTTATTTGATAGACGATCTTCCAAAATCTTTACAA
* * * *
1378198 AAGCATCAAATAAGGCGTTTCATTTTACAAACGCCTTATTTTATGCTTTTTCCAACATATTTACA
66 AA-CATCAAATAAGGCATTTCATTTAACAAACACCTTATTTGATGCTTTTTCCAACATATTTACA
** * *
1378263 AAGCCCAT
130 AAAACAAG
* *
1378271 TCAAATAAAGCATTTCCATTTTACAAACGCCTTATTTGATAGACGATCTTCCAGAATCTTTAC-A
1 TCAAATAAAGCATTTCCATTTTACAAACACCTTATTTGATAGACGATCTTCCAAAATCTTTACAA
* * *
1378335 AA-TTCAAATAAGGTATTT-ACTTTGAATAAACACCTTATTTGATGCTTTTTCCAACATATTTAC
66 AACATCAAATAAGGCATTTCA-TTT-AACAAACACCTTATTTGATGCTTTTTCCAACATATTTAC
1378398 AAAAACAAG
129 AAAAACAAG
1378407 T
1 T
1378408 AAGGTGTTCA
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
134 1 0.01
135 16 0.14
136 41 0.35
137 18 0.15
138 41 0.35
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (137 bp):
TCAAATAAAGCATTTCCATTTTACAAACACCTTATTTGATAGACGATCTTCCAAAATCTTTACAA
AACATCAAATAAGGCATTTCATTTAACAAACACCTTATTTGATGCTTTTTCCAACATATTTACAA
AAACAAG
Found at i:1387282 original size:22 final size:20
Alignment explanation
Indices: 1387249--1387288 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
1387239 ATAAAATATA
1387249 TATTTTTATTTTATTAAATT
1 TATTTTTATTTTATTAAATT
1387269 TATTTATTATTTTTATTAAA
1 TATTT-TTA-TTTTATTAAA
1387289 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTTTATTTTATTAAATT
Found at i:1387299 original size:22 final size:22
Alignment explanation
Indices: 1387257--1387300 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1387247 TATATTTTTA
**
1387257 TTTTATTAAATTTATTTATTAT
1 TTTTATTAAATTTATAAATTAT
1387279 TTTTATTAAAATTT-TAAATTAT
1 TTTTATT-AAATTTATAAATTAT
1387301 ATTATTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATTAAATTTATAAATTAT
Found at i:1388695 original size:20 final size:21
Alignment explanation
Indices: 1388655--1388719 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
1388645 CTAACATAAA
*
1388655 AATAATATAATTTAAATTTTT
1 AATAATATAATATAAATTTTT
*
1388676 AATAATA-AATATATATTTTT
1 AATAATATAATATAAATTTTT
* *
1388696 TATAATATAAAAATAATATTTTT
1 AATAATAT-AATATAA-ATTTTT
1388719 A
1 A
1388720 TATTTTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 17 0.49
21 7 0.20
22 5 0.14
23 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATAATATAATATAAATTTTT
Found at i:1388705 original size:22 final size:23
Alignment explanation
Indices: 1388671--1388718 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1388661 ATAATTTAAA
*
1388671 TTTTTAATAATAAATAT-ATATT
1 TTTTTAATAATAAAAATAATATT
1388693 TTTTATAAT-ATAAAAATAATATT
1 TTTT-TAATAATAAAAATAATATT
1388716 TTT
1 TTT
1388719 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTTAATAATAAAAATAATATT
Found at i:1389714 original size:31 final size:31
Alignment explanation
Indices: 1389671--1389734 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1389661 ATTTTAAGAT
* *
1389671 TTGTCTATAATAAGGTCGCAATATATTGATC
1 TTGTCTACAATAAGGTCGCAATATATCGATC
* *
1389702 TTGTCTACAATAAGGTTGTAATATATCGATC
1 TTGTCTACAATAAGGTCGCAATATATCGATC
1389733 TT
1 TT
1389735 AGTATAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (31 bp):
TTGTCTACAATAAGGTCGCAATATATCGATC
Found at i:1389769 original size:10 final size:10
Alignment explanation
Indices: 1389746--1389787 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1389736 GTATAAAGTC
*
1389746 ATGAGATATT
1 ATGATATATT
1389756 ATGATAT-TT
1 ATGATATATT
1389765 AATGATATATT
1 -ATGATATATT
*
1389776 ATGATAAATT
1 ATGATATATT
1389786 AT
1 AT
1389788 AAGATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 2 0.07
10 24 0.86
11 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (10 bp):
ATGATATATT
Found at i:1390511 original size:17 final size:18
Alignment explanation
Indices: 1390491--1390536 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
1390481 TAAACACTTA
*
1390491 TTTTTT-TATTGAATTAT
1 TTTTTTATATTGAATAAT
*
1390508 TTTTTTATAAT-AATAAT
1 TTTTTTATATTGAATAAT
1390525 TTTTTTATATTG
1 TTTTTTATATTG
1390537 TCAACTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTTTATATTGAATAAT
Found at i:1390821 original size:21 final size:21
Alignment explanation
Indices: 1390789--1390860 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 21
1390779 GGTTTAGAAT
1390789 TTTTTTAT-TTATAATAATAA
1 TTTTTTATGTTATAATAATAA
*
1390809 TTTTTTATGTTATCAAT-TTAA
1 TTTTTTATGTTAT-AATAATAA
* **
1390830 TTATTTACATTATAATAA-AA
1 TTTTTTATGTTATAATAATAA
* *
1390850 TCTGTTATGTT
1 TTTTTTATGTT
1390861 TTTTCTTACA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 19 0.49
21 17 0.44
22 3 0.08
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTTTTATGTTATAATAATAA
Found at i:1390935 original size:282 final size:282
Alignment explanation
Indices: 1390450--1390975 Score: 600
Period size: 282 Copynumber: 1.9 Consensus size: 282
1390440 CCAAATAATG
* * *
1390450 CAAATTTTACGGTCATTCTCACATTTTTACATAAACACTTATTTTTTTATTGAATTATTTTTTTA
1 CAAATTTTACGATCATTCTCACAATTTTACATAAACACTTATTTTTTTATAGAATTATTTTTTTA
* ** * * *
1390515 TAATAATAATTTTTTTATATTGTCAACTTAATTATTTATGTTAAAATAATATTTTTTACGCTTGT
66 TAATAATAATTTTTTTATATTATCAACTTAATTATTTACATTAAAATAAAATCTGTTACGCTTGT
* * * * * * * * **
1390580 TCTTATATTTATTATGTTTAGAATTATCTCAACTTTTTTTTTAAGATATTACGATAGTTCTAGCT
131 TCTTACATTTATTATATTCAGAATTATCACAACTTTTTTCTTAAGATATTACCACACTTCTAAAT
*
1390645 TGATTTTACACT-AAATGATA-CTAATTTTATGATTATTCTCACATTTTTACGTTACAATACTTT
196 TGATTTTAC-CTCAAATGATATC-AATTTTATGATGATTCTCACATTTTTACGTTACAATACTTT
1390708 TAACATATTTTACATTAAATTATA
259 TAACATATTTTACATTAAATTATA
** * * * *
1390732 CAAATTTTACGATCATTCTCACAATTTTATGTTAATATTTATTTTTAGGTT-TAGAATTTTTTTA
1 CAAATTTTACGATCATTCTCACAATTTTACATAAACACTTATTTTT---TTATAGAATTATTTT-
* * * * *
1390796 TTTATAATAATAA-TTTTTTATGTTATCAATTTAATTATTTACATTATAATAAAATCTGTTATGT
62 TTTATAATAATAATTTTTTTATATTATCAACTTAATTATTTACATTAAAATAAAATCTGTTACGC
*
1390860 TTTTTCTTACATTTTATTATATTCAGAATTATCACAA-TTTTTTCTTAA-ATATTACCACACTTC
127 TTGTTCTTACA-TTTATTATATTCAGAATTATCACAACTTTTTTCTTAAGATATTACCACACTTC
* * **
1390923 -AAATAT-ATTTTACGTCAAATTATATCAATTTTATGATGATTCTTGCATTTTTA
191 TAAAT-TGATTTTACCTCAAATGATATCAATTTTATGATGATTCTCACATTTTTA
1390976 ATTTAACACT
Statistics
Matches: 200, Mismatches: 36, Indels: 16
0.79 0.14 0.06
Matches are distributed among these distances:
281 1 0.00
282 79 0.40
283 14 0.07
284 69 0.34
285 37 0.19
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (282 bp):
CAAATTTTACGATCATTCTCACAATTTTACATAAACACTTATTTTTTTATAGAATTATTTTTTTA
TAATAATAATTTTTTTATATTATCAACTTAATTATTTACATTAAAATAAAATCTGTTACGCTTGT
TCTTACATTTATTATATTCAGAATTATCACAACTTTTTTCTTAAGATATTACCACACTTCTAAAT
TGATTTTACCTCAAATGATATCAATTTTATGATGATTCTCACATTTTTACGTTACAATACTTTTA
ACATATTTTACATTAAATTATA
Found at i:1391006 original size:18 final size:19
Alignment explanation
Indices: 1390970--1391009 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1390960 GATTCTTGCA
*
1390970 TTTTTAATTTAACACTTAT
1 TTTTTAATTTAACAATTAT
*
1390989 TTTTTTATTTAA-AATTAT
1 TTTTTAATTTAACAATTAT
1391007 TTT
1 TTT
1391010 GATTTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTAATTTAACAATTAT
Found at i:1391455 original size:20 final size:20
Alignment explanation
Indices: 1391430--1391492 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
1391420 TTTTGTTTAA
1391430 AATTATTATTTATTTATAAT
1 AATTATTATTTATTTATAAT
1391450 AATTATT-TTATATTT-TCAA-
1 AATTATTATT-TATTTAT-AAT
*
1391469 AAATATTATTTATATTATAAT
1 AATTATTATTTAT-TTATAAT
1391490 AAT
1 AAT
1391493 ATTTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
19 12 0.34
20 20 0.57
21 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTATTATTTATTTATAAT
Found at i:1391482 original size:21 final size:20
Alignment explanation
Indices: 1391425--1391506 Score: 62
Period size: 21 Copynumber: 4.1 Consensus size: 20
1391415 TATTTTTTTG
*
1391425 TTTAAAATTATTATTTAT-T
1 TTTAAAAATATTATTTATAT
* *
1391444 TAT-AATA-ATTATTTTATAT
1 TTTAAAAATATTA-TTTATAT
1391463 TTTCAAAAATATTATTTATAT
1 TTT-AAAAATATTATTTATAT
* * *
1391484 TATAATAATATTTTTTTATAT
1 TTTAAAAATA-TTATTTATAT
1391505 TT
1 TT
1391507 GTTCATACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
17 4 0.08
18 7 0.15
19 5 0.10
20 6 0.12
21 22 0.46
22 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAAAAATATTATTTATAT
Found at i:1392280 original size:220 final size:221
Alignment explanation
Indices: 1391986--1392410 Score: 525
Period size: 220 Copynumber: 1.9 Consensus size: 221
1391976 TGTTGTTATT
* * * * *
1391986 TTTTATTGCATTTAGAATTATTACAAATTTTTTTCTTAAGGTGTAACAATACTTTTAATTATTTT
1 TTTTATTACATTTAAAAGTATTACAAATTTTTTTCTAAAGGTGTAACAACACTTTTAATTATTTT
* * ** *
1392051 ACGTTAAATAATATAAATTTTACAATTATTCTCACAATTTT-ATGTTAACTCTTAACTTTTAATT
66 ACATTAAATAATACAAATTTTACAATTATTCTCACAATTTTCATACTAACACTTAACTTTTAATT
** * **
1392115 TAAAATTATTTTTTTGTTTGTAATAATAATTCTTTTATATTGCC-AATTTAATTATTTATGTTAT
131 TAAAATTA-TTAATTATTTGTAATAATAATTCTTTTATATTGCCAAAAAT-ATTATTTATGTTAT
*
1392179 ATTAATTTTTTTTACATTTATTTTTACC
194 AATAATTTTTTTTACATTTATTTTTACC
* * * *
1392207 TTTTATTACGTTTAAAAGTATTACAACTTTTTTT-TAAAGGTGTTACGACACTTCTT-ATTATTT
1 TTTTATTACATTTAAAAGTATTACAAATTTTTTTCTAAAGGTGTAACAACACTT-TTAATTATTT
** ** ** **
1392270 TACATTAAATAATACAAATTTTATGATTATTCTCACCTTTTTCATACTAACACTTATTTTTTGGT
65 TACATTAAATAATACAAATTTTACAATTATTCTCACAATTTTCATACTAACACTTAACTTTTAAT
* *
1392335 TTAAAATTATTAATTATTTGTAGTAATAATTCTTTTATATTGCTAAAAATATTATTTATGTTATA
130 TTAAAATTATTAATTATTTGTAATAATAATTCTTTTATATTGCCAAAAATATTATTTATGTTATA
1392400 ATAATTTTTTT
195 ATAATTTTTTT
1392411 GTTTAAACTT
Statistics
Matches: 171, Mismatches: 30, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
220 113 0.66
221 58 0.34
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (221 bp):
TTTTATTACATTTAAAAGTATTACAAATTTTTTTCTAAAGGTGTAACAACACTTTTAATTATTTT
ACATTAAATAATACAAATTTTACAATTATTCTCACAATTTTCATACTAACACTTAACTTTTAATT
TAAAATTATTAATTATTTGTAATAATAATTCTTTTATATTGCCAAAAATATTATTTATGTTATAA
TAATTTTTTTTACATTTATTTTTACC
Found at i:1392610 original size:20 final size:19
Alignment explanation
Indices: 1392587--1392631 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1392577 TTAACACTTC
* *
1392587 TTTTTTTGT-TAATAATTA
1 TTTTTTTTTATAATAATAA
1392605 TTTTTTATTTATAATAATAA
1 TTTTTT-TTTATAATAATAA
1392625 TTTTTTT
1 TTTTTTT
1392632 AAGTTGTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 3 0.13
20 14 0.61
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTTTTTATAATAATAA
Found at i:1393213 original size:217 final size:213
Alignment explanation
Indices: 1392820--1393222 Score: 470
Period size: 216 Copynumber: 1.9 Consensus size: 213
1392810 ATGTAGGATT
* **
1392820 ATTTTTTATTTATAATACTCATTTTTTTCATTACCAATTTAATTATGTACATTTTAATATTTCTT
1 ATTTTTTATTTATAATACTCATTTTTTTCATTACCAATTTAATTATGTACATTATAATACATCTT
* * * * *
1392885 TTACACTTGTTGTTACTTTTCATTACGTTTAGAATTATCACAATATTTTATTAAGGTGTAACGAT
66 TTACACCTGTTATTACTTTTCATTACGTTTAGAACTATCACAATATTTTATTAAGGTGTAACAAC
* * * * * *
1392950 ATTTGTAATCATTTTACGTCAAATAATACTAATTTTATGATTATTCTCATTTTTTTTACATTAAC
131 ACTTCTAATCATTTTACATCAAATAACACAAATTTTATGATTATTCTCACTTTTTTTACATTAAC
1393015 TTTTATTTTTTGTTTAAA
196 TTTTATTTTTTGTTTAAA
* * * **
1393033 ATTTTTTATTTGTAATAGT-ATTTATTTTACATTACCAATTTAATTATTTTTATTATAATAACAT
1 ATTTTTTATTTATAATACTCATTT-TTTT-CATTACCAATTTAATTATGTACATTATAAT-ACAT
* * * *
1393097 CTTTTTATACCTGTTATTATTTTTCATTACGTTTATAACTATCACAAT-TCTTTGTT-AGGATGT
63 C-TTTTACACCTGTTATTACTTTTCATTACGTTTAGAACTATCACAATAT-TTTATTAAGG-TGT
* * * * *
1393160 TACAACACTTCTAACTTATTTTACATTAAATGACACAAATTTTATGATTATTCTTACTTTTTT
125 AACAACACTTCTAA-TCATTTTACATCAAATAACACAAATTTTATGATTATTCTCACTTTTTT
1393223 ATGTTAAAAC
Statistics
Matches: 155, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
212 4 0.03
213 21 0.14
214 26 0.17
215 7 0.05
216 57 0.37
217 40 0.26
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (213 bp):
ATTTTTTATTTATAATACTCATTTTTTTCATTACCAATTTAATTATGTACATTATAATACATCTT
TTACACCTGTTATTACTTTTCATTACGTTTAGAACTATCACAATATTTTATTAAGGTGTAACAAC
ACTTCTAATCATTTTACATCAAATAACACAAATTTTATGATTATTCTCACTTTTTTTACATTAAC
TTTTATTTTTTGTTTAAA
Found at i:1394805 original size:31 final size:29
Alignment explanation
Indices: 1394750--1394807 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 29
1394740 TGAAAGAATT
*
1394750 TTATGTTTTTTTTTTAAATTTTTTTAGAA
1 TTATGTTTTTTTTTTAAATCTTTTTAGAA
1394779 TTAT-TTTTTTATTTTATAATACTTTTTAG
1 TTATGTTTTTT-TTTTA-AAT-CTTTTTAG
1394808 CTATTTAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 6 0.24
29 9 0.36
30 3 0.12
31 7 0.28
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (29 bp):
TTATGTTTTTTTTTTAAATCTTTTTAGAA
Found at i:1418078 original size:15 final size:15
Alignment explanation
Indices: 1418060--1418095 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1418050 ATATGATTTT
*
1418060 TATTTTTTTAATTCA
1 TATTATTTTAATTCA
1418075 TATTATTTTAATTCA
1 TATTATTTTAATTCA
1418090 TATTAT
1 TATTAT
1418096 ATTTTTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTATTTTAATTCA
Found at i:1418098 original size:17 final size:17
Alignment explanation
Indices: 1418065--1418118 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 17
1418055 ATTTTTATTT
1418065 TTTTAATTCATA-T-TA
1 TTTTAATTCATATTATA
1418080 TTTTAATTCATATTATA
1 TTTTAATTCATATTATA
* *
1418097 TTTTTA-TCATATCATCA
1 TTTTAATTCATATTAT-A
1418114 TTTTA
1 TTTTA
1418119 TATTTAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 12 0.36
16 9 0.27
17 12 0.36
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAATTCATATTATA
Found at i:1418663 original size:11 final size:11
Alignment explanation
Indices: 1418647--1418679 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1418637 CATGATAAGG
1418647 TGGCTGGTTCT
1 TGGCTGGTTCT
1418658 TGGCTGGTTCT
1 TGGCTGGTTCT
*
1418669 TGGCTTGTTCT
1 TGGCTGGTTCT
1418680 GAACAGCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.18, G:0.33, T:0.48
Consensus pattern (11 bp):
TGGCTGGTTCT
Found at i:1419588 original size:27 final size:27
Alignment explanation
Indices: 1419546--1419642 Score: 106
Period size: 27 Copynumber: 3.5 Consensus size: 27
1419536 GTCTGAACTC
*
1419546 AAGAAGCTCAATTCCACTTCCCTGTTA
1 AAGAAGCTCAACTCCACTTCCCTGTTA
*
1419573 AAGAAGCTCAACTCCACTTCTCTCCTG-AA
1 AAGAAGCTCAACTCCAC-T-TC-CCTGTTA
* * *
1419602 GAAGAAACTCAATTCCACTTTCCTGTTA
1 -AAGAAGCTCAACTCCACTTCCCTGTTA
1419630 AAGAAGCTCAACT
1 AAGAAGCTCAACT
1419643 TCACATCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
27 31 0.54
28 3 0.05
29 4 0.07
30 19 0.33
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.27
Consensus pattern (27 bp):
AAGAAGCTCAACTCCACTTCCCTGTTA
Found at i:1419634 original size:30 final size:29
Alignment explanation
Indices: 1419546--1419635 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 29
1419536 GTCTGAACTC
*
1419546 AAGAAGCTCAATTCCACTTCCCTGTTAAAG
1 AAGAA-CTCAATTCCACTTTCCTGTTAAAG
* ** *
1419576 AAG--CTCAACTCCAC-TTCTCTCCTGAAG
1 AAGAACTCAATTCCACTTTC-CTGTTAAAG
1419603 AAGAAACTCAATTCCACTTTCCTGTTAAAG
1 AAG-AACTCAATTCCACTTTCCTGTTAAAG
1419633 AAG
1 AAG
1419636 CTCAACTTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
26 2 0.04
27 19 0.41
30 22 0.48
31 3 0.07
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (29 bp):
AAGAACTCAATTCCACTTTCCTGTTAAAG
Found at i:1421823 original size:36 final size:36
Alignment explanation
Indices: 1421772--1421840 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
1421762 TAAATTTAAC
* *
1421772 TTAAAATTTATTTTTTGAAATTT-GATTTGATTTTGA
1 TTAAAATTTAATTTTT-AAATTTAAATTTGATTTTGA
*
1421808 TTAAATTTTAATTTTTAAATTTAAATTTGATTT
1 TTAAAATTTAATTTTTAAATTTAAATTTGATTT
1421841 GAAATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 6 0.21
36 23 0.79
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (36 bp):
TTAAAATTTAATTTTTAAATTTAAATTTGATTTTGA
Found at i:1422470 original size:401 final size:399
Alignment explanation
Indices: 1421691--1422488 Score: 1219
Period size: 401 Copynumber: 2.0 Consensus size: 399
1421681 TAATTAAAGG
* *
1421691 TTTGTGAAGCATTCTAGTCTACGGGTGTAATTGATTCAGTTAGTTAAATTCGTATAGTGAGAATT
1 TTTGTGAAGCATTCTAGTCTACGGGTGTAATTGATTCAATTAGTTAAATTCATATAGTGAGAATT
* *
1421756 TGAGTTTAAATTTAACTTAAAATTTATTTTTTGAAATTTGATTTGATTTTGATTAAATTTTAATT
66 TGAGTTTAAATTTAACTTAAAATTTATTATTTGAAATTTGATTTGAATTTGATTAAATTTTAATT
* * * *
1421821 TTTAAATTTAAATTTGATTTGAAATAAAAATTAAATTACTTAAACTTATTCTATTAGATTTATTT
131 TTTAAATTTAAATTCGATTTAAAATAAAAATAAAATTACTTAAACTTATTCGATTAGATTTATTT
*
1421886 ATAAAATAAAAAAAGTTCAATTTTTTTATTTGACTTTAAATTAGATCATTTTTATTCAAATTATA
196 ATAAAATAAAAAAAGTTCAATTTTTATATTTGACTTTAAATTAGATCATTTTTATTCAAATTATA
* *
1421951 GCTTGAACTCAATTTAATTTATATATATGGATAAAATAATAAATTTTTAATTAAAATCTTAAAAA
261 GCTTGAACTCAAATTAA-TTATATATATGGACAAAATAATAAATTTTTAATTAAAATCTTAAAAA
* * * *
1422016 TATATATTAAAATAAAAAAATTTGATTAGATTTTTGAGCTATTTGAATTTAAAATTAAGATACTT
325 TATATATTAAAATAAAAAAATTTAATTAGACTTATGAACTATTTGAATTTAAAATTAAGATACTT
1422081 GAATTTATTA
390 GAATTTATTA
* * *
1422091 TTTGTGATGCATTCTAGTCTACGGGTGTAATTGATTCAATTAGTTGAGTTCATATAGTGA-AATT
1 TTTGTGAAGCATTCTAGTCTACGGGTGTAATTGATTCAATTAGTTAAATTCATATAGTGAGAA-T
* *
1422155 TTGAGTTTAAATTCT-ATTTAAAATTTATTATTTGAAATTTGATTTGAATTTGATTAATTTTTAA
65 TTGAGTTTAAATT-TAACTTAAAATTTATTATTTGAAATTTGATTTGAATTTGATTAAATTTTAA
* * * *
1422219 TTTTTAAGTTTGAATTCGATTTAAAAATAAAAATAAAATTATTTGAA-TTCATTCGATTAGATTT
129 TTTTTAAATTTAAATTCGATTT-AAAATAAAAATAAAATTACTTAAACTT-ATTCGATTAGATTT
* * *
1422283 ATTTATCAAATAAAAAAAGATTTTAATTTTTATATTTGATTTTAAATTAGATCATTTTTATTCAA
192 ATTTATAAAATAAAAAAAG--TTCAATTTTTATATTTGACTTTAAATTAGATCATTTTTATTCAA
1422348 ATTATAGCTTGAACTCAAATTAA-TATATATATGGACAAAATAATAAATTTTTAATTAAAA-CAT
255 ATTATAGCTTGAACTCAAATTAATTATATATATGGACAAAATAATAAATTTTTAATTAAAATC-T
* * *
1422411 TAAAAATATATATTAAAATAAAAAATTTTAATTAGACTTATGAATTATTTGAGTTTAAAATTAAG
319 TAAAAATATATATTAAAATAAAAAAATTTAATTAGACTTATGAACTATTTGAATTTAAAATTAAG
1422476 ATACTTGAATTTA
384 ATACTTGAATTTA
1422489 ACTCATTAAA
Statistics
Matches: 361, Mismatches: 30, Indels: 13
0.89 0.07 0.03
Matches are distributed among these distances:
399 2 0.01
400 136 0.38
401 160 0.44
403 63 0.17
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (399 bp):
TTTGTGAAGCATTCTAGTCTACGGGTGTAATTGATTCAATTAGTTAAATTCATATAGTGAGAATT
TGAGTTTAAATTTAACTTAAAATTTATTATTTGAAATTTGATTTGAATTTGATTAAATTTTAATT
TTTAAATTTAAATTCGATTTAAAATAAAAATAAAATTACTTAAACTTATTCGATTAGATTTATTT
ATAAAATAAAAAAAGTTCAATTTTTATATTTGACTTTAAATTAGATCATTTTTATTCAAATTATA
GCTTGAACTCAAATTAATTATATATATGGACAAAATAATAAATTTTTAATTAAAATCTTAAAAAT
ATATATTAAAATAAAAAAATTTAATTAGACTTATGAACTATTTGAATTTAAAATTAAGATACTTG
AATTTATTA
Found at i:1424696 original size:9 final size:9
Alignment explanation
Indices: 1424675--1424707 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1424665 TAAATTTCTT
*
1424675 TTATTTTTA
1 TTATTTTAA
1424684 -TATTTTAA
1 TTATTTTAA
1424692 TTATTTTAA
1 TTATTTTAA
1424701 TTATTTT
1 TTATTTT
1424708 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTATTTTAA
Found at i:1424766 original size:26 final size:28
Alignment explanation
Indices: 1424716--1424776 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 28
1424706 TTTTTAATAA
1424716 AATTTAATATAAAAAATTATGAAAATTT
1 AATTTAATATAAAAAATTATGAAAATTT
* *
1424744 AATTTTATA-AAAAAATT-TTAAAATTT
1 AATTTAATATAAAAAATTATGAAAATTT
1424770 AATTTAA
1 AATTTAA
1424777 ATAGATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 14 0.47
27 8 0.27
28 8 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
AATTTAATATAAAAAATTATGAAAATTT
Found at i:1431864 original size:17 final size:18
Alignment explanation
Indices: 1431842--1431883 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1431832 ATAATAAAAA
1431842 TTTTATTTTA-TTTTATT
1 TTTTATTTTATTTTTATT
1431859 TTTTA-TTTATTTTTATT
1 TTTTATTTTATTTTTATT
1431876 TTTATATT
1 TTT-TATT
1431884 GTATATTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.18
17 15 0.68
18 2 0.09
19 1 0.05
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTATTTTATTTTTATT
Found at i:1434534 original size:19 final size:20
Alignment explanation
Indices: 1434510--1434551 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1434500 ACTCAAAATC
*
1434510 TAATTTTAAATA-GATATAA
1 TAATTTTAAATATGATAAAA
1434529 TAATTTTAAATATGATAAAA
1 TAATTTTAAATATGATAAAA
1434549 TAA
1 TAA
1434552 CGTGATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
TAATTTTAAATATGATAAAA
Found at i:1435194 original size:2 final size:2
Alignment explanation
Indices: 1435187--1435211 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1435177 AACTCAACTT
1435187 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 T
1435212 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1435465 original size:19 final size:19
Alignment explanation
Indices: 1435443--1435485 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1435433 GCTTTAGAAC
1435443 AAAAATTGGAATATAAAAA
1 AAAAATTGGAATATAAAAA
1435462 AAAAATTGGAATATAAAAA
1 AAAAATTGGAATATAAAAA
1435481 AAAAA
1 AAAAA
1435486 ATCCGGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (19 bp):
AAAAATTGGAATATAAAAA
Found at i:1440988 original size:133 final size:134
Alignment explanation
Indices: 1440805--1441045 Score: 353
Period size: 133 Copynumber: 1.8 Consensus size: 134
1440795 ACAACATATG
* *
1440805 GAGGAACATTAAGCACTTTCTAAGCAACCTCTGAAATCTTATCAGTTGCATCC-CTAAAATTCTT
1 GAGGAACATTAAGCACTTTCTAAGCAACCTCTGAAATCTTATCACTTGCATCCTC-AAAATTCAT
**
1440869 GATGAA-ATGTTGCTTATTCAGTAATAATTGTTGATTATTACAAGAAAGAACTTGAGTGAGACAG
65 GATGAATATGTTGCACATTCAGTAATAATTGTTGATTATTACAAGAAAGAACTTGAGTGAGACAG
1440933 GGATA
130 GGATA
* * *
1440938 GAGGGACATTAAGCACTTTCTTAGCAACCTCTGAAATCTTA-CCCTATGCATCCTCAAAATTCAT
1 GAGGAACATTAAGCACTTTCTAAGCAACCTCTGAAATCTTATCACT-TGCATCCTCAAAATTCAT
* **
1441002 GATGAATATGTTTCACATTCAGTAATGGTTGTTGATTATTACAA
65 GATGAATATGTTGCACATTCAGTAATAATTGTTGATTATTACAA
1441046 CTAAAATGTG
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
132 2 0.02
133 60 0.63
134 33 0.35
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (134 bp):
GAGGAACATTAAGCACTTTCTAAGCAACCTCTGAAATCTTATCACTTGCATCCTCAAAATTCATG
ATGAATATGTTGCACATTCAGTAATAATTGTTGATTATTACAAGAAAGAACTTGAGTGAGACAGG
GATA
Found at i:1452354 original size:27 final size:26
Alignment explanation
Indices: 1452324--1452380 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
1452314 TAAAAATAAA
1452324 ATAAAATGATATTATTTAATTTAATTT
1 ATAAAATGATATTATTTAATTTAA-TT
* * * *
1452351 ATAATATTATATTATTTTATTTTATT
1 ATAAAATGATATTATTTAATTTAATT
1452377 ATAA
1 ATAA
1452381 TTTTGTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
ATAAAATGATATTATTTAATTTAATT
Found at i:1455289 original size:16 final size:18
Alignment explanation
Indices: 1455268--1455300 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1455258 TCCTATTTTC
1455268 ATATTAT-GT-TTATATA
1 ATATTATCGTATTATATA
1455284 ATATTATCGTATTATAT
1 ATATTATCGTATTATAT
1455301 TTTAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (18 bp):
ATATTATCGTATTATATA
Found at i:1473912 original size:3 final size:3
Alignment explanation
Indices: 1473904--1473942 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1473894 GTTTCTTAAC
1473904 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1473943 TGAATGCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1474119 original size:26 final size:26
Alignment explanation
Indices: 1474089--1474140 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1474079 TTATATATAT
1474089 ATATATATATATATATGCACATATTG
1 ATATATATATATATATGCACATATTG
*
1474115 ATATATATATATATATGCATATATTG
1 ATATATATATATATATGCACATATTG
1474141 TTTCTCAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (26 bp):
ATATATATATATATATGCACATATTG
Found at i:1474138 original size:2 final size:2
Alignment explanation
Indices: 1474080--1474130 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
1474070 AGAGTTGTAT
* * *
1474080 TA TA TA TA TA TA TA TA TA TA TA TA TG CA CA TA T- TGA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
1474122 TA TA TA TA T
1 TA TA TA TA T
1474131 GCATATATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.95
3 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1484410 original size:13 final size:13
Alignment explanation
Indices: 1484392--1484419 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1484382 GTCAAGCCGA
1484392 AATCTTAAGACCT
1 AATCTTAAGACCT
1484405 AATCTTAAGACCT
1 AATCTTAAGACCT
1484418 AA
1 AA
1484420 GGTAGGTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (13 bp):
AATCTTAAGACCT
Found at i:1488066 original size:9 final size:9
Alignment explanation
Indices: 1488049--1488078 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1488039 GTTTTGATTG
1488049 GAGGAGAAA
1 GAGGAGAAA
*
1488058 GATGAGAAA
1 GAGGAGAAA
1488067 GAGGAGAAA
1 GAGGAGAAA
1488076 GAG
1 GAG
1488079 TTAATTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.43, T:0.03
Consensus pattern (9 bp):
GAGGAGAAA
Found at i:1488695 original size:25 final size:25
Alignment explanation
Indices: 1488665--1488717 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1488655 TTCTCTACTC
*
1488665 AAATATTATTTTAAGTTATGTCATT
1 AAATATTATTTCAAGTTATGTCATT
1488690 AAATATTATTTCAAGTTATGTCATT
1 AAATATTATTTCAAGTTATGTCATT
1488715 AAA
1 AAA
1488718 CATTGATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (25 bp):
AAATATTATTTCAAGTTATGTCATT
Found at i:1489058 original size:32 final size:32
Alignment explanation
Indices: 1488983--1489093 Score: 89
Period size: 32 Copynumber: 3.4 Consensus size: 32
1488973 ATATGGATTT
* *
1488983 AAATATAAAAATTTATGTATTTATGTGATATA
1 AAATATAAAAATTTATATATTTATATGATATA
* ** *
1489015 AAATATTAAAATTTATATATTTATATTTTATT
1 AAATATAAAAATTTATATATTTATATGATATA
** * *
1489047 TTATATAAAAATTATATTATAATTAATAT-AAATAA
1 AAATATAAAAATT-TA-TAT-ATTTATATGATAT-A
1489082 AAATATAAAAAT
1 AAATATAAAAAT
1489094 ATTTTTTTAT
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
32 36 0.60
33 2 0.03
34 5 0.08
35 17 0.28
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (32 bp):
AAATATAAAAATTTATATATTTATATGATATA
Found at i:1489075 original size:23 final size:23
Alignment explanation
Indices: 1489035--1489078 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1489025 ATTTATATAT
* * *
1489035 TTATATTTTATTTTATATAAAAA
1 TTATATTATAATTAATATAAAAA
1489058 TTATATTATAATTAATATAAA
1 TTATATTATAATTAATATAAA
1489079 TAAAAATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATATTATAATTAATATAAAAA
Found at i:1489130 original size:22 final size:21
Alignment explanation
Indices: 1489105--1489152 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
1489095 TTTTTTTATT
1489105 TTATT-AAATTTATAAATAATAA
1 TTATTAAAATTT-TAAATAAT-A
*
1489127 TTATTAAAATTTTAAATTATA
1 TTATTAAAATTTTAAATAATA
1489148 TTATT
1 TTATT
1489153 TTTATATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 6 0.25
22 12 0.50
23 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTAAAATTTTAAATAATA
Found at i:1506329 original size:36 final size:37
Alignment explanation
Indices: 1506273--1506348 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 37
1506263 TAAATAGGAA
1506273 CATAGAAAAAGTGAAAAAAAAACAACTAAATTGATTTC
1 CATAGAAAAAGTG-AAAAAAAACAACTAAATTGATTTC
*
1506311 CATAGAAAAAGTG-CAAAAAACAACTAAATTGATTTC
1 CATAGAAAAAGTGAAAAAAAACAACTAAATTGATTTC
1506347 CA
1 CA
1506349 AATTCTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 24 0.65
38 13 0.35
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (37 bp):
CATAGAAAAAGTGAAAAAAAACAACTAAATTGATTTC
Found at i:1510810 original size:3 final size:3
Alignment explanation
Indices: 1510791--1510828 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1510781 AAACATAGTT
* *
1510791 TTA TTT TTA TGA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1510829 TGCTTTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1511566 original size:16 final size:16
Alignment explanation
Indices: 1511545--1511582 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1511535 ATTATTTTTA
1511545 ATATAAATATAAAATT
1 ATATAAATATAAAATT
1511561 ATATAAATATAAAATT
1 ATATAAATATAAAATT
*
1511577 AAATAA
1 ATATAA
1511583 TTAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAATATAAAATT
Found at i:1517616 original size:113 final size:113
Alignment explanation
Indices: 1517418--1517629 Score: 379
Period size: 113 Copynumber: 1.9 Consensus size: 113
1517408 ATCAAGCAAC
* *
1517418 TAACTGTGCTAAATGCCTTGCAGAGTTCAACGACGAGGAGGAGGAGGATTGTAGGGTTTGTTTTT
1 TAACTGTGCTAAATGCCCTGAAGAGTTCAACGACGAGGAGGAGGAGGATTGTAGGGTTTGTTTTT
1517483 AGTGCAAACATCAATACCATAGAATTTGTATAGAGGAAGCCACAAATT
66 AGTGCAAACATCAATACCATAGAATTTGTATAGAGGAAGCCACAAATT
* *
1517531 TAACTGTGCTAAATGCCCTGAAGAGTTCAACGACGAGGAGGAGGATGCTTGTAGGGTTTGTTTTT
1 TAACTGTGCTAAATGCCCTGAAGAGTTCAACGACGAGGAGGAGGAGGATTGTAGGGTTTGTTTTT
*
1517596 AGTGCAAACATCAATACCATAGACTTTGTATAGA
66 AGTGCAAACATCAATACCATAGAATTTGTATAGA
1517630 TAAATGGTTG
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 94 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (113 bp):
TAACTGTGCTAAATGCCCTGAAGAGTTCAACGACGAGGAGGAGGAGGATTGTAGGGTTTGTTTTT
AGTGCAAACATCAATACCATAGAATTTGTATAGAGGAAGCCACAAATT
Found at i:1519032 original size:79 final size:79
Alignment explanation
Indices: 1518887--1519032 Score: 215
Period size: 79 Copynumber: 1.8 Consensus size: 79
1518877 GATAAGAGTG
* * *
1518887 ATATGATTCTAATAAATTTATTAAAAATTTTTTTAGATAAATTAATCAAAATTAAGATAAGGTAA
1 ATATGATTCTAACAAATTTATTAAAAATTTTTTTAGATAAATTAATCAAAATTAAAATAACGTAA
1518952 AATATCTTAAAAGA
66 AATATCTTAAAAGA
* *
1518966 ATATGATT-TCAACAAATTTATTGTAAAA-TTTTTTAGATAAATTAATCAAAATTAAAATAACTT
1 ATATGATTCT-AACAAATTTATT-AAAAATTTTTTTAGATAAATTAATCAAAATTAAAATAACGT
1519029 AAAA
64 AAAA
1519033 GAAGAGTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
78 1 0.02
79 55 0.92
80 4 0.07
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.38
Consensus pattern (79 bp):
ATATGATTCTAACAAATTTATTAAAAATTTTTTTAGATAAATTAATCAAAATTAAAATAACGTAA
AATATCTTAAAAGA
Found at i:1519901 original size:47 final size:47
Alignment explanation
Indices: 1519832--1519921 Score: 153
Period size: 47 Copynumber: 1.9 Consensus size: 47
1519822 ATTGTTTGTC
* *
1519832 AGTAATTGATTTGACTATTTTTGAGAATTTAAATTTTTAATGATTAT
1 AGTAATTGATTTAACTATTTTTGAGAATTTAAATTTTAAATGATTAT
*
1519879 AGTAATTGATTTAATTATTTTTGAGAATTTAAATTTTAAATGA
1 AGTAATTGATTTAACTATTTTTGAGAATTTAAATTTTAAATGA
1519922 AGATTTTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (47 bp):
AGTAATTGATTTAACTATTTTTGAGAATTTAAATTTTAAATGATTAT
Found at i:1520343 original size:18 final size:17
Alignment explanation
Indices: 1520320--1520357 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1520310 TGCCTTTTCT
*
1520320 TTTAAAGATATTGGTTAA
1 TTTAAA-ATATTGATTAA
1520338 TTT-AAATATTGATTAA
1 TTTAAAATATTGATTAA
1520354 TTTA
1 TTTA
1520358 GATAAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 13 0.72
17 2 0.11
18 3 0.17
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTAAAATATTGATTAA
Found at i:1520348 original size:16 final size:16
Alignment explanation
Indices: 1520327--1520357 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1520317 TCTTTTAAAG
*
1520327 ATATTGGTTAATTTAA
1 ATATTGATTAATTTAA
1520343 ATATTGATTAATTTA
1 ATATTGATTAATTTA
1520358 GATAAGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
ATATTGATTAATTTAA
Found at i:1520384 original size:37 final size:35
Alignment explanation
Indices: 1520343--1520441 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 35
1520333 GTTAATTTAA
1520343 ATATTGATTAATTTAGATAAGATTTCACGTTTTAAAG
1 ATATTGATTAATTTAGATAA-ATTTCAC-TTTTAAAG
1520380 ATATTGATTAA--T-GACT---TTT-ACTTTTAAAG
1 ATATTGATTAATTTAGA-TAAATTTCACTTTTAAAG
* *
1520409 ATATTGATTAATTTAGGTAAAATTTCACATTTA
1 ATATTGATTAATTTAGAT-AAATTTCACTTTTA
1520442 TAAGTGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 19
0.71 0.03 0.26
Matches are distributed among these distances:
29 19 0.37
30 2 0.04
31 5 0.10
32 1 0.02
34 2 0.04
35 5 0.10
36 6 0.12
37 11 0.22
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.45
Consensus pattern (35 bp):
ATATTGATTAATTTAGATAAATTTCACTTTTAAAG
Found at i:1526851 original size:114 final size:113
Alignment explanation
Indices: 1526488--1526916 Score: 335
Period size: 114 Copynumber: 3.7 Consensus size: 113
1526478 GACTTACATT
* * * * * * * * * **
1526488 TTCCAGTTATTTGATATCGACTCAGGTTAGATCATCTTTAGACCCGTAACGTCAGTTTGATCATT
1 TTCCAGTCATTTGATCT-TACTTAGGTCAGATCATCTTCAGACCTGTGATGTCAGTCCGATCATT
* * * * * *
1526553 TATTTTCATCCTCGACTTAGTCTTGGTCATTTTATTTTGACTCATGGTATCA
65 T-TTTT-AACCTCAACTCAGTCCTGATCGTTTTATTTTGACTCATGG-ATCA
* * * **
1526605 TTTC-GATCATTTGATCTCTACTCAAGTCAGATCATCTTCAGACCCATGATGTCAGTCCGATCAT
1 TTCCAG-TCATTTGATCT-TACTTAGGTCAGATCATCTTCAGACCTGTGATGTCAGTCCGATCA-
* * * ** * *
1526669 TTTTTTTTACCTCGATTCAGTTTTGATCGCTTTATTTTGACTTAT-GAT-A
63 TTTTTTTAACCTCAACTCAGTCCTGATCGTTTTATTTTGACTCATGGATCA
** * *
1526718 TATCTCAGTCATTTGATCTTAACTTAGGTTGGATCATCTTCAAACCTGTGATATCAGTCCGATCA
1 T-TC-CAGTCATTTGATCTT-ACTTAGGTCAGATCATCTTCAGACCTGTGATGTCAGTCCGATCA
* *
1526783 TTTTTTTAACCTCAACTCAGTCCT-ATCTTTTTATTTTGACTCGTGGCATCA
63 TTTTTTTAACCTCAACTCAGTCCTGATCGTTTTATTTTGACTCATGG-ATCA
* * * * *
1526834 TTCCAGTCATTTGATCTTGACTTAGGTCAAATCATCTTTAGACCTGCGACGTTAGTCCGATCATT
1 TTCCAGTCATTTGATCTT-ACTTAGGTCAGATCATCTTCAGACCTGTGATGTCAGTCCGATCATT
*
1526899 TCTTTTCAACGTCAACTC
65 T-TTTT-AACCTCAACTC
1526917 GATTTTGGTA
Statistics
Matches: 251, Mismatches: 50, Indels: 23
0.77 0.15 0.07
Matches are distributed among these distances:
113 18 0.07
114 77 0.31
115 57 0.23
116 43 0.17
117 53 0.21
118 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (113 bp):
TTCCAGTCATTTGATCTTACTTAGGTCAGATCATCTTCAGACCTGTGATGTCAGTCCGATCATTT
TTTTAACCTCAACTCAGTCCTGATCGTTTTATTTTGACTCATGGATCA
Found at i:1527900 original size:21 final size:22
Alignment explanation
Indices: 1527855--1527896 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1527845 TCAAAGTTTC
*
1527855 GGTGAGATTTTGAGTTTCTAGA
1 GGTGAGATTTTGAGTTTCTAAA
1527877 GGTGA-ATTTTGAG-TTCTAAA
1 GGTGAGATTTTGAGTTTCTAAA
1527897 AGGTTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.29, T:0.40
Consensus pattern (22 bp):
GGTGAGATTTTGAGTTTCTAAA
Found at i:1527966 original size:23 final size:22
Alignment explanation
Indices: 1527929--1527975 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1527919 GATTTAGGAA
*
1527929 TTTTTTAGAATTTTTTTGGATTT
1 TTTTTTAGAA-ATTTTTGGATTT
* *
1527952 TTTTTTCGAAATTTTTGGGTTT
1 TTTTTTAGAAATTTTTGGATTT
1527974 TT
1 TT
1527976 CTGGGTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.15, C:0.02, G:0.15, T:0.68
Consensus pattern (22 bp):
TTTTTTAGAAATTTTTGGATTT
Found at i:1528383 original size:5 final size:5
Alignment explanation
Indices: 1528375--1528417 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
1528365 TAGGTTTTCT
*
1528375 TTTTA TTTTA TTTTA TTTT- TATTT- TTTGA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTT
1528418 TAACCCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 3 0.09
5 31 0.91
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1528408 original size:19 final size:17
Alignment explanation
Indices: 1528380--1528418 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
1528370 TTTCTTTTTA
1528380 TTTTATTTTATTTTTATT
1 TTTTATTTTA-TTTTATT
1528398 TTTTGATTTTATTTTATT
1 TTTT-ATTTTATTTTATT
1528416 TTT
1 TTT
1528419 AACCCATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTATTTTATTTTATT
Found at i:1528427 original size:29 final size:23
Alignment explanation
Indices: 1528374--1528419 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
1528364 GTAGGTTTTC
1528374 TTTTTATTTTATTTTATTTTTAT
1 TTTTTATTTTATTTTATTTTTAT
1528397 TTTTTGATTTTATTTTATTTTTA
1 TTTTT-ATTTTATTTTATTTTTA
1528420 ACCCATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTTATTTTATTTTATTTTTAT
Found at i:1530946 original size:48 final size:48
Alignment explanation
Indices: 1530867--1530963 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
1530857 GATAATTGTT
*
1530867 TATCAATAATTGATTTGATTGTCTTTAAGAATTTAAATTTTTAATGAA
1 TATCAATAATCGATTTGATTGTCTTTAAGAATTTAAATTTTTAATGAA
* * *
1530915 TATCAGTAATCGATTTGATTGTTTTTTAGAATTTAAATTTTTAATGAA
1 TATCAATAATCGATTTGATTGTCTTTAAGAATTTAAATTTTTAATGAA
1530963 T
1 T
1530964 TTTTTTATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.49
Consensus pattern (48 bp):
TATCAATAATCGATTTGATTGTCTTTAAGAATTTAAATTTTTAATGAA
Found at i:1539417 original size:26 final size:26
Alignment explanation
Indices: 1539381--1539435 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
1539371 CTTTTAAGGC
1539381 ATTCAAAATGACATTGATATGCGCTA
1 ATTCAAAATGACATTGATATGCGCTA
1539407 ATTCAAAATGACATTGATATGCGCTA
1 ATTCAAAATGACATTGATATGCGCTA
1539433 ATT
1 ATT
1539436 ATATATTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (26 bp):
ATTCAAAATGACATTGATATGCGCTA
Found at i:1548580 original size:21 final size:20
Alignment explanation
Indices: 1548555--1548595 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1548545 AATTCATGTA
1548555 AATTTTAAAAAAATCTAATTT
1 AATTTT-AAAAAATCTAATTT
* *
1548576 AATTTTATAAATTCTAATTT
1 AATTTTAAAAAATCTAATTT
1548596 CTACTGGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTTAAAAAATCTAATTT
Found at i:1548855 original size:13 final size:14
Alignment explanation
Indices: 1548830--1548858 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1548820 AGCTATGAAA
1548830 ATTATGAAAATAAG
1 ATTATGAAAATAAG
1548844 ATTATG-AAATAAG
1 ATTATGAAAATAAG
1548857 AT
1 AT
1548859 GAAAATTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (14 bp):
ATTATGAAAATAAG
Found at i:1550489 original size:20 final size:20
Alignment explanation
Indices: 1550448--1550489 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1550438 GAGTCTTGGA
*
1550448 TTTAATTATTTTGATATGAT
1 TTTAATTATTTTGATATAAT
*
1550468 TTTAATTATATTTTAT-TAAT
1 TTTAATTAT-TTTGATATAAT
1550488 TT
1 TT
1550490 AAAAGATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTAATTATTTTGATATAAT
Found at i:1551226 original size:12 final size:12
Alignment explanation
Indices: 1551209--1551235 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1551199 TGAACCTGCA
1551209 AATGTTAATCTC
1 AATGTTAATCTC
1551221 AATGTTAATCTC
1 AATGTTAATCTC
1551233 AAT
1 AAT
1551236 TTGTTACACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (12 bp):
AATGTTAATCTC
Found at i:1556056 original size:3 final size:3
Alignment explanation
Indices: 1556050--1556078 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1556040 GGTAGGGATG
1556050 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1556079 TCTTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1558226 original size:48 final size:48
Alignment explanation
Indices: 1558145--1558240 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
1558135 AATAATTGTT
*
1558145 TATCAGTAATTGATTTGATTGTCATTGAAAATTTAAAATTTTAATGAA
1 TATCAGTAATTGATTTGATTATCATTGAAAATTTAAAATTTTAATGAA
** * * *
1558193 TATCAGTAATTGATTTGATTATTTTTGAGAATTTAAATTTTTTATGAA
1 TATCAGTAATTGATTTGATTATCATTGAAAATTTAAAATTTTAATGAA
1558241 GAAATTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (48 bp):
TATCAGTAATTGATTTGATTATCATTGAAAATTTAAAATTTTAATGAA
Found at i:1559044 original size:24 final size:24
Alignment explanation
Indices: 1559017--1559062 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1559007 AGTTATTATA
*
1559017 AAATTTTTTAGATAAATTAATCTT
1 AAATTTATTAGATAAATTAATCTT
1559041 AAATTTATTAGATAAATTAATC
1 AAATTTATTAGATAAATTAATC
1559063 AAAATTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTTATTAGATAAATTAATCTT
Found at i:1561239 original size:24 final size:24
Alignment explanation
Indices: 1561212--1561259 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1561202 GATTTCACAA
*
1561212 TAAGATTTAACGTTCATAAAATTT
1 TAAGATTTAACATTCATAAAATTT
* *
1561236 TAAGATTTAATATTTATAAAATTT
1 TAAGATTTAACATTCATAAAATTT
1561260 AATGCTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (24 bp):
TAAGATTTAACATTCATAAAATTT
Found at i:1561453 original size:22 final size:22
Alignment explanation
Indices: 1561425--1561469 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1561415 CAAAATATTG
1561425 ATTAATTTGAAT-GAGATTTCAC
1 ATTAATTTGAATAGA-ATTTCAC
1561447 ATTAATTTGAATAGAATTTCAC
1 ATTAATTTGAATAGAATTTCAC
1561469 A
1 A
1561470 AAAAATTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (22 bp):
ATTAATTTGAATAGAATTTCAC
Found at i:1570953 original size:16 final size:16
Alignment explanation
Indices: 1570928--1570961 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1570918 CTATTTTTAA
1570928 AGATAATAATTAATTT
1 AGATAATAATTAATTT
*
1570944 AGATATTAATTAATTT
1 AGATAATAATTAATTT
1570960 AG
1 AG
1570962 CTAGGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
AGATAATAATTAATTT
Found at i:1571342 original size:24 final size:24
Alignment explanation
Indices: 1571301--1571349 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1571291 TTGATAGGAT
** * *
1571301 AAGATTTAATGTTTATAAGATTTA
1 AAGATTTAACATTCATAAAATTTA
1571325 AAGATTTAACATTCATAAAATTTA
1 AAGATTTAACATTCATAAAATTTA
1571349 A
1 A
1571350 CACTTGCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (24 bp):
AAGATTTAACATTCATAAAATTTA
Found at i:1571371 original size:24 final size:24
Alignment explanation
Indices: 1571340--1571398 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
1571330 TTAACATTCA
* *
1571340 TAAA-ATTTAACACTTGCAAGATT
1 TAAAGATTTAACACTTACAAAATT
* * *
1571363 TAAAGATTTAATATTTATAAAATT
1 TAAAGATTTAACACTTACAAAATT
1571387 TAAAGATTTAAC
1 TAAAGATTTAAC
1571399 GTTCATAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (24 bp):
TAAAGATTTAACACTTACAAAATT
Found at i:1571406 original size:24 final size:24
Alignment explanation
Indices: 1571360--1571413 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1571350 CACTTGCAAG
* *
1571360 ATTTAAAGATTTAATATTTATAAA
1 ATTTAAAGATTTAACATTCATAAA
*
1571384 ATTTAAAGATTTAACGTTCATAAA
1 ATTTAAAGATTTAACATTCATAAA
1571408 ATTTAA
1 ATTTAA
1571414 CACTCATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (24 bp):
ATTTAAAGATTTAACATTCATAAA
Found at i:1571609 original size:23 final size:23
Alignment explanation
Indices: 1571578--1571621 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1571568 AGAATATTGT
1571578 TTAAATTGAAT-AGAATTTCACCA
1 TTAAATTGAATAAG-ATTTCACCA
*
1571601 TTAATTTGAATAAGATTTCAC
1 TTAAATTGAATAAGATTTCAC
1571622 AAAAGATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (23 bp):
TTAAATTGAATAAGATTTCACCA
Found at i:1571909 original size:79 final size:79
Alignment explanation
Indices: 1571816--1571975 Score: 275
Period size: 79 Copynumber: 2.0 Consensus size: 79
1571806 GGATAAGAGC
* * *
1571816 AATATGATTGCAACACATTTATTATAAAAGTTTTTAGATAAATTAATCAAAATTAAGATAAGTTA
1 AATATGATTGCAACAAATTTATTATAAAAGTTTTTAGATAAATTAATCAAAATTAAAATAAATTA
1571881 AAATATCTTAAAAG
66 AAATATCTTAAAAG
* *
1571895 AATATGATTTCAACAAATTTATTATAAAATTTTTTAGATAAATTAATCAAAATTAAAATAAATTA
1 AATATGATTGCAACAAATTTATTATAAAAGTTTTTAGATAAATTAATCAAAATTAAAATAAATTA
1571960 AAATATCTTAAAAG
66 AAATATCTTAAAAG
1571974 AA
1 AA
1571976 GTGTTTTAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (79 bp):
AATATGATTGCAACAAATTTATTATAAAAGTTTTTAGATAAATTAATCAAAATTAAAATAAATTA
AAATATCTTAAAAG
Found at i:1575630 original size:29 final size:30
Alignment explanation
Indices: 1575597--1575704 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 30
1575587 GCCCTTTTTT
1575597 TATTGATT-ATTTGTCTTTATTTTTAAAGA
1 TATTGATTAATTTGTCTTTATTTTTAAAGA
* *
1575626 TATTGATTAATTTAAATAAAATTTCATATTTTAAAGA
1 TATTGATTAATTT--GT---CTTT-AT-TTTTAAAGA
*
1575663 TATTGATT-ATTTG-CTTTTCTTTTTAAA-A
1 TATTGATTAATTTGTC-TTTATTTTTAAAGA
*
1575691 TATTTATTAATTTG
1 TATTGATTAATTTG
1575705 AATATTTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
28 8 0.13
29 20 0.32
30 5 0.08
31 3 0.05
32 1 0.02
35 3 0.05
36 6 0.10
37 17 0.27
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (30 bp):
TATTGATTAATTTGTCTTTATTTTTAAAGA
Found at i:1575673 original size:18 final size:18
Alignment explanation
Indices: 1575617--1575674 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
1575607 TTGTCTTTAT
1575617 TTTTAAAGATATTGATTA
1 TTTTAAAGATATTGATTA
* * * *
1575635 ATTTAAATAAAATTTCA-TA
1 TTTTAAA-GATA-TTGATTA
1575654 TTTTAAAGATATTGATTA
1 TTTTAAAGATATTGATTA
1575672 TTT
1 TTT
1575675 GCTTTTCTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 3 0.10
18 13 0.45
19 10 0.34
20 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (18 bp):
TTTTAAAGATATTGATTA
Found at i:1575710 original size:16 final size:16
Alignment explanation
Indices: 1575689--1575719 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1575679 TTCTTTTTAA
1575689 AATATTTATTAATTTG
1 AATATTTATTAATTTG
1575705 AATATTTATTAATTT
1 AATATTTATTAATTT
1575720 ATATAGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
AATATTTATTAATTTG
Found at i:1581778 original size:20 final size:20
Alignment explanation
Indices: 1581753--1581800 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1581743 TGATATTATT
1581753 AATTATTAAA-AATAAAAATA
1 AATTA-TAAACAATAAAAATA
* *
1581773 AATTATAAACAATGAACATA
1 AATTATAAACAATAAAAATA
1581793 AATT-TAAA
1 AATTATAAA
1581801 TGAATCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
AATTATAAACAATAAAAATA
Found at i:1582097 original size:2 final size:2
Alignment explanation
Indices: 1582090--1582120 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1582080 CGGTAATTCT
1582090 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1582121 GCGCATGTAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1587176 original size:48 final size:48
Alignment explanation
Indices: 1587095--1587190 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
1587085 AATAATTGTT
*
1587095 TATCAGTAATTGATTTGATTGTCGTTCAGAATTTAAAATTTTAATGAA
1 TATCAGTAATTGATTTGATTGTCGTTCAAAATTTAAAATTTTAATGAA
** * *
1587143 TATCAGTAATTGATTTGATTGTTTTTGAAAATTTAAATTTTTAATGAA
1 TATCAGTAATTGATTTGATTGTCGTTCAAAATTTAAAATTTTAATGAA
1587191 GAATTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (48 bp):
TATCAGTAATTGATTTGATTGTCGTTCAAAATTTAAAATTTTAATGAA
Found at i:1602657 original size:19 final size:18
Alignment explanation
Indices: 1602578--1602657 Score: 56
Period size: 19 Copynumber: 4.1 Consensus size: 18
1602568 GTATGATTGT
*
1602578 ATAATTATATT-TCAATTA
1 ATAATT-TATTATTAATTA
*
1602596 ACTAATTAATTATTCAATTA
1 A-TAATTTATTATT-AATTA
1602616 GTATAATTTGATTA-TAATATA
1 --ATAATTT-ATTATTAAT-TA
1602637 ATAATTTATTATTAAATTA
1 ATAATTTATTATT-AATTA
1602656 AT
1 AT
1602658 TATATAAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 17
0.71 0.04 0.24
Matches are distributed among these distances:
18 8 0.16
19 18 0.36
20 11 0.22
21 8 0.16
22 5 0.10
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (18 bp):
ATAATTTATTATTAATTA
Found at i:1605094 original size:14 final size:14
Alignment explanation
Indices: 1605075--1605103 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1605065 GTTCATTTTT
1605075 ATTAAATAAATTTA
1 ATTAAATAAATTTA
1605089 ATTAAATAAATTTA
1 ATTAAATAAATTTA
1605103 A
1 A
1605104 ATAATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAATAAATTTA
Found at i:1605115 original size:14 final size:14
Alignment explanation
Indices: 1605077--1605107 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1605067 TCATTTTTAT
*
1605077 TAAATAAATTTAAT
1 TAAATAAATTTAAA
1605091 TAAATAAATTTAAA
1 TAAATAAATTTAAA
1605105 TAA
1 TAA
1605108 TTTAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATAAATTTAAA
Found at i:1607579 original size:110 final size:110
Alignment explanation
Indices: 1607386--1607618 Score: 421
Period size: 110 Copynumber: 2.1 Consensus size: 110
1607376 TTTGTGGCTT
* *
1607386 TATTTGGATTATGGTCAAATTTAACTGCTTTTTGAGGTGATCCTTAGTGCACTGCAATGTGTATT
1 TATTTGGATTATGGTCAAATTTAACTGCTTTTTGAAGTGATCCTTAGTGCACTACAATGTGTATT
1607451 GGGTAGATACAGTTGATAACTTGATGGACTGTTATCTTTGCCAGA
66 GGGTAGATACAGTTGATAACTTGATGGACTGTTATCTTTGCCAGA
* * *
1607496 TATTTGGATTATGGTTAAATTTAACTGCTTTTTGAAGTGATCTTTAGTGCACTACAATGTGTGTT
1 TATTTGGATTATGGTCAAATTTAACTGCTTTTTGAAGTGATCCTTAGTGCACTACAATGTGTATT
1607561 GGGTAGATACAGTTGATAACTTGATGGACTGTTATCTTTGCCAGA
66 GGGTAGATACAGTTGATAACTTGATGGACTGTTATCTTTGCCAGA
1607606 TATTTGGATTATG
1 TATTTGGATTATG
1607619 CCATTTCCTT
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 118 1.00
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (110 bp):
TATTTGGATTATGGTCAAATTTAACTGCTTTTTGAAGTGATCCTTAGTGCACTACAATGTGTATT
GGGTAGATACAGTTGATAACTTGATGGACTGTTATCTTTGCCAGA
Found at i:1612267 original size:15 final size:15
Alignment explanation
Indices: 1612247--1612276 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1612237 TGCAACCAAA
1612247 AGATTAATGCACTTT
1 AGATTAATGCACTTT
1612262 AGATTAATGCACTTT
1 AGATTAATGCACTTT
1612277 TGACTTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
AGATTAATGCACTTT
Found at i:1626776 original size:37 final size:39
Alignment explanation
Indices: 1626708--1626803 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
1626698 AATTTCATCC
* * *
1626708 CAAAAAAAATAAAAATAATAATATTACAAAATAC-GAAATA
1 CAAAAAATATAAAAA-AATAATATTA-AAAATACAAAAAAA
1626748 CAAAAAATATATAAAAAATAATA-T-AAAATACAAAAAAA
1 CAAAAAATATA-AAAAAATAATATTAAAAATACAAAAAAA
*
1626786 CAAAAAATAAAAAAAAAT
1 CAAAAAATATAAAAAAAT
1626804 CGAGGATGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
37 14 0.28
38 14 0.28
39 1 0.02
40 17 0.34
41 4 0.08
ACGTcount: A:0.75, C:0.06, G:0.01, T:0.18
Consensus pattern (39 bp):
CAAAAAATATAAAAAAATAATATTAAAAATACAAAAAAA
Found at i:1626802 original size:17 final size:17
Alignment explanation
Indices: 1626758--1626802 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1626748 CAAAAAATAT
* * *
1626758 ATAAAAAATAATATAAA
1 ATAAAAAAAAACAAAAA
*
1626775 ATACAAAAAAACAAAAA
1 ATAAAAAAAAACAAAAA
1626792 ATAAAAAAAAA
1 ATAAAAAAAAA
1626803 TCGAGGATGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.13
Consensus pattern (17 bp):
ATAAAAAAAAACAAAAA
Done.