Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 155 of 160
Found at i:31333636 original size:17 final size:17
Alignment explanation
Indices: 31333610--31333642 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31333600 TTTAATTAAG
31333610 TTTTTATA-TTTAATTT
1 TTTTTATATTTTAATTT
31333626 TTTTTATTATTTTAATT
1 TTTTTA-TATTTTAATT
31333643 AATAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTATATTTTAATTT
Found at i:31338367 original size:19 final size:17
Alignment explanation
Indices: 31338336--31338370 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
31338326 GATTTATTGA
31338336 TTTATAATTTTTTAATT
1 TTTATAATTTTTTAATT
31338353 TTTATATATTATTTTAAT
1 TTTATA-ATT-TTTTAAT
31338371 ATAAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATAATTTTTTAATT
Found at i:31338372 original size:13 final size:13
Alignment explanation
Indices: 31338350--31338389 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
31338340 TAATTTTTTA
*
31338350 ATTTTTATATATT
1 ATTTTAATATATT
**
31338363 ATTTTAATATAAA
1 ATTTTAATATATT
31338376 ATTTTAATATATT
1 ATTTTAATATATT
31338389 A
1 A
31338390 AAATAAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:31355430 original size:11 final size:11
Alignment explanation
Indices: 31355414--31355438 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31355404 TAATTTATGC
31355414 ATTTATATTAT
1 ATTTATATTAT
31355425 ATTTATATTAT
1 ATTTATATTAT
31355436 ATT
1 ATT
31355439 AAATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:31356932 original size:16 final size:15
Alignment explanation
Indices: 31356911--31356941 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
31356901 TTTCACATAT
31356911 ATAAATATATATATTA
1 ATAAATATA-ATATTA
31356927 ATAAATATAATATTA
1 ATAAATATAATATTA
31356942 GTGCATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATATAATATTA
Found at i:31357587 original size:216 final size:216
Alignment explanation
Indices: 31357213--31357658 Score: 892
Period size: 216 Copynumber: 2.1 Consensus size: 216
31357203 TCAAAACTAT
31357213 ATCTAATTTAATTTAGTTTATTTTTTATTTATTTTGACCCTTTAATAATGTAAATTAAAATATGA
1 ATCTAATTTAATTTAGTTTATTTTTTATTTATTTTGACCCTTTAATAATGTAAATTAAAATATGA
31357278 AACAAAAAAAAATCTCTAAAATTTAATTTGATAGTGTTTGATAAATAATAAATCTCATTTATTTA
66 AACAAAAAAAAATCTCTAAAATTTAATTTGATAGTGTTTGATAAATAATAAATCTCATTTATTTA
31357343 ACTGTATCTTTATAAAAATATTATTATATTATTTAGTTTGATTTAAATTGATTTCAAAATAACAA
131 ACTGTATCTTTATAAAAATATTATTATATTATTTAGTTTGATTTAAATTGATTTCAAAATAACAA
31357408 GAAAATGAGAGCAAGATTTTA
196 GAAAATGAGAGCAAGATTTTA
31357429 ATCTAATTTAATTTAGTTTATTTTTTATTTATTTTGACCCTTTAATAATGTAAATTAAAATATGA
1 ATCTAATTTAATTTAGTTTATTTTTTATTTATTTTGACCCTTTAATAATGTAAATTAAAATATGA
31357494 AACAAAAAAAAATCTCTAAAATTTAATTTGATAGTGTTTGATAAATAATAAATCTCATTTATTTA
66 AACAAAAAAAAATCTCTAAAATTTAATTTGATAGTGTTTGATAAATAATAAATCTCATTTATTTA
31357559 ACTGTATCTTTATAAAAATATTATTATATTATTTAGTTTGATTTAAATTGATTTCAAAATAACAA
131 ACTGTATCTTTATAAAAATATTATTATATTATTTAGTTTGATTTAAATTGATTTCAAAATAACAA
31357624 GAAAATGAGAGCAAGATTTTA
196 GAAAATGAGAGCAAGATTTTA
31357645 ATCTAATTTAATTT
1 ATCTAATTTAATTT
31357659 GGATTTTGAT
Statistics
Matches: 230, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 230 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.44
Consensus pattern (216 bp):
ATCTAATTTAATTTAGTTTATTTTTTATTTATTTTGACCCTTTAATAATGTAAATTAAAATATGA
AACAAAAAAAAATCTCTAAAATTTAATTTGATAGTGTTTGATAAATAATAAATCTCATTTATTTA
ACTGTATCTTTATAAAAATATTATTATATTATTTAGTTTGATTTAAATTGATTTCAAAATAACAA
GAAAATGAGAGCAAGATTTTA
Found at i:31360090 original size:18 final size:17
Alignment explanation
Indices: 31360069--31360103 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
31360059 AAAATTTAAA
31360069 TTATATTATTTTTATATT
1 TTATATTATTTTT-TATT
31360087 TTATATTATTTTTTATT
1 TTATATTATTTTTTATT
31360104 ATATCGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATATTATTTTTTATT
Found at i:31360098 original size:10 final size:10
Alignment explanation
Indices: 31360069--31360105 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
31360059 AAAATTTAAA
31360069 TTATATTATT
1 TTATATTATT
31360079 TT-TA-TATT
1 TTATATTATT
31360087 TTATATTATT
1 TTATATTATT
*
31360097 TTTTATTAT
1 TTATATTAT
31360106 ATCGTGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
8 6 0.25
9 4 0.17
10 14 0.58
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTATATTATT
Found at i:31361857 original size:12 final size:12
Alignment explanation
Indices: 31361840--31361864 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31361830 ATGGTCATCT
31361840 TTTGTTTCTTTA
1 TTTGTTTCTTTA
31361852 TTTGTTTCTTTA
1 TTTGTTTCTTTA
31361864 T
1 T
31361865 CTTCTGTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTGTTTCTTTA
Found at i:31366443 original size:29 final size:30
Alignment explanation
Indices: 31366411--31366494 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 30
31366401 TATTACATTT
31366411 AAATAAACTCTTAATTTTTAATTTACA-CC
1 AAATAAACTCTTAATTTTTAATTTACATCC
* * * * *
31366440 AAATAAGCTCTTAATCTTAAATTTGCATTC
1 AAATAAACTCTTAATTTTTAATTTACATCC
*
31366470 AAATAAATTCTTAAATTTTTAATTT
1 AAATAAACTCTT-AATTTTTAATTT
31366495 TGATTTAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 23 0.52
30 11 0.25
31 10 0.23
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (30 bp):
AAATAAACTCTTAATTTTTAATTTACATCC
Found at i:31366612 original size:29 final size:30
Alignment explanation
Indices: 31366550--31366629 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
31366540 ATAAAAATTT
* *
31366550 AAAATATAAAAACTTATTTTAATATAAATC
1 AAAATATAAAAACTTATTTAAATATAAATA
* *
31366580 AAAATCTAATAACTTATTTAAATAT-AATA
1 AAAATATAAAAACTTATTTAAATATAAATA
* *
31366609 AAAATATAACAGCTTATTTAA
1 AAAATATAAAAACTTATTTAA
31366630 GAAAAAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 21 0.49
30 22 0.51
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAATATAAAAACTTATTTAAATATAAATA
Found at i:31374400 original size:23 final size:25
Alignment explanation
Indices: 31374355--31374411 Score: 91
Period size: 23 Copynumber: 2.3 Consensus size: 25
31374345 TTAATTAATT
31374355 TATTTATATATTTATATTAAAAATAA
1 TATTT-TATATTTATATTAAAAATAA
31374381 TATTTTATATTT-T-TTAAAAATAA
1 TATTTTATATTTATATTAAAAATAA
31374404 TATTTTAT
1 TATTTTAT
31374412 TAATTTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.58
24 1 0.03
25 7 0.23
26 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTTATATTTATATTAAAAATAA
Found at i:31374418 original size:24 final size:23
Alignment explanation
Indices: 31374371--31374418 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
31374361 TATATTTATA
*
31374371 TTAAAAATAATATTTTATATTTT
1 TTAAAAATAATATTTTATAATTT
31374394 TTAAAAATAATATTTTATTAATTT
1 TTAAAAATAATATTTTA-TAATTT
31374418 T
1 T
31374419 AAGTTTGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAAAAATAATATTTTATAATTT
Found at i:31375287 original size:31 final size:31
Alignment explanation
Indices: 31375219--31375287 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
31375209 TTTTTATATT
** * *
31375219 TATATTTGATTTAATTTGATATTATATAAAT
1 TATATTTGATTTAATTAAAAATTATATAAAA
*
31375250 TATATTTGATTTGATTAAAAATTA-ATAAAA
1 TATATTTGATTTAATTAAAAATTATATAAAA
31375280 TATTATTT
1 TA-TATTT
31375288 TTTAAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (31 bp):
TATATTTGATTTAATTAAAAATTATATAAAA
Found at i:31375307 original size:19 final size:18
Alignment explanation
Indices: 31375283--31375324 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
31375273 AATAAAATAT
31375283 TATTTTTTAAAATATAAAA
1 TATTTTTT-AAATATAAAA
31375302 TATTTTTTAAATATAAAA
1 TATTTTTTAAATATAAAA
31375320 TATTT
1 TATTT
31375325 AAATATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTTTTTAAATATAAAA
Found at i:31375365 original size:17 final size:18
Alignment explanation
Indices: 31375343--31375377 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
31375333 AATTATATAT
31375343 ATAAATAA-AAAAATTAA
1 ATAAATAATAAAAATTAA
31375360 ATAAATAATTAAAAATTA
1 ATAAATAA-TAAAAATTA
31375378 TTTTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATAATAAAAATTAA
Found at i:31375367 original size:21 final size:21
Alignment explanation
Indices: 31375333--31375374 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31375323 TTAAATATAT
* *
31375333 AATTATATATATAAATAAAAA
1 AATTAAATAAATAAATAAAAA
*
31375354 AATTAAATAAATAATTAAAAA
1 AATTAAATAAATAAATAAAAA
31375375 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTAAATAAATAAATAAAAA
Found at i:31377818 original size:29 final size:29
Alignment explanation
Indices: 31377760--31377818 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
31377750 TAATTGTGAA
**
31377760 ACTTGTGGTTTGATTGGAGATGTTGGATC
1 ACTTGTGGTTTGACCGGAGATGTTGGATC
* *
31377789 ACTTGTGGTTTGCACCGTAGAT-TTGTATC
1 ACTTGTGGTTTG-ACCGGAGATGTTGGATC
31377818 A
1 A
31377819 ATGTTCATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.41
Consensus pattern (29 bp):
ACTTGTGGTTTGACCGGAGATGTTGGATC
Found at i:31415685 original size:15 final size:16
Alignment explanation
Indices: 31415644--31415685 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
31415634 TTCATAAAAA
*
31415644 TTAATATTTATATTAT
1 TTAATATATATATTAT
31415660 TT-ATATATATA-TAT
1 TTAATATATATATTAT
31415674 TTAATATATATA
1 TTAATATATATA
31415686 CATATGAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 17 0.71
16 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATATATATATTAT
Found at i:31423946 original size:3 final size:3
Alignment explanation
Indices: 31423940--31423971 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
31423930 GGACGGTGGT
*
31423940 GGA GGA GGT GGA GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
31423972 TGATGGTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.69, T:0.03
Consensus pattern (3 bp):
GGA
Found at i:31436625 original size:17 final size:17
Alignment explanation
Indices: 31436590--31436640 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
31436580 TATAAATATA
31436590 TTAAAATAATATATAAAT
1 TTAAAA-AATATATAAAT
31436608 TTAAAAAATAT-TACAAT
1 TTAAAAAATATATA-AAT
*
31436625 TTAAAAATTA-ATAAAT
1 TTAAAAAATATATAAAT
31436641 ACAATTGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.17
17 19 0.63
18 6 0.20
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAAAATATATAAAT
Found at i:31444814 original size:29 final size:26
Alignment explanation
Indices: 31444750--31444803 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
31444740 ATGATATAGG
*
31444750 ATGATTATCATCTTATCCTATCAATA
1 ATGATTATCATCATATCCTATCAATA
*
31444776 ATGATTATCATCATATCTTATCAATA
1 ATGATTATCATCATATCCTATCAATA
31444802 AT
1 AT
31444804 CTTATGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.43
Consensus pattern (26 bp):
ATGATTATCATCATATCCTATCAATA
Found at i:31449981 original size:42 final size:42
Alignment explanation
Indices: 31449922--31450068 Score: 224
Period size: 42 Copynumber: 3.5 Consensus size: 42
31449912 GCCATGGATG
* * * *
31449922 ATCAGTT-ATATTCAGAAGATATGGATGAAAATGACACAGACA
1 ATCAGTTGA-ATTTAGAAGATATGGATGAGACTGACACGGACA
*
31449964 ATCAGTTGAATTTAGAAGATGTGGATGAGACTGACACGGACA
1 ATCAGTTGAATTTAGAAGATATGGATGAGACTGACACGGACA
*
31450006 ATCAGTGGAATTTAGAAGATATGGATGAGACTGACACGGACA
1 ATCAGTTGAATTTAGAAGATATGGATGAGACTGACACGGACA
31450048 ATCAGTTGAATTTAGAAGATA
1 ATCAGTTGAATTTAGAAGATA
31450069 CAAATGTGAT
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
42 95 0.99
43 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.24
Consensus pattern (42 bp):
ATCAGTTGAATTTAGAAGATATGGATGAGACTGACACGGACA
Found at i:31451482 original size:76 final size:76
Alignment explanation
Indices: 31451400--31451553 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 76
31451390 ACTTTTTTAC
* *
31451400 ATTACATCCTTTTGATACTCTGGAGGTCGCATCTTCAATTTGTATTTTCTTCACT-TGGACTTTC
1 ATTACATCCTTTTGATACTCTGGAGGTAGCATCTTCAATTGGTATTTTCTTCACTCT-GACTTTC
31451464 TAGAATTGCTTG
65 TAGAATTGCTTG
31451476 ATTACATCCTTTTGATACTCTGGAGGTAGCATCTTCAATTGGTATTTTCTTCACTCTGACTTTCT
1 ATTACATCCTTTTGATACTCTGGAGGTAGCATCTTCAATTGGTATTTTCTTCACTCTGACTTTCT
31451541 AGAATTGCTTG
66 AGAATTGCTTG
31451552 AT
1 AT
31451554 CTTACATGCT
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
76 74 0.99
77 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (76 bp):
ATTACATCCTTTTGATACTCTGGAGGTAGCATCTTCAATTGGTATTTTCTTCACTCTGACTTTCT
AGAATTGCTTG
Found at i:31453589 original size:21 final size:22
Alignment explanation
Indices: 31453563--31453606 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
31453553 CCTGAGGAGG
31453563 ATGATA-AGAGATGAT-AATCAA
1 ATGATATAGA-ATGATAAATCAA
*
31453584 ATGATATAGAATTATAAATCAA
1 ATGATATAGAATGATAAATCAA
31453606 A
1 A
31453607 ATGTTTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (22 bp):
ATGATATAGAATGATAAATCAA
Found at i:31464642 original size:36 final size:38
Alignment explanation
Indices: 31464600--31464672 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
31464590 AATAAGTACA
31464600 TATACCACAGT-AGACCCAAAAAGGAAA-GTACTCCAT
1 TATACCACAGTAAGACCCAAAAAGGAAAGGTACTCCAT
*
31464636 TATACCACAGTAAGGCCCAAAAAGGAAAGGTACTCCA
1 TATACCACAGTAAGACCCAAAAAGGAAAGGTACTCCA
31464673 GCAGCCAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 11 0.32
37 15 0.44
38 8 0.24
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.15
Consensus pattern (38 bp):
TATACCACAGTAAGACCCAAAAAGGAAAGGTACTCCAT
Found at i:31466439 original size:96 final size:97
Alignment explanation
Indices: 31466294--31466487 Score: 282
Period size: 96 Copynumber: 2.0 Consensus size: 97
31466284 CAAGTTATAT
* * * *
31466294 AAAAATTTTGAAAGATTAAATAATTAAATAAACACCTAAAACCAGTTCGATAATAATACATTCCG
1 AAAAATTTTAAAAGATTAAATAATTAAATAAACACCTAAAACCAATTCGATAACAATACAGTCCG
* *
31466359 GTTTAACTGACTGGTTCTTGGCCAATCCAATC
66 GTTTAACTGACTGGTCCTTGACCAATCCAATC
* * **
31466391 AAAAATTTTAAAAGATTAAATAA-TAAATAAACACCTATAACCAATTCGATACCAATATGGTCCG
1 AAAAATTTTAAAAGATTAAATAATTAAATAAACACCTAAAACCAATTCGATAACAATACAGTCCG
*
31466455 GTTTAACTGACTGGTCCTTGACCAGTCCAATC
66 GTTTAACTGACTGGTCCTTGACCAATCCAATC
31466487 A
1 A
31466488 GCCAGCCCCA
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
96 64 0.74
97 22 0.26
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (97 bp):
AAAAATTTTAAAAGATTAAATAATTAAATAAACACCTAAAACCAATTCGATAACAATACAGTCCG
GTTTAACTGACTGGTCCTTGACCAATCCAATC
Found at i:31475441 original size:16 final size:15
Alignment explanation
Indices: 31475408--31475437 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31475398 ATCTCAATTT
*
31475408 GAAAGAAAAGTTAAA
1 GAAAAAAAAGTTAAA
31475423 GAAAAAAAAGTTAAA
1 GAAAAAAAAGTTAAA
31475438 AGAATTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
GAAAAAAAAGTTAAA
Found at i:31475460 original size:20 final size:20
Alignment explanation
Indices: 31475435--31475474 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31475425 AAAAAAAGTT
*
31475435 AAAAGAATT-TTATTTTTATA
1 AAAAG-ATTGTTATATTTATA
31475455 AAAAGATTGTTATATTTATA
1 AAAAGATTGTTATATTTATA
31475475 TTTTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
AAAAGATTGTTATATTTATA
Found at i:31475943 original size:15 final size:15
Alignment explanation
Indices: 31475923--31475964 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
31475913 GATACATATA
*
31475923 TCTTTTCCTTTCCTT
1 TCTTTTCTTTTCCTT
*
31475938 TCTTTTCTTTTTCTT
1 TCTTTTCTTTTCCTT
*
31475953 TCATTTCTTTTC
1 TCTTTTCTTTTC
31475965 TTTAATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTTTCTTTTCCTT
Found at i:31475948 original size:20 final size:20
Alignment explanation
Indices: 31475923--31475967 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
31475913 GATACATATA
*
31475923 TCTTTTCCTTTCCTTTCTTT
1 TCTTTTCCTTTCATTTCTTT
*
31475943 TCTTTTTCTTTCATTTCTTT
1 TCTTTTCCTTTCATTTCTTT
31475963 TCTTT
1 TCTTT
31475968 AATTAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTTTCCTTTCATTTCTTT
Found at i:31476975 original size:24 final size:24
Alignment explanation
Indices: 31476947--31476993 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
31476937 ATACATTTAA
31476947 TTTTA-CTATTAATTTTTCACACAG
1 TTTTATCTATTAATTTTTC-CACAG
* *
31476971 TTTTATTTTTTAATTTTTCCACA
1 TTTTATCTATTAATTTTTCCACA
31476994 TTCCACATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.26, C:0.15, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTATCTATTAATTTTTCCACAG
Found at i:31480087 original size:3 final size:3
Alignment explanation
Indices: 31480079--31480123 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
31480069 ATCATTCCCT
*
31480079 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCT TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
31480124 GCCCCCTCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
TCC
Found at i:31483525 original size:3 final size:3
Alignment explanation
Indices: 31483517--31483578 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
31483507 TTTGCATTCA
31483517 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
31483565 ATC ATC ATC ATC AT
1 ATC ATC ATC ATC AT
31483579 ATTTTGAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:31484511 original size:20 final size:21
Alignment explanation
Indices: 31484477--31484516 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
31484467 AATTTCAAAT
*
31484477 AAAATTTATATTATTAAATAA
1 AAAATTAATATTATTAAATAA
31484498 AAAATTAATA-TATTAAATA
1 AAAATTAATATTATTAAATA
31484517 TATATCCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTAATATTATTAAATAA
Found at i:31497832 original size:23 final size:23
Alignment explanation
Indices: 31497793--31497858 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 23
31497783 ATGAAAAACT
31497793 AAAA-ATAATTTTTAAATATAAACA
1 AAAACATAA-TTTTAAATATAAA-A
*
31497817 AATAA-A-AATTTTAAATGTAAAA
1 AA-AACATAATTTTAAATATAAAA
31497839 AAAACATAATTTTAGAATAT
1 AAAACATAATTTTA-AATAT
31497859 CTAAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
21 2 0.06
22 4 0.11
23 19 0.53
24 8 0.22
25 3 0.08
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (23 bp):
AAAACATAATTTTAAATATAAAA
Found at i:31501428 original size:49 final size:49
Alignment explanation
Indices: 31501375--31501472 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
31501365 AATATACTTA
31501375 GCATTGAAAAATGTTACTTTTGTCTACTTATCCAAGGTTTAGATTGCAC
1 GCATTGAAAAATGTTACTTTTGTCTACTTATCCAAGGTTTAGATTGCAC
31501424 GCATTGAAAAATGTTACTTTTGTCTACTTATCCAAGGTTTAGATTGCAC
1 GCATTGAAAAATGTTACTTTTGTCTACTTATCCAAGGTTTAGATTGCAC
31501473 TAGCCTACTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (49 bp):
GCATTGAAAAATGTTACTTTTGTCTACTTATCCAAGGTTTAGATTGCAC
Found at i:31507027 original size:18 final size:19
Alignment explanation
Indices: 31506993--31507029 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
31506983 GACTCGGATG
31506993 GTTTCAAGTCAATAAATTT
1 GTTTCAAGTCAATAAATTT
*
31507012 GTTTCAA-TCTATAAATTT
1 GTTTCAAGTCAATAAATTT
31507030 CATGATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (19 bp):
GTTTCAAGTCAATAAATTT
Found at i:31517475 original size:17 final size:17
Alignment explanation
Indices: 31517450--31517492 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
31517440 TAATTGATTA
*
31517450 TTTAATTTTAAAATAAT
1 TTTATTTTTAAAATAAT
**
31517467 TTTATTTTTAATTTAAT
1 TTTATTTTTAAAATAAT
*
31517484 TTAATTTTT
1 TTTATTTTT
31517493 GAATCGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATTTTTAAAATAAT
Found at i:31518233 original size:10 final size:10
Alignment explanation
Indices: 31518218--31518243 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
31518208 TATAAAATTA
31518218 AATATATATC
1 AATATATATC
31518228 AATATATATC
1 AATATATATC
31518238 AATATA
1 AATATA
31518244 AAATTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (10 bp):
AATATATATC
Found at i:31519153 original size:15 final size:14
Alignment explanation
Indices: 31519133--31519170 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
31519123 TTTATTTGAT
31519133 TTTATATTTATAATA
1 TTTATATTT-TAATA
*
31519148 TTTATATTTTATTA
1 TTTATATTTTAATA
31519162 TTT-TATTTT
1 TTTATATTTT
31519171 TATTCGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.27
14 7 0.32
15 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATATTTTAATA
Found at i:31520583 original size:20 final size:20
Alignment explanation
Indices: 31520527--31520583 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
31520517 TTTGTCAACG
*
31520527 AATTT-AATTGAATTATAAAA
1 AATTTAAATTTAATT-TAAAA
* *
31520547 AATTTAATATTTTATTTATAA
1 AATTTAA-ATTTAATTTAAAA
31520568 AATTTAAATTTAATTT
1 AATTTAAATTTAATTT
31520584 TTATTGTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 13 0.42
21 12 0.39
22 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AATTTAAATTTAATTTAAAA
Found at i:31524760 original size:2 final size:2
Alignment explanation
Indices: 31524753--31524782 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31524743 ATATCCTTTA
31524753 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
31524783 GTTTCAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31527147 original size:14 final size:15
Alignment explanation
Indices: 31527125--31527161 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
31527115 TTTTAATTAA
31527125 TATTT-TTTGTTTT-
1 TATTTATTTGTTTTG
31527138 TATTTATTTGTTTTG
1 TATTTATTTGTTTTG
*
31527153 TATTAATTT
1 TATTTATTT
31527162 TCATGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.24
14 8 0.38
15 8 0.38
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (15 bp):
TATTTATTTGTTTTG
Found at i:31527817 original size:21 final size:22
Alignment explanation
Indices: 31527772--31527814 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
31527762 TATTTTTATT
31527772 ATTTTAGATTATAAAAAATTAA
1 ATTTTAGATTATAAAAAATTAA
*
31527794 ATTTT-GATTAT-TAAAATTAA
1 ATTTTAGATTATAAAAAATTAA
31527814 A
1 A
31527815 ATTCCATCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 6 0.30
22 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTTTAGATTATAAAAAATTAA
Found at i:31527962 original size:3 final size:3
Alignment explanation
Indices: 31527956--31527982 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31527946 ATAATAATAA
31527956 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
31527983 AAATAATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31529735 original size:31 final size:31
Alignment explanation
Indices: 31529699--31529758 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
31529689 TTTTCACATC
*
31529699 ATTTTAGTTTAATAATTAAATTTATCAAATT
1 ATTTTAGTTTAATAATTAAATCTATCAAATT
31529730 ATTTTAGTTTAATAATTAAATCTATCAAA
1 ATTTTAGTTTAATAATTAAATCTATCAAA
31529759 ATTAACACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTTTAGTTTAATAATTAAATCTATCAAATT
Found at i:31536959 original size:2 final size:2
Alignment explanation
Indices: 31536952--31536980 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31536942 TACCCCCGTT
31536952 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 T
31536981 GGCAGTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31538337 original size:24 final size:24
Alignment explanation
Indices: 31538283--31538339 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
31538273 TATTAAAATT
* *
31538283 TATAAATTTTTATTATATTTTATA
1 TATAAATTTGTATTATAATTTATA
*
31538307 TAAAAATTTGGTATTATAATTTATA
1 TATAAATTT-GTATTATAATTTATA
31538332 T-TAAATTT
1 TATAAATTT
31538340 ATGTATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
TATAAATTTGTATTATAATTTATA
Found at i:31538345 original size:25 final size:25
Alignment explanation
Indices: 31538283--31538376 Score: 76
Period size: 25 Copynumber: 4.0 Consensus size: 25
31538273 TATTAAAATT
*
31538283 TATAAATTTT-TATTATATTTTATA
1 TATAAATTTTGTATTATAATTTATA
* *
31538307 TAAAAATTTGGTATTATAATTTATA
1 TATAAATTTTGTATTATAATTTATA
* *
31538332 T-TAAATTTATGTATAATTA-TTAT-
1 TATAAATTT-TGTATTATAATTTATA
*
31538355 TA-AAATTTT-AATTA-AATTTATA
1 TATAAATTTTGTATTATAATTTATA
31538377 AATTCTAGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
20 1 0.02
21 7 0.13
22 1 0.02
23 7 0.13
24 18 0.33
25 21 0.38
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (25 bp):
TATAAATTTTGTATTATAATTTATA
Found at i:31541754 original size:24 final size:26
Alignment explanation
Indices: 31541702--31541754 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
31541692 ACGTACGGAC
* *
31541702 AAAATTTTTACAAATTTTTTTTTGTT
1 AAAATTTGTACAAATTTTTTTTTGAT
*
31541728 AAAATTTGTA-AAGTTTTTTTTT-AT
1 AAAATTTGTACAAATTTTTTTTTGAT
31541752 AAA
1 AAA
31541755 TGATTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 11 0.46
26 9 0.38
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (26 bp):
AAAATTTGTACAAATTTTTTTTTGAT
Found at i:31541879 original size:29 final size:28
Alignment explanation
Indices: 31541834--31541892 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
31541824 TATAAAAAAA
**
31541834 TTATTTATAATTTAAATT-TGATTAATAT
1 TTATTTATAATAAAAATTAT-ATTAATAT
31541862 TTATTTAATAATAAAAATTATATTAATAT
1 TTATTT-ATAATAAAAATTATATTAATAT
31541891 TT
1 TT
31541893 TTATTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 20 0.74
30 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTATTTATAATAAAAATTATATTAATAT
Found at i:31542611 original size:16 final size:16
Alignment explanation
Indices: 31542586--31542620 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31542576 ATCAAAATTT
* *
31542586 TAATTGAAATATAATA
1 TAATTCAAATATAAAA
31542602 TAATTCAAATATAAAA
1 TAATTCAAATATAAAA
31542618 TAA
1 TAA
31542621 AAGATGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
TAATTCAAATATAAAA
Found at i:31542782 original size:4 final size:4
Alignment explanation
Indices: 31542749--31542828 Score: 52
Period size: 4 Copynumber: 18.2 Consensus size: 4
31542739 ATTTAAAATA
* * * *
31542749 TAAT ATAAT ATAAT TATAT TTAT TATT TAAT TAAT TAAA AAAT TAAT TAAATT
1 TAAT -TAAT -TAAT TA-AT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T-AA-T
*
31542802 TAAT GAAT TAAATT TAAT TAAT TAAT T
1 TAAT TAAT T-AA-T TAAT TAAT TAAT T
31542829 TTTAAAATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
4 36 0.60
5 20 0.33
6 4 0.07
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (4 bp):
TAAT
Found at i:31542812 original size:14 final size:14
Alignment explanation
Indices: 31542793--31542826 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
31542783 TTAAAAAATT
31542793 AATTAAATTTAATG
1 AATTAAATTTAATG
*
31542807 AATTAAATTTAATT
1 AATTAAATTTAATG
31542821 AATTAA
1 AATTAA
31542827 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
AATTAAATTTAATG
Found at i:31545566 original size:10 final size:10
Alignment explanation
Indices: 31545551--31545575 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31545541 CATTGTATAA
31545551 ATATATGTAT
1 ATATATGTAT
31545561 ATATATGTAT
1 ATATATGTAT
31545571 ATATA
1 ATATA
31545576 CATATATTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (10 bp):
ATATATGTAT
Found at i:31547024 original size:19 final size:19
Alignment explanation
Indices: 31546966--31547018 Score: 97
Period size: 19 Copynumber: 2.7 Consensus size: 19
31546956 TGTACATTTA
31546966 TTGGATTTTCAAAAAAATT
1 TTGGATTTTCAAAAAAATT
31546985 TTGGATTTTCAAAAAAATT
1 TTGGATTTTCAAAAAAATT
31547004 TTGGATTTTTCAAAA
1 TTGGA-TTTTCAAAA
31547019 TTTTTTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 24 0.73
20 9 0.27
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (19 bp):
TTGGATTTTCAAAAAAATT
Found at i:31550354 original size:2 final size:2
Alignment explanation
Indices: 31550347--31550376 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31550337 ACACAACTGC
31550347 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31550377 TTAAATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31557087 original size:21 final size:21
Alignment explanation
Indices: 31557030--31557099 Score: 59
Period size: 24 Copynumber: 3.1 Consensus size: 21
31557020 TCGTTATTGA
* *
31557030 TTTTAATATTATTATTATAAT
1 TTTTAATTTTATTAATATAAT
* *
31557051 ATTTAATCTTAATATTAATATTAT
1 TTTTAAT-TT--TATTAATATAAT
*
31557075 TTTTAATTTTATTAAAACTAAT
1 TTTTAATTTTATTAATA-TAAT
31557097 TTT
1 TTT
31557100 ATCGTTCATC
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
21 13 0.34
22 7 0.18
23 2 0.05
24 16 0.42
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTAATTTTATTAATATAAT
Found at i:31557145 original size:18 final size:19
Alignment explanation
Indices: 31557110--31557149 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
31557100 ATCGTTCATC
*
31557110 TAAATTAATATTTAATATG
1 TAAATTAATATGTAATATG
31557129 TAAATTAA-ATGTAATATG
1 TAAATTAATATGTAATATG
31557147 TAA
1 TAA
31557150 TAGAGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (19 bp):
TAAATTAATATGTAATATG
Found at i:31560229 original size:3 final size:3
Alignment explanation
Indices: 31560215--31560303 Score: 61
Period size: 3 Copynumber: 29.7 Consensus size: 3
31560205 TGAGATAGAA
* * * * * * * * *
31560215 GAT GAC GAT GAT GAT GAA GGT GAT GAG GAT GAT GAA GAG GAA GAG GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * * *
31560263 GAG GAA GAG GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
31560304 AGAAAGGAAA
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.39, C:0.01, G:0.40, T:0.19
Consensus pattern (3 bp):
GAT
Found at i:31560238 original size:12 final size:12
Alignment explanation
Indices: 31560215--31560306 Score: 85
Period size: 12 Copynumber: 7.7 Consensus size: 12
31560205 TGAGATAGAA
*
31560215 GATGACGATGAT
1 GATGAAGATGAT
*
31560227 GATGAAGGTGAT
1 GATGAAGATGAT
* * *
31560239 GAGGATGATGAA
1 GATGAAGATGAT
* * *
31560251 GAGGAAGAGGAA
1 GATGAAGATGAT
* *
31560263 GAGGAAGAGGAT
1 GATGAAGATGAT
31560275 GATGAAGATGAT
1 GATGAAGATGAT
*
31560287 GATGATGATGAT
1 GATGAAGATGAT
31560299 GATGAAGA
1 GATGAAGA
31560307 AAGGAAAACC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 67 1.00
ACGTcount: A:0.40, C:0.01, G:0.40, T:0.18
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:31568491 original size:19 final size:20
Alignment explanation
Indices: 31568449--31568505 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
31568439 CACTTTGGCC
*
31568449 AAAAAAGCTCAGCTTAATCG
1 AAAAAAGCTCAGCTCAATCG
* *
31568469 AAAAAAGCTCAGCTCGA-CT
1 AAAAAAGCTCAGCTCAATCG
* *
31568488 AAAAAAGTTCACCTCAAT
1 AAAAAAGCTCAGCTCAAT
31568506 TATCTCGATC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.46, C:0.23, G:0.12, T:0.19
Consensus pattern (20 bp):
AAAAAAGCTCAGCTCAATCG
Found at i:31568796 original size:55 final size:55
Alignment explanation
Indices: 31568674--31568817 Score: 155
Period size: 55 Copynumber: 2.6 Consensus size: 55
31568664 ATCAAAGAGA
* * * * *
31568674 TTATCTCAATAAATTGTA-TTCACAAAGGCTTAGCTCGATCATTTTGGTCAAAGAGC
1 TTATCTCGATAAA-T-TACTTCACAAAGGCTTAGCTCGATCATTTTAGTAAAAAAAC
* * * *
31568730 TCATCTTGATAAATTACTTCACAAAGGCTTAGCTCGATCGTTTTAGTAAAAAAAT
1 TTATCTCGATAAATTACTTCACAAAGGCTTAGCTCGATCATTTTAGTAAAAAAAC
* *
31568785 TTATCTCGATAAATTACCTTCATAAAGGTTTAG
1 TTATCTCGATAAATTA-CTTCACAAAGGCTTAG
31568818 ATAAACCATC
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
54 2 0.03
55 47 0.64
56 24 0.33
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (55 bp):
TTATCTCGATAAATTACTTCACAAAGGCTTAGCTCGATCATTTTAGTAAAAAAAC
Found at i:31569146 original size:19 final size:19
Alignment explanation
Indices: 31569124--31569168 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
31569114 TAGCTAAGCC
*
31569124 AAAAGAGATTAATTCAGCT
1 AAAAGAGATCAATTCAGCT
* * *
31569143 AAAAGAAATCAGTTTAGCT
1 AAAAGAGATCAATTCAGCT
31569162 AAAAGAG
1 AAAAGAG
31569169 CTCGGCCTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (19 bp):
AAAAGAGATCAATTCAGCT
Found at i:31569479 original size:31 final size:31
Alignment explanation
Indices: 31569403--31569479 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
31569393 TTAGAATCAC
* * *
31569403 CAAATTCACCTCGATGAAAATCACTTCAGTA
1 CAAATTCACCTTGGTAAAAATCACTTCAGTA
*
31569434 CAAATTCACTTTGGTAAAAATCATCTT-AGTA
1 CAAATTCACCTTGGTAAAAATCA-CTTCAGTA
*
31569465 CACATTCACCTTGGT
1 CAAATTCACCTTGGT
31569480 GTAAATTACC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 36 0.92
32 3 0.08
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.31
Consensus pattern (31 bp):
CAAATTCACCTTGGTAAAAATCACTTCAGTA
Found at i:31570909 original size:21 final size:20
Alignment explanation
Indices: 31570884--31570940 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
31570874 AATCATAATT
*
31570884 ATGAGATTAATTATTGTAACG
1 ATGAGATTAA-TATTATAACG
* *
31570905 GTGAGATTGAATATTATAATG
1 ATGAGATT-AATATTATAACG
*
31570926 ATGAGATTAAAATTA
1 ATGAGATTAATATTA
31570941 ACAGTGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 6 0.20
21 22 0.73
22 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (20 bp):
ATGAGATTAATATTATAACG
Found at i:31571570 original size:7 final size:7
Alignment explanation
Indices: 31571558--31571583 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31571548 ATAGTCATTG
31571558 AAATTTA
1 AAATTTA
31571565 AAATTTA
1 AAATTTA
31571572 AAATTTA
1 AAATTTA
31571579 AAATT
1 AAATT
31571584 AGTTACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:31576165 original size:7 final size:7
Alignment explanation
Indices: 31576153--31576178 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31576143 ACCAATGAAA
31576153 ATGTTTC
1 ATGTTTC
31576160 ATGTTTC
1 ATGTTTC
31576167 ATGTTTC
1 ATGTTTC
31576174 ATGTT
1 ATGTT
31576179 CAGATATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (7 bp):
ATGTTTC
Found at i:31576843 original size:2 final size:2
Alignment explanation
Indices: 31576836--31576865 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31576826 AGCATATAGA
31576836 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
31576866 GAATTAGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31577247 original size:2 final size:2
Alignment explanation
Indices: 31577240--31577264 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31577230 GAAATTCCAA
31577240 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 T
31577265 TTTTGCATTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31578339 original size:26 final size:25
Alignment explanation
Indices: 31578300--31578348 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
31578290 TTTATTAAAA
* *
31578300 TTTTTTAATTATAATTATAATAATT
1 TTTTTTAATCATAATTACAATAATT
31578325 TTTTTTCAATCATAATTACAATAA
1 TTTTTT-AATCATAATTACAATAA
31578349 ATATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTTTTAATCATAATTACAATAATT
Found at i:31589151 original size:34 final size:34
Alignment explanation
Indices: 31589108--31589175 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
31589098 TTAAATTGGT
31589108 TTTTTTTTTTTAATCTTACTTTCGTTCTGGTCCA
1 TTTTTTTTTTTAATCTTACTTTCGTTCTGGTCCA
* *
31589142 TTTTTTTTTTTAATCTTACTTTTGTTGTGGTCCA
1 TTTTTTTTTTTAATCTTACTTTCGTTCTGGTCCA
31589176 CATATAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.12, C:0.15, G:0.10, T:0.63
Consensus pattern (34 bp):
TTTTTTTTTTTAATCTTACTTTCGTTCTGGTCCA
Found at i:31597295 original size:99 final size:100
Alignment explanation
Indices: 31597182--31597385 Score: 308
Period size: 101 Copynumber: 2.0 Consensus size: 100
31597172 CCAGTATCTG
*
31597182 CTATTGGATCTTGGATGATGA-TCTC-T-CATGATAATTGATCAATCAACTAGGTTTTTTCAATT
1 CTATTGGATCTTGGATGATGACTCTCATACATGATAATTGATCAATCAA--A-GTTTTTCCAATT
* *
31597244 GGGGTCCCA-CTCTAATCGGAATCAAAGATAAAAAGTA
63 GGAGTCCCAGCTCCAATCGGAATCAAAGATAAAAAGTA
31597281 CTATTGGATCTTGGATGATGATCTCTCATACATGATAATTGATCAATCAAAGTTTTTCCAATTGG
1 CTATTGGATCTTGGATGATGA-CTCTCATACATGATAATTGATCAATCAAAGTTTTTCCAATTGG
*
31597346 AGTCCCAGCTCCAATTGGAATCAAAGATAAAAAGTA
65 AGTCCCAGCTCCAATCGGAATCAAAGATAAAAAGTA
31597382 CTAT
1 CTAT
31597386 GTACTAATTG
Statistics
Matches: 96, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
99 21 0.22
100 19 0.20
101 35 0.36
102 1 0.01
103 20 0.21
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (100 bp):
CTATTGGATCTTGGATGATGACTCTCATACATGATAATTGATCAATCAAAGTTTTTCCAATTGGA
GTCCCAGCTCCAATCGGAATCAAAGATAAAAAGTA
Found at i:31599483 original size:12 final size:12
Alignment explanation
Indices: 31599466--31599490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31599456 CTACTAAAGA
31599466 GACGATGATGAT
1 GACGATGATGAT
31599478 GACGATGATGAT
1 GACGATGATGAT
31599490 G
1 G
31599491 GAGATAAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.36, T:0.24
Consensus pattern (12 bp):
GACGATGATGAT
Found at i:31602466 original size:22 final size:22
Alignment explanation
Indices: 31602441--31602500 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 22
31602431 CCCGAAATTA
*
31602441 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATATTTTAAAAT
31602463 ATAAAATATTATATTTTAAAAT
1 ATAAAATATTATATTTTAAAAT
31602485 ATAAATATATATATAT
1 ATAAA-ATAT-TATAT
31602501 AAATAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 26 0.74
23 4 0.11
24 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAAATATTATATTTTAAAAT
Found at i:31604678 original size:60 final size:60
Alignment explanation
Indices: 31604607--31604730 Score: 230
Period size: 60 Copynumber: 2.1 Consensus size: 60
31604597 AAAAACACCC
* *
31604607 TACTCACAGGGCATGAGCGACTCGGATAAACTGACACATGATCGAATGGATTTACTATTT
1 TACTCACAGGGCATGAGCAACTAGGATAAACTGACACATGATCGAATGGATTTACTATTT
31604667 TACTCACAGGGCATGAGCAACTAGGATAAACTGACACATGATCGAATGGATTTACTATTT
1 TACTCACAGGGCATGAGCAACTAGGATAAACTGACACATGATCGAATGGATTTACTATTT
31604727 TACT
1 TACT
31604731 AAATGCGAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (60 bp):
TACTCACAGGGCATGAGCAACTAGGATAAACTGACACATGATCGAATGGATTTACTATTT
Found at i:31606016 original size:15 final size:15
Alignment explanation
Indices: 31605994--31606036 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
31605984 TCCATCCATC
*
31605994 AAAATATTATTATTT
1 AAAATATTATTATTA
* *
31606009 AGAATATTACTATTA
1 AAAATATTATTATTA
*
31606024 AAAATATTTTTAT
1 AAAATATTATTAT
31606037 ATTAATATTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
AAAATATTATTATTA
Found at i:31613658 original size:23 final size:23
Alignment explanation
Indices: 31613630--31613673 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
31613620 TTAATAAAAA
*
31613630 TTATTATAATTATGATTAAAATT
1 TTATTATAATTATAATTAAAATT
31613653 TTATTATAATTATAATTAAAA
1 TTATTATAATTATAATTAAAA
31613674 AAAATTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTATTATAATTATAATTAAAATT
Found at i:31614096 original size:27 final size:28
Alignment explanation
Indices: 31614065--31614129 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
31614055 ATATATATAC
*
31614065 TTTTTAATTTTA-TATATTTAATGATTA
1 TTTTTAATTTTATTATATTTAATCATTA
* *
31614092 TTTTT-ATTATATTATATTTTATCATTA
1 TTTTTAATTTTATTATATTTAATCATTA
*
31614119 TTGTTACATTT
1 TTTTTA-ATTT
31614130 AAATTTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 5 0.17
27 22 0.73
29 3 0.10
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTTAATTTTATTATATTTAATCATTA
Found at i:31614113 original size:21 final size:21
Alignment explanation
Indices: 31614049--31614113 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
31614039 ATTTGTAAAA
*
31614049 TTTATTATATATATACTTTTTAAT
1 TTTATTATAT-TATA--TTTTATT
*
31614073 TTTA-TATATT-TAATGATTATT
1 TTTATTATATTAT-AT-TTTATT
31614094 TTTATTATATTATATTTTAT
1 TTTATTATATTATATTTTAT
31614114 CATTATTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 10 0.29
23 6 0.18
24 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTATTATATTATATTTTATT
Found at i:31620477 original size:28 final size:28
Alignment explanation
Indices: 31620445--31620502 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
31620435 GAAACTCTGT
31620445 ATCAGAAAAAAGAGTTGTATTTGCATAA
1 ATCAGAAAAAAGAGTTGTATTTGCATAA
*
31620473 ATCAGAAAATAGAGTTGTATTTGCATAA
1 ATCAGAAAAAAGAGTTGTATTTGCATAA
31620501 AT
1 AT
31620503 TTTGATTACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (28 bp):
ATCAGAAAAAAGAGTTGTATTTGCATAA
Found at i:31624947 original size:223 final size:223
Alignment explanation
Indices: 31624559--31625239 Score: 1019
Period size: 223 Copynumber: 3.1 Consensus size: 223
31624549 AAGGGTATAA
* * * *
31624559 CTCTCCAGCATCGTCACCTGT-AATCTCGTTTCATAAGCATCAACATACAAGAAATGCAAGAACC
1 CTCTCCAGCATTGTCGCCT-TCAATCTCATTTCATAAGCATCAACATACACGAAATGCAAGAACC
* *
31624623 AGTCCTGCTCCGGCATCATCATTCCTGATTTCACCTGCGCCTTTGAAACAGCAAGGTCTGATATC
65 AGTCCTGCTCCTGCATCATCATACCTGATTTCACCTGCGCCTTTGAAACAGCAAGGTCTGATATC
** * * * * * *
31624688 TTGTGCCCAAGACTTGTCTTAGT-CATTCTAACATTATAAGGTCTCAGCATATCCTGTTAATGTT
130 TTGTGCCCAAGACTTGTCCCA-TCCATACTAACATTATATGGGCTTATCACATCCTGTTAATGTT
31624752 TCATTTTAATATTTATACAGGTCCAGTCAT
194 TCATTTTAATATTTATACAGGTCCAGTCAT
*
31624782 CTCTCCAGCATTGTCGCCTTCAATCTCATTTCATAGGCATCAACATACACGAAATGCAAGAACCA
1 CTCTCCAGCATTGTCGCCTTCAATCTCATTTCATAAGCATCAACATACACGAAATGCAAGAACCA
*
31624847 GTCCTGCTCCTGCATCATCATACCTGATTTCACCTGCGCCCTTGAAACAGCAAGGTCTGATATCT
66 GTCCTGCTCCTGCATCATCATACCTGATTTCACCTGCGCCTTTGAAACAGCAAGGTCTGATATCT
* *
31624912 TGTGCCCAAGACTTGTCCCATCCATACTAACATTATATGGGCTTATTACATCCCGTTAATGTTTC
131 TGTGCCCAAGACTTGTCCCATCCATACTAACATTATATGGGCTTATCACATCCTGTTAATGTTTC
* *
31624977 ATTTCAATATTTATACAGGTCCGGTCAT
196 ATTTTAATATTTATACAGGTCCAGTCAT
* * * *
31625005 CTCTCCTGCATTGTCGCCTTCAATCTCAGTTCATAAGCATCAACATACACGAAATGTAAGAACCG
1 CTCTCCAGCATTGTCGCCTTCAATCTCATTTCATAAGCATCAACATACACGAAATGCAAGAACCA
31625070 GTCCTGCTCCTGCATCATCATACCTGATTTCACCTGCGCCTTTGAAACAGCAAGGTCTGATATCT
66 GTCCTGCTCCTGCATCATCATACCTGATTTCACCTGCGCCTTTGAAACAGCAAGGTCTGATATCT
* * * *
31625135 TGTTCCCAAGACTTGTCCCAGCCATACTAACAATATATGGGCTTATCACATCCCT-TTAATTTTT
131 TGTGCCCAAGACTTGTCCCATCCATACTAACATTATATGGGCTTATCACAT-CCTGTTAATGTTT
* * *
31625199 C-TTTTCTATATTTATATAGGTCCTGTCAT
195 CATTTT-AATATTTATACAGGTCCAGTCAT
31625228 CTCTCCAGCATT
1 CTCTCCAGCATT
31625240 TCTTCCGGGA
Statistics
Matches: 417, Mismatches: 37, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
222 5 0.01
223 410 0.98
224 2 0.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.32
Consensus pattern (223 bp):
CTCTCCAGCATTGTCGCCTTCAATCTCATTTCATAAGCATCAACATACACGAAATGCAAGAACCA
GTCCTGCTCCTGCATCATCATACCTGATTTCACCTGCGCCTTTGAAACAGCAAGGTCTGATATCT
TGTGCCCAAGACTTGTCCCATCCATACTAACATTATATGGGCTTATCACATCCTGTTAATGTTTC
ATTTTAATATTTATACAGGTCCAGTCAT
Found at i:31625301 original size:16 final size:16
Alignment explanation
Indices: 31625280--31625310 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31625270 TCCTGCACCC
31625280 CTTCATCCTGGTATCG
1 CTTCATCCTGGTATCG
31625296 CTTCATCCTGGTATC
1 CTTCATCCTGGTATC
31625311 AAAATAGCAA
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:0.13, C:0.32, G:0.16, T:0.39
Consensus pattern (16 bp):
CTTCATCCTGGTATCG
Found at i:31627901 original size:22 final size:22
Alignment explanation
Indices: 31627874--31627915 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
31627864 TATTCTGTGG
31627874 TTAA-TTCTAGAGATACAAATTC
1 TTAATTTC-AGAGATACAAATTC
*
31627896 TTAATTTCAGGGATACAAAT
1 TTAATTTCAGAGATACAAAT
31627916 ATATAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (22 bp):
TTAATTTCAGAGATACAAATTC
Found at i:31632847 original size:22 final size:22
Alignment explanation
Indices: 31632822--31632863 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31632812 TATTCTGTCT
31632822 TTAATTCTAGAGATACAAATTC
1 TTAATTCTAGAGATACAAATTC
* * *
31632844 TTAATTTTAGGGATTCAAAT
1 TTAATTCTAGAGATACAAAT
31632864 ATATACAAAT
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:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (22 bp):
TTAATTCTAGAGATACAAATTC
Found at i:31635604 original size:15 final size:18
Alignment explanation
Indices: 31635567--31635601 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31635557 ATAATTTTAC
31635567 TTAA-AAATAATATTATA
1 TTAATAAATAATATTATA
31635584 TTAATAAATAATATTATA
1 TTAATAAATAATATTATA
31635602 ATATATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAATAAATAATATTATA
Found at i:31635635 original size:23 final size:23
Alignment explanation
Indices: 31635580--31635635 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
31635570 AAAATAATAT
* * *
31635580 TATATTAATAAATAATATTATAA
1 TATATAAATAAATAATATAAGAA
*
31635603 TATATTAATAAATAATATAAAGAA
1 TATATAAATAAATAATAT-AAGAA
31635627 TA-ATAAATA
1 TATATAAATA
31635636 GTATTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 24 0.83
24 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TATATAAATAAATAATATAAGAA
Found at i:31635693 original size:13 final size:14
Alignment explanation
Indices: 31635677--31635707 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31635667 AATATTTTAA
31635677 TATT-AAATATAAT
1 TATTAAAATATAAT
31635690 TATTAAAATATAAT
1 TATTAAAATATAAT
31635704 TATT
1 TATT
31635708 TCTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATTAAAATATAAT
Found at i:31635721 original size:16 final size:15
Alignment explanation
Indices: 31635682--31635732 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 15
31635672 TTTAATATTA
**
31635682 AATATAATT-ATTAA
1 AATATAATTAATTTT
*
31635696 AATATAATTATTTCTT
1 AATATAATTAATT-TT
*
31635712 AATATTATTAATTTT
1 AATATAATTAATTTT
31635727 AATATA
1 AATATA
31635733 TTTTAATAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 9 0.31
15 9 0.31
16 11 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
AATATAATTAATTTT
Found at i:31663390 original size:5 final size:5
Alignment explanation
Indices: 31663380--31663406 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
31663370 ATTAATATAT
31663380 ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT
31663407 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:31667588 original size:2 final size:2
Alignment explanation
Indices: 31667583--31667607 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31667573 TATATATGTA
31667583 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
31667608 AAGAGCGGCT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:31677300 original size:24 final size:23
Alignment explanation
Indices: 31677258--31677304 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
31677248 GTATGAAAAT
*
31677258 ATTTAATATTTATTCTTTTATTAA
1 ATTTAATATTTAATCTTTT-TTAA
31677282 ATTTAATATTTAAAT-TTTTTTAA
1 ATTTAATATTT-AATCTTTTTTAA
31677305 TTAAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 15 0.71
25 2 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTAATATTTAATCTTTTTTAA
Found at i:31685175 original size:26 final size:26
Alignment explanation
Indices: 31685146--31685195 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
31685136 TACCCATAAC
31685146 TTAAGGAAAATTTAAAAAGGAACAAT
1 TTAAGGAAAATTTAAAAAGGAACAAT
* *
31685172 TTAAGGAAATTTTAAGAAGGAACA
1 TTAAGGAAAATTTAAAAAGGAACA
31685196 TTATTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.18, T:0.24
Consensus pattern (26 bp):
TTAAGGAAAATTTAAAAAGGAACAAT
Found at i:31690331 original size:14 final size:13
Alignment explanation
Indices: 31690306--31690340 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
31690296 TGATAGTTAA
31690306 TAAATTTAAAATT
1 TAAATTTAAAATT
31690319 TAAATTATAAAATT
1 TAAATT-TAAAATT
31690333 TATAATTT
1 TA-AATTT
31690341 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 10 0.50
15 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:31723181 original size:27 final size:25
Alignment explanation
Indices: 31723117--31723182 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
31723107 ATAATTTGAC
* *
31723117 TTTTAATTATATTATATGTATTATATA
1 TTTTAATT-TA-TATAAGTATTAAATA
*
31723144 TTTTAA-ATATATAAGTGATTAAATAA
1 TTTTAATTTATATAAGT-ATTAAAT-A
31723170 TTTTAATTTATAT
1 TTTTAATTTATAT
31723183 TTTTATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 6 0.19
25 8 0.25
26 7 0.22
27 11 0.34
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (25 bp):
TTTTAATTTATATAAGTATTAAATA
Found at i:31729983 original size:20 final size:20
Alignment explanation
Indices: 31729960--31730007 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
31729950 TTTCAGTTGG
*
31729960 TATTTTCTGCTGCTGGAACT
1 TATTTTCCGCTGCTGGAACT
31729980 TATTTTCCGCTGCTGGAACT
1 TATTTTCCGCTGCTGGAACT
31730000 TATTTTCC
1 TATTTTCC
31730008 TTTAGTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (20 bp):
TATTTTCCGCTGCTGGAACT
Found at i:31733985 original size:3 final size:3
Alignment explanation
Indices: 31733977--31734010 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
31733967 ATGGGCGTTG
31733977 TTA TTA TTA TTA TTA TTA TTA TTA TT- TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31734011 GTTAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:31734447 original size:3 final size:3
Alignment explanation
Indices: 31734439--31734469 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31734429 ATAGTATCTT
31734439 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
31734470 AGAACCCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:31736841 original size:23 final size:23
Alignment explanation
Indices: 31736781--31736841 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
31736771 AACAATTCAC
31736781 GAGTTAATTTTTGGAGAAAGAAA
1 GAGTTAATTTTTGGAGAAAGAAA
* * * *
31736804 GAGTGAACTTCTGGAGAAA-AGAT
1 GAGTTAATTTTTGGAGAAAGA-AA
31736827 GAGTTAATTTTTGGA
1 GAGTTAATTTTTGGA
31736842 AGGAAATATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (23 bp):
GAGTTAATTTTTGGAGAAAGAAA
Found at i:31736934 original size:13 final size:14
Alignment explanation
Indices: 31736912--31736945 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
31736902 TTTGAATTTC
31736912 TGAA-TTTTGG-TT
1 TGAAGTTTTGGATT
31736924 TGAAGTTTTGGATT
1 TGAAGTTTTGGATT
31736938 TGAAGTTT
1 TGAAGTTT
31736946 GAAAATTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 6 0.30
14 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (14 bp):
TGAAGTTTTGGATT
Found at i:31752025 original size:2 final size:2
Alignment explanation
Indices: 31752020--31752044 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31752010 GCGCGCGGGC
31752020 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
31752045 AGAGAGAGAG
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:31767561 original size:51 final size:51
Alignment explanation
Indices: 31767485--31767583 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
31767475 CTCAAAACCC
**
31767485 CAACAAACTCAACCCTCTATGCACCTACGCCGTATCCAATAACACCAACGG
1 CAACAAACTCAACCCTCTATGCACCTACGCCACATCCAATAACACCAACGG
* *
31767536 CAACAAACTCAACCTTCTATGCACCTATGCCACATCCAATAACACCAA
1 CAACAAACTCAACCCTCTATGCACCTACGCCACATCCAATAACACCAA
31767584 TAGCAACAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.37, C:0.38, G:0.07, T:0.17
Consensus pattern (51 bp):
CAACAAACTCAACCCTCTATGCACCTACGCCACATCCAATAACACCAACGG
Found at i:31774406 original size:20 final size:20
Alignment explanation
Indices: 31774378--31774415 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31774368 AAATCCAGCA
*
31774378 TAAAGGAAAGAAGAAAAAAC
1 TAAAAGAAAGAAGAAAAAAC
*
31774398 TAAAAGAAATAAGAAAAA
1 TAAAAGAAAGAAGAAAAA
31774416 GAATTAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.08
Consensus pattern (20 bp):
TAAAAGAAAGAAGAAAAAAC
Found at i:31782216 original size:16 final size:16
Alignment explanation
Indices: 31782157--31782218 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
31782147 TATTTTTAAT
31782157 TAATTAAATTTATAAA
1 TAATTAAATTTATAAA
* *
31782173 T-ATCATAAATTAATGAA
1 TAAT--TAAATTTATAAA
*
31782190 TGATTAAATTTATAAA
1 TAATTAAATTTATAAA
31782206 TAATTAAATTTAT
1 TAATTAAATTTAT
31782219 TTATTTTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 2 0.05
16 23 0.61
17 11 0.29
18 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (16 bp):
TAATTAAATTTATAAA
Found at i:31790571 original size:16 final size:15
Alignment explanation
Indices: 31790550--31790585 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
31790540 TTCTTTTTTC
*
31790550 TTTTTTTCTTCATCAT
1 TTTTTTTCATCATC-T
31790566 TTTTTTTCATCATCT
1 TTTTTTTCATCATCT
31790581 TTTTT
1 TTTTT
31790586 CTTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTTCATCATCT
Found at i:31790574 original size:13 final size:13
Alignment explanation
Indices: 31790551--31790586 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
31790541 TCTTTTTTCT
31790551 TTTTTTCTTCATCA
1 TTTTTT-TTCATCA
31790565 TTTTTTTTCATCA
1 TTTTTTTTCATCA
*
31790578 TCTTTTTTC
1 TTTTTTTTC
31790587 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTTCATCA
Found at i:31794606 original size:59 final size:58
Alignment explanation
Indices: 31794483--31794813 Score: 456
Period size: 59 Copynumber: 5.7 Consensus size: 58
31794473 TTGTGTAGGA
*
31794483 AAAATTGATACTTTCAACTTTTTCC-CAAAAATA-TTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
* * * *
31794540 AAAATTGATAGTTTTAACTTTTCCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTT-ATTTTTAAGG
* **
31794599 AAAATTGATACTTTCAACTTTTTCTCAAAAACCCTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTTTGAAAATTTATTTTTAAGG
* *
31794658 AAAATTGATGCTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
* * *
31794715 AAAATTGATACTTTCAACTTTT-CTCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTGAAAATTT-ATTTTTAAGG
31794774 AAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTT
31794814 TTGGAAATTT
Statistics
Matches: 243, Mismatches: 23, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
56 8 0.03
57 76 0.31
58 24 0.10
59 120 0.49
60 15 0.06
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
Found at i:31794628 original size:116 final size:114
Alignment explanation
Indices: 31794483--31794813 Score: 472
Period size: 116 Copynumber: 2.8 Consensus size: 114
31794473 TTGTGTAGGA
*
31794483 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTGA
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTGA
* *
31794548 TAGTTTTAACTTTTCCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGG
66 TAGTTTCAACTTTTCC-CAAAAATATTTTTTTGAAAATTT-ATTTTCAAGG
*
31794599 AAAATTGATACTTTCAACTTTTTCTCAAAAACCCT-TTTTTTGAAAATTTATTTTTAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAA---TATTTTTTGGAAATTTATTTTTAAGGAAAAT
*
31794663 TGAT-GCTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTTATTTTTAAGG
63 TGATAG-TTTCAACTTTT-CCCAAAAATATTTTTTTGAAAATTTATTTTCAAGG
*
31794715 AAAATTGATACTTTCAAC-TTTTCTCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTTCTC-AAAAATATTTTTTGGAAA-TTT-ATTTTTAAGGAAAAT
*
31794779 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTT
63 TGATAGTTTCAACTTTTCCC-AAAAATATTTTTTT
31794814 TTGGAAATTT
Statistics
Matches: 195, Mismatches: 8, Indels: 23
0.86 0.04 0.10
Matches are distributed among these distances:
113 1 0.01
114 10 0.05
115 13 0.07
116 98 0.50
117 20 0.10
118 50 0.26
119 3 0.02
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (114 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTGA
TAGTTTCAACTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTCAAGG
Found at i:31794814 original size:175 final size:178
Alignment explanation
Indices: 31794483--31794832 Score: 539
Period size: 175 Copynumber: 2.0 Consensus size: 178
31794473 TTGTGTAGGA
* *
31794483 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAAGGAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGGAAAATTGA
* * *
31794548 TAGTTTTAACTTTTCCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGGAAAATTGATACTTT
66 TACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGATTTTCAAGGAAAATTGATACTTT
* *
31794613 CAACTTTTTCTCAAAAAC-CCTTTTTTT-GAAAATTT-ATTTTTAAGG
131 CAACTTTTCCTCAAAAACATCTTTTTTTGGAAAATTTGATTTTTAAGG
*
31794658 AAAATTGATGCTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGGAAAATTGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGGAAAATTGA
*
31794723 TACTTTCAACTTTT-CTCTAAAAATATTTTTTGGAAATTTTGATTTTCAAGGAAAATTGATACTT
66 TACTTTCAACTTTTCCTC-AAAAATATTTTTTGGAAACTTTGATTTTCAAGGAAAATTGATACTT
* * *
31794787 TCAACTTTTCC-CTAAAAATATTTTTTTTTGGAAATTTTGATTTTTA
130 TCAACTTTTCCTC-AAAAACATCTTTTTTTGGAAAATTTGATTTTTA
31794833 TTTAAAGAAA
Statistics
Matches: 158, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
174 4 0.03
175 133 0.84
176 7 0.04
177 7 0.04
178 7 0.04
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (178 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAAGGAAAATTGA
TACTTTCAACTTTTCCTCAAAAATATTTTTTGGAAACTTTGATTTTCAAGGAAAATTGATACTTT
CAACTTTTCCTCAAAAACATCTTTTTTTGGAAAATTTGATTTTTAAGG
Found at i:31794845 original size:6 final size:6
Alignment explanation
Indices: 31794846--31794920 Score: 54
Period size: 6 Copynumber: 13.3 Consensus size: 6
31794836 AAAGAAAAAG
* * *
31794846 AATAATA AAT-AA AAT-A- AATAAA AATAAA AA-ATA AAGAAA AGT-AA
1 AATAA-A AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
* *
31794890 AACAAA AATAAA AAT-AA AATAAA GATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AA
31794921 GAATATTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
4 3 0.06
5 18 0.33
6 30 0.56
7 3 0.06
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:31794859 original size:16 final size:15
Alignment explanation
Indices: 31794835--31794934 Score: 57
Period size: 16 Copynumber: 6.5 Consensus size: 15
31794825 GATTTTTATT
*
31794835 TAAAGAAAAAGAATAA
1 TAAATAAAAA-AATAA
31794851 TAAATAAAATAAATAA
1 TAAATAAAA-AAATAA
31794867 -AAAT-AAAAAATAAA
1 TAAATAAAAAAAT-AA
*
31794881 GAAAAGTAAAACAAA-AA
1 -TAAA-TAAAA-AAATAA
*
31794898 TAAA-AATAAAATAA
1 TAAATAAAAAAATAA
* *
31794912 -AGATAAAAAGAATAT
1 TAAATAAAAA-AATAA
31794927 TAAATAAA
1 TAAATAAA
31794935 CCTAATCTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
13 9 0.14
14 14 0.21
15 8 0.12
16 25 0.38
17 4 0.06
18 3 0.05
19 3 0.05
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (15 bp):
TAAATAAAAAAATAA
Found at i:31794877 original size:22 final size:22
Alignment explanation
Indices: 31794846--31794920 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
31794836 AAAGAAAAAG
*
31794846 AATAATAAATAAAATAAATAAA
1 AATAAAAAATAAAATAAATAAA
31794868 AATAAAAAATAAAGA-AAAGT-AA
1 AATAAAAAATAAA-ATAAA-TAAA
*
31794890 AA-CAAAAATAAAAATAAAATAAA
1 AATAAAAAAT-AAAAT-AAATAAA
*
31794913 GATAAAAA
1 AATAAAAA
31794921 GAATATTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
21 7 0.17
22 23 0.55
23 8 0.19
24 4 0.10
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (22 bp):
AATAAAAAATAAAATAAATAAA
Found at i:31794878 original size:17 final size:17
Alignment explanation
Indices: 31794856--31794908 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
31794846 AATAATAAAT
31794856 AAAATAAATAAAAATAA
1 AAAATAAATAAAAATAA
* *
31794873 AAAATAAAGAAAAGTAA
1 AAAATAAATAAAAATAA
31794890 AACAA-AAATAAAAATAA
1 AA-AATAAATAAAAATAA
31794907 AA
1 AA
31794909 TAAAGATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 29 0.94
18 2 0.06
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (17 bp):
AAAATAAATAAAAATAA
Found at i:31794917 original size:17 final size:17
Alignment explanation
Indices: 31794842--31794920 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 17
31794832 ATTTAAAGAA
31794842 AAAGAATAATAAATAAAAT
1 AAAG-ATAA-AAATAAAAT
31794861 -AA-ATAAAAATAAAAAAT
1 AAAGATAAAAAT--AAAAT
* *
31794878 AAAG--AAAAGTAAAAC
1 AAAGATAAAAATAAAAT
*
31794893 AAAAATAAAAATAAAAT
1 AAAGATAAAAATAAAAT
31794910 AAAGATAAAAA
1 AAAGATAAAAA
31794921 GAATATTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
15 11 0.23
16 4 0.08
17 29 0.60
18 4 0.08
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAGATAAAAATAAAAT
Found at i:31795988 original size:25 final size:26
Alignment explanation
Indices: 31795937--31796011 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 26
31795927 AAAAACAAAA
*
31795937 AAATATAATA-AAATAATAATAAATAT
1 AAATCTAATATAAATAA-AATAAATAT
31795963 ATAA-CT-ATATAAATAAAATAAATAT
1 A-AATCTAATATAAATAAAATAAATAT
*
31795988 AAATCTAATCTAAAT-AAATAAATA
1 AAATCTAATATAAATAAAATAAATA
31796012 AAGATATACA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
24 2 0.05
25 24 0.56
26 15 0.35
27 2 0.05
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATCTAATATAAATAAAATAAATAT
Found at i:31796066 original size:18 final size:20
Alignment explanation
Indices: 31796028--31796085 Score: 75
Period size: 18 Copynumber: 3.0 Consensus size: 20
31796018 TACATATATT
31796028 AATACATAATAATAATAATAA
1 AATACATAA-AATAATAATAA
31796049 AATACATAAAAT-AT-ATAA
1 AATACATAAAATAATAATAA
* *
31796067 AATACAAAAAAAAATAATA
1 AATACATAAAATAATAATA
31796086 TAAGATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 14 0.42
19 4 0.12
20 6 0.18
21 9 0.27
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
AATACATAAAATAATAATAA
Found at i:31797547 original size:37 final size:37
Alignment explanation
Indices: 31797506--31797623 Score: 111
Period size: 37 Copynumber: 3.1 Consensus size: 37
31797496 CATTTATAAT
31797506 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACA
1 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACA
* * *
31797543 TTAAT-TA-TG--CTTTTT-AATTTAAATATCACCATTAACATA
1 TTAATACATTGTTCTTTTTCAA-TTAAA-A--AACAAT-AC--A
31797582 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACA
1 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACA
31797619 TTAAT
1 TTAAT
31797624 TATACTTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 24
0.68 0.06 0.26
Matches are distributed among these distances:
32 2 0.03
33 11 0.17
34 1 0.02
35 2 0.03
36 5 0.08
37 13 0.21
39 8 0.13
40 5 0.08
41 2 0.03
42 1 0.02
43 11 0.17
44 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.43
Consensus pattern (37 bp):
TTAATACATTGTTCTTTTTCAATTAAAAAACAATACA
Found at i:31797565 original size:33 final size:33
Alignment explanation
Indices: 31797519--31797637 Score: 89
Period size: 33 Copynumber: 3.3 Consensus size: 33
31797509 ATACATTGTT
31797519 CTTTTTCAATTAAAAAACAATACATTAATTATG
1 CTTTTTCAATTAAAAAACAATACATTAATTATG
* * *
31797552 CTTTTT-AATTTAAATATCACCATTAACATATTAATACATTG
1 CTTTTTCAA-TTAAA-A--AACAAT-AC--ATTAAT-TA-TG
*
31797593 TTCTTTTTCAATTAAAAAACAATACATTAATTATA
1 --CTTTTTCAATTAAAAAACAATACATTAATTATG
31797628 CTTTTT-AATT
1 CTTTTTCAATT
31797638 TAAATATCAT
Statistics
Matches: 67, Mismatches: 7, Indels: 25
0.68 0.07 0.25
Matches are distributed among these distances:
32 6 0.09
33 17 0.25
34 1 0.01
35 1 0.01
36 5 0.07
37 8 0.12
39 8 0.12
40 5 0.07
41 2 0.03
42 1 0.01
43 11 0.16
44 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.45
Consensus pattern (33 bp):
CTTTTTCAATTAAAAAACAATACATTAATTATG
Found at i:31797658 original size:76 final size:76
Alignment explanation
Indices: 31797506--31797646 Score: 273
Period size: 76 Copynumber: 1.9 Consensus size: 76
31797496 CATTTATAAT
*
31797506 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACATTAATTATGCTTTTTAATTTAAATATCA
1 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATCA
31797571 CCATTAACATA
66 CCATTAACATA
31797582 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATCA
1 TTAATACATTGTTCTTTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATCA
31797647 TCGTTGACAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (76 bp):
TTAATACATTGTTCTTTTTCAATTAAAAAACAATACATTAATTATACTTTTTAATTTAAATATCA
CCATTAACATA
Done.