Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 1 of 145
Found at i:28566 original size:20 final size:19
Alignment explanation
Indices: 28541--28586 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
28531 GAAGTTAATT
*
28541 TTATTTTTATTAATTTATAA
1 TTATTTTAATTAATTT-TAA
*
28561 TTATTTAAATTAATTTTAA
1 TTATTTTAATTAATTTTAA
28580 TT-TTTTA
1 TTATTTTA
28587 TGATGCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.17
19 5 0.22
20 14 0.61
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTTAATTAATTTTAA
Found at i:36672 original size:62 final size:62
Alignment explanation
Indices: 36575--36706 Score: 192
Period size: 62 Copynumber: 2.1 Consensus size: 62
36565 CAATCACATT
* * *
36575 TTTCACAACGAATTTTGATTCTAAATCTTTGAATCAATAATGCCAAGTTATATTAGAAGTCA
1 TTTCACAACGAATTTTGATTCTAAATCTTTGAATCAATAATGCCAAGTTAGAATACAAGTCA
* * * * *
36637 TTTCACAATGAATTTTGCTTCTAAATCTTTGAATCAATGATGTCAATTTAGAATACAAGTCA
1 TTTCACAACGAATTTTGATTCTAAATCTTTGAATCAATAATGCCAAGTTAGAATACAAGTCA
36699 TTTCACAA
1 TTTCACAA
36707 ATTTAATTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (62 bp):
TTTCACAACGAATTTTGATTCTAAATCTTTGAATCAATAATGCCAAGTTAGAATACAAGTCA
Found at i:57163 original size:43 final size:42
Alignment explanation
Indices: 57092--57198 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
57082 TGTCCTAGAC
* * *
57092 ATGGTCTTACATGGAAATCTCATATCGATGCCCATAGCCCAGCT
1 ATGGTCTTACA-CGAAATCTCACATCGAT-CCCATAGCCCAGAT
* * *
57136 ATGGTCTTACACGAAGTCTCACATCGATCTCATATCCCAGAT
1 ATGGTCTTACACGAAATCTCACATCGATCCCATAGCCCAGAT
*
57178 ATGGTCTTATACGAAATCTCA
1 ATGGTCTTACACGAAATCTCA
57199 AATCAATGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 30 0.55
43 14 0.25
44 11 0.20
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (42 bp):
ATGGTCTTACACGAAATCTCACATCGATCCCATAGCCCAGAT
Found at i:57182 original size:42 final size:42
Alignment explanation
Indices: 57092--57301 Score: 150
Period size: 48 Copynumber: 4.7 Consensus size: 42
57082 TGTCCTAGAC
* * * * *
57092 ATGGTCTTACATGGAAATCTCATATCGATGCCCATAGCCCAGCT
1 ATGGTCTTACA-CGAAATCTCACATCGAT-CTCATATCCCAGAT
*
57136 ATGGTCTTACACGAAGTCTCACATCGATCTCATATCCCAGAT
1 ATGGTCTTACACGAAATCTCACATCGATCTCATATCCCAGAT
* *
57178 ATGGTCTTATACGAAATCTCAAATCAATGTCGATGTCATATCCCAGAT
1 ATGGTCTTACACGAAATCTC--A-C-A--TCGATCTCATATCCCAGAT
* * * * *
57226 ATGGTCTTATACGAGATCTCAAAACGATGCCGATGTCATATCCTAGAC
1 ATGGTCTTACACGAAATCTC---AC-AT--CGATCTCATATCCCAGAT
* * *
57274 ATGGTCTTATACGAGATCTCAAATCGAT
1 ATGGTCTTACACGAAATCTCACATCGAT
57302 GCCGATGCCA
Statistics
Matches: 143, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
42 33 0.23
43 14 0.10
44 14 0.10
45 2 0.01
46 2 0.01
48 75 0.52
49 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (42 bp):
ATGGTCTTACACGAAATCTCACATCGATCTCATATCCCAGAT
Found at i:57230 original size:48 final size:48
Alignment explanation
Indices: 57160--57394 Score: 319
Period size: 48 Copynumber: 4.9 Consensus size: 48
57150 AGTCTCACAT
* * * *
57160 CGATCTCATATCCCAGATATGGTCTTATACGAAATCTCAAATCAATGT
1 CGATGTCATATCCCAGATATGGTCTTATACGAGATCTCAAATCGATGC
*
57208 CGATGTCATATCCCAGATATGGTCTTATACGAGATCTCAAAACGATGC
1 CGATGTCATATCCCAGATATGGTCTTATACGAGATCTCAAATCGATGC
* *
57256 CGATGTCATATCCTAGACATGGTCTTATACGAGATCTCAAATCGATGC
1 CGATGTCATATCCCAGATATGGTCTTATACGAGATCTCAAATCGATGC
* * *
57304 CGATGCCATATTCCAGACATGGTCTTATAC-AGGATCTCAAATCGATGC
1 CGATGTCATATCCCAGATATGGTCTTATACGA-GATCTCAAATCGATGC
* * * * *
57352 CGATGTCATATCTCAAATATAGTCTTATACGGGATCTTAAATC
1 CGATGTCATATCCCAGATATGGTCTTATACGAGATCTCAAATC
57395 AATTTGGCAA
Statistics
Matches: 166, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
47 1 0.01
48 165 0.99
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (48 bp):
CGATGTCATATCCCAGATATGGTCTTATACGAGATCTCAAATCGATGC
Found at i:57424 original size:30 final size:30
Alignment explanation
Indices: 57390--57487 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
57380 ACGGGATCTT
*
57390 AAATCAATTTGGCAATATATATACATATAC
1 AAATCAATTCGGCAATATATATACATATAC
*
57420 AAATCAATTCGGCAATATATATATATATCTAC
1 AAATCAATTCGGCAATATATATACATA--TAC
*
57452 ATATAAATCAATTCGGCAATATATAAAACATATAC
1 ----AAATCAATTCGGCAATATAT-ATACATATAC
57487 A
1 A
57488 TTTGAATTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
30 25 0.44
31 1 0.02
32 3 0.05
35 3 0.05
36 20 0.35
37 5 0.09
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATCAATTCGGCAATATATATACATATAC
Found at i:57460 original size:36 final size:37
Alignment explanation
Indices: 57404--57476 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 37
57394 CAATTTGGCA
57404 ATATATATACATATACAAATCAATTCGGCAATATATAT
1 ATATATATACATATA-AAATCAATTCGGCAATATATAT
*
57442 ATATATCTACATAT-AAATCAATTCGGCAATATATA
1 ATATATATACATATAAAATCAATTCGGCAATATATA
57477 AAACATATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 21 0.62
38 13 0.38
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (37 bp):
ATATATATACATATAAAATCAATTCGGCAATATATAT
Found at i:61665 original size:2 final size:2
Alignment explanation
Indices: 61658--61691 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
61648 GAATAATGAA
*
61658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61692 GCCACATATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:67589 original size:3 final size:3
Alignment explanation
Indices: 67581--67616 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
67571 TTAAAGTCAC
67581 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
67617 TTCTAACTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:73424 original size:31 final size:31
Alignment explanation
Indices: 73389--73488 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
73379 AGTTAATATT
* * *
73389 TGAACTTGGTAATTGTTCTTATATTG-GGACC
1 TGAACTTGGCAATTGTTCTCACATTGAGG-CC
* *
73420 TGAACTTAGCAATTGTTCTCACATTGAGGTC
1 TGAACTTGGCAATTGTTCTCACATTGAGGCC
* *
73451 TGAACTTGGCAATTATTC-CTTCATTGAGGCC
1 TGAACTTGGCAATTGTTCTC-ACATTGAGGCC
*
73482 TAAACTT
1 TGAACTT
73489 TAGGGTTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
30 1 0.02
31 54 0.95
32 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (31 bp):
TGAACTTGGCAATTGTTCTCACATTGAGGCC
Found at i:79455 original size:97 final size:97
Alignment explanation
Indices: 79289--79479 Score: 355
Period size: 97 Copynumber: 2.0 Consensus size: 97
79279 GCAGCCCCGA
* *
79289 GAAAAATAAGGCTTCGAAGCAGAGGAAACGATGCGATTTCTGGTTCTAAGATGATTTCTCTTTGC
1 GAAAAAGAAGGCTTCGAAGCAGAGGAAACGACGCGATTTCTGGTTCTAAGATGATTTCTCTTTGC
79354 TTTTGTATGCTTGAATAGAAGCTAGAAGGCCC
66 TTTTGTATGCTTGAATAGAAGCTAGAAGGCCC
*
79386 GAAAAAGAAGGCTTCGAAGCAGAGGAAACGACGCGATTTCTGGTTCTAAGGTGATTTCTCTTTGC
1 GAAAAAGAAGGCTTCGAAGCAGAGGAAACGACGCGATTTCTGGTTCTAAGATGATTTCTCTTTGC
79451 TTTTGTATGCTTGAATAGAAGCTAGAAGG
66 TTTTGTATGCTTGAATAGAAGCTAGAAGG
79480 TGTGAGGATT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (97 bp):
GAAAAAGAAGGCTTCGAAGCAGAGGAAACGACGCGATTTCTGGTTCTAAGATGATTTCTCTTTGC
TTTTGTATGCTTGAATAGAAGCTAGAAGGCCC
Found at i:90101 original size:16 final size:17
Alignment explanation
Indices: 90071--90103 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
90061 AACAGGGACC
*
90071 AAAAGCAAATTAATTTT
1 AAAAGCAAATCAATTTT
90088 AAAA-CAAATCAATTTT
1 AAAAGCAAATCAATTTT
90104 GTTGTGTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAAGCAAATCAATTTT
Found at i:96281 original size:20 final size:20
Alignment explanation
Indices: 96256--96333 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 20
96246 TTTAGATTAG
*
96256 AATTTTGTATGAATATTTTA
1 AATTTTGTATGAATATTATA
96276 AATTTTTTGTATGAATATTATA
1 AA--TTTTGTATGAATATTATA
* * *
96298 ATTTTTTTATGAATATTGT-
1 AATTTTGTATGAATATTATA
*
96317 AATGTTGTATGAATATT
1 AATTTTGTATGAATATT
96334 GTAATATTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
19 14 0.29
20 17 0.35
22 18 0.37
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (20 bp):
AATTTTGTATGAATATTATA
Found at i:96329 original size:19 final size:19
Alignment explanation
Indices: 96256--96442 Score: 123
Period size: 19 Copynumber: 10.2 Consensus size: 19
96246 TTTAGATTAG
*
96256 AATTTTGTATGAATATTTT
1 AATTTTGTATGAATATTGT
*
96275 AAATTTTTTGTATGAATATTAT
1 -AA--TTTTGTATGAATATTGT
*
96297 AATTTTTTTATGAATATTGT
1 AA-TTTTGTATGAATATTGT
*
96317 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
* *
96336 AA-TAT-TAT-AATTTTGTAT
1 AATTTTGTATGAATATTG--T
* *
96354 GAATATTG--T-AATTTTGT
1 -AATTTTGTATGAATATTGT
96371 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
96390 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
*
96404 AATATTG--T-AATATTGT
1 AATTTTGTATGAATATTGT
96420 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
96439 AATT
1 AATT
96443 ATTTTATAAT
Statistics
Matches: 134, Mismatches: 15, Indels: 37
0.72 0.08 0.20
Matches are distributed among these distances:
13 1 0.01
14 7 0.05
15 4 0.03
16 20 0.15
17 4 0.03
18 7 0.05
19 52 0.39
20 21 0.16
21 2 0.01
22 16 0.12
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:96339 original size:8 final size:8
Alignment explanation
Indices: 96309--96428 Score: 55
Period size: 8 Copynumber: 14.1 Consensus size: 8
96299 TTTTTTTATG
96309 AATATTGT
1 AATATTGT
*
96317 AATGTTGTAT
1 AATATTG--T
96327 GAATATTGT
1 -AATATTGT
*
96336 AATATTAT
1 AATATTGT
*
96344 AATTTTGTAT
1 AATATTG--T
96354 GAATATTGT
1 -AATATTGT
*
96363 AATTTTGT
1 AATATTGT
*
96371 AATTTTGTAT
1 AATATTG--T
96381 GAATATTGT
1 -AATATTGT
* *
96390 AATTTTTT
1 AATATTGT
**
96398 TGTA-TG-
1 AATATTGT
96404 AATATTGT
1 AATATTGT
96412 AATATTGT
1 AATATTGT
*
96420 AATTTTGT
1 AATATTGT
96428 A
1 A
96429 TGAATATTGT
Statistics
Matches: 84, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
6 2 0.02
7 3 0.04
8 55 0.65
9 3 0.04
10 3 0.04
11 18 0.21
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (8 bp):
AATATTGT
Found at i:96351 original size:27 final size:27
Alignment explanation
Indices: 96309--96441 Score: 204
Period size: 27 Copynumber: 5.1 Consensus size: 27
96299 TTTTTTTATG
*
96309 AATATTGTAATGTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
*
96336 AATATTATAATTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
*
96363 AATTTTGTAATTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
96390 -A-ATT-T--TTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
96412 AATATTGTAATTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
96439 AAT
1 AAT
96442 TATTTTATAA
Statistics
Matches: 96, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.18
23 1 0.01
24 4 0.04
25 3 0.03
26 1 0.01
27 70 0.73
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
AATATTGTAATTTTGTATGAATATTGT
Found at i:96420 original size:49 final size:49
Alignment explanation
Indices: 96309--96447 Score: 206
Period size: 49 Copynumber: 2.7 Consensus size: 49
96299 TTTTTTTATG
*
96309 AATATTGTAATGTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT-A-ATT-T--TTTTGTATGAATATTGT
*
96363 AATTTTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
*
96412 AATATTGTAATTTTGTATGAATATTGTAATTATTTT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTT
96448 ATAATTAATT
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
49 51 0.63
51 1 0.01
52 3 0.04
53 1 0.01
54 25 0.31
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
Found at i:96525 original size:27 final size:27
Alignment explanation
Indices: 96494--96561 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
96484 ATATTTTGTT
96494 CACCATTGGCGCCTCCCAAATAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
*
96521 CACCATTGGCGCCTCCTAAATAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
96548 CACCATTGGCGCCT
1 CACCATTGGCGCCT
96562 TCCAGATATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.24, C:0.40, G:0.19, T:0.18
Consensus pattern (27 bp):
CACCATTGGCGCCTCCCAAATAGGCAC
Found at i:100607 original size:37 final size:36
Alignment explanation
Indices: 100564--100661 Score: 96
Period size: 37 Copynumber: 2.8 Consensus size: 36
100554 ATATCATCTT
* *
100564 AAACAAATGAAATATAGCACCAGTTTAAGGTATTACA
1 AAACAAATGAAATATAGCACTAGTTTAAGGGA-TACA
* * **
100601 AAAC-AA--AAGTATAG-ATTAGTTTAAGGGATATG
1 AAACAAATGAAATATAGCACTAGTTTAAGGGATACA
100633 AAACAAAATGAAATATAGCACTAGTTTAA
1 AAAC-AAATGAAATATAGCACTAGTTTAA
100662 CGAATATCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
32 6 0.12
33 11 0.23
34 9 0.19
36 9 0.19
37 13 0.27
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (36 bp):
AAACAAATGAAATATAGCACTAGTTTAAGGGATACA
Found at i:102570 original size:93 final size:94
Alignment explanation
Indices: 102402--102588 Score: 349
Period size: 93 Copynumber: 2.0 Consensus size: 94
102392 TTGAAGAGAG
*
102402 TAATGAGTTGGATCTGAAAATGTTAAGCTTTTTTTTTTTTTTTTTTTGTACAAATTTTAATCCGG
1 TAATGAGTTGGATCTGAAAATGTTAAGCTTTTTTTTTTTTTTTTTTTGTACAAATTCTAATCCGG
102467 AGAGAGCTATAATTGAAGGGGGAAAATAA
66 AGAGAGCTATAATTGAAGGGGGAAAATAA
102496 TAATGAGTTGGATCTGAAAATGTTAAGC-TTTTTTTTTTTTTTTTTTGTACAAATTCTAATCCGG
1 TAATGAGTTGGATCTGAAAATGTTAAGCTTTTTTTTTTTTTTTTTTTGTACAAATTCTAATCCGG
*
102560 AGAGAGCTATAATTGAAGGTGGAAAATAA
66 AGAGAGCTATAATTGAAGGGGGAAAATAA
102589 AAAAAAAAAA
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
93 63 0.69
94 28 0.31
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (94 bp):
TAATGAGTTGGATCTGAAAATGTTAAGCTTTTTTTTTTTTTTTTTTTGTACAAATTCTAATCCGG
AGAGAGCTATAATTGAAGGGGGAAAATAA
Found at i:107560 original size:13 final size:13
Alignment explanation
Indices: 107542--107567 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
107532 TTGGATGAAC
107542 CATAGTACTAGCT
1 CATAGTACTAGCT
107555 CATAGTACTAGCT
1 CATAGTACTAGCT
107568 TTGGAGCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
CATAGTACTAGCT
Found at i:113428 original size:5 final size:5
Alignment explanation
Indices: 113418--113459 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
113408 TGTGTCTCGG
*
113418 TCTCT TCTCT TCTCT TCTCG TCTCT TCTCT TCTCT TCTCT TC
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TC
113460 ACATTTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.57
Consensus pattern (5 bp):
TCTCT
Found at i:113442 original size:20 final size:21
Alignment explanation
Indices: 113412--113456 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
113402 AAGGTATGTG
113412 TCTCGGTCTCTTCTCTTCTCT
1 TCTCGGTCTCTTCTCTTCTCT
113433 TCTC-GTCTCTTCTCTTCTCT
1 TCTCGGTCTCTTCTCTTCTCT
113453 TCTC
1 TCTC
113457 TTCACATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.00, C:0.40, G:0.07, T:0.53
Consensus pattern (21 bp):
TCTCGGTCTCTTCTCTTCTCT
Found at i:116329 original size:38 final size:37
Alignment explanation
Indices: 116260--116338 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 37
116250 GCCTTTAAAG
* *
116260 TTTACACATTCTATCAAATTGTTATTGATTTAAAAAAA
1 TTTACACATTCTATCAAATTGTCATTAATTT-AAAAAA
* *
116298 TTTACACATTCTGTCAAATTAGTCA-TAATTTAACAAA
1 TTTACACATTCTATCAAATT-GTCATTAATTTAAAAAA
116335 TTTA
1 TTTA
116339 GCCTGTAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 9 0.25
38 24 0.67
39 3 0.08
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.42
Consensus pattern (37 bp):
TTTACACATTCTATCAAATTGTCATTAATTTAAAAAA
Found at i:129752 original size:3 final size:3
Alignment explanation
Indices: 129744--129792 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
129734 GACTTTGGAC
129744 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
129792 T
1 T
129793 TTGTTTGGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:138488 original size:24 final size:23
Alignment explanation
Indices: 138456--138500 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
138446 ATGAATGTTG
138456 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTATCACA-ATTATTAT
*
138480 TTTAAATTTATCATAATTATT
1 TTTAAATTTATCACAATTATT
138501 TTAAGTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTAAATTTATCACAATTATTAT
Found at i:141000 original size:16 final size:16
Alignment explanation
Indices: 140969--141002 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
140959 TTGCTTCTGT
*
140969 TAAGTGTGTATGTATA
1 TAAGTGTGTATCTATA
*
140985 TAAGTGTGTGTCTATA
1 TAAGTGTGTATCTATA
141001 TA
1 TA
141003 TATATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.44
Consensus pattern (16 bp):
TAAGTGTGTATCTATA
Found at i:152425 original size:2 final size:2
Alignment explanation
Indices: 152420--152451 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
152410 AGCTTTTAAC
152420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
152452 TTAGCTTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:162130 original size:3 final size:3
Alignment explanation
Indices: 162124--162160 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
162114 GTTGGTTCGC
* *
162124 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TGT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
162161 TGTGTGATTT
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:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:162444 original size:179 final size:179
Alignment explanation
Indices: 162140--162502 Score: 719
Period size: 179 Copynumber: 2.0 Consensus size: 179
162130 TATTATTATT
162140 ATTA-TTATTGTTATTGTTATTTGTGTGATTTAATTTGTTTGAATATTTTGAATATAATAAAATT
1 ATTAGTTATTGTTATTGTTATTTGTGTGATTTAATTTGTTTGAATATTTTGAATATAATAAAATT
162204 TGATACAATGTATGTCATATTCGAATTTATATTTAACCCCAAGCGAATTACTAGATCGATGAAAA
66 TGATACAATGTATGTCATATTCGAATTTATATTTAACCCCAAGCGAATTACTAGATCGATGAAAA
162269 GACTGAGTTGATATGAACCTCACACTTTAAGTTTCAATTTTTTTGTCTA
131 GACTGAGTTGATATGAACCTCACACTTTAAGTTTCAATTTTTTTGTCTA
162318 ATTAGTTATTGTTATTGTTATTTGTGTGATTTAATTTGTTTGAATATTTTGAATATAATAAAATT
1 ATTAGTTATTGTTATTGTTATTTGTGTGATTTAATTTGTTTGAATATTTTGAATATAATAAAATT
162383 TGATACAATGTATGTCATATTCGAATTTATATTTAACCCCAAGCGAATTACTAGATCGATGAAAA
66 TGATACAATGTATGTCATATTCGAATTTATATTTAACCCCAAGCGAATTACTAGATCGATGAAAA
162448 GACTGAGTTGATATGAACCTCACACTTTAAGTTTCAATTTTTTTGTCTA
131 GACTGAGTTGATATGAACCTCACACTTTAAGTTTCAATTTTTTTGTCTA
162497 ATTAGT
1 ATTAGT
162503 ATCTATTTTT
Statistics
Matches: 184, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
178 4 0.02
179 180 0.98
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.44
Consensus pattern (179 bp):
ATTAGTTATTGTTATTGTTATTTGTGTGATTTAATTTGTTTGAATATTTTGAATATAATAAAATT
TGATACAATGTATGTCATATTCGAATTTATATTTAACCCCAAGCGAATTACTAGATCGATGAAAA
GACTGAGTTGATATGAACCTCACACTTTAAGTTTCAATTTTTTTGTCTA
Found at i:172196 original size:42 final size:42
Alignment explanation
Indices: 172150--172240 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
172140 TTTCGTTCAA
* * *
172150 CTCTTTTGAGCCTCTGTTTAACCCTTATAGGTTTCCGTTTAG
1 CTCTTATGAGCCTCCGTTCAACCCTTATAGGTTTCCGTTTAG
* * *
172192 CTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAG
1 CTCTTATGAGCCTCCGTTCAACCCTTATAGGTTTCCGTTTAG
*
172234 CACTTAT
1 CTCTTAT
172241 TGTAACGACC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.15, C:0.24, G:0.16, T:0.44
Consensus pattern (42 bp):
CTCTTATGAGCCTCCGTTCAACCCTTATAGGTTTCCGTTTAG
Found at i:172197 original size:21 final size:20
Alignment explanation
Indices: 172173--172240 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
172163 CTGTTTAACC
*
172173 CTTATAGGTTTCCGTTTAGCT
1 CTTAT-GGTTTCCGTTTAGCA
* * * *
172194 CTTATGAGCTTCCGTTCAACC
1 CTTATG-GTTTCCGTTTAGCA
*
172215 CTTATGGGTTTCTGTTTAGCA
1 CTTAT-GGTTTCCGTTTAGCA
172236 CTTAT
1 CTTAT
172241 TGTAACGACC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (20 bp):
CTTATGGTTTCCGTTTAGCA
Found at i:172569 original size:22 final size:21
Alignment explanation
Indices: 172527--172586 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
172517 TTTATTTGTC
172527 TAAATATATAATTAATGATAT
1 TAAATATATAATTAATGATAT
*
172548 TAAA-ATATAATTTATATTATAT
1 TAAATATATAA-TTA-ATGATAT
*
172570 GAATATATGATAATTAA
1 TAA-ATAT-ATAATTAA
172587 ATTATAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 6 0.19
21 7 0.22
22 8 0.25
23 2 0.06
24 5 0.16
25 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
TAAATATATAATTAATGATAT
Found at i:172599 original size:24 final size:25
Alignment explanation
Indices: 172554--172612 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
172544 ATATTAAAAT
*
172554 ATAATTTATATTATATGAATA-TATG
1 ATAA-TTAAATTATATGAATATTATG
172579 ATAATTAAATTATAATG-ATATTATG
1 ATAATTAAATTAT-ATGAATATTATG
*
172604 -TTATTAAAT
1 ATAATTAAAT
172613 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (25 bp):
ATAATTAAATTATATGAATATTATG
Found at i:172909 original size:3 final size:3
Alignment explanation
Indices: 172896--172935 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
172886 TAGGTAAATA
*
172896 ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
172936 CATATTGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:174334 original size:42 final size:42
Alignment explanation
Indices: 174265--174403 Score: 152
Period size: 42 Copynumber: 3.3 Consensus size: 42
174255 TAGCTCTCAC
* * *
174265 GAGCTTCTGTTCAACTCATATGAGTTTCCGTTCAACTCTTTT
1 GAGCTTCTGTTCAACCCTTATGAGTTTCCGTTCAACTCTTAT
* * * * *
174307 GAGCCTCTGTTTAACCCTTATGGGTTTCCGTTTAGCTCTTAT
1 GAGCTTCTGTTCAACCCTTATGAGTTTCCGTTCAACTCTTAT
* * * *
174349 GAGCTTCTGTTCAACCCTTATGAGTTTCTGTTTAGCACTTAT
1 GAGCTTCTGTTCAACCCTTATGAGTTTCCGTTCAACTCTTAT
**
174391 GTTCTTCTGTTCA
1 GAGCTTCTGTTCA
174404 GCCTTCGGAC
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (42 bp):
GAGCTTCTGTTCAACCCTTATGAGTTTCCGTTCAACTCTTAT
Found at i:174377 original size:21 final size:21
Alignment explanation
Indices: 174269--174380 Score: 107
Period size: 21 Copynumber: 5.3 Consensus size: 21
174259 TCTCACGAGC
*
174269 TTCTGTTCAACTCATATGAGT
1 TTCTGTTCAACTCTTATGAGT
* * *
174290 TTCCGTTCAACTCTTTTGAGC
1 TTCTGTTCAACTCTTATGAGT
* * * *
174311 CTCTGTTTAACCCTTATGGGT
1 TTCTGTTCAACTCTTATGAGT
* * * *
174332 TTCCGTTTAGCTCTTATGAGC
1 TTCTGTTCAACTCTTATGAGT
*
174353 TTCTGTTCAACCCTTATGAGT
1 TTCTGTTCAACTCTTATGAGT
174374 TTCTGTT
1 TTCTGTT
174381 TAGCACTTAT
Statistics
Matches: 69, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAACTCTTATGAGT
Found at i:185565 original size:18 final size:18
Alignment explanation
Indices: 185531--185569 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
185521 TGAAAGGGTC
185531 ACAAAGAAAAGAAAAATT
1 ACAAAGAAAAGAAAAATT
*
185549 ACAAA-AAAAGATCAAATT
1 ACAAAGAAAAGA-AAAATT
185567 ACA
1 ACA
185570 CAACGTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.69, C:0.10, G:0.08, T:0.13
Consensus pattern (18 bp):
ACAAAGAAAAGAAAAATT
Found at i:188425 original size:2 final size:2
Alignment explanation
Indices: 188418--188444 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
188408 CTGCTCGACC
188418 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
188445 CACTCATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:191106 original size:17 final size:18
Alignment explanation
Indices: 191079--191112 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
191069 AAATAATTTA
191079 AAAAATATAAAAAAAATT
1 AAAAATATAAAAAAAATT
191097 AAAAAT-TAAAAAAAAT
1 AAAAATATAAAAAAAAT
191113 AACATGGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAATATAAAAAAAATT
Found at i:197486 original size:27 final size:27
Alignment explanation
Indices: 197447--197532 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
197437 CTGGTTTAGA
*
197447 CACCTGCGAAGGCGCCTTTGAAGGTCC
1 CACCTGCGAAGGCACCTTTGAAGGTCC
197474 CACCTGCCG-AGGCACCTTTGAAGGTCC
1 CACCTG-CGAAGGCACCTTTGAAGGTCC
* *
197501 CACCTGTGAAGGCACCTTCGAAGGTCC
1 CACCTGCGAAGGCACCTTTGAAGGTCC
197528 CACCT
1 CACCT
197533 CTTCAGCCAC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
26 1 0.02
27 51 0.94
28 2 0.04
ACGTcount: A:0.20, C:0.36, G:0.26, T:0.19
Consensus pattern (27 bp):
CACCTGCGAAGGCACCTTTGAAGGTCC
Found at i:203289 original size:20 final size:22
Alignment explanation
Indices: 203249--203291 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
203239 ACGTGTACAT
*
203249 TTTGCTAACGTATAAAGATAAA
1 TTTGCTAACGTATAAAAATAAA
203271 TTTG-TAACG-ATAAAAATAAA
1 TTTGCTAACGTATAAAAATAAA
203291 T
1 T
203292 AAAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 5 0.25
22 4 0.20
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.33
Consensus pattern (22 bp):
TTTGCTAACGTATAAAAATAAA
Found at i:218593 original size:2 final size:2
Alignment explanation
Indices: 218588--218628 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
218578 AGATTGTGTG
218588 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
218629 TTGTTGCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:220287 original size:77 final size:78
Alignment explanation
Indices: 220188--220344 Score: 307
Period size: 77 Copynumber: 2.0 Consensus size: 78
220178 TAGAATGATC
220188 TTATAACTTGGTGTCACTTTATGTGCTGAATAATAAGAGAAATCACTCTTTATATTTCAATTAAT
1 TTATAACTTGGTGTCACTTTATGTGCTGAATAATAAGAGAAATCACTCTTTATATTTCAATTAAT
220253 TTAATTCTAGTGT
66 TTAATTCTAGTGT
220266 TTATAACTTGG-GTCACTTTATGTGCTGAATAATAAGAGAAATCACTCTTTATATTTCAATTAAT
1 TTATAACTTGGTGTCACTTTATGTGCTGAATAATAAGAGAAATCACTCTTTATATTTCAATTAAT
220330 TTAATTCTAGTGT
66 TTAATTCTAGTGT
220343 TT
1 TT
220345 TTGTTAGCAA
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 68 0.86
78 11 0.14
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (78 bp):
TTATAACTTGGTGTCACTTTATGTGCTGAATAATAAGAGAAATCACTCTTTATATTTCAATTAAT
TTAATTCTAGTGT
Found at i:222527 original size:19 final size:18
Alignment explanation
Indices: 222487--222523 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
222477 ATTTTTAGAT
*
222487 TAATTTTTTTATTTAAAA
1 TAATTTTTTTATTAAAAA
222505 TAATTTTTTT-TTAAAAA
1 TAATTTTTTTATTAAAAA
222522 TA
1 TA
222524 TAATGCACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAATTTTTTTATTAAAAA
Found at i:223792 original size:2 final size:2
Alignment explanation
Indices: 223785--223818 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
223775 AGGTTGGATT
223785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
223819 AGTTGGGNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:231223 original size:26 final size:27
Alignment explanation
Indices: 231171--231233 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 27
231161 ATAAAAAATA
231171 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
231198 ACCAAAATATTATAA-TTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
*
231224 ACTAAAATAT
1 ACCAAAATAT
231234 ACTTAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 20 0.57
27 15 0.43
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAACTTTTTTTATTT
Found at i:231311 original size:27 final size:27
Alignment explanation
Indices: 231281--231363 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 27
231271 GTCAGATCAG
*
231281 GCCAATCACATTGCCGGCACCAAAGGT
1 GCCAAACACATTGCCGGCACCAAAGGT
* * ** *
231308 GCCAAAGAGATTGGGGGCACCAATGGT
1 GCCAAACACATTGCCGGCACCAAAGGT
* * * * *
231335 GCCAAAGAGATTGGCGGCACGAATGGT
1 GCCAAACACATTGCCGGCACCAAAGGT
231362 GC
1 GC
231364 TAAAGGACTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.29, C:0.24, G:0.33, T:0.14
Consensus pattern (27 bp):
GCCAAACACATTGCCGGCACCAAAGGT
Found at i:231368 original size:27 final size:27
Alignment explanation
Indices: 231290--231368 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
231280 GGCCAATCAC
* *
231290 ATTGCCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
*
231317 ATTGGGGGCACCAATGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
* *
231344 ATTGGCGGCACGAATGGTGCTAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
231369 GACTAAAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.34, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:231948 original size:18 final size:18
Alignment explanation
Indices: 231927--232032 Score: 126
Period size: 18 Copynumber: 5.8 Consensus size: 18
231917 AGTAATAACT
231927 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
231945 CTATTCTT-ATTTAATAAA
1 CTATT-TTAATTTAATAAA
*
231963 CTATTCTT-ATTTAATAACT
1 CTATT-TTAATTTAATAA-A
231982 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
* * *
232000 CTATTCTCATTTAATAACT
1 CTATTTTAATTTAATAA-A
232019 CTATTTTAATTTAA
1 CTATTTTAATTTAA
232033 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
18 49 0.64
19 28 0.36
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:231960 original size:37 final size:36
Alignment explanation
Indices: 231927--232032 Score: 135
Period size: 37 Copynumber: 2.9 Consensus size: 36
231917 AGTAATAACT
231927 CTATTTTAATTTAATAA-ACTATTCTT-ATTTAATAAA
1 CTATTTT-ATTTAATAACACTATT-TTAATTTAATAAA
*
231963 CTATTCTTATTTAATAACTCTATTTTAATTTAATAAA
1 CTATT-TTATTTAATAACACTATTTTAATTTAATAAA
* *
232000 CTATTCTCATTTAATAACTCTATTTTAATTTAA
1 CTATT-TTATTTAATAACACTATTTTAATTTAA
232033 NNNNNNNNNN
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
36 16 0.25
37 49 0.75
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (36 bp):
CTATTTTATTTAATAACACTATTTTAATTTAATAAA
Found at i:232116 original size:19 final size:19
Alignment explanation
Indices: 232092--232156 Score: 96
Period size: 19 Copynumber: 3.5 Consensus size: 19
232082 NNAGAATAGT
232092 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
232111 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
232129 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
232148 TTATTAAAT
1 TTATTAAAT
232157 GAGAATAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.38
19 24 0.62
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:232134 original size:37 final size:37
Alignment explanation
Indices: 232084--232163 Score: 160
Period size: 37 Copynumber: 2.2 Consensus size: 37
232074 NNNNNNNNNN
232084 AGAATAGTTTATTAAATTAAAATAGAGTTATTAAATG
1 AGAATAGTTTATTAAATTAAAATAGAGTTATTAAATG
232121 AGAATAGTTTATTAAATTAAAATAGAGTTATTAAATG
1 AGAATAGTTTATTAAATTAAAATAGAGTTATTAAATG
232158 AGAATA
1 AGAATA
232164 AAGAATAGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (37 bp):
AGAATAGTTTATTAAATTAAAATAGAGTTATTAAATG
Found at i:233804 original size:21 final size:18
Alignment explanation
Indices: 233763--233811 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 18
233753 AATATATATA
*
233763 TTTAAAAATCAACAAATT
1 TTTAAAAATCAACAAACT
233781 TTTAAAAAGTTCATACAAACT
1 TTTAAAAA--TCA-ACAAACT
233802 TTTAGAAAAT
1 TTTA-AAAAT
233812 TTATCCATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.31
20 4 0.15
21 10 0.38
22 4 0.15
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (18 bp):
TTTAAAAATCAACAAACT
Found at i:244700 original size:2 final size:2
Alignment explanation
Indices: 244695--244740 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
244685 AGCAAAAGAT
244695 AG AG AG AG AG AG 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 AG AG AG AG AG AG
244737 AG AG
1 AG AG
244741 TTGCTTGGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:246741 original size:14 final size:17
Alignment explanation
Indices: 246697--246735 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
246687 CAAATTATAA
*
246697 TATTATATTATTAAAAT
1 TATTATATTGTTAAAAT
246714 TATTATATTGTTAAAAT
1 TATTATATTGTTAAAAT
246731 TATTA
1 TATTA
246736 ATTTAACCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TATTATATTGTTAAAAT
Found at i:262027 original size:49 final size:48
Alignment explanation
Indices: 261929--262024 Score: 185
Period size: 47 Copynumber: 2.0 Consensus size: 48
261919 GTTATATATC
261929 ATACATCATATATATATATATATATAAAGAGCTATAATTTTTTTAAAA
1 ATACATCATATATATATATATATATAAAGAGCTATAATTTTTTTAAAA
261977 ATACATCATATA-ATATATATATATAAAGAGCTATAATTTTTTTAAAA
1 ATACATCATATATATATATATATATAAAGAGCTATAATTTTTTTAAAA
262024 A
1 A
262025 AATTAGCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 36 0.75
48 12 0.25
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (48 bp):
ATACATCATATATATATATATATATAAAGAGCTATAATTTTTTTAAAA
Found at i:264615 original size:19 final size:20
Alignment explanation
Indices: 264591--264628 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
264581 TATTTTTATC
*
264591 AATTTAATCCTT-TTATTTA
1 AATTTAATCATTATTATTTA
264610 AATTTAATCATTATTATTT
1 AATTTAATCATTATTATTT
264629 TAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTAATCATTATTATTTA
Found at i:293803 original size:77 final size:78
Alignment explanation
Indices: 293711--293862 Score: 297
Period size: 77 Copynumber: 2.0 Consensus size: 78
293701 TATGATAGTA
293711 AAAATATAATTTTACAATTTTAATATTATATCTTTTTAATTTTTAAAGAATTAAATCAAAATTTT
1 AAAATATAATTTTACAATTTTAATATTATATCTTTTTAATTTTTAAAGAATTAAATCAAAATTTT
293776 ATCATTTATAAGT
66 ATCATTTATAAGT
293789 AAAA-ATAATTTTACAATTTTAATATTATATCTTTTTAATTTTTAAAGAATTAAATCAAAATTTT
1 AAAATATAATTTTACAATTTTAATATTATATCTTTTTAATTTTTAAAGAATTAAATCAAAATTTT
293853 ATCATTTATA
66 ATCATTTATA
293863 GGAGGGCCAT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 70 0.95
78 4 0.05
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (78 bp):
AAAATATAATTTTACAATTTTAATATTATATCTTTTTAATTTTTAAAGAATTAAATCAAAATTTT
ATCATTTATAAGT
Found at i:328151 original size:39 final size:39
Alignment explanation
Indices: 328070--328176 Score: 180
Period size: 39 Copynumber: 2.8 Consensus size: 39
328060 CTTAGAGTTG
* * *
328070 GACTTTAGTTTTATTTTTATTGGGTT-TGTAATTTGGTA
1 GACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGTA
328108 GACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGTA
1 GACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGTA
328147 GACTTTAGTTTTAGTTTTATTGGGTTGGGT
1 GACTTTAGTTTTAGTTTTATTGGGTTGGGT
328177 TGGTAATTGG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 25 0.38
39 40 0.62
ACGTcount: A:0.17, C:0.03, G:0.27, T:0.53
Consensus pattern (39 bp):
GACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGTA
Found at i:328196 original size:13 final size:13
Alignment explanation
Indices: 328174--328219 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
328164 TATTGGGTTG
*
328174 GGTT-GGTAATTG
1 GGTTGGGTAATTA
328186 GGTTGGGTAATTA
1 GGTTGGGTAATTA
328199 GGTTGGGTAATTA
1 GGTTGGGTAATTA
328212 GGTTGGGT
1 GGTTGGGT
328220 TGGATAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 4 0.12
13 28 0.88
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.39
Consensus pattern (13 bp):
GGTTGGGTAATTA
Found at i:329998 original size:15 final size:15
Alignment explanation
Indices: 329949--329999 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
329939 TTACCTTAGG
329949 TTACGTTTTAGTCAT
1 TTACGTTTTAGTCAT
* **
329964 TTATG-TTT-GAAAT
1 TTACGTTTTAGTCAT
329977 ATTACGTTTTAGTCAT
1 -TTACGTTTTAGTCAT
329993 TTACGTT
1 TTACGTT
330000 ATCATGTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 14 0.52
16 3 0.11
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (15 bp):
TTACGTTTTAGTCAT
Found at i:332663 original size:22 final size:21
Alignment explanation
Indices: 332637--332680 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
332627 TATATGTTAC
*
332637 ATCAACAAATAATTTTAAAAAA
1 ATCAA-AAATAAATTTAAAAAA
**
332659 ATCAAAGTTAAATTTAAAAAA
1 ATCAAAAATAAATTTAAAAAA
332680 A
1 A
332681 ATAAAAAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (21 bp):
ATCAAAAATAAATTTAAAAAA
Found at i:332859 original size:31 final size:33
Alignment explanation
Indices: 332796--332863 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
332786 TAAAAACATC
* *
332796 ATTTCGACTTTTTTTCAAAAAGTTAATGGTCAA
1 ATTTCGACTCTTTTTCAAAAAGTTAAGGGTCAA
* *
332829 ATTT-GACTCTTTTT-AAAAGGTTGAGGGTCAA
1 ATTTCGACTCTTTTTCAAAAAGTTAAGGGTCAA
332860 ATTT
1 ATTT
332864 AGATTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 18 0.58
32 9 0.29
33 4 0.13
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (33 bp):
ATTTCGACTCTTTTTCAAAAAGTTAAGGGTCAA
Found at i:337909 original size:34 final size:35
Alignment explanation
Indices: 337866--337937 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
337856 TTTGATGAAT
337866 GTTTTGTGTTTCTCA-TTTTTTATCCCCATAAATG
1 GTTTTGTGTTTCTCATTTTTTTATCCCCATAAATG
337900 GTTTTGTGTTTCTCATTTTTTTATCCCCATAAATG
1 GTTTTGTGTTTCTCATTTTTTTATCCCCATAAATG
337935 GTT
1 GTT
337938 GCTCTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 15 0.41
35 22 0.59
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (35 bp):
GTTTTGTGTTTCTCATTTTTTTATCCCCATAAATG
Found at i:357582 original size:14 final size:14
Alignment explanation
Indices: 357563--357589 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
357553 TTACCAATTT
357563 AAGTACTAAAGTAC
1 AAGTACTAAAGTAC
357577 AAGTACTAAAGTA
1 AAGTACTAAAGTA
357590 GACTTAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (14 bp):
AAGTACTAAAGTAC
Found at i:358236 original size:19 final size:19
Alignment explanation
Indices: 358212--358249 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
358202 TGTATCATTC
*
358212 GAATTTGATATAGTGAATT
1 GAATTTGACATAGTGAATT
358231 GAATTTGACATAGTGAATT
1 GAATTTGACATAGTGAATT
358250 TTCTTTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (19 bp):
GAATTTGACATAGTGAATT
Found at i:358715 original size:24 final size:24
Alignment explanation
Indices: 358681--358728 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
358671 TCAAACTAAA
* *
358681 ACTTAATTAATAATATTTTTATAC
1 ACTTAAATAATAACATTTTTATAC
*
358705 ACTTAAATAATAGCATTTTTATAC
1 ACTTAAATAATAACATTTTTATAC
358729 TTTCAACAGA
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:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (24 bp):
ACTTAAATAATAACATTTTTATAC
Found at i:365333 original size:14 final size:15
Alignment explanation
Indices: 365314--365342 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
365304 GTAAAATGAA
365314 ATTTTTT-AATTTAC
1 ATTTTTTAAATTTAC
365328 ATTTTTTAAATTTAC
1 ATTTTTTAAATTTAC
365343 TTGCTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTTAAATTTAC
Found at i:370854 original size:23 final size:23
Alignment explanation
Indices: 370824--370869 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
370814 GTTACGAATG
370824 ACTTGGTTGATGAGATTGGGAAC
1 ACTTGGTTGATGAGATTGGGAAC
370847 ACTTGGTTGATGAGATTGGGAAC
1 ACTTGGTTGATGAGATTGGGAAC
370870 CCAAACCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.35, T:0.30
Consensus pattern (23 bp):
ACTTGGTTGATGAGATTGGGAAC
Found at i:373046 original size:31 final size:31
Alignment explanation
Indices: 372987--373068 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
372977 AAAGTGCTGT
* *
372987 ATTTAGTCTCTATAC-TTT-AATTTGATCAA
1 ATTTAGTCCCTATACTTTTCAAATTGATCAA
*
373016 ATTTAGTCCCTGTACTTTTCAAATTGATCAA
1 ATTTAGTCCCTATACTTTTCAAATTGATCAA
*
373047 ATTTAATCCCTATACTTTTCAA
1 ATTTAGTCCCTATACTTTTCAA
373069 GTTTTAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 13 0.28
30 3 0.07
31 30 0.65
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (31 bp):
ATTTAGTCCCTATACTTTTCAAATTGATCAA
Found at i:378599 original size:32 final size:32
Alignment explanation
Indices: 378561--378625 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
378551 CCAATATTAC
*
378561 GATCGGCTCTCCATTGAGCCGTGTTCACCTTT
1 GATCGGCTCTCCATTGAGCCATGTTCACCTTT
378593 GATCGGCTCTCCATTGAGCCATGTTCACCTTT
1 GATCGGCTCTCCATTGAGCCATGTTCACCTTT
378625 G
1 G
378626 CCCTCATCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.14, C:0.31, G:0.22, T:0.34
Consensus pattern (32 bp):
GATCGGCTCTCCATTGAGCCATGTTCACCTTT
Found at i:387659 original size:12 final size:12
Alignment explanation
Indices: 387642--387668 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
387632 TACATAGATT
387642 GTGTCATTTTTA
1 GTGTCATTTTTA
387654 GTGTCATTTTTA
1 GTGTCATTTTTA
387666 GTG
1 GTG
387669 ATCCAAGAGA
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:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (12 bp):
GTGTCATTTTTA
Found at i:393067 original size:12 final size:12
Alignment explanation
Indices: 393050--393085 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
393040 TGATACATGT
393050 GAAACTGTTCCA
1 GAAACTGTTCCA
393062 GAAACTGTTCCA
1 GAAACTGTTCCA
393074 GAAACTGTTCCA
1 GAAACTGTTCCA
393086 AATGAAGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (12 bp):
GAAACTGTTCCA
Found at i:393810 original size:42 final size:42
Alignment explanation
Indices: 393751--393922 Score: 344
Period size: 42 Copynumber: 4.1 Consensus size: 42
393741 CAAATTATGG
393751 AATGCTGGCAAGTTTGAGCTCCAGGTTCTGCCTAATCGGGAT
1 AATGCTGGCAAGTTTGAGCTCCAGGTTCTGCCTAATCGGGAT
393793 AATGCTGGCAAGTTTGAGCTCCAGGTTCTGCCTAATCGGGAT
1 AATGCTGGCAAGTTTGAGCTCCAGGTTCTGCCTAATCGGGAT
393835 AATGCTGGCAAGTTTGAGCTCCAGGTTCTGCCTAATCGGGAT
1 AATGCTGGCAAGTTTGAGCTCCAGGTTCTGCCTAATCGGGAT
393877 AATGCTGGCAAGTTTGAGCTCCAGGTTCTGCCTAATCGGGAT
1 AATGCTGGCAAGTTTGAGCTCCAGGTTCTGCCTAATCGGGAT
393919 AATG
1 AATG
393923 TTTCTGGTTG
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 130 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (42 bp):
AATGCTGGCAAGTTTGAGCTCCAGGTTCTGCCTAATCGGGAT
Found at i:401571 original size:78 final size:78
Alignment explanation
Indices: 401442--401592 Score: 248
Period size: 78 Copynumber: 1.9 Consensus size: 78
401432 CTCATATTCT
* * *
401442 ACCATTAAACCATGATCCCTTGATCTTACCAGCTGGGAGAGTCGGTGATCATGTTGATAATGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
401507 ACCATGGAGTTCG
66 ACCATGGAGTTCG
* * *
401520 ACCATTAAACCATGATCCCTTGATCTCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
401585 ACCATGGA
66 ACCATGGA
401593 CTTTGTGTAC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (78 bp):
ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
ACCATGGAGTTCG
Found at i:404574 original size:15 final size:15
Alignment explanation
Indices: 404554--404610 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
404544 ACGTAGTTAA
404554 TGGGATATCCCGGCT
1 TGGGATATCCCGGCT
***
404569 TGGGATATTCCATTCT
1 TGGGATA-TCCCGGCT
**
404585 ACGGATATCCCGGCT
1 TGGGATATCCCGGCT
404600 TGGGATATCCC
1 TGGGATATCCC
404611 ATTTTAGGGA
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
15 21 0.68
16 10 0.32
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (15 bp):
TGGGATATCCCGGCT
Found at i:404594 original size:31 final size:31
Alignment explanation
Indices: 404556--404630 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
404546 GTAGTTAATG
*
404556 GGATATCCCGGCTTGGGATATTCCATTCTAC
1 GGATATCCCGGCTTGGGATATCCCATTCTAC
* *
404587 GGATATCCCGGCTTGGGATATCCCATTTTAG
1 GGATATCCCGGCTTGGGATATCCCATTCTAC
*
404618 GGATATTCCGGCT
1 GGATATCCCGGCT
404631 GGGGGTCTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (31 bp):
GGATATCCCGGCTTGGGATATCCCATTCTAC
Found at i:411989 original size:20 final size:19
Alignment explanation
Indices: 411964--412002 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
411954 CAACTCTAGG
*
411964 CCATTGATGACTTTTATCCA
1 CCATTGATGA-TTTAATCCA
411984 CCATTGATGATTTAATCCA
1 CCATTGATGATTTAATCCA
412003 ACAAACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (19 bp):
CCATTGATGATTTAATCCA
Found at i:414736 original size:21 final size:21
Alignment explanation
Indices: 414712--414751 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
414702 AATTTCCCCC
414712 GTCCGGGTCAG-TTGTTTTAGT
1 GTCCGGGTCAGATT-TTTTAGT
*
414733 GTCCGGTTCAGATTTTTTA
1 GTCCGGGTCAGATTTTTTA
414752 TGCTTCTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.12, C:0.15, G:0.28, T:0.45
Consensus pattern (21 bp):
GTCCGGGTCAGATTTTTTAGT
Found at i:414839 original size:16 final size:16
Alignment explanation
Indices: 414809--414880 Score: 121
Period size: 16 Copynumber: 4.6 Consensus size: 16
414799 CCCATTCCGC
414809 GGATATCCC-GGTTTG
1 GGATATCCCGGGTTTG
414824 GGATATCCCGGGTTTG
1 GGATATCCCGGGTTTG
414840 GGATATCCCGGGTTTG
1 GGATATCCCGGGTTTG
*
414856 GAATATCCC-GGTTTG
1 GGATATCCCGGGTTTG
414871 GGATATCCCG
1 GGATATCCCG
414881 AAAACGGATA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
15 23 0.43
16 30 0.57
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.31
Consensus pattern (16 bp):
GGATATCCCGGGTTTG
Found at i:414844 original size:31 final size:30
Alignment explanation
Indices: 414809--414880 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 30
414799 CCCATTCCGC
*
414809 GGATATCCCGGTTTGGGATATCCCGGGTTTG
1 GGATATCCCGGTTTGGAATATCCC-GGTTTG
414840 GGATATCCCGGGTTTGGAATATCCCGGTTTG
1 GGATATCCC-GGTTTGGAATATCCCGGTTTG
414871 GGATATCCCG
1 GGATATCCCG
414881 AAAACGGATA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 1 0.03
31 24 0.62
32 14 0.36
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.31
Consensus pattern (30 bp):
GGATATCCCGGTTTGGAATATCCCGGTTTG
Found at i:415183 original size:27 final size:29
Alignment explanation
Indices: 415129--415183 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
415119 AGTCCGATAT
**
415129 TTTTTTAAAAATAAAATAAAATTCAAACC
1 TTTTTTAAAAATAAAATAAAATAAAAACC
*
415158 TTTTTT-AAAAT-AAATAATATAAAAAC
1 TTTTTTAAAAATAAAATAAAATAAAAAC
415184 TCATTCTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 5 0.22
29 6 0.26
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (29 bp):
TTTTTTAAAAATAAAATAAAATAAAAACC
Found at i:422570 original size:33 final size:33
Alignment explanation
Indices: 422524--422589 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
422514 AACGTACATA
*
422524 ATAGTCCGCTGTTTTGTCTTTCAAAGATGAAAT
1 ATAGTCCGATGTTTTGTCTTTCAAAGATGAAAT
* *
422557 ATAGTCTGATGTTTTGTCTTTCAAAGATTAAAT
1 ATAGTCCGATGTTTTGTCTTTCAAAGATGAAAT
422590 TTTCCTCTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (33 bp):
ATAGTCCGATGTTTTGTCTTTCAAAGATGAAAT
Found at i:423424 original size:33 final size:32
Alignment explanation
Indices: 423339--423425 Score: 84
Period size: 33 Copynumber: 2.7 Consensus size: 32
423329 CAGGTAGGGA
* * *
423339 TATCCCATTCGAAGGATATCCCGGTTTAGATT
1 TATCCCATTCTAAGGATATCCCGGATCAGATT
* * ** *
423371 TATCCAATTATGCGGTTATCCCGGATCAGGATT
1 TATCCCATTCTAAGGATATCCCGGATCA-GATT
*
423404 TATCCCATTCTTAGGATATCCC
1 TATCCCATTCTAAGGATATCCC
423426 AACCTGGATT
Statistics
Matches: 41, Mismatches: 13, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
32 20 0.49
33 21 0.51
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (32 bp):
TATCCCATTCTAAGGATATCCCGGATCAGATT
Found at i:423592 original size:234 final size:233
Alignment explanation
Indices: 423183--423691 Score: 822
Period size: 234 Copynumber: 2.2 Consensus size: 233
423173 GATAACCCGG
* * *
423183 GGATATCCCAACCT-GATTTAAGCTATTCCCGGGTTATTCCTTTTAAATGCCGTCCCGGTTCGTT
1 GGATATCCCAACCTGGA-TTAAGCTATTCCCCGGTTATTCCTTTCAAATGCCGTCCCGGTTCGGT
* * *
423247 ATCCTATAGCCGGTTTTAGATGGTTTAGACTCCGGTTCATCGTTTTTTCGAGTTTAGACCGGGTA
65 ATCCTATAGCCGGTTTTAGATGGTTTAGACACCGGTTCATCGTTTTTTCGAGCTTAGACCGGGGA
* *
423312 ATCTACCGTAGTTATTCCAGGTAGGGATATCCCATTCGAAGGATATCCCGGTTTAGATTTATCCA
130 ACCTACCGTAGTTATTCCAGGTAGGGATATCCCATTCGAAGGATATCCCGGTTTAGAGTTATCCA
423377 ATTATGCGGTTATCCCGGATCAGGATTTATCCCATTCTTA
195 ATTATGCGGTTATCCCGG-TCAGGATTTATCCCATTCTTA
*
423417 GGATATCCCAACCTGGATTAAGCTATTCCCCGGTTATTCCTTTCAATTGCCGTCCCGGTTCGGTA
1 GGATATCCCAACCTGGATTAAGCTATTCCCCGGTTATTCCTTTCAAATGCCGTCCCGGTTCGGTA
423482 TCCTATAGCCGGTTTTAGATGGTTTAGACACCGGTTCATCGTTTTTTCGAGCTTAGACCGGGGAA
66 TCCTATAGCCGGTTTTAGATGGTTTAGACACCGGTTCATCGTTTTTTCGAGCTTAGACCGGGGAA
* *
423547 CCTACCGTAGTTATTCCAGGTAGGGATATCCCATTCGGAGGATATCCCGGTTTAGAGTTATCCTA
131 CCTACCGTAGTTATTCCAGGTAGGGATATCCCATTCGAAGGATATCCCGGTTTAGAGTTATCCAA
* ** *
423612 TTCTGCGGTTATCCCGGTTTGGATTTATCCCATTCTTC
196 TTATGCGGTTATCCCGGTCAGGATTTATCCCATTCTTA
* * * *
423650 GGATATCCTAACTTGGATTAAGCTATTCCCTGTTTATTCCTT
1 GGATATCCCAACCTGGATTAAGCTATTCCCCGGTTATTCCTT
423692 AGGGTTTAAG
Statistics
Matches: 255, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
233 56 0.22
234 197 0.77
235 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (233 bp):
GGATATCCCAACCTGGATTAAGCTATTCCCCGGTTATTCCTTTCAAATGCCGTCCCGGTTCGGTA
TCCTATAGCCGGTTTTAGATGGTTTAGACACCGGTTCATCGTTTTTTCGAGCTTAGACCGGGGAA
CCTACCGTAGTTATTCCAGGTAGGGATATCCCATTCGAAGGATATCCCGGTTTAGAGTTATCCAA
TTATGCGGTTATCCCGGTCAGGATTTATCCCATTCTTA
Found at i:423625 original size:32 final size:32
Alignment explanation
Indices: 423573--423657 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 32
423563 CAGGTAGGGA
* *
423573 TATCCCATTCGGAGGATATCCCGGTTTAGAGT
1 TATCCCATTCTGCGGATATCCCGGTTTAGAGT
* * * *
423605 TATCCTATTCTGCGGTTATCCCGGTTTGGATT
1 TATCCCATTCTGCGGATATCCCGGTTTAGAGT
*
423637 TATCCCATTCTTCGGATATCC
1 TATCCCATTCTGCGGATATCC
423658 TAACTTGGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.38
Consensus pattern (32 bp):
TATCCCATTCTGCGGATATCCCGGTTTAGAGT
Found at i:423714 original size:7 final size:7
Alignment explanation
Indices: 423690--423885 Score: 153
Period size: 7 Copynumber: 26.9 Consensus size: 7
423680 TGTTTATTCC
423690 TTAGGGT
1 TTAGGGT
*
423697 TTAAGGT
1 TTAGGGT
423704 TTAGGGT
1 TTAGGGT
*
423711 TTAGGAT
1 TTAGGGT
423718 TTAGGGGTT
1 TTA-GGG-T
**
423727 TTAAAGT
1 TTAGGGT
*
423734 TTAGGAT
1 TTAGGGT
*
423741 TTTGGGT
1 TTAGGGT
423748 TTAGGGTT
1 TTAGGG-T
423756 TTAGGGT
1 TTAGGGT
*
423763 TTTGGTGT
1 TTAGG-GT
*
423771 TTGGGGT
1 TTAGGGT
423778 TTAGGGT
1 TTAGGGT
*
423785 TTAAGGT
1 TTAGGGT
423792 TTAGGGT
1 TTAGGGT
423799 TTAGGGGT
1 TTA-GGGT
*
423807 TTGGGGT
1 TTAGGGT
423814 TTGAGGG-
1 TT-AGGGT
** *
423821 TGGGGGG
1 TTAGGGT
423828 TTA-GGT
1 TTAGGGT
*
423834 TTAAGGT
1 TTAGGGT
423841 TTAGGGT
1 TTAGGGT
423848 TTAGGGAGGT
1 TTA--G-GGT
423858 TTAGGGT
1 TTAGGGT
423865 TTAGGGT
1 TTAGGGT
*
423872 ATATGGGT
1 TTA-GGGT
423880 TTAGGG
1 TTAGGG
423886 GGGTTTGGGG
Statistics
Matches: 150, Mismatches: 27, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
6 8 0.05
7 99 0.66
8 32 0.21
9 5 0.03
10 6 0.04
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (7 bp):
TTAGGGT
Found at i:423730 original size:30 final size:29
Alignment explanation
Indices: 423690--423871 Score: 140
Period size: 29 Copynumber: 6.2 Consensus size: 29
423680 TGTTTATTCC
*
423690 TTAGGG-TTTAAGGTTTAGGGTTTAGGAT
1 TTAGGGTTTTAAGGTTTAGGGTTTAGGGT
* * *
423718 TTAGGGGTTTTAAAGTTTAGGATTTTGGGT
1 TTA-GGGTTTTAAGGTTTAGGGTTTAGGGT
* * *
423748 TTAGGGTTTTAGGGTTTTGGTGTTTGGGGT
1 TTAGGGTTTTAAGGTTTAGG-GTTTAGGGT
423778 TTAGGG-TTTAAGGTTTAGGGTTTAGGGGT
1 TTAGGGTTTTAAGGTTTAGGGTTTA-GGGT
* * * ** *
423807 TT-GGGGTTTGAGGGTGGGGGGTTA-GGT
1 TTAGGGTTTTAAGGTTTAGGGTTTAGGGT
* *
423834 TTAAGG-TTTAGGGTTTAGGGAGGTTTAGGGT
1 TTAGGGTTTTAAGGTTTA--G-GGTTTAGGGT
423865 TTAGGGT
1 TTAGGGT
423872 ATATGGGTTT
Statistics
Matches: 118, Mismatches: 25, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
27 11 0.09
28 12 0.10
29 48 0.41
30 39 0.33
31 8 0.07
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.42
Consensus pattern (29 bp):
TTAGGGTTTTAAGGTTTAGGGTTTAGGGT
Found at i:423785 original size:37 final size:35
Alignment explanation
Indices: 423701--423821 Score: 116
Period size: 37 Copynumber: 3.3 Consensus size: 35
423691 TAGGGTTTAA
** *
423701 GGTTTAGGGTTTAGGATTTAGGGGTTTTAAAGTTTAG
1 GGTTTAGGGTTTAGG-TTTA-GGGTTTTGGAGTTTGG
* * *
423738 GATTTTGGGTTTAGGGTTTTAGGGTTTTGGTGTTTGG
1 GGTTTAGGGTTTA-GG-TTTAGGGTTTTGGAGTTTGG
* *
423775 GGTTTAGGGTTTAAGGTTTAGGGTTTAGGGGTTTGG
1 GGTTTAGGGTTT-AGGTTTAGGGTTTTGGAGTTTGG
423811 GGTTTGAGGGT
1 GGTTT-AGGGT
423822 GGGGGGTTAG
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
36 23 0.33
37 40 0.57
38 7 0.10
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.45
Consensus pattern (35 bp):
GGTTTAGGGTTTAGGTTTAGGGTTTTGGAGTTTGG
Found at i:423844 original size:49 final size:51
Alignment explanation
Indices: 423755--423871 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
423745 GGTTTAGGGT
* * *
423755 TTTAGGGTTTTGGTGTTTGGGGTTTAGGGTTTAAGGTTTAGGGTTTA-GG-GG
1 TTTAGGGTTTAGG-G-TGGGGGGTTAGGGTTTAAGGTTTAGGGTTTAGGGAGG
*
423806 TTTGGGGTTTGAGGGTGGGGGGTTA-GGTTTAAGGTTTAGGGTTTAGGGAGG
1 TTTAGGGTTT-AGGGTGGGGGGTTAGGGTTTAAGGTTTAGGGTTTAGGGAGG
423857 TTTAGGGTTTAGGGT
1 TTTAGGGTTTAGGGT
423872 ATATGGGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
49 20 0.34
50 15 0.26
51 21 0.36
52 2 0.03
ACGTcount: A:0.13, C:0.00, G:0.46, T:0.41
Consensus pattern (51 bp):
TTTAGGGTTTAGGGTGGGGGGTTAGGGTTTAAGGTTTAGGGTTTAGGGAGG
Found at i:423859 original size:17 final size:17
Alignment explanation
Indices: 423837--423870 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
423827 GTTAGGTTTA
423837 AGGTTTAGGGTTTAGGG
1 AGGTTTAGGGTTTAGGG
423854 AGGTTTAGGGTTTAGGG
1 AGGTTTAGGGTTTAGGG
423871 TATATGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.35
Consensus pattern (17 bp):
AGGTTTAGGGTTTAGGG
Found at i:424976 original size:21 final size:19
Alignment explanation
Indices: 424924--424977 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
424914 CACATCGTTA
424924 TTTAAAATTATTATTAACATG
1 TTTAAAA-T-TTATTAACATG
* *
424945 TTTAGAGTTTATTAACATTG
1 TTTAAAATTTATTAACA-TG
424965 TTTTAAAATTTAT
1 -TTTAAAATTTAT
424978 CCTTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 9 0.33
20 3 0.11
21 15 0.56
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTAAAATTTATTAACATG
Found at i:426155 original size:16 final size:16
Alignment explanation
Indices: 426136--426181 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
426126 TCAAATTTTC
426136 TTTTCAAAGGATCGTA
1 TTTTCAAAGGATCGTA
426152 TTTT-AAA--ATC---
1 TTTTCAAAGGATCGTA
426162 TTTTCAAAGGATCGTA
1 TTTTCAAAGGATCGTA
426178 TTTT
1 TTTT
426182 AAAATCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 12
0.67 0.00 0.33
Matches are distributed among these distances:
10 4 0.17
11 3 0.12
13 6 0.25
15 3 0.12
16 8 0.33
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (16 bp):
TTTTCAAAGGATCGTA
Found at i:426167 original size:26 final size:26
Alignment explanation
Indices: 426134--426196 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
426124 ACTCAAATTT
426134 TCTTTTCAAAGGATCGTATTTTAAAA
1 TCTTTTCAAAGGATCGTATTTTAAAA
426160 TCTTTTCAAAGGATCGTATTTTAAAA
1 TCTTTTCAAAGGATCGTATTTTAAAA
426186 TCTTTTCAAAG
1 TCTTTTCAAAG
426197 TTTCGACACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (26 bp):
TCTTTTCAAAGGATCGTATTTTAAAA
Found at i:440584 original size:29 final size:29
Alignment explanation
Indices: 440551--440610 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
440541 TATATTGTCC
440551 TTTTCAATTTTTATAACTTCATATTTAAG
1 TTTTCAATTTTTATAACTTCATATTTAAG
440580 TTTTCAATTTTTATAACTTCATATTTAAG
1 TTTTCAATTTTTATAACTTCATATTTAAG
440609 TT
1 TT
440611 ATTTAAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (29 bp):
TTTTCAATTTTTATAACTTCATATTTAAG
Found at i:458731 original size:16 final size:16
Alignment explanation
Indices: 458712--458743 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
458702 AAATGATACA
458712 AACCCAAAATGACATG
1 AACCCAAAATGACATG
*
458728 AACCCGAAATGACATG
1 AACCCAAAATGACATG
458744 TGCAAGTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
AACCCAAAATGACATG
Found at i:460266 original size:27 final size:28
Alignment explanation
Indices: 460219--460274 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
460209 TATAATTTAC
* *
460219 TTAGAATTTTTTAAATGTTTTTTTATTT
1 TTAGAATTTTATAAATGTTTTTTAATTT
460247 TTAG-ATTTTATATAAT-TTTTTTAATTT
1 TTAGAATTTTATA-AATGTTTTTTAATTT
460274 T
1 T
460275 CATGTGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (28 bp):
TTAGAATTTTATAAATGTTTTTTAATTT
Found at i:464088 original size:14 final size:15
Alignment explanation
Indices: 464058--464091 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
464048 TCAACATGTT
464058 TTTTA-ATATTTACA
1 TTTTATATATTTACA
464072 TTTTATATATTTA-A
1 TTTTATATATTTACA
464086 TTTTAT
1 TTTTAT
464092 GTGATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTATATATTTACA
Found at i:467139 original size:149 final size:149
Alignment explanation
Indices: 466966--467263 Score: 580
Period size: 149 Copynumber: 2.0 Consensus size: 149
466956 CACAAGCAAG
466966 GTAAAAAAGTTAACAAGTGTCTTATAATGGTAAGTTTTTAAGCTTGCTTGTGGAATAAAAAAAAC
1 GTAAAAAAGTTAACAAGTGTCTTATAATGGTAAGTTTTTAAGCTTGCTTGTGGAATAAAAAAAAC
467031 ATACTGCCAATGTATCAAACATTTATTACTTAATA-TTATAAATTATAAATATATTTTTTAATTA
66 ATACTGCCAATGTATCAAACATTTATTACTTAATATTTATAAATTAT-AATATATTTTTTAATTA
467095 AAATAAAAATTATTAATAAT
130 AAATAAAAATTATTAATAAT
467115 GTAAAAAAGTTAACAAGTGTCTTATAATGGTAAGTTTTTAAGCTTGCTTGTGGAATAAAAAAAAC
1 GTAAAAAAGTTAACAAGTGTCTTATAATGGTAAGTTTTTAAGCTTGCTTGTGGAATAAAAAAAAC
467180 ATACTGCCAATGTATCAAACATTTATTACTTAATATTTATAAATTATAATATATTTTTTAATTAA
66 ATACTGCCAATGTATCAAACATTTATTACTTAATATTTATAAATTATAATATATTTTTTAATTAA
467245 AATAAAAATTATTAATAAT
131 AATAAAAATTATTAATAAT
467264 ATAATAAGTT
Statistics
Matches: 148, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
149 137 0.93
150 11 0.07
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (149 bp):
GTAAAAAAGTTAACAAGTGTCTTATAATGGTAAGTTTTTAAGCTTGCTTGTGGAATAAAAAAAAC
ATACTGCCAATGTATCAAACATTTATTACTTAATATTTATAAATTATAATATATTTTTTAATTAA
AATAAAAATTATTAATAAT
Found at i:467407 original size:24 final size:24
Alignment explanation
Indices: 467375--467422 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
467365 GGCAGTGAAC
467375 ATCCTTAACCATTAGACCATTACA
1 ATCCTTAACCATTAGACCATTACA
467399 ATCCTTAACCATTAGACCATTACA
1 ATCCTTAACCATTAGACCATTACA
467423 TAGAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (24 bp):
ATCCTTAACCATTAGACCATTACA
Found at i:468376 original size:15 final size:15
Alignment explanation
Indices: 468358--468391 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
468348 TAAAGTCCTC
*
468358 TCAATAATGTCGATT
1 TCAACAATGTCGATT
468373 TCAACAATGTCGATT
1 TCAACAATGTCGATT
468388 TCAA
1 TCAA
468392 GATTTGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (15 bp):
TCAACAATGTCGATT
Found at i:474397 original size:3 final size:3
Alignment explanation
Indices: 474389--474423 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
474379 TTCACTCTCC
474389 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
474424 TAAAAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:479719 original size:2 final size:2
Alignment explanation
Indices: 479714--479752 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
479704 CACGCAAAAA
479714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
479753 ATTTACTCAT
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:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:481515 original size:22 final size:22
Alignment explanation
Indices: 481487--481538 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
481477 ACGGTGGTTT
481487 CCTCCTCC-CTCTCTCACACGTG
1 CCTCCTCCTCTC-CTCACACGTG
*
481509 CCTCCTCCTCTCCTCGCACGTG
1 CCTCCTCCTCTCCTCACACGTG
*
481531 ACT-CTCCT
1 CCTCCTCCT
481539 ACCCCCCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 5 0.19
22 19 0.70
23 3 0.11
ACGTcount: A:0.08, C:0.54, G:0.10, T:0.29
Consensus pattern (22 bp):
CCTCCTCCTCTCCTCACACGTG
Found at i:484464 original size:29 final size:29
Alignment explanation
Indices: 484423--484481 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
484413 GTACAAAAAT
484423 TTTTATGATACTTTTATCGTTGAGTTTTA
1 TTTTATGATACTTTTATCGTTGAGTTTTA
484452 TTTTATGATACTTTTATCGTTGAGTTTTA
1 TTTTATGATACTTTTATCGTTGAGTTTTA
484481 T
1 T
484482 CTTGAGTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.07, G:0.14, T:0.59
Consensus pattern (29 bp):
TTTTATGATACTTTTATCGTTGAGTTTTA
Found at i:492175 original size:17 final size:17
Alignment explanation
Indices: 492153--492185 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
492143 TAATTAAATT
*
492153 ATTCGTTAGATATTTGA
1 ATTCGTTAAATATTTGA
492170 ATTCGTTAAATATTTG
1 ATTCGTTAAATATTTG
492186 GATTTAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (17 bp):
ATTCGTTAAATATTTGA
Found at i:493562 original size:2 final size:2
Alignment explanation
Indices: 493555--493594 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
493545 TATATCTACA
493555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
493595 CAGTTCTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:495559 original size:4 final size:4
Alignment explanation
Indices: 495550--495580 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
495540 AAATGAGAAA
495550 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
495581 TGGCTGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:497713 original size:16 final size:16
Alignment explanation
Indices: 497692--497722 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
497682 TTAGGGCATT
*
497692 GAATAGAGGTGTAATG
1 GAATAGAGCTGTAATG
497708 GAATAGAGCTGTAAT
1 GAATAGAGCTGTAAT
497723 AGTAATTCAA
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:0.03, G:0.32, T:0.26
Consensus pattern (16 bp):
GAATAGAGCTGTAATG
Found at i:497791 original size:44 final size:45
Alignment explanation
Indices: 497708--497795 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 45
497698 AGGTGTAATG
*
497708 GAATAGAGCTGTAATAGTAATTCAATTGTTTGGTTGAATGGAATA
1 GAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGGAATA
* *
497753 GAATAGAACTGTAATGGT-ATTC-TTGTGTTTGGTTGAATGGAAT
1 GAATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGGAAT
497796 GATGTTGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 1 0.03
44 22 0.56
45 16 0.41
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.38
Consensus pattern (45 bp):
GAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGGAATA
Found at i:520509 original size:21 final size:22
Alignment explanation
Indices: 520469--520513 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
520459 TGAGTTAGTT
*
520469 TTTGAATTTAGATCAATTTAAA
1 TTTGAATTTAGATAAATTTAAA
*
520491 TTTGAGTTTA-ATAAATTTAAA
1 TTTGAATTTAGATAAATTTAAA
520512 TT
1 TT
520514 ATTTACCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
TTTGAATTTAGATAAATTTAAA
Found at i:531001 original size:21 final size:21
Alignment explanation
Indices: 530977--531016 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
530967 TGTTCAATTT
530977 TTATTTTCCCATGACTTTTGA
1 TTATTTTCCCATGACTTTTGA
* *
530998 TTATTTTCTCATGTCTTTT
1 TTATTTTCCCATGACTTTT
531017 CTCCTATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.17, G:0.07, T:0.60
Consensus pattern (21 bp):
TTATTTTCCCATGACTTTTGA
Found at i:532623 original size:21 final size:21
Alignment explanation
Indices: 532599--532642 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
532589 TTAAATAGAT
532599 TAAATTAA-TGTTTGCTAATAA
1 TAAATTAAGT-TTTGCTAATAA
*
532620 TAAATTAAGTTTTGTTAATAA
1 TAAATTAAGTTTTGCTAATAA
532641 TA
1 TA
532643 TATATCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (21 bp):
TAAATTAAGTTTTGCTAATAA
Found at i:536907 original size:72 final size:73
Alignment explanation
Indices: 536827--536973 Score: 260
Period size: 72 Copynumber: 2.0 Consensus size: 73
536817 TAAATTTTTT
* **
536827 TTAGCAAAGATTAGAATTTAATTATATTTTTTTCATAGATCAAAATTTTGGTTTATTATGTA-TA
1 TTAGCAAAGATTAGAATTTAATTATATTTTTTTCATAGATCAAAATATAAGTTTATTATGTATTA
536891 ATTTATAA
66 ATTTATAA
536899 TTAGCAAAGATTAGAATTTAATTATATTTTTTTCATAGATCAAAATATAAGTTTATTATGTATTA
1 TTAGCAAAGATTAGAATTTAATTATATTTTTTTCATAGATCAAAATATAAGTTTATTATGTATTA
536964 ATTTATAA
66 ATTTATAA
536972 TT
1 TT
536974 TCATCAGTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 59 0.83
73 12 0.17
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (73 bp):
TTAGCAAAGATTAGAATTTAATTATATTTTTTTCATAGATCAAAATATAAGTTTATTATGTATTA
ATTTATAA
Found at i:537047 original size:84 final size:81
Alignment explanation
Indices: 536950--537164 Score: 208
Period size: 83 Copynumber: 2.6 Consensus size: 81
536940 AAAATATAAG
* *
536950 TTTATTATGTATTAATTTATAATTTCATCAGTTT-TGAAGA-GACTATAA-AAAATATTTT-ATT
1 TTTACTATATATTAATTTATAATTTC-TCAGTTTAT-AAGAGGACTA-AATAAAAT-TTTTCA-T
* *
537011 TTTACGGGG-GCTAAAGTGTAATT
61 TTTA-GGGGATC-AAAGAGT-ATT
**
537034 TTTACTATATATTAATTTATAATTTCTTTGTTTATAAGAGGACTAAATTGAAAATTTTTCATTTT
1 TTTACTATATATTAATTTATAATTTCTCAGTTTATAAGAGGACTAAA-T-AAAATTTTTCATTTT
537099 AGGGGATCAAAGAGTATT
64 AGGGGATCAAAGAGTATT
* * *
537117 TTTACTATATACTAATTTATAATTTATTTA-TTTATAAGAGGACTAAAT
1 TTTACTATATATTAATTTATAATTT-CTCAGTTTATAAGAGGACTAAAT
537165 TGAAAAAAAT
Statistics
Matches: 114, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
82 1 0.01
83 55 0.48
84 42 0.37
85 10 0.09
86 6 0.05
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (81 bp):
TTTACTATATATTAATTTATAATTTCTCAGTTTATAAGAGGACTAAATAAAATTTTTCATTTTAG
GGGATCAAAGAGTATT
Found at i:541659 original size:31 final size:31
Alignment explanation
Indices: 541624--541702 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
541614 AATTAAACTG
541624 TTAATATATT-ATTTAGTACTT-GAGTTTAGTT
1 TTAATAT-TTAATTTAGTA-TTCGAGTTTAGTT
* * *
541655 TTAATGTTTAATTTTGTATTCGAGTTTATTT
1 TTAATATTTAATTTAGTATTCGAGTTTAGTT
* *
541686 TTAATATTCATTTTAGT
1 TTAATATTTAATTTAGT
541703 GCCTAAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 4 0.10
31 35 0.90
ACGTcount: A:0.27, C:0.04, G:0.11, T:0.58
Consensus pattern (31 bp):
TTAATATTTAATTTAGTATTCGAGTTTAGTT
Found at i:554241 original size:141 final size:143
Alignment explanation
Indices: 553987--554270 Score: 554
Period size: 141 Copynumber: 2.0 Consensus size: 143
553977 AACAATACTC
553987 ATACCAATTGAATTAAGATAAAATTGTTTTAATTTCTTTTCTGATTGATATCTTCAATGCATTAG
1 ATACCAATTGAATTAAGATAAAATTGTTTTAATTTCTTTTCTGATTGATATCTTCAATGCATTAG
554052 CCATGTTGTAATAGTGGTTGATTTTTTTTTAAGTTGCATCTTTTATTGTATTTTATATACAA-TT
66 CCATGTTGTAATAGTGGTTGATTTTTTTTTAAGTTGCATCTTTTATTGTATTTTATATACAATTT
554116 -TAAAAATAAATA
131 ATAAAAATAAATA
554128 ATACCAATTGAATTAAGATAAAATTGTTTTAATTTCTTTTCTGATTGATATCTTCAATGCATTAG
1 ATACCAATTGAATTAAGATAAAATTGTTTTAATTTCTTTTCTGATTGATATCTTCAATGCATTAG
554193 CCATGTTGTAATAGTGGTTGATTTTTTTTTAAGTTGCATCTTTTATTGTATTTTATATACAATTT
66 CCATGTTGTAATAGTGGTTGATTTTTTTTTAAGTTGCATCTTTTATTGTATTTTATATACAATTT
554258 ATAAAAATAAATA
131 ATAAAAATAAATA
554271 TAATTTAGTA
Statistics
Matches: 141, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
141 127 0.90
142 2 0.01
143 12 0.09
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (143 bp):
ATACCAATTGAATTAAGATAAAATTGTTTTAATTTCTTTTCTGATTGATATCTTCAATGCATTAG
CCATGTTGTAATAGTGGTTGATTTTTTTTTAAGTTGCATCTTTTATTGTATTTTATATACAATTT
ATAAAAATAAATA
Found at i:554271 original size:21 final size:21
Alignment explanation
Indices: 554247--554289 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
554237 ATTGTATTTT
554247 ATATACAATT-TATAAAAATAA
1 ATATA-AATTATATAAAAATAA
*
554268 ATATAATTTAGTATAAAAATAA
1 ATATAAATTA-TATAAAAATAA
554290 TTTAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 5 0.26
22 11 0.58
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATATAAATTATATAAAAATAA
Found at i:554289 original size:16 final size:16
Alignment explanation
Indices: 554264--554298 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
554254 ATTTATAAAA
* *
554264 ATAAATATAATTTAGT
1 ATAAAAATAATTTAAT
554280 ATAAAAATAATTTAAT
1 ATAAAAATAATTTAAT
554296 ATA
1 ATA
554299 TTTTAATTAA
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:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
ATAAAAATAATTTAAT
Done.