Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 61 of 344
Found at i:19650919 original size:26 final size:25
Alignment explanation
Indices: 19650875--19650950 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
19650865 CTCTGAATGG
**
19650875 ATTGCCTTATGGCAAATTCTGTATA
1 ATTGCCTTATGGCGTATTCTGTATA
* *
19650900 ATTGCCCTTGTGGCGTATTCTATAATA
1 ATTG-CCTTATGGCGTATTCTGT-ATA
* *
19650927 A-GGCCTTATGGCGTATTTTGTATA
1 ATTGCCTTATGGCGTATTCTGTATA
19650951 TCGTTTGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
24 3 0.07
25 19 0.46
26 15 0.37
27 4 0.10
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.41
Consensus pattern (25 bp):
ATTGCCTTATGGCGTATTCTGTATA
Found at i:19657636 original size:20 final size:21
Alignment explanation
Indices: 19657596--19657636 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
19657586 AATATGTTAC
**
19657596 ATAATTTTTTTTAGATTTTAT
1 ATAATTTTTTTTAGAAATTAT
19657617 ATAA-TTTTTTTAGAAATTAT
1 ATAATTTTTTTTAGAAATTAT
19657637 GTATAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
ATAATTTTTTTTAGAAATTAT
Found at i:19658394 original size:15 final size:15
Alignment explanation
Indices: 19658376--19658405 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19658366 TTAATGATTA
*
19658376 TCCTTTAAATATTTT
1 TCCTTTAAAAATTTT
19658391 TCCTTTAAAAATTTT
1 TCCTTTAAAAATTTT
19658406 AAAATTATAT
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:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (15 bp):
TCCTTTAAAAATTTT
Found at i:19662402 original size:15 final size:15
Alignment explanation
Indices: 19662344--19662400 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 15
19662334 TGTTTATATA
*
19662344 TTTTATTAAATTATT
1 TTTTATTAAATTAGT
19662359 TTTTAGTTAAATTAGT
1 TTTTA-TTAAATTAGT
* *
19662375 TTTTATTTATTTA-T
1 TTTTATTAAATTAGT
*
19662389 TTTTGTTAAATT
1 TTTTATTAAATT
19662401 TAGCTATCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
14 10 0.29
15 11 0.31
16 14 0.40
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (15 bp):
TTTTATTAAATTAGT
Found at i:19662574 original size:20 final size:20
Alignment explanation
Indices: 19662538--19662589 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
19662528 TACATGTCAT
*
19662538 ATTAACAAATA-TT-AAAAA
1 ATTAAAAAATATTTAAAAAA
19662556 ATTATAAAAATATTTAAAAAA
1 ATTA-AAAAATATTTAAAAAA
19662577 ATTAAAAAATATT
1 ATTAAAAAATATT
19662590 CTATAACGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 4 0.13
19 6 0.20
20 11 0.37
21 9 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTAAAAAATATTTAAAAAA
Found at i:19673542 original size:36 final size:36
Alignment explanation
Indices: 19673499--19673570 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
19673489 CCAAATACGC
19673499 CACCTACCTCCACTACACCTATCCCATCACATTCAA
1 CACCTACCTCCACTACACCTATCCCATCACATTCAA
* * *
19673535 CACCTACCTCCACTACACCTTTTCCATCCCATTCAA
1 CACCTACCTCCACTACACCTATCCCATCACATTCAA
19673571 TGTCTCACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.25
Consensus pattern (36 bp):
CACCTACCTCCACTACACCTATCCCATCACATTCAA
Found at i:19676926 original size:61 final size:61
Alignment explanation
Indices: 19676778--19676949 Score: 186
Period size: 61 Copynumber: 2.8 Consensus size: 61
19676768 ACATACCATT
* * * *
19676778 CTTAACCTTAAAATCAAACTCTAAACCCCCAAATCATTAAACCTTAAACTTTATTATCATC
1 CTTATCCTTAAAATCAAACCCTAAACCCCCAAACCATTAAACCTTAAACCTTATTATCATC
* * * * *
19676839 TTTATCCTTAAAATCAATCCTTAAACCCCTAAACCATTAAA-CTATAAACCTTCTTATCATC
1 CTTATCCTTAAAATCAAACCCTAAACCCCCAAACCATTAAACCT-TAAACCTTATTATCATC
* * * **
19676900 CTTATCCTCAAAATCAAACCCCAAA-CCTCAAATTTATTAAACCTTAAACC
1 CTTATCCTTAAAATCAAACCCTAAACCCCCAAA-CCATTAAACCTTAAACC
19676950 CTCTTTATCA
Statistics
Matches: 90, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
60 7 0.08
61 81 0.90
62 2 0.02
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (61 bp):
CTTATCCTTAAAATCAAACCCTAAACCCCCAAACCATTAAACCTTAAACCTTATTATCATC
Found at i:19680055 original size:16 final size:17
Alignment explanation
Indices: 19680024--19680056 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19680014 TTAAGATTCA
*
19680024 ATGATTTTGGGATTTAG
1 ATGATTTTGAGATTTAG
19680041 ATGATTTTGAG-TTTAG
1 ATGATTTTGAGATTTAG
19680057 GGATGGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (17 bp):
ATGATTTTGAGATTTAG
Found at i:19681805 original size:22 final size:22
Alignment explanation
Indices: 19681771--19681819 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
19681761 TGGTGTAAAA
19681771 TTTTCATTTTAAATAATTACAT
1 TTTTCATTTTAAATAATTACAT
*
19681793 TTTTC-TTTATAAATAATTATAT
1 TTTTCATTT-TAAATAATTACAT
19681815 TTTTC
1 TTTTC
19681820 CGTCATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTCATTTTAAATAATTACAT
Found at i:19682590 original size:16 final size:15
Alignment explanation
Indices: 19682565--19682625 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
19682555 TAAAAATATA
19682565 TTTATAATTATTTTAT
1 TTTAT-ATTATTTTAT
*
19682581 TTTAATATTA-TTAAT
1 TTT-ATATTATTTTAT
19682596 TTTATA-TATTTTTAT
1 TTTATATTA-TTTTAT
* *
19682611 TTTTTATAATTTTAT
1 TTTATATTATTTTAT
19682626 ATATAGCGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
13 2 0.05
14 3 0.08
15 22 0.59
16 8 0.22
17 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATATTATTTTAT
Found at i:19682608 original size:25 final size:25
Alignment explanation
Indices: 19682561--19682629 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
19682551 ATTTTAAAAA
19682561 TATATT-TATAATTATT-T-TATTTT
1 TATATTATATAATT-TTATATATTTT
*
19682584 AATATTAT-TAATTTTATATATTTT
1 TATATTATATAATTTTATATATTTT
* *
19682608 TATTTTTTATAATTTTATATAT
1 TATATTATATAATTTTATATAT
19682630 AGCGATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 2 0.05
23 11 0.29
24 12 0.32
25 13 0.34
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TATATTATATAATTTTATATATTTT
Found at i:19682612 original size:15 final size:15
Alignment explanation
Indices: 19682575--19682625 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
19682565 TTTATAATTA
19682575 TTTTATTTTA-ATAT
1 TTTTATTTTATATAT
*
19682589 TATTAATTTTATATAT
1 T-TTTATTTTATATAT
* *
19682605 TTTTATTTTTTATAA
1 TTTTATTTTATATAT
19682620 TTTTAT
1 TTTTAT
19682626 ATATAGCGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 1 0.03
15 25 0.81
16 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATTTTATATAT
Found at i:19682623 original size:8 final size:9
Alignment explanation
Indices: 19682578--19682629 Score: 51
Period size: 8 Copynumber: 6.3 Consensus size: 9
19682568 ATAATTATTT
19682578 TATTTTA-A
1 TATTTTATA
*
19682586 TATTAT-TA
1 TATTTTATA
19682594 -ATTTTATA
1 TATTTTATA
19682602 TATTTT-TA
1 TATTTTATA
*
19682610 TTTTTTATA
1 TATTTTATA
19682619 -ATTTTATA
1 TATTTTATA
19682627 TAT
1 TAT
19682630 AGCGATATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
7 4 0.11
8 22 0.63
9 9 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTTATA
Found at i:19682696 original size:15 final size:16
Alignment explanation
Indices: 19682669--19682716 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
19682659 TCATAGTAGT
*
19682669 ATTATATATTTTATAA
1 ATTATAAATTTTATAA
**
19682685 ATT-TAAATTTTATGT
1 ATTATAAATTTTATAA
*
19682700 ATTATAAATTATATAA
1 ATTATAAATTTTATAA
19682716 A
1 A
19682717 ATAAAACATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATTATAAATTTTATAA
Found at i:19683146 original size:2 final size:2
Alignment explanation
Indices: 19683101--19683129 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19683091 TATATTTAGA
19683101 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 A
19683130 CGTGTGTTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19684343 original size:14 final size:14
Alignment explanation
Indices: 19684324--19684354 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
19684314 TACATAACCA
19684324 ATTGGCCCTTTTTT
1 ATTGGCCCTTTTTT
19684338 ATTGGCCCTTTTTT
1 ATTGGCCCTTTTTT
19684352 ATT
1 ATT
19684355 TTTTTACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.10, C:0.19, G:0.13, T:0.58
Consensus pattern (14 bp):
ATTGGCCCTTTTTT
Found at i:19684681 original size:27 final size:27
Alignment explanation
Indices: 19684644--19684696 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
19684634 AGTGTGAAGA
*
19684644 AAACTTGTACTATTGACTCTACTATGG
1 AAACTTATACTATTGACTCTACTATGG
*
19684671 AAACTTATACTGTTGACTCTACTATG
1 AAACTTATACTATTGACTCTACTATG
19684697 AAGGTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (27 bp):
AAACTTATACTATTGACTCTACTATGG
Found at i:19685314 original size:9 final size:9
Alignment explanation
Indices: 19685298--19685340 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
19685288 GGTATTTTTC
19685298 GGTAATTCG
1 GGTAATTCG
*
19685307 GTTAATTCG
1 GGTAATTCG
19685316 GGTAATTCG
1 GGTAATTCG
19685325 GGTAATTCG
1 GGTAATTCG
19685334 GGTAATT
1 GGTAATT
19685341 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.37
Consensus pattern (9 bp):
GGTAATTCG
Found at i:19685518 original size:12 final size:12
Alignment explanation
Indices: 19685501--19685525 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19685491 AGTAATTTCG
19685501 GGTCGGTTAACC
1 GGTCGGTTAACC
19685513 GGTCGGTTAACC
1 GGTCGGTTAACC
19685525 G
1 G
19685526 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:19691225 original size:22 final size:22
Alignment explanation
Indices: 19691198--19691249 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
19691188 GTCATAATAG
*
19691198 TTTTATATATTATAT--TATATA
1 TTTT-TATATTATATAATTTATA
19691219 TTTTTATATTATATAATTTATA
1 TTTTTATATTATATAATTTATA
*
19691241 TTATTATAT
1 TTTTTATAT
19691250 GTTTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 4 0.15
22 13 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTATATTATATAATTTATA
Found at i:19691227 original size:15 final size:15
Alignment explanation
Indices: 19691207--19691257 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
19691197 GTTTTATATA
19691207 TTATATTATATATTT
1 TTATATTATATATTT
19691222 TTATATTATATAATTT
1 TTATATTATAT-ATTT
* *
19691238 ATATTATTATATGTTT
1 TTA-TATTATATATTT
19691254 TTAT
1 TTAT
19691258 TTGTAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 12 0.39
16 11 0.35
17 8 0.26
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATATTATATATTT
Found at i:19691268 original size:29 final size:30
Alignment explanation
Indices: 19691201--19691273 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
19691191 ATAATAGTTT
*
19691201 TATATATTATATTA-TATATTTTTATATTA
1 TATAAATTATATTATTATATTTTTATATTA
*
19691230 TATAATTTATATTATTATATGTTTT-TATT-
1 TATAAATTATATTATTATAT-TTTTATATTA
* *
19691259 TGTAAATTATGTTAT
1 TATAAATTATATTAT
19691274 ACACTACATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 24 0.65
30 9 0.24
31 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (30 bp):
TATAAATTATATTATTATATTTTTATATTA
Found at i:19695621 original size:39 final size:39
Alignment explanation
Indices: 19695561--19695686 Score: 191
Period size: 39 Copynumber: 3.2 Consensus size: 39
19695551 TTCAGTGATG
19695561 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
19695600 TATATCCAGACTT-AGGATCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGG-TCCGCAGGCTATGTGCTGGAAT
* * *
19695639 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCCGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
*
19695678 TATGTCCGG
1 TATATCCGG
19695687 GCTAAAGTCC
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
38 3 0.04
39 73 0.92
40 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAAT
Found at i:19698683 original size:14 final size:16
Alignment explanation
Indices: 19698664--19698700 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
19698654 CGATGTCCTT
19698664 TTTGCAT-TCAT-GCA
1 TTTGCATCTCATAGCA
19698678 TTTGCATCTCATAGCA
1 TTTGCATCTCATAGCA
19698694 TTT-CATC
1 TTTGCATC
19698701 GCATTGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (16 bp):
TTTGCATCTCATAGCA
Found at i:19706129 original size:175 final size:175
Alignment explanation
Indices: 19705933--19706260 Score: 577
Period size: 175 Copynumber: 1.9 Consensus size: 175
19705923 ACTGAAACAG
19705933 ATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTT
1 ATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTT
* *
19705998 CAGATGATTTCACTGGAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGA-ACAAATC
66 CAGATGATTTCACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTCACAAGGAGA-AAATC
*
19706062 GAAGACATAGCAGATTTGACTTTCGGATGTTCCCACACCAACGCAC
130 GAAGACACAGCAGATTTGACTTTCGGATGTTCCCACACCAACGCAC
19706108 ATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTT
1 ATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTT
* * *
19706173 CAGATGATTTCATTGAAGTAGATCCAAGATGATTTGGCATCCTTGTGTTCACAAGGAGAAAATCT
66 CAGATGATTTCACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTCACAAGGAGAAAATCG
*
19706238 AAGACACAGCAGATTTGGCTTTC
131 AAGACACAGCAGATTTGACTTTC
19706261 ACGTGTTTAT
Statistics
Matches: 145, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
175 144 0.99
176 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (175 bp):
ATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTT
CAGATGATTTCACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTCACAAGGAGAAAATCG
AAGACACAGCAGATTTGACTTTCGGATGTTCCCACACCAACGCAC
Found at i:19708215 original size:22 final size:22
Alignment explanation
Indices: 19708188--19708239 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
19708178 GTCATAATAG
*
19708188 TTTTATATATTATAT--TATATA
1 TTTT-TATATTATATAATTTATA
19708209 TTTTTATATTATATAATTTATA
1 TTTTTATATTATATAATTTATA
*
19708231 TTATTATAT
1 TTTTTATAT
19708240 GTTTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 4 0.15
22 13 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTATATTATATAATTTATA
Found at i:19708217 original size:15 final size:15
Alignment explanation
Indices: 19708197--19708247 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
19708187 GTTTTATATA
19708197 TTATATTATATATTT
1 TTATATTATATATTT
19708212 TTATATTATATAATTT
1 TTATATTATAT-ATTT
* *
19708228 ATATTATTATATGTTT
1 TTA-TATTATATATTT
19708244 TTAT
1 TTAT
19708248 TTGTAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 12 0.39
16 11 0.35
17 8 0.26
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATATTATATATTT
Found at i:19708258 original size:29 final size:30
Alignment explanation
Indices: 19708191--19708263 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
19708181 ATAATAGTTT
*
19708191 TATATATTATATTA-TATATTTTTATATTA
1 TATAAATTATATTATTATATTTTTATATTA
*
19708220 TATAATTTATATTATTATATGTTTT-TATT-
1 TATAAATTATATTATTATAT-TTTTATATTA
* *
19708249 TGTAAATTATGTTAT
1 TATAAATTATATTAT
19708264 ACACTACATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 24 0.65
30 9 0.24
31 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (30 bp):
TATAAATTATATTATTATATTTTTATATTA
Found at i:19712930 original size:18 final size:19
Alignment explanation
Indices: 19712901--19712949 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
19712891 TAGTGTGTTA
19712901 ATAATA-TTTTATAATATT
1 ATAATATTTTTATAATATT
*
19712919 -TAATATTTTTAT-ATTTT
1 ATAATATTTTTATAATATT
*
19712936 ATAAAATTTTTATA
1 ATAATATTTTTATA
19712950 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATAATATTTTTATAATATT
Found at i:19713132 original size:20 final size:20
Alignment explanation
Indices: 19713084--19713132 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
19713074 TAAATTATTC
19713084 TATTTATATTTTATTATATA
1 TATTTATATTTTATTATATA
** *
19713104 TATAAATATTTGT-TTATTTA
1 TATTTATATTT-TATTATATA
19713124 TATTTATAT
1 TATTTATAT
19713133 ATTTTGTTCG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TATTTATATTTTATTATATA
Found at i:19713134 original size:22 final size:23
Alignment explanation
Indices: 19713093--19713136 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
19713083 CTATTTATAT
19713093 TTTATTATATATATAAATATTTG
1 TTTATTATATATATAAATATTTG
* *
19713116 TTTATT-TATATTTATATATTT
1 TTTATTATATATATAAATATTT
19713137 TGTTCGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTATTATATATATAAATATTTG
Found at i:19713942 original size:17 final size:18
Alignment explanation
Indices: 19713900--19713949 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
19713890 TTACGTGTTA
19713900 ATAATATTTTATAATATT
1 ATAATATTTTATAATATT
*
19713918 -TAATATTTTAT-ATTTT
1 ATAATATTTTATAATATT
*
19713934 ATAAAATTTTTATAAT
1 ATAATA-TTTTATAAT
19713950 TTGAAGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 15 0.56
18 6 0.22
19 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATAATATTTTATAATATT
Found at i:19714567 original size:12 final size:12
Alignment explanation
Indices: 19714536--19714572 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
19714526 TTTTGATATG
*
19714536 ATACAATTCTT-
1 ATACAATTATTA
19714547 ATA-AATTATTA
1 ATACAATTATTA
19714558 ATACAATTATTA
1 ATACAATTATTA
19714570 ATA
1 ATA
19714573 TAATATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
10 6 0.26
11 6 0.26
12 11 0.48
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (12 bp):
ATACAATTATTA
Found at i:19728725 original size:24 final size:24
Alignment explanation
Indices: 19728696--19728764 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
19728686 ACTTAAGATT
19728696 TTATGCTAATAAATGCTAAATATA
1 TTATGCTAATAAATGCTAAATATA
*
19728720 TTATGCTAATAAATGATAAATATA
1 TTATGCTAATAAATGCTAAATATA
* *
19728744 TTATACTAATAAATACTAAAT
1 TTATGCTAATAAATGCTAAAT
19728765 CTTCTAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.38
Consensus pattern (24 bp):
TTATGCTAATAAATGCTAAATATA
Found at i:19734091 original size:16 final size:16
Alignment explanation
Indices: 19734070--19734126 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
19734060 TTTGGTTCGC
*
19734070 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
19734086 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
19734102 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
19734118 TGTAATGGA
1 TGTAATGGA
19734127 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:19734393 original size:18 final size:17
Alignment explanation
Indices: 19734372--19734406 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19734362 TTATTATTAA
*
19734372 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
19734390 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
19734407 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19734543 original size:16 final size:16
Alignment explanation
Indices: 19734506--19734547 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
19734496 TTAATCATAT
*
19734506 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
19734522 TT-AAATATATTATAA
1 TTAAAATATATTATAA
19734537 TTAAAATATAT
1 TTAAAATATAT
19734548 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:19734544 original size:154 final size:156
Alignment explanation
Indices: 19734259--19734572 Score: 560
Period size: 154 Copynumber: 2.0 Consensus size: 156
19734249 TAGAATACCC
19734259 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTGAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTGAAATTTTAATAAGATTA-TA
*
19734324 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
*
19734389 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAAAAA
* * *
19734416 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTGAAATTTTAATAAGATTATAT
19734479 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
19734544 ATATAATTTAATAAAATTCTTAAAAA
131 ATATAATTTAATAAAATTCTTAAAAA
19734570 TTA
1 TTA
19734573 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
154 92 0.61
155 1 0.01
157 59 0.39
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTGAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAAAAA
Found at i:19734554 original size:14 final size:15
Alignment explanation
Indices: 19734515--19734556 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
19734505 TTTAAACATA
*
19734515 ATTATTATTAAATAT
1 ATTATAATTAAATAT
19734530 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
19734544 A-TATAATTTAATA
1 ATTATAATTAAATA
19734557 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:19734643 original size:120 final size:120
Alignment explanation
Indices: 19734509--19734731 Score: 412
Period size: 120 Copynumber: 1.9 Consensus size: 120
19734499 ATCATATTTA
19734509 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA-AAATTA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAA-TA
*
19734573 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
65 AAATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
19734629 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
*
19734694 AATTCTTCTATGAATTTACTCAAATCATAATATATGAT
66 AATTCTTATATGAATTTACTCAAATCATAATATATGAT
19734732 TATAACTAAT
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
120 97 0.97
121 3 0.03
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
AATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:19734674 original size:14 final size:15
Alignment explanation
Indices: 19734625--19734676 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
19734615 GTAAAATATA
19734625 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
19734640 TATTAAATATATTAT
1 AATTAAATATATTAT
19734655 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
19734668 AATTTAATA
1 AATTAAATA
19734677 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:19734691 original size:44 final size:43
Alignment explanation
Indices: 19734602--19734692 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
19734592 CTCAAATCAT
* * *
19734602 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
19734645 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
19734689 AATA
1 AATA
19734693 AAATTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:19734727 original size:59 final size:59
Alignment explanation
Indices: 19734544--19734727 Score: 148
Period size: 59 Copynumber: 3.1 Consensus size: 59
19734534 TAATTAAAAT
19734544 ATATAATTTAATAAAATTCTTAA-AAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAA-TAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * * *
19734603 ATAT-ATGATACTGTAAAA-TATAAATTAACATAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATAAT-TTA--ATAAAATTCTTAA-TAA-ATAA-TATTCTTATATGA-ATT-TACTCAAATCA
19734663 T-
58 TA
* *
19734664 ATATAATTTAATAAAATTCTTAATAAATAAAATTCTTCTATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
19734723 ATATA
1 ATATA
19734728 TGATTATAAC
Statistics
Matches: 92, Mismatches: 18, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
56 6 0.07
57 10 0.11
58 9 0.10
59 19 0.21
60 8 0.09
61 11 0.12
62 10 0.11
63 13 0.14
64 6 0.07
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
Found at i:19734743 original size:17 final size:16
Alignment explanation
Indices: 19734721--19734767 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
19734711 ACTCAAATCA
19734721 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
19734738 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
19734752 TAAATATATGATTTAA
1 T-AATATATGATTTAA
19734768 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:19734768 original size:17 final size:17
Alignment explanation
Indices: 19734740--19734773 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19734730 ATTATAACTA
*
19734740 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
19734757 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
19734774 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:19734916 original size:93 final size:92
Alignment explanation
Indices: 19734806--19735000 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
19734796 GATTATAGTT
* * *
19734806 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
19734869 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
19734899 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
19734964 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
19734991 TATGAATTTA
1 TATGAATTTA
19735001 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:19741113 original size:20 final size:20
Alignment explanation
Indices: 19741051--19741113 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
19741041 GAAAATTTTT
* * *
19741051 AATTTTTTAACTTTCTTATA
1 AATTTTTTAATTTTTTTAAA
* **
19741071 TA-TTTTTAATTTGTTTTTGA
1 AATTTTTTAATTT-TTTTAAA
19741091 AATTTTTTAATTTTTTTAAA
1 AATTTTTTAATTTTTTTAAA
19741111 AAT
1 AAT
19741114 ATAAATTTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 9 0.27
20 14 0.42
21 10 0.30
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
AATTTTTTAATTTTTTTAAA
Found at i:19741149 original size:19 final size:20
Alignment explanation
Indices: 19741118--19741189 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 20
19741108 AAAAATATAA
19741118 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAATTTTTATAAAT
*
19741138 ATTTTG-AA-TTTTAAAAATT
1 ATTTTGAAATTTTTATAAA-T
* *
19741157 ATTTTGAAATTTTGATAATT
1 ATTTTGAAATTTTTATAAAT
19741177 ATTTT-AAATTTTT
1 ATTTTGAAATTTTT
19741190 TTCTGTAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.18
19 16 0.36
20 14 0.32
21 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
ATTTTGAAATTTTTATAAAT
Found at i:19741166 original size:39 final size:41
Alignment explanation
Indices: 19741104--19741188 Score: 120
Period size: 39 Copynumber: 2.1 Consensus size: 41
19741094 TTTTTAATTT
* *
19741104 TTTTAAAAATATAAATTTTGAAATTTTTATAAATATTTTGAA
1 TTTTAAAAATAT-AATTTTGAAATTTTGATAAATATTTTAAA
*
19741146 TTTTAAAAAT-T-ATTTTGAAATTTTGATAATTATTTTAAA
1 TTTTAAAAATATAATTTTGAAATTTTGATAAATATTTTAAA
19741185 TTTT
1 TTTT
19741189 TTTCTGTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 29 0.73
41 1 0.03
42 10 0.25
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (41 bp):
TTTTAAAAATATAATTTTGAAATTTTGATAAATATTTTAAA
Found at i:19756286 original size:416 final size:420
Alignment explanation
Indices: 19755749--19756583 Score: 1243
Period size: 418 Copynumber: 2.0 Consensus size: 420
19755739 AAAATTATGA
*
19755749 ATTATGAATTTTTTTAAATATTTTTTATTTAAAAAAAATAATTAATTTTTAACATGACATACACA
1 ATTATGAATTTTTTTAAATACTTTTTATTTAAAAAAAATAATTAATTTTTAACATGACATACACA
* *
19755814 TGGACTTCCAAGCTGGTTGCCTTGTCAAAAAAGTTAATCAACTTTTAACTTTTTCATCTATTTTA
66 TGGACTTCCAAGCTGGTTGCCATGTCAAAAAAGTTAATCAACTTTTAACCTTTTCATCTATTTTA
* * *
19755879 GGCTGATTTCATAAACAATACAAGTTTAAAAACTACAGATGTAAAAAATTAAATGAAGGGATAAA
131 GGCTGATTTCATAAACAATACAAGTTTAAAAACTACAGATGCAAAAAATTAAATAAAAGGATAAA
* * *
19755944 ATAATTTTTTTATAATG-TTAGATAGCCAAATAAGTTATTATGACATTTATTTTCGATTTGTCTA
196 ATAATTTTTTTATAACGTTTAAAGAGCCAAATAAGTTATTATGACATTTATTTTCGATTTGTCTA
* * * * *
19756008 TAATACTT-ATGTGAAAATAAAAGAGAGACTAAAAAATCAGTTGCATCTAAATTTCTTA-GTTGT
261 TAATACTTGAGGCGAAAATAAAAGAGAGACTAAAAAATCAGTTACATCT-AAGTTCTTACATTGT
*
19756071 TACAGGGTTTTTGTTGTACTTAATTGAAGTTTGAAACATAATAAATACAACAAAAGTGATGGAGT
325 TACAGGGTTTTTGTTGTACTTAATTGAAGTTTGAAACATAATAAATACAACAAAACTGATGGAGT
*
19756136 TTAAATTCAAGTTTAATGTAATATATCTAAC
390 TTAAAATCAAGTTTAATGTAATATATCTAAC
* * *
19756167 ATTATGAA-TTTTTT-AATACTTTTTATTTTTAAAAAATTAATTAATTTTTAACATGATATACAC
1 ATTATGAATTTTTTTAAATACTTTTTA-TTTAAAAAAAATAATTAATTTTTAACATGACATACAC
* * * * *
19756230 GTGGACTTCTAAG-TCGGTTGTCATGT-AGAAAAGTTAATTAACTTTTAACCTTTTCATCTATTT
65 ATGGACTTCCAAGCT-GGTTGCCATGTCAAAAAAGTTAATCAACTTTTAACCTTTTCATCTATTT
* * * *
19756293 TAGGTTGATTTTATAAACAATACAAGTTTAAGAACTACATATGCAAAAAATTAAATAAAAGGATA
129 TAGGCTGATTTCATAAACAATACAAGTTTAAAAACTACAGATGCAAAAAATTAAATAAAAGGATA
* * * *
19756358 AAATGATTTTTTTATAACGTTTAAAGAGTCAAATAAGTTATTATGTCATTTCTTTTCGATTTGTC
194 AAATAATTTTTTTATAACGTTTAAAGAGCCAAATAAGTTATTATGACATTTATTTTCGATTTGTC
* *
19756423 TATAATACTTGAGGCGAAAATAAAAGAGAGACTAAAATATCAGTTACATCTAAGTTGTTACATTG
259 TATAATACTTGAGGCGAAAATAAAAGAGAGACTAAAAAATCAGTTACATCTAAGTTCTTACATTG
* * * * *
19756488 TTACAGGGTTTTTGTTGTACTTGATTGAAGTTTGAAACTTAATAACTATAACAAAACTGATGGGG
324 TTACAGGGTTTTTGTTGTACTTAATTGAAGTTTGAAACATAATAAATACAACAAAACTGATGGAG
19756553 TTTAAAATCAAGTTTAATGTAATATATCTAA
389 TTTAAAATCAAGTTTAATGTAATATATCTAA
19756584 TATGATACCA
Statistics
Matches: 373, Mismatches: 39, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
416 120 0.32
417 117 0.31
418 136 0.36
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (420 bp):
ATTATGAATTTTTTTAAATACTTTTTATTTAAAAAAAATAATTAATTTTTAACATGACATACACA
TGGACTTCCAAGCTGGTTGCCATGTCAAAAAAGTTAATCAACTTTTAACCTTTTCATCTATTTTA
GGCTGATTTCATAAACAATACAAGTTTAAAAACTACAGATGCAAAAAATTAAATAAAAGGATAAA
ATAATTTTTTTATAACGTTTAAAGAGCCAAATAAGTTATTATGACATTTATTTTCGATTTGTCTA
TAATACTTGAGGCGAAAATAAAAGAGAGACTAAAAAATCAGTTACATCTAAGTTCTTACATTGTT
ACAGGGTTTTTGTTGTACTTAATTGAAGTTTGAAACATAATAAATACAACAAAACTGATGGAGTT
TAAAATCAAGTTTAATGTAATATATCTAAC
Found at i:19764421 original size:46 final size:46
Alignment explanation
Indices: 19764368--19764630 Score: 323
Period size: 46 Copynumber: 5.7 Consensus size: 46
19764358 TGATGCCATA
* * * *
19764368 GTATCTTTCAACTATGATTTTACTCGTTTTC-TGTCATGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATGTCATGTTGTCATG
* ** *
19764414 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCATGTTGTCATG
* *
19764461 GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGTCATG
* * *
19764507 GTATCTTTCAACCATGGTTTTACACATTTCATATCATGTT-TCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGT-CATG
* * * *
19764553 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGTCATG
*
19764599 GTATCTTTCAACCATGGTCTTACACATTTCAT
1 GTATCTTTCAACCATGGTCTTACTCATTTCAT
19764631 TTCAAAGAGC
Statistics
Matches: 194, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
45 1 0.01
46 154 0.79
47 39 0.20
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGTCATG
Found at i:19765676 original size:17 final size:17
Alignment explanation
Indices: 19765654--19765690 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
19765644 TTTCTCTTGA
19765654 AAATAGACTCATTCAGG
1 AAATAGACTCATTCAGG
*
19765671 AAATAGACTGATTCAGG
1 AAATAGACTCATTCAGG
19765688 AAA
1 AAA
19765691 CTTTCTCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.22
Consensus pattern (17 bp):
AAATAGACTCATTCAGG
Found at i:19766998 original size:16 final size:17
Alignment explanation
Indices: 19766966--19766998 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19766956 TTTATAAGTA
*
19766966 TATATCAATCGTTTCAT
1 TATATCAATCATTTCAT
19766983 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
19766999 GTTTCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:19767441 original size:92 final size:92
Alignment explanation
Indices: 19767294--19767504 Score: 350
Period size: 92 Copynumber: 2.3 Consensus size: 92
19767284 TGCCATAGTG
* * *
19767294 TCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
* *
19767359 TTCTTTTCATGTCACGTTGCCACGGTA
66 TTCGTTTCATATCACGTTGCCACGGTA
*
19767386 TCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
*
19767451 TTCGTTTCATATCACGTTGCCATGGTA
66 TTCGTTTCATATCACGTTGCCACGGTA
*
19767478 TCTTTCAACCATGGTCTTACACATTTC
1 TCTTTCAACCATGGTCTTACTCATTTC
19767505 ATATCAGAGA
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 110 1.00
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.42
Consensus pattern (92 bp):
TCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
TTCGTTTCATATCACGTTGCCACGGTA
Found at i:19767510 original size:46 final size:46
Alignment explanation
Indices: 19767284--19767506 Score: 304
Period size: 46 Copynumber: 4.8 Consensus size: 46
19767274 TTTGACATGA
* * * * *
19767284 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGTCACGT
*
19767330 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
* ** *
19767376 TGCCACGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
* *
19767422 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
**
19767468 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCAT
19767507 ATCAGAGAGC
Statistics
Matches: 156, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 4 0.03
46 152 0.97
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
Found at i:19771712 original size:20 final size:20
Alignment explanation
Indices: 19771687--19771726 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19771677 GCTGGGATCA
19771687 CTAACTAATACTAATCTAAT
1 CTAACTAATACTAATCTAAT
*
19771707 CTAACTAGTACTAATCTAAT
1 CTAACTAATACTAATCTAAT
19771727 ACTATGTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (20 bp):
CTAACTAATACTAATCTAAT
Found at i:19771861 original size:15 final size:15
Alignment explanation
Indices: 19771841--19771871 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19771831 GACAGTTCCA
19771841 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
*
19771856 TGTGCTTTGATTCAT
1 TGTGCTCTGATTCAT
19771871 T
1 T
19771872 ACTGATACAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.19, T:0.52
Consensus pattern (15 bp):
TGTGCTCTGATTCAT
Found at i:19775256 original size:15 final size:15
Alignment explanation
Indices: 19775226--19775292 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
19775216 TCTATATTTC
*
19775226 TATATTATTTATTTAT
1 TATATTATCTA-TTAT
19775242 TAT-TCTATCTATTAT
1 TATAT-TATCTATTAT
19775257 TATATTATCTATT-T
1 TATATTATCTATTAT
*
19775271 ATATATTAT-TTTTA-
1 -TATATTATCTATTAT
19775285 TATATTAT
1 TATATTAT
19775293 TATATATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
13 8 0.18
14 4 0.09
15 24 0.53
16 9 0.20
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATTATCTATTAT
Found at i:19775264 original size:23 final size:22
Alignment explanation
Indices: 19775220--19775307 Score: 79
Period size: 23 Copynumber: 3.8 Consensus size: 22
19775210 TATAAATCTA
*
19775220 TATTTCTATATTATT-TATTTAT
1 TATTTATATATTATTATA-TTAT
*
19775242 TATTCTATCTATTATTATATTAT
1 TATT-TATATATTATTATATTAT
*
19775265 CTATTTATATATTATTTTTATATAT
1 -TATTTATATATTA-TTATAT-TAT
*
19775290 TATTATATATATTTTTAT
1 TATT-TATATATTATTAT
19775308 CCAATTTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
22 4 0.07
23 21 0.39
24 18 0.33
25 11 0.20
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTTATATATTATTATATTAT
Found at i:19776872 original size:21 final size:20
Alignment explanation
Indices: 19776848--19776903 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
19776838 AAAATCTTAT
19776848 AATATAATTATTTAATTAATA
1 AATAT-ATTATTTAATTAATA
*
19776869 AATATATT-TTATAAAATAATA
1 AATATATTATT-T-AATTAATA
19776890 AATAT-TTATTTAAT
1 AATATATTATTTAAT
19776904 ATCTAATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
19 4 0.13
20 7 0.23
21 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATATTATTTAATTAATA
Found at i:19778914 original size:49 final size:49
Alignment explanation
Indices: 19778841--19778966 Score: 162
Period size: 49 Copynumber: 2.6 Consensus size: 49
19778831 AGATGTTGAC
* * *
19778841 ACCATGTCCCAAACATGGTCTTACACTGGCTTTCATATAGCGAGGCCGAT
1 ACCATGTCCCAGACA-GGTCTTACACTGGCTCTAATATAGCGAGGCCGAT
* * * * *
19778891 ACCATGTCCTAGACAGGTCTTACACTGGCTCTAATCTATCGATGTCGAT
1 ACCATGTCCCAGACAGGTCTTACACTGGCTCTAATATAGCGAGGCCGAT
*
19778940 GCCATGTCCCAGACAGGTCTTACACTG
1 ACCATGTCCCAGACAGGTCTTACACTG
19778967 ACACACCACA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 53 0.80
50 13 0.20
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (49 bp):
ACCATGTCCCAGACAGGTCTTACACTGGCTCTAATATAGCGAGGCCGAT
Found at i:19779928 original size:13 final size:13
Alignment explanation
Indices: 19779910--19779934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19779900 CTAAAAGTGC
19779910 AAAAATCATCAAG
1 AAAAATCATCAAG
19779923 AAAAATCATCAA
1 AAAAATCATCAA
19779935 AATCACTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:19784345 original size:19 final size:17
Alignment explanation
Indices: 19784303--19784350 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
19784293 TATATTTGGT
*
19784303 AATAATA-ATATAAAAT
1 AATAATATATATAAAAA
*
19784319 AATAATATGTATAAAAA
1 AATAATATATATAAAAA
19784336 AACTACATATATATA
1 AA-TA-ATATATATA
19784351 TGCATATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.27
17 9 0.35
18 2 0.08
19 8 0.31
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (17 bp):
AATAATATATATAAAAA
Found at i:19784714 original size:13 final size:12
Alignment explanation
Indices: 19784696--19784740 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
19784686 GCATTAAAAA
19784696 AATATATATACAT
1 AATATATATA-AT
19784709 AATATATATAA-
1 AATATATATAAT
*
19784720 AATACATATAAT
1 AATATATATAAT
19784732 -ATATATATA
1 AATATATATA
19784741 CGTATTAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 18 0.62
12 1 0.03
13 10 0.34
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATATATAAT
Found at i:19784728 original size:24 final size:22
Alignment explanation
Indices: 19784694--19784740 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
19784684 TGGCATTAAA
*
19784694 AAAATATATATACATAATATATAT
1 AAAATACATATA-AT-ATATATAT
19784718 AAAATACATATAATATATATAT
1 AAAATACATATAATATATATAT
19784740 A
1 A
19784741 CGTATTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 2 0.09
24 11 0.50
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATACATATAATATATATAT
Found at i:19785393 original size:13 final size:13
Alignment explanation
Indices: 19785347--19785399 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
19785337 AAAAGGTAAA
*
19785347 ATTTTTTT-TAAT
1 ATTTTTTTATTAT
*
19785359 ATTTGTTTTGTATAT
1 ATTT-TTTTAT-TAT
*
19785374 ATATTTTTATTAT
1 ATTTTTTTATTAT
19785387 ATTTTTTTATTAT
1 ATTTTTTTATTAT
19785400 GATGTATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.12
13 19 0.56
14 6 0.18
15 5 0.15
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
ATTTTTTTATTAT
Found at i:19785471 original size:17 final size:17
Alignment explanation
Indices: 19785451--19785489 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
19785441 AAATAAAATA
*
19785451 AAAATAA-AAATAAGAGT
1 AAAATAATAAAGAAGA-T
19785468 AAAATAATAAAGAAGAT
1 AAAATAATAAAGAAGAT
19785485 AAAAT
1 AAAAT
19785490 CACCTTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAATAATAAAGAAGAT
Found at i:19785803 original size:17 final size:18
Alignment explanation
Indices: 19785778--19785823 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
19785768 AGGGTTTCTT
19785778 GGTTTTTTTTTTGGGTTA
1 GGTTTTTTTTTTGGGTTA
19785796 GGTTTTTTTTTTGGGTTA
1 GGTTTTTTTTTTGGGTTA
19785814 GGTTTTTTTT
1 GGTTTTTTTT
19785824 GGGGGGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.00, G:0.26, T:0.70
Consensus pattern (18 bp):
GGTTTTTTTTTTGGGTTA
Found at i:19787711 original size:7 final size:7
Alignment explanation
Indices: 19787699--19787740 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
19787689 AGATTTTGAT
19787699 ATATGAA
1 ATATGAA
19787706 ATATGAA
1 ATATGAA
19787713 ATATGAA
1 ATATGAA
19787720 ATATGAA
1 ATATGAA
19787727 ATATGAA
1 ATATGAA
19787734 ATATGAA
1 ATATGAA
19787741 TTTTAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (7 bp):
ATATGAA
Found at i:19792486 original size:40 final size:40
Alignment explanation
Indices: 19792430--19792588 Score: 210
Period size: 40 Copynumber: 4.0 Consensus size: 40
19792420 GAGGAAGTAC
* *
19792430 TGACAGTTTATTTGCAATACTAGTGGCTTGTCCACAATAT
1 TGACAGTTTATCTGCAATACTGGTGGCTTGTCCACAATAT
* *
19792470 TGACAGTTTATCTGCAATACGGGTGGCTTGTCCACAATAC
1 TGACAGTTTATCTGCAATACTGGTGGCTTGTCCACAATAT
* * * *
19792510 TGGCAATTTATCTGCAATACTGGTGGCTAGTCCATAATAT
1 TGACAGTTTATCTGCAATACTGGTGGCTTGTCCACAATAT
* * * *
19792550 TGGCAGTTTATATGCAATACTGGTGGTTTGACCACAATA
1 TGACAGTTTATCTGCAATACTGGTGGCTTGTCCACAATA
19792589 CTGGTAGATT
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 103 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (40 bp):
TGACAGTTTATCTGCAATACTGGTGGCTTGTCCACAATAT
Found at i:19792603 original size:80 final size:80
Alignment explanation
Indices: 19792427--19792592 Score: 233
Period size: 80 Copynumber: 2.1 Consensus size: 80
19792417 AAGGAGGAAG
* * * * *
19792427 TACTGACAGTTTATTTGCAATACTAGTGGCTTGTCCACAATATTGACAGTTTATCTGCAATACGG
1 TACTGGCAATTTATCTGCAATACTAGTGGCTAGTCCACAATATTGACAGTTTATATGCAATACGG
*
19792492 GTGGCTTGTCCACAA
66 GTGGCTTGACCACAA
* * * *
19792507 TACTGGCAATTTATCTGCAATACTGGTGGCTAGTCCATAATATTGGCAGTTTATATGCAATACTG
1 TACTGGCAATTTATCTGCAATACTAGTGGCTAGTCCACAATATTGACAGTTTATATGCAATACGG
*
19792572 GTGGTTTGACCACAA
66 GTGGCTTGACCACAA
19792587 TACTGG
1 TACTGG
19792593 TAGATTATCT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (80 bp):
TACTGGCAATTTATCTGCAATACTAGTGGCTAGTCCACAATATTGACAGTTTATATGCAATACGG
GTGGCTTGACCACAA
Found at i:19795387 original size:73 final size:73
Alignment explanation
Indices: 19795220--19795391 Score: 200
Period size: 73 Copynumber: 2.4 Consensus size: 73
19795210 AAGGCCAAGT
* * * * **
19795220 CACACGCCCGTGTGCTTAGGCCGTGTGGTGAGTTAAATTCCAAAAATCAGGTGCAAACTTCACAC
1 CACACGCCCATGTCCTGAGGCCGTGTGGTGAATTAAATTCCAAAAATCAACTGCAAACTTCACAC
* * *
19795285 GGCTGGGG
66 AGATAGGG
* * * * * *
19795293 TATACGCCCGTGTGCTTAGGCCGTGTGGTGAATTAAATTCCAAAAATCAACTGCAGACTTCACAC
1 CACACGCCCATGTCCTGAGGCCGTGTGGTGAATTAAATTCCAAAAATCAACTGCAAACTTCACAC
19795358 AGATAGGG
66 AGATAGGG
*
19795366 CACATGCCCATGTCCTGAGGCCGTGT
1 CACACGCCCATGTCCTGAGGCCGTGT
19795392 CCTTCACACG
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (73 bp):
CACACGCCCATGTCCTGAGGCCGTGTGGTGAATTAAATTCCAAAAATCAACTGCAAACTTCACAC
AGATAGGG
Found at i:19810202 original size:27 final size:27
Alignment explanation
Indices: 19810172--19810347 Score: 174
Period size: 27 Copynumber: 6.5 Consensus size: 27
19810162 AAATTGTACA
19810172 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTT
** * *
19810199 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGATTTGACTATGTT
* * **
19810226 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTT
* * *
19810253 GCACTAAGTGTGTGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTT
* *
19810281 GCACTAAGTGTGCGATTTGATTACG-T
1 GCACTAAGTGTGCGATTTGACTATGTT
* * * *
19810307 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTT
*
19810334 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
19810348 GCTCATATAC
Statistics
Matches: 122, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
26 22 0.18
27 79 0.65
28 21 0.17
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTT
Found at i:19810317 original size:81 final size:81
Alignment explanation
Indices: 19810172--19810326 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 81
19810162 AAATTGTACA
* * *
19810172 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
19810237 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
19810253 GCACTAAGTGTGTGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGCACTAAGTG
1 GCACTAAGTGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
*
19810317 TGCGAGTTGA
65 TGCGAATTGA
19810327 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
81 34 0.52
82 31 0.48
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:19810338 original size:81 final size:81
Alignment explanation
Indices: 19810168--19810347 Score: 218
Period size: 81 Copynumber: 2.2 Consensus size: 81
19810158 GATTAAATTG
* * *
19810168 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
19810233 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
19810249 TGCGGCACTAAGTGTGTGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGCACTA
1 TACAGCACTAAGTGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTA
* **
19810313 AGTGTGCGAGTTGATTA
65 AGTGTGCGAATTGACCA
* *
19810330 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
19810348 GCTCATATAC
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
81 50 0.62
82 31 0.38
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:19818256 original size:27 final size:27
Alignment explanation
Indices: 19818225--19818402 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
19818215 TAAATTGTAC
19818225 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
19818252 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
19818278 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
19818306 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
19818334 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
19818361 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
19818388 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
19818403 GGATCAATAT
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 103 0.82
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:19818340 original size:82 final size:81
Alignment explanation
Indices: 19818226--19818381 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
19818216 AAATTGTACA
* * *
19818226 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
19818290 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
19818307 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
19818372 TGCGAGTTGA
65 TGCGAATTGA
19818382 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:19818393 original size:82 final size:81
Alignment explanation
Indices: 19818222--19818402 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
19818212 GATTAAATTG
* * *
19818222 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
19818287 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
19818303 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
19818367 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
19818385 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
19818403 GGATCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:19819867 original size:21 final size:21
Alignment explanation
Indices: 19819842--19819884 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
19819832 GTTCTGCTCT
*
19819842 GCCTCCCTCGCTGTTGCCTCC
1 GCCTCCCTCGCTGCTGCCTCC
19819863 GCCTCCCTCGCTGCTGCCTCC
1 GCCTCCCTCGCTGCTGCCTCC
19819884 G
1 G
19819885 TTCTAAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.53, G:0.21, T:0.26
Consensus pattern (21 bp):
GCCTCCCTCGCTGCTGCCTCC
Found at i:19823495 original size:19 final size:20
Alignment explanation
Indices: 19823456--19823507 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
19823446 TTTTGATTTT
*
19823456 GATTTGGGGAAATATTTAGG
1 GATTTGGGGAAATAGTTAGG
*
19823476 GATTAGGGGAAA-AGTTAGG
1 GATTTGGGGAAATAGTTAGG
19823495 GATTTGGGGAAAT
1 GATTTGGGGAAAT
19823508 TTGGGTGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.29
Consensus pattern (20 bp):
GATTTGGGGAAATAGTTAGG
Found at i:19825457 original size:10 final size:10
Alignment explanation
Indices: 19825442--19825466 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19825432 TATCTCAGTT
19825442 TTTTGCGGCG
1 TTTTGCGGCG
19825452 TTTTGCGGCG
1 TTTTGCGGCG
19825462 TTTTG
1 TTTTG
19825467 AATAAAACGC
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:0.00, C:0.16, G:0.36, T:0.48
Consensus pattern (10 bp):
TTTTGCGGCG
Found at i:19825488 original size:50 final size:51
Alignment explanation
Indices: 19825401--19825506 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 51
19825391 TAGCTCAACC
* **
19825401 TTTTGTGGCGTTTGGAACTAAAGTGCCACTATATCTCAGTTTTTTGCGGCG
1 TTTTGCGGCGTTTGGAACTAAAACGCCACTATATCTCAGTTTTTTGCGGCG
* *
19825452 TTTTGCGGCGTTTTGAA-TAAAACGCCACTATTTCTCAGTTTTTTGCGGCG
1 TTTTGCGGCGTTTGGAACTAAAACGCCACTATATCTCAGTTTTTTGCGGCG
19825502 TTTTG
1 TTTTG
19825507 GATGAAAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 35 0.70
51 15 0.30
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.42
Consensus pattern (51 bp):
TTTTGCGGCGTTTGGAACTAAAACGCCACTATATCTCAGTTTTTTGCGGCG
Found at i:19825504 original size:40 final size:41
Alignment explanation
Indices: 19825459--19825588 Score: 190
Period size: 41 Copynumber: 3.2 Consensus size: 41
19825449 GCGTTTTGCG
* * * *
19825459 GCGTTTTGAAT-AAAACGCCACTATTTCTCAGTTTTTTGCG
1 GCGTTTTGGATAAAAACGCCACTATTACTCAGTTTTTAGCA
* *
19825499 GCGTTTTGGATGAAAATGCCACTATTACTCAGTTTTTAGCA
1 GCGTTTTGGATAAAAACGCCACTATTACTCAGTTTTTAGCA
*
19825540 GCGTTTTGGATAAAAACGCCACTATTGCTCAGTTTTTAGCA
1 GCGTTTTGGATAAAAACGCCACTATTACTCAGTTTTTAGCA
19825581 GCGTTTTG
1 GCGTTTTG
19825589 TTTCAAACGC
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 10 0.12
41 71 0.88
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (41 bp):
GCGTTTTGGATAAAAACGCCACTATTACTCAGTTTTTAGCA
Found at i:19836433 original size:367 final size:367
Alignment explanation
Indices: 19835760--19836496 Score: 1474
Period size: 367 Copynumber: 2.0 Consensus size: 367
19835750 CTCATGGACT
19835760 AATGATATTATTTTTGGACTATGATTGTGGATATTTTGATGCTTGACAATGAATTGATAATGGAT
1 AATGATATTATTTTTGGACTATGATTGTGGATATTTTGATGCTTGACAATGAATTGATAATGGAT
19835825 GCTATATTTTCTTTATGAATATGTAATAATATGGCATGTAAATTGGTTAAAAAGTGGTAATAGGA
66 GCTATATTTTCTTTATGAATATGTAATAATATGGCATGTAAATTGGTTAAAAAGTGGTAATAGGA
19835890 TTGAAACAATATTCTGATAATTTGAGCATGTTTAAAGTGACCAAATGATTCCAAATGGACATTTA
131 TTGAAACAATATTCTGATAATTTGAGCATGTTTAAAGTGACCAAATGATTCCAAATGGACATTTA
19835955 AAATCCTTAGAAAACCTTGAGATGATGATTTGTTATGTTCACTAATGATTTCTTGAAGTAAAAGT
196 AAATCCTTAGAAAACCTTGAGATGATGATTTGTTATGTTCACTAATGATTTCTTGAAGTAAAAGT
19836020 ATGGCTGCTAGCATGAAGGTTATTTAGTACGTCAAATTTTGCTATGATAGGTTATGGTGCATGTG
261 ATGGCTGCTAGCATGAAGGTTATTTAGTACGTCAAATTTTGCTATGATAGGTTATGGTGCATGTG
19836085 AACATTTCCTAATTGATGTATGAATGTATTCTGACTTGTTCA
326 AACATTTCCTAATTGATGTATGAATGTATTCTGACTTGTTCA
19836127 AATGATATTATTTTTGGACTATGATTGTGGATATTTTGATGCTTGACAATGAATTGATAATGGAT
1 AATGATATTATTTTTGGACTATGATTGTGGATATTTTGATGCTTGACAATGAATTGATAATGGAT
19836192 GCTATATTTTCTTTATGAATATGTAATAATATGGCATGTAAATTGGTTAAAAAGTGGTAATAGGA
66 GCTATATTTTCTTTATGAATATGTAATAATATGGCATGTAAATTGGTTAAAAAGTGGTAATAGGA
19836257 TTGAAACAATATTCTGATAATTTGAGCATGTTTAAAGTGACCAAATGATTCCAAATGGACATTTA
131 TTGAAACAATATTCTGATAATTTGAGCATGTTTAAAGTGACCAAATGATTCCAAATGGACATTTA
19836322 AAATCCTTAGAAAACCTTGAGATGATGATTTGTTATGTTCACTAATGATTTCTTGAAGTAAAAGT
196 AAATCCTTAGAAAACCTTGAGATGATGATTTGTTATGTTCACTAATGATTTCTTGAAGTAAAAGT
19836387 ATGGCTGCTAGCATGAAGGTTATTTAGTACGTCAAATTTTGCTATGATAGGTTATGGTGCATGTG
261 ATGGCTGCTAGCATGAAGGTTATTTAGTACGTCAAATTTTGCTATGATAGGTTATGGTGCATGTG
19836452 AACATTTCCTAATTGATGTATGAATGTATTCTGACTTGTTCA
326 AACATTTCCTAATTGATGTATGAATGTATTCTGACTTGTTCA
19836494 AAT
1 AAT
19836497 TCAGTTTAGA
Statistics
Matches: 370, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
367 370 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (367 bp):
AATGATATTATTTTTGGACTATGATTGTGGATATTTTGATGCTTGACAATGAATTGATAATGGAT
GCTATATTTTCTTTATGAATATGTAATAATATGGCATGTAAATTGGTTAAAAAGTGGTAATAGGA
TTGAAACAATATTCTGATAATTTGAGCATGTTTAAAGTGACCAAATGATTCCAAATGGACATTTA
AAATCCTTAGAAAACCTTGAGATGATGATTTGTTATGTTCACTAATGATTTCTTGAAGTAAAAGT
ATGGCTGCTAGCATGAAGGTTATTTAGTACGTCAAATTTTGCTATGATAGGTTATGGTGCATGTG
AACATTTCCTAATTGATGTATGAATGTATTCTGACTTGTTCA
Found at i:19838499 original size:12 final size:12
Alignment explanation
Indices: 19838482--19838511 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19838472 TAATATAAAA
19838482 ATATAACATAAT
1 ATATAACATAAT
*
19838494 ATATAATATAAT
1 ATATAACATAAT
19838506 ATATAA
1 ATATAA
19838512 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATAACATAAT
Found at i:19839866 original size:21 final size:22
Alignment explanation
Indices: 19839830--19839884 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
19839820 AGGGTCGTGG
* *
19839830 TGCATTGAAAGGCCTGTGACA-A
1 TGCATTG-ATGGCCTGAGACAGA
19839852 TGCATTGATGGCCTGAGACAGA
1 TGCATTGATGGCCTGAGACAGA
*
19839874 -ACATTGATGGC
1 TGCATTGATGGC
19839885 AGATGCTCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (22 bp):
TGCATTGATGGCCTGAGACAGA
Found at i:19849247 original size:19 final size:19
Alignment explanation
Indices: 19849223--19849260 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
19849213 TTGCAACTTA
19849223 AATTTTT-ATTTTATTTTCT
1 AATTTTTCA-TTTATTTTCT
19849242 AATTTTTCATTTATTTTCT
1 AATTTTTCATTTATTTTCT
19849261 TCTGATAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTCATTTATTTTCT
Found at i:19857314 original size:25 final size:27
Alignment explanation
Indices: 19857274--19857329 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
19857264 TCCTCTTTCA
19857274 AGCCATATAATAGG-AAGCTCACAAAG
1 AGCCATATAATAGGAAAGCTCACAAAG
* *
19857300 AGCCAT-TAATCGGAAAGCTCACAACG
1 AGCCATATAATAGGAAAGCTCACAAAG
19857326 AGCC
1 AGCC
19857330 TATCAAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (27 bp):
AGCCATATAATAGGAAAGCTCACAAAG
Found at i:19862697 original size:52 final size:52
Alignment explanation
Indices: 19862640--19862741 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 52
19862630 TCTAAGTTAG
* * *
19862640 CCAAGCCTAGTCGAGTATTTTTCTTGCTTATAGCAGTCCACATTTTCTTTAC
1 CCAAGCCTACTCAAATATTTTTCTTGCTTATAGCAGTCCACATTTTCTTTAC
*
19862692 CCAAGCCTACTCAAATATTTTTCTTGCTTATAGTAGTCCACATTTTCTTT
1 CCAAGCCTACTCAAATATTTTTCTTGCTTATAGCAGTCCACATTTTCTTT
19862742 CATTTCACAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.42
Consensus pattern (52 bp):
CCAAGCCTACTCAAATATTTTTCTTGCTTATAGCAGTCCACATTTTCTTTAC
Found at i:19863890 original size:25 final size:25
Alignment explanation
Indices: 19863862--19863911 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
19863852 CTCAGTTTGC
19863862 CCTTTCGACCAAATCTCAAGACCTT
1 CCTTTCGACCAAATCTCAAGACCTT
19863887 CCTTTCGACCAAATCTCAAGACCTT
1 CCTTTCGACCAAATCTCAAGACCTT
19863912 TCTCCATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.28
Consensus pattern (25 bp):
CCTTTCGACCAAATCTCAAGACCTT
Found at i:19886264 original size:10 final size:10
Alignment explanation
Indices: 19886249--19886276 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
19886239 GTAAAAGTGG
19886249 AATCCAAACT
1 AATCCAAACT
19886259 AATCCAAACT
1 AATCCAAACT
19886269 AATCCAAA
1 AATCCAAA
19886277 GCTTTAGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.18
Consensus pattern (10 bp):
AATCCAAACT
Found at i:19898619 original size:6 final size:6
Alignment explanation
Indices: 19898608--19898634 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19898598 CTATTAGCAT
19898608 GACTCG GACTCG GACTCG GACTCG GAC
1 GACTCG GACTCG GACTCG GACTCG GAC
19898635 AGATACACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.15
Consensus pattern (6 bp):
GACTCG
Found at i:19901505 original size:96 final size:96
Alignment explanation
Indices: 19901355--19901534 Score: 272
Period size: 96 Copynumber: 1.9 Consensus size: 96
19901345 AAGATCTCTA
* * *
19901355 ATTTACGATCATAACTTCAGTTTATTGTTTACGATCATGAGCAATTCATTAAGATTTCGTCAATT
1 ATTTACGATCACAACTTCAG-TTATTGTTTACGATCATGAACAATTCATTAAGATTTCGTCAATC
19901420 TACAATTGCGACTCCACTTTAACAGTTTGTTG
65 TACAATTGCGACTCCACTTTAACAGTTTGTTG
* * *
19901452 ATTTACGATCACAACTTCAG-TATTGATTTACGATTATGAACAATTCATTAAGATTTTGTCGATC
1 ATTTACGATCACAACTTCAGTTATTG-TTTACGATCATGAACAATTCATTAAGATTTCGTCAATC
*
19901516 TACGATTGCGACTCCACTT
65 TACAATTGCGACTCCACTT
19901535 AAATAGTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
95 5 0.07
96 51 0.68
97 19 0.25
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (96 bp):
ATTTACGATCACAACTTCAGTTATTGTTTACGATCATGAACAATTCATTAAGATTTCGTCAATCT
ACAATTGCGACTCCACTTTAACAGTTTGTTG
Found at i:19901550 original size:96 final size:96
Alignment explanation
Indices: 19901355--19901564 Score: 269
Period size: 96 Copynumber: 2.2 Consensus size: 96
19901345 AAGATCTCTA
* *
19901355 ATTTACGATCATAACTTCAGTTTATTGTTTACGATCATGAGCAATTCATTAAGATTTCGTCAATT
1 ATTTACGATCATAACTTCAG-TTATTGTTTACGATCATGAACAATTCATTAAGATTTCGTCAATC
* ***
19901420 TACAATTGCGACTCCACTTTAACAGTTTGTTG
65 TACAATTGCGACTCCACTTAAACAGTTCACTG
* * * *
19901452 ATTTACGATCACAACTTCAG-TATTGATTTACGATTATGAACAATTCATTAAGATTTTGTCGATC
1 ATTTACGATCATAACTTCAGTTATTG-TTTACGATCATGAACAATTCATTAAGATTTCGTCAATC
* *
19901516 TACGATTGCGACTCCACTTAAATAGTTCACTG
65 TACAATTGCGACTCCACTTAAACAGTTCACTG
* *
19901548 ATTCACTATCATAACTT
1 ATTTACGATCATAACTT
19901565 TCATTTTTAA
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
95 5 0.05
96 73 0.75
97 19 0.20
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (96 bp):
ATTTACGATCATAACTTCAGTTATTGTTTACGATCATGAACAATTCATTAAGATTTCGTCAATCT
ACAATTGCGACTCCACTTAAACAGTTCACTG
Found at i:19901818 original size:134 final size:135
Alignment explanation
Indices: 19901452--19901931 Score: 526
Period size: 135 Copynumber: 3.6 Consensus size: 135
19901442 CAGTTTGTTG
* *
19901452 ATTTACGATCACAACTTCAG-T-ATTGATTTACGATTATGAACAATTCATTAAGATTTTGTC-GA
1 ATTTACGATCACAACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTTGTCTGA
* ** * * * * * *
19901514 TCTACGATTGCGACTCCACTTAAATAGTTCACTGATTCACTATCATAACTTTCATTTTTAAAGCT
66 TTTACGATTGTAACTCCACTTAAACAGTTCATTGATTTACGATCACAACTGTCATTTTTAAAGCT
19901579 CGCTA
131 CGCTA
* * ** *
19901584 ATTTACGACCACAACTTCAGTTCATTGATTTACGAATGATGAACAATTCATTAAGAG-TTCACTA
1 ATTTACGATCACAACTTCAGTTCATTGATTTACG-ATCATGAACAATTCATTAAGAGTTTGTCTG
* * * * * * *
19901648 ATTTATGACTGCT-ACTCCACTTAAACAGTTCGTTGATTTACGATTACAAATGTCATTTTTTATG
65 ATTTACGATTG-TAACTCCACTTAAACAGTTCATTGATTTACGATCACAACTGTCATTTTTAAAG
* *
19901712 CTTGGTA
129 CTCGCTA
**
19901719 ATTTACGATCACAGTTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTTGTC-GA
1 ATTTACGATCACAACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTTGTCTGA
* * *
19901783 TTTACAATTGTAACTCCACCTAAACAGTCCATTGATTTACGATCACAACTGTCA-TTTTAAAGCT
66 TTTACGATTGTAACTCCACTTAAACAGTTCATTGATTTACGATCACAACTGTCATTTTTAAAGCT
** *
19901847 CATTG
131 CGCTA
* * *** * *
19901852 ATTTATGATCACAATTTCAGTTCATTGATTTGTTATCATGAACAGTTCATTAAGAGTTCG-CTGA
1 ATTTACGATCACAACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTTGTCTGA
19901916 TTTACGATTGTAACTC
66 TTTACGATTGTAACTC
19901932 TATTCTCACG
Statistics
Matches: 288, Mismatches: 52, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
132 20 0.07
133 81 0.28
134 80 0.28
135 107 0.37
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (135 bp):
ATTTACGATCACAACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTTGTCTGA
TTTACGATTGTAACTCCACTTAAACAGTTCATTGATTTACGATCACAACTGTCATTTTTAAAGCT
CGCTA
Found at i:19901951 original size:133 final size:133
Alignment explanation
Indices: 19901449--19901968 Score: 431
Period size: 133 Copynumber: 3.9 Consensus size: 133
19901439 TAACAGTTTG
* * * *
19901449 TTGATTTACGATCACAACTTCAG-T-ATTGATTTACGATTATGAACAATTCATTAAGATTTTGTC
1 TTGATTTACGATCACAATTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTCGTC
* * ** * * * * * * * * *
19901512 GATCTACGATTGCGACTCCACTTAAATAGTTCACTGATTCACTATCATAACTTTCATTTTTAAAG
66 GATTTACAATTGTAACTCCACCTAAACAGTCCATTGATTTACAACCACAACTGTCA-TTTTAAAG
*
19901577 CTCG
130 CTCA
* * * * * *
19901581 CTAATTTACGACCACAACTTCAGTTCATTGATTTACGAATGATGAACAATTCATTAAGAGTTC-A
1 TTGATTTACGATCACAATTTCAGTTCATTGATTTACG-ATCATGAACAATTCATTAAGAGTTCGT
* ** * * * * * ** * *
19901645 CTAATTTATGACTGCT-ACTCCACTTAAACAGTTCGTTGATTTACGATTACAAATGTCATTTTTT
65 C-GATTTACAATTG-TAACTCCACCTAAACAGTCCATTGATTTACAACCACAACTGTCA-TTTTA
* **
19901709 ATGCTTG
127 AAGCTCA
* * * *
19901716 GTAATTTACGATCACAGTTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTTGTC
1 TTGATTTACGATCACAATTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTCGTC
* *
19901781 GATTTACAATTGTAACTCCACCTAAACAGTCCATTGATTTACGATCACAACTGTCATTTTAAAGC
66 GATTTACAATTGTAACTCCACCTAAACAGTCCATTGATTTACAACCACAACTGTCATTTTAAAGC
19901846 TCA
131 TCA
* *** *
19901849 TTGATTTATGATCACAATTTCAGTTCATTGATTTGTTATCATGAACAGTTCATTAAGAGTTCG-C
1 TTGATTTACGATCACAATTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTCGTC
* * * * * *
19901913 TGATTTACGATTGTAACTCTATTCT-CACGGTCCCTTGATTTACAACCACAACTGTC
66 -GATTTACAATTGTAACTCCA-CCTAAACAGTCCATTGATTTACAACCACAACTGTC
19901969 TGCTTACGAA
Statistics
Matches: 318, Mismatches: 61, Indels: 17
0.80 0.15 0.04
Matches are distributed among these distances:
132 21 0.07
133 108 0.34
134 82 0.26
135 107 0.34
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (133 bp):
TTGATTTACGATCACAATTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTCGTC
GATTTACAATTGTAACTCCACCTAAACAGTCCATTGATTTACAACCACAACTGTCATTTTAAAGC
TCA
Found at i:19918549 original size:21 final size:21
Alignment explanation
Indices: 19918525--19918684 Score: 135
Period size: 21 Copynumber: 7.6 Consensus size: 21
19918515 GAAGCTCGAA
19918525 AGCTGAACAGAAACTCATAAG
1 AGCTGAACAGAAACTCATAAG
*
19918546 AGCTGAACAGAAACTTATAAG
1 AGCTGAACAGAAACTCATAAG
* * *
19918567 AGTTGAACAGAAGCTCGTAAG
1 AGCTGAACAGAAACTCATAAG
* *
19918588 AGCTTAACAGAATCTCATAAG
1 AGCTGAACAGAAACTCATAAG
* * ** **
19918609 AGTTGAATAGATGCTTGTAAG
1 AGCTGAACAGAAACTCATAAG
* * *
19918630 AGTTGAACAGAAGCTCGTAAG
1 AGCTGAACAGAAACTCATAAG
*
19918651 AGCTGAACA-AAAGCTCGA-AAA
1 AGCTGAACAGAAA-CTC-ATAAG
*
19918672 AGCTAAACAGAAA
1 AGCTGAACAGAAA
19918685 GTAAAACACT
Statistics
Matches: 112, Mismatches: 24, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
20 2 0.02
21 107 0.96
22 3 0.03
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (21 bp):
AGCTGAACAGAAACTCATAAG
Found at i:19918588 original size:42 final size:42
Alignment explanation
Indices: 19918528--19918684 Score: 170
Period size: 42 Copynumber: 3.7 Consensus size: 42
19918518 GCTCGAAAGC
* * *
19918528 TGAACAGAAACTCATAAGAGCTGAACAGAAACTTATAAGAGT
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGT
* *
19918570 TGAACAGAAGCTCGTAAGAGCTTAACAGAATCTCATAAGAGT
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGT
* * * * * * *
19918612 TGAATAGATGCTTGTAAGAGTTGAACAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGT
* * * *
19918654 TGAACAAAAGCTCGAAAAAGCTAAACAGAAA
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAA
19918685 GTAAAACACT
Statistics
Matches: 93, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.19
Consensus pattern (42 bp):
TGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGT
Found at i:19918630 original size:63 final size:63
Alignment explanation
Indices: 19918514--19918684 Score: 215
Period size: 63 Copynumber: 2.7 Consensus size: 63
19918504 ATATGCCAAA
19918514 AGAAGCTCG-AA-AGCTGAACAGAAACTCATAAGAGCTGAACAGAAACTTATAAGAGTTGAAC
1 AGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGCTGAACAGAAACTTATAAGAGTTGAAC
* * * * ** *
19918575 AGAAGCTCGTAAGAGCTTAACAGAATCTCATAAGAGTTGAATAGATGCTTGTAAGAGTTGAAC
1 AGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGCTGAACAGAAACTTATAAGAGTTGAAC
* *
19918638 AGAAGCTCGTAAGAGCTGAACA-AAAGCTCGA-AAAAGCTAAACAGAAA
1 AGAAGCTCGTAAGAGCTGAACAGAAA-CTC-ATAAGAGCTGAACAGAAA
19918685 GTAAAACACT
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
61 9 0.10
62 4 0.04
63 77 0.85
64 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.18
Consensus pattern (63 bp):
AGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGCTGAACAGAAACTTATAAGAGTTGAAC
Found at i:19922790 original size:26 final size:26
Alignment explanation
Indices: 19922761--19922811 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
19922751 ACCAGCACAC
* *
19922761 CAATATCGTAGCAAAGCTGCCAGTAA
1 CAATAACGCAGCAAAGCTGCCAGTAA
**
19922787 CAATAACGCAGCGTAGCTGCCAGTA
1 CAATAACGCAGCAAAGCTGCCAGTA
19922812 GCAGTAAGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (26 bp):
CAATAACGCAGCAAAGCTGCCAGTAA
Found at i:19930965 original size:4 final size:4
Alignment explanation
Indices: 19930956--19930990 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
19930946 CTTTTCCTAT
* *
19930956 ATAC ATAC ATAC ATAC ATAC ATAC GTAC GTAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
19930991 TATGTATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:19931019 original size:16 final size:16
Alignment explanation
Indices: 19930960--19931019 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
19930950 TCCTATATAC
* *
19930960 ATACATACATACATAC
1 ATACATACGTACATAT
*
19930976 ATACGTACGTACATAT
1 ATACATACGTACATAT
** *
19930992 ATGTATATGTACATAT
1 ATACATACGTACATAT
*
19931008 GTACATACGTAC
1 ATACATACGTAC
19931020 GTACATATAC
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (16 bp):
ATACATACGTACATAT
Found at i:19931027 original size:28 final size:29
Alignment explanation
Indices: 19930996--19931061 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
19930986 ACATATATGT
19930996 ATATGTACATATGTACATACGTACGTAC-
1 ATATGTACATATGTACATACGTACGTACG
** * *
19931024 ATATACATATATGTACATACGTATGTACG
1 ATATGTACATATGTACATACGTACGTACG
19931053 TATATGTAC
1 -ATATGTAC
19931062 GTACGTATGT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
28 24 0.83
30 5 0.17
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (29 bp):
ATATGTACATATGTACATACGTACGTACG
Found at i:19931041 original size:16 final size:16
Alignment explanation
Indices: 19930984--19931042 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
19930974 ACATACGTAC
**
19930984 GTACATATATGTATAT
1 GTACATATACATATAT
*
19931000 GTACATATGTACATACGTAC
1 GTACATA--TACATA--TAT
19931020 GTACATATACATATAT
1 GTACATATACATATAT
19931036 GTACATA
1 GTACATA
19931043 CGTATGTACG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 16 0.46
18 10 0.29
20 9 0.26
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.36
Consensus pattern (16 bp):
GTACATATACATATAT
Found at i:19931052 original size:8 final size:8
Alignment explanation
Indices: 19931044--19931097 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
19931034 ATGTACATAC
*
19931044 GTATGTAC
1 GTATGTAT
19931052 GTAT--AT
1 GTATGTAT
* *
19931058 GTACGTAC
1 GTATGTAT
19931066 GTATGTAT
1 GTATGTAT
19931074 GTATGTAT
1 GTATGTAT
19931082 GTATGTAT
1 GTATGTAT
19931090 GTATGTAT
1 GTATGTAT
19931098 ATGTAGATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 4 0.10
8 35 0.90
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (8 bp):
GTATGTAT
Found at i:19931054 original size:36 final size:36
Alignment explanation
Indices: 19930965--19931046 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
19930955 TATACATACA
* **
19930965 TACATACATACATACGTACGTACATATATGTATATG
1 TACATACGTACATACGTACGTACATATACATATATG
*
19931001 TACATATGTACATACGTACGTACATATACATATATG
1 TACATACGTACATACGTACGTACATATACATATATG
19931037 TACATACGTA
1 TACATACGTA
19931047 TGTACGTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (36 bp):
TACATACGTACATACGTACGTACATATACATATATG
Found at i:19931073 original size:4 final size:4
Alignment explanation
Indices: 19931055--19931097 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
19931045 TATGTACGTA
* *
19931055 TATG TACG TACG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
19931098 ATGTAGATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:19934930 original size:18 final size:18
Alignment explanation
Indices: 19934909--19934944 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
19934899 ATATAAAATT
19934909 TAAACTAAAT-AAAATAAA
1 TAAA-TAAATAAAAATAAA
19934927 TAAATAAATAAAAATAAA
1 TAAATAAATAAAAATAAA
19934945 ACTTTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAATAAATAAAAATAAA
Found at i:19935751 original size:17 final size:16
Alignment explanation
Indices: 19935730--19935813 Score: 69
Period size: 17 Copynumber: 4.9 Consensus size: 16
19935720 ACTACGCAGC
19935730 TTTGGTGAGCTCGCAT
1 TTTGGTGAGCTCGCAT
*
19935746 TATTGGAGAGCTCGCAGT
1 T-TTGGTGAGCTCGCA-T
* * *
19935764 CTTGATGAGCTCGTAGT
1 TTTGGTGAGCTCGCA-T
*
19935781 TTTGGGTGAGCTCGCACA
1 TTT-GGTGAGCTCGCA-T
*
19935799 TTTGGTGAGTTCGCA
1 TTTGGTGAGCTCGCA
19935814 ATCTTGCGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
16 1 0.02
17 39 0.72
18 14 0.26
ACGTcount: A:0.17, C:0.18, G:0.32, T:0.33
Consensus pattern (16 bp):
TTTGGTGAGCTCGCAT
Found at i:19938908 original size:45 final size:45
Alignment explanation
Indices: 19938859--19939027 Score: 212
Period size: 45 Copynumber: 3.8 Consensus size: 45
19938849 CATTGATTCG
* *
19938859 TGATGCCATAACATCTTTTAGCTATGGTCTTTCTTGATAGAATCA
1 TGATGCCATAACATCTTTCAGCTATGGTCTTACTTGATAGAATCA
* * * * * *
19938904 TGATGCCGTAACGTCTTTCAGCTATCGTCTTACTTAATAAAATCG
1 TGATGCCATAACATCTTTCAGCTATGGTCTTACTTGATAGAATCA
* * * **
19938949 TGATGTCATAACGTCTTTCAGCTATGGTCTTACTCGATAGAATTT
1 TGATGCCATAACATCTTTCAGCTATGGTCTTACTTGATAGAATCA
*
19938994 TGATGCCATAACATTTTTCAGCTATGGTCTTACT
1 TGATGCCATAACATCTTTCAGCTATGGTCTTACT
19939028 CATTTCTGGT
Statistics
Matches: 105, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 105 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGATGCCATAACATCTTTCAGCTATGGTCTTACTTGATAGAATCA
Found at i:19939048 original size:90 final size:90
Alignment explanation
Indices: 19938856--19939027 Score: 245
Period size: 90 Copynumber: 1.9 Consensus size: 90
19938846 TTTCATTGAT
* * * * * * *
19938856 TCGTGATGCCATAACATCTTTTAGCTATGGTCTTTCTTGATAGAATCATGATGCCGTAACGTCTT
1 TCGTGATGTCATAACGTCTTTCAGCTATGGTCTTACTCGATAGAATCATGATGCCATAACATCTT
19938921 TCAGCTATCGTCTTACTTAATAAAA
66 TCAGCTATCGTCTTACTTAATAAAA
** *
19938946 TCGTGATGTCATAACGTCTTTCAGCTATGGTCTTACTCGATAGAATTTTGATGCCATAACATTTT
1 TCGTGATGTCATAACGTCTTTCAGCTATGGTCTTACTCGATAGAATCATGATGCCATAACATCTT
*
19939011 TCAGCTATGGTCTTACT
66 TCAGCTATCGTCTTACT
19939028 CATTTCTGGT
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 71 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (90 bp):
TCGTGATGTCATAACGTCTTTCAGCTATGGTCTTACTCGATAGAATCATGATGCCATAACATCTT
TCAGCTATCGTCTTACTTAATAAAA
Found at i:19939058 original size:45 final size:46
Alignment explanation
Indices: 19939009--19939123 Score: 128
Period size: 45 Copynumber: 2.5 Consensus size: 46
19938999 CCATAACATT
* * *
19939009 TTTCAGCTATGGTCTTACTCATTTCT-GGTACGA-TGTCATAGTGTC
1 TTTCAACTATGGTCTTAATCATTTCTCGGTA-GAGTGCCATAGTGTC
* * * *
19939054 TTTCAACTATAGTCTTATTTATTT-TCGGTATAGTGCCATAGTGTC
1 TTTCAACTATGGTCTTAATCATTTCTCGGTAGAGTGCCATAGTGTC
*
19939099 TTTCAACTACGGTCTTAATCATTTC
1 TTTCAACTATGGTCTTAATCATTTC
19939124 CTTCAAGCCA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
44 2 0.04
45 55 0.96
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (46 bp):
TTTCAACTATGGTCTTAATCATTTCTCGGTAGAGTGCCATAGTGTC
Found at i:19941613 original size:18 final size:18
Alignment explanation
Indices: 19941576--19941615 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19941566 TCTATTCTCC
* *
19941576 CTTCTTTCTCGACTGCAT
1 CTTCTTTCTCAACTACAT
*
19941594 CTTCTTTCTCAACTATAT
1 CTTCTTTCTCAACTACAT
19941612 CTTC
1 CTTC
19941616 ATTGTCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.33, G:0.05, T:0.47
Consensus pattern (18 bp):
CTTCTTTCTCAACTACAT
Found at i:19946211 original size:16 final size:15
Alignment explanation
Indices: 19946190--19946223 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
19946180 AAGAGTTCAC
19946190 TTCTTTTTCTTTTCTT
1 TTCTTTTT-TTTTCTT
*
19946206 TTCTTTTTTTTTTTT
1 TTCTTTTTTTTTCTT
19946221 TTC
1 TTC
19946224 CATTTCAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTCTTTTTTTTTCTT
Found at i:19961438 original size:42 final size:43
Alignment explanation
Indices: 19961345--19961442 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 43
19961335 TTAACTACAG
* * *
19961345 GGGTCACACGGCCGTGTGGCTAGGCCGTGTAACCTTCGAACTG
1 GGGTCACACGGCCGTGTGCCTAGCCCGTGTAACCTTCGAACTA
* * * *
19961388 GGGACACACGGCCGTGT-CCTTGCCCGTGTGACCTTCTG-AGTA
1 GGGTCACACGGCCGTGTGCCTAGCCCGTGTAACCTTC-GAACTA
19961430 GGGTCACACGGCC
1 GGGTCACACGGCC
19961443 AAACCACACG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 29 0.63
43 17 0.37
ACGTcount: A:0.15, C:0.31, G:0.34, T:0.20
Consensus pattern (43 bp):
GGGTCACACGGCCGTGTGCCTAGCCCGTGTAACCTTCGAACTA
Found at i:19969483 original size:48 final size:48
Alignment explanation
Indices: 19969412--19969508 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
19969402 TTGTGTTAGG
19969412 ACATAAAATTTCTAGTAAAGGGATTAAGGTCGATAAATCTAAAATTGA
1 ACATAAAATTTCTAGTAAAGGGATTAAGGTCGATAAATCTAAAATTGA
19969460 ACATAAAATTTCTAGTAAAGGGATTAAGGTCGATAAATCTAAAATTGA
1 ACATAAAATTTCTAGTAAAGGGATTAAGGTCGATAAATCTAAAATTGA
19969508 A
1 A
19969509 GCCATTGAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.29
Consensus pattern (48 bp):
ACATAAAATTTCTAGTAAAGGGATTAAGGTCGATAAATCTAAAATTGA
Found at i:19976997 original size:12 final size:12
Alignment explanation
Indices: 19976980--19977004 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19976970 ATGTAAGTGA
19976980 TCTTGATGATTT
1 TCTTGATGATTT
19976992 TCTTGATGATTT
1 TCTTGATGATTT
19977004 T
1 T
19977005 TACATTTTCG
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:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:19977791 original size:46 final size:46
Alignment explanation
Indices: 19977690--19978112 Score: 293
Period size: 50 Copynumber: 8.8 Consensus size: 46
19977680 TAATTTGTGT
*
19977690 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGATGAGA
* * * *
19977738 GCCAGTGTAAGATATGTCCGGGACATGCATCGGCCTTTAGATGTA-A
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATG-AGA
* *
19977784 GCTAGTGTAAGACATGTCTGGGACATGCATCGGC--T-ACGA-GACA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGA-GATGAGA
* ** * *
19977827 TGTCAGTGTAAGATCATGTCTGGGACATGGCATAAGCATGGATATGCAAGA
1 -GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGATG--AGA
* * * * *
19977878 GCTAGTGTAAGACCATGTCTGGGACATGGAATCAGCACGTAAGTATGAGA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-TTGAG-ATGAGA
* * *
19977928 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTCGATGAGGATA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATT-GA-GATGAGA
* ** * *
19977977 GCCAGTGTAAGACCATGTCTGGGACATGGAATTAGCACGTAAGTATGAGA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-TTGAG-ATGAGA
* * * *
19978027 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTCGATAAGGATA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATT-GA-GATGAGA
19978076 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
19978113 ACTTAACCCA
Statistics
Matches: 305, Mismatches: 48, Indels: 42
0.77 0.12 0.11
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 13 0.04
45 14 0.05
46 52 0.17
47 13 0.04
48 15 0.05
49 80 0.26
50 107 0.35
51 4 0.01
52 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGAGA
Found at i:19977896 original size:50 final size:48
Alignment explanation
Indices: 19977831--19978108 Score: 295
Period size: 50 Copynumber: 5.6 Consensus size: 48
19977821 GAGACATGTC
* *
19977831 AGTGTAAGATCATGTCTGGGACATGGCATAAGCATGGATATGCAAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGATATG--AGAGCT
* * *
19977881 AGTGTAAGACCATGTCTGGGACATGGAATCAGCACGTAAGTATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATG-GA-TATGAGAGCT
* * * * * *
19977931 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGATGAGGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGAT-ATGAGAGCT
* * * *
19977980 AGTGTAAGACCATGTCTGGGACATGGAATTAGCACGTAAGTATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATG-GA-TATGAGAGCT
* * * * * *
19978030 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGATAAGGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGAT-ATGAGAGCT
19978079 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
19978109 GGCAACTTAA
Statistics
Matches: 188, Mismatches: 34, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
48 2 0.01
49 74 0.39
50 106 0.56
51 2 0.01
52 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCATGGATATGAGAGCT
Found at i:19977988 original size:149 final size:141
Alignment explanation
Indices: 19977689--19978111 Score: 480
Period size: 149 Copynumber: 2.9 Consensus size: 141
19977679 GTAATTTGTG
** * * * * *
19977689 TGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGTGCCAGTGTAAGA-TAT
1 TGCCAGTGTAAGACCATGTCTGGGACATGGCATAAGCATGGATATGAGAGCTAGTGTAAGACCAT
* * *
19977753 GTCCGGGACAT-GCATCGGCCTTTAGATGTAAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATC
66 GTCTGGGACATGGCATCGGCCGTAAGATG-AAGCTAGTGTAAGACCATGTCTGGGACATGGCATC
19977815 GGCTACGAGACA
130 GGCTACGAGACA
* *
19977827 TGTCAGTGTAAGATCATGTCTGGGACATGGCATAAGCATGGATATGCAAGAGCTAGTGTAAGACC
1 TGCCAGTGTAAGACCATGTCTGGGACATGGCATAAGCATGGATATG--AGAGCTAGTGTAAGACC
* *
19977892 ATGTCTGGGACATGGAATCAGCACGTAAGTATGAGAGCTAGTGTAAGACCATGTCTGGGACATGG
64 ATGTCTGGGACATGGCATCGGC-CGTAAG-ATGA-AGCTAGTGTAAGACCATGTCTGGGACATGG
* *
19977957 CATCGGCTTCGATGAGGA
126 CATCGGCTACGA-GA-CA
* * * *
19977975 TAGCCAGTGTAAGACCATGTCTGGGACATGGAATTAGCACGTAAGTATGAGAGCTAGTGTAAGAC
1 T-GCCAGTGTAAGACCATGTCTGGGACATGGCATAAGCATG-GA-TATGAGAGCTAGTGTAAGAC
*
19978040 CATGTCTGGGACATGGCATCGGCTTCGATAAG--GATAGCCAGTGTAAGACCATGTCTGGGACAT
63 CATGTCTGGGACATGGCATCGGC--CG-TAAGATGA-AGCTAGTGTAAGACCATGTCTGGGACAT
19978103 GGCATCGGC
124 GGCATCGGC
19978112 AACTTAACCC
Statistics
Matches: 242, Mismatches: 27, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
138 40 0.17
140 13 0.05
141 12 0.05
142 6 0.02
143 5 0.02
144 16 0.07
145 14 0.06
146 12 0.05
147 2 0.01
148 40 0.17
149 71 0.29
150 3 0.01
151 8 0.03
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (141 bp):
TGCCAGTGTAAGACCATGTCTGGGACATGGCATAAGCATGGATATGAGAGCTAGTGTAAGACCAT
GTCTGGGACATGGCATCGGCCGTAAGATGAAGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
GCTACGAGACA
Done.