Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 12 of 64
Found at i:1344963 original size:32 final size:32
Alignment explanation
Indices: 1344927--1344992 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
1344917 ATAAATAAAT
* *
1344927 AATCATACAAATAAATATATTAATAATCATGC
1 AATCATACAAAAAAATAAATTAATAATCATGC
*
1344959 AATCATGCAAAAAAATAAATTAATAATCATGC
1 AATCATACAAAAAAATAAATTAATAATCATGC
1344991 AA
1 AA
1344993 ATAGATATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (32 bp):
AATCATACAAAAAAATAAATTAATAATCATGC
Found at i:1345024 original size:20 final size:20
Alignment explanation
Indices: 1344999--1345275 Score: 92
Period size: 21 Copynumber: 13.3 Consensus size: 20
1344989 GCAAATAGAT
1344999 ATGCAATTAAATATATAATC
1 ATGCAATTAAATATATAATC
* *
1345019 ATGCAATTAACA-ATGTAAAAC
1 ATGCAATTAA-ATATAT-AATC
* *
1345040 ATGCAATCAAATATATGATC
1 ATGCAATTAAATATATAATC
*
1345060 ATGCAAAT-AATAATATAAATC
1 ATGCAATTAAAT-ATAT-AATC
*
1345081 ACGC----AAATA-A-AA--
1 ATGCAATTAAATATATAATC
*
1345093 ATACAATTAAATATATAATC
1 ATGCAATTAAATATATAATC
*
1345113 ATGCAAATAAATATATTAATAATC
1 ATGC-AATTAA-ATA-T-ATAATC
*
1345137 AAGCAATTAAATACATTATTAATC
1 ATGCAATTAAAT--A-TA-TAATC
*
1345161 ATGCAATTGAATTAAATATAATC
1 ATGCAATT-AA--ATATATAATC
* *
1345184 ATACAAATAAATATATTAATAATC
1 ATGC-AATTAA-ATA-T-ATAATC
* *
1345208 ATGCAAATATAT-TAATAAATC
1 ATGCAATTAAATAT-AT-AATC
** *
1345229 ACACAAATAAATATATTAATC
1 ATGCAATTAAATATA-TAATC
* *
1345250 ATGCAAATATAATAT-TAGTC
1 ATGCAATTA-AATATATAATC
1345270 ATGCAA
1 ATGCAA
1345276 AGTCATGCAA
Statistics
Matches: 195, Mismatches: 31, Indels: 62
0.68 0.11 0.22
Matches are distributed among these distances:
12 2 0.01
14 2 0.01
16 6 0.03
17 2 0.01
18 5 0.03
19 3 0.02
20 43 0.22
21 52 0.27
22 17 0.09
23 21 0.11
24 38 0.19
25 3 0.02
27 1 0.01
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (20 bp):
ATGCAATTAAATATATAATC
Found at i:1345135 original size:24 final size:24
Alignment explanation
Indices: 1345107--1345264 Score: 136
Period size: 24 Copynumber: 6.8 Consensus size: 24
1345097 AATTAAATAT
1345107 ATAATCATGCAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
* * *
1345131 ATAATCAAGCAATTAAATACATTA
1 ATAATCATGCAAATAAATATATTA
* * * *
1345155 TTAATCATGCAATTGAAT-TA-AA
1 ATAATCATGCAAATAAATATATTA
*
1345177 TATAATCATACAAATAAATATATTA
1 -ATAATCATGCAAATAAATATATTA
1345202 ATAATCATGC----AAATATATTA
1 ATAATCATGCAAATAAATATATTA
**
1345222 ATAAATCACACAAATAAATATA-T-
1 AT-AATCATGCAAATAAATATATTA
1345245 -TAATCATGCAAATATAATAT
1 ATAATCATGCAAATA-AATAT
1345265 TAGTCATGCA
Statistics
Matches: 107, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
20 12 0.11
21 17 0.16
22 7 0.07
23 15 0.14
24 48 0.45
25 8 0.07
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAATCATGCAAATAAATATATTA
Found at i:1345195 original size:47 final size:44
Alignment explanation
Indices: 1345108--1345260 Score: 152
Period size: 47 Copynumber: 3.4 Consensus size: 44
1345098 ATTAAATATA
* * *
1345108 TAATCATGCAAATAAATATATTAATAATCAAGCAATTAAATACATTAT
1 TAATCATGCAAATATAT-TAAT-ATAATCAA-CAAATAAATA-ATTAT
* *
1345156 TAATCATGCAATTGA-ATTAAATATAATCATACAAATAAATATATTAA
1 TAATCATGCAAAT-ATATT-AATATAATCA-ACAAATAAATA-ATTAT
1345203 TAATCATGCAAATATATTAATA-AATCACACAAATAAAT-A-TAT
1 TAATCATGCAAATATATTAATATAATCA-ACAAATAAATAATTAT
1345245 TAATCATGCAAATATA
1 TAATCATGCAAATATA
1345261 ATATTAGTCA
Statistics
Matches: 93, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
42 18 0.19
43 1 0.01
45 15 0.16
46 5 0.05
47 36 0.39
48 17 0.18
49 1 0.01
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (44 bp):
TAATCATGCAAATATATTAATATAATCAACAAATAAATAATTAT
Found at i:1352042 original size:25 final size:26
Alignment explanation
Indices: 1352014--1352065 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1352004 GAACATTATC
* *
1352014 ATTTGAGATTTTTA-ATTTCTTTTAA
1 ATTTGAGATTTTAAGATTTCTTCTAA
*
1352039 ATTTTAGATTTTAAGATTTCTTCTAA
1 ATTTGAGATTTTAAGATTTCTTCTAA
1352065 A
1 A
1352066 AGAAAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (26 bp):
ATTTGAGATTTTAAGATTTCTTCTAA
Found at i:1352884 original size:18 final size:17
Alignment explanation
Indices: 1352861--1352931 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 17
1352851 TGCAAAAAAA
1352861 AAAATGAAAAAGAGAAAG
1 AAAATGAAAAA-AGAAAG
*
1352879 AAAATGAAAAAAGAAAAAAT
1 AAAATGAAAAAAG---AAAG
1352899 AAAATGAAATGAAATGAAAG
1 AAAATGAAA--AAA-GAAAG
1352919 AAAA-GAAAAAAGA
1 AAAATGAAAAAAGA
1352932 GGAATATTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
16 2 0.04
17 5 0.11
18 11 0.24
19 4 0.09
20 19 0.42
22 3 0.07
23 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (17 bp):
AAAATGAAAAAAGAAAG
Found at i:1353407 original size:15 final size:16
Alignment explanation
Indices: 1353369--1353410 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1353359 CAAAGTAAGG
*
1353369 GAAAAGAAAAGTGAAA
1 GAAAAAAAAAGTGAAA
*
1353385 GAAAAAAAAATTGAAA
1 GAAAAAAAAAGTGAAA
1353401 -AACAAAAAAA
1 GAA-AAAAAAA
1353411 AAGGAAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.07
Consensus pattern (16 bp):
GAAAAAAAAAGTGAAA
Found at i:1353424 original size:23 final size:23
Alignment explanation
Indices: 1353398--1353455 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
1353388 AAAAAAATTG
1353398 AAAAACAAAAA-AAAAGGAAAAAC
1 AAAAA-AAAAAGAAAAGGAAAAAC
*
1353421 AAAAAAAAAAGAAAAGG-AAAAG
1 AAAAAAAAAAGAAAAGGAAAAAC
*
1353443 AAAAAGAAAAGAA
1 AAAAAAAAAAGAA
1353456 TGATTAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 21 0.66
23 11 0.34
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAGAAAAGGAAAAAC
Found at i:1353440 original size:6 final size:6
Alignment explanation
Indices: 1353382--1353452 Score: 60
Period size: 6 Copynumber: 12.3 Consensus size: 6
1353372 AAGAAAAGTG
* * * *
1353382 AAAGAA AAA-AA AATTGAA AAACAA AAA-AA AAGGAA AAACAA AAA-AA
1 AAAGAA AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
1353428 AAAG-A AAAGGA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA
1353453 GAATGATTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
5 18 0.34
6 31 0.58
7 4 0.08
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:1353441 original size:11 final size:11
Alignment explanation
Indices: 1353368--1353455 Score: 54
Period size: 11 Copynumber: 7.8 Consensus size: 11
1353358 TCAAAGTAAG
1353368 GGAAAAGAAAA
1 GGAAAAGAAAA
1353379 GTG-AAAGAAAA
1 G-GAAAAGAAAA
*
1353390 -AAAAATTGAAAA
1 GGAAAA--GAAAA
** *
1353402 ACAAAAAAAAA
1 GGAAAAGAAAA
*
1353413 GGAAAAACAAAA
1 GG-AAAAGAAAA
**
1353425 AAAAAAGAAAA
1 GGAAAAGAAAA
1353436 GGAAAAGAAAA
1 GGAAAAGAAAA
*
1353447 AGAAAAGAA
1 GGAAAAGAA
1353456 TGATTAAGTA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
10 3 0.05
11 38 0.64
12 14 0.24
13 4 0.07
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.03
Consensus pattern (11 bp):
GGAAAAGAAAA
Found at i:1353441 original size:17 final size:17
Alignment explanation
Indices: 1353386--1353452 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
1353376 AAAGTGAAAG
*
1353386 AAAAAAAAATTGAAAAAC
1 AAAAAAAAA-AGAAAAAC
*
1353404 AAAAAAAAAGGAAAAAC
1 AAAAAAAAAAGAAAAAC
**
1353421 AAAAAAAAAAGAAAAGG
1 AAAAAAAAAAGAAAAAC
*
1353438 AAAAGAAAAAGAAAA
1 AAAAAAAAAAGAAAA
1353453 GAATGATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 35 0.80
18 9 0.20
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAC
Found at i:1353850 original size:18 final size:17
Alignment explanation
Indices: 1353790--1353846 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 17
1353780 GTGTAATAAT
*
1353790 AAAAAAAAA-AGAAGAG
1 AAAAAAAAAGAGAAAAG
*
1353806 ACAAAAAAAGAGAATAAG
1 AAAAAAAAAGAGAA-AAG
* *
1353824 AGAAAGAAAGAGAAAAG
1 AAAAAAAAAGAGAAAAG
1353841 AAAAAA
1 AAAAAA
1353847 GAAAAAAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 8 0.24
17 11 0.33
18 14 0.42
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAGAGAAAAG
Found at i:1355197 original size:6 final size:6
Alignment explanation
Indices: 1355186--1355217 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1355176 ACAAAGATTC
*
1355186 TTGCAT TTGCAT TTGCAT TTGCAT TCGCAT TT
1 TTGCAT TTGCAT TTGCAT TTGCAT TTGCAT TT
1355218 TTTATTGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (6 bp):
TTGCAT
Found at i:1355446 original size:25 final size:24
Alignment explanation
Indices: 1355418--1355477 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
1355408 GAAAGAGTTT
* *
1355418 GAAAAAAGAGAGACAAGAAAATAAA
1 GAAAAAAGAAAGAAAAGAAAA-AAA
*
1355443 GAAAAAAAAAAGAAAAGAAAAAAA
1 GAAAAAAGAAAGAAAAGAAAAAAA
1355467 GCAAACAAAGA
1 G-AAA-AAAGA
1355478 TAAAGTATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.14
25 21 0.72
26 4 0.14
ACGTcount: A:0.77, C:0.05, G:0.17, T:0.02
Consensus pattern (24 bp):
GAAAAAAGAAAGAAAAGAAAAAAA
Found at i:1355853 original size:33 final size:32
Alignment explanation
Indices: 1355745--1355928 Score: 134
Period size: 33 Copynumber: 5.6 Consensus size: 32
1355735 AGTACTAAGA
* *
1355745 AGATTTAAGCCTAGTTTAATTAACACCCAGATG
1 AGATTTAAGCCTAGTTT-AGTAGCACCCAGATG
* * * * * *
1355778 AGGTTTAAGCCCAATTTAATTAGCACCCAAATA
1 AGATTTAAGCCTAGTTT-AGTAGCACCCAGATG
** * *
1355811 AGAACTAAGCCTAATTTAGTAGGCACCCAAATG
1 AGATTTAAGCCTAGTTTAGTA-GCACCCAGATG
** * *
1355844 AGATTTAAGCCTAGTTTAGCCGGCGCCTAGATG
1 AGATTTAAGCCTAGTTTAG-TAGCACCCAGATG
* * * *
1355877 AGAATTAAGCCCATTTTAGCTAGCACTCAGATG
1 AGATTTAAGCCTAGTTTAG-TAGCACCCAGATG
*
1355910 AGATTTAAGCATAGTTTAG
1 AGATTTAAGCCTAGTTTAG
1355929 CTGGTATTAA
Statistics
Matches: 117, Mismatches: 32, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
32 3 0.03
33 114 0.97
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (32 bp):
AGATTTAAGCCTAGTTTAGTAGCACCCAGATG
Found at i:1356166 original size:46 final size:46
Alignment explanation
Indices: 1356091--1356295 Score: 279
Period size: 46 Copynumber: 4.4 Consensus size: 46
1356081 TAGTCCAAGA
* *
1356091 TAAATTTTATTTTCAAAAGTTATTAAGCCTTTACCTAAATGAGCTTT
1 TAAA-TTTATCTTCAAAAGTTATTGAGCCTTTACCTAAATGAGCTTT
*
1356138 TAAATTTATCTTCAAAAGTTGTTGAGCCTTTACCTAAA-GAAGCTTT
1 TAAATTTATCTTCAAAAGTTATTGAGCCTTTACCTAAATG-AGCTTT
* * *
1356184 TAAATTTATCTTCAAAAATTATTGAGCATTTACCTAAAAT-AACTTT
1 TAAATTTATCTTCAAAAGTTATTGAGCCTTTACCT-AAATGAGCTTT
* * *
1356230 TATATTTATCTTCAAATGTTATTGAGTCTTTACCTAAATGAGCTTT
1 TAAATTTATCTTCAAAAGTTATTGAGCCTTTACCTAAATGAGCTTT
*
1356276 TAAATTTATTTTCAAAAGTT
1 TAAATTTATCTTCAAAAGTT
1356296 GTAAAGCCTT
Statistics
Matches: 138, Mismatches: 16, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
45 5 0.04
46 126 0.91
47 7 0.05
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.44
Consensus pattern (46 bp):
TAAATTTATCTTCAAAAGTTATTGAGCCTTTACCTAAATGAGCTTT
Found at i:1356372 original size:10 final size:9
Alignment explanation
Indices: 1356326--1356381 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
1356316 AATTTTTTTT
1356326 AATTCAAAAA
1 AATT-AAAAA
*
1356336 AATAAAAAA
1 AATTAAAAA
1356345 AATTAATTAAA
1 AATTAA--AAA
*
1356356 AA-CAAAAA
1 AATTAAAAA
*
1356364 ATTTAAAAA
1 AATTAAAAA
1356373 AATTAAAAA
1 AATTAAAAA
1356382 GAAAAAAACA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
8 4 0.11
9 23 0.62
10 5 0.14
11 5 0.14
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (9 bp):
AATTAAAAA
Found at i:1356395 original size:24 final size:26
Alignment explanation
Indices: 1356331--1356395 Score: 53
Period size: 27 Copynumber: 2.5 Consensus size: 26
1356321 TTTTTAATTC
*
1356331 AAAAAAATAAAAAAAATTAATTAAAAA
1 AAAAAAATAAAAAAAAATAA-TAAAAA
* **
1356358 CAAAAAATTTAAAAAAAT--TAAAAA
1 AAAAAAATAAAAAAAAATAATAAAAA
*
1356382 GAAAAAAACAAAAA
1 -AAAAAAATAAAAA
1356396 TTCAAAGAGT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
24 6 0.21
25 9 0.31
27 14 0.48
ACGTcount: A:0.80, C:0.03, G:0.02, T:0.15
Consensus pattern (26 bp):
AAAAAAATAAAAAAAAATAATAAAAA
Found at i:1362112 original size:16 final size:16
Alignment explanation
Indices: 1362093--1362127 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1362083 ATATAAGCTT
*
1362093 ATACCAATTGTTAAGG
1 ATACCAATTGTTAAAG
1362109 ATACCAATTGTTAAAG
1 ATACCAATTGTTAAAG
1362125 ATA
1 ATA
1362128 TGTTATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (16 bp):
ATACCAATTGTTAAAG
Found at i:1367424 original size:20 final size:21
Alignment explanation
Indices: 1367400--1367451 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1367390 TTTGGTACCA
* *
1367400 ATCGATCCCTT-TTTTAGGTG
1 ATCGATCCCTTAATCTAGGTG
*
1367420 GTCGATCCCTTAATCTAGGTG
1 ATCGATCCCTTAATCTAGGTG
1367441 ATCGATCCCTT
1 ATCGATCCCTT
1367452 CTCAAATCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (21 bp):
ATCGATCCCTTAATCTAGGTG
Found at i:1369535 original size:62 final size:62
Alignment explanation
Indices: 1369351--1369672 Score: 269
Period size: 62 Copynumber: 5.1 Consensus size: 62
1369341 GAAAAAGTAT
* * * * *
1369351 GATTATTGAAGGCATTTCATGCAAAAAACACCTTCAATAATCCCTTTCAAATTTTTACAAGG
1 GATTATTAAAGGTATTTCATGCAAAAAACACCTTCAATAATCCCCTTCAATTTTTTATAAGG
* * ***
1369413 GATTATTAAAAGCGT-TTTC-TACCAAAAATGCAAACACCTTCAATAGT-CCCGAAAACTTTTTT
1 GATTATT-AAAG-GTATTTCAT-GC--AAA---AAACACCTTCAATAATCCCCTTCAA-TTTTTT
1369475 ATAAGG
57 ATAAGG
* *
1369481 GATTATTAAAGGTATTTCAGGCAAAAAACACCTTCAATAATCCCCTTCAATTTTTTACATA-G
1 GATTATTAAAGGTATTTCATGCAAAAAACACCTTCAATAATCCCCTTCAATTTTTTATA-AGG
* * * * * *
1369543 GATTATTGAAGGTGTTTTC-TGCTAAAAACGCCTTCAATAAT-CCCTTCCATTTTTTATGAGG
1 GATTATTAAAGGT-ATTTCATGCAAAAAACACCTTCAATAATCCCCTTCAATTTTTTATAAGG
* * * ** * * *
1369604 GATTATCAAAGGTGTTTCAAGCAAAAAATGCCTTTAATAATCCCCTCCAATTTTTTATGAGG
1 GATTATTAAAGGTATTTCATGCAAAAAACACCTTCAATAATCCCCTTCAATTTTTTATAAGG
1369666 GATTATT
1 GATTATT
1369673 GAAGCGTTCC
Statistics
Matches: 208, Mismatches: 35, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
60 5 0.02
61 44 0.21
62 87 0.42
63 18 0.09
64 1 0.00
65 6 0.03
66 2 0.01
67 13 0.06
68 32 0.15
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (62 bp):
GATTATTAAAGGTATTTCATGCAAAAAACACCTTCAATAATCCCCTTCAATTTTTTATAAGG
Found at i:1369617 original size:61 final size:61
Alignment explanation
Indices: 1369469--1369706 Score: 250
Period size: 61 Copynumber: 3.9 Consensus size: 61
1369459 TCCCGAAAAC
* * * * *
1369469 TTTTTTATAAGGGATTATTAAAGGTATTTCAGGCAAAAAACACCTTCAATAATCCCCTTCAA
1 TTTTTTATGAGGGATTATTAAAGGTGTTTCAAGCAAAAAACGCCTTCAATAAT-CCCTTCCA
* * *
1369531 TTTTTTACAT-A-GGATTATTGAAGGTGTTTTC-TGCTAAAAACGCCTTCAATAATCCCTTCCA
1 TTTTTT--ATGAGGGATTATTAAAGGTG-TTTCAAGCAAAAAACGCCTTCAATAATCCCTTCCA
* * * *
1369592 TTTTTTATGAGGGATTATCAAAGGTGTTTCAAGCAAAAAATGCCTTTAATAATCCCCTCCAA
1 TTTTTTATGAGGGATTATTAAAGGTGTTTCAAGCAAAAAACGCCTTCAATAATCCCTTCC-A
* * * * *
1369654 TTTTTTATGAGGGATTATTGAA-GCGTTCCAAGCAAAAAATGCCTTAAATAATC
1 TTTTTTATGAGGGATTATTAAAGGTGTTTCAAGCAAAAAACGCCTTCAATAATC
1369707 TACTCATAAA
Statistics
Matches: 151, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
59 2 0.01
60 5 0.03
61 78 0.52
62 59 0.39
63 5 0.03
64 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (61 bp):
TTTTTTATGAGGGATTATTAAAGGTGTTTCAAGCAAAAAACGCCTTCAATAATCCCTTCCA
Found at i:1383442 original size:29 final size:29
Alignment explanation
Indices: 1383392--1383457 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
1383382 GAATTATATA
*
1383392 TTTATATAATTATGCATAAAAATATTATT
1 TTTATATAATTATACATAAAAATATTATT
*
1383421 TTTATATAATTATACATCAAAATATTATT
1 TTTATATAATTATACATAAAAATATTATT
1383450 TTTA-ATAA
1 TTTATATAA
1383458 AAATATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (29 bp):
TTTATATAATTATACATAAAAATATTATT
Found at i:1384003 original size:34 final size:36
Alignment explanation
Indices: 1383953--1384050 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 36
1383943 AGTATATGCT
* * * *
1383953 GAACCAAATATTTATTATATATGTTTGAGAAA-AAA
1 GAACCAAAGATTTATTATATATATATGAAAAAGAAA
*
1383988 -AATCAAAGATTTATTATACATATATATGAAAAAGAAA
1 GAACCAAAGATTTATTAT--ATATATATGAAAAAGAAA
*
1384025 GAACCAAAGATTTATTGTATATATAT
1 GAACCAAAGATTTATTATATATATAT
1384051 ATTGTCATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
34 15 0.29
36 19 0.37
37 3 0.06
38 15 0.29
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (36 bp):
GAACCAAAGATTTATTATATATATATGAAAAAGAAA
Found at i:1384033 original size:38 final size:36
Alignment explanation
Indices: 1383953--1384052 Score: 105
Period size: 38 Copynumber: 2.8 Consensus size: 36
1383943 AGTATATGCT
* * * *
1383953 GAACCAAATATTTATTAT-ATATGTTTGAGAAAAAA
1 GAACCAAAGATTTATTATAATATATATGAAAAAAAA
*
1383988 -AATCAAAGATTTATTATACATATATATGAAAAAGAAA
1 GAACCAAAGATTTATTATA-ATATATATGAAAAA-AAA
*
1384025 GAACCAAAGATTTATTGTATATATATAT
1 GAACCAAAGATTTATTATA-ATATATAT
1384053 TGTCATAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 15 0.28
36 11 0.21
37 3 0.06
38 24 0.45
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (36 bp):
GAACCAAAGATTTATTATAATATATATGAAAAAAAA
Found at i:1386091 original size:15 final size:15
Alignment explanation
Indices: 1386071--1386103 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1386061 CGGTCAAATG
1386071 TTTATTATTTTTA-TT
1 TTTATT-TTTTTACTT
1386086 TTTATTTTTTTACTT
1 TTTATTTTTTTACTT
1386101 TTT
1 TTT
1386104 TCATTATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTATTTTTTTACTT
Found at i:1386235 original size:4 final size:4
Alignment explanation
Indices: 1386226--1386273 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
1386216 ATAAAACCCA
* * * *
1386226 AAAT AAAT AAAT AAAC AAAC AAAC ATAT AAAT AAAT AAAT AACAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAA
1386274 ATAATGAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 35 0.90
5 4 0.10
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:1386464 original size:9 final size:9
Alignment explanation
Indices: 1386450--1386474 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1386440 CATGTTCATT
1386450 TTTTTTTTG
1 TTTTTTTTG
1386459 TTTTTTTTG
1 TTTTTTTTG
1386468 TTTTTTT
1 TTTTTTT
1386475 AATCAGACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1386582 original size:44 final size:44
Alignment explanation
Indices: 1386528--1386642 Score: 112
Period size: 41 Copynumber: 2.7 Consensus size: 44
1386518 GTAGAGGTTT
*
1386528 ACAACTTTTGGAAAAATAAAAATAACTCCTCTAAACAAAGGCTCA
1 ACAAC-TTTGGAAAAATAAAAATAACTCCTCTAAACAAAAGCTCA
** * * **
1386573 ATGACTTTGGAAAAGT--AAATAA-ACCTCTAATTAAAAGCTCA
1 ACAACTTTGGAAAAATAAAAATAACTCCTCTAAACAAAAGCTCA
*
1386614 ACAACTTTGGAAACATAAATAA-AACTCCT
1 ACAACTTTGGAAAAATAAA-AATAACTCCT
1386643 ATAATTAGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
41 27 0.50
42 6 0.11
43 3 0.06
44 15 0.28
45 3 0.06
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.24
Consensus pattern (44 bp):
ACAACTTTGGAAAAATAAAAATAACTCCTCTAAACAAAAGCTCA
Found at i:1387216 original size:44 final size:44
Alignment explanation
Indices: 1387166--1387312 Score: 149
Period size: 44 Copynumber: 3.2 Consensus size: 44
1387156 TCTTTATTTT
1387166 AGTTCAAAGATTCACATTCAATAAATCTTAGAGTTTCACGTCTA
1 AGTTCAAAGATTCACATTCAATAAATCTTAGAGTTTCACGTCTA
*
1387210 AGTTCAAAGATTCTA-ATTCAA-AAAT-TTAGAGATTCACATCCAAAAGTTCT-
1 AGTTCAAAGATTC-ACATTCAATAAATCTTAGAG-TT----T-C--ACG-TCTA
* *
1387260 AGTTCAAAGATTCACATTCGATAAATCTTAGAGTTTCACATCTA
1 AGTTCAAAGATTCACATTCAATAAATCTTAGAGTTTCACGTCTA
1387304 AGTTCAAAG
1 AGTTCAAAG
1387313 GTTTTCATTC
Statistics
Matches: 85, Mismatches: 4, Indels: 28
0.73 0.03 0.24
Matches are distributed among these distances:
42 6 0.07
43 9 0.11
44 29 0.34
45 1 0.01
46 1 0.01
47 2 0.02
48 1 0.01
49 1 0.01
50 20 0.24
51 9 0.11
52 6 0.07
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.33
Consensus pattern (44 bp):
AGTTCAAAGATTCACATTCAATAAATCTTAGAGTTTCACGTCTA
Found at i:1387298 original size:94 final size:94
Alignment explanation
Indices: 1387165--1387348 Score: 305
Period size: 94 Copynumber: 2.0 Consensus size: 94
1387155 CTCTTTATTT
*
1387165 TAGTTCAAAGATTCACATTCAATAAATCTTAGAGTTTCACGTCTAAGTTCAAAGATTCTAATTCA
1 TAGTTCAAAGATTCACATTCAATAAATCTTAGAGTTTCACATCTAAGTTCAAAGATTCTAATTCA
1387230 AAAATTTAGAGATTCACATCCAAAAGTTC
66 AAAATTTAGAGATTCACATCCAAAAGTTC
* * * *
1387259 TAGTTCAAAGATTCACATTCGATAAATCTTAGAGTTTCACATCTAAGTTCAAAGGTTTTCATTCA
1 TAGTTCAAAGATTCACATTCAATAAATCTTAGAGTTTCACATCTAAGTTCAAAGATTCTAATTCA
* *
1387324 AATATTTAGAGATTCGCATCCAAAA
66 AAAATTTAGAGATTCACATCCAAAA
1387349 TTTTGAAGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 83 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (94 bp):
TAGTTCAAAGATTCACATTCAATAAATCTTAGAGTTTCACATCTAAGTTCAAAGATTCTAATTCA
AAAATTTAGAGATTCACATCCAAAAGTTC
Found at i:1388566 original size:10 final size:10
Alignment explanation
Indices: 1388553--1388586 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1388543 TTTTCATTCA
1388553 TTTTTCTCTT
1 TTTTTCTCTT
1388563 TTTTTCTC--
1 TTTTTCTCTT
1388571 TTTTTCTCTT
1 TTTTTCTCTT
1388581 TTTTTC
1 TTTTTC
1388587 ATTTCTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:1388591 original size:15 final size:16
Alignment explanation
Indices: 1388529--1388606 Score: 68
Period size: 16 Copynumber: 4.6 Consensus size: 16
1388519 TTCTTTTACA
*
1388529 TTTTCATTTTTCATTT
1 TTTTCATTTCTCATTT
*
1388545 TTCATTCATTTTTCTCTTTT
1 TT--TTCA--TTTCTCATTT
*
1388565 TTTCTCTTTTTCTC-TTT
1 TTT-TC-ATTTCTCATTT
1388582 TTTTCATTTCTCATTT
1 TTTTCATTTCTCATTT
1388598 TTTTCATTT
1 TTTTCATTT
1388607 TTTTCATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
15 6 0.12
16 16 0.31
17 6 0.12
18 11 0.22
19 2 0.04
20 10 0.20
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTCATTTCTCATTT
Found at i:1388617 original size:11 final size:9
Alignment explanation
Indices: 1388535--1388618 Score: 70
Period size: 9 Copynumber: 9.3 Consensus size: 9
1388525 TACATTTTCA
1388535 TTTTTCATT
1 TTTTTCATT
1388544 TTTCATTCATT
1 TTT--TTCATT
*
1388555 TTTCTC-TT
1 TTTTTCATT
1388563 TTTTTC-TCT
1 TTTTTCAT-T
1388572 TTTTCTC-TT
1 TTTT-TCATT
1388581 TTTTTCA--
1 TTTTTCATT
*
1388588 TTTCTCATT
1 TTTTTCATT
1388597 TTTTTCATT
1 TTTTTCATT
1388606 TTTTTCATAT
1 TTTTTCAT-T
1388616 TTT
1 TTT
1388619 CACCCATTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
7 6 0.10
8 10 0.16
9 31 0.49
10 7 0.11
11 9 0.14
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTCATT
Found at i:1393573 original size:11 final size:11
Alignment explanation
Indices: 1393557--1393586 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1393547 TTTCTCCCTC
1393557 TTTTTCCTTTT
1 TTTTTCCTTTT
1393568 TTTTTCCTTTT
1 TTTTTCCTTTT
1393579 TTTTTCCT
1 TTTTTCCT
1393587 CTTCTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTCCTTTT
Found at i:1393594 original size:11 final size:11
Alignment explanation
Indices: 1393557--1393600 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1393547 TTTCTCCCTC
*
1393557 TTTTTCCTTTT
1 TTTTTCCTCTT
*
1393568 TTTTTCCTTTT
1 TTTTTCCTCTT
1393579 TTTTTCCTCTT
1 TTTTTCCTCTT
*
1393590 CTTTTCTCTCT
1 TTTTTC-CTCT
1393601 AAACCCTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 26 0.87
12 4 0.13
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTCCTCTT
Found at i:1393770 original size:30 final size:30
Alignment explanation
Indices: 1393734--1393800 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
1393724 AAACCTGTCG
* *
1393734 AAAAATTTAACCGATGCTGGAAA-ATTCACC
1 AAAAATTCAACCGATGC-CGAAACATTCACC
*
1393764 AAAAATTCAACCGATGCCGAAACATTCATC
1 AAAAATTCAACCGATGCCGAAACATTCACC
1393794 AAAAATT
1 AAAAATT
1393801 AGAAAGTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 4 0.12
30 29 0.88
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.22
Consensus pattern (30 bp):
AAAAATTCAACCGATGCCGAAACATTCACC
Found at i:1395695 original size:272 final size:269
Alignment explanation
Indices: 1395274--1396010 Score: 1194
Period size: 271 Copynumber: 2.7 Consensus size: 269
1395264 CTCATAAATC
*
1395274 AATTACATATTATTATAAAGGTTTATATTTTAAATATATAATTTGATCTATCAG-TTTTTTCTAT
1 AATTACATATTATTATAAA-GTTTAAATTTTAAATATATAATTTGATCTATCAGCTTTTTTCTAT
* * *
1395338 TTTTGAAATCAAACACCCAAAATTAAGGTAATGTAAGCATAAAAATTTTAGAGAATTAAAAATAA
65 TTTTGAAATCAAA-TCCCAAAATTAAGGTAATGTAAGTATAAAAATTTTAGAGAATTCAAAATAA
1395403 AATTAAAACTATTGAATGCATGCTCAATAAGATTTTAATTTATTGT-AAAAAATAGAAAGAAATA
129 AATTAAAACTATTGAATGCATGCTCAATAAGATTTTAATTTATTGTAAAAAAATAGAAAGAAATA
1395467 ATATATATATATATATAGACAACATACATA-TCACAAATCAATTACATATTATTATGAAAAATTT
194 ATATATATATATATATAGACAACATACATACTCACAAATCAATTACATATTATTATGAAAAATTT
*
1395531 TTGTCTTCCTT
259 TTGTCTCCCTT
*
1395542 AATTACATATTATTATAAAGTTTAAATTTTAAATATATAATTTGATCTATCAGCTTTTCTTTTTT
1 AATTACATATTATTATAAAGTTTAAATTTTAAATATATAATTTGATCTATCAGC--TT-TTTTCT
*
1395607 ATTTTTGAAATCAAATGCCCAAAATTAAGGTAACGTAAGTATAAAAAGTTTTAGAGAATTCAAAA
63 ATTTTTGAAATCAAAT-CCCAAAATTAAGGTAATGTAAGTATAAAAA-TTTTAGAGAATTCAAAA
* * *
1395672 TAAAATTAGAACTATTGAATGCATGCTCAATCAGATTTTAATTTATTGTAAAAAAAAGAGAAAGA
126 TAAAATTAAAACTATTGAATGCATGCTCAATAAGATTTTAATTTATTGT-AAAAAAATAGAAAGA
* *
1395737 AATAATATATATATATATATAGACAACATACATACTCATAAATCAATTACTTATTATTATGAAAA
190 AATAATATATATATATATATAGACAACATACATACTCACAAATCAATTACATATTATTATGAAAA
1395802 ATTTTTGTCTCCCTT
255 ATTTTTGTCTCCCTT
* * * * *
1395817 AATTATATATTATTATAGAGTTTACACTTTAAATATATAATTTGATCTACCA-CTTTTTTCTATT
1 AATTACATATTATTATAAAGTTTAAATTTTAAATATATAATTTGATCTATCAGCTTTTTTCTATT
1395881 TTTGAAATCAAACTCCCAAAATTAAGGTAATGTAAGTATAAAAAATTTTAGAGAATTCAAAATAA
66 TTTGAAATCAAA-TCCCAAAATTAAGGTAATGTAAGTAT-AAAAATTTTAGAGAATTCAAAATAA
*
1395946 AATTAAAACTATTGAATGCATGCTCAATAAGATTTTAATTTGTTGTAAAAAAATAGAAAGAAATA
129 AATTAAAACTATTGAATGCATGCTCAATAAGATTTTAATTTATTGTAAAAAAATAGAAAGAAATA
1396011 TTCATACTTA
Statistics
Matches: 435, Mismatches: 23, Indels: 20
0.91 0.05 0.04
Matches are distributed among these distances:
267 33 0.08
268 19 0.04
270 20 0.05
271 155 0.36
272 71 0.16
274 48 0.11
275 89 0.20
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (269 bp):
AATTACATATTATTATAAAGTTTAAATTTTAAATATATAATTTGATCTATCAGCTTTTTTCTATT
TTTGAAATCAAATCCCAAAATTAAGGTAATGTAAGTATAAAAATTTTAGAGAATTCAAAATAAAA
TTAAAACTATTGAATGCATGCTCAATAAGATTTTAATTTATTGTAAAAAAATAGAAAGAAATAAT
ATATATATATATATAGACAACATACATACTCACAAATCAATTACATATTATTATGAAAAATTTTT
GTCTCCCTT
Found at i:1396903 original size:301 final size:300
Alignment explanation
Indices: 1396326--1396913 Score: 971
Period size: 301 Copynumber: 2.0 Consensus size: 300
1396316 AATAAATATG
* *
1396326 CAAAATTATTCATGATTAATTAGTTTTCTATTTAAATTTTGACTTTTTGAATTAATGATCAAATT
1 CAAAATTATTCACGATTAATTAGCTTTCTATTTAAATTTTGACTTTTTGAATTAATGATCAAATT
* * * * *
1396391 AATTATGGCTAATTTATAGGCGGCAAGAATATTGATATTTAAACATAATTAATTTAGCCATAATA
66 AATTATGGCCAAATAATAAGAGGCAAGAATATTGATATTTAAACATAATTAATTTAGCCATAATA
1396456 AATTTTTTAAAATTAATTATATAATCAAATTCATTAATTATATAACACATGGCATTTATCTATGA
131 AATTTTTTAAAATTAATTATATAATCAAATTCATTAATTATATAACACATGGCATTTATCTATGA
* * * *
1396521 CATTCCACATGTGAAAAATGTAACCTATGTACATAGAATTATTTCCTTTTATGCTAAAGGTTTTG
196 CAATCCACATGTCAAAAATGTAACCTATGTACATAAAATAATTTCCTTTTATGCTAAAGGTTTTG
* *
1396586 ATTTTTATATATTTATATAAGATTAATATGTTTATATAAT
261 ACTTTGATATATTTATATAAGATTAATATGTTTATATAAT
* *
1396626 CAAAATTATTCACGATTAATTAGCTTTCTATTTAAATTTTGATTTTTTGAATTGATGATCAAATT
1 CAAAATTATTCACGATTAATTAGCTTTCTATTTAAATTTTGACTTTTTGAATTAATGATCAAATT
*
1396691 AATTATGGCCAAATAATAAGAGGCAAGATTATTGATATTTAAACATAATTAATTTAGCCATAATA
66 AATTATGGCCAAATAATAAGAGGCAAGAATATTGATATTTAAACATAATTAATTTAGCCATAATA
*
1396756 AATTATTTTAAAATTAATTATATAATTAAATTCATTAATTATATAACACATGGCATTTATCTATG
131 AATT-TTTTAAAATTAATTATATAATCAAATTCATTAATTATATAACACATGGCATTTATCTATG
* *
1396821 ACAATCCACATGTCAAAAATGTAACCTAT-TCACATAAAATAATTTTCTTTTATGCTAAATGTTT
195 ACAATCCACATGTCAAAAATGTAACCTATGT-ACATAAAATAATTTCCTTTTATGCTAAAGGTTT
*
1396885 TGACTTTGATATATTTATATATGATTAAT
259 TGACTTTGATATATTTATATAAGATTAAT
1396914 GATAATATAA
Statistics
Matches: 266, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
300 125 0.47
301 141 0.53
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.43
Consensus pattern (300 bp):
CAAAATTATTCACGATTAATTAGCTTTCTATTTAAATTTTGACTTTTTGAATTAATGATCAAATT
AATTATGGCCAAATAATAAGAGGCAAGAATATTGATATTTAAACATAATTAATTTAGCCATAATA
AATTTTTTAAAATTAATTATATAATCAAATTCATTAATTATATAACACATGGCATTTATCTATGA
CAATCCACATGTCAAAAATGTAACCTATGTACATAAAATAATTTCCTTTTATGCTAAAGGTTTTG
ACTTTGATATATTTATATAAGATTAATATGTTTATATAAT
Found at i:1398052 original size:10 final size:10
Alignment explanation
Indices: 1398039--1398085 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
1398029 TCTAAAAAAA
1398039 TTTAAAAATT
1 TTTAAAAATT
1398049 TTT---AATT
1 TTTAAAAATT
1398056 TTTAAAAA-T
1 TTTAAAAATT
1398065 TTTAAAATATT
1 TTTAAAA-ATT
1398076 TTTAAAAATT
1 TTTAAAAATT
1398086 CAAAACAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
7 7 0.22
9 8 0.25
10 9 0.28
11 8 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTAAAAATT
Found at i:1398195 original size:28 final size:27
Alignment explanation
Indices: 1398162--1398234 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 27
1398152 TTATAAAACA
1398162 TAAAAAATATGAAATATTTTTATAAAT
1 TAAAAAATATGAAATATTTTTATAAAT
*
1398189 TACAAAAAT-TG--TTA-TTTTA-AAAT
1 TA-AAAAATATGAAATATTTTTATAAAT
1398212 TAAAAAATA--AAA-ATTTTTATAAA
1 TAAAAAATATGAAATATTTTTATAAA
1398235 GAATAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 15
0.69 0.04 0.27
Matches are distributed among these distances:
22 7 0.18
23 11 0.29
24 8 0.21
25 2 0.05
27 4 0.11
28 6 0.16
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (27 bp):
TAAAAAATATGAAATATTTTTATAAAT
Found at i:1398327 original size:7 final size:8
Alignment explanation
Indices: 1398306--1398347 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
1398296 CACAAAAACA
*
1398306 TAAAAAAA
1 TAAAAAAT
*
1398314 TAGAAAAT
1 TAAAAAAT
1398322 TAAAAAAT
1 TAAAAAAT
1398330 TAAAAAAT
1 TAAAAAAT
1398338 CTAAAAAAT
1 -TAAAAAAT
1398347 T
1 T
1398348 TTTGAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (8 bp):
TAAAAAAT
Found at i:1398342 original size:17 final size:17
Alignment explanation
Indices: 1398288--1398347 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 17
1398278 TCTTGAACTG
*
1398288 TAAAAAATCACAAAAA-C
1 TAAAAAATTA-AAAAATC
* *
1398305 ATAAAAAAATAGAAAAT-
1 -TAAAAAATTAAAAAATC
1398322 TAAAAAATTAAAAAATC
1 TAAAAAATTAAAAAATC
1398339 TAAAAAATT
1 TAAAAAATT
1398348 TTTGAACATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 14 0.40
17 13 0.37
18 8 0.23
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.20
Consensus pattern (17 bp):
TAAAAAATTAAAAAATC
Found at i:1399082 original size:10 final size:11
Alignment explanation
Indices: 1399037--1399090 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
1399027 TTTTTGTAAC
1399037 TTTAAAAATTT
1 TTTAAAAATTT
**
1399048 TTTAAAAAAGT
1 TTTAAAAATTT
*
1399059 TTTAAGAAA--A
1 TTTAA-AAATTT
1399069 TTT-AAAATTT
1 TTTAAAAATTT
1399079 TTTAAAAATTT
1 TTTAAAAATTT
1399090 T
1 T
1399091 CTTTTAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
8 3 0.09
9 1 0.03
10 6 0.17
11 22 0.63
12 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (11 bp):
TTTAAAAATTT
Found at i:1401099 original size:7 final size:7
Alignment explanation
Indices: 1401087--1401161 Score: 57
Period size: 7 Copynumber: 10.6 Consensus size: 7
1401077 AAATTAAGGG
1401087 AAAATAA
1 AAAATAA
1401094 AAAATAA
1 AAAATAA
*
1401101 AAAGTGTAA
1 AAA--ATAA
*
1401110 AAACTAA
1 AAAATAA
1401117 AAAA-AA
1 AAAATAA
1401123 AAAATAA
1 AAAATAA
1401130 ACAAA-AA
1 A-AAATAA
* *
1401137 AGCAA-AC
1 A-AAATAA
1401144 AAAATAA
1 AAAATAA
1401151 AAAATAA
1 AAAATAA
1401158 AAAA
1 AAAA
1401162 AAGATACTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
6 8 0.15
7 38 0.69
8 3 0.05
9 6 0.11
ACGTcount: A:0.80, C:0.05, G:0.04, T:0.11
Consensus pattern (7 bp):
AAAATAA
Found at i:1401163 original size:16 final size:16
Alignment explanation
Indices: 1401092--1401163 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
1401082 AAGGGAAAAT
* **
1401092 AAAAAATAAAAAGTGT
1 AAAAAATAAAAAATAA
* *
1401108 AAAAACTAAAAAAAAA
1 AAAAAATAAAAAATAA
* *
1401124 AAATAAACAAAAAAGCAA
1 AAA-AAATAAAAAA-TAA
*
1401142 ACAAAATAAAAAATAA
1 AAAAAATAAAAAATAA
1401158 AAAAAA
1 AAAAAA
1401164 GATACTTTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
16 21 0.50
17 17 0.40
18 4 0.10
ACGTcount: A:0.81, C:0.06, G:0.04, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAAAATAA
Found at i:1405703 original size:17 final size:16
Alignment explanation
Indices: 1405670--1405719 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
1405660 GAAATGCCCT
1405670 AAAA-AGAAAAGAAAA
1 AAAAGAGAAAAGAAAA
1405685 AAAAGAGAAAAGAAAA
1 AAAAGAGAAAAGAAAA
1405701 AAAAGATGAAAAGATAAA
1 AAAAGA-GAAAAGA-AAA
1405719 A
1 A
1405720 GAGTGAAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.12
16 17 0.53
17 7 0.22
18 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAGAGAAAAGAAAA
Found at i:1405726 original size:16 final size:16
Alignment explanation
Indices: 1405675--1405737 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
1405665 GCCCTAAAAA
*
1405675 GAAAAGAAAAAAAAGA
1 GAAAAGAAAAAAAAGT
1405691 GAAAAGAAAAAAAAGAT
1 GAAAAGAAAAAAAAG-T
* *
1405708 GAAAAGATAAAAGAGT
1 GAAAAGAAAAAAAAGT
1405724 GAAGAGAGAAAAAA
1 GAA-A-AGAAAAAA
1405738 TAAAGTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
16 19 0.47
17 14 0.35
18 7 0.17
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (16 bp):
GAAAAGAAAAAAAAGT
Found at i:1405736 original size:33 final size:33
Alignment explanation
Indices: 1405675--1405737 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1405665 GCCCTAAAAA
1405675 GAAAAGAAAAAAAAGAGAAAAGAAAAAAAAGAT
1 GAAAAGAAAAAAAAGAGAAAAGAAAAAAAAGAT
* * * * *
1405708 GAAAAGATAAAAGAGTGAAGAGAGAAAAAA
1 GAAAAGAAAAAAAAGAGAAAAGAAAAAAAA
1405738 TAAAGTTTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (33 bp):
GAAAAGAAAAAAAAGAGAAAAGAAAAAAAAGAT
Found at i:1406424 original size:18 final size:18
Alignment explanation
Indices: 1406397--1406459 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
1406387 GAGGCGTGCA
1406397 AAAAAAAATGAAAAAGAG-
1 AAAAAAAATGAAAAA-AGC
*
1406415 AAAGAAAATGAAAAAAGC
1 AAAAAAAATGAAAAAAGC
1406433 AAAAAAAATGAAATGAAAG-
1 AAAAAAAATGAAA--AAAGC
1406452 AAAAAAAA
1 AAAAAAAA
1406460 GGATTATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.05
18 26 0.65
19 8 0.20
20 4 0.10
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAAAAATGAAAAAAGC
Found at i:1406946 original size:20 final size:20
Alignment explanation
Indices: 1406892--1406972 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 20
1406882 GTATTCACTC
* *
1406892 AAAGAAAAGGAAAA-AAAATG
1 AAAGAAAA-AAAAAGAAAAAG
1406912 AAAGAAAATTGAAAAAGAAAAAG
1 AAAGAAAA---AAAAAGAAAAAG
1406935 AAAGAACAAAAAAA-AAAAAG
1 AAAGAA-AAAAAAAGAAAAAG
*
1406955 AAGGAAAAAAAAAGAAAA
1 AAAGAAAAAAAAAGAAAA
1406973 GAATGATTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
19 7 0.13
20 23 0.43
21 5 0.09
22 5 0.09
23 11 0.21
24 2 0.04
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (20 bp):
AAAGAAAAAAAAAGAAAAAG
Found at i:1406954 original size:16 final size:18
Alignment explanation
Indices: 1406924--1406971 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1406914 AGAAAATTGA
1406924 AAAAGAAAAAGAAAGAA-C
1 AAAA-AAAAAGAAAGAAGC
*
1406942 AAAAAAAAA-AAAGAAGG
1 AAAAAAAAAGAAAGAAGC
1406959 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
1406972 AGAATGATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 6 0.22
17 14 0.52
18 7 0.26
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAGAAGC
Found at i:1406973 original size:19 final size:20
Alignment explanation
Indices: 1406923--1406975 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
1406913 AAGAAAATTG
1406923 AAAAAGAAAAAGAAAGAACAA
1 AAAAAG-AAAAGAAAGAACAA
* *
1406944 AAAAAAAAAAGAAGGAA-AA
1 AAAAAGAAAAGAAAGAACAA
1406963 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
1406976 TGATTAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 14 0.48
20 10 0.34
21 5 0.17
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAGAAAGAACAA
Found at i:1407337 original size:30 final size:30
Alignment explanation
Indices: 1407303--1407359 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1407293 AGCATGGTGT
*
1407303 AATAATAAAAAAGA-AAAGAAAAGAAAAGAG
1 AATAA-AAAAAAGAGAAAGAAAAAAAAAGAG
* *
1407333 AATAAGAGAAAGAGAAAGAAAAAAAAA
1 AATAAAAAAAAGAGAAAGAAAAAAAAA
1407360 AGGAAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 6 0.26
30 17 0.74
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (30 bp):
AATAAAAAAAAGAGAAAGAAAAAAAAAGAG
Found at i:1407347 original size:6 final size:5
Alignment explanation
Indices: 1407311--1407378 Score: 50
Period size: 5 Copynumber: 13.2 Consensus size: 5
1407301 GTAATAATAA
* * * *
1407311 AAAAG AAAAG AAAAG AAAAG AGAAT AAGAG -AAAG AGAAAG AAAAAA AAAAGG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG -AAAAG AAAA-G
1407363 AAAAAG AAAA- AAAAG A
1 -AAAAG AAAAG AAAAG A
1407379 TATGGCTTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
4 7 0.14
5 29 0.59
6 8 0.16
7 5 0.10
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:1408046 original size:21 final size:19
Alignment explanation
Indices: 1408004--1408047 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1407994 TTTAAACAAG
* *
1408004 TTTTCATTTAAAAAAATGT
1 TTTTCATTAAAAAAAATAT
1408023 TTTTCATTGAAAAATAAATAT
1 TTTTCATT-AAAAA-AAATAT
1408044 TTTT
1 TTTT
1408048 GAAAATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 4 0.19
21 9 0.43
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTTCATTAAAAAAAATAT
Found at i:1408228 original size:18 final size:18
Alignment explanation
Indices: 1408205--1408244 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1408195 AATAATTGAG
1408205 TGAAAATGAAACAATGTC
1 TGAAAATGAAACAATGTC
*
1408223 TGAAAATGAAACAATGTT
1 TGAAAATGAAACAATGTC
1408241 TGAA
1 TGAA
1408245 GAAAAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.25
Consensus pattern (18 bp):
TGAAAATGAAACAATGTC
Found at i:1408982 original size:26 final size:27
Alignment explanation
Indices: 1408952--1409007 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1408942 AGGTTTAAAG
* *
1408952 AAAGAAAGAAAAGAA-AATAAAGCAAA
1 AAAGAAAGAAAAAAATAAAAAAGCAAA
*
1408978 AAAGAGAGAAAAAAATAAAAAAGCAAA
1 AAAGAAAGAAAAAAATAAAAAAGCAAA
1409005 AAA
1 AAA
1409008 AAGATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.04
Consensus pattern (27 bp):
AAAGAAAGAAAAAAATAAAAAAGCAAA
Found at i:1409000 original size:27 final size:26
Alignment explanation
Indices: 1408952--1409016 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 26
1408942 AGGTTTAAAG
* * *
1408952 AAAGAAAGAAAAGAAAATAAAGCAAA
1 AAAGAGAGAAAAAAAAAAAAAGCAAA
1408978 AAAGAGAGAAAAAAATAAAAAAGCAAA
1 AAAGAGAGAAAAAAA-AAAAAAGCAAA
* *
1409005 AAAAAGATAAAA
1 AAAGAGAGAAAA
1409017 TATGTCATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
26 13 0.39
27 20 0.61
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (26 bp):
AAAGAGAGAAAAAAAAAAAAAGCAAA
Found at i:1409286 original size:31 final size:31
Alignment explanation
Indices: 1409209--1409275 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1409199 AAAATGAGAC
* *
1409209 TTAAACCTAGTTTTAGTTGGTACTAAGAAAAT
1 TTAAACCTA-ATTTAGTTAGTACTAAGAAAAT
* *
1409241 TTAAGCCTAATTTAGTTAGTACTAAGAAGAT
1 TTAAACCTAATTTAGTTAGTACTAAGAAAAT
1409272 TTAA
1 TTAA
1409276 TACCAGTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (31 bp):
TTAAACCTAATTTAGTTAGTACTAAGAAAAT
Found at i:1409377 original size:33 final size:33
Alignment explanation
Indices: 1409268--1409587 Score: 155
Period size: 33 Copynumber: 9.8 Consensus size: 33
1409258 AGTACTAAGA
** **
1409268 AGATTTAATACCAGTTTAGCTAACACCCAGATG
1 AGATTTAAGCCCAGTTTAGCTGGCACCCAGATG
* * * ** * *
1409301 AGGTTTAAGCCCAATTTAGTTAACACCCAAATA
1 AGATTTAAGCCCAGTTTAGCTGGCACCCAGATG
* * *
1409334 AGAATAAAGCCCAATTTAGCTGGCACCCAGATG
1 AGATTTAAGCCCAGTTTAGCTGGCACCCAGATG
* * * * *
1409367 AGATTTAAGCCTAGTTTAGTTGTCACCCATATA
1 AGATTTAAGCCCAGTTTAGCTGGCACCCAGATG
* * * * * *
1409400 AAAATTAAGCTCATTTTAGGTAGCACCCAGATG
1 AGATTTAAGCCCAGTTTAGCTGGCACCCAGATG
* * * **
1409433 AGATTTAAGCCTAGTTTAGTTGGTACTAAGA-G
1 AGATTTAAGCCCAGTTTAGCTGGCACCCAGATG
* **** * * *
1409465 -GATATAAATTTAGTTTAGCTGACAACCAAATG
1 AGATTTAAGCCCAGTTTAGCTGGCACCCAGATG
* * * *
1409497 A-AGTTTAAGTCTAGTTTAGCT-G-ACACTGATG
1 AGA-TTTAAGCCCAGTTTAGCTGGCACCCAGATG
* * * *
1409528 AGATTTAAGCCTAGTTTAGTTAGCACCCATATG
1 AGATTTAAGCCCAGTTTAGCTGGCACCCAGATG
* * *
1409561 AGAATTGAGCCCAATTTAGCTGGCACC
1 AGATTTAAGCCCAGTTTAGCTGGCACC
1409588 GATTAGATGT
Statistics
Matches: 208, Mismatches: 73, Indels: 12
0.71 0.25 0.04
Matches are distributed among these distances:
31 41 0.20
32 5 0.02
33 162 0.78
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (33 bp):
AGATTTAAGCCCAGTTTAGCTGGCACCCAGATG
Found at i:1409454 original size:66 final size:66
Alignment explanation
Indices: 1409282--1409454 Score: 229
Period size: 66 Copynumber: 2.6 Consensus size: 66
1409272 TTAATACCAG
* * * * * *
1409282 TTTAGCTAACACCCAGATGAGGTTTAAGCCCAATTTAGTTAACACCCAAATAAGAATAAAGCCCA
1 TTTAGCTAGCACCCAGATGAGATTTAAGCCTAGTTTAGTTGACACCCAAATAAAAATAAAGCCCA
1409347 A
66 A
* * * * *
1409348 TTTAGCTGGCACCCAGATGAGATTTAAGCCTAGTTTAGTTGTCACCCATATAAAAATTAAGCTCA
1 TTTAGCTAGCACCCAGATGAGATTTAAGCCTAGTTTAGTTGACACCCAAATAAAAATAAAGCCCA
*
1409413 T
66 A
*
1409414 TTTAGGTAGCACCCAGATGAGATTTAAGCCTAGTTTAGTTG
1 TTTAGCTAGCACCCAGATGAGATTTAAGCCTAGTTTAGTTG
1409455 GTACTAAGAG
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 93 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (66 bp):
TTTAGCTAGCACCCAGATGAGATTTAAGCCTAGTTTAGTTGACACCCAAATAAAAATAAAGCCCA
A
Found at i:1409542 original size:31 final size:31
Alignment explanation
Indices: 1409429--1409546 Score: 87
Period size: 31 Copynumber: 3.7 Consensus size: 31
1409419 GTAGCACCCA
* **
1409429 GATGAGATTTAAGCCTAGTTTAGTTGGTACT
1 GATGAGATTTAAGCCTAGTTTAGCTGACACT
* * *** *
1409460 -AAGAGGATATAAATTTAGTTTAGCTGACAACCA
1 GATGA-GATTTAAGCCTAGTTTAGCTGAC-A-CT
* *
1409493 AATGA-AGTTTAAGTCTAGTTTAGCTGACACT
1 GATGAGA-TTTAAGCCTAGTTTAGCTGACACT
1409524 GATGAGATTTAAGCCTAGTTTAG
1 GATGAGATTTAAGCCTAGTTTAG
1409547 TTAGCACCCA
Statistics
Matches: 65, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
30 3 0.05
31 36 0.55
32 4 0.06
33 19 0.29
34 3 0.05
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (31 bp):
GATGAGATTTAAGCCTAGTTTAGCTGACACT
Found at i:1409663 original size:24 final size:23
Alignment explanation
Indices: 1409636--1409709 Score: 55
Period size: 24 Copynumber: 3.2 Consensus size: 23
1409626 TCAAATGTTA
1409636 TTAAGCCTTTACCTAAATAAGCTT
1 TTAAGCCTTTACCTAAA-AAGCTT
* * *
1409660 TTAA--ATTTATCTTCAAAAG-TT
1 TTAAGCCTTTA-CCTAAAAAGCTT
*
1409681 GTTGAGCCTTTACCTAAAGAAGCTT
1 -TTAAGCCTTTACCTAAA-AAGCTT
1409706 TTAA
1 TTAA
1409710 ATTTAACTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
21 2 0.06
22 10 0.28
23 8 0.22
24 14 0.39
25 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (23 bp):
TTAAGCCTTTACCTAAAAAGCTT
Found at i:1409689 original size:46 final size:46
Alignment explanation
Indices: 1409616--1409828 Score: 237
Period size: 46 Copynumber: 4.6 Consensus size: 46
1409606 GTCCAAGATG
* * *
1409616 AAATTTATTTTCAAATGTTATTAAGCCTTTACCTAAATAAGCTTTT
1 AAATTTATCTTCAAAAGTTGTTAAGCCTTTACCTAAATAAGCTTTT
* *
1409662 AAATTTATCTTCAAAAGTTGTTGAGCCTTTACCTAAAGAAGCTTTT
1 AAATTTATCTTCAAAAGTTGTTAAGCCTTTACCTAAATAAGCTTTT
* * * ** * *
1409708 AAATTTAACTTCAAAAGTTATTGAGTATTTACCTAAAAAAAACTTTT
1 AAATTTATCTTCAAAAGTTGTTAAGCCTTTACCT-AAATAAGCTTTT
* ** * *
1409755 AACTTTATCTTCAAAAGTTGTTAAATCTTTACTTAAATGAGCTTTT
1 AAATTTATCTTCAAAAGTTGTTAAGCCTTTACCTAAATAAGCTTTT
* * *
1409801 GAATTTATTTTCAAAAGTTGTAAAGCCT
1 AAATTTATCTTCAAAAGTTGTTAAGCCT
1409829 CTGATGTGAG
Statistics
Matches: 139, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
46 102 0.73
47 37 0.27
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (46 bp):
AAATTTATCTTCAAAAGTTGTTAAGCCTTTACCTAAATAAGCTTTT
Found at i:1409785 original size:93 final size:92
Alignment explanation
Indices: 1409616--1409819 Score: 257
Period size: 93 Copynumber: 2.2 Consensus size: 92
1409606 GTCCAAGATG
* * * *
1409616 AAATTTATTTTCAAATGTTATTAAGCCTTTACCTAAATAAGCTTTTAAATTTATCTTCAAAAGTT
1 AAATTTATTTTCAAAAGTTATTAAGCATTTACCTAAAAAAACTTTTAAATTTATCTTCAAAAGTT
* *
1409681 GTTGAGCCTTTACCTAAA-GAAGCTTTT
66 GTTAAACCTTTACCTAAATG-AGCTTTT
** * * *
1409708 AAATTTAACTTCAAAAGTTATTGAGTATTTACCTAAAAAAAACTTTTAACTTTATCTTCAAAAGT
1 AAATTTATTTTCAAAAGTTATTAAGCATTTACCT-AAAAAAACTTTTAAATTTATCTTCAAAAGT
* *
1409773 TGTTAAATCTTTACTTAAATGAGCTTTT
65 TGTTAAACCTTTACCTAAATGAGCTTTT
*
1409801 GAATTTATTTTCAAAAGTT
1 AAATTTATTTTCAAAAGTT
1409820 GTAAAGCCTC
Statistics
Matches: 94, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
92 28 0.30
93 65 0.69
94 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (92 bp):
AAATTTATTTTCAAAAGTTATTAAGCATTTACCTAAAAAAACTTTTAAATTTATCTTCAAAAGTT
GTTAAACCTTTACCTAAATGAGCTTTT
Found at i:1410012 original size:20 final size:20
Alignment explanation
Indices: 1409987--1410064 Score: 61
Period size: 21 Copynumber: 3.9 Consensus size: 20
1409977 GTCAAAAACT
1409987 AAAAAAACAACAAAGAATAA
1 AAAAAAACAACAAAGAATAA
* * *
1410007 AAAAAAGCAAACAAAAAACAA
1 AAAAAAAC-AACAAAGAATAA
* *
1410028 AAAATAAC-A-AAAGCATACA
1 AAAAAAACAACAAAGAATA-A
*
1410047 AAACAAAACAAAAAAGAA
1 AAA-AAAACAACAAAGAA
1410065 CAAGAGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
18 5 0.12
19 5 0.12
20 11 0.26
21 17 0.40
22 5 0.12
ACGTcount: A:0.78, C:0.13, G:0.05, T:0.04
Consensus pattern (20 bp):
AAAAAAACAACAAAGAATAA
Found at i:1410026 original size:31 final size:29
Alignment explanation
Indices: 1409988--1410060 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 29
1409978 TCAAAAACTA
1409988 AAAAAACAACAAAGAATAAAAAAAAGCAAAC
1 AAAAAACAACAAA-AAT-AAAAAAAGCAAAC
* *
1410019 AAAAAAC-A-AAAAATAACAAAAGCATAC
1 AAAAAACAACAAAAATAAAAAAAGCAAAC
1410046 AAAACAA-AACAAAAA
1 AAAA-AACAACAAAAA
1410061 AGAACAAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 15 0.41
28 6 0.16
29 8 0.22
30 1 0.03
31 7 0.19
ACGTcount: A:0.78, C:0.14, G:0.04, T:0.04
Consensus pattern (29 bp):
AAAAAACAACAAAAATAAAAAAAGCAAAC
Found at i:1410067 original size:20 final size:19
Alignment explanation
Indices: 1409987--1410067 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 19
1409977 GTCAAAAACT
* *
1409987 AAAAAAACAACAAAGAATA
1 AAAAAAACAAAAAAGAACA
*
1410006 AAAAAAAGCAAACAAAAAACA
1 AAAAAAA-CAAA-AAAGAACA
1410027 AAAAATAAC--AAAAGCATACA
1 AAAAA-AACAAAAAAG-A-ACA
1410047 AAACAAAACAAAAAAGAACA
1 AAA-AAAACAAAAAAGAACA
1410067 A
1 A
1410068 GAGAAAAGCT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
18 3 0.06
19 9 0.18
20 16 0.32
21 15 0.30
22 7 0.14
ACGTcount: A:0.78, C:0.14, G:0.05, T:0.04
Consensus pattern (19 bp):
AAAAAAACAAAAAAGAACA
Found at i:1412576 original size:23 final size:22
Alignment explanation
Indices: 1412560--1412602 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1412550 ATAAAAGGCT
1412560 AAAATAATAAAAAATAATAAACA
1 AAAATAATAAAAAATAA-AAACA
*
1412583 AAAATGATAAAAAATAAAAA
1 AAAATAATAAAAAATAAAAA
1412603 AATTTAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAATAATAAAAAATAAAAACA
Found at i:1414832 original size:16 final size:16
Alignment explanation
Indices: 1414811--1414842 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1414801 CATGCTTATG
*
1414811 CCAATTGTTAAGGATA
1 CCAATTGTTAAAGATA
1414827 CCAATTGTTAAAGATA
1 CCAATTGTTAAAGATA
1414843 TGTTATTACA
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:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (16 bp):
CCAATTGTTAAAGATA
Found at i:1419725 original size:3 final size:3
Alignment explanation
Indices: 1419717--1419748 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
1419707 ATGTCTTTTA
1419717 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A
1419749 GTTAACTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1422772 original size:28 final size:29
Alignment explanation
Indices: 1422735--1422794 Score: 113
Period size: 28 Copynumber: 2.1 Consensus size: 29
1422725 GAATTATATA
1422735 TTTATATAATTATGCAT-AAAAATATTAT
1 TTTATATAATTATGCATAAAAAATATTAT
1422763 TTTATATAATTATGCATAAAAAATATTAT
1 TTTATATAATTATGCATAAAAAATATTAT
1422792 TTT
1 TTT
1422795 TAATAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTATATAATTATGCATAAAAAATATTAT
Found at i:1422820 original size:17 final size:18
Alignment explanation
Indices: 1422781--1422824 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1422771 ATTATGCATA
*
1422781 AAAAATATTATTTTTAAT
1 AAAAATATTACTTTTAAT
*
1422799 AAAAATATTACTTTTAGT
1 AAAAATATTACTTTTAAT
1422817 AAAAATAT
1 AAAAATAT
1422825 AAAATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
AAAAATATTACTTTTAAT
Found at i:1422950 original size:16 final size:14
Alignment explanation
Indices: 1422922--1422949 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1422912 TAAATATTTG
1422922 ATAAAATTTATATA
1 ATAAAATTTATATA
1422936 ATAAAATTTATATA
1 ATAAAATTTATATA
1422950 TTTATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAAAATTTATATA
Found at i:1424273 original size:40 final size:40
Alignment explanation
Indices: 1424218--1424304 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
1424208 CACCATTATA
1424218 TATATATATATATAGACAACATAAATACTCATAAATCAAT
1 TATATATATATATAGACAACATAAATACTCATAAATCAAT
1424258 TATATATATATATAGACAACATAAATACTCATAAATCAAT
1 TATATATATATATAGACAACATAAATACTCATAAATCAAT
*
1424298 TAGATAT
1 TATATAT
1424305 TATTATGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.33
Consensus pattern (40 bp):
TATATATATATATAGACAACATAAATACTCATAAATCAAT
Found at i:1425376 original size:301 final size:301
Alignment explanation
Indices: 1424828--1425405 Score: 998
Period size: 301 Copynumber: 1.9 Consensus size: 301
1424818 AATAAATATG
1424828 CAAAATTATTCATGATTAATTAGCTTTCTAATTAAATTTTAACTTTTTGAATTAATGATCAAATT
1 CAAAATTATTCATGATTAATTAGCTTTCTAATTAAATTTTAACTTTTTGAATTAATGATCAAATT
* * * *
1424893 AATTATGGCTAATTTATAGGAGGCAAGAATATTGATATTTAAACATAATTAATTTAGCCATAATA
66 AATTATAGCTAAATAATAAGAGGCAAGAATATTGATATTTAAACATAATTAATTTAGCCATAATA
*
1424958 AATTATTTTAAAATTAATTATATAATCAAATTCATTAATTATATAACACATGGCATTTATTTATG
131 AATTATTTTAAAATTAATTATATAATCAAATTCATTAATTATATAACACATGGCATTTATCTATG
* * *
1425023 ACATTCCACATGTGAAAAATGTAAGCTATCTACTTAGAATTATTTCCTTTTATGCTAAAGGTTTT
196 ACATTCCACATGTCAAAAATGTAACCTATCTACATAGAATTATTTCCTTTTATGCTAAAGGTTTT
1425088 GACTTTTATATATTTATATAAGATTAATATGTTTATATAAT
261 GACTTTTATATATTTATATAAGATTAATATGTTTATATAAT
* *
1425129 CAAAATTATTCATGATTAATTAGCTTTCTATTTAAATTTTGACTTTTTGAATTAATGATCAAATT
1 CAAAATTATTCATGATTAATTAGCTTTCTAATTAAATTTTAACTTTTTGAATTAATGATCAAATT
*
1425194 AATTATTATC-AAATAATAAGAGGCAAGAATATTGATATTTAAACATAATTAATTTAGCCATAAT
66 AATTA-TAGCTAAATAATAAGAGGCAAGAATATTGATATTTAAACATAATTAATTTAGCCATAAT
*
1425258 AAATTATTTTAAAATTAATTATATAATTAAATTCATTAATTATATAACACATGGCATTTATCTAT
130 AAATTATTTTAAAATTAATTATATAATCAAATTCATTAATTATATAACACATGGCATTTATCTAT
* *
1425323 GACATTCCACATGTCAAAAATGTAACCTAT-TCACATAGAATTATTTTCTTTTATGCTAAATGTT
195 GACATTCCACATGTCAAAAATGTAACCTATCT-ACATAGAATTATTTCCTTTTATGCTAAAGGTT
1425387 TTGACTTTTATATATTTAT
259 TTGACTTTTATATATTTAT
1425406 TTATATATGA
Statistics
Matches: 261, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
300 1 0.00
301 258 0.99
302 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (301 bp):
CAAAATTATTCATGATTAATTAGCTTTCTAATTAAATTTTAACTTTTTGAATTAATGATCAAATT
AATTATAGCTAAATAATAAGAGGCAAGAATATTGATATTTAAACATAATTAATTTAGCCATAATA
AATTATTTTAAAATTAATTATATAATCAAATTCATTAATTATATAACACATGGCATTTATCTATG
ACATTCCACATGTCAAAAATGTAACCTATCTACATAGAATTATTTCCTTTTATGCTAAAGGTTTT
GACTTTTATATATTTATATAAGATTAATATGTTTATATAAT
Found at i:1426366 original size:13 final size:13
Alignment explanation
Indices: 1426350--1426391 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 13
1426340 GCATAAAAGG
1426350 AAATTTTAAAAAA
1 AAATTTTAAAAAA
1426363 AAATTTTAATTAAAA
1 AAATTTTAA--AAAA
1426378 AAATCTTTAAAAAA
1 AAAT-TTTAAAAAA
1426392 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.35
14 4 0.15
15 8 0.31
16 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATTTTAAAAAA
Found at i:1427332 original size:9 final size:10
Alignment explanation
Indices: 1427310--1427343 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1427300 GTCATCGGTG
1427310 AATAAAATGA
1 AATAAAATGA
*
1427320 AATAAAA-GT
1 AATAAAATGA
1427329 AATAAAATGA
1 AATAAAATGA
1427339 AATAA
1 AATAA
1427344 GAGTATCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (10 bp):
AATAAAATGA
Found at i:1427334 original size:19 final size:19
Alignment explanation
Indices: 1427310--1427348 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1427300 GTCATCGGTG
1427310 AATAAAATGAAATAAAAGT
1 AATAAAATGAAATAAAAGT
*
1427329 AATAAAATGAAATAAGAGT
1 AATAAAATGAAATAAAAGT
1427348 A
1 A
1427349 TCCTCCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.21
Consensus pattern (19 bp):
AATAAAATGAAATAAAAGT
Found at i:1427741 original size:79 final size:79
Alignment explanation
Indices: 1427610--1427768 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
1427600 CACTGGTTTC
1427610 TCGACATTTATGTTGAAAGCATCATTATTTAATTTAAGAACATACAAACCATTATCATACATTCC
1 TCGACATTTATGTTGAAAGCATCATTATTTAATTTAAGAACATACAAACCATTATCATACATTCC
1427675 CATACCATAAAAGA
66 CATACCATAAAAGA
*
1427689 TCGACATTTATGTTGAAAGCATCATTATTTAATTTAAGAACATACAAACCATTATCATATATTCC
1 TCGACATTTATGTTGAAAGCATCATTATTTAATTTAAGAACATACAAACCATTATCATACATTCC
1427754 CATACCATAAAAGA
66 CATACCATAAAAGA
1427768 T
1 T
1427769 ATCACTTAAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.33
Consensus pattern (79 bp):
TCGACATTTATGTTGAAAGCATCATTATTTAATTTAAGAACATACAAACCATTATCATACATTCC
CATACCATAAAAGA
Found at i:1431647 original size:20 final size:20
Alignment explanation
Indices: 1431603--1431666 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
1431593 ATTTGAGCTT
* *
1431603 AAAGTTGATTGCAA-ATGTG
1 AAAGTTTATTGCAAGATTTG
1431622 -AAGTTTATTGCAAGATTTG
1 AAAGTTTATTGCAAGATTTG
1431641 AAAGTTTATTGCAAGATTTG
1 AAAGTTTATTGCAAGATTTG
1431661 AAAGTT
1 AAAGTT
1431667 CACATGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.29
19 4 0.10
20 25 0.61
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (20 bp):
AAAGTTTATTGCAAGATTTG
Found at i:1444805 original size:21 final size:20
Alignment explanation
Indices: 1444780--1444821 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
1444770 TTTTAATTTC
1444780 TATTTATTTGT-TTATTGAATT
1 TATTTATTT-TCTT-TTGAATT
1444801 TATTTATTTTCTTTTGAATT
1 TATTTATTTTCTTTTGAATT
1444821 T
1 T
1444822 TTTGCTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.69
Consensus pattern (20 bp):
TATTTATTTTCTTTTGAATT
Found at i:1447585 original size:8 final size:8
Alignment explanation
Indices: 1447572--1447613 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
1447562 CATCACATTA
1447572 TTTTTCTT
1 TTTTTCTT
1447580 TTTTTCTT
1 TTTTTCTT
1447588 TTTTT-TT
1 TTTTTCTT
*
1447595 TCTTTGCTT
1 T-TTTTCTT
1447604 TTTTTCTT
1 TTTTTCTT
1447612 TT
1 TT
1447614 CCACTTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 3 0.10
8 24 0.80
9 3 0.10
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1452702 original size:24 final size:24
Alignment explanation
Indices: 1452673--1452718 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1452663 GTGCAATTTT
* * *
1452673 ATTTATCTTTTTTTTTTTTTTATC
1 ATTTATCTCTCTTTGTTTTTTATC
1452697 ATTTATCTCTCTTTGTTTTTTA
1 ATTTATCTCTCTTTGTTTTTTA
1452719 AAGGATTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (24 bp):
ATTTATCTCTCTTTGTTTTTTATC
Found at i:1458466 original size:20 final size:16
Alignment explanation
Indices: 1458434--1458491 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
1458424 TTAAATGCAT
1458434 AAATAA-GTAAATAAA
1 AAATAAGGTAAATAAA
1458449 CAAATCAATGGTAGAATAAA
1 -AAAT-AA-GGTA-AATAAA
1458469 TAAATAAGGTAAATAAA
1 -AAATAAGGTAAATAAA
1458486 AAATAA
1 AAATAA
1458492 ACAAAGTACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
16 10 0.27
17 8 0.22
18 4 0.11
19 5 0.14
20 10 0.27
ACGTcount: A:0.66, C:0.03, G:0.10, T:0.21
Consensus pattern (16 bp):
AAATAAGGTAAATAAA
Found at i:1459078 original size:43 final size:43
Alignment explanation
Indices: 1459032--1459278 Score: 273
Period size: 43 Copynumber: 5.7 Consensus size: 43
1459022 AAAACTCCTT
* * *
1459032 TATACAAAGGCAAAACAACTTTAAAATAAGAAATGGGCTCTTT
1 TATACAGAGGCTAAACAACTTTAAAATAAGAAATGGGCTCTTC
* * * * * *
1459075 TATATAGAGGCTAAGCAATTTTAAATTAAGAAATAGGCTCCTC
1 TATACAGAGGCTAAACAACTTTAAAATAAGAAATGGGCTCTTC
*
1459118 TATACAGAGGTTAAACAA-TTCTAAAATAAGAAATGGGCT-TCTC
1 TATACAGAGGCTAAACAACTT-TAAAATAAGAAATGGGCTCT-TC
* * * * *
1459161 TATACAGAGGTTACACAACTTTAAATTAAGAAATGGACTCTTT
1 TATACAGAGGCTAAACAACTTTAAAATAAGAAATGGGCTCTTC
* *
1459204 TATACAGAGGCTAAACAACTTTAAAAAAAGAAATGGGCTCCTC
1 TATACAGAGGCTAAACAACTTTAAAATAAGAAATGGGCTCTTC
* * * *
1459247 CATACAAAGGCTAAACAACTCTAAATTAAGAA
1 TATACAGAGGCTAAACAACTTTAAAATAAGAA
1459279 TCATCTAATT
Statistics
Matches: 169, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
42 2 0.01
43 164 0.97
44 3 0.02
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (43 bp):
TATACAGAGGCTAAACAACTTTAAAATAAGAAATGGGCTCTTC
Found at i:1459184 original size:86 final size:85
Alignment explanation
Indices: 1459025--1459278 Score: 307
Period size: 86 Copynumber: 3.0 Consensus size: 85
1459015 ACAAAATAAA
* * * *
1459025 ACTCCTTTATACAAAGGCAAAACAACTTTAAAATAAGAAATGGGC-TCTTTTATATAGAGGCTAA
1 ACTCCTTTATACAGAGGCTAAACAACTTTAAAATAAGAAATGGGCTTC-TCTATACAGAGGCTAA
*
1459089 GCAATTTTAAATTAAGAAATAGG
65 -CAACTTTAAATTAAGAAAT-GG
* * *
1459112 -CTCCTCTATACAGAGGTTAAACAA-TTCTAAAATAAGAAATGGGCTTCTCTATACAGAGGTTAC
1 ACTCCTTTATACAGAGGCTAAACAACTT-TAAAATAAGAAATGGGCTTCTCTATACAGAGGCTA-
1459175 ACAACTTTAAATTAAGAAATGG
64 ACAACTTTAAATTAAGAAATGG
* * * * *
1459197 ACTCTTTTATACAGAGGCTAAACAACTTTAAAAAAAGAAATGGGCTCCTCCATACAAAGGCTAAA
1 ACTCCTTTATACAGAGGCTAAACAACTTTAAAATAAGAAATGGGCTTCTCTATACAGAGGCT-AA
*
1459262 CAACTCTAAATTAAGAA
65 CAACTTTAAATTAAGAA
1459279 TCATCTAATT
Statistics
Matches: 144, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
85 4 0.03
86 134 0.93
87 6 0.04
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (85 bp):
ACTCCTTTATACAGAGGCTAAACAACTTTAAAATAAGAAATGGGCTTCTCTATACAGAGGCTAAC
AACTTTAAATTAAGAAATGG
Found at i:1459262 original size:129 final size:129
Alignment explanation
Indices: 1459046--1459278 Score: 349
Period size: 129 Copynumber: 1.8 Consensus size: 129
1459036 CAAAGGCAAA
* * * * **
1459046 ACAACTTTAAAATAAGAAATGGGCTCTTTTATATAGAGGCTAAGCAATTTTAAATTAAGAAATAG
1 ACAACTTTAAAATAAGAAATGGACTCTTTTATACAGAGGCTAAACAACTTTAAAAAAAGAAATAG
* * * *
1459111 GCTCCTCTATACAGAGGTTAAACAATTCTAAAATAAGAAATGGGCTTCTCTATACAGAGGTTAC
66 GCTCCTCCATACAAAGGCTAAACAACTCTAAAATAAGAAATGGGCTTCTCTATACAGAGGTTAC
* *
1459175 ACAACTTTAAATTAAGAAATGGACTCTTTTATACAGAGGCTAAACAACTTTAAAAAAAGAAATGG
1 ACAACTTTAAAATAAGAAATGGACTCTTTTATACAGAGGCTAAACAACTTTAAAAAAAGAAATAG
*
1459240 GCTCCTCCATACAAAGGCTAAACAACTCTAAATTAAGAA
66 GCTCCTCCATACAAAGGCTAAACAACTCTAAAATAAGAA
1459279 TCATCTAATT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
129 91 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (129 bp):
ACAACTTTAAAATAAGAAATGGACTCTTTTATACAGAGGCTAAACAACTTTAAAAAAAGAAATAG
GCTCCTCCATACAAAGGCTAAACAACTCTAAAATAAGAAATGGGCTTCTCTATACAGAGGTTAC
Found at i:1463724 original size:21 final size:23
Alignment explanation
Indices: 1463700--1463745 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
1463690 ATGCTTTGAC
1463700 TAGAAGGAA-AAATAAAAA-GAA
1 TAGAAGGAATAAATAAAAATGAA
* *
1463721 TAGAGGGAATGAATAAAAATGAA
1 TAGAAGGAATAAATAAAAATGAA
1463744 TA
1 TA
1463746 CTCTTATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (23 bp):
TAGAAGGAATAAATAAAAATGAA
Found at i:1464796 original size:27 final size:27
Alignment explanation
Indices: 1464753--1464827 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 27
1464743 ACTGTAGACA
*
1464753 CCCATTTTT-GTCCGGGCTCAATTAGG
1 CCCATTTTTGGTTCGGGCTCAATTAGG
*
1464779 CCCATTTTTGGTTTGGGCTCAATTAGG
1 CCCATTTTTGGTTCGGGCTCAATTAGG
*
1464806 CCCA-TCTTGGTTCGGGCTCAAT
1 CCCATTTTTGGTTCGGGCTCAAT
1464828 ATAGTTTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 25 0.57
27 19 0.43
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.36
Consensus pattern (27 bp):
CCCATTTTTGGTTCGGGCTCAATTAGG
Found at i:1464822 original size:26 final size:27
Alignment explanation
Indices: 1464765--1464827 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
1464755 CATTTTTGTC
*
1464765 CGGGCTCAATTAGGCCCATTTTTGGTT
1 CGGGCTCAATTAGGCCCATTCTTGGTT
*
1464792 TGGGCTCAATTAGGCCCA-TCTTGGTT
1 CGGGCTCAATTAGGCCCATTCTTGGTT
1464818 CGGGCTCAAT
1 CGGGCTCAAT
1464828 ATAGTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 16 0.48
27 17 0.52
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (27 bp):
CGGGCTCAATTAGGCCCATTCTTGGTT
Found at i:1464995 original size:3 final size:3
Alignment explanation
Indices: 1464976--1465034 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
1464966 TTAGGTGCTC
*
1464976 TTA TTA TTG TT- TCTA TTA TTA TTA TTA TTA TT- TCTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
1465021 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
1465035 TCTTTTTCTA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1465002 original size:21 final size:21
Alignment explanation
Indices: 1464976--1465028 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1464966 TTAGGTGCTC
*
1464976 TTATTATTGTTTCTATTATTA
1 TTATTATTATTTCTATTATTA
1464997 TTATTATTATTTCTATTATTA
1 TTATTATTATTTCTATTATTA
1465018 TTATTATTATT
1 TTATTATTATT
1465029 ATTATTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (21 bp):
TTATTATTATTTCTATTATTA
Found at i:1465978 original size:18 final size:19
Alignment explanation
Indices: 1465952--1465996 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1465942 TCTATCTTTT
*
1465952 TATAAAATAAATGAAAATA
1 TATAAAATAAATAAAAATA
*
1465971 TA-AAAATATATAAAAATA
1 TATAAAATAAATAAAAATA
1465989 TATAAAAT
1 TATAAAAT
1465997 TTGTTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
TATAAAATAAATAAAAATA
Found at i:1465981 original size:10 final size:10
Alignment explanation
Indices: 1465968--1465995 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1465958 ATAAATGAAA
1465968 ATATAAAAAT
1 ATATAAAAAT
1465978 ATATAAAAAT
1 ATATAAAAAT
1465988 ATATAAAA
1 ATATAAAA
1465996 TTTGTTATTT
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:1470157 original size:35 final size:37
Alignment explanation
Indices: 1470086--1470157 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 37
1470076 TAGATAGAAG
* *
1470086 TATCTTTCAATATGTTAGTAATATTTTTTATCAAAAAT
1 TATCATTCAATATGTTAGTAAGA-TTTTTATCAAAAAT
*
1470124 TATCATTCAATATGTT-GTAAGA-TTTTATGAAAAA
1 TATCATTCAATATGTTAGTAAGATTTTTATCAAAAA
1470158 ACAAGAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 11 0.35
37 5 0.16
38 15 0.48
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (37 bp):
TATCATTCAATATGTTAGTAAGATTTTTATCAAAAAT
Found at i:1477437 original size:104 final size:104
Alignment explanation
Indices: 1477252--1477654 Score: 558
Period size: 104 Copynumber: 3.9 Consensus size: 104
1477242 AAATAAAATA
* * * *
1477252 AGAGATTATGCTTGAAGGTCTTATAAATCTTGACATTTATGAAAGCTCCTTTAATCGGAGGCATT
1 AGAGATTATGCTTGAAGGTCTTACAAATCTTGACATCTATGAAAGCTCCTCTAATCAGAGGCATT
* * *
1477317 GAAAGTTTAAAGATTTAAAATATTTTGCCTAGAGGACTT
66 GAAACTTTAAAAATTTAAAATGTTTTGCCTAGAGGACTT
* ** *
1477356 AGAGATTATGCTTAAAGGTCTTACAAATCTCAACATCTATGAAAGCTCCTCTAACCAGAGGCATT
1 AGAGATTATGCTTGAAGGTCTTACAAATCTTGACATCTATGAAAGCTCCTCTAATCAGAGGCATT
* * * *
1477421 AAAACTTTAAAAATTTAAAATGTTTCGCTTGGAGGACTT
66 GAAACTTTAAAAATTTAAAATGTTTTGCCTAGAGGACTT
* *
1477460 AGAGATTATGTTTGTAGGTCTTACAAATCTTGACATCTATGGAAA-CTCCTCTAATCAGAGGCAT
1 AGAGATTATGCTTGAAGGTCTTACAAATCTTGACATCTAT-GAAAGCTCCTCTAATCAGAGGCAT
* *
1477524 TCAAACTTTAAAAATTTAAAATGTTTTGCCCAGAGGACTT
65 TGAAACTTTAAAAATTTAAAATGTTTTGCCTAGAGGACTT
* * * *
1477564 AGAGATTATG-TCCGAAGGTCTTACAAATCTTGATATCTATAAAAGCTCCTCTAATCAAAGGCAT
1 AGAGATTATGCT-TGAAGGTCTTACAAATCTTGACATCTATGAAAGCTCCTCTAATCAGAGGCAT
*
1477628 TGAAACTTTAAAAATCTAAAATGTTTT
65 TGAAACTTTAAAAATTTAAAATGTTTT
1477655 ACTTGAAGGT
Statistics
Matches: 263, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
103 4 0.02
104 255 0.97
105 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (104 bp):
AGAGATTATGCTTGAAGGTCTTACAAATCTTGACATCTATGAAAGCTCCTCTAATCAGAGGCATT
GAAACTTTAAAAATTTAAAATGTTTTGCCTAGAGGACTT
Found at i:1479313 original size:9 final size:8
Alignment explanation
Indices: 1479287--1479337 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
1479277 ACATTCATAT
*
1479287 TTTTTTTA
1 TTTTTTTC
1479295 TTTTTTT-
1 TTTTTTTC
*
1479302 TTTGTTTC
1 TTTTTTTC
*
1479310 TTTTCTTC
1 TTTTTTTC
1479318 TTTTTCTTC
1 TTTTT-TTC
1479327 TTTTTCTTC
1 TTTTT-TTC
1479336 TT
1 TT
1479338 CTTCTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
7 6 0.16
8 17 0.46
9 14 0.38
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1479342 original size:9 final size:9
Alignment explanation
Indices: 1479310--1479343 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1479300 TTTTTGTTTC
1479310 TTTTCTTCT
1 TTTTCTTCT
1479319 TTTTCTTCT
1 TTTTCTTCT
1479328 TTTTCTTCT
1 TTTTCTTCT
*
1479337 TCTTCTT
1 TTTTCTT
1479344 TTATTATTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:1479819 original size:6 final size:6
Alignment explanation
Indices: 1479722--1479821 Score: 50
Period size: 6 Copynumber: 17.0 Consensus size: 6
1479712 TTTTTTTCCA
* * * *
1479722 CTTTTT CTTTGT CTTTTT -TATTT -TTTTT ATTTTCT CATTTTT -TCTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT-T C-TTTTT CTTTTT
* * * *
1479769 CTTTGT GTTTTT -TTTTT -TATGTT CTTGTT C-TTTT CATTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CT-TTTT CTTTTT CTTTTT C-TTTTT CTTTTT
1479816 CTTTTT
1 CTTTTT
1479822 ATCTCTTTCC
Statistics
Matches: 74, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
5 22 0.30
6 40 0.54
7 8 0.11
8 4 0.05
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:1479874 original size:25 final size:25
Alignment explanation
Indices: 1479800--1479876 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
1479790 TTCTTGTTCT
* **
1479800 TTTCATTTTTCTTTTTCTTTTTATCTC
1 TTTCACTTTTCTTTTTC-TTTCCT-TC
* *
1479827 TTTCCCTTTTCTTATTT-TCTCCTTC
1 TTTCACTTTTCTT-TTTCTTTCCTTC
1479852 TTTCACTTTTCTTTTTCTTTCCTTC
1 TTTCACTTTTCTTTTTCTTTCCTTC
1479877 AAGTGGATTC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
24 3 0.07
25 21 0.51
26 3 0.07
27 11 0.27
28 3 0.07
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTCACTTTTCTTTTTCTTTCCTTC
Found at i:1480222 original size:21 final size:21
Alignment explanation
Indices: 1480184--1480223 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1480174 GAAGAAAATT
* *
1480184 TTTTTTGTTTGGGGTTTTTTC
1 TTTTTTGTTTGAGATTTTTTC
1480205 TTTTTTGTTTGAGATTTTT
1 TTTTTTGTTTGAGATTTTT
1480224 CTGGTTGTTA
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:0.05, C:0.03, G:0.20, T:0.72
Consensus pattern (21 bp):
TTTTTTGTTTGAGATTTTTTC
Found at i:1480350 original size:28 final size:28
Alignment explanation
Indices: 1480319--1480394 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 28
1480309 AATCAAAGAT
1480319 TTTTTTCCTCTTTTTTTCT-TTCTTTC-C
1 TTTTTTCCTCTTTTTTTCTCTT-TTTCTC
*
1480346 ATTTTTCTCTTCTTGTTTTTCTCTTTTTCTC
1 -TTTTT-TCCTCTT-TTTTTCTCTTTTTCTC
*
1480377 TTTCTTTCCTTTTTTTTT
1 TTT-TTTCCTCTTTTTTT
1480395 TTGCATGTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 5 0.12
29 11 0.28
30 19 0.47
31 5 0.12
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.75
Consensus pattern (28 bp):
TTTTTTCCTCTTTTTTTCTCTTTTTCTC
Found at i:1483462 original size:38 final size:37
Alignment explanation
Indices: 1483396--1483476 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 37
1483386 AATGGAGTAG
* * *
1483396 TGTACTATCTATTGAGATGTGCATGAGATAGAA-TGCA
1 TGTACTATCTATTAAGATGTACAAGAGAT-GAAGTGCA
*
1483433 TGTACTATCTAATTAAGATGTATAAGAGATGAAGTGCA
1 TGTACTATCT-ATTAAGATGTACAAGAGATGAAGTGCA
*
1483471 TTTACT
1 TGTACT
1483477 CTCTTATTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 13 0.35
38 24 0.65
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.35
Consensus pattern (37 bp):
TGTACTATCTATTAAGATGTACAAGAGATGAAGTGCA
Found at i:1484344 original size:20 final size:19
Alignment explanation
Indices: 1484266--1484374 Score: 91
Period size: 20 Copynumber: 5.7 Consensus size: 19
1484256 TGCAAGAATG
1484266 TCATGCAAATATATTAATTA
1 TCATGCAAATATA-TAATTA
* **
1484286 TCATAC-AATA-ATAACAA
1 TCATGCAAATATATAATTA
*
1484303 TCATGTAAATATATAA-TA
1 TCATGCAAATATATAATTA
*
1484321 TCATGCAAATACATTAATTA
1 TCATGCAAATATA-TAATTA
*
1484341 TCATGC-AATATTATAAAATA
1 TCATGCAAATA-TAT-AATTA
*
1484361 CCATGCAAATATAT
1 TCATGCAAATATAT
1484375 TAATAACCAT
Statistics
Matches: 71, Mismatches: 11, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
17 8 0.11
18 17 0.24
19 16 0.23
20 26 0.37
21 4 0.06
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.34
Consensus pattern (19 bp):
TCATGCAAATATATAATTA
Found at i:1484384 original size:20 final size:20
Alignment explanation
Indices: 1484266--1484380 Score: 93
Period size: 18 Copynumber: 6.0 Consensus size: 20
1484256 TGCAAGAATG
*
1484266 TCATGCAAATATATTAATTA
1 TCATGCAAATATATTAATAA
* *
1484286 TCATAC-AATA-A-TAACAA
1 TCATGCAAATATATTAATAA
*
1484303 TCATGTAAATATA-TAAT-A
1 TCATGCAAATATATTAATAA
* *
1484321 TCATGCAAATACATTAATTA
1 TCATGCAAATATATTAATAA
1484341 TCATGC-AATAT-TATAA-AA
1 TCATGCAAATATAT-TAATAA
1484359 TACCATGCAAATATATTAATAA
1 T--CATGCAAATATATTAATAA
1484381 CCATTCATGC
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
17 8 0.11
18 20 0.27
19 19 0.25
20 17 0.23
21 8 0.11
22 3 0.04
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (20 bp):
TCATGCAAATATATTAATAA
Found at i:1484547 original size:25 final size:24
Alignment explanation
Indices: 1484503--1484550 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
1484493 TATCATTCAA
*
1484503 ATATAATATTAATCATGCAATAAC
1 ATATAATATCAATCATGCAATAAC
1484527 ATATAATATCATATCATGCAATAA
1 ATATAATATCA-ATCATGCAATAA
1484551 AAATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
ATATAATATCAATCATGCAATAAC
Found at i:1484559 original size:25 final size:24
Alignment explanation
Indices: 1484501--1484556 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
1484491 AATATCATTC
*
1484501 AAATATAATATTAATCATGCAATA
1 AAATATAATATCAATCATGCAATA
*
1484525 ACATATAATATCATATCATGCAATA
1 AAATATAATATCA-ATCATGCAATA
1484550 AAA-ATAA
1 AAATATAA
1484557 ATAAATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATATAATATCAATCATGCAATA
Found at i:1484706 original size:56 final size:56
Alignment explanation
Indices: 1484558--1484787 Score: 183
Period size: 56 Copynumber: 4.2 Consensus size: 56
1484548 TAAAAATAAA
* * * * * *
1484558 TAAATAAATAAAT-ATGCAAATAAATATATTAATAATCATACAATCATACAAAT--AAA
1 TAAATATAT-AATCATGCAAAAAAAAATATTAATAATCATGCAATTA-AC-AATGCAAT
** *
1484614 TAAAT-TAATAATCATGC--AATTAAATA-T-ATAATCATGCCATTAACAATGCAAT
1 TAAATAT-ATAATCATGCAAAAAAAAATATTAATAATCATGCAATTAACAATGCAAT
* *
1484666 TAAATATATAATTATGCAAAAAAAAATATTAATAATCATGCAATTAGAC-ATGCTAT
1 TAAATATATAATCATGCAAAAAAAAATATTAATAATCATGCAATTA-ACAATGCAAT
* * * * * *
1484722 CAAATATATAATCATGCAAATAATAATATTCATAATCATGTAAATAA-ACATGCAAT
1 TAAATATATAATCATGCAAAAAAAAATATTAATAATCATGCAATTAACA-ATGCAAT
1484778 TAAATATATA
1 TAAATATATA
1484788 TAAACCATGC
Statistics
Matches: 139, Mismatches: 23, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
50 3 0.02
51 2 0.01
52 28 0.20
53 2 0.01
54 12 0.09
55 5 0.04
56 85 0.61
57 2 0.01
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.31
Consensus pattern (56 bp):
TAAATATATAATCATGCAAAAAAAAATATTAATAATCATGCAATTAACAATGCAAT
Found at i:1484798 original size:23 final size:22
Alignment explanation
Indices: 1484765--1484807 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1484755 AATCATGTAA
*
1484765 ATAAACATGCAATTAAATATAT
1 ATAAACATGCAAATAAATATAT
1484787 ATAAACCATGCAAATAAATAT
1 ATAAA-CATGCAAATAAATAT
1484808 GCAATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.28
Consensus pattern (22 bp):
ATAAACATGCAAATAAATATAT
Found at i:1484829 original size:20 final size:22
Alignment explanation
Indices: 1484800--1484855 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1484790 AACCATGCAA
*
1484800 ATAAAT-ATGCAATTA-AATAT
1 ATAAATAATGCAATAATAATAT
*
1484820 AT-AATCATGCAAATAATAATAT
1 ATAAATAATGC-AATAATAATAT
1484842 ATAAATAATGCAAT
1 ATAAATAATGCAAT
1484856 CATGTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.10
20 6 0.20
21 4 0.13
22 10 0.33
23 7 0.23
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.32
Consensus pattern (22 bp):
ATAAATAATGCAATAATAATAT
Found at i:1484849 original size:14 final size:14
Alignment explanation
Indices: 1484830--1484877 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
1484820 ATAATCATGC
1484830 AAATAATAATATAT
1 AAATAATAATATAT
*
1484844 AAATAATGCAATCATGT
1 AAATAAT--AAT-ATAT
1484861 AAATAATAATATAT
1 AAATAATAATATAT
1484875 AAA
1 AAA
1484878 CCATGCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 13 0.45
15 3 0.10
16 3 0.10
17 10 0.34
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (14 bp):
AAATAATAATATAT
Found at i:1484865 original size:17 final size:15
Alignment explanation
Indices: 1484813--1484870 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 15
1484803 AATATGCAAT
1484813 TAAATATATAATCATG
1 TAAATA-ATAATCATG
* *
1484829 CAAATAATAAT-ATA
1 TAAATAATAATCATG
1484843 TAAATAATGCAATCATG
1 TAAATAAT--AATCATG
1484860 TAAATAATAAT
1 TAAATAATAAT
1484871 ATATAAACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 9 0.26
15 8 0.23
16 8 0.23
17 10 0.29
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (15 bp):
TAAATAATAATCATG
Found at i:1484884 original size:31 final size:31
Alignment explanation
Indices: 1484822--1484885 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1484812 TTAAATATAT
*
1484822 AATCATGCAAATAATAATATATAAATAATGC
1 AATCATGCAAATAATAATATATAAACAATGC
* *
1484853 AATCATGTAAATAATAATATATAAACCATGC
1 AATCATGCAAATAATAATATATAAACAATGC
1484884 AA
1 AA
1484886 AATATGCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (31 bp):
AATCATGCAAATAATAATATATAAACAATGC
Found at i:1485901 original size:36 final size:37
Alignment explanation
Indices: 1485764--1485942 Score: 181
Period size: 38 Copynumber: 4.9 Consensus size: 37
1485754 TTGAAACTTT
* *
1485764 AAATAAAAGTACTCCTCCACTGAGGCTTCAACTTTGAGA
1 AAAT-AAAGAACTCCTCCACTAAGGCTTCAACTTTGA-A
*
1485803 AAAT----AACTCCACCA-TCAAGGCTTCAACTTTGAA
1 AAATAAAGAACTCCTCCACT-AAGGCTTCAACTTTGAA
** * *
1485836 AAATAAAGAACTCCTAAACCAAGGGTTCAAC-TTGAA
1 AAATAAAGAACTCCTCCACTAAGGCTTCAACTTTGAA
* *
1485872 AAGTAAAGAACTCCTCCACTAAAGCTTCAACTTTGAAA
1 AAATAAAGAACTCCTCCACTAAGGCTTCAACTTTG-AA
* *
1485910 AAATAAAAAACTCCTCCACTGAGGCTTCAACTT
1 AAATAAAGAACTCCTCCACTAAGGCTTCAACTT
1485943 GGAACTTTTG
Statistics
Matches: 114, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
33 6 0.05
34 23 0.20
36 30 0.26
37 20 0.18
38 31 0.27
39 4 0.04
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (37 bp):
AAATAAAGAACTCCTCCACTAAGGCTTCAACTTTGAA
Found at i:1486152 original size:41 final size:43
Alignment explanation
Indices: 1485945--1486215 Score: 299
Period size: 42 Copynumber: 6.5 Consensus size: 43
1485935 TTCAACTTGG
* * *
1485945 AACTTTTGAAAAATAAAATGCTCCCCCACAATTGAAGCTTTGA
1 AACTTTTGAAAAATAAAATGCTCCCTCACAACTGAGGCTTTGA
* * *
1485988 AACTTTTG-AAAATAAAATTC-CCCCCTACAACTGAGGCTTTGG
1 AACTTTTGAAAAATAAAATGCTCCCTC-ACAACTGAGGCTTTGA
* * *
1486030 AACTTTTG-AAAATAAAATACTCCCTTACAATTGAGGCTTT-A
1 AACTTTTGAAAAATAAAATGCTCCCTCACAACTGAGGCTTTGA
* * * * *
1486071 GAACTTTTCAAAAATAAAATGCT-GCTCATAATTAAGGCTTTGA
1 -AACTTTTGAAAAATAAAATGCTCCCTCACAACTGAGGCTTTGA
* *
1486114 AAC-TTTGAAAAA-AAAATGCTCCCTCACAACTAAAGCTTTGA
1 AACTTTTGAAAAATAAAATGCTCCCTCACAACTGAGGCTTTGA
* *
1486155 AACTTTCGAAAAATAAAATGC-CCC-CCCAACTGAGGCTTTGA
1 AACTTTTGAAAAATAAAATGCTCCCTCACAACTGAGGCTTTGA
1486196 AACTTTTGAAAAATAAAATG
1 AACTTTTGAAAAATAAAATG
1486216 AGATCATTAT
Statistics
Matches: 195, Mismatches: 25, Indels: 18
0.82 0.11 0.08
Matches are distributed among these distances:
40 8 0.04
41 65 0.33
42 91 0.47
43 31 0.16
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (43 bp):
AACTTTTGAAAAATAAAATGCTCCCTCACAACTGAGGCTTTGA
Found at i:1487691 original size:15 final size:15
Alignment explanation
Indices: 1487671--1487700 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1487661 TATAATTTAA
1487671 GTTTTAATTTTTTTT
1 GTTTTAATTTTTTTT
*
1487686 GTTTTACTTTTTTTT
1 GTTTTAATTTTTTTT
1487701 TGCTTTTCTT
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:0.10, C:0.03, G:0.07, T:0.80
Consensus pattern (15 bp):
GTTTTAATTTTTTTT
Found at i:1491584 original size:26 final size:26
Alignment explanation
Indices: 1491543--1491592 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1491533 GTACTAACAA
1491543 TTATATTTCTTGAAAGGCT-ATTTTAT
1 TTATATTTCTTGAAA-GCTAATTTTAT
* *
1491569 TTATATTTGTTTAAAGCTAATTTT
1 TTATATTTCTTGAAAGCTAATTTT
1491593 TAAAAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.28, C:0.06, G:0.10, T:0.56
Consensus pattern (26 bp):
TTATATTTCTTGAAAGCTAATTTTAT
Found at i:1491852 original size:18 final size:17
Alignment explanation
Indices: 1491818--1491861 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1491808 TTAAAATCTC
*
1491818 ATTTTATTTTTTTTATT
1 ATTTTATTTTTTATATT
1491835 ATTTTATATTTTTATATT
1 ATTTTAT-TTTTTATATT
*
1491853 -TGTTATTTT
1 ATTTTATTTT
1491862 AACAAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 12 0.50
18 9 0.38
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (17 bp):
ATTTTATTTTTTATATT
Done.