Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, 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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 6 of 131
Found at i:1244852 original size:21 final size:22
Alignment explanation
Indices: 1244811--1244852 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1244801 TGCTTTAAAA
*
1244811 TTGATTTAAAAAAATATTACAG
1 TTGATTTAAAAAAATAATACAG
1244833 TTGATTTAAAAAAA-AATACA
1 TTGATTTAAAAAAATAATACA
1244853 TAATGGAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (22 bp):
TTGATTTAAAAAAATAATACAG
Found at i:1257940 original size:4 final size:4
Alignment explanation
Indices: 1257931--1257973 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
1257921 CATAACAAGT
* * * *
1257931 ATAC ATAC ATAC ATAC AAAC AAAC ATAT ATAC ATAT ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1257974 TATATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1257968 original size:2 final size:2
Alignment explanation
Indices: 1257955--1257989 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1257945 ACAAACAAAC
* *
1257955 AT AT AT AC AT AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1257990 ATCATGGGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1258678 original size:84 final size:84
Alignment explanation
Indices: 1258537--1258708 Score: 256
Period size: 84 Copynumber: 2.0 Consensus size: 84
1258527 AAGCGAAAGC
** *
1258537 ATACCAGTTCCTGTTGCAGCTGCAGTGTTTTCCGAACTGCTGCATCTCTTTCATCCTTCAGAGG-
1 ATACCAGTTCCTGTTGCAGCCACAGTGTTTGCCGAACTGCTGCATCTCTTTCATCCTTCAG-GGA
*
1258601 TTGCACAGCCTGATTCATGA
65 GTGCACAGCCTGATTCATGA
* * * *
1258621 ATACCAGTTCTTGTTGGAGCCACATTGTTTGCTGAACTGCTGCATCTCTTTCATCCTTCAGGGAG
1 ATACCAGTTCCTGTTGCAGCCACAGTGTTTGCCGAACTGCTGCATCTCTTTCATCCTTCAGGGAG
1258686 TGCACAGCCTGATTCATGA
66 TGCACAGCCTGATTCATGA
1258705 ATAC
1 ATAC
1258709 AGAAAGGAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
83 2 0.03
84 77 0.97
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.33
Consensus pattern (84 bp):
ATACCAGTTCCTGTTGCAGCCACAGTGTTTGCCGAACTGCTGCATCTCTTTCATCCTTCAGGGAG
TGCACAGCCTGATTCATGA
Found at i:1263144 original size:23 final size:23
Alignment explanation
Indices: 1263110--1263164 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1263100 CTGGGCTGGA
*
1263110 AAAGAACCAAAGAATGATAGCAC
1 AAAGAACGAAAGAATGATAGCAC
1263133 AAAGAACGAAAGAATGATAGCAC
1 AAAGAACGAAAGAATGATAGCAC
1263156 AAAGAACGA
1 AAAGAACGA
1263165 GAAGGAGAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.58, C:0.15, G:0.20, T:0.07
Consensus pattern (23 bp):
AAAGAACGAAAGAATGATAGCAC
Found at i:1263666 original size:11 final size:10
Alignment explanation
Indices: 1263623--1263674 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
1263613 TAAGTGTTTT
* *
1263623 TTTATTTAAT
1 TTTAATTAAA
1263633 TTTAATTAAA
1 TTTAATTAAA
*
1263643 TATATATTAAA
1 TTTA-ATTAAA
1263654 TTTAGATTAAA
1 TTTA-ATTAAA
*
1263665 TTTAAATAAA
1 TTTAATTAAA
1263675 AAATAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 16 0.46
11 19 0.54
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (10 bp):
TTTAATTAAA
Found at i:1263800 original size:33 final size:35
Alignment explanation
Indices: 1263752--1263816 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
1263742 ATAAAATAAA
*
1263752 ATTAATAATTTTATATTAAAAT-TTATTTAAATAT
1 ATTAATAATTTTATATTAAAATAATATTTAAATAT
1263786 ATTAA-AATTTTATATTAAAATAATATTTAAA
1 ATTAATAATTTTATATTAAAATAATATTTAAA
1263817 AATAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 16 0.55
34 13 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATTAATAATTTTATATTAAAATAATATTTAAATAT
Found at i:1263801 original size:13 final size:13
Alignment explanation
Indices: 1263752--1263806 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 13
1263742 ATAAAATAAA
1263752 ATTAATAATTTTAT
1 ATTAA-AATTTTAT
1263766 ATTAAAA-TTTAT
1 ATTAAAATTTTAT
1263778 -TT-AAA---TAT
1 ATTAAAATTTTAT
1263786 ATTAAAATTTTAT
1 ATTAAAATTTTAT
1263799 ATTAAAAT
1 ATTAAAAT
1263807 AATATTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
8 3 0.08
9 2 0.06
10 6 0.17
11 2 0.06
12 5 0.14
13 13 0.36
14 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTAAAATTTTAT
Found at i:1267537 original size:22 final size:22
Alignment explanation
Indices: 1267512--1267581 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
1267502 ATTTAATTTG
* *
1267512 AATAAAATTCATATTCAATTCA
1 AATAAAATTCAAATTCAACTCA
1267534 AATAAAATTCAAATTCAACTCA
1 AATAAAATTCAAATTCAACTCA
* **
1267556 ATTATTA-TCAAA-TCAAACTCA
1 AATAAAATTCAAATTC-AACTCA
1267577 AATAA
1 AATAA
1267582 CTCAATTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 2 0.05
21 14 0.35
22 24 0.60
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAAAATTCAAATTCAACTCA
Found at i:1267578 original size:32 final size:30
Alignment explanation
Indices: 1267531--1267591 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 30
1267521 CATATTCAAT
*
1267531 TCAAATAAAATTCAAATTCAACTCAATTATTA
1 TCAAATAAAACTCAAA-T-AACTCAATTATTA
*
1267563 TCAAATCAAACTCAAATAACTCAATTATT
1 TCAAATAAAACTCAAATAACTCAATTATT
1267592 TATAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 12 0.44
31 1 0.04
32 14 0.52
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (30 bp):
TCAAATAAAACTCAAATAACTCAATTATTA
Found at i:1267855 original size:14 final size:14
Alignment explanation
Indices: 1267821--1267860 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1267811 ATTAAAATTT
1267821 TATCAAA-TTCAAA
1 TATCAAATTTCAAA
1267834 T-T-AAATTTCAAA
1 TATCAAATTTCAAA
*
1267846 TATCAAATTTTAAA
1 TATCAAATTTCAAA
1267860 T
1 T
1267861 CGATCTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
11 3 0.13
12 8 0.35
13 2 0.09
14 10 0.43
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (14 bp):
TATCAAATTTCAAA
Found at i:1267894 original size:22 final size:22
Alignment explanation
Indices: 1267868--1267916 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1267858 AATCGATCTC
1267868 AAACTTATTATTGTATTCACTT
1 AAACTTATTATTGTATTCACTT
1267890 AAACTTATTATTGTATTCACTT
1 AAACTTATTATTGTATTCACTT
1267912 AAACT
1 AAACT
1267917 AGATCAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (22 bp):
AAACTTATTATTGTATTCACTT
Found at i:1267943 original size:15 final size:15
Alignment explanation
Indices: 1267923--1267954 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1267913 AACTAGATCA
*
1267923 ATTTTATCTCTATTC
1 ATTTTACCTCTATTC
1267938 ATTTTACCTCTATTC
1 ATTTTACCTCTATTC
1267953 AT
1 AT
1267955 CACCTCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTACCTCTATTC
Found at i:1268008 original size:38 final size:38
Alignment explanation
Indices: 1267947--1268024 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 38
1267937 CATTTTACCT
* * * *
1267947 CTATTCATCACCTCAAGGAGGCCTGGCAAAACACCACC
1 CTATTCACCACCACAAGGAGGCCTAGCAAAAAACCACC
* * *
1267985 CTATTCACCACCACAGGGCGGCCTAGTAAAAAACCACC
1 CTATTCACCACCACAAGGAGGCCTAGCAAAAAACCACC
1268023 CT
1 CT
1268025 GAAGCCTCCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.32, C:0.37, G:0.15, T:0.15
Consensus pattern (38 bp):
CTATTCACCACCACAAGGAGGCCTAGCAAAAAACCACC
Found at i:1272394 original size:24 final size:24
Alignment explanation
Indices: 1272348--1272394 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1272338 AAATTTTAAA
* *
1272348 TTAAATTATTTTTATATCTTATTT
1 TTAAATTATATTTATATCGTATTT
* *
1272372 TTAATTTATATTTATGTCGTATT
1 TTAAATTATATTTATATCGTATT
1272395 ATCATATCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (24 bp):
TTAAATTATATTTATATCGTATTT
Found at i:1279447 original size:19 final size:21
Alignment explanation
Indices: 1279423--1279463 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
1279413 TTTATATCAT
1279423 ATTATCATA-TT-ATTTTAAA
1 ATTATCATATTTAATTTTAAA
1279442 ATTATCATATTTAATTTTAAA
1 ATTATCATATTTAATTTTAAA
1279463 A
1 A
1279464 AAATTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTATCATATTTAATTTTAAA
Found at i:1280186 original size:23 final size:24
Alignment explanation
Indices: 1280143--1280192 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
1280133 AACAGAGTGA
*
1280143 ATATTTATTATTTTTTAAATATTT
1 ATATTTATAATTTTTTAAATATTT
1280167 ATATTTA-AATTTATTT-AATATTT
1 ATATTTATAATTT-TTTAAATATTT
1280190 ATA
1 ATA
1280193 ATATTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATTTATAATTTTTTAAATATTT
Found at i:1280197 original size:16 final size:15
Alignment explanation
Indices: 1280156--1280200 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
1280146 TTTATTATTT
1280156 TTTAAATATTT-ATA
1 TTTAAATATTTAATA
1280170 TTTAAATTTATTTAATA
1 TTTAAA--TATTTAATA
1280187 TTTATAATATTTAA
1 TTTA-AATATTTAA
1280201 ATTCGTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.22
16 12 0.44
17 7 0.26
18 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATATTTAATA
Found at i:1291394 original size:22 final size:23
Alignment explanation
Indices: 1291352--1291395 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1291342 TGCATTTCAC
* *
1291352 TTATAATTATTTTTATTATAATT
1 TTATAATTAGTTTAATTATAATT
1291375 TTATAATT-GTTTAATTATAAT
1 TTATAATTAGTTTAATTATAAT
1291396 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATAATTAGTTTAATTATAATT
Found at i:1292008 original size:25 final size:26
Alignment explanation
Indices: 1291979--1292042 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 26
1291969 AATTTTAAAT
1291979 TATATAAATTATA-TAT-TTTTTATA
1 TATATAAATTATATTATCTTTTTATA
* *
1292003 TCATATTTATATTATATTATCTTATTATA
1 T-ATA--TAAATTATATTATCTTTTTATA
1292032 T-TATAAATTAT
1 TATATAAATTAT
1292043 CAAATATTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
24 1 0.03
25 10 0.31
27 10 0.31
28 3 0.09
29 8 0.25
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (26 bp):
TATATAAATTATATTATCTTTTTATA
Found at i:1297385 original size:3 final size:3
Alignment explanation
Indices: 1297377--1297451 Score: 64
Period size: 3 Copynumber: 25.0 Consensus size: 3
1297367 CCAAGAAAGA
*
1297377 AAT AAT AAT AAT AA- AAT AAAT AAT GAT AAT AAT AAT AAT GAAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT AAT
** * * *
1297423 AA- ACG AAA AAA AAT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1297452 TACTATTATA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
2 3 0.05
3 51 0.85
4 6 0.10
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1297392 original size:27 final size:27
Alignment explanation
Indices: 1297369--1297447 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 27
1297359 ATAAAAATCC
1297369 AAGAAAGA-AATAATAATAATAAAATA
1 AAGAAAGATAATAATAATAATAAAATA
* *
1297395 AATAATGATAATAATAATAATGAATAATA
1 AAGAAAGATAATAATAATAAT-AA-AATA
* * *
1297424 AACGAAAAAAAATAATACTAATAA
1 AA-GAAAGATAATAATAATAATAA
1297448 TAATTACTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
26 6 0.14
27 12 0.29
28 2 0.05
29 8 0.19
30 14 0.33
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (27 bp):
AAGAAAGATAATAATAATAATAAAATA
Found at i:1297877 original size:14 final size:15
Alignment explanation
Indices: 1297853--1297885 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1297843 TTATTATATA
1297853 ATAATTTTTTAAAAC
1 ATAATTTTTTAAAAC
*
1297868 ATAA-TTTTTAAAAT
1 ATAATTTTTTAAAAC
1297882 ATAA
1 ATAA
1297886 ATAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTTTTTAAAAC
Found at i:1297896 original size:6 final size:6
Alignment explanation
Indices: 1297875--1297911 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
1297865 AACATAATTT
1297875 TTAAAA -TATAAA -TAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTA-AAA TTAAAA TTAAAA TTAAAA TTAAAA TT
1297912 TATTTATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TTAAAA
Found at i:1297904 original size:17 final size:18
Alignment explanation
Indices: 1297875--1297911 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1297865 AACATAATTT
1297875 TTAAAATATAAA-TAAAA
1 TTAAAATATAAATTAAAA
1297892 TTAAAAT-TAAAATTAAAA
1 TTAAAATAT-AAATTAAAA
1297910 TT
1 TT
1297912 TATTTATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.06
17 10 0.56
18 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAAATATAAATTAAAA
Found at i:1303614 original size:12 final size:12
Alignment explanation
Indices: 1303597--1303621 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1303587 GAGAAAGAGT
1303597 AAAAAAAAATTA
1 AAAAAAAAATTA
1303609 AAAAAAAAATTA
1 AAAAAAAAATTA
1303621 A
1 A
1303622 GATTTTTTTA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:1304132 original size:4 final size:4
Alignment explanation
Indices: 1304123--1304178 Score: 69
Period size: 4 Copynumber: 13.8 Consensus size: 4
1304113 CATAATTGTC
* *
1304123 TATT TATT TATT TATT TATTT TATT TATT TGA-C TATT TATG TATT TATT
1 TATT TATT TATT TATT TA-TT TATT TATT T-ATT TATT TATT TATT TATT
1304172 TATT TAT
1 TATT TAT
1304179 AAATATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 1 0.02
4 39 0.87
5 5 0.11
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:1304592 original size:19 final size:17
Alignment explanation
Indices: 1304558--1304605 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
1304548 AAACTTTATG
1304558 ATTTTTA-AATAAAAATTA
1 ATTTTTATAA-AAAAA-TA
1304576 ATTTTTATAAAAGAAATA
1 ATTTTTATAAAA-AAATA
*
1304594 ATTTTCATAAAA
1 ATTTTTATAAAA
1304606 CCCTAACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTTTTATAAAAAAATA
Found at i:1308646 original size:15 final size:15
Alignment explanation
Indices: 1308626--1308670 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1308616 CACACATTTT
1308626 ATTTTTTTATTTAAA
1 ATTTTTTTATTTAAA
***
1308641 ATTTTTTTATTTTTT
1 ATTTTTTTATTTAAA
1308656 A-TTTTTTATTTAAA
1 ATTTTTTTATTTAAA
1308670 A
1 A
1308671 CTTTGAAGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTTTTATTTAAA
Found at i:1309866 original size:22 final size:19
Alignment explanation
Indices: 1309829--1309877 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
1309819 TTTGTTTTAG
1309829 TTTTTTTTTTGCAAAAATAT
1 TTTTTTTTTTGCAAAAA-AT
* *
1309849 TTTTTTTTTATTCTAAAAACT
1 TTTTTTTTT-TGC-AAAAAAT
1309870 TTTTTTTT
1 TTTTTTTT
1309878 ACCCACCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.36
21 11 0.44
22 5 0.20
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTTTTTTGCAAAAAAT
Found at i:1311101 original size:24 final size:25
Alignment explanation
Indices: 1311074--1311126 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
1311064 AAAAAAGATG
*
1311074 TGAAAA-ATAAAAGAAT-CGAAAAAA
1 TGAAAAGA-AAAAAAATGCGAAAAAA
*
1311098 TGAAAAGAAAAAAAATGTGAAAAAA
1 TGAAAAGAAAAAAAATGCGAAAAAA
1311123 TGAA
1 TGAA
1311127 GCAAAATGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.70, C:0.02, G:0.15, T:0.13
Consensus pattern (25 bp):
TGAAAAGAAAAAAAATGCGAAAAAA
Found at i:1311466 original size:27 final size:24
Alignment explanation
Indices: 1311408--1311475 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 24
1311398 ATCGAAAAAG
*
1311408 AAATAAAAAGAAAAAAATAATGAGA
1 AAATGAAAA-AAAAAAATAATGAGA
1311433 AAATGAAAAATAAAAAA-AATGAGA
1 AAATGAAAAA-AAAAAATAATGAGA
1311457 AAGATGTGAAAAAAAAAAA
1 AA-A--TGAAAAAAAAAAA
1311476 GACTCAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
24 10 0.26
25 15 0.39
26 6 0.16
27 7 0.18
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (24 bp):
AAATGAAAAAAAAAAATAATGAGA
Found at i:1313271 original size:18 final size:19
Alignment explanation
Indices: 1313248--1313499 Score: 115
Period size: 18 Copynumber: 13.9 Consensus size: 19
1313238 AATCTTGAAA
1313248 TTTGTGAATCTTTGAA-CT
1 TTTGTGAATCTTTGAATCT
* * *
1313266 TTTGTGAATTTTTAAAT-A
1 TTTGTGAATCTTTGAATCT
* *
1313284 TTTGTGAATC-TTAAATCA
1 TTTGTGAATCTTTGAATCT
* * *
1313302 CTTATGAATCTTTAAATCT
1 TTTGTGAATCTTTGAATCT
* *
1313321 CTTGTAAATC-TTGAAT-T
1 TTTGTGAATCTTTGAATCT
*
1313338 TTTGTGAATC-TTGAATAT
1 TTTGTGAATCTTTGAATCT
* *
1313356 TTTGTGAATTTTTGAAAATGT
1 TTTGTGAATCTTTG--AATCT
* *
1313377 TTTGTCAATC-TTGAATCA
1 TTTGTGAATCTTTGAATCT
* **
1313395 CTTGCAAATC--TGAAATCT
1 TTTGTGAATCTTTG-AATCT
* **
1313413 CTTGCAAATCTTT-ACA-CT
1 TTTGTGAATCTTTGA-ATCT
*
1313431 TTTGTAAATC-TTGAAT-T
1 TTTGTGAATCTTTGAATCT
*
1313448 TTT-TAAAATC-TTGAATCT
1 TTTGT-GAATCTTTGAATCT
*
1313466 TTTGCGAA-CTTTGAA-CT
1 TTTGTGAATCTTTGAATCT
*
1313483 TTTGTAAATCTTTGAAT
1 TTTGTGAATCTTTGAAT
1313500 TCAATTTATT
Statistics
Matches: 187, Mismatches: 28, Indels: 37
0.74 0.11 0.15
Matches are distributed among these distances:
16 1 0.01
17 50 0.27
18 101 0.54
19 19 0.10
20 4 0.02
21 12 0.06
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (19 bp):
TTTGTGAATCTTTGAATCT
Found at i:1314722 original size:16 final size:16
Alignment explanation
Indices: 1314685--1314723 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1314675 ATTTTATCAT
* *
1314685 ATTATTTATTTATTTG
1 ATTATTTATGTATTTA
*
1314701 ACTATTTATGTATTTA
1 ATTATTTATGTATTTA
1314717 ATTATTT
1 ATTATTT
1314724 GTAAATATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (16 bp):
ATTATTTATGTATTTA
Found at i:1315011 original size:18 final size:18
Alignment explanation
Indices: 1314970--1315011 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1314960 AAACTTTATT
*
1314970 ATTTTTAAATAAAAATTA
1 ATTTTTAAATAAAAAATA
*
1314988 AATTTTAAA-AAATAAATA
1 ATTTTTAAATAAA-AAATA
1315006 ATTTTT
1 ATTTTT
1315012 CATAAAATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTTTAAATAAAAAATA
Found at i:1321059 original size:12 final size:12
Alignment explanation
Indices: 1321042--1321078 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1321032 ATTTTTGTTC
*
1321042 TTTCATTCATGA
1 TTTCATCCATGA
1321054 TTTCATCCATGA
1 TTTCATCCATGA
1321066 TTTCATCCATGA
1 TTTCATCCATGA
1321078 T
1 T
1321079 CCAGCTCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (12 bp):
TTTCATCCATGA
Found at i:1338935 original size:2 final size:2
Alignment explanation
Indices: 1338928--1338966 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1338918 ATGTACTTAG
* * *
1338928 TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1338967 TTTTGTTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1342284 original size:2 final size:2
Alignment explanation
Indices: 1342277--1342305 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1342267 ATCATATTGC
1342277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1342306 CATAGTGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1343793 original size:17 final size:18
Alignment explanation
Indices: 1343771--1343808 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1343761 AATCTCAAGT
1343771 ATCATA-TTT-TTTTAGAA
1 ATCATACTTTCTTTT-GAA
1343788 ATCATACTTTCTTTTGAA
1 ATCATACTTTCTTTTGAA
1343806 ATC
1 ATC
1343809 TATGATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 9 0.47
19 4 0.21
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (18 bp):
ATCATACTTTCTTTTGAA
Found at i:1345866 original size:17 final size:14
Alignment explanation
Indices: 1345839--1345881 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1345829 ATAAAATTAT
*
1345839 TTTTTTAATTTTATA
1 TTTTATAATTTTA-A
1345854 TTTGGTATAATTTTAA
1 TTT--TATAATTTTAA
1345870 TTTTATAATTTT
1 TTTTATAATTTT
1345882 GTATATCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 9 0.36
15 3 0.12
16 4 0.16
17 9 0.36
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
TTTTATAATTTTAA
Found at i:1345867 original size:24 final size:24
Alignment explanation
Indices: 1345841--1345886 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
1345831 AAAATTATTT
1345841 TTTTAATTTTAT-ATTTGGTATAA
1 TTTTAATTTTATAATTTGGTATAA
*
1345864 TTTTAATTTTATAATTTTGTATA
1 TTTTAATTTTATAATTTGGTATA
1345887 TCTTTTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (24 bp):
TTTTAATTTTATAATTTGGTATAA
Found at i:1346042 original size:22 final size:23
Alignment explanation
Indices: 1346007--1346063 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1345997 ATAAAATATT
* *
1346007 TTTTATAAAATAAAATCATAA-AA
1 TTTT-TAAATTAAAATAATAATAA
*
1346030 TTTTTAAATTAAAATAATAATAC
1 TTTTTAAATTAAAATAATAATAA
*
1346053 TTTATAAATTA
1 TTTTTAAATTA
1346064 TATACGATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTTTAAATTAAAATAATAATAA
Found at i:1347831 original size:3 final size:3
Alignment explanation
Indices: 1347825--1347868 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1347815 TAACCTTTTT
1347825 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1347869 TTAGATTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1349730 original size:31 final size:30
Alignment explanation
Indices: 1349673--1349747 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
1349663 ATTTTAAAAA
*
1349673 AATTTATTTAATAATGAAATATTATCATTT
1 AATTTATTTAATAATGAAATATTATCATCT
*
1349703 AATTTATATTATTAAT-AAATTATTATCATCT
1 AATTTAT-TTAATAATGAAA-TATTATCATCT
*
1349734 AATTCA-TTAATAAT
1 AATTTATTTAATAAT
1349748 ATATAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 7 0.18
30 10 0.26
31 22 0.56
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (30 bp):
AATTTATTTAATAATGAAATATTATCATCT
Found at i:1352200 original size:2 final size:2
Alignment explanation
Indices: 1352159--1352187 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1352149 TATGAATCTA
1352159 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1352188 GACAACATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1352334 original size:17 final size:17
Alignment explanation
Indices: 1352308--1352340 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1352298 TTAGATAATT
*
1352308 TTAAATTTATTCAAATA
1 TTAAAATTATTCAAATA
1352325 TTAAAATTATTCAAAT
1 TTAAAATTATTCAAAT
1352341 TATAATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAAATTATTCAAATA
Found at i:1352772 original size:12 final size:12
Alignment explanation
Indices: 1352755--1352779 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1352745 TCCATTTTAA
1352755 AATTTAAAAATT
1 AATTTAAAAATT
1352767 AATTTAAAAATT
1 AATTTAAAAATT
1352779 A
1 A
1352780 TCTATCTAAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATTTAAAAATT
Found at i:1354474 original size:3 final size:3
Alignment explanation
Indices: 1354466--1354493 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1354456 AGAAAAAGGG
1354466 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1354494 GCTTCCTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1360485 original size:15 final size:16
Alignment explanation
Indices: 1360455--1360488 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1360445 GTCTTATTTC
1360455 TTTTAATATTTAATAT
1 TTTTAATATTTAATAT
*
1360471 TTTTATTATTT-ATAT
1 TTTTAATATTTAATAT
1360486 TTT
1 TTT
1360489 AAAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAATATTTAATAT
Found at i:1360575 original size:29 final size:29
Alignment explanation
Indices: 1360516--1360577 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1360506 TTGTTTTACT
***
1360516 TTTTAATATTAAAAATCATAAAATTTTAA
1 TTTTAATATTAAAAATCATAAAATCAAAA
*
1360545 TTTTAATATTAAATAT-ATTAAAATCAAAA
1 TTTTAATATTAAAAATCA-TAAAATCAAAA
1360574 TTTT
1 TTTT
1360578 TTAAAATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTTAATATTAAAAATCATAAAATCAAAA
Found at i:1361828 original size:21 final size:21
Alignment explanation
Indices: 1361804--1361843 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1361794 TAATTAATAA
1361804 AATC-TTAAATATTTTATTTCG
1 AATCATTAAATA-TTTATTTCG
1361825 AATCATTAAATATTTATTT
1 AATCATTAAATATTTATTT
1361844 TTACCTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
AATCATTAAATATTTATTTCG
Found at i:1365970 original size:21 final size:21
Alignment explanation
Indices: 1365946--1365995 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1365936 GTTTTGGGGA
1365946 AAATTTTGAAAAATTTTCTTC
1 AAATTTTGAAAAATTTTCTTC
1365967 AAATTTTGAAAAATTTTCTTC
1 AAATTTTGAAAAATTTTCTTC
1365988 AAATTTTG
1 AAATTTTG
1365996 GGCATGAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (21 bp):
AAATTTTGAAAAATTTTCTTC
Found at i:1367437 original size:24 final size:25
Alignment explanation
Indices: 1367386--1367439 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
1367376 CCCTTGCTTA
* * **
1367386 TTATTGTAAAAAAATTTTCATTTTT
1 TTATTGTAAAAAAAATATCATTCAT
1367411 TTATTG-AAAAAAAATATCATTCAT
1 TTATTGTAAAAAAAATATCATTCAT
1367435 TTATT
1 TTATT
1367440 ATTTTGTCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (25 bp):
TTATTGTAAAAAAAATATCATTCAT
Found at i:1369888 original size:10 final size:10
Alignment explanation
Indices: 1369875--1369901 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1369865 GTGTGTGTGC
1369875 GCGCGTGCGT
1 GCGCGTGCGT
1369885 GCGCGTGCGT
1 GCGCGTGCGT
1369895 GCGCGTG
1 GCGCGTG
1369902 TCTGTAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.52, T:0.19
Consensus pattern (10 bp):
GCGCGTGCGT
Found at i:1374599 original size:21 final size:22
Alignment explanation
Indices: 1374562--1374612 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
1374552 TATAAAAATA
*
1374562 TAAAATATATATTTAATT-TTAT
1 TAAAAT-TATATATAATTATTAT
1374584 TAAAATTATATATAATTATTAT
1 TAAAATTATATATAATTATTAT
1374606 TAAAATT
1 TAAAATT
1374613 TTAATTCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAAATTATATATAATTATTAT
Found at i:1374647 original size:24 final size:23
Alignment explanation
Indices: 1374620--1374680 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1374610 ATTTTAATTC
* *
1374620 ATATTATTTTTATATTTATTTTTT
1 ATATTATTTTTAT-GTTATTTTAT
**
1374644 ATATTAAATTTATGTTATTTTAT
1 ATATTATTTTTATGTTATTTTAT
1374667 AGTATTATATTTTA
1 A-TATTAT-TTTTA
1374681 AATTATTAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 9 0.31
24 16 0.55
25 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (23 bp):
ATATTATTTTTATGTTATTTTAT
Found at i:1376875 original size:181 final size:181
Alignment explanation
Indices: 1376566--1377102 Score: 835
Period size: 181 Copynumber: 3.0 Consensus size: 181
1376556 ACCTAATTTA
* ** * * * **
1376566 CTTTCTGTTTGGTTCCCGAGAACATGTCCGAAAAGAATGAAGCCAATGTTTGGGCTTTGGCGTCT
1 CTTTATGTTTGGTTCCCGAGAACATGTGGGAAAAGAACGAAGCTAAAGTTTGGAATTTGGCGTCT
* * * * *
1376631 TGTTGTTAATTAGTTTGAAAAGCTATTGTTTAAAATAATCCCTTGTAAT-AACATTTGTTTTACT
66 TGTTGTTAATTGGTTTGAAAAGATATTGTTTAAAATAATCTCTTAT-ATCAACATGTGTTTTACT
*
1376695 GTTTGTTTCTCACGAAAATGTAGGAAGAAATCCAATTTTCTGTTTGTTGTTT
130 GTTTGTTTCTCACGAAAATGTAGGAAGAAATCCAATTTTCTGTTTGGTGTTT
*
1376747 CTTTATGTTTGGTTCCCGAGAACATGTGGGAAAAGAACGAAGCTAAAGTTTGGAATTTGGGGTCT
1 CTTTATGTTTGGTTCCCGAGAACATGTGGGAAAAGAACGAAGCTAAAGTTTGGAATTTGGCGTCT
*
1376812 TGTTGTTAATTGGTTTGAAAAGATATTGTTTACAATAATCTCTTATATCAACATGTGTTTTACTG
66 TGTTGTTAATTGGTTTGAAAAGATATTGTTTAAAATAATCTCTTATATCAACATGTGTTTTACTG
*
1376877 TTTGTTTCTCACGAAAATGTAGGAGGAAATCCAATTTTCTGTTTGGTGTTT
131 TTTGTTTCTCACGAAAATGTAGGAAGAAATCCAATTTTCTGTTTGGTGTTT
* *
1376928 C-TTATTGTTTGGTTCCCGAGAACATGTGGGAAAAGAACGGAGCTAAAGTTTGGATTTTGGCGTC
1 CTTTA-TGTTTGGTTCCCGAGAACATGTGGGAAAAGAACGAAGCTAAAGTTTGGAATTTGGCGTC
*
1376992 TTGTTGTTAATTGGTTTGAAAAGATATTGTTTAAAATAATCTCTTATAACAACATGTGTTTTACT
65 TTGTTGTTAATTGGTTTGAAAAGATATTGTTTAAAATAATCTCTTATATCAACATGTGTTTTACT
* * *
1377057 GTTGGTTTCTCACAAAAATGTAGGAAGAAATCCAATTTTTTGTTTG
130 GTTTGTTTCTCACGAAAATGTAGGAAGAAATCCAATTTTCTGTTTG
1377103 ATGTCTTAAA
Statistics
Matches: 328, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
180 5 0.02
181 323 0.98
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (181 bp):
CTTTATGTTTGGTTCCCGAGAACATGTGGGAAAAGAACGAAGCTAAAGTTTGGAATTTGGCGTCT
TGTTGTTAATTGGTTTGAAAAGATATTGTTTAAAATAATCTCTTATATCAACATGTGTTTTACTG
TTTGTTTCTCACGAAAATGTAGGAAGAAATCCAATTTTCTGTTTGGTGTTT
Found at i:1384468 original size:13 final size:13
Alignment explanation
Indices: 1384450--1384475 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1384440 GCCAACTGCC
1384450 AATAATACGAAGG
1 AATAATACGAAGG
1384463 AATAATACGAAGG
1 AATAATACGAAGG
1384476 CTAATTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (13 bp):
AATAATACGAAGG
Found at i:1385877 original size:3 final size:3
Alignment explanation
Indices: 1385869--1385894 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1385859 ACGATCTATG
1385869 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1385895 ATTTAGATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1386799 original size:28 final size:30
Alignment explanation
Indices: 1386745--1386801 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
1386735 TTTATAATTT
* *
1386745 TATTTAAATAAATTGTTGTATTTTTTATTG
1 TATTAAAATAAATTGTTGTATTCTTTATTG
*
1386775 TATTAAAATAGATT-TT-TATTCTTTATT
1 TATTAAAATAAATTGTTGTATTCTTTATT
1386802 TTACATCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.42
29 2 0.08
30 12 0.50
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.60
Consensus pattern (30 bp):
TATTAAAATAAATTGTTGTATTCTTTATTG
Found at i:1391105 original size:11 final size:11
Alignment explanation
Indices: 1391089--1391119 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1391079 ATAACTGCCT
1391089 CTCTAGTCTGG
1 CTCTAGTCTGG
1391100 CTCTAGTCTGG
1 CTCTAGTCTGG
*
1391111 CTCTTGTCT
1 CTCTAGTCT
1391120 ATCAAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.06, C:0.29, G:0.23, T:0.42
Consensus pattern (11 bp):
CTCTAGTCTGG
Found at i:1392337 original size:9 final size:9
Alignment explanation
Indices: 1392323--1392382 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
1392313 AATATAAATT
1392323 TTTTATTAA
1 TTTTATTAA
1392332 TTTTATTAA
1 TTTTATTAA
1392341 --TTA-TAA
1 TTTTATTAA
* *
1392347 TTATAATAA
1 TTTTATTAA
1392356 TTTTTATT-A
1 -TTTTATTAA
*
1392365 TTTTTTTAA
1 TTTTATTAA
1392374 TTTTATTAA
1 TTTTATTAA
1392383 AATTAATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 8 0.20
9 22 0.54
10 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTATTAA
Found at i:1392390 original size:33 final size:34
Alignment explanation
Indices: 1392297--1392391 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 34
1392287 GCTCATCTTA
1392297 TTATTAATTA-AATTTAAATATAAATTTTTTATTAATT
1 TTATTAATTATAA-TTAAA-AT-AA-TTTTTATTAATT
*
1392334 TTATTAATTATAATTATAATAATTTTTATT-ATT
1 TTATTAATTATAATTAAAATAATTTTTATTAATT
* *
1392367 TTTTTAATT-TTATTAAAATTAATTT
1 TTATTAATTATAATTAAAA-TAATTT
1392392 AATCATCCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
32 7 0.13
33 17 0.33
34 8 0.15
35 2 0.04
36 2 0.04
37 14 0.27
38 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TTATTAATTATAATTAAAATAATTTTTATTAATT
Found at i:1401598 original size:20 final size:20
Alignment explanation
Indices: 1401569--1401614 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1401559 GGTCTTGGTA
*
1401569 AACTTAATATATAGTTGTCT
1 AACTTTATATATAGTTGTCT
1401589 AACTTTATATATAGTTGTCT
1 AACTTTATATATAGTTGTCT
*
1401609 GACTTT
1 AACTTT
1401615 TCTTAACTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (20 bp):
AACTTTATATATAGTTGTCT
Found at i:1401880 original size:22 final size:23
Alignment explanation
Indices: 1401823--1401890 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 23
1401813 ATTAAAAAAT
* *
1401823 AATTTAAATTAATTTAATTTTAA
1 AATTTAAAATAATTTAAATTTAA
* *
1401846 AATTTTAAA-AATTTAAATTTAG
1 AATTTAAAATAATTTAAATTTAA
*
1401868 AA-TTAAAATAA-TTCAATTTAA
1 AATTTAAAATAATTTAAATTTAA
1401889 AA
1 AA
1401891 CTATTCAATC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.41
22 15 0.41
23 7 0.19
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (23 bp):
AATTTAAAATAATTTAAATTTAA
Found at i:1406255 original size:18 final size:18
Alignment explanation
Indices: 1406232--1406272 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1406222 ATTGTTGTTG
1406232 TATATTCTATTATATGAT
1 TATATTCTATTATATGAT
1406250 TATATTCTATTATATGAT
1 TATATTCTATTATATGAT
*
1406268 AATAT
1 TATAT
1406273 ATGAACATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
TATATTCTATTATATGAT
Found at i:1422453 original size:49 final size:49
Alignment explanation
Indices: 1422377--1422473 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
1422367 CTCGCCCTTT
* *
1422377 AAATTTTCAAATTTTGTTGAATAGTTCTGCAGTCTTGATGTATTGCAAA
1 AAATTTTCAAATTTTCTTGAATAGTTCTACAGTCTTGATGTATTGCAAA
* *
1422426 AAATTTTCAAATTTTCTTGAATGGTTCTACAGTCTTTATGTATTGCAA
1 AAATTTTCAAATTTTCTTGAATAGTTCTACAGTCTTGATGTATTGCAA
1422474 TTGGTTGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.44
Consensus pattern (49 bp):
AAATTTTCAAATTTTCTTGAATAGTTCTACAGTCTTGATGTATTGCAAA
Found at i:1425682 original size:23 final size:25
Alignment explanation
Indices: 1425645--1425706 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 25
1425635 AATCAAATCA
*
1425645 AATTTTATCTATATTTTTTTAATTT
1 AATTTTATCTATATTATTTTAATTT
*
1425670 AATTTT-T-TATATTATTTTAATAT
1 AATTTTATCTATATTATTTTAATTT
*
1425693 -ATTTTA-ATATATTA
1 AATTTTATCTATATTA
1425707 AAATAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 5 0.15
23 21 0.64
24 1 0.03
25 6 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
AATTTTATCTATATTATTTTAATTT
Found at i:1425773 original size:16 final size:16
Alignment explanation
Indices: 1425752--1425783 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1425742 ATAAAAATTT
1425752 AATATATATAAGTTAA
1 AATATATATAAGTTAA
*
1425768 AATATATATAATTTAA
1 AATATATATAAGTTAA
1425784 TTTTTTTATT
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:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATATATATAAGTTAA
Found at i:1428283 original size:5 final size:5
Alignment explanation
Indices: 1428273--1428297 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1428263 CTAAGTTATA
1428273 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
1428298 GCAGATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:1435864 original size:6 final size:6
Alignment explanation
Indices: 1435853--1435880 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1435843 ATTATTCATG
1435853 CTCGAA CTCGAA CTCGAA CTCGAA CTCG
1 CTCGAA CTCGAA CTCGAA CTCGAA CTCG
1435881 GATTCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.18
Consensus pattern (6 bp):
CTCGAA
Found at i:1437371 original size:10 final size:10
Alignment explanation
Indices: 1437358--1437387 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1437348 ATCGAATTTT
1437358 TATATTTTAA
1 TATATTTTAA
1437368 TATATTTTAA
1 TATATTTTAA
1437378 T-TATTTTAA
1 TATATTTTAA
1437387 T
1 T
1437388 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:1437384 original size:9 final size:9
Alignment explanation
Indices: 1437360--1437389 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1437350 CGAATTTTTA
1437360 TATTTTAAT
1 TATTTTAAT
1437369 ATATTTTAAT
1 -TATTTTAAT
1437379 TATTTTAAT
1 TATTTTAAT
1437388 TA
1 TA
1437390 ATAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:1437558 original size:6 final size:6
Alignment explanation
Indices: 1437539--1437585 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
1437529 ATTAAAAAAA
*
1437539 TTAAAT TT-AA- TTAAAT TTAAAA TTAAAT TTAAAAT TTAAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TT-AAAT TTAAA
1437586 ATCGAGTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 2 0.06
5 4 0.11
6 17 0.47
7 13 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:1437564 original size:12 final size:12
Alignment explanation
Indices: 1437535--1437587 Score: 74
Period size: 12 Copynumber: 4.4 Consensus size: 12
1437525 TCAAATTAAA
1437535 AAAATTAAATTT
1 AAAATTAAATTT
1437547 --AATTAAATTT
1 AAAATTAAATTT
1437557 AAAATTAAATTT
1 AAAATTAAATTT
1437569 AAAATTTAAAATTT
1 AAAA-TT-AAATTT
1437583 AAAAT
1 AAAAT
1437588 CGAGTTTGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.27
12 14 0.38
13 3 0.08
14 10 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAATTAAATTT
Found at i:1437573 original size:7 final size:7
Alignment explanation
Indices: 1437551--1437587 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1437541 AAATTTAATT
1437551 AAATTTA
1 AAATTTA
1437558 AAA-TT-
1 AAATTTA
1437563 AAATTTA
1 AAATTTA
1437570 AAATTTA
1 AAATTTA
1437577 AAATTTA
1 AAATTTA
1437584 AAAT
1 AAAT
1437588 CGAGTTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 3 0.11
6 4 0.14
7 21 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:1445874 original size:24 final size:24
Alignment explanation
Indices: 1445824--1445880 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1445814 AAATTGACTT
*
1445824 CTGCAGCTGTTGCAATAGCAGCTG
1 CTGCAGCTGTTGCAATAGCAGCAG
* *
1445848 CTGCTGCTGTTGCAA-AGGCTGCAG
1 CTGCAGCTGTTGCAATA-GCAGCAG
*
1445872 CTGCGGCTG
1 CTGCAGCTG
1445881 CCAATGTTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (24 bp):
CTGCAGCTGTTGCAATAGCAGCAG
Found at i:1463526 original size:22 final size:22
Alignment explanation
Indices: 1463483--1463526 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1463473 TCAAATCAAT
* * *
1463483 AAATTAATAAAATTTAATATAA
1 AAATCAATAAAATGTAAAATAA
*
1463505 AAATCAATAATATGTAAAATAA
1 AAATCAATAAAATGTAAAATAA
1463527 TTATTAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
AAATCAATAAAATGTAAAATAA
Found at i:1465384 original size:101 final size:101
Alignment explanation
Indices: 1465172--1465474 Score: 524
Period size: 101 Copynumber: 3.0 Consensus size: 101
1465162 TTAGCCTATT
* *
1465172 AGGCATAGAAACACTTTTCCTTCAAGGGTGTTTGACAAATACCCACCTTGCATCGGATA---G-G
1 AGGCATAGAAACACTTTTTCTTCAAGGGTGTTTGACAAATACCCACCTTGCATTGGATAGGTGAG
*
1465233 TGAGTCATGCACCCTTAAAAACATGTCTTTCAAATC
66 TGAGTCATGCACCCTTAAAAACGTGTCTTTCAAATC
*
1465269 AGGCATAGAGACACTTTTTCTTCAAGGGTGTTTGACAAATACCCACCTTGCATTGGATAGGTGAG
1 AGGCATAGAAACACTTTTTCTTCAAGGGTGTTTGACAAATACCCACCTTGCATTGGATAGGTGAG
1465334 TGAGTCATGCACCCTTAAAAACGTGTCTTTCAAATC
66 TGAGTCATGCACCCTTAAAAACGTGTCTTTCAAATC
*
1465370 AGGCATAGAAACACTTTTTCTTCAAGGGAGTTTGACAAATACCCACCTTGCATTGGATAGGTGAG
1 AGGCATAGAAACACTTTTTCTTCAAGGGTGTTTGACAAATACCCACCTTGCATTGGATAGGTGAG
*
1465435 TGAGTCATGTACCCTTAAAAACGTGTCTTTCAAATC
66 TGAGTCATGCACCCTTAAAAACGTGTCTTTCAAATC
1465471 AGGC
1 AGGC
1465475 TTATGAGTTA
Statistics
Matches: 195, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
97 56 0.29
100 1 0.01
101 138 0.71
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (101 bp):
AGGCATAGAAACACTTTTTCTTCAAGGGTGTTTGACAAATACCCACCTTGCATTGGATAGGTGAG
TGAGTCATGCACCCTTAAAAACGTGTCTTTCAAATC
Found at i:1470457 original size:33 final size:32
Alignment explanation
Indices: 1470381--1470463 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 32
1470371 ATTTTTTTTC
*
1470381 ATAATTTTTTAAAAATAAATTCTTAAAAAATT
1 ATAATTTTTCAAAAATAAATTCTTAAAAAATT
* *
1470413 ATAATTTTTTTCGAAAATAAATT-TTCAAAAATCAT
1 ATAA--TTTTTCAAAAATAAATTCTTAAAAAAT--T
1470448 ATAATTTTTCAAAAAT
1 ATAATTTTTCAAAAAT
1470464 CCATTTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
32 4 0.09
33 19 0.44
34 15 0.35
35 5 0.12
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (32 bp):
ATAATTTTTCAAAAATAAATTCTTAAAAAATT
Found at i:1471118 original size:55 final size:57
Alignment explanation
Indices: 1471053--1471162 Score: 136
Period size: 55 Copynumber: 2.0 Consensus size: 57
1471043 ATTTAAAATT
* * *
1471053 TTAATAATTATTATATATAAATTTAAT-AAAATTAATATTTTATAT-TTTTATATTGA
1 TTAATAATTATTATACATAAATTTAATAAAAATT-ATAATTTAAATATTTTATATTGA
* * *
1471109 TTAA-AATTATTTTACATAATTTTTATAAAAATTATAATTTAAATATTTTATATT
1 TTAATAATTATTATACATAAATTTAATAAAAATTATAATTTAAATATTTTATATT
1471163 ATATAAATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 27 0.59
56 19 0.41
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (57 bp):
TTAATAATTATTATACATAAATTTAATAAAAATTATAATTTAAATATTTTATATTGA
Found at i:1479956 original size:13 final size:13
Alignment explanation
Indices: 1479938--1479963 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1479928 GTATATAAAT
1479938 GACAAAAAATGCA
1 GACAAAAAATGCA
1479951 GACAAAAAATGCA
1 GACAAAAAATGCA
1479964 CTTGCAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (13 bp):
GACAAAAAATGCA
Found at i:1484396 original size:7 final size:7
Alignment explanation
Indices: 1484374--1484407 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
1484364 AGTTTAATTC
1484374 TATTTATT
1 TATTT-TT
1484382 TA-TTTT
1 TATTTTT
1484388 TATTTTT
1 TATTTTT
1484395 TATTTTT
1 TATTTTT
1484402 TATTTT
1 TATTTT
1484408 AATATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.16
7 19 0.76
8 2 0.08
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TATTTTT
Found at i:1487682 original size:30 final size:31
Alignment explanation
Indices: 1487646--1487704 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
1487636 ATTCAATTAT
1487646 TTTTAAATGA-TAATATTT-AATAAATTTAAA
1 TTTTAAAT-ATTAATATTTAAATAAATTTAAA
1487676 TTTTAAATATTAATATTTACAATAAATTT
1 TTTTAAATATTAATATTTA-AATAAATTT
1487705 TTTATCTTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 1 0.04
30 16 0.62
32 9 0.35
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (31 bp):
TTTTAAATATTAATATTTAAATAAATTTAAA
Found at i:1489609 original size:31 final size:29
Alignment explanation
Indices: 1489551--1489610 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 29
1489541 GGCCTTTAAG
*
1489551 TTTCTCTTGGGCTAGAATTTTATTTTCCT
1 TTTCTCTTGGACTAGAATTTTATTTTCCT
1489580 TTTCTC-TGGACTAGAAGCTTTTAATTTTCCT
1 TTTCTCTTGGACTAGAA--TTTT-ATTTTCCT
1489611 CGTAACTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 9 0.33
29 6 0.22
30 4 0.15
31 8 0.30
ACGTcount: A:0.17, C:0.18, G:0.13, T:0.52
Consensus pattern (29 bp):
TTTCTCTTGGACTAGAATTTTATTTTCCT
Found at i:1492398 original size:182 final size:183
Alignment explanation
Indices: 1492091--1492450 Score: 607
Period size: 182 Copynumber: 2.0 Consensus size: 183
1492081 ACAACATGTG
1492091 GGCTTTAGGCCTTCCGCTGTTTATAAGTCTCGGCTCATCACATCACTTAATTATAGATCCGACTG
1 GGCTTTAGGCCTTCCGCTGTTTATAAGTCTCGGCTCATCACATCACTTAATTATAGATCCGACTG
*
1492156 ACAAGAACTCATTGACGAAGCCAAGCCCAAAACGGGTTTGCGATGATGGCGTTGGATTCACATCA
66 ACAAGAACTCATGGACGAAGCCAAGCCCAAAACGGGTTTGCGATGATGGCGTTGGATTCACATCA
* *
1492221 GTTGCAAGACATAAATCCCACGGTGCATTGCC-TTTTCCAGACAACCGGGCTT
131 GTTGCAAGACATAAATCCCACGGTACATAGCCTTTTTCCAGACAACCGGGCTT
* * * *
1492273 GGCTTTAGGCCTTCGGCTGTTTCTAAGTCTCGGGTCATCATATCACTTAATTATAGATCCGACTG
1 GGCTTTAGGCCTTCCGCTGTTTATAAGTCTCGGCTCATCACATCACTTAATTATAGATCCGACTG
* *
1492338 ACAAGCAA-TCATGGACGAAGCCAAGCCCAAAACGGGTTTGCTATGATGGGGTTGGATTCACATC
66 ACAAG-AACTCATGGACGAAGCCAAGCCCAAAACGGGTTTGCGATGATGGCGTTGGATTCACATC
*
1492402 AGTTGCAAGACATAAATCCCACGGTACATAGCCTTTTTTCAGACAACCG
130 AGTTGCAAGACATAAATCCCACGGTACATAGCCTTTTTCCAGACAACCG
1492451 TGCGCAAATA
Statistics
Matches: 166, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
182 150 0.90
183 16 0.10
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (183 bp):
GGCTTTAGGCCTTCCGCTGTTTATAAGTCTCGGCTCATCACATCACTTAATTATAGATCCGACTG
ACAAGAACTCATGGACGAAGCCAAGCCCAAAACGGGTTTGCGATGATGGCGTTGGATTCACATCA
GTTGCAAGACATAAATCCCACGGTACATAGCCTTTTTCCAGACAACCGGGCTT
Found at i:1496073 original size:148 final size:148
Alignment explanation
Indices: 1495805--1496099 Score: 590
Period size: 148 Copynumber: 2.0 Consensus size: 148
1495795 GATGTGTGGT
1495805 ACTTCTTTCAACAAAGATAGAATCATACAAATAGCTTGACTCAACTTATTATCTCAATTTTGGTG
1 ACTTCTTTCAACAAAGATAGAATCATACAAATAGCTTGACTCAACTTATTATCTCAATTTTGGTG
1495870 CCATGATTTAATAATAAAACTAATATTGTAGCTAAATCTTATTTTCTACATATATTCTCTACTTG
66 CCATGATTTAATAATAAAACTAATATTGTAGCTAAATCTTATTTTCTACATATATTCTCTACTTG
1495935 CATCTAATTTCTCATGGC
131 CATCTAATTTCTCATGGC
1495953 ACTTCTTTCAACAAAGATAGAATCATACAAATAGCTTGACTCAACTTATTATCTCAATTTTGGTG
1 ACTTCTTTCAACAAAGATAGAATCATACAAATAGCTTGACTCAACTTATTATCTCAATTTTGGTG
1496018 CCATGATTTAATAATAAAACTAATATTGTAGCTAAATCTTATTTTCTACATATATTCTCTACTTG
66 CCATGATTTAATAATAAAACTAATATTGTAGCTAAATCTTATTTTCTACATATATTCTCTACTTG
1496083 CATCTAATTTCTCATGG
131 CATCTAATTTCTCATGG
1496100 TAAATTCCTT
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 147 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (148 bp):
ACTTCTTTCAACAAAGATAGAATCATACAAATAGCTTGACTCAACTTATTATCTCAATTTTGGTG
CCATGATTTAATAATAAAACTAATATTGTAGCTAAATCTTATTTTCTACATATATTCTCTACTTG
CATCTAATTTCTCATGGC
Found at i:1499042 original size:30 final size:30
Alignment explanation
Indices: 1499006--1499067 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1498996 TTTTGAACCT
*
1499006 TGAAATCAAGCAAAACACAATCTGCTCACA
1 TGAAATCAAACAAAACACAATCTGCTCACA
1499036 TGAAATCAAACAAAACACAATCTGCTCACA
1 TGAAATCAAACAAAACACAATCTGCTCACA
1499066 TG
1 TG
1499068 CCTCATGCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.47, C:0.26, G:0.10, T:0.18
Consensus pattern (30 bp):
TGAAATCAAACAAAACACAATCTGCTCACA
Found at i:1501303 original size:17 final size:18
Alignment explanation
Indices: 1501278--1501319 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1501268 ATTTTTTTAA
*
1501278 TTATAATTA-TAATAATT
1 TTATCATTATTAATAATT
**
1501295 TTATCATTATTTTTAATT
1 TTATCATTATTAATAATT
1501313 TTATCAT
1 TTATCAT
1501320 CTACCAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATCATTATTAATAATT
Found at i:1502578 original size:15 final size:15
Alignment explanation
Indices: 1502558--1502589 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1502548 ACCTTTCTTC
1502558 AATTTAAATATAATA
1 AATTTAAATATAATA
1502573 AATTTAAATATAATA
1 AATTTAAATATAATA
1502588 AA
1 AA
1502590 ATAATATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTTAAATATAATA
Found at i:1502606 original size:16 final size:15
Alignment explanation
Indices: 1502579--1502627 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1502569 AATAAATTTA
1502579 AATAT-AAT-AAAAT
1 AATATGAATAAAAAT
1502592 AATATGATATAAAAAT
1 AATATGA-ATAAAAAT
*
1502608 AATACGAATAAAAAT
1 AATATGAATAAAAAT
*
1502623 TATAT
1 AATAT
1502628 AATTTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 5 0.17
14 1 0.03
15 13 0.43
16 11 0.37
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (15 bp):
AATATGAATAAAAAT
Found at i:1502621 original size:15 final size:16
Alignment explanation
Indices: 1502587--1502622 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1502577 TAAATATAAT
*
1502587 AAAATAATATGATATA
1 AAAATAATACGATATA
1502603 AAAATAATACGA-ATA
1 AAAATAATACGATATA
1502618 AAAAT
1 AAAAT
1502623 TATATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAATAATACGATATA
Found at i:1504799 original size:25 final size:24
Alignment explanation
Indices: 1504728--1504799 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 24
1504718 TAAAAATAAT
*
1504728 AATTATTATAATTATGATTTAAAAA
1 AATTATTAAAATTAT-ATTTAAAAA
* *
1504753 AATTA-TAAAATTTTTATGTTAAATA
1 AATTATTAAAA-TTATAT-TTAAAAA
1504778 AATTATTAAAATTAATATTTAA
1 AATTATTAAAATT-ATATTTAA
1504800 TTATGATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 6 0.15
25 25 0.64
26 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (24 bp):
AATTATTAAAATTATATTTAAAAA
Found at i:1504835 original size:20 final size:20
Alignment explanation
Indices: 1504812--1504853 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1504802 ATGATGAATT
*
1504812 TAATAGCATCATACTGAAAA
1 TAATACCATCATACTGAAAA
*
1504832 TAATACCGTCATACTGAAAA
1 TAATACCATCATACTGAAAA
1504852 TA
1 TA
1504854 CCGTGTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.26
Consensus pattern (20 bp):
TAATACCATCATACTGAAAA
Found at i:1505061 original size:26 final size:26
Alignment explanation
Indices: 1505032--1505083 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1505022 TTAAAAAAAA
*
1505032 ATTTTAAATAATTTTTTATTTGAATT
1 ATTTTAAATAATATTTTATTTGAATT
* *
1505058 ATTTTAAATTATATTTTATTTTAATT
1 ATTTTAAATAATATTTTATTTGAATT
1505084 TAAAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
ATTTTAAATAATATTTTATTTGAATT
Found at i:1505641 original size:23 final size:21
Alignment explanation
Indices: 1505583--1505643 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1505573 TTGATAATAT
* *
1505583 TAAAAATAATAATTAAAATTAA
1 TAAAAAT-TTAATTATAATTAA
*
1505605 TAAAAATTTTATTATAATTAA
1 TAAAAATTTAATTATAATTAA
*
1505626 TATTTAAATTTAATTATA
1 TA--AAAATTTAATTATA
1505644 CCGTACGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 13 0.41
22 7 0.22
23 12 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAAATTTAATTATAATTAA
Found at i:1514381 original size:2 final size:2
Alignment explanation
Indices: 1514374--1514420 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1514364 TGTTCAGTAT
1514374 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1514416 TC TC T
1 TC TC T
1514421 TTGTTTGGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1516045 original size:6 final size:6
Alignment explanation
Indices: 1516029--1516073 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1516019 GCCGTCTAAG
* * * *
1516029 ATATAT TTATAG ATATAT ATATAT ATATAT AAATAT ATATTT ATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATA
1516074 ATAGAGTCTG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
ATATAT
Found at i:1516050 original size:4 final size:4
Alignment explanation
Indices: 1516029--1516073 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
1516019 GCCGTCTAAG
* * * *
1516029 ATAT ATTT ATAG ATAT ATAT ATAT ATAT ATAA ATAT ATAT TTAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
1516074 ATAGAGTCTG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:1536760 original size:33 final size:32
Alignment explanation
Indices: 1536696--1536764 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
1536686 CTCTTCATTT
1536696 ATTTATATTTTGAAAATCTTTAAAAAATTTTA
1 ATTTATATTTTGAAAATCTTTAAAAAATTTTA
* *
1536728 GATTTATATTTTCTAAAATCTTT-AAAATTTTTA
1 -ATTTATATTTT-GAAAATCTTTAAAAAATTTTA
1536761 ATTT
1 ATTT
1536765 TGTATTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 4 0.12
33 20 0.61
34 9 0.27
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (32 bp):
ATTTATATTTTGAAAATCTTTAAAAAATTTTA
Found at i:1537349 original size:2 final size:2
Alignment explanation
Indices: 1537342--1537366 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1537332 CTCTTCCCCA
1537342 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1537367 AGCCCGTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1537385 original size:2 final size:2
Alignment explanation
Indices: 1537380--1537410 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1537370 CCGTAGCCCG
*
1537380 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1537411 CCATCTCGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1538717 original size:26 final size:26
Alignment explanation
Indices: 1538688--1538739 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1538678 CAATAGACCA
*
1538688 ATATAAACGCATTTTTTAAAAAAACT
1 ATATAAACGCATTTTCTAAAAAAACT
* *
1538714 ATATAGATGCATTTTCTAAAAAAACT
1 ATATAAACGCATTTTCTAAAAAAACT
1538740 GAAATCATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (26 bp):
ATATAAACGCATTTTCTAAAAAAACT
Found at i:1538749 original size:26 final size:26
Alignment explanation
Indices: 1538696--1538750 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1538686 CAATATAAAC
* * *
1538696 GCATTTTTTAAAAAAACTATATAGAT
1 GCATTTTCTAAAAAAACTAAATACAT
1538722 GCATTTTCTAAAAAAACTGAAAT-CAT
1 GCATTTTCTAAAAAAACT-AAATACAT
1538748 GCA
1 GCA
1538751 GGATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (26 bp):
GCATTTTCTAAAAAAACTAAATACAT
Found at i:1538870 original size:16 final size:17
Alignment explanation
Indices: 1538836--1538874 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1538826 TTTCTTTGTC
1538836 TTTTAAAGATTTCACTT
1 TTTTAAAGATTTCACTT
* *
1538853 TTTTAAAGGTTTC-TTT
1 TTTTAAAGATTTCACTT
1538869 TTTTAA
1 TTTTAA
1538875 TTTTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (17 bp):
TTTTAAAGATTTCACTT
Found at i:1540329 original size:21 final size:22
Alignment explanation
Indices: 1540305--1540347 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1540295 AAATAATTAA
*
1540305 TTAAAATATAATTAAA-TAAAT
1 TTAAAATAGAATTAAATTAAAT
*
1540326 TTAATATAGAATTAAATTAAAT
1 TTAAAATAGAATTAAATTAAAT
1540348 CCAAAACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAAATAGAATTAAATTAAAT
Found at i:1540929 original size:15 final size:16
Alignment explanation
Indices: 1540909--1540951 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
1540899 TTAATTAACA
1540909 TAATTGATTAAAA-AT
1 TAATTGATTAAAATAT
1540924 TAATTGATATAAAATAT
1 TAATTGAT-TAAAATAT
1540941 TAATT-ATTAAA
1 TAATTGATTAAA
1540952 CAAAATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.46
16 7 0.27
17 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (16 bp):
TAATTGATTAAAATAT
Found at i:1546479 original size:11 final size:11
Alignment explanation
Indices: 1546463--1546505 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
1546453 ATACGATAAC
1546463 ATAATAAAATA
1 ATAATAAAATA
1546474 ATAATAAAATA
1 ATAATAAAATA
1546485 ATAAATACAAA-A
1 AT-AATA-AAATA
1546497 ATAATAAAA
1 ATAATAAAA
1546506 ATTATAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.10
11 17 0.57
12 7 0.23
13 3 0.10
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (11 bp):
ATAATAAAATA
Found at i:1546491 original size:23 final size:23
Alignment explanation
Indices: 1546465--1546517 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
1546455 ACGATAACAT
1546465 AATAAAATAATAAT-AAAATAATA
1 AATAAAA-AATAATAAAAATAATA
*
1546488 AATACAAAAATAATAAAAATTATA
1 AATA-AAAAATAATAAAAATAATA
1546512 AATAAA
1 AATAAA
1546518 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (23 bp):
AATAAAAAATAATAAAAATAATA
Found at i:1550443 original size:7 final size:7
Alignment explanation
Indices: 1550431--1550459 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1550421 TTAGGCTGAC
1550431 AGTTGAA
1 AGTTGAA
1550438 AGTTGAA
1 AGTTGAA
1550445 AGTTGAA
1 AGTTGAA
1550452 AGTTGAA
1 AGTTGAA
1550459 A
1 A
1550460 AGAGCCCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (7 bp):
AGTTGAA
Found at i:1556023 original size:2 final size:2
Alignment explanation
Indices: 1556016--1556045 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1556006 GCCTAAAACA
1556016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1556046 TTAAGGAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1556495 original size:17 final size:17
Alignment explanation
Indices: 1556473--1556511 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1556463 GAGGGGAGAG
*
1556473 AGAAAGAAGAAAGAAAT
1 AGAAAGAAGAAAAAAAT
1556490 AGAAAGAAGAAAAAAAT
1 AGAAAGAAGAAAAAAAT
1556507 -GAAAG
1 AGAAAG
1556512 TGTGGGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (17 bp):
AGAAAGAAGAAAAAAAT
Found at i:1556949 original size:26 final size:25
Alignment explanation
Indices: 1556908--1556975 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 25
1556898 AAGAATAAAG
*
1556908 AAAAATATACAATAAATAATAATA-AT
1 AAAAATA-AAAATAAATAA-AATAGAT
*
1556934 AATAATGAAAAATAAATAAAATATGAT
1 AAAAAT-AAAAATAAATAAAATA-GAT
1556961 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
1556976 ATCATAAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 4 0.11
26 24 0.67
27 8 0.22
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (25 bp):
AAAAATAAAAATAAATAAAATAGAT
Found at i:1556982 original size:20 final size:20
Alignment explanation
Indices: 1556921--1556982 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
1556911 AATATACAAT
*
1556921 AAATAATAATAATAATAATGAA
1 AAATAAAAATAA-AATAAT-AA
1556943 AAAT--AAATAAAATATGATAA
1 AAATAAAAATAAAATA--ATAA
*
1556963 AAATAAAAATAAAATCATAA
1 AAATAAAAATAAAATAATAA
1556983 GTGGTGATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
19 4 0.12
20 15 0.44
21 2 0.06
22 13 0.38
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (20 bp):
AAATAAAAATAAAATAATAA
Found at i:1559830 original size:172 final size:172
Alignment explanation
Indices: 1559531--1559880 Score: 601
Period size: 172 Copynumber: 2.0 Consensus size: 172
1559521 TATACTCACT
* * *
1559531 AATTTAATCATATCTTGAGCTATATAAATTCAAATTAAAAATCATTTGAAGATTTAAAAACTAGA
1 AATTTAATCATATCTTGAGCTATATAAATCCAAATTAAAAACCATTTGAAGATTAAAAAACTAGA
*
1559596 CTCAAAGGACTTTCTATCCATATAAAATTCATCACCTAATTCATTGTATATGTAGCTTTTAGACA
66 CTCAAAGGACTTTCTATCCATATAAAATTCATCACCTAATTCATTGTATATGTAACTTTTAGACA
*
1559661 ACTGTAAAATGTCTAGTAAAAATTTAAAATATTTTCTTAAAA
131 ACTGTAAAATATCTAGTAAAAATTTAAAATATTTTCTTAAAA
*
1559703 AATTTGATCATATCTTGAGCTATATAAATCCAAATTAAAAACCATTTGAAGATTAAAAAACTAGA
1 AATTTAATCATATCTTGAGCTATATAAATCCAAATTAAAAACCATTTGAAGATTAAAAAACTAGA
* * *
1559768 CTTAAAGGACTTTCTATCCTTATAAAATTCATCACCTAATTCATTGTATATGTAATTTTTAGACA
66 CTCAAAGGACTTTCTATCCATATAAAATTCATCACCTAATTCATTGTATATGTAACTTTTAGACA
* *
1559833 ACTGTAAAATATTTAGTAAAAATTTAAAATATTTTTTTAAAA
131 ACTGTAAAATATCTAGTAAAAATTTAAAATATTTTCTTAAAA
1559875 AATTTA
1 AATTTA
1559881 GATTTTAATT
Statistics
Matches: 166, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
172 166 1.00
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (172 bp):
AATTTAATCATATCTTGAGCTATATAAATCCAAATTAAAAACCATTTGAAGATTAAAAAACTAGA
CTCAAAGGACTTTCTATCCATATAAAATTCATCACCTAATTCATTGTATATGTAACTTTTAGACA
ACTGTAAAATATCTAGTAAAAATTTAAAATATTTTCTTAAAA
Found at i:1561202 original size:16 final size:16
Alignment explanation
Indices: 1561181--1561214 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1561171 ATACGATACG
1561181 ATGATAT-AATATAAAA
1 ATGATATGAATA-AAAA
1561197 ATGATATGAATAAAAA
1 ATGATATGAATAAAAA
1561213 AT
1 AT
1561215 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (16 bp):
ATGATATGAATAAAAA
Found at i:1561236 original size:24 final size:23
Alignment explanation
Indices: 1561188--1561257 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
1561178 ACGATGATAT
*
1561188 AATATAAAAATGATATGAATAAAA
1 AATATAAAAATAATATGAAT-AAA
* *
1561212 AATATAAAAATAATATGATTTAA
1 AATATAAAAATAATATGAATAAA
* *
1561235 AATTTAAAAA-AATCATAAATAAA
1 AATATAAAAATAAT-ATGAATAAA
1561258 TTTAATAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 3 0.08
23 17 0.45
24 18 0.47
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (23 bp):
AATATAAAAATAATATGAATAAA
Found at i:1561275 original size:21 final size:21
Alignment explanation
Indices: 1561234--1561275 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1561224 ATATGATTTA
*
1561234 AAATTTAAAAAAATCATAAAT
1 AAATTTAAAAAAATCAAAAAT
* *
1561255 AAATTTAATAAAATTAAAAAT
1 AAATTTAAAAAAATCAAAAAT
1561276 TATATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATTTAAAAAAATCAAAAAT
Found at i:1561876 original size:20 final size:21
Alignment explanation
Indices: 1561843--1561891 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1561833 CGAAATTAAA
*
1561843 AAAAAATTATTTTTTAAATAT
1 AAAATATTATTTTTTAAATAT
1561864 AAAATATTATTTTTTAAATAT
1 AAAATATTATTTTTTAAATAT
1561885 -AAATATT
1 AAAATATT
1561892 TAAAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATATTATTTTTTAAATAT
Found at i:1561900 original size:16 final size:16
Alignment explanation
Indices: 1561879--1561929 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
1561869 ATTATTTTTT
*
1561879 AAATATAAATATTTAA
1 AAATATAAATATATAA
*
1561895 AAATATAATTATATAA
1 AAATATAAATATATAA
* * *
1561911 ATATATATATAAATAA
1 AAATATAAATATATAA
1561927 AAA
1 AAA
1561930 ATTAAAAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATAAATATATAA
Done.