Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008999.1 Hibiscus syriacus cultivar Beakdansim tig00112380_pilon, 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: 605736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1185 original size:31 final size:31
Alignment explanation
Indices: 1142--1209 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
1132 ACACTTTTTA
*
1142 TCACTTACGTTATCGTTTTATTAAGTTTTGG
1 TCACTTACGTTATCGTTTTATCAAGTTTTGG
*
1173 TCACTTATGTTATCGTTTTATCAAGTTTTGG
1 TCACTTACGTTATCGTTTTATCAAGTTTTGG
1204 TCACTT
1 TCACTT
1210 GGAAATGAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (31 bp):
TCACTTACGTTATCGTTTTATCAAGTTTTGG
Found at i:1417 original size:2 final size:2
Alignment explanation
Indices: 1369--1399 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1359 CGGTTTTTGA
1369 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1400 GTTTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1425 original size:25 final size:26
Alignment explanation
Indices: 1386--1460 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 26
1376 TATATATATA
1386 TATATATATATATAGTTTTTAAAAAC-
1 TATATA-ATATATAGTTTTTAAAAACT
1412 TATATAATATATAG-TTTTAGAAAACT
1 TATATAATATATAGTTTTTA-AAAACT
*
1438 TATATAATATATAGTTTTGAAAA
1 TATATAATATATAGTTTTTAAAA
1461 TATTTTTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
24 5 0.11
25 13 0.29
26 23 0.51
27 4 0.09
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.44
Consensus pattern (26 bp):
TATATAATATATAGTTTTTAAAAACT
Found at i:1485 original size:37 final size:36
Alignment explanation
Indices: 1426--1905 Score: 335
Period size: 36 Copynumber: 13.8 Consensus size: 36
1416 TAATATATAG
* * *
1426 TTTTAGAAAACTTATATAATATATAGTTTTGAAAATA
1 TTTTTGAAAACATATAT-ATATATAGTTTTGAAAACA
*
1463 TTTTTAAAAACATATA-ATATATAGTTTTTGAAAACA
1 TTTTTGAAAACATATATATATATAG-TTTTGAAAACA
* *
1499 -TTTTGAAAAC-T-TATATA-ATA----T--ATA-G
1 TTTTTGAAAACATATATATATATAGTTTTGAAAACA
*
1524 TTTTTGAAAACATATATAATGTATAGTTTTGAAAACA
1 TTTTTGAAAACATATAT-ATATATAGTTTTGAAAACA
* *
1561 TATTTGAAAACTTATATAATATATAGTTTTGAAAACA
1 TTTTTGAAAACATATAT-ATATATAGTTTTGAAAACA
* *
1598 -TTTTGAAATCTTATATAATATATAGTTTTGAAAACA
1 TTTTTGAAAACATATAT-ATATATAGTTTTGAAAACA
*
1634 ----T------ATATA-ATGTATAGTTTTGAAAACA
1 TTTTTGAAAACATATATATATATAGTTTTGAAAACA
* *
1659 TATTTGAAAACTTATATAATATATAG-TTTGAAAACA
1 TTTTTGAAAACATATAT-ATATATAGTTTTGAAAACA
**
1695 TTTTTGAAAACATATA-ATATATAGTTTTGAAATTA
1 TTTTTGAAAACATATATATATATAGTTTTGAAAACA
1730 TTTTTGAAAACATATAATATATATATAGTTTTTGAAAACA
1 TTTTTGAAAAC--AT-ATATATATATAG-TTTTGAAAACA
***
1770 -TTTTGAAAACATATATATAATATATAGTTTTTG-AATTT
1 TTTTTGAAAAC--ATATAT-ATATATAG-TTTTGAAAACA
* * *
1808 TTTTTGAATATATATAT-TATATAGTTTTGAAAATAA
1 TTTTTGAAAACATATATATATATAGTTTTGAAAA-CA
* *
1844 TTTTTG-AAA-ATACATATATATA--TTTGAAAGCAA
1 TTTTTGAAAACATATATATATATAGTTTTGAAAAC-A
* *
1877 TTTCTTGAAAACATAT-TATTTTTAGTTTT
1 TTT-TTGAAAACATATATATATATAGTTTT
1906 TTATATATTA
Statistics
Matches: 360, Mismatches: 40, Indels: 86
0.74 0.08 0.18
Matches are distributed among these distances:
25 18 0.05
26 12 0.03
27 5 0.01
28 4 0.01
29 3 0.01
30 3 0.01
33 17 0.05
34 26 0.07
35 66 0.18
36 79 0.22
37 65 0.18
38 9 0.03
39 44 0.12
40 9 0.03
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (36 bp):
TTTTTGAAAACATATATATATATAGTTTTGAAAACA
Found at i:1518 original size:98 final size:96
Alignment explanation
Indices: 1402--1726 Score: 494
Period size: 98 Copynumber: 3.3 Consensus size: 96
1392 TATATATAGT
* * * * *
1402 TTTTAAAAACTATATAATATATAGTTTTAGAAAACTTATATAATATATAGTTTTGAAAATATTTT
1 TTTTGAAAACTATATAATATATAGTTTT-GAAAACATATATAATGTATAGTTTTGAAAACATATT
*
1467 TAAAAAC-ATATAATATATAGTTTTTGAAAACA
65 TGAAAACTATATAATATATAG-TTTTGAAAACA
1499 TTTTGAAAACTTATATAATATATAGTTTTTGAAAACATATATAATGTATAGTTTTGAAAACATAT
1 TTTTGAAAAC-TATATAATATATAG-TTTTGAAAACATATATAATGTATAGTTTTGAAAACATAT
1564 TTGAAAACTTATATAATATATAGTTTTGAAAACA
64 TTGAAAAC-TATATAATATATAGTTTTGAAAACA
*
1598 TTTTGAAATCTTATATAATATATAGTTTTGAAAACATATATAATGTATAGTTTTGAAAACATATT
1 TTTTGAAAAC-TATATAATATATAGTTTTGAAAACATATATAATGTATAGTTTTGAAAACATATT
1663 TGAAAACTTATATAATATATAG-TTTGAAAACA
65 TGAAAAC-TATATAATATATAGTTTTGAAAACA
1695 TTTTTGAAAAC-ATATAATATATAGTTTTGAAA
1 -TTTTGAAAACTATATAATATATAGTTTTGAAA
1727 TTATTTTTGA
Statistics
Matches: 215, Mismatches: 8, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
96 21 0.10
97 19 0.09
98 123 0.57
99 39 0.18
100 13 0.06
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (96 bp):
TTTTGAAAACTATATAATATATAGTTTTGAAAACATATATAATGTATAGTTTTGAAAACATATTT
GAAAACTATATAATATATAGTTTTGAAAACA
Found at i:1528 original size:26 final size:25
Alignment explanation
Indices: 1499--1661 Score: 120
Period size: 25 Copynumber: 6.6 Consensus size: 25
1489 TTTGAAAACA
*
1499 TTTTGAAAACTTATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
*
1524 TTTTTGAAAACATATATAATGTATAG
1 -TTTTGAAAACATATATAATATATAG
* * *
1550 TTTTGAAAACATATTTGA-A-A-AC
1 TTTTGAAAACATATATAATATATAG
* * * ** * *
1572 TTAT-ATAATATATAGTTTTGA-AAACA
1 TTTTGAAAACATATA-TAAT-ATATA-G
* *
1598 TTTTGAAATCTTATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
*
1623 TTTTGAAAACATATATAATGTATAG
1 TTTTGAAAACATATATAATATATAG
1648 TTTTGAAAACATAT
1 TTTTGAAAACATAT
1662 TTGAAAACTT
Statistics
Matches: 105, Mismatches: 25, Indels: 15
0.72 0.17 0.10
Matches are distributed among these distances:
21 7 0.07
22 5 0.05
23 1 0.01
24 2 0.02
25 54 0.51
26 30 0.29
27 6 0.06
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (25 bp):
TTTTGAAAACATATATAATATATAG
Found at i:1567 original size:63 final size:62
Alignment explanation
Indices: 1474--1598 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 62
1464 TTTTAAAAAC
1474 ATATAATATATAGTTTTTGAAAACATTTTGAAAACTTATATAATATATAGTTTTTGAAAACAT
1 ATATAATATATAGTTTTTGAAAACATTTTGAAAACTTATATAATATATAG-TTTTGAAAACAT
*
1537 ATATAATGTATAG-TTTTGAAAACATATTTGAAAACTTATATAATATATAGTTTTGAAAACAT
1 ATATAATATATAGTTTTTGAAAACAT-TTTGAAAACTTATATAATATATAGTTTTGAAAACAT
1599 TTTGAAATCT
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
62 24 0.40
63 36 0.60
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (62 bp):
ATATAATATATAGTTTTTGAAAACATTTTGAAAACTTATATAATATATAGTTTTGAAAACAT
Found at i:1946 original size:24 final size:23
Alignment explanation
Indices: 1892--1946 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
1882 TGAAAACATA
*
1892 TTATTTTTAGTTTTTTATATATT
1 TTATATTTAGTTTTTTATATATT
*
1915 ATATTATTTAGTTTCATTTATAT-TT
1 TTA-TATTTAGTTT--TTTATATATT
1940 TTATATT
1 TTATATT
1947 AATATATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 2 0.08
24 13 0.50
25 4 0.15
26 7 0.27
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (23 bp):
TTATATTTAGTTTTTTATATATT
Found at i:2429 original size:22 final size:22
Alignment explanation
Indices: 2388--2429 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2378 GCACAACAAA
* *
2388 AACATCAAAATATCAGCAAAAC
1 AACAACAAAATAACAGCAAAAC
*
2410 AACAACAAAATAACATCAAA
1 AACAACAAAATAACAGCAAA
2430 CAAACCCGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.21, G:0.02, T:0.12
Consensus pattern (22 bp):
AACAACAAAATAACAGCAAAAC
Found at i:4620 original size:33 final size:33
Alignment explanation
Indices: 4578--4642 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
4568 TTCCTGAGTA
*
4578 ATGATGTTGCCAAATGAGTTGATCACCTTCATT
1 ATGATGTTGCCAAATGAATTGATCACCTTCATT
* *
4611 ATGATGTTGCCAGATGAATTGATCGCCTTCAT
1 ATGATGTTGCCAAATGAATTGATCACCTTCAT
4643 GGGGGGTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (33 bp):
ATGATGTTGCCAAATGAATTGATCACCTTCATT
Found at i:6009 original size:17 final size:18
Alignment explanation
Indices: 5936--6010 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
5926 TCTACGTCTA
* **
5936 ATAACTGTAAAACATCAA
1 ATAACTGTAAATCATCTG
*
5954 ATAACTGT-AATCATTTG
1 ATAACTGTAAATCATCTG
* *
5971 ATAACTGAAAATCATTTG
1 ATAACTGTAAATCATCTG
5989 ATAACTGTAAAT-ATCTG
1 ATAACTGTAAATCATCTG
6006 ATAAC
1 ATAAC
6011 GGTGAAATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
17 21 0.43
18 28 0.57
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (18 bp):
ATAACTGTAAATCATCTG
Found at i:11793 original size:37 final size:37
Alignment explanation
Indices: 11751--11826 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
11741 CATATCAGAT
*
11751 CAGTAATATCTACATCCTAGTGGCATGTACATATTTC
1 CAGTAATATCGACATCCTAGTGGCATGTACATATTTC
11788 CAGTAATATCGACATCCTAGTGGCATGTACATATTTC
1 CAGTAATATCGACATCCTAGTGGCATGTACATATTTC
11825 CA
1 CA
11827 ACATAAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (37 bp):
CAGTAATATCGACATCCTAGTGGCATGTACATATTTC
Found at i:11931 original size:22 final size:22
Alignment explanation
Indices: 11891--11938 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
11881 CCAATAAATG
*
11891 TAACACTCATAACATGTATATA
1 TAACACTCATAACACGTATATA
* * *
11913 TAACACTCGTAACCCGTATATG
1 TAACACTCATAACACGTATATA
11935 TAAC
1 TAAC
11939 GCCCTTAGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (22 bp):
TAACACTCATAACACGTATATA
Found at i:13076 original size:18 final size:18
Alignment explanation
Indices: 13053--13138 Score: 86
Period size: 18 Copynumber: 4.8 Consensus size: 18
13043 TTAATCTACG
*
13053 TCTGATAACTATAAATTA
1 TCTGATAACTGTAAATTA
* *
13071 TCTGATAACTGAAAATCA
1 TCTGATAACTGTAAATTA
* *
13089 TCTAATAATTGTAAA-TA
1 TCTGATAACTGTAAATTA
*
13106 TATGATAACTGTGAAATT-
1 TCTGATAACTGT-AAATTA
*
13124 TCTGCTAACTGTAAA
1 TCTGATAACTGTAAA
13139 CATTTAGAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
17 13 0.24
18 40 0.74
19 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (18 bp):
TCTGATAACTGTAAATTA
Found at i:13460 original size:2 final size:2
Alignment explanation
Indices: 13453--13493 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
13443 TATTATTCTG
13453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13494 TGAAAACTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14003 original size:35 final size:35
Alignment explanation
Indices: 13954--14030 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
13944 CAACATTGGC
* * *
13954 TCATCGCAATACTTAAGTATTTGAAAACTTGTAATT
1 TCATC-CAACACTTAAATATTTGAAAACTTGTAACT
13990 TCATCCAACACTTAAATATTTGAAAACTTGTAACT
1 TCATCCAACACTTAAATATTTGAAAACTTGTAACT
14025 TCATCC
1 TCATCC
14031 TTCATTTTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (35 bp):
TCATCCAACACTTAAATATTTGAAAACTTGTAACT
Found at i:20998 original size:22 final size:21
Alignment explanation
Indices: 20973--21167 Score: 162
Period size: 22 Copynumber: 8.9 Consensus size: 21
20963 ACTTTTTTTT
*
20973 AAACTATGCTATATATTTTCAA
1 AAACTAT-ATATATATTTTCAA
20995 AAACAATATATTATATATGTTTTCAA
1 AAAC--TATA-TATATA--TTTTCAA
* *
21021 AAACTATATCATATGTTTT-TA
1 AAACTATAT-ATATATTTTCAA
21042 AAACTATACTATATATTTTCAA
1 AAACTATA-TATATATTTTCAA
* **
21064 AAACTATATATTATGTTTTTTA
1 AAACTATATA-TATATTTTCAA
*
21086 AAACTATATAATATGTTTTCAA
1 AAACTATAT-ATATATTTTCAA
* *
21108 AAACTATATCATATGTTTTTAA
1 AAACTATAT-ATATATTTTCAA
*
21130 ATACTATACTATATATTTT-AA
1 AAACTATA-TATATATTTTCAA
*
21151 AAACCATATAT-TATTTT
1 AAACTATATATATATTTT
21168 TTTGATAAAA
Statistics
Matches: 146, Mismatches: 16, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
19 6 0.04
20 3 0.02
21 27 0.18
22 79 0.54
23 3 0.02
24 17 0.12
26 11 0.08
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (21 bp):
AAACTATATATATATTTTCAA
Found at i:21105 original size:44 final size:43
Alignment explanation
Indices: 21008--21159 Score: 220
Period size: 44 Copynumber: 3.5 Consensus size: 43
20998 CAATATATTA
*
21008 TATATGTTTTCAAAAACTATATCATATGTTTTTAAAACTATAC
1 TATATATTTTCAAAAACTATATCATATGTTTTTAAAACTATAC
21051 TATATATTTTCAAAAACTATAT-ATTATGTTTTTTAAAACTATA-
1 TATATATTTTCAAAAACTATATCA-TATG-TTTTTAAAACTATAC
*
21094 TAATATGTTTTCAAAAACTATATCATATGTTTTTAAATACTATAC
1 T-ATATATTTTCAAAAACTATATCATATGTTTTTAAA-ACTATAC
*
21139 TATATATTTT-AAAAACCATAT
1 TATATATTTTCAAAAACTATAT
21160 ATTATTTTTT
Statistics
Matches: 99, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
42 1 0.01
43 44 0.44
44 52 0.53
45 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (43 bp):
TATATATTTTCAAAAACTATATCATATGTTTTTAAAACTATAC
Found at i:21112 original size:87 final size:88
Alignment explanation
Indices: 21009--21184 Score: 302
Period size: 87 Copynumber: 2.0 Consensus size: 88
20999 AATATATTAT
*
21009 ATATGTTTTCAAAAACTATATCATATGTTTTTAAA-ACTATACTATATATTTTCAAAAACTATAT
1 ATATGTTTTCAAAAACTATATCATATGTTTTTAAATACTATACTATATATTTT-AAAAACCATAT
21073 ATTATGTTTTT-TAAAACTATATA
65 ATTATGTTTTTATAAAACTATATA
21096 ATATGTTTTCAAAAACTATATCATATGTTTTTAAATACTATACTATATATTTTAAAAACCATATA
1 ATATGTTTTCAAAAACTATATCATATGTTTTTAAATACTATACTATATATTTTAAAAACCATATA
*
21161 TTATTTTTTTGATAAAACTATATA
66 TTATGTTTTT-ATAAAACTATATA
21185 TTATATGATA
Statistics
Matches: 84, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
87 55 0.65
88 17 0.20
89 12 0.14
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.46
Consensus pattern (88 bp):
ATATGTTTTCAAAAACTATATCATATGTTTTTAAATACTATACTATATATTTTAAAAACCATATA
TTATGTTTTTATAAAACTATATA
Found at i:26144 original size:44 final size:44
Alignment explanation
Indices: 26030--26424 Score: 435
Period size: 44 Copynumber: 8.9 Consensus size: 44
26020 AAATGAATGA
* * *
26030 ATAAATAAAAAGGCATAAC-ATTGCATTATTGGCAGAAAAGGTGCC
1 ATAAATGAAAATGCATAACGA-TGCATTATTGGCAG-AAAGGTGTC
* *
26075 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGG-GCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAG-AAAGGTGTC
* * * *
26119 AAAAATGAAAATTCATAACGATGCATTATTGGAAGAAAGATGTC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGTC
* * * ** * *
26163 ATAAATGAAAATGCATAATGTTACAACATTGGCAAAAAGGTTTC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGTC
26207 ATAAATGAAAATGCATAAC-AGTGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGA-TGCATTATTGGCAGAAAGGTGTC
26251 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGTC
* *
26295 ATAAATGAAAATGCATAATTG-TGCATTAATT-GCAGAAAGGTGCC
1 ATAAATGAAAATGCATAA-CGATGCATT-ATTGGCAGAAAGGTGTC
* * *
26339 ATAAATGAAAATGCATAACGGTGCATTATTGGCATAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGTC
*
26383 ACT-AATGACAATTAAATGCATAACGATGCATT-TTGGAAGAAA
1 A-TAAATG---A--AAATGCATAACGATGCATTATTGGCAGAAA
26425 TGTGCCACTC
Statistics
Matches: 302, Mismatches: 34, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
43 8 0.03
44 224 0.74
45 43 0.14
47 1 0.00
48 8 0.03
49 18 0.06
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.25
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGTC
Found at i:26223 original size:132 final size:132
Alignment explanation
Indices: 26057--26424 Score: 494
Period size: 132 Copynumber: 2.8 Consensus size: 132
26047 ACATTGCATT
26057 ATTGGCAGAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGG-GCCAA
1 ATTGGCA-AAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAG-AAAGGTGCCAA
*
26121 AAATGAAAATTCATAACGATGCATTATTGGAAGAAAGATGTCATAAATGAAAATGCATAA-TGTT
64 AAATGAAAATGCATAACGATGCATTATTGGAAGAAAGATGTCATAAATGAAAATGCATAATTG-T
26185 ACA-A
128 ACATA
** * * *
26189 CATTGGCAAAAAGGTTTCATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGTCATA
1 -ATTGGCAAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCAAA
* * *
26254 AATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAATTGTGC
65 AATGAAAATGCATAACGATGCATTATTGGAAGAAAGATGTCATAAATGAAAATGCATAATTGTAC
26319 ATTA
130 A-TA
* * **
26323 ATT-GCAGAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCATAAAGGTGCCACTA
1 ATTGGCAAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCAAAA
26387 ATGACAATTAAATGCATAACGATGCATT-TTGGAAGAAA
66 ATG---A--AAATGCATAACGATGCATTATTGGAAGAAA
26425 TGTGCCACTC
Statistics
Matches: 208, Mismatches: 18, Indels: 15
0.86 0.07 0.06
Matches are distributed among these distances:
131 5 0.02
132 161 0.77
133 12 0.06
134 1 0.00
135 1 0.00
136 9 0.04
137 19 0.09
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (132 bp):
ATTGGCAAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCAAAA
ATGAAAATGCATAACGATGCATTATTGGAAGAAAGATGTCATAAATGAAAATGCATAATTGTACA
TA
Found at i:31647 original size:21 final size:21
Alignment explanation
Indices: 31621--31660 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31611 CAGAACCCCA
*
31621 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
31642 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
31661 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:31689 original size:20 final size:21
Alignment explanation
Indices: 31643--31703 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
31633 TTCCCCTGTG
31643 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
31666 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
31686 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
31704 TGCACTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:37960 original size:45 final size:46
Alignment explanation
Indices: 37904--38025 Score: 169
Period size: 45 Copynumber: 2.7 Consensus size: 46
37894 TATAAAATTT
* *
37904 CTTATCATTTA-TCCTAGAAGCTCGTAAGCTTATTCTACCAATATA
1 CTTACCATTTACTCCTATAAGCTCGTAAGCTTATTCTACCAATATA
* * *
37949 CTTTCCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTACTCCTATAAGCTCGTAAGCTTATTCTACCAATATA
*
37994 CTTACCATTTACTCCT-TAAGCTTGTAAGCTTA
1 CTTACCATTTACTCCTATAAGCTCGTAAGCTTA
38026 GTTTCATGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
45 65 0.96
46 3 0.04
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (46 bp):
CTTACCATTTACTCCTATAAGCTCGTAAGCTTATTCTACCAATATA
Found at i:44670 original size:44 final size:44
Alignment explanation
Indices: 44620--44939 Score: 378
Period size: 44 Copynumber: 7.3 Consensus size: 44
44610 AATAAAAAAA
* * * *
44620 ATAAATGAAAATACATAACATTGCTTTATTGGAAGAAAAGTGTC
1 ATAAATGAAAATGCATAACAGTGCATTATTGGAAGAAAGGTGTC
** * *
44664 ATAAATGAAAATGCATAATGGTGCATTGTTGGACGAAAGGTGTC
1 ATAAATGAAAATGCATAACAGTGCATTATTGGAAGAAAGGTGTC
* * *
44708 ATAAATGAAATTGCATAACAGTGCATTATT-GACAGAAATGAGTC
1 ATAAATGAAAATGCATAACAGTGCATTATTGGA-AGAAAGGTGTC
* *
44752 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACAGTGCATTATTGGAAGAAAGGTGTC
* *
44796 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACAGTGCATTATTGGAAGAAAGGTGTC
* * *
44840 ATAAATGAAAATGCATAAC-GATGCATTAATT-GCAGAAATGTGCC
1 ATAAATGAAAATGCATAACAG-TGCATT-ATTGGAAGAAAGGTGTC
* * * *
44884 ATAAATGAAAATGCATAACGGTGCATTATTGGCATAAAGGTGCC
1 ATAAATGAAAATGCATAACAGTGCATTATTGGAAGAAAGGTGTC
44928 ACT-AATGAAAAT
1 A-TAAATGAAAAT
44940 TAAATGCATA
Statistics
Matches: 245, Mismatches: 24, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
43 6 0.02
44 233 0.95
45 6 0.02
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.26
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACAGTGCATTATTGGAAGAAAGGTGTC
Found at i:44857 original size:132 final size:132
Alignment explanation
Indices: 44620--44939 Score: 459
Period size: 132 Copynumber: 2.4 Consensus size: 132
44610 AATAAAAAAA
* ** * * * *
44620 ATAAATGAAAATACATAACATTGCTTTATTGGAAGAAAAGTGTCATAAATGAAAATGCATAATGG
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAACGG
* *
44685 TGCATTGTTGGACGAAAGGTGTCATAAATGAAATTGCATAAC-AGTGCATT-ATTGACAGAAATG
66 TGCATTATTGGACGAAAGGTGTCATAAATGAAAATGCATAACGA-TGCATTAATTG-CAGAAATG
*
44748 AGTC
129 AGCC
44752 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAACGG
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAACGG
*
44817 TGCATTATTGG-CAGAAAGGTGTCATAAATGAAAATGCATAACGATGCATTAATTGCAGAAATGT
66 TGCATTATTGGAC-GAAAGGTGTCATAAATGAAAATGCATAACGATGCATTAATTGCAGAAATGA
44881 GCC
130 GCC
* *
44884 ATAAATGAAAATGCATAACGGTGCATTATTGGCATAAAGGTGCCACT-AATGAAAAT
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTCA-TAAATGAAAAT
44940 TAAATGCATA
Statistics
Matches: 171, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
131 1 0.01
132 164 0.96
133 6 0.04
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.26
Consensus pattern (132 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAACGG
TGCATTATTGGACGAAAGGTGTCATAAATGAAAATGCATAACGATGCATTAATTGCAGAAATGAG
CC
Found at i:44916 original size:88 final size:87
Alignment explanation
Indices: 44620--44939 Score: 426
Period size: 88 Copynumber: 3.6 Consensus size: 87
44610 AATAAAAAAA
* * * * * *
44620 ATAAATGAAAATACATAACATTGCTTTATTGGAAGAAAAGTGTCATAAATGAAAATGCATAATGG
1 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAACGG
* *
44685 TGCATTGTTGGACGAAAGGTGTC
66 TGCATTATTGCA-GAAAGGTGTC
* * * *
44708 ATAAATGAAATTGCATAACAGTGCATTATTGACAGAAATGAGTCATAAATGAAAATGCATAACGG
1 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAACGG
44773 TGCATTATTGGCAGAAAGGTGTC
66 TGCATTATT-GCAGAAAGGTGTC
* *
44796 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAACGA
1 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAACGG
* *
44861 TGCATTAATTGCAGAAATGTGCC
66 TGCATT-ATTGCAGAAAGGTGTC
* * *
44884 ATAAATGAAAATGCATAACGGTGCATTATTGGCATAAAGGTGCCACT-AATGAAAAT
1 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGTCA-TAAATGAAAAT
44940 TAAATGCATA
Statistics
Matches: 208, Mismatches: 21, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
88 202 0.97
89 6 0.03
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.26
Consensus pattern (87 bp):
ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAACGG
TGCATTATTGCAGAAAGGTGTC
Found at i:49255 original size:12 final size:12
Alignment explanation
Indices: 49238--49268 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
49228 AATGCTTCTT
49238 TTCCCTCCTTAG
1 TTCCCTCCTTAG
49250 TTCCCTCCTTAG
1 TTCCCTCCTTAG
49262 TTCCCTC
1 TTCCCTC
49269 ACATCTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.45, G:0.06, T:0.42
Consensus pattern (12 bp):
TTCCCTCCTTAG
Found at i:50558 original size:21 final size:22
Alignment explanation
Indices: 50528--50587 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
50518 TATATTATAT
50528 ATATATATATATTTTCTAAAA-A
1 ATATA-ATATATTTTCTAAAATA
* *
50550 ATATAATATATATTTTTAAAATC
1 ATATAATATAT-TTTCTAAAATA
*
50573 ATATAATATGTTTTC
1 ATATAATATATTTTC
50588 AAGTATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 6 0.19
22 16 0.50
23 10 0.31
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATAATATATTTTCTAAAATA
Found at i:50558 original size:23 final size:23
Alignment explanation
Indices: 50526--50581 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
50516 TATATATTAT
50526 ATATATATATATATTTTCTAAAA-A
1 ATATA-ATATATATTTT-TAAAATA
*
50550 ATATAATATATATTTTTAAAATC
1 ATATAATATATATTTTTAAAATA
50573 ATATAATAT
1 ATATAATAT
50582 GTTTTCAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.17
23 20 0.67
24 5 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATAATATATATTTTTAAAATA
Found at i:50648 original size:21 final size:21
Alignment explanation
Indices: 50547--50648 Score: 72
Period size: 21 Copynumber: 5.0 Consensus size: 21
50537 TATTTTCTAA
*
50547 AAAATATAAT-ATATATTTTT
1 AAAATATAATAATATGTTTTT
*
50567 AAAATCAT-ATAATATGTTTTC
1 AAAAT-ATAATAATATGTTTTT
* * *
50588 AAGTATATATTACGTAT-TTTTT
1 AA-AATATAATA-ATATGTTTTT
* *
50610 --CA-ATAATTATATGTTTTT
1 AAAATATAATAATATGTTTTT
50628 AAAATATAATAATATGTTTTT
1 AAAATATAATAATATGTTTTT
50649 TTTAAATTAT
Statistics
Matches: 61, Mismatches: 12, Indels: 17
0.68 0.13 0.19
Matches are distributed among these distances:
17 3 0.05
18 9 0.15
19 1 0.02
20 8 0.13
21 29 0.48
22 8 0.13
23 3 0.05
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (21 bp):
AAAATATAATAATATGTTTTT
Found at i:50717 original size:17 final size:17
Alignment explanation
Indices: 50660--50719 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
50650 TTAAATTATG
50660 CTATATATTTTC-AAAA
1 CTATATATTTTCAAAAA
* * * *
50676 CCATATGTTTTTGAAATA
1 CTATAT-ATTTTCAAAAA
50694 -TACTATATTTTCAAAAA
1 CTA-TATATTTTCAAAAA
50711 CTATATATT
1 CTATATATT
50720 AGTGTTGTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 7
0.68 0.17 0.15
Matches are distributed among these distances:
16 5 0.16
17 19 0.59
18 8 0.25
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (17 bp):
CTATATATTTTCAAAAA
Found at i:50805 original size:22 final size:20
Alignment explanation
Indices: 50763--50813 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
50753 AAACTATGCC
**
50763 ATATGATTTTAAAAATTATATT
1 ATAT-ATTTTAAAAACCATA-T
50785 ATATATTTTCAAAAACCATAT
1 ATATATTTT-AAAAACCATAT
50806 AT-TATTTT
1 ATATATTTT
50814 TTTTTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 6 0.23
21 8 0.31
22 12 0.46
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (20 bp):
ATATATTTTAAAAACCATAT
Found at i:51745 original size:55 final size:55
Alignment explanation
Indices: 51627--52104 Score: 676
Period size: 55 Copynumber: 8.7 Consensus size: 55
51617 CTACCAATAT
* * * * *
51627 GGAAATTTATACACTTGGTATGAATTTCCT-AGTTTTTGCACATATAA-TGCCCATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAG--TTTACACATA-AAGTGCCCATAC
** *
51683 AAAAATTCATCCACTTAGTATGAATTTCTTAAATTTACACATAAAGTGCCCATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC
* * *
51738 GGAAATTCATCCACTTAGTCTGAATTCCTTAAGTTTACACATATAA-CGCCCATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATA-AAGTGCCCATAC
* *
51793 GAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACAGAAAGTGCCCATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC
* * *
51848 GTAAATTCATCCACTTAGTATGAATTTCTTAATTTTTACACATATAGTGCCCATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAA-GTTTACACATAAAGTGCCCATAC
* *
51904 GGAAATTCATCCACTTAGTATGAATTTCTTAATTTTACACCTAAAGTGCCCATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC
*
51959 GAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAA-TGCCCATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATA-AAGTGCCCATAC
* *
52014 GGAAATTCATCCACTTAGTAGGAATTTCTTAAGTTTACACATATAGTGCCCATAC
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC
*
52069 GGAAATTCATCCACTTGGTATGAATTTCTTAAGTTT
1 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
52105 TTGCACACTT
Statistics
Matches: 381, Mismatches: 34, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
54 5 0.01
55 296 0.78
56 79 0.21
57 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (55 bp):
GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC
Found at i:52027 original size:221 final size:221
Alignment explanation
Indices: 51627--52120 Score: 783
Period size: 221 Copynumber: 2.2 Consensus size: 221
51617 CTACCAATAT
* * * * *
51627 GGAAATTTATACACTTGGTATGAATTTCCTAGTTTTTGCACATATAATGCCCATACAAAAATTCA
1 GGAAATTCATCCACTTGGTATGAATTTCTTAATTTTTGCACATATAGTGCCCATACAAAAATTCA
*
51692 TCCACTTAGTATGAATTTCTTAAATTTACACATAAAGTGCCCATACGGAAATTCATCCACTTAGT
66 TCCACTTAGTATGAATTTCTTAAATTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAGT
* *
51757 CTGAATTCCTTAAGTTTACACATATAACGCCCATACGAAAATTCATCCACTTAGTATGAATTTCT
131 ATGAATTCCTTAAGTTTACACATATAACGCCCATACGAAAATTCATCCACTTAGTAGGAATTTCT
51822 TAAGTTTACACAGAAAGTGCCCATAC
196 TAAGTTTACACAGAAAGTGCCCATAC
* * * **
51848 GTAAATTCATCCACTTAGTATGAATTTCTTAATTTTTACACATATAGTGCCCATACGGAAATTCA
1 GGAAATTCATCCACTTGGTATGAATTTCTTAATTTTTGCACATATAGTGCCCATACAAAAATTCA
* *
51913 TCCACTTAGTATGAATTTCTTAATTTTACACCTAAAGTGCCCATACGAAAATTCATCCACTTAGT
66 TCCACTTAGTATGAATTTCTTAAATTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAGT
* * *
51978 ATGAATTTCTTAAGTTTACACATATAATGCCCATACGGAAATTCATCCACTTAGTAGGAATTTCT
131 ATGAATTCCTTAAGTTTACACATATAACGCCCATACGAAAATTCATCCACTTAGTAGGAATTTCT
* *
52043 TAAGTTTACACATATAGTGCCCATAC
196 TAAGTTTACACAGAAAGTGCCCATAC
52069 GGAAATTCATCCACTTGGTATGAATTTCTTAAGTTTTTGCACACT-TAGTGCC
1 GGAAATTCATCCACTTGGTATGAATTTCTTAA-TTTTTGCACA-TATAGTGCC
52121 ATTTGGTAAT
Statistics
Matches: 248, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
221 231 0.93
222 16 0.06
223 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (221 bp):
GGAAATTCATCCACTTGGTATGAATTTCTTAATTTTTGCACATATAGTGCCCATACAAAAATTCA
TCCACTTAGTATGAATTTCTTAAATTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAGT
ATGAATTCCTTAAGTTTACACATATAACGCCCATACGAAAATTCATCCACTTAGTAGGAATTTCT
TAAGTTTACACAGAAAGTGCCCATAC
Found at i:52486 original size:22 final size:19
Alignment explanation
Indices: 52460--52514 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 19
52450 TACCCCTACC
52460 ATGGTATCGATACTACCATACT
1 ATGGTATCGATAC--CCA-ACT
*
52482 ATGGTACCGATACCCAACT
1 ATGGTATCGATACCCAACT
52501 ATGGTATCGATACC
1 ATGGTATCGATACC
52515 ATTTTTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 16 0.52
20 3 0.10
22 12 0.39
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (19 bp):
ATGGTATCGATACCCAACT
Found at i:52501 original size:19 final size:20
Alignment explanation
Indices: 52443--52514 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 20
52433 TTGCTCCTCA
* * *
52443 GTATTGATACCCCTACCATG
1 GTATCGATACCCATACTATG
52463 GTATCGATACTACCATACTATG
1 GTATCGATAC--CCATACTATG
*
52485 GTACCGATACCCA-ACTATG
1 GTATCGATACCCATACTATG
52504 GTATCGATACC
1 GTATCGATACC
52515 ATTTTTTCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.36
20 12 0.27
22 17 0.38
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCATACTATG
Found at i:58618 original size:55 final size:55
Alignment explanation
Indices: 58511--58983 Score: 671
Period size: 55 Copynumber: 8.5 Consensus size: 55
58501 AAATTTATAT
* * * * **
58511 ACTTAGTATGAATTTCGTAGTTTTTTACCCATATAGTGCCCATATAGAAATTCATCC
1 ACTTAGTATGAATTTCTTA--ATTTTACACATAAAGTGCCCATACGGAAATTCATCC
* *
58568 ACTTAGTATGAATTTCTTAAATTTACACATAAAGTGCCCATACGGAAATTCAACC
1 ACTTAGTATGAATTTCTTAATTTTACACATAAAGTGCCCATACGGAAATTCATCC
* ** * * *
58623 ACTTAGTATGAATTCCTTAGGTTTACACATATAGTGCTCATACAGAAATTCATCC
1 ACTTAGTATGAATTTCTTAATTTTACACATAAAGTGCCCATACGGAAATTCATCC
58678 ACTTAGTATGAATTTCTTAATTTTACACATAAAGTGCCCATACGGAAATTCATCC
1 ACTTAGTATGAATTTCTTAATTTTACACATAAAGTGCCCATACGGAAATTCATCC
*
58733 ACTTAGTATGAATTTCTTAATTTTTACACATATAGTGCCCATACGGAAATT-ATCC
1 ACTTAGTATGAATTTCTTAA-TTTTACACATAAAGTGCCCATACGGAAATTCATCC
* * *
58788 ACTTAGTATGAATTTCTTAATTTTACACATAAAATGCCCATACAGAAATCCATCC
1 ACTTAGTATGAATTTCTTAATTTTACACATAAAGTGCCCATACGGAAATTCATCC
* * *
58843 ACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCTATACGGAAATTCATCC
1 ACTTAGTATGAATTTCTTAATTTTACACATAAAGTGCCCATACGGAAATTCATCC
* *
58898 ACTTAGTATGAATTTCTTAAGTTTACATATATAA-TGCCCATACGGAAATTCATCC
1 ACTTAGTATGAATTTCTTAATTTTACACATA-AAGTGCCCATACGGAAATTCATCC
58953 ACTTAGTATGAATTTCTTAAGTTTTTACACA
1 ACTTAGTATGAATTTCTTAA--TTTTACACA
58984 CTTAGTGTCA
Statistics
Matches: 374, Mismatches: 37, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
54 26 0.07
55 293 0.78
56 30 0.08
57 25 0.07
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (55 bp):
ACTTAGTATGAATTTCTTAATTTTACACATAAAGTGCCCATACGGAAATTCATCC
Found at i:59384 original size:19 final size:20
Alignment explanation
Indices: 59315--59386 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 20
59305 TGGCTGCTCA
* *
59315 GTATCGATACCCCTACCATG
1 GTATCGATACCCATACTATG
59335 GTATCGATACTACCATACTATG
1 GTATCGATAC--CCATACTATG
*
59357 GTA-CTGATACCCA-ATTATG
1 GTATC-GATACCCATACTATG
59376 GTATCGATACC
1 GTATCGATACC
59387 ATTTTTACAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 14 0.31
20 14 0.31
21 1 0.02
22 16 0.36
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (20 bp):
GTATCGATACCCATACTATG
Found at i:63788 original size:26 final size:27
Alignment explanation
Indices: 63748--63808 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
63738 AATAAGCTTA
*
63748 ATAT-ATATATATATATTCTAAAAATT
1 ATATAATATATATATATTCTAAAAATC
* *
63774 ATATAATATAT-TATATTTTTAAAATC
1 ATATAATATATATATATTCTAAAAATC
63800 ATATAATAT
1 ATATAATAT
63809 GTTTTCAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 25 0.81
27 6 0.19
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATAATATATATATATTCTAAAAATC
Found at i:63942 original size:38 final size:38
Alignment explanation
Indices: 63868--63940 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
63858 AAATATAATA
* * *
63868 ATATGTTTTTTTAAATTATGCTATATATTTTCAAAACC
1 ATATGTTTTTTAAAACTATACTATATATTTTCAAAACC
63906 ATATG-TTTTTAAAACTATACTATATATTTTCAAAA
1 ATATGTTTTTTAAAACTATACTATATATTTTCAAAA
63941 ACTATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 27 0.84
38 5 0.16
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (38 bp):
ATATGTTTTTTAAAACTATACTATATATTTTCAAAACC
Found at i:63944 original size:22 final size:21
Alignment explanation
Indices: 63916--64047 Score: 97
Period size: 22 Copynumber: 5.9 Consensus size: 21
63906 ATATGTTTTT
63916 AAAACTATACTATATATTTTCA
1 AAAACTATA-TATATATTTTCA
**
63938 AAAACTATATATTATATGTTTGTTTT
1 AAAACTATATA-TATA---TT-TTCA
*
63964 AAAACTATATAATATGTTTTCA
1 AAAACTATAT-ATATATTTTCA
**
63986 AAAACTATGCCATATGATTTT-A
1 AAAACTAT-ATATAT-ATTTTCA
*
64008 AAAATTATATTATATATTTTCA
1 AAAACTATA-TATATATTTTCA
*
64030 AAAACCATATAT-TATTTT
1 AAAACTATATATATATTTT
64048 TTTTTTGAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
20 6 0.07
21 10 0.11
22 47 0.54
23 6 0.07
25 2 0.02
26 15 0.17
27 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (21 bp):
AAAACTATATATATATTTTCA
Found at i:63946 original size:17 final size:17
Alignment explanation
Indices: 63888--63950 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
63878 TTAAATTATG
63888 CTATATATTTTC-AAAA
1 CTATATATTTTCAAAAA
* * *
63904 CCATATGTTTTTAAAACTATA
1 CTATAT-ATTTTCAAA--A-A
63925 CTATATATTTTCAAAAA
1 CTATATATTTTCAAAAA
63942 CTATATATT
1 CTATATATT
63951 ATATGTTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
16 5 0.14
17 14 0.39
18 3 0.08
20 8 0.22
21 6 0.17
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.44
Consensus pattern (17 bp):
CTATATATTTTCAAAAA
Found at i:63953 original size:24 final size:24
Alignment explanation
Indices: 63921--64073 Score: 95
Period size: 24 Copynumber: 6.4 Consensus size: 24
63911 TTTTTAAAAC
*
63921 TATACTATATATTTTCAAAAACTA
1 TATATTATATATTTTCAAAAACTA
* **
63945 TATATTATATGTTTGTTTTAAAACTA
1 TATATTATAT-ATT-TTCAAAAACTA
*
63971 TATA--ATATGTTTTCAAAAACTA
1 TATATTATATATTTTCAAAAACTA
** *
63993 TGCCA-TAT-GATTTT-AAAAA-T-
1 T-ATATTATATATTTTCAAAAACTA
*
64013 TATATTATATATTTTCAAAAACCA
1 TATATTATATATTTTCAAAAACTA
* * *
64037 TATATTATTTTTTTTTTGAAAAAACTA
1 TATATTA--TATATTTT-CAAAAACTA
64064 TATATTATAT
1 TATATTATAT
64074 GATATAAAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 23
0.69 0.14 0.16
Matches are distributed among these distances:
19 1 0.01
20 4 0.04
21 6 0.06
22 20 0.21
23 7 0.07
24 22 0.23
25 4 0.04
26 19 0.20
27 14 0.14
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (24 bp):
TATATTATATATTTTCAAAAACTA
Found at i:68286 original size:191 final size:193
Alignment explanation
Indices: 67935--68292 Score: 420
Period size: 191 Copynumber: 1.9 Consensus size: 193
67925 CAATGACAAC
* * ** *
67935 TAGTTACGTCATTAAATTATATGAAATTTTGTTATTAATAATTCACATTGTCAAGAATAATACAT
1 TAGTTACATCACTAAATTATATGAAATTTTGTTATTAATAATTCACATCATCAAGAATAATACAA
* * * * *
68000 TAAAATCAATCTATATGTGACGAAAGAAATATTGTCACATATTCAGTGTCGTAATATAATGTTAC
66 TAAAATCAACCTATATGTGACGAAAGAAATATTGTCAAATATTCAGGGACATAATATAATGTTAC
*
68065 CTAATAGCATTAAGAATGACACTTATGCATAACGTCATTTTATAACTTATATTGCATTACAGT
131 CTAATAGCATTAAGAATGACACTAATGCATAACGTCATTTTATAACTTATATTGCATTACAGT
* * * *
68128 TAGTTACATCACTAAATTATAT--AATATTT-TTATTAATAATTTATATCATCATGAATACTACA
1 TAGTTACATCACTAAATTATATGAAAT-TTTGTTATTAATAATTCACATCATCAAGAATAATACA
* * * * *
68190 ATAAAATCAACCTATATGTTACGAAAGAGATATTGTCAAAT-TTATAGGGACATTATATAATTTT
65 ATAAAATCAACCTATATGTGACGAAAGAAATATTGTCAAATATT-CAGGGACATAATATAATGTT
** * ** *
68254 ATGTAATAGTATTTTGAATGATGA-TAATGCATAACGTCA
129 ACCTAATAGCATTAAGAATGA-CACTAATGCATAACGTCA
68293 CCATATTCAA
Statistics
Matches: 136, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
190 2 0.01
191 110 0.81
192 4 0.03
193 20 0.15
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (193 bp):
TAGTTACATCACTAAATTATATGAAATTTTGTTATTAATAATTCACATCATCAAGAATAATACAA
TAAAATCAACCTATATGTGACGAAAGAAATATTGTCAAATATTCAGGGACATAATATAATGTTAC
CTAATAGCATTAAGAATGACACTAATGCATAACGTCATTTTATAACTTATATTGCATTACAGT
Found at i:69487 original size:41 final size:41
Alignment explanation
Indices: 69430--69523 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
69420 CAAACTTAGG
69430 GCACCTTGAAAGGGGAATTCAAAGCTGATAAATAAAGATAC
1 GCACCTTGAAAGGGGAATTCAAAGCTGATAAATAAAGATAC
* *
69471 GCACCTTGAAAGGGGAATTCAAAGCTGATAAATAACGATGC
1 GCACCTTGAAAGGGGAATTCAAAGCTGATAAATAAAGATAC
69512 GCACCTTGAAAG
1 GCACCTTGAAAG
69524 CTACATAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (41 bp):
GCACCTTGAAAGGGGAATTCAAAGCTGATAAATAAAGATAC
Found at i:73225 original size:15 final size:15
Alignment explanation
Indices: 73205--73237 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
73195 CCTGACCATT
73205 GAATTTTGCAACTTC
1 GAATTTTGCAACTTC
73220 GAATTTTGCAACTTC
1 GAATTTTGCAACTTC
73235 GAA
1 GAA
73238 CATCTGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (15 bp):
GAATTTTGCAACTTC
Found at i:74783 original size:2 final size:2
Alignment explanation
Indices: 74778--74831 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
74768 CTCTCTAAAC
74778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
74820 AT AT AT GT AT AT
1 AT AT AT AT AT AT
74832 TAGAATTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76272 original size:29 final size:29
Alignment explanation
Indices: 76230--76287 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
76220 ATTTTCTCTC
76230 ATTAAATGATCTTAAACAAGTATAAACTT
1 ATTAAATGATCTTAAACAAGTATAAACTT
76259 ATTAAATGATCTTAAACAAGTATAAACTT
1 ATTAAATGATCTTAAACAAGTATAAACTT
76288 TTACATTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (29 bp):
ATTAAATGATCTTAAACAAGTATAAACTT
Found at i:77043 original size:39 final size:39
Alignment explanation
Indices: 76964--77057 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 39
76954 GCAAACATTC
* * *
76964 TTCATAACATTTTAGGTTGCAACCGAAAATATTATCTAT
1 TTCATAATATTTTAGGTTGAAACCGAAAATATTATATAT
* * *
77003 TTCATAATATTTTCGGTT-AAATCGAAAATGTTATGATAT
1 TTCATAATATTTTAGGTTGAAACCGAAAATATTAT-ATAT
77042 TT-ATAATATTTTAGGT
1 TTCATAATATTTTAGGT
77058 CGCGTTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
38 26 0.55
39 21 0.45
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (39 bp):
TTCATAATATTTTAGGTTGAAACCGAAAATATTATATAT
Found at i:80061 original size:22 final size:21
Alignment explanation
Indices: 80009--80061 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
79999 TTTTCAGTTC
* *
80009 AACGAACAATGAGTCAAGTCG
1 AACGAACAACGAGTCAAATCG
80030 AACGAACAACGAGTCAAATCG
1 AACGAACAACGAGTCAAATCG
*
80051 AATTGAACAAC
1 AA-CGAACAAC
80062 AATTTCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (21 bp):
AACGAACAACGAGTCAAATCG
Found at i:86479 original size:16 final size:17
Alignment explanation
Indices: 86447--86479 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
86437 TCCAGCTACA
*
86447 CCATTTTGATCCGAAAC
1 CCATTTTGATCCAAAAC
86464 CCATTTT-ATCCAAAAC
1 CCATTTTGATCCAAAAC
86480 TTTAAAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (17 bp):
CCATTTTGATCCAAAAC
Found at i:94675 original size:18 final size:18
Alignment explanation
Indices: 94654--94689 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
94644 CCTTCAACTT
*
94654 TTTTTGTTTTCTTTATTG
1 TTTTTGTTTTCTTGATTG
*
94672 TTTTTTTTTTCTTGATTG
1 TTTTTGTTTTCTTGATTG
94690 ATGAGAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTTGTTTTCTTGATTG
Found at i:99637 original size:60 final size:60
Alignment explanation
Indices: 99503--99649 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 60
99493 AATATAATAA
* * *
99503 ATAGTCGGGTGACCATTTTATAACTTTTAATAGTTGAGAGATTAAACAAAGCAATACTCT
1 ATAGTTGGGAGACCATTTTGTAACTTTTAATAGTTGAGAGATTAAACAAAGCAATACTCT
** * * *
99563 ATAG-TCAGAGGACCATTTTGTAACTTTTAATAGTTGAGAGACTT-AATATAGCATTA-TCCT
1 ATAGTTGGGA-GACCATTTTGTAACTTTTAATAGTTGAGAGA-TTAAACAAAGCAATACT-CT
99623 ATAGTTGGGAGACCA-TTTGTATACTTT
1 ATAGTTGGGAGACCATTTTGTA-ACTTT
99650 ACCCTATTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
59 8 0.11
60 59 0.82
61 5 0.07
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (60 bp):
ATAGTTGGGAGACCATTTTGTAACTTTTAATAGTTGAGAGATTAAACAAAGCAATACTCT
Found at i:114036 original size:3 final size:3
Alignment explanation
Indices: 114028--114061 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
114018 TGGCCCACAA
114028 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
114062 TCGGGATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:114513 original size:132 final size:132
Alignment explanation
Indices: 114263--114592 Score: 396
Period size: 132 Copynumber: 2.5 Consensus size: 132
114253 TGCTCTGCTG
* * * * * *
114263 TTTCTTCAGGGTAGATCAGATCTTGAAATGTTGATTCATTTCAATATTCTTCAGGGAAGATTGAA
1 TTTCTTCAGGGAAAATCAGAT-ATGGAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAA
* * **
114328 TCGTGGCAGTCTTGTTCCACTGTTGCTCAGGGAAGATCAAATATGGAAAGAGGGGATC-AGTTCC
65 CCGTGGCAGACTTGTTCCACTACTGCTCAGGGAAGATCAAATATGGAAAGAGGGGATCTA-TTCC
114392 ACTA
129 ACTA
* * *
114396 TTTCTTTAGGGAAAATCAGATATGGAGATGTTGATTAATTCCACTGTTCTTCAGGGAAGATTGAA
1 TTTCTTCAGGGAAAATCAGATATGGA-ATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAA
* * **
114461 CCG-GGTAGACTTGTTCCACTACTGCTCAGGGAAGATCAAATCTGGAAAGAGGGGATCTATTCTG
65 CCGTGGCAGACTTGTTCCACTACTGCTCAGGGAAGATCAAATATGGAAAGAGGGGATCTATTCCA
* *
114525 TTG
130 CTA
* * *
114528 CTTCTTCAGGGAAAATAAGATATGGAA-GCATTGATTCATTCCACTATTCTTTAGGGAAGATTGA
1 TTTCTTCAGGGAAAATCAGATATGGAATG--TTGATTCATTCCACTATTCTTCAGGGAAGATTGA
114592 A
64 A
114593 TCGATTTCGA
Statistics
Matches: 168, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
130 1 0.01
131 1 0.01
132 111 0.66
133 55 0.33
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (132 bp):
TTTCTTCAGGGAAAATCAGATATGGAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAAC
CGTGGCAGACTTGTTCCACTACTGCTCAGGGAAGATCAAATATGGAAAGAGGGGATCTATTCCAC
TA
Found at i:115846 original size:11 final size:11
Alignment explanation
Indices: 115832--115859 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
115822 TTTTTTTAAT
115832 TTTTTCAATTG
1 TTTTTCAATTG
115843 TTTTTCAATTG
1 TTTTTCAATTG
115854 TTTTTC
1 TTTTTC
115860 TTCTTTCAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.11, G:0.07, T:0.68
Consensus pattern (11 bp):
TTTTTCAATTG
Found at i:135253 original size:20 final size:20
Alignment explanation
Indices: 135208--135253 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
135198 TCATTGAATC
135208 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT-CTTAAT
135228 ATTAGTTCTTAGCT-TTAAT
1 ATTAGTTCTTAGCTCTTAAT
135247 AATTAGT
1 -ATTAGT
135254 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.21
20 10 0.42
21 9 0.38
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (20 bp):
ATTAGTTCTTAGCTCTTAAT
Found at i:148363 original size:3 final size:3
Alignment explanation
Indices: 148355--148449 Score: 156
Period size: 3 Copynumber: 31.3 Consensus size: 3
148345 TAGGAGAGTT
148355 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
148402 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGAGA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A-A TAA TAA TAA TAA
148449 T
1 T
148450 TGTATGGAAA
Statistics
Matches: 87, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
2 2 0.02
3 81 0.93
4 2 0.02
5 2 0.02
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:149910 original size:17 final size:17
Alignment explanation
Indices: 149890--149922 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
149880 ATATTTATTT
149890 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
149907 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
149923 TGTGATCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:151757 original size:28 final size:28
Alignment explanation
Indices: 151702--151775 Score: 141
Period size: 28 Copynumber: 2.7 Consensus size: 28
151692 AGCTTGTTAA
151702 TGAACTTAAACAAAC-AGCTCTTGTTTG
1 TGAACTTAAACAAACAAGCTCTTGTTTG
151729 TGAACTTAAACAAACAAGCTCTTGTTTG
1 TGAACTTAAACAAACAAGCTCTTGTTTG
151757 TGAACTTAAACAAACAAGC
1 TGAACTTAAACAAACAAGC
151776 CGATAAACGA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 15 0.33
28 31 0.67
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (28 bp):
TGAACTTAAACAAACAAGCTCTTGTTTG
Found at i:156902 original size:43 final size:43
Alignment explanation
Indices: 156819--156958 Score: 167
Period size: 43 Copynumber: 3.2 Consensus size: 43
156809 GCTAAAGTTC
* * *
156819 GCGGCGTTTG-TTAACCAAAAACGCCACAATAGGTAACGATATATA
1 GCGGCGTTTGTTTAA-C--AAACGCCGCAATAGGTATCGATATTTA
*
156864 GCGGCGTTTGTTTAACAAATGCCGCAATAGGTATCGATATTTA
1 GCGGCGTTTGTTTAACAAACGCCGCAATAGGTATCGATATTTA
* * *
156907 GCGGCGTTTGTCTTAA-AAACGCCGCAATTGGTGTCAATATTTA
1 GCGGCGTTTGT-TTAACAAACGCCGCAATAGGTATCGATATTTA
156950 GCGGCGTTT
1 GCGGCGTTT
156959 TTATCACAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
43 66 0.78
44 4 0.05
45 11 0.13
46 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (43 bp):
GCGGCGTTTGTTTAACAAACGCCGCAATAGGTATCGATATTTA
Found at i:161537 original size:166 final size:167
Alignment explanation
Indices: 161293--161604 Score: 405
Period size: 166 Copynumber: 1.9 Consensus size: 167
161283 CGTTTACTTA
* * * ** **
161293 AAAAACGCCACTACTGTCCAAATGTTGAGCAGCGTTTGTGTTTCAAAACGCCACTAACTTAAGCC
1 AAAAACGCCACTAATGTCCAAATATTGAGCAGCGTTTGTGTTTAAAAACAACACTAAAGTAAGCC
** *
161358 TCTATAGCGGCGTTTTCTTAAAAACGCTGCTAAAGTTATATTATATTGCGGCGTTGAT-TAAAAA
66 TCTATAGCGGCGTTTTAATAAAAACGCCGCTAAAGTTATATTATATTGCGGCGTTGATAT-AAAA
161422 ACGCCACTAAAT-ATTAAATCTATTGCTGCATTTGTAT
130 ACGCCACTAAATCATTAAATCTATTGCTGCATTTGTAT
** * *
161459 AAAAACGCCACTAATGTCCAAATATTTTGCGGCGTTTTTGTTTAAAAACAACACTAAAGTAA-CA
1 AAAAACGCCACTAATGTCCAAATATTGAGCAGCGTTTGTGTTTAAAAACAACACTAAAGTAAGC-
* * * * *
161523 CTTTATAGCGGCGTTTTAATAACAACGCCGCTAAAGTTCTATTATTTTGCGGCGTTTATATAAAA
65 CTCTATAGCGGCGTTTTAATAAAAACGCCGCTAAAGTTATATTATATTGCGGCGTTGATATAAAA
*
161588 ACGCCGCTAAATCATTA
130 ACGCCACTAAATCATTA
161605 TCCTTGAAAC
Statistics
Matches: 123, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
165 1 0.01
166 117 0.95
167 5 0.04
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (167 bp):
AAAAACGCCACTAATGTCCAAATATTGAGCAGCGTTTGTGTTTAAAAACAACACTAAAGTAAGCC
TCTATAGCGGCGTTTTAATAAAAACGCCGCTAAAGTTATATTATATTGCGGCGTTGATATAAAAA
CGCCACTAAATCATTAAATCTATTGCTGCATTTGTAT
Found at i:161792 original size:41 final size:40
Alignment explanation
Indices: 161737--161874 Score: 136
Period size: 41 Copynumber: 3.4 Consensus size: 40
161727 AAATTACTTA
* * *
161737 TCTATAGCGTCGTTTGTTGAACAAACGCCAATATAAACAAC
1 TCTATTGCGGCGTTTGTTGAA-AAACGCCACTATAAACAAC
* * * *
161778 ACTATCGCGGCGTTTG-TGTAAAAACGCCGCTA-AATTACCAC
1 TCTATTGCGGCGTTTGTTG-AAAAACGCCACTATAA--ACAAC
* *
161819 TCTATTGCGGCGTTTATTGAAAAAACGCCACTATAAACATC
1 TCTATTGCGGCGTTTGTTG-AAAAACGCCACTATAAACAAC
161860 TCTATTGCGGCGTTT
1 TCTATTGCGGCGTTT
161875 TAGCTATAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
39 2 0.03
40 11 0.14
41 50 0.63
42 14 0.18
43 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (40 bp):
TCTATTGCGGCGTTTGTTGAAAAACGCCACTATAAACAAC
Found at i:161833 original size:82 final size:83
Alignment explanation
Indices: 161737--161930 Score: 248
Period size: 82 Copynumber: 2.3 Consensus size: 83
161727 AAATTACTTA
* * *
161737 TCTATAGCGTCGTTTGTTGAACAAACGCCAATATAAACAACACTATCGCGGCGTTTGT-G-TAAA
1 TCTATTGCGGCGTTTGTTGAAAAAACGCCAATATAAACAACACTATCGCGGCGTTT-TAGCTAAA
161800 AACGCCGCTAAATTACCAC
65 AACGCCGCTAAATTACCAC
* * * * * *
161819 TCTATTGCGGCGTTTATTGAAAAAACGCCACTATAAACATCTCTATTGCGGCGTTTTAGCTATAA
1 TCTATTGCGGCGTTTGTTGAAAAAACGCCAATATAAACAACACTATCGCGGCGTTTTAGCTAAAA
*
161884 ATGCCGCTAAATTACCAC
66 ACGCCGCTAAATTACCAC
* * *
161902 TCTATTACGGCTTTTGTTTAAAAAACGCC
1 TCTATTGCGGCGTTTGTTGAAAAAACGCC
161931 GCTAAAGTAT
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 1 0.01
82 49 0.51
83 46 0.48
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (83 bp):
TCTATTGCGGCGTTTGTTGAAAAAACGCCAATATAAACAACACTATCGCGGCGTTTTAGCTAAAA
ACGCCGCTAAATTACCAC
Found at i:161928 original size:83 final size:82
Alignment explanation
Indices: 161747--161930 Score: 244
Period size: 83 Copynumber: 2.2 Consensus size: 82
161737 TCTATAGCGT
*
161747 CGTTTGTTGAACAAACGCCAATATAAACAACACTATCGCGGCGTTTGTGTAAAAACGCCGCTAAA
1 CGTTTGTTGAAAAAACGCCAATATAAACAACACTATCGCGGCGTTTGTGTAAAAACGCCGCTAAA
*
161812 TTACCACTCTATTGCGG
66 TTACCACTCTATTACGG
* * * * * * *
161829 CGTTTATTGAAAAAACGCCACTATAAACATCTCTATTGCGGCGTTT-TAGCTATAAATGCCGCTA
1 CGTTTGTTGAAAAAACGCCAATATAAACAACACTATCGCGGCGTTTGT-G-TAAAAACGCCGCTA
161893 AATTACCACTCTATTACGG
64 AATTACCACTCTATTACGG
* *
161912 CTTTTGTTTAAAAAACGCC
1 CGTTTGTTGAAAAAACGCC
161931 GCTAAAGTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 1 0.01
82 41 0.47
83 46 0.52
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (82 bp):
CGTTTGTTGAAAAAACGCCAATATAAACAACACTATCGCGGCGTTTGTGTAAAAACGCCGCTAAA
TTACCACTCTATTACGG
Found at i:161932 original size:42 final size:42
Alignment explanation
Indices: 161779--161936 Score: 139
Period size: 41 Copynumber: 3.8 Consensus size: 42
161769 ATAAACAACA
* * *
161779 CTATCGCGGCGTTTGTGT-AAAAACGCCGCTAAATTACCACT
1 CTATTGCGGCTTTTGTTTAAAAAACGCCGCTAAATTACCACT
* * * *
161820 CTATTGCGGCGTTTATTGAAAAAACGCCACTATAA--A-CATCT
1 CTATTGCGGCTTTTGTTTAAAAAACGCCGCTA-AATTACCA-CT
* * *
161861 CTATTGCGGCGTTTTAG-CT-ATAAATGCCGCTAAATTACCACT
1 CTATTGCGGC-TTTT-GTTTAAAAAACGCCGCTAAATTACCACT
*
161903 CTATTACGGCTTTTGTTTAAAAAACGCCGCTAAA
1 CTATTGCGGCTTTTGTTTAAAAAACGCCGCTAAA
161937 GTATCATTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
40 5 0.05
41 42 0.46
42 40 0.44
43 4 0.04
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (42 bp):
CTATTGCGGCTTTTGTTTAAAAAACGCCGCTAAATTACCACT
Found at i:180228 original size:27 final size:28
Alignment explanation
Indices: 180190--180255 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
180180 AAGGGAATTC
180190 AGCAACCAATGGAG-TTTTTCATCATTA
1 AGCAACCAATGGAGTTTTTTCATCATTA
180217 AGCAACCAATGGAGTTTTTTCATCATTA
1 AGCAACCAATGGAGTTTTTTCATCATTA
180245 AGCAACCAATG
1 AGCAACCAATG
180256 CCCATTAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 14 0.37
28 24 0.63
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (28 bp):
AGCAACCAATGGAGTTTTTTCATCATTA
Found at i:185174 original size:23 final size:23
Alignment explanation
Indices: 185130--185174 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
185120 TAGAAACATA
*
185130 TAAACGAACATATACTCAAACGT
1 TAAACGAACATATACACAAACGT
* *
185153 TAAACGAACATATTCACGAACG
1 TAAACGAACATATACACAAACG
185175 AACACGAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.22, G:0.11, T:0.20
Consensus pattern (23 bp):
TAAACGAACATATACACAAACGT
Found at i:186039 original size:77 final size:77
Alignment explanation
Indices: 185912--186069 Score: 262
Period size: 77 Copynumber: 2.1 Consensus size: 77
185902 CTAAATAATT
*
185912 CGTTATTTAATTACGCGATCATCTTCACACAATATTCCTTAGCATGATTGTATTTATCATCGATT
1 CGTTATTTAATTACGCGATCATCTTAACACAATATTCCTTAGCATGATTGTATTTATCATCGATT
185977 ATCCTCTTTCCC
66 ATCCTCTTTCCC
* * * *
185989 CGTTATTTAATTACGCGATCATCTTAACACCATATTGCTTAGCATGATTGTATTTCTCATCTATT
1 CGTTATTTAATTACGCGATCATCTTAACACAATATTCCTTAGCATGATTGTATTTATCATCGATT
*
186054 ATCCTTTTTCCC
66 ATCCTCTTTCCC
186066 CGTT
1 CGTT
186070 GGTCAAGCGT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.43
Consensus pattern (77 bp):
CGTTATTTAATTACGCGATCATCTTAACACAATATTCCTTAGCATGATTGTATTTATCATCGATT
ATCCTCTTTCCC
Found at i:199257 original size:71 final size:71
Alignment explanation
Indices: 199137--199276 Score: 183
Period size: 71 Copynumber: 2.0 Consensus size: 71
199127 AATCAATCCC
* * * * * *
199137 TTGACCAAAAGGATTGATCCCAAACTTTCGGTTATGCAAATGATTGACCACTTTTCAAAAGGATT
1 TTGACCAAAAGGATTGATCCCAAACTTTCGGTTATACAAAGGATCGACCACATTCCAAAAGGATC
199202 GATCTT
66 GATCTT
* * *
199208 TTGACCAAAATGATTGATCCCAAACTTTCTG-TAGTACAAAGGATCGACCACATTCCAATAGGAT
1 TTGACCAAAAGGATTGATCCCAAACTTTCGGTTA-TACAAAGGATCGACCACATTCCAAAAGGAT
199272 CGATC
65 CGATC
199277 CATCGGAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
70 2 0.03
71 57 0.97
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (71 bp):
TTGACCAAAAGGATTGATCCCAAACTTTCGGTTATACAAAGGATCGACCACATTCCAAAAGGATC
GATCTT
Found at i:202180 original size:21 final size:20
Alignment explanation
Indices: 202134--202186 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
202124 CCCTTTAAGG
*
202134 AGTATCGATATTCAGGGTCT
1 AGTATCGATACTCAGGGTCT
202154 AGTATCGATACTCAGAGGGTC-
1 AGTATCGATACTC--AGGGTCT
*
202175 AGTATCAATACT
1 AGTATCGATACT
202187 GAGGCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.41
21 11 0.38
22 6 0.21
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTCAGGGTCT
Found at i:210051 original size:9 final size:9
Alignment explanation
Indices: 210037--210079 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
210027 TTTTTTTACA
210037 AAAAAAAAC
1 AAAAAAAAC
**
210046 AAAAAAGGC
1 AAAAAAAAC
210055 AAAAAAAAC
1 AAAAAAAAC
*
210064 ACAAAAAAAT
1 A-AAAAAAAC
210074 AAAAAA
1 AAAAAA
210080 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.02
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:210078 original size:20 final size:19
Alignment explanation
Indices: 210036--210079 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
210026 ATTTTTTTAC
*
210036 AAAAAAAAACAAAAAAGGCA
1 AAAAAAAAACAAAAAAAG-A
* *
210056 AAAAAAACACAAAAAAATA
1 AAAAAAAAACAAAAAAAGA
210075 AAAAA
1 AAAAA
210080 GCCAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.02
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAAGA
Found at i:219962 original size:19 final size:19
Alignment explanation
Indices: 219938--219974 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
219928 CGGCCAAGAG
219938 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
*
219957 CATGTATTTTCATTAAAA
1 CATGTATCTTCATTAAAA
219975 AAAATCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:220546 original size:12 final size:13
Alignment explanation
Indices: 220507--220570 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
220497 CCTTTGATAG
220507 CATTTCTTTCCATTT
1 CATTTCTTT--ATTT
220522 CATTTCTTTATTT
1 CATTTCTTTATTT
220535 CATTTC-TTATTT
1 CATTTCTTTATTT
** *
220547 CCATTTAATCATTT
1 -CATTTCTTTATTT
220561 C-TTTCTTTAT
1 CATTTCTTTAT
220571 ATTGTGTAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
12 12 0.29
13 16 0.38
14 5 0.12
15 9 0.21
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.62
Consensus pattern (13 bp):
CATTTCTTTATTT
Found at i:221617 original size:3 final size:3
Alignment explanation
Indices: 221609--221634 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
221599 CCACTATTTG
221609 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
221635 GTATTTGTGA
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:225096 original size:173 final size:175
Alignment explanation
Indices: 224807--225152 Score: 678
Period size: 173 Copynumber: 2.0 Consensus size: 175
224797 TCTAATTTCC
224807 AAGGGTCTTCTTCTTCCAAGGCTGTAGCTCCAATGCCTCAACAGCAGCAGCAACAACAGGAGCAA
1 AAGGGTCTTCTTCTTCCAAGGCTGTAGCTCCAATGCCTCAACAGCAGCAGCAACAACAGGAGCAA
224872 CCATTCAATATGGACTCCATGTGGTGAAAAGCTGTAAGCCAAATATATCTGAAAGAGTGG-AAAG
66 CCATTCAATATGGACTCCATGTGGTGAAAAGCTGTAAGCCAAATATATCTGAAAGAGTGGAAAAG
224936 ATATCAC-TTATGAATATTCCATGACATGAAAGGGTTGATTAAAA
131 ATATCACTTTATGAATATTCCATGACATGAAAGGGTTGATTAAAA
224980 AAGGGTCTTCTTCTTCCAAGGCTGTAGCTCCAATGCCTCAACAGCAGCAGCAACAACAGGAGCAA
1 AAGGGTCTTCTTCTTCCAAGGCTGTAGCTCCAATGCCTCAACAGCAGCAGCAACAACAGGAGCAA
225045 CCATTCAATATGGACTCCATGTGGTGAAAAGCTGTAAGCCAAATATATCTGAAAGAGTGGAAAAG
66 CCATTCAATATGGACTCCATGTGGTGAAAAGCTGTAAGCCAAATATATCTGAAAGAGTGGAAAAG
225110 ATATCACTTTATGAATATTCCATGACATGAAAGGGTTGATTAA
131 ATATCACTTTATGAATATTCCATGACATGAAAGGGTTGATTAA
225153 GATGAAAATA
Statistics
Matches: 171, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
173 125 0.73
174 11 0.06
175 35 0.20
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (175 bp):
AAGGGTCTTCTTCTTCCAAGGCTGTAGCTCCAATGCCTCAACAGCAGCAGCAACAACAGGAGCAA
CCATTCAATATGGACTCCATGTGGTGAAAAGCTGTAAGCCAAATATATCTGAAAGAGTGGAAAAG
ATATCACTTTATGAATATTCCATGACATGAAAGGGTTGATTAAAA
Found at i:225626 original size:19 final size:19
Alignment explanation
Indices: 225602--225644 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
225592 TTCTTCTAAA
225602 ATTTTAAAAATTATTATAT
1 ATTTTAAAAATTATTATAT
** *
225621 ATTTTAAATTTTCTTATAT
1 ATTTTAAAAATTATTATAT
225640 ATTTT
1 ATTTT
225645 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTAAAAATTATTATAT
Found at i:229608 original size:26 final size:26
Alignment explanation
Indices: 229575--229640 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
229565 TGCACATACC
229575 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
229601 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
229627 ATGCATCGATGCAC
1 ATGCATCGATGCAC
229641 AAGACCATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (26 bp):
ATGCATCGATGCACTCAGTGCATTTG
Found at i:235177 original size:24 final size:24
Alignment explanation
Indices: 235150--235232 Score: 59
Period size: 24 Copynumber: 3.6 Consensus size: 24
235140 CACTTAACAG
*
235150 TGCACCGATGCATCCCTTTGAATA
1 TGCACCGATGCATCCCCTTGAATA
* * **
235174 TGCATCGATACAT-CAGTTG---A
1 TGCACCGATGCATCCCCTTGAATA
*
235194 TGCACCGATGCA-CGCCCTTGAATG
1 TGCACCGATGCATC-CCCTTGAATA
*
235218 TGCATCGATGCATCC
1 TGCACCGATGCATCC
235233 GTCGGGTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
20 11 0.26
21 4 0.09
23 4 0.09
24 23 0.53
25 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (24 bp):
TGCACCGATGCATCCCCTTGAATA
Found at i:253809 original size:11 final size:11
Alignment explanation
Indices: 253795--253858 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
253785 GGAAGTGAAA
*
253795 AAGAAGAGGAG
1 AAGAAGAAGAG
253806 AAGAAGAAGAG
1 AAGAAGAAGAG
253817 -A-AAG-AG-G
1 AAGAAGAAGAG
*
253824 AAGAAATAAGAG
1 AAG-AAGAAGAG
253836 AA-AAGAA-AG
1 AAGAAGAAGAG
253845 AAAGAAGAAGAG
1 -AAGAAGAAGAG
253857 AA
1 AA
253859 TATGTTCGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
7 1 0.02
8 3 0.07
9 5 0.12
10 9 0.21
11 19 0.45
12 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.02
Consensus pattern (11 bp):
AAGAAGAAGAG
Found at i:253828 original size:18 final size:19
Alignment explanation
Indices: 253805--253858 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
253795 AAGAAGAGGA
253805 GAAGAAGAAGAGAAAG-AG
1 GAAGAAGAAGAGAAAGAAG
*
253823 GAAGAAATAAGAGAAAAGAAAG
1 GAAG-AAGAAGAG-AAAG-AAG
*
253845 AAAGAAGAAGAGAA
1 GAAGAAGAAGAGAA
253859 TATGTTCGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.14
19 7 0.24
20 6 0.21
21 7 0.24
22 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (19 bp):
GAAGAAGAAGAGAAAGAAG
Found at i:254848 original size:4 final size:4
Alignment explanation
Indices: 254836--254869 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
254826 ATGTACATAC
* *
254836 ATAT TTAT ATAT ATAT ATAT ATAT ATAT ACAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
254870 TTAAAACTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:254850 original size:6 final size:6
Alignment explanation
Indices: 254836--254869 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
254826 ATGTACATAC
* *
254836 ATATTT ATATAT ATATAT ATATAT ATATAC ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
254870 TTAAAACTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:254988 original size:35 final size:35
Alignment explanation
Indices: 254949--255017 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
254939 TTTAAAAAAA
254949 TATATATATATATTTTT-AAAATCA-TTTTGAAAACT
1 TATATATATA-ATTTTTGAAAA-CATTTTTGAAAACT
254984 TATATATATAATTTTTGAAAACATTTTTGAAAAC
1 TATATATATAATTTTTGAAAACATTTTTGAAAAC
255018 ATTTTGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
34 8 0.25
35 24 0.75
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (35 bp):
TATATATATAATTTTTGAAAACATTTTTGAAAACT
Found at i:255011 original size:12 final size:12
Alignment explanation
Indices: 254994--255032 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
254984 TATATATATA
254994 ATTTTTGAAAAC
1 ATTTTTGAAAAC
255006 ATTTTTGAAAAC
1 ATTTTTGAAAAC
255018 A-TTTTGAAAAC
1 ATTTTTGAAAAC
255029 ATTT
1 ATTT
255033 ATATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
ATTTTTGAAAAC
Found at i:255022 original size:11 final size:11
Alignment explanation
Indices: 254996--255032 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
254986 TATATATAAT
254996 TTTTGAAAACA
1 TTTTGAAAACA
255007 TTTTTGAAAACA
1 -TTTTGAAAACA
255019 TTTTGAAAACA
1 TTTTGAAAACA
255030 TTT
1 TTT
255033 ATATATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:255062 original size:39 final size:36
Alignment explanation
Indices: 255007--255167 Score: 134
Period size: 39 Copynumber: 4.4 Consensus size: 36
254997 TTTGAAAACA
255007 TTTTTGAAAACATTTTGAAAACATTTATATATTATATAG
1 TTTTT-AAAACATTTTGAAAA-ATTTATATATTATAT-G
*
255046 TTTTTAAAACGTTTTTGAAAAA-TTATATA--ATAT-
1 TTTTTAAAAC-ATTTTGAAAAATTTATATATTATATG
* * **
255079 TTTTGAAAACATGTTGAAAACATTCGTATATTATATAG
1 TTTTTAAAACATTTTGAAAA-ATTTATATATTATAT-G
** *
255117 TTTAAAAAAACATTTTG-AAAATTTATATATTATGTG
1 TTT-TTAAAACATTTTGAAAAATTTATATATTATATG
*
255153 TTTTTGAAAATATTT
1 TTTTT-AAAACATTT
255168 ACGTATATAT
Statistics
Matches: 98, Mismatches: 15, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
32 8 0.08
33 10 0.10
34 5 0.05
35 4 0.04
36 16 0.16
37 19 0.19
38 12 0.12
39 24 0.24
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (36 bp):
TTTTTAAAACATTTTGAAAAATTTATATATTATATG
Found at i:255084 original size:71 final size:71
Alignment explanation
Indices: 255006--255145 Score: 201
Period size: 71 Copynumber: 2.0 Consensus size: 71
254996 TTTTGAAAAC
* * ** *
255006 ATTTTTGAAAACATTTTGAAAACATTTATATATTATATAGTTT-TTAAAACGTTTTTGAAAAATT
1 ATTTTTGAAAACATGTTGAAAACATTCATATATTATATAGTTTAAAAAAAC-ATTTTGAAAAATT
255070 ATATAAT
65 ATATAAT
* *
255077 ATTTTTGAAAACATGTTGAAAACATTCGTATATTATATAGTTTAAAAAAACATTTTGAAAATTTA
1 ATTTTTGAAAACATGTTGAAAACATTCATATATTATATAGTTTAAAAAAACATTTTGAAAAATTA
255142 TATA
66 TATA
255146 TTATGTGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 56 0.92
72 5 0.08
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (71 bp):
ATTTTTGAAAACATGTTGAAAACATTCATATATTATATAGTTTAAAAAAACATTTTGAAAAATTA
TATAAT
Found at i:261621 original size:84 final size:81
Alignment explanation
Indices: 261437--262068 Score: 637
Period size: 84 Copynumber: 7.7 Consensus size: 81
261427 TAAACAAACT
* ** *
261437 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGACTACACTC
* *
261501 AGCTTCGAGGGCACATC
66 AGC-TCCAAGGCACATC
* * * *
261518 TTTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---ACCAAAGACCTTCGAGTTCGACTACA
261583 CTCAGCTCCAAGGCACATC
63 CTCAGCTCCAAGGCACATC
* * ** *
261602 ATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGACTACACTC
* *
261666 AGCTTCGAGGGCACATC
66 AGC-TCCAAGGCACATC
* * * * * * * *
261683 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTAGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC--TGACC-AAAGACCTTCGAGTTCGACTACA
261748 CTCAGCT-CAACGGCACATC
63 CTCAGCTCCAA-GGCACATC
* * ** * *
261767 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATTTG-CCAAAGACCCCCGAGTTTGATTACACTC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGACTACACTC
* *
261831 AGCTTCGAGGGCACATC
66 AGC-TCCAAGGCACATC
* *
261848 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---ACCAAAGACCTTCGAGTTCGACTACA
261913 CTCAGCTCCAAGGCACATC
63 CTCAGCTCCAAGGCACATC
* * * * * * * *
261932 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTTTGCCAACAAAAGACCTTTGAGTTTGACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---ACCAAAGACCTTCGAGTTCGACTACA
*
261997 CTCAGCT-CAACGACACATC
63 CTCAGCTCCAA-GGCACATC
* * * *
262016 ATTTGCAGTATAGCTTAAGTCCAGAAGGGCTATCTG-CTAAAGACCTTCGAGTT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTT
262069 TAATTATATT
Statistics
Matches: 456, Mismatches: 78, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
80 64 0.14
81 116 0.25
82 3 0.01
83 6 0.01
84 192 0.42
85 75 0.16
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGACTACACTC
AGCTCCAAGGCACATC
Found at i:261711 original size:165 final size:165
Alignment explanation
Indices: 261437--262052 Score: 887
Period size: 165 Copynumber: 3.7 Consensus size: 165
261427 TAAACAAACT
261437 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
261502 GCTTCGAGGGCACATCTTTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
261567 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
261602 ATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * **
261667 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGAC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGAC
*
261731 CTTTGAGTTAGACTACGCTCAGCT-CAACGGCACATC
130 CTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
* *
261767 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATTTGCCAAAGACCCCCGAGTTTGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
261832 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
*
261897 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * * * * *** * *
261932 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTTTGCCAACAAAAGACCTTTGAGTTTGACTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTCGATTACA
* * * * * * *
261997 CTCAGC-TCAACGACACATCATTTGCAGTATAGCTTAAGTCCAGAAGGGCTATCTGC
62 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
262053 TAAAGACCTT
Statistics
Matches: 407, Mismatches: 36, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
164 6 0.01
165 325 0.80
166 7 0.02
168 44 0.11
169 25 0.06
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:262814 original size:39 final size:39
Alignment explanation
Indices: 262768--262934 Score: 130
Period size: 39 Copynumber: 4.3 Consensus size: 39
262758 TTTTTAAAAC
* *
262768 TATATAATGTATAGTTTTTAAAAAACATTTT-AAAAAATA
1 TATATAATATATAATTTTT-AAAAACATTTTGAAAAAATA
* **
262807 TATATAATATATAATTTTTAAAATCATTTTGAAAACTTA
1 TATATAATATATAATTTTTAAAAACATTTTGAAAAAATA
* * * *
262846 TATATAATTTTTGAAAACATTTTTGAAAACATTTTGAAAACAT-
1 TATATAA--TAT--ATA-ATTTTTAAAAACATTTTGAAAAAATA
* *
262889 T-TATATTATATAGTTTTT-AAAACATTTTTG-AAAAAT-
1 TATATAATATATAATTTTTAAAAACA-TTTTGAAAAAATA
262925 TATATAATAT
1 TATATAATAT
262935 TTTTGAAAAC
Statistics
Matches: 104, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
36 12 0.12
37 17 0.16
38 12 0.12
39 30 0.29
40 2 0.02
41 2 0.02
42 4 0.04
43 3 0.03
44 22 0.21
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (39 bp):
TATATAATATATAATTTTTAAAAACATTTTGAAAAAATA
Found at i:262853 original size:32 final size:33
Alignment explanation
Indices: 262813--262875 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 33
262803 AATATATATA
262813 ATATATAATTTTT-AAAATCA-TTTTGAAAACTT
1 ATATATAATTTTTGAAAA-CATTTTTGAAAACTT
262845 ATATATAATTTTTGAAAACATTTTTGAAAAC
1 ATATATAATTTTTGAAAACATTTTTGAAAAC
262876 ATTTTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (33 bp):
ATATATAATTTTTGAAAACATTTTTGAAAACTT
Found at i:262880 original size:11 final size:11
Alignment explanation
Indices: 262854--262890 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
262844 TATATATAAT
262854 TTTTGAAAACA
1 TTTTGAAAACA
262865 TTTTTGAAAACA
1 -TTTTGAAAACA
262877 TTTTGAAAACA
1 TTTTGAAAACA
262888 TTT
1 TTT
262891 ATATTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:262910 original size:81 final size:81
Alignment explanation
Indices: 262789--262958 Score: 231
Period size: 81 Copynumber: 2.1 Consensus size: 81
262779 TAGTTTTTAA
*
262789 AAAACATTTTAAAAAATATATATAATATATAATTTTTAAAATCA-TTTTGAAAACTTATAT-ATA
1 AAAACATTTTAAAAAATATATATAATATATAATTTTTAAAA-CATTTTTGAAAAATTATATAAT-
*
262852 ATTTTTGAAAACATTTTTG
64 ATTTTTGAAAACA-TGTTG
* * *
262871 AAAACATTTTGAAAACAT-T-TATATTATATAGTTTTTAAAACATTTTTGAAAAATTATATAATA
1 AAAACATTTT-AAAAAATATATATAATATATAATTTTTAAAACATTTTTGAAAAATTATATAATA
262934 TTTTTGAAAACATGTTG
65 TTTTTGAAAACATGTTG
262951 AAAACATT
1 AAAACATT
262959 CGTATATTAT
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
80 14 0.17
81 47 0.59
82 13 0.16
83 6 0.08
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (81 bp):
AAAACATTTTAAAAAATATATATAATATATAATTTTTAAAACATTTTTGAAAAATTATATAATAT
TTTTGAAAACATGTTG
Found at i:262952 original size:69 final size:70
Alignment explanation
Indices: 262864--263010 Score: 208
Period size: 71 Copynumber: 2.1 Consensus size: 70
262854 TTTTGAAAAC
* **
262864 ATTTTTGAAAACATTTTGAAAACATT-TATATTATATAGTTT-TTAAAACATTTTTGAAAAATTA
1 ATTTTTGAAAACATGTTGAAAACATTCTATATTATATAGTTTAAAAAAACA-TTTTGAAAAATTA
262927 TATAAT
65 TATAAT
*
262933 ATTTTTGAAAACATGTTGAAAACATTCGTATATTATATAGTTTAAAAAAACATTTTGAAAATTTA
1 ATTTTTGAAAACATGTTGAAAACATTC-TATATTATATAGTTTAAAAAAACATTTTGAAAAATTA
*
262998 TATATT
65 TATAAT
263004 ATGTTTT
1 AT-TTTT
263011 TTGAAAATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
69 25 0.36
71 34 0.49
72 10 0.14
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (70 bp):
ATTTTTGAAAACATGTTGAAAACATTCTATATTATATAGTTTAAAAAAACATTTTGAAAAATTAT
ATAAT
Found at i:263040 original size:3 final size:3
Alignment explanation
Indices: 263032--263066 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
263022 TATGTATATA
263032 TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
263067 CATTTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:263043 original size:19 final size:19
Alignment explanation
Indices: 263021--263066 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
263011 TTGAAAATAT
263021 TTATGTA-TATATATTATTA
1 TTATGTATTAT-TATTATTA
*
263040 TTATTTATTATTATTATTA
1 TTATGTATTATTATTATTA
263059 TTAT-TATT
1 TTATGTATT
263067 CATTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 18 0.72
20 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATGTATTATTATTATTA
Found at i:265669 original size:13 final size:13
Alignment explanation
Indices: 265653--265677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
265643 TTTATGTATT
265653 TTAATTAAAATTC
1 TTAATTAAAATTC
265666 TTAATTAAAATT
1 TTAATTAAAATT
265678 TATTTATTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAATTAAAATTC
Found at i:267048 original size:20 final size:20
Alignment explanation
Indices: 267011--267070 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
267001 CGAACCGATA
*
267011 TTCTCTTCT-TCTTCTTTCT
1 TTCTCTTTTCTCTTCTTTCT
*
267030 TTCTCTTTTCTCTTATTTCT
1 TTCTCTTTTCTCTTCTTTCT
*
267050 TCCTCTTTTCTCTTCTTTCT
1 TTCTCTTTTCTCTTCTTTCT
267070 T
1 T
267071 CTTCTCTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 8 0.22
20 28 0.78
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTCTTTTCTCTTCTTTCT
Found at i:267080 original size:20 final size:20
Alignment explanation
Indices: 267011--267080 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
267001 CGAACCGATA
267011 TTCTCTTCTTCTTCTTTCTT-
1 TTCTCTTC-TCTTCTTTCTTC
* *
267031 TCTCTTTTCTCTTATTTCTTC
1 T-TCTCTTCTCTTCTTTCTTC
* *
267052 CTCTTTTCTCTTCTTTCTTC
1 TTCTCTTCTCTTCTTTCTTC
267072 TTCTCTTCT
1 TTCTCTTCT
267081 TTTTTTCACT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 36 0.86
21 6 0.14
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTCTTCTCTTCTTTCTTC
Found at i:272479 original size:36 final size:35
Alignment explanation
Indices: 272426--272503 Score: 81
Period size: 35 Copynumber: 2.2 Consensus size: 35
272416 ATATAATAAT
272426 ATAAAAAAATGAAGT-AA-ATAAAACGAGATAAAGAAA
1 ATAAAAAAATGAAGTAAAGATAAAA--AG-TAAAGAAA
* *
272462 ATAAAAAAAT-AGTGTAAAGATAAAAAGTAAATAAA
1 ATAAAAAAATGA-AGTAAAGATAAAAAGTAAAGAAA
272497 ATAAAAA
1 ATAAAAA
272504 TAAATAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
35 15 0.41
36 14 0.38
37 2 0.05
38 6 0.16
ACGTcount: A:0.71, C:0.01, G:0.12, T:0.17
Consensus pattern (35 bp):
ATAAAAAAATGAAGTAAAGATAAAAAGTAAAGAAA
Found at i:272517 original size:60 final size:64
Alignment explanation
Indices: 272426--272631 Score: 200
Period size: 60 Copynumber: 3.3 Consensus size: 64
272416 ATATAATAAT
** * * *
272426 ATAAA-AAA-ATGAAGTAAATAAAA-CGAGATAAAGAAAATAAAAAA-ATAGTGTAAAGATAAAA
1 ATAAATAAATATGAA-TAAATAAAATAAAGATAAAGAAAATAAAAAATAAAG-ATAAAGACAAAA
272487 A
64 A
* * *
272488 GTAAATAAA-AT-AA-AAAT-AAATAAATATAAAGAAATTAAAAAATAAAGATAAAGACAAAAA
1 ATAAATAAATATGAATAAATAAAATAAAGATAAAGAAAATAAAAAATAAAGATAAAGACAAAAA
* *
272548 ATAAATAAATATGAATAAATAAAATGAAGATAAAGAAAAT-AAAAATAAA-ATAAAGAGAAGAAA
1 ATAAATAAATATGAATAAATAAAATAAAGATAAAGAAAATAAAAAATAAAGATAAAGA-CA-AAA
272611 A
64 A
*
272612 ATAAATAAA-ATAAATAAATA
1 ATAAATAAATATGAATAAATA
272632 TGATAAGGAA
Statistics
Matches: 121, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
59 3 0.02
60 40 0.33
61 5 0.04
62 15 0.12
63 29 0.24
64 29 0.24
ACGTcount: A:0.72, C:0.01, G:0.09, T:0.18
Consensus pattern (64 bp):
ATAAATAAATATGAATAAATAAAATAAAGATAAAGAAAATAAAAAATAAAGATAAAGACAAAAA
Found at i:272548 original size:45 final size:41
Alignment explanation
Indices: 272499--272603 Score: 124
Period size: 45 Copynumber: 2.5 Consensus size: 41
272489 TAAATAAAAT
272499 AAAAATAAATAAATATAAAGAAATTAAAAAATAAAGATAAAGACA
1 AAAAATAAATAAATATAAAGAAA-T--AAAATAAAGATAAAGA-A
* * *
272544 AAAAATAAATAAATATGAATAAATAAAATGAAGATAAAGAA
1 AAAAATAAATAAATATAAAGAAATAAAATAAAGATAAAGAA
*
272585 AATAA-AAATAAA-ATAAAGA
1 AAAAATAAATAAATATAAAGA
272604 GAAGAAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 5 0.09
40 7 0.13
41 5 0.09
42 15 0.28
44 1 0.02
45 21 0.39
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (41 bp):
AAAAATAAATAAATATAAAGAAATAAAATAAAGATAAAGAA
Found at i:272566 original size:14 final size:13
Alignment explanation
Indices: 272547--272598 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
272537 AAAGACAAAA
272547 AATAAATAAATATG
1 AATAAATAAA-ATG
272561 AATAAATAAAATG
1 AATAAATAAAATG
*
272574 AAGATAAAGAAAAT-
1 -A-ATAAATAAAATG
272588 AA-AAATAAAAT
1 AATAAATAAAAT
272599 AAAGAGAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 8 0.24
12 1 0.03
13 4 0.12
14 11 0.32
15 10 0.29
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (13 bp):
AATAAATAAAATG
Found at i:272637 original size:13 final size:13
Alignment explanation
Indices: 272414--272631 Score: 92
Period size: 13 Copynumber: 16.4 Consensus size: 13
272404 ACAAATAAGA
*
272414 AAATATAATAATAT
1 AAATAAAATAA-AT
*
272428 AAA-AAAATGAAGT
1 AAATAAAAT-AAAT
* *
272441 AAATAAAACGAGAT
1 AAATAAAA-TAAAT
* *
272455 AAAGAAAATAAAA
1 AAATAAAATAAAT
*** *
272468 AAATAGTGTAAAG
1 AAATAAAATAAAT
*
272481 ATAA-AAAGTAAAT
1 A-AATAAAATAAAT
272494 AAAATAAAAATAAAT
1 -AAAT-AAAATAAAT
*
272509 AAATATAAAGAAAT
1 AAATA-AAATAAAT
*
272523 TAA-AAAATAAAGAT
1 AAATAAAAT-AA-AT
*
272537 AAAGACAAA-AAAT
1 AAATA-AAATAAAT
*
272550 AAATAAATATGAAT
1 AAATAAA-ATAAAT
272564 AAATAAAATGAAGAT
1 AAATAAAAT-AA-AT
*
272579 AAAGAAAAT-AA-
1 AAATAAAATAAAT
*
272590 AAATAAAATAAAG
1 AAATAAAATAAAT
* *
272603 AGA-AGAA-AAAT
1 AAATAAAATAAAT
272614 AAATAAAATAAAT
1 AAATAAAATAAAT
272627 AAATA
1 AAATA
272632 TGATAAGGAA
Statistics
Matches: 152, Mismatches: 32, Indels: 41
0.68 0.14 0.18
Matches are distributed among these distances:
11 13 0.09
12 14 0.09
13 52 0.34
14 51 0.34
15 19 0.12
16 3 0.02
ACGTcount: A:0.72, C:0.01, G:0.09, T:0.19
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:274806 original size:117 final size:117
Alignment explanation
Indices: 274656--274884 Score: 307
Period size: 117 Copynumber: 2.0 Consensus size: 117
274646 AAGGATGGAT
* * *
274656 GTTGCTGGTGGACACGGTATCCTTCGTCGTGAAGTTGAAATCACAGATGGCCCTTTCGTTGTGAA
1 GTTGCTGGTGGACACGATATCCTTCATCGTGAAGTTGAAATCACAGATGGCCCATTCGTTGTGAA
274721 GTTAAGCCTTGAATTGGATAT-CATTCATCATGAAATTGAAATCCAATATTGA
66 GTTAAGCCTTGAATTGGATATAC-TTCATCATGAAATTGAAATCCAATATTGA
* * * *** * *
274773 GTTGCTTGTGGGCACGATATCCTTTATCGTGAAGTTGAAATCGTGGGTGGCTCATTCGTTGTGAA
1 GTTGCTGGTGGACACGATATCCTTCATCGTGAAGTTGAAATCACAGATGGCCCATTCGTTGTGAA
* * * *
274838 GTTGAGCCTTGGATTGGATATACTTCGTCGTGAAATTGAAATCCAAT
66 GTTAAGCCTTGAATTGGATATACTTCATCATGAAATTGAAATCCAAT
274885 CTTTTTGTTT
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
117 95 0.99
118 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (117 bp):
GTTGCTGGTGGACACGATATCCTTCATCGTGAAGTTGAAATCACAGATGGCCCATTCGTTGTGAA
GTTAAGCCTTGAATTGGATATACTTCATCATGAAATTGAAATCCAATATTGA
Found at i:275856 original size:7 final size:6
Alignment explanation
Indices: 275836--275888 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
275826 CCCACCTTAT
* *
275836 TTTTTC TTTTTC TTTTCTC TTTTCTC TTTTTC -TTTTG TTTTT- TTTCTC
1 TTTTTC TTTTTC TTTT-TC TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC
275884 TTTTT
1 TTTTT
275889 TCAATTTAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
5 8 0.20
6 20 0.49
7 13 0.32
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:275878 original size:20 final size:21
Alignment explanation
Indices: 275835--275888 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
275825 ACCCACCTTA
275835 TTTTT-TCTTTTTCTTTTC-T
1 TTTTTCTCTTTTTCTTTTCTT
* *
275854 CTTTTCTCTTTTTCTTTTGTTT
1 TTTTTCTCTTTTTCTTTT-CTT
275876 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
275889 TCAATTTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 12 0.41
22 13 0.45
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTTCTCTTTTTCTTTTCTT
Found at i:286839 original size:30 final size:30
Alignment explanation
Indices: 286783--286841 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
286773 ACAAGAATAA
*
286783 AAGTGGGTGAGCCATTATCCTCTGTCGAGG
1 AAGTGGGTGAGCCATTAACCTCTGTCGAGG
*
286813 AAGTGGGTGAGCC-TGTAACCTTTGTCGAG
1 AAGTGGGTGAGCCAT-TAACCTCTGTCGAG
286842 AATGTTGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.27
Consensus pattern (30 bp):
AAGTGGGTGAGCCATTAACCTCTGTCGAGG
Found at i:290826 original size:11 final size:11
Alignment explanation
Indices: 290812--290849 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
290802 AATTATATAT
290812 TAATTTCATTA
1 TAATTTCATTA
*
290823 TAATTAT-ATTT
1 TAATT-TCATTA
290834 TAATTTCATTA
1 TAATTTCATTA
290845 TAATT
1 TAATT
290850 ATAATATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.04
11 21 0.91
12 1 0.04
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (11 bp):
TAATTTCATTA
Found at i:290828 original size:22 final size:22
Alignment explanation
Indices: 290802--290852 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
290792 AAATTTTAAA
290802 AATTATATATTAATTTCATTAT
1 AATTATATATTAATTTCATTAT
*
290824 AATTATATTTTAATTTCATTAT
1 AATTATATATTAATTTCATTAT
290846 AATTATA
1 AATTATA
290853 ATATGTTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTATATATTAATTTCATTAT
Found at i:293429 original size:21 final size:21
Alignment explanation
Indices: 293388--293430 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
293378 GCTTCACTGC
**
293388 AAGACTTTATGGCCTTGACAA
1 AAGACTTTATGGCCTCAACAA
293409 AAGA-TTTCATGGCCTCAACAA
1 AAGACTTT-ATGGCCTCAACAA
293430 A
1 A
293431 GACCTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (21 bp):
AAGACTTTATGGCCTCAACAA
Found at i:293644 original size:19 final size:19
Alignment explanation
Indices: 293622--293664 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
293612 TTACTTGTAT
*
293622 CGATTGTGTTTACATGCAC
1 CGATTGTGTATACATGCAC
*
293641 CGATTGTGTATACTTGCAC
1 CGATTGTGTATACATGCAC
293660 CGATT
1 CGATT
293665 TGCATGCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
CGATTGTGTATACATGCAC
Found at i:305683 original size:21 final size:20
Alignment explanation
Indices: 305638--305684 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
305628 TATTCCTTGT
305638 GTTTTTGGCTGAAAATTTCA
1 GTTTTTGGCTGAAAATTTCA
305658 GTTTTTGGCTGAAAATTTCA
1 GTTTTTGGCTGAAAATTTCA
*
305678 ATTTTTG
1 GTTTTTG
305685 CTTGTTCTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.09, G:0.19, T:0.49
Consensus pattern (20 bp):
GTTTTTGGCTGAAAATTTCA
Found at i:317535 original size:26 final size:25
Alignment explanation
Indices: 317499--317579 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 25
317489 ATCCAAGTGC
317499 TAATACACATAAGGTCGTTCCCACCA
1 TAATACACATAAGGTC-TTCCCACCA
* *
317525 TAATACACATAAGGTCATACCCATCAA
1 TAATACACATAAGGTC-TTCCCA-CCA
*
317552 TAATACACATAAAGTCTTGCCCACCA
1 TAATACACATAAGGTCTT-CCCACCA
317578 TA
1 TA
317580 TGCATTTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 26 0.55
27 21 0.45
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (25 bp):
TAATACACATAAGGTCTTCCCACCA
Found at i:337074 original size:17 final size:17
Alignment explanation
Indices: 337052--337122 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
337042 AATTAAGAGA
*
337052 TAGTTTAATAAATAAAC
1 TAGTTTAATAAATGAAC
* **
337069 TAGTTTGATGGATGAAC
1 TAGTTTAATAAATGAAC
*
337086 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
337103 TAACTTTATTAAATG-AC
1 T-AGTTTAATAAATGAAC
337120 TAG
1 TAG
337123 ATGCATGAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
16 1 0.02
17 31 0.74
18 10 0.24
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:337181 original size:33 final size:33
Alignment explanation
Indices: 337096--337171 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
337086 TAGTTTAATT
* * *
337096 AATGAACTAACTTTATTAAATGACTAGATGCATG
1 AATGAACTAGC-TTACTAAATGACTAGATGCATA
*
337130 AATGAAGTAGCTTACTAAATGACTAGATGCATA
1 AATGAACTAGCTTACTAAATGACTAGATGCATA
*
337163 AATTAACTA
1 AATGAACTA
337172 CTTCCCTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 27 0.75
34 9 0.25
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (33 bp):
AATGAACTAGCTTACTAAATGACTAGATGCATA
Found at i:340330 original size:20 final size:21
Alignment explanation
Indices: 340300--340343 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
340290 CTAAAATTAG
*
340300 TACCACTAAGGCCAGTATCTA
1 TACCACTAAGGCCAGTATCAA
340321 TACC-CTAAGGCCAGTATCAA
1 TACCACTAAGGCCAGTATCAA
340341 TAC
1 TAC
340344 TTATATGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.23
Consensus pattern (21 bp):
TACCACTAAGGCCAGTATCAA
Done.