Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007853.1 Hibiscus syriacus cultivar Beakdansim tig00110213_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: 2309479
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1390217 original size:18 final size:18
Alignment explanation
Indices: 1390194--1390242 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1390184 AATTCTTACA
1390194 ATATATAAATTTAAATAT
1 ATATATAAATTTAAATAT
* *
1390212 ATATATTAAAATT-CATAT
1 ATATA-TAAATTTAAATAT
*
1390230 ATACATAAATTTA
1 ATATATAAATTTA
1390243 CGATTAGTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.24
18 13 0.52
19 6 0.24
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATAAATTTAAATAT
Found at i:1394460 original size:29 final size:29
Alignment explanation
Indices: 1394427--1394487 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
1394417 TTTGTCCATC
*
1394427 ACAAGCCGTTAGATTTACATGACGACGAA
1 ACAAGCCGTTAGATTTACATCACGACGAA
1394456 ACAAGCCGTTAGATTTACATCACGACGAA
1 ACAAGCCGTTAGATTTACATCACGACGAA
1394485 ACA
1 ACA
1394488 GTCAACGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (29 bp):
ACAAGCCGTTAGATTTACATCACGACGAA
Found at i:1411168 original size:10 final size:10
Alignment explanation
Indices: 1411155--1411183 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1411145 AAAAAGCTAC
1411155 AAAAAAT-AA
1 AAAAAATAAA
1411164 AAAAAATAAA
1 AAAAAATAAA
1411174 AAAAAATAAA
1 AAAAAATAAA
1411184 GCATCCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:1412406 original size:30 final size:30
Alignment explanation
Indices: 1412345--1412409 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1412335 AACTGTATAT
* **
1412345 AAAACAAAATTTAAGGACCAAATTGTATTC
1 AAAACAAAATTCAAGGACCAAATTACATTC
*
1412375 AAAACAAAA-TCAATGACCAAATTACATTTC
1 AAAACAAAATTCAAGGACCAAATTACA-TTC
1412405 AAAAC
1 AAAAC
1412410 TAAACTCGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (30 bp):
AAAACAAAATTCAAGGACCAAATTACATTC
Found at i:1416032 original size:15 final size:15
Alignment explanation
Indices: 1416008--1416037 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1415998 GGTGTTGTCG
1416008 GTACACTAATATCTT
1 GTACACTAATATCTT
*
1416023 GTACAGTAATATCTT
1 GTACACTAATATCTT
1416038 TAGGTACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (15 bp):
GTACACTAATATCTT
Found at i:1437249 original size:84 final size:84
Alignment explanation
Indices: 1437105--1437457 Score: 546
Period size: 84 Copynumber: 4.2 Consensus size: 84
1437095 AAAGGAGGAT
* * **
1437105 CTCGAAGCAAAGGAGGAAAAGCTCCATTCGAAAGAGAAACAACTCAGCTCGGTCCAAATATGGAT
1 CTCGAAGCAAAGGAGGAAGAGCTCCATTCGAAAGAGAAACAACTCAGCTCGGTCCTAATATCCAT
1437170 CGAAGGATGCACCAAGCAG
66 CGAAGGATGCACCAAGCAG
* *
1437189 CTCGAAGGAAAGGAGGAAGAGCTCCATTCGAAAGAGAAACAACTCGGCTCGGTCCTAATATCCAT
1 CTCGAAGCAAAGGAGGAAGAGCTCCATTCGAAAGAGAAACAACTCAGCTCGGTCCTAATATCCAT
1437254 CGAAGGATGCACCAAGCAG
66 CGAAGGATGCACCAAGCAG
* * *
1437273 CTCGAAGGAAAGGAGGAAGAGCTCCATTCGAAAGAGAAACAACTCGGCTCGGTCCTCATATCCAT
1 CTCGAAGCAAAGGAGGAAGAGCTCCATTCGAAAGAGAAACAACTCAGCTCGGTCCTAATATCCAT
*
1437338 TGAAGGATGCACCAAGCAG
66 CGAAGGATGCACCAAGCAG
* * *
1437357 CTCGAAGCAAAGGAGGAAGAGCTCCATTCGAAAGAGAAACAACTCAGCTCTGTCCAAATGT-CAG
1 CTCGAAGCAAAGGAGGAAGAGCTCCATTCGAAAGAGAAACAACTCAGCTCGGTCCTAATATCCA-
* *
1437421 TCAAAGGATGCACCAAGCTG
65 TCGAAGGATGCACCAAGCAG
*
1437441 CTTGAAGCAAAGGAGGA
1 CTCGAAGCAAAGGAGGA
1437458 TGAACTTACC
Statistics
Matches: 250, Mismatches: 18, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
83 2 0.01
84 248 0.99
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (84 bp):
CTCGAAGCAAAGGAGGAAGAGCTCCATTCGAAAGAGAAACAACTCAGCTCGGTCCTAATATCCAT
CGAAGGATGCACCAAGCAG
Found at i:1437820 original size:21 final size:21
Alignment explanation
Indices: 1437778--1437817 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1437768 AAAAAGTCGG
1437778 TTGAACAGCAAAGAAAAGAAC
1 TTGAACAGCAAAGAAAAGAAC
* *
1437799 TTGAACTG-AAAGAGAAGAA
1 TTGAACAGCAAAGAAAAGAA
1437818 ACTAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.55, C:0.10, G:0.23, T:0.12
Consensus pattern (21 bp):
TTGAACAGCAAAGAAAAGAAC
Found at i:1442455 original size:14 final size:14
Alignment explanation
Indices: 1442436--1442462 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1442426 TTCATTCGAG
1442436 TTAAATCAAATAAC
1 TTAAATCAAATAAC
1442450 TTAAATCAAATAA
1 TTAAATCAAATAA
1442463 TACAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TTAAATCAAATAAC
Found at i:1442726 original size:23 final size:23
Alignment explanation
Indices: 1442699--1442749 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1442689 TTTTTAATAA
* *
1442699 CTCTACTTTTATGACACGTTTTT
1 CTCTACCTTTATGACACATTTTT
*
1442722 CTCTACCTTTATGACATATTTTT
1 CTCTACCTTTATGACACATTTTT
1442745 CTCTA
1 CTCTA
1442750 TCTCTTGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.51
Consensus pattern (23 bp):
CTCTACCTTTATGACACATTTTT
Found at i:1442766 original size:23 final size:23
Alignment explanation
Indices: 1442699--1442767 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
1442689 TTTTTAATAA
* * **
1442699 CTCTACTTTTATGACACGTTTTT
1 CTCTACCTCTATGACATATTTTT
*
1442722 CTCTACCTTTATGACATATTTTT
1 CTCTACCTCTATGACATATTTTT
* *
1442745 CTCTATCTCT-TGACATGTTTTT
1 CTCTACCTCTATGACATATTTTT
1442767 C
1 C
1442768 GGTTGTTTAG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 12 0.30
23 28 0.70
ACGTcount: A:0.17, C:0.23, G:0.07, T:0.52
Consensus pattern (23 bp):
CTCTACCTCTATGACATATTTTT
Found at i:1452104 original size:19 final size:19
Alignment explanation
Indices: 1452043--1452105 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
1452033 ATTATTTATA
*
1452043 TATTTATTTTTTAAAAATT
1 TATTTATTATTTAAAAATT
* *
1452062 TATATTTTTATATAAATAATATT
1 TAT-TTATTAT-TTAA-AA-ATT
*
1452085 TATTTATTGTTTAAAAATT
1 TATTTATTATTTAAAAATT
1452104 TA
1 TA
1452106 ATGTATATGG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 8 0.24
20 7 0.21
21 6 0.18
22 7 0.21
23 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTTATTATTTAAAAATT
Found at i:1455850 original size:2 final size:2
Alignment explanation
Indices: 1455843--1455905 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1455833 TAATGTGTCT
1455843 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1455885 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
1455906 GAAGTTGAGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1461385 original size:2 final size:2
Alignment explanation
Indices: 1461378--1461408 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1461368 ATGTTATGTT
1461378 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 T
1461409 TTTGGTAAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1463114 original size:20 final size:20
Alignment explanation
Indices: 1463062--1463114 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
1463052 ATATATATTA
*
1463062 ATTATAA-ATTTGATAATTT
1 ATTATAATATTTGACAATTT
* *
1463081 ATTGTAATAATTGACAA-TT
1 ATTATAATATTTGACAATTT
1463100 ATTATAATTATTTGA
1 ATTATAA-TATTTGA
1463115 ACTATTGAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (20 bp):
ATTATAATATTTGACAATTT
Found at i:1471958 original size:16 final size:15
Alignment explanation
Indices: 1471920--1471977 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
1471910 TATTAATATA
1471920 TAATTGAAAGTTA-GAG
1 TAATT-AAA-TTATGAG
1471936 TAATTAAATTATGAG
1 TAATTAAATTATGAG
*
1471951 TAATTTAAAATT-TAAG
1 TAA-TT-AAATTATGAG
1471967 TAATTAAATTA
1 TAATTAAATTA
1471978 AAAAAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
14 8 0.22
15 11 0.30
16 13 0.35
17 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (15 bp):
TAATTAAATTATGAG
Found at i:1474614 original size:78 final size:78
Alignment explanation
Indices: 1474524--1474675 Score: 216
Period size: 78 Copynumber: 1.9 Consensus size: 78
1474514 AATTTCATAC
* * * * **
1474524 TTGTGTACGTTTATTTATTTAC-GAAGATGTTTATGTTCGTTTGTTTAGCATTCGTGCATGTTCG
1 TTGTGTACGTTTAATTATTT-CTAAAGAGGTTCATGTTCGTTTGTTTAGCATTCACGCATGTTCG
1474588 TTTAACATTCGTAT
65 TTTAACATTCGTAT
* *
1474602 TTGTGTACGTTTAATTATTTCTAAAGGGGTTCATGTTCGTTTGTTTAGCATTTACGCATGTTCGT
1 TTGTGTACGTTTAATTATTTCTAAAGAGGTTCATGTTCGTTTGTTTAGCATTCACGCATGTTCGT
1474667 TTAACATTC
66 TTAACATTC
1474676 AAGAACATGT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
77 1 0.02
78 64 0.98
ACGTcount: A:0.20, C:0.12, G:0.19, T:0.49
Consensus pattern (78 bp):
TTGTGTACGTTTAATTATTTCTAAAGAGGTTCATGTTCGTTTGTTTAGCATTCACGCATGTTCGT
TTAACATTCGTAT
Found at i:1478075 original size:18 final size:20
Alignment explanation
Indices: 1478037--1478090 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
1478027 TATTATTTTT
*
1478037 CTTTCTATTCTTTTAACAATTA
1 CTTTCTATT-TTTTTA-AATTA
*
1478059 CTTT-T-TTTTTTTAAATTT
1 CTTTCTATTTTTTTAAATTA
1478077 CTTTCTATTTTTTT
1 CTTTCTATTTTTTT
1478091 GACGTTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 8 0.29
19 6 0.21
20 9 0.32
21 1 0.04
22 4 0.14
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.69
Consensus pattern (20 bp):
CTTTCTATTTTTTTAAATTA
Found at i:1478778 original size:33 final size:33
Alignment explanation
Indices: 1478736--1478866 Score: 127
Period size: 33 Copynumber: 4.2 Consensus size: 33
1478726 TGGTGCCCAA
1478736 GGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGT
1 GGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGT
* *
1478769 GGTGCAGGAGTTAGAGCCCAAGGTCCGGTTGGT
1 GGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGT
* * ***
1478802 GTTGCA-G-G-T--A-CCGAAGG-T--GTCCAT
1 GGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGT
1478826 GGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGT
1 GGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGT
*
1478859 GTTGCAGG
1 GGTGCAGG
1478867 TACCGAAGGT
Statistics
Matches: 75, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
24 8 0.11
25 1 0.01
26 1 0.01
27 7 0.09
28 1 0.01
29 1 0.01
30 7 0.09
31 2 0.03
32 1 0.01
33 46 0.61
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.24
Consensus pattern (33 bp):
GGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGT
Found at i:1479047 original size:27 final size:27
Alignment explanation
Indices: 1479016--1479104 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
1479006 GCCGGAGCCC
1479016 AAGGTTCGGTTGGTGTTGCAGGTACCG
1 AAGGTTCGGTTGGTGTTGCAGGTACCG
** ** * *
1479043 AAGGTGTC-CATGGTGCAGGC-GCCGGAGCCC
1 AAGGT-TCGGTTGGTG-TTGCAG--GTA-CCG
1479073 AAGGTTCGGTTGGTGTTGCAGGTACCG
1 AAGGTTCGGTTGGTGTTGCAGGTACCG
1479100 AAGGT
1 AAGGT
1479105 GTCCATGGTG
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
27 18 0.42
28 6 0.14
29 6 0.14
30 13 0.30
ACGTcount: A:0.17, C:0.19, G:0.40, T:0.24
Consensus pattern (27 bp):
AAGGTTCGGTTGGTGTTGCAGGTACCG
Found at i:1479087 original size:30 final size:30
Alignment explanation
Indices: 1478997--1479087 Score: 75
Period size: 30 Copynumber: 3.1 Consensus size: 30
1478987 AGGTGTCCAC
1478997 GGTGCAGGCGCCGGAGCCCAAGGTTCGGTT
1 GGTGCAGGCGCCGGAGCCCAAGGTTCGGTT
** * * **
1479027 GGTG-TTGCAG--GTA-CCGAAGGTGTC-CAT
1 GGTGCAGGC-GCCGGAGCCCAAGGT-TCGGTT
1479054 GGTGCAGGCGCCGGAGCCCAAGGTTCGGTT
1 GGTGCAGGCGCCGGAGCCCAAGGTTCGGTT
1479084 GGTG
1 GGTG
1479088 TTGCAGGTAC
Statistics
Matches: 42, Mismatches: 12, Indels: 14
0.62 0.18 0.21
Matches are distributed among these distances:
27 13 0.31
28 6 0.14
29 6 0.14
30 17 0.40
ACGTcount: A:0.14, C:0.23, G:0.43, T:0.20
Consensus pattern (30 bp):
GGTGCAGGCGCCGGAGCCCAAGGTTCGGTT
Found at i:1479113 original size:27 final size:27
Alignment explanation
Indices: 1479026--1479114 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
1479016 AAGGTTCGGT
1479026 TGGTGTTGCAGGTACCGAAGGTGTCCA
1 TGGTGTTGCAGGTACCGAAGGTGTCCA
** * * **
1479053 TGGTGCAGGC-GCCGGAGCCCAAGGT-TCGGT
1 TGGTG-TTGCAG--GTA-CCGAAGGTGTC-CA
1479083 TGGTGTTGCAGGTACCGAAGGTGTCCA
1 TGGTGTTGCAGGTACCGAAGGTGTCCA
1479110 TGGTG
1 TGGTG
1479115 CAGGAGTTGG
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
27 18 0.42
28 6 0.14
29 6 0.14
30 13 0.30
ACGTcount: A:0.16, C:0.20, G:0.40, T:0.24
Consensus pattern (27 bp):
TGGTGTTGCAGGTACCGAAGGTGTCCA
Found at i:1479315 original size:57 final size:57
Alignment explanation
Indices: 1478768--1479307 Score: 796
Period size: 57 Copynumber: 9.5 Consensus size: 57
1478758 GTTCGGTTGG
* *
1478768 TGGTGCAGGAGTTAGAGCCCAAGGTCCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
1478825 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
* * * *
1478882 TGGTGCAGGAGTTGGAGCCCAAGGTTCAGTTGGCT-TTACTGGTACTGAAGGTGTCCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGG-TGTTGCAGGTACCGAAGGTGTCCA
* *
1478939 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTAGGTGTTGCAGGTATCGAAGGTGTCCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
* * **
1478996 CGGTGCAGGCGCCGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
* **
1479053 TGGTGCAGGCGCCGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
* * *
1479110 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGCT-TTACTGGTACTGAAGGTGTCCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGG-TGTTGCAGGTACCGAAGGTGTCCA
* *
1479167 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGCTGTTGCAGGTATCGAAGGTGTCCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
* * * *
1479224 TGGTGCAGGGGCTGGAGTCCAAGGTTCGGTTGGTGTTGCAGGTATCGAAGGTGTCCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
* ** *
1479281 TGGTGCAGGCGCGGGAGTCCAAGGTTC
1 TGGTGCAGGAGTTGGAGCCCAAGGTTC
1479308 AACTGGTGAT
Statistics
Matches: 443, Mismatches: 36, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
56 2 0.00
57 439 0.99
58 2 0.00
ACGTcount: A:0.17, C:0.19, G:0.39, T:0.24
Consensus pattern (57 bp):
TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
Found at i:1479350 original size:171 final size:167
Alignment explanation
Indices: 1478768--1479382 Score: 711
Period size: 171 Copynumber: 3.6 Consensus size: 167
1478758 GTTCGGTTGG
* * * * *
1478768 TGGTGCAGGAGTTAGAGCCCAAGGTCCGGTTGGTGT-TGCAGGTACCGAAGGTGTCCATGGTGCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTC-GCTGGTGTCT-C-GGTA-TGAAGGTGTCCACGGTGCA
*
1478832 GGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCATGGTGCAGGAGTTGG
62 GGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCATGGTGCAGGAGCTGG
* * *
1478897 AGCCCAAGGTTCAGTTGGCT-TTACTGGTACTGAAGGTGTCCA
127 AGCCCAAGGTTCGGTTGG-TGTTGCAGGTAC-GAAGGTGTCCA
*
1478939 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTAGGTGT-TGCAGGTATCGAAGGTGTCCACGGTGCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTCGCT-GGTGTCT-C-GGTAT-GAAGGTGTCCACGGTGCA
* ** * *
1479003 GGCGCCGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCATGGTGCAGGCGCCGG
62 GGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCATGGTGCAGGAGCTGG
1479068 AGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCA
127 AGCCCAAGGTTCGGTTGGTGTTGCAGGTA-CGAAGGTGTCCA
* * *
1479110 TGGTGCAGGAGTTGGAGCCCAAGGTTCGGTTGGCTTTACT-GGTACTGAAGGTGTCCATGGTGCA
1 TGGTGCAGGAGTTGGAGCCCAAGGTTC-GCTGG-TGT-CTCGGTA-TGAAGGTGTCCACGGTGCA
* * *
1479174 GGAGTTGGAGCCCAAGGTTCGGTTGCTGTTGCAGGTATCGAAGGTGTCCATGGTGCAGGGGCTGG
62 GGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCATGGTGCAGGAGCTGG
*
1479239 AGTCCAAGGTTCGGTTGGTGTTGCAGGTATCGAAGGTGTCCA
127 AGCCCAAGGTTCGGTTGGTGTTGCAGGTA-CGAAGGTGTCCA
* ** * * * * **
1479281 TGGTGCAGGCGCGGGAGTCCAAGGTTCAACTGGTGATCTCGGTGT-AACTGGT-TCCCACGATAT
1 TGGTGCAGGAGTTGGAGCCCAAGGTTC-GCTGGTG-TCTCGGTATGAA--GGTGT-CCACGGTGC
*
1479344 AGGAGTTGGAGCCCAAGGTTCAGTTGGTGTTGCAGGTAC
61 AGGAGTTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTAC
1479383 TGTCCATGGT
Statistics
Matches: 388, Mismatches: 42, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
169 2 0.01
170 8 0.02
171 371 0.96
172 6 0.02
174 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.39, T:0.25
Consensus pattern (167 bp):
TGGTGCAGGAGTTGGAGCCCAAGGTTCGCTGGTGTCTCGGTATGAAGGTGTCCACGGTGCAGGAG
TTGGAGCCCAAGGTTCGGTTGGTGTTGCAGGTACCGAAGGTGTCCATGGTGCAGGAGCTGGAGCC
CAAGGTTCGGTTGGTGTTGCAGGTACGAAGGTGTCCA
Found at i:1489600 original size:8 final size:8
Alignment explanation
Indices: 1489587--1489619 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1489577 AACCACAAAC
1489587 CTAAATAT
1 CTAAATAT
1489595 CTAAATAT
1 CTAAATAT
*
1489603 CTAAATCT
1 CTAAATAT
1489611 CTAAA-AT
1 CTAAATAT
1489618 CT
1 CT
1489620 CCCATGCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 3 0.13
8 20 0.87
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (8 bp):
CTAAATAT
Found at i:1490023 original size:30 final size:28
Alignment explanation
Indices: 1489955--1490023 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
1489945 AGAGTTGAAA
*
1489955 TTAAATATTTTAAGATTTTAGATGTTTT
1 TTAAATATTTTAAGATTTAAGATGTTTT
* *
1489983 ATAAAAATTTTAGAGAAATTTAAGAT-TTTT
1 TTAAATATTTTA-AG--ATTTAAGATGTTTT
1490013 TTAAATATTTT
1 TTAAATATTTT
1490024 TTTGTTTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 10 0.30
29 2 0.06
30 13 0.39
31 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (28 bp):
TTAAATATTTTAAGATTTAAGATGTTTT
Found at i:1495497 original size:6 final size:6
Alignment explanation
Indices: 1495486--1495514 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1495476 TTATCCCAAT
1495486 GTTTTC GTTTTC GTTTTC GTTTTC GTTTT
1 GTTTTC GTTTTC GTTTTC GTTTTC GTTTT
1495515 TCAATTTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.17, T:0.69
Consensus pattern (6 bp):
GTTTTC
Found at i:1496194 original size:37 final size:37
Alignment explanation
Indices: 1496121--1496195 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
1496111 GTTGAAAAAT
* *
1496121 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
1496158 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
1496195 A
1 A
1496196 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:1503392 original size:24 final size:23
Alignment explanation
Indices: 1503314--1503401 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
1503304 AAATCTTATA
*
1503314 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1503337 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1503360 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
1503384 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
1503402 TATATGAGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 1 0.02
23 35 0.64
24 18 0.33
25 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1505461 original size:18 final size:19
Alignment explanation
Indices: 1505421--1505463 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1505411 AAATTTAGAA
*
1505421 TAAAAATCAATATAAATTC
1 TAAAATTCAATATAAATTC
1505440 TAAAATTCAATA-AACATT-
1 TAAAATTCAATATAA-ATTC
1505458 TAAAAT
1 TAAAAT
1505464 GGTTTAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATTCAATATAAATTC
Found at i:1516007 original size:2 final size:2
Alignment explanation
Indices: 1516000--1516072 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1515990 ACTTCTGTTC
1516000 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
1516042 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
1516073 AAAATGAGAG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1517449 original size:60 final size:60
Alignment explanation
Indices: 1517353--1517508 Score: 170
Period size: 60 Copynumber: 2.6 Consensus size: 60
1517343 GTTTGAGATA
* * * * * * **
1517353 AAATTTAAATGTTTAAAAGTATGGGGACCAACTTAAAATGAGGGTCATAATTTGGAG-GTG
1 AAATTTAAATATTTAAAAGTTTGAGGATCAATTTAAAATGAGAGTCAT-ATTTGGAGAAAG
* * *
1517413 AAATTAAAATATTTAAAAGTTTGAGGATTAATTTAAAATGAGAGTCATATTTTGAGAAAG
1 AAATTTAAATATTTAAAAGTTTGAGGATCAATTTAAAATGAGAGTCATATTTGGAGAAAG
* * *
1517473 AAATTTAAATATTTAAAATTTTAAAGATCAATTTAA
1 AAATTTAAATATTTAAAAGTTTGAGGATCAATTTAA
1517509 GATAAGAATC
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
59 7 0.09
60 72 0.91
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.35
Consensus pattern (60 bp):
AAATTTAAATATTTAAAAGTTTGAGGATCAATTTAAAATGAGAGTCATATTTGGAGAAAG
Found at i:1529795 original size:36 final size:36
Alignment explanation
Indices: 1529746--1529850 Score: 101
Period size: 36 Copynumber: 2.9 Consensus size: 36
1529736 ATAATTTGCG
*
1529746 TTATAAT-TCTTTATTCTAGTTGTAATAAGTTTGAAA
1 TTATAATCT-TTTATTCTAGTTGTAAGAAGTTTGAAA
* * *
1529782 TTATAATCTTTTATT-TTGATTATAAGAATTTTGAAA
1 TTATAATCTTTTATTCTAG-TTGTAAGAAGTTTGAAA
*
1529818 TTATAATCCTTTGT-TTCGA-TTGTAAGAAGTTTG
1 TTATAAT-CTTT-TATTCTAGTTGTAAGAAGTTTG
1529851 TAAGGAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
35 2 0.04
36 46 0.82
37 7 0.12
38 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (36 bp):
TTATAATCTTTTATTCTAGTTGTAAGAAGTTTGAAA
Found at i:1544401 original size:2 final size:2
Alignment explanation
Indices: 1544394--1544421 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1544384 TGGTTCCCAC
1544394 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
1544422 TCCTTTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1550407 original size:72 final size:72
Alignment explanation
Indices: 1550329--1550470 Score: 223
Period size: 72 Copynumber: 2.0 Consensus size: 72
1550319 CTTTTAGAAA
** *
1550329 TAAATAAATAAATATTAATATAATATTAAAAATTTAAATGAACACGAATAAAATATAAATACA-T
1 TAAATAAATAAATACGAATATAATATTAAAAATTT-AATAAACACGAATAAAATATAAATACATT
1550393 TAAAAAGC
65 TAAAAAGC
* *
1550401 TAAATAAATAAATACGAATATAATATTAAAAATTTAATAAATACGAATAAAATATAAATATATTT
1 TAAATAAATAAATACGAATATAATATTAAAAATTTAATAAACACGAATAAAATATAAATACATTT
1550466 AAAAA
66 AAAAA
1550471 AACTAATAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 24 0.38
72 40 0.62
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (72 bp):
TAAATAAATAAATACGAATATAATATTAAAAATTTAATAAACACGAATAAAATATAAATACATTT
AAAAAGC
Found at i:1551097 original size:16 final size:17
Alignment explanation
Indices: 1551073--1551106 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1551063 ATAAAAACAA
*
1551073 TAATTAAATC-TTTAAT
1 TAATAAAATCGTTTAAT
1551089 TAATAAAATCGTTTAAT
1 TAATAAAATCGTTTAAT
1551106 T
1 T
1551107 TGACACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATAAAATCGTTTAAT
Found at i:1554160 original size:2 final size:2
Alignment explanation
Indices: 1554153--1554182 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1554143 ATCTAACTGA
1554153 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
1554183 GAAAAGGGGT
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:1555154 original size:39 final size:40
Alignment explanation
Indices: 1555099--1555176 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 40
1555089 ATAAATTGAC
*
1555099 ATATAATCAAAATAAAATAATATTGATAATTTGAAAGTTG
1 ATATAATCAAAATAAAATAATATTGATAATTTAAAAGTTG
*
1555139 ATATAAT-AAAATAAAATGATATTGATAATTTAAAAGTT
1 ATATAATCAAAATAAAATAATATTGATAATTTAAAAGTT
1555177 ATACTATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 29 0.81
40 7 0.19
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (40 bp):
ATATAATCAAAATAAAATAATATTGATAATTTAAAAGTTG
Found at i:1571845 original size:17 final size:18
Alignment explanation
Indices: 1571813--1571846 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1571803 AAAAAGTTCA
*
1571813 TAAAAAAACTTGAGATTT
1 TAAAAAAAATTGAGATTT
1571831 TAAAAAAAATT-AGATT
1 TAAAAAAAATTGAGATT
1571847 ATTATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (18 bp):
TAAAAAAAATTGAGATTT
Found at i:1576550 original size:207 final size:207
Alignment explanation
Indices: 1576195--1576602 Score: 807
Period size: 207 Copynumber: 2.0 Consensus size: 207
1576185 CCATCCTCAC
1576195 TATGAATATCCCTAGGATCCAAATCATCATTCACCAACAGTTTATAAGGAACAGAACCAACATTT
1 TATGAATATCCCTAGGATCCAAATCATCATTCACCAACAGTTTATAAGGAACAGAACCAACATTT
*
1576260 TCCTCGACTTCACTGACATCATTATCCACCAAACTAGCTTTCTCCTCAGCATCCTCAACTATACC
66 TCCTCGACTTCACTGACATCATTATCCACCAAACTAACTTTCTCCTCAGCATCCTCAACTATACC
1576325 CCTCCTCTTCCCTGCATGTCTTTCTATGACAAAATCATCATCACCAGCATATCTCTCCACAACAG
131 CCTCCTCTTCCCTGCATGTCTTTCTATGACAAAATCATCATCACCAGCATATCTCTCCACAACAG
1576390 TATGATACTCGG
196 TATGATACTCGG
1576402 TATGAATATCCCTAGGATCCAAATCATCATTCACCAACAGTTTATAAGGAACAGAACCAACATTT
1 TATGAATATCCCTAGGATCCAAATCATCATTCACCAACAGTTTATAAGGAACAGAACCAACATTT
1576467 TCCTCGACTTCACTGACATCATTATCCACCAAACTAACTTTCTCCTCAGCATCCTCAACTATACC
66 TCCTCGACTTCACTGACATCATTATCCACCAAACTAACTTTCTCCTCAGCATCCTCAACTATACC
1576532 CCTCCTCTTCCCTGCATGTCTTTCTATGACAAAATCATCATCACCAGCATATCTCTCCACAACAG
131 CCTCCTCTTCCCTGCATGTCTTTCTATGACAAAATCATCATCACCAGCATATCTCTCCACAACAG
1576597 TATGAT
196 TATGAT
1576603 CCTCAGTAGC
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 200 1.00
ACGTcount: A:0.31, C:0.32, G:0.09, T:0.29
Consensus pattern (207 bp):
TATGAATATCCCTAGGATCCAAATCATCATTCACCAACAGTTTATAAGGAACAGAACCAACATTT
TCCTCGACTTCACTGACATCATTATCCACCAAACTAACTTTCTCCTCAGCATCCTCAACTATACC
CCTCCTCTTCCCTGCATGTCTTTCTATGACAAAATCATCATCACCAGCATATCTCTCCACAACAG
TATGATACTCGG
Found at i:1577566 original size:2 final size:2
Alignment explanation
Indices: 1577559--1577620 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1577549 TAAAAAGGTT
1577559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1577601 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1577621 AATAGATTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1588638 original size:30 final size:30
Alignment explanation
Indices: 1588604--1588665 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1588594 TGGCGGTAAT
*
1588604 GGTTTCGAG-TCCAGAGTGCTGCCAAGTCAA
1 GGTTTCAAGTTCC-GAGTGCTGCCAAGTCAA
*
1588634 GGTTTCAAGTTCCGAGTGCTTCCAAGTCAA
1 GGTTTCAAGTTCCGAGTGCTGCCAAGTCAA
1588664 GG
1 GG
1588666 ATAACGAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (30 bp):
GGTTTCAAGTTCCGAGTGCTGCCAAGTCAA
Found at i:1591465 original size:15 final size:15
Alignment explanation
Indices: 1591442--1591471 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1591432 TTATTAACAT
1591442 TTATAAAAGAAAAAG
1 TTATAAAAGAAAAAG
*
1591457 TTATGAAAGAAAAAG
1 TTATAAAAGAAAAAG
1591472 ATACAAAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (15 bp):
TTATAAAAGAAAAAG
Found at i:1597829 original size:19 final size:19
Alignment explanation
Indices: 1597805--1597844 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1597795 TACGAGTATG
1597805 TATTGATTCGTTGTCTTGC
1 TATTGATTCGTTGTCTTGC
1597824 TATTGATTCGTTGTCTTGC
1 TATTGATTCGTTGTCTTGC
1597843 TA
1 TA
1597845 ATCTTCTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.15, G:0.20, T:0.53
Consensus pattern (19 bp):
TATTGATTCGTTGTCTTGC
Found at i:1603412 original size:25 final size:23
Alignment explanation
Indices: 1603369--1603418 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
1603359 ATAATTTGTT
*
1603369 TTCTTCCCTTAAAATTTTATAAA
1 TTCTTCCCTTAAAATTTTAAAAA
*
1603392 TTCTTCCCTTCTAAAGTTTTAAAAA
1 TTCTTCCC-T-TAAAATTTTAAAAA
1603417 TT
1 TT
1603419 TATTCTCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 1 0.04
25 14 0.61
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.48
Consensus pattern (23 bp):
TTCTTCCCTTAAAATTTTAAAAA
Found at i:1603414 original size:23 final size:23
Alignment explanation
Indices: 1603369--1603414 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1603359 ATAATTTGTT
*
1603369 TTCTTCCCTTAAAATTTTATAAA
1 TTCTTCCCTTAAAAGTTTATAAA
*
1603392 TTCTTCCCTTCTAAAGTTT-TAAA
1 TTCTTCCCTT-AAAAGTTTATAAA
1603415 AATTTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (23 bp):
TTCTTCCCTTAAAAGTTTATAAA
Found at i:1604848 original size:9 final size:9
Alignment explanation
Indices: 1604834--1604858 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1604824 TGGGAGGGTG
1604834 GGGTTGGTT
1 GGGTTGGTT
1604843 GGGTTGGTT
1 GGGTTGGTT
1604852 GGGTTGG
1 GGGTTGG
1604859 ATAGTGCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (9 bp):
GGGTTGGTT
Found at i:1612756 original size:94 final size:94
Alignment explanation
Indices: 1612595--1612779 Score: 370
Period size: 94 Copynumber: 2.0 Consensus size: 94
1612585 CACGTTCATT
1612595 TCCCTTTGCTAAAAGATGGCAGAAACAAAACATGATTGGTGGGAGCTCTTTTTTTTAATGAAATG
1 TCCCTTTGCTAAAAGATGGCAGAAACAAAACATGATTGGTGGGAGCTCTTTTTTTTAATGAAATG
1612660 ATGATATTTTTTTTGTATTTCAACATAAA
66 ATGATATTTTTTTTGTATTTCAACATAAA
1612689 TCCCTTTGCTAAAAGATGGCAGAAACAAAACATGATTGGTGGGAGCTCTTTTTTTTAATGAAATG
1 TCCCTTTGCTAAAAGATGGCAGAAACAAAACATGATTGGTGGGAGCTCTTTTTTTTAATGAAATG
1612754 ATGATATTTTTTTTGTATTTCAACAT
66 ATGATATTTTTTTTGTATTTCAACAT
1612780 GTTAAATGAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (94 bp):
TCCCTTTGCTAAAAGATGGCAGAAACAAAACATGATTGGTGGGAGCTCTTTTTTTTAATGAAATG
ATGATATTTTTTTTGTATTTCAACATAAA
Found at i:1613658 original size:21 final size:21
Alignment explanation
Indices: 1613629--1613668 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1613619 GGTTTAAACC
* *
1613629 GGAGATGGTGCCGGTGTTCAA
1 GGAGATGGTGACGGAGTTCAA
*
1613650 GGAGTTGGTGACGGAGTTC
1 GGAGATGGTGACGGAGTTC
1613669 GCGGTTTGTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.12, G:0.45, T:0.25
Consensus pattern (21 bp):
GGAGATGGTGACGGAGTTCAA
Found at i:1618356 original size:61 final size:59
Alignment explanation
Indices: 1618284--1618429 Score: 145
Period size: 61 Copynumber: 2.4 Consensus size: 59
1618274 TTATTCAATT
* *
1618284 ATGACTCTCATTTTAAATTGGTCCCT-AAACTTTTAAATATTTTAATTTCAT-CCTTAAAACC
1 ATGACT-TCATTTTAAATTGGTCCCTCAAACTTTTAAACATTTCAATTTCATGCC--AAAA-C
* * * * *
1618345 ATGACTATCATTTTAGATTAGT-CTTCAAACTTTTGAACATTTCAATTTCATGCCAAAAT
1 ATGACT-TCATTTTAAATTGGTCCCTCAAACTTTTAAACATTTCAATTTCATGCCAAAAC
*
1618404 ATGATCTTCATTCTAAATTGGTCCCT
1 ATGA-CTTCATTTTAAATTGGTCCCT
1618430 TGACTAATTC
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
59 16 0.23
60 10 0.14
61 41 0.59
62 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.42
Consensus pattern (59 bp):
ATGACTTCATTTTAAATTGGTCCCTCAAACTTTTAAACATTTCAATTTCATGCCAAAAC
Found at i:1618711 original size:3 final size:3
Alignment explanation
Indices: 1618703--1618784 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
1618693 TCCCATTATC
1618703 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1618750 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1618785 AGTACTAATT
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1624948 original size:64 final size:66
Alignment explanation
Indices: 1624872--1625017 Score: 217
Period size: 64 Copynumber: 2.2 Consensus size: 66
1624862 ACCCATTCAA
* *
1624872 GGGGAACCGATACCCCTCAACGAATATGAATTTCCAGAATACTAGA-GGGAATCGATA-CCCCCA
1 GGGGAACCGATACCCCTCAACGAATATGAAATTCCAG-ATACTAGAGGGGAACCGATACCCCCCA
1624935 -G
65 GG
* *
1624936 GGGGAACCGATACCCCTCAACGGATATGAAATTCCAGATGCTAGAGGGGAACCGATACCCCCCAG
1 GGGGAACCGATACCCCTCAACGAATATGAAATTCCAGATACTAGAGGGGAACCGATACCCCCCAG
1625001 G
66 G
*
1625002 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
1625018 CATGAGAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
63 7 0.09
64 45 0.61
65 6 0.08
66 16 0.22
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (66 bp):
GGGGAACCGATACCCCTCAACGAATATGAAATTCCAGATACTAGAGGGGAACCGATACCCCCCAG
G
Found at i:1625657 original size:23 final size:23
Alignment explanation
Indices: 1625613--1625657 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1625603 ATCATTATAT
*
1625613 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1625636 GGCACTTCGGTGCAGTTATACG
1 GGCACTACGGTGCAATTATACG
1625658 AGCTGTGGTG
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:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1631510 original size:21 final size:21
Alignment explanation
Indices: 1631468--1631510 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1631458 TTTCTGGGTT
* * *
1631468 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1631489 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1631510 A
1 A
1631511 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1631571 original size:67 final size:68
Alignment explanation
Indices: 1631490--1631641 Score: 252
Period size: 67 Copynumber: 2.2 Consensus size: 68
1631480 ACCCATTCAA
* *
1631490 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
1631555 -GG
66 GGG
* *
1631557 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
1631622 GGG
66 GGG
*
1631625 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1631642 ATGAGAAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
67 61 0.77
68 18 0.23
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.14
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCA
GGG
Found at i:1632296 original size:23 final size:23
Alignment explanation
Indices: 1632252--1632296 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1632242 ATCATTATAT
*
1632252 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1632275 GGCACTTCGGTGCAGTTATACG
1 GGCACTACGGTGCAATTATACG
1632297 AGCTGTGGTG
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:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1633405 original size:230 final size:230
Alignment explanation
Indices: 1632872--1633405 Score: 745
Period size: 229 Copynumber: 2.3 Consensus size: 230
1632862 GGGGGTGTTA
* * * * *
1632872 CAGTGTTGGTCTTCGATCATGAACTCAAGCAGTTGTGTATGTGAATTGACAATGGTTAAAAGAGA
1 CAGTGTTGGTATTCAATCTTGAACTCAAGCAGTTGTGTATATGAATTGACAATGGTTAAAAAAGA
* * * *
1632937 TTTTGAATAGATTCAACTAATTTTTAGTTTCTTCGAATTCAAACCCGAAACCAGTTTGAGTATGA
66 -TATGAACAAATTCAACTAATTTTTAATTTCTTCGAATTCAAACCCGAAACCAGTTTGAGTATGA
* *
1633002 AAAAAATGTAGCTACATGAATCAATTAACATTTAATTATTATCTACTTTTAATTTATGTTAAGGT
130 AAAAAATGTAGCTACATGAATCAAATAACATTTAATTATTATCTACTTCTAATTTATGTTAAGGT
* *
1633067 TTAAATTATTGAGTTACCTCCTTGGTTGGTTGAAGG
195 TTAAATTATTGAGTTACCTCCTTGGTTAGTTAAAGG
* * * * ** *
1633103 CAGTGTTGGTATTCAATCTTGAGCTCAAACAATTATGTATGA-GAATTGACAAAAGCTAAAAAA-
1 CAGTGTTGGTATTCAATCTTGAACTCAAGCAGTTGTGTAT-ATGAATTGACAATGGTTAAAAAAG
*
1633166 ATCATGAACAAATTCAACTAATTTTTAATTTCTTCGAATTCAAACCTGAAA-CAGTTTGAGTATG
65 AT-ATGAACAAATTCAACTAATTTTTAATTTCTTCGAATTCAAACCCGAAACCAGTTTGAGTATG
* *
1633230 AAAAAAAATGTA-ATCACATGAATCAAATAACA-TTAATTATTATCTACTTCTAATTTATGTTAG
129 -AAAAAAATGTAGCT-ACATGAATCAAATAACATTTAATTATTATCTACTTCTAATTTATGTTAA
*
1633293 GGTTTAAATTATTGAGTTATCTCCTTGGTTAGTTAAAGG
192 GGTTTAAATTATTGAGTTACCTCCTTGGTTAGTTAAAGG
* *
1633332 GAGTGTTGTTATTCAATCTTGAACTCAAGCAGTTGTGTATATGAATTGACAATGGTTAAAAAAGA
1 CAGTGTTGGTATTCAATCTTGAACTCAAGCAGTTGTGTATATGAATTGACAATGGTTAAAAAAGA
1633397 CTATGAACA
66 -TATGAACA
1633406 TATGTTACCT
Statistics
Matches: 263, Mismatches: 33, Indels: 15
0.85 0.11 0.05
Matches are distributed among these distances:
228 1 0.00
229 132 0.50
230 79 0.30
231 51 0.19
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (230 bp):
CAGTGTTGGTATTCAATCTTGAACTCAAGCAGTTGTGTATATGAATTGACAATGGTTAAAAAAGA
TATGAACAAATTCAACTAATTTTTAATTTCTTCGAATTCAAACCCGAAACCAGTTTGAGTATGAA
AAAAATGTAGCTACATGAATCAAATAACATTTAATTATTATCTACTTCTAATTTATGTTAAGGTT
TAAATTATTGAGTTACCTCCTTGGTTAGTTAAAGG
Found at i:1634416 original size:2 final size:2
Alignment explanation
Indices: 1634409--1634441 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1634399 TGTATCTATC
1634409 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 T
1634442 GATTTTCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1639271 original size:21 final size:21
Alignment explanation
Indices: 1639238--1639277 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1639228 AAGTTTAAAT
1639238 TTTAAATTGTAGGAGTTAGAA
1 TTTAAATTGTAGGAGTTAGAA
* * *
1639259 TTTAGATTTTAGGATTTAG
1 TTTAAATTGTAGGAGTTAG
1639278 GATTAGAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (21 bp):
TTTAAATTGTAGGAGTTAGAA
Found at i:1647657 original size:105 final size:105
Alignment explanation
Indices: 1647463--1647664 Score: 278
Period size: 105 Copynumber: 1.9 Consensus size: 105
1647453 GACCACATAT
* *
1647463 AAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCCCAAAAGACCTCATACAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCCCAAAAGACCTCATACAT
1647528 GCTCCAAAGAATACATATACGTCCCGAAGGACTACGTAAA
66 GCTCCAAAGAATACATATACGTCCCGAAGGACTACGTAAA
* * * * * * *
1647568 AAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATATGTGTCGCAAAGGACCTCATAGAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCCCAAAAGACCTCATACAT
* * * * *
1647633 GTTCCATAGGATACCTATATGTCCCGAAGGAC
66 GCTCCAAAGAATACATATACGTCCCGAAGGAC
1647665 CGCGTAGACC
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 83 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.23
Consensus pattern (105 bp):
AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCCCAAAAGACCTCATACAT
GCTCCAAAGAATACATATACGTCCCGAAGGACTACGTAAA
Found at i:1650473 original size:2 final size:2
Alignment explanation
Indices: 1650466--1650499 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1650456 TAAAATAATA
1650466 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
1650500 CCGAAGTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1651739 original size:22 final size:22
Alignment explanation
Indices: 1651714--1651757 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1651704 AAGGATCCAC
1651714 CACCATCATCCAA-ATCCTCTAT
1 CACCATCATCCAACAT-CTCTAT
1651736 CACCATCATCCAACATCTCTAT
1 CACCATCATCCAACATCTCTAT
1651758 GACCTCCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (22 bp):
CACCATCATCCAACATCTCTAT
Found at i:1657591 original size:24 final size:24
Alignment explanation
Indices: 1657563--1657609 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1657553 CCAAATAACC
1657563 AACAAACCATAACAAACTAATAAT
1 AACAAACCATAACAAACTAATAAT
*
1657587 AACAAACCATAATAAACTAATAA
1 AACAAACCATAACAAACTAATAA
1657610 CAAACTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.64, C:0.19, G:0.00, T:0.17
Consensus pattern (24 bp):
AACAAACCATAACAAACTAATAAT
Found at i:1659256 original size:11 final size:11
Alignment explanation
Indices: 1659235--1659316 Score: 87
Period size: 11 Copynumber: 7.4 Consensus size: 11
1659225 CCAAATAACC
1659235 AACAAAC-AAT
1 AACAAACTAAT
1659245 AACAAACTAATAAT
1 AACAAAC---TAAT
1659259 AACAAACTAAT
1 AACAAACTAAT
**
1659270 AACAAGTTAAT
1 AACAAACTAAT
*
1659281 AACAAAC-CAT
1 AACAAACTAAT
1659291 AACAAACTAAT
1 AACAAACTAAT
*
1659302 AACAAACTAGT
1 AACAAACTAAT
1659313 AACA
1 AACA
1659317 CTCTAACACT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
10 16 0.27
11 34 0.57
14 10 0.17
ACGTcount: A:0.62, C:0.18, G:0.02, T:0.17
Consensus pattern (11 bp):
AACAAACTAAT
Found at i:1659266 original size:14 final size:14
Alignment explanation
Indices: 1659228--1659271 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1659218 ATATAGCCCA
* * *
1659228 AATAACCAACAAAC
1 AATAACAAACTAAT
1659242 AATAACAAACTAAT
1 AATAACAAACTAAT
1659256 AATAACAAACTAAT
1 AATAACAAACTAAT
1659270 AA
1 AA
1659272 CAAGTTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.66, C:0.18, G:0.00, T:0.16
Consensus pattern (14 bp):
AATAACAAACTAAT
Found at i:1659294 original size:21 final size:22
Alignment explanation
Indices: 1659235--1659316 Score: 87
Period size: 21 Copynumber: 3.7 Consensus size: 22
1659225 CCAAATAACC
1659235 AACAAAC-AATAACAAACTAATAAT
1 AACAAACTAATAACAAAC---TAAT
**
1659259 AACAAACTAATAACAAGTTAAT
1 AACAAACTAATAACAAACTAAT
*
1659281 AACAAAC-CATAACAAACTAAT
1 AACAAACTAATAACAAACTAAT
*
1659302 AACAAACTAGTAACA
1 AACAAACTAATAACA
1659317 CTCTAACACT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
21 18 0.37
22 16 0.33
24 7 0.14
25 8 0.16
ACGTcount: A:0.62, C:0.18, G:0.02, T:0.17
Consensus pattern (22 bp):
AACAAACTAATAACAAACTAAT
Found at i:1660706 original size:6 final size:6
Alignment explanation
Indices: 1660669--1660695 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1660659 GTTATTGATT
1660669 TTGCAA TTGCAA TTGCAA TTGCAA TTG
1 TTGCAA TTGCAA TTGCAA TTGCAA TTG
1660696 TAGTTGCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (6 bp):
TTGCAA
Found at i:1662897 original size:14 final size:14
Alignment explanation
Indices: 1662878--1662933 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1662868 CGTTCGTGAA
1662878 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
1662892 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
1662905 --TT-GTTTATGTT
1 CGTTCGATTATGTT
1662916 CGTTCGATTATGTT
1 CGTTCGATTATGTT
1662930 CGTT
1 CGTT
1662934 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:1662912 original size:24 final size:24
Alignment explanation
Indices: 1662885--1662954 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
1662875 GAACGTTCGA
*
1662885 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
1662909 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
1662933 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
1662955 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:1663693 original size:10 final size:10
Alignment explanation
Indices: 1663678--1663752 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1663668 GGGTCTCCAA
1663678 CGTTTATGTT
1 CGTTTATGTT
1663688 CGTTTATGTT
1 CGTTTATGTT
1663698 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
1663709 ATGTTCGTGTT
1 -CGTTTATGTT
1663720 CGTTTATGTT
1 CGTTTATGTT
1663730 CG----TGTT
1 CGTTTATGTT
1663736 CGTTTATGTT
1 CGTTTATGTT
1663746 CGTTTAT
1 CGTTTAT
1663753 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1663709 original size:16 final size:16
Alignment explanation
Indices: 1663684--1663748 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1663674 CCAACGTTTA
1663684 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1663700 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
1663716 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1663732 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1663748 T
1 T
1663749 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1680664 original size:21 final size:21
Alignment explanation
Indices: 1680638--1680677 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1680628 CAGAACCCCA
*
1680638 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1680659 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1680678 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:1702767 original size:2 final size:2
Alignment explanation
Indices: 1702760--1702787 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1702750 ACAGTCCTTC
1702760 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1702788 AAATTGGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1704066 original size:36 final size:36
Alignment explanation
Indices: 1704026--1704095 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
1704016 TTTGATACAA
* * *
1704026 TTCTATGATTGCACCACATGTATTTATGTTTGTTAT
1 TTCTATGATTACACCACATGCATTCATGTTTGTTAT
* *
1704062 TTCTATGGTTACACCATATGCATTCATGTTTGTT
1 TTCTATGATTACACCACATGCATTCATGTTTGTT
1704096 GCTGAGTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (36 bp):
TTCTATGATTACACCACATGCATTCATGTTTGTTAT
Found at i:1709278 original size:31 final size:31
Alignment explanation
Indices: 1709240--1709308 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 31
1709230 AATAGTTATG
1709240 AATTACAAGAGGTAGTAATTAAACCTCCTGT
1 AATTACAAGAGGTAGTAATTAAACCTCCTGT
* *
1709271 AATTAC-A-AGGTAGTAATTACACCTCTTGT
1 AATTACAAGAGGTAGTAATTAAACCTCCTGT
*
1709300 AGTTACAAG
1 AATTACAAG
1709309 GAACTAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 25 0.76
30 2 0.06
31 6 0.18
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (31 bp):
AATTACAAGAGGTAGTAATTAAACCTCCTGT
Found at i:1709316 original size:29 final size:29
Alignment explanation
Indices: 1709255--1709317 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1709245 CAAGAGGTAG
* *
1709255 TAATTAAACCTCCTGTAATTACAAGGTAG
1 TAATTAAACCTCCTGTAATTACAAGGAAC
* * *
1709284 TAATTACACCTCTTGTAGTTACAAGGAAC
1 TAATTAAACCTCCTGTAATTACAAGGAAC
1709313 TAATT
1 TAATT
1709318 CCCTAGACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (29 bp):
TAATTAAACCTCCTGTAATTACAAGGAAC
Found at i:1735916 original size:31 final size:32
Alignment explanation
Indices: 1735858--1735918 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1735848 TTTTTTGAAA
***
1735858 TGGTGGGAATACATTATCTTTTGTTATTTATT
1 TGGTGGGAATACATTATCTTAAATTATTTATT
1735890 TGGTGGGAATA-ATTATCTTAAATTATTTA
1 TGGTGGGAATACATTATCTTAAATTATTTA
1735919 GTATTTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
TGGTGGGAATACATTATCTTAAATTATTTATT
Found at i:1736414 original size:9 final size:9
Alignment explanation
Indices: 1736400--1736442 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1736390 AAATTATTTG
1736400 TATAAAAAT
1 TATAAAAAT
1736409 TATAAAAA-
1 TATAAAAAT
*
1736417 TATACAAAT
1 TATAAAAAT
1736426 TATAAATAAT
1 TATAAA-AAT
*
1736436 AATAAAA
1 TATAAAA
1736443 TATTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
TATAAAAAT
Found at i:1736425 original size:17 final size:18
Alignment explanation
Indices: 1736400--1736442 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1736390 AAATTATTTG
1736400 TATAAAAATTATAAA-AA
1 TATAAAAATTATAAATAA
*
1736417 TATACAAATTATAAATAA
1 TATAAAAATTATAAATAA
1736435 TAATAAAA
1 T-ATAAAA
1736443 TATTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 14 0.64
18 3 0.14
19 5 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TATAAAAATTATAAATAA
Found at i:1738592 original size:24 final size:24
Alignment explanation
Indices: 1738564--1738613 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1738554 TTGGGAAAGA
1738564 TAATTTAAATCATCTATAAGAGAT
1 TAATTTAAATCATCTATAAGAGAT
*
1738588 TAATTTAAATCATCTATATGAGAT
1 TAATTTAAATCATCTATAAGAGAT
1738612 TA
1 TA
1738614 TTGGACTGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (24 bp):
TAATTTAAATCATCTATAAGAGAT
Found at i:1742364 original size:235 final size:237
Alignment explanation
Indices: 1741943--1742422 Score: 910
Period size: 235 Copynumber: 2.0 Consensus size: 237
1741933 AAGACACCCA
*
1741943 CACTATCGTCTTTCTCGCTCTCATTGTTGATGTGGTCCATTGAAGCTGGCTGCACTTTTTCCTTG
1 CACTTTCGTCTTTCTCGCTCTCATTGTTGATGTGGTCCATTGAAGCTGGCTGCACTTTTTCC---
1742008 GCTTGGCATTGGAAGCATAAGTTAAATTGCTTGAGTTGGAATCAAGGAAGAGGCAGACCACAGCA
63 GCTTGGCATTGGAAGCATAAGTTAAATTGCTTGAGTTGGAATCAAGGAAGAGGCAGACCACAGCA
1742073 CAATCATCAACTTTTGAAGTCGGGTATTTGTATCTCCAAGCTCGAACTGCTGAATGAACCAAGGC
128 CAATCATCAACTTTTGAAGTCGGGTATTTGTATCTCCAAGCTCGAACTGCTGAATGAACCAAGGC
1742138 TCGAGCAGCAGAGGAACGAGCAGGGGCAGATGCTACAATATCTAC
193 TCGAGCAGCAGAGGAACGAGCAGGGGCAGATGCTACAATATCTAC
1742183 CACTTTCGTCTTTCTCGCTCTCATTGTTGATGTGGTCCATTGAAGCTGGCTGCACTTTTT-C-CT
1 CACTTTCGTCTTTCTCGCTCTCATTGTTGATGTGGTCCATTGAAGCTGGCTGCACTTTTTCCGCT
1742246 TGGCATTGGAAGCATAAGTTAAATTGCTTGAGTTGGAATCAAGGAAGAGGCAGACCACAGCACAA
66 TGGCATTGGAAGCATAAGTTAAATTGCTTGAGTTGGAATCAAGGAAGAGGCAGACCACAGCACAA
1742311 TCATCAACTTTTGAAGTCGGGTATTTGTATCTCCAAGCTCGAACTGCTGAATGAACCAAGGCTCG
131 TCATCAACTTTTGAAGTCGGGTATTTGTATCTCCAAGCTCGAACTGCTGAATGAACCAAGGCTCG
1742376 AGCAGCAGAGGAACGAGCAGGGGCAGATGCTACAATATCTAC
196 AGCAGCAGAGGAACGAGCAGGGGCAGATGCTACAATATCTAC
1742418 CACTT
1 CACTT
1742423 CGTTGTTTGA
Statistics
Matches: 239, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
235 179 0.75
239 1 0.00
240 59 0.25
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (237 bp):
CACTTTCGTCTTTCTCGCTCTCATTGTTGATGTGGTCCATTGAAGCTGGCTGCACTTTTTCCGCT
TGGCATTGGAAGCATAAGTTAAATTGCTTGAGTTGGAATCAAGGAAGAGGCAGACCACAGCACAA
TCATCAACTTTTGAAGTCGGGTATTTGTATCTCCAAGCTCGAACTGCTGAATGAACCAAGGCTCG
AGCAGCAGAGGAACGAGCAGGGGCAGATGCTACAATATCTAC
Found at i:1747469 original size:13 final size:13
Alignment explanation
Indices: 1747453--1747504 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
1747443 ATTTACTTAT
1747453 TTAATTTTATATA
1 TTAATTTTATATA
*
1747466 TTAATTTTTTTAATTTA
1 TTAA---TTTT-ATATA
1747483 CTTAATTTTATATA
1 -TTAATTTTATATA
1747497 TTAATTTT
1 TTAATTTT
1747505 TTTGTCACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 12 0.38
14 4 0.12
15 4 0.12
16 4 0.12
17 4 0.12
18 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
TTAATTTTATATA
Found at i:1747481 original size:35 final size:35
Alignment explanation
Indices: 1747415--1747507 Score: 126
Period size: 31 Copynumber: 2.8 Consensus size: 35
1747405 ATCTTTTATT
*
1747415 TTATTT-ATTGTAT-TATTAATTTTTTTTAATTTAC
1 TTATTTAATTTTATATATTAA-TTTTTTTAATTTAC
1747449 TTATTTAATTTTATATATTAATTTTTTTAATTTAC
1 TTATTTAATTTTATATATTAATTTTTTTAATTTAC
1747484 ----TTAATTTTATATATTAATTTTTTT
1 TTATTTAATTTTATATATTAATTTTTTT
1747508 GTCACTCTAC
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
31 24 0.43
34 6 0.11
35 20 0.36
36 6 0.11
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (35 bp):
TTATTTAATTTTATATATTAATTTTTTTAATTTAC
Found at i:1747747 original size:44 final size:43
Alignment explanation
Indices: 1747683--1747874 Score: 166
Period size: 44 Copynumber: 4.5 Consensus size: 43
1747673 CTATAATAGT
*
1747683 AGAAGTGAGATTGAAAAAAATTAGAGGTCTCAATTATAAAGGTA
1 AGAAGTGGGATTG-AAAAAATTAGAGGTCTCAATTATAAAGGTA
* * *
1747727 AGAAGTGGGATTGAAGAAAATTAGATGTCTCGATTATAAAAGTA
1 AGAAGTGGGATTGAA-AAAATTAGAGGTCTCAATTATAAAGGTA
*
1747771 AAAAGTAGGG-TTGAAAACAA-T--AGGTCTCAATTATAAAGGTA
1 AGAAGT-GGGATTGAAAA-AATTAGAGGTCTCAATTATAAAGGTA
*
1747812 A-AA-TGCGAGATT-ATAAAAATTAGAGG-CTTCAATTATAAAGATA
1 AGAAGTG-G-GATTGA-AAAAATTAGAGGTC-TCAATTATAAAGGTA
* * * *
1747855 AAAAATGGGAATAAAAAAAT
1 AGAAGTGGGATTGAAAAAAT
1747875 ATGAGCTCAA
Statistics
Matches: 124, Mismatches: 10, Indels: 29
0.76 0.06 0.18
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 6 0.05
41 24 0.19
42 1 0.01
43 32 0.26
44 53 0.43
45 5 0.04
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.25
Consensus pattern (43 bp):
AGAAGTGGGATTGAAAAAATTAGAGGTCTCAATTATAAAGGTA
Found at i:1747884 original size:84 final size:84
Alignment explanation
Indices: 1747796--1747959 Score: 197
Period size: 84 Copynumber: 2.0 Consensus size: 84
1747786 AACAATAGGT
* * * * * *
1747796 CTCAATTATAAAGGTAAAATGCGAGATTATAAAAATTA-GAGGCTTCAATTATAAAGATAAAAAA
1 CTCAATTAAAAAGATAAAATACAAGATTATAAAAATTAGGA-GCATCAATTATAAAAATAAAAAA
*
1747860 TGGGAA-TAAAAAAATATGAG
65 T-GAAACTAAAAAAATATGAG
* * * *
1747880 CTCAATTAAAAAGATAAAATATAATATTATAAAAGTTAGGAGCATCAATTATAAAAATAGAAAAT
1 CTCAATTAAAAAGATAAAATACAAGATTATAAAAATTAGGAGCATCAATTATAAAAATAAAAAAT
1747945 GAAACTAAAAAAATA
66 GAAACTAAAAAAATA
1747960 AAGACATCAA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
83 3 0.04
84 62 0.93
85 2 0.03
ACGTcount: A:0.56, C:0.06, G:0.13, T:0.25
Consensus pattern (84 bp):
CTCAATTAAAAAGATAAAATACAAGATTATAAAAATTAGGAGCATCAATTATAAAAATAAAAAAT
GAAACTAAAAAAATATGAG
Found at i:1747994 original size:42 final size:42
Alignment explanation
Indices: 1747826--1747998 Score: 136
Period size: 42 Copynumber: 4.1 Consensus size: 42
1747816 GCGAGATTAT
* * * *
1747826 AAAAATTAGAGGCTTCAATTATAAAGATAAAAAATGGGAATAA
1 AAAAATAAGA-GCATCAATTATAAAGATAAAAAATAGGACTAA
* * * ** *
1747869 AAAAATATGAGC-TCAATTAAAAAGATAAAATATAATATTATA
1 AAAAATAAGAGCATCAATTATAAAGATAAAAAATAGGACTA-A
** * * * *
1747911 AAAGTTAGGAGCATCAATTATAAAAATAGAAAAT-GAAACTAA
1 AAAAATAAGAGCATCAATTATAAAGATAAAAAATAG-GACTAA
*
1747953 AAAAATAA-AGACATCAATTATGAAGATAAAAAATAGGACTAA
1 AAAAATAAGAG-CATCAATTATAAAGATAAAAAATAGGACTAA
1747995 AAAA
1 AAAA
1747999 TTAATGGTAC
Statistics
Matches: 100, Mismatches: 25, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
41 24 0.24
42 47 0.47
43 29 0.29
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.23
Consensus pattern (42 bp):
AAAAATAAGAGCATCAATTATAAAGATAAAAAATAGGACTAA
Found at i:1748151 original size:2 final size:2
Alignment explanation
Indices: 1748144--1748182 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1748134 TATGAAACTT
1748144 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 T
1748183 GACGATTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1762277 original size:44 final size:47
Alignment explanation
Indices: 1762206--1762301 Score: 144
Period size: 44 Copynumber: 2.1 Consensus size: 47
1762196 TATTTTCGTT
*
1762206 TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTA
* *
1762252 TTTTTGAAT-AA-GCATGCGAATTAGATATCATGCAGTTAGGATTTC
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTA
1762297 TTTTT
1 TTTTT
1762302 ATGGATAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 27 0.59
45 10 0.22
46 9 0.20
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (47 bp):
TTTTTGAATAAATGCATGCGAACTAGATATCATGCAGTTAGGATTTA
Found at i:1771980 original size:10 final size:10
Alignment explanation
Indices: 1771955--1771992 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1771945 TGCTTGAAGA
*
1771955 AGAAATAAAAG
1 AGAAA-AAATG
1771966 AGAAAAAATG
1 AGAAAAAATG
1771976 AG-AAAAATG
1 AGAAAAAATG
1771985 AGAAAAAA
1 AGAAAAAA
1771993 GAAAAATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 9 0.36
10 11 0.44
11 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (10 bp):
AGAAAAAATG
Found at i:1771981 original size:8 final size:9
Alignment explanation
Indices: 1771969--1772001 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1771959 ATAAAAGAGA
1771969 AAAAATGAG
1 AAAAATGAG
1771978 AAAAATGAG
1 AAAAATGAG
1771987 AAAAA--AG
1 AAAAATGAG
1771994 AAAAATGA
1 AAAAATGA
1772002 TGGAAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.32
9 15 0.68
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (9 bp):
AAAAATGAG
Found at i:1772009 original size:19 final size:16
Alignment explanation
Indices: 1771976--1772090 Score: 68
Period size: 16 Copynumber: 7.3 Consensus size: 16
1771966 AGAAAAAATG
1771976 AGAAAAATGAGAAAAA
1 AGAAAAATGAGAAAAA
1771992 AGAAAAATGATGGAAAAA
1 AGAAAAATGA--GAAAAA
1772010 ACG--AAA--AG-AAAA
1 A-GAAAAATGAGAAAAA
1772022 A-AAAAA-GA-AAAAA
1 AGAAAAATGAGAAAAA
**
1772035 AGGAAAAGGGAAGAAAAA
1 A-GAAAAATG-AGAAAAA
*
1772053 ATGAAAAATGAAAAAAA
1 A-GAAAAATGAGAAAAA
*
1772070 AGGAAAATGA-AAAAA
1 AGAAAAATGAGAAAAA
1772085 GAGAAA
1 -AGAAA
1772091 TAAAAGGAGG
Statistics
Matches: 79, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
12 8 0.10
13 7 0.09
15 10 0.13
16 23 0.29
17 11 0.14
18 19 0.24
19 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.20, T:0.05
Consensus pattern (16 bp):
AGAAAAATGAGAAAAA
Found at i:1772033 original size:25 final size:26
Alignment explanation
Indices: 1772005--1772060 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
1771995 AAAATGATGG
1772005 AAAAAACGAAAA-GAAAAAAAAAAGA
1 AAAAAACGAAAAGGAAAAAAAAAAGA
* * *
1772030 AAAAAAGGAAAAGGGAAGAAAAAATGA
1 AAAAAACGAAAA-GGAAAAAAAAAAGA
1772057 AAAA
1 AAAA
1772061 TGAAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 11 0.42
27 15 0.58
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (26 bp):
AAAAAACGAAAAGGAAAAAAAAAAGA
Found at i:1772050 original size:61 final size:60
Alignment explanation
Indices: 1771954--1772084 Score: 149
Period size: 61 Copynumber: 2.1 Consensus size: 60
1771944 TTGCTTGAAG
* * * * *
1771954 AAGAAATAAAAGAGAAAAAATGAGAAAAATGAGAAAAAA-GAAAAATGATGGAAAAAACGAA
1 AAGAAAAAAAAAAGAAAAAAAGAGAAAAAGGAGAAAAAATGAAAAATGA--AAAAAAACGAA
* *
1772015 AAGAAAAAAAAAAGAAAAAAAG-GAAAAGGGAAGAAAAAATGAAAAATGAAAAAAAAGGAA
1 AAGAAAAAAAAAAGAAAAAAAGAGAAAAAGG-AGAAAAAATGAAAAATGAAAAAAAACGAA
1772075 AATGAAAAAA
1 AA-GAAAAAA
1772085 GAGAAATAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
60 17 0.28
61 34 0.57
62 9 0.15
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (60 bp):
AAGAAAAAAAAAAGAAAAAAAGAGAAAAAGGAGAAAAAATGAAAAATGAAAAAAAACGAA
Found at i:1772084 original size:25 final size:25
Alignment explanation
Indices: 1771969--1772084 Score: 85
Period size: 25 Copynumber: 4.5 Consensus size: 25
1771959 ATAAAAGAGA
* *
1771969 AAAAATGAGAAAAATGAGAAAAAAG
1 AAAAATGAAAAAAATGAAAAAAAAG
*
1771994 AAAAATGATGGAAAAAACGAAAAGAAAA-
1 AAAAATGA---AAAAAATGAAAA-AAAAG
* * **
1772022 AAAAAAGAAAAAAAGGAAAAGGGAAG
1 AAAAATGAAAAAAATGAAAA-AAAAG
1772048 AAAAAATG--AAAAATGAAAAAAAAG
1 -AAAAATGAAAAAAATGAAAAAAAAG
*
1772072 GAAAATGAAAAAA
1 AAAAATGAAAAAA
1772085 GAGAAATAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
23 6 0.08
24 3 0.04
25 36 0.51
27 6 0.08
28 16 0.23
29 4 0.06
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (25 bp):
AAAAATGAAAAAAATGAAAAAAAAG
Found at i:1773478 original size:51 final size:51
Alignment explanation
Indices: 1773401--1773946 Score: 561
Period size: 51 Copynumber: 10.3 Consensus size: 51
1773391 GAAGCAAACT
*
1773401 CGTTTGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACC
1 CGTTT-TTGAAGATTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACC
* * *
1773452 AGTTTGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTT-TTGAAGATTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACC
* * * *
1773503 AGTTCGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTT-TTTGAAGATTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACC
* * * * *
1773554 AGTTCGTTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACA
1 CGTT-TTTGAAGATTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACC
*
1773605 CGTTTATTGAAGA-TCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACC
1 CGTTT-TTGAAGATTCGAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACC
*
1773656 CGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACC
1 CGTTTT-TGAAGA---TTCGAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACC
*
1773711 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTT-TGAAGA---TTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACC
*
1773766 CGTTTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACC
1 CG-TTT-TTGAAGA---TTCGAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACC
* *
1773822 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACC
1 CGTTTT-TGAAGA---TTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACC
* *
1773877 CGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCAGACC
1 CGTTTT-TGAAGA---TTCGAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACC
1773932 CGTTATTTGAAGATT
1 CGTT-TTTGAAGATT
1773947 TTTTAAGTCT
Statistics
Matches: 459, Mismatches: 19, Indels: 33
0.90 0.04 0.06
Matches are distributed among these distances:
50 2 0.00
51 198 0.43
52 4 0.01
54 5 0.01
55 195 0.42
56 52 0.11
57 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (51 bp):
CGTTTTTGAAGATTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACC
Found at i:1773693 original size:55 final size:55
Alignment explanation
Indices: 1773416--1773946 Score: 599
Period size: 55 Copynumber: 9.9 Consensus size: 55
1773406 GTTGAAGATT
* *
1773416 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCAGTTTGT-TGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTT-TATGAAGATTGTTC
* ** *
1773467 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT-TGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTT-TTATGAAGATTGTTC
* ** *
1773518 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT-TGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTT-TTATGAAGATTGTTC
* * *
1773569 GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTATTGAAGA----TC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTA-TGAAGATTGTTC
*
1773620 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
*
1773675 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
* *
1773730 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTT-ATGAAGATTGTTC
*
1773786 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
* *
1773841 GAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
* *
1773896 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCAGACCCGTTATT-TGAAGATT
1 GAGTTCTATACTCTCTGAA-GGAATAGGGAGCGGACCCGTT-TTATGAAGATT
1773947 TTTTAAGTCT
Statistics
Matches: 444, Mismatches: 20, Indels: 28
0.90 0.04 0.06
Matches are distributed among these distances:
49 1 0.00
50 2 0.00
51 178 0.40
52 6 0.01
54 4 0.01
55 198 0.45
56 53 0.12
57 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (55 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
Found at i:1773818 original size:166 final size:162
Alignment explanation
Indices: 1773416--1773946 Score: 671
Period size: 166 Copynumber: 3.3 Consensus size: 162
1773406 GTTGAAGATT
* * *
1773416 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCAGTTTGTTGAAGATT-GAGTCCTATACTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTCGAGTTCTATACTC
* ** * *
1773480 TCTGAA-GGAATAGGGAGCGGACAAGTTCGT-TGAAGA---TT-GAGTCCTATACTCTCTGAAGG
66 CCTGAACGG-ATAGGGAGCGGACCCGTT-TTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGG
** *
1773539 AATAGGGAGCGGACAAGTTCGT-TGAAGA---TT-
129 AATAGGGAGCGGACCCGTT-TTATGAAGATTGTTC
* *
1773569 GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTATTGAAGA-TCGAGTTCTATACTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTCGAGTTCTATACTC
*
1773633 CCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-
66 CCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAA-GGA
1773697 ATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
130 ATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
* * *
1773730 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACCCG-TTTGTTGAAGA---TTCGAGTTCTAT
1773795 ACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAA
62 ACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAA
* *
1773860 GGAATAGAGAGCAGACCCGTTTTATGAAGATTGTTC
127 GGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
* *
1773896 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCAGACCCGTTAT-TTGAAGATT
1 GAGTCCTATACTCTCTGAA-GGAATAGGGAGCAGACCCGTT-TGTTGAAGATT
1773947 TTTTAAGTCT
Statistics
Matches: 332, Mismatches: 25, Indels: 33
0.85 0.06 0.08
Matches are distributed among these distances:
152 2 0.01
153 84 0.25
154 2 0.01
156 3 0.01
157 39 0.12
158 2 0.01
160 2 0.01
161 34 0.10
162 12 0.04
165 11 0.03
166 139 0.42
167 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (162 bp):
GAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTCGAGTTCTATACTC
CCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAA
TAGGGAGCGGACCCGTTTTATGAAGATTGTTC
Found at i:1779056 original size:14 final size:14
Alignment explanation
Indices: 1779037--1779098 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
1779027 ATTTGTATTA
1779037 TTTAGAGTTTAGGG
1 TTTAGAGTTTAGGG
1779051 TTTAGAGTTTTA-GG
1 TTTAGAG-TTTAGGG
* *
1779065 TTTAGGGTTTAGGTT
1 TTTAGAGTTTAGG-G
*
1779080 TTTAGATTTTAGGG
1 TTTAGAGTTTAGGG
*
1779094 CTTAG
1 TTTAG
1779099 GATTGAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.10
14 20 0.51
15 15 0.38
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (14 bp):
TTTAGAGTTTAGGG
Found at i:1779068 original size:21 final size:21
Alignment explanation
Indices: 1779037--1779099 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
1779027 ATTTGTATTA
1779037 TTTAGAGTTTAGGGTTTAGAGT
1 TTTAGAGTTTAGGGTTTAG-GT
1779059 TTTAG-GTTTAGGGTTTAGGTT
1 TTTAGAGTTTAGGGTTTAGG-T
* *
1779080 TTTAGATTTTAGGGCTTAGG
1 TTTAGAGTTTAGGGTTTAGG
1779100 ATTGAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.03
21 19 0.51
22 17 0.46
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.48
Consensus pattern (21 bp):
TTTAGAGTTTAGGGTTTAGGT
Found at i:1789223 original size:15 final size:16
Alignment explanation
Indices: 1789203--1789236 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1789193 CCTTAAGTCT
1789203 AAAATTT-TAGTTATA
1 AAAATTTCTAGTTATA
1789218 AAAATTTCTAGTTATA
1 AAAATTTCTAGTTATA
1789234 AAA
1 AAA
1789237 TAATATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (16 bp):
AAAATTTCTAGTTATA
Found at i:1789237 original size:15 final size:14
Alignment explanation
Indices: 1789202--1789237 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
1789192 TCCTTAAGTC
1789202 TAAAATTTTAGTTA
1 TAAAATTTTAGTTA
1789216 TAAAAATTTCTAGTTA
1 T-AAAATTT-TAGTTA
1789232 TAAAAT
1 TAAAAT
1789238 AATATTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 12 0.60
16 7 0.35
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (14 bp):
TAAAATTTTAGTTA
Found at i:1792436 original size:278 final size:277
Alignment explanation
Indices: 1791934--1792486 Score: 1079
Period size: 278 Copynumber: 2.0 Consensus size: 277
1791924 AGATACTATG
*
1791934 CCAACGTTAAATTATGAAGTTCATAGTCTTTTACATTGTAATTAGCTTGAATAGTTTTTTTCCCT
1 CCAACATTAAATTATGAAGTTCATAGTCTTTTACATTGTAATTAGCTTGAATAGTTTTTTTCCCT
1791999 ATAACCATCCATAAATTATTCAGGTTTCTGGAATTTCTTCTTTCCATTTGAGGAACATTGACCAG
66 ATAACCATCCATAAATTATTCAGGTTTCTGGAATTTCTTCTTTCCATTTGAGGAACATTGACCAG
1792064 AGGTAATTTTTGGTTGTTAGATATGTATGAATGTATTTGCATGTTCTATAGCTTCAAATTAAATG
131 AGGTAATTTTTGGTTGTTAGATATGTATGAATGTATTTGCATGTTCTATAGCTTCAAATTAAATG
1792129 TGATTCACCAAAAATTGCTTTAGTTGCACTTGGAAACCTAAACTTGATTTAGTTGAAAAGTGGGC
196 TGATTCACCAAAAATTGCTTTAGTTGCACTTGGAAACCTAAACTTGATTTAGTTGAAAAGTGGGC
1792194 AATCAGGCTCAGGAATA
261 AATCAGGCTCAGGAATA
*
1792211 CCAACATTAAATTATTAAGTTCATAGTCTTTTACATTGTAATTAGCTTGAATAGTTTTTTTCCCC
1 CCAACATTAAATTATGAAGTTCATAGTCTTTTACATTGTAATTAGCTTGAATAGTTTTTTT-CCC
1792276 TATAACCATCCATAAATTATTCAGGTTTCTGGAATTTCTTCTTTCCATTTGAGGAACATTGACCA
65 TATAACCATCCATAAATTATTCAGGTTTCTGGAATTTCTTCTTTCCATTTGAGGAACATTGACCA
1792341 GAGGTAATTTTTGGTTGTTAGATATGTATGAATGTATTTGCATGTTCTATAGCTTCAAATTAAAT
130 GAGGTAATTTTTGGTTGTTAGATATGTATGAATGTATTTGCATGTTCTATAGCTTCAAATTAAAT
1792406 GTGATTCACCAAAAATTGCTTTAGTTGCACTTGGAAACCTAAACTTGATTTAGTTGAAAAGTGGG
195 GTGATTCACCAAAAATTGCTTTAGTTGCACTTGGAAACCTAAACTTGATTTAGTTGAAAAGTGGG
1792471 CAATCAGGCTCAGGAA
260 CAATCAGGCTCAGGAA
1792487 AAATGGCATT
Statistics
Matches: 273, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
277 59 0.22
278 214 0.78
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (277 bp):
CCAACATTAAATTATGAAGTTCATAGTCTTTTACATTGTAATTAGCTTGAATAGTTTTTTTCCCT
ATAACCATCCATAAATTATTCAGGTTTCTGGAATTTCTTCTTTCCATTTGAGGAACATTGACCAG
AGGTAATTTTTGGTTGTTAGATATGTATGAATGTATTTGCATGTTCTATAGCTTCAAATTAAATG
TGATTCACCAAAAATTGCTTTAGTTGCACTTGGAAACCTAAACTTGATTTAGTTGAAAAGTGGGC
AATCAGGCTCAGGAATA
Found at i:1793091 original size:21 final size:21
Alignment explanation
Indices: 1793057--1793096 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1793047 TTCCGATATA
*
1793057 CCCGCTACACCCGCGATAGTG
1 CCCGCTACACCCGCAATAGTG
**
1793078 CCCGCTACGGCCGCAATAG
1 CCCGCTACACCCGCAATAG
1793097 CGGTAAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.42, G:0.25, T:0.12
Consensus pattern (21 bp):
CCCGCTACACCCGCAATAGTG
Found at i:1799061 original size:19 final size:19
Alignment explanation
Indices: 1799017--1799063 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1799007 TCTTCAACTC
*
1799017 CAAGGGCCTTGCTCTCCCT
1 CAAGGGTCTTGCTCTCCCT
1799036 CAAGGGTCTTGCTCTCCCT
1 CAAGGGTCTTGCTCTCCCT
1799055 CAAGGGTCT
1 CAAGGGTCT
1799064 CTCCACTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.13, C:0.36, G:0.23, T:0.28
Consensus pattern (19 bp):
CAAGGGTCTTGCTCTCCCT
Found at i:1800718 original size:3 final size:3
Alignment explanation
Indices: 1800710--1800742 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1800700 TTTCTTTATA
1800710 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1800743 ATGTCGTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1802502 original size:36 final size:38
Alignment explanation
Indices: 1802462--1802538 Score: 88
Period size: 40 Copynumber: 2.0 Consensus size: 38
1802452 GGGGGCTAAT
1802462 ATAAT-ATATTT-TTAT-TTAACATGTTTTATTAATAAA
1 ATAATAATATTTATTATATT-ACATGTTTTATTAATAAA
**
1802498 ATAATAAATATTTAATTATATTTTATGTTTTATTAATAAA
1 ATAAT-AATATTT-ATTATATTACATGTTTTATTAATAAA
1802538 A
1 A
1802539 ATATTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
36 5 0.15
38 6 0.18
40 21 0.62
41 2 0.06
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (38 bp):
ATAATAATATTTATTATATTACATGTTTTATTAATAAA
Found at i:1805571 original size:15 final size:15
Alignment explanation
Indices: 1805547--1805596 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
1805537 ATAATATGTT
*
1805547 TAATAGTATATTAAA
1 TAATATTATATTAAA
1805562 TAATATTATATTAAA
1 TAATATTATATTAAA
*
1805577 TAATTTTATTATTAAA
1 TAATATTA-TATTAAA
1805593 -AATA
1 TAATA
1805597 ACATTACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 24 0.77
16 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TAATATTATATTAAA
Found at i:1810351 original size:21 final size:21
Alignment explanation
Indices: 1810327--1810368 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1810317 TTCATAGATA
*
1810327 TTTATAAAATAAA-AGTTTAAT
1 TTTAAAAAATAAATA-TTTAAT
1810348 TTTAAAAAATAAATATTTAAT
1 TTTAAAAAATAAATATTTAAT
1810369 CTATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTAAAAAATAAATATTTAAT
Found at i:1811811 original size:18 final size:17
Alignment explanation
Indices: 1811775--1811818 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1811765 ATGGAATTGG
*
1811775 ATTCCAATTCCTGACAA
1 ATTCCAATTCCTCACAA
*
1811792 ATTCTAATTCCTTCACAA
1 ATTCCAATTCC-TCACAA
*
1811810 ATTTCAATT
1 ATTCCAATT
1811819 ACTTCATAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTCCAATTCCTCACAA
Found at i:1811823 original size:18 final size:18
Alignment explanation
Indices: 1811788--1811836 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1811778 CCAATTCCTG
*
1811788 ACAAA-TTCTAATTCCTTC
1 ACAAATTTC-AATTACTTC
1811806 ACAAATTTCAATTACTTC
1 ACAAATTTCAATTACTTC
* *
1811824 ATAGATTTCAATT
1 ACAAATTTCAATT
1811837 CCCTCAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (18 bp):
ACAAATTTCAATTACTTC
Found at i:1814728 original size:525 final size:529
Alignment explanation
Indices: 1813707--1814764 Score: 2072
Period size: 525 Copynumber: 2.0 Consensus size: 529
1813697 TGCACCCCGC
1813707 CTTATGTGAAGTTTCACTTCTTGGGTACTTGAATTTGTCTGGTAATAGCTTCAACGGCATAATTC
1 CTTATGTGAAGTTTCACTTCTTGGGTACTTGAATTTGTCTGGTAATAGCTTCAACGGCATAATTC
1813772 CAACATGTTTTGGCTCTTTGGGTAGTCTTAAAACTCTGGATCTTAGTCACAATAGCTTTGTTGGG
66 CAACATGTTTTGGCTCTTTGGGTAGTCTTAAAACTCTGGATCTTAGTCACAATAGCTTTGTTGGG
1813837 TTTGTACCTGATGATATCATGAAGCTGAGGCAATTGAAGGAACTTGTGCTGAATGGAAACCGAGA
131 TTTGTACCTGATGATATCATGAAGCTGAGGCAATTGAAGGAACTTGTGCTGAATGGAAACCGAGA
1813902 ACTCAGTGGCTTTTTGCCGTCATGGATCGGTAACTTTTCCACTAATCTCGAAAAACTCAATCTCG
196 ACTCAGTGGCTTTTTGCCGTCATGGATCGGTAACTTTTCCACTAATCTCGAAAAACTCAATCTCG
1813967 GCTCCAATTCCTTTCATGGGGAGATGCCTGACAGCTTGTTTCATTTGAAGTCCTTGAAGCACTTG
261 GCTCCAATTCCTTTCATGGGGAGATGCCTGACAGCTTGTTTCATTTGAAGTCCTTGAAGCACTTG
1814032 GATCTCGGAGACAATTGTTTATCAGGCAATATTCATGAGTTTCATCAGTCCTTGGAGTTCCTCAA
326 GATCTCGGAGACAATTGTTTATCAGGCAATATTCATGAGTTTCATCAGTCCTTGGAGTTCCTCAA
1814097 TCTTTCTTCGAATCAATTATTCGGTACTTTGCCGTGTTTCGCTGCTTCGACTCGGGAGTCTAACT
391 TCTTTCTTCGAATCAATTATTCGGTACTTTGCCGTGTTTCGCTGCTTCGACTCGGGAGTCTAACT
1814162 GTTCTGACATTGGCTAACAATTCACTTGTAGGAGGATACCTACATGTA-TGCCTCACTGCAA-TG
456 GTTCTGACATTGGCTAACAATTCACTTGTAGGAGGATACCTACATGTATTGCCTCACTGCAAGTG
1814225 TTGGCAC-T
521 TTGGCACAT
1814233 CTTATGTGAAGTTTCACTTCTT-GGTACTTGAATTTGTCTGGTAATAGCTTCAACGGCATAATTC
1 CTTATGTGAAGTTTCACTTCTTGGGTACTTGAATTTGTCTGGTAATAGCTTCAACGGCATAATTC
1814297 CAACATGTTTTGGCTCTTTGGGTAGTCTTAAAACTCTGGATCTTAGTCACAATAGCTTTGTTGGG
66 CAACATGTTTTGGCTCTTTGGGTAGTCTTAAAACTCTGGATCTTAGTCACAATAGCTTTGTTGGG
1814362 TTTGTACCTGATGATATCATGAAGCTGAGGCAATTGAAGGAACTTGTGCTGAATGGAAACCGAGA
131 TTTGTACCTGATGATATCATGAAGCTGAGGCAATTGAAGGAACTTGTGCTGAATGGAAACCGAGA
1814427 ACTCAGTGGCTTTTTGCCGTCATGGATCGGTAACTTTTCCACTAATCTCGAAAAACTCAATCTCG
196 ACTCAGTGGCTTTTTGCCGTCATGGATCGGTAACTTTTCCACTAATCTCGAAAAACTCAATCTCG
1814492 GCTCCAATTCCTTTCATGGGGAGATGCCTGACAGCTTGTTTCATTTGAAGTCCTTGAAGCACTTG
261 GCTCCAATTCCTTTCATGGGGAGATGCCTGACAGCTTGTTTCATTTGAAGTCCTTGAAGCACTTG
1814557 GATCTCGGAGACAATTGTTTATCAGGCAATATTCATGAGTTTCATCAGTCCTTGGAGTTCCTCAA
326 GATCTCGGAGACAATTGTTTATCAGGCAATATTCATGAGTTTCATCAGTCCTTGGAGTTCCTCAA
1814622 TCTTTCTTCGAATCAATTATTCGGTACTTTGCCGTGTTTCGCTGCTTCGACTC-GGAGTCTAACT
391 TCTTTCTTCGAATCAATTATTCGGTACTTTGCCGTGTTTCGCTGCTTCGACTCGGGAGTCTAACT
1814686 GTTCTGACATTGGCTAACAATTCACTTGTAGGAGGAATACCTACATGTATTGCCTCACTGCAAGT
456 GTTCTGACATTGGCTAACAATTCACTTGTAGGAGG-ATACCTACATGTATTGCCTCACTGCAAGT
1814751 GTTGGCACAT
520 GTTGGCACAT
1814761 CTTA
1 CTTA
1814765 ACCTATCATT
Statistics
Matches: 528, Mismatches: 0, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
524 46 0.09
525 433 0.82
526 35 0.07
527 9 0.02
528 5 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (529 bp):
CTTATGTGAAGTTTCACTTCTTGGGTACTTGAATTTGTCTGGTAATAGCTTCAACGGCATAATTC
CAACATGTTTTGGCTCTTTGGGTAGTCTTAAAACTCTGGATCTTAGTCACAATAGCTTTGTTGGG
TTTGTACCTGATGATATCATGAAGCTGAGGCAATTGAAGGAACTTGTGCTGAATGGAAACCGAGA
ACTCAGTGGCTTTTTGCCGTCATGGATCGGTAACTTTTCCACTAATCTCGAAAAACTCAATCTCG
GCTCCAATTCCTTTCATGGGGAGATGCCTGACAGCTTGTTTCATTTGAAGTCCTTGAAGCACTTG
GATCTCGGAGACAATTGTTTATCAGGCAATATTCATGAGTTTCATCAGTCCTTGGAGTTCCTCAA
TCTTTCTTCGAATCAATTATTCGGTACTTTGCCGTGTTTCGCTGCTTCGACTCGGGAGTCTAACT
GTTCTGACATTGGCTAACAATTCACTTGTAGGAGGATACCTACATGTATTGCCTCACTGCAAGTG
TTGGCACAT
Found at i:1817270 original size:20 final size:20
Alignment explanation
Indices: 1817245--1817283 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1817235 ATGAAAAGCA
1817245 TGTTTTAGGTAGGAATAGAC
1 TGTTTTAGGTAGGAATAGAC
1817265 TGTTTTAGGTAGGAATAGA
1 TGTTTTAGGTAGGAATAGA
1817284 TGATTAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.36
Consensus pattern (20 bp):
TGTTTTAGGTAGGAATAGAC
Found at i:1827117 original size:90 final size:90
Alignment explanation
Indices: 1826951--1827118 Score: 239
Period size: 90 Copynumber: 1.9 Consensus size: 90
1826941 TTGCTCGATA
**
1826951 TGTTTTGAAATGATAAAAAGTATCATCAAATTAAATTATTACGGGTGCAATTTCTGGTAAGATCT
1 TGTTTTGAAATGATAAAAAGTATCATCAAATTAAATTATTACGGGTGCAATTTCTGCCAAGATCT
** *
1827016 TCTGGCCTATTTGCAAAGACTCGAG
66 TCTAACATATTTGCAAAGACTCGAG
* * *
1827041 TGTTTTGAAATGATAAAAAGTATCATCAAATTAAATTATTACGGGTGTGAATTTCTTCCAAG-TG
1 TGTTTTGAAATGATAAAAAGTATCATCAAATTAAATTATTACGGGTG-CAATTTCTGCCAAGATC
*
1827105 TTCTAATATATTTG
65 TTCTAACATATTTG
1827119 AAGGATTCTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
90 58 0.85
91 10 0.15
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (90 bp):
TGTTTTGAAATGATAAAAAGTATCATCAAATTAAATTATTACGGGTGCAATTTCTGCCAAGATCT
TCTAACATATTTGCAAAGACTCGAG
Found at i:1830259 original size:35 final size:35
Alignment explanation
Indices: 1830212--1830282 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1830202 TTCCAACTCA
1830212 TTTTCATAGTTGCTAATCTAAAAAAGAAAAGATTT
1 TTTTCATAGTTGCTAATCTAAAAAAGAAAAGATTT
* *
1830247 TTTTCATGGTTGCTAATCTAAAATAGAAAAGATTT
1 TTTTCATAGTTGCTAATCTAAAAAAGAAAAGATTT
1830282 T
1 T
1830283 ACAAGTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (35 bp):
TTTTCATAGTTGCTAATCTAAAAAAGAAAAGATTT
Found at i:1834103 original size:52 final size:54
Alignment explanation
Indices: 1834019--1834156 Score: 174
Period size: 52 Copynumber: 2.6 Consensus size: 54
1834009 TCCTCCCTCT
* *
1834019 CTCTCTCTCTCTCTCTCTATATATATATATAAAAGAGACTCGATGGCCGCTTACC
1 CTCTC-CTATCTCTCTCTATATATATATATAAAAGAAACTCGATGGCCGCTTACC
*
1834074 CTCTCCTATCTCTCTCT-T-TTTATATATAAAAGAAACTCGATGGCCGCTTACC
1 CTCTCCTATCTCTCTCTATATATATATATAAAAGAAACTCGATGGCCGCTTACC
* **
1834126 CTTTCCTCGCT-TCCTCATATATATATATATA
1 CTCTCCTATCTCT-CTC-TATATATATATATA
1834157 TATAAAATAG
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
51 1 0.01
52 43 0.60
53 2 0.03
54 12 0.17
55 14 0.19
ACGTcount: A:0.25, C:0.28, G:0.09, T:0.38
Consensus pattern (54 bp):
CTCTCCTATCTCTCTCTATATATATATATAAAAGAAACTCGATGGCCGCTTACC
Found at i:1836712 original size:18 final size:17
Alignment explanation
Indices: 1836691--1836730 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
1836681 TTATGAATAG
1836691 AAAATATA-AAAATTATTT
1 AAAATATATAAAA--ATTT
1836709 AAAATATATAAAAATTT
1 AAAATATATAAAAATTT
1836726 AAAAT
1 AAAAT
1836731 CTTTAAGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 8 0.38
19 4 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATATATAAAAATTT
Found at i:1845597 original size:38 final size:37
Alignment explanation
Indices: 1845554--1845628 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 37
1845544 TTGAAAATTA
*
1845554 TGAAGTTTAATACGAGGTTAAGAAAGGGCATTGAAACT
1 TGAAGTTTAAGACGAGGTTAAGAAAGGG-ATTGAAACT
1845592 TGAAGTTTAAGACGAGGTTAAGAAAGGGATTGAAACT
1 TGAAGTTTAAGACGAGGTTAAGAAAGGGATTGAAACT
1845629 CCTAACTCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 9 0.25
38 27 0.75
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (37 bp):
TGAAGTTTAAGACGAGGTTAAGAAAGGGATTGAAACT
Found at i:1849419 original size:23 final size:24
Alignment explanation
Indices: 1849367--1849413 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1849357 GTCAGGTTTA
* *
1849367 AATAATAAATTTTAAATTTATTAT
1 AATAATAAATTTTAAATATATAAT
1849391 AATAAT-AATTTTAAATATATAAT
1 AATAATAAATTTTAAATATATAAT
1849414 GTTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AATAATAAATTTTAAATATATAAT
Found at i:1850268 original size:3 final size:3
Alignment explanation
Indices: 1850262--1850295 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
1850252 AGTAATCTTA
1850262 AAT AAT AAT AAT AAT AAT AAT AACTT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT AA
1850296 CGGGACGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 26 0.90
5 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1850583 original size:30 final size:31
Alignment explanation
Indices: 1850524--1850583 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
1850514 ATTCCTTTTC
* *
1850524 AAAAATTAAGGAATCAATTCAAATCAATGAG
1 AAAAATTAAGGAACCAAGTCAAATCAATGAG
* *
1850555 AAAAA-TAAGGAACCAAGTCCAATTAATGA
1 AAAAATTAAGGAACCAAGTCAAATCAATGA
1850584 AACATTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.55, C:0.12, G:0.13, T:0.20
Consensus pattern (31 bp):
AAAAATTAAGGAACCAAGTCAAATCAATGAG
Found at i:1853362 original size:14 final size:14
Alignment explanation
Indices: 1853343--1853399 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
1853333 ATTGGTTTTC
* *
1853343 TGGAAATTGAATTT
1 TGGAAAATGAATTA
1853357 TGGAAAATGAATTA
1 TGGAAAATGAATTA
* **
1853371 CTAGAATTTGAATTA
1 -TGGAAAATGAATTA
1853386 TGGAAAATGAATTA
1 TGGAAAATGAATTA
1853400 CATTTCTGGA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 23 0.68
15 11 0.32
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (14 bp):
TGGAAAATGAATTA
Done.