Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 31
Found at i:1233160 original size:51 final size:51
Alignment explanation
Indices: 1233084--1233194 Score: 222
Period size: 51 Copynumber: 2.2 Consensus size: 51
1233074 CCAAAAAAAG
1233084 CCCAATCCTTCTATAAAGAACTAACCCCAATCCTTCTATAACGAGATAAAC
1 CCCAATCCTTCTATAAAGAACTAACCCCAATCCTTCTATAACGAGATAAAC
1233135 CCCAATCCTTCTATAAAGAACTAACCCCAATCCTTCTATAACGAGATAAAC
1 CCCAATCCTTCTATAAAGAACTAACCCCAATCCTTCTATAACGAGATAAAC
1233186 CCCAATCCT
1 CCCAATCCT
1233195 ATAAACAATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.23
Consensus pattern (51 bp):
CCCAATCCTTCTATAAAGAACTAACCCCAATCCTTCTATAACGAGATAAAC
Found at i:1237595 original size:39 final size:39
Alignment explanation
Indices: 1237542--1237621 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
1237532 GTATCAATAC
*
1237542 TATTATATAGTAGTATTGATACCATAACATCAATATCAA
1 TATTATATAGTAGTATCGATACCATAACATCAATATCAA
*
1237581 TATTATATATTAGTATCGATACCATAACATCAATATCAA
1 TATTATATAGTAGTATCGATACCATAACATCAATATCAA
1237620 TA
1 TA
1237622 CTCACTCAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (39 bp):
TATTATATAGTAGTATCGATACCATAACATCAATATCAA
Found at i:1238981 original size:3 final size:3
Alignment explanation
Indices: 1238973--1239017 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
1238963 GAAACTCCAA
* *
1238973 AAG AAG AAG AAAG AAG AAG AAG AAG AA- AAG AAC AAG AAA AAG AAG
1 AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1239018 GGTGAAATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1239004 original size:17 final size:17
Alignment explanation
Indices: 1238973--1239016 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1238963 GAAACTCCAA
*
1238973 AAGAAGAAG-AAAGAAG
1 AAGAAGAAGAAAAGAAC
1238989 AAGAAGAAGAAAAGAAC
1 AAGAAGAAGAAAAGAAC
*
1239006 AAGAAAAAGAA
1 AAGAAGAAGAA
1239017 GGGTGAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (17 bp):
AAGAAGAAGAAAAGAAC
Found at i:1240868 original size:64 final size:66
Alignment explanation
Indices: 1240799--1240923 Score: 182
Period size: 64 Copynumber: 1.9 Consensus size: 66
1240789 GGAACATTTA
* * *
1240799 GTGCATCGATGCATAAAATGCATTCGATG-TATCA-AACAAGCCTGAGTGCATCGATGCATGGTC
1 GTGCATCGATGCATAAAATACATTCGATGTTATCATAAAAAACCTGAGTGCATCGATGCATGGTC
1240862 T
66 T
* * *
1240863 GTGCATCGATGCATAAAATACATTTGATGTTTTCATAAAAAACTTGAGTGCATCGATGCAT
1 GTGCATCGATGCATAAAATACATTCGATGTTATCATAAAAAACCTGAGTGCATCGATGCAT
1240924 CAATGAGTGC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 27 0.51
65 4 0.08
66 22 0.42
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (66 bp):
GTGCATCGATGCATAAAATACATTCGATGTTATCATAAAAAACCTGAGTGCATCGATGCATGGTC
T
Found at i:1240932 original size:20 final size:20
Alignment explanation
Indices: 1240907--1241024 Score: 209
Period size: 20 Copynumber: 5.9 Consensus size: 20
1240897 ATAAAAAACT
*
1240907 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGGTGCATCAA
1240927 TGAGTGCATCGGTGCATCAA
1 TGAGTGCATCGGTGCATCAA
*
1240947 TGAGTGCATCCGTGCATCAA
1 TGAGTGCATCGGTGCATCAA
1240967 TGAGTGCATCGGTGCATCAA
1 TGAGTGCATCGGTGCATCAA
1240987 TGAGTGCATCGGTGCATCAA
1 TGAGTGCATCGGTGCATCAA
*
1241007 TGAGTGCATCGTTGCATC
1 TGAGTGCATCGGTGCATC
1241025 CCTTCAAAAA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 94 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGGTGCATCAA
Found at i:1243704 original size:21 final size:23
Alignment explanation
Indices: 1243642--1243728 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 23
1243632 GCATGGCATT
1243642 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
*
1243665 GTGCATCGATGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
*
1243687 -TGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
1243709 GATGCATCGATGCACATTCA
1 G-TGCATCGATGCACATTCA
1243729 TAGTGTATCG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.02
21 14 0.26
22 3 0.06
23 19 0.35
24 17 0.31
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:1243717 original size:24 final size:22
Alignment explanation
Indices: 1243643--1243728 Score: 104
Period size: 24 Copynumber: 3.8 Consensus size: 22
1243633 CATGGCATTG
1243643 TGCATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
*
1243665 GTGCATCGATGCATC-TTC-ATGA
1 -TGCATCGATGCA-CATTCAAGGA
*
1243687 TGTATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AA-GGA
1243711 TGCATCGATGCACATTCA
1 TGCATCGATGCACATTCA
1243729 TAGTGTATCG
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.26
22 3 0.06
23 17 0.31
24 19 0.35
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:1243740 original size:21 final size:22
Alignment explanation
Indices: 1243643--1243743 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 22
1243633 CATGGCATTG
1243643 TGCATCGATGCACATTCA-AGGA
1 TGCATCGATGCACATTCATA-GA
1243665 GTGCATCGATGCATC-TTCAT-GA
1 -TGCATCGATGCA-CATTCATAGA
* *
1243687 TGTATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTCATA--GA
1243711 TGCATCGATGCACATTCATAG-
1 TGCATCGATGCACATTCATAGA
*
1243732 TGTATCGATGCA
1 TGCATCGATGCA
1243744 TTATGCACAA
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
20 1 0.01
21 26 0.39
22 3 0.04
23 16 0.24
24 21 0.31
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACATTCATAGA
Found at i:1249473 original size:64 final size:64
Alignment explanation
Indices: 1249405--1249558 Score: 231
Period size: 64 Copynumber: 2.4 Consensus size: 64
1249395 TGCACTATGG
1249405 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGACTGAGTGCATCGATGCATGGTC
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAGACTGAGTGCATCGATGCATGG-C
*
1249468 T
64 A
** *
1249469 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAATCCTGAGTGCATCGATGTATGGCA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAGACTGAGTGCATCGATGCATGGCA
*
1249533 GTGCATCTATGCATAAAATGCATTCG
1 GTGCATCGATGCATAAAATGCATTCG
1249559 GAATGGTGTG
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
64 55 0.66
65 26 0.31
66 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAGACTGAGTGCATCGATGCATGGCA
Found at i:1250796 original size:59 final size:59
Alignment explanation
Indices: 1250731--1251094 Score: 496
Period size: 59 Copynumber: 6.2 Consensus size: 59
1250721 TTTCTATAAA
* * * *
1250731 ATGAAAGGTTAACTGCCTAACTGTGCATTTGGAAAAAAGGTACCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTACCAATATTGCAAGTTAG
* * * *
1250790 ATGAAAGGTAAAATGCCTAACTGTGCATTTGGCAGAAATGTTCCAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTACCAATATTGCAAGTTAG
* * * * *
1250849 ATGAAATGATAAATGTCTAACTGTGCATTTGGCATAAAGGTGCCAATATTGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTACCAATATTGCAAGTTAG
*
1250908 ATGAAAGGTTAACTGCCTAACTGTGCATTTGGCAGAAAGGTGA-CAATATTGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGT-ACCAATATTGCAAGTTAG
* * *
1250967 ATTAAAGGTTAAATGCCTAACTGTGCATTTGGAAAAAAGGTACCAATATTGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTACCAATATTGCAAGTTAG
* * * * * * *
1251026 GTGAAAGGTTAACTGCCTAATTGTGCATTTAGCAGAAAGGTGCCTATATTGCAAGTTTG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTACCAATATTGCAAGTTAG
1251085 ATGAAAGGTT
1 ATGAAAGGTT
1251095 CCAATATGGC
Statistics
Matches: 268, Mismatches: 35, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
58 1 0.00
59 267 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (59 bp):
ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTACCAATATTGCAAGTTAG
Found at i:1251090 original size:27 final size:27
Alignment explanation
Indices: 1251060--1251117 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1251050 GCATTTAGCA
* *
1251060 GAAAGGTGCCTATATTGCAAGTT-TGAT
1 GAAAGGTGCCAATATGGCAAGTTAT-AT
*
1251087 GAAAGGTTCCAATATGGCAAGTTATAT
1 GAAAGGTGCCAATATGGCAAGTTATAT
1251114 GAAA
1 GAAA
1251118 TATTAAATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.29
Consensus pattern (27 bp):
GAAAGGTGCCAATATGGCAAGTTATAT
Found at i:1251093 original size:118 final size:118
Alignment explanation
Indices: 1250731--1251094 Score: 548
Period size: 118 Copynumber: 3.1 Consensus size: 118
1250721 TTTCTATAAA
* *
1250731 ATGAAAGGTTAACTGCCTAACTGTGCATTTGGAAAAAAGGTACCAATAATGCAAGTTAGATGAAA
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGAAAAAAGGTACCAATATTGCAAGTTAGATGAAA
* * * * *
1250796 GGTAAAATGCCTAACTGTGCATTTGGCAGAAATGTTCCAATAATGCAAGTTAG
66 GGTTAACTGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAG
* * * * * *
1250849 ATGAAATGATAAATGTCTAACTGTGCATTTGGCATAAAGGTGCCAATATTGCAAGTTAGATGAAA
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGAAAAAAGGTACCAATATTGCAAGTTAGATGAAA
*
1250914 GGTTAACTGCCTAACTGTGCATTTGGCAGAAAGGTGACAATATTGCAAGTTAG
66 GGTTAACTGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAG
* *
1250967 ATTAAAGGTTAAATGCCTAACTGTGCATTTGGAAAAAAGGTACCAATATTGCAAGTTAGGTGAAA
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGAAAAAAGGTACCAATATTGCAAGTTAGATGAAA
* * * *
1251032 GGTTAACTGCCTAATTGTGCATTTAGCAGAAAGGTGCCTATATTGCAAGTTTG
66 GGTTAACTGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAG
1251085 ATGAAAGGTT
1 ATGAAAGGTT
1251095 CCAATATGGC
Statistics
Matches: 218, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 218 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (118 bp):
ATGAAAGGTTAAATGCCTAACTGTGCATTTGGAAAAAAGGTACCAATATTGCAAGTTAGATGAAA
GGTTAACTGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAG
Found at i:1251101 original size:86 final size:86
Alignment explanation
Indices: 1251002--1251168 Score: 226
Period size: 86 Copynumber: 1.9 Consensus size: 86
1250992 CATTTGGAAA
* * * * *
1251002 AAAGGTACCAATATTGCAAGTTAGGTGAAAGGTTAACTGCCTAATTGTGCATTTAGCAGAAAGGT
1 AAAGGTACCAATATGGCAAGTTAGATGAAAGATTAAATGCCTAACTGTGCATTTAGCAGAAAGGT
* *
1251067 GCCTATATTGCAAGTTTGATG
66 GCCAATAATGCAAGTTTGATG
* * * * *
1251088 AAAGGTTCCAATATGGCAAGTTATATGAAATATTAAATGCCTAACTGTGCATTTGGCATAAAGGT
1 AAAGGTACCAATATGGCAAGTTAGATGAAAGATTAAATGCCTAACTGTGCATTTAGCAGAAAGGT
1251153 GCCAATAATGCAAGTT
66 GCCAATAATGCAAGTT
1251169 AGTGAAAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (86 bp):
AAAGGTACCAATATGGCAAGTTAGATGAAAGATTAAATGCCTAACTGTGCATTTAGCAGAAAGGT
GCCAATAATGCAAGTTTGATG
Found at i:1257915 original size:20 final size:20
Alignment explanation
Indices: 1257890--1257964 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
1257880 AAAATGTTTA
**
1257890 TATGAATAGTACCGATACTG
1 TATGAATAGTAATGATACTG
1257910 TATGAATAGTAATGATACTG
1 TATGAATAGTAATGATACTG
1257930 TATGAATAGTAATGATACTG
1 TATGAATAGTAATGATACTG
*
1257950 TGTGAATAGTAATGA
1 TATGAATAGTAATGA
1257965 ATAGTATCGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGAATAGTAATGATACTG
Found at i:1258041 original size:20 final size:20
Alignment explanation
Indices: 1258008--1258046 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1257998 ATGGGTACCA
*
1258008 ATACTACTACAGTAGTATCG
1 ATACTACTACAGTAATATCG
* *
1258028 ATACTGCTATAGTAATATC
1 ATACTACTACAGTAATATC
1258047 AAACCCCATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
ATACTACTACAGTAATATCG
Found at i:1258448 original size:34 final size:34
Alignment explanation
Indices: 1258405--1258471 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
1258395 TGTAAATGGA
* *
1258405 AAGGTTCTAGTTGAGCCCTTGAAAAGCTAGGGAT
1 AAGGTTCTAGTTGAGCCCGTGAAAAACTAGGGAT
*
1258439 AAGGTTCTAGTTTAGCCCGTGAAAAACTAGGGA
1 AAGGTTCTAGTTGAGCCCGTGAAAAACTAGGGA
1258472 GTTGTAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.25
Consensus pattern (34 bp):
AAGGTTCTAGTTGAGCCCGTGAAAAACTAGGGAT
Found at i:1258497 original size:36 final size:36
Alignment explanation
Indices: 1258451--1258523 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1258441 GGTTCTAGTT
1258451 TAGCCCGTGAAAAACTAGGGAGTTGTAAAGGTTATC
1 TAGCCCGTGAAAAACTAGGGAGTTGTAAAGGTTATC
1258487 TAGCCCGTGAAAAACTAGGGAGTTGTAAAGGTTATC
1 TAGCCCGTGAAAAACTAGGGAGTTGTAAAGGTTATC
1258523 T
1 T
1258524 CTTTGTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (36 bp):
TAGCCCGTGAAAAACTAGGGAGTTGTAAAGGTTATC
Found at i:1259924 original size:91 final size:92
Alignment explanation
Indices: 1259820--1260009 Score: 364
Period size: 91 Copynumber: 2.1 Consensus size: 92
1259810 ATGACTCCAA
*
1259820 TGATGATGAATAATAGTTAACCCATGCCTTATGGCCAACGAAGAAGAATCCGAGGTATCTTCCAA
1 TGATGAGGAATAATAGTTAACCCATGCCTTATGGCCAACGAAGAAGAATCCGAGGTATCTTCCAA
1259885 CTCAAATGAATTAAATTCTTGTTC-TT
66 CTCAAATGAATTAAATTCTTGTTCTTT
1259911 TGATGAGGAATAATAGTTAACCCATGCCTTATGGCCAACGAAGAAGAATCCGAGGTATCTTCCAA
1 TGATGAGGAATAATAGTTAACCCATGCCTTATGGCCAACGAAGAAGAATCCGAGGTATCTTCCAA
1259976 CTCAAATGAATTAAATTCTTGTTCTTT
66 CTCAAATGAATTAAATTCTTGTTCTTT
1260003 TGATGAG
1 TGATGAG
1260010 CTACAAGATT
Statistics
Matches: 97, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
91 88 0.91
92 9 0.09
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (92 bp):
TGATGAGGAATAATAGTTAACCCATGCCTTATGGCCAACGAAGAAGAATCCGAGGTATCTTCCAA
CTCAAATGAATTAAATTCTTGTTCTTT
Found at i:1260793 original size:17 final size:17
Alignment explanation
Indices: 1260771--1260809 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1260761 AATTGATATA
1260771 AATTTTTCA-AATTTTTT
1 AATTTTT-AGAATTTTTT
1260788 AA-TTTTAGAATTTTTT
1 AATTTTTAGAATTTTTT
1260804 AATTTT
1 AATTTT
1260810 AGACCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.05
16 14 0.70
17 5 0.25
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (17 bp):
AATTTTTAGAATTTTTT
Found at i:1260799 original size:16 final size:16
Alignment explanation
Indices: 1260780--1260812 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1260770 AAATTTTTCA
1260780 AATTTTTTAATTTTAG
1 AATTTTTTAATTTTAG
1260796 AATTTTTTAATTTTAG
1 AATTTTTTAATTTTAG
1260812 A
1 A
1260813 CCTAAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
AATTTTTTAATTTTAG
Found at i:1261549 original size:21 final size:21
Alignment explanation
Indices: 1261519--1261569 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1261509 CTGTATGAAT
*
1261519 AGTACTGATACTCATTGAAGG
1 AGTACCGATACTCATTGAAGG
1261540 AGTACCGATACTCATTGAAGG
1 AGTACCGATACTCATTGAAGG
*
1261561 AGTATCGAT
1 AGTACCGAT
1261570 GCTAAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (21 bp):
AGTACCGATACTCATTGAAGG
Found at i:1261640 original size:20 final size:20
Alignment explanation
Indices: 1261597--1261640 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1261587 GCAAAATGGG
*
1261597 TATCGATACTGCTAAAGTAG
1 TATCGATACTGCTAAAGTAA
* *
1261617 TATCGATACTGTTATAGTAA
1 TATCGATACTGCTAAAGTAA
1261637 TATC
1 TATC
1261641 AAGCCTAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
TATCGATACTGCTAAAGTAA
Found at i:1263100 original size:15 final size:15
Alignment explanation
Indices: 1263080--1263120 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1263070 ACCATCACCC
1263080 AAAATCCCTAAATCT
1 AAAATCCCTAAATCT
*
1263095 AAAATCTCCAAAATCT
1 AAAATC-CCTAAATCT
1263111 -AAATCCCTAA
1 AAAATCCCTAA
1263121 TTCTCATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 4 0.17
15 11 0.48
16 8 0.35
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATCCCTAAATCT
Found at i:1268540 original size:15 final size:15
Alignment explanation
Indices: 1268502--1268532 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1268492 ATTCGATCTG
1268502 ATCCAAATAACATAT
1 ATCCAAATAACATAT
1268517 ATCCAAATAACATAT
1 ATCCAAATAACATAT
1268532 A
1 A
1268533 CTCGAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (15 bp):
ATCCAAATAACATAT
Found at i:1271669 original size:3 final size:3
Alignment explanation
Indices: 1271661--1271700 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
1271651 ACTAGTATGT
1271661 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1271701 CGAACATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1299439 original size:21 final size:21
Alignment explanation
Indices: 1299409--1299452 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1299399 AGAAGAACTA
*
1299409 TGGCTTTGAAGTAAGGCACCT
1 TGGCTCTGAAGTAAGGCACCT
*
1299430 TGGCTCTGAAGTAAGGCTCCT
1 TGGCTCTGAAGTAAGGCACCT
1299451 TG
1 TG
1299453 ATTCTTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (21 bp):
TGGCTCTGAAGTAAGGCACCT
Found at i:1311779 original size:22 final size:22
Alignment explanation
Indices: 1311732--1311779 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1311722 AATTGAAAAA
*
1311732 TGAAAGTATTGAATATGAAATG
1 TGAAAGTATTGAATATGAAATC
*
1311754 TGAAAGTATTGATTATGAGAA-C
1 TGAAAGTATTGAATATGA-AATC
1311776 TGAA
1 TGAA
1311780 TATGTGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.31
Consensus pattern (22 bp):
TGAAAGTATTGAATATGAAATC
Found at i:1312231 original size:3 final size:3
Alignment explanation
Indices: 1312223--1312337 Score: 149
Period size: 3 Copynumber: 38.3 Consensus size: 3
1312213 AACTGGTATG
* *
1312223 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
1312271 TAA TAA CAA CAA CAA CAA CAA CAA CAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1312319 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
1312338 GACCTAGTAT
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 106 1.00
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:1316333 original size:21 final size:21
Alignment explanation
Indices: 1316309--1316372 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 21
1316299 ATTGTTGTAC
1316309 CACTGAACAAAAGTGCATTCG
1 CACTGAACAAAAGTGCATTCG
* *
1316330 CACTAAATCAAAAGTGCATTTG
1 CACTGAA-CAAAAGTGCATTCG
1316352 CACTGATACAAAAGTGTCATT
1 CACTGA-ACAAAAGTG-CATT
1316373 TCACTGGGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 6 0.16
22 26 0.70
23 5 0.14
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (21 bp):
CACTGAACAAAAGTGCATTCG
Found at i:1320803 original size:187 final size:186
Alignment explanation
Indices: 1320469--1320850 Score: 712
Period size: 187 Copynumber: 2.0 Consensus size: 186
1320459 CTAGTAAAAA
*
1320469 TTTGGTAAATCGGATAATCGATTTTTTTAGAAAATTTGAAGAATGATCAATTTAATCTTATAAAT
1 TTTGGTAAATCGGATAATCGATTTTTTTAGAAAATTTGAAGAATGATAAATTTAATCTTATAAAT
1320534 ATTATTCCACTTTAAAATGATGTAAAATAATATGGAGCATTGGATTTGAGAATGTATTTTCATGT
66 ATTATTCCACTTTAAAATGATGTAAAATAATATGGAGCATTGGATTTGAGAATGTATTTTCATGT
1320599 TCAATTTGGATCGTCAGATGAAAAATGGCAAGATTGATTTTTTTTTTGAAAATAAC
131 TCAATTTGGATCGTCAGATGAAAAATGGCAAGATTGATTTTTTTTTTGAAAATAAC
1320655 TTTGGT-AATCGGATAATCGATTTTTTTAGAAAATTTGAAGAATGATAAATTTAATCTTATAAAT
1 TTTGGTAAATCGGATAATCGATTTTTTTAGAAAATTTGAAGAATGATAAATTTAATCTTATAAAT
1320719 ATTATTCCACTTTTCAAAATGATGTAAAATAATATGGAGCATTGGATTTGAGAATGTATTTTCAT
66 ATTATTCCAC-TTT-AAAATGATGTAAAATAATATGGAGCATTGGATTTGAGAATGTATTTTCAT
1320784 GTTCAATTTGGATCGTCAGATGAAAAATGGCAAGATTGATTTTTTTTTTGAAAATAAC
129 GTTCAATTTGGATCGTCAGATGAAAAATGGCAAGATTGATTTTTTTTTTGAAAATAAC
* *
1320842 ATGGGTAAA
1 TTTGGTAAA
1320851 GTTGTAAAGG
Statistics
Matches: 190, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
185 67 0.35
186 9 0.05
187 112 0.59
188 2 0.01
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (186 bp):
TTTGGTAAATCGGATAATCGATTTTTTTAGAAAATTTGAAGAATGATAAATTTAATCTTATAAAT
ATTATTCCACTTTAAAATGATGTAAAATAATATGGAGCATTGGATTTGAGAATGTATTTTCATGT
TCAATTTGGATCGTCAGATGAAAAATGGCAAGATTGATTTTTTTTTTGAAAATAAC
Found at i:1322961 original size:20 final size:22
Alignment explanation
Indices: 1322919--1322961 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
1322909 CACTAGTTAT
* *
1322919 TATATATATGATTTTTTATAAA
1 TATATATATGATTTATTACAAA
1322941 TATATA-ATG-TTTATTACAAA
1 TATATATATGATTTATTACAAA
1322961 T
1 T
1322962 GTTACTTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (22 bp):
TATATATATGATTTATTACAAA
Found at i:1333989 original size:104 final size:104
Alignment explanation
Indices: 1333809--1334016 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
1333799 ATATCTGATC
1333809 TGTTTCGAATAACATTACTCAAATATCATATATCTGAACTTTGATCTGATTCGAATGTAATAATT
1 TGTTTCGAATAACATTACTCAAATATCATATATCTGAACTTTGATCTGATTCGAATGTAATAATT
1333874 ACCAATACAAATTATTCGAATGCATCTCATAAATTTTCA
66 ACCAATACAAATTATTCGAATGCATCTCATAAATTTTCA
1333913 TGTTTCGAATAACATTACTCAAATATCATATATCTGAACTTTGATCTGATTCGAATGTAATAATT
1 TGTTTCGAATAACATTACTCAAATATCATATATCTGAACTTTGATCTGATTCGAATGTAATAATT
1333978 ACCAATACAAATTATTCGAATGCATCTCATAAATTTTCA
66 ACCAATACAAATTATTCGAATGCATCTCATAAATTTTCA
1334017 ACATGACATA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (104 bp):
TGTTTCGAATAACATTACTCAAATATCATATATCTGAACTTTGATCTGATTCGAATGTAATAATT
ACCAATACAAATTATTCGAATGCATCTCATAAATTTTCA
Found at i:1340323 original size:38 final size:37
Alignment explanation
Indices: 1340272--1340417 Score: 109
Period size: 38 Copynumber: 3.9 Consensus size: 37
1340262 TGTTCCCTCG
1340272 AAAAATTTTCATCTCACTCGAGACAGTTTCCCTTAAAAC
1 AAAAA-TTTCATCTCACTCGAGACAGTTTCCCTT-AAAC
* * * * *
1340311 AAAAATTTCATCTTC-CTTGAGATATTTTTCCCCT-GA-
1 AAAAATTTCATC-TCACTCGAGACA-GTTTCCCTTAAAC
* ** *
1340347 AAATATTTTGTCTCATTCGAGACAGTTTCCCTTGAAAC
1 AAAAATTTCATCTCACTCGAGACAGTTTCCCTT-AAAC
* * * *
1340385 AAAAATTTCATCTCCCTTGAGATATTTTCCCTT
1 AAAAATTTCATCTCACTCGAGACAGTTTCCCTT
1340418 GAAAGCTTTC
Statistics
Matches: 79, Mismatches: 22, Indels: 13
0.69 0.19 0.11
Matches are distributed among these distances:
35 9 0.11
36 15 0.19
37 2 0.03
38 39 0.49
39 14 0.18
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (37 bp):
AAAAATTTCATCTCACTCGAGACAGTTTCCCTTAAAC
Found at i:1340370 original size:74 final size:73
Alignment explanation
Indices: 1340205--1340521 Score: 334
Period size: 73 Copynumber: 4.3 Consensus size: 73
1340195 CCTCAATTTT
* ** * ** * *
1340205 TTTTGTCTCACTCGAGACAATTTCTTTTGAAATGAAAAGTTCATCTCCCTTGAGATATGTT-CCC
1 TTTTGTCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTCATCTCCCTTGAGATATTTTCCCC
1340269 TCGAAAA-A
66 T-GAAAATA
* *
1340277 TTTTCATCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTCATCTTCCTTGAGATATTTTTCC
1 TTTT-GTCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTCATCTCCCTTGAGATA-TTTTCC
1340342 CCTGAAAATA
64 CCTGAAAATA
* * *
1340352 TTTTGTCTCATTCGAGACAGTTTCCCTTGAAACAAAAATTTCATCTCCCTTGAGATATTTTCCCT
1 TTTTGTCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTCATCTCCCTTGAGATATTTTCCCC
*
1340417 TGAAAGCT-
66 TGAAA-ATA
** * * ** * * *
1340425 TTCCGTCTCACTCGAGATAGTTTCTCTTAAAATGAAAATTTAATCTCCATTGAGATATTTTCCCT
1 TTTTGTCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTCATCTCCCTTGAGATATTTTCCCC
*
1340490 TGAAAATG
66 TGAAAATA
* * *
1340498 TTTTGTATCACTTGAGATAGTTTC
1 TTTTGTCTCACTCGAGACAGTTTC
1340522 AATATTTTGT
Statistics
Matches: 208, Mismatches: 31, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
72 5 0.02
73 136 0.65
74 58 0.28
75 9 0.04
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (73 bp):
TTTTGTCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTCATCTCCCTTGAGATATTTTCCCC
TGAAAATA
Found at i:1340397 original size:147 final size:146
Alignment explanation
Indices: 1340205--1340521 Score: 395
Period size: 147 Copynumber: 2.2 Consensus size: 146
1340195 CCTCAATTTT
* * ** **
1340205 TTTTGTCTCACTCGAGACAATTTCTTTTGAAATGAAAAGTTCATCTCCCTTGAGATATGTTCCCT
1 TTTTGTCTCATTCGAGACAGTTTCCCTTGAAACAAAAAGTTCATCTCCCTTGAGATATGTTCCCT
* *
1340270 CGAAAAATTTTCATCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTCATCTTCC-TTGAGAT
66 CGAAAAATTTCCATCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTAATC-TCCATTGAGAT
1340334 ATTTTTCCCCTGAAAATA
130 A-TTTTCCCCTGAAAATA
* *
1340352 TTTTGTCTCATTCGAGACAGTTTCCCTTGAAACAAAAATTTCATCTCCCTTGAGATATTTTCCCT
1 TTTTGTCTCATTCGAGACAGTTTCCCTTGAAACAAAAAGTTCATCTCCCTTGAGATATGTTCCCT
* ** * * * **
1340417 TGAAAGCTTTCCGTCTCACTCGAGATAGTTTCTCTTAAAATGAAAATTTAATCTCCATTGAGATA
66 CGAAAAATTTCCATCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTAATCTCCATTGAGATA
* *
1340482 TTTTCCCTTGAAAATG
131 TTTTCCCCTGAAAATA
* *
1340498 TTTTGTATCACTT-GAGATAGTTTC
1 TTTTGTCTCA-TTCGAGACAGTTTC
1340522 AATATTTTGT
Statistics
Matches: 146, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
146 36 0.25
147 110 0.75
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (146 bp):
TTTTGTCTCATTCGAGACAGTTTCCCTTGAAACAAAAAGTTCATCTCCCTTGAGATATGTTCCCT
CGAAAAATTTCCATCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTAATCTCCATTGAGATA
TTTTCCCCTGAAAATA
Found at i:1340610 original size:101 final size:101
Alignment explanation
Indices: 1340429--1340622 Score: 257
Period size: 101 Copynumber: 1.9 Consensus size: 101
1340419 AAAGCTTTCC
* * **
1340429 GTCTCACTCGAGATAGTTTCTCTTAAAATGAAAATTTAATCTCCATTGAGATATTTTCCCTTGAA
1 GTCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTAATCTCCATTGAGATATTTTCCCTTGAA
* *
1340494 AATGTTTTGTATCACTTGAGATAGTTTCAATATTTT
66 AATGTTTCGTATCACTCGAGATAGTTTCAATATTTT
* * * *
1340530 GTCTCATTCGAGACAGTTTCCCTTGAAACAAAAATTTCATCTCCCTTGAGATATTTTCCCTTG-A
1 GTCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTAATCTCCATTGAGATATTTTCCCTTGAA
*
1340594 AA-GCTTTCCGTCTCACTCGAGATAGTTTC
66 AATG-TTT-CGTATCACTCGAGATAGTTTC
1340623 TCTTAAAAAC
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
99 1 0.01
100 6 0.08
101 73 0.91
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (101 bp):
GTCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTAATCTCCATTGAGATATTTTCCCTTGAA
AATGTTTCGTATCACTCGAGATAGTTTCAATATTTT
Found at i:1340653 original size:74 final size:73
Alignment explanation
Indices: 1340530--1340669 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 73
1340520 TCAATATTTT
* * *
1340530 GTCTCATTCGAGACAGTTTCCCTTGAAACAAAAATTTCATCTCCCTTGAGATATTTTCCCTTGAA
1 GTCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTCATCTCACTTGAGATATTTTCCCTTGAA
1340595 AGCTTTCC
66 AGCTTTCC
* * * * *
1340603 GTCTCACTCGAGATAGTTTCTCTTAAAAACCAAAATTTCATCTCAGTTGAGATATTTTCTCTTGA
1 GTCTCACTCGAGACAGTTTCCCTT-AAAACAAAAATTTCATCTCACTTGAGATATTTTCCCTTGA
1340668 AA
65 AA
1340670 ATTTTTGTCC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 21 0.36
74 37 0.64
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (73 bp):
GTCTCACTCGAGACAGTTTCCCTTAAAACAAAAATTTCATCTCACTTGAGATATTTTCCCTTGAA
AGCTTTCC
Found at i:1342045 original size:21 final size:21
Alignment explanation
Indices: 1342019--1342058 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1342009 TTTTTTAATT
1342019 TTATTT-CTATTACTTATATTA
1 TTATTTACTATTAC-TATATTA
1342040 TTATTTACTATTACTATAT
1 TTATTTACTATTACTATAT
1342059 GATATGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTTACTATTACTATATTA
Found at i:1342799 original size:16 final size:16
Alignment explanation
Indices: 1342778--1342809 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1342768 AAAATAATTT
*
1342778 AAAAATTATAAATAAA
1 AAAAATCATAAATAAA
1342794 AAAAATCATAAATAAA
1 AAAAATCATAAATAAA
1342810 GGACTTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATCATAAATAAA
Found at i:1344956 original size:4 final size:4
Alignment explanation
Indices: 1344947--1344988 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
1344937 TTATTATTGA
*
1344947 TATT TATT TATA TATAT TATTT TATT TATT TATT TA-T TATT T
1 TATT TATT TATT TAT-T TA-TT TATT TATT TATT TATT TATT T
1344989 CTTACTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 3 0.09
4 24 0.73
5 5 0.15
6 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:1346477 original size:15 final size:15
Alignment explanation
Indices: 1346455--1346496 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1346445 ATTATTTTAA
*
1346455 ATATTTTAAACAATTT
1 ATATTTTAAA-AATAT
1346471 A-ATTTTATAAAATAT
1 ATATTTTA-AAAATAT
1346486 ATATTTTAAAA
1 ATATTTTAAAA
1346497 CTACATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATTTTAAAAATAT
Found at i:1347924 original size:21 final size:21
Alignment explanation
Indices: 1347879--1347927 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1347869 ATCGCTTCAT
**
1347879 AAAAGGATCGATCCCTTAAGG
1 AAAAGGATCGATCCCTTAACC
* *
1347900 AAAAGGATTGATCCCTTCACC
1 AAAAGGATCGATCCCTTAACC
1347921 AAAAGGA
1 AAAAGGA
1347928 GATTCATTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (21 bp):
AAAAGGATCGATCCCTTAACC
Found at i:1352008 original size:20 final size:21
Alignment explanation
Indices: 1351983--1352034 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1351973 TGAGATGTGG
1351983 GTATCGATACTCG-TCAGGGA
1 GTATCGATACTCGTTCAGGGA
* * *
1352003 GTATCGATA-TTGTTCATGTA
1 GTATCGATACTCGTTCAGGGA
1352023 GTATCGATACTC
1 GTATCGATACTC
1352035 AAGGGTTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 23 0.88
21 1 0.04
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
GTATCGATACTCGTTCAGGGA
Found at i:1360080 original size:22 final size:22
Alignment explanation
Indices: 1360048--1360100 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1360038 TTTTCATTCC
* *
1360048 TAATTAATT-AAAACTGTTATTT
1 TAATTATTTAAAAACTCTTA-TT
1360070 TAATTATTTAAAAACTCTTATT
1 TAATTATTTAAAAACTCTTATT
1360092 TAATTATTT
1 TAATTATTT
1360101 GAAATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATTATTTAAAAACTCTTATT
Found at i:1378954 original size:35 final size:34
Alignment explanation
Indices: 1378915--1379009 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 34
1378905 TATACACTAA
* * *
1378915 GTGTCTTGGGTATAAACTCTAGTGTTTTACACCAT
1 GTGTCTTTGGTAGAAACTCTAGTG-CTTACACCAT
* * * *
1378950 GTGTCTTTAGAAGAAACTCTAATGCTTGCACCAT
1 GTGTCTTTGGTAGAAACTCTAGTGCTTACACCAT
*
1378984 GTGTCTTTGCTAGAAACTCTAGTGCT
1 GTGTCTTTGGTAGAAACTCTAGTGCT
1379010 ACAAGTTATA
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 30 0.61
35 19 0.39
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (34 bp):
GTGTCTTTGGTAGAAACTCTAGTGCTTACACCAT
Found at i:1382992 original size:30 final size:30
Alignment explanation
Indices: 1382956--1383022 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
1382946 CAAAATACAT
*
1382956 AACTTTTTAAAATTACACTTTTGCTCCCTA
1 AACTTTTGAAAATTACACTTTTGCTCCCTA
** * *
1382986 AACTTTTGAAAATTACTTTTTTGGTCTCTA
1 AACTTTTGAAAATTACACTTTTGCTCCCTA
1383016 AACTTTT
1 AACTTTT
1383023 CCAAACATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (30 bp):
AACTTTTGAAAATTACACTTTTGCTCCCTA
Found at i:1395645 original size:19 final size:20
Alignment explanation
Indices: 1395621--1395666 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1395611 CATAATGGCC
*
1395621 CAATTTCAA-ATTCTAACAT
1 CAATTTCAACACTCTAACAT
1395640 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
1395660 TAATTTC
1 CAATTTC
1395667 CAGCATAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:1396342 original size:22 final size:22
Alignment explanation
Indices: 1396317--1396361 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1396307 TGGAGAGATG
1396317 TCAT-GAAATTTCTACATTAATT
1 TCATAGAAATTTCT-CATTAATT
* *
1396339 TCATATAAATTTCTCATTTATT
1 TCATAGAAATTTCTCATTAATT
1396361 T
1 T
1396362 AATCTTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.51
Consensus pattern (22 bp):
TCATAGAAATTTCTCATTAATT
Found at i:1396370 original size:23 final size:23
Alignment explanation
Indices: 1396322--1396364 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1396312 AGATGTCATG
*
1396322 AAATTTCTACATTAATTTCATAT
1 AAATTTCTACATTAATTTAATAT
*
1396345 AAATTTCT-CATTTATTTAAT
1 AAATTTCTACATTAATTTAAT
1396365 CTTAAACGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTCTACATTAATTTAATAT
Found at i:1398499 original size:35 final size:35
Alignment explanation
Indices: 1398470--1398544 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1398460 TGCTATGGTG
*
1398470 AAAGTTTATCAAAATTGAAAAAGTATGCTAAGGAA
1 AAAGTTTAACAAAATTGAAAAAGTATGCTAAGGAA
* * *
1398505 AAAGTTTAACAAAATTGTAAAAGTATGCTAAAGCA
1 AAAGTTTAACAAAATTGAAAAAGTATGCTAAGGAA
1398540 AAAGT
1 AAAGT
1398545 AAAATTGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (35 bp):
AAAGTTTAACAAAATTGAAAAAGTATGCTAAGGAA
Found at i:1408441 original size:15 final size:16
Alignment explanation
Indices: 1408404--1408441 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1408394 GGAAGCATAG
1408404 AGATGATGAACACGAT
1 AGATGATGAACACGAT
*
1408420 AGA-GATGAGCA-GAT
1 AGATGATGAACACGAT
1408434 AGATGATG
1 AGATGATG
1408442 CTAATGGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 11 0.55
16 3 0.15
ACGTcount: A:0.42, C:0.08, G:0.32, T:0.18
Consensus pattern (16 bp):
AGATGATGAACACGAT
Found at i:1418418 original size:129 final size:129
Alignment explanation
Indices: 1418188--1418445 Score: 516
Period size: 129 Copynumber: 2.0 Consensus size: 129
1418178 CACTTTAGTT
1418188 TCTTCTACTCACACTATGTCGAAAAGTATTTCTTCTTGTTTCTGACCATTTATTATACTTAAAAC
1 TCTTCTACTCACACTATGTCGAAAAGTATTTCTTCTTGTTTCTGACCATTTATTATACTTAAAAC
1418253 ATTTTTTTATCTTGACAACAATATGTTCAATGACCTTAAGGTTATCCTTAAAGATGAGATTCAA
66 ATTTTTTTATCTTGACAACAATATGTTCAATGACCTTAAGGTTATCCTTAAAGATGAGATTCAA
1418317 TCTTCTACTCACACTATGTCGAAAAGTATTTCTTCTTGTTTCTGACCATTTATTATACTTAAAAC
1 TCTTCTACTCACACTATGTCGAAAAGTATTTCTTCTTGTTTCTGACCATTTATTATACTTAAAAC
1418382 ATTTTTTTATCTTGACAACAATATGTTCAATGACCTTAAGGTTATCCTTAAAGATGAGATTCAA
66 ATTTTTTTATCTTGACAACAATATGTTCAATGACCTTAAGGTTATCCTTAAAGATGAGATTCAA
1418446 CACATGTGCA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (129 bp):
TCTTCTACTCACACTATGTCGAAAAGTATTTCTTCTTGTTTCTGACCATTTATTATACTTAAAAC
ATTTTTTTATCTTGACAACAATATGTTCAATGACCTTAAGGTTATCCTTAAAGATGAGATTCAA
Found at i:1420461 original size:59 final size:60
Alignment explanation
Indices: 1420387--1420549 Score: 188
Period size: 60 Copynumber: 2.7 Consensus size: 60
1420377 TTAAATTATG
* * ** *
1420387 AATCTTATTTTAAATTAGTCCTTAAAC-TTTAAATATTTCAATTTCATCTTTAAAATATA
1 AATCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCCCTAAAATACA
* * * *
1420446 AATTTCATTCTAAATTAGTCCTTAAACTTTTAAACA-TTCGAATTTCATCCCTAAACTACG
1 AATCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTC-AATTTCATCCCTAAAATACA
* *
1420506 AATCTCATTCTAAATTAGT-CTCTAAACTTTTAGATCTTTCAATT
1 AATCTCATTCTAAATTAGTCCT-TAAACTTTTAAATATTTCAATT
1420550 CCACCCCCCA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 29 0.33
60 55 0.63
61 3 0.03
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.44
Consensus pattern (60 bp):
AATCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCCCTAAAATACA
Found at i:1425335 original size:2 final size:2
Alignment explanation
Indices: 1425330--1425355 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1425320 CTCTCTCTCT
1425330 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
1425356 TTCATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1426743 original size:21 final size:21
Alignment explanation
Indices: 1426717--1426758 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1426707 TATATTCTTA
1426717 TATATCTTATACTCAAACTTG
1 TATATCTTATACTCAAACTTG
1426738 TATATCTTATACTCAAACTTG
1 TATATCTTATACTCAAACTTG
1426759 AGACCTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (21 bp):
TATATCTTATACTCAAACTTG
Found at i:1429031 original size:29 final size:27
Alignment explanation
Indices: 1428998--1429052 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
1428988 TGATATATGA
* *
1428998 TTACCGTATATTTTTTATATGATCTCTGG
1 TTACCGTAT-TTCTATATATGAT-TCTGG
1429027 TTACCGTATTTCTATATATGATTCTG
1 TTACCGTATTTCTATATATGATTCTG
1429053 AAAAATGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 11 0.46
29 9 0.38
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.51
Consensus pattern (27 bp):
TTACCGTATTTCTATATATGATTCTGG
Found at i:1435589 original size:3 final size:3
Alignment explanation
Indices: 1435581--1435616 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1435571 ATTAAAAAAC
*
1435581 AAG AAG AAG AAG AAG AAG AAAG AAA AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AA
1435617 AATGAATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1435609 original size:16 final size:16
Alignment explanation
Indices: 1435584--1435617 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1435574 AAAAAACAAG
*
1435584 AAGAAGAAGAAGAAGA
1 AAGAAAAAGAAGAAGA
1435600 AAGAAAAAGAAGAAGA
1 AAGAAAAAGAAGAAGA
1435616 AA
1 AA
1435618 ATGAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAGAAGA
Found at i:1441587 original size:32 final size:31
Alignment explanation
Indices: 1441543--1441626 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 31
1441533 ATACGTTTTT
* *
1441543 GCCTTAGAGCCTACCCAAGGAAGCACCTTAGG
1 GCCTAAGAGCCTACCCAAGGAA-CACCTCAGG
* * * *
1441575 GCCTGAGAGCCTACCTAAGAGAATATCTCAGG
1 GCCTAAGAGCCTACCCAAG-GAACACCTCAGG
1441607 GCCTAAGAGCCTACCCAAGG
1 GCCTAAGAGCCTACCCAAGG
1441627 GTCACCTTAG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 1 0.02
32 40 0.91
33 3 0.07
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (31 bp):
GCCTAAGAGCCTACCCAAGGAACACCTCAGG
Found at i:1442420 original size:22 final size:22
Alignment explanation
Indices: 1442375--1442420 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1442365 GGTCAAAGTT
*
1442375 AAAGTCAAAGTCAATGTTGTTC
1 AAAGTCAAAGTCAATGTTGGTC
*
1442397 AAAGTTAAAGTCAAT-TATGGTC
1 AAAGTCAAAGTCAATGT-TGGTC
1442419 AA
1 AA
1442421 TGTTTTGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (22 bp):
AAAGTCAAAGTCAATGTTGGTC
Found at i:1455126 original size:62 final size:63
Alignment explanation
Indices: 1455029--1455157 Score: 206
Period size: 62 Copynumber: 2.1 Consensus size: 63
1455019 AGAAAATGAA
* * *
1455029 TAGGTTTTTAAATTCATGAGTTGCCTTGGCGGCCCAGTGTAGCACTTTAGGCACAATCGGGT-
1 TAGGTTTTTAAATTCAGGAGTTGCCTTGGCGGCCCAGTGTAGAACTTTAGGCACAATCAGGTG
* *
1455091 TAGGTTTTTAAATTCAGGAGTTGCCTTGGTGGCCCAGTGTAGAACTTTAGGCCCAATCAGGTG
1 TAGGTTTTTAAATTCAGGAGTTGCCTTGGCGGCCCAGTGTAGAACTTTAGGCACAATCAGGTG
1455154 TAGG
1 TAGG
1455158 GTGTTACATA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
62 57 0.93
63 4 0.07
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.32
Consensus pattern (63 bp):
TAGGTTTTTAAATTCAGGAGTTGCCTTGGCGGCCCAGTGTAGAACTTTAGGCACAATCAGGTG
Found at i:1456195 original size:20 final size:22
Alignment explanation
Indices: 1456170--1456223 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
1456160 TTGGAGAGGT
*
1456170 AGTATCGATACTCTT-GGCT-G
1 AGTATCGATACTCTTAGACTAG
1456190 AGTATCGATACTCTTAGACTAG
1 AGTATCGATACTCTTAGACTAG
*
1456212 GGTATCGATACT
1 AGTATCGATACT
1456224 GCTCTTAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 15 0.50
21 3 0.10
22 12 0.40
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (22 bp):
AGTATCGATACTCTTAGACTAG
Found at i:1457661 original size:21 final size:22
Alignment explanation
Indices: 1457622--1457662 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1457612 ACGCGCAAGA
1457622 TGATAAAACTGTAAATTCTTAT
1 TGATAAAACTGTAAATTCTTAT
*
1457644 TGATAAAA-TGTAAGTTCTT
1 TGATAAAACTGTAAATTCTT
1457663 TTAGTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (22 bp):
TGATAAAACTGTAAATTCTTAT
Found at i:1460852 original size:2 final size:2
Alignment explanation
Indices: 1460845--1460873 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1460835 AGCAAACATA
1460845 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1460874 CACACTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1461023 original size:25 final size:25
Alignment explanation
Indices: 1460994--1461048 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1460984 TAATGTGTTT
1460994 ATATATC-ATATTA-TTATATATAATA
1 ATATATCAAT-TTATTTATATA-AATA
*
1461019 ATATATTAATTTATTTATATAAATA
1 ATATATCAATTTATTTATATAAATA
1461044 ATATA
1 ATATA
1461049 ATACATTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATATCAATTTATTTATATAAATA
Found at i:1462264 original size:11 final size:11
Alignment explanation
Indices: 1462248--1462303 Score: 52
Period size: 9 Copynumber: 5.5 Consensus size: 11
1462238 TCTGGAAATG
1462248 AACCGGCTGAA
1 AACCGGCTGAA
1462259 AACCGG-T-AA
1 AACCGGCTGAA
*
1462268 AACCGGGGTG--
1 AACC-GGCTGAA
1462278 AACCGGCTGAA
1 AACCGGCTGAA
1462289 AACCGGC--AA
1 AACCGGCTGAA
1462298 AACCGG
1 AACCGG
1462304 TTTGAACCGC
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 18 0.46
10 7 0.18
11 14 0.36
ACGTcount: A:0.36, C:0.27, G:0.30, T:0.07
Consensus pattern (11 bp):
AACCGGCTGAA
Found at i:1462282 original size:30 final size:30
Alignment explanation
Indices: 1462246--1462312 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1462236 GATCTGGAAA
*
1462246 TGAACCGGCTGAAAACCGGTAAAACCGGGG
1 TGAACCGGCTGAAAACCGGCAAAACCGGGG
**
1462276 TGAACCGGCTGAAAACCGGCAAAACCGGTT
1 TGAACCGGCTGAAAACCGGCAAAACCGGGG
1462306 TGAACCG
1 TGAACCG
1462313 CCGTTTCACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.25, G:0.30, T:0.12
Consensus pattern (30 bp):
TGAACCGGCTGAAAACCGGCAAAACCGGGG
Found at i:1467181 original size:29 final size:29
Alignment explanation
Indices: 1467126--1467226 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 29
1467116 ATACAATCTA
* *
1467126 ATGCAGAATCAGG-GAGGACATATAATCCC
1 ATGCAGAATCAGGATAGTA-ATATAATCCC
*
1467155 ATGCAGAATCAGGATAGTAATAAAATCCC
1 ATGCAGAATCAGGATAGTAATATAATCCC
* * *
1467184 ATGCAGAATCAAGATAATGATATAATCCC
1 ATGCAGAATCAGGATAGTAATATAATCCC
* * *
1467213 GTACAGAAACAGGA
1 ATGCAGAATCAGGA
1467227 ATGCATCAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 57 0.95
30 3 0.05
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.19
Consensus pattern (29 bp):
ATGCAGAATCAGGATAGTAATATAATCCC
Found at i:1473174 original size:54 final size:54
Alignment explanation
Indices: 1473126--1473453 Score: 505
Period size: 54 Copynumber: 6.1 Consensus size: 54
1473116 TTGCAGACCC
* * *
1473126 AGTGCCCATATAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACGT
1 AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
* *
1473180 AGTGCCAATACGGAAATTCATAAACTCATTATGAACTTCTTAAGTTGCACACAT
1 AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
* *
1473234 AGCGCCAATACATAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
1 AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
* *
1473288 AGTGCTAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
1 AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
* *
1473342 AGTGCCAATACGGAAATTCATAAACTCATTATGAAATTCTTAAGTTGCACACAT
1 AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
** * *
1473396 AG-GTCCAATAGGGAAATTCATAAGCTCATTATGAATTTCTTAAGTTGCAGACAT
1 AGTG-CCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
1473450 AGTG
1 AGTG
1473454 TCATTCGATA
Statistics
Matches: 253, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
53 1 0.00
54 251 0.99
55 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (54 bp):
AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
Found at i:1473935 original size:94 final size:95
Alignment explanation
Indices: 1473801--1473993 Score: 253
Period size: 94 Copynumber: 2.0 Consensus size: 95
1473791 CATGGTATCA
* * * * * * *
1473801 ATACTTCTATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTG-GATC
1 ATACTTCTATACTAAGGTACCAATACTCCATTACAATATCGATACCATTTCTACATTCTGAAATC
** * *
1473865 CTTGGTATCGATACCTTTCTCTTAGTACCG
66 AATGGTATCGATACCTTCCTCATAGTACCG
* *
1473895 ATACTTCTATACTAAGGTATCAATACTCTATTACAATATCGATACCATTTCTACATTCTGAAATC
1 ATACTTCTATACTAAGGTACCAATACTCCATTACAATATCGATACCATTTCTACATTCTGAAATC
*
1473960 AATGGTATCGATACCTTCCTCATAGTATCG
66 AATGGTATCGATACCTTCCTCATAGTACCG
1473990 ATAC
1 ATAC
1473994 CTACATCAGT
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
94 52 0.62
95 32 0.38
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (95 bp):
ATACTTCTATACTAAGGTACCAATACTCCATTACAATATCGATACCATTTCTACATTCTGAAATC
AATGGTATCGATACCTTCCTCATAGTACCG
Found at i:1474006 original size:18 final size:19
Alignment explanation
Indices: 1473964--1474011 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1473954 GAAATCAATG
* *
1473964 GTATCGATACCTTCCTCATA
1 GTATCGATACCTACATCA-A
1473984 GTATCGATACCTACATC-A
1 GTATCGATACCTACATCAA
1474002 GTATCGATAC
1 GTATCGATAC
1474012 TAATTGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
20 15 0.58
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (19 bp):
GTATCGATACCTACATCAA
Found at i:1479882 original size:54 final size:54
Alignment explanation
Indices: 1479809--1480088 Score: 393
Period size: 54 Copynumber: 5.2 Consensus size: 54
1479799 ACGCAGTGCC
*
1479809 CATAGTGCCAATATGGAAATTCATAAAC-CTGTTATGAATTTCTTAAGTTGCACA
1 CATAGTGCCAATACGGAAATTCATAAACTC-GTTATGAATTTCTTAAGTTGCACA
* *
1479863 CATTGTGCCAATACAGAAATTCATAAACTCGTTATGAATTTCTTAAGTTGCACA
1 CATAGTGCCAATACGGAAATTCATAAACTCGTTATGAATTTCTTAAGTTGCACA
* **
1479917 CATTGTGCCAATACGGAAATTCATAAACTCGTTATGAATTTCTTAAGTTATACA
1 CATAGTGCCAATACGGAAATTCATAAACTCGTTATGAATTTCTTAAGTTGCACA
* * *
1479971 CATAGTGCCAATACGGAAATTCATAAACTCATTATGAAATTCTTAATTTGCACA
1 CATAGTGCCAATACGGAAATTCATAAACTCGTTATGAATTTCTTAAGTTGCACA
** * * * *
1480025 CATAGTGCCAATAAAGAAATTCATATACGC-ATAGTGAATTTCTTAAATTGCACA
1 CATAGTGCCAATACGGAAATTCATAAACTCGTTA-TGAATTTCTTAAGTTGCACA
1480079 CATAGTGCCA
1 CATAGTGCCA
1480089 TTCGAAAATC
Statistics
Matches: 205, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
53 2 0.01
54 202 0.99
55 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (54 bp):
CATAGTGCCAATACGGAAATTCATAAACTCGTTATGAATTTCTTAAGTTGCACA
Found at i:1480527 original size:73 final size:74
Alignment explanation
Indices: 1480415--1480564 Score: 257
Period size: 73 Copynumber: 2.0 Consensus size: 74
1480405 ATAGTATCAG
1480415 TACTTCTATATTGTGGTACCAATACTCCCTTTCAATATCGATA-CATTTCTACATTTTGGATCCT
1 TACTTCTATATTGTGGTACCAATACTCCCTTTCAATATCGATACCATTTCTACATTTTGGATCCT
1480479 TGGTATCGA
66 TGGTATCGA
*** *
1480488 TACTTCTATATTGTGGTATTGATACTCCCTTTCAGTATCGATACCATTTCTACATTTTGGATCCT
1 TACTTCTATATTGTGGTACCAATACTCCCTTTCAATATCGATACCATTTCTACATTTTGGATCCT
1480553 TGGTATCGA
66 TGGTATCGA
1480562 TAC
1 TAC
1480565 CTTTCTCTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
73 39 0.54
74 33 0.46
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.42
Consensus pattern (74 bp):
TACTTCTATATTGTGGTACCAATACTCCCTTTCAATATCGATACCATTTCTACATTTTGGATCCT
TGGTATCGA
Found at i:1492018 original size:34 final size:34
Alignment explanation
Indices: 1491980--1492066 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 34
1491970 TGTATATTAT
*
1491980 ATGATTGCATTTGGAGTGTATATTTTTGTATCTG
1 ATGATTGCATTTGGAGTGCATATTTTTGTATCTG
* ** * *
1492014 ATGATTTCAACTGGAATGCATATTTTTGTTTCTG
1 ATGATTGCATTTGGAGTGCATATTTTTGTATCTG
*
1492048 ATGATAGCATTTGGAGTGC
1 ATGATTGCATTTGGAGTGC
1492067 TCATTACACA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (34 bp):
ATGATTGCATTTGGAGTGCATATTTTTGTATCTG
Found at i:1495557 original size:41 final size:42
Alignment explanation
Indices: 1495500--1495582 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 42
1495490 AGTACATTCA
1495500 CGCAGAATATGGCTCAAGTTCTTCAA-GGACATCCACAACCT
1 CGCAGAATATGGCTCAAGTTCTTCAAGGGACATCCACAACCT
1495541 CGCAGAATATGGCTCAAGTTCTTCAAGGGACATCCACAACCT
1 CGCAGAATATGGCTCAAGTTCTTCAAGGGACATCCACAACCT
1495583 GTACAGCTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 26 0.63
42 15 0.37
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (42 bp):
CGCAGAATATGGCTCAAGTTCTTCAAGGGACATCCACAACCT
Found at i:1505399 original size:2 final size:2
Alignment explanation
Indices: 1505392--1505432 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1505382 TTTATTATTA
1505392 AT AT AT AT AT AT AT AT AT AT A- 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
1505433 TATTTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1505416 original size:21 final size:21
Alignment explanation
Indices: 1505390--1505432 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1505380 CATTTATTAT
1505390 TAATATATATATATATATATA
1 TAATATATATATATATATATA
1505411 TAATATATATATATATATATA
1 TAATATATATATATATATATA
1505432 T
1 T
1505433 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATATATATATATATATATA
Found at i:1505463 original size:25 final size:25
Alignment explanation
Indices: 1505432--1505482 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
1505422 TATATATATA
*
1505432 TTATTTTTTT-ATTCTTATACTCTT
1 TTATTTTTTTCTTTCTTATACTCTT
* *
1505456 TTATTTTTTTCTTTTTTATTCTCTT
1 TTATTTTTTTCTTTCTTATACTCTT
1505481 TT
1 TT
1505483 TACTAGTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (25 bp):
TTATTTTTTTCTTTCTTATACTCTT
Found at i:1505659 original size:26 final size:27
Alignment explanation
Indices: 1505630--1505681 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1505620 CTTCTAGTTT
*
1505630 TTATTTATTTA-TTTAATTTTTTTTCG
1 TTATTTATTTACTTTAATTATTTTTCG
*
1505656 TTATTTATTTACTTTCATTATTTTTC
1 TTATTTATTTACTTTAATTATTTTTC
1505682 CTCTAACAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (27 bp):
TTATTTATTTACTTTAATTATTTTTCG
Found at i:1505679 original size:30 final size:28
Alignment explanation
Indices: 1505575--1505680 Score: 94
Period size: 30 Copynumber: 3.7 Consensus size: 28
1505565 ATTCATTTTC
*
1505575 TTTATCTT-TTTCTTATTTTTTCTCTTTA
1 TTTAT-TTATTTCTTATTTTTTCTCGTTA
*
1505603 TTTA-TTATTTC-TATTTTCTTCTAGTT-
1 TTTATTTATTTCTTATTTT-TTCTCGTTA
* *
1505629 TTTATTTATTTATTTAATTTTTTTTCGTTA
1 TTTATTTATTT-CTT-ATTTTTTCTCGTTA
1505659 TTTATTTACTTTCATTATTTTT
1 TTTATTTA-TTTC-TTATTTTT
1505681 CCTCTAACAA
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
26 12 0.19
27 16 0.25
28 4 0.06
29 7 0.11
30 19 0.30
31 5 0.08
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (28 bp):
TTTATTTATTTCTTATTTTTTCTCGTTA
Found at i:1507469 original size:20 final size:20
Alignment explanation
Indices: 1507444--1507482 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1507434 ACCGTATAAG
1507444 ACTGGGGGGTATCGGTACCT
1 ACTGGGGGGTATCGGTACCT
1507464 ACTGGGGGGTATCGGTACC
1 ACTGGGGGGTATCGGTACC
1507483 CTCCGAGCAT
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:0.15, C:0.21, G:0.41, T:0.23
Consensus pattern (20 bp):
ACTGGGGGGTATCGGTACCT
Found at i:1511001 original size:90 final size:90
Alignment explanation
Indices: 1510873--1511050 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
1510863 TAATCCCGAA
* * *
1510873 TATTTAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1510938 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
* *
1510963 TATTAAATTCCAATTAATTTAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
* *
1511028 TAGGGTAACTTGGCTATGAAAGG
66 TAGGGTAACTTGGATATAAAAGG
1511051 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:1517369 original size:90 final size:90
Alignment explanation
Indices: 1517250--1517417 Score: 275
Period size: 90 Copynumber: 1.9 Consensus size: 90
1517240 TAATCCCGAA
* * *
1517250 TATTTAATTTCAATTCATTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCCTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAT-CCTAATATGA
*
1517314 TTAGGGTAGCTTGGATATAAATGGAT
65 TTAGGGTAACTTGGATATAAATGGAT
*
1517340 TATTAAATTCCAATTAATTAAATATAGATTTAGTTAATTTGAAATAATAAAAATCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGAT
1517405 TAGGGTAACTTGG
66 TAGGGTAACTTGG
1517418 CCATAAAAGT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
90 67 0.93
91 5 0.07
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGAT
TAGGGTAACTTGGATATAAATGGAT
Found at i:1519238 original size:6 final size:6
Alignment explanation
Indices: 1519220--1519264 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
1519210 TCTAATTTAC
* *
1519220 TTTGAT TTCGAT TTTGAT TTCGAT TTTGAT TTTGAT TTTGAT TTT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT TTT
1519265 TATCAAGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (6 bp):
TTTGAT
Found at i:1519293 original size:15 final size:15
Alignment explanation
Indices: 1519273--1519301 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1519263 TTTATCAAGT
1519273 ATTTATTTTTATTTC
1 ATTTATTTTTATTTC
1519288 ATTTATTTTTATTT
1 ATTTATTTTTATTT
1519302 TTTAGTACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTATTTTTATTTC
Found at i:1521374 original size:17 final size:17
Alignment explanation
Indices: 1521352--1521386 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1521342 TTGGGAATTA
1521352 TTATTTAGGATTTTATT
1 TTATTTAGGATTTTATT
* *
1521369 TTATTTGGGGTTTTATT
1 TTATTTAGGATTTTATT
1521386 T
1 T
1521387 GAATTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (17 bp):
TTATTTAGGATTTTATT
Found at i:1539441 original size:57 final size:56
Alignment explanation
Indices: 1539321--1539506 Score: 206
Period size: 57 Copynumber: 3.4 Consensus size: 56
1539311 ATGGCACTGA
* *
1539321 GTGTGCAAAAATTTAAGAAATT--TAATTAGTTTATGAA-TT-TTATGGG-A-TGGGT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTTATGGGCACT--TT
1539373 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCT-TATGGGCACTTT
* * * * *
1539430 GTGTACAAAAAGTTAAAAAATTCATAATTACTTTATGAATTTCCATATGGGCACCTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTT-CTTATGGGCACTTT
* *
1539487 GTGCGCAAAAA-CTAAGAAAT
1 GTGTGCAAAAAGTTAAGAAAT
1539507 ATATACTAAC
Statistics
Matches: 115, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
52 21 0.18
54 15 0.13
55 2 0.02
56 8 0.07
57 66 0.57
58 2 0.02
59 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.35
Consensus pattern (56 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCTTATGGGCACTTT
Found at i:1544149 original size:23 final size:23
Alignment explanation
Indices: 1544123--1544177 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1544113 GTCGCAAAAT
1544123 GTTTAACATTTCAGCAAGTGAAC
1 GTTTAACATTTCAGCAAGTGAAC
1544146 GTTTAACATTTCAGCAAGTGAAC
1 GTTTAACATTTCAGCAAGTGAAC
*
1544169 GTTGAACAT
1 GTTTAACAT
1544178 CAAGTGCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (23 bp):
GTTTAACATTTCAGCAAGTGAAC
Found at i:1547598 original size:57 final size:57
Alignment explanation
Indices: 1547438--1547716 Score: 248
Period size: 57 Copynumber: 5.0 Consensus size: 57
1547428 ATTACCAAAT
* ** * * *
1547438 GGCACTGA-GTGTGCAAAAAGTTAAGAAATTCATAATTGGTTTATGAACTTCCGTATG
1 GGCACT-ATGTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATA
* * * * * *
1547495 GGCACTTTGTGTTCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTTCGTATA
1 GGCACTATGTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATA
* * * * * *
1547552 GGCACTTTGTTTGCAAAAAGCTAAGAAATTCATACTAAGTGCATGAATTTACGTATG
1 GGCACTATGTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATA
* * * * *
1547609 GGCACTATGTGTG--TAAA-CTAAGAAATTCATACTAATTGTGTGAATTTCCATATA
1 GGCACTATGTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATA
* * * *
1547663 GGAACTATATGTGCAAACA--TAAGAAATTCATAATAAGTAG-GTGAATTTCCGTAT
1 GGCACTATGTGTGCAAAAAGCTAAGAAATTCATAATAAGT-GTATGAATTTCCGTAT
1547717 TGGTAGTGGG
Statistics
Matches: 187, Mismatches: 31, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
54 42 0.22
55 33 0.18
56 3 0.02
57 109 0.58
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (57 bp):
GGCACTATGTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATA
Found at i:1547707 original size:55 final size:54
Alignment explanation
Indices: 1547572--1547712 Score: 167
Period size: 54 Copynumber: 2.6 Consensus size: 54
1547562 TTGCAAAAAG
* * * * * * *
1547572 CTAAGAAATTCATACTAAGTGCATGAATTTACGTATGGGCACTATGTGTGTAAA
1 CTAAGAAATTCATACTAAGTGCGTGAATTTCCATATAGGAACTATATGTGCAAA
* *
1547626 CTAAGAAATTCATACTAATTGTGTGAATTTCCATATAGGAACTATATGTGCAAA
1 CTAAGAAATTCATACTAAGTGCGTGAATTTCCATATAGGAACTATATGTGCAAA
*
1547680 CATAAGAAATTCATAATAAGTAG-GTGAATTTCC
1 C-TAAGAAATTCATACTAAGT-GCGTGAATTTCC
1547713 GTATTGGTAG
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
54 46 0.62
55 27 0.36
56 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (54 bp):
CTAAGAAATTCATACTAAGTGCGTGAATTTCCATATAGGAACTATATGTGCAAA
Found at i:1554940 original size:2 final size:2
Alignment explanation
Indices: 1554929--1554966 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1554919 AATCAAAGAG
*
1554929 TA TA -A TA TA TA TA TA TA TA CA 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
1554967 GAATTGTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1555690 original size:2 final size:2
Alignment explanation
Indices: 1555679--1555713 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1555669 GTTAGATCTC
1555679 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1555714 CATTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1558823 original size:25 final size:25
Alignment explanation
Indices: 1558789--1558878 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 25
1558779 GCCACATAGA
* *
1558789 TTTATCCTGAAGGATCGCGTAGAAT
1 TTTATCCTGAAGGACCGCATAGAAT
* *
1558814 TTTTTCCTGAAGGACCACATAGAAT
1 TTTATCCTGAAGGACCGCATAGAAT
* *
1558839 TTTATCCCGAAAGACCGCATAGAAT
1 TTTATCCTGAAGGACCGCATAGAAT
* *
1558864 TTTGTCCGGAAGGAC
1 TTTATCCTGAAGGAC
1558879 TGAGTAGAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (25 bp):
TTTATCCTGAAGGACCGCATAGAAT
Found at i:1558887 original size:50 final size:50
Alignment explanation
Indices: 1558780--1558878 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
1558770 AACTGAAGTG
* * * * * *
1558780 CCACATAG-A-TTTATCCTGAAGGATCGCGTAGAATTTTTTCCTGAAGGA
1 CCACATAGAATTTTATCCCGAAAGACCGCATAGAATTTTGTCCGGAAGGA
1558828 CCACATAGAATTTTATCCCGAAAGACCGCATAGAATTTTGTCCGGAAGGA
1 CCACATAGAATTTTATCCCGAAAGACCGCATAGAATTTTGTCCGGAAGGA
1558878 C
1 C
1558879 TGAGTAGAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 8 0.19
49 1 0.02
50 34 0.79
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (50 bp):
CCACATAGAATTTTATCCCGAAAGACCGCATAGAATTTTGTCCGGAAGGA
Found at i:1559036 original size:15 final size:15
Alignment explanation
Indices: 1559018--1559102 Score: 73
Period size: 15 Copynumber: 5.7 Consensus size: 15
1559008 CACATAGGGT
*
1559018 ATTTTCACGTAGAAC
1 ATTTTCACATAGAAC
* * *
1559033 A-TTTCACTTGGCAC
1 ATTTTCACATAGAAC
*
1559047 ATTTTCACATGGAAC
1 ATTTTCACATAGAAC
* *
1559062 ATTTTCATATAAAAC
1 ATTTTCACATAGAAC
* *
1559077 ATATTCACATATAAC
1 ATTTTCACATAGAAC
*
1559092 ATTTTTACATA
1 ATTTTCACATA
1559103 CCAATAAAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
14 11 0.20
15 45 0.80
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (15 bp):
ATTTTCACATAGAAC
Found at i:1565825 original size:25 final size:25
Alignment explanation
Indices: 1565793--1565892 Score: 87
Period size: 25 Copynumber: 4.0 Consensus size: 25
1565783 TGCCACATAG
* *
1565793 ATTTGTCCCGAATGACCACGTAGAA
1 ATTTGTCCCAAAGGACCACGTAGAA
**
1565818 ATTTGTCCCAAAGGACTGCGTA-AA
1 ATTTGTCCCAAAGGACCACGTAGAA
* **
1565842 AGTTTGTCCTAAACAACCACGTAGAA
1 A-TTTGTCCCAAAGGACCACGTAGAA
* *
1565868 TTTTGTCCCGAAGGA-CAGCGTAGAA
1 ATTTGTCCCAAAGGACCA-CGTAGAA
1565893 CCATCGACTC
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
24 5 0.09
25 51 0.88
26 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (25 bp):
ATTTGTCCCAAAGGACCACGTAGAA
Found at i:1566056 original size:15 final size:15
Alignment explanation
Indices: 1566022--1566103 Score: 78
Period size: 15 Copynumber: 5.5 Consensus size: 15
1566012 TGCATAGGGT
* *
1566022 ATTTTCACGTACAAC
1 ATTTTCACTTAGAAC
*
1566037 A-TTTCACTTAGCAC
1 ATTTTCACTTAGAAC
*
1566051 ATTTTCACATAGAAC
1 ATTTTCACTTAGAAC
*
1566066 ATTTTCA-TATAAAAC
1 ATTTTCACT-TAGAAC
* *
1566081 ATATTCACTTATAAC
1 ATTTTCACTTAGAAC
1566096 ATTTTCAC
1 ATTTTCAC
1566104 ATACCAATAA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
14 11 0.20
15 42 0.78
16 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.38
Consensus pattern (15 bp):
ATTTTCACTTAGAAC
Found at i:1566501 original size:22 final size:22
Alignment explanation
Indices: 1566476--1566523 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1566466 GGTATCCCTC
*
1566476 CTATAATACCGATAATTTTCTT
1 CTATAATACCGATAACTTTCTT
** *
1566498 CTATGGTACCGATACCTTTCTT
1 CTATAATACCGATAACTTTCTT
1566520 CTAT
1 CTAT
1566524 GGTACTGATA
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:0.25, C:0.23, G:0.08, T:0.44
Consensus pattern (22 bp):
CTATAATACCGATAACTTTCTT
Found at i:1566541 original size:25 final size:22
Alignment explanation
Indices: 1566482--1566536 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1566472 CCTCCTATAA
**
1566482 TACCGATAATTTTCTTCTATGG
1 TACCGATACCTTTCTTCTATGG
1566504 TACCGATACCTTTCTTCTATGG
1 TACCGATACCTTTCTTCTATGG
*
1566526 TACTGATACCT
1 TACCGATACCT
1566537 CCTTTAGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.42
Consensus pattern (22 bp):
TACCGATACCTTTCTTCTATGG
Found at i:1566650 original size:21 final size:20
Alignment explanation
Indices: 1566624--1566679 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
1566614 ATACCTCCAC
1566624 ATCAGTATCAATACTACTTCA
1 ATCAGTATCAATA-TACTTCA
*
1566645 ATCAGTATCGATTATACTTCA
1 ATCAGTATC-AATATACTTCA
*
1566666 TTCAGTATCAATAT
1 ATCAGTATCAATAT
1566680 TGTTCATTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 24 0.77
22 3 0.10
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (20 bp):
ATCAGTATCAATATACTTCA
Found at i:1567070 original size:12 final size:13
Alignment explanation
Indices: 1567033--1567062 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1567023 CTATACCACT
1567033 CCAAACTTCAAAA
1 CCAAACTTCAAAA
1567046 CCAAACTTCAAAA
1 CCAAACTTCAAAA
1567059 CCAA
1 CCAA
1567063 CTCAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.13
Consensus pattern (13 bp):
CCAAACTTCAAAA
Found at i:1568650 original size:23 final size:23
Alignment explanation
Indices: 1568621--1568664 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1568611 TCCGGAGTTT
* *
1568621 TTTTTAATAACATATAGTTTTAG
1 TTTTTAAAAAAATATAGTTTTAG
*
1568644 TTTTTAAAAAAATATATTTTT
1 TTTTTAAAAAAATATAGTTTT
1568665 GAAAATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTTAAAAAAATATAGTTTTAG
Found at i:1568712 original size:39 final size:37
Alignment explanation
Indices: 1568659--1568859 Score: 124
Period size: 39 Copynumber: 5.6 Consensus size: 37
1568649 AAAAAAATAT
*
1568659 ATTTTTGAAAATATATATAATATATAGTTTTGCAAAC
1 ATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
*
1568696 ATTTTTGAAAACATATATATATTATATAGTTTTGAAAAC
1 ATTTTTG-AAA-ATATATATAATATATAGTTTTGAAAAC
* * * *
1568735 A----T--ATATATA-AT-ATATA-ATTTTTAAAAAT
1 ATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
* *
1568763 ATTTTT-AATATATATATAATATAATATAGTTTTGGAAAAT
1 ATTTTTGAAAATATATAT-A-AT-ATATAGTTTT-GAAAAC
* * **
1568803 ATTTTTG-AAA-GTATAT--TATATAGATTAAAAAAC
1 ATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
*
1568836 TATTTTTGAAAATATATATTATAT
1 -ATTTTTGAAAATATATATAATAT
1568860 GGTTTTAAAA
Statistics
Matches: 128, Mismatches: 16, Indels: 39
0.70 0.09 0.21
Matches are distributed among these distances:
28 10 0.08
29 4 0.03
30 2 0.02
31 5 0.04
32 2 0.02
33 11 0.09
34 17 0.13
35 5 0.04
36 5 0.04
37 9 0.07
38 9 0.07
39 36 0.28
40 13 0.10
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (37 bp):
ATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
Found at i:1568771 original size:26 final size:27
Alignment explanation
Indices: 1568698--1568776 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
1568688 TTGCAAACAT
* *
1568698 TTTTGAAAACATATATATATTATATAG
1 TTTTGAAAACATATATATAATATATAA
1568725 TTTTGAAAACATATATATAATATATAA
1 TTTTGAAAACATATATATAATATATAA
* * *
1568752 TTTTTAAAA-ATATTTTTAATATATA
1 TTTTGAAAACATATATATAATATATA
1568777 TATAATATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 14 0.30
27 33 0.70
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (27 bp):
TTTTGAAAACATATATATAATATATAA
Found at i:1568779 original size:66 final size:66
Alignment explanation
Indices: 1568654--1568804 Score: 182
Period size: 66 Copynumber: 2.3 Consensus size: 66
1568644 TTTTTAAAAA
* * *
1568654 AATATATTTTTG-AAAATATATATAATATATAGTTTTGCAAACATTTTTGAAAACATATAT-ATA
1 AATATAGTTTTGAAAAATATATATAATATATAATTTTGCAAAAATTTTTGAAAACATATATAATA
1568717 T
66 T
* * * * *
1568718 TATATAGTTTTGAAAACATATATATAATATATAATTTT-TAAAAATATTTTTAATATATATATAA
1 AATATAGTTTTGAAAA-ATATATATAATATATAATTTTGCAAAAAT-TTTTGAAAACATATATAA
1568782 TAT
64 TAT
*
1568785 AATATAGTTTTGGAAAATAT
1 AATATAGTTTTGAAAAATAT
1568805 TTTTGAAAGT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
64 10 0.14
65 8 0.11
66 37 0.51
67 18 0.25
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (66 bp):
AATATAGTTTTGAAAAATATATATAATATATAATTTTGCAAAAATTTTTGAAAACATATATAATA
T
Found at i:1568802 original size:40 final size:37
Alignment explanation
Indices: 1568735--1568808 Score: 103
Period size: 40 Copynumber: 1.9 Consensus size: 37
1568725 TTTTGAAAAC
*
1568735 ATATATATAATATATAATTTTTAAAAATATTTTTAAT
1 ATATATATAATATATAATTTTGAAAAATATTTTTAAT
*
1568772 ATATATATAATATAATATAGTTTTGGAAAATATTTTT
1 ATATATATAATAT-ATA-A-TTTTGAAAAATATTTTT
1568809 GAAAGTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 13 0.41
38 3 0.09
39 1 0.03
40 15 0.47
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (37 bp):
ATATATATAATATATAATTTTGAAAAATATTTTTAAT
Found at i:1568824 original size:34 final size:35
Alignment explanation
Indices: 1568652--1568878 Score: 132
Period size: 36 Copynumber: 6.3 Consensus size: 35
1568642 AGTTTTTAAA
1568652 AAAATATATTTTTGAAAATATATATAATATATAGTTTT
1 AAAA-ATATTTTTGAAAATATATAT--TATATAGTTTT
** *
1568690 GCAAACATTTTTGAAAACATATATATATTATATAGTTTT
1 AAAAATATTTTTG--AA-A-ATATATATTATATAGTTTT
* * * * *
1568729 GAAAACA--TAT--ATATA-ATA-TATA-ATTTTT
1 AAAAATATTTTTGAAAATATATATTATATAGTTTT
1568757 AAAAATATTTTT-AATATATATATAATATAATATAGTTTT
1 AAAAATATTTTTGAA-A-ATATAT-AT-T-ATATAGTTTT
* * * *
1568796 GGAAAATATTTTTG-AAA-GTATATTATATAGATTA
1 -AAAAATATTTTTGAAAATATATATTATATAGTTTT
*
1568830 AAAAACTATTTTTGAAAATATATATTATATGGTTTT
1 AAAAA-TATTTTTGAAAATATATATTATATAGTTTT
1568866 AAAAATGATTTTT
1 AAAAAT-ATTTTT
1568879 TTATTTTTAT
Statistics
Matches: 147, Mismatches: 21, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
28 10 0.07
29 4 0.03
30 5 0.03
31 4 0.03
33 8 0.05
34 18 0.12
35 6 0.04
36 26 0.18
37 14 0.10
38 6 0.04
39 25 0.17
40 13 0.09
41 8 0.05
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (35 bp):
AAAAATATTTTTGAAAATATATATTATATAGTTTT
Found at i:1572650 original size:17 final size:17
Alignment explanation
Indices: 1572610--1572644 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1572600 TGTCCTTTAC
*
1572610 TAGCTTTAACCCTCGGA
1 TAGCTTTAACCTTCGGA
1572627 TAGCTTTAACCTTCGGA
1 TAGCTTTAACCTTCGGA
1572644 T
1 T
1572645 CTCTTTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (17 bp):
TAGCTTTAACCTTCGGA
Found at i:1573000 original size:25 final size:25
Alignment explanation
Indices: 1572966--1573065 Score: 114
Period size: 25 Copynumber: 4.0 Consensus size: 25
1572956 TTCCACATAG
*
1572966 ATTTTTCCCGAAGGACCACGTAGAA
1 ATTTGTCCCGAAGGACCACGTAGAA
* *
1572991 ATTTGTCCCGAAGGATCGCGTA-AA
1 ATTTGTCCCGAAGGACCACGTAGAA
**
1573015 ATTTTGTCTTGAAGGACCACGTAGAA
1 A-TTTGTCCCGAAGGACCACGTAGAA
*
1573041 TTTTGTCCCGAAGGA-CAGCGTAGAA
1 ATTTGTCCCGAAGGACCA-CGTAGAA
1573066 CCCTCGACTC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
24 5 0.08
25 55 0.89
26 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (25 bp):
ATTTGTCCCGAAGGACCACGTAGAA
Found at i:1573213 original size:15 final size:15
Alignment explanation
Indices: 1573195--1573280 Score: 77
Period size: 15 Copynumber: 5.8 Consensus size: 15
1573185 TGCGTAGGGT
*
1573195 ATTTTCACGTACAAC
1 ATTTTCACATACAAC
*
1573210 A-TTTCACTTAGC-AC
1 ATTTTCACATA-CAAC
*
1573224 ATTTTCACATAGAAC
1 ATTTTCACATACAAC
*
1573239 ATTTTCACATAAAAC
1 ATTTTCACATACAAC
* * * *
1573254 ATATTAACATATAAA
1 ATTTTCACATACAAC
1573269 ATTTTCACATAC
1 ATTTTCACATAC
1573281 CAATAAAATC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
14 11 0.19
15 46 0.81
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (15 bp):
ATTTTCACATACAAC
Found at i:1573705 original size:22 final size:22
Alignment explanation
Indices: 1573648--1573706 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1573638 AGTATCCCTC
* *
1573648 CTACAGTAACGATACTTTTCTT
1 CTACGGTACCGATACTTTTCTT
* *
1573670 CTATGGT-CCTGATAGTTTTCTT
1 CTACGGTACC-GATACTTTTCTT
1573692 CTACGGTACCGATAC
1 CTACGGTACCGATAC
1573707 CTCTTTTAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 26 0.90
23 2 0.07
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (22 bp):
CTACGGTACCGATACTTTTCTT
Found at i:1573825 original size:21 final size:21
Alignment explanation
Indices: 1573796--1573850 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1573786 ATACCTCCAC
*
1573796 ATCAGTATCAATACTACTTCA
1 ATCAGTATCAATAATACTTCA
* *
1573817 ATCAATATCGATAATACTTCA
1 ATCAGTATCAATAATACTTCA
*
1573838 TTCAGTATCAATA
1 ATCAGTATCAATA
1573851 TTGTTTATTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (21 bp):
ATCAGTATCAATAATACTTCA
Found at i:1575905 original size:25 final size:26
Alignment explanation
Indices: 1575877--1575959 Score: 105
Period size: 27 Copynumber: 3.2 Consensus size: 26
1575867 AAAAAAATAT
*
1575877 TTTTGAAA-ATTTATATAATATATAG
1 TTTTGAAACATATATATAATATATAG
* * *
1575902 TTTTGAATATATATATATATTATATTG
1 TTTTGAA-ACATATATATAATATATAG
1575929 TTTTGAAAACATATATATAATATATAG
1 TTTTG-AAACATATATATAATATATAG
1575956 TTTT
1 TTTT
1575960 TAAAAACATT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.14
26 1 0.02
27 39 0.80
28 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (26 bp):
TTTTGAAACATATATATAATATATAG
Found at i:1575926 original size:27 final size:27
Alignment explanation
Indices: 1575888--1575964 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 27
1575878 TTTGAAAATT
* *
1575888 TATATAATATATAGTTTTGAATATATA
1 TATATAATATATAGTTTTGAAAACATA
* *
1575915 TATATATTATATTGTTTTGAAAACATA
1 TATATAATATATAGTTTTGAAAACATA
*
1575942 TATATAATATATAGTTTTTAAAA
1 TATATAATATATAGTTTTGAAAA
1575965 ACATTTTGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.48
Consensus pattern (27 bp):
TATATAATATATAGTTTTGAAAACATA
Found at i:1575981 original size:2 final size:2
Alignment explanation
Indices: 1575974--1576000 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1575964 AACATTTTGA
1575974 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 A
1576001 GTTTGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1576016 original size:45 final size:45
Alignment explanation
Indices: 1575939--1576033 Score: 115
Period size: 45 Copynumber: 2.1 Consensus size: 45
1575929 TTTTGAAAAC
*
1575939 ATATATATAATATATAGTTTTTAAAAACA-TTTTGAATA-TATATAT
1 ATATATATAATATATAGTTTTGAAAAACATTTTTGAA-AGTATAT-T
* *
1575984 ATATATATATATATATAG-TTTGGAAAATATTTTTGAAAGTATATT
1 ATATATATA-ATATATAGTTTTGAAAAACATTTTTGAAAGTATATT
1576029 ATATA
1 ATATA
1576034 GATTAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
45 24 0.55
46 20 0.45
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (45 bp):
ATATATATAATATATAGTTTTGAAAAACATTTTTGAAAGTATATT
Found at i:1576018 original size:46 final size:44
Alignment explanation
Indices: 1575939--1576033 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 44
1575929 TTTTGAAAAC
**
1575939 ATATATATAATATATAGTTTTTAAAAACATTTTGAATA-TATATAT
1 ATATATATAATATATAGTTTGGAAAAACATTTTGAA-AGTATAT-T
*
1575984 ATATATATATATATATAGTTTGGAAAATA-TTTTTGAAAGTATATT
1 ATATATATA-ATATATAGTTTGGAAAA-ACATTTTGAAAGTATATT
1576029 ATATA
1 ATATA
1576034 GATTAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
45 16 0.36
46 27 0.61
47 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (44 bp):
ATATATATAATATATAGTTTGGAAAAACATTTTGAAAGTATATT
Found at i:1576027 original size:36 final size:35
Alignment explanation
Indices: 1575986--1576087 Score: 109
Period size: 36 Copynumber: 2.9 Consensus size: 35
1575976 ATATATATAT
**
1575986 ATATATATATATATAGTTTGGAAAATATTTTTG-AA
1 ATATATAT-TATATAGTTTAAAAAATATTTTTGAAA
* *
1576021 A-GTATATTATATAGATTAAAAAACTATTTTTGAAA
1 ATATATATTATATAGTTTAAAAAA-TATTTTTGAAA
* *
1576056 ATATATATTATATGGTTTTAAAAATGATTTTT
1 ATATATATTATATAGTTTAAAAAAT-ATTTTT
1576088 ATTTATTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
33 13 0.24
34 13 0.24
35 5 0.09
36 24 0.44
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (35 bp):
ATATATATTATATAGTTTAAAAAATATTTTTGAAA
Found at i:1576049 original size:34 final size:34
Alignment explanation
Indices: 1575988--1576087 Score: 103
Period size: 34 Copynumber: 2.9 Consensus size: 34
1575978 ATATATATAT
* **
1575988 ATATATATATATAGTTTGGAAAATATTTTTGAAA
1 ATATATATATATAGATTAAAAAATATTTTTGAAA
*
1576022 GTATAT-TATATAGATTAAAAAACTATTTTTGAAA
1 ATATATATATATAGATTAAAAAA-TATTTTTGAAA
* * *
1576056 ATATATATTATATGGTTTTAAAAATGATTTTT
1 ATATATA-TATATAGATTAAAAAAT-ATTTTT
1576088 ATTTATTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
33 13 0.24
34 21 0.39
35 1 0.02
36 19 0.35
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (34 bp):
ATATATATATATAGATTAAAAAATATTTTTGAAA
Done.