Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008702.1 Hibiscus syriacus cultivar Beakdansim tig00111741_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: 3201804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 14
Found at i:1565540 original size:2 final size:2
Alignment explanation
Indices: 1565533--1565575 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1565523 TACCCAAATA
1565533 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
1565575 A
1 A
1565576 CCCACATGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1569319 original size:18 final size:18
Alignment explanation
Indices: 1569295--1569348 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1569285 GGTGTGAAAC
1569295 TATAAAAGTGTTTATAAAA
1 TATAAAAGTGTTTA-AAAA
* *
1569314 -ATAAAATTAACTTTAAAAA
1 TATAAAAGT--GTTTAAAAA
1569333 TATAAAAGTGTTTAAA
1 TATAAAAGTGTTTAAA
1569349 TTATAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
18 13 0.46
19 4 0.14
20 11 0.39
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (18 bp):
TATAAAAGTGTTTAAAAA
Found at i:1581746 original size:19 final size:20
Alignment explanation
Indices: 1581712--1581751 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1581702 AAATTTTGCT
* *
1581712 AAAAATAAAGCGAAA-TAAA
1 AAAAATAAAACAAAATTAAA
1581731 AAAAATAAAACAAAATTAAA
1 AAAAATAAAACAAAATTAAA
1581751 A
1 A
1581752 CGAAATGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (20 bp):
AAAAATAAAACAAAATTAAA
Found at i:1594838 original size:29 final size:28
Alignment explanation
Indices: 1594805--1594859 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
1594795 GGAAGAAGAA
1594805 GAAGAATAACTAA-AACAAAGTAAAAAAGT
1 GAAGAA-AA-TAAGAACAAAGTAAAAAAGT
*
1594834 GAAGAAGATAAGAACAAAGTAAAAAA
1 GAAGAAAATAAGAACAAAGTAAAAAA
1594860 TAAGGGGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 3 0.12
28 15 0.62
29 6 0.25
ACGTcount: A:0.67, C:0.05, G:0.16, T:0.11
Consensus pattern (28 bp):
GAAGAAAATAAGAACAAAGTAAAAAAGT
Found at i:1596558 original size:20 final size:20
Alignment explanation
Indices: 1596533--1596570 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1596523 TGGCATTCTG
1596533 AAATGATCT-CTAGCCTAGAT
1 AAATGATCTAC-AGCCTAGAT
1596553 AAATGATCTACAGCCTAG
1 AAATGATCTACAGCCTAG
1596571 TTCTCAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (20 bp):
AAATGATCTACAGCCTAGAT
Found at i:1598203 original size:45 final size:46
Alignment explanation
Indices: 1598146--1598234 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
1598136 AATTTCTTAT
* *
1598146 CAATATATTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTAATCCCATAAGCTCGTAACCTTATTTTAC
1598191 CAATATACTTACCATTTAATCCCATAAGCTCGTAACCTTATTTT
1 CAATATACTTACCATTTAATCCCATAAGCTCGTAACCTTATTTT
1598235 CATGCTTACC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 16 0.39
46 25 0.61
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (46 bp):
CAATATACTTACCATTTAATCCCATAAGCTCGTAACCTTATTTTAC
Found at i:1598248 original size:41 final size:42
Alignment explanation
Indices: 1598154--1598248 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 42
1598144 ATCAATATAT
*
1598154 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATCCCATAAGCTCGTAACCTTATTTTA-C-A-ATAC
*
1598199 TTACCATTTAATCCCATAAGCTCGTAACCTTATTTT-C-ATGC
1 TTACCATTT-ATCCCATAAGCTCGTAACCTTATTTTACAATAC
1598240 TTACCATTT
1 TTACCATTT
1598249 GATAAGCAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
41 12 0.26
44 1 0.02
45 9 0.19
46 25 0.53
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.40
Consensus pattern (42 bp):
TTACCATTTATCCCATAAGCTCGTAACCTTATTTTACAATAC
Found at i:1598724 original size:64 final size:64
Alignment explanation
Indices: 1598623--1598750 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
1598613 AATGTCATGA
1598623 CAATTCCAAAGGAATTAACTCAAAAATTGAAAATAAAATATTTTCTTACCTTTAAAGCTAACTC
1 CAATTCCAAAGGAATTAACTCAAAAATTGAAAATAAAATATTTTCTTACCTTTAAAGCTAACTC
1598687 CAATTCCAAAGGAATTAACTCAAAAATTGAAAATAAAATATTTTCTTACCTTTAAAGCTAACTC
1 CAATTCCAAAGGAATTAACTCAAAAATTGAAAATAAAATATTTTCTTACCTTTAAAGCTAACTC
1598751 ACGTCAATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.31
Consensus pattern (64 bp):
CAATTCCAAAGGAATTAACTCAAAAATTGAAAATAAAATATTTTCTTACCTTTAAAGCTAACTC
Found at i:1606918 original size:10 final size:10
Alignment explanation
Indices: 1606903--1606955 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
1606893 TCATCACTCA
1606903 TTTTTTTCTC
1 TTTTTTTCTC
1606913 TTTTTTTCTC
1 TTTTTTTCTC
1606923 TTTTTCTTCT-
1 TTTTT-TTCTC
*
1606933 TTGTTTTTGT-
1 TT-TTTTTCTC
1606943 TTTTTTT-TC
1 TTTTTTTCTC
1606952 TTTT
1 TTTT
1606956 CCTGTTTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 1 0.03
9 9 0.23
10 22 0.56
11 7 0.18
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:1606948 original size:9 final size:9
Alignment explanation
Indices: 1606903--1606970 Score: 55
Period size: 10 Copynumber: 6.8 Consensus size: 9
1606893 TCATCACTCA
1606903 TTTTTTTCTC
1 TTTTTTT-TC
1606913 TTTTTTTCTC
1 TTTTTTT-TC
*
1606923 TTTTTCTTC
1 TTTTTTTTC
*
1606932 TTTGTTTTTGT
1 TTT-TTTTT-C
1606943 TTTTTTTTC
1 TTTTTTTTC
1606952 TTTTCCTGTTTC
1 TTTT--T-TTTC
1606964 TTTTTTT
1 TTTTTTT
1606971 AATGTTTCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
9 11 0.22
10 26 0.53
11 4 0.08
12 8 0.16
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1606967 original size:28 final size:29
Alignment explanation
Indices: 1606913--1606968 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
1606903 TTTTTTTCTC
* *
1606913 TTTTTTTCTCTTTTTCTTCTTTGTTTTTG
1 TTTTTTTCTCTTTTTCCTCTTTCTTTTTG
* *
1606942 TTTTTTTTTC-TTTTCCTGTTTCTTTTT
1 TTTTTTTCTCTTTTTCCTCTTTCTTTTT
1606969 TTAATGTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.80
Consensus pattern (29 bp):
TTTTTTTCTCTTTTTCCTCTTTCTTTTTG
Found at i:1609697 original size:45 final size:46
Alignment explanation
Indices: 1609640--1609727 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
1609630 AATTTCTTAT
*
1609640 CAATATATTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTAC
1609685 CAATATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATTT
1609728 GAATGCTTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 16 0.39
46 25 0.61
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (46 bp):
CAATATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:1613642 original size:11 final size:11
Alignment explanation
Indices: 1613626--1613650 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1613616 TCATCACTCA
1613626 TTTTTTATCTT
1 TTTTTTATCTT
1613637 TTTTTTATCTT
1 TTTTTTATCTT
1613648 TTT
1 TTT
1613651 CTTCTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTATCTT
Found at i:1613649 original size:20 final size:19
Alignment explanation
Indices: 1613626--1613680 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
1613616 TCATCACTCA
1613626 TTTTTTATCTTTTTTTTATC
1 TTTTTTATCTTTTTTTT-TC
1613646 TTTTTCT-TCTTTTCTTTTTC
1 TTTTT-TATCTTTT-TTTTTC
*
1613666 TGTTTCTAT-TTTTTT
1 T-TTTTTATCTTTTTT
1613681 AGCTCTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
19 2 0.07
20 19 0.63
21 9 0.30
ACGTcount: A:0.05, C:0.13, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTATCTTTTTTTTTC
Found at i:1624274 original size:90 final size:88
Alignment explanation
Indices: 1624160--1624331 Score: 272
Period size: 90 Copynumber: 1.9 Consensus size: 88
1624150 TCCCGAATAT
* * * *
1624160 TTAATTTCAATTAATTAAATATAGAATTAATTAATTTGAAATAATAAAATCCCTGATATGATTAG
1 TTAAATTCAATTAATTAAATATAGAATTAATAAATTTGAAATAATAAAA-CCCTAATATGACTAG
1624225 GGTAACTTGGATATAAAAGGATTA
65 GGTAACTTGGATATAAAAGGATTA
*
1624249 TTAAATTCTAATTAATTAAATATAGATTTAATAAATTTGAAATAATAAAACCCTAATATGACTAG
1 TTAAATTC-AATTAATTAAATATAGAATTAATAAATTTGAAATAATAAAACCCTAATATGACTAG
*
1624314 GGTAACTTGGCTATAAAA
65 GGTAACTTGGATATAAAA
1624332 TGGTGTGTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
89 37 0.49
90 39 0.51
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGAATTAATAAATTTGAAATAATAAAACCCTAATATGACTAGG
GTAACTTGGATATAAAAGGATTA
Found at i:1624740 original size:14 final size:14
Alignment explanation
Indices: 1624721--1624752 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1624711 ACCATAAACC
1624721 ATAGACAATAGCCA
1 ATAGACAATAGCCA
*
1624735 ATAGACAATAGCCC
1 ATAGACAATAGCCA
1624749 ATAG
1 ATAG
1624753 CCCAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.16
Consensus pattern (14 bp):
ATAGACAATAGCCA
Found at i:1632104 original size:27 final size:27
Alignment explanation
Indices: 1632073--1632137 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
1632063 TTAAAGGACT
*
1632073 AAAATACCCTTAAACTCTAAAATAACT
1 AAAATACCCTTAAACTCTAAAATAACC
* * *
1632100 GAAATACCCTTAAACTTTAAAATGACC
1 AAAATACCCTTAAACTCTAAAATAACC
1632127 AAAATACCCTT
1 AAAATACCCTT
1632138 GGGCTCCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (27 bp):
AAAATACCCTTAAACTCTAAAATAACC
Found at i:1634505 original size:39 final size:39
Alignment explanation
Indices: 1634480--1634576 Score: 144
Period size: 39 Copynumber: 2.5 Consensus size: 39
1634470 CTCTCCATCT
1634480 TTCAAGA-ACTCTTAAATTCACAATAAAACACTCTAACG
1 TTCAAGAGACTCTTAAATTCACAATAAAACACTCTAACG
* *
1634518 TTCAAGAGATTCTTAATTTCACAATAAAACACTCTAAC-
1 TTCAAGAGACTCTTAAATTCACAATAAAACACTCTAACG
*
1634556 TACTAAGAGACTCTTAAATTC
1 TTC-AAGAGACTCTTAAATTC
1634577 CCCCCTTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
38 9 0.17
39 43 0.83
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (39 bp):
TTCAAGAGACTCTTAAATTCACAATAAAACACTCTAACG
Found at i:1634508 original size:38 final size:39
Alignment explanation
Indices: 1634466--1634576 Score: 127
Period size: 39 Copynumber: 2.9 Consensus size: 39
1634456 AATAAAAATA
* * *
1634466 AAAACTCTCCATCTTTCAAGA-ACTCTTAAATTCACAAT
1 AAAACACTCCAACGTTCAAGAGACTCTTAAATTCACAAT
* * *
1634504 AAAACACTCTAACGTTCAAGAGATTCTTAATTTCACAAT
1 AAAACACTCCAACGTTCAAGAGACTCTTAAATTCACAAT
* *
1634543 AAAACACTCTAAC-TACTAAGAGACTCTTAAATTC
1 AAAACACTCCAACGTTC-AAGAGACTCTTAAATTC
1634577 CCCCCTTAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
38 19 0.31
39 43 0.69
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.30
Consensus pattern (39 bp):
AAAACACTCCAACGTTCAAGAGACTCTTAAATTCACAAT
Found at i:1636244 original size:57 final size:57
Alignment explanation
Indices: 1636156--1636268 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 57
1636146 AATCCTATTG
*
1636156 TTAAATGTAAGATACGAGTATGTGCCCACCAAATACATTTTCTAGAAAGGGTCTCTA
1 TTAAATGTAAGATACGAGTACGTGCCCACCAAATACATTTTCTAGAAAGGGTCTCTA
* * *
1636213 TTAAATGTAAGATACGAGTACGTGCCGACCAAGTACATTTTCTGGAAAGGGTCTCT
1 TTAAATGTAAGATACGAGTACGTGCCCACCAAATACATTTTCTAGAAAGGGTCTCT
1636269 TTGGCCATTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (57 bp):
TTAAATGTAAGATACGAGTACGTGCCCACCAAATACATTTTCTAGAAAGGGTCTCTA
Found at i:1636944 original size:45 final size:45
Alignment explanation
Indices: 1636871--1636981 Score: 150
Period size: 45 Copynumber: 2.5 Consensus size: 45
1636861 TATATATATA
*
1636871 TTGCAATTCCAGTGAGCATATCAGGGTGTTTATCCCGTTAAAATT
1 TTGCAATTCCAGTGAGAATATCAGGGTGTTTATCCCGTTAAAATT
* * * * *
1636916 TTGCAATTCCAGTGAGAATTTTATGGTGTTTATTCTGTTAAAATT
1 TTGCAATTCCAGTGAGAATATCAGGGTGTTTATCCCGTTAAAATT
* *
1636961 TTGCAATTCCAGAGAGCATAT
1 TTGCAATTCCAGTGAGAATAT
1636982 ATGTATATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (45 bp):
TTGCAATTCCAGTGAGAATATCAGGGTGTTTATCCCGTTAAAATT
Found at i:1644877 original size:45 final size:45
Alignment explanation
Indices: 1644828--1644929 Score: 141
Period size: 45 Copynumber: 2.3 Consensus size: 45
1644818 TAATTTAAGT
* * * *
1644828 GGTGTGGCCCCATGTTCATGCGTAATATCTCGTATAGCTCCAAGC
1 GGTGTGGTCCCATGGTCATGAGCAATATCTCGTATAGCTCCAAGC
* * *
1644873 GGTGTAGTCCCATGGTCATGAGCATTATCTTGTATAGCTCCAAGC
1 GGTGTGGTCCCATGGTCATGAGCAATATCTCGTATAGCTCCAAGC
1644918 GGTGTGGTCCCA
1 GGTGTGGTCCCA
1644930 AGGTTATCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (45 bp):
GGTGTGGTCCCATGGTCATGAGCAATATCTCGTATAGCTCCAAGC
Found at i:1662282 original size:6 final size:6
Alignment explanation
Indices: 1662265--1662338 Score: 87
Period size: 6 Copynumber: 11.8 Consensus size: 6
1662255 CATCACTCAT
*
1662265 TTTTTC TCTTTC TTTTTC TTTTTC TTCTTTC TTCTTTC TTTTTC TTCTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TT-TTTC TTTTTC -T-TTTTC
*
1662317 TTTTTC TGTTTC TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTT
1662339 ATGTTTCTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
5 5 0.08
6 36 0.59
7 15 0.25
8 5 0.08
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:1662300 original size:26 final size:24
Alignment explanation
Indices: 1662265--1662338 Score: 96
Period size: 26 Copynumber: 3.0 Consensus size: 24
1662255 CATCACTCAT
1662265 TTTTTCTCTTTCTTTTTCTTTTTC
1 TTTTTCTCTTTCTTTTTCTTTTTC
1662289 TTCTTTCTTCTTTCTTTTTCTTCTTTTC
1 TT-TTTC-TCTTTCTTTTTC-T-TTTTC
*
1662317 TTTTTCTGTTTCTTTTT-TTTTT
1 TTTTTCTCTTTCTTTTTCTTTTT
1662339 ATGTTTCTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
23 4 0.09
24 3 0.07
25 4 0.09
26 22 0.49
27 5 0.11
28 7 0.16
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (24 bp):
TTTTTCTCTTTCTTTTTCTTTTTC
Found at i:1662302 original size:20 final size:19
Alignment explanation
Indices: 1662265--1662338 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 19
1662255 CATCACTCAT
1662265 TTTTTC-TCTTTCTTTTTC
1 TTTTTCTTCTTTCTTTTTC
1662283 TTTTTCTTCTTTCTTCTTTC
1 TTTTTCTTCTTTCTT-TTTC
1662303 TTTTTCTTCTTTTCTTTTTC
1 TTTTTCTTC-TTTCTTTTTC
*
1662323 TGTTTCTT-TTT-TTTTT
1 TTTTTCTTCTTTCTTTTT
1662339 ATGTTTCTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
17 5 0.10
18 9 0.17
19 8 0.15
20 24 0.46
21 6 0.12
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (19 bp):
TTTTTCTTCTTTCTTTTTC
Found at i:1662338 original size:17 final size:17
Alignment explanation
Indices: 1662264--1662354 Score: 87
Period size: 17 Copynumber: 5.2 Consensus size: 17
1662254 TCATCACTCA
1662264 TTTTTTCTCTTTCTTTT
1 TTTTTTCTCTTTCTTTT
1662281 TCTTTTTCTTCTTTCTTCTT
1 T-TTTTTC-TCTTTCTT-TT
*
1662301 TCTTTT-TC-TTCTTTT
1 TTTTTTCTCTTTCTTTT
* *
1662316 CTTTTTCTGTTTCTTTT
1 TTTTTTCTCTTTCTTTT
* *
1662333 TTTTTTATGTTTCTATTT
1 TTTTTTCTCTTTCT-TTT
1662351 TTTT
1 TTTT
1662355 AGCTCTTATG
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.10
16 6 0.10
17 22 0.35
18 13 0.21
19 12 0.19
20 3 0.05
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTTCTCTTTCTTTT
Found at i:1673045 original size:90 final size:88
Alignment explanation
Indices: 1672931--1673102 Score: 265
Period size: 90 Copynumber: 1.9 Consensus size: 88
1672921 TCCCGAATAT
* * *
1672931 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGA-TATGATTA
1 TTAAATTCAATTAATTAAATATAGATTTAATAAATTTGAAATAATAAAA-CCCT-ATTATGACTA
1672995 GGGTAACTTAGATATAAAAGGATTA
64 GGGTAACTTAGATATAAAAGGATTA
1673020 TTAAATTCTAATTAATTAAATATAGATTTAATAAATTTGAAATAATAAAACCCTATTATGACTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATAAATTTGAAATAATAAAACCCTATTATGACTAG
* *
1673085 GGTAACTTGGCTATAAAA
65 GGTAACTTAGATATAAAA
1673103 TGGTGTGTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
88 1 0.01
89 35 0.46
90 40 0.53
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATAAATTTGAAATAATAAAACCCTATTATGACTAGG
GTAACTTAGATATAAAAGGATTA
Found at i:1673516 original size:14 final size:14
Alignment explanation
Indices: 1673497--1673528 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1673487 ACCATAAACC
1673497 ATAGACAATAGCCA
1 ATAGACAATAGCCA
*
1673511 ATAGACAATAGCCC
1 ATAGACAATAGCCA
1673525 ATAG
1 ATAG
1673529 CCCAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.16
Consensus pattern (14 bp):
ATAGACAATAGCCA
Found at i:1680403 original size:32 final size:32
Alignment explanation
Indices: 1680362--1680423 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
1680352 GTAAGTTCTT
1680362 ACCGTAATCTCATTTGCTTCGTGCATAGGGGA
1 ACCGTAATCTCATTTGCTTCGTGCATAGGGGA
1680394 ACCGTAATCTCATTTGCTTCGTGCATAGGG
1 ACCGTAATCTCATTTGCTTCGTGCATAGGG
1680424 AAAAACCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (32 bp):
ACCGTAATCTCATTTGCTTCGTGCATAGGGGA
Found at i:1680480 original size:40 final size:40
Alignment explanation
Indices: 1680406--1680505 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 40
1680396 CGTAATCTCA
* **
1680406 TTTGCTTCGTGCATAGGGAAAAACCTTATTGTATGCCCAT
1 TTTGCATCGTGCATAGGGAAAAACCTTACCGTATGCCCAT
* **
1680446 TTTGCATCGTGCATAAGGG-AAAACTTTACCGTATGCTTAT
1 TTTGCATCGTGCAT-AGGGAAAAACCTTACCGTATGCCCAT
* *
1680486 TTT-CTTTGTGCATAGGGAAA
1 TTTGCATCGTGCATAGGGAAA
1680506 TTTGTCTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
38 4 0.08
39 10 0.20
40 32 0.64
41 4 0.08
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (40 bp):
TTTGCATCGTGCATAGGGAAAAACCTTACCGTATGCCCAT
Found at i:1681637 original size:39 final size:39
Alignment explanation
Indices: 1681612--1681708 Score: 144
Period size: 39 Copynumber: 2.5 Consensus size: 39
1681602 CTCTCCATCT
1681612 TTCAAGA-ACTCTTAAATTCACAATAAAACACTCTAACG
1 TTCAAGAGACTCTTAAATTCACAATAAAACACTCTAACG
* *
1681650 TTCAAGAGATTCTTAATTTCACAATAAAACACTCTAAC-
1 TTCAAGAGACTCTTAAATTCACAATAAAACACTCTAACG
*
1681688 TACTAAGAGACTCTTAAATTC
1 TTC-AAGAGACTCTTAAATTC
1681709 CCCCCTTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
38 9 0.17
39 43 0.83
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (39 bp):
TTCAAGAGACTCTTAAATTCACAATAAAACACTCTAACG
Found at i:1681640 original size:38 final size:39
Alignment explanation
Indices: 1681598--1681708 Score: 127
Period size: 39 Copynumber: 2.9 Consensus size: 39
1681588 AATAAAAATA
* * *
1681598 AAAACTCTCCATCTTTCAAGA-ACTCTTAAATTCACAAT
1 AAAACACTCCAACGTTCAAGAGACTCTTAAATTCACAAT
* * *
1681636 AAAACACTCTAACGTTCAAGAGATTCTTAATTTCACAAT
1 AAAACACTCCAACGTTCAAGAGACTCTTAAATTCACAAT
* *
1681675 AAAACACTCTAAC-TACTAAGAGACTCTTAAATTC
1 AAAACACTCCAACGTTC-AAGAGACTCTTAAATTC
1681709 CCCCCTTAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
38 19 0.31
39 43 0.69
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.30
Consensus pattern (39 bp):
AAAACACTCCAACGTTCAAGAGACTCTTAAATTCACAAT
Found at i:1683374 original size:57 final size:57
Alignment explanation
Indices: 1683286--1683398 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 57
1683276 AATCCTATTG
* *
1683286 TTAAATGTAAGATACGAGTATGTGCCAACCAAATACATTTTTTGGAAAGGGTCTCTA
1 TTAAATGTAAGATACGAGTACGTGCCAACCAAATACATTTTCTGGAAAGGGTCTCTA
* *
1683343 TTAAATGTAAGATACGAGTACGTGCCGACCAAGTACATTTTCTGGAAAGGGTCTCT
1 TTAAATGTAAGATACGAGTACGTGCCAACCAAATACATTTTCTGGAAAGGGTCTCT
1683399 TTGGCCATTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (57 bp):
TTAAATGTAAGATACGAGTACGTGCCAACCAAATACATTTTCTGGAAAGGGTCTCTA
Found at i:1684076 original size:45 final size:45
Alignment explanation
Indices: 1684003--1684113 Score: 159
Period size: 45 Copynumber: 2.5 Consensus size: 45
1683993 TATATATATA
*
1684003 TTGCAATTCCAGTGAGCATATCAGGGTGTTTATCCCGTTAAAATT
1 TTGCAATTCCAGTGAGAATATCAGGGTGTTTATCCCGTTAAAATT
* * * * *
1684048 TTGCAATTCCAGTGAGAATTTTATGGTGTTTATTCTGTTAAAATT
1 TTGCAATTCCAGTGAGAATATCAGGGTGTTTATCCCGTTAAAATT
*
1684093 TTGCAATTCCAGTGAGCATAT
1 TTGCAATTCCAGTGAGAATAT
1684114 ATGTATATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (45 bp):
TTGCAATTCCAGTGAGAATATCAGGGTGTTTATCCCGTTAAAATT
Found at i:1691962 original size:45 final size:45
Alignment explanation
Indices: 1691911--1692017 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
1691901 TAATTTAAGT
1691911 GGTGTGGCCCCATGTTCATGCA-CAATATCTCGCATAGCTCCAAGC
1 GGTGTGGCCCCATGTTCATG-AGCAATATCTCGCATAGCTCCAAGC
* * * *
1691956 GGTGTGGTCCCATGGTCATGAGCATTATCTCGTATAGCTCCAAGC
1 GGTGTGGCCCCATGTTCATGAGCAATATCTCGCATAGCTCCAAGC
*
1692001 GGTGTGGTCCCAATGTT
1 GGTGTGG-CCCCATGTT
1692018 ATCACCATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 1 0.02
45 46 0.87
46 6 0.11
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (45 bp):
GGTGTGGCCCCATGTTCATGAGCAATATCTCGCATAGCTCCAAGC
Found at i:1705515 original size:52 final size:52
Alignment explanation
Indices: 1705437--1705541 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
1705427 GGGAATGCTT
1705437 TGGTTGTATGGAAAAAGGGTAAATCATATACAGGTCCTCCCTGTTTAGCATG
1 TGGTTGTATGGAAAAAGGGTAAATCATATACAGGTCCTCCCTGTTTAGCATG
1705489 TGGTTGTATGGAAAAAGGGTAAATCATATACAGGTCCTCCCTGTTTAGCATG
1 TGGTTGTATGGAAAAAGGGTAAATCATATACAGGTCCTCCCTGTTTAGCATG
1705541 T
1 T
1705542 CACGTTTTAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (52 bp):
TGGTTGTATGGAAAAAGGGTAAATCATATACAGGTCCTCCCTGTTTAGCATG
Found at i:1709003 original size:31 final size:31
Alignment explanation
Indices: 1708965--1709028 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1708955 ACCGTCAAGT
* * *
1708965 CCAGTAAGGCCCTGAGCACACAGCCGAGGAG
1 CCAGTAAGGCCCTCAGCACAAAGCCGAGCAG
* *
1708996 CCAGTAAGGTCCTCAGTACAAAGCCGAGCAG
1 CCAGTAAGGCCCTCAGCACAAAGCCGAGCAG
1709027 CC
1 CC
1709029 TCCAGGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.33, G:0.28, T:0.09
Consensus pattern (31 bp):
CCAGTAAGGCCCTCAGCACAAAGCCGAGCAG
Found at i:1711583 original size:15 final size:15
Alignment explanation
Indices: 1711563--1711600 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1711553 GGAAGACGAA
1711563 GAAGTTGATTAAAGG
1 GAAGTTGATTAAAGG
1711578 GAAGTTGATTAAAGG
1 GAAGTTGATTAAAGG
*
1711593 GGAGTTGA
1 GAAGTTGA
1711601 GCCAAAGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (15 bp):
GAAGTTGATTAAAGG
Found at i:1712307 original size:16 final size:16
Alignment explanation
Indices: 1712286--1712320 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1712276 CCATTGAATA
*
1712286 AGATTTTCTTAAGGAT
1 AGATTTTCTCAAGGAT
1712302 AGATTTTCTCAAGGAT
1 AGATTTTCTCAAGGAT
1712318 AGA
1 AGA
1712321 ATAATAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (16 bp):
AGATTTTCTCAAGGAT
Found at i:1712944 original size:15 final size:15
Alignment explanation
Indices: 1712924--1712973 Score: 100
Period size: 15 Copynumber: 3.3 Consensus size: 15
1712914 GTCTGTGTTC
1712924 ATTTCGAATTTAATA
1 ATTTCGAATTTAATA
1712939 ATTTCGAATTTAATA
1 ATTTCGAATTTAATA
1712954 ATTTCGAATTTAATA
1 ATTTCGAATTTAATA
1712969 ATTTC
1 ATTTC
1712974 TTCTCTCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (15 bp):
ATTTCGAATTTAATA
Found at i:1715631 original size:18 final size:18
Alignment explanation
Indices: 1715608--1715672 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
1715598 GACCGGTCAC
*
1715608 AACCCGACCCGACTCGTT
1 AACCCGACCCGACCCGTT
1715626 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
* *
1715644 GACCCGACCTGACCCGTT
1 AACCCGACCCGACCCGTT
*
1715662 GACCCGACCCG
1 AACCCGACCCG
1715673 TTGACCGTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.20, C:0.48, G:0.20, T:0.12
Consensus pattern (18 bp):
AACCCGACCCGACCCGTT
Found at i:1715647 original size:13 final size:13
Alignment explanation
Indices: 1715631--1715678 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
1715621 TCGTTAACCC
1715631 GACCCGACCCGTT
1 GACCCGACCCGTT
1715644 GACCCGACCTGACCCGTT
1 GA--C--CC-GACCCGTT
1715662 GACCCGACCCGTT
1 GACCCGACCCGTT
1715675 GACC
1 GACC
1715679 GTTGACCGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 14 0.47
14 2 0.07
15 1 0.03
16 1 0.03
17 2 0.07
18 10 0.33
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1718253 original size:24 final size:23
Alignment explanation
Indices: 1718178--1718260 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
1718168 ATATTTTATC
* *
1718178 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATT-TGTTT
* *
1718202 TGACATCTGATCTGAAATTTGTTC
1 TGATATCTGATCTG-AATTTGTTT
*
1718226 TGATATCTGTTCTGAATTATGTTT
1 TGATATCTGATCTGAATT-TGTTT
*
1718250 TGATTTCTGAT
1 TGATATCTGAT
1718261 ATCTCCGTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
23 4 0.08
24 40 0.83
25 4 0.08
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (23 bp):
TGATATCTGATCTGAATTTGTTT
Found at i:1718425 original size:2 final size:2
Alignment explanation
Indices: 1718420--1718444 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1718410 GGGATGGGGG
1718420 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 T
1718445 GTTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1721858 original size:24 final size:24
Alignment explanation
Indices: 1721826--1721936 Score: 141
Period size: 24 Copynumber: 4.6 Consensus size: 24
1721816 AAATGTTTTA
*
1721826 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
1721850 TCTGATTTCTGATATGAATTATGT
1 TCTGATTTCTGATATGAATTCTGT
* * * *
1721874 TCTGATTTTTTATCTGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* *
1721898 TCTTATATCTGATATGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
1721922 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
1721937 CTCTGTATAC
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.54
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:1721859 original size:12 final size:12
Alignment explanation
Indices: 1721826--1721932 Score: 58
Period size: 12 Copynumber: 8.9 Consensus size: 12
1721816 AAATGTTTTA
1721826 TCTGATTTCTGAT
1 TCTGATTTCTG-T
*
1721839 T-TGAATTCTGT
1 TCTGATTTCTGT
*
1721850 TCTGATTTCTGA
1 TCTGATTTCTGT
* * *
1721862 TATGAATTATGT
1 TCTGATTTCTGT
*
1721874 TCTGATTT-TTT
1 TCTGATTTCTGT
1721885 ATCTGGA-TTCTGT
1 -TCT-GATTTCTGT
* * *
1721898 TCTTATATCTGA
1 TCTGATTTCTGT
* *
1721910 TATGAATTCTGT
1 TCTGATTTCTGT
*
1721922 TTTGATTTCTG
1 TCTGATTTCTG
1721933 ATATCTCTGT
Statistics
Matches: 68, Mismatches: 21, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
11 5 0.07
12 58 0.85
13 5 0.07
ACGTcount: A:0.19, C:0.11, G:0.16, T:0.54
Consensus pattern (12 bp):
TCTGATTTCTGT
Found at i:1724026 original size:60 final size:60
Alignment explanation
Indices: 1723939--1724051 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
1723929 AATGGTCCCT
* * * * *
1723939 GACTATAGGGTGATGCTTCGTTGAGTCTCTCGACTATTAAAAGTTATAAAATGATCTTTC
1 GACTATAAGGTGATGCTTCGTTCAGTCTCCCGACTATCAAAAGTTACAAAATGATCTTTC
* *
1723999 GACTATAAGGTGTTGCTTTGTTCAGTCTCCCGACTATCAAAAGTTACAAAATG
1 GACTATAAGGTGATGCTTCGTTCAGTCTCCCGACTATCAAAAGTTACAAAATG
1724052 GTTATCCAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (60 bp):
GACTATAAGGTGATGCTTCGTTCAGTCTCCCGACTATCAAAAGTTACAAAATGATCTTTC
Found at i:1725184 original size:40 final size:40
Alignment explanation
Indices: 1725140--1725233 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
1725130 TAACACGATC
1725140 TCAAATTCGCAACGC-AAGTTCCAAAATTGCAACGC-AAAAG
1 TCAAATTCGCAACGCAAAG-T-CAAAATTGCAACGCGAAAAG
* *
1725180 TCAAATTCGCAACGCGAAAGTCAAATTTGCAACGCGAATAG
1 TCAAATTCGCAACGC-AAAGTCAAAATTGCAACGCGAAAAG
*
1725221 TTAAA-TCGCAACG
1 TCAAATTCGCAACG
1725234 ATAATATGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
40 36 0.75
41 9 0.19
42 3 0.06
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (40 bp):
TCAAATTCGCAACGCAAAGTCAAAATTGCAACGCGAAAAG
Found at i:1725215 original size:20 final size:20
Alignment explanation
Indices: 1725140--1725233 Score: 97
Period size: 20 Copynumber: 4.7 Consensus size: 20
1725130 TAACACGATC
1725140 TCAAATTCGCAACGC--AAG
1 TCAAATTCGCAACGCGAAAG
*
1725158 TTCCAAAATT-GCAACGCAAAAG
1 -T-C-AAATTCGCAACGCGAAAG
1725180 TCAAATTCGCAACGCGAAAG
1 TCAAATTCGCAACGCGAAAG
*
1725200 TCAAATTTGCAACGCGAATAG
1 TCAAATTCGCAACGCGAA-AG
*
1725221 TTAAA-TCGCAACG
1 TCAAATTCGCAACG
1725234 ATAATATGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
19 6 0.09
20 44 0.68
21 12 0.18
22 3 0.05
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (20 bp):
TCAAATTCGCAACGCGAAAG
Found at i:1725239 original size:20 final size:20
Alignment explanation
Indices: 1725222--1725293 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
1725212 CGCGAATAGT
1725222 TAAATCGCAACGATAATATG
1 TAAATCGCAACGATAATATG
* ** *
1725242 TAATTCGCAACGCGAATAGG
1 TAAATCGCAACGATAATATG
1725262 TAAATCGCAACGATAATATG
1 TAAATCGCAACGATAATATG
*
1725282 TAAATCACAACG
1 TAAATCGCAACG
1725294 CAAATTCTCC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGATAATATG
Found at i:1725252 original size:40 final size:40
Alignment explanation
Indices: 1725203--1725294 Score: 148
Period size: 40 Copynumber: 2.3 Consensus size: 40
1725193 GCGAAAGTCA
* *
1725203 AATTTGCAACGCGAATAGTTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
1725243 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
* *
1725283 AAATCACAACGC
1 AATTCGCAACGC
1725295 AAATTCTCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.23
Consensus pattern (40 bp):
AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
Found at i:1725598 original size:20 final size:21
Alignment explanation
Indices: 1725555--1725623 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
1725545 GGTTCCAAAT
* **
1725555 TCGCAACACGAATTCAGAAAA
1 TCGCAACGCGAATTTGGAAAA
*
1725576 TCGCAACGCGAATTT-GTAAA
1 TCGCAACGCGAATTTGGAAAA
1725596 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAATTTGGAAAA
1725617 TCGCAAC
1 TCGCAAC
1725624 ACAGAAGTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 19 0.44
21 24 0.56
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAATTTGGAAAA
Found at i:1725641 original size:41 final size:41
Alignment explanation
Indices: 1725550--1725645 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 41
1725540 ACCCAGGTTC
*
1725550 CAAATTCGCAACACGAATTCAGAAAATCGCAACGCGAATTTGT
1 CAAATTCGCAACACGAATTCAGAAAATCGCAACACGAA--TGT
* **
1725593 -AAA-TCGCAACGCGAATTTGGAAAATCGCAACACAGAA-GT
1 CAAATTCGCAACACGAATTCAGAAAATCGCAACAC-GAATGT
1725632 CAAATTCGCAACAC
1 CAAATTCGCAACAC
1725646 AGAAGTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
39 2 0.04
40 3 0.07
41 34 0.76
42 6 0.13
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.18
Consensus pattern (41 bp):
CAAATTCGCAACACGAATTCAGAAAATCGCAACACGAATGT
Found at i:1725642 original size:20 final size:20
Alignment explanation
Indices: 1725617--1725655 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1725607 ATTTGGAAAA
1725617 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
1725637 TCGCAACACAGAAGTCAAA
1 TCGCAACACAGAAGTCAAA
1725656 GCGCTTTATT
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:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:1726204 original size:20 final size:20
Alignment explanation
Indices: 1726181--1726286 Score: 158
Period size: 20 Copynumber: 5.3 Consensus size: 20
1726171 AAACTTAAAT
*
1726181 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1726201 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1726221 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
** *
1726241 TAACAACGTGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1726261 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1726281 TCGCAA
1 TCGCAA
1726287 AGCAAAACTA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1726335 original size:20 final size:20
Alignment explanation
Indices: 1726310--1726415 Score: 131
Period size: 20 Copynumber: 5.3 Consensus size: 20
1726300 TCTTGTTGCG
* *
1726310 ATTTTCTCGTTGCGGTTTTC
1 ATTTTCGCGTTGCGATTTTC
* * *
1726330 ATTTTCGAGGTGCAATTTTC
1 ATTTTCGCGTTGCGATTTTC
*
1726350 ATTTTTGCGTTGCGATTTTC
1 ATTTTCGCGTTGCGATTTTC
* *
1726370 ATGTTCGCGTTGTGATTTTC
1 ATTTTCGCGTTGCGATTTTC
*
1726390 ATTTTCGCATTGCGATTTTC
1 ATTTTCGCGTTGCGATTTTC
1726410 ATTTTC
1 ATTTTC
1726416 AGAAACTACT
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATTTTC
Found at i:1728584 original size:21 final size:21
Alignment explanation
Indices: 1728558--1728674 Score: 94
Period size: 21 Copynumber: 5.6 Consensus size: 21
1728548 TGCACCTTTC
*
1728558 ATCGTTCAAGAGGCTCCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
1728579 ATCGTTCAAGAGGCCCCT-CT
1 ATCGTTCAAGAGGCCCCTCCT
* ** *
1728599 CATCATAGAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* *
1728621 ACCGTTCAAGAGGCCCCT-AT
1 ATCGTTCAAGAGGCCCCTCCT
* * * *
1728641 CATCGTTGAAGAGGTCCCGCCC
1 -ATCGTTCAAGAGGCCCCTCCT
*
1728663 GTCGTTCAAGAG
1 ATCGTTCAAGAG
1728675 CCCGATTCAT
Statistics
Matches: 73, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.03
21 70 0.96
22 1 0.01
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.21
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:1728619 original size:42 final size:42
Alignment explanation
Indices: 1728565--1728674 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
1728555 TTCATCGTTC
* * *
1728565 AAGAGGCTCCTCCTATCGTTCAAGAGGCCCCTCTCATCATAG
1 AAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTATCATCATAG
* * *
1728607 AAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCGTTG
1 AAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTATCATCATAG
* * *
1728649 AAGAGGTCCCGCCCGTCGTTCAAGAG
1 AAGAGGCCCCTCCCATCGTTCAAGAG
1728675 CCCGATTCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.20
Consensus pattern (42 bp):
AAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTATCATCATAG
Found at i:1730112 original size:65 final size:67
Alignment explanation
Indices: 1729977--1730145 Score: 204
Period size: 67 Copynumber: 2.6 Consensus size: 67
1729967 TGGGGTACAC
* * ***
1729977 TTTGCTTGTTTAATTGATTTTTAAGAGTTGATTTGATTTGTTTAATTGATGAGGAAATAAGAATT
1 TTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTG--TTAAATAATTGATGAGGAAATAAGAATT
1730042 -TTT
64 ATTT
* *
1730045 TTT-CTTGTTCAATTGATTTGTAAAAGTTGATTTGTTAAATAATTGATGTA-TAAATAAGAATTA
1 TTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTAAATAATTGATG-AGGAAATAAGAATTA
1730108 TTT
65 TTT
*
1730111 TTTGCTTGTTTAATTGA--TGTTAAAGTTGATTTGTT
1 TTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1730146 GTTTTGAATT
Statistics
Matches: 89, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
65 39 0.44
66 7 0.08
67 40 0.45
68 3 0.03
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.51
Consensus pattern (67 bp):
TTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTAAATAATTGATGAGGAAATAAGAATTAT
TT
Found at i:1730228 original size:20 final size:20
Alignment explanation
Indices: 1730203--1730279 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
1730193 GTTGAAACTA
*
1730203 CAAATTTGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
**
1730223 CAAATTCGCATTGC-AATAGT
1 CAAATTCGCAACGCGAA-AGT
* **
1730243 CAAATTCGTAACATGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
1730263 CAAATTCGCAATGCGAA
1 CAAATTCGCAACGCGAA
1730280 TTTGACTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 2 0.05
20 39 0.91
21 2 0.05
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1730555 original size:18 final size:18
Alignment explanation
Indices: 1730532--1730567 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1730522 AAGCCGGTTG
*
1730532 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1730550 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1730568 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1734907 original size:31 final size:31
Alignment explanation
Indices: 1734850--1734910 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1734840 TGTCAAGTCC
*
1734850 AGTAAGGCCCTGAGCACACATCTGAGGAGCT
1 AGTAAGGCCCTGAGCACAAATCTGAGGAGCT
*
1734881 AGTAAGGTCCTGAGCACAAAGT-TGAGGAGC
1 AGTAAGGCCCTGAGCACAAA-TCTGAGGAGC
1734911 CTCCAGGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.16
Consensus pattern (31 bp):
AGTAAGGCCCTGAGCACAAATCTGAGGAGCT
Found at i:1735953 original size:29 final size:29
Alignment explanation
Indices: 1735880--1735953 Score: 116
Period size: 28 Copynumber: 2.6 Consensus size: 29
1735870 TAGAAATTAG
1735880 TTACAAAACTAACACCCTTTTAACAATAT
1 TTACAAAACTAACACCCTTTTAACAATAT
1735909 TT-CAAAACTAACACCCTTTATAA-AATAT
1 TTACAAAACTAACACCCTTT-TAACAATAT
*
1735937 TTACAAAACTTACACCC
1 TTACAAAACTAACACCC
1735954 GGTCAGCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 24 0.57
29 18 0.43
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (29 bp):
TTACAAAACTAACACCCTTTTAACAATAT
Found at i:1735979 original size:13 final size:13
Alignment explanation
Indices: 1735961--1735994 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1735951 CCCGGTCAGC
1735961 GGTCAACG-GTTCG
1 GGTCAACGAGTT-G
1735974 GGTCAACGAGTTG
1 GGTCAACGAGTTG
1735987 GGTCAACG
1 GGTCAACG
1735995 CGCAGTAGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (13 bp):
GGTCAACGAGTTG
Found at i:1736743 original size:21 final size:18
Alignment explanation
Indices: 1736713--1736756 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
1736703 TGAAGATGAT
1736713 GATGACGAAGAATACGACAAC
1 GATGACGAAG-AT--GACAAC
*
1736734 GATGAGGAAGATGACAAC
1 GATGACGAAGATGACAAC
1736752 GATGA
1 GATGA
1736757 AGATGGTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
20 2 0.09
21 9 0.41
ACGTcount: A:0.45, C:0.14, G:0.30, T:0.11
Consensus pattern (18 bp):
GATGACGAAGATGACAAC
Found at i:1738221 original size:24 final size:23
Alignment explanation
Indices: 1738193--1738239 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1738183 TGGATATCTT
* *
1738193 ATTTTCTTTATTCTTTTCTTCAAA
1 ATTTTCCTTATTATTTT-TTCAAA
1738217 ATTTTCCTTATTATTTTTTCAAA
1 ATTTTCCTTATTATTTTTTCAAA
1738240 TGTTATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTCCTTATTATTTTTTCAAA
Found at i:1738466 original size:29 final size:29
Alignment explanation
Indices: 1738433--1738489 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1738423 TTAAACCACC
*
1738433 CTTTTAACAATATTTACAAAACTAACACA
1 CTTTTAAAAATATTTACAAAACTAACACA
1738462 CTTTTAAAAATATTTACAAAACTAACAC
1 CTTTTAAAAATATTTACAAAACTAACAC
1738490 CTGGTCAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (29 bp):
CTTTTAAAAATATTTACAAAACTAACACA
Found at i:1738504 original size:7 final size:7
Alignment explanation
Indices: 1738492--1738527 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1738482 ACTAACACCT
1738492 GGTCAAC
1 GGTCAAC
1738499 GGTCAAC
1 GGTCAAC
*
1738506 GGTTAAC
1 GGTCAAC
1738513 GGT-AAC
1 GGTCAAC
1738519 GGTCAAC
1 GGTCAAC
1738526 GG
1 GG
1738528 GTCGGGTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.28, C:0.22, G:0.33, T:0.17
Consensus pattern (7 bp):
GGTCAAC
Found at i:1738521 original size:13 final size:14
Alignment explanation
Indices: 1738492--1738527 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1738482 ACTAACACCT
1738492 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
*
1738506 GGTTAACGGT-AAC
1 GGTCAACGGTCAAC
1738519 GGTCAACGG
1 GGTCAACGG
1738528 GTCGGGTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.28, C:0.22, G:0.33, T:0.17
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:1739469 original size:14 final size:15
Alignment explanation
Indices: 1739450--1739486 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
1739440 CCTTATTGCA
1739450 TTTGCATCTCCCA-T
1 TTTGCATCTCCCATT
1739464 TTTGCA-CTCCCATT
1 TTTGCATCTCCCATT
1739478 TTTGCATCT
1 TTTGCATCT
1739487 TTTCATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 13 0.62
15 2 0.10
ACGTcount: A:0.14, C:0.32, G:0.08, T:0.46
Consensus pattern (15 bp):
TTTGCATCTCCCATT
Found at i:1739531 original size:2 final size:2
Alignment explanation
Indices: 1739524--1739558 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1739514 TTTGCATTAG
1739524 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 T
1739559 GTACATTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1740892 original size:11 final size:10
Alignment explanation
Indices: 1740878--1740940 Score: 54
Period size: 10 Copynumber: 5.9 Consensus size: 10
1740868 AAAAATACAT
*
1740878 AAAAAGATAA
1 AAAAAGAAAA
* *
1740888 AAAAACAACA
1 AAAAAGAAAA
1740898 AAAAAGAAAA
1 AAAAAGAAAA
1740908 AAAAGAGGAAAA
1 AAAA-A-GAAAA
*
1740920 AAAGAGAAAA
1 AAAAAGAAAA
1740930 AGGAAAAGAAA
1 A--AAAAGAAA
1740941 GAAAGAAAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 25 0.60
11 2 0.05
12 15 0.36
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:1740909 original size:9 final size:9
Alignment explanation
Indices: 1740878--1740949 Score: 63
Period size: 9 Copynumber: 7.4 Consensus size: 9
1740868 AAAAATACAT
1740878 AAAAAGATAA
1 AAAAAGA-AA
*
1740888 AAAAACAACA
1 AAAAAGAA-A
1740898 AAAAAGAAA
1 AAAAAGAAA
1740907 AAAAAGAGGAA
1 AAAAAGA--AA
*
1740918 AAAAAGAGA
1 AAAAAGAAA
*
1740927 AAAAGGAAA
1 AAAAAGAAA
*
1740936 AGAAAGAAA
1 AAAAAGAAA
1740945 GAAAA
1 -AAAA
1740950 CATATCCAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
9 24 0.48
10 17 0.34
11 9 0.18
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:1740947 original size:20 final size:20
Alignment explanation
Indices: 1740897--1740949 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1740887 AAAAAACAAC
*
1740897 AAAAAAGAAAAAAAAGAGGA
1 AAAAAAGAAAGAAAAGAGGA
1740917 AAAAAAG--AGAAAA-AGGA
1 AAAAAAGAAAGAAAAGAGGA
1740934 AAAGAAAGAAAGAAAA
1 AAA-AAAGAAAGAAAA
1740950 CATATCCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 7 0.24
18 9 0.31
20 13 0.45
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAGAAAAGAGGA
Found at i:1744329 original size:91 final size:92
Alignment explanation
Indices: 1744174--1744717 Score: 689
Period size: 91 Copynumber: 6.0 Consensus size: 92
1744164 AAGATAACCA
* * * * *** *
1744174 ATCAACATTTCTAGCG-GGGAGTTTATAATGAAAAGAACTCATTTGACGAGGTAGAAGAAGTTCA
1 ATCAACATTTCCAGCGAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
1744238 TAATGAGAAGAACTTGTTCAACCTTGC
66 TAATGAGAAGAACTTGTTCAACCTTGC
* * * *
1744265 ATCAACATTTCCAGCGAG-GAGTTCATAATAAGAAGAACTCATCCGAA-TAGAGAGAACAAGTTC
1 ATCAACATTTCCAGCGAGAGAGTTCATAATGAGAAGAACTCATCC-AACGAGGGAGAAGAAGTTC
*
1744328 ATAATGAGAAGAACTTGTTCATCCTTG-
65 ATAATGAGAAGAACTTGTTCAACCTTGC
* * *
1744355 ATTCAACATTTCC-G-GTAGAGAGTTCATAATGAGAAGAACCCATCCAACAAGGGAGATGAAGTT
1 A-TCAACATTTCCAGCG-AGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTT
*
1744418 AATAATGAGAAGAACTTGTTCAACCTTAGC
64 CATAATGAGAAGAACTTGTTCAACCTT-GC
* * *
1744448 -TCAACATTTCCAGTG-GAGGGTTCATAATGAGAAGAATTCATCCAACGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGCGAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
1744511 TAATGAGAAGAACTTGTTCAACCTTG-
66 TAATGAGAAGAACTTGTTCAACCTTGC
* *** * *
1744537 ATTCAAAATTTATGGTG-GAGAGTTCATAATGAGAAGAATTCATCCAACGAGGGAGAAGAAGTTC
1 A-TCAACATTTCCAGCGAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTC
1744601 ATAATGAGAAGAACTTGTTCAACCTTGGC
65 ATAATGAGAAGAACTTGTTCAACCTT-GC
*
1744630 -TCAATATTTCCAGCG-GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAGCGAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
* *
1744693 TAATGAGAAGAATTTGTTTAACCTT
66 TAATGAGAAGAACTTGTTCAACCTT
1744718 AGCTGGATTC
Statistics
Matches: 400, Mismatches: 39, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
89 1 0.00
90 7 0.02
91 386 0.96
92 5 0.01
93 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (92 bp):
ATCAACATTTCCAGCGAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTGC
Found at i:1744870 original size:90 final size:92
Alignment explanation
Indices: 1744746--1744924 Score: 299
Period size: 91 Copynumber: 2.0 Consensus size: 92
1744736 AATAAATCGA
1744746 TCAACATTTCCAGTGCAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAA-GAAGTTCAT
1 TCAACATTTCCAGTGCAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAATGAAGTTCAT
*
1744810 AATGAGAAGAACTTGTTCAACCTTGGC
66 AATGAGAAGAACTTGTACAACCTTGGC
* * * *
1744837 TCAACATTTCCAGTG-TGAGTTCATAATGAGAAGAACTCGTCCGATGAGGGAGAATGAAGTTCGT
1 TCAACATTTCCAGTGCAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAATGAAGTTCAT
1744901 AATGAGAAGAACTTGTACAACCTT
66 AATGAGAAGAACTTGTACAACCTT
1744925 AGTTAGATTC
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 36 0.44
91 46 0.56
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (92 bp):
TCAACATTTCCAGTGCAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAATGAAGTTCAT
AATGAGAAGAACTTGTACAACCTTGGC
Found at i:1744910 original size:207 final size:207
Alignment explanation
Indices: 1744555--1745042 Score: 780
Period size: 207 Copynumber: 2.4 Consensus size: 207
1744545 TTTATGGTGG
*
1744555 AGAGTTCATAATGAGAAGAATTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1744620 CAACCTTGGCTCAATATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAA
66 CAACCTTGGCTCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAA
* ** *
1744685 GAAGTTCATAATGAGAAGAATTTGTTTAACCTTAGCTGGATTCCATCACAGAATAAATCGATCAA
131 GAAGTTCATAATGAGAAGAACTTGTACAACCTTAGCTAGATTCCATCACAGAATAAATCGATCAA
1744750 CATTTCCAGTGC
196 CATTTCCAGTGC
*
1744762 AGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
1744827 CAACCTTGGCTCAACATTTCCAG-TGTGAGTTCATAATGAGAAGAACTCGTCCGATGAGGGAGAA
66 CAACCTTGGCTCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAA
* * * *
1744891 TGAAGTTCGTAATGAGAAGAACTTGTACAACCTTAGTTAGATTCCATCATAGAATAAATCGATTA
131 -GAAGTTCATAATGAGAAGAACTTGTACAACCTTAGCTAGATTCCATCACAGAATAAATCGATCA
*
1744956 ACATTTCCAGTGG
195 ACATTTCCAGTGC
* * *
1744969 AGAGTTAATAATGAGAAGAACTTATCTAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1745034 CAACCTTGG
66 CAACCTTGG
1745043 TGATTCCATC
Statistics
Matches: 259, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
206 36 0.14
207 223 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (207 bp):
AGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTGGCTCAACATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAA
GAAGTTCATAATGAGAAGAACTTGTACAACCTTAGCTAGATTCCATCACAGAATAAATCGATCAA
CATTTCCAGTGC
Found at i:1746606 original size:22 final size:22
Alignment explanation
Indices: 1746562--1746607 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1746552 AATTAGATCC
* *
1746562 TTATTTTATGTTTATTTCATTT
1 TTATTCTATGTTTATTACATTT
1746584 TTATTCTATGTTT-TTACAGTTT
1 TTATTCTATGTTTATTACA-TTT
1746606 TT
1 TT
1746608 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (22 bp):
TTATTCTATGTTTATTACATTT
Found at i:1748537 original size:2 final size:2
Alignment explanation
Indices: 1748530--1748562 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1748520 ATAAAAACAT
1748530 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
1748563 TTCTTTTCTC
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:1749663 original size:17 final size:17
Alignment explanation
Indices: 1749633--1749676 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1749623 TTTTAATAAA
*
1749633 AAAACTC-AAAACTTTG
1 AAAACTCTAATACTTTG
1749649 AAAACTCTAATACTTTG
1 AAAACTCTAATACTTTG
1749666 AAAACTCTAAT
1 AAAACTCTAAT
1749677 TCCAAATCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (17 bp):
AAAACTCTAATACTTTG
Found at i:1755693 original size:35 final size:36
Alignment explanation
Indices: 1755644--1755716 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 36
1755634 ATAAGTTATT
* **
1755644 CAAGGAGTATCGATACC-TAAAGGGTAGTATCGATAC
1 CAAGGAGTACCGATACCAT-AAGGCAAGTATCGATAC
1755680 CAAGG-GTACCGATACCATAAGGCAAGTATCGATAC
1 CAAGGAGTACCGATACCATAAGGCAAGTATCGATAC
1755715 CA
1 CA
1755717 TTTTGAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 27 0.82
36 6 0.18
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (36 bp):
CAAGGAGTACCGATACCATAAGGCAAGTATCGATAC
Found at i:1755717 original size:20 final size:17
Alignment explanation
Indices: 1755645--1755715 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 17
1755635 TAAGTTATTC
1755645 AAGGAGTATCGATACCT
1 AAGGAGTATCGATACCT
1755662 AAAGGGTAGTATCGATACC-
1 -AA-GG-AGTATCGATACCT
*
1755681 AAGG-GTACCGATACCAT
1 AAGGAGTATCGATACC-T
1755698 AAGGCAAGTATCGATACC
1 AAGG--AGTATCGATACC
1755716 ATTTTGAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
15 10 0.23
17 6 0.14
18 4 0.09
19 2 0.05
20 22 0.50
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (17 bp):
AAGGAGTATCGATACCT
Found at i:1756578 original size:21 final size:21
Alignment explanation
Indices: 1756549--1756609 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1756539 TCGAGGGTTC
* *
1756549 TATGGGGTCTTTCGGGACATA
1 TATGAGGTCCTTCGGGACATA
* * *
1756570 TATGTGGTCCTTCGAGACATC
1 TATGAGGTCCTTCGGGACATA
*
1756591 TACGAGGTCCTTCGGGACA
1 TATGAGGTCCTTCGGGACA
1756610 ATTTTATATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TATGAGGTCCTTCGGGACATA
Found at i:1757337 original size:16 final size:17
Alignment explanation
Indices: 1757303--1757337 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1757293 ATTTAAATTT
*
1757303 GTAACTATTTTGTAAAA
1 GTAAATATTTTGTAAAA
1757320 GTAAATATTTTG-AAAA
1 GTAAATATTTTGTAAAA
1757336 GT
1 GT
1757338 CAATGTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (17 bp):
GTAAATATTTTGTAAAA
Found at i:1759972 original size:16 final size:17
Alignment explanation
Indices: 1759941--1759975 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1759931 CCATTGACTA
1759941 AAAAGTCAAAATTTTTG
1 AAAAGTCAAAATTTTTG
* *
1759958 AAAAGTCATATTTTTTG
1 AAAAGTCAAAATTTTTG
1759975 A
1 A
1759976 CTTCTTGAGT
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:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (17 bp):
AAAAGTCAAAATTTTTG
Found at i:1765143 original size:60 final size:59
Alignment explanation
Indices: 1765028--1765154 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 59
1765018 CATGAGATCG
* * *
1765028 TTTTGTAACTTCTAATAGTCGATGAACTCAACAAAACAACACCCTATAGTTGAGGAACCA
1 TTTTGTAACTTCTAATAGTCGATGAACTAAACAAAACAACAACATATAGTTGAGG-ACCA
* *
1765088 TTTTGTAACTTGC-AATAGTCG--GAGACTAAATAAAATAACAACATATAGTTAGAGGACCA
1 TTTTGTAACTT-CTAATAGTCGATGA-ACTAAACAAAACAACAACATATAGTT-GAGGACCA
1765147 TTTATGTA
1 TTT-TGTA
1765155 TTTTACCCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
58 2 0.03
59 28 0.48
60 27 0.47
61 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (59 bp):
TTTTGTAACTTCTAATAGTCGATGAACTAAACAAAACAACAACATATAGTTGAGGACCA
Found at i:1765490 original size:27 final size:27
Alignment explanation
Indices: 1765443--1765496 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1765433 TTTAAGTATT
* *
1765443 TATTTTGATACAAGAAAATACTTTATA
1 TATTTGGATACAAAAAAATACTTTATA
1765470 TATTTGGATA-AAAAAATATACTTTATA
1 TATTTGGATACAAAAAA-ATACTTTATA
1765497 ATATAAACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (27 bp):
TATTTGGATACAAAAAAATACTTTATA
Found at i:1766968 original size:35 final size:37
Alignment explanation
Indices: 1766915--1767150 Score: 239
Period size: 37 Copynumber: 6.3 Consensus size: 37
1766905 TTGCAAATGG
* ***
1766915 TTTTTGAAAATATGTATATAATATATAGTTTTT-AATTT
1 TTTTTGAAAA-CT-TATATAATATATAGTTTTTAAAACA
* *
1766953 TTTTTTAAAAC-TATATAATATATTGTTTTTAAAACA
1 TTTTTGAAAACTTATATAATATATAGTTTTTAAAACA
*
1766989 TTTTAGAAAA-TATATATAATATATAGTTTTTAAAATCA
1 TTTTTGAAAACT-TATATAATATATAGTTTTTAAAA-CA
1767027 -TTTTGAAAACTTATATAATATATA-TTTTTGAAAACA
1 TTTTTGAAAACTTATATAATATATAGTTTTT-AAAACA
**
1767063 TTTTTGAAAACTTATATAATATATAGTTTGAAAAACA
1 TTTTTGAAAACTTATATAATATATAGTTTTTAAAACA
* **
1767100 TTTTTTGAAAAAATTATATAATATATAGGTTTAAAAAAACA
1 -TTTTTG-AAAACTTATATAATATATA-GTTT-TTAAAACA
*
1767141 TTTTTAAAAA
1 TTTTTGAAAA
1767151 AAACTTATAT
Statistics
Matches: 171, Mismatches: 15, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
35 18 0.11
36 17 0.10
37 77 0.45
38 21 0.12
39 22 0.13
40 9 0.05
41 7 0.04
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAACTTATATAATATATAGTTTTTAAAACA
Found at i:1769059 original size:17 final size:18
Alignment explanation
Indices: 1769019--1769060 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1769009 AAAAACTAAT
*
1769019 TTATGTAAAATCAAATTA
1 TTATTTAAAATCAAATTA
**
1769037 AGATTTAAAAT-AAATTA
1 TTATTTAAAATCAAATTA
1769054 TTATTTA
1 TTATTTA
1769061 TTATATATAT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
TTATTTAAAATCAAATTA
Found at i:1770332 original size:113 final size:113
Alignment explanation
Indices: 1770134--1770612 Score: 450
Period size: 113 Copynumber: 4.1 Consensus size: 113
1770124 GCAATGTTGG
* * * * *
1770134 TTCTCATTATGAACTCTGC-CTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTG
1 TTCTCATTATGAACTC-GCTCTGGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTG
*
1770198 AACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATAAGTTC
65 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTC
** *
1770247 TTCTCATTATGAACTTTCTCTTGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGA
1 TTCTCATTATGAACTCGCTCTGGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGA
** *
1770312 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
66 ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTC
** * ***
1770360 TTCTCATTATGAACTCGAACTGGAAATGTTAATGCTGATCTATCTTTTTCTGTGATAGAA-TCAA
1 TTCTCATTATGAACTCGCTCTGGAAATG---A---TGATCCATC-----GAATGAT-GAATTCAA
* ** * *
1770424 GCAAAAAGGTTGAACAAGCTCTTCTCATT-TGAACTTCTTCTTCC-TC-AGATGATAACTTA
54 ACAAAAA-GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATAAGTTC
* * * * * *
1770483 TTCTCATTATGAAC-C-TTCTGGCAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTGA
1 TTCTCATTATGAACTCGCTCTGGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGA
* * *
1770546 ACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTGTTC
66 ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A--AGTTC
*
1770597 TTCTTATTATGAACTC
1 TTCTCATTATGAACTC
1770613 TAACTGAAAA
Statistics
Matches: 296, Mismatches: 47, Indels: 44
0.76 0.12 0.11
Matches are distributed among these distances:
109 23 0.08
110 28 0.09
111 4 0.01
112 3 0.01
113 122 0.41
114 15 0.05
115 9 0.03
116 1 0.00
119 8 0.03
121 8 0.03
122 2 0.01
123 22 0.07
124 29 0.10
125 22 0.07
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTCATTATGAACTCGCTCTGGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGA
ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTC
Found at i:1770547 original size:234 final size:239
Alignment explanation
Indices: 1770189--1770626 Score: 654
Period size: 234 Copynumber: 1.8 Consensus size: 239
1770179 GAATTTAAAC
* * * *
1770189 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
1 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTACAGATAACTTATTCTCAT
* *
1770254 TATGAACTTTCTCTTGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATT
66 TATGAACTCTCTCTGGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATT
* *
1770319 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-GTTCTTCTCATTATGAACTCGAACTGG
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGATGTTCTTCTCATTATGAACTCGAACTGA
1770383 AAATGTTAATGCTGATCTATCTTTTTCTGTGATAGAATCAAGCA
196 AAATGTTAATGCTGATCTATCTTTTTCTGTGATAGAATCAAGCA
*
1770427 AAAAGGTTGAACAAGCTCTTCTCATT-TGAACTTCTTCTTCC-TC-AGATGATAACTTATTCTCA
1 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTACA-GATAACTTATTCTCA
* * * * * *
1770489 TTATGAAC-CT-TCTGGCAATGCTGATCCATCGAATGATGAATTCGAGCAAAAGGTTGAACAAGT
65 TTATGAACTCTCTCTGGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAAT
* *
1770552 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTGTTCTTCTTATTATGAACTCTAAC
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGA--TGTTCTTCTCATTATGAACTCGAAC
1770617 TGAAAATGTT
193 TGAAAATGTT
1770627 GATCCATTAA
Statistics
Matches: 179, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
234 83 0.46
235 2 0.01
236 23 0.13
237 45 0.25
238 26 0.15
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (239 bp):
AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTACAGATAACTTATTCTCAT
TATGAACTCTCTCTGGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGATGTTCTTCTCATTATGAACTCGAACTGA
AAATGTTAATGCTGATCTATCTTTTTCTGTGATAGAATCAAGCA
Found at i:1772140 original size:10 final size:10
Alignment explanation
Indices: 1772125--1772192 Score: 63
Period size: 10 Copynumber: 7.0 Consensus size: 10
1772115 ATCTTGACCC
1772125 CTTTTTTTCT
1 CTTTTTTTCT
*
1772135 CTTTTTTTTT
1 CTTTTTTTCT
1772145 CTTCTTTTT-T
1 CTT-TTTTTCT
*
1772155 C-TTCTTTCT
1 CTTTTTTTCT
1772164 -TCTTTTTTCT
1 CT-TTTTTTCT
1772174 CTTTTTTT-T
1 CTTTTTTTCT
*
1772183 CTTTTCTTCT
1 CTTTTTTTCT
1772193 TTTCATTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
8 4 0.08
9 10 0.21
10 28 0.58
11 6 0.12
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
CTTTTTTTCT
Found at i:1772164 original size:17 final size:16
Alignment explanation
Indices: 1772128--1772207 Score: 78
Period size: 16 Copynumber: 5.0 Consensus size: 16
1772118 TTGACCCCTT
1772128 TTTTTCTCTTTTT-TT-
1 TTTTTCT-TTTTTCTTC
*
1772143 TTCTTCTTTTTTCTTC
1 TTTTTCTTTTTTCTTC
1772159 TTTCTTCTTTTTTC-TC
1 TTT-TTCTTTTTTCTTC
*
1772175 TTTTTTTTCTTTTCTTC
1 TTTTTCTT-TTTTCTTC
1772192 -TTTTCATTTTTTCTTC
1 TTTTTC-TTTTTTCTTC
1772208 AAGCATAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
14 5 0.09
15 12 0.22
16 24 0.44
17 14 0.25
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTTTCTTC
Found at i:1772170 original size:39 final size:42
Alignment explanation
Indices: 1772127--1772207 Score: 123
Period size: 39 Copynumber: 2.0 Consensus size: 42
1772117 CTTGACCCCT
1772127 TTTTTTCTCTTTTTTTT-TCTTCTT-TTTTC-TTCTTTCTTC
1 TTTTTTCTCTTTTTTTTCTCTTCTTCTTTTCATTCTTTCTTC
* *
1772166 TTTTTTCTCTTTTTTTTCTTTTCTTCTTTTCATTTTTTCTTC
1 TTTTTTCTCTTTTTTTTCTCTTCTTCTTTTCATTCTTTCTTC
1772208 AAGCATAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 17 0.46
40 6 0.16
41 5 0.14
42 9 0.24
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (42 bp):
TTTTTTCTCTTTTTTTTCTCTTCTTCTTTTCATTCTTTCTTC
Found at i:1772176 original size:26 final size:27
Alignment explanation
Indices: 1772126--1772195 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 27
1772116 TCTTGACCCC
* *
1772126 TTTTT-TTCTCTTTTTTTTTCTTCTTT
1 TTTTTCTTTTCTTCTTTTTTCTTCTTT
1772152 TTTCTTC-TTTCTTCTTTTTTC-TCTTT
1 TTT-TTCTTTTCTTCTTTTTTCTTCTTT
1772178 TTTTTCTTTTCTTCTTTT
1 TTTTTCTTTTCTTCTTTT
1772196 CATTTTTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 3 0.08
26 22 0.56
27 14 0.36
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTTCTTTTCTTCTTTTTTCTTCTTT
Found at i:1783666 original size:17 final size:18
Alignment explanation
Indices: 1783626--1783667 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1783616 AAAAAATAAT
*
1783626 TTATATAAAATCAAATTA
1 TTATTTAAAATCAAATTA
**
1783644 AGATTTAAAAT-AAATTA
1 TTATTTAAAATCAAATTA
1783661 TTATTTA
1 TTATTTA
1783668 TTATATATAT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TTATTTAAAATCAAATTA
Found at i:1785033 original size:3 final size:3
Alignment explanation
Indices: 1785027--1785084 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
1785017 TAATATTTAT
*
1785027 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1785074 T-A TAAA TAA TA
1 TAA T-AA TAA TA
1785085 TTTAAATGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 4 0.08
3 44 0.88
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1785085 original size:9 final size:10
Alignment explanation
Indices: 1785014--1785085 Score: 77
Period size: 9 Copynumber: 7.9 Consensus size: 10
1785004 TTTGGGCCTG
*
1785014 TAATAATATT
1 TAATAATATA
*
1785024 TATTAATA-A
1 TAATAATATA
1785033 TAA-AATA-A
1 TAATAATATA
1785041 TAATAATA-A
1 TAATAATATA
1785050 TAATAAT-TA
1 TAATAATATA
1785059 TAATAATA-A
1 TAATAATATA
1785068 TAATAATATA
1 TAATAATATA
1785078 -AATAATAT
1 TAATAATAT
1785086 TTAAATGAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
8 8 0.15
9 39 0.71
10 8 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAATAATATA
Found at i:1785272 original size:2 final size:2
Alignment explanation
Indices: 1785267--1785298 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1785257 AATGCTTTGC
*
1785267 AT AT AT AT AT GT 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
1785299 TATTCTTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1785335 original size:13 final size:14
Alignment explanation
Indices: 1785313--1785415 Score: 50
Period size: 14 Copynumber: 7.3 Consensus size: 14
1785303 CTTACTCTTA
1785313 TTTTATTTTTATTT
1 TTTTATTTTTATTT
1785327 TTTTATTTTATTATTGT
1 TTTTA-TTT-TTATT-T
*
1785344 TTTTGGTTTTTATTT
1 TTTT-ATTTTTATTT
* * * *
1785359 CTTTGTTCTT-TTA
1 TTTTATTTTTATTT
* * *
1785372 ATTCATTTTTATAT
1 TTTTATTTTTATTT
* * *
1785386 TATTA-TTATA-TC
1 TTTTATTTTTATTT
1785398 TTTTATTTTTATTT
1 TTTTATTTTTATTT
1785412 TTTT
1 TTTT
1785416 TGCAATTAAA
Statistics
Matches: 63, Mismatches: 19, Indels: 14
0.66 0.20 0.15
Matches are distributed among these distances:
12 4 0.06
13 16 0.25
14 18 0.29
15 7 0.11
16 10 0.16
17 8 0.13
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:1788875 original size:95 final size:96
Alignment explanation
Indices: 1788768--1788954 Score: 281
Period size: 95 Copynumber: 2.0 Consensus size: 96
1788758 AGATTATAAT
1788768 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTA-AAGCAATTGGTTAAACGCCCCGGCTTT
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAA-CAATTGGTTAAACGCCCCGGCTTT
1788832 ATGAATAAGA-TCAAGCTAGCCTGATAAAGGTG
65 ATGAATAAGATTC-AGCTAGCCTGATAAAGGTG
* * *
1788864 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAACCATTGGTTAAACGCCTCGGCTTTT
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAACAATTGGTTAAACGCCCCGGCTTTA
* * *
1788928 TGGATAATATTCAGCTTGCCTGATAAA
66 TGAATAAGATTCAGCTAGCCTGATAAA
1788955 ATATCTATAC
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
95 73 0.88
96 10 0.12
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (96 bp):
ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAACAATTGGTTAAACGCCCCGGCTTTA
TGAATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:1790258 original size:84 final size:84
Alignment explanation
Indices: 1790112--1790832 Score: 775
Period size: 84 Copynumber: 8.7 Consensus size: 84
1790102 CTATCGGCAA
* * * * *
1790112 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
1790177 CAAGGCATATCATTTGCAG
66 CAAGGCACATCATTTGCAG
* * * * * * *
1790196 TATAGCTCAAGGCTTGAAGGGCTATCTGCCACCAAAATACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1790261 CAAGGCACATCATTTGCAG
66 CAAGGCACATCATTTGCAG
** * * *
1790280 CATAACTCAAGGCTAGAAGGTTTATCTGCCAACAAAAGACCTTCAAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
1790345 CAAGGCACATCATTTGTAA
66 CAAGGCACATCATTTGCAG
* * * * *
1790364 CATAGCTCAAGGCAAGAAGGGCTATTTACCAACAAAAGACCTTTGAGTTCGATTACACTCAGCT-
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
1790428 TAACGGCACATCATTTGTAG
66 CAA-GGCACATCATTTGCAG
* * *
1790448 TATAACTCAAGGCTAGAAGGGCTATCT----ATAAAAGACCCTCGAGTTCGATTACACTCAGCTT
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC-T
* * * * *
1790509 CGAGGGAACATCATTTACAA
65 CCAAGGCACATCATTTGCAG
* * * * *
1790529 CATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTTGAGTTTGATTACACTTAGCT-
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1790592 CAACGGCACATCATTTGCAG
66 CAA-GGCACATCATTTGCAG
* * ** * *
1790612 TATAGCTCAAGGCTAGAACAAG-TATCTG-C--C-AAAGACCTTCAAGTTCGATTACACTCAACT
1 CATAACTCAAGGCTAGAA-GGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC-
* * *
1790672 TCGAGGGCACATCATTTACAG
64 TCCAAGGCACATCATTTGCAG
** * *
1790693 CATAACTCAAGGCTAGAAGGATTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTAAGCTC
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
1790757 AAAGGCACATCATTTGCAG
66 CAAGGCACATCATTTGCAG
* * * * *
1790776 CATAGCTTAAAGCGAGAAGGGCTATCTGCCAACAAAATACCTTCGAGTTCGATTACA
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACA
1790833 TTTAGCCTAA
Statistics
Matches: 534, Mismatches: 87, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
80 54 0.10
81 76 0.14
82 5 0.01
83 82 0.15
84 316 0.59
85 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (84 bp):
CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
CAAGGCACATCATTTGCAG
Found at i:1790414 original size:168 final size:168
Alignment explanation
Indices: 1790112--1790832 Score: 782
Period size: 164 Copynumber: 4.3 Consensus size: 168
1790102 CTATCGGCAA
* * * *
1790112 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGC-T
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTT
* * ** * * * *
1790176 CCAAGGCATATCATTTGCAGTATAGCTCAAGGCTTGAAGGGCTATCTGCCACCAAAATACCTTCG
66 CCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGCTATCTGCCAAC-AAAGACCTTCG
* *
1790241 AGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAG
130 AGTTCGATTACACTCAGCT-CAACGGCACATCATTTGCAG
** * *
1790280 CATAACTCAAGGCTAGAAGGTTTATCTGCCAACAAAAGACCTTCAAGTTCGACTACGCTCAGC-T
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTT
** * * * * *
1790344 CCAAGGCACATCATTTGTAACATAGCTCAAGGCAAGAAGGGCTATTTACCAACAAAAGACCTTTG
66 CCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGCTATCTGCCAAC-AAAGACCTTCG
* *
1790409 AGTTCGATTACACTCAGCTTAACGGCACATCATTTGTAG
130 AGTTCGATTACACTCAGCTCAACGGCACATCATTTGCAG
* * * *
1790448 TATAACTCAAGGCTAGAAGGGCTATCT----ATAAAAGACCCTCGAGTTCGATTACACTCAGCTT
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTT
* * * * * *
1790509 CGAGGGAACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTTGA
66 CCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAGACCTTCGA
* *
1790574 GTTTGATTACACTTAGCTCAACGGCACATCATTTGCAG
131 GTTCGATTACACTCAGCTCAACGGCACATCATTTGCAG
* * ** * * *
1790612 TATAGCTCAAGGCTAGAACAAG-TATCTG-C--C-AAAGACCTTCAAGTTCGATTACACTCAACT
1 CATAACTCAAGGCTAGAA-GGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCT
* * * ** *
1790672 TCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGATTATCTGTCAACAAAGACCTTCG
65 TCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAGACCTTCG
* *
1790737 AGTTCGATTACACTAAGCTCAAAGGCACATCATTTGCAG
130 AGTTCGATTACACTCAGCTCAACGGCACATCATTTGCAG
* * * * * *
1790776 CATAGCTTAAAGCGAGAAGGGCTATCTGCCAACAAAATACCTTCGAGTTCGATTACA
1 CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACA
1790833 TTTAGCCTAA
Statistics
Matches: 479, Mismatches: 64, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
163 1 0.00
164 239 0.50
165 45 0.09
167 3 0.01
168 191 0.40
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (168 bp):
CATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTT
CCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGCTATCTGCCAACAAAGACCTTCGA
GTTCGATTACACTCAGCTCAACGGCACATCATTTGCAG
Found at i:1791614 original size:37 final size:35
Alignment explanation
Indices: 1791510--1791736 Score: 258
Period size: 37 Copynumber: 6.1 Consensus size: 35
1791500 TTTTTAAAAA
1791510 AAAAACATTTTGAAAATATATATAATATATAGCTTTT
1 AAAAACATTTTGAAAAT-TATATAATATATAG-TTTT
*
1791547 -AAAACATTTTTGAAAACTATATAATATATAGTTTT
1 AAAAACA-TTTTGAAAATTATATAATATATAGTTTT
*
1791582 CAAAACATTTTAGAAAATATATATAATATATAGTTTTT
1 AAAAACATTTT-GAAAAT-TATATAATATATAG-TTTT
*
1791620 AAAATCATTTTGAAAACTTATATAATATATAGTTTT
1 AAAAACATTTTGAAAA-TTATATAATATATAGTTTT
* *** *
1791656 GAACATTTTTTTGAAAACTTATATAACATATAGTTTT
1 -AAAAACATTTTGAAAA-TTATATAATATATAGTTTT
1791693 AAAAACATTTTTTGAGAAAATTATATAATATATAGTTTT
1 AAAAACA--TTTT--GAAAATTATATAATATATAGTTTT
1791732 AAAAA
1 AAAAA
1791737 AACATTTTTT
Statistics
Matches: 166, Mismatches: 13, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
35 8 0.05
36 38 0.23
37 74 0.45
38 18 0.11
39 23 0.14
40 5 0.03
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (35 bp):
AAAAACATTTTGAAAATTATATAATATATAGTTTT
Found at i:1791672 original size:74 final size:73
Alignment explanation
Indices: 1791511--1791745 Score: 289
Period size: 74 Copynumber: 3.2 Consensus size: 73
1791501 TTTTAAAAAA
1791511 AAAACA-TTTTGAAAATATATATAATATATAGCTTTTAAAACATTTTTGAAAAC-TATATAATAT
1 AAAACATTTTTGAAAATATATATAATATATAG-TTTTAAAACATTTTTGAAAACTTATATAATAT
1791574 ATAGTTTTC
65 ATAGTTTTC
*
1791583 AAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCA-TTTTGAAAACTTATATAATA
1 AAAACATTTTTGAAAATATATATAATATATAG-TTTTAAAA-CATTTTTGAAAACTTATATAATA
*
1791647 TATAGTTTTG
64 TATAGTTTTC
* ** * *
1791657 AACATTTTTTTGAAAACT-TATATAACATATAGTTTTAAAAACATTTTTTGAGAAAATTATATAA
1 AAAACATTTTTGAAAA-TATATATAATATATAGTTTT-AAAACA-TTTTTGA-AAACTTATATAA
*
1791721 TATATAGTTTTAAA
62 TATATAGTTTT--C
1791735 AAAACATTTTT
1 AAAACATTTTT
1791746 TTTTGAAAAT
Statistics
Matches: 140, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
72 6 0.04
73 48 0.34
74 49 0.35
75 7 0.05
76 22 0.16
78 8 0.06
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (73 bp):
AAAACATTTTTGAAAATATATATAATATATAGTTTTAAAACATTTTTGAAAACTTATATAATATA
TAGTTTTC
Found at i:1791898 original size:14 final size:14
Alignment explanation
Indices: 1791865--1791891 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1791855 TTAAATAGAT
1791865 TATATTATTATTAG
1 TATATTATTATTAG
1791879 TATATTATTATTA
1 TATATTATTATTA
1791892 TTTTATTTTA
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:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
TATATTATTATTAG
Found at i:1791904 original size:10 final size:11
Alignment explanation
Indices: 1791863--1791908 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1791853 TATTAAATAG
1791863 ATTA-TATTATT
1 ATTATTATT-TT
* *
1791874 ATTAGTATATT
1 ATTATTATTTT
1791885 ATTATTATTTT
1 ATTATTATTTT
1791896 ATT-TTATTTT
1 ATTATTATTTT
1791906 ATT
1 ATT
1791909 CATTTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 10 0.32
11 18 0.58
12 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:1792586 original size:18 final size:18
Alignment explanation
Indices: 1792563--1792601 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1792553 GCATCAAATG
1792563 AAGTGCCGCCGGAAGTCA
1 AAGTGCCGCCGGAAGTCA
1792581 AAGTGCCGCCGGAAGTCA
1 AAGTGCCGCCGGAAGTCA
1792599 AAG
1 AAG
1792602 GGCCACCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.33, T:0.10
Consensus pattern (18 bp):
AAGTGCCGCCGGAAGTCA
Found at i:1793163 original size:17 final size:14
Alignment explanation
Indices: 1793127--1793165 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
1793117 TTATACGTAT
1793127 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
1793141 TTTTTATTTCTTTCTA
1 TTTTTATTT-TTT-TA
1793157 GTTTTTATT
1 -TTTTTATT
1793166 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.41
15 3 0.14
16 2 0.09
17 8 0.36
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:1793325 original size:46 final size:45
Alignment explanation
Indices: 1793228--1793328 Score: 111
Period size: 46 Copynumber: 2.2 Consensus size: 45
1793218 TCTTGTTTAA
*
1793228 TTTTTATTTTATTTATTTTATTATTTTTAGTTTTTATTTATTTGT
1 TTTTTAATTTATTTATTTTATTATTTTTAGTTTTTATTTATTTGT
1793273 TCTTTTAATTTATTT-TTTATATTATTATTATA-TCTTTTATTT-TTAT-T
1 T-TTTTAATTTATTTATTT-TATTATT-TT-TAGT-TTTTATTTATT-TGT
1793320 TTTTTAATT
1 TTTTTAATT
1793329 GTTTGCCTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
45 4 0.08
46 27 0.55
47 7 0.14
48 11 0.22
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (45 bp):
TTTTTAATTTATTTATTTTATTATTTTTAGTTTTTATTTATTTGT
Found at i:1793339 original size:61 final size:59
Alignment explanation
Indices: 1793228--1793357 Score: 133
Period size: 61 Copynumber: 2.2 Consensus size: 59
1793218 TCTTGTTTAA
* * *
1793228 TTTT-TATTTTATTTATTTTATTATTTTTAGTTTTTATTTATTTGTTCTTTTAATTTATT
1 TTTTATATTTTATTTATCTTATTATTTTTAGTTTTTAATTATTTGTCCTTTT-ATTTATT
* * *
1793287 TTTTATATTATTATTATATCTT-TTATTTTTATTTTTTTAATTGTTTG-CCTTTTATTTTTT
1 TTTTATATT-TTATT-TATCTTATTATTTTTA-GTTTTTAATTATTTGTCCTTTTATTTATT
1793347 TATTTAT-TTTT
1 T-TTTATATTTT
1793358 CTATCTAACA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
59 6 0.10
60 13 0.22
61 24 0.40
62 17 0.28
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (59 bp):
TTTTATATTTTATTTATCTTATTATTTTTAGTTTTTAATTATTTGTCCTTTTATTTATT
Found at i:1797894 original size:2 final size:2
Alignment explanation
Indices: 1797887--1797915 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1797877 TCCCAAATTA
1797887 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
1797916 ACTGAACATG
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:1800799 original size:21 final size:21
Alignment explanation
Indices: 1800772--1800830 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1800762 GTCCGAGTTA
*
1800772 CCCGCGACGGCCGCAATATCG
1 CCCGCGACGGCCGCAATAGCG
* * **
1800793 TCCGCGAAGATCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
1800814 CCCGCGACGGCCGCAAT
1 CCCGCGACGGCCGCAAT
1800831 CACTGTAAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.39, G:0.29, T:0.10
Consensus pattern (21 bp):
CCCGCGACGGCCGCAATAGCG
Found at i:1801200 original size:122 final size:122
Alignment explanation
Indices: 1800938--1801299 Score: 618
Period size: 122 Copynumber: 3.0 Consensus size: 122
1800928 CTTAAAGAGT
* * * * * **
1800938 CCAACTTGGAAGTCTCAGATTAAACTATGTGAGAGTACCGAGTTGGATTTAGCAGAATACTGGAA
1 CCAACTTGGAAGTCTCAGATTGAACTATGTGAAAGTAACGAGTTGGATTTAGCAGAATGCCGGTG
**
1801003 TTCTACGTTCATTGTAT-GCCATTGGTAGTTTGGTACCATGATCTCCATATGTATGG
66 GGCTACGTTCATTGTATGGCCATTGGTAGTTTGGTACCATGATCTCCATATGTATGG
*
1801059 CCAACTTGGAAGTCTCAGATTGAACTATGTGAAAGTAGCGAGTTGGATTTAGCAGAATGCCGGTG
1 CCAACTTGGAAGTCTCAGATTGAACTATGTGAAAGTAACGAGTTGGATTTAGCAGAATGCCGGTG
1801124 GGCTACGTTCATTGTATGGCCATTGGTAGTTTGGTACCATGATCTCCATATGTATGG
66 GGCTACGTTCATTGTATGGCCATTGGTAGTTTGGTACCATGATCTCCATATGTATGG
1801181 CCAACTTGGAAGTCTCAGATTGAACTATGTGAAAGTAACGAGTTGGATTTAGCAGAATGCCGGTG
1 CCAACTTGGAAGTCTCAGATTGAACTATGTGAAAGTAACGAGTTGGATTTAGCAGAATGCCGGTG
*
1801246 GGCTACGTTCATTGTATGGCCATTGGTAGTTTGGTACCATAATCTCCATATGTA
66 GGCTACGTTCATTGTATGGCCATTGGTAGTTTGGTACCATGATCTCCATATGTA
1801300 CCATAATAAA
Statistics
Matches: 229, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
121 73 0.32
122 156 0.68
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (122 bp):
CCAACTTGGAAGTCTCAGATTGAACTATGTGAAAGTAACGAGTTGGATTTAGCAGAATGCCGGTG
GGCTACGTTCATTGTATGGCCATTGGTAGTTTGGTACCATGATCTCCATATGTATGG
Found at i:1810570 original size:361 final size:361
Alignment explanation
Indices: 1809901--1810612 Score: 1264
Period size: 361 Copynumber: 2.0 Consensus size: 361
1809891 CAAGGTTACC
* * *
1809901 TGGTCTCACCAGTTGAAGGATCGCTGGAGGTTTGTTGAGTTGTTGGGATGATAGTATTTTTAAAG
1 TGGTCTCACCAGTTAAAGGATCGATGGAGGTTTCTTGAGTTGTTGGGATGATAGTATTTTTAAAG
* *
1809966 TCAAGGAACATTTTGTAAATAAGAGGTTTATTGCCATATTCAGGTATTTTAGAGAGAATCTTTTT
66 TCAAGGAACATTTTGTAAATAAGAGGTTTATTGCCATATTCAGGCATTTTAGAGAGAATATTTTT
1810031 AGTTATGGTCTTATTAATGTATACGAGCCGACCACAGAGGATGAGAAAGCAATCTTTTTGAAAGA
131 AGTTATGGTCTTATTAATGTATACGAGCCGACCACAGAGGATGAGAAAGCAATCTTTTTGAAAGA
*
1810096 GTTCTCTTCCTATTTGGAAATTCAAAGTCTCTTTTATGCGTGGGAAGGGACTTCAATTTGTATCT
196 GTTCTCTTCCTATTTGGAAATTCAAAGTCTCTTTTATGCGTGGGAAGGGACTTCAATGTGTATCT
* * *
1810161 ATTTCCAAAAGATAAGGAAGTCAAATCTCAAAATTGGAATTTAATAGAGCCTTTTAGGTCTTTCA
261 ATCTCCAAAAGATAAGGAAGGCAAATCTCAAAATTGGAATTCAATAGAGCCTTTTAGGTCTTTCA
*
1810226 TTCATCAAATAGGTCTCATAGACCTTTAGGGTTAGA
326 TTCATCAAATAGGCCTCATAGACCTTTAGGGTTAGA
1810262 TGGTCTCACCAGTTAAAGGATCGATGGAGGTTTCTTGAGTTGTTGGGATGATAGTATTTTTAAAG
1 TGGTCTCACCAGTTAAAGGATCGATGGAGGTTTCTTGAGTTGTTGGGATGATAGTATTTTTAAAG
* * *
1810327 TCAAGGCACATTTTGTAAATAAGAGGTTTATTGCCATATTTAGGCATTTTAGAGATAATATTTTT
66 TCAAGGAACATTTTGTAAATAAGAGGTTTATTGCCATATTCAGGCATTTTAGAGAGAATATTTTT
* *
1810392 AGTTGTGGTCTTATTAATGTATACGGGCCGACCACAGAGGATGAGAAAGCAATCTTTTT-AGAAG
131 AGTTATGGTCTTATTAATGTATACGAGCCGACCACAGAGGATGAGAAAGCAATCTTTTTGA-AAG
1810456 AGTTCTCTTCCTATTTGGAAATTCAAAGTCTCTTTTATGCGTGGGAAGGGACTTCAATGTGTATC
195 AGTTCTCTTCCTATTTGGAAATTCAAAGTCTCTTTTATGCGTGGGAAGGGACTTCAATGTGTATC
*
1810521 TATCTCCAAAAGATAAGGAAGGCAAATCTCAACATTGGAATTCAATAGAGCCTTTTAGGTCTTTC
260 TATCTCCAAAAGATAAGGAAGGCAAATCTCAAAATTGGAATTCAATAGAGCCTTTTAGGTCTTTC
1810586 ATTCATCAAATAGGCCTCATAGACCTT
325 ATTCATCAAATAGGCCTCATAGACCTT
1810613 CCTCTAATTG
Statistics
Matches: 334, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
360 1 0.00
361 333 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (361 bp):
TGGTCTCACCAGTTAAAGGATCGATGGAGGTTTCTTGAGTTGTTGGGATGATAGTATTTTTAAAG
TCAAGGAACATTTTGTAAATAAGAGGTTTATTGCCATATTCAGGCATTTTAGAGAGAATATTTTT
AGTTATGGTCTTATTAATGTATACGAGCCGACCACAGAGGATGAGAAAGCAATCTTTTTGAAAGA
GTTCTCTTCCTATTTGGAAATTCAAAGTCTCTTTTATGCGTGGGAAGGGACTTCAATGTGTATCT
ATCTCCAAAAGATAAGGAAGGCAAATCTCAAAATTGGAATTCAATAGAGCCTTTTAGGTCTTTCA
TTCATCAAATAGGCCTCATAGACCTTTAGGGTTAGA
Found at i:1822356 original size:453 final size:451
Alignment explanation
Indices: 1821481--1822387 Score: 1374
Period size: 453 Copynumber: 2.0 Consensus size: 451
1821471 TTGCTAAAGC
* *
1821481 AAATGAGATTTGTAAGTTACTGGAAAAAAGCCTAAAGGTAGCACACTAGGCTGACATAAATGCTA
1 AAATGAGATTTGTAAGTCACTGGAAAAAAGCCTAAAGGTAGCACACTAGGCTAACATAAATGCTA
* * *
1821546 CCATTCTATATTGTAGCACAACCACCTTTATTGTTCAGAATATGTATTTTCCCATTAGTTTCAAT
66 CCATTCTATATTGTAGCACAACCACCTTCATTGTGCAGAATATGTATTTTCCCATTAGATTCAAT
* * * *
1821611 CATTCCAAAAGTAGAGGACATTAACGGATCCAGGTCCAGCGAACCTAGGGTGAGTAAAAAGTTGA
131 CATTCCAAAAGTAGAGGACATCAACGAATCCAGGTCCAACGAACCCAGGGTGAGTAAAAAGTTGA
* * * *
1821676 TTCGGTTGCAGGTAAGAAGGATGCATAAGTACATTACCATGGTTGAAAGGTAAAGTCCAAAAAGG
196 TTCGGCTACAAGTAAGAAGGATGCATAAGTACATTACCACGGTTGAAAGGTAAAGTCCAAAAAGG
* * * *
1821741 CTTAACAAATAGAAGGTAGTTATGTTTATCACCCAACCTATAATTAATAACAATAGGTGCAGAGG
261 CTTAACAAATAGAAGGTAGTTATGTTGATCACCCAACCTAAAACTAATAACAATAGATGCAGAGG
* * *
1821806 CCCTAAAATTGAATACAAAGACAAAACTAACTGTAAATGAAGCTAATGTGAGATGAGACCACTTA
326 CCCTAAAATTGAATACAAAGACAAAACAAACTGTAAATGAAACTAATGTAAGATGAGACCACTTA
1821871 ACAGTTATTAGTTGAACTAAAAGATGAATTTAAAAATCATTAGCCTAAGAAGATATAAAAT
391 ACAGTTATTAGTTGAACTAAAAGATGAATTTAAAAATCATTAGCCTAAGAAGATATAAAAT
* *
1821932 AAATGAGCTTTGTAAGTCACTGGAAAAAA-CCTAAAGGTAGCATACTAGGCTAACATAAATGCTA
1 AAATGAGATTTGTAAGTCACTGGAAAAAAGCCTAAAGGTAGCACACTAGGCTAACATAAATGCTA
* *
1821996 CCATTC-CTGTTGTAGCACAACCACCTTCATTAG-GCAGAATATGTATTTTTTTCCCATTAGATT
66 CCATTCTATATTGTAGCACAACCACCTTCATT-GTGCAGAATATGTA---TTTTCCCATTAGATT
* * * * * *
1822059 CAATTATTCCAAAGGTAGAGGATATCATCGAATCTAGGTCCAACGAACCCAGGGTGAGTAAAAAT
127 CAATCATTCCAAAAGTAGAGGACATCAACGAATCCAGGTCCAACGAACCCAGGGTGAGTAAAAAG
* * *
1822124 TTGATTTGGCTACAAGTAAGAGGGGTGCATAAGTACATTACCACGGTTGAAAGGTAAAGTCCAAA
192 TTGATTCGGCTACAAGTAAGAAGGATGCATAAGTACATTACCACGGTTGAAAGGTAAAGTCCAAA
* * *
1822189 AAGGCTTAAATAAATAGAAGGTAGTTCA-GTTGATCATCCAACCTAAAACTAATAGCAATAGATG
257 AAGGCTT-AACAAATAGAAGGTAGTT-ATGTTGATCACCCAACCTAAAACTAATAACAATAGATG
*
1822253 CAGATGCCCTAAAATTGAATACAAAGACAAAACAAACT-TCAAATGAAACTAATGTAAGATGAGA
320 CAGAGGCCCTAAAATTGAATACAAAGACAAAACAAACTGT-AAATGAAACTAATGTAAGATGAGA
*
1822317 CCACTTAACAGTTATTAGTTGAACTAAAAGATTAATTTAAAAATCATTAGCCTAAGAAGATATAA
384 CCACTTAACAGTTATTAGTTGAACTAAAAGATGAATTTAAAAATCATTAGCCTAAGAAGATATAA
1822382 AAT
449 AAT
1822385 AAA
1 AAA
1822388 GCCCATTGGG
Statistics
Matches: 411, Mismatches: 38, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
449 33 0.08
450 40 0.10
451 27 0.07
452 135 0.33
453 175 0.43
454 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (451 bp):
AAATGAGATTTGTAAGTCACTGGAAAAAAGCCTAAAGGTAGCACACTAGGCTAACATAAATGCTA
CCATTCTATATTGTAGCACAACCACCTTCATTGTGCAGAATATGTATTTTCCCATTAGATTCAAT
CATTCCAAAAGTAGAGGACATCAACGAATCCAGGTCCAACGAACCCAGGGTGAGTAAAAAGTTGA
TTCGGCTACAAGTAAGAAGGATGCATAAGTACATTACCACGGTTGAAAGGTAAAGTCCAAAAAGG
CTTAACAAATAGAAGGTAGTTATGTTGATCACCCAACCTAAAACTAATAACAATAGATGCAGAGG
CCCTAAAATTGAATACAAAGACAAAACAAACTGTAAATGAAACTAATGTAAGATGAGACCACTTA
ACAGTTATTAGTTGAACTAAAAGATGAATTTAAAAATCATTAGCCTAAGAAGATATAAAAT
Found at i:1828997 original size:17 final size:18
Alignment explanation
Indices: 1828975--1829011 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1828965 ATCAAGCTAA
1828975 AAGTAT-TGAACGAG-AGG
1 AAGTATCTGAA-GAGAAGG
1828992 AAGTATCTGAAGAGAAGG
1 AAGTATCTGAAGAGAAGG
1829010 AA
1 AA
1829012 ATAACTGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.46, C:0.05, G:0.32, T:0.16
Consensus pattern (18 bp):
AAGTATCTGAAGAGAAGG
Found at i:1838542 original size:20 final size:21
Alignment explanation
Indices: 1838505--1838544 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1838495 AAATTAAGTT
1838505 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1838526 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1838545 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1838868 original size:19 final size:19
Alignment explanation
Indices: 1838844--1838895 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1838834 AATGCATTTG
1838844 ATGCATCGATGCACAAGCC
1 ATGCATCGATGCACAAGCC
1838863 ATGCATCGATGCACAAGCC
1 ATGCATCGATGCACAAGCC
1838882 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1838896 TCAGGCTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACAAGCC
Found at i:1844745 original size:20 final size:21
Alignment explanation
Indices: 1844716--1844771 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1844706 TTTATGCTTC
*
1844716 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1844736 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1844758 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1844772 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Done.