Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 109 of 226
Found at i:37377357 original size:24 final size:24
Alignment explanation
Indices: 37377302--37377357 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
37377292 TATGGTGCTT
37377302 CCTGATTAATTGCTCTTCAGAGCTA
1 CCTG-TTAATTGCTCTTCAGAGCTA
* *
37377327 CCCGTTAATTGCTC-TCTGGAGCTA
1 CCTGTTAATTGCTCTTC-AGAGCTA
37377351 CCTGTTA
1 CCTGTTA
37377358 TAGGCTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 22 0.81
25 3 0.11
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (24 bp):
CCTGTTAATTGCTCTTCAGAGCTA
Found at i:37397979 original size:50 final size:49
Alignment explanation
Indices: 37397916--37398044 Score: 170
Period size: 50 Copynumber: 2.6 Consensus size: 49
37397906 GATGAGACCC
**
37397916 CATGTAAGACCATGTCTGGGACATGGCGATGGTG-CCGAGATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGC-ATGG-GACCGAGATGAGAACTCT
* *
37397966 CCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGACATGGCATGGG-ACCGAGATGAGAACTCT
* *
37398016 CATGTAAGACCATATCTGGGAAATGGCAT
1 CATGTAAGACCATGTCTGGGACATGGCAT
37398045 TTGCAGTACA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
48 1 0.01
49 4 0.06
50 65 0.93
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (49 bp):
CATGTAAGACCATGTCTGGGACATGGCATGGGACCGAGATGAGAACTCT
Found at i:37398081 original size:49 final size:49
Alignment explanation
Indices: 37398019--37398144 Score: 200
Period size: 49 Copynumber: 2.6 Consensus size: 49
37398009 GAACTCTCAT
37398019 GTAAGACCATATCTGGGAAATGGCATTTGCAGTACAGGAAACATCCCAC
1 GTAAGACCATATCTGGGAAATGGCATTTGCAGTACAGGAAACATCCCAC
* * *
37398068 GTAAGACCATATCTGGGATATGTCATTTGCAGTACAGGAAACATCCCAT
1 GTAAGACCATATCTGGGAAATGGCATTTGCAGTACAGGAAACATCCCAC
* *
37398117 GTAAGACCATGTCTGGGACATGGC-TTTG
1 GTAAGACCATATCTGGGAAATGGCATTTG
37398145 GCATGTTATT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
48 4 0.06
49 67 0.94
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (49 bp):
GTAAGACCATATCTGGGAAATGGCATTTGCAGTACAGGAAACATCCCAC
Found at i:37398375 original size:20 final size:20
Alignment explanation
Indices: 37398350--37398388 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
37398340 TGAGTTATTT
37398350 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
37398370 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
37398389 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:37399560 original size:6 final size:6
Alignment explanation
Indices: 37399549--37399579 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
37399539 ATTGATAATA
37399549 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
37399580 AAAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:37407779 original size:20 final size:20
Alignment explanation
Indices: 37407756--37407820 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
37407746 ACTTCGGTGT
*
37407756 CCCTGTTTGCACAAC-TGTGC
1 CCCTGATTGCAC-ACTTGTGC
37407776 CCCTGATTGCACACTTGTGC
1 CCCTGATTGCACACTTGTGC
*
37407796 CCCTGATTGCAC-TTTGGTGC
1 CCCTGATTGCACACTT-GTGC
37407816 CCCTG
1 CCCTG
37407821 TTTTGCATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.10
20 37 0.90
ACGTcount: A:0.12, C:0.35, G:0.22, T:0.31
Consensus pattern (20 bp):
CCCTGATTGCACACTTGTGC
Found at i:37407838 original size:22 final size:20
Alignment explanation
Indices: 37407772--37407843 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
37407762 TTGCACAACT
*
37407772 GTGCCCCTGATTGCAC-ACTT
1 GTGCCCCTGATTGCACTA-TG
*
37407792 GTGCCCCTGATTGCACTTTG
1 GTGCCCCTGATTGCACTATG
*
37407812 GTGCCCCTGTTTTGCATCTATG
1 GTGCCCCTG-ATTGCA-CTATG
37407834 GTGCCCCTGA
1 GTGCCCCTGA
37407844 AAATGAGTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 26 0.59
21 5 0.11
22 13 0.30
ACGTcount: A:0.11, C:0.32, G:0.24, T:0.33
Consensus pattern (20 bp):
GTGCCCCTGATTGCACTATG
Found at i:37411192 original size:17 final size:17
Alignment explanation
Indices: 37411158--37411192 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
37411148 CTTGTATTTA
*
37411158 AGTGTGAACACTCCTCT
1 AGTGTGAACACACCTCT
*
37411175 AGTGTGAACACACTTCT
1 AGTGTGAACACACCTCT
37411192 A
1 A
37411193 AGACAATAAG
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:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (17 bp):
AGTGTGAACACACCTCT
Found at i:37411768 original size:20 final size:18
Alignment explanation
Indices: 37411729--37411771 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
37411719 CCCCCTCTTC
37411729 TTCTTCTTCTTCCTTATT
1 TTCTTCTTCTTCCTTATT
37411747 TTCTT-TTCTTCTCTTCATT
1 TTCTTCTTCTTC-CTT-ATT
37411766 TT-TTCT
1 TTCTTCT
37411772 CCTATTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.27
18 10 0.45
19 6 0.27
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.70
Consensus pattern (18 bp):
TTCTTCTTCTTCCTTATT
Found at i:37411779 original size:26 final size:26
Alignment explanation
Indices: 37411757--37411824 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
37411747 TTCTTTTCTT
37411757 CTCTTCATTTTTTCTCCTATTTTCTCC
1 CTCTTC-TTTTTTCTCCTATTTTCTCC
*
37411784 CTCTTCCTTTTTCTCCTATTTTCTCC
1 CTCTTCTTTTTTCTCCTATTTTCTCC
*
37411810 CTCTTCCTTTTTCTC
1 CTCTTCTTTTTTCTC
37411825 GATCGTGGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 34 0.85
27 6 0.15
ACGTcount: A:0.04, C:0.37, G:0.00, T:0.59
Consensus pattern (26 bp):
CTCTTCTTTTTTCTCCTATTTTCTCC
Found at i:37423012 original size:22 final size:22
Alignment explanation
Indices: 37422984--37423042 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
37422974 TTTATTGTTC
37422984 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
37423006 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
37423028 AGCCATGAGAGCTTA
1 AAACATGAGAGCTTA
37423043 CTAGTGGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:37425113 original size:23 final size:22
Alignment explanation
Indices: 37425070--37425113 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
37425060 TTTCAAAATC
* * *
37425070 CCCCTGTCGAATGGCCTGTTCT
1 CCCCGGTCGAATGGACAGTTCT
37425092 CCCCGGTCGAAATGGACAGTTC
1 CCCCGGTCG-AATGGACAGTTC
37425114 AATTCCTTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.16, C:0.34, G:0.25, T:0.25
Consensus pattern (22 bp):
CCCCGGTCGAATGGACAGTTCT
Found at i:37430299 original size:16 final size:16
Alignment explanation
Indices: 37430280--37430333 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
37430270 AAAAATAAAA
*
37430280 TATAATTAAAAATATT
1 TATAATTTAAAATATT
* *
37430296 TATAATTTAATATAAT
1 TATAATTTAAAATATT
*
37430312 AATTAATTTAAAATATT
1 TA-TAATTTAAAATATT
37430329 TATAA
1 TATAA
37430334 AAATATTGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAATTTAAAATATT
Found at i:37430305 original size:17 final size:17
Alignment explanation
Indices: 37430280--37430333 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
37430270 AAAAATAAAA
37430280 TATAA-TTAAAAATATT
1 TATAATTTAAAAATATT
*
37430296 TATAATTTAATATAATA-A
1 TATAATTTAA-A-AATATT
37430314 T-TAATTT-AAAATATT
1 TATAATTTAAAAATATT
37430329 TATAA
1 TATAA
37430334 AAATATTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 4 0.13
15 2 0.06
16 9 0.29
17 10 0.32
18 2 0.06
19 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATAATTTAAAAATATT
Found at i:37430755 original size:27 final size:27
Alignment explanation
Indices: 37430714--37430816 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
37430704 TAGTATTGGC
* *
37430714 GCCTATCTAGAAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
* *
37430741 GCCTATTTGGGAGGCGCCAATGGTAGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
37430768 GCCTATCTGGGAGGCACCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
**
37430795 GCC-ATACTGAAAGGCGCCAATG
1 GCCTAT-CTGGGAGGCGCCAATG
37430817 CTGTGATTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 2 0.03
27 63 0.97
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.21
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:37430910 original size:22 final size:21
Alignment explanation
Indices: 37430882--37430926 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
37430872 CGGAAGAAAG
*
37430882 AAGAAGGAAAGAAGCAGAAGAA
1 AAGAAGGAAAGAA-AAGAAGAA
*
37430904 AAGAAGGAAGGAAAAGAAGAA
1 AAGAAGGAAAGAAAAGAAGAA
37430925 AA
1 AA
37430927 AAATTAGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (21 bp):
AAGAAGGAAAGAAAAGAAGAA
Found at i:37433165 original size:16 final size:15
Alignment explanation
Indices: 37433134--37433175 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
37433124 ACAAAATCAA
*
37433134 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
37433149 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
37433165 ATAAAAATTAA
1 ATAAAAGTTAA
37433176 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:37433255 original size:39 final size:38
Alignment explanation
Indices: 37433212--37433294 Score: 148
Period size: 39 Copynumber: 2.2 Consensus size: 38
37433202 AAAAAGTCAG
37433212 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAA-TTTTT
*
37433251 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
37433289 TTATAA
1 TTATAA
37433295 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 11 0.26
39 32 0.74
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:37433419 original size:59 final size:59
Alignment explanation
Indices: 37433329--37433448 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 59
37433319 TACTAAACTA
* * * * * * *
37433329 AACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATTTTTAGATAATTAC
1 AACACAAAAACTTATAGCATAATCCCAAATTACTAACAAATT-AATTATAAAATAATTAC
*
37433389 AACACAAAAATTTATA-CATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
1 AACACAAAAACTTATAGCATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
37433447 AA
1 AA
37433449 TATTCATACA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 16 0.31
59 22 0.42
60 14 0.27
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.32
Consensus pattern (59 bp):
AACACAAAAACTTATAGCATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:37433541 original size:30 final size:27
Alignment explanation
Indices: 37433489--37433575 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
37433479 ATATCCCCAC
37433489 ATTACAATATTCATACAAAATTGCAAT
1 ATTACAATATTCATACAAAATTGCAAT
37433516 ATTACAATATTCATACAAAA----AA-
1 ATTACAATATTCATACAAAATTGCAAT
* **
37433538 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTGCAAT
37433565 ATTACAATATT
1 ATTACAATATT
37433576 NNNNNNNNNN
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
22 19 0.36
23 2 0.04
26 2 0.04
27 30 0.57
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTGCAAT
Found at i:37433923 original size:3 final size:3
Alignment explanation
Indices: 37433917--37433960 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
37433907 TTTTTTTTCT
*
37433917 TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TCC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
37433961 CCTTTCTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:37433937 original size:14 final size:14
Alignment explanation
Indices: 37433913--37433961 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
37433903 CCTTTTTTTT
37433913 TTCTT-TCTTCTTC
1 TTCTTCTCTTCTTC
37433926 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
37433940 TTCTTCTCCTTC-TC
1 TTCTTCT-CTTCTTC
37433954 TTCTTCTC
1 TTCTTCTC
37433962 CTTTCTCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.18
14 24 0.71
15 4 0.12
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
TTCTTCTCTTCTTC
Found at i:37433942 original size:20 final size:20
Alignment explanation
Indices: 37433917--37433960 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
37433907 TTTTTTTTCT
*
37433917 TTCTTCTTCTTCTTCTCTTC
1 TTCTTCTTCTCCTTCTCTTC
37433937 TTCTTCTTCTCCTTCTCTTC
1 TTCTTCTTCTCCTTCTCTTC
37433957 TTCT
1 TTCT
37433961 CCTTTCTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
TTCTTCTTCTCCTTCTCTTC
Found at i:37433962 original size:14 final size:15
Alignment explanation
Indices: 37433919--37433964 Score: 78
Period size: 14 Copynumber: 3.2 Consensus size: 15
37433909 TTTTTTCTTT
37433919 CTTCTTCTTCTTCT-
1 CTTCTTCTTCTTCTC
37433933 CTTCTTCTTCTTCTC
1 CTTCTTCTTCTTCTC
37433948 CTTC-TCTTCTTCTC
1 CTTCTTCTTCTTCTC
37433962 CTT
1 CTT
37433965 TCTCTCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 27 0.87
15 4 0.13
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (15 bp):
CTTCTTCTTCTTCTC
Found at i:37433972 original size:14 final size:13
Alignment explanation
Indices: 37433923--37433972 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 13
37433913 TTCTTTCTTC
*
37433923 TTCTTCTTCTCTT
1 TTCTTCTTCTCCT
37433936 CTTCTTCTTCTCCT
1 -TTCTTCTTCTCCT
37433950 TCTCTTCTTCTCCT
1 T-TCTTCTTCTCCT
37433964 TTCTCTCTT
1 TTCT-TCTT
37433973 TTTTTTCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 4 0.12
14 29 0.88
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTTCTTCTCCT
Found at i:37434128 original size:27 final size:27
Alignment explanation
Indices: 37434096--37434161 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
37434086 GCAGAGGGCA
37434096 CCATTGGCGCCTCTCCATGAGGCTCCT
1 CCATTGGCGCCTCTCCATGAGGCTCCT
*
37434123 TCATTGGCGCCTCTCCATGAGGCTCCT
1 CCATTGGCGCCTCTCCATGAGGCTCCT
37434150 CCATTGGCGCCT
1 CCATTGGCGCCT
37434162 ACTAGACAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.11, C:0.39, G:0.23, T:0.27
Consensus pattern (27 bp):
CCATTGGCGCCTCTCCATGAGGCTCCT
Found at i:37434270 original size:27 final size:25
Alignment explanation
Indices: 37434223--37434279 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
37434213 TTAAAAAAAA
37434223 TATT-AAAAAAAGTATAAATTATATTT
1 TATTCAAAAAAAGTATAAA-T-TATTT
*
37434249 TATTCAAAAAAA-TATATTATTATTT
1 TATTCAAAAAAAGTATA-AATTATTT
37434274 TATTCA
1 TATTCA
37434280 TTGGCTCCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 11 0.39
26 9 0.32
27 8 0.29
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
TATTCAAAAAAAGTATAAATTATTT
Found at i:37434590 original size:7 final size:7
Alignment explanation
Indices: 37434578--37434602 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
37434568 CATATATAAA
37434578 ATTTATT
1 ATTTATT
37434585 ATTTATT
1 ATTTATT
37434592 ATTTATT
1 ATTTATT
37434599 ATTT
1 ATTT
37434603 GATCTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTATT
Found at i:37435057 original size:33 final size:33
Alignment explanation
Indices: 37435020--37435087 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 33
37435010 TGTATTTTTT
*
37435020 TATTT-TAAAAAACTAATAATATAAATAACTTGA
1 TATTTATAAAAAACTAAAAATATAAA-AACTTGA
* *
37435053 TATTTAATAAAAAATTAAAAATATATAAACTTGA
1 TATTT-ATAAAAAACTAAAAATATAAAAACTTGA
37435087 T
1 T
37435088 TGCATCTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 5 0.17
34 8 0.27
35 17 0.57
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (33 bp):
TATTTATAAAAAACTAAAAATATAAAAACTTGA
Found at i:37436934 original size:18 final size:17
Alignment explanation
Indices: 37436911--37436945 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
37436901 AAGCAAAACA
37436911 AATCTAAAAAATGGAGTT
1 AATCTAAAAAAT-GAGTT
*
37436929 AATCTAAGAAATGAGTT
1 AATCTAAAAAATGAGTT
37436946 CAAGCTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.29
Consensus pattern (17 bp):
AATCTAAAAAATGAGTT
Found at i:37441644 original size:19 final size:19
Alignment explanation
Indices: 37441609--37441652 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
37441599 TGCAAATAAT
* *
37441609 TTCTAA-ATATTATTTTAA
1 TTCTAATATAGTACTTTAA
37441627 TTCTAATATAGTACTTTAA
1 TTCTAATATAGTACTTTAA
*
37441646 TTATAAT
1 TTCTAAT
37441653 TTTATTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (19 bp):
TTCTAATATAGTACTTTAA
Found at i:37446403 original size:2 final size:2
Alignment explanation
Indices: 37446396--37446437 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
37446386 GAATTGAGAA
37446396 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
37446438 TTTTGCTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:37449460 original size:23 final size:23
Alignment explanation
Indices: 37449433--37449509 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
37449423 ATCCCAACGC
37449433 TATCATGAAAATGAATTAACAAA
1 TATCATGAAAATGAATTAACAAA
* * * *
37449456 TATCA-CAAGATTTGTGAGATCAACATA
1 TATCATGAA-A---ATGA-ATTAACAAA
37449483 -ATCATGAAAATGAATTAACAAA
1 TATCATGAAAATGAATTAACAAA
37449505 TATCA
1 TATCA
37449510 AATTCTAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 14
0.64 0.13 0.23
Matches are distributed among these distances:
22 9 0.23
23 13 0.33
26 8 0.21
27 9 0.23
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (23 bp):
TATCATGAAAATGAATTAACAAA
Found at i:37455279 original size:32 final size:31
Alignment explanation
Indices: 37455216--37455279 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
37455206 ACTTGTCCTT
** *
37455216 CAAAACTTTTACTCCTTCCCACTTTCTCCCC
1 CAAAACTTTTACTCCTTCCCACTCCCACCCC
37455247 CAAAACTTTTACTCCCTTCCC-CTCCCAACCCC
1 CAAAACTTTTACT-CCTTCCCACTCCC-ACCCC
37455279 C
1 C
37455280 CAATCTAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.20, C:0.50, G:0.00, T:0.30
Consensus pattern (31 bp):
CAAAACTTTTACTCCTTCCCACTCCCACCCC
Found at i:37463406 original size:51 final size:51
Alignment explanation
Indices: 37463300--37463406 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 51
37463290 CCACTTCAGC
* **
37463300 TTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCTATCTTTAGC
1 TTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCTATCTTCAAA
* ** *
37463351 TTTAATCTATTCCACTGCAACGCCAGGGCAATGAGATTCGCTGA-CTTCAAA
1 TTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCT-ATCTTCAAA
37463402 TTTAA
1 TTTAA
37463407 CGCCGGGGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 47 0.98
52 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (51 bp):
TTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCTATCTTCAAA
Found at i:37463744 original size:258 final size:257
Alignment explanation
Indices: 37463155--37463915 Score: 1059
Period size: 258 Copynumber: 2.9 Consensus size: 257
37463145 TAATGCCAAG
*
37463155 GAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGTCAGGG-AA-CAGATTTGC
1 GAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAAACCAGATTTGC
* * * *
37463218 TACCTTTAGCTTTAATCTGTTCCACTGTAACGCCTAGGAGATAGGATTCGCTGCCTTCAACTTTA
66 TACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCTCAACTTTA
* * * *
37463283 ATCCGCTCCACTTCAGCTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGAGTCGCTATCTTT
131 ATCCGCTCCACTTCAGC--TATTCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTTT
* * * * *
37463348 AGCTTTAATCTATTCCACTGCAACGCCAGGGCAATGAGATTCGCTGACTTCAAATTTAACGCCGG
194 AGCTTTAATCTGTTCCACTGCAACGCCAGGG-AATAAGATT-GGTGACTTCAAATTTAACACCAG
*
37463413 G
257 A
* * * *
37463414 GAGATAAGATTCGCTGCCTTCATCTTTAATCTGCTCCGCTACAACGCCAGGGAAACAAGATTCGC
1 GAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAAACCAGATTTGC
* *
37463479 TACCTTTAGCTTTAATCTGTTCCACTGAAATGCCAAAGAGATAGGATTCGCTGCCCTCAGCTTTA
66 TACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCTCAACTTTA
* *
37463544 ATCGGCTCCACTTCAGCTATTCTATTCCACTGCAATGCTAGGGAAACAAGATTCGCTACCTTTAG
131 ATCCGCTCCACTTCAGCTATTCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTTTAG
* *
37463609 CTTTAATCTGTTCC-CTGCAACGCCAGGGAAGTAAGATTGGTTACTTTC-AGTCTTAACACCAGA
196 CTTTAATCTGTTCCACTGCAACGCCAGGGAA-TAAGATTGGTGAC-TTCAAAT-TTAACACCAGA
* *
37463672 GAGATAAGATTCGCTGCCCTT-AGCTTTAATCTGCTCCGCTGCAACACCAGGGAAACCAGGTTTG
1 GAGATAAGATTCGCTG-CCTTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAAACCAGATTTG
* *
37463736 CTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGATATAGGATTCACTGCCCTCAACTTT
65 CTACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCTCAACTTT
* * * *
37463801 AATCTGCTCCACTTCAGCTATT-TCATTCAATTGCAATGCCAGGGAAACAAAATTCGCTACC-TT
130 AATCCGCTCCACTTCAGCTATTCT-ATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTTT
* * *
37463864 AGCTTTAATCTGTTCCACTGTAACGCCAGGGAAATAAGACTGGTGTCTTCAA
194 AGCTTTAATCTGTTCCACTGCAACGCCAGGG-AATAAGATTGGTGACTTCAA
37463916 TCCACTCCAC
Statistics
Matches: 448, Mismatches: 44, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
257 30 0.07
258 223 0.50
259 111 0.25
260 2 0.00
261 82 0.18
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (257 bp):
GAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAAACCAGATTTGC
TACCTTTAGCTTTAATCTGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCTCAACTTTA
ATCCGCTCCACTTCAGCTATTCTATTCCACTGCAATGCCAGGGAAACAAGATTCGCTACCTTTAG
CTTTAATCTGTTCCACTGCAACGCCAGGGAATAAGATTGGTGACTTCAAATTTAACACCAGA
Found at i:37466234 original size:7 final size:8
Alignment explanation
Indices: 37466217--37466256 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
37466207 TGTTTCATCA
*
37466217 TTTTCATT
1 TTTTGATT
37466225 TTTTGATT
1 TTTTGATT
37466233 TTTTGATTT
1 TTTTGA-TT
37466242 TTTTGA-T
1 TTTTGATT
37466249 TTTTGATT
1 TTTTGATT
37466257 GAATCTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.24
8 14 0.48
9 8 0.28
ACGTcount: A:0.12, C:0.03, G:0.10, T:0.75
Consensus pattern (8 bp):
TTTTGATT
Found at i:37466235 original size:9 final size:9
Alignment explanation
Indices: 37466223--37466252 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
37466213 ATCATTTTCA
37466223 TTTTTTGA-
1 TTTTTTGAT
37466231 TTTTTTGAT
1 TTTTTTGAT
37466240 TTTTTTGAT
1 TTTTTTGAT
37466249 TTTT
1 TTTT
37466253 GATTGAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (9 bp):
TTTTTTGAT
Found at i:37468225 original size:50 final size:50
Alignment explanation
Indices: 37468117--37468358 Score: 322
Period size: 50 Copynumber: 4.7 Consensus size: 50
37468107 ACATGCTAAA
** * *
37468117 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAAT
* *
37468168 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
37468218 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
* * *
37468268 GCTATGTCCCAGACATGGTCTTACATGAGACCTTTCATGATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACC--TC-TCATCTC--GG-TGCCAAT
* *
37468324 GCCATGTCCCAGACATGATCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
37468359 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
50 93 0.55
51 29 0.17
52 2 0.01
53 7 0.04
54 2 0.01
55 2 0.01
56 35 0.21
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
Found at i:37469210 original size:13 final size:13
Alignment explanation
Indices: 37469194--37469260 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
37469184 TTTAAACTAA
37469194 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
37469207 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* * *
37469220 GCTTTTTCTACAGC
1 AC-TTTTCAAAAGC
37469234 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
37469247 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
37469260 A
1 A
37469261 ATGAAGAACT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
13 36 0.80
14 9 0.20
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:37469426 original size:30 final size:29
Alignment explanation
Indices: 37469391--37469447 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
37469381 CCTCGACTCT
37469391 AACTTTGT-CAAAATTACGATTTTGCCCCTA
1 AACTTT-TACAAAATTAC-ATTTTGCCCCTA
* *
37469421 AACTTTTACATAATTACATTTTTCCCC
1 AACTTTTACAAAATTACATTTTGCCCC
37469448 AAGGCTCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (29 bp):
AACTTTTACAAAATTACATTTTGCCCCTA
Found at i:37474620 original size:41 final size:41
Alignment explanation
Indices: 37474575--37474664 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
37474565 AATTCGGCCA
* * *
37474575 AACATGTAGTAGCAGCATTAAATTCGTCTAGGCATATTTAT
1 AACATGTAGTAGCAGCATTAAATTCATCCAGACATATTTAT
*
37474616 AACATGTAGTGGCAGCATTAAATTCATCCAGACATATTTAT
1 AACATGTAGTAGCAGCATTAAATTCATCCAGACATATTTAT
37474657 AACATGTA
1 AACATGTA
37474665 TGAAAATAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (41 bp):
AACATGTAGTAGCAGCATTAAATTCATCCAGACATATTTAT
Found at i:37476096 original size:16 final size:18
Alignment explanation
Indices: 37476065--37476097 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
37476055 ACTCTTCAAT
37476065 CCATCATCCAAATCAAAG
1 CCATCATCCAAATCAAAG
37476083 CCATCA-CC-AATCAAA
1 CCATCATCCAAATCAAA
37476098 AATTGATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.45, C:0.36, G:0.03, T:0.15
Consensus pattern (18 bp):
CCATCATCCAAATCAAAG
Found at i:37476794 original size:15 final size:17
Alignment explanation
Indices: 37476774--37476816 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
37476764 TTTTGATATC
37476774 TCATTTTCATC-TT-TT
1 TCATTTTCATCATTCTT
*
37476789 TCATTTTCTTCATTTCTT
1 TCATTTTCATCA-TTCTT
37476807 TCATTTTCAT
1 TCATTTTCAT
37476817 TTTCTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 10 0.43
17 2 0.09
18 11 0.48
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.65
Consensus pattern (17 bp):
TCATTTTCATCATTCTT
Found at i:37476803 original size:24 final size:24
Alignment explanation
Indices: 37476778--37476822 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
37476768 GATATCTCAT
*
37476778 TTTC-ATCTTTTTCATTTTCTTCA
1 TTTCTATCATTTTCATTTTCTTCA
*
37476801 TTTCTTTCATTTTCATTTTCTT
1 TTTCTATCATTTTCATTTTCTT
37476823 TGTTCTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTCTATCATTTTCATTTTCTTCA
Found at i:37476832 original size:24 final size:23
Alignment explanation
Indices: 37476786--37476830 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
37476776 ATTTTCATCT
37476786 TTTTCATTTTCTTCATTTCTTTCA
1 TTTTCATTTTCTT-ATTTCTTTCA
37476810 TTTTCATTTTCTT-TGTTCTTT
1 TTTTCATTTTCTTAT-TTCTTT
37476831 TCTCGCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 6 0.30
24 13 0.65
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTTCATTTTCTTATTTCTTTCA
Found at i:37477775 original size:21 final size:20
Alignment explanation
Indices: 37477748--37477797 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 20
37477738 TACAAACTTC
*
37477748 TTTTTTTTTGAATTTTTTTGAA
1 TTTTTTTTCG-ATTTTTTTG-A
37477770 TTTTTTTTCGATTTTTTTGA
1 TTTTTTTTCGATTTTTTTGA
37477790 TTTTTTTT
1 TTTTTTTT
37477798 ACAATACCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 9 0.33
21 9 0.33
22 9 0.33
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (20 bp):
TTTTTTTTCGATTTTTTTGA
Found at i:37477797 original size:10 final size:10
Alignment explanation
Indices: 37477749--37477797 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
37477739 ACAAACTTCT
37477749 TTTTTTTTGA
1 TTTTTTTTGA
*
37477759 ATTTTTTTGAA
1 TTTTTTTTG-A
37477770 TTTTTTTTCGA
1 TTTTTTTT-GA
37477781 -TTTTTTTGA
1 TTTTTTTTGA
37477790 TTTTTTTT
1 TTTTTTTT
37477798 ACAATACCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 22 0.65
11 9 0.26
12 1 0.03
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:37479397 original size:41 final size:41
Alignment explanation
Indices: 37479352--37479441 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
37479342 AATTCGGCCA
*
37479352 AACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTAT
1 AACATGTAGTAGCAGCATTAAATTCGTCCAGACATATTTAT
*
37479393 AACATGTAGTGGCAGCATTAAATTCGTCCAGACATATTTAT
1 AACATGTAGTAGCAGCATTAAATTCGTCCAGACATATTTAT
37479434 AACATGTA
1 AACATGTA
37479442 TGAAAATAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (41 bp):
AACATGTAGTAGCAGCATTAAATTCGTCCAGACATATTTAT
Found at i:37480372 original size:18 final size:19
Alignment explanation
Indices: 37480351--37480435 Score: 63
Period size: 18 Copynumber: 4.7 Consensus size: 19
37480341 GATAAAAAAG
37480351 ACAAAT-ATAATAATAACA
1 ACAAATAATAATAATAACA
*** *
37480369 AC-AACGGTAATAATAATA
1 ACAAATAATAATAATAACA
* *
37480387 A-TAATAATAATAATAATA
1 ACAAATAATAATAATAACA
*
37480405 A-TAATAATAATAATAAC-
1 ACAAATAATAATAATAACA
*
37480422 ACAAACAATAATAA
1 ACAAATAATAATAA
37480436 AGATAGTGGA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
17 3 0.05
18 52 0.95
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (19 bp):
ACAAATAATAATAATAACA
Found at i:37480435 original size:3 final size:3
Alignment explanation
Indices: 37480376--37480420 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
37480366 ACAACAACGG
37480376 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37480421 CACAAACAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:37482824 original size:19 final size:17
Alignment explanation
Indices: 37482800--37482838 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
37482790 GATTTTATTA
37482800 AATTAATTAATCTTAAGCT
1 AATTAATTAAT-TTAA-CT
*
37482819 AATTAATTTATTTAACT
1 AATTAATTAATTTAACT
37482836 AAT
1 AAT
37482839 CAACAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (17 bp):
AATTAATTAATTTAACT
Found at i:37485275 original size:22 final size:22
Alignment explanation
Indices: 37485245--37485313 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
37485235 TATGCACTAT
* *
37485245 TAAATAGAGAGCACTAAAGTGC
1 TAAACAGAGAGCACTAATGTGC
*
37485267 TATACAGAGAGCAC-AGATGTGC
1 TAAACAGAGAGCACTA-ATGTGC
*
37485289 TAAACGGAGAGCACTAATGTGC
1 TAAACAGAGAGCACTAATGTGC
37485311 TAA
1 TAA
37485314 TAATCGGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.19
Consensus pattern (22 bp):
TAAACAGAGAGCACTAATGTGC
Found at i:37491379 original size:26 final size:26
Alignment explanation
Indices: 37491344--37491420 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
37491334 GTAGCTCTTA
*
37491344 TGAGCGTCCCG-TTATATGGCTCTTCG
1 TGAGCTTCCCGATTA-ATGGCTCTTCG
* *
37491370 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAATGGCTCTTCG
*
37491396 TGAGCTTCCTGATTAATGGCTCTTC
1 TGAGCTTCCCGATTAATGGCTCTTC
37491421 AGAGTTACCT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 41 0.93
27 3 0.07
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (26 bp):
TGAGCTTCCCGATTAATGGCTCTTCG
Found at i:37491499 original size:25 final size:25
Alignment explanation
Indices: 37491471--37491536 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
37491461 GGCTCTCATG
* **
37491471 AGCTTCCCGTTATATGTCCCGGATA
1 AGCTTCCCGTTATATGACCCACATA
* * * *
37491496 AGCTTCCTGTTACATGACTCACATG
1 AGCTTCCCGTTATATGACCCACATA
37491521 AGCTTCCCGTTATATG
1 AGCTTCCCGTTATATG
37491537 GCTCGAGAGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.33
Consensus pattern (25 bp):
AGCTTCCCGTTATATGACCCACATA
Found at i:37493076 original size:9 final size:9
Alignment explanation
Indices: 37493062--37493095 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
37493052 ACAAGTTAGA
37493062 TAAAATAAT
1 TAAAATAAT
*
37493071 TAAAATAAA
1 TAAAATAAT
*
37493080 TAAGATAAT
1 TAAAATAAT
37493089 TAAAATA
1 TAAAATA
37493096 GAATAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (9 bp):
TAAAATAAT
Found at i:37493087 original size:18 final size:19
Alignment explanation
Indices: 37493061--37493101 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
37493051 TACAAGTTAG
37493061 ATAAAATAATTAAAATA-A
1 ATAAAATAATTAAAATAGA
*
37493079 ATAAGATAATTAAAATAGA
1 ATAAAATAATTAAAATAGA
37493098 ATAA
1 ATAA
37493102 TAAATCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
ATAAAATAATTAAAATAGA
Found at i:37495941 original size:21 final size:21
Alignment explanation
Indices: 37495911--37495950 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
37495901 TTACTATTAC
*
37495911 TATTAATATAAATTTTAAATT
1 TATTAATATAAATATTAAATT
* *
37495932 TATTATTATATATATTAAA
1 TATTAATATAAATATTAAA
37495951 AATATTTATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTAATATAAATATTAAATT
Found at i:37496800 original size:8 final size:8
Alignment explanation
Indices: 37496787--37496814 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
37496777 TAAAAATTAT
37496787 ATAAAATG
1 ATAAAATG
37496795 ATAAAATG
1 ATAAAATG
37496803 ATAAAATG
1 ATAAAATG
37496811 ATAA
1 ATAA
37496815 TCATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (8 bp):
ATAAAATG
Found at i:37496905 original size:10 final size:10
Alignment explanation
Indices: 37496882--37496915 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
37496872 ATTTTAAAAT
37496882 TTTATTATATA
1 TTTATTA-ATA
37496893 TTTATTAATA
1 TTTATTAATA
37496903 TTTATTAATA
1 TTTATTAATA
37496913 TTT
1 TTT
37496916 TACTATACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTATTAATA
Found at i:37496905 original size:22 final size:20
Alignment explanation
Indices: 37496875--37496915 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
37496865 TAAAATAATT
37496875 TTAAAATTTTATTATATATTTA
1 TTAAAA-TTTATTA-ATATTTA
*
37496897 TTAATATTTATTAATATTT
1 TTAAAATTTATTAATATTT
37496916 TACTATACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAAAATTTATTAATATTTA
Found at i:37501157 original size:51 final size:51
Alignment explanation
Indices: 37501057--37501164 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
37501047 TAAAATATTC
* *
37501057 ATAATAAAAATAAATTTTTATGGGTGGAAGGAGAGAGATGAGCTTCACCAAT
1 ATAA-AAAAATAAATTTTTATGGGTGGAAGGAGAGAGATGAGATACACCAAT
* * * * *
37501109 ATAAAAAAATTATTTTTTATGGGTGGAGGGAGAGAGTTG-GATGACACCAGT
1 ATAAAAAAATAAATTTTTATGGGTGGAAGGAGAGAGATGAGAT-ACACCAAT
37501160 ATAAA
1 ATAAA
37501165 TTTTTTTTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 2 0.04
51 42 0.88
52 4 0.08
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (51 bp):
ATAAAAAAATAAATTTTTATGGGTGGAAGGAGAGAGATGAGATACACCAAT
Found at i:37519793 original size:46 final size:46
Alignment explanation
Indices: 37519742--37519840 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
37519732 TTAAAAATTT
*
37519742 AAATTAAGTCAAGCATTTGTTATAGTTTAATAAATTAATACAAACA
1 AAATTAAGTCAAGCATTTGTTATAATTTAATAAATTAATACAAACA
* *
37519788 AAATTAAGTCAAGCATTTTTTATAATTTAATAAATTAATTCAAACA
1 AAATTAAGTCAAGCATTTGTTATAATTTAATAAATTAATACAAACA
37519834 AAATTAA
1 AAATTAA
37519841 CACAATCTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.36
Consensus pattern (46 bp):
AAATTAAGTCAAGCATTTGTTATAATTTAATAAATTAATACAAACA
Found at i:37527499 original size:54 final size:54
Alignment explanation
Indices: 37527413--37527530 Score: 132
Period size: 54 Copynumber: 2.2 Consensus size: 54
37527403 TTAAGTAAAT
* * * *
37527413 GAGTTACACGGCCTAGCACACGGCTTGTGACACGGCCATGTG-CCACAAGTTAGA
1 GAGTTACACGGCCTAGCACACGACTTGCGACACGACCATGTGACC-CAACTTAGA
* * * * *
37527467 GAGTTACACGGTCTGGCACATGACTTGCGACACGACCGTGTGACCCAACTTAGT
1 GAGTTACACGGCCTAGCACACGACTTGCGACACGACCATGTGACCCAACTTAGA
37527521 G-GTTACACGG
1 GAGTTACACGG
37527531 GTGGAGGCAC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
53 9 0.17
54 43 0.80
55 2 0.04
ACGTcount: A:0.25, C:0.27, G:0.28, T:0.20
Consensus pattern (54 bp):
GAGTTACACGGCCTAGCACACGACTTGCGACACGACCATGTGACCCAACTTAGA
Found at i:37529043 original size:16 final size:16
Alignment explanation
Indices: 37529004--37529044 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
37528994 AATGAGCCAT
* *
37529004 ATCCATGAATCCAGCC
1 ATCCATGTACCCAGCC
37529020 ATCCATGTACCCAGCC
1 ATCCATGTACCCAGCC
*
37529036 ATTCATGTA
1 ATCCATGTA
37529045 TGCTCCCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.34, G:0.12, T:0.24
Consensus pattern (16 bp):
ATCCATGTACCCAGCC
Found at i:37530186 original size:28 final size:28
Alignment explanation
Indices: 37530125--37530187 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
37530115 AGATGAACTG
* *
37530125 CACAATT--AATAACATAGATGTAATAA
1 CACAATTAAAATAAAATAGAGGTAATAA
** *
37530151 CATGATTAAAATAAAATAGAGGTAGTAA
1 CACAATTAAAATAAAATAGAGGTAATAA
37530179 CACAATTAA
1 CACAATTAA
37530188 TAACATGTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 5 0.18
28 23 0.82
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.25
Consensus pattern (28 bp):
CACAATTAAAATAAAATAGAGGTAATAA
Found at i:37531872 original size:10 final size:9
Alignment explanation
Indices: 37531846--37531870 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
37531836 CTAGTTAATT
37531846 AAAAAAACA
1 AAAAAAACA
37531855 AAAAAAACA
1 AAAAAAACA
37531864 AAAAAAA
1 AAAAAAA
37531871 ACTAATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:37533979 original size:28 final size:29
Alignment explanation
Indices: 37533939--37533998 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
37533929 ATTTAATTTT
*
37533939 AATTTTAATTAAATAAATAA-AAATAATTA
1 AATTCTAATTAAA-AAATAACAAATAATTA
*
37533968 AATTCTAA-TAAAAAATAACATATAATTA
1 AATTCTAATTAAAAAATAACAAATAATTA
37533996 AAT
1 AAT
37533999 GAAGGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 6 0.21
28 15 0.54
29 7 0.25
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
AATTCTAATTAAAAAATAACAAATAATTA
Found at i:37538160 original size:148 final size:147
Alignment explanation
Indices: 37537906--37538175 Score: 351
Period size: 148 Copynumber: 1.8 Consensus size: 147
37537896 AGTCTATTCT
* * * *
37537906 ACTGCAACCTCAGTGAGATAAGACTTGTAGCTTCAATAAAGTCTGATGCGATCTGCTCTACTGCA
1 ACTGCAACCTCAGGGAGATAAGACTCGTAACTTCAATAAAGTCTGATGCGATCCGCTCTACTGCA
* * * * * *
37537971 ACTTCGGAGAGATAAGATCCATCCTTTTAATCTACTTCACTGCAACTTTAGGAAGATTGGACTAG
66 ACTTCAGAGAGATAAGATCCATCATTTTAACCCACTCCACTGCAACTTCAGGAAGATTGGACTAG
37538036 TAACTTCAATCTGCTCC
131 TAACTTCAATCTGCTCC
* * * * *
37538053 ACTGCAACTTCAGGGAGATAAGGCTCGTAATTTCCAATAAAGTCTGATGTGATCCGTTCTACTGC
1 ACTGCAACCTCAGGGAGATAAGACTCGTAACTT-CAATAAAGTCTGATGCGATCCGCTCTACTGC
* * * * *
37538118 AACTTCAGAGAGATAAGGTCTATCATTTTGACCCGCTCCACTGCAACTTCAGGGAGAT
65 AACTTCAGAGAGATAAGATCCATCATTTTAACCCACTCCACTGCAACTTCAGGAAGAT
37538176 AAGACTTATA
Statistics
Matches: 102, Mismatches: 20, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
147 27 0.26
148 75 0.74
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (147 bp):
ACTGCAACCTCAGGGAGATAAGACTCGTAACTTCAATAAAGTCTGATGCGATCCGCTCTACTGCA
ACTTCAGAGAGATAAGATCCATCATTTTAACCCACTCCACTGCAACTTCAGGAAGATTGGACTAG
TAACTTCAATCTGCTCC
Found at i:37538703 original size:46 final size:46
Alignment explanation
Indices: 37538636--37538899 Score: 384
Period size: 46 Copynumber: 5.7 Consensus size: 46
37538626 AACCTAGTCT
* *
37538636 GCTGCCAAATACAGGAAGACAAGATCTACTATCCACGATCTACTCC
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
* * * * *
37538682 GCTGCCAAATATAGGAAGACAAAATCTGCTATCTTCAATCTACTTC
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
* * * *
37538728 GCTGCCAAATATAGGAAGACAATATCTGCTATCTTCGATCTACTCT
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
* * *
37538774 GCTACCAAATACAGGAAGACAAGATATGCTATCTACGATCTACTCT
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
37538820 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
* *
37538866 TCTGCCAAATACAGGAAGATAAGATCTGCTATCT
1 GCTGCCAAATACAGGAAGACAAGATCTGCTATCT
37538900 TTAATCTGTT
Statistics
Matches: 197, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 197 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (46 bp):
GCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACTCC
Found at i:37539392 original size:24 final size:24
Alignment explanation
Indices: 37539354--37539411 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
37539344 CGGATTGCTC
*
37539354 CCACTGTAATCTTC-AGAGTTCAAT
1 CCACTGTAATATTCAAG-GTTCAAT
* *
37539378 CCATTGTAATATTCAAGGTTCAGT
1 CCACTGTAATATTCAAGGTTCAAT
37539402 CCACTGTAAT
1 CCACTGTAAT
37539412 TTTGGGACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (24 bp):
CCACTGTAATATTCAAGGTTCAAT
Found at i:37540421 original size:5 final size:5
Alignment explanation
Indices: 37540402--37540452 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
37540392 GGCCTCTCCT
*
37540402 TTTTC TTTT- TCTTC TTTTC TTTTC -TTT- TTTTC TTTTC TTTTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC --TTTTC TTTTC
37540451 TT
1 TT
37540453 CTTTTTTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 9 0.23
5 25 0.64
7 5 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:37540421 original size:8 final size:7
Alignment explanation
Indices: 37540401--37540459 Score: 63
Period size: 7 Copynumber: 8.7 Consensus size: 7
37540391 AGGCCTCTCC
37540401 TTTTTC-
1 TTTTTCT
37540407 TTTTTCT
1 TTTTTCT
37540414 TCTTTTC-
1 T-TTTTCT
37540421 -TTTTCT
1 TTTTTCT
37540427 TTTTT-T
1 TTTTTCT
*
37540433 CTTTTCT
1 TTTTTCT
37540440 TTTTTCT
1 TTTTTCT
37540447 TTTCTTCT
1 TTT-TTCT
37540455 TTTTT
1 TTTTT
37540460 TGTTTATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
5 5 0.11
6 11 0.24
7 17 0.38
8 12 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:37540426 original size:13 final size:13
Alignment explanation
Indices: 37540402--37540457 Score: 87
Period size: 13 Copynumber: 4.3 Consensus size: 13
37540392 GGCCTCTCCT
37540402 TTTTCTTTTTCTTC
1 TTTTC-TTTTCTTC
*
37540416 TTTTCTTTTCTTT
1 TTTTCTTTTCTTC
37540429 TTTTCTTTTCTT-
1 TTTTCTTTTCTTC
37540441 TTTTCTTTTCTTC
1 TTTTCTTTTCTTC
37540454 TTTT
1 TTTT
37540458 TTTGTTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
12 12 0.30
13 23 0.57
14 5 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTCTTC
Found at i:37542793 original size:12 final size:12
Alignment explanation
Indices: 37542762--37542795 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
37542752 CTTTTCTAGT
37542762 TGTTCTTGCATC
1 TGTTCTTGCATC
**
37542774 TGGGCTTGCATC
1 TGTTCTTGCATC
37542786 TGTTCTTGCA
1 TGTTCTTGCA
37542796 ATTGCTCTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TGTTCTTGCATC
Found at i:37542951 original size:19 final size:20
Alignment explanation
Indices: 37542927--37542973 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
37542917 TGTGAAAATC
*
37542927 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGCAATG
*
37542946 TAATGCAAATGCATGGAATG
1 TAATGCAAATGCATGCAATG
37542966 -AATGCAAA
1 TAATGCAAA
37542974 AAGAAAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (20 bp):
TAATGCAAATGCATGCAATG
Found at i:37552763 original size:8 final size:8
Alignment explanation
Indices: 37552745--37552776 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
37552735 TGGAACTCAG
37552745 AGATT-AA
1 AGATTCAA
37552752 AGATTCAA
1 AGATTCAA
37552760 AGATTCAA
1 AGATTCAA
37552768 AGATTCAA
1 AGATTCAA
37552776 A
1 A
37552777 CACCAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.21
8 19 0.79
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (8 bp):
AGATTCAA
Found at i:37557778 original size:50 final size:50
Alignment explanation
Indices: 37557719--37557955 Score: 219
Period size: 50 Copynumber: 4.7 Consensus size: 50
37557709 AAAGTGATGG
* *
37557719 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGA-ACGAAAGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GAATGA
* * ** **
37557769 TCACATGTGTAGTACTATGTGCAAGCTACTATGCATACCGGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAAT-GA
** *** * *
37557820 TCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTGTTGGATATTAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GAATGA
* * * **
37557871 T--CATGTGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGTTTGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAATGA
* * *
37557919 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA
37557956 TCAAATAATA
Statistics
Matches: 145, Mismatches: 37, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
48 3 0.02
49 33 0.23
50 68 0.47
51 40 0.28
52 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAATGA
Found at i:37557945 original size:99 final size:100
Alignment explanation
Indices: 37557719--37557955 Score: 266
Period size: 99 Copynumber: 2.4 Consensus size: 100
37557709 AAAGTGATGG
* *
37557719 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAACGAAAGATCACATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGAACGAAAGAT-ACATGTGTAGTAC
* *
37557784 TATGTGCAAGCTACTATGCATACCGGATAGCTTCGA
65 TATGTGCAAGCTACTATGCATACCAGAAAGCTTCGA
* * *** ** * *
37557820 TCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTGTTGGATATTAATGGT-CATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGA-ACGAAAGATACATGTGTAGTAC
* *
37557884 TATGTGCAGGCTACTACGTG-A-ACCAGAAAG-TTTGA
65 TATGTGCAAGCTACTA--TGCATACCAGAAAGCTTCGA
*
37557919 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
37557956 TCAAATAATA
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
99 37 0.32
100 34 0.30
101 37 0.32
102 7 0.06
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (100 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGGAACGAAAGATACATGTGTAGTACT
ATGTGCAAGCTACTATGCATACCAGAAAGCTTCGA
Found at i:37573153 original size:18 final size:19
Alignment explanation
Indices: 37573130--37573178 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
37573120 GTTGTAAAGT
*
37573130 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
37573148 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
37573167 TTTAATTTTTAT
1 TTT-ATTTTTAT
37573179 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:37573158 original size:22 final size:22
Alignment explanation
Indices: 37573129--37573178 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
37573119 AGTTGTAAAG
* *
37573129 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
37573150 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
37573173 TTTTAT
1 TTTTAT
37573179 GTAAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:37573402 original size:14 final size:15
Alignment explanation
Indices: 37573379--37573407 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
37573369 AGAATTCTCT
37573379 TTGAGTTTTTCTCCA
1 TTGAGTTTTTCTCCA
37573394 TTGAG-TTTTCTCCA
1 TTGAGTTTTTCTCCA
37573408 AGAAGTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (15 bp):
TTGAGTTTTTCTCCA
Found at i:37579674 original size:12 final size:12
Alignment explanation
Indices: 37579657--37579683 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
37579647 TAAAGTTTTA
37579657 TTTTTATTTATT
1 TTTTTATTTATT
37579669 TTTTTATTTATT
1 TTTTTATTTATT
37579681 TTT
1 TTT
37579684 ACTTAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTATTTATT
Found at i:37579700 original size:22 final size:21
Alignment explanation
Indices: 37579652--37579701 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
37579642 AGTTGTAAAG
* **
37579652 TTTTATTTTTATTTATTTTTT
1 TTTTATTTTTACTTATTTAAT
37579673 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTA-TTTAAT
37579696 TTTTAT
1 TTTTAT
37579702 GTAAATATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.75
23 5 0.21
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTATTTTTACTTATTTAAT
Found at i:37584226 original size:20 final size:20
Alignment explanation
Indices: 37584196--37584246 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
37584186 AATTTAACTT
37584196 AGTCTAGCTCACTCGAGCTCA
1 AGTC-AGCTCACTCGAGCTCA
* *
37584217 AGTCAGCTCATTTGAGCTCA
1 AGTCAGCTCACTCGAGCTCA
*
37584237 ATTCAGCTCA
1 AGTCAGCTCA
37584247 ATCTTAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (20 bp):
AGTCAGCTCACTCGAGCTCA
Found at i:37586817 original size:21 final size:19
Alignment explanation
Indices: 37586745--37586818 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 19
37586735 GGGAAACGAA
37586745 AAAAAGAAATGAAAGAAAAAG
1 AAAAAGAAATG--AGAAAAAG
*
37586766 AACAAGAAAT-AG-AAAAG
1 AAAAAGAAATGAGAAAAAG
* *
37586783 AAAATGAGAGTGAGAAAAAG
1 AAAAAGA-AATGAGAAAAAG
37586803 AAAAAAGAAATTGAGA
1 -AAAAAGAAA-TGAGA
37586819 TTGAAAAAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
17 10 0.24
18 4 0.10
19 2 0.05
20 6 0.14
21 20 0.48
ACGTcount: A:0.69, C:0.01, G:0.22, T:0.08
Consensus pattern (19 bp):
AAAAAGAAATGAGAAAAAG
Found at i:37590906 original size:34 final size:34
Alignment explanation
Indices: 37590863--37590930 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
37590853 AAATCTTGTG
*
37590863 TTAGCTTGAAATGATGAAAACTGTTAATCGTGAC
1 TTAGCTTGAAATGATGAAAACTATTAATCGTGAC
37590897 TTAGCTTGAAATGATGAAAACTATTAATCGTGAC
1 TTAGCTTGAAATGATGAAAACTATTAATCGTGAC
37590931 CCAATATCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (34 bp):
TTAGCTTGAAATGATGAAAACTATTAATCGTGAC
Found at i:37592739 original size:20 final size:20
Alignment explanation
Indices: 37592714--37592755 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
37592704 AATATAATTG
*
37592714 TTATTTGCTTCT-ATAACATT
1 TTATTTACTTCTCA-AACATT
37592734 TTATTTACTTCTCAAACATT
1 TTATTTACTTCTCAAACATT
37592754 TT
1 TT
37592756 CATTCCCCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATTTACTTCTCAAACATT
Found at i:37597171 original size:14 final size:16
Alignment explanation
Indices: 37597152--37597184 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
37597142 GGCAACCCAT
37597152 ATTTATTT-ATTTT-A
1 ATTTATTTAATTTTGA
37597166 ATTTATTTAATTTTGA
1 ATTTATTTAATTTTGA
37597182 ATT
1 ATT
37597185 AAGTTTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 5 0.29
16 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTATTTAATTTTGA
Found at i:37600415 original size:18 final size:18
Alignment explanation
Indices: 37600371--37600415 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
37600361 AAATTGCTAG
37600371 TAGTT-AAATTAATTAAT
1 TAGTTAAAATTAATTAAT
*
37600388 TAGTTTAAATTAATTAATT
1 TAGTTAAAATTAATTAA-T
37600407 TA-TTAAAAT
1 TAGTTAAAAT
37600416 CTGGACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 17 0.68
19 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TAGTTAAAATTAATTAAT
Found at i:37616146 original size:20 final size:20
Alignment explanation
Indices: 37616121--37616171 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
37616111 CATTTTTGGT
*
37616121 TCATTCGAGCTCAAGTTAGC
1 TCATTCGAGCTCAAGTCAGC
37616141 TCATTCGAGCTCAAGTCAGC
1 TCATTCGAGCTCAAGTCAGC
*
37616161 ACATT-GAGCTC
1 TCATTCGAGCTC
37616172 GTTATTAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
TCATTCGAGCTCAAGTCAGC
Found at i:37619393 original size:11 final size:11
Alignment explanation
Indices: 37619377--37619405 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
37619367 CGAGATTGTA
37619377 AAAAAAATTCG
1 AAAAAAATTCG
37619388 AAAAAAATTCG
1 AAAAAAATTCG
37619399 AAAAAAA
1 AAAAAAA
37619406 AGTTTGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:37621827 original size:20 final size:20
Alignment explanation
Indices: 37621802--37621852 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
37621792 CATTTTTGGT
*
37621802 TCATTCGAGCTCAAGTTAGC
1 TCATTCGAGCTCAAGTCAGC
37621822 TCATTCGAGCTCAAGTCAGC
1 TCATTCGAGCTCAAGTCAGC
*
37621842 ACATT-GAGCTC
1 TCATTCGAGCTC
37621853 GTTATTAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
TCATTCGAGCTCAAGTCAGC
Found at i:37621996 original size:11 final size:11
Alignment explanation
Indices: 37621980--37622007 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
37621970 TTTAATTAGG
37621980 TGTTTTAAATA
1 TGTTTTAAATA
37621991 TGTTTTAAATA
1 TGTTTTAAATA
37622002 TGTTTT
1 TGTTTT
37622008 TTTTAATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (11 bp):
TGTTTTAAATA
Found at i:37622078 original size:41 final size:41
Alignment explanation
Indices: 37622029--37622159 Score: 244
Period size: 41 Copynumber: 3.2 Consensus size: 41
37622019 CCTATTTTCA
*
37622029 TACATGTTATAAATATGTCTGGACGAATTTAATGCTGCCAC
1 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
37622070 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
1 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
*
37622111 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCTAC
1 TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
37622152 TACATGTT
1 TACATGTT
37622160 TGGCCGTGTC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 88 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (41 bp):
TACATGTTATAAATATGCCTGGACGAATTTAATGCTGCCAC
Found at i:37625489 original size:22 final size:22
Alignment explanation
Indices: 37625446--37625510 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
37625436 CCTTTTTGAA
*
37625446 CCATTTCCATTTTCGTACCAAAT
1 CCATTACCA-TTTCGTACCAAAT
**
37625469 CCATTACCATTTCGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
* * *
37625491 CCCTTACCGTTTCATACCAA
1 CCATTACCATTTCGTACCAA
37625511 TTCCCAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:37631779 original size:20 final size:22
Alignment explanation
Indices: 37631754--37631803 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
37631744 GAACATGGAC
*
37631754 TAAACAGCAT-GT-AGACAAAT
1 TAAACAACATGGTAAGACAAAT
*
37631774 TAAACAATATGGTAAGACAAAT
1 TAAACAACATGGTAAGACAAAT
37631796 TAAA-AACA
1 TAAACAACA
37631804 CTTAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 8 0.32
21 5 0.20
22 12 0.48
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (22 bp):
TAAACAACATGGTAAGACAAAT
Found at i:37633996 original size:14 final size:14
Alignment explanation
Indices: 37633977--37634012 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
37633967 TCAAGTTGTG
37633977 AAAAAAAATTTGAA
1 AAAAAAAATTTGAA
*
37633991 AAAAAAATTTTGAA
1 AAAAAAAATTTGAA
37634005 AAAAAAAA
1 AAAAAAAA
37634013 GAGAGCTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTTGAA
Found at i:37642725 original size:17 final size:17
Alignment explanation
Indices: 37642703--37642735 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
37642693 AAAGAAAGAA
37642703 AAAAATTGAAAAAAAAT
1 AAAAATTGAAAAAAAAT
37642720 AAAAATTGAAAAAAAA
1 AAAAATTGAAAAAAAA
37642736 GAGGATTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAATTGAAAAAAAAT
Found at i:37644631 original size:12 final size:12
Alignment explanation
Indices: 37644614--37644640 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
37644604 ATCGTCAAGC
37644614 CAAGGTGAGTAT
1 CAAGGTGAGTAT
37644626 CAAGGTGAGTAT
1 CAAGGTGAGTAT
37644638 CAA
1 CAA
37644641 ATTGAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (12 bp):
CAAGGTGAGTAT
Found at i:37648164 original size:11 final size:10
Alignment explanation
Indices: 37648139--37648199 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
37648129 ACCAATAAAA
37648139 TAAA-TGAGC
1 TAAATTGAGC
*
37648148 TGAATTGTAGC
1 TAAATTG-AGC
37648159 TAAATTGAGC
1 TAAATTGAGC
**
37648169 TTGATTGAGC
1 TAAATTGAGC
37648179 TGAAA-TGAGC
1 T-AAATTGAGC
*
37648189 TCAATTGAGC
1 TAAATTGAGC
37648199 T
1 T
37648200 GGTCGGAGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:37648200 original size:20 final size:20
Alignment explanation
Indices: 37648140--37648200 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
37648130 CCAATAAAAT
*
37648140 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
**
37648160 AAATTGAGCTTGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
37648181 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
37648201 GTCGGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:37648209 original size:30 final size:30
Alignment explanation
Indices: 37648144--37648250 Score: 85
Period size: 30 Copynumber: 3.5 Consensus size: 30
37648134 TAAAATAAAT
* *
37648144 GAGCTGAATTGTAGCTAAATTGAGCTTGATT
1 GAGCTGAAATG-AGCTAAATTGAGCTTGATG
* *
37648175 GAGCTGAAATGAGCTCAATTGAGC-TGGTCG
1 GAGCTGAAATGAGCTAAATTGAGCTTGAT-G
* * *
37648205 GAGCTGAAACGAGCTAGAA--AAGCTAAGATG
1 GAGCTGAAATGAGCTA-AATTGAGCT-TGATG
37648235 GAGCTGAAATTGAGCT
1 GAGCTGAAA-TGAGCT
37648251 GAAGTTAGCT
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
29 6 0.10
30 36 0.59
31 19 0.31
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.24
Consensus pattern (30 bp):
GAGCTGAAATGAGCTAAATTGAGCTTGATG
Found at i:37649736 original size:18 final size:18
Alignment explanation
Indices: 37649696--37649736 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
37649686 GCTGCTAGTT
* *
37649696 AAATTAATCAATTAGTTT
1 AAATTAATCAATTAATTA
*
37649714 TAATTAATCAATTAATTA
1 AAATTAATCAATTAATTA
37649732 AAATT
1 AAATT
37649737 TGGACATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
AAATTAATCAATTAATTA
Found at i:37655762 original size:20 final size:20
Alignment explanation
Indices: 37655739--37655785 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
37655729 GGGATGAGGT
37655739 TGAGCTGAATTGAACTCGAA
1 TGAGCTGAATTGAACTCGAA
* * *
37655759 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAACTCGAA
37655779 TGAGCTG
1 TGAGCTG
37655786 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAACTCGAA
Found at i:37657016 original size:13 final size:12
Alignment explanation
Indices: 37656984--37657017 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
37656974 TTTTCTTTCA
*
37656984 TTTCTTTTTCTT
1 TTTCATTTTCTT
37656996 TTTCATTTTCTT
1 TTTCATTTTCTT
*
37657008 TTTCAATTTC
1 TTTCATTTTC
37657018 ATTACAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:37657020 original size:18 final size:16
Alignment explanation
Indices: 37656965--37657011 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 16
37656955 TATCTCACAC
*
37656965 TCATCTTCTTTTTCTT
1 TCATTTTCTTTTTCTT
37656981 TCA-TTTCTTTTTCTTTT
1 TCATTTTCTTTTTC--TT
37656998 TCATTTTCTTTTTC
1 TCATTTTCTTTTTC
37657012 AATTTCATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 9 0.33
16 3 0.11
17 5 0.19
18 10 0.37
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATTTTCTTTTTCTT
Found at i:37660000 original size:20 final size:20
Alignment explanation
Indices: 37659977--37660023 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
37659967 GGGATGAGGT
37659977 TGAGCTGAATTGAACTCGAA
1 TGAGCTGAATTGAACTCGAA
* * *
37659997 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAACTCGAA
37660017 TGAGCTG
1 TGAGCTG
37660024 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAACTCGAA
Found at i:37674303 original size:20 final size:20
Alignment explanation
Indices: 37674280--37674326 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
37674270 GGGATGAGGT
37674280 TGAGCTGAATTGAACTCGAA
1 TGAGCTGAATTGAACTCGAA
* * *
37674300 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAACTCGAA
37674320 TGAGCTG
1 TGAGCTG
37674327 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAACTCGAA
Found at i:37675553 original size:13 final size:12
Alignment explanation
Indices: 37675521--37675554 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
37675511 TTTTCTTTCA
*
37675521 TTTCTTTTTCTT
1 TTTCATTTTCTT
37675533 TTTCATTTTCTT
1 TTTCATTTTCTT
*
37675545 TTTCAATTTC
1 TTTCATTTTC
37675555 ATTACAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:37675557 original size:18 final size:16
Alignment explanation
Indices: 37675502--37675548 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 16
37675492 TATCTCACAC
*
37675502 TCATCTTCTTTTTCTT
1 TCATTTTCTTTTTCTT
37675518 TCA-TTTCTTTTTCTTTT
1 TCATTTTCTTTTTC--TT
37675535 TCATTTTCTTTTTC
1 TCATTTTCTTTTTC
37675549 AATTTCATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 9 0.33
16 3 0.11
17 5 0.19
18 10 0.37
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATTTTCTTTTTCTT
Found at i:37683991 original size:29 final size:29
Alignment explanation
Indices: 37683957--37684029 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
37683947 ATGTATTAGT
* *
37683957 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
37683986 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
37684015 TTAGGACATATTTAA
1 TTAGGACATATTTAA
37684030 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:37687663 original size:22 final size:22
Alignment explanation
Indices: 37687604--37687663 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
37687594 CCATTTCCAT
* *
37687604 TTTCGTACCAAATCCATTACCA
1 TTTCATACCAAATCCCTTACCA
** *
37687626 TTTCATTTCAAATCCCTTACCG
1 TTTCATACCAAATCCCTTACCA
*
37687648 TTTCATACCAATTCCC
1 TTTCATACCAAATCCC
37687664 AAATACCAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.27, C:0.33, G:0.03, T:0.37
Consensus pattern (22 bp):
TTTCATACCAAATCCCTTACCA
Found at i:37690847 original size:15 final size:14
Alignment explanation
Indices: 37690811--37690852 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
37690801 TCTATTGAAC
37690811 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
37690825 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
37690839 GAGTGAAAAGAAAA
1 GAG-AAAAAGAAAA
37690853 GGAAAGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:37694470 original size:20 final size:20
Alignment explanation
Indices: 37694424--37694470 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
37694414 AGCTCATTTC
*
37694424 CAGCTCACTTGAGCTCAAGT
1 CAGCTCACTTGAGATCAAGT
* *
37694444 CAACTCA-TTCGAGATCAATT
1 CAGCTCACTT-GAGATCAAGT
37694464 CAGCTCA
1 CAGCTCA
37694471 ATTTTAACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (20 bp):
CAGCTCACTTGAGATCAAGT
Found at i:37703280 original size:17 final size:17
Alignment explanation
Indices: 37703255--37703295 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
37703245 CCGTATGCAA
37703255 TTTTT-TTTTCAAATTT
1 TTTTTCTTTTCAAATTT
* *
37703271 TTTTTCTTTTCGATTTT
1 TTTTTCTTTTCAAATTT
37703288 TTTTTCTT
1 TTTTTCTT
37703296 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTCAAATTT
Found at i:37717920 original size:13 final size:13
Alignment explanation
Indices: 37717902--37717927 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37717892 ATTGAGTTTA
37717902 AATGTGTCTTAGT
1 AATGTGTCTTAGT
37717915 AATGTGTCTTAGT
1 AATGTGTCTTAGT
37717928 TCATACATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
AATGTGTCTTAGT
Found at i:37719555 original size:21 final size:21
Alignment explanation
Indices: 37719529--37719569 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
37719519 CCAAATACCT
37719529 TACCATTTCATACCAATTCCA
1 TACCATTTCATACCAATTCCA
*
37719550 TACCATTTCGTACCAATTCC
1 TACCATTTCATACCAATTCC
37719570 CAAATACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.02, T:0.34
Consensus pattern (21 bp):
TACCATTTCATACCAATTCCA
Found at i:37721862 original size:41 final size:41
Alignment explanation
Indices: 37721806--37721912 Score: 180
Period size: 41 Copynumber: 2.6 Consensus size: 41
37721796 TTTAATATGT
* *
37721806 CGAA-TTAATGCTGCCACTACATGTTATAAATGTGTCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
37721846 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
*
37721887 CGAATTTAATGCTGCTACTACATGTT
1 CGAATTTAATGCTGCCACTACATGTT
37721913 TGGCCGAATT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
40 4 0.06
41 59 0.94
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
Found at i:37728047 original size:17 final size:17
Alignment explanation
Indices: 37727997--37728047 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
37727987 TCAAATTAGG
* *
37727997 TTCGTGAATTAAAAAAA
1 TTCGTGCATAAAAAAAA
*
37728014 TTCGTGCAAAAAAAAAA
1 TTCGTGCATAAAAAAAA
37728031 TTCGTGCATAAAAAAAA
1 TTCGTGCATAAAAAAAA
37728048 AGAGGTTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (17 bp):
TTCGTGCATAAAAAAAA
Done.