Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold166
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: 2719372
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17868 characters in sequence are not A, C, G, or T
File 12 of 18
Found at i:2068262 original size:13 final size:13
Alignment explanation
Indices: 2068244--2068269 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2068234 ACATATTTAT
2068244 GTGTATCGATACA
1 GTGTATCGATACA
2068257 GTGTATCGATACA
1 GTGTATCGATACA
2068270 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:2070287 original size:145 final size:143
Alignment explanation
Indices: 2070021--2070430 Score: 480
Period size: 145 Copynumber: 2.8 Consensus size: 143
2070011 CAATATTTAT
** * *
2070021 CATTTTTGTTTCTTTTAGGGTTACCGTGATACTTTAATGTCGAAGGTATACACTGAGGGTATTTT
1 CATTTTTGAGTCTTTTAGGGTTACCGTGATACTTTAATGTCGAAGGTATAC-CTAAGAGTATTTT
* * *
2070086 AGTAATTTTTTAAGAACCAAGTCTTAGGTAACCATCAAGATGCTTTTATGCTAAGGGTGCATATT
65 AGTAATTTTTT-AGAACCGAGTCTTAGGTAACCATCAGGATGCTTTTATGCCAAGGGTGCATATT
2070151 TAGGATAGGGTCACC
129 TAGGATAGGGTCACC
* * * *
2070166 CATTTTTGAGTCTTTTAGAGTTACCGGGATACTTTTATGTCGAAGGTATATCCTAAGAGTGTTTT
1 CATTTTTGAGTCTTTTAGGGTTACCGTGATACTTTAATGTCGAAGGTATA-CCTAAGAGTATTTT
* * * *
2070231 AGTAATTTTCTTAGAATCGAGTCCTAGGTCACCACCAGGATGCTTTTATGCCAAGGGTGCATATT
65 AGTAATTTT-TTAGAACCGAGTCTTAGGTAACCATCAGGATGCTTTTATGCCAAGGGTGCATATT
*
2070296 TAGGATAGGTTCACC
129 TAGGATAGGGTCACC
** * * * * * * *
2070311 CATTTTAAAGTCCTTGAGGGTTGCCGTGATGCTTTCATATCGAAGGTATACTTATAGGAGTATTT
1 CATTTTTGAGTCTTTTAGGGTTACCGTGATACTTTAATGTCGAAGGTATACCTA-A-GAGTATTT
*** *
2070376 TCA-TAATTTTTTTAGAACCGAGTCTTAGGTTGTCATCGGGATGCTTTTATGCCAA
64 T-AGTAA-TTTTTTAGAACCGAGTCTTAGGTAACCATCAGGATGCTTTTATGCCAA
2070431 AGATATGTAT
Statistics
Matches: 224, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
144 3 0.01
145 165 0.74
146 51 0.23
147 5 0.02
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (143 bp):
CATTTTTGAGTCTTTTAGGGTTACCGTGATACTTTAATGTCGAAGGTATACCTAAGAGTATTTTA
GTAATTTTTTAGAACCGAGTCTTAGGTAACCATCAGGATGCTTTTATGCCAAGGGTGCATATTTA
GGATAGGGTCACC
Found at i:2071983 original size:10 final size:10
Alignment explanation
Indices: 2071970--2072025 Score: 67
Period size: 10 Copynumber: 5.5 Consensus size: 10
2071960 AATAAAAAAT
*
2071970 AAAAAAACAA
1 AAAAAAAGAA
*
2071980 AAAAAGAGAA
1 AAAAAAAGAA
2071990 AAAAAAGAGAA
1 AAAAAA-AGAA
**
2072001 AAAATGAGAA
1 AAAAAAAGAA
2072011 AAAAAAAGAA
1 AAAAAAAGAA
2072021 AAAAA
1 AAAAA
2072026 GCATGGAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 30 0.79
11 8 0.21
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:2071992 original size:11 final size:11
Alignment explanation
Indices: 2071978--2072025 Score: 73
Period size: 10 Copynumber: 4.5 Consensus size: 11
2071968 ATAAAAAAAC
2071978 AAAAAAAGAGA
1 AAAAAAAGAGA
2071989 AAAAAAAGAG-
1 AAAAAAAGAGA
*
2071999 AAAAAATGAGA
1 AAAAAAAGAGA
2072010 AAAAAAA-AGA
1 AAAAAAAGAGA
2072020 AAAAAA
1 AAAAAA
2072026 GCATGGAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 18 0.53
11 16 0.47
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:2072002 original size:21 final size:20
Alignment explanation
Indices: 2071970--2072026 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 20
2071960 AATAAAAAAT
*
2071970 AAAAAAACAAAAAAAGAGAA
1 AAAAAAAGAAAAAAAGAGAA
*
2071990 AAAAAAGAGAAAAAATGAGAA
1 AAAAAA-AGAAAAAAAGAGAA
2072011 AAAAAAAGAAAAAAAG
1 AAAAAAAGAAAAAAAG
2072027 CATGGAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAGAGAA
Found at i:2072080 original size:18 final size:19
Alignment explanation
Indices: 2072059--2072109 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
2072049 TAGATAGTAA
2072059 GAAAAAATAAAGAAAA-AT
1 GAAAAAATAAAGAAAAGAT
*
2072077 GAAAAAA-AGAGAAAAGAT
1 GAAAAAATAAAGAAAAGAT
**
2072095 GAGGAAATAAAGAAA
1 GAAAAAATAAAGAAA
2072110 TGCTGTATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 7 0.26
18 14 0.52
19 6 0.22
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.08
Consensus pattern (19 bp):
GAAAAAATAAAGAAAAGAT
Found at i:2072863 original size:109 final size:111
Alignment explanation
Indices: 2072646--2072967 Score: 359
Period size: 109 Copynumber: 2.9 Consensus size: 111
2072636 AAAATTAAAT
* * * * * * *
2072646 TTGTCTGATTTTCAAAGAAATTCATGTTTTATACTACCTAATCCATTCATGCTTAGGAAAATAAG
1 TTGTCTGATTTTCAAAAAAATTCATATTTTATACAACCTGATCCATTCGTGCTTACGAAAAT-GG
*
2072711 GA-ATGTATCTTATTAGTTTTGAAATTTTTAAGACAACGACATCAAA
65 GACATGTATCTTATTAGTTTTGAAATTTTTGAGACAACGACATCAAA
2072757 -TGTCTGATTTT-AAAAAAATTCATATTTTATACAACCTGATCCATTCGTGCTTACGAAAATGGG
1 TTGTCTGATTTTCAAAAAAATTCATATTTTATACAACCTGATCCATTCGTGCTTACGAAAATGGG
* * * *
2072820 ACATGTATCTTATTAGTTTTAAAATTTTTGAGGCAATGGCATCAAA
66 ACATGTATCTTATTAGTTTTGAAATTTTTGAGACAACGACATCAAA
* * ** * * * *
2072866 TTTGTCTGATTTTCAAAAAATTTCATATCTTATATGACTTGATCCATTTGTACGTAGCG-AAATG
1 -TTGTCTGATTTTCAAAAAAATTCATATTTTATACAACCTGATCCATTCGTGCTTA-CGAAAATG
* * *
2072930 GG-CATGCAT-TCTCTTAGTTTTGAAATTTTTGAGCCAAC
64 GGACATGTATCT-TATTAGTTTTGAAATTTTTGAGACAAC
2072968 CAAAGTTTTT
Statistics
Matches: 180, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
108 3 0.02
109 82 0.46
110 12 0.07
111 40 0.22
112 41 0.23
113 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (111 bp):
TTGTCTGATTTTCAAAAAAATTCATATTTTATACAACCTGATCCATTCGTGCTTACGAAAATGGG
ACATGTATCTTATTAGTTTTGAAATTTTTGAGACAACGACATCAAA
Found at i:2078077 original size:14 final size:13
Alignment explanation
Indices: 2078058--2078142 Score: 73
Period size: 14 Copynumber: 6.4 Consensus size: 13
2078048 TTTTTGAGAT
*
2078058 AAAAAATATATATA
1 AAAAAATA-AAATA
2078072 AAAAAATAAAATA
1 AAAAAATAAAATA
*
2078085 AAATAATAATAATA
1 AAAAAATAA-AATA
* *
2078099 ATAACATAAAA-A
1 AAAAAATAAAATA
* *
2078111 ATAAAATAGAATA
1 AAAAAATAAAATA
*
2078124 AAAATATAATAATA
1 AAAAAATAA-AATA
2078138 AAAAA
1 AAAAA
2078143 TGTTCCACTG
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.18
13 21 0.37
14 26 0.46
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:2078084 original size:5 final size:5
Alignment explanation
Indices: 2078074--2078126 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
2078064 TATATATAAA
* *
2078074 AAAAT AAAAT AAAAT AATAAT AATAAT AACATAA AAAAT AAAAT AGAAT
1 AAAAT AAAAT AAAAT AA-AAT AA-AAT AA-A-AT AAAAT AAAAT AAAAT
2078123 AAAA
1 AAAA
2078127 ATATAATAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
5 25 0.61
6 13 0.32
7 3 0.07
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:2078113 original size:34 final size:31
Alignment explanation
Indices: 2078059--2078143 Score: 102
Period size: 34 Copynumber: 2.7 Consensus size: 31
2078049 TTTTGAGATA
2078059 AAAAATAT-AT-ATAAAAAAATAAAATAAAAT
1 AAAAATATAATAAT-AAAAAATAAAATAAAAT
* *
2078089 AATAATAATAATAACATAAAAAATAAAATAGAAT
1 AAAAAT-ATAAT-A-ATAAAAAATAAAATAAAAT
2078123 AAAAATATAATAATAAAAAAT
1 AAAAATATAATAATAAAAAAT
2078144 GTTCCACTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
30 5 0.11
31 11 0.23
32 3 0.06
33 5 0.11
34 21 0.45
35 2 0.04
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.24
Consensus pattern (31 bp):
AAAAATATAATAATAAAAAATAAAATAAAAT
Found at i:2078659 original size:51 final size:50
Alignment explanation
Indices: 2078563--2078660 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 50
2078553 AGATAACTAT
* * **
2078563 AGCAAAAGAAAAAGCAAAATAGCTATAGCAAAAGAGAAATGGACAGCTGC
1 AGCAAAAGAAAAAACAAAATAGCAATAGCAAAAGAGAAACAGACAGCTGC
* *
2078613 AGCAAAAGAAAAAAACAAAGTAG-AAGTAGCGAAAGAGAAACAGACAGC
1 AGCAAAAG-AAAAAACAAAATAGCAA-TAGCAAAAGAGAAACAGACAGC
2078661 AAAGCAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 9 0.22
51 31 0.77
ACGTcount: A:0.57, C:0.13, G:0.22, T:0.07
Consensus pattern (50 bp):
AGCAAAAGAAAAAACAAAATAGCAATAGCAAAAGAGAAACAGACAGCTGC
Found at i:2078732 original size:35 final size:35
Alignment explanation
Indices: 2078693--2078759 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
2078683 AACGAAATAG
*
2078693 CAATAGTAAGAGGGAGAAAGTAAGAAATGAAACAA
1 CAATAGTAAGAGGGAGAAAGCAAGAAATGAAACAA
2078728 CAATAGTAAGAGGGAGAAAGCAAGAAATGAAA
1 CAATAGTAAGAGGGAGAAAGCAAGAAATGAAA
2078760 TAGCAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.57, C:0.06, G:0.27, T:0.10
Consensus pattern (35 bp):
CAATAGTAAGAGGGAGAAAGCAAGAAATGAAACAA
Found at i:2086634 original size:20 final size:20
Alignment explanation
Indices: 2086580--2086634 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
2086570 ATTGGGCTTA
* *
2086580 ATGTATCGATACATTTTACC
1 ATGTATCGATACAATTCACC
* *
2086600 ATGTATC-ATTGCAATTCATC
1 ATGTATCGA-TACAATTCACC
2086620 ATGTATCGATACAAT
1 ATGTATCGATACAAT
2086635 GTATCGATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:2086636 original size:13 final size:13
Alignment explanation
Indices: 2086620--2086644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2086610 GCAATTCATC
2086620 ATGTATCGATACA
1 ATGTATCGATACA
2086633 ATGTATCGATAC
1 ATGTATCGATAC
2086645 TAAGTGAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2086730 original size:13 final size:13
Alignment explanation
Indices: 2086712--2086736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2086702 TACTATGAAC
2086712 ATGTATCGATACA
1 ATGTATCGATACA
2086725 ATGTATCGATAC
1 ATGTATCGATAC
2086737 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2089518 original size:20 final size:20
Alignment explanation
Indices: 2089493--2089539 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2089483 GGTTTTCTAG
2089493 ATGTATCAGTACATTATTCA
1 ATGTATCAGTACATTATTCA
2089513 ATGTATCAGTACATTATTCA
1 ATGTATCAGTACATTATTCA
2089533 ATGTATC
1 ATGTATC
2089540 GACACATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCAGTACATTATTCA
Found at i:2090017 original size:51 final size:51
Alignment explanation
Indices: 2089962--2090061 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
2089952 GCCTTTATCC
* * *
2089962 TTATTGATTACTATTAGGATTGTGATTAGGATTGTCCTTGTTTAGTTAGGA
1 TTATTGATTACTATTAGGACTGTGATTAGAATTGTCCTTGTTTAATTAGGA
*
2090013 TTATTGATTACTATTAGGACTGTGATTAGAATTGTCCTTTTTTAATTAG
1 TTATTGATTACTATTAGGACTGTGATTAGAATTGTCCTTGTTTAATTAG
2090062 TACTTTACAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.48
Consensus pattern (51 bp):
TTATTGATTACTATTAGGACTGTGATTAGAATTGTCCTTGTTTAATTAGGA
Found at i:2090493 original size:16 final size:17
Alignment explanation
Indices: 2090468--2090521 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
2090458 AATCAATAAC
*
2090468 AAAATAAAAAGAAGAAA
1 AAAAGAAAAAGAAGAAA
2090485 AAAAGAAAAA-AAG-AA
1 AAAAGAAAAAGAAGAAA
*
2090500 AAAGGAAAAAGAAGAAA
1 AAAAGAAAAAGAAGAAA
2090517 AAAAG
1 AAAAG
2090522 TGTTCTAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 11 0.34
16 6 0.19
17 15 0.47
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAGAAGAAA
Found at i:2090495 original size:7 final size:8
Alignment explanation
Indices: 2090468--2090521 Score: 65
Period size: 8 Copynumber: 6.6 Consensus size: 8
2090458 AATCAATAAC
*
2090468 AAAATAAA
1 AAAAGAAA
2090476 AAGAAGAAA
1 AA-AAGAAA
2090485 AAAAGAAA
1 AAAAGAAA
2090493 AAAAG-AA
1 AAAAGAAA
*
2090500 AAAGGAAA
1 AAAAGAAA
2090508 AAGAAGAAA
1 AA-AAGAAA
2090517 AAAAG
1 AAAAG
2090522 TGTTCTAGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.15
8 20 0.50
9 14 0.35
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAAGAAA
Found at i:2090684 original size:27 final size:29
Alignment explanation
Indices: 2090610--2090684 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 29
2090600 TTTTGTTTCC
*
2090610 TTCTTGTTGATTTCTCTT-TCTTTGATAT
1 TTCTTGTTGATTTCACTTCTCTTTGATAT
* * *
2090638 TTCTTGCTAATTTCAATTCTC-TT-ATAT
1 TTCTTGTTGATTTCACTTCTCTTTGATAT
*
2090665 TTCTTGTTGATTTCGCTTCT
1 TTCTTGTTGATTTCACTTCT
2090685 TTGAACTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
27 20 0.53
28 16 0.42
29 2 0.05
ACGTcount: A:0.13, C:0.17, G:0.09, T:0.60
Consensus pattern (29 bp):
TTCTTGTTGATTTCACTTCTCTTTGATAT
Found at i:2092484 original size:13 final size:13
Alignment explanation
Indices: 2092466--2092490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2092456 ATATTGCACA
2092466 GTATCGATACATT
1 GTATCGATACATT
2092479 GTATCGATACAT
1 GTATCGATACAT
2092491 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2092538 original size:16 final size:16
Alignment explanation
Indices: 2092517--2092568 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
2092507 ACTTGTTAAG
2092517 AATGCGAATGCACATT
1 AATGCGAATGCACATT
* ** *
2092533 AATGCG--TTCTTATG
1 AATGCGAATGCACATT
2092547 AATGCGAATGCACATT
1 AATGCGAATGCACATT
2092563 AATGCG
1 AATGCG
2092569 TTCTTATGAA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 10 0.38
16 16 0.62
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (16 bp):
AATGCGAATGCACATT
Found at i:2092550 original size:30 final size:30
Alignment explanation
Indices: 2092516--2092578 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
2092506 TACTTGTTAA
2092516 GAATGCGAATGCACATTAATGCGTTCTTAT
1 GAATGCGAATGCACATTAATGCGTTCTTAT
2092546 GAATGCGAATGCACATTAATGCGTTCTTAT
1 GAATGCGAATGCACATTAATGCGTTCTTAT
2092576 GAA
1 GAA
2092579 AATGAATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (30 bp):
GAATGCGAATGCACATTAATGCGTTCTTAT
Found at i:2092586 original size:30 final size:30
Alignment explanation
Indices: 2092521--2092586 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
2092511 GTTAAGAATG
**
2092521 CGAATGCACATTAATGCGTTCTTATGAATG
1 CGAATGCACATTAATGCGTTCTTATGAAAA
2092551 CGAATGCACATTAATGCGTTCTTATGAAAA
1 CGAATGCACATTAATGCGTTCTTATGAAAA
*
2092581 TGAATG
1 CGAATG
2092587 TACGTGAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (30 bp):
CGAATGCACATTAATGCGTTCTTATGAAAA
Found at i:2092597 original size:30 final size:30
Alignment explanation
Indices: 2092521--2092597 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
2092511 GTTAAGAATG
* **
2092521 CGAATGCACATTAATGCGTTCTTATGAATG
1 CGAATGCACATGAATGCGTTCTTATGAAAA
*
2092551 CGAATGCACATTAATGCGTTCTTATGAAAA
1 CGAATGCACATGAATGCGTTCTTATGAAAA
* * *
2092581 TGAATGTACGTGAATGC
1 CGAATGCACATGAATGC
2092598 ATATGTTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (30 bp):
CGAATGCACATGAATGCGTTCTTATGAAAA
Found at i:2093838 original size:20 final size:20
Alignment explanation
Indices: 2093737--2093848 Score: 70
Period size: 20 Copynumber: 5.7 Consensus size: 20
2093727 GTATCAATAC
*
2093737 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTAAA
* ***
2093757 TGTATCGATAGATGTCTCAAA
1 TGTATCGATACATAAGT-AAA
* ** *
2093778 TGTATCGATACAAAACCACA
1 TGTATCGATACATAAGTAAA
*
2093798 TGTATTCTG-T--A-AAGAAAA
1 TGTA-TC-GATACATAAGTAAA
2093816 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAAGTAAA
*
2093836 TGTATCGCTACAT
1 TGTATCGATACAT
2093849 GCTCACGATT
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
16 1 0.01
17 3 0.04
18 8 0.12
19 2 0.03
20 37 0.54
21 17 0.25
22 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAAGTAAA
Found at i:2104819 original size:20 final size:20
Alignment explanation
Indices: 2104794--2104832 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2104784 TTGAAGCTTG
*
2104794 TTTGGAGCTTGTTTCCACTA
1 TTTGGAGCTTGTTCCCACTA
2104814 TTTGGAGCTTGTTCCCACT
1 TTTGGAGCTTGTTCCCACT
2104833 CTTTCATGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (20 bp):
TTTGGAGCTTGTTCCCACTA
Found at i:2110669 original size:50 final size:50
Alignment explanation
Indices: 2110300--2110693 Score: 205
Period size: 50 Copynumber: 7.9 Consensus size: 50
2110290 AGTGTGCATT
*
2110300 TTTGACTCTATAAGA-TTCGACCCTCTTATTAGGTGCTAGCTAGTGT-GAAC
1 TTTGACTCTATAAGACTT-GACCTTCTTATTAGGTGCTAGCTAGTGTAG-AC
* * * * * **
2110350 TTTGACTCCAT-AGGCTT-AGTCTTCTTATCAGGTGCCAATTAGTGTAGAC
1 TTTGACTCTATAAGACTTGA-CCTTCTTATTAGGTGCTAGCTAGTGTAGAC
* * * * * * * *
2110399 TTTGGCTCTATAGGAGTTGA-CTTTTCTATCAAGTGCCAGCTAGTGTCGAC
1 TTTGACTCTATAAGACTTGACCTTCT-TATTAGGTGCTAGCTAGTGTAGAC
* * * * *
2110449 TTTAACTCTATAGGACTTGACTTTCCTATTAGGTGCTAGCTAGTGTTG-C
1 TTTGACTCTATAAGACTTGACCTTCTTATTAGGTGCTAGCTAGTGTAGAC
* * * * ** * * * *
2110498 TTTGATTTTAT-AGTACTTGACATTTTCTATTAAATGCTAGTTATTATGGAC
1 TTTGACTCTATAAG-ACTTGACCTTCT-TATTAGGTGCTAGCTAGTGTAGAC
* * * * * * * *
2110549 TTTTGACTTTATAAGATTTGACCATCCTATTAGGTGCTAGCTACTATGGAT
1 -TTTGACTCTATAAGACTTGACCTTCTTATTAGGTGCTAGCTAGTGTAGAC
* * * *
2110600 TTTGACT-TGAT-AGAGCTTAACCTTCTTATCAAGTGCCAGCTAGTGTAGAC
1 TTTGACTCT-ATAAGA-CTTGACCTTCTTATTAGGTGCTAGCTAGTGTAGAC
* * * *
2110650 TTTGACTCTATAAGACTTAATCC-TCCTACTAAGTGCTAGCTAGT
1 TTTGACTCTATAAGACTTGA-CCTTCTTATTAGGTGCTAGCTAGT
2110694 ATGGACTCTA
Statistics
Matches: 260, Mismatches: 67, Indels: 34
0.72 0.19 0.09
Matches are distributed among these distances:
48 2 0.01
49 59 0.23
50 151 0.58
51 29 0.11
52 17 0.07
53 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (50 bp):
TTTGACTCTATAAGACTTGACCTTCTTATTAGGTGCTAGCTAGTGTAGAC
Found at i:2110831 original size:53 final size:52
Alignment explanation
Indices: 2110768--2110898 Score: 140
Period size: 53 Copynumber: 2.5 Consensus size: 52
2110758 ACTTCATAAG
* * * * *
2110768 AGCCAATTAGTTAGAACTAATCTACATGA-ATTATTAGGCTTAATCTTAATAT
1 AGCCAATTAGTCAGAACTAACCTAC-TAACATCATTACGCTTAATCTTAATAT
* *
2110820 AAGCCAATTAGTCGGAGCTAACCTACTAACATCATTACGCTTAATCTTAATAT
1 -AGCCAATTAGTCAGAACTAACCTACTAACATCATTACGCTTAATCTTAATAT
*
2110873 AGCCTAATTAG-CTGAAACTAACCTAC
1 AGCC-AATTAGTCAG-AACTAACCTAC
2110899 CAATGTCATT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
52 8 0.12
53 58 0.88
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (52 bp):
AGCCAATTAGTCAGAACTAACCTACTAACATCATTACGCTTAATCTTAATAT
Found at i:2110908 original size:53 final size:52
Alignment explanation
Indices: 2110800--2110951 Score: 153
Period size: 53 Copynumber: 2.8 Consensus size: 52
2110790 TACATGAATT
* * *
2110800 ATTAGGCTTAATCTTAATATAAGCCAATTAGTCGGAGCTAACCTACTAACATC
1 ATTAGGCTTAATCTTAATATAAGCCAATTAGT-GAAACTAACCTACCAACATC
* **
2110853 ATTACGCTTAATCTTAATAT-AGCCTAATTAGCTGAAACTAACCTACCAATGTC
1 ATTAGGCTTAATCTTAATATAAGCC-AATTAG-TGAAACTAACCTACCAACATC
* * ** *
2110906 ATTGGGCTTATATCTTAGTATGGGCCAATTAGTTGAAACCAACCTA
1 ATTAGGCTTA-ATCTTAATATAAGCCAATTAG-TGAAACTAACCTA
2110952 TCGGCATCAT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
52 4 0.05
53 48 0.58
54 28 0.34
55 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (52 bp):
ATTAGGCTTAATCTTAATATAAGCCAATTAGTGAAACTAACCTACCAACATC
Found at i:2120217 original size:13 final size:13
Alignment explanation
Indices: 2120199--2120223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2120189 AGATTGCACA
2120199 GTATCGATACATT
1 GTATCGATACATT
2120212 GTATCGATACAT
1 GTATCGATACAT
2120224 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2120255 original size:21 final size:20
Alignment explanation
Indices: 2120211--2120263 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2120201 ATCGATACAT
**
2120211 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
2120231 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAA-AA
*
2120252 TGTATTGATACA
1 TGTATCGATACA
2120264 GGTCATTGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:2120329 original size:19 final size:20
Alignment explanation
Indices: 2120305--2120352 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2120295 CTTAACTGTT
*
2120305 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
2120324 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
2120344 TGTATCGAT
1 TGTATCGAT
2120353 GCATTGGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:2125796 original size:13 final size:13
Alignment explanation
Indices: 2125778--2125802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2125768 AGATTGCACA
2125778 GTATCGATACATT
1 GTATCGATACATT
2125791 GTATCGATACAT
1 GTATCGATACAT
2125803 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2125834 original size:21 final size:20
Alignment explanation
Indices: 2125790--2125842 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2125780 ATCGATACAT
* **
2125790 TGTATCGATACATGACCAAA
1 TGTATCGATACTTGAAAAAA
2125810 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACTTGAAAA-AA
2125831 TGTATCGATACT
1 TGTATCGATACT
2125843 GGTCATTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (20 bp):
TGTATCGATACTTGAAAAAA
Found at i:2125927 original size:20 final size:20
Alignment explanation
Indices: 2125884--2125935 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2125874 CTTAACTGTT
*
2125884 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
2125903 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
2125923 TGTATCGATACAT
1 TGTATCGATACAT
2125936 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:2130848 original size:19 final size:20
Alignment explanation
Indices: 2130821--2130870 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2130811 CAATATATTC
2130821 ATCGATACATGCTC-ATTGT
1 ATCGATACATGCTCAATTGT
* *
2130840 ATTGATACATACTCAATTGT
1 ATCGATACATGCTCAATTGT
2130860 ATCGATACATG
1 ATCGATACATG
2130871 AAACTAGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (20 bp):
ATCGATACATGCTCAATTGT
Found at i:2133179 original size:30 final size:28
Alignment explanation
Indices: 2133145--2133200 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 28
2133135 TCGATGATTA
2133145 GAAAATAAATCGAGATTGGAGTATCCCCTC
1 GAAAAT-AA-CGAGATTGGAGTATCCCCTC
*
2133175 GAAAATAACGGGATTGGAGTATCCCC
1 GAAAATAACGAGATTGGAGTATCCCC
2133201 AATTATGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 17 0.68
29 2 0.08
30 6 0.24
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (28 bp):
GAAAATAACGAGATTGGAGTATCCCCTC
Found at i:2133186 original size:78 final size:79
Alignment explanation
Indices: 2133082--2133282 Score: 235
Period size: 78 Copynumber: 2.6 Consensus size: 79
2133072 AATAACAGGG
* * * * *
2133082 TTGGAGTGTTCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG
*
2133146 AAAATAAA-TCGAGA
65 AAAATAAAGCCGAGA
* * * * *
2133160 TTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * *
2133225 GAATAAAGCCGGGG
66 AAATAAAGCCGAGA
* *
2133239 TTGGAGTATCCCCTTGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGAT
2133283 GAAATAACGA
Statistics
Matches: 102, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
77 1 0.01
78 59 0.58
79 42 0.41
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (79 bp):
TTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAATAAAGCCGAGA
Found at i:2133274 original size:28 final size:28
Alignment explanation
Indices: 2133234--2133310 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
2133224 GGAATAAAGC
* *
2133234 CGGGGTTGGAGTATCCCC-TTGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAT-GAAATAA
2133262 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
2133290 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
2133311 TATGAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 43 0.98
29 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2133410 original size:53 final size:52
Alignment explanation
Indices: 2133330--2133518 Score: 161
Period size: 52 Copynumber: 3.6 Consensus size: 52
2133320 TTGGTATTTT
* * ** *
2133330 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGGTG
1 TTTTGAAAATAAAACCGG-GTTGGAGTATCCCCGATTAAAGAAAAAATTAGTG
* **
2133383 TTTTGAAAATAAAACCGAGGTTAGAGTATCCCCGATT-GTGAAAAAATTAGTG
1 TTTTGAAAATAAAACCG-GGTTGGAGTATCCCCGATTAAAGAAAAAATTAGTG
* * * * *
2133435 TTTT-AGCAATAAAACCGGGATTGGAGTATCCCCGATT-ATG-AAAAATCAATA
1 TTTTGA-AAATAAAACCGGG-TTGGAGTATCCCCGATTAAAGAAAAAATTAGTG
* * *
2133486 TTTTGGAGATAAAATCGGGGTTGGAGTATCCCC
1 TTTTGAAAATAAAA-CCGGGTTGGAGTATCCCC
2133519 TCGGAAATAA
Statistics
Matches: 113, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
51 34 0.30
52 46 0.41
53 32 0.28
54 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (52 bp):
TTTTGAAAATAAAACCGGGTTGGAGTATCCCCGATTAAAGAAAAAATTAGTG
Found at i:2133449 original size:52 final size:52
Alignment explanation
Indices: 2133298--2133479 Score: 154
Period size: 52 Copynumber: 3.4 Consensus size: 52
2133288 AACGAGGTTG
* * * * * * *
2133298 GAGTATCCTCGATTATGAAAAATTGGTATTTTTTTTGGAAATAAAATC-GGAGTTG
1 GAGTATCCCCGATTATGAAAAAAT--TA-GTGTTTTGAAAATAAAACCGGGA-TTA
* ** *
2133353 GAGTATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGAGG-TTA
1 GAGTATCCCCGATT-ATGAAAAAATTAGTGTTTTGAAAATAAAACCG-GGATTA
* * *
2133406 GAGTATCCCCGATTGTGAAAAAATTAGTGTTTT-AGCAATAAAACCGGGATTG
1 GAGTATCCCCGATTATGAAAAAATTAGTGTTTTGA-AAATAAAACCGGGATTA
2133458 GAGTATCCCCGATTATGAAAAA
1 GAGTATCCCCGATTATGAAAAA
2133480 TCAATATTTT
Statistics
Matches: 103, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
51 3 0.03
52 47 0.46
53 31 0.30
54 1 0.01
55 15 0.15
56 6 0.06
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (52 bp):
GAGTATCCCCGATTATGAAAAAATTAGTGTTTTGAAAATAAAACCGGGATTA
Found at i:2133510 original size:51 final size:51
Alignment explanation
Indices: 2133293--2133681 Score: 218
Period size: 51 Copynumber: 7.4 Consensus size: 51
2133283 GAAATAACGA
* * * *
2133293 GGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAA-T--TA-GTGTTTTGGAAATAAAACCGG
* * * * * *
2133348 AGTTGGAGTATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGA
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * *
2133401 GGTTAGAGTATCCCCGATTGTGAAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATG-AAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * * *
2133453 GATTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAGATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
** ** *
2133504 GGTTGGAGTATCCCC---TCGGAAATAA-T-G-GGGTTGGAGTATCCCCGATGATTAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AATTAGTGTTTTGGA--A------AT-A-AAACCGG
* * * *
2133559 GGTTGGAGTATCCCCGATTGTGAAAATTTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTG--TTTTGGAAATAAAACCGG
* * * *
2133612 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAACCGG
* *
2133663 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
2133682 GTGGAGAATT
Statistics
Matches: 257, Mismatches: 53, Indels: 52
0.71 0.15 0.14
Matches are distributed among these distances:
46 5 0.02
48 5 0.02
49 2 0.01
51 71 0.28
52 45 0.18
53 64 0.25
54 5 0.02
55 36 0.14
56 3 0.01
57 7 0.03
58 6 0.02
59 1 0.00
60 2 0.01
62 5 0.02
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:2133568 original size:27 final size:28
Alignment explanation
Indices: 2133501--2133576 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
2133491 GAGATAAAAT
***
2133501 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
2133529 TGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
2133556 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2133577 TGTGAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2136075 original size:13 final size:13
Alignment explanation
Indices: 2136057--2136082 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2136047 ACAAAGATCC
2136057 ATGTATCGATACA
1 ATGTATCGATACA
2136070 ATGTATCGATACA
1 ATGTATCGATACA
2136083 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2136078 original size:33 final size:33
Alignment explanation
Indices: 2136036--2136102 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2136026 AAAATTTCCA
***
2136036 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2136069 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2136102 A
1 A
2136103 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2136146 original size:19 final size:18
Alignment explanation
Indices: 2136122--2136189 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2136112 CAGTAGCTAA
2136122 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2136141 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2136156 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2136173 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2136190 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2136162 original size:13 final size:13
Alignment explanation
Indices: 2136144--2136168 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2136134 ACAATACTTA
2136144 TGTATCGATACAT
1 TGTATCGATACAT
2136157 TGTATCGATACA
1 TGTATCGATACA
2136169 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2136166 original size:32 final size:32
Alignment explanation
Indices: 2136125--2136187 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2136115 TAGCTAATTA
*
2136125 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2136157 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2136188 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2137413 original size:55 final size:55
Alignment explanation
Indices: 2137329--2137951 Score: 956
Period size: 55 Copynumber: 11.3 Consensus size: 55
2137319 ATAAACTGCA
* * * * * *
2137329 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
2137384 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
2137439 TCCTGCTCTTT-AGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGA-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2137494 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
2137549 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2137604 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2137659 TCCTGCTCTTTGGGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
2137714 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
2137769 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
2137824 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2137879 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
2137934 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
2137952 AAAAAGAGGA
Statistics
Matches: 531, Mismatches: 26, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
54 14 0.03
55 504 0.95
56 13 0.02
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:2137683 original size:26 final size:26
Alignment explanation
Indices: 2137654--2137739 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
2137644 GGGCTTTAAG
2137654 AGGTGTCCTGCTCTTTGGGGACTAAA
1 AGGTGTCCTGCTCTTTGGGGACTAAA
** * *
2137680 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
1 AGGTGTCCTGC-TCTT-TG-GGGAC--TAAA
*
2137709 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTAAA
2137735 AGGTG
1 AGGTG
2137740 CCACCAACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.07
26 15 0.34
27 6 0.14
28 6 0.14
29 11 0.25
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTAAA
Found at i:2137844 original size:26 final size:26
Alignment explanation
Indices: 2137815--2137904 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
2137805 GGGTGGGCTT
2137815 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
2137841 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
* *
2137868 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
2137896 TGAAAGGTG
1 TGAAAGGTG
2137905 CCACCAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
25 3 0.06
26 17 0.35
27 8 0.17
28 9 0.19
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:2138963 original size:17 final size:17
Alignment explanation
Indices: 2138917--2138990 Score: 62
Period size: 17 Copynumber: 4.3 Consensus size: 17
2138907 CTTAAGTAGG
*
2138917 TTTTTTCTTTTCTCTCTTT
1 TTTTTTTTTTTC-CT-TTT
* * *
2138936 TTCTTTGTTTT-GTTTT
1 TTTTTTTTTTTCCTTTT
2138952 TTTGTTTTTTTTCC-TTT
1 TTT-TTTTTTTTCCTTTT
*
2138969 TTTTTTTTTTGCCTTTT
1 TTTTTTTTTTTCCTTTT
2138986 TTTTT
1 TTTTT
2138991 GAAGAGAAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
16 14 0.31
17 22 0.49
19 9 0.20
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTTCCTTTT
Found at i:2138983 original size:16 final size:16
Alignment explanation
Indices: 2138949--2138990 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2138939 TTTGTTTTGT
*
2138949 TTTTTTGTTTTTTTTCC
1 TTTTTT-TTTTTTTGCC
2138966 TTTTTTTTTTTTTGCC
1 TTTTTTTTTTTTTGCC
2138982 TTTTTTTTT
1 TTTTTTTTT
2138991 GAAGAGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.86
Consensus pattern (16 bp):
TTTTTTTTTTTTTGCC
Found at i:2151415 original size:30 final size:28
Alignment explanation
Indices: 2151381--2151436 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 28
2151371 TCGATGATTA
2151381 GAAAATAAATCGAGATTGGAGTATCCCCTC
1 GAAAAT-AA-CGAGATTGGAGTATCCCCTC
*
2151411 GAAAATAACGGGATTGGAGTATCCCC
1 GAAAATAACGAGATTGGAGTATCCCC
2151437 AATTATGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 17 0.68
29 2 0.08
30 6 0.24
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (28 bp):
GAAAATAACGAGATTGGAGTATCCCCTC
Found at i:2151418 original size:78 final size:79
Alignment explanation
Indices: 2151318--2151518 Score: 226
Period size: 78 Copynumber: 2.6 Consensus size: 79
2151308 AATAACAGGG
* * * * *
2151318 TTGGAGTGTTCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG
*
2151382 AAAATAAA-TCGAGA
65 AAAATAAAGCCGAGA
* * * * *
2151396 TTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* *
2151461 GAATAAAGCCGAGG
66 AAATAAAGCCGAGA
** * *
2151475 TTACAGTATCCCCTTGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGAT
2151519 GAAATAACGA
Statistics
Matches: 101, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
77 1 0.01
78 59 0.58
79 41 0.41
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (79 bp):
TTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAATAAAGCCGAGA
Found at i:2151646 original size:53 final size:52
Alignment explanation
Indices: 2151566--2151754 Score: 161
Period size: 52 Copynumber: 3.6 Consensus size: 52
2151556 TTGGTATTTT
* * * *
2151566 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTGGTG
1 TTTTGAAAATAAAACCGG-GTTGGAGTATCCCCGATTAAAGGAAAAATTAGTG
* **
2151619 TTTTGAAAATAAAACCGAGGTTAGAGTATCCCCGATT-GTGGAAAAATTAGTG
1 TTTTGAAAATAAAACCG-GGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTG
* * * * * *
2151671 TTTT-AGCAATAAAACAGGGATTGGAGTATCCCCGATT--ATGAAAAATCAATA
1 TTTTGA-AAATAAAACCGGG-TTGGAGTATCCCCGATTAAAGGAAAAATTAGTG
* * *
2151722 TTTTGGAGATAAAATCGGGGTTGGAGTATCCCC
1 TTTTGAAAATAAAA-CCGGGTTGGAGTATCCCC
2151755 TCGGAAATAA
Statistics
Matches: 112, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
51 35 0.31
52 44 0.39
53 32 0.29
54 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (52 bp):
TTTTGAAAATAAAACCGGGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTG
Found at i:2151746 original size:51 final size:51
Alignment explanation
Indices: 2151529--2151917 Score: 202
Period size: 51 Copynumber: 7.4 Consensus size: 51
2151519 GAAATAACGA
* * * *
2151529 GGTTGGAGTATCCTCGATTACGAAAAATTGGTATTTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAA-T--TA-GTGTTTTGGAAATAAAATCGG
* * * * * * *
2151584 AGTTGGAGTATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGA
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTAGTGTTTTGGAAATAAAATCGG
* * * *
2151637 GGTTAGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAA-CAGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAATC-GG
* * * * *
2151689 GATTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAGATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGG
** ** *
2151740 GGTTGGAGTATCCCC---TCGGAAATAA-T-G-GGGTTGGAGTATCCCCGATGATTAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AATTAGTGTTTTGGA--A------AT-A-AAATCGG
* * * *
2151795 GGTTGGAGTATCCCCGATTGTGAAAATTTGGTGTTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTG--TTTTGGAAATAAAATCGG
* * * *
2151848 AGTTTGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAATCGG
* *
2151899 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
2151918 GTGGAGAATT
Statistics
Matches: 252, Mismatches: 56, Indels: 56
0.69 0.15 0.15
Matches are distributed among these distances:
46 5 0.02
48 5 0.02
49 2 0.01
51 69 0.27
52 44 0.17
53 62 0.25
54 5 0.02
55 36 0.14
56 3 0.01
57 7 0.03
58 6 0.02
59 1 0.00
60 2 0.01
62 5 0.02
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGG
Found at i:2151804 original size:27 final size:28
Alignment explanation
Indices: 2151737--2151812 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
2151727 GAGATAAAAT
***
2151737 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
2151765 TGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
2151792 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2151813 TGTGAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2154309 original size:13 final size:13
Alignment explanation
Indices: 2154291--2154316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2154281 ACAAAGATCC
2154291 ATGTATCGATACA
1 ATGTATCGATACA
2154304 ATGTATCGATACA
1 ATGTATCGATACA
2154317 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2154312 original size:33 final size:33
Alignment explanation
Indices: 2154270--2154336 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2154260 AAAATTTCCA
***
2154270 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2154303 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2154336 A
1 A
2154337 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2154380 original size:19 final size:18
Alignment explanation
Indices: 2154356--2154423 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2154346 CAGTAGCTAA
2154356 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2154375 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2154390 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2154407 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2154424 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2154396 original size:13 final size:13
Alignment explanation
Indices: 2154378--2154402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2154368 ACAATACTTA
2154378 TGTATCGATACAT
1 TGTATCGATACAT
2154391 TGTATCGATACA
1 TGTATCGATACA
2154403 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2154400 original size:32 final size:32
Alignment explanation
Indices: 2154359--2154421 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2154349 TAGCTAATTA
*
2154359 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2154391 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2154422 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2155192 original size:20 final size:20
Alignment explanation
Indices: 2155169--2155206 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2155159 AGAGAGCTTT
2155169 AATTTTATCAAGAAGGAGAA
1 AATTTTATCAAGAAGGAGAA
* *
2155189 AATTTTATTAAGAGGGAG
1 AATTTTATCAAGAAGGAG
2155207 TTTTATTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.29
Consensus pattern (20 bp):
AATTTTATCAAGAAGGAGAA
Found at i:2155964 original size:20 final size:20
Alignment explanation
Indices: 2155906--2155970 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
2155896 CTAAGTGAAA
2155906 TGTATCGATACATGGGACAT
1 TGTATCGATACATGGGACAT
*
2155926 TGTAT-GA-ATAT---A-A-
1 TGTATCGATACATGGGACAT
2155939 TGTATCGATACATGGGACAT
1 TGTATCGATACATGGGACAT
2155959 TGTATCGATACA
1 TGTATCGATACA
2155971 ATGTATCGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 5 0.14
14 3 0.08
15 4 0.11
18 4 0.11
19 3 0.08
20 17 0.47
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGGGACAT
Found at i:2155977 original size:13 final size:13
Alignment explanation
Indices: 2155959--2155983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2155949 CATGGGACAT
2155959 TGTATCGATACAA
1 TGTATCGATACAA
2155972 TGTATCGATACA
1 TGTATCGATACA
2155984 TGGTAAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2155997 original size:33 final size:33
Alignment explanation
Indices: 2155904--2155986 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
2155894 CCCTAAGTGA
*
2155904 AATGTATCGATACATGGGACATTGTAT-GAATAT
1 AATGTATCGATACATGGGACATTGTATCG-ATAC
2155937 AATGTATCGATACATGGGACATTGTATCGATAC
1 AATGTATCGATACATGGGACATTGTATCGATAC
2155970 AATGTATCGATACATGG
1 AATGTATCGATACATGG
2155987 TAAAAAGTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 47 0.98
34 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (33 bp):
AATGTATCGATACATGGGACATTGTATCGATAC
Found at i:2156053 original size:15 final size:15
Alignment explanation
Indices: 2156033--2156074 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
2156023 TCAAATGCAT
*
2156033 GTATCGATACATTAA
1 GTATCGATACATGAA
* *
2156048 GTATCGAAATATGAA
1 GTATCGATACATGAA
2156063 GTATCGATACAT
1 GTATCGATACAT
2156075 AATAATGGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (15 bp):
GTATCGATACATGAA
Found at i:2157657 original size:20 final size:20
Alignment explanation
Indices: 2157634--2157671 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2157624 AGAGAGCTTT
2157634 AATTTTATCAAGAAGGAGAA
1 AATTTTATCAAGAAGGAGAA
* *
2157654 AATTTTATTAAGAGGGAG
1 AATTTTATCAAGAAGGAG
2157672 TTTTATTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.29
Consensus pattern (20 bp):
AATTTTATCAAGAAGGAGAA
Found at i:2158440 original size:33 final size:34
Alignment explanation
Indices: 2158369--2158452 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 34
2158359 CCCTAAGTGA
* *
2158369 AATGTATCGATACATGGGACACTTGTATTAATAT
1 AATGTATCGATACATGGGACACTTGTATCAATAC
*
2158403 AATGTATCGATACATGGGACA-TTGTATCGATAC
1 AATGTATCGATACATGGGACACTTGTATCAATAC
2158436 AATGTATCGATACATGG
1 AATGTATCGATACATGG
2158453 TAAAAAGTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 26 0.55
34 21 0.45
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (34 bp):
AATGTATCGATACATGGGACACTTGTATCAATAC
Found at i:2158443 original size:13 final size:13
Alignment explanation
Indices: 2158425--2158449 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2158415 CATGGGACAT
2158425 TGTATCGATACAA
1 TGTATCGATACAA
2158438 TGTATCGATACA
1 TGTATCGATACA
2158450 TGGTAAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2158463 original size:33 final size:33
Alignment explanation
Indices: 2158369--2158469 Score: 103
Period size: 33 Copynumber: 3.0 Consensus size: 33
2158359 CCCTAAGTGA
*** * *
2158369 AATGTATCGATACATGGGACACTTGTATTAATAT
1 AATGTATCGATACATGGGA-AAAAGTATCAATAC
* ** *
2158403 AATGTATCGATACATGGGACATTGTATCGATAC
1 AATGTATCGATACATGGGAAAAAGTATCAATAC
*
2158436 AATGTATCGATACATGGTAAAAAGTATCAATAC
1 AATGTATCGATACATGGGAAAAAGTATCAATAC
2158469 A
1 A
2158470 TGCCCAACAG
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
33 38 0.67
34 19 0.33
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (33 bp):
AATGTATCGATACATGGGAAAAAGTATCAATAC
Found at i:2158524 original size:20 final size:20
Alignment explanation
Indices: 2158499--2158550 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2158489 TCAAATGCAT
2158499 GTATCGATACATTATGAAAA
1 GTATCGATACATTATGAAAA
2158519 GTATCGATACATTATGAAAA
1 GTATCGATACATTATGAAAA
2158539 GTATCGATACAT
1 GTATCGATACAT
2158551 AATAATGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (20 bp):
GTATCGATACATTATGAAAA
Found at i:2160134 original size:20 final size:20
Alignment explanation
Indices: 2160111--2160148 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2160101 AGAGAGCTTT
2160111 AATTTTATCAAGAAGGAGAA
1 AATTTTATCAAGAAGGAGAA
* *
2160131 AATTTTATTAAGAGGGAG
1 AATTTTATCAAGAAGGAG
2160149 TTTTATTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.29
Consensus pattern (20 bp):
AATTTTATCAAGAAGGAGAA
Found at i:2160906 original size:20 final size:20
Alignment explanation
Indices: 2160848--2160912 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
2160838 CTAAGTGAAA
2160848 TGTATCGATACATGGGACAT
1 TGTATCGATACATGGGACAT
*
2160868 TGTAT-GA-ATAT---A-A-
1 TGTATCGATACATGGGACAT
2160881 TGTATCGATACATGGGACAT
1 TGTATCGATACATGGGACAT
2160901 TGTATCGATACA
1 TGTATCGATACA
2160913 ATGTATCGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 5 0.14
14 3 0.08
15 4 0.11
18 4 0.11
19 3 0.08
20 17 0.47
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGGGACAT
Found at i:2160919 original size:13 final size:13
Alignment explanation
Indices: 2160901--2160925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2160891 CATGGGACAT
2160901 TGTATCGATACAA
1 TGTATCGATACAA
2160914 TGTATCGATACA
1 TGTATCGATACA
2160926 TGGTAAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2160939 original size:33 final size:33
Alignment explanation
Indices: 2160846--2160928 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
2160836 CCCTAAGTGA
*
2160846 AATGTATCGATACATGGGACATTGTAT-GAATAT
1 AATGTATCGATACATGGGACATTGTATCG-ATAC
2160879 AATGTATCGATACATGGGACATTGTATCGATAC
1 AATGTATCGATACATGGGACATTGTATCGATAC
2160912 AATGTATCGATACATGG
1 AATGTATCGATACATGG
2160929 TAAAAAGTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 47 0.98
34 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (33 bp):
AATGTATCGATACATGGGACATTGTATCGATAC
Found at i:2169570 original size:13 final size:13
Alignment explanation
Indices: 2169552--2169576 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2169542 ATAATGCACA
2169552 GTATCGATACATT
1 GTATCGATACATT
2169565 GTATCGATACAT
1 GTATCGATACAT
2169577 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2169694 original size:13 final size:13
Alignment explanation
Indices: 2169676--2169714 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2169666 TACACACAAG
*
2169676 ATGTATTGATACA
1 ATGTATCGATACA
2169689 ATGTATCGATACA
1 ATGTATCGATACA
2169702 ATGTATCGATACA
1 ATGTATCGATACA
2169715 TCCCAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2177162 original size:32 final size:30
Alignment explanation
Indices: 2177126--2177184 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
2177116 GAAATCAAAT
2177126 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
2177158 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
2177185 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:2177431 original size:9 final size:9
Alignment explanation
Indices: 2177417--2177442 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2177407 TTTGAAAATA
2177417 TAGCCGTTC
1 TAGCCGTTC
2177426 TAGCCGTTC
1 TAGCCGTTC
2177435 TAGCCGTT
1 TAGCCGTT
2177443 ACAAGCCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.31, G:0.23, T:0.35
Consensus pattern (9 bp):
TAGCCGTTC
Found at i:2177492 original size:19 final size:20
Alignment explanation
Indices: 2177452--2177503 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
2177442 TACAAGCCAA
2177452 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA-TTTTTG
2177473 TGTATCGATACATA-TTTTG
1 TGTATCGATACATATTTTTG
2177492 TGTATCGATACA
1 TGTATCGATACA
2177504 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 17 0.55
21 14 0.45
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATATTTTTG
Found at i:2179595 original size:20 final size:21
Alignment explanation
Indices: 2179556--2179598 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2179546 GACTAGTGTG
* *
2179556 GGGACTGCCCGGTTGTGACCT
1 GGGACTGCCCGGTCGCGACCT
2179577 GGGACTG-CCGGTCGCGACCT
1 GGGACTGCCCGGTCGCGACCT
2179597 GG
1 GG
2179599 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.09, C:0.30, G:0.42, T:0.19
Consensus pattern (21 bp):
GGGACTGCCCGGTCGCGACCT
Found at i:2180030 original size:11 final size:12
Alignment explanation
Indices: 2179999--2180046 Score: 64
Period size: 11 Copynumber: 4.1 Consensus size: 12
2179989 ATAATCCCCC
2179999 TGTATCGATACA
1 TGTATCGATACA
2180011 GTGTATCGATACA
1 -TGTATCGATACA
*
2180024 T-TATCGATA-G
1 TGTATCGATACA
2180034 TGTATCGATACA
1 TGTATCGATACA
2180046 T
1 T
2180047 TACAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 1 0.03
11 16 0.52
12 2 0.06
13 12 0.39
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:2180038 original size:22 final size:23
Alignment explanation
Indices: 2180001--2180071 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 23
2179991 AATCCCCCTG
2180001 TATCGATACAGTGTATCGATACAT
1 TATCGATA-AGTGTATCGATACAT
2180025 TATCGAT-AGTGTATCGATACAT
1 TATCGATAAGTGTATCGATACAT
* *
2180047 TA-CAAGAAAAATGTATCGATACAT
1 TATC--GATAAGTGTATCGATACAT
2180071 T
1 T
2180072 GAATTTCCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.02
22 17 0.40
23 2 0.05
24 22 0.52
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.32
Consensus pattern (23 bp):
TATCGATAAGTGTATCGATACAT
Found at i:2185001 original size:52 final size:52
Alignment explanation
Indices: 2184920--2185040 Score: 206
Period size: 52 Copynumber: 2.3 Consensus size: 52
2184910 GAAAATTTAT
* *
2184920 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGCATATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGC
* *
2184972 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGC
2185024 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
2185041 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGC
Found at i:2185053 original size:52 final size:51
Alignment explanation
Indices: 2184920--2185060 Score: 194
Period size: 52 Copynumber: 2.7 Consensus size: 51
2184910 GAAAATTTAT
*
2184920 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGCATATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAATTTGC
* * *
2184972 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAATTTGC
*
2185024 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2185061 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGCAAATTTGC
Found at i:2185067 original size:13 final size:13
Alignment explanation
Indices: 2185049--2185107 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
2185039 CAAAGATCAG
2185049 TGTATCGATACAA
1 TGTATCGATACAA
2185062 TGTATCGATAC-A
1 TGTATCGATACAA
2185074 TG--T-GAGT--AA
1 TGTATCGA-TACAA
2185083 TGTATCGATACAA
1 TGTATCGATACAA
2185096 TGTATCGATACA
1 TGTATCGATACA
2185108 TGTGAGTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 5 0.13
10 2 0.05
11 2 0.05
12 5 0.13
13 25 0.64
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2185092 original size:34 final size:34
Alignment explanation
Indices: 2185049--2185128 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
2185039 CAAAGATCAG
2185049 TGTATCGATACAATGTATCGATACATGTGAGTAA
1 TGTATCGATACAATGTATCGATACATGTGAGTAA
2185083 TGTATCGATACAATGTATCGATACATGTGAGTAA
1 TGTATCGATACAATGTATCGATACATGTGAGTAA
2185117 TGTATCGATACA
1 TGTATCGATACA
2185129 TTTTTTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (34 bp):
TGTATCGATACAATGTATCGATACATGTGAGTAA
Found at i:2185190 original size:33 final size:33
Alignment explanation
Indices: 2185148--2185217 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2185138 AGCAGTAGCT
2185148 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
2185181 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
2185214 TACA
1 TACA
2185218 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:2185191 original size:13 final size:13
Alignment explanation
Indices: 2185173--2185197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2185163 CAAAAAAATA
2185173 TGTATCGATACAT
1 TGTATCGATACAT
2185186 TGTATCGATACA
1 TGTATCGATACA
2185198 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2185774 original size:15 final size:15
Alignment explanation
Indices: 2185738--2185775 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2185728 TTCATCAATT
* *
2185738 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
2185753 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
2185768 TCATTTTG
1 TCATTTTG
2185776 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:2187595 original size:21 final size:21
Alignment explanation
Indices: 2187566--2187610 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2187556 AAATTTTTAT
*
2187566 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2187586 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2187608 TTT
1 TTT
2187611 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2189528 original size:32 final size:30
Alignment explanation
Indices: 2189492--2189550 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
2189482 GAAATCAAAT
2189492 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
2189524 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
2189551 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:2189850 original size:19 final size:20
Alignment explanation
Indices: 2189810--2189861 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
2189800 TACAAGCCAA
2189810 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA-TTTTTG
2189831 TGTATCGATACATA-TTTTG
1 TGTATCGATACATATTTTTG
2189850 TGTATCGATACA
1 TGTATCGATACA
2189862 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 17 0.55
21 14 0.45
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATATTTTTG
Found at i:2191781 original size:20 final size:20
Alignment explanation
Indices: 2191714--2191787 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
2191704 CAAAACCCTG
****
2191714 AAATGTATCGATACACCTTC
1 AAATGTATCGATACATAACC
*
2191734 AAATGTATCGATACATAATGC
1 AAATGTATCGATACATAA-CC
* *
2191755 ACA-GTATCGATACATGACC
1 AAATGTATCGATACATAACC
*
2191774 AAATGTATTGATAC
1 AAATGTATCGATAC
2191788 TTGTTAAGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (20 bp):
AAATGTATCGATACATAACC
Found at i:2191883 original size:20 final size:20
Alignment explanation
Indices: 2191840--2191891 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2191830 CTTAACTGTT
*
2191840 TGTATCGATACA-CACAAGA
1 TGTATCGATACATCACAAAA
*
2191859 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
2191879 TGTATCGATACAT
1 TGTATCGATACAT
2191892 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:2200018 original size:68 final size:68
Alignment explanation
Indices: 2199871--2200032 Score: 157
Period size: 68 Copynumber: 2.4 Consensus size: 68
2199861 CTAGCCTTTG
* * * * * * *
2199871 TTAATGATGTTTTCAGAAATTTCACTACCTTTTTCTTAAGGATGTTTTAAGAGATTCCATAAGCC
1 TTAAAGATGTTTTCAAAAATTTCACAACC-TTTTCTTAAGGATGTTTGAAAAGATTCCACAAGAC
*
2199936 TCTT
65 TCTC
* *
2199940 TTAAATATGTTTTCAAAAATTTCACAAGCC-TTTCTTGAA-GATGTTTGAAAAGATTTCACAAGA
1 TTAAAGATGTTTTCAAAAATTTCACAA-CCTTTTCTT-AAGGATGTTTGAAAAGATTCCACAAGA
2200003 CTCTC
64 CTCTC
* * *
2200008 TTGAGGATGTTTTAAAATAATTTCA
1 TTAAAGATGTTTTCAAA-AATTTCA
2200033 AATGCCACTC
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
68 42 0.55
69 32 0.42
70 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (68 bp):
TTAAAGATGTTTTCAAAAATTTCACAACCTTTTCTTAAGGATGTTTGAAAAGATTCCACAAGACT
CTC
Found at i:2200065 original size:69 final size:68
Alignment explanation
Indices: 2199946--2200105 Score: 157
Period size: 69 Copynumber: 2.3 Consensus size: 68
2199936 TCTTTTAAAT
* ** *
2199946 ATGTTTTCAAAAATTTCACAAGCCTTTCTTGAAGATGTTTGAAAAGATTTCACAAGAC-TCTCTT
1 ATGTTTTAAAAAATTTCACAAGCCACTCTTGAAGATGTTTGAAAAGATTTCAAAAGACTTC-CTT
2200010 GAGG
65 GAGG
* *
2200014 ATGTTTTAAAATAATTTCA-AATGCCACTCTTGAGGATGCTTT-AAGAA-ATTTCAAAAGCCTTC
1 ATGTTTTAAAA-AATTTCACAA-GCCACTCTTGAAGATG-TTTGAA-AAGATTTCAAAAGACTTC
2200076 CTTGAGG
62 CTTGAGG
* * * *
2200083 ATATTTTAAGAGATTTCAAAAGC
1 ATGTTTTAAAAAATTTCACAAGC
2200106 TTTTCTTAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
68 20 0.26
69 50 0.65
70 7 0.09
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (68 bp):
ATGTTTTAAAAAATTTCACAAGCCACTCTTGAAGATGTTTGAAAAGATTTCAAAAGACTTCCTTG
AGG
Found at i:2200080 original size:34 final size:34
Alignment explanation
Indices: 2199904--2200105 Score: 167
Period size: 34 Copynumber: 5.9 Consensus size: 34
2199894 ACTACCTTTT
* * * *
2199904 TCTTAAGGATGTTTTAAGAGATTCCATAAGCCTC
1 TCTTGAGGATGTTTTAAGAAATTTCAAAAGCCTC
* * ** * *
2199938 TTTTAAATATGTTTTCAA-AAATTTCACAAGCCTT
1 TCTTGAGGATGTTTT-AAGAAATTTCAAAAGCCTC
* * * *
2199972 TCTTGAAGATGTTTGAA-AAGATTTCACAAGACTC
1 TCTTGAGGATGTTTTAAGAA-ATTTCAAAAGCCTC
* * *
2200006 TCTTGAGGATGTTTTAAAATAATTTCAAATGCCAC
1 TCTTGAGGATGTTTTAAGA-AATTTCAAAAGCCTC
*
2200041 TCTTGAGGATGCTTTAAGAAATTTCAAAAGCCT-
1 TCTTGAGGATGTTTTAAGAAATTTCAAAAGCCTC
* *
2200074 TCCTTGAGGATATTTTAAGAGATTTCAAAAGC
1 T-CTTGAGGATGTTTTAAGAAATTTCAAAAGC
2200106 TTTTCTTAAG
Statistics
Matches: 137, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
33 5 0.04
34 101 0.74
35 30 0.22
36 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (34 bp):
TCTTGAGGATGTTTTAAGAAATTTCAAAAGCCTC
Found at i:2200118 original size:34 final size:34
Alignment explanation
Indices: 2200053--2200120 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
2200043 TTGAGGATGC
*
2200053 TTTAAGAAATTTCAAAAGCCTTCCTTGAGGATAT
1 TTTAAGAAATTTCAAAAGCCTTCCTTAAGGATAT
* * *
2200087 TTTAAGAGATTTCAAAAGCTTTTCTTAAGGATAT
1 TTTAAGAAATTTCAAAAGCCTTCCTTAAGGATAT
2200121 GCTTCATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (34 bp):
TTTAAGAAATTTCAAAAGCCTTCCTTAAGGATAT
Found at i:2206066 original size:9 final size:9
Alignment explanation
Indices: 2206043--2206115 Score: 76
Period size: 9 Copynumber: 7.9 Consensus size: 9
2206033 AGACATCTTT
2206043 AAAAAAACAC
1 AAAAAAA-AC
2206053 TAAAAAATAA-
1 -AAAAAA-AAC
2206063 AAAAAAAAC
1 AAAAAAAAC
* *
2206072 AAGAAACAC
1 AAAAAAAAC
*
2206081 AAAAAAAAT
1 AAAAAAAAC
*
2206090 AAAAAACAC
1 AAAAAAAAC
2206099 AAAAAAAAC
1 AAAAAAAAC
2206108 AAAAAAAA
1 AAAAAAAA
2206116 AGGTCTAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
8 2 0.04
9 42 0.81
11 7 0.13
12 1 0.02
ACGTcount: A:0.84, C:0.11, G:0.01, T:0.04
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:2206084 original size:18 final size:18
Alignment explanation
Indices: 2206043--2206113 Score: 88
Period size: 18 Copynumber: 3.8 Consensus size: 18
2206033 AGACATCTTT
* *
2206043 AAAAAAACACTAAAAAATAA
1 AAAAAAA-AC-AAAAAACAC
*
2206063 AAAAAAAACAAGAAACAC
1 AAAAAAAACAAAAAACAC
*
2206081 AAAAAAAATAAAAAACAC
1 AAAAAAAACAAAAAACAC
2206099 AAAAAAAACAAAAAA
1 AAAAAAAACAAAAAA
2206114 AAAGGTCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 36 0.80
19 2 0.04
20 7 0.16
ACGTcount: A:0.83, C:0.11, G:0.01, T:0.04
Consensus pattern (18 bp):
AAAAAAAACAAAAAACAC
Found at i:2207463 original size:26 final size:27
Alignment explanation
Indices: 2207395--2207465 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 27
2207385 CAAAATTGTT
* *
2207395 GTCAAGAAAT-TTTCGTCAAGAACTTTT
1 GTCAAGAAATGTTT-GTCAAAAACTTTC
* * *
2207422 GTCGAG-AACGTGTGTCAAAAAC-TTC
1 GTCAAGAAATGTTTGTCAAAAACTTTC
2207447 GTCAAGAAATGTTTGTCAA
1 GTCAAGAAATGTTTGTCAA
2207466 CATGAATCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
25 7 0.21
26 20 0.59
27 7 0.21
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (27 bp):
GTCAAGAAATGTTTGTCAAAAACTTTC
Found at i:2207768 original size:32 final size:32
Alignment explanation
Indices: 2207727--2207950 Score: 217
Period size: 32 Copynumber: 7.0 Consensus size: 32
2207717 CTAGTGGAGA
2207727 AACCTTCTCCAAAGGCCACACAAGTTGGTGGC
1 AACCTTCTCCAAAGGCCACACAAGTTGGTGGC
2207759 AACCTTCTCCAAAGGCCACACAAGTTGGTGGC
1 AACCTTCTCCAAAGGCCACACAAGTTGGTGGC
*
2207791 AACCTTCTTCAAA-GCCTACACAAGTTGGTGGC
1 AACCTTCTCCAAAGGCC-ACACAAGTTGGTGGC
* * * *
2207823 AATC-TCTTCAAAAGCCCACACAAGTTGGTGGT
1 AACCTTC-TCCAAAGGCCACACAAGTTGGTGGC
* * * * * *
2207855 AACC-CCTTCAAAGCCCACACAAGCTAGTGGT
1 AACCTTCTCCAAAGGCCACACAAGTTGGTGGC
* ** *
2207886 AACCCTTCT-TAAACCCCACACAAGTCGGTGGC
1 AA-CCTTCTCCAAAGGCCACACAAGTTGGTGGC
*
2207918 AACCCTT-T-CAAAAGCCTACACAAGTTGGTGGC
1 AA-CCTTCTCCAAAGGCC-ACACAAGTTGGTGGC
2207950 A
1 A
2207951 TCTCCATCTT
Statistics
Matches: 163, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
31 34 0.21
32 125 0.77
33 4 0.02
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.21
Consensus pattern (32 bp):
AACCTTCTCCAAAGGCCACACAAGTTGGTGGC
Found at i:2207842 original size:64 final size:64
Alignment explanation
Indices: 2207727--2207954 Score: 243
Period size: 64 Copynumber: 3.6 Consensus size: 64
2207717 CTAGTGGAGA
* * * *
2207727 AACCTTCTCCAAAGGCC-ACACAAGTTGGTGGCAACCT-TCTCCAAAGGCCACACAAGTTGGTGG
1 AACCTTCTTCAAA-GCCTACACAAGTTGGTGGCAATCTCT-TCAAAAGCCCACACAAGTTGGTGG
2207790 C
64 C
*
2207791 AACCTTCTTCAAAGCCTACACAAGTTGGTGGCAATCTCTTCAAAAGCCCACACAAGTTGGTGGT
1 AACCTTCTTCAAAGCCTACACAAGTTGGTGGCAATCTCTTCAAAAGCCCACACAAGTTGGTGGC
* * * * * * * * *
2207855 AACC-CCTTCAAAGCCCACACAAGCTAGTGGTAA-CCCTTCTTAAACCCCACACAAGTCGGTGGC
1 AACCTTCTTCAAAGCCTACACAAGTTGGTGGCAATCTCTTC-AAAAGCCCACACAAGTTGGTGGC
*
2207918 AACCCT-TTCAAAAGCCTACACAAGTTGGTGGC-ATCTC
1 AACCTTCTTC-AAAGCCTACACAAGTTGGTGGCAATCTC
2207955 CATCTTTAAG
Statistics
Matches: 137, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
62 5 0.04
63 54 0.39
64 77 0.56
65 1 0.01
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.21
Consensus pattern (64 bp):
AACCTTCTTCAAAGCCTACACAAGTTGGTGGCAATCTCTTCAAAAGCCCACACAAGTTGGTGGC
Found at i:2207904 original size:63 final size:63
Alignment explanation
Indices: 2207774--2207950 Score: 203
Period size: 63 Copynumber: 2.8 Consensus size: 63
2207764 TCTCCAAAGG
* * * * *
2207774 CCACACAAGTTGGTGGCAACCTTCTTCAAAGCCTACACAAGTTGGTGGCAATCTCTTCAAAAGC
1 CCACACAAGTTGGTGGCAACC-CCTTCAAAGCCTACACAAGCTAGTGGCAATCCCTTCAAAACC
* * * *
2207838 CCACACAAGTTGGTGGTAACCCCTTCAAAGCCCACACAAGCTAGTGGTAA-CCCTTCTTAAACC
1 CCACACAAGTTGGTGGCAACCCCTTCAAAGCCTACACAAGCTAGTGGCAATCCCTTC-AAAACC
* * * *
2207901 CCACACAAGTCGGTGGCAACCCTTTCAAAAGCCTACACAAGTTGGTGGCA
1 CCACACAAGTTGGTGGCAACCCCTTC-AAAGCCTACACAAGCTAGTGGCA
2207951 TCTCCATCTT
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
62 5 0.05
63 51 0.54
64 39 0.41
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.21
Consensus pattern (63 bp):
CCACACAAGTTGGTGGCAACCCCTTCAAAGCCTACACAAGCTAGTGGCAATCCCTTCAAAACC
Found at i:2207916 original size:95 final size:96
Alignment explanation
Indices: 2207737--2207950 Score: 272
Period size: 95 Copynumber: 2.2 Consensus size: 96
2207727 AACCTTCTCC
* * * * *
2207737 AAAGGCCACACAAGTTGGTGGCAACCTTCTCCAAAGGCCACACAAGTTGGTGGCAACCTTCTTCA
1 AAAGCCCACACAAGTTGGTGGCAACCTCCTCCAAAGCCCACACAAGCTAGTGGCAACCTTCTTCA
* * * *
2207802 AAGCCTACACAAGTTGGTGGCAA-TCTCTTCA
66 AACCCCACACAAGTCGGTGGCAACCCT-TTCA
* * *
2207833 AAAGCCCACACAAGTTGGTGGTAACC-CCTTCAAAGCCCACACAAGCTAGTGGTAACCCTTCTT-
1 AAAGCCCACACAAGTTGGTGGCAACCTCCTCCAAAGCCCACACAAGCTAGTGGCAA-CCTTCTTC
2207896 AAACCCCACACAAGTCGGTGGCAACCCTTTCA
65 AAACCCCACACAAGTCGGTGGCAACCCTTTCA
*
2207928 AAAGCCTACACAAGTTGGTGGCA
1 AAAGCCCACACAAGTTGGTGGCA
2207951 TCTCCATCTT
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
95 69 0.68
96 33 0.32
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (96 bp):
AAAGCCCACACAAGTTGGTGGCAACCTCCTCCAAAGCCCACACAAGCTAGTGGCAACCTTCTTCA
AACCCCACACAAGTCGGTGGCAACCCTTTCA
Found at i:2208125 original size:52 final size:52
Alignment explanation
Indices: 2207955--2208204 Score: 249
Period size: 52 Copynumber: 4.9 Consensus size: 52
2207945 GTGGCATCTC
* *
2207955 CATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCA-CCTT--
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTTCA
* * * *
2208004 CATCTTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCATAT-TTAA
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAT-TCTTCA
* * * * *
2208056 CAT-TCCTAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCATTTTTCT
1 CATCT-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTTCA
* * * * **
2208108 CATCTTCAAGTCTAATGTCGCTAGCCGTGAATCAGCACATTTACATTCTTCA
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTTCA
* * * * *
2208160 CATCTTTAAGCCCAATATTGCTGGCCTTGAATCAACATATTGGCA
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
2208205 CATTTATCAT
Statistics
Matches: 159, Mismatches: 35, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
49 41 0.26
50 2 0.01
51 2 0.01
52 113 0.71
53 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (52 bp):
CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTTCA
Found at i:2208281 original size:61 final size:61
Alignment explanation
Indices: 2208142--2208274 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 61
2208132 CCGTGAATCA
* * * * * *
2208142 GCACATTTA-CATTCTTCACATCTTTAAGCCCAATATTGCTGGCCTTGAATCAACATATTG
1 GCACATTTATCATCCTTCTCTTTTTTAAGCCCAATATTGCTGGCCCTAAATCAACATATTG
*
2208202 GCACATTTATCATCCTTCTCTTTTTTAAGCCCAATATTGCTGGCCCTAAATCAGCATATTG
1 GCACATTTATCATCCTTCTCTTTTTTAAGCCCAATATTGCTGGCCCTAAATCAACATATTG
2208263 GCATC-TTTATCA
1 GCA-CATTTATCA
2208275 CTCTTCTGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
60 9 0.14
61 54 0.84
62 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (61 bp):
GCACATTTATCATCCTTCTCTTTTTTAAGCCCAATATTGCTGGCCCTAAATCAACATATTG
Found at i:2208898 original size:13 final size:13
Alignment explanation
Indices: 2208880--2208918 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2208870 TCTATAATTT
2208880 GTATCGATACAAA
1 GTATCGATACAAA
2208893 GTATCGATACAATA
1 GTATCGATACAA-A
*
2208907 -TATGGATACAAA
1 GTATCGATACAAA
2208919 ACTACCCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (13 bp):
GTATCGATACAAA
Found at i:2217738 original size:10 final size:10
Alignment explanation
Indices: 2217719--2217782 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
2217709 AATCAAGAGC
2217719 AAAAGAAAAAA
1 AAAAG-AAAAA
2217730 AAAAGAAAAA
1 AAAAGAAAAA
* *
2217740 GAAAGTAAAGA
1 AAAAG-AAAAA
* *
2217751 AAGAGAAAGA
1 AAAAGAAAAA
* *
2217761 GAAAGAGAAA
1 AAAAGAAAAA
2217771 AAAAGAAAAA
1 AAAAGAAAAA
2217781 AA
1 AA
2217783 CTCAAGTATG
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
10 30 0.71
11 12 0.29
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:2217744 original size:21 final size:20
Alignment explanation
Indices: 2217720--2217780 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
2217710 ATCAAGAGCA
2217720 AAAGAAAAAAAAAAGAAAAAG
1 AAAG-AAAAAAAAAGAAAAAG
* * *
2217741 AAAGTAAAGAAAGAGAAAGAG
1 AAAG-AAAAAAAAAGAAAAAG
*
2217762 AAAGAGAAAAAAAGAAAAA
1 AAAGAAAAAAAAAGAAAAA
2217781 AACTCAAGTA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAGAAAAAAAAAGAAAAAG
Found at i:2217990 original size:20 final size:21
Alignment explanation
Indices: 2217947--2217990 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2217937 TTAAGTATAG
*
2217947 ATGTTTTTCAAGCATAAAAGTA
1 ATGTTTTTCAAG-ATAAAAATA
2217969 ATGTTTTTCAAG-TAAAAATA
1 ATGTTTTTCAAGATAAAAATA
2217989 AT
1 AT
2217991 TCAAAGTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (21 bp):
ATGTTTTTCAAGATAAAAATA
Found at i:2218110 original size:20 final size:19
Alignment explanation
Indices: 2218087--2218136 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
2218077 ACACCCAGAT
* *
2218087 GTATCGATACTTATTGCTTA
1 GTATCGATACATATT-CCTA
* *
2218107 GTATCGACACATATTCCTG
1 GTATCGATACATATTCCTA
2218126 GTATCGATACA
1 GTATCGATACA
2218137 CCTTGAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (19 bp):
GTATCGATACATATTCCTA
Found at i:2218225 original size:20 final size:20
Alignment explanation
Indices: 2218200--2218250 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2218190 CGATACATTA
2218200 TATCGATACATAATGAATTG
1 TATCGATACATAATGAATTG
**
2218220 TATCGATACATGGTGAATTG
1 TATCGATACATAATGAATTG
2218240 TATCGATACAT
1 TATCGATACAT
2218251 TGAGCCCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (20 bp):
TATCGATACATAATGAATTG
Found at i:2221602 original size:20 final size:20
Alignment explanation
Indices: 2221574--2221658 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
2221564 TTTTAACTAG
*
2221574 ATGTGTCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
2221594 ATGTATCGATACATCTATGTAAAAA
1 ATGTATCGATACA--T-TG--AAAA
2221619 GATAGAATGTATCGATACATTGAAAA
1 -AT-G--T--ATCGATACATTGAAAA
2221645 ATGTATCGATACAT
1 ATGTATCGATACAT
2221659 CTGGGTACTT
Statistics
Matches: 53, Mismatches: 1, Indels: 22
0.70 0.01 0.29
Matches are distributed among these distances:
20 22 0.42
22 2 0.04
23 2 0.04
24 1 0.02
25 6 0.11
26 6 0.11
27 1 0.02
28 2 0.04
29 2 0.04
31 9 0.17
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:2222629 original size:28 final size:28
Alignment explanation
Indices: 2222525--2222783 Score: 329
Period size: 28 Copynumber: 9.0 Consensus size: 28
2222515 TAAAAAAAAA
* *
2222525 GGTGCCACTAACTTGTGTGGGCTTTGAAAAAA
1 GGTGCCACTGAC-T-TGTGGGCTTTG--AAAG
* *
2222557 GTTGCCACCGACTTGTGTGGGCTTTGAAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAG
* *
2222588 AGTGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
2222616 GGTGCCACTAACTTATGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
2222644 GGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
**
2222673 AATGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2222701 GGTGCCACGGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
2222729 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2222757 GATGCCACTGACTTGTGGGCTTTGAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAA
2222784 ATAGTTGCCA
Statistics
Matches: 203, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
28 131 0.65
29 36 0.18
30 1 0.00
31 12 0.06
32 23 0.11
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:2222679 original size:85 final size:85
Alignment explanation
Indices: 2222525--2222783 Score: 376
Period size: 85 Copynumber: 3.0 Consensus size: 85
2222515 TAAAAAAAAA
* * *
2222525 GGTGCCACTAACTTGTGTGGGCTTTGAAAAAAGTTGCCACCGACTTGTGTGGGCTTTGAAAAGAG
1 GGTGCCACTAAC-T-TGTGGGCTTTG--AAAAGGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAA
*
2222590 TGCCATTGACTTGTGGGCTTTGAAAG
60 TGCCACTGACTTGTGGGCTTTGAAAG
*
2222616 GGTGCCACTAACTTATGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAATGCCAC
1 GGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAATGCCAC
2222681 TGACTTGTGGGCTTTGAAAG
66 TGACTTGTGGGCTTTGAAAG
** * *
2222701 GGTGCCACGGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCAC
1 GGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAATGCCAC
2222765 TGACTTGTGGGCTTTGAAA
66 TGACTTGTGGGCTTTGAAA
2222784 ATAGTTGCCA
Statistics
Matches: 158, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
84 30 0.19
85 90 0.57
86 1 0.01
87 14 0.09
89 10 0.06
90 1 0.01
91 12 0.08
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (85 bp):
GGTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAATGCCAC
TGACTTGTGGGCTTTGAAAG
Done.