Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 89 of 167
Found at i:29314340 original size:65 final size:65
Alignment explanation
Indices: 29314262--29314397 Score: 272
Period size: 65 Copynumber: 2.1 Consensus size: 65
29314252 ACCCGAATCC
29314262 TTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGAAGAATCCATGTAGAATTACACTTCTT
1 TTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGAAGAATCCATGTAGAATTACACTTCTT
29314327 TTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGAAGAATCCATGTAGAATTACACTTCTT
1 TTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGAAGAATCCATGTAGAATTACACTTCTT
29314392 TTATTT
1 TTATTT
29314398 TATTTTAGAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 71 1.00
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (65 bp):
TTATTTAAATAAAATACAGTGGTAAAATAAAATAAAAGAAGAATCCATGTAGAATTACACTTCTT
Found at i:29317202 original size:31 final size:31
Alignment explanation
Indices: 29317146--29317211 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
29317136 AGAAAGTAAC
* * * *
29317146 AATTCTACTCTTTTTGATAGGTTGAT-GTTCA
1 AATTCAACTCTTTTTAAAAGATTGATGGTT-A
29317177 AATTCAACTCTTTTTAAAAGATTGATGGTTA
1 AATTCAACTCTTTTTAAAAGATTGATGGTTA
29317208 AATT
1 AATT
29317212 TAGTAAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (31 bp):
AATTCAACTCTTTTTAAAAGATTGATGGTTA
Found at i:29318109 original size:54 final size:54
Alignment explanation
Indices: 29318044--29318151 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
29318034 ATTTCAATTA
*
29318044 GGGAAATAAAGTTTTATAAATAGCCAATTTCATTCAAACCTTAGAATTTTTACC
1 GGGAAAGAAAGTTTTATAAATAGCCAATTTCATTCAAACCTTAGAATTTTTACC
29318098 GGGAAAGAAAGTTTTATAAATAGCCAATTTCATTCAAACCTTAGAATTTTTACC
1 GGGAAAGAAAGTTTTATAAATAGCCAATTTCATTCAAACCTTAGAATTTTTACC
29318152 TAGCAAATTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (54 bp):
GGGAAAGAAAGTTTTATAAATAGCCAATTTCATTCAAACCTTAGAATTTTTACC
Found at i:29318843 original size:17 final size:16
Alignment explanation
Indices: 29318821--29318896 Score: 80
Period size: 17 Copynumber: 4.6 Consensus size: 16
29318811 CTATACATGT
29318821 GAACCCTCTTTGTATGC
1 GAACCC-CTTTGTATGC
*
29318838 GAACCCCCTTGTATGC
1 GAACCCCTTTGTATGC
* *
29318854 GAGCCCCTTTTGTACGC
1 GAACCCC-TTTGTATGC
* *
29318871 GAACACCCTTGGTATGT
1 GAAC-CCCTTTGTATGC
29318888 GAACCCCTT
1 GAACCCCTT
29318897 ATAGTGAGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
16 20 0.41
17 26 0.53
18 3 0.06
ACGTcount: A:0.18, C:0.33, G:0.20, T:0.29
Consensus pattern (16 bp):
GAACCCCTTTGTATGC
Found at i:29318866 original size:33 final size:34
Alignment explanation
Indices: 29318824--29318896 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
29318814 TACATGTGAA
* * *
29318824 CCCTCTTTGTATGCGAACCCCCTT-GTATGCGAGC
1 CCCT-TTTGTACGCGAACACCCTTGGTATGCGAAC
*
29318858 CCCTTTTGTACGCGAACACCCTTGGTATGTGAAC
1 CCCTTTTGTACGCGAACACCCTTGGTATGCGAAC
29318892 CCCTT
1 CCCTT
29318897 ATAGTGAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.16, C:0.34, G:0.19, T:0.30
Consensus pattern (34 bp):
CCCTTTTGTACGCGAACACCCTTGGTATGCGAAC
Found at i:29325487 original size:46 final size:46
Alignment explanation
Indices: 29325402--29325526 Score: 119
Period size: 46 Copynumber: 2.7 Consensus size: 46
29325392 CTCGCACACT
* * * * *
29325402 AAGTACCTATACCATGGCCCAAAGCCAATTCAAGGTAACT-TATCCA
1 AAGTA-CTATACCATGGCCCGAAGCCAAATCAAGATAACTCCACCCA
*
29325448 AAGTACTGATACCATGGCCCGAAGCCAAATC-AGTATAACTCGCACCCG
1 AAGTACT-ATACCATGGCCCGAAGCCAAATCAAG-ATAACTC-CACCCA
* *
29325496 AAGTGCTAATATCATGGCCCGAAGCCAAATC
1 AAGTACT-ATACCATGGCCCGAAGCCAAATC
29325527 CATGTATCTC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
45 4 0.06
46 31 0.47
48 31 0.47
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (46 bp):
AAGTACTATACCATGGCCCGAAGCCAAATCAAGATAACTCCACCCA
Found at i:29337516 original size:20 final size:21
Alignment explanation
Indices: 29337493--29337534 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29337483 TATGTATGAG
*
29337493 TTTTGAA-GTTTCTTGATAGA
1 TTTTGAATGCTTCTTGATAGA
*
29337513 TTTTGAATGCTTGTTGATAGA
1 TTTTGAATGCTTCTTGATAGA
29337534 T
1 T
29337535 ATATAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.24, C:0.05, G:0.21, T:0.50
Consensus pattern (21 bp):
TTTTGAATGCTTCTTGATAGA
Found at i:29338184 original size:29 final size:28
Alignment explanation
Indices: 29338151--29338206 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
29338141 GAGTTATACC
29338151 GATTTGGCTACGGGCCATGCATATCAGTT
1 GATTTGGCTACGGGCCATG-ATATCAGTT
*
29338180 GATTTGGCTTCGGGCCATGATATCAGT
1 GATTTGGCTACGGGCCATGATATCAGT
29338207 ACATTGAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (28 bp):
GATTTGGCTACGGGCCATGATATCAGTT
Found at i:29339210 original size:37 final size:37
Alignment explanation
Indices: 29339018--29339199 Score: 285
Period size: 37 Copynumber: 4.9 Consensus size: 37
29339008 GCTCAGATGA
** * *
29339018 AATCTCCACACAAAGTTATCGGGTCTTACCCGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
29339055 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
29339092 AATCTCCATACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
29339129 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA-AT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
* *
29339165 ATATTTCCACACGTAGTCATCGGGTCTTACTCGGA
1 A-ATCTCCACACGTAGTCATCGGGTCTTACCCGGA
29339200 ATATATTTCC
Statistics
Matches: 136, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
36 3 0.02
37 133 0.98
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:29339401 original size:48 final size:48
Alignment explanation
Indices: 29339346--29340312 Score: 1808
Period size: 48 Copynumber: 20.1 Consensus size: 48
29339336 ACACATCGCC
* * *
29339346 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
* *
29339394 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTC--A
* * * *
29339444 TATATATTTCACATTAGCCATTCGGCTTTACCATATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
*
29339492 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29339540 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29339588 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29339636 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29339684 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29339732 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29339780 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29339828 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29339876 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29339924 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29339972 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29340020 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29340068 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29340116 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29340164 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29340212 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
* *
29340260 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
29340308 TACAT
1 TACAT
29340313 CAATTTCCGC
Statistics
Matches: 908, Mismatches: 9, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
48 862 0.95
50 46 0.05
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.37
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGATTTACCACATATACTTATCTCA
Found at i:29343644 original size:30 final size:30
Alignment explanation
Indices: 29343609--29343669 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
29343599 AATTGGTATA
29343609 TTTGTGGAATTGAGCATATTAATGCATATT
1 TTTGTGGAATTGAGCATATTAATGCATATT
29343639 TTTGTGGAATTGAGCATATTAATGCATATT
1 TTTGTGGAATTGAGCATATTAATGCATATT
29343669 T
1 T
29343670 GTAAATGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.44
Consensus pattern (30 bp):
TTTGTGGAATTGAGCATATTAATGCATATT
Found at i:29344077 original size:12 final size:12
Alignment explanation
Indices: 29344060--29344089 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29344050 TATAGGTTTG
29344060 GCATGGCCTGGC
1 GCATGGCCTGGC
29344072 GCATGGCCTGGC
1 GCATGGCCTGGC
*
29344084 ACATGG
1 GCATGG
29344090 GCGTGTATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.30, G:0.40, T:0.17
Consensus pattern (12 bp):
GCATGGCCTGGC
Found at i:29344437 original size:16 final size:17
Alignment explanation
Indices: 29344413--29344450 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
29344403 AAATTGATTA
*
29344413 GTATTGATTGA-TAAAT
1 GTATGGATTGATTAAAT
29344429 GTATGGATTGATTAAAT
1 GTATGGATTGATTAAAT
29344446 GTATG
1 GTATG
29344451 TGAAAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (17 bp):
GTATGGATTGATTAAAT
Found at i:29346701 original size:49 final size:50
Alignment explanation
Indices: 29346393--29346713 Score: 198
Period size: 46 Copynumber: 6.7 Consensus size: 50
29346383 TTATGGGAGC
* * * *
29346393 CAGTGTAAGACCATGTCTGGGACATGGCATC-GAATTTGAGA--CGAGAG-
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAGCA-TAGATATGTGAGAGT
** * * * *
29346440 CTAGTGTAAGA-CATGTCTGGGACAT-GCATTGGCCTCGAGATGT-A-AGC
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCAGCATAGATATGTGAGAGT
* * *
29346487 CAGTGTAAGA-CATGTCTAGGACAT-GCATCGGC-TACGAGATGT----GT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAGCATA-GATATGTGAGAGT
* * * * * ** *
29346531 AAGTGTAAGACCATGTCTCGGACATGGCATCGGCACATATA-AAG-GTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAGCATAGATATGTGAGAGT
29346579 CAGTGTAAGACCATGTCTGGGACATGGCATCAGCATAGATATGTGAGAG-
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAGCATAGATATGTGAGAGT
* * * * *
29346628 CTAGTGCAAGACCATGTCTAGGACATGGCGTCAGCCTCA-AT-T-TCGATAGT
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCAGCAT-AGATATGT-GAGAGT
*
29346678 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAGCAT
29346714 TATACCTTAT
Statistics
Matches: 222, Mismatches: 34, Indels: 34
0.77 0.12 0.12
Matches are distributed among these distances:
44 10 0.05
45 14 0.06
46 57 0.26
47 19 0.09
48 48 0.22
49 37 0.17
50 36 0.16
51 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (50 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCAGCATAGATATGTGAGAGT
Found at i:29347359 original size:37 final size:37
Alignment explanation
Indices: 29347311--29347392 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 37
29347301 CTATGGTTTT
*
29347311 TTGGCTGAGAAATCATATTAAGTTAGATTTTGATTTA
1 TTGGTTGAGAAATCATATTAAGTTAGATTTTGATTTA
29347348 TTGGTTGAGAAATCATATTAAGTTAGATTTTGATTTA
1 TTGGTTGAGAAATCATATTAAGTTAGATTTTGATTTA
29347385 TTGGTTGA
1 TTGGTTGA
29347393 TGATAGATTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (37 bp):
TTGGTTGAGAAATCATATTAAGTTAGATTTTGATTTA
Found at i:29359483 original size:24 final size:24
Alignment explanation
Indices: 29359395--29359484 Score: 98
Period size: 23 Copynumber: 3.9 Consensus size: 24
29359385 GAGCTGATGG
29359395 ACAGTAAGCT-TTATTGAGCTAAA
1 ACAGTAAGCTCTTATTGAGCTAAA
**
29359418 ATGGTAAGCTC-TATTGAGCTAAA
1 ACAGTAAGCTCTTATTGAGCTAAA
* * *
29359441 ACGGTAAGCTCTGA-CGAGCTAAAA
1 ACAGTAAGCTCTTATTGAGCT-AAA
29359465 ACAGTAAGCTCTTA-TGAGCT
1 ACAGTAAGCTCTTATTGAGCT
29359485 GATATATCGG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
23 35 0.62
24 21 0.38
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (24 bp):
ACAGTAAGCTCTTATTGAGCTAAA
Found at i:29375538 original size:36 final size:36
Alignment explanation
Indices: 29375495--29375568 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
29375485 TTTAACTTGG
* *
29375495 GATAATTTTTTGTTTTTATTGAATAAAGTCTGACTT
1 GATAATTTTTTCTTTTTATTGAATAAAGCCTGACTT
29375531 GATAATTTTTTCTTTTTATTGAATAAAGCCTGACTT
1 GATAATTTTTTCTTTTTATTGAATAAAGCCTGACTT
29375567 GA
1 GA
29375569 GGTCAGTTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (36 bp):
GATAATTTTTTCTTTTTATTGAATAAAGCCTGACTT
Found at i:29376892 original size:38 final size:39
Alignment explanation
Indices: 29376801--29376894 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 39
29376791 CGGTACCTTT
* * *
29376801 TGGTGTGTAGGGTTGGATGGGTTGATTATATCCCTATACT
1 TGGTGTGTAGGGTTGGATGGGTCGATTATATCCC-ACACA
* *
29376841 TGGTGTGTAGGGTTGGGTGGGTCGATTCTATCCC-CACA
1 TGGTGTGTAGGGTTGGATGGGTCGATTATATCCCACACA
*
29376879 TGGTGTGTTGGGTTGG
1 TGGTGTGTAGGGTTGG
29376895 TCGGAGATGG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
38 17 0.35
40 31 0.65
ACGTcount: A:0.13, C:0.12, G:0.38, T:0.37
Consensus pattern (39 bp):
TGGTGTGTAGGGTTGGATGGGTCGATTATATCCCACACA
Found at i:29384628 original size:27 final size:27
Alignment explanation
Indices: 29384598--29384776 Score: 191
Period size: 27 Copynumber: 6.6 Consensus size: 27
29384588 ATATTGAGCC
* * * *
29384598 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAGTCATAT
* * *
29384625 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCATAT
*
29384652 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCATA-T
** *
29384680 CGCACACTTAGTGCCGCATGGTCA-ATT
1 CGCACACTTAGTGCTACATAGTCATA-T
* *
29384707 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCATAT
*
29384734 CGCACACTTAGTGCAACATAGTCATAT
1 CGCACACTTAGTGCTACATAGTCATAT
29384761 CGCACACTTAGTGCTA
1 CGCACACTTAGTGCTA
29384777 TACAATTTAA
Statistics
Matches: 130, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 107 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCATAT
Found at i:29384737 original size:82 final size:81
Alignment explanation
Indices: 29384624--29384774 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 81
29384614 TATAATCATC
* *
29384624 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
29384689 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* ** *
29384706 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCATATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
29384770 AGTGC
65 AGTGC
29384775 TATACAATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAAT
Found at i:29385346 original size:13 final size:13
Alignment explanation
Indices: 29385328--29385352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29385318 TACTAAATTT
29385328 TCATGGATTCAAG
1 TCATGGATTCAAG
29385341 TCATGGATTCAA
1 TCATGGATTCAA
29385353 TATACCATTA
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:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:29392477 original size:27 final size:27
Alignment explanation
Indices: 29392447--29392625 Score: 191
Period size: 27 Copynumber: 6.6 Consensus size: 27
29392437 ATATTGAGCC
* * * *
29392447 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAGTCATAT
* * *
29392474 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCATAT
*
29392501 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCATA-T
** *
29392529 CGCACACTTAGTGCCGCATGGTCA-ATT
1 CGCACACTTAGTGCTACATAGTCATA-T
* *
29392556 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCATAT
*
29392583 CGCACACTTAGTGCAACATAGTCATAT
1 CGCACACTTAGTGCTACATAGTCATAT
29392610 CGCACACTTAGTGCTA
1 CGCACACTTAGTGCTA
29392626 TACAATTTAA
Statistics
Matches: 130, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 107 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCATAT
Found at i:29392586 original size:82 final size:81
Alignment explanation
Indices: 29392473--29392623 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 81
29392463 TATAATCATC
* *
29392473 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
29392538 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* ** *
29392555 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCATATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
29392619 AGTGC
65 AGTGC
29392624 TATACAATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAAT
Found at i:29393191 original size:13 final size:13
Alignment explanation
Indices: 29393173--29393197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29393163 TACTAAATTT
29393173 TCATGGATTCAAG
1 TCATGGATTCAAG
29393186 TCATGGATTCAA
1 TCATGGATTCAA
29393198 TATACCATTA
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:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:29407744 original size:28 final size:28
Alignment explanation
Indices: 29407704--29407768 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
29407694 ATGTACTAGA
* *
29407704 ATACCACTATGTATGCAAAATTACCAT-T
1 ATACCCCTATGTATGCAAAATGACC-TGT
29407732 ATACCCCTATGTATGCAAAATGACCTGT
1 ATACCCCTATGTATGCAAAATGACCTGT
29407760 ATACCCCTA
1 ATACCCCTA
29407769 GGGTTAATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.29
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCTGT
Found at i:29407935 original size:27 final size:28
Alignment explanation
Indices: 29407874--29407988 Score: 92
Period size: 27 Copynumber: 4.1 Consensus size: 28
29407864 AGGAAGCATC
* * * *
29407874 CTGGTGGCTATGCGACAAATTATATG-TT
1 CTGGTGGCTCTGCCACATA-TATCTGTTT
29407902 CTGGTGGCTCTGCCACATATATCT-TTT
1 CTGGTGGCTCTGCCACATATATCTGTTT
* * *
29407929 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCTCTGCCAC-ATATATCTGTTT
* * * *
29407958 CTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTCTGCCACATATATCTGTTT
29407985 CTGG
1 CTGG
29407989 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
27 33 0.46
28 24 0.33
29 15 0.21
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (28 bp):
CTGGTGGCTCTGCCACATATATCTGTTT
Found at i:29407974 original size:29 final size:28
Alignment explanation
Indices: 29407874--29407974 Score: 105
Period size: 27 Copynumber: 3.6 Consensus size: 28
29407864 AGGAAGCATC
* * * *
29407874 CTGGTGGCTATGCGACAAATTATATGTT
1 CTGGTGGCTCTGCCACAAAATATCTGTT
* *
29407902 CTGGTGGCTCTGCCAC-ATATATCTTTT
1 CTGGTGGCTCTGCCACAAAATATCTGTT
*
29407929 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCTCTGCCACAAAATATCTGT-T
* *
29407958 CTGGTGACTCTGTCACA
1 CTGGTGGCTCTGCCACA
29407975 TTTTCTGTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
27 22 0.37
28 22 0.37
29 15 0.25
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (28 bp):
CTGGTGGCTCTGCCACAAAATATCTGTT
Found at i:29407988 original size:56 final size:55
Alignment explanation
Indices: 29407874--29407988 Score: 126
Period size: 55 Copynumber: 2.1 Consensus size: 55
29407864 AGGAAGCATC
* * * *
29407874 CTGGTGGCTATGCGACAAATTATATGTTCTGGTGGCTCTGCCACATATATCTTTT
1 CTGGTGGCTATGCCACAAAATATATGTTCTGGTGACTCTGCCACATATATCTTAT
* * *
29407929 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATATGT-TCTGGTGACTCTGCCACATATATCT-TAT
29407985 CTGG
1 CTGG
29407989 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 26 0.52
56 23 0.46
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (55 bp):
CTGGTGGCTATGCCACAAAATATATGTTCTGGTGACTCTGCCACATATATCTTAT
Found at i:29413252 original size:79 final size:81
Alignment explanation
Indices: 29413112--29413296 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
29413102 TTGAATGATG
* *
29413112 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
29413176 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * * **
29413191 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCTGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
29413253 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
29413271 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29413297 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:29413310 original size:40 final size:40
Alignment explanation
Indices: 29413113--29413296 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
29413103 TGAATGATGT
* * * *
29413113 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
29413153 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
29413193 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* * *
29413231 TCTGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29413272 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
29413297 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:29413318 original size:79 final size:79
Alignment explanation
Indices: 29413165--29413329 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
29413155 GGACTAAGAT
* * **
29413165 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
* *
29413230 ATCTGGGTTAAGTC
66 ATCTCGGTTAAATC
* *
29413244 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
29413307 TATATC-CGGTTAAATT
63 TAAATCTCGGTTAAATC
29413323 CCGAAGG
1 CCGAAGG
29413330 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCTCGGTTAAATC
Found at i:29418798 original size:28 final size:28
Alignment explanation
Indices: 29418758--29418822 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
29418748 ATGTACTAGA
*
29418758 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
29418786 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
29418814 ATACCCCTA
1 ATACCCCTA
29418823 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:29418986 original size:27 final size:27
Alignment explanation
Indices: 29418928--29419017 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
29418918 AGGAAGCGTC
29418928 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
29418956 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
29418983 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
29419012 CTGGTG
1 CTGGTG
29419018 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:29419036 original size:55 final size:56
Alignment explanation
Indices: 29418928--29419042 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
29418918 AGGAAGCGTC
* *
29418928 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
29418983 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
29419039 CTGG
1 CTGG
29419043 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.58
56 21 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:29419505 original size:19 final size:19
Alignment explanation
Indices: 29419481--29419519 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29419471 TTTTAATTAT
* *
29419481 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
29419500 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
29419519 T
1 T
29419520 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:29420138 original size:11 final size:10
Alignment explanation
Indices: 29420110--29420143 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
29420100 AGCCTGTAAG
29420110 TATTCTGAAT
1 TATTCTGAAT
*
29420120 TTTTCTGAAT
1 TATTCTGAAT
29420130 ATATTCTGAAT
1 -TATTCTGAAT
29420141 TAT
1 TAT
29420144 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:29424241 original size:8 final size:8
Alignment explanation
Indices: 29424228--29424259 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
29424218 CTAGATCGGC
29424228 AAAAGCCG
1 AAAAGCCG
29424236 AAAAGCCG
1 AAAAGCCG
*
29424244 AAATGCCG
1 AAAAGCCG
29424252 AAAAGCCG
1 AAAAGCCG
29424260 TTATTTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:29424547 original size:28 final size:28
Alignment explanation
Indices: 29424507--29424598 Score: 148
Period size: 28 Copynumber: 3.3 Consensus size: 28
29424497 TGTACTAGAT
*
29424507 TACCCCTATGTATGCAAAATTACCATAA
1 TACCCCTATGTATGCAAAATTACCATTA
*
29424535 TACCCCTATGTATGGAAAATTACCATTA
1 TACCCCTATGTATGCAAAATTACCATTA
* *
29424563 TACCCCTATGTATGCAAAATGACCTTTA
1 TACCCCTATGTATGCAAAATTACCATTA
29424591 TACCCCTA
1 TACCCCTA
29424599 GGGTTAATTC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATTACCATTA
Found at i:29424758 original size:27 final size:28
Alignment explanation
Indices: 29424704--29424793 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
29424694 AGGAAGCGTC
*
29424704 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* * *
29424732 CTGGTGGCCCTGCTAC-ATATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
29424759 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
29424788 CTGGTG
1 CTGGTG
29424794 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:29424812 original size:55 final size:56
Alignment explanation
Indices: 29424704--29424818 Score: 139
Period size: 55 Copynumber: 2.1 Consensus size: 56
29424694 AGGAAGCGTC
* *
29424704 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCTACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCTACATATATCTGTAT
* *
29424759 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTG-TCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCT-ACATATATCTGTAT
29424815 CTGG
1 CTGG
29424819 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
54 1 0.02
55 31 0.60
56 20 0.38
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCTACATATATCTGTAT
Found at i:29434285 original size:41 final size:42
Alignment explanation
Indices: 29434240--29434322 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 42
29434230 ATATGTCTCT
*
29434240 AGAAATTTTCTAAAATAATTTCTTCA-AGAATTTTTTCCCTA
1 AGAAATTTTCTAAAATAATCTCTTCAGAGAATTTTTTCCCTA
* * *
29434281 AGAAATTTTTTGAAATAATCTCTTTAGAGAATTTTTTCCCTA
1 AGAAATTTTCTAAAATAATCTCTTCAGAGAATTTTTTCCCTA
29434323 CAACTTTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 22 0.59
42 15 0.41
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (42 bp):
AGAAATTTTCTAAAATAATCTCTTCAGAGAATTTTTTCCCTA
Found at i:29442827 original size:13 final size:13
Alignment explanation
Indices: 29442809--29442836 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29442799 TTTGGGGTAA
29442809 ACGGCCATGGAAC
1 ACGGCCATGGAAC
29442822 ACGGCCATGGAAC
1 ACGGCCATGGAAC
29442835 AC
1 AC
29442837 ACCCGTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.29, T:0.07
Consensus pattern (13 bp):
ACGGCCATGGAAC
Found at i:29455960 original size:22 final size:19
Alignment explanation
Indices: 29455918--29455960 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
29455908 TTCATCACTC
*
29455918 AATTATTAATTTTTTATTT
1 AATTATTAATTTTTTAATT
29455937 AATTATTCAAATTTTTTAAATT
1 AATTATT--AATTTTTT-AATT
29455959 AA
1 AA
29455961 ATAATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.35
21 8 0.40
22 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTATTAATTTTTTAATT
Found at i:29457266 original size:78 final size:77
Alignment explanation
Indices: 29457136--29457399 Score: 285
Period size: 78 Copynumber: 3.5 Consensus size: 77
29457126 AGCCCCAAAA
* * * * *
29457136 CCCCAAATTCTTTTCCCCAGATTAATTCCCCCTCTTCTCAAAATCCCTAAGTTTTTTTTCCCAAA
1 CCCCAATTTCTTTTCCCCAAATCAATT-CCCCTCTCCCCAAAATCCCTAAG-TTTTTTTCCCAAA
29457201 CCCCTTTCTTTTTT
64 CCCCTTTCTTTTTT
* * *
29457215 CCCCAATTTC-TTTCCCCAAATCAATTCTCCCTCTCCCCGAAATCCCTAAGTTTCTTTCCCAGAC
1 CCCCAATTTCTTTTCCCCAAATCAATTC-CCCTCTCCCCAAAATCCCTAAGTTTTTTTCCCAAAC
29457279 CCCTTTCTGTTTTT
65 CCCTTTCT-TTTTT
* ** *
29457293 -CCCAATTT-TTTT-CCCAAATCAATTCCCCT-ACCCCAAAATCCCTAA-TTTTTTT-AGAAATC
1 CCCCAATTTCTTTTCCCCAAATCAATTCCCCTCTCCCCAAAATCCCTAAGTTTTTTTCCCAAACC
*
29457352 CCGTT-TTTTTT
66 CCTTTCTTTTTT
** *
29457363 CCTGAATTTCTTTTCCCCAAATCAGTTCCCC-CTCCCC
1 CCCCAATTTCTTTTCCCCAAATCAATTCCCCTCTCCCC
29457400 GATATATGCG
Statistics
Matches: 158, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
70 5 0.03
71 7 0.04
72 11 0.07
73 25 0.16
74 14 0.09
75 4 0.03
76 13 0.08
77 32 0.20
78 38 0.24
79 9 0.06
ACGTcount: A:0.20, C:0.37, G:0.04, T:0.39
Consensus pattern (77 bp):
CCCCAATTTCTTTTCCCCAAATCAATTCCCCTCTCCCCAAAATCCCTAAGTTTTTTTCCCAAACC
CCTTTCTTTTTT
Found at i:29458036 original size:12 final size:12
Alignment explanation
Indices: 29458019--29458044 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29458009 ATAATTAAAA
29458019 TATTTTATTTGT
1 TATTTTATTTGT
29458031 TATTTTATTTGT
1 TATTTTATTTGT
29458043 TA
1 TA
29458045 AGGCAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (12 bp):
TATTTTATTTGT
Found at i:29464083 original size:42 final size:43
Alignment explanation
Indices: 29463971--29464085 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
29463961 ACATTTTCCA
* * ** * * *
29463971 AAAAACGCCGCTAAAGAACATAATCTTTAACAGCACTTTTCCC
1 AAAAACGCCACTAAAGATCATGTTCTTTAGCAACACTTTTACC
29464014 AAAAACGCCACTAAAGATCATGTTCTTTAGCAACACTTTTACC
1 AAAAACGCCACTAAAGATCATGTTCTTTAGCAACACTTTTACC
** *
29464057 ACTAACGCC-CTAAAGGTCATGTTCTTTAG
1 AAAAACGCCACTAAAGATCATGTTCTTTAG
29464086 TGGCGTTTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 19 0.31
43 43 0.69
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (43 bp):
AAAAACGCCACTAAAGATCATGTTCTTTAGCAACACTTTTACC
Found at i:29464585 original size:19 final size:20
Alignment explanation
Indices: 29464549--29464588 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
29464539 GGTGGATTTT
29464549 TATTTTATTTAATATTAATA
1 TATTTTATTTAATATTAATA
29464569 TATTTATATTT-AT-TTAATA
1 TATTT-TATTTAATATTAATA
29464588 T
1 T
29464589 TAATATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTATTTAATATTAATA
Found at i:29464585 original size:25 final size:24
Alignment explanation
Indices: 29464547--29464595 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
29464537 GTGGTGGATT
29464547 TTTATTTTATTTAATATTAATATA
1 TTTATTTTATTTAATATTAATATA
29464571 TTTATATTTATTTAATATTAATATA
1 TTTAT-TTTATTTAATATTAATATA
29464596 AAATGTGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTATTTTATTTAATATTAATATA
Found at i:29468236 original size:314 final size:314
Alignment explanation
Indices: 29467851--29468481 Score: 1262
Period size: 314 Copynumber: 2.0 Consensus size: 314
29467841 TTATATGCAT
29467851 ATGACACAGATATCATGTGCTAAAATCTATGTAAAATAAATCATTAATTTAGAAGATAAAAAATG
1 ATGACACAGATATCATGTGCTAAAATCTATGTAAAATAAATCATTAATTTAGAAGATAAAAAATG
29467916 ATAATGCAAATATAATATGAATATATGTTTTTTTTTTACAAATTAAATTTTTATGATAAATTATA
66 ATAATGCAAATATAATATGAATATATGTTTTTTTTTTACAAATTAAATTTTTATGATAAATTATA
29467981 TAAAATACAATATAAATTGAAACATAATAGGCTCAAAATTGAATAATTATCACAAACTATATAAA
131 TAAAATACAATATAAATTGAAACATAATAGGCTCAAAATTGAATAATTATCACAAACTATATAAA
29468046 ATATATTACAAAATGGAAGTAACATAATGCGTCACAATATACATACAACTATTTTTTAACATGAG
196 ATATATTACAAAATGGAAGTAACATAATGCGTCACAATATACATACAACTATTTTTTAACATGAG
29468111 AAATATATATATATATATATATATTTGGGTAGAATGAAATATATATATAAAAAC
261 AAATATATATATATATATATATATTTGGGTAGAATGAAATATATATATAAAAAC
29468165 ATGACACAGATATCATGTGCTAAAATCTATGTAAAATAAATCATTAATTTAGAAGATAAAAAATG
1 ATGACACAGATATCATGTGCTAAAATCTATGTAAAATAAATCATTAATTTAGAAGATAAAAAATG
29468230 ATAATGCAAATATAATATGAATATATGTTTTTTTTTTACAAATTAAATTTTTATGATAAATTATA
66 ATAATGCAAATATAATATGAATATATGTTTTTTTTTTACAAATTAAATTTTTATGATAAATTATA
29468295 TAAAATACAATATAAATTGAAACATAATAGGCTCAAAATTGAATAATTATCACAAACTATATAAA
131 TAAAATACAATATAAATTGAAACATAATAGGCTCAAAATTGAATAATTATCACAAACTATATAAA
29468360 ATATATTACAAAATGGAAGTAACATAATGCGTCACAATATACATACAACTATTTTTTAACATGAG
196 ATATATTACAAAATGGAAGTAACATAATGCGTCACAATATACATACAACTATTTTTTAACATGAG
29468425 AAATATATATATATATATATATATTTGGGTAGAATGAAATATATATATAAAAAC
261 AAATATATATATATATATATATATTTGGGTAGAATGAAATATATATATAAAAAC
29468479 ATG
1 ATG
29468482 GGTATGAAAA
Statistics
Matches: 317, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
314 317 1.00
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (314 bp):
ATGACACAGATATCATGTGCTAAAATCTATGTAAAATAAATCATTAATTTAGAAGATAAAAAATG
ATAATGCAAATATAATATGAATATATGTTTTTTTTTTACAAATTAAATTTTTATGATAAATTATA
TAAAATACAATATAAATTGAAACATAATAGGCTCAAAATTGAATAATTATCACAAACTATATAAA
ATATATTACAAAATGGAAGTAACATAATGCGTCACAATATACATACAACTATTTTTTAACATGAG
AAATATATATATATATATATATATTTGGGTAGAATGAAATATATATATAAAAAC
Found at i:29473780 original size:27 final size:27
Alignment explanation
Indices: 29473750--29473927 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29473740 ATATTGAGTC
* * * *
29473750 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29473777 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29473804 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29473832 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29473859 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29473886 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29473913 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29473928 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29473889 original size:82 final size:81
Alignment explanation
Indices: 29473771--29473926 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29473761 TGCTATATAA
* *
29473771 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29473836 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29473853 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29473917 CACTTAGTGC
65 CACTTAGTGC
29473927 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29478993 original size:14 final size:13
Alignment explanation
Indices: 29478976--29479024 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
29478966 AAATTAAAAA
29478976 AAAAAGAATCAATC
1 AAAAA-AATCAATC
**
29478990 -AAAAAATCAAAA
1 AAAAAAATCAATC
29479002 AAAAAGAATCAATC
1 AAAAA-AATCAATC
29479016 AAAAAAATC
1 AAAAAAATC
29479025 GAAAAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 6 0.21
13 12 0.41
14 11 0.38
ACGTcount: A:0.71, C:0.12, G:0.04, T:0.12
Consensus pattern (13 bp):
AAAAAAATCAATC
Found at i:29479022 original size:27 final size:27
Alignment explanation
Indices: 29478962--29479038 Score: 111
Period size: 26 Copynumber: 2.8 Consensus size: 27
29478952 TTGAGACCTT
*
29478962 AAAAAAATTAAAAAAAAAAGAATCAATC
1 AAAAAAA-TCAAAAAAAAAGAATCAATC
29478990 -AAAAAATCAAAAAAAAAGAATCAATC
1 AAAAAAATCAAAAAAAAAGAATCAATC
29479016 AAAAAAATCGAAAAAAGAAAGAA
1 AAAAAAATC-AAAAAA-AAAGAA
29479039 AAATGAGAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 19 0.42
27 14 0.31
28 6 0.13
29 6 0.13
ACGTcount: A:0.75, C:0.08, G:0.06, T:0.10
Consensus pattern (27 bp):
AAAAAAATCAAAAAAAAAGAATCAATC
Found at i:29487780 original size:116 final size:116
Alignment explanation
Indices: 29487636--29487869 Score: 398
Period size: 116 Copynumber: 2.0 Consensus size: 116
29487626 TCCAAATCAC
**
29487636 TTGCCGTTAATTTTTCCTGAATATAGACTCGTATATCTTCCATTCATAAAATTTCCAGAATTTTA
1 TTGCCGTTAATTTTTCCTGAATATAGACTCGTATATCTTCCACCCATAAAATTTCCAGAATTTTA
* * *
29487701 GGTTTGTCCAATCAATACCAGATTTTTCTTAAAGTTTCCCCTGTTTCACTG
66 GGCTAGGCCAATCAATACCAGATTTTTCTTAAAGTTTCCCCTGTTTCACTG
*
29487752 TTGCCGTTAA-TTTTCTCTGAATATAGACTCGTATATCTTCCACCCATAAAATTTTCAGAATTTT
1 TTGCCGTTAATTTTTC-CTGAATATAGACTCGTATATCTTCCACCCATAAAATTTCCAGAATTTT
29487816 AGGCTAGGCCAATCAATACCAGATTTTTCTTAAAGTTTCCCCTGTTTCACTG
65 AGGCTAGGCCAATCAATACCAGATTTTTCTTAAAGTTTCCCCTGTTTCACTG
29487868 TT
1 TT
29487870 TGACTAATCT
Statistics
Matches: 111, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
115 5 0.05
116 106 0.95
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (116 bp):
TTGCCGTTAATTTTTCCTGAATATAGACTCGTATATCTTCCACCCATAAAATTTCCAGAATTTTA
GGCTAGGCCAATCAATACCAGATTTTTCTTAAAGTTTCCCCTGTTTCACTG
Found at i:29489751 original size:44 final size:44
Alignment explanation
Indices: 29489697--29490136 Score: 248
Period size: 44 Copynumber: 9.5 Consensus size: 44
29489687 GATTGAATAC
* * **
29489697 CTTATTTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGTAGTAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGTAAGT
*
29489741 CTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCTAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-TAG-TAAGT
* * * * * *
29489786 CTTATTTACCTGAAGATGCAGTGGAACAGATTGAAGCTATAAATAAATAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG---T-AGT--A-AG-T
* * * * * * **
29489838 ATTATCTCTCTGAAGTTGCAGTAGAGTAGA-T-CA-TAGCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGTAAGT
* * *
29489879 CTTATCTCCCTGAAGTTGCAGTGAAGCAGTTGCAGTGAAGCAGGTTGAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCA---G-ACTGAAGTA-G-T-AAGT
* * * *
29489930 AGC-AAGTCTTATCCCTCTGAAGTTGCAATGGAGCAGACTGAAG-ATTGAAGAC
1 --CTTA-TC---TCCCT--GAAGTTGCAGTGGAGCAGACTGAAGTAGT-AAG-T
** *
29489982 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAATTAGTAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGTAAGT
* *
29490026 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGTTA-TGAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-TAGTAAGT
* *
29490070 CTTATCTCTCTGAAGTTGCAGTGGAGCAAACTGAAGATAGTGAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-TAGT-AAGT
*
29490115 CTTATCTCTCTGAAGTTGCAGT
1 CTTATCTCCCTGAAGTTGCAGT
29490137 AAAAGAGATC
Statistics
Matches: 304, Mismatches: 58, Indels: 67
0.71 0.14 0.16
Matches are distributed among these distances:
41 23 0.08
42 1 0.00
43 1 0.00
44 103 0.34
45 86 0.28
46 8 0.03
47 9 0.03
48 2 0.01
49 2 0.01
50 5 0.02
51 9 0.03
52 24 0.08
53 4 0.01
54 6 0.02
55 1 0.00
56 5 0.02
58 15 0.05
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTAGTAAGT
Found at i:29489911 original size:14 final size:14
Alignment explanation
Indices: 29489892--29489921 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29489882 ATCTCCCTGA
29489892 AGTTGCAGTGAAGC
1 AGTTGCAGTGAAGC
29489906 AGTTGCAGTGAAGC
1 AGTTGCAGTGAAGC
29489920 AG
1 AG
29489922 GTTGAAGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.37, T:0.20
Consensus pattern (14 bp):
AGTTGCAGTGAAGC
Found at i:29490057 original size:89 final size:88
Alignment explanation
Indices: 29489906--29490136 Score: 279
Period size: 89 Copynumber: 2.6 Consensus size: 88
29489896 GCAGTGAAGC
* * * *
29489906 AGTTGCAGTGAAGCAGGTTGAAGTAGCAAGTCTTATC-CCTCTGAAGTTGCAATGGAGCAGACTG
1 AGTTGCAGTGGAGCAGGTTGAAATAGTAAGTCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTG
29489970 AAGATTGAAGA-CCTTATCTCCCTGA
65 AAG-TT-AAGAGCCTTATCTCCCTGA
* *
29489995 AGTTGCAGTGGAGCAGGTTGAATTAGTAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGA
1 AGTTGCAGTGGAGCAGGTTGAAATAGTAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA
* * *
29490060 AGTTATGAGTCTTATCTCTCTGA
66 AGTTAAGAGCCTTATCTCCCTGA
*** *
29490083 AGTTGCAGTGGAGCAAACTGAAGATAGTGAA-TCTTATCTCTCTGAAGTTGCAGT
1 AGTTGCAGTGGAGCAGGTTGAA-ATAGT-AAGTCTTATCTCCCTGAAGTTGCAGT
29490137 AAAAGAGATC
Statistics
Matches: 125, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
87 3 0.02
88 33 0.26
89 85 0.68
90 4 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (88 bp):
AGTTGCAGTGGAGCAGGTTGAAATAGTAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA
AGTTAAGAGCCTTATCTCCCTGA
Found at i:29490245 original size:94 final size:91
Alignment explanation
Indices: 29490025--29490274 Score: 224
Period size: 94 Copynumber: 2.7 Consensus size: 91
29490015 AATTAGTAAG
* * * * * *
29490025 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGTTATGAGTCTTATCTCTCTGAAGTTGC-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTATAAATCCTATC-CTCTGAAGTTGCA
*
29490089 --AGTGGAGCAAACTGAAGATAGTGAA
65 GTAGTGGAGCAAACTGAACATAGTGAA
* ** *
29490114 TCTTATCTCTCTGAAGTTGCAGTAAAAG-AGATCAAAGCTATAAATCCTATACCTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGT-GGAGTAGATTAAAGCTATAAATCCTAT-CCTCTGAAGTTGC
* * *
29490178 AGTAGCTCGGATCAAACCT-ACCATGGTGAA
64 AGTAG-T-GGAGCAAA-CTGAACATAGTGAA
* * * *
29490208 TCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTAAAGCCACAAA-CCTTATCCCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTATAAATCC-TAT-CCTCTGAAGTTGC
29490272 AGT
64 AGT
29490275 GGGGTAAGTT
Statistics
Matches: 128, Mismatches: 23, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
89 49 0.38
90 3 0.02
92 2 0.02
93 5 0.04
94 67 0.52
95 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (91 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTATAAATCCTATCCTCTGAAGTTGCAG
TAGTGGAGCAAACTGAACATAGTGAA
Found at i:29490376 original size:88 final size:88
Alignment explanation
Indices: 29490212--29490376 Score: 188
Period size: 88 Copynumber: 1.9 Consensus size: 88
29490202 GGTGAATCTT
* * * * *
29490212 ATCTCCCTGAAGTTGTAGTGGAGTAGATTAAAGCCACAAACCTTATCCCCCTGAAGTTGCAGTGG
1 ATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGACACAAACCTTATCCCCCTGAAGTTGCAATGA
* *
29490277 GGTAAGTTCAAGTTACAAGTCTA
66 AGTAAGATCAAGTTACAAGTCTA
* * * * * *
29490300 ATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAGATCTTATCTCCTTGAAGTTGCAATG
1 ATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGACA-CAAACCTTATCCCCCTGAAGTTGCAATG
*
29490365 AAG-CAGATCAAG
65 AAGTAAGATCAAG
29490377 CTTAAATCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
88 38 0.61
89 24 0.39
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (88 bp):
ATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGACACAAACCTTATCCCCCTGAAGTTGCAATGA
AGTAAGATCAAGTTACAAGTCTA
Found at i:29493770 original size:13 final size:13
Alignment explanation
Indices: 29493753--29493787 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
29493743 CAAGACACAC
29493753 ACCCGTGTGTCCT
1 ACCCGTGTGTCCT
*
29493766 GCCCGTGTGTCCT
1 ACCCGTGTGTCCT
29493779 ACCCGTGTG
1 ACCCGTGTG
29493788 CTAATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.37, G:0.29, T:0.29
Consensus pattern (13 bp):
ACCCGTGTGTCCT
Found at i:29512192 original size:26 final size:25
Alignment explanation
Indices: 29512163--29512212 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
29512153 GTACATGTAA
*
29512163 ATTTTGTTATTATATAAATAAATATG
1 ATTTTATTATTATAT-AATAAATATG
*
29512189 ATTTTATTTTTATATAATAAATAT
1 ATTTTATTATTATATAATAAATAT
29512213 ATAAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
ATTTTATTATTATATAATAAATATG
Found at i:29514622 original size:20 final size:21
Alignment explanation
Indices: 29514589--29514627 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
29514579 TTTAATTTCA
*
29514589 AAAAATTGAGTAATTAAATTG
1 AAAAATTGAATAATTAAATTG
29514610 AAAAATT-AATAATTAAAT
1 AAAAATTGAATAATTAAAT
29514628 ATCTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (21 bp):
AAAAATTGAATAATTAAATTG
Found at i:29515871 original size:34 final size:34
Alignment explanation
Indices: 29515833--29515900 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
29515823 TAATTAGTGT
29515833 TTGATTGAAACAAATAAACAGAGTTTAACTAAAA
1 TTGATTGAAACAAATAAACAGAGTTTAACTAAAA
29515867 TTGATTGAAACAAATAAACAGAGTTTAACTAAAA
1 TTGATTGAAACAAATAAACAGAGTTTAACTAAAA
29515901 GATTATTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (34 bp):
TTGATTGAAACAAATAAACAGAGTTTAACTAAAA
Found at i:29519029 original size:42 final size:42
Alignment explanation
Indices: 29518981--29519063 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
29518971 CAGAAATTTA
*
29518981 GTCGCATAAAGAGTTTTTAACCTTTTCCACAAGGCAAATGAT
1 GTCGCATAAAGAGTTTTTAACCTTTTCCACAAGGAAAATGAT
*
29519023 GTCGCATAAGGAGTTTTTAACCTTTTCCACAAGGAAAATGA
1 GTCGCATAAAGAGTTTTTAACCTTTTCCACAAGGAAAATGA
29519064 GGTTTTCTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (42 bp):
GTCGCATAAAGAGTTTTTAACCTTTTCCACAAGGAAAATGAT
Found at i:29525403 original size:57 final size:57
Alignment explanation
Indices: 29525315--29525422 Score: 171
Period size: 57 Copynumber: 1.9 Consensus size: 57
29525305 TTGTTCCAAC
* * * *
29525315 GAACATTATTATCTCTTGCTATCTCATGGACAGTTTGAGTTAATGTTAAAAGCTGAG
1 GAACATGACTATCTCTTGCTATCTCATGGACAATTTGAATTAATGTTAAAAGCTGAG
*
29525372 GAACATGACTATCTCTTGCTATTTCATGGACAATTTGAATTAATGTTAAAA
1 GAACATGACTATCTCTTGCTATCTCATGGACAATTTGAATTAATGTTAAAA
29525423 TAGTGTATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (57 bp):
GAACATGACTATCTCTTGCTATCTCATGGACAATTTGAATTAATGTTAAAAGCTGAG
Found at i:29526164 original size:22 final size:20
Alignment explanation
Indices: 29526121--29526179 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
29526111 TCAAATAGAG
*
29526121 AAAAATAAGTTTTTAATCTTTT
1 AAAAATAA-TTTTT-ATATTTT
*
29526143 AAAGATTATATTTTTATATTTT
1 AAA-AATA-ATTTTTATATTTT
29526165 AAAAATAATTTTTAT
1 AAAAATAATTTTTAT
29526180 TATAATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 8 0.25
21 3 0.09
22 12 0.38
23 8 0.25
24 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
AAAAATAATTTTTATATTTT
Found at i:29527059 original size:13 final size:14
Alignment explanation
Indices: 29527040--29527116 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
29527030 TACAATATTC
29527040 ATATATTTTAATTTT
1 ATAT-TTTTAATTTT
*
29527055 ATATTTTTAATTTCG
1 ATATTTTTAATTT-T
* *
29527070 AGAATTTTTAAATTT
1 A-TATTTTTAATTTT
29527085 ATATATTTTAAGTTTTT
1 ATAT-TTTTAA--TTTT
* *
29527102 ATAATTTTATTTTT
1 ATATTTTTAATTTT
29527116 A
1 A
29527117 GATAATTGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 16 0.33
15 12 0.24
16 15 0.31
17 6 0.12
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (14 bp):
ATATTTTTAATTTT
Found at i:29527723 original size:18 final size:19
Alignment explanation
Indices: 29527684--29527724 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
29527674 ATTATTTGGA
*
29527684 TATTATATAATTCTTGTTT
1 TATTATATAATTCTTGTAT
29527703 TATTAT-TAATT-TTGCTAT
1 TATTATATAATTCTTG-TAT
29527721 TATT
1 TATT
29527725 TTAGTGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 11 0.55
19 6 0.30
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TATTATATAATTCTTGTAT
Found at i:29533179 original size:14 final size:14
Alignment explanation
Indices: 29533160--29533188 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29533150 GAGAAATAAG
29533160 AAGCTGACGTGGAT
1 AAGCTGACGTGGAT
29533174 AAGCTGACGTGGAT
1 AAGCTGACGTGGAT
29533188 A
1 A
29533189 CTTTTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (14 bp):
AAGCTGACGTGGAT
Found at i:29535826 original size:69 final size:69
Alignment explanation
Indices: 29535715--29535852 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
29535705 CTTCCCATTG
* *
29535715 GATGTCTATTAGTAGATAATGTGCCTCATTAAAACCTTATTAGGAAAAACCCTGT-AGGATAAAA
1 GATGTCCATTAGTAGATAATGTGCCTCATTAAAACCTTATTAGGAAAAACCCTATGA-GATAAAA
29535779 ACCTA
65 ACCTA
* * *
29535784 GATGTCCATTGGTAGATAATGTGCCTCGTTAAAACCTTATTAGGAAAAGCCCTATGAGATAAAAA
1 GATGTCCATTAGTAGATAATGTGCCTCATTAAAACCTTATTAGGAAAAACCCTATGAGATAAAAA
29535849 CCTA
66 CCTA
29535853 ATGAATGAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 62 0.98
70 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (69 bp):
GATGTCCATTAGTAGATAATGTGCCTCATTAAAACCTTATTAGGAAAAACCCTATGAGATAAAAA
CCTA
Found at i:29549765 original size:20 final size:20
Alignment explanation
Indices: 29549740--29549782 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
29549730 AATAACCATA
29549740 GGCCATATCATAATGACATT
1 GGCCATATCATAATGACATT
29549760 GGCCATATCATAATGACATT
1 GGCCATATCATAATGACATT
29549780 GGC
1 GGC
29549783 ACATGCATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (20 bp):
GGCCATATCATAATGACATT
Found at i:29551355 original size:21 final size:19
Alignment explanation
Indices: 29551316--29551372 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
29551306 AATCTTTAAG
29551316 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29551335 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
* *
29551356 GATCTTGTAATCTTAGA
1 GAT-ATGCAATCTTAGA
29551373 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 13 0.39
20 3 0.09
21 9 0.27
22 8 0.24
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29551356 original size:16 final size:17
Alignment explanation
Indices: 29551306--29551356 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
29551296 ATGGAAATAT
*
29551306 AATCTTTAAGGATATGC
1 AATCTTGAAGGATATGC
*
29551323 AATCTTAGATATGATATGC
1 AATCTT-GA-AGGATATGC
29551342 AATCTTGAA-GATATG
1 AATCTTGAAGGATATG
29551357 ATCTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 3 0.10
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
AATCTTGAAGGATATGC
Found at i:29551375 original size:22 final size:21
Alignment explanation
Indices: 29551316--29551358 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
29551306 AATCTTTAAG
29551316 GATATGCAATCTT--AGATAT
1 GATATGCAATCTTGAAGATAT
29551335 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTTGAAGATAT
29551356 GAT
1 GAT
29551359 CTTGTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (21 bp):
GATATGCAATCTTGAAGATAT
Found at i:29554853 original size:44 final size:44
Alignment explanation
Indices: 29554646--29554976 Score: 210
Period size: 44 Copynumber: 7.5 Consensus size: 44
29554636 GGGACAATGT
* *
29554646 AGATCAAAGA-AACAAGATTTGACATCCCTGTGTTTATAGGGAAAC
1 AGATCAAAGATAGC-AGATCTGACATCCCTGTGTTTATAGGG-AAC
* * * *
29554691 AGATCGAAGATAGCAGATCTGACA-CTCCTGTGCTTACAGTGAAAC
1 AGATCAAAGATAGCAGATCTGACATC-CCTGTGTTTATAG-GGAAC
* ** * *
29554736 AGATCGAAGATTTCAG--CATGGCATCCCTATGTTTATAGGGAAC
1 AGATCAAAGATAGCAGATC-TGACATCCCTGTGTTTATAGGGAAC
* ** * *
29554779 AAATTGAAGATAGCAGAT-TTAGTATCCCTGTGTTTATAGGGAAC
1 AGATCAAAGATAGCAGATCTGA-CATCCCTGTGTTTATAGGGAAC
* * * *
29554823 AGATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAGCGAAAC
1 AGATCAAAGATAGCAGATCTGACATCCCTGTGTTTATAG-GGAAC
*** *
29554868 AGATCAAAGATTTTA-A-CATGGCATCCCTGTGTTTATAGGGAAC
1 AGATCAAAGATAGCAGATC-TGACATCCCTGTGTTTATAGGGAAC
** * * * * *
29554911 A-AGTTGAAGATAGCAAATTTGGCATCCCTGTGTTTACAAGGAAC
1 AGA-TCAAAGATAGCAGATCTGACATCCCTGTGTTTATAGGGAAC
* *
29554955 AAATCGAAGACATAGCAGATCT
1 AGATC-AA-AGATAGCAGATCT
29554977 AATTTTCGGA
Statistics
Matches: 218, Mismatches: 51, Indels: 33
0.72 0.17 0.11
Matches are distributed among these distances:
42 1 0.00
43 31 0.14
44 106 0.49
45 67 0.31
46 13 0.06
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (44 bp):
AGATCAAAGATAGCAGATCTGACATCCCTGTGTTTATAGGGAAC
Found at i:29554901 original size:132 final size:132
Alignment explanation
Indices: 29554668--29554976 Score: 456
Period size: 132 Copynumber: 2.3 Consensus size: 132
29554658 CAAGATTTGA
* *
29554668 CATCCCTGTGTTTATAGGGAAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTTACAGTGA
1 CATCCCTGTGTTTATAGGG-AACAGATCAAAGATAGCAGATCTGACACTCCTGTGCTTACAGCGA
* * *
29554733 AACAGATCGAAGATTTCAGCATGGCATCCCTATGTTTATAGGGAACAAATTGAAGATAGCAGATT
65 AACAGATCAAAGATTTCAACATGGCATCCCTATGTTTATAGGGAACAAATTGAAGATAGCAAATT
29554798 TAG
130 TAG
* *
29554801 TATCCCTGTGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAGCGAA
1 CATCCCTGTGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACACTCCTGTGCTTACAGCGAA
* * *
29554866 ACAGATCAAAGATTTTAACATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAAATTT
66 ACAGATCAAAGATTTCAACATGGCATCCCTATGTTTATAGGGAACAAATTGAAGATAGCAAATTT
*
29554931 GG
131 AG
* * * *
29554933 CATCCCTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATCT
1 CATCCCTGTGTTTATAGGGAACAGATC-AA-AGATAGCAGATCT
29554977 AATTTTCGGA
Statistics
Matches: 158, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
132 126 0.80
133 20 0.13
134 12 0.08
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (132 bp):
CATCCCTGTGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACACTCCTGTGCTTACAGCGAA
ACAGATCAAAGATTTCAACATGGCATCCCTATGTTTATAGGGAACAAATTGAAGATAGCAAATTT
AG
Found at i:29555126 original size:175 final size:175
Alignment explanation
Indices: 29554927--29555852 Score: 1555
Period size: 175 Copynumber: 5.3 Consensus size: 175
29554917 AAGATAGCAA
* * * * *
29554927 ATTTGGCATCCCTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATCTAATTTTCGGATGTTC
1 ATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTC
*
29554992 TCACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
66 TTACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
* *
29555057 GCTGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATG
131 GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCTAAGATG
* * *
29555102 ATTTGGCATTATTGTGTTTACAAGGAACAAATCGAAAACATAGCAGATTTGACTTTTGGATGTTC
1 ATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTC
* * *
29555167 TCACACCAAAGCAGATCCAAGATAACAGATCTGGCATCTCCACTTCGACGGAGAGCAGGTACATA
66 TTACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
* *
29555232 GTAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATG
131 GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCTAAGATG
* *
29555277 ATTTGGCATTCTTGTGTTTACAAGGAACAAATTGAAGACATAGTAGATTTGACTTTCGGATGTTC
1 ATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTC
* *
29555342 TTACACCAAAGTAGATCCAAGATAACAGATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
66 TTACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
*
29555407 GCAGGTCTAACCTTCAGATGTTTATATTGAAGCAGATCTAAGATG
131 GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCTAAGATG
* * **
29555452 ATTTGGCATTCTTGTGTTTACAAGAAACAAATTGAAGACATAGCAGATTTGACTTTCAAATGTTC
1 ATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTC
*
29555517 TTACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCTATTTCGACGGAGAGCAGGTACATA
66 TTACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
*
29555582 GAAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCTAAGATG
131 GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCTAAGATG
29555627 ATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTC
1 ATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTC
* *
29555692 TTACACCAAAGCAGATCCAAGATAACTAATCTGGCATCTCCATTTCGATGGAGAGCAGGTACATA
66 TTACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
*
29555757 GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATTTAAGATG
131 GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCTAAGATG
* * *
29555802 ATTTGGTATTCTTGTGTTTATAAGGAACAAATCAAAGACATAGCAGATTTG
1 ATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTG
29555853 GCATTCACGT
Statistics
Matches: 707, Mismatches: 44, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 707 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (175 bp):
ATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTC
TTACACCAAAGCAGATCCAAGATAACAAATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATA
GCAGGTCTAACCTTCAGATGTTTATACTGAAGCAGATCTAAGATG
Found at i:29556345 original size:19 final size:19
Alignment explanation
Indices: 29556321--29556382 Score: 106
Period size: 19 Copynumber: 3.2 Consensus size: 19
29556311 AATCTTTAAG
29556321 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29556340 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29556359 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
29556380 GAT
1 GAT
29556383 CTTGTAATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 32 0.78
21 9 0.22
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29559642 original size:44 final size:45
Alignment explanation
Indices: 29559589--29559688 Score: 130
Period size: 44 Copynumber: 2.2 Consensus size: 45
29559579 CTTTGACATA
* * *
29559589 GACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAATATG
1 GACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAATATG
** *
29559633 GACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAATATG
1 GACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAATATG
29559679 GACTTACATG
1 GACTTACATG
29559689 GCTCATTTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
44 30 0.62
46 18 0.38
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (45 bp):
GACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAATATG
Found at i:29559690 original size:46 final size:44
Alignment explanation
Indices: 29559605--29559693 Score: 142
Period size: 46 Copynumber: 2.0 Consensus size: 44
29559595 CATGAATTAT
*
29559605 TCCTGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAA
1 TCCTGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAA
*
29559649 TCCTGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TCCTGTCTCCAAAGCCATA--TATAATATGGACTTACATGGCTCA
29559694 TTTCTGTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 18 0.44
46 23 0.56
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (44 bp):
TCCTGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAA
Found at i:29564999 original size:24 final size:24
Alignment explanation
Indices: 29564945--29564999 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
29564935 CTTGTTGGTA
* * *
29564945 TTATATTCTTTGTATTGTGTTTTAG
1 TTAT-TTCTCTGTATTGTCTTGTAG
29564970 TTATTTCTCTGTATTGTCTTGT-G
1 TTATTTCTCTGTATTGTCTTGTAG
29564993 TTCATTT
1 TT-ATTT
29565000 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 3 0.12
24 19 0.73
25 4 0.15
ACGTcount: A:0.13, C:0.09, G:0.15, T:0.64
Consensus pattern (24 bp):
TTATTTCTCTGTATTGTCTTGTAG
Found at i:29570115 original size:23 final size:23
Alignment explanation
Indices: 29570085--29570131 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
29570075 TAGGTATTAC
29570085 CTATAAAAAAGTGTTCTCTTTTT
1 CTATAAAAAAGTGTTCTCTTTTT
29570108 CTATAAAAAAGTGTTCTCTTTTT
1 CTATAAAAAAGTGTTCTCTTTTT
29570131 C
1 C
29570132 ATTGGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.47
Consensus pattern (23 bp):
CTATAAAAAAGTGTTCTCTTTTT
Found at i:29578009 original size:25 final size:25
Alignment explanation
Indices: 29577972--29578082 Score: 98
Period size: 25 Copynumber: 4.4 Consensus size: 25
29577962 ATACATGTAT
* *
29577972 GCTCATACAAGCTATGAATCGGTAT
1 GCTCATACGAGCTATGAATCGGTAA
* *
29577997 GCTC-TCACGAGCTGTGAATTGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
* *
29578022 CCTCATACGAGCTAAGAATCGGTAA
1 GCTCATACGAGCTATGAATCGGTAA
* * * * *
29578047 GCTCTTACAAGCTGTAAATCGGGAA
1 GCTCATACGAGCTATGAATCGGTAA
*
29578072 ACTCATACGAG
1 GCTCATACGAG
29578083 TCGTGTTGTG
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
24 1 0.02
25 64 0.97
26 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATCGGTAA
Found at i:29578051 original size:50 final size:50
Alignment explanation
Indices: 29577973--29578082 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
29577963 TACATGTATG
* * * * * * * *
29577973 CTCATACAAGCTATGAATCGGTATGCTCTCACGAGCTGTGAATTGGTAAC
1 CTCATACGAGCTAAGAATCGGTAAGCTCTCACAAGCTGTAAATCGGGAAA
*
29578023 CTCATACGAGCTAAGAATCGGTAAGCTCTTACAAGCTGTAAATCGGGAAA
1 CTCATACGAGCTAAGAATCGGTAAGCTCTCACAAGCTGTAAATCGGGAAA
29578073 CTCATACGAG
1 CTCATACGAG
29578083 TCGTGTTGTG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (50 bp):
CTCATACGAGCTAAGAATCGGTAAGCTCTCACAAGCTGTAAATCGGGAAA
Found at i:29578409 original size:15 final size:15
Alignment explanation
Indices: 29578389--29578427 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
29578379 TATACGAATG
29578389 AATTTAA-CTCATTTC
1 AATTTAATCTCA-TTC
29578404 AATTTAATTCTCATTC
1 AATTTAA-TCTCATTC
29578420 AATTTAAT
1 AATTTAAT
29578428 TCAACATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.36
16 10 0.45
17 4 0.18
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTTAATCTCATTC
Found at i:29578422 original size:16 final size:17
Alignment explanation
Indices: 29578396--29578429 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
29578386 ATGAATTTAA
29578396 CTCATTTCAATTTAATT
1 CTCATTTCAATTTAATT
29578413 CTCA-TTCAATTTAATT
1 CTCATTTCAATTTAATT
29578429 C
1 C
29578430 AACATGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (17 bp):
CTCATTTCAATTTAATT
Found at i:29584267 original size:53 final size:53
Alignment explanation
Indices: 29584204--29584314 Score: 222
Period size: 53 Copynumber: 2.1 Consensus size: 53
29584194 GAATGAAAGC
29584204 AAATTCAAATTCTCAACAATTTTCTTGATGGAAAATTTCAATGGCTAATCGAG
1 AAATTCAAATTCTCAACAATTTTCTTGATGGAAAATTTCAATGGCTAATCGAG
29584257 AAATTCAAATTCTCAACAATTTTCTTGATGGAAAATTTCAATGGCTAATCGAG
1 AAATTCAAATTCTCAACAATTTTCTTGATGGAAAATTTCAATGGCTAATCGAG
29584310 AAATT
1 AAATT
29584315 TCGGATTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (53 bp):
AAATTCAAATTCTCAACAATTTTCTTGATGGAAAATTTCAATGGCTAATCGAG
Found at i:29586960 original size:22 final size:21
Alignment explanation
Indices: 29586924--29586965 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
29586914 GTTAGGATTT
*
29586924 GGTATTTAAATTTAAGTTTTA
1 GGTATTTAAATTTAACTTTTA
*
29586945 GGTATTATATATTTAACTTTT
1 GGTATT-TAAATTTAACTTTT
29586966 TTTAGTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (21 bp):
GGTATTTAAATTTAACTTTTA
Found at i:29589344 original size:19 final size:20
Alignment explanation
Indices: 29589306--29589347 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
29589296 CAAAAAAATT
**
29589306 TATAAAAACAATATTTAAAA
1 TATAAAAACAATATAAAAAA
29589326 TATAAAAA-AATATAAAAAA
1 TATAAAAACAATATAAAAAA
29589345 TAT
1 TAT
29589348 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
TATAAAAACAATATAAAAAA
Found at i:29589344 original size:31 final size:32
Alignment explanation
Indices: 29589297--29589359 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
29589287 TAAAAATTTC
*
29589297 AAAAAAATTTATAAAAACAATATTTAAAATAT
1 AAAAAAATATATAAAAACAATATTTAAAATAT
* * *
29589329 AAAAAAATATA-AAAAATATTTTTTAAAATAT
1 AAAAAAATATATAAAAACAATATTTAAAATAT
29589360 TTTAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (32 bp):
AAAAAAATATATAAAAACAATATTTAAAATAT
Found at i:29590355 original size:30 final size:30
Alignment explanation
Indices: 29590312--29590369 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
29590302 ACAAGAAAAT
29590312 GCCTCTAAAATAATAACAAAATTAACAAAC
1 GCCTCTAAAATAATAACAAAATTAACAAAC
* *
29590342 GCCTTTAATATAATAACAAAATTAACAA
1 GCCTCTAAAATAATAACAAAATTAACAA
29590370 TAAAATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.24
Consensus pattern (30 bp):
GCCTCTAAAATAATAACAAAATTAACAAAC
Found at i:29592880 original size:39 final size:37
Alignment explanation
Indices: 29592794--29592872 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
29592784 ATTTTTGTAC
* * * *
29592794 ATACACTTATACACATACCTTTTTTTGTAATATATAT
1 ATACACATATAAACATACCTATTTTTATAATATATAT
*
29592831 ATACACATATAAACATACCTATTTTTATAATATATTT
1 ATACACATATAAACATACCTATTTTTATAATATATAT
29592868 ATACA
1 ATACA
29592873 TGTATATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.15, G:0.01, T:0.43
Consensus pattern (37 bp):
ATACACATATAAACATACCTATTTTTATAATATATAT
Found at i:29592914 original size:44 final size:44
Alignment explanation
Indices: 29592875--29592958 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
29592865 TTTATACATG
* * *
29592875 TATATATTTATAATACATGCACATATTTCCT-ATTTTTATAAACC
1 TATATATATAT-ATACATACACATATTTCATAATTTTTATAAACC
* *
29592919 TATATGTATATATACTTACACATATTTCATAATTTTTATA
1 TATATATATATATACATACACATATTTCATAATTTTTATA
29592959 TATATCTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 16 0.47
44 18 0.53
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (44 bp):
TATATATATATATACATACACATATTTCATAATTTTTATAAACC
Found at i:29592969 original size:44 final size:43
Alignment explanation
Indices: 29592894--29592977 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
29592884 ATAATACATG
* * *
29592894 CACATATTTCCTATTTTTATAAACCTATATGTATATATACTTA
1 CACATATTTCATATTTTTATAAACATATATGTACATATACTTA
* * *
29592937 CACATATTTCATAATTTTTATATATATCTATGTACATATAC
1 CACATATTTCAT-ATTTTTATAAACATATATGTACATATAC
29592978 ATATTTTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 11 0.32
44 23 0.68
ACGTcount: A:0.36, C:0.15, G:0.02, T:0.46
Consensus pattern (43 bp):
CACATATTTCATATTTTTATAAACATATATGTACATATACTTA
Found at i:29599826 original size:28 final size:28
Alignment explanation
Indices: 29599795--29599859 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
29599785 AGCTTTTGGC
* * *
29599795 TTTAGGGTTTATTATTTAATATTTTAAG
1 TTTAGGGTTTAGTATTTAAGATTTAAAG
* * * *
29599823 TTTAAGGTGTAGTGTTTAAGGTTTAAAG
1 TTTAGGGTTTAGTATTTAAGATTTAAAG
29599851 TTTAGGGTT
1 TTTAGGGTT
29599860 CATGTGTTTT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (28 bp):
TTTAGGGTTTAGTATTTAAGATTTAAAG
Found at i:29600452 original size:20 final size:21
Alignment explanation
Indices: 29600415--29600459 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
29600405 GAGGTCAAGA
*
29600415 TTTATGGTTTCATGTTTTGGG
1 TTTATGGTTTCATGTTTTGAG
* *
29600436 TTTAT-GTTTTATTTTTTGAG
1 TTTATGGTTTCATGTTTTGAG
29600456 TTTA
1 TTTA
29600460 AAGTTTTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.13, C:0.02, G:0.20, T:0.64
Consensus pattern (21 bp):
TTTATGGTTTCATGTTTTGAG
Found at i:29606347 original size:13 final size:13
Alignment explanation
Indices: 29606329--29606356 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29606319 TGAACATGCT
29606329 TTGTAATAATTAA
1 TTGTAATAATTAA
29606342 TTGTAATAATTAA
1 TTGTAATAATTAA
29606355 TT
1 TT
29606357 TTTATAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
TTGTAATAATTAA
Found at i:29621665 original size:16 final size:16
Alignment explanation
Indices: 29621644--29621674 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29621634 TAAAATTTTT
29621644 AAATAAAAAATAACAA
1 AAATAAAAAATAACAA
*
29621660 AAATAAAGAATAACA
1 AAATAAAAAATAACA
29621675 TTTATTCACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.13
Consensus pattern (16 bp):
AAATAAAAAATAACAA
Found at i:29650534 original size:47 final size:47
Alignment explanation
Indices: 29650466--29650560 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
29650456 GTATGTTGGT
*
29650466 TATATAAACAAAATATTATTCATAATATTTACATAAACTGACTTTGA
1 TATATAAACAAAATATTATTCATAATATTTACATAAACTAACTTTGA
29650513 TATATAAACAAAATATTATTCATAATATTTACATAAACTAACTTTGA
1 TATATAAACAAAATATTATTCATAATATTTACATAAACTAACTTTGA
29650560 T
1 T
29650561 GAAGTCCATA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (47 bp):
TATATAAACAAAATATTATTCATAATATTTACATAAACTAACTTTGA
Found at i:29650818 original size:21 final size:20
Alignment explanation
Indices: 29650785--29650831 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
29650775 ATAAATAAAA
29650785 TCATTCATGTCAATTCCCTG
1 TCATTCATGTCAATTCCCTG
*
29650805 TCATTCACTGTCAATTTCCTG
1 TCATTCA-TGTCAATTCCCTG
29650826 TCATTC
1 TCATTC
29650832 TTAACTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.19, C:0.30, G:0.09, T:0.43
Consensus pattern (20 bp):
TCATTCATGTCAATTCCCTG
Found at i:29651038 original size:19 final size:19
Alignment explanation
Indices: 29651012--29651071 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
29651002 CGAATACGCC
*
29651012 AACAGAAGCTCGAAAGTTG
1 AACAGAAGCTCGAAAGCTG
* *
29651031 AGCAGAAGCTCGTAAGCTG
1 AACAGAAGCTCGAAAGCTG
29651050 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCG-AA-AGCTG
29651071 A
1 A
29651072 TTCACCCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 27 0.79
20 1 0.03
21 6 0.18
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.15
Consensus pattern (19 bp):
AACAGAAGCTCGAAAGCTG
Found at i:29653675 original size:17 final size:16
Alignment explanation
Indices: 29653647--29653699 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
29653637 TTTGGTTCGC
29653647 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
29653663 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
29653680 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
29653696 TGTA
1 TGTA
29653700 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:29653764 original size:44 final size:45
Alignment explanation
Indices: 29653680--29653770 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
29653670 GGATTAGAGG
* * *
29653680 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
29653725 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
29653769 TG
1 TG
29653771 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:29653956 original size:18 final size:17
Alignment explanation
Indices: 29653935--29653969 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29653925 TTATTATTAA
*
29653935 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29653953 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29653970 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29654068 original size:15 final size:15
Alignment explanation
Indices: 29654050--29654107 Score: 80
Period size: 16 Copynumber: 3.7 Consensus size: 15
29654040 CATAATTATT
29654050 ATTAAATATATTTTA
1 ATTAAATATATTTTA
29654065 ATTAAAATATATTTTA
1 ATT-AAATATATTTTA
*
29654081 ATTAAATATAATTTA
1 ATTAAATATATTTTA
*
29654096 ATAATAATATAT
1 ATTA-AATATAT
29654108 AATTTCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 17 0.45
16 21 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTAAATATATTTTA
Found at i:29654088 original size:31 final size:31
Alignment explanation
Indices: 29654034--29654107 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
29654024 GTAAAATATA
* *
29654034 AATTAACATA-ATTATTATTAAATATATTTT
1 AATTAAAATATATTATTATTAAATATAATTT
29654064 AATTAAAATATATT-TTAATTAAATATAATTT
1 AATTAAAATATATTATT-ATTAAATATAATTT
29654095 AA-TAATAATATAT
1 AATTAA-AATATAT
29654108 AATTTCATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 14 0.36
31 25 0.64
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (31 bp):
AATTAAAATATATTATTATTAAATATAATTT
Found at i:29654109 original size:18 final size:18
Alignment explanation
Indices: 29654055--29654117 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
29654045 TTATTATTAA
*
29654055 ATATATTTTAATTAA-AAT
1 ATATAATTTAA-TAATAAT
29654073 ATAT--TTTAAT--TAA-
1 ATATAATTTAATAATAAT
29654086 ATATAATTTAATAATAAT
1 ATATAATTTAATAATAAT
*
29654104 ATATAATTTCATAA
1 ATATAATTTAATAA
29654118 AATTCTTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 4 0.11
14 2 0.05
15 7 0.18
16 5 0.13
17 3 0.08
18 17 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATAATTTAATAATAAT
Found at i:29654134 original size:47 final size:46
Alignment explanation
Indices: 29654083--29654227 Score: 156
Period size: 47 Copynumber: 3.2 Consensus size: 46
29654073 ATATTTTAAT
*
29654083 TAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAA
1 TAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTAATAA
* * ** *
29654130 TAAAT-T-TTCTTATATGAATTTATATAA-TT--TAAAATAATTAATAT
1 TAAATATAAT-TTA-AT-AATATATATAATTTCATAAAATTCTTAATAA
29654174 TAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAA
1 TAAATATAATTTAATAAT-ATATATAATTTCATAAAATTCTTAATAA
29654221 TAAATAT
1 TAAATAT
29654228 TCTTATATAA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
43 3 0.04
44 25 0.32
45 7 0.09
46 7 0.09
47 33 0.42
48 3 0.04
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (46 bp):
TAAATATAATTTAATAATATATATAATTTCATAAAATTCTTAATAA
Found at i:29654198 original size:44 final size:43
Alignment explanation
Indices: 29654081--29654203 Score: 106
Period size: 44 Copynumber: 2.7 Consensus size: 43
29654071 ATATATTTTA
** *
29654081 ATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTGAT
1 ATTAAATATAATTTAATAAT-ATATATAA-TT--TAAAATAATTAAT
* * *
29654128 AATAAAT-T-TTCTTATATGAATTTATATAATTTAAAATAATTAAT
1 ATTAAATATAAT-TTA-AT-AATATATATAATTTAAAATAATTAAT
29654172 ATTAAATATAATTTAATAATGATATATAATTT
1 ATTAAATATAATTTAATAAT-ATATATAATTT
29654204 CATAAAATTC
Statistics
Matches: 61, Mismatches: 9, Indels: 15
0.72 0.11 0.18
Matches are distributed among these distances:
43 3 0.05
44 28 0.46
45 5 0.08
46 7 0.11
47 15 0.25
48 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (43 bp):
ATTAAATATAATTTAATAATATATATAATTTAAAATAATTAAT
Found at i:29654231 original size:16 final size:16
Alignment explanation
Indices: 29654205--29654238 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
29654195 ATATAATTTC
29654205 ATAAAATTCTTA-ATA
1 ATAAAATTCTTATATA
29654220 ATAAATATTCTTATATA
1 ATAAA-ATTCTTATATA
29654237 AT
1 AT
29654239 TTACTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAATTCTTATATA
Found at i:29654585 original size:66 final size:66
Alignment explanation
Indices: 29654479--29654609 Score: 217
Period size: 66 Copynumber: 2.0 Consensus size: 66
29654469 CGCAAATGTG
* *
29654479 ATTTGAGTTCAAATTAGATTCATAGTAAGCTCAAATTTTTATTAATGCCAATGCCAACACTACCA
1 ATTTGAGTTCAAATTAGACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
29654544 C
66 C
* * *
29654545 ATTTGGGTTCAAATTATACTCATAGTAAGCTCAAACTTTTATTGATGCCAATGCCAACACTACCA
1 ATTTGAGTTCAAATTAGACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
29654610 AAACCTTTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (66 bp):
ATTTGAGTTCAAATTAGACTCATAGTAAGCTCAAACTTTTATTAATGCCAATGCCAACACTACCA
C
Found at i:29659604 original size:23 final size:23
Alignment explanation
Indices: 29659576--29659619 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
29659566 AAAATTTTCT
*
29659576 AATTTAGTATCTAAATTTGATTC
1 AATTTAGAATCTAAATTTGATTC
*
29659599 AATTTAGAATTTAAATTTGAT
1 AATTTAGAATCTAAATTTGAT
29659620 AAATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (23 bp):
AATTTAGAATCTAAATTTGATTC
Found at i:29666768 original size:32 final size:33
Alignment explanation
Indices: 29666710--29666774 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
29666700 ATGATGAAAA
29666710 ACCTTGTTTGCTGGTGCTTTTTTTCTTCTTGTT
1 ACCTTGTTTGCTGGTGCTTTTTTTCTTCTTGTT
*
29666743 ACCTTGTTTTCTGGTG-TTTTTTTCTTCTTGTT
1 ACCTTGTTTGCTGGTGCTTTTTTTCTTCTTGTT
29666775 GTCGAAATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.03, C:0.17, G:0.17, T:0.63
Consensus pattern (33 bp):
ACCTTGTTTGCTGGTGCTTTTTTTCTTCTTGTT
Found at i:29671962 original size:3 final size:3
Alignment explanation
Indices: 29671954--29671978 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29671944 ATAAACCCAT
29671954 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
29671979 ACAGAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:29674386 original size:26 final size:26
Alignment explanation
Indices: 29674357--29674443 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 26
29674347 AGACACGAAG
29674357 AAAAATATAAATTTAACGAAAGACAAAA
1 AAAAATATAAATTTAACGAAAGAC--AA
* * * *
29674385 AAAAAAAAAAACGTTTCAA-GACACGA-AG
1 AAAAATATAAA--TTT-AACGA-AAGACAA
29674413 AAAAATATAAATTTAACGAAAGACAA
1 AAAAATATAAATTTAACGAAAGACAA
29674439 AAAAA
1 AAAAA
29674444 AAAACACGGG
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 5 0.11
26 11 0.24
28 19 0.42
30 5 0.11
31 5 0.11
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.15
Consensus pattern (26 bp):
AAAAATATAAATTTAACGAAAGACAA
Found at i:29674391 original size:30 final size:30
Alignment explanation
Indices: 29674357--29674447 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
29674347 AGACACGAAG
29674357 AAAAATATAAATTTAACGAAAGACAAAAAA
1 AAAAATATAAATTTAACGAAAGACAAAAAA
** *
29674387 AAAAA-A-AAACGTTT--C--AAGACACGAAG
1 AAAAATATAAA--TTTAACGAAAGACAAAAAA
29674413 AAAAATATAAATTTAACGAAAGACAAAAAA
1 AAAAATATAAATTTAACGAAAGACAAAAAA
29674443 AAAAA
1 AAAAA
29674448 CACGGGTAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
26 16 0.34
27 1 0.02
28 8 0.17
29 1 0.02
30 21 0.45
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.14
Consensus pattern (30 bp):
AAAAATATAAATTTAACGAAAGACAAAAAA
Found at i:29674428 original size:56 final size:56
Alignment explanation
Indices: 29674342--29674447 Score: 212
Period size: 56 Copynumber: 1.9 Consensus size: 56
29674332 CTTTTTGTTA
29674342 TTTCAAGACACGAAGAAAAATATAAATTTAACGAAAGACAAAAAAAAAAAAAAACG
1 TTTCAAGACACGAAGAAAAATATAAATTTAACGAAAGACAAAAAAAAAAAAAAACG
29674398 TTTCAAGACACGAAGAAAAATATAAATTTAACGAAAGACAAAAAAAAAAA
1 TTTCAAGACACGAAGAAAAATATAAATTTAACGAAAGACAAAAAAAAAAA
29674448 CACGGGTAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.15
Consensus pattern (56 bp):
TTTCAAGACACGAAGAAAAATATAAATTTAACGAAAGACAAAAAAAAAAAAAAACG
Found at i:29675090 original size:221 final size:221
Alignment explanation
Indices: 29674830--29675271 Score: 875
Period size: 221 Copynumber: 2.0 Consensus size: 221
29674820 TTCGTACTTG
29674830 ACTCAGTACTTTGAGGACTTACTCTCTTTTCTTTTTTTTTGTTTTAATTAATATAAAAAAAATCT
1 ACTCAGTACTTTGAGGACTTACTCTCTTTTCTTTTTTTTTGTTTTAATTAATATAAAAAAAATCT
29674895 CAATTAAATTATCGATTGAACTTTAACACAATTGACATTGTTGCTATTACAACAATTAAGAAGAC
66 CAATTAAATTATCGATTGAACTTTAACACAATTGACATTGTTGCTATTACAACAATTAAGAAGAC
29674960 CTGTGCTTAAACACATTTTTTTGAGAGGGATTATAAGTAAAAAATAAGTTTTGTACACAAAAAAA
131 CTGTGCTTAAACACATTTTTTTGAGAGGGATTATAAGTAAAAAATAAGTTTTGTACACAAAAAAA
29675025 AAGTCTCAATTTAAATTCAAAATTGA
196 AAGTCTCAATTTAAATTCAAAATTGA
*
29675051 ACTCAGTACTTTGAGGACTTCCTCTCTTTTCTTTTTTTTTGTTTTAATTAATATAAAAAAAATCT
1 ACTCAGTACTTTGAGGACTTACTCTCTTTTCTTTTTTTTTGTTTTAATTAATATAAAAAAAATCT
29675116 CAATTAAATTATCGATTGAACTTTAACACAATTGACATTGTTGCTATTACAACAATTAAGAAGAC
66 CAATTAAATTATCGATTGAACTTTAACACAATTGACATTGTTGCTATTACAACAATTAAGAAGAC
29675181 CTGTGCTTAAACACATTTTTTTGAGAGGGATTATAAGTAAAAAATAAGTTTTGTACACAAAAAAA
131 CTGTGCTTAAACACATTTTTTTGAGAGGGATTATAAGTAAAAAATAAGTTTTGTACACAAAAAAA
29675246 AAGTCTCAATTTAAATTCAAAATTGA
196 AAGTCTCAATTTAAATTCAAAATTGA
29675272 TTATTTTTTA
Statistics
Matches: 220, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 220 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.38
Consensus pattern (221 bp):
ACTCAGTACTTTGAGGACTTACTCTCTTTTCTTTTTTTTTGTTTTAATTAATATAAAAAAAATCT
CAATTAAATTATCGATTGAACTTTAACACAATTGACATTGTTGCTATTACAACAATTAAGAAGAC
CTGTGCTTAAACACATTTTTTTGAGAGGGATTATAAGTAAAAAATAAGTTTTGTACACAAAAAAA
AAGTCTCAATTTAAATTCAAAATTGA
Found at i:29703027 original size:61 final size:61
Alignment explanation
Indices: 29702932--29703058 Score: 254
Period size: 61 Copynumber: 2.1 Consensus size: 61
29702922 GTGGGAGTCC
29702932 AAATAGGTTTTAAATGCTAACTTGGATGTCCAGTTGCTGGAATGAAAATAAGTTTTTAATT
1 AAATAGGTTTTAAATGCTAACTTGGATGTCCAGTTGCTGGAATGAAAATAAGTTTTTAATT
29702993 AAATAGGTTTTAAATGCTAACTTGGATGTCCAGTTGCTGGAATGAAAATAAGTTTTTAATT
1 AAATAGGTTTTAAATGCTAACTTGGATGTCCAGTTGCTGGAATGAAAATAAGTTTTTAATT
29703054 AAATA
1 AAATA
29703059 AATTTAATTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (61 bp):
AAATAGGTTTTAAATGCTAACTTGGATGTCCAGTTGCTGGAATGAAAATAAGTTTTTAATT
Found at i:29714337 original size:100 final size:99
Alignment explanation
Indices: 29714159--29714352 Score: 289
Period size: 100 Copynumber: 1.9 Consensus size: 99
29714149 TCTTCTGGAG
* * * * *
29714159 TCATCTTATTCCTCGGGTGCCATGCTTTATCTGCTAAAAACCCTTTGGTTTATGTTTGTTTGAGA
1 TCATCTTATTCCTCGGGTGCCAAGCTTTATCTGCTAAAAACCATTTGCTTAATGTCTGTTTGAGA
* * *
29714224 ATATATTTCTTAAAATTATTCAATACCATGTTCCA
66 AAACATTTATT-AAATTATTCAATACCATGTTCCA
* *
29714259 TCATCTTATTCCTTGGGTGCCAAGCTTTATCTGCTAAAAACCATTTGCTTAATGTCTGTTTGTGA
1 TCATCTTATTCCTCGGGTGCCAAGCTTTATCTGCTAAAAACCATTTGCTTAATGTCTGTTTGAGA
29714324 AAACATTTATTAAATTATTCAATACCATG
66 AAACATTTATTAAATTATTCAATACCATG
29714353 CGTCATTACT
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 18 0.21
100 66 0.79
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.42
Consensus pattern (99 bp):
TCATCTTATTCCTCGGGTGCCAAGCTTTATCTGCTAAAAACCATTTGCTTAATGTCTGTTTGAGA
AAACATTTATTAAATTATTCAATACCATGTTCCA
Done.