Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 115 of 210
Found at i:38703550 original size:53 final size:53
Alignment explanation
Indices: 38703492--38703599 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
38703482 TTATATTGTT
*
38703492 TATGTAGTTAAATATTCTTGTACTTCTTCTACTAATTAAATAATCGGTCCATG
1 TATGTAGTTAAATAATCTTGTACTTCTTCTACTAATTAAATAATCGGTCCATG
*
38703545 TATGTAGTTAAATAATCTTGTACTTCTTCTATTAATTAAATAATCGGTCCATG
1 TATGTAGTTAAATAATCTTGTACTTCTTCTACTAATTAAATAATCGGTCCATG
38703598 TA
1 TA
38703600 AACATGACAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (53 bp):
TATGTAGTTAAATAATCTTGTACTTCTTCTACTAATTAAATAATCGGTCCATG
Found at i:38703899 original size:15 final size:15
Alignment explanation
Indices: 38703879--38703908 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38703869 CCGATCATCG
38703879 GGTCCGAGCTATAGA
1 GGTCCGAGCTATAGA
38703894 GGTCCGAGCTATAGA
1 GGTCCGAGCTATAGA
38703909 ATGTCACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (15 bp):
GGTCCGAGCTATAGA
Found at i:38706424 original size:15 final size:15
Alignment explanation
Indices: 38706404--38706433 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38706394 TTCACTATTA
*
38706404 TGTCTTTTGTATTTT
1 TGTCTTTTATATTTT
38706419 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
38706434 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (15 bp):
TGTCTTTTATATTTT
Found at i:38707787 original size:23 final size:23
Alignment explanation
Indices: 38707761--38707882 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
38707751 ATAAGTGCCA
38707761 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
38707784 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
38707807 CACTGAAATGGAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
38707830 CACTGATATGGAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
38707853 CACTGA-ATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
38707876 CACTGAT
1 CACTGAT
38707883 CAATAACACT
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
22 1 0.01
23 86 0.99
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:38707828 original size:46 final size:46
Alignment explanation
Indices: 38707761--38707882 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
38707751 ATAAGTGCCA
* *
38707761 CACTGATATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGGAGCCGTAGCTAC
* *
38707807 CACTGAAATGGAGCCGAAGCTACCACTGATATGGAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGGAGCCGTAGCTAC
*
38707853 CACTGAATTGTAGCCGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
38707883 CAATAACACT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATACGGAGCCGTAGCTAC
Found at i:38710143 original size:13 final size:13
Alignment explanation
Indices: 38710122--38710170 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
38710112 ATTACTCAAC
*
38710122 TAAATAATTTGAT
1 TAAAGAATTTGAT
*
38710135 TAAAGAATTTAAT
1 TAAAGAATTTGAT
*
38710148 TAAGGAATTTGAT
1 TAAAGAATTTGAT
*
38710161 TAAGGAATTT
1 TAAAGAATTT
38710171 TCTTGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (13 bp):
TAAAGAATTTGAT
Found at i:38710577 original size:71 final size:69
Alignment explanation
Indices: 38710493--38710662 Score: 243
Period size: 71 Copynumber: 2.4 Consensus size: 69
38710483 AATACTTATC
*
38710493 TATTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAAAAATTAAATTTAATATTTATCT
1 TATTTTATTAATTTAATATTAAAGTGATTATCTTAATATT---AAATTAAATCTAATATTTATCT
*
38710558 TAAT-AG
63 TAATAAA
* * *
38710564 TATTTTATTAATTTAAAATTAAAGTGATTATCTTAATATTAAATTTAATCTAATATTTATCTTGA
1 TATTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAAATCTAATATTTATCTTAA
38710629 TAAA
66 TAAA
* *
38710633 TATTATATTAATTTATTATTAAAGTGATTA
1 TATTTTATTAATTTAATATTAAAGTGATTA
38710663 AGTTTAATCA
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
68 23 0.26
69 28 0.31
71 39 0.43
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (69 bp):
TATTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAAATCTAATATTTATCTTAA
TAAA
Found at i:38714376 original size:23 final size:23
Alignment explanation
Indices: 38714345--38714395 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
38714335 ACCTACTTTC
* * *
38714345 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGAGATA
38714368 TTACAGTAGTAATTTTCGAGATA
1 TTACAGTAGTAATTTTCGAGATA
38714391 TTACA
1 TTACA
38714396 ACGACATTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGAGATA
Found at i:38731329 original size:180 final size:181
Alignment explanation
Indices: 38731027--38731387 Score: 656
Period size: 180 Copynumber: 2.0 Consensus size: 181
38731017 CATCATGTTG
*
38731027 TTTTTATTGTGTGGGGGCGACGGAATGAGGAGCGATAGAAATGGGAGTAGGGAATTGACGGTGAT
1 TTTTTATTGTGTGGGGGCGACGGAATGAGGAGCGATAGAAATAGGAGTAGGGAATTGACGGTGAT
38731092 GAAATTTAGTGATTTTTATGGTGGATGTTGAGGGTAATGAAAATGGGTGGTTCTTATTTTGCAAA
66 GAAATTTAGTGATTTTTATGGTGGATGTTGAGGGTAATGAAAATGGGTGGTTCTTATTTTGCAAA
*
38731157 TAAAAAAATTGTTTTGGACTAATTGTAGAAAGGA-CCTAACTTTAGTCAAA
131 TAAAAAAAGTGTTTTGGACTAATTGTAGAAAGGACCCTAACTTTAGTCAAA
38731207 TTTTTATTGTGTGGGGGCGAC-GAAGTGAGGAGCGATA-AAGATAGGAGTAGGGAATTGACGGTG
1 TTTTTATTGTGTGGGGGCGACGGAA-TGAGGAGCGATAGAA-ATAGGAGTAGGGAATTGACGGTG
38731270 ATGAAATTTAGTGATTTTTATGGTGGATGTTGAGGGTAATGAAAATGGGTGGTTCTTATTTTGCA
64 ATGAAATTTAGTGATTTTTATGGTGGATGTTGAGGGTAATGAAAATGGGTGGTTCTTATTTTGCA
*
38731335 AATAAAAAAAGTGTTTTGGACTAATTGTAGAGAGGACCCTAACTTTAGTCAAA
129 AATAAAAAAAGTGTTTTGGACTAATTGTAGAAAGGACCCTAACTTTAGTCAAA
38731388 AGTAAAAAAA
Statistics
Matches: 175, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
179 5 0.03
180 154 0.88
181 16 0.09
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.32
Consensus pattern (181 bp):
TTTTTATTGTGTGGGGGCGACGGAATGAGGAGCGATAGAAATAGGAGTAGGGAATTGACGGTGAT
GAAATTTAGTGATTTTTATGGTGGATGTTGAGGGTAATGAAAATGGGTGGTTCTTATTTTGCAAA
TAAAAAAAGTGTTTTGGACTAATTGTAGAAAGGACCCTAACTTTAGTCAAA
Found at i:38731811 original size:16 final size:15
Alignment explanation
Indices: 38731786--38731830 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
38731776 TACAACTCTC
38731786 TAATTAGTTTAAATT
1 TAATTAGTTTAAATT
38731801 TAATGTAGTTTAAATT
1 TAAT-TAGTTTAAATT
*
38731817 TGATT--TTTAAATT
1 TAATTAGTTTAAATT
38731830 T
1 T
38731831 TAAATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 9 0.32
15 5 0.18
16 14 0.50
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (15 bp):
TAATTAGTTTAAATT
Found at i:38734842 original size:22 final size:22
Alignment explanation
Indices: 38734817--38734863 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
38734807 AAAACACGTG
* *
38734817 AATTTATACTTATTGCATGAAA
1 AATTTAAACTTAATGCATGAAA
*
38734839 AATTTAAACTTAATGCATTAAA
1 AATTTAAACTTAATGCATGAAA
38734861 AAT
1 AAT
38734864 GTCATTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (22 bp):
AATTTAAACTTAATGCATGAAA
Found at i:38752187 original size:23 final size:22
Alignment explanation
Indices: 38752161--38752203 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
38752151 GAGATCAAAA
*
38752161 TATAATTTTATCATTTATTGATT
1 TATAATTTGATCATTT-TTGATT
38752184 TATAATTTGATCATTTTTGA
1 TATAATTTGATCATTTTTGA
38752204 AGTAATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (22 bp):
TATAATTTGATCATTTTTGATT
Found at i:38753859 original size:137 final size:138
Alignment explanation
Indices: 38753697--38753972 Score: 545
Period size: 137 Copynumber: 2.0 Consensus size: 138
38753687 TCTAGTATCA
38753697 ATTCCAATCCAGCTCAATAAAAACAATAAAACATTGTTAATTTTTTTTCATAATAAATATTAAAA
1 ATTCCAATCCAGCTCAATAAAAACAATAAAACATTGTTAATTTTTTTTCATAATAAATATTAAAA
38753762 TAAACTATCTAAATAGAGGTTAATAAAACACGGGTACTCACAAATTATTTAAATTCCATTTAAAA
66 TAAACTATCTAAATAGAGGTTAATAAAACACGGGTACTCACAAATTATTTAAATTCCATTTAAAA
38753827 AATATTTG
131 AATATTTG
38753835 ATTCCAATCCA-CTCAATAAAAACAATAAAACATTGTTAATTTTTTTTCATAATAAATATTAAAA
1 ATTCCAATCCAGCTCAATAAAAACAATAAAACATTGTTAATTTTTTTTCATAATAAATATTAAAA
38753899 TAAACTATCTAAATAGAGGTTAATAAAACACGGGTACTCACAAATTATTTAAATTCCATTTAAAA
66 TAAACTATCTAAATAGAGGTTAATAAAACACGGGTACTCACAAATTATTTAAATTCCATTTAAAA
38753964 AATATTTG
131 AATATTTG
38753972 A
1 A
38753973 ATTTAATTTG
Statistics
Matches: 138, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
137 127 0.92
138 11 0.08
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (138 bp):
ATTCCAATCCAGCTCAATAAAAACAATAAAACATTGTTAATTTTTTTTCATAATAAATATTAAAA
TAAACTATCTAAATAGAGGTTAATAAAACACGGGTACTCACAAATTATTTAAATTCCATTTAAAA
AATATTTG
Found at i:38760767 original size:3 final size:3
Alignment explanation
Indices: 38760759--38760789 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
38760749 ACCAGTTTTT
*
38760759 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38760790 GATAGAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:38763799 original size:20 final size:19
Alignment explanation
Indices: 38763766--38763808 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
38763756 TCACACTAAT
*
38763766 AAATAATTTAAAAACTATAA
1 AAATAATTTAAAAAATA-AA
* *
38763786 AAATATTTTTAAAAATAAA
1 AAATAATTTAAAAAATAAA
38763805 AAAT
1 AAAT
38763809 TCAAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATTTAAAAAATAAA
Found at i:38769121 original size:53 final size:52
Alignment explanation
Indices: 38769013--38769162 Score: 162
Period size: 53 Copynumber: 2.9 Consensus size: 52
38769003 GTATACAAAA
38769013 AAAATAAAAAAAAATTTGGGTGCT-TGCCTGTCAATGGGT-GGCACCACCTAGG
1 AAAATAAAAAAAAATTTGGGTGCTGT-CCTGTCAAT-GGTCGGCACCACCTAGG
* * * **
38769065 AAAATGAAAAAAAAATTTGGGTGCTGTCGTGTCAATGGTCGGCACCGCTTTTG
1 AAAAT-AAAAAAAAATTTGGGTGCTGTCCTGTCAATGGTCGGCACCACCTAGG
* * * * *
38769118 AAAA-CAAAAAAAATTTGGGCGCTGGCCTGTCAATAGCCGGCACCA
1 AAAATAAAAAAAAATTTGGGTGCTGTCCTGTCAATGGTCGGCACCA
38769163 ACACTAAAAC
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
51 34 0.41
52 8 0.10
53 40 0.48
54 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (52 bp):
AAAATAAAAAAAAATTTGGGTGCTGTCCTGTCAATGGTCGGCACCACCTAGG
Found at i:38769280 original size:194 final size:195
Alignment explanation
Indices: 38768981--38769347 Score: 427
Period size: 194 Copynumber: 1.9 Consensus size: 195
38768971 ACCAGTGTAT
* *
38768981 TTTTTTGAATCGTATCATACTGGTATACAAAAAAAATAAAAAAAAATTTGGGTGCTTGCCTGTCA
1 TTTTTTGAATCGTATCATACTGGTATACAAAAAAAACAAAAAAAAATTTGGGTGCTGGCCTGTCA
** * * * * * *
38769046 ATGGGTGGCACCACCTAGGAAAATGAAAAAAAAATTTGGGTGCTGTCGTGTCAATGGTCGGCACC
66 ATGGCCGACACCACCTAGGAAAACGAAAAAAAAATTTGGGTACTGGCCTATCAATGGTCGGCACC
**
38769111 -GCTTTTGAAAAC-AAAAAAAA-TTTGGGCGCTGGCCTGTCAATAGCCGGCACCAACACTAAAAC
131 AGC--ACGAAAACGAAAAAAAATTTTGGGCGCTGGCCTGTCAATAGCCGGCACCAACACTAAAAC
38769173 AA
194 AA
* * *** ** * *
38769175 TTTTTTG-TTCGTATTATACTGGTATACAAAAAAAACAACAAAATTTTTTTTGTGCTGGCTTGTT
1 TTTTTTGAATCGTATCATACTGGTATACAAAAAAAACAA-AAAAAAATTTGGGTGCTGGCCTGTC
**** *
38769239 AATGGCCGACACCACCTAGGAAAACGAAAAATTTTTTTGGGTACTGGCCTATCAATGGTCTGCAC
65 AATGGCCGACACCACCTAGGAAAACGAAAAAAAAATTTGGGTACTGGCCTATCAATGGTCGGCAC
*
38769304 CAGCACGAAAACGGAAAAAAAATTTTGGGTGCTGGCCTGTCAAT
130 CAGCACGAAAAC-GAAAAAAAATTTTGGGCGCTGGCCTGTCAAT
38769348 GGCGAACACC
Statistics
Matches: 141, Mismatches: 27, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
193 34 0.24
194 77 0.55
195 10 0.07
196 20 0.14
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (195 bp):
TTTTTTGAATCGTATCATACTGGTATACAAAAAAAACAAAAAAAAATTTGGGTGCTGGCCTGTCA
ATGGCCGACACCACCTAGGAAAACGAAAAAAAAATTTGGGTACTGGCCTATCAATGGTCGGCACC
AGCACGAAAACGAAAAAAAATTTTGGGCGCTGGCCTGTCAATAGCCGGCACCAACACTAAAACAA
Found at i:38769296 original size:53 final size:52
Alignment explanation
Indices: 38769239--38769477 Score: 180
Period size: 53 Copynumber: 4.4 Consensus size: 52
38769229 CTGGCTTGTT
* ***
38769239 AATGGCCGACACCACCTAGGAAAACGAAAAATTTTTTTGGGTACTGGCCTATC
1 AATGGCCGACACCA-CTACGAAAACGAAAAAAAATTTTGGGTACTGGCCTATC
* * *
38769292 AATGGTCTG-CACCAGC-ACGAAAACGGAAAAAAAATTTTGGGTGCTGGCCTGTC
1 AATGG-CCGACACCA-CTACGAAAAC-GAAAAAAAATTTTGGGTACTGGCCTATC
* * *** *
38769345 AATGG-CGAACACCAATACGAAAACGAAAAAAAAATTTTGGGTGCTGATTTGTC
1 AATGGCCG-ACACCACTACGAAAACG-AAAAAAAATTTTGGGTACTGGCCTATC
* * *
38769398 AATGGCTGGCACTACCAGTACGAAAACAGAAAAAAAAATTTTGGGTGCTAGG-CTATC
1 AATGGC-CG-AC-ACCACTACGAAAAC-G-AAAAAAAATTTTGGGTACT-GGCCTATC
*
38769455 AATGGCCGACACCAGTACTGAAA
1 AATGGCCGACACCACTAC-GAAA
38769478 CAAATTCTTT
Statistics
Matches: 154, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
51 1 0.01
52 8 0.05
53 81 0.53
54 10 0.06
55 9 0.06
56 14 0.09
57 30 0.19
58 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (52 bp):
AATGGCCGACACCACTACGAAAACGAAAAAAAATTTTGGGTACTGGCCTATC
Found at i:38769443 original size:57 final size:53
Alignment explanation
Indices: 38769301--38769477 Score: 196
Period size: 53 Copynumber: 3.2 Consensus size: 53
38769291 CAATGGTCTG
* * *
38769301 CACCAGCACGAAAACGGAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCGAA
1 CACCAGTACGAAAACGAAAAAAAAATTTTGGGTGCTGACCTGTCAATGGCGAA
* ** *
38769354 CACCAATACGAAAACGAAAAAAAAATTTTGGGTGCTGATTTGTCAATGGCTGGCA
1 CACCAGTACGAAAACGAAAAAAAAATTTTGGGTGCTGACCTGTCAATGGC--GAA
* *
38769409 CTACCAGTACGAAAACAGAAAAAAAAATTTTGGGTGCT-AGGCTATCAATGGCCG-A
1 C-ACCAGTACGAAAAC-GAAAAAAAAATTTTGGGTGCTGA-CCTGTCAATGG-CGAA
38769464 CACCAGTACTGAAA
1 CACCAGTAC-GAAA
38769478 CAAATTCTTT
Statistics
Matches: 106, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
53 44 0.42
54 8 0.08
55 9 0.08
56 15 0.14
57 29 0.27
58 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (53 bp):
CACCAGTACGAAAACGAAAAAAAAATTTTGGGTGCTGACCTGTCAATGGCGAA
Found at i:38770582 original size:17 final size:19
Alignment explanation
Indices: 38770556--38770598 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
38770546 AAATTAAATT
*
38770556 AATA-TTAAAAA-ATAAGA
1 AATATTTAAAAATAAAAGA
38770573 AA-ATTTAAAAATAAAAGA
1 AATATTTAAAAATAAAAGA
38770591 AATATTTA
1 AATATTTA
38770599 TAGAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 9 0.41
18 7 0.32
19 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AATATTTAAAAATAAAAGA
Found at i:38772704 original size:33 final size:33
Alignment explanation
Indices: 38772661--38772723 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
38772651 ATGGAGTGAT
* * *
38772661 CGGCGATCGTTGGCGGTGGTTGAGGGTGAATAG
1 CGGCGATCGTTAGCGGCGGTTGAAGGTGAATAG
* *
38772694 CGGCGGTCGTTAGCTGCGGTTGAAGGTGAA
1 CGGCGATCGTTAGCGGCGGTTGAAGGTGAA
38772724 CCGCGGTGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.16, C:0.14, G:0.46, T:0.24
Consensus pattern (33 bp):
CGGCGATCGTTAGCGGCGGTTGAAGGTGAATAG
Found at i:38773771 original size:5 final size:5
Alignment explanation
Indices: 38773763--38773841 Score: 50
Period size: 5 Copynumber: 14.6 Consensus size: 5
38773753 AACTTTTTTT
* * *
38773763 TTTCA TTTCA TTTTA TTTTTA TTTCA TTTCA TTCTAA TTTCA TTTTCA
1 TTTCA TTTCA TTTCA -TTTCA TTTCA TTTCA TT-TCA TTTCA -TTTCA
* * *
38773811 TTACCA TTACCA TTTCCC TTTCA TTTCA TTT
1 TT-TCA TT-TCA TTT-CA TTTCA TTTCA TTT
38773842 AAAAAATATT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
5 33 0.54
6 28 0.46
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.59
Consensus pattern (5 bp):
TTTCA
Found at i:38773781 original size:16 final size:16
Alignment explanation
Indices: 38773757--38773808 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
38773747 CATTTCAACT
* *
38773757 TTTTTTTTTCATTTCA
1 TTTTATTTTAATTTCA
*
38773773 TTTTATTTTTATTTCA
1 TTTTATTTTAATTTCA
* *
38773789 TTTCATTCTAATTTCA
1 TTTTATTTTAATTTCA
38773805 TTTT
1 TTTT
38773809 CATTACCATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTTTAATTTCA
Found at i:38773807 original size:21 final size:22
Alignment explanation
Indices: 38773762--38773812 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
38773752 CAACTTTTTT
* * *
38773762 TTTTCATTTCATTTTATTTTTA
1 TTTTCATTTCATTCTAATTTCA
38773784 -TTTCATTTCATTCTAATTTCA
1 TTTTCATTTCATTCTAATTTCA
38773805 TTTTCATT
1 TTTTCATT
38773813 ACCATTACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTCATTTCATTCTAATTTCA
Found at i:38775612 original size:55 final size:55
Alignment explanation
Indices: 38775545--38776587 Score: 786
Period size: 55 Copynumber: 18.8 Consensus size: 55
38775535 TTGATAAATT
* *
38775545 TGGTGCCGGCCATTGACAGACTAGCACCCAAAATTTTTTTTTGTTTTCGTACTGA
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTGTTTTCGTACTGA
* * * *
38775600 TGGTGTCGGCCATTGACAGGCCAGTACCAAAAAAAATATTTTTTTTCGTTTTCGTACTGG
1 TGGTGCCGGCCATTGACAGGCCAGCACC---CAAAAT-TTTTTTTT-GTTTTCGTACTGA
* * * *
38775660 TAGTGCCGGCCATTGACAGGCCAGTACCTAAAATATTTTTTTCGTTTTCGTACTGA
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT-TTTTTTTTGTTTTCGTACTGA
** * * * * * * *
38775716 TGGTGCCAACCATTGATAAGTCAACACCC-AAATTTTTTTTCCCGTTTTTGTACTGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTT--TGTTTTCGTACTGA
* * * * ** * *
38775772 TGATGTCAGCCATTGACAGGCAAGCAGGCAAAAATTTTTTTCGTTTTCGTAC---
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTGTTTTCGTACTGA
* * * * * *
38775824 TGGTGTCGGCCATTTATATGTCAGCACCCAAAATTTTTTTTCCCT-TTTTCCTACT-A
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTT---TGTTTTCGTACTGA
* * *
38775880 GTGGTGCCGGCCATTGACAGGACATCACCC--AATTTTTTTTTCGTTTTTGTACT-A
1 -TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT-GTTTTCGTACTGA
* * * * *
38775934 GTGGTGTCGACTATTTACAGGCCAGCACCCAAATTTTTTTTTTGTTTTCGTACT-A
1 -TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTGTTTTCGTACTGA
* * *
38775989 GTGGTGCCGGCCATTGACAGGTCAGTACCAAAAAAAATATTTTTTTTCGTTTTCGTACT-A
1 -TGGTGCCGGCCATTGACAGGCCAGCACC---CAAAAT-TTTTTTTT-GTTTTCGTACTGA
* * * *
38776049 GTAGTGCCGGCCATTGACAGGCCAGTACCTAAAATATTTTTTTCGTTTTCGTACTGA
1 -TGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT-TTTTTTTTGTTTTCGTACTGA
** * **
38776106 TGGTGCTAGCCATTGATAAACCAGCACCCAAAACTTTTTTTTCTGTTTTCGTA-T--
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAA-TTTTTTTT-TGTTTTCGTACTGA
* * * * *
38776160 TGGTGTCGGCCATTTACAGGCCAGCATCCAAAATTTTTTTTCCT-TTTTCGTATTGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTT--TGTTTTCGTACTGA
* * * ** * *
38776216 TGGTGCCGACCATTGACAAAG-CATCACCC-AAA-TTTTTTCCGTTTTTGTACTGG
1 TGGTGCCGGCCATTGAC-AGGCCAGCACCCAAAATTTTTTTTTGTTTTCGTACTGA
* * * * *
38776269 TGGTGTCAGCCATTTACAGGCCAGCACCCAAAATTTTTTTTCGTTTTCGTACTGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTGTTTTCGTACTGA
* * *
38776324 TGGTGCCGGCCATTGACAGGCCAGCACAC-AAATTTTTTTTTCGTTTTCATACTGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT-GTTTTCGTACTGA
* * * *
38776379 TGGTGCCAGCCATTGATAGGCCAGCACCCAAAATTTTTTTTCGTTTTCATAC---
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTGTTTTCGTACTGA
* * * ** *
38776431 TGGTGCCGGCCATTGATAAGCCGGCACAGAAAAAAACTTTATTTTTTCATTTTCGTAC---
1 TGGTGCCGGCCATTGACAGGCCAGCAC---CCAAAA-TTT-TTTTTT-GTTTTCGTACTGA
* * ** *
38776489 TGGTGCTGGCCATTGACAGGCCAGCATCCAATTTTTTTTTTTGTTTTCGTACTGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTGTTTTCGTACTGA
* **
38776544 TGGTGCCGACCATTGACAGGCCAGCACCCCCAATTTTTTTTTGT
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTGT
38776588 ATACCAGTAT
Statistics
Matches: 798, Mismatches: 144, Indels: 92
0.77 0.14 0.09
Matches are distributed among these distances:
52 67 0.08
53 52 0.07
54 99 0.12
55 220 0.28
56 151 0.19
57 77 0.10
58 39 0.05
59 16 0.02
60 77 0.10
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (55 bp):
TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTGTTTTCGTACTGA
Found at i:38776078 original size:390 final size:386
Alignment explanation
Indices: 38775545--38776446 Score: 1121
Period size: 390 Copynumber: 2.3 Consensus size: 386
38775535 TTGATAAATT
* * * * *
38775545 TGGTGCCGGCCATTGACAGACTAGCACCCAAAATTTTTTTTTGTTTTCGTACTGATGGTGTCGGC
1 TGGTGCCGACCATTGACAGGCCAGCACCCAAATTTTTTTTTTGTTTTCGTACTG-TGGTGCCGGC
38775610 CATTGACAGGCCAGTACCAAAAAAAATATTTTTTTTCGTTTTCGTACTGGTAGTGCCGGCCATTG
65 CATTGACAGGCCAGTACCAAAAAAAATATTTTTTTTCGTTTTCGTACT-GTAGTGCCGGCCATTG
**
38775675 ACAGGCCAGTACCTAAAATATTTTTTTCGTTTTCGTACTGATGGTGCCAACCATTGATAAGTCAA
129 ACAGGCCAGTACCTAAAATATTTTTTTCGTTTTCGTACTGATGGTGCCAACCATTGATAAACCAA
* *
38775740 CACCC-AAA-TTTTTTTTCCCGTTTTTGTACTGGTGATGTCAGCCATTGACAGGCAAGCAGGCAA
194 CACCCAAAACTTTTTTTT-CCGTTTTCGTA-T--TGATGTCAGCCATTGACAGGCAAGCAGCCAA
* * * *
38775803 AAATTTTTTT-CGTTTTCGTACTGGT-GT-CGGCCATTTA-TATGTCAGCACCCAAAATTTTTTT
255 AAATTTTTTTCCGTTTTCGTACTGGTGGTCCGACCATTGACAAAG-CAGCACCC-AAA--TTTTT
* * * *
38775864 TCCCTTTTTCCTACTAGTGGTGCCGGCCATTGACAGGACATCACCC-AATTTTTTTTTCGTTTTT
316 TCCCTTTTT-CTACTAGTGGTGCCAGCCATTGACAGGACAGCACCCAAAATTTTTTTTCGTTTTC
38775928 GTACTAG
380 GTACTAG
* * *
38775935 TGGTGTCGACTATTTACAGGCCAGCACCCAAATTTTTTTTTTGTTTTCGTACTAGTGGTGCCGGC
1 TGGTGCCGACCATTGACAGGCCAGCACCCAAATTTTTTTTTTGTTTTCGTACT-GTGGTGCCGGC
*
38776000 CATTGACAGGTCAGTACCAAAAAAAATATTTTTTTTCGTTTTCGTACTAGTAGTGCCGGCCATTG
65 CATTGACAGGCCAGTACCAAAAAAAATATTTTTTTTCGTTTTCGTACT-GTAGTGCCGGCCATTG
* * *
38776065 ACAGGCCAGTACCTAAAATATTTTTTTCGTTTTCGTACTGATGGTGCTAGCCATTGATAAACCAG
129 ACAGGCCAGTACCTAAAATATTTTTTTCGTTTTCGTACTGATGGTGCCAACCATTGATAAACCAA
* * * * * * *
38776130 CACCCAAAACTTTTTTTTCTGTTTTCGTATTGGTGTCGGCCATTTACAGGCCAGCATCCAAAATT
194 CACCCAAAACTTTTTTTTCCGTTTTCGTATTGATGTCAGCCATTGACAGGCAAGCAGCCAAAAAT
* * * *
38776195 TTTTTTCCTTTTTCGTATTGGTGGTGCCGACCATTGACAAAGCATCACCCAAATTTTTTCCGTTT
259 TTTTTTCCGTTTTCGTACTGGTGGT-CCGACCATTGACAAAGCAGCACCCAAATTTTTTCCCTTT
* * * * * *
38776260 TTGTACTGGTGGTGTCAGCCATTTACAGGCCAGCACCCAAAATTTTTTTTCGTTTTCGTACTGG
323 TTCTACTAGTGGTGCCAGCCATTGACAGGACAGCACCCAAAATTTTTTTTCGTTTTCGTACTAG
* * * * *
38776324 TGGTGCCGGCCATTGACAGGCCAGCACACAAATTTTTTTTTCGTTTTCATACTGGTGGTGCCAGC
1 TGGTGCCGACCATTGACAGGCCAGCACCCAAATTTTTTTTTTGTTTTCGTACT-GTGGTGCCGGC
* * * *
38776389 CATTGATAGGCCAGCACC----CAAA-ATTTTTTTTCGTTTTCATACTG--GTGCCGGCCATTGA
65 CATTGACAGGCCAGTACCAAAAAAAATATTTTTTTTCGTTTTCGTACTGTAGTGCCGGCCATTGA
38776447 TAAGCCGGCA
Statistics
Matches: 447, Mismatches: 56, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
381 14 0.03
383 1 0.00
384 20 0.04
385 3 0.01
388 63 0.14
389 119 0.27
390 186 0.42
391 16 0.04
392 23 0.05
393 2 0.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (386 bp):
TGGTGCCGACCATTGACAGGCCAGCACCCAAATTTTTTTTTTGTTTTCGTACTGTGGTGCCGGCC
ATTGACAGGCCAGTACCAAAAAAAATATTTTTTTTCGTTTTCGTACTGTAGTGCCGGCCATTGAC
AGGCCAGTACCTAAAATATTTTTTTCGTTTTCGTACTGATGGTGCCAACCATTGATAAACCAACA
CCCAAAACTTTTTTTTCCGTTTTCGTATTGATGTCAGCCATTGACAGGCAAGCAGCCAAAAATTT
TTTTCCGTTTTCGTACTGGTGGTCCGACCATTGACAAAGCAGCACCCAAATTTTTTCCCTTTTTC
TACTAGTGGTGCCAGCCATTGACAGGACAGCACCCAAAATTTTTTTTCGTTTTCGTACTAG
Found at i:38776193 original size:110 final size:108
Alignment explanation
Indices: 38775545--38776584 Score: 884
Period size: 110 Copynumber: 9.4 Consensus size: 108
38775535 TTGATAAATT
* * *
38775545 TGGTGCCGGCCATTGACAGACTAGCACCCAAAATTTTTTTTTGTTTTCGTACTGATGGTGTCGGC
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTTTTCGTACTG-TGGTGTCGGC
*
38775610 CATTGACAGGCCAGTACCAAAAAAAATATTTTTTTTCGTTTTCGTACTGG
65 CATTGACAGGCCAGCACC-----AAA-ATTTTTTTTCGTTTTCGTACTGG
* * * * **
38775660 TAGTGCCGGCCATTGACAGGCCAGTACCTAAAATATTTTTTTCGTTTTCGTACTGATGGTGCCAA
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT-TTTTTTTCGTTTTCGTACTG-TGGTGTCGG
* * * * * *
38775725 CCATTGATAAGTCAACACCCAAATTTTTTTTCCCGTTTTTGTACTGG
64 CCATTGACAGGCCAGCACCAAAATTTTTTTT--CGTTTTCGTACTGG
* * * * ** *
38775772 TGATGTCAGCCATTGACAGGCAAGCAGGCAAAAATTTTTTTCGTTTTCGTAC--TGGTGTCGGCC
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTTTTCGTACTGTGGTGTCGGCC
* * * * * * *
38775835 ATTTATATGTCAGCACCCAAAATTTTTTTTCCCTTTTTCCTACTAG
66 ATTGACAGGCCAGCA-CCAAAATTTTTTTT--CGTTTTCGTACTGG
* * * * *
38775881 TGGTGCCGGCCATTGACAGGACATCACCC-AATTTTTTTTTCGTTTTTGTACTAGTGGTGTCGAC
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTTTTCGTACT-GTGGTGTCGGC
* * * * *
38775945 TATTTACAGGCCAGCACCCAAATTTTTTTTTTGTTTTCGTACTAG
65 CATTGACAGGCCAGCA-CCAAAATTTTTTTTCGTTTTCGTACTGG
* * * *
38775990 TGGTGCCGGCCATTGACAGGTCAGTACCAAAAAAAATATTTTTTTTCGTTTTCGTACTAGTAGTG
1 TGGTGCCGGCCATTGACAGGCCAGCACC----CAAA-ATTTTTTTTCGTTTTCGTACT-GTGGTG
* * *
38776055 CCGGCCATTGACAGGCCAGTACCTAAAATATTTTTTTCGTTTTCGTACTGA
60 TCGGCCATTGACAGGCCAGCACC-AAAAT-TTTTTTTCGTTTTCGTACTGG
** * **
38776106 TGGTGCTAGCCATTGATAAACCAGCACCCAAAACTTTTTTTTCTGTTTTCGTA-T-TGGTGTCGG
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAA-TTTTTTTTC-GTTTTCGTACTGTGGTGTCGG
* * *
38776169 CCATTTACAGGCCAGCATCCAAAATTTTTTTTCCTTTTTCGTATTGG
64 CCATTGACAGGCCAGCA-CCAAAATTTTTTTT-CGTTTTCGTACTGG
* * * * * *
38776216 TGGTGCCGACCATTGACAAAG-CATCACCC-AAA-TTTTTTCCGTTTTTGTACTGGTGGTGTCAG
1 TGGTGCCGGCCATTGAC-AGGCCAGCACCCAAAATTTTTTTTCGTTTTCGTACT-GTGGTGTCGG
*
38776278 CCATTTACAGGCCAGCACCCAAAATTTTTTTTCGTTTTCGTACTGG
64 CCATTGACAGGCCAGCA-CCAAAATTTTTTTTCGTTTTCGTACTGG
* * * * *
38776324 TGGTGCCGGCCATTGACAGGCCAGCACACAAATTTTTTTTTCGTTTTCATACTGGTGGTGCCAGC
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTTTTCGTACT-GTGGTGTCGGC
* *
38776389 CATTGATAGGCCAGCACCCAAAATTTTTTTTCGTTTTCATAC---
65 CATTGACAGGCCAGCA-CCAAAATTTTTTTTCGTTTTCGTACTGG
* * * ** *
38776431 TGGTGCCGGCCATTGATAAGCCGGCACAGAAAAAAACTTTATTTTTTCATTTTCGTAC--TGGTG
1 TGGTGCCGGCCATTGACAGGCCAGCAC---CCAAAA--TT-TTTTTTCGTTTTCGTACTGTGGTG
** *
38776494 -CTGGCCATTGACAGGCCAGCATCCAATTTTTTTTTTTGTTTTCGTACTGG
60 TC-GGCCATTGACAGGCCAGCA-CCAAAATTTTTTTTCGTTTTCGTACTGG
* **
38776544 TGGTGCCGACCATTGACAGGCCAGCACCCCCAATTTTTTTT
1 TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTT
38776585 TGTATACCAG
Statistics
Matches: 755, Mismatches: 134, Indels: 80
0.78 0.14 0.08
Matches are distributed among these distances:
106 8 0.01
107 40 0.05
108 75 0.10
109 134 0.18
110 182 0.24
111 60 0.08
112 52 0.07
113 47 0.06
114 4 0.01
115 74 0.10
116 79 0.10
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (108 bp):
TGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTTTTCGTACTGTGGTGTCGGCC
ATTGACAGGCCAGCACCAAAATTTTTTTTCGTTTTCGTACTGG
Found at i:38776714 original size:53 final size:52
Alignment explanation
Indices: 38776602--38776725 Score: 128
Period size: 52 Copynumber: 2.4 Consensus size: 52
38776592 CAGTATGATA
* * *
38776602 CAAAATTTTTTTTATCATTTTCAGGCTGGTGCCGACCATTAACAGGCTAGTACC
1 CAAAA-TTTTTTT-TCGTTTTCAGGCTGGTGCCGACCATTAACAGGCCAGCACC
* * *
38776656 C-AAATTTTTTTTCGTTTTCCTAGG-TGGTGCTGGCCATTGACAGGCCAGCACC
1 CAAAATTTTTTTTCGTTTT-C-AGGCTGGTGCCGACCATTAACAGGCCAGCACC
*
38776708 CAAAATTTATTTT-GTTTT
1 CAAAATTTTTTTTCGTTTT
38776726 TTTTTTGTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
51 6 0.10
52 37 0.62
53 16 0.27
54 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.39
Consensus pattern (52 bp):
CAAAATTTTTTTTCGTTTTCAGGCTGGTGCCGACCATTAACAGGCCAGCACC
Found at i:38778368 original size:5 final size:5
Alignment explanation
Indices: 38778358--38778385 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
38778348 ACCTATATTA
38778358 CAAAC CAAAC CAAAC CAAAC CAAAC CAA
1 CAAAC CAAAC CAAAC CAAAC CAAAC CAA
38778386 GTATTCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.39, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAC
Found at i:38781499 original size:35 final size:35
Alignment explanation
Indices: 38781463--38781530 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
38781453 CTACAAAAAT
*
38781463 TTTAACTTTAAAA-CTAAATATAA-AAATTAATAAA
1 TTTAAATTTAAAATCTAAA-ATAATAAATTAATAAA
*
38781497 TTTAAATTTAAAATTTAAAATAATAAATTAATAA
1 TTTAAATTTAAAATCTAAAATAATAAATTAATAA
38781531 CACAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (35 bp):
TTTAAATTTAAAATCTAAAATAATAAATTAATAAA
Found at i:38781663 original size:43 final size:43
Alignment explanation
Indices: 38781614--38781697 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
38781604 ATATGCAAGG
* *
38781614 TAATAAAACATACAATACT-TTTTCTTAATCAAGTAAATCTTAA
1 TAATAAAACATACAATA-TATTTACTTAATCAAGGAAATCTTAA
* *
38781657 TAATAAAAGATATAATATATTTACTTAATCAAGGAAATCTT
1 TAATAAAACATACAATATATTTACTTAATCAAGGAAATCTT
38781698 GTAATGAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (43 bp):
TAATAAAACATACAATATATTTACTTAATCAAGGAAATCTTAA
Found at i:38786698 original size:79 final size:81
Alignment explanation
Indices: 38786586--38786733 Score: 210
Period size: 79 Copynumber: 1.9 Consensus size: 81
38786576 CACTAGTTAA
* * *
38786586 TCTAAACCCTAAACCTTAAAACCCTAAAATCCTAAACCCTTAACACATAACCTTTAAACTTTAAA
1 TCTAAACACTAAACCTTAAAACCCTAAAATCCTAAACCCTTAACACATAACCTCTAAACCTTAAA
38786651 CCCCGGCCTTTTAAAC
66 CCCCGGCCTTTTAAAC
* * ** *
38786667 TCTAAACATTAAACC-T-AAACCCTAAAATCCTAAACTCTTAACGTATACCCTCTAAACCTTAAA
1 TCTAAACACTAAACCTTAAAACCCTAAAATCCTAAACCCTTAACACATAACCTCTAAACCTTAAA
38786730 CCCC
66 CCCC
38786734 AACCTTTAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
79 45 0.76
80 1 0.02
81 13 0.22
ACGTcount: A:0.40, C:0.32, G:0.02, T:0.26
Consensus pattern (81 bp):
TCTAAACACTAAACCTTAAAACCCTAAAATCCTAAACCCTTAACACATAACCTCTAAACCTTAAA
CCCCGGCCTTTTAAAC
Found at i:38786769 original size:79 final size:79
Alignment explanation
Indices: 38786604--38786771 Score: 198
Period size: 79 Copynumber: 2.1 Consensus size: 79
38786594 CTAAACCTTA
* * **
38786604 AAACCCTAAAATCCTAAACCCTTAACACATAACCTTTAAACTTTAAACCCCGGCCTTTTAAACTC
1 AAACCCTAAAATCCTAAACCCTTAACACATAACCTCTAAACCTTAAACCCCAACCTTTTAAACTC
*
38786669 TAAACATTAAACCT
66 TAAACATTAAACAT
* ** *
38786683 AAACCCTAAAATCCTAAACTCTTAACGTATACCCTCTAAACCTTAAACCCCAACC-TTTAAAC-C
1 AAACCCTAAAATCCTAAACCCTTAACACATAACCTCTAAACCTTAAACCCCAACCTTTTAAACTC
38786746 ATAAATCA-TAAATCAT
66 -TAAA-CATTAAA-CAT
*
38786762 AACCCCTAAA
1 AAACCCTAAA
38786772 CCCATAATCC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 15 0.20
79 60 0.79
ACGTcount: A:0.42, C:0.31, G:0.02, T:0.25
Consensus pattern (79 bp):
AAACCCTAAAATCCTAAACCCTTAACACATAACCTCTAAACCTTAAACCCCAACCTTTTAAACTC
TAAACATTAAACAT
Found at i:38786957 original size:41 final size:41
Alignment explanation
Indices: 38786910--38787023 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
38786900 CGATAGTATT
**
38786910 AATTAGCGGCAATTTTTCAAAAACGCAGCTAAAGCCCCGAG
1 AATTAGCGGCGCTTTTTCAAAAACGCAGCTAAAGCCCCGAG
* *
38786951 AATTAGCGGCGCTTTTTCAAAAGCGCCGCTAAAGCCCCGAG
1 AATTAGCGGCGCTTTTTCAAAAACGCAGCTAAAGCCCCGAG
* * *
38786992 CATTAGCGGTGCTTTTTCAAAAACGCTGCTAA
1 AATTAGCGGCGCTTTTTCAAAAACGCAGCTAA
38787024 TGCTCATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (41 bp):
AATTAGCGGCGCTTTTTCAAAAACGCAGCTAAAGCCCCGAG
Found at i:38793122 original size:25 final size:24
Alignment explanation
Indices: 38793063--38793153 Score: 76
Period size: 25 Copynumber: 3.7 Consensus size: 24
38793053 TACGAACGAT
* * *
38793063 TATCGGTAAACTCCTCCGAGCTGAA
1 TATCGGTAAGCTCATACGAGCTG-A
*
38793088 TATTGGTAAGCTCATACGAGCTGA
1 TATCGGTAAGCTCATACGAGCTGA
*
38793112 GTATCGGTAAGTTC-TCACGAGCTGCA
1 -TATCGGTAAGCTCAT-ACGAGCTG-A
* *
38793138 AATCAGTAAGCTCATA
1 TATCGGTAAGCTCATA
38793154 TGAACTGCGA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
24 2 0.04
25 49 0.92
26 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
TATCGGTAAGCTCATACGAGCTGA
Found at i:38794391 original size:20 final size:20
Alignment explanation
Indices: 38794368--38794452 Score: 61
Period size: 20 Copynumber: 4.2 Consensus size: 20
38794358 AATATGATTA
38794368 AAATTAATCAATTTAATATT
1 AAATTAATCAATTTAATATT
* *
38794388 AAATTAATATAATGATATATATT
1 AAATTAAT-CAAT-TTA-ATATT
* *
38794411 AGATT-A--AATTTGATATT
1 AAATTAATCAATTTAATATT
*
38794428 AAGA-TAATCACTTTAATATT
1 AA-ATTAATCAATTTAATATT
38794448 AAATT
1 AAATT
38794453 TAAAAAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
17 7 0.14
18 3 0.06
19 4 0.08
20 20 0.41
21 3 0.06
22 3 0.06
23 9 0.18
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (20 bp):
AAATTAATCAATTTAATATT
Found at i:38796991 original size:19 final size:21
Alignment explanation
Indices: 38796960--38797005 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
38796950 TAAGATAACT
*
38796960 TAATT-AAACAAAATT-AAGA
1 TAATTGAAACAAAATTAAAAA
38796979 TAATTGAAA-AAAATTAAAAA
1 TAATTGAAACAAAATTAAAAA
38796999 TAATTGA
1 TAATTGA
38797006 GATTGTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (21 bp):
TAATTGAAACAAAATTAAAAA
Found at i:38802224 original size:18 final size:18
Alignment explanation
Indices: 38802204--38802275 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 18
38802194 TATATTTATT
38802204 TTTTAAAA-ATTTTTTAA
1 TTTTAAAATATTTTTTAA
*
38802221 TTTTAAAATATTTTTAAAATAC
1 TTTTAAAATATTTTT----TAA
** *
38802243 TTTTTTATTATTTTTTAA
1 TTTTAAAATATTTTTTAA
38802261 TTTTAAAATATTTTT
1 TTTTAAAATATTTTT
38802276 AAAATACTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
17 8 0.19
18 20 0.48
22 14 0.33
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTAAAATATTTTTTAA
Found at i:38802235 original size:11 final size:11
Alignment explanation
Indices: 38802221--38802287 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
38802211 AATTTTTTAA
38802221 TTTTAAAATAT
1 TTTTAAAATAT
38802232 TTTTAAAATACT
1 TTTTAAAATA-T
* *
38802244 TTTT-TATTAT
1 TTTTAAAATAT
*
38802254 TTTT----TAA
1 TTTTAAAATAT
38802261 TTTTAAAATAT
1 TTTTAAAATAT
38802272 TTTTAAAATACT
1 TTTTAAAATA-T
38802284 TTTT
1 TTTT
38802288 TTAATTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
7 6 0.13
10 5 0.11
11 25 0.54
12 10 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:38802288 original size:40 final size:39
Alignment explanation
Indices: 38802211--38802296 Score: 154
Period size: 40 Copynumber: 2.2 Consensus size: 39
38802201 ATTTTTTAAA
38802211 AATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAT
1 AATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT-T
*
38802251 TATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
1 AATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
38802290 AATTTTT
1 AATTTTT
38802297 AAAATAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 7 0.16
40 37 0.84
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (39 bp):
AATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
Found at i:38802308 original size:21 final size:21
Alignment explanation
Indices: 38802270--38802309 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38802260 ATTTTAAAAT
**
38802270 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
38802291 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
38802310 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:38802316 original size:22 final size:20
Alignment explanation
Indices: 38802269--38802323 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
38802259 AATTTTAAAA
* *
38802269 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
38802289 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
38802312 TATTTATTAAAA
1 TATTT-TTAAAA
38802324 CCTGGCTGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:38803959 original size:38 final size:38
Alignment explanation
Indices: 38803892--38804316 Score: 433
Period size: 38 Copynumber: 11.2 Consensus size: 38
38803882 ATAGAAATGT
** *
38803892 GGTGATATTTAGGCTATGTGCCTAGCAGGCTTTGTATC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
** * * * *
38803930 AATGTTATTCGAGCTCTGTGCCTAGCAGGCTTTGTGCC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
* * * * *
38803968 AGTGATATTTGGGCTTTGTGCCTAGCAGGCTTTGTGCT
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
* * * *
38804006 GGTCATATTCGGGATATGTGCTTAGCAGGCTTTGTGCC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
* * * * *
38804044 GGTGATATTCAGGATATATGCCTAGTAGGTTTTGTACC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
* *
38804082 AGTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTACC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
* * * * *
38804120 GATGTTATTCGAGG-TCTGTGCCTAGCAGGCTTTGTGCT
1 GGTGATATTCG-GGCTATGTGCCTAGCAGGCTTTGTACC
* * * *
38804158 GTTGATATTCGGGCTATGTGCCTAGCAGGCTTTATGCT
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
* * *
38804196 AGTGATATTCGGGCTATGTGCCTAGTAGGCTTTGTGCC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
*
38804234 GGTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTACC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
* ** * *
38804272 GGTGTTATTCGGGCCCTGTGCCTAGTAGGC-TTGTGCC
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
38804309 GGTG-TATT
1 GGTGATATT
38804317 GAAAATTTAC
Statistics
Matches: 323, Mismatches: 62, Indels: 6
0.83 0.16 0.02
Matches are distributed among these distances:
36 4 0.01
37 12 0.04
38 305 0.94
39 2 0.01
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (38 bp):
GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACC
Found at i:38804282 original size:114 final size:114
Alignment explanation
Indices: 38803892--38804316 Score: 487
Period size: 114 Copynumber: 3.7 Consensus size: 114
38803882 ATAGAAATGT
** * ** * * *
38803892 GGTGATATTTAGGCTATGTGCCTAGCAGGCTTTGTATCAATGTTATTCGAGCTCTGTGCCTAGCA
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACCGGTGATATTCGGGCTATGTGCCTAGCA
* *
38803957 GGCTTTGTGCCAGTGATATTTGGGCTTTGTGCCTAGCAGGCTTTGTGCT
66 GGCTTTGTGCCAGTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCC
* * * * * * * *
38804006 GGTCATATTCGGGATATGTGCTTAGCAGGCTTTGTGCCGGTGATATTCAGGATATATGCCTAGTA
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACCGGTGATATTCGGGCTATGTGCCTAGCA
* * *
38804071 GGTTTTGTACCAGTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTACC
66 GGCTTTGTGCCAGTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCC
* * * * * *
38804120 GATGTTATTCGAGG-TCTGTGCCTAGCAGGCTTTGTGCTGTTGATATTCGGGCTATGTGCCTAGC
1 GGTGATATTCG-GGCTATGTGCCTAGCAGGCTTTGTACCGGTGATATTCGGGCTATGTGCCTAGC
* * * *
38804184 AGGCTTTATGCTAGTGATATTCGGGCTATGTGCCTAGTAGGCTTTGTGCC
65 AGGCTTTGTGCCAGTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCC
* * ** *
38804234 GGTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTACCGGTGTTATTCGGGCCCTGTGCCTAGTA
1 GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACCGGTGATATTCGGGCTATGTGCCTAGCA
*
38804299 GGC-TTGTGCCGGTG-TATT
66 GGCTTTGTGCCAGTGATATT
38804317 GAAAATTTAC
Statistics
Matches: 256, Mismatches: 53, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
112 4 0.02
113 10 0.04
114 240 0.94
115 2 0.01
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (114 bp):
GGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTACCGGTGATATTCGGGCTATGTGCCTAGCA
GGCTTTGTGCCAGTGATATTTGGGCTATGTGCCTAGCAGGCTTTGTGCC
Found at i:38810361 original size:23 final size:23
Alignment explanation
Indices: 38810335--38810379 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
38810325 ATTTCATGCC
38810335 ATAATCATCGACCAAAATGACAT
1 ATAATCATCGACCAAAATGACAT
*
38810358 ATAATCATCGACCATAATGACA
1 ATAATCATCGACCAAAATGACA
38810380 AATATTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (23 bp):
ATAATCATCGACCAAAATGACAT
Found at i:38817669 original size:5 final size:5
Alignment explanation
Indices: 38817661--38817686 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38817651 GAGATGGAAT
38817661 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
38817687 ATATTTNNNN
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:38817686 original size:26 final size:26
Alignment explanation
Indices: 38817635--38817686 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
38817625 TGAAGTTTTC
* * *
38817635 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
38817661 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
38817687 ATATTTNNNN
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:38818480 original size:9 final size:9
Alignment explanation
Indices: 38818463--38818493 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
38818453 TCGAGTTGAT
38818463 TCGAATAAC
1 TCGAATAAC
*
38818472 TCGATTAAC
1 TCGAATAAC
38818481 TCGAATAAC
1 TCGAATAAC
38818490 TCGA
1 TCGA
38818494 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:38819406 original size:15 final size:15
Alignment explanation
Indices: 38819386--38819415 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38819376 GGCTAATCTC
38819386 AATAAAATATTTGTA
1 AATAAAATATTTGTA
38819401 AATAAAATATTTGTA
1 AATAAAATATTTGTA
38819416 TGTTATCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
AATAAAATATTTGTA
Found at i:38820023 original size:25 final size:25
Alignment explanation
Indices: 38819995--38820054 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
38819985 CATGTAAACA
*
38819995 GGAAGCTCTTTTGAG-TCATATAACG
1 GGAAGCTCTTGTGAGCT-ATATAACG
* *
38820020 GGAAGCTCATGTGAGCTGTATAACG
1 GGAAGCTCTTGTGAGCTATATAACG
38820045 GGAAGCTCTT
1 GGAAGCTCTT
38820055 AGGAGCCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 29 0.97
26 1 0.03
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (25 bp):
GGAAGCTCTTGTGAGCTATATAACG
Found at i:38821442 original size:38 final size:38
Alignment explanation
Indices: 38821399--38821710 Score: 389
Period size: 38 Copynumber: 8.3 Consensus size: 38
38821389 AATAGAAAAG
* *
38821399 CGGTGATATTCGGGATATGTGCCTAGCAGGCTTTGTGT
1 CGGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* **
38821437 TGGTGATATTCGGGCTATGTGCCTAATAGGCTTTGTGC
1 CGGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
** *
38821475 CAATGATATTCGGGCTACT-TGCCTAGCAGGCTTTGTAC
1 CGGTGATATTCGGGCTA-TGTGCCTAGCAGGCTTTGTGC
*
38821513 CGGTGATATTCGGGCTATGTGCCTAGCAAGCTTTGTGC
1 CGGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
** *
38821551 CAATGATATTCGGGCTACT-TGCCTAGCAGGCTTTGTAC
1 CGGTGATATTCGGGCTA-TGTGCCTAGCAGGCTTTGTGC
*
38821589 CGGTGATATTCGAGCTATGTGCCTAGCAGGCTTTGTGC
1 CGGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
* * *
38821627 AGATGTTATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
1 CGGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
** * *
38821665 AAGTGTTATTCGGGCTCTGTGCCTAGCAGGC-TTGTGC
1 CGGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
*
38821702 CAGTG-TATT
1 CGGTGATATT
38821711 AAAAATTTAC
Statistics
Matches: 239, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
36 4 0.02
37 12 0.05
38 221 0.92
39 2 0.01
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.33
Consensus pattern (38 bp):
CGGTGATATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
Found at i:38822401 original size:17 final size:17
Alignment explanation
Indices: 38822379--38822437 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 17
38822369 ATACGGCTTA
*
38822379 AGACACGAGCATGTGTG
1 AGACACGAGCGTGTGTG
*
38822396 AGACACGGGCGTGTGTG
1 AGACACGAGCGTGTGTG
* *
38822413 AGACATGGGCGTGTGTG
1 AGACACGAGCGTGTGTG
*
38822430 ACACACGA
1 AGACACGA
38822438 CCATATGACA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.39, T:0.17
Consensus pattern (17 bp):
AGACACGAGCGTGTGTG
Found at i:38826225 original size:23 final size:23
Alignment explanation
Indices: 38826196--38826271 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
38826186 ATAAGTGCCA
*
38826196 CACTGATATATAGCCGAATG-TAC
1 CACTGATATGTAGCCGAA-GCTAC
*
38826219 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
38826242 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
38826265 CACTGAT
1 CACTGAT
38826272 TAGTAACACT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 1 0.02
23 48 0.98
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:38826435 original size:18 final size:17
Alignment explanation
Indices: 38826409--38826447 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
38826399 ATTTTCCTTC
38826409 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
38826426 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
38826444 CACA
1 CACA
38826448 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:38826560 original size:20 final size:20
Alignment explanation
Indices: 38826522--38826560 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38826512 GTAAATTAGT
* *
38826522 CGATAACTTTCTCTTTTCCC
1 CGATAACTTTCACTATTCCC
*
38826542 CGATCACTTTCACTATTCC
1 CGATAACTTTCACTATTCC
38826561 TTCTTTCTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.36, G:0.05, T:0.41
Consensus pattern (20 bp):
CGATAACTTTCACTATTCCC
Found at i:38828560 original size:20 final size:18
Alignment explanation
Indices: 38828513--38828561 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
38828503 CAAGATAAAC
38828513 ATTAAATT-ATATTTAAT
1 ATTAAATTAATATTTAAT
38828530 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
38828550 ATTAAATTAATA
1 ATTAAATTAATA
38828562 AAATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 6 0.22
18 3 0.11
19 3 0.11
20 15 0.56
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:38829057 original size:19 final size:18
Alignment explanation
Indices: 38829033--38829084 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
38829023 AAAGTATCAT
*
38829033 ATTAATTTTAATTTATTTG
1 ATTAA-TTTAATTTACTTG
38829052 ATTAATTTAATTTTACTTG
1 ATTAATTTAA-TTTACTTG
*
38829071 ATCAAATTTAATTT
1 AT-TAATTTAATTT
38829085 TTCCAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 5 0.17
19 17 0.59
20 7 0.24
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (18 bp):
ATTAATTTAATTTACTTG
Found at i:38835723 original size:15 final size:15
Alignment explanation
Indices: 38835703--38835732 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38835693 CTAAGGAAAT
38835703 CCAAGCCGCTGCTTC
1 CCAAGCCGCTGCTTC
*
38835718 CCAAGCTGCTGCTTC
1 CCAAGCCGCTGCTTC
38835733 AACATATCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.43, G:0.20, T:0.23
Consensus pattern (15 bp):
CCAAGCCGCTGCTTC
Found at i:38836181 original size:2 final size:2
Alignment explanation
Indices: 38836174--38836202 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38836164 TTCTTTGTTT
38836174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38836203 TTCTGTTAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38837481 original size:40 final size:38
Alignment explanation
Indices: 38837437--38837527 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 38
38837427 ACCAAATATA
*
38837437 TTTATAAAATGTTATAAGAATTAAAA-AAATGTCATAAAAT
1 TTTATAAAAT-TTAT-A-AATTAAAATAAAGGTCATAAAAT
* *
38837477 TTTATACAATATTTATAAATTAAAATATAGGTTATAAAAT
1 TTTATA-AA-ATTTATAAATTAAAATAAAGGTCATAAAAT
*
38837517 TTTATGAAATT
1 TTTATAAAATT
38837528 AAGAACTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
38 3 0.07
39 10 0.23
40 23 0.52
41 6 0.14
42 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (38 bp):
TTTATAAAATTTATAAATTAAAATAAAGGTCATAAAAT
Found at i:38844188 original size:22 final size:23
Alignment explanation
Indices: 38844158--38844227 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 23
38844148 ACTAATTTTT
38844158 AACATAGTCTTGTTCCATTTTCG
1 AACATAGTCTTGTTCCATTTTCG
38844181 AACA-AGTC----T-CATTTT--
1 AACATAGTCTTGTTCCATTTTCG
*
38844196 ATCATAGTCTTGTTCCATTTTCG
1 AACATAGTCTTGTTCCATTTTCG
38844219 AACA-AGTCT
1 AACATAGTCT
38844228 CATTTTATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 17
0.66 0.04 0.30
Matches are distributed among these distances:
15 3 0.08
16 4 0.11
17 6 0.16
18 1 0.03
20 1 0.03
21 6 0.16
22 9 0.24
23 7 0.19
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.41
Consensus pattern (23 bp):
AACATAGTCTTGTTCCATTTTCG
Found at i:38844204 original size:38 final size:38
Alignment explanation
Indices: 38844154--38844238 Score: 161
Period size: 38 Copynumber: 2.2 Consensus size: 38
38844144 CCTCACTAAT
*
38844154 TTTTAACATAGTCTTGTTCCATTTTCGAACAAGTCTCA
1 TTTTATCATAGTCTTGTTCCATTTTCGAACAAGTCTCA
38844192 TTTTATCATAGTCTTGTTCCATTTTCGAACAAGTCTCA
1 TTTTATCATAGTCTTGTTCCATTTTCGAACAAGTCTCA
38844230 TTTTATCAT
1 TTTTATCAT
38844239 TTATAATCTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (38 bp):
TTTTATCATAGTCTTGTTCCATTTTCGAACAAGTCTCA
Found at i:38846215 original size:33 final size:33
Alignment explanation
Indices: 38846178--38846241 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
38846168 AGTCTGTCGG
* *
38846178 GATAATAAATACAGAATAGAGATAA-TCTATCAA
1 GATAATAAACACAGAACAGAG-TAAGTCTATCAA
38846211 GATAATAAACACAGAACAGAGTAAGTCTATC
1 GATAATAAACACAGAACAGAGTAAGTCTATC
38846242 GGGACGGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (33 bp):
GATAATAAACACAGAACAGAGTAAGTCTATCAA
Found at i:38847503 original size:9 final size:9
Alignment explanation
Indices: 38847489--38847525 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
38847479 TATAGTTTAA
38847489 TATTCGAAT
1 TATTCGAAT
38847498 TATTCGAAT
1 TATTCGAAT
*
38847507 TATTCGAGT
1 TATTCGAAT
38847516 TATTCGAAT
1 TATTCGAAT
38847525 T
1 T
38847526 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:38856209 original size:25 final size:25
Alignment explanation
Indices: 38856170--38856218 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38856160 TATAAAATAT
38856170 AAAAATATACATATGT-ACATATAAG
1 AAAAATATACATATGTGA-ATATAAG
**
38856195 AAAAATATATGTATGTGAATATAA
1 AAAAATATACATATGTGAATATAA
38856219 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (25 bp):
AAAAATATACATATGTGAATATAAG
Found at i:38856238 original size:11 final size:11
Alignment explanation
Indices: 38856212--38856250 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
38856202 TATGTATGTG
38856212 AATATA-ATAT
1 AATATATATAT
38856222 ATATATATATAT
1 A-ATATATATAT
*
38856234 AATATATGTAT
1 AATATATATAT
38856245 AATATA
1 AATATA
38856251 CATGTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 1 0.04
11 20 0.77
12 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
AATATATATAT
Found at i:38856245 original size:19 final size:19
Alignment explanation
Indices: 38856198--38856250 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
38856188 ATATAAGAAA
*
38856198 AATATATGTATGTGA-ATAT
1 AATATATGTATAT-ATATAT
38856217 AATATA--TATATATATAT
1 AATATATGTATATATATAT
38856234 AATATATGTATA-ATATA
1 AATATATGTATATATATA
38856251 CATGTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.03
17 14 0.47
18 5 0.17
19 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
AATATATGTATATATATAT
Found at i:38864889 original size:35 final size:35
Alignment explanation
Indices: 38864840--38864908 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
38864830 TGTCCCATGA
38864840 AAATGTATCCATTGAATGATAAATTATCACTTTCT
1 AAATGTATCCATTGAATGATAAATTATCACTTTCT
* *
38864875 AAATGTATCTATTGACTGATAAATTATCACTTTC
1 AAATGTATCCATTGAATGATAAATTATCACTTTC
38864909 CAAAATTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (35 bp):
AAATGTATCCATTGAATGATAAATTATCACTTTCT
Found at i:38867435 original size:32 final size:33
Alignment explanation
Indices: 38867399--38867461 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
38867389 AATAAAATTA
*
38867399 AATACG-AATACAAAAAATGCTTTAAAAAACGT
1 AATACGAAATAAAAAAAATGCTTTAAAAAACGT
*
38867431 AATACGAAATAAAAAAAATGCTTTAAGAAAC
1 AATACGAAATAAAAAAAATGCTTTAAAAAAC
38867462 AAGAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.59, C:0.11, G:0.10, T:0.21
Consensus pattern (33 bp):
AATACGAAATAAAAAAAATGCTTTAAAAAACGT
Found at i:38867599 original size:9 final size:9
Alignment explanation
Indices: 38867581--38867627 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
38867571 CGACTTGGGC
*
38867581 TTTTTCCTT
1 TTTTTTCTT
38867590 TTTTTTCTT
1 TTTTTTCTT
38867599 TTTTTTCTT
1 TTTTTTCTT
*
38867608 TTTTCTCTT
1 TTTTTTCTT
38867617 CTTTTTT-TT
1 -TTTTTTCTT
38867626 TT
1 TT
38867628 GCTGCCTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
8 2 0.06
9 27 0.79
10 5 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:38867609 original size:16 final size:17
Alignment explanation
Indices: 38867588--38867627 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
38867578 GGCTTTTTCC
38867588 TTTTTTTTCT-TT-TTT
1 TTTTTTTTCTCTTCTTT
38867603 TTCTTTTTTCTCTTCTTT
1 TT-TTTTTTCTCTTCTTT
38867621 TTTTTTT
1 TTTTTTT
38867628 GCTGCCTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.09
16 8 0.36
17 7 0.32
18 5 0.23
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTTCTCTTCTTT
Found at i:38867977 original size:13 final size:12
Alignment explanation
Indices: 38867954--38868025 Score: 73
Period size: 12 Copynumber: 6.2 Consensus size: 12
38867944 ATTATTTTTA
38867954 TTTTTTCTTCTC
1 TTTTTTCTTCTC
38867966 TTTTTTCTT-TC
1 TTTTTTCTTCTC
38867977 -TTTTTCTT-TC
1 TTTTTTCTTCTC
38867987 TTCTTCTTCTTC-C
1 TT-TT-TTCTTCTC
*
38868000 TTCTTTCTTTCTC
1 TTTTTTC-TTCTC
38868013 TTTTTTCTT-TC
1 TTTTTTCTTCTC
38868024 TT
1 TT
38868026 CTTCTCCGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
10 10 0.19
11 10 0.19
12 17 0.33
13 15 0.29
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTTCTTCTC
Found at i:38867984 original size:17 final size:17
Alignment explanation
Indices: 38867957--38868030 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
38867947 ATTTTTATTT
38867957 TTTCTTC-TCTTTTTTC
1 TTTCTTCTTCTTTTTTC
*
38867973 TTTC-T-TT-TTCTTTC
1 TTTCTTCTTCTTTTTTC
**
38867987 -TTCTTCTTCTTCCTTC
1 TTTCTTCTTCTTTTTTC
38868003 TTTCTT-TCTCTTTTTTC
1 TTTCTTCT-TCTTTTTTC
38868020 TTTCTTCTTCT
1 TTTCTTCTTCT
38868031 CCGTTCGGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
13 3 0.06
14 7 0.15
15 4 0.09
16 11 0.23
17 21 0.45
18 1 0.02
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTCTTCTTTTTTC
Found at i:38868320 original size:16 final size:16
Alignment explanation
Indices: 38868275--38868330 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
38868265 CTGCCTTCCC
* *
38868275 CTCTTTTCTCTTCTTC
1 CTCTTTTCTCTCCTTT
38868291 CT-TTCTTCCTCTCCTTT
1 CTCTT-TT-CTCTCCTTT
38868308 CTCTTTTCTCTCCTATT
1 CTCTTTTCTCTCCT-TT
38868325 -TCTTTT
1 CTCTTTT
38868331 TTTCGAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 2 0.06
16 17 0.50
17 13 0.38
18 2 0.06
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (16 bp):
CTCTTTTCTCTCCTTT
Found at i:38868601 original size:13 final size:13
Alignment explanation
Indices: 38868583--38868630 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
38868573 AATTTAGGGG
38868583 TCAAAATGTAATT
1 TCAAAATGTAATT
* *
38868596 TCAAAAAGTTAATGGG
1 TCAAAATG-TAAT--T
38868612 TCAAAATGTAATT
1 TCAAAATGTAATT
38868625 TCAAAA
1 TCAAAA
38868631 AATTCAGGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 13 0.46
14 4 0.14
15 4 0.14
16 7 0.25
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (13 bp):
TCAAAATGTAATT
Found at i:38868641 original size:29 final size:29
Alignment explanation
Indices: 38868571--38868647 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
38868561 AAATTTTGAG
*
38868571 AAAATTTAGGGGTCAAAATGTAATTTCAA
1 AAAATTAAGGGGTCAAAATGTAATTTCAA
* *
38868600 AAAGTTAATGGGTCAAAATGTAATTTCAA
1 AAAATTAAGGGGTCAAAATGTAATTTCAA
* *
38868629 AAAATTCAGGGGTCGAAAT
1 AAAATTAAGGGGTCAAAAT
38868648 ATATTTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (29 bp):
AAAATTAAGGGGTCAAAATGTAATTTCAA
Found at i:38870411 original size:21 final size:21
Alignment explanation
Indices: 38870385--38870424 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38870375 TACAAATATA
38870385 ATTAATAAAATTATTATTTTT
1 ATTAATAAAATTATTATTTTT
*
38870406 ATTAATAAATTTATTATTT
1 ATTAATAAAATTATTATTT
38870425 AATCTCACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTAATAAAATTATTATTTTT
Found at i:38870523 original size:60 final size:60
Alignment explanation
Indices: 38870451--38870582 Score: 228
Period size: 60 Copynumber: 2.2 Consensus size: 60
38870441 TTACGGTATT
*
38870451 CAATCTTACCGCTATAGTAATTAATCTCACCGCCACCGCTATTTTTAACCTCATCAAAAG
1 CAATCTTACCGCTATAGTAATTAATCTCACCGCCACCACTATTTTTAACCTCATCAAAAG
* *
38870511 CAATCTTACCGCTATAGTAATTAATCTCACCGCCACTACTATTTTTAATCTCATCAAAAG
1 CAATCTTACCGCTATAGTAATTAATCTCACCGCCACCACTATTTTTAACCTCATCAAAAG
*
38870571 CAATCTCACCGC
1 CAATCTTACCGC
38870583 CCATCTAAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.30
Consensus pattern (60 bp):
CAATCTTACCGCTATAGTAATTAATCTCACCGCCACCACTATTTTTAACCTCATCAAAAG
Found at i:38871647 original size:3 final size:3
Alignment explanation
Indices: 38871639--38871670 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
38871629 TGTTTCCTTT
38871639 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38871671 TTTTGTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:38874778 original size:2 final size:2
Alignment explanation
Indices: 38874760--38874800 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
38874750 ACCATAGGTA
* *
38874760 AT AT AC AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38874801 GTTCAACTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38875734 original size:2 final size:2
Alignment explanation
Indices: 38875727--38875752 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38875717 GGTAAGTTCA
38875727 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38875753 TTACTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38877302 original size:181 final size:180
Alignment explanation
Indices: 38876925--38877305 Score: 437
Period size: 181 Copynumber: 2.1 Consensus size: 180
38876915 TTCAGGGTTT
* * * * * *
38876925 TAATCACTTCACGTTCAAGTTATTCAAATTCAATTCAATTTGGGTTTAGGGTTGGGTGGTTTGAG
1 TAATCACTTAATGTTCAAGTTATCCAAATTCAATTCAATTTGGATTTAAGGTTAGGTGGTTTGAG
* * *
38876990 ATTTTTAATGATCAAATAGGATGGGGTGAATTGGAGTTTGAATTGATCGATTCGAATATTCAAAT
66 ATTTTTAATGATCAAATAGGATGAGATGAATTGGAGTTTGAATCGATCGATTCGAATATTCAAAT
* * * * *
38877055 TCGGATATTTCCAAATTGGGTCATTAAGAAGTTCGAATCAGTTCAAGTTT
131 TCGAATATTTCCAAATCGGGTCATTAAGAAGTTCGAACCAATTCAAGTTC
* * **
38877105 TACTCACTTTATGTTCAAGTTAATCCAAATTTGATTCAATTTGGATTTAAGGTTAGGTGGTTTGA
1 TAATCACTTAATGTTCAAGTT-ATCCAAATTCAATTCAATTTGGATTTAAGGTTAGGTGGTTTGA
* * * *
38877170 GTTTTTTAATGATCAAATTGGATGAGATCGAATTTGAGTTTGAATCGATTGATTCGAATATTCAA
65 GATTTTTAATGATCAAATAGGATGAGAT-GAATTGGAGTTTGAATCGATCGATTCGAATATTCAA
* * * ** *
38877235 ATTTGAATTTTTTCAGGTCGGGTCATTAAG-GGTTC-AGACCAATTCAA-TGTC
129 ATTCGAATATTTCCAAATCGGGTCATTAAGAAGTTCGA-ACCAATTCAAGT-TC
38877286 TAATCA-TTAAATGTTCAAGT
1 TAATCACTT-AATGTTCAAGT
38877306 CAATTTGGAT
Statistics
Matches: 167, Mismatches: 29, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
180 22 0.13
181 89 0.53
182 56 0.34
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (180 bp):
TAATCACTTAATGTTCAAGTTATCCAAATTCAATTCAATTTGGATTTAAGGTTAGGTGGTTTGAG
ATTTTTAATGATCAAATAGGATGAGATGAATTGGAGTTTGAATCGATCGATTCGAATATTCAAAT
TCGAATATTTCCAAATCGGGTCATTAAGAAGTTCGAACCAATTCAAGTTC
Found at i:38877338 original size:181 final size:181
Alignment explanation
Indices: 38876925--38877350 Score: 405
Period size: 181 Copynumber: 2.4 Consensus size: 181
38876915 TTCAGGGTTT
* * * * ** * ** * *
38876925 TAATCACTTCACGTTCAAGT-TATTCAAATTCAATTCAATTTGGGTTTAGGGTTGGGTGGTTTGA
1 TAATCACTTAATGTTCAAGTCAATCCAAATTTGATTCAATTCGGACTTAAGGTTAGGTGGTTTGA
* * *
38876989 GATTTTTAATGATCAAATAGGATGGGGTGAATTGGAGTTTGAATTGATCGATTCGAATATTCAAA
66 GATTTTTAATGATCAAATAGGATGAGATGAATTGGAGTTTGAATCGATCGATTCGAATATTCAAA
* * * * *
38877054 TTCGGATATTTCCAAATTGGGTCATTAAGAAGTTCGAATCAGTTCAAGTTT
131 TTCGAATATTTCCAAATCGGGTCATTAAGAAGTTCGAACCAATTCAAGTTC
* * * * *
38877105 TACTCACTTTATGTTCAAGTTAATCCAAATTTGATTCAATTTGGATTTAAGGTTAGGTGGTTTGA
1 TAATCACTTAATGTTCAAGTCAATCCAAATTTGATTCAATTCGGACTTAAGGTTAGGTGGTTTGA
* * * *
38877170 GTTTTTTAATGATCAAATTGGATGAGATCGAATTTGAGTTTGAATCGATTGATTCGAATATTCAA
66 GATTTTTAATGATCAAATAGGATGAGAT-GAATTGGAGTTTGAATCGATCGATTCGAATATTCAA
* * * ** *
38877235 ATTTGAATTTTTTCAGGTCGGGTCATTAAG-GGTTC-AGACCAATTCAA-TGTC
130 ATTCGAATATTTCCAAATCGGGTCATTAAGAAGTTCGA-ACCAATTCAAGT-TC
**** * *
38877286 TAATCA-TTAAATGTTCAAGTCAATTTGGATTTGATTCAATTC-GAGCTTAAGGTTAGATGATTT
1 TAATCACTT-AATGTTCAAGTCAATCCAAATTTGATTCAATTCGGA-CTTAAGGTTAGGTGGTTT
38877349 GA
64 GA
38877351 TTTGTTGACT
Statistics
Matches: 201, Mismatches: 39, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
180 23 0.11
181 122 0.61
182 56 0.28
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.39
Consensus pattern (181 bp):
TAATCACTTAATGTTCAAGTCAATCCAAATTTGATTCAATTCGGACTTAAGGTTAGGTGGTTTGA
GATTTTTAATGATCAAATAGGATGAGATGAATTGGAGTTTGAATCGATCGATTCGAATATTCAAA
TTCGAATATTTCCAAATCGGGTCATTAAGAAGTTCGAACCAATTCAAGTTC
Found at i:38879029 original size:4 final size:4
Alignment explanation
Indices: 38879020--38879072 Score: 106
Period size: 4 Copynumber: 13.2 Consensus size: 4
38879010 GACTCCCAAG
38879020 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
38879068 GTAT G
1 GTAT G
38879073 AGTTATAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:38882297 original size:13 final size:15
Alignment explanation
Indices: 38882279--38882310 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38882269 TTGTTAAAAC
38882279 AAAAGG-AAAT-AAG
1 AAAAGGAAAATAAAG
38882292 AAAAGGAAAATAAAG
1 AAAAGGAAAATAAAG
38882307 AAAA
1 AAAA
38882311 AAATTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 4 0.24
15 7 0.41
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (15 bp):
AAAAGGAAAATAAAG
Found at i:38882917 original size:26 final size:24
Alignment explanation
Indices: 38882867--38882918 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
38882857 TTTTCATATA
**
38882867 TTTTTTTGAAAGTATTTATGTATT
1 TTTTTTTGAAAGTATTTATAAATT
*
38882891 TTTTTTTCTAAAGTCATTTATAAATT
1 TTTTTTT-GAAAGT-ATTTATAAATT
38882917 TT
1 TT
38882919 GAGGGTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 5 0.22
26 11 0.48
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.62
Consensus pattern (24 bp):
TTTTTTTGAAAGTATTTATAAATT
Found at i:38883443 original size:25 final size:26
Alignment explanation
Indices: 38883421--38883475 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
38883411 AGCTTTTTTC
38883421 CCACATTTTCACGG-TTTTGTTTTAT
1 CCACATTTTCACGGTTTTTGTTTTAT
* ** *
38883446 CCATATTTTCGTGGTTTTTGTTTTGT
1 CCACATTTTCACGGTTTTTGTTTTAT
38883472 CCAC
1 CCAC
38883476 TTTGTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.13, C:0.20, G:0.15, T:0.53
Consensus pattern (26 bp):
CCACATTTTCACGGTTTTTGTTTTAT
Found at i:38884895 original size:31 final size:31
Alignment explanation
Indices: 38884859--38884919 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
38884849 CAACCCAACT
*
38884859 ACTTAAAT-AAGAACTTTTGCATAATTCAGTA
1 ACTTAAATGAA-AACTTTTGAATAATTCAGTA
*
38884890 ACTTAAATGAAAACTTTTGAATAGTTCAGT
1 ACTTAAATGAAAACTTTTGAATAATTCAGT
38884920 GACCATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (31 bp):
ACTTAAATGAAAACTTTTGAATAATTCAGTA
Found at i:38885834 original size:16 final size:16
Alignment explanation
Indices: 38885810--38885843 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
38885800 TTTTTTTATA
38885810 TATTCTTTAGAATTTT
1 TATTCTTTAGAATTTT
*
38885826 TATTTTTTAGAATTTT
1 TATTCTTTAGAATTTT
38885842 TA
1 TA
38885844 CAAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (16 bp):
TATTCTTTAGAATTTT
Found at i:38885880 original size:18 final size:19
Alignment explanation
Indices: 38885857--38885893 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38885847 ATTTTTAAAA
38885857 TATAAAT-TTTGAAATTTT
1 TATAAATATTTGAAATTTT
*
38885875 TATAAATATTTTAAATTTT
1 TATAAATATTTGAAATTTT
38885894 AAAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGAAATTTT
Found at i:38885911 original size:18 final size:18
Alignment explanation
Indices: 38885846--38885911 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 18
38885836 AATTTTTACA
38885846 AATTTTTAAAATATAAATTTT
1 AATTTTTAAAAT-T--ATTTT
38885867 GAAATTTTTATAAA-TATTTT
1 --AATTTTTA-AAATTATTTT
*
38885887 AAATTTTAAAATTATTTT
1 AATTTTTAAAATTATTTT
38885905 AATTTTT
1 AATTTTT
38885912 TTGAAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 3 0.08
18 19 0.49
20 5 0.13
22 1 0.03
23 8 0.21
24 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
AATTTTTAAAATTATTTT
Found at i:38885922 original size:12 final size:12
Alignment explanation
Indices: 38885905--38885942 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
38885895 AAATTATTTT
38885905 AATTTTTTTGAA
1 AATTTTTTTGAA
38885917 AATTTTTTTTG-A
1 AA-TTTTTTTGAA
38885929 AATTTTTGTTGAA
1 AATTTTT-TTGAA
38885942 A
1 A
38885943 GGGACTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.22
12 8 0.35
13 10 0.43
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
AATTTTTTTGAA
Found at i:38885925 original size:13 final size:13
Alignment explanation
Indices: 38885907--38885942 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
38885897 ATTATTTTAA
38885907 TTTTTTTGAAAAT
1 TTTTTTTGAAAAT
38885920 TTTTTTTG-AAAT
1 TTTTTTTGAAAAT
*
38885932 TTTTGTTGAAA
1 TTTTTTTGAAA
38885943 GGGACTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (13 bp):
TTTTTTTGAAAAT
Found at i:38888757 original size:205 final size:205
Alignment explanation
Indices: 38888395--38888783 Score: 595
Period size: 205 Copynumber: 1.9 Consensus size: 205
38888385 AGATACCCTC
38888395 ATTTTTCCTAACTAGTTGGACAGGAAACCAAACACACATTCAGCCAAACCCCCTACTTAAATTCT
1 ATTTTTCCTAACTAGTTGGACAGGAAACCAAACACACATTCAGCCAAACCCCCTACTTAAATTCT
*
38888460 GCTATATAAGTCCCTATATTTTATAAAAATTGTGGATATAGTTTCTATACTTTTCAAGTTTTGAA
66 GCTATATAAGTCCCTATACTTTATAAAAATTGTGGATATAGTTTCTATACTTTTCAAGTTTTGAA
38888525 ATTTTAATCTTGACCCAAATGGTAACAATTAAATCTATTTGGTTAAATTCAATTACTAGTATTAT
131 ATTTTAATCTTGACCCAAATGGTAACAATTAAATCTATTTGGTTAAATTCAATTACTAGTATTAT
38888590 AGATATGCCT
196 AGATATGCCT
* * * *
38888600 ATTTTTCTTAACTAGTTGGACTAGGAAACCAAACACACATTCTGCCAAACCCCTGTACTTATATT
1 ATTTTTCCTAACTAGTTGGAC-AGGAAACCAAACACACATTCAGCCAAACCCC-CTACTTAAATT
* * * * ** *
38888665 CTGCTATA-AA-TCCCTATACTTTATGAAAATTGTGGATTTAGTTTTTATATTTTTCGGGTTTTT
64 CTGCTATATAAGTCCCTATACTTTATAAAAATTGTGGATATAGTTTCTATACTTTTCAAGTTTTG
* * *
38888728 AAATTTTAATCTTGACTC-AATCTGTAACAATTAGATCTATTTGGTTAAATTCAATT
129 AAATTTTAATCTTGACCCAAAT-GGTAACAATTAAATCTATTTGGTTAAATTCAATT
38888784 TTTAGTCTTG
Statistics
Matches: 166, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
204 3 0.02
205 114 0.69
206 32 0.19
207 17 0.10
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (205 bp):
ATTTTTCCTAACTAGTTGGACAGGAAACCAAACACACATTCAGCCAAACCCCCTACTTAAATTCT
GCTATATAAGTCCCTATACTTTATAAAAATTGTGGATATAGTTTCTATACTTTTCAAGTTTTGAA
ATTTTAATCTTGACCCAAATGGTAACAATTAAATCTATTTGGTTAAATTCAATTACTAGTATTAT
AGATATGCCT
Found at i:38896245 original size:13 final size:12
Alignment explanation
Indices: 38896229--38896275 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
38896219 AAACTTATTA
38896229 TTAATTATTATAT
1 TTAATT-TTATAT
*
38896242 TTAAATTTAT-T
1 TTAATTTTATAT
38896253 ATTAATTGTTATAT
1 -TTAATT-TTATAT
38896267 TTAATTTTA
1 TTAATTTTA
38896276 GAAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 1 0.03
12 12 0.41
13 15 0.52
14 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (12 bp):
TTAATTTTATAT
Found at i:38896257 original size:25 final size:25
Alignment explanation
Indices: 38896223--38896275 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
38896213 AAATGAAAAC
38896223 TTATTATTAATTATTATATTTAAAT
1 TTATTATTAATTATTATATTTAAAT
* *
38896248 TTATTATTAATTGTTATATTTAATT
1 TTATTATTAATTATTATATTTAAAT
38896273 TTA
1 TTA
38896276 GAAATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTATTATTAATTATTATATTTAAAT
Found at i:38897549 original size:20 final size:20
Alignment explanation
Indices: 38897524--38897697 Score: 70
Period size: 20 Copynumber: 8.7 Consensus size: 20
38897514 CACATATGTG
*
38897524 CCCCTGTTTGTACTCCGGTA
1 CCCCTGTTTGTACTACGGTA
* * *
38897544 CCCCTGATTGCACATAC-GTG
1 CCCCTGTTTGTAC-TACGGTA
** *
38897564 CCGTTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTACGGTA
** * * *
38897584 CCCCTAATTGCACATAC-ATG
1 CCCCTGTTTGTAC-TACGGTA
*
38897604 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTACGGTA
* ** *
38897624 CCCCTGATTACACATAC-GTG
1 CCCCTGTTTGTAC-TACGGTA
* **
38897644 CCCCTGTTTGTACTTCAATA
1 CCCCTGTTTGTACTACGGTA
* *
38897664 CCCCT-TGTTGTACATA-AGTG
1 CCCCTGT-TTGTAC-TACGGTA
38897684 CCCCTGTTTGTACT
1 CCCCTGTTTGTACT
38897698 TTGATACCCC
Statistics
Matches: 107, Mismatches: 38, Indels: 19
0.65 0.23 0.12
Matches are distributed among these distances:
19 8 0.07
20 91 0.85
21 8 0.07
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.34
Consensus pattern (20 bp):
CCCCTGTTTGTACTACGGTA
Found at i:38897565 original size:40 final size:40
Alignment explanation
Indices: 38897508--38897771 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
38897498 AATTATTGTA
* *
38897508 TGATTGCACATATGTGCCCCTGTTTGTACTCCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
**
38897548 TGATTGCACATACGTGCCGTTGTTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
38897588 TAATTGCACATACATGCCCCTGTTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* **
38897628 TGATTACACATACGTGCCCCTGTTTGTACTTCAATACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
38897668 TTG-TTGTACATAAGTGCCCCTGTTTGTACTTTGATACCCC
1 -TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
38897708 TGATTGCACATATGTGCCCCTGTTTGTAATTCGGTA-CTC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * **
38897747 TGAATGCACTTTTGTGCCCCTGTTT
1 TGATTGCACATACGTGCCCCTGTTT
38897772 ATACCTCGAC
Statistics
Matches: 195, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
39 26 0.13
40 167 0.86
41 2 0.01
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.36
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:38897707 original size:20 final size:20
Alignment explanation
Indices: 38897644--38897709 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
38897634 CACATACGTG
*
38897644 CCCCTGTTTGTACTTCAATA
1 CCCCTGTTTGTACTTTAATA
* *
38897664 CCCCT-TGTTGTAC-ATAAGTG
1 CCCCTGT-TTGTACTTTAA-TA
*
38897684 CCCCTGTTTGTACTTTGATA
1 CCCCTGTTTGTACTTTAATA
38897704 CCCCTG
1 CCCCTG
38897710 ATTGCACATA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
19 3 0.08
20 30 0.83
21 3 0.08
ACGTcount: A:0.17, C:0.30, G:0.15, T:0.38
Consensus pattern (20 bp):
CCCCTGTTTGTACTTTAATA
Found at i:38899731 original size:45 final size:45
Alignment explanation
Indices: 38899662--38899804 Score: 169
Period size: 45 Copynumber: 3.0 Consensus size: 45
38899652 ATTTATCACT
38899662 TGTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
1 TGTCACTTGT-CCTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
* * * *
38899708 TGTTACTTGTCTTGATAAGATAAGTGCAGCTAAAGCTACCACTTATCA
1 TGTCACTTGTCCTGATCAGATAAGTGTAGCTAAAGCTACCAC-T-T-A
* *
38899756 CTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAACGCTACCACTTA
1 --TGTCACTTGTC-CTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
38899804 T
1 T
38899805 CATTTGTCAC
Statistics
Matches: 81, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
45 29 0.36
46 11 0.14
47 1 0.01
48 2 0.02
49 1 0.01
50 11 0.14
51 26 0.32
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (45 bp):
TGTCACTTGTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTA
Found at i:38910018 original size:27 final size:26
Alignment explanation
Indices: 38909978--38910028 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 26
38909968 AAGCAATTCT
38909978 TACAAACAATATGATTGAATAACAATA
1 TACAAACAATATGA-TGAATAACAATA
38910005 TACAAAGCAA-ATGATGAATAACAA
1 TACAAA-CAATATGATGAATAACAA
38910029 ACAAATTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 10 0.43
27 10 0.43
28 3 0.13
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.22
Consensus pattern (26 bp):
TACAAACAATATGATGAATAACAATA
Found at i:38910142 original size:15 final size:17
Alignment explanation
Indices: 38910122--38910153 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
38910112 ACAAAACGAG
38910122 AATAA-TTAAT-ACAAA
1 AATAATTTAATCACAAA
38910137 AATAATTTAATCACAAA
1 AATAATTTAATCACAAA
38910154 TAAACCAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATTTAATCACAAA
Found at i:38910345 original size:19 final size:20
Alignment explanation
Indices: 38910312--38910351 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
38910302 AAGTAAAAAG
*
38910312 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
38910332 AATTT-AAATGATGTGGATA
1 AATTTAAAATAATGTGGATA
38910351 A
1 A
38910352 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:38911328 original size:16 final size:16
Alignment explanation
Indices: 38911279--38911346 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 16
38911269 AAATACATCC
38911279 TCTTTTCTGTTCTTTTT
1 TCTTTT-TGTTCTTTTT
*
38911296 TCTTTTT-TTGCTATTT
1 TCTTTTTGTT-CTTTTT
38911312 TCTTTTTGTTTTCTTTTCT
1 TCTTTTTG--TTCTTTT-T
38911331 TCCTTTTTGTTCTTTT
1 T-CTTTTTGTTCTTTT
38911347 GTGTGCTACG
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
15 2 0.05
16 13 0.30
17 6 0.14
18 11 0.26
19 4 0.09
20 7 0.16
ACGTcount: A:0.01, C:0.16, G:0.06, T:0.76
Consensus pattern (16 bp):
TCTTTTTGTTCTTTTT
Found at i:38913811 original size:24 final size:23
Alignment explanation
Indices: 38913784--38913859 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
38913774 AGATATTTAT
*
38913784 ATTATTTATTTATATAATATATAA
1 ATTAATTATTTATATAATAT-TAA
** *
38913808 ATTAATTATAAAGTATATTATTAA
1 ATTAATTATTTA-TATAATATTAA
*
38913832 ATTAATTATATTATA-AATATTAT
1 ATTAATTAT-TTATATAATATTAA
38913855 ATTAA
1 ATTAA
38913860 GAAATAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.26
24 23 0.55
25 8 0.19
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTAATTATTTATATAATATTAA
Found at i:38913827 original size:12 final size:11
Alignment explanation
Indices: 38913798--38913841 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
38913788 TTTATTTATA
38913798 TAATATATAAAT
1 TAAT-TATAAAT
*
38913810 TAATTATAAAG
1 TAATTATAAAT
38913821 TATATTATTAAAT
1 TA-ATTA-TAAAT
38913834 TAATTATA
1 TAATTATA
38913842 TTATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
12 12 0.43
13 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:38913853 original size:14 final size:17
Alignment explanation
Indices: 38913821--38913858 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
38913811 AATTATAAAG
38913821 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
38913838 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
38913852 TATATTA
1 TATATTA
38913859 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:38914095 original size:15 final size:17
Alignment explanation
Indices: 38914077--38914108 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38914067 CAGAATAGAA
38914077 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
38914092 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
38914109 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:38916112 original size:3 final size:3
Alignment explanation
Indices: 38916104--38916131 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38916094 TACAAAATTT
38916104 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38916132 AGAGATGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38919192 original size:20 final size:21
Alignment explanation
Indices: 38919169--38919207 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38919159 TACGCCAACT
*
38919169 AAAA-CTCGTTAGAGCTGAAC
1 AAAAGCTCGTAAGAGCTGAAC
38919189 AAAAGCTCGTAAGAGCTGA
1 AAAAGCTCGTAAGAGCTGA
38919208 TCCACCCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (21 bp):
AAAAGCTCGTAAGAGCTGAAC
Found at i:38932886 original size:37 final size:37
Alignment explanation
Indices: 38932845--38932961 Score: 104
Period size: 37 Copynumber: 3.3 Consensus size: 37
38932835 ACTAAAAACA
38932845 TTAAAATAAATGTTTCTCAGCAAATTGAAAATAAATT
1 TTAAAATAAATGTTTCTCAGCAAATTGAAAATAAATT
* * ** **
38932882 TTAAAATATAA----T-ACATCAAATACAACAA-AAAAC
1 TTAAAATA-AATGTTTCTCAGCAAATTGAA-AATAAATT
*
38932915 TTAAAATAAATGTTTCTCAGCAAATTGAAAATACATT
1 TTAAAATAAATGTTTCTCAGCAAATTGAAAATAAATT
38932952 TTAAAA-AAAT
1 TTAAAATAAAT
38932962 CTTTATACTT
Statistics
Matches: 59, Mismatches: 13, Indels: 17
0.66 0.15 0.19
Matches are distributed among these distances:
32 2 0.03
33 20 0.34
34 3 0.05
36 7 0.12
37 25 0.42
38 2 0.03
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (37 bp):
TTAAAATAAATGTTTCTCAGCAAATTGAAAATAAATT
Found at i:38932919 original size:70 final size:70
Alignment explanation
Indices: 38932800--38932957 Score: 264
Period size: 70 Copynumber: 2.2 Consensus size: 70
38932790 TTTTTATACA
*
38932800 AAAATAAATTTTAAAAAATATAATACATCAAATACACTAAAAACATTAAAATAAATGTTTCTCAG
1 AAAATAAATTTT--AAAATATAATACATCAAATACACAAAAAACATTAAAATAAATGTTTCTCAG
38932865 CAAATTG
64 CAAATTG
38932872 AAAATAAATTTTAAAATATAATACATCAAATACAACAAAAAAC-TTAAAATAAATGTTTCTCAGC
1 AAAATAAATTTTAAAATATAATACATCAAATAC-ACAAAAAACATTAAAATAAATGTTTCTCAGC
38932936 AAATTG
65 AAATTG
*
38932942 AAAATACATTTTAAAA
1 AAAATAAATTTTAAAA
38932958 AAATCTTTAT
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
70 63 0.76
71 8 0.10
72 12 0.14
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (70 bp):
AAAATAAATTTTAAAATATAATACATCAAATACACAAAAAACATTAAAATAAATGTTTCTCAGCA
AATTG
Found at i:38939035 original size:20 final size:20
Alignment explanation
Indices: 38939012--38939050 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38939002 GGGTTAAAGT
*
38939012 TAAAAGTTTTATAT-TAAAAA
1 TAAAAATTTT-TATCTAAAAA
38939032 TAAAAATTTTTATCTAAAA
1 TAAAAATTTTTATCTAAAA
38939051 TAAGCTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
TAAAAATTTTTATCTAAAAA
Found at i:38942834 original size:31 final size:31
Alignment explanation
Indices: 38942796--38942858 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
38942786 TTTACGAAGT
38942796 TAGTTGTGTAGTTAATTAGGTTTTAATTAAG
1 TAGTTGTGTAGTTAATTAGGTTTTAATTAAG
38942827 TAGTTGTGTAGTTAATTAGGTTTTAATTAAG
1 TAGTTGTGTAGTTAATTAGGTTTTAATTAAG
38942858 T
1 T
38942859 GAATTTGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (31 bp):
TAGTTGTGTAGTTAATTAGGTTTTAATTAAG
Found at i:38944596 original size:35 final size:32
Alignment explanation
Indices: 38944546--38944640 Score: 136
Period size: 35 Copynumber: 2.9 Consensus size: 32
38944536 TACTGTGATA
*
38944546 ATTTATAACAGTATATTAAAATAGTATATTAC
1 ATTTATAACAGTATATTAAAACAGTATATTAC
* *
38944578 AAATTTTATAACAATATATTAAACCAGTATATTAC
1 --A-TTTATAACAGTATATTAAAACAGTATATTAC
38944613 ATTTATAACAGTATATTAAAACAGTATA
1 ATTTATAACAGTATATTAAAACAGTATA
38944641 CTAAAACAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 25 0.45
33 1 0.02
34 1 0.02
35 28 0.51
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (32 bp):
ATTTATAACAGTATATTAAAACAGTATATTAC
Found at i:38944610 original size:13 final size:13
Alignment explanation
Indices: 38944552--38944657 Score: 76
Period size: 13 Copynumber: 8.0 Consensus size: 13
38944542 GATAATTTAT
38944552 AACAGTATATTAA
1 AACAGTATATTAA
* *
38944565 AATAGTATATTAC
1 AACAGTATATTAA
*
38944578 AA-A-T-T-TTAT
1 AACAGTATATTAA
*
38944587 AACAATATATTAA
1 AACAGTATATTAA
*
38944600 ACCAGTATATTACATTTA
1 AACAGTATATT--A---A
38944618 TAACAGTATATTAA
1 -AACAGTATATTAA
*
38944632 AACAGTATACTAA
1 AACAGTATATTAA
38944645 AACAGTATATTAA
1 AACAGTATATTAA
38944658 CTACAATAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
11 2 0.03
12 2 0.03
13 49 0.66
14 1 0.01
15 1 0.01
17 1 0.01
18 1 0.01
19 10 0.14
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (13 bp):
AACAGTATATTAA
Found at i:38945924 original size:7 final size:7
Alignment explanation
Indices: 38945912--38945953 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
38945902 ACACGGGGTC
38945912 GGGAAAT
1 GGGAAAT
38945919 GGGAAAT
1 GGGAAAT
38945926 GGGAAAT
1 GGGAAAT
* *
38945933 GGG-GAG
1 GGGAAAT
*
38945939 GGGAATT
1 GGGAAAT
38945946 GGGAAAT
1 GGGAAAT
38945953 G
1 G
38945954 TAACTGTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
6 4 0.14
7 24 0.86
ACGTcount: A:0.36, C:0.00, G:0.50, T:0.14
Consensus pattern (7 bp):
GGGAAAT
Found at i:38952845 original size:18 final size:18
Alignment explanation
Indices: 38952819--38952860 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
38952809 TATATATATG
*
38952819 TATACATAC-TTATATATT
1 TATATATACATTATA-ATT
*
38952837 TTTATATACATTATAATT
1 TATATATACATTATAATT
38952855 TATATA
1 TATATA
38952861 CATAACGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (18 bp):
TATATATACATTATAATT
Found at i:38953053 original size:18 final size:18
Alignment explanation
Indices: 38953008--38953059 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
38952998 TTTATATTTT
* *
38953008 TTTACAATTTATATATAC
1 TTTATAATTTTTATATAC
*
38953026 -ATATATATTTTTATATAC
1 TTTATA-ATTTTTATATAC
*
38953044 TTTATAATTTTCATAT
1 TTTATAATTTTTATAT
38953060 GCATACATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 20 0.74
19 4 0.15
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATAATTTTTATATAC
Found at i:38953053 original size:36 final size:35
Alignment explanation
Indices: 38952952--38953072 Score: 118
Period size: 36 Copynumber: 3.3 Consensus size: 35
38952942 ATACCCTTTT
* * *
38952952 TACATATTTATTTTTTTATTTTTATAATTCATATA
1 TACATATATATTTTTATATTTTTATAATTTATATA
* *
38952987 CACATATAT-TTTTTATATTTTTTTACAATTTATATA
1 TACATATATATTTTTATA--TTTTTATAATTTATATA
*
38953023 TACATATATATTTTTATATACTTTATAATTTTCATATGCA
1 TACATATATATTTTTATAT-TTTTATAA-TTT-ATAT--A
38953063 TACATATATA
1 TACATATATA
38953073 CATATTTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
34 7 0.10
35 8 0.11
36 29 0.41
37 11 0.16
38 4 0.06
40 11 0.16
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (35 bp):
TACATATATATTTTTATATTTTTATAATTTATATA
Done.