Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 100 of 349
Found at i:31089417 original size:16 final size:18
Alignment explanation
Indices: 31089396--31089437 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
31089386 GGGATAATTG
31089396 AATCAAT-T-TTGATTAA
1 AATCAATCTATTGATTAA
31089412 AATCAAATCTCATTGATTAA
1 AATC-AATCT-ATTGATTAA
31089432 AATCAA
1 AATCAA
31089438 ATAATTCAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 3 0.14
18 1 0.05
19 2 0.09
20 12 0.55
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.36
Consensus pattern (18 bp):
AATCAATCTATTGATTAA
Found at i:31093271 original size:47 final size:47
Alignment explanation
Indices: 31092996--31093236 Score: 437
Period size: 47 Copynumber: 5.1 Consensus size: 47
31092986 GATTTTATGA
31092996 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
31093043 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* *
31093090 GATGAATGTGAACTTGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
31093137 AATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
**
31093184 GATGAATGTGAACATGCATATATGTGATAAGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
31093231 GATGAA
1 GATGAA
31093237 CGTGGAAGTG
Statistics
Matches: 186, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 186 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
Found at i:31093314 original size:46 final size:46
Alignment explanation
Indices: 31093264--31093478 Score: 322
Period size: 46 Copynumber: 4.7 Consensus size: 46
31093254 GTGGCGAAGT
* *
31093264 CGAATGGCTAATACGAAATATGTATGAGATGGATATGAGGTAAAGC
1 CGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTAAAGC
31093310 CGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTAAAGC
1 CGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTAAAGC
* * *
31093356 CGAATGGCTAATGTGAAACGTGTATGATATGGATATGAGGTAAAGC
1 CGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTAAAGC
* * *
31093402 TGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTACAGC
1 CGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTAAAGC
* * * *
31093448 CAAATGGCTAATGTGAGATATGTATGAGATG
1 CGAATGGCTAATGCGAAATGTGTATGAGATG
31093479 TGTATATATA
Statistics
Matches: 154, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 154 1.00
ACGTcount: A:0.35, C:0.09, G:0.31, T:0.25
Consensus pattern (46 bp):
CGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTAAAGC
Found at i:31095053 original size:13 final size:13
Alignment explanation
Indices: 31095035--31095060 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31095025 ACATTGCCTC
31095035 CAAGAAAGTGCTT
1 CAAGAAAGTGCTT
31095048 CAAGAAAGTGCTT
1 CAAGAAAGTGCTT
31095061 AAAAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CAAGAAAGTGCTT
Found at i:31095731 original size:126 final size:125
Alignment explanation
Indices: 31095589--31096022 Score: 541
Period size: 125 Copynumber: 3.5 Consensus size: 125
31095579 GTCAAACGGT
* * * * * * * *
31095589 AAATCGAAACCTAGCACGATTGGGCACAATTTATCGAA-TTTCCAAATACGAAATATTGCCTCCT
1 AAATCAAAACCCAGCACGATTGGGCACGA-TTCTCAAACTTCCCAAATTCGAAATATTGCCTCAT
*
31095653 GTTAATTTAAGAAAACATAGACGAATTTTCAAAAAGAATATTCCGCACTTTAGTCGAATGAA
65 TTTAATTTAAGAAAACATAGACGAA-TTTCAAAAAGAATATTCCGCACTTTAGTCGAATGAA
* * * * *
31095715 AAATCGAAACCCAGCACGATTAGGCATGA-TCTCAAACTCCCCAAATTCGAAATATTGCCTCGTT
1 AAATCAAAACCCAGCACGATTGGGCACGATTCTCAAACTTCCCAAATTCGAAATATTGCCTCATT
* * *
31095779 TTAATTTAAGAAAACATGGACGAAATTTCAAAAGGAATATTCCGCACTTTAGTCGAATGGA
66 TTAATTTAAGAAAACATAGACG-AATTTCAAAAAGAATATTCCGCACTTTAGTCGAATGAA
31095840 AAATCAAAACCCAGCACGATTGGGCACGATCTCTCAAACTTCCCAAATTCGAAATATTGCCTCAT
1 AAATCAAAACCCAGCACGATTGGGCACGAT-TCTCAAACTTCCCAAATTCGAAATATTGCCTCAT
* * * * ** * * *
31095905 TTTAATTTAAGGAAACATAGACGAAATTCCAAAAGGATATTTTGTATTTTAGTCAAATGAA
65 TTTAATTTAAGAAAACATAGACGAATTTCAAAAAGAATATTCCGCACTTTAGTCGAATGAA
* **
31095966 AAATCAAAACCCAGCACGATTGGGCATGATCTCTCAAAC-TCCCAAACACGAAATATT
1 AAATCAAAACCCAGCACGATTGGGCACGAT-TCTCAAACTTCCCAAATTCGAAATATT
31096023 TCCTTATGTT
Statistics
Matches: 270, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
124 5 0.02
125 119 0.44
126 93 0.34
127 53 0.20
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (125 bp):
AAATCAAAACCCAGCACGATTGGGCACGATTCTCAAACTTCCCAAATTCGAAATATTGCCTCATT
TTAATTTAAGAAAACATAGACGAATTTCAAAAAGAATATTCCGCACTTTAGTCGAATGAA
Found at i:31098403 original size:84 final size:84
Alignment explanation
Indices: 31098261--31098539 Score: 407
Period size: 84 Copynumber: 3.3 Consensus size: 84
31098251 AGAAGCCTAA
* * * *
31098261 TACCCTACTGCTTAGGGGGTTAAGGCTTGCTGTCTTCGATTTGTTCCACTACTGTTTAGGGGAGA
1 TACCCTACTGCTTAAGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTGTTTAGGGGAGA
*
31098326 TCTGTATTTTCCAGCATGT
66 TCTGTATTTTCCAGCCTGT
* *
31098345 TACCCTACTGCTTAAGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTATTTAGGAGAGA
1 TACCCTACTGCTTAAGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTGTTTAGGGGAGA
* *
31098410 TCTGTATTTTCCAACCTAT
66 TCTGTATTTTCCAGCCTGT
* * * * *
31098429 TACCCTATTACTTAAGAGGTTAAGGCTTACTGTCTTTGTTCTGCTCCACTACTGTTTAGGGGAGA
1 TACCCTACTGCTTAAGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTGTTTAGGGGAGA
*
31098494 TCTGTATTTTCTAGCCTGT
66 TCTGTATTTTCCAGCCTGT
31098513 TACCCTACTGCTT-AGGGAGTTAAGGCT
1 TACCCTACTGCTTAAGGG-GTTAAGGCT
31098540 CGTATCTTCA
Statistics
Matches: 172, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
83 3 0.02
84 169 0.98
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (84 bp):
TACCCTACTGCTTAAGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTGTTTAGGGGAGA
TCTGTATTTTCCAGCCTGT
Found at i:31098897 original size:177 final size:177
Alignment explanation
Indices: 31098491--31099245 Score: 1162
Period size: 177 Copynumber: 4.3 Consensus size: 177
31098481 TGTTTAGGGG
*
31098491 AGATCTGT-ATTTTCTAGCCTGTTACCCTACTGCTTAGGGAGTTAAGGCTCGTATCTTCAACCTG
1 AGATCTGTAATTTT-TAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTCAACCTG
* *
31098555 CTCTCTTGCTACCTCAGAGAGATAAGG-TCAGTGGCTAAAATCTTCTCCATAGCCGATACATGGA
65 CTCTCTTGCTACCTCAGAGAGATAAGGCT-GGTGGCTAAAATCTGCTCCATAGCCGATACATGGA
* * * * *
31098619 GATAAG-CTCGCCATCTTTGATCTGCTCCATAGTCAATACTTGAAGATA
129 GATAAGACTCGCCATCTTTGATCTACTCCATAGCCGATACATGGAGATA
* *
31098667 AGATTTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGACTCGTATCTTCAACCTGC
1 AGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTCAACCTGC
* * *
31098732 TCTCTTGCTACCTTAGAGAGATAAGG-TCGGTGGCTAAAATCTGCTCCATAGTCGATACATGGGG
66 TCTCTTGCTACCTCAGAGAGATAAGGCT-GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAG
31098796 ATAAGACTCGCCATCTTTGATCTGA-TCCATAGCCGATACATGGAGATA
130 ATAAGACTCGCCATCTTTGATCT-ACTCCATAGCCGATACATGGAGATA
* *
31098844 AGATCTGTAATTTTTAGCTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTCAATCTGC
1 AGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTCAACCTGC
* * *
31098909 TCTCTTGTTATCTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTCCATAGCCGATACATGGAGA
66 TCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGA
31098974 TAAGACTCGCCAT-TTTCGATCTACTCCATAGCCGATACATGGAGATA
131 TAAGACTCGCCATCTTT-GATCTACTCCATAGCCGATACATGGAGATA
* * * *
31099021 AGATCTGCAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTTAACCTGT
1 AGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTCAACCTGC
*
31099086 TCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCATAGCCGATACATGGAGA
66 TCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGA
* * *
31099151 TAAGACTCGCCATTTTTGATCTACTCTATAGTCGATACATGGAGATA
131 TAAGACTCGCCATCTTTGATCTACTCCATAGCCGATACATGGAGATA
* * *
31099198 AGATCTGTAATTTTTAGTCTGTTACCCTACTGTTTAAGGGGTTAAGGC
1 AGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
31099246 ACGTGACTTC
Statistics
Matches: 532, Mismatches: 40, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
176 124 0.23
177 404 0.76
178 4 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (177 bp):
AGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTCAACCTGC
TCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGA
TAAGACTCGCCATCTTTGATCTACTCCATAGCCGATACATGGAGATA
Found at i:31099034 original size:45 final size:45
Alignment explanation
Indices: 31098947--31099035 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
31098937 GGTGGCTTAA
* *
31098947 ATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTTCG
1 ATCTACTCCATAGCCGATACATGGAGATAAGACTCGCAATTTTCG
31098992 ATCTACTCCATAGCCGATACATGGAGATAAGA-TCTGCAATTTTC
1 ATCTACTCCATAGCCGATACATGGAGATAAGACTC-GCAATTTTC
31099036 AGCCTGTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (45 bp):
ATCTACTCCATAGCCGATACATGGAGATAAGACTCGCAATTTTCG
Found at i:31099421 original size:64 final size:64
Alignment explanation
Indices: 31099320--31099442 Score: 201
Period size: 64 Copynumber: 1.9 Consensus size: 64
31099310 GTATCTATGC
* * * *
31099320 TTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCTTAGCTAGATGTGATAT
1 TTATGCCAAATAATTAGGATGCTATAATCAAAATGAATCAAATGCTCCTAACTAGATGTGATAT
*
31099384 TTATGTCAAATAATTAGGATGCTATAATCAAAATGAATCAAATGCTCCTAACTAGATGT
1 TTATGCCAAATAATTAGGATGCTATAATCAAAATGAATCAAATGCTCCTAACTAGATGT
31099443 ACTATGAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (64 bp):
TTATGCCAAATAATTAGGATGCTATAATCAAAATGAATCAAATGCTCCTAACTAGATGTGATAT
Found at i:31110118 original size:40 final size:40
Alignment explanation
Indices: 31110073--31110152 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
31110063 TGAAAAAAGG
31110073 ATAGAAAATAATCAATTTTACGGCTTGACTCTCTTATTGT
1 ATAGAAAATAATCAATTTTACGGCTTGACTCTCTTATTGT
31110113 ATAGAAAATAATCAATTTTACGGCTTGACTCTCTTATTGT
1 ATAGAAAATAATCAATTTTACGGCTTGACTCTCTTATTGT
31110153 CCCCAGTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (40 bp):
ATAGAAAATAATCAATTTTACGGCTTGACTCTCTTATTGT
Found at i:31110833 original size:127 final size:127
Alignment explanation
Indices: 31110648--31111093 Score: 592
Period size: 127 Copynumber: 3.5 Consensus size: 127
31110638 GCCAAATGGT
* * * * * * **
31110648 AAATCGAAACCTAGCACGATTGGACACGATTTATCGAA-TTTCCAAATACGAAATATTGCCTCAT
1 AAATCGAAACCCAGCACGATTGGGCATGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCAT
31110712 GTTAATTTAAGAAAACATGGACGAAATTTCAAAAGGAATATTCTGCACTTTAGTCGAATGAA
66 GTTAATTTAAGAAAACATGGACGAAATTTCAAAAGGAATATTCTGCACTTTAGTCGAATGAA
* * *
31110774 AAATTGAAACCCAGCACGATTGGGCATGATCTCTCAAACTCCCCAAATTCGAAATATTGCCTCGT
1 AAATCGAAACCCAGCACGATTGGGCATGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCAT
* * * *
31110839 TTTAATTTAAGAAAACATGGATGAAATTTCAAAAGGAATATTCCGCACTTTAGTCGAATGGA
66 GTTAATTTAAGAAAACATGGACGAAATTTCAAAAGGAATATTCTGCACTTTAGTCGAATGAA
* * * *
31110901 AAATCGAAACCCAGCACGATTGGGCACGATCTCTCAAGCTCCCCAAATTCGAAATATTGCCTCGT
1 AAATCGAAACCCAGCACGATTGGGCATGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCAT
* * * * * * * *
31110966 TTTAATTTAAGAAAACATAGACAAAATTCCAAAAGG-ATATTTTGTATTTTAGTCAAATGAA
66 GTTAATTTAAGAAAACATGGACGAAATTTCAAAAGGAATATTCTGCACTTTAGTCGAATGAA
* * * *
31111027 AAATCGAAACCCAGCACAATTGGGCATGATCTCTCAAACT-CCCAAACACGAAATATTTCCTTAT
1 AAATCGAAACCCAGCACGATTGGGCATGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCAT
31111091 GTT
66 GTT
31111094 GAGGGGACTC
Statistics
Matches: 282, Mismatches: 37, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
125 21 0.07
126 87 0.31
127 174 0.62
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (127 bp):
AAATCGAAACCCAGCACGATTGGGCATGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCAT
GTTAATTTAAGAAAACATGGACGAAATTTCAAAAGGAATATTCTGCACTTTAGTCGAATGAA
Found at i:31114112 original size:12 final size:11
Alignment explanation
Indices: 31114093--31114123 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
31114083 TGTATAAAAC
31114093 TTATTTTATTA
1 TTATTTTATTA
31114104 TTAATTTTATTA
1 TT-ATTTTATTA
31114116 TTATTTTA
1 TTATTTTA
31114124 AAGGAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:31114140 original size:30 final size:30
Alignment explanation
Indices: 31114104--31114163 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
31114094 TATTTTATTA
31114104 TTAATTTTATTATTATTTTAAAGGAATTTG
1 TTAATTTTATTATTATTTTAAAGGAATTTG
* *
31114134 TTAATTTTATTATTATTTTAGAGGTATTTG
1 TTAATTTTATTATTATTTTAAAGGAATTTG
31114164 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGAATTTG
Found at i:31125432 original size:13 final size:14
Alignment explanation
Indices: 31125414--31125442 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31125404 TTGGTGATTC
31125414 TTTC-TTTTCTTTT
1 TTTCTTTTTCTTTT
31125427 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
31125441 TT
1 TT
31125443 CCCATCTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTCTTTTTCTTTT
Found at i:31126549 original size:51 final size:51
Alignment explanation
Indices: 31126490--31126588 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
31126480 ATGCATGTCT
* * *
31126490 AAGTCCACTTGAAACTTTATTTTATATAGTCTCCAAAGAAAGTGAGTGGGC
1 AAGTCCACTTAAAACTTTAATTTATATAGTCTCCAAAGAAAATGAGTGGGC
* *
31126541 AAGTCCACTTAAAACTTTAATTTATCTAGTCTCCTAAGAAAATGAGTG
1 AAGTCCACTTAAAACTTTAATTTATATAGTCTCCAAAGAAAATGAGTG
31126589 TGCATTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (51 bp):
AAGTCCACTTAAAACTTTAATTTATATAGTCTCCAAAGAAAATGAGTGGGC
Found at i:31126873 original size:13 final size:13
Alignment explanation
Indices: 31126852--31126922 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
31126842 AGTTTGGCAA
*
31126852 TGCTTTTGAAAAG
1 TGCTTTTGAGAAG
*
31126865 TGTTTTTGAGAAG
1 TGCTTTTGAGAAG
*
31126878 TACTTTTGAGAAG
1 TGCTTTTGAGAAG
31126891 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
31126904 TACTTTTGAGAAG
1 TGCTTTTGAGAAG
31126917 TGCTTT
1 TGCTTT
31126923 AGAAAAATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:31126885 original size:26 final size:26
Alignment explanation
Indices: 31126854--31126922 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
31126844 TTTGGCAATG
* *
31126854 CTTTTGAAAAGTGTTTTTGAGAAGTA
1 CTTTTGAGAAGTGCTTTTGAGAAGTA
31126880 CTTTTGAGAAGTGCTTTTGAGAAGTA
1 CTTTTGAGAAGTGCTTTTGAGAAGTA
31126906 CTTTTGAGAAGTGCTTT
1 CTTTTGAGAAGTGCTTT
31126923 AGAAAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (26 bp):
CTTTTGAGAAGTGCTTTTGAGAAGTA
Found at i:31127212 original size:21 final size:19
Alignment explanation
Indices: 31127144--31127216 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 19
31127134 AGTAATTAAT
* *
31127144 ATTAATTATTTATTAAATTTA
1 ATTAAATATTTA--AAATATA
*
31127165 ATTAGAATATATAAAATATA
1 ATTA-AATATTTAAAATATA
*
31127185 TTTAAATATTTAAATATAATA
1 ATTAAATATTTAAA-AT-ATA
31127206 ATTAAATATTT
1 ATTAAATATTT
31127217 GTAATTAGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 9 0.21
20 11 0.26
21 17 0.40
22 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (19 bp):
ATTAAATATTTAAAATATA
Found at i:31128173 original size:10 final size:10
Alignment explanation
Indices: 31128145--31128174 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
31128135 GTCGAGATGC
*
31128145 CAATACTACT
1 CAATACTATT
31128155 CAATACTATT
1 CAATACTATT
31128165 CAATACTATT
1 CAATACTATT
31128175 TATTTCAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (10 bp):
CAATACTATT
Found at i:31133397 original size:59 final size:58
Alignment explanation
Indices: 31133323--31133433 Score: 159
Period size: 59 Copynumber: 1.9 Consensus size: 58
31133313 TTGTTATTAA
* *
31133323 ATTTTAATAACATTATTATTAAATATAATTTAATAAAATATAATAAATAATATAATCAT
1 ATTTTAATAAAATTATTATTAAATATAATTTAACAAAA-ATAATAAATAATATAATCAT
* * * *
31133382 ATTTTTATAAAATTATTATTATATATAATTTAACAATAATAATATATAATAT
1 ATTTTAATAAAATTATTATTAAATATAATTTAACAAAAATAATAAATAATAT
31133434 TAGAAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 13 0.28
59 33 0.72
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (58 bp):
ATTTTAATAAAATTATTATTAAATATAATTTAACAAAAATAATAAATAATATAATCAT
Found at i:31133427 original size:21 final size:21
Alignment explanation
Indices: 31133402--31133450 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
31133392 AATTATTATT
31133402 ATATATAAT-TTA-ACAATAATA
1 ATATATAATATTAGA-AA-AATA
31133423 ATATATAATATTAGAAAAATA
1 ATATATAATATTAGAAAAATA
31133444 ATATATA
1 ATATATA
31133451 GCCATAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 20 0.77
22 5 0.19
23 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATATAATATTAGAAAAATA
Found at i:31134381 original size:26 final size:26
Alignment explanation
Indices: 31134352--31134404 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
31134342 TGCGATCTCC
31134352 TCACGTTCTAAGAATTTCATACCAAG
1 TCACGTTCTAAGAATTTCATACCAAG
*
31134378 TCACGTTCTAAGAATTTCATAGCAAG
1 TCACGTTCTAAGAATTTCATACCAAG
31134404 T
1 T
31134405 TGCTGCAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (26 bp):
TCACGTTCTAAGAATTTCATACCAAG
Found at i:31139209 original size:19 final size:18
Alignment explanation
Indices: 31139187--31139238 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
31139177 CTTTTACATT
*
31139187 TATTTAATATAAATAATTA
1 TATTTAATATAAATAA-AA
*
31139206 TATTT-ATCTAATATAAAA
1 TATTTAATATAA-ATAAAA
31139224 TATTTTAATATAAAT
1 TA-TTTAATATAAAT
31139239 TTTTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 8 0.30
19 14 0.52
20 5 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTTAATATAAATAAAA
Found at i:31146672 original size:23 final size:21
Alignment explanation
Indices: 31146598--31146664 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
31146588 CCTGATCAGT
** * *
31146598 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
31146619 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
31146640 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
31146661 ATAC
1 ATAC
31146665 ACGACACATA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.15
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:31146680 original size:23 final size:22
Alignment explanation
Indices: 31146600--31146685 Score: 86
Period size: 21 Copynumber: 4.0 Consensus size: 22
31146590 TGATCAGTAT
* *
31146600 ACGACACATAAAGTGCCT-AAA
1 ACGACACACAAAGTGCCTGATA
* *
31146621 ACGACACACGAGGTGCCTGAT-
1 ACGACACACAAAGTGCCTGATA
* *
31146642 ACGACACACGAGGTGCCTGATA
1 ACGACACACAAAGTGCCTGATA
*
31146664 CACGACACATAAAGTGCCTGAT
1 -ACGACACACAAAGTGCCTGAT
31146686 CGATAAAGCC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 36 0.65
22 1 0.02
23 18 0.33
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.15
Consensus pattern (22 bp):
ACGACACACAAAGTGCCTGATA
Found at i:31147080 original size:15 final size:15
Alignment explanation
Indices: 31147055--31147112 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
31147045 TCATATATAT
31147055 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
31147071 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
31147086 AATAATTTCAATCAA
1 TATAAATTCAATCAA
31147101 TATAAATTCAAT
1 TATAAATTCAAT
31147113 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:31153142 original size:21 final size:21
Alignment explanation
Indices: 31153118--31153185 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
31153108 GTAAGTATAT
31153118 CAATGTGAAATGTAGGTTCAC
1 CAATGTGAAATGTAGGTTCAC
** * *
31153139 CAATGTGTTGA-GTAAGTAT-AT
1 CAATGTG-AAATGTAGGT-TCAC
31153160 CAATGTGAAATGTAGGTTCAC
1 CAATGTGAAATGTAGGTTCAC
31153181 CAATG
1 CAATG
31153186 GGTTTGGGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (21 bp):
CAATGTGAAATGTAGGTTCAC
Found at i:31153165 original size:42 final size:42
Alignment explanation
Indices: 31153106--31153185 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
31153096 GATTGAACTG
31153106 GAGTAAGTATATCAATGTGAAATGTAGGTTCACCAATGTGTT
1 GAGTAAGTATATCAATGTGAAATGTAGGTTCACCAATGTGTT
31153148 GAGTAAGTATATCAATGTGAAATGTAGGTTCACCAATG
1 GAGTAAGTATATCAATGTGAAATGTAGGTTCACCAATG
31153186 GGTTTGGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (42 bp):
GAGTAAGTATATCAATGTGAAATGTAGGTTCACCAATGTGTT
Found at i:31155521 original size:68 final size:67
Alignment explanation
Indices: 31155348--31155596 Score: 237
Period size: 69 Copynumber: 3.6 Consensus size: 67
31155338 TCATTGTGAA
* * * *
31155348 CCTTAATGTGACAACTGGGAGCTTTTCTCTCATTAACTGTGTTTGAGGCTGTGACTCTTCGCCTA
1 CCTTAATATGACAACTGGGAGCTTTGCTCTCACTAACTGTG-TTG-GGCTGTGGCTCTTCGCCTA
*
31155413 CGAG
64 CAAG
** * * ** * * * *
31155417 CCTTAATATGACAGTTGGAAGCTTTACTCTTGCTAACTATGCTAGGGCTGCGGCTCCTCGCCTAC
1 CCTTAATATGACAACTGGGAGCTTTGCTCTCACTAACTGTG-TTGGGCTGTGGCTCTTCGCCTAC
*
31155482 TAG
65 AAG
* * * * * *
31155485 CCTTAATATGACAGCTGGGAGCTTTGCTCTCACTAACTGTGTTGGAGATTATAGATTTTCGCCTA
1 CCTTAATATGACAACTGGGAGCTTTGCTCTCACTAACTGTGTTGG-G-CTGTGGCTCTTCGCCTA
31155550 CAAG
64 CAAG
* *
31155554 CCTTAATATGACAACTAGGAGCTTTGCTCTCACTAACAGTGTT
1 CCTTAATATGACAACTGGGAGCTTTGCTCTCACTAACTGTGTT
31155597 AGAGATTACG
Statistics
Matches: 145, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
67 3 0.02
68 55 0.38
69 87 0.60
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (67 bp):
CCTTAATATGACAACTGGGAGCTTTGCTCTCACTAACTGTGTTGGGCTGTGGCTCTTCGCCTACA
AG
Found at i:31155602 original size:69 final size:69
Alignment explanation
Indices: 31155474--31155635 Score: 243
Period size: 69 Copynumber: 2.3 Consensus size: 69
31155464 CTGCGGCTCC
* * * * * *
31155474 TCGCCTACTAGCCTTAATATGACAGCTGGGAGCTTTGCTCTCACTAACTGTGTTGGAGATTATAG
1 TCGCCTACAAGCCTTAATATGACAACTAGGAGCTTTGCTCTCACTAACAGTGTTAGAGATTACAG
31155539 ATTT
66 ATTT
*
31155543 TCGCCTACAAGCCTTAATATGACAACTAGGAGCTTTGCTCTCACTAACAGTGTTAGAGATTACGG
1 TCGCCTACAAGCCTTAATATGACAACTAGGAGCTTTGCTCTCACTAACAGTGTTAGAGATTACAG
31155608 ATTT
66 ATTT
* *
31155612 TCACCTACGAGCCTTAATATGACA
1 TCGCCTACAAGCCTTAATATGACA
31155636 CGAATGTTGT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 84 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (69 bp):
TCGCCTACAAGCCTTAATATGACAACTAGGAGCTTTGCTCTCACTAACAGTGTTAGAGATTACAG
ATTT
Found at i:31164127 original size:68 final size:69
Alignment explanation
Indices: 31163979--31164146 Score: 207
Period size: 68 Copynumber: 2.4 Consensus size: 69
31163969 ATGATTCTGC
* * * * * *
31163979 GCCCAGCACTAGTTAGACAAGCTGACAAAA-GTTGCGCCCAGTGCTAATCGAATGAACTGACAAT
1 GCCCAGCACTAGTCAGACAAGCTGA-AAAAGGCTGCGCCCAATGCTAATAGAATGAACTCAAAAT
31164043 TGTGT
65 TGTGT
* *
31164048 GCCCAGCACTAGTCAGACAAGCTGAAAAAGGCTGCGTCCAATGCTAATTAGATTG-AC-CAAAAT
1 GCCCAGCACTAGTCAGACAAGCTGAAAAAGGCTGCGCCCAATGCTAA-TAGAATGAACTCAAAAT
*
31164111 TGTTT
65 TGTGT
*
31164116 GCCCAACACTAGTCAGACAAGCTGAAAAAGG
1 GCCCAGCACTAGTCAGACAAGCTGAAAAAGG
31164147 TTGTGTAACA
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
68 42 0.48
69 40 0.46
70 5 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (69 bp):
GCCCAGCACTAGTCAGACAAGCTGAAAAAGGCTGCGCCCAATGCTAATAGAATGAACTCAAAATT
GTGT
Found at i:31167369 original size:48 final size:48
Alignment explanation
Indices: 31167298--31167511 Score: 200
Period size: 48 Copynumber: 4.5 Consensus size: 48
31167288 AAGCTGACGC
* * * **
31167298 CATGTCCTAGCCAGGTCTTACACTAGCTTGTATATCACGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCACGAGGCCGATG
* * ** * * ** * *
31167346 CATGTCCTAGACATATCTTACACTAGCTCT-CGTCTTA--ATACTGATC
1 CATGTCCCAGACATGTCTTACACTAGCT-TAAATATCACGAGGCCGATG
* * * *
31167392 CACGTCCCAGACATGTCTTACATTGGCTTAAATATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCACGAGGCCGATG
* * *
31167440 CATGTCCCAGGCATGTCTTACACTAGCTTAAATATCTCGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTAAATATCACGAGGCCGATG
31167488 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
31167512 GTCTCTCATG
Statistics
Matches: 131, Mismatches: 31, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
45 1 0.01
46 30 0.23
48 99 0.76
49 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTAAATATCACGAGGCCGATG
Found at i:31167554 original size:142 final size:141
Alignment explanation
Indices: 31167298--31167555 Score: 322
Period size: 142 Copynumber: 1.8 Consensus size: 141
31167288 AAGCTGACGC
* ** *
31167298 CATGTCCTAGCCAGGTCTTACACTAGCTTGTATATCACGAGGCCGATGCATGTCCTAGACATATC
1 CATGTCCCAGCCAGGTCTTACACTAGCTTAAATATCACGAGGCCGATGCATGTCCCAGACATATC
* * *
31167363 TTACACTAGCTCTCGTCTTAATACTGATCCACGTCCCAGACATGTCTTACATTGGCTTAAATATC
66 TTACACTAGCTCTCATCTT-AGACTAATCCACGTCCCAGACATGTCTTACATTGGCTTAAATATC
31167428 TCGAGGCCGATG
130 TCGAGGCCGATG
* * * * *
31167440 CATGTCCCAGGCATGTCTTACACTAGCTTAAATATCTCGAGGCTGATGCATGTCCCAGACATGTC
1 CATGTCCCAGCCAGGTCTTACACTAGCTTAAATATCACGAGGCCGATGCATGTCCCAGACATATC
* * * *
31167505 TTACACT-GTCTCTCATGCTGT-GGCTAATGCATGTCTCAGACATGTCTTACA
66 TTACACTAG-CTCTCAT-CT-TAGACTAATCCACGTCCCAGACATGTCTTACA
31167556 CTAGCACACA
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
141 1 0.01
142 93 0.96
143 2 0.02
144 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (141 bp):
CATGTCCCAGCCAGGTCTTACACTAGCTTAAATATCACGAGGCCGATGCATGTCCCAGACATATC
TTACACTAGCTCTCATCTTAGACTAATCCACGTCCCAGACATGTCTTACATTGGCTTAAATATCT
CGAGGCCGATG
Found at i:31176035 original size:24 final size:25
Alignment explanation
Indices: 31176000--31176047 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
31175990 TCTTGTTTTA
31176000 ATATTTATTTTA-ATATTTTTAAAT
1 ATATTTATTTTATATATTTTTAAAT
31176024 ATATTTGA-TTTATTATATTTTTAA
1 ATATTT-ATTTTA-TATATTTTTAA
31176048 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 10 0.48
25 1 0.05
26 10 0.48
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
ATATTTATTTTATATATTTTTAAAT
Found at i:31176047 original size:26 final size:24
Alignment explanation
Indices: 31176000--31176047 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
31175990 TCTTGTTTTA
31176000 ATATTTATTTTAATATTTTTAAAT
1 ATATTTATTTTAATATTTTTAAAT
*
31176024 ATATTTGATTTATTATATTTTTAA
1 ATATTT-ATTT-TAATATTTTTAA
31176048 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
ATATTTATTTTAATATTTTTAAAT
Found at i:31181505 original size:19 final size:20
Alignment explanation
Indices: 31181483--31181524 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
31181473 AAAAAAAAAG
*
31181483 AAATTATAAAAAT-TATTAT
1 AAATTACAAAAATATATTAT
31181502 AAATTACAAAAATATATTAT
1 AAATTACAAAAATATATTAT
31181522 AAA
1 AAA
31181525 AATTGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTACAAAAATATATTAT
Found at i:31182204 original size:19 final size:20
Alignment explanation
Indices: 31182174--31182218 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
31182164 TGTTTTATAA
31182174 TTTTTATGATTTTGT-AATAT
1 TTTTTATGATTTT-TAAATAT
31182194 TTTTTAT-ATTTTTAAATAT
1 TTTTTATGATTTTTAAATAT
31182213 TATTTT
1 T-TTTT
31182219 TCATAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.04
19 11 0.48
20 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTTATGATTTTTAAATAT
Found at i:31182258 original size:29 final size:31
Alignment explanation
Indices: 31182201--31182258 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
31182191 TATTTTTTAT
31182201 ATTTTTAAATATTATTTTTCATAACTTTAAC
1 ATTTTTAAATATTATTTTTCATAACTTTAAC
*
31182232 ATTTTTATATATT-TTTTTCATAA-TTTA
1 ATTTTTAAATATTATTTTTCATAACTTTA
31182259 TATAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 10 0.38
31 12 0.46
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (31 bp):
ATTTTTAAATATTATTTTTCATAACTTTAAC
Found at i:31182963 original size:18 final size:18
Alignment explanation
Indices: 31182936--31182985 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
31182926 ACAAGTTTAT
*
31182936 AAAACTATAAAACTT-AGG
1 AAAA-TATAAAAATTAAGG
*
31182954 AAAATAATAAAAATTAATG
1 AAAAT-ATAAAAATTAAGG
31182973 AAAATATAAAAAT
1 AAAATATAAAAAT
31182986 ATTATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 20 0.71
19 7 0.25
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (18 bp):
AAAATATAAAAATTAAGG
Found at i:31182995 original size:19 final size:19
Alignment explanation
Indices: 31182954--31182995 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
31182944 AAAACTTAGG
*
31182954 AAAATAATAAAAATTAATG
1 AAAATAATAAAAATTAATA
*
31182973 AAAAT-ATAAAAATATTATA
1 AAAATAATAAAAAT-TAATA
31182992 AAAA
1 AAAA
31182996 ATTTGAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATAATAAAAATTAATA
Found at i:31183021 original size:18 final size:19
Alignment explanation
Indices: 31182982--31183031 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
31182972 GAAAATATAA
*
31182982 AAATATTATAAAAAATTTG
1 AAATATTATAAAAAATTGG
31183001 AAATA-TATAAAAACA-TGG
1 AAATATTATAAAAA-ATTGG
*
31183019 AAAAATTATAAAA
1 AAATATTATAAAA
31183032 TATTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (19 bp):
AAATATTATAAAAAATTGG
Found at i:31183937 original size:13 final size:13
Alignment explanation
Indices: 31183885--31183937 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
31183875 TTTAAACCAA
31183885 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
31183898 CCTTCTT-AAAAGC
1 ACTT-TTCAAAAGC
*
31183911 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
31183924 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
31183937 A
1 A
31183938 TTGCCAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 5 0.16
13 23 0.72
14 4 0.12
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:31184758 original size:134 final size:134
Alignment explanation
Indices: 31184509--31184768 Score: 313
Period size: 134 Copynumber: 1.9 Consensus size: 134
31184499 GGAACTAAAA
* * * * *
31184509 CTATCGATACCAAAAGAAATTTATCGATATCAAACAAAAGGTATCGATACTATATCGATACTTAA
1 CTATCGATACCAAAAGAAATTTATCAATACCAAACAAAACGTATCGATACCATATCGAAACTTAA
* ** ** * * *
31184574 TAAATCTTTTGGAAGTCAGAATGCCAATTTGGTATCGATATTAAAGAAGGTATCGATAAATGTGT
66 TAAATATTTTAAAAAACAGAATGCCAATTTGGTATCGATATCAAAAAAGGTATCAATAAATGTGT
31184639 ACTT
131 ACTT
** * * * * **
31184643 CTATCGATACTTAAATAATTTTATCAATACCAAGCAAAACGTATCGATACCATATTGAAACTTGG
1 CTATCGATACCAAAAGAAATTTATCAATACCAAACAAAACGTATCGATACCATATCGAAACTTAA
* *
31184708 TAAATATTTTAAAAAACAGAATGCCATTTTTGTATCGATATCAAAAAAGGTATCAATAAAT
66 TAAATATTTTAAAAAACAGAATGCCAATTTGGTATCGATATCAAAAAAGGTATCAATAAAT
31184769 TTGTGAATAT
Statistics
Matches: 103, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
134 103 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.32
Consensus pattern (134 bp):
CTATCGATACCAAAAGAAATTTATCAATACCAAACAAAACGTATCGATACCATATCGAAACTTAA
TAAATATTTTAAAAAACAGAATGCCAATTTGGTATCGATATCAAAAAAGGTATCAATAAATGTGT
ACTT
Found at i:31184834 original size:134 final size:134
Alignment explanation
Indices: 31184510--31184806 Score: 301
Period size: 134 Copynumber: 2.2 Consensus size: 134
31184500 GAACTAAAAC
* * * * * * * * * **
31184510 TATCGATAC-CAAAAGAAATTTATCGATATCAAACAAAAGGTATCGATACTATATCGATACTTAA
1 TATCGATACTC-AAATAAATTTATCAATACCAAGCAAAACGTATCGATACCAGATTGAAACTTGG
* ** ** * * *
31184574 TAAATCTTTTGGAAGTCAGAATGCCAATTTGGTATCGATATTAAAGAAGGTATCGATAAATGTGT
65 TAAATATTTTAAAAAACAGAATGCCAATTTGGTATCGATATCAAAAAAGGTATCAATAAATGTGT
* *
31184639 ACTTC
130 ACATA
* * *
31184644 TATCGATACTTAAATAATTTTATCAATACCAAGCAAAACGTATCGATACCATATTGAAACTTGGT
1 TATCGATACTCAAATAAATTTATCAATACCAAGCAAAACGTATCGATACCAGATTGAAACTTGGT
* * *
31184709 AAATATTTTAAAAAACAGAATGCCATTTTTGTATCGATATCAAAAAAGGTATCAATAAATTTGTG
66 AAATATTTTAAAAAACAGAATGCCAATTTGGTATCGATATCAAAAAAGGTATCAATAAATGTGT-
31184774 A-ATA
130 ACATA
**
31184778 TATCGATACTCATTTAAATTTATCAATAC
1 TATCGATACTCAAATAAATTTATCAATAC
31184807 TTGACAAGAA
Statistics
Matches: 132, Mismatches: 29, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
134 131 0.99
135 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (134 bp):
TATCGATACTCAAATAAATTTATCAATACCAAGCAAAACGTATCGATACCAGATTGAAACTTGGT
AAATATTTTAAAAAACAGAATGCCAATTTGGTATCGATATCAAAAAAGGTATCAATAAATGTGTA
CATA
Found at i:31187083 original size:19 final size:20
Alignment explanation
Indices: 31187054--31187098 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
31187044 GGTATCGACA
31187054 ATTTTTCAT-AAGTATCAAT
1 ATTTTTCATAAAGTATCAAT
*
31187073 ACTTTTT-ATAAAGTATCTAT
1 A-TTTTTCATAAAGTATCAAT
31187093 ATTTTT
1 ATTTTT
31187099 GTATCAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.53
Consensus pattern (20 bp):
ATTTTTCATAAAGTATCAAT
Found at i:31187148 original size:21 final size:21
Alignment explanation
Indices: 31187119--31187163 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
31187109 CGATACCAAA
31187119 TGCCCATTCTATTTTGCTAAG
1 TGCCCATTCTATTTTGCTAAG
* *
31187140 TGCCTATTCTGTTTTGCTAAG
1 TGCCCATTCTATTTTGCTAAG
31187161 TGC
1 TGC
31187164 AAATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (21 bp):
TGCCCATTCTATTTTGCTAAG
Found at i:31196797 original size:35 final size:35
Alignment explanation
Indices: 31196719--31196800 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
31196709 CAAACATCAA
* *
31196719 ACAAATACAAAT-TAGGGCCTAAGCCTATTATAGAT
1 ACAAATACAGATAT-GGGCCTAAGCCTATTACAGAT
*
31196754 GCAAATACAGATATGGGCCTAAGCCTATCT-CAGAT
1 ACAAATACAGATATGGGCCTAAGCCTAT-TACAGAT
*
31196789 ACAGATACAGAT
1 ACAAATACAGAT
31196801 GTGCAATTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 38 0.95
36 2 0.05
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (35 bp):
ACAAATACAGATATGGGCCTAAGCCTATTACAGAT
Found at i:31202316 original size:48 final size:47
Alignment explanation
Indices: 31202134--31202358 Score: 191
Period size: 48 Copynumber: 4.8 Consensus size: 47
31202124 CATAGGGTAT
* * *
31202134 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTTACATATC
1 AATGCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCAT-C-TCTC
* * *
31202184 CATGCCGATG-CATGTCCTAGACATGTCTTACACTAGCACATCTCGT-
1 AATGCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCATCTC-TC
* * *
31202230 -A-GCTGAT-ACATGTCCCAGACATGTCTTACACTATCTC-TCGTCTC
1 AATGCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCATC-TCTC
* *
31202274 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TC-AT-
1 AATGCCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCATCTCTC
*
31202319 AATGTGGCCGATG-CATGTCCAAGACATGTCTTACACTAGC
1 AA--T-GCCGATGCCATGTCCCAGACATGTCTTACACTAGC
31202359 ACACACACAT
Statistics
Matches: 147, Mismatches: 17, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
43 3 0.02
44 33 0.22
45 4 0.03
46 19 0.13
47 30 0.20
48 36 0.24
49 13 0.09
50 9 0.06
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (47 bp):
AATGCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCATCTCTC
Found at i:31202352 original size:94 final size:92
Alignment explanation
Indices: 31202137--31202358 Score: 243
Period size: 94 Copynumber: 2.4 Consensus size: 92
31202127 AGGGTATAAT
* * *
31202137 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTTACATATCCATGCCGATGCATGTCCT
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTTACATATCAATGCCGATGCATGTCCC
31202202 AGACATGTCTTACACTAGCACATCTCGTA
64 AGACATGTCTTACACTAGCACATCTCGTA
* * * * *
31202231 GCTGATACATGTCCCAGACATGTCTTACACTATCTC-T-CGTCTCAATGCCGATGCCATGTCCCA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTTACATATCAATGCCGATG-CATGTCCCA
* * * *
31202294 GACATGGTCTTACACTGGCTC-TCATAATGTG
65 GACAT-GTCTTACACTAGCACATC-T--CGTA
*
31202325 GCCGATGCATGTCCAAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
31202359 ACACACACAT
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
90 13 0.12
91 16 0.15
92 27 0.25
93 14 0.13
94 37 0.35
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.28
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTTACATATCAATGCCGATGCATGTCCCAG
ACATGTCTTACACTAGCACATCTCGTA
Found at i:31213568 original size:40 final size:40
Alignment explanation
Indices: 31213492--31213568 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
31213482 ACACACTATG
* * *
31213492 TGGGGATAAAATCGACCCACCCAGCCCTAGACACCAAGTA
1 TGGGGATAAAATCAACCCACCCAACCCTACACACCAAGTA
* *
31213532 TGGGGATAAAATCAACCCATCCAACCCTACATACCAA
1 TGGGGATAAAATCAACCCACCCAACCCTACACACCAA
31213569 ATGGTACCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.38, C:0.32, G:0.16, T:0.14
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCACCCAACCCTACACACCAAGTA
Found at i:31216092 original size:24 final size:25
Alignment explanation
Indices: 31216058--31216154 Score: 80
Period size: 24 Copynumber: 4.1 Consensus size: 25
31216048 TCCGGGCTAT
31216058 ATAA-CGGGAAGCTCA-TAAGAGCC
1 ATAATCGGGAAGCTCACTAAGAGCC
* * * * *
31216081 ATAATCAGGAAGTTCACAAAGAACT
1 ATAATCGGGAAGCTCACTAAGAGCC
* *
31216106 TTAATCGGGAAG-TCACGAAGAGCC
1 ATAATCGGGAAGCTCACTAAGAGCC
31216130 -T-ATCGGGAAGCTCA-TCAAGAGCC
1 ATAATCGGGAAGCTCACT-AAGAGCC
31216153 AT
1 AT
31216155 GTAACAAGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
22 9 0.16
23 15 0.26
24 19 0.33
25 15 0.26
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.18
Consensus pattern (25 bp):
ATAATCGGGAAGCTCACTAAGAGCC
Found at i:31216137 original size:22 final size:23
Alignment explanation
Indices: 31216109--31216152 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31216099 AAGAACTTTA
31216109 ATCGGGAAG-TCA-CGAAGAGCCT
1 ATCGGGAAGCTCATC-AAGAGCCT
31216131 ATCGGGAAGCTCATCAAGAGCC
1 ATCGGGAAGCTCATCAAGAGCC
31216153 ATGTAACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 10 0.50
24 1 0.05
ACGTcount: A:0.32, C:0.25, G:0.30, T:0.14
Consensus pattern (23 bp):
ATCGGGAAGCTCATCAAGAGCCT
Found at i:31222399 original size:174 final size:174
Alignment explanation
Indices: 31222094--31222419 Score: 483
Period size: 174 Copynumber: 1.9 Consensus size: 174
31222084 CTTCCCCTTG
** *
31222094 GTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATCTTCTTCCTCTATTGGACTTCAGGAATCT
1 GTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATCTTCTTCCTCTATTAAACGTCAGGAATCT
* ** *
31222159 CTTCAACCTCCTAATAAACATGGTCATCTCTTTGTTTTCATCCACCTCTTCGCTTGATTAACTAT
66 CTTCAACCTCCTAACAAACATGAACATCTCTTTGTTTTCATCCACATCTTCGCTTGATTAACTAT
31222224 CTTCATTTGTGGTAGATTTAAGCTTTAACCCCTCATTCTTCTTA
131 CTTCATTTGTGGTAGATTTAAGCTTTAACCCCTCATTCTTCTTA
* * *
31222268 GTAGATTCAAGCTTTAACCCCTCCTTCTTTTGGAATCTTCTTCCTCTATTAAAGGTCATGAATCT
1 GTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATCTTCTTCCTCTATTAAACGTCAGGAATCT
* * * * * *
31222333 CTTGAATCTCCTAGCAAACATGAACATCTCTTT-TTCTTCATCCACATCTTTGGTTGATTCACTA
66 CTTCAACCTCCTAACAAACATGAACATCTCTTTGTT-TTCATCCACATCTTCGCTTGATTAACTA
*
31222397 TCTTCATTTGTGGTGGATTTAAG
130 TCTTCATTTGTGGTAGATTTAAG
31222420 AGCAACTCCA
Statistics
Matches: 134, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
173 2 0.01
174 132 0.99
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (174 bp):
GTAGATTCAAGCTTTAACCCCTCATTCTTTTGGAATCTTCTTCCTCTATTAAACGTCAGGAATCT
CTTCAACCTCCTAACAAACATGAACATCTCTTTGTTTTCATCCACATCTTCGCTTGATTAACTAT
CTTCATTTGTGGTAGATTTAAGCTTTAACCCCTCATTCTTCTTA
Found at i:31224647 original size:12 final size:12
Alignment explanation
Indices: 31224630--31224674 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
31224620 TTCATTATTG
31224630 TTTCATGCACAT
1 TTTCATGCACAT
*
31224642 TTTCATATCACATT
1 TTTCAT-GCACA-T
31224656 GTTTCATGCACAT
1 -TTTCATGCACAT
31224669 TTTCAT
1 TTTCAT
31224675 ATCACATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 12 0.43
13 5 0.18
14 5 0.18
15 6 0.21
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Consensus pattern (12 bp):
TTTCATGCACAT
Found at i:31224655 original size:13 final size:13
Alignment explanation
Indices: 31224637--31224696 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
31224627 TTGTTTCATG
31224637 CACATTTTCATAT
1 CACATTTTCATAT
*
31224650 CACATTGTTTCAT-G
1 CACA-T-TTTCATAT
31224664 CACATTTTCATAT
1 CACATTTTCATAT
*
31224677 CACATTTGTCACAT
1 CACATTT-TCATAT
31224691 -ACATTT
1 CACATTT
31224697 CACTTTTTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 6 0.15
13 18 0.45
14 10 0.25
15 6 0.15
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.43
Consensus pattern (13 bp):
CACATTTTCATAT
Found at i:31224657 original size:27 final size:27
Alignment explanation
Indices: 31224626--31224682 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
31224616 ATGTTTCATT
31224626 ATTGTTTCATGCACATTTTCATATCAC
1 ATTGTTTCATGCACATTTTCATATCAC
31224653 ATTGTTTCATGCACATTTTCATATCAC
1 ATTGTTTCATGCACATTTTCATATCAC
31224680 ATT
1 ATT
31224683 TGTCACATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (27 bp):
ATTGTTTCATGCACATTTTCATATCAC
Found at i:31224669 original size:14 final size:14
Alignment explanation
Indices: 31224626--31224669 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
31224616 ATGTTTCATT
31224626 ATTGTTTCATGCAC
1 ATTGTTTCATGCAC
*
31224640 A-T-TTTCATATCAC
1 ATTGTTTCAT-GCAC
31224653 ATTGTTTCATGCAC
1 ATTGTTTCATGCAC
31224667 ATT
1 ATT
31224670 TTCATATCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 6 0.24
13 5 0.20
14 8 0.32
15 6 0.24
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.45
Consensus pattern (14 bp):
ATTGTTTCATGCAC
Found at i:31227578 original size:20 final size:20
Alignment explanation
Indices: 31227533--31227614 Score: 57
Period size: 19 Copynumber: 4.2 Consensus size: 20
31227523 AAAGCTTAGT
*
31227533 TTAACAAAAATTATAAAAAA
1 TTAATAAAAATTATAAAAAA
*
31227553 TT-ATAAAAAGTTAT-AAAAC
1 TTAATAAAAA-TTATAAAAAA
* * *
31227572 TTAAT--AATTTATTAAATAG
1 TTAATAAAAATTA-TAAAAAA
31227591 TT-ATAAAAATTATAAAAATA
1 TTAATAAAAATTATAAAAA-A
31227611 TTAA
1 TTAA
31227615 AGAGTATATA
Statistics
Matches: 46, Mismatches: 8, Indels: 15
0.67 0.12 0.22
Matches are distributed among these distances:
17 3 0.07
18 5 0.11
19 22 0.48
20 15 0.33
21 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
TTAATAAAAATTATAAAAAA
Found at i:31227612 original size:28 final size:28
Alignment explanation
Indices: 31227538--31227627 Score: 85
Period size: 28 Copynumber: 3.1 Consensus size: 28
31227528 TTAGTTTAAC
31227538 AAAAATTATAAAAA-ATTATAAAAAGTTAT
1 AAAAATTATAAAAATA-T-TAAAAAGTTAT
* ** *
31227567 AAAACTTA-ATAATTTATTAAATAGTTAT
1 AAAAATTATA-AAAATATTAAAAAGTTAT
*
31227595 AAAAATTATAAAAATATTAAAGAGTATAT
1 AAAAATTATAAAAATATTAAAAAGT-TAT
31227624 AAAA
1 AAAA
31227628 TTGTATTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
28 30 0.61
29 18 0.37
30 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAAATTATAAAAATATTAAAAAGTTAT
Found at i:31227615 original size:9 final size:9
Alignment explanation
Indices: 31227538--31227609 Score: 65
Period size: 10 Copynumber: 7.7 Consensus size: 9
31227528 TTAGTTTAAC
31227538 AAAAATTAT
1 AAAAATTAT
31227547 AAAAAATTAT
1 -AAAAATTAT
31227557 AAAAAGTTAT
1 AAAAA-TTAT
*
31227567 AAAACTTA-
1 AAAAATTAT
* *
31227575 ATAATTTATT
1 AAAAATTA-T
*
31227585 AAATAGTTAT
1 AAA-AATTAT
31227595 AAAAATTAT
1 AAAAATTAT
31227604 AAAAAT
1 AAAAAT
31227610 ATTAAAGAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
8 6 0.12
9 19 0.37
10 23 0.44
11 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:31231138 original size:81 final size:81
Alignment explanation
Indices: 31231039--31231204 Score: 314
Period size: 81 Copynumber: 2.0 Consensus size: 81
31231029 ATAAATACAA
*
31231039 TCTTAGGGGTTTGATGTAACTAAGTCATCTTAGACGCATCCAAAAACCTTTGTAGTTTAGGAGTA
1 TCTTAGGGGTTTGATGTAACTAAGTCATCTTAGACGCATCCAAAAACCCTTGTAGTTTAGGAGTA
31231104 GGATTAGATTAAGTTT
66 GGATTAGATTAAGTTT
*
31231120 TCTTAGGGGTTTGATGTAACTAAGTCATCTTCGACGCATCCAAAAACCCTTGTAGTTTAGGAGTA
1 TCTTAGGGGTTTGATGTAACTAAGTCATCTTAGACGCATCCAAAAACCCTTGTAGTTTAGGAGTA
31231185 GGATTAGATTAAGTTT
66 GGATTAGATTAAGTTT
31231201 TCTT
1 TCTT
31231205 TTATTTTTCA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (81 bp):
TCTTAGGGGTTTGATGTAACTAAGTCATCTTAGACGCATCCAAAAACCCTTGTAGTTTAGGAGTA
GGATTAGATTAAGTTT
Found at i:31246214 original size:416 final size:416
Alignment explanation
Indices: 31245432--31246229 Score: 1192
Period size: 416 Copynumber: 1.9 Consensus size: 416
31245422 ATAGTACGCT
*
31245432 TGAGAAGGAAAAGGGTAAAGGGGCAAGTTCAAAAGAACTTAGTGAGTTCCATAGAGATCTTAAGC
1 TGAGAAGGAAAAGGGTAAAGAGGCAAGTTCAAAAGAACTTAGTGAGTTCCATAGAGATCTTAAGC
* * *
31245497 AGAATACTAAAAGCACAATCCAATCTTTCAAAAGAATTACTCAACACGAAAGAGTATGCCTAATG
66 AGAATACTAAAAGCACAATCCAATCTTTCAAAAGAATCACTCAACACGAAAGAGTACGCCCAATG
* * *
31245562 ACGTATACAAAACTCAGACAGACTCAGTACGCCAATGGCATGTCACATAGGTGAATACTATATGC
131 AAGTATACAAAACTCAGACAGACTCAGTACGCCAATGGCATGTCACATAGGGGAATACTATACGC
* * * *
31245627 CAAGACAACATAACTCAGACATTCCATTTTCATGCTAGCCACATACTTAAAGTTCAGAGTCAGAT
196 CAAGACAACATAACTCAGACATTCCATTTTCATGCCAACCACATACCTAAAGTTCAGAGTCAAAT
* * *
31245692 TCATATAAGATGTTTTCGTTTCATTCATATACATTCTCTCCTTATAGCTCCTCATTTAGAATCAT
261 TCATATAAGATGTTTTCGTTTAATTCATATACATTCTCTCCTTATAGCTCCTAATTTAGAATCAC
*
31245757 TCAGTAACATGTTTAATTATGTTATACCAATTCAGTTTGTAATATATATTTTCCCTAGCAGATAT
326 TCAGTAACATGTTTAATTATGTTATACCAATTCAGTTTGTAATATATATTTACCCTAGCAGATAT
31245822 CCTCTGGCATAGTCCTTTAGAAAGCC
391 CCTCTGGCATAGTCCTTTAGAAAGCC
* *
31245848 TGAGAAGGAAGAGGGTAACA-AGGTAAGTTCAAAAGAA-TTAAGTGAGTTCCATAGAGATCTTAA
1 TGAGAAGGAAAAGGGTAA-AGAGGCAAGTTCAAAAGAACTT-AGTGAGTTCCATAGAGATCTTAA
* * *
31245911 GTAGAATACTAAAAGC-CAAATCTAATCTTTCAAAAGAATCACTCAACATGACAA-AGTACGCCC
64 GCAGAATACTAAAAGCAC-AATCCAATCTTTCAAAAGAATCACTCAACACGA-AAGAGTACGCCC
* * * * * *
31245974 AATGAAGTATACAAAACTTATACAGACTTAGTACGCCAATGGCATGTTATATGGGGGAATACTAT
127 AATGAAGTATACAAAACTCAGACAGACTCAGTACGCCAATGGCATGTCACATAGGGGAATACTAT
* * *
31246039 ACGCCAATACAACATAACTCAGACATTCCATTTTCATGCCAACCACATACCTAGAGTTCATAGTC
192 ACGCCAAGACAACATAACTCAGACATTCCATTTTCATGCCAACCACATACCTAAAGTTCAGAGTC
* * *
31246104 AAATTCATATAAGATGTTTTTGTTTAATTCATATACATTCTCTCCTTATATCTCTTAATTTAGAA
257 AAATTCATATAAGATGTTTTCGTTTAATTCATATACATTCTCTCCTTATAGCTCCTAATTTAGAA
* * **
31246169 TCACTCAGTAGCATGTTTAATTGTGTTATGTCAATTC-GATTTGTAATATATATTTACCCTA
322 TCACTCAGTAACATGTTTAATTATGTTATACCAATTCAG-TTTGTAATATATATTTACCCTA
31246230 CTAGAGGCTA
Statistics
Matches: 341, Mismatches: 36, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
415 4 0.01
416 334 0.98
417 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (416 bp):
TGAGAAGGAAAAGGGTAAAGAGGCAAGTTCAAAAGAACTTAGTGAGTTCCATAGAGATCTTAAGC
AGAATACTAAAAGCACAATCCAATCTTTCAAAAGAATCACTCAACACGAAAGAGTACGCCCAATG
AAGTATACAAAACTCAGACAGACTCAGTACGCCAATGGCATGTCACATAGGGGAATACTATACGC
CAAGACAACATAACTCAGACATTCCATTTTCATGCCAACCACATACCTAAAGTTCAGAGTCAAAT
TCATATAAGATGTTTTCGTTTAATTCATATACATTCTCTCCTTATAGCTCCTAATTTAGAATCAC
TCAGTAACATGTTTAATTATGTTATACCAATTCAGTTTGTAATATATATTTACCCTAGCAGATAT
CCTCTGGCATAGTCCTTTAGAAAGCC
Found at i:31255137 original size:10 final size:10
Alignment explanation
Indices: 31255124--31255158 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
31255114 TCCCTTTTGC
*
31255124 AAATCAATCA
1 AAATTAATCA
31255134 AAATTAATCA
1 AAATTAATCA
*
31255144 AAATTAATAA
1 AAATTAATCA
31255154 AAATT
1 AAATT
31255159 TGATAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATTAATCA
Found at i:31256597 original size:25 final size:25
Alignment explanation
Indices: 31256568--31256637 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
31256558 ACAACCCAAC
31256568 CAGAACAG-GACAGAGCAGAACATAA
1 CAGAACAGAG-CAGAGCAGAACATAA
* * *
31256593 CAGAACATAGTAGAGCAGAGCATAA
1 CAGAACAGAGCAGAGCAGAACATAA
*
31256618 CAAAACAGAGCAGAGCAGAA
1 CAGAACAGAGCAGAGCAGAA
31256638 TAGAATAGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
25 36 0.97
26 1 0.03
ACGTcount: A:0.51, C:0.19, G:0.24, T:0.06
Consensus pattern (25 bp):
CAGAACAGAGCAGAGCAGAACATAA
Found at i:31256706 original size:15 final size:15
Alignment explanation
Indices: 31256661--31256709 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
31256651 AACATAACAT
*
31256661 AACATAGCAAAATAG
1 AACAGAGCAAAATAG
*
31256676 AATAGAG-AAGAATAG
1 AACAGAGCAA-AATAG
*
31256691 AACAGAGCAAAGTAG
1 AACAGAGCAAAATAG
31256706 AACA
1 AACA
31256710 TAATAGAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 24 0.86
16 2 0.07
ACGTcount: A:0.59, C:0.10, G:0.20, T:0.10
Consensus pattern (15 bp):
AACAGAGCAAAATAG
Found at i:31256796 original size:31 final size:30
Alignment explanation
Indices: 31256755--31256820 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
31256745 GTGCAGAATG
* * *
31256755 GAACATAATAGAACAAAGCAAAAGCATAACA
1 GAACAGAATAGAACAAAACAAAA-CAAAACA
* *
31256786 GAACAGAATAGAGCAAAACATAACAAAACA
1 GAACAGAATAGAACAAAACAAAACAAAACA
31256816 GAACA
1 GAACA
31256821 ATGCATAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.62, C:0.17, G:0.14, T:0.08
Consensus pattern (30 bp):
GAACAGAATAGAACAAAACAAAACAAAACA
Found at i:31260812 original size:21 final size:20
Alignment explanation
Indices: 31260786--31260825 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
31260776 AAAAATATGG
31260786 ATAAAAACTTAGAAATAAAAA
1 ATAAAAACTTA-AAATAAAAA
*
31260807 ATAAAAACTTAAAGTAAAA
1 ATAAAAACTTAAAATAAAA
31260826 CCTACCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (20 bp):
ATAAAAACTTAAAATAAAAA
Found at i:31262554 original size:20 final size:20
Alignment explanation
Indices: 31262526--31262573 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
31262516 TTTATCTATA
31262526 TTTATATTATTTTATAAAGTT
1 TTTA-ATTATTTTATAAAGTT
31262547 TTTAATTATTTTATAAAGTT
1 TTTAATTATTTTATAAAGTT
*
31262567 GTTAATT
1 TTTAATT
31262574 CAATTGGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
TTTAATTATTTTATAAAGTT
Found at i:31300081 original size:21 final size:22
Alignment explanation
Indices: 31300041--31300092 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
31300031 CAGGGCTCAC
*
31300041 ACGCCCATGTGGACCATGGGATA
1 ACGCCCGTGTGGACCATGGGA-A
*
31300064 A-GCCCGTGT-GACCCTGGGAA
1 ACGCCCGTGTGGACCATGGGAA
31300084 ACGCCCGTG
1 ACGCCCGTG
31300093 CTACAGGTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 2 0.08
21 16 0.62
22 7 0.27
23 1 0.04
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.15
Consensus pattern (22 bp):
ACGCCCGTGTGGACCATGGGAA
Found at i:31301663 original size:50 final size:48
Alignment explanation
Indices: 31301524--31301663 Score: 172
Period size: 48 Copynumber: 2.9 Consensus size: 48
31301514 AGACATGTCT
* ***
31301524 ATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGTATCGGCATTGAG
1 ATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGTATCGGCACAAAG
* * * * *
31301572 ACGAGAGCTAGTGTAAGACCATGCCTGGGACATGGCATCGGCACAAAT
1 ATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGTATCGGCACAAAG
*
31301620 ATGTGAGAGCTAGTGTAAGACCATGTCTAGGACATGGTGTCGGC
1 A--TGAGAGCTAGTGTAAGACCATGTCTAGGACATGGTATCGGC
31301664 CTCGATTTCA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
48 40 0.53
50 36 0.47
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (48 bp):
ATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGTATCGGCACAAAG
Found at i:31314473 original size:22 final size:23
Alignment explanation
Indices: 31314447--31314493 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
31314437 CACCTCATAA
*
31314447 AATTGACTAGAT-TTT-GAATTAT
1 AATTGA-TAGATGTTTACAATTAT
31314469 AATTGATAGATGTTTACAATTAT
1 AATTGATAGATGTTTACAATTAT
31314492 AA
1 AA
31314494 ATTTATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 9 0.41
23 8 0.36
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (23 bp):
AATTGATAGATGTTTACAATTAT
Found at i:31316354 original size:18 final size:18
Alignment explanation
Indices: 31316331--31316367 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31316321 ACCCTTATGC
31316331 ATGCAAAATTACAATTTT
1 ATGCAAAATTACAATTTT
31316349 ATGCAAAATTACAATTTT
1 ATGCAAAATTACAATTTT
31316367 A
1 A
31316368 CCCCTAGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (18 bp):
ATGCAAAATTACAATTTT
Found at i:31316543 original size:27 final size:26
Alignment explanation
Indices: 31316499--31316549 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
31316489 CTCGCTGCAA
*
31316499 TCTGGTGGCCTCGCCACATATATCTAT
1 TCTGGTGACCTCGCCACA-ATATCTAT
* *
31316526 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
31316550 GGCAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTAT
Found at i:31316616 original size:33 final size:32
Alignment explanation
Indices: 31316566--31316629 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 32
31316556 CTCGCTGCAA
*
31316566 TCTGGTGGCTTCACCACATATATATATATCTGT
1 TCTGGTGGCCTCACCACA-ATATATATATCTGT
* *
31316599 TCTGGTGGCCT-AGCCACAATATCTGTATCTG
1 TCTGGTGGCCTCA-CCACAATATATATATCTG
31316630 GTGACTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (32 bp):
TCTGGTGGCCTCACCACAATATATATATCTGT
Found at i:31316643 original size:27 final size:27
Alignment explanation
Indices: 31316613--31316677 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
31316603 GTGGCCTAGC
31316613 CACAATATCTGTATCTGGTGACTTCAT
1 CACAATATCTGTATCTGGTGACTTCAT
*
31316640 CACAATATCTGTATCTGGTGACTTCGT
1 CACAATATCTGTATCTGGTGACTTCAT
31316667 CACAATATCTG
1 CACAATATCTG
31316678 GCAGCCTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (27 bp):
CACAATATCTGTATCTGGTGACTTCAT
Found at i:31323774 original size:18 final size:18
Alignment explanation
Indices: 31323751--31323786 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
31323741 AGTTAGATCG
31323751 AGGAAAAGAAAAAGTATC
1 AGGAAAAGAAAAAGTATC
31323769 AGGAAAAGAAAAAGTATC
1 AGGAAAAGAAAAAGTATC
31323787 GGATTAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.22, T:0.11
Consensus pattern (18 bp):
AGGAAAAGAAAAAGTATC
Found at i:31324237 original size:25 final size:24
Alignment explanation
Indices: 31324195--31324247 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
31324185 CACAAACGTA
*
31324195 GCTCTTTATAAGCGTCCTGCTATAG
1 GCTCTTTATAAGCGTCCTGATAT-G
* * *
31324220 GCTCTTTGTGAGCTTCCTGATATG
1 GCTCTTTATAAGCGTCCTGATATG
31324244 GCTC
1 GCTC
31324248 ACTTGAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.38
Consensus pattern (24 bp):
GCTCTTTATAAGCGTCCTGATATG
Found at i:31330515 original size:38 final size:38
Alignment explanation
Indices: 31330459--31330534 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
31330449 CTTACAGTGA
*
31330459 AAAATCGATCAAAATTCTTGCACGGGAAACGAAAGAGT
1 AAAACCGATCAAAATTCTTGCACGGGAAACGAAAGAGT
31330497 AAAACCGATCAAAATTCTTGCACGGGAAACGAAAGAGT
1 AAAACCGATCAAAATTCTTGCACGGGAAACGAAAGAGT
31330535 TAAGAAACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (38 bp):
AAAACCGATCAAAATTCTTGCACGGGAAACGAAAGAGT
Found at i:31347793 original size:12 final size:13
Alignment explanation
Indices: 31347771--31347797 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31347761 AAGATGATGA
31347771 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
31347784 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
31347797 T
1 T
31347798 ATAATTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:31350920 original size:61 final size:60
Alignment explanation
Indices: 31350800--31350933 Score: 137
Period size: 61 Copynumber: 2.2 Consensus size: 60
31350790 AAAGAAATTG
* * * * * *
31350800 AAAAATTATGATTTTTCATTGAAATTTTTAGAAAATTTTAATTAAGTGTTCAACTTTTTT
1 AAAAATTATTATTTTTCATTGAAATTTTTAAAAAATTTGAATTAACTCTTCAACATTTTT
* * *
31350860 GTAAAATT-TTATTTTTCTCTTGAAGTTTTTAAAAAATTTGAATTAAACTCTTCAA-ATTTTT
1 -AAAAATTATTATTTTTC-ATTGAAATTTTTAAAAAATTTGAATT-AACTCTTCAACATTTTT
*
31350921 AAAAATTCTTATT
1 AAAAATTATTATT
31350934 ATACCTTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
60 14 0.23
61 38 0.63
62 8 0.13
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (60 bp):
AAAAATTATTATTTTTCATTGAAATTTTTAAAAAATTTGAATTAACTCTTCAACATTTTT
Found at i:31364458 original size:41 final size:40
Alignment explanation
Indices: 31364387--31364539 Score: 164
Period size: 41 Copynumber: 3.8 Consensus size: 40
31364377 AAATAGGGCT
** *
31364387 TTAGCGGCG-TTTTGACAAAAACGCCGCTAAAAACTGAGCA
1 TTAGCGGCGTTTTTG-GTAAAACGCCGCTAAAAACAGAGCA
* * *
31364427 ATAGCGGCGTTTTTTGTTAAAACGCCACTAAAAACAGAGCA
1 TTAGCGGCG-TTTTTGGTAAAACGCCGCTAAAAACAGAGCA
* * *
31364468 TTAGCGGCGCTTTTGGTGAAACGCCGCTAAAGACCAGAGCA
1 TTAGCGGCGTTTTTGGTAAAACGCCGCTAAA-AACAGAGCA
* * *
31364509 TTAGCGGCGCTTTTGGTGAAATGCCGCTAAA
1 TTAGCGGCGTTTTTGGTAAAACGCCGCTAAA
31364540 GATACCAACT
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
40 26 0.27
41 67 0.68
42 5 0.05
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.23
Consensus pattern (40 bp):
TTAGCGGCGTTTTTGGTAAAACGCCGCTAAAAACAGAGCA
Found at i:31364541 original size:41 final size:40
Alignment explanation
Indices: 31364405--31364539 Score: 180
Period size: 41 Copynumber: 3.3 Consensus size: 40
31364395 GTTTTGACAA
* * * * *
31364405 AAACGCCGCTAAAAACTGAGCAATAGCGGCGTTTTTTGTTA
1 AAACGCCGCTAAAAACAGAGCATTAGCGGCG-CTTTTGGTG
*
31364446 AAACGCCACTAAAAACAGAGCATTAGCGGCGCTTTTGGTG
1 AAACGCCGCTAAAAACAGAGCATTAGCGGCGCTTTTGGTG
*
31364486 AAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGTG
1 AAACGCCGCTAAA-AACAGAGCATTAGCGGCGCTTTTGGTG
*
31364527 AAATGCCGCTAAA
1 AAACGCCGCTAAA
31364540 GATACCAACT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
40 18 0.21
41 66 0.79
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.21
Consensus pattern (40 bp):
AAACGCCGCTAAAAACAGAGCATTAGCGGCGCTTTTGGTG
Found at i:31364639 original size:14 final size:15
Alignment explanation
Indices: 31364620--31364693 Score: 75
Period size: 14 Copynumber: 5.2 Consensus size: 15
31364610 TTTAAAGGTA
31364620 GTTTAAGGGTT-GGG
1 GTTTAAGGGTTAGGG
*
31364634 GTTTAAGGTTTAGGG
1 GTTTAAGGGTTAGGG
*
31364649 G-TTAGGGGTTAGGG
1 GTTTAAGGGTTAGGG
*
31364663 G-TTAGGGGTTAGGG
1 GTTTAAGGGTTAGGG
* *
31364677 G-TTAGGGGTTATGG
1 GTTTAAGGGTTAGGG
31364691 GTT
1 GTT
31364694 ATGGGTTTAG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
14 49 0.91
15 5 0.09
ACGTcount: A:0.15, C:0.00, G:0.50, T:0.35
Consensus pattern (15 bp):
GTTTAAGGGTTAGGG
Found at i:31364706 original size:7 final size:7
Alignment explanation
Indices: 31364632--31364774 Score: 108
Period size: 7 Copynumber: 20.1 Consensus size: 7
31364622 TTAAGGGTTG
31364632 GGGTTTA
1 GGGTTTA
*
31364639 AGGTTTA
1 GGGTTTA
*
31364646 GGGGTTA
1 GGGTTTA
*
31364653 GGGGTTA
1 GGGTTTA
*
31364660 GGGGTTA
1 GGGTTTA
*
31364667 GGGGTTA
1 GGGTTTA
*
31364674 GGGGTTA
1 GGGTTTA
*
31364681 GGGGTTA
1 GGGTTTA
31364688 TGGG-TTA
1 -GGGTTTA
31364695 TGGGTTTA
1 -GGGTTTA
*
31364703 GGGTTCA
1 GGGTTTA
*
31364710 GGGTTCA
1 GGGTTTA
*
31364717 GGGTTCA
1 GGGTTTA
31364724 GGGTTTA
1 GGGTTTA
* *
31364731 TGTTTTA
1 GGGTTTA
*
31364738 AGGTTTA
1 GGGTTTA
**
31364745 ATGTTTA
1 GGGTTTA
*
31364752 GGGATTA
1 GGGTTTA
31364759 GGAGTTTA
1 GG-GTTTA
31364767 GGGTTTA
1 GGGTTTA
31364774 G
1 G
31364775 ATTGGTTAAT
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
7 107 0.90
8 12 0.10
ACGTcount: A:0.17, C:0.02, G:0.43, T:0.38
Consensus pattern (7 bp):
GGGTTTA
Found at i:31365401 original size:16 final size:16
Alignment explanation
Indices: 31365380--31365411 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31365370 AAAAATTTTC
*
31365380 ATAAAAAATTTAAAAA
1 ATAAAAAACTTAAAAA
31365396 ATAAAAAACTTAAAAA
1 ATAAAAAACTTAAAAA
31365412 TTTAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAAAAACTTAAAAA
Found at i:31369184 original size:27 final size:28
Alignment explanation
Indices: 31369149--31369202 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
31369139 TATTTTGATA
31369149 ATGAATTTTAAAAT-TTTTATATTTTTC
1 ATGAATTTTAAAATATTTTATATTTTTC
* * *
31369176 ATGATTTTTATAATATTTTATTTTTTT
1 ATGAATTTTAAAATATTTTATATTTTT
31369203 AAATTTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (28 bp):
ATGAATTTTAAAATATTTTATATTTTTC
Found at i:31369208 original size:15 final size:16
Alignment explanation
Indices: 31369179--31369211 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31369169 ATTTTTCATG
31369179 ATTTTTATAATATTTT
1 ATTTTTATAATATTTT
*
31369195 ATTTTTTTAA-ATTTT
1 ATTTTTATAATATTTT
31369210 AT
1 AT
31369212 GACCTTTAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTATAATATTTT
Found at i:31369280 original size:43 final size:43
Alignment explanation
Indices: 31369215--31369353 Score: 174
Period size: 43 Copynumber: 3.3 Consensus size: 43
31369205 ATTTTATGAC
****
31369215 CTTTAGCGGCGTTTGCGGGAAAAGCGCCG-TGAAAAGTCTTGGA
1 CTTTAGCGGCGTTTTTTAGAAAAGCGCCGCT-AAAAGTCTTGGA
31369258 CTTTAGCGGCGTTTTTTAGAAAAGCGCCGCTAAAAGTCTTGGA
1 CTTTAGCGGCGTTTTTTAGAAAAGCGCCGCTAAAAGTCTTGGA
* * * * *
31369301 ATTTAGCGGC-ATTTTTAGAAAAGCGTCGCTAAAAGTCCTGGT
1 CTTTAGCGGCGTTTTTTAGAAAAGCGCCGCTAAAAGTCTTGGA
31369343 CTTTAGCGGCG
1 CTTTAGCGGCG
31369354 CTTAAAAATG
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
42 37 0.44
43 46 0.55
44 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTTAGAAAAGCGCCGCTAAAAGTCTTGGA
Found at i:31369331 original size:42 final size:43
Alignment explanation
Indices: 31369233--31369353 Score: 174
Period size: 42 Copynumber: 2.8 Consensus size: 43
31369223 GCGTTTGCGG
*
31369233 GAAAAGCGCCG-TGAAAAGTCTTGGACTTTAGCGGCGTTTTTTA
1 GAAAAGCGCCGCT-AAAAGTCTTGGACTTTAGCGGCGATTTTTA
*
31369276 GAAAAGCGCCGCTAAAAGTCTTGGAATTTAGCGGC-ATTTTTA
1 GAAAAGCGCCGCTAAAAGTCTTGGACTTTAGCGGCGATTTTTA
* * *
31369318 GAAAAGCGTCGCTAAAAGTCCTGGTCTTTAGCGGCG
1 GAAAAGCGCCGCTAAAAGTCTTGGACTTTAGCGGCG
31369354 CTTAAAAATG
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
42 37 0.53
43 32 0.46
44 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (43 bp):
GAAAAGCGCCGCTAAAAGTCTTGGACTTTAGCGGCGATTTTTA
Found at i:31372794 original size:161 final size:161
Alignment explanation
Indices: 31372536--31372856 Score: 579
Period size: 161 Copynumber: 2.0 Consensus size: 161
31372526 TAACCAAATA
31372536 ATATTTACATCAACCAACCACGATAAATTTAGTTACAAATCATCATTTTCATGCACACAACAACC
1 ATATTTACATCAACCAACCACGATAAATTTAGTTACAAATCATCATTTTCATGCACACAACAACC
* * *
31372601 AAACATATACTTAAATCATACATTAAAATAAGCATGAGAATAGGGTTAACAAAAGCTTAGAAATC
66 AAACATATACTCAAATCATACATCAAAATAAGCATAAGAATAGGGTTAACAAAAGCTTAGAAATC
31372666 TCTTTATGGATGCTTGAAGAAGACAATAATT
131 TCTTTATGGATGCTTGAAGAAGACAATAATT
*
31372697 ATATTTACATCAATCAACCACGATAAATTTAGTTACAAATCATCATTTTCATGCACACAACAACC
1 ATATTTACATCAACCAACCACGATAAATTTAGTTACAAATCATCATTTTCATGCACACAACAACC
* *
31372762 AAACATATACTCAAATCATACATCAAAATAAGCATAAGAATAGGGTTAAGAAACGCTTAGAAATC
66 AAACATATACTCAAATCATACATCAAAATAAGCATAAGAATAGGGTTAACAAAAGCTTAGAAATC
*
31372827 TCTTTGTGGATGCTTGAAGAAGACAATAAT
131 TCTTTATGGATGCTTGAAGAAGACAATAAT
31372857 AGCAACAATG
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
161 153 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (161 bp):
ATATTTACATCAACCAACCACGATAAATTTAGTTACAAATCATCATTTTCATGCACACAACAACC
AAACATATACTCAAATCATACATCAAAATAAGCATAAGAATAGGGTTAACAAAAGCTTAGAAATC
TCTTTATGGATGCTTGAAGAAGACAATAATT
Found at i:31374790 original size:47 final size:47
Alignment explanation
Indices: 31374736--31375283 Score: 900
Period size: 47 Copynumber: 11.6 Consensus size: 47
31374726 TATTTGAATA
*
31374736 AATGTGAAAGTGTATATATGTGATAAGGCATAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
31374783 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
31374830 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
31374879 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCTATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
31374926 AATGTGAAAGTGTATATATGTGATAAGGTCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
31374973 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
31375020 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
31375069 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCTGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
31375116 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
31375163 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
31375210 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT-G
*
31375258 AA-GTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
31375284 TCCCGAAGGG
Statistics
Matches: 470, Mismatches: 26, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
47 377 0.80
48 3 0.01
49 90 0.19
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:31375059 original size:190 final size:189
Alignment explanation
Indices: 31374736--31375283 Score: 951
Period size: 190 Copynumber: 2.9 Consensus size: 189
31374726 TATTTGAATA
31374736 AATGTGAAAGTGTATATATGTGATAAGGCATAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGC-TAATGGCCGATGTGATGAATGTGAAAGTGTATATA
31374801 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
65 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
31374866 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCT-ATGTGATG
130 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAG-CTGATGTGATG
31374926 AATGTGAAAGTGTATATATGTGATAAGGTCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGG-CTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
31374991 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
65 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
31375056 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCTGATGTGATG
130 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCTGATGTGATG
31375116 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGG-CTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * *
31375181 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAGGGCCGAGT
65 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
* * *
31375244 GGCCAACGTGATGGAA-GTGAAAGTGTATAAATGTGATAAG
130 GGCCGATGTGAT-GAATGTGAAAGTGTATATATGTGATAAG
31375284 TCCCGAAGGG
Statistics
Matches: 346, Mismatches: 9, Indels: 8
0.95 0.02 0.02
Matches are distributed among these distances:
188 52 0.15
189 5 0.01
190 288 0.83
191 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (189 bp):
AATGTGAAAGTGTATATATGTGATAAGGCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATG
GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCTGATGTGATG
Found at i:31381694 original size:20 final size:20
Alignment explanation
Indices: 31381671--31381708 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31381661 TTATTCATAA
* *
31381671 AATTTTAGAATTTTTCATCG
1 AATTTTACAACTTTTCATCG
31381691 AATTTTACAACTTTTCAT
1 AATTTTACAACTTTTCAT
31381709 TTTAGTCCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (20 bp):
AATTTTACAACTTTTCATCG
Found at i:31387238 original size:41 final size:41
Alignment explanation
Indices: 31386976--31387338 Score: 401
Period size: 41 Copynumber: 8.9 Consensus size: 41
31386966 CGTTTGTCCG
* * * *** **
31386976 AAACGCCACTAAAAACTAAACTATAACAGCGTTTTTGGCCA
1 AAACGCCACTAAAAACTGATCAATAGTGGCGTTTTTATCCA
* * * **
31387017 AAATGCCACTAAAAACTGGTCAATAGCGGCGTTTTTGGCCA
1 AAACGCCACTAAAAACTGATCAATAGTGGCGTTTTTATCCA
* *
31387058 AAACGCCACTAAAAACTGGTCAATAGCGGCGTTTTTCA-CC-
1 AAACGCCACTAAAAACTGATCAATAGTGGCGTTTTT-ATCCA
* * * *
31387098 AAACGCCACTAAAAGCTGATCAATAGCGGCGTTTTAATCCC
1 AAACGCCACTAAAAACTGATCAATAGTGGCGTTTTTATCCA
* *
31387139 AAACGCCACTAAAAACTGATCAATTGCT-GCGTTTTTATCCC
1 AAACGCCACTAAAAACTGATCAATAG-TGGCGTTTTTATCCA
*
31387180 AAACGCCACTAAAAACTGATCAATTGTGGCGTTTTTATCCA
1 AAACGCCACTAAAAACTGATCAATAGTGGCGTTTTTATCCA
* * * *
31387221 AAATGCCACTAAAAACTGATCAATTGTGGCGTTTTGGAT-AA
1 AAACGCCACTAAAAACTGATCAATAGTGGCGTTTT-TATCCA
* *
31387262 AAACGCCACAAAAAACTGATCAATTGTGGCGTTTTTATCCA
1 AAACGCCACTAAAAACTGATCAATAGTGGCGTTTTTATCCA
* *
31387303 AAACACCACTAAAAACTGATTAATAGTGGCGTTTTT
1 AAACGCCACTAAAAACTGATCAATAGTGGCGTTTTT
31387339 GGTCCAAACG
Statistics
Matches: 287, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.00
40 38 0.13
41 246 0.86
42 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (41 bp):
AAACGCCACTAAAAACTGATCAATAGTGGCGTTTTTATCCA
Found at i:31387711 original size:20 final size:21
Alignment explanation
Indices: 31387656--31387730 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 21
31387646 CTTAAATCTT
* * *
31387656 AAACATTAAACCCTAAACCCT
1 AAACACTAAACCATAAACCCA
*** *
31387677 AAATTTTAAAACATAAA-CCA
1 AAACACTAAACCATAAACCCA
31387697 AAACACTAAACCATAAACTCCA
1 AAACACTAAACCATAAAC-CCA
*
31387719 AAACCCTAAACC
1 AAACACTAAACC
31387731 CCCCCAAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
20 15 0.36
21 13 0.31
22 14 0.33
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.17
Consensus pattern (21 bp):
AAACACTAAACCATAAACCCA
Found at i:31389092 original size:40 final size:41
Alignment explanation
Indices: 31389048--31389141 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 41
31389038 GCGTTTTTAC
* *
31389048 AAAAACGCCACTAAAAA-TAGAGAATTAGTGGCGCTTTCGTA
1 AAAAACGCCACTAAAAACT-GAGAATTAGCGACGCTTTCGTA
* * * *
31389089 AAAAATGCCGC-AAAAACTTAGAATTAGCGACGCTTTTGT-
1 AAAAACGCCACTAAAAACTGAGAATTAGCGACGCTTTCGTA
31389128 -AAAACGCCACTAAA
1 AAAAACGCCACTAAA
31389142 TGTTTAATTG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
38 8 0.19
39 3 0.07
40 22 0.51
41 10 0.23
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAAACGCCACTAAAAACTGAGAATTAGCGACGCTTTCGTA
Found at i:31389751 original size:18 final size:19
Alignment explanation
Indices: 31389717--31389752 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31389707 CTTCTTTCTG
31389717 TAGAATTGCAAAGATGAAA
1 TAGAATTGCAAAGATGAAA
*
31389736 TAGAATTG-AGAGATGAA
1 TAGAATTGCAAAGATGAA
31389753 GAATTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.03, G:0.25, T:0.22
Consensus pattern (19 bp):
TAGAATTGCAAAGATGAAA
Found at i:31390147 original size:11 final size:11
Alignment explanation
Indices: 31390131--31390180 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
31390121 CAACTTGTAT
31390131 ATTTGTCAAGA
1 ATTTGTCAAGA
31390142 ATTTGTCAAGA
1 ATTTGTCAAGA
* *
31390153 ATTTGACAAAATA
1 ATTTGTC--AAGA
31390166 ATTTGTCAAGA
1 ATTTGTCAAGA
31390177 ATTT
1 ATTT
31390181 TTAAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.73
13 9 0.27
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (11 bp):
ATTTGTCAAGA
Found at i:31397220 original size:31 final size:31
Alignment explanation
Indices: 31397174--31397240 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
31397164 TGGTTGTATT
* *
31397174 TTTTATGTTAAATTTGCTGTTTTTGGCTGCA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
* * * *
31397205 TTTTATATTATATTTGTTGTATTTGGTTGGA
1 TTTTATATTAAATTTGCTGTATTTGGCTGCA
31397236 TTTTA
1 TTTTA
31397241 ATGCAGGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.60
Consensus pattern (31 bp):
TTTTATATTAAATTTGCTGTATTTGGCTGCA
Found at i:31397340 original size:43 final size:42
Alignment explanation
Indices: 31397309--31397391 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
31397299 GTGTTTGTAG
*
31397309 AAAAAGCGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCC
1 AAAAA-CGCCGCTAAAAGCCTTGACCTTTAGCGGCG-TTTTCAC
* * *
31397353 ACAAATGCCGCTAAAAGCCTTGACCTTTAACGGCGTTTT
1 AAAAACGCCGCTAAAAGCCTTGACCTTTAGCGGCGTTTT
31397392 TTTTCAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 4 0.11
43 28 0.78
44 4 0.11
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (42 bp):
AAAAACGCCGCTAAAAGCCTTGACCTTTAGCGGCGTTTTCAC
Found at i:31405520 original size:24 final size:24
Alignment explanation
Indices: 31405488--31405534 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
31405478 CTCTGGATAT
31405488 CAGAAAGGACGTCAAGCATAACTC
1 CAGAAAGGACGTCAAGCATAACTC
31405512 CAGAAAGGACGTCAAGCATAACT
1 CAGAAAGGACGTCAAGCATAACT
31405535 GTCAAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (24 bp):
CAGAAAGGACGTCAAGCATAACTC
Found at i:31413188 original size:27 final size:26
Alignment explanation
Indices: 31413151--31413264 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
31413141 AACATGGCTG
* *
31413151 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
31413177 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
31413205 CCA-AACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
31413231 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
31413258 CCAGAAC
1 CCAGAAC
31413265 GCTTCCTCCA
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
26 27 0.35
27 38 0.49
28 13 0.17
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:31413213 original size:53 final size:53
Alignment explanation
Indices: 31413155--31413260 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 53
31413145 TGGCTGCCAG
*
31413155 AACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCACCA
1 AACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCACCA
* * * *
31413208 AACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCACCA
1 AACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCACCA
31413261 GAACGCTTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 29 0.62
54 18 0.38
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (53 bp):
AACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCACCA
Found at i:31414915 original size:26 final size:26
Alignment explanation
Indices: 31414879--31414988 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
31414869 CATGAAATTC
31414879 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
31414905 TTATCATGAAACATTTACCTGACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
31414931 TTATCATGGAATATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
31414957 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
31414983 TTATCA
1 TTATCA
31414989 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:31421324 original size:28 final size:28
Alignment explanation
Indices: 31421304--31421465 Score: 80
Period size: 29 Copynumber: 5.6 Consensus size: 28
31421294 AAATTGATAT
31421304 AAACTTATAAAAATTAAAAAAATCATAA
1 AAACTTATAAAAATTAAAAAAATCATAA
* * * *
31421332 AAACTTATAAATATTATGAAAATTTATAA
1 AAACTTATAAAAATTA-AAAAAATCATAA
* * *
31421361 AAA-TTCTAATATATTATAAAAAATTA-ATA
1 AAACTTATAA-AAATTA-AAAAAATCATA-A
* * ** *
31421390 AAACATATTTAAAACATTTAAAATTTTATAA
1 AAAC-T-TATAAAA-ATTAAAAAAATCATAA
* *
31421421 AAACTTAATAGAAATTCAAAAAAATTATAA
1 AAACTT-ATAAAAATT-AAAAAAATCATAA
31421451 ATAA--TATAAAAATTA
1 A-AACTTATAAAAATTA
31421466 TGAAAAATTA
Statistics
Matches: 105, Mismatches: 18, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
27 1 0.01
28 29 0.28
29 35 0.33
30 16 0.15
31 16 0.15
32 8 0.08
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.33
Consensus pattern (28 bp):
AAACTTATAAAAATTAAAAAAATCATAA
Found at i:31421333 original size:18 final size:19
Alignment explanation
Indices: 31421254--31421384 Score: 69
Period size: 19 Copynumber: 6.9 Consensus size: 19
31421244 TAACAAGTTT
*
31421254 ATAAAAAATATAAAAAAT-
1 ATAAAAATTATAAAAAATC
*
31421272 ACTAAAAATT-TAAAAAA-A
1 A-TAAAAATTATAAAAAATC
* * *
31421290 ACT-AAAATTGATATAAACTT
1 A-TAAAAATT-ATAAAAAATC
31421310 ATAAAAATTA-AAAAAATC
1 ATAAAAATTATAAAAAATC
* *
31421328 ATAAAAACTTAT-AAATATT
1 ATAAAAA-TTATAAAAAATC
* *
31421347 ATGAAAATTTATAAAAATTC
1 AT-AAAAATTATAAAAAATC
*
31421367 -TAATATATTATAAAAAAT
1 ATAA-AAATTATAAAAAAT
31421385 TAATAAAACA
Statistics
Matches: 86, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
17 6 0.07
18 25 0.29
19 40 0.47
20 15 0.17
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAATTATAAAAAATC
Found at i:31421348 original size:9 final size:9
Alignment explanation
Indices: 31421252--31421475 Score: 123
Period size: 9 Copynumber: 23.3 Consensus size: 9
31421242 ATTAACAAGT
31421252 TTATAAAAA
1 TTATAAAAA
*
31421261 ATATAAAAA
1 TTATAAAAA
*
31421270 ATACTAAAAA
1 TTA-TAAAAA
31421280 TT-TAAAAA
1 TTATAAAAA
**
31421288 AAACT-AAAA
1 TTA-TAAAAA
*
31421297 TTGATATAAAC
1 TT-ATA-AAAA
31421308 TTATAAAAA
1 TTATAAAAA
*
31421317 TTAAAAAAA
1 TTATAAAAA
*
31421326 TCATAAAAA
1 TTATAAAAA
*
31421335 CTTATAAATA
1 -TTATAAAAA
*
31421345 TTATGAAAAT
1 TTAT-AAAAA
31421355 TTATAAAAA
1 TTATAAAAA
* *
31421364 TTCTAATATA
1 TTATAA-AAA
31421374 TTATAAAAAA
1 TTAT-AAAAA
31421384 TTAATAAAACA
1 TT-ATAAAA-A
*
31421395 TATTTAAAACA
1 T-TATAAAA-A
*
31421406 TT-TAAAATT
1 TTATAAAA-A
31421415 TTATAAAAA
1 TTATAAAAA
*
31421424 CTTAATAGAAA
1 -TT-ATAAAAA
*
31421435 TTCAAAAAAA
1 TT-ATAAAAA
31421445 TTATAAATAA
1 TTATAAA-AA
31421455 -TATAAAAA
1 TTATAAAAA
31421463 TTATGAAAAA
1 TTAT-AAAAA
31421473 TTA
1 TTA
31421476 GATATTATTA
Statistics
Matches: 167, Mismatches: 29, Indels: 37
0.72 0.12 0.16
Matches are distributed among these distances:
8 8 0.05
9 67 0.40
10 66 0.40
11 25 0.15
12 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:31438210 original size:47 final size:47
Alignment explanation
Indices: 31438132--31438637 Score: 814
Period size: 47 Copynumber: 10.6 Consensus size: 47
31438122 CCCTTCGGGA
* * * * * *
31438132 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
31438179 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31438226 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31438273 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31438320 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
31438367 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31438416 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31438465 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31438512 CTTATCACATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
31438559 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31438608 CTTATCACATATATACACTTTCACATTCAT
1 CTTATCACATATATACACTTTCACATTCAT
31438638 TCAAATATAC
Statistics
Matches: 433, Mismatches: 22, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
47 298 0.69
49 135 0.31
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31438478 original size:192 final size:190
Alignment explanation
Indices: 31438132--31438637 Score: 872
Period size: 192 Copynumber: 2.7 Consensus size: 190
31438122 CCCTTCGGGA
* * * * * * * *
31438132 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
31438195 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
31438260 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
31438320 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
31438385 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCATCA
*
31438450 CATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
129 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
31438512 CTTATCACATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
31438577 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCAT
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCAT
31438638 TCAAATATAC
Statistics
Matches: 302, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
188 47 0.16
190 67 0.22
192 188 0.62
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (190 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:31440905 original size:85 final size:85
Alignment explanation
Indices: 31440776--31440954 Score: 340
Period size: 85 Copynumber: 2.1 Consensus size: 85
31440766 TATTTTATTG
* *
31440776 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATATTTT
31440841 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
31440861 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATATTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATATTTT
31440926 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
31440946 CCCATGCTC
1 CCCATGCTC
31440955 ATGGACGGCC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.27, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATATTTT
TAGCCATAACATCTTGTCCA
Found at i:31471478 original size:23 final size:25
Alignment explanation
Indices: 31471419--31471479 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 25
31471409 GTGTTTTGTT
31471419 TTAATT-AAAA-TAACCTTTAATAA
1 TTAATTCAAAATTAACCTTTAATAA
*
31471442 TTAAATACCAAAATTAACCTTT-A-AA
1 TT-AAT-TCAAAATTAACCTTTAATAA
31471467 TTAATTCAAAATT
1 TTAATTCAAAATT
31471480 TCGTTTATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
23 9 0.28
24 6 0.19
25 4 0.12
26 5 0.16
27 8 0.25
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (25 bp):
TTAATTCAAAATTAACCTTTAATAA
Found at i:31472533 original size:144 final size:144
Alignment explanation
Indices: 31472273--31472672 Score: 663
Period size: 144 Copynumber: 2.8 Consensus size: 144
31472263 TTTTATCTCC
*
31472273 CACTTAATAATTTAATCCAACCCAATACTTGTTTTCTATTTCCCAAAATTAATATTATTTATTTA
1 CACTTCATAATTTAATCCAACCCAATACTTGTTTTCTATTTCCCAAAATTAATATTATTTATTTA
31472338 ATTAATGAAATCAACTAAACCAATTTCCTAATTAAATAATTTTTTCAATCCAGTTCTAACCAGTC
66 ATTAATGAAATCAACTAAACCAATTTCCTAATTAAATAATTTTTTCAATCCAGTTCTAACCAGTC
31472403 CAATTTTGATCTTG
131 CAATTTTGATCTTG
*
31472417 CACTTCATAATTTAATCCAACCCAATATTTGTTTTCTATTTCCCAAAATTAATATTATTTATTTA
1 CACTTCATAATTTAATCCAACCCAATACTTGTTTTCTATTTCCCAAAATTAATATTATTTATTTA
31472482 ATTAATGAAATCAACTAAACCAATTTCCTAATTAAATAATTTTTTCAATCCAGTTCTAACCAGTC
66 ATTAATGAAATCAACTAAACCAATTTCCTAATTAAATAATTTTTTCAATCCAGTTCTAACCAGTC
31472547 CAATTTTGATCTTG
131 CAATTTTGATCTTG
*
31472561 CACTTCATAATTTAATCCAACCCAATACTTGTTTTCTATTTTCCAAAA-T-A-A--A--TA-TTA
1 CACTTCATAATTTAATCCAACCCAATACTTGTTTTCTATTTCCCAAAATTAATATTATTTATTTA
* ** ** *
31472618 ATTAATTAAATCAACTAAATTAATTTTTTAATTAAATAATTTTCTCAATCCAGTT
66 ATTAATGAAATCAACTAAACCAATTTCCTAATTAAATAATTTTTTCAATCCAGTT
31472673 TTAATTCCAT
Statistics
Matches: 246, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
136 52 0.21
137 2 0.01
139 1 0.00
141 1 0.00
142 1 0.00
143 1 0.00
144 188 0.76
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.42
Consensus pattern (144 bp):
CACTTCATAATTTAATCCAACCCAATACTTGTTTTCTATTTCCCAAAATTAATATTATTTATTTA
ATTAATGAAATCAACTAAACCAATTTCCTAATTAAATAATTTTTTCAATCCAGTTCTAACCAGTC
CAATTTTGATCTTG
Found at i:31474560 original size:18 final size:17
Alignment explanation
Indices: 31474536--31474581 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
31474526 TTTTACATAC
31474536 TTTTTAATATTTATAAT
1 TTTTTAATATTTATAAT
* *
31474553 TTTCTTAAAAATTATAAT
1 TTT-TTAATATTTATAAT
31474571 TTTTT-ATATTT
1 TTTTTAATATTT
31474582 CATTAGAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.17
17 5 0.21
18 15 0.62
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTAATATTTATAAT
Found at i:31474739 original size:10 final size:9
Alignment explanation
Indices: 31474603--31474832 Score: 69
Period size: 9 Copynumber: 23.7 Consensus size: 9
31474593 ATTATGAATC
31474603 TTTTATAACT
1 TTTTATAA-T
*
31474613 TTTGATAA-
1 TTTTATAAT
31474621 TTTTATAAGT
1 TTTTATAA-T
* *
31474631 TTATAGAAT
1 TTTTATAAT
31474640 GTTTT-TATAT
1 -TTTTATA-AT
31474650 TTTT-TACAT
1 TTTTATA-AT
*
31474659 TTTT-TATT
1 TTTTATAAT
31474667 TTTTATAATT
1 TTTTATAA-T
31474677 ACTTTTATAA-
1 --TTTTATAAT
*
31474687 TTTAATAGTAT
1 TTTTATA--AT
31474698 CTTTTATAAT
1 -TTTTATAAT
*
31474708 TTTTGTAAT
1 TTTTATAAT
*
31474717 ATTTATAAGT
1 TTTTATAA-T
31474727 TTTTATGAATTTT
1 TTTTAT-AA---T
* **
31474740 TTTTGTAGC
1 TTTTATAAT
31474749 TTTTATAAGT
1 TTTTATAA-T
31474759 TTCTGTA-AAT
1 TT-T-TATAAT
*
31474769 ATTTCATACAT
1 -TTTTATA-AT
31474780 TTTT-TAAT
1 TTTTATAAT
*
31474788 TTTTTTAAAT
1 TTTTAT-AAT
*
31474798 TTGTAATAAT
1 TT-TTATAAT
*
31474808 CTTTTATGAT
1 -TTTTATAAT
31474818 TTTTATAAT
1 TTTTATAAT
31474827 TTTTAT
1 TTTTAT
31474833 GAGAAAAATA
Statistics
Matches: 165, Mismatches: 29, Indels: 53
0.67 0.12 0.21
Matches are distributed among these distances:
8 24 0.15
9 56 0.34
10 49 0.30
11 13 0.08
12 17 0.10
13 6 0.04
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:31475927 original size:20 final size:20
Alignment explanation
Indices: 31475902--31475946 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
31475892 CAAATCCTTT
31475902 TCTTTTCTTCTTTCT-TTTCC
1 TCTTTTCTT-TTTCTATTTCC
31475922 TCTTTTCTTTTTCTATTTCC
1 TCTTTTCTTTTTCTATTTCC
31475942 TCTTT
1 TCTTT
31475947 CAATTGAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTTTCTTTTTCTATTTCC
Found at i:31475928 original size:13 final size:13
Alignment explanation
Indices: 31475898--31475932 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
31475888 AAGTCAAATC
*
31475898 CTTTTCTTTTCTT
1 CTTTTCTTTTCCT
31475911 C-TTTCTTTTCCT
1 CTTTTCTTTTCCT
31475923 CTTTTCTTTT
1 CTTTTCTTTT
31475933 TCTATTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
CTTTTCTTTTCCT
Found at i:31479136 original size:31 final size:31
Alignment explanation
Indices: 31479101--31479176 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
31479091 TGCCCCAAGA
* *
31479101 TACACGGGCGTGTGAGTCCACATGGGCCCCC
1 TACACGGGCGTGTGAGTCCACACGAGCCCCC
*
31479132 TACACGGGTGTGTGAGTCCACACGAGCCCCC
1 TACACGGGCGTGTGAGTCCACACGAGCCCCC
31479163 TACACGGGCGTGTG
1 TACACGGGCGTGTG
31479177 TCCCTTTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (31 bp):
TACACGGGCGTGTGAGTCCACACGAGCCCCC
Found at i:31493394 original size:8 final size:9
Alignment explanation
Indices: 31493376--31493405 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
31493366 TGAGAGTTAA
31493376 TTTTTATTT
1 TTTTTATTT
31493385 TTTTTATTT
1 TTTTTATTT
31493394 TTTTTATTT
1 TTTTTATTT
31493403 TTT
1 TTT
31493406 CTCTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:31497116 original size:72 final size:72
Alignment explanation
Indices: 31496987--31497129 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 72
31496977 CAGGGGCGAT
* * * *
31496987 GGCTTGCTGTTTTGAACGGTTGAGGAGAGCGAGGAAGCAGCGGCTGAATCTAATCGGGAGGAGAC
1 GGCTGGCTGTTTTGAACGGTTGAGGAGAGCAAAGAAGCAGCAGCTGAATCTAATCGGGAGGAGAC
31497052 AGCTTCG
66 AGCTTCG
* *
31497059 GGCTGGCTGTTTTGAATGGTTGAGGAGAGCAAAGAAGCAGCAGCTGAAT-TGATTCGGGAGGAGA
1 GGCTGGCTGTTTTGAACGGTTGAGGAGAGCAAAGAAGCAGCAGCTGAATCT-AATCGGGAGGAGA
31497123 CAGCTTC
65 CAGCTTC
31497130 AGACAGTACT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 1 0.02
72 63 0.98
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.22
Consensus pattern (72 bp):
GGCTGGCTGTTTTGAACGGTTGAGGAGAGCAAAGAAGCAGCAGCTGAATCTAATCGGGAGGAGAC
AGCTTCG
Found at i:31501490 original size:28 final size:28
Alignment explanation
Indices: 31501451--31501532 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 28
31501441 ATAAAATTTT
* ** *
31501451 GGGAAAGA-TGTAAAATTTGTAAAGTAG
1 GGGAAAGATTGTAAAATCTAAAAAATAG
*
31501478 GGGACAGATTGTAAAATCTAAAAAATAG
1 GGGAAAGATTGTAAAATCTAAAAAATAG
*
31501506 GGGAAAAATTGTAAAATC-AAAGAAATA
1 GGGAAAGATTGTAAAATCTAAA-AAATA
31501533 AGGACAAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
27 10 0.22
28 36 0.78
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.22
Consensus pattern (28 bp):
GGGAAAGATTGTAAAATCTAAAAAATAG
Done.