Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 102 of 208
Found at i:30792126 original size:18 final size:18
Alignment explanation
Indices: 30792043--30792127 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 18
30792033 CAAAAAAGAA
30792043 GAAAAAGAAAAAGAAAGT-
1 GAAAAAGAAAAAGAAA-TC
* *
30792061 GAAAAAGAAAAAGAGTGCGAGC
1 GAAAAAGAAAAAGA----AATC
*
30792083 GAGAAAATGAAAAAGAAATT
1 GA-AAAA-GAAAAAGAAATC
*
30792103 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATC
30792121 GAAAAAG
1 GAAAAAG
30792128 TGAGAGAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
18 31 0.60
19 4 0.08
20 2 0.04
22 3 0.06
23 4 0.08
24 8 0.15
ACGTcount: A:0.65, C:0.05, G:0.24, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATC
Found at i:30792178 original size:18 final size:18
Alignment explanation
Indices: 30792157--30792191 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30792147 AGAAAAGAAA
30792157 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
30792175 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
30792192 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:30792200 original size:16 final size:17
Alignment explanation
Indices: 30792179--30792217 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
30792169 ATTGAGATTG
30792179 AGAAAAAAA-TTGAAAA
1 AGAAAAAAAGTTGAAAA
30792195 AGAAAAAAATGTTGAAAA
1 AGAAAAAAA-GTTGAAAA
30792213 AGAAA
1 AGAAA
30792218 CGAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.43
18 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (17 bp):
AGAAAAAAAGTTGAAAA
Found at i:30801089 original size:15 final size:17
Alignment explanation
Indices: 30801069--30801125 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 17
30801059 ATTAGTTTCT
30801069 TATAGTCTT-ATAA-TC
1 TATAGTCTTCATAATTC
*
30801084 TATAGTTTTCATAATTC
1 TATAGTCTTCATAATTC
*
30801101 TATACT-TTCA-AATTC
1 TATAGTCTTCATAATTC
30801116 TATAGT-TTCA
1 TATAGTCTTCA
30801126 CATCTAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 22 0.59
16 8 0.22
17 7 0.19
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (17 bp):
TATAGTCTTCATAATTC
Found at i:30803904 original size:23 final size:23
Alignment explanation
Indices: 30803857--30803907 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
30803847 ACCTACTTTC
* * * *
30803857 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTCGAGATA
30803880 TTACAGTAGTAATTTTCGAGATA
1 TTACAGTAGTAATTTTCGAGATA
30803903 TTACA
1 TTACA
30803908 ACCCTGCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGAGATA
Found at i:30804984 original size:26 final size:27
Alignment explanation
Indices: 30804955--30805182 Score: 140
Period size: 27 Copynumber: 8.5 Consensus size: 27
30804945 AATTTACCAA
* *
30804955 ACAGAGGTATTACAGTCATTTTA-CCT
1 ACAGAGGTATTTCAGTAATTTTACCCT
* * *
30804981 ACAGGGGCA--TCATGATCATTTTACCCT
1 ACAGAGGTATTTCA-G-TAATTTTACCCT
30805008 ACA-AGGGTATTTCAGTAATTTTACCCT
1 ACAGA-GGTATTTCAGTAATTTTACCCT
*
30805035 ACAGGGGTATTTCAGTAATTTTACCC-
1 ACAGAGGTATTTCAGTAATTTTACCCT
* *
30805061 ATCGGGGGTATTTC-GATAATTTTACCC-
1 A-CAGAGGTATTTCAG-TAATTTTACCCT
30805088 ATC-GAAGGTATTTC-GATAATTTTACCC-
1 A-CAG-AGGTATTTCAG-TAATTTTACCCT
** *
30805115 ATTGAGGGTATTTCGGTAATTTTACCC-
1 ACAGA-GGTATTTCAGTAATTTTACCCT
*
30805142 ATCA-ACGGTATTTTAGTAATTTTACCC-
1 A-CAGA-GGTATTTCAGTAATTTTACCCT
*
30805169 ATCAGGGGTATTTC
1 A-CAGAGGTATTTC
30805183 GATAAATTTA
Statistics
Matches: 170, Mismatches: 17, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
24 2 0.01
25 1 0.01
26 19 0.11
27 143 0.84
28 2 0.01
29 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (27 bp):
ACAGAGGTATTTCAGTAATTTTACCCT
Found at i:30805028 original size:27 final size:27
Alignment explanation
Indices: 30804998--30805182 Score: 209
Period size: 27 Copynumber: 6.9 Consensus size: 27
30804988 CATCATGATC
30804998 ATTTTACCC-TACAAGGGTATTTCAGTA
1 ATTTTACCCAT-CAAGGGTATTTCAGTA
*
30805025 ATTTTACCC-TACAGGGGTATTTCAGTA
1 ATTTTACCCAT-CAAGGGTATTTCAGTA
**
30805052 ATTTTACCCATCGGGGGTATTTC-GATA
1 ATTTTACCCATCAAGGGTATTTCAG-TA
30805079 ATTTTACCCATCGAA-GGTATTTC-GATA
1 ATTTTACCCATC-AAGGGTATTTCAG-TA
** *
30805106 ATTTTACCCATTGAGGGTATTTCGGTA
1 ATTTTACCCATCAAGGGTATTTCAGTA
* *
30805133 ATTTTACCCATCAACGGTATTTTAGTA
1 ATTTTACCCATCAAGGGTATTTCAGTA
*
30805160 ATTTTACCCATCAGGGGTATTTC
1 ATTTTACCCATCAAGGGTATTTC
30805183 GATAAATTTA
Statistics
Matches: 139, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.01
27 135 0.97
28 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (27 bp):
ATTTTACCCATCAAGGGTATTTCAGTA
Found at i:30805058 original size:54 final size:55
Alignment explanation
Indices: 30804960--30805182 Score: 196
Period size: 54 Copynumber: 4.1 Consensus size: 55
30804950 ACCAAACAGA
* * * * *
30804960 GGTATTACAGTCATTTTACCTA-CAGGGGCA--TCATGATCATTTTACCC-TACAAG
1 GGTATTTCAGTAATTTTACCCATCAGGGGTATTTCA-GATAATTTTACCCAT-CAAG
**
30805013 GGTATTTCAGTAATTTTACCC-TACAGGGGTATTTCAG-TAATTTTACCCATCGGG
1 GGTATTTCAGTAATTTTACCCAT-CAGGGGTATTTCAGATAATTTTACCCATCAAG
* **
30805067 GGTATTTC-GATAATTTTACCCATC-GAAGGTATTTC-GATAATTTTACCCATTGAG
1 GGTATTTCAG-TAATTTTACCCATCAG-GGGTATTTCAGATAATTTTACCCATCAAG
* ** * *
30805121 GGTATTTCGGTAATTTTACCCATCAACGGTATTTTAG-TAATTTTACCCATCAGG
1 GGTATTTCAGTAATTTTACCCATCAGGGGTATTTCAGATAATTTTACCCATCAAG
30805175 GGTATTTC
1 GGTATTTC
30805183 GATAAATTTA
Statistics
Matches: 142, Mismatches: 16, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
53 21 0.15
54 113 0.80
55 5 0.04
56 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (55 bp):
GGTATTTCAGTAATTTTACCCATCAGGGGTATTTCAGATAATTTTACCCATCAAG
Found at i:30809774 original size:20 final size:20
Alignment explanation
Indices: 30809749--30809787 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
30809739 TAAATTAAAC
*
30809749 TGAGCTAGGTTTGAGCTTAT
1 TGAGCTAAGTTTGAGCTTAT
30809769 TGAGCTAAGTTTGAGCTTA
1 TGAGCTAAGTTTGAGCTTA
30809788 GTTCAGCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.38
Consensus pattern (20 bp):
TGAGCTAAGTTTGAGCTTAT
Found at i:30815770 original size:15 final size:17
Alignment explanation
Indices: 30815752--30815783 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
30815742 TAAAATAGAA
30815752 AATATAA-ATA-ACAAC
1 AATATAACATATACAAC
30815767 AATATAACATATACAAC
1 AATATAACATATACAAC
30815784 TACAAGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (17 bp):
AATATAACATATACAAC
Found at i:30819873 original size:28 final size:28
Alignment explanation
Indices: 30819813--30819873 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
30819803 TGAGCCTTAT
* * *
30819813 TCAGTGTGGGCCTTAGCCCAATATAGAA
1 TCAGTGTGAGCCTAAGCCCAATACAGAA
* * *
30819841 ACAGTGTGAGCCTAAGCCCGATACAGTA
1 TCAGTGTGAGCCTAAGCCCAATACAGAA
30819869 TCAGT
1 TCAGT
30819874 ATGGTGCAAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (28 bp):
TCAGTGTGAGCCTAAGCCCAATACAGAA
Found at i:30820071 original size:22 final size:22
Alignment explanation
Indices: 30820041--30820092 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
30820031 AATGGCTAAG
* * *
30820041 AGCCGTAAACAAGATAGCTATA
1 AGCCATAAACAAAATAGCTACA
* *
30820063 AGCTATAAACAAAATGGCTACA
1 AGCCATAAACAAAATAGCTACA
30820085 AGCCATAA
1 AGCCATAA
30820093 GTACAATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.17
Consensus pattern (22 bp):
AGCCATAAACAAAATAGCTACA
Found at i:30820152 original size:32 final size:32
Alignment explanation
Indices: 30820104--30820314 Score: 176
Period size: 32 Copynumber: 6.6 Consensus size: 32
30820094 TACAATAATG
* *
30820104 TGATTGGCACAAAGCCATCAGTAGCAGTGATA
1 TGATCGGCACAAAGCCATCAGTAACAGTGATA
* * * **
30820136 TGATCGGCACACAGCCATCAGTAACGGTAACG
1 TGATCGGCACAAAGCCATCAGTAACAGTGATA
* * *
30820168 TGATCAGTACAAAGCCATCAGTAGCAGTGATA
1 TGATCGGCACAAAGCCATCAGTAACAGTGATA
* * * *
30820200 TGATCAGCACATAGCCAAT-AATAACAGTGAAA
1 TGATCGGCACAAAGCC-ATCAGTAACAGTGATA
* * * * *
30820232 TGATCGGCATACAA-CCATTAGTATCGGTAATA
1 TGATCGGCACA-AAGCCATCAGTAACAGTGATA
* *
30820264 TGATCGGCACAAAGCCATCACTAACGGT-ACTA
1 TGATCGGCACAAAGCCATCAGTAACAGTGA-TA
*
30820296 TGATTGGCACAAAGCCATC
1 TGATCGGCACAAAGCCATC
30820315 TGATGTGAGC
Statistics
Matches: 141, Mismatches: 33, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
31 5 0.04
32 133 0.94
33 3 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (32 bp):
TGATCGGCACAAAGCCATCAGTAACAGTGATA
Found at i:30820306 original size:96 final size:97
Alignment explanation
Indices: 30820104--30820312 Score: 235
Period size: 96 Copynumber: 2.2 Consensus size: 97
30820094 TACAATAATG
* * * * *
30820104 TGATTGGCACAAAGCC-ATCAGTAGCAGTGATATGATCGGCACACAGCCATCAGTAACGGTAACG
1 TGATTGGCACAAAGCCAATCAATAACAGTGAAATGATCGGCACACAACCATCAGTAACGGTAACA
* * *
30820168 TGATCAGTACAAAGCCATCAGTAGCAGTGATA
66 TGATCAGCACAAAGCCATCACTAACAGTGATA
** * * * * *
30820200 TGATCAGCACATAGCCAAT-AATAACAGTGAAATGATCGGCATACAACCATTAGTATCGGTAATA
1 TGATTGGCACAAAGCCAATCAATAACAGTGAAATGATCGGCACACAACCATCAGTAACGGTAACA
* *
30820264 TGATCGGCACAAAGCCATCACTAACGGT-ACTA
66 TGATCAGCACAAAGCCATCACTAACAGTGA-TA
30820296 TGATTGGCACAAAGCCA
1 TGATTGGCACAAAGCCA
30820313 TCTGATGTGA
Statistics
Matches: 91, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
95 1 0.01
96 88 0.97
97 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (97 bp):
TGATTGGCACAAAGCCAATCAATAACAGTGAAATGATCGGCACACAACCATCAGTAACGGTAACA
TGATCAGCACAAAGCCATCACTAACAGTGATA
Found at i:30820559 original size:20 final size:20
Alignment explanation
Indices: 30820534--30820581 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
30820524 TTAACTTAGT
30820534 TCAGCTCACTCGAGATCAAG
1 TCAGCTCACTCGAGATCAAG
* * *
30820554 TCAGCTCATTCGAGCTCAAT
1 TCAGCTCACTCGAGATCAAG
30820574 TCAGCTCA
1 TCAGCTCA
30820582 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (20 bp):
TCAGCTCACTCGAGATCAAG
Found at i:30822142 original size:24 final size:23
Alignment explanation
Indices: 30822115--30822196 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 23
30822105 CCATGCTCAG
*
30822115 AATCAATCATTCAAATCACAAACA
1 AATCAATCATTCAAA-CACAGACA
* *
30822139 AATCATTCATACCAAACACAGACA
1 AATCAATCAT-TCAAACACAGACA
* *
30822163 AAT-AAGTCATTTAACCACAGACA
1 AATCAA-TCATTCAAACACAGACA
*
30822186 AAACAATCATT
1 AATCAATCATT
30822197 TGACCTCGAG
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
23 18 0.38
24 25 0.53
25 4 0.09
ACGTcount: A:0.51, C:0.24, G:0.04, T:0.21
Consensus pattern (23 bp):
AATCAATCATTCAAACACAGACA
Found at i:30822276 original size:27 final size:27
Alignment explanation
Indices: 30822237--30822486 Score: 365
Period size: 27 Copynumber: 9.3 Consensus size: 27
30822227 CCACCAGGGC
*
30822237 ATTACGGTCATTTTACCCTACAGGGAT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
30822264 ATTACGATTATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* **
30822291 ATTACGGTCATTTTATCCTACAGATGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** *
30822318 ATTATAGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
*
30822345 ATTACGGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
*
30822372 ATTACGGTCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
30822399 ATTACGATCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
30822426 ATTACGGTCATATTACCCTACAAGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
30822453 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
30822480 ATTACGG
1 ATTACGG
30822487 ACAAGGGCAT
Statistics
Matches: 196, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 196 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.34
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:30822486 original size:54 final size:54
Alignment explanation
Indices: 30822233--30822593 Score: 379
Period size: 54 Copynumber: 6.9 Consensus size: 54
30822223 TTACCCACCA
* * *
30822233 GGGCATTACGGTCATTTTACCCTACAGGGATATTACGATTATTTTACCCTACAG
1 GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAG
* * ** **
30822287 GGGTATTACGGTCATTTTATCCTACAGATGTATTATAGTCATTTTACCCTACAG
1 GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAG
* *
30822341 GGGCATTACGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTATAG
1 GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAG
* * * *
30822395 GGGTATTACGATCATTTTACCCTACAGGGGTATTACGGTCATATTACCCTACAA
1 GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAG
30822449 GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGG-------A--C-A-A-
1 GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAG
* * * * *
30822491 GGGCATTACGGTCACTTTACCCTGCAGAGGTAGTACGGTCATTTTATCCTACAG
1 GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAG
* * * * * * * *
30822545 TGGCATTACGGT-AATTTCCCCTTCAGGAGTATTTCGATAATTTTACCCT
1 GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCT
30822594 TCGAGGTATT
Statistics
Matches: 255, Mismatches: 40, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
42 34 0.13
43 1 0.00
44 1 0.00
45 1 0.00
47 1 0.00
49 1 0.00
51 1 0.00
52 1 0.00
53 28 0.11
54 186 0.73
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (54 bp):
GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTACAG
Found at i:30822496 original size:42 final size:42
Alignment explanation
Indices: 30822445--30822528 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
30822435 ATATTACCCT
* * *
30822445 ACAAGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGG
1 ACAAGGGCATTACGGTCACTTTACCCTACAGAGGTAGTACGG
*
30822487 ACAAGGGCATTACGGTCACTTTACCCTGCAGAGGTAGTACGG
1 ACAAGGGCATTACGGTCACTTTACCCTACAGAGGTAGTACGG
30822529 TCATTTTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (42 bp):
ACAAGGGCATTACGGTCACTTTACCCTACAGAGGTAGTACGG
Found at i:30822554 original size:27 final size:27
Alignment explanation
Indices: 30822492--30822561 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
30822482 TACGGACAAG
* *
30822492 GGCATTACGGTCACTTTACCCTGCAGA
1 GGCATTACGGTCATTTTACCCTACAGA
* * * *
30822519 GGTAGTACGGTCATTTTATCCTACAGT
1 GGCATTACGGTCATTTTACCCTACAGA
*
30822546 GGCATTACGGTAATTT
1 GGCATTACGGTCATTT
30822562 CCCCTTCAGG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (27 bp):
GGCATTACGGTCATTTTACCCTACAGA
Found at i:30822641 original size:26 final size:27
Alignment explanation
Indices: 30822555--30822640 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
30822545 TGGCATTACG
*
30822555 GTAA-TTTCCCCTTC-AGGAGTATTTC-
1 GTAATTTTACCCTTCGAGG-GTATTTCA
30822580 GATAATTTTACCCTTCGA-GGTATTTCA
1 G-TAATTTTACCCTTCGAGGGTATTTCA
30822607 GTAATTTTACCCTTCGAGGGTATTTCA
1 GTAATTTTACCCTTCGAGGGTATTTCA
30822634 GTAATTT
1 GTAATTT
30822641 AACAACCTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
25 1 0.02
26 26 0.47
27 27 0.49
28 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (27 bp):
GTAATTTTACCCTTCGAGGGTATTTCA
Found at i:30829384 original size:3 final size:3
Alignment explanation
Indices: 30829376--30829403 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
30829366 ATTAAGGTGC
30829376 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
30829404 GAAAATGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:30837306 original size:33 final size:33
Alignment explanation
Indices: 30837264--30837330 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
30837254 TCATGCGTCG
30837264 TCACAAGTTACAGTATCTTTGTTTCACACACCA
1 TCACAAGTTACAGTATCTTTGTTTCACACACCA
* *
30837297 TCACAAGTTACGGTATCTTTGTTTCACGCACCA
1 TCACAAGTTACAGTATCTTTGTTTCACACACCA
30837330 T
1 T
30837331 GCGTGGCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (33 bp):
TCACAAGTTACAGTATCTTTGTTTCACACACCA
Found at i:30850251 original size:23 final size:22
Alignment explanation
Indices: 30850208--30850251 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
30850198 TTCTAAGTCG
30850208 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
30850231 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
30850252 TTAGTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:30850364 original size:45 final size:45
Alignment explanation
Indices: 30850296--30850384 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
30850286 AACAGATACT
* * * *
30850296 CGGTGGATTCAGCACATATCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGTC
*
30850341 CGGTGGAATCAGTACATAGCAACCACCTTACTAATCAATAATGT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGT
30850385 TTGGTTCACA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGTC
Found at i:30850454 original size:51 final size:51
Alignment explanation
Indices: 30850395--30850581 Score: 216
Period size: 51 Copynumber: 3.7 Consensus size: 51
30850385 TTGGTTCACA
* * * * *
30850395 TAGTAGCCTGCACATAGTGCTACACATGTGGCCATTACCATCCGATACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTACACG
* ** * * * *
30850446 TAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTACACG
* * *
30850497 TAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCA-TCCGGTACACG
30850547 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
30850582 CACTTTCACT
Statistics
Matches: 110, Mismatches: 23, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.35
51 69 0.63
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTACACG
Found at i:30857007 original size:20 final size:20
Alignment explanation
Indices: 30856982--30857024 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30856972 AAAAGAAAAG
30856982 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
30857002 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
30857022 AAA
1 AAA
30857025 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:30859816 original size:14 final size:14
Alignment explanation
Indices: 30859797--30859828 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
30859787 TCGTCAACTT
30859797 GTGTGAGCGGCATC
1 GTGTGAGCGGCATC
30859811 GTGTGAGCGGCATC
1 GTGTGAGCGGCATC
30859825 GTGT
1 GTGT
30859829 AGCTTACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.44, T:0.25
Consensus pattern (14 bp):
GTGTGAGCGGCATC
Found at i:30863304 original size:15 final size:15
Alignment explanation
Indices: 30863286--30863316 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30863276 TGAACTTTTA
30863286 TTTCTTTTATGTTAT
1 TTTCTTTTATGTTAT
*
30863301 TTTCTTTTATTTTAT
1 TTTCTTTTATGTTAT
30863316 T
1 T
30863317 ATTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTTATGTTAT
Found at i:30866927 original size:101 final size:102
Alignment explanation
Indices: 30866801--30866983 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 102
30866791 AAAGTGATGG
*
30866801 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGG-ATGATAATGGTCACATGTGTAGT
*
30866864 ACTACGTGCAGGCTACTATGCGCACCAGATAGTTTCGA
65 ACTACGTGCAGGCAACTATGCGCACCAGATAGTTTCGA
* * *
30866902 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATGATAATGGTCACATGTGTAGTA
*
30866967 CTATGTGCAGGCAACTA
66 CTACGTGCAGGCAACTA
30866984 GGTGAACCGA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.54
102 30 0.41
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGATGATAATGGTCACATGTGTAGTA
CTACGTGCAGGCAACTATGCGCACCAGATAGTTTCGA
Found at i:30866962 original size:51 final size:50
Alignment explanation
Indices: 30866797--30866992 Score: 205
Period size: 51 Copynumber: 3.9 Consensus size: 50
30866787 AGTGAAAGTG
* * *
30866797 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGGT
* * * * * * *
30866848 A-GGTCGCATGTGTAGTACTACGTGCAGGCTACTATGCGCACCAGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
* * * *
30866897 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
* * *
30866948 AATGGTCACATGTGTAGTACTATGTGCAGGCAACTAGGTGAACCG
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
30866993 AACATCATTG
Statistics
Matches: 114, Mismatches: 28, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
49 3 0.03
50 35 0.31
51 75 0.66
52 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGT
Found at i:30867045 original size:45 final size:45
Alignment explanation
Indices: 30866989--30867083 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
30866979 AACTAGGTGA
* *
30866989 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
* *
30867034 ACCGGACATCATTGATTAATAAGGTTGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
30867079 ACCGA
1 ACCGA
30867084 GTCTCTGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:30875218 original size:23 final size:23
Alignment explanation
Indices: 30875199--30875289 Score: 139
Period size: 23 Copynumber: 4.0 Consensus size: 23
30875189 CCACACTAAT
* *
30875199 ATGTAGCCGAAGCTACCACTCAT
1 ATGTAGCCGAAGCTACCACTGAA
30875222 ATGTAGCCGACA-CTACCACTGAA
1 ATGTAGCCGA-AGCTACCACTGAA
*
30875245 ATGTAGCCAAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
30875268 ATGTAGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
30875290 TCAATAACAC
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
22 1 0.02
23 60 0.97
24 1 0.02
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.19
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:30880341 original size:36 final size:36
Alignment explanation
Indices: 30880289--30880369 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 36
30880279 GTATTAAAAA
30880289 TAAAGAGGTAAATGACATGGCTTACCATAAACAAGTG
1 TAAA-AGGTAAATGACATGGCTTACCATAAACAAGTG
30880326 TAAAAGGTAAATGACATGGCTTACCATAAACAAGTG
1 TAAAAGGTAAATGACATGGCTTACCATAAACAAGTG
30880362 TAAAAGGT
1 TAAAAGGT
30880370 GACATCCTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 40 0.91
37 4 0.09
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.22
Consensus pattern (36 bp):
TAAAAGGTAAATGACATGGCTTACCATAAACAAGTG
Found at i:30882858 original size:23 final size:23
Alignment explanation
Indices: 30882827--30882871 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
30882817 TCCAAACCAA
*
30882827 TTCGCACCTAAACCTAAATCATT
1 TTCGAACCTAAACCTAAATCATT
30882850 TTCGAACCTAAACCTAAATCAT
1 TTCGAACCTAAACCTAAATCAT
30882872 AACCATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (23 bp):
TTCGAACCTAAACCTAAATCATT
Found at i:30887916 original size:23 final size:23
Alignment explanation
Indices: 30887885--30887929 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
30887875 TCCAAACCAA
*
30887885 TTCGCACCTAAACCTAAATCATT
1 TTCGAACCTAAACCTAAATCATT
30887908 TTCGAACCTAAACCTAAATCAT
1 TTCGAACCTAAACCTAAATCAT
30887930 AACCATTCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (23 bp):
TTCGAACCTAAACCTAAATCATT
Found at i:30906348 original size:27 final size:27
Alignment explanation
Indices: 30906317--30906464 Score: 106
Period size: 27 Copynumber: 5.5 Consensus size: 27
30906307 ACCCTAAAGT
30906317 AGGGTAAAATGACCGAAATA-CCCTCGA
1 AGGGTAAAATGACCGAAATACCCCT-GA
* * *
30906344 AGGGTAAAATTATCGAAATACCCCTGT
1 AGGGTAAAATGACCGAAATACCCCTGA
** * *
30906371 AGGGTAAAATGACCGTGATGCCCCTGT
1 AGGGTAAAATGACCGAAATACCCCTGA
* * * *
30906398 A-GGTAAAATGACTGTAATACCTCTGTT
1 AGGGTAAAATGACCGAAATACCCCTG-A
* **
30906425 A-GGTAAATTGACC-AATATACCCCCAA
1 AGGGTAAAATGACCGAA-ATACCCCTGA
30906451 AGAGGTAAAATGAC
1 AG-GGTAAAATGAC
30906465 TATTTTACCC
Statistics
Matches: 96, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
26 22 0.23
27 60 0.62
28 14 0.15
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (27 bp):
AGGGTAAAATGACCGAAATACCCCTGA
Found at i:30906597 original size:24 final size:24
Alignment explanation
Indices: 30906562--30906620 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
30906552 TTATGTTATG
* *
30906562 TATGACTCATTTGTCTGTGATTTT
1 TATGACTGATTTGTCTGTGATTTC
*
30906586 TATGACTGATTTGTTTGTGATTTC
1 TATGACTGATTTGTCTGTGATTTC
*
30906610 TATGACCGATT
1 TATGACTGATT
30906621 CTGAGCATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.51
Consensus pattern (24 bp):
TATGACTGATTTGTCTGTGATTTC
Found at i:30906820 original size:32 final size:32
Alignment explanation
Indices: 30906784--30906946 Score: 184
Period size: 32 Copynumber: 5.1 Consensus size: 32
30906774 CAGTTTTGCT
*
30906784 GCTTTGTGCCGATTATATTACTGTTACTGATG
1 GCTTTGTGCCGATCATATTACTGTTACTGATG
* * *
30906816 GCTTTGTACCGATCATACTACCGTTACTGATG
1 GCTTTGTGCCGATCATATTACTGTTACTGATG
* * *
30906848 GCTTTGTGCCGGTCATATTACAGTTATTGATG
1 GCTTTGTGCCGATCATATTACTGTTACTGATG
* * * **
30906880 GCTGTGTGCCGGTCATATCACTACTACTGATG
1 GCTTTGTGCCGATCATATTACTGTTACTGATG
* * *
30906912 GCTTTGTGCCAAACATATTACT-TTACTTATG
1 GCTTTGTGCCGATCATATTACTGTTACTGATG
30906943 GCTT
1 GCTT
30906947 GTAGCCATTC
Statistics
Matches: 109, Mismatches: 22, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
31 11 0.10
32 98 0.90
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (32 bp):
GCTTTGTGCCGATCATATTACTGTTACTGATG
Found at i:30906968 original size:22 final size:21
Alignment explanation
Indices: 30906938--30907002 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
30906928 ATTACTTTAC
30906938 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* * *
30906960 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTT-TAGCCATTCTGT
30906982 TTATGGCTCTTAGCCATTCTG
1 TTATGGCT-TTAGCCATTCTG
30907003 ACTACTGGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:30918530 original size:27 final size:29
Alignment explanation
Indices: 30918488--30918552 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
30918478 TCCTTTTCAC
30918488 TCATTTTCTTTCCAATGTCTTTTTC-TTT
1 TCATTTTCTTTCCAATGTCTTTTTCATTT
* *
30918516 TTATTTTCTTT-CAATTTCTTTTTCATTT
1 TCATTTTCTTTCCAATGTCTTTTTCATTT
30918544 TCATTTTCT
1 TCATTTTCT
30918553 CGCTCGCCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 12 0.36
28 21 0.64
ACGTcount: A:0.12, C:0.18, G:0.02, T:0.68
Consensus pattern (29 bp):
TCATTTTCTTTCCAATGTCTTTTTCATTT
Found at i:30921093 original size:10 final size:10
Alignment explanation
Indices: 30921078--30921127 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
30921068 TTGGGTTAAG
30921078 ATTGAGCTGA
1 ATTGAGCTGA
30921088 ATTGAGCTCGA
1 ATTGAGCT-GA
30921099 A-TGAGCTGA
1 ATTGAGCTGA
* *
30921108 CTTGAGCTCA
1 ATTGAGCTGA
*
30921118 AGTGAGCTGA
1 ATTGAGCTGA
30921128 CCTAAGTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 28 0.85
11 3 0.09
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:30921128 original size:20 final size:20
Alignment explanation
Indices: 30921080--30921128 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
30921070 GGGTTAAGAT
*
30921080 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGACTTGAGCTCGAA
30921100 TGAGCTGACTTGAGCTC-AA
1 TGAGCTGACTTGAGCTCGAA
30921119 GTGAGCTGAC
1 -TGAGCTGAC
30921129 CTAAGTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (20 bp):
TGAGCTGACTTGAGCTCGAA
Found at i:30927090 original size:36 final size:36
Alignment explanation
Indices: 30927048--30927120 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
30927038 CGAAATTTCC
*
30927048 TAAGGGGGAGAGTTGTAACAACCTGTTTTTCATTGG
1 TAAGGGGGAGAGTTGTAACAACCTGTTTTTCAATGG
*
30927084 TAAGGGGGAGAGTTGTAACAACTTGTTTTTCAATGG
1 TAAGGGGGAGAGTTGTAACAACCTGTTTTTCAATGG
30927120 T
1 T
30927121 GACGAAACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.10, G:0.30, T:0.34
Consensus pattern (36 bp):
TAAGGGGGAGAGTTGTAACAACCTGTTTTTCAATGG
Found at i:30928279 original size:40 final size:40
Alignment explanation
Indices: 30928220--30928371 Score: 196
Period size: 40 Copynumber: 3.8 Consensus size: 40
30928210 TAATTATTGC
* * * * *
30928220 CTGAATGCACATATGTGCCCCTATTTGTACTTTGGTACCT
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGATACCA
* * * *
30928260 CTAAATGCACATACATGCCCCTGTTTGTACTCCGATACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGATACCA
*
30928300 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGATACAA
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGATACCA
* *
30928340 CTGAATGCACATATGTGCCCCTGTTAGTACTT
1 CTGAATGCACATACGTGCCCCTGTTTGTACTT
30928372 TGGTAACCTT
Statistics
Matches: 97, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 97 1.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.32
Consensus pattern (40 bp):
CTGAATGCACATACGTGCCCCTGTTTGTACTTCGATACCA
Found at i:30936776 original size:21 final size:20
Alignment explanation
Indices: 30936752--30936790 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
30936742 TAGTGGAAAT
30936752 AGGGGAACCAAAGTGCAAACA
1 AGGGGAACCAAA-TGCAAACA
* *
30936773 AGGGGCACCGAATGCAAA
1 AGGGGAACCAAATGCAAA
30936791 TCATGTACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.21, G:0.31, T:0.05
Consensus pattern (20 bp):
AGGGGAACCAAATGCAAACA
Found at i:30947918 original size:13 final size:13
Alignment explanation
Indices: 30947900--30947924 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30947890 GCAAAAAAAT
30947900 AGAAAATTCAAAC
1 AGAAAATTCAAAC
30947913 AGAAAATTCAAA
1 AGAAAATTCAAA
30947925 TTATCACCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.12, G:0.08, T:0.16
Consensus pattern (13 bp):
AGAAAATTCAAAC
Found at i:30948685 original size:14 final size:13
Alignment explanation
Indices: 30948649--30948735 Score: 52
Period size: 14 Copynumber: 6.3 Consensus size: 13
30948639 TCAATCTCTC
*
30948649 TTTCAATTTCTTT
1 TTTCAATTTTTTT
**
30948662 TTTCGCTTTTTCTT
1 TTTCAATTTTT-TT
30948676 TTTCAATTTTTTTT
1 TTTCAA-TTTTTTT
*
30948690 CATTCTCAATTTCTTT
1 --TT-TCAATTTTTTT
30948706 TTT-AATTTTCTTT
1 TTTCAATTTT-TTT
*
30948719 TCTTC-ATTTTCTT
1 T-TTCAATTTTTTT
30948732 TTTC
1 TTTC
30948736 TCTCACTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
12 8 0.14
13 16 0.28
14 17 0.29
15 5 0.09
16 8 0.14
17 4 0.07
ACGTcount: A:0.11, C:0.17, G:0.01, T:0.70
Consensus pattern (13 bp):
TTTCAATTTTTTT
Found at i:30948690 original size:17 final size:18
Alignment explanation
Indices: 30948667--30948707 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
30948657 TCTTTTTTCG
* *
30948667 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTCTCAATTT
30948685 -TTTTTCATTCTCAATTT
1 CTTTTTCATTCTCAATTT
30948702 CTTTTT
1 CTTTTT
30948708 TAATTTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTTTCATTCTCAATTT
Found at i:30948761 original size:17 final size:17
Alignment explanation
Indices: 30948741--30948792 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
30948731 TTTTCTCTCA
30948741 CTTTTTCGATTTCTTTT
1 CTTTTTCGATTTCTTTT
*
30948758 CTTTTGT-AATTTCTTTTT
1 CTTTT-TCGATTTC-TTTT
*
30948776 CTTTTTCGTTTTCTTTT
1 CTTTTTCGATTTCTTTT
30948793 TGTTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (17 bp):
CTTTTTCGATTTCTTTT
Found at i:30948788 original size:18 final size:18
Alignment explanation
Indices: 30948741--30948798 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
30948731 TTTTCTCTCA
*
30948741 CTTTTTCGATTTC-TTTT
1 CTTTTTCGTTTTCTTTTT
30948758 C-TTTT-GTAATTTCTTTTT
1 CTTTTTCGT--TTTCTTTTT
30948776 CTTTTTCGTTTTCTTTTT
1 CTTTTTCGTTTTCTTTTT
*
30948794 GTTTT
1 CTTTT
30948799 CTTTCAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 1 0.03
16 4 0.12
17 5 0.15
18 18 0.53
19 4 0.12
20 2 0.06
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.74
Consensus pattern (18 bp):
CTTTTTCGTTTTCTTTTT
Found at i:30948797 original size:11 final size:12
Alignment explanation
Indices: 30948741--30948802 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
30948731 TTTTCTCTCA
*
30948741 CTTTTTCGATTT
1 CTTTTTCGTTTT
30948753 C-TTTTC-TTTT
1 CTTTTTCGTTTT
* * *
30948763 GTAATTTCTTTTT
1 CT-TTTTCGTTTT
30948776 CTTTTTCGTTTT
1 CTTTTTCGTTTT
30948788 CTTTTT-GTTTT
1 CTTTTTCGTTTT
30948799 CTTT
1 CTTT
30948803 CAATTTCTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
10 3 0.07
11 14 0.34
12 19 0.46
13 5 0.12
ACGTcount: A:0.05, C:0.15, G:0.06, T:0.74
Consensus pattern (12 bp):
CTTTTTCGTTTT
Found at i:30951917 original size:23 final size:23
Alignment explanation
Indices: 30951887--30951933 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
30951877 TTTACCAAGT
30951887 AGGCGTACATCAAATGTAATGGC
1 AGGCGTACATCAAATGTAATGGC
30951910 AGGCGTACATCAAATGTAATGGC
1 AGGCGTACATCAAATGTAATGGC
30951933 A
1 A
30951934 AAGGCTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (23 bp):
AGGCGTACATCAAATGTAATGGC
Found at i:30958404 original size:20 final size:19
Alignment explanation
Indices: 30958379--30958434 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 19
30958369 TTGATGTGGT
30958379 TCAGCTCACTTGAGCTCAAG
1 TCAGCTCA-TTGAGCTCAAG
*
30958399 TCAGCTCATTCGAGCTCAAT
1 TCAGCTCATT-GAGCTCAAG
30958419 TCAGCTCATTGAGCTC
1 TCAGCTCATTGAGCTC
30958435 GTTATTAGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 8 0.24
20 26 0.76
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (19 bp):
TCAGCTCATTGAGCTCAAG
Found at i:30962274 original size:5 final size:5
Alignment explanation
Indices: 30962264--30962296 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
30962254 GCATTTGAAC
30962264 TTTAT TTTAT TTTAT TTTAT TTTACT TTT-T TTT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTT
30962297 CTAGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:30977124 original size:14 final size:14
Alignment explanation
Indices: 30977107--30977134 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30977097 GACATATGTG
30977107 ATGACTATTGTGAA
1 ATGACTATTGTGAA
30977121 ATGACTATTGTGAA
1 ATGACTATTGTGAA
30977135 TTGTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
ATGACTATTGTGAA
Found at i:30982453 original size:51 final size:51
Alignment explanation
Indices: 30982371--30982706 Score: 333
Period size: 51 Copynumber: 6.6 Consensus size: 51
30982361 GATGAACATG
* * * * *
30982371 TGTGTAGTACTGTGTGAAGGCTCCTACGTGTATCGATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAAGTTGGTCACA
* * *
30982422 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG--AAAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAAG--TTGGTCACA
* * * * *
30982473 TATGTAGTACTATGTGAAGGCTACCACGTGAACCG-TAAAACTTGATCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAAGTTGGTCACA
* * * * * * *
30982523 TGTGTAGTACTGTGTGAAGACTACTACGTGAATCGACAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAAGTTGGTCACA
* * *
30982574 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACC-A-AAAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAAG--TTGGTCACA
* * * * * *
30982625 TGTGTAATAATATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAAGTTGGTCACA
30982675 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
30982707 TCGAATGATA
Statistics
Matches: 232, Mismatches: 45, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
49 8 0.03
50 75 0.32
51 141 0.61
52 8 0.03
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (51 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAAGTTGGTCACA
Found at i:30982570 original size:101 final size:99
Alignment explanation
Indices: 30982370--30982706 Score: 338
Period size: 101 Copynumber: 3.3 Consensus size: 99
30982360 CGATGAACAT
* * ***
30982370 GTGTGTAGTACTGTGTGAAGGCT-CCTACGTGTATCGATAAATGATGGTCACATGTGTAGTACTA
1 GTGTGTAGTACTATGTGAAGGCTACC-ACGTGTACCG-TAAAACTTGGTCACATGTGTAGTACTA
* * * *
30982434 AGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCAC
64 TGTGAAGGCTACTACGTGAACCGAAAA--TGTGGTCAC
* * * *
30982472 GTATGTAGTACTATGTGAAGGCTACCACGTGAACCGTAAAACTTGATCACATGTGTAGTACTGTG
1 GTGTGTAGTACTATGTGAAGGCTACCACGTGTACCGTAAAACTTGGTCACATGTGTAGTACTATG
* *
30982537 TGAAGACTACTACGTGAATCGACAAATGATGGTCAC
66 TGAAGGCTACTACGTGAACCGA-AAATG-TGGTCAC
* * * * * * * *
30982573 ATGTGTAGTACTAAGTGAAGGCTACTATGTGTACC-AAAAAGCTTTGGTCACGTGTGTAATAATA
1 GTGTGTAGTACTATGTGAAGGCTACCACGTGTACCGTAAAA-C-TTGGTCACATGTGTAGTACTA
*
30982637 TGTGAAGGCTACTACGTGAACCGTAAAACT-TGATCAC
64 TGTGAAGGCTACTACGTGAACCG-AAAA-TGTGGTCAC
*
30982674 GTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 GTGTGTAGTACTATGTGAAGGCTACCACGTGTA
30982707 TCGAATGATA
Statistics
Matches: 195, Mismatches: 33, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
100 5 0.03
101 114 0.58
102 72 0.37
103 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (99 bp):
GTGTGTAGTACTATGTGAAGGCTACCACGTGTACCGTAAAACTTGGTCACATGTGTAGTACTATG
TGAAGGCTACTACGTGAACCGAAAATGTGGTCAC
Found at i:30982647 original size:152 final size:152
Alignment explanation
Indices: 30982371--30982710 Score: 581
Period size: 152 Copynumber: 2.2 Consensus size: 152
30982361 GATGAACATG
* *
30982371 TGTGTAGTACTGTGTGAAGGCTCCTACGTGTATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGACAAATGATGGTCACATGTGTAGTACTAAG
* * *
30982436 TGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTATGTAGTACTATGTGAAGGCTACCACG
66 TGAAGGCTACTATGTGTACCAAAAAGCTTTGGTCACGTATGTAATAATATGTGAAGGCTACCACG
30982501 TGAACCGTAAAACTTGATCACA
131 TGAACCGTAAAACTTGATCACA
* *
30982523 TGTGTAGTACTGTGTGAAGACTACTACGTGAATCGACAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGACAAATGATGGTCACATGTGTAGTACTAAG
* *
30982588 TGAAGGCTACTATGTGTACCAAAAAGCTTTGGTCACGTGTGTAATAATATGTGAAGGCTACTACG
66 TGAAGGCTACTATGTGTACCAAAAAGCTTTGGTCACGTATGTAATAATATGTGAAGGCTACCACG
*
30982653 TGAACCGTAAAACTTGATCACG
131 TGAACCGTAAAACTTGATCACA
*
30982675 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGA
30982711 ATGATAAAAG
Statistics
Matches: 175, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
152 175 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (152 bp):
TGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGACAAATGATGGTCACATGTGTAGTACTAAG
TGAAGGCTACTATGTGTACCAAAAAGCTTTGGTCACGTATGTAATAATATGTGAAGGCTACCACG
TGAACCGTAAAACTTGATCACA
Found at i:31001525 original size:21 final size:21
Alignment explanation
Indices: 31001499--31001539 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31001489 CGGTTTGTGT
31001499 ACACGGACATGTGAAATAGCC
1 ACACGGACATGTGAAATAGCC
* *
31001520 ACACGGGCATGTGAAGTAGC
1 ACACGGACATGTGAAATAGC
31001540 GACATGTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.29, T:0.15
Consensus pattern (21 bp):
ACACGGACATGTGAAATAGCC
Found at i:31011754 original size:24 final size:25
Alignment explanation
Indices: 31011709--31011757 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
31011699 ATATGAAACA
*
31011709 TTTATTTTATAAATGAAAATAATATT
1 TTTATTTAATAAATG-AAATAATATT
*
31011735 TTTATTTAATAAATG-GATAATAT
1 TTTATTTAATAAATGAAATAATAT
31011758 CCTTACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
26 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (25 bp):
TTTATTTAATAAATGAAATAATATT
Found at i:31028474 original size:16 final size:16
Alignment explanation
Indices: 31028453--31028494 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
31028443 TTCGTGAATT
31028453 AAAAAAAAATTCGTGC
1 AAAAAAAAATTCGTGC
31028469 AAAAAAAAATTCGTGC
1 AAAAAAAAATTCGTGC
31028485 ATAAAAAAAA
1 A-AAAAAAAA
31028495 AGAGGTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.17
Consensus pattern (16 bp):
AAAAAAAAATTCGTGC
Found at i:31029446 original size:14 final size:13
Alignment explanation
Indices: 31029427--31029464 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
31029417 AATAGTGAGA
31029427 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
31029439 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
31029454 GAAAAAGAAAA
1 GAAAAAGAAAA
31029465 AGATGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:31040534 original size:23 final size:23
Alignment explanation
Indices: 31040508--31040604 Score: 169
Period size: 23 Copynumber: 4.2 Consensus size: 23
31040498 ACCTACTTTC
*
31040508 TTACTGTAGTAATTTTCGAGGTA
1 TTACAGTAGTAATTTTCGAGGTA
31040531 TTACAGTAGTAATTTTCGAGGTA
1 TTACAGTAGTAATTTTCGAGGTA
31040554 TTACAGTAGTAATTTTCGAGGTA
1 TTACAGTAGTAATTTTCGAGGTA
31040577 TTACAGTAGTAATTTTCG-GGATA
1 TTACAGTAGTAATTTTCGAGG-TA
31040600 TTACA
1 TTACA
31040605 TTTCTCTCCC
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
22 2 0.03
23 70 0.97
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGAGGTA
Found at i:31042190 original size:50 final size:50
Alignment explanation
Indices: 31042072--31042708 Score: 734
Period size: 50 Copynumber: 12.7 Consensus size: 50
31042062 TGATAATAAC
* * * ** *
31042072 ATGCCAAAGCCATGTCCTAGACATGGTCTTACATGAGATGTTTC--CT-G
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * ** *
31042119 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * **
31042171 ATGCCCATGCCATGTCCCAGACATGGCCTTACGGGGGACCTCTCATC-CTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC-G
* * *
31042221 GTGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * *
31042271 GTGCCAACGCCATGTCCCAGACGTGGTCTTACATGGGACCTCTCATCTC-
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
31042320 AGTGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
1 A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* *
31042371 GTGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * *
31042421 ATGCCAACGCCATGTCCCAGACATGGTCGTACATGGGACCTGTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * *
31042471 GTGCCAATGCCATGTCCCAGAGATGGT-GTACATGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * *
31042520 GTGCCAATACCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* *
31042570 GTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCATA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--G
* *
31042625 ATGCCAATGCCATGTCCCAGACATGGTCTTACACT-GG--CTCACATATCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCG
** * * * *
31042673 ATATCGATGCCATATCTCAGATATGGTCTTACATGG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGG
31042709 AAATCACATA
Statistics
Matches: 513, Mismatches: 60, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
47 1 0.00
48 29 0.06
49 81 0.16
50 354 0.69
51 3 0.01
52 1 0.00
53 9 0.02
55 34 0.07
56 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:31042733 original size:249 final size:247
Alignment explanation
Indices: 31042229--31042747 Score: 627
Period size: 249 Copynumber: 2.1 Consensus size: 247
31042219 TGGTGCCAAC
* * * *
31042229 GCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACG
1 GCCATGTCCCAGACATGGTCGTACATGGGACCTCTCATCTCGGTGCCAACACCATGTCCCAGACA
31042294 TGGTCTTACATGGGACCTCTCATCTCAGTGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGA
66 TGGTCTTACATGGGACCTCTCATCTCAGTGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGA
** * * *
31042359 CCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGATG
131 CCTCTCATCTCAATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGA-CTCACATATCGATA
* ** ** * **
31042424 CCAACGCCATGTCCCAGACATGGTCGTACATGGGACCTGTCATCTCGGTGCCAAT
195 CCAACGCCATATCCCAGACATGGTCGTACATGGGAAATCACATATCCATG-C-AT
* * *
31042479 GCCATGTCCCAGAGATGGT-GTACATGGGACCTCTCATCTCGGTGCCAATACCATGTCCTAGACA
1 GCCATGTCCCAGACATGGTCGTACATGGGACCTCTCATCTCGGTGCCAACACCATGTCCCAGACA
* *
31042543 TGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
66 TGGTCTTACATGGGACCTCTCATCTCAGTGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGA
31042608 CCTCTCATAATCTCATAATGCCAATGCCATGTCCCAGACATGGTCTTACACTG-G-CTCACATAT
131 CCTCTC---ATCTC--AATGCCAATGCCATGTCCCAGACATGGTCTTACA-TGAGACTCACATAT
* * * * * * *
31042671 CGATATCGATGCCATATCTCAGATATGGTCTTACAT-GGAAATCACATATCACATG-TT
190 CGATACCAACGCCATATCCCAGACATGGTCGTACATGGGAAATCACATATC-CATGCAT
*
31042728 GCCATGTTCCA-ACCATGGTC
1 GCCATGTCCCAGA-CATGGTC
31042748 TTTTCCATCA
Statistics
Matches: 229, Mismatches: 31, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
248 1 0.00
249 124 0.54
250 18 0.08
251 9 0.04
252 42 0.18
254 33 0.14
255 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (247 bp):
GCCATGTCCCAGACATGGTCGTACATGGGACCTCTCATCTCGGTGCCAACACCATGTCCCAGACA
TGGTCTTACATGGGACCTCTCATCTCAGTGCCAATGCCAAGTCCCAGACATGGTCTTACATGGGA
CCTCTCATCTCAATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACTCACATATCGATAC
CAACGCCATATCCCAGACATGGTCGTACATGGGAAATCACATATCCATGCAT
Found at i:31045723 original size:23 final size:23
Alignment explanation
Indices: 31045697--31045747 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
31045687 ACCTACTTTC
*
31045697 TTACAGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
*
31045720 TTACAGTAGTAGTTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
31045743 TTACA
1 TTACA
31045748 CTTGGCACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:31049527 original size:16 final size:15
Alignment explanation
Indices: 31049486--31049528 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
31049476 AAAGATGATA
31049486 ATATTAATATATAATT
1 ATATTAAT-TATAATT
**
31049502 ATATCCATTATAATAT
1 ATATTAATTATAAT-T
31049518 ATATTAATTAT
1 ATATTAATTAT
31049529 TATCAGCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTAATTATAATT
Found at i:31053085 original size:22 final size:22
Alignment explanation
Indices: 31053059--31053103 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31053049 ATTATATGTA
31053059 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
* *
31053081 TTAATTTATATCTAATTTAATT
1 TTAATTCATATATAATTTAATT
31053103 T
1 T
31053104 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:31056005 original size:40 final size:39
Alignment explanation
Indices: 31055961--31056175 Score: 180
Period size: 41 Copynumber: 5.3 Consensus size: 39
31055951 ACTATGTTTT
* *
31055961 GCACTTAGTGTGCGATTTGAGATAACTTCGGCTATTTATG
1 GCACTTAGTGTGCGA-TTGAGATAGCTTCGGCTATATATG
* *
31056001 GCACTTAGTGTGCGATTGGGAATAGCTTCGGCTACATATG
1 GCACTTAGTGTGCGATTGAG-ATAGCTTCGGCTATATATG
* * * * *
31056041 GCACTTAATGTGTGAGACTGAGATAGCTTCGACTATGTAAG
1 GCACTT-A-GTGTGCGATTGAGATAGCTTCGGCTATATATG
* * *
31056082 GCACTTACTGTGCGGGATT-ATAATAGCTTCGGCTAGATATG
1 GCACTTAGTGTGC--GATTGA-GATAGCTTCGGCTATATATG
* * * * * *
31056123 GCACTTAGTGTGTTAGACTAAGATAACTTCGGCTATGTAAG
1 GCACTTAGTGTG--CGATTGAGATAGCTTCGGCTATATATG
31056164 GCACTTAGTGTG
1 GCACTTAGTGTG
31056176 TGGGATTATA
Statistics
Matches: 139, Mismatches: 27, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
39 8 0.06
40 39 0.28
41 81 0.58
42 11 0.08
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (39 bp):
GCACTTAGTGTGCGATTGAGATAGCTTCGGCTATATATG
Found at i:31056124 original size:82 final size:82
Alignment explanation
Indices: 31055978--31056198 Score: 302
Period size: 82 Copynumber: 2.7 Consensus size: 82
31055968 GTGTGCGATT
* * **
31055978 TGAGATAACTTCGGCTATTTATGGCACTTAGTGTGC--GATTGGGAATAGCTTCGGCTACATATG
1 TGAGATAACTTCGGCTATGTAAGGCACTTAGTGTGCGGGATT-ATAATAGCTTCGGCTACATATG
31056041 GCACTTAATGTGTGAGAC
65 GCACTTAATGTGTGAGAC
* * * *
31056059 TGAGATAGCTTCGACTATGTAAGGCACTTACTGTGCGGGATTATAATAGCTTCGGCTAGATATGG
1 TGAGATAACTTCGGCTATGTAAGGCACTTAGTGTGCGGGATTATAATAGCTTCGGCTACATATGG
* *
31056124 CACTTAGTGTGTTAGAC
66 CACTTAATGTGTGAGAC
* * *
31056141 TAAGATAACTTCGGCTATGTAAGGCACTTAGTGTGTGGGATTATAATAGCTTCAGCTA
1 TGAGATAACTTCGGCTATGTAAGGCACTTAGTGTGCGGGATTATAATAGCTTCGGCTA
31056199 TGCGATGGCA
Statistics
Matches: 122, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
81 31 0.25
82 87 0.71
83 4 0.03
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (82 bp):
TGAGATAACTTCGGCTATGTAAGGCACTTAGTGTGCGGGATTATAATAGCTTCGGCTACATATGG
CACTTAATGTGTGAGAC
Found at i:31056199 original size:41 final size:41
Alignment explanation
Indices: 31055986--31056200 Score: 170
Period size: 41 Copynumber: 5.3 Consensus size: 41
31055976 TTTGAGATAA
* * * **
31055986 CTTCGGCTATTTATGGCACTTA--GTGTGCGATTGGGAATAG
1 CTTCGGCTATGTAAGGCACTTAGTGTGTGGGATT-ATAATAG
** * * * * *
31056026 CTTCGGCTACATATGGCACTTAATGTGTGAGACTGA-GATAG
1 CTTCGGCTATGTAAGGCACTTAGTGTGTGGGA-TTATAATAG
* * *
31056067 CTTCGACTATGTAAGGCACTTACTGTGCGGGATTATAATAG
1 CTTCGGCTATGTAAGGCACTTAGTGTGTGGGATTATAATAG
* ** * *
31056108 CTTCGGCTA-GATATGGCACTTAGTGTGTTAGACTA-AGATAA
1 CTTCGGCTATG-TAAGGCACTTAGTGTGTGGGATTATA-ATAG
31056149 CTTCGGCTATGTAAGGCACTTAGTGTGTGGGATTATAATAG
1 CTTCGGCTATGTAAGGCACTTAGTGTGTGGGATTATAATAG
*
31056190 CTTCAGCTATG
1 CTTCGGCTATG
31056201 CGATGGCATT
Statistics
Matches: 138, Mismatches: 29, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
40 24 0.17
41 104 0.75
42 9 0.07
43 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (41 bp):
CTTCGGCTATGTAAGGCACTTAGTGTGTGGGATTATAATAG
Found at i:31064945 original size:41 final size:40
Alignment explanation
Indices: 31064839--31065076 Score: 187
Period size: 41 Copynumber: 5.8 Consensus size: 40
31064829 GTGAATTGAG
* * * * **
31064839 ATAGCTTCGGCTATTTATGGCACTTAATGTGC-GATTGGGA
1 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGGACT-ATA
* ** *
31064879 ATAGCTTCGGGTACATATGGCACTTAGTGTGCGTGACTA-A
1 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCG-GACTATA
* * *
31064919 GATAGCTTCGGCTATGTAAGGGACTTAGTGTGTGGGATTATA
1 -ATAGCTTCGGCTATGTAAGGCACTTAGTGTG-CGGACTATA
* * *
31064961 ATAGCTTCAGG-TATTTATGGCACTTAGTGTGCGAGACTGA-G
1 ATAGCTTC-GGCTATGTAAGGCACTTAGTGTGCG-GACT-ATA
*
31065002 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATTATA
1 ATAGCTTCGGCTATGTAAGGCACTTAGTGTGC-GGACTATA
* * *
31065043 ATAGCTTCGGCTATGCGATGGCATTTAGTGTGCG
1 ATAGCTTCGGCTATG-TAAGGCACTTAGTGTGCG
31065077 AAACATTGAG
Statistics
Matches: 160, Mismatches: 26, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
40 33 0.21
41 104 0.65
42 23 0.14
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (40 bp):
ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGGACTATA
Found at i:31064987 original size:82 final size:81
Alignment explanation
Indices: 31064818--31065077 Score: 292
Period size: 82 Copynumber: 3.2 Consensus size: 81
31064808 ACTATGTTTA
* * * * * * **
31064818 GCACTTAGTGTGTGA-ATTGAGATAGCTTCGGCTATTTATGGCACTTAATGTGC--GATTGGGAA
1 GCACTTAGTGTGCGAGACTAAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATT-ATAA
*
31064880 TAGCTTCGGGTACATATG
65 TAGCTTC-GGTATATATG
* * **
31064898 GCACTTAGTGTGCGTGACTAAGATAGCTTCGGCTATGTAAGGGACTTAGTGTGTGGGATTATAAT
1 GCACTTAGTGTGCGAGACTAAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATTATAAT
*
31064963 AGCTTCAGGTATTTATG
66 AGCTTC-GGTATATATG
*
31064980 GCACTTAGTGTGCGAGACTGAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATTATAAT
1 GCACTTAGTGTGCGAGACTAAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATTATAAT
**
31065045 AGCTTCGGCTATGCGATG
66 AGCTTCGG-TAT-ATATG
*
31065063 GCATTTAGTGTGCGA
1 GCACTTAGTGTGCGA
31065078 AACATTGAGT
Statistics
Matches: 153, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
80 13 0.08
81 33 0.22
82 86 0.56
83 21 0.14
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (81 bp):
GCACTTAGTGTGCGAGACTAAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATTATAAT
AGCTTCGGTATATATG
Found at i:31072299 original size:51 final size:51
Alignment explanation
Indices: 31072239--31072409 Score: 184
Period size: 51 Copynumber: 3.4 Consensus size: 51
31072229 GATGAACACG
*
31072239 TGTGTAGTACTATGTGAAGACTACTACGTGTATCGATAAA-AAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA-AAAGAAATGGTCACA
* * * *** *
31072290 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAAGAAATGGTCACA
* * * *
31072341 TGTGTAGTACTATGTGAAGGCTACTACATGTATCG-AATGATAATAGTAACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAAGA-AATGGTCACA
* *
31072392 TGGGTGGTACTATGTGAA
1 TGTGTAGTACTATGTGAA
31072410 AACCCCCAAA
Statistics
Matches: 97, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
50 6 0.06
51 91 0.94
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAAGAAATGGTCACA
Found at i:31074577 original size:17 final size:18
Alignment explanation
Indices: 31074552--31074594 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
31074542 GGAATCTCAC
* *
31074552 TCTTCTTCATTTTA-ATT
1 TCTTTTTCATTTGATATT
*
31074569 TCTTTTTCATTTGATTTT
1 TCTTTTTCATTTGATATT
31074587 TCTTTTTC
1 TCTTTTTC
31074595 TTTCCTCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.70
Consensus pattern (18 bp):
TCTTTTTCATTTGATATT
Found at i:31074640 original size:28 final size:27
Alignment explanation
Indices: 31074609--31074672 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
31074599 CTCTCACACT
*
31074609 TTTTTTAATATCTCTTTCATTTTT-TTTC
1 TTTTTTAATA-CACTTTC-TTTTTCTTTC
*
31074637 TTTTTTTATACACTTTCTTTTTCTTTC
1 TTTTTTAATACACTTTCTTTTTCTTTC
*
31074664 CTTTTTAAT
1 TTTTTTAAT
31074673 TTCCTCACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 5 0.16
27 17 0.55
28 9 0.29
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTTTAATACACTTTCTTTTTCTTTC
Found at i:31077187 original size:31 final size:31
Alignment explanation
Indices: 31077089--31077204 Score: 117
Period size: 31 Copynumber: 3.7 Consensus size: 31
31077079 TGAGATGCTT
* * * **
31077089 TAATGCATGACTTCATTAAATGCTACTCACA
1 TAATGCAAGACATAATTAAATGCTAAACACA
*
31077120 TAATGCAAGACAAAATTTAAAGATGC-AAACACA
1 TAATGCAAGACATAA-TT-AA-ATGCTAAACACA
* *
31077153 TAATGCAAGTCATAATTAAATGCTAAACATA
1 TAATGCAAGACATAATTAAATGCTAAACACA
*
31077184 TAATGCAAGGCATAATTAAAT
1 TAATGCAAGACATAATTAAAT
31077205 ATGCAAGTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
30 4 0.06
31 39 0.55
32 4 0.06
33 20 0.28
34 4 0.06
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.27
Consensus pattern (31 bp):
TAATGCAAGACATAATTAAATGCTAAACACA
Found at i:31082919 original size:32 final size:33
Alignment explanation
Indices: 31082873--31082934 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
31082863 CTAAATGCAA
*
31082873 AACATATAATGTAAGACATAA-TTAAAGATGCT
1 AACATATAAGGTAAGACATAATTTAAAGATGCT
31082905 AACATATAAGGTAAGACATAATTTAAAGAT
1 AACATATAAGGTAAGACATAATTTAAAGAT
31082935 ACAAAGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (33 bp):
AACATATAAGGTAAGACATAATTTAAAGATGCT
Found at i:31095588 original size:33 final size:34
Alignment explanation
Indices: 31095540--31095608 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
31095530 ATACAACAAG
* *
31095540 CAGTGACAGTCTGGGCCTGAGCCCTATTCAGTAA
1 CAGTGACAGTCTGGGCCTGAGCCCAATACAGTAA
* *
31095574 CAGT-ACAGTGTGGGCCTTAGCCCAATACAGTAA
1 CAGTGACAGTCTGGGCCTGAGCCCAATACAGTAA
31095607 CA
1 CA
31095609 ATGTGGGCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 27 0.87
34 4 0.13
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.22
Consensus pattern (34 bp):
CAGTGACAGTCTGGGCCTGAGCCCAATACAGTAA
Found at i:31095615 original size:28 final size:28
Alignment explanation
Indices: 31095573--31095633 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
31095563 CTATTCAGTA
* *
31095573 ACAGT-ACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTACCCCAAT
31095600 ACAGTAACAATGTGGGCCTTACCCCAAT
1 ACAGTAACAATGTGGGCCTTACCCCAAT
31095628 ACAGTA
1 ACAGTA
31095634 TCCGTATAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTACCCCAAT
Found at i:31095697 original size:21 final size:21
Alignment explanation
Indices: 31095671--31095723 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
31095661 CCCAATCCAG
31095671 CCAACACACCACTCCGTACCA
1 CCAACACACCACTCCGTACCA
31095692 CCAACACACCACTCCGTACCA
1 CCAACACACCACTCCGTACCA
31095713 CCAACACACCA
1 CCAACACACCA
31095724 TGTGGGGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.53, G:0.04, T:0.08
Consensus pattern (21 bp):
CCAACACACCACTCCGTACCA
Found at i:31096169 original size:27 final size:27
Alignment explanation
Indices: 31095977--31096172 Score: 252
Period size: 27 Copynumber: 7.3 Consensus size: 27
31095967 GCGTATAACA
* *
31095977 GTCATTTTACCCTGTAGGGGTAATTCA
1 GTCATTTTACCCTGTGGGGGTAATTCG
* *
31096004 GTCATTTTACCCTATGGGAGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCG
* *
31096031 GCCATTTTACCCAGTGGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCG
* ** *
31096058 ATCATTTTACCCTGTGGGCTTAATTTG
1 GTCATTTTACCCTGTGGGGGTAATTCG
31096085 AG-CATTTTACCCTGTGGGGGTAATTCG
1 -GTCATTTTACCCTGTGGGGGTAATTCG
* *
31096112 ATCATTTTACCCTGTGGGGGTAATTCA
1 GTCATTTTACCCTGTGGGGGTAATTCG
31096139 GTCATTTTACCCTGTGGGGGTAA-TCTG
1 GTCATTTTACCCTGTGGGGGTAATTC-G
31096166 GTCATTT
1 GTCATTT
31096173 ATTGATCTCT
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
26 2 0.01
27 142 0.99
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCCTGTGGGGGTAATTCG
Found at i:31098916 original size:41 final size:41
Alignment explanation
Indices: 31098855--31099134 Score: 231
Period size: 41 Copynumber: 6.8 Consensus size: 41
31098845 ACACATAATT
* ** *
31098855 ATACCCTTGAATTGTGCTTACATTCCCCTGTTTGTACTTCG
1 ATACCCCTGAATTGCACTTACATGCCCCTGTTTGTACTTCG
*
31098896 ATACCCTTGAATTGCACTTACATGCCCCTGTTTGTACTTCG
1 ATACCCCTGAATTGCACTTACATGCCCCTGTTTGTACTTCG
* * * * * **
31098937 ATATCCCTGAATTACACTTACGTGCCCTTATTCATACTTCG
1 ATACCCCTGAATTGCACTTACATGCCCCTGTTTGTACTTCG
* ** ** * * *
31098978 GTATGCCTGAATTGCACTTATGTGCCCTTTTTTTGTACTTTG
1 ATACCCCTGAATTGCACTTACATGCCC-CTGTTTGTACTTCG
* ** *
31099020 GTACCCCTGAATTGCACTTATGTGCCCCTG-TTGCACTTC-
1 ATACCCCTGAATTGCACTTACATGCCCCTGTTTGTACTTCG
* * * *
31099059 AGTACCCCCTAAATTGCACTTACATGCCTCTATTTGTAGTTCG
1 A-TA-CCCCTGAATTGCACTTACATGCCCCTGTTTGTACTTCG
* * * *
31099102 GTACCCCTGAATTGCACATACGTGCCCTTGTTT
1 ATACCCCTGAATTGCACTTACATGCCCCTGTTT
31099135 AAACTCTGAT
Statistics
Matches: 194, Mismatches: 40, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
40 9 0.05
41 141 0.73
42 44 0.23
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (41 bp):
ATACCCCTGAATTGCACTTACATGCCCCTGTTTGTACTTCG
Found at i:31098944 original size:20 final size:19
Alignment explanation
Indices: 31098880--31098945 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
31098870 GCTTACATTC
31098880 CCCTGTTTGTACTTCGATA
1 CCCTGTTTGTACTTCGATA
* * *
31098899 CCCTTGAATTGCACTTAC-ATGC
1 CCC-TG-TTTGTACTT-CGAT-A
31098921 CCCTGTTTGTACTTCGATA
1 CCCTGTTTGTACTTCGATA
31098940 TCCCTG
1 -CCCTG
31098946 AATTACACTT
Statistics
Matches: 35, Mismatches: 6, Indels: 11
0.67 0.12 0.21
Matches are distributed among these distances:
19 4 0.11
20 16 0.46
21 11 0.31
22 4 0.11
ACGTcount: A:0.17, C:0.30, G:0.15, T:0.38
Consensus pattern (19 bp):
CCCTGTTTGTACTTCGATA
Found at i:31099046 original size:124 final size:124
Alignment explanation
Indices: 31098885--31099130 Score: 291
Period size: 124 Copynumber: 2.0 Consensus size: 124
31098875 CATTCCCCTG
* * * *
31098885 TTTGTACTTCGATACCCTTGAATTGCACTTACATGCCCCTGTTTGTACTTC-GATA-TCCCTGAA
1 TTTGTACTTCGATACCCCTGAATTGCACTTACATGCCCCTG-TTGCACTTCAG-TACCCCCTAAA
* ** * *
31098948 TTACACTTACGTGCC-CTTATTCATACTTCGGTATGCCTGAATTGCACTTATGTGCCCTTTT
64 TTACACTTACATGCCTC-TATTCATACTTCGGTACCCCTGAATTGCACATACGTGCCCTTTT
* * **
31099009 TTTGTACTTTGGTACCCCTGAATTGCACTTATGTGCCCCTGTTGCACTTCAGTACCCCCTAAATT
1 TTTGTACTTCGATACCCCTGAATTGCACTTACATGCCCCTGTTGCACTTCAGTACCCCCTAAATT
* ** *
31099074 GCACTTACATGCCTCTATTTGTAGTTCGGTACCCCTGAATTGCACATACGTGCCCTT
66 ACACTTACATGCCTCTATTCATACTTCGGTACCCCTGAATTGCACATACGTGCCCTT
31099131 GTTTAAACTC
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
123 10 0.10
124 91 0.89
125 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.37
Consensus pattern (124 bp):
TTTGTACTTCGATACCCCTGAATTGCACTTACATGCCCCTGTTGCACTTCAGTACCCCCTAAATT
ACACTTACATGCCTCTATTCATACTTCGGTACCCCTGAATTGCACATACGTGCCCTTTT
Found at i:31099066 original size:19 final size:20
Alignment explanation
Indices: 31099020--31099080 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 20
31099010 TTGTACTTTG
31099020 GTACCCCTGAATTGCACTTAT
1 GTACCCCTG-ATTGCACTTAT
*
31099041 GTGCCCCTG-TTGCACTTCA-
1 GTACCCCTGATTGCACTT-AT
*
31099060 GTACCCCCTAAATTGCACTTA
1 GTA-CCCCT-GATTGCACTTA
31099081 CATGCCTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 10 0.30
20 6 0.18
21 9 0.27
22 8 0.24
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (20 bp):
GTACCCCTGATTGCACTTAT
Found at i:31101945 original size:38 final size:39
Alignment explanation
Indices: 31101903--31101990 Score: 117
Period size: 40 Copynumber: 2.3 Consensus size: 39
31101893 GAAATTCTTG
31101903 TTATAATTATTGCAATTGT-AA-TTTAGGATCAAATATTA
1 TTATAATTATTGCAATTGTAAATTTTAGG-TCAAATATTA
* * *
31101941 TTATAATTATTGTAATTTTAAATTTTTTGGTCAAATATTA
1 TTATAATTATTGCAATTGTAAA-TTTTAGGTCAAATATTA
31101981 TTATAATTAT
1 TTATAATTAT
31101991 GGTAATTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 17 0.39
39 2 0.05
40 20 0.45
41 5 0.11
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (39 bp):
TTATAATTATTGCAATTGTAAATTTTAGGTCAAATATTA
Found at i:31102021 original size:17 final size:18
Alignment explanation
Indices: 31101999--31102034 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
31101989 ATGGTAATTA
31101999 TAATTATTAT-ATTTGGT
1 TAATTATTATGATTTGGT
31102016 TAATTATTATGATTTGGT
1 TAATTATTATGATTTGGT
31102034 T
1 T
31102035 CATATAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (18 bp):
TAATTATTATGATTTGGT
Found at i:31105473 original size:12 final size:11
Alignment explanation
Indices: 31105456--31105490 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
31105446 TTAAGGATGG
31105456 GGGAAGGGGAA
1 GGGAAGGGGAA
31105467 TGGGAAGGGGAA
1 -GGGAAGGGGAA
*
31105479 GGGAAAGGGAA
1 GGGAAGGGGAA
31105490 G
1 G
31105491 ATCGGGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.60, T:0.03
Consensus pattern (11 bp):
GGGAAGGGGAA
Found at i:31105488 original size:17 final size:18
Alignment explanation
Indices: 31105455--31105490 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
31105445 GTTAAGGATG
*
31105455 GGGGAAGGGGAATGGGAA
1 GGGGAAGGGGAAAGGGAA
31105473 GGGGAA-GGGAAAGGGAA
1 GGGGAAGGGGAAAGGGAA
31105490 G
1 G
31105491 ATCGGGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.61, T:0.03
Consensus pattern (18 bp):
GGGGAAGGGGAAAGGGAA
Found at i:31105752 original size:28 final size:28
Alignment explanation
Indices: 31105712--31105766 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
31105702 TGAATATGTG
31105712 ATATTCATTAATACTGCTTTAAGTCATA
1 ATATTCATTAATACTGCTTTAAGTCATA
31105740 ATATTCATTAATACTGCTTTAAGTCAT
1 ATATTCATTAATACTGCTTTAAGTCAT
31105767 TAATTTGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.44
Consensus pattern (28 bp):
ATATTCATTAATACTGCTTTAAGTCATA
Found at i:31110176 original size:38 final size:39
Alignment explanation
Indices: 31110125--31110200 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 39
31110115 TAGTACTTCG
31110125 TTACTTTCACTGATGATTTTAGTAGA-AAGGGTATGTTA
1 TTACTTTCACTGATGATTTTAGTAGATAAGGGTATGTTA
* *
31110163 TTACTTTCGCTGATGATTTTAGTAGATATGGGTATGTT
1 TTACTTTCACTGATGATTTTAGTAGATAAGGGTATGTT
31110201 TATCTAATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 25 0.71
39 10 0.29
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (39 bp):
TTACTTTCACTGATGATTTTAGTAGATAAGGGTATGTTA
Found at i:31115402 original size:24 final size:24
Alignment explanation
Indices: 31115375--31115420 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
31115365 ACCTGAATCA
*
31115375 TGTAAACCCTAATGACATGTCATT
1 TGTAAACCCTAATGAAATGTCATT
31115399 TGTAAACCCTAATGAAATGTCA
1 TGTAAACCCTAATGAAATGTCA
31115421 ATTTAGGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (24 bp):
TGTAAACCCTAATGAAATGTCATT
Found at i:31116043 original size:7 final size:7
Alignment explanation
Indices: 31116031--31116056 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31116021 ATCTTTCTGT
31116031 TTCTTAA
1 TTCTTAA
31116038 TTCTTAA
1 TTCTTAA
31116045 TTCTTAA
1 TTCTTAA
31116052 TTCTT
1 TTCTT
31116057 TCATTGTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (7 bp):
TTCTTAA
Found at i:31117417 original size:39 final size:39
Alignment explanation
Indices: 31117363--31117440 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
31117353 GCTAAGATTG
* *
31117363 AACCATGACCCGATAATGTCAAACGTGTATTCATCGCTC
1 AACCATCACCCGATAATGTCAAACATGTATTCATCGCTC
*
31117402 AACCATCACCCGATAATGTCAAATATGTATTCATCGCTC
1 AACCATCACCCGATAATGTCAAACATGTATTCATCGCTC
31117441 GTAGGGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (39 bp):
AACCATCACCCGATAATGTCAAACATGTATTCATCGCTC
Found at i:31117916 original size:19 final size:20
Alignment explanation
Indices: 31117892--31117934 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
31117882 TCACTTGAGT
31117892 TCAAGTCAGCTCA-TCGAGC
1 TCAAGTCAGCTCATTCGAGC
31117911 TCAAGTCAGCTCATTCGAGC
1 TCAAGTCAGCTCATTCGAGC
31117931 TCAA
1 TCAA
31117935 TTCATCTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (20 bp):
TCAAGTCAGCTCATTCGAGC
Found at i:31126308 original size:25 final size:25
Alignment explanation
Indices: 31126274--31126333 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
31126264 CTGCAACTCA
* *
31126274 TGAGAGCATAATGATTTGTAAATCG
1 TGAGAGCATAATAATTTATAAATCG
* **
31126299 TGAGAGCATACTAATTTATAGCTCG
1 TGAGAGCATAATAATTTATAAATCG
31126324 TGAGAGCATA
1 TGAGAGCATA
31126334 TCAATCTACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (25 bp):
TGAGAGCATAATAATTTATAAATCG
Found at i:31130525 original size:15 final size:15
Alignment explanation
Indices: 31130505--31130534 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31130495 AGATTTCAAT
*
31130505 TTGGTGTTGTGACTA
1 TTGGTGGTGTGACTA
31130520 TTGGTGGTGTGACTA
1 TTGGTGGTGTGACTA
31130535 GCTATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.07, G:0.37, T:0.43
Consensus pattern (15 bp):
TTGGTGGTGTGACTA
Found at i:31133353 original size:15 final size:15
Alignment explanation
Indices: 31133331--31133363 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
31133321 ATCGAAGTTT
31133331 AAAAAAA-TCAAAAA
1 AAAAAAATTCAAAAA
31133345 AAAAGAAATTCAAAAA
1 AAAA-AAATTCAAAAA
31133361 AAA
1 AAA
31133364 GGTCAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 3 0.18
16 10 0.59
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (15 bp):
AAAAAAATTCAAAAA
Found at i:31133359 original size:25 final size:26
Alignment explanation
Indices: 31133305--31133362 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
31133295 AGAGAATTTG
** * *
31133305 AAAAAAATTCAAAAAAATCGAAGTTT
1 AAAAAAATTCAAAAAAAAAGAAATTC
31133331 AAAAAAA-TCAAAAAAAAAGAAATTC
1 AAAAAAATTCAAAAAAAAAGAAATTC
31133356 AAAAAAA
1 AAAAAAA
31133363 AGGTCAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (26 bp):
AAAAAAATTCAAAAAAAAAGAAATTC
Found at i:31133360 original size:26 final size:25
Alignment explanation
Indices: 31133305--31133374 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
31133295 AGAGAATTTG
* ** *
31133305 AAAAAAATTCAAAAAAATCGAAGTT
1 AAAAAAAATCAAAAAAAAAGAAATT
*
31133330 TAAAAAAATCAAAAAAAAAGAAATT
1 AAAAAAAATCAAAAAAAAAGAAATT
31133355 CAAAAAAAAGGTCAAAAAAA
1 -AAAAAAAA--TCAAAAAAA
31133375 GGTGAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 20 0.56
26 7 0.19
28 9 0.25
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (25 bp):
AAAAAAAATCAAAAAAAAAGAAATT
Found at i:31136215 original size:10 final size:9
Alignment explanation
Indices: 31136200--31136256 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 9
31136190 CATGTGGTTC
31136200 AGCTCACTTG
1 AGCTCA-TTG
* *
31136210 AGCTCAAGTC
1 AGCTC-ATTG
31136220 AGCTCATTCG
1 AGCTCATT-G
*
31136230 AGCTCAATTC
1 AGCTC-ATTG
31136240 AGCTCATTG
1 AGCTCATTG
31136249 AGCTCATT
1 AGCTCATT
31136257 ATTAGCTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
9 13 0.34
10 21 0.55
11 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (9 bp):
AGCTCATTG
Found at i:31136223 original size:20 final size:19
Alignment explanation
Indices: 31136198--31136254 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 19
31136188 TTCATGTGGT
31136198 TCAGCTCACTTGAGCTCAAG
1 TCAGCTCA-TTGAGCTCAAG
*
31136218 TCAGCTCATTCGAGCTCAAT
1 TCAGCTCATT-GAGCTCAAG
31136238 TCAGCTCATTGAGCTCA
1 TCAGCTCATTGAGCTCA
31136255 TTATTAGCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 9 0.26
20 26 0.74
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (19 bp):
TCAGCTCATTGAGCTCAAG
Found at i:31136263 original size:20 final size:21
Alignment explanation
Indices: 31136197--31136275 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 21
31136187 TTTCATGTGG
31136197 TTCAGCTCACTTGAGCTCA--A
1 TTCAGCTCA-TTGAGCTCATTA
*
31136217 GTCAGCTCATTCGAGCTCA--A
1 TTCAGCTCATT-GAGCTCATTA
31136237 TTCAGCTCATTGAGCTCATTA
1 TTCAGCTCATTGAGCTCATTA
*
31136258 TT-AGCTC-TTTAGCTCATT
1 TTCAGCTCATTGAGCTCATT
31136276 TAATTTTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
19 19 0.36
20 31 0.58
21 3 0.06
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (21 bp):
TTCAGCTCATTGAGCTCATTA
Found at i:31143014 original size:20 final size:20
Alignment explanation
Indices: 31142991--31143031 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
31142981 CCTCAACTGT
*
31142991 CTCGACGCATAAGCAACTAC
1 CTCGACGCATAAGAAACTAC
*
31143011 CTCGGCGCATAAGAAACTAC
1 CTCGACGCATAAGAAACTAC
31143031 C
1 C
31143032 CTAACCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.15
Consensus pattern (20 bp):
CTCGACGCATAAGAAACTAC
Found at i:31144732 original size:15 final size:15
Alignment explanation
Indices: 31144712--31144740 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31144702 TCCCTCAAGT
31144712 CTGATTGCAAACAAA
1 CTGATTGCAAACAAA
31144727 CTGATTGCAAACAA
1 CTGATTGCAAACAA
31144741 CAATGGCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (15 bp):
CTGATTGCAAACAAA
Found at i:31154062 original size:17 final size:16
Alignment explanation
Indices: 31154042--31154080 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
31154032 CAAATTAACC
*
31154042 TTTTATTCACATAATTT
1 TTTTATT-ACATAATTG
31154059 TTTTA-TACATAATTG
1 TTTTATTACATAATTG
31154074 TTTTATT
1 TTTTATT
31154081 TCTTAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 13 0.65
16 2 0.10
17 5 0.25
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTATTACATAATTG
Found at i:31166430 original size:44 final size:44
Alignment explanation
Indices: 31166381--31166738 Score: 195
Period size: 44 Copynumber: 7.7 Consensus size: 44
31166371 TTACAGATCT
* **
31166381 TATCTCCATGAGATTACAGTGGAGCAGATTGAAGCTATTAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCC
** ** * *
31166425 TATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAAAGATCA
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAA-ATCC
** * *
31166469 TATCTCTTTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCT
1 TATCTCCCTGAGA-TTACAGT---G--GA--G---CAGATTGAAGCTAGAAATCC
* * * *
31166523 TATCTCCTTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCC
* ** *
31166567 TATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATA-AAGGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAA--ATCC
** * *
31166611 TATCTCTTTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCT
1 TATCTCCCTGAGA-TTACAGT---G--GA--G---CAGATTGAAGCTAGAAATCC
* * *
31166665 TATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCC
*
31166709 TATCTCCCTGAGATTACAGTGGAGCGGATT
1 TATCTCCCTGAGATTACAGTGGAGCAGATT
31166739 AAAACAAAGG
Statistics
Matches: 237, Mismatches: 47, Indels: 60
0.69 0.14 0.17
Matches are distributed among these distances:
42 1 0.00
43 11 0.05
44 152 0.64
47 4 0.02
49 7 0.03
51 4 0.02
54 46 0.19
55 10 0.04
56 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCC
Found at i:31166633 original size:142 final size:142
Alignment explanation
Indices: 31166377--31166796 Score: 714
Period size: 142 Copynumber: 3.0 Consensus size: 142
31166367 GAAATTACAG
* *
31166377 ATCTTATCTCCATGAGATTACAGTGGAGCAGATTGAAGCTATTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCATGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
* * *
31166442 AGTGGAGTGGATTAAAATAAAAGATCATATCTCTTTGAAGTTACAGTAGAGTAGATCGCATCAGA
66 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGTAGATCGCATCAGA
31166507 TTGAAGCCAGAA
131 TTGAAGCCAGAA
* *
31166519 ATCTTATCTCCTTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCATGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
31166584 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGTAGATCGCATCAGA
66 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGTAGATCGCATCAGA
31166649 TTGAAGCCAGAA
131 TTGAAGCCAGAA
* *
31166661 ATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCATGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
* * **
31166726 AGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGCGGAGTAGATCGCATCAGA
66 AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGTAGATCGCATCAGA
*
31166791 ATGAAG
131 TTGAAG
31166797 TTACAATAGC
Statistics
Matches: 263, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 263 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (142 bp):
ATCTTATCTCCATGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAGTAGATCGCATCAGA
TTGAAGCCAGAA
Found at i:31166757 original size:44 final size:44
Alignment explanation
Indices: 31166660--31166781 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 44
31166650 TGAAGCCAGA
* * * *
31166660 AATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAACAAGT
* * *
31166704 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAG-
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAC-AAGT
* * *
31166748 GATCTTATCTCTCTGA-AGTTACAGCGGAGTAGAT
1 AATCTTATCTCCCTGAGA-TTACAGCGGAGCAGAT
31166782 CGCATCAGAA
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
43 1 0.02
44 60 0.95
45 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAACAAGT
Found at i:31170427 original size:28 final size:28
Alignment explanation
Indices: 31170395--31170451 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
31170385 TATGGAAAGT
31170395 ATGAACTTAAAGGCATTATGTTCATGTA
1 ATGAACTTAAAGGCATTATGTTCATGTA
31170423 ATGAACTTAAAGGCATTATGTTCATGTA
1 ATGAACTTAAAGGCATTATGTTCATGTA
31170451 A
1 A
31170452 ATCTAGCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (28 bp):
ATGAACTTAAAGGCATTATGTTCATGTA
Found at i:31171622 original size:13 final size:14
Alignment explanation
Indices: 31171598--31171626 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31171588 ATTGGTTGAA
31171598 TTGAATTTGGTCAT
1 TTGAATTTGGTCAT
31171612 TTGAA-TTGGTCAT
1 TTGAATTTGGTCAT
31171625 TT
1 TT
31171627 TATGCATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (14 bp):
TTGAATTTGGTCAT
Found at i:31178795 original size:27 final size:27
Alignment explanation
Indices: 31178765--31179001 Score: 223
Period size: 27 Copynumber: 8.8 Consensus size: 27
31178755 TATAACAGTT
*
31178765 ATTTTACCCTAT-GGGGGTATTTTAGTA
1 ATTTTACCC-ATCGAGGGTATTTTAGTA
* * * *
31178792 ATTTTACACTTCGAAGGTA-TTTCGATA
1 ATTTTACCCATCGAGGGTATTTTAG-TA
* *
31178819 ATTTTAACCATCGAGGGTA-TTTCGATA
1 ATTTTACCCATCGAGGGTATTTTAG-TA
* *
31178846 ATTTTATCCATTGAGGGTATTTTAGTA
1 ATTTTACCCATCGAGGGTATTTTAGTA
* *
31178873 ATTTTACCCATCAAGGGTA-TTTCGATA
1 ATTTTACCCATCGAGGGTATTTTAG-TA
*
31178900 ATTTTACCTATCGAGGGTATTTTAGTA
1 ATTTTACCCATCGAGGGTATTTTAGTA
* * *
31178927 ATTTTACGCATTGAGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTTAGTA
* * *
31178954 ATTTTACCCATC-AGAGTTATTTCAATA
1 ATTTTACCCATCGAG-GGTATTTTAGTA
*
31178981 ATTTTACCTATCGAGGGTATT
1 ATTTTACCCATCGAGGGTATT
31179002 ATGGTCATTT
Statistics
Matches: 174, Mismatches: 29, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
26 11 0.06
27 153 0.88
28 10 0.06
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTTAGTA
Found at i:31178892 original size:81 final size:81
Alignment explanation
Indices: 31178779--31179001 Score: 312
Period size: 81 Copynumber: 2.8 Consensus size: 81
31178769 TACCCTATGG
* *
31178779 GGGTATTTTAGTAATTTTACACTTCGAA-GGTATTTCGATAATTTTAACC-ATCGAGGGTATTTC
1 GGGTATTTTAGTAATTTTACCCATC-AAGGGTATTTCGATAATTTT-ACCTATCGAGGGTATTT-
31178842 GA-TAATTTTATC-CATTGA
63 GAGTAATTTTA-CGCATTGA
*
31178860 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGATAATTTTACCTATCGAGGGTATTTTAG
1 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGATAATTTTACCTATCGAGGGTATTTGAG
31178925 TAATTTTACGCATTGA
66 TAATTTTACGCATTGA
* * *
31178941 GGGTATTTCAGTAATTTTACCCATC-AGAGTTATTTCAATAATTTTACCTATCGAGGGTATT
1 GGGTATTTTAGTAATTTTACCCATCAAG-GGTATTTCGATAATTTTACCTATCGAGGGTATT
31179002 ATGGTCATTT
Statistics
Matches: 131, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
80 9 0.07
81 122 0.93
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (81 bp):
GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGATAATTTTACCTATCGAGGGTATTTGAG
TAATTTTACGCATTGA
Found at i:31179039 original size:81 final size:80
Alignment explanation
Indices: 31178779--31179041 Score: 266
Period size: 81 Copynumber: 3.2 Consensus size: 80
31178769 TACCCTATGG
* * * *
31178779 GGGTATTTTAGTAATTTTACACTTCGAA-GGTATTTCGATAATTTTAACC-ATCGAGGGTATT-T
1 GGGTATTTCAGTAATTTTACCCATC-AAGGGTATTTCAATAATTTT-ACCTATCGAGGGTATTAT
* * *
31178841 CGATAATTTTATCCATTGA
64 AG-TAATTTTA-CAATTCA
* * *
31178860 GGGTATTTTAGTAATTTTACCCATCAAGGGTATTTCGATAATTTTACCTATCGAGGGTATTTTAG
1 GGGTATTTCAGTAATTTTACCCATCAAGGGTATTTCAATAATTTTACCTATCGAGGGTATTATAG
* *
31178925 TAATTTTACGCATTGA
66 TAATTTTAC-AATTCA
* *
31178941 GGGTATTTCAGTAATTTTACCCATC-AGAGTTATTTCAATAATTTTACCTATCGAGGGTATTATG
1 GGGTATTTCAGTAATTTTACCCATCAAG-GGTATTTCAATAATTTTACCTATCGAGGGTATTATA
*
31179005 GTCATTTTA-AATTACA
65 GTAATTTTACAATT-CA
* *
31179021 GAGGTATTTCGGTCATTTTAC
1 G-GGTATTTCAGTAATTTTAC
31179042 AACCTTTCCG
Statistics
Matches: 162, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
79 3 0.02
80 10 0.06
81 147 0.91
82 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (80 bp):
GGGTATTTCAGTAATTTTACCCATCAAGGGTATTTCAATAATTTTACCTATCGAGGGTATTATAG
TAATTTTACAATTCA
Found at i:31179420 original size:22 final size:21
Alignment explanation
Indices: 31179374--31179423 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
31179364 CATTACGGCT
*
31179374 ATAAAAAGCCATTGAAATACT
1 ATAAAAAGCCATTGAAATACA
*
31179395 ATAAAAAGGCATTGAGAA-ATCA
1 ATAAAAAGCCATTGA-AATA-CA
31179417 ATAAAAA
1 ATAAAAA
31179424 ACTGAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (21 bp):
ATAAAAAGCCATTGAAATACA
Found at i:31180436 original size:20 final size:21
Alignment explanation
Indices: 31180399--31180439 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
31180389 TATGTAATCA
31180399 TTATTTTCATAATCTATATAT
1 TTATTTTCATAATCTATATAT
31180420 TTATTTT-ATAA-CTTATATAT
1 TTATTTTCATAATC-TATATAT
31180440 GTACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 11 0.58
21 7 0.37
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTCATAATCTATATAT
Found at i:31180505 original size:12 final size:12
Alignment explanation
Indices: 31180433--31180508 Score: 57
Period size: 12 Copynumber: 6.2 Consensus size: 12
31180423 TTTTATAACT
* *
31180433 TATATATGTACA
1 TATATATTTATA
*
31180445 TATATATATATA
1 TATATATTTATA
31180457 TATATATTT-TAA
1 TATATATTTAT-A
*
31180469 TACATATTT-TA
1 TATATATTTATA
* *
31180480 TAATCTAATCTATA
1 T-ATAT-ATTTATA
31180494 TATATATTTATA
1 TATATATTTATA
31180506 TAT
1 TAT
31180509 TTTTCTTTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 3 0.06
12 39 0.76
13 6 0.12
14 3 0.06
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.51
Consensus pattern (12 bp):
TATATATTTATA
Found at i:31187319 original size:22 final size:21
Alignment explanation
Indices: 31187284--31187341 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
31187274 AAAGGATATA
* *
31187284 TACAAATTAAATCTCTAAAAT
1 TACAAATCATATCTCTAAAAT
*
31187305 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAAAT
* *
31187328 TGCACATCATATCT
1 TACAAATCATATCT
31187342 TGATAGAGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (21 bp):
TACAAATCATATCTCTAAAAT
Done.