Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 132 of 250
Found at i:42674509 original size:100 final size:100
Alignment explanation
Indices: 42674313--42674707 Score: 433
Period size: 100 Copynumber: 4.1 Consensus size: 100
42674303 CGCTGAGGTA
*** *
42674313 TTTTCAATTTCCATTTTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTG
1 TTTTCAATTTCTGCTTTT-AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* * ** *
42674378 AGCCTCGGGGCACGCCAAGGTATTTTTAATTTATGT
65 AGCCTCAGGACACGCTGAGGTATTTTCAATTTATGT
* *
42674414 TTTTCAATTTCTGCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 TTTTCAATTTCTGCTTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* *
42674479 GCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGT
66 GCCTCAGGACACGCTGAGGTATTTTCAATTTATGT
* ** * *
42674514 TTTTCAATTTTTGCCTTACAAATTCTGCTTTTC--AAATCAACTCATATTGCGAGAGGTGAGTTG
1 TTTTCAATTTCTG-CTTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
42674577 AGCCTCAGGACACGCTGAGGTATTTTC-A---A---
65 AGCCTCAGGACACGCTGAGGTATTTTCAATTTATGT
* * * *
42674606 TTTTC-A-TT-T--TTTTAATTTATG-TTTCTAAAAAATAAATTCATATTGCGAGAAGTGAGTTG
1 TTTTCAATTTCTGCTTTTAATTTATGCTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* *
42674665 AGCCTCAGGACACGCTGAGGTAGTTTCAATTTTTGT
65 AGCCTCAGGACACGCTGAGGTATTTTCAATTTATGT
*
42674701 TTGTCAA
1 TTTTCAA
42674708 AAATCAACTC
Statistics
Matches: 253, Mismatches: 29, Indels: 29
0.81 0.09 0.09
Matches are distributed among these distances:
85 3 0.01
86 9 0.04
88 53 0.21
89 2 0.01
90 2 0.01
91 1 0.00
92 5 0.02
95 4 0.02
96 1 0.00
98 1 0.00
99 56 0.22
100 86 0.34
101 30 0.12
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (100 bp):
TTTTCAATTTCTGCTTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
GCCTCAGGACACGCTGAGGTATTTTCAATTTATGT
Found at i:42674738 original size:73 final size:72
Alignment explanation
Indices: 42674614--42675067 Score: 520
Period size: 73 Copynumber: 6.2 Consensus size: 72
42674604 AATTTTCATT
* * * * * * *
42674614 TTTTTAATTTATGTTTCTAAAAAATAAATTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACG
1 TTTTCAATTTTTGTTT-TAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACG
*
42674679 CTGAGGTA
65 TTGAGGTA
* * * *
42674687 GTTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACG
1 TTTTCAATTTTTGTTT-TAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACG
42674752 TTGAGGTA
65 TTGAGGTA
* *
42674760 TTTTCAATTTCTGTCTTTAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACAC
1 TTTTCAATTTTTGT-TTT-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACAC
42674825 GTTGAGGTA
64 GTTGAGGTA
* * * *
42674834 TTTTCAATTTCTGTTTTTTTAAAAAATCAACTCATATTGCGATAGGTGAGATGAACCTTAAG--A
1 TTTTCAA-TT-T-TTGTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
*
42674897 CGCTGAGGTA
63 CGTTGAGGTA
* * * * *
42674907 ATTTCAATTTTTATTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATG
1 TTTTCAATTTTTGTTT-TAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACG
42674972 TTGAGGTA
65 TTGAGGTA
* *
42674980 TTTTCAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--A
1 TTTTCAATTTTTGT-TTT--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
*
42675043 CGTTGAGGTG
63 CGTTGAGGTA
* *
42675053 TTTTCCATTTCTGTT
1 TTTTCAATTTTTGTT
42675068 CTTCAATTTC
Statistics
Matches: 328, Mismatches: 42, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
70 5 0.02
71 39 0.12
72 3 0.01
73 134 0.41
74 62 0.19
75 79 0.24
76 4 0.01
77 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (72 bp):
TTTTCAATTTTTGTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGT
TGAGGTA
Found at i:42675182 original size:15 final size:14
Alignment explanation
Indices: 42675146--42675178 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
42675136 CGTTGAGGTA
42675146 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
42675160 TTTTCAAATTTTGT
1 TTTTCAAATTCTGT
42675174 TTTTC
1 TTTTC
42675179 CAAAAAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:42675307 original size:182 final size:180
Alignment explanation
Indices: 42675000--42675334 Score: 444
Period size: 182 Copynumber: 1.9 Consensus size: 180
42674990 CTGTCTTTAA
* * * * * *
42675000 AAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGTTGAGGTGTTTTCCATTTCT
1 AAAAAATCAGCTCATATTGCGAGAGGTGAGTTCAACCTCAACACGCTGAGATATTTTCAATTTCT
* * * *
42675065 GTTCTTCAATTTCCGTGTTTCAAAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCT-TG
66 GTTCTTCAATTTACGTGTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
**
42675129 ACTCACACGTTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
131 A-TCACACGCCGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
*
42675180 AAAAAATC-GACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGACACGCTGAGATATTTTCAATT
1 AAAAAATCAG-CTCATATTGCGAGAGGTGAGTTCAACCTCA--ACACGCTGAGATATTTTCAATT
* * *
42675244 TCTTTTTTTTCAATTTATGT-TTGTC-AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
63 TC-TGTTCTTCAATTTACGTGTT-TCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
42675307 CTCAGATCACACGCCGAGGTATTTTCAA
126 CTCAGATCACACGCCGAGGTATTTTCAA
42675335 TTGATTTTTA
Statistics
Matches: 133, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
179 1 0.01
180 36 0.27
182 79 0.59
183 17 0.13
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (180 bp):
AAAAAATCAGCTCATATTGCGAGAGGTGAGTTCAACCTCAACACGCTGAGATATTTTCAATTTCT
GTTCTTCAATTTACGTGTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
ATCACACGCCGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
Found at i:42675343 original size:91 final size:91
Alignment explanation
Indices: 42674980--42675534 Score: 395
Period size: 91 Copynumber: 6.0 Consensus size: 91
42674970 TGTTGAGGTA
* *
42674980 TTTTCAATTTCTGTCTTT-AAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTC--A-A
1 TTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACA
* * * *
42675041 GACGTTGAGGTGTTTTCCATTTCTGT
66 CACGCTGAGGTATTTTCAATTTCTGT
* * * * * *
42675067 TCTTCAATTTCCGTGTTTCAAAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCT-TGAC
1 TTTTCAATTTCTGTCTTTC-AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA-
* *
42675131 TCACACGTTGAGGTATTTTCAAATTCTGT
64 -CACACGCTGAGGTATTTTCAATTTCTGT
* * * * *
42675160 TTTTCAAATTT-TGTTTTTC-CAAAAAATCGACTCATATTGCGAGAGGTGAGTTCAGCCTCAG-G
1 TTTTC-AATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAC
* *
42675222 ACACGCTGAGATATTTTCAATTTCTTTT
65 ACACGCTGAGGTATTTTCAATTTC-TGT
*
42675250 TTTTCAATTTATGT-TTGTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
1 TTTTCAATTTCTGTCTT-TCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA-
* * *
42675314 CACACGCCGAGGTATTTTCAATTGATTTTT
64 CACACGCTGAGGTATTTTCAATT--TCTGT
* * * * *** * *
42675344 ATTTTTATTTTTTTTCAATTTATGCTTTGCAAAAATCAACTCATATTACGAGAGGTAAGTTGAGC
1 -TTTTCAATTTCTGTC---TT-T-C--AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * ** * **
42675409 CTCGGGTCACATACCGAGGTATTTTCAAAATCTGT
58 CTC-AGACACACGCTGAGGTATTTTCAATTTCTGT
* * *
42675444 TTTACAAATTT-TGT-TTT----AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTAG-C
1 TTTTC-AATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAC
* *
42675502 TCACGTGCTGAGCTATTTTCAATTTCTGT
65 ACAC--GCTGAGGTATTTTCAATTTCTGT
42675531 TTTT
1 TTTT
42675535 TAATGTTTAG
Statistics
Matches: 374, Mismatches: 65, Indels: 58
0.75 0.13 0.12
Matches are distributed among these distances:
85 3 0.01
86 1 0.00
87 70 0.19
89 66 0.18
90 13 0.03
91 73 0.20
92 1 0.00
93 53 0.14
94 9 0.02
95 13 0.03
99 8 0.02
100 8 0.02
102 55 0.15
103 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (91 bp):
TTTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACA
CACGCTGAGGTATTTTCAATTTCTGT
Found at i:42675419 original size:102 final size:103
Alignment explanation
Indices: 42675246--42675436 Score: 287
Period size: 102 Copynumber: 1.8 Consensus size: 103
42675236 TTTCAATTTC
* *
42675246 TTTTTTTTCAATTTATGTTTGTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
1 TTTTTTTTCAATTTATGTTTGTC--AAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCA
*
42675311 GATCACACGCCGAGGTATTTTCAATTGATTTTTATTTTTA
64 GATCACACACCGAGGTATTTTCAATTGATTTTTATTTTTA
*
42675351 TTTTTTTTCAATTTATGCTTTG-C-AAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCGG
1 TTTTTTTTCAATTTATG-TTTGTCAAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAG
* *
42675414 GTCACATACCGAGGTATTTTCAA
65 ATCACACACCGAGGTATTTTCAA
42675437 AATCTGTTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
102 57 0.72
105 18 0.23
106 4 0.05
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (103 bp):
TTTTTTTTCAATTTATGTTTGTCAAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAGA
TCACACACCGAGGTATTTTCAATTGATTTTTATTTTTA
Found at i:42675520 original size:87 final size:88
Alignment explanation
Indices: 42675374--42675602 Score: 230
Period size: 87 Copynumber: 2.6 Consensus size: 88
42675364 TATGCTTTGC
* * * * * *
42675374 AAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGCTCACATACCGAGCTATTTTCAAAA
42675439 TCTGTTTTACAAAT-TTT-GTTTT
66 TCTGTTTT-CAAATGTTTAGTTTT
* * * * **
42675461 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTAGCTCACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGCTCACATACCGAGCTATTTTCAAAA
**
42675526 TCTGTTTTTTAATGTTTAGTTTT
66 TCTGTTTTCAAATGTTTAGTTTT
* * * * * *
42675549 AAAGAGTCAATTCATATTGCGAGAAATGAGTTAAG-CTCAAGATCACATGCCGAG
1 AAA-AATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-AGCTCACATACCGAG
42675603 TAAAGAATAA
Statistics
Matches: 116, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
86 3 0.03
87 64 0.55
88 10 0.09
89 39 0.34
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (88 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGCTCACATACCGAGCTATTTTCAAAA
TCTGTTTTCAAATGTTTAGTTTT
Found at i:42676252 original size:30 final size:30
Alignment explanation
Indices: 42676216--42676314 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
42676206 CTAGCCTTTG
42676216 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
42676246 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
42676276 CTACCACCTACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
42676306 CCACCACCA
1 CCACCACCA
42676315 CTTGTACCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.18
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:42676881 original size:23 final size:25
Alignment explanation
Indices: 42676833--42676910 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 25
42676823 ATTCTTTTAA
* * *
42676833 TATATTAGGTATAT-TC-TAAATTC
1 TATATTACGTATATATCATTAATAC
42676856 TATATTACGTATATAT-ATT-ATAC
1 TATATTACGTATATATCATTAATAC
* * *
42676879 TATTTTATGTATATATCTTTAATAC
1 TATATTACGTATATATCATTAATAC
42676904 TATATTA
1 TATATTA
42676911 TTTACATATT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 30 0.68
24 4 0.09
25 10 0.23
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (25 bp):
TATATTACGTATATATCATTAATAC
Found at i:42676965 original size:22 final size:23
Alignment explanation
Indices: 42676935--42677000 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
42676925 TTTCTACATG
*
42676935 TTATCTTATGTATATATTTTA-A
1 TTATATTATGTATATATTTTACA
*
42676957 TTATATTATGTATGTATTTTTACA
1 TTATATTATGTATATA-TTTTACA
* *
42676981 CTATATTATGTACATATTTT
1 TTATATTATGTATATATTTT
42677001 TTTATATCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 14 0.38
23 9 0.24
24 14 0.38
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATATTATGTATATATTTTACA
Found at i:42676990 original size:24 final size:23
Alignment explanation
Indices: 42676940--42677001 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
42676930 ACATGTTATC
*
42676940 TTATGTATATA-TTTTAATTATA
1 TTATGTATATATTTTTAACTATA
*
42676962 TTATGTATGTATTTTTACACTATA
1 TTATGTATATATTTTTA-ACTATA
*
42676986 TTATGTACATATTTTT
1 TTATGTATATATTTTT
42677002 TTATATCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 10 0.29
23 5 0.15
24 19 0.56
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATGTATATATTTTTAACTATA
Found at i:42677030 original size:79 final size:79
Alignment explanation
Indices: 42676864--42677036 Score: 192
Period size: 78 Copynumber: 2.2 Consensus size: 79
42676854 TCTATATTAC
* * * *
42676864 GTATATATATTATACTATTTTATGTATATATCTTTAATACTATATTATTTACATATTTTTTTTTC
1 GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTTTC
*
42676929 TACATGTTATCTTAT
66 TA-ATGTTATCATAT
* * *
42676944 GTATATATTTTA-ATTATATTATGTATGTAT-TTTTACACTATATTATGTACATATTTTTTTATA
1 GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTT-T-
42677007 TCT-AT-TTCATACATAT
64 TCTAATGTT-AT-CATAT
*
42677023 GTATATATTATATA
1 GTATATATTTTATA
42677037 TATCTTAACA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
77 2 0.03
78 31 0.39
79 31 0.39
80 15 0.19
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.56
Consensus pattern (79 bp):
GTATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTTTC
TAATGTTATCATAT
Found at i:42677091 original size:25 final size:24
Alignment explanation
Indices: 42677063--42677118 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
42677053 GTTATATTTT
*
42677063 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
42677088 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
42677111 CACTATTA
1 CACTATTA
42677119 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:42682503 original size:30 final size:31
Alignment explanation
Indices: 42682469--42682527 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 31
42682459 ACCAGCTAAC
42682469 AGCTAACCATACTAACTG-AAGAC-GTTACAA
1 AGCTAACCA-ACTAACTGTAAGACAGTTACAA
42682499 AGCTAACCAACTAACTGTAAGACAGTTAC
1 AGCTAACCAACTAACTGTAAGACAGTTAC
42682528 TCCTAACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 8 0.30
30 14 0.52
31 5 0.19
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (31 bp):
AGCTAACCAACTAACTGTAAGACAGTTACAA
Found at i:42683021 original size:5 final size:5
Alignment explanation
Indices: 42683011--42683035 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42683001 GGTTTTATAC
42683011 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
42683036 ATGTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:42683066 original size:19 final size:18
Alignment explanation
Indices: 42683003--42683098 Score: 72
Period size: 19 Copynumber: 5.3 Consensus size: 18
42682993 GGGGAAGGGG
*
42683003 TTTTATACTTTTATTTT-A
1 TTTTATAATTTT-TTTTAA
*
42683021 TTTTAT--TTTATTTTAA
1 TTTTATAATTTTTTTTAA
* * *
42683037 TGTAATTATTTTTATTTAA
1 TTTTATAATTTTT-TTTAA
*
42683056 TTTTATAATTTTTTATAA
1 TTTTATAATTTTTTTTAA
*
42683074 TTCTTATAATATTTTTTATA
1 TT-TTATAATTTTTTTTA-A
42683094 TTTTA
1 TTTTA
42683099 ATTTATTTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
15 4 0.06
16 8 0.13
18 16 0.26
19 31 0.50
20 3 0.05
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (18 bp):
TTTTATAATTTTTTTTAA
Found at i:42683068 original size:20 final size:20
Alignment explanation
Indices: 42683043--42683089 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
42683033 TTAATGTAAT
42683043 TATTTTTATTTAATT-TTATAA
1 TATTTTTA--TAATTCTTATAA
42683064 T-TTTTTATAATTCTTATAA
1 TATTTTTATAATTCTTATAA
42683083 TATTTTT
1 TATTTTT
42683090 TATATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
19 7 0.29
20 11 0.46
21 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTTTATAATTCTTATAA
Found at i:42683105 original size:19 final size:19
Alignment explanation
Indices: 42683003--42683107 Score: 54
Period size: 21 Copynumber: 5.1 Consensus size: 19
42682993 GGGGAAGGGG
*
42683003 TTTTATACTTTTATTTTATT
1 TTTTATA-TTTTAATTTATT
* *
42683023 TTATTTTATTTTAATGTAATT
1 TT-TTATATTTTAAT-TTATT
42683044 ATTTT-TA-TTTAATTTTATAATT
1 -TTTTATATTTTAA--TT-T-ATT
*
42683066 TTTTATAATTCTT-ATAATATT
1 TTTTAT-ATT-TTAAT-TTATT
42683087 TTTTATATTTTAATTTATT
1 TTTTATATTTTAATTTATT
42683106 TT
1 TT
42683108 AAAGATTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 27
0.67 0.06 0.27
Matches are distributed among these distances:
19 13 0.20
20 16 0.24
21 24 0.36
22 8 0.12
23 1 0.02
24 2 0.03
25 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.70
Consensus pattern (19 bp):
TTTTATATTTTAATTTATT
Found at i:42683140 original size:13 final size:13
Alignment explanation
Indices: 42683119--42683159 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
42683109 AAGATTTTTT
42683119 TATATCAAAATAA
1 TATATCAAAATAA
*
42683132 TATAACAAAAATAA
1 TATATC-AAAATAA
*
42683146 TATTTCAAAATAA
1 TATATCAAAATAA
42683159 T
1 T
42683160 GTCAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (13 bp):
TATATCAAAATAA
Found at i:42688854 original size:16 final size:15
Alignment explanation
Indices: 42688830--42688881 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
42688820 AAATTTATAT
42688830 TTTTCATCCTTTCAA
1 TTTTCATCCTTTCAA
*
42688845 TTTTCTATCCCTTCAAA
1 TTTTC-ATCCTTTC-AA
42688862 TTTTCAT-CTTTCCAA
1 TTTTCATCCTTT-CAA
42688877 TTTTC
1 TTTTC
42688882 TTTCCACTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 15 0.47
16 10 0.31
17 7 0.22
ACGTcount: A:0.19, C:0.27, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTCATCCTTTCAA
Found at i:42688863 original size:17 final size:15
Alignment explanation
Indices: 42688830--42688869 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
42688820 AAATTTATAT
*
42688830 TTTTCATCCTTTCAA
1 TTTTCATCCCTTCAA
42688845 TTTTCTATCCCTTCAAA
1 TTTTC-ATCCCTTC-AA
42688862 TTTTCATC
1 TTTTCATC
42688870 TTTCCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 10 0.45
17 7 0.32
ACGTcount: A:0.20, C:0.28, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTCATCCCTTCAA
Found at i:42693799 original size:46 final size:44
Alignment explanation
Indices: 42693740--42693854 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
42693730 ACAGGACAGA
* *
42693740 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
42693786 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
42693830 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
42693855 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:42693835 original size:44 final size:45
Alignment explanation
Indices: 42693740--42693873 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
42693730 ACAGGACAGA
* *
42693740 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
42693786 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
42693830 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
42693874 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:42701127 original size:46 final size:44
Alignment explanation
Indices: 42701068--42701182 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
42701058 ACAGGACAGA
* *
42701068 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
42701114 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
42701158 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
42701183 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:42701163 original size:44 final size:45
Alignment explanation
Indices: 42701068--42701201 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
42701058 ACAGGACAGA
* *
42701068 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
42701114 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
42701158 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
42701202 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:42703159 original size:15 final size:15
Alignment explanation
Indices: 42703134--42703191 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
42703124 TCATATATAT
42703134 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
42703150 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
42703165 AATAATTTCAATCAA
1 TATAAATTCAATCAA
42703180 TATAAATTCAAT
1 TATAAATTCAAT
42703192 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:42704459 original size:5 final size:5
Alignment explanation
Indices: 42704446--42704487 Score: 75
Period size: 5 Copynumber: 8.2 Consensus size: 5
42704436 TTCTTTAGTT
42704446 TATATA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
42704488 TAAAACATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 32 0.89
6 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:42704523 original size:8 final size:8
Alignment explanation
Indices: 42704510--42704538 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
42704500 TATTTTTATT
42704510 ATATAATA
1 ATATAATA
42704518 ATATAATA
1 ATATAATA
42704526 ATATAATA
1 ATATAATA
42704534 ATATA
1 ATATA
42704539 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:42711817 original size:75 final size:75
Alignment explanation
Indices: 42711722--42711871 Score: 228
Period size: 75 Copynumber: 2.0 Consensus size: 75
42711712 CATTTGCAAG
* * * * *
42711722 ATTGTTTGTTTAAACAATTAATTTCAGATCATGCAATAAAGACAGTTCATCTTACTAGTACTGAT
1 ATTGCTTGTTTAAACAATTAATTTCAAACCATGCAATAAAGACAATTCATCTTACTAATACTGAT
42711787 GAGTTTATAT
66 GAGTTTATAT
* **
42711797 ATTGCTTGTTTAAATAATTAATTTCAAACCATGCAATAAAGACAATTCATCTTGGTAATACTGAT
1 ATTGCTTGTTTAAACAATTAATTTCAAACCATGCAATAAAGACAATTCATCTTACTAATACTGAT
42711862 GAGTTTATAT
66 GAGTTTATAT
42711872 CTTAGTCTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (75 bp):
ATTGCTTGTTTAAACAATTAATTTCAAACCATGCAATAAAGACAATTCATCTTACTAATACTGAT
GAGTTTATAT
Found at i:42715594 original size:131 final size:130
Alignment explanation
Indices: 42715438--42715696 Score: 383
Period size: 131 Copynumber: 2.0 Consensus size: 130
42715428 TAACTATTCA
* * *
42715438 TTTAAAAATTTTCAAAACGAAGGCAACATTCAAGGTTTGGGAATTTGGGGAATCGTGCCCAATCT
1 TTTAAAAATTTTCAAAACGAAGGCAACATTCAAGGTTTGGCAATTCGGGGAATCGTGCCCAATCG
* * * * *
42715503 TGTTGGGTTGCAATTTCCCGTTTCTTCAAAATAATCGAATATTCTTTTCGAATTTCAATCATGCC
66 TGCTAGGTTGCAATTTCCCATTTCTTCAAAATAATCGAATATTCCTTTAGAATTTCAATCATGCC
* * * * *
42715568 TTTAAAAATTCTTTAAAACGAAGGCAACGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
1 TTTAAAAATT-TTCAAAACGAAGGCAACATTCAAGGTTTGGCAATTCGGGGAATCGTGCCCAATC
*
42715633 GTGCTAGGTTGCAATTTCCCATTTCTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATG
65 GTGCTAGGTTGCAATTTCCCATTTCTTCAAAATAATCGAATATTCCTTTAGAATTTCAATCATG
42715697 TTTTCAAGAT
Statistics
Matches: 114, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
130 10 0.09
131 104 0.91
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (130 bp):
TTTAAAAATTTTCAAAACGAAGGCAACATTCAAGGTTTGGCAATTCGGGGAATCGTGCCCAATCG
TGCTAGGTTGCAATTTCCCATTTCTTCAAAATAATCGAATATTCCTTTAGAATTTCAATCATGCC
Found at i:42719153 original size:21 final size:20
Alignment explanation
Indices: 42719127--42719179 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
42719117 AAAAATAGGG
42719127 TTTTATAAGAAATTACTTGG-T
1 TTTTATAAGAAATT--TTGGAT
*
42719148 TTTTATATGAAAATTTTGGAT
1 TTTTATAAG-AAATTTTGGAT
42719169 TTTTAT-AGAAA
1 TTTTATAAGAAA
42719180 AAGTTATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 5 0.18
21 15 0.54
22 5 0.18
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTTATAAGAAATTTTGGAT
Found at i:42719181 original size:21 final size:20
Alignment explanation
Indices: 42719143--42719180 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42719133 AAGAAATTAC
42719143 TTGGTTTTTATATGAAAATT
1 TTGGTTTTTATATGAAAATT
42719163 TTGGATTTTTATA-GAAAA
1 TTGG-TTTTTATATGAAAA
42719181 AGTTATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (20 bp):
TTGGTTTTTATATGAAAATT
Found at i:42719473 original size:31 final size:31
Alignment explanation
Indices: 42719438--42719498 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
42719428 GTATGACGGG
* *
42719438 TGACTAAAATGATAAATGTATGTAACAATAA
1 TGACTAAAATAATAAAAGTATGTAACAATAA
*
42719469 TGACTAAAATAATAAAAGTATGTAAGAATA
1 TGACTAAAATAATAAAAGTATGTAACAATA
42719499 GTGTTTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (31 bp):
TGACTAAAATAATAAAAGTATGTAACAATAA
Found at i:42732509 original size:14 final size:14
Alignment explanation
Indices: 42732490--42732557 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 14
42732480 AATTGTTGGT
42732490 TTCTTTTGTTCTTG
1 TTCTTTTGTTCTTG
*
42732504 TTCTTTTGGTTTTTG
1 TTCTTTT-GTTCTTG
* *
42732519 AATCTTTTATTTTTCTT-
1 --T-TCTT-TTGTTCTTG
42732536 TTCTTTTGTTCTTG
1 TTCTTTTGTTCTTG
42732550 TTCTTTTG
1 TTCTTTTG
42732558 GTTTTTGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
13 7 0.17
14 18 0.43
15 7 0.17
17 1 0.02
18 7 0.17
19 2 0.05
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.72
Consensus pattern (14 bp):
TTCTTTTGTTCTTG
Found at i:42732526 original size:16 final size:15
Alignment explanation
Indices: 42732491--42732578 Score: 54
Period size: 15 Copynumber: 5.8 Consensus size: 15
42732481 ATTGTTGGTT
* *
42732491 TCTTTTGTTCTTG-T
1 TCTTTTGTTTTTGAA
42732505 TCTTTTGGTTTTTGAA
1 TCTTTT-GTTTTTGAA
* ***
42732521 TCTTTTATTTTTCTTT
1 TCTTTTGTTTTT-GAA
* *
42732537 TCTTTTGTTCTTG-T
1 TCTTTTGTTTTTGAA
42732551 TCTTTTGGTTTTTGAA
1 TCTTTT-GTTTTTGAA
*
42732567 TCTTTTATTTTT
1 TCTTTTGTTTTT
42732579 CTTTCTTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
14 13 0.23
15 22 0.39
16 22 0.39
ACGTcount: A:0.07, C:0.10, G:0.11, T:0.72
Consensus pattern (15 bp):
TCTTTTGTTTTTGAA
Found at i:42732539 original size:46 final size:46
Alignment explanation
Indices: 42732489--42732582 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
42732479 GAATTGTTGG
42732489 TTTCTTTTGTTCTTGTTCTTTTGGTTTTTGAATCTTTTATTTTTCT
1 TTTCTTTTGTTCTTGTTCTTTTGGTTTTTGAATCTTTTATTTTTCT
42732535 TTTCTTTTGTTCTTGTTCTTTTGGTTTTTGAATCTTTTATTTTTCT
1 TTTCTTTTGTTCTTGTTCTTTTGGTTTTTGAATCTTTTATTTTTCT
42732581 TT
1 TT
42732583 CTTATTTCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (46 bp):
TTTCTTTTGTTCTTGTTCTTTTGGTTTTTGAATCTTTTATTTTTCT
Found at i:42734924 original size:187 final size:182
Alignment explanation
Indices: 42734602--42734972 Score: 661
Period size: 187 Copynumber: 2.0 Consensus size: 182
42734592 TGATTAAATA
*
42734602 TTGTGATTTAATGCATCCAAGTCCAATAAGCTCATGTTCATATAGTTGCACAGTACCATCTGCGA
1 TTGTGATTTAATGCATCCAAGTCCAATAAGCTCATGTTCATATAGTTGCACAGTACCATATGCGA
*
42734667 TATCTTAAACCTAGATTTGACATTCTATTTATATTCCATAGTAGCTATAGTTCCATTTGTTAAAG
66 TATCTTAAACCTAGATTTGACATGCTATTTATATTCCATAGTAGCTATAGTTCCATTTGTTAAAG
*
42734732 GGCAGATTAAAATGACACTCTAGTCTAGATGCTCATGTTTTGACTTGGTCTATATTT
131 GGCAGATTAAAAGGACA--C---TCTAGATGCTCATGTTTTGACTTGGTCTATATTT
42734789 TTGTGATTTAATGCATCCAAGTCCAATAAGCTCATGTTCATATAGTTGCACAGTACCATATGCGA
1 TTGTGATTTAATGCATCCAAGTCCAATAAGCTCATGTTCATATAGTTGCACAGTACCATATGCGA
*
42734854 TATCTTAAACCTAGATTTGACATGCTATTTATATTCCATAGTAGCTATAGTTCCATTTGTTAATG
66 TATCTTAAACCTAGATTTGACATGCTATTTATATTCCATAGTAGCTATAGTTCCATTTGTTAAAG
42734919 GGCAGATTAAAAGGACACTCTAGATGCTCATGTTTTGACTTGGTCTATATTT
131 GGCAGATTAAAAGGACACTCTAGATGCTCATGTTTTGACTTGGTCTATATTT
42734971 TT
1 TT
42734973 AAACATTGTT
Statistics
Matches: 180, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
182 36 0.20
185 1 0.01
187 143 0.79
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (182 bp):
TTGTGATTTAATGCATCCAAGTCCAATAAGCTCATGTTCATATAGTTGCACAGTACCATATGCGA
TATCTTAAACCTAGATTTGACATGCTATTTATATTCCATAGTAGCTATAGTTCCATTTGTTAAAG
GGCAGATTAAAAGGACACTCTAGATGCTCATGTTTTGACTTGGTCTATATTT
Found at i:42736181 original size:20 final size:22
Alignment explanation
Indices: 42736141--42736190 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
42736131 GAAAATAACT
42736141 AAAATAAAAAATTTAAGAATAA
1 AAAATAAAAAATTTAAGAATAA
*
42736163 AAAATAAATAA-TTAA-AATAA
1 AAAATAAAAAATTTAAGAATAA
*
42736183 TAAATAAA
1 AAAATAAA
42736191 CAGATAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 12 0.46
21 4 0.15
22 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATAAAAAATTTAAGAATAA
Found at i:42736184 original size:16 final size:15
Alignment explanation
Indices: 42736160--42736189 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42736150 AATTTAAGAA
42736160 TAAAAAATAAATAAT
1 TAAAAAATAAATAAT
42736175 TAAAATAATAAATAA
1 TAAAA-AATAAATAA
42736190 ACAGATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAAAATAAATAAT
Found at i:42736201 original size:20 final size:20
Alignment explanation
Indices: 42736141--42736202 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
42736131 GAAAATAACT
*
42736141 AAAATAAAAAATTTAAGAATAA
1 AAAATAAACAA-TT-AGAATAA
* *
42736163 AAAATAAATAATTAAAATAA
1 AAAATAAACAATTAGAATAA
*
42736183 TAAATAAACAGA-TAGAATAA
1 AAAATAAACA-ATTAGAATAA
42736203 GAAGTGGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 21 0.62
21 3 0.09
22 10 0.29
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAATAAACAATTAGAATAA
Found at i:42741577 original size:17 final size:17
Alignment explanation
Indices: 42741555--42741587 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42741545 TCTGATGGTT
*
42741555 TATTTTTAGTAATTTTA
1 TATTTTTAATAATTTTA
42741572 TATTTTTAATAATTTT
1 TATTTTTAATAATTTT
42741588 GAAAAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TATTTTTAATAATTTTA
Found at i:42742731 original size:34 final size:34
Alignment explanation
Indices: 42742686--42742756 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
42742676 TAACAAAAAG
* *
42742686 TCCTTATTTTAACCATTTTTAACCAGTAACTAAT
1 TCCTTAGTTTAACCATTTTTAACCAGTAACCAAT
42742720 TCCTTAGTTTAACCATTTTTAACCAGTAACCAAT
1 TCCTTAGTTTAACCATTTTTAACCAGTAACCAAT
42742754 TCC
1 TCC
42742757 GAGATCCCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (34 bp):
TCCTTAGTTTAACCATTTTTAACCAGTAACCAAT
Found at i:42742904 original size:18 final size:20
Alignment explanation
Indices: 42742883--42742925 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
42742873 ACAAAATCAA
*
42742883 ATTCAACTACA-A-ATGCAG
1 ATTCAAATACATATATGCAG
*
42742901 ATTCAAATACATATATGTAG
1 ATTCAAATACATATATGCAG
42742921 ATTCA
1 ATTCA
42742926 GAACAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 10 0.48
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.30
Consensus pattern (20 bp):
ATTCAAATACATATATGCAG
Found at i:42745218 original size:35 final size:34
Alignment explanation
Indices: 42745179--42745297 Score: 96
Period size: 35 Copynumber: 3.4 Consensus size: 34
42745169 ATGTAGATAA
42745179 AACAGATCAGAACATACTAGTTGCACATATAGTTT
1 AACAGATCAGAACATACTA-TTGCACATATAGTTT
* * **
42745214 AACAGATCAAAAACATGCTATTG-ACATATTCAGATAA
1 AACAGATC-AGAACATACTATTGCACATA-T-AG-TTT
* * * * *
42745251 AACATATTAGGACATATTAATTGCAAATATAGTTT
1 AACAGATCAGAACATACT-ATTGCACATATAGTTT
42745286 AACAGATCAGAA
1 AACAGATCAGAA
42745298 ACAGGTATTG
Statistics
Matches: 62, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
34 5 0.08
35 22 0.35
36 19 0.31
37 12 0.19
38 4 0.06
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (34 bp):
AACAGATCAGAACATACTATTGCACATATAGTTT
Found at i:42748830 original size:50 final size:50
Alignment explanation
Indices: 42748753--42748853 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
42748743 ATATTCTATG
*
42748753 AACCTTCAACATGGGATAAATTGCCGATGCCATGTCCCAGACATGGTCTT
1 AACCTTCAACATGGGATAAATTACCGATGCCATGTCCCAGACATGGTCTT
42748803 AACCTTCAACATGGGATAAATTACCGATGCCATGTCCCAGACATGGTCTT
1 AACCTTCAACATGGGATAAATTACCGATGCCATGTCCCAGACATGGTCTT
42748853 A
1 A
42748854 CACTGGTTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (50 bp):
AACCTTCAACATGGGATAAATTACCGATGCCATGTCCCAGACATGGTCTT
Found at i:42749022 original size:47 final size:47
Alignment explanation
Indices: 42748826--42749138 Score: 211
Period size: 47 Copynumber: 6.7 Consensus size: 47
42748816 GGATAAATTA
** * *
42748826 CCGATGCCATGTCCCAGACATGGTCTTACACTGGTTCTCAT-ATATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATCTTGTG
* * * * *
42748872 CGTGATG-CATGTCCTAGACAT-GTCTTACACTAGCAC-AACCCTTG-G
1 C-CGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCA-TCTTGTG
* * *
42748917 CCGATG-CGTGTCCCAGACA-CGTCTTACACTGGCTA-TC-TCTGTCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC-ACTCATCT-T-G-TG
* * * *
42748964 TCGATG-AATGTCCCAAACAT-GTCTTACTCTGGCACTCATCTCTGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATCT-TGTG
* * ** *
42749010 CCGATGCCATGTCCCCGACATGGTCTTACACTGGCTCTCATAATATAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATCTTGT-G
* * * * *
42749058 CTGATG-CATGTCCCAGACAT-GTCTTACACTAGCCCTCATCTGGATA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATCTTG-TG
*
42749104 CCGATGCCATGCCCCAGACATGGTCTTACACTGGC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC
42749139 GCACAAATCA
Statistics
Matches: 205, Mismatches: 43, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
43 2 0.01
44 29 0.14
45 16 0.08
46 44 0.21
47 75 0.37
48 39 0.19
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (47 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATCTTGTG
Found at i:42749072 original size:94 final size:93
Alignment explanation
Indices: 42748826--42749138 Score: 336
Period size: 94 Copynumber: 3.4 Consensus size: 93
42748816 GGATAAATTA
* *
42748826 CCGATGCCATGTCCCAGACATGGTCTTACACTGGTTCTCATATAT-GCGTGATGCATGTCCTAGA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATAGC-TGATGCATGTCCCAGA
* *
42748890 CATGTCTTACACTAGCA--CAACCCT-TGG
65 CATGTCTTACACTAGCACTCATCTCTGT-G
* * * ** * *
42748917 CCGATG-CGTGTCCCAGACA-CGTCTTACACTGGCTATCTC-TGTCGAGGTCGATGAATGTCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTCATATATAGCT-GATGCATGTCCCA
* * *
42748979 AACATGTCTTACTCTGGCACTCATCTCTGTG
63 GACATGTCTTACACTAGCACTCATCTCTGTG
*
42749010 CCGATGCCATGTCCCCGACATGGTCTTACACTGGCTCTCATAATATAGCTGATGCATGTCCCAGA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATATAGCTGATGCATGTCCCAGA
* * *
42749075 CATGTCTTACACTAGCCCTCATCT-GGATA
65 CATGTCTTACACTAGCACTCATCTCTG-TG
*
42749104 CCGATGCCATGCCCCAGACATGGTCTTACACTGGC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC
42749139 GCACAAATCA
Statistics
Matches: 180, Mismatches: 30, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
89 12 0.07
90 15 0.08
91 38 0.21
93 17 0.09
94 81 0.45
95 17 0.09
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (93 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATAGCTGATGCATGTCCCAGAC
ATGTCTTACACTAGCACTCATCTCTGTG
Found at i:42755632 original size:42 final size:43
Alignment explanation
Indices: 42755514--42755636 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
42755504 CCACATATTG
* * * *
42755514 ATGCCACTGTCCCAGACATGGTCTTACACGAAATCA-TATAACG
1 ATGCCAATGT-CCAGACATGGTCTTACACGTAATCACAATAACA
42755557 ATGCCAATGTCCTAGACATGGTCTTACACGTAATCACAAT-ACA
1 ATGCCAATGTCC-AGACATGGTCTTACACGTAATCACAATAACA
*
42755600 ATGCCAATGTCCAGACATGGTCTTACATGTAATCACA
1 ATGCCAATGTCCAGACATGGTCTTACACGTAATCACA
42755637 TCTCGATAAC
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
42 26 0.36
43 45 0.62
44 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCAGACATGGTCTTACACGTAATCACAATAACA
Found at i:42762005 original size:46 final size:46
Alignment explanation
Indices: 42761932--42762190 Score: 358
Period size: 46 Copynumber: 5.6 Consensus size: 46
42761922 TGATGTCATA
* * *
42761932 GTATCTTTCAACTATGGTTTTACTCATTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGTTGCCATG
* * ** *
42761978 GTATCTTTCAACCATTGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGTTGCCATG
* *
42762025 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTAGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* *
42762071 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* *
42762117 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
*
42762163 GTATCTTTCAACCATGGTCTTATTCATT
1 GTATCTTTCAACCATGGTCTTACTCATT
42762191 CCATATCAGA
Statistics
Matches: 193, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 155 0.80
47 38 0.20
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
Found at i:42765002 original size:70 final size:70
Alignment explanation
Indices: 42764910--42765133 Score: 270
Period size: 70 Copynumber: 3.2 Consensus size: 70
42764900 CAATTTATTA
* * * *
42764910 CTAATTAATATGATGCTATTATATTGTAAATCATTGGTTGTCCAAATTAGGACAAATTCGTGGTG
1 CTAATTAATATGCTGCTGTTATATTGTAAATCATTGGCTGTCCAAATTAGGACAAATTCATGGTG
42764975 TTTAG
66 TTTAG
* * *
42764980 CTAATTAATATGCTGCTGTTATATTGTAAACCATTGACTGTCTAAATTAGGACAAATTCATGGTG
1 CTAATTAATATGCTGCTGTTATATTGTAAATCATTGGCTGTCCAAATTAGGACAAATTCATGGTG
42765045 TTTAG
66 TTTAG
* * * * * * * *
42765050 CTAATGAAAATGCTGTTGTTATAGTATGAATCATTGGCTGTCCAAATTAGGGCATACTT-ATGGT
1 CTAATTAATATGCTGCTGTTATATTGTAAATCATTGGCTGTCCAAATTAGGACA-AATTCATGGT
*
42765114 ATTTAG
65 GTTTAG
* *
42765120 ATAATTAAAATGCT
1 CTAATTAATATGCT
42765134 AATGTTATGA
Statistics
Matches: 132, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
70 129 0.98
71 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTTATATTGTAAATCATTGGCTGTCCAAATTAGGACAAATTCATGGTG
TTTAG
Found at i:42768438 original size:43 final size:43
Alignment explanation
Indices: 42768303--42768437 Score: 168
Period size: 43 Copynumber: 3.2 Consensus size: 43
42768293 GTTATACTTT
*
42768303 GGTTTATCCGATGATGCACTGATGTGT--CAGTATATTTAATTC
1 GGTTTATCCGATGATGCACTG-TGTGTGCCAGTATATTTTATTC
* *
42768345 GGTTTATCCGATGATGCATTGTGTGTGCC-GATATATTTTCTTC
1 GGTTTATCCGATGATGCACTGTGTGTGCCAG-TATATTTTATTC
* * * *
42768388 GGTTTATTCGATGATGTACTGTGTGTGCCAGTATATTTTTTTG
1 GGTTTATCCGATGATGCACTGTGTGTGCCAGTATATTTTATTC
42768431 GGTTTAT
1 GGTTTAT
42768438 TTGATTTCTG
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
41 5 0.06
42 21 0.26
43 54 0.67
44 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.24, T:0.45
Consensus pattern (43 bp):
GGTTTATCCGATGATGCACTGTGTGTGCCAGTATATTTTATTC
Found at i:42769881 original size:20 final size:20
Alignment explanation
Indices: 42769856--42769894 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
42769846 GTTGAGGAAT
42769856 GATATCTCTTCCTTTGTACC
1 GATATCTCTTCCTTTGTACC
42769876 GATATCTCTTCCTTTGTAC
1 GATATCTCTTCCTTTGTAC
42769895 AGATGAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.28, G:0.10, T:0.46
Consensus pattern (20 bp):
GATATCTCTTCCTTTGTACC
Found at i:42775805 original size:40 final size:40
Alignment explanation
Indices: 42775760--42775943 Score: 244
Period size: 40 Copynumber: 4.6 Consensus size: 40
42775750 CTCGCACAAG
* *
42775760 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
42775800 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
*
42775840 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * * *
42775880 GCTTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
42775920 GCCTTCGGGACTTAGCCTGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
42775944 CATTCGAATA
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 122 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:42779325 original size:25 final size:26
Alignment explanation
Indices: 42779291--42779362 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 26
42779281 ATCTATTCAT
*
42779291 TTATTATTATTTTTTATTCTTATTAG
1 TTATTATTATTTTTTATTCTTATTAC
42779317 TTA-TATTATTTTATT-TGT-TTATTAC
1 TTATTATTATTTT-TTAT-TCTTATTAC
*
42779342 TTATTGTTA-TTTTTATTCTTA
1 TTATTATTATTTTTTATTCTTA
42779363 GTTATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
24 3 0.08
25 26 0.67
26 10 0.26
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (26 bp):
TTATTATTATTTTTTATTCTTATTAC
Found at i:42779550 original size:3 final size:3
Alignment explanation
Indices: 42779542--42779566 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42779532 TTTCTTTATG
42779542 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
42779567 GTGTTCGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42781735 original size:42 final size:42
Alignment explanation
Indices: 42781673--42781802 Score: 215
Period size: 42 Copynumber: 3.1 Consensus size: 42
42781663 CTAAGTCCGG
* *
42781673 ATATAGTACCAGCACTAAGCCTGCGGGATTTGACCCGGATAT
1 ATATATTACCAGCACGAAGCCTGCGGGATTTGACCCGGATAT
*
42781715 ATATATTACCAGCACGAAGCCTGCGGGATTTGACCTGGATAT
1 ATATATTACCAGCACGAAGCCTGCGGGATTTGACCCGGATAT
* *
42781757 ATATATTACCAGAACGAAGCCTGCGGGATTTAACCCGGATAT
1 ATATATTACCAGCACGAAGCCTGCGGGATTTGACCCGGATAT
42781799 ATAT
1 ATAT
42781803 TATATCGAGA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (42 bp):
ATATATTACCAGCACGAAGCCTGCGGGATTTGACCCGGATAT
Found at i:42783957 original size:6 final size:6
Alignment explanation
Indices: 42783937--42783984 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
42783927 ATTGAGTCCA
* *
42783937 TTTA-T TTTA-T TTTATT TTTATT TTTATT TTTATG TTTATT GTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
42783983 TT
1 TT
42783985 CTTAGATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
5 9 0.24
6 29 0.76
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:42786579 original size:63 final size:62
Alignment explanation
Indices: 42786456--42786579 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
42786446 GATCAAGACG
42786456 CAAGTGAATAAATCATTTAATTCAGATTCAGAACAATAGGTGAAGTCTAGGTGGATTCTTTA
1 CAAGTGAATAAATCATTTAATTCAGATTCAGAACAATAGGTGAAGTCTAGGTGGATTCTTTA
* * *
42786518 CAAGTGAATAAATCGTTTAATTCAGATTTAGAATTAATAGGTGAAGTCTAGGTGGATTCTTT
1 CAAGTGAATAAATCATTTAATTCAGATTCAGAA-CAATAGGTGAAGTCTAGGTGGATTCTTT
42786580 TCTAGGTATT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
62 31 0.53
63 27 0.47
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (62 bp):
CAAGTGAATAAATCATTTAATTCAGATTCAGAACAATAGGTGAAGTCTAGGTGGATTCTTTA
Found at i:42788897 original size:41 final size:40
Alignment explanation
Indices: 42788834--42788924 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 40
42788824 TGTTTTTCAG
*
42788834 AAAATGCCGCTATAGGTAGAGTATTAGTGGCGTTTGTTTTGA
1 AAAACGCCGCTATAGGTAGAGTATTAGTGGC-TTT-TTTTGA
*
42788876 AAAACGCCGCTATAGGT-GAGTATTAGTGGCTTTTTTTTA
1 AAAACGCCGCTATAGGTAGAGTATTAGTGGCTTTTTTTGA
42788915 AAAACGCCGC
1 AAAACGCCGC
42788925 AAAAAATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 15 0.32
40 3 0.06
41 13 0.28
42 16 0.34
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.33
Consensus pattern (40 bp):
AAAACGCCGCTATAGGTAGAGTATTAGTGGCTTTTTTTGA
Found at i:42789290 original size:15 final size:15
Alignment explanation
Indices: 42789270--42789307 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
42789260 ATATTTTAAG
**
42789270 GTTTAGGGATTATGT
1 GTTTAGGGATTATCA
42789285 GTTTAGGGATTATCA
1 GTTTAGGGATTATCA
42789300 GTTTAGGG
1 GTTTAGGG
42789308 GTTGTGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.03, G:0.34, T:0.42
Consensus pattern (15 bp):
GTTTAGGGATTATCA
Found at i:42789351 original size:7 final size:7
Alignment explanation
Indices: 42789341--42789426 Score: 73
Period size: 7 Copynumber: 11.4 Consensus size: 7
42789331 TAGTGGGTAG
42789341 GGGTTAA
1 GGGTTAA
42789348 GGGTTTTAA
1 GGG--TTAA
*
42789357 GGGTTAT
1 GGGTTAA
42789364 GGGTTTAA
1 GGG-TTAA
42789372 GGGTTAA
1 GGGTTAA
*
42789379 GGGTTAT
1 GGGTTAA
42789386 GGGTTTAA
1 GGG-TTAA
*
42789394 TGGTTAA
1 GGGTTAA
*
42789401 GGGGATAA
1 -GGGTTAA
*
42789409 TGGTTAA
1 GGGTTAA
42789416 GGGGTTAA
1 -GGGTTAA
42789424 GGG
1 GGG
42789427 GTTTAATGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
7 34 0.54
8 22 0.35
9 7 0.11
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.34
Consensus pattern (7 bp):
GGGTTAA
Found at i:42789372 original size:15 final size:15
Alignment explanation
Indices: 42789341--42789438 Score: 76
Period size: 15 Copynumber: 6.4 Consensus size: 15
42789331 TAGTGGGTAG
42789341 GGGTTAAGGGTTTTAA
1 GGGTTAAGGG-TTTAA
*
42789357 GGGTTATGGGTTTAA
1 GGGTTAAGGGTTTAA
*
42789372 GGGTTAAGGG-TTAT
1 GGGTTAAGGGTTTAA
*
42789386 GGGTTTAATGG-TTAA
1 GGG-TTAAGGGTTTAA
* *
42789401 GGGGATAATGG-TTAA
1 -GGGTTAAGGGTTTAA
42789416 GGGGTTAAGGGGTTTAA
1 -GGGTTAA-GGGTTTAA
*
42789433 TGGTTA
1 GGGTTA
42789439 TGGGGACATG
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
14 6 0.09
15 40 0.58
16 19 0.28
17 4 0.06
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (15 bp):
GGGTTAAGGGTTTAA
Found at i:42789378 original size:22 final size:22
Alignment explanation
Indices: 42789344--42789403 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 22
42789334 TGGGTAGGGG
42789344 TTAAGGGTTTTAAGGGTTATGGGT
1 TTAAGGG--TTAAGGGTTATGGGT
42789368 TTAAGGGTTAAGGGTTATGGGT
1 TTAAGGGTTAAGGGTTATGGGT
*
42789390 TTAATGGTTAAGGG
1 TTAAGGGTTAAGGG
42789404 GATAATGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 28 0.80
24 7 0.20
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (22 bp):
TTAAGGGTTAAGGGTTATGGGT
Found at i:42789423 original size:8 final size:8
Alignment explanation
Indices: 42789339--42789429 Score: 66
Period size: 8 Copynumber: 11.9 Consensus size: 8
42789329 ATTAGTGGGT
42789339 AGGGGTTA
1 AGGGGTTA
*
42789347 AGGGTTTTA
1 AGGG-GTTA
42789356 A-GGGTTA
1 AGGGGTTA
* *
42789363 TGGGTTTA
1 AGGGGTTA
42789371 A-GGGTTA
1 AGGGGTTA
42789378 A-GGGTTA
1 AGGGGTTA
* *
42789385 TGGGTTTA
1 AGGGGTTA
*
42789393 A-TGGTTA
1 AGGGGTTA
*
42789400 AGGGGATA
1 AGGGGTTA
*
42789408 A-TGGTTA
1 AGGGGTTA
42789415 AGGGGTTA
1 AGGGGTTA
42789423 AGGGGTT
1 AGGGGTT
42789430 TAATGGTTAT
Statistics
Matches: 62, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
7 25 0.40
8 33 0.53
9 4 0.06
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.34
Consensus pattern (8 bp):
AGGGGTTA
Found at i:42789433 original size:24 final size:23
Alignment explanation
Indices: 42789395--42789443 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
42789385 TGGGTTTAAT
42789395 GGTTAAGGGGATAATGGTTAAGG
1 GGTTAAGGGGATAATGGTTAAGG
* *
42789418 GGTTAAGGGGTTTAATGGTTATGG
1 GGTTAAGGGG-ATAATGGTTAAGG
42789442 GG
1 GG
42789444 ACATGGGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.24, C:0.00, G:0.45, T:0.31
Consensus pattern (23 bp):
GGTTAAGGGGATAATGGTTAAGG
Found at i:42789437 original size:8 final size:8
Alignment explanation
Indices: 42789339--42789437 Score: 64
Period size: 7 Copynumber: 12.8 Consensus size: 8
42789329 ATTAGTGGGT
*
42789339 AGGGGTTA
1 AGGGTTTA
42789347 AGGGTTTTA
1 AGGG-TTTA
42789356 AGGG-TTA
1 AGGGTTTA
*
42789363 TGGGTTTA
1 AGGGTTTA
42789371 AGGG-TTA
1 AGGGTTTA
42789378 AGGG-TTA
1 AGGGTTTA
*
42789385 TGGGTTTA
1 AGGGTTTA
*
42789393 ATGG-TTA
1 AGGGTTTA
**
42789400 AGGGGATA
1 AGGGTTTA
*
42789408 ATGG-TTA
1 AGGGTTTA
*
42789415 AGGGGTTA
1 AGGGTTTA
42789423 AGGGGTTTA
1 A-GGGTTTA
*
42789432 ATGGTT
1 AGGGTT
42789438 ATGGGGACAT
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
7 30 0.42
8 28 0.39
9 14 0.19
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.35
Consensus pattern (8 bp):
AGGGTTTA
Found at i:42789503 original size:22 final size:22
Alignment explanation
Indices: 42789458--42789503 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
42789448 GGGTTAGGGG
* *
42789458 TTTATGGTTTATGAGTTAATAT
1 TTTAAGGTTTATGAGTTAAGAT
42789480 TTTAAGGTTTATGA-TTATAGAT
1 TTTAAGGTTTATGAGTTA-AGAT
42789502 TT
1 TT
42789504 AGGGATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.54
Consensus pattern (22 bp):
TTTAAGGTTTATGAGTTAAGAT
Found at i:42789823 original size:26 final size:26
Alignment explanation
Indices: 42789723--42789816 Score: 145
Period size: 26 Copynumber: 3.6 Consensus size: 26
42789713 TAAAGATTTA
42789723 AAGATTTCAAA-TTTAGAATAATTTTC
1 AAGATTTCAAATTTTA-AATAATTTTC
* *
42789749 AAGAATTAAAATTTTAAATAATTTTC
1 AAGATTTCAAATTTTAAATAATTTTC
42789775 AAGATTTCAAATTTTAAATAATTTTC
1 AAGATTTCAAATTTTAAATAATTTTC
*
42789801 AATATTTCAAATTTTA
1 AAGATTTCAAATTTTA
42789817 TCTAATTCTT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
26 58 0.94
27 4 0.06
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (26 bp):
AAGATTTCAAATTTTAAATAATTTTC
Found at i:42792162 original size:34 final size:34
Alignment explanation
Indices: 42792124--42792193 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
42792114 ATTAAATTAC
*
42792124 TTTTT-AAAAATTATT-TTATTTGATTTTATTTTTA
1 TTTTTCAAAAATTATTATTATTT--TTATATTTTTA
* *
42792158 TTTTTCACAATTTATTATTATTTTTATATTTTTA
1 TTTTTCAAAAATTATTATTATTTTTATATTTTTA
42792192 TT
1 TT
42792194 GAAAATACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 17 0.55
35 8 0.26
36 6 0.19
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (34 bp):
TTTTTCAAAAATTATTATTATTTTTATATTTTTA
Found at i:42792878 original size:67 final size:67
Alignment explanation
Indices: 42792770--42792907 Score: 267
Period size: 67 Copynumber: 2.1 Consensus size: 67
42792760 CTCAATTTAT
*
42792770 AATGGCAAACCACATAGACAACTAAGATTAGCCGTTGGAGTAGCAACTAGCATGCTTTACATCAT
1 AATGGCAAACCACATAGACAACTAAGATTAGCCATTGGAGTAGCAACTAGCATGCTTTACATCAT
42792835 AA
66 AA
42792837 AATGGCAAACCACATAGACAACTAAGATTAGCCATTGGAGTAGCAACTAGCATGCTTTACATCAT
1 AATGGCAAACCACATAGACAACTAAGATTAGCCATTGGAGTAGCAACTAGCATGCTTTACATCAT
42792902 AA
66 AA
42792904 AATG
1 AATG
42792908 CAGGTGTATG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.22
Consensus pattern (67 bp):
AATGGCAAACCACATAGACAACTAAGATTAGCCATTGGAGTAGCAACTAGCATGCTTTACATCAT
AA
Found at i:42793775 original size:15 final size:15
Alignment explanation
Indices: 42793757--42793811 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
42793747 ATTTGGATTA
*
42793757 ATTTATTTAAATATT
1 ATTTAATTAAATATT
42793772 ATTTAATTAATATAATT
1 ATTTAATTAA-AT-ATT
42793789 -TTT-A-TAAATATT
1 ATTTAATTAAATATT
42793801 ATTTAATTAAA
1 ATTTAATTAAA
42793812 ATAATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
14 4 0.12
15 14 0.41
16 5 0.15
17 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTAATTAAATATT
Found at i:42793787 original size:29 final size:29
Alignment explanation
Indices: 42793755--42793820 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
42793745 TAATTTGGAT
*
42793755 TAATTTATT-TAAATATTATTTAATTAATA
1 TAATTT-TTATAAATATTATTTAATTAAAA
42793784 TAATTTTTATAAATATTATTTAATTAAAA
1 TAATTTTTATAAATATTATTTAATTAAAA
42793813 TAATTTTT
1 TAATTTTT
42793821 TTCCATGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 2 0.06
29 33 0.94
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TAATTTTTATAAATATTATTTAATTAAAA
Found at i:42793793 original size:20 final size:20
Alignment explanation
Indices: 42793734--42793793 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
42793724 TCAATCTTAT
**
42793734 TTTAATTAATATAATTTGGA
1 TTTAATTAATATAATTTTTA
* * * *
42793754 -TTAATTTATTTAAATATTA
1 TTTAATTAATATAATTTTTA
42793773 TTTAATTAATATAATTTTTA
1 TTTAATTAATATAATTTTTA
42793793 T
1 T
42793794 AAATATTATT
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTAATTAATATAATTTTTA
Found at i:42794106 original size:9 final size:9
Alignment explanation
Indices: 42794092--42794160 Score: 102
Period size: 9 Copynumber: 7.7 Consensus size: 9
42794082 TATATACTTG
42794092 AACTTACAT
1 AACTTACAT
42794101 AACTTACAT
1 AACTTACAT
42794110 AACTTACAT
1 AACTTACAT
*
42794119 AACTCACAT
1 AACTTACAT
*
42794128 AACTCACAT
1 AACTTACAT
* *
42794137 AATTTACAG
1 AACTTACAT
42794146 AACTTACAT
1 AACTTACAT
42794155 AACTTA
1 AACTTA
42794161 ATTATACTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:42799218 original size:13 final size:14
Alignment explanation
Indices: 42799202--42799230 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42799192 TTATAATTAT
42799202 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
42799215 TTATAATGGTTTAA
1 TTATAATGGTTTAA
42799229 TT
1 TT
42799231 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:42799668 original size:21 final size:21
Alignment explanation
Indices: 42799644--42799714 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
42799634 AGAGCGAGAA
* *
42799644 GGAGGCAGCGAAAGCAGTAAG
1 GGAGGCAGCGACAGCAGTGAG
* * *
42799665 GGAGGCAGTGGCAGCAATGAG
1 GGAGGCAGCGACAGCAGTGAG
42799686 GGAGGCAGCGACAGCAGTGAG
1 GGAGGCAGCGACAGCAGTGAG
42799707 GGAGGCAG
1 GGAGGCAG
42799715 AGGTAACAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.31, C:0.15, G:0.48, T:0.06
Consensus pattern (21 bp):
GGAGGCAGCGACAGCAGTGAG
Found at i:42800177 original size:43 final size:43
Alignment explanation
Indices: 42800114--42800476 Score: 476
Period size: 43 Copynumber: 8.5 Consensus size: 43
42800104 GTGGAAGCGT
* * * * ** * *
42800114 CGCT-AAAGCCATGACTTTTAACGGCACTTTTATCACTAACAC
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * * ** *
42800156 CGCTAAAAGCTTTGACCTTTAACGGTGCTTTTATCACAAAAGC
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * * *
42800199 CACTAAAAGCCTTGACCTTTAGTGGCACTTTTCCCACAAATGC
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
42800242 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
* ** *
42800285 CGCTAAAAGCCTTGACCTTTAGCGACGCTTTTATCACAAAAGC
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
* *
42800328 CACTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAATGC
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
42800371 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
*
42800414 CGCTAAAAGCCTTGACCTTTAGCGACGCTTTTCCCACAAACGC
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
* *
42800457 CGCTAAAAGTCTTGATCTTT
1 CGCTAAAAGCCTTGACCTTT
42800477 TGTGGTGTTT
Statistics
Matches: 285, Mismatches: 35, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
42 4 0.01
43 281 0.99
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (43 bp):
CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGC
Found at i:42800348 original size:129 final size:129
Alignment explanation
Indices: 42800114--42800481 Score: 540
Period size: 129 Copynumber: 2.9 Consensus size: 129
42800104 GTGGAAGCGT
* * * * ** * * * *
42800114 CGCT-AAAGCCATGACTTTTAACGGCACTTTTATCACTAACACCGCTAAAAGCTTTGACCTTTAA
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACCTTTAG
**
42800178 CGGTGCTTTTATCACAAAAGCCACTAAAAGCCTTGACCTTTAGTGGCACTTTTCCCACAAATGC
66 CGACGCTTTTATCACAAAAGCCACTAAAAGCCTTGACCTTTAGTGGCACTTTTCCCACAAATGC
42800242 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACCTTTAG
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACCTTTAG
* *
42800307 CGACGCTTTTATCACAAAAGCCACTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAATGC
66 CGACGCTTTTATCACAAAAGCCACTAAAAGCCTTGACCTTTAGTGGCACTTTTCCCACAAATGC
42800371 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACCTTTAG
1 CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACCTTTAG
** * * * * *
42800436 CGACGCTTTTCCCACAAACGCCGCTAAAAGTCTTGATCTTTTGTGG
66 CGACGCTTTTATCACAAAAGCCACTAAAAGCCTTGACCTTTAGTGG
42800482 TGTTTTTTTC
Statistics
Matches: 217, Mismatches: 22, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
128 4 0.02
129 213 0.98
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (129 bp):
CGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACCTTTAG
CGACGCTTTTATCACAAAAGCCACTAAAAGCCTTGACCTTTAGTGGCACTTTTCCCACAAATGC
Found at i:42801650 original size:11 final size:11
Alignment explanation
Indices: 42801634--42801660 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
42801624 GATACACTCA
42801634 AAATATGATTT
1 AAATATGATTT
42801645 AAATATGATTT
1 AAATATGATTT
42801656 AAATA
1 AAATA
42801661 CTAATCCGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (11 bp):
AAATATGATTT
Found at i:42803995 original size:18 final size:18
Alignment explanation
Indices: 42803972--42804008 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
42803962 GCTATGAAAG
42803972 TTAGATGTTAGATAAACA
1 TTAGATGTTAGATAAACA
42803990 TTAGATGTTAGATAAACA
1 TTAGATGTTAGATAAACA
42804008 T
1 T
42804009 CTTTTACTAG
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:0.43, C:0.05, G:0.16, T:0.35
Consensus pattern (18 bp):
TTAGATGTTAGATAAACA
Found at i:42806763 original size:16 final size:17
Alignment explanation
Indices: 42806742--42806777 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
42806732 AATAATCATA
42806742 AATTAATTAATTTTC-C
1 AATTAATTAATTTTCTC
42806758 AATTAATTAATTTTCTC
1 AATTAATTAATTTTCTC
42806775 AAT
1 AAT
42806778 CCGATTCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTAATTAATTTTCTC
Found at i:42808175 original size:28 final size:28
Alignment explanation
Indices: 42808144--42808205 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
42808134 TTCAAATGAT
** *
42808144 TTCATACATGCAGGTTCGTAGATACAGA
1 TTCATACATGCAGAATCATAGATACAGA
* *
42808172 TTCATACATGCTGAATCATAGTTACAGA
1 TTCATACATGCAGAATCATAGATACAGA
42808200 TTCATA
1 TTCATA
42808206 AAGGCAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (28 bp):
TTCATACATGCAGAATCATAGATACAGA
Found at i:42808260 original size:14 final size:14
Alignment explanation
Indices: 42808144--42808278 Score: 56
Period size: 14 Copynumber: 9.6 Consensus size: 14
42808134 TTCAAATGAT
*
42808144 TTCATACATGCAGG
1 TTCATACATGCAGA
* * *
42808158 TTCGTAGATACAGA
1 TTCATACATGCAGA
*
42808172 TTCATACATGCTGA
1 TTCATACATGCAGA
* ** *
42808186 ATCATAGTTACAGA
1 TTCATACATGCAGA
* * *
42808200 TTCATAAAGGCAAA
1 TTCATACATGCAGA
** **
42808214 TTTGTACATGTGGA
1 TTCATACATGCAGA
* * **
42808228 TTTATAGACACAGA
1 TTCATACATGCAGA
*
42808242 CTCATACATGCAGA
1 TTCATACATGCAGA
*
42808256 TTCAT-CAATACAGA
1 TTCATAC-ATGCAGA
42808270 TTCATACAT
1 TTCATACAT
42808279 ATGAACTCAT
Statistics
Matches: 80, Mismatches: 39, Indels: 4
0.65 0.32 0.03
Matches are distributed among these distances:
13 1 0.01
14 78 0.98
15 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (14 bp):
TTCATACATGCAGA
Found at i:42808401 original size:28 final size:28
Alignment explanation
Indices: 42808364--42808448 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 28
42808354 TAGTTAGTTT
*
42808364 ATGCAGACTCTTACTT-AAATGATAGTCC
1 ATGCAAACTCTTACTTGAAA-GATAGTCC
*
42808392 ATGCGAACTCTTACTTGAAAGATAGTCC
1 ATGCAAACTCTTACTTGAAAGATAGTCC
* *
42808420 ATGCAAACTCTTGCTTGGAAGATAGTCC
1 ATGCAAACTCTTACTTGAAAGATAGTCC
42808448 A
1 A
42808449 AGCAGGGTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
28 48 0.94
29 3 0.06
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (28 bp):
ATGCAAACTCTTACTTGAAAGATAGTCC
Found at i:42811971 original size:17 final size:18
Alignment explanation
Indices: 42811949--42811984 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
42811939 TAATCTTGTT
42811949 TTAATAAATTAATA-GCA
1 TTAATAAATTAATATGCA
*
42811966 TTAATAATTTAATATGCA
1 TTAATAAATTAATATGCA
42811984 T
1 T
42811985 ATATTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (18 bp):
TTAATAAATTAATATGCA
Found at i:42814829 original size:43 final size:42
Alignment explanation
Indices: 42814766--42814922 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 42
42814756 TATGTGTTCT
* * * *
42814766 CGTGTAAGAACACGTCTGGGACGTTGGCATTGATATGTGATTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATATATGA-TA
* * ** * *
42814809 CGTGTAAGACCATGTTTGGGACATCAGAATCG-TATTTGACT-
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATATATGA-TA
* *
42814850 CGTGTAAGACC-CTGTGTGGGACAGTGGCATCGATATATGATA
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCGATATATGATA
*
42814892 GCATGTAAGACCACGTCTGGGACATTGGCAT
1 -CGTGTAAGACCACGTCTGGGACATTGGCAT
42814923 TGTACAATAT
Statistics
Matches: 89, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
41 26 0.29
42 13 0.15
43 49 0.55
44 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGATATATGATA
Found at i:42816564 original size:645 final size:648
Alignment explanation
Indices: 42815319--42816619 Score: 2419
Period size: 645 Copynumber: 2.0 Consensus size: 648
42815309 AGATTAAATG
*
42815319 ATATTTTGATATTGGATATATATAAATTCAGCTAAATGAAAGTACATGTTGTATATGAAATCGTG
1 ATATATTGATATTGGATATATATAAATTCAGCTAAATGAAAGTACATGTTGTATATGAAATCGTG
42815384 AGCTTGAAAATAAATGTTACCATGATAGCATAAATTAGTTTGGTTAAGTTGAGTTGATATTAACA
66 AGCTTGAAAATAAATGTTACCATGATAGCATAAATTAGTTTGGTTAAGTTGAGTTGATATTAACA
42815449 TCGAGTTATTTATTTGCTTATAACTTATTAAGCTATGATAGCTTACTATGTGTGTTTATGTTTGC
131 TCGAGTTATTTATTTGCTTATAACTTATTAAGCTATGATAGCTTACTATGTGTGTTTATGTTTGC
*
42815514 CTTTGTTTTGTAGCTTTTGGAGATTAGTTACGAGCTCGGGCATCGTCAGCAAAGTCTATCACACT
196 CTTTGTTTTATAGCTTTTGGAGATTAGTTACGAGCTCGGGCATCGTCAGCAAAGTCTATCACACT
*
42815579 ATCGACTGTTTTGGGTATTTTATAAGTTTGAACTTGAACCTATGGCATGTATAGGCTAGGTCATA
261 ATCGACTATTTTGGGTATTTTATAAGTTTGAACTTGAACCTATGGCATGTATAGGCTAGGTCATA
42815644 TTTGGTTAAGTTTGAAGTTGTGTATATATTAAGCCATGCGAAAAATGGCTATTATGATATGTGAG
326 TTTGGTTAAGTTTGAAGTTGTGTATATATTAAGCCATGCGAAAAATGGCTATTATGATATGTGAG
*
42815709 TATATTAAATTCTAGTCAAGTTTATATGTGTTATATGCATTGAAAATGGTTGGTGATTTTGGATG
391 TATATGAAATTCTAGTCAAGTTTATATGTGTTATATGCATTGAAAATGGTTGGTGATTTTGGATG
42815774 TGTGTTTGGTTGATTCAGCTTTGGTTCATGCATAGATAAATATATATATGTGAACTTGGTTGATG
456 TGTGTTTGGTTGATTCAGCTTTGGTTCATGCATAGATAAATATATATATGTGAACTTGGTTGATG
* *
42815839 TGCTTTGTTAAGGTATCACAAATAGCCTATGGTTAGCTCAGTTTTGGTAAGTTTGATGTATGGTA
521 TGCTTTGTTAAGGTATCACAAATAGCCTATGGTTAGCTCACTTTTGGTAAGTTTGATATATGGTA
*
42815904 TGTTTTGTCTTTGAGAATGGCTTATTAATTTGGCTTAGTAATGGAGTAAAATGATAATGATAT
586 TGTTTTGTATTTGAGAATGGCTTATTAATTTGGCTTAGTAATGGAGTAAAATGATAATGATAT
*
42815967 ATATATTGATATTGGATATATGTAAATTCAGCTAAATGAAAGTACATGTTGTATATGAAATCGTG
1 ATATATTGATATTGGATATATATAAATTCAGCTAAATGAAAGTACATGTTGTATATGAAATCGTG
* *
42816032 AGCTTGAAAATAAATGTTACCATGATATCATAAATTAGTTTGGTTAGGTTGAGTTGATATTAACA
66 AGCTTGAAAATAAATGTTACCATGATAGCATAAATTAGTTTGGTTAAGTTGAGTTGATATTAACA
* *
42816097 TTGAGTTATTTATTTGC-TATAACTTATTAAGCTATGATAGCTTACTATGTGTGTTTATGTTTTC
131 TCGAGTTATTTATTTGCTTATAACTTATTAAGCTATGATAGCTTACTATGTGTGTTTATGTTTGC
* *
42816161 CTTTGTTTTATAGCTTTTGGAGATTAGTTACGAGCTCGGGGATCGTTAGCAAAGTCTATCACACT
196 CTTTGTTTTATAGCTTTTGGAGATTAGTTACGAGCTCGGGCATCGTCAGCAAAGTCTATCACACT
*
42816226 ATCGACTATTTTTGGTATTTTATAAGTTTGAACTTGAACCTATGGCATGTATAGGCTAGGTCAT-
261 ATCGACTATTTTGGGTATTTTATAAGTTTGAACTTGAACCTATGGCATGTATAGGCTAGGTCATA
42816290 TTTGGTTAAGTTTGAAGTTGTGTATATATTAAGCCATGCG-AAAATGGCTATTATGATATGTGAG
326 TTTGGTTAAGTTTGAAGTTGTGTATATATTAAGCCATGCGAAAAATGGCTATTATGATATGTGAG
42816354 TATATGAAATTCTAGTCAAGTTTATATGTGTTATATGCATTGAAAATGGTTGGTGATTTTGGATG
391 TATATGAAATTCTAGTCAAGTTTATATGTGTTATATGCATTGAAAATGGTTGGTGATTTTGGATG
*
42816419 TGTGTTTGGTTGATTCGGCTTTGGTTCATGCATAGATAAATATATATATGTGAACTTGGTTGATG
456 TGTGTTTGGTTGATTCAGCTTTGGTTCATGCATAGATAAATATATATATGTGAACTTGGTTGATG
42816484 TGCTTTGTTAAGGTATCACAAATAGCCTATGGTTAGCTCACTTTTGGTAAGTTTGATATATGGTA
521 TGCTTTGTTAAGGTATCACAAATAGCCTATGGTTAGCTCACTTTTGGTAAGTTTGATATATGGTA
* *
42816549 TGTTTTGTATTTGAGAATGGTTTATTAATTTGGCTTAGTAATGGAGTAAAATGTTAATGATAT
586 TGTTTTGTATTTGAGAATGGCTTATTAATTTGGCTTAGTAATGGAGTAAAATGATAATGATAT
42816612 ATATATTG
1 ATATATTG
42816620 GAATGGGTAC
Statistics
Matches: 635, Mismatches: 18, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
645 283 0.45
646 40 0.06
647 170 0.27
648 142 0.22
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (648 bp):
ATATATTGATATTGGATATATATAAATTCAGCTAAATGAAAGTACATGTTGTATATGAAATCGTG
AGCTTGAAAATAAATGTTACCATGATAGCATAAATTAGTTTGGTTAAGTTGAGTTGATATTAACA
TCGAGTTATTTATTTGCTTATAACTTATTAAGCTATGATAGCTTACTATGTGTGTTTATGTTTGC
CTTTGTTTTATAGCTTTTGGAGATTAGTTACGAGCTCGGGCATCGTCAGCAAAGTCTATCACACT
ATCGACTATTTTGGGTATTTTATAAGTTTGAACTTGAACCTATGGCATGTATAGGCTAGGTCATA
TTTGGTTAAGTTTGAAGTTGTGTATATATTAAGCCATGCGAAAAATGGCTATTATGATATGTGAG
TATATGAAATTCTAGTCAAGTTTATATGTGTTATATGCATTGAAAATGGTTGGTGATTTTGGATG
TGTGTTTGGTTGATTCAGCTTTGGTTCATGCATAGATAAATATATATATGTGAACTTGGTTGATG
TGCTTTGTTAAGGTATCACAAATAGCCTATGGTTAGCTCACTTTTGGTAAGTTTGATATATGGTA
TGTTTTGTATTTGAGAATGGCTTATTAATTTGGCTTAGTAATGGAGTAAAATGATAATGATAT
Found at i:42845264 original size:43 final size:43
Alignment explanation
Indices: 42845157--42845257 Score: 141
Period size: 43 Copynumber: 2.3 Consensus size: 43
42845147 GAGATGTGAA
* *
42845157 TATGTGTAAGACCATGTCTAGGACATTGGCATCATTATGAGAT
1 TATGTGTAAGACCATGTCTGGGACATTAGCATCATTATGAGAT
* **
42845200 TATGCGTAAGACCATGTCTGGGACATTAGCATCATTATTTGAT
1 TATGTGTAAGACCATGTCTGGGACATTAGCATCATTATGAGAT
42845243 T-TCGTGTAAGACCAT
1 TAT-GTGTAAGACCAT
42845258 AGCTGGGCTA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 1 0.02
43 50 0.98
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (43 bp):
TATGTGTAAGACCATGTCTGGGACATTAGCATCATTATGAGAT
Found at i:42847455 original size:45 final size:45
Alignment explanation
Indices: 42847391--42847482 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
42847381 TTACCCGTGA
*
42847391 ATGCACAAAATTTATTTCCAAACTTGAGGATAAACCTAAATGCAT
1 ATGCACAAAATTTATTTCCAAACCTGAGGATAAACCTAAATGCAT
*
42847436 ATGCACAAAATTTATTTCCAAACCTGAGGATAAACTTAAATGCAT
1 ATGCACAAAATTTATTTCCAAACCTGAGGATAAACCTAAATGCAT
42847481 AT
1 AT
42847483 AACTCAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.29
Consensus pattern (45 bp):
ATGCACAAAATTTATTTCCAAACCTGAGGATAAACCTAAATGCAT
Found at i:42850866 original size:50 final size:49
Alignment explanation
Indices: 42850813--42850979 Score: 167
Period size: 50 Copynumber: 3.4 Consensus size: 49
42850803 CTAAATAATG
* * *
42850813 GTAAGCTCATACGAGCTGAGTATCGATAAGCTCTCACGAGATGAAAATCG
1 GTAAGCTCATACGAGCTGAGTAT-GATAAGCTCTCATGAGCTGAAAATCA
* ** ** *
42850863 GTAAGCTCATACGAGCTGTA-AATGGCAAGCTCTTTTGAGCT-AAATAACA
1 GTAAGCTCATACGAGCTG-AGTATGATAAGCTCTCATGAGCTGAAA-ATCA
* * *
42850912 GCAAGCTAATACGAGTTGAGTATTGATAAGCTCTCATGAGCTGAAAATCA
1 GTAAGCTCATACGAGCTGAGTA-TGATAAGCTCTCATGAGCTGAAAATCA
*
42850962 GTAAGCTCACACGAGCTG
1 GTAAGCTCATACGAGCTG
42850980 TCGTGTGTCC
Statistics
Matches: 90, Mismatches: 22, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
48 4 0.04
49 30 0.33
50 52 0.58
51 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (49 bp):
GTAAGCTCATACGAGCTGAGTATGATAAGCTCTCATGAGCTGAAAATCA
Found at i:42850885 original size:25 final size:24
Alignment explanation
Indices: 42850768--42850894 Score: 105
Period size: 25 Copynumber: 5.2 Consensus size: 24
42850758 GTACATGTAT
*
42850768 GCTCATACGAGCT-ATAAATGATAA
1 GCTCATACGAGCTGA-AAATGGTAA
* * *
42850792 GCTCCTTCGAGCTAAATAATGGTAA
1 GCTCATACGAGCTGAA-AATGGTAA
** *
42850817 GCTCATACGAGCTGAGTATCGATAA
1 GCTCATACGAGCTGAAAAT-GGTAA
*
42850842 GCTC-TCACGAGATGAAAATCGGTAA
1 GCTCAT-ACGAGCTGAAAAT-GGTAA
* *
42850867 GCTCATACGAGCTGTAAATGGCAA
1 GCTCATACGAGCTGAAAATGGTAA
42850891 GCTC
1 GCTC
42850895 TTTTGAGCTA
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
24 23 0.28
25 58 0.71
26 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (24 bp):
GCTCATACGAGCTGAAAATGGTAA
Found at i:42850940 original size:99 final size:99
Alignment explanation
Indices: 42850768--42850980 Score: 291
Period size: 99 Copynumber: 2.2 Consensus size: 99
42850758 GTACATGTAT
* * ** * *
42850768 GCTCATACGAGCTATAAATGATAAGCTCCTTCGAGCTAAATAATGGTAAGCTCATACGAGCTGAG
1 GCTCATACGAGCTGTAAATGACAAGCTCCTTCGAGCTAAATAACAGCAAGCTAATACGAGCTGAG
*
42850833 TATCGATAAGCTCTCACGAGATGAAAATCGGTAA
66 TATCGATAAGCTCTCACGAGATGAAAATCAGTAA
* * * *
42850867 GCTCATACGAGCTGTAAATGGCAAGCTCTTTTGAGCTAAATAACAGCAAGCTAATACGAGTTGAG
1 GCTCATACGAGCTGTAAATGACAAGCTCCTTCGAGCTAAATAACAGCAAGCTAATACGAGCTGAG
* * *
42850932 TATTGATAAGCTCTCATGAGCTGAAAATCAGTAA
66 TATCGATAAGCTCTCACGAGATGAAAATCAGTAA
*
42850966 GCTCACACGAGCTGT
1 GCTCATACGAGCTGT
42850981 CGTGTGTCCG
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (99 bp):
GCTCATACGAGCTGTAAATGACAAGCTCCTTCGAGCTAAATAACAGCAAGCTAATACGAGCTGAG
TATCGATAAGCTCTCACGAGATGAAAATCAGTAA
Found at i:42855274 original size:41 final size:40
Alignment explanation
Indices: 42855131--42855495 Score: 423
Period size: 41 Copynumber: 8.9 Consensus size: 40
42855121 TTTTAAAATA
* *
42855131 CAGAGCAATAGCGGCG-TTTTAAGAAAAACGCCGCTAAAAA-
1 CAGAGCATTAGCGGCGCTTTT--GTAAAACGCCGCTAAAAAC
** * * * * *
42855171 CAGAGCAACAGCAGTGTTTTTTACTAAAACACCGCTAAAAA-
1 CAGAGCATTAGCGGCG-CTTTT-GTAAAACGCCGCTAAAAAC
*
42855212 CAGAGCATTAGCGGCACTTTTGTCAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTTGT-AAAACGCCGCTAAAAAC
* *
42855253 CAGATCATTAGCGGCGCTTTTGCTAAAACGCCACTAAAAAC
1 CAGAGCATTAGCGGCGCTTTTG-TAAAACGCCGCTAAAAAC
* *
42855294 CAGATCATTAGCGGCG-TTTGGGTAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTT-TGTAAAACGCCGCTAAAAAC
*
42855334 CAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTTG-TAAAACGCCGCTAAAAAC
**
42855375 CAGAGCATTAGCGGCGCTTTCAATAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTT-TGTAAAACGCCGCTAAAAAC
* *
42855416 CAAAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTT-TGTAAAACGCCGCTAAAAAC
*
42855457 CAGAGCATTAGCGGCGCTTTTGGTAAAATGCCGCTAAAA
1 CAGAGCATTAGCGGCGCTTTT-GTAAAACGCCGCTAAAA
42855496 GTCATAGAAC
Statistics
Matches: 286, Mismatches: 29, Indels: 19
0.86 0.09 0.06
Matches are distributed among these distances:
39 1 0.00
40 68 0.24
41 212 0.74
42 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (40 bp):
CAGAGCATTAGCGGCGCTTTTGTAAAACGCCGCTAAAAAC
Found at i:42855279 original size:81 final size:82
Alignment explanation
Indices: 42855131--42855495 Score: 434
Period size: 81 Copynumber: 4.5 Consensus size: 82
42855121 TTTTAAAATA
* * ** * ** * * * **
42855131 CAGAGCAATAGCGGCGTTTTAAGAAAAACGCCGCTAAAAA-CAGAGCAACAGCAGTGTTTTTTAC
1 CAGAGCATTAGCGGCGCTTTCTGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCG-CTTTCGC
*
42855195 TAAAACACCGCTAAAAA-
65 TAAAACGCCGCTAAAAAC
* * *
42855212 CAGAGCATTAGCGGCACTTT-TGTCAAAACGCCGCTAAAAACCAGATCATTAGCGGCGCTTTTGC
1 CAGAGCATTAGCGGCGCTTTCTGT-AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGC
*
42855276 TAAAACGCCACTAAAAAC
65 TAAAACGCCGCTAAAAAC
* ** *
42855294 CAGATCATTAGCGGCG-TTTGGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGAT
1 CAGAGCATTAGCGGCGCTTTCTGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGCT
42855358 AAAACGCCGCTAAAAAC
66 AAAACGCCGCTAAAAAC
** * *
42855375 CAGAGCATTAGCGGCGCTTTCAATAAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTTCGGT
1 CAGAGCATTAGCGGCGCTTTCTGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGCT
42855440 AAAACGCCGCTAAAAAC
66 AAAACGCCGCTAAAAAC
*
42855457 CAGAGCATTAGCGGCGCTTT-TGGTAAAATGCCGCTAAAA
1 CAGAGCATTAGCGGCGCTTTCT-GTAAAACGCCGCTAAAA
42855496 GTCATAGAAC
Statistics
Matches: 248, Mismatches: 30, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
80 1 0.00
81 125 0.50
82 122 0.49
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (82 bp):
CAGAGCATTAGCGGCGCTTTCTGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGCT
AAAACGCCGCTAAAAAC
Found at i:42855341 original size:122 final size:122
Alignment explanation
Indices: 42855195--42855495 Score: 453
Period size: 122 Copynumber: 2.5 Consensus size: 122
42855185 TGTTTTTTAC
* * *
42855195 TAAAACACCGCTAAAAA-CAGAGCATTAGCGGCACTTTTGTCAAAACGCCGCTAAAAACCAGATC
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGT-AAAACGCCGCTAAAAACCAGAGC
*** * * *
42855259 ATTAGCGGCGCTTTTGCTAAAACGCCACTAAAAACCAGATCATTAGCGGCG-TTTGGG
65 ATTAGCGGCGCTTTCAATAAAACGCCACTAAAAACCAAAGCATTAGCGGCGCTTTCGG
*
42855316 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGC
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTG-TAAAACGCCGCTAAAAACCAGAGC
*
42855381 ATTAGCGGCGCTTTCAATAAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTTCGG
65 ATTAGCGGCGCTTTCAATAAAACGCCACTAAAAACCAAAGCATTAGCGGCGCTTTCGG
*
42855439 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAATGCCGCTAAAA
1 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTT-GTAAAACGCCGCTAAAA
42855496 GTCATAGAAC
Statistics
Matches: 163, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
121 16 0.10
122 87 0.53
123 59 0.36
124 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (122 bp):
TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGTAAAACGCCGCTAAAAACCAGAGCA
TTAGCGGCGCTTTCAATAAAACGCCACTAAAAACCAAAGCATTAGCGGCGCTTTCGG
Found at i:42855745 original size:36 final size:39
Alignment explanation
Indices: 42855675--42855750 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 39
42855665 ATAGTTTAAG
* * *
42855675 ATATATGGTTTAGGGTTTAAGCAGGTTTATGAGTTAACT
1 ATATATGGTTTAAGATTTAAGCAGGTTTAGGAGTTAACT
42855714 ATATATGGTTTAAGATTT-A-C-GGTTTAGGAGTTAACT
1 ATATATGGTTTAAGATTTAAGCAGGTTTAGGAGTTAACT
42855750 A
1 A
42855751 GTAATTGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 16 0.47
37 1 0.03
38 1 0.03
39 16 0.47
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (39 bp):
ATATATGGTTTAAGATTTAAGCAGGTTTAGGAGTTAACT
Found at i:42855938 original size:25 final size:25
Alignment explanation
Indices: 42855909--42855960 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
42855899 GTGATTTTGA
42855909 ATGTGGAATTAGCATTTGTTGAACT
1 ATGTGGAATTAGCATTTGTTGAACT
42855934 ATGTGGAATTAGCATTTGTTGAACT
1 ATGTGGAATTAGCATTTGTTGAACT
42855959 AT
1 AT
42855961 TAGCTAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (25 bp):
ATGTGGAATTAGCATTTGTTGAACT
Found at i:42856342 original size:17 final size:17
Alignment explanation
Indices: 42856320--42856353 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42856310 TTTAATTTAG
*
42856320 AAGATAAATGTATATAT
1 AAGATAAATATATATAT
42856337 AAGATAAATATATATAT
1 AAGATAAATATATATAT
42856354 TATTATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (17 bp):
AAGATAAATATATATAT
Found at i:42856386 original size:22 final size:21
Alignment explanation
Indices: 42856331--42856388 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
42856321 AGATAAATGT
*
42856331 ATATATAAGATAAATATATATA
1 ATATATATGA-AAATATATATA
* *
42856353 TTATTATTTGAAAATATATATAA
1 ATA-TATATGAAAATATATAT-A
42856376 ATATATATGAAAA
1 ATATATATGAAAA
42856389 GTGGTTTAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
ATATATATGAAAATATATATA
Found at i:42858576 original size:23 final size:23
Alignment explanation
Indices: 42858550--42858596 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
42858540 GAGCTTGGTC
42858550 CTATTTCTCCTGTTAATGGTATA
1 CTATTTCTCCTGTTAATGGTATA
*
42858573 CTATTTCTCCTGTTAATGTTATA
1 CTATTTCTCCTGTTAATGGTATA
42858596 C
1 C
42858597 CAAATTGCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.49
Consensus pattern (23 bp):
CTATTTCTCCTGTTAATGGTATA
Found at i:42861571 original size:468 final size:466
Alignment explanation
Indices: 42860568--42861814 Score: 2401
Period size: 468 Copynumber: 2.7 Consensus size: 466
42860558 CAATAGCTGA
42860568 GCTTGTCCATTCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGG
1 GCTTGTCCATTCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGG
42860633 TTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATG
66 TTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATG
* *
42860698 AATCTTAAAAAATTCAAAAAGAATTGAAAAAAGTTCTATCACTATTGAATATTTATATAACCTTA
131 AATCTTAAAAAATTCAAGAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTA
42860763 ATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAA-
196 ATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAAT
42860827 TACTATTTTGTTATATTAATAATG-TTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGT
261 TACTATTTTGTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGT
42860891 TATAAATAATTTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTT
326 TATAAATAATTTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTT
42860956 TTATATTTTGGTTCAACTTAATTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCAT
391 TTATATTTTGGTTCAACTTAATTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCAT
42861021 ATATGTAGCTT
456 ATATGTAGCTT
* *
42861032 GCTTGTCCATTCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTAGAAACCTGACGGA
1 GCTTGTCCATTCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGG
*
42861097 TTGCCTTATATCGAGTTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATG
66 TTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATG
42861162 AATCTTAAAAAATTCAAGAAGAATTGAAAAAAGTTC-ATCGCTATTGAATATTTATATAACCTTA
131 AATCTTAAAAAATTCAAGAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTA
42861226 ATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAAT
196 ATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAAT
42861291 TACTATTTTGTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGT
261 TACTATTTTGTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGT
42861356 TATAAATAATTTTTATCAAAATAGTATTAATTATTATTTGAAGTAATGAATAAGTATGAATAAGT
326 TATAAATAA-TTTTATCAAAATAGTATTAATTATTATTTGAAGT-ATGAATAAGTATGAATAAGT
42861421 TTTTATATTTTGGTTCAACTTAATTTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTAC
389 TTTTATATTTTGGTTCAACTTAA-TTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTAC
42861486 CATATATGTAGCTT
453 CATATATGTAGCTT
42861500 GCTTGTCCATTCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGG
1 GCTTGTCCATTCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGG
42861565 TTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATG
66 TTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATG
42861630 AATCTTAAAAAATTCAAGAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTA
131 AATCTTAAAAAATTCAAGAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTA
42861695 ATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAAT
196 ATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAAT
42861760 TACTATTTTGTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGT
261 TACTATTTTGTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGT
42861815 ATTTGTTATA
Statistics
Matches: 769, Mismatches: 8, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
463 91 0.12
464 186 0.24
465 49 0.06
466 34 0.04
467 43 0.06
468 218 0.28
469 148 0.19
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (466 bp):
GCTTGTCCATTCCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGG
TTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATG
AATCTTAAAAAATTCAAGAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTA
ATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAAT
TACTATTTTGTTATATTAATAATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGT
TATAAATAATTTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTT
TTATATTTTGGTTCAACTTAATTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCAT
ATATGTAGCTT
Found at i:42867634 original size:21 final size:21
Alignment explanation
Indices: 42867608--42867655 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
42867598 TCAACTTAGA
*
42867608 GCGGAGGTAGCAGCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
42867629 GCGGAGGCAGCAGCGAGGGAG
1 GCGGAGGCAGCAGCGAGGGAG
42867650 GCGGAG
1 GCGGAG
42867656 CAGAACAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.17, G:0.58, T:0.02
Consensus pattern (21 bp):
GCGGAGGCAGCAGCGAGGGAG
Found at i:42868002 original size:43 final size:43
Alignment explanation
Indices: 42867954--42868328 Score: 484
Period size: 43 Copynumber: 8.7 Consensus size: 43
42867944 ACTGGGCAAA
* * * * *
42867954 TTAGCGGCGTTTTTTAAAAAAGCACCGCTAAAAGTACAGGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
*
42867997 ATAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* * *
42868040 TTAGCGGTGTTTTTTATAAAAGCACCGCTAAAGGTCCTGATCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* * * *
42868083 TTAGCGGCGTTTTTTCTAAAAGCGCCGCTAAAAGTACAGGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* *
42868126 ATAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTTT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
*
42868169 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGGTCCTGGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* * * *
42868212 TTGGCGGCG-TTTTTATAAGAGCACCGCTAAAGGTCCTGGTCA
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* *
42868254 TTGGCGGCG-TTTTTATAAGAGCGCCGCTAAAGGTCCTGGTCT
1 TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
* * * *
42868296 TTAACAGCGCTTTTTTCTGAAAAACGCCGCTAA
1 TTAGCGGCG-TTTTTTAT-AAAAGCGCCGCTAA
42868329 TTTTTGTGGC
Statistics
Matches: 290, Mismatches: 39, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
42 75 0.26
43 197 0.68
44 6 0.02
45 12 0.04
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGGTCCTGGTCT
Found at i:42869821 original size:55 final size:55
Alignment explanation
Indices: 42869738--42869859 Score: 201
Period size: 55 Copynumber: 2.2 Consensus size: 55
42869728 GCACTTAAAA
* * * *
42869738 TTTT-AAGTCATTCTTGTACACGGGCAGGCCACACGGGCGTGTGCCATGGCCGTG
1 TTTTAAAGTCAGTATTGTACACGGGCAGGCCACACGGGCGTATGCCATGGCCGGG
42869792 TTTTAAAGTCAGTATTGTACACGGGCAGGCCACACGGGCGTATGCCATGGCCGGG
1 TTTTAAAGTCAGTATTGTACACGGGCAGGCCACACGGGCGTATGCCATGGCCGGG
42869847 TTTTAAAGTCAGT
1 TTTTAAAGTCAGT
42869860 GTTGCATACG
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
54 4 0.06
55 59 0.94
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.26
Consensus pattern (55 bp):
TTTTAAAGTCAGTATTGTACACGGGCAGGCCACACGGGCGTATGCCATGGCCGGG
Found at i:42878857 original size:15 final size:13
Alignment explanation
Indices: 42878819--42878860 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
42878809 ACCTCTTGTA
*
42878819 AAAAGAAAATGAG
1 AAAAGAAAAAGAG
42878832 AAAAGAAAAAGATG
1 AAAAGAAAAAGA-G
42878846 AAAAGCAAAAAGAG
1 AAAAG-AAAAAGAG
42878860 A
1 A
42878861 TCAAAAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 8 0.31
15 7 0.27
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.05
Consensus pattern (13 bp):
AAAAGAAAAAGAG
Found at i:42880388 original size:46 final size:46
Alignment explanation
Indices: 42880338--42880513 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
42880328 TGGTTGAGCA
*
42880338 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
42880384 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
42880431 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
42880477 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42880514 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 62 0.58
47 28 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:42880494 original size:93 final size:93
Alignment explanation
Indices: 42880335--42880506 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
42880325 GGATGGTTGA
* * *
42880335 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
*
42880400 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
42880428 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
42880493 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42880507 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42883486 original size:14 final size:15
Alignment explanation
Indices: 42883437--42883486 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
42883427 GTATCTTGGG
*
42883437 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
42883452 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
42883467 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
42883481 TTTCTT
1 TTTCTT
42883487 GTTATCTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.10, C:0.18, G:0.12, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:42885923 original size:46 final size:45
Alignment explanation
Indices: 42885870--42886039 Score: 179
Period size: 47 Copynumber: 3.8 Consensus size: 45
42885860 TTGAGCATCT
42885870 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA-GTCC
* * *
42885916 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A-G--TCC
* * *
42885963 GAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGC-GAGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGTCC
* *
42886007 GAGCTCGTTGA-TTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42886040 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
43 26 0.25
44 12 0.11
45 4 0.04
46 27 0.26
47 30 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGTCC
Found at i:42895906 original size:34 final size:36
Alignment explanation
Indices: 42895868--42895943 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 36
42895858 TTATTACTAA
*
42895868 AATAAATTTGTAAT-ATTAAATAATTTAATA-AAAT
1 AATAAATTTGTAATAATTAAATAATTAAATACAAAT
* * *
42895902 AATAAA-TTGTATTAATTATATTATTAAATACAAAT
1 AATAAATTTGTAATAATTAAATAATTAAATACAAAT
42895937 AATAAAT
1 AATAAAT
42895944 ACGTATGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 6 0.17
34 19 0.54
35 10 0.29
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (36 bp):
AATAAATTTGTAATAATTAAATAATTAAATACAAAT
Found at i:42903990 original size:142 final size:142
Alignment explanation
Indices: 42903733--42904016 Score: 541
Period size: 142 Copynumber: 2.0 Consensus size: 142
42903723 GCTGCTAAGG
42903733 ATATTTGGGCTCAAGTTAATCAAGGTAAGTATATTTCTAATTTTTTTTCAATTCCCACTCAAGAC
1 ATATTTGGGCTCAAGTTAATCAAGGTAAGTATATTTCTAATTTTTTTTCAATTCCCACTCAAGAC
42903798 TGGATTCTTCTTAATTTACAGGTAAATAGGTTGATCCATGCGGGAAGAGCTAATTGGGCTTGTTT
66 TGGATTCTTCTTAATTTACAGGTAAATAGGTTGATCCATGCGGGAAGAGCTAATTGGGCTTGTTT
42903863 ATTTGGTCTTCT
131 ATTTGGTCTTCT
*
42903875 ATATTTGGGCTCAAGTTAATCAAGGTAAGTATATTTCTATTTTTTTTTCAATTCCCACTCAAGAC
1 ATATTTGGGCTCAAGTTAATCAAGGTAAGTATATTTCTAATTTTTTTTCAATTCCCACTCAAGAC
* *
42903940 TGGATTCTTCTTAATTTATAGGTAAATAGGTTGATCCATGCGGGAGGAGCTAATTGGGCTTGTTT
66 TGGATTCTTCTTAATTTACAGGTAAATAGGTTGATCCATGCGGGAAGAGCTAATTGGGCTTGTTT
42904005 ATTTGGTCTTCT
131 ATTTGGTCTTCT
42904017 TATGTGGCAT
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 139 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (142 bp):
ATATTTGGGCTCAAGTTAATCAAGGTAAGTATATTTCTAATTTTTTTTCAATTCCCACTCAAGAC
TGGATTCTTCTTAATTTACAGGTAAATAGGTTGATCCATGCGGGAAGAGCTAATTGGGCTTGTTT
ATTTGGTCTTCT
Found at i:42906552 original size:12 final size:12
Alignment explanation
Indices: 42906530--42906562 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42906520 AAAAATTTAA
42906530 ATTTT-ATTTTG
1 ATTTTAATTTTG
42906541 ATTTTAATTTTG
1 ATTTTAATTTTG
*
42906553 ATTCTAATTT
1 ATTTTAATTT
42906563 ATGTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (12 bp):
ATTTTAATTTTG
Found at i:42914622 original size:41 final size:41
Alignment explanation
Indices: 42914565--42914649 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
42914555 ACATGGGCTG
*
42914565 ATTCAATTGGATCAATGATTATATGATTAATTGT-ACAATTT
1 ATTCAATTGGATCAATGATTATATAATTAA-TGTCACAATTT
*
42914606 ATTCAATTGGATCAATGATTGTATAATTAATGTCACAATTT
1 ATTCAATTGGATCAATGATTATATAATTAATGTCACAATTT
42914647 ATT
1 ATT
42914650 TGATTACGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 3 0.07
41 38 0.93
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (41 bp):
ATTCAATTGGATCAATGATTATATAATTAATGTCACAATTT
Found at i:42915133 original size:40 final size:41
Alignment explanation
Indices: 42915066--42915143 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42915056 ATGGACTAAT
*
42915066 TCAATTGGATAAATGATTGTACGATTAATAT-ACAATTTAC
1 TCAATTGGATAAATGATTGTACAATTAATATCACAATTTAC
* * *
42915106 TCAATTGGATTATTGAATT-TACAATTAATGTCACAATT
1 TCAATTGGATAAATG-ATTGTACAATTAATATCACAATT
42915144 CATTGGACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 23 0.72
41 9 0.28
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (41 bp):
TCAATTGGATAAATGATTGTACAATTAATATCACAATTTAC
Found at i:42915403 original size:498 final size:494
Alignment explanation
Indices: 42914441--42916203 Score: 2132
Period size: 498 Copynumber: 3.6 Consensus size: 494
42914431 CAAGTGTCAT
* *
42914441 ATAAATACTCTTAAATTAATCAAATATTTGAAATTAAACATAAGTGATCCAAAGTTTTGA-TATA
1 ATAAATACTCTTAAATTAATCAAATATTTGAAATTAAACATAGGTGGTCCAAAGTTTT-ATTATA
** * *
42914505 TTTCATGATATGATATTGAATTCTAAACATGTATACTCAATGTTGTGTTTACATGGGCTGATTCA
65 TTTCAT-ATATGATATTGAATT-TAAACATGTATACT-AATGTTAAGTTTACATGGACTAATTCA
* * * * * * *
42914570 ATTGGATCAATGATTATATGATTAATTGTACAATTTATTCAATTGGATCAATGATTGTATAATTA
127 ATTGGATAAATGATTGTACGATTAATTATACAATTTATTCAATTGGATCATTGATTATACAATTA
* * *
42914635 ATGTCACAATTTATTTGATTACGCTAGTAATTAG-AGAAATATACAATTGATCAAAACTTTTAAA
192 ATGTCACAATTCATTGGATTTC-CTAGTAATTAGAAG-AATATACAATTGAT-AAAACTTTTAAA
** * * * * * *
42914699 AATACTTTTACACTACAATGTTATTACCTTCATACATAGATTCATTCAATTCGATCAACGATTGT
254 AATACTTACACACTATAATGTCATCACCTTCATACATAGATTCATTCAATTAGATCAATGAGTGT
* * * * *
42914764 ACAAGTATTGTCATAACTCATTCAAATAAATTAGAAATCAGAAAAATGTAAAAGTGACCATTACT
319 ACAACTAATGTCATAACTCATTCAAATACATTAGAAATTAGAAAAATGTAAAAGTGA-TATTACT
* *
42914829 CGTCAAATTACTTGTACACCACAATGTTAGTACATTTGTATATAGACCCAATTCAATTGGTTCAA
383 CTTCAAATTACTTGTACACCACAATGTTAGTACATTTATATATAGACCCAATTCAATTGGTTCAA
* * *
42914894 TTTCGTAATCATTCAATTACATTAGTGGTTAGAGGAATGCATAATTG
448 TGTCATAATCATTCAATTACATTAGTAGTTAGAGGAATGCATAATTG
* *
42914941 ATAAATACTCTTAAATTAATCAAATATTTGAAATTAATCATAGGTGGTCCATAGTTTTATTATAT
1 ATAAATACTCTTAAATTAATCAAATATTTGAAATTAAACATAGGTGGTCCAAAGTTTTATTATAT
*
42915006 TTCACTATATGATATTCAATTTAAACATGTATACTAGATGTTAAGTTTACATGGACTAATTCAAT
66 TTCA-TATATGATATTGAATTTAAACATGTATACTA-ATGTTAAGTTTACATGGACTAATTCAAT
* *
42915071 TGGATAAATGATTGTACGATTAA-TATACAATTTACTCAATTGGATTATTGAATT-TACAATTAA
129 TGGATAAATGATTGTACGATTAATTATACAATTTATTCAATTGGATCATTG-ATTATACAATTAA
*
42915134 TGTCACAATTCATTGGACTTTCCTAGTAATTAGAAGAATATACAATTGATAAATATTTTTAAAAA
193 TGTCACAATTCATTGGA-TTTCCTAGTAATTAGAAGAATATACAATTGATAAA-ACTTTT-AAAA
* *
42915199 ATACTTACACACTGTAATGTCATCACCTTCATATATAGATTCATTCAATTAGATCAATGAGTGTA
255 ATACTTACACACTATAATGTCATCACCTTCATACATAGATTCATTCAATTAGATCAATGAGTGTA
* *
42915264 CAATTAATGTAATAACTCATTCAAATACATTAGAAATTAGAAAAATGTAAAAGTGATATTACTCT
320 CAACTAATGTCATAACTCATTCAAATACATTAGAAATTAGAAAAATGTAAAAGTGATATTACTCT
* * *
42915329 TCAAATTACTTGTACGCCACAATGTTAGTATATTCATATATAGACCCAATTCAATTGGTTCAATG
385 TCAAATTACTTGTACACCACAATGTTAGTACATTTATATATAGACCCAATTCAATTGGTTCAATG
*
42915394 TCATAATCATTCAATTACATTAGTAGTTATAGGAATGCATAATTG
450 TCATAATCATTCAATTACATTAGTAGTTAGAGGAATGCATAATTG
*
42915439 ATAAATACTCTTAAATTAATCAAATATTTGAAATTAAACATAGGTGGTCCAAAGTTTTAATATAT
1 ATAAATACTCTTAAATTAATCAAATATTTGAAATTAAACATAGGTGGTCCAAAGTTTTATTATAT
* * *
42915504 TTCACTACATGATATTGAATTTAAACATGTATACTAGATGTTAAGTTTATATGGACTAATTCATT
66 TTCA-TATATGATATTGAATTTAAACATGTATACTA-ATGTTAAGTTTACATGGACTAATTCAAT
* * *
42915569 TGGATAAAT-ACTTGTACGACTAATTATACAATTTATTCTATTGGATCATTGGA-TGTACAATTA
129 TGGATAAATGA-TTGTACGATTAATTATACAATTTATTCAATTGGATCATT-GATTATACAATTA
* *
42915632 ATGTCACAATTCATTGGAATTTCCTAGTAATTAGAGGAATATGCAATTG-----A----T--AAA
192 ATGTCACAATTCATTGG-ATTTCCTAGTAATTAGAAGAATATACAATTGATAAAACTTTTAAAAA
*
42915686 TACTTACACACTATAATGTCATCACCTTCATACATAGATTCGTTCAATTAGATCAATGAGTGTAC
256 TACTTACACACTATAATGTCATCACCTTCATACATAGATTCATTCAATTAGATCAATGAGTGTAC
** * * * * * * *
42915751 AACTAATGTCATAACTCATGATCAGTTACGTTAG-TATTAGAGAAATGTACAATTAATCAATACT
321 AACTAATGTCATAACTCAT--TCAAATACATTAGAAATTAGAAAAATGTAAAAGTGAT-ATTACT
* *
42915815 CTTCAAATTACTTGTACACCACAATGTTAGTACATTTTATATATAGATCCGATTCAATTGGTTCA
383 CTTCAAATTACTTGTACACCACAATGTTAGTACA-TTTATATATAGACCCAATTCAATTGGTTCA
* * * *
42915880 ATGTCATAAGCATTCGA-TAGCGTTTGTAGTTAGAGGAATGCATAATTG
447 ATGTCATAATCATTCAATTA-CATTAGTAGTTAGAGGAATGCATAATTG
* * * * * *
42915928 ATAAATACTCTTAAATTGATCAAATATTTAAAATTAAACATTGATAGTCCAAACTTTT-TATATA
1 ATAAATACTCTTAAATTAATCAAATATTTGAAATTAAACATAGGTGGTCCAAAGTTTTAT-TATA
* * * ** * * ** *
42915992 TTTCGATATATGTTATTGAATTTCAAACATGTATATTTAATTTTGTGTTTATATGAACCGATTGA
65 TTTC-ATATATGATATTGAATTT-AAACATGTATA-CTAATGTTAAGTTTACATGGACTAATTCA
* * * * * *
42916057 ATT-GATCAATGGTTGTACGA-TACATTATACAATTTATTCAGTTAGATTATTGGTTATACAATT
127 ATTGGATAAATGATTGTACGATTA-ATTATACAATTTATTCAATTGGATCATTGATTATACAATT
* * * * * * *
42916120 AATGCCATAGATT-ATTTGATTATGCTAATAATTAGAAGAATATACAATTCATTAATACTTTTAA
191 AATGTCACA-ATTCATTGGATT-TCCTAGTAATTAGAAGAATATACAATTGA-TAAAACTTTTAA
* * *
42916184 AAATACATATACATTATAAT
253 AAATACTTACACACTATAAT
42916204 TTTTTAAAGT
Statistics
Matches: 1104, Mismatches: 120, Indels: 77
0.85 0.09 0.06
Matches are distributed among these distances:
486 82 0.07
487 18 0.02
488 55 0.05
489 223 0.20
490 36 0.03
491 2 0.00
493 1 0.00
495 1 0.00
497 4 0.00
498 330 0.30
499 255 0.23
500 79 0.07
501 18 0.02
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (494 bp):
ATAAATACTCTTAAATTAATCAAATATTTGAAATTAAACATAGGTGGTCCAAAGTTTTATTATAT
TTCATATATGATATTGAATTTAAACATGTATACTAATGTTAAGTTTACATGGACTAATTCAATTG
GATAAATGATTGTACGATTAATTATACAATTTATTCAATTGGATCATTGATTATACAATTAATGT
CACAATTCATTGGATTTCCTAGTAATTAGAAGAATATACAATTGATAAAACTTTTAAAAATACTT
ACACACTATAATGTCATCACCTTCATACATAGATTCATTCAATTAGATCAATGAGTGTACAACTA
ATGTCATAACTCATTCAAATACATTAGAAATTAGAAAAATGTAAAAGTGATATTACTCTTCAAAT
TACTTGTACACCACAATGTTAGTACATTTATATATAGACCCAATTCAATTGGTTCAATGTCATAA
TCATTCAATTACATTAGTAGTTAGAGGAATGCATAATTG
Found at i:42918070 original size:28 final size:26
Alignment explanation
Indices: 42918022--42918093 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 26
42918012 ACAGGGCTCG
* * *
42918022 CATATAGGGTTTGCTTGTAAGGCTTGCA
1 CATATAGGGTTCGCATATAAGG-TT-CA
42918050 CATATAGGGTTCGCATATAAGGTTCA
1 CATATAGGGTTCGCATATAAGGTTCA
* *
42918076 CACATAAGGTTC-CATATA
1 CATATAGGGTTCGCATATA
42918094 GTAATTCATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 6 0.15
26 12 0.31
27 2 0.05
28 19 0.49
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (26 bp):
CATATAGGGTTCGCATATAAGGTTCA
Found at i:42918086 original size:26 final size:27
Alignment explanation
Indices: 42918039--42918093 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
42918029 GGTTTGCTTG
* *
42918039 TAAGGCTTGCACATATAGGGTTCGCATA
1 TAAGGCTTGCACACATAAGGTTC-CATA
42918067 TAAGG-TT-CACACATAAGGTTCCATA
1 TAAGGCTTGCACACATAAGGTTCCATA
42918092 TA
1 TA
42918094 GTAATTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 12 0.48
27 2 0.08
28 5 0.20
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (27 bp):
TAAGGCTTGCACACATAAGGTTCCATA
Found at i:42918121 original size:23 final size:24
Alignment explanation
Indices: 42918078--42918137 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
42918068 AAGGTTCACA
*
42918078 CATA-AGGTTC-CATATAGTAATT
1 CATATAGGTTCGCATATACTAATT
42918100 CATATAGGTTCGCATA-ACTAATT
1 CATATAGGTTCGCATATACTAATT
* *
42918123 CATATGGGTTTGCAT
1 CATATAGGTTCGCAT
42918138 GATAACCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.12
23 25 0.76
24 4 0.12
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (24 bp):
CATATAGGTTCGCATATACTAATT
Found at i:42918200 original size:22 final size:22
Alignment explanation
Indices: 42918174--42918220 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
42918164 TCACTAAGAG
* * *
42918174 GGGTTCACCTAGCGTTCCTTAA
1 GGGTTCACATAACATTCCTTAA
*
42918196 GGGTTCGCATAACATTCCTTAA
1 GGGTTCACATAACATTCCTTAA
42918218 GGG
1 GGG
42918221 CTTGCAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (22 bp):
GGGTTCACATAACATTCCTTAA
Found at i:42918509 original size:18 final size:17
Alignment explanation
Indices: 42918485--42918535 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
42918475 AATTCTTTAA
42918485 AGGTTCACATGATATCT
1 AGGTTCACATGATATCT
*
42918502 ATGGTTCACAT-AGTACCT
1 A-GGTTCACATGA-TATCT
42918520 AGAGTTCACATGATAT
1 AG-GTTCACATGATAT
42918536 GTATAGCTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 3 0.11
18 24 0.86
19 1 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (17 bp):
AGGTTCACATGATATCT
Done.