Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 556 of 770
Found at i:173043744 original size:20 final size:20
Alignment explanation
Indices: 173043684--173043744 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
173043674 ATAAATATGG
*
173043684 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
173043704 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
173043724 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
173043744 T
1 T
173043745 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:173043862 original size:23 final size:24
Alignment explanation
Indices: 173043794--173043934 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
173043784 GAGGAAGTGA
173043794 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
173043818 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
173043842 AAAAGGGCTTATG-CCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
173043864 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* *
173043888 GAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
173043911 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
173043935 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 3, Indels: 9
0.90 0.02 0.07
Matches are distributed among these distances:
22 13 0.12
23 36 0.33
24 52 0.48
25 8 0.07
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:173043879 original size:46 final size:47
Alignment explanation
Indices: 173043794--173043934 Score: 198
Period size: 46 Copynumber: 3.0 Consensus size: 47
173043784 GAGGAAGTGA
173043794 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
173043842 AAAAGGGCTTATG-CCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* *
173043888 GAAAGGGCTT-TGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
173043935 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
45 2 0.02
46 40 0.47
47 20 0.23
48 24 0.28
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:173044185 original size:31 final size:30
Alignment explanation
Indices: 173044126--173044214 Score: 125
Period size: 31 Copynumber: 3.1 Consensus size: 30
173044116 CGTTTACAGT
173044126 AAAGGCTTCGGCCCAG--TA-GAAAT-T-A
1 AAAGGCTTCGGCCCAGTATATGAAATATGA
173044151 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGT-ATATGAAATATGA
173044182 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTA-TATGAAATATGA
173044213 AA
1 AA
173044215 TATGAAAAGG
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
25 16 0.28
28 2 0.04
29 5 0.09
30 2 0.04
31 32 0.56
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTATATGAAATATGA
Found at i:173045355 original size:27 final size:28
Alignment explanation
Indices: 173045325--173045424 Score: 107
Period size: 27 Copynumber: 3.7 Consensus size: 28
173045315 TTTAGTTTAC
*
173045325 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCAAAATACCCTTAGATTTG
* * *
173045352 TAAAAATACTAAAATACCC-TCGATTTG
1 TAAAATTACCAAAATACCCTTAGATTTG
* * *
173045379 TAAAATTACTAAAATA-CCTTCGACTTG
1 TAAAATTACCAAAATACCCTTAGATTTG
*
173045406 TAAAATTACCAAAGTACCC
1 TAAAATTACCAAAATACCC
173045425 CCGATTTACA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
26 4 0.06
27 56 0.90
28 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (28 bp):
TAAAATTACCAAAATACCCTTAGATTTG
Found at i:173045384 original size:54 final size:54
Alignment explanation
Indices: 173045325--173045431 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 54
173045315 TTTAGTTTAC
* * * *
173045325 TAAAATTACCGAAATACCCTTAG-TTTGTAAAAATACTAAAATACCCTCGATTTG
1 TAAAATTACCAAAATA-CCTTAGACTTGTAAAAATACCAAAATACCCCCGATTTG
* * * *
173045379 TAAAATTACTAAAATACCTTCGACTTGTAAAATTACCAAAGTACCCCCGATTT
1 TAAAATTACCAAAATACCTTAGACTTGTAAAAATACCAAAATACCCCCGATTT
173045432 ACAGAACTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
53 5 0.11
54 39 0.89
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (54 bp):
TAAAATTACCAAAATACCTTAGACTTGTAAAAATACCAAAATACCCCCGATTTG
Found at i:173045492 original size:81 final size:81
Alignment explanation
Indices: 173045420--173045676 Score: 329
Period size: 81 Copynumber: 3.2 Consensus size: 81
173045410 ATTACCAAAG
* * * * * * *
173045420 TACCCCCGATTTACAGAACTATCATTTTACCCCCGATTTACATAATTACCGTTTTACCCTCGATT
1 TACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTTGATT
*
173045485 TACAAAATTACCGTTT
66 TACAAAATTACCATTT
173045501 TACCCTCGATTTACAGAATTA-CTGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTTGAT
1 TACCCTCGATTTACAGAATTATC-GTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTTGAT
* **
173045565 TTACAGAATTATTATTT
65 TTACAAAATTACCATTT
* * **
173045582 TACCCTCGATTTACA-AATTATCGTTTTACCGTCGATTTATAGAATTACTATTTTACCCTTGATT
1 TACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTTGATT
* *
173045646 TACAGAATTACTATTT
66 TACAAAATTACCATTT
*
173045662 TACCCTTGATTTACA
1 TACCCTCGATTTACA
173045677 AAGTTACAGA
Statistics
Matches: 157, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
80 73 0.46
81 84 0.54
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (81 bp):
TACCCTCGATTTACAGAATTATCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCTTGATT
TACAAAATTACCATTT
Found at i:173045683 original size:27 final size:27
Alignment explanation
Indices: 173045420--173045676 Score: 295
Period size: 27 Copynumber: 9.6 Consensus size: 27
173045410 ATTACCAAAG
* * *
173045420 TACCCCCGATTTACAGAACTA-TCATTT
1 TACCCTCGATTTACAGAATTACT-GTTT
* * *
173045447 TACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
173045474 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
173045501 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
173045528 TACCCTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
173045555 TACCCTTGATTTACAGAATTATTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
173045582 TACCCTCGATTTACA-AATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
* * *
173045608 TACCGTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
173045635 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
173045662 TACCCTTGATTTACA
1 TACCCTCGATTTACA
173045677 AAGTTACAGA
Statistics
Matches: 201, Mismatches: 25, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
25 1 0.00
26 21 0.10
27 178 0.89
28 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:173045693 original size:107 final size:108
Alignment explanation
Indices: 173045420--173045694 Score: 286
Period size: 107 Copynumber: 2.6 Consensus size: 108
173045410 ATTACCAAAG
* * * * ** * * ****
173045420 TACCCCCGATTTACAGAACTATCATTTTACCCCCGATTTACATAATTACCGTTTTACCCTCGATT
1 TACCCTCGATTTACAAAATTACCATTTTACCCTTGATTTACAGAATTATCAAAATACCCTCGATT
*
173045485 TACAAAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTT
66 TACAAAATTACCGTTTTACCCTCGATTTACAGAATTACTATTT
* * * ***
173045528 TACCCTCGATTTATAAAATTACCGTTTTACCCTTGATTTACAGAATTATTATTTTACCCTCGATT
1 TACCCTCGATTTACAAAATTACCATTTTACCCTTGATTTACAGAATTATCAAAATACCCTCGATT
* * *
173045593 TAC-AAATTATCGTTTTACCGTCGATTTATAGAATTACTATTT
66 TACAAAATTACCGTTTTACCCTCGATTTACAGAATTACTATTT
* * *
173045635 TACCCTTGATTTACAGAATTACTATTTTACCCTTGATTTACA-AAGTTA-CAGAAATACCCT
1 TACCCTCGATTTACAAAATTACCATTTTACCCTTGATTTACAGAA-TTATCA-AAATACCCT
173045695 TGACTTTCTA
Statistics
Matches: 140, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
106 3 0.02
107 81 0.58
108 56 0.40
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (108 bp):
TACCCTCGATTTACAAAATTACCATTTTACCCTTGATTTACAGAATTATCAAAATACCCTCGATT
TACAAAATTACCGTTTTACCCTCGATTTACAGAATTACTATTT
Found at i:173045756 original size:27 final size:27
Alignment explanation
Indices: 173045635--173045752 Score: 107
Period size: 27 Copynumber: 4.3 Consensus size: 27
173045625 ATTACTATTT
* **
173045635 TACCCTTGATTTACAGAATTACT-ATTT
1 TACCCTTGATTTACAAAATTACTGA-AA
* *
173045662 TACCCTTGATTTACAAAGTTACAGAAA
1 TACCCTTGATTTACAAAATTACTGAAA
173045689 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTAC--AAAATTACT-GAAA
* *
173045718 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACTGAAA
173045745 TACCCTTG
1 TACCCTTG
173045753 GTTTGTAGAT
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
27 48 0.65
28 8 0.11
29 18 0.24
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACTGAAA
Found at i:173045840 original size:27 final size:27
Alignment explanation
Indices: 173045809--173045901 Score: 125
Period size: 27 Copynumber: 3.4 Consensus size: 27
173045799 TACCCCTATT
*
173045809 AGGTAAAAAGACCGTAAAGCCCCTGTA
1 AGGTAAAATGACCGTAAAGCCCCTGTA
* *
173045836 GGGTAAAGTGACCGTAAAGCCCCTGTA
1 AGGTAAAATGACCGTAAAGCCCCTGTA
*
173045863 AGGTAAAGTGACCGTAATA-CCCCTGTA
1 AGGTAAAATGACCGTAA-AGCCCCTGTA
*
173045890 TGGTAAAATGAC
1 AGGTAAAATGAC
173045902 GAATATGCCC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 58 0.98
28 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.19
Consensus pattern (27 bp):
AGGTAAAATGACCGTAAAGCCCCTGTA
Found at i:173047086 original size:25 final size:25
Alignment explanation
Indices: 173047058--173047105 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
173047048 TTATACCATG
* * *
173047058 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
173047083 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
173047106 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:173047208 original size:20 final size:20
Alignment explanation
Indices: 173047148--173047208 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
173047138 ATAAATATGG
*
173047148 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
173047168 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
173047188 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
173047208 T
1 T
173047209 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:173047327 original size:47 final size:48
Alignment explanation
Indices: 173047258--173047376 Score: 152
Period size: 47 Copynumber: 2.5 Consensus size: 48
173047248 GAGGAAGTGA
* *
173047258 AAAAGGGCTTATGCCCGAGTTATCAAAAGGGCTTATGCCCTAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
173047305 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
173047353 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
173047377 ATGATAAAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
47 41 0.65
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:173047372 original size:25 final size:24
Alignment explanation
Indices: 173047258--173047376 Score: 152
Period size: 24 Copynumber: 5.0 Consensus size: 24
173047248 GAGGAAGTGA
* *
173047258 AAAAGGGCTTATGCCCGAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
173047282 AAAAGGGCTTATGCCCTAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
173047305 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
173047329 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
173047353 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
173047377 ATGATAAAGC
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
23 21 0.25
24 52 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:173047603 original size:31 final size:31
Alignment explanation
Indices: 173047568--173047631 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
173047558 CGTTTACAGT
173047568 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
173047599 AAAGGCTTCGGCCCAGTGTTATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
173047630 AA
1 AA
173047632 CATGAAAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:173060218 original size:49 final size:49
Alignment explanation
Indices: 173060152--173060389 Score: 271
Period size: 49 Copynumber: 4.8 Consensus size: 49
173060142 TAGCCAAAGC
*
173060152 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
* * * ** *
173060201 TATCTAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACC-AAT
* * * * * *
173060251 CATCTGATACACGTAGTAGCTTGCACTTAGTACTACACACGTG-ATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA--TGCAACCAA-T
* ** *
173060302 TATCGGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
*
173060351 AATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
173060390 CGTGACCTCA
Statistics
Matches: 154, Mismatches: 30, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
49 78 0.51
50 42 0.27
51 33 0.21
52 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
Found at i:173062903 original size:25 final size:25
Alignment explanation
Indices: 173062872--173062938 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
173062862 AATCAAAATA
* *
173062872 AGAATCAGAATCAGAATCAGGTGAT
1 AGAATCAAAATCAGAATCAGGTAAT
* *
173062897 AGAATCAAAATCGGTATCAGGTAAT
1 AGAATCAAAATCAGAATCAGGTAAT
*
173062922 AGAATCAAAATTAGAAT
1 AGAATCAAAATCAGAAT
173062939 GTGAATGTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (25 bp):
AGAATCAAAATCAGAATCAGGTAAT
Found at i:173063097 original size:27 final size:26
Alignment explanation
Indices: 173063056--173063120 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 26
173063046 AGCATGGCTG
* * *
173063056 CCAGAATAGATATTGCGATAGAGTCA
1 CCAGAACAGATATTGCGACAGAGCCA
* *
173063082 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGCGACAGAGCCA
173063109 CCAGAACAGATA
1 CCAGAACAGATA
173063121 ATGTGGCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATATTGCGACAGAGCCA
Found at i:173063125 original size:26 final size:27
Alignment explanation
Indices: 173063075--173063128 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
173063065 ATATTGCGAT
* *
173063075 AGAGTCACCAGATACAGATATTGTGGC
1 AGAGCCACCAGATACAGATAATGTGGC
173063102 AGAGCCACCAGA-ACAGATAATGTGGC
1 AGAGCCACCAGATACAGATAATGTGGC
173063128 A
1 A
173063129 AAACCACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (27 bp):
AGAGCCACCAGATACAGATAATGTGGC
Found at i:173063135 original size:26 final size:27
Alignment explanation
Indices: 173063080--173063135 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
173063070 GCGATAGAGT
* * *
173063080 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAAAC
173063107 CACCAGA-ACAGATAATGTGGCAAAAC
1 CACCAGATACAGATAATGTGGCAAAAC
173063133 CAC
1 CAC
173063136 TTAAAAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.14
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAAAC
Found at i:173063955 original size:6 final size:6
Alignment explanation
Indices: 173063934--173064012 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
173063924 TATTAGAACT
* * *
173063934 AGAATC AAAATG AGAATC AGAATC AGAATC AG-GTGAC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * *
173063983 AGTATC AGGTAA-C AGAGTC AGAATT AGAAT
1 AGAATC A-G-AATC AGAATC AGAATC AGAAT
173064013 GTGAATGCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
5 2 0.04
6 46 0.82
7 6 0.11
8 2 0.04
ACGTcount: A:0.47, C:0.13, G:0.22, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:173063979 original size:25 final size:25
Alignment explanation
Indices: 173063946--173064012 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
173063936 AATCAAAATG
*
173063946 AGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGGTAAC
*
173063971 AGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
* *
173063996 AGAGTCAGAATTAGAAT
1 AGAATCAGAATCAGAAT
173064013 GTGAATGCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.19
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTAAC
Found at i:173064201 original size:27 final size:27
Alignment explanation
Indices: 173064130--173064208 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
173064120 AGCATGGCTG
* *
173064130 CCAGAACAGATATTGTGACAGAG-TCA
1 CCAGAACAGATATTGTGGCAGAGCCCA
173064156 CCAGATACAGATATTGTGGCAGAGCCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCCA
* *
173064184 CCAGAACAGATAATGTGGCAAAGCC
1 CCAGAACAGATATTGTGGCAGAGCC
173064209 ACTTAACAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
26 5 0.11
27 35 0.74
28 7 0.15
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATATTGTGGCAGAGCCCA
Found at i:173064403 original size:22 final size:22
Alignment explanation
Indices: 173064372--173064433 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
173064362 AATACGTTTA
*
173064372 GCACACAGCCATAATCAGGTTG
1 GCACAAAGCCATAATCAGGTTG
* *
173064394 GCACAGAGCCAT-ATGTAGGTTG
1 GCACAAAGCCATAAT-CAGGTTG
*
173064416 GCGCAAAGCCATAATCAG
1 GCACAAAGCCATAATCAG
173064434 AAGGCTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (22 bp):
GCACAAAGCCATAATCAGGTTG
Found at i:173064899 original size:27 final size:27
Alignment explanation
Indices: 173064865--173065183 Score: 453
Period size: 27 Copynumber: 11.9 Consensus size: 27
173064855 CAAAATGGTG
* *
173064865 ATTT-TACCCCACAAGGGTATCTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
* * * *
173064891 AATTCTACCCTGCAGGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATTTCGGT
173064918 ATTTCTACCCTACAAGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
* * * *
173064945 AATTCTATCCTATAAGGGTATTTCAGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
* * *
173064972 AATTCTACCCTACAGGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATTTCGGT
*
173064999 ATTTCTACCCTATAAGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
*
173065026 ATTTCTACCCTACAAGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATTTCGGT
* *
173065053 AATTCTACCCTACAGGGGTA-TTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
* *
173065079 AATTCTACCCTACAGGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
173065106 ATTTCTACCCTACAAGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
173065133 ATTTCTACCCTACAAGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
173065160 ATTTCTACCCTACAAGGGTATTTC
1 ATTTCTACCCTACAAGGGTATTTC
173065184 AATAATTTTG
Statistics
Matches: 261, Mismatches: 30, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
26 28 0.11
27 233 0.89
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (27 bp):
ATTTCTACCCTACAAGGGTATTTCGGT
Found at i:173065259 original size:27 final size:26
Alignment explanation
Indices: 173065223--173065406 Score: 124
Period size: 27 Copynumber: 6.9 Consensus size: 26
173065213 TAATTCTGTA
*
173065223 AATCGGGGGTACTTTGA-TAATTTTAC
1 AATCGAGGGTA-TTTGAGTAATTTTAC
*
173065249 AAGTCGAGGGTATTTCAGTAATTTTAC
1 AA-TCGAGGGTATTTGAGTAATTTTAC
* * *
173065276 AAATCGAGTGTATTTAAGTAATTTTGC
1 -AATCGAGGGTATTTGAGTAATTTTAC
*
173065303 AAACTGAGGGTATTTCG-GTAATTTTAC
1 AATC-GAGGGTATTT-GAGTAATTTTAC
* * * * *
173065330 AAATCAAGGATGTTTGGGTAATTTTAT
1 -AATCGAGGGTATTTGAGTAATTTTAC
* *
173065357 AAACTGGGGGTACTTTG-GTAATTTTAC
1 AATC-GAGGGTA-TTTGAGTAATTTTAC
* *
173065384 AA-CTGGGGGTATTTCAGTAATTT
1 AATC-GAGGGTATTTGAGTAATTT
173065407 GGTAAACTAA
Statistics
Matches: 127, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
25 3 0.02
26 29 0.23
27 86 0.68
28 9 0.07
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (26 bp):
AATCGAGGGTATTTGAGTAATTTTAC
Found at i:173065280 original size:54 final size:54
Alignment explanation
Indices: 173065222--173065406 Score: 162
Period size: 54 Copynumber: 3.4 Consensus size: 54
173065212 GTAATTCTGT
* * *
173065222 AAATCGGGGGTACTTTGA-TAATTTTAC-AAGTCGAGGGTATTTCAGTAATTTTAC
1 AAATCGAGGGTA-TTTAAGTAATTTTACAAACT-GAGGGTATTTCAGTAATTTTAC
* * *
173065276 AAATCGAGTGTATTTAAGTAATTTTGCAAACTGAGGGTATTTCGGTAATTTTAC
1 AAATCGAGGGTATTTAAGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTAC
* * * ** * * *
173065330 AAATCAAGGATGTTTGGGTAATTTTATAAACTGGGGGTACTTT-GGTAATTTTAC
1 AAATCGAGGGTATTTAAGTAATTTTACAAACTGAGGGTA-TTTCAGTAATTTTAC
* * *
173065384 AACT-GGGGGTATTTCAGTAATTT
1 AAATCGAGGGTATTTAAGTAATTT
173065407 GGTAAACTAA
Statistics
Matches: 106, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
53 17 0.16
54 83 0.78
55 6 0.06
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (54 bp):
AAATCGAGGGTATTTAAGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTAC
Found at i:173065414 original size:27 final size:25
Alignment explanation
Indices: 173065347--173065406 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
173065337 GGATGTTTGG
*
173065347 GTAATTTTATAAACTGGGGGTACTTTG
1 GTAA-TTT-TAAACTGGGGGTACTTTA
173065374 GTAATTTTACAACTGGGGGTA-TTTCA
1 GTAATTTTA-AACTGGGGGTACTTT-A
173065400 GTAATTT
1 GTAATTT
173065407 GGTAAACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.17
26 21 0.70
27 4 0.13
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (25 bp):
GTAATTTTAAACTGGGGGTACTTTA
Found at i:173068692 original size:40 final size:40
Alignment explanation
Indices: 173068647--173068813 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
173068637 CGGAATATAA
173068647 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
173068687 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
173068727 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
173068767 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
173068806 CCGGATAT
1 CCGGATAT
173068814 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:173088175 original size:40 final size:40
Alignment explanation
Indices: 173088130--173088297 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
173088120 CGGAATATAA
173088130 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
173088170 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
173088210 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
173088250 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
173088290 CCGGATAT
1 CCGGATAT
173088298 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:173097103 original size:25 final size:24
Alignment explanation
Indices: 173097044--173097103 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 24
173097034 AAAAGATAAT
173097044 AATTATTA-ATATATAATTATATC
1 AATTATTATATATATAATTATATC
* *
173097067 CATTATAATATATATTAATTATTATC
1 AATTATTATATATA-TAATTA-TATC
173097093 AACTTATTATA
1 AA-TTATTATA
173097104 GAGTTAGGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.21
24 5 0.17
25 6 0.21
26 5 0.17
27 7 0.24
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTATTATATATATAATTATATC
Found at i:173097292 original size:17 final size:18
Alignment explanation
Indices: 173097270--173097303 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
173097260 TTTTTGTTTA
173097270 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
173097287 AATAAATTAATATGCAT
1 AATAAATTAATATGCAT
173097304 ATATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:173107296 original size:24 final size:24
Alignment explanation
Indices: 173107269--173107426 Score: 255
Period size: 24 Copynumber: 6.6 Consensus size: 24
173107259 CTTATTATGT
* * *
173107269 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
*
173107293 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
173107317 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
173107341 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
173107365 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
173107389 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
173107413 TC-CACACATAGTGC
1 TCGCACACATAGTGC
173107427 ATTTGAGATA
Statistics
Matches: 126, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
23 12 0.10
24 114 0.90
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:173107303 original size:48 final size:48
Alignment explanation
Indices: 173107269--173107426 Score: 282
Period size: 48 Copynumber: 3.3 Consensus size: 48
173107259 CTTATTATGT
* * *
173107269 TCGCACACATAGAGCTATAGCAAATCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTGAA
173107317 TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTGAA
173107365 TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTGAA
173107413 TC-CACACATAGTGC
1 TCGCACACATAGTGC
173107427 ATTTGAGATA
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
47 12 0.11
48 95 0.89
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (48 bp):
TCGCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTGAA
Found at i:173107883 original size:2 final size:2
Alignment explanation
Indices: 173107876--173107901 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
173107866 TGGGCATACT
173107876 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
173107902 CATACCCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:173110888 original size:20 final size:21
Alignment explanation
Indices: 173110852--173110899 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
173110842 ATTTTGATAT
*
173110852 ACATGATTTGATATGATATGC
1 ACATGATATGATATGATATGC
173110873 ACATGATATG-TATGATATGC
1 ACATGATATGATATGATATGC
173110893 ACATGAT
1 ACATGAT
173110900 GTATTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (21 bp):
ACATGATATGATATGATATGC
Found at i:173110984 original size:25 final size:25
Alignment explanation
Indices: 173110950--173111015 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
173110940 GGAACTGCAC
*
173110950 AAGGGCTTTGCCCCAGTTTACCGAA
1 AAGGGCTTTGCCCCAGTTTACCAAA
* *
173110975 AAGGGCTTTGCCCAAGTTTATCAAA
1 AAGGGCTTTGCCCCAGTTTACCAAA
173111000 AAGGGCTTTGCCCCAG
1 AAGGGCTTTGCCCCAG
173111016 CTATTAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (25 bp):
AAGGGCTTTGCCCCAGTTTACCAAA
Found at i:173113165 original size:42 final size:42
Alignment explanation
Indices: 173113054--173113175 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 42
173113044 TACCGTACCA
* *
173113054 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCC
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCC
* * *
173113096 ATGCAAATAGT-CCAGCTATGGTCTTACACG-AAGTCTCATATCG
1 ATGC-CATA-TCCCAGATATGGTCTTACACGTAA-TCTCATATCC
173113139 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
173113176 ATAACCCTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 32 0.47
43 34 0.50
44 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGTAATCTCATATCC
Found at i:173121588 original size:39 final size:40
Alignment explanation
Indices: 173121530--173121630 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
173121520 AAATTGAATG
* *
173121530 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
173121569 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
173121609 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
173121631 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:173121623 original size:40 final size:40
Alignment explanation
Indices: 173121530--173121712 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
173121520 AAATTGAATG
* * * * *
173121530 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
173121569 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
173121609 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
173121649 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
173121689 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
173121713 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 32 0.26
40 87 0.72
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:173129741 original size:40 final size:40
Alignment explanation
Indices: 173129639--173129822 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
173129629 AAATTGAATG
* * * * *
173129639 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
173129679 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
173129719 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
173129759 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
173129799 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
173129823 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:173134767 original size:30 final size:30
Alignment explanation
Indices: 173134731--173134861 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
173134721 GACAAGATTG
* * * * *
173134731 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
173134761 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
173134789 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
173134819 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
173134848 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
173134862 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:173134822 original size:58 final size:58
Alignment explanation
Indices: 173134731--173134861 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
173134721 GACAAGATTG
* * * * * *
173134731 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
173134789 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
173134848 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
173134862 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:173137715 original size:3 final size:3
Alignment explanation
Indices: 173137709--173137761 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
173137699 TTACGACTAC
* *
173137709 TAT TAT TAAA TAT TAT TAAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
173137756 TAT TAT
1 TAT TAT
173137762 CTTTTTTACA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 40 0.91
4 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:173144292 original size:20 final size:20
Alignment explanation
Indices: 173144267--173144307 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
173144257 ATAACAAATT
*
173144267 ACACCATACATAACCTATGA
1 ACACCATACATAACCCATGA
173144287 ACACCATACATAACCCATGA
1 ACACCATACATAACCCATGA
173144307 A
1 A
173144308 TCAGACTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.32, G:0.05, T:0.17
Consensus pattern (20 bp):
ACACCATACATAACCCATGA
Found at i:173144631 original size:14 final size:14
Alignment explanation
Indices: 173144614--173144643 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
173144604 TCATTTCATT
173144614 AATATCAATAAACC
1 AATATCAATAAACC
*
173144628 AATATCACTAAACC
1 AATATCAATAAACC
173144642 AA
1 AA
173144644 ATTTATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (14 bp):
AATATCAATAAACC
Found at i:173146762 original size:40 final size:40
Alignment explanation
Indices: 173146706--173146949 Score: 348
Period size: 40 Copynumber: 6.1 Consensus size: 40
173146696 CGGGATTGAA
* * * *
173146706 CCGGATATAGCT-ACTCGCTCGAATACCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
173146746 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
173146786 CCGGATATAGTATCTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
173146826 CCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
173146866 TCGGATATAGTAACTCGGACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * **
173146906 CCGGA-ACTAGTCACTAGTGCAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
173146946 CCGG
1 CCGG
173146950 TTATCATCCA
Statistics
Matches: 187, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 2 0.01
40 185 0.99
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:173153735 original size:29 final size:29
Alignment explanation
Indices: 173153702--173153833 Score: 219
Period size: 29 Copynumber: 4.6 Consensus size: 29
173153692 CCTTCGAGCT
** * *
173153702 CGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
173153731 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
173153760 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
173153789 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
173153818 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
173153834 ATCTCGTCAC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 97 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:173153736 original size:58 final size:58
Alignment explanation
Indices: 173153673--173153833 Score: 187
Period size: 58 Copynumber: 2.8 Consensus size: 58
173153663 AATTTAAGCC
* * * * * *
173153673 CGCACACATAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
* * * **
173153731 TGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
* * **
173153789 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCA
173153834 ATCTCGTCAC
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 91 1.00
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (58 bp):
CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
Found at i:173153764 original size:87 final size:87
Alignment explanation
Indices: 173153673--173153833 Score: 223
Period size: 87 Copynumber: 1.9 Consensus size: 87
173153663 AATTTAAGCC
* * * * * *
173153673 CGCACACATAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCATGCACAC
1 CGCACACATAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCACGCACAC
173153738 TTAGTGCCATATATTTCCAGCA
66 TTAGTGCCATATATTTCCAGCA
* * * **
173153760 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCACGCACAC
1 CGCACACATAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCACGCACAC
173153825 TTAGTGCCA
66 TTAGTGCCA
173153834 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 63 1.00
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (87 bp):
CGCACACATAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCACGCACAC
TTAGTGCCATATATTTCCAGCA
Found at i:173165174 original size:27 final size:25
Alignment explanation
Indices: 173165136--173165197 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
173165126 ATATATGTAG
173165136 ATATAGTA-ATACATAATATAGTTAAAA
1 ATATA-TATATACAT-ATAT-GTTAAAA
*
173165163 ATATATATATACATATATGTTGAAA
1 ATATATATATACATATATGTTAAAA
*
173165188 ATAAATATAT
1 ATATATATAT
173165198 GGTGATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 15 0.47
26 6 0.19
27 11 0.34
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.37
Consensus pattern (25 bp):
ATATATATATACATATATGTTAAAA
Found at i:173165195 original size:25 final size:27
Alignment explanation
Indices: 173165144--173165197 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
173165134 AGATATAGTA
*
173165144 ATACATAATATAGTTAAAAATATATAT
1 ATACATAATATAGTTAAAAATAAATAT
*
173165171 ATACAT-ATAT-GTTGAAAATAAATAT
1 ATACATAATATAGTTAAAAATAAATAT
173165196 AT
1 AT
173165198 GGTGATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.60
26 4 0.16
27 6 0.24
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (27 bp):
ATACATAATATAGTTAAAAATAAATAT
Found at i:173168805 original size:13 final size:13
Alignment explanation
Indices: 173168787--173168811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173168777 TTACTTGCTA
173168787 TGATCATAGTGGC
1 TGATCATAGTGGC
173168800 TGATCATAGTGG
1 TGATCATAGTGG
173168812 TGAGAGAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (13 bp):
TGATCATAGTGGC
Found at i:173170095 original size:26 final size:26
Alignment explanation
Indices: 173170066--173170128 Score: 92
Period size: 25 Copynumber: 2.4 Consensus size: 26
173170056 CAATTGTAAG
173170066 TTCATTTTTTCTCGTTTTTTAATGAT
1 TTCATTTTTTCTCGTTTTTTAATGAT
*
173170092 TTCA-TTTTGCTCGTTTTTTAATGAT
1 TTCATTTTTTCTCGTTTTTTAATGAT
173170117 TTCTATGTTTTT
1 TTC-AT-TTTTT
173170129 GAGATCGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 23 0.72
26 5 0.16
28 4 0.12
ACGTcount: A:0.14, C:0.11, G:0.10, T:0.65
Consensus pattern (26 bp):
TTCATTTTTTCTCGTTTTTTAATGAT
Found at i:173172861 original size:22 final size:22
Alignment explanation
Indices: 173172833--173172884 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
173172823 AACTTACCAT
*
173172833 TTCAGCTCTTATGAGCATACCG
1 TTCAGCTCTTAGGAGCATACCG
* *
173172855 TTCAGCTCTTCGGAGCTTACCG
1 TTCAGCTCTTAGGAGCATACCG
173172877 TTCAGCTC
1 TTCAGCTC
173172885 AGTTGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (22 bp):
TTCAGCTCTTAGGAGCATACCG
Found at i:173172892 original size:22 final size:20
Alignment explanation
Indices: 173172833--173172900 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 20
173172823 AACTTACCAT
*
173172833 TTCAGCTCTTATGAGCATACCG
1 TTCAGCTC-T-TGAGCTTACCG
173172855 TTCAGCTCTTCGGAGCTTACCG
1 TTCAGCTCTT--GAGCTTACCG
173172877 TTCAGCTCAGTTGAGCTTACCG
1 TTCAGCTC--TTGAGCTTACCG
173172899 TT
1 TT
173172901 TATTGGCTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 37 0.90
24 2 0.05
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.34
Consensus pattern (20 bp):
TTCAGCTCTTGAGCTTACCG
Found at i:173176425 original size:45 final size:43
Alignment explanation
Indices: 173176353--173176442 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 43
173176343 GGCTATTGCC
*
173176353 TAAAATGAGTAAAACCTAGTTGAAAGATGTTATGACATCATGA
1 TAAAATGAGTAAAACCTAGCTGAAAGATGTTATGACATCATGA
* *
173176396 TAAAGATGAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGA
1 TAAA-ATGAGTAAAACC-TAGCTGAAAGATGTTATGACATCATGA
173176441 TA
1 TA
173176443 GAAACAGGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 4 0.10
44 11 0.26
45 27 0.64
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (43 bp):
TAAAATGAGTAAAACCTAGCTGAAAGATGTTATGACATCATGA
Found at i:173178456 original size:39 final size:40
Alignment explanation
Indices: 173178402--173178539 Score: 192
Period size: 40 Copynumber: 3.5 Consensus size: 40
173178392 AAACCAAGTA
* *
173178402 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
173178441 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
173178481 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
173178521 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
173178540 TTATCATCCG
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
39 15 0.17
40 75 0.83
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:173182092 original size:48 final size:49
Alignment explanation
Indices: 173181964--173182109 Score: 163
Period size: 48 Copynumber: 3.0 Consensus size: 49
173181954 GGTTATGTAC
* *
173181964 GATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCATC-ATCATGA
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATCATGA
*** * *
173182012 GATCCCCCATAAGACCATGTCTAGGACATGGCATTGGCATCGA-CATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATCATGA
* * ** *
173182060 GATCCCATGTAAGACCATATTTGGGATGTGGCATTGTCATCGAT-ATGA
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATCATGA
173182108 GA
1 GA
173182110 CATTGTGTAA
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
48 78 0.99
49 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (49 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATCATGA
Found at i:173184673 original size:27 final size:27
Alignment explanation
Indices: 173184601--173184684 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
173184591 GCATCATAGT
* *
173184601 TAGTCCAATAGGACATTAAACACGGGA
1 TAGTCCAATGGGACATTAAACACAGGA
* *
173184628 TAGTCCAATGAGACATTAAACTCAGGA
1 TAGTCCAATGGGACATTAAACACAGGA
** *
173184655 TAGTCCAATGGGATGTTAAACA-AGGG
1 TAGTCCAATGGGACATTAAACACAGGA
173184681 TAGT
1 TAGT
173184685 TCGCTGGGAC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
26 7 0.15
27 41 0.85
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (27 bp):
TAGTCCAATGGGACATTAAACACAGGA
Found at i:173190303 original size:46 final size:46
Alignment explanation
Indices: 173190250--173190422 Score: 206
Period size: 46 Copynumber: 3.7 Consensus size: 46
173190240 TGGTTGAGCA
*
173190250 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
* * * * * *
173190296 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATACGA-ACG
*
173190343 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
* * *
173190389 CCCGAGCTCGTTGAGGTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
173190423 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
45 1 0.01
46 68 0.65
47 35 0.33
48 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
Found at i:173190409 original size:93 final size:93
Alignment explanation
Indices: 173190247--173190417 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
173190237 GGATGGTTGA
* * *
173190247 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGG
173190312 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
173190340 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGG
173190405 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
173190418 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAGG
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:173192446 original size:29 final size:29
Alignment explanation
Indices: 173192412--173192543 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
173192402 TACTCGATTT
** * *
173192412 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* **** * *
173192441 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
173192470 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
173192499 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
173192528 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
173192544 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:173200366 original size:29 final size:29
Alignment explanation
Indices: 173200333--173200406 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
173200323 CCTTCGAGCT
173200333 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
173200362 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
173200391 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
173200407 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:173200367 original size:57 final size:58
Alignment explanation
Indices: 173200275--173200406 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
173200265 ATACTCGATT
* * * * *
173200275 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACAC-AAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACTAAGTGCCATACACTTCCAGC
* * * * * *
173200332 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACTAAGTGCCATACACTTCCAGC
*
173200390 ACGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
173200407 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
56 4 0.07
57 27 0.44
58 30 0.49
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACTAAGTGCCATACACTTCCAGC
Found at i:173203473 original size:80 final size:80
Alignment explanation
Indices: 173203389--173203537 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
173203379 TATGGTAACC
* * * *
173203389 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
173203453 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
173203469 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
173203534 CCGG
66 CCGG
173203538 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:173203479 original size:40 final size:38
Alignment explanation
Indices: 173203430--173203537 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
173203420 ATCACGATTT
*
173203430 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
173203470 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
173203510 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
173203538 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:173211561 original size:80 final size:80
Alignment explanation
Indices: 173211477--173211625 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
173211467 TATGGTAACC
* * * *
173211477 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
173211541 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
173211557 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
173211622 CCGG
66 CCGG
173211626 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:173211567 original size:40 final size:38
Alignment explanation
Indices: 173211518--173211625 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
173211508 ATCACGATTT
*
173211518 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
173211558 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
173211598 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
173211626 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:173214201 original size:40 final size:40
Alignment explanation
Indices: 173214127--173214282 Score: 206
Period size: 40 Copynumber: 3.9 Consensus size: 40
173214117 GATAATCGGA
* * * *
173214127 CTAAGATCCAAAGGCATTCGTGCGAGTTGCTATATCTGGG
1 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCTGGG
* * * *
173214167 CTATGTCCCGAAGGCATTTATGCTAG-TGATTATATCTGGG
1 CTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATATCTGGG
* *
173214207 CTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGG
1 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCTGGG
173214247 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATC
1 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATC
173214283 CGGGTAATTT
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 95 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCTGGG
Found at i:173214568 original size:22 final size:22
Alignment explanation
Indices: 173214526--173214569 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
173214516 AGAATGTGCA
* *
173214526 TATATGAAGTTATTCATTTAGC
1 TATATGAAGTTATACACTTAGC
173214548 TATATGAATGTTATAC-CTTAGC
1 TATATGAA-GTTATACACTTAGC
173214570 CGAAACTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATATGAAGTTATACACTTAGC
Found at i:173217647 original size:27 final size:26
Alignment explanation
Indices: 173217603--173217654 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
173217593 CTCGCTGCAA
*
173217603 TCTGGTGGCCTCGCCACATATATCTAT
1 TCTGGTGACCTCGCCACA-ATATCTAT
* *
173217630 TCTGGTGACTTCGTCACAATATCTA
1 TCTGGTGACCTCGCCACAATATCTA
173217655 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTAT
Found at i:173224924 original size:42 final size:42
Alignment explanation
Indices: 173224862--173224946 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
173224852 CAACTAAGGA
*
173224862 TCTTAAAGGCTAGCACAGTTGGGCATCAAGACTAGTCTGTAT
1 TCTTAAAGGCTAGCACAGTTGGGCATCAAGACTAGTCTATAT
* *
173224904 TCTTAAAGGCTAGCATAGTTGGGCATCGAGACTAGTCTATAT
1 TCTTAAAGGCTAGCACAGTTGGGCATCAAGACTAGTCTATAT
173224946 T
1 T
173224947 TGGCAGAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
TCTTAAAGGCTAGCACAGTTGGGCATCAAGACTAGTCTATAT
Found at i:173229124 original size:40 final size:39
Alignment explanation
Indices: 173229080--173229386 Score: 314
Period size: 40 Copynumber: 7.7 Consensus size: 39
173229070 TAACCACAAT
* * * *** *
173229080 CACAATTGCCTTTGGGTCTTAACCCGGATTTGGTAACTTG
1 CACAA-TGCCTTCGGGTCTTAGCCCGGATATAACAACTCG
173229120 CACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCG
1 CAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTCG
*
173229160 CACGAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTAG
1 CAC-AATGCCTTCGGGTCTTAGCCCGGATATAA-CAACTCG
* * * *
173229200 CATAAATGCCTTCGGGACTTAGCCTGGGTATAACAACTCG
1 CA-CAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCG
*
173229240 CACGAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTAG
1 CAC-AATGCCTTCGGGTCTTAGCCCGGATATAA-CAACTCG
* * * *
173229280 CATAAATGCCTTCGGGACTTAGCTCGGGTATAACAACTCG
1 CA-CAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCG
*
173229320 CACGAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTAG
1 CAC-AATGCCTTCGGGTCTTAGCCCGGATATAA-CAACTCG
* *
173229360 CATAAATGCCTTCGGGACTTAGCCCGG
1 CA-CAATGCCTTCGGGTCTTAGCCCGG
173229387 GTATCATTCA
Statistics
Matches: 225, Mismatches: 31, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
39 2 0.01
40 218 0.97
41 5 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CACAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCG
Found at i:173229207 original size:80 final size:80
Alignment explanation
Indices: 173229086--173229390 Score: 502
Period size: 80 Copynumber: 3.8 Consensus size: 80
173229076 CAATCACAAT
* * * ** * * * * *
173229086 TGCCTTTGGGTCTTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGGTAT
173229151 AACAACTCGCACGAA
66 AACAACTCGCACGAA
*
173229166 TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCTGGGTAT
1 TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGGTAT
173229231 AACAACTCGCACGAA
66 AACAACTCGCACGAA
*
173229246 TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCTCGGGTAT
1 TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGGTAT
173229311 AACAACTCGCACGAA
66 AACAACTCGCACGAA
173229326 TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGGTAT
1 TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGGTAT
173229391 CATTCAAATG
Statistics
Matches: 211, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 211 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (80 bp):
TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGGTAT
AACAACTCGCACGAA
Found at i:173229288 original size:120 final size:121
Alignment explanation
Indices: 173229059--173229386 Score: 353
Period size: 120 Copynumber: 2.7 Consensus size: 121
173229049 TCATCGGAAT
* * * * * * * * ** *
173229059 TTAG-CCGGATATAACCACAATCACAATTGCCTTTGGGTCTTAACCCGGATTTGGT-AACTTGCA
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAATCAACTAGCA
* * *
173229122 CAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
66 CAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGAC
* * * *
173229178 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGACTTAGCCTGGGTATAA-CAACTCGC
1 TTAGCCCGGATATAA-CAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAATCAACTAGC
* *
173229241 ACGAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
65 ACAAATGCCTTCGGGTCTTAGCCCGGATATAA-CAACTAGCACAAATGCCTTCGGGAC
* * * * *
173229298 TTAGCTCGGGTATAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTAGCA
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAATCAACTAGCA
* *
173229362 TAAATGCCTTCGGGACTTAGCCCGG
66 CAAATGCCTTCGGGTCTTAGCCCGG
173229387 GTATCATTCA
Statistics
Matches: 173, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
119 5 0.03
120 165 0.95
121 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (121 bp):
TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAATCAACTAGCA
CAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGAC
Found at i:173237432 original size:28 final size:28
Alignment explanation
Indices: 173237371--173237468 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
173237361 TCACAAATTG
** * *
173237371 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
173237400 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
173237428 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
173237456 GCACTAAGTGTGC
1 GCACTAAGTGTGC
173237469 GGGCTTATGC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:173250582 original size:28 final size:28
Alignment explanation
Indices: 173250521--173250618 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
173250511 TCACAAATTG
** * *
173250521 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
173250550 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
173250578 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
173250606 GCACTAAGTGTGC
1 GCACTAAGTGTGC
173250619 GGGCTTATGC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:173258244 original size:28 final size:28
Alignment explanation
Indices: 173258183--173258280 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
173258173 TCACAAATTG
** * *
173258183 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
173258212 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
173258240 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
173258268 GCACTAAGTGTGC
1 GCACTAAGTGTGC
173258281 GGGCTTATGC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:173265911 original size:28 final size:28
Alignment explanation
Indices: 173265850--173265947 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
173265840 TCACAAATTG
** * *
173265850 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
173265879 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
173265907 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
173265935 GCACTAAGTGTGC
1 GCACTAAGTGTGC
173265948 GGGCTTATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:173275491 original size:79 final size:80
Alignment explanation
Indices: 173275408--173275555 Score: 183
Period size: 79 Copynumber: 1.9 Consensus size: 80
173275398 TATGGTAACC
* * *
173275408 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGA-TTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
173275471 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
173275487 CGCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTAGCACCATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
173275552 CCGG
66 CCGG
173275556 TTATAATTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
78 1 0.02
79 30 0.53
80 26 0.46
ACGTcount: A:0.23, C:0.31, G:0.24, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:173275500 original size:40 final size:40
Alignment explanation
Indices: 173275448--173275555 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 40
173275438 TATCACGATT
** *
173275448 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
173275488 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
173275528 GCACCATTGCCTTCGGGTCTTAACCCGG
1 GCACAAATGCCTTCGGGTCTTAGCCCGG
173275556 TTATAATTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
Found at i:173284392 original size:39 final size:39
Alignment explanation
Indices: 173284344--173284575 Score: 296
Period size: 39 Copynumber: 6.0 Consensus size: 39
173284334 GATGTGTATG
173284344 AATGTTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
1 AATG-TGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
*
173284384 AATGTGCGAATTGTGATATCTGGGCTAAG-CCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
173284422 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
* *
173284461 ATTGTGCGAGA-TATGATATCC-GGCT-AGCCCG-AGGCA
1 AATGTGCGA-ATTGTGATATCCGGGCTAAGCCCGAAGGCA
* * *
173284497 ATTGTGCGAGA-TATGATATCCGGGCTAAGCCCGAAGGCG
1 AATGTGCGA-ATTGTGATATCCGGGCTAAGCCCGAAGGCA
* * * *
173284536 ATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCAAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCA
173284576 TTTGTGCGGG
Statistics
Matches: 175, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
36 26 0.15
37 10 0.06
38 47 0.27
39 79 0.45
40 13 0.07
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (39 bp):
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
Found at i:173284436 original size:77 final size:76
Alignment explanation
Indices: 173284344--173284564 Score: 288
Period size: 75 Copynumber: 2.9 Consensus size: 76
173284334 GATGTGTATG
*
173284344 AATGTTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAATGTGCGAATTGTGATATCTGGGC
1 AATG-TGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATATC-GGGC
173284409 TAAG-CCGAAGGCA
64 TAAGCCCG-AGGCA
* *
173284422 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGA-TATGATATCCGGCT
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGA-ATTGTGATATCGGGCT
173284486 -AGCCCGAGGCA
65 AAGCCCGAGGCA
* * * * *
173284497 ATTGTGCGAGA-TATGATATCCGGGCTAAGCCCGAAGGCGATTGTGCGAGTTGTGATATCCGGGT
1 AATGTGCGA-ATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATAT-CGGGC
173284561 TAAG
64 TAAG
173284565 TCCCAAAGGC
Statistics
Matches: 127, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
75 57 0.45
76 12 0.09
77 53 0.42
78 5 0.04
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.24
Consensus pattern (76 bp):
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATATCGGGCTA
AGCCCGAGGCA
Found at i:173293222 original size:29 final size:29
Alignment explanation
Indices: 173293188--173293265 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
173293178 GTGACGAGAT
* *
173293188 CGGCACTAAGTGTGCGTGCTGGAAATATA
1 CGGCACTAAGTGTGCGAGCTGGAAAAATA
* *
173293217 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 CGGCACTAAGTGTGCGAGCTGGAAAAATA
**
173293246 CGGCACTGGGTGTGCGAGCT
1 CGGCACTAAGTGTGCGAGCT
173293266 CGGAGGGTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (29 bp):
CGGCACTAAGTGTGCGAGCTGGAAAAATA
Found at i:173306809 original size:29 final size:29
Alignment explanation
Indices: 173306777--173306908 Score: 246
Period size: 29 Copynumber: 4.5 Consensus size: 29
173306767 ATAGTGAATC
173306777 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
173306806 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
173306836 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
*
173306865 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
173306894 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
173306909 GTACAATTTT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 72 0.71
30 29 0.29
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:173306918 original size:59 final size:59
Alignment explanation
Indices: 173306777--173306908 Score: 248
Period size: 59 Copynumber: 2.3 Consensus size: 59
173306767 ATAGTGAATC
173306777 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
*
173306836 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATAT-ATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
173306894 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
173306909 GTACAATTTT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
58 24 0.33
59 48 0.67
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (59 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:173314338 original size:18 final size:18
Alignment explanation
Indices: 173314315--173314349 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
173314305 TAAGCCGAAC
173314315 TGGGCTATGT-GGGCCCAA
1 TGGGCT-TGTAGGGCCCAA
173314333 TGGGCTTGTAGGGCCCA
1 TGGGCTTGTAGGGCCCA
173314350 CGTGGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.14, C:0.23, G:0.40, T:0.23
Consensus pattern (18 bp):
TGGGCTTGTAGGGCCCAA
Found at i:173317530 original size:80 final size:80
Alignment explanation
Indices: 173317446--173317594 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
173317436 TATGGTAACC
* * * *
173317446 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
173317510 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
173317526 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
173317591 CCGG
66 CCGG
173317595 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:173317536 original size:40 final size:38
Alignment explanation
Indices: 173317487--173317594 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
173317477 ATCACGATTT
*
173317487 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
173317527 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
173317567 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
173317595 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:173325648 original size:80 final size:80
Alignment explanation
Indices: 173325564--173325712 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
173325554 TATGGTAACC
* * * *
173325564 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
173325628 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
173325644 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
173325709 CCGG
66 CCGG
173325713 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:173325654 original size:40 final size:38
Alignment explanation
Indices: 173325605--173325712 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
173325595 ATCACGATTT
*
173325605 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
173325645 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
173325685 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
173325713 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:173328577 original size:25 final size:25
Alignment explanation
Indices: 173328548--173328595 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
173328538 TTATAATATG
* * *
173328548 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
173328573 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
173328596 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:173328704 original size:5 final size:5
Alignment explanation
Indices: 173328634--173328724 Score: 57
Period size: 5 Copynumber: 18.4 Consensus size: 5
173328624 TTTGATAAAC
* * *
173328634 TGATA TG-TA TGATA TGACA TGACA TGATGA TGCACA TGATA TG-T- TGATA
1 TGATA TGATA TGATA TGATA TGATA TGAT-A TG-ATA TGATA TGATA TGATA
* * *
173328683 TGCACA TGACA TG-TA TGATA TGCACA TGATA TG-TA TGATA TG
1 TG-ATA TGATA TGATA TGATA TG-ATA TGATA TGATA TGATA TG
173328725 CACACGAGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
3 2 0.03
4 13 0.19
5 39 0.57
6 14 0.20
7 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (5 bp):
TGATA
Found at i:173328736 original size:20 final size:20
Alignment explanation
Indices: 173328638--173328728 Score: 129
Period size: 20 Copynumber: 4.8 Consensus size: 20
173328628 ATAAACTGAT
173328638 ATGTATGATATG-ACATGAC
1 ATGTATGATATGCACATGAC
*
173328657 ATG-ATG--ATGCACATGAT
1 ATGTATGATATGCACATGAC
173328674 ATGT-TGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
173328693 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
173328713 ATGTATGATATGCACA
1 ATGTATGATATGCACA
173328729 CGAGATGTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
16 3 0.05
17 11 0.17
18 3 0.05
19 17 0.27
20 30 0.47
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:173328838 original size:24 final size:24
Alignment explanation
Indices: 173328782--173328924 Score: 258
Period size: 23 Copynumber: 6.1 Consensus size: 24
173328772 GAGGAAGTGC
173328782 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
173328806 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
173328829 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
173328853 AAAAGGGCTTATG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
173328876 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
173328899 AAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
173328922 AAA
1 AAA
173328925 GAGGCTAGGC
Statistics
Matches: 116, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
22 12 0.10
23 59 0.51
24 45 0.39
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:173328930 original size:23 final size:24
Alignment explanation
Indices: 173328783--173328944 Score: 216
Period size: 23 Copynumber: 7.0 Consensus size: 24
173328773 AGGAAGTGCA
173328783 AAAG-GGCTTATGCCCCAGTTATT
1 AAAGAGGCTTATGCCCCAGTTATT
173328806 AAAG-GGCTTATGCCCCAGTTATT
1 AAAGAGGCTTATGCCCCAGTTATT
173328829 AAA-AGGGCTTATGCCCCAGTTATT
1 AAAGA-GGCTTATGCCCCAGTTATT
173328853 AAA-AGGGCTTATG-CCCAGTTATT
1 AAAGA-GGCTTATGCCCCAGTTATT
173328876 AAAG-GGCTTATGCCCCAGTTATT
1 AAAGAGGCTTATGCCCCAGTTATT
173328899 AAA-AGGGCTT-TGCCCCAGTTATT
1 AAAGA-GGCTTATGCCCCAGTTATT
*
173328922 AAAGAGGC-TAGGCCTCCAGTTAT
1 AAAGAGGCTTATGCC-CCAGTTAT
173328945 ATGATAAAGC
Statistics
Matches: 129, Mismatches: 1, Indels: 17
0.88 0.01 0.12
Matches are distributed among these distances:
22 9 0.07
23 74 0.57
24 46 0.36
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
AAAGAGGCTTATGCCCCAGTTATT
Found at i:173328944 original size:70 final size:70
Alignment explanation
Indices: 173328782--173328924 Score: 252
Period size: 70 Copynumber: 2.0 Consensus size: 70
173328772 GAGGAAGTGC
*
173328782 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTA-GGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCA
173328847 GTTATT
65 GTTATT
*
173328853 AAAAGGGCTTATGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTT-TGCCCCAG
1 AAAAGGGCTTAGGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAG
173328917 TTATT
66 TTATT
173328922 AAA
1 AAA
173328925 GAGGCTAGGC
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
69 16 0.23
70 43 0.61
71 11 0.16
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (70 bp):
AAAAGGGCTTAGGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAG
TTATT
Found at i:173329193 original size:30 final size:31
Alignment explanation
Indices: 173329133--173329195 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
173329123 CGTTTACAGT
173329133 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
173329164 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
173329194 AA
1 AA
173329196 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:173336805 original size:40 final size:40
Alignment explanation
Indices: 173336761--173336860 Score: 200
Period size: 40 Copynumber: 2.5 Consensus size: 40
173336751 TTGATAAACC
173336761 TGATATGTATGATATGCACATGACATGTATGATATGCACA
1 TGATATGTATGATATGCACATGACATGTATGATATGCACA
173336801 TGATATGTATGATATGCACATGACATGTATGATATGCACA
1 TGATATGTATGATATGCACATGACATGTATGATATGCACA
173336841 TGATATGTATGATATGCACA
1 TGATATGTATGATATGCACA
173336861 CGAGATGTTC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (40 bp):
TGATATGTATGATATGCACATGACATGTATGATATGCACA
Found at i:173336868 original size:20 final size:20
Alignment explanation
Indices: 173336765--173336860 Score: 174
Period size: 20 Copynumber: 4.8 Consensus size: 20
173336755 TAAACCTGAT
173336765 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
173336785 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
173336805 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
173336825 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
173336845 ATGTATGATATGCACA
1 ATGTATGATATGCACA
173336861 CGAGATGTTC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:173336941 original size:24 final size:24
Alignment explanation
Indices: 173336914--173337011 Score: 128
Period size: 24 Copynumber: 4.0 Consensus size: 24
173336904 GAGGAAGTGC
173336914 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
173336938 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
173336962 AAAAAAAGGGCTT-TGCCCCAGTTATT
1 ---AAAAGGGCTTATGCCCCAGTTATT
*
173336988 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
173337012 ATGATAAAGC
Statistics
Matches: 67, Mismatches: 1, Indels: 11
0.85 0.01 0.14
Matches are distributed among these distances:
23 6 0.09
24 30 0.45
25 8 0.12
26 13 0.19
27 10 0.15
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:173336990 original size:50 final size:52
Alignment explanation
Indices: 173336914--173337011 Score: 157
Period size: 50 Copynumber: 1.9 Consensus size: 52
173336904 GAGGAAGTGC
*
173336914 AAAAGGGCTTATGCCCCAGTTATTAAAAG-GGCTTATGCC-CCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATTAAA
173336965 AAAAGGGCTT-TGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
173337012 ATGATAAAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
50 23 0.52
51 21 0.48
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTATTAAA
Found at i:173337239 original size:31 final size:31
Alignment explanation
Indices: 173337204--173337267 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
173337194 CGTTTACAGT
173337204 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
173337235 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
173337266 AA
1 AA
173337268 TATGAACAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:173339168 original size:39 final size:40
Alignment explanation
Indices: 173339054--173339238 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
173339044 GCTACTCGTT
*
173339054 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
173339094 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
173339134 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
** * * * *
173339173 CAAATGCCTTC-GGATCTTAGTTCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
173339214 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
173339239 CATCATTCGA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.26
40 77 0.62
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:173339199 original size:79 final size:81
Alignment explanation
Indices: 173339056--173339238 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
173339046 TACTCGTTCA
* *
173339056 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
173339120 TTTAGTAAC-TCGCACC
66 TATAGTAACTTAGCA-C
***
173339136 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTTCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
173339198 ATATGGTCACTTAGCAC
65 ATATAGTAACTTAGCAC
*
173339215 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
173339239 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:173343996 original size:25 final size:23
Alignment explanation
Indices: 173343957--173344036 Score: 85
Period size: 22 Copynumber: 3.5 Consensus size: 23
173343947 GCCATGATCG
*
173343957 GTAAGCTCCTCTTGAGCTGATGAACA
1 GTAAGCT-CTATTGAGCT--TGAACA
*
173343983 GTAAGCTTTATTGAGC-TGAACA
1 GTAAGCTCTATTGAGCTTGAACA
*
173344005 GTAAGCTCTATCGAG-TTGAACA
1 GTAAGCTCTATTGAGCTTGAACA
173344027 GTAAGC-CTAT
1 GTAAGCTCTAT
173344037 ACAAGCTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
21 4 0.08
22 31 0.63
25 7 0.14
26 7 0.14
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (23 bp):
GTAAGCTCTATTGAGCTTGAACA
Found at i:173344005 original size:22 final size:22
Alignment explanation
Indices: 173343977--173344076 Score: 105
Period size: 22 Copynumber: 4.5 Consensus size: 22
173343967 CTTGAGCTGA
* *
173343977 TGAACAGTAAGCTTTATTGAGC
1 TGAACAGTAAGCTCTATCGAGC
*
173343999 TGAACAGTAAGCTCTATCGAGT
1 TGAACAGTAAGCTCTATCGAGC
*
173344021 TGAACAGTAAGC-CTATACAAGC
1 TGAACAGTAAGCTCTAT-CGAGC
* *
173344043 TGAACAATAAGCTCATAT-GATC
1 TGAACAGTAAGCTC-TATCGAGC
173344065 TGAAACAGTAAG
1 TG-AACAGTAAG
173344077 ATCCAATGAG
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
21 4 0.06
22 49 0.75
23 9 0.14
24 3 0.05
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (22 bp):
TGAACAGTAAGCTCTATCGAGC
Found at i:173348417 original size:27 final size:27
Alignment explanation
Indices: 173348375--173348491 Score: 137
Period size: 27 Copynumber: 4.3 Consensus size: 27
173348365 TGGATAAGTT
* *
173348375 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCAAAATACCCTTGTAGG
* *
173348402 ATAGAATTACTAAAATACCCTTGTAGG
1 GTAGAATTACCAAAATACCCTTGTAGG
* *
173348429 GTAGAAATACCAAAATGCCCTTGTAGG
1 GTAGAATTACCAAAATACCCTTGTAGG
* *
173348456 GTAGAATTA-CAGAGATACCCTTGTGGG
1 GTAGAATTACCA-AAATACCCTTGTAGG
*
173348483 GTAAAATTA
1 GTAGAATTA
173348492 AATGACTATT
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
26 2 0.03
27 74 0.97
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (27 bp):
GTAGAATTACCAAAATACCCTTGTAGG
Found at i:173349190 original size:27 final size:26
Alignment explanation
Indices: 173349146--173349196 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
173349136 CTCGCTGTAA
*
173349146 TCTGGTGGCCTCGCCACATATATCTAT
1 TCTGGTGACCTCGCCACA-ATATCTAT
* *
173349173 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
173349197 GGCAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTAT
Found at i:173349274 original size:2 final size:2
Alignment explanation
Indices: 173349267--173349292 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
173349257 GCCTAGTCAC
173349267 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
173349293 TTGTTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:173349295 original size:47 final size:46
Alignment explanation
Indices: 173349230--173349318 Score: 151
Period size: 47 Copynumber: 1.9 Consensus size: 46
173349220 GCTTCTCCAC
*
173349230 ATATATATATATATATTTGTTCTGGTGGCCTAGTCACATATATATAT
1 ATATATATATATATATTTGTTCTGGTGGCCTAGCCACA-ATATATAT
*
173349277 ATATATATATATATATTTGTTTTGGTGGCCTAGCCACAATAT
1 ATATATATATATATATTTGTTCTGGTGGCCTAGCCACAATAT
173349319 CTGTATTTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 4 0.10
47 36 0.90
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (46 bp):
ATATATATATATATATTTGTTCTGGTGGCCTAGCCACAATATATAT
Found at i:173360960 original size:93 final size:93
Alignment explanation
Indices: 173360848--173361019 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
173360838 CGCCCATAAG
* *
173360848 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
173360913 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
173360941 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
173361006 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
173361020 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:173361016 original size:46 final size:46
Alignment explanation
Indices: 173360841--173361016 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
173360831 TGTAACCCGC
* * *
173360841 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
173360887 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
173360937 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
173360980 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
173361017 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:173368544 original size:93 final size:93
Alignment explanation
Indices: 173368385--173368556 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
173368375 CGCCCATAAG
* *
173368385 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
173368450 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
173368478 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
173368543 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
173368557 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:173368553 original size:46 final size:46
Alignment explanation
Indices: 173368378--173368553 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
173368368 TGTAACCCGC
* * *
173368378 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
173368424 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
173368474 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
173368517 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
173368554 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:173372080 original size:40 final size:39
Alignment explanation
Indices: 173372013--173372174 Score: 245
Period size: 40 Copynumber: 4.1 Consensus size: 39
173372003 CGGGCTTTAA
* *
173372013 CCGGATATAGCACTCGCTCAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGC
*
173372052 CCGGATATAGTAGTTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTA-CTCGCACAAATGCCTTCGGGACTTAGC
173372092 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGC
*
173372132 CCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGC
173372172 CCG
1 CCG
173372175 TTATCATCCG
Statistics
Matches: 114, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
39 12 0.11
40 101 0.89
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:173383176 original size:29 final size:29
Alignment explanation
Indices: 173383140--173383361 Score: 399
Period size: 29 Copynumber: 7.7 Consensus size: 29
173383130 TGTTGAAAAA
* *
173383140 CTCGCACACACAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
* *
173383169 CTCGCACACGTAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
173383198 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
173383227 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
173383256 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
*
173383285 CTCGCACACATAGTGCCTCAATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
173383314 CTCGCACACATAGTGCCTCGATTACTGAT
1 CTCGCACACATAGTGCCTCGATTACTGAT
173383343 CTCGCACACATAGTGCCTC
1 CTCGCACACATAGTGCCTC
173383362 TATTCATTCG
Statistics
Matches: 187, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 187 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCGATTACTGAT
Found at i:173383592 original size:40 final size:40
Alignment explanation
Indices: 173383535--173383779 Score: 355
Period size: 40 Copynumber: 6.1 Consensus size: 40
173383525 CGAATACACG
* * *
173383535 TCACTAGCATGATTGCTCTTCGGGACCTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
* * *
173383575 TCACTAGCACGAATGCTCTTCGGGACTTTGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
* * *
173383615 TCACTAGCACGAATGCTCTTCGGGACTTTGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
* *
173383655 TCACTAGCATGAATGCTCTTCGGAACTTAGTCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
* *
173383695 TCACTAGCATGAATGCTCTTCGGAACTTAGTCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
* *
173383735 TCACTAGCATGAATGCTCTTCGGAACTTAGTCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
173383775 TCACT
1 TCACT
173383780 CTCAATTCTC
Statistics
Matches: 196, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 196 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
Done.