Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, whole genome shotgun sequence
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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 8 of 20
Found at i:2894221 original size:71 final size:73
Alignment explanation
Indices: 2894125--2894261 Score: 251
Period size: 71 Copynumber: 1.9 Consensus size: 73
2894115 AAATTATAGT
2894125 GAGGACAATTTTGGAAAAAAATTATAACTTTACTTTCAC-GGGGAAAAGTAACTTTCTCT-CATG
1 GAGGACAATTTTGGAAAAAAATTATAACTTTACTTTCACGGGGGAAAAGTAACTTTCTCTCCATG
2894188 ATTATAAC
66 ATTATAAC
*
2894196 GAGGACAATTTTGGAAAAAATTTATAACTTTACTTTCACGGGGGAAAAGTAACTTTCTCTCCATG
1 GAGGACAATTTTGGAAAAAAATTATAACTTTACTTTCACGGGGGAAAAGTAACTTTCTCTCCATG
2894261 A
66 A
2894262 GAGAAAGGAA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
71 38 0.60
72 20 0.32
73 5 0.08
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (73 bp):
GAGGACAATTTTGGAAAAAAATTATAACTTTACTTTCACGGGGGAAAAGTAACTTTCTCTCCATG
ATTATAAC
Found at i:2894547 original size:14 final size:15
Alignment explanation
Indices: 2894517--2894556 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
2894507 AATAAACATT
2894517 AAAACATAGGGGAAA
1 AAAACATAGGGGAAA
*
2894532 AAAATATAGGGGAAA
1 AAAACATAGGGGAAA
*
2894547 AAAACCTAGG
1 AAAACATAGG
2894557 TATGTAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.57, C:0.07, G:0.25, T:0.10
Consensus pattern (15 bp):
AAAACATAGGGGAAA
Found at i:2895009 original size:22 final size:22
Alignment explanation
Indices: 2894984--2895028 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2894974 AGGGTTTAGA
*
2894984 AATTAGTCAATGGTTATAGCCT
1 AATTAGTCAATGATTATAGCCT
2895006 AATTAGTCAATGATTATAGCCT
1 AATTAGTCAATGATTATAGCCT
2895028 A
1 A
2895029 CAATCAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (22 bp):
AATTAGTCAATGATTATAGCCT
Found at i:2904681 original size:3 final size:3
Alignment explanation
Indices: 2904673--2904697 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2904663 AGAAAACAAA
2904673 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2904698 TTACATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2910111 original size:6 final size:6
Alignment explanation
Indices: 2910100--2910130 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
2910090 AGGGAGAGTC
2910100 CAAAGG CAAAGG CAAAGG CAAAGG CACAAGG
1 CAAAGG CAAAGG CAAAGG CAAAGG CA-AAGG
2910131 ACGAGAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.48, C:0.19, G:0.32, T:0.00
Consensus pattern (6 bp):
CAAAGG
Found at i:2913126 original size:39 final size:39
Alignment explanation
Indices: 2913072--2913148 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
2913062 TTTTCATAGG
*
2913072 TTTGTGCCTCTTTAGGGCCAATAGGCTCTTTTGGAGCAA
1 TTTGTGCCTCTTTAGGGCCAATAGGCTCTTCTGGAGCAA
* * *
2913111 TTTGTGCCTCTTTAGGGGCAATGGGTTCTTCTGGAGCA
1 TTTGTGCCTCTTTAGGGCCAATAGGCTCTTCTGGAGCA
2913149 GATTCATGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.16, C:0.19, G:0.29, T:0.36
Consensus pattern (39 bp):
TTTGTGCCTCTTTAGGGCCAATAGGCTCTTCTGGAGCAA
Found at i:2922704 original size:37 final size:37
Alignment explanation
Indices: 2922582--2922704 Score: 108
Period size: 37 Copynumber: 3.3 Consensus size: 37
2922572 CAAGAAAATA
2922582 AACCCATATGTATCTAGAATAATCATCAACTATAATG
1 AACCCATATGTATCTAGAATAATCATCAACTATAATG
* *** * * * *
2922619 AACCCATATG-ATTTACCTCTTAAACTAGT-TA-TGTCAATA
1 AACCCATATGTATCTA--GAATAATC-A-TCAACTAT-AATG
2922658 AACCCATATGTATCTAGAATAATCATCAACTATAATG
1 AACCCATATGTATCTAGAATAATCATCAACTATAATG
2922695 AACCCATATG
1 AACCCATATG
2922705 ATTTACCTCC
Statistics
Matches: 62, Mismatches: 16, Indels: 16
0.66 0.17 0.17
Matches are distributed among these distances:
36 5 0.08
37 25 0.40
38 12 0.19
39 15 0.24
40 5 0.08
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (37 bp):
AACCCATATGTATCTAGAATAATCATCAACTATAATG
Found at i:2922704 original size:76 final size:76
Alignment explanation
Indices: 2922578--2922732 Score: 301
Period size: 76 Copynumber: 2.0 Consensus size: 76
2922568 TAAGCAAGAA
*
2922578 AATAAACCCATATGTATCTAGAATAATCATCAACTATAATGAACCCATATGATTTACCTCTTAAA
1 AATAAACCCATATGTATCTAGAATAATCATCAACTATAATGAACCCATATGATTTACCTCCTAAA
2922643 CTAGTTATGTC
66 CTAGTTATGTC
2922654 AATAAACCCATATGTATCTAGAATAATCATCAACTATAATGAACCCATATGATTTACCTCCTAAA
1 AATAAACCCATATGTATCTAGAATAATCATCAACTATAATGAACCCATATGATTTACCTCCTAAA
2922719 CTAGTTATGTC
66 CTAGTTATGTC
2922730 AAT
1 AAT
2922733 TGGACCAAAT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (76 bp):
AATAAACCCATATGTATCTAGAATAATCATCAACTATAATGAACCCATATGATTTACCTCCTAAA
CTAGTTATGTC
Found at i:2929338 original size:18 final size:18
Alignment explanation
Indices: 2929299--2929338 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2929289 AATTTTAGCT
* * *
2929299 AAAATTATTAAAAATAAT
1 AAAATAATTAAAAAGAAA
2929317 AAAATAATTAAAAAGAAA
1 AAAATAATTAAAAAGAAA
2929335 AAAA
1 AAAA
2929339 AGGATGAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATAATTAAAAAGAAA
Found at i:2929667 original size:14 final size:14
Alignment explanation
Indices: 2929648--2929675 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2929638 ATTTAACTGG
2929648 TTTTGGTAGTTTGT
1 TTTTGGTAGTTTGT
2929662 TTTTGGTAGTTTGT
1 TTTTGGTAGTTTGT
2929676 AGAGATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.29, T:0.64
Consensus pattern (14 bp):
TTTTGGTAGTTTGT
Found at i:2932469 original size:18 final size:18
Alignment explanation
Indices: 2932442--2932476 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2932432 TAAGAACCAA
*
2932442 AAATAATAAAATAATAAT
1 AAATAATAAAAAAATAAT
*
2932460 AAATACTAAAAAAATAA
1 AAATAATAAAAAAATAA
2932477 GTGAAGCGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAATAAAAAAATAAT
Found at i:2941301 original size:43 final size:43
Alignment explanation
Indices: 2941193--2941372 Score: 141
Period size: 43 Copynumber: 4.1 Consensus size: 43
2941183 GCTTCTAGTG
* * * * * *
2941193 CATTTTCTAAAATCTTTGGGTATATATTCAAAACCTCCAAGTA
1 CATTCTCTAAAATCTCTAGGTACATCTCCAAAACCTCCAAGTA
* * * **
2941236 TA-TCTCTAAAA-CTTCCAAGTACATCTCCAAAACCTTTAAGTA
1 CATTCTCTAAAATC-TCTAGGTACATCTCCAAAACCTCCAAGTA
*
2941278 CATTCTCTAAAATCTCTAGGTACAT-TCTTAAAACCTCCAAGTA
1 CATTCTCTAAAATCTCTAGGTACATCTC-CAAAACCTCCAAGTA
* * * * *
2941321 CATTCTTATAAAACCTCTAGGTACATTCTCAAGAAACCTCTAGGTA
1 CATTC-TCTAAAATCTCTAGGTACA-TCTCCA-AAACCTCCAAGTA
2941367 CATTCT
1 CATTCT
2941373 TAGGAAACTT
Statistics
Matches: 107, Mismatches: 22, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
41 1 0.01
42 31 0.29
43 36 0.34
44 18 0.17
45 3 0.03
46 18 0.17
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (43 bp):
CATTCTCTAAAATCTCTAGGTACATCTCCAAAACCTCCAAGTA
Found at i:2941321 original size:21 final size:22
Alignment explanation
Indices: 2941222--2941372 Score: 146
Period size: 21 Copynumber: 6.9 Consensus size: 22
2941212 GTATATATTC
* *
2941222 AAAACCTCCAAGTATA-TCTCT
1 AAAACCTCTAAGTACATTCTCT
* * *
2941243 AAAACTTCCAAGTACA-TCTCC
1 AAAACCTCTAAGTACATTCTCT
*
2941264 AAAACCTTTAAGTACATTCTCT
1 AAAACCTCTAAGTACATTCTCT
* *
2941286 AAAATCTCTAGGTACATTCT-T
1 AAAACCTCTAAGTACATTCTCT
* *
2941307 AAAACCTCCAAGTACATTCTTAT
1 AAAACCTCTAAGTACATTC-TCT
* *
2941330 AAAACCTCTAGGTACATTCTCA
1 AAAACCTCTAAGTACATTCTCT
*
2941352 AGAAACCTCTAGGTACATTCT
1 A-AAACCTCTAAGTACATTCT
2941373 TAGGAAACTT
Statistics
Matches: 109, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
21 48 0.44
22 24 0.22
23 37 0.34
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.30
Consensus pattern (22 bp):
AAAACCTCTAAGTACATTCTCT
Found at i:2941379 original size:23 final size:21
Alignment explanation
Indices: 2941264--2941389 Score: 126
Period size: 23 Copynumber: 5.7 Consensus size: 21
2941254 GTACATCTCC
* *
2941264 AAAACCTTTAAGTACATTCTCT
1 AAAACCTCTAGGTACATTCT-T
*
2941286 AAAATCTCTAGGTACATTCTT
1 AAAACCTCTAGGTACATTCTT
* *
2941307 AAAACCTCCAAGTACATTCTTAT
1 AAAACCTCTAGGTACATTC-T-T
*
2941330 AAAACCTCTAGGTACATTCTCA
1 AAAACCTCTAGGTACATTCT-T
2941352 AGAAACCTCTAGGTACATTCTT
1 A-AAACCTCTAGGTACATTCTT
*
2941374 AGGAAACTTCTAGGTA
1 A--AAACCTCTAGGTA
2941390 ACTAGCATCA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
21 17 0.19
22 21 0.24
23 50 0.57
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (21 bp):
AAAACCTCTAGGTACATTCTT
Found at i:2941979 original size:17 final size:18
Alignment explanation
Indices: 2941957--2941993 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2941947 AGCTAAAATT
*
2941957 ATTAAAAA-TAATAAAAA
1 ATTAAAAATTAAAAAAAA
2941974 ATTAAAAATTAAAAAAAA
1 ATTAAAAATTAAAAAAAA
2941992 AT
1 AT
2941994 AAGTTGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
ATTAAAAATTAAAAAAAA
Found at i:2942182 original size:14 final size:13
Alignment explanation
Indices: 2942147--2942193 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2942137 AATCAAATGA
2942147 AAAAACATAAAAAC
1 AAAAA-ATAAAAAC
2942161 AAAAAATAAAAA-
1 AAAAAATAAAAAC
*
2942173 AATAATAATAAATAC
1 AA-AA-AATAAAAAC
2942188 AAAAAA
1 AAAAAA
2942194 AAGGTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 2 0.07
13 11 0.38
14 14 0.48
15 2 0.07
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAATAAAAAC
Found at i:2942463 original size:14 final size:15
Alignment explanation
Indices: 2942444--2942480 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2942434 ATAAGGTAAA
2942444 TAAAAATAAAAT-AC
1 TAAAAATAAAATCAC
*
2942458 TAAAAAGAAAATCAC
1 TAAAAATAAAATCAC
2942473 -AAAAATAA
1 TAAAAATAA
2942481 TAAATTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 18 0.90
15 2 0.10
ACGTcount: A:0.73, C:0.08, G:0.03, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAATCAC
Found at i:2944379 original size:28 final size:28
Alignment explanation
Indices: 2944347--2944404 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2944337 GAATAAAACA
2944347 GCCTTGCCTTTGTTTCAAATCCCAGCTG
1 GCCTTGCCTTTGTTTCAAATCCCAGCTG
2944375 GCCTTGCCTTTGTTTCAAATCCCAGCTG
1 GCCTTGCCTTTGTTTCAAATCCCAGCTG
2944403 GC
1 GC
2944405 TTTGATAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.14, C:0.33, G:0.19, T:0.34
Consensus pattern (28 bp):
GCCTTGCCTTTGTTTCAAATCCCAGCTG
Found at i:2945054 original size:4 final size:4
Alignment explanation
Indices: 2945045--2945070 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2945035 TAATTATAGT
2945045 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
2945071 AGATGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:2959251 original size:31 final size:29
Alignment explanation
Indices: 2959210--2959292 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 29
2959200 AATAAAAAAT
2959210 ATTAAAAAATTAAATTAAAATAATTTTTAAA
1 ATTAAAAAATTAAATTAAAATAA-TTTT-AA
* * **
2959241 ATTAATAAATTAAAATATCATAATTTTAA
1 ATTAAAAAATTAAATTAAAATAATTTTAA
* *
2959270 A-TAGAGAGATTAAATTAAAATAA
1 ATTA-AAAAATTAAATTAAAATAA
2959293 ATATCTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
28 2 0.05
29 17 0.40
30 4 0.10
31 19 0.45
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (29 bp):
ATTAAAAAATTAAATTAAAATAATTTTAA
Found at i:2960802 original size:20 final size:19
Alignment explanation
Indices: 2960773--2960811 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2960763 TTAGGCATAA
2960773 TATTTAAAAAAAATTTAAAT
1 TATTT-AAAAAAATTTAAAT
*
2960793 TATTTGAAAAAATTTAAAT
1 TATTTAAAAAAATTTAAAT
2960812 AAATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TATTTAAAAAAATTTAAAT
Found at i:2962172 original size:4 final size:4
Alignment explanation
Indices: 2962163--2962205 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
2962153 GGTGAATGTG
* *
2962163 ACAA ACAA ACAA ACAA ATAA ACAA ACAA ACAA A-AA AAAA ACAA
1 ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA
2962206 TAAGTTAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.79, C:0.19, G:0.00, T:0.02
Consensus pattern (4 bp):
ACAA
Found at i:2977674 original size:23 final size:22
Alignment explanation
Indices: 2977648--2977691 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2977638 TATTTCTTCT
* *
2977648 TTTTCTTTCTATTTTGTTTTTAA
1 TTTTATTTCTATCTT-TTTTTAA
2977671 TTTTATTTCTATCTTTTTTTA
1 TTTTATTTCTATCTTTTTTTA
2977692 GACTTTGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTATTTCTATCTTTTTTTAA
Found at i:2978100 original size:14 final size:14
Alignment explanation
Indices: 2978065--2978115 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
2978055 TTTATCTCTC
2978065 ATTTT-TTTATTTG
1 ATTTTATTTATTTG
** *
2978078 ATTCAATTTTTTTG
1 ATTTTATTTATTTG
2978092 ATTTTATTTATTT-
1 ATTTTATTTATTTG
2978105 ATTATTATTTA
1 ATT-TTATTTA
2978116 ATAAAAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 6 0.20
14 24 0.80
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (14 bp):
ATTTTATTTATTTG
Found at i:2978459 original size:10 final size:11
Alignment explanation
Indices: 2978430--2978459 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2978420 ATTATTATTT
2978430 TTTTATAAAAA
1 TTTTATAAAAA
2978441 TTTTATAAAAA
1 TTTTATAAAAA
2978452 TTTT-TAAA
1 TTTTATAAA
2978460 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTTATAAAAA
Found at i:2984716 original size:2 final size:2
Alignment explanation
Indices: 2984711--2984743 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2984701 TTTTTTGTGG
*
2984711 TC TC TC TC TC TC TT TC TC TC TC TC TC -C TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2984744 ACGCACATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2985686 original size:25 final size:26
Alignment explanation
Indices: 2985638--2985694 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
2985628 TTGTTATTTT
2985638 TTTATTATGTTGAATTAGATATTATA
1 TTTATTATGTTGAATTAGATATTATA
*
2985664 TTTA-TATTTTGAATTA-ATAATTA-A
1 TTTATTATGTTGAATTAGAT-ATTATA
2985688 -TTATTAT
1 TTTATTAT
2985695 TTTAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 3 0.11
24 6 0.21
25 15 0.54
26 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (26 bp):
TTTATTATGTTGAATTAGATATTATA
Found at i:2992685 original size:17 final size:17
Alignment explanation
Indices: 2992658--2992697 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
2992648 TACTTGAGTG
2992658 CAATGGCATAGTGAAGCT
1 CAAT-GCATAGTGAAGCT
*
2992676 CAATGCATAGTGGAGCT
1 CAATGCATAGTGAAGCT
2992693 CAATG
1 CAATG
2992698 ATACTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (17 bp):
CAATGCATAGTGAAGCT
Found at i:2996619 original size:1 final size:1
Alignment explanation
Indices: 2996615--2996641 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2996605 CCCCCCCTTT
2996615 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
2996642 TGGGCGTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3000773 original size:23 final size:21
Alignment explanation
Indices: 3000741--3000782 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3000731 CGGCTGCCAA
3000741 TTTTACATTTTTTAATAATTTAG
1 TTTTACA-TTTTTAA-AATTTAG
*
3000764 TTTTATATTTTTAAAATTT
1 TTTTACATTTTTAAAATTT
3000783 TATAATTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTACATTTTTAAAATTTAG
Found at i:3000783 original size:32 final size:33
Alignment explanation
Indices: 3000741--3000826 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 33
3000731 CGGCTGCCAA
*
3000741 TTTTACATTTTTTAATAATTTAGT-TTTAT-AT
1 TTTTAAATTTTTTAATAATTTAGTCTTTATAAT
* *
3000772 TTTTAAA-ATTTT-ATAATTTCGTCTTTATAAAAT
1 TTTTAAATTTTTTAATAATTTAGTCTTTAT--AAT
3000805 TTTTAAATTTTTTAATATATTT
1 TTTTAAATTTTTTAATA-ATTT
3000827 TTATTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
29 9 0.20
30 9 0.20
31 6 0.14
33 9 0.20
34 4 0.09
35 3 0.07
36 4 0.09
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (33 bp):
TTTTAAATTTTTTAATAATTTAGTCTTTATAAT
Found at i:3003802 original size:35 final size:35
Alignment explanation
Indices: 3003763--3003837 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
3003753 CGCGAAGTAA
* * *
3003763 TTGTTCTGCATGAAGTAGTACTTTACTTGTTCTAG
1 TTGTTCTGCATGAAATAGTACTTCACTTGCTCTAG
* *
3003798 TTGTTCTGGATGAAATAGTTCTTCACTTGCTCTAG
1 TTGTTCTGCATGAAATAGTACTTCACTTGCTCTAG
3003833 TTGTT
1 TTGTT
3003838 TTATGTCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.47
Consensus pattern (35 bp):
TTGTTCTGCATGAAATAGTACTTCACTTGCTCTAG
Found at i:3003861 original size:35 final size:34
Alignment explanation
Indices: 3003775--3003876 Score: 93
Period size: 35 Copynumber: 3.0 Consensus size: 34
3003765 GTTCTGCATG
* *
3003775 AAGTAGTACTTTACTTGTTCTAGTTGTTCTGGATG-
1 AAGTAGTACTTTACTTGCTCTAGTTGTT-T-TATGT
* * *
3003810 AAATAGTTCTTCACTTGCTCTAGTTGTTTTATGT
1 AAGTAGTACTTTACTTGCTCTAGTTGTTTTATGT
* *
3003844 CAAGTAGTGCTTTACTTGCTTTAG-TG-TTTATGT
1 -AAGTAGTACTTTACTTGCTCTAGTTGTTTTATGT
3003877 GTAAAGCAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
33 10 0.18
34 3 0.05
35 43 0.77
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.48
Consensus pattern (34 bp):
AAGTAGTACTTTACTTGCTCTAGTTGTTTTATGT
Found at i:3008567 original size:26 final size:25
Alignment explanation
Indices: 3008524--3008582 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
3008514 AAAAGGAGCC
*
3008524 CTCAACTTTACATCAAGGAGATTAA
1 CTCAACTTGACATCAAGGAGATTAA
*
3008549 CTCTAACTTGACATGAAGGAGATTAA
1 CTC-AACTTGACATCAAGGAGATTAA
*
3008575 TTCAACTT
1 CTCAACTT
3008583 TTAAAATAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.31
Consensus pattern (25 bp):
CTCAACTTGACATCAAGGAGATTAA
Found at i:3009951 original size:35 final size:35
Alignment explanation
Indices: 3009903--3010011 Score: 137
Period size: 35 Copynumber: 3.1 Consensus size: 35
3009893 CTGTGCAAAA
* * *
3009903 TAGTTGTTCTGCATGAAATAGTACTTTACTTGTTC
1 TAGTTGTTTTGCATGAAATAGTACTTCACTTGCTC
* *
3009938 TAGTTGTTTTGCATGAAATAGTGCTTCACTTACTC
1 TAGTTGTTTTGCATGAAATAGTACTTCACTTGCTC
*** *
3009973 TAGTTGTTTTATGTGAAGTAGTACTTCACTTGCTC
1 TAGTTGTTTTGCATGAAATAGTACTTCACTTGCTC
3010008 TAGT
1 TAGT
3010012 GACTGTGTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (35 bp):
TAGTTGTTTTGCATGAAATAGTACTTCACTTGCTC
Found at i:3011651 original size:20 final size:20
Alignment explanation
Indices: 3011626--3011665 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3011616 CTTCGTAATC
3011626 GGGTCTAACTTGTGAAAATT
1 GGGTCTAACTTGTGAAAATT
3011646 GGGTCTAACTTGTGAAAATT
1 GGGTCTAACTTGTGAAAATT
3011666 TTGAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (20 bp):
GGGTCTAACTTGTGAAAATT
Found at i:3011709 original size:16 final size:16
Alignment explanation
Indices: 3011688--3011722 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3011678 GAACCAAGGC
* *
3011688 TAATTAATGAATTAAT
1 TAATTAAAGAAATAAT
3011704 TAATTAAAGAAATAAT
1 TAATTAAAGAAATAAT
3011720 TAA
1 TAA
3011723 AAATCACTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (16 bp):
TAATTAAAGAAATAAT
Found at i:3013844 original size:19 final size:19
Alignment explanation
Indices: 3013820--3013858 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3013810 TTTATTTTAA
3013820 CATGATGTAAGTTATTCAT
1 CATGATGTAAGTTATTCAT
3013839 CATGATGTAAGTTATTCAT
1 CATGATGTAAGTTATTCAT
3013858 C
1 C
3013859 TAAATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (19 bp):
CATGATGTAAGTTATTCAT
Found at i:3015312 original size:30 final size:30
Alignment explanation
Indices: 3015276--3015333 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3015266 TTAATAAAAC
*
3015276 TTTTATACTTTTATTTTGAATCGAATAATT
1 TTTTATACTTTTATTTTGAATCAAATAATT
*
3015306 TTTTATATTTTTATTTTGAATCAAATAA
1 TTTTATACTTTTATTTTGAATCAAATAA
3015334 GTTCTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (30 bp):
TTTTATACTTTTATTTTGAATCAAATAATT
Found at i:3016448 original size:31 final size:29
Alignment explanation
Indices: 3016410--3016533 Score: 100
Period size: 31 Copynumber: 4.2 Consensus size: 29
3016400 ATAATATTAT
3016410 AATTAAAATAAATATATAATATAAGAATAAA
1 AATTAAAATAAATATATAATAT-AGAA-AAA
*
3016441 AATTAAAATAAA-ATA-AA-ATA-TAAAA
1 AATTAAAATAAATATATAATATAGAAAAA
**
3016466 AATT--AATATTTATATAATATAGATAAAACA
1 AATTAAAATAAATATATAATATAG--AAAA-A
3016496 AATTAAAATAAAATATATAATATA-AAAAA
1 AATTAAAAT-AAATATATAATATAGAAAAA
3016525 TATATTAAA
1 -A-ATTAAA
3016534 GAAATGAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
23 4 0.05
24 3 0.04
25 9 0.12
26 4 0.05
27 1 0.01
28 2 0.03
29 6 0.08
30 13 0.17
31 18 0.24
32 3 0.04
33 12 0.16
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (29 bp):
AATTAAAATAAATATATAATATAGAAAAA
Found at i:3016463 original size:24 final size:25
Alignment explanation
Indices: 3016414--3016871 Score: 111
Period size: 26 Copynumber: 17.0 Consensus size: 25
3016404 TATTATAATT
*
3016414 AAAA-TAAATATATAATATAAGA-ATA
1 AAAATTAAA-ATAAAATATAA-ATATA
3016439 AAAATTAAAATAAAATA-AAATATAA
1 AAAATTAAAATAAAATATAAATAT-A
* * *
3016464 AAAATTAATATTTATATAATATAGATAAA
1 AAAATTAA-A---ATAAAATATAAATATA
3016493 ACAAATTAAAATAAAATATATAATATA
1 A-AAATTAAAATAAAATATA-AATATA
* * * *
3016520 AAAAATATATTAAAGAAATGAAA-A-A
1 AAAATTAAAATAAA-ATAT-AAATATA
* *
3016545 AATATATAAAATTATAATA-ATAA-ATA
1 AAAAT-TAAAA-TAAAATATA-AATATA
*
3016571 AAAA-TAAAATATATGACAT-TAAAAAT-
1 AAAATTAAAATA-A--A-ATATAAATATA
* * * *
3016597 ATATTTAAAATATAATAT-TATATA
1 AAAATTAAAATAAAATATAAATATA
3016621 AAAATTAATAATATAAATATAAATATATTA
1 AAAATTAA-AATA-AAATAT-AA-ATA-TA
*
3016651 AAAATAAAATATAAAATATTATAATA-A
1 AAAATTAAA-ATAAAATA-TA-AATATA
* * *
3016678 TAAATAAAAATAAAATATATGATATTA
1 AAAATTAAAATAAAATATA-AATA-TA
* * *
3016705 AAAATATATTTAA-GAAATGATATTATATA
1 AAAAT-TA--AAATAAAAT-ATA-AATATA
3016734 AAAATTAATAA-AAAATATAAATATATTA
1 AAAATTAA-AATAAAATAT-AA-ATA-TA
*
3016762 AAAATAAAAAATAAAATAT-AATAATA
1 AAAAT-TAAAATAAAATATAAAT-ATA
* *
3016788 ATAAATAAAAATAAAATATATGATATTA
1 A-AAATTAAAATAAAATATA-AATA-TA
** *
3016816 AAAA-TATATTTAAAAATGATATTATATA
1 AAAATTA-AAAT-AAAAT-ATA-AATATA
3016844 AAAATTAATAATAAAAAATATAAATATA
1 AAAATTAA-AAT--AAAATATAAATATA
3016872 TTAAACTTAT
Statistics
Matches: 328, Mismatches: 48, Indels: 111
0.67 0.10 0.23
Matches are distributed among these distances:
23 8 0.02
24 18 0.05
25 37 0.11
26 73 0.22
27 61 0.19
28 35 0.11
29 56 0.17
30 40 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAATTAAAATAAAATATAAATATA
Found at i:3016560 original size:10 final size:10
Alignment explanation
Indices: 3016514--3016800 Score: 59
Period size: 10 Copynumber: 28.4 Consensus size: 10
3016504 TAAAATATAT
3016514 AATATA-AAA
1 AATATATAAA
3016523 AATATATTAAA
1 AATATA-TAAA
*
3016534 GAA-ATGAAAAA
1 -AATAT-ATAAA
3016545 AATATAT-AA
1 AATATATAAA
*
3016554 AAT-TATAAT
1 AATATATAAA
*
3016563 AATAAATAAA
1 AATATATAAA
3016573 AATA-A-AATA
1 AATATATAA-A
* *
3016582 TATGACATTAAA
1 AAT-ATA-TAAA
**
3016594 AATATATTTA
1 AATATATAAA
*
3016604 AA-ATATAAT
1 AATATATAAA
*
3016613 ATTATATAAA
1 AATATATAAA
3016623 AAT-TAATAATA
1 AATAT-ATAA-A
3016634 TAA-ATATAAA
1 -AATATATAAA
*
3016644 TATAT-TAAA
1 AATATATAAA
*
3016653 AATAAAATATAA
1 AAT-ATATA-AA
*
3016665 AATATTATAAT
1 AATA-TATAAA
*
3016676 AATAAATAAA
1 AATATATAAA
3016686 AATA-A-AATA
1 AATATATAA-A
*
3016695 TATGATATTAAA
1 AAT-ATA-TAAA
*
3016707 AATATATTTAA
1 AATATA-TAAA
* * *
3016718 GA-A-ATGAT
1 AATATATAAA
*
3016726 ATTATATAAA
1 AATATATAAA
3016736 AAT-TAATAAA
1 AATAT-ATAAA
3016746 AA-ATATAAA
1 AATATATAAA
*
3016755 TATAT-TAAA
1 AATATATAAA
* *
3016764 AATAAAAAATAA
1 AAT-ATATA-AA
*
3016776 AATATAATAAT
1 AATAT-ATAAA
*
3016787 AATAAATAAA
1 AATATATAAA
3016797 AATA
1 AATA
3016801 AAATATATGA
Statistics
Matches: 199, Mismatches: 43, Indels: 71
0.64 0.14 0.23
Matches are distributed among these distances:
8 9 0.05
9 51 0.26
10 66 0.33
11 42 0.21
12 27 0.14
13 4 0.02
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
AATATATAAA
Found at i:3016596 original size:27 final size:26
Alignment explanation
Indices: 3016550--3016865 Score: 198
Period size: 27 Copynumber: 11.5 Consensus size: 26
3016540 AAAAAAATAT
3016550 ATAAAAT-TATA-A-TAATAAATAAAA
1 ATAAAATATATATATTAA-AAATAAAA
* * *
3016574 ATAAAATATATGACATTAAAAATATAT
1 ATAAAATATAT-ATATTAAAAATAAAA
*
3016601 TTAAAATATAATATTATATAAAAATTAATAA
1 ATAAAATAT-ATA-TAT-TAAAAA-TAA-AA
*
3016632 TATAAATATAAATATATTAAAAATAAAA
1 -ATAAA-ATATATATATTAAAAATAAAA
*
3016660 TATAAAATAT-TATAATAATAAATAAAA
1 -ATAAAATATATATATTAA-AAATAAAA
* *
3016687 ATAAAATATATGATATTAAAAATATAT
1 ATAAAATATAT-ATATTAAAAATAAAA
*
3016714 TTAAGAA-ATGATATTATATAAAAATTAATAA
1 ATAA-AATAT-ATA-TAT-TAAAAA-TAA-AA
*
3016745 A-AAATATAAATATATTAAAAATAAAAA
1 ATAAA-ATATATATATTAAAAAT-AAAA
*
3016772 ATAAAATATA-ATAATAATAAATAAAA
1 ATAAAATATATATATTAA-AAATAAAA
* *
3016798 ATAAAATATATGATATTAAAAATATAT
1 ATAAAATATAT-ATATTAAAAATAAAA
* *
3016825 TTAAAA-ATGATATTATATAAAAATTAATA
1 ATAAAATAT-ATA-TAT-TAAAAA-TAAAA
*
3016854 ATAAAAAATATA
1 ATAAAATATATA
3016866 AATATATTAA
Statistics
Matches: 232, Mismatches: 28, Indels: 59
0.73 0.09 0.18
Matches are distributed among these distances:
24 7 0.03
25 3 0.01
26 40 0.17
27 68 0.29
28 51 0.22
29 29 0.12
30 18 0.08
31 6 0.03
32 7 0.03
33 3 0.01
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAAAATATATATATTAAAAATAAAA
Found at i:3016599 original size:113 final size:106
Alignment explanation
Indices: 3016503--3016865 Score: 430
Period size: 113 Copynumber: 3.2 Consensus size: 106
3016493 ACAAATTAAA
3016503 ATAAAATATATAATATAAAAAATATATTAAAGAAATGAAAAAAATATATAAAATTATAATAATAA
1 ATAAAA-ATATAATATAAAAAATATATT-AA-AAAT--AAAAAATATA-AAAATTATAATAATAA
*
3016568 ATAAAAATAAAATATATGACATTAAAAATATATTTAAAATATAATATTAT
60 ATAAAAATAAAATATATGATATTAAAAATATATTTAAAA-AT-A-ATTAT
3016618 ATAAAAATTAATAATATAAATATAAATATATTAAAAAT--AAAATATAAAATATTATAATAATAA
1 ATAAAAA-T-ATAATAT-AA-A-AAATATATTAAAAATAAAAAATATAAAA-ATTATAATAATAA
3016681 ATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGATATTAT
60 ATAAAAATAAAATATATGATATTAAAAATATATTTAA-AAAT-A-ATTAT
* * *
3016731 ATAAAAAT-TAATAAAAAATATAAATATATTAAAAATAAAAAATA-AAATATAATAATAATAAAT
1 ATAAAAATATAAT--ATAA-A-AAATATATTAAAAATAAAAAATATAAAAATTATAATAATAAAT
3016794 AAAAATAAAATATATGATATTAAAAATATATTTAAAAATGATATTAT
62 AAAAATAAAATATATGATATTAAAAATATATTTAAAAAT-A-ATTAT
3016841 ATAAAAAT-TAATAATAAAAAATATA
1 ATAAAAATATAAT-ATAAAAAATATA
3016866 AATATATTAA
Statistics
Matches: 231, Mismatches: 6, Indels: 30
0.87 0.02 0.11
Matches are distributed among these distances:
107 7 0.03
108 1 0.00
109 4 0.02
110 28 0.12
111 69 0.30
112 8 0.03
113 79 0.34
114 3 0.01
115 7 0.03
116 7 0.03
117 6 0.03
118 3 0.01
119 9 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (106 bp):
ATAAAAATATAATATAAAAAATATATTAAAAATAAAAAATATAAAAATTATAATAATAAATAAAA
ATAAAATATATGATATTAAAAATATATTTAAAAATAATTAT
Found at i:3016641 original size:6 final size:6
Alignment explanation
Indices: 3016630--3016696 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
3016620 AAAAATTAAT
* *
3016630 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
3016680 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
3016697 TGATATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:3016812 original size:111 final size:109
Alignment explanation
Indices: 3016550--3016876 Score: 539
Period size: 113 Copynumber: 2.9 Consensus size: 109
3016540 AAAAAAATAT
* *
3016550 ATAAAAT-TATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAAATATAATA
1 ATAAAATATATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAA-ATGATA
*
3016614 TTATATAAAAATTAATAATATAAATATAAATATATTAAAAATAAAAT
65 TTATATAAAAATTAATAA-A-AAATATAAATATATTAAAAATAAAAA
3016661 ATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAAATGAT
1 ATAAAATA-TATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAA-AAATGAT
3016726 ATTATATAAAAATTAATAAAAAATATAAATATATTAAAAATAAAAA
64 ATTATATAAAAATTAATAAAAAATATAAATATATTAAAAATAAAAA
3016772 ATAAAATATAATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAAATGATA
1 ATAAAATAT-ATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAAATGATA
3016837 TTATATAAAAATTAATAATAAAAAATATAAATATATTAAA
65 TTATATAAAAA-T--TAATAAAAAATATAAATATATTAAA
3016877 CTTATATTTT
Statistics
Matches: 206, Mismatches: 3, Indels: 12
0.93 0.01 0.05
Matches are distributed among these distances:
110 20 0.10
111 88 0.43
112 1 0.00
113 95 0.46
114 2 0.01
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (109 bp):
ATAAAATATATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAAAATGATAT
TATATAAAAATTAATAAAAAATATAAATATATTAAAAATAAAAA
Found at i:3016830 original size:33 final size:31
Alignment explanation
Indices: 3016740--3016832 Score: 87
Period size: 33 Copynumber: 2.9 Consensus size: 31
3016730 TATAAAAATT
* *
3016740 AATAAAAAATATAAATATATTAAAAATAAAA
1 AATAAAATATAAAAATATATTAAAAATAAAA
* *
3016771 AATAAAATATAATAATAATAAATAAAAATAAAA
1 AATAAAATATAAAAAT-AT-ATTAAAAATAAAA
* **
3016804 TATATGATATTAAAAATATATTTAAAAAT
1 AATAAAATA-TAAAAATATA-TTAAAAAT
3016833 GATATTATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
31 13 0.27
32 3 0.06
33 27 0.55
34 6 0.12
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (31 bp):
AATAAAATATAAAAATATATTAAAAATAAAA
Found at i:3016859 original size:28 final size:27
Alignment explanation
Indices: 3016611--3016864 Score: 175
Period size: 28 Copynumber: 9.1 Consensus size: 27
3016601 TTAAAATATA
3016611 ATATTATATAAAAATTAATAATATAAAT
1 ATATTATATAAAAATTAATAATA-AAAT
*
3016639 ATAAATATATTAAAAA-TAA-AATATAAA-
1 AT-ATTATA-TAAAAATTAATAATA-AAAT
*
3016666 ATATTATAATAATAAA-TAAAAATAAAAT
1 ATATTAT-ATAA-AAATTAATAATAAAAT
* * *
3016694 ATATGATATTAAAAATATATTTAA-GAAAT
1 ATATTATA-TAAAAAT-TA-ATAATAAAAT
3016723 GATATTATATAAAAATTAATAA-AAAAT
1 -ATATTATATAAAAATTAATAATAAAAT
* * *
3016750 ATAAATATATTAAAAATAAAAAATAAAAT
1 AT-ATTATA-TAAAAATTAATAATAAAAT
* *
3016779 ATAATA-ATAATAAA-TAAAAATAAAAT
1 ATATTATATAA-AAATTAATAATAAAAT
* * *
3016805 ATATGATATTAAAAATATATTTA-AAAAT
1 ATATTATA-TAAAAAT-TAATAATAAAAT
*
3016833 GATATTATATAAAAATTAATAATAAAAA
1 -ATATTATATAAAAATTAATAATAAAAT
3016861 ATAT
1 ATAT
3016865 AAATATATTA
Statistics
Matches: 183, Mismatches: 22, Indels: 43
0.74 0.09 0.17
Matches are distributed among these distances:
26 27 0.15
27 44 0.24
28 59 0.32
29 38 0.21
30 15 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
ATATTATATAAAAATTAATAATAAAAT
Found at i:3017044 original size:15 final size:15
Alignment explanation
Indices: 3017021--3017079 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
3017011 TGTTATTTTC
* *
3017021 CTTGTAATCACATTG
1 CTTGCAATCACATTA
3017036 CTTGCAATCACATTA
1 CTTGCAATCACATTA
3017051 CTTGCAATCACATTA
1 CTTGCAATCACATTA
* *
3017066 CCTGTAATCACATT
1 CTTGCAATCACATT
3017080 GCATTGTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (15 bp):
CTTGCAATCACATTA
Found at i:3018136 original size:2 final size:2
Alignment explanation
Indices: 3018129--3018154 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3018119 GATCCTTTAA
3018129 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
3018155 TCTGTATTAT
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:3020460 original size:19 final size:19
Alignment explanation
Indices: 3020438--3020475 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3020428 AGTTTCACCC
3020438 CTTGTTGATCTTTTCTCCA
1 CTTGTTGATCTTTTCTCCA
3020457 CTTGTTGATCTTTTCTCCA
1 CTTGTTGATCTTTTCTCCA
3020476 AAAGGGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.11, T:0.53
Consensus pattern (19 bp):
CTTGTTGATCTTTTCTCCA
Found at i:3021333 original size:18 final size:18
Alignment explanation
Indices: 3021310--3021344 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3021300 CTCGCTGTTT
3021310 TCTCTG-CTGTGGCCCTGG
1 TCTCTGTCT-TGGCCCTGG
3021328 TCTCTGTCTTGGCCCTG
1 TCTCTGTCTTGGCCCTG
3021345 CATGGTACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.00, C:0.34, G:0.29, T:0.37
Consensus pattern (18 bp):
TCTCTGTCTTGGCCCTGG
Found at i:3024761 original size:21 final size:20
Alignment explanation
Indices: 3024729--3024767 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3024719 CGGTCCAATT
3024729 CAAAATTATTAAATTTAAAA
1 CAAAATTATTAAATTTAAAA
* *
3024749 CAAATATTTTTAATTTTAA
1 CAAA-ATTATTAAATTTAA
3024768 TAGCTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
CAAAATTATTAAATTTAAAA
Found at i:3026481 original size:2 final size:2
Alignment explanation
Indices: 3026476--3026511 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3026466 CTACAAAAAG
*
3026476 GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3026512 AGCATCCAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3040969 original size:39 final size:37
Alignment explanation
Indices: 3040915--3041013 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 37
3040905 TTTAGTTTAA
3040915 AAATA-TTTTAGTTAAATATTAATTTGTTTTAATTTTTT
1 AAATATTTTTAGTTAAATATTAATTTG--TTAATTTTTT
3040953 AAATATTTTTAGTTAAATATTGATATTTGTTAATTTTTT
1 AAATATTTTTAGTTAAATATT-A-ATTTGTTAATTTTTT
* *
3040992 --ATATTTTAAATTAAATATTAAT
1 AAATATTTTTAGTTAAATATTAAT
3041014 ATTTATCAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
35 2 0.04
36 1 0.02
37 17 0.30
38 5 0.09
39 25 0.45
40 1 0.02
41 5 0.09
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (37 bp):
AAATATTTTTAGTTAAATATTAATTTGTTAATTTTTT
Found at i:3042693 original size:30 final size:30
Alignment explanation
Indices: 3042624--3042694 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
3042614 TATGTTTAAT
* * ** *
3042624 TAAGTTTTTATATTTTTATTTTAAGTCGAA
1 TAAGTTTTTATACTCTTATTTTAAACCAAA
**
3042654 TAAACTTTTATACTCTTATTTTAAACCAAA
1 TAAGTTTTTATACTCTTATTTTAAACCAAA
3042684 TAAGTTTTTAT
1 TAAGTTTTTAT
3042695 CACAAATAGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (30 bp):
TAAGTTTTTATACTCTTATTTTAAACCAAA
Found at i:3043065 original size:2 final size:2
Alignment explanation
Indices: 3043054--3043106 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
3043044 ATATCAAAAT
* * * * * *
3043054 TA TA TG TA TA TA TA TA CA TA TA CA CA TA TA TA TA CA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3043096 TA TA TA TA TA T
1 TA TA TA TA TA T
3043107 GACTTAATTA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (2 bp):
TA
Found at i:3043082 original size:18 final size:18
Alignment explanation
Indices: 3043061--3043105 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3043051 AATTATATGT
*
3043061 ATATATATACATATACAC
1 ATATATATACAAATACAC
* *
3043079 ATATATATACAAATATAT
1 ATATATATACAAATACAC
3043097 ATATATATA
1 ATATATATA
3043106 TGACTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATATATACAAATACAC
Found at i:3043795 original size:6 final size:6
Alignment explanation
Indices: 3043784--3043815 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3043774 TAGTGCATTA
3043784 TTAATT TTAATT TTAATT TTAATT TTAATT TT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TT
3043816 CTCAATCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTAATT
Found at i:3044030 original size:21 final size:20
Alignment explanation
Indices: 3043998--3044036 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3043988 TTAAAATTTA
*
3043998 AAAATAAATAAAACTACCTT
1 AAAATAAATAAAAATACCTT
*
3044018 AAAATATATTAAAAATACC
1 AAAATA-AATAAAAATACC
3044037 AGTATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAAATAAAAATACCTT
Found at i:3051475 original size:33 final size:34
Alignment explanation
Indices: 3051393--3051525 Score: 112
Period size: 34 Copynumber: 3.9 Consensus size: 34
3051383 TAAAATCTGT
* * * *
3051393 CTTTTCA-AGGATCAAGCATAACCTTTACACATTGC
1 CTTTTCATGGGATCAAGCATAACC--CACACACTAC
*
3051428 CTTTTCGA-GAGGATCAAGTATAACCTCA-AC-CTAC
1 CTTTTC-ATG-GGATCAAGCATAACC-CACACACTAC
*
3051462 TTTTTCATGGGATCAAGCATAACCCACACACTAC
1 CTTTTCATGGGATCAAGCATAACCCACACACTAC
* * *
3051496 CTTTTCACGGAAACAAGCATAACCCACACA
1 CTTTTCATGGGATCAAGCATAACCCACACA
3051526 ATGCCATTTC
Statistics
Matches: 82, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
32 2 0.02
33 17 0.21
34 38 0.46
35 8 0.10
36 3 0.04
37 14 0.17
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.26
Consensus pattern (34 bp):
CTTTTCATGGGATCAAGCATAACCCACACACTAC
Found at i:3051580 original size:27 final size:28
Alignment explanation
Indices: 3051549--3051602 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
3051539 GAGCAAACAT
3051549 AACCTCAGTCTTCTCAA-GATCAAGTAG
1 AACCTCAGTCTTCTCAAGGATCAAGTAG
* * *
3051576 AACCTTAGTCTTTTTAAGGATCAAGTA
1 AACCTCAGTCTTCTCAAGGATCAAGTA
3051603 AAAGGTTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (28 bp):
AACCTCAGTCTTCTCAAGGATCAAGTAG
Found at i:3051611 original size:28 final size:28
Alignment explanation
Indices: 3051562--3051637 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 28
3051552 CTCAGTCTTC
* *
3051562 TCAA-GATCAAGTAGAACCTTAGTCTTT
1 TCAAGGATCAAGTAAAACCTTAGCCTTT
* **
3051589 TTAAGGATCAAGTAAAAGGTTAGCCTTT
1 TCAAGGATCAAGTAAAACCTTAGCCTTT
* * *
3051617 TCAAGTATCAGGCAAAACCTT
1 TCAAGGATCAAGTAAAACCTT
3051638 TACAACATTG
Statistics
Matches: 37, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
27 3 0.08
28 34 0.92
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (28 bp):
TCAAGGATCAAGTAAAACCTTAGCCTTT
Found at i:3052235 original size:21 final size:21
Alignment explanation
Indices: 3052211--3052263 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
3052201 ATGAAGTTAG
3052211 GTATCAAGACTTTGAAACCAA
1 GTATCAAGACTTTGAAACCAA
*
3052232 GTATCAAGATTTTGAAACCAA
1 GTATCAAGACTTTGAAACCAA
*
3052253 GTGTCAAGACT
1 GTATCAAGACT
3052264 CTATGAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (21 bp):
GTATCAAGACTTTGAAACCAA
Found at i:3052563 original size:21 final size:21
Alignment explanation
Indices: 3052537--3052581 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3052527 TGGGAAGTTG
3052537 TCTCGATACATCCAAT-CATGC
1 TCTCGATAC-TCCAATACATGC
*
3052558 TCTCGATACTTCAATACATGC
1 TCTCGATACTCCAATACATGC
3052579 TCT
1 TCT
3052582 TTGGAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (21 bp):
TCTCGATACTCCAATACATGC
Found at i:3054053 original size:18 final size:17
Alignment explanation
Indices: 3054021--3054071 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
3054011 ACATATGAGC
*
3054021 AAATAGAATAAAAATAAAT
1 AAATAGAATATAAAT--AT
3054040 AAATA-AATATAAATAT
1 AAATAGAATATAAATAT
*
3054056 AAATAATAATATAAAT
1 AAAT-AGAATATAAAT
3054072 TGAAAGAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 6 0.21
17 1 0.03
18 17 0.59
19 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAATAGAATATAAATAT
Found at i:3054059 original size:16 final size:18
Alignment explanation
Indices: 3054028--3054071 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
3054018 AGCAAATAGA
*
3054028 ATAAAAATAAATAAATAAAT
1 ATAAATATAAAT-AAT-AAT
3054048 ATAAATATAAATAATAAT
1 ATAAATATAAATAATAAT
3054066 ATAAAT
1 ATAAAT
3054072 TGAAAGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 3 0.13
20 11 0.48
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAATATAAATAATAAT
Found at i:3054773 original size:18 final size:18
Alignment explanation
Indices: 3054726--3054804 Score: 54
Period size: 18 Copynumber: 4.4 Consensus size: 18
3054716 TCAAGCATTC
* *
3054726 ATATATGTTCAAATATTT
1 ATATTTGTTCAAATAGTT
* *
3054744 CTGTTT-TTCAAATAGTT
1 ATATTTGTTCAAATAGTT
* *
3054761 ATATTTGTTCAAACAATT
1 ATATTTGTTCAAATAGTT
* **
3054779 ATATCTACTCAAA-AGGTT
1 ATATTTGTTCAAATA-GTT
3054797 ATATTTGT
1 ATATTTGT
3054805 GCAAGCAAAC
Statistics
Matches: 44, Mismatches: 15, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
17 15 0.34
18 29 0.66
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (18 bp):
ATATTTGTTCAAATAGTT
Found at i:3062595 original size:22 final size:22
Alignment explanation
Indices: 3062566--3062608 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3062556 TTTAAGTTTT
*
3062566 ATTGTTT-GAAAAATTAAAAAG
1 ATTGTTTGGAAAAATAAAAAAG
3062587 ATTGTTTTGGAAAAATAAAAAA
1 ATTG-TTTGGAAAAATAAAAAA
3062609 CGAAAACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (22 bp):
ATTGTTTGGAAAAATAAAAAAG
Found at i:3062658 original size:2 final size:2
Alignment explanation
Indices: 3062653--3062682 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3062643 AAAGAATAGA
3062653 AT AT 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 AT AT
3062683 TCTTCCAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3063806 original size:14 final size:14
Alignment explanation
Indices: 3063787--3063819 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3063777 TAACGGTTAG
3063787 TTTTATTTTT-TTAT
1 TTTTATTTTTATT-T
3063801 TTTTATTTTTATTT
1 TTTTATTTTTATTT
3063815 TTTTA
1 TTTTA
3063820 GGGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:3069719 original size:25 final size:26
Alignment explanation
Indices: 3069657--3069719 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
3069647 CATACAAATG
3069657 ATATTTTTATTATAAAACAACAAACTA
1 ATATTTTTATTATAAAACAACAAAC-A
* *
3069684 ATATTTTTATTATAAAATAATAAA-A
1 ATATTTTTATTATAAAACAACAAACA
*
3069709 ATATTTATATT
1 ATATTTTTATT
3069720 GATTTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 11 0.33
27 22 0.67
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (26 bp):
ATATTTTTATTATAAAACAACAAACA
Found at i:3070139 original size:5 final size:5
Alignment explanation
Indices: 3070123--3070153 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
3070113 GCACATGCCT
3070123 CCATC ACCATC CCATC CCATC CCATC CCATC
1 CCATC -CCATC CCATC CCATC CCATC CCATC
3070154 ATCCCATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.23, C:0.58, G:0.00, T:0.19
Consensus pattern (5 bp):
CCATC
Found at i:3072382 original size:3 final size:3
Alignment explanation
Indices: 3072376--3072426 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
3072366 GCATCAACAA
* * *
3072376 CAG CAG CAG CAG CAA CAG CAA CAG CAA CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
3072424 CAG
1 CAG
3072427 TTCCTCCACA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.39, C:0.33, G:0.27, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:3079076 original size:15 final size:13
Alignment explanation
Indices: 3079037--3079078 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
3079027 AACAGCTACA
3079037 ACAGCAACAGCA-
1 ACAGCAACAGCAG
*
3079049 ACAGCATCAGCAG
1 ACAGCAACAGCAG
3079062 ACACCGCAACAGCAG
1 ACA--GCAACAGCAG
3079077 AC
1 AC
3079079 GAAGGCTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.44
13 3 0.12
15 11 0.44
ACGTcount: A:0.43, C:0.36, G:0.19, T:0.02
Consensus pattern (13 bp):
ACAGCAACAGCAG
Found at i:3080875 original size:19 final size:19
Alignment explanation
Indices: 3080848--3080886 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3080838 AGATGACATG
*
3080848 CGTGGCACCAACATGATAA
1 CGTGCCACCAACATGATAA
*
3080867 CGTGCCACCAGCATGATAA
1 CGTGCCACCAACATGATAA
3080886 C
1 C
3080887 TAAATTGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.21, T:0.15
Consensus pattern (19 bp):
CGTGCCACCAACATGATAA
Found at i:3082181 original size:30 final size:30
Alignment explanation
Indices: 3082120--3082181 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
3082110 AATCAAAATT
*
3082120 TTGTACTTTTATTTTAAGCTAAATAAACTC
1 TTGTACTTTTATTTTAAGCTAAACAAACTC
* * *
3082150 TTGTATTTTTATTTTGAG-TGAAACAAGCTC
1 TTGTACTTTTATTTTAAGCT-AAACAAACTC
3082180 TT
1 TT
3082182 ATAACTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.48
Consensus pattern (30 bp):
TTGTACTTTTATTTTAAGCTAAACAAACTC
Found at i:3092735 original size:15 final size:15
Alignment explanation
Indices: 3092693--3092735 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
3092683 TATTTTAAAT
3092693 TAAATATTAATATTCA
1 TAAAT-TTAATATTCA
*
3092709 TCAAACTT-ATATTCA
1 T-AAATTTAATATTCA
3092724 TAAATTTAATAT
1 TAAATTTAATAT
3092736 AAAACTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 5 0.22
15 12 0.52
16 3 0.13
17 3 0.13
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTTAATATTCA
Found at i:3094764 original size:26 final size:26
Alignment explanation
Indices: 3094735--3094789 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3094725 ATTTAAAATC
* *
3094735 AATAATTATAAAAAT-AATTATAATAA
1 AATAATAAT-AAAATCAAATATAATAA
*
3094761 AATAATAATAACATCAAATATAATAA
1 AATAATAATAAAATCAAATATAATAA
3094787 AAT
1 AAT
3094790 TGAACATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
AATAATAATAAAATCAAATATAATAA
Found at i:3094780 original size:21 final size:21
Alignment explanation
Indices: 3094756--3094802 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
3094746 AAATAATTAT
3094756 AATAAAATAATAA-T-AACATCA
1 AATAAAATAA-AATTGAACAT-A
*
3094777 AATATAATAAAATTGAACATA
1 AATAAAATAAAATTGAACATA
3094798 AATAA
1 AATAA
3094803 CATACATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 15 0.68
22 5 0.23
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (21 bp):
AATAAAATAAAATTGAACATA
Found at i:3095869 original size:15 final size:14
Alignment explanation
Indices: 3095845--3095878 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3095835 ATACTTGAAA
3095845 AGATAAAAAAGAAC
1 AGATAAAAAAGAAC
*
3095859 AGATGAAAAAATAAC
1 AGAT-AAAAAAGAAC
3095874 AGATA
1 AGATA
3095879 CTTAACAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.12
Consensus pattern (14 bp):
AGATAAAAAAGAAC
Found at i:3123888 original size:23 final size:23
Alignment explanation
Indices: 3123846--3123891 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3123836 TAGGTTAATA
*
3123846 TGTGAAATTGTGGTTGTTGTTTG
1 TGTGAAATTGTGGTTATTGTTTG
**
3123869 TGTGAAATTGTTTTTATTGTTTG
1 TGTGAAATTGTGGTTATTGTTTG
3123892 AATGTTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.28, T:0.57
Consensus pattern (23 bp):
TGTGAAATTGTGGTTATTGTTTG
Found at i:3124481 original size:37 final size:36
Alignment explanation
Indices: 3124410--3124481 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
3124400 TCAAATAAAG
* *
3124410 TTCAATATAATACTTTTCATGGATCAAGCACAACCT
1 TTCAATATAATACCTTTCATAGATCAAGCACAACCT
* * *
3124446 TTCAATATAATGCCTTTCTATAGTTCAAGTACAACC
1 TTCAATATAATACCTTTC-ATAGATCAAGCACAACC
3124482 ATTCTACCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 16 0.53
37 14 0.47
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (36 bp):
TTCAATATAATACCTTTCATAGATCAAGCACAACCT
Found at i:3125704 original size:27 final size:27
Alignment explanation
Indices: 3125670--3125724 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
3125660 ATAATTTATT
* *
3125670 TAATTAAGTAATGTA-ATGTGTTATAAG
1 TAATTAAGAAAT-TACATGTGCTATAAG
3125697 TAATTAAGAAATTACATGTGCTATAAG
1 TAATTAAGAAATTACATGTGCTATAAG
3125724 T
1 T
3125725 TGTAATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (27 bp):
TAATTAAGAAATTACATGTGCTATAAG
Found at i:3138875 original size:2 final size:2
Alignment explanation
Indices: 3138868--3138896 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3138858 AAAAGGCAAA
3138868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3138897 AAAAGGAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3142908 original size:19 final size:19
Alignment explanation
Indices: 3142871--3142909 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3142861 TTCTTTTCTC
* **
3142871 TTTCTTTTTTTTTTTCATT
1 TTTCTTTTTGTTTACCATT
3142890 TTTCTTTTTGTTTACCATT
1 TTTCTTTTTGTTTACCATT
3142909 T
1 T
3142910 CAGTTTACAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTCTTTTTGTTTACCATT
Found at i:3143709 original size:2 final size:2
Alignment explanation
Indices: 3143702--3143726 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3143692 ACCTCTGAGA
3143702 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3143727 ACACACAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3149183 original size:39 final size:39
Alignment explanation
Indices: 3149140--3149218 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3149130 TTTTCCCACG
3149140 ATTTGGTGTCATCATTAACATATACATAACAGAGAAGGT
1 ATTTGGTGTCATCATTAACATATACATAACAGAGAAGGT
3149179 ATTTGGTGTCATCATTAACATATACATAACAGAGAAGGT
1 ATTTGGTGTCATCATTAACATATACATAACAGAGAAGGT
3149218 A
1 A
3149219 GATCACCTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (39 bp):
ATTTGGTGTCATCATTAACATATACATAACAGAGAAGGT
Found at i:3155731 original size:9 final size:9
Alignment explanation
Indices: 3155717--3155809 Score: 56
Period size: 9 Copynumber: 10.7 Consensus size: 9
3155707 GAATTAATCT
3155717 AAAAATATA
1 AAAAATATA
3155726 AAAAAT-TA
1 AAAAATATA
3155734 AAAAA-ATTA
1 AAAAATA-TA
*
3155743 AAAAAAATTA
1 AAAAATA-TA
3155753 AAAAAT-T-
1 AAAAATATA
* * *
3155760 CAAAA-GTC
1 AAAAATATA
3155768 AAAAATGA-A
1 AAAAAT-ATA
3155777 AAAAATA-A
1 AAAAATATA
*
3155785 AAAAATAAA
1 AAAAATATA
3155794 AAAAATTATA
1 AAAAA-TATA
3155804 AAAAAT
1 AAAAAT
3155810 GGACAAACCA
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
7 5 0.07
8 21 0.30
9 26 0.38
10 17 0.25
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (9 bp):
AAAAATATA
Found at i:3155797 original size:8 final size:8
Alignment explanation
Indices: 3155716--3155797 Score: 67
Period size: 8 Copynumber: 10.0 Consensus size: 8
3155706 AGAATTAATC
*
3155716 TAAAAATA
1 TAAAAAAA
*
3155724 TAAAAAAT
1 TAAAAAAA
3155732 TAAAAAAA
1 TAAAAAAA
3155740 TTAAAAAAAA
1 -T-AAAAAAA
*
3155750 TTAAAAAA
1 TAAAAAAA
** *
3155758 TTCAAAAG
1 TAAAAAAA
*
3155766 T-CAAAAA
1 TAAAAAAA
3155773 TGAAAAAAA
1 T-AAAAAAA
3155782 TAAAAAAA
1 TAAAAAAA
3155790 TAAAAAAA
1 TAAAAAAA
3155798 ATTATAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
7 6 0.10
8 41 0.66
9 8 0.13
10 7 0.11
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (8 bp):
TAAAAAAA
Found at i:3156649 original size:25 final size:25
Alignment explanation
Indices: 3156619--3156677 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
3156609 AATGGCTAAT
*
3156619 AATATTAATCTCCATGTAATAAATA
1 AATATTAATCTCCATATAATAAATA
**
3156644 AATATTAATCTTTATATAATAAATA
1 AATATTAATCTCCATATAATAAATA
*
3156669 AACATTAAT
1 AATATTAAT
3156678 TTCAAAAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (25 bp):
AATATTAATCTCCATATAATAAATA
Found at i:3157962 original size:23 final size:23
Alignment explanation
Indices: 3157936--3157984 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
3157926 TTCGACAATA
*
3157936 TTAAATTTTTTTCTTGAAGTGTC
1 TTAAATTTTTTTCTTGAAATGTC
3157959 TTAAATTTTTTTCTTGAAATGTC
1 TTAAATTTTTTTCTTGAAATGTC
3157982 TTA
1 TTA
3157985 TTGCGACATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.57
Consensus pattern (23 bp):
TTAAATTTTTTTCTTGAAATGTC
Found at i:3159379 original size:2 final size:2
Alignment explanation
Indices: 3159374--3159406 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3159364 TATATATATA
3159374 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3159407 TGATCGGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3165409 original size:23 final size:23
Alignment explanation
Indices: 3165372--3165423 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3165362 ATTGCCAGAT
* *
3165372 TAGTTT-TTAGGTATTATGTGAC
1 TAGTTTGTTAGATATTACGTGAC
* *
3165394 TAGTTTGTTAGATATTGCGTGGC
1 TAGTTTGTTAGATATTACGTGAC
3165417 TAGTTTG
1 TAGTTTG
3165424 GTAGGCATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.19, C:0.06, G:0.27, T:0.48
Consensus pattern (23 bp):
TAGTTTGTTAGATATTACGTGAC
Found at i:3167321 original size:15 final size:15
Alignment explanation
Indices: 3167298--3167334 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3167288 TACCTAATTA
*
3167298 TGTCGTGTGATTGGT
1 TGTCTTGTGATTGGT
3167313 TGTCTTGTGATTGGT
1 TGTCTTGTGATTGGT
3167328 TGTCTTG
1 TGTCTTG
3167335 AAAATGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.08, G:0.35, T:0.51
Consensus pattern (15 bp):
TGTCTTGTGATTGGT
Found at i:3171613 original size:38 final size:38
Alignment explanation
Indices: 3171564--3171649 Score: 129
Period size: 38 Copynumber: 2.3 Consensus size: 38
3171554 AAACACCAGC
* *
3171564 CACACAGTGCCTTAGTTACACAATGACTATGAA-CTAGG
1 CACACAATGCCTTAGTTACACAATGACTATCAATC-AGG
*
3171602 CACGCAATGCCTTAGTTACACAATGACTATCAATCAGG
1 CACACAATGCCTTAGTTACACAATGACTATCAATCAGG
3171640 CACACAATGC
1 CACACAATGC
3171650 TTTATCGGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 42 0.98
39 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (38 bp):
CACACAATGCCTTAGTTACACAATGACTATCAATCAGG
Found at i:3174438 original size:23 final size:23
Alignment explanation
Indices: 3174412--3174457 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3174402 TCGCACAAGG
*
3174412 CCTATCAACAAGTCACGCAATGC
1 CCTATCAACAAGTCACACAATGC
* **
3174435 CCTATTAACTTGTCACACAATGC
1 CCTATCAACAAGTCACACAATGC
3174458 ACTTTGATCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.24
Consensus pattern (23 bp):
CCTATCAACAAGTCACACAATGC
Found at i:3174672 original size:296 final size:296
Alignment explanation
Indices: 3174126--3174692 Score: 646
Period size: 296 Copynumber: 1.9 Consensus size: 296
3174116 ACAATGCCTT
* ** *
3174126 AGTCACGTAATGCCCTATCAACTTGTCATGCAATGCACTTTGATCGTGGTCAATTTCGATTGGCA
1 AGTCACGCAATGCCCTATCAACTTGTCACACAATGCACTTTGATCGTGGTCAATTTCGATTGGAA
* * ** *
3174191 AACTATTGATAGATTCTACAAATATATCTATAGTTTTCGAGCCTCTTTAATTTGTAAAGTTCTCG
66 AACTATAGATAGATTCTACAAATATATCAATAGTTTTCGAGCCTCTTTAATTTACAAAGTTCTCA
* * *
3174256 AGTGGTCATTTATTGATAGTTAGCGTAATCTATTGATAGATGTTCATCTAAATTACCTTCCATGC
131 AGTGGTCATTTATTAATAGTTAGAGTAATCTATTGATAGATGTTCATCCAAATTACCTTCCATGC
* * * ** * * *
3174321 TCTGAACAAACCATTCACGCAATGCCTATGGACTAGGCATGAGATGCCCTATACCCAAGTTAGGC
196 TCTGAACAAACCACTCACACAATGCCCATCAACTAGGCATCAGATGCCCTATACCCAAGTCACGC
3174386 AATGAATAAAAACCAGTCGCACAAGGCCTATCAACA
261 AATGAATAAAAACCAGTCGCACAAGGCCTATCAACA
* *
3174422 AGTCACGCAATGCCCTATTAACTTGTCACACAATGCACTTTGATC-TAAGGT-AATTTC-ATTTG
1 AGTCACGCAATGCCCTATCAACTTGTCACACAATGCACTTTGATCGT--GGTCAATTTCGATTGG
** * * * **
3174484 AAAATCTATAGATAGATTCTA-AGGGTCTATCAATAGTTTCTTG-GCTTCTTTGCTTTACAAAGT
64 AAAA-CTATAGATAGATTCTACA-AATATATCAATAGTTT-TCGAGCCTCTTTAATTTACAAAGT
* *
3174547 TCTCAAGTGGTCATTTATTAATAGTTAGTAG-AATTTATTGATAGATTTTCATCCAAATTACCTT
126 TCTCAAGTGGTCATTTATTAATAGTTAG-AGTAATCTATTGATAGATGTTCATCCAAATTACCTT
** *** * * * *
3174611 CCATGCT-TGATGTAAAGTGCTCACATAATGCCCATCAAGTAGGCA-CATGATGCCTTATACCCT
190 CCATGCTCTGA-ACAAACCACTCACACAATGCCCATCAACTAGGCATCA-GATGCCCTATACCCA
3174674 AGTCACGCAATGAATAAAA
253 AGTCACGCAATGAATAAAA
3174693 TAAGTCACGT
Statistics
Matches: 223, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
295 13 0.06
296 204 0.91
297 6 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (296 bp):
AGTCACGCAATGCCCTATCAACTTGTCACACAATGCACTTTGATCGTGGTCAATTTCGATTGGAA
AACTATAGATAGATTCTACAAATATATCAATAGTTTTCGAGCCTCTTTAATTTACAAAGTTCTCA
AGTGGTCATTTATTAATAGTTAGAGTAATCTATTGATAGATGTTCATCCAAATTACCTTCCATGC
TCTGAACAAACCACTCACACAATGCCCATCAACTAGGCATCAGATGCCCTATACCCAAGTCACGC
AATGAATAAAAACCAGTCGCACAAGGCCTATCAACA
Found at i:3174981 original size:22 final size:23
Alignment explanation
Indices: 3174956--3175012 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
3174946 GCAAAGCTTA
3174956 AGTCACGCAATGCTCAAT-AACT
1 AGTCACGCAATGCTCAATCAACT
**
3174978 AGTCACGCAATGCTTTATCAACT
1 AGTCACGCAATGCTCAATCAACT
*
3175001 AGTCATGCAATG
1 AGTCACGCAATG
3175013 ACCTAAAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (23 bp):
AGTCACGCAATGCTCAATCAACT
Found at i:3175625 original size:13 final size:13
Alignment explanation
Indices: 3175609--3175634 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3175599 TTTTTTCAGG
3175609 CCTTTAATGGTGT
1 CCTTTAATGGTGT
3175622 CCTTTAATGGTGT
1 CCTTTAATGGTGT
3175635 TTGTCTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
CCTTTAATGGTGT
Found at i:3177056 original size:33 final size:33
Alignment explanation
Indices: 3176994--3177057 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
3176984 CCTTTAGTCC
* *
3176994 TTGCATCTCTCGTTAAATTTCCAATTGCATTGA
1 TTGCATCTCTCGTTAAATCTCCAACTGCATTGA
* *
3177027 TTGCATCTCTCGTTGAATCTCCAGCTGCATT
1 TTGCATCTCTCGTTAAATCTCCAACTGCATT
3177058 CACTATATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (33 bp):
TTGCATCTCTCGTTAAATCTCCAACTGCATTGA
Found at i:3180962 original size:2 final size:2
Alignment explanation
Indices: 3180955--3180981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3180945 TAATTGAGTC
3180955 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3180982 ATTTTGATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3181172 original size:2 final size:2
Alignment explanation
Indices: 3181167--3181191 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3181157 ATAAATTTTA
3181167 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3181192 GAGCAGATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3185100 original size:2 final size:2
Alignment explanation
Indices: 3185093--3185119 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3185083 CCTTCTTCTT
3185093 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3185120 TTCAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3193560 original size:80 final size:80
Alignment explanation
Indices: 3193325--3193557 Score: 351
Period size: 80 Copynumber: 2.9 Consensus size: 80
3193315 TTATCTCCCA
3193325 AAATAATTTAGAGATAATATTCATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTA
1 AAATAATTTAGAGATAATATTCATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTA
*
3193390 TCTCTAAATAAATCT
66 TCTCTAAATAAATCC
* *
3193405 AAATTATTTAGAGATAATATTTATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTA
1 AAATAATTTAGAGATAATATTCATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTA
3193470 TCTCTAAATAAATCC
66 TCTCTAAATAAATCC
* * * * ** *
3193485 AAATAATTTGGAGATAATCTTCATATTTTTGACCAATTAAA-ATTTAGTTATTGGTCATTTAAAT
1 AAATAATTTAGAGATAATATTCATA-TTTTGACCAATCAAATA-TTAGCTATTGGTCATCCAATT
3193549 TATCTCTAA
64 TATCTCTAA
3193558 TAATTATATT
Statistics
Matches: 139, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
80 99 0.71
81 40 0.29
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (80 bp):
AAATAATTTAGAGATAATATTCATATTTTGACCAATCAAATATTAGCTATTGGTCATCCAATTTA
TCTCTAAATAAATCC
Found at i:3193908 original size:23 final size:23
Alignment explanation
Indices: 3193879--3194043 Score: 267
Period size: 23 Copynumber: 7.2 Consensus size: 23
3193869 GGTGAAGATC
3193879 AAGCAACGGCGAAGTTCGTGATA
1 AAGCAACGGCGAAGTTCGTGATA
* *
3193902 AATCAACGGCGAAGTTCGTGATC
1 AAGCAACGGCGAAGTTCGTGATA
*
3193925 AAGCAACGGCGAAGTTCGTGATC
1 AAGCAACGGCGAAGTTCGTGATA
3193948 AAGCAACGGCGAAGTTCGTGATA
1 AAGCAACGGCGAAGTTCGTGATA
3193971 AAGCAACGGCGAAGTTCGTGATA
1 AAGCAACGGCGAAGTTCGTGATA
* *
3193994 AAGCAACGGCGAAGTTCGTAATC
1 AAGCAACGGCGAAGTTCGTGATA
* *
3194017 AAGCAACAGCGAAGTTCGTGATC
1 AAGCAACGGCGAAGTTCGTGATA
3194040 AAGC
1 AAGC
3194044 GACGACGTCA
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 134 1.00
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (23 bp):
AAGCAACGGCGAAGTTCGTGATA
Found at i:3195705 original size:72 final size:72
Alignment explanation
Indices: 3195525--3195689 Score: 330
Period size: 72 Copynumber: 2.3 Consensus size: 72
3195515 TGAATTTCCA
3195525 TTAAAATGTATCGATACATTTGTATATGTATTGATACATTTCAACTTTTCTGCAAGGGTTTTGAC
1 TTAAAATGTATCGATACATTTGTATATGTATTGATACATTTCAACTTTTCTGCAAGGGTTTTGAC
3195590 ATTTTGC
66 ATTTTGC
3195597 TTAAAATGTATCGATACATTTGTATATGTATTGATACATTTCAACTTTTCTGCAAGGGTTTTGAC
1 TTAAAATGTATCGATACATTTGTATATGTATTGATACATTTCAACTTTTCTGCAAGGGTTTTGAC
3195662 ATTTTGC
66 ATTTTGC
3195669 TTAAAATGTATCGATACATTT
1 TTAAAATGTATCGATACATTT
3195690 ATTCATGTAT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 93 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (72 bp):
TTAAAATGTATCGATACATTTGTATATGTATTGATACATTTCAACTTTTCTGCAAGGGTTTTGAC
ATTTTGC
Found at i:3201617 original size:17 final size:17
Alignment explanation
Indices: 3201583--3201641 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
3201573 TAGTAATGCT
*
3201583 TATGTATAAATTAA-ATA
1 TATGTATATA-TAATATA
3201600 TATGTATATATAATATA
1 TATGTATATATAATATA
*
3201617 TTACTTTAT-TATAGATATA
1 -TA-TGTATATATA-ATATA
3201636 TATGTA
1 TATGTA
3201642 ATTAATGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.09
17 15 0.43
18 8 0.23
19 9 0.26
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
TATGTATATATAATATA
Found at i:3201804 original size:216 final size:215
Alignment explanation
Indices: 3201415--3202050 Score: 900
Period size: 216 Copynumber: 2.9 Consensus size: 215
3201405 CCATAATTAT
* * *
3201415 ATATATATGAAATTAATGATATAAATTATATGTTATAATGTTTTAGATCAAAGGTTGCATAAATA
1 ATATATATGAAATTAATGATACAAATTATATGTTATAATGTTTTATATCAAA-GTTGTATAAATA
*
3201480 ATAACTAATTATAAACAATTTGTTATAAAATCTAAGGTGATAGCTAATAAAT-TTATCAAGTGTA
65 ATAACTAATTATAAACAATTTGTTATAAAATCTAAGGTGATAACTAAT-AATGTTATCAAGTGTA
* * * * *
3201544 ATGATATAAATAAAGTTTATTGTAAGCTGTAGTAATGCTTATGTATAAATTAAATATATGTATAT
129 ATCATATAAATAAAGTTTATTATAAACTATAGTAATGTTTATGTATAAATTAAATATATGTATAT
3201609 ATAATATATTACTTTATTATAG
194 ATAATATATTACTTTATTATAG
* * * * *
3201631 ATATATATGTAATTAATGATACAAATTATAGGCTAAAATGTTTTATATCAAAGTCTATATAAATA
1 ATATATATGAAATTAATGATACAAATTATATGTTATAATGTTTTATATCAAAGT-TGTATAAATA
* ** * *
3201696 ATAACTAATTATAAATAACATGTCATAAAATCTAAGGTGATAACTAATAATGTTATTAAGTGTAA
65 ATAACTAATTATAAACAATTTGTTATAAAATCTAAGGTGATAACTAATAATGTTATCAAGTGTAA
* * * *
3201761 TCATATAAATAAAGTCTATTATAAACTATAGCAATGTTTATGTATAAATTAAATATATGGATACA
130 TCATATAAATAAAGTTTATTATAAACTATAGTAATGTTTATGTATAAATTAAATATATGTATATA
* * *
3201826 TAATATATGACTTTATTTTAT
195 TAATATATTACTTTATTATAG
* *
3201847 ATATATATGAAATTAAT-A-ACATAACTTAGATGTTATAATGTTTTATATCAAAGTTTGTATCAA
1 ATATATATGAAATTAATGATACA-AA-TTATATGTTATAATGTTTTATATCAAAG-TTGTATAAA
* * *
3201910 TAATAATTAATTATAAACAATTTGTTATAAAATCTAAGATGATAACTAATAAAGTTATCAAGTGT
63 TAATAACTAATTATAAACAATTTGTTATAAAATCTAAGGTGATAACTAATAATGTTATCAAGTGT
* *
3201975 AATCATATAAATAAAGTTTATTATAAATTATAGTAATGTTTATGTATAAATTAAATATATGTATT
128 AATCATATAAATAAAGTTTATTATAAACTATAGTAATGTTTATGTATAAATTAAATATATGTATA
3202040 TATAATATATT
193 TATAATATATT
3202051 TATACAATTA
Statistics
Matches: 367, Mismatches: 48, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
214 3 0.01
215 8 0.02
216 355 0.97
217 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (215 bp):
ATATATATGAAATTAATGATACAAATTATATGTTATAATGTTTTATATCAAAGTTGTATAAATAA
TAACTAATTATAAACAATTTGTTATAAAATCTAAGGTGATAACTAATAATGTTATCAAGTGTAAT
CATATAAATAAAGTTTATTATAAACTATAGTAATGTTTATGTATAAATTAAATATATGTATATAT
AATATATTACTTTATTATAG
Found at i:3202036 original size:23 final size:21
Alignment explanation
Indices: 3201982--3202044 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
3201972 TGTAATCATA
*
3201982 TAAATAAAGTTTATTATAAAT
1 TAAATAATGTTTATTATAAAT
*
3202003 TATAGTAATGTTTATGTATAAAT
1 TA-AATAATGTTTAT-TATAAAT
*
3202026 TAAATATATGTAT-TTATAA
1 TAAATA-ATGTTTATTATAA
3202045 TATATTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 7 0.20
22 14 0.40
23 14 0.40
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (21 bp):
TAAATAATGTTTATTATAAAT
Found at i:3211157 original size:12 final size:14
Alignment explanation
Indices: 3211134--3211170 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
3211124 CATATGAGCA
*
3211134 AATAGTATAAAAAT
1 AATAATATAAAAAT
3211148 -ATAA-ATAAAAAT
1 AATAATATAAAAAT
3211160 AATAATATAAA
1 AATAATATAAA
3211171 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 8 0.40
13 7 0.35
14 5 0.25
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
AATAATATAAAAAT
Found at i:3211787 original size:46 final size:46
Alignment explanation
Indices: 3211732--3211821 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
3211722 CCCAACAAGT
*
3211732 AGAGTCACAAAATCACACATAAAAAAAAAACTTCTAGTGAGTAGTA
1 AGAGCCACAAAATCACACATAAAAAAAAAACTTCTAGTGAGTAGTA
* *
3211778 AGAGCCACAAAATCACACATCAAAAAGAAACTTCTAGTGAGTAG
1 AGAGCCACAAAATCACACATAAAAAAAAAACTTCTAGTGAGTAG
3211822 AAACTTCTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (46 bp):
AGAGCCACAAAATCACACATAAAAAAAAAACTTCTAGTGAGTAGTA
Found at i:3211825 original size:17 final size:17
Alignment explanation
Indices: 3211803--3211838 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3211793 CACATCAAAA
3211803 AGAAACTTCTAGTGAGT
1 AGAAACTTCTAGTGAGT
3211820 AGAAACTTCTAGTGAGT
1 AGAAACTTCTAGTGAGT
3211837 AG
1 AG
3211839 TAAGGGTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (17 bp):
AGAAACTTCTAGTGAGT
Found at i:3212281 original size:2 final size:2
Alignment explanation
Indices: 3212276--3212304 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3212266 TGTATGTAGA
3212276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3212305 ACATATGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3218892 original size:21 final size:21
Alignment explanation
Indices: 3218866--3218938 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
3218856 TTTGTATGTA
* * *
3218866 GCGTGTAACAACTTAACCATG
1 GCGTGTAACAGCCTATCCATG
3218887 GCGTGTAACAGCCTATCCATG
1 GCGTGTAACAGCCTATCCATG
*
3218908 ACGTGTAACAGCCTATCCATG
1 GCGTGTAACAGCCTATCCATG
3218929 GCGTGTAACA
1 GCGTGTAACA
3218939 TATTTTTGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (21 bp):
GCGTGTAACAGCCTATCCATG
Found at i:3226196 original size:26 final size:27
Alignment explanation
Indices: 3226167--3226224 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
3226157 CTTATGTTTG
3226167 TTATTAT-TATTATTATCTTTTTT-ATT
1 TTATTATCTATT-TTATCTTTTTTCATT
*
3226193 TTATT-TCTATTTTATGTTTTTTCATT
1 TTATTATCTATTTTATCTTTTTTCATT
3226219 TTATTA
1 TTATTA
3226225 ATATCTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (27 bp):
TTATTATCTATTTTATCTTTTTTCATT
Found at i:3232260 original size:331 final size:334
Alignment explanation
Indices: 3231716--3232377 Score: 904
Period size: 332 Copynumber: 2.0 Consensus size: 334
3231706 TTTATAAGGA
* * * *
3231716 ATATATACTTTTAGTATATATACTTTTAACATAAACATATTTGCTTTCTATTTTGTGTTAACTCT
1 ATATATACTTTTAGTACATATACTTTAAACATAAACATATTTACTTTCTATTTTATGTTAACTCT
* * *
3231781 AAAAAAATTATAACTTATAAAATTATTAATTATAATATGTATGTATACCTTTGTTTATATAAACG
66 AAAAAAATTATAACTTATAAAACTATTAATTATAATA-GTA-GCATACCTTTATTTATATAAACG
*
3231846 TATAATACATATACCTAAAAAGAAGTTGTGAGATTAGAATAGTTTGAGAACCTAACTATTTTTTT
129 TATAATACATATACCTAAAAAGAAGTTGTAAGATTAGAATAGTTTGAGAACCTAACTATTTTTTT
* * * * **
3231911 TAATTTCATGTAATTAAGG-ATAACCCATATACCTAATTAAATTAATTTATGAAATTATGATTAT
194 TAATTTCATGTAATTAAGGAAAAACCCATACAACTAATTAAATTAATTCATGAAACCATGATTAT
* * * *
3231975 TAATTAACTTGTAATGTCTTTTAATATATATAATTTATATATTGTCTTAATTTAT-AAGAAATAT
259 TAATTAACTCGTAATATCTTTTAATATATATAATCTATATATTGTCTTAAATTATAAAG-AATAT
3232039 AATTACTATTAT
323 AATTACTATTAT
* *
3232051 ATATATACTTTTAGTACATATACTTTAAATATAAATATATTTACTTTCTATTTTATGTTAACAT-
1 ATATATACTTTTAGTACATATACTTTAAACATAAACATATTTACTTTCTATTTTATGTTAAC-TC
* * * *
3232115 TATAAAAATTATTACTTATAGAACTATTAATTATAATA-TA-CATACCTTTATTTATATAAACTT
65 TAAAAAAATTATAACTTATAAAACTATTAATTATAATAGTAGCATACCTTTATTTATATAAACGT
* * * * * **
3232178 GTAATATATGTCCCTAAAGAGAAGTTGTAAGATTAGAATAGTTTTG-GAATTTAACTATTTTTTT
130 ATAATACATATACCTAAAAAGAAGTTGTAAGATTAGAATAG-TTTGAGAACCTAACTATTTTTTT
* * * *
3232242 TAATTTTATGTAATTAAGGAAAAACTCTTACAATTAATTAAATTAATTCATGAAACCATGATTAT
194 TAATTTCATGTAATTAAGGAAAAACCCATACAACTAATTAAATTAATTCATGAAACCATGATTAT
* *
3232307 TAATTAACTCGTAATATCTTTTAATATATATACTCTATATATTGTGTTAAATTATAAAGAATATA
259 TAATTAACTCGTAATATCTTTTAATATATATAATCTATATATTGTCTTAAATTATAAAGAATATA
3232372 ATTACT
324 ATTACT
3232378 TGTGAATTAT
Statistics
Matches: 286, Mismatches: 37, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
331 89 0.31
332 101 0.35
333 5 0.02
335 90 0.31
336 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.44
Consensus pattern (334 bp):
ATATATACTTTTAGTACATATACTTTAAACATAAACATATTTACTTTCTATTTTATGTTAACTCT
AAAAAAATTATAACTTATAAAACTATTAATTATAATAGTAGCATACCTTTATTTATATAAACGTA
TAATACATATACCTAAAAAGAAGTTGTAAGATTAGAATAGTTTGAGAACCTAACTATTTTTTTTA
ATTTCATGTAATTAAGGAAAAACCCATACAACTAATTAAATTAATTCATGAAACCATGATTATTA
ATTAACTCGTAATATCTTTTAATATATATAATCTATATATTGTCTTAAATTATAAAGAATATAAT
TACTATTAT
Found at i:3233290 original size:13 final size:13
Alignment explanation
Indices: 3233272--3233297 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3233262 ATAATTTTTA
3233272 CTATTTGATAAAT
1 CTATTTGATAAAT
3233285 CTATTTGATAAAT
1 CTATTTGATAAAT
3233298 TTACTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
CTATTTGATAAAT
Found at i:3233722 original size:22 final size:22
Alignment explanation
Indices: 3233675--3233723 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
3233665 TAAATTTTTG
* **
3233675 TTTTTTTAAAAAAAGTTATTTG
1 TTTTTTTAAAAAAAATTATTAA
3233697 TTTTTTTAAAAAAAATT-TTAA
1 TTTTTTTAAAAAAAATTATTAA
*
3233718 ATTTTT
1 TTTTTT
3233724 ATTTGACCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTTTTTAAAAAAAATTATTAA
Found at i:3238619 original size:2 final size:2
Alignment explanation
Indices: 3238612--3238641 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3238602 CATAAAAGAA
*
3238612 CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3238642 TTCTGTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Done.