Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold138
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: 1735418
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 2489 characters in sequence are not A, C, G, or T
File 2 of 11
Found at i:183703 original size:15 final size:15
Alignment explanation
Indices: 183676--183716 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
183666 ATATAATTTT
183676 AATTATATATTATAA
1 AATTATATATTATAA
183691 AATTGATAT-TTATAA
1 AATT-ATATATTATAA
*
183706 AAGTATATATT
1 AATTATATATT
183717 TTTTATACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.17
15 15 0.65
16 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (15 bp):
AATTATATATTATAA
Found at i:183741 original size:22 final size:23
Alignment explanation
Indices: 183714--183767 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
183704 AAAAGTATAT
183714 ATTTTTTATA-CATAATTA-ATAA
1 ATTTTTTATATCATAATTATA-AA
* * *
183736 ATTTTTAAAATTATAATTATAAA
1 ATTTTTTATATCATAATTATAAA
183759 ATTTTTTAT
1 ATTTTTTAT
183768 TAACCTCTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 8 0.32
23 16 0.64
24 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTTTTATATCATAATTATAAA
Found at i:184180 original size:22 final size:22
Alignment explanation
Indices: 184155--184200 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
184145 TAACTCTTTG
*
184155 TATTATAAATTATTTATTACTA
1 TATTATAAAGTATTTATTACTA
* *
184177 TATTATGAAGTGTTTATTACTA
1 TATTATAAAGTATTTATTACTA
184199 TA
1 TA
184201 ATATTAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (22 bp):
TATTATAAAGTATTTATTACTA
Found at i:186114 original size:33 final size:33
Alignment explanation
Indices: 186036--186120 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 33
186026 GGAAAAAAAC
*
186036 CACCATTTAGTCAACAATGGTAAACCACCAAAT
1 CACCATTTAATCAACAATGGTAAACCACCAAAT
*
186069 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAACCACCAAAT
186103 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
186121 TCTCCCACTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 18 0.37
34 31 0.63
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.24
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAACCACCAAAT
Found at i:190575 original size:34 final size:34
Alignment explanation
Indices: 190529--190746 Score: 251
Period size: 34 Copynumber: 6.4 Consensus size: 34
190519 TAAAAAACCA
* *
190529 TCATTTAATCAACAATGGCAACCTACCAAATCTAC
1 TCATTTAATCAACAATGGTAAACTACCAAATC-AC
* * *
190564 -CATTTAGTCAACAATGGTAAGCCACCAAATCAC
1 TCATTTAATCAACAATGGTAAACTACCAAATCAC
* * * **
190597 CCATTTAATCAATAATGGTAAGCTACCAAATTTC
1 TCATTTAATCAACAATGGTAAACTACCAAATCAC
* **
190631 TCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 TCATTTAATCAACAATGGTAAACTACCAAATCAC
* * **
190665 TCATTTAGTCAACGATGACAAACTACCAAATCAC
1 TCATTTAATCAACAATGGTAAACTACCAAATCAC
*
190699 TCATTTAATCAACAATAGTAAACTACCAAATCAC
1 TCATTTAATCAACAATGGTAAACTACCAAATCAC
190733 -CATTTAATCAACAA
1 TCATTTAATCAACAA
190747 ATATATCAGT
Statistics
Matches: 159, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
33 16 0.10
34 143 0.90
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (34 bp):
TCATTTAATCAACAATGGTAAACTACCAAATCAC
Found at i:190705 original size:102 final size:102
Alignment explanation
Indices: 190529--190746 Score: 287
Period size: 102 Copynumber: 2.1 Consensus size: 102
190519 TAAAAAACCA
** *
190529 TCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 TCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAAAT
* * * **
190594 CACCCATTTAATCAATAATGGTAAGCTACCAAATTTC
66 CACCCATTTAATCAACAATAGTAAACTACCAAATCAC
* * * * *
190631 TCATTTAATCAACAATGGTAAGCTACCAAAT-TTCTCATTTAGTCAACGATGACAAACTACCAAA
1 TCATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGACAAACCACCAAA
*
190695 TCACTCATTTAATCAACAATAGTAAACTACCAAATCAC
65 TCACCCATTTAATCAACAATAGTAAACTACCAAATCAC
190733 -CATTTAATCAACAA
1 TCATTTAATCAACAA
190747 ATATATCAGT
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
101 16 0.16
102 85 0.84
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (102 bp):
TCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAAAT
CACCCATTTAATCAACAATAGTAAACTACCAAATCAC
Found at i:191492 original size:23 final size:23
Alignment explanation
Indices: 191465--191510 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
191455 TGATACTTTA
*
191465 TGAATCATTGGCATTTAAATTTG
1 TGAATCATTAGCATTTAAATTTG
*
191488 TGAATCATTAGTATTTAAATTTG
1 TGAATCATTAGCATTTAAATTTG
191511 AAGTAAAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.46
Consensus pattern (23 bp):
TGAATCATTAGCATTTAAATTTG
Found at i:192982 original size:20 final size:19
Alignment explanation
Indices: 192941--192994 Score: 60
Period size: 17 Copynumber: 3.0 Consensus size: 19
192931 ATTTTGTGCA
* *
192941 AATAA-AATAAAATAATAT
1 AATAATAATAAATTAATTT
*
192959 AATAAT-AT-TATTAATTT
1 AATAATAATAAATTAATTT
192976 AATAATAATAAATTAATTT
1 AATAATAATAAATTAATTT
192995 TTTAAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 12 0.41
18 9 0.31
19 8 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAATAATAAATTAATTT
Found at i:200953 original size:20 final size:20
Alignment explanation
Indices: 200928--200966 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
200918 CTCTGTCAAT
200928 GTCCCTCAATTGCTTCTCAC
1 GTCCCTCAATTGCTTCTCAC
*
200948 GTCCCTCAGTTGCTTCTCA
1 GTCCCTCAATTGCTTCTCA
200967 AAATTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.38, G:0.13, T:0.36
Consensus pattern (20 bp):
GTCCCTCAATTGCTTCTCAC
Found at i:208188 original size:16 final size:16
Alignment explanation
Indices: 208167--208199 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
208157 TCCACGAAAG
208167 AGGCAATTTTTCAATC
1 AGGCAATTTTTCAATC
208183 AGGCAATTTTTCAATC
1 AGGCAATTTTTCAATC
208199 A
1 A
208200 AAACAGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (16 bp):
AGGCAATTTTTCAATC
Found at i:209184 original size:2 final size:2
Alignment explanation
Indices: 209177--209223 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
209167 TTTTTCTCTT
* *
209177 TA TA TA TA TA TA TA TT TA TA TA TGA AA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
209219 TA TA T
1 TA TA T
209224 TTCATTTGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:209264 original size:2 final size:2
Alignment explanation
Indices: 209257--209284 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
209247 GCTTTCGTTT
209257 TA 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 TA
209285 AACTGATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:213445 original size:13 final size:13
Alignment explanation
Indices: 213427--213478 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
213417 AGCTTCGTAG
213427 CGATACATTGTAT
1 CGATACATTGTAT
213440 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
213459 CGATACATTGTAT
1 CGATACATTGTAT
213472 CGATACA
1 CGATACA
213479 ACACTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:213459 original size:19 final size:19
Alignment explanation
Indices: 213435--213499 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
213425 AGCGATACAT
213435 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
213454 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
213467 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
213486 TATATCGATACAAA
1 TGTATCGATACAAA
213500 TTGTTGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:213468 original size:32 final size:32
Alignment explanation
Indices: 213427--213497 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
213417 AGCTTCGTAG
*
213427 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATATAT
*
213459 CGATACATTGTATCGATACAACACTTATATAT
1 CGATACATTGTATCGATACAAAACTTATATAT
213491 CGATACA
1 CGATACA
213498 AATTGTTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATATAT
Found at i:215430 original size:26 final size:26
Alignment explanation
Indices: 215394--215448 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
215384 CACGATGTCT
*
215394 TGAACTATTTATGCTTTCTTATAAAC
1 TGAACTATTTAGGCTTTCTTATAAAC
*
215420 TGAACTATTTAGGCTTTCTTGTAAAC
1 TGAACTATTTAGGCTTTCTTATAAAC
215446 TGA
1 TGA
215449 GACAATAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (26 bp):
TGAACTATTTAGGCTTTCTTATAAAC
Found at i:218536 original size:2 final size:2
Alignment explanation
Indices: 218485--218522 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
218475 TGTAAAAGTT
*
218485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
218523 AAAGGACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:224175 original size:28 final size:28
Alignment explanation
Indices: 224116--224180 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
224106 CTACCCATTT
*
224116 ATTTGTCAAAAATGGTGGTTATTTTGTG
1 ATTTGTCAAAAATAGTGGTTATTTTGTG
224144 -TTTGTCAAAAATAGTGGTT-TCCTTTG-G
1 ATTTGTCAAAAATAGTGGTTAT--TTTGTG
224171 ATTTGTCAAA
1 ATTTGTCAAA
224181 TATGGAGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 1 0.03
27 19 0.58
28 13 0.39
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.45
Consensus pattern (28 bp):
ATTTGTCAAAAATAGTGGTTATTTTGTG
Found at i:226230 original size:17 final size:16
Alignment explanation
Indices: 226205--226262 Score: 59
Period size: 15 Copynumber: 3.7 Consensus size: 16
226195 ATTTTATTTG
226205 TTTAATATTTATAAAA
1 TTTAATATTTATAAAA
*
226221 TTTGAATA-TTA-AATA
1 TTT-AATATTTATAAAA
*
226236 TTT-ATAATTATAAAA
1 TTTAATATTTATAAAA
226251 TTTATATATTTA
1 TTTA-ATATTTA
226263 CATATAAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
13 3 0.09
14 3 0.09
15 12 0.35
16 6 0.18
17 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TTTAATATTTATAAAA
Found at i:226979 original size:4 final size:4
Alignment explanation
Indices: 226970--227033 Score: 74
Period size: 4 Copynumber: 16.0 Consensus size: 4
226960 AAGTAACATG
* * *
226970 TATA TATA TATA TATA TATA TATA TGTA TGTA TGTA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
227018 TGTA TGTA TGTA TATA
1 TATA TATA TATA TATA
227034 ATTAGATGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:227012 original size:24 final size:24
Alignment explanation
Indices: 226980--227033 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
226970 TATATATATA
226980 TATATATATATATATGTATGTATG
1 TATATATATATATATGTATGTATG
227004 TATATATATATATATGTATGTATG
1 TATATATATATATATGTATGTATG
227028 TATATA
1 TATATA
227034 ATTAGATGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (24 bp):
TATATATATATATATGTATGTATG
Found at i:230259 original size:20 final size:19
Alignment explanation
Indices: 230215--230309 Score: 113
Period size: 19 Copynumber: 4.9 Consensus size: 19
230205 GTATTAATAT
*
230215 ATTGTATCCATACATGATC
1 ATTGTATCGATACATGATC
230234 ATTGTATCGATACATGCA-C
1 ATTGTATCGATACATG-ATC
*
230253 AATTGTATCGATACACGATC
1 -ATTGTATCGATACATGATC
*
230273 ATTGTATCAATACATGCA-C
1 ATTGTATCGATACATG-ATC
230292 AATTGTATCGATACATGA
1 -ATTGTATCGATACATGA
230310 AACTGGCAGT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
19 33 0.50
20 33 0.50
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (19 bp):
ATTGTATCGATACATGATC
Found at i:230273 original size:39 final size:39
Alignment explanation
Indices: 230215--230306 Score: 157
Period size: 39 Copynumber: 2.4 Consensus size: 39
230205 GTATTAATAT
* * *
230215 ATTGTATCCATACATGATCATTGTATCGATACATGCACA
1 ATTGTATCGATACACGATCATTGTATCAATACATGCACA
230254 ATTGTATCGATACACGATCATTGTATCAATACATGCACA
1 ATTGTATCGATACACGATCATTGTATCAATACATGCACA
230293 ATTGTATCGATACA
1 ATTGTATCGATACA
230307 TGAAACTGGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (39 bp):
ATTGTATCGATACACGATCATTGTATCAATACATGCACA
Found at i:234138 original size:13 final size:13
Alignment explanation
Indices: 234120--234145 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
234110 ACATTTTATG
234120 ATGTATCGATACA
1 ATGTATCGATACA
234133 ATGTATCGATACA
1 ATGTATCGATACA
234146 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:234162 original size:32 final size:33
Alignment explanation
Indices: 234098--234165 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
234088 TGTTACAAGC
* **
234098 CAATGTATTGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATACTATGATGTATCGATA
*
234131 CAATGTATCGATACATACTGTG-TGTATCGATA
1 CAATGTATCGATACATACTATGATGTATCGATA
234163 CAA
1 CAA
234166 GTTTAGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGATGTATCGATA
Found at i:234244 original size:20 final size:21
Alignment explanation
Indices: 234197--234249 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
234187 ACCAATGACT
**
234197 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
234218 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
234238 TGTATCGATACA
1 TGTATCGATACA
234250 ATGTATTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:234294 original size:20 final size:20
Alignment explanation
Indices: 234251--234301 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
234241 ATCGATACAA
*
234251 TGTATTGATACAATGCAATC
1 TGTATTGATACAATGAAATC
* * *
234271 TGTATTGATACATTTAAATG
1 TGTATTGATACAATGAAATC
*
234291 TGTATCGATAC
1 TGTATTGATAC
234302 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (20 bp):
TGTATTGATACAATGAAATC
Found at i:234843 original size:21 final size:21
Alignment explanation
Indices: 234817--234869 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
234807 TTTTCTTTTC
234817 TCTCCCCCTTAATCAAAAATT
1 TCTCCCCCTTAATCAAAAATT
**
234838 TCTCCCCCTTAATCAAACGTT
1 TCTCCCCCTTAATCAAAAATT
234859 TCTCCCCCTTA
1 TCTCCCCCTTA
234870 GTAAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.40, G:0.02, T:0.34
Consensus pattern (21 bp):
TCTCCCCCTTAATCAAAAATT
Found at i:236744 original size:13 final size:13
Alignment explanation
Indices: 236726--236750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
236716 ATAATCCCCT
236726 TGTATCGATACAA
1 TGTATCGATACAA
236739 TGTATCGATACA
1 TGTATCGATACA
236751 GAGAATGCTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:242957 original size:33 final size:32
Alignment explanation
Indices: 242920--242987 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
242910 CGTTACAAGC
**
242920 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATACTATG-TGTATCGATA
*
242953 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
242985 CAA
1 CAA
242988 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:242960 original size:13 final size:13
Alignment explanation
Indices: 242942--242967 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
242932 ACATTTTATG
242942 ATGTATCGATACA
1 ATGTATCGATACA
242955 ATGTATCGATACA
1 ATGTATCGATACA
242968 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:243066 original size:20 final size:21
Alignment explanation
Indices: 243019--243071 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
243009 GCCAATGACT
**
243019 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
243040 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
243060 TGTATCGATACA
1 TGTATCGATACA
243072 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:243077 original size:13 final size:13
Alignment explanation
Indices: 243059--243087 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
243049 ACATTTGGTC
243059 ATGTATCGATACA
1 ATGTATCGATACA
243072 ATGTATCGATACA
1 ATGTATCGATACA
243085 ATG
1 ATG
243088 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:243098 original size:20 final size:20
Alignment explanation
Indices: 243073--243123 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
243063 ATCGATACAA
*
243073 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
243093 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
243113 TGTATCGATAC
1 TGTATCGATAC
243124 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:249163 original size:34 final size:34
Alignment explanation
Indices: 249120--249187 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
249110 ATCATATTTT
*
249120 TTGTTTATTTCCAACCTCAATTGCCCATAAAAAA
1 TTGTTTATTTCCAACCTCAATTACCCATAAAAAA
* * * *
249154 TTGTTTATTTTCAACTTTAATTACTCATAAAAAA
1 TTGTTTATTTCCAACCTCAATTACCCATAAAAAA
249188 AAGAACAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (34 bp):
TTGTTTATTTCCAACCTCAATTACCCATAAAAAA
Found at i:251071 original size:17 final size:16
Alignment explanation
Indices: 251049--251084 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
251039 TTTTTTAAGA
*
251049 ATATTTATATTTAAAAT
1 ATATTTATATAT-AAAT
251066 ATATTTATATATAAAT
1 ATATTTATATATAAAT
251082 ATA
1 ATA
251085 AAAATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTTATATATAAAT
Found at i:251093 original size:24 final size:24
Alignment explanation
Indices: 251061--251151 Score: 75
Period size: 22 Copynumber: 4.0 Consensus size: 24
251051 ATTTATATTT
251061 AAAATATATTTATATATAAATATA
1 AAAATATATTTATATATAAATATA
* *
251085 AAAATATATTT-TTTA-AAATTTA
1 AAAATATATTTATATATAAATATA
* * * *
251107 TAAATATATTTCTTTAAAAAT-TA
1 AAAATATATTTATATATAAATATA
* *
251130 AAGA-ATATTTATAT-TATATATA
1 AAAATATATTTATATATAAATATA
251152 CACATATTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
21 3 0.05
22 26 0.47
23 11 0.20
24 15 0.27
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
AAAATATATTTATATATAAATATA
Found at i:251103 original size:22 final size:23
Alignment explanation
Indices: 251061--251141 Score: 78
Period size: 22 Copynumber: 3.6 Consensus size: 23
251051 ATTTATATTT
*
251061 AAAATATATTTATATATAAATATA
1 AAAATATATTTATTTA-AAATATA
*
251085 AAAATATATTT-TTTAAAATTTA
1 AAAATATATTTATTTAAAATATA
* *
251107 TAAATATATTTCTTTAAAA-ATTA
1 AAAATATATTTATTTAAAATA-TA
*
251130 AAGA-ATATTTAT
1 AAAATATATTTAT
251142 ATTATATATA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 23 0.48
23 14 0.29
24 11 0.23
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
AAAATATATTTATTTAAAATATA
Found at i:251187 original size:23 final size:23
Alignment explanation
Indices: 251049--251188 Score: 72
Period size: 23 Copynumber: 5.9 Consensus size: 23
251039 TTTTTTAAGA
* *
251049 ATATTTATATTTAAAATATATTT
1 ATATTTAAATTTAAAAAATATTT
* *
251072 ATATATAAATATAAAAATATATTT
1 ATATTTAAATTTAAAAA-ATATTT
* *
251096 -T-TTAAAATTTATAAATATATTT
1 ATATTTAAATTTA-AAAAATATTT
* * * *
251118 CT-TTAAAAATTAAAGAATATTT
1 ATATTTAAATTTAAAAAATATTT
* *
251140 ATA-TTATATATACACATATTTAATATTT
1 ATATTTAAATTTA-A-A-A---AATATTT
251168 ATATTTAAATTTAAAAAATAT
1 ATATTTAAATTTAAAAAATAT
251189 AACTCTTTAA
Statistics
Matches: 87, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
22 27 0.31
23 33 0.38
24 7 0.08
26 1 0.01
27 1 0.01
28 11 0.13
29 7 0.08
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (23 bp):
ATATTTAAATTTAAAAAATATTT
Found at i:251692 original size:26 final size:28
Alignment explanation
Indices: 251663--251718 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
251653 TAAAAATATC
* *
251663 AAAATATGATT-ATTTTAATA-ATTTTT
1 AAAAAATGATTAATTTTAAAATATTTTT
*
251689 AAAAAATTATTAATTTTAAAATATTTTT
1 AAAAAATGATTAATTTTAAAATATTTTT
251717 AA
1 AA
251719 TTTTTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.36
27 8 0.32
28 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
AAAAAATGATTAATTTTAAAATATTTTT
Found at i:251704 original size:18 final size:18
Alignment explanation
Indices: 251681--251723 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
251671 ATTATTTTAA
251681 TAATTTTTAAAAAATTAT
1 TAATTTTTAAAAAATTAT
* *
251699 TAA-TTTTAAAATATTTT
1 TAATTTTTAAAAAATTAT
251716 TAATTTTT
1 TAATTTTT
251724 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATTTTTAAAAAATTAT
Found at i:251755 original size:25 final size:25
Alignment explanation
Indices: 251721--251793 Score: 114
Period size: 24 Copynumber: 3.0 Consensus size: 25
251711 ATTTTTAATT
251721 TTTTTTAAAAAAATAAGTATATTTA
1 TTTTTTAAAAAAATAAGTATATTTA
251746 TTTTTT-AAAAAATAAGTATATTTA
1 TTTTTTAAAAAAATAAGTATATTTA
*
251770 TTTTTTAAAAATATATA-TATATTT
1 TTTTTTAAAAAAATA-AGTATATTT
251794 TTTCACTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
24 24 0.53
25 20 0.44
26 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (25 bp):
TTTTTTAAAAAAATAAGTATATTTA
Found at i:252686 original size:17 final size:17
Alignment explanation
Indices: 252664--252725 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 17
252654 ATTATTTTCA
252664 TAATTTTTAAAAATTAT
1 TAATTTTTAAAAATTAT
252681 TAA-TTTTAAAATATTAT
1 TAATTTTTAAAA-ATTAT
*
252698 TAATTTTTTTAAAATATAT
1 TAA-TTTTTAAAAAT-TAT
252717 ATAATTTTT
1 -TAATTTTT
252726 TCATTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
16 8 0.21
17 11 0.28
18 2 0.05
19 15 0.38
20 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTTTTAAAAATTAT
Found at i:252689 original size:16 final size:17
Alignment explanation
Indices: 252668--252704 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
252658 TTTTCATAAT
252668 TTTTAAAA-ATTATTAA
1 TTTTAAAATATTATTAA
252684 TTTTAAAATATTATTAA
1 TTTTAAAATATTATTAA
252701 TTTT
1 TTTT
252705 TTTAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAAAATATTATTAA
Found at i:252707 original size:20 final size:20
Alignment explanation
Indices: 252667--252726 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
252657 ATTTTCATAA
252667 TTTTTAAAA-ATTATTAA--
1 TTTTTAAAATATTATTAATT
252684 -TTTTAAAATATTATTAATT
1 TTTTTAAAATATTATTAATT
252703 TTTTTAAAATA-TATATAATT
1 TTTTTAAAATATTAT-TAATT
252723 TTTT
1 TTTT
252727 CATTATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.21
17 8 0.21
19 3 0.08
20 19 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTAAAATATTATTAATT
Found at i:252886 original size:14 final size:14
Alignment explanation
Indices: 252869--252913 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
252859 ATATATTTAT
252869 TAAAATTTATATAA
1 TAAAATTTATATAA
*
252883 TAAAATTATTAATATAT
1 TAAAA-T-TT-ATATAA
252900 TAAAATTTATATAA
1 TAAAATTTATATAA
252914 ATATTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.38
15 3 0.12
16 3 0.12
17 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAATTTATATAA
Found at i:252903 original size:17 final size:16
Alignment explanation
Indices: 252866--252931 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 16
252856 TAAATATATT
252866 TATTAAAA-TTT-ATA
1 TATTAAAATTTTAATA
*
252880 TAATAAAATTATTAATA
1 TATTAAAATT-TTAATA
*
252897 TATTAAAATTTATATAAA
1 TATTAAAATTT-TA-ATA
252915 TATTAAATATTTTAATA
1 TATTAAA-ATTTTAATA
252932 AAATATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
14 7 0.17
15 1 0.02
16 3 0.07
17 16 0.38
18 11 0.26
19 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTAAAATTTTAATA
Found at i:252928 original size:20 final size:18
Alignment explanation
Indices: 252883--252938 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
252873 ATTTATATAA
* *
252883 TAAAA-TTATTAATATAT
1 TAAAATTTAATAAAATAT
252900 TAAAATTT-ATATAAATAT
1 TAAAATTTAATA-AAATAT
252918 TAAATATTTTAATAAAATAT
1 TAAA-A-TTTAATAAAATAT
252938 T
1 T
252939 TAAACATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 7 0.22
18 11 0.34
19 1 0.03
20 10 0.31
21 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATTTAATAAAATAT
Found at i:258316 original size:2 final size:2
Alignment explanation
Indices: 258309--258341 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
258299 ATATTAGACT
258309 TA TA TA 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 TA TA TA T
258342 CACAAAAGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:263161 original size:2 final size:2
Alignment explanation
Indices: 263154--263193 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
263144 ACTATATGAA
263154 AT AT AT AT AT 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 AT AT AT AT AT
263194 GACAATCCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:264498 original size:2 final size:2
Alignment explanation
Indices: 264491--264520 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
264481 TCAAATATTT
*
264491 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
264521 ACATATTTTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:265059 original size:17 final size:18
Alignment explanation
Indices: 265030--265065 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
265020 AGATTTAGTA
265030 GCCTAATTTTTTTTAAAT
1 GCCTAATTTTTTTTAAAT
265048 GCCTAA-TTTTTTTAAAT
1 GCCTAATTTTTTTTAAAT
265065 G
1 G
265066 AAAAAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (18 bp):
GCCTAATTTTTTTTAAAT
Found at i:265112 original size:23 final size:23
Alignment explanation
Indices: 265084--265159 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 23
265074 GACCAAGACA
265084 TAAAAAATTTAAAAATTAATTTT
1 TAAAAAATTTAAAAATTAATTTT
* *
265107 TAAAAAA-TGAAATAAATAATTTTTT
1 TAAAAAATTTAAA-AATTAA--TTTT
265132 TAAAGAAATATTAAAAAATTAAATTTT
1 TAAA-AAAT-TT-AAAAATT-AATTTT
265159 T
1 T
265160 TTACCAACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
22 4 0.10
23 12 0.29
25 8 0.20
26 3 0.07
27 5 0.12
28 4 0.10
29 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (23 bp):
TAAAAAATTTAAAAATTAATTTT
Found at i:267056 original size:14 final size:15
Alignment explanation
Indices: 267032--267060 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
267022 TATTATTAGC
267032 TCCATCATATCCTTG
1 TCCATCATATCCTTG
267047 TCCA-CATATCCTTG
1 TCCATCATATCCTTG
267061 GCAAGTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.34, G:0.07, T:0.38
Consensus pattern (15 bp):
TCCATCATATCCTTG
Found at i:275252 original size:31 final size:29
Alignment explanation
Indices: 275192--275253 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
275182 ATTTTAATTT
*
275192 AATTTTTAATAATTTCTATTGGTAATAAA
1 AATTTTTAATAATTTCTATTGATAATAAA
* *
275221 AATTTATTAATAATTTTTATATTATAATAAA
1 AATTT-TTAATAATTTCTAT-TGATAATAAA
275252 AA
1 AA
275254 ATTAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.18
30 13 0.46
31 10 0.36
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (29 bp):
AATTTTTAATAATTTCTATTGATAATAAA
Found at i:275297 original size:15 final size:15
Alignment explanation
Indices: 275259--275301 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
275249 AAAAAATTAA
*
275259 TTTATATTATTAAAT
1 TTTATATTTTTAAAT
*
275274 TTAAT-TTTTTAAAT
1 TTTATATTTTTAAAT
275288 TTTATATTTTTAAA
1 TTTATATTTTTAAA
275302 ATAATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATTTTTAAAT
Found at i:275380 original size:20 final size:20
Alignment explanation
Indices: 275328--275382 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
275318 AATAAATAAT
275328 TATGTTAAAAAAATTATTTGA
1 TATGTTAAAAAAA-TATTTGA
* *
275349 -ATATTAATAAAATA-TTGA
1 TATGTTAAAAAAATATTTGA
275367 TATGTCTAAAAAAATA
1 TATGT-TAAAAAAATA
275383 ACTTATGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 4 0.14
19 5 0.18
20 19 0.68
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (20 bp):
TATGTTAAAAAAATATTTGA
Found at i:275710 original size:31 final size:32
Alignment explanation
Indices: 275675--275736 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
275665 TTTTGATACA
275675 TTTTAAATTTATTATATAAT-ATTATTTTTAT
1 TTTTAAATTTATTATATAATAATTATTTTTAT
** **
275706 TTTTATTTTTATTATATTTTAATTATTTTTA
1 TTTTAAATTTATTATATAATAATTATTTTTA
275737 ATTAAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (32 bp):
TTTTAAATTTATTATATAATAATTATTTTTAT
Found at i:275735 original size:10 final size:10
Alignment explanation
Indices: 275708--275740 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
275698 ATTTTTATTT
275708 TTATTTTT-A
1 TTATTTTTAA
275717 TTATATTTTAA
1 TTAT-TTTTAA
275728 TTATTTTTAA
1 TTATTTTTAA
275738 TTA
1 TTA
275741 AATTTATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.18
10 13 0.59
11 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATTTTTAA
Found at i:275735 original size:21 final size:22
Alignment explanation
Indices: 275694--275745 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
275684 TATTATATAA
* *
275694 TATTAT-TTTTATTTTTATTTT
1 TATTATATTTTAATTATATTTT
275715 TATTATATTTTAATTAT-TTTT
1 TATTATATTTTAATTATATTTT
* *
275736 AATTAAATTT
1 TATTATATTT
275746 ATGATACCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TATTATATTTTAATTATATTTT
Found at i:275746 original size:20 final size:20
Alignment explanation
Indices: 275708--275746 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
275698 ATTTTTATTT
*
275708 TTATTTTTATTATATTTTAA
1 TTATTTTTATTATAATTTAA
275728 TTATTTTTAATTA-AATTTA
1 TTATTTTT-ATTATAATTTA
275747 TGATACCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTTATTATAATTTAA
Found at i:276271 original size:18 final size:18
Alignment explanation
Indices: 276248--276286 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
276238 AAGTTAAAAC
276248 ATAAATTTTCCTATATAT
1 ATAAATTTTCCTATATAT
276266 ATAAATTTTCCTATATAT
1 ATAAATTTTCCTATATAT
276284 ATA
1 ATA
276287 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAAATTTTCCTATATAT
Found at i:276282 original size:2 final size:2
Alignment explanation
Indices: 276277--276312 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
276267 TAAATTTTCC
276277 TA TA TA TA TA 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 TA TA TA TA TA
276313 AGATTCCGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:277931 original size:18 final size:18
Alignment explanation
Indices: 277910--277944 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
277900 GTATATCAGA
277910 AAAAAAAACAAATAAAAT
1 AAAAAAAACAAATAAAAT
**
277928 AAAAAATTCAAATAAAA
1 AAAAAAAACAAATAAAA
277945 GTAAGTACAA
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:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAAAAACAAATAAAAT
Found at i:284025 original size:20 final size:21
Alignment explanation
Indices: 283993--284041 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 21
283983 ATAATTTATA
*
283993 ATATAATTT-TAT-TT-TTTC
1 ATATAATTTGTATATTATTTT
284011 ATAT-ATTTGTATATTATTTT
1 ATATAATTTGTATATTATTTT
284031 ATATAATTTGT
1 ATATAATTTGT
284042 GTGATGCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.15
18 7 0.27
19 2 0.08
20 7 0.27
21 6 0.23
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
ATATAATTTGTATATTATTTT
Found at i:284140 original size:2 final size:2
Alignment explanation
Indices: 284106--284130 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
284096 AAGAAATTGC
284106 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
284131 CCATTATATA
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:298401 original size:269 final size:270
Alignment explanation
Indices: 297922--298435 Score: 847
Period size: 269 Copynumber: 1.9 Consensus size: 270
297912 TGATCATCAA
* * * *
297922 TGTAAAGATATATTTATTATTTTAGAATAAATTGGTTATGGGTATTGGTACGACCTAACTCCTTA
1 TGTAAAGATATATTCATTATTCTAAAATAAATTGGTTATGGGTATTGGTACGACCTAACTCCCTA
* * *
297987 CTCCTCCTTAGTTATTCGATAATCAAGGTATGACTGTTAATTATTTCCTTTATTGATTACACAAA
66 CTCCTCCTTAGTTATTCGATAATCAAAGTACGACCGTTAATTATTTCCTTTATTGATTACACAAA
* **
298052 CCCTAAATATGATCTTAGAGTTTTAATGTATCAATAGCATTAATAATTAGAGAGGGATCGTCAAT
131 CCCTAAATATGATCTTAGAGTTTTAATGCATCAATAGCATTAATAATTAGAGAGGGATCACCAAT
298117 TCTAATTAATAAACTCACAAGCG-GGTTTATTTAAATTAGATTGTGAATTCTTTATAGAGTTTTA
196 TCTAATTAATAAACTCACAAGCGAGGTTTATTTAAATTAGATTGTGAATTCTTTATAGAGTTTTA
298181 AATTAGATTG
261 AATTAGATTG
298191 TGTAAAGATATATTCATTATTCTAAAATAAATTGGTTATGGGTATTGGTACGACCTAACTCCCTA
1 TGTAAAGATATATTCATTATTCTAAAATAAATTGGTTATGGGTATTGGTACGACCTAACTCCCTA
298256 -TCCCTCCTTAGTTATTCGATAATCAAAGTACGACCGTTAATTATTTCCTTTATTGATTACACAA
66 CT-CCTCCTTAGTTATTCGATAATCAAAGTACGACCGTTAATTATTTCCTTTATTGATTACACAA
* *
298320 ACCCTAGATACT-ATCTTAGAGTTTTAGTGCATCAATAGCATTAATAATTAGAG-GGAGATCACC
130 ACCCTAAATA-TGATCTTAGAGTTTTAATGCATCAATAGCATTAATAATTAGAGAGG-GATCACC
* *
298383 AATTCTAATTAATAAACTCACAAGCGAGTTTTTTTTAAATTAGATTGTGAATT
193 AATTCTAATTAATAAACTCACAAGCGAGGTTTATTTAAATTAGATTGTGAATT
298436 TTTCCTAACC
Statistics
Matches: 227, Mismatches: 14, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
268 3 0.01
269 199 0.88
270 25 0.11
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (270 bp):
TGTAAAGATATATTCATTATTCTAAAATAAATTGGTTATGGGTATTGGTACGACCTAACTCCCTA
CTCCTCCTTAGTTATTCGATAATCAAAGTACGACCGTTAATTATTTCCTTTATTGATTACACAAA
CCCTAAATATGATCTTAGAGTTTTAATGCATCAATAGCATTAATAATTAGAGAGGGATCACCAAT
TCTAATTAATAAACTCACAAGCGAGGTTTATTTAAATTAGATTGTGAATTCTTTATAGAGTTTTA
AATTAGATTG
Found at i:305405 original size:2 final size:2
Alignment explanation
Indices: 305398--305424 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
305388 CTAAAGTATC
305398 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
305425 AAGATGGCAT
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:306660 original size:28 final size:28
Alignment explanation
Indices: 306616--306674 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
306606 ATTTTTTGTT
306616 ATAAAAAAATTATAAATTTAAGA-TAAAA
1 ATAAAAAAATTATAAATTTAA-ATTAAAA
*
306644 ATAATAAATATTA-AAATTTAAATTAAAA
1 ATAA-AAAAATTATAAATTTAAATTAAAA
306672 ATA
1 ATA
306675 TATTTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 1 0.04
28 20 0.71
29 7 0.25
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
ATAAAAAAATTATAAATTTAAATTAAAA
Found at i:307051 original size:32 final size:32
Alignment explanation
Indices: 307012--307089 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 32
307002 TATAATAATA
307012 ATAATAATAATATATAACAATATT-TTAAAATTTAT
1 ATAAT-ATAA-AT-TAACAAT-TTATTAAAATTTAT
*
307047 ATAATATAAATTAATAATTTATTAAAATTTAT
1 ATAATATAAATTAACAATTTATTAAAATTTAT
307079 ATAAATATAAA
1 AT-AATATAAA
307090 ATAATTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 2 0.05
32 19 0.47
33 10 0.25
34 4 0.10
35 5 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
ATAATATAAATTAACAATTTATTAAAATTTAT
Found at i:307097 original size:20 final size:19
Alignment explanation
Indices: 307072--307110 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
307062 AATTTATTAA
*
307072 AATTTATATAAATATAAAAT
1 AATTTAAATAAA-ATAAAAT
*
307092 AATTTAAATATAATAAAAT
1 AATTTAAATAAAATAAAAT
307111 TTAGGAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTTAAATAAAATAAAAT
Found at i:307101 original size:16 final size:16
Alignment explanation
Indices: 307080--307113 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
307070 AAAATTTATA
307080 TAAATATAA-AATAATT
1 TAAATATAATAA-AATT
307096 TAAATATAATAAAATT
1 TAAATATAATAAAATT
307112 TA
1 TA
307114 GGAATATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATAATAAAATT
Found at i:314071 original size:15 final size:16
Alignment explanation
Indices: 314053--314086 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
314043 TATTTTTAAA
*
314053 TTTATTAA-ATATTAT
1 TTTATTAATATAATAT
314068 TTTATTAATATAATAT
1 TTTATTAATATAATAT
314084 TTT
1 TTT
314087 TTTATGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATTAATATAATAT
Found at i:315406 original size:56 final size:55
Alignment explanation
Indices: 315346--315462 Score: 132
Period size: 55 Copynumber: 2.1 Consensus size: 55
315336 ATTTTTGCAT
*
315346 GTAATTCCATATGCTGT-ATGGCAGGAGTGATCTT-CTCTAT-TAGTGTATTTTTACGC
1 GTAATTCCATATG-GGTCATGG-AGGAGTGAT-TTCCTCTATAT-GTGTATTTTTACGC
*** *
315402 GTAATTTTGTATGGGTCATGGTGGAGTGATTTCCTCTATATGTGTATTTTTACGC
1 GTAATTCCATATGGGTCATGGAGGAGTGATTTCCTCTATATGTGTATTTTTACGC
315457 GTAATT
1 GTAATT
315463 TTGTATGTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
54 2 0.04
55 36 0.68
56 15 0.28
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.44
Consensus pattern (55 bp):
GTAATTCCATATGGGTCATGGAGGAGTGATTTCCTCTATATGTGTATTTTTACGC
Found at i:323514 original size:3 final size:3
Alignment explanation
Indices: 323506--323543 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
323496 CCATATCATT
323506 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
323544 GAAAAAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:325705 original size:49 final size:50
Alignment explanation
Indices: 325648--326204 Score: 252
Period size: 47 Copynumber: 11.5 Consensus size: 50
325638 TAATTACTAT
*
325648 TTAAAAAAATTAAAATAATTTACATTAAATCTTGAATT-CTATTTAAAAA
1 TTAAAAAAATTAAAATAATTTATATTAAATCTTGAATTACTATTTAAAAA
*
325697 TTAAAAAAATT---AT-A-TTAAATTCAAA-CTT--ATTA--A-TTAAAAA
1 TTAAAAAAATTAAAATAATTTATATT-AAATCTTGAATTACTATTTAAAAA
* ** * *
325737 -TAATAAAATTTTAAAATTTTTTATATTAAATTTTGAATTATTATTT-AAAA
1 TTAA-AAAA-ATTAAAATAATTTATATTAAATCTTGAATTACTATTTAAAAA
* *
325787 -TAATAAAGATTTAAAAT-TTTTATATTAAATCTTGAATTACTATTTAAAAA
1 TTAA-AAA-AATTAAAATAATTTATATTAAATCTTGAATTACTATTTAAAAA
* * * * *
325837 AT-AATAAA--AAATTATTTTATATTAAATCTTGTATTACTATTTAAAAA
1 TTAAAAAAATTAAAATAATTTATATTAAATCTTGAATTACTATTTAAAAA
* * * *
325884 TTATAAAAATTAATAACAATTT-TAATTAAATCCTAAATTACT-TTTGAAAAA
1 TTAAAAAAATTAA-AATAATTTAT-ATTAAATCTTGAATTACTATTT-AAAAA
* * * * * * * *
325935 ATAATAAAA--AATAT-TTTTATATTAAATCTTGAATGAATATCTATAAA
1 TTAAAAAAATTAAAATAATTTATATTAAATCTTGAATTACTATTTAAAAA
* * ** * *
325982 TAATAAAAAATTAAAAATATTTTATATTAAATCCCGAAGTATTATTTAAAAA
1 TTA-AAAAAATT-AAAATAATTTATATTAAATCTTGAATTACTATTTAAAAA
* * * * * * *
326034 -T---AATATAAAAATATTTTATAGTAAACCCTAAATTAC-ATTTTAAAAA
1 TTAAAAAAATTAAAATAATTTATATTAAATCTTGAATTACTA-TTTAAAAA
* * * * *
326080 TAATAAAAAATCAAAAACATAGTTTATAGTAAATCCTGAATTACTATTTAAAAA
1 TTA-AAAAAAT--TAAA-ATAATTTATATTAAATCTTGAATTACTATTTAAAAA
* **
326134 -T-----AATTAAAA-ATTTTGATATTAAATCCAGAATTACTATTTAAAAA
1 TTAAAAAAATTAAAATAATTT-ATATTAAATCTTGAATTACTATTTAAAAA
*
326178 TAGTAAAAAAATAAAAAT-ATTTCATAT
1 T--TAAAAAAATTAAAATAATTT-ATAT
326205 ATGTATTAGA
Statistics
Matches: 391, Mismatches: 65, Indels: 101
0.70 0.12 0.18
Matches are distributed among these distances:
39 3 0.01
40 11 0.03
41 3 0.01
42 3 0.01
43 4 0.01
44 39 0.10
45 11 0.03
46 45 0.12
47 63 0.16
48 18 0.05
49 41 0.10
50 31 0.08
51 43 0.11
52 40 0.10
53 4 0.01
54 31 0.08
55 1 0.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.40
Consensus pattern (50 bp):
TTAAAAAAATTAAAATAATTTATATTAAATCTTGAATTACTATTTAAAAA
Found at i:325767 original size:51 final size:48
Alignment explanation
Indices: 325706--325844 Score: 145
Period size: 51 Copynumber: 2.8 Consensus size: 48
325696 ATTAAAAAAA
325706 TTATATTAAATTCAAACTTATTAATTAAAAATAATAAA-ATTTTAAAATTTT
1 TTATATTAAATTCAAA-TTATT-ATTAAAAATAATAAAGA-TTTAAAA-TTT
** *
325757 TTATATTAAATTTTGAATTATTATTTAAAATAATAAAGATTTAAAATTT
1 TTATATTAAA-TTCAAATTATTATTAAAAATAATAAAGATTTAAAATTT
** *
325806 TTATATTAAATCTTGAATTACTATTTAAAAAATAATAAA
1 TTATATTAAAT-TCAAATTATTA-TT-AAAAATAATAAA
325845 AAATTATTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
48 1 0.01
49 23 0.29
50 23 0.29
51 27 0.35
52 4 0.05
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (48 bp):
TTATATTAAATTCAAATTATTATTAAAAATAATAAAGATTTAAAATTT
Found at i:325923 original size:98 final size:97
Alignment explanation
Indices: 325749--326204 Score: 455
Period size: 98 Copynumber: 4.7 Consensus size: 97
325739 ATAAAATTTT
* * * * *
325749 AAAATTTTTTATATTAAATTTTGAATTATTATTT-AAAATAATAAAGATTTA-AAAT-TTTTATA
1 AAAATATTTTATATTAAATCTTGAATTACTATTTAAAAATAATAAAAATTAATAAATATTTTATA
*
325811 TTAAATCTTGAATTACTATTTAAAAAATAATAA
66 TTAAATCCTGAATTACTATTT-AAAAATAATAA
* *
325844 AAAATTATTTTATATTAAATCTTGTATTACTATTTAAAAATTATAAAAATTAATAACA-ATTTTA
1 AAAA-TATTTTATATTAAATCTTGAATTACTATTTAAAAATAATAAAAATTAATAA-ATATTTTA
*
325908 -ATTAAATCCTAAATTACT-TTTGAAAAAATAATAA
64 TATTAAATCCTGAATTACTATTT--AAAAATAATAA
* * * *
325942 AAAATATTTTTATATTAAATCTTGAATGAATATCTATAAATAATAAAAAATTAA-AAATATTTTA
1 AAAATA-TTTTATATTAAATCTTGAATTACTATTTAAAAATAAT-AAAAATTAATAAATATTTTA
* * *
326006 TATTAAATCCCGAAGTATTATTTAAAAATAATATA
64 TATTAAATCCTGAATTACTATTTAAAAATAATA-A
* * * * * * *
326041 AAAATATTTTATAGTAAACCCTAAATTAC-ATTTTAAAAATAATAAAAAATCAAAAACATAGTTT
1 AAAATATTTTATATTAAATCTTGAATTACTA-TTTAAAAATAAT-AAAAATTAATAA-ATATTTT
* *
326105 ATAGTAAATCCTGAATTACTATTTAAAAATAATTA
63 ATATTAAATCCTGAATTACTATTTAAAAATAATAA
* ** * * *
326140 AAAAT-TTTGATATTAAATCCAGAATTACTATTTAAAAATAGTAAAAAAATAA-AAATATTTCAT
1 AAAATATTTTATATTAAATCTTGAATTACTATTTAAAAATAAT-AAAAATTAATAAATATTTTAT
326203 AT
65 AT
326205 ATGTATTAGA
Statistics
Matches: 300, Mismatches: 45, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
95 4 0.01
96 34 0.11
97 23 0.08
98 156 0.52
99 45 0.15
100 38 0.13
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (97 bp):
AAAATATTTTATATTAAATCTTGAATTACTATTTAAAAATAATAAAAATTAATAAATATTTTATA
TTAAATCCTGAATTACTATTTAAAAATAATAA
Found at i:326051 original size:196 final size:197
Alignment explanation
Indices: 325749--326204 Score: 511
Period size: 196 Copynumber: 2.3 Consensus size: 197
325739 ATAAAATTTT
* * * *
325749 AAAAT-TTTTTATATTAAATTTTGAATTATTATTTAAAATAAT-AAAGATTTAAAAT-TTTTATA
1 AAAATATTTTTATATTAAATCTTGAATTAATATTTAAAATAATAAAAAATTAAAAATATTTTATA
** * * * * **
325811 TTAAATCTTGAATTACTATTTAAAAAATAATAAAAAATTATTTTATATTAAATCTTGTATTAC-T
66 TTAAATCCCGAAGTACTATTTAAAAAATAATAAAAAATTATTTTATAGTAAACCCTAAATTACAT
* * * * *
325875 ATTTAAAAATTAT-AAAAATTAATAACA-ATTTTA-ATTAAATCCTAAATTACT-TTTGAAAAAA
131 -TTTAAAAATAATAAAAAATCAAAAACATAGTTTATAGTAAATCCTAAATTACTATTT--AAAAA
325936 TAATAA
193 TAAT-A
* *
325942 AAAATATTTTTATATTAAATCTTGAATGAATATCTATAAATAATAAAAAATTAAAAATATTTTAT
1 AAAATATTTTTATATTAAATCTTGAATTAATATTTA-AAATAATAAAAAATTAAAAATATTTTAT
*
326007 ATTAAATCCCGAAGTATTATTT-AAAAATAATATAAAAA-TATTTTATAGTAAACCCTAAATTAC
65 ATTAAATCCCGAAGTACTATTTAAAAAATAATA-AAAAATTATTTTATAGTAAACCCTAAATTAC
*
326070 ATTTTAAAAATAATAAAAAATCAAAAACATAGTTTATAGTAAATCCTGAATTACTATTTAAAAAT
129 ATTTTAAAAATAATAAAAAATCAAAAACATAGTTTATAGTAAATCCTAAATTACTATTTAAAAAT
*
326135 AATT
194 AATA
* ** * * * *
326139 AAAA-ATTTTGATATTAAATCCAGAATTACTATTTAAAAATAGTAAAAAAATAAAAATATTTCAT
1 AAAATATTTTTATATTAAATCTTGAATTAATATTT-AAAATAATAAAAAATTAAAAATATTTTAT
326203 AT
65 AT
326205 ATGTATTAGA
Statistics
Matches: 221, Mismatches: 31, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
193 5 0.02
194 26 0.12
195 7 0.03
196 103 0.47
197 47 0.21
198 14 0.06
199 16 0.07
200 3 0.01
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (197 bp):
AAAATATTTTTATATTAAATCTTGAATTAATATTTAAAATAATAAAAAATTAAAAATATTTTATA
TTAAATCCCGAAGTACTATTTAAAAAATAATAAAAAATTATTTTATAGTAAACCCTAAATTACAT
TTTAAAAATAATAAAAAATCAAAAACATAGTTTATAGTAAATCCTAAATTACTATTTAAAAATAA
TA
Found at i:326064 original size:145 final size:140
Alignment explanation
Indices: 325802--326191 Score: 326
Period size: 144 Copynumber: 2.7 Consensus size: 140
325792 AAGATTTAAA
* * * * **
325802 ATTTTTATATTAAATCTTGAATTACTATTTAAAAAATAATAAAAAATTATTTTATATTAAATCTT
1 ATTTTTATATTAAATCTTGAATGAATATTTAAAAAATAAAAAAAAAATATTTTATATTAAATCCC
* * * * *
325867 GTATTACTATTTAAAAATTATAAAAATTAATAACAATTTTAATTAAATCCTAAATTAC-TTTTGA
66 GAAGTACTATTTAAAAATAATAAAAA-TAAT---AATTTTAAGTAAACCCTAAATTACATTTT--
325931 AAAAATAATAAAAAAT
125 AAAAATAATAAAAAAT
*
325947 ATTTTTATATTAAATCTTGAATGAATATCTATAAATAATAAAAAATTAAAAATATTTTATATTAA
1 ATTTTTATATTAAATCTTGAATGAATAT-T-TAAAAAAT-AAAAA--AAAAATATTTTATATTAA
* *
326012 ATCCCGAAGTATTATTTAAAAATAATATAAA-AAT-ATTTTATAGTAAACCCTAAATTACATTTT
61 ATCCCGAAGTACTATTTAAAAATAATAAAAATAATAATTTTA-AGTAAACCCTAAATTACATTTT
326075 AAAAATAATAAAAAAT
125 AAAAATAATAAAAAAT
* * * * * ** *
326091 CAAAAACATAGTTTATAGTAAATCCTGAATTACTATTT-AAAAAT-AATTAAAAAT-TTTGATAT
1 -------AT-TTTTATATTAAATCTTGAATGAATATTTAAAAAATAAAAAAAAAATATTTTATAT
* * *
326153 TAAATCCAGAATTACTATTTAAAAATAGTAAAAA-AATAA
58 TAAATCCCGAAGTACTATTTAAAAATAATAAAAATAATAA
326192 AAATATTTCA
Statistics
Matches: 201, Mismatches: 28, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
144 61 0.30
145 48 0.24
146 5 0.02
147 9 0.04
148 7 0.03
149 5 0.02
150 42 0.21
151 3 0.01
152 21 0.10
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (140 bp):
ATTTTTATATTAAATCTTGAATGAATATTTAAAAAATAAAAAAAAAATATTTTATATTAAATCCC
GAAGTACTATTTAAAAATAATAAAAATAATAATTTTAAGTAAACCCTAAATTACATTTTAAAAAT
AATAAAAAAT
Found at i:326107 original size:54 final size:53
Alignment explanation
Indices: 326040--326144 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 53
326030 AAAATAATAT
*
326040 AAAAATATTTTATAGTAAACCCTAAATTAC-ATTTTAAAAATAATAAAAAATCA
1 AAAAATAGTTTATAGTAAACCCTAAATTACTA-TTTAAAAATAATAAAAAATCA
* * *
326093 AAAACATAGTTTATAGTAAATCCTGAATTACTATTTAAAAATAATTAAAAAT
1 AAAA-ATAGTTTATAGTAAACCCTAAATTACTATTTAAAAATAATAAAAAAT
326145 TTTGATATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
53 4 0.09
54 41 0.89
55 1 0.02
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (53 bp):
AAAAATAGTTTATAGTAAACCCTAAATTACTATTTAAAAATAATAAAAAATCA
Found at i:328063 original size:20 final size:20
Alignment explanation
Indices: 328038--328095 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 20
328028 AAACTCTTTT
*
328038 TTATAATTATATATATTTAA
1 TTATAATTATATATATTCAA
328058 TTATAATTATATGTATATTCAA
1 TTATAATTATA--TATATTCAA
*
328080 TCATAATTATATATAT
1 TTATAATTATATATAT
328096 GTACATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.47
22 18 0.53
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (20 bp):
TTATAATTATATATATTCAA
Found at i:328126 original size:21 final size:22
Alignment explanation
Indices: 328102--328147 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
328092 ATATGTACAT
*
328102 AATTTAA-TGCTTGAA-ATAAAA
1 AATTTAACT-CTTGAAGAAAAAA
328123 AA-TTAACTCTTGAAGAAAAAA
1 AATTTAACTCTTGAAGAAAAAA
328144 AATT
1 AATT
328148 GACCTATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 10 0.48
21 10 0.48
22 1 0.05
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (22 bp):
AATTTAACTCTTGAAGAAAAAA
Found at i:328464 original size:19 final size:21
Alignment explanation
Indices: 328437--328480 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
328427 AAAATTATTT
*
328437 TTATTTAAATA-TAAT-TAAA
1 TTATATAAATATTAATATAAA
328456 TTATATAAATATTAATATAAA
1 TTATATAAATATTAATATAAA
328477 TTAT
1 TTAT
328481 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 4 0.18
21 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATATAAATATTAATATAAA
Found at i:328479 original size:46 final size:46
Alignment explanation
Indices: 328428--328592 Score: 141
Period size: 46 Copynumber: 3.2 Consensus size: 46
328418 AATGAATAAA
328428 AAATTATTTTTATTTAAATATAATTAAATTATATAAATATTAATAT
1 AAATTATTTTTATTTAAATATAATTAAATTATATAAATATTAATAT
* * * * *
328474 AAATTATTTTTTAATTTTTAAATTTCAAATAAGACAATACGTATATATTTAAAATGAATAAA
1 AAATTA-TTTTT-A--TTTAAATAT--AAT--TA-AAT---TATATA---AATATTAAT-AT
328536 AAATTATTTTTATTTAAATATAATTAAATTATATAAATATTAATAT
1 AAATTATTTTTATTTAAATATAATTAAATTATATAAATATTAATAT
328582 AAATTATTTTT
1 AAATTATTTTT
328593 TAATTTTTAA
Statistics
Matches: 93, Mismatches: 10, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
46 18 0.19
47 12 0.13
48 1 0.01
50 14 0.15
52 3 0.03
53 3 0.03
54 2 0.02
55 3 0.03
56 3 0.03
58 14 0.15
60 1 0.01
61 12 0.13
62 7 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (46 bp):
AAATTATTTTTATTTAAATATAATTAAATTATATAAATATTAATAT
Found at i:328572 original size:19 final size:21
Alignment explanation
Indices: 328545--328588 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
328535 AAAATTATTT
*
328545 TTATTTAAATA-TAAT-TAAA
1 TTATATAAATATTAATATAAA
328564 TTATATAAATATTAATATAAA
1 TTATATAAATATTAATATAAA
328585 TTAT
1 TTAT
328589 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 4 0.18
21 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATATAAATATTAATATAAA
Found at i:328577 original size:108 final size:109
Alignment explanation
Indices: 328386--328604 Score: 422
Period size: 108 Copynumber: 2.0 Consensus size: 109
328376 AAATTGATTC
328386 TTTCAAATAAGACAATACGTATATATATTTAAAATGAATAAAAAATTATTTTTATTTAAATATAA
1 TTTCAAATAAGACAATACG-ATATATATTTAAAATGAATAAAAAATTATTTTTATTTAAATATAA
328451 TTAAATTATATAAATATTAATATAAATTATTTTTTAATTTTTAAA
65 TTAAATTATATAAATATTAATATAAATTATTTTTTAATTTTTAAA
328496 TTTCAAATAAGACAATACG-TATATATTTAAAATGAATAAAAAATTATTTTTATTTAAATATAAT
1 TTTCAAATAAGACAATACGATATATATTTAAAATGAATAAAAAATTATTTTTATTTAAATATAAT
328560 TAAATTATATAAATATTAATATAAATTATTTTTTAATTTTTAAA
66 TAAATTATATAAATATTAATATAAATTATTTTTTAATTTTTAAA
328604 T
1 T
328605 AGTAATGTGA
Statistics
Matches: 109, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
108 90 0.83
110 19 0.17
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (109 bp):
TTTCAAATAAGACAATACGATATATATTTAAAATGAATAAAAAATTATTTTTATTTAAATATAAT
TAAATTATATAAATATTAATATAAATTATTTTTTAATTTTTAAA
Found at i:328712 original size:102 final size:100
Alignment explanation
Indices: 328587--328815 Score: 300
Period size: 102 Copynumber: 2.2 Consensus size: 100
328577 AATATAAATT
* * * *
328587 ATTTTTTAATTTTTAAATAGTAATGTGAGA-TTTAATATAAAATATTTTTAAAATTTTTATTGTT
1 ATTTTTTATTTTTTAAATAGTAAT-TGAAATTTTAAT-TAAAATATTTTT--AATTTTTAATATT
* * *
328651 TTTAAATAGTAATTTGAGATTTAATATAAAAT-TTTTTA
62 TTTAAATAATAATTTAAGATTTAATATAAAATATGTTTA
* *
328689 ATTTTTTATTTTTTAAATAGTAATTTAAATTTTAATTATAATATTTTTAATTTTTAATATTTTTA
1 ATTTTTTATTTTTTAAATAGTAATTGAAATTTTAATTAAAATATTTTTAATTTTTAATATTTTTA
328754 AATAATAATTTAAGATTTAATATAAAATATGTTTA
66 AATAATAATTTAAGATTTAATATAAAATATGTTTA
*
328789 ATTTTTTATAATTTTTAAATAATAATT
1 ATTTTTTAT--TTTTTAAATAGTAATT
328816 TAAGATTATT
Statistics
Matches: 113, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
99 41 0.36
100 14 0.12
101 14 0.12
102 44 0.39
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (100 bp):
ATTTTTTATTTTTTAAATAGTAATTGAAATTTTAATTAAAATATTTTTAATTTTTAATATTTTTA
AATAATAATTTAAGATTTAATATAAAATATGTTTA
Found at i:328738 original size:15 final size:16
Alignment explanation
Indices: 328718--328754 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
328708 GTAATTTAAA
328718 TTTTAA-TTATAATAT
1 TTTTAATTTATAATAT
*
328733 TTTTAATTTTTAATAT
1 TTTTAATTTATAATAT
328749 TTTTAA
1 TTTTAA
328755 ATAATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATTTATAATAT
Found at i:329111 original size:14 final size:14
Alignment explanation
Indices: 329092--329130 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
329082 ATAAAATATA
329092 ATATAAAAATTAAT
1 ATATAAAAATTAAT
329106 ATATAAAAA-TAAT
1 ATATAAAAATTAAT
*
329119 -TATATAAATTAA
1 ATATAAAAATTAA
329131 AAAAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 7 0.30
13 7 0.30
14 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATAAAAATTAAT
Found at i:329148 original size:23 final size:21
Alignment explanation
Indices: 329110--329152 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
329100 ATTAATATAT
*
329110 AAAAATAATTATATAAATTAA
1 AAAAATAATTACATAAATTAA
329131 AAAAATTATATTACATAAATTA
1 AAAAA-TA-ATTACATAAATTA
329153 TTAATATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAATAATTACATAAATTAA
Found at i:329149 original size:18 final size:17
Alignment explanation
Indices: 329087--329141 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
329077 TTTAAATAAA
*
329087 ATAT-AATATAAAAATT
1 ATATAAATAAAAAAATT
*
329103 A-ATATATAAAAATAATT
1 ATATAAATAAAAA-AATT
329120 ATATAAATTAAAAAAATT
1 ATATAAA-TAAAAAAATT
329138 ATAT
1 ATAT
329142 TACATAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 2 0.06
16 7 0.22
17 5 0.16
18 12 0.38
19 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAAATAAAAAAATT
Found at i:329209 original size:57 final size:57
Alignment explanation
Indices: 329139--329247 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
329129 AAAAAAATTA
* * * * *
329139 TATTACATAAATTATTAATATCTTAAAATTTTAATGTTACTATTTTAAAAATTATTT
1 TATTAAATAAATTATTAATATATTAAAATTTAAATATTAATATTTTAAAAATTATTT
329196 TATTAAATAAATTATTAATATATTAAAATTTAAATATTAATATTTTAAAAAT
1 TATTAAATAAATTATTAATATATTAAAATTTAAATATTAATATTTTAAAAAT
329248 ATCATCAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.49
Consensus pattern (57 bp):
TATTAAATAAATTATTAATATATTAAAATTTAAATATTAATATTTTAAAAATTATTT
Found at i:329219 original size:20 final size:20
Alignment explanation
Indices: 329196--329244 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
329186 AAAATTATTT
329196 TATTAAA-TAAATTATTAATA
1 TATTAAATTAAA-TATTAATA
329216 TATTAAAATTTAAATATTAATA
1 TATT-AAA-TTAAATATTAATA
*
329238 TTTTAAA
1 TATTAAA
329245 AATATCATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 6 0.24
22 11 0.44
23 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTAAATTAAATATTAATA
Found at i:329236 original size:22 final size:23
Alignment explanation
Indices: 329203--329245 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
329193 TTTTATTAAA
329203 TAAATTATTAATATATTAAAATT
1 TAAATTATTAATATATTAAAATT
*
329226 TAAA-TATTAATATTTTAAAA
1 TAAATTATTAATATATTAAAA
329246 ATATCATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATTATTAATATATTAAAATT
Found at i:336701 original size:15 final size:15
Alignment explanation
Indices: 336683--336726 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
336673 TGATCCTATC
336683 CATCCACCACCTGTG
1 CATCCACCACCTGTG
* *
336698 CATCCACAACCCGTG
1 CATCCACCACCTGTG
336713 CATCCACCACCTGT
1 CATCCACCACCTGT
336727 TTACCCACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.23, C:0.48, G:0.11, T:0.18
Consensus pattern (15 bp):
CATCCACCACCTGTG
Found at i:337293 original size:75 final size:75
Alignment explanation
Indices: 337180--337423 Score: 353
Period size: 75 Copynumber: 3.3 Consensus size: 75
337170 ATGTGAAATA
* *
337180 TGCAGATTATCTCGGATTAGTTGTTGATAGTAATAATGTGAAATATGCAGAAACATTTGTTGATT
1 TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATT
337245 GTAGTTATCG
66 GTAGTTATCG
* * *
337255 TGCAGATTATCTCAGATTAGTTGTTGATAATAGCAATGTGAAATATGCAAAAACATTTGTTGATT
1 TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATT
*
337320 GTAGTTATTG
66 GTAGTTATCG
* * *** *
337330 TGCAGATTATCTCGGATTAGTTGTTGATAGTAGTACTGTGAAATATATTGAAAAATTTGTTGATT
1 TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATT
* *
337395 GTAATTATCA
66 GTAGTTATCG
*
337405 TGCGGATTATCTCAGATTA
1 TGCAGATTATCTCAGATTA
337424 TCATTTTATC
Statistics
Matches: 149, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 149 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (75 bp):
TGCAGATTATCTCAGATTAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTGATT
GTAGTTATCG
Found at i:338324 original size:43 final size:45
Alignment explanation
Indices: 338223--338325 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 45
338213 TAAAAATATT
* *
338223 TATTTAAATTTTATTAAATTTAAGTATTTTTTAAATTATTTTTTTA
1 TATTTAAATTAT-TTAAATTTAAGTATTTTTTAAATTATTTTTGTA
** * *
338269 TATTTTTA-TATTTAAA-TTATGTATTTATTTAAA-TATTTTTGTG
1 TATTTAAATTATTTAAATTTAAGTATTT-TTTAAATTATTTTTGTA
338312 T-TTTAAATTATTTA
1 TATTTAAATTATTTA
338326 TTTAAATATG
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
42 4 0.09
43 24 0.51
44 11 0.23
45 2 0.04
46 6 0.13
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (45 bp):
TATTTAAATTATTTAAATTTAAGTATTTTTTAAATTATTTTTGTA
Found at i:340601 original size:25 final size:26
Alignment explanation
Indices: 340563--340626 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
340553 ATAAGTAATT
* * *
340563 AATATAACACAAAAAATTA-AAATAA
1 AATATAATATAAAAAATAATAAATAA
340588 AATATAATATAAAAAAATAATAAATAA
1 AATATAATAT-AAAAAATAATAAATAA
*
340615 AATACAAT-TAAA
1 AATATAATATAAA
340627 TAAACATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 11 0.33
26 9 0.27
27 13 0.39
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (26 bp):
AATATAATATAAAAAATAATAAATAA
Found at i:340612 original size:27 final size:25
Alignment explanation
Indices: 340573--340638 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 25
340563 AATATAACAC
* *
340573 AAAAAATTAAAATAAAATATAATATA
1 AAAAAATAAAAATAAAATACAAT-TA
340599 AAAAAATAATAAATAAAATACAATTA
1 AAAAAATAA-AAATAAAATACAATTA
340625 AATAAACATAAAAA
1 AA-AAA-ATAAAAA
340639 AATTTATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 12 0.34
27 19 0.54
28 4 0.11
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAAAATAAAAATAAAATACAATTA
Found at i:340626 original size:15 final size:14
Alignment explanation
Indices: 340576--340636 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 14
340566 ATAACACAAA
340576 AAATTAAAATAAAAT
1 AAATT-AAATAAAAT
340591 ATAATATAAA-AAAAT
1 A-AAT-TAAATAAAAT
340606 -AA-TAAATAAAAT
1 AAATTAAATAAAAT
340618 ACAATTAAATAAACAT
1 A-AATTAAATAAA-AT
340634 AAA
1 AAA
340637 AAAATTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
11 4 0.10
12 5 0.13
13 2 0.05
14 2 0.05
15 16 0.41
16 9 0.23
17 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATTAAATAAAAT
Found at i:341722 original size:15 final size:15
Alignment explanation
Indices: 341704--341733 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
341694 AGGTTTAGGG
341704 TAATTAGTTGATGGT
1 TAATTAGTTGATGGT
*
341719 TAATTAGTTTATGGT
1 TAATTAGTTGATGGT
341734 ATAAAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (15 bp):
TAATTAGTTGATGGT
Found at i:346647 original size:15 final size:15
Alignment explanation
Indices: 346627--346664 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
346617 TGATTGTATC
346627 CATCCACCACCCGTG
1 CATCCACCACCCGTG
**
346642 CATCCATAACCCGTG
1 CATCCACCACCCGTG
346657 CATCCACC
1 CATCCACC
346665 CCCTATTTAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.50, G:0.11, T:0.16
Consensus pattern (15 bp):
CATCCACCACCCGTG
Found at i:346801 original size:27 final size:27
Alignment explanation
Indices: 346767--346825 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
346757 CACCATATTT
*
346767 TCCTACTCAACCTCCATACCGGTCATA
1 TCCTACTCAACCTCCATACCGATCATA
* *
346794 TCCTACTCAACCTCCATATCTATCATA
1 TCCTACTCAACCTCCATACCGATCATA
346821 TCCTA
1 TCCTA
346826 GACAAGTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.39, G:0.03, T:0.31
Consensus pattern (27 bp):
TCCTACTCAACCTCCATACCGATCATA
Found at i:349593 original size:127 final size:127
Alignment explanation
Indices: 349367--349618 Score: 459
Period size: 127 Copynumber: 2.0 Consensus size: 127
349357 AAATAACACC
*
349367 AAATTTAATTATTCAAATTATACAATTATGGTCGATGAGATGGTCCGGGATAATCTCCACAAGGA
1 AAATTTAATTATTCAAATTATACAATTATAGTCGATGAGATGGTCCGGGATAATCTCCACAAGGA
* * *
349432 GGATGTGAACTCGAGCCAAGCTGCTAGGTTATGGTAGGATATGATGGGTATGGAGGTTGAGT
66 GGATGGGAACTCGAGCCAAACTGCTAGGTCATGGTAGGATATGATGGGTATGGAGGTTGAGT
*
349494 AAATTTAATTATTCAAATTATACAATTATAGTCGATGAGATGGTCCGGGATAATCTCCACGAGGA
1 AAATTTAATTATTCAAATTATACAATTATAGTCGATGAGATGGTCCGGGATAATCTCCACAAGGA
349559 GGATGGGAACTCGAGCCAAACTGCTAGGTCATGGTAGGATATGATGGGTATGGAGGTTGA
66 GGATGGGAACTCGAGCCAAACTGCTAGGTCATGGTAGGATATGATGGGTATGGAGGTTGA
349619 ATAGGATATT
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 120 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (127 bp):
AAATTTAATTATTCAAATTATACAATTATAGTCGATGAGATGGTCCGGGATAATCTCCACAAGGA
GGATGGGAACTCGAGCCAAACTGCTAGGTCATGGTAGGATATGATGGGTATGGAGGTTGAGT
Found at i:355151 original size:32 final size:33
Alignment explanation
Indices: 355079--355153 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 33
355069 CTAAAGCACG
*
355079 TAGCGC-TTCCACGTGGGATATGCTAAGCCGCT
1 TAGCGCATTCCACGTGGGATACGCTAAGCCGCT
* * *
355111 AAGTGCATTCCACGT-GGATACGCTATG-CGCCT
1 TAGCGCATTCCACGTGGGATACGCTAAGCCG-CT
355143 TAGCGCATTCC
1 TAGCGCATTCC
355154 GTGGCATGCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 2 0.06
32 25 0.71
33 8 0.23
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.25
Consensus pattern (33 bp):
TAGCGCATTCCACGTGGGATACGCTAAGCCGCT
Found at i:356949 original size:23 final size:24
Alignment explanation
Indices: 356912--356958 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
356902 ATACCTAGAA
356912 ATTTTAGTCTTAATTTGAACTTTTT
1 ATTTTAGTCTTAATTT-AACTTTTT
*
356937 ATTTTA-T-TTAATTTTACTTTTT
1 ATTTTAGTCTTAATTTAACTTTTT
356959 TAGGTACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 7 0.33
24 1 0.05
25 6 0.29
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.66
Consensus pattern (24 bp):
ATTTTAGTCTTAATTTAACTTTTT
Found at i:360532 original size:33 final size:33
Alignment explanation
Indices: 360490--360554 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
360480 TACCACTGTT
* *
360490 TGTATCGATACATGGCACA-TTGTATCGATACAA
1 TGTATCGATACAT-GAAAAGTTGTATCGATACAA
*
360523 TGTATCGATATATGAAAAGTTGTATCGATACA
1 TGTATCGATACATGAAAAGTTGTATCGATACA
360555 TTGTCTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGAAAAGTTGTATCGATACAA
Found at i:369199 original size:13 final size:13
Alignment explanation
Indices: 369181--369206 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
369171 TATATCCAGA
369181 TATATCGATACAT
1 TATATCGATACAT
369194 TATATCGATACAT
1 TATATCGATACAT
369207 ACACAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:376480 original size:12 final size:12
Alignment explanation
Indices: 376465--376489 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
376455 TAAAAATTTT
376465 ATAAAAATAATA
1 ATAAAAATAATA
376477 ATAAAAATAATA
1 ATAAAAATAATA
376489 A
1 A
376490 AAATGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:376578 original size:14 final size:15
Alignment explanation
Indices: 376566--376684 Score: 100
Period size: 14 Copynumber: 8.5 Consensus size: 15
376556 ACATTTCATG
376566 CATGCATTTTCATTT
1 CATGCATTTTCATTT
376581 CATGCA-TTTCA---
1 CATGCATTTTCATTT
*
376592 CAT-AATTTTCATTT
1 CATGCATTTTCATTT
376606 CATGCA-TTTCATTTCAT
1 CATGCATTTTCA-TT--T
376623 GCATGCATTTTCATTT
1 -CATGCATTTTCATTT
376639 CATGCA-TTTCA---
1 CATGCATTTTCATTT
*
376650 CAT-AATTTTCATTT
1 CATGCATTTTCATTT
376664 CATGCA-TTTCATTT
1 CATGCATTTTCATTT
376678 CATGCAT
1 CATGCAT
376685 GCATTTCATA
Statistics
Matches: 84, Mismatches: 4, Indels: 32
0.70 0.03 0.27
Matches are distributed among these distances:
10 2 0.02
11 16 0.19
14 35 0.42
15 16 0.19
16 1 0.01
17 1 0.01
18 8 0.10
19 5 0.06
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (15 bp):
CATGCATTTTCATTT
Found at i:376626 original size:58 final size:58
Alignment explanation
Indices: 376557--376690 Score: 268
Period size: 58 Copynumber: 2.3 Consensus size: 58
376547 TTTCACGTAA
376557 CATTTCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATTT
1 CATTTCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATTT
376615 CATTTCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATTT
1 CATTTCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATTT
376673 CATTTCATGCATGCATTT
1 CATTTCATGCATGCATTT
376691 CATAAACATT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 76 1.00
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (58 bp):
CATTTCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATTT
Found at i:376660 original size:44 final size:44
Alignment explanation
Indices: 376612--376765 Score: 206
Period size: 44 Copynumber: 3.5 Consensus size: 44
376602 ATTTCATGCA
376612 TTTCATTTCATGCATGCATTTTCATTTCATGCATTTCACATAAT
1 TTTCATTTCATGCATGCATTTTCATTTCATGCATTTCACATAAT
* * * *
376656 TTTCATTTCATGCATTTCA-TTTCA-TGCATGCATTTCATA-AACA
1 TTTCATTTCATGCA-TGCATTTTCATTTCATGCATTTCACATAA-T
*
376699 TTTCAAGCTTCATGCATGCATTTTCATTTCATGCATTTCACATAAT
1 TTTC-A-TTTCATGCATGCATTTTCATTTCATGCATTTCACATAAT
376745 TTTCATTTCATGCATGCATTT
1 TTTCATTTCATGCATGCATTT
376766 CATAAACATT
Statistics
Matches: 93, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
42 2 0.02
43 17 0.18
44 38 0.41
45 17 0.18
46 17 0.18
47 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (44 bp):
TTTCATTTCATGCATGCATTTTCATTTCATGCATTTCACATAAT
Found at i:376733 original size:15 final size:15
Alignment explanation
Indices: 376713--376759 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 15
376703 AAGCTTCATG
376713 CATGCATTTTCATTT
1 CATGCATTTTCATTT
376728 CATGCA-TTTCA---
1 CATGCATTTTCATTT
*
376739 CAT-AATTTTCATTT
1 CATGCATTTTCATTT
376753 CATGCAT
1 CATGCAT
376760 GCATTTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
10 1 0.04
11 8 0.32
14 8 0.32
15 8 0.32
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (15 bp):
CATGCATTTTCATTT
Found at i:376737 original size:14 final size:14
Alignment explanation
Indices: 376557--376738 Score: 99
Period size: 14 Copynumber: 13.5 Consensus size: 14
376547 TTTCACGTAA
*
376557 CATTTCA-TGCATG
1 CATTTCATTTCATG
376570 CATTTTCATTTCATG
1 CA-TTTCATTTCATG
376585 CATTTCA---CAT-
1 CATTTCATTTCATG
*
376595 AATTTTCATTTCATG
1 CA-TTTCATTTCATG
376610 CATTTCATTTCATGCATG
1 CATTTCA-TT--T-CATG
376628 CATTTTCATTTCATG
1 CA-TTTCATTTCATG
376643 CATTTCA---CAT-
1 CATTTCATTTCATG
*
376653 AATTTTCATTTCATG
1 CA-TTTCATTTCATG
376668 CATTTCATTTCATG
1 CATTTCATTTCATG
*
376682 CA-TGCATTTCAT-
1 CATTTCATTTCATG
** *
376694 -A-AACATTTCAAG
1 CATTTCATTTCATG
*
376706 C--TTCA-TGCATG
1 CATTTCATTTCATG
376717 CATTTTCATTTCATG
1 CA-TTTCATTTCATG
376732 CATTTCA
1 CATTTCA
376739 CATAATTTTC
Statistics
Matches: 132, Mismatches: 14, Indels: 45
0.69 0.07 0.24
Matches are distributed among these distances:
10 2 0.02
11 29 0.22
12 2 0.02
13 11 0.08
14 49 0.37
15 24 0.18
16 1 0.01
17 1 0.01
18 8 0.06
19 5 0.04
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (14 bp):
CATTTCATTTCATG
Found at i:376762 original size:29 final size:30
Alignment explanation
Indices: 376728--376793 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
376718 ATTTTCATTT
*
376728 CATGCATTTCACATAA-TTTTCAT-TTCATG
1 CATGCATTTCACA-AACATTTCATCTTCATG
*
376757 CATGCATTTCATAAACATTTCATGCTTCATG
1 CATGCATTTCACAAACATTTCAT-CTTCATG
376788 CATGCA
1 CATGCA
376794 AATTTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.06
29 18 0.56
31 12 0.38
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (30 bp):
CATGCATTTCACAAACATTTCATCTTCATG
Found at i:376821 original size:75 final size:73
Alignment explanation
Indices: 376669--376825 Score: 237
Period size: 75 Copynumber: 2.1 Consensus size: 73
376659 CATTTCATGC
*
376669 ATTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATGCATGCATTTTCATTTCATGCA
1 ATTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATGCATGCATTTTCATTTCATACA
376734 TTTCACATA
66 -TTCACATA
*
376743 ATTTTCATTTCATGCATGCATTTCATAAACATTTCATGCTTCATGCATGCAAATTTTCATTTCAT
1 A-TTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATGCATGC--ATTTTCATTTCAT
376808 ACA-T-ACATGA
63 ACATTCACAT-A
376818 ATTTCATT
1 ATTTCATT
376826 GCATTTGCTT
Statistics
Matches: 77, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
74 12 0.16
75 50 0.65
77 15 0.19
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (73 bp):
ATTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATGCATGCATTTTCATTTCATACA
TTCACATA
Found at i:377249 original size:22 final size:22
Alignment explanation
Indices: 377222--377264 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
377212 AGTTTTCTTC
*
377222 CAGCTTTCACGGATAG-CTCCAG
1 CAGCTTCCACGG-TAGCCTCCAG
377244 CAGCTTCCACGGTAGCCTCCA
1 CAGCTTCCACGGTAGCCTCCA
377265 ATCCACGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.21, C:0.37, G:0.21, T:0.21
Consensus pattern (22 bp):
CAGCTTCCACGGTAGCCTCCAG
Found at i:377479 original size:22 final size:22
Alignment explanation
Indices: 377427--377481 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
377417 TCTAGCAAGT
* *
377427 TCTATCAGCTCCCACGACAGCC
1 TCTAACAGCTCCCACGACAACC
* *
377449 TCTAGCAGCTCCCACGGCAACC
1 TCTAACAGCTCCCACGACAACC
377471 T-TCAACAGCTC
1 TCT-AACAGCTC
377482 AGCAACCACG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.24, C:0.44, G:0.15, T:0.18
Consensus pattern (22 bp):
TCTAACAGCTCCCACGACAACC
Found at i:377528 original size:22 final size:22
Alignment explanation
Indices: 377503--377551 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
377493 ACAGCCCCCC
* *
377503 ACAGCTCCTACAGTAACTTCCA
1 ACAGCTCCCACAGCAACTTCCA
377525 ACAGCTCCCACAGCAACTTCCA
1 ACAGCTCCCACAGCAACTTCCA
377547 ACAGC
1 ACAGC
377552 GACGTAGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.41, G:0.10, T:0.16
Consensus pattern (22 bp):
ACAGCTCCCACAGCAACTTCCA
Done.