Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 8 of 17
Found at i:1095908 original size:32 final size:32
Alignment explanation
Indices: 1095064--1095888 Score: 1090
Period size: 32 Copynumber: 26.6 Consensus size: 32
1095054 AGTGGCATCT
* * *
1095064 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1095092 TTTCAAAGTCCACACAAGTTGGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1095122 TTTCAAAG-CC-CACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1095152 TTTCAAAG-CC-CACAACTCAGTGGC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1095180 TTTCAAAGCCCACACAAGTCGGTGG-TA-CTA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1095210 TTTCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1095242 TTTCAAATCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1095274 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1095306 TTTCAAAG-CC-CACAAGTCAGTGGC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1095334 TTTCAAAGCCCACACAAGTCAGTGAC-A-CTA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
**
1095364 TTTCAAAGCCCACGTAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1095396 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1095428 TTTTAAAGCCCACACAAGTTGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1095460 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1095492 TTTCAAAGCCCAAACAAGTCGATGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1095524 TTTCAAATCCCATACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1095556 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1095588 TTTTAAAG-CC-CACAAGTCAGTGGC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1095616 TTTCAAAGCCCACACAAGTCGGTGGC-A-CTA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
** *
1095646 TTTCAAAGCCCACGTAAGTCGGTGGTAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1095678 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1095710 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1095742 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1095774 TTTCAAAGCCCACACAAGTCGATGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1095806 TTTCAAACCCCACACAAGTCGGTGGTAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1095838 TTTCAAAGCCGACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1095870 TTTCAAAGCCCACACAAGT
1 TTTCAAAGCCCACACAAGT
1095889 TGATGGGGAC
Statistics
Matches: 712, Mismatches: 67, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
28 50 0.07
29 16 0.02
30 185 0.26
31 8 0.01
32 453 0.64
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:1096528 original size:20 final size:20
Alignment explanation
Indices: 1096500--1096574 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1096490 TTTTACCTTG
1096500 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1096520 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1096540 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1096560 ATGTATCGATACATT
1 ATGTATCGATACATT
1096575 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1096567 original size:40 final size:39
Alignment explanation
Indices: 1096500--1096577 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1096490 TTTTACCTTG
* *
1096500 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1096540 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1096578 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1100312 original size:21 final size:21
Alignment explanation
Indices: 1100286--1100338 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1100276 TCAATATATT
1100286 TAATTTTAATA-ATTATAAAA
1 TAATTTTAATATATTATAAAA
* * *
1100306 TATATTTTAAAATATTTTAAAT
1 TA-ATTTTAATATATTATAAAA
1100328 TAATTTTAATA
1 TAATTTTAATA
1100339 GTTTACTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.07
21 16 0.59
22 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTTTAATATATTATAAAA
Found at i:1100710 original size:2 final size:2
Alignment explanation
Indices: 1100703--1100731 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1100693 GCATCCTTCA
1100703 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
1100732 CTTCTTCAAT
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:1105420 original size:2 final size:2
Alignment explanation
Indices: 1105413--1105441 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1105403 GAAAATGAAT
1105413 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 T
1105442 CTTGTTGATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1106945 original size:22 final size:21
Alignment explanation
Indices: 1106917--1106963 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1106907 TGAATGTTAG
1106917 AGATGATCTTTAAAATTTTTAA
1 AGATGAT-TTTAAAATTTTTAA
** *
1106939 AGATGATTTTTTATTTTTTAA
1 AGATGATTTTAAAATTTTTAA
1106960 AGAT
1 AGAT
1106964 AATTATTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (21 bp):
AGATGATTTTAAAATTTTTAA
Found at i:1110882 original size:22 final size:22
Alignment explanation
Indices: 1110817--1110883 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 22
1110807 TTTTCTATGG
* *
1110817 TAAATCTTATTACTATTTATAATA
1 TAAATATTATTACTA--TATAAAA
* **
1110841 TAAAATATTAATAAGA-ATAAAA
1 T-AAATATTATTACTATATAAAA
1110863 TAAATATTATTACTATATAAA
1 TAAATATTATTACTATATAAA
1110884 TAATTGGAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
21 11 0.33
22 11 0.33
24 1 0.03
25 10 0.30
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (22 bp):
TAAATATTATTACTATATAAAA
Found at i:1113489 original size:22 final size:22
Alignment explanation
Indices: 1113462--1113503 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1113452 TATTAAAAAT
1113462 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1113484 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1113504 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1114650 original size:29 final size:30
Alignment explanation
Indices: 1114613--1114670 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1114603 ATTAAAAGAT
1114613 AATTATTAAAAATT-ATTTTTTATCTTTAA
1 AATTATTAAAAATTAATTTTTTATCTTTAA
* *
1114642 AATTTTTAAAAATTAATTTTTTATTTTTA
1 AATTATTAAAAATTAATTTTTTATCTTTA
1114671 GTGATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (30 bp):
AATTATTAAAAATTAATTTTTTATCTTTAA
Found at i:1116859 original size:32 final size:33
Alignment explanation
Indices: 1116818--1116881 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
1116808 AGTAGCTTAA
1116818 ATTGTATCGATACAAAAC-TTATGTATCGATAT
1 ATTGTATCGATACAAAACTTTATGTATCGATAT
*
1116850 ATTGTATCGATACAACACTTTATGTATCGATA
1 ATTGTATCGATACAAAACTTTATGTATCGATA
1116882 CAAATCGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAT
Found at i:1119002 original size:21 final size:22
Alignment explanation
Indices: 1118958--1119013 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
1118948 TCATATATTT
1118958 TAAAAT-TT-TATATTTATATA
1 TAAAATATTATATATTTATATA
*
1118978 TAAAATATTATATATTT-TTTA
1 TAAAATATTATATATTTATATA
1118999 T-AAATATTAATATAT
1 TAAAATATT-ATATAT
1119014 CGATAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 13 0.41
21 12 0.38
22 7 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAAAATATTATATATTTATATA
Found at i:1119510 original size:19 final size:19
Alignment explanation
Indices: 1119487--1119524 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1119477 TAGTTTTTAA
1119487 AAAAATGTGAATTTTTTTTG
1 AAAAA-GTGAATTTTTTTTG
*
1119507 AAAAAGTTAATTTTTTTT
1 AAAAAGTGAATTTTTTTT
1119525 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (19 bp):
AAAAAGTGAATTTTTTTTG
Found at i:1119754 original size:22 final size:22
Alignment explanation
Indices: 1119729--1119787 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
1119719 TACTATTTAT
1119729 TATTAAAAATTAATTAT-ATAAA
1 TATTAAAAATT-ATTATAATAAA
* *
1119751 TATTTTAAAATT-TTATAATAAT
1 TA-TTAAAAATTATTATAATAAA
1119773 TATTAAAATATTATT
1 TATTAAAA-ATTATT
1119788 TTACAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
21 9 0.30
22 11 0.37
23 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTAAAAATTATTATAATAAA
Found at i:1119843 original size:14 final size:13
Alignment explanation
Indices: 1119818--1119931 Score: 51
Period size: 13 Copynumber: 8.6 Consensus size: 13
1119808 TATTGAGATA
1119818 AATATTAAATATT
1 AATATTAAATATT
1119831 AATATTAAAATATT
1 AATATT-AAATATT
*
1119845 AA-A--AACTATT
1 AATATTAAATATT
*
1119855 TATCATTAAACTATT
1 AAT-ATTAAA-TATT
* *
1119870 AATTTTCAATATT
1 AATATTAAATATT
*
1119883 AA-ATTGCAATATTTT
1 AATATT--AA-ATATT
*
1119898 AATAAT-AATATTT
1 AATATTAAATA-TT
*
1119911 AATGATAAAATATT
1 AAT-ATTAAATATT
1119925 -ATATTAA
1 AATATTAA
1119932 TACTAAATAT
Statistics
Matches: 74, Mismatches: 14, Indels: 27
0.64 0.12 0.23
Matches are distributed among these distances:
10 7 0.09
12 9 0.12
13 21 0.28
14 19 0.26
15 16 0.22
16 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (13 bp):
AATATTAAATATT
Found at i:1120207 original size:21 final size:22
Alignment explanation
Indices: 1120175--1120217 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
1120165 TTACAATTTA
1120175 TTATTAAAATAATATTTTTATT
1 TTATTAAAATAATATTTTTATT
1120197 TTATT-AAATAATATTTTTATT
1 TTATTAAAATAATATTTTTATT
1120218 AAAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTAAAATAATATTTTTATT
Found at i:1120216 original size:16 final size:17
Alignment explanation
Indices: 1120170--1120226 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 17
1120160 TAATGTTACA
1120170 ATTTATTATTAAAATAAT
1 ATTT-TTATTAAAATAAT
1120188 ATTTTTATTTTATTAAATAAT
1 ATTTTTA--TTA--AAATAAT
1120209 ATTTTTATTAAAATAAT
1 ATTTTTATTAAAATAAT
1120226 A
1 A
1120227 AATTAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 11 0.31
18 4 0.11
19 6 0.17
21 14 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTTATTAAAATAAT
Found at i:1120339 original size:177 final size:175
Alignment explanation
Indices: 1120099--1120420 Score: 529
Period size: 177 Copynumber: 1.8 Consensus size: 175
1120089 TTATTTAAAT
* *
1120099 AGTCATATAAAAATATTTTTCAAAAAATATTAAAAATACTGTTCTAAATTTAAAATATTGATAAT
1 AGTCATATAAAAATATTTTTCAAAAAATATAAAAAATACTATTCTAAATTTAAAATATTGATAAT
* * * *
1120164 GTTACAATTTATTATTAAAATAATATTTTTATTTTATTAAATAATATTTTTATTAAAATAATAAA
66 GTTACAACTTATTATTAAAATAATAATATTATTTTATTAAATAATATTATTATTAAAATAATAAA
*
1120229 TTAAAAATTCAATTTCAATTATTTAGTGTCTGACGTATTGAAAAA
131 TAAAAAATTCAATTTCAATTATTTAGTGTCTGACGTATTGAAAAA
*
1120274 AGTCATA-GAAAATATTTTTCAAAAAAATTATAAAAAATTACTATTCTAAATTTAAAATATTGAT
1 AGTCATATAAAAATATTTTTC-AAAAAA-TATAAAAAA-TACTATTCTAAATTTAAAATATTGAT
*
1120338 AATGTTACAACTTATTATTGAAATAATAATATTATTTTATTAAATAATATTATTATTAAAATAAT
63 AATGTTACAACTTATTATTAAAATAATAATATTATTTTATTAAATAATATTATTATTAAAATAAT
1120403 AAATAAAAAATTCAATTT
128 AAATAAAAAATTCAATTT
1120421 TAATAATAAT
Statistics
Matches: 135, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
174 12 0.09
175 13 0.10
176 8 0.06
177 102 0.76
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.42
Consensus pattern (175 bp):
AGTCATATAAAAATATTTTTCAAAAAATATAAAAAATACTATTCTAAATTTAAAATATTGATAAT
GTTACAACTTATTATTAAAATAATAATATTATTTTATTAAATAATATTATTATTAAAATAATAAA
TAAAAAATTCAATTTCAATTATTTAGTGTCTGACGTATTGAAAAA
Found at i:1120383 original size:21 final size:22
Alignment explanation
Indices: 1120352--1120394 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1120342 TTACAACTTA
1120352 TTATTGAAATAATAATATTATT
1 TTATTGAAATAATAATATTATT
*
1120374 TTATT-AAATAATATTATTATT
1 TTATTGAAATAATAATATTATT
1120395 AAAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATTGAAATAATAATATTATT
Found at i:1120407 original size:21 final size:20
Alignment explanation
Indices: 1120349--1120404 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 20
1120339 ATGTTACAAC
*
1120349 TTATTATTGAAATAATAATA
1 TTATTATTAAAATAATAATA
**
1120369 TTATT-TTATTA-AATAATA
1 TTATTATTAAAATAATAATA
1120387 TTATTATTAAAATAATAA
1 TTATTATTAAAATAATAA
1120405 ATAAAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 12 0.41
19 7 0.24
20 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTATTATTAAAATAATAATA
Found at i:1120822 original size:17 final size:18
Alignment explanation
Indices: 1120800--1120833 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1120790 AATAACATAA
1120800 TATTTTTTA-AAATTTAT
1 TATTTTTTATAAATTTAT
1120817 TATTTTTTATAAATTTA
1 TATTTTTTATAAATTTA
1120834 AATTTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTTTTATAAATTTAT
Found at i:1120838 original size:17 final size:17
Alignment explanation
Indices: 1120801--1120839 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1120791 ATAACATAAT
*
1120801 ATTTTTTAAAATTTATT
1 ATTTTTTAAAATTTATA
1120818 ATTTTTTATAAATTTA-A
1 ATTTTTTA-AAATTTATA
1120835 ATTTT
1 ATTTT
1120840 AAATTATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTTAAAATTTATA
Found at i:1121836 original size:2 final size:2
Alignment explanation
Indices: 1121829--1121858 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1121819 CCACTTTTTA
1121829 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
1121859 TTAAAAAAAT
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:1125598 original size:8 final size:8
Alignment explanation
Indices: 1125587--1125619 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
1125577 ATAATAATTT
1125587 TATTTTAA
1 TATTTTAA
1125595 TATTTTAA
1 TATTTTAA
1125603 TATTTTAA
1 TATTTTAA
1125611 TATCTTTAA
1 TAT-TTTAA
1125620 ATTAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.79
9 5 0.21
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTTAA
Found at i:1130058 original size:2 final size:2
Alignment explanation
Indices: 1130051--1130081 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1130041 GATTTTCAAA
*
1130051 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1130082 AATAACAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1130881 original size:15 final size:16
Alignment explanation
Indices: 1130856--1130885 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1130846 ATTCATTCTT
1130856 TTTTATTTATTTTTTA
1 TTTTATTTATTTTTTA
1130872 TTTT-TTTATTTTTT
1 TTTTATTTATTTTTT
1130886 CAAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTATTTATTTTTTA
Found at i:1133056 original size:20 final size:21
Alignment explanation
Indices: 1133018--1133066 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1133008 ATTTAATTAA
1133018 TAATTTAAATTAAATTAAA-T
1 TAATTTAAATTAAATTAAACT
*
1133038 TAATTTAAATTATCA-TAAACT
1 TAATTTAAATTA-AATTAAACT
1133059 T-ATTTAAA
1 TAATTTAAA
1133067 ACTCGATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATTTAAATTAAATTAAACT
Found at i:1133472 original size:21 final size:21
Alignment explanation
Indices: 1133448--1133503 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1133438 AATAAAAACC
1133448 ATAATTATTATTTAAATATTA
1 ATAATTATTATTTAAATATTA
** **
1133469 ATAAAAATTATTTTTATATTA
1 ATAATTATTATTTAAATATTA
*
1133490 ATAGTTATATATTT
1 ATAATTAT-TATTT
1133504 TATAATTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
ATAATTATTATTTAAATATTA
Found at i:1133754 original size:2 final size:2
Alignment explanation
Indices: 1133747--1133777 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1133737 TTGGGTCCTT
1133747 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 T
1133778 GTTTGTATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1136238 original size:1 final size:1
Alignment explanation
Indices: 1136232--1136256 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1136222 ATTAGAGGCT
1136232 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1136257 AAGAAATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1137090 original size:2 final size:2
Alignment explanation
Indices: 1137083--1137107 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1137073 TATTGTTCTT
1137083 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 T
1137108 TAATGGGGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1139299 original size:26 final size:26
Alignment explanation
Indices: 1139259--1139326 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
1139249 TTTATTTTGA
* * *
1139259 AACACAATATACTTCGTTCTCGCTGC
1 AACACAAAATGCTTCGTTCTCGCTAC
* *
1139285 AACACAAAATGCTTCATTCTGGCTAC
1 AACACAAAATGCTTCGTTCTCGCTAC
**
1139311 AATGCAAAATGCTTCG
1 AACACAAAATGCTTCG
1139327 AAAAAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (26 bp):
AACACAAAATGCTTCGTTCTCGCTAC
Found at i:1140433 original size:2 final size:2
Alignment explanation
Indices: 1140426--1140453 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1140416 CATAAAATGT
1140426 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
1140454 GAAGTTTAGA
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:1147682 original size:2 final size:2
Alignment explanation
Indices: 1147675--1147707 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1147665 GTGGAATATA
1147675 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1147708 TAGTAGTTGA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1149723 original size:3 final size:3
Alignment explanation
Indices: 1149715--1149740 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1149705 GTTAAAGCAC
1149715 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
1149741 ATGTAAGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:1153322 original size:18 final size:18
Alignment explanation
Indices: 1153299--1153336 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1153289 GAATTTTATT
**
1153299 TTTAAAATTTAAATTTAA
1 TTTAAAATAAAAATTTAA
1153317 TTTAAAATAAAAATTTAA
1 TTTAAAATAAAAATTTAA
1153335 TT
1 TT
1153337 GATTAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAAATAAAAATTTAA
Found at i:1153470 original size:26 final size:26
Alignment explanation
Indices: 1153418--1153473 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1153408 TCGGTTATTT
* * *
1153418 ATTTTTAATTTAAGTTTAAATTGAAA
1 ATTTTTAATTTAAGTTAAAAATAAAA
1153444 ATTTTTAATATTAA-TTAAAAATAAAA
1 ATTTTTAAT-TTAAGTTAAAAATAAAA
1153470 ATTT
1 ATTT
1153474 AGACTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
ATTTTTAATTTAAGTTAAAAATAAAA
Found at i:1153732 original size:17 final size:17
Alignment explanation
Indices: 1153710--1153743 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1153700 AAATGGCGAC
1153710 AATAATACAATATTACA
1 AATAATACAATATTACA
*
1153727 AATAATATAATATTACA
1 AATAATACAATATTACA
1153744 TAATTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATACAATATTACA
Found at i:1153785 original size:17 final size:16
Alignment explanation
Indices: 1153759--1153800 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1153749 ATTTTAAAAA
1153759 TTTTGAATTTATTTATT
1 TTTTGAATTTA-TTATT
*
1153776 TTTTGCATTTATTATT
1 TTTTGAATTTATTATT
*
1153792 TTTTTAATT
1 TTTTGAATT
1153801 ACAATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (16 bp):
TTTTGAATTTATTATT
Found at i:1155589 original size:2 final size:2
Alignment explanation
Indices: 1155582--1155625 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1155572 TGATCTAATC
1155582 AT 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 AT
1155624 AT
1 AT
1155626 GCATGCATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1156207 original size:22 final size:21
Alignment explanation
Indices: 1156179--1156220 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1156169 GATTAGATAT
1156179 TTATATTATACATCAATTTATC
1 TTATATTATACAT-AATTTATC
*
1156201 TTATATTTTACATAATTTAT
1 TTATATTATACATAATTTAT
1156221 TATAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATATTATACATAATTTATC
Found at i:1156593 original size:3 final size:3
Alignment explanation
Indices: 1156585--1156614 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1156575 AGCATTTATC
1156585 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1156615 AAGCAACTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1157837 original size:13 final size:13
Alignment explanation
Indices: 1157810--1157847 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1157800 TATATATATG
*
1157810 AATAAAAT-ATGA
1 AATAAAATAATTA
1157822 AATAAAATAATTA
1 AATAAAATAATTA
*
1157835 AATTAAATAATTA
1 AATAAAATAATTA
1157848 TAAATAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (13 bp):
AATAAAATAATTA
Found at i:1158953 original size:12 final size:12
Alignment explanation
Indices: 1158936--1158960 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1158926 TAGGCGTTGA
1158936 TTAGTGAAAATT
1 TTAGTGAAAATT
1158948 TTAGTGAAAATT
1 TTAGTGAAAATT
1158960 T
1 T
1158961 AAGTTTCAAC
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TTAGTGAAAATT
Found at i:1159790 original size:20 final size:20
Alignment explanation
Indices: 1159762--1159799 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1159752 TAAAATTTTA
*
1159762 ATAT-TTTTTATTTTTAAACT
1 ATATATTTTT-TTTGTAAACT
1159782 ATATATTTTTTTTGTAAA
1 ATATATTTTTTTTGTAAA
1159800 AAAAACATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
ATATATTTTTTTTGTAAACT
Found at i:1161347 original size:2 final size:2
Alignment explanation
Indices: 1161340--1161366 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1161330 TCACGAGATC
1161340 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
1161367 CGATAACTTT
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:1162203 original size:13 final size:13
Alignment explanation
Indices: 1162185--1162209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1162175 ATGATAAATT
1162185 TTTAAATTTAAAG
1 TTTAAATTTAAAG
1162198 TTTAAATTTAAA
1 TTTAAATTTAAA
1162210 ACTCACACTC
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTAAATTTAAAG
Found at i:1162432 original size:24 final size:24
Alignment explanation
Indices: 1162404--1162459 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1162394 TTAAATAAAA
* *
1162404 TAATTTTTTTATTTTTTTA-TTTT
1 TAATTTTTTTATTTATTTACATTT
*
1162427 TAAATTTATTTATTTATTTACATTT
1 T-AATTTTTTTATTTATTTACATTT
1162452 TAATTTTT
1 TAATTTTT
1162460 CACTATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 1 0.04
24 22 0.81
25 4 0.15
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (24 bp):
TAATTTTTTTATTTATTTACATTT
Found at i:1162662 original size:17 final size:16
Alignment explanation
Indices: 1162640--1162687 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
1162630 AAAAATTTAA
1162640 AATTTAATATAAAATAT
1 AATTTAATATAAAA-AT
1162657 AATTTAATATAAAAAT
1 AATTTAATATAAAAAT
1162673 AA-TTAA-A-AAAAAT
1 AATTTAATATAAAAAT
1162686 AA
1 AA
1162688 AATACAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.26
14 1 0.03
15 4 0.13
16 4 0.13
17 14 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTTAATATAAAAAT
Found at i:1162749 original size:41 final size:39
Alignment explanation
Indices: 1162628--1162752 Score: 96
Period size: 41 Copynumber: 3.1 Consensus size: 39
1162618 ATTAACGAAG
1162628 TAAAA-AATTTAAAATTTAATATAAA-ATATAATTTAATATA
1 TAAAATAA-TTAAAATTT-ATATAAATATATAA-TTAATATA
*** * * *
1162668 -AAAATAATTAAAAAAAATA-AAATACAACAATTTATAATA
1 TAAAATAATTAAAATTTATATAAATA-TATAATTAAT-ATA
*
1162707 TATAAATTATTAAAATTTATATAAATATATAATATAATATA
1 TA-AAATAATTAAAATTTATATAAATATATAAT-TAATATA
1162748 TAAAA
1 TAAAA
1162753 ATATATACAC
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
37 3 0.05
38 8 0.12
39 16 0.25
40 6 0.09
41 23 0.36
42 8 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (39 bp):
TAAAATAATTAAAATTTATATAAATATATAATTAATATA
Found at i:1162755 original size:10 final size:10
Alignment explanation
Indices: 1162704--1162759 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
1162694 ACAATTTATA
*
1162704 ATATATAAAT
1 ATATAAAAAT
*
1162714 -TATTAAAAT
1 ATATAAAAAT
* *
1162723 TTATATAAAT
1 ATATAAAAAT
1162733 ATATAATATAAT
1 ATATAA-A-AAT
1162745 ATATAAAAAT
1 ATATAAAAAT
1162755 ATATA
1 ATATA
1162760 CACGCAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 7 0.19
10 19 0.51
11 2 0.05
12 9 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:1163030 original size:16 final size:16
Alignment explanation
Indices: 1163006--1163059 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
1162996 ATAAAATAAA
*
1163006 AATTTAATTTATATTT
1 AATTAAATTTATATTT
1163022 AATTAAATTT-TA-TT
1 AATTAAATTTATATTT
1163036 --TTAAATTTATATTT
1 AATTAAATTTATATTT
*
1163050 AAATAAATTT
1 AATTAAATTT
1163060 TTAACGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 8 0.25
13 2 0.06
14 4 0.12
15 2 0.06
16 16 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTAAATTTATATTT
Found at i:1163062 original size:18 final size:18
Alignment explanation
Indices: 1163041--1163083 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1163031 TTATTTTAAA
1163041 TTTATATTTAAATAAATT
1 TTTATATTTAAATAAATT
**
1163059 TTTA-ACGTAAATAAATT
1 TTTATATTTAAATAAATT
1163076 TTT-TATTT
1 TTTATATTT
1163084 TAAGTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTATATTTAAATAAATT
Found at i:1163254 original size:18 final size:17
Alignment explanation
Indices: 1163216--1163253 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1163206 AGGTTGATAG
*
1163216 TTTTGAATTGAGTTTAA
1 TTTTGAATTGAGCTTAA
1163233 TTTTGAAATT-AGCTTAA
1 TTTTG-AATTGAGCTTAA
1163250 TTTT
1 TTTT
1163254 TTATTATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (17 bp):
TTTTGAATTGAGCTTAA
Found at i:1169116 original size:21 final size:20
Alignment explanation
Indices: 1169086--1169126 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1169076 TGTTTAAAGA
1169086 AAATTATAAATTAATTGAATT
1 AAATTATAAATTAATT-AATT
* *
1169107 AAATTCTAAATTTATTAATT
1 AAATTATAAATTAATTAATT
1169127 TTTTCTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
AAATTATAAATTAATTAATT
Found at i:1169616 original size:3 final size:3
Alignment explanation
Indices: 1169608--1169644 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1169598 ATCTATAACC
1169608 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1169645 GAATGATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1169952 original size:23 final size:22
Alignment explanation
Indices: 1169926--1169991 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
1169916 TTTTTATAAT
1169926 ATAAATAAAATTATATTTATATA
1 ATAAATAAAATTATA-TTATATA
* * *
1169949 ATAATTTAAAAATATATAATATA
1 ATAA-ATAAAATTATATTATATA
* *
1169972 ATATAT-AATTTATATTATAT
1 ATAAATAAAATTATATTATAT
1169992 TATATTATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 11 0.32
22 1 0.03
23 13 0.38
24 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATAAAATTATATTATATA
Found at i:1170332 original size:10 final size:10
Alignment explanation
Indices: 1170313--1170349 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1170303 TTTTACTATC
1170313 AAAAGAAAAT
1 AAAAGAAAAT
*
1170323 AAAAGGAAAT
1 AAAAGAAAAT
*
1170333 AAAATAAAAT
1 AAAAGAAAAT
1170343 AAAAGAA
1 AAAAGAA
1170350 GTCCTTCGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:1170515 original size:2 final size:2
Alignment explanation
Indices: 1170508--1170546 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1170498 TTATACTTAT
* *
1170508 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1170547 GTAAAGTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1170853 original size:28 final size:28
Alignment explanation
Indices: 1170773--1170856 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 28
1170763 ATCAATAAGC
* *
1170773 TTTTATTAATATTTTGTTTTTATTTATTAT
1 TTTTATTAA-ATTTT-TTTTTATTCATAAT
* *
1170803 TTTTA-AAAATTATATTTATTATTCATAAT
1 TTTTATTAAATT-T-TTTTTTATTCATAAT
1170832 TTTTATTAAATTTTTTTTTATTCAT
1 TTTTATTAAATTTTTTTTTATTCAT
1170857 GACTTTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
28 14 0.31
29 20 0.44
30 11 0.24
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (28 bp):
TTTTATTAAATTTTTTTTTATTCATAAT
Found at i:1170863 original size:28 final size:28
Alignment explanation
Indices: 1170767--1170864 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 28
1170757 CTAATGATCA
*
1170767 ATAAGCTTTTATTAATATTTTGTTTTTATTT
1 ATAA-CTTTTATTAA-ATTTT-TTTTTATTC
* * * *
1170798 ATTATTTTTA-AAAATTATATTTATTATTC
1 ATAACTTTTATTAAATT-T-TTTTTTATTC
*
1170827 ATAATTTTTATTAAATTTTTTTTTATTC
1 ATAACTTTTATTAAATTTTTTTTTATTC
*
1170855 ATGACTTTTA
1 ATAACTTTTA
1170865 AAAGTTAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
28 20 0.37
29 20 0.37
30 11 0.20
31 3 0.06
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (28 bp):
ATAACTTTTATTAAATTTTTTTTTATTC
Found at i:1170866 original size:57 final size:60
Alignment explanation
Indices: 1170773--1170886 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 60
1170763 ATCAATAAGC
* * * *
1170773 TTTTATTAATATTTTGTTTTTATTTATTATTTTTAAAAATTATATTTATT-ATTCATAAT
1 TTTTATTAATATTTTGTTTTTATTCATGACTTTTAAAAATTAAATTTATTCATTCATAAT
*
1170832 TTTTATTAA-ATTTT-TTTTTATTCATGACTTTTAAAAGTTAAATTTATTCATTCAT
1 TTTTATTAATATTTTGTTTTTATTCATGACTTTTAAAAATTAAATTTATTCATTCAT
1170887 GACCTTTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 29 0.59
58 11 0.22
59 9 0.18
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (60 bp):
TTTTATTAATATTTTGTTTTTATTCATGACTTTTAAAAATTAAATTTATTCATTCATAAT
Found at i:1170907 original size:30 final size:30
Alignment explanation
Indices: 1170851--1170907 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1170841 ATTTTTTTTT
* * *
1170851 ATTCATGACTTTTAAAAGTTAAATTTATTC
1 ATTCATGACCTTTAAAAATCAAATTTATTC
*
1170881 ATTCATGACCTTTAAAAATCATATTTA
1 ATTCATGACCTTTAAAAATCAAATTTA
1170908 CCATTTACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (30 bp):
ATTCATGACCTTTAAAAATCAAATTTATTC
Found at i:1171618 original size:16 final size:14
Alignment explanation
Indices: 1171599--1171650 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1171589 ATTTATTGAC
1171599 ATTAATATTAAAAATT
1 ATTAATATT-AAAA-T
1171615 ATTAAT-TTAAAAT
1 ATTAATATTAAAAT
**
1171628 ATTAATATTTTAAT
1 ATTAATATTAAAAT
*
1171642 AGTAATATT
1 ATTAATATT
1171651 CAATACGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 7 0.22
14 17 0.53
15 2 0.06
16 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTAATATTAAAAT
Found at i:1171717 original size:20 final size:19
Alignment explanation
Indices: 1171692--1171742 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1171682 TTAAAATAAT
1171692 AATATTATTATAAATATTGA
1 AATATTATTATAAATATT-A
* *
1171712 AATATTATGATAATTATTA
1 AATATTATTATAAATATTA
* *
1171731 AAAAATATTATA
1 AATATTATTATA
1171743 TTCATATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
AATATTATTATAAATATTA
Found at i:1171782 original size:27 final size:25
Alignment explanation
Indices: 1171721--1171784 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 25
1171711 AAATATTATG
1171721 ATAATTATTAAAAAATATTATATTC
1 ATAATTATTAAAAAATATTATATTC
*
1171746 AT-ATTTTTAAATAGAA-A-TATATTGAC
1 ATAATTATTAAA-A-AATATTATATT--C
1171772 ATAATTATTAAAA
1 ATAATTATTAAAA
1171785 TATTAAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
24 14 0.44
25 4 0.12
26 6 0.19
27 8 0.25
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (25 bp):
ATAATTATTAAAAAATATTATATTC
Found at i:1171866 original size:45 final size:43
Alignment explanation
Indices: 1171817--1171906 Score: 101
Period size: 44 Copynumber: 2.0 Consensus size: 43
1171807 ACTACTAATT
* * *
1171817 TTAATTATTAATAT-TTCAAATAATAATATCTACTAAAATATTATA
1 TTAA-TATTAA-ATCTTAAAATAATAATAT-TACAAAAAAATTATA
*
1171862 TTAATATTAAATGCTTAAAATAATACTATTACAAAAAAATTATA
1 TTAATATTAAAT-CTTAAAATAATAATATTACAAAAAAATTATA
1171906 T
1 T
1171907 ATAAATGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
43 2 0.05
44 20 0.51
45 17 0.44
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (43 bp):
TTAATATTAAATCTTAAAATAATAATATTACAAAAAAATTATA
Found at i:1172177 original size:15 final size:15
Alignment explanation
Indices: 1172138--1172233 Score: 76
Period size: 15 Copynumber: 6.4 Consensus size: 15
1172128 AATAATTTAT
*
1172138 TATTAAAATA-GTAA
1 TATTAAAATATATAA
*
1172152 TATTTATAATATATAA
1 TA-TTAAAATATATAA
1172168 TATTAAAATATA-AA
1 TATTAAAATATATAA
**
1172182 TATATATCCATA-ATAA
1 TAT-TA-AAATATATAA
1172198 TATTTAAAATATA-AA
1 TA-TTAAAATATATAA
1172213 TATTAAAA-ATTATAA
1 TATTAAAATA-TATAA
1172228 TATTAA
1 TATTAA
1172234 TATAATTTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
13 1 0.02
14 15 0.23
15 34 0.52
16 15 0.23
17 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (15 bp):
TATTAAAATATATAA
Found at i:1172184 original size:30 final size:30
Alignment explanation
Indices: 1172138--1172233 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
1172128 AATAATTTAT
1172138 TATTAAAATAGT-AATATTTATAATATATAA
1 TATTAAAATA-TAAATATTTATAATATATAA
* *
1172168 TATTAAAATATAAATATATATCCATA-ATAA
1 TATTAAAATATAAATATTTAT-AATATATAA
* *
1172198 TATTTAAAATATAAATATTAAAAAT-TATAA
1 TA-TTAAAATATAAATATTTATAATATATAA
1172228 TATTAA
1 TATTAA
1172234 TATAATTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
29 5 0.09
30 32 0.57
31 19 0.34
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (30 bp):
TATTAAAATATAAATATTTATAATATATAA
Found at i:1172229 original size:21 final size:21
Alignment explanation
Indices: 1172155--1172236 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 21
1172145 ATAGTAATAT
1172155 TTATAATATATAATATTAAAATA
1 TTATAATATA-AATATTAAAA-A
* ** * * *
1172178 TAAATATATATCCATAATAATAT
1 T-TATA-ATATAAATATTAAAAA
*
1172201 TTAAAATATAAATATTAAAAA
1 TTATAATATAAATATTAAAAA
*
1172222 TTATAATATTAATAT
1 TTATAATATAAATAT
1172237 AATTTTAGAT
Statistics
Matches: 42, Mismatches: 15, Indels: 6
0.67 0.24 0.10
Matches are distributed among these distances:
21 24 0.57
22 2 0.05
23 2 0.05
24 10 0.24
25 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTATAATATAAATATTAAAAA
Found at i:1173195 original size:14 final size:15
Alignment explanation
Indices: 1173176--1173213 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1173166 CTTAAACAGT
*
1173176 AAAATAAATGTAT-A
1 AAAATAAATATATCA
1173190 AAAAT-AATATATCA
1 AAAATAAATATATCA
1173204 AAAATAAATA
1 AAAATAAATA
1173214 ATTCTTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 6 0.29
14 11 0.52
15 4 0.19
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (15 bp):
AAAATAAATATATCA
Found at i:1173626 original size:19 final size:19
Alignment explanation
Indices: 1173589--1173627 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1173579 TGATTTAACA
*
1173589 TTTATTATGAGCTTTTGAT
1 TTTATTATGAGCTTATGAT
1173608 TTTATTTATGAG-TTATGAT
1 TTTA-TTATGAGCTTATGAT
1173627 T
1 T
1173628 AATTAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.59
Consensus pattern (19 bp):
TTTATTATGAGCTTATGAT
Found at i:1183531 original size:26 final size:26
Alignment explanation
Indices: 1183502--1183562 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
1183492 TGGTGCGAAT
*
1183502 AAAATCTTATACAAGTATCTGCAGAA
1 AAAATCTCATACAAGTATCTGCAGAA
1183528 AAAATCTCATACAAGTATCTGCAGAA
1 AAAATCTCATACAAGTATCTGCAGAA
1183554 AAAATCTCA
1 AAAATCTCA
1183563 GACCTAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.25
Consensus pattern (26 bp):
AAAATCTCATACAAGTATCTGCAGAA
Found at i:1186533 original size:23 final size:24
Alignment explanation
Indices: 1186489--1186533 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1186479 AACTTAATTT
*
1186489 TATACGTTATAATTTATAAATAAA
1 TATACGTTATAATTGATAAATAAA
* *
1186513 TATAC-TTATTATTGATCAATA
1 TATACGTTATAATTGATAAATA
1186534 GACTATATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (24 bp):
TATACGTTATAATTGATAAATAAA
Found at i:1186626 original size:8 final size:8
Alignment explanation
Indices: 1186615--1186694 Score: 54
Period size: 8 Copynumber: 9.4 Consensus size: 8
1186605 TTTAATTTTG
1186615 AAAATATA
1 AAAATATA
1186623 AAAATTATA
1 AAAA-TATA
1186632 AAAATATA
1 AAAATATA
*
1186640 AAAATTAGA
1 AAAA-TATA
*
1186649 AATTAATTTA
1 AA--AATATA
1186659 AAAATA-A
1 AAAATATA
*
1186666 AATAAGTAAA
1 AA-AA-TATA
*
1186676 AAAATTTA
1 AAAATATA
*
1186684 AAAATTTA
1 AAAATATA
1186692 AAA
1 AAA
1186695 TTTTATAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
7 3 0.05
8 30 0.51
9 17 0.29
10 7 0.12
11 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (8 bp):
AAAATATA
Found at i:1186628 original size:17 final size:17
Alignment explanation
Indices: 1186615--1186694 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 17
1186605 TTTAATTTTG
1186615 AAAATATAAAAATTATA
1 AAAATATAAAAATTATA
*
1186632 AAAATATAAAAATTAGA
1 AAAATATAAAAATTATA
*
1186649 AATTAATTTAAAAA-TA-A
1 AA--AATATAAAAATTATA
*
1186666 AATAAGTAAAAAAATT-TA
1 AA-AA-TATAAAAATTATA
*
1186684 AAAATTTAAAA
1 AAAATATAAAA
1186695 TTTTATAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
16 8 0.15
17 29 0.56
18 6 0.12
19 9 0.17
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATATAAAAATTATA
Found at i:1186696 original size:44 final size:45
Alignment explanation
Indices: 1186599--1186696 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 45
1186589 TATATTTATT
* * * *
1186599 TTTAAATTTAATTTTGAAAATATAAAAATTATAAAAATATAAAAA
1 TTTAAAATTAATTTTAAAAATATAAAAAGTAAAAAAATATAAAAA
*
1186644 -TTAGAAATTAA-TTTAAAAATA-AAATAAGTAAAAAAATTTAAAAA
1 TTTA-AAATTAATTTTAAAAATATAAA-AAGTAAAAAAATATAAAAA
1186688 TTTAAAATT
1 TTTAAAATT
1186697 TTATAATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
43 3 0.07
44 33 0.73
45 9 0.20
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (45 bp):
TTTAAAATTAATTTTAAAAATATAAAAAGTAAAAAAATATAAAAA
Found at i:1187330 original size:40 final size:39
Alignment explanation
Indices: 1187266--1187362 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 39
1187256 TTTATATAAA
* *
1187266 TTTTAATATATTTATAT-TT-TGTATTGTA-TTTACATTAT
1 TTTTTATAT-TTTATATATTATGTATTATACTTTA-ATTAT
1187304 TTTTTAT-TTTATAATATATTATGTATTATACTTTAATTAT
1 TTTTTATATTT-T-ATATATTATGTATTATACTTTAATTAT
1187344 TTTTTATATTTTATATATT
1 TTTTTATATTTTATATATT
1187363 TATATTAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
36 2 0.04
37 2 0.04
38 10 0.20
39 9 0.18
40 21 0.41
41 7 0.14
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (39 bp):
TTTTTATATTTTATATATTATGTATTATACTTTAATTAT
Found at i:1187362 original size:18 final size:18
Alignment explanation
Indices: 1187253--1187363 Score: 50
Period size: 18 Copynumber: 5.8 Consensus size: 18
1187243 ATCAATAATG
* *
1187253 TATTTTATATAAATTTTAA
1 TATTTTATAT-ATTTTTTA
*
1187272 TATATTTATAT-TTTGTATTG
1 TAT-TTTATATATTT-T-TTA
*
1187292 TA-TTTACATTATTTTTTA
1 TATTTTATA-TATTTTTTA
1187310 T-TTTATAATATATTATGTATTA
1 TATTT-T-ATATATT-T-T-TTA
*
1187332 TACTTTA-ATTATTTTTTA
1 TATTTTATA-TATTTTTTA
1187350 TATTTTATATATTT
1 TATTTTATATATTT
1187364 ATATTAAATA
Statistics
Matches: 70, Mismatches: 8, Indels: 29
0.65 0.07 0.27
Matches are distributed among these distances:
18 26 0.37
19 13 0.19
20 18 0.26
21 6 0.09
22 5 0.07
23 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (18 bp):
TATTTTATATATTTTTTA
Found at i:1187672 original size:43 final size:43
Alignment explanation
Indices: 1187606--1187700 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 43
1187596 TTAATAATAG
*
1187606 ATATATAAATTTTAAGTATGAAAAATCTATTTTATTATATAAAA
1 ATAT-TAAATCTTAAGTATGAAAAATCTATTTTATTATATAAAA
* *
1187650 ATATTAAATCTTAGGTATGAAAAATTTATTTTATTATATAAAA
1 ATATTAAATCTTAAGTATGAAAAATCTATTTTATTATATAAAA
1187693 ATATTAAA
1 ATATTAAA
1187701 AAGCTTAAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 44 0.92
44 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.43
Consensus pattern (43 bp):
ATATTAAATCTTAAGTATGAAAAATCTATTTTATTATATAAAA
Found at i:1187694 original size:20 final size:20
Alignment explanation
Indices: 1187626--1187694 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
1187616 TTTAAGTATG
*
1187626 AAAAATCTATTTTATTATAT
1 AAAAATTTATTTTATTATAT
* * *
1187646 AAAAATATTAAATCTTAGGTAT-G
1 AAAAAT-TT--ATTTTA-TTATAT
1187669 AAAAATTTATTTTATTATAT
1 AAAAATTTATTTTATTATAT
1187689 AAAAAT
1 AAAAAT
1187695 ATTAAAAAGC
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.46
21 1 0.03
22 2 0.05
23 11 0.30
24 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (20 bp):
AAAAATTTATTTTATTATAT
Found at i:1187721 original size:43 final size:42
Alignment explanation
Indices: 1187617--1187712 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 42
1187607 TATATAAATT
* * *
1187617 TTAAGTATGAAAAATCTATTTTATTATATAAAAATATTAAATC
1 TTAAGCAT-AAAAATTTATTTTATTATATAAAAATATTAAAGC
* *
1187660 TTAGGTATGAAAAATTTATTTTATTATATAAAAATATTAAAAAGC
1 TTAAGCAT-AAAAATTTATTTTATTATATAAAAATATT--AAAGC
1187705 TTAAGCAT
1 TTAAGCAT
1187713 TTAATTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 36 0.78
45 10 0.22
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (42 bp):
TTAAGCATAAAAATTTATTTTATTATATAAAAATATTAAAGC
Found at i:1188890 original size:2 final size:2
Alignment explanation
Indices: 1188883--1188912 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1188873 CAAGCCAAGC
1188883 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
1188913 GAATAAATTA
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:1190098 original size:26 final size:25
Alignment explanation
Indices: 1190037--1190099 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
1190027 TATTTTATGA
1190037 TTTAAAAATATTAAAAAATTATTTT
1 TTTAAAAATATTAAAAAATTATTTT
* *
1190062 TATAATTAAAT-TTAAATAAATATTTTTT
1 TTTAA--AAATATTAAA-AAAT-TATTTT
1190090 TTTAAAAATA
1 TTTAAAAATA
1190100 AACAACGGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
25 4 0.13
26 9 0.30
27 8 0.27
28 9 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAAAAATATTAAAAAATTATTTT
Found at i:1191147 original size:14 final size:14
Alignment explanation
Indices: 1191128--1191154 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1191118 TTTTGGCAAG
1191128 AAAAATTATTTATT
1 AAAAATTATTTATT
1191142 AAAAATTATTTAT
1 AAAAATTATTTAT
1191155 AATAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAAATTATTTATT
Found at i:1193194 original size:4 final size:4
Alignment explanation
Indices: 1193185--1193212 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1193175 AACTCATTCC
1193185 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1193213 CATTAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:1193478 original size:21 final size:22
Alignment explanation
Indices: 1193447--1193500 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
1193437 TCGTGAAAAG
*
1193447 TATAAATA-AATTTAATA-ATT
1 TATAAATATAAATTAATATATT
1193467 T-TAAATATAAATTAATATATT
1 TATAAATATAAATTAATATATT
1193488 TAATAAATATAAA
1 T-ATAAATATAAA
1193501 AATTATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.21
20 9 0.31
21 4 0.14
23 10 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATAAATATAAATTAATATATT
Found at i:1193584 original size:14 final size:16
Alignment explanation
Indices: 1193542--1193596 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 16
1193532 TTTTATTTAA
* *
1193542 ATTTAAAAATTTAACAT
1 ATTTAATAATTT-ATAT
1193559 ATTTAATAATTTATAT
1 ATTTAATAATTTATAT
*
1193575 ATTT-AT-ATTTACAT
1 ATTTAATAATTTATAT
*
1193589 AATTAATA
1 ATTTAATA
1193597 TAAAAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.31
15 4 0.12
16 7 0.22
17 11 0.34
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAATAATTTATAT
Found at i:1193605 original size:23 final size:22
Alignment explanation
Indices: 1193557--1193605 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
1193547 AAAATTTAAC
* ***
1193557 ATATTTAATAATTTATATATTT
1 ATATTTAATAATTAATATAAAA
1193579 ATATTTACATAATTAATATAAAA
1 ATATTTA-ATAATTAATATAAAA
1193602 ATAT
1 ATAT
1193606 AAAAATTAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTTAATAATTAATATAAAA
Found at i:1194617 original size:14 final size:15
Alignment explanation
Indices: 1194598--1194627 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1194588 GTTCTTCAAG
1194598 AGAAAAAA-AAAAAA
1 AGAAAAAAGAAAAAA
1194612 AGAAAAAAGAAAAAA
1 AGAAAAAAGAAAAAA
1194627 A
1 A
1194628 AATGGTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AGAAAAAAGAAAAAA
Found at i:1196446 original size:17 final size:16
Alignment explanation
Indices: 1196419--1196471 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
1196409 ATATATAAAG
1196419 TTAAAATATATATATTAT
1 TTAAAA-ATATAT-TTAT
1196437 TTAAAAATAT-TTTAT
1 TTAAAAATATATTTAT
*
1196452 TTAACAATATATTTTAT
1 TTAAAAATATA-TTTAT
1196469 TTA
1 TTA
1196472 TTTCTAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
15 13 0.41
16 1 0.03
17 12 0.38
18 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAAATATATTTAT
Found at i:1203253 original size:23 final size:23
Alignment explanation
Indices: 1203226--1203276 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
1203216 TTCATAAGAT
*
1203226 TATTTAAAATTTAATATTTAATAA
1 TATTTAAAAATTAATATTT-ATAA
1203250 -ATTTAAAAATTAATATTTATAA
1 TATTTAAAAATTAATATTTATAA
1203272 TATTT
1 TATTT
1203277 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTAAAAATTAATATTTATAA
Found at i:1208315 original size:64 final size:64
Alignment explanation
Indices: 1208214--1208341 Score: 211
Period size: 64 Copynumber: 2.0 Consensus size: 64
1208204 CCCTTCTAAT
* * *
1208214 CAAATACTGCATACTTACAACATTGGGCAAAACAAAACTGGGACCAGTGGAACCCTTTTGATAG
1 CAAATACTACATACTTACAACATTGGACAAAACAAAACTGGCACCAGTGGAACCCTTTTGATAG
**
1208278 CAAATACTACATACTTACGGCATTGGACAAAACAAAACTGGCACCAGTGGAACCCTTTTGATAG
1 CAAATACTACATACTTACAACATTGGACAAAACAAAACTGGCACCAGTGGAACCCTTTTGATAG
1208342 TTCATAGTCA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (64 bp):
CAAATACTACATACTTACAACATTGGACAAAACAAAACTGGCACCAGTGGAACCCTTTTGATAG
Found at i:1211558 original size:27 final size:26
Alignment explanation
Indices: 1211512--1211563 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1211502 TTCTTGAACC
*
1211512 TAATGCCTTTTAAAATAAAAACATAG
1 TAATGCCCTTTAAAATAAAAACATAG
1211538 TAATGCCCTTTAAAATAAAAACATAG
1 TAATGCCCTTTAAAATAAAAACATAG
1211564 CTGCGAAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (26 bp):
TAATGCCCTTTAAAATAAAAACATAG
Found at i:1215436 original size:24 final size:26
Alignment explanation
Indices: 1215409--1215470 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 26
1215399 ATATCAATCG
1215409 AATTATATTATTTTTAA-TA-TTTTA
1 AATTATATTATTTTTAATTATTTTTA
* *
1215433 AATTA-A-TA-TATTAATTATTTTTT
1 AATTATATTATTTTTAATTATTTTTA
1215456 AATTATATTATTTTT
1 AATTATATTATTTTT
1215471 TACAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 5 0.17
22 4 0.13
23 10 0.33
24 6 0.20
25 2 0.07
26 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
AATTATATTATTTTTAATTATTTTTA
Found at i:1215460 original size:15 final size:16
Alignment explanation
Indices: 1215442--1215472 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1215432 AAATTAATAT
1215442 ATTA-ATTATTTTTTA
1 ATTATATTATTTTTTA
1215457 ATTATATTATTTTTTA
1 ATTATATTATTTTTTA
1215473 CAATTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTATATTATTTTTTA
Found at i:1215494 original size:15 final size:15
Alignment explanation
Indices: 1215474--1215503 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1215464 TATTTTTTAC
1215474 AATTTAATATTTAAA
1 AATTTAATATTTAAA
1215489 AATTTAATATTTAAA
1 AATTTAATATTTAAA
1215504 CTTTATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAATATTTAAA
Found at i:1215804 original size:20 final size:20
Alignment explanation
Indices: 1215781--1215821 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1215771 ATTTAAGTAC
*
1215781 TTATAAATCTTTTTATGTAT
1 TTATAAATCTTTTTATATAT
*
1215801 TTATAAATTTTTTTATATAT
1 TTATAAATCTTTTTATATAT
1215821 T
1 T
1215822 AAATCATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTATAAATCTTTTTATATAT
Found at i:1217502 original size:3 final size:3
Alignment explanation
Indices: 1217488--1217517 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1217478 CATTCTAAAG
*
1217488 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1217518 CTTTTGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1218712 original size:21 final size:21
Alignment explanation
Indices: 1218688--1218748 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1218678 TTTTGTTAAA
* *
1218688 TTTTGATACGATTTTAATAGC
1 TTTTAATATGATTTTAATAGC
* *
1218709 TTTTTATATGATTTTAAAAGC
1 TTTTAATATGATTTTAATAGC
*
1218730 CTTTAATATGATTTTAATA
1 TTTTAATATGATTTTAATA
1218749 AATTTAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTTAATATGATTTTAATAGC
Found at i:1218780 original size:21 final size:20
Alignment explanation
Indices: 1218734--1218787 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1218724 AAAAGCCTTT
* *
1218734 AATATGATTTTAATAAATTT
1 AATATAATTTTAATAAATTA
*
1218754 AATATAATTTTGATAACATTA
1 AATATAATTTTAATAA-ATTA
*
1218775 AATATAATATTAA
1 AATATAATTTTAA
1218788 CAATCTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
AATATAATTTTAATAAATTA
Found at i:1218851 original size:10 final size:10
Alignment explanation
Indices: 1218838--1218881 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
1218828 TTTGATTCGA
*
1218838 TTTTGATAATT
1 TTTTAATAA-T
1218849 TTTTATATAAT
1 TTTTA-ATAAT
1218860 TTTTAATAAT
1 TTTTAATAAT
*
1218870 TTTTATTAAT
1 TTTTAATAAT
1218880 TT
1 TT
1218882 ATAACATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 16 0.53
11 10 0.33
12 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:1218860 original size:12 final size:11
Alignment explanation
Indices: 1218843--1218881 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
1218833 TTCGATTTTG
1218843 ATAATTTTTTAT
1 ATAA-TTTTTAT
1218855 ATAATTTTTA-
1 ATAATTTTTAT
1218865 ATAATTTTTAT
1 ATAATTTTTAT
1218876 -TAATTT
1 ATAATTT
1218882 ATAACATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 16 0.62
11 6 0.23
12 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATAATTTTTAT
Found at i:1218863 original size:22 final size:20
Alignment explanation
Indices: 1218838--1218881 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
1218828 TTTGATTCGA
*
1218838 TTTTGATAATTTTTTATATAAT
1 TTTTAATAA-TTTTTAT-TAAT
1218860 TTTTAATAATTTTTATTAAT
1 TTTTAATAATTTTTATTAAT
1218880 TT
1 TT
1218882 ATAACATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 7 0.33
22 8 0.38
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTAATAATTTTTATTAAT
Found at i:1218892 original size:20 final size:21
Alignment explanation
Indices: 1218846--1218892 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1218836 GATTTTGATA
* *
1218846 ATTTTTTATATAATTTTTAAT
1 ATTTTTTATATAATTTATAAC
*
1218867 AATTTTTAT-TAATTTATAAC
1 ATTTTTTATATAATTTATAAC
1218887 ATTTTT
1 ATTTTT
1218893 GCAATTTTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTTATATAATTTATAAC
Found at i:1219106 original size:21 final size:21
Alignment explanation
Indices: 1219056--1219488 Score: 133
Period size: 21 Copynumber: 20.9 Consensus size: 21
1219046 CTTTAAACAA
* *
1219056 TTTTGATGTAATTTTGATCAC
1 TTTTGATATAATTTTGATAAC
* * *
1219077 CTTTAATATTATTTTGATAA-
1 TTTTGATATAATTTTGATAAC
1219097 TGTTTGATATAATTTAT-ATAAC
1 T-TTTGATATAATTT-TGATAAC
* *
1219119 TTTTGTTATAATTTTGAT-AG
1 TTTTGATATAATTTTGATAAC
* * *
1219139 TTTT-CTAT--TTTTAATAAT
1 TTTTGATATAATTTTGATAAC
*
1219157 TTTTTATATAATTTTGATAA-
1 TTTTGATATAATTTTGATAAC
* * ** *
1219177 TCTTAGATACAATTTTCTTAGC
1 T-TTTGATATAATTTTGATAAC
* * * *
1219199 TTTTAAAATGATTTTGACAAC
1 TTTTGATATAATTTTGATAAC
* ** * *
1219220 TTTTTATACGATTTTAATAGC
1 TTTTGATATAATTTTGATAAC
*
1219241 TTTTGATATAAATTTGATATA-
1 TTTTGATATAATTTTGATA-AC
* * *
1219262 TTTTGATATAATTATGGTTAC
1 TTTTGATATAATTTTGATAAC
* ** * * * *
1219283 GTTAAATATAGTCTAGGTAAC
1 TTTTGATATAATTTTGATAAC
* *
1219304 TTTAGAAATAATTTT-AGTAAC
1 TTTTGATATAATTTTGA-TAAC
* *
1219325 ATTTGATATAA-TTTAATAAC
1 TTTTGATATAATTTTGATAAC
* ** *** *
1219345 TTTTAATATGGTTGCAAT-AG
1 TTTTGATATAATTTTGATAAC
* *
1219365 TATTTGATATGATTTTGATGAC
1 T-TTTGATATAATTTTGATAAC
1219387 TTTTGATATAATTTT-AGTAA-
1 TTTTGATATAATTTTGA-TAAC
* * *
1219407 TCGTTAATATAATTTTCATAA-
1 T-TTTGATATAATTTTGATAAC
* *
1219428 TATTTGATATAATCTTGACAAC
1 T-TTTGATATAATTTTGATAAC
* * *
1219450 TTTTTACATGATTTT-ATTAA-
1 TTTTGATATAATTTTGA-TAAC
*
1219470 TTTTTAGTATAATTTTGAT
1 TTTTGA-TATAATTTTGAT
1219489 TTTGATAACT
Statistics
Matches: 294, Mismatches: 94, Indels: 48
0.67 0.22 0.11
Matches are distributed among these distances:
17 6 0.02
18 5 0.02
19 6 0.02
20 33 0.11
21 236 0.80
22 8 0.03
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTTGATATAATTTTGATAAC
Found at i:1219513 original size:21 final size:21
Alignment explanation
Indices: 1219487--1219688 Score: 68
Period size: 21 Copynumber: 9.8 Consensus size: 21
1219477 TATAATTTTG
1219487 ATTTTGATAACTTTTGAAATA
1 ATTTTGATAACTTTTGAAATA
* **
1219508 ATTTTG-TAA-TCATTGGTATA
1 ATTTTGATAACT-TTTGAAATA
* *
1219528 GTTTTGATAACTTAT-AATATA
1 ATTTTGATAACTTTTGAA-ATA
* *
1219549 ATTTTGATGATGCGTTTTG---TG
1 ATTTTGAT-A-AC-TTTTGAAATA
* * *
1219570 ATTTTAATAACTTTTCATATA
1 ATTTTGATAACTTTTGAAATA
*
1219591 ATTTTGAT-ACATTTT-AATTTA
1 ATTTTGATAAC-TTTTGAA-ATA
* *
1219612 ATTTTGAT-ATTATTTGATATA
1 ATTTTGATAACT-TTTGAAATA
*
1219633 ATTTTGAT-ACATTTTGTAATA
1 ATTTTGATAAC-TTTTGAAATA
* * * *
1219654 GTTTTAATAA--TATGATATA
1 ATTTTGATAACTTTTGAAATA
*
1219673 ATTTTGATAACCTTTG
1 ATTTTGATAACTTTTG
1219689 TAATTGTTAT
Statistics
Matches: 129, Mismatches: 33, Indels: 38
0.64 0.17 0.19
Matches are distributed among these distances:
18 4 0.03
19 16 0.12
20 19 0.15
21 81 0.63
22 5 0.04
23 1 0.01
24 3 0.02
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (21 bp):
ATTTTGATAACTTTTGAAATA
Found at i:1219629 original size:10 final size:11
Alignment explanation
Indices: 1219576--1219681 Score: 73
Period size: 11 Copynumber: 10.1 Consensus size: 11
1219566 TGTGATTTTA
*
1219576 ATAACTTTTCAT
1 ATAA-TTTTGAT
1219588 ATAATTTTGAT
1 ATAATTTTGAT
* *
1219599 A-CATTTTAAT
1 ATAATTTTGAT
*
1219609 TTAATTTTGAT
1 ATAATTTTGAT
*
1219620 ATTA-TTTGAT
1 ATAATTTTGAT
1219630 ATAATTTTGAT
1 ATAATTTTGAT
*
1219641 A-CATTTTG-T
1 ATAATTTTGAT
*
1219650 AATAGTTTT-A-
1 -ATAATTTTGAT
*
1219660 ATAA-TATGAT
1 ATAATTTTGAT
1219670 ATAATTTTGAT
1 ATAATTTTGAT
1219681 A
1 A
1219682 ACCTTTGTAA
Statistics
Matches: 71, Mismatches: 15, Indels: 17
0.69 0.15 0.17
Matches are distributed among these distances:
8 2 0.03
9 5 0.07
10 27 0.38
11 33 0.46
12 4 0.06
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (11 bp):
ATAATTTTGAT
Found at i:1223644 original size:2 final size:2
Alignment explanation
Indices: 1223637--1223662 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1223627 TCATTTAAAA
1223637 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1223663 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1223667 original size:2 final size:2
Alignment explanation
Indices: 1223662--1223686 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1223652 TCTCTCTCTC
1223662 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 T
1223687 CCTAATTGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1223892 original size:33 final size:34
Alignment explanation
Indices: 1223821--1223888 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
1223811 ATTTTTAGCA
* *
1223821 TTAAAAAATATTTACTTATTTTTTTAAGATTTAT
1 TTAAAAAATATTTACTCATTTTTTTAAGATTAAT
1223855 TTAAAAATATATTTA-TCA-TTTTTTAA-ATTAAT
1 TTAAAAA-ATATTTACTCATTTTTTTAAGATTAAT
1223887 TT
1 TT
1223889 TAAATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 7 0.23
33 8 0.26
34 9 0.29
35 7 0.23
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (34 bp):
TTAAAAAATATTTACTCATTTTTTTAAGATTAAT
Found at i:1224044 original size:26 final size:26
Alignment explanation
Indices: 1223993--1224044 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1223983 GTTAATCTTA
* *
1223993 AAATTATCCTTAATTACTGTTAAATT
1 AAATTATCATTAATTACTATTAAATT
*
1224019 AAATTATTATTAATTA-TATTACAATT
1 AAATTATCATTAATTACTATTA-AATT
1224045 CAGGGCATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (26 bp):
AAATTATCATTAATTACTATTAAATT
Found at i:1227608 original size:29 final size:29
Alignment explanation
Indices: 1227576--1227635 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
1227566 TTTATTTTAT
* *
1227576 AAAATTATTTAAATATAAATTAAAAATTA
1 AAAATTAATTAAATACAAATTAAAAATTA
* * *
1227605 AAAATTAATTCAGTACAAATTAAAAGTTA
1 AAAATTAATTAAATACAAATTAAAAATTA
1227634 AA
1 AA
1227636 CTGAATGAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTAATTAAATACAAATTAAAAATTA
Found at i:1229303 original size:19 final size:18
Alignment explanation
Indices: 1229252--1229314 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
1229242 TAATAGAGTA
1229252 ATAATTTTTTTAAGAA--
1 ATAATTTTTTTAAGAATG
*
1229268 AT--TTTTTTTAAAAAATG
1 ATAATTTTTTT-AAGAATG
1229285 ATAATTTTTTTAATGAATG
1 ATAATTTTTTTAA-GAATG
* *
1229304 GTAGTTTTTTT
1 ATAATTTTTTT
1229315 TTAAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 7 0.19
15 4 0.11
16 2 0.05
17 2 0.05
18 2 0.05
19 20 0.54
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.56
Consensus pattern (18 bp):
ATAATTTTTTTAAGAATG
Found at i:1229463 original size:20 final size:18
Alignment explanation
Indices: 1229438--1229478 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1229428 ATTTATTTTT
1229438 TATTATTTTAATTAAATTAA
1 TATTA-TTTAATTAAA-TAA
*
1229458 TATTATTTAATTTAATAA
1 TATTATTTAATTAAATAA
1229476 TAT
1 TAT
1229479 CAAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 9 0.45
20 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATTTAATTAAATAA
Found at i:1230398 original size:41 final size:39
Alignment explanation
Indices: 1230319--1230411 Score: 145
Period size: 38 Copynumber: 2.4 Consensus size: 39
1230309 TGTTAGGTGC
1230319 AAAA-TGCAACCAATTATTGAACAATAATAATAAT-AAA
1 AAAATTGCAACCAATTATTGAACAATAATAATAATAAAA
1230356 AAAATTGCAACCAATTATTGAACAATAATAATAATAATAAAA
1 AAAATTGCAACCAATTATTGAAC---AATAATAATAATAAAA
1230398 AAAATTGCAACCAA
1 AAAATTGCAACCAA
1230412 GTAAGTCATC
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
37 4 0.08
38 18 0.35
41 12 0.24
42 17 0.33
ACGTcount: A:0.59, C:0.12, G:0.05, T:0.24
Consensus pattern (39 bp):
AAAATTGCAACCAATTATTGAACAATAATAATAATAAAA
Found at i:1231219 original size:2 final size:2
Alignment explanation
Indices: 1231206--1231253 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1231196 GCTATAATTA
*
1231206 AT AT AT AC 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 AT
1231248 AT AT AT
1 AT AT AT
1231254 TGCAAGAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1232484 original size:60 final size:61
Alignment explanation
Indices: 1232376--1232493 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 61
1232366 ACTTATGTTC
1232376 GATCTCTATTGCTATCACATCCTCATCCCGGAGTCATTTCTTTAATAACCTCAATGATTTT
1 GATCTCTATTGCTATCACATCCTCATCCCGGAGTCATTTCTTTAATAACCTCAATGATTTT
*
1232437 GATCTCTATTGCTATCACATCCTC-TCCCGGAGTCATTTCTTTAATAACCTCGATGAT
1 GATCTCTATTGCTATCACATCCTCATCCCGGAGTCATTTCTTTAATAACCTCAATGAT
1232494 CAAATTCATA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 32 0.57
61 24 0.43
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (61 bp):
GATCTCTATTGCTATCACATCCTCATCCCGGAGTCATTTCTTTAATAACCTCAATGATTTT
Found at i:1238640 original size:30 final size:30
Alignment explanation
Indices: 1238604--1238668 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
1238594 AATGGTGTTA
*
1238604 GTATTGAAGGTAGAGATCTTAGTATTTGGG
1 GTATTGAAGGTAGAGATCTTAATATTTGGG
* *
1238634 GTATTGAAGGTGGAGATCTTAATATTTTGG
1 GTATTGAAGGTAGAGATCTTAATATTTGGG
1238664 GTATT
1 GTATT
1238669 ATGAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.03, G:0.31, T:0.40
Consensus pattern (30 bp):
GTATTGAAGGTAGAGATCTTAATATTTGGG
Found at i:1241494 original size:11 final size:11
Alignment explanation
Indices: 1241480--1241515 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1241470 CTCTTTCCTC
1241480 TCTTTTTTTTT
1 TCTTTTTTTTT
*
1241491 TCTTTATTTTT
1 TCTTTTTTTTT
*
1241502 TATTTTTTTTT
1 TCTTTTTTTTT
1241513 TCT
1 TCT
1241516 CTTCGAGGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.06, C:0.08, G:0.00, T:0.86
Consensus pattern (11 bp):
TCTTTTTTTTT
Done.