Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 9 of 16
Found at i:1354025 original size:12 final size:13
Alignment explanation
Indices: 1354006--1354040 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1353996 TACCTATCTT
1354006 TAAAATAAATAAA
1 TAAAATAAATAAA
*
1354019 T-AAATAAATAAG
1 TAAAATAAATAAA
1354031 TAAAATAAAT
1 TAAAATAAAT
1354041 GAAAAATCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:1361163 original size:2 final size:2
Alignment explanation
Indices: 1361156--1361184 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1361146 TCTGACCCTT
1361156 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
1361185 GTATGTAATA
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:1361759 original size:24 final size:25
Alignment explanation
Indices: 1361696--1361759 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 25
1361686 ATATATTAAA
1361696 AATAAAATTTTTATTATTAGTATTTTT
1 AATAAAATTTTT-TTATTA-TATTTTT
*
1361723 AA-GAAATTGTTTTTATT-TATTTTT
1 AATAAAATT-TTTTTATTATATTTTT
1361747 AATAAAATTTTTT
1 AATAAAATTTTTT
1361760 AAAATTAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
24 13 0.39
25 5 0.15
26 10 0.30
27 5 0.15
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (25 bp):
AATAAAATTTTTTTATTATATTTTT
Found at i:1365212 original size:3 final size:3
Alignment explanation
Indices: 1365206--1365243 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1365196 AATCTTATAT
* *
1365206 ATA ATA AT- ATA ACA ATA ATA ATA ATA TTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1365244 CGTGTATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1370719 original size:2 final size:2
Alignment explanation
Indices: 1370712--1370754 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1370702 CCCACCATCT
1370712 TA TA TA 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 TA TA TA
1370754 T
1 T
1370755 TCTATACAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1376149 original size:15 final size:15
Alignment explanation
Indices: 1376129--1376158 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1376119 TTGAGTAAAA
1376129 GGATTAATTAGAGAG
1 GGATTAATTAGAGAG
*
1376144 GGATTATTTAGAGAG
1 GGATTAATTAGAGAG
1376159 CTTTGGCAGC
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:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (15 bp):
GGATTAATTAGAGAG
Found at i:1376696 original size:23 final size:24
Alignment explanation
Indices: 1376665--1376711 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1376655 AATTATATAT
*
1376665 TAAATTAAAATATTTTTATTTAAA
1 TAAATTAAAATATTATTATTTAAA
*
1376689 TAAA-TAAATTATTATTATTTAAA
1 TAAATTAAAATATTATTATTTAAA
1376712 AATTTTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAAATTAAAATATTATTATTTAAA
Found at i:1376827 original size:21 final size:22
Alignment explanation
Indices: 1376803--1376845 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1376793 AGAAATAAAT
1376803 TTAC-TCTTATTATTTTAAAAA
1 TTACATCTTATTATTTTAAAAA
* *
1376824 TTACATTTTATTTTTTTAAAAA
1 TTACATCTTATTATTTTAAAAA
1376846 ATAGCTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (22 bp):
TTACATCTTATTATTTTAAAAA
Found at i:1377165 original size:20 final size:20
Alignment explanation
Indices: 1377140--1377180 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1377130 GTATAAATTG
1377140 TCCTTTCATTATAATTAACC
1 TCCTTTCATTATAATTAACC
*
1377160 TCCTTTCATTGTAATTAACC
1 TCCTTTCATTATAATTAACC
1377180 T
1 T
1377181 ATATGCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.02, T:0.46
Consensus pattern (20 bp):
TCCTTTCATTATAATTAACC
Found at i:1378344 original size:24 final size:23
Alignment explanation
Indices: 1378317--1378375 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
1378307 ATATGTCCTA
1378317 TTTTTTATATATAA-AATATTA-T
1 TTTTTTATATATAATAAT-TTATT
*
1378339 ATTTTTATATATTAATAATTTATT
1 TTTTTTATATA-TAATAATTTATT
* *
1378363 TATTTTATGTATA
1 TTTTTTATATATA
1378376 TTTTTATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
22 10 0.33
23 8 0.27
24 12 0.40
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTTTATATATAATAATTTATT
Found at i:1378355 original size:21 final size:22
Alignment explanation
Indices: 1378318--1378363 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1378308 TATGTCCTAT
1378318 TTTTTATATATAAAAT-ATTATA
1 TTTTTATATATAAAATAATT-TA
*
1378340 TTTTTATATAT-TAATAATTTA
1 TTTTTATATATAAAATAATTTA
1378361 TTT
1 TTT
1378364 ATTTTATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTTATATATAAAATAATTTA
Found at i:1378552 original size:24 final size:23
Alignment explanation
Indices: 1378508--1378553 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1378498 TTTTTACACG
*
1378508 TTAATTATTCATTTATCTATATT
1 TTAATTATTCATATATCTATATT
* *
1378531 TTAATATATTCGTATATTTATAT
1 TTAAT-TATTCATATATCTATAT
1378554 CGTGTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (23 bp):
TTAATTATTCATATATCTATATT
Found at i:1380049 original size:16 final size:16
Alignment explanation
Indices: 1380030--1380066 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1380020 GCTTTTTCTC
1380030 TTTTTTTT-TT-TTAA
1 TTTTTTTTATTATTAA
1380044 TTTTTTTTATTATTAA
1 TTTTTTTTATTATTAA
1380060 TTTTTTT
1 TTTTTTT
1380067 GTTTCTGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 2 0.10
16 11 0.52
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTATTATTAA
Found at i:1383817 original size:2 final size:2
Alignment explanation
Indices: 1383810--1383837 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1383800 TTTCCTAAAC
1383810 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
1383838 TATTGGAAAA
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):
AT
Found at i:1386984 original size:29 final size:28
Alignment explanation
Indices: 1386930--1386984 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
1386920 CCATTATATC
* * *
1386930 TTTTATTATGCATGGATATTCTTAATCA
1 TTTTATTAAGCATGGATATCCGTAATCA
*
1386958 TTTTATTTAAGCATGTATATCCGTAAT
1 TTTTA-TTAAGCATGGATATCCGTAAT
1386985 AATATATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 5 0.23
29 17 0.77
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (28 bp):
TTTTATTAAGCATGGATATCCGTAATCA
Found at i:1392517 original size:25 final size:25
Alignment explanation
Indices: 1392466--1392518 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1392456 AAAATTTATT
* *
1392466 TTAAAATTATTTATATGTATTATTA
1 TTAAAATAATTTATATGTATTAATA
* * *
1392491 TTAAAATAATTTTTATTTTTTAATA
1 TTAAAATAATTTATATGTATTAATA
1392516 TTA
1 TTA
1392519 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTAAAATAATTTATATGTATTAATA
Found at i:1392878 original size:2 final size:2
Alignment explanation
Indices: 1392871--1392905 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1392861 AACTCATGTG
1392871 TA 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 TA T
1392906 TATTTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1393559 original size:24 final size:25
Alignment explanation
Indices: 1393522--1393569 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1393512 ACAAAATTAT
1393522 AAATAAAACATAAA-ATATAATAATC
1 AAATAAAACATAAATATA-AATAATC
*
1393547 AAATTAAA-ATAAATATAAATAAT
1 AAATAAAACATAAATATAAATAAT
1393570 ATAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (25 bp):
AAATAAAACATAAATATAAATAATC
Found at i:1394510 original size:19 final size:19
Alignment explanation
Indices: 1394486--1394524 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1394476 CCATTGTTTG
* *
1394486 AATATAATATAAATAATAT
1 AATATAATAAAAAAAATAT
1394505 AATATAATAAAAAAAATAT
1 AATATAATAAAAAAAATAT
1394524 A
1 A
1394525 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATATAATAAAAAAAATAT
Found at i:1394569 original size:18 final size:18
Alignment explanation
Indices: 1394537--1394596 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
1394527 TTTAAATTTT
1394537 TATATTATAAA-TTATTAA
1 TATATTA-AAATTTATTAA
1394555 TATATTAAAATTTATATAA
1 TATATTAAAATTTAT-TAA
1394574 -ATA-TAAAATATT-TTACA
1 TATATTAAAAT-TTATTA-A
1394591 TATATT
1 TATATT
1394597 TATAATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.06
17 11 0.31
18 19 0.53
19 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATTAAAATTTATTAA
Found at i:1395262 original size:13 final size:14
Alignment explanation
Indices: 1395228--1395256 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1395218 AAATAATGAG
1395228 ATAATATTTTTACT
1 ATAATATTTTTACT
1395242 ATAATATTTTTACT
1 ATAATATTTTTACT
1395256 A
1 A
1395257 CATATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
ATAATATTTTTACT
Found at i:1396721 original size:15 final size:15
Alignment explanation
Indices: 1396679--1396731 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1396669 TAAAAATATT
1396679 TTAAAATTTATATAATA
1 TTAAAATTTAT-T-ATA
*
1396696 TT-AATTATTATTATA
1 TTAAAAT-TTATTATA
1396711 TTAAAATTTATTATA
1 TTAAAATTTATTATA
1396726 -TAAAAT
1 TTAAAAT
1396732 AAAATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 6 0.19
15 13 0.41
16 7 0.22
17 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAAATTTATTATA
Found at i:1398685 original size:3 final size:3
Alignment explanation
Indices: 1398666--1398699 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1398656 TTTATTTTTT
* *
1398666 TTA TTG TTA TTA CTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1398700 AGTTGCTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1402718 original size:18 final size:18
Alignment explanation
Indices: 1402695--1402735 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1402685 TTTCTCTCTC
* *
1402695 TATATATGTATATATATA
1 TATATATGTACATAAATA
1402713 TATATATGTACATAAATA
1 TATATATGTACATAAATA
1402731 TATAT
1 TATAT
1402736 TACATATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATATGTACATAAATA
Found at i:1402854 original size:3 final size:3
Alignment explanation
Indices: 1402840--1402874 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1402830 TATCATTGTC
*
1402840 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1402875 GGAGTGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1402855 original size:12 final size:12
Alignment explanation
Indices: 1402828--1402874 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1402818 TGATATTGAG
* *
1402828 ATTATCATTGTC
1 ATTATCATTATT
1402840 ATTATCATTATT
1 ATTATCATTATT
*
1402852 ATTATTATTATT
1 ATTATCATTATT
*
1402864 ATTATTATTAT
1 ATTATCATTAT
1402875 GGAGTGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (12 bp):
ATTATCATTATT
Found at i:1404479 original size:2 final size:2
Alignment explanation
Indices: 1404472--1404498 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1404462 GATGATTGCC
1404472 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1404499 TATTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1404653 original size:31 final size:30
Alignment explanation
Indices: 1404613--1404719 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 30
1404603 ATTAAAGATT
*
1404613 TTTTTAAAATTTTTAATATTTAATTAATTA
1 TTTTAAAAATTTTTAATATTTAATTAATTA
1404643 TTTTACAAAATTTTTAAATATATATAATT-ATTA
1 TTTTA-AAAATTTTT-AATAT-T-TAATTAATTA
*
1404676 TTTT-AAATTTTTTAA-ATTTAA--AATATA
1 TTTTAAAAATTTTTAATATTTAATTAAT-TA
1404703 TTTTTAAAAATTTTTAA
1 -TTTTAAAAATTTTTAA
1404720 ATAAAATTAG
Statistics
Matches: 66, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
26 2 0.03
27 5 0.08
28 5 0.08
29 12 0.18
30 6 0.09
31 17 0.26
32 5 0.08
33 9 0.14
34 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (30 bp):
TTTTAAAAATTTTTAATATTTAATTAATTA
Found at i:1404998 original size:16 final size:16
Alignment explanation
Indices: 1404964--1405000 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1404954 TTTTAAATTA
* *
1404964 TTATTATAAATATATT
1 TTATTATAAATAAAAT
1404980 TTATTATAAATAAAAT
1 TTATTATAAATAAAAT
1404996 TTATT
1 TTATT
1405001 TAACCAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTATAAATAAAAT
Found at i:1407993 original size:2 final size:2
Alignment explanation
Indices: 1407986--1408011 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1407976 ACAAAGATTC
1407986 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
1408012 CACTTGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1414285 original size:4 final size:4
Alignment explanation
Indices: 1414276--1414302 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1414266 GTTTAAAGAT
1414276 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1414303 TATTGAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1414490 original size:2 final size:2
Alignment explanation
Indices: 1414485--1414513 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1414475 TTAGCTATTT
1414485 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
1414514 TCTTGTACAG
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:1417243 original size:11 final size:11
Alignment explanation
Indices: 1417219--1417279 Score: 54
Period size: 10 Copynumber: 5.5 Consensus size: 11
1417209 TTTTAAATTT
1417219 TTTATTTA-AA
1 TTTATTTATAA
1417229 TTTATTTATAA
1 TTTATTTATAA
*
1417240 TTTAATT-TAA
1 TTTATTTATAA
* *
1417250 TTTGTTAATAA
1 TTTATTTATAA
1417261 TTTTATATTATATA
1 -TTTAT-TTATA-A
1417275 TTTAT
1 TTTAT
1417280 AATAAATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
10 15 0.38
11 11 0.28
12 4 0.10
13 9 0.22
14 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TTTATTTATAA
Found at i:1417251 original size:21 final size:21
Alignment explanation
Indices: 1417222--1417282 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1417212 TAAATTTTTT
1417222 ATTTAAATTTATTTATAATTTA
1 ATTT-AATTTATTTATAATTTA
* * *
1417244 ATTTAATTTGTTAATAATTTT
1 ATTTAATTTATTTATAATTTA
*
1417265 ATATT-ATATATTTATAAT
1 AT-TTAATTTATTTATAAT
1417283 AAATAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 26 0.81
22 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTAATTTATTTATAATTTA
Found at i:1417348 original size:20 final size:21
Alignment explanation
Indices: 1417303--1417348 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1417293 TTAAAAATAT
* *
1417303 ATTTTTATATTTTATAACTGA
1 ATTTATATATTTTATAAATGA
*
1417324 ATTTATATATTTT-TAAATTA
1 ATTTATATATTTTATAAATGA
1417344 ATTTA
1 ATTTA
1417349 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTATATATTTTATAAATGA
Found at i:1417378 original size:22 final size:23
Alignment explanation
Indices: 1417323--1417383 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 23
1417313 TTTATAACTG
1417323 AATTTATATATTT-TTAAATTAATTT
1 AATTTA-A-ATTTATTAAATT-ATTT
1417348 AATTTAAATTTATTAAATT-TTT
1 AATTTAAATTTATTAAATTATTT
1417370 -ATTTAAAATTTATT
1 AATTT-AAATTTATT
1417384 GGTGAATAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.12
22 12 0.35
23 4 0.12
24 8 0.24
25 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTTAAATTTATTAAATTATTT
Found at i:1418366 original size:21 final size:20
Alignment explanation
Indices: 1418315--1418367 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1418305 TTAAAATATG
1418315 ATAAAAATATTATTAATTATT
1 ATAAAAATA-TATTAATTATT
**
1418336 ATATTTAATATATTAATTAATT
1 ATA-AAAATATATTAATT-ATT
*
1418358 TTAAAAATAT
1 ATAAAAATAT
1418368 TTTTCAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAAAATATATTAATTATT
Found at i:1418748 original size:4 final size:4
Alignment explanation
Indices: 1418739--1418764 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1418729 ATGTATTTAA
1418739 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
1418765 AAAATTATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1419379 original size:22 final size:20
Alignment explanation
Indices: 1419353--1419399 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
1419343 ATGTATTTGA
*
1419353 TTATTAAATTTATTATTTTTAG
1 TTATTAAATTTA-T-TTATTAG
*
1419375 TTATT-TATTTATTTATTAG
1 TTATTAAATTTATTTATTAG
1419394 TTATTA
1 TTATTA
1419400 TATAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 5 0.23
22 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (20 bp):
TTATTAAATTTATTTATTAG
Found at i:1419408 original size:22 final size:19
Alignment explanation
Indices: 1419363--1419408 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 19
1419353 TTATTAAATT
1419363 TATTATTTTTAGTTATTTA
1 TATTATTTTTAGTTATTTA
1419382 T-TTATTTATTAGTTATTATA
1 TATTATTT-TTAGTTATT-TA
1419402 TAATTAT
1 T-ATTAT
1419409 ATAAATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 6 0.26
19 10 0.43
20 3 0.13
22 4 0.17
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (19 bp):
TATTATTTTTAGTTATTTA
Found at i:1419735 original size:2 final size:2
Alignment explanation
Indices: 1419728--1419772 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
1419718 GGTGGTCTAT
* *
1419728 TA TA TA TA TA TA TA TA TA TA TA GCA TC 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 TA TA TA
1419771 TA
1 TA
1419773 AAGGAACTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 37 0.97
3 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1420488 original size:2 final size:2
Alignment explanation
Indices: 1420481--1420513 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1420471 CTTAGCCTAA
1420481 AT AT 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 AT AT A
1420514 AAAAGCAGTG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1420908 original size:18 final size:19
Alignment explanation
Indices: 1420874--1420910 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1420864 TATTATTAAT
*
1420874 TATAATAGATTAAAATTTA
1 TATAATAGATAAAAATTTA
1420893 TATAATA-ATAAAAATTTA
1 TATAATAGATAAAAATTTA
1420911 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TATAATAGATAAAAATTTA
Found at i:1420914 original size:19 final size:20
Alignment explanation
Indices: 1420869--1420914 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1420859 AAAATTATTA
*
1420869 TTAATTATAATAGATTAAAAT
1 TTAA-TATAATAGATAAAAAT
1420890 TT-ATATAATA-ATAAAAAT
1 TTAATATAATAGATAAAAAT
1420908 TTAATAT
1 TTAATAT
1420915 TTTTTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 9 0.39
19 11 0.48
20 1 0.04
21 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAATATAATAGATAAAAAT
Found at i:1421617 original size:17 final size:18
Alignment explanation
Indices: 1421595--1421628 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1421585 AGTTAAAAAA
1421595 TAAATAA-AATTCAATTC
1 TAAATAAGAATTCAATTC
*
1421612 TAAATAAGAATTTAATT
1 TAAATAAGAATTCAATT
1421629 TAATTTGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAATAAGAATTCAATTC
Found at i:1421962 original size:3 final size:3
Alignment explanation
Indices: 1421948--1421991 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
1421938 CTCTCAATTG
* *
1421948 ATT ATT AGT ATT ATT ATT ATT ATA ATAT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT A
1421992 AATAACACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1422134 original size:29 final size:29
Alignment explanation
Indices: 1422099--1422158 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1422089 TTTTATATAT
1422099 TTTTAAAAAAT-AATATTTAATAATAATAA
1 TTTTAAAAAATAAAT-TTTAATAATAATAA
***
1422128 TTTTAAATTTTAAATTTTAATAATAATAA
1 TTTTAAAAAATAAATTTTAATAATAATAA
1422157 TT
1 TT
1422159 CTTATCTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTTAAAAAATAAATTTTAATAATAATAA
Found at i:1426930 original size:14 final size:14
Alignment explanation
Indices: 1426913--1426953 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1426903 ATTTTTATTT
1426913 ATTTATTTATTTAA
1 ATTTATTTATTTAA
* *
1426927 ATTTATATA-ATAA
1 ATTTATTTATTTAA
1426940 ATTT-TTTATTTAA
1 ATTTATTTATTTAA
1426953 A
1 A
1426954 AATATAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
12 3 0.14
13 11 0.50
14 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTATTTATTTAA
Found at i:1426981 original size:17 final size:17
Alignment explanation
Indices: 1426926--1426984 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 17
1426916 TATTTATTTA
1426926 AATTTATA-TAATAAATT
1 AATTTATATTAA-AAATT
*
1426943 -TTTTAT-TTAAAAATAT
1 AATTTATATTAAAAAT-T
1426959 AA--TATATTAAAAATT
1 AATTTATATTAAAAATT
1426974 AATTTATATTA
1 AATTTATATTA
1426985 GTATTTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 10 0.29
16 17 0.50
17 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTATATTAAAAATT
Found at i:1427818 original size:25 final size:28
Alignment explanation
Indices: 1427744--1427819 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 28
1427734 GGCTGGATCA
1427744 CAATTAA-TTTTTATTTTAATAGATCGATT
1 CAATTAATTTTTTATTTTAATAGA--GATT
* *
1427773 CAATTAAATTGTTT-TTATAAT-G-G-TT
1 CAATT-AATTTTTTATTTTAATAGAGATT
1427798 CAATTAATTTTTTATTTTAATA
1 CAATTAATTTTTTATTTTAATA
1427820 TATATGCCGG
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
24 7 0.18
25 13 0.33
26 1 0.03
29 6 0.15
30 8 0.21
31 4 0.10
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (28 bp):
CAATTAATTTTTTATTTTAATAGAGATT
Found at i:1428220 original size:6 final size:6
Alignment explanation
Indices: 1428209--1428241 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1428199 CTATACATAC
1428209 ATACAT ATACAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATA
1428242 TATAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:1428467 original size:14 final size:14
Alignment explanation
Indices: 1428450--1428496 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1428440 TTTTTATTTT
1428450 TTAATTTATTAAAA
1 TTAATTTATTAAAA
*
1428464 TTAATATATT-AAA
1 TTAATTTATTAAAA
*
1428477 TGTAATTTTTTAAAA
1 T-TAATTTATTAAAA
*
1428492 ATAAT
1 TTAAT
1428497 AATTAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 4 0.15
14 20 0.74
15 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
TTAATTTATTAAAA
Found at i:1428482 original size:28 final size:25
Alignment explanation
Indices: 1428450--1428520 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 25
1428440 TTTTTATTTT
1428450 TTAATTTATTAAAATTAATATATTAAA
1 TTAATTT-TTAAAATTAATATATT-AA
*
1428477 TGTAATTTTTTAAAAATAATA-ATTAA
1 T-TAA-TTTTTAAAATTAATATATTAA
1428503 TTAATTTTT--AATTAATAT
1 TTAATTTTTAAAATTAATAT
1428521 GGGTAAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 7 0.18
24 5 0.13
25 3 0.08
26 3 0.08
27 4 0.10
28 14 0.36
29 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
TTAATTTTTAAAATTAATATATTAA
Found at i:1428519 original size:25 final size:27
Alignment explanation
Indices: 1428462--1428519 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 27
1428452 AATTTATTAA
1428462 AATTAAT-ATATTAAATGTAATTTTTT
1 AATTAATAATATTAAATGTAATTTTTT
*
1428488 AA-AAATAATAATT-AAT-TAA-TTTTT
1 AATTAATAAT-ATTAAATGTAATTTTTT
1428512 AATTAATA
1 AATTAATA
1428520 TGGGTAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
24 7 0.26
25 10 0.37
26 7 0.26
27 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
AATTAATAATATTAAATGTAATTTTTT
Found at i:1431202 original size:30 final size:32
Alignment explanation
Indices: 1431168--1431237 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
1431158 TTAAATATGC
1431168 AATTATATACAAAAATTAGT-ATTTTTTTA-T
1 AATTATATACAAAAATTAGTAATTTTTTTAGT
** **
1431198 AATTATAT-GTAAAATTTTTAATTTTTTTAGT
1 AATTATATACAAAAATTAGTAATTTTTTTAGT
1431229 AATTATATA
1 AATTATATA
1431238 TATGAACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 7 0.21
30 17 0.52
31 9 0.27
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (32 bp):
AATTATATACAAAAATTAGTAATTTTTTTAGT
Found at i:1432155 original size:26 final size:26
Alignment explanation
Indices: 1432126--1432205 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 26
1432116 CTCAATAATA
1432126 ATAATATTTAATATAATTATATAAAT
1 ATAATATTTAATATAATTATATAAAT
* *
1432152 ATAATATAT-ATATAA-TA-ATTAA-
1 ATAATATTTAATATAATTATATAAAT
1432174 A-AA-A-TTAATATAATTATA-AAAT
1 ATAATATTTAATATAATTATATAAAT
* *
1432196 TTAAAATTTA
1 ATAATATTTA
1432206 TAAAATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
19 1 0.02
20 7 0.17
21 6 0.14
22 2 0.05
23 6 0.14
24 3 0.07
25 9 0.21
26 8 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAATATTTAATATAATTATATAAAT
Found at i:1432167 original size:37 final size:35
Alignment explanation
Indices: 1432119--1432192 Score: 87
Period size: 37 Copynumber: 2.1 Consensus size: 35
1432109 TTATTTACTC
* *
1432119 AATAATAATAATATTTAATATAATT-ATATAAATAT
1 AATAATAATAATAATTAA-AAAATTAATATAAATAT
*
1432154 AATATATATATAATAATTAAAAAATTAATATAATTAT
1 AATA-ATA-ATAATAATTAAAAAATTAATATAAATAT
1432191 AA
1 AA
1432193 AATTTAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 4 0.12
36 8 0.24
37 21 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
AATAATAATAATAATTAAAAAATTAATATAAATAT
Found at i:1432191 original size:28 final size:28
Alignment explanation
Indices: 1432126--1432201 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 28
1432116 CTCAATAATA
* *
1432126 ATAATATTTA-AT-ATAATTATATAAAT
1 ATAATATATATATAATAATTATAAAAAT
1432152 ATAATATATATATAATAATTA-AAAAAT
1 ATAATATATATATAATAATTATAAAAAT
1432179 -TAATATA-ATTATAA-AATT-TAAAA
1 ATAATATATA-TATAATAATTATAAAA
1432202 TTTATAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
25 9 0.20
26 21 0.48
27 7 0.16
28 7 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAATATATATATAATAATTATAAAAAT
Found at i:1432208 original size:16 final size:17
Alignment explanation
Indices: 1432187--1432219 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1432177 ATTAATATAA
1432187 TTATAAAAT-TTAAAAT
1 TTATAAAATATTAAAAT
1432203 TTATAAAATATTAAAAT
1 TTATAAAATATTAAAAT
1432220 ATCAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTATAAAATATTAAAAT
Found at i:1432674 original size:3 final size:3
Alignment explanation
Indices: 1432666--1432702 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1432656 TCTTGGGCTT
1432666 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1432703 CTTAGTTTCC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1433294 original size:69 final size:69
Alignment explanation
Indices: 1433183--1433322 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
1433173 ATGGGGGTAA
1433183 TGTCTATAATTAGAGCTCACCAGCAAGGTTGCATAAATATTTGATTGTTCTTAGGGCAATTGAAT
1 TGTCTATAATTAGAGCTCACCAGCAAGGTTGCATAAATATTTGATTGTTCTTAGGGCAATTGAAT
1433248 CAAT
66 CAAT
1433252 TGTCTATAATTAGAGCTCACCAGCAAGGTTGCATAAATATTTGATTGTTCTTAGGGCAATTGAAT
1 TGTCTATAATTAGAGCTCACCAGCAAGGTTGCATAAATATTTGATTGTTCTTAGGGCAATTGAAT
1433317 CAAT
66 CAAT
1433321 TG
1 TG
1433323 GTTCTTTAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.35
Consensus pattern (69 bp):
TGTCTATAATTAGAGCTCACCAGCAAGGTTGCATAAATATTTGATTGTTCTTAGGGCAATTGAAT
CAAT
Found at i:1441982 original size:24 final size:23
Alignment explanation
Indices: 1441933--1441993 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
1441923 ATATAGTTTA
1441933 AAAAT-TATTATTTTAAAATTGT
1 AAAATATATTATTTTAAAATTGT
1441955 --AATATATTATTTTATTAAATT-T
1 AAAATATATTATTTTA--AAATTGT
* *
1441977 AAAATATAATATATTAA
1 AAAATATATTATTTTAA
1441994 TTATATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
20 3 0.09
21 10 0.31
22 2 0.06
23 5 0.16
24 12 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AAAATATATTATTTTAAAATTGT
Found at i:1449470 original size:22 final size:22
Alignment explanation
Indices: 1449425--1449470 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1449415 AAATTTTATT
*
1449425 ATATTTTTTAATAATAATATAA
1 ATATTTTTTAATAATAATAAAA
*
1449447 ATATTATTTT-ATAATATTAAAA
1 ATATT-TTTTAATAATAATAAAA
1449469 AT
1 AT
1449471 TATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTTTTTAATAATAATAAAA
Found at i:1449838 original size:17 final size:17
Alignment explanation
Indices: 1449812--1449860 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
1449802 AAAATTATTG
1449812 ATTATATTTAATATAAT
1 ATTATATTTAATATAAT
*
1449829 ATTATTTTTAATATTAAT
1 ATTATATTTAATA-TAAT
1449847 -TTATATTTAATATA
1 ATTATATTTAATATA
1449861 TTAAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 2 0.07
17 23 0.79
18 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATATTTAATATAAT
Found at i:1450114 original size:2 final size:2
Alignment explanation
Indices: 1450107--1450139 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1450097 CGATTTTGAC
*
1450107 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1450140 ATTTTACGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:1450518 original size:17 final size:16
Alignment explanation
Indices: 1450496--1450546 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1450486 AACATTATAT
1450496 TAAAAAATAAAATTAAA
1 TAAAAAAT-AAATTAAA
* *
1450513 TAAAAAATTAAATTTAT
1 TAAAAAA-TAAATTAAA
*
1450530 TTAAAAATAAATTAAA
1 TAAAAAATAAATTAAA
1450546 T
1 T
1450547 TTTAATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 8 0.29
17 19 0.68
18 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAAATAAATTAAA
Found at i:1450534 original size:18 final size:17
Alignment explanation
Indices: 1450489--1450540 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
1450479 GAATAAAAAC
1450489 ATTATATTAAAAAATAAA
1 ATTAT-TTAAAAAATAAA
**
1450507 ATTAAATAAAAAATTAAA
1 ATTATTTAAAAAA-TAAA
*
1450525 TTTATTT-AAAAATAAA
1 ATTATTTAAAAAATAAA
1450541 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 4 0.14
17 12 0.43
18 12 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTATTTAAAAAATAAA
Found at i:1450550 original size:22 final size:22
Alignment explanation
Indices: 1450508--1450548 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1450498 AAAAATAAAA
1450508 TTAAATAAAAAATTAAATTTAT
1 TTAAATAAAAAATTAAATTTAT
*
1450530 TTAAA-AATAAATTAAATTT
1 TTAAATAAAAAATTAAATTT
1450549 TAATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAATAAAAAATTAAATTTAT
Found at i:1450697 original size:19 final size:19
Alignment explanation
Indices: 1450651--1450703 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1450641 ATGTAAATAA
* *
1450651 TAAATATATAATAGTATATG
1 TAAATAT-TAAAAATATATG
1450671 TAAATATTAAAAATATAT-
1 TAAATATTAAAAATATATG
1450689 TAAATTATTAAAAAT
1 TAAA-TATTAAAAAT
1450704 TAAATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 4 0.13
19 19 0.63
20 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
TAAATATTAAAAATATATG
Found at i:1450707 original size:15 final size:15
Alignment explanation
Indices: 1450687--1450741 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
1450677 TTAAAAATAT
1450687 ATTAAATTATTAAAA
1 ATTAAATTATTAAAA
1450702 ATTAAATT-TTAAAA
1 ATTAAATTATTAAAA
* * *
1450716 AATATATTTTTATAAAA
1 ATTA-AATTAT-TAAAA
1450733 ATTAAATTA
1 ATTAAATTA
1450742 AAAATATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.28
15 11 0.34
16 4 0.12
17 8 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAAATTATTAAAA
Found at i:1450735 original size:31 final size:32
Alignment explanation
Indices: 1450671--1450749 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 32
1450661 ATAGTATATG
*
1450671 TAAATATTAAAAATATATTAAATTATTAAAAAT
1 TAAATTTTAAAAATATATT-AATTATTAAAAAT
*
1450704 TAAATTTTAAAAAATATATT-TTTA-TAAAAAT
1 TAAATTTT-AAAAATATATTAATTATTAAAAAT
1450735 TAAA--TTAAAAATATA
1 TAAATTTTAAAAATATA
1450750 ATATGAATGA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 9 0.21
29 2 0.05
31 11 0.26
32 3 0.07
33 7 0.16
34 11 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TAAATTTTAAAAATATATTAATTATTAAAAAT
Found at i:1453085 original size:51 final size:51
Alignment explanation
Indices: 1453003--1453129 Score: 134
Period size: 51 Copynumber: 2.5 Consensus size: 51
1452993 GAATGTTACG
* * * * **
1453003 TAATAATTACAAAATATCATACTTTATTAAATTATTGTACAGAATA-TTCTA
1 TAATAATTACACAATGTCAAACCTTCCTAAATTATTGTACAGAATATTTC-A
* *
1453054 TAATAATTACACAATGTCAAACCTTCCTAAATTGTTGTACATAATATTTCA
1 TAATAATTACACAATGTCAAACCTTCCTAAATTATTGTACAGAATATTTCA
* *
1453105 CAATAATT--ACATTGTCAAACCTTCC
1 TAATAATTACACAATGTCAAACCTTCC
1453130 AATATTACAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 16 0.25
51 46 0.71
52 3 0.05
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.38
Consensus pattern (51 bp):
TAATAATTACACAATGTCAAACCTTCCTAAATTATTGTACAGAATATTTCA
Found at i:1453738 original size:3 final size:3
Alignment explanation
Indices: 1453730--1453776 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1453720 ACTAAGGTTT
1453730 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1453777 TAAGTGGTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1455980 original size:27 final size:28
Alignment explanation
Indices: 1455948--1456000 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
1455938 AATTTAAATC
1455948 GATTAAATTAAATTTAAT-AATTTTTTT
1 GATTAAATTAAATTTAATCAATTTTTTT
*
1455975 GATTAAATTAATTTTAATCAATTTTT
1 GATTAAATTAAATTTAATCAATTTTT
1456001 ATTTTCTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (28 bp):
GATTAAATTAAATTTAATCAATTTTTTT
Found at i:1470466 original size:40 final size:38
Alignment explanation
Indices: 1470422--1470496 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 38
1470412 AGATTCAATA
*
1470422 TTTAATATATATATATATATTTTAAATAAATAAATTTAAT
1 TTTAAAATATATATATATA-TTTAAA-AAATAAATTTAAT
* * *
1470462 TTTAAAATATTTTTATATATTTAAAAAATATATTT
1 TTTAAAATATATATATATATTTAAAAAATAAATTT
1470497 TATAATCGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 9 0.29
39 6 0.19
40 16 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
TTTAAAATATATATATATATTTAAAAAATAAATTTAAT
Found at i:1470483 original size:20 final size:22
Alignment explanation
Indices: 1470425--1470500 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 22
1470415 TTCAATATTT
*
1470425 AATATATATATATATATTTTAAATA
1 AATATAT-TTTATATA-TTTAAA-A
*
1470450 AATA-AATTTA-AT-TTT--AA
1 AATATATTTTATATATTTAAAA
1470467 AATAT-TTTTATATATTTAAAA
1 AATATATTTTATATATTTAAAA
1470488 AATATATTTTATA
1 AATATATTTTATA
1470501 ATCGTATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
17 9 0.21
18 3 0.07
19 3 0.07
20 3 0.07
21 7 0.17
22 9 0.21
23 3 0.07
24 1 0.02
25 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATATTTTATATATTTAAAA
Found at i:1470849 original size:26 final size:27
Alignment explanation
Indices: 1470803--1470864 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
1470793 TATTCACATT
1470803 TAAA-TTACTATAAAAAATTAT-TATTA
1 TAAATTTA-TATAAAAAATTATATATTA
**
1470829 TAAATTTATATAAAATTTTATATATTA
1 TAAATTTATATAAAAAATTATATATTA
1470856 -ATAATTTAT
1 TA-AATTTAT
1470865 TTTATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
TAAATTTATATAAAAAATTATATATTA
Found at i:1470876 original size:11 final size:10
Alignment explanation
Indices: 1470861--1470916 Score: 64
Period size: 9 Copynumber: 5.7 Consensus size: 10
1470851 TATTAATAAT
1470861 TTATTTTATA
1 TTATTTTATA
1470871 TATATTTTATA
1 T-TATTTTATA
*
1470882 -TGTTTTATA
1 TTATTTTATA
1470891 TT-TTTTA-A
1 TTATTTTATA
1470899 TTAATTTTATA
1 TT-ATTTTATA
1470910 TTATTTT
1 TTATTTT
1470917 TGTAGATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 3 0.08
9 13 0.32
10 12 0.30
11 12 0.30
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TTATTTTATA
Found at i:1471255 original size:20 final size:21
Alignment explanation
Indices: 1471207--1471274 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 21
1471197 ATTTTATTTT
1471207 TAAATTATATATTTAAAATTATA
1 TAAATT-TA-ATTTAAAATTATA
1471230 TAAA-TTAATTTAAAA-TATCA
1 TAAATTTAATTTAAAATTAT-A
* *
1471250 TTAATTTAATTTTATAATTA-A
1 TAAATTTAA-TTTAAAATTATA
1471271 TAAA
1 TAAA
1471275 ATATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
19 3 0.08
20 12 0.32
21 10 0.26
22 7 0.18
23 6 0.16
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAATTTAATTTAAAATTATA
Found at i:1474743 original size:15 final size:15
Alignment explanation
Indices: 1474720--1474749 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1474710 AGGCAACCTT
*
1474720 TTAAGGGAAAAAGGC
1 TTAAAGGAAAAAGGC
1474735 TTAAAGGAAAAAGGC
1 TTAAAGGAAAAAGGC
1474750 AGCCTAGACG
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:0.50, C:0.07, G:0.30, T:0.13
Consensus pattern (15 bp):
TTAAAGGAAAAAGGC
Found at i:1475282 original size:25 final size:28
Alignment explanation
Indices: 1475254--1475305 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1475244 TGATTATATA
1475254 AATATCAA-ATAAAAA-A-TTAAAATTC
1 AATATCAATATAAAAATATTTAAAATTC
*
1475279 AATATGAATATAAAAATATTTAAAATT
1 AATATCAATATAAAAATATTTAAAATT
1475306 TTATTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 7 0.30
27 1 0.04
28 8 0.35
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (28 bp):
AATATCAATATAAAAATATTTAAAATTC
Found at i:1476623 original size:22 final size:22
Alignment explanation
Indices: 1476597--1476638 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1476587 ATAAATAGAG
1476597 ATTTAATAAATATAATATATAT
1 ATTTAATAAATATAATATATAT
* *
1476619 ATTTAATATATTTAATATAT
1 ATTTAATAAATATAATATAT
1476639 GTATCGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTAATAAATATAATATATAT
Found at i:1477300 original size:18 final size:18
Alignment explanation
Indices: 1477269--1477304 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1477259 TTTTTAAAAA
*
1477269 ATATAATTACATATATAT
1 ATATAATTAAATATATAT
*
1477287 ATATATTTAAATATATAT
1 ATATAATTAAATATATAT
1477305 TTGATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATAATTAAATATATAT
Found at i:1478717 original size:17 final size:20
Alignment explanation
Indices: 1478676--1478719 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 20
1478666 TCATATGCGA
1478676 ATTTATATTTTATATAAATAT
1 ATTTA-ATTTTATATAAATAT
1478697 ATTTAATTTT-T-TAAA-AT
1 ATTTAATTTTATATAAATAT
1478714 ATTTAA
1 ATTTAA
1478720 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.35
18 4 0.17
19 1 0.04
20 5 0.22
21 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAATTTTATATAAATAT
Found at i:1478771 original size:18 final size:18
Alignment explanation
Indices: 1478711--1478771 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
1478701 AATTTTTTAA
* *
1478711 AATATTTAAAAAATT-TT
1 AATATTTAAATATTTATT
*
1478728 AATATGATTAAATTATGTATT
1 AATAT--TTAAA-TATTTATT
*
1478749 TATATTTAAATATTTATT
1 AATATTTAAATATTTATT
1478767 AATAT
1 AATAT
1478772 AAATATTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
17 5 0.15
18 11 0.32
19 10 0.29
20 2 0.06
21 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AATATTTAAATATTTATT
Found at i:1479373 original size:30 final size:30
Alignment explanation
Indices: 1479337--1479396 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1479327 CTAAATTTTT
*
1479337 TTAATAAATTAA-TGTAAATAATATAATTTA
1 TTAATAAATTAAGT-TAAATAATACAATTTA
* *
1479367 TTAATAATTTAAGTTTAATAATACAATTTA
1 TTAATAAATTAAGTTAAATAATACAATTTA
1479397 ATAAAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (30 bp):
TTAATAAATTAAGTTAAATAATACAATTTA
Found at i:1479411 original size:30 final size:30
Alignment explanation
Indices: 1479353--1479413 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1479343 AATTAATGTA
* * *
1479353 AATAATATAATTTATTAATAATTTAAGTTT
1 AATAATACAATTTAATAATAATTAAAGTTT
1479383 AATAATACAATTTAATAA-AATTAAAAGTTT
1 AATAATACAATTTAATAATAATT-AAAGTTT
1479413 A
1 A
1479414 TTCTCTTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (30 bp):
AATAATACAATTTAATAATAATTAAAGTTT
Found at i:1480181 original size:14 final size:13
Alignment explanation
Indices: 1480159--1480193 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1480149 TTATTTATAT
1480159 TTAATTAAAAATA
1 TTAATTAAAAATA
1480172 TTAATATAAAAATA
1 TTAAT-TAAAAATA
*
1480186 TTATTTAA
1 TTAATTAA
1480194 TATTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAATTAAAAATA
Found at i:1480412 original size:3 final size:3
Alignment explanation
Indices: 1480398--1480432 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
1480388 TGTCTCAAGC
1480398 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1480433 TCAACTGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1480848 original size:2 final size:2
Alignment explanation
Indices: 1480841--1480874 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1480831 CCCACCAAAA
1480841 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
1480875 GCTTACAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1483085 original size:13 final size:13
Alignment explanation
Indices: 1483067--1483091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1483057 TTTTTCTTAA
1483067 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
1483080 AAAAAAGAAAAA
1 AAAAAAGAAAAA
1483092 CTGAAGATTT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:1495218 original size:2 final size:2
Alignment explanation
Indices: 1495211--1495247 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1495201 TTATACATAC
1495211 AT AT AT AT 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 AT AT AT AT A
1495248 GAAAGAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1496428 original size:2 final size:2
Alignment explanation
Indices: 1496423--1496447 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1496413 TACACACATT
1496423 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
1496448 TTGTCCTTTT
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:1502325 original size:2 final size:2
Alignment explanation
Indices: 1502318--1502352 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1502308 TTATACATAC
1502318 AT AT AT 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 AT AT AT A
1502353 GAAAGAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1506294 original size:21 final size:20
Alignment explanation
Indices: 1506262--1506302 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
1506252 GCTTCCATAA
1506262 TCTTCTTTCTTTCTTTCTTTT
1 TCTTCTTTCTTT-TTTCTTTT
1506283 TCTT-TTTCCTTTTTT-TTTT
1 TCTTCTTT-CTTTTTTCTTTT
1506302 T
1 T
1506303 TGAAAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.26
20 6 0.32
21 8 0.42
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TCTTCTTTCTTTTTTCTTTT
Found at i:1511204 original size:4 final size:4
Alignment explanation
Indices: 1511195--1511224 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1511185 GTTTTCTTCC
1511195 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1511225 CAATTGGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1511900 original size:2 final size:2
Alignment explanation
Indices: 1511893--1511919 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1511883 CTTTGGGTGC
1511893 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
1511920 ATTTCATTGC
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:1512073 original size:2 final size:2
Alignment explanation
Indices: 1512066--1512090 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1512056 CTTAGACACA
1512066 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 A
1512091 TCTTTTACAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1513432 original size:21 final size:21
Alignment explanation
Indices: 1513406--1513448 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1513396 AAATATATAA
1513406 ATATATAGATATACTTT-TATT
1 ATATATAGATATA-TTTGTATT
*
1513427 ATATATATATATATTTGTATT
1 ATATATAGATATATTTGTATT
1513448 A
1 A
1513449 GTTTATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
ATATATAGATATATTTGTATT
Found at i:1515081 original size:13 final size:12
Alignment explanation
Indices: 1515063--1515144 Score: 55
Period size: 14 Copynumber: 6.6 Consensus size: 12
1515053 TTATTTTTAA
1515063 AATATTCATATTT
1 AATATT-ATATTT
1515076 AATATTTATATTT
1 AATA-TTATATTT
1515089 AATA-TATATTT
1 AATATTATATTT
*
1515100 AAATATAATTATTT
1 -AATATTA-TATTT
*
1515114 AAATATAAATATATT
1 -AATAT-TATAT-TT
1515129 AA-A-TATATTT
1 AATATTATATTT
1515139 -ATATTA
1 AATATTA
1515145 AAATATATAT
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
9 1 0.02
10 3 0.05
11 13 0.22
12 4 0.07
13 16 0.27
14 18 0.31
15 4 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (12 bp):
AATATTATATTT
Found at i:1515095 original size:15 final size:15
Alignment explanation
Indices: 1515077--1515213 Score: 82
Period size: 15 Copynumber: 9.9 Consensus size: 15
1515067 TTCATATTTA
*
1515077 ATATTTATATTTAAT
1 ATATTTATATTAAAT
1515092 ATA--TAT-TTAAAT
1 ATATTTATATTAAAT
*
1515104 ATAATTAT-TTAAAT
1 ATATTTATATTAAAT
**
1515118 ATAAATATATTAAAT
1 ATATTTATATTAAAT
1515133 ATATTTATATTAAA-
1 ATATTTATATTAAAT
*
1515147 ATA--TATA-TCAAT
1 ATATTTATATTAAAT
1515159 ATA-TT-TATTAAA-
1 ATATTTATATTAAAT
* *
1515171 AAATTTAATATAAAAT
1 ATATTT-ATATTAAAT
* * *
1515187 AAATTTTTATT-TAT
1 ATATTTATATTAAAT
*
1515201 ATATTTAAATTAA
1 ATATTTATATTAA
1515214 TTCAATTCAA
Statistics
Matches: 96, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
11 3 0.03
12 19 0.20
13 9 0.09
14 29 0.30
15 30 0.31
16 6 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTTATATTAAAT
Found at i:1515114 original size:14 final size:14
Alignment explanation
Indices: 1515084--1515151 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
1515074 TTAATATTTA
1515084 TATTT-AATAT-A-
1 TATTTAAATATAAT
1515095 TATTTAAATATAAT
1 TATTTAAATATAAT
*
1515109 TATTTAAATATAAA
1 TATTTAAATATAAT
*
1515123 TATATTAAATATATT
1 TAT-TTAAATATAAT
1515138 TATATTAAAATATA
1 TAT-TT-AAATATA
1515152 TATCAATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
11 5 0.10
12 5 0.10
13 1 0.02
14 16 0.33
15 15 0.31
16 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATTTAAATATAAT
Found at i:1516700 original size:13 final size:13
Alignment explanation
Indices: 1516664--1516693 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1516654 GCACTATTTA
*
1516664 TTATTATTAATAT
1 TTATCATTAATAT
1516677 TTATCATTAATAT
1 TTATCATTAATAT
1516690 TTAT
1 TTAT
1516694 TGATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATCATTAATAT
Found at i:1517477 original size:30 final size:31
Alignment explanation
Indices: 1517424--1517517 Score: 81
Period size: 32 Copynumber: 3.1 Consensus size: 31
1517414 AATTATTATT
* *
1517424 TAATAATTAAAAAAT--ATTTTTA-TTTAAA
1 TAATAAATAAAAAATAAAATTTTATTTTAAA
*
1517452 T-ATAAATATAAAAATAAAATTTTATTTTAAT
1 TAATAAATA-AAAAATAAAATTTTATTTTAAA
* *
1517483 TAATAAATAAATAAT-AAATTTAAATTTTTAAA
1 TAATAAATAAAAAATAAAATTT-TA-TTTTAAA
1517515 TAA
1 TAA
1517518 AATTTAATTC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
27 6 0.11
28 7 0.13
30 12 0.23
31 12 0.23
32 16 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TAATAAATAAAAAATAAAATTTTATTTTAAA
Found at i:1517526 original size:24 final size:24
Alignment explanation
Indices: 1517445--1517534 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 24
1517435 AAATATTTTT
* * *
1517445 ATTTAAATATAAATATAAAAATAAA
1 ATTT-AATTTAAATTTATAAATAAA
* * *
1517470 ATTTTATTTTAATTAATAAATAAA
1 ATTTAATTTAAATTTATAAATAAA
* * *
1517494 TAATAAATTTAAATTTTTAAATAAA
1 -ATTTAATTTAAATTTATAAATAAA
*
1517519 ATTTAATTCAAATTTA
1 ATTTAATTTAAATTTA
1517535 AACAGAAACA
Statistics
Matches: 48, Mismatches: 16, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
24 26 0.54
25 22 0.46
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTTAATTTAAATTTATAAATAAA
Found at i:1517776 original size:2 final size:2
Alignment explanation
Indices: 1517769--1517798 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1517759 GGGTGTGACC
1517769 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1517799 TGGGTTCTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1520657 original size:19 final size:19
Alignment explanation
Indices: 1520635--1520674 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1520625 TTAAATATAA
*
1520635 AATATAATTTTAAAA-ATTT
1 AATA-AATTTAAAAATATTT
1520654 AATAAATTTAAAAATATTT
1 AATAAATTTAAAAATATTT
1520673 AA
1 AA
1520675 ATTAAACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAAATTTAAAAATATTT
Found at i:1523769 original size:42 final size:40
Alignment explanation
Indices: 1523698--1523778 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 40
1523688 TAAATCTATA
* *
1523698 TATTAAATATTTTATATTATGTTATAAAATTATATTAAAAAT
1 TATTAAATATTTTATATCATGCTATAAAATT-T-TTAAAAAT
1523740 TATTAAA-ATTATTATA-CATGCTATCAAAATTTTTAAAAA
1 TATTAAATATT-TTATATCATGCTAT-AAAATTTTTAAAAA
1523779 ATAAACAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
40 7 0.20
41 10 0.29
42 18 0.51
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (40 bp):
TATTAAATATTTTATATCATGCTATAAAATTTTTAAAAAT
Found at i:1523880 original size:21 final size:21
Alignment explanation
Indices: 1523855--1523916 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
1523845 TCTCAAAAGA
* *
1523855 TATATTAAAAATTATGAAAAT
1 TATATTAAATATTATCAAAAT
* *
1523876 TATATCAAATATTATTAAAAT
1 TATATTAAATATTATCAAAAT
1523897 TATATTAAATATTATCAAAA
1 TATATTAAATATTATCAAAA
1523917 AATTACTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (21 bp):
TATATTAAATATTATCAAAAT
Found at i:1523926 original size:21 final size:20
Alignment explanation
Indices: 1523882--1523951 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
1523872 AAATTATATC
* * *
1523882 AAATATTATTAAAATTATATT
1 AAATATTATCAAAAAT-TACT
1523903 AAATATTATCAAAAAATTACT
1 AAATATTATC-AAAAATTACT
*
1523924 AAAT-TATATCAAATATTACT
1 AAATAT-TATCAAAAATTACT
1523944 AAA-ATTAT
1 AAATATTAT
1523952 ATCAAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.07
20 14 0.33
21 20 0.48
22 5 0.12
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATATTATCAAAAATTACT
Found at i:1523943 original size:20 final size:21
Alignment explanation
Indices: 1523909--1524031 Score: 87
Period size: 21 Copynumber: 5.9 Consensus size: 21
1523899 TATTAAATAT
*
1523909 TATCAAAAAATTACT-AAATTA
1 TATC-AAATATTACTAAAATTA
1523930 TATCAAATATTACTAAAATTA
1 TATCAAATATTACTAAAATTA
* *
1523951 TATCAAATATTA-TCAGAACTA
1 TATCAAATATTACT-AAAATTA
*
1523972 TATCAAA-ATTTA-TCAAATTTA
1 TATCAAATA-TTACT-AAAATTA
*
1523993 TTAT-AAACATTA-TAAAAATTA
1 -TATCAAATATTACT-AAAATTA
* *
1524014 TATAAAATATTACCAAAA
1 TATCAAATATTACTAAAA
1524032 CTCTTATAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
20 14 0.16
21 67 0.79
22 4 0.05
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.36
Consensus pattern (21 bp):
TATCAAATATTACTAAAATTA
Found at i:1523952 original size:21 final size:21
Alignment explanation
Indices: 1523924--1524031 Score: 105
Period size: 21 Copynumber: 5.1 Consensus size: 21
1523914 AAAAATTACT
1523924 AAATTATATCAAATATTA-CTA
1 AAATTATATCAAATATTATC-A
1523945 AAATTATATCAAATATTATCA
1 AAATTATATCAAATATTATCA
* *
1523966 GAACTATATCAAA-ATTTATCA
1 AAATTATATCAAATA-TTATCA
* * *
1523987 AATTTATTAT-AAACATTATAA
1 AAATTA-TATCAAATATTATCA
* *
1524008 AAATTATATAAAATATTACCA
1 AAATTATATCAAATATTATCA
1524029 AAA
1 AAA
1524032 CTCTTATAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.06
21 63 0.88
22 5 0.07
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (21 bp):
AAATTATATCAAATATTATCA
Found at i:1523986 original size:52 final size:51
Alignment explanation
Indices: 1523861--1524006 Score: 161
Period size: 52 Copynumber: 2.7 Consensus size: 51
1523851 AAGATATATT
* *
1523861 AAAAATTATGAAAATTATATCAAATATTATTAAAATTATATTAAATATTATCA
1 AAAAATTA-CAAAATTATATCAAATATTA-TAAAATTATATCAAATATTATCA
*
1523914 AAAAATTACTAAATTATATCAAATATTACTAAAATTATATCAAATATTATC-
1 AAAAATTACAAAATTATATCAAATATTA-TAAAATTATATCAAATATTATCA
* *
1523965 AGAACTATATCAAAATT-TATCAAATTTATTATAAACATTATA
1 AAAAAT-TA-CAAAATTATATCAAA--TATTATAAA-ATTATA
1524007 AAAATTATAT
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
51 4 0.05
52 48 0.59
53 18 0.22
54 11 0.14
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (51 bp):
AAAAATTACAAAATTATATCAAATATTATAAAATTATATCAAATATTATCA
Found at i:1525771 original size:23 final size:23
Alignment explanation
Indices: 1525725--1525771 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1525715 ACCGATGATT
** * *
1525725 TTTAAAATTTAAAATCTTTCCTA
1 TTTAAAATAAAAAATCATTACTA
1525748 TTTAAAATAAAAAATCATTACTA
1 TTTAAAATAAAAAATCATTACTA
1525771 T
1 T
1525772 ATGTTCCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAAATAAAAAATCATTACTA
Found at i:1526351 original size:14 final size:14
Alignment explanation
Indices: 1526328--1526371 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
1526318 CTTACAAAAT
1526328 ATAATATATAATTA
1 ATAATATATAATTA
*
1526342 ATAATTTATAATTA
1 ATAATATATAATTA
1526356 ATAATAATATATATTA
1 ATAAT-ATATA-ATTA
1526372 TATTTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 18 0.69
15 4 0.15
16 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAATATATAATTA
Found at i:1528950 original size:3 final size:3
Alignment explanation
Indices: 1528942--1528973 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1528932 GAAAGTTTAA
1528942 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1528974 AAACGTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1536423 original size:27 final size:26
Alignment explanation
Indices: 1536355--1536423 Score: 61
Period size: 27 Copynumber: 2.6 Consensus size: 26
1536345 CTAGATATTT
*
1536355 TGTTGATTATCGATGCTTTTAAGCAG
1 TGTTGATTATCAATGCTTTTAAGCAG
* *
1536381 TGTTAGGCTTGA--AATGCTTTTATGCATG
1 TGTT--GATT-ATCAATGCTTTTAAGCA-G
1536409 TGTTGATTATCAATG
1 TGTTGATTATCAATG
1536424 TTTAATGGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
25 1 0.03
26 7 0.21
27 16 0.48
28 8 0.24
29 1 0.03
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.43
Consensus pattern (26 bp):
TGTTGATTATCAATGCTTTTAAGCAG
Found at i:1541507 original size:21 final size:20
Alignment explanation
Indices: 1541481--1541541 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 20
1541471 ATATTATAAA
1541481 ATTATATGTATTAATAAAATT
1 ATTATAT-TATTAATAAAATT
*
1541502 ATTATAATATTTTTAA-AAAATT
1 A-T-T-ATATTATTAATAAAATT
1541524 -TTATATTATT-ATAAAATT
1 ATTATATTATTAATAAAATT
1541542 CAATCATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
17 1 0.03
18 13 0.38
19 1 0.03
20 1 0.03
21 1 0.03
22 7 0.21
23 6 0.18
24 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTATATTATTAATAAAATT
Found at i:1541538 original size:20 final size:21
Alignment explanation
Indices: 1541481--1541539 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1541471 ATATTATAAA
*
1541481 ATTATATGTATTA-ATAAAATT
1 ATTATAT-TATTATAAAAAATT
* *
1541502 ATTATAATATTTTTAAAAAATT
1 ATTATATTA-TTATAAAAAATT
1541524 -TTATATTATTATAAAA
1 ATTATATTATTATAAAA
1541540 TTCAATCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 9 0.29
21 15 0.48
22 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTATATTATTATAAAAAATT
Found at i:1541539 original size:18 final size:18
Alignment explanation
Indices: 1541472--1541541 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 18
1541462 TAATAAAAAA
1541472 TATTATAAAA--TTATAT
1 TATTATAAAATTTTATAT
1541488 GTATTAATAAAATTATTATAATAT
1 -TATT-ATAAAA-T-TT-T-ATAT
* *
1541512 TTTTAAAAAATTTTATAT
1 TATTATAAAATTTTATAT
1541530 TATTATAAAATT
1 TATTATAAAATT
1541542 CAATCATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
17 4 0.10
18 20 0.48
19 1 0.02
20 2 0.05
21 1 0.02
22 6 0.14
23 4 0.10
24 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (18 bp):
TATTATAAAATTTTATAT
Done.