Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold114
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: 3219552
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 36736 characters in sequence are not A, C, G, or T
File 11 of 13
Found at i:2648272 original size:2 final size:2
Alignment explanation
Indices: 2648265--2648290 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2648255 TTGTCTAGAA
2648265 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
2648291 TTATTATTTC
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:2652957 original size:2 final size:2
Alignment explanation
Indices: 2652950--2652974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2652940 GCATAAATAC
2652950 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2652975 ATTTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2654675 original size:10 final size:10
Alignment explanation
Indices: 2654660--2654684 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2654650 ACAAAGAAAC
2654660 AATTACTAGT
1 AATTACTAGT
2654670 AATTACTAGT
1 AATTACTAGT
2654680 AATTA
1 AATTA
2654685 ATTTGCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (10 bp):
AATTACTAGT
Found at i:2659217 original size:6 final size:6
Alignment explanation
Indices: 2659180--2659222 Score: 50
Period size: 6 Copynumber: 6.5 Consensus size: 6
2659170 TTTCACATAG
2659180 TATTTA TATTTTA TATTATAA TATTATA TATTTA TATTTA TAT
1 TATTTA TA-TTTA TATT-T-A TATT-TA TATTTA TATTTA TAT
2659223 GGTATCAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 15 0.44
7 12 0.35
8 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:2659379 original size:21 final size:19
Alignment explanation
Indices: 2659355--2659397 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2659345 CTCGGTATTA
*
2659355 ATAAAAATAACTATATAATAT
1 ATAAAAATAA-TA-ATAACAT
*
2659376 ATAAATATAATAATAACAT
1 ATAAAAATAATAATAACAT
2659395 ATA
1 ATA
2659398 GTATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAAATAATAATAACAT
Found at i:2659385 original size:13 final size:13
Alignment explanation
Indices: 2659355--2659397 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
2659345 CTCGGTATTA
*
2659355 ATAAAAATAACTAT
1 ATAATAATAAC-AT
2659369 ATAATATATAA-AT
1 ATAATA-ATAACAT
2659382 ATAATAATAACAT
1 ATAATAATAACAT
2659395 ATA
1 ATA
2659398 GTATTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.50
14 5 0.19
15 4 0.15
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAATAATAACAT
Found at i:2660408 original size:21 final size:21
Alignment explanation
Indices: 2660362--2660409 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2660352 TAATATTTAT
*
2660362 ATTATTTTTTTAGATCATATT
1 ATTATTTTTTTAGATCATATA
* **
2660383 TTTATTTTTTTATTTCATATA
1 ATTATTTTTTTAGATCATATA
2660404 ATTATT
1 ATTATT
2660410 AAATATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTATTTTTTTAGATCATATA
Found at i:2660761 original size:13 final size:12
Alignment explanation
Indices: 2660739--2660789 Score: 59
Period size: 13 Copynumber: 4.1 Consensus size: 12
2660729 GATTTTTTAT
2660739 TAAAAAATAATA
1 TAAAAAATAATA
*
2660751 CTAAAATATAA-A
1 -TAAAAAATAATA
2660763 TAAAAAATAATA
1 TAAAAAATAATA
2660775 TAATATAAATAATA
1 TAA-A-AAATAATA
2660789 T
1 T
2660790 TTTAAGAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 9 0.27
12 5 0.15
13 10 0.30
14 9 0.27
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAAAAATAATA
Found at i:2660766 original size:24 final size:21
Alignment explanation
Indices: 2660739--2660786 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 21
2660729 GATTTTTTAT
2660739 TAAAAAATAATACTAAAATATAAA
1 TAAAAAATAATA-T--AATATAAA
2660763 TAAAAAATAATATAATATAAA
1 TAAAAAATAATATAATATAAA
2660784 TAA
1 TAA
2660787 TATTTTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.46
23 1 0.04
24 12 0.50
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAAAAATAATATAATATAAA
Found at i:2668374 original size:32 final size:32
Alignment explanation
Indices: 2668303--2668374 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
2668293 AATCTTAAAT
* **
2668303 TAAAATAATAATAAATTATTAATTATTATATC
1 TAAAATAATAATAAATTATTAATTATTAAAAA
*
2668335 TAAAATAATAATATATTAATTAATT-TTAAAAA
1 TAAAATAATAATAAATT-ATTAATTATTAAAAA
*
2668367 TATAATAA
1 TAAAATAA
2668375 AAATTTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 27 0.79
33 7 0.21
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
TAAAATAATAATAAATTATTAATTATTAAAAA
Found at i:2672417 original size:2 final size:2
Alignment explanation
Indices: 2672412--2672436 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2672402 ATATATGTAT
2672412 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
2672437 ACCAAACACA
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:2677953 original size:28 final size:30
Alignment explanation
Indices: 2677922--2677987 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
2677912 TTATTTTTTT
* *
2677922 TATAAAAATTTAAAATTT-TTTATT-AAAA
1 TATAAAAATTCAAAATTTCTTAATTAAAAA
* *
2677950 TATATAAA-TCACAATTTCTTAATTAAAAA
1 TATAAAAATTCAAAATTTCTTAATTAAAAA
2677979 TATAAAAAT
1 TATAAAAAT
2677988 AACACTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
27 7 0.23
28 12 0.40
29 11 0.37
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (30 bp):
TATAAAAATTCAAAATTTCTTAATTAAAAA
Found at i:2677958 original size:21 final size:20
Alignment explanation
Indices: 2677917--2677958 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2677907 ACTTATTATT
*
2677917 TTTTTTATAAAAATTTAAAA
1 TTTTTTATAAAAATATAAAA
*
2677937 TTTTTTATTAAAATATATAAA
1 TTTTTTATAAAAATATA-AAA
2677958 T
1 T
2677959 CACAATTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTTTATAAAAATATAAAA
Found at i:2678155 original size:3 final size:3
Alignment explanation
Indices: 2678147--2678176 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2678137 TAAAATATGT
*
2678147 TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2678177 AAAATTTAAA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:2679357 original size:2 final size:2
Alignment explanation
Indices: 2679350--2679383 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2679340 CTATGTTATT
2679350 TA TA TA TA TA TA TA TA TA T- 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
2679384 CTATGTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2688207 original size:3 final size:3
Alignment explanation
Indices: 2688199--2688246 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
2688189 TGATTACATC
* *
2688199 TTA TTA TTA GTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2688247 ATCTTGCATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2688397 original size:3 final size:3
Alignment explanation
Indices: 2688389--2688415 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2688379 GAAAGCACAG
2688389 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2688416 GCCATAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2689765 original size:2 final size:2
Alignment explanation
Indices: 2689758--2689794 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2689748 TCAATGCATT
2689758 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2689795 ATATATATAT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2689799 original size:2 final size:2
Alignment explanation
Indices: 2689794--2689826 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2689784 TCTCTCTCTC
2689794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2689827 TCTTCTTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2691668 original size:2 final size:2
Alignment explanation
Indices: 2691644--2691692 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
2691634 AATTCTAGTC
2691644 TA TA -A TA TA -A TA T- TA TA TA -A 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
2691682 TA TA TA TA TA T
1 TA TA TA TA TA T
2691693 GTCAGTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2693248 original size:2 final size:2
Alignment explanation
Indices: 2693236--2693277 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
2693226 CTTTCTCTTG
*
2693236 TA TA CA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2693275 TA T
1 TA T
2693278 TATTTTAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2693854 original size:18 final size:18
Alignment explanation
Indices: 2693833--2693867 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2693823 TATTAATATT
*
2693833 AAATAATAAATAAATAAA
1 AAATAAAAAATAAATAAA
*
2693851 AAATAAAAAATTAATAA
1 AAATAAAAAATAAATAA
2693868 CTGTATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAAAAATAAATAAA
Found at i:2695342 original size:31 final size:32
Alignment explanation
Indices: 2695270--2695360 Score: 112
Period size: 32 Copynumber: 2.9 Consensus size: 32
2695260 TTAAAATCGG
** *
2695270 TAAAAAATCAAAATTAAGCGATAAAATTTAAT
1 TAAAAAATCAAAATTAAGTAACAAAATTTAAT
*
2695302 TAAAAAATCAAAATTCAGTAACAAAATTTAAT
1 TAAAAAATCAAAATTAAGTAACAAAATTTAAT
* * *
2695334 T-AAAAATCAAATTTTAGTTACAAAATT
1 TAAAAAATCAAAATTAAGTAACAAAATT
2695361 CAATCAAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
31 23 0.44
32 29 0.56
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (32 bp):
TAAAAAATCAAAATTAAGTAACAAAATTTAAT
Found at i:2695739 original size:1 final size:1
Alignment explanation
Indices: 2695733--2695759 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2695723 GTAATTTGAG
2695733 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
2695760 CTGTTGATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2703777 original size:71 final size:72
Alignment explanation
Indices: 2703648--2703809 Score: 209
Period size: 71 Copynumber: 2.3 Consensus size: 72
2703638 AAAGGGTTTT
* * * *
2703648 AGAATCCGACCTTCCAATCACTAATTGCCCTGTCCAGTGTCTTTAATTATACCATCTTCAATTAT
1 AGAATCCAACCTTCAAATCACTAATTGCCATGTCCAGTGTCTGTAATTATACCATCTTCAATTAT
2703713 TTTATAA
66 TTTATAA
* ****
2703720 AG-ATCCAACCTTCAAATCACTAATTGCCATGTTCAGTGTCTGTAATTATGTTTTCTTCAATTAT
1 AGAATCCAACCTTCAAATCACTAATTGCCATGTCCAGTGTCTGTAATTATACCATCTTCAATTAT
* *
2703784 TTTGTGA
66 TTTATAA
*
2703791 AGAATCCAACCTACAAATC
1 AGAATCCAACCTTCAAATC
2703810 GTGTGAGGGT
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
71 60 0.78
72 17 0.22
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (72 bp):
AGAATCCAACCTTCAAATCACTAATTGCCATGTCCAGTGTCTGTAATTATACCATCTTCAATTAT
TTTATAA
Found at i:2704589 original size:11 final size:11
Alignment explanation
Indices: 2704561--2704604 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2704551 TTAAAATATG
2704561 TATTCTATATTA
1 TATT-TATATTA
2704573 TAATTTATATTA
1 T-ATTTATATTA
*
2704585 TATTTATATAA
1 TATTTATATTA
*
2704596 TTTTTATAT
1 TATTTATAT
2704605 AATTCTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 17 0.59
12 9 0.31
13 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTTATATTA
Found at i:2705403 original size:3 final size:3
Alignment explanation
Indices: 2705395--2705447 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
2705385 TTAGGTGCAG
2705395 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2705443 TTA TT
1 TTA TT
2705448 TTACATTTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2705985 original size:2 final size:2
Alignment explanation
Indices: 2705978--2706008 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2705968 CTCAAAACAG
2705978 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
2706009 TAAAAAGTTA
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:2706972 original size:17 final size:17
Alignment explanation
Indices: 2706937--2706987 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
2706927 TAATATTTTT
*
2706937 ATTA-TTTTAATTGAAAA
1 ATTATTTTTAA-TGATAA
2706954 ATTATTTTTAATGATAA
1 ATTATTTTTAATGATAA
*
2706971 A-TATTTTTTAT-ATAA
1 ATTATTTTTAATGATAA
2706986 AT
1 AT
2706988 AAATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 5 0.17
16 9 0.30
17 10 0.33
18 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
ATTATTTTTAATGATAA
Found at i:2706985 original size:15 final size:16
Alignment explanation
Indices: 2706941--2706988 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2706931 ATTTTTATTA
*
2706941 TTTTAATTGAAAAATTAT
1 TTTTAA-TGATAAA-TAT
2706959 TTTTAATGATAAATAT
1 TTTTAATGATAAATAT
*
2706975 TTTTTAT-ATAAATA
1 TTTTAATGATAAATA
2706989 AATATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.25
16 9 0.32
17 6 0.21
18 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (16 bp):
TTTTAATGATAAATAT
Found at i:2712853 original size:2 final size:2
Alignment explanation
Indices: 2712846--2712878 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2712836 TGTAAACTTG
2712846 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2712879 TCCCTCTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2714805 original size:33 final size:35
Alignment explanation
Indices: 2714751--2714819 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 35
2714741 AATTAAATTA
* * *
2714751 ATTTATATTATATTATA-TTTTTAAA-AAAATAAT
1 ATTTATAATATATTAAATTTTTTAAATAAAAAAAT
2714784 ATTTATAATAT-TTAAATTTTTTTAAATAAAAAAAT
1 ATTTATAATATATTAAA-TTTTTTAAATAAAAAAAT
2714819 A
1 A
2714820 AATGAGCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 4 0.13
33 10 0.33
34 8 0.27
35 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATTTATAATATATTAAATTTTTTAAATAAAAAAAT
Found at i:2719318 original size:16 final size:17
Alignment explanation
Indices: 2719297--2719332 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2719287 TCTAAGACGG
2719297 ATCTTA-ATTAATTTGC
1 ATCTTACATTAATTTGC
*
2719313 ATCTTACATTGATTTGC
1 ATCTTACATTAATTTGC
2719330 ATC
1 ATC
2719333 AATTTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (17 bp):
ATCTTACATTAATTTGC
Found at i:2722637 original size:2 final size:2
Alignment explanation
Indices: 2722630--2722661 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2722620 ACATACATAC
2722630 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
2722662 GACTGGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2723967 original size:44 final size:44
Alignment explanation
Indices: 2723904--2724030 Score: 254
Period size: 44 Copynumber: 2.9 Consensus size: 44
2723894 AAAAAAGTAA
2723904 GAAGAATAAGAACGAGAATAGAGAGGAAATAAATGATTTGTTAT
1 GAAGAATAAGAACGAGAATAGAGAGGAAATAAATGATTTGTTAT
2723948 GAAGAATAAGAACGAGAATAGAGAGGAAATAAATGATTTGTTAT
1 GAAGAATAAGAACGAGAATAGAGAGGAAATAAATGATTTGTTAT
2723992 GAAGAATAAGAACGAGAATAGAGAGGAAATAAATGATTT
1 GAAGAATAAGAACGAGAATAGAGAGGAAATAAATGATTT
2724031 CAAAATAACT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 83 1.00
ACGTcount: A:0.51, C:0.02, G:0.25, T:0.21
Consensus pattern (44 bp):
GAAGAATAAGAACGAGAATAGAGAGGAAATAAATGATTTGTTAT
Found at i:2725102 original size:32 final size:32
Alignment explanation
Indices: 2725066--2725139 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
2725056 CAGCGATTTG
*
2725066 TATCGGTACATAAGTGTTGTATCGATACAATA
1 TATCGATACATAAGTGTTGTATCGATACAATA
*
2725098 TATCGATACATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATA
*
2725130 TATCGTTACA
1 TATCGATACA
2725140 AAGCTATTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATA
Found at i:2725122 original size:19 final size:19
Alignment explanation
Indices: 2725063--2725126 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
2725053 TTTCAGCGAT
*
2725063 TTGTATCGGTACATAAGTG
1 TTGTATCGATACATAAGTG
2725082 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
2725096 -TATATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
2725114 TTGTATCGATACA
1 TTGTATCGATACA
2725127 ATGTATCGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:2727597 original size:51 final size:51
Alignment explanation
Indices: 2727541--2727653 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
2727531 AATTCTCCGC
2727541 AATCGGGGATA-TCCTAACTCCGATTTTATTT-TCAAAACA-CTAATTTTCTAT
1 AATCGGGGATACTCC-AACTCCGATTTTATTTCT-AAAACATC-AATTTTCTAT
2727592 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAA-TTT-T-T
1 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTCTAT
*
2727640 CATCGGGGATACTC
1 AATCGGGGATACTC
2727654 TAACCCCGTT
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
48 14 0.24
49 1 0.02
50 3 0.05
51 35 0.60
52 5 0.09
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTCTAT
Found at i:2727670 original size:27 final size:27
Alignment explanation
Indices: 2727639--2727715 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
2727629 CATCAATTTT
*
2727639 TCATCGGGGATACTCTAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
*
2727666 TCATCGGGGATACTCCGACCCCGTT-A
1 TCATCGGGGATACTCCAACCCCGTTAA
**
2727692 TTTTCGAGGGGATACTCCAACCCC
1 TCATC--GGGGATACTCCAACCCC
2727716 CGGCTTTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.09
27 23 0.53
28 16 0.37
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:2727840 original size:79 final size:79
Alignment explanation
Indices: 2727668--2727984 Score: 433
Period size: 79 Copynumber: 4.0 Consensus size: 79
2727658 CCCGTTAATC
* *
2727668 ATCGGGGATACTCCGACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA-CCCCGGCTTTATTTCTAAAA
*
2727733 TATTGATTTCTCATA
65 TATTAATTTCTCATA
2727748 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAT
2727813 ATTAATTTCTCATA
66 ATTAATTTCTCATA
* * * * *
2727827 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCAGTTTTATTTC-CAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAT
** * *
2727891 CATCGATTTTTCACA
66 -ATTAATTTCTCATA
* * *
2727906 ATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCC-G-TTACTATCTCCAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTT--TATTTCTAAA
2727969 ATATTAAATTTCTCAT
64 ATATT-AATTTCTCAT
2727985 CGGGAAATAT
Statistics
Matches: 211, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
77 2 0.01
78 5 0.02
79 150 0.71
80 54 0.26
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAT
ATTAATTTCTCATA
Found at i:2742572 original size:3 final size:3
Alignment explanation
Indices: 2742564--2742596 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2742554 CTGCTTCCTG
2742564 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2742597 CCAAATAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2744421 original size:1 final size:1
Alignment explanation
Indices: 2744415--2744439 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2744405 GTGAGAAATG
2744415 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2744440 GAGAGTCCAA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2756764 original size:16 final size:16
Alignment explanation
Indices: 2756717--2756766 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
2756707 TGACTAGTAT
*
2756717 TAAATTAAATTTAAATA
1 TAAATT-AATTAAAATA
*
2756734 -AAATT-TTTAATAATA
1 TAAATTAATTAA-AATA
2756749 TAAATTAATTAAAATA
1 TAAATTAATTAAAATA
2756765 TA
1 TA
2756767 TTAAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
14 3 0.11
15 4 0.15
16 16 0.59
17 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTAATTAAAATA
Found at i:2757430 original size:23 final size:24
Alignment explanation
Indices: 2757404--2757473 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
2757394 AAATTATTTG
2757404 TTAATAAAATATTATAATATAAT-
1 TTAATAAAATATTATAATATAATA
* *
2757427 TTAATGATAATA-TATAAATTTATATA
1 TTAAT-AAAATATTAT-AATATA-ATA
*
2757453 TTAATAATATATTA-AATATAA
1 TTAATAAAATATTATAATATAA
2757474 ATCTATTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
23 9 0.24
24 15 0.41
25 6 0.16
26 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
TTAATAAAATATTATAATATAATA
Found at i:2757481 original size:26 final size:25
Alignment explanation
Indices: 2757404--2757473 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 25
2757394 AAATTATTTG
* *
2757404 TTAATAAAATATTATAATATAATTTA
1 TTAATAATATATTA-AATATAATATA
* * *
2757430 ATGATAATATA-TAAAT-TTATATA
1 TTAATAATATATTAAATATAATATA
2757453 TTAATAATATATTAAATATAA
1 TTAATAATATATTAAATATAA
2757474 ATCTATTATA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
23 14 0.41
24 8 0.24
25 4 0.12
26 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (25 bp):
TTAATAATATATTAAATATAATATA
Found at i:2766077 original size:2 final size:2
Alignment explanation
Indices: 2766070--2766095 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2766060 AAGTAAAAAG
2766070 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
2766096 GAGATTAAAA
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:2766227 original size:30 final size:30
Alignment explanation
Indices: 2766115--2766228 Score: 83
Period size: 30 Copynumber: 3.8 Consensus size: 30
2766105 ATAAAAAAGT
* * *
2766115 AAAAGATATTTC-TACTTTAAAATTTTATAA
1 AAAATATATTTCAT-CTTCAAAATTTAATAA
* *
2766145 AAAATATATTT-ATTTTCAATCATTTAA-AA
1 AAAATATATTTCATCTTCAA-AATTTAATAA
* * * *
2766174 AATATTTACTTAAT-TTCTTAAAATTTAATAA
1 AAAATATATTTCATCTTC--AAAATTTAATAA
2766205 AAAATATATTTCATCTTCAAAATT
1 AAAATATATTTCATCTTCAAAATT
2766229 ATTATTTTTA
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
29 17 0.27
30 30 0.47
31 14 0.22
32 3 0.05
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.45
Consensus pattern (30 bp):
AAAATATATTTCATCTTCAAAATTTAATAA
Found at i:2775311 original size:15 final size:15
Alignment explanation
Indices: 2775293--2775333 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2775283 TAAAGATTTT
2775293 TTTATTAATATTAAA
1 TTTATTAATATTAAA
2775308 TTTATTAATA--AAA
1 TTTATTAATATTAAA
*
2775321 -TTATTATTATTAA
1 TTTATTAATATTAA
2775334 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
14 2 0.09
15 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTATTAATATTAAA
Found at i:2775767 original size:2 final size:2
Alignment explanation
Indices: 2775760--2775784 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2775750 CATTATTTAC
2775760 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2775785 AAACCTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2775957 original size:22 final size:20
Alignment explanation
Indices: 2775915--2775971 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
2775905 AAATTACTTA
* *
2775915 AAAATAAAAT-AATATAATT
1 AAAATAAAATAAAAAAAATT
2775934 AAACATAAAACTAAAAAAAATT
1 AAA-ATAAAA-TAAAAAAAATT
*
2775956 AAATTAAAATAAAAAA
1 AAAATAAAATAAAAAA
2775972 TTTTACTGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 3 0.09
20 13 0.41
21 6 0.19
22 10 0.31
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATAAAATAAAAAAAATT
Found at i:2776265 original size:220 final size:221
Alignment explanation
Indices: 2776005--2776447 Score: 703
Period size: 224 Copynumber: 2.0 Consensus size: 221
2775995 TAAAATATTA
*
2776005 ACTATTTTATTCGTATTATTTAAAAATAAAATAATTTTTAAAATAAATTATTAAAAAATAATATA
1 ACTATTTTACTCGTATTATTTAAAAATAAAATAATTTTTAAAATAAATTATTAAAAAATAATATA
* *
2776070 AATTAAATAACGAAACTAAAAGTTAAAACTAAAAAACAAATAAAACTAAC-AAA-AAAAAACTTG
66 AATTAAATAACGAAACTAAAAGTTAAAACTAAAAAA-AAATAAAACTAACAAAATAAAAAAATTA
* *
2776133 ACATATATATTACACAAAATTATTTTTTAATTTTTTTAAAAAATCAAATATTAATTTTAAATTAT
130 ACATACATATTACACAAAATTATTTTTTAATTTTTTTAAAAAATCAAATATAAATTTTAAATTAT
* * *
2776198 CGTGTAAAATATGTGATAAATTTTTTT
195 CGTATAAAATATATGACAAATTTTTTT
2776225 ACTATTTTACTCGTATTATTT-AAAATAAAATAATTTTTTAAAATAAATTATTAAAAAATAATAT
1 ACTATTTTACTCGTATTATTTAAAAATAAAATAA-TTTTTAAAATAAATTATTAAAAAATAATAT
*
2776289 AAATTAAATAACGAAACTAAAAGTTAAAACTTAAAAAAAATAAAACTAACAAAAAAATAAAAAAA
65 AAATTAAATAACGAAACTAAAAGTTAAAACTAAAAAAAAATAAAACTAAC---AAAATAAAAAAA
* * *
2776354 TTAACATACATATTACATAAAATTATTTTTTAATTTTTTTTAAAAATCATATATAAATTTTAAAT
127 TTAACATACATATTACACAAAATTATTTTTTAATTTTTTTAAAAAATCAAATATAAATTTTAAAT
*
2776419 TATCGTATGAAATATATGACAAATTTTTT
192 TATCGTATAAAATATATGACAAATTTTTT
2776448 ATTATATTAT
Statistics
Matches: 204, Mismatches: 13, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
219 25 0.12
220 86 0.42
223 3 0.01
224 90 0.44
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (221 bp):
ACTATTTTACTCGTATTATTTAAAAATAAAATAATTTTTAAAATAAATTATTAAAAAATAATATA
AATTAAATAACGAAACTAAAAGTTAAAACTAAAAAAAAATAAAACTAACAAAATAAAAAAATTAA
CATACATATTACACAAAATTATTTTTTAATTTTTTTAAAAAATCAAATATAAATTTTAAATTATC
GTATAAAATATATGACAAATTTTTTT
Found at i:2776332 original size:16 final size:17
Alignment explanation
Indices: 2776313--2776350 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2776303 AACTAAAAGT
*
2776313 TAAAACTTA-AAAAAAA
1 TAAAACTAACAAAAAAA
2776329 TAAAACTAACAAAAAAA
1 TAAAACTAACAAAAAAA
2776346 TAAAA
1 TAAAA
2776351 AAATTAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (17 bp):
TAAAACTAACAAAAAAA
Found at i:2776353 original size:20 final size:19
Alignment explanation
Indices: 2776321--2776359 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2776311 GTTAAAACTT
*
2776321 AAAAAAAATAAAACTAACA
1 AAAAAAAAAAAAACTAACA
*
2776340 AAAAAATAAAAAAATTAACA
1 AAAAAA-AAAAAAACTAACA
2776360 TACATATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (19 bp):
AAAAAAAAAAAAACTAACA
Found at i:2785702 original size:24 final size:24
Alignment explanation
Indices: 2785670--2785718 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2785660 GGTTGAGCTA
2785670 TTCGTCTTCTGGAAGTGAGAATGC
1 TTCGTCTTCTGGAAGTGAGAATGC
2785694 TTCGTCTTCTGGAAGTGAGAATGC
1 TTCGTCTTCTGGAAGTGAGAATGC
2785718 T
1 T
2785719 GGTGATGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (24 bp):
TTCGTCTTCTGGAAGTGAGAATGC
Found at i:2791873 original size:15 final size:17
Alignment explanation
Indices: 2791853--2791889 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2791843 TAGCTGCCTA
2791853 TTTTTCA-TTCA-TTTT
1 TTTTTCAGTTCAGTTTT
2791868 TTTTTCAGTTTCAGTTTT
1 TTTTTCAG-TTCAGTTTT
2791886 TTTT
1 TTTT
2791890 ATTAAAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
17 4 0.21
18 8 0.42
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTTCAGTTCAGTTTT
Found at i:2803964 original size:14 final size:14
Alignment explanation
Indices: 2803947--2803976 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2803937 ATTTTTGTGT
2803947 TTAAATTTATTTTA
1 TTAAATTTATTTTA
2803961 TTAAATTTATTTTA
1 TTAAATTTATTTTA
2803975 TT
1 TT
2803977 TTTTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTAAATTTATTTTA
Found at i:2803972 original size:18 final size:16
Alignment explanation
Indices: 2803951--2803991 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 16
2803941 TTGTGTTTAA
2803951 ATTTATTTTATTAAATTT
1 ATTTATTTT-TTAAA-TT
2803969 ATTTTATTTTTTAAATT
1 A-TTTATTTTTTAAATT
2803986 ATTTAT
1 ATTTAT
2803992 ATCTGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.23
17 3 0.14
18 6 0.27
19 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTATTTTTTAAATT
Found at i:2810916 original size:2 final size:2
Alignment explanation
Indices: 2810909--2810941 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2810899 TGGCCATAAA
2810909 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2810942 TAGCTTAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2811969 original size:2 final size:2
Alignment explanation
Indices: 2811962--2811995 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2811952 TATCATTCTT
* *
2811962 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2811996 ATGACATGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2812581 original size:6 final size:6
Alignment explanation
Indices: 2812572--2812626 Score: 51
Period size: 7 Copynumber: 8.8 Consensus size: 6
2812562 GTTATAAGAT
*
2812572 ATTTAA ATTT-A ATTTGAA ATTTAAA ATTTAAA ATTTGAA GTTT-A ATTTAA
1 ATTTAA ATTTAA ATTT-AA ATTT-AA ATTT-AA ATTT-AA ATTTAA ATTTAA
2812622 ATTTA
1 ATTTA
2812627 TAAAAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
5 9 0.21
6 10 0.24
7 23 0.55
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (6 bp):
ATTTAA
Found at i:2812844 original size:22 final size:22
Alignment explanation
Indices: 2812813--2812856 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2812803 TAAAATAAAA
* *
2812813 AATTATATTAAATCTATAAATT
1 AATTAAATTAAATATATAAATT
*
2812835 AATTAAATTAAATATTTAAATT
1 AATTAAATTAAATATATAAATT
2812857 TAACTCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTAAATTAAATATATAAATT
Found at i:2821506 original size:34 final size:34
Alignment explanation
Indices: 2821468--2821552 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
2821458 TGTGGTAACT
2821468 TTTAAGCAAGAATTAAATGGGATTTGTTGTATTG
1 TTTAAGCAAGAATTAAATGGGATTTGTTGTATTG
2821502 TTTAAGCAAGAATTAAATGGGATTTGTTGTATTG
1 TTTAAGCAAGAATTAAATGGGATTTGTTGTATTG
* *
2821536 TTTAAGCATGGATTAAA
1 TTTAAGCAAGAATTAAA
2821553 CTTGGGTTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTAAGCAAGAATTAAATGGGATTTGTTGTATTG
Found at i:2822530 original size:2 final size:2
Alignment explanation
Indices: 2822523--2822573 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2822513 GGGCACAGAA
2822523 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2822565 AG AG AG AG A
1 AG AG AG AG A
2822574 TTCCAGCTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2834632 original size:18 final size:19
Alignment explanation
Indices: 2834592--2834632 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
2834582 GTCCCCCTTT
2834592 TGCATGCTTGATACTTTTA
1 TGCATGCTTGATACTTTTA
* *
2834611 -GCATGTTTGTTA-TTTTA
1 TGCATGCTTGATACTTTTA
2834628 TGCAT
1 TGCAT
2834633 CTTCATATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (19 bp):
TGCATGCTTGATACTTTTA
Found at i:2839100 original size:2 final size:2
Alignment explanation
Indices: 2839093--2839126 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2839083 TCTTTCTAAA
2839093 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2839127 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2839131 original size:2 final size:2
Alignment explanation
Indices: 2839126--2839150 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2839116 CTCTCTCTCT
2839126 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
2839151 TCACTCTTGC
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2845051 original size:2 final size:2
Alignment explanation
Indices: 2845044--2845078 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2845034 AGACTGCTCT
2845044 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
2845079 TTGTTTAAAT
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:2849331 original size:2 final size:2
Alignment explanation
Indices: 2849324--2849354 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2849314 GTAATTGGGG
2849324 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2849355 CATGTATACT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2857306 original size:27 final size:28
Alignment explanation
Indices: 2857272--2857342 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
2857262 GTCACCCATT
2857272 TATTTGTCAAAAATGGTGGTTAT-TTTA
1 TATTTGTCAAAAATGGTGGTTATCTTTA
* * * *
2857299 TGTTTGTCAAAAATGATGGTTTTCTTTG
1 TATTTGTCAAAAATGGTGGTTATCTTTA
*
2857327 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
2857343 AGGCTTGTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.27, C:0.06, G:0.20, T:0.48
Consensus pattern (28 bp):
TATTTGTCAAAAATGGTGGTTATCTTTA
Found at i:2857462 original size:20 final size:20
Alignment explanation
Indices: 2857439--2857478 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2857429 AGGCTCCCAA
2857439 ATCCATCTCTAGCATCCCTC
1 ATCCATCTCTAGCATCCCTC
* * *
2857459 ATCCTTCTCTTGTATCCCTC
1 ATCCATCTCTAGCATCCCTC
2857479 TTCAATTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.42, G:0.05, T:0.38
Consensus pattern (20 bp):
ATCCATCTCTAGCATCCCTC
Found at i:2859960 original size:21 final size:22
Alignment explanation
Indices: 2859931--2859976 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2859921 TGTTCAGACA
** *
2859931 AGTAGTACTCCGTAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2859953 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2859974 AGT
1 AGT
2859977 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2861914 original size:28 final size:27
Alignment explanation
Indices: 2861859--2861929 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
2861849 GCCACCCATT
2861859 TATTTGTCAAAAATGGTAGTGATTTTG
1 TATTTGTCAAAAATGGTAGTGATTTTG
* * *
2861886 TGTTTGTCAAAAATGGTGGT-TTCCTTTG
1 TATTTGTCAAAAATGGTAGTGAT--TTTG
*
2861914 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
2861930 AGGCTTGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.49
28 18 0.49
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTAGTGATTTTG
Found at i:2862049 original size:20 final size:20
Alignment explanation
Indices: 2862026--2862065 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2862016 AGGCTCCCAA
2862026 ATCCATCTCTAGCATCCCTC
1 ATCCATCTCTAGCATCCCTC
* * *
2862046 ATCCTTCTCTTGTATCCCTC
1 ATCCATCTCTAGCATCCCTC
2862066 TTCAATTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.42, G:0.05, T:0.38
Consensus pattern (20 bp):
ATCCATCTCTAGCATCCCTC
Found at i:2875740 original size:17 final size:18
Alignment explanation
Indices: 2875718--2875752 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2875708 CTTCAAATGC
2875718 TAATG-AGAAAAAAAAAT
1 TAATGAAGAAAAAAAAAT
2875735 TAATGAAAGAAAAAAAAA
1 TAATG-AAGAAAAAAAAA
2875753 ACTGAAGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
19 11 0.69
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (18 bp):
TAATGAAGAAAAAAAAAT
Found at i:2876452 original size:20 final size:17
Alignment explanation
Indices: 2876426--2876468 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2876416 AATTTATTAA
*
2876426 ATATTATATTTAATATAAT
1 ATATTAT-TATAA-ATAAT
2876445 ATTATTATTATAAATAAT
1 A-TATTATTATAAATAAT
2876463 ATATTA
1 ATATTA
2876469 ATTAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 5 0.23
20 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATTATAAATAAT
Found at i:2887457 original size:2 final size:2
Alignment explanation
Indices: 2887450--2887502 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2887440 CTAGCTAATC
2887450 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
2887492 AT AT AT AT AT A
1 AT AT AT AT AT A
2887503 AATTTTTGTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2888836 original size:3 final size:3
Alignment explanation
Indices: 2888828--2888853 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2888818 ACGCCACCCA
2888828 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2888854 AAACAAAACA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2895390 original size:3 final size:3
Alignment explanation
Indices: 2895382--2895412 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2895372 ATTTACAACC
*
2895382 ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2895413 CATTGCATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:2900372 original size:2 final size:2
Alignment explanation
Indices: 2900367--2900391 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2900357 TTAACTTAAA
2900367 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
2900392 AACTTGACGT
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:2901974 original size:23 final size:20
Alignment explanation
Indices: 2901933--2901981 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
2901923 AAAATGACTC
*
2901933 AAATCTGTTGAATTCAACTGTT
1 AAATCTGTTGAATTAAAC--TT
*
2901955 AAATCTGATTGACTTAAACTT
1 AAATCTG-TTGAATTAAACTT
2901976 AAATCT
1 AAATCT
2901982 AAAATTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 7 0.29
23 9 0.38
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (20 bp):
AAATCTGTTGAATTAAACTT
Found at i:2902696 original size:22 final size:21
Alignment explanation
Indices: 2902658--2902703 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
2902648 AAACATTTTT
2902658 TAATGTAAATATTATTTTAACTA
1 TAATGTAAATATTA-TTTAA-TA
*
2902681 TAATTTAAA-ATTATTTAATA
1 TAATGTAAATATTATTTAATA
2902701 TAA
1 TAA
2902704 ATATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 4 0.18
23 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TAATGTAAATATTATTTAATA
Found at i:2903056 original size:25 final size:24
Alignment explanation
Indices: 2902988--2903066 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
2902978 GGAAAAAAAA
**
2902988 TTTATATATTTGT-ATTTATGTTATT
1 TTTATATATTAATAATTTAT-TT-TT
*
2903013 TTTATATA--AAAAATATTATATTTT
1 TTTATATATTAATAAT-TTAT-TTTT
2903037 TTTATATATTAATAATTTATTTTAT
1 TTTATATATTAATAATTTATTTT-T
2903062 TTTAT
1 TTTAT
2903067 GTATATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
24 15 0.34
25 24 0.55
26 5 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (24 bp):
TTTATATATTAATAATTTATTTTT
Found at i:2904184 original size:13 final size:13
Alignment explanation
Indices: 2904147--2904216 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
2904137 TATTTTATAT
*
2904147 TTTATATATTAAA
1 TTTATTTATTAAA
*
2904160 TTTCAATT-TTAAA
1 TTT-ATTTATTAAA
2904173 TTTATTTATTAAA
1 TTTATTTATTAAA
*
2904186 TAT-TTTATATAAA
1 TTTATTTAT-TAAA
*
2904199 TTTTATTAACTTAAA
1 -TTTATTTA-TTAAA
2904214 TTT
1 TTT
2904217 CATAATATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
12 8 0.18
13 22 0.49
14 7 0.16
15 7 0.16
16 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTATTTATTAAA
Found at i:2906900 original size:18 final size:18
Alignment explanation
Indices: 2906879--2906918 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2906869 TCCACGACCA
2906879 CCTCCACCTCCACCTCCG
1 CCTCCACCTCCACCTCCG
* * *
2906897 CCTCCGCGTCCACCTCGG
1 CCTCCACCTCCACCTCCG
2906915 CCTC
1 CCTC
2906919 TAGAATTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.07, C:0.62, G:0.12, T:0.17
Consensus pattern (18 bp):
CCTCCACCTCCACCTCCG
Found at i:2909404 original size:2 final size:2
Alignment explanation
Indices: 2909397--2909441 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2909387 GAAAGCATAC
*
2909397 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2909438 AT AT
1 AT AT
2909442 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2910858 original size:2 final size:2
Alignment explanation
Indices: 2910851--2910880 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2910841 TTATCGCTCT
2910851 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
2910881 TGGGATATTC
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:2912532 original size:2 final size:2
Alignment explanation
Indices: 2912464--2912514 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2912454 TAAGGCAAAA
2912464 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2912506 AG AG AG AG A
1 AG AG AG AG A
2912515 AGGGGTGGGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2916685 original size:6 final size:6
Alignment explanation
Indices: 2916674--2916707 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2916664 GTCTAAAGCA
* *
2916674 CCATGT CCATGT CCATAT CCATAT CCATAT CCAT
1 CCATAT CCATAT CCATAT CCATAT CCATAT CCAT
2916708 GGGTTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.26, C:0.35, G:0.06, T:0.32
Consensus pattern (6 bp):
CCATAT
Found at i:2918888 original size:13 final size:14
Alignment explanation
Indices: 2918861--2918892 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2918851 ACTTAATTTA
2918861 TTAATAATAAAAAT
1 TTAATAATAAAAAT
2918875 TTAATAAT-AAAAT
1 TTAATAATAAAAAT
2918888 TTAAT
1 TTAAT
2918893 TATATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAATAATAAAAAT
Found at i:2922831 original size:23 final size:23
Alignment explanation
Indices: 2922800--2922845 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2922790 CATAAAATTT
2922800 AATTAATTTATAAAACCATCCAA
1 AATTAATTTATAAAACCATCCAA
*
2922823 AATTGATTTATAAAACCATCCAA
1 AATTAATTTATAAAACCATCCAA
2922846 TTGTAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.30
Consensus pattern (23 bp):
AATTAATTTATAAAACCATCCAA
Found at i:2926631 original size:2 final size:2
Alignment explanation
Indices: 2926599--2926623 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2926589 TATATTACTT
2926599 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
2926624 GCATATATCA
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:2927075 original size:6 final size:6
Alignment explanation
Indices: 2927058--2927098 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
2927048 GTTTTTGTAC
* * *
2927058 CCATGA CTATGA CAATGA CCATGA CCATGA CCATGA TCATG
1 CCATGA CCATGA CCATGA CCATGA CCATGA CCATGA CCATG
2927099 TAGATGTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (6 bp):
CCATGA
Found at i:2929647 original size:3 final size:3
Alignment explanation
Indices: 2929639--2929680 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2929629 GCAAATCCCA
2929639 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2929681 TTAAAAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2932555 original size:2 final size:2
Alignment explanation
Indices: 2932548--2932578 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2932538 CATTCTCTTT
2932548 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2932579 GCTTCGGAAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2933411 original size:13 final size:13
Alignment explanation
Indices: 2933389--2933421 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2933379 GGCATTTTTA
2933389 GATG-TTATTCTT
1 GATGATTATTCTT
2933401 GATGATTATTCTT
1 GATGATTATTCTT
*
2933414 GATTATTA
1 GATGATTA
2933422 CAAAGAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (13 bp):
GATGATTATTCTT
Found at i:2934475 original size:2 final size:2
Alignment explanation
Indices: 2934468--2934502 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2934458 TGTAATTATG
2934468 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
2934503 GGGAAACATG
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:2935014 original size:18 final size:18
Alignment explanation
Indices: 2934973--2935011 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
2934963 TTTTATTATT
2934973 TATTTAATTATAAAAATA
1 TATTTAATTATAAAAATA
2934991 TATTTAA-TATAAAAAT-
1 TATTTAATTATAAAAATA
2935007 TATTT
1 TATTT
2935012 TTATTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 9 0.43
18 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTAATTATAAAAATA
Found at i:2935975 original size:3 final size:3
Alignment explanation
Indices: 2935967--2936000 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2935957 TCCTTTTAAG
* *
2935967 TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2936001 GTCATAGCAG
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:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2937446 original size:10 final size:10
Alignment explanation
Indices: 2937433--2937484 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
2937423 ACCCCTTCCA
2937433 TTTTTTAAAT
1 TTTTTTAAAT
2937443 TTTTTTAAAT
1 TTTTTTAAAT
* *
2937453 ATTTTTATAT
1 TTTTTTAAAT
2937463 TTGTTTTAGTAAT
1 TT-TTTTA--AAT
*
2937476 TATTTTAAA
1 TTTTTTAAA
2937485 ATAAATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 21 0.62
11 5 0.15
12 5 0.15
13 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (10 bp):
TTTTTTAAAT
Found at i:2937504 original size:27 final size:28
Alignment explanation
Indices: 2937472--2937526 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2937462 TTTGTTTTAG
2937472 TAATTATT-TTAAA-ATAAATATAATTTT
1 TAATTATTATTAAATAT-AATATAATTTT
*
2937499 TAATTATTATTTAATATAATATAATTTT
1 TAATTATTATTAAATATAATATAATTTT
2937527 ATCATTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 8 0.32
28 15 0.60
29 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TAATTATTATTAAATATAATATAATTTT
Found at i:2937648 original size:38 final size:35
Alignment explanation
Indices: 2937605--2937691 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
2937595 ATTGTTTAGT
*
2937605 ATATAATTTTAATAATTTTCAATTATTATTGAAAATAA
1 ATATAATTTTAATAATATT---TTATTATTGAAAATAA
* * * *
2937643 ATATAATTTTATTTATATTTTATTATTTAATATAA
1 ATATAATTTTAATAATATTTTATTATTGAAAATAA
2937678 ATATAAATTTTAAT
1 ATAT-AATTTTAAT
2937692 TATTAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
35 18 0.43
36 8 0.19
38 16 0.38
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (35 bp):
ATATAATTTTAATAATATTTTATTATTGAAAATAA
Found at i:2937678 original size:35 final size:36
Alignment explanation
Indices: 2937627--2937694 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
2937617 TAATTTTCAA
*
2937627 TTATTATTGAAAATAAATAT-AATTTTATTTATATT
1 TTATTATTGAAAATAAATATAAATTTTAATTATATT
* *
2937662 TTATTATTTAATATAAATATAAATTTTAATTAT
1 TTATTATTGAAAATAAATATAAATTTTAATTAT
2937695 TAAATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 18 0.62
36 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
TTATTATTGAAAATAAATATAAATTTTAATTATATT
Found at i:2937711 original size:22 final size:19
Alignment explanation
Indices: 2937667--2937714 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
2937657 ATATTTTATT
2937667 ATTTAA-TATAAATATAAA
1 ATTTAATTATAAATATAAA
*
2937685 TTTTAATTATTAAATATATATA
1 ATTTAATTA-TAAATATA-A-A
2937707 ATTTAATT
1 ATTTAATT
2937715 GTATATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 5 0.21
19 2 0.08
20 8 0.33
21 1 0.04
22 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAATTATAAATATAAA
Found at i:2937848 original size:27 final size:27
Alignment explanation
Indices: 2937818--2937873 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
2937808 TAATCTCTCC
* *
2937818 ATTATTATTTTTTTAATCTCATCGTCT
1 ATTATTATTTTTTTAACCTCATCATCT
2937845 ATTATTATTTTTTTAACCTCATCATCT
1 ATTATTATTTTTTTAACCTCATCATCT
2937872 AT
1 AT
2937874 CTAATGGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.02, T:0.57
Consensus pattern (27 bp):
ATTATTATTTTTTTAACCTCATCATCT
Found at i:2944869 original size:3 final size:3
Alignment explanation
Indices: 2944861--2944919 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
2944851 TAGATTCGTC
2944861 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2944909 TTA TTA TTA TT
1 TTA TTA TTA TT
2944920 GTCTAAAAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2947133 original size:2 final size:2
Alignment explanation
Indices: 2947126--2947171 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2947116 GCGGCCGCCC
2947126 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
2947168 AT AT
1 AT AT
2947172 CACCCTCTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2948069 original size:2 final size:2
Alignment explanation
Indices: 2948062--2948088 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2948052 CATAGCTAGC
2948062 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2948089 GAGGGGGGGG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2950946 original size:2 final size:2
Alignment explanation
Indices: 2950933--2950970 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2950923 ATCAATGACA
* *
2950933 AT AT AC AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2950971 GCAAATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2953284 original size:189 final size:189
Alignment explanation
Indices: 2952963--2953343 Score: 521
Period size: 189 Copynumber: 2.0 Consensus size: 189
2952953 CATTTCTTCT
* * * * *
2952963 GGATATTTTAGTTATCGCTCTGACTAGATCTTTGGAATGGTATGATAATTACAGGTTGAGCATTT
1 GGATATTCTAGTTATCACTCTGACGAGATCTGTGGAATGGTATGATAATTACAGGTTGAGCATTG
* * * * *
2953028 AGCTGGTGTTATTGAAAGGCCGTAATGTCTACTAGGATCATCTGGAGTTATAATTGTTGATGGTA
66 AGCTGGTGTTATTGAAAGGCCATAACGTCTACCAGGATCATCTGGAGTTATAATTGTTAAGGGTA
* * *
2953093 TTAAGAATTAGATCAGGAATCTGCTGCAAATTAGGCTGCAAGTTATTCAATATTGTTTA
131 TTAAGAATTAGATCAGGAATCTGCTGCAAATTAGGCTACAACTTATTCAATATCGTTTA
**
2953152 GGATATTCTAGTTATCACTCTGACGAGATCTGTGGAATGGTATGATAATTGTAGGTTGAGCATTG
1 GGATATTCTAGTTATCACTCTGACGAGATCTGTGGAATGGTATGATAATTACAGGTTGAGCATTG
* * * * * * *
2953217 GGCTGGTGTTATTGAAAGGCTATTACGTCT-CCCGGTTTCATTTGGAGTTATTATTGTTAAGGGT
66 AGCTGGTGTTATTGAAAGGCCATAACGTCTACCAGG-ATCATCTGGAGTTATAATTGTTAAGGGT
* * *
2953281 ATTAAGAATTAGTTCAGGAATTTGCTGCAAATTAGGTTACAACTTATTCAATATCGTTTA
130 ATTAAGAATTAGATCAGGAATCTGCTGCAAATTAGGCTACAACTTATTCAATATCGTTTA
2953341 GGA
1 GGA
2953344 AACCCAGAAT
Statistics
Matches: 166, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
188 3 0.02
189 163 0.98
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (189 bp):
GGATATTCTAGTTATCACTCTGACGAGATCTGTGGAATGGTATGATAATTACAGGTTGAGCATTG
AGCTGGTGTTATTGAAAGGCCATAACGTCTACCAGGATCATCTGGAGTTATAATTGTTAAGGGTA
TTAAGAATTAGATCAGGAATCTGCTGCAAATTAGGCTACAACTTATTCAATATCGTTTA
Found at i:2955622 original size:2 final size:2
Alignment explanation
Indices: 2955615--2955676 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
2955605 CCTCCTCTTC
*
2955615 CT CT CT CT TT CT CT CT 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 CT CT CT CT CT CT CT CT
2955657 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
2955677 ATATATATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:2958712 original size:2 final size:2
Alignment explanation
Indices: 2958705--2958738 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2958695 GTACTCTCAC
2958705 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
2958739 TAGTCAGTAG
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:2959792 original size:2 final size:2
Alignment explanation
Indices: 2959785--2959821 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2959775 TATCTTGAAA
2959785 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
2959822 AATAGTTGAC
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:2960790 original size:2 final size:2
Alignment explanation
Indices: 2960780--2960809 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2960770 ACACACACAC
*
2960780 AT AT CT 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
2960810 TGTTTGGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2966927 original size:2 final size:2
Alignment explanation
Indices: 2966916--2966953 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2966906 TTCTATGAAG
2966916 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
2966954 TCTCTCTCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2966958 original size:2 final size:2
Alignment explanation
Indices: 2966953--2966980 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2966943 CACACACACA
2966953 CT 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 CT
2966981 GAAAAAAGGA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2967784 original size:2 final size:2
Alignment explanation
Indices: 2967777--2967803 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2967767 CCAAGCATAA
2967777 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
2967804 CACAACACTA
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:2972768 original size:6 final size:6
Alignment explanation
Indices: 2972757--2972784 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2972747 GAAAAACAAC
2972757 ACTAAA ACTAAA ACTAAA ACTAAA ACTA
1 ACTAAA ACTAAA ACTAAA ACTAAA ACTA
2972785 GAATTAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (6 bp):
ACTAAA
Found at i:2972924 original size:7 final size:7
Alignment explanation
Indices: 2972906--2972934 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2972896 GTTTTTTTTA
2972906 TTATTA-
1 TTATTAT
2972912 TTATTAT
1 TTATTAT
2972919 TTATTAT
1 TTATTAT
2972926 TTATTAT
1 TTATTAT
2972933 TT
1 TT
2972935 TAAGCTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTAT
Found at i:2974161 original size:2 final size:2
Alignment explanation
Indices: 2974154--2974191 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2974144 GTTCGTCATC
2974154 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
2974192 TTTCGGGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2984867 original size:13 final size:13
Alignment explanation
Indices: 2984849--2984879 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2984839 GACCCTAACT
2984849 ATATTAATAATTA
1 ATATTAATAATTA
*
2984862 ATATTAATATTTA
1 ATATTAATAATTA
2984875 ATATT
1 ATATT
2984880 GTAGGTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTAATAATTA
Done.