Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
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: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 21 of 24
Found at i:2722926 original size:13 final size:13
Alignment explanation
Indices: 2722908--2722937 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2722898 TAAAATATAA
*
2722908 AATTTATTTAATT
1 AATTTATATAATT
2722921 AATTTATATAATT
1 AATTTATATAATT
2722934 AATT
1 AATT
2722938 ATTAATAAAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTTATATAATT
Found at i:2723544 original size:37 final size:37
Alignment explanation
Indices: 2723472--2723547 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
2723462 TAGATCAAAT
* *
2723472 TTTTTAAAAAATTATAATTAATATATAATATTTTAAA
1 TTTTTAAAAAATTATAATTAAAATATAATAATTTAAA
*
2723509 TTTTT-AAAAATTA-AATTAAAAATTATATTAATTTAAA
1 TTTTTAAAAAATTATAATT-AAAA-TATAATAATTTAAA
2723546 TT
1 TT
2723548 AAATTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 4 0.12
36 11 0.32
37 19 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TTTTTAAAAAATTATAATTAAAATATAATAATTTAAA
Found at i:2723620 original size:25 final size:24
Alignment explanation
Indices: 2723582--2723628 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
2723572 AGATTTATTC
2723582 ATTTTTTAAAATTTTAAAAATTAT
1 ATTTTTTAAAATTTTAAAAATTAT
*
2723606 ATTTTTATAATATTTTAAAAATT
1 ATTTTT-TAAAATTTTAAAAATT
2723629 TTATACTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTTTAAAATTTTAAAAATTAT
Found at i:2723632 original size:19 final size:19
Alignment explanation
Indices: 2723608--2723646 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2723598 AAAATTATAT
*
2723608 TTTTATAATATTTTAAAAA
1 TTTTATAATAATTTAAAAA
*
2723627 TTTTATACTAATTTAAAAA
1 TTTTATAATAATTTAAAAA
2723646 T
1 T
2723647 AAAATATTTA
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTATAATAATTTAAAAA
Found at i:2724830 original size:21 final size:22
Alignment explanation
Indices: 2724801--2724854 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 22
2724791 TCAATTATGA
2724801 TAAATATTAATAAAA-AATAAAT
1 TAAATATT-ATAAAATAATAAAT
2724823 TAAA-ATTATAAAATAAT-AAT
1 TAAATATTATAAAATAATAAAT
2724843 TATAATATTATA
1 TA-AATATTATA
2724855 TTACGATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 11 0.38
21 8 0.28
22 10 0.34
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATATTATAAAATAATAAAT
Found at i:2727580 original size:2 final size:2
Alignment explanation
Indices: 2727573--2727603 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2727563 TTTTGCATCT
2727573 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
2727604 TTGTAAAGGG
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:2728068 original size:1 final size:1
Alignment explanation
Indices: 2728062--2728098 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
2728052 TAACCACCTG
2728062 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2728099 CCAAATTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2728545 original size:62 final size:62
Alignment explanation
Indices: 2728448--2728878 Score: 434
Period size: 62 Copynumber: 6.9 Consensus size: 62
2728438 TAATCTGAAG
* * * *
2728448 TGAGCAAAACCCAT-AAAGCTGAGCATCAAATCAAGCATTAAAATGCAGAGAAAACAGAGAAA
1 TGAGCAAAACCCATGAAA-CTGAACATCAAAACAAGCATAAAAATGCAAAGAAAACAGAGAAA
** * * ** * * * *
2728510 TGAGCAAAATTCTTGAAATTGAACATCAACTCAAGCGTACAAATGCAAAGACAACTGAGAAA
1 TGAGCAAAACCCATGAAACTGAACATCAAAACAAGCATAAAAATGCAAAGAAAACAGAGAAA
* * * * * * *
2728572 TGTGCAAAATCCAAGAAGCTGAACATCAAAACAAGCATAAAAATACAAAGAAACCAGAGATA
1 TGAGCAAAACCCATGAAACTGAACATCAAAACAAGCATAAAAATGCAAAGAAAACAGAGAAA
* * * * * * *
2728634 TAAGCAAAACCCATGAAGCCGAGCATTAAACCAAGCATAAAAATGCAAACAAAACAGAGAAA
1 TGAGCAAAACCCATGAAACTGAACATCAAAACAAGCATAAAAATGCAAAGAAAACAGAGAAA
* * * * * *
2728696 TGAGGCAAAAACCAAGAAGCTGAACATCAAAACAAGCATAAAAATGCAACGAAACCAGAGATA
1 TGA-GCAAAACCCATGAAACTGAACATCAAAACAAGCATAAAAATGCAAAGAAAACAGAGAAA
* * * *
2728759 TGAGCAAAACCCATAAAATTGAACATCAAAACAAGCATTAAAATGCAAAGAAAATAGAGAAA
1 TGAGCAAAACCCATGAAACTGAACATCAAAACAAGCATAAAAATGCAAAGAAAACAGAGAAA
* * * * *
2728821 TAAGCAAAACTCATGAAGA-TAAACATCAAACCAAGGATAAAAATGCAAAGAAAACAGA
1 TGAGCAAAACCCATGAA-ACTGAACATCAAAACAAGCATAAAAATGCAAAGAAAACAGA
2728879 AAAAGATAAT
Statistics
Matches: 298, Mismatches: 68, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
62 242 0.81
63 56 0.19
ACGTcount: A:0.54, C:0.18, G:0.15, T:0.13
Consensus pattern (62 bp):
TGAGCAAAACCCATGAAACTGAACATCAAAACAAGCATAAAAATGCAAAGAAAACAGAGAAA
Found at i:2728810 original size:187 final size:186
Alignment explanation
Indices: 2728450--2728878 Score: 511
Period size: 187 Copynumber: 2.3 Consensus size: 186
2728440 ATCTGAAGTG
* * * *
2728450 AGCAAAACCCATAAAGCTGAGCATCAAATCAAGCATTAAAATGCAGAGAAAACAGAGAAATGAGC
1 AGCAAAACCCATGAAGCTGAGCATCAAACCAAGCATAAAAATGCAAAGAAAACAGAGAAATGAGC
** ** * ** * * * *
2728515 AAAATTCTTGAAATTGAACATCAACTCAAGCGTACAAATGCAAAGACAACTGAGAAATGTGCAAA
66 AAAAACCAAGAAACTGAACATCAAAACAAGCATAAAAATGCAAAGACAACAGAGAAATGAGCAAA
* * * *
2728580 ATCCAAGAAGCTGAACATCAAAACAAGCATAAAAATACAAAGAAACCAGAGATATA
131 ACCCAAGAAACTGAACATCAAAACAAGCATAAAAATACAAAGAAAACAGAGAAATA
* * *
2728636 AGCAAAACCCATGAAGCCGAGCATTAAACCAAGCATAAAAATGCAAACAAAACAGAGAAATGAGG
1 AGCAAAACCCATGAAGCTGAGCATCAAACCAAGCATAAAAATGCAAAGAAAACAGAGAAATGA-G
* * *
2728701 CAAAAACCAAGAAGCTGAACATCAAAACAAGCATAAAAATGCAACGA-AACCAGAGATATGAGCA
65 CAAAAACCAAGAAACTGAACATCAAAACAAGCATAAAAATGCAAAGACAA-CAGAGAAATGAGCA
* * * *
2728765 AAACCCATA-AAATTGAACATCAAAACAAGCATTAAAATGCAAAGAAAATAGAGAAATA
129 AAACCCA-AGAAACTGAACATCAAAACAAGCATAAAAATACAAAGAAAACAGAGAAATA
* * * * *
2728823 AGCAAAACTCATGAAGATAAACATCAAACCAAGGATAAAAATGCAAAGAAAACAGA
1 AGCAAAACCCATGAAGCTGAGCATCAAACCAAGCATAAAAATGCAAAGAAAACAGA
2728879 AAAAGATAAT
Statistics
Matches: 203, Mismatches: 37, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
186 58 0.29
187 144 0.71
188 1 0.00
ACGTcount: A:0.54, C:0.18, G:0.15, T:0.13
Consensus pattern (186 bp):
AGCAAAACCCATGAAGCTGAGCATCAAACCAAGCATAAAAATGCAAAGAAAACAGAGAAATGAGC
AAAAACCAAGAAACTGAACATCAAAACAAGCATAAAAATGCAAAGACAACAGAGAAATGAGCAAA
ACCCAAGAAACTGAACATCAAAACAAGCATAAAAATACAAAGAAAACAGAGAAATA
Found at i:2730371 original size:14 final size:14
Alignment explanation
Indices: 2730348--2730384 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2730338 TATATAACTA
2730348 TTATAA-TATTATG
1 TTATAATTATTATG
*
2730361 TTATAATTATTATT
1 TTATAATTATTATG
2730375 TTATAATTAT
1 TTATAATTAT
2730385 AATTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
TTATAATTATTATG
Found at i:2730374 original size:3 final size:3
Alignment explanation
Indices: 2730361--2730417 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
2730351 TAATATTATG
* * *
2730361 TTA TAA TTA TTA TT- TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
2730409 TTA TAA TTA
1 TTA TTA TTA
2730418 ATTACGATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2731031 original size:22 final size:22
Alignment explanation
Indices: 2731006--2731047 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2730996 TTTAAAAATA
2731006 TTTAAA-TATTCATATTATATAT
1 TTTAAATTA-TCATATTATATAT
*
2731028 TTTATATTATCATATTATAT
1 TTTAAATTATCATATTATAT
2731048 TTCTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTAAATTATCATATTATATAT
Found at i:2734607 original size:20 final size:21
Alignment explanation
Indices: 2734560--2734609 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
2734550 TTTTCAGTTT
2734560 TAATTAAAAATAATAAAAATA
1 TAATTAAAAATAATAAAAATA
2734581 TATATTAAAAATAA-AAAAAT-
1 TA-ATTAAAAATAATAAAAATA
2734601 TCAATTAAA
1 T-AATTAAA
2734610 CTCATAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
TAATTAAAAATAATAAAAATA
Found at i:2735741 original size:2 final size:2
Alignment explanation
Indices: 2735736--2735760 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2735726 TAATTTTTTC
2735736 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
2735761 GGAAAAGCAT
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:2735943 original size:23 final size:23
Alignment explanation
Indices: 2735917--2735965 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2735907 AATATTACGG
*
2735917 ATATTAAATTTTAAATTTTAAAT
1 ATATTAAATATTAAATTTTAAAT
**
2735940 ATATTAAATATTATTTTTTAAAT
1 ATATTAAATATTAAATTTTAAAT
2735963 ATA
1 ATA
2735966 ATTATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTAAATATTAAATTTTAAAT
Found at i:2735982 original size:13 final size:14
Alignment explanation
Indices: 2735943--2735982 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2735933 TTTAAATATA
* *
2735943 TTAAATATTATTTT
1 TTAAATATAATTAT
2735957 TTAAATATAATTAT
1 TTAAATATAATTAT
2735971 TTAAAT-TAATTA
1 TTAAATATAATTA
2735983 AATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAAATATAATTAT
Found at i:2736941 original size:19 final size:19
Alignment explanation
Indices: 2736917--2736953 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2736907 AAAAATTATA
*
2736917 TTTTTATAATATTTTAAAG
1 TTTTTATAATAATTTAAAG
*
2736936 TTTTTATATTAATTTAAA
1 TTTTTATAATAATTTAAA
2736954 AATAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTTATAATAATTTAAAG
Found at i:2737278 original size:28 final size:28
Alignment explanation
Indices: 2737199--2737278 Score: 74
Period size: 31 Copynumber: 2.8 Consensus size: 28
2737189 GCTCCTTTTG
*
2737199 TTTT-TTATAATATAATAA-ATATAAAA
1 TTTTATTATTATATAATAATATATAAAA
* **
2737225 GTTTATTTATTATATAATGTGTATATAATAAA
1 TTTTA-TTATTATATAAT-AATATAT-A-AAA
2737257 TTTTATTATTATATAATAATAT
1 TTTTATTATTATATAATAATAT
2737279 TAATGATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
26 3 0.07
28 11 0.27
30 7 0.17
31 13 0.32
32 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
TTTTATTATTATATAATAATATATAAAA
Found at i:2737305 original size:13 final size:13
Alignment explanation
Indices: 2737287--2737311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2737277 ATTAATGATT
2737287 TAAAAATAAATAA
1 TAAAAATAAATAA
2737300 TAAAAATAAATA
1 TAAAAATAAATA
2737312 TTATTTTTAT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAATAAATAA
Found at i:2737870 original size:6 final size:6
Alignment explanation
Indices: 2737861--2737927 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
2737851 TAGAATATAG
* * * *
2737861 TAATTA TAATTA TAATTTT TAA-AA TAATT- T-ATTA TACTTTA TGATTA
1 TAATTA TAATTA TAA-TTA TAATTA TAATTA TAATTA TA-ATTA TAATTA
2737908 -AATTA TAATTA TAATTA TAA
1 TAATTA TAATTA TAATTA TAA
2737928 AATTTTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 26 0.55
7 9 0.19
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (6 bp):
TAATTA
Found at i:2741550 original size:28 final size:28
Alignment explanation
Indices: 2741519--2741581 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
2741509 CATTTTTTAC
* *
2741519 ATACAAAA-ATAACTACCATATTTGACTA
1 ATACAAAAGA-AACCACCATATTTGACAA
2741547 ATACAAAAGAAACCACCATATTTGACAA
1 ATACAAAAGAAACCACCATATTTGACAA
2741575 ATACAAA
1 ATACAAA
2741582 GGGTGGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.54, C:0.19, G:0.05, T:0.22
Consensus pattern (28 bp):
ATACAAAAGAAACCACCATATTTGACAA
Found at i:2746100 original size:28 final size:28
Alignment explanation
Indices: 2746069--2746127 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
2746059 TTTTACATAC
* *
2746069 AAAAATAACTACCATATTTGACAAATAT
1 AAAAAAAACCACCATATTTGACAAATAT
2746097 AAAAAAAACCACCATATTTGACAAATAT
1 AAAAAAAACCACCATATTTGACAAATAT
2746125 AAA
1 AAA
2746128 GAGTAACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (28 bp):
AAAAAAAACCACCATATTTGACAAATAT
Found at i:2749106 original size:2 final size:2
Alignment explanation
Indices: 2749101--2749137 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2749091 ATAACACTAC
2749101 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
2749138 CGCACACACA
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:2750489 original size:19 final size:20
Alignment explanation
Indices: 2750460--2750502 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
2750450 ATTTTTCTAT
2750460 TTTTTTCATTATTATCATTA
1 TTTTTTCATTATTATCATTA
*
2750480 TTTTTT-ATTATTATTATTA
1 TTTTTTCATTATTATCATTA
2750499 TTTT
1 TTTT
2750503 GGATAAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTCATTATTATCATTA
Found at i:2750795 original size:6 final size:7
Alignment explanation
Indices: 2750783--2750814 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
2750773 GTTTGATTTA
2750783 ATTTATT
1 ATTTATT
2750790 -TTTATT
1 ATTTATT
2750796 ATTTATT
1 ATTTATT
2750803 -TTTATT
1 ATTTATT
2750809 ATTTAT
1 ATTTAT
2750815 AAGTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 12 0.52
7 11 0.48
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
ATTTATT
Found at i:2750801 original size:13 final size:13
Alignment explanation
Indices: 2750783--2750814 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2750773 GTTTGATTTA
2750783 ATTTATTTTTATT
1 ATTTATTTTTATT
2750796 ATTTATTTTTATT
1 ATTTATTTTTATT
2750809 ATTTAT
1 ATTTAT
2750815 AAGTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTTATTTTTATT
Found at i:2752445 original size:5 final size:5
Alignment explanation
Indices: 2752407--2752444 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
2752397 TTTATCGATG
* *
2752407 AATCA AATCA AATCA AATCA AATCA AATTA AATTA AAT
1 AATCA AATCA AATCA AATCA AATCA AATCA AATCA AAT
2752445 TTAAATAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (5 bp):
AATCA
Found at i:2752681 original size:15 final size:16
Alignment explanation
Indices: 2752650--2752682 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2752640 ATATCAGTCA
2752650 AATATAAATAAATATTT
1 AATATAAAT-AATATTT
2752667 AATATAAAT-ATATTT
1 AATATAAATAATATTT
2752682 A
1 A
2752683 TTTTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATAAATAATATTT
Found at i:2752694 original size:26 final size:27
Alignment explanation
Indices: 2752661--2752724 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
2752651 ATATAAATAA
2752661 ATATTTAATATAAATATATTTATT-TTT
1 ATATTTAATAT-AATATATTTATTATTT
* *
2752688 -TATTTAA-ATATTATATTTTTTATTT
1 ATATTTAATATAATATATTTATTATTT
2752713 ATATTTGAATAT
1 ATATTT-AATAT
2752725 GTTAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
24 10 0.32
25 5 0.16
26 12 0.39
27 2 0.06
28 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
ATATTTAATATAATATATTTATTATTT
Found at i:2752697 original size:21 final size:20
Alignment explanation
Indices: 2752676--2752713 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2752666 TAATATAAAT
2752676 ATATT-TATTTTTTATTTAA
1 ATATTATATTTTTTATTTAA
2752695 ATATTATATTTTTTATTTA
1 ATATTATATTTTTTATTTA
2752714 TATTTGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATATTATATTTTTTATTTAA
Found at i:2755814 original size:16 final size:18
Alignment explanation
Indices: 2755783--2755823 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2755773 TTATCACTAG
*
2755783 TTTATATTTATTTAAAT-
1 TTTAAATTTATTTAAATA
2755800 TTTAAATTT-TTTAAATA
1 TTTAAATTTATTTAAATA
2755817 TTTAAAT
1 TTTAAAT
2755824 ATATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATTTATTTAAATA
Found at i:2755841 original size:27 final size:27
Alignment explanation
Indices: 2755811--2755862 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
2755801 TTAAATTTTT
2755811 TAAATATTTAAATATATATAAAAAATA
1 TAAATATTTAAATATATATAAAAAATA
*
2755838 TAAATTTTTAAATATATATAAAAAA
1 TAAATATTTAAATATATATAAAAAA
2755863 AATTAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
TAAATATTTAAATATATATAAAAAATA
Found at i:2756396 original size:17 final size:18
Alignment explanation
Indices: 2756356--2756397 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2756346 TAATATTATA
2756356 TTTA-AAATATTATATTT
1 TTTATAAATATTATATTT
*
2756373 TTATATAAATTTTA-ATTT
1 TT-TATAAATATTATATTT
2756391 TTTATAA
1 TTTATAA
2756398 TTTATATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 8 0.36
19 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATAAATATTATATTT
Found at i:2756416 original size:24 final size:23
Alignment explanation
Indices: 2756389--2756483 Score: 56
Period size: 24 Copynumber: 4.2 Consensus size: 23
2756379 AAATTTTAAT
2756389 TTTTTATAATTTATATCATATAAA
1 TTTTTATAATTTATAT-ATATAAA
* * *
2756413 TTTTAATACGTTTATATATATATA
1 TTTTTATA-ATTTATATATATAAA
* **
2756437 -TATTA-AATTTATAT-TATTTA
1 TTTTTATAATTTATATATATAAA
* *
2756457 TTTATATAATATT-TTTAT-TAAA
1 TTTTTATAAT-TTATATATATAAA
2756479 TTTTT
1 TTTTT
2756484 TTCGTATTAT
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
20 5 0.09
21 10 0.19
22 12 0.23
23 6 0.11
24 13 0.25
25 7 0.13
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (23 bp):
TTTTTATAATTTATATATATAAA
Found at i:2756435 original size:31 final size:30
Alignment explanation
Indices: 2756374--2756446 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
2756364 ATTATATTTT
** *
2756374 TATATAAATTTTAATTTTTTATAATTTATA
1 TATATAAATTTTAATCGTTTATAATATATA
2756404 TCATATAAATTTTAATACGTTTAT-ATATATA
1 T-ATATAAATTTTAAT-CGTTTATAATATATA
2756435 TATATTAAATTT
1 TATA-TAAATTT
2756447 ATATTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 4 0.11
31 28 0.76
32 5 0.14
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (30 bp):
TATATAAATTTTAATCGTTTATAATATATA
Found at i:2758194 original size:101 final size:100
Alignment explanation
Indices: 2757936--2758245 Score: 356
Period size: 102 Copynumber: 3.0 Consensus size: 100
2757926 TTTTACATAA
* *
2757936 TTATATTTATAAAAATTTTAAGAAATTTGTAATTAATATTATATAATTTAAATATA-TTTTAAAT
1 TTATA-TT-TAAAAATTTTAA-TAATTTATAATTAATATTATATAATTTAAATATATTTTTAAA-
* * * *
2758000 TTTAAACTACTCTTATTAATTTTTTATACCA-TCATAT-T
62 TTTAAATTATTTTTATTAA-TTTTTATACCATTAATATAT
* *
2758038 TATATATTTATAAAATTTTAATAAATTTATAATTTATATTATATAATTTAGATATATTTTTAAAT
1 T-TATATTTA-AAAATTTTAAT-AATTTATAATTAATATTATATAATTTAAATATATTTTTAAAT
*
2758103 TTAAATTATTTTGTATTAATTATTATACCATTAATATAT
63 TTAAATTATTTT-TATTAATTTTTATACCATTAATATAT
* * * * *
2758142 TTATATTTAAAATTTTTAATAATTTATAATTCATATTATATAATTTAAATATATTCTGAAATCTA
1 TTATATTTAAAAATTTTAATAATTTATAATTAATATTATATAATTTAAATATATTTTTAAATTTA
* *
2758207 AATTATTATTATATTAATTTTTATATCATAAATATAT
66 AATTATT-TT-TATTAATTTTTATACCATTAATATAT
2758244 TT
1 TT
2758246 TACGTTATAT
Statistics
Matches: 181, Mismatches: 19, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
101 49 0.27
102 100 0.55
103 30 0.17
104 2 0.01
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (100 bp):
TTATATTTAAAAATTTTAATAATTTATAATTAATATTATATAATTTAAATATATTTTTAAATTTA
AATTATTTTTATTAATTTTTATACCATTAATATAT
Found at i:2762850 original size:13 final size:13
Alignment explanation
Indices: 2762814--2762872 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
2762804 ATTAAAATTT
*
2762814 TATAAAATATAAA
1 TATATAATATAAA
2762827 -A-ATAAT-T-AA
1 TATATAATATAAA
2762836 TATATAATATAAA
1 TATATAATATAAA
2762849 TATATAATATAAA
1 TATATAATATAAA
2762862 T-TATTAATATA
1 TATA-TAATATA
2762873 TTAAAATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
9 2 0.05
10 2 0.05
11 9 0.22
12 4 0.10
13 23 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATATAATATAAA
Found at i:2762856 original size:20 final size:19
Alignment explanation
Indices: 2762767--2762873 Score: 59
Period size: 20 Copynumber: 5.7 Consensus size: 19
2762757 TACATTCGAT
2762767 AATATTAAATATAT--TATA
1 AATA-TAAATATATAATATA
2762785 AATAT-AATAT-TAA-A-A
1 AATATAAATATATAATATA
* *
2762800 AATAATTAAA-ATTTTATA-A
1 AAT-A-TAAATATATAATATA
*
2762819 AATATAAAAATAATTAATATA
1 AATATAAATAT-A-TAATATA
2762840 TAATATAAATATATAATATA
1 -AATATAAATATATAATATA
*
2762860 AATTATTAATATAT
1 AA-TATAAATATAT
2762874 TAAAATTTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
15 5 0.07
16 7 0.10
17 8 0.11
18 11 0.15
19 7 0.10
20 21 0.30
21 2 0.03
22 10 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATAAATATATAATATA
Found at i:2762857 original size:27 final size:27
Alignment explanation
Indices: 2762773--2762879 Score: 76
Period size: 27 Copynumber: 3.9 Consensus size: 27
2762763 CGATAATATT
*
2762773 AAATATATTATAAATATAAT--ATTA-AA
1 AAATA-ATTA-AAATATAATAAAATATAA
* *
2762799 AAATAATTAAAATTTTATAAAATATAA
1 AAATAATTAAAATATAATAAAATATAA
*
2762826 AAATAATTAATATATAATATAAATATATA
1 AAATAATTAAAATATAATA-AAATATA-A
* * *
2762855 ATATAAATTATTAATATATTAAAAT
1 AAAT-AATTA-AAATATAATAAAAT
2762880 TTAATTATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
24 7 0.11
25 4 0.06
26 8 0.12
27 18 0.28
28 7 0.11
29 4 0.06
30 9 0.14
31 7 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATAATTAAAATATAATAAAATATAA
Found at i:2762863 original size:51 final size:51
Alignment explanation
Indices: 2762767--2762893 Score: 122
Period size: 51 Copynumber: 2.5 Consensus size: 51
2762757 TACATTCGAT
*
2762767 AATATT-AAATAT-ATTATAAATATAATATTAAAAAATAATTAAAATTTTATAA
1 AATATTAAAATATAATTAT--ATATAATATTAAAAAATAATTAAAATTAT-TAA
*
2762819 AATA-TAAAA-ATAATTAATATATAATA-TAAATATATAA-TATAAATTATTAA
1 AATATTAAAATATAATT-ATATATAATATTAAA-AAATAATTA-AAATTATTAA
* *
2762869 TATATTAAAATTTAATTATATATAA
1 AATATTAAAATATAATTATATATAA
2762894 AATTTTTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
50 12 0.19
51 35 0.55
52 15 0.23
53 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (51 bp):
AATATTAAAATATAATTATATATAATATTAAAAAATAATTAAAATTATTAA
Found at i:2762892 original size:33 final size:32
Alignment explanation
Indices: 2762820--2762894 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
2762810 ATTTTATAAA
* *
2762820 ATATAAAAATAATTAATATATAATATAAATAT
1 ATATATAAATAATTAATATATAAAATAAATAT
* *
2762852 ATAATATAAATTATTAATATATTAAAATTTAAT-T
1 AT-ATATAAATAATTAATATA-TAAAA-TAAATAT
2762886 ATATATAAA
1 ATATATAAA
2762895 ATTTTTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 2 0.06
33 23 0.64
34 7 0.19
35 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATATAAATAATTAATATATAAAATAAATAT
Found at i:2762892 original size:68 final size:69
Alignment explanation
Indices: 2762777--2762964 Score: 174
Period size: 68 Copynumber: 2.8 Consensus size: 69
2762767 AATATTAAAT
* * * * *
2762777 ATATTATAAATATAATATTA-AAAAATAATTAAAATTTTATAAAATATAAAAATAATTAATATAT
1 ATATAATAAATATAA-ATTATTAATAT-ATTAAAATTTAATTAAATATAAAAATAATTAAT-TAT
2762841 AATATA-A
63 AAT-TACA
* * **
2762848 ATAT-AT-AATATAAATTATTAATATATTAAAATTTAATTATATATAAAATTTTTTAATTATAAT
1 ATATAATAAATATAAATTATTAATATATTAAAATTTAATTAAATATAAAAATAATTAATTATAAT
2762911 TACA
66 TACA
* * *
2762915 ATATAATAAAATATATATTTTTAAAATATT--AATTTAA-TAAATATAAAAAT
1 ATATAAT-AAATATAAATTATTAATATATTAAAATTTAATTAAATATAAAAAT
2762965 TATTTTTAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
66 2 0.02
67 22 0.22
68 40 0.40
69 11 0.11
70 20 0.20
71 4 0.04
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.43
Consensus pattern (69 bp):
ATATAATAAATATAAATTATTAATATATTAAAATTTAATTAAATATAAAAATAATTAATTATAAT
TACA
Found at i:2762896 original size:17 final size:17
Alignment explanation
Indices: 2762806--2762898 Score: 59
Period size: 17 Copynumber: 5.5 Consensus size: 17
2762796 AAAAAATAAT
* * *
2762806 TAAAATTTTATAAAATA
1 TAAAATTTAATTATATA
*
2762823 TAAAA-ATAATTA-ATA
1 TAAAATTTAATTATATA
* * *
2762838 TATAATATAAATATATAA
1 TAAAATTTAATTATAT-A
2762856 TATAAA-TT-ATTAATATA
1 TA-AAATTTAATT-ATATA
2762873 TTAAAATTTAATTATATA
1 -TAAAATTTAATTATATA
2762891 TAAAATTT
1 TAAAATTT
2762899 TTTAATTATA
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
15 7 0.12
16 10 0.17
17 21 0.35
18 17 0.28
19 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTTAATTATATA
Found at i:2762962 original size:22 final size:23
Alignment explanation
Indices: 2762936--2762991 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
2762926 TATATATTTT
2762936 TAAAATATTAATTTAAT-AAATA
1 TAAAATATTAATTTAATAAAATA
* *
2762958 TAAAA-ATTATTTTTAATAAAATT
1 TAAAATATTA-ATTTAATAAAATA
*
2762981 TATAATATTAA
1 TAAAATATTAA
2762992 ATACGATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
21 4 0.15
22 11 0.41
23 8 0.30
24 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAATATTAATTTAATAAAATA
Found at i:2762988 original size:70 final size:72
Alignment explanation
Indices: 2762829--2762994 Score: 166
Period size: 70 Copynumber: 2.3 Consensus size: 72
2762819 AATATAAAAA
* * *
2762829 TAATTAATA-TATAATATAAATATATAATATAAATTATTAATATATTAAAATTTAATTATATATA
1 TAATTAAAATTATAATATAAATATATAATATAAATTATTAAAATATT-AAATTTAATAATATATA
2762893 AAATTTTT
65 AAATTTTT
* * * *
2762901 TAATTATAATTACAATAT-AATA-A-AATATATATTTTTAAAATATT-AATTTAATAA-ATATAA
1 TAATTAAAATTATAATATAAATATATAATATAAATTATTAAAATATTAAATTTAATAATATAT-A
2762961 AAATTATTTT
65 AAA-T-TTTT
2762971 TAA-TAAAATTTATAATATTAAATA
1 TAATTAAAA-TTATAATA-TAAATA
2762995 CGATTATATA
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
67 4 0.05
68 13 0.17
69 5 0.06
70 32 0.41
71 2 0.03
72 15 0.19
73 7 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.46
Consensus pattern (72 bp):
TAATTAAAATTATAATATAAATATATAATATAAATTATTAAAATATTAAATTTAATAATATATAA
AATTTTT
Found at i:2763561 original size:15 final size:16
Alignment explanation
Indices: 2763534--2763574 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
2763524 TTTTAACATT
2763534 TAAATTAAATAATTTA
1 TAAATTAAATAATTTA
*
2763550 TAAATT-AATAATTTT
1 TAAATTAAATAATTTA
*
2763565 TAATTTAAAT
1 TAAATTAAAT
2763575 TAATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATTAAATAATTTA
Found at i:2764524 original size:15 final size:15
Alignment explanation
Indices: 2764488--2764526 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2764478 ACTTTGAAAA
* *
2764488 AAAAAACTATCAATT
1 AAAAAATTATCAACT
*
2764503 AAAAAATTATCTACT
1 AAAAAATTATCAACT
2764518 AAAAAATTA
1 AAAAAATTA
2764527 CTGATCACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAAATTATCAACT
Found at i:2766553 original size:21 final size:20
Alignment explanation
Indices: 2766516--2766574 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
2766506 TGTTATTAAA
*
2766516 AATATTATTAATGATAAAATT
1 AATATTA-TAATAATAAAATT
2766537 AATTATTATAATAATAAAATT
1 AA-TATTATAATAATAAAATT
*
2766558 AA-AAT-TAATAATAAAAT
1 AATATTATAATAATAAAAT
2766575 ATATATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.34
19 2 0.06
21 16 0.46
22 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AATATTATAATAATAAAATT
Found at i:2766706 original size:27 final size:27
Alignment explanation
Indices: 2766676--2766750 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 27
2766666 ATATAATAAA
* *
2766676 TAAATATTATTAAAATTATATTTATAT
1 TAAATATTATTAAAATTAAATTAATAT
* *
2766703 TAAATAATAATTAAAAATAAATTAATAT
1 TAAAT-ATTATTAAAATTAAATTAATAT
*
2766731 AAAATACTT-TTAAAA-TAAAT
1 TAAATA-TTATTAAAATTAAAT
2766751 AATTAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 5 0.12
27 12 0.30
28 23 0.57
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATATTATTAAAATTAAATTAATAT
Found at i:2766735 original size:44 final size:44
Alignment explanation
Indices: 2766649--2766727 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
2766639 TTAAATTAAA
*
2766649 ATATTTATATAATAAATATATAATAAATAAATATTATTAAAATT
1 ATATTTATATAATAAATATATAATAAATAAATAATATTAAAATT
*
2766693 ATATTTATAT--TAAATA-ATAATTAA-AAATAA-ATTAA
1 ATATTTATATAATAAATATATAATAAATAAATAATATTAA
2766728 TATAAAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
39 5 0.15
40 5 0.15
41 7 0.21
42 6 0.18
44 10 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (44 bp):
ATATTTATATAATAAATATATAATAAATAAATAATATTAAAATT
Found at i:2771395 original size:2 final size:2
Alignment explanation
Indices: 2771390--2771425 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2771380 AAAAAGGGTG
2771390 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
2771426 GCAGACTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2771637 original size:27 final size:27
Alignment explanation
Indices: 2771607--2771662 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2771597 AATTATTGTA
*
2771607 ATAATTATA-TTAATATTATATATTT-TT
1 ATAATTAAATTTAA-ATTA-ATATTTATT
2771634 ATAATTAAATTTAAATTAATATTTATT
1 ATAATTAAATTTAAATTAATATTTATT
2771661 AT
1 AT
2771663 TAAGTAGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 6 0.23
27 16 0.62
28 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATAATTAAATTTAAATTAATATTTATT
Found at i:2772614 original size:2 final size:2
Alignment explanation
Indices: 2772607--2772636 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2772597 ATGCTTTTCC
*
2772607 CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2772637 GTCTTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:2776341 original size:29 final size:29
Alignment explanation
Indices: 2776299--2776354 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
2776289 CATTTAAGCA
*
2776299 CTAACTTACTATTTTTCTCGGACTCGGCG
1 CTAACTTACTATTTTACTCGGACTCGGCG
*
2776328 CTAAGTTACTATTTTACTCGGACTCGG
1 CTAACTTACTATTTTACTCGGACTCGG
2776355 ATATGAATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (29 bp):
CTAACTTACTATTTTACTCGGACTCGGCG
Found at i:2778012 original size:2 final size:2
Alignment explanation
Indices: 2778005--2778031 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2777995 TAACAGTTAC
2778005 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
2778032 AGCGATGGTA
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:2781834 original size:19 final size:19
Alignment explanation
Indices: 2781810--2781847 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2781800 ATTGATTCAG
*
2781810 AATATTATTTGTTTAATTA
1 AATATTATTTATTTAATTA
*
2781829 AATATTTTTTATTTAATTA
1 AATATTATTTATTTAATTA
2781848 TAAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
AATATTATTTATTTAATTA
Found at i:2781870 original size:18 final size:18
Alignment explanation
Indices: 2781849--2781883 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2781839 ATTTAATTAT
2781849 AAAATAAATATTAATATA
1 AAAATAAATATTAATATA
* *
2781867 AAAATAATTTTTAATAT
1 AAAATAAATATTAATAT
2781884 TTTATTATTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATAAATATTAATATA
Found at i:2782786 original size:13 final size:12
Alignment explanation
Indices: 2782740--2782803 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 12
2782730 CATACGGCTG
2782740 ATAAAAAATAAT
1 ATAAAAAATAAT
* * *
2782752 -TAAGATATGAT
1 ATAAAAAATAAT
*
2782763 ATAAAATATAAT
1 ATAAAAAATAAT
2782775 ATGAAAAAATAAT
1 AT-AAAAAATAAT
* *
2782788 A-AAAATATGAT
1 ATAAAAAATAAT
2782799 ATAAA
1 ATAAA
2782804 TATATATAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
11 17 0.41
12 14 0.34
13 10 0.24
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:2782808 original size:13 final size:12
Alignment explanation
Indices: 2782756--2782812 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
2782746 AATAATTAAG
2782756 ATATGATATAAA
1 ATATGATATAAA
*
2782768 ATATAATATGAAA
1 ATATGATAT-AAA
* *
2782781 AAATAATA-AAA
1 ATATGATATAAA
2782792 ATATGATAT-AA
1 ATATGATATAAA
2782803 ATAT-ATATAA
1 ATATGATATAA
2782813 TTTTTAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 4 0.11
11 16 0.42
12 8 0.21
13 10 0.26
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (12 bp):
ATATGATATAAA
Found at i:2782869 original size:17 final size:18
Alignment explanation
Indices: 2782797--2782872 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 18
2782787 TAAAAATATG
2782797 ATAT-AAATA-TATATAA
1 ATATAAAATATTATATAA
* * * *
2782813 TTTTTAAATGTTATAT-A
1 ATATAAAATATTATATAA
*
2782830 ATATAAATTATTA-ATAA
1 ATATAAAATATTATATAA
2782847 AT-TAAAAT-TTATATAA
1 ATATAAAATATTATATAA
2782863 ATATAAAATA
1 ATATAAAATA
2782873 ATTTGAACAT
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
15 3 0.07
16 15 0.33
17 22 0.49
18 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (18 bp):
ATATAAAATATTATATAA
Found at i:2783563 original size:25 final size:23
Alignment explanation
Indices: 2783515--2783563 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
2783505 ATTTAATATA
*
2783515 TTAATAATTTATAGTATATATTT
1 TTAATAATTTATAATATATATTT
2783538 TTAATATATTTATATATATATATTT
1 TTAATA-ATTTATA-ATATATATTT
2783563 T
1 T
2783564 ATTTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.26
24 7 0.30
25 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTAATAATTTATAATATATATTT
Found at i:2783570 original size:17 final size:17
Alignment explanation
Indices: 2783550--2783601 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
2783540 AATATATTTA
2783550 TATATATATATTTTATT
1 TATATATATATTTTATT
*
2783567 TATATA-ATATCTTTCAGAT
1 TATATATATAT-TTT-A-TT
2783586 TATAT-TATATTTTATT
1 TATATATATATTTTATT
2783602 CCTATTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 5 0.17
17 10 0.34
18 4 0.14
19 10 0.34
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (17 bp):
TATATATATATTTTATT
Found at i:2783571 original size:25 final size:24
Alignment explanation
Indices: 2783515--2783564 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 24
2783505 ATTTAATATA
2783515 TTAATA-ATTTATAGTATATATTT
1 TTAATATATTTATAGTATATATTT
2783538 TTAATATATTTATA-TATATATATT
1 TTAATATATTTATAGTATATAT-TT
2783562 TTA
1 TTA
2783565 TTTATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTAATATATTTATAGTATATATTT
Found at i:2784364 original size:12 final size:12
Alignment explanation
Indices: 2784308--2784382 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
2784298 AAGTGATCAC
2784308 AATATTA-TATT
1 AATATTATTATT
*
2784319 ATTATTATTATTT
1 AATATTATTA-TT
*
2784332 AATAATTTTTA-T
1 AAT-ATTATTATT
*
2784344 ATATTTTATTATT
1 A-ATATTATTATT
* *
2784357 GATATTATAATT
1 AATATTATTATT
2784369 AATATT-TTA-T
1 AATATTATTATT
2784379 AATA
1 AATA
2784383 ATTAATCAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
10 5 0.10
11 8 0.16
12 23 0.47
13 7 0.14
14 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (12 bp):
AATATTATTATT
Found at i:2789247 original size:29 final size:30
Alignment explanation
Indices: 2789178--2789250 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 30
2789168 TAAACGTAAC
*
2789178 TAATATAATAAATTTAATATATTTATGTTTA
1 TAAT-TAATACATTTAATATATTTATGTTTA
*
2789209 AAATTTTAATACATTTAATA-ATTTAT-TTATA
1 TAA--TTAATACATTTAATATATTTATGTT-TA
2789240 TAATTAATACA
1 TAATTAATACA
2789251 AAAAAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 8 0.22
30 2 0.06
31 12 0.33
32 13 0.36
33 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (30 bp):
TAATTAATACATTTAATATATTTATGTTTA
Found at i:2789735 original size:22 final size:22
Alignment explanation
Indices: 2789709--2789767 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
2789699 AATTTTAATG
2789709 ATTTAAGTTAATTAAAAT-TATT
1 ATTTAA-TTAATTAAAATATATT
* * *
2789731 ATTTAAATAATAAAAATATTTT
1 ATTTAATTAATTAAAATATATT
2789753 ATTTAAAATTAATTA
1 ATTT--AATTAATTA
2789768 TAAAATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 9 0.31
22 13 0.45
24 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTAATTAATTAAAATATATT
Found at i:2789746 original size:21 final size:22
Alignment explanation
Indices: 2789717--2789759 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2789707 TGATTTAAGT
*
2789717 TAATTAAAAT-TATTATTTAAA
1 TAATAAAAATATATTATTTAAA
*
2789738 TAATAAAAATATTTTATTTAAA
1 TAATAAAAATATATTATTTAAA
2789760 ATTAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATAAAAATATATTATTTAAA
Found at i:2789786 original size:21 final size:18
Alignment explanation
Indices: 2789753--2789791 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 18
2789743 AAAATATTTT
2789753 ATTTAAAATTAATTATAAA
1 ATTTAAAATTAA-TATAAA
2789772 ATTTATAATATTAATATAAA
1 ATTTA-AA-ATTAATATAAA
2789792 TAAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAAAATTAATATAAA
Found at i:2792049 original size:47 final size:47
Alignment explanation
Indices: 2791998--2792091 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
2791988 GTATAGGTGG
*
2791998 CTAATATAATTATATTTAAATTTTTAAAA-TTTTTTATGTATTTAAAA
1 CTAATATAATTATATTT-AATTTTTAAAATTTTTTTATGTATTGAAAA
2792045 CTAATATAATTATATTTAATTTTTAAAATTTTTTTATGTATTGAAAA
1 CTAATATAATTATATTTAATTTTTAAAATTTTTTTATGTATTGAAAA
2792092 GTTTTTAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 11 0.24
47 34 0.76
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (47 bp):
CTAATATAATTATATTTAATTTTTAAAATTTTTTTATGTATTGAAAA
Found at i:2792877 original size:17 final size:19
Alignment explanation
Indices: 2792842--2792881 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
2792832 AATAAATTTC
2792842 AAAAATAATAAATAATTAAT
1 AAAAATAATAAAT-ATTAAT
2792862 AAAAAT-ATAAAT-TTAAT
1 AAAAATAATAAATATTAAT
2792879 AAA
1 AAA
2792882 GAGATTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATAATAAATATTAAT
Found at i:2806780 original size:15 final size:15
Alignment explanation
Indices: 2806746--2806777 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2806736 AGTTTAATTC
2806746 TTTATATAATTTATA
1 TTTATATAATTTATA
2806761 TTTATATAATTTA-A
1 TTTATATAATTTATA
2806775 TTT
1 TTT
2806778 TATTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATATAATTTATA
Found at i:2812063 original size:31 final size:31
Alignment explanation
Indices: 2812026--2812086 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2812016 CACCACGCAT
* *
2812026 CATCAAATGATTAATGCTTCATTTGAATGTG
1 CATCAAATAATTAATGCTTCATTCGAATGTG
*
2812057 CATCAAATAATTAATGCTTCGTTCGAATGT
1 CATCAAATAATTAATGCTTCATTCGAATGT
2812087 ACAATGCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (31 bp):
CATCAAATAATTAATGCTTCATTCGAATGTG
Found at i:2812421 original size:19 final size:19
Alignment explanation
Indices: 2812397--2812436 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2812387 AATTTACTTT
**
2812397 TAAATATAATTAAAAAATA
1 TAAATATAAAGAAAAAATA
2812416 TAAATATAAAGAAAAAATA
1 TAAATATAAAGAAAAAATA
2812435 TA
1 TA
2812437 TTAGTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
TAAATATAAAGAAAAAATA
Found at i:2814026 original size:2 final size:2
Alignment explanation
Indices: 2814019--2814051 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2814009 GAGTCTTACA
2814019 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2814052 CCTGAGAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2815953 original size:3 final size:3
Alignment explanation
Indices: 2815945--2815985 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2815935 TAATACACAA
2815945 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2815986 AAGAAAGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2816872 original size:17 final size:17
Alignment explanation
Indices: 2816842--2816911 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
2816832 AATTGTTTTA
* *
2816842 AATAAAATTA-TAATGT
1 AATAAAAATATTAATAT
2816858 AATAAAAATATTAATAT
1 AATAAAAATATTAATAT
* *
2816875 GATATAAATATATAA-AT
1 AATAAAAATAT-TAATAT
2816892 AATAAAAA-ATTAATAAT
1 AATAAAAATATTAAT-AT
2816909 AAT
1 AAT
2816912 TTTATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
15 3 0.07
16 11 0.25
17 27 0.61
18 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAAAAATATTAATAT
Found at i:2816917 original size:29 final size:30
Alignment explanation
Indices: 2816885--2816943 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
2816875 GATATAAATA
*
2816885 TATAAATAATAAAA-AATT-AATAATAATTT
1 TATAAAAAATAAAATAATTAAATAA-AATTT
2816914 TATAAAAAATAAAATAATTAAATAAAATTT
1 TATAAAAAATAAAATAATTAAATAAAATTT
2816944 ATATTTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 13 0.48
30 9 0.33
31 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
TATAAAAAATAAAATAATTAAATAAAATTT
Found at i:2816918 original size:22 final size:20
Alignment explanation
Indices: 2816893--2816932 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
2816883 TATATAAATA
2816893 ATAAAAAATTAATAATAATTTT
1 ATAAAAAA-TAA-AATAATTTT
2816915 ATAAAAAATAAAATAATT
1 ATAAAAAATAAAATAATT
2816933 AAATAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAAAAATAAAATAATTTT
Found at i:2816944 original size:29 final size:27
Alignment explanation
Indices: 2816880--2816946 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 27
2816870 AATATGATAT
* *
2816880 AAATATATAAATAATAAAAAATTAATA
1 AAATTTATAAAAAATAAAAAATTAATA
2816907 ATAATTTTATAAAAAATAAAATAATTAAATA
1 A-AA-TTTATAAAAAATAAAA-AATT-AATA
2816938 AAATTTATA
1 AAATTTATA
2816947 TTTATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 1 0.03
28 2 0.06
29 20 0.59
30 6 0.18
31 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
AAATTTATAAAAAATAAAAAATTAATA
Found at i:2817017 original size:18 final size:18
Alignment explanation
Indices: 2816994--2817035 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
2816984 TTATATTTAT
2816994 TTTAATATTTAAATATTA
1 TTTAATATTTAAATATTA
2817012 TTTAATATTTAAATATTA
1 TTTAATATTTAAATATTA
2817030 TTTAAT
1 TTTAAT
2817036 GATAGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAATATTTAAATATTA
Found at i:2817022 original size:25 final size:26
Alignment explanation
Indices: 2816980--2817028 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
2816970 TTGAGTGTAT
*
2816980 AATATTATATTTATTTT-AATATTTA
1 AATATTATATTAATTTTAAATATTTA
2817005 AATATTAT-TTAATATTTAAATATT
1 AATATTATATTAAT-TTTAAATATT
2817029 ATTTAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATATTATATTAATTTTAAATATTTA
Found at i:2819041 original size:8 final size:8
Alignment explanation
Indices: 2819028--2819052 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2819018 TTTATTCTTT
2819028 AAATATTA
1 AAATATTA
2819036 AAATATTA
1 AAATATTA
2819044 AAATATTA
1 AAATATTA
2819052 A
1 A
2819053 TTTTATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATATTA
Found at i:2819917 original size:23 final size:26
Alignment explanation
Indices: 2819891--2819940 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
2819881 GCTACATTGC
2819891 TTTA-ATTTT-TATTTTT-TTAAATA
1 TTTATATTTTATATTTTTATTAAATA
*
2819914 TTTATATTTTATATTTTTATTTAATA
1 TTTATATTTTATATTTTTATTAAATA
2819940 T
1 T
2819941 ATATTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 5 0.22
25 7 0.30
26 7 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTATATTTTATATTTTTATTAAATA
Found at i:2820001 original size:19 final size:19
Alignment explanation
Indices: 2819979--2820032 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 19
2819969 TTATATAATT
2819979 TTTTTAAATATATAAAAAA
1 TTTTTAAATATATAAAAAA
* *
2819998 -TTTTAAAAATAATAAAAAT
1 TTTTTAAATAT-ATAAAAAA
2820017 TTATATTAAATATATA
1 TT-T-TTAAATATATA
2820033 TTATTCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 1 0.04
21 4 0.14
22 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTTAAATATATAAAAAA
Found at i:2820642 original size:21 final size:21
Alignment explanation
Indices: 2820618--2820657 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2820608 AAAAAATAAT
2820618 ATTTATAA-AATTAAAATTTAA
1 ATTT-TAATAATTAAAATTTAA
*
2820639 ATTTTAATAATTATAATTT
1 ATTTTAATAATTAAAATTT
2820658 TTTTACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTAATAATTAAAATTTAA
Found at i:2821136 original size:19 final size:19
Alignment explanation
Indices: 2821110--2821150 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2821100 TTTTATGTAA
2821110 ATTT-TAATATATTTATAT
1 ATTTATAATATATTTATAT
*
2821128 ATTTATAATGTATTTATAT
1 ATTTATAATATATTTATAT
2821147 -TTTA
1 ATTTA
2821151 AGTATTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTTATAATATATTTATAT
Found at i:2822386 original size:22 final size:22
Alignment explanation
Indices: 2822361--2822407 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2822351 GATTAAATAA
2822361 TGATTTGATAATTTATCATTGT
1 TGATTTGATAATTTATCATTGT
** *
2822383 TGATTTGATGGTTTGTCATTGT
1 TGATTTGATAATTTATCATTGT
2822405 TGA
1 TGA
2822408 CTAAGTGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.53
Consensus pattern (22 bp):
TGATTTGATAATTTATCATTGT
Found at i:2822524 original size:34 final size:34
Alignment explanation
Indices: 2822419--2822532 Score: 120
Period size: 34 Copynumber: 3.4 Consensus size: 34
2822409 TAAGTGAAAA
* * * *
2822419 ATTTGGTAGTTTACCATGGTTAATTAAATGGCTG
1 ATTTGGTAGTTTACTATTGTTGATTAAATGGGTG
* * * * * * * *
2822453 ATTTGGTTGTTTATTATTATGGACTAAACGAGAG
1 ATTTGGTAGTTTACTATTGTTGATTAAATGGGTG
2822487 ATTTGGTAGTTTACTATTGTTGATTAAATGGGTG
1 ATTTGGTAGTTTACTATTGTTGATTAAATGGGTG
2822521 ATTTGGTAGTTT
1 ATTTGGTAGTTT
2822533 TTACATAGTG
Statistics
Matches: 60, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (34 bp):
ATTTGGTAGTTTACTATTGTTGATTAAATGGGTG
Found at i:2822846 original size:19 final size:19
Alignment explanation
Indices: 2822822--2822875 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
2822812 GGTTGTCGAT
2822822 GCATTATTCACGTATATAG
1 GCATTATTCACGTATATAG
2822841 GCATTATTCACGTATATAG
1 GCATTATTCACGTATATAG
* * *
2822860 GTACTATTTACGTATA
1 GCATTATTCACGTATA
2822876 CGACACTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (19 bp):
GCATTATTCACGTATATAG
Found at i:2826616 original size:22 final size:22
Alignment explanation
Indices: 2826584--2826630 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2826574 GATTAAATGG
*
2826584 TGATTTGGTAGTTTGCCATTAT
1 TGATTTAGTAGTTTGCCATTAT
*
2826606 TGATTTAGTAGTTTGCCATTGT
1 TGATTTAGTAGTTTGCCATTAT
2826628 TGA
1 TGA
2826631 CTAAATGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.09, G:0.23, T:0.49
Consensus pattern (22 bp):
TGATTTAGTAGTTTGCCATTAT
Found at i:2826651 original size:34 final size:34
Alignment explanation
Indices: 2826607--2826755 Score: 156
Period size: 34 Copynumber: 4.4 Consensus size: 34
2826597 TGCCATTATT
*
2826607 GATTTAGTAGTTTGCCATTGTTGACTAAATGAGA
1 GATTTGGTAGTTTGCCATTGTTGACTAAATGAGA
* * * * *
2826641 GATTTGGTAGTTTGACGTTGTTGATTAAATGGGT
1 GATTTGGTAGTTTGCCATTGTTGACTAAATGAGA
* *
2826675 GATTTGGTAGTTTACCATTATTGACTAAAT-AGGA
1 GATTTGGTAGTTTGCCATTGTTGACTAAATGA-GA
* * * * *
2826709 GATCTGGTAGTTTGTCATTGTTGATTAAATGGGT
1 GATTTGGTAGTTTGCCATTGTTGACTAAATGAGA
*
2826743 GATTTGGTGGTTT
1 GATTTGGTAGTTT
2826756 TTACCAAACC
Statistics
Matches: 91, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
34 91 1.00
ACGTcount: A:0.24, C:0.06, G:0.28, T:0.42
Consensus pattern (34 bp):
GATTTGGTAGTTTGCCATTGTTGACTAAATGAGA
Found at i:2826717 original size:68 final size:68
Alignment explanation
Indices: 2826606--2826755 Score: 221
Period size: 68 Copynumber: 2.2 Consensus size: 68
2826596 TTGCCATTAT
* * * * *
2826606 TGATTTAGTAGTTTGCCATTGTTGACTAAATGAGAGATTTGGTAGTTTGACGTTGTTGATTAAAT
1 TGATTTGGTAGTTTACCATTATTGACTAAATGAGAGATCTGGTAGTTTGACATTGTTGATTAAAT
2826671 GGG
66 GGG
*
2826674 TGATTTGGTAGTTTACCATTATTGACTAAAT-AGGAGATCTGGTAGTTTGTCATTGTTGATTAAA
1 TGATTTGGTAGTTTACCATTATTGACTAAATGA-GAGATCTGGTAGTTTGACATTGTTGATTAAA
2826738 TGGG
65 TGGG
*
2826742 TGATTTGGTGGTTT
1 TGATTTGGTAGTTT
2826756 TTACCAAACC
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
67 1 0.01
68 73 0.99
ACGTcount: A:0.24, C:0.06, G:0.27, T:0.43
Consensus pattern (68 bp):
TGATTTGGTAGTTTACCATTATTGACTAAATGAGAGATCTGGTAGTTTGACATTGTTGATTAAAT
GGG
Found at i:2830414 original size:30 final size:32
Alignment explanation
Indices: 2830380--2830442 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
2830370 ATATTAAAGA
*
2830380 TATT-ATATA-TTTGTATAAAGTTTAATATAT
1 TATTAATATATTTTATATAAAGTTTAATATAT
* * *
2830410 TATTAATTTATTTTATATAAATTTTGATATAT
1 TATTAATATATTTTATATAAAGTTTAATATAT
2830442 T
1 T
2830443 TATCTATTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 4 0.15
31 4 0.15
32 19 0.70
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (32 bp):
TATTAATATATTTTATATAAAGTTTAATATAT
Found at i:2830986 original size:19 final size:20
Alignment explanation
Indices: 2830964--2831014 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
2830954 TAATTAAATA
2830964 ATTTAATTTTAATAT-TTTT
1 ATTTAATTTTAATATATTTT
* *
2830983 ATTTGA-TTAATATATATTTT
1 ATTTAATTTTA-ATATATTTT
*
2831003 ATTTATTTTTAA
1 ATTTAATTTTAA
2831015 ACTGAATTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
18 3 0.12
19 9 0.38
20 9 0.38
21 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTAATTTTAATATATTTT
Found at i:2831201 original size:24 final size:24
Alignment explanation
Indices: 2831174--2831219 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2831164 AAATTATAAT
*
2831174 TATTTAAATTAA-ATTTTTATTTAA
1 TATTT-AATTAATAATTTTATTTAA
2831198 TATTTAATTAATAATTTTATTT
1 TATTTAATTAATAATTTTATTT
2831220 TTAATTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTAATTAATAATTTTATTTAA
Found at i:2831672 original size:15 final size:16
Alignment explanation
Indices: 2831631--2831701 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 16
2831621 TTAAAATTAA
*
2831631 AAATTTAATATTTTAT
1 AAATATAATATTTTAT
* *
2831647 TAATAAAAATATTTT-T
1 AAAT-ATAATATTTTAT
*
2831663 AAATATAATA---TAA
1 AAATATAATATTTTAT
2831676 AAATATAATATATTTAAT
1 AAATATAATAT-TTT-AT
2831694 AAATATAA
1 AAATATAA
2831702 AAAAATAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
12 1 0.02
13 10 0.24
15 5 0.12
16 7 0.17
17 9 0.22
18 9 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATAATATTTTAT
Found at i:2831681 original size:13 final size:13
Alignment explanation
Indices: 2831663--2831709 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
2831653 AAATATTTTT
2831663 AAATATAATATAA
1 AAATATAATATAA
*
2831676 AAATATAATATATT
1 AAATATAATATA-A
*
2831690 TAATA-AATATAA
1 AAATATAATATAA
*
2831702 AAAAATAA
1 AAATATAA
2831710 ATTTAATATG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 3 0.11
13 20 0.74
14 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:2831685 original size:18 final size:18
Alignment explanation
Indices: 2831664--2831701 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2831654 AATATTTTTA
2831664 AATATAATATAA-AAATAT
1 AATAT-ATATAATAAATAT
*
2831682 AATATATTTAATAAATAT
1 AATATATATAATAAATAT
2831700 AA
1 AA
2831702 AAAAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATATATAATAAATAT
Found at i:2831686 original size:28 final size:26
Alignment explanation
Indices: 2831654--2831713 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
2831644 TATTAATAAA
*
2831654 AATATTTTTAAATATAATATAAAAATAT
1 AATATTTTT-AATA-AATATAAAAAAAT
*
2831682 AATATATTTAATAAATATAAAAAAAT
1 AATATTTTTAATAAATATAAAAAAAT
2831708 AA-ATTT
1 AATATTT
2831714 AATATGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 3 0.10
26 14 0.48
27 4 0.14
28 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AATATTTTTAATAAATATAAAAAAAT
Found at i:2831693 original size:22 final size:22
Alignment explanation
Indices: 2831619--2831694 Score: 55
Period size: 22 Copynumber: 3.4 Consensus size: 22
2831609 CTGATTTGAC
* *
2831619 ATTTAAAATTAAAAATTTAATAT
1 ATTTAATA-TAAAAATATAATAT
* ** *
2831642 -TTTATTAATAAAAATATTTTTAA
1 ATTTAAT-ATAAAAATA-TAATAT
*
2831665 ATATAATATAAAAATATAATAT
1 ATTTAATATAAAAATATAATAT
2831687 ATTTAATA
1 ATTTAATA
2831695 AATATAAAAA
Statistics
Matches: 38, Mismatches: 12, Indels: 7
0.67 0.21 0.12
Matches are distributed among these distances:
22 21 0.55
23 13 0.34
24 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTAATATAAAAATATAATAT
Found at i:2832274 original size:29 final size:27
Alignment explanation
Indices: 2832229--2832287 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 27
2832219 ATTTAATAAA
* *
2832229 TAAAAAAATTATTTAAATTTAATTTTT
1 TAAAAAAATTATATAAAATTAATTTTT
2832256 TAAAAAATATATATATAAAATTAATTTTT
1 TAAAAAA-AT-TATATAAAATTAATTTTT
2832285 TAA
1 TAA
2832288 TATTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 7 0.25
28 2 0.07
29 19 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAAAAAATTATATAAAATTAATTTTT
Found at i:2835329 original size:2 final size:2
Alignment explanation
Indices: 2835322--2835349 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2835312 ATGATTGTGA
2835322 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
2835350 TATTGTGATT
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:2837140 original size:176 final size:174
Alignment explanation
Indices: 2836799--2837156 Score: 465
Period size: 176 Copynumber: 2.0 Consensus size: 174
2836789 GCTTAAGTTG
* *
2836799 ATAAGAAATGATTAAATTATTATTTCATTAAATGCTTCTCAAGTGCAATTTGATTGAATGATAAC
1 ATAAAAAATGATTAAATTATTATTTCATTAAATGCTTCTCAAGTGCAAGTTGATTGAATGATAAC
* * * *
2836864 TTGCATGTGGACGTAGATATAGGGAAAAAAAAAGTATAAATTGAAGAAAGATTAAAGTGGTGATG
66 TTGCATATGGACGTAAATATA-GGAAAAAAAAAGTATAAATTAAAGAAAGATTAAAGAGGTGATG
* ** * *
2836929 GCAGTCTGATGGGTAATAATATGTTGGGGTGAAGAAATATTAAAGA
130 GCAGTCTAATGAATAATAATAGGTTGGGCTGAAGAAATATTAAA-A
* *
2836975 CTAAAAAATGATTAAATTATTATTTCATTAAATGCTTCTCAAGTGCAAGTTGATTGAATTATAAC
1 ATAAAAAATGATTAAATTATTATTTCATTAAATGCTTCTCAAGTGCAAGTTGATTGAATGATAAC
* *
2837040 TTGCGTATGGATGTAAATATA-GAAAAAAATATA-TATACAAATTAAAGAAAGATTAAAGCAGG-
66 TTGCATATGGACGTAAATATAGGAAAAAAA-A-AGTAT--AAATTAAAGAAAGATTAAAG-AGGT
*
2837102 GATGGCAGTTTAATGAATAATAA-AGGATT-GGCTGAAGAAATATTAAAA
126 GATGGCAGTCTAATGAATAATAATAGG-TTGGGCTGAAGAAATATTAAAA
2837150 ATAAAAA
1 ATAAAAA
2837157 TAGTTATCAA
Statistics
Matches: 159, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
174 8 0.05
175 11 0.07
176 98 0.62
177 40 0.25
178 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.30
Consensus pattern (174 bp):
ATAAAAAATGATTAAATTATTATTTCATTAAATGCTTCTCAAGTGCAAGTTGATTGAATGATAAC
TTGCATATGGACGTAAATATAGGAAAAAAAAAGTATAAATTAAAGAAAGATTAAAGAGGTGATGG
CAGTCTAATGAATAATAATAGGTTGGGCTGAAGAAATATTAAAA
Found at i:2842236 original size:3 final size:3
Alignment explanation
Indices: 2842228--2842274 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2842218 GTTAGATCAA
2842228 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2842275 ACTTTCTTTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2842869 original size:21 final size:21
Alignment explanation
Indices: 2842845--2842884 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2842835 TTTTATATAT
2842845 ATTTAATAAT-TAAAATTTAAA
1 ATTTAA-AATATAAAATTTAAA
*
2842866 ATTTAAAATATATAATTTA
1 ATTTAAAATATAAAATTTA
2842885 TATGAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTAAAATATAAAATTTAAA
Found at i:2844853 original size:14 final size:15
Alignment explanation
Indices: 2844829--2844857 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2844819 AGAAAATATT
2844829 TATATAATATTAAAA
1 TATATAATATTAAAA
2844844 TATA-AATATTAAAA
1 TATATAATATTAAAA
2844858 AATTGTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TATATAATATTAAAA
Found at i:2844957 original size:16 final size:18
Alignment explanation
Indices: 2844936--2844969 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2844926 TATATATTTT
2844936 AAAAATA-ATAAA-ATAA
1 AAAAATAGATAAATATAA
2844952 AAAAATAGATAAATATAA
1 AAAAATAGATAAATATAA
2844970 TCGAACTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAAATAGATAAATATAA
Found at i:2845758 original size:18 final size:18
Alignment explanation
Indices: 2845735--2845783 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
2845725 TAAAAACAAG
2845735 TACAAAATATAAATATTT
1 TACAAAATATAAATATTT
2845753 TACAAAATATAAATATTT
1 TACAAAATATAAATATTT
*
2845771 TAAAAAATATAAA
1 TACAAAATATAAA
2845784 AAGTCTAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
TACAAAATATAAATATTT
Found at i:2845792 original size:18 final size:18
Alignment explanation
Indices: 2845756--2845799 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2845746 AATATTTTAC
* * *
2845756 AAAATATAAATATTTTAA
1 AAAATATAAAAAGTCTAA
2845774 AAAATATAAAAAGTCTAA
1 AAAATATAAAAAGTCTAA
*
2845792 ACAATATA
1 AAAATATA
2845800 CATCAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAATATAAAAAGTCTAA
Found at i:2847201 original size:21 final size:23
Alignment explanation
Indices: 2847159--2847205 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2847149 ATTTTTAAAT
2847159 TTTTTTATAATTAAATTAAATAA
1 TTTTTTATAATTAAATTAAATAA
**
2847182 TTTTTTATTGTTAAA-T-AATAA
1 TTTTTTATAATTAAATTAAATAA
2847203 TTT
1 TTT
2847206 GAATTGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 1 0.05
23 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTTTATAATTAAATTAAATAA
Found at i:2848955 original size:16 final size:17
Alignment explanation
Indices: 2848934--2848969 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2848924 CATGTTATAA
*
2848934 TTATATTTA-ATATATT
1 TTATATTTATATAAATT
2848950 TTATATTTATATAAATT
1 TTATATTTATATAAATT
2848967 TTA
1 TTA
2848970 ATATATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:2851081 original size:18 final size:19
Alignment explanation
Indices: 2851052--2851087 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2851042 AAGGTTCGTA
2851052 ATTATATATTAAAATTTAT
1 ATTATATATTAAAATTTAT
*
2851071 ATTAT-TATTAATATTTA
1 ATTATATATTAAAATTTA
2851088 AAAATCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATATATTAAAATTTAT
Found at i:2851189 original size:28 final size:28
Alignment explanation
Indices: 2851153--2851215 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
2851143 TCATAGCACT
*
2851153 TGGACAAACACATTTTCTAACATAATAC
1 TGGAAAAACACATTTTCTAACATAATAC
2851181 TGGAAAAACACATTTTCTAACATAATAC
1 TGGAAAAACACATTTTCTAACATAATAC
2851209 TAGGAAA
1 T-GGAAA
2851216 GGGTTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (28 bp):
TGGAAAAACACATTTTCTAACATAATAC
Found at i:2852762 original size:51 final size:50
Alignment explanation
Indices: 2852640--2852775 Score: 139
Period size: 51 Copynumber: 2.6 Consensus size: 50
2852630 AAAATTAGTA
* * *
2852640 TTTTAGAGATAACAACGGGGCTAGAGTATCCCCGATTATGGAAAAACGGTG
1 TTTTAGAAATAA-AACGGGGTTAGAGTATCCCCGATTATGGAAAAACGATG
* * * * *
2852691 TTCTAAAAAATAAAATCGGGGTTAGAGTATTCTCGATTAT-GAAAAATTGATG
1 TT-TTAGAAATAAAA-CGGGGTTAGAGTATCCCCGATTATGGAAAAA-CGATG
*
2852743 TTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 TTTTAGAAATAAAA-CGGGGTTAGAGTATCCCC
2852776 TCAGAAATAA
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
51 35 0.51
52 33 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (50 bp):
TTTTAGAAATAAAACGGGGTTAGAGTATCCCCGATTATGGAAAAACGATG
Found at i:2852838 original size:79 final size:79
Alignment explanation
Indices: 2852707--2853201 Score: 864
Period size: 79 Copynumber: 6.3 Consensus size: 79
2852697 AAAATAAAAT
* * *
2852707 CGGGGTTAGAGTATTCTCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
2852772 CCCCTCAGAAATAA
66 CCCCTCGGAAATAA
*
2852786 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
2852851 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
*
2852865 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
2852930 CCCCTCAGAAATAA
66 CCCCTCGGAAATAA
* *
2852944 CGGGGTTGGAGTATCCCTGATTATGAAAAATTGATGTTATAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
2853009 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
*
2853023 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
2853088 CCCCTCGAAAATAA
66 CCCCTCGGAAATAA
* * *
2853102 TGGGGTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
2853167 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
2853181 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2853202 GATTAACGGG
Statistics
Matches: 395, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 395 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCTCGGAAATAA
Found at i:2853216 original size:27 final size:28
Alignment explanation
Indices: 2853153--2853228 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
2853143 GAAATAAAGC
***
2853153 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
2853181 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
2853208 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2853229 TGTGAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2855416 original size:1 final size:1
Alignment explanation
Indices: 2855412--2855439 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2855402 AGTAAATGGG
2855412 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
2855440 GTGGACGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2855643 original size:30 final size:32
Alignment explanation
Indices: 2855609--2855671 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
2855599 ATATTAAAGA
*
2855609 TATT-ATATA-TTTGTATAAAGTTTAATATAT
1 TATTAATATATTTTATATAAAGTTTAATATAT
* * *
2855639 TATTAATTTATTTTATATAAATTTTGATATAT
1 TATTAATATATTTTATATAAAGTTTAATATAT
2855671 T
1 T
2855672 TATCTATTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 4 0.15
31 4 0.15
32 19 0.70
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (32 bp):
TATTAATATATTTTATATAAAGTTTAATATAT
Found at i:2856215 original size:19 final size:20
Alignment explanation
Indices: 2856193--2856243 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
2856183 TAATTAAATA
2856193 ATTTAATTTTAATAT-TTTT
1 ATTTAATTTTAATATATTTT
* *
2856212 ATTTGA-TTAATATATATTTT
1 ATTTAATTTTA-ATATATTTT
*
2856232 ATTTATTTTTAA
1 ATTTAATTTTAA
2856244 ACTGAATTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
18 3 0.12
19 9 0.38
20 9 0.38
21 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTAATTTTAATATATTTT
Found at i:2856430 original size:24 final size:24
Alignment explanation
Indices: 2856403--2856448 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2856393 AAATTATAAT
*
2856403 TATTTAAATTAA-ATTTTTATTTAA
1 TATTT-AATTAATAATTTTATTTAA
2856427 TATTTAATTAATAATTTTATTT
1 TATTTAATTAATAATTTTATTT
2856449 TTAATTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTAATTAATAATTTTATTTAA
Done.