Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 21 of 28
Found at i:3146864 original size:27 final size:28
Alignment explanation
Indices: 3146808--3146871 Score: 103
Period size: 27 Copynumber: 2.3 Consensus size: 28
3146798 AGCCTTCATA
3146808 TTTGACAAATACAAAAGAAATCACCATT
1 TTTGACAAATACAAAAGAAATCACCATT
*
3146836 TTTGACAAATACAAAA-TAATCACCATT
1 TTTGACAAATACAAAAGAAATCACCATT
*
3146863 TTTAACAAA
1 TTTGACAAA
3146872 CAAATGGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 18 0.53
28 16 0.47
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (28 bp):
TTTGACAAATACAAAAGAAATCACCATT
Found at i:3148370 original size:3 final size:3
Alignment explanation
Indices: 3148364--3148396 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3148354 ATTAAAAAAA
3148364 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3148397 GTAAATGTGA
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):
TAT
Found at i:3148435 original size:40 final size:37
Alignment explanation
Indices: 3148391--3148471 Score: 103
Period size: 37 Copynumber: 2.1 Consensus size: 37
3148381 TTATTATTAT
3148391 TATTATGTAAATGTGATAT-TTTAGATATAATATAAAAATA
1 TATTAT-T-AATGTGATATATTTA-ATA-AATATAAAAATA
*
3148431 TATTATTAATTTGATATATTTAATAAATATAAAAATA
1 TATTATTAATGTGATATATTTAATAAATATAAAAATA
3148468 -ATTA
1 TATTA
3148472 AATAAATATG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
36 4 0.10
37 12 0.31
38 12 0.31
39 5 0.13
40 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.44
Consensus pattern (37 bp):
TATTATTAATGTGATATATTTAATAAATATAAAAATA
Found at i:3148484 original size:38 final size:38
Alignment explanation
Indices: 3148398--3148484 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
3148388 TATTATTATG
*
3148398 TAAATGTGATATTTTAGATATAATATAAAAATATATTA
1 TAAATATGATATTTTAGATATAATATAAAAATATATTA
* *
3148436 TTAATTTGATATATTTA-ATA-AATATAAAAATA-ATTAAA
1 TAAATATGATAT-TTTAGATATAATATAAAAATATATT--A
3148474 TAAATATGATA
1 TAAATATGATA
3148485 CGATATATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
36 3 0.07
37 12 0.29
38 23 0.55
39 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (38 bp):
TAAATATGATATTTTAGATATAATATAAAAATATATTA
Found at i:3150664 original size:36 final size:36
Alignment explanation
Indices: 3150623--3150730 Score: 216
Period size: 36 Copynumber: 3.0 Consensus size: 36
3150613 AATCTAATTT
3150623 AATATGGACCAAACCATACAAATTGCGATCAATAAG
1 AATATGGACCAAACCATACAAATTGCGATCAATAAG
3150659 AATATGGACCAAACCATACAAATTGCGATCAATAAG
1 AATATGGACCAAACCATACAAATTGCGATCAATAAG
3150695 AATATGGACCAAACCATACAAATTGCGATCAATAAG
1 AATATGGACCAAACCATACAAATTGCGATCAATAAG
3150731 TTCTATTCCA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.19
Consensus pattern (36 bp):
AATATGGACCAAACCATACAAATTGCGATCAATAAG
Found at i:3152803 original size:16 final size:15
Alignment explanation
Indices: 3152784--3152813 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
3152774 TTGATTAATT
3152784 AAATATTATTTTTTAA
1 AAATATT-TTTTTTAA
3152800 AAATATTTTTTTTA
1 AAATATTTTTTTTA
3152814 CCCACCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AAATATTTTTTTTAA
Found at i:3153582 original size:14 final size:14
Alignment explanation
Indices: 3153545--3153588 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
3153535 AACACGATAC
3153545 AAATACAATAT-TA
1 AAATACAATATATA
3153558 AAA-A-AATTATATA
1 AAATACAA-TATATA
3153571 AAATACAATATA-A
1 AAATACAATATATA
3153584 AAATA
1 AAATA
3153589 ATATGAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 2 0.07
12 4 0.15
13 14 0.52
14 5 0.19
15 2 0.07
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATACAATATATA
Found at i:3153773 original size:14 final size:14
Alignment explanation
Indices: 3153754--3153827 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
3153744 TTCCCTTCCC
3153754 TTTTTTCTCTTTCT
1 TTTTTTCTCTTTCT
*
3153768 TTTTTTCTCTCTCAT
1 TTTTTTCTCTTTC-T
* * *
3153783 TTCGTTTC-ATTTCC
1 TT-TTTTCTCTTTCT
*
3153797 TTTATT-TCTTTC-
1 TTTTTTCTCTTTCT
3153809 TTTTTTCT-TTTCT
1 TTTTTTCTCTTTCT
3153822 TTTTTT
1 TTTTTT
3153828 TTTCTCCTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
12 9 0.20
13 13 0.28
14 14 0.30
15 6 0.13
16 4 0.09
ACGTcount: A:0.04, C:0.20, G:0.01, T:0.74
Consensus pattern (14 bp):
TTTTTTCTCTTTCT
Found at i:3153822 original size:16 final size:16
Alignment explanation
Indices: 3153801--3153832 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3153791 ATTTCCTTTA
3153801 TTTCTTTCTTTTTTCT
1 TTTCTTTCTTTTTTCT
*
3153817 TTTCTTTTTTTTTTCT
1 TTTCTTTCTTTTTTCT
3153833 CCTTTCCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTCTTTCTTTTTTCT
Found at i:3153925 original size:2 final size:2
Alignment explanation
Indices: 3153918--3153942 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3153908 TAATTAAAAT
3153918 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
3153943 GTTAGATTGA
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:3154306 original size:17 final size:19
Alignment explanation
Indices: 3154252--3154299 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
3154242 AAATTAAAAT
3154252 TATCAATGATCTATAATATTA
1 TATCAA-GA-CTATAATATTA
3154273 TATCAAGCACTATAATATTA
1 TATCAAG-ACTATAATATTA
3154293 TATCAAG
1 TATCAAG
3154300 CATAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (19 bp):
TATCAAGACTATAATATTA
Found at i:3154308 original size:20 final size:20
Alignment explanation
Indices: 3154262--3154301 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3154252 TATCAATGAT
3154262 CTATAATATTATATCAAGCA
1 CTATAATATTATATCAAGCA
3154282 CTATAATATTATATCAAGCA
1 CTATAATATTATATCAAGCA
3154302 TAATAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (20 bp):
CTATAATATTATATCAAGCA
Found at i:3157600 original size:20 final size:20
Alignment explanation
Indices: 3157575--3157641 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
3157565 AGATTAAATT
3157575 TAAAAATTTATATTATTATA
1 TAAAAATTTATATTATTATA
*
3157595 TAAAAATTTA-A--AATAT-
1 TAAAAATTTATATTATTATA
*
3157611 TAAAAA--AATATTATTATA
1 TAAAAATTTATATTATTATA
*
3157629 TAAATATTTATAT
1 TAAAAATTTATAT
3157642 ATTTTTATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
14 1 0.03
15 1 0.03
16 6 0.17
17 8 0.22
18 5 0.14
19 1 0.03
20 14 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAAATTTATATTATTATA
Found at i:3158957 original size:16 final size:18
Alignment explanation
Indices: 3158937--3158984 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
3158927 ATTTAATTTA
3158937 ATTTAAAAATAAATTA-T
1 ATTTAAAAATAAATTATT
**
3158954 -TTTAAATTTAAATTATT
1 ATTTAAAAATAAATTATT
3158971 ATTTAATAAATAAA
1 ATTTAA-AAATAAA
3158985 AATATATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 13 0.54
17 1 0.04
18 5 0.21
19 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTAAAAATAAATTATT
Found at i:3159021 original size:10 final size:10
Alignment explanation
Indices: 3158996--3159029 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3158986 ATATATTATA
3158996 TAAAATAATTT
1 TAAAAT-ATTT
3159007 T-AAATATTT
1 TAAAATATTT
3159016 TAAAATATTT
1 TAAAATATTT
3159026 TAAA
1 TAAA
3159030 TAATAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 16 0.73
11 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TAAAATATTT
Found at i:3159292 original size:2 final size:2
Alignment explanation
Indices: 3159287--3159340 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3159277 TAAGAGAGAA
3159287 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
3159329 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3159341 GGAGCACCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3160561 original size:3 final size:3
Alignment explanation
Indices: 3160548--3160601 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
3160538 ATCATTTTAG
3160548 TTA TT- 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
*
3160595 TTT TTA T
1 TTA TTA T
3160602 AACTGATAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3162096 original size:15 final size:16
Alignment explanation
Indices: 3162050--3162096 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
3162040 CTATGTAAAA
*
3162050 ATAAATTTTAAAAT-T
1 ATAAATTTTTAAATAT
*
3162065 ATAAATATTT-AATAT
1 ATAAATTTTTAAATAT
3162080 ATAAAATTTTTAAATAT
1 AT-AAATTTTTAAATAT
3162097 CAATAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 3 0.12
15 11 0.42
16 7 0.27
17 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAATTTTTAAATAT
Found at i:3162101 original size:23 final size:23
Alignment explanation
Indices: 3162058--3162101 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3162048 AAATAAATTT
*
3162058 TAAAATTATAAATATTTAATATA
1 TAAAATTATAAATATTCAATATA
*
3162081 TAAAATTTTTAAATA-TCAATA
1 TAAAA-TTATAAATATTCAATA
3162102 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAAATTATAAATATTCAATATA
Found at i:3163165 original size:23 final size:23
Alignment explanation
Indices: 3163139--3163217 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
3163129 AATTGTTCAA
3163139 ATTTTTAAAAAATATATTAAAAT
1 ATTTTTAAAAAATATATTAAAAT
* * *
3163162 ATTTAT-AAAAATAAATTTTAAAT
1 ATTTTTAAAAAATATA-TTAAAAT
*
3163185 ATTTTTTAATAAAAT-TAAATAAAACT
1 A-TTTTTAA-AAAATAT-ATTAAAA-T
3163211 ATTTTTA
1 ATTTTTA
3163218 TTTATTAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
22 8 0.19
23 12 0.28
24 4 0.09
25 11 0.26
26 8 0.19
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTTTAAAAAATATATTAAAAT
Found at i:3164984 original size:17 final size:19
Alignment explanation
Indices: 3164964--3165007 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
3164954 GTTAATATTA
3164964 TTTTTATATTAT-A-TAAT
1 TTTTTATATTATAATTAAT
3164981 TTTTTATATTATAATTTAAT
1 TTTTTATATTATAA-TTAAT
3165001 TTTTTAT
1 TTTTTAT
3165008 TATATTTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.50
18 1 0.04
20 11 0.46
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTATATTATAATTAAT
Found at i:3165414 original size:23 final size:24
Alignment explanation
Indices: 3165381--3165436 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
3165371 AGTAGGTACT
*
3165381 ATATAATATATTTAAATATGAT-TA
1 ATAT-ATATATATAAATATGATATA
*
3165405 ATATATATATATATATATGATATA
1 ATATATATATATAAATATGATATA
3165429 AGTATATA
1 A-TATATA
3165437 GTTATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 15 0.54
24 7 0.25
25 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (24 bp):
ATATATATATATAAATATGATATA
Found at i:3165442 original size:23 final size:21
Alignment explanation
Indices: 3165386--3165443 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 21
3165376 GTACTATATA
* *
3165386 ATATATTTAAATATGATTAAT
1 ATATAATTATATATGATTAAT
3165407 ATATATATATATATATGATATAAGT
1 ATATA-AT-TATATATGAT-TAA-T
*
3165432 ATATAGTTATAT
1 ATATAATTATAT
3165444 TTAAAGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.17
22 1 0.03
23 14 0.47
24 4 0.13
25 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (21 bp):
ATATAATTATATATGATTAAT
Found at i:3165640 original size:31 final size:30
Alignment explanation
Indices: 3165578--3165646 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
3165568 TTACACTAAA
* ** **
3165578 AATTTATTTAAGTAAAAATTAATGATTAAG
1 AATTTATTTAAGAAAAAATTAAAAAACAAG
3165608 AATTTATTTAAGAAAAAAATTAAAAAACAAG
1 AATTTATTTAAG-AAAAAATTAAAAAACAAG
3165639 AATTTATT
1 AATTTATT
3165647 CAAATACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (30 bp):
AATTTATTTAAGAAAAAATTAAAAAACAAG
Found at i:3171664 original size:2 final size:2
Alignment explanation
Indices: 3171657--3171688 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3171647 AAGATATTAA
3171657 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
3171689 TAATAAAGGT
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:3171862 original size:60 final size:60
Alignment explanation
Indices: 3171789--3171903 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
3171779 TTCATCAGTC
3171789 AGTTTAGGCGTATACTTTATGAAAGAATGCCATATTTC-AGCCTCCTTAAAAGTCATTGCA
1 AGTTTAGGCGTATACTTTATGAAAGAATGCCATATTTCTA-CCTCCTTAAAAGTCATTGCA
3171849 AGTTTAGGCGTATACTTTATGAAAGAATGCCATATTTCTACCTCCTTAAAAGTCA
1 AGTTTAGGCGTATACTTTATGAAAGAATGCCATATTTCTACCTCCTTAAAAGTCA
3171904 CAGCAAAATG
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
60 53 0.98
61 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (60 bp):
AGTTTAGGCGTATACTTTATGAAAGAATGCCATATTTCTACCTCCTTAAAAGTCATTGCA
Found at i:3172849 original size:28 final size:30
Alignment explanation
Indices: 3172786--3172850 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
3172776 AATATTAATA
*
3172786 TAATTTAAAATAATAAAATAAATGTTTATAC
1 TAATTTAAAATAATAAAAT-AATGTTTAAAC
* * *
3172817 CAATTTTAAATAATAAAAT-AT-TTTAAAT
1 TAATTTAAAATAATAAAATAATGTTTAAAC
3172845 TAATTT
1 TAATTT
3172851 GATATAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 10 0.34
29 2 0.07
31 17 0.59
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (30 bp):
TAATTTAAAATAATAAAATAATGTTTAAAC
Found at i:3174328 original size:30 final size:30
Alignment explanation
Indices: 3174289--3174396 Score: 98
Period size: 30 Copynumber: 3.6 Consensus size: 30
3174279 GTTAATAGCC
* *
3174289 TATTCAGATATAAATTAAA-GTTAAAGAACA
1 TATTTAGATATAAATTAAATATTAAA-AACA
**
3174319 TATTTAGATATAAATTAAATATTAAAAATT
1 TATTTAGATATAAATTAAATATTAAAAACA
* *
3174349 TATTT-GAATATAAATTAAA-ATTTAAACACC
1 TATTTAG-ATATAAATTAAATA-TTAAAAACA
*
3174379 TATTTAAATAT-AATTAAA
1 TATTTAGATATAAATTAAA
3174397 ATATAAATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
29 9 0.14
30 52 0.79
31 5 0.08
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (30 bp):
TATTTAGATATAAATTAAATATTAAAAACA
Found at i:3177101 original size:16 final size:17
Alignment explanation
Indices: 3177077--3177117 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
3177067 ATAATTTAAA
*
3177077 AAATCAAATATAA-ATG
1 AAATAAAATATAATATG
3177093 AAATAAAATATAATATG
1 AAATAAAATATAATATG
*
3177110 ATATAAAA
1 AAATAAAA
3177118 AAAATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (17 bp):
AAATAAAATATAATATG
Found at i:3177107 original size:21 final size:18
Alignment explanation
Indices: 3177083--3177132 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
3177073 TAAAAAATCA
3177083 AATATAAATGAAATAAAATAT
1 AATATAAAT-AAA-AAAA-AT
*
3177104 AATATGATATAAAAAAAAT
1 AATAT-AAATAAAAAAAAT
3177123 AATATAAATA
1 AATATAAATA
3177133 TGATATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.15
19 7 0.27
20 4 0.15
21 8 0.31
22 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (18 bp):
AATATAAATAAAAAAAAT
Found at i:3177115 original size:26 final size:25
Alignment explanation
Indices: 3177084--3177138 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
3177074 AAAAAATCAA
**
3177084 ATATAAATGAAATAAAATATAATATG
1 ATATAAAAAAAATAAAATA-AATATG
*
3177110 ATATAAAAAAAATAATATAAATATG
1 ATATAAAAAAAATAAAATAAATATG
3177135 ATAT
1 ATAT
3177139 GAATAGATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (25 bp):
ATATAAAAAAAATAAAATAAATATG
Found at i:3177200 original size:26 final size:26
Alignment explanation
Indices: 3177119--3177216 Score: 64
Period size: 26 Copynumber: 3.8 Consensus size: 26
3177109 GATATAAAAA
3177119 AAATA-ATATAAATATGATATGAA-TAGAT
1 AAATATATATAAATAT-ATA--AATTA-AT
* * *
3177147 AAATATAT-TAAAT-TTTATATTAAA
1 AAATATATATAAATATATAAATTAAT
*
3177171 AAATATATATAAATATATAAATTATT
1 AAATATATATAAATATATAAATTAAT
3177197 AAAT-T-TAGTAAATAATATAA
1 AAATATATA-TAAAT-ATATAA
3177217 GAGACTAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
24 12 0.21
25 13 0.23
26 19 0.33
27 1 0.02
28 10 0.18
29 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
AAATATATATAAATATATAAATTAAT
Found at i:3181297 original size:27 final size:28
Alignment explanation
Indices: 3181229--3181298 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 28
3181219 AATAAATTTA
3181229 ATAA-TTTAATA-ATTTATATCATATAT
1 ATAATTTTAATATATTTATATCATATAT
* * * *
3181255 ATTATTTTTATTTA-TTATAATTATATAT
1 ATAATTTTAATATATTTAT-ATCATATAT
3181283 A-AATTTTAATATATTT
1 ATAATTTTAATATATTT
3181299 TTTATATATT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
26 3 0.09
27 18 0.55
28 12 0.36
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (28 bp):
ATAATTTTAATATATTTATATCATATAT
Found at i:3182246 original size:2 final size:2
Alignment explanation
Indices: 3182239--3182271 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3182229 TTAAATCATT
3182239 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
3182272 GATGCGAATG
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:3183197 original size:22 final size:20
Alignment explanation
Indices: 3183161--3183208 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 20
3183151 ACAAATATTT
3183161 AATTTATTATTTTAT-ATTA
1 AATTTATTATTTTATAATTA
3183180 ATATTTATATAATTTTATAATTA
1 A-ATTTAT-T-ATTTTATAATTA
3183203 AATTTA
1 AATTTA
3183209 AATTAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 6 0.24
21 1 0.04
22 12 0.48
23 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTATTATTTTATAATTA
Found at i:3183215 original size:23 final size:22
Alignment explanation
Indices: 3183169--3183216 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
3183159 TTAATTTATT
*
3183169 ATTTTATATTAATATTTATATA
1 ATTTTATATTAATATTTAAATA
3183191 ATTTTATAATTAA-ATTTAAATTA
1 ATTTTAT-ATTAATATTTAAA-TA
3183214 ATT
1 ATT
3183217 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTATATTAATATTTAAATA
Found at i:3183217 original size:15 final size:15
Alignment explanation
Indices: 3183197--3183235 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3183187 TATAATTTTA
3183197 TAATTAAATTTAAAT
1 TAATTAAATTTAAAT
* **
3183212 TAATTAATTTTTTAT
1 TAATTAAATTTAAAT
3183227 TAATTAAAT
1 TAATTAAAT
3183236 AACAATAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTAAATTTAAAT
Found at i:3184900 original size:2 final size:2
Alignment explanation
Indices: 3184893--3184928 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3184883 TCATCTCCAA
3184893 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
3184929 TAAAAAAAAA
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:3185395 original size:16 final size:16
Alignment explanation
Indices: 3185374--3185404 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3185364 ATTTAACAAC
3185374 GTTTATTTTGTTAAAT
1 GTTTATTTTGTTAAAT
3185390 GTTTATTTTGTTAAA
1 GTTTATTTTGTTAAA
3185405 AGATACTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (16 bp):
GTTTATTTTGTTAAAT
Found at i:3185671 original size:31 final size:30
Alignment explanation
Indices: 3185614--3185674 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3185604 GTAAGGTTTT
* * * *
3185614 TATTTTTTTTCGACCTTGTTTGGACTATAA
1 TATTTTTTTTCAACCATATTTAGACTATAA
3185644 TATTTTTTTCTCAACCATATTTAGACTATAA
1 TATTTTTTT-TCAACCATATTTAGACTATAA
3185675 GTTGTTCACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (30 bp):
TATTTTTTTTCAACCATATTTAGACTATAA
Found at i:3185823 original size:28 final size:30
Alignment explanation
Indices: 3185764--3185823 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
3185754 ATTTTTTAAT
*
3185764 TTTTTATATTTATATTTAAAAAATTATATA
1 TTTTTATATTAATATTTAAAAAATTATATA
3185794 TTTTTATATTAATATTT-AAAAA-TATATA
1 TTTTTATATTAATATTTAAAAAATTATATA
3185822 TT
1 TT
3185824 AAATATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 8 0.28
29 5 0.17
30 16 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTTTATATTAATATTTAAAAAATTATATA
Found at i:3185835 original size:13 final size:13
Alignment explanation
Indices: 3185799--3185841 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3185789 ATATATTTTT
*
3185799 ATATTAATATTTAA
1 ATATAAATA-TTAA
* *
3185813 AAATATATATTAA
1 ATATAAATATTAA
3185826 ATATAAATATTAA
1 ATATAAATATTAA
3185839 ATA
1 ATA
3185842 AATATACTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAAATATTAA
Found at i:3186796 original size:34 final size:34
Alignment explanation
Indices: 3186730--3186914 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
3186720 ATTTATTTTT
* *
3186730 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
3186763 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3186797 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
3186831 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
3186865 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3186899 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
3186915 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:3187277 original size:19 final size:19
Alignment explanation
Indices: 3187221--3187283 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
3187211 TGGTTGTCGA
**
3187221 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
3187240 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
3187259 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
3187278 GTTACT
1 GGTACT
3187284 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:3191415 original size:34 final size:34
Alignment explanation
Indices: 3191349--3191533 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
3191339 AAGTGGGAGA
* *
3191349 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
3191382 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3191416 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
3191450 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
3191484 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3191518 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
3191534 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:3191923 original size:16 final size:16
Alignment explanation
Indices: 3191899--3191941 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
3191889 AGATTTTTTT
* *
3191899 AAAATATTAAAATATA
1 AAAAAATTAAAAGATA
*
3191915 AAAAAATTAAAGGATA
1 AAAAAATTAAAAGATA
3191931 AAAAAA-TAAAA
1 AAAAAATTAAAA
3191942 AATACTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (16 bp):
AAAAAATTAAAAGATA
Found at i:3191925 original size:24 final size:24
Alignment explanation
Indices: 3191897--3191943 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3191887 TAAGATTTTT
* * *
3191897 TTAAAATATTAAAATATAAAAAAA
1 TTAAAAGATAAAAAAATAAAAAAA
*
3191921 TTAAAGGATAAAAAAATAAAAAA
1 TTAAAAGATAAAAAAATAAAAAA
3191944 TACTCTAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (24 bp):
TTAAAAGATAAAAAAATAAAAAAA
Found at i:3192198 original size:20 final size:21
Alignment explanation
Indices: 3192175--3192215 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3192165 AATTTTTACT
3192175 TAATTTAAAT-TATTATTTAA
1 TAATTTAAATATATTATTTAA
*
3192195 TAATTTAAATATATTTTTTAA
1 TAATTTAAATATATTATTTAA
3192216 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATTTAAATATATTATTTAA
Found at i:3197059 original size:2 final size:2
Alignment explanation
Indices: 3197052--3197083 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
3197042 AATAACAACA
3197052 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
3197084 AAAGAATCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3198597 original size:2 final size:2
Alignment explanation
Indices: 3198590--3198617 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3198580 AAATCAAAAC
3198590 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
3198618 GAAGCTTTAC
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:3198801 original size:24 final size:25
Alignment explanation
Indices: 3198758--3198804 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3198748 CTAAAAATTT
3198758 ATTTTATTATTTAAAATAATATTAA
1 ATTTTATTATTTAAAATAATATTAA
* *
3198783 ATTTTATT-TTTATATTAATATT
1 ATTTTATTATTTAAAATAATATT
3198805 TATAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTATTATTTAAAATAATATTAA
Found at i:3199305 original size:11 final size:10
Alignment explanation
Indices: 3199262--3199313 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 10
3199252 CTCGCCTTCC
3199262 TTTTTTTTTCA
1 TTTTTTTTT-A
*
3199273 GTTTTTTATTTT
1 -TTTTTT-TTTA
3199285 TTATTTTTTTA
1 TT-TTTTTTTA
3199296 TTTCTTTTTTA
1 TTT-TTTTTTA
3199307 TTTTTTT
1 TTTTTTT
3199314 GCCTATTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 5 0.14
11 17 0.49
12 10 0.29
13 3 0.09
ACGTcount: A:0.10, C:0.04, G:0.02, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:3200522 original size:5 final size:5
Alignment explanation
Indices: 3200489--3200521 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3200479 GCCAGCTAGG
*
3200489 AATCC AATCC AATCC AATCC AATCC AATAC AAT
1 AATCC AATCC AATCC AATCC AATCC AATCC AAT
3200522 AGGAGCCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (5 bp):
AATCC
Found at i:3200788 original size:28 final size:29
Alignment explanation
Indices: 3200743--3200799 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
3200733 TATAAATGTA
3200743 GTTTTTTTTAAAGATTA-TT-ATATTTTT
1 GTTTTTTTTAAAGATTATTTAATATTTTT
**
3200770 GTTTTTTTATAAATTTTATTTAATATTTTT
1 GTTTTTTT-TAAAGATTATTTAATATTTTT
3200800 ATTATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.32
28 7 0.28
29 2 0.08
30 8 0.32
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (29 bp):
GTTTTTTTTAAAGATTATTTAATATTTTT
Found at i:3204489 original size:26 final size:23
Alignment explanation
Indices: 3204443--3204498 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 23
3204433 TTCAAAAATT
3204443 TAATAAAAATTTTAATAATTTAA
1 TAATAAAAATTTTAATAATTTAA
*
3204466 TAATAATAAATTTTATTTATATTTAA
1 TAATAA-AAATTTTA-ATA-ATTTAA
*
3204492 TTATAAA
1 TAATAAA
3204499 TATATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 6 0.21
24 8 0.29
25 3 0.11
26 11 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATAAAAATTTTAATAATTTAA
Found at i:3204492 original size:23 final size:23
Alignment explanation
Indices: 3204440--3204499 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
3204430 AGATTCAAAA
3204440 ATTTAATAA-AAATTTTAATAAT
1 ATTTAATAATAAATTTTAATAAT
* *
3204462 -TTAATAATAATAAATTTTATTTAT
1 ATT--TAATAATAAATTTTAATAAT
*
3204486 ATTTAATTATAAAT
1 ATTTAATAATAAAT
3204500 ATATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 2 0.06
23 16 0.52
24 11 0.35
25 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTAATAATAAATTTTAATAAT
Found at i:3205916 original size:15 final size:15
Alignment explanation
Indices: 3205896--3205928 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3205886 ATCATATATT
3205896 AAAAAAG-AGAGAAAA
1 AAAAAAGAAG-GAAAA
3205911 AAAAAAGAAGGAAAA
1 AAAAAAGAAGGAAAA
3205926 AAA
1 AAA
3205929 CCCAATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAGGAAAA
Found at i:3207333 original size:11 final size:12
Alignment explanation
Indices: 3207310--3207338 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3207300 ATATAATACG
3207310 AATATAATATAA
1 AATATAATATAA
3207322 AATATAAT-TAA
1 AATATAATATAA
3207333 AATATA
1 AATATA
3207339 GCTTGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AATATAATATAA
Found at i:3209312 original size:19 final size:19
Alignment explanation
Indices: 3209288--3209324 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3209278 TCATGAATAT
3209288 TTATAATTTTTTTTTTAAA
1 TTATAATTTTTTTTTTAAA
3209307 TTATAATTTTTTTTTTAA
1 TTATAATTTTTTTTTTAA
3209325 TATTCTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATAATTTTTTTTTTAAA
Found at i:3210140 original size:2 final size:2
Alignment explanation
Indices: 3210133--3210171 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3210123 TTAACAAATA
3210133 AT 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 AT A
3210172 CACTTTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3211477 original size:84 final size:84
Alignment explanation
Indices: 3211336--3211498 Score: 263
Period size: 84 Copynumber: 1.9 Consensus size: 84
3211326 ATCACATTTT
* *
3211336 ATTCAAATTTAGGTTGAAACTTCAATTCTCTAGTCCCATCCCATAAGTTTTATCGAACTTCAAGT
1 ATTCAAATTTAGGTTGAAACTTCAATTCTCAAGTCCCATCCCATAAGTTTTATCGAACTTAAAGT
*
3211401 CAATGGGTCAAAAAGATAA
66 CAATGGCTCAAAAAGATAA
** *
3211420 ATTCAAATTTAGGTTGGCACTTCAATTCTCAAGTCCCATCCCATATGTTTTATCGAACTTAAAGT
1 ATTCAAATTTAGGTTGAAACTTCAATTCTCAAGTCCCATCCCATAAGTTTTATCGAACTTAAAGT
*
3211485 CGATGGCTCAAAAA
66 CAATGGCTCAAAAA
3211499 ATATGAAGAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (84 bp):
ATTCAAATTTAGGTTGAAACTTCAATTCTCAAGTCCCATCCCATAAGTTTTATCGAACTTAAAGT
CAATGGCTCAAAAAGATAA
Found at i:3212332 original size:28 final size:28
Alignment explanation
Indices: 3212300--3212353 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
3212290 TGAAACCAGG
*
3212300 TCATACATATAAATATACATATACATGT
1 TCATACATATAAACATACATATACATGT
* * *
3212328 TCATACATGTATACATGCATATACAT
1 TCATACATATAAACATACATATACAT
3212354 ATGTATGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.35
Consensus pattern (28 bp):
TCATACATATAAACATACATATACATGT
Found at i:3212553 original size:20 final size:20
Alignment explanation
Indices: 3212528--3212565 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3212518 GTATAAAAAA
* *
3212528 ATATATTCATACATATATAC
1 ATATATGCATACAAATATAC
3212548 ATATATGCATACAAATAT
1 ATATATGCATACAAATAT
3212566 TTATTTATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (20 bp):
ATATATGCATACAAATATAC
Found at i:3213374 original size:2 final size:2
Alignment explanation
Indices: 3213367--3213396 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3213357 CTCTTTGTTC
3213367 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
3213397 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3213401 original size:2 final size:2
Alignment explanation
Indices: 3213396--3213422 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3213386 TATATATATA
3213396 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3213423 TAATTAACGA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3215559 original size:3 final size:3
Alignment explanation
Indices: 3215551--3215586 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3215541 ATAATATCAT
3215551 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3215587 TATCAACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3217362 original size:19 final size:18
Alignment explanation
Indices: 3217336--3217376 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 18
3217326 AAATTTTAAT
3217336 ATATATATATATATAATATAA
1 ATATAT-TA-ATATAATA-AA
3217357 ATATATTAATATAATAAA
1 ATATATTAATATAATAAA
3217375 AT
1 AT
3217377 TTAAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 2 0.10
21 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATATTAATATAATAAA
Found at i:3218022 original size:20 final size:20
Alignment explanation
Indices: 3217985--3218031 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
3217975 TTAATCACTT
*
3217985 TTTACTATAATTAAATATGATAA
1 TTTA-TATAATT-AATATCAT-A
3218008 TTTATATAATT-ATATCATA
1 TTTATATAATTAATATCATA
3218027 TTTAT
1 TTTAT
3218032 TTTATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
22 7 0.30
23 4 0.17
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTATATAATTAATATCATA
Found at i:3218105 original size:35 final size:37
Alignment explanation
Indices: 3218024--3218107 Score: 90
Period size: 35 Copynumber: 2.4 Consensus size: 37
3218014 TAATTATATC
*
3218024 ATATTTATTTTATTTTTATATATTATAACTATATTTAAA
1 ATATTT-TTATATTTTTATATATTATAAC-ATATTTAAA
3218063 ATA---TTATATTTTTATACT-TTATAA-AT-TTTAAA
1 ATATTTTTATATTTTTATA-TATTATAACATATTTAAA
3218095 ATATTTTTATATT
1 ATATTTTTATATT
3218108 CAAAACATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
32 9 0.22
33 2 0.05
35 25 0.62
36 1 0.03
39 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (37 bp):
ATATTTTTATATTTTTATATATTATAACATATTTAAA
Found at i:3218152 original size:17 final size:18
Alignment explanation
Indices: 3218132--3218178 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
3218122 TTATTTTTTA
3218132 TATTATATTATATATT-T
1 TATTATATTATATATTAT
*
3218149 TATTATATTTTA-ATTAT
1 TATTATATTATATATTAT
*
3218166 TTTTATATTATAT
1 TATTATATTATAT
3218179 TCATGTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTATATTATATATTAT
Found at i:3218157 original size:22 final size:22
Alignment explanation
Indices: 3218117--3218190 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
3218107 TCAAAACATG
*
3218117 ATTATTTATTTT-TTATATTAT
1 ATTATATATTTTATTATATTAT
*
3218138 ATTATATATTTTATTATATTTT
1 ATTATATATTTTATTATATTAT
3218160 AATTAT-T-TTTATATTATATTCAT
1 -ATTATATATTT-TATTATATT-AT
*
3218183 GTTATATA
1 ATTATATA
3218191 ATTATATCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 14 0.33
22 22 0.51
23 7 0.16
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (22 bp):
ATTATATATTTTATTATATTAT
Found at i:3220308 original size:2 final size:2
Alignment explanation
Indices: 3220296--3220328 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
3220286 ACTGCTCTCA
3220296 AT AT A- AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
3220329 CAAGAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3221675 original size:2 final size:2
Alignment explanation
Indices: 3221670--3221707 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3221660 CGGAGCTCTT
3221670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3221708 AACTTTTTCA
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):
TA
Found at i:3228921 original size:12 final size:12
Alignment explanation
Indices: 3228904--3228952 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
3228894 CATATCATTT
3228904 ATTTTTTTATTA
1 ATTTTTTTATTA
3228916 ATTTTTTTATT-
1 ATTTTTTTATTA
*
3228927 ATTTTTTAATTTTA
1 ATTTTTT--TATTA
3228941 ATTTTATTTATT
1 ATTTT-TTTATT
3228953 TTATAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 7 0.23
12 11 0.35
13 6 0.19
14 5 0.16
15 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTTTTATTA
Found at i:3228928 original size:23 final size:25
Alignment explanation
Indices: 3228902--3228952 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
3228892 ATCATATCAT
3228902 TTATTTTTT-TATTAATTTT-TTTA
1 TTATTTTTTATATTAATTTTATTTA
*
3228925 TTATTTTTTAATTTTAATTTTATTTA
1 TTATTTTTT-ATATTAATTTTATTTA
3228951 TT
1 TT
3228953 TTATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
25 9 0.38
26 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (25 bp):
TTATTTTTTATATTAATTTTATTTA
Found at i:3228947 original size:19 final size:18
Alignment explanation
Indices: 3228901--3228952 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
3228891 AATCATATCA
3228901 TTTATTTT-TTTATTAAT
1 TTTATTTTATTTATTAAT
* *
3228918 TTTTTTATTATTTTTTAAT
1 TTTATT-TTATTTATTAAT
3228937 TTTAATTTTATTTATT
1 TTT-ATTTTATTTATT
3228953 TTATAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.18
18 2 0.07
19 19 0.68
20 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTTATTTATTAAT
Found at i:3228953 original size:23 final size:21
Alignment explanation
Indices: 3228901--3228956 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
3228891 AATCATATCA
3228901 TTTATTT-TTTTATTAATTTT
1 TTTATTTATTTTATTAATTTT
3228921 TTTA-TTATTTT-TTAATTTTAAT
1 TTTATTTATTTTATTAA-TTT--T
3228943 TTTATTTATTTTAT
1 TTTATTTATTTTAT
3228957 AAATATCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 6 0.20
20 11 0.37
22 5 0.17
23 7 0.23
24 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTATTTATTTTATTAATTTT
Found at i:3234628 original size:11 final size:11
Alignment explanation
Indices: 3234606--3234636 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
3234596 ATATCAAAAT
3234606 ATATATATAACC
1 ATATA-ATAACC
3234618 ATATAATAACC
1 ATATAATAACC
3234629 ATATAATA
1 ATATAATA
3234637 CTTTAAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (11 bp):
ATATAATAACC
Found at i:3234748 original size:72 final size:72
Alignment explanation
Indices: 3234663--3234810 Score: 269
Period size: 72 Copynumber: 2.1 Consensus size: 72
3234653 GACACATGAA
* * *
3234663 ATACATGAACATGATACAAATAAATGAATTTCTAGGTCTAAATCTAGCTGACTAATATGAAGAAG
1 ATACACGAACATGATACAAATAAATGAATTGCTAGGTCTAAATCTAGCTGACTAATATGAAGAAC
3234728 AACAACC
66 AACAACC
3234735 ATACACGAACATGATACAAATAAATGAATTGCTAGGTCTAAATCTAGCTGACTAATATGAAGAAC
1 ATACACGAACATGATACAAATAAATGAATTGCTAGGTCTAAATCTAGCTGACTAATATGAAGAAC
3234800 AACAACC
66 AACAACC
3234807 ATAC
1 ATAC
3234811 CGAGAAACAT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (72 bp):
ATACACGAACATGATACAAATAAATGAATTGCTAGGTCTAAATCTAGCTGACTAATATGAAGAAC
AACAACC
Found at i:3238205 original size:21 final size:21
Alignment explanation
Indices: 3238130--3238236 Score: 58
Period size: 21 Copynumber: 4.8 Consensus size: 21
3238120 AGGATATCCT
* *
3238130 AATATATATATATATA-TATA
1 AATATAAATATAAATATTATA
*
3238150 TAATATAAATTATTAATATATTAAA
1 -AATATAAA-TA-TAA-ATATTATA
*
3238175 ATTTATATAAATATAAATATTTTA
1 A---ATATAAATATAAATATTATA
* *
3238199 AATATAATTGT-AATATTATA
1 AATATAAATATAAATATTATA
3238219 AA-ATAAAAGTATAAATAT
1 AATAT-AAA-TATAAATAT
3238237 ACGAATTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
19 2 0.03
20 12 0.18
21 17 0.26
22 7 0.11
23 2 0.03
24 11 0.17
25 6 0.09
26 2 0.03
27 7 0.11
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATAAATATAAATATTATA
Found at i:3241319 original size:1 final size:1
Alignment explanation
Indices: 3241313--3241339 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3241303 CACTACTGAA
3241313 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
3241340 ACATTTGGAA
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:3242826 original size:24 final size:23
Alignment explanation
Indices: 3242799--3242843 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
3242789 AATTTTTTAA
*
3242799 TTATATAATATATTAATTTTATTT
1 TTATATAATAGA-TAATTTTATTT
*
3242823 TTATATATTAGATAATTTTAT
1 TTATATAATAGATAATTTTAT
3242844 CACAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTATATAATAGATAATTTTATTT
Found at i:3242910 original size:30 final size:33
Alignment explanation
Indices: 3242876--3242944 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 33
3242866 TAAATATATT
3242876 AAATTATTTAAA-TTTTAAAAT-TTTA-TAAAA
1 AAATTATTTAAATTTTTAAAATATTTATTAAAA
*
3242906 AAATTA-TTAAATTTTTAAAATATTTATTTAAA
1 AAATTATTTAAATTTTTAAAATATTTATTAAAA
3242938 AAATTAT
1 AAATTAT
3242945 AAATAAACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 5 0.15
30 15 0.44
31 4 0.12
32 10 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
AAATTATTTAAATTTTTAAAATATTTATTAAAA
Found at i:3242937 original size:21 final size:21
Alignment explanation
Indices: 3242885--3242925 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3242875 TAAATTATTT
3242885 AAATT-TTAAAATTTTATAAAA
1 AAATTATT-AAATTTTATAAAA
3242906 AAATTATTAAATTTT-TAAAA
1 AAATTATTAAATTTTATAAAA
3242926 TATTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 12 0.63
22 2 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTATTAAATTTTATAAAA
Found at i:3247888 original size:16 final size:16
Alignment explanation
Indices: 3247876--3247909 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3247866 TAATTTTTTT
3247876 ATTTTTATGTTTTTAA
1 ATTTTTATGTTTTTAA
3247892 ATTTTTAT-TATTTTAA
1 ATTTTTATGT-TTTTAA
3247908 AT
1 AT
3247910 ATATCATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTTTATGTTTTTAA
Found at i:3249215 original size:12 final size:12
Alignment explanation
Indices: 3249170--3249218 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
3249160 AAAAATATAG
*
3249170 TATAAATTATTT
1 TATAAGTTATTT
* *
3249182 TATAAGTAACTTA
1 TATAAGTTA-TTT
*
3249195 TAAAAGTTATTT
1 TATAAGTTATTT
3249207 TATAAGTTATTT
1 TATAAGTTATTT
3249219 ATATTACTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (12 bp):
TATAAGTTATTT
Found at i:3249658 original size:27 final size:28
Alignment explanation
Indices: 3249628--3249682 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
3249618 TATTAATTTT
*
3249628 TATATCATA-ATAATATTTAA-AATATTA
1 TATAT-ATATATAAAATTTAATAATATTA
*
3249655 TATATTTATATAAAATTTAATAATATTA
1 TATATATATATAAAATTTAATAATATTA
3249683 ATAATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.08
27 15 0.62
28 7 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TATATATATATAAAATTTAATAATATTA
Found at i:3249668 original size:20 final size:20
Alignment explanation
Indices: 3249649--3249752 Score: 71
Period size: 19 Copynumber: 5.3 Consensus size: 20
3249639 AATATTTAAA
*
3249649 ATATTATATATTTATATAAA
1 ATATTATATATTTATATAAT
3249669 AT-TTA-ATAATATTA-ATAATTT
1 ATATTATAT-AT-TTATATAA--T
* *
3249690 ATTTTATATATTT-TTTAAT
1 ATATTATATATTTATATAAT
3249709 ATATTCATATATTTATAT--T
1 ATATT-ATATATTTATATAAT
3249728 ATCATTATAT-TTTATATAAT
1 AT-ATTATATATTTATATAAT
3249748 -TATTA
1 ATATTA
3249753 ATTATTTTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 26
0.69 0.04 0.27
Matches are distributed among these distances:
18 13 0.19
19 22 0.32
20 17 0.25
21 9 0.13
22 5 0.07
23 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTATATATTTATATAAT
Found at i:3249689 original size:28 final size:27
Alignment explanation
Indices: 3249637--3249691 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
3249627 TTATATCATA
*
3249637 ATAATATTTAAAATATTATATATTTAT
1 ATAAAATTTAAAATATTATATATTTAT
3249664 ATAAAATTTAATAATATTA-ATAATTTAT
1 ATAAAATTTAA-AATATTATAT-ATTTAT
3249692 TTTATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAAAATTTAAAATATTATATATTTAT
Found at i:3249736 original size:39 final size:39
Alignment explanation
Indices: 3249696--3249771 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
3249686 ATTTATTTTA
*
3249696 TATATTTT-T-TAATATATTCA-TATATTTATATTATCAT
1 TATATTTTATATAAT-TATTAATTATATTTATATTATCAT
* *
3249733 TATATTTTATATAATTATTAATTATTTTTATTTTATCAT
1 TATATTTTATATAATTATTAATTATATTTATATTATCAT
3249772 ATTTAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 8 0.24
38 6 0.18
39 19 0.58
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (39 bp):
TATATTTTATATAATTATTAATTATATTTATATTATCAT
Found at i:3249743 original size:18 final size:17
Alignment explanation
Indices: 3249696--3249775 Score: 54
Period size: 18 Copynumber: 4.4 Consensus size: 17
3249686 ATTTATTTTA
* *
3249696 TATATTTTTTAATATAT
1 TATATTTTATATTATAT
3249713 TCATATATTTATATTATCAT
1 T-ATAT-TTTATATTAT-AT
*
3249733 TATATTTTATATAATTAT
1 TATATTTTATATTA-TAT
*
3249751 TAATTATTTT-TATTTTAT
1 T-A-TATTTTATATTATAT
*
3249769 CATATTT
1 TATATTT
3249776 AAAATTATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
16 5 0.10
17 2 0.04
18 18 0.35
19 17 0.33
20 9 0.18
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTTTATATTATAT
Found at i:3249744 original size:26 final size:25
Alignment explanation
Indices: 3249689--3249776 Score: 71
Period size: 26 Copynumber: 3.6 Consensus size: 25
3249679 ATTAATAATT
3249689 TATTTTATATATTT-T-TTA-A-TA
1 TATTTTATATATTTATATTATATTA
*
3249710 TA-TTCATATATTTATATTATCATTA
1 TATTTTATATATTTATATTAT-ATTA
* *
3249735 TATTTTATATAATTATTAATTAT-TTT
1 TATTTTATATATTTA-T-ATTATATTA
3249761 TATTTTATCATATTTA
1 TATTTTAT-ATATTTA
3249777 AAATTATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
20 10 0.19
21 3 0.06
22 3 0.06
24 1 0.02
25 4 0.08
26 20 0.38
27 7 0.13
28 5 0.09
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTTTATATATTTATATTATATTA
Found at i:3249781 original size:26 final size:26
Alignment explanation
Indices: 3249735--3249784 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3249725 ATTATCATTA
*
3249735 TATTTTATATAATTATTAATTATTTT
1 TATTTTATATAATTATAAATTATTTT
*
3249761 TATTTTATCATATTTA-AAATTATT
1 TATTTTAT-ATAATTATAAATTATT
3249785 AGATAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTTTATATAATTATAAATTATTTT
Found at i:3252238 original size:15 final size:16
Alignment explanation
Indices: 3252211--3252247 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
3252201 TTTAACGTAT
3252211 ATATATTTAATTTTAA
1 ATATATTTAATTTTAA
3252227 ATATATTT-ATTTTAA
1 ATATATTTAATTTTAA
3252242 ATATAT
1 ATATAT
3252248 GTTCAGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATATTTAATTTTAA
Found at i:3252611 original size:19 final size:21
Alignment explanation
Indices: 3252560--3252612 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3252550 ATTTTTTATT
3252560 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
3252581 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
*
3252601 -ATATTTTAATAT
1 TAAATTTTAATAT
3252613 TATTATAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 11 0.39
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:3256432 original size:17 final size:18
Alignment explanation
Indices: 3256406--3256444 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3256396 TATATTTATA
*
3256406 TAAATATTTTTA-ATTTT
1 TAAATATTTTTATATATT
*
3256423 TAAATTTTTTTATATATT
1 TAAATATTTTTATATATT
3256441 TAAA
1 TAAA
3256445 AAATTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TAAATATTTTTATATATT
Found at i:3258463 original size:17 final size:17
Alignment explanation
Indices: 3258443--3258512 Score: 55
Period size: 17 Copynumber: 4.5 Consensus size: 17
3258433 ATATTTAACA
*
3258443 TAAATATATTTATTTTT
1 TAAATATATTTATATTT
* *
3258460 TAAATTTTTTTATATTT
1 TAAATATATTTATATTT
*
3258477 T-AATA-A-TTATAATT
1 TAAATATATTTATATTT
3258491 T---TATATTTATA-TT
1 TAAATATATTTATATTT
3258504 TAAATATAT
1 TAAATATAT
3258513 GATAAATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
12 2 0.05
13 4 0.10
14 13 0.31
16 8 0.19
17 15 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAAATATATTTATATTT
Found at i:3258573 original size:2 final size:2
Alignment explanation
Indices: 3258566--3258592 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3258556 AATATAAATC
3258566 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
3258593 AAAGAAAAGT
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:3261013 original size:2 final size:2
Alignment explanation
Indices: 3261006--3261058 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3260996 AACATATGTG
3261006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3261048 TA TA TA TA TA T
1 TA TA TA TA TA T
3261059 CCAACAATTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3261138 original size:57 final size:57
Alignment explanation
Indices: 3261046--3261155 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 57
3261036 TATATATATA
*
3261046 TATATATATATATCCAACAATTACTCGTTCATAACACATACTTATTCATGAATTTTG
1 TATATATATATATCCAACAATTACTCGTTCATAACACATACTCATTCATGAATTTTG
* ** *
3261103 TATATATA-AGTATCCAACAATTGCTAC-TTTGTAACATATACTCATTCATGAAT
1 TATATATATA-TATCCAACAATTACT-CGTTCATAACACATACTCATTCATGAAT
3261156 CTGCTCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 1 0.02
57 44 0.96
58 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.39
Consensus pattern (57 bp):
TATATATATATATCCAACAATTACTCGTTCATAACACATACTCATTCATGAATTTTG
Found at i:3264514 original size:2 final size:2
Alignment explanation
Indices: 3264509--3264545 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3264499 ACACACATAC
*
3264509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3264546 ATTTGGAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3265126 original size:3 final size:3
Alignment explanation
Indices: 3265118--3265158 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3265108 CTTGTTTATG
3265118 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3265159 TATACCTTCT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3265834 original size:21 final size:21
Alignment explanation
Indices: 3265808--3265849 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3265798 TTAATCCTTT
3265808 TTAATGGAACATATTTTCCAC
1 TTAATGGAACATATTTTCCAC
3265829 TTAATGGAACATATTTTCCAC
1 TTAATGGAACATATTTTCCAC
3265850 ATTTCTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (21 bp):
TTAATGGAACATATTTTCCAC
Found at i:3266097 original size:2 final size:2
Alignment explanation
Indices: 3266090--3266122 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3266080 GCATTTCTCT
3266090 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
3266123 TAAAGACATT
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:3267456 original size:2 final size:2
Alignment explanation
Indices: 3267449--3267488 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3267439 GATTTTATGG
3267449 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
3267489 CACATGTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3270974 original size:2 final size:2
Alignment explanation
Indices: 3270967--3271004 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3270957 CATTATCAAA
*
3270967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3271005 TAAAGAGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3271862 original size:16 final size:16
Alignment explanation
Indices: 3271843--3271875 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3271833 TACCTTTTTC
*
3271843 TTTTTTAACATCTTTA
1 TTTTTAAACATCTTTA
3271859 TTTTTAAACATCTTTA
1 TTTTTAAACATCTTTA
3271875 T
1 T
3271876 GTATTGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTAAACATCTTTA
Found at i:3272802 original size:3 final size:3
Alignment explanation
Indices: 3272794--3272828 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3272784 TATGACCCCT
*
3272794 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTCC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC T
3272829 CTCAGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3276752 original size:17 final size:15
Alignment explanation
Indices: 3276706--3276741 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3276696 TTAATTATAA
3276706 AAATAATTTAATATTTT
1 AAATAA-TTAA-ATTTT
3276723 AAATAATTAAATTTT
1 AAATAATTAAATTTT
3276738 AAAT
1 AAAT
3276742 TCAATTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 4 0.21
17 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATAATTAAATTTT
Found at i:3279258 original size:2 final size:2
Alignment explanation
Indices: 3279251--3279285 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3279241 AGCAGTATTC
3279251 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3279286 AGATTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3280837 original size:28 final size:29
Alignment explanation
Indices: 3280769--3280837 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
3280759 AATATATTTT
*
3280769 ATTTATATTTAAATATTAATTTTACATAAA
1 ATTTA-ATTTAAATATTAATTATACATAAA
*
3280799 A-TAAATATTAAATA-TAATTAATA-ATAAA
1 ATTTAAT-TTAAATATTAATT-ATACATAAA
3280827 ATTTAATTTAA
1 ATTTAATTTAA
3280838 TAATATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
28 17 0.52
29 15 0.45
30 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTAATTTAAATATTAATTATACATAAA
Found at i:3281036 original size:16 final size:14
Alignment explanation
Indices: 3280990--3281030 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
3280980 CATAAATTAT
*
3280990 TTTTAATATATTAA
1 TTTTAATATATAAA
*
3281004 TATT--TATATAAA
1 TTTTAATATATAAA
3281016 TTTTAATATATAAA
1 TTTTAATATATAAA
3281030 T
1 T
3281031 AATTTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTAATATATAAA
Found at i:3284909 original size:165 final size:165
Alignment explanation
Indices: 3284637--3284970 Score: 668
Period size: 165 Copynumber: 2.0 Consensus size: 165
3284627 TCAATTTCAA
3284637 CACTTGGGAACTCCTTGATAAGAACTCAAGCTCCAACAATGGTTTCATTCATTCCCTGCGGTTGT
1 CACTTGGGAACTCCTTGATAAGAACTCAAGCTCCAACAATGGTTTCATTCATTCCCTGCGGTTGT
3284702 ACCATCCTGTCAGTACATAAGAACCGTTGCAAATGATATCTAATGGATCTTTGATTAGTATTGTC
66 ACCATCCTGTCAGTACATAAGAACCGTTGCAAATGATATCTAATGGATCTTTGATTAGTATTGTC
3284767 ATGCACACAGTTTAGAATAAACAGAAAAATGGAAG
131 ATGCACACAGTTTAGAATAAACAGAAAAATGGAAG
3284802 CACTTGGGAACTCCTTGATAAGAACTCAAGCTCCAACAATGGTTTCATTCATTCCCTGCGGTTGT
1 CACTTGGGAACTCCTTGATAAGAACTCAAGCTCCAACAATGGTTTCATTCATTCCCTGCGGTTGT
3284867 ACCATCCTGTCAGTACATAAGAACCGTTGCAAATGATATCTAATGGATCTTTGATTAGTATTGTC
66 ACCATCCTGTCAGTACATAAGAACCGTTGCAAATGATATCTAATGGATCTTTGATTAGTATTGTC
3284932 ATGCACACAGTTTAGAATAAACAGAAAAATGGAAG
131 ATGCACACAGTTTAGAATAAACAGAAAAATGGAAG
3284967 CACT
1 CACT
3284971 GCAGAATATG
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 169 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (165 bp):
CACTTGGGAACTCCTTGATAAGAACTCAAGCTCCAACAATGGTTTCATTCATTCCCTGCGGTTGT
ACCATCCTGTCAGTACATAAGAACCGTTGCAAATGATATCTAATGGATCTTTGATTAGTATTGTC
ATGCACACAGTTTAGAATAAACAGAAAAATGGAAG
Found at i:3286188 original size:3 final size:3
Alignment explanation
Indices: 3286180--3286204 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3286170 TTCCTTCTGA
3286180 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3286205 TGATGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3286539 original size:21 final size:19
Alignment explanation
Indices: 3286513--3286564 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 19
3286503 TTTAAATTTT
3286513 TTTAAAATTTTTAAATAATAA
1 TTTAAAATTTTT-AATAA-AA
3286534 TTT-AAATTATTTAATAAAA
1 TTTAAAATT-TTTAATAAAA
3286553 TTAATAAAATTT
1 TT--TAAAATTT
3286565 AAATCAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
19 4 0.15
20 10 0.37
21 8 0.30
22 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAAAATTTTTAATAAAA
Found at i:3286549 original size:20 final size:19
Alignment explanation
Indices: 3286517--3286599 Score: 52
Period size: 19 Copynumber: 4.5 Consensus size: 19
3286507 AATTTTTTTA
3286517 AAATTTTTAAATAATAATTT
1 AAATTTTTAAATAA-AATTT
3286537 AAATTATTT-AATAAAATTAAT
1 AAATT-TTTAAATAAAATT--T
* *
3286558 AAA-ATTTAAAT-CAATTT
1 AAATTTTTAAATAAAATTT
*
3286575 -AA--TTTAAATATAATTT
1 AAATTTTTAAATAAAATTT
*
3286591 AATTTTTTA
1 AAATTTTTA
3286600 CTATTTGTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
15 7 0.14
16 7 0.14
17 2 0.04
19 15 0.29
20 13 0.25
21 7 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATTTTTAAATAAAATTT
Found at i:3286578 original size:15 final size:16
Alignment explanation
Indices: 3286560--3286595 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3286550 AAATTAATAA
3286560 AATTTAAAT-CAATTT
1 AATTTAAATACAATTT
*
3286575 AATTTAAATATAATTT
1 AATTTAAATACAATTT
3286591 AATTT
1 AATTT
3286596 TTTACTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTAAATACAATTT
Found at i:3295409 original size:18 final size:18
Alignment explanation
Indices: 3295347--3295411 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
3295337 CCATCCATTG
*
3295347 CCTCTTCATCGTCCTCAT
1 CCTCTTCATCGTCATCAT
* *
3295365 CCTCGTCATCATCGGACTCAT
1 CCTCTTCATCGTC--A-TCAT
* *
3295386 CATCTTCATCGTCATCCT
1 CCTCTTCATCGTCATCAT
3295404 CCTCTTCA
1 CCTCTTCA
3295412 CTGCCTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 21 0.58
19 1 0.03
21 14 0.39
ACGTcount: A:0.15, C:0.42, G:0.08, T:0.35
Consensus pattern (18 bp):
CCTCTTCATCGTCATCAT
Found at i:3297101 original size:20 final size:20
Alignment explanation
Indices: 3297057--3297101 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3297047 TTAAAATAAT
* **
3297057 ATAAAATTTTTATTTTTATA
1 ATAAAATTTTAATTTAAATA
*
3297077 TTAAAATTTTAATTTAAATA
1 ATAAAATTTTAATTTAAATA
3297097 ATAAA
1 ATAAA
3297102 TTATTATTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAAAATTTTAATTTAAATA
Found at i:3298021 original size:21 final size:22
Alignment explanation
Indices: 3297997--3298046 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
3297987 AAAATATTTT
3297997 TATTTAAAT-TTAATAAAAAAA
1 TATTTAAATATTAATAAAAAAA
3298018 TA-TT-AATATTAATAAAAAAA
1 TATTTAAATATTAATAAAAAAA
3298038 TAATTTAAA
1 T-ATTTAAA
3298047 ATTTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.12
20 15 0.60
21 3 0.12
22 2 0.08
23 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TATTTAAATATTAATAAAAAAA
Done.