Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 12 of 24
Found at i:2448391 original size:19 final size:18
Alignment explanation
Indices: 2448319--2448393 Score: 51
Period size: 20 Copynumber: 3.8 Consensus size: 18
2448309 GGTTAAACTT
2448319 AAATTATTATTTATATAATAA
1 AAATTATT-TTTA-ATAA-AA
*
2448340 AAATTATTTTTATTTATAAA
1 AAATTATTTTTA-ATA-AAA
* * * *
2448360 ATATAAATATTAATAAAA
1 AAATTATTTTTAATAAAA
2448378 AAATTAATTTTTAATA
1 AAATT-ATTTTTAATA
2448394 TTTTAATATT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
18 6 0.14
19 10 0.24
20 17 0.40
21 9 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTATTTTTAATAAAA
Found at i:2449085 original size:26 final size:27
Alignment explanation
Indices: 2449046--2449136 Score: 78
Period size: 27 Copynumber: 3.2 Consensus size: 27
2449036 AAAAAAATAA
*
2449046 TTAAAATATAATATAATATTA-AATATT
1 TTAAAA-ATTATATAATATTATAATATT
*
2449073 TTAAAAATTATATTATATAAATTATAAAATTT
1 TTAAAAATTATA-TA-AT--ATTATAATA-TT
*
2449105 TTAAAATTTATATAA-ATATATAATATT
1 TTAAAAATTATATAATAT-TATAATATT
2449132 TTAAA
1 TTAAA
2449137 TAAATACACG
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
26 5 0.09
27 17 0.32
28 8 0.15
30 5 0.09
31 5 0.09
32 13 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TTAAAAATTATATAATATTATAATATT
Found at i:2449105 original size:31 final size:29
Alignment explanation
Indices: 2449048--2449142 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 29
2449038 AAAAATAATT
*
2449048 AAAATATAATATAATATTA-AATATTTTAA
1 AAAATATTATATAA-ATTATAATATTTTAA
* *
2449077 AAATTATATTATATAAATTATAAAATTTT-T
1 AAA--ATATTATATAAATTATAATATTTTAA
2449107 AAAAT-TTATATAAATATATAATATTTTAA
1 AAAATATTATATAAAT-TATAATATTTTAA
2449136 ATAAATA
1 A-AAATA
2449143 CACGAATGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
27 10 0.19
28 12 0.22
29 4 0.07
30 11 0.20
31 17 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATATTATATAAATTATAATATTTTAA
Found at i:2453293 original size:23 final size:23
Alignment explanation
Indices: 2453249--2453295 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
2453239 TTTTATTTAA
*
2453249 TTTTAAATTATTATTTACTAATAT
1 TTTTAAATTATTA-TTAATAATAT
2453273 TTTTAAAATTATTA-TAATAATAT
1 TTTT-AAATTATTATTAATAATAT
2453296 ATAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 4 0.19
25 9 0.43
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTAAATTATTATTAATAATAT
Found at i:2453312 original size:23 final size:22
Alignment explanation
Indices: 2453286--2453329 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2453276 TAAAATTATT
* *
2453286 ATAATAATATATAATTTTTAAAA
1 ATAATAAAATA-AATTATTAAAA
2453309 ATAATAAAATAAATTATTAAA
1 ATAATAAAATAAATTATTAAA
2453330 TCAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATAAAATAAATTATTAAAA
Found at i:2453736 original size:21 final size:23
Alignment explanation
Indices: 2453710--2453753 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
2453700 TTTACATTAT
2453710 TAATTTAT-T-TTATATAATAAA
1 TAATTTATATATTATATAATAAA
2453731 TAATTTATATAATTATATAATAA
1 TAATTTATAT-ATTATATAATAA
2453754 TTAGTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
24 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAATTTATATATTATATAATAAA
Found at i:2454107 original size:17 final size:18
Alignment explanation
Indices: 2454081--2454118 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2454071 ATTTAATATA
*
2454081 AATTAATTAAA-ATTAAT
1 AATTAATTAAATATAAAT
*
2454098 AATTATTTAAATATAAAT
1 AATTAATTAAATATAAAT
2454116 AAT
1 AAT
2454119 ATTCTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTAATTAAATATAAAT
Found at i:2454173 original size:21 final size:22
Alignment explanation
Indices: 2454096--2454178 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 22
2454086 ATTAAAATTA
2454096 ATAATTATT--TAAATATAAAT
1 ATAATTATTAATAAATATAAAT
* *
2454116 A-ATATTCTTAATATAATATTTAATT
1 ATA-ATTATTAATA-AATA--TAAAT
*
2454141 ATTTATTATTAATAAATATAAAT
1 A-TAATTATTAATAAATATAAAT
2454164 ATAATT-TTAATAAAT
1 ATAATTATTAATAAAT
2454179 TTTAATTAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
19 1 0.02
20 6 0.12
21 9 0.18
22 6 0.12
23 9 0.18
25 9 0.18
26 9 0.18
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAATTATTAATAAATATAAAT
Found at i:2454193 original size:45 final size:48
Alignment explanation
Indices: 2454105--2454194 Score: 125
Period size: 45 Copynumber: 1.9 Consensus size: 48
2454095 AATAATTATT
**
2454105 TAAATATAAATAATATTCTTAATATAATATTTAATTATTTATTATTAA
1 TAAATATAAATAATATTCTTAATATAATATTTAATTAACTATTATTAA
2454153 TAAATATAAAT-ATAATT-TTAATA-AAT-TTTAATTAACTATTAT
1 TAAATATAAATAAT-ATTCTTAATATAATATTTAATTAACTATTAT
2454195 ACATACATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 14 0.36
46 3 0.08
47 8 0.21
48 14 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (48 bp):
TAAATATAAATAATATTCTTAATATAATATTTAATTAACTATTATTAA
Found at i:2458973 original size:3 final size:3
Alignment explanation
Indices: 2458965--2458990 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2458955 TTTATTTCTT
2458965 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2458991 TTAATCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2459606 original size:3 final size:3
Alignment explanation
Indices: 2459598--2459643 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
2459588 CACCTCTTTT
* *
2459598 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2459644 ATAACTCAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2461254 original size:2 final size:2
Alignment explanation
Indices: 2461247--2461282 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2461237 GAAGGAAAGA
2461247 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
2461283 TATGAAACTG
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:2465057 original size:27 final size:28
Alignment explanation
Indices: 2465015--2465133 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 28
2465005 TTTATTATAT
2465015 TTTTATA-TTATAATTATA-TTTAAAATA
1 TTTTATATTTAT-ATTATATTTTAAAATA
**
2465042 TTTTATATTTATATTA-ATTTTAGTATA
1 TTTTATATTTATATTATATTTTAAAATA
* * *
2465069 TTAATAATTTTTATTATATAAATTTTAAAATA
1 TT--TTATATTTA-TAT-TATATTTTAAAATA
*
2465101 ---TATATTTATATTATATTTT-AATTA
1 TTTTATATTTATATTATATTTTAAAATA
2465125 TTTTATATT
1 TTTTATATT
2465134 ATTATATTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
24 4 0.06
25 7 0.10
26 4 0.06
27 32 0.44
28 4 0.06
29 7 0.10
30 3 0.04
31 2 0.03
32 9 0.12
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (28 bp):
TTTTATATTTATATTATATTTTAAAATA
Found at i:2465143 original size:14 final size:14
Alignment explanation
Indices: 2465009--2465154 Score: 59
Period size: 13 Copynumber: 11.0 Consensus size: 14
2464999 TACTTATTTA
*
2465009 TTATATTTTTATA-
1 TTATATTATTATAT
2465022 TTATA--ATTATAT
1 TTATATTATTATAT
2465034 TTAAAATATT-TTATAT
1 TT---ATATTATTATAT
*
2465050 TTATATTAATTTTA-
1 TTATATT-ATTATAT
* *
2465064 GTATATTAATA-AT
1 TTATATTATTATAT
* *
2465077 TTTTATTATATAAAT
1 TTATATTAT-TATAT
* *
2465092 TT-TA-AAATATAT
1 TTATATTATTATAT
2465104 ATT-TA-TATTATAT
1 -TTATATTATTATAT
2465117 TT-TA--ATTAT-T
1 TTATATTATTATAT
2465127 TTATATTATTATAT
1 TTATATTATTATAT
*
2465141 TTATATAATTATAT
1 TTATATTATTATAT
2465155 CATATTTAAT
Statistics
Matches: 103, Mismatches: 14, Indels: 31
0.70 0.09 0.21
Matches are distributed among these distances:
10 3 0.03
11 12 0.12
12 11 0.11
13 34 0.33
14 24 0.23
15 11 0.11
16 8 0.08
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.60
Consensus pattern (14 bp):
TTATATTATTATAT
Found at i:2465179 original size:43 final size:41
Alignment explanation
Indices: 2465099--2465186 Score: 99
Period size: 43 Copynumber: 2.1 Consensus size: 41
2465089 AATTTTAAAA
* * *
2465099 TATATATTTATATTATATTTTAATTATTTTATATTATTATATT
1 TATATAATTATATCATATTTTAATTATTTTAAATTATT-T-TT
2465142 TATATAATTATATCATA-TTTAA-TATTATTAAATTTATTTTT
1 TATATAATTATATCATATTTTAATTATT-TTAAA-TTATTTTT
2465183 TATA
1 TATA
2465187 AATGTTACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 10 0.25
42 10 0.25
43 20 0.50
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (41 bp):
TATATAATTATATCATATTTTAATTATTTTAAATTATTTTT
Found at i:2467444 original size:5 final size:5
Alignment explanation
Indices: 2467409--2467441 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2467399 ACAAAAACAG
*
2467409 AAGGA AAGGA AAGGA AAGGA AAGGA AAGCA AAG
1 AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAG
2467442 CAAGAAACGT
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:0.61, C:0.03, G:0.36, T:0.00
Consensus pattern (5 bp):
AAGGA
Found at i:2473754 original size:2 final size:2
Alignment explanation
Indices: 2473749--2473782 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2473739 ATATAGATTT
2473749 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2473783 GAGGGATCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2475707 original size:10 final size:10
Alignment explanation
Indices: 2475692--2475723 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2475682 TTGTACCAAC
2475692 GAGAGAGATA
1 GAGAGAGATA
2475702 GAGAGAGATA
1 GAGAGAGATA
*
2475712 GAGAGAGGTA
1 GAGAGAGATA
2475722 GA
1 GA
2475724 CGTGATGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.44, T:0.09
Consensus pattern (10 bp):
GAGAGAGATA
Found at i:2483003 original size:15 final size:16
Alignment explanation
Indices: 2482963--2483005 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2482953 AATAATTATG
2482963 TAATATAAATATAATA
1 TAATATAAATATAATA
*
2482979 TAACAT-AATATAA-A
1 TAATATAAATATAATA
*
2482993 TTATATAAATATA
1 TAATATAAATATA
2483006 TTAAAATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 13 0.57
16 5 0.22
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATATAAATATAATA
Found at i:2491718 original size:18 final size:19
Alignment explanation
Indices: 2491697--2491732 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2491687 CAATTAATAA
2491697 TAAATAAAAAATT-TAATT
1 TAAATAAAAAATTATAATT
*
2491715 TAAATATAAAATTATAAT
1 TAAATAAAAAATTATAAT
2491733 AAATACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAATAAAAAATTATAATT
Found at i:2491909 original size:23 final size:24
Alignment explanation
Indices: 2491878--2491922 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
2491868 GATAAAATTT
2491878 AAATATAAAATT-ATAAAAAATAAA
1 AAATAT-AAATTGATAAAAAATAAA
*
2491902 AAAT-TAAATTGATATAAAATA
1 AAATATAAATTGATAAAAAATA
2491923 CTAGTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATATAAATTGATAAAAAATAAA
Found at i:2502227 original size:2 final size:2
Alignment explanation
Indices: 2502220--2502266 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2502210 TCTCAAGGGG
*
2502220 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GT GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2502262 GA GA G
1 GA GA G
2502267 GTTGATTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.51, T:0.02
Consensus pattern (2 bp):
GA
Found at i:2502494 original size:16 final size:16
Alignment explanation
Indices: 2502468--2502506 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2502458 ATTAAAATTA
2502468 AATATTAAAT-ATAATAT
1 AATA-TAAATAAT-ATAT
2502485 AATATAAATAATATAT
1 AATATAAATAATATAT
2502501 AATATA
1 AATATA
2502507 TCAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAAATAATATAT
Found at i:2502521 original size:16 final size:15
Alignment explanation
Indices: 2502502--2502552 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
2502492 ATAATATATA
*
2502502 ATATATCAAAATTTAT
1 ATATAT-AAATTTTAT
2502518 ATATTATAAATTATTA-
1 ATA-TATAAATT-TTAT
2502534 ATATATTAAATTTTAT
1 ATATA-TAAATTTTAT
2502550 ATA
1 ATA
2502553 AATATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 5 0.17
16 19 0.63
17 6 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATAAATTTTAT
Found at i:2503351 original size:25 final size:26
Alignment explanation
Indices: 2503286--2503352 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
2503276 CTAATTTAAT
* *
2503286 TTAAAAA-A-TTATATATAAATCAAA
1 TTAAAAATATTTAAATATAAATAAAA
*
2503310 TTAAAAATATACT-AATA-AAATAAAA
1 TTAAAAATAT-TTAAATATAAATAAAA
2503335 TTAAAAATATTTAAATAT
1 TTAAAAATATTTAAATAT
2503353 TTCAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
24 8 0.24
25 22 0.65
26 3 0.09
27 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (26 bp):
TTAAAAATATTTAAATATAAATAAAA
Found at i:2504100 original size:18 final size:20
Alignment explanation
Indices: 2504073--2504114 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
2504063 AAATAAAATA
*
2504073 ATTACAATTT-TA-TTTTTT
1 ATTACAATTTATACATTTTT
*
2504091 ATTACTATTTATACATTTTT
1 ATTACAATTTATACATTTTT
2504111 ATTA
1 ATTA
2504115 TTTAAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTACAATTTATACATTTTT
Found at i:2506735 original size:31 final size:29
Alignment explanation
Indices: 2506698--2506766 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
2506688 ATTTGACAAT
*
2506698 ATAAAATAATTAAAATATAATATATAATATA
1 ATAAAATAATTAAAA-ATAATATA-AATAAA
*
2506729 ATAAAAT-TTTAAAAATAATATAAATAAA
1 ATAAAATAATTAAAAATAATATAAATAAA
2506757 ATATAAATAA
1 ATA-AAATAA
2506767 ATAATTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 8 0.24
29 12 0.36
30 6 0.18
31 7 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
ATAAAATAATTAAAAATAATATAAATAAA
Found at i:2506775 original size:14 final size:13
Alignment explanation
Indices: 2506695--2506782 Score: 53
Period size: 14 Copynumber: 7.0 Consensus size: 13
2506685 TAGATTTGAC
*
2506695 AATATAAAATAATT
1 AATAT-AAATAAAT
* *
2506709 AAAATATAATATAT
1 AATATA-AATAAAT
2506723 AATAT-AAT-AA-
1 AATATAAATAAAT
* *
2506733 AATTTTAA-AAAT
1 AATATAAATAAAT
2506745 AATATAAAT-AA-
1 AATATAAATAAAT
2506756 AATATAAATAAAT
1 AATATAAATAAAT
*
2506769 AATTATATATAAAT
1 AA-TATAAATAAAT
2506783 TCATATTATA
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
10 4 0.07
11 14 0.25
12 13 0.23
13 3 0.05
14 23 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATATAAATAAAT
Found at i:2507796 original size:18 final size:18
Alignment explanation
Indices: 2507773--2507807 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2507763 ATCGAATTAT
2507773 AAAAAAATTATATTAATC
1 AAAAAAATTATATTAATC
*
2507791 AAAAAAATTATTTTAAT
1 AAAAAAATTATATTAAT
2507808 TAATTTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAAAATTATATTAATC
Found at i:2510776 original size:29 final size:30
Alignment explanation
Indices: 2510744--2510804 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
2510734 AACTTATTAA
*
2510744 AATTTAT-ATA-AATAAAATATTTAAAATAT
1 AATTTATGATATAATAAAATATAT-AAATAT
2510773 AA-TTATGATATAATAAAATATATAAATAT
1 AATTTATGATATAATAAAATATATAAATAT
2510802 AAT
1 AAT
2510805 ATAAATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.14
29 13 0.46
30 11 0.39
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
AATTTATGATATAATAAAATATATAAATAT
Found at i:2511098 original size:15 final size:14
Alignment explanation
Indices: 2511051--2511100 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 14
2511041 TATATATTTA
2511051 TTTTTTAAAATATAT
1 TTTTTTAAAAT-TAT
*
2511066 TTTATTAAATACTTAT
1 TTTTTTAAA-A-TTAT
2511082 TTTTTTATAAATTAT
1 TTTTTTA-AAATTAT
2511097 TTTT
1 TTTT
2511101 ATTTCACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 16 0.53
16 11 0.37
17 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTAAAATTAT
Found at i:2511356 original size:18 final size:18
Alignment explanation
Indices: 2511333--2511375 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2511323 AATTAAGTGA
*
2511333 TAAATTATTTTAAAATTT
1 TAAATTATTTAAAAATTT
*
2511351 TAAATTAATTAAAAATTT
1 TAAATTATTTAAAAATTT
2511369 T-AATTAT
1 TAAATTAT
2511376 AATACCTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAATTATTTAAAAATTT
Found at i:2515275 original size:30 final size:29
Alignment explanation
Indices: 2515231--2515300 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
2515221 ATCTATTTTA
2515231 ATTTAAAT-ATAAAAT-ATTTTTTAATATT
1 ATTTAAATAATAAAATAATTTTTTAAT-TT
2515259 ATTTTAAATAATAAAATAAATTTTTTAATTT
1 A-TTTAAATAATAAAAT-AATTTTTTAATTT
*
2515290 ACTTAAATAAT
1 ATTTAAATAAT
2515301 TTAAATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 7 0.19
30 16 0.43
31 3 0.08
32 10 0.27
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTAAATAATAAAATAATTTTTTAATTT
Found at i:2517590 original size:3 final size:3
Alignment explanation
Indices: 2517582--2517625 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2517572 GATCTCTTTT
2517582 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2517626 GCGACGATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2521062 original size:29 final size:28
Alignment explanation
Indices: 2520998--2521054 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
2520988 TATTAAAAAA
*
2520998 TATAATTATTTTTAATTGATTATTAATTT
1 TATAATTATATTTAATT-ATTATTAATTT
*
2521027 TATAATTATATTTAATT-TTATTTATTT
1 TATAATTATATTTAATTATTATTAATTT
2521054 T
1 T
2521055 CATTAATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 10 0.38
29 16 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (28 bp):
TATAATTATATTTAATTATTATTAATTT
Found at i:2522496 original size:17 final size:17
Alignment explanation
Indices: 2522474--2522522 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
2522464 AATATTATTA
2522474 TGAATATTCATTAATTT
1 TGAATATTCATTAATTT
* *
2522491 TGAATAGTCATAAATTT
1 TGAATATTCATTAATTT
*
2522508 TGAATATACATTAAT
1 TGAATATTCATTAAT
2522523 GTTATTATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (17 bp):
TGAATATTCATTAATTT
Found at i:2522639 original size:2 final size:2
Alignment explanation
Indices: 2522632--2522656 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2522622 ATTCATTAAT
2522632 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
2522657 TCATGAATCC
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:2523997 original size:2 final size:2
Alignment explanation
Indices: 2523992--2524036 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
2523982 TGTGATAATT
2523992 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2524031 TA TA TA
1 TA TA TA
2524037 GTTATTTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2524365 original size:20 final size:18
Alignment explanation
Indices: 2524328--2524385 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
2524318 TTTAAATACG
2524328 ATATAAAT-T-AAGATATA
1 ATATAAATATGAA-ATATA
*
2524345 ATATAAATATGATATAT-
1 ATATAAATATGAAATATA
2524362 ATAATAAATATGAAA-ATA
1 AT-ATAAATATGAAATATA
2524380 ATATAA
1 ATATAA
2524386 TAAACATAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 16 0.46
18 18 0.51
19 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
ATATAAATATGAAATATA
Found at i:2524368 original size:18 final size:18
Alignment explanation
Indices: 2524339--2524389 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
2524329 TATAAATTAA
2524339 GATATA-AT-ATAAATAT
1 GATATATATAATAAATAT
2524355 GATATATATAATAAATAT
1 GATATATATAATAAATAT
*
2524373 GAAAATAATATAATAAA
1 G-ATAT-ATATAATAAA
2524390 CATAACATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 6 0.20
17 2 0.07
18 9 0.30
19 3 0.10
20 10 0.33
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
GATATATATAATAAATAT
Found at i:2525992 original size:2 final size:2
Alignment explanation
Indices: 2525979--2526015 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2525969 GACAACATCA
*
2525979 AT AT AA 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
2526016 AATTACGGAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2526896 original size:21 final size:20
Alignment explanation
Indices: 2526872--2526959 Score: 90
Period size: 21 Copynumber: 4.3 Consensus size: 20
2526862 AAATTTAAAA
2526872 ATAATTTTAATAGCTTTTAAT
1 ATAATTTTAATA-CTTTTAAT
*
2526893 ATAATTTTAATACTTTTTAAC
1 ATAATTTTAATAC-TTTTAAT
* * *
2526914 ATCATTTTGATAACTGTTAAT
1 ATAATTTTAAT-ACTTTTAAT
*
2526935 ATAATTTTAATAATTTT--T
1 ATAATTTTAATACTTTTAAT
2526953 ATAATTT
1 ATAATTT
2526960 GAGAACATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
18 8 0.14
20 5 0.09
21 41 0.73
22 2 0.04
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (20 bp):
ATAATTTTAATACTTTTAAT
Found at i:2526900 original size:42 final size:42
Alignment explanation
Indices: 2526832--2526947 Score: 117
Period size: 42 Copynumber: 2.8 Consensus size: 42
2526822 TTTTCTATAC
* * *
2526832 AATTTTAATAA-TGTTCCATATGATTTTCATAAATTTAAAAAT
1 AATTTTAATAACTGTT-AATATAATTTTAATAAATTTAAAAAT
* * ** * *
2526874 AATTTTAATAGCTTTTAATATAATTTTAATACTTTTTAACAT
1 AATTTTAATAACTGTTAATATAATTTTAATAAATTTAAAAAT
* *
2526916 CATTTTGATAACTGTTAATATAATTTTAATAA
1 AATTTTAATAACTGTTAATATAATTTTAATAA
2526948 TTTTTATAAT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
42 56 0.95
43 3 0.05
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (42 bp):
AATTTTAATAACTGTTAATATAATTTTAATAAATTTAAAAAT
Found at i:2526902 original size:11 final size:11
Alignment explanation
Indices: 2526849--2526946 Score: 53
Period size: 11 Copynumber: 9.3 Consensus size: 11
2526839 ATAATGTTCC
* *
2526849 ATATGATTTTC
1 ATATAATTTTA
*
2526860 ATA-AATTTAA
1 ATATAATTTTA
*
2526870 AAATAATTTTA
1 ATATAATTTTA
**
2526881 ATA-GCTTTTA
1 ATATAATTTTA
2526891 ATATAATTTTA
1 ATATAATTTTA
2526902 ATACT--TTTTA
1 ATA-TAATTTTA
* * *
2526912 ACATCATTTTG
1 ATATAATTTTA
* *
2526923 ATA-ACTGTTA
1 ATATAATTTTA
2526933 ATATAATTTTA
1 ATATAATTTTA
2526944 ATA
1 ATA
2526947 ATTTTTATAA
Statistics
Matches: 62, Mismatches: 19, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
9 1 0.02
10 27 0.44
11 33 0.53
12 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (11 bp):
ATATAATTTTA
Found at i:2528788 original size:2 final size:2
Alignment explanation
Indices: 2528781--2528817 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2528771 AGAATATTAA
* *
2528781 AT AT AT AT AT AT AT AT AA AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2528818 AAGGAAGACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2529584 original size:16 final size:17
Alignment explanation
Indices: 2529563--2529595 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2529553 TTTAAATAAT
2529563 ATTAAAT-TATTTAAAA
1 ATTAAATATATTTAAAA
2529579 ATTAAATATATTTAAAA
1 ATTAAATATATTTAAAA
2529596 TTCAAGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAAATATATTTAAAA
Found at i:2535931 original size:24 final size:22
Alignment explanation
Indices: 2535891--2535952 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 22
2535881 GATATAAATT
2535891 AATTTAATTTATTAATA-ATATA
1 AATTTAATTTATTAATATAT-TA
2535913 AATTTATATATTATTAATATATTA
1 AATTTA-AT-TTATTAATATATTA
* *
2535937 AATATAATTTTTTAAT
1 AATTTAATTTATTAAT
2535953 GAATTATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 13 0.37
23 4 0.11
24 16 0.46
25 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTAATTTATTAATATATTA
Found at i:2535978 original size:17 final size:16
Alignment explanation
Indices: 2535940--2535984 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2535930 TATATTAAAT
2535940 ATAAT-TTTTTAATGA
1 ATAATATTTTTAATGA
* *
2535955 ATTATATTTTTAATTA
1 ATAATATTTTTAATGA
2535971 ATAAATATTTTTAA
1 AT-AATATTTTTAA
2535985 ATTACTGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.16
16 11 0.44
17 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATAATATTTTTAATGA
Found at i:2541574 original size:2 final size:2
Alignment explanation
Indices: 2541567--2541593 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2541557 AAACCATTCT
2541567 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2541594 GAGGGGGAGG
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2544767 original size:24 final size:23
Alignment explanation
Indices: 2544705--2544767 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 23
2544695 TAGATACGAT
*
2544705 TAAAATATTAAAATA-TAATATA
1 TAAATTATTAAAATATTAATATA
*
2544727 -AATATT-TTAATAT-TTAATGATA
1 TAA-ATTATTAAAATATTAAT-ATA
2544749 TAAATTATTAAAATATTAA
1 TAAATTATTAAAATATTAA
2544768 ATTTTATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
21 12 0.38
22 8 0.25
23 8 0.25
24 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAATTATTAAAATATTAATATA
Found at i:2545999 original size:20 final size:20
Alignment explanation
Indices: 2545922--2545999 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
2545912 ATTTTTATAA
2545922 TTAAATTTAAATAAAATT-AT
1 TTAAATTTAAA-AAAATTAAT
** * *
2545942 TTTTA-TTAAATAAATAAAAT
1 TTAAATTTAAAAAAAT-TAAT
** *
2545962 TTAAATTTAATCATATTAAT
1 TTAAATTTAAAAAAATTAAT
2545982 TTAAATTTAAAAAAATTA
1 TTAAATTTAAAAAAATTA
2546000 CCCCAAATTT
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
18 4 0.10
19 5 0.12
20 26 0.62
21 7 0.17
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATTTAAAAAAATTAAT
Found at i:2546464 original size:6 final size:6
Alignment explanation
Indices: 2546453--2546538 Score: 52
Period size: 6 Copynumber: 14.2 Consensus size: 6
2546443 TGATATATTA
* * * * *
2546453 TTATAT TTATA- TTAAAT TTACA- TTATTTT TTATAT TTATTAT ATTTTAA
1 TTATAT TTATAT TTATAT TTATAT TTA-TAT TTATAT TTA-TAT -TTATAT
* *
2546502 TTATTT TTATA- TTATAT TTATATT TTATAG TTATAT T
1 TTATAT TTATAT TTATAT TTATA-T TTATAT TTATAT T
2546539 AATTGTAACG
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
5 12 0.20
6 32 0.53
7 14 0.23
8 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (6 bp):
TTATAT
Found at i:2546492 original size:38 final size:37
Alignment explanation
Indices: 2546439--2546540 Score: 102
Period size: 38 Copynumber: 2.8 Consensus size: 37
2546429 TATTTTTAAA
*
2546439 ATTTTGATATATTATTATATTTATATTAAATTTACATT
1 ATTTTTATAT-TTATTATATTTATATTAAATTTACATT
** *
2546477 ATTTTTTATATTTATTATATTT-TAATTATTTTTATATT
1 A-TTTTTATATTTATTATATTTAT-ATTAAATTTACATT
* *
2546515 ATATTTATA-TT-TTATAGTTATATTAA
1 ATTTTTATATTTATTATATTTATATTAA
2546541 TTGTAACGTA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
35 11 0.20
36 3 0.06
37 8 0.15
38 24 0.44
39 8 0.15
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (37 bp):
ATTTTTATATTTATTATATTTATATTAAATTTACATT
Found at i:2546515 original size:11 final size:11
Alignment explanation
Indices: 2546451--2546525 Score: 54
Period size: 11 Copynumber: 7.4 Consensus size: 11
2546441 TTTGATATAT
*
2546451 TATTATATTTA
1 TATTATTTTTA
**
2546462 TATTAAATTTA
1 TATTATTTTTA
*
2546473 CATTATTTTT-
1 TATTATTTTTA
*
2546483 TA-TATTTAT-
1 TATTATTTTTA
2546492 TA-TA-TTTTA
1 TATTATTTTTA
2546501 -ATTATTTTTA
1 TATTATTTTTA
*
2546511 TATTATATTTA
1 TATTATTTTTA
2546522 TATT
1 TATT
2546526 TTATAGTTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
8 4 0.08
9 12 0.23
10 6 0.12
11 30 0.58
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:2546522 original size:17 final size:17
Alignment explanation
Indices: 2546485--2546538 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
2546475 TTATTTTTTA
* *
2546485 TATTTATTATATTTTAAT
1 TATTT-TTATATTATATT
2546503 TATTTTTATATTATATT
1 TATTTTTATATTATATT
2546520 TATATTTTATAGTTATATT
1 TAT-TTTTATA-TTATATT
2546539 AATTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 13 0.41
18 12 0.38
19 7 0.22
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTTTTATATTATATT
Found at i:2546529 original size:13 final size:13
Alignment explanation
Indices: 2546491--2546538 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2546481 TTTATATTTA
2546491 TTATATTTTAATTAT
1 TTATATTTT-A-TAT
* *
2546506 TTTTATATTATAT
1 TTATATTTTATAT
*
2546519 TTATATTTTATAG
1 TTATATTTTATAT
2546532 TTATATT
1 TTATATT
2546539 AATTGTAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 20 0.71
14 1 0.04
15 7 0.25
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATATTTTATAT
Found at i:2546535 original size:24 final size:23
Alignment explanation
Indices: 2546453--2546539 Score: 69
Period size: 22 Copynumber: 3.9 Consensus size: 23
2546443 TGATATATTA
* *
2546453 TTATA-TTTATATTAAATTTACA-
1 TTATATTTTATATTATA-TTATAT
*
2546475 TTATTTTTTATATT-TATTATAT
1 TTATATTTTATATTATATTATAT
2546497 TT-TAATTATT-T-TTATATTATAT
1 TTAT-ATT-TTATATTATATTATAT
2546519 TTATATTTTATAGTTATATTA
1 TTATATTTTATA-TTATATTA
2546540 ATTGTAACGT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
21 9 0.17
22 24 0.46
23 11 0.21
24 8 0.15
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (23 bp):
TTATATTTTATATTATATTATAT
Found at i:2549988 original size:3 final size:3
Alignment explanation
Indices: 2549982--2550016 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2549972 AATCATCATC
2549982 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2550017 AAAATATGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2551562 original size:15 final size:15
Alignment explanation
Indices: 2551542--2551572 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2551532 ATAAATCTAG
2551542 ATAGATAATTAATTT
1 ATAGATAATTAATTT
*
2551557 ATAGATAATTTATTT
1 ATAGATAATTAATTT
2551572 A
1 A
2551573 CTCAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
ATAGATAATTAATTT
Found at i:2551638 original size:5 final size:5
Alignment explanation
Indices: 2551618--2551655 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
2551608 TATGAAACAA
*
2551618 AAAAT -AAAT AAGAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
2551656 GCCTATGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:2559653 original size:15 final size:16
Alignment explanation
Indices: 2559633--2559665 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2559623 AACTCATATT
2559633 AATC-AAAAGAAAACA
1 AATCAAAAAGAAAACA
2559648 AATCAAAAAGAAAACA
1 AATCAAAAAGAAAACA
2559664 AA
1 AA
2559666 CCCAGAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.76, C:0.12, G:0.06, T:0.06
Consensus pattern (16 bp):
AATCAAAAAGAAAACA
Found at i:2564096 original size:13 final size:13
Alignment explanation
Indices: 2564056--2564086 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2564046 AAAACTTTGA
2564056 ATTTT-ATTAATT
1 ATTTTAATTAATT
2564068 ATTTTAATTAATT
1 ATTTTAATTAATT
2564081 ATTTTA
1 ATTTTA
2564087 TATTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTAATTAATT
Found at i:2565573 original size:2 final size:2
Alignment explanation
Indices: 2565566--2565600 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2565556 TGTAATGATA
2565566 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
2565601 AAAGAAATTG
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:2566102 original size:29 final size:30
Alignment explanation
Indices: 2566039--2566102 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
2566029 AAAACATAAT
* * **
2566039 ATAATTAATTAGATTGTTTATAATCTATGA
1 ATAATTAATTAGATTGTTCAAAATCTAAAA
2566069 A-AATTAATTAGATTGTTCAAAAT-TAAAA
1 ATAATTAATTAGATTGTTCAAAATCTAAAA
2566097 ATAATT
1 ATAATT
2566103 TTTATTAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.14
29 24 0.83
30 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (30 bp):
ATAATTAATTAGATTGTTCAAAATCTAAAA
Found at i:2568280 original size:2 final size:2
Alignment explanation
Indices: 2568273--2568302 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2568263 CTCTTTGTGC
2568273 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
2568303 TTGTCCAGTA
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:2573236 original size:18 final size:18
Alignment explanation
Indices: 2573200--2573257 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
2573190 ATAAATTAAT
**
2573200 TAATTTTATATATTTTTA
1 TAATTTTATATATAATTA
*
2573218 TAATTTTATGTATAATTA
1 TAATTTTATATATAATTA
* * *
2573236 TTATTTTA-ATAAAATAA
1 TAATTTTATATATAATTA
2573253 TAATT
1 TAATT
2573258 AAATTTAATA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 10 0.31
18 22 0.69
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TAATTTTATATATAATTA
Found at i:2573559 original size:16 final size:16
Alignment explanation
Indices: 2573540--2573571 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2573530 AAATAAAATG
*
2573540 AATTTTTAATAATTTA
1 AATTATTAATAATTTA
2573556 AATTATTAATAATTTA
1 AATTATTAATAATTTA
2573572 CTAATTTTTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTATTAATAATTTA
Found at i:2585761 original size:19 final size:18
Alignment explanation
Indices: 2585737--2585785 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 18
2585727 AATATTAAAA
2585737 AAATTTAACTAAAAATATT
1 AAATTTAACTAAAAA-ATT
2585756 AAATTT---TAAAAAA-T
1 AAATTTAACTAAAAAATT
2585770 AAATTTAACTAAAAAA
1 AAATTTAACTAAAAAA
2585786 ATTATGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 7 0.26
15 1 0.04
16 6 0.22
17 7 0.26
19 6 0.22
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTTAACTAAAAAATT
Found at i:2585898 original size:18 final size:18
Alignment explanation
Indices: 2585863--2585918 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
2585853 TGGTTCATTT
* *
2585863 TTAATTATATAATATATA
1 TTAATTATATATTTTATA
*
2585881 TTAATTTTATATTTTATA
1 TTAATTATATATTTTATA
*
2585899 -T-ATTATATATTTTTTA
1 TTAATTATATATTTTATA
2585915 TTAA
1 TTAA
2585919 ATAAAAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.42
17 2 0.06
18 16 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAATTATATATTTTATA
Found at i:2585964 original size:21 final size:21
Alignment explanation
Indices: 2585917--2585964 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2585907 ATTTTTTATT
2585917 AAATA-AAAATAAATATATAA
1 AAATATAAAATAAATATATAA
* * * *
2585937 TATTATAATATAAATATTTAA
1 AAATATAAAATAAATATATAA
2585958 AAATATA
1 AAATATA
2585965 TTACATTATT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATAAAATAAATATATAA
Found at i:2586019 original size:30 final size:29
Alignment explanation
Indices: 2585984--2586057 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
2585974 TTATATTTTA
2585984 AAATTTAATAAA-ATTAAATTATTAAAAATT
1 AAATTTAA-AAATATTAAATTA-TAAAAATT
***
2586014 AAATTTAAAAATATTTTTTTATAAAAATT
1 AAATTTAAAAATATTAAATTATAAAAATT
2586043 AAATTTTAAAAATAT
1 AAA-TTTAAAAATAT
2586058 AATATAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 14 0.36
30 25 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATTTAAAAATATTAAATTATAAAAATT
Found at i:2586024 original size:14 final size:14
Alignment explanation
Indices: 2585984--2586055 Score: 65
Period size: 15 Copynumber: 4.9 Consensus size: 14
2585974 TTATATTTTA
2585984 AAATTTAATAAAATT
1 AAATTTAA-AAAATT
*
2585999 AAATTATTAAAAATT
1 AAATT-TAAAAAATT
2586014 AAATTTAAAAATATT
1 AAATTTAAAAA-ATT
**
2586029 -TTTTTATAAAAATT
1 AAATTTA-AAAAATT
*
2586043 AAATTTTAAAAAT
1 AAATTTAAAAAAT
2586056 ATAATATAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
14 18 0.39
15 26 0.57
16 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTTAAAAAATT
Found at i:2586330 original size:29 final size:28
Alignment explanation
Indices: 2586273--2586333 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
2586263 ATTTAATTGG
* **
2586273 TTTTTAATTATTAAATTTATTAATGACA
1 TTTTTAAATATTAAATTTATTAAAAACA
2586301 TTTTTAAAT-TTATAATTTATTATAAAACA
1 TTTTTAAATATTA-AATTTATTA-AAAACA
2586330 TTTT
1 TTTT
2586334 CTGGTTATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.11
28 17 0.61
29 8 0.29
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTTTAAATATTAAATTTATTAAAAACA
Found at i:2586811 original size:11 final size:11
Alignment explanation
Indices: 2586787--2586859 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
2586777 TAAAATATTA
2586787 TATATTTATAT
1 TATATTTATAT
*
2586798 ATTTATATTATAT
1 -TATAT-TTATAT
*
2586811 TACATTTAATAT
1 TATATTT-ATAT
* *
2586823 AATATTTAAAT
1 TATATTTATAT
*
2586834 TAT-TTT-CAT
1 TATATTTATAT
*
2586843 TAGATTTATAT
1 TATATTTATAT
2586854 TATATT
1 TATATT
2586860 ATTTTTATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
9 4 0.09
10 6 0.13
11 14 0.30
12 16 0.35
13 6 0.13
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2587040 original size:2 final size:2
Alignment explanation
Indices: 2587028--2587068 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2587018 GTAGGCAGTC
2587028 AT AT AT A- 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
2587069 CACTTTTCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2593017 original size:14 final size:14
Alignment explanation
Indices: 2592994--2593038 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2592984 TTTAAAAATA
2592994 AATTTAATAAATTT
1 AATTTAATAAATTT
*
2593008 AATTTTATAAATTAT
1 AATTTAATAAATT-T
* *
2593023 TATTTAATATATTT
1 AATTTAATAAATTT
2593037 AA
1 AA
2593039 AAAAATTAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTAATAAATTT
Found at i:2593038 original size:38 final size:39
Alignment explanation
Indices: 2592990--2593063 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
2592980 ATATTTTAAA
* *
2592990 AATAAATTTAATAAATTTAA-TTTTATAAAT-TATTATTT
1 AATAAATTTAAAAAAATTAACTTTT-TAAATATATTATTT
*
2593028 AATATATTTAAAAAAATTAACTTTTTAAATATATTA
1 AATAAATTTAAAAAAATTAACTTTTTAAATATATTA
2593064 AAATATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 22 0.71
39 9 0.29
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (39 bp):
AATAAATTTAAAAAAATTAACTTTTTAAATATATTATTT
Found at i:2593131 original size:26 final size:28
Alignment explanation
Indices: 2593102--2593165 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 28
2593092 TTTTTATATT
2593102 TTAATATATTTAA-AAT-ATATAATAAA
1 TTAATATATTTAACAATAATATAATAAA
* * *
2593128 TTAAAATTTTTAACTAATAATATATTAAA
1 TTAATATATTTAAC-AATAATATAATAAA
2593157 -TAAT-TATTT
1 TTAATATATTT
2593166 TCAATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
26 11 0.37
27 4 0.13
28 6 0.20
29 9 0.30
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TTAATATATTTAACAATAATATAATAAA
Found at i:2593601 original size:26 final size:26
Alignment explanation
Indices: 2593552--2593600 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
2593542 AAATAGTGAA
2593552 AAAAATTTATGATGTCAAATAAAAGT
1 AAAAATTTATGATGTCAAATAAAAGT
2593578 AAAAA-TTATGGATGT-AAATAAAA
1 AAAAATTTAT-GATGTCAAATAAAA
2593601 AACTTACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (26 bp):
AAAAATTTATGATGTCAAATAAAAGT
Found at i:2594240 original size:25 final size:24
Alignment explanation
Indices: 2594169--2594241 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 24
2594159 AAAAGGTAAG
*
2594169 TTAATTAAAATATAAAA-AATAAATA
1 TTAATT-AAAT-TAAAATAATTAATA
*
2594194 TTAATTAAA-TAAAATATTTTAATA
1 TTAATTAAATTAAAATA-ATTAATA
2594218 TTAAATTAAATTAAAATAATTAAT
1 TT-AATTAAATTAAAATAATTAAT
2594242 TTTTTACACA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.12
23 1 0.02
24 10 0.24
25 18 0.44
26 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TTAATTAAATTAAAATAATTAATA
Found at i:2599613 original size:2 final size:2
Alignment explanation
Indices: 2599606--2599648 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
2599596 ACTTTTAGCC
2599606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
2599649 AAACTACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2601124 original size:3 final size:3
Alignment explanation
Indices: 2601116--2601156 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2601106 CTAACATCAA
2601116 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
2601157 AGAAATTACA
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:2604128 original size:4 final size:4
Alignment explanation
Indices: 2604114--2604145 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
2604104 GAGTATGCGT
*
2604114 ATAC GTAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2604146 TCTAATATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:2609207 original size:21 final size:21
Alignment explanation
Indices: 2609166--2609205 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2609156 TTATCATACC
*
2609166 AAATTCAATTAAATATTTATA
1 AAATTAAATTAAATATTTATA
2609187 AAATTAAATT-AAT-TTTATA
1 AAATTAAATTAAATATTTATA
2609206 TATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTAAATTAAATATTTATA
Found at i:2609234 original size:27 final size:29
Alignment explanation
Indices: 2609204--2609269 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
2609194 ATTAATTTTA
* *
2609204 TATATTTTTTTAATTT-TTTA-TATAATT
1 TATATTTTTTTAATTTGATCATTATAATT
* *
2609231 TATATTTATTTAATTTGATCATTATATTT
1 TATATTTTTTTAATTTGATCATTATAATT
2609260 TATATTTTTT
1 TATATTTTTT
2609270 GTTACATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 15 0.47
28 2 0.06
29 15 0.47
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (29 bp):
TATATTTTTTTAATTTGATCATTATAATT
Found at i:2612234 original size:29 final size:30
Alignment explanation
Indices: 2612179--2612245 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 30
2612169 TTAGTTCCAT
*
2612179 TTTATAATATTATTTTATGATTTTATAATAA
1 TTTA-AATATTATTTTATGATTATATAATAA
*
2612210 -TTAAATATT-TTATTATTATTATATAATAA
1 TTTAAATATTATT-TTATGATTATATAATAA
2612239 TTTAAAT
1 TTTAAAT
2612246 TAATTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 2 0.06
29 21 0.66
30 9 0.28
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
TTTAAATATTATTTTATGATTATATAATAA
Found at i:2613782 original size:19 final size:19
Alignment explanation
Indices: 2613726--2613783 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
2613716 AATTTAAATA
*
2613726 TAAAAATA-TAATTATTTT
1 TAAAAATATTAAATATTTT
* * *
2613744 TAAATATATAAAATAATTT
1 TAAAAATATTAAATATTTT
*
2613763 TAAAAATATTAAACATTTT
1 TAAAAATATTAAATATTTT
2613782 TA
1 TA
2613784 TATCAAATTT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 7 0.23
19 24 0.77
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAAATATTAAATATTTT
Found at i:2621795 original size:21 final size:21
Alignment explanation
Indices: 2621771--2621828 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2621761 ATTATTAATT
*
2621771 TTTAATCTCATCATTACAGTA
1 TTTAATCTCATCATTACAATA
2621792 TTTAATCTCA-CTATTACAATA
1 TTTAATCTCATC-ATTACAATA
* *
2621813 ATTAATTTCATCATTA
1 TTTAATCTCATCATTA
2621829 TTATTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTAATCTCATCATTACAATA
Found at i:2622622 original size:22 final size:22
Alignment explanation
Indices: 2622597--2622657 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
2622587 ATAAATATTT
2622597 TTTTAGAAAAAATAAT-TATAAA
1 TTTTAGAAAAAATAATCTA-AAA
*
2622619 TTTTCGAATAAAATTAATCTAAAA
1 TTTTAGAA-AAAA-TAATCTAAAA
*
2622643 TTATA-AAATAAATAA
1 TTTTAGAAA-AAATAA
2622658 AGATATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 11 0.34
23 9 0.28
24 10 0.31
25 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (22 bp):
TTTTAGAAAAAATAATCTAAAA
Found at i:2623764 original size:17 final size:18
Alignment explanation
Indices: 2623742--2623778 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2623732 ACTTTATACC
2623742 ATTAT-AAAATAAAAAAA
1 ATTATAAAAATAAAAAAA
2623759 ATTATAAAAATAAAAAAA
1 ATTATAAAAATAAAAAAA
2623777 AT
1 AT
2623779 AATATCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
ATTATAAAAATAAAAAAA
Found at i:2623776 original size:9 final size:9
Alignment explanation
Indices: 2623747--2623780 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2623737 ATACCATTAT
2623747 AAAATAAAA
1 AAAATAAAA
* *
2623756 AAAATTATA
1 AAAATAAAA
2623765 AAAATAAAA
1 AAAATAAAA
2623774 AAAATAA
1 AAAATAA
2623781 TATCATCATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAATAAAA
Found at i:2624010 original size:21 final size:22
Alignment explanation
Indices: 2623984--2624024 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2623974 AAATTTAACC
* *
2623984 ATTAATTAA-TTTCAAAAATAA
1 ATTAATCAACTTTAAAAAATAA
2624005 ATTAATCAACTTTAAAAAAT
1 ATTAATCAACTTTAAAAAAT
2624025 TACCAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTAATCAACTTTAAAAAATAA
Found at i:2624229 original size:22 final size:23
Alignment explanation
Indices: 2624199--2624243 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2624189 ATTAACATTT
2624199 ATAAATATTAA-TTAAAAATTAC
1 ATAAATATTAATTTAAAAATTAC
*
2624221 ATAATTATTAATTTTAAAAATTA
1 ATAAATATTAA-TTTAAAAATTA
2624244 ATATTTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
24 10 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAAATATTAATTTAAAAATTAC
Found at i:2624673 original size:3 final size:3
Alignment explanation
Indices: 2624665--2624693 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2624655 CTTTTATATT
2624665 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2624694 TTTGCTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2625513 original size:18 final size:20
Alignment explanation
Indices: 2625490--2625529 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2625480 CTATATAAAC
2625490 AAAATAT-TA-TACAAAGTA
1 AAAATATATATTACAAAGTA
*
2625508 AAAATATATATTATAAAGTA
1 AAAATATATATTACAAAGTA
2625528 AA
1 AA
2625530 TTTTTTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 10 0.53
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAATATATATTACAAAGTA
Found at i:2631763 original size:18 final size:18
Alignment explanation
Indices: 2631719--2631763 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2631709 AATTATTTAA
* *
2631719 TTAATTTAAAAATATCAT
1 TTAATTTAAAAACAACAT
*
2631737 TTAAATTTAAATACAACAT
1 TT-AATTTAAAAACAACAT
2631756 TTAATTTA
1 TTAATTTA
2631764 TAGTTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATTTAAAAACAACAT
Found at i:2631833 original size:24 final size:23
Alignment explanation
Indices: 2631806--2631856 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
2631796 ATGATTATAT
2631806 AAATATGACATAAAAATATAATTA
1 AAATATGACATAAAAATAT-ATTA
* * *
2631830 AAATATGATATAAATATATTTTA
1 AAATATGACATAAAAATATATTA
2631853 AAAT
1 AAAT
2631857 TTATATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
AAATATGACATAAAAATATATTA
Found at i:2631847 original size:22 final size:21
Alignment explanation
Indices: 2631819--2631869 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
2631809 TATGACATAA
2631819 AAATATAATTAAAATATGATAT
1 AAATATAATTAAAAT-TGATAT
* *
2631841 AAATATATTTTAAAATTTATAT
1 AAATATA-ATTAAAATTGATAT
2631863 -AATATAA
1 AAATATAA
2631870 ATTATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 6 0.24
22 12 0.48
23 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAATATAATTAAAATTGATAT
Found at i:2631889 original size:18 final size:17
Alignment explanation
Indices: 2631851--2631952 Score: 56
Period size: 18 Copynumber: 6.1 Consensus size: 17
2631841 AAATATATTT
*
2631851 TAAAATTTATAT-AATA
1 TAAAAATTATATAAATA
2631867 T--AAATTAT-TAATATA
1 TAAAAATTATATAA-ATA
2631882 TCAAAAATTATATAAATA
1 T-AAAAATTATATAAATA
*
2631900 TAAAATATTTTATATAAT-
1 TAAAA-ATTATATA-AATA
* *
2631918 TATAATATGATA-AAATA
1 TA-AAAATTATATAAATA
* *
2631935 TATAAA-TATAAAAATA
1 TAAAAATTATATAAATA
2631951 TA
1 TA
2631953 TGATTTATTC
Statistics
Matches: 67, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
13 1 0.01
14 7 0.10
15 7 0.10
16 13 0.19
17 7 0.10
18 24 0.36
19 8 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (17 bp):
TAAAAATTATATAAATA
Found at i:2631940 original size:43 final size:45
Alignment explanation
Indices: 2631820--2631947 Score: 126
Period size: 43 Copynumber: 2.8 Consensus size: 45
2631810 ATGACATAAA
* *
2631820 AATATAATTAAAATATGATATAAATATAT---TTTAAAATTTATAT
1 AATATAATTATAATATGATA-AAATATATAAATATAAAATTTATAT
2631863 AATATAAATTATTAATAT-ATCAAAAATTATATAAATATAAAATATT-T-T
1 AATAT-AATTA-TAATATGAT--AAAA-TATATAAATATAAAAT-TTATAT
2631911 -ATATAATTATAATATGATAAAATATATAAATATAAAA
1 AATATAATTATAATATGATAAAATATATAAATATAAAA
2631948 ATATATGATT
Statistics
Matches: 73, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
43 20 0.27
44 11 0.15
45 14 0.19
46 13 0.18
47 4 0.05
48 1 0.01
49 8 0.11
50 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.41
Consensus pattern (45 bp):
AATATAATTATAATATGATAAAATATATAAATATAAAATTTATAT
Found at i:2632220 original size:17 final size:17
Alignment explanation
Indices: 2632184--2632222 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2632174 TTAAATATAA
* **
2632184 ATATTAAATATAGATGT
1 ATATTAAATATAAAAAT
2632201 ATATTAAATATAAAAAT
1 ATATTAAATATAAAAAT
2632218 ATATT
1 ATATT
2632223 TTAAATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
ATATTAAATATAAAAAT
Found at i:2632470 original size:14 final size:14
Alignment explanation
Indices: 2632451--2632478 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2632441 TCTTTCCACA
2632451 TTATTATTATTTTT
1 TTATTATTATTTTT
2632465 TTATTATTATTTTT
1 TTATTATTATTTTT
2632479 GGTCTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTATTATTTTT
Found at i:2634809 original size:19 final size:19
Alignment explanation
Indices: 2634772--2634809 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2634762 ATAATTAAAT
*
2634772 TTAAATAAAAATATTTTTA
1 TTAAATAAAAATATATTTA
2634791 TTAAATAAATAATA-ATTTA
1 TTAAATAAA-AATATATTTA
2634810 AATCAGGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATAAAAATATATTTA
Found at i:2635188 original size:36 final size:35
Alignment explanation
Indices: 2635140--2635218 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 35
2635130 AATATGACAT
2635140 AATTATATGATATGAATATAATATAAA-A-A-ATTAAA
1 AATTATATGATAT-AA-AT-ATATAAATATATATTAAA
2635175 ATATTATATGATATAAATATATAAATATATATTAAA
1 A-ATTATATGATATAAATATATAAATATATATTAAA
2635211 AATTATAT
1 AATTATAT
2635219 ATAATTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
33 7 0.17
34 3 0.08
35 11 0.28
36 19 0.47
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (35 bp):
AATTATATGATATAAATATATAAATATATATTAAA
Found at i:2635294 original size:17 final size:17
Alignment explanation
Indices: 2635247--2635305 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
2635237 AACATTTATT
*
2635247 AAAATATAAATTTTAATA
1 AAAATATAAA-TATAATA
* *
2635265 TAATTAT-AATATAA-A
1 AAAATATAAATATAATA
2635280 AAATATATAAATATAATA
1 AAA-ATATAAATATAATA
2635298 AAAATATA
1 AAAATATA
2635306 TGTATTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 3 0.09
16 7 0.21
17 14 0.42
18 9 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATATAAATATAATA
Found at i:2635294 original size:22 final size:21
Alignment explanation
Indices: 2635262--2635306 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2635252 ATAAATTTTA
*
2635262 ATATAATTATAATATAAAAAAT
1 ATATAAATATAATA-AAAAAAT
*
2635284 ATATAAATATAATAAAAATAT
1 ATATAAATATAATAAAAAAAT
2635305 AT
1 AT
2635307 GTATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATAAATATAATAAAAAAAT
Found at i:2636841 original size:16 final size:16
Alignment explanation
Indices: 2636822--2636878 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
2636812 AGAAAGATGC
2636822 AAAGAAAA-AAAGTAAA
1 AAAGAAAAGAAAG-AAA
2636838 AAAGAAAAGAAAGAAA
1 AAAGAAAAGAAAGAAA
* *
2636854 AAA-AAAGGAGAGAAATA
1 AAAGAAAAGAAAG-AA-A
2636871 AAAGAAAA
1 AAAGAAAA
2636879 ATTTAATGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 7 0.21
16 16 0.47
17 8 0.24
18 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (16 bp):
AAAGAAAAGAAAGAAA
Found at i:2636859 original size:19 final size:19
Alignment explanation
Indices: 2636835--2636879 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2636825 GAAAAAAAGT
2636835 AAAAAAGAAAAGAAAGAAA
1 AAAAAAGAAAAGAAAGAAA
* * *
2636854 AAAAAAGGAGAGAAATAAA
1 AAAAAAGAAAAGAAAGAAA
2636873 AGAAAAA
1 A-AAAAA
2636880 TTTAATGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAAAGAAAGAAA
Found at i:2637290 original size:15 final size:15
Alignment explanation
Indices: 2637272--2637306 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2637262 TTAATTTATT
2637272 TATTTTAAAATAATA
1 TATTTTAAAATAATA
2637287 TA-TTTAAAATAATA
1 TATTTTAAAATAATA
*
2637301 AATTTT
1 TATTTT
2637307 TGTATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTTTAAAATAATA
Found at i:2637305 original size:37 final size:35
Alignment explanation
Indices: 2637222--2637305 Score: 82
Period size: 37 Copynumber: 2.3 Consensus size: 35
2637212 AAATATTTTT
2637222 TAATAAATTTAATTTTTATTAAAAATAATTAAAAA
1 TAATAAATTTAATTTTTATTAAAAATAATTAAAAA
* *
2637257 TATTATTAATTT-ATTTATT-TTAAAATAATATATTTAAAA
1 TA--ATAAATTTAATTT-TTATT-AAA-AATA-ATTAAAAA
2637296 TAATAAATTT
1 TAATAAATTT
2637306 TTGTATTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
35 2 0.05
36 6 0.15
37 19 0.47
38 4 0.10
39 9 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
TAATAAATTTAATTTTTATTAAAAATAATTAAAAA
Found at i:2637369 original size:16 final size:16
Alignment explanation
Indices: 2637348--2637404 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
2637338 AATTTTAAAT
2637348 ATAAAATTATTATTTA
1 ATAAAATTATTATTTA
2637364 ATAAAATTATT-TTATA
1 ATAAAATTATTATT-TA
* *
2637380 ATTAAATTTTTA-TTA
1 ATAAAATTATTATTTA
2637395 ATAACAATTA
1 ATAA-AATTA
2637405 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 7 0.21
16 27 0.79
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAAATTATTATTTA
Found at i:2637418 original size:21 final size:20
Alignment explanation
Indices: 2637379--2637427 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
2637369 ATTATTTTAT
* **
2637379 AATTAAATTTTTATTAATAA
1 AATTAAAATTTTAAAAATAA
2637399 CAATTAAAATTTTAAAAATAA
1 -AATTAAAATTTTAAAAATAA
*
2637420 AAATAAAA
1 AATTAAAA
2637428 GACCCGAGCG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTAAAATTTTAAAAATAA
Found at i:2637554 original size:68 final size:68
Alignment explanation
Indices: 2637444--2637578 Score: 234
Period size: 68 Copynumber: 2.0 Consensus size: 68
2637434 AGCGAAACGG
* * *
2637444 GATATACATCTAAAATCAACTCTATCAATCATTTTGGTGCTGACATGTAGCGCCATGTTTTTTTT
1 GATATACATCTAAAATCAACTATACCAATCATTTTGGCGCTGACATGTAGCGCCATGTTTTTTTT
2637509 TTC
66 TTC
*
2637512 GATATACATCTAAAATCAACTATACCAATCATTTTGGCGCTGACATGTGGCGCCATGTTTTTTTT
1 GATATACATCTAAAATCAACTATACCAATCATTTTGGCGCTGACATGTAGCGCCATGTTTTTTTT
2637577 TT
66 TT
2637579 TGCTTTCAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (68 bp):
GATATACATCTAAAATCAACTATACCAATCATTTTGGCGCTGACATGTAGCGCCATGTTTTTTTT
TTC
Found at i:2637638 original size:19 final size:19
Alignment explanation
Indices: 2637614--2637650 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2637604 TAGGTAGGTG
*
2637614 AAAAAGAAAGAAAGAAAAA
1 AAAAAGAAAAAAAGAAAAA
2637633 AAAAAGAAAAAAAGAAAA
1 AAAAAGAAAAAAAGAAAA
2637651 TTTTTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAAAGAAAAA
Found at i:2637686 original size:15 final size:16
Alignment explanation
Indices: 2637666--2637765 Score: 64
Period size: 15 Copynumber: 6.2 Consensus size: 16
2637656 TATGTGTTTA
2637666 TATTTATAATTT-TTT
1 TATTTATAATTTATTT
* *
2637681 TATTTAAAATATTATAT
1 TATTTATAAT-TTATTT
2637698 T-TTTATATATTT-TTT
1 TATTTATA-ATTTATTT
2637713 ATATATTAATAATTTATTT
1 -TAT-TT-ATAATTTATTT
* * **
2637732 TATTTTTTACATA-TT
1 TATTTATAATTTATTT
*
2637747 TATGTATAATTTATTT
1 TATTTATAATTTATTT
2637763 TAT
1 TAT
2637766 ATATGGGAGA
Statistics
Matches: 63, Mismatches: 13, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
15 21 0.33
16 19 0.30
17 8 0.13
18 9 0.14
19 6 0.10
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (16 bp):
TATTTATAATTTATTT
Found at i:2637733 original size:31 final size:30
Alignment explanation
Indices: 2637662--2637769 Score: 89
Period size: 31 Copynumber: 3.5 Consensus size: 30
2637652 TTTTTATGTG
*
2637662 TTTATATTTATA-ATTTTTT-TATTTAAAATA
1 TTTAT-TTTATATATTTTTTATATTTAATA-A
2637692 TTATATTTTTATATATTTTTTATATATTAATAA
1 TT-TA-TTTTATATATTTTTTATAT-TTAATAA
**
2637725 TTTATTTTAT-T-TTTTACATATTTATGTATAA
1 TTTATTTTATATATTTTTTATATTTA---ATAA
2637756 TTTATTTTATATAT
1 TTTATTTTATATAT
2637770 GGGAGAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
28 3 0.05
29 8 0.12
30 3 0.05
31 28 0.43
32 11 0.17
33 7 0.11
34 5 0.08
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (30 bp):
TTTATTTTATATATTTTTTATATTTAATAA
Found at i:2637833 original size:19 final size:19
Alignment explanation
Indices: 2637805--2637860 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
2637795 TTTTATTAAA
2637805 AATA-TTATAAATTTATGT
1 AATATTTATAAATTTATGT
*
2637823 AATATTTATAAATATT-TTT
1 AATATTTATAAAT-TTATGT
* *
2637842 TATATTTATATATTTATGT
1 AATATTTATAAATTTATGT
2637861 CATTTTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 6 0.19
19 23 0.74
20 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
AATATTTATAAATTTATGT
Found at i:2638937 original size:4 final size:4
Alignment explanation
Indices: 2638930--2638959 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2638920 CACATGTGGA
2638930 AAAG AAAG AAAG AAAG AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
2638960 AAAATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2638975 original size:13 final size:13
Alignment explanation
Indices: 2638957--2638982 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2638947 AAGAAAGAAG
2638957 AAAAAAATTTATA
1 AAAAAAATTTATA
2638970 AAAAAAATTTATA
1 AAAAAAATTTATA
2638983 TGTTTGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAAAATTTATA
Found at i:2639007 original size:24 final size:24
Alignment explanation
Indices: 2638977--2639040 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
2638967 ATAAAAAAAA
2638977 TTTATATGTTTGTAT-TTATATTTT
1 TTTATAT-TTTGTATATTATATTTT
***
2639001 TTTATATTTAAAATATTATATTTT
1 TTTATATTTTGTATATTATATTTT
*
2639025 TATATATTTTGTATAT
1 TTTATATTTTGTATAT
2639041 ATTAATAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (24 bp):
TTTATATTTTGTATATTATATTTT
Done.