Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 9 of 27
Found at i:1290499 original size:47 final size:48
Alignment explanation
Indices: 1290428--1290521 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 48
1290418 GCCAAATCAA
* *
1290428 AGAAAAAACCTTAGTTGAAGGAATAATAC-AAAAAGACTGCTTCATAG
1 AGAAAAAACCTTAGTTGAAAGAATAATACAAAAAAGACTGCTGCATAG
*
1290475 AGAAAGAACCTTAGTTGAAAGAATAATACAAAAAAGACTGCTGCATA
1 AGAAAAAACCTTAGTTGAAAGAATAATACAAAAAAGACTGCTGCATA
1290522 CAGACATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
47 27 0.63
48 16 0.37
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (48 bp):
AGAAAAAACCTTAGTTGAAAGAATAATACAAAAAAGACTGCTGCATAG
Found at i:1292211 original size:3 final size:3
Alignment explanation
Indices: 1292203--1292241 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
1292193 TCTGGAGTTG
1292203 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
1292242 TATTAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1296480 original size:20 final size:20
Alignment explanation
Indices: 1296455--1296494 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1296445 AAAATAGTAT
1296455 TTTAT-ATTAATATTTATATA
1 TTTATAATTAAT-TTTATATA
1296475 TTTATAATTAATTTTATATA
1 TTTATAATTAATTTTATATA
1296495 AAATTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATAATTAATTTTATATA
Found at i:1296787 original size:2 final size:2
Alignment explanation
Indices: 1296780--1296807 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1296770 GATACACATA
1296780 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
1296808 GGGGTTTTCC
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:1297165 original size:10 final size:10
Alignment explanation
Indices: 1297148--1297183 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1297138 AAAATTTAAG
1297148 TAATATTTTT
1 TAATATTTTT
* *
1297158 TTATATTTAT
1 TAATATTTTT
1297168 TAATATTTTT
1 TAATATTTTT
1297178 TAATAT
1 TAATAT
1297184 GACTTTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TAATATTTTT
Found at i:1297654 original size:18 final size:18
Alignment explanation
Indices: 1297625--1297666 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1297615 TATTTTTATA
1297625 ATAAATTTAAATAAAAATT
1 ATAAA-TTAAATAAAAATT
*
1297644 ATAAATTAAATAATAATT
1 ATAAATTAAATAAAAATT
1297662 -TAAAT
1 ATAAAT
1297667 AAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 12 0.55
19 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATTAAATAAAAATT
Found at i:1297672 original size:18 final size:17
Alignment explanation
Indices: 1297633--1297683 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1297623 TAATAAATTT
* *
1297633 AAATAAAAATTATAAATT
1 AAATAATAATT-TAAATA
1297651 AAATAATAATTTAAATA
1 AAATAATAATTTAAATA
*
1297668 AAA-ATTATATTTAAAT
1 AAATAATA-ATTTAAAT
1297684 TTGCTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.10
17 16 0.55
18 10 0.34
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATAATAATTTAAATA
Found at i:1299217 original size:103 final size:104
Alignment explanation
Indices: 1299032--1299234 Score: 291
Period size: 103 Copynumber: 2.0 Consensus size: 104
1299022 ATTTTTTTAT
* * ** *
1299032 TTAAATTTAATTATAAAAATATATGTTAATATACAAATAATTTATATTAATTTTTACATAATAAT
1 TTAAATTTAATTATAAAAACATATGTTAATATACAAAAAAAATATATTAATTTTCACATAATAAT
*
1299097 TTTAATTTTCAAGTCAGATCGAGTTTGATTTAAATCTAC
66 TTTAATTTTCAAGTCAGAGCGAGTTTGATTTAAATCTAC
* * * *
1299136 TTAAATTTAATTATAAAAACATATGTTAATGTATAAAAAAAAT-TATTAATTTTCATATAATGAT
1 TTAAATTTAATTATAAAAACATATGTTAATATACAAAAAAAATATATTAATTTTCACATAATAAT
* *
1299200 TTTAGTTTTTAAGTCAGAGCGAGTTTGATTTAAAT
66 TTTAATTTTCAAGTCAGAGCGAGTTTGATTTAAAT
1299235 ATAACCAAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
103 50 0.57
104 37 0.43
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (104 bp):
TTAAATTTAATTATAAAAACATATGTTAATATACAAAAAAAATATATTAATTTTCACATAATAAT
TTTAATTTTCAAGTCAGAGCGAGTTTGATTTAAATCTAC
Found at i:1300203 original size:7 final size:7
Alignment explanation
Indices: 1300180--1300214 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
1300170 AATACTAAAA
1300180 AAATTTAT
1 AAATTT-T
*
1300188 AAATATT
1 AAATTTT
1300195 AAATTTT
1 AAATTTT
1300202 AAATTTT
1 AAATTTT
1300209 AAATTT
1 AAATTT
1300215 AATAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (7 bp):
AAATTTT
Found at i:1300210 original size:14 final size:15
Alignment explanation
Indices: 1300180--1300226 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
1300170 AATACTAAAA
1300180 AAATTTATAAATATT
1 AAATTTATAAATATT
*
1300195 AAATTT-TAAATTTT
1 AAATTTATAAATATT
1300209 AAATTTAATAAATTATT
1 AAATTT-ATAAA-TATT
1300226 A
1 A
1300227 TTGTGACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.48
15 6 0.22
16 4 0.15
17 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTATAAATATT
Found at i:1300974 original size:78 final size:76
Alignment explanation
Indices: 1300882--1301037 Score: 258
Period size: 78 Copynumber: 2.0 Consensus size: 76
1300872 AATGTACTAT
* *
1300882 TTATTAATTATTATTTTTTATCATTTTTACTAAAAATAATTTTAATTATAAAATAATGAGATTTA
1 TTATTAATTATTATTTTTCATCATTTTTACTAAAAATAATTTTAA-T-TAAAATAATGACATTTA
1300947 ATTAATCTTAAAA
64 ATTAATCTTAAAA
* *
1300960 TTATTAATTATTATTTTTCATCATTTTTACTAAAAATAATTTTAATTACAATAATGACATTTAGT
1 TTATTAATTATTATTTTTCATCATTTTTACTAAAAATAATTTTAATTAAAATAATGACATTTAAT
1301025 TAATCTTAAAA
66 TAATCTTAAAA
1301036 TT
1 TT
1301038 TACTATTAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
76 29 0.39
77 1 0.01
78 44 0.59
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (76 bp):
TTATTAATTATTATTTTTCATCATTTTTACTAAAAATAATTTTAATTAAAATAATGACATTTAAT
TAATCTTAAAA
Found at i:1301112 original size:22 final size:22
Alignment explanation
Indices: 1301087--1301167 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 22
1301077 TAAGTACATG
1301087 TTAAATAATTTTAAATTTATTT
1 TTAAATAATTTTAAATTTATTT
* * *
1301109 TTAATTCAATTAT-ATTTTATTT
1 TTAAAT-AATTTTAAATTTATTT
* *
1301131 TTAATTAAGTTATTAAAATTTTTTAT
1 TTAAATAA-TT-TT-AAATTTATT-T
1301157 TTAAATTAATT
1 TTAAA-TAATT
1301168 AATTATTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
21 2 0.04
22 21 0.47
23 6 0.13
25 6 0.13
26 7 0.16
27 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (22 bp):
TTAAATAATTTTAAATTTATTT
Found at i:1304420 original size:29 final size:31
Alignment explanation
Indices: 1304368--1304435 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
1304358 AAATAAAAAT
* *
1304368 TATTAAATATATTAAAATTTTAAATACGA-TA
1 TATTATATATATTAAAATTATAAATA-GATTA
*
1304399 TATTATATATATT-AAA-TATAAATATATTA
1 TATTATATATATTAAAATTATAAATAGATTA
1304428 TATTATAT
1 TATTATAT
1304436 TTTATTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 17 0.52
30 3 0.09
31 12 0.36
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (31 bp):
TATTATATATATTAAAATTATAAATAGATTA
Found at i:1304431 original size:5 final size:5
Alignment explanation
Indices: 1304397--1304453 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
1304387 TTAAATACGA
* * *
1304397 TATAT TATA- TATAT TA-AA TATAAA TATAT TATAT TATAT TTTAT TATAT
1 TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT TATAT
1304446 TATTAT TA
1 TA-TAT TA
1304454 CACTAAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
4 7 0.16
5 27 0.61
6 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:1304996 original size:25 final size:25
Alignment explanation
Indices: 1304898--1304996 Score: 62
Period size: 25 Copynumber: 4.0 Consensus size: 25
1304888 GTTTAAAATT
*
1304898 AATTTTAAAAATCGTTA--TTTATTA
1 AATTTTAAAAAT-ATTATTTTTATTA
* * * *
1304922 TATTATCAAAATATTATTTTTATAA
1 AATTTTAAAAATATTATTTTTATTA
* * * *
1304947 TAATATTT-AAACT-CTATTATAATTA
1 -AAT-TTTAAAAATATTATTTTTATTA
1304972 AATTTTAAAAATATTATTTTTATTA
1 AATTTTAAAAATATTATTTTTATTA
1304997 GTGAAAAGTA
Statistics
Matches: 53, Mismatches: 16, Indels: 11
0.66 0.20 0.14
Matches are distributed among these distances:
23 6 0.11
24 16 0.30
25 23 0.43
26 6 0.11
27 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (25 bp):
AATTTTAAAAATATTATTTTTATTA
Found at i:1305957 original size:50 final size:51
Alignment explanation
Indices: 1305860--1305961 Score: 120
Period size: 50 Copynumber: 2.0 Consensus size: 51
1305850 TAAACTTGAA
** ** *
1305860 TTAAATAAAAAATTATTTTATATTAATATTTATATATTTTTATAATTAAAT
1 TTAAATAAAAAATTATTTTATATTAATATAAATATATAATTAAAATTAAAT
1305911 TTAAAT-AAAAATTATTATTTATATTAA-ATAAATA-ATAATTAAAATTAAAT
1 TTAAATAAAAAATTA-T-TTTATATTAATATAAATATATAATTAAAATTAAAT
1305961 T
1 T
1305962 AGTTCGACTC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 22 0.50
51 12 0.27
52 10 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (51 bp):
TTAAATAAAAAATTATTTTATATTAATATAAATATATAATTAAAATTAAAT
Found at i:1306330 original size:47 final size:46
Alignment explanation
Indices: 1306244--1306333 Score: 112
Period size: 46 Copynumber: 1.9 Consensus size: 46
1306234 ATTTTTCTAA
* **
1306244 TATCCACTTAAAAAAACTTATCTATTTTTTATTATTTTTTAAAAGT
1 TATCCACTTAAAAAAACTTATCAATTTTAGATTATTTTTTAAAAGT
1306290 TATCCACTTAAAAAAA-TTAT-AACTTTTAGATTTAATTTTTTAAA
1 TATCCACTTAAAAAAACTTATCAA-TTTTAGA-TT-ATTTTTTAAA
1306334 CATAATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
44 1 0.03
45 9 0.24
46 18 0.47
47 10 0.26
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (46 bp):
TATCCACTTAAAAAAACTTATCAATTTTAGATTATTTTTTAAAAGT
Found at i:1306743 original size:15 final size:14
Alignment explanation
Indices: 1306723--1306765 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1306713 TTTTAATTTT
1306723 TTTATATATTATATA
1 TTTATATA-TATATA
1306738 TTTATATA-ATATA
1 TTTATATATATATA
* *
1306751 TTTAAATATAAATA
1 TTTATATATATATA
1306765 T
1 T
1306766 AAAACATGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.48
14 5 0.20
15 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTATATATATATA
Found at i:1308951 original size:29 final size:29
Alignment explanation
Indices: 1308918--1308974 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1308908 AAATATTTAT
* *
1308918 ATAAAAT-AATTTTTAATATTATTTTAATA
1 ATAAAATAAAATTTTAAT-TAATTTTAATA
1308947 ATAAAATAAAATTTTAATTAATTTTAAT
1 ATAAAATAAAATTTTAATTAATTTTAAT
1308975 TTAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATAAAATAAAATTTTAATTAATTTTAATA
Found at i:1308980 original size:11 final size:11
Alignment explanation
Indices: 1308956--1308989 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1308946 AATAAAATAA
1308956 AATTTTAA-TT
1 AATTTTAATTT
1308966 AATTTTAATTT
1 AATTTTAATTT
*
1308977 AATTTAAATTT
1 AATTTTAATTT
1308988 AA
1 AA
1308990 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTTAATTT
Found at i:1310338 original size:29 final size:25
Alignment explanation
Indices: 1310306--1310362 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 25
1310296 TTATTTTAGT
1310306 TTAAAATTTTATCTTATTATTTATTAATA
1 TTAAAATTTTAT-TT-TTA--TATTAATA
1310335 TTAAAATTTTATTTTTATATTAATA
1 TTAAAATTTTATTTTTATATTAATA
1310360 TTA
1 TTA
1310363 TATTTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.39
27 3 0.11
28 2 0.07
29 12 0.43
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TTAAAATTTTATTTTTATATTAATA
Found at i:1310356 original size:19 final size:19
Alignment explanation
Indices: 1310322--1310376 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
1310312 TTTTATCTTA
1310322 TTATTTATTAATATTAAAATT
1 TTATTT-TT-ATATTAAAATT
*
1310343 TTATTTTTATATTAATATT
1 TTATTTTTATATTAAAATT
* *
1310362 ATATTTATA-ATTAAA
1 TTATTTTTATATTAAA
1310377 TTTAAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 5 0.17
19 17 0.57
20 2 0.07
21 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATTTTTATATTAAAATT
Found at i:1311141 original size:12 final size:12
Alignment explanation
Indices: 1311126--1311166 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1311116 TTTACATTAT
1311126 TATTTAAAATAA
1 TATTTAAAATAA
*
1311138 TATTAAAAATAA
1 TATTTAAAATAA
*
1311150 T-TTTAAATTAA
1 TATTTAAAATAA
1311161 TATTTA
1 TATTTA
1311167 TATTTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TATTTAAAATAA
Found at i:1311242 original size:21 final size:20
Alignment explanation
Indices: 1311205--1311243 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1311195 ATAAATAAAT
**
1311205 TTAAATTTAAATTAAATCAC
1 TTAAATTTAAAAAAAATCAC
1311225 TTAAATTATAAAAAAAATC
1 TTAAATT-TAAAAAAAATC
1311244 CAACCCAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAATTTAAAAAAAATCAC
Found at i:1314163 original size:18 final size:17
Alignment explanation
Indices: 1314135--1314168 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1314125 TTTTATTTTT
1314135 ATTTTATTTTTAATTAA
1 ATTTTATTTTTAATTAA
*
1314152 ATTTTAATTTTTTATTA
1 ATTTT-ATTTTTAATTA
1314169 GATAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATTTTTAATTAA
Found at i:1316648 original size:17 final size:17
Alignment explanation
Indices: 1316606--1316652 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1316596 AATATAAAAT
*
1316606 ATAATAAT-TAATTAAT
1 ATAATAATATAATTAAC
* * *
1316622 AAAATTATATATTTAAC
1 ATAATAATATAATTAAC
1316639 ATAATAATATAATT
1 ATAATAATATAATT
1316653 CTTAATATAT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATAATATAATTAAC
Found at i:1318201 original size:32 final size:34
Alignment explanation
Indices: 1318165--1318234 Score: 101
Period size: 32 Copynumber: 2.1 Consensus size: 34
1318155 TAACATAAAT
*
1318165 ATATTAAAATTTATAT-AATATAA-AT-TATTAA
1 ATATTAAAATTTAAATAAATATAATATATATTAA
1318196 CATATTAAAATTTAAATAAATATAATATATATTAA
1 -ATATTAAAATTTAAATAAATATAATATATATTAA
1318231 ATAT
1 ATAT
1318235 AAATATGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
32 15 0.44
33 7 0.21
34 6 0.18
35 6 0.18
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (34 bp):
ATATTAAAATTTAAATAAATATAATATATATTAA
Found at i:1330362 original size:14 final size:14
Alignment explanation
Indices: 1330343--1330375 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1330333 AATTTTTTAA
1330343 TAAAA-TAAAAAATT
1 TAAAATTAAAAAA-T
1330357 TAAAATTAAAAAAT
1 TAAAATTAAAAAAT
1330371 TAAAA
1 TAAAA
1330376 AGTAAGTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAAATTAAAAAAT
Found at i:1330557 original size:74 final size:72
Alignment explanation
Indices: 1330389--1330787 Score: 368
Period size: 74 Copynumber: 5.5 Consensus size: 72
1330379 AAGTGTCATG
* * * * * *
1330389 GGTATTATTTATCTTTATTTGTAAAAGTTT-AATTTGTTTTTTACGTATGATTATATGAGTAAAA
1 GGTATAATTTATTTTTATTTGTAAAAGTTTAAATGTGTTTTTT-GGTATGATTATATGAATTAAA
1330453 GTTTTT-A-
65 -TTTTTGAT
* ** *
1330460 GAATATAATTTATTTTTATTTGTAGTAGTTTAAATGTGTTTTTTGGGTATGCTTATATGAATTTA
1 G-GTATAATTTATTTTTATTTGTAAAAGTTTAAATGTGTTTTTT-GGTATGATTATATGAA-TTA
1330525 AATTTTTGAT
63 AATTTTTGAT
* * * *
1330535 GGTATAATTTATTTTTATTTGTAAAAGTTTAAATGTAGTTTTTTGGTACGATTTTAT-AAGTATA
1 GGTATAATTTATTTTTATTTGTAAAAGTTTAAATGT-GTTTTTTGGTATGATTATATGAATTAAA
1330599 TATTTTGTAT
65 T-TTTTG-AT
* * *
1330609 GGTATAATTTATTTTTATTTGTAAAAGTTTAAATGTAGTTTTTTGGTATGATTTTAT-AAGTATA
1 GGTATAATTTATTTTTATTTGTAAAAGTTTAAATGT-GTTTTTTGGTATGATTATATGAATTAAA
1330673 TATTTTGTAT
65 T-TTTTG-AT
* * * *
1330683 GGTATAATTCATTTTTATTTGTAAAAATTTTAAAT-T-TTTTTTGGGT-TGATTAAATGAGTTTA
1 GGTATAATTTATTTTTATTTGT-AAAAGTTTAAATGTGTTTTTT-GGTATGATTATATGA-ATTA
*
1330745 AATTTTT-AA
63 AATTTTTGAT
* * *
1330754 GATAGT-ATTTATCTTTATTTGTAAAAATTTAAAT
1 GGTA-TAATTTATTTTTATTTGTAAAAGTTTAAAT
1330788 TTTTATTTAA
Statistics
Matches: 283, Mismatches: 32, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
70 11 0.04
71 19 0.07
72 42 0.15
73 44 0.16
74 148 0.52
75 19 0.07
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.54
Consensus pattern (72 bp):
GGTATAATTTATTTTTATTTGTAAAAGTTTAAATGTGTTTTTTGGTATGATTATATGAATTAAAT
TTTTGAT
Found at i:1330969 original size:23 final size:22
Alignment explanation
Indices: 1330939--1330982 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1330929 GAGATACTAT
*
1330939 AATTTTATTAATCATATATTTA
1 AATTTTATTAATCATAAATTTA
*
1330961 AATTATTATTAATTATAAATTT
1 AATT-TTATTAATCATAAATTT
1330983 TGTAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTTTATTAATCATAAATTTA
Found at i:1331195 original size:17 final size:17
Alignment explanation
Indices: 1331168--1331200 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1331158 AAAAAATAAG
1331168 AAAATTATTGATATTATT
1 AAAATTATTGAT-TTATT
1331186 AAAA-TATTGATTTAT
1 AAAATTATTGATTTAT
1331201 ACATATCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
AAAATTATTGATTTATT
Found at i:1331307 original size:12 final size:12
Alignment explanation
Indices: 1331275--1331317 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1331265 AATTTTTTTT
1331275 AAATATAATATAA
1 AAATATAAT-TAA
* *
1331288 AAAAATAATTCA
1 AAATATAATTAA
*
1331300 AAATATAAATAA
1 AAATATAATTAA
1331312 AAATAT
1 AAATAT
1331318 TTAATAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (12 bp):
AAATATAATTAA
Found at i:1331326 original size:22 final size:21
Alignment explanation
Indices: 1331279--1331327 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1331269 TTTTTTAAAT
1331279 ATAATATAAAAAAATAATTCA
1 ATAATATAAAAAAATAATTCA
*
1331300 A-AATATAAATAAAA-ATATTTA
1 ATAATATAAA-AAAATA-ATTCA
1331321 ATAATAT
1 ATAATAT
1331328 CTCGAGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 9 0.38
21 10 0.42
22 5 0.21
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATATAAAAAAATAATTCA
Found at i:1332164 original size:3 final size:3
Alignment explanation
Indices: 1332156--1332181 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1332146 TGGCAATTTC
1332156 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1332182 CATTTTCATT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1337980 original size:23 final size:22
Alignment explanation
Indices: 1337940--1337993 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
1337930 TAAAAAAAAT
* *
1337940 TAAAAAAATTATTAAATTTAGA
1 TAAAAAAATTAGTAAATTTAAA
*
1337962 TAAAAAAATTAAGTCAATTTAAA
1 TAAAAAAATT-AGTAAATTTAAA
*
1337985 AAAAAAAAT
1 TAAAAAAAT
1337994 AGAGTCCTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
TAAAAAAATTAGTAAATTTAAA
Found at i:1337999 original size:23 final size:23
Alignment explanation
Indices: 1337954--1337999 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1337944 AAAATTATTA
* *
1337954 AATTTAGATAAAAAAATTAAGTC
1 AATTTAGAAAAAAAAAATAAGTC
1337977 AATTTA-AAAAAAAAAATAGAGTC
1 AATTTAGAAAAAAAAAATA-AGTC
1338000 CTGGCTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26
Consensus pattern (23 bp):
AATTTAGAAAAAAAAAATAAGTC
Found at i:1338246 original size:13 final size:13
Alignment explanation
Indices: 1338207--1338246 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
1338197 CTAAAAGTTA
1338207 AAATTTTAAAAAT
1 AAATTTTAAAAAT
1338220 ATATATTTTAAAAAT
1 A-A-ATTTTAAAAAT
*
1338235 AAATTATAAAAA
1 AAATTTTAAAAA
1338247 AATAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.42
14 2 0.08
15 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:1339395 original size:15 final size:15
Alignment explanation
Indices: 1339375--1339403 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1339365 ATAATAAATC
1339375 CAAGAAAAGAAAAGA
1 CAAGAAAAGAAAAGA
1339390 CAAGAAAAGAAAAG
1 CAAGAAAAGAAAAG
1339404 GTATAGTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.21, T:0.00
Consensus pattern (15 bp):
CAAGAAAAGAAAAGA
Found at i:1340764 original size:1 final size:1
Alignment explanation
Indices: 1340760--1340785 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1340750 TTTTTTTTTT
1340760 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
1340786 ATTTGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1346143 original size:40 final size:40
Alignment explanation
Indices: 1346069--1346208 Score: 113
Period size: 38 Copynumber: 3.7 Consensus size: 40
1346059 AATATCAATG
*
1346069 TATATATTTTATGTAAAAATTATATAAAAAATAATTAAAA
1 TATATATTATATGTAAAAATTATATAAAAAATAATTAAAA
*
1346109 TATATATTAATATGTAAAAATT-T-T-AAAAAT-A-T-AAT
1 TATATATT-ATATGTAAAAATTATATAAAAAATAATTAAAA
* * *
1346144 TAT-TATCATAT-TAAAAATTTATATAAATATATAATTATAA
1 TATATATTATATGTAAAAA-TTATATAAA-AAATAATTAAAA
* *
1346184 T-TA-A-TATATATAAAAATAATATAAA
1 TATATATTATATGTAAAAATTATATAAA
1346209 TATATAAATA
Statistics
Matches: 81, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
32 6 0.07
33 6 0.07
34 4 0.05
35 6 0.07
36 3 0.04
37 4 0.05
38 19 0.23
39 10 0.12
40 11 0.14
41 12 0.15
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (40 bp):
TATATATTATATGTAAAAATTATATAAAAAATAATTAAAA
Found at i:1346192 original size:19 final size:19
Alignment explanation
Indices: 1346151--1346216 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
1346141 AATTATTATC
*
1346151 ATAT-TAAAAATTTATATAA
1 ATATATAAAAA-TAATATAA
**
1346170 ATATATAATTATAAT-TAA
1 ATATATAAAAATAATATAA
1346188 TATATATAAAAATAATATAA
1 -ATATATAAAAATAATATAA
1346208 ATATATAAA
1 ATATATAAA
1346217 TATGTTATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 3 0.08
19 29 0.74
20 7 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATATAAAAATAATATAA
Found at i:1346205 original size:11 final size:12
Alignment explanation
Indices: 1346151--1346214 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 12
1346141 AATTATTATC
1346151 ATAT-TAAAAAT
1 ATATATAAAAAT
* *
1346162 TTATATAAATAT
1 ATATATAAAAAT
*
1346174 ATAATTATAATTAAT
1 AT-A-TATAA-AAAT
1346189 ATATATAAAAAT
1 ATATATAAAAAT
*
1346201 A-ATATAAATAT
1 ATATATAAAAAT
1346212 ATA
1 ATA
1346215 AATATGTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
11 13 0.32
12 12 0.29
13 6 0.15
14 6 0.15
15 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATAAAAAT
Found at i:1346210 original size:21 final size:19
Alignment explanation
Indices: 1346134--1346216 Score: 62
Period size: 19 Copynumber: 4.2 Consensus size: 19
1346124 AAAAATTTTA
*
1346134 AAAATATAATTATTATCATATT
1 AAAA-ATAATTAATAT-ATA-T
*
1346156 AAAAATTTATATAA-ATATAT
1 AAAAA-TAAT-TAATATATAT
**
1346176 AATTATAATTAATATATAT
1 AAAAATAATTAATATATAT
1346195 AAAAATAATATAA-ATATAT
1 AAAAATAAT-TAATATATAT
1346214 AAA
1 AAA
1346217 TATGTTATCA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
18 3 0.06
19 25 0.50
20 7 0.14
21 4 0.08
22 9 0.18
23 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATAATTAATATATAT
Found at i:1346211 original size:38 final size:41
Alignment explanation
Indices: 1346138--1346215 Score: 117
Period size: 38 Copynumber: 2.0 Consensus size: 41
1346128 ATTTTAAAAA
* *
1346138 TATAATTATTATCATATTAAAAATTTATATAAATATATAAT
1 TATAATTAATATCATATTAAAAATTAATATAAATATATAAT
1346179 TATAATTAATAT-ATA-TAAAAA-TAATATAAATATATAA
1 TATAATTAATATCATATTAAAAATTAATATAAATATATAA
1346216 ATATGTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 15 0.43
39 6 0.17
40 3 0.09
41 11 0.31
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (41 bp):
TATAATTAATATCATATTAAAAATTAATATAAATATATAAT
Found at i:1347176 original size:22 final size:22
Alignment explanation
Indices: 1347134--1347186 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1347124 AATATTTTTA
1347134 TATAAAT-TTAATGATAAAATT
1 TATAAATATTAATGATAAAATT
1347155 TATAAATATTAATG-TAATAATT
1 TATAAATATTAATGATAA-AATT
*
1347177 TTTAAATATT
1 TATAAATATT
1347187 TTATTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TATAAATATTAATGATAAAATT
Found at i:1347217 original size:19 final size:18
Alignment explanation
Indices: 1347164--1347217 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
1347154 TTATAAATAT
1347164 TAATGTAATAATTTTTAAA
1 TAAT-TAATAATTTTTAAA
* * *
1347183 TATTTTATTATATTTTAAA
1 TAATTAATAAT-TTTTAAA
1347202 TAATTAATGAATTTTT
1 TAATTAAT-AATTTTT
1347218 CATGCTTAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 5 0.19
19 20 0.74
20 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TAATTAATAATTTTTAAA
Found at i:1349128 original size:20 final size:20
Alignment explanation
Indices: 1349105--1349143 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1349095 AATATACAAA
1349105 AACATTTT-CAAATAATTTTC
1 AACATTTTAC-AATAATTTTC
1349125 AACATTTTACAATAATTTT
1 AACATTTTACAATAATTTT
1349144 ATTTTAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (20 bp):
AACATTTTACAATAATTTTC
Found at i:1356015 original size:2 final size:2
Alignment explanation
Indices: 1356008--1356041 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1355998 GCATTAGTAA
1356008 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
1356042 TAAGCAGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1360462 original size:19 final size:19
Alignment explanation
Indices: 1360438--1360509 Score: 85
Period size: 19 Copynumber: 3.8 Consensus size: 19
1360428 TATATAATTA
1360438 TTAAAATATATATTTATAT
1 TTAAAATATATATTTATAT
1360457 TTAAAATATATATTTATATT
1 TTAAAATATATATTTATA-T
* * * *
1360477 TTATATTAAATATTTTTAT
1 TTAAAATATATATTTATAT
1360496 TT-AAAT-TATATTTA
1 TTAAAATATATATTTA
1360510 AATAATTATA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
17 6 0.14
18 2 0.05
19 21 0.48
20 15 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAAAATATATATTTATAT
Found at i:1360793 original size:19 final size:20
Alignment explanation
Indices: 1360756--1360819 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
1360746 TATTAGTAAC
*
1360756 TAAAAAATAATTAATAATAT
1 TAAAAAATTATTAATAATAT
*
1360776 TAAAAAATTATTTA-AATAT
1 TAAAAAATTATTAATAATAT
* *
1360795 TAATAAATTATGAAT-ATATT
1 TAAAAAATTATTAATAATA-T
1360815 TAAAA
1 TAAAA
1360820 TTTAAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TAAAAAATTATTAATAATAT
Found at i:1360994 original size:14 final size:14
Alignment explanation
Indices: 1360977--1361027 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1360967 TTATAATTTA
1360977 AAAATATTAAAATT
1 AAAATATTAAAATT
*
1360991 AAAATATTAAATTT
1 AAAATATTAAAATT
*
1361005 AATAATA-AAATAATT
1 AA-AATATTAA-AATT
1361020 AAAATATT
1 AAAATATT
1361028 TCTCGCATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 21 0.70
15 9 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATATTAAAATT
Found at i:1361004 original size:29 final size:30
Alignment explanation
Indices: 1360965--1361027 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
1360955 ATTTTTTATT
*
1360965 TATTATAATTTAAAAATATTAA-AATTAAAA
1 TATTATAATTTAAAAATA-AAATAATTAAAA
*
1360995 TATTA-AATTTAATAATAAAATAATTAAAA
1 TATTATAATTTAAAAATAAAATAATTAAAA
1361024 TATT
1 TATT
1361028 TCTCGCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 23 0.77
30 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TATTATAATTTAAAAATAAAATAATTAAAA
Found at i:1361282 original size:21 final size:22
Alignment explanation
Indices: 1361242--1361287 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1361232 AGAATAAATT
1361242 TATTAAATTATTTTAATTTA-A
1 TATTAAATTATTTTAATTTACA
*
1361263 TATTAAATT-TTATTACTTTACA
1 TATTAAATTATT-TTAATTTACA
1361285 TAT
1 TAT
1361288 ATTTAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 2 0.09
21 16 0.73
22 4 0.18
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTAAATTATTTTAATTTACA
Found at i:1361691 original size:30 final size:29
Alignment explanation
Indices: 1361640--1361708 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
1361630 CAAATTATCT
* *
1361640 AAAATCAATATTGAGGGATAAAATTTAATCA
1 AAAATCAA-ATTGAGGAATAAAATTCAAT-A
*
1361671 AAAATCAAATTGAGTAATAAAATTCAATA
1 AAAATCAAATTGAGGAATAAAATTCAATA
1361700 AAAATCAAA
1 AAAATCAAA
1361709 GTTTAGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 10 0.29
30 17 0.49
31 8 0.23
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (29 bp):
AAAATCAAATTGAGGAATAAAATTCAATA
Found at i:1365012 original size:2 final size:2
Alignment explanation
Indices: 1365007--1365033 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1364997 GTTTCTCTTC
1365007 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
1365034 CTGTTAGTGT
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:1370871 original size:44 final size:44
Alignment explanation
Indices: 1370777--1370875 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
1370767 ATATTATATT
* * *
1370777 AAAATATATATAAATAATAAAAAATTTTAAATTATTTTATATTTAT
1 AAAAT-TAT-TAAATAATAAAAAATTTTAAATTATTTTATAGTCAA
*
1370823 AAAATTATTAAATAATTAAAAATTATTAAATTATATTT-T-GTCAA
1 AAAATTATTAAATAATAAAAAATT-TTAAATTAT-TTTATAGTCAA
1370867 AAAATTATT
1 AAAATTATT
1370876 TTATTAATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 26 0.55
45 13 0.28
46 8 0.17
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (44 bp):
AAAATTATTAAATAATAAAAAATTTTAAATTATTTTATAGTCAA
Found at i:1373527 original size:20 final size:19
Alignment explanation
Indices: 1373480--1373537 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
1373470 ATGTTTTGAT
*
1373480 TTTATTATTTT-ATTTAGTCA
1 TTTATTATTTTAATTT--TTA
1373500 TTTATTATTTATATATTTTTA
1 TTTATTATTT-TA-ATTTTTA
1373521 TTT-TTATTTTAATTTTT
1 TTTATTATTTTAATTTTT
1373538 CATGAATCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 6 0.18
19 2 0.06
20 16 0.47
21 6 0.18
23 4 0.12
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTATTATTTTAATTTTTA
Found at i:1373682 original size:13 final size:12
Alignment explanation
Indices: 1373647--1373691 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 12
1373637 GAGTGTAATG
1373647 AATTTT-AAATT
1 AATTTTAAAATT
*
1373658 AAATTT--AATT
1 AATTTTAAAATT
1373668 AATTTATAAAATT
1 AATTT-TAAAATT
1373681 AATTTTAAAAT
1 AATTTTAAAAT
1373692 ATGTATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 8 0.28
11 6 0.21
12 6 0.21
13 9 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATTTTAAAATT
Found at i:1373859 original size:19 final size:20
Alignment explanation
Indices: 1373835--1373882 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1373825 AAAATATTAA
1373835 AAATTTAAT-TATTAT-ATT
1 AAATTTAATATATTATAATT
*
1373853 AATATTTATATATTTTATAATT
1 AA-ATTTA-ATATATTATAATT
1373875 AAATTTAA
1 AAATTTAA
1373883 ATTAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
19 5 0.20
20 3 0.12
21 10 0.40
22 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATTTAATATATTATAATT
Found at i:1374539 original size:7 final size:7
Alignment explanation
Indices: 1374527--1374572 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
1374517 CTAGCCATCT
1374527 TCATTAA
1 TCATTAA
1374534 TCATTAA
1 TCATTAA
*
1374541 CCATTAA
1 TCATTAA
1374548 TCATTAA
1 TCATTAA
1374555 TCATTAA
1 TCATTAA
1374562 TCATTAA
1 TCATTAA
1374569 TCAT
1 TCAT
1374573 ATTTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (7 bp):
TCATTAA
Found at i:1374655 original size:29 final size:29
Alignment explanation
Indices: 1374623--1374692 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1374613 TTAACTAAAA
* * *
1374623 ATTATTTAT-TTATAATTTATATTTAATAT
1 ATTATTTATATTA-AATTGAAATATAATAT
*
1374652 ATTATTTTTATTAAATTGAAATATAATAT
1 ATTATTTATATTAAATTGAAATATAATAT
*
1374681 ATTAATTATATT
1 ATTATTTATATT
1374693 TTTTATAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 31 0.91
30 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (29 bp):
ATTATTTATATTAAATTGAAATATAATAT
Found at i:1375314 original size:29 final size:29
Alignment explanation
Indices: 1375248--1375318 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 29
1375238 ATATATTCTT
1375248 TTTTTAATTTAATAAAAGTAATAAATTAA
1 TTTTTAATTTAATAAAAGTAATAAATTAA
* * * *
1375277 ATATAAATTT-TTAAAAGATAATGAAA-TAA
1 TTTTTAATTTAATAAAAG-TAAT-AAATTAA
1375306 TTTTTAA-TTAATA
1 TTTTTAATTTAATA
1375319 TTTATCAACT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
28 8 0.26
29 20 0.65
30 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (29 bp):
TTTTTAATTTAATAAAAGTAATAAATTAA
Found at i:1382960 original size:8 final size:8
Alignment explanation
Indices: 1382949--1382977 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1382939 GGATTTAAAA
1382949 ATTTATAT
1 ATTTATAT
1382957 ATTTATAT
1 ATTTATAT
1382965 ATTTATAT
1 ATTTATAT
1382973 ATTTA
1 ATTTA
1382978 AATTATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTATAT
Found at i:1383048 original size:29 final size:29
Alignment explanation
Indices: 1383004--1383085 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
1382994 AAAATATTTT
*
1383004 TTTGGGTCAGAGTAAAAGATAATTAAATA
1 TTTGGGTCAGAATAAAAGATAATTAAATA
1383033 TTTGGGTCAGAATAAAAGATAATTAAATA
1 TTTGGGTCAGAATAAAAGATAATTAAATA
1383062 TTTGGGTCAGAATAAAAGATAATT
1 TTTGGGTCAGAATAAAAGATAATT
1383086 GAATTATAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.32
Consensus pattern (29 bp):
TTTGGGTCAGAATAAAAGATAATTAAATA
Found at i:1383542 original size:2 final size:2
Alignment explanation
Indices: 1383535--1383561 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1383525 ATATGCTTTA
1383535 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1383562 CTTGCAAGTG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1384591 original size:36 final size:34
Alignment explanation
Indices: 1384532--1384610 Score: 88
Period size: 36 Copynumber: 2.3 Consensus size: 34
1384522 TTTAGTTATG
* * *
1384532 TATATTAAATTTAAATAAATTAAAAATATATAATTA
1 TATATTTAATATAAATAAATT-AAAATAT-TAAATA
*
1384568 TTTATTTAATATAAA-AAATTTAAAATATTAAATA
1 TATATTTAATATAAATAAA-TTAAAATATTAAATA
1384602 TATATTTAA
1 TATATTTAA
1384611 AAATAATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 13 0.35
35 10 0.27
36 14 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
TATATTTAATATAAATAAATTAAAATATTAAATA
Found at i:1385437 original size:13 final size:14
Alignment explanation
Indices: 1385410--1385438 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1385400 GATAAAAAAT
1385410 TTTAAATATTTAAA
1 TTTAAATATTTAAA
1385424 TTTAAATA-TTAAA
1 TTTAAATATTTAAA
1385437 TT
1 TT
1385439 AATTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAAATATTTAAA
Found at i:1385924 original size:2 final size:2
Alignment explanation
Indices: 1385917--1385955 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1385907 TACGTGCGTG
1385917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1385956 GGATAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1388167 original size:29 final size:30
Alignment explanation
Indices: 1388054--1388161 Score: 114
Period size: 29 Copynumber: 3.7 Consensus size: 30
1388044 GTACACATAC
* * *
1388054 TTTTA-TTATATTTAAATAAATTTTTAACT
1 TTTTATTTATATCTAAATAAACTCTTAACT
* * *
1388083 TTTTATTTGTAT-TAAACAAACCCTTAACT
1 TTTTATTTATATCTAAATAAACTCTTAACT
* * *
1388112 TTTAATTTACA-CTAAATAAGCTCTTAACT
1 TTTTATTTATATCTAAATAAACTCTTAACT
1388141 TTTTATTTATATCTAAATAAA
1 TTTTATTTATATCTAAATAAA
1388162 TTTTAATATT
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
29 49 0.79
30 13 0.21
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (30 bp):
TTTTATTTATATCTAAATAAACTCTTAACT
Found at i:1388364 original size:261 final size:263
Alignment explanation
Indices: 1387898--1388429 Score: 759
Period size: 261 Copynumber: 2.0 Consensus size: 263
1387888 AGAATTACTT
* * * * * * *
1387898 ATTTTAATGTTAATTTATTGATTTTTACTTTATGATTGATAGTAAAAAAATATGCTTCTTGATCT
1 ATTTTAATATTAATTTATCGATTTATACTTCATAATCGATAATAAAAAAATATGCTTCTTGATCT
* * **
1387963 ATCATTATTGACTATTTTTTTATTTTTGACTAAATTAATAATTAAAAAAACTCTAAAATTTTATC
66 ATAATTATTGACTATTTTTTAATCATTGACTAAATTAATAATTAAAAAAACTCTAAAATTTTATC
* *
1388028 ACTTTATTCAAATTAAGTACACATACTTTTATTATATTTAAATAAATTTTTAACTTTTTATTTGT
131 ACTTTATTCAAATTAAGTACACATACTTTTATTACATTCAAATAAATTTTTAACTTTTTATTTGT
* * *
1388093 ATTAAACAAACCCTTAACTTTTAATTTACACTAAATAAGCTCTTAACTTTTTATTTATATCTAAA
196 ATCAAACAAACCCTTAACCTTTAATTTACACTAAATAAGCTCTTAACTTTTTATTTATACCTAAA
1388158 TAA
261 TAA
*
1388161 ATTTTAATATTAATTTATCGATTTATACTTCATAATCGATAAT-AAAAAATATGCTTCTTGGTCT
1 ATTTTAATATTAATTTATCGATTTATACTTCATAATCGATAATAAAAAAATATGCTTCTTGATCT
* *
1388225 ATAATTATTGAC-AGCTTTTTTAATCATTGATTAAATTAATAATT-AAAAAATTCTAAAATTTTA
66 ATAATTATTGACTA--TTTTTTAATCATTGACTAAATTAATAATTAAAAAAACTCTAAAATTTTA
* * *
1388288 TCATTTTATTTAAA-TAAGTACATC-TATTTTTATTACATTCAAATAAATTTTTAACTTTTTATT
129 TCACTTTATTCAAATTAAGTACA-CATACTTTTATTACATTCAAATAAATTTTTAACTTTTTATT
* * * *
1388351 TGTATCAAACAAACTCTTAACCTTTAATTTATACTAAATAGGCTCTTAATTTTTTATTTATACCT
193 TGTATCAAACAAACCCTTAACCTTTAATTTACACTAAATAAGCTCTTAACTTTTTATTTATACCT
1388416 AAATAA
258 AAATAA
1388422 ACTTTTAA
1 A-TTTTAA
1388430 CCTTTAATTT
Statistics
Matches: 239, Mismatches: 26, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
261 110 0.46
262 68 0.28
263 61 0.26
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.47
Consensus pattern (263 bp):
ATTTTAATATTAATTTATCGATTTATACTTCATAATCGATAATAAAAAAATATGCTTCTTGATCT
ATAATTATTGACTATTTTTTAATCATTGACTAAATTAATAATTAAAAAAACTCTAAAATTTTATC
ACTTTATTCAAATTAAGTACACATACTTTTATTACATTCAAATAAATTTTTAACTTTTTATTTGT
ATCAAACAAACCCTTAACCTTTAATTTACACTAAATAAGCTCTTAACTTTTTATTTATACCTAAA
TAA
Found at i:1388370 original size:29 final size:30
Alignment explanation
Indices: 1388328--1388450 Score: 97
Period size: 29 Copynumber: 4.2 Consensus size: 30
1388318 TATTACATTC
* * * * *
1388328 AAATAAATTTTTAACTTTTTATTTGTATC-
1 AAATAAACTCTTAACCTTTAATTTATATCT
*
1388357 AAACAAACTCTTAACCTTTAATTTATA-CT
1 AAATAAACTCTTAACCTTTAATTTATATCT
** ** * *
1388386 AAATAGGCTCTTAATTTTTTATTTATACCT
1 AAATAAACTCTTAACCTTTAATTTATATCT
* * *
1388416 AAATAAACTTTTAACCTTTAATTTGTATTT
1 AAATAAACTCTTAACCTTTAATTTATATCT
1388446 AAATA
1 AAATA
1388451 GATCCCTAAC
Statistics
Matches: 71, Mismatches: 21, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
28 1 0.01
29 42 0.59
30 28 0.39
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.47
Consensus pattern (30 bp):
AAATAAACTCTTAACCTTTAATTTATATCT
Found at i:1388450 original size:30 final size:29
Alignment explanation
Indices: 1388361--1388439 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
1388351 TGTATCAAAC
1388361 AAACTCTTAACCTTTAATTTATACTAAAT
1 AAACTCTTAACCTTTAATTTATACTAAAT
** ** *
1388390 AGGCTCTTAATTTTTTATTTATACCTAAAT
1 AAACTCTTAACCTTTAATTTATA-CTAAAT
*
1388420 AAACTTTTAACCTTTAATTT
1 AAACTCTTAACCTTTAATTT
1388440 GTATTTAAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
29 18 0.47
30 20 0.53
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (29 bp):
AAACTCTTAACCTTTAATTTATACTAAAT
Found at i:1394092 original size:20 final size:20
Alignment explanation
Indices: 1394059--1394122 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1394049 TTAAATTAAC
* * *
1394059 TCTAAACCTCAACCTTAAAT
1 TCTAATCCTAAACCCTAAAT
1394079 TCTAATCCTAAACCCTAAAT
1 TCTAATCCTAAACCCTAAAT
* * *
1394099 TTTAATCATAAACACT-AAT
1 TCTAATCCTAAACCCTAAAT
1394118 TCTAA
1 TCTAA
1394123 ACCCTTAATC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 7 0.19
20 30 0.81
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (20 bp):
TCTAATCCTAAACCCTAAAT
Found at i:1395399 original size:4 final size:4
Alignment explanation
Indices: 1395384--1395426 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
1395374 TTGATGCCTT
* * * *
1395384 TATA TGTA TATA TATA CATA TATA TATA TATA CATA CATA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
1395427 CATTTTTAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (4 bp):
TATA
Found at i:1395409 original size:16 final size:16
Alignment explanation
Indices: 1395385--1395426 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1395375 TGATGCCTTT
*
1395385 ATATGTATATATATAC
1 ATATATATATATATAC
1395401 ATATATATATATATAC
1 ATATATATATATATAC
*
1395417 ATACATATAT
1 ATATATATAT
1395427 CATTTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATATATATATATAC
Found at i:1396276 original size:14 final size:15
Alignment explanation
Indices: 1396257--1396295 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1396247 TTATATTTAA
*
1396257 AAATTTTAAAAATT-
1 AAATTTAAAAAATTG
1396271 AAATTTAAAAAATTG
1 AAATTTAAAAAATTG
1396286 AAA-TTAAAAA
1 AAATTTAAAAA
1396296 TCTTACATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 20 0.87
15 3 0.13
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAATTTAAAAAATTG
Found at i:1396727 original size:18 final size:18
Alignment explanation
Indices: 1396695--1396762 Score: 82
Period size: 18 Copynumber: 3.6 Consensus size: 18
1396685 AATGGTCGTT
*
1396695 ATAATTAAAAATAATATTA
1 ATAA-TAAAATTAATATTA
1396714 ATAATAAAATTAATTATTATA
1 ATAATAAAATTAA-TA-T-TA
*
1396735 ATAATAAAATTAAAATTA
1 ATAATAAAATTAATATTA
1396753 ATAATAAAAT
1 ATAATAAAAT
1396763 ATATTATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
18 20 0.45
19 7 0.16
20 2 0.05
21 15 0.34
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATAAAATTAATATTA
Found at i:1396738 original size:21 final size:20
Alignment explanation
Indices: 1396711--1396773 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
1396701 AAAAATAATA
1396711 TTAATAATAAAATTAATTAT
1 TTAATAATAAAATTAATTAT
*
1396731 TATAATAATAAAATTAA--AA
1 T-TAATAATAAAATTAATTAT
1396750 TTAATAATAAAA-TATATTAT
1 TTAATAATAAAATTA-ATTAT
1396770 TTAA
1 TTAA
1396774 ATGCAAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 2 0.05
18 12 0.32
19 2 0.05
20 6 0.16
21 15 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATAATAAAATTAATTAT
Found at i:1396753 original size:39 final size:40
Alignment explanation
Indices: 1396695--1396770 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
1396685 AATGGTCGTT
*
1396695 ATAATTAAAAATAATATTAATAATAAAAT-TAATTATTATA
1 ATAATTAAAAATAAAATTAATAATAAAATAT-ATTATTATA
*
1396735 ATAA-TAAAATTAAAATTAATAATAAAATATATTATT
1 ATAATTAAAAATAAAATTAATAATAAAATATATTATT
1396771 TAAATGCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 28 0.85
40 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (40 bp):
ATAATTAAAAATAAAATTAATAATAAAATATATTATTATA
Found at i:1396916 original size:17 final size:17
Alignment explanation
Indices: 1396894--1396940 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1396884 TTTTAATACA
*
1396894 TATTTATTTTATATATT
1 TATTTATTTTATATAAT
**
1396911 TATTTAAATTATATAAT
1 TATTTATTTTATATAAT
*
1396928 TAATTATTTTATA
1 TATTTATTTTATA
1396941 ATTATATAGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTATTTTATATAAT
Found at i:1397478 original size:19 final size:18
Alignment explanation
Indices: 1397454--1397510 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
1397444 AATTAATAAT
1397454 TAATAA-AATAAAATTATCA
1 TAATAATAATAAAA-TAT-A
*
1397473 TAATAATTATAAAATATA
1 TAATAATAATAAAATATA
*
1397491 TAAT-ATTATAAAAATATA
1 TAATAATAAT-AAAATATA
1397509 TA
1 TA
1397511 TTTTGTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
17 5 0.14
18 15 0.43
19 9 0.26
20 6 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAATAATAAAATATA
Found at i:1397495 original size:18 final size:17
Alignment explanation
Indices: 1397461--1397510 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 17
1397451 AATTAATAAA
1397461 ATAAAATTATCATAATAATT
1 ATAAAA-TAT-ATAAT-ATT
1397481 ATAAAATATATAATATT
1 ATAAAATATATAATATT
1397498 ATAAAAATATATA
1 AT-AAAATATATA
1397511 TTTTGTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.17
18 15 0.52
19 3 0.10
20 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAATATATAATATT
Found at i:1397693 original size:16 final size:17
Alignment explanation
Indices: 1397672--1397703 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1397662 TAAATTTAAA
1397672 TAAAT-AATTTAATTTT
1 TAAATAAATTTAATTTT
1397688 TAAATAAATTTAATTT
1 TAAATAAATTTAATTT
1397704 AAACTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATAAATTTAATTTT
Found at i:1397711 original size:20 final size:18
Alignment explanation
Indices: 1397664--1397711 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1397654 TAAATTTTTA
1397664 AATTTAAATAAATAATTT
1 AATTTAAATAAATAATTT
*
1397682 AATTT--TTAAATAAATTT
1 AATTTAAATAAAT-AATTT
1397699 AATTTAAACTAAA
1 AATTTAAA-TAAA
1397712 AAAGGTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
16 5 0.21
17 10 0.42
18 5 0.21
20 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAAATAAATAATTT
Found at i:1397886 original size:12 final size:12
Alignment explanation
Indices: 1397860--1397923 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
1397850 CAAATTAAAC
* *
1397860 AAAATAAATTTA
1 AAAATAAAATAA
*
1397872 AAAATTAAATAA
1 AAAATAAAATAA
1397884 AAAATAAAAT--
1 AAAATAAAATAA
1397894 AAAAT-AAATAA
1 AAAATAAAATAA
1397905 AAATATCAAAATAA
1 AAA-AT-AAAATAA
1397919 TAAAA
1 -AAAA
1397924 AATATCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 4 0.10
10 5 0.12
11 3 0.07
12 20 0.48
14 7 0.17
15 3 0.07
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:1397903 original size:21 final size:23
Alignment explanation
Indices: 1397872--1397927 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 23
1397862 AATAAATTTA
1397872 AAAATTAAATAAAAA-AT-AAAAT
1 AAAA-TAAATAAAAATATCAAAAT
1397894 AAAATAAATAAAAATATCAAAAT
1 AAAATAAATAAAAATATCAAAAT
*
1397917 AATAAAAAATA
1 AA-AATAAATA
1397928 TCAAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 10 0.33
22 6 0.20
23 7 0.23
24 7 0.23
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (23 bp):
AAAATAAATAAAAATATCAAAAT
Found at i:1397917 original size:18 final size:18
Alignment explanation
Indices: 1397894--1397934 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1397884 AAAATAAAAT
1397894 AAAATAA-ATAAAAATATC
1 AAAATAATA-AAAAATATC
1397912 AAAATAATAAAAAATATC
1 AAAATAATAAAAAATATC
1397930 AAAAT
1 AAAAT
1397935 TTATATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAATAATAAAAAATATC
Found at i:1397963 original size:49 final size:49
Alignment explanation
Indices: 1397907--1398005 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 49
1397897 ATAAATAAAA
*
1397907 ATATCAAA-ATAATAAAAAATATCAA-AA-TTTATATAATAAAAATTAATAT
1 ATATCAAATATAAT-AAAAATATAAATAATTTTA-AT-ATAAAAATTAATAT
* * *
1397956 ATATCAAATTTCATAAAATTATAAATAATTTTAATATAAAAATTAATAT
1 ATATCAAATATAATAAAAATATAAATAATTTTAATATAAAAATTAATAT
1398005 A
1 A
1398006 AAAATTAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
49 32 0.74
50 7 0.16
51 4 0.09
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (49 bp):
ATATCAAATATAATAAAAATATAAATAATTTTAATATAAAAATTAATAT
Found at i:1398001 original size:12 final size:12
Alignment explanation
Indices: 1397986--1398015 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1397976 ATAAATAATT
1397986 TTAATATAAAAA
1 TTAATATAAAAA
1397998 TTAATATAAAAA
1 TTAATATAAAAA
1398010 TTAATA
1 TTAATA
1398016 AATTTATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAATATAAAAA
Found at i:1398517 original size:2 final size:2
Alignment explanation
Indices: 1398510--1398539 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1398500 CCACGAAATT
1398510 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1398540 CGCAGTTTGC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1399433 original size:2 final size:2
Alignment explanation
Indices: 1399426--1399454 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1399416 AAATTGAAGA
1399426 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1399455 TATTGAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1401120 original size:2 final size:2
Alignment explanation
Indices: 1401115--1401144 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1401105 AGTCTTTTTT
1401115 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
1401145 AAACAGGGAG
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):
TA
Found at i:1403919 original size:2 final size:2
Alignment explanation
Indices: 1403912--1403939 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1403902 TGTTGACTGC
1403912 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
1403940 GTATTTTTTT
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:1407376 original size:2 final size:2
Alignment explanation
Indices: 1407371--1407400 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1407361 GTTTCAAAAA
*
1407371 AT AT AT AA 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
1407401 TAGTGCTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1413666 original size:15 final size:15
Alignment explanation
Indices: 1413646--1413684 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1413636 TTGTTTTCTT
* *
1413646 AATTTTTTATTTTTA
1 AATTTTTTATATTAA
1413661 AATTTTTTATATTAA
1 AATTTTTTATATTAA
*
1413676 AAATTTTTA
1 AATTTTTTA
1413685 AATATTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
AATTTTTTATATTAA
Found at i:1413816 original size:19 final size:18
Alignment explanation
Indices: 1413781--1413826 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
1413771 ATTCATATCG
1413781 TATTATTATTATTTTTTTA
1 TATTA-TATTATTTTTTTA
*
1413800 TGTTATATTATTATTTTTA
1 TATTATATTATT-TTTTTA
1413819 TATTATAT
1 TATTATAT
1413827 CTAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TATTATATTATTTTTTTA
Found at i:1414980 original size:20 final size:20
Alignment explanation
Indices: 1414957--1415022 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
1414947 TATTATTTAA
1414957 AAATTTAAAAAATTATAATT
1 AAATTTAAAAAATTATAATT
* *
1414977 AAATTTAAATAAA-AATTATT
1 AAATTTAAA-AAATTATAATT
** *
1414997 TTATTTATAAAATTATAATCT
1 AAATTTAAAAAATTATAAT-T
1415018 AAATT
1 AAATT
1415023 AAATTATTTA
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
19 3 0.09
20 24 0.71
21 7 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTTAAAAAATTATAATT
Found at i:1416622 original size:139 final size:140
Alignment explanation
Indices: 1416473--1416749 Score: 477
Period size: 141 Copynumber: 2.0 Consensus size: 140
1416463 AATTTTGATT
* *
1416473 ATTAACATTTTAAATATTTTATTAAACTAATTTTTTATAAAGTTATATTT-AAAAACCTATTTAT
1 ATTAACATTTTAAATATTTTATTAAACTAAATTTTTATAAAGTTATATTTAAAAAACCTATTCAT
*
1416537 TCAAGGTTTATGAA-TTTTTTTTAATTTTAAATATATTTACAATAAAATAAAACCAAACTTGAAT
66 TCAAGGTTTATGAATTTTTTTTTAATTTTAAATATATTTACAATAAAATAAAACAAAACTTGAAT
1416601 TTGACTTTCAA
131 TTGA-TTTCAA
* *
1416612 ATTAAGATTTTAAATATTTTATTAAACTAAATTTTTATAAAGTTATATTTAAAAAACTTATTCAT
1 ATTAACATTTTAAATATTTTATTAAACTAAATTTTTATAAAGTTATATTTAAAAAACCTATTCAT
*
1416677 TCAAGGTTTATGAATTTTTTTTTAATTTTAAATATATTTACAATAAAATAAAACAAAACTTTAAT
66 TCAAGGTTTATGAATTTTTTTTTAATTTTAAATATATTTACAATAAAATAAAACAAAACTTGAAT
1416742 TTGATTTC
131 TTGATTTC
1416750 TTAAAATTCA
Statistics
Matches: 130, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
139 48 0.37
140 30 0.23
141 52 0.40
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (140 bp):
ATTAACATTTTAAATATTTTATTAAACTAAATTTTTATAAAGTTATATTTAAAAAACCTATTCAT
TCAAGGTTTATGAATTTTTTTTTAATTTTAAATATATTTACAATAAAATAAAACAAAACTTGAAT
TTGATTTCAA
Found at i:1417639 original size:17 final size:17
Alignment explanation
Indices: 1417616--1417655 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1417606 TTGTATGTTT
1417616 ATTTATTAATTATATAA
1 ATTTATTAATTATATAA
* * *
1417633 TTTTATTTATTATTTAA
1 ATTTATTAATTATATAA
1417650 ATTTAT
1 ATTTAT
1417656 CACGTTATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTATTAATTATATAA
Found at i:1417900 original size:14 final size:14
Alignment explanation
Indices: 1417881--1417929 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
1417871 ATTTTTTTAA
1417881 TTTTTAAAATATAT
1 TTTTTAAAATATAT
*
1417895 TTTTTAAAAAATAT
1 TTTTTAAAATATAT
*
1417909 TTTTTAAAATGTAT
1 TTTTTAAAATATAT
1417923 GTTTTTA
1 -TTTTTA
1417930 CGAATCTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
14 25 0.81
15 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (14 bp):
TTTTTAAAATATAT
Found at i:1418764 original size:67 final size:66
Alignment explanation
Indices: 1418661--1418798 Score: 172
Period size: 67 Copynumber: 2.1 Consensus size: 66
1418651 TAAATGTAAT
* *
1418661 TAATACATATATTGCTATGAAAATTAGATTCATTCTGATAT-AAAAAAAGTTGATAAAATTAATA
1 TAATACATATATTGCTATGAAAATCAGATTCATTCTGATATGAAAAAAA-TTGATAAAACTAATA
1418725 AA
65 AA
* * * *
1418727 TAATGCATATATT-CTTGATGAGAATCAGATTCCTTCTGATATGAAAAAAATTGATAAGACTAAT
1 TAATACATATATTGC-T-ATGAAAATCAGATTCATTCTGATATGAAAAAAATTGATAAAACTAAT
*
1418791 ACA
64 AAA
1418794 TAATA
1 TAATA
1418799 GTAAATGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
65 1 0.02
66 13 0.21
67 40 0.66
68 7 0.11
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (66 bp):
TAATACATATATTGCTATGAAAATCAGATTCATTCTGATATGAAAAAAATTGATAAAACTAATAA
A
Found at i:1418970 original size:92 final size:92
Alignment explanation
Indices: 1418800--1418981 Score: 235
Period size: 92 Copynumber: 2.0 Consensus size: 92
1418790 TACATAATAG
*
1418800 TAAATGTCAGACTACAAAAATTAGACTAATACATAAATTATATTTGAGAATCAGATTTCTTTTGG
1 TAAATGTCAGACTACAAAAATTAGACTAATACATAAATTATATTTGAGAATCACATTTCTTTTGG
* **
1418865 TAGATAAAAAGAAATTTTGATTGATCA
66 TAGAAAAAAAGAAAAGTTGATTGATCA
** * * *
1418892 TAAATGTCAGACTGTAAGAATTAGACTAATATATAAATTATA-TTGAGAATCACA-TTCTTTTTT
1 TAAATGTCAGACTACAAAAATTAGACTAATACATAAATTATATTTGAGAATCACATTTC-TTTTG
1418955 GT-GAAAAAAAGAGAAAAGTTGATTGAT
65 GTAG-AAAAAA-AGAAAAGTTGATTGAT
1418982 TGTAAATATT
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
90 4 0.05
91 22 0.28
92 52 0.67
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (92 bp):
TAAATGTCAGACTACAAAAATTAGACTAATACATAAATTATATTTGAGAATCACATTTCTTTTGG
TAGAAAAAAAGAAAAGTTGATTGATCA
Found at i:1419674 original size:4 final size:4
Alignment explanation
Indices: 1419667--1419701 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1419657 TTTTTTTTGT
*
1419667 TTTC TTTC TTTC -TTC TTTC TTTC TTTC TTTA TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1419702 CTTGTTCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:1419685 original size:15 final size:15
Alignment explanation
Indices: 1419667--1419695 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1419657 TTTTTTTTGT
1419667 TTTCTTTCTTTCTTC
1 TTTCTTTCTTTCTTC
1419682 TTTCTTTCTTTCTT
1 TTTCTTTCTTTCTT
1419696 TATTTCCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCTTTCTTTCTTC
Found at i:1419919 original size:75 final size:72
Alignment explanation
Indices: 1419796--1420003 Score: 235
Period size: 74 Copynumber: 2.9 Consensus size: 72
1419786 TCGTGTCTAG
*
1419796 AAATTTAAATTTGTATAATCAA-ACTAAAAAATA-AATTTTAAATTTTTACAATTAAAAATAAAT
1 AAATTTAAATTTGTATAATCAACA-TAAAAAA-ACAA-TTTAAATTTTTACAAATAAAAATAAAT
1419859 TATACCATAAA
63 TATACCAT-AA
* * *
1419870 AAATTTAAATTTATATAATCATACATAAAAAAACACATTTAAATTTTTACAAATCAAAATAAGTT
1 AAATTTAAATTTGTATAATCA-ACATAAAAAAACA-ATTTAAATTTTTACAAATAAAAATAAATT
*
1419935 ATACCCTAA
64 ATACCATAA
* * * * * *
1419944 AAATTTAAACTCGCATAATCAA-ATAAAAACA-AATTTAAACTTTTATAAATAAAAATAAAT
1 AAATTTAAATTTGTATAATCAACATAAAAAAACAATTTAAATTTTTACAAATAAAAATAAAT
1420004 AATAACTTTG
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
70 24 0.21
71 1 0.01
72 8 0.07
73 1 0.01
74 40 0.34
75 40 0.34
76 2 0.02
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (72 bp):
AAATTTAAATTTGTATAATCAACATAAAAAAACAATTTAAATTTTTACAAATAAAAATAAATTAT
ACCATAA
Found at i:1420453 original size:73 final size:75
Alignment explanation
Indices: 1420302--1420445 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 75
1420292 ATTTAAAATT
* ** *
1420302 TTTTATTTTATTAAATAATTAATAATTAATAATTTGAATTTTTATACAATTTTTTTCAAATTTAA
1 TTTTATTTTATTAAATAATTAAAAATTAATAATTTGAATTTCAATACAATTTTTTTAAAATTTAA
1420367 TTAAATAAAA
66 TTAAATAAAA
*
1420377 TTTTATTTTATTAAA-AATTAAAAATTAATACA-TT-AATTTCAATATGAA-TTTTTTAAAATTT
1 TTTTATTTTATTAAATAATTAAAAATTAATA-ATTTGAATTTCAATA-CAATTTTTTTAAAATTT
1420438 AATTAAAT
64 AATTAAAT
1420446 TTTATTTTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
73 28 0.45
74 18 0.29
75 16 0.26
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (75 bp):
TTTTATTTTATTAAATAATTAAAAATTAATAATTTGAATTTCAATACAATTTTTTTAAAATTTAA
TTAAATAAAA
Found at i:1420578 original size:13 final size:12
Alignment explanation
Indices: 1420551--1420575 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1420541 AATATATTCG
1420551 TAAAAAATATTT
1 TAAAAAATATTT
1420563 TAAAAAATATTT
1 TAAAAAATATTT
1420575 T
1 T
1420576 TAAGAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATATTT
Found at i:1420826 original size:14 final size:15
Alignment explanation
Indices: 1420795--1420830 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1420785 CCTAAATCAA
1420795 TTAATTTAATTAATT
1 TTAATTTAATTAATT
*
1420810 TTAATTTGATT-ATT
1 TTAATTTAATTAATT
1420824 TTAATTT
1 TTAATTT
1420831 TTTTAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TTAATTTAATTAATT
Found at i:1426937 original size:34 final size:34
Alignment explanation
Indices: 1426894--1426961 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
1426884 GTGATCATCA
1426894 GACTTTTTGTTTTGTCTATAACATTTTCTTTCTT
1 GACTTTTTGTTTTGTCTATAACATTTTCTTTCTT
*
1426928 GACTTTTTGTTTTGTCTTTAACATTTTCTTTCTT
1 GACTTTTTGTTTTGTCTATAACATTTTCTTTCTT
1426962 TAGTTTCCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.13, C:0.15, G:0.09, T:0.63
Consensus pattern (34 bp):
GACTTTTTGTTTTGTCTATAACATTTTCTTTCTT
Found at i:1429689 original size:3 final size:3
Alignment explanation
Indices: 1429681--1429724 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1429671 CCATGGTATA
1429681 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1429725 ATAAATAATA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1430084 original size:38 final size:38
Alignment explanation
Indices: 1430028--1430103 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
1430018 GTCATTCGTC
*
1430028 CTGGAAACATGTGAAACTTTGATTT-GAATGGTTAAATA
1 CTGGAAACATGTGAAACTTT-ATTTCGAATGATTAAATA
* *
1430066 CTGGTAACATGTGAAACTTTATTTCGATTGATTAAATA
1 CTGGAAACATGTGAAACTTTATTTCGAATGATTAAATA
1430104 TTTCGAGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 4 0.12
38 30 0.88
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (38 bp):
CTGGAAACATGTGAAACTTTATTTCGAATGATTAAATA
Found at i:1430648 original size:2 final size:2
Alignment explanation
Indices: 1430637--1430681 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1430627 GAAGAAAGTG
1430637 TA TA TA -A 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
1430678 TA TA
1 TA TA
1430682 GAGAGAGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1430738 original size:2 final size:2
Alignment explanation
Indices: 1430681--1430719 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1430671 ATATATATAT
1430681 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1430720 TTAATTGACC
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1434316 original size:23 final size:23
Alignment explanation
Indices: 1434274--1434317 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1434264 TTTTAAATAA
*
1434274 ATTTAAATAAAAATATTTTTATT
1 ATTTAAATAAAAATAATTTTATT
1434297 ATTTAAA-AAAAATAAATTTTA
1 ATTTAAATAAAAAT-AATTTTA
1434318 AGTCGTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTAAATAAAAATAATTTTATT
Found at i:1435708 original size:17 final size:17
Alignment explanation
Indices: 1435653--1435704 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
1435643 GAAATTAAAT
1435653 TTAAATTTTAATATTTATA
1 TTAAATTTTAAT-TTT-TA
*
1435672 TT--TTTTTAATTTTTA
1 TTAAATTTTAATTTTTA
1435687 TTAAATTTT-ATTTTTA
1 TTAAATTTTAATTTTTA
1435703 TT
1 TT
1435705 TAAAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 4 0.14
16 12 0.41
17 11 0.38
19 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTAAATTTTAATTTTTA
Found at i:1438329 original size:18 final size:16
Alignment explanation
Indices: 1438298--1438337 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
1438288 ATTTTAGATG
1438298 AAATTTTTATAAATTT
1 AAATTTTTATAAATTT
1438314 AAATTTTTAAATAAATTT
1 AAATTTTT--ATAAATTT
1438332 AAATTT
1 AAATTT
1438338 AATTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTTTTATAAATTT
Found at i:1438332 original size:10 final size:10
Alignment explanation
Indices: 1438306--1438374 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
1438296 TGAAATTTTT
1438306 ATAAATTTAA
1 ATAAATTTAA
*
1438316 AT--TTTTAA
1 ATAAATTTAA
1438324 ATAAATTTAA
1 ATAAATTTAA
*
1438334 ATTTAATTTAA
1 A-TAAATTTAA
*
1438345 ATAAAATTAA
1 ATAAATTTAA
* *
1438355 AAAAAATTAA
1 ATAAATTTAA
*
1438365 A-AATTTTAA
1 ATAAATTTAA
1438374 A
1 A
1438375 CTGCAATCCG
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
8 7 0.15
9 7 0.15
10 25 0.52
11 9 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATAAATTTAA
Found at i:1438362 original size:21 final size:21
Alignment explanation
Indices: 1438319--1438362 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1438309 AATTTAAATT
* ***
1438319 TTTAAATAAATTTAAATTTAA
1 TTTAAATAAAATTAAAAAAAA
1438340 TTTAAATAAAATTAAAAAAAA
1 TTTAAATAAAATTAAAAAAAA
1438361 TT
1 TT
1438363 AAAAATTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTAAATAAAATTAAAAAAAA
Found at i:1438984 original size:28 final size:29
Alignment explanation
Indices: 1438935--1438996 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
1438925 TTTAATTTTT
*
1438935 TATATATATTTAAAAAATTAT-AATTATA
1 TATATATATTTAAAAAATTATAAATGATA
*
1438963 TATATATATTT-AAATATATATAAATGATA
1 TATATATATTTAAAAAAT-TATAAATGATA
1438992 TATAT
1 TATAT
1438997 TAGATGCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 5 0.17
28 14 0.47
29 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATATATATTTAAAAAATTATAAATGATA
Found at i:1441555 original size:22 final size:22
Alignment explanation
Indices: 1441530--1441571 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1441520 TATGTTTAAT
1441530 TAAAT-TTAATTATTAAAATATA
1 TAAATATTAA-TATTAAAATATA
1441552 TAAATATTAATATTAAAATA
1 TAAATATTAATATTAAAATA
1441572 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATTAATATTAAAATATA
Done.