Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 4 of 328
Found at i:1037317 original size:53 final size:53
Alignment explanation
Indices: 1037236--1037381 Score: 204
Period size: 53 Copynumber: 2.7 Consensus size: 53
1037226 CTTACACGGT
* *
1037236 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
1037291 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
1037344 TCACATTGCACTGATGCCATAGCCCAGCTATGGTCTTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTA
1037382 AACAGGCGCA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 76 0.90
54 1 0.01
55 6 0.07
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:1044078 original size:3 final size:3
Alignment explanation
Indices: 1044070--1044100 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1044060 GCAAAGACGA
1044070 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1044101 TAACATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1044334 original size:3 final size:3
Alignment explanation
Indices: 1044328--1044398 Score: 56
Period size: 3 Copynumber: 24.0 Consensus size: 3
1044318 GTAGCAGTAT
** * * *
1044328 ATA ATA ATA ATA ATA ATA ATA ACC GTA GTA GTA ATA A-A AGT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
* *
1044372 ATA GTA ATG ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1044399 TAAAATATAG
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
2 3 0.05
3 52 0.95
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1044567 original size:3 final size:3
Alignment explanation
Indices: 1044559--1044638 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
1044549 TGAAAATATT
1044559 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1044607 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1044639 GGTGTTAGAC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1045612 original size:23 final size:23
Alignment explanation
Indices: 1045577--1045620 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1045567 TGCAGGTGGA
*
1045577 ACAAGTGGAGGAGCAGGTGGTTG
1 ACAAGCGGAGGAGCAGGTGGTTG
*
1045600 ACAAGCGGTGGAGCAGGTGGT
1 ACAAGCGGAGGAGCAGGTGGT
1045621 CAGAAGGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.48, T:0.16
Consensus pattern (23 bp):
ACAAGCGGAGGAGCAGGTGGTTG
Found at i:1046870 original size:15 final size:15
Alignment explanation
Indices: 1046846--1046890 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
1046836 CGATATAAAC
1046846 ATGAATAAATTAAATT
1 ATGAA-AAATTAAATT
*
1046862 ATGAAAAATTAAAAT
1 ATGAAAAATTAAATT
1046877 AT-AAAAATTAAATT
1 ATGAAAAATTAAATT
1046891 TAGTAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 11 0.41
15 11 0.41
16 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (15 bp):
ATGAAAAATTAAATT
Found at i:1046884 original size:14 final size:15
Alignment explanation
Indices: 1046846--1046888 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1046836 CGATATAAAC
*
1046846 ATGAATAAATTAAATT
1 ATGAA-AAATTAAAAT
1046862 ATGAAAAATTAAAAT
1 ATGAAAAATTAAAAT
1046877 AT-AAAAATTAAA
1 ATGAAAAATTAAA
1046889 TTTAGTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 10 0.38
15 11 0.42
16 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
ATGAAAAATTAAAAT
Found at i:1063086 original size:22 final size:22
Alignment explanation
Indices: 1063035--1063086 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
1063025 GCTATTTTGT
** * *
1063035 TACTATTTTTTCATTGTTTTGC
1 TACTATTTCGTCATTATATTGC
1063057 TA-TCATTTCGTCATTATATTGC
1 TACT-ATTTCGTCATTATATTGC
1063079 TACTATTT
1 TACTATTT
1063087 TGTTGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 22 0.92
23 1 0.04
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (22 bp):
TACTATTTCGTCATTATATTGC
Found at i:1063714 original size:20 final size:21
Alignment explanation
Indices: 1063668--1063720 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
1063658 TACTAATTAA
1063668 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
1063689 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
*
1063709 ATATATTCTAAT
1 AAATATT-TAAT
1063721 TAAATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.14
20 11 0.39
21 13 0.46
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:1063775 original size:30 final size:30
Alignment explanation
Indices: 1063735--1063791 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1063725 TTTTATAAAT
1063735 AATTAATA-TTTAT-TACTTAAAAATATTTTA
1 AATTAATATTTTATATA-TT-AAAATATTTTA
*
1063765 AATTTATATTTTATATATTAAAATATT
1 AATTAATATTTTATATATTAAAATATT
1063792 AACAAGAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 15 0.62
31 7 0.29
32 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
AATTAATATTTTATATATTAAAATATTTTA
Found at i:1067456 original size:11 final size:12
Alignment explanation
Indices: 1067440--1067468 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1067430 ATTCTTCAGT
1067440 TTTTTTG-TTTG
1 TTTTTTGTTTTG
1067451 TTTTTTGTTTTG
1 TTTTTTGTTTTG
1067463 TTTTTT
1 TTTTTT
1067469 AAGTGGCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (12 bp):
TTTTTTGTTTTG
Found at i:1073795 original size:63 final size:63
Alignment explanation
Indices: 1073691--1073824 Score: 252
Period size: 63 Copynumber: 2.1 Consensus size: 63
1073681 TTCAGGTCAT
*
1073691 GATTA-GTAGCTTTAGTCGATTCTTAGCTTCACAAATCTAATTGAATACATATATTGTTGCGG
1 GATTAGGTAGCTCTAGTCGATTCTTAGCTTCACAAATCTAATTGAATACATATATTGTTGCGG
1073753 GATTAGGTAGCTCTAGTCGATTCTTAGCTTCACAAATCTAATTGAATACATATATTGTTGCGG
1 GATTAGGTAGCTCTAGTCGATTCTTAGCTTCACAAATCTAATTGAATACATATATTGTTGCGG
1073816 GATTAGGTA
1 GATTAGGTA
1073825 TTGTATGGAG
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 5 0.07
63 65 0.93
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.37
Consensus pattern (63 bp):
GATTAGGTAGCTCTAGTCGATTCTTAGCTTCACAAATCTAATTGAATACATATATTGTTGCGG
Found at i:1077240 original size:25 final size:25
Alignment explanation
Indices: 1077207--1077270 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
1077197 AATTTGATAA
* * *
1077207 TTTTTTTCACATTGAAGTCTAAATT
1 TTTTTTTCAAATTAAAGTCTAAACT
* *
1077232 TTTTTTTCAAATTAAATTTTAAACT
1 TTTTTTTCAAATTAAAGTCTAAACT
1077257 TTTTTTTCTAAATT
1 TTTTTTTC-AAATT
1077271 TATCCTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 28 0.85
26 5 0.15
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTTTTTCAAATTAAAGTCTAAACT
Found at i:1082711 original size:19 final size:20
Alignment explanation
Indices: 1082687--1082737 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1082677 ATATATTTAA
1082687 AATTTAAATTTAAGAT-ATT
1 AATTTAAATTTAAGATAATT
*
1082706 AATTT-AATTTAATATAATT
1 AATTTAAATTTAAGATAATT
* *
1082725 AATATAATTTTAA
1 AATTTAAATTTAA
1082738 TTTTTTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.33
19 12 0.44
20 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AATTTAAATTTAAGATAATT
Found at i:1088654 original size:21 final size:23
Alignment explanation
Indices: 1088602--1088654 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
1088592 TGGAGTGTTA
1088602 ATAAGTT-ATTATTAAAGTTTCG
1 ATAAGTTAATTATTAAAGTTTCG
* *
1088624 TTAAG-AAATT-TTAAAGTTTCG
1 ATAAGTTAATTATTAAAGTTTCG
1088645 AT-AGTTAATT
1 ATAAGTTAATT
1088655 GAATAAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
20 2 0.08
21 16 0.64
22 7 0.28
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (23 bp):
ATAAGTTAATTATTAAAGTTTCG
Found at i:1090418 original size:51 final size:51
Alignment explanation
Indices: 1090342--1090455 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
1090332 AGTGACAAGC
* *
1090342 GACAAGCGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
*
1090393 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
1090444 GACAAGTGATAA
1 GACAAGTGATAA
1090456 ATGTGATCAG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (51 bp):
GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
Found at i:1093980 original size:48 final size:48
Alignment explanation
Indices: 1093913--1094009 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1093903 CAAACTTAAA
1093913 TTTTTCGCAAACTTATTTTCGAGTATAACAGTTTTGTTTGAACCATTT
1 TTTTTCGCAAACTTATTTTCGAGTATAACAGTTTTGTTTGAACCATTT
1093961 TTTTTCGCAAACTTATTTTCGAGTATAACAGTTTTGTTTGAACCATTT
1 TTTTTCGCAAACTTATTTTCGAGTATAACAGTTTTGTTTGAACCATTT
1094009 T
1 T
1094010 ATATATTAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.48
Consensus pattern (48 bp):
TTTTTCGCAAACTTATTTTCGAGTATAACAGTTTTGTTTGAACCATTT
Found at i:1096505 original size:14 final size:14
Alignment explanation
Indices: 1096486--1096515 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1096476 TCCAAAGATC
1096486 GAACCCGAGATTGA
1 GAACCCGAGATTGA
1096500 GAACCCGAGATTGA
1 GAACCCGAGATTGA
1096514 GA
1 GA
1096516 TACACTCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.13
Consensus pattern (14 bp):
GAACCCGAGATTGA
Found at i:1099219 original size:23 final size:24
Alignment explanation
Indices: 1099193--1099243 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1099183 TTTATGCATT
1099193 TAATTT-TTAATTAATTATT-TAAA
1 TAATTTATT-ATTAATTATTGTAAA
* *
1099216 TAATTTATTTTTAATTATTGTAAT
1 TAATTTATTATTAATTATTGTAAA
1099240 TAAT
1 TAAT
1099244 ACAAACTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TAATTTATTATTAATTATTGTAAA
Found at i:1100706 original size:20 final size:20
Alignment explanation
Indices: 1100668--1100725 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1100658 TATATTTGAA
1100668 ATAAAAAT-TTAATATATTTTT
1 ATAAAAATATTAA-A-ATTTTT
* *
1100689 GTAAAAATATTGAAATTTTT
1 ATAAAAATATTAAAATTTTT
*
1100709 ATAAATATATTAAAATT
1 ATAAAAATATTAAAATT
1100726 CTAAATATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 20 0.65
21 8 0.26
22 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
ATAAAAATATTAAAATTTTT
Found at i:1100881 original size:16 final size:16
Alignment explanation
Indices: 1100860--1100891 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1100850 TGAAAAACTG
1100860 AATAACACGATTAGAT
1 AATAACACGATTAGAT
1100876 AATAACACGATTAGAT
1 AATAACACGATTAGAT
1100892 TAACTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (16 bp):
AATAACACGATTAGAT
Found at i:1104546 original size:21 final size:21
Alignment explanation
Indices: 1104522--1104562 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1104512 TTATAGTAAG
1104522 TAAATTTTGACAATAATTAGT
1 TAAATTTTGACAATAATTAGT
1104543 TAAATTTTGACAATAATTAG
1 TAAATTTTGACAATAATTAG
1104563 ATCAAGCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (21 bp):
TAAATTTTGACAATAATTAGT
Found at i:1104854 original size:69 final size:69
Alignment explanation
Indices: 1104768--1104898 Score: 262
Period size: 69 Copynumber: 1.9 Consensus size: 69
1104758 CCCACCCATG
1104768 TAAATAATTTGTAAGTTTTATCCATATTTTAGTTTAGTTTAAATCTTACTATGTGTAGGTTTACT
1 TAAATAATTTGTAAGTTTTATCCATATTTTAGTTTAGTTTAAATCTTACTATGTGTAGGTTTACT
1104833 CATA
66 CATA
1104837 TAAATAATTTGTAAGTTTTATCCATATTTTAGTTTAGTTTAAATCTTACTATGTGTAGGTTT
1 TAAATAATTTGTAAGTTTTATCCATATTTTAGTTTAGTTTAAATCTTACTATGTGTAGGTTT
1104899 TATTTAGATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (69 bp):
TAAATAATTTGTAAGTTTTATCCATATTTTAGTTTAGTTTAAATCTTACTATGTGTAGGTTTACT
CATA
Found at i:1105510 original size:2 final size:2
Alignment explanation
Indices: 1105499--1105527 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1105489 TTGACGACAA
1105499 AT AT -T 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
1105528 GGATTGTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1109101 original size:20 final size:20
Alignment explanation
Indices: 1109078--1109117 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1109068 TATTTTAACA
* *
1109078 ATTTAATTCTTATATTTTAT
1 ATTTAATTCATATATATTAT
*
1109098 ATTTTATTCATATATATTAT
1 ATTTAATTCATATATATTAT
1109118 GCATATTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTAATTCATATATATTAT
Found at i:1109313 original size:15 final size:17
Alignment explanation
Indices: 1109293--1109324 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1109283 TTTAATAATT
1109293 AATTAT-TAAA-ATATA
1 AATTATATAAATATATA
1109308 AATTATATAAATATATA
1 AATTATATAAATATATA
1109325 TTTAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTATATAAATATATA
Found at i:1111530 original size:2 final size:2
Alignment explanation
Indices: 1111523--1111554 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1111513 AATATTTAAA
1111523 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
1111555 TTATGAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1111622 original size:19 final size:19
Alignment explanation
Indices: 1111583--1111620 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1111573 GGTTAATTAG
*
1111583 AGTTTAATTAAGTGAATTT
1 AGTTTAATTAAGAGAATTT
1111602 AGTTTAATTAAGAGTAATT
1 AGTTTAATTAAGAG-AATT
1111621 AGGAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (19 bp):
AGTTTAATTAAGAGAATTT
Found at i:1111877 original size:19 final size:19
Alignment explanation
Indices: 1111855--1111893 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1111845 TTTTAAATAG
*
1111855 ATACACATGTATTAATAAT
1 ATACACATGTATAAATAAT
1111874 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
1111893 A
1 A
1111894 AATAAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:1112766 original size:15 final size:15
Alignment explanation
Indices: 1112743--1112791 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1112733 TATCAAATTT
1112743 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
1112758 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
*
1112773 ATATTGATTGAAATT
1 ATATTGATTGAAATC
1112788 ATAT
1 ATAT
1112792 ATATATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:1125301 original size:14 final size:14
Alignment explanation
Indices: 1125284--1125326 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1125274 ACCCACAGAA
1125284 TTTTTT-TATTTTT
1 TTTTTTGTATTTTT
* *
1125297 TTTTTCGTATTTTA
1 TTTTTTGTATTTTT
1125311 TTTTTTGTACTTTTT
1 TTTTTTGTA-TTTTT
1125326 T
1 T
1125327 ATCACTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 5 0.21
14 14 0.58
15 5 0.21
ACGTcount: A:0.09, C:0.05, G:0.05, T:0.81
Consensus pattern (14 bp):
TTTTTTGTATTTTT
Found at i:1127017 original size:14 final size:14
Alignment explanation
Indices: 1126998--1127026 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1126988 AGAAGGGTAT
1126998 GTAAACTATATCAG
1 GTAAACTATATCAG
1127012 GTAAACTATATCAG
1 GTAAACTATATCAG
1127026 G
1 G
1127027 GTCACCTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (14 bp):
GTAAACTATATCAG
Found at i:1130684 original size:2 final size:2
Alignment explanation
Indices: 1130677--1130710 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1130667 GACAAGTACA
1130677 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
1130711 TGACCCATTT
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:1130876 original size:2 final size:2
Alignment explanation
Indices: 1130869--1130903 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1130859 TAACTCTATC
1130869 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
1130904 AAAGAATTTG
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:1137315 original size:21 final size:21
Alignment explanation
Indices: 1137289--1137344 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1137279 TTATTGGTTT
*
1137289 CTTGCATATTAAGTCAAATTA
1 CTTGCAGATTAAGTCAAATTA
* *
1137310 CTTGCAGATTAGGTCAGATTA
1 CTTGCAGATTAAGTCAAATTA
*
1137331 CTTGTAGATTAAGT
1 CTTGCAGATTAAGT
1137345 AAAGCCACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (21 bp):
CTTGCAGATTAAGTCAAATTA
Found at i:1137435 original size:33 final size:33
Alignment explanation
Indices: 1137393--1137458 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1137383 GAGACTCTTG
1137393 TGGAAGTATTATCTTATGCTGATTTTTAACCTT
1 TGGAAGTATTATCTTATGCTGATTTTTAACCTT
1137426 TGGAAGTATTATCTTATGCTGATTTTTAACCTT
1 TGGAAGTATTATCTTATGCTGATTTTTAACCTT
1137459 ACTTTATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (33 bp):
TGGAAGTATTATCTTATGCTGATTTTTAACCTT
Found at i:1138660 original size:21 final size:20
Alignment explanation
Indices: 1138634--1138680 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1138624 ATAAGTAATA
*
1138634 ATAATATTAGAA-ATATGCAAT
1 ATAATATTA-AAGATATAC-AT
1138655 ATAATATTAAAGATATACAT
1 ATAATATTAAAGATATACAT
1138675 ATAATA
1 ATAATA
1138681 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (20 bp):
ATAATATTAAAGATATACAT
Found at i:1138860 original size:14 final size:14
Alignment explanation
Indices: 1138841--1138867 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1138831 ATACATATTA
1138841 AAAAGAAAAAAAAG
1 AAAAGAAAAAAAAG
1138855 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
1138868 TAATATTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:1139034 original size:3 final size:3
Alignment explanation
Indices: 1139026--1139079 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
1139016 ATGTACTATG
* ** *
1139026 ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA AGG ATA ATA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1139074 ATA ATA
1 ATA ATA
1139080 GAAAAATACA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1139170 original size:36 final size:36
Alignment explanation
Indices: 1139122--1139194 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 36
1139112 AAGGTAAGGA
1139122 AAATAAAGTAGTAAATAATAAT-ATATTAAAAATAAT
1 AAATAAAGTAGTAAA-AATAATAATATTAAAAATAAT
*
1139158 AAATATAA-TAGTAAAAATAATAATGTTAAAAATAAT
1 AAATA-AAGTAGTAAAAATAATAATATTAAAAATAAT
1139194 A
1 A
1139195 CCATATGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
35 6 0.18
36 26 0.76
37 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (36 bp):
AAATAAAGTAGTAAAAATAATAATATTAAAAATAAT
Found at i:1139172 original size:21 final size:18
Alignment explanation
Indices: 1139134--1139180 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 18
1139124 ATAAAGTAGT
1139134 AAATAAT-AATATATTAA
1 AAATAATAAATATATTAA
1139151 AAATAATAAATATAATAGTAA
1 AAATAATAAATAT-AT--TAA
1139172 AAATAATAA
1 AAATAATAA
1139181 TGTTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.27
18 5 0.19
19 2 0.08
21 12 0.46
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAATAATAAATATATTAA
Found at i:1139839 original size:16 final size:16
Alignment explanation
Indices: 1139820--1139862 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
1139810 AAAAGAAGAA
1139820 AGAGAAGGGAGAAAAG
1 AGAGAAGGGAGAAAAG
1139836 AGAGAAGGGAGAAAAG
1 AGAGAAGGGAGAAAAG
1139852 AGAGAAGGGAG
1 AGAGAAGGGAG
1139863 GAAGGAGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (16 bp):
AGAGAAGGGAGAAAAG
Found at i:1141404 original size:15 final size:17
Alignment explanation
Indices: 1141384--1141418 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1141374 TTAAAACTTT
1141384 AAATTT-AAA-TAATTC
1 AAATTTAAAATTAATTC
1141399 AAATTTAAAATTAATTC
1 AAATTTAAAATTAATTC
1141416 AAA
1 AAA
1141419 CTGATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 3 0.17
17 9 0.50
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTTAAAATTAATTC
Found at i:1141407 original size:21 final size:22
Alignment explanation
Indices: 1141372--1141412 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1141362 AAACTTGAAG
*
1141372 AATTAAAACTTTAAATTTAAAT
1 AATTAAAACTTTAAAATTAAAT
*
1141394 AATTCAAA-TTTAAAATTAA
1 AATTAAAACTTTAAAATTAA
1141413 TTCAAACTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAAAACTTTAAAATTAAAT
Found at i:1149680 original size:65 final size:65
Alignment explanation
Indices: 1149576--1149708 Score: 248
Period size: 65 Copynumber: 2.0 Consensus size: 65
1149566 AATTACTCTC
* *
1149576 GTTATAGCAATTTTTCATACTCTTAACGATGTGAACTTCCATAAGAAGCCACCTTTACATTTTAT
1 GTTATAGCAATTTTTCATACTCTTAACGATGTAAACTTCCATAAGAAACCACCTTTACATTTTAT
1149641 GTTATAGCAATTTTTCATACTCTTAACGATGTAAACTTCCATAAGAAACCACCTTTACATTTTAT
1 GTTATAGCAATTTTTCATACTCTTAACGATGTAAACTTCCATAAGAAACCACCTTTACATTTTAT
1149706 GTT
1 GTT
1149709 GTTACAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (65 bp):
GTTATAGCAATTTTTCATACTCTTAACGATGTAAACTTCCATAAGAAACCACCTTTACATTTTAT
Found at i:1151205 original size:25 final size:25
Alignment explanation
Indices: 1151176--1151224 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1151166 TTTTTCTTAA
1151176 TTCCCAAATTTTCTTCTTCACAAAC
1 TTCCCAAATTTTCTTCTTCACAAAC
1151201 TTCCCAAATTTTCTTCTTCACAAA
1 TTCCCAAATTTTCTTCTTCACAAA
1151225 TAATTGACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.41
Consensus pattern (25 bp):
TTCCCAAATTTTCTTCTTCACAAAC
Found at i:1153052 original size:42 final size:42
Alignment explanation
Indices: 1152993--1153076 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
1152983 ATGAAACAAG
1152993 GTAAATTGAAAAATTTCCCATATGAATTCAAATCTCAGTGTT
1 GTAAATTGAAAAATTTCCCATATGAATTCAAATCTCAGTGTT
1153035 GTAAATTGAAAAATTTCCCATATGAATTCAAATCTCAGTGTT
1 GTAAATTGAAAAATTTCCCATATGAATTCAAATCTCAGTGTT
1153077 ATCTCAAGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (42 bp):
GTAAATTGAAAAATTTCCCATATGAATTCAAATCTCAGTGTT
Found at i:1157084 original size:2 final size:2
Alignment explanation
Indices: 1157077--1157104 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1157067 CAATTTACCC
1157077 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
1157105 TCCAAACGTG
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:1158415 original size:19 final size:20
Alignment explanation
Indices: 1158388--1158428 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
1158378 GTTTGAAAAA
*
1158388 AATTATTAAATTCAAAAATT
1 AATTATTAAATTAAAAAATT
1158408 AATT-TTAAATTAAAAAATT
1 AATTATTAAATTAAAAAATT
1158427 AA
1 AA
1158429 GTCGGCCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTATTAAATTAAAAAATT
Found at i:1162074 original size:16 final size:17
Alignment explanation
Indices: 1162034--1162067 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1162024 ACAAAACTGT
1162034 GACACTTTTTCTCGTGA
1 GACACTTTTTCTCGTGA
1162051 GACACTTTTTCTCGTGA
1 GACACTTTTTCTCGTGA
1162068 ACCCTTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (17 bp):
GACACTTTTTCTCGTGA
Found at i:1164746 original size:20 final size:20
Alignment explanation
Indices: 1164707--1164746 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1164697 TAGAACTTAT
*
1164707 AATTTAAAAAGTTAGTTAAA
1 AATTTAAAAAGTTAGATAAA
1164727 AATTTAGAAAAGTT-GATAAA
1 AATTTA-AAAAGTTAGATAAA
1164747 TTTTTTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (20 bp):
AATTTAAAAAGTTAGATAAA
Found at i:1181253 original size:49 final size:49
Alignment explanation
Indices: 1181158--1181254 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 49
1181148 TAATTGCTCA
* * * * * *
1181158 GTTAACCTTGTTGGTATGCTGATCTGTCTAATAATTAGTTTATTGGTTG
1 GTTAACCTTGCTGGCATGCTGATCTATCTAACAACTAGCTTATTGGTTG
* *
1181207 GTTATCCTTGCTGGCATGCTGATCTATCTAACAACTAGCTTGTTGGTT
1 GTTAACCTTGCTGGCATGCTGATCTATCTAACAACTAGCTTATTGGTT
1181255 TATGCTTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (49 bp):
GTTAACCTTGCTGGCATGCTGATCTATCTAACAACTAGCTTATTGGTTG
Found at i:1181342 original size:51 final size:51
Alignment explanation
Indices: 1181263--1181519 Score: 325
Period size: 51 Copynumber: 5.0 Consensus size: 51
1181253 TTTATGCTTA
* *
1181263 TTAATTGTTCGGTTAACCTTGCTGGCATGTTGATCTGTCTAATAACTAGTT
1 TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
* *
1181314 TTAATTGTTTGGTTAACCTTGCTAGCATGCTCATCTGTCTAATAACTAGTT
1 TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
* * * * *
1181365 TTAATTATTTGTTTAACCTTGTTGGCATGCTGACCTGTCTAATAATTAGTT
1 TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
** * * * * *
1181416 TTAATTGTTTGGTTAACCTTGCCAGTATGTTGATCTGTCTAAAAATTAATT
1 TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
** * * *
1181467 TTAATTGTTCAGTTAACCTTGCTGGCGTGCTAATCTATCTAATAACTAGTT
1 TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
1181518 TT
1 TT
1181520 TATACTATAG
Statistics
Matches: 173, Mismatches: 33, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 173 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.44
Consensus pattern (51 bp):
TTAATTGTTTGGTTAACCTTGCTGGCATGCTGATCTGTCTAATAACTAGTT
Found at i:1181623 original size:40 final size:40
Alignment explanation
Indices: 1181559--1181882 Score: 189
Period size: 40 Copynumber: 8.2 Consensus size: 40
1181549 CGTTTGAATA
* * * *
1181559 AAAAACACCGTTACAGATTGAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* * * * **
1181599 AAAAACGCCACTATAGATCAAGCATTAGCTGCGCATTTCA
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* * *
1181639 AAAAACACTGCTATAGATCGACCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* *** * * * ** *
1181679 AAAAATGCCAAAAAAAATCAAGCACAATGCCGTCG-TTTTATG
1 AAAAACGCCGCTATAGATCGAGCATTA-G-CGGCGCTTTT-TG
** * *
1181721 -TTAA----GCTTTAG-T-G-GCATTAGCGACGCTTTTTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* * *
1181753 AAAAACACTGCTATAGGTCGAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* ***
1181793 AAAAATCGCCGCTATAGATCGAGCATTAGCGACGCTTTCCA
1 AAAAA-CGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
* * ** * *
1181834 AAAAACGCCGCTATAGGTCGACCATTAGCAACGCTGTCTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
1181874 AAAAACGCC
1 AAAAACGCC
1181883 ACAAAAAAAT
Statistics
Matches: 210, Mismatches: 61, Indels: 26
0.71 0.21 0.09
Matches are distributed among these distances:
32 6 0.03
33 7 0.03
34 4 0.02
36 1 0.00
37 7 0.03
38 1 0.00
39 1 0.00
40 137 0.65
41 40 0.19
42 6 0.03
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTG
Found at i:1181819 original size:41 final size:40
Alignment explanation
Indices: 1181734--1181882 Score: 190
Period size: 40 Copynumber: 3.7 Consensus size: 40
1181724 AGCTTTAGTG
* *
1181734 GCATTAGCGACGCTTTTTGAAAAACACTGCTATAGGTCGA
1 GCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGGTCGA
* *
1181774 GCATTAGCGGCGCTTTTTGAAAAATCGCCGCTATAGATCGA
1 GCATTAGCGACGCTTTTTGAAAAA-CGCCGCTATAGGTCGA
***
1181815 GCATTAGCGACGCTTTCCAAAAAACGCCGCTATAGGTCGA
1 GCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGGTCGA
* * * *
1181855 CCATTAGCAACGCTGTCTGAAAAACGCC
1 GCATTAGCGACGCTTTTTGAAAAACGCC
1181883 ACAAAAAAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 61 0.65
41 33 0.35
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (40 bp):
GCATTAGCGACGCTTTTTGAAAAACGCCGCTATAGGTCGA
Found at i:1181876 original size:81 final size:80
Alignment explanation
Indices: 1181734--1181882 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 80
1181724 AGCTTTAGTG
*** * * ** * *
1181734 GCATTAGCGACGCTTTTTGAAAAACACTGCTATAGGTCGAGCATTAGCGGCGCTTTTTGAAAAAT
1 GCATTAGCGACGCTTTCCAAAAAACACCGCTATAGGTCGACCATTAGCAACGCTGTCTGAAAAA-
1181799 CGCCGCTATAGATCGA
65 CGCCGCTATAGATCGA
*
1181815 GCATTAGCGACGCTTTCCAAAAAACGCCGCTATAGGTCGACCATTAGCAACGCTGTCTGAAAAAC
1 GCATTAGCGACGCTTTCCAAAAAACACCGCTATAGGTCGACCATTAGCAACGCTGTCTGAAAAAC
1181880 GCC
66 GCC
1181883 ACAAAAAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
80 4 0.07
81 54 0.93
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (80 bp):
GCATTAGCGACGCTTTCCAAAAAACACCGCTATAGGTCGACCATTAGCAACGCTGTCTGAAAAAC
GCCGCTATAGATCGA
Found at i:1181947 original size:196 final size:194
Alignment explanation
Indices: 1181578--1181978 Score: 563
Period size: 196 Copynumber: 2.1 Consensus size: 194
1181568 GTTACAGATT
1181578 GAGCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCAAGCATTAGCTGCGCATTTCAAAAA
1 GAGCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCAAGCATTAGCTGCGCATTTCAAAAA
* ** * * * *
1181643 ACACTGCTATAGATCGACCATTAGCGGCGCTTTTTGAAAAATGCCAAAAAAAATCAAGCACAATG
66 ACACCGCTATAGATCGACCATTAGCAACGCTGTCTGAAAAACGCCAAAAAAAATCAAGCACAACG
* * ** * *
1181708 CCGTCGTTTTATGTTAAGCTTTAGTGGCATTAGCGACGCTTTTTGAAAAACACTGCTATAGGTC
131 CCATCATTTTATGTTAAGCTTTAGTGGCATTAGCGACGCTTTTTGAAAAACACCACTATAAGCC
* *
1181772 GAGCATTAGCGGCGCTTTTTGAAAAATCGCCGCTATAGATCGAGCATTAGC-GACGC-TTTCCAA
1 GAGCATTAGCGGCGCTTTTTGAAAAA-CGCCACTATAGATCAAGCATTAGCTG-CGCATTT-CAA
* * *
1181835 AAAACGCCGCTATAGGTCGACCATTAGCAACGCTGTCTGAAAAACGCCACAAAAAAATTAAGCAC
63 AAAACACCGCTATAGATCGACCATTAGCAACGCTGTCTGAAAAACGCCA-AAAAAAATCAAGCAC
* * *
1181900 AACGCCATCATTTTATGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTGAAAAACGCCACTATAA
127 AACGCCATCATTTTATGTTAAGCTTTAGTGGCATTAGCGACGCTTTTTGAAAAACACCACTATAA
1181965 GCC
192 GCC
1181968 GAGCATTAGCG
1 GAGCATTAGCG
1181979 ATGCTTTCCA
Statistics
Matches: 182, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
194 30 0.16
195 69 0.38
196 83 0.46
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (194 bp):
GAGCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCAAGCATTAGCTGCGCATTTCAAAAA
ACACCGCTATAGATCGACCATTAGCAACGCTGTCTGAAAAACGCCAAAAAAAATCAAGCACAACG
CCATCATTTTATGTTAAGCTTTAGTGGCATTAGCGACGCTTTTTGAAAAACACCACTATAAGCC
Found at i:1182035 original size:196 final size:195
Alignment explanation
Indices: 1181599--1182038 Score: 506
Period size: 196 Copynumber: 2.3 Consensus size: 195
1181589 GCGCTTTTTG
* * * * * *
1181599 AAAAACGCCACTATAGATCAAGCATTAGCTG-CGCATTT-CAAAAAACACTGCTATAGATCGACC
1 AAAAACGCCGCTATAGATCGACCATTAGC-GACAC-TTTCCAAAAAACGCCGCTATAGATCGACC
** * * * * * *
1181662 ATTAGCGGCGCTTTTTGAAAAATGCCAAAAAAAATCAAGCACAATGCCGTCGTTTTATGTTAAGC
64 ATTAGCAACGCTGTCTGAAAAACGCCAAAAAAAATCAAGCACAACGCCATCATTTTATGTTAAGC
** * * * **
1181727 TTTAGTGGCATTAGCGACGCTTTTTGAAAAACACTGCTATAGGTCGAGCATTAGCGGCGCTTTTT
129 TTTAGTGGCATTAGCGACGCTTTTTGAAAAACACCACTATAAGCCGAGCATTAGCGACGCTTTCC
*
1181792 GA
194 AA
* * * *
1181794 AAAATCGCCGCTATAGATCGAGCATTAGCGACGCTTTCCAAAAAACGCCGCTATAGGTCGACCAT
1 AAAAACGCCGCTATAGATCGACCATTAGCGACACTTTCCAAAAAACGCCGCTATAGATCGACCAT
* *
1181859 TAGCAACGCTGTCTGAAAAACGCCACAAAAAAATTAAGCACAACGCCATCATTTTATGTTGAGCT
66 TAGCAACGCTGTCTGAAAAACGCCA-AAAAAAATCAAGCACAACGCCATCATTTTATGTTAAGCT
* * *
1181924 TTAGTGGCATTAGCGGCGCTTTTTGAAAAACGCCACTATAAGCCGAGCATTAGCGATGCTTTCCA
130 TTAGTGGCATTAGCGACGCTTTTTGAAAAACACCACTATAAGCCGAGCATTAGCGACGCTTTCCA
1181989 A
195 A
* * * * **
1181990 AAAAACTCCGCTATAGGTCGACCATTAGTGCCACTTTTTAAAAAACGCC
1 AAAAACGCCGCTATAGATCGACCATTAGCGACACTTTCCAAAAAACGCC
1182039 ACAAAAAAAT
Statistics
Matches: 206, Mismatches: 36, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
194 4 0.02
195 73 0.35
196 129 0.63
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (195 bp):
AAAAACGCCGCTATAGATCGACCATTAGCGACACTTTCCAAAAAACGCCGCTATAGATCGACCAT
TAGCAACGCTGTCTGAAAAACGCCAAAAAAAATCAAGCACAACGCCATCATTTTATGTTAAGCTT
TAGTGGCATTAGCGACGCTTTTTGAAAAACACCACTATAAGCCGAGCATTAGCGACGCTTTCCAA
Found at i:1182058 original size:156 final size:154
Alignment explanation
Indices: 1181774--1182117 Score: 485
Period size: 156 Copynumber: 2.2 Consensus size: 154
1181764 TATAGGTCGA
*
1181774 GCATTAGCGGCGCTTTTTGAAAAATCGCCGCTAT-AGATCGAGCATTAGCGACGCTTTCCAAAAA
1 GCATTAGCGGCGCTTTTTGAAAAA-CGCCGCTATAAGACCGAGCATTAGCGACGCTTTCCAAAAA
* * *
1181838 ACGCCGCTATAGGTCGACCATTAGCAACGCTGTCTGAAAAACGCCACAAAAAAATTAAGCACAAC
65 ACGCCGCTATAGGTCGACCATTAGCAACACTGTCTAAAAAACGCCACAAAAAAATTAAACACAAC
*
1181903 GCCATCATTTTATGTTGAGCTTTAGTG
130 GACATCATTTTATGTT--GCTTTAGTG
* *
1181930 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAAG-CCGAGCATTAGCGATGCTTTCCAAAAAA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAGACCGAGCATTAGCGACGCTTTCC-AAAAA
* *** * *
1181994 ACTCCGCTATAGGTCGACCATTAGTGCCACTTTTTAAAAAACGCCACAAAAAAATTAAACACAAC
65 ACGCCGCTATAGGTCGACCATTAGCAACACTGTCTAAAAAACGCCACAAAAAAATTAAACACAAC
1182059 GACATCATTTTATGTTGCTTTAGTG
130 GACATCATTTTATGTTGCTTTAGTG
* * * *
1182084 GTATTAGCAGCGATTTCTGAAAAACGCCGCTATA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATA
1182118 GATAAGCATT
Statistics
Matches: 168, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
154 38 0.23
155 28 0.17
156 102 0.61
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (154 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAAGACCGAGCATTAGCGACGCTTTCCAAAAAA
CGCCGCTATAGGTCGACCATTAGCAACACTGTCTAAAAAACGCCACAAAAAAATTAAACACAACG
ACATCATTTTATGTTGCTTTAGTG
Found at i:1186714 original size:5 final size:5
Alignment explanation
Indices: 1186673--1186751 Score: 61
Period size: 5 Copynumber: 14.8 Consensus size: 5
1186663 CAACCCAATC
* * *
1186673 TTTATT TTTATT TATTAT TTTCT TTTCT TTTCT TTTAT TTTATT ATTTAT
1 TTTA-T TTTA-T T-TTAT TTTAT TTTAT TTTAT TTTAT TTTA-T -TTTAT
*
1186723 TATT-T ATTAT TTTAT TTTAT TTTAT TTTA
1 T-TTAT TTTAT TTTAT TTTAT TTTAT TTTA
1186752 GTTAAATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
4 2 0.03
5 42 0.66
6 13 0.20
7 7 0.11
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:1186904 original size:42 final size:42
Alignment explanation
Indices: 1186858--1186962 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
1186848 ATCCATGGTA
1186858 CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTGCT-G
1 CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTG-TAG
* * *
1186900 CCAAACAGTTCTATTCCAGCCCAGAATGTCATATCTCTGTAG
1 CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTGTAG
* * *
1186942 CCAAACAATCCTATTTCAGCC
1 CCAAACAGTTCTATTCCAGCC
1186963 TTAGAATCCC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.02
42 55 0.98
ACGTcount: A:0.30, C:0.33, G:0.11, T:0.26
Consensus pattern (42 bp):
CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTGTAG
Found at i:1188516 original size:20 final size:20
Alignment explanation
Indices: 1188491--1188538 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1188481 ATGTGTTTAT
*
1188491 TTTGAGCTTGAGCCTACTAA
1 TTTGAGCTTGAGCCTACCAA
1188511 TTTGAGCTTGAGCCTACCAA
1 TTTGAGCTTGAGCCTACCAA
1188531 TTTGAGCT
1 TTTGAGCT
1188539 ATTTATGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
TTTGAGCTTGAGCCTACCAA
Found at i:1193025 original size:14 final size:14
Alignment explanation
Indices: 1193001--1193035 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1192991 TTAAATATTT
1193001 ATAAT-GTTTAATC
1 ATAATGGTTTAATC
*
1193014 ATAATGGTTTAATT
1 ATAATGGTTTAATC
1193028 ATAATGGT
1 ATAATGGT
1193036 ATATTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (14 bp):
ATAATGGTTTAATC
Found at i:1193795 original size:43 final size:43
Alignment explanation
Indices: 1193756--1193994 Score: 239
Period size: 43 Copynumber: 5.6 Consensus size: 43
1193746 GAGAAAAGTA
* *
1193756 CCGCTAAAAGTCACGTTCTTTAGCGGCATTTGTATGAAAAGCG
1 CCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTATGAAAAGCG
* * * *
1193799 CCGCTATAAGTTAAGTTCTTTAGCGGCGTTTTTGA-GAAAAGCG
1 CCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT-ATGAAAAGCG
* * * *
1193842 CCACTAAAGGTCATTTTCTTTAGCGGCGTTTGTATGAAATGCG
1 CCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTATGAAAAGCG
* * * * *
1193885 CCGTTAAAAGTCATATTCTTTAACGGCATTTTTGA-GAAAAGCG
1 CCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGT-ATGAAAAGCG
* * * * * *
1193928 TCGCTAAAGGTCACGTTCTTTAGCAGCGTTTGTGTGAACAGCG
1 CCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTATGAAAAGCG
* *
1193971 CCGCTAGAGGTCATGTTCTTTAGC
1 CCGCTAAAAGTCATGTTCTTTAGC
1193995 TAGGGGTGAG
Statistics
Matches: 157, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
42 1 0.01
43 154 0.98
44 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
CCGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTATGAAAAGCG
Found at i:1193849 original size:86 final size:86
Alignment explanation
Indices: 1193732--1193994 Score: 321
Period size: 86 Copynumber: 3.1 Consensus size: 86
1193722 TCTGCTAAAA
* ** * *
1193732 TTAGTGGCGTTTTTGAGAAAAGTACCGCTAAAAGTCACGTTCTTTAGCGGCATTTGTATGAAAAG
1 TTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTATGAAAAG
* *
1193797 CGCCGCTATAAGTTAAGTTCT
66 CGCCGCTAAAAGTCAAGTTCT
* ** *
1193818 TTAGCGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCATTTTCTTTAGCGGCGTTTGTATGAAATG
1 TTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTATGAAAAG
*
1193883 CGCCGTTAAAAGTCATA-TTCT
66 CGCCGCTAAAAGTCA-AGTTCT
* * * * * *
1193904 TTAACGGCATTTTTGAGAAAAGCGTCGCTAAAGGTCACGTTCTTTAGCAGCGTTTGTGTGAACAG
1 TTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTATGAAAAG
* * *
1193969 CGCCGCTAGAGGTCATGTTCT
66 CGCCGCTAAAAGTCAAGTTCT
1193990 TTAGC
1 TTAGC
1193995 TAGGGGTGAG
Statistics
Matches: 148, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
86 147 0.99
87 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (86 bp):
TTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTATGAAAAG
CGCCGCTAAAAGTCAAGTTCT
Found at i:1193971 original size:129 final size:129
Alignment explanation
Indices: 1193760--1193994 Score: 312
Period size: 129 Copynumber: 1.8 Consensus size: 129
1193750 AAAGTACCGC
* * * *
1193760 TAAAAGTCACGTTCTTTAGCGGCATTTGTATGAAAAGCGCCGCTATAAGTTAAGTTCTTTAGCGG
1 TAAAAGTCACATTCTTTAACGGCATTTGTATGAAAAGCGCCGCTATAAGTCAAGTTCTTTAGCAG
* *
1193825 CGTTTTTGAGAAAAGCGCCACTAAAGGTCATTTTCTTTAGCGGCGTTTGTATGAAATGCGCCGT
66 CGTTTGTGAGAAAAGCGCCACTAAAGGTCATGTTCTTTAGCGGCGTTTGTATGAAATGCGCCGT
* * * *
1193889 TAAAAGTCATATTCTTTAACGGCATTTTTGA-GAAAAGCGTCGCTA-AAGGTCACGTTCTTTAGC
1 TAAAAGTCACATTCTTTAACGGCATTTGT-ATGAAAAGCGCCGCTATAA-GTCAAGTTCTTTAGC
* * * *
1193952 AGCGTTTGTGTGAACAGCGCCGCTAGAGGTCATGTTCTTTAGC
64 AGCGTTTGTGAGAAAAGCGCCACTAAAGGTCATGTTCTTTAGC
1193995 TAGGGGTGAG
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
128 2 0.02
129 87 0.97
130 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (129 bp):
TAAAAGTCACATTCTTTAACGGCATTTGTATGAAAAGCGCCGCTATAAGTCAAGTTCTTTAGCAG
CGTTTGTGAGAAAAGCGCCACTAAAGGTCATGTTCTTTAGCGGCGTTTGTATGAAATGCGCCGT
Found at i:1194806 original size:67 final size:68
Alignment explanation
Indices: 1194697--1194837 Score: 178
Period size: 67 Copynumber: 2.1 Consensus size: 68
1194687 ATAACTAATT
* * * *
1194697 TTAATTGTTTTGGTTAATCTTGCTAACATGCTGATCTGTCTAATAATT-AGTTTGTTGGTTCATG
1 TTAATTGTTTTGGTTAATCTTGCTAACATGCTAACCTGTCTAATAATTGA-TTTATTAGTTCATG
*
1194761 CTTG
65 CTTA
** * *
1194765 TTAATTG-TTTGGTTAATCTTGCTGGCCTGCTAACCTGTCTAATAATTGATTTATTAGTTTATGC
1 TTAATTGTTTTGGTTAATCTTGCTAACATGCTAACCTGTCTAATAATTGATTTATTAGTTCATGC
1194829 TTA
66 TTA
1194832 TTAATT
1 TTAATT
1194838 TCTCGGTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
67 55 0.87
68 8 0.13
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (68 bp):
TTAATTGTTTTGGTTAATCTTGCTAACATGCTAACCTGTCTAATAATTGATTTATTAGTTCATGC
TTA
Found at i:1194869 original size:67 final size:67
Alignment explanation
Indices: 1194697--1194869 Score: 152
Period size: 67 Copynumber: 2.6 Consensus size: 67
1194687 ATAACTAATT
* * * * * * * *
1194697 TTAATTGTTTTGGTTAATCTTGCTAACATGCTGATCTGTCTAATAATTAGTTTGTTGGTTCATGC
1 TTAATTG-TTCGGTTAACCTTGCTAGCAAGCTAACCTGTCTAATAATTAGTTTATTAGTTCATGC
*
1194762 TTG
65 TTA
* * * ** *
1194765 TTAATTGTTTGGTTAATCTTGCTGGCCTGCTAACCTGTCTAATAATT-GATTTATTAGTTTATGC
1 TTAATTGTTCGGTTAACCTTGCTAGCAAGCTAACCTGTCTAATAATTAG-TTTATTAGTTCATGC
1194829 TTA
65 TTA
* *
1194832 TTAATT-TCTCGGTTAACCTTGTTAGCAAGCTAGCCTGT
1 TTAATTGT-TCGGTTAACCTTGCTAGCAAGCTAACCTGT
1194870 AGATAGTGCA
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
66 2 0.02
67 78 0.90
68 7 0.08
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.46
Consensus pattern (67 bp):
TTAATTGTTCGGTTAACCTTGCTAGCAAGCTAACCTGTCTAATAATTAGTTTATTAGTTCATGCT
TA
Found at i:1200595 original size:5 final size:6
Alignment explanation
Indices: 1200581--1200619 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
1200571 CAACCGCTTG
* *
1200581 AAAATA AAAATA AAAATA AAAATTA TAAACA AAAATA AA
1 AAAATA AAAATA AAAATA AAAA-TA AAAATA AAAATA AA
1200620 TAAAAAGGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:1203057 original size:20 final size:20
Alignment explanation
Indices: 1203032--1203074 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1203022 AACATTTACT
*
1203032 TTGTTAGCTTATACATGCCA
1 TTGTTAGCTCATACATGCCA
1203052 TTGTTAGCTCATACATGCCA
1 TTGTTAGCTCATACATGCCA
1203072 TTG
1 TTG
1203075 ATTTCCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (20 bp):
TTGTTAGCTCATACATGCCA
Found at i:1207503 original size:65 final size:64
Alignment explanation
Indices: 1207386--1207517 Score: 210
Period size: 65 Copynumber: 2.0 Consensus size: 64
1207376 AGGTCATCCA
* * *
1207386 TTAATAAGAGTCTCAACTAAGTTGGGGAATTACTAAAAAAAGATCAATTTTTAACAAAAATAAG
1 TTAATAAGAGACTCAACTAAGTTAGGGAATTACTAAAAAAAGATCAAATTTTAACAAAAATAAG
* *
1207450 TTAATCAGAGACTCAACTAAGTTAAGGGAATTACTAAAAAAATATCAAATTTTAACAAAAATAAG
1 TTAATAAGAGACTCAACTAAGTT-AGGGAATTACTAAAAAAAGATCAAATTTTAACAAAAATAAG
1207515 TTA
1 TTA
1207518 TATGATTATG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
64 21 0.34
65 41 0.66
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (64 bp):
TTAATAAGAGACTCAACTAAGTTAGGGAATTACTAAAAAAAGATCAAATTTTAACAAAAATAAG
Found at i:1208297 original size:115 final size:115
Alignment explanation
Indices: 1208083--1208305 Score: 283
Period size: 115 Copynumber: 1.9 Consensus size: 115
1208073 AAAGGAATAT
* * *
1208083 TTTAGTCCCTATACATTTCAAAAGCTAACATTTTAATCCTTGCCTGTTGAGTTTGTTGTTAAATG
1 TTTAGTCCCTATACATTTCAAAAGCTAACATTTTAATCCTTGCCTATTAAGTTTGATGTTAAATG
* * *
1208148 AATGACATGACTTAACTGTTGTTAACGTGACATTAAATCAAATTAAACAC
66 AATGACATGACTTAACAGTTGCTAACATGACATTAAATCAAATTAAACAC
* ** *
1208198 TTTAGTCCCTATACATTTGAAAAGCTGGCATTTTAATTCTTGCAC-ATTAAGTTTGATGTT-AAT
1 TTTAGTCCCTATACATTTCAAAAGCTAACATTTTAATCCTTGC-CTATTAAGTTTGATGTTAAAT
*
1208261 GGAATGACATGACTTAACAG-TGACTGACATCG-CATTAAATCAAAT
65 -GAATGACATGACTTAACAGTTG-CTAACAT-GACATTAAATCAAAT
1208306 ATTAAATTAA
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
114 5 0.05
115 86 0.92
116 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (115 bp):
TTTAGTCCCTATACATTTCAAAAGCTAACATTTTAATCCTTGCCTATTAAGTTTGATGTTAAATG
AATGACATGACTTAACAGTTGCTAACATGACATTAAATCAAATTAAACAC
Found at i:1209702 original size:20 final size:20
Alignment explanation
Indices: 1209672--1209710 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1209662 TTCTCTCAAA
1209672 ATATTATTAATATT-TTTTC
1 ATATTATTAATATTATTTTC
1209691 ATATTAATTAATATTATTTT
1 ATATT-ATTAATATTATTTT
1209711 TAGAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTATTAATATTATTTTC
Found at i:1214431 original size:21 final size:22
Alignment explanation
Indices: 1214406--1214446 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1214396 TTATTATTTT
1214406 ATAATAAAAATA-GAAAAATAA
1 ATAATAAAAATAGGAAAAATAA
*
1214427 ATAATCAAAATAGGAAAAAT
1 ATAATAAAAATAGGAAAAAT
1214447 TAGTTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (22 bp):
ATAATAAAAATAGGAAAAATAA
Found at i:1220558 original size:22 final size:22
Alignment explanation
Indices: 1220543--1220584 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1220533 TAAAAATTAT
*
1220543 TTAAT-ATTATAATAAATAATA
1 TTAATAATAATAATAAATAATA
1220564 TTAATAATAATAAT-AATAATA
1 TTAATAATAATAATAAATAATA
1220585 GAGTGTGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAATAATAATAATAAATAATA
Found at i:1220563 original size:3 final size:3
Alignment explanation
Indices: 1220551--1220584 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1220541 ATTTAATATT
*
1220551 ATA ATAA ATA ATA TTA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
1220585 GAGTGTGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1220564 original size:15 final size:15
Alignment explanation
Indices: 1220544--1220584 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1220534 AAAAATTATT
1220544 TAATATT-ATAATAAA
1 TAATATTAATAAT-AA
1220559 TAATATTAATAATAA
1 TAATATTAATAATAA
*
1220574 TAATAATAATA
1 TAATATTAATA
1220585 GAGTGTGAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATATTAATAATAA
Found at i:1232728 original size:21 final size:21
Alignment explanation
Indices: 1232698--1232750 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1232688 TTATTCTGAG
*
1232698 TTTTTTATTTATAATATAATTA
1 TTTTATATTTAT-ATATAATTA
* *
1232720 -TTTATATTTATATTTGATTA
1 TTTTATATTTATATATAATTA
1232740 TTTTATATTTA
1 TTTTATATTTA
1232751 AAAAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTATATTTATATATAATTA
Found at i:1244376 original size:7 final size:7
Alignment explanation
Indices: 1244360--1244393 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1244350 ACCCTTAGGG
1244360 TTTT-TT
1 TTTTGTT
1244366 TTTTGTT
1 TTTTGTT
1244373 TTTTGTT
1 TTTTGTT
1244380 TTTTG-T
1 TTTTGTT
1244386 TTTTGTT
1 TTTTGTT
1244393 T
1 T
1244394 AAATAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 10 0.38
7 16 0.62
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:1244381 original size:13 final size:14
Alignment explanation
Indices: 1244360--1244393 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1244350 ACCCTTAGGG
1244360 TTTT-TTTTTTGTT
1 TTTTGTTTTTTGTT
1244373 TTTTGTTTTTTG-T
1 TTTTGTTTTTTGTT
1244386 TTTTGTTT
1 TTTTGTTT
1244394 AAATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (14 bp):
TTTTGTTTTTTGTT
Found at i:1245686 original size:12 final size:12
Alignment explanation
Indices: 1245664--1245692 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1245654 TAATAATAAA
1245664 TTAAT-GTTTAT
1 TTAATAGTTTAT
1245675 TTAATAGTTTAT
1 TTAATAGTTTAT
1245687 TTAATA
1 TTAATA
1245693 TAATAATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
TTAATAGTTTAT
Found at i:1247001 original size:3 final size:3
Alignment explanation
Indices: 1246993--1247019 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1246983 TTGAGACAAA
1246993 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1247020 TGACTAACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1247078 original size:28 final size:30
Alignment explanation
Indices: 1247019--1247078 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
1247009 TTATTATTAT
* *
1247019 TTGACTAACTGACTTTATTACATTTACTTA
1 TTGACTAACTGAATTTATTACATTTACATA
1247049 TTGACTAA-TGAATTT-TTA-ACTTTACATA
1 TTGACTAACTGAATTTATTACA-TTTACATA
1247077 TT
1 TT
1247079 ATGTTGGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 12 0.44
29 6 0.22
30 8 0.30
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (30 bp):
TTGACTAACTGAATTTATTACATTTACATA
Found at i:1247109 original size:2 final size:2
Alignment explanation
Indices: 1247102--1247128 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1247092 TGAAATTTTA
1247102 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
1247129 AAAGTATTAA
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:1253029 original size:20 final size:20
Alignment explanation
Indices: 1252992--1253028 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1252982 CCGTAAGTTC
1252992 TGATTTCCTTTTTCTTTTGG
1 TGATTTCCTTTTTCTTTTGG
*
1253012 TGATTTCGTTTTT-TTTT
1 TGATTTCCTTTTTCTTTT
1253029 TAACAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.05, C:0.11, G:0.14, T:0.70
Consensus pattern (20 bp):
TGATTTCCTTTTTCTTTTGG
Found at i:1254390 original size:22 final size:23
Alignment explanation
Indices: 1254363--1254419 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1254353 TTTAATATTT
*
1254363 TAAAAATTATATTTTTACTATCA
1 TAAAAATTACATTTTTACTATCA
* *
1254386 TAAAAATTACATTTTTGCTATTA
1 TAAAAATTACATTTTTACTATCA
1254409 TAAAAATTACA
1 TAAAAATTACA
1254420 ATTTAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAAAATTACATTTTTACTATCA
Found at i:1267669 original size:16 final size:16
Alignment explanation
Indices: 1267634--1267666 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1267624 TTAATTTTTT
*
1267634 AATTTAAAATATATAA
1 AATTCAAAATATATAA
1267650 AATTCAAAAT-TATAA
1 AATTCAAAATATATAA
1267665 AA
1 AA
1267667 ATTATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTCAAAATATATAA
Found at i:1267683 original size:20 final size:19
Alignment explanation
Indices: 1267655--1267692 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1267645 TATAAAATTC
*
1267655 AAAATTATAAAAATTATTTA
1 AAAACTATAAAAA-TATTTA
1267675 AAAACTATAAAAATATTT
1 AAAACTATAAAAATATTT
1267693 TTAAATATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAACTATAAAAATATTTA
Found at i:1268454 original size:7 final size:7
Alignment explanation
Indices: 1268442--1268468 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1268432 TTAACATAAA
1268442 AAAAAAT
1 AAAAAAT
1268449 AAAAAAT
1 AAAAAAT
1268456 AAAAAAT
1 AAAAAAT
1268463 AAAAAA
1 AAAAAA
1268469 CATAGGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:1286571 original size:25 final size:26
Alignment explanation
Indices: 1286539--1286595 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
1286529 CAGGTTGTAT
* **
1286539 TTTATTTTT-CTGTT-AAATTTTTTA
1 TTTATTTTTACTGTTGAAAGTTGATA
1286563 TTTATTTTTACTGTTGAAAGTTGATA
1 TTTATTTTTACTGTTGAAAGTTGATA
1286589 TTTATTT
1 TTTATTT
1286596 GTCAACATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 9 0.32
25 5 0.18
26 14 0.50
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.65
Consensus pattern (26 bp):
TTTATTTTTACTGTTGAAAGTTGATA
Found at i:1287916 original size:2 final size:2
Alignment explanation
Indices: 1287900--1287955 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
1287890 AAATTGTTTG
*
1287900 AT AT AT TT AT A- 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
1287941 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1287956 AAAGCAAGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1288397 original size:20 final size:22
Alignment explanation
Indices: 1288369--1288412 Score: 56
Period size: 20 Copynumber: 2.0 Consensus size: 22
1288359 ATAACATCAA
*
1288369 TATATTGAA-TAAATA-TATTT
1 TATAATGAACTAAATATTATTT
1288389 TATAATGAACTTAAATATTATTT
1 TATAATGAAC-TAAATATTATTT
1288412 T
1 T
1288413 TTATAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
22 6 0.30
23 6 0.30
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TATAATGAACTAAATATTATTT
Found at i:1292613 original size:17 final size:17
Alignment explanation
Indices: 1292591--1292626 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1292581 CCGTTTATTA
1292591 TAATTTGATTTGGATTT
1 TAATTTGATTTGGATTT
1292608 TAATTTGATTTGGATTT
1 TAATTTGATTTGGATTT
1292625 TA
1 TA
1292627 GTTTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (17 bp):
TAATTTGATTTGGATTT
Found at i:1294126 original size:35 final size:35
Alignment explanation
Indices: 1294087--1294157 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1294077 CACTTGCCTC
*
1294087 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
*
1294122 TTCCCATTCTCCCATGCTGTCTGCCACCAACACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
1294157 T
1 T
1294158 CACACTCCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.18, C:0.46, G:0.10, T:0.25
Consensus pattern (35 bp):
TTCCCACTCTCCCATGCTGTCTGCCACCAACACCA
Found at i:1294560 original size:12 final size:12
Alignment explanation
Indices: 1294545--1294579 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1294535 TAAAACATAA
1294545 AAAAAAATATAC
1 AAAAAAATATAC
*
1294557 AAAAAGATATAC
1 AAAAAAATATAC
1294569 AAAAAAATATA
1 AAAAAAATATA
1294580 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (12 bp):
AAAAAAATATAC
Found at i:1294698 original size:11 final size:11
Alignment explanation
Indices: 1294665--1294698 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1294655 CGAATTCCCC
1294665 TCCCT-TCTCT
1 TCCCTCTCTCT
1294675 CTCCCTCTCTCT
1 -TCCCTCTCTCT
1294687 TCCCTCTCTCT
1 TCCCTCTCTCT
1294698 T
1 T
1294699 TTTTTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (11 bp):
TCCCTCTCTCT
Found at i:1295184 original size:3 final size:3
Alignment explanation
Indices: 1295176--1295206 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1295166 TGCATTTCAA
1295176 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1295207 GAAATACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1295317 original size:3 final size:3
Alignment explanation
Indices: 1295309--1295352 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1295299 TTGTGTTTCA
1295309 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
1295353 ATATCCTTGT
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:1295625 original size:33 final size:30
Alignment explanation
Indices: 1295567--1295639 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 30
1295557 TAATATTATG
*
1295567 TATATATTTTAATATTATCAGTTATATATA
1 TATATATTTTAATACTATCAGTTATATATA
* *
1295597 CTATATGATTTCTAATACTATTATTTATATATA
1 -TATAT-ATTT-TAATACTATCAGTTATATATA
1295630 TATATATTTT
1 TATATATTTT
1295640 CTTAGTACCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 1 0.03
31 9 0.24
32 9 0.24
33 18 0.49
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (30 bp):
TATATATTTTAATACTATCAGTTATATATA
Found at i:1310867 original size:20 final size:20
Alignment explanation
Indices: 1310835--1310877 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1310825 TTCAAAATAA
1310835 TTATTTTAGGTTG-AGATTAT
1 TTATTTTAGGTTGAAG-TTAT
1310855 TTATTTT-GAGTTGAAGTTAT
1 TTATTTTAG-GTTGAAGTTAT
1310875 TTA
1 TTA
1310878 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.05
20 18 0.86
21 2 0.10
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (20 bp):
TTATTTTAGGTTGAAGTTAT
Found at i:1310938 original size:39 final size:40
Alignment explanation
Indices: 1310855--1310940 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 40
1310845 TTGAGATTAT
* *
1310855 TTATTTTGAGTTGAAGTTATTTAAATTTTTTTATTTTCATA
1 TTATTTTGAGTT-AAGTTATTTAAATTATTTCATTTTCATA
* *
1310896 TTATTTTGAGTT-ATTTATTTAAATTATTTCATGTTTGA-A
1 TTATTTTGAGTTAAGTTATTTAAATTATTTCAT-TTTCATA
1310935 TTATTT
1 TTATTT
1310941 AAGGTTTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
39 24 0.60
40 4 0.10
41 12 0.30
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (40 bp):
TTATTTTGAGTTAAGTTATTTAAATTATTTCATTTTCATA
Found at i:1317208 original size:5 final size:5
Alignment explanation
Indices: 1317198--1317224 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1317188 TTATGTTTTA
1317198 ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT
1317225 AAACTAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:1318521 original size:15 final size:14
Alignment explanation
Indices: 1318496--1318552 Score: 78
Period size: 15 Copynumber: 3.9 Consensus size: 14
1318486 CGATGAATTT
1318496 ATTGAATTTATATTG
1 ATTGAA-TTATATTG
*
1318511 ATTGCAATTATTTTG
1 ATTG-AATTATATTG
1318526 ATTGAAATTATATTG
1 ATTG-AATTATATTG
1318541 ATTGAATTATAT
1 ATTGAATTATAT
1318553 AATATATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.21
15 28 0.74
16 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:1318955 original size:23 final size:22
Alignment explanation
Indices: 1318925--1319031 Score: 114
Period size: 21 Copynumber: 5.0 Consensus size: 22
1318915 GCTTTATCGA
* *
1318925 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTA-T
*
1318948 TCAGGCACCTCGTGTGTCGTA-
1 TCAGGCACCTCATGTGTCGTAT
*
1318969 TCAGGCACCTCGTGTGTCGTA-
1 TCAGGCACCTCATGTGTCGTAT
1318990 TCAGGCACCTCATGTGTCGT-T
1 TCAGGCACCTCATGTGTCGTAT
* * *
1319011 TTAGGCACTTTATG-GTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
1319032 ACTGATCAGG
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
20 5 0.07
21 52 0.69
23 18 0.24
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAGGCACCTCATGTGTCGTAT
Found at i:1318972 original size:21 final size:21
Alignment explanation
Indices: 1318937--1319018 Score: 119
Period size: 21 Copynumber: 3.8 Consensus size: 21
1318927 AGGCACTTTA
1318937 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
1318960 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
*
1318981 TGTGTCGTATCAGGCACCTCA
1 TGTGTCGTATCAGGCACCTCG
* *
1319002 TGTGTCGTTTTAGGCAC
1 TGTGTCGTATCAGGCAC
1319019 TTTATGGTCG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
21 47 0.84
23 9 0.16
ACGTcount: A:0.15, C:0.26, G:0.27, T:0.33
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:1320186 original size:19 final size:21
Alignment explanation
Indices: 1320150--1320188 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1320140 CATAAATTAT
*
1320150 AAAAAATTGATATGAAAATAA
1 AAAAAAATGATATGAAAATAA
1320171 AAAAAAATGAT-T-AAAATA
1 AAAAAAATGATATGAAAATA
1320189 GTAAAGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (21 bp):
AAAAAAATGATATGAAAATAA
Found at i:1320385 original size:13 final size:13
Alignment explanation
Indices: 1320369--1320393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1320359 ATATTCCCAC
1320369 ATTATTTTGTATG
1 ATTATTTTGTATG
1320382 ATTATTTTGTAT
1 ATTATTTTGTAT
1320394 ATAAATGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
ATTATTTTGTATG
Found at i:1323572 original size:28 final size:28
Alignment explanation
Indices: 1323541--1323602 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1323531 TAGTACAATC
* * *
1323541 GATTAACTGTTTGAAATTAAAATACCGA
1 GATTAACCGTTTCAAATTAAAATACAGA
*
1323569 GATTAACCGTTTCAAATTAAAATATAGA
1 GATTAACCGTTTCAAATTAAAATACAGA
1323597 GATTAA
1 GATTAA
1323603 ATCTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (28 bp):
GATTAACCGTTTCAAATTAAAATACAGA
Found at i:1328041 original size:2 final size:2
Alignment explanation
Indices: 1328034--1328059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1328024 CAATAATTAC
1328034 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
1328060 TTTGATTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1328538 original size:17 final size:17
Alignment explanation
Indices: 1328499--1328540 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1328489 TGATGAAAAC
*
1328499 ATTTTTTATTGTTTTCT
1 ATTTTTTATTATTTTCT
*
1328516 AATTTTTATATATTTT-T
1 ATTTTTTAT-TATTTTCT
1328533 ATTTTTTA
1 ATTTTTTA
1328541 AAAATCATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTTTATTATTTTCT
Found at i:1329594 original size:15 final size:15
Alignment explanation
Indices: 1329576--1329617 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
1329566 AATGAAAGGG
*
1329576 AAAGAAAGGAAAAAA
1 AAAGAAAAGAAAAAA
1329591 AAAGAAAAG-AAAAA
1 AAAGAAAAGAAAAAA
1329605 AAAGAAGAAGAAA
1 AAAGAA-AAGAAA
1329618 GATTAGTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 11 0.46
15 11 0.46
16 2 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAA
Found at i:1329605 original size:14 final size:14
Alignment explanation
Indices: 1329576--1329617 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1329566 AATGAAAGGG
*
1329576 AAAGAAAGGAAAAAA
1 AAAGAAAAG-AAAAA
1329591 AAAGAAAAGAAAAA
1 AAAGAAAAGAAAAA
1329605 AAAGAAGAAGAAA
1 AAAGAA-AAGAAA
1329618 GATTAGTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAA
Found at i:1342173 original size:23 final size:24
Alignment explanation
Indices: 1342142--1342186 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1342132 TTCGAGAATT
*
1342142 ATTTGAATAAATAATTA-AAAATA
1 ATTTAAATAAATAATTAGAAAATA
*
1342165 ATTTAAATAAGTAATTAGAAAA
1 ATTTAAATAAATAATTAGAAAA
1342187 GACTTGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (24 bp):
ATTTAAATAAATAATTAGAAAATA
Found at i:1348325 original size:180 final size:178
Alignment explanation
Indices: 1347828--1348521 Score: 773
Period size: 180 Copynumber: 4.0 Consensus size: 178
1347818 CAAAGCTGTC
* *
1347828 AAAAATGACCCAATTTCTAAATTAAAACAAATAG-AAATACAAAGTACACAATTTTTTTCAAATA
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGTAAAC-ATTTTTTTCAAATA
* * * * * *
1347892 CCCTTTGTACATTTTTTTTATAAACCTTATTAATTATTTA-AACTTTTTCCAGTACTTTCTCAGG
65 CCCTTTGTACAATTTTTAT-TAAACCTTATTAATT-TCTACAAC-TTCTCCACTACTTTCTCAGC
*
1347956 AAACAAACACCAAATAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCC-A
127 AAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
* * * * * *
1348007 AAAAATGACCCAATTTCTAAATTAAAACACACAGAAAACACAAAGCAAGCA-CTTCTTCAAATAC
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGTAAACATTTTTTTCAAATAC
* * * * * * *
1348071 CGTTTGCAGAATATTTTA-TAAACCTTACTAATTTGTACAACTTCCCCTCTACTTTCTCAGCAAA
66 CCTTTGTACAAT-TTTTATTAAACCTTATTAATTTCTACAACTTCTCCACTACTTTCTCAGCAAA
* * * *
1348135 CAAACACCAAGTAATGGCGGGTAATTAAAGAGTACCACAAAACCGCCAA
130 CAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
* * *
1348184 AAAAAAGACCCAATTTCTAATTTAAAACACATAGAAAATACAAAGTAAACATTTTTTTTCTAATA
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGTAAACA-TTTTTTTCAAATA
* *
1348249 CCCTTTGTATAATTTTTATTAAACCTTATTAATTTCAACAACTTCTCCGACTACTTTCTCAGCAA
65 CCCTTTGTACAATTTTTATTAAACCTTATTAATTTCTACAACTTCTCC-ACTACTTTCTCAGCAA
* * *
1348314 ACAAACACCAAGTAATGGTGAGTAATTAAAAAGCACCTCAAAGCTGCCAA
129 ACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
*
1348364 AAAAATGACCCAATTTCTAAATTCAAACACATAG-----A-AAA-T--AC---TTTTTCAAATAC
1 AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGTAAACATTTTTTTCAAATAC
* * * *
1348417 CCTTTGCT-C-ATTTTT-TTATGAACCTTATTAAATTGT-TAACTTTTCCCACTACTTTCTCAGC
66 CCTTTG-TACAATTTTTATTA--AACCTTATTAATTTCTACAACTTCT-CCACTACTTTCTCAGC
* *
1348478 AAACAAACACCAAGTAATGATGGGTAACTAAAGAGTACCTCAAA
127 AAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAA
1348522 CAAGGCCATC
Statistics
Matches: 439, Mismatches: 64, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
165 3 0.01
166 65 0.15
167 32 0.07
168 1 0.00
171 2 0.00
173 1 0.00
174 3 0.01
175 1 0.00
176 63 0.14
177 63 0.14
178 24 0.05
179 81 0.18
180 100 0.23
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.30
Consensus pattern (178 bp):
AAAAATGACCCAATTTCTAAATTAAAACACATAGAAAATACAAAGTAAACATTTTTTTCAAATAC
CCTTTGTACAATTTTTATTAAACCTTATTAATTTCTACAACTTCTCCACTACTTTCTCAGCAAAC
AAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAA
Found at i:1351986 original size:59 final size:60
Alignment explanation
Indices: 1351894--1352013 Score: 179
Period size: 59 Copynumber: 2.0 Consensus size: 60
1351884 CTTTCCGCCT
* *
1351894 TTGCATTATGTCCACTAAAGACAGATGACAATCTACAA-TATATATATATAGGGGGTATC
1 TTGCATTATGTCCACTAAAGACAGATGACAATCTACAACAATATATATACAGGGGGTATC
* * * *
1351953 TTGCATTATGTCCACTCAAGAGAGATGACAATCTACAACAATATGTATACATGGGGTATC
1 TTGCATTATGTCCACTAAAGACAGATGACAATCTACAACAATATATATACAGGGGGTATC
1352013 T
1 T
1352014 AGCAAACCTA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
59 36 0.67
60 18 0.33
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (60 bp):
TTGCATTATGTCCACTAAAGACAGATGACAATCTACAACAATATATATACAGGGGGTATC
Found at i:1359577 original size:3 final size:3
Alignment explanation
Indices: 1359569--1359650 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
1359559 ACTTAATCTC
1359569 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1359617 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1359651 CTTTGCCAGT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1361600 original size:11 final size:10
Alignment explanation
Indices: 1361569--1361606 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
1361559 TTAAATTAAC
1361569 TTTTAATATT
1 TTTTAATATT
1361579 TTTTAATATT
1 TTTTAATATT
1361589 TTTTAATAATT
1 TTTTAAT-ATT
1361600 TTTTAAT
1 TTTTAAT
1361607 CTAACCTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTAATATT
Found at i:1374656 original size:16 final size:17
Alignment explanation
Indices: 1374628--1374660 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1374618 AATTAAAATG
1374628 TAATTTCATATTTTTAT
1 TAATTTCATATTTTTAT
1374645 TAATTT-ATATTTTTAT
1 TAATTTCATATTTTTAT
1374661 GATTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTCATATTTTTAT
Found at i:1386525 original size:19 final size:19
Alignment explanation
Indices: 1386503--1386541 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1386493 TAGATACATG
1386503 ATAATTGAATTAAGGTTGT
1 ATAATTGAATTAAGGTTGT
1386522 ATAATTGAATTAAGGTTGT
1 ATAATTGAATTAAGGTTGT
1386541 A
1 A
1386542 CTCTTTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (19 bp):
ATAATTGAATTAAGGTTGT
Found at i:1394339 original size:38 final size:39
Alignment explanation
Indices: 1394235--1394351 Score: 112
Period size: 38 Copynumber: 3.1 Consensus size: 39
1394225 ATTCTTACAT
* * * * **
1394235 TAAATCGATAAATCCAATTCAAT-CTAAAATATAAAAAA
1 TAAATCAATAAATCCGATACAATCCAAAAATATAAAAGG
* *
1394273 TTAATCAATAAATCCGATACAATTC-AAAATATAAAAGG
1 TAAATCAATAAATCCGATACAATCCAAAAATATAAAAGG
* ***
1394311 TAAATCAATAAATCTGATTGGATCCAAAAATATAAAAGG
1 TAAATCAATAAATCCGATACAATCCAAAAATATAAAAGG
1394350 TA
1 TA
1394352 GAATAAAAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
38 49 0.75
39 16 0.25
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.26
Consensus pattern (39 bp):
TAAATCAATAAATCCGATACAATCCAAAAATATAAAAGG
Done.