Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 106 of 175
Found at i:33775694 original size:34 final size:35
Alignment explanation
Indices: 33775650--33775716 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
33775640 CAGTAAAATA
*
33775650 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
33775684 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
33775717 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:33775720 original size:14 final size:15
Alignment explanation
Indices: 33775644--33775720 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
33775634 GATTGCCAGT
* *
33775644 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
33775658 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
33775672 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
33775692 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
33775707 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
33775721 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:33778275 original size:3 final size:3
Alignment explanation
Indices: 33778267--33778306 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
33778257 AATCATGCCA
33778267 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
33778307 GAATATTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:33784400 original size:84 final size:84
Alignment explanation
Indices: 33784259--33784431 Score: 328
Period size: 84 Copynumber: 2.1 Consensus size: 84
33784249 GGTAATTTCC
33784259 CTATTCTGTTGAAATAAAATGAAAAAGACTTAGGAATGGAGTGGTTTAAACTTAGTTGTGCTAGG
1 CTATTCTGTTGAAATAAAATGAAAAAGACTTAGGAATGGAGTGGTTTAAACTTAGTTGTGCTAGG
*
33784324 AGAATGAGTAAGTGCTTAA
66 AGAAGGAGTAAGTGCTTAA
*
33784343 CTATTCTGTTGAAATAAAATGAAAGAGACTTAGGAATGGAGTGGTTTAAACTTAGTTGTGCTAGG
1 CTATTCTGTTGAAATAAAATGAAAAAGACTTAGGAATGGAGTGGTTTAAACTTAGTTGTGCTAGG
33784408 AGAAGGAGTAAGTGCTTAA
66 AGAAGGAGTAAGTGCTTAA
33784427 CTATT
1 CTATT
33784432 GGGTTGCTGC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (84 bp):
CTATTCTGTTGAAATAAAATGAAAAAGACTTAGGAATGGAGTGGTTTAAACTTAGTTGTGCTAGG
AGAAGGAGTAAGTGCTTAA
Found at i:33787565 original size:34 final size:34
Alignment explanation
Indices: 33787503--33787569 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
33787493 AGTAGCAATC
*
33787503 ATTATGCTTATAATAGTTCGATTTAGTGGCAAAT
1 ATTATGCTTATAATAGTTCGATTCAGTGGCAAAT
33787537 ATTATGCTTATAACATA-TT-GATTCAGTGGCAAA
1 ATTATGCTTAT-A-ATAGTTCGATTCAGTGGCAAA
33787570 AAACATGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 24 0.80
35 3 0.10
36 3 0.10
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (34 bp):
ATTATGCTTATAATAGTTCGATTCAGTGGCAAAT
Found at i:33787578 original size:34 final size:34
Alignment explanation
Indices: 33787506--33787581 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
33787496 AGCAATCATT
* * **
33787506 ATGCTTATAATAGTTCGATTTAGTGGCAAATATT
1 ATGCTTATAATAGTTCGATTCAGTGGCAAAAAAC
33787540 ATGCTTATAACATA-TT-GATTCAGTGGCAAAAAAC
1 ATGCTTAT-A-ATAGTTCGATTCAGTGGCAAAAAAC
33787574 ATGCTTAT
1 ATGCTTAT
33787582 CATGTGTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 30 0.83
35 3 0.08
36 3 0.08
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (34 bp):
ATGCTTATAATAGTTCGATTCAGTGGCAAAAAAC
Found at i:33787639 original size:6 final size:6
Alignment explanation
Indices: 33787628--33787656 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
33787618 TGTGTACCAT
33787628 TACAAA TACAAA TACAAA TACAAA TACAA
1 TACAAA TACAAA TACAAA TACAAA TACAA
33787657 TAGACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
TACAAA
Found at i:33790364 original size:20 final size:19
Alignment explanation
Indices: 33790317--33790364 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
33790307 TTTAATTTAA
*
33790317 CAAGTATCGATACCTTGCT
1 CAAGTATCAATACCTTGCT
* *
33790336 GAAGGTATCAATACCTTTCT
1 CAA-GTATCAATACCTTGCT
33790356 CAAGATATC
1 CAAG-TATC
33790365 GGTACTTTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (19 bp):
CAAGTATCAATACCTTGCT
Found at i:33797955 original size:10 final size:11
Alignment explanation
Indices: 33797924--33797953 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
33797914 CTAATTTTAA
33797924 TTAAATAAATTC
1 TTAAA-AAATTC
33797936 TTAAAAAATTC
1 TTAAAAAATTC
33797947 TTAAAAA
1 TTAAAAA
33797954 TTAAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (11 bp):
TTAAAAAATTC
Found at i:33808935 original size:16 final size:16
Alignment explanation
Indices: 33808914--33808968 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
33808904 GTTTGGTTCA
33808914 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
33808930 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
33808946 TTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
33808962 CTGTAAT
1 CTGTAAT
33808969 CAGTAACTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:33809232 original size:20 final size:20
Alignment explanation
Indices: 33809207--33809300 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 20
33809197 TTATTATTAA
33809207 ATATAATTTAATAAAATAAT
1 ATATAATTTAATAAAATAAT
33809227 ATATAATTTAATAAAATTATTATT
1 ATATAATTTAATAAAA-TA--A-T
*
33809251 ATATGAA-TTAAAAAATCATAAT
1 ATAT-AATTTAATAAA--ATAAT
*
33809273 ATATAATACT-ATAAAAATAAT
1 ATATAAT-TTAAT-AAAATAAT
33809294 ATATAAT
1 ATATAAT
33809301 CTACTTTATT
Statistics
Matches: 61, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
20 16 0.26
21 16 0.26
22 6 0.10
23 6 0.10
24 12 0.20
25 4 0.07
26 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (20 bp):
ATATAATTTAATAAAATAAT
Found at i:33811013 original size:23 final size:23
Alignment explanation
Indices: 33810969--33811013 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
33810959 CAGTAATTTG
* *
33810969 CAACACTTTAACATCTCTATTAA
1 CAACACTTTAACACCTCAATTAA
33810992 CAACA-TTTATACACCTCAATTA
1 CAACACTTTA-ACACCTCAATTA
33811014 CAGCAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (23 bp):
CAACACTTTAACACCTCAATTAA
Found at i:33811099 original size:23 final size:23
Alignment explanation
Indices: 33810991--33811156 Score: 65
Period size: 23 Copynumber: 7.3 Consensus size: 23
33810981 ATCTCTATTA
* *
33810991 ACAACATTTATACACCTCAA-TT
1 ACAACATTTAAACACTTCAATTT
* * *
33811013 ACAGCAATAAAACA-TCTCAATTT
1 ACAACATTTAAACACT-TCAATTT
* * ** *
33811036 CCAGCAACTAAACAATTCAATTT
1 ACAACATTTAAACACTTCAATTT
* *
33811059 GCGATAC-TTAAAACACTTCAATTT
1 AC-A-ACATTTAAACACTTCAATTT
*
33811083 ACAACATTTAAACACTTTAATTT
1 ACAACATTTAAACACTTCAATTT
** * * *
33811106 GTAGCACTTT-AACA-TCTCTATTA
1 ACAACA-TTTAAACACT-TCAATTT
* *
33811129 ACAACATTTATACACCTCAA-TT
1 ACAACATTTAAACACTTCAATTT
33811151 ACAACA
1 ACAACA
33811157 ATAAAATATC
Statistics
Matches: 104, Mismatches: 30, Indels: 20
0.68 0.19 0.13
Matches are distributed among these distances:
22 27 0.26
23 57 0.55
24 19 0.18
25 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.04, T:0.31
Consensus pattern (23 bp):
ACAACATTTAAACACTTCAATTT
Found at i:33811210 original size:138 final size:138
Alignment explanation
Indices: 33810962--33811225 Score: 467
Period size: 138 Copynumber: 1.9 Consensus size: 138
33810952 AGAGCTTCAG
*
33810962 TAATTTGCAACACTTTAACATCTCTATTAACAACATTTATACACCTCAATTACAGCAATAAAACA
1 TAATTTGCAACACTTTAACATCTCTATTAACAACATTTATACACCTCAATTACAACAATAAAACA
33811027 TCTCAATTTCCAGCAACTAAACAATTCAATTTGCGATACTTAAAACACTTCAATTTACAACATTT
66 TCTCAATTTCCAGCAACTAAACAATTCAATTTGCGATACTTAAAACACTTCAATTTACAACATTT
33811092 AAACACTT
131 AAACACTT
* * *
33811100 TAATTTGTAGCACTTTAACATCTCTATTAACAACATTTATACACCTCAATTACAACAATAAAATA
1 TAATTTGCAACACTTTAACATCTCTATTAACAACATTTATACACCTCAATTACAACAATAAAACA
*
33811165 TCTCAATTTCCAGCAACTAAATAATTCAATTTGC-AGTACTTAAAACACTTCAATTTACAAC
66 TCTCAATTTCCAGCAACTAAACAATTCAATTTGCGA-TACTTAAAACACTTCAATTTACAAC
33811226 TTAAGACAGA
Statistics
Matches: 120, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
137 1 0.01
138 119 0.99
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (138 bp):
TAATTTGCAACACTTTAACATCTCTATTAACAACATTTATACACCTCAATTACAACAATAAAACA
TCTCAATTTCCAGCAACTAAACAATTCAATTTGCGATACTTAAAACACTTCAATTTACAACATTT
AAACACTT
Found at i:33813853 original size:28 final size:28
Alignment explanation
Indices: 33813796--33813857 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
33813786 ATGTTTTGTT
** *
33813796 GAACTTAACTTGTATTTACTGTCCCGAC
1 GAACTTAACCCGTATTTACTGTCCCAAC
**
33813824 GAACTTAACCCGTATTTACTGTCTTAAC
1 GAACTTAACCCGTATTTACTGTCCCAAC
33813852 GAACTT
1 GAACTT
33813858 TATTTGTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (28 bp):
GAACTTAACCCGTATTTACTGTCCCAAC
Found at i:33814072 original size:51 final size:51
Alignment explanation
Indices: 33814007--33814149 Score: 142
Period size: 51 Copynumber: 2.8 Consensus size: 51
33813997 TTGTACCATG
* * *
33814007 CTGCCATGGTGTCTTTCATCCATGGTCTTACACTACGTACCTCATACCAAA
1 CTGCCATAGCGTCTTTCATCCATGGTCTTACACTACATACCTCATACCAAA
* ** * * * *
33814058 TTGCCATAGCGTCTTTCATATATGGTCTTACACTATATACCTTATACTAGA
1 CTGCCATAGCGTCTTTCATCCATGGTCTTACACTACATACCTCATACCAAA
* * * * * *
33814109 CTACCATAACATTTTTCATCCATGGTCTTACGCTATATACC
1 CTGCCATAGCGTCTTTCATCCATGGTCTTACACTACATACC
33814150 GTCGTCATGG
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (51 bp):
CTGCCATAGCGTCTTTCATCCATGGTCTTACACTACATACCTCATACCAAA
Found at i:33815478 original size:2 final size:2
Alignment explanation
Indices: 33815471--33815495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33815461 CACAAACGTG
33815471 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
33815496 TCTATCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:33818487 original size:21 final size:21
Alignment explanation
Indices: 33818418--33818500 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
33818408 ATTGGGTGAA
* *
33818418 TTAGCTCTTATGAGCTTCTGT
1 TTAGCTTTTACGAGCTTCTGT
*
33818439 TTAGCTCTTT-CGAG-TTACAGT
1 TTAGCT-TTTACGAGCTT-CTGT
* *
33818460 TCAGCTTTTACGAGCTTTTGT
1 TTAGCTTTTACGAGCTTCTGT
*
33818481 TTAGC-TTT-CAAGCTTCTGT
1 TTAGCTTTTACGAGCTTCTGT
33818500 T
1 T
33818501 GACATATTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
19 10 0.20
20 8 0.16
21 27 0.55
22 4 0.08
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (21 bp):
TTAGCTTTTACGAGCTTCTGT
Found at i:33823588 original size:62 final size:62
Alignment explanation
Indices: 33823491--33823614 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
33823481 ACATACGCAT
33823491 GGTCAGTCGCTAACTTAGGATTTAGGTAAATCACACCATGGATGTCACAAGTGAATTAATTC
1 GGTCAGTCGCTAACTTAGGATTTAGGTAAATCACACCATGGATGTCACAAGTGAATTAATTC
33823553 GGTCAGTCGCTAACTTAGGATTTAGGTAAATCACACCATGGATGTCACAAGTGAATTAATTC
1 GGTCAGTCGCTAACTTAGGATTTAGGTAAATCACACCATGGATGTCACAAGTGAATTAATTC
33823615 ACAAACAGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (62 bp):
GGTCAGTCGCTAACTTAGGATTTAGGTAAATCACACCATGGATGTCACAAGTGAATTAATTC
Found at i:33824176 original size:28 final size:28
Alignment explanation
Indices: 33824133--33824189 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
33824123 TAATATACTT
33824133 ACATTTTACTTGCCTAATGTTTTGATCC
1 ACATTTTACTTGCCTAATGTTTTGATCC
* *
33824161 ACATTTTACTTTCCTAGTGTTTTGATCC
1 ACATTTTACTTGCCTAATGTTTTGATCC
33824189 A
1 A
33824190 ATGTCTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (28 bp):
ACATTTTACTTGCCTAATGTTTTGATCC
Found at i:33824931 original size:31 final size:31
Alignment explanation
Indices: 33824893--33824956 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
33824883 CGTGTTTCGG
33824893 GTTAGTTAGTTTTAGGCTTGGAATTGTTGTT
1 GTTAGTTAGTTTTAGGCTTGGAATTGTTGTT
33824924 GTTAGTTAGTTTTAGGCTTGGAATTGTTGTT
1 GTTAGTTAGTTTTAGGCTTGGAATTGTTGTT
33824955 GT
1 GT
33824957 GTTTTGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.16, C:0.03, G:0.30, T:0.52
Consensus pattern (31 bp):
GTTAGTTAGTTTTAGGCTTGGAATTGTTGTT
Found at i:33829752 original size:28 final size:28
Alignment explanation
Indices: 33829695--33829754 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
33829685 TCATAGGAAT
*
33829695 TAATAGGATAAAATAAATAATTAGTTAA
1 TAATAGGATAAAATAAATAATTAATTAA
*
33829723 TAATAGTA-AAAAT-AATAATTAAATTCAA
1 TAATAGGATAAAATAAATAATT-AATT-AA
33829751 TAAT
1 TAAT
33829755 TATGGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 7 0.25
27 8 0.29
28 13 0.46
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (28 bp):
TAATAGGATAAAATAAATAATTAATTAA
Found at i:33841274 original size:102 final size:102
Alignment explanation
Indices: 33841147--33841377 Score: 417
Period size: 102 Copynumber: 2.3 Consensus size: 102
33841137 ATTGAATAAA
* * * *
33841147 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCTATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTAATTCCCCGACTCATTGGT
33841212 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
*
33841249 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTAATTCCTCGACTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTAATTCCCCGACTCATTGGT
33841314 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
33841351 AAGGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
33841378 GAATCATTGG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 124 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTAATTCCCCGACTCATTGGT
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
Found at i:33841288 original size:27 final size:31
Alignment explanation
Indices: 33841252--33841333 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 31
33841242 AAATGTGAAG
33841252 GGGGTTGCTAAGTGCTGATTCC-C-C-CA-A
1 GGGGTTGCTAAGTGCTGATTCCTCACTCATA
* *
33841279 GGGGTTGCTAAGTGCTAATTCCTCGACTCATT
1 GGGGTTGCTAAGTGCTGATTCCTC-ACTCATA
33841311 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
33841334 ACCGTATCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 21 0.46
28 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 19 0.41
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (31 bp):
GGGGTTGCTAAGTGCTGATTCCTCACTCATA
Found at i:33841373 original size:42 final size:41
Alignment explanation
Indices: 33841314--33841454 Score: 145
Period size: 42 Copynumber: 3.6 Consensus size: 41
33841304 ACTCATTGGT
*
33841314 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGAATCCACCGTATC-TAAATGTGAAGGG
* * *
33841356 GGTTGCTAAGTGCTGATTCC-CCGAATC---AT-T---GGT
1 GGTTGCTAAGTGCTGAATCCACCGTATCTAAATGTGAAGGG
* * *
33841389 GGTTGCTAACTGCTGAAACCACCGTATCATAAATGTGAAAGG
1 GGTTGCTAAGTGCTGAATCCACCGTATC-TAAATGTGAAGGG
33841431 GGTTGCTAAGTGCTGAATCCACCG
1 GGTTGCTAAGTGCTGAATCCACCG
33841455 ATAACGGTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
33 19 0.24
34 6 0.08
36 1 0.01
37 2 0.03
38 2 0.03
39 1 0.01
41 6 0.08
42 43 0.54
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGAATCCACCGTATCTAAATGTGAAGGG
Found at i:33841445 original size:75 final size:75
Alignment explanation
Indices: 33841277--33841455 Score: 268
Period size: 75 Copynumber: 2.4 Consensus size: 75
33841267 TGATTCCCCC
* * * * **
33841277 AAGGGGTTGCTAAGTGCTAATTCCTCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAACTGCTGAAACCACCGTATC
*
33841342 TTAAATGTGA
66 ATAAATGTGA
*
33841352 AGGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAACTGCTGAAACCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAACTGCTGAAACCACCGTATC
33841417 ATAAATGTGA
66 ATAAATGTGA
*
33841427 AAGGGGTTGCTAAGTGCTGAATCCACCGA
1 AAGGGGTTGCTAAGTGCTGATTCC-CCGA
33841456 TAACGGTTAA
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 89 0.96
76 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAACTGCTGAAACCACCGTATC
ATAAATGTGA
Found at i:33845014 original size:78 final size:78
Alignment explanation
Indices: 33844930--33845085 Score: 285
Period size: 78 Copynumber: 2.0 Consensus size: 78
33844920 CCGTTATACA
* * *
33844930 CACAATTTATTTATGTTTTTTTGAGTTAATAATAATTCTCTTTGAGTTTTTCTTCAAGAATTGCT
1 CACAATTGATTTATGTTTTATTGAGTTAATAATAATTCTCTTTGAATTTTTCTTCAAGAATTGCT
33844995 CTTGAGTTTCTTT
66 CTTGAGTTTCTTT
33845008 CACAATTGATTTATGTTTTATTGAGTTAATAATAATTCTCTTTGAATTTTTCTTCAAGAATTGCT
1 CACAATTGATTTATGTTTTATTGAGTTAATAATAATTCTCTTTGAATTTTTCTTCAAGAATTGCT
33845073 CTTGAGTTTCTTT
66 CTTGAGTTTCTTT
33845086 TAGAAGCTGT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (78 bp):
CACAATTGATTTATGTTTTATTGAGTTAATAATAATTCTCTTTGAATTTTTCTTCAAGAATTGCT
CTTGAGTTTCTTT
Found at i:33846876 original size:21 final size:21
Alignment explanation
Indices: 33846843--33846888 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33846833 ACTTGGATCT
33846843 AGTCCAATATCCTGTCAGTCC
1 AGTCCAATATCCTGTCAGTCC
* * *
33846864 AGTCTAATGTCCTGTTAGTCC
1 AGTCCAATATCCTGTCAGTCC
33846885 AGTC
1 AGTC
33846889 AGTTACATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (21 bp):
AGTCCAATATCCTGTCAGTCC
Found at i:33847749 original size:32 final size:33
Alignment explanation
Indices: 33847707--33847768 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
33847697 AAACCCCTTT
33847707 TAAAAGTATCCCATAAAATCCTAATCAATCTCA
1 TAAAAGTATCCCATAAAATCCTAATCAATCTCA
*
33847740 TAAAA-TATCCTATAAAATCCTAATCAATC
1 TAAAAGTATCCCATAAAATCCTAATCAATC
33847769 CCTAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.29
Consensus pattern (33 bp):
TAAAAGTATCCCATAAAATCCTAATCAATCTCA
Found at i:33847777 original size:32 final size:32
Alignment explanation
Indices: 33847707--33847778 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
33847697 AAACCCCTTT
* *
33847707 TAAAAGTATCCCATAAAATCCTAATCAATCTC
1 TAAAAATATCCCATAAAATCCTAATCAATCCC
*
33847739 -ATAAAATATCCTATAAAATCCTAATCAATCCC
1 TA-AAAATATCCCATAAAATCCTAATCAATCCC
33847771 TAAAAATA
1 TAAAAATA
33847779 GAGTTTCTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 1 0.03
32 33 0.94
33 1 0.03
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.28
Consensus pattern (32 bp):
TAAAAATATCCCATAAAATCCTAATCAATCCC
Found at i:33853360 original size:12 final size:11
Alignment explanation
Indices: 33853334--33853359 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
33853324 TCAAATATTC
33853334 AAAATATTTTT
1 AAAATATTTTT
33853345 AAAATATTTTT
1 AAAATATTTTT
33853356 AAAA
1 AAAA
33853360 AAGATTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:33858367 original size:67 final size:66
Alignment explanation
Indices: 33858248--33858533 Score: 231
Period size: 67 Copynumber: 4.3 Consensus size: 66
33858238 GAGGTATAAG
* * ** *** *
33858248 GTGTAAGACCATAACTCGAATATGGCAGCATAA-AGAGTCCACCAAGATAGTAAACATGAGGTAT
1 GTGTAAGACCATAGCTCGACTATGGCAGCA-AAGAGAGTCTGCTGGGACAGTAAACATG-GGTAT
33858312 GTT
64 GTT
* * * * * * *
33858315 ATGTATGATCATAGTTCGGCTATGGCAGCAAAGAGAGTCTG-TCGGGAGAGTAAACACGGGGTAT
1 GTGTAAGACCATAGCTCGACTATGGCAGCAAAGAGAGTCTGCT-GGGACAGTAAACA-TGGGTAT
33858379 GTT
64 GTT
* * * * * *
33858382 GCGTAAGACCAAAGCTCAACTATGGCAACATAGAGAGTCTGCTGGGACAATAAACATGGTGTATG
1 GTGTAAGACCATAGCTCGACTATGGCAGCAAAGAGAGTCTGCTGGGACAGTAAACATGG-GTATG
33858447 TT
65 TT
* ** *
33858449 GTGTAAGACCATAGCTCGACTATGGCAGCATAA-AAAGT-TCGCCAGGACAATAAACACAT-GGT
1 GTGTAAGACCATAGCTCGACTATGGCAGCA-AAGAGAGTCT-GCTGGGACAGT-AA-ACATGGGT
33858511 ATGTT
62 ATGTT
33858516 GTGTAAGACCATAGCTCG
1 GTGTAAGACCATAGCTCG
33858534 CCTACGACGG
Statistics
Matches: 175, Mismatches: 35, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
66 5 0.03
67 160 0.91
68 6 0.03
69 4 0.02
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (66 bp):
GTGTAAGACCATAGCTCGACTATGGCAGCAAAGAGAGTCTGCTGGGACAGTAAACATGGGTATGT
T
Found at i:33864339 original size:29 final size:30
Alignment explanation
Indices: 33864289--33864345 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
33864279 GTAATTTGGG
*
33864289 CTAAATTGTGAAAATAATAAAT-TGAGGGA
1 CTAAAATGTGAAAATAATAAATGTGAGGGA
33864318 CTAAAATGTGAAAA-AATAAAATGTGAGG
1 CTAAAATGTGAAAATAAT-AAATGTGAGG
33864346 ACTTATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 17 0.68
30 5 0.20
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.25
Consensus pattern (30 bp):
CTAAAATGTGAAAATAATAAATGTGAGGGA
Found at i:33864901 original size:43 final size:43
Alignment explanation
Indices: 33864813--33864924 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 43
33864803 CCGATAAGTG
* **
33864813 TTACAGTGTAAGACCTTGTGTGGGACAGTGGCATCAATTTATAA
1 TTACA-TGTAAGACCTTGTGTGGGACAGCGGCATCAATACATAA
* ** *
33864857 TTGCGA-GTAAGACCTTGTGTGGGACAGCGGCATCGCTACGTAA
1 TTAC-ATGTAAGACCTTGTGTGGGACAGCGGCATCAATACATAA
**
33864900 TTACATGTAAGACCACGTGTGGGAC
1 TTACATGTAAGACCTTGTGTGGGAC
33864925 GTTGGTATTG
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 1 0.02
43 51 0.91
44 3 0.05
45 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
TTACATGTAAGACCTTGTGTGGGACAGCGGCATCAATACATAA
Found at i:33870207 original size:3 final size:3
Alignment explanation
Indices: 33870199--33870250 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
33870189 AAAGTGAATG
* * *
33870199 AAT AAT AAT AATT ATT ATT AAT AAT AAT AAT TAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33870245 AAT AAT
1 AAT AAT
33870251 TATTATTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:33875636 original size:14 final size:14
Alignment explanation
Indices: 33875617--33875646 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33875607 AATGAAAAAC
33875617 GCAAATAATCATTG
1 GCAAATAATCATTG
*
33875631 GCAAATAGTCATTG
1 GCAAATAATCATTG
33875645 GC
1 GC
33875647 TTCATTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (14 bp):
GCAAATAATCATTG
Found at i:33876037 original size:19 final size:18
Alignment explanation
Indices: 33876014--33876054 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
33876004 ATCTTTGTAC
33876014 CAAAAAGCAAAAAA-AAAA
1 CAAAAA-CAAAAAAGAAAA
33876032 CAAAAACAAAAAAGGAAAA
1 CAAAAACAAAAAA-GAAAA
33876051 CAAA
1 CAAA
33876055 TCTTTGTGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 6 0.29
19 8 0.38
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (18 bp):
CAAAAACAAAAAAGAAAA
Found at i:33886335 original size:20 final size:20
Alignment explanation
Indices: 33886312--33886378 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
33886302 AAATAAGTTT
*
33886312 AATAAAATGGAAATTTATTG
1 AATAAATTGGAAATTTATTG
33886332 AATAAATTGGAAATTTATTG
1 AATAAATTGGAAATTTATTG
* *
33886352 AATAAATTAGAATTTTATTG
1 AATAAATTGGAAATTTATTG
33886372 AATAAAT
1 AATAAAT
33886379 AAAAGGAACA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (20 bp):
AATAAATTGGAAATTTATTG
Found at i:33890929 original size:16 final size:16
Alignment explanation
Indices: 33890908--33890940 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33890898 TTTGCTCGTC
33890908 CTACGTGGTGCGCTTT
1 CTACGTGGTGCGCTTT
33890924 CTACGTGGTGCGCTTT
1 CTACGTGGTGCGCTTT
33890940 C
1 C
33890941 CTTCTGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.27, G:0.30, T:0.36
Consensus pattern (16 bp):
CTACGTGGTGCGCTTT
Found at i:33898687 original size:17 final size:18
Alignment explanation
Indices: 33898661--33898699 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
33898651 GTTATTGTGG
33898661 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
33898677 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
33898695 AAAAT
1 AAAAT
33898700 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:33898876 original size:15 final size:15
Alignment explanation
Indices: 33898856--33898886 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33898846 AAAACAATAT
33898856 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
33898871 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
33898886 A
1 A
33898887 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:33900476 original size:15 final size:15
Alignment explanation
Indices: 33900466--33900495 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33900456 TCCCTTCTTG
33900466 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
33900481 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
33900496 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:33901452 original size:15 final size:15
Alignment explanation
Indices: 33901432--33901462 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33901422 AAAACAATAT
33901432 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
33901447 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
33901462 A
1 A
33901463 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:33903385 original size:9 final size:9
Alignment explanation
Indices: 33903371--33903395 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
33903361 GGAAAAATCA
33903371 GCTTGATTT
1 GCTTGATTT
33903380 GCTTGATTT
1 GCTTGATTT
33903389 GCTTGAT
1 GCTTGAT
33903396 GTATGGCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.52
Consensus pattern (9 bp):
GCTTGATTT
Found at i:33914146 original size:16 final size:16
Alignment explanation
Indices: 33914127--33914157 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33914117 ACTTCTCATC
*
33914127 ATTCTCTCATCTCTCA
1 ATTCTCTCAACTCTCA
33914143 ATTCTCTCAACTCTC
1 ATTCTCTCAACTCTC
33914158 TTAGCTCTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.39, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTCTCTCAACTCTCA
Found at i:33921180 original size:51 final size:52
Alignment explanation
Indices: 33921120--33921220 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 52
33921110 AAGGTGGAAG
* * *
33921120 CAGTGGCAGTATATCTGCAATTCAGTTGTGGCTTGTCCAC-ATTAGTGTTAT
1 CAGTGGCAGTATATCTGCAAATCAGTGGTGGCTTGTCCACAAATAGTGTTAT
* *
33921171 CAGTGGCAGTTTATTTGCAAATCAGTGGTGGCTTGTCCACAAATAGTGTT
1 CAGTGGCAGTATATCTGCAAATCAGTGGTGGCTTGTCCACAAATAGTGTT
33921221 TTGGATGGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 36 0.82
52 8 0.18
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (52 bp):
CAGTGGCAGTATATCTGCAAATCAGTGGTGGCTTGTCCACAAATAGTGTTAT
Found at i:33921304 original size:16 final size:16
Alignment explanation
Indices: 33921283--33921314 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33921273 AGGAACTTTA
*
33921283 TAAAATGTGCATCGAT
1 TAAAATATGCATCGAT
33921299 TAAAATATGCATCGAT
1 TAAAATATGCATCGAT
33921315 ATGTCCTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (16 bp):
TAAAATATGCATCGAT
Found at i:33927502 original size:14 final size:15
Alignment explanation
Indices: 33927480--33927556 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
33927470 CAATCAAACA
33927480 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
33927494 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
33927509 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
33927529 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
33927543 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
33927557 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:33927521 original size:20 final size:20
Alignment explanation
Indices: 33927496--33927535 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
33927486 AATATTTTCC
*
33927496 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
33927516 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
33927536 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:33927541 original size:34 final size:35
Alignment explanation
Indices: 33927484--33927550 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
33927474 CAAACACCAG
*
33927484 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
33927519 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
33927551 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:33930270 original size:114 final size:114
Alignment explanation
Indices: 33930065--33930309 Score: 409
Period size: 114 Copynumber: 2.1 Consensus size: 114
33930055 CTTAAGTTTT
*
33930065 AATAATGGAATTGCAATATTTAGAAATTGTAATATTTTCTATAATGGATGGATGTCAAATAATAT
1 AATAATGGAATTGCAATATTTAGAAATTGTAATATTTTCTATAATAGATGGATGTCAAATAATAT
*
33930130 CTACTTTATCAAATCAAAGATCTACACATTGATTGAGACTAAAATATCG
66 CTACTTTATCAAATCAAAGATCTACACATTGATTGAGACTAAAATATCA
* *
33930179 AATAATGGAATTGCAATATTTAGAAATTGTAATATTTTCTGTAATAGATGGATGTTAAATAATAT
1 AATAATGGAATTGCAATATTTAGAAATTGTAATATTTTCTATAATAGATGGATGTCAAATAATAT
* * * *
33930244 CTACTTTATCAAATCAAAGATGTACACATTGTTTGAGACTGAAATATTA
66 CTACTTTATCAAATCAAAGATCTACACATTGATTGAGACTAAAATATCA
*
33930293 AATAATAGAATTGCAAT
1 AATAATGGAATTGCAAT
33930310 TTTTTCTGTA
Statistics
Matches: 122, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 122 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (114 bp):
AATAATGGAATTGCAATATTTAGAAATTGTAATATTTTCTATAATAGATGGATGTCAAATAATAT
CTACTTTATCAAATCAAAGATCTACACATTGATTGAGACTAAAATATCA
Found at i:33930317 original size:98 final size:94
Alignment explanation
Indices: 33930203--33930382 Score: 270
Period size: 94 Copynumber: 1.9 Consensus size: 94
33930193 AATATTTAGA
* * *
33930203 AATTGTAATATTTTCTGTAATAGATGGATGTTAAATAATATCTACTTTATCAAATCAAAGATGTA
1 AATTGCAATATTTTCTGTAAT--A--GATGTCAAATAATATCTACCTTATCAAATCAAAGATGTA
*
33930268 CACATTGTTTGAGACTGAAATATTAAATAATAG
62 CACATTATTTGAGACTGAAATATTAAATAATAG
*
33930301 AATTGCAATTTTTTCTGTAATAGATGTCAAATAATATCTACCTTATCAAATCAAAGATGTACACA
1 AATTGCAATATTTTCTGTAATAGATGTCAAATAATATCTACCTTATCAAATCAAAGATGTACACA
*
33930366 TTATTTGAGATTGAAAT
66 TTATTTGAGACTGAAAT
33930383 CTAGAATAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 56 0.74
96 1 0.01
98 19 0.25
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (94 bp):
AATTGCAATATTTTCTGTAATAGATGTCAAATAATATCTACCTTATCAAATCAAAGATGTACACA
TTATTTGAGACTGAAATATTAAATAATAG
Found at i:33930869 original size:32 final size:32
Alignment explanation
Indices: 33930828--33930894 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
33930818 ATATTTATCT
33930828 GATGAGTTCATAGGGTACCTCATAGAGAATGA
1 GATGAGTTCATAGGGTACCTCATAGAGAATGA
33930860 GATGAGTTCATAGGGTACCTCATAGAGAATGA
1 GATGAGTTCATAGGGTACCTCATAGAGAATGA
33930892 GAT
1 GAT
33930895 TCTATCCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.25
Consensus pattern (32 bp):
GATGAGTTCATAGGGTACCTCATAGAGAATGA
Found at i:33941881 original size:6 final size:6
Alignment explanation
Indices: 33941870--33941902 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
33941860 TTTTTGAAAA
33941870 AAAATT AAAATT AAAA-T AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
33941903 ATTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (6 bp):
AAAATT
Found at i:33941891 original size:11 final size:12
Alignment explanation
Indices: 33941870--33941902 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
33941860 TTTTTGAAAA
33941870 AAAATTAAAATT
1 AAAATTAAAATT
33941882 AAAA-TAAAATT
1 AAAATTAAAATT
33941893 AAAATTAAAA
1 AAAATTAAAA
33941903 ATTTTGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAATTAAAATT
Found at i:33941892 original size:17 final size:16
Alignment explanation
Indices: 33941866--33941903 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
33941856 TTTATTTTTG
33941866 AAAAAAAATTAAAATT
1 AAAAAAAATTAAAATT
33941882 AAAATAAAATTAAAATT
1 AAAA-AAAATTAAAATT
33941899 AAAAA
1 AAAAA
33941904 TTTTGCTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAAAATTAAAATT
Found at i:33942600 original size:46 final size:47
Alignment explanation
Indices: 33942543--33942636 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
33942533 GACCCAAGCC
* * *
33942543 CCGTTATAACCTAAC-AAAACCCTTTGATCTTTGCATCTGATTCTAA
1 CCGTTACAACCTAACAAAAACCCTTTGATCTTTACATCCGATTCTAA
33942589 CCGTTACAACCTAACAAAAACCCTTTGATCTTTACATCCGATTCTAA
1 CCGTTACAACCTAACAAAAACCCTTTGATCTTTACATCCGATTCTAA
33942636 C
1 C
33942637 TCTAGTGGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 14 0.32
47 30 0.68
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (47 bp):
CCGTTACAACCTAACAAAAACCCTTTGATCTTTACATCCGATTCTAA
Found at i:33943792 original size:13 final size:13
Alignment explanation
Indices: 33943774--33943798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33943764 TTAAGTTTTT
33943774 TTATATTATTATC
1 TTATATTATTATC
33943787 TTATATTATTAT
1 TTATATTATTAT
33943799 TTAATTTCAT
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATATTATTATC
Found at i:33947199 original size:4 final size:4
Alignment explanation
Indices: 33947190--33947215 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
33947180 TTTTCTTCCA
33947190 ATTC ATTC ATTC ATTC ATTC ATTC AT
1 ATTC ATTC ATTC ATTC ATTC ATTC AT
33947216 AATCATACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTC
Found at i:33948082 original size:8 final size:8
Alignment explanation
Indices: 33948041--33948065 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
33948031 AGAGTATTTC
33948041 AAAAAAAT
1 AAAAAAAT
33948049 AAAAAAAT
1 AAAAAAAT
33948057 AAAAAAAT
1 AAAAAAAT
33948065 A
1 A
33948066 TTTCAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:33948104 original size:6 final size:6
Alignment explanation
Indices: 33948087--33948133 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
33948077 TGAAAATGAT
* *
33948087 GAAAAA -AAAAA GAAAAA GAGAAG GAAAAA G-AAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
33948133 G
1 G
33948134 GAGAGGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:33949993 original size:24 final size:24
Alignment explanation
Indices: 33949956--33950017 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
33949946 TTTATGTCTC
*
33949956 AAAAGTACAGTGGATTGAACCTTG
1 AAAATTACAGTGGATTGAACCTTG
*
33949980 AAGATTACAGTGGATTGAACCTTG
1 AAAATTACAGTGGATTGAACCTTG
33950004 AAAATTACAGTGGA
1 AAAATTACAGTGGA
33950018 GGCAATCTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAATTACAGTGGATTGAACCTTG
Found at i:33950406 original size:44 final size:43
Alignment explanation
Indices: 33950343--33950866 Score: 307
Period size: 44 Copynumber: 11.8 Consensus size: 43
33950333 GAAGATGGTG
33950343 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCAAT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAA-CAAT
* * *** *
33950387 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTTAC
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACAAT
* ** * * *
33950430 AAGTCTTTTCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAAAAC
1 AA-TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA-ACAAT
* * * * * ***
33950475 AAGTCTTATCCCCCTAAAGTTGTAGTGGGGCAGAATGAAGATGGT
1 AA-TCTTATCTCCCTGAAGTTGTAGTGGAGCAG-ATTAAAACAAT
* * * * *
33950520 GAATTTTATCTCCTTGAAGTTGTAGTGGAGCAAATTAAAGCCGAT
1 -AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA-ACAAT
* * * *** *
33950565 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTGAC
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACAAT
* * **
33950608 AAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATAGCG
1 AA-TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA-ACA-AT
* * * * *
33950654 AATCTTATTTCTCTGCAGTTGTAGTGGAACAGATTAAAGCTATAAAT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA---A-CAAT
* * * * ***
33950701 CACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATGGC-A-
1 ---A-ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACAAT
** **
33950746 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTACAGCCAAT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTA-AAACAAT
* * * **
33950790 AAT-TCTATCTCCTTGAAGTTGTAGTGGAGCGGATTGAAGACACC
1 AATCT-TATCTCCCTGAAGTTGTAGTGGAGCAGATT-AAAACAAT
* *
33950834 ACTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGA
33950867 CTGAAGATAG
Statistics
Matches: 367, Mismatches: 92, Indels: 42
0.73 0.18 0.08
Matches are distributed among these distances:
41 31 0.08
42 3 0.01
43 9 0.02
44 194 0.53
45 90 0.25
46 8 0.02
47 1 0.00
48 1 0.00
50 1 0.00
51 29 0.08
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACAAT
Found at i:33950630 original size:88 final size:88
Alignment explanation
Indices: 33950345--33950863 Score: 364
Period size: 88 Copynumber: 5.8 Consensus size: 88
33950335 AGATGGTGAA
*
33950345 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACCAATAATCCTATCTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGTA
*
33950410 GTGGAGCGGATTAAAGTTACAAG
66 GTGGAGCGGATTAAAGTGACAAG
* ** * ** * * * *
33950433 TCTTTTCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAAAACAAGTCTTATCCCCCTAAAGTTGT
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAA-TCCTATCTCCCTGAAGTTGT
* * * * **
33950498 AGTGGGGCAGAATGAAGATGGTGAA-
65 AGTGGAGCGGATTAAAG-T-GACAAG
* * * * *
33950523 TTTTATCTCCTTGAAGTTGTAGTGGAGCAAATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGTA
33950588 GTGGAGCGGATTAAAGTGACAAG
66 GTGGAGCGGATTAAAGTGACAAG
* ** ** * * * *
33950611 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATAGCGAATCTTATTTCTCTGCAGTTGT
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCA-ATAATCCTATCTCCCTGAAGTTGT
* * *
33950676 AGTGGAACAGATTAAAGCTATAAATCACAG
65 AGTGGAGCGGATTAAAG---T-GA-CA-AG
* * * * * * * **
33950706 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCATGGC-A-AATCTTATCTCCCTGAAGTTAC
1 -TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGT
* * ** * *
33950768 AGTGGAGCAGATTACAGCCAATAAT
65 AGTGGAGCGGATTAAAG-TGACAAG
* * * * ** * * *
33950793 TC-TATCTCCTTGAAGTTGTAGTGGAGCGGATTGAAGACACCACTCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGTA
33950857 GTGGAGC
66 GTGGAGC
33950864 AGACTGAAGA
Statistics
Matches: 330, Mismatches: 86, Indels: 30
0.74 0.19 0.07
Matches are distributed among these distances:
85 23 0.07
86 6 0.02
87 4 0.01
88 99 0.30
89 93 0.28
90 34 0.10
91 2 0.01
92 33 0.10
93 1 0.00
94 2 0.01
95 5 0.02
96 28 0.08
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGTA
GTGGAGCGGATTAAAGTGACAAG
Found at i:33950690 original size:133 final size:134
Alignment explanation
Indices: 33950345--33950911 Score: 402
Period size: 133 Copynumber: 4.2 Consensus size: 134
33950335 AGATGGTGAA
* * * *
33950345 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA-ACCA-ATAATCCTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGAATAAAGA-TAGAGAATCTTATCT-CCTGAAGTTG
* ** * *
33950408 TAGTGGAGCGGATTAAAG-TTACAAGTCTTTTCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAA
64 TAGTGGAGCAGATTAAAGCCGACAAGTCCTATCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAA
33950472 AACAAG
129 AACAAG
* * * * * * *
33950478 TCTTATCCCCCTAAAGTTGTAGTGGGGCAGAATGAAGATGGTGAATTTTATCTCCTTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGAATAAAGATAGAGAATCTTATCTCC-TGAAGTTGT
* * * * * **
33950543 AGTGGAGCAAATTAAAGCCGATAA-TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAG-TG
65 AGTGGAGCAGATTAAAGCCGACAAGTCCTATCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAAA
33950606 ACAAG
130 ACAAG
* * * *
33950611 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATAGCGAATCTTATTTCTCTGCAGTTGT
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGAATAAAGATAGAGAATCTTATCTC-CTGAAGTTGT
* ** * * * * *
33950676 AGTGGAACAGATTAAAGCTATAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TC
65 AGTGGAGCAGATTAAAGC---CGA-CA-AG-TCCTATCTCCCTGAAGTTACAGTGGAGCAGACTA
* * *
33950740 ATG---GCAAA
124 AAGAAAACAAG
** * * ** *
33950748 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTACAGCCA-ATAAT-TCTATCTCCTTGAAGTTG
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGAATAAAGATAGAGAATCT-TATCTCC-TGAAGTTG
* * * * * * * * *
33950811 TAGTGGAGCGGATTGAAGAC-ACCACTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT
64 TAGTGGAGCAGATTAAAGCCGACAAGTCCTATCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAA
* **
33950875 AGCGGG
129 AACAAG
* * *
33950881 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGA
33950912 CCATAACAAG
Statistics
Matches: 343, Mismatches: 73, Indels: 36
0.76 0.16 0.08
Matches are distributed among these distances:
129 29 0.08
130 4 0.01
131 1 0.00
132 1 0.00
133 137 0.40
134 66 0.19
135 5 0.01
136 31 0.09
137 38 0.11
138 1 0.00
139 3 0.01
140 27 0.08
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (134 bp):
TCTTATCTCCCTGAAGTTGTAGTGGAGCAGAATAAAGATAGAGAATCTTATCTCCTGAAGTTGTA
GTGGAGCAGATTAAAGCCGACAAGTCCTATCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAAAA
CAAG
Found at i:33950872 original size:44 final size:42
Alignment explanation
Indices: 33950701--33950953 Score: 165
Period size: 44 Copynumber: 5.9 Consensus size: 42
33950691 AGCTATAAAT
* * * * *
33950701 CACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATGG
1 CACA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAGA
* * *
33950744 CA-AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTACAGC
1 CACAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGA-AGA
* * * *
33950786 CAATAAT-TCTATCTCCTTGAAGTTGTAGTGGAGCGGATTGAAGA
1 C-ACAATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAGA
*
33950830 CACCACTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
1 CA-CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAGA
* ** * * **
33950874 TAGCGGGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGACCATA-A
1 CA-C-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGA-AGA
* * *
33950918 CA-AGTCCTATCCCCCTGAAGTTGCAGTAGG-GCAGAT
1 CACAATCTTATCTCCCTGAAGTTGCAGT-GGAGCAGAT
33950954 TGAATATAGC
Statistics
Matches: 167, Mismatches: 33, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
41 57 0.34
42 4 0.02
43 5 0.03
44 68 0.41
45 33 0.20
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.26
Consensus pattern (42 bp):
CACAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAGA
Found at i:33952414 original size:3 final size:3
Alignment explanation
Indices: 33952406--33952444 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
33952396 ACTGGTTTAA
* *
33952406 TAT TAT TAT TAC TAT TAT TAT TAT TAG T-T TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
33952445 TTTTATATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 30 0.97
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:33952535 original size:13 final size:13
Alignment explanation
Indices: 33952517--33952541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33952507 TTTAAGTTTT
33952517 TTATATTATTATA
1 TTATATTATTATA
33952530 TTATATTATTAT
1 TTATATTATTAT
33952542 TTAATTTCAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATATTATTATA
Found at i:33959294 original size:45 final size:46
Alignment explanation
Indices: 33959224--33959319 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 46
33959214 CCCTTGATCA
* *
33959224 AGTATAGATAATTAATAATAAATACTATCTAATTTAGTTAA-ATTT
1 AGTATAAATAATTAATAATAAATACTATCTAATTTAGGTAATATTT
* *
33959269 AGTATAAATAATTTAA-AATATATACTATGTAATTTAGGTAATTATTT
1 AGTATAAATAA-TTAATAATAAATACTATCTAATTTAGGTAA-TATTT
33959316 AGTA
1 AGTA
33959320 GGTCAAATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
45 32 0.73
46 4 0.09
47 8 0.18
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (46 bp):
AGTATAAATAATTAATAATAAATACTATCTAATTTAGGTAATATTT
Found at i:33963054 original size:162 final size:163
Alignment explanation
Indices: 33962786--33963099 Score: 567
Period size: 162 Copynumber: 1.9 Consensus size: 163
33962776 AAAATATTGT
* *
33962786 ATGTGAAACTTTGAAATTGTACCACATCATCACCTGAAAATTCATATAATTTTTTTAAATTTTCA
1 ATGTGAAACTTTGAAATTGTACCACATCATCACCTAAAAATTCATATAATATTTTTAAATTTTCA
* *
33962851 AGTGATGATGTAGCACAATCTCATAGTGCCACATCATCAAACTTTTATAGTTTTCAAGTTTGGGA
66 AGTGATGATGTAGCACAATCTCATAATGCCACATCATCAAACTTTTATAGGTTTCAAGTTTGGGA
33962916 CTAAAATGGACTCAGTTGTCAAATTTAAGTGCC
131 CTAAAATGGACTCAGTTGTCAAATTTAAGTGCC
*
33962949 ATGTGAAACTTTGAAATTGTATCACATCATCACCTAAAAATTCATAT-ATATTTTTAAATTTTCA
1 ATGTGAAACTTTGAAATTGTACCACATCATCACCTAAAAATTCATATAATATTTTTAAATTTTCA
*
33963013 AGTGATGATGTTGCACAATCTCATAATGCCACATCATCAAACTTTTATAGGTTTCAAGTTTGGGA
66 AGTGATGATGTAGCACAATCTCATAATGCCACATCATCAAACTTTTATAGGTTTCAAGTTTGGGA
33963078 CTAAAATGGACTCAGTTGTCAA
131 CTAAAATGGACTCAGTTGTCAA
33963100 GTTGGTACCT
Statistics
Matches: 145, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
162 100 0.69
163 45 0.31
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (163 bp):
ATGTGAAACTTTGAAATTGTACCACATCATCACCTAAAAATTCATATAATATTTTTAAATTTTCA
AGTGATGATGTAGCACAATCTCATAATGCCACATCATCAAACTTTTATAGGTTTCAAGTTTGGGA
CTAAAATGGACTCAGTTGTCAAATTTAAGTGCC
Found at i:33964969 original size:18 final size:18
Alignment explanation
Indices: 33964946--33964981 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
33964936 TTTTCATACT
33964946 CTTCATCATCTTCTTCTC
1 CTTCATCATCTTCTTCTC
*
33964964 CTTCATCTTCTTCTTCTC
1 CTTCATCATCTTCTTCTC
33964982 AGCATAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.39, G:0.00, T:0.53
Consensus pattern (18 bp):
CTTCATCATCTTCTTCTC
Found at i:33974507 original size:83 final size:82
Alignment explanation
Indices: 33974364--33974526 Score: 211
Period size: 83 Copynumber: 2.0 Consensus size: 82
33974354 TTAGAGGGCT
* * * *
33974364 AAAGTATAATTTTACTATATATTAATTAACAATTTCTTTATTTATAAGAGGACTATATTGAAAAA
1 AAAGTACAATTTCACTATATATTAATTAACAAATTCTCTATTTATAAGAGGACTATATTG-AAAA
33974429 TTTTAATTTTAAGGGGTC
65 TTTTAATTTTAAGGGGTC
* * * *
33974447 AAAGTACAATTTCACTATATATTAATTTATAAATTCTCTATTTATAAGAGGATTGA-ATTGAAAT
1 AAAGTACAATTTCACTATATATTAATTAACAAATTCTCTATTTATAAGAGGACT-ATATTGAAAA
* *
33974511 TTTTATTTTTGAGGGG
65 TTTTAATTTTAAGGGG
33974527 CCAAGGTGTA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
82 17 0.25
83 51 0.74
84 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (82 bp):
AAAGTACAATTTCACTATATATTAATTAACAAATTCTCTATTTATAAGAGGACTATATTGAAAAT
TTTAATTTTAAGGGGTC
Found at i:33977691 original size:13 final size:13
Alignment explanation
Indices: 33977673--33977697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33977663 ACTTACAAAT
33977673 TTTTTTAAATATA
1 TTTTTTAAATATA
33977686 TTTTTTAAATAT
1 TTTTTTAAATAT
33977698 TTTCAATTCT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTAAATATA
Found at i:33981914 original size:17 final size:18
Alignment explanation
Indices: 33981892--33981926 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
33981882 AATTGGGCCA
33981892 TGTGGG-CCACACGGGTG
1 TGTGGGCCCACACGGGTG
33981909 TGTGGGCCCACACGGGTG
1 TGTGGGCCCACACGGGTG
33981927 AACCACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.11, C:0.26, G:0.46, T:0.17
Consensus pattern (18 bp):
TGTGGGCCCACACGGGTG
Found at i:33987231 original size:34 final size:32
Alignment explanation
Indices: 33987192--33987303 Score: 107
Period size: 34 Copynumber: 3.3 Consensus size: 32
33987182 ATTATGTATT
**
33987192 TAATAGAAGAATACAGTAGTAATAAATATGCTTA
1 TAATAGATCAATACAGTA-TAAT-AATATGCTTA
* *
33987226 TAATAGTTCAATACAATATCAATTAATATGCTTA
1 TAATAGATCAATACAGTAT-AA-TAATATGCTTA
* * *
33987260 TAACAGTTCAATACAGTAACAAGTAATATGCTTA
1 TAATAGATCAATACAGT-ATAA-TAATATGCTTA
33987294 TAATAGATCA
1 TAATAGATCA
33987304 GCTTAGTAGT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
33 1 0.02
34 62 0.95
35 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (32 bp):
TAATAGATCAATACAGTATAATAATATGCTTA
Found at i:33991366 original size:24 final size:26
Alignment explanation
Indices: 33991337--33991384 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
33991327 ATATCAGAGA
*
33991337 AAAATACT-ATACA-TAGTTATACTG
1 AAAATACTAATAAAGTAGTTATACTG
*
33991361 AAAATAGTAATAAAGTAGTTATAC
1 AAAATACTAATAAAGTAGTTATAC
33991385 AAAATATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 4 0.20
26 9 0.45
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.31
Consensus pattern (26 bp):
AAAATACTAATAAAGTAGTTATACTG
Found at i:33991741 original size:99 final size:99
Alignment explanation
Indices: 33991570--33991766 Score: 394
Period size: 99 Copynumber: 2.0 Consensus size: 99
33991560 TTCCTCGGAG
33991570 ACGAACAAAAGTCTACAAATCTAAACATGAAGACAATTTGGAGATTGAGCTTTACAAGCTTAGTG
1 ACGAACAAAAGTCTACAAATCTAAACATGAAGACAATTTGGAGATTGAGCTTTACAAGCTTAGTG
33991635 GTACACAACAAATCTACCATATTTCAAGCAATTC
66 GTACACAACAAATCTACCATATTTCAAGCAATTC
33991669 ACGAACAAAAGTCTACAAATCTAAACATGAAGACAATTTGGAGATTGAGCTTTACAAGCTTAGTG
1 ACGAACAAAAGTCTACAAATCTAAACATGAAGACAATTTGGAGATTGAGCTTTACAAGCTTAGTG
33991734 GTACACAACAAATCTACCATATTTCAAGCAATT
66 GTACACAACAAATCTACCATATTTCAAGCAATT
33991767 TATAAATATA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (99 bp):
ACGAACAAAAGTCTACAAATCTAAACATGAAGACAATTTGGAGATTGAGCTTTACAAGCTTAGTG
GTACACAACAAATCTACCATATTTCAAGCAATTC
Found at i:33995531 original size:31 final size:31
Alignment explanation
Indices: 33995465--33995532 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
33995455 AATTTTTTTT
* * *
33995465 ATTTTTGTGCAAATATACACATTAAAGTTTG
1 ATTTTTGTGCAAATATACACATAAAACTTTA
* *
33995496 ATTTTTGTTG-AAATATATATATAAAACTTTA
1 ATTTTTG-TGCAAATATACACATAAAACTTTA
33995527 ATTTTT
1 ATTTTT
33995533 ATTAATTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (31 bp):
ATTTTTGTGCAAATATACACATAAAACTTTA
Found at i:33999216 original size:23 final size:23
Alignment explanation
Indices: 33999186--33999232 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
33999176 TGTTACTAGA
33999186 ATTTTTTGTTTTCTCCAAGTATT
1 ATTTTTTGTTTTCTCCAAGTATT
33999209 ATTTTTTGTTTTCTCCAAGTATT
1 ATTTTTTGTTTTCTCCAAGTATT
33999232 A
1 A
33999233 GTGCATTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.60
Consensus pattern (23 bp):
ATTTTTTGTTTTCTCCAAGTATT
Found at i:34000212 original size:14 final size:14
Alignment explanation
Indices: 34000193--34000222 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
34000183 TACTAAGAAC
34000193 ATTGTTAAGAATAT
1 ATTGTTAAGAATAT
34000207 ATTGTTAAGAATAT
1 ATTGTTAAGAATAT
34000221 AT
1 AT
34000223 GTCATAAAAA
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:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
ATTGTTAAGAATAT
Found at i:34005867 original size:18 final size:18
Alignment explanation
Indices: 34005844--34005879 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
34005834 TACTACACTT
34005844 TATACC-TTATATGATTTA
1 TATACCTTTATAT-ATTTA
34005862 TATACCTTTATATATTTA
1 TATACCTTTATATATTTA
34005880 AGAACTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.53
Consensus pattern (18 bp):
TATACCTTTATATATTTA
Found at i:34008267 original size:6 final size:6
Alignment explanation
Indices: 34008256--34008288 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
34008246 ACTAACCACC
*
34008256 TTCCCT TTCCCT TTCCCT TT-CCT TTTCCT TTCC
1 TTCCCT TTCCCT TTCCCT TTCCCT TTCCCT TTCC
34008289 ATAATTCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (6 bp):
TTCCCT
Found at i:34008273 original size:12 final size:12
Alignment explanation
Indices: 34008256--34008288 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
34008246 ACTAACCACC
34008256 TTCCCTTTCCCT
1 TTCCCTTTCCCT
34008268 TTCCCTTT-CCT
1 TTCCCTTTCCCT
*
34008279 TTTCCTTTCC
1 TTCCCTTTCC
34008289 ATAATTCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (12 bp):
TTCCCTTTCCCT
Found at i:34008279 original size:17 final size:17
Alignment explanation
Indices: 34008254--34008288 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34008244 TCACTAACCA
34008254 CCTTCCCTTTCCCTTTC
1 CCTTCCCTTTCCCTTTC
* *
34008271 CCTTTCCTTTTCCTTTC
1 CCTTCCCTTTCCCTTTC
34008288 C
1 C
34008289 ATAATTCCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (17 bp):
CCTTCCCTTTCCCTTTC
Found at i:34008738 original size:17 final size:15
Alignment explanation
Indices: 34008716--34008757 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
34008706 TTCATTTTTC
34008716 TTGTTACTTATTATTAT
1 TTGTTA-TTATTATT-T
34008733 TTGTTATT-TTATTT
1 TTGTTATTATTATTT
*
34008747 TTCTTATTATT
1 TTGTTATTATT
34008758 GTCAGTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 8 0.35
15 7 0.30
16 2 0.09
17 6 0.26
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (15 bp):
TTGTTATTATTATTT
Found at i:34008794 original size:14 final size:14
Alignment explanation
Indices: 34008723--34008795 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
34008713 TTCTTGTTAC
34008723 TTATTATTATTTG-
1 TTATTATTATTTGT
*
34008736 TTATT-TTATTTTT
1 TTATTATTATTTGT
* **
34008749 CTTATTATTGTCAGTT
1 -TTATTATTATTTG-T
* * *
34008765 TTCTTATCATTAGT
1 TTATTATTATTTGT
34008779 TTATTATTATTTGT
1 TTATTATTATTTGT
34008793 TTA
1 TTA
34008796 CTGTTTTAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
12 6 0.14
13 5 0.11
14 20 0.45
15 12 0.27
16 1 0.02
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (14 bp):
TTATTATTATTTGT
Found at i:34008901 original size:3 final size:3
Alignment explanation
Indices: 34008879--34008945 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
34008869 TGTTTACTCG
* * * * *
34008879 TAT TAT TTT TAAT TAG TAT TAT TAG TAT TAG TAT TAT TTT TACT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
34008926 TAT T-T TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
34008946 TAGTACTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
2 4 0.08
3 41 0.82
4 5 0.10
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:34008935 original size:8 final size:8
Alignment explanation
Indices: 34008922--34008946 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
34008912 TTATTTTTAC
34008922 TTATTATT
1 TTATTATT
34008930 TTATTATT
1 TTATTATT
34008938 TTATTATT
1 TTATTATT
34008946 T
1 T
34008947 AGTACTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTATT
Found at i:34010484 original size:26 final size:23
Alignment explanation
Indices: 34010441--34010492 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 23
34010431 CTGATTTTAT
*
34010441 TTTTAGTTTTATTTTTTATTTTGC
1 TTTTAGTTTTAATTTTTATTTT-C
34010465 TTTTAGTTGTTTAATTTTTATTTTC
1 TTTTAG-T-TTTAATTTTTATTTTC
34010490 TTT
1 TTT
34010493 GACTTATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 5 0.20
26 14 0.56
ACGTcount: A:0.13, C:0.04, G:0.08, T:0.75
Consensus pattern (23 bp):
TTTTAGTTTTAATTTTTATTTTC
Found at i:34010511 original size:26 final size:26
Alignment explanation
Indices: 34010448--34010511 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
34010438 TATTTTTAGT
* * * *
34010448 TTTATTTTTTATTTTGCTTTTAGTTG
1 TTTAATTTTTATTTTGCTTTGACTTA
34010474 TTTAATTTTTATTTT-CTTTGACTTA
1 TTTAATTTTTATTTTGCTTTGACTTA
*
34010499 TTTCATTTATTAT
1 TTTAATTT-TTAT
34010512 CTTTTGAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.70
Consensus pattern (26 bp):
TTTAATTTTTATTTTGCTTTGACTTA
Found at i:34012824 original size:105 final size:105
Alignment explanation
Indices: 34012631--34012827 Score: 231
Period size: 105 Copynumber: 1.9 Consensus size: 105
34012621 AATGTTCAAA
* ** *
34012631 TGTAAGACCATAGTTGGGCTATGGCATTGTAATGGAAAGACCATAACTGTGTTATGGCACCTTCA
1 TGTAAGACCATAGCTGGGCTATGGCATCCTAATGGAAAGACCATAACTGTGTTATGGCACATTCA
**
34012696 ACGTAAGACCATAGTTGGACCATGGCAGTAAATATATATG
66 ACGTAAGACCATAGCAGGACCATGGCAGTAAATATATATG
*
34012736 TGTAAGACCATAGCTGGGCTATGGCATCCTAAT-GATAATACCATAACTAG-GTTAT-G-ACATT
1 TGTAAGACCATAGCTGGGCTATGGCATCCTAATGGA-AAGACCATAACT-GTGTTATGGCACATT
** * *
34012797 ACGAGTGTAAGACCATGGCAGGGCCATGGCA
64 -C-AACGTAAGACCATAGCAGGACCATGGCA
34012828 ATTGTGTAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
103 4 0.05
104 4 0.05
105 68 0.88
106 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGCTATGGCATCCTAATGGAAAGACCATAACTGTGTTATGGCACATTCA
ACGTAAGACCATAGCAGGACCATGGCAGTAAATATATATG
Found at i:34017212 original size:21 final size:21
Alignment explanation
Indices: 34017188--34017230 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
34017178 GTATACTATA
*
34017188 TATATTGCCCTTGTGGCGTAT
1 TATATTGCCCTTGTGGCATAT
*
34017209 TATATTGCCTTTGTGGCATAT
1 TATATTGCCCTTGTGGCATAT
34017230 T
1 T
34017231 CTGTCTAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (21 bp):
TATATTGCCCTTGTGGCATAT
Found at i:34022259 original size:19 final size:17
Alignment explanation
Indices: 34022215--34022251 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
34022205 TTAAAACCTT
*
34022215 AAACCCTAATTCTTAAA
1 AAACCTTAATTCTTAAA
34022232 AAACCTTAATTCTTAAA
1 AAACCTTAATTCTTAAA
34022249 AAA
1 AAA
34022252 AATCTTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (17 bp):
AAACCTTAATTCTTAAA
Found at i:34022856 original size:42 final size:42
Alignment explanation
Indices: 34022808--34022892 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
34022798 GTTTTATTTT
34022808 TAATTATAGTAATTTACATAAAATAATTTTTTATTTGAATTA
1 TAATTATAGTAATTTACATAAAATAATTTTTTATTTGAATTA
34022850 TAATTATAGTAATTTACATAAAATAATTTTTTATTTGAATTA
1 TAATTATAGTAATTTACATAAAATAATTTTTTATTTGAATTA
34022892 T
1 T
34022893 TGAATATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (42 bp):
TAATTATAGTAATTTACATAAAATAATTTTTTATTTGAATTA
Found at i:34023562 original size:30 final size:30
Alignment explanation
Indices: 34023528--34023605 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
34023518 TGAGAAAAGC
*
34023528 ATTTAAATTTTAAATTTTTGAAAAAA-AAA
1 ATTTAAATTTTAAAATTTTGAAAAAAGAAA
*
34023557 TATTTAGATTTTAAAATTTTGAAAAAAGAAA
1 -ATTTAAATTTTAAAATTTTGAAAAAAGAAA
*
34023588 ACTTAAATTTTCAAAATT
1 ATTTAAATTTT-AAAATT
34023606 ATATATTCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 33 0.79
31 9 0.21
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (30 bp):
ATTTAAATTTTAAAATTTTGAAAAAAGAAA
Found at i:34026585 original size:33 final size:30
Alignment explanation
Indices: 34026511--34026588 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 30
34026501 TGAATAAATG
* * *
34026511 ATGTTAAATTGAA-TGTATTTATTTTATAC
1 ATGTTGAATTGAATTGTATGTATTATATAC
34026540 ATAGTTGAATTGAATTGTATGTATGTATACTAC
1 AT-GTTGAATTGAATTGTATGTAT-TATA-TAC
34026573 AATGTTGAATTGAATT
1 -ATGTTGAATTGAATT
34026589 TAGCATAGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 2 0.05
30 10 0.24
31 8 0.20
32 3 0.07
33 16 0.39
34 2 0.05
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (30 bp):
ATGTTGAATTGAATTGTATGTATTATATAC
Found at i:34026784 original size:42 final size:44
Alignment explanation
Indices: 34026682--34026836 Score: 138
Period size: 43 Copynumber: 3.6 Consensus size: 44
34026672 TGATATCGTA
** * *
34026682 TAAGACCACATCTGGGACGTTGGCATCGATTTGAGATTTACGTG
1 TAAGACCATGTCTGGGACATTGGCATCGATATGAGATTTACGTG
34026726 TAAGACCATGTCTGGGACATTGGCATC-ATAT-ATGATTT-CGTG
1 TAAGACCATGTCTGGGACATTGGCATCGATATGA-GATTTACGTG
* * * * * ** * *
34026768 TAAGACCCTGTTTGGGATAGTGGCATCGTTATTTGA-ATACATG
1 TAAGACCATGTCTGGGACATTGGCATCGATATGAGATTTACGTG
* *
34026811 TAAGACCACGTCTGGGACGTTGGCAT
1 TAAGACCATGTCTGGGACATTGGCAT
34026837 TGTACGAGCT
Statistics
Matches: 89, Mismatches: 18, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
42 29 0.33
43 36 0.40
44 24 0.27
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (44 bp):
TAAGACCATGTCTGGGACATTGGCATCGATATGAGATTTACGTG
Found at i:34043415 original size:18 final size:18
Alignment explanation
Indices: 34043368--34043415 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
34043358 GGAAAACATA
34043368 AATAAAAATA-A-AAAAT
1 AATAAAAATATATAAAAT
*
34043384 ACATAAAAATATATAAATT
1 A-ATAAAAATATATAAAAT
34043403 AATAAAAATATAT
1 AATAAAAATATAT
34043416 TTTTTTCTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 1 0.04
17 9 0.32
18 13 0.46
19 5 0.18
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAAAAATATATAAAAT
Found at i:34044964 original size:98 final size:99
Alignment explanation
Indices: 34044827--34045036 Score: 325
Period size: 100 Copynumber: 2.1 Consensus size: 99
34044817 AAGAAAAACG
*
34044827 AAAAAAAAATTTGGGTCCTGGCCTGACAATTGCCAGCACCCAGTACAA-TTTAAAAAAAAATTT-
1 AAAAAAAAATTTGGGTCCTGGCCTGACAATGGCCAGCACCCAGTACAATTTTAAAAAAAAATTTC
*
34044890 GTGTCAGAGTCAGATATCAGTATACGAAAAAAAT
66 GTGTCAGAATCAGATATCAGTATACGAAAAAAAT
** * * *
34044924 AAAAAAAAATTTAGGGTGTTGGCCTGTCAATGGCCGGCACCTAGTACAATTTTAAAAAAAAATTT
1 AAAAAAAAATTT-GGGTCCTGGCCTGACAATGGCCAGCACCCAGTACAATTTTAAAAAAAAATTT
34044989 CGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
65 CGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
34045024 AAAAGAAAAATTT
1 AAAA-AAAAATTT
34045037 TCGTACATTG
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
97 12 0.12
98 30 0.29
99 15 0.15
100 37 0.36
101 8 0.08
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (99 bp):
AAAAAAAAATTTGGGTCCTGGCCTGACAATGGCCAGCACCCAGTACAATTTTAAAAAAAAATTTC
GTGTCAGAATCAGATATCAGTATACGAAAAAAAT
Found at i:34045170 original size:109 final size:109
Alignment explanation
Indices: 34045048--34045478 Score: 536
Period size: 109 Copynumber: 4.0 Consensus size: 109
34045038 CGTACATTGA
* *
34045048 TTTTTATTTTTTTCGTATACTAATATCTGATTCTGACACGAAAAAAAAAGAAAAAAAATTTTAA-
1 TTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAG-AAAAAAATTTAAAT
* * * * *
34045112 TATATTGGGTGCCGGCCAATGACAGGCCTGCACCCAAAAAATTTT
65 TGTACTGGGTGCCAGCCATTGACAGGCCAGCACCCAAAAAATTTT
* ***
34045157 TTTTTATTTTTTTCGTATACTGATATTTGATTCTGACACGAAAAAAAAAGAAAATTTTTTTTTAA
1 TTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAGAAAA---AAATTTAA
*
34045222 TTTGTACTGGGTGCCAGCCATTGACAGGCCAGCACCC-AAAAATTTT
63 ATTGTACTGGGTGCCAGCCATTGACAGGCCAGCACCCAAAAAATTTT
* *
34045268 TTTTTATTTTTTTCATATACTGATATCTGATTCTGAGC-C--AAAAAAGAGAAAAAAA-TTAAAT
1 TTTTTATTTTTTTCGTATACTGATATCTGATTCTGA-CACGAAAAAAAAAGAAAAAAATTTAAAT
* * **
34045329 TGTACTGAGTGCCAGCCATTGACAGGCCAACA-CCAAAATTTTTT
65 TGTACTGGGTGCCAGCCATTGACAGGCCAGCACCCAAAAAATTTT
34045373 TTTTTA-TTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAGAAAAAAATTTAAAAA
1 TTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAGAAAAAAATTT--AAA
* * * * *
34045437 TTGTATTGGGTACCGGCCATTGACAGGCCAACACCAAAAAAA
64 TTGTACTGGGTGCCAGCCATTGACAGGCCAGCACCCAAAAAA
34045479 AATTTTCGTT
Statistics
Matches: 277, Mismatches: 32, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
103 1 0.00
104 31 0.11
105 48 0.17
106 15 0.05
107 2 0.01
108 4 0.01
109 92 0.33
110 5 0.02
111 48 0.17
112 31 0.11
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (109 bp):
TTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAGAAAAAAATTTAAATT
GTACTGGGTGCCAGCCATTGACAGGCCAGCACCCAAAAAATTTT
Found at i:34050682 original size:33 final size:32
Alignment explanation
Indices: 34050645--34050757 Score: 156
Period size: 32 Copynumber: 3.5 Consensus size: 32
34050635 CGTGTGGTTC
* *
34050645 TGTGAAATGATAACAAATATCAGCTTTTCATTT
1 TGTGAAATGATAACAAATATCAAC-TTTAATTT
34050678 TGTGAAATGATAACAAAT-TACAACTTTAATTT
1 TGTGAAATGATAACAAATAT-CAACTTTAATTT
*
34050710 TGTAAAATGATAACAAATATCAACTTTAATTT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
* *
34050742 TATTAAATGATAACAA
1 TGTGAAATGATAACAA
34050758 TATTCCTCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
32 51 0.70
33 22 0.30
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (32 bp):
TGTGAAATGATAACAAATATCAACTTTAATTT
Found at i:34051881 original size:13 final size:13
Alignment explanation
Indices: 34051863--34051897 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
34051853 ACAAGGGACA
34051863 CATGGTCGTGTCG
1 CATGGTCGTGTCG
34051876 CATGGTCGTGTCG
1 CATGGTCGTGTCG
34051889 CATGGTCGT
1 CATGGTCGT
34051898 ATGTCACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.09, C:0.23, G:0.37, T:0.31
Consensus pattern (13 bp):
CATGGTCGTGTCG
Found at i:34052680 original size:41 final size:40
Alignment explanation
Indices: 34052634--34052728 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 40
34052624 GCACGTATGA
34052634 GCAATTCAGAGGTACTGAAGTACAAATAGGGGCACATAAGT
1 GCAATTCAG-GGTACTGAAGTACAAATAGGGGCACATAAGT
*
34052675 GCAATTTAGGGGTACTGAAGTACAAATAGGGGCACATAAGT
1 GCAATTCA-GGGTACTGAAGTACAAATAGGGGCACATAAGT
34052716 GCAATTCAGGGTA
1 GCAATTCAGGGTA
34052729 TAATTAAGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
40 5 0.10
41 45 0.88
42 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (40 bp):
GCAATTCAGGGTACTGAAGTACAAATAGGGGCACATAAGT
Found at i:34052684 original size:21 final size:21
Alignment explanation
Indices: 34052660--34052726 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
34052650 GAAGTACAAA
34052660 TAGGGGCACATAAGTGCAATT
1 TAGGGGCACATAAGTGCAATT
* * *
34052681 TAGGGGTAC-TGAAGTACAA-A
1 TAGGGGCACAT-AAGTGCAATT
34052701 TAGGGGCACATAAGTGCAATT
1 TAGGGGCACATAAGTGCAATT
*
34052722 CAGGG
1 TAGGG
34052727 TATAATTAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.21
Consensus pattern (21 bp):
TAGGGGCACATAAGTGCAATT
Found at i:34052706 original size:20 final size:20
Alignment explanation
Indices: 34052644--34052706 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
34052634 GCAATTCAGA
34052644 GGTACTGAAGTACAAATAGG
1 GGTACTGAAGTACAAATAGG
* * *
34052664 GGCACAT-AAGTGCAATTTAGG
1 GGTAC-TGAAGTACAA-ATAGG
34052685 GGTACTGAAGTACAAATAGG
1 GGTACTGAAGTACAAATAGG
34052705 GG
1 GG
34052707 CACATAAGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.21
Consensus pattern (20 bp):
GGTACTGAAGTACAAATAGG
Found at i:34052715 original size:20 final size:20
Alignment explanation
Indices: 34052651--34052715 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
34052641 AGAGGTACTG
34052651 AAGTACAAATAGGGGCACAT
1 AAGTACAAATAGGGGCACAT
* * *
34052671 AAGTGCAATTTAGGGGTAC-T
1 AAGTACAA-ATAGGGGCACAT
34052691 GAAGTACAAATAGGGGCACAT
1 -AAGTACAAATAGGGGCACAT
34052712 AAGT
1 AAGT
34052716 GCAATTCAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20
Consensus pattern (20 bp):
AAGTACAAATAGGGGCACAT
Found at i:34054906 original size:12 final size:12
Alignment explanation
Indices: 34054891--34054915 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34054881 TATTAGAATT
34054891 AATAAAGAAGAA
1 AATAAAGAAGAA
34054903 AATAAAGAAGAA
1 AATAAAGAAGAA
34054915 A
1 A
34054916 GATGGAAAGA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AATAAAGAAGAA
Found at i:34057795 original size:7 final size:7
Alignment explanation
Indices: 34057785--34057809 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34057775 AGAAATTCGA
34057785 AATAATG
1 AATAATG
34057792 AATAATG
1 AATAATG
34057799 AATAATG
1 AATAATG
34057806 AATA
1 AATA
34057810 GACATCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (7 bp):
AATAATG
Found at i:34063716 original size:20 final size:20
Alignment explanation
Indices: 34063682--34063737 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
34063672 TTAAAATATT
*
34063682 AAAAACTTATAAAAATCAGAA
1 AAAAATTTATAAAAAT-AGAA
*
34063703 AAAAATTTATAAAAATATAA
1 AAAAATTTATAAAAATAGAA
34063723 AAAAATTT-TAAAAAT
1 AAAAATTTATAAAAAT
34063738 TTAAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.21
20 11 0.33
21 15 0.45
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAATTTATAAAAATAGAA
Found at i:34063791 original size:9 final size:9
Alignment explanation
Indices: 34063703--34063946 Score: 97
Period size: 10 Copynumber: 25.6 Consensus size: 9
34063693 AAAATCAGAA
34063703 AAAAATTTAT
1 AAAAA-TTAT
*
34063713 AAAAATATAA
1 AAAAAT-TAT
*
34063723 AAAAATTTT
1 AAAAATTAT
34063732 AAAAATT-T
1 AAAAATTAT
*
34063740 AAATATTA-
1 AAAAATTAT
34063748 AAAAATATAT
1 AAAAAT-TAT
*
34063758 GAAAATTGATT
1 AAAAATT-A-T
* * *
34063769 TAAACTTTT
1 AAAAATTAT
34063778 AAAAATTAT
1 AAAAATTAT
34063787 AAAAAATTAAT
1 -AAAAATT-AT
* *
34063798 AAATACTAT
1 AAAAATTAT
34063807 CAAAAA-TAT
1 -AAAAATTAT
34063816 AATAAATCTA-
1 AA-AAAT-TAT
*
34063826 ATAAATTAT
1 AAAAATTAT
34063835 AGAAAATTAT
1 A-AAAATTAT
34063845 -AAAATTAAT
1 AAAAATT-AT
*
34063854 AAAACATATTT
1 AAAA-AT-TAT
*
34063865 AAAATTTTAT
1 AAAA-ATTAT
34063875 AAAAATGTATT
1 AAAAAT-TA-T
*
34063886 AAAATTCTAT
1 AAAAAT-TAT
*
34063896 AAAAATAAT
1 AAAAATTAT
34063905 AAAACA--AT
1 AAAA-ATTAT
*
34063913 AAAAAGTATT
1 AAAAATTA-T
*
34063923 AAAATTTAT
1 AAAAATTAT
*
34063932 ATAAAATCAT
1 A-AAAATTAT
34063942 AAAAA
1 AAAAA
34063947 ACTGAATTGA
Statistics
Matches: 179, Mismatches: 30, Indels: 51
0.69 0.12 0.20
Matches are distributed among these distances:
7 1 0.01
8 28 0.16
9 48 0.27
10 75 0.42
11 26 0.15
12 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:34063878 original size:21 final size:21
Alignment explanation
Indices: 34063831--34063902 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
34063821 ATCTAATAAA
34063831 TTATAGAAAAT-TA-TAAAA-T
1 TTATA-AAAATATATTAAAATT
*
34063850 TAATAAAACATAT-TTAAAATT
1 TTATAAAA-ATATATTAAAATT
*
34063871 TTATAAAAATGTATTAAAATT
1 TTATAAAAATATATTAAAATT
*
34063892 CTATAAAAATA
1 TTATAAAAATA
34063903 ATAAAACAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 3 0.07
19 6 0.14
20 9 0.21
21 25 0.58
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TTATAAAAATATATTAAAATT
Found at i:34063924 original size:37 final size:38
Alignment explanation
Indices: 34063873--34063945 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 38
34063863 TTAAAATTTT
34063873 ATAAAAATGTATTAAAATTCTATA-AAAATAATAAAACA
1 ATAAAAATGTATTAAAATT-TATATAAAATAATAAAACA
*
34063911 ATAAAAA-GTATTAAAATTTATATAAAATCATAAAA
1 ATAAAAATGTATTAAAATTTATATAAAATAATAAAA
34063946 AACTGAATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 4 0.12
37 22 0.67
38 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (38 bp):
ATAAAAATGTATTAAAATTTATATAAAATAATAAAACA
Found at i:34063937 original size:21 final size:20
Alignment explanation
Indices: 34063844--34063937 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
34063834 TAGAAAATTA
34063844 TAAAATTA-ATAAAACA-TATT
1 TAAAATTATATAAAA-AGTA-T
*
34063864 TAAAATTTTATAAAAATGTAT
1 TAAAATTATATAAAAA-GTAT
* *
34063885 TAAAATTCTATAAAAA-TAA
1 TAAAATTATATAAAAAGTAT
*
34063904 TAAAA-CA-ATAAAAAGTAT
1 TAAAATTATATAAAAAGTAT
34063922 TAAAATTTATATAAAA
1 TAAAA-TTATATAAAA
34063938 TCATAAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
17 7 0.12
18 7 0.12
19 7 0.12
20 9 0.15
21 28 0.47
22 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAAATTATATAAAAAGTAT
Found at i:34064449 original size:5 final size:5
Alignment explanation
Indices: 34064439--34064470 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
34064429 TAAAGCATCA
34064439 ATATC ATATC ATATC ATATC ATATC ATATC AT
1 ATATC ATATC ATATC ATATC ATATC ATATC AT
34064471 TTTGTTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:34067928 original size:28 final size:30
Alignment explanation
Indices: 34067854--34067926 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
34067844 ACAACAGACG
* *
34067854 AAGAACCTTTTGTGTTTTTTTCGGGACAAC
1 AAGAATCTTTTGTGTTTTTTTCCGGACAAC
*
34067884 AAGAATCTTTTGTGTTTTTTTCCGGACAAT
1 AAGAATCTTTTGTGTTTTTTTCCGGACAAC
34067914 AAGAATCTTTTGT
1 AAGAATCTTTTGT
34067927 TTAATCACGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.44
Consensus pattern (30 bp):
AAGAATCTTTTGTGTTTTTTTCCGGACAAC
Found at i:34068173 original size:46 final size:46
Alignment explanation
Indices: 34068106--34068198 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
34068096 AAATAACAAC
*
34068106 CATTTCTATCACTTAAAAATTAAATTAATTAAATTCATCACTTTAT
1 CATTTCTATCACTTAAAAATTAAATTAACTAAATTCATCACTTTAT
34068152 CATTTCTATCACTTAAAAATTAAATTAACTAAATTCATCACTTTAT
1 CATTTCTATCACTTAAAAATTAAATTAACTAAATTCATCACTTTAT
34068198 C
1 C
34068199 GTTAAACAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.42
Consensus pattern (46 bp):
CATTTCTATCACTTAAAAATTAAATTAACTAAATTCATCACTTTAT
Found at i:34069273 original size:108 final size:109
Alignment explanation
Indices: 34068915--34069339 Score: 658
Period size: 109 Copynumber: 3.9 Consensus size: 109
34068905 TGGATTAAGA
* * * * * *
34068915 TTTAAGAGGATATTCGGCTATTTGGTCCAACGAG--AAATCGAAACCCAGCGCATTAGAGCAAGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
34068978 TTTCTCGAGTTTCCAAACGCAAAACATTGCCTTATTTTGAAATC
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
* * * *
34069022 TTTGAAAGGATATTTAGCTATTTGGTCGAGCGAGAAAAATCGAAACCCAGCACATTAGGGCACAT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
34069087 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
*
34069131 TTTAAAAGGATATTTGGTTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
* * *
34069196 TTTCTCGAATTTTCAAACGC-GAACATTGCCTTATGTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
* *
34069239 TTTAAAAGGATATTTTGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGACACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
*
34069304 TTTCTCGAATTTTCAAACGCAAAACATTGCCTTATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
34069340 GAAAAAAACA
Statistics
Matches: 290, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
107 28 0.10
108 103 0.36
109 159 0.55
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (109 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
Found at i:34069295 original size:217 final size:216
Alignment explanation
Indices: 34068915--34069339 Score: 663
Period size: 217 Copynumber: 2.0 Consensus size: 216
34068905 TGGATTAAGA
* *
34068915 TTTAAGAGGATATTCGGCTATTTGGTCCAACGAGAAATCGAAACCCAGCGCATTAGAGCAAGTTT
1 TTTAAAAGGATATTCGGCTATTTGGTCCAACGAGAAATCGAAACCCAGCACATTAGAGCAAGTTT
* * *
34068980 TCTCGAGTTTCCAAACGCAAAACATTGCCTTATTTTGAAATCTTTGAAAGGATATTTAGCTATTT
66 TCTCGAATTTCCAAACGCAAAACATTGCCTTATGTTGAAATCTTTAAAAGGATATTTAGCTATTT
* *
34069045 GGTCGAGCGAGAAAAATCGAAACCCAGCACATTAGGGCACATTTTCTCGAATTTCCAAACGCAAA
131 GGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGACACATTTTCTCGAATTTCCAAACGCAAA
34069110 ACATTGCCTTATTTTGAAATT
196 ACATTGCCTTATTTTGAAATT
* * * * *
34069131 TTTAAAAGGATATTTGGTTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTCGGCTATTTGGTCCAACGAG--AAATCGAAACCCAGCACATTAGAGCAAGT
* * * *
34069196 TTTCTCGAATTTTCAAACGC-GAACATTGCCTTATGTTGAAATTTTTAAAAGGATATTTTGCTAT
64 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATGTTGAAATCTTTAAAAGGATATTTAGCTAT
* *
34069260 TTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGACACGTTTTCTCGAATTTTCAAACGCA
129 TTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGACACATTTTCTCGAATTTCCAAACGCA
34069325 AAACATTGCCTTATT
194 AAACATTGCCTTATT
34069340 GAAAAAAACA
Statistics
Matches: 189, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
216 30 0.16
217 115 0.61
218 44 0.23
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (216 bp):
TTTAAAAGGATATTCGGCTATTTGGTCCAACGAGAAATCGAAACCCAGCACATTAGAGCAAGTTT
TCTCGAATTTCCAAACGCAAAACATTGCCTTATGTTGAAATCTTTAAAAGGATATTTAGCTATTT
GGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGACACATTTTCTCGAATTTCCAAACGCAAA
ACATTGCCTTATTTTGAAATT
Found at i:34070850 original size:66 final size:67
Alignment explanation
Indices: 34070769--34070895 Score: 186
Period size: 66 Copynumber: 1.9 Consensus size: 67
34070759 TGTTGTAACT
* *
34070769 TCAATCTATTTAATTGCAATGTTG-GGTAAGAAAGATTCGTCATTGTAGCTTCAATCTATTCGTG
1 TCAATCTATTTAATTGCAATGTCGAGG-AAGAAAGATTCGCCATTGTAGCTTCAATCTATTCGTG
34070833 CCC
65 CCC
** *
34070836 TCAATCT-TTTAATTGCAATGTCGAGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTATTC
1 TCAATCTATTTAATTGCAATGTCGAGGAAGAAAGATTCGCCATTGTAGCTTCAATCTATTC
34070896 CACTGCACCG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
66 45 0.83
67 9 0.17
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (67 bp):
TCAATCTATTTAATTGCAATGTCGAGGAAGAAAGATTCGCCATTGTAGCTTCAATCTATTCGTGC
CC
Found at i:34070924 original size:50 final size:50
Alignment explanation
Indices: 34070867--34071469 Score: 263
Period size: 50 Copynumber: 12.1 Consensus size: 50
34070857 CGAGGAAGCG
* *
34070867 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCTTGAGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGAAGTA
* * ** * ** * **
34070917 AGATTCGCCGTTGTGGCCTCAATCT-TTTAATTGCAATG-TCGGGGAAGCG
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCT-AGGGAAGTA
* *
34070966 AGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGAAGTA
* * * ** * ** * *
34071016 AGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAATG-TCGGGGAAGCA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCT-AGGGAAGTA
* * *
34071066 AGATTCACCGTTGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGAAGTA
** * * ** * *** * **
34071116 AGATTCATCGTTGTGGCTTCAATCTTTTTAATTGCA-ATATCGGGGAAGCG
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCT-AGGGAAGTA
* * * ** * * ** * *
34071166 AGATTCACCGTTGTAGCCTCAATAT-TTTAATTACAATG-TCGGGGAAGCA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCT-AGGGAAGTA
*** * * *
34071215 AGATTCATTGTTGTAGCTTCAATCTGTTCCACTACACCGCCT-GAGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCG-CTAGGGAAGTA
* * * * * * ** * ** *
34071265 AGATTTGCCATTGTGGCCTAAATCTTTTTAATTGCAATG-TCAGGGAAGCA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCT-AGGGAAGTA
* * ** * *
34071315 AGATTCACCGTTGTAGCTTCGATCTGCTCCACTGCACCGCCAGGGAAATA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGAAGTA
* * * * ** * ** * **
34071365 AGATTTGCTGTTGTGGCCTCAATCT-TTTAATTGCAATG-TCGAGGAAGCC
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAG-GGAAGTA
* * *
34071414 AGATTCGCCATTGTAGCTTCAATCTATTCCACTGCACCACCAGGGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGAAGTA
34071464 AGATTC
1 AGATTC
34071470 ACTGTCTTCG
Statistics
Matches: 392, Mismatches: 145, Indels: 32
0.69 0.25 0.06
Matches are distributed among these distances:
48 3 0.01
49 107 0.27
50 280 0.71
51 1 0.00
52 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (50 bp):
AGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCTAGGGAAGTA
Done.