Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003929.1 Hibiscus syriacus cultivar Beakdansim tig00008493_pilon, whole genome shotgun sequence
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: 81941
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1572 original size:2 final size:2
Alignment explanation
Indices: 1565--1597 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1555 CTGTATAGGA
1565 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 A
1598 ATGTATGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8039 original size:29 final size:29
Alignment explanation
Indices: 7997--8053 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
7987 AGTGTTGGCC
*
7997 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGAGACCTT
8026 GTAGGTCGCCATGCACTCCGGGAGACCT
1 GTAGGTCGCCATGCACTCCGGGAGACCT
8054 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.33, G:0.32, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGAGACCTT
Found at i:8145 original size:29 final size:29
Alignment explanation
Indices: 8112--8167 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
8102 TCCCAACACA
* *
8112 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGACATGCACTCCGGGCGACCTTG
8141 TAGGTCGACATGCACTCCGGGCGACCT
1 TAGGTCGACATGCACTCCGGGCGACCT
8168 ACCCTCGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.36, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGACATGCACTCCGGGCGACCTTG
Found at i:8212 original size:33 final size:33
Alignment explanation
Indices: 8171--8255 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
8161 GCGACCTACC
*
8171 CTCGCTCGGCTT-CCCTCGGATTCCATCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCATCGCATAG
*
8204 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCATCGCATAG
* * *
8237 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
8256 TCGGATGGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 44 0.96
ACGTcount: A:0.09, C:0.38, G:0.27, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCATCGCATAG
Found at i:8259 original size:14 final size:14
Alignment explanation
Indices: 8237--8283 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
8227 CCTCGCATAG
*
8237 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
8251 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
*
8265 CTCGGTCAGATGGC
1 CTCGGTCGGATGGC
8279 CTCGG
1 CTCGG
8284 ATGCCCAGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.09, C:0.30, G:0.38, T:0.23
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:8363 original size:29 final size:29
Alignment explanation
Indices: 8326--8383 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
8316 GCAATCTCTT
*
8326 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
8355 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
8384 CTGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:10578 original size:20 final size:20
Alignment explanation
Indices: 10553--10605 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
10543 ACAAGTTCCA
10553 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
* **
10573 AAATCGCAATGATAATATGT
1 AAATCGCAACGCGAATATGT
*
10593 AAATCACAACGCG
1 AAATCGCAACGCG
10606 GTTTTCCAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:10631 original size:21 final size:21
Alignment explanation
Indices: 10593--10641 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
10583 GATAATATGT
* **
10593 AAATCACAACGCGGTTTTCCA
1 AAATCGCAACGCCATTTTCCA
*
10614 AAATCGCAACGCCATTTTCTA
1 AAATCGCAACGCCATTTTCCA
*
10635 AATTCGC
1 AAATCGC
10642 TACGATGATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (21 bp):
AAATCGCAACGCCATTTTCCA
Found at i:10720 original size:57 final size:57
Alignment explanation
Indices: 10616--11149 Score: 332
Period size: 57 Copynumber: 9.3 Consensus size: 57
10606 GTTTTCCAAA
* * * *
10616 ATCGCAACGCCATTTTCTAAATTCGCTACGATGATTACCGATGTAGGTAAACAGTACT
1 ATCGCAACGCGATTTTC-AAATTCGCAACGATAATTACCGATATAGGTAAACAGTACT
* *
10674 ATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACT
1 ATCGCAACGCGATTTTCAAATTCGCAACGATAATTACCGATATAGGTAAACAGTACT
* * * * * ***
10731 ATCGCAACGCGATTTACAAATTCGCAACGAGATTTTCAACTTCGCA-ACGAGATTTTCA--ACT
1 ATCGCAACGCGATTTTCAAATTCGCAACGATA-ATT--AC--CG-ATA-TAGGTAAACAGTACT
* * ** * ** * * * * * ** *
10792 -TCGCAACTCTAATTACCGATATAGGTAAAC-AGT-ACTATCGCA-ACTCGATTTACA--AAT
1 ATCGCAACGC-GATTTTC-AAATTCG-CAACGA-TAATTACCG-ATA-TAGGTAAACAGTACT
* * * *
10849 -TCGCAACGAGATTTTCAAATTCGCAACGCTAATTGCCGATATAGGTAAATAGTACT
1 ATCGCAACGCGATTTTCAAATTCGCAACGATAATTACCGATATAGGTAAACAGTACT
* * * * * * * * **
10905 AGCGCAACACAATTTACAAATTCGCAAAGCTACTTACCGATAGAGGTAAACAGTGTT
1 ATCGCAACGCGATTTTCAAATTCGCAACGATAATTACCGATATAGGTAAACAGTACT
* * *
10962 ATCGCAACGCGATTTTCCAAAATCGCAACGCTAATTACCGATGTAGGTAAACAGTACT
1 ATCGCAACGCGATTTT-CAAATTCGCAACGATAATTACCGATATAGGTAAACAGTACT
* * ** * **
11020 ATCGAAACGCGATTTTCAAATTCGCAACGCTAATTATTGATGTAGGTAAACAGTGTT
1 ATCGCAACGCGATTTTCAAATTCGCAACGATAATTACCGATATAGGTAAACAGTACT
* * * * *
11077 ATCGCAACACGATTTTCAAATTTGCAACGCTAATTACCGATATAGGTAAACAATATT
1 ATCGCAACGCGATTTTCAAATTCGCAACGATAATTACCGATATAGGTAAACAGTACT
*
11134 ATCGCAACGCTATTTT
1 ATCGCAACGCGATTTT
11150 GGAAACTATG
Statistics
Matches: 368, Mismatches: 90, Indels: 37
0.74 0.18 0.07
Matches are distributed among these distances:
54 10 0.03
55 9 0.02
56 6 0.02
57 241 0.65
58 67 0.18
59 1 0.00
60 10 0.03
61 8 0.02
62 7 0.02
63 9 0.02
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (57 bp):
ATCGCAACGCGATTTTCAAATTCGCAACGATAATTACCGATATAGGTAAACAGTACT
Found at i:10757 original size:20 final size:20
Alignment explanation
Indices: 10732--10798 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
10722 AACAGTACTA
* * *
10732 TCGCAACGCGATTTACAAAT
1 TCGCAACGAGATTTTCAACT
10752 TCGCAACGAGATTTTCAACT
1 TCGCAACGAGATTTTCAACT
10772 TCGCAACGAGATTTTCAACT
1 TCGCAACGAGATTTTCAACT
10792 TCGCAAC
1 TCGCAAC
10799 TCTAATTACC
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:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (20 bp):
TCGCAACGAGATTTTCAACT
Found at i:10833 original size:77 final size:77
Alignment explanation
Indices: 10752--10931 Score: 254
Period size: 77 Copynumber: 2.3 Consensus size: 77
10742 ATTTACAAAT
* * * *
10752 TCGCAACGAGATTTTCAACTTCGCAACGAGATTTTCAACTTCGCAACTCTAATTACCGATATAGG
1 TCGCAACGAGATTTACAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGG
10817 TAAACAGTACTA
66 TAAACAGTACTA
** *
10829 TCGCAACTCGATTTACAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTGCCGATATAGG
1 TCGCAACGAGATTTACAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGG
*
10894 TAAATAGTACTA
66 TAAACAGTACTA
* *
10906 GCGCAAC-ACAATTTACAAATTCGCAA
1 TCGCAACGA-GATTTACAAATTCGCAA
10932 AGCTACTTAC
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
77 91 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (77 bp):
TCGCAACGAGATTTACAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGG
TAAACAGTACTA
Found at i:10841 original size:97 final size:97
Alignment explanation
Indices: 10675--10876 Score: 350
Period size: 97 Copynumber: 2.1 Consensus size: 97
10665 AACAGTACTA
* *
10675 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGCAACG
1 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
*
10740 CGATTTACAAATTCGCAACGAGATTTTCAACT
66 CGATTTACAAATTCGCAACGAGATTTTCAAAT
* * *
10772 TCGCAACGAGATTTTCAACTTCGCAACTCTAATTACCGATATAGGTAAACAGTACTATCGCAACT
1 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
10837 CGATTTACAAATTCGCAACGAGATTTTCAAAT
66 CGATTTACAAATTCGCAACGAGATTTTCAAAT
10869 TCGCAACG
1 TCGCAACG
10877 CTAATTGCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 99 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (97 bp):
TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
CGATTTACAAATTCGCAACGAGATTTTCAAAT
Found at i:10854 original size:20 final size:20
Alignment explanation
Indices: 10838--10876 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10828 ATCGCAACTC
10838 GATTTACAAATTCGCAACGA
1 GATTTACAAATTCGCAACGA
*
10858 GATTTTCAAATTCGCAACG
1 GATTTACAAATTCGCAACG
10877 CTAATTGCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
GATTTACAAATTCGCAACGA
Found at i:11010 original size:115 final size:114
Alignment explanation
Indices: 10849--11128 Score: 391
Period size: 115 Copynumber: 2.4 Consensus size: 114
10839 ATTTACAAAT
* * * *
10849 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTGCCGATATAGGTAAATAGTACTAGCGCAACA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTAGCGAAACA
*
10914 CAATTTACAAATTCGCAAAGCTACTTACCGATAG-AGGTAAACAGTGTTA
66 CAATTTACAAATTCGCAAAGCTAATTACCGAT-GTAGGTAAACAGTGTTA
* * *
10963 TCGCAACGCGATTTTCCAAAATCGCAACGCTAATTACCGATGTAGGTAAACAGTACTATCGAAAC
1 TCGCAACGCGATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTAGCGAAAC
* * * * **
11028 GCGATTTTCAAATTCGCAACGCTAATTATTGATGTAGGTAAACAGTGTTA
65 ACAATTTACAAATTCGCAAAGCTAATTACCGATGTAGGTAAACAGTGTTA
* *
11078 TCGCAACACGATTTTCAAATTTGCAACGCTAATTACCGATATAGGTAAACA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACA
11129 ATATTATCGC
Statistics
Matches: 146, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
114 48 0.33
115 98 0.67
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (114 bp):
TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTAGCGAAACA
CAATTTACAAATTCGCAAAGCTAATTACCGATGTAGGTAAACAGTGTTA
Found at i:13174 original size:20 final size:20
Alignment explanation
Indices: 13149--13198 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
13139 ACAGATTCTA
*
13149 AAATCGCAACGCGAATATGT
1 AAATCGCAACGAGAATATGT
* *
13169 AAATCGCAATGATAATATGT
1 AAATCGCAACGAGAATATGT
*
13189 AAATCACAAC
1 AAATCGCAAC
13199 CAGGGTTTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGAGAATATGT
Found at i:13230 original size:21 final size:21
Alignment explanation
Indices: 13204--13244 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
13194 ACAACCAGGG
13204 TTTTCCAAAATCGCAACGCTA
1 TTTTCCAAAATCGCAACGCTA
*
13225 TTTTCCAAATTCGCAACGCT
1 TTTTCCAAAATCGCAACGCT
13245 GATTATCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (21 bp):
TTTTCCAAAATCGCAACGCTA
Found at i:13297 original size:20 final size:20
Alignment explanation
Indices: 13272--13339 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
13262 AACAGTACTA
* *
13272 TCGCAACGCGGTTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
*
13292 TCGCAATGAGATTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
13312 TCGCAACGAGATTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
13332 TCGCAACG
1 TCGCAACG
13340 CTAATTACTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (20 bp):
TCGCAACGAGATTTTCAAAT
Found at i:13340 original size:97 final size:99
Alignment explanation
Indices: 13204--13386 Score: 255
Period size: 97 Copynumber: 1.9 Consensus size: 99
13194 ACAACCAGGG
** * *
13204 TTTTCCAAAATCGCAACGCTATTTTCCAAATTCGCAACGCTGATTA-TCGATGTAGGTAAACAGT
1 TTTTCCAAAATCGCAACGAGATTTTCCAAATTCGCAACGCTAATTACT-GATATAGGTAAACAGT
* *
13268 ACTATCGCAACGCGGTTTTCAAATTCGCAATGAGA
65 ACTATCGCAACGAGATTTTCAAATTCGCAATGAGA
* * *
13303 TTTT-CAAATTCGCAACGAGATTTT-CAAATTCGCAACGCTAATTACTGATATATGTGAACAGTA
1 TTTTCCAAAATCGCAACGAGATTTTCCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTA
13366 CTATCGCAACGAGATTTTCAA
66 CTATCGCAACGAGATTTTCAA
13387 CTTCACAACT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
97 52 0.70
98 18 0.24
99 4 0.05
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (99 bp):
TTTTCCAAAATCGCAACGAGATTTTCCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTA
CTATCGCAACGAGATTTTCAAATTCGCAATGAGA
Found at i:13702 original size:172 final size:172
Alignment explanation
Indices: 13312--13783 Score: 705
Period size: 172 Copynumber: 2.8 Consensus size: 172
13302 ATTTTCAAAT
* * *
13312 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACTGATATATGTGAACAGTACTATCGCAACG
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGCAAC-
* * * * *
13377 A-GATTTTCAACTTCACAACTCTAATTACCGATATAGGTAAACAGTACTATCACAACGCGA-TTT
65 ACGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTATTATCGCAACGCGATTTT
* * *
13440 ACAAATTCGCAACGCTAATTGCCGATATAGGTAAACAGTACTA
130 ACAAAATCACAACGCTAATTACCGATATAGGTAAACAGTACTA
13483 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGCAACA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGCAACA
* * * * * *
13548 CAATTTACAAATTCGCAAAGCTAATTACCGATAGAGGTAAACAGTGTTATCGCAACGCGATTTTC
66 CGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTATTATCGCAACGCGATTTTA
*
13613 CAAAATCACAACGCTAATTACCGATGTAGGTAAACAGTACTA
131 CAAAATCACAACGCTAATTACCGATATAGGTAAACAGTACTA
* * **
13655 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTATTGATGTAGGTAAACAGTGTTATCGCAACA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGCAACA
* *
13720 CGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATATTATCGCAACGCTATTTT
66 CGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTATTATCGCAACGCGATTTT
13784 GGAAACTATG
Statistics
Matches: 270, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
170 1 0.00
171 110 0.41
172 159 0.59
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (172 bp):
TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACTATCGCAACA
CGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTATTATCGCAACGCGATTTTA
CAAAATCACAACGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:13783 original size:57 final size:57
Alignment explanation
Indices: 13312--13783 Score: 656
Period size: 57 Copynumber: 8.3 Consensus size: 57
13302 ATTTTCAAAT
* * * *
13312 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACTGATATATGTGAACAGTACTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* * * *
13369 TCGCAACGAGATTTTCAACTTCACAACTCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* * *
13426 TCACAACGCGATTTACAAATTCGCAACGCTAATTGCCGATATAGGTAAACAGTACTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
*
13483 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACTGATATAGGTAAACAGTACTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* * * * * **
13540 TCGCAACACAATTTACAAATTCGCAAAGCTAATTACCGATAGAGGTAAACAGTGTTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* * *
13597 TCGCAACGCGATTTTCCAAAATCACAACGCTAATTACCGATGTAGGTAAACAGTACTA
1 TCGCAACGCGATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
** * **
13655 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTATTGATGTAGGTAAACAGTGTTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* * *
13712 TCGCAACACGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATATTA
1 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
*
13769 TCGCAACGCTATTTT
1 TCGCAACGCGATTTT
13784 GGAAACTATG
Statistics
Matches: 365, Mismatches: 49, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
57 315 0.86
58 50 0.14
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (57 bp):
TCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:14162 original size:16 final size:17
Alignment explanation
Indices: 14141--14181 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
14131 CCCGCCCACT
14141 AATTATCAACCA-TATA
1 AATTATCAACCATTATA
14157 AATTAT-AGACCATTATA
1 AATTATCA-ACCATTATA
14174 AATT-TCAA
1 AATTATCAA
14182 AGACTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.05
16 12 0.55
17 9 0.41
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (17 bp):
AATTATCAACCATTATA
Found at i:14632 original size:2 final size:2
Alignment explanation
Indices: 14627--14661 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14617 ATTTTAAATT
14627 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14662 TGTTAAACTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15909 original size:33 final size:33
Alignment explanation
Indices: 15861--15930 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
15851 TTTAAAGTTT
* * *
15861 AAATTGAATTATAAAGTACAACTCGAATAATTC
1 AAATCGAATTATAAAGTACAACTCAAATAACTC
*
15894 AAATCGAATTTTAAAGTACAACTCAAATAACTC
1 AAATCGAATTATAAAGTACAACTCAAATAACTC
15927 AAAT
1 AAAT
15931 TTTTTAGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (33 bp):
AAATCGAATTATAAAGTACAACTCAAATAACTC
Found at i:20794 original size:2 final size:2
Alignment explanation
Indices: 20787--20827 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
20777 TATTTTGGAT
* * *
20787 TA TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20828 TAAATTCAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:21063 original size:31 final size:31
Alignment explanation
Indices: 21025--21096 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
21015 AGTAATTTTT
21025 AGGTACTAAACGCATTAAATTTTTAAAGGTG
1 AGGTACTAAACGCATTAAATTTTTAAAGGTG
21056 AGGTACTAAACGCATTAAATTTTTAAAGGTG
1 AGGTACTAAACGCATTAAATTTTTAAAGGTG
21087 AGGTACTAAA
1 AGGTACTAAA
21097 ATGAAACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (31 bp):
AGGTACTAAACGCATTAAATTTTTAAAGGTG
Found at i:21552 original size:2 final size:2
Alignment explanation
Indices: 21545--21576 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21535 TTCTAAAATC
21545 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21577 ATTCATATGG
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):
TA
Found at i:22841 original size:59 final size:59
Alignment explanation
Indices: 22705--22851 Score: 138
Period size: 59 Copynumber: 2.5 Consensus size: 59
22695 AATAAAATGA
* *
22705 ATAGTCG-GGTGACCATTTTGTAACCCTTAATAGTCAAGGGACTCAACAAAATAACACTCT
1 ATAGTCGAGG-GACCATTTTGTAA-CTTTAATAGTCAAGGAACTCAACAAAATAACACTCT
** * * * * * **
22765 ATAGTCGAATGATCATTTTGTAACTTTAATAGTCGATGAACTTAATAAAATAGTAC-CAT
1 ATAGTCGAGGGACCATTTTGTAACTTTAATAGTCAAGGAACTCAACAAAATAACACTC-T
22824 ATAGTCGAGGGACCATTTGTGT-ACTTTA
1 ATAGTCGAGGGACCATTT-TGTAACTTTA
22852 CCCATTATTG
Statistics
Matches: 70, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
58 1 0.01
59 47 0.67
60 22 0.31
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (59 bp):
ATAGTCGAGGGACCATTTTGTAACTTTAATAGTCAAGGAACTCAACAAAATAACACTCT
Found at i:24495 original size:21 final size:22
Alignment explanation
Indices: 24468--24538 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
24458 CCTAAAATAG
*
24468 GGTTTATGGTTTATTGTTTAGA
1 GGTTTATGGTTTATAGTTTAGA
* *
24490 GG-TTATGGGGTTATGGTTTAG-
1 GGTTTAT-GGTTTATAGTTTAGA
* *
24511 GGTTTAGGGTTTATAATTTAGA
1 GGTTTATGGTTTATAGTTTAGA
*
24533 GTTTTA
1 GGTTTA
24539 AGTTAGGATT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
21 17 0.44
22 22 0.56
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (22 bp):
GGTTTATGGTTTATAGTTTAGA
Found at i:25684 original size:2 final size:2
Alignment explanation
Indices: 25677--25721 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
25667 AGGCAAAAAC
25677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25719 AT A
1 AT A
25722 ATAGTAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26908 original size:16 final size:15
Alignment explanation
Indices: 26882--26912 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
26872 ATGTGTGGCC
26882 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
26897 GGTCAGTCCCGGGATG
1 GGTCA-TCCCGGGATG
26913 TCGGCCGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:27083 original size:19 final size:19
Alignment explanation
Indices: 27059--27117 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
27049 CCTGAAACGA
*
27059 AAATAAATAA-AATAAAAAT
1 AAAT-AATAATAATAATAAT
*
27078 AAATAATAATAATAATGAT
1 AAATAATAATAATAATAAT
27097 AAATAATAATAATAATAAT
1 AAATAATAATAATAATAAT
27116 AA
1 AA
27118 TGTATCCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 5 0.14
19 31 0.86
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATAATAATAATAATAAT
Found at i:27087 original size:3 final size:3
Alignment explanation
Indices: 27064--27118 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
27054 AACGAAAATA
* *
27064 AAT AA- AAT AAA AAT AAAT AAT AAT AAT AAT GAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
27110 AAT AAT AAT
1 AAT AAT AAT
27119 GTATCCTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 38 0.84
4 5 0.11
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:27336 original size:40 final size:39
Alignment explanation
Indices: 27240--27471 Score: 207
Period size: 36 Copynumber: 6.1 Consensus size: 39
27230 TATATAAGTT
27240 AAAAAAATGTTTTTTTAAAATTATATATTATATAATTTTTC
1 AAAAAAATG--TTTTTAAAATTATATATTATATAATTTTTC
*
27281 --AAAAATGTTTTTAAAATTATATGTTATATAATTTTTC
1 AAAAAAATGTTTTTAAAATTATATATTATATAATTTTTC
27318 AAAAAAAATGTTTTTAAAATTATATATTATATAA--TTTC
1 -AAAAAAATGTTTTTAAAATTATATATTATATAATTTTTC
** ** * * *
27356 CCAAAAAT-TTTAAAAAACTATATACTATATAAGTTTTC
1 AAAAAAATGTTTTTAAAATTATATATTATATAATTTTTC
* * * *
27394 ---AAAATGTGTTAAAAACTATATATTATATAAGTTTTC
1 AAAAAAATGTTTTTAAAATTATATATTATATAATTTTTC
* * *
27430 ---AAAATGTTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAAAAATGTTTTTAAAATTATATATTATAT-AAT-TTTTC
27468 AAAA
1 AAAA
27472 CTATATATTA
Statistics
Matches: 166, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
35 5 0.03
36 73 0.44
37 37 0.22
38 13 0.08
39 7 0.04
40 30 0.18
41 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (39 bp):
AAAAAAATGTTTTTAAAATTATATATTATATAATTTTTC
Found at i:27478 original size:29 final size:27
Alignment explanation
Indices: 27431--27485 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
27421 TAAGTTTTCA
27431 AAATGTTTTAAAAACTATATAATATAT
1 AAATGTTTTAAAAACTATATAATATAT
* *
27458 AAATGTTTTCAAAACTATATATTATAT
1 AAATGTTTTAAAAACTATATAATATAT
27485 A
1 A
27486 TATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATGTTTTAAAAACTATATAATATAT
Found at i:27484 original size:34 final size:36
Alignment explanation
Indices: 27444--27530 Score: 90
Period size: 35 Copynumber: 2.4 Consensus size: 36
27434 TGTTTTAAAA
**
27444 ACTATATAATATATAAATGTTTTCA-AAACTATA-T
1 ACTATATAATATATAAACATTTTCACAAACTATATT
* *
27478 ATTATAT-ATATTTTAAAACATTTTCACAAACTATATT
1 ACTATATAATA-TAT-AAACATTTTCACAAACTATATT
27515 ACTATATATATATATA
1 ACTATATA-ATATATA
27531 TATATATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
33 3 0.07
34 8 0.20
35 9 0.22
36 8 0.20
37 8 0.20
38 2 0.05
39 3 0.07
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (36 bp):
ACTATATAATATATAAACATTTTCACAAACTATATT
Found at i:27486 original size:36 final size:38
Alignment explanation
Indices: 27446--27532 Score: 99
Period size: 36 Copynumber: 2.3 Consensus size: 38
27436 TTTTAAAAAC
** *
27446 TATATAATATATAAATGTTTTCA-AAACTATA-TATTA
1 TATATAATATATAAACATTTTCACAAACTATATTACTA
* *
27482 TATATATTTTA-AAACATTTTCACAAACTATATTACTA
1 TATATAATATATAAACATTTTCACAAACTATATTACTA
27519 TATATATATATATA
1 TATATA-ATATATA
27533 TATATAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
35 9 0.22
36 17 0.43
37 10 0.25
38 3 0.08
39 1 0.03
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.45
Consensus pattern (38 bp):
TATATAATATATAAACATTTTCACAAACTATATTACTA
Found at i:27491 original size:25 final size:26
Alignment explanation
Indices: 27431--27496 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
27421 TAAGTTTTCA
*
27431 AAATGTTTTAAAAACTATATAATATAT
1 AAATATTTT-AAAACTATATAATATAT
*
27458 AAATGTTTTCAAAACTATAT-AT-TAT
1 AAATATTTT-AAAACTATATAATATAT
*
27483 ATATATTTTAAAAC
1 AAATATTTTAAAAC
27497 ATTTTCACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.14
25 10 0.28
26 2 0.06
27 19 0.53
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (26 bp):
AAATATTTTAAAACTATATAATATAT
Found at i:27509 original size:63 final size:64
Alignment explanation
Indices: 27395--27522 Score: 163
Period size: 63 Copynumber: 2.0 Consensus size: 64
27385 TAAGTTTTCA
* *
27395 AAATGTGTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTATA-TAATATAT
1 AAATGTGTTAAAAACTATATATTATATAAGTTTTAAAAATGTTTCAAAAACTATATTAATATAT
* * * *
27458 AAATGTTTTCAAAACTATATATTATATATA-TTTTAAAACAT-TTTCACAAACTATATTACTATA
1 AAATGTGTTAAAAACTATATATTATATA-AGTTTTAAAA-ATGTTTCAAAAACTATATTAATATA
27521 T
64 T
27522 A
1 A
27523 TATATATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
63 45 0.80
64 11 0.20
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (64 bp):
AAATGTGTTAAAAACTATATATTATATAAGTTTTAAAAATGTTTCAAAAACTATATTAATATAT
Found at i:45780 original size:16 final size:16
Alignment explanation
Indices: 45735--45796 Score: 81
Period size: 16 Copynumber: 3.8 Consensus size: 16
45725 TGTTTATAGG
45735 AGAATTGAAATCTGTGA
1 AGAATTGAAATCTGT-A
45752 AGGAATT-ATAATCTGTA
1 A-GAATTGA-AATCTGTA
45769 AGAATTGAAATCTGTA
1 AGAATTGAAATCTGTA
*
45785 AGAATTGGAATC
1 AGAATTGAAATC
45797 CAATTCCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
16 24 0.59
17 5 0.12
18 12 0.29
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (16 bp):
AGAATTGAAATCTGTA
Found at i:50584 original size:21 final size:21
Alignment explanation
Indices: 50560--50600 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
50550 ATTTATTAAT
*
50560 ATTTATGGATGATTTTAAATA
1 ATTTATGAATGATTTTAAATA
* *
50581 ATTTATTAATTATTTTAAAT
1 ATTTATGAATGATTTTAAAT
50601 CATTATTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (21 bp):
ATTTATGAATGATTTTAAATA
Found at i:61055 original size:59 final size:60
Alignment explanation
Indices: 60978--61114 Score: 145
Period size: 59 Copynumber: 2.3 Consensus size: 60
60968 TTAATGTTCT
* * * * * * *
60978 AATTTCATCCCTAGACTATTAATATT-AATTTAAATTAGTCCTCAAAGT-TTTAAACATTTC
1 AATTTCATCCC-AAACTATTAATATTCAATCTAAATT-GGCCCCAAACTAGTTAAACATTCC
* * *
61038 AATTTCATCTCAAACTA-TAATCTTCAATCTAAATTGGCCCCAAACTAGTTGAACATTCC
1 AATTTCATCCCAAACTATTAATATTCAATCTAAATTGGCCCCAAACTAGTTAAACATTCC
61097 AATTTCATCCCAAACTAT
1 AATTTCATCCCAAACTAT
61115 ACCTATATAC
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
58 14 0.22
59 39 0.62
60 10 0.16
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (60 bp):
AATTTCATCCCAAACTATTAATATTCAATCTAAATTGGCCCCAAACTAGTTAAACATTCC
Found at i:61402 original size:16 final size:16
Alignment explanation
Indices: 61377--61409 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
61367 CAATTTAATA
61377 TATATATATATATGTG
1 TATATATATATATGTG
*
61393 TATATGTATATATGTG
1 TATATATATATATGTG
61409 T
1 T
61410 GTCCATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (16 bp):
TATATATATATATGTG
Found at i:61402 original size:18 final size:18
Alignment explanation
Indices: 61375--61411 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
61365 ACCAATTTAA
61375 TATATATATATATATGTG
1 TATATATATATATATGTG
* *
61393 TATATGTATATATGTGTG
1 TATATATATATATATGTG
61411 T
1 T
61412 CCATAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (18 bp):
TATATATATATATATGTG
Found at i:65068 original size:59 final size:59
Alignment explanation
Indices: 64938--65107 Score: 148
Period size: 59 Copynumber: 2.9 Consensus size: 59
64928 AATTATTACC
* * *
64938 CTCATTCTAAAA-TGATCCTTAAACTTTTGAATATTTAATTTCATCCTCAACCTAAGATT
1 CTCATTC-AAAATTAATCCTTAAACTTTTGAATATTCAATTTCATCCTCAAACTAAGATT
* * * * *
64997 ATCGTTCTAAATTAATCCTTAAACTTTTGAA-ATTCCAATTTTATACC-CAAACTATGATT
1 CTCATTCAAAATTAATCCTTAAACTTTTGAATATT-CAATTTCAT-CCTCAAACTAAGATT
** ** * * *
65056 CTCATTCAAAATTGGTCCCCAAACTATTGAATCTTCCAATTTCATCCCCAAA
1 CTCATTCAAAATTAATCCTTAAACTTTTGAATATT-CAATTTCATCCTCAAA
65108 TTTATCCAAA
Statistics
Matches: 88, Mismatches: 18, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
58 6 0.07
59 65 0.74
60 17 0.19
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (59 bp):
CTCATTCAAAATTAATCCTTAAACTTTTGAATATTCAATTTCATCCTCAAACTAAGATT
Found at i:65320 original size:60 final size:60
Alignment explanation
Indices: 65241--65399 Score: 180
Period size: 60 Copynumber: 2.6 Consensus size: 60
65231 GAAATTTTCA
* * *
65241 AAAAGTTTAAGGATCAATTTATAATAAATA-TCATACTTTAGGGAT-ATAACTGAAATATTT
1 AAAAGTTTAAGGATCAATTTAGAAT-AATAGTCATAATTTAGGGATCA-AACTAAAATATTT
* * *
65301 AAAAGTTTAAGGA-CAAATTTAGAATGATAGTCATAATTTAGTGATCAAATTAAAATATTT
1 AAAAGTTTAAGGATC-AATTTAGAATAATAGTCATAATTTAGGGATCAAACTAAAATATTT
* * * *
65361 AAAAATTTAAGAATCAATTTAGAATGATTGTCATAATTT
1 AAAAGTTTAAGGATCAATTTAGAATAATAGTCATAATTT
65400 GAAGAAGCCC
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
59 4 0.05
60 80 0.93
61 2 0.02
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (60 bp):
AAAAGTTTAAGGATCAATTTAGAATAATAGTCATAATTTAGGGATCAAACTAAAATATTT
Found at i:66143 original size:2 final size:2
Alignment explanation
Indices: 66131--66175 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
66121 TCAAAGACGA
66131 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66174 AT
1 AT
66176 TTAAACTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:69252 original size:2 final size:2
Alignment explanation
Indices: 69231--69284 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
69221 AAATTTGATA
* * *
69231 AT AT AA AT AA AT AA 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
69273 AT AT AT AT AT AT
1 AT AT AT AT AT AT
69285 TGCATGCTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:72275 original size:2 final size:2
Alignment explanation
Indices: 72268--72303 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
72258 TTGAGAGCAA
72268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72304 GACACTAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76040 original size:13 final size:13
Alignment explanation
Indices: 76022--76058 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
76012 GTGTAATAAT
*
76022 TAAAATATTTTTA
1 TAAAATATTTATA
76035 TAAAAT-TTTATA
1 TAAAATATTTATA
76047 T-AAATATTTATA
1 TAAAATATTTATA
76059 ATTTAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 4 0.18
12 12 0.55
13 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAAAATATTTATA
Done.