Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005373.1 Hibiscus syriacus cultivar Beakdansim tig00012233_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: 312417
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:5432 original size:21 final size:21
Alignment explanation
Indices: 5406--5457 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
5396 TTTTACACTA
5406 AGTGTACCGAAACAATTTGAT
1 AGTGTACCGAAACAATTTGAT
5427 AGTGTACCGAAACAATTTGAT
1 AGTGTACCGAAACAATTTGAT
5448 AGTGTACCGA
1 AGTGTACCGA
5458 TACACCTACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (21 bp):
AGTGTACCGAAACAATTTGAT
Found at i:6222 original size:39 final size:39
Alignment explanation
Indices: 6167--6242 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
6157 AGTCATCAAT
*
6167 GGCTTCTACTTTAAACTTCGACTTCGTTCTTAATTCTTA
1 GGCTTCTACTTCAAACTTCGACTTCGTTCTTAATTCTTA
*
6206 GGCTTCTACTTCAAACTTTGACTTCGTTCTTAATTCT
1 GGCTTCTACTTCAAACTTCGACTTCGTTCTTAATTCT
6243 CAGCCCGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.46
Consensus pattern (39 bp):
GGCTTCTACTTCAAACTTCGACTTCGTTCTTAATTCTTA
Found at i:11877 original size:15 final size:15
Alignment explanation
Indices: 11857--11885 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11847 TAGGACATTT
11857 GGTTTAGATAACGAC
1 GGTTTAGATAACGAC
11872 GGTTTAGATAACGA
1 GGTTTAGATAACGA
11886 AAAAGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (15 bp):
GGTTTAGATAACGAC
Found at i:16029 original size:21 final size:20
Alignment explanation
Indices: 15999--16039 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
15989 ATAAAACAAC
15999 AAATAATAAAA-AACAGTAAA
1 AAATAATAAAATAACA-TAAA
16019 AAATAAATAAAATAACATAAA
1 AAAT-AATAAAATAACATAAA
16040 TATAAGGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (20 bp):
AAATAATAAAATAACATAAA
Found at i:17721 original size:60 final size:60
Alignment explanation
Indices: 17640--17828 Score: 202
Period size: 60 Copynumber: 3.1 Consensus size: 60
17630 TGCATCATAT
* * * *
17640 ATCCCCAAATTAT-AATCCTCATTTTACATTGGTCCTTAAACTTTTGAATATTTCAATTTC
1 ATCCCCAAACTATGAAT-CTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTC
** * * *
17700 ATCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAATTTTTTTAACA-TTCTAAATTC
1 ATCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTC-AATTTC
* * * ** * *
17760 ATCCCTAAACTATGACTCTTATTCTAAATTAGTCCCCAAACTTTTGAGTGTTTCAATTTC
1 ATCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTC
17820 ATCCCCAAA
1 ATCCCCAAA
17829 TCCATCCAAA
Statistics
Matches: 104, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
59 3 0.03
60 95 0.91
61 6 0.06
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.40
Consensus pattern (60 bp):
ATCCCCAAACTATGAATCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTC
Found at i:21164 original size:32 final size:31
Alignment explanation
Indices: 21087--21175 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 31
21077 CCCTAAGGGA
* *
21087 ACATCTTAGGGCC-TGAGAGCCTACCCAAGAT
1 ACATCTTAGGGCCGTG-GGGCCTACCCAAGAC
* * * *
21118 AGATTTTGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCGTGGGGCCTACCCAAG-AC
*
21150 ACATCTTAGGGCCGTAGGGCCTACCC
1 ACATCTTAGGGCCGTGGGGCCTACCC
21176 GAGAATGATC
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
31 21 0.47
32 24 0.53
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.20
Consensus pattern (31 bp):
ACATCTTAGGGCCGTGGGGCCTACCCAAGAC
Found at i:21193 original size:63 final size:63
Alignment explanation
Indices: 21087--21210 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
21077 CCCTAAGGGA
* ** ** *
21087 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTTGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
21150 ACATCTTAGGGCC-GTAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
21211 GTCATATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.27, G:0.28, T:0.19
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:22102 original size:13 final size:13
Alignment explanation
Indices: 22084--22129 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
22074 AAGAAAGTCA
*
22084 ACGGTCAACGATC
1 ACGGTCAACGGTC
22097 ACGGTCAACGGTC
1 ACGGTCAACGGTC
22110 ACGGTCAACGGTC
1 ACGGTCAACGGTC
22123 AACGGTC
1 -ACGGTC
22130 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 25 0.81
14 6 0.19
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:22105 original size:20 final size:20
Alignment explanation
Indices: 22080--22129 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
22070 GTCAAAGAAA
22080 GTCAACGGTCAACGATC-ACG
1 GTCAACGGTC-ACGATCAACG
*
22100 GTCAACGGTCACGGTCAACG
1 GTCAACGGTCACGATCAACG
22120 GTCAACGGTC
1 GTCAACGGTC
22130 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (20 bp):
GTCAACGGTCACGATCAACG
Found at i:22141 original size:17 final size:17
Alignment explanation
Indices: 22119--22168 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
22109 CACGGTCAAC
22119 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
22136 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
* *
22153 AGTCAACAGTCGGGTC
1 GGTCAACGGTCGGGTC
22169 AACCCGGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.16, C:0.24, G:0.42, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:22146 original size:7 final size:7
Alignment explanation
Indices: 22080--22129 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
22070 GTCAAAGAAA
22080 GTCAACG
1 GTCAACG
22087 GTCAACG
1 GTCAACG
*
22094 ATC-ACG
1 GTCAACG
22100 GTCAACG
1 GTCAACG
22107 GTC-ACG
1 GTCAACG
22113 GTCAACG
1 GTCAACG
22120 GTCAACG
1 GTCAACG
22127 GTC
1 GTC
22130 GGGTCGGGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 11 0.28
7 28 0.72
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:22189 original size:19 final size:19
Alignment explanation
Indices: 22165--22254 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
22155 TCAACAGTCG
*
22165 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
22184 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
22203 GGTCAAACCGATTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
22222 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
22242 GGTCAAACCGGTT
1 GGTCAAACCGGTT
22255 TTCCAGCAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 47 0.75
20 15 0.24
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:22237 original size:10 final size:10
Alignment explanation
Indices: 22167--22254 Score: 85
Period size: 9 Copynumber: 9.1 Consensus size: 10
22157 AACAGTCGGG
*
22167 TCAACCCGGT
1 TCAAACCGGT
*
22177 TCAGACCGG-
1 TCAAACCGGT
22186 TCAAACCGGT
1 TCAAACCGGT
*
22196 TCAGACCGG-
1 TCAAACCGGT
*
22205 TCAAACCGAT
1 TCAAACCGGT
*
22215 TCGAACCGG-
1 TCAAACCGGT
22224 TCAAACCGGT
1 TCAAACCGGT
*
22234 TCAAAACTGG-
1 TC-AAACCGGT
22244 TCAAACCGGT
1 TCAAACCGGT
22254 T
1 T
22255 TTCCAGCAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 29 0.47
10 27 0.44
11 6 0.10
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:28467 original size:32 final size:31
Alignment explanation
Indices: 28431--28507 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
28421 CGGGGCCGTG
*
28431 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
28463 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
28494 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
28508 GTCATATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:28490 original size:63 final size:63
Alignment explanation
Indices: 28384--28507 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
28374 CCCTAAGGGA
* * ** *
28384 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
28447 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
28508 GTCATATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:29399 original size:13 final size:13
Alignment explanation
Indices: 29381--29426 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
29371 AAGAAAGTCA
29381 ACGGTCAACGGTC
1 ACGGTCAACGGTC
29394 ACGGTCAACGGTC
1 ACGGTCAACGGTC
29407 ACGGTCAACGGTC
1 ACGGTCAACGGTC
29420 AACGGTC
1 -ACGGTC
29427 GGGTCGGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 26 0.81
14 6 0.19
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:29402 original size:20 final size:20
Alignment explanation
Indices: 29377--29426 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
29367 GTCAAAGAAA
29377 GTCAACGGTCAACGGTC-ACG
1 GTCAACGGTC-ACGGTCAACG
29397 GTCAACGGTCACGGTCAACG
1 GTCAACGGTCACGGTCAACG
29417 GTCAACGGTC
1 GTCAACGGTC
29427 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (20 bp):
GTCAACGGTCACGGTCAACG
Found at i:29438 original size:17 final size:17
Alignment explanation
Indices: 29416--29465 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
29406 CACGGTCAAC
29416 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
29433 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
* *
29450 AGTCAACAGTCGGGTC
1 GGTCAACGGTCGGGTC
29466 AACCCGGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.16, C:0.24, G:0.42, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:29443 original size:7 final size:7
Alignment explanation
Indices: 29377--29426 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
29367 GTCAAAGAAA
29377 GTCAACG
1 GTCAACG
29384 GTCAACG
1 GTCAACG
29391 GTC-ACG
1 GTCAACG
29397 GTCAACG
1 GTCAACG
29404 GTC-ACG
1 GTCAACG
29410 GTCAACG
1 GTCAACG
29417 GTCAACG
1 GTCAACG
29424 GTC
1 GTC
29427 GGGTCGGGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.29
7 29 0.71
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:29492 original size:9 final size:9
Alignment explanation
Indices: 29462--29541 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
29452 TCAACAGTCG
*
29462 GGTCAACCC
1 GGTCAAACC
*
29471 GGTTCAGACC
1 GG-TCAAACC
*
29481 GGTAAAACC
1 GGTCAAACC
*
29490 GGTTCAGACC
1 GG-TCAAACC
29500 GGTCAAACC
1 GGTCAAACC
*
29509 GGTTCGAACC
1 GG-TCAAACC
*
29519 GGTCCAAAACT
1 GGT-C-AAACC
*
29530 GGTTAAACC
1 GGTCAAACC
29539 GGT
1 GGT
29542 TTTCCAGCAG
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
9 25 0.46
10 23 0.43
11 6 0.11
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:29500 original size:10 final size:10
Alignment explanation
Indices: 29464--29542 Score: 65
Period size: 10 Copynumber: 8.1 Consensus size: 10
29454 AACAGTCGGG
*
29464 TCAACCCGGT
1 TCAAACCGGT
*
29474 TCAGACCGG-
1 TCAAACCGGT
*
29483 TAAAACCGGT
1 TCAAACCGGT
*
29493 TCAGACCGG-
1 TCAAACCGGT
29502 TCAAACCGGT
1 TCAAACCGGT
*
29512 TCGAACCGGT
1 TCAAACCGGT
* *
29522 CCAAAACTGGT
1 TC-AAACCGGT
29533 T-AAACCGGT
1 TCAAACCGGT
29542 T
1 T
29543 TTCCAGCAGC
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
9 23 0.43
10 24 0.45
11 6 0.11
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:29519 original size:19 final size:19
Alignment explanation
Indices: 29462--29522 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
29452 TCAACAGTCG
*
29462 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
29481 GGTAAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
29500 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
29519 GGTC
1 GGTC
29523 CAAAACTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 1 0.03
19 37 0.97
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:32798 original size:19 final size:19
Alignment explanation
Indices: 32764--32800 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
32754 ATGACCAACA
*
32764 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
32783 AAATCGCAACGTGATCTC
1 AAATCGCAACGCGATCTC
32801 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:32930 original size:21 final size:21
Alignment explanation
Indices: 32904--33026 Score: 212
Period size: 21 Copynumber: 5.9 Consensus size: 21
32894 TCCAAAATCA
32904 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
32925 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
32946 TTGCGATAGCACTGTTAACCG
1 TTGCGATAGCACTGTTCACCG
*
32967 TTGCGATAGCACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
*
32988 TTGCGATAGTACTGTTCACC-
1 TTGCGATAGCACTGTTCACCG
33008 TTGCGATAGCACTGTTCAC
1 TTGCGATAGCACTGTTCAC
33027 ATTTTATAAT
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
20 18 0.19
21 79 0.81
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:33759 original size:21 final size:21
Alignment explanation
Indices: 33733--33816 Score: 123
Period size: 21 Copynumber: 4.0 Consensus size: 21
33723 AATTCGCAAT
* *
33733 GTGAACAGTGTTATCACAACG
1 GTGAACAGTGCTATCGCAACG
33754 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
* *
33775 GTGAACAGTACTATTGCAACG
1 GTGAACAGTGCTATCGCAACG
*
33796 GTAAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
33817 CGAATTCGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:33830 original size:42 final size:42
Alignment explanation
Indices: 33744--33837 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
33734 TGAACAGTGT
* * * *
33744 TATCACAACGGTGAACAGTGCTATCGCAACGGTGAACAGTAC
1 TATCGCAACGGTAAACAGTGCTATCGCAACGGCGAACAGGAC
*
33786 TATTGCAACGGTAAACAGTGCTATCGCAAC-GCGAATTC-GGAC
1 TATCGCAACGGTAAACAGTGCTATCGCAACGGCGAA--CAGGAC
33828 TATCGCAACG
1 TATCGCAACG
33838 CGAATTTGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 39 0.89
43 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (42 bp):
TATCGCAACGGTAAACAGTGCTATCGCAACGGCGAACAGGAC
Found at i:33861 original size:21 final size:21
Alignment explanation
Indices: 33806--33855 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
33796 GTAAACAGTG
33806 CTATCGCAACGCGAATTCGGA
1 CTATCGCAACGCGAATTCGGA
*
33827 CTATCGCAACGCGAATTTGGA
1 CTATCGCAACGCGAATTCGGA
33848 CTATCGCA
1 CTATCGCA
33856 TTGCGATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (21 bp):
CTATCGCAACGCGAATTCGGA
Found at i:33940 original size:20 final size:19
Alignment explanation
Indices: 33917--33962 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
33907 AAAAATTTAT
* *
33917 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
33937 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
33956 TTGCGAT
1 TTGCGAT
33963 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:33952 original size:19 final size:19
Alignment explanation
Indices: 33928--33964 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
33918 TGCGATACTG
*
33928 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
33947 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
33965 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:34541 original size:156 final size:156
Alignment explanation
Indices: 34248--34554 Score: 544
Period size: 156 Copynumber: 2.0 Consensus size: 156
34238 AAAAATTCTT
34248 AAAGTTTGACTTTCATAAAAAAGAAAAACACAAATAAGATTGATATGAAAGGACTTGTGGTAGAT
1 AAAGTTTGACTTTCATAAAAAAGAAAAACACAAATAAGATTGATATGAAAGGACTTGTGGTAGAT
* * *
34313 GGTGAAGATGCAGCTTATAATTTGTATAATGATTGTGGTAATGGCATGGTTTCAGTGTTCGAAAA
66 GGTGAAGATGCAACTTATAATTTGTATAACGATTATGGTAATGGCATGGTTTCAGTGTTCGAAAA
34378 GGAAAAAAAATAGATATCTTTATCTC
131 GGAAAAAAAATAGATATCTTTATCTC
* *
34404 AAAGTTTGACTTTCATAAAAAAGACAAACACAAATAAGGTTGATATGAAAGGACTTGTGGTAGAT
1 AAAGTTTGACTTTCATAAAAAAGAAAAACACAAATAAGATTGATATGAAAGGACTTGTGGTAGAT
34469 GGTGAAGATGCAACTTATAATTTGTATAACGATTATGGTAATGGCATGGGTTTCAGTGTTCGAAA
66 GGTGAAGATGCAACTTATAATTTGTATAACGATTATGGTAATGGCAT-GGTTTCAGTGTTCGAAA
*
34534 A-GTAAAAAAATAGATATCTTT
130 AGGAAAAAAAATAGATATCTTT
34555 CTGGCACTAA
Statistics
Matches: 144, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
156 126 0.88
157 18 0.12
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (156 bp):
AAAGTTTGACTTTCATAAAAAAGAAAAACACAAATAAGATTGATATGAAAGGACTTGTGGTAGAT
GGTGAAGATGCAACTTATAATTTGTATAACGATTATGGTAATGGCATGGTTTCAGTGTTCGAAAA
GGAAAAAAAATAGATATCTTTATCTC
Found at i:36694 original size:18 final size:19
Alignment explanation
Indices: 36671--36711 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
36661 GTTCAATTAA
36671 TTTTTTAAAAATA-TATAT
1 TTTTTTAAAAATATTATAT
*
36689 TTTTTTATAAATATTATAT
1 TTTTTTAAAAATATTATAT
36708 TTTT
1 TTTT
36712 ATAGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTAAAAATATTATAT
Found at i:47375 original size:10 final size:10
Alignment explanation
Indices: 47357--47446 Score: 51
Period size: 10 Copynumber: 8.7 Consensus size: 10
47347 ATGTTAGATC
47357 AAATAAATAA
1 AAATAAATAA
*
47367 AACTAAATAA
1 AAATAAATAA
*
47377 AAAAAAATAA
1 AAATAAATAA
47387 AAA-AACATAA
1 AAATAA-ATAA
* *
47397 TAAAAAACAAAA
1 -AAATAA-ATAA
* *
47409 GAAAAAAATGA
1 -AAATAAATAA
47420 AAATAAA-AA
1 AAATAAATAA
47429 CAAA-AAGATAA
1 -AAATAA-ATAA
47440 AAATAAA
1 AAATAAA
47447 AATGAAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
9 5 0.08
10 38 0.59
11 9 0.14
12 12 0.19
ACGTcount: A:0.80, C:0.04, G:0.03, T:0.12
Consensus pattern (10 bp):
AAATAAATAA
Found at i:47402 original size:24 final size:24
Alignment explanation
Indices: 47357--47434 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 24
47347 ATGTTAGATC
47357 AAATAAATAAAAC-TAA-ATAAAAAA
1 AAATAAA-AAAACATAATA-AAAAAA
47381 AAATAAAAAAACATAATAAAAAACA
1 AAATAAAAAAACATAATAAAAAA-A
* * *
47406 AAAGAAAAAAATGAAAATAAAAACAA
1 AAATAAAAAAA-CATAATAAAAA-AA
47432 AAA
1 AAA
47435 GATAAAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 5 0.11
24 15 0.33
25 12 0.26
26 13 0.28
27 1 0.02
ACGTcount: A:0.81, C:0.05, G:0.03, T:0.12
Consensus pattern (24 bp):
AAATAAAAAAACATAATAAAAAAA
Found at i:47413 original size:25 final size:25
Alignment explanation
Indices: 47371--47455 Score: 84
Period size: 26 Copynumber: 3.4 Consensus size: 25
47361 AAATAAAACT
*
47371 AAATAAAAA-AAAATAAAAAAA-CA
1 AAATAAAAACAAAAGAAAAAAATCA
* *
47394 TAATAAAAAACAAAAGAAAAAAATGA
1 AAAT-AAAAACAAAAGAAAAAAATCA
* *
47420 AAATAAAAACAAAAAGATAAAAATAA
1 AAATAAAAAC-AAAAGAAAAAAATCA
47446 AAATGAAAAA
1 AAAT-AAAAA
47456 AGAATGAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
23 3 0.06
24 5 0.10
25 17 0.33
26 21 0.41
27 5 0.10
ACGTcount: A:0.81, C:0.04, G:0.05, T:0.11
Consensus pattern (25 bp):
AAATAAAAACAAAAGAAAAAAATCA
Found at i:47428 original size:20 final size:20
Alignment explanation
Indices: 47361--47456 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
47351 TAGATCAAAT
**
47361 AAATAAAACTAAATAAAA-AA
1 AAATAAAAAGAAA-AAAATAA
* *
47381 AAATAAAAA-AACATAATAA
1 AAATAAAAAGAAAAAAATAA
*
47400 AAA-ACAAAAGAAAAAAATGA
1 AAATA-AAAAGAAAAAAATAA
* *
47420 AAATAAAAACAAAAAGATAA
1 AAATAAAAAGAAAAAAATAA
47440 AAATAAAAATGAAAAAA
1 AAATAAAAA-GAAAAAA
47457 GAATGAAATA
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
18 4 0.07
19 11 0.18
20 39 0.65
21 6 0.10
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.11
Consensus pattern (20 bp):
AAATAAAAAGAAAAAAATAA
Found at i:47469 original size:2 final size:2
Alignment explanation
Indices: 47464--47494 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
47454 AAAGAATGAA
*
47464 AT AT AT AC 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 A
47495 CATAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:47475 original size:8 final size:8
Alignment explanation
Indices: 47464--47498 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
47454 AAAGAATGAA
47464 ATATATAC
1 ATATATAC
*
47472 ATATATAT
1 ATATATAC
*
47480 ATATATAT
1 ATATATAC
47488 ATATATAC
1 ATATATAC
47496 ATA
1 ATA
47499 ATAAAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATATAC
Found at i:47550 original size:29 final size:31
Alignment explanation
Indices: 47517--47579 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 31
47507 TGTTAGATTA
47517 AATAAATAAAA-T-AAAAAGAAAAAAATAAT
1 AATAAATAAAACTGAAAAAGAAAAAAATAAT
* **
47546 AATAATTAAAACGTGAGGAAGAAAAAAATAAT
1 AATAAATAAAAC-TGAAAAAGAAAAAAATAAT
47578 AA
1 AA
47580 AGGACCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.36
31 1 0.04
32 17 0.61
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (31 bp):
AATAAATAAAACTGAAAAAGAAAAAAATAAT
Found at i:50383 original size:20 final size:21
Alignment explanation
Indices: 50350--50390 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
50340 ACCCACCTTA
*
50350 TTTTCTTTTCTTTTTCAATTT
1 TTTTCTTATCTTTTTCAATTT
50371 TTTTCTTAT-TTTTTCAATTT
1 TTTTCTTATCTTTTTCAATTT
50391 AGGGCGCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCTTATCTTTTTCAATTT
Found at i:60863 original size:13 final size:14
Alignment explanation
Indices: 60840--60870 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
60830 TAAGAGGGAA
60840 AAATAAAAAAAATG
1 AAATAAAAAAAATG
60854 AAAT-AAAAAAATG
1 AAATAAAAAAAATG
60867 AAAT
1 AAAT
60871 TAATATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (14 bp):
AAATAAAAAAAATG
Found at i:60978 original size:13 final size:13
Alignment explanation
Indices: 60962--61029 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 13
60952 AATTGAATAG
60962 AGAAATAAAAAAA
1 AGAAATAAAAAAA
60975 AGAAATGAAAAACAA
1 AGAAAT-AAAAA-AA
*
60990 AAAAATAAAACAAA
1 AGAAATAAAA-AAA
*
61004 AGGAAAGGAAAAAATA
1 A-GAAA-TAAAAAA-A
61020 A-AAATAAAAA
1 AGAAATAAAAA
61030 TAAAAAGGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
13 11 0.24
14 15 0.33
15 13 0.29
16 6 0.13
ACGTcount: A:0.79, C:0.03, G:0.10, T:0.07
Consensus pattern (13 bp):
AGAAATAAAAAAA
Found at i:61191 original size:3 final size:3
Alignment explanation
Indices: 61174--61212 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
61164 TGTTAGATTA
61174 AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61213 TAAAACTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:63665 original size:380 final size:380
Alignment explanation
Indices: 62964--63732 Score: 1430
Period size: 380 Copynumber: 2.0 Consensus size: 380
62954 TTAAATTAAT
* **
62964 AATTTTATATTATTTTAGATCGGGTTGGGTCGGAGTCCAATTTTTTCTGAAAAATCAGATCGAGT
1 AATTTTATATTATTTTAGATCGGGTTGAGTCGGAGTCCAATTTTAGCTGAAAAATCAGATCGAGT
*
63029 ATCAAATTTTCAGATGGGAACTAATTATTCAGAAATCCAACCCAAACCGACCCATGCCGATGACT
66 ATCAAATTTTCAGATGGGAACTAATTATTCAGAAATCCAACCCAAACCGACCCATGCCGATAACT
*
63094 AAATGCAAGTCCAAAATTTTGAACTATTAACGCCACAACTTTCTGTCGTTCAAAATTGTGATATT
131 AAATGCAAGTCCAAAATTTTGAACTATTAACGCCACAACTTTATGTCGTTCAAAATTGTGATATT
63159 AGAACAACACATGGCAGGGAAAAATATTTTATCTAATGATATGTAAATCGAAATTGTCATATAAT
196 AGAACAACACATGGCAGGGAAAAATATTTTATCTAATGATATGTAAATCGAAATTGTCATATAAT
*
63224 CGTGTTTTTTAAACTATCCTAATCGTATTATCGCGTATGTTGAATATTCTTGCCTTTTTCATTAA
261 CGTGTTTTTTAAACTATCCTAATCGTATTATCGCGTATGTTGAATATTATTGCCTTTTTCATTAA
63289 CATTTTTAAAGATTTTGTATCTTAGAATGTGGATAAACTACACGTCTAGTACCTA
326 CATTTTTAAAGATTTTGTATCTTAGAATGTGGATAAACTACACGTCTAGTACCTA
63344 AATTTTATATTATTTTAGATCGGGTTGAGTCGGAGTCCAATTTTAGCTGAAAAATCAGATCGAGT
1 AATTTTATATTATTTTAGATCGGGTTGAGTCGGAGTCCAATTTTAGCTGAAAAATCAGATCGAGT
* *
63409 ATCAAATTTTCAGATGGGAACTAATTATTCAGAAATCCGACCCAAACCGACCCATGCGGATAACT
66 ATCAAATTTTCAGATGGGAACTAATTATTCAGAAATCCAACCCAAACCGACCCATGCCGATAACT
* *
63474 AAATGCAAGTCCAAAATTTTGAACTATTAACGCCACAACTTTATGTGGTTCGAAATTGTGATATT
131 AAATGCAAGTCCAAAATTTTGAACTATTAACGCCACAACTTTATGTCGTTCAAAATTGTGATATT
63539 AGAACAACACATGGCAGGGAAAAATATTTTATCTAATGATATGTAAATCGAAATTGTCATATAAT
196 AGAACAACACATGGCAGGGAAAAATATTTTATCTAATGATATGTAAATCGAAATTGTCATATAAT
63604 CGTGTTTTTTAAACTATCCTAATCGTATTATCGCGTATGTTGAATATTATTGCCTTTTTCATTAA
261 CGTGTTTTTTAAACTATCCTAATCGTATTATCGCGTATGTTGAATATTATTGCCTTTTTCATTAA
*
63669 CATTTTTAAAGATTTTGTATCTTAGAATGTGGATAAACTACATGTCTAGTACCTA
326 CATTTTTAAAGATTTTGTATCTTAGAATGTGGATAAACTACACGTCTAGTACCTA
63724 AATTATTAT
1 AATT-TTAT
63733 TTTTATTCTA
Statistics
Matches: 377, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
380 373 0.99
381 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (380 bp):
AATTTTATATTATTTTAGATCGGGTTGAGTCGGAGTCCAATTTTAGCTGAAAAATCAGATCGAGT
ATCAAATTTTCAGATGGGAACTAATTATTCAGAAATCCAACCCAAACCGACCCATGCCGATAACT
AAATGCAAGTCCAAAATTTTGAACTATTAACGCCACAACTTTATGTCGTTCAAAATTGTGATATT
AGAACAACACATGGCAGGGAAAAATATTTTATCTAATGATATGTAAATCGAAATTGTCATATAAT
CGTGTTTTTTAAACTATCCTAATCGTATTATCGCGTATGTTGAATATTATTGCCTTTTTCATTAA
CATTTTTAAAGATTTTGTATCTTAGAATGTGGATAAACTACACGTCTAGTACCTA
Found at i:65665 original size:27 final size:27
Alignment explanation
Indices: 65597--65714 Score: 111
Period size: 27 Copynumber: 4.4 Consensus size: 27
65587 ATAATAGAAG
* *
65597 TGCAACAAAAGAATGTCCCAATT-CCAAA
1 TGCAACAAAA-TATGTCTC-ATTACCAAA
*
65625 TGCAA-AAAATATGTCTCATTATCAAA
1 TGCAACAAAATATGTCTCATTACCAAA
* *
65651 TGCAACAAAATATGTATC-TAAACCAAA
1 TGCAACAAAATATGTCTCAT-TACCAAA
* *
65678 TTCAAC-AAA-ATGTCTCAATACCAAA
1 TGCAACAAAATATGTCTCATTACCAAA
65703 TGCAACAAAATA
1 TGCAACAAAATA
65715 AATAAATAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 13
0.75 0.11 0.13
Matches are distributed among these distances:
25 20 0.27
26 22 0.30
27 26 0.36
28 5 0.07
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.23
Consensus pattern (27 bp):
TGCAACAAAATATGTCTCATTACCAAA
Found at i:65700 original size:25 final size:25
Alignment explanation
Indices: 65608--65713 Score: 106
Period size: 25 Copynumber: 4.1 Consensus size: 25
65598 GCAACAAAAG
* * *
65608 AATGTCCCAATTCCAAATGCAAAAA
1 AATGTCTCAATACCAAATGCAACAA
* *
65633 ATATGTCTCATTATCAAATGCAACAAA
1 A-ATGTCTCAATACCAAATGCAAC-AA
* *
65660 ATATGTATCTAA-ACCAAATTCAACAA
1 A-ATGTCTC-AATACCAAATGCAACAA
65686 AATGTCTCAATACCAAATGCAACAA
1 AATGTCTCAATACCAAATGCAACAA
65711 AAT
1 AAT
65714 AAATAAATAA
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
24 2 0.03
25 23 0.35
26 20 0.30
27 20 0.30
28 1 0.02
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.25
Consensus pattern (25 bp):
AATGTCTCAATACCAAATGCAACAA
Found at i:73250 original size:42 final size:42
Alignment explanation
Indices: 73173--73252 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
73163 TAGACATTTA
* * *
73173 AAACGCCGCAATAGAGTGTTAATGTAGCGGTGTTTATAGCAC
1 AAACGCCGCAATAGAGTGTAAATGTAACGGCGTTTATAGCAC
*
73215 AAACGCTGCAATAGAGTGGTAAAT-TAACGGCGTTTATA
1 AAACGCCGCAATAGAGT-GTAAATGTAACGGCGTTTATA
73253 TATAAAAAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 28 0.85
43 5 0.15
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAATAGAGTGTAAATGTAACGGCGTTTATAGCAC
Found at i:79488 original size:21 final size:21
Alignment explanation
Indices: 79464--79507 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
79454 CGGAAAATGA
* *
79464 AGCAAGGGAAGCAGAGAGAGC
1 AGCAACGGAAGCAGACAGAGC
*
79485 AGCAACGGAAGCAGCCAGAGC
1 AGCAACGGAAGCAGACAGAGC
79506 AG
1 AG
79508 TAGCGAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.39, T:0.00
Consensus pattern (21 bp):
AGCAACGGAAGCAGACAGAGC
Found at i:79553 original size:21 final size:21
Alignment explanation
Indices: 79525--79594 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
79515 ACACAAAAAC
79525 AAGCAGCGGCAGCACAGAGAG
1 AAGCAGCGGCAGCACAGAGAG
* *
79546 AAGTAGCGGTAGCACAGAGAG
1 AAGCAGCGGCAGCACAGAGAG
*
79567 AAGCAGCGGCAACACAGAGAG
1 AAGCAGCGGCAGCACAGAGAG
79588 AAGCAGC
1 AAGCAGC
79595 ATATCAACAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.40, C:0.21, G:0.36, T:0.03
Consensus pattern (21 bp):
AAGCAGCGGCAGCACAGAGAG
Found at i:79605 original size:42 final size:42
Alignment explanation
Indices: 79525--79607 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
79515 ACACAAAAAC
* * *
79525 AAGCAGCGGCAGCACAGAGAGAAGTAGCGGTAGCACAGAGAG
1 AAGCAGCGGCAACACAGAGAGAAGCAGCGATAGCACAGAGAG
*
79567 AAGCAGCGGCAACACAGAGAGAAGCAGC-ATATCAACAGAGA
1 AAGCAGCGGCAACACAGAGAGAAGCAGCGATAGC-ACAGAGA
79608 TGTGAAGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 3 0.08
42 33 0.92
ACGTcount: A:0.42, C:0.20, G:0.33, T:0.05
Consensus pattern (42 bp):
AAGCAGCGGCAACACAGAGAGAAGCAGCGATAGCACAGAGAG
Found at i:79997 original size:44 final size:44
Alignment explanation
Indices: 79910--80026 Score: 159
Period size: 44 Copynumber: 2.7 Consensus size: 44
79900 ATTCTGTGTT
* *
79910 ATTTAGCGGCGTTTGTA-A--AAAAAAGCCGCAATATACCATAC
1 ATTTAGCGGCGTTTGTATACTAGAAACGCCGCAATATACCATAC
* *
79951 ATTTAGCGGCGTTTGTATACTAGAAACGTCGCAATATATCATAC
1 ATTTAGCGGCGTTTGTATACTAGAAACGCCGCAATATACCATAC
**
79995 ATTTAGCGATGTTTGTATACTAGAAACGCCGC
1 ATTTAGCGGCGTTTGTATACTAGAAACGCCGC
80027 TAATGCTCAA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 17 0.26
42 1 0.02
44 48 0.73
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (44 bp):
ATTTAGCGGCGTTTGTATACTAGAAACGCCGCAATATACCATAC
Found at i:80210 original size:43 final size:43
Alignment explanation
Indices: 80061--80201 Score: 140
Period size: 43 Copynumber: 3.3 Consensus size: 43
80051 TTTTCGATAC
* * * *
80061 AAACGCCGCTAAATCTGAAAACCTACTACGACATTTGT-GGGA
1 AAACGCCGCTAAATCTCAAAACCTACTACGACGTTTTTAGGAA
* * * * * * *
80103 AAATGCCGCAAAATATCAAAACCTACTGCGGCGTTTTTAAGTA
1 AAACGCCGCTAAATCTCAAAACCTACTACGACGTTTTTAGGAA
* * * *
80146 AAACGCCACTAAATCCCAACACATACTACGACGTTTTTAGGAA
1 AAACGCCGCTAAATCTCAAAACCTACTACGACGTTTTTAGGAA
80189 AAACGCCGCTAAA
1 AAACGCCGCTAAA
80202 CATCAACACC
Statistics
Matches: 76, Mismatches: 22, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
42 30 0.39
43 46 0.61
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAATCTCAAAACCTACTACGACGTTTTTAGGAA
Found at i:80269 original size:43 final size:42
Alignment explanation
Indices: 80135--80287 Score: 110
Period size: 43 Copynumber: 3.5 Consensus size: 42
80125 CTACTGCGGC
* * * ** * *
80135 GTTTTTAAGTAAAACGCCACTAAATCCCAACACATACTACGA
1 GTTTTTAGGAAAAACGCCGCTAAATAACAACACCTATTACGA
* * *
80177 CGTTTTTAGGAAAAACGCCGCTAAACATCAACACCTATTGC-A
1 -GTTTTTAGGAAAAACGCCGCTAAATAACAACACCTATTACGA
** *
80219 GCATTTTTCTGACAAACGCCGCTAAATAACAACACCTATTACGA
1 G--TTTTTAGGAAAAACGCCGCTAAATAACAACACCTATTACGA
** *
80263 TGTTTTTTAAAAAAAACGCTGCTAA
1 -G-TTTTTAGGAAAAACGCCGCTAA
80288 CTTTAGCGAC
Statistics
Matches: 85, Mismatches: 21, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 64 0.75
44 18 0.21
45 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (42 bp):
GTTTTTAGGAAAAACGCCGCTAAATAACAACACCTATTACGA
Found at i:81252 original size:25 final size:25
Alignment explanation
Indices: 81206--81253 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
81196 CGTGGTGTAT
* * *
81206 TTTTTTATTAATGCTTATTGTTTTC
1 TTTTTTATTAATACATAATGTTTTC
81231 TTTTTTATTAATACATAATGTTT
1 TTTTTTATTAATACATAATGTTT
81254 GTGGCATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (25 bp):
TTTTTTATTAATACATAATGTTTTC
Found at i:84618 original size:27 final size:28
Alignment explanation
Indices: 84588--84643 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
84578 CATATTAAGG
*
84588 ATTTGGTATTGAGACA-TATTTTGTTGC
1 ATTTGGTATTGAGAAATTATTTTGTTGC
*
84615 ATTTGGTATTGAGAAATTTTTTTGTTGC
1 ATTTGGTATTGAGAAATTATTTTGTTGC
84643 A
1 A
84644 CTTTTGTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.50
Consensus pattern (28 bp):
ATTTGGTATTGAGAAATTATTTTGTTGC
Found at i:86352 original size:23 final size:23
Alignment explanation
Indices: 86300--86360 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
86290 TTTCACTTGG
*
86300 TTCTTTTACTTTTATTTATTTAT
1 TTCTTTTAATTTTATTTATTTAT
* * *
86323 TTATTTTAATTTTCTTT-TTCTTT
1 TTCTTTTAATTTTATTTATT-TAT
*
86346 TTCTTTTATTTTTAT
1 TTCTTTTAATTTTAT
86361 ACAGGCCAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (23 bp):
TTCTTTTAATTTTATTTATTTAT
Found at i:87568 original size:109 final size:109
Alignment explanation
Indices: 87346--87541 Score: 261
Period size: 109 Copynumber: 1.8 Consensus size: 109
87336 GTTTAGCGCA
* * * *
87346 TTTTTGCATGTTGATCACCTGTGAGGACCGAAGTTGCTATTTACCCGTTTTCTTGCATGTTATAT
1 TTTTTACATGTTGATCACCTGTGAGGACCAAAGTTGCTATTTACCCATTTTCGTGCATGTTATAT
* * * *
87411 ATTTTTTGGGATATTTTTTGTTTAGTCCCCCGTAATTTAGTGTG
66 AATTTTTAGAATATTTTCTGTTTAGTCCCCCGTAATTTAGTGTG
* * * *
87455 TTTTTACATGTTGATCACTTGT-AGGGACCAAAGTTGTTATTTACCCATTTT-GTGCTTGTTATG
1 TTTTTACATGTTGATCACCTGTGA-GGACCAAAGTTGCTATTTACCCATTTTCGTGCATGTTATA
87518 TAATTTTTAGAATATTTTCTGTTT
65 TAATTTTTAGAATATTTTCTGTTT
87542 GATCTCCCTT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
108 30 0.41
109 44 0.59
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.48
Consensus pattern (109 bp):
TTTTTACATGTTGATCACCTGTGAGGACCAAAGTTGCTATTTACCCATTTTCGTGCATGTTATAT
AATTTTTAGAATATTTTCTGTTTAGTCCCCCGTAATTTAGTGTG
Found at i:88848 original size:36 final size:36
Alignment explanation
Indices: 88744--89064 Score: 375
Period size: 37 Copynumber: 8.8 Consensus size: 36
88734 AGAAAATGAT
*
88744 TTTTGAAAA-TGTATATATTATATAGTTTTTGAAAACA
1 TTTTGAAAACT-TATATAATATATAG-TTTTGAAAACA
*
88781 TTTTGAAAA-TATATATAATATATAATTTTTTGAAAACA
1 TTTTGAAAACT-TATATAATATAT-A-GTTTTGAAAACA
* *
88819 TTTTGAAAACTTATGTAATATATAGTTTTGAAATCA
1 TTTTGAAAACTTATATAATATATAGTTTTGAAAACA
* *
88855 TTTTGAAATAGTTATATAATATATAGTTTTGAAATCA
1 TTTTGAAA-ACTTATATAATATATAGTTTTGAAAACA
88892 TTTTGAAAAACTTATATAATATATAGTTTTGAAAACA
1 TTTTG-AAAACTTATATAATATATAGTTTTGAAAACA
* * *
88929 TTTTTTGAAAACATATATAATAAATAGTTTTAAAAAACA
1 --TTTTGAAAACTTATATAATATATAGTTTT-GAAAACA
* *
88968 -TTTGAAAACATATATAATATATAGTTTT-AAAATA
1 TTTTGAAAACTTATATAATATATAGTTTTGAAAACA
89002 TTTTTGAAAAC-TATATAATATATAGTTTTGAAAACA
1 -TTTTGAAAACTTATATAATATATAGTTTTGAAAACA
* * *
89038 TTTTTAAAA-TTATATAACATAGAGTTT
1 TTTTGAAAACTTATATAATATATAGTTT
89065 AAAAATATTT
Statistics
Matches: 253, Mismatches: 19, Indels: 26
0.85 0.06 0.09
Matches are distributed among these distances:
34 5 0.02
35 41 0.16
36 59 0.23
37 79 0.31
38 57 0.23
39 12 0.05
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTTGAAAACTTATATAATATATAGTTTTGAAAACA
Found at i:88936 original size:13 final size:13
Alignment explanation
Indices: 88918--88942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88908 TAATATATAG
88918 TTTTGAAAACATT
1 TTTTGAAAACATT
88931 TTTTGAAAACAT
1 TTTTGAAAACAT
88943 ATATAATAAA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAACATT
Found at i:89102 original size:14 final size:14
Alignment explanation
Indices: 89083--89125 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
89073 TTTTGAAATA
89083 TATATATTATATAT
1 TATATATTATATAT
89097 TATATAGTT-TATAT
1 TATATA-TTATATAT
89111 TAT-TATTAT-TAT
1 TATATATTATATAT
89123 TAT
1 TAT
89126 TTTATTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.30
13 3 0.11
14 14 0.52
15 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TATATATTATATAT
Found at i:90470 original size:20 final size:20
Alignment explanation
Indices: 90419--90476 Score: 84
Period size: 19 Copynumber: 2.9 Consensus size: 20
90409 ATCTTATTTC
90419 ATTTTCCCTTTGATTTATTAT
1 ATTTT-CCTTTGATTTATTAT
90440 -TCTTT-CTTTGATTTATTAT
1 AT-TTTCCTTTGATTTATTAT
90459 ATTTTCCTTTGATTTATT
1 ATTTTCCTTTGATTTATT
90477 TAATATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 17 0.50
20 14 0.41
21 3 0.09
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTTCCTTTGATTTATTAT
Found at i:90506 original size:32 final size:31
Alignment explanation
Indices: 90455--90519 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
90445 CTTTGATTTA
*
90455 TTATATTTTCCTTTGATTTAT-TTAATATTTTT
1 TTATATTTTCCTTCGATTTATATT--TATTTTT
* *
90487 TTATTTTTTTCTTCGATTTATATTTATTTTT
1 TTATATTTTCCTTCGATTTATATTTATTTTT
90518 TT
1 TT
90520 CCCTCGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 9 0.31
32 18 0.62
33 2 0.07
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.72
Consensus pattern (31 bp):
TTATATTTTCCTTCGATTTATATTTATTTTT
Found at i:90526 original size:24 final size:25
Alignment explanation
Indices: 90480--90546 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 25
90470 ATTTATTTAA
* *
90480 TATTTTTTTATTTTTTTCTTCGATT
1 TATTATTTTATTTTTTTCCTCGATT
90505 TA-TA-TTTATTTTTTTCCCTCGATT
1 TATTATTTTATTTTTTT-CCTCGATT
90529 TATTATTTTATTATTTTT
1 TATTATTTTATT-TTTTT
90547 ATGTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 11 0.31
24 10 0.28
25 4 0.11
26 6 0.17
27 5 0.14
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (25 bp):
TATTATTTTATTTTTTTCCTCGATT
Found at i:90556 original size:19 final size:19
Alignment explanation
Indices: 90529--90586 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
90519 TCCCTCGATT
*
90529 TATTATTTTATTATTTTTA
1 TATTTTTTTATTATTTTTA
* *
90548 TGTTTTTTTATT-TATTTAA
1 TATTTTTTTATTAT-TTTTA
90567 TATTTTTTTATTATTTTTA
1 TATTTTTTTATTATTTTTA
90586 T
1 T
90587 CTAACATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 1 0.03
19 30 0.94
20 1 0.03
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TATTTTTTTATTATTTTTA
Found at i:90583 original size:11 final size:11
Alignment explanation
Indices: 90527--90584 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
90517 TTTCCCTCGA
90527 TTTATTATTTT
1 TTTATTATTTT
* *
90538 ATTATTTTTATGT
1 TTTATTATT-T-T
* *
90551 TTTTTTATTTA
1 TTTATTATTTT
*
90562 TTTAATATTTT
1 TTTATTATTTT
90573 TTTATTATTTT
1 TTTATTATTTT
90584 T
1 T
90585 ATCTAACATT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
11 26 0.74
12 2 0.06
13 7 0.20
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTATTATTTT
Found at i:97529 original size:95 final size:95
Alignment explanation
Indices: 97361--97554 Score: 345
Period size: 95 Copynumber: 2.1 Consensus size: 95
97351 CAGATACCTG
97361 GAAT-TTGTTAATGCCATATTCATGGATGAGGAAAAGAAGATATTTAAGCCTAGACTGTCCAATT
1 GAATGTTGTTAATGCCATATTCATGGATGAGGAAAAGAAGATATTTAAGCCTAGACTGTCCAATT
* * *
97425 GTACGAGAATGGAATTAAAGATAACTTTTT
66 ATACCAGAATGGAATTAAAGATAACTTTGT
*
97455 GAATGTTGTTAATTCCATATTCATGGATGAGGAAAAGAAGATATTTAAGCCTAGACTGTCCAATT
1 GAATGTTGTTAATGCCATATTCATGGATGAGGAAAAGAAGATATTTAAGCCTAGACTGTCCAATT
97520 ATACCAGAATGGAATTAAAGATAACTTTGT
66 ATACCAGAATGGAATTAAAGATAACTTTGT
97550 GAATG
1 GAATG
97555 AGAGCCAAGG
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
94 4 0.04
95 91 0.96
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (95 bp):
GAATGTTGTTAATGCCATATTCATGGATGAGGAAAAGAAGATATTTAAGCCTAGACTGTCCAATT
ATACCAGAATGGAATTAAAGATAACTTTGT
Found at i:101575 original size:13 final size:13
Alignment explanation
Indices: 101557--101618 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
101547 TTTGCCTAAA
101557 GAAAGAAAAAAAT
1 GAAAGAAAAAAAT
101570 GAAAGAAAAAAAT
1 GAAAGAAAAAAAT
* *
101583 AAAATAAAAAAAT
1 GAAAGAAAAAAAT
*
101596 AAAAAGAAAAAAA-
1 -GAAAGAAAAAAAT
101609 GAAAGAAAAA
1 GAAAGAAAAA
101619 TAATAGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
12 9 0.20
13 24 0.55
14 11 0.25
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.06
Consensus pattern (13 bp):
GAAAGAAAAAAAT
Found at i:101602 original size:40 final size:42
Alignment explanation
Indices: 101558--101637 Score: 121
Period size: 40 Copynumber: 1.9 Consensus size: 42
101548 TTGCCTAAAG
101558 AAAGAAAAAAATGAAAGAAAAA-AAT-AAAATAAA-AAAATAA
1 AAAGAAAAAAA-GAAAGAAAAATAATAAAAATAAATAAAATAA
101598 AAAGAAAAAAAGAAAGAAAAATAATAGAAAATAAATAAAA
1 AAAGAAAAAAAGAAAGAAAAATAATA-AAAATAAATAAAA
101638 AGGGGTTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
39 10 0.28
40 14 0.39
42 8 0.22
43 4 0.11
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.10
Consensus pattern (42 bp):
AAAGAAAAAAAGAAAGAAAAATAATAAAAATAAATAAAATAA
Found at i:101618 original size:27 final size:27
Alignment explanation
Indices: 101554--101637 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
101544 TACTTTGCCT
*
101554 AAAGAAAG-AAAAAAAT-GAAAGAAAA
1 AAAGAAAGAAAAAAAATAAAAAGAAAA
*
101579 AAATAAA-ATAAAAAAATAAAAAGAAAA
1 AAAGAAAGA-AAAAAAATAAAAAGAAAA
* *
101606 AAAGAAAGAAAAATAATAGAAAATAAATA
1 AAAGAAAGAAAAAAAATA-AAAAGAAA-A
101635 AAA
1 AAA
101638 AGGGGTTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 6 0.12
26 8 0.17
27 22 0.46
28 8 0.17
29 4 0.08
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (27 bp):
AAAGAAAGAAAAAAAATAAAAAGAAAA
Found at i:103217 original size:138 final size:133
Alignment explanation
Indices: 102926--103435 Score: 575
Period size: 138 Copynumber: 3.8 Consensus size: 133
102916 GCAAATCAAA
* * *
102926 CTCGATTCAATATTCCCTGAAGAATAGTGGAATGAATCAACATTTCCAGATTTGATCTACCCTAA
1 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATCTACCCTGA
* * * * * * * *
102991 AGAAGTAGCAGA-ACAAATCT--CTTTTCTCAAGATTTGATATTCTCTAAAGAAACAGTAGAACA
66 AGAAGCAGCGGAGA-AGATCTCCCTTTT-TCTAGATTTGATCTTCCCTGAAG-AACAGTGGAACA
*
103053 AGACTAC
128 A-ACTGC
* * * *
103060 TTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTTCGGATCTGATTTACCCTGA
1 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATCTACCCTGA
103125 AGAAGCAGCGGAGAAGATCCCCTCCCTTTTTCTAGATTTGATCTTCCCTGAAGAAGCAGTGGAAC
66 AGAAGCAGCGGAGAAGAT---CTCCCTTTTTCTAGATTTGATCTTCCCTGAAGAA-CAGTGGAAC
103190 AAACCTGC
127 AAA-CTGC
* * * *
103198 CTCGATCCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCTAGATCTGATTTACCCTGA
1 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATCTACCCTGA
* * * * * *
103263 AAAAGTAGCGGAGCAGATC-CCCTTTTTCTAGATTTGATCTTCCTTGAGGAATAGTGGAACAAAT
66 AGAAGCAGCGGAGAAGATCTCCCTTTTTCTAGATTTGATCTTCCCTGAAGAACAGTGGAACAAA-
103327 CTGC
130 CTGC
* * ** *
103331 CTCGATTCAATATTCCCTGAACAACGGTGGAATGAATCAACGCTTCCAGATTTGATCTACCCTGA
1 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATCTACCCTGA
* * *
103396 AGAAGCAGCGGAGCATATC-CCC-CTTTC-AGATTTGATCTTC
66 AGAAGCAGCGGAGAAGATCTCCCTTTTTCTAGATTTGATCTTC
103436 AAAAATCTCT
Statistics
Matches: 326, Mismatches: 42, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
131 13 0.04
132 4 0.01
133 90 0.28
134 101 0.31
135 2 0.01
137 5 0.02
138 106 0.33
139 5 0.02
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (133 bp):
CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATCTACCCTGA
AGAAGCAGCGGAGAAGATCTCCCTTTTTCTAGATTTGATCTTCCCTGAAGAACAGTGGAACAAAC
TGC
Found at i:103636 original size:13 final size:13
Alignment explanation
Indices: 103615--103662 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
103605 GTTCTTTATT
*
103615 TTTTGTTTATTTA
1 TTTTATTTATTTA
*
103628 TTTTATTTATCTA
1 TTTTATTTATTTA
103641 TTTTAATTT-TTTA
1 TTTT-ATTTATTTA
103654 TATTTATTT
1 T-TTTATTT
103663 TTATACAGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 23 0.77
14 7 0.23
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:104486 original size:12 final size:12
Alignment explanation
Indices: 104469--104494 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
104459 GGGGAGAGAA
104469 TTTTTTAGTTTT
1 TTTTTTAGTTTT
104481 TTTTTTAGTTTT
1 TTTTTTAGTTTT
104493 TT
1 TT
104495 GGTCGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTTTAGTTTT
Found at i:106701 original size:20 final size:20
Alignment explanation
Indices: 106676--106714 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
106666 TTAAAAGATC
106676 AGTTGTAAATGATATAGTTG
1 AGTTGTAAATGATATAGTTG
* *
106696 AGTTGTTAATGGTATAGTT
1 AGTTGTAAATGATATAGTT
106715 TACCATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.44
Consensus pattern (20 bp):
AGTTGTAAATGATATAGTTG
Found at i:107616 original size:11 final size:11
Alignment explanation
Indices: 107602--107633 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
107592 AATTTTATTC
*
107602 TAATTTTAATA
1 TAATTATAATA
107613 TAATTATAATA
1 TAATTATAATA
107624 TAATTATAAT
1 TAATTATAAT
107634 TTTTATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATTATAATA
Found at i:108912 original size:28 final size:28
Alignment explanation
Indices: 108881--108937 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
108871 TTTAATGATT
* *
108881 ATATATAAAGAGTAAATATAGTTTAAAA
1 ATATAAAAAAAGTAAATATAGTTTAAAA
* * *
108909 ATATAAAAAAATTAAATTTATTTTAAAA
1 ATATAAAAAAAGTAAATATAGTTTAAAA
108937 A
1 A
108938 AAAACTCAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (28 bp):
ATATAAAAAAAGTAAATATAGTTTAAAA
Found at i:110064 original size:17 final size:18
Alignment explanation
Indices: 110042--110077 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
110032 ATTCTAATTA
*
110042 AATTTT-AATAAATGATT
1 AATTTTAAATAAATCATT
110059 AATTTTAAATAAATCATT
1 AATTTTAAATAAATCATT
110077 A
1 A
110078 TACTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
AATTTTAAATAAATCATT
Found at i:110582 original size:20 final size:20
Alignment explanation
Indices: 110554--110591 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
110544 TGGATTTTCA
* *
110554 AAATTTATTTTTGAAATTTT
1 AAATATATTTTTAAAATTTT
110574 AAATATATTTTTAAAATT
1 AAATATATTTTTAAAATT
110592 ATATTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
AAATATATTTTTAAAATTTT
Found at i:111362 original size:21 final size:21
Alignment explanation
Indices: 111309--111389 Score: 110
Period size: 21 Copynumber: 3.8 Consensus size: 21
111299 AATATTAAGA
* *
111309 GGTACCGATACCACTATGAAT
1 GGTATCGATACCCCTATGAAT
*
111330 GGGTATCAATACCCCTATGAAT
1 -GGTATCGATACCCCTATGAAT
111352 GGTA-CTGATACCCCTATGAAT
1 GGTATC-GATACCCCTATGAAT
111373 GGTATCGATACCCCTAT
1 GGTATCGATACCCCTAT
111390 CAATACCTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
20 1 0.02
21 33 0.62
22 19 0.36
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (21 bp):
GGTATCGATACCCCTATGAAT
Found at i:111370 original size:43 final size:42
Alignment explanation
Indices: 111309--111389 Score: 126
Period size: 43 Copynumber: 1.9 Consensus size: 42
111299 AATATTAAGA
111309 GGTACCGATACCACTATGAATGGGTATCAATACCCCTATGAAT
1 GGTACCGATACCACTATGAAT-GGTATCAATACCCCTATGAAT
* * *
111352 GGTACTGATACCCCTATGAATGGTATCGATACCCCTAT
1 GGTACCGATACCACTATGAATGGTATCAATACCCCTAT
111390 CAATACCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 16 0.46
43 19 0.54
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (42 bp):
GGTACCGATACCACTATGAATGGTATCAATACCCCTATGAAT
Found at i:111422 original size:55 final size:55
Alignment explanation
Indices: 111333--111442 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 55
111323 TATGAATGGG
* *
111333 TATCAATACCCCTATGAATGGTACTGATACCCCTATGAAT-GGTATCGATACCCC
1 TATCAATACCCCTATGAAGGGTACTGATACCCCTATGAATGGGTATCAATACCCC
* *
111387 TATCAATACCTCTTATGAACGGGTACTGAT-GCCCTATGAATGGGTATCAATACCCC
1 TATCAATACC-CCTATGAA-GGGTACTGATACCCCTATGAATGGGTATCAATACCCC
111443 ATGAAGGCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
54 10 0.20
55 17 0.35
56 22 0.45
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (55 bp):
TATCAATACCCCTATGAAGGGTACTGATACCCCTATGAATGGGTATCAATACCCC
Found at i:112933 original size:17 final size:17
Alignment explanation
Indices: 112911--112945 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
112901 TGTTGAAGGA
112911 AGAAGAAAAAGAAGAAG
1 AGAAGAAAAAGAAGAAG
*
112928 AGAAGAAAAATAAGAAG
1 AGAAGAAAAAGAAGAAG
112945 A
1 A
112946 ATGAGGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (17 bp):
AGAAGAAAAAGAAGAAG
Found at i:113460 original size:19 final size:20
Alignment explanation
Indices: 113436--113473 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
113426 TAAAGATAAA
113436 TCGATTTTGAAAAT-AAAAG
1 TCGATTTTGAAAATCAAAAG
113455 TCGATTTTGAAAATCAAAA
1 TCGATTTTGAAAATCAAAA
113474 TGAAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (20 bp):
TCGATTTTGAAAATCAAAAG
Found at i:114611 original size:18 final size:19
Alignment explanation
Indices: 114588--114639 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
114578 TATATTTTCC
*
114588 AACAATTGGTATCTTTT-T
1 AACAATTGGTATCTTTTAA
*
114606 AACAATTGTTATCCTTTTGAA
1 AACAATTGGTAT-CTTTT-AA
114627 AACAATTGGTATC
1 AACAATTGGTATC
114640 AGAGCTTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.39
19 5 0.18
20 1 0.04
21 11 0.39
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (19 bp):
AACAATTGGTATCTTTTAA
Found at i:116600 original size:35 final size:35
Alignment explanation
Indices: 116561--116690 Score: 251
Period size: 35 Copynumber: 3.7 Consensus size: 35
116551 CTAATACCCC
*
116561 TATGAATGGGTACTGATACCCCTATCAATACGTCT
1 TATGAACGGGTACTGATACCCCTATCAATACGTCT
116596 TATGAACGGGTACTGATACCCCTATCAATACGTCT
1 TATGAACGGGTACTGATACCCCTATCAATACGTCT
116631 TATGAACGGGTACTGATACCCCTATCAATACGTCT
1 TATGAACGGGTACTGATACCCCTATCAATACGTCT
116666 TATGAACGGGTACTGATACCCCTAT
1 TATGAACGGGTACTGATACCCCTAT
116691 GAATGGGTAT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
35 94 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (35 bp):
TATGAACGGGTACTGATACCCCTATCAATACGTCT
Found at i:117658 original size:18 final size:18
Alignment explanation
Indices: 117635--117669 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
117625 AAGTATAAGT
117635 ATTTATTTAAA-ATTAATC
1 ATTTA-TTAAATATTAATC
117653 ATTTATTAAATATTAAT
1 ATTTATTAAATATTAAT
117670 TTTAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTATTAAATATTAATC
Found at i:119493 original size:14 final size:15
Alignment explanation
Indices: 119462--119498 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
119452 ATAAATTAGT
*
119462 TAAAA-ATTTAAAGG
1 TAAAATATTTAAAGA
119476 TAAAATATTTAAA-A
1 TAAAATATTTAAAGA
119490 TAAAATATT
1 TAAAATATT
119499 AATTACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (15 bp):
TAAAATATTTAAAGA
Found at i:120588 original size:25 final size:23
Alignment explanation
Indices: 120543--120589 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
120533 TAATTATAGA
*
120543 AATTATAATTTTAATAGAATTAT
1 AATTATAATTTTAATAAAATTAT
*
120566 AATTATAAATATTTATTAAAATTA
1 AATTAT-AAT-TTTAATAAAATTA
120590 ATCATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTATAATTTTAATAAAATTAT
Found at i:123245 original size:6 final size:6
Alignment explanation
Indices: 123229--123261 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
123219 CACTTGTATA
123229 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
123262 GCATGTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:124852 original size:20 final size:20
Alignment explanation
Indices: 124827--124868 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
124817 GGGCCTAATC
*
124827 ATAAAATAAAAATG-AAAAGA
1 ATAAAA-AAAAAAGAAAAAGA
124847 ATAAAAAAAAAAGAAAAAGA
1 ATAAAAAAAAAAGAAAAAGA
124867 AT
1 AT
124869 TTGATGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (20 bp):
ATAAAAAAAAAAGAAAAAGA
Found at i:125533 original size:20 final size:19
Alignment explanation
Indices: 125486--125538 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
125476 AAAAATTATA
125486 ATTAA-TTTTTAATAAATC
1 ATTAACTTTTTAATAAATC
**
125504 ATTATTTTTTTAATAAATC
1 ATTAACTTTTTAATAAATC
*
125523 CTTAAACTTTTTAATA
1 ATT-AACTTTTTAATA
125539 TTTACATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 4 0.14
19 15 0.52
20 10 0.34
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTAACTTTTTAATAAATC
Found at i:128536 original size:2 final size:2
Alignment explanation
Indices: 128501--128525 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
128491 TAAATATGAG
128501 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
128526 CTCAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:128625 original size:2 final size:2
Alignment explanation
Indices: 128618--128653 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
128608 ATGAGTATTG
128618 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
128654 GATGTAGGAT
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:133077 original size:20 final size:20
Alignment explanation
Indices: 133022--133091 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
133012 TACTGTTTAT
* * *
133022 TACTGTTCACACAGTATCGA
1 TACTATTCATACAGTACCGA
* *
133042 TACTATTTATATAGTACCGA
1 TACTATTCATACAGTACCGA
*
133062 TACTATTCATACAGTACAG-
1 TACTATTCATACAGTACCGA
133081 TACTATTCATA
1 TACTATTCATA
133092 AAAACATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 11 0.26
20 31 0.74
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAGTACCGA
Found at i:138456 original size:20 final size:19
Alignment explanation
Indices: 138418--138456 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
138408 CAATAGTCAC
*
138418 ACAAAAAATTATACATAAA
1 ACAAAAAATTAAACATAAA
*
138437 ACAAAAATATTAAACCTAAA
1 ACAAAAA-ATTAAACATAAA
138457 TATACGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.21
Consensus pattern (19 bp):
ACAAAAAATTAAACATAAA
Found at i:142640 original size:21 final size:20
Alignment explanation
Indices: 142602--142640 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
142592 TAATGAATAG
*
142602 TTGTTTTTGTATGTTGTTAT
1 TTGTTTTTGTATGATGTTAT
*
142622 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TGTATGATGTT
142641 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:142772 original size:20 final size:20
Alignment explanation
Indices: 142747--142790 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
142737 GAGAGAAAAT
142747 AGGGAGGATCCACATAAGAA
1 AGGGAGGATCCACATAAGAA
142767 AGGGAGGATCCACATAAGAA
1 AGGGAGGATCCACATAAGAA
142787 AGGG
1 AGGG
142791 GTTCTAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.34, T:0.09
Consensus pattern (20 bp):
AGGGAGGATCCACATAAGAA
Found at i:143313 original size:16 final size:17
Alignment explanation
Indices: 143279--143320 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
143269 TTGCTACCAT
*
143279 ATTCCA-TTACACCACC
1 ATTCCATTTACACCAAC
143295 ATTCCATTTACA-CAAC
1 ATTCCATTTACACCAAC
143311 ATTCTCATTT
1 ATTC-CATTT
143321 GTAAATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTCCATTTACACCAAC
Found at i:161855 original size:27 final size:27
Alignment explanation
Indices: 161825--161935 Score: 141
Period size: 27 Copynumber: 4.1 Consensus size: 27
161815 CTCTCAATTG
161825 TTTTTAACTTTTTCCATTTCTCTTTCA
1 TTTTTAACTTTTTCCATTTCTCTTTCA
*
161852 TTTTTAACCTTTTCCATTTCTCTTTCA
1 TTTTTAACTTTTTCCATTTCTCTTTCA
* * *
161879 TTTCTAACTTTTCCCATTTCCCTTTCA
1 TTTTTAACTTTTTCCATTTCTCTTTCA
* * ** *
161906 TTTGTAACTTTTACTTTTTCTCTCTCA
1 TTTTTAACTTTTTCCATTTCTCTTTCA
161933 TTT
1 TTT
161936 CTTCATCTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.14, C:0.25, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTTTAACTTTTTCCATTTCTCTTTCA
Found at i:181394 original size:76 final size:76
Alignment explanation
Indices: 181265--181410 Score: 186
Period size: 76 Copynumber: 1.9 Consensus size: 76
181255 ACGCATTTAA
** * * ** * *
181265 CTTAAAATTCGAATTTTCTTCGATTAGTTATCTATTTTATTAATGGTGTTTACCTTTAAATTTTA
1 CTTAAAACCCGAATTTTCTTCGATTAATTATCTATTTTACTAATAATGCTTACCTTAAAATTTTA
181330 TTTGTACCCAC
66 TTTGTACCCAC
* *
181341 CTTAAAACCCGAATTTTCTTCGGTTAATTA-CTTATTTTACTGATAATGCTTACCTTAAAATTTT
1 CTTAAAACCCGAATTTTCTTCGATTAATTATC-TATTTTACTAATAATGCTTACCTTAAAATTTT
181405 ATTTGT
65 ATTTGT
181411 GCTCATTTCA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 1 0.02
76 58 0.98
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (76 bp):
CTTAAAACCCGAATTTTCTTCGATTAATTATCTATTTTACTAATAATGCTTACCTTAAAATTTTA
TTTGTACCCAC
Found at i:184018 original size:16 final size:16
Alignment explanation
Indices: 183999--184033 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
183989 GGCGTGACAC
*
183999 GTGACACTAGTGATAT
1 GTGACACTAGTAATAT
184015 GTGACACTAGTAATAT
1 GTGACACTAGTAATAT
184031 GTG
1 GTG
184034 TCACAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (16 bp):
GTGACACTAGTAATAT
Found at i:188958 original size:17 final size:17
Alignment explanation
Indices: 188936--188968 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
188926 GGCTTGGAGG
188936 CACTTTAAGTCATTTTA
1 CACTTTAAGTCATTTTA
*
188953 CACTTTAGGTCATTTT
1 CACTTTAAGTCATTTT
188969 GGTCATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.48
Consensus pattern (17 bp):
CACTTTAAGTCATTTTA
Found at i:192204 original size:36 final size:35
Alignment explanation
Indices: 192137--192329 Score: 192
Period size: 36 Copynumber: 5.4 Consensus size: 35
192127 TCTTAGGTCC
* *
192137 ATAAGAAATTACCAGTTGATCAGTACCGAACCTAT
1 ATAAGAAATTACCAGTTGATCAGAACTGAACCTAT
192172 ATAAGAAATTACCAGCTTGATCAGAACTGAACCTGCA-
1 ATAAGAAATTACCAG-TTGATCAGAACTGAACCT--AT
** * **
192209 ATAAGGGATTAACAGTTGATCAGTGCTGAACCTAT
1 ATAAGAAATTACCAGTTGATCAGAACTGAACCTAT
* * *
192244 ATAAGGAATTACCAGCTTGATTAGAACTGAACCTAC
1 ATAAGAAATTACCAG-TTGATCAGAACTGAACCTAT
* * **
192280 AAATAGGAATTACCAGTTGATC-GATGTTGAACCTAT
1 ATA-AGAAATTACCAGTTGATCAGA-ACTGAACCTAT
192316 ATAAGAAATTACCA
1 ATAAGAAATTACCA
192330 ACTTGAAGAT
Statistics
Matches: 131, Mismatches: 20, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
34 1 0.01
35 40 0.31
36 65 0.50
37 24 0.18
38 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (35 bp):
ATAAGAAATTACCAGTTGATCAGAACTGAACCTAT
Found at i:192254 original size:72 final size:72
Alignment explanation
Indices: 192143--192335 Score: 273
Period size: 72 Copynumber: 2.7 Consensus size: 72
192133 GTCCATAAGA
* * *
192143 AATTACCAGTTGATCAGTACCGAACCTATATAAGAAATTACCAGCTTGATCAGAACTGAACCTGC
1 AATTACCAGTTGATCAGTGCTGAACCTATATAAGAAATTACCAGCTTGATCAGAACTGAACCTAC
192208 -AATAAGG
66 AAAT-AGG
* * * *
192215 GATTAACAGTTGATCAGTGCTGAACCTATATAAGGAATTACCAGCTTGATTAGAACTGAACCTAC
1 AATTACCAGTTGATCAGTGCTGAACCTATATAAGAAATTACCAGCTTGATCAGAACTGAACCTAC
192280 AAATAGG
66 AAATAGG
* *
192287 AATTACCAGTTGATC-GATGTTGAACCTATATAAGAAATTACCAACTTGA
1 AATTACCAGTTGATCAG-TGCTGAACCTATATAAGAAATTACCAGCTTGA
192336 AGATTTCATA
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
71 1 0.01
72 103 0.96
73 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (72 bp):
AATTACCAGTTGATCAGTGCTGAACCTATATAAGAAATTACCAGCTTGATCAGAACTGAACCTAC
AAATAGG
Found at i:194038 original size:19 final size:19
Alignment explanation
Indices: 193988--194040 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
193978 TCAACTCTTA
* *
193988 TCAAAGTCAACGAGTCGTG
1 TCAAAGTCAACGGGTCGGG
*
194007 TCAGAGTCAACGGGTCGGG
1 TCAAAGTCAACGGGTCGGG
194026 TCAAAGTCAACGGGT
1 TCAAAGTCAACGGGT
194041 AAGGTCAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.32, T:0.19
Consensus pattern (19 bp):
TCAAAGTCAACGGGTCGGG
Found at i:194046 original size:19 final size:18
Alignment explanation
Indices: 193988--194048 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
193978 TCAACTCTTA
* *
193988 TCAAAGTCAACGAGTCGTG
1 TCAAAGTCAACGGGTAG-G
* *
194007 TCAGAGTCAACGGGTCGGG
1 TCAAAGTCAACGGGT-AGG
194026 TCAAAGTCAACGGGTAAGG
1 TCAAAGTCAACGGGT-AGG
194045 TCAA
1 TCAA
194049 GTTGACTCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 34 0.97
20 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (18 bp):
TCAAAGTCAACGGGTAGG
Found at i:196705 original size:35 final size:35
Alignment explanation
Indices: 196660--196783 Score: 110
Period size: 35 Copynumber: 3.5 Consensus size: 35
196650 TAAACCTACA
*
196660 ATAAGGAATTACCAGCTGATCAATACTGAACCTAT
1 ATAAGAAATTACCAGCTGATCAATACTGAACCTAT
* *
196695 ATAAGAAATTACCAACTTGGTCAGA-ACTGAACCTGCA-
1 ATAAGAAATTACCAGC-TGATCA-ATACTGAACCT--AT
* * *
196732 ATAA-AGAATTACTAGTTGATCAATATTGAACCTAT
1 ATAAGA-AATTACCAGCTGATCAATACTGAACCTAT
* *
196767 ATAAGGAATTACAAGCT
1 ATAAGAAATTACCAGCT
196784 TGATTAGAGC
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
34 1 0.01
35 28 0.40
36 28 0.40
37 12 0.17
38 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.27
Consensus pattern (35 bp):
ATAAGAAATTACCAGCTGATCAATACTGAACCTAT
Found at i:196741 original size:72 final size:72
Alignment explanation
Indices: 196652--196801 Score: 203
Period size: 72 Copynumber: 2.1 Consensus size: 72
196642 GTTGAATCTA
* * *
196652 AACCTACAATAAGGAATTACCAGCTGATCAATACTGAACCTATATAAGAAATTACCAA-CTTGGT
1 AACCTGCAATAAAGAATTACCAGCTGATCAATACTGAACCTATATAAGAAATTA-CAAGCTTGAT
196716 CAGAACTG
65 CAGAACTG
* * * * *
196724 AACCTGCAATAAAGAATTACTAGTTGATCAATATTGAACCTATATAAGGAATTACAAGCTTGATT
1 AACCTGCAATAAAGAATTACCAGCTGATCAATACTGAACCTATATAAGAAATTACAAGCTTGATC
*
196789 AGAGCTG
66 AGAACTG
196796 AACCTG
1 AACCTG
196802 TAAAGACTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 3 0.04
72 65 0.96
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (72 bp):
AACCTGCAATAAAGAATTACCAGCTGATCAATACTGAACCTATATAAGAAATTACAAGCTTGATC
AGAACTG
Found at i:196800 original size:36 final size:36
Alignment explanation
Indices: 196660--196787 Score: 131
Period size: 36 Copynumber: 3.6 Consensus size: 36
196650 TAAACCTACA
*
196660 ATAAGGAATTACCAGC-TGATCAATACTGAACCTAT
1 ATAAGGAATTACAAGCTTGATCAATACTGAACCTAT
* *
196695 ATAAGAAATTACCAA-CTTGGTCAGA-ACTGAACCTGCA-
1 ATAAGGAATTA-CAAGCTTGATCA-ATACTGAACCT--AT
* * *
196732 ATAAAGAATTACTAG-TTGATCAATATTGAACCTAT
1 ATAAGGAATTACAAGCTTGATCAATACTGAACCTAT
196767 ATAAGGAATTACAAGCTTGAT
1 ATAAGGAATTACAAGCTTGAT
196788 TAGAGCTGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
34 1 0.01
35 25 0.34
36 37 0.50
37 10 0.14
38 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.27
Consensus pattern (36 bp):
ATAAGGAATTACAAGCTTGATCAATACTGAACCTAT
Found at i:198805 original size:22 final size:22
Alignment explanation
Indices: 198777--198818 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
198767 CCCATGGCGA
*
198777 ATGAACAGATGAGCATCAACAG
1 ATGAACAAATGAGCATCAACAG
198799 ATGAACAAATGAGCATCAAC
1 ATGAACAAATGAGCATCAAC
198819 GGACGACCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.14
Consensus pattern (22 bp):
ATGAACAAATGAGCATCAACAG
Found at i:202077 original size:21 final size:20
Alignment explanation
Indices: 202049--202087 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
202039 CATTGTAGGA
*
202049 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
202069 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
202088 GACTTTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:202266 original size:20 final size:20
Alignment explanation
Indices: 202241--202285 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
202231 ACCCACAAGG
202241 AAGTCTCCCTAGTGATACTA
1 AAGTCTCCCTAGTGATACTA
* *
202261 AAGTCTTCCTAGTGATACTG
1 AAGTCTCCCTAGTGATACTA
202281 AAGTC
1 AAGTC
202286 ATTAAATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (20 bp):
AAGTCTCCCTAGTGATACTA
Found at i:210412 original size:18 final size:18
Alignment explanation
Indices: 210391--210426 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
210381 CGAGATATTA
*
210391 TCATTTTTCTAGAGATTG
1 TCATTTTTCTAGAAATTG
210409 TCATTTTTCTAGAAATTG
1 TCATTTTTCTAGAAATTG
210427 AATCTTAGAT
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:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (18 bp):
TCATTTTTCTAGAAATTG
Found at i:213331 original size:21 final size:21
Alignment explanation
Indices: 213307--213376 Score: 131
Period size: 21 Copynumber: 3.3 Consensus size: 21
213297 GGTAGTACAG
213307 ATACCCCTTGAAAGGGTACCA
1 ATACCCCTTGAAAGGGTACCA
213328 ATACCCCTTGAAAGGGTACCA
1 ATACCCCTTGAAAGGGTACCA
*
213349 ATACCCCTTGAAAGGGTACCG
1 ATACCCCTTGAAAGGGTACCA
213370 ATACCCC
1 ATACCCC
213377 CTGTTATGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (21 bp):
ATACCCCTTGAAAGGGTACCA
Found at i:216372 original size:34 final size:34
Alignment explanation
Indices: 216329--216395 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
216319 TGTAAAAGGA
216329 AAGGTTCTAGCTAAGCCCT-TGAAAAACTAGGGAT
1 AAGGTTCTAGCTAAG-CCTGTGAAAAACTAGGGAT
* *
216363 AAGGTTCTAGTTTAGCCTGTGAAAAACTAGGGA
1 AAGGTTCTAGCTAAGCCTGTGAAAAACTAGGGA
216396 GATGTAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 3 0.10
34 27 0.90
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (34 bp):
AAGGTTCTAGCTAAGCCTGTGAAAAACTAGGGAT
Found at i:217471 original size:21 final size:20
Alignment explanation
Indices: 217438--217477 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
217428 TTTTGCAAAA
*
217438 CAAATCATCCCCAAATGGCTC
1 CAAAACATCCCC-AATGGCTC
*
217459 CAAAACATTCCCAATGGCT
1 CAAAACATCCCCAATGGCT
217478 ATATATGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.20
Consensus pattern (20 bp):
CAAAACATCCCCAATGGCTC
Found at i:217736 original size:34 final size:33
Alignment explanation
Indices: 217674--217737 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
217664 TCCTTTTTAA
* *
217674 AAGGAAAGGTTCTAGCTGAGCCCTTGAAAAGCT
1 AAGGAAAGGTTCTAGCTGAGCACGTGAAAAGCT
* *
217707 AAGGATAAGGTTCTAGTTTAGCACGTGAAAA
1 AAGGA-AAGGTTCTAGCTGAGCACGTGAAAA
217738 ACTGAGAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 5 0.19
34 21 0.81
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (33 bp):
AAGGAAAGGTTCTAGCTGAGCACGTGAAAAGCT
Found at i:218542 original size:72 final size:72
Alignment explanation
Indices: 218425--218633 Score: 310
Period size: 72 Copynumber: 2.9 Consensus size: 72
218415 TGCCTTAGGT
* ** ** * *
218425 CAATAAGAAATTACTATTTGATTTGTGCTGAACATATATAAGGAATTACCAGCTTGATCAGAACT
1 CAATAAGAAATTACCAGCTGATCGGTGATGAACCTATATAAGGAATTACCAGCTTGATCAGAACT
218490 GAACCTG
66 GAACCTG
* *
218497 CAATAAGAAATTTCCAGCTGATCGGTGATGAACCTATATAAGGAATTGCCAGCTTGATCAGAACT
1 CAATAAGAAATTACCAGCTGATCGGTGATGAACCTATATAAGGAATTACCAGCTTGATCAGAACT
218562 GAACCTG
66 GAACCTG
* * *
218569 CAATAAGGAATTACCAGCTGATCGGTGCTAAACCTATATAAGGAATTACCAGCTTGATCAGAACT
1 CAATAAGAAATTACCAGCTGATCGGTGATGAACCTATATAAGGAATTACCAGCTTGATCAGAACT
218634 AAACATGTAG
Statistics
Matches: 123, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 123 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (72 bp):
CAATAAGAAATTACCAGCTGATCGGTGATGAACCTATATAAGGAATTACCAGCTTGATCAGAACT
GAACCTG
Found at i:218637 original size:36 final size:36
Alignment explanation
Indices: 218452--218633 Score: 194
Period size: 36 Copynumber: 5.1 Consensus size: 36
218442 TTGATTTGTG
*
218452 CTGAACATATATAAGGAATTACCAGCTTGATCAGAA
1 CTGAACCTATATAAGGAATTACCAGCTTGATCAGAA
* * * *
218488 CTGAACCTGCA-ATAAGAAATTTCCAGC-TGATCGGTGA
1 CTGAACCT--ATATAAGGAATTACCAGCTTGATCAG-AA
*
218525 -TGAACCTATATAAGGAATTGCCAGCTTGATCAGAA
1 CTGAACCTATATAAGGAATTACCAGCTTGATCAGAA
* **
218560 CTGAACCTGCA-ATAAGGAATTACCAGC-TGATCGGTG
1 CTGAACCT--ATATAAGGAATTACCAGCTTGATCAGAA
*
218596 CTAAACCTATATAAGGAATTACCAGCTTGATCAGAA
1 CTGAACCTATATAAGGAATTACCAGCTTGATCAGAA
218632 CT
1 CT
218634 AAACATGTAG
Statistics
Matches: 119, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
34 2 0.02
35 31 0.26
36 54 0.45
37 30 0.25
38 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (36 bp):
CTGAACCTATATAAGGAATTACCAGCTTGATCAGAA
Found at i:218656 original size:72 final size:70
Alignment explanation
Indices: 218449--218656 Score: 235
Period size: 72 Copynumber: 2.9 Consensus size: 70
218439 TATTTGATTT
*
218449 GTGCTGAACATATATAAGGAATTACCAGCTTGATCAGAACTGAACCTGCAATAAGAAATT-T-CC
1 GTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAACTGAACCTG---TAAG-AATTATACC
218512 AGCTGATCG
62 AGCTGATCG
* *
218521 GTGATGAACCTATATAAGGAATTGCCAGCTTGATCAGAACTGAACCTGCAATAAGGAA-T-TACC
1 GTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAACTGAACCTG---TAA-GAATTATACC
218584 AGCTGATCG
62 AGCTGATCG
* * * *
218593 GTGCTAAACCTATATAAGGAATTACCAGCTTGATCAGAACTAAACATGTAGAGACTTCATACCA
1 GTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAACTGAACCTGTA-AGAATT-ATACCA
218657 ATTCCCATAT
Statistics
Matches: 121, Mismatches: 9, Indels: 12
0.85 0.06 0.08
Matches are distributed among these distances:
69 4 0.03
70 2 0.02
71 2 0.02
72 112 0.93
73 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (70 bp):
GTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAACTGAACCTGTAAGAATTATACCAGCT
GATCG
Found at i:223827 original size:23 final size:23
Alignment explanation
Indices: 223797--223847 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
223787 TCCTTGCTAC
223797 CTGTTACTCATAACATGTGCCAA
1 CTGTTACTCATAACATGTGCCAA
223820 CTGTTACTCATAACATGTGCCAA
1 CTGTTACTCATAACATGTGCCAA
223843 CTGTT
1 CTGTT
223848 CAACTTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (23 bp):
CTGTTACTCATAACATGTGCCAA
Found at i:227136 original size:9 final size:9
Alignment explanation
Indices: 227099--227129 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
227089 TCAAAGAAAT
*
227099 AATGTTATC
1 AATGTCATC
227108 AATGTCATC
1 AATGTCATC
227117 AATGTCATC
1 AATGTCATC
227126 AATG
1 AATG
227130 CTATCAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (9 bp):
AATGTCATC
Done.