Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006303.1 Hibiscus syriacus cultivar Beakdansim tig00015062_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: 108195
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2272 original size:2 final size:2
Alignment explanation
Indices: 2265--2315 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2255 AAGAAGTGTT
2265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2307 TA TA TA TA T
1 TA TA TA TA T
2316 TAATTTTTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5334 original size:15 final size:16
Alignment explanation
Indices: 5303--5336 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5293 TGAACATTTA
*
5303 AAATGAGAAACGAAAC
1 AAATAAGAAACGAAAC
5319 AAATAAGAAA-GAAAC
1 AAATAAGAAACGAAAC
5334 AAA
1 AAA
5337 AAACTTGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.71, C:0.09, G:0.15, T:0.06
Consensus pattern (16 bp):
AAATAAGAAACGAAAC
Found at i:7166 original size:182 final size:181
Alignment explanation
Indices: 6666--7440 Score: 973
Period size: 182 Copynumber: 4.3 Consensus size: 181
6656 ATACAAAATG
* * * * * * *
6666 AAAAATGTATCGCTCCATAGCAATATTACAT-GTAAATATATGATAAAACCGGTCTCGAAATGAC
1 AAAAATGTATCGATCCATAACAATA-TA-ATAGTAAAAATATGACAAAACCAGTCCCAAAATGAC
* * * *
6730 AAAATCGGTAAAACGATACC-GATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACA-TT
64 AAAACCGGTAAAGCAATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
*
6793 TT-GAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAATGTCGATACTTTAAA
129 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTT-AA
* *
6846 AAAAATATATCGATCCATAACAATATGACAT-GTAAAAATATGACAAAA-CATGTCTCAAAAATG
1 AAAAATGTATCGATCCATAACAATAT-A-ATAGTAAAAATATGACAAAACCA-GTC-CCAAAATG
* *
6909 ACAAAACCGGTAAA--AATACGGGATATGTTGAAA-TGTCGATAATTTAATATAAGTATTGA-AT
62 ACAAAACCGGTAAAGCAATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACA-
* *
6970 TTTTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTCTATAAAGTGTCGATACTTTAA
126 --CTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
7028 AAAAATGTATCGATCCATAACAATATAATAGCTAAAAATATGACAAAACCAGTCCCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAATAG-TAAAAATATGACAAAACCAGTCCCAAAATGACA
* ** * * *
7093 AATCCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGACAATTTAAAATAAGTTTCGACACTTT
65 AAACCGGTAAAGCAATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* * *
7158 CT-GAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTAGATACTTTAT
130 -TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
* * ** *
7210 GAAAATATATCGATCCATAACAATATAATAGCTAAAAATATGACAAAACTGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAATAG-TAAAAATATGACAAAACCAGTCCCAAAATGACA
* * * *
7275 AAACCGATAAAG-AACTATCGGATATGTTGAGAGTGTCGATACTTTAATATAAGTATCGACACTT
65 AAACCGGTAAAGCAA-TACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
*
7339 TTGGAATTTAAAAGAGAAGAAGTTATAGC-ACTATAAAGTGTCGATACTTTAA
129 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
* *
7391 AAAAATGTATCGATCGATAACAATATAACAGGTAAAAATATGACAAAACC
1 AAAAATGTATCGATCCATAACAATATAATA-GTAAAAATATGACAAAACC
7441 GGTAAAGCGC
Statistics
Matches: 520, Mismatches: 55, Indels: 39
0.85 0.09 0.06
Matches are distributed among these distances:
178 1 0.00
179 31 0.06
180 57 0.11
181 103 0.20
182 240 0.46
183 65 0.12
184 22 0.04
185 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (181 bp):
AAAAATGTATCGATCCATAACAATATAATAGTAAAAATATGACAAAACCAGTCCCAAAATGACAA
AACCGGTAAAGCAATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTT
GGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:7429 original size:363 final size:360
Alignment explanation
Indices: 6666--7440 Score: 1102
Period size: 363 Copynumber: 2.1 Consensus size: 360
6656 ATACAAAATG
* * * * * * * * *
6666 AAAAATGTATCGCTCCATAGCAATATTACATGTAAATATATGATAAAACCGGTCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCCCAAAATGACA
* *
6731 AAATCGGTAAAACGATACCGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACATTTTG
66 AAATCGGTAAAACGATACCGATATATTGAAAGTGTCGACAATTTAAAATAAGTATCGACATTTTG
*
6796 AATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAATGTCGATACTTTAAAAAAAATATATCGATC
131 AATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAATGTAGATACTTTAAAAAAAATATATCGATC
*
6861 CATAACAATATGACATGTAAAAATATGACAAAACATGTCTCAAAAATGACAAAACCGGTAAAAAT
196 CATAACAATATGACATGTAAAAATATGACAAAACATGTCTCAAAAATGACAAAACCGATAAAAAT
* *
6926 ACGGGATATGTTGAAATGTCGATAATTTAATATAAGTATTGAATTTTTTTTGGAATTTAAAAGAG
261 ACGGGATATGTTGAAATGTCGATAATTTAATATAAGTATCGAA--TCTTTTGGAATTTAAAAGAG
*
6991 AAGAAGTTATAGCGTCTATAAAGTGTCGATACTTTAA
324 AAGAAGTTATAGCGACTATAAAGTGTCGATACTTTAA
* *
7028 AAAAATGTATCGATCCATAACAATATAATAGCTAAAAATATGACAAAACCAGTCCCAAAATGAC-
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCCCAAAATGACA
* * * *
7092 AAATCCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGACAATTTAAAATAAGTTTCGACACTT
66 AAAT-CGGTAAAACGATACC-GATATATTGAAAGTGTCGACAATTTAAAATAAGTATCGACA-TT
**
7157 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTA-AAAAGTGTAGATACTTT-ATGAAAATATAT
128 T-TGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAA-TGTAGATACTTTAAAAAAAATATAT
7220 CGATCCATAACAATAT-A-ATAGCTAAAAATATGACAAAAC-TGGTCTC-AAAATGACAAAACCG
191 CGATCCATAACAATATGACAT-G-TAAAAATATGACAAAACAT-GTCTCAAAAATGACAAAACCG
* *
7281 ATAAAGAACTATC-GGATATGTTGAGAGTGTCGATACTTTAATATAAGTATCGACA-CTTTTGGA
253 ATAAA-AA-TA-CGGGATATGTTGA-AATGTCGATAATTTAATATAAGTATCGA-ATCTTTTGGA
7344 ATTTAAAAGAGAAGAAGTTATAGC-ACTATAAAGTGTCGATACTTTAA
313 ATTTAAAAGAGAAGAAGTTATAGCGACTATAAAGTGTCGATACTTTAA
*
7391 AAAAATGTATCGATCGATAACAATATAACAGGTAAAAATATGACAAAACC
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACC
7441 GGTAAAGCGC
Statistics
Matches: 371, Mismatches: 29, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
361 4 0.01
362 68 0.18
363 128 0.35
364 88 0.24
365 56 0.15
366 26 0.07
367 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (360 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCAGTCCCAAAATGACA
AAATCGGTAAAACGATACCGATATATTGAAAGTGTCGACAATTTAAAATAAGTATCGACATTTTG
AATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAATGTAGATACTTTAAAAAAAATATATCGATC
CATAACAATATGACATGTAAAAATATGACAAAACATGTCTCAAAAATGACAAAACCGATAAAAAT
ACGGGATATGTTGAAATGTCGATAATTTAATATAAGTATCGAATCTTTTGGAATTTAAAAGAGAA
GAAGTTATAGCGACTATAAAGTGTCGATACTTTAA
Found at i:7937 original size:18 final size:19
Alignment explanation
Indices: 7902--7944 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
7892 CTTTTATTTA
*
7902 ATATTATAGGCAAAAAATT
1 ATATTATAGGCAAAAAATG
*
7921 ATATTATAGG-TAAAAATG
1 ATATTATAGGCAAAAAATG
7939 ATATTA
1 ATATTA
7945 CATGTAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (19 bp):
ATATTATAGGCAAAAAATG
Found at i:11524 original size:19 final size:19
Alignment explanation
Indices: 11500--11548 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
11490 AATGTAGGGT
11500 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
* *
11519 TAATTTTGTATACGGTTTA
1 TAATTTTGTATAAGATTTA
11538 TAATTTTGTAT
1 TAATTTTGTAT
11549 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:12323 original size:198 final size:198
Alignment explanation
Indices: 11920--13214 Score: 1937
Period size: 198 Copynumber: 6.5 Consensus size: 198
11910 ATAAACTTAT
* * *
11920 GTGTCGATACATTTATAACAAATATCGATCCCAAAAACATTGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
** **
11985 GGTAAATTAACAATGTAGTCGGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAAAAATA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACC-GGTTTTGAGAAAACAGGTGTACAAAAAATA
*
12050 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGTACGA
130 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGA
*
12115 AAAG
195 AAAA
*
12119 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATATAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
12184 GGTAAGTTAACAATGTAACCTGTCTAAATATACCGGTTTTGAGAAAACAGGTGTACAAAAAATAT
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTGAGAAAACAGGTGTACAAAAAATAT
* * * *
12249 CGACACAAATAAAGCAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCTAGTACATGAA
131 CGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAA
12314 AAA
196 AAA
12317 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * *
12382 GGTAAATTAACAGTGTAACCAGTCTAAATATATCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGG-TTTTGAGAAAACAGGTGTACAAAAAATA
* * * *
12447 TCGACACAAATAAAACAAGTGTTGATACTTTTGATCCAAAATGTATTTCTAAACCTAGTGCACGA
130 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGA
12512 AAAA
195 AAAA
* *
12516 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAATATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
12581 GGTAAATTAACAATGTAACCAGTCTAAATATATCGGTTTTTGAGAAAACATGTGTAC-AAAAATA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGG-TTTTGAGAAAACAGGTGTACAAAAAATA
* * * *
12645 TCAACAAAAATAAAACAAGTGTCCATACTTTTGGTCCATAATGTATTTCTAAACCAAGTGCACGA
130 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGA
12710 AAAA
195 AAAA
* * *
12714 GTGTCGATACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
** *
12779 GGTAAATTAACAATGTAACCGGTCTAAATATACCAATTTTGAGAAAACAGGTGTACAAAAAGTAT
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTGAGAAAACAGGTGTACAAAAAATAT
* * * *
12844 CAACAAAAATAAAACAAGTGTCGATACTTTTTGTCCATAATGTATTTCTAAACCAAGTGCACGAA
131 CGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAA
*
12909 TAA
196 AAA
* * *
12912 GTATCTATACATTTATAACAAGTGTCTATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
12977 GGTAAATTAACAATGTAACCGGTCTAAATATACTAGTTTTTTTAGAAAACAAGTGTA-AAAAAGT
66 GGTAAATTAACAATGTAACCGGTCTAAATATAC-CG-GTTTTGAGAAAACAGGTGTACAAAAAAT
*
13041 ATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGCATTTCTAAACCAAGTGCACG
129 ATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACG
13106 AAAAA
194 AAAAA
* * * * *
13111 GTGTCGATACATTTATAACAAGTATCGATCCTAAGAACATCGAAACCCAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * ** * * * *
13176 GGTCATTTTGCAATGTAATCGGTATAATTATACCTGTTT
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTT
13215 AATTTGAAAA
Statistics
Matches: 1003, Mismatches: 89, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
197 22 0.02
198 511 0.51
199 453 0.45
200 17 0.02
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (198 bp):
GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTGAGAAAACAGGTGTACAAAAAATAT
CGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGAA
AAA
Found at i:12658 original size:397 final size:395
Alignment explanation
Indices: 11920--13178 Score: 1957
Period size: 397 Copynumber: 3.2 Consensus size: 395
11910 ATAAACTTAT
* * *
11920 GTGTCGATACATTTATAACAAATATCGATCCCAAAAACATTGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACCCAAAATTATAATGTAATA
** *
11985 GGTAAATTAACAATGTAGTCGGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAAAAATA
66 GGTAAATTAACAATGTAACCGGTCTAAATATA-CAATTTTTGAGAAAACAGGTGTACAAAAAGTA
* *
12050 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGTACGA
130 TCGACACAAATAAAACAAGTGTCGATACTTTT-GTCCAAAATGTATTTCTAAACCAAGTGCACGA
* *
12115 AAAGGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATAT
194 AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
* * * *
12180 AATAGGTAAGTTAACAATGTAACCTGTCTAAATATACCGG-TTTTGAGAAAACAGGTGTACAAAA
259 AATAGGTAAATTAACAATGTAACCAGTCTAAATATATCGGTTTTTGAGAAAACAAGTGTAC-AAA
* * *
12244 AATATCGACACAAATAAAGCAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCTAGTAC
323 AATATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGC
*
12309 ATGAAAAA
388 ACGAAAAA
* *
12317 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACCCAAAATTATAATGTAATA
* * **
12382 GGTAAATTAACAGTGTAACCAGTCTAAATATATCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATA-CAATTTTTGAGAAAACAGGTGTACAAAAAGTA
* *
12447 TCGACACAAATAAAACAAGTGTTGATACTTTTGATCCAAAATGTATTTCTAAACCTAGTGCACGA
130 TCGACACAAATAAAACAAGTGTCGATACTTTTG-TCCAAAATGTATTTCTAAACCAAGTGCACGA
* *
12512 AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAATATCGAAACTCATAATTATAATGT
194 AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
*
12577 AATAGGTAAATTAACAATGTAACCAGTCTAAATATATCGGTTTTTGAGAAAACATGTGTACAAAA
259 AATAGGTAAATTAACAATGTAACCAGTCTAAATATATCGGTTTTTGAGAAAACAAGTGTACAAAA
* * * *
12642 ATATCAACAAAAATAAAACAAGTGTCCATACTTTTGGTCCATAATGTATTTCTAAACCAAGTGCA
324 ATATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCA
12707 CGAAAAA
389 CGAAAAA
* * *
12714 GTGTCGATACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACCCAAAATTATAATGTAATA
12779 GGTAAATTAACAATGTAACCGGTCTAAATATACCAA-TTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATA-CAATTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
12843 TCAACAAAAATAAAACAAGTGTCGATACTTTTTGTCCATAATGTATTTCTAAACCAAGTGCACGA
130 TCGACACAAATAAAACAAGTGTCGATAC-TTTTGTCCAAAATGTATTTCTAAACCAAGTGCACGA
* * * *
12908 ATAAGTATCTATACATTTATAACAAGTGTCTATCCCAAAAACATCGAAACCCATAATTATAATGT
194 AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
* * * *
12973 AATAGGTAAATTAACAATGTAACCGGTCTAAATATACTAGTTTTTTTAGAAAACAAGTGTA-AAA
259 AATAGGTAAATTAACAATGTAACCAGTCTAAATATA-TCGGTTTTTGAGAAAACAAGTGTACAAA
*
13037 AAGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGCATTTCTAAACCAAGTG
323 AA-TATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTG
13102 CACGAAAAA
387 CACGAAAAA
* * *
13111 GTGTCGATACATTTATAACAAGTATCGATCCTAAGAACATCGAAACCCAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACCCAAAATTATAATGTAATA
13176 GGT
66 GGT
13179 CATTTTGCAA
Statistics
Matches: 793, Mismatches: 64, Indels: 10
0.91 0.07 0.01
Matches are distributed among these distances:
396 182 0.23
397 592 0.75
398 19 0.02
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (395 bp):
GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACCCAAAATTATAATGTAATA
GGTAAATTAACAATGTAACCGGTCTAAATATACAATTTTTGAGAAAACAGGTGTACAAAAAGTAT
CGACACAAATAAAACAAGTGTCGATACTTTTGTCCAAAATGTATTTCTAAACCAAGTGCACGAAA
AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAA
TAGGTAAATTAACAATGTAACCAGTCTAAATATATCGGTTTTTGAGAAAACAAGTGTACAAAAAT
ATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACG
AAAAA
Found at i:13193 original size:595 final size:596
Alignment explanation
Indices: 11920--13178 Score: 2009
Period size: 595 Copynumber: 2.1 Consensus size: 596
11910 ATAAACTTAT
* *
11920 GTGTCGATACATTTATAACAAATATCGATCCCAAAAACATTGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
** *
11985 GGTAAATTAACAATGTAGTCGGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAAAAATA
66 GGTAAATTAACAATGTAACCAGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAAAAATA
* * * *
12050 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGTACGA
131 TCAACAAAAATAAAACAAGTGTCCATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGA
* *
12115 AAAGGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATAT
196 AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTATAATAT
* * **
12180 AATAGGTAAGTTAACAATGTAACCTGTCTAAATATACCGGTTTTGAGAAAACAGGTGTACAAAAA
261 AATAGGTAAATTAACAATGTAACCGGTCTAAATATACCAATTTTGAGAAAACAGGTGTACAAAAA
* * * *
12245 ATATCGACACAAATAAAGCAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCTAGTACA
326 ATATCAACAAAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTACA
* *
12310 TGAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAA
391 CGAAAAAGTATCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAA
* * *
12375 TGTAATAGGTAAATTAACAGTGTAACCAGTCTAAATATATCGGTTTTTGAGAAAACAGGTGTACA
456 TGTAATAGGTAAATTAACAATGTAACCAGTCTAAATATATAGGTTTTTGAGAAAACAAGTGTACA
* * *
12440 AAAAGTATCGACACAAATAAAACAAGTGTTGATACTTTTGATCCAAAATGTATTTCTAAACCTAG
521 AAAAGTATCGACACAAATAAAACAAGTGTCGATACTTTTGATCCAAAATGCATTTCTAAACCAAG
12505 TGCACGAAAAA
586 TGCACGAAAAA
* * *
12516 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAATATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* ** *
12581 GGTAAATTAACAATGTAACCAGTCTAAATATATCGGTTTTTGAGAAAACATGTGTAC-AAAAATA
66 GGTAAATTAACAATGTAACCAGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAAAAATA
*
12645 TCAACAAAAATAAAACAAGTGTCCATACTTTTGGTCCATAATGTATTTCTAAACCAAGTGCACGA
131 TCAACAAAAATAAAACAAGTGTCCATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGA
* * *
12710 AAAAGTGTCGATACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGT
196 AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTATAATAT
12775 AATAGGTAAATTAACAATGTAACCGGTCTAAATATACCAATTTTGAGAAAACAGGTGTACAAAAA
261 AATAGGTAAATTAACAATGTAACCGGTCTAAATATACCAATTTTGAGAAAACAGGTGTACAAAAA
* * * *
12840 GTATCAACAAAAATAAAACAAGTGTCGATACTTTTTGTCCATAATGTATTTCTAAACCAAGTGCA
326 ATATCAACAAAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTACA
* * *
12905 CGAATAAGTATCTATACATTTATAACAAGTGTCTATCCCAAAAACATCGAAACCCATAATTATAA
391 CGAAAAAGTATCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAA
* * *
12970 TGTAATAGGTAAATTAACAATGTAACCGGTCTAAATATACTAGTTTTTTTAGAAAACAAGTGTA-
456 TGTAATAGGTAAATTAACAATGTAACCAGTCTAAATATA-TAGGTTTTTGAGAAAACAAGTGTAC
* *
13034 AAAAAGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGCATTTCTAAACCAA
520 AAAAAGTATCGACACAAATAAAACAAGTGTCGATACTTTTGATCCAAAATGCATTTCTAAACCAA
13099 GTGCACGAAAAA
585 GTGCACGAAAAA
* * * *
13111 GTGTCGATACATTTATAACAAGTATCGATCCTAAGAACATCGAAACCCAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
13176 GGT
66 GGT
13179 CATTTTGCAA
Statistics
Matches: 605, Mismatches: 57, Indels: 3
0.91 0.09 0.00
Matches are distributed among these distances:
595 475 0.79
596 130 0.21
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (596 bp):
GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTAACAATGTAACCAGTCTAAATATACCAATTTTTGAGAAAACAGGTGTACAAAAAATA
TCAACAAAAATAAAACAAGTGTCCATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACGA
AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTATAATAT
AATAGGTAAATTAACAATGTAACCGGTCTAAATATACCAATTTTGAGAAAACAGGTGTACAAAAA
ATATCAACAAAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTACA
CGAAAAAGTATCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAA
TGTAATAGGTAAATTAACAATGTAACCAGTCTAAATATATAGGTTTTTGAGAAAACAAGTGTACA
AAAAGTATCGACACAAATAAAACAAGTGTCGATACTTTTGATCCAAAATGCATTTCTAAACCAAG
TGCACGAAAAA
Found at i:13566 original size:15 final size:15
Alignment explanation
Indices: 13546--13587 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
13536 TTTCTCAAAT
13546 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAC
* *
13561 CTCTTCCCAACCCAG
1 CTCTTCTCAACCCAC
13576 CTCTTCTCAACC
1 CTCTTCTCAACC
13588 ACAACCTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.19, C:0.52, G:0.02, T:0.26
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:13930 original size:2 final size:2
Alignment explanation
Indices: 13923--13956 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13913 ATGGAGAAGG
13923 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
13957 CTCCGGAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14800 original size:6 final size:6
Alignment explanation
Indices: 14763--14796 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
14753 CAAGCGGTCA
* *
14763 ATGAAG ATGACG ATGAAG ATGAAG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
14797 TGATCCAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.32, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:16725 original size:200 final size:200
Alignment explanation
Indices: 16375--17537 Score: 923
Period size: 200 Copynumber: 5.9 Consensus size: 200
16365 CATTTATAAC
* * * * *
16375 AAAAACATCGAAACACATA-ATTATAATGTAATAAGTAAATTAACAATGTAACCAATCTAAATAA
1 AAAATCATCGAAACACATAGA-TATAATGTAATAGGTAAAATAACAATGTAACCGATCTAAATAT
* * * *
16439 ACTGGTTTTTGAGAAAACAAGTATACATAAAGTATCAACACAAATCTAACAAGTGTCGATACTTT
65 ACCGGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTT
* *
16504 TTGTCTAGAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAACAAGTGTC
130 TTGTCCATAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAACAAGTGTC
16569 GATACT
195 GATACT
* *
16575 AAAATCATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGACCTAAATACA
1 AAAATCATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGATCTAAATATA
16640 CCGGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTTT
66 CCGGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTTT
* ** *
16705 TGTCCATAATGTAGTTTCCAAACCAA-TGCAAAAAAAAGTGTCGATACATTTATAACATGTGTCG
131 TGTCCATAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAACAAGTGTCG
16769 AT-C-
196 ATACT
* * ** * * *
16772 ACAAATACATCGAAAC-CTATA-ATTAAAATGTAATAGGTCACTTTACAATATAACCGATTTAAA
1 A-AAAT-CATCGAAACAC-ATAGA-TATAATGTAATAGGTAAAATAACAATGTAACCGATCTAAA
* * * * *
16835 TTTACCAGTTTTATGAGAAAATATGTATACATAAAGTATCGACACAAATGCAACAAGTGTCGATA
62 TATACC-GGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATA
*
16900 CTTTTTGTCCATAATGTATTTTCCAAATCAAGTGCACGACAAAA-TGTCGATACA---A-AA-AA
126 CTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGA-AAAAGTGTCGATACATTTATAACAA
* *
16959 --ATCGAAACACAT
190 GTGTCG--ATAC-T
* * * * * * * ** ** * * *
16971 AGATATAAT-GTAATAGATAAAATAACAATGTAACCGGCCT-AAAT-ACACCGGTTTA-TGA--G
1 A-AAATCATCGAAACACAT-AGAT-ATAATGTAATAGG--TAAAATAACA-ATG-TAACCGATCT
* * * * * ***
17030 AAA-ATA--GG--TAT-A-CATA-AAGTATCGACACAAA-T-TC-A-ACAAGTGTCGATACTTTT
59 AAATATACCGGTTTATGAGAAAACAAGTAT--ACATAAAGTATCGACACAA--ATCCA-AC-AAG
* * *
17083 TGTCCATAATGTATTT-TCC---A---A--------ACCAAGTGCACGACAAAGTGTCGATACAT
118 TGTCGATACT-T-TTTGTCCATAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACAT
17133 TTATAACAAGTGTCGATACT
181 TTATAACAAGTGTCGATACT
* ** **
17153 AAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAATGCA
1 AAAATCATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGATCTAAATATA
*
17218 CCGGTTTATGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTTT
66 CCGGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTTT
* *
17283 TGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTATCGATACATTTATAACAAGTGTCG
131 TGTCCATAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAACAAGTGTCG
17348 ATACT
196 ATACT
* ** * * * *
17353 AAAAAT-ATCGAAACACATAGATATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTT
1 -AAAATCATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGATCTAAATAT
* * * ** ** ***
17417 ACCGGTTTTATGAGAAAATAGGTATATATAAAGTATCGACACTTTAT-TTATTTGTGTCGATACT
65 ACCGG-TTTATGAGAAAACAAGTATACATAAAGTATCGACAC-AAATCCAACAAGTGTCGATACT
* * * * * *
17481 TTTTATCCATAATG-AATTCCCAAACTATGTGCACGCATAAAGTGTCGATACATTTAT
128 TTTTGTCCATAATGTATTTTCCAAACCAAGTGCACG-AAAAAGTGTCGATACATTTAT
17538 TAAACGTATC
Statistics
Matches: 761, Mismatches: 128, Indels: 147
0.73 0.12 0.14
Matches are distributed among these distances:
177 3 0.00
178 25 0.03
179 6 0.01
180 13 0.02
181 11 0.01
182 11 0.01
183 5 0.01
184 2 0.00
185 6 0.01
186 8 0.01
187 19 0.02
188 6 0.01
189 21 0.03
190 6 0.01
191 19 0.02
192 8 0.01
193 3 0.00
194 4 0.01
196 2 0.00
197 11 0.01
198 15 0.02
199 103 0.14
200 348 0.46
201 100 0.13
202 6 0.01
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.29
Consensus pattern (200 bp):
AAAATCATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGATCTAAATATA
CCGGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTTT
TGTCCATAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAACAAGTGTCG
ATACT
Found at i:17014 original size:378 final size:384
Alignment explanation
Indices: 16373--17656 Score: 1354
Period size: 378 Copynumber: 3.3 Consensus size: 384
16363 TACATTTATA
* * * * * ** * *
16373 ACAAAAACATCGAAACACATAATTATAATGTAATAAGTAAATTAACAATGTAACCAATCTAAATA
1 ACAAATACATCGAAAC-CATAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATT
* * * * * *
16438 AACTGGTTTT-TGAGAAAACAAGTATACATAAAGTATCAACACAAATCTAACAAGTGTCGATACT
65 TAC-CGTTTTATGAGAAAATATGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACT
* * *
16502 TTTTGTCTAGAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAACAAGTG
129 TTTTGTCCATAATGTATTTTCCAAACCAAGT---CG-ACAA---TCGA-AC-----TAACAAGTG
** *
16567 TCGATACTAAAATCATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGACC
181 TCGATACTAAAAAAATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCC
* *
16632 TAAATACACCGGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGTCG
246 TAAATACACCGGTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAAT-CAACAAGTGTCG
*
16697 ATACTTTTTGTCCATAATGTAGTTTCCAAACCAATGCAAAAAAAAGTGTCGATACATTTATAACA
310 ATACTTTTTGTCCATAATGTAATTTCCAAACCAATGCAAAAAAAAGTGTCGATACATTTATAACA
*
16762 TGTGTCGATC
375 AGTGTCGATC
* * *
16772 ACAAATACATCGAAACCTATAATTAAAATGTAATAGGTCACTTTACAATATAACCGATTTAAATT
1 ACAAATACATCGAAACC-ATAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATT
*
16837 TACCAGTTTTATGAGAAAATATGTATACATAAAGTATCGACACAAATGCAACAAGTGTCGATACT
65 TACC-GTTTTATGAGAAAATATGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACT
*
16902 TTTTGTCCATAATGTATTTTCCAAATCAAGT-G-C-A-CG-AC-AA-AA-TGTCGATAC-AAAAA
129 TTTTGTCCATAATGTATTTTCCAAACCAAGTCGACAATCGAACTAACAAGTGTCGATACTAAAAA
*
16958 AATCGAAACACATAGATATAATGTAATAGATAAAATAACAATGTAACCGGCCTAAATACACCGGT
194 AATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAATACACCGGT
17023 TTATGAGAAAATAGGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTTTGTCC
259 TTATGAGAAAATAGGTATACATAAAGTATCGACACAAA-TCAACAAGTGTCGATACTTTTTGTCC
* ** *
17088 ATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGAT-
323 ATAATGTAATTTCCAAACCAA-TGCAAAAAAAAGTGTCGATACATTTATAACAAGTGTCGATC
* * ** * **
17150 ACTAAAAACATCGAAACACATAGA-TATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAA
1 AC-AAATACATCGAAAC-CATA-ATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAA
** * *
17214 TGCACCGGTTTATGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATAC
63 TTTACCGTTTTATGAGAAAATATGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATAC
17279 TTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTATCGATACATTTATAACAAGT
128 TTTTTGTCCATAATGTATTTTCCAAACCAAGT---CGAC--A--ATCGA-AC-----TAACAAGT
* * ** * *
17344 GTCGATACTAAAAATATCGAAACACATAGATATAATGTAATAGGTCACTTTACAATGTAACCGGT
180 GTCGATACTAAAAAAATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGGC
* ** * ** ** ***
17409 TTAAATTTACCGGTTTTATGAGAAAATAGGTATATATAAAGTATCGACACTTTATTTATTTGTGT
245 CTAAATACACCGG-TTTATGAGAAAATAGGTATACATAAAGTATCGACAC-AAATCAACAAGTGT
* * * * ** *
17474 CGATACTTTTTATCCATAATG-AATTCCCAAACTATGTGCACGCATAAAGTGTCGATACATTTAT
308 CGATACTTTTTGTCCATAATGTAATTTCCAAACCA-ATGCA-AAAAAAAGTGTCGATACATTTA-
* * *
17538 TAA-ACGTATCGACC
370 TAACAAGTGTCGATC
* * *
17552 CCAAATACATCGAGACCGAAAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATT
1 ACAAATACATCGAAACC-ATAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATT
* * * * *
17617 TACCGATTTTATGAGCAAATAGGTCTACGTAATGTATCGA
65 TACCG-TTTTATGAGAAAATATGTATACATAAAGTATCGA
17657 TACTTTTTGC
Statistics
Matches: 750, Mismatches: 96, Indels: 75
0.81 0.10 0.08
Matches are distributed among these distances:
378 236 0.31
379 97 0.13
380 4 0.01
381 2 0.00
382 1 0.00
383 1 0.00
387 2 0.00
388 1 0.00
389 4 0.01
391 2 0.00
393 1 0.00
396 1 0.00
397 2 0.00
398 3 0.00
399 69 0.09
400 152 0.20
401 140 0.19
402 32 0.04
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (384 bp):
ACAAATACATCGAAACCATAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTT
ACCGTTTTATGAGAAAATATGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTT
TTGTCCATAATGTATTTTCCAAACCAAGTCGACAATCGAACTAACAAGTGTCGATACTAAAAAAA
TCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAATACACCGGTTT
ATGAGAAAATAGGTATACATAAAGTATCGACACAAATCAACAAGTGTCGATACTTTTTGTCCATA
ATGTAATTTCCAAACCAATGCAAAAAAAAGTGTCGATACATTTATAACAAGTGTCGATC
Found at i:17515 original size:578 final size:579
Alignment explanation
Indices: 16373--17532 Score: 1766
Period size: 578 Copynumber: 2.0 Consensus size: 579
16363 TACATTTATA
* * *
16373 ACAAAAACATCGAAACACATAATTATAATGTAATAAGTAAATTAACAATGTAACCAATCTAAATA
1 ACAAAAAAATCGAAACACATAATTATAATGTAATAAGTAAAATAACAATGTAACCAACCTAAATA
* *
16438 AACTGGTTTTTGAGAAAACAAGTATACATAAAGTATCAACACAAATCTAACAAGTGTCGATACTT
66 AACCGGTTTATGAGAAAACAAGTATACATAAAGTATCAACACAAATCTAACAAGTGTCGATACTT
*
16503 TTTGTCTAGAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAACAAGTGT
131 TTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAACAAGTGT
*
16568 CGATACTAAAATCATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGACCT
196 CGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGACCT
16633 AAATACACCGGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGA
261 AAATACACCGGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGA
* *
16698 TACTTTTTGTCCATAATGTAGTTTCCAAACCAATGCAAAAAAAAGTGTCGATACATTTATAACAT
326 TACTTTTTGTCCATAATGTAGTTTCCAAACCAATGCAAAAAAAAGTATCGATACATTTATAACAA
*
16763 GTGTCGATCACAAATACATCGAAACCTATAATTAAAATGTAATAGGTCACTTTACAATATAACCG
391 GTGTCGATCACAAAAACATCGAAACCTATAATTAAAATGTAATAGGTCACTTTACAATATAACCG
*
16828 ATTTAAATTTACCAGTTTTATGAGAAAATATGTATACATAAAGTATCGACACAAATGCAACAAGT
456 ATTTAAATTTACCAGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATGCAACAAGT
* * *
16893 GTCGATACTTTTTGTCCATAATGTATTTTCCAAATCAAGTGCACGACA-AAA-TGTCGAT
521 GTCGATACTTTTTATCCATAATGTAATTCCCAAATCAAGTGCACG-CATAAAGTGTCGAT
**
16951 ACAAAAAAATCGAAACACATAGA-TATAATGTAAT-AGATAAAATAACAATGTAACCGGCCTAAA
1 ACAAAAAAATCGAAACACATA-ATTATAATGTAATAAG-TAAAATAACAATGTAACCAACCTAAA
* * * *
17014 TACACCGGTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAAT-TCAACAAGTGTCGATA
64 TAAACCGGTTTATGAGAAAACAAGTATACATAAAGTATCAACACAAATCT-AACAAGTGTCGATA
* *
17078 CTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAG
128 CTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAACAAG
*
17143 TGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGG
193 TGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGA
* *
17208 CCTAAATGCACCGGTTTATGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAAGTGT
258 CCTAAATACACCGGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGT
* ** *
17273 CGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTATCGATACATTTATA
323 CGATACTTTTTGTCCATAATGTAGTTTCCAAACCAA-TGCAAAAAAAAGTATCGATACATTTATA
* *
17338 ACAAGTGTCGAT-ACTAAAAATATCGAAACAC-ATAGA-TATAATGTAATAGGTCACTTTACAAT
387 ACAAGTGTCGATCAC-AAAAACATCGAAAC-CTATA-ATTAAAATGTAATAGGTCACTTTACAAT
* * * * **
17400 GTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTATATATAAAGTATCGACACTTTAT-
449 ATAACCGATTTAAATTTACCAGTTTTATGAGAAAATAGGTATACATAAAGTATCGACAC-AAATG
** *** *
17464 TTATTTGTGTCGATACTTTTTATCCATAATG-AATTCCCAAA-CTATGTGCACGCATAAAGTGTC
513 CAACAAGTGTCGATACTTTTTATCCATAATGTAATTCCCAAATC-AAGTGCACGCATAAAGTGTC
17527 GAT
577 GAT
17530 ACA
1 ACA
17533 TTTATTAAAC
Statistics
Matches: 528, Mismatches: 43, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
577 6 0.01
578 353 0.67
579 165 0.31
580 4 0.01
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (579 bp):
ACAAAAAAATCGAAACACATAATTATAATGTAATAAGTAAAATAACAATGTAACCAACCTAAATA
AACCGGTTTATGAGAAAACAAGTATACATAAAGTATCAACACAAATCTAACAAGTGTCGATACTT
TTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGAAAAAGTGTCGATACATTTATAACAAGTGT
CGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGACCT
AAATACACCGGTTTATGAGAAAACAAGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGA
TACTTTTTGTCCATAATGTAGTTTCCAAACCAATGCAAAAAAAAGTATCGATACATTTATAACAA
GTGTCGATCACAAAAACATCGAAACCTATAATTAAAATGTAATAGGTCACTTTACAATATAACCG
ATTTAAATTTACCAGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATGCAACAAGT
GTCGATACTTTTTATCCATAATGTAATTCCCAAATCAAGTGCACGCATAAAGTGTCGAT
Found at i:17581 original size:201 final size:201
Alignment explanation
Indices: 16952--17848 Score: 904
Period size: 200 Copynumber: 4.5 Consensus size: 201
16942 AATGTCGATA
* * * * * * ** **
16952 CAAAAAAATCGAAACACATAGATATAATGTAATAGATAAAATAACAATGTAACCGGCCTAAATAC
1 CAAAAACATCGAAACACATAAATATAATGTAATAGGTCAATTTACAATGTAACCGGTTTAAATTT
17017 ACCGG-TTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGATACTT
66 ACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGATACTT
* *
17081 TTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGT
131 TTTGTCCATAATGTAATTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTAT
*
17146 CGATAC
196 CGACAC
* * * * * ** **
17152 TAAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAATGC
1 CAAAAACATCGAAACACATAAATATAATGTAATAGGTCAATTTACAATGTAACCGGTTTAAATTT
* * *
17217 ACCGG-TTTATGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTT
66 ACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGATACTT
* * *
17281 TTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTATCGATACATTTATAACAAGTGT
131 TTTGTCCATAATGTAATTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTAT
*
17346 CGATAC
196 CGACAC
* * * *
17352 TAAAAATATCGAAACACATAGATATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTT
1 CAAAAACATCGAAACACATAAATATAATGTAATAGGTCAATTTACAATGTAACCGGTTTAAATTT
* ** * ***
17417 ACCGGTTTTATGAGAAAATAGGTATATATAAAGTATCGACACTTTATT-TATTTGTGTCGATACT
66 ACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACAC-AAATTCAACAAGTGTCGATACT
* * * * * *
17481 TTTTATCCATAATG-AATTCCCAAACTATGTGCACGCATAAAGTGTCGATACATTTATTAA-ACG
130 TTTTGTCCATAATGTAATTTCCAAACCAAGTGCACG-ACAAAGTGTCGATACATTTA-TAACAAG
*
17544 TATCGACCC
193 TATCGACAC
* * *
17553 CAAATACATCGAGAC-CGA-AAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAAT
1 CAAAAACATCGAAACAC-ATAAA-TATAATGTAATAGGTCAATTTACAATGTAACCGGTTTAAAT
* * * * * * *** ***
17616 TTACCGATTTTATGAGCAAATAGGTCTACGTAATGTATCGATACTTTTTGC-ATTTGTGTCGATA
64 TTACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATT-CAACAAGTGTCGATA
* * * * * *
17680 CTTTATGTCGATAATG-AA-TACCAAA-CAATGTCCACGCATAAAGTGTCGATACATTTATAAAA
128 CTTTTTGTCCATAATGTAATTTCCAAACCAA-GTGCACG-ACAAAGTGTCGATACATTTATAACA
* *
17742 AGTATCAACCC
191 AGTATCGACAC
* * * * *
17753 CAAATATATTGAAAC-CAAAAATTATAATGTAATAGGTCAATTTACAATGTAACCGGTTGAAATT
1 CAAAAACATCGAAACACATAAA-TATAATGTAATAGGTCAATTTACAATGTAACCGGTTTAAATT
**
17817 TACCGGTGTAAAT-AGAAAATAGGTCA-ACATAA
65 TACCGGT-TTTATGAGAAAATAGGT-ATACATAA
17849 TGTGTAGACA
Statistics
Matches: 613, Mismatches: 71, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
199 5 0.01
200 398 0.65
201 205 0.33
202 5 0.01
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (201 bp):
CAAAAACATCGAAACACATAAATATAATGTAATAGGTCAATTTACAATGTAACCGGTTTAAATTT
ACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATTCAACAAGTGTCGATACTT
TTTGTCCATAATGTAATTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTAT
CGACAC
Found at i:17731 original size:401 final size:400
Alignment explanation
Indices: 16940--17848 Score: 937
Period size: 401 Copynumber: 2.3 Consensus size: 400
16930 AGTGCACGAC
* * * * *
16940 AAAA-TGTCGATACAAAAAAATCGAAACACATAGATATAATGTAATAGATAAAATAACAATGTAA
1 AAAAGTGTCGATACAAAAATATCGAAACACATAGATATAATGTAATAGGTCAATTTACAATGTAA
** **
17004 CCGGCCTAAATACACCGG-TTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATTCAACA
66 CCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATTCAACA
* * *
17068 AGTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACAT
131 AGTGTCGATACTTTTTATCCATAATGTAATTCCCAAACCAAGTGCACGACAAAGTGTCGATACAT
* * * *
17133 TTATAACAAGTGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACA
196 TTATAACAAGTATCGACACCAAAAACATCGAAACACATAAATATAATGTAATAGGTAAAATAACA
*
17198 ATGTAACCGGCCTAAATGCACCGGTTTATGAGAAAACATGTATACATAAAGTATCGACACAAATC
261 ATGTAACCGGCCTAAATGCACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATC
* * * *
17263 CAACAAGTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTATCGA
326 CAACAAGTGTCGATACTTTATGTCCATAATGTATATACCAAACCAAGTCCACGACAAAGTATCGA
17328 TACATTTATA
391 TACATTTATA
* *
17338 ACAAGTGTCGATACTAAAAATATCGAAACACATAGATATAATGTAATAGGTCACTTTACAATGTA
1 AAAAGTGTCGATAC-AAAAATATCGAAACACATAGATATAATGTAATAGGTCAATTTACAATGTA
* ** *
17403 ACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTATATATAAAGTATCGACACTTTATT-TA
65 ACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACAC-AAATTCAA
*** * * *
17467 TTTGTGTCGATACTTTTTATCCATAATG-AATTCCCAAACTATGTGCACGCATAAAGTGTCGATA
129 CAAGTGTCGATACTTTTTATCCATAATGTAATTCCCAAACCAAGTGCACG-ACAAAGTGTCGATA
* * * * * *
17531 CATTTATTAA-ACGTATCGACCCCAAATACATCGAGAC-CGA-AAATTATAATGTAATAGGTCAC
193 CATTTA-TAACAAGTATCGACACCAAAAACATCGAAACAC-ATAAA-TATAATGTAATAGGTAAA
* * ** ** * * * * * * *
17593 TTTACAATGTAACCGGTTTAAATTTACCGATTTTATGAGCAAATAGGTCTACGTAATGTATCGAT
255 ATAACAATGTAACCGGCCTAAATGCACCG-GTTTATGAGAAAACAGGTATACATAAAGTATCGAC
*** * *** * *
17658 ACTTTTTGC-ATTTGTGTCGATACTTTATGTCGATAATG-A-ATACCAAA-CAATGTCCACGCAT
319 AC-AAATCCAACAAGTGTCGATACTTTATGTCCATAATGTATATACCAAACCAA-GTCCACG-AC
*
17719 AAAGTGTCGATACATTTATA
381 AAAGTATCGATACATTTATA
* * ** * * * *
17739 AAAAGTATCAACCCCAAATATATTGAAAC-CAAAAATTATAATGTAATAGGTCAATTTACAATGT
1 AAAAGTGTCGA-TACAAAAATATCGAAACACATAGA-TATAATGTAATAGGTCAATTTACAATGT
* **
17803 AACCGGTTGAAATTTACCGGTGTAAAT-AGAAAATAGGTCA-ACATAA
64 AACCGGTTTAAATTTACCGGT-TTTATGAGAAAATAGGT-ATACATAA
17849 TGTGTAGACA
Statistics
Matches: 419, Mismatches: 76, Indels: 29
0.80 0.15 0.06
Matches are distributed among these distances:
398 3 0.01
399 12 0.03
400 95 0.23
401 243 0.58
402 64 0.15
403 2 0.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (400 bp):
AAAAGTGTCGATACAAAAATATCGAAACACATAGATATAATGTAATAGGTCAATTTACAATGTAA
CCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATTCAACA
AGTGTCGATACTTTTTATCCATAATGTAATTCCCAAACCAAGTGCACGACAAAGTGTCGATACAT
TTATAACAAGTATCGACACCAAAAACATCGAAACACATAAATATAATGTAATAGGTAAAATAACA
ATGTAACCGGCCTAAATGCACCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAAATC
CAACAAGTGTCGATACTTTATGTCCATAATGTATATACCAAACCAAGTCCACGACAAAGTATCGA
TACATTTATA
Found at i:21731 original size:87 final size:87
Alignment explanation
Indices: 21629--21791 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 87
21619 AAATAGGTCA
* * * * *
21629 ATATAAGTGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTATTTGGTAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
*
21694 CCGGTTAAATGCGTATTTTATT
66 CCAGTTAAATGCGTATTTTATT
*
21716 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
21781 CCAGTTAAATG
66 CCAGTTAAATG
21792 ATATAACATA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
CCAGTTAAATGCGTATTTTATT
Found at i:21733 original size:23 final size:23
Alignment explanation
Indices: 21707--21763 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
21697 GTTAAATGCG
*
21707 TATTTTATTATATAAGCGCTACC
1 TATTATATTATATAAGCGCTACC
*
21730 TATTACATTATATAAGCGCTACC
1 TATTATATTATATAAGCGCTACC
*
21753 TAATATATTAT
1 TATTATATTAT
21764 TGTGCTTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (23 bp):
TATTATATTATATAAGCGCTACC
Found at i:23103 original size:19 final size:18
Alignment explanation
Indices: 23043--23130 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 18
23033 TTTATGTTAG
23043 TATTTTT-TTAAATAGTTA
1 TATTTTTATTAAATA-TTA
23061 T-TATTTT-TT--ATATTAA
1 TAT-TTTTATTAAATATT-A
*
23077 TATATTTATGTAAATATTA
1 TATTTTTAT-TAAATATTA
*
23096 TATTTTTATTAAA-ATAA
1 TATTTTTATTAAATATTA
* *
23113 TATTTATA-TAATTATTA
1 TATTTTTATTAAATATTA
23130 T
1 T
23131 TTATTTAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
15 2 0.04
16 11 0.20
17 17 0.30
18 12 0.21
19 9 0.16
20 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TATTTTTATTAAATATTA
Found at i:23136 original size:36 final size:33
Alignment explanation
Indices: 23049--23137 Score: 85
Period size: 34 Copynumber: 2.7 Consensus size: 33
23039 TTAGTATTTT
* *
23049 TTTAAATAGTTATTATTT-TTTATATTAATATA
1 TTTATATAATTATTATTTATTTATATTAATATA
* * *
23081 TTTATGTAAATATTATATT-TTTAT-TAAAATAATA
1 TTTATATAATTATTAT-TTATTTATAT-TAAT-ATA
23115 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTATTTA
23138 GAATTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 13 0.28
33 12 0.26
34 21 0.46
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (33 bp):
TTTATATAATTATTATTTATTTATATTAATATA
Found at i:23299 original size:17 final size:17
Alignment explanation
Indices: 23277--23330 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
23267 AATGTTAATA
23277 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
23294 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
23311 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
23328 TTT
1 TTT
23331 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:24940 original size:21 final size:21
Alignment explanation
Indices: 24914--25007 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
24904 TATGCCATCT
24914 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
24935 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
24956 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
24977 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
24998 CCGCAGGGTT
1 CCGCAGGGTT
25008 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.28, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:25589 original size:33 final size:34
Alignment explanation
Indices: 25530--25626 Score: 126
Period size: 33 Copynumber: 2.9 Consensus size: 34
25520 AAATGTTTTT
*
25530 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
25564 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
*
25597 AAAATATAAATTAT-TGTATTCGAAATTTAA
1 AAAATAAAAATTATAT-TATTCGAAATTTAA
25627 CATTAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.02
33 27 0.49
34 27 0.49
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:25633 original size:34 final size:33
Alignment explanation
Indices: 25528--25633 Score: 126
Period size: 34 Copynumber: 3.2 Consensus size: 33
25518 ATAAATGTTT
*
25528 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
25562 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
*
25594 TTTAAAATATAAATTAT-TGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATAT-TATTCGAAATTTAA-A
25629 TTAAA
1 TTAAA
25634 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
32 4 0.06
33 24 0.39
34 33 0.53
35 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.39
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:26313 original size:128 final size:128
Alignment explanation
Indices: 26027--27034 Score: 1738
Period size: 128 Copynumber: 7.9 Consensus size: 128
26017 TTACCTGATT
*
26027 TACTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
26091 TGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
26153 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
26218 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
26281 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** * *
26346 TGACGAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCATGTCCCTTGAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
26409 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
26474 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGTGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
26537 TACTGATATATCTAGTGTCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
26602 TGACGAAATAATGGAAGGCGCGCCCCCGGGGATGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
26665 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
26730 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
26793 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
26858 TGATGAAATAATGGAAGGCACGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
26921 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
26986 TGACGAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCATGTGAATA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
27035 ATACTCCGAT
Statistics
Matches: 833, Mismatches: 44, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
126 18 0.02
127 95 0.11
128 719 0.86
129 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:27120 original size:8 final size:8
Alignment explanation
Indices: 27107--27147 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
27097 TCACAATCTT
27107 TCAAATTC
1 TCAAATTC
27115 TCAAATTC
1 TCAAATTC
* *
27123 CCAAACTC
1 TCAAATTC
27131 T-AAATTC
1 TCAAATTC
27138 TCAAATTC
1 TCAAATTC
27146 TC
1 TC
27148 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:40839 original size:22 final size:22
Alignment explanation
Indices: 40814--40858 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
40804 TCGGTGCCCC
*
40814 CCTTAGCCCCTTAATTGACTTT
1 CCTTAGCACCTTAATTGACTTT
40836 CCTTAGCACCTTAATTGACTTT
1 CCTTAGCACCTTAATTGACTTT
40858 C
1 C
40859 AACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (22 bp):
CCTTAGCACCTTAATTGACTTT
Found at i:66344 original size:2 final size:2
Alignment explanation
Indices: 66339--66366 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
66329 TTTTTTTAAT
66339 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
66367 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71293 original size:33 final size:33
Alignment explanation
Indices: 71226--71324 Score: 139
Period size: 33 Copynumber: 3.1 Consensus size: 33
71216 AAAGATGAAA
* *
71226 AATAAGTTGGCCACCTACCAA-A-GATTTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
*
71257 AATAAGTTGGTCACCAACCAAGATGAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
* *
71290 AATAAGTTGGCCACCAACCAAGATAAAATTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
71323 AA
1 AA
71325 CTTGCCAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 19 0.32
32 1 0.02
33 40 0.67
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATGAATTTTCC
Found at i:75234 original size:65 final size:63
Alignment explanation
Indices: 75156--75315 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 63
75146 AAATAAATTG
* *
75156 AACATCGAATGCATTTCATGCATCGATGCACACACCATGCATCGATGCACTGGGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATCGATGCACTAGGGATATTT-TG-
75220 A
63 A
* * * *
75221 AACATCGAATGCATTTGATGCATCGATGTATCAGCCATGCATCGATGCACTATGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCATCGATGCACTAGGGATATTTTGA
*
75285 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
75316 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.34
65 50 0.59
66 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATCGATGCACTAGGGATATTTTGA
Found at i:75315 original size:17 final size:19
Alignment explanation
Indices: 75287--75335 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
75277 TATTTTGAAA
75287 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
75305 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
75324 CACCGATGCACT
1 CATCGATGCACT
75336 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:81161 original size:23 final size:21
Alignment explanation
Indices: 81073--81167 Score: 95
Period size: 21 Copynumber: 4.4 Consensus size: 21
81063 TTGTGCTTAA
*
81073 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
*
81093 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
81115 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
*
81136 TGCACCGATACACGCCTTGAATG
1 TGCATCGATACA--CCTTGAATG
81159 TGCATCGAT
1 TGCATCGAT
81168 GCACAAGGCC
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.18
21 20 0.33
22 13 0.21
23 17 0.28
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:81163 original size:44 final size:42
Alignment explanation
Indices: 81073--81167 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
81063 TTGTGCTTAA
* * *
81073 TGCATCGATACACCTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATACAGCCTTGAATG
*
81115 TGCATCGATACACCATGAA-GGTGCACCGATACACGCCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATACA-GCCTTGAATG
81159 TGCATCGAT
1 TGCATCGAT
81168 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 14 0.30
43 12 0.26
44 20 0.43
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATACAGCCTTGAATG
Found at i:85490 original size:33 final size:33
Alignment explanation
Indices: 85449--85522 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
85439 TACCAAAGAT
** *
85449 TTTTCCAATAAGTTGGTTACCAACCAAGATGAA
1 TTTTCCAATAAGTTGGCCACCAACCAAGATAAA
85482 TTTTCCAATAAGTTGGCCACCAACCAAGATAAA
1 TTTTCCAATAAGTTGGCCACCAACCAAGATAAA
*
85515 ATTTCCAA
1 TTTTCCAA
85523 CTTGCCAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (33 bp):
TTTTCCAATAAGTTGGCCACCAACCAAGATAAA
Found at i:85686 original size:25 final size:23
Alignment explanation
Indices: 85657--85710 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
85647 TCCATTTTCA
*
85657 ACTTTAAAATCTTCTCTTTATTTTT
1 ACTTTAAAATC-TCT-TTTATTATT
85682 ACTTT-AAATCTCTTTTATTATT
1 ACTTTAAAATCTCTTTTATTATT
85704 A-TTTAAA
1 ACTTTAAA
85711 TATATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 11 0.41
23 3 0.11
24 5 0.19
25 5 0.19
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (23 bp):
ACTTTAAAATCTCTTTTATTATT
Found at i:85718 original size:21 final size:22
Alignment explanation
Indices: 85673--85718 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
85663 AAATCTTCTC
* * *
85673 TTTATTTTTACTTTAAATCTCT
1 TTTATTATTACTTTAAATATAT
85695 TTTATTATTA-TTTAAATATAT
1 TTTATTATTACTTTAAATATAT
85716 TTT
1 TTT
85719 TACTAAAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATTATTACTTTAAATATAT
Found at i:85921 original size:10 final size:10
Alignment explanation
Indices: 85908--85932 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
85898 TGTTTATATT
85908 TGTTCATTTA
1 TGTTCATTTA
85918 TGTTCATTTA
1 TGTTCATTTA
85928 TGTTC
1 TGTTC
85933 TTTCGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (10 bp):
TGTTCATTTA
Found at i:85953 original size:24 final size:24
Alignment explanation
Indices: 85883--85969 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
85873 CAAAACAACA
* *
85883 TTTG-TCATTTATGTTTGTTTATA
1 TTTGTTCATTTATGTTCGTTTATG
*
85906 TTTGTTCATTTATGTTCATTTATG
1 TTTGTTCATTTATGTTCGTTTATG
*
85930 TTCT-TTCGTTTATGTTCGTTTATG
1 TT-TGTTCATTTATGTTCGTTTATG
** *
85954 TGCGTTCAATTATGTT
1 TTTGTTCATTTATGTT
85970 TAGCCCAATC
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
23 4 0.08
24 47 0.90
25 1 0.02
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.61
Consensus pattern (24 bp):
TTTGTTCATTTATGTTCGTTTATG
Found at i:89545 original size:29 final size:25
Alignment explanation
Indices: 89488--89539 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
89478 ACTCTTAGAA
89488 AGTTAAATAGATAAGGATAACTACT
1 AGTTAAATAGATAAGGATAACTACT
*
89513 AGTTAAATAGATAATGATAACTACT
1 AGTTAAATAGATAAGGATAACTACT
89538 AG
1 AG
89540 GTAGTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (25 bp):
AGTTAAATAGATAAGGATAACTACT
Found at i:104903 original size:45 final size:45
Alignment explanation
Indices: 104841--104927 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
104831 ATCATAATAC
*
104841 CATGATTGTTTTCATGCACAACACTGGATGAAATAATCATGACGT
1 CATGATTCTTTTCATGCACAACACTGGATGAAATAATCATGACGT
* *
104886 CATGATTACTTTT-ATGCACAACACTTGATGAGATAATCATGA
1 CATGATT-CTTTTCATGCACAACACTGGATGAAATAATCATGA
104928 ATCATATCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 34 0.89
46 4 0.11
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (45 bp):
CATGATTCTTTTCATGCACAACACTGGATGAAATAATCATGACGT
Done.