Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 5 of 173
Found at i:1377882 original size:5 final size:5
Alignment explanation
Indices: 1377872--1377922 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
1377862 TTAAATATAT
*
1377872 TATTA TATTA T-TT- TATTA TAAAATA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA T--ATTA TATTA TATTA TATTA TATTA TATTA
1377922 T
1 T
1377923 TATATAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.10
5 31 0.77
7 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:1377918 original size:20 final size:18
Alignment explanation
Indices: 1377872--1377927 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
1377862 TTAAATATAT
1377872 TATTATATTATTTTATTA
1 TATTATATTATTTTATTA
** *
1377890 TAAAATA-TATTATATTA
1 TATTATATTATTTTATTA
*
1377907 TATTATATTATATTATTA
1 TATTATATTATTTTATTA
1377925 TAT
1 TAT
1377928 AAAATAAACC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATATTATTTTATTA
Found at i:1378167 original size:16 final size:17
Alignment explanation
Indices: 1378148--1378179 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1378138 AGGGGAGAAA
1378148 AGAAAGAAA-GAAAAAG
1 AGAAAGAAAGGAAAAAG
1378164 AGAAAGAAAGGAAAAA
1 AGAAAGAAAGGAAAAA
1378180 CTAAGGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAGGAAAAAG
Found at i:1379203 original size:39 final size:38
Alignment explanation
Indices: 1379150--1379290 Score: 219
Period size: 39 Copynumber: 3.6 Consensus size: 38
1379140 CAGGCACTTA
* *
1379150 TGTGCCGACTACTGTTACTGTTACCGATTCAGCACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGATTC-GCACTTTG
1379189 TGTGTCGAATACTGTTACTGTTACCGATTCGGCACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGATTC-GCACTTTG
1379228 TGTGTCGAATACTGTTACTGTTACCGATTCGACACTTTG
1 TGTGTCGAATACTGTTACTGTTACCGATTCG-CACTTTG
* *
1379267 TGTGTCGAATACTGTCACCGTTAC
1 TGTGTCGAATACTGTTACTGTTAC
1379291 TAATTACTGT
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 1 0.01
39 95 0.99
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (38 bp):
TGTGTCGAATACTGTTACTGTTACCGATTCGCACTTTG
Found at i:1382125 original size:25 final size:23
Alignment explanation
Indices: 1382066--1382141 Score: 61
Period size: 25 Copynumber: 3.3 Consensus size: 23
1382056 AAATAAATGA
*
1382066 AAGAAAAA-GA-ATAGAA-AAAG
1 AAGAAAAAGGAGAAAGAACAAAG
* *
1382086 AAGAACAAAGTAGAACGAAACAAAG
1 AAGAA-AAAGGAGAAAG-AACAAAG
*
1382111 AAGAAAAAGAGAGAAAGAAGAAAG
1 AAGAAAAAG-GAGAAAGAACAAAG
1382135 -AGAAAAA
1 AAGAAAAA
1382142 AATTAGGGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 5 0.11
21 3 0.07
22 1 0.02
23 9 0.20
24 12 0.27
25 14 0.32
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.03
Consensus pattern (23 bp):
AAGAAAAAGGAGAAAGAACAAAG
Found at i:1382804 original size:41 final size:37
Alignment explanation
Indices: 1382759--1382848 Score: 101
Period size: 41 Copynumber: 2.3 Consensus size: 37
1382749 CTTCAAGTCA
*
1382759 ATGAGACACTGGGTG-TCAATTTACTACTTCGGATTAATTCG
1 ATGAGACACTGGGTGCT-AA-TT--TACTTCGGATTAACT-G
* *
1382800 ATGAGATACTGGGTGCTAATTTACTTCGGTTTAACTG
1 ATGAGACACTGGGTGCTAATTTACTTCGGATTAACTG
1382837 ATGAGACACTGG
1 ATGAGACACTGG
1382849 AAATCAACTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
37 12 0.27
38 13 0.30
40 2 0.05
41 16 0.36
42 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (37 bp):
ATGAGACACTGGGTGCTAATTTACTTCGGATTAACTG
Found at i:1383861 original size:51 final size:51
Alignment explanation
Indices: 1383785--1383886 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
1383775 TGACTGGACC
1383785 ATGTAAGACACACGGCTAACACATGGGCGTGTATCCCCTGTTTCTTTGAAA
1 ATGTAAGACACACGGCTAACACATGGGCGTGTATCCCCTGTTTCTTTGAAA
1383836 ATGTAAGACACACGGCTAACACATGGGCGTGTATCCCCTGTTTCTTTGAAA
1 ATGTAAGACACACGGCTAACACATGGGCGTGTATCCCCTGTTTCTTTGAAA
1383887 TTTTTTGATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (51 bp):
ATGTAAGACACACGGCTAACACATGGGCGTGTATCCCCTGTTTCTTTGAAA
Found at i:1384917 original size:19 final size:20
Alignment explanation
Indices: 1384866--1384917 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1384856 CCAATTACAT
1384866 TATATAACCAATTTTCATATCA
1 TATATAACCAA--TTCATATCA
* *
1384888 T-TATTATCAATTCATAT-A
1 TATATAACCAATTCATATCA
1384906 TATATAACCAAT
1 TATATAACCAAT
1384918 ACCACATAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 2 0.08
19 15 0.60
21 7 0.28
22 1 0.04
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATAACCAATTCATATCA
Found at i:1391262 original size:40 final size:41
Alignment explanation
Indices: 1391207--1391284 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
1391197 TTTCTAGAAT
1391207 TAGGAACATGCC-TTTTCTGTACAACTTAGCCAACTTAACG
1 TAGGAACATGCCTTTTTCTGTACAACTTAGCCAACTTAACG
* *
1391247 TAGGAATATGGCTTTTTCTGTACAACTTAGCCAACTTA
1 TAGGAACATGCCTTTTTCTGTACAACTTAGCCAACTTA
1391285 TACCCTACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 10 0.29
41 25 0.71
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (41 bp):
TAGGAACATGCCTTTTTCTGTACAACTTAGCCAACTTAACG
Found at i:1395560 original size:6 final size:6
Alignment explanation
Indices: 1395543--1395572 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1395533 AACTTAATCT
1395543 TCTGCTC TCTGCC TCTGCC TCTGCC TCTGC
1 TCTGC-C TCTGCC TCTGCC TCTGCC TCTGC
1395573 GTCTCATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.00, C:0.47, G:0.17, T:0.37
Consensus pattern (6 bp):
TCTGCC
Found at i:1395566 original size:12 final size:13
Alignment explanation
Indices: 1395543--1395577 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
1395533 AACTTAATCT
1395543 TCTGCTCTCTGCC
1 TCTGCTCTCTGCC
1395556 TCTGC-CTCTGCC
1 TCTGCTCTCTGCC
1395568 TCTGCGTCTC
1 TCTGC-TCTC
1395578 ATACTCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.60
13 5 0.25
14 3 0.15
ACGTcount: A:0.00, C:0.46, G:0.17, T:0.37
Consensus pattern (13 bp):
TCTGCTCTCTGCC
Found at i:1398791 original size:18 final size:18
Alignment explanation
Indices: 1398768--1398811 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1398758 ATTACTTCTC
*
1398768 AAAAGTATTTTTGGGACA
1 AAAAGTATTTTTGAGACA
* *
1398786 AAAAGTACTTTTGAGATA
1 AAAAGTATTTTTGAGACA
1398804 AAAA-TATT
1 AAAAGTATT
1398812 GCTAAACAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (18 bp):
AAAAGTATTTTTGAGACA
Found at i:1408547 original size:127 final size:128
Alignment explanation
Indices: 1408369--1408624 Score: 426
Period size: 127 Copynumber: 2.0 Consensus size: 128
1408359 ATTAAATTTT
1408369 ATCTAAACTTAACTATCGATATTTTACAAAAAGTCAAATTAATTTTTTCAAGGCTAAATATTAAA
1 ATCTAAACTTAACTATCGATATTTTACAAAAAGTCAAATTAATTTTTTCAAGGCTAAATATTAAA
* *
1408434 AATTA-GAGTCCAATTTTTTAGGAGTTATACACGTAAGGGCCAAATCTTTTCATGATCATAACA
66 AATTAGGA-TCCAATTTTTTAGGAGTTATACACGCAAAGGCCAAATCTTTTCATGATCATAACA
* * *
1408497 ATCTAAACTTAATTATCGATATTTTA-AAAAAGTTAAATTAATTTTTTCAAGGTTAAATATTAAA
1 ATCTAAACTTAACTATCGATATTTTACAAAAAGTCAAATTAATTTTTTCAAGGCTAAATATTAAA
* *
1408561 AATTAGGATCTAATTTTTTAGGAGTTATACACGCAAAGGCTAAATCTTTTCATGATCATAACA
66 AATTAGGATCCAATTTTTTAGGAGTTATACACGCAAAGGCCAAATCTTTTCATGATCATAACA
1408624 A
1 A
1408625 AGTGCTCTAA
Statistics
Matches: 120, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
127 93 0.77
128 27 0.22
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.37
Consensus pattern (128 bp):
ATCTAAACTTAACTATCGATATTTTACAAAAAGTCAAATTAATTTTTTCAAGGCTAAATATTAAA
AATTAGGATCCAATTTTTTAGGAGTTATACACGCAAAGGCCAAATCTTTTCATGATCATAACA
Found at i:1409186 original size:14 final size:14
Alignment explanation
Indices: 1409167--1409206 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1409157 CTCACCCCAC
*
1409167 TTCCATATACCATA
1 TTCCATAGACCATA
1409181 TTCCATAGACCATA
1 TTCCATAGACCATA
**
1409195 GACCATAGACCA
1 TTCCATAGACCA
1409207 AAGATCCACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.30, G:0.07, T:0.25
Consensus pattern (14 bp):
TTCCATAGACCATA
Found at i:1413441 original size:18 final size:18
Alignment explanation
Indices: 1413406--1413442 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1413396 CGTTCGCACT
*
1413406 TGCATATTCATCCTCAAC
1 TGCATATTCATCCGCAAC
*
1413424 TGCATATTCATTCGCAAC
1 TGCATATTCATCCGCAAC
1413442 T
1 T
1413443 TTCGGCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.30, G:0.08, T:0.35
Consensus pattern (18 bp):
TGCATATTCATCCGCAAC
Found at i:1420077 original size:23 final size:22
Alignment explanation
Indices: 1420027--1420077 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
1420017 TTATATATTT
*
1420027 TTAA-AAAAAAATTCAAAAGAA
1 TTAATAAAAAAATTCAAAAAAA
*
1420048 -TATATAAAGAAAATTTAAAAAAA
1 TTA-ATAAA-AAAATTCAAAAAAA
1420071 TTAATAA
1 TTAATAA
1420078 TAATTTTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 2 0.08
21 1 0.04
22 3 0.12
23 16 0.67
24 2 0.08
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (22 bp):
TTAATAAAAAAATTCAAAAAAA
Found at i:1420796 original size:11 final size:11
Alignment explanation
Indices: 1420780--1420804 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1420770 CTCCAAAATT
1420780 ATTATTTTAAA
1 ATTATTTTAAA
1420791 ATTATTTTAAA
1 ATTATTTTAAA
1420802 ATT
1 ATT
1420805 TTAACTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTTTAAA
Found at i:1420868 original size:20 final size:19
Alignment explanation
Indices: 1420847--1420885 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1420837 TAAAAATATA
*
1420847 TATAAAT-TTTAAAATTTT
1 TATAAATATTTTAAATTTT
*
1420865 TATAAATATTTTGAATTTT
1 TATAAATATTTTAAATTTT
1420884 TA
1 TA
1420886 AAGAGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:1420884 original size:28 final size:28
Alignment explanation
Indices: 1420816--1420887 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
1420806 TAACTTTATT
**
1420816 TTTTAGAATTTTTAATTTTTTTAAAAATA
1 TTTT-GAATTTTTAAAATTTTTAAAAATA
* * *
1420845 TATAT-AAATTTTAAAATTTTTATAAATA
1 T-TTTGAATTTTTAAAATTTTTAAAAATA
1420873 TTTTGAATTTTTAAA
1 TTTTGAATTTTTAAA
1420888 GAGAAAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
27 2 0.06
28 29 0.85
29 1 0.03
30 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (28 bp):
TTTTGAATTTTTAAAATTTTTAAAAATA
Found at i:1424378 original size:22 final size:22
Alignment explanation
Indices: 1424348--1424390 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1424338 ACACCAAAAC
* *
1424348 AGGCATTTAGTGGCGCTTTTTT
1 AGGCATTTAGCGGCACTTTTTT
*
1424370 AGGCCTTTAGCGGCACTTTTT
1 AGGCATTTAGCGGCACTTTTT
1424391 AGCGCCACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCATTTAGCGGCACTTTTTT
Found at i:1424528 original size:43 final size:43
Alignment explanation
Indices: 1424479--1424689 Score: 266
Period size: 43 Copynumber: 4.9 Consensus size: 43
1424469 TAAAGACCCT
1424479 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAC
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAC
* * *
1424522 GACCTTTAACGGTGCTTTTTCCACAAACGCCGCTAAAGACCAC
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAC
* * *
1424565 GACCTTTAACGGCGCTTTTCCCTACAAACGCCGCTAAAGACCAC
1 GACCTTTAGCGGCGCTTTTTCC-ACAAACGCCGCTAAAAACCAC
1424609 GACCTTTAGCGGCG-TTTTTCCACAAACGCCGCTAAAGAA-CA-
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAA-AACCAC
* * * ** * *
1424650 AACCTTTAGCGACGCTTCTGGCAAAAACGCCACTAAAAAC
1 GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAAC
1424690 ATAATCTTTA
Statistics
Matches: 149, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
41 14 0.09
42 34 0.23
43 67 0.45
44 34 0.23
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.21
Consensus pattern (43 bp):
GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAACCAC
Found at i:1424607 original size:44 final size:43
Alignment explanation
Indices: 1424467--1424646 Score: 283
Period size: 43 Copynumber: 4.2 Consensus size: 43
1424457 GCTAACTTTA
*
1424467 GCTAAAGACC-CTGACCTTTAGCGGCGCTTTTTCCACAAACGCC
1 GCTAAAGACCAC-GACCTTTAACGGCGCTTTTTCCACAAACGCC
* *
1424510 GCTAAAAACCACGACCTTTAACGGTGCTTTTTCCACAAACGCC
1 GCTAAAGACCACGACCTTTAACGGCGCTTTTTCCACAAACGCC
*
1424553 GCTAAAGACCACGACCTTTAACGGCGCTTTTCCCTACAAACGCC
1 GCTAAAGACCACGACCTTTAACGGCGCTTTTTCC-ACAAACGCC
*
1424597 GCTAAAGACCACGACCTTTAGCGGCG-TTTTTCCACAAACGCC
1 GCTAAAGACCACGACCTTTAACGGCGCTTTTTCCACAAACGCC
1424639 GCTAAAGA
1 GCTAAAGA
1424647 ACAAACCTTT
Statistics
Matches: 127, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
42 17 0.13
43 75 0.59
44 35 0.28
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (43 bp):
GCTAAAGACCACGACCTTTAACGGCGCTTTTTCCACAAACGCC
Found at i:1424678 original size:42 final size:42
Alignment explanation
Indices: 1424546--1424699 Score: 114
Period size: 42 Copynumber: 3.6 Consensus size: 42
1424536 CTTTTTCCAC
* * * * * * *
1424546 AAACGCCGCTAAAGACCACGACCTTTAACGGCGCTTTTCCCTAC
1 AAACGCCGCTAAAGAACACAACCTTTAGCGACG-TTCTGCC-AA
* * * * * *
1424590 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGTTTTTCCAC
1 AAACGCCGCTAAAGAACACAACCTTTAGCGACGTTCTGCCAA
*
1424632 AAACGCCGCTAAAGAACA-AACCTTTAGCGACGCTTCTGGCAA
1 AAACGCCGCTAAAGAACACAACCTTTAGCGACG-TTCTGCCAA
* * *
1424674 AAACGCCACTAAA-AACATAATCTTTA
1 AAACGCCGCTAAAGAACACAACCTTTA
1424700 AAAAAATTTA
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
41 16 0.16
42 43 0.44
43 6 0.06
44 32 0.33
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACACAACCTTTAGCGACGTTCTGCCAA
Found at i:1431799 original size:3 final size:3
Alignment explanation
Indices: 1431791--1431859 Score: 97
Period size: 3 Copynumber: 23.7 Consensus size: 3
1431781 AATAAATAGG
* * *
1431791 TAA TAA TAA T-A TAG T-A TAG TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1431837 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
1431860 GGACTAATTC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 3 0.05
3 55 0.95
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1432319 original size:10 final size:9
Alignment explanation
Indices: 1432294--1432318 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1432284 ATGAAAAGAG
1432294 AAAAAAATA
1 AAAAAAATA
1432303 AAAAAAATA
1 AAAAAAATA
1432312 AAAAAAA
1 AAAAAAA
1432319 AGAAACAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:1433597 original size:26 final size:26
Alignment explanation
Indices: 1433561--1433612 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1433551 TTATTTAAAT
**
1433561 AATAAAAAATAATGTTATTTTAATTA
1 AATAAAAAATAACATTATTTTAATTA
* *
1433587 AATAATAAATAACATTATTTTCATTA
1 AATAAAAAATAACATTATTTTAATTA
1433613 TTTAAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (26 bp):
AATAAAAAATAACATTATTTTAATTA
Found at i:1433852 original size:18 final size:18
Alignment explanation
Indices: 1433822--1433901 Score: 67
Period size: 18 Copynumber: 4.3 Consensus size: 18
1433812 TGTTTAGTAA
1433822 ATTTTTTATATTTTATATT
1 ATTTTTTA-ATTTTATATT
1433841 ATTTTTTAATTTTATAATGT
1 ATTTTTTAATTTTAT-AT-T
* *
1433861 -TATTTTTAATTCTT-TGTA
1 AT-TTTTTAATT-TTATATT
*
1433879 ATTTTTTATTTTTA-ATT
1 ATTTTTTAATTTTATATT
1433896 ATTTTT
1 ATTTTT
1433902 AAGGTTTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
17 9 0.18
18 15 0.30
19 13 0.26
20 11 0.22
21 2 0.04
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (18 bp):
ATTTTTTAATTTTATATT
Found at i:1433909 original size:24 final size:24
Alignment explanation
Indices: 1433860--1433909 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1433850 TTTTATAATG
* **
1433860 TTATTTTTAATTCTTTGTAATTTT
1 TTATTTTTAATTATTTGTAAGGTT
*
1433884 TTATTTTTAATTATTTTTAAGGTT
1 TTATTTTTAATTATTTGTAAGGTT
1433908 TT
1 TT
1433910 TCGAATGATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (24 bp):
TTATTTTTAATTATTTGTAAGGTT
Found at i:1438051 original size:19 final size:20
Alignment explanation
Indices: 1438019--1438057 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1438009 AACAATTTTC
1438019 TTTTTAAGTAGTAATAAAAT
1 TTTTTAAGTAGTAATAAAAT
1438039 TTTTTAAGT-GTAATAAAAT
1 TTTTTAAGTAGTAATAAAAT
1438058 AAAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTTTAAGTAGTAATAAAAT
Found at i:1441521 original size:16 final size:17
Alignment explanation
Indices: 1441490--1441522 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1441480 TAAATTATTA
*
1441490 CAAATTTAAATACTCAC
1 CAAATTAAAATACTCAC
1441507 CAAATTAAAAT-CTCAC
1 CAAATTAAAATACTCAC
1441523 TTTTACATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (17 bp):
CAAATTAAAATACTCAC
Found at i:1442024 original size:18 final size:20
Alignment explanation
Indices: 1441990--1442026 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1441980 TAAAATATAT
1441990 ATTTTTATAACATTTTAATG
1 ATTTTTATAACATTTTAATG
1442010 ATTTTTA-AA-ATTTTAAT
1 ATTTTTATAACATTTTAAT
1442027 TTTTTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
ATTTTTATAACATTTTAATG
Found at i:1442032 original size:18 final size:18
Alignment explanation
Indices: 1441991--1442033 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1441981 AAAATATATA
* *
1441991 TTTTTATAACATTTTAAT
1 TTTTTTTAAAATTTTAAT
**
1442009 GATTTTTAAAATTTTAAT
1 TTTTTTTAAAATTTTAAT
1442027 TTTTTTT
1 TTTTTTT
1442034 GAAGTTTTTG
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTTTAAAATTTTAAT
Found at i:1442516 original size:20 final size:20
Alignment explanation
Indices: 1442478--1442514 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1442468 AACAATTTTC
*
1442478 TTTTTAAGTAGTAATAAATT
1 TTTTTAAGTAGTAAAAAATT
1442498 TTTTTAAGT-GTAAAAAA
1 TTTTTAAGTAGTAAAAAA
1442515 ATAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (20 bp):
TTTTTAAGTAGTAAAAAATT
Found at i:1444031 original size:43 final size:44
Alignment explanation
Indices: 1443983--1444069 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
1443973 TATTATATCT
1443983 ATTGTTTTTTTTT-CCAAGGCATCTATGGGAGCAAACCCACTAA
1 ATTGTTTTTTTTTCCCAAGGCATCTATGGGAGCAAACCCACTAA
1444026 ATTGTTTTTTTTTCCCAAGGCATCTATGGGAGCAAACCCACTAA
1 ATTGTTTTTTTTTCCCAAGGCATCTATGGGAGCAAACCCACTAA
1444070 TTATTTGCGT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 13 0.30
44 30 0.70
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (44 bp):
ATTGTTTTTTTTTCCCAAGGCATCTATGGGAGCAAACCCACTAA
Found at i:1444828 original size:15 final size:14
Alignment explanation
Indices: 1444807--1444840 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1444797 GAATAAAAAA
1444807 TAATAAAAAATTTT
1 TAATAAAAAATTTT
*
1444821 TGAATAAAATATTTT
1 T-AATAAAAAATTTT
1444836 TAATA
1 TAATA
1444841 TTTTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
TAATAAAAAATTTT
Found at i:1444951 original size:27 final size:27
Alignment explanation
Indices: 1444919--1444982 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
1444909 CTATCAAGTT
1444919 GGCGCCAATGAAGGTGCCTCATAGAGA
1 GGCGCCAATGAAGGTGCCTCATAGAGA
*
1444946 GTCGCCAATGAAGGTGCCTCATAGAGA
1 GGCGCCAATGAAGGTGCCTCATAGAGA
1444973 GGCGCCAATG
1 GGCGCCAATG
1444983 GTGGCCTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.33, T:0.16
Consensus pattern (27 bp):
GGCGCCAATGAAGGTGCCTCATAGAGA
Found at i:1445213 original size:12 final size:12
Alignment explanation
Indices: 1445196--1445221 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1445186 TTTGTGAATT
1445196 TTTTAGAAGATA
1 TTTTAGAAGATA
1445208 TTTTAGAAGATA
1 TTTTAGAAGATA
1445220 TT
1 TT
1445222 GTGAATTTTT
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTTAGAAGATA
Found at i:1445317 original size:22 final size:21
Alignment explanation
Indices: 1445290--1445565 Score: 232
Period size: 22 Copynumber: 13.0 Consensus size: 21
1445280 TAGATTAGAA
*
1445290 TTTTGTATGAATATTCTAATTT
1 TTTTGTATGAATATTGTAA-TT
1445312 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
1445333 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
1445351 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
1445372 ATTTTATAATTAA-ATT-TATATT
1 -TTTTGT-ATGAATATTGTA-ATT
* * * * *
1445394 TATAGTTTTGGAT-TAGT-A--
1 TTTTG-TATGAATATTGTAATT
1445412 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATATTGTAA-TT
*
1445434 TTTTGTATGAATATTGCAATTT
1 TTTTGTATGAATATTGTAA-TT
1445456 TTTTGTATGAATATTGTAATTTTGT
1 TTTTGTATGAATATTGTAA---T-T
1445481 AATTTTGTATGAATATTGTAATTT
1 --TTTTGTATGAATATTGTAA-TT
*
1445505 TTTTGTATGAATATTATAA--
1 TTTTGTATGAATATTGTAATT
*
1445524 TTTTGTATGAATATTGCAATTT
1 TTTTGTATGAATATTGTAA-TT
1445546 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
1445566 ATTGTAATAT
Statistics
Matches: 209, Mismatches: 23, Indels: 45
0.75 0.08 0.16
Matches are distributed among these distances:
17 5 0.02
18 9 0.04
19 32 0.15
20 15 0.07
21 14 0.07
22 105 0.50
23 4 0.02
24 3 0.01
25 3 0.01
27 19 0.09
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:1445326 original size:61 final size:60
Alignment explanation
Indices: 1445261--1445448 Score: 188
Period size: 61 Copynumber: 3.1 Consensus size: 60
1445251 TAAATTATCT
* *
1445261 ATATTTACTGTTTATAGTTTAGATTAGAATTTTGTATGAATATTCTAATTTTTTTGTATGA
1 ATATTTA-TATTTATAGTTTAGATTAGAATTTTGTATGAATATTGTAATTTTTTTGTATGA
* * * * *
1445322 ATATTGTA-ATTT-T--TTTATGAATATTGTAATGTTGTATGAATATTGTAATTATTTTATAATT
1 ATATT-TATATTTATAGTTTA-G-AT-TAG-AATTTTGTATGAATATTGTAATTTTTTTGT-ATG
1445383 A
60 A
* *
1445384 A-ATTTATATTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAATTTTTTTGTATGA
1 ATATTTATATTTATAG-TTTAGATTAGAATTTTGTATGAATATTGTAATTTTTTTGTATGA
1445444 ATATT
1 ATATT
1445449 GCAATTTTTT
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
57 4 0.04
58 1 0.01
59 3 0.03
60 11 0.11
61 67 0.66
62 9 0.09
63 2 0.02
64 1 0.01
65 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (60 bp):
ATATTTATATTTATAGTTTAGATTAGAATTTTGTATGAATATTGTAATTTTTTTGTATGA
Found at i:1445480 original size:19 final size:19
Alignment explanation
Indices: 1445288--1445640 Score: 170
Period size: 19 Copynumber: 18.2 Consensus size: 19
1445278 TTTAGATTAG
*
1445288 AATTTTGTATGAATATTCT
1 AATTTTGTATGAATATTGT
1445307 AATTTTTTTGTATGAATATTGT
1 AA---TTTTGTATGAATATTGT
*
1445329 AATTTTTTTATGAATATTGT
1 AA-TTTTGTATGAATATTGT
*
1445349 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
1445368 AATTATTTTAT-AATTAAATT-T
1 AATT-TTGTATGAA-T--ATTGT
* * *
1445389 ATATTTATAGTTTTGGAT-TAGT
1 A-ATTT-T-G-TATGAATATTGT
1445411 -ATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
1445429 AATTTTTTTGTATGAATATTGC
1 AA---TTTTGTATGAATATTGT
*
1445451 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
1445465 AATATTG--T-AATTTTGT
1 AATTTTGTATGAATATTGT
1445481 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
1445500 AATTTTTTTGTATGAATATTAT
1 AA---TTTTGTATGAATATTGT
*
1445522 AATTTTGTATGAATATTGC
1 AATTTTGTATGAATATTGT
*
1445541 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
*
1445555 AATATTG--T-AATATTGT
1 AATTTTGTATGAATATTGT
*
1445571 AATATTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
1445590 AATGTTGGGATATATTGTAATATTGT
1 AAT-TT----TGTA-TG-AATATTGT
1445616 AATTTTTTGTATGAATATTGT
1 AA--TTTTGTATGAATATTGT
1445637 AATT
1 AATT
1445641 ATTTTATAAT
Statistics
Matches: 261, Mismatches: 27, Indels: 92
0.69 0.07 0.24
Matches are distributed among these distances:
13 2 0.01
14 13 0.05
15 8 0.03
16 17 0.07
17 5 0.02
18 12 0.05
19 71 0.27
20 30 0.11
21 14 0.05
22 64 0.25
23 3 0.01
24 6 0.02
25 3 0.01
26 10 0.04
27 2 0.01
28 1 0.00
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:1445506 original size:49 final size:49
Alignment explanation
Indices: 1445434--1445645 Score: 250
Period size: 49 Copynumber: 4.5 Consensus size: 49
1445424 ATTGTAATTT
* *
1445434 TTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTGTAA
1445483 TTTTGTATGAATATTGTAATTTTTTTGTATGAATA---T--TA---TAA
1 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTGTAA
*
1445524 TTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTGTAA
* * * *
1445573 TATTGTATGAATATTGTAA--TGTTGGGAT--ATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTGTAA
*
1445618 TTTTTTGTATGAATATTGTAATTATTTT
1 --TTTTGTATGAATATTGTAATTTTTTT
1445646 ATAATTAATT
Statistics
Matches: 139, Mismatches: 12, Indels: 24
0.79 0.07 0.14
Matches are distributed among these distances:
41 37 0.27
44 2 0.01
45 17 0.12
46 3 0.02
47 24 0.17
49 56 0.40
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (49 bp):
TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTGTAA
Found at i:1445540 original size:90 final size:91
Alignment explanation
Indices: 1445412--1445592 Score: 310
Period size: 90 Copynumber: 2.0 Consensus size: 91
1445402 TGGATTAGTA
* *
1445412 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTATAA--TTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATA
*
1445477 TTGTAATTTTGTATGAATATTGTAATTT
64 TTGTAATATTGTATGAATATTGTAATTT
1445505 TTTTGTATGAATATTATAA-TTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATT
1 TTTTGTATGAATATTATAATTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATT
1445569 GTAATATTGTATGAATATTGTAAT
66 GTAATATTGTATGAATATTGTAAT
1445593 GTTGGGATAT
Statistics
Matches: 85, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
90 67 0.79
93 18 0.21
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (91 bp):
TTTTGTATGAATATTATAATTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATT
GTAATATTGTATGAATATTGTAATTT
Found at i:1445568 original size:8 final size:8
Alignment explanation
Indices: 1445555--1445618 Score: 65
Period size: 8 Copynumber: 7.4 Consensus size: 8
1445545 TTTTTGTATG
1445555 AATATTGT
1 AATATTGT
1445563 AATATTGT
1 AATATTGT
1445571 AATATTGTAT
1 AATATTG--T
1445581 GAATATTGT
1 -AATATTGT
* *
1445590 AATGTTGGG
1 AATATT-GT
1445599 ATATATTGT
1 A-ATATTGT
1445608 AATATTGT
1 AATATTGT
1445616 AAT
1 AAT
1445619 TTTTTGTATG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
8 30 0.64
9 5 0.11
10 5 0.11
11 7 0.15
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (8 bp):
AATATTGT
Found at i:1445602 original size:27 final size:24
Alignment explanation
Indices: 1445414--1445640 Score: 157
Period size: 22 Copynumber: 9.8 Consensus size: 24
1445404 GATTAGTATT
*
1445414 TTGTATGAATATTGTAATTT--TT
1 TTGTATGAATATTGTAATTTGATA
* *
1445436 TTGTATGAATATTGCAATTT--TT
1 TTGTATGAATATTGTAATTTGATA
*
1445458 TTGTATGAATATTGTAATTTTGTAATT
1 TTGTATGAATATTGTAA-TTTG--ATA
*
1445485 TTGTATGAATATTGTAATTT--TT
1 TTGTATGAATATTGTAATTTGATA
*
1445507 TTGTATGAATATTATAA--T--T-
1 TTGTATGAATATTGTAATTTGATA
* *
1445526 TTGTATGAATATTGCAATTT--TT
1 TTGTATGAATATTGTAATTTGATA
1445548 TTGTATGAATATTGTAATATTGTAATA
1 TTGTATGAATATTGTAAT-TTG--ATA
1445575 TTGTATGAATATTGTAATGTTGGGATA
1 TTGTATGAATATTGTAAT-TT--GATA
*
1445602 -TAT-TGTAATATTGTAATTT--T-
1 TTGTATG-AATATTGTAATTTGATA
1445622 TTGTATGAATATTGTAATT
1 TTGTATGAATATTGTAATT
1445641 ATTTTATAAT
Statistics
Matches: 177, Mismatches: 10, Indels: 37
0.79 0.04 0.17
Matches are distributed among these distances:
19 15 0.08
20 2 0.01
21 17 0.10
22 74 0.42
23 5 0.03
25 4 0.02
26 16 0.09
27 43 0.24
29 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (24 bp):
TTGTATGAATATTGTAATTTGATA
Found at i:1445714 original size:60 final size:60
Alignment explanation
Indices: 1445633--1445754 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
1445623 TGTATGAATA
* * * * * *
1445633 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTGGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
1445693 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
1445753 TT
1 TT
1445755 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 6 0.11
60 48 0.89
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:1445833 original size:38 final size:38
Alignment explanation
Indices: 1445788--1445869 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 38
1445778 CATATAAAGT
*
1445788 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCACTAAAAGTTTAA
* *
1445826 TTATAAAAAAATTTAAAATCATTTTACTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCACTAAAAGTTTAA
1445864 TTATAA
1 TTATAA
1445870 CTGACTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCACTAAAAGTTTAA
Found at i:1446263 original size:22 final size:21
Alignment explanation
Indices: 1446228--1446272 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
1446218 TACGTTATTT
*
1446228 TTTTCTTCTTTTCCTTCCTTC
1 TTTTCTTCTCTTCCTTCCTTC
1446249 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCT-CTTCCTTCCTTC
1446271 TT
1 TT
1446273 ATTTCTTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTCTTCTCTTCCTTCCTTC
Found at i:1446408 original size:26 final size:26
Alignment explanation
Indices: 1446338--1446417 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
1446328 AAAATCAGAG
1446338 CATTGGCGCCTCTCAGTATGGCACCAA
1 CATTGGCGCCTCTCAG-ATGGCACCAA
* * * *
1446365 TAATGGCGCCTCCCAGATGGCACCAC
1 CATTGGCGCCTCTCAGATGGCACCAA
* *
1446391 CATTGGCGCCTCTGAGATAGGCGCCAA
1 CATTGGCGCCTCTCAGAT-GGCACCAA
1446418 TACTATGTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
26 23 0.55
27 19 0.45
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.19
Consensus pattern (26 bp):
CATTGGCGCCTCTCAGATGGCACCAA
Found at i:1448688 original size:7 final size:7
Alignment explanation
Indices: 1448678--1448718 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
1448668 CTTAACCTCT
*
1448678 AACCCCC
1 AACCCCA
*
1448685 AACCCCT
1 AACCCCA
*
1448692 AACTCCA
1 AACCCCA
1448699 AACCCCA
1 AACCCCA
1448706 AACCCCA
1 AACCCCA
1448713 AACCCC
1 AACCCC
1448719 TAACTACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.37, C:0.59, G:0.00, T:0.05
Consensus pattern (7 bp):
AACCCCA
Found at i:1448688 original size:14 final size:14
Alignment explanation
Indices: 1448671--1448722 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
1448661 ACTAACTCTT
* *
1448671 AACCTCTAACCCCC
1 AACCCCTAACCCCA
*
1448685 AACCCCTAACTCCA
1 AACCCCTAACCCCA
*
1448699 AACCCCAAACCCCA
1 AACCCCTAACCCCA
1448713 AACCCCTAAC
1 AACCCCTAAC
1448723 TACTAACCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.37, C:0.54, G:0.00, T:0.10
Consensus pattern (14 bp):
AACCCCTAACCCCA
Found at i:1448730 original size:28 final size:28
Alignment explanation
Indices: 1448678--1448731 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1448668 CTTAACCTCT
* *
1448678 AACCCCCAACCCCTAACTCCAAACCCCA
1 AACCCCAAACCCCTAACTACAAACCCCA
*
1448706 AACCCCAAACCCCTAACTACTAACCC
1 AACCCCAAACCCCTAACTACAAACCC
1448732 ATAAACCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.37, C:0.54, G:0.00, T:0.09
Consensus pattern (28 bp):
AACCCCAAACCCCTAACTACAAACCCCA
Found at i:1449438 original size:39 final size:40
Alignment explanation
Indices: 1449367--1449455 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
1449357 TTCGAAAAAA
* * *
1449367 CGCCGCTAATGCTCATTTTTGGCTGCGCTTTTA-GGAAAG
1 CGCCGCTAATGCTCATCTTTAGCAGCGCTTTTATGGAAAG
* **
1449406 CGCCGCTAATGTTCAGTCTTTAGCAGCG-TTTTATTTAAAG
1 CGCCGCTAATGCTCA-TCTTTAGCAGCGCTTTTATGGAAAG
1449446 CGCCGCTAAT
1 CGCCGCTAAT
1449456 ACTTGATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 19 0.45
40 23 0.55
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (40 bp):
CGCCGCTAATGCTCATCTTTAGCAGCGCTTTTATGGAAAG
Found at i:1449468 original size:40 final size:40
Alignment explanation
Indices: 1449402--1449477 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
1449392 CGCTTTTAGG
*
1449402 AAAGCGCCGCTAATGTTCAGTCTTTAGCAGCGTTTTATTT
1 AAAGCGCCGCTAATCTTCAGTCTTTAGCAGCGTTTTATTT
* * *
1449442 AAAGCGCCGCTAATACTTGA-TTTTTAGCGGCGTTTT
1 AAAGCGCCGCTAAT-CTTCAGTCTTTAGCAGCGTTTT
1449478 TTGTCCAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 28 0.90
41 3 0.10
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (40 bp):
AAAGCGCCGCTAATCTTCAGTCTTTAGCAGCGTTTTATTT
Found at i:1457847 original size:21 final size:21
Alignment explanation
Indices: 1457806--1457848 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1457796 AATAAAGTAG
*
1457806 ATTATATACTATTTTTATAGT
1 ATTATATACTATATTTATAGT
*
1457827 ATTATATATTATGATTT-TAGT
1 ATTATATACTAT-ATTTATAGT
1457848 A
1 A
1457849 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTATATACTATATTTATAGT
Found at i:1457944 original size:21 final size:21
Alignment explanation
Indices: 1457920--1457961 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1457910 ATATTTAATA
*
1457920 ATTATTATGGTTAAATTATTT
1 ATTATTATGATTAAATTATTT
* *
1457941 ATTATTTTTATTAAATTATTT
1 ATTATTATGATTAAATTATTT
1457962 TTAATAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
ATTATTATGATTAAATTATTT
Found at i:1457981 original size:47 final size:45
Alignment explanation
Indices: 1457879--1457981 Score: 134
Period size: 48 Copynumber: 2.2 Consensus size: 45
1457869 TATTAAGAAT
* *
1457879 TTTATTAAATTATATATTATTTTATTAAATTATATTTAATAATTA
1 TTTATTAAATTATATATTATTTTATTAAATTATTTTTAATAATAA
* *
1457924 TTATGGTTAAATTATTTATTATTTTTATTAAATTATTTTTAATAATAA
1 TT-T-ATTAAATTATATATTA-TTTTATTAAATTATTTTTAATAATAA
1457972 TCTTATTAAA
1 T-TTATTAAA
1457982 ATTTAATAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
45 2 0.04
46 1 0.02
47 19 0.39
48 26 0.53
49 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (45 bp):
TTTATTAAATTATATATTATTTTATTAAATTATTTTTAATAATAA
Found at i:1457984 original size:48 final size:46
Alignment explanation
Indices: 1457866--1457981 Score: 133
Period size: 47 Copynumber: 2.5 Consensus size: 46
1457856 ATAATAATAA
* * *
1457866 TTTTATTAAGAATTTTATTAAATTATATATTATTTTATTAAATTAT
1 TTTTAATAATAATATTATTAAATTATATATTATTTTATTAAATTAT
* * ** *
1457912 ATTTAATAATTATTATGGTTAAATTATTTATTATTTTTATTAAATTAT
1 TTTTAATAA-TAATATTATTAAATTATATATTA-TTTTATTAAATTAT
*
1457960 TTTTAATAATAATCTTATTAAA
1 TTTTAATAATAATATTATTAAA
1457982 ATTTAATAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
46 7 0.13
47 26 0.47
48 22 0.40
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (46 bp):
TTTTAATAATAATATTATTAAATTATATATTATTTTATTAAATTAT
Found at i:1458174 original size:16 final size:16
Alignment explanation
Indices: 1458150--1458203 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
1458140 TAAATTACTG
*
1458150 ATTATAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
1458166 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
1458182 ATTACA-CTCCTATTCC
1 ATTACAGCT-CTATTCC
1458198 ATTACA
1 ATTACA
1458204 ATGAAACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 2 0.06
16 32 0.94
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:1459605 original size:31 final size:32
Alignment explanation
Indices: 1459527--1459606 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 32
1459517 ACAAGTTTCA
1459527 AAAT-TATGCAT-AAACTTTGATTCAATGCTC
1 AAATATATGCATGAAACTTTGATTCAATGCTC
* * *
1459557 AATTATATACATG-AACTTTGA-TC-GTGGCTC
1 AAATATATGCATGAAACTTTGATTCAAT-GCTC
1459587 AAATATATGCATGAAACTTT
1 AAATATATGCATGAAACTTT
1459607 TATTTTGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
29 1 0.02
30 20 0.49
31 20 0.49
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (32 bp):
AAATATATGCATGAAACTTTGATTCAATGCTC
Found at i:1462911 original size:14 final size:15
Alignment explanation
Indices: 1462889--1462965 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1462879 CAATCAAACA
1462889 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
1462903 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
1462918 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
1462938 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
1462952 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
1462966 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:1462930 original size:20 final size:20
Alignment explanation
Indices: 1462905--1462944 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1462895 AATATTTTCC
*
1462905 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
1462925 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
1462945 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:1462950 original size:34 final size:35
Alignment explanation
Indices: 1462893--1462959 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1462883 CAAACACCAG
*
1462893 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1462928 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1462960 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1463397 original size:19 final size:20
Alignment explanation
Indices: 1463356--1463394 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1463346 TTTAATCCTT
1463356 TTAAAATGATAAAAATATAA
1 TTAAAATGATAAAAATATAA
*
1463376 TTAAAATGATAAAATTATA
1 TTAAAATGATAAAAATATA
1463395 TTATTACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
TTAAAATGATAAAAATATAA
Found at i:1469265 original size:9 final size:9
Alignment explanation
Indices: 1469234--1469376 Score: 57
Period size: 9 Copynumber: 15.6 Consensus size: 9
1469224 TTATAAAAAA
1469234 TTATAATTT
1 TTATAATTT
*
1469243 CTTA-GATTT
1 -TTATAATTT
1469252 ATTATAATTT
1 -TTATAATTT
*
1469262 TTATAAGTTA
1 TTATAA-TTT
*
1469272 ATATCAATTT
1 TTAT-AATTT
*
1469282 TCAT-A-TT
1 TTATAATTT
*
1469289 TT-TAATAT
1 TTATAATTT
1469297 TTA-ATATTT
1 TTATA-ATTT
1469306 TTAT--TTT
1 TTATAATTT
1469313 TTAATAATTT
1 TT-ATAATTT
* *
1469323 TTTTGATTT
1 TTATAATTT
*
1469332 TTCATAAATT
1 TT-ATAATTT
*
1469342 TTATGATTT
1 TTATAATTT
1469351 TTATAACATTT
1 TTAT-A-ATTT
*
1469362 TTAATCATTT
1 TT-ATAATTT
1469372 TTATA
1 TTATA
1469377 GGAAAAGTAT
Statistics
Matches: 97, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
6 1 0.01
7 9 0.09
8 7 0.07
9 37 0.38
10 33 0.34
11 8 0.08
12 2 0.02
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (9 bp):
TTATAATTT
Found at i:1469305 original size:16 final size:16
Alignment explanation
Indices: 1469284--1469324 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1469274 ATCAATTTTC
1469284 ATATTTTTAATATTTA
1 ATATTTTTAATATTTA
* *
1469300 ATATTTTTATTTTTTA
1 ATATTTTTAATATTTA
1469316 ATAATTTTT
1 AT-ATTTTT
1469325 TTGATTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATTTTTAATATTTA
Found at i:1469331 original size:20 final size:20
Alignment explanation
Indices: 1469298--1469352 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
1469288 TTTTAATATT
*
1469298 TAATATTTTT-ATTTTTTAA
1 TAATTTTTTTGATTTTTTAA
*
1469317 TAATTTTTTTGA-TTTTTCA
1 TAATTTTTTTGATTTTTTAA
* *
1469336 TAAATTTTATGATTTTT
1 TAATTTTTTTGATTTTT
1469353 ATAACATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 25 0.83
20 5 0.17
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
TAATTTTTTTGATTTTTTAA
Found at i:1469338 original size:19 final size:18
Alignment explanation
Indices: 1469310--1469376 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 18
1469300 ATATTTTTAT
* *
1469310 TTTTTAATAATTTTTTTGA
1 TTTTT-ATAAATTTTATGA
1469329 TTTTTCATAAATTTTATGA
1 TTTTT-ATAAATTTTATGA
*
1469348 TTTTTATAACATTTTTAATCA
1 TTTTTATAA-A-TTTT-ATGA
1469369 TTTTTATA
1 TTTTTATA
1469377 GGAAAAGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.10
19 22 0.54
20 4 0.10
21 11 0.27
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTTATAAATTTTATGA
Found at i:1471619 original size:35 final size:35
Alignment explanation
Indices: 1471552--1471621 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
1471542 ATAAATGTGC
*
1471552 AAATATATGTATATAAAAATTATAGAATATAAAAA
1 AAATATATGTATATAAAAATTATAGAAAATAAAAA
* * *
1471587 AAATATATGTATGTATATATTCAT-GAAAATAAAAA
1 AAATATATGTATATAAAAATT-ATAGAAAATAAAAA
1471622 TATGTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 28 0.93
36 2 0.07
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (35 bp):
AAATATATGTATATAAAAATTATAGAAAATAAAAA
Found at i:1471866 original size:15 final size:16
Alignment explanation
Indices: 1471836--1471884 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
1471826 AAAATAATAG
*
1471836 TAATAATATTTAAAAA
1 TAATAATATGTAAAAA
1471852 TAATAATA-GTAAAAA
1 TAATAATATGTAAAAA
* *
1471867 TAATGATAATGTTAAAA
1 TAATAAT-ATGTAAAAA
1471884 T
1 T
1471885 TAATTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 12 0.43
16 9 0.32
17 7 0.25
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TAATAATATGTAAAAA
Found at i:1477085 original size:14 final size:14
Alignment explanation
Indices: 1477054--1477091 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1477044 TTATTTACTA
*
1477054 TTATT-TTACTATT
1 TTATTGTTATTATT
*
1477067 ATATTGTTATTATT
1 TTATTGTTATTATT
1477081 TTATTGTTATT
1 TTATTGTTATT
1477092 GTCTAGATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (14 bp):
TTATTGTTATTATT
Found at i:1479930 original size:18 final size:18
Alignment explanation
Indices: 1479907--1479946 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1479897 ATGACTTTTA
*
1479907 AATAATTTTTTATTAAGT
1 AATAATATTTTATTAAGT
*
1479925 AATAATATTTTATTAATT
1 AATAATATTTTATTAAGT
1479943 AATA
1 AATA
1479947 TTATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AATAATATTTTATTAAGT
Found at i:1487014 original size:287 final size:287
Alignment explanation
Indices: 1486498--1487074 Score: 1154
Period size: 287 Copynumber: 2.0 Consensus size: 287
1486488 TAATTGAAAA
1486498 AAAGAGGAGCGTGTTACCGTCCTGTCACGTTGCGGTAGGGCTGTCAGATACCAAAAACTTAAATA
1 AAAGAGGAGCGTGTTACCGTCCTGTCACGTTGCGGTAGGGCTGTCAGATACCAAAAACTTAAATA
1486563 AAAACCAAAACATTCAACAGACATAGATTTTTGGCTGAGGTGGGGTTATATATTTTGGGTGGTGT
66 AAAACCAAAACATTCAACAGACATAGATTTTTGGCTGAGGTGGGGTTATATATTTTGGGTGGTGT
1486628 CGCCTAACAATGATGCGGGACCACCAATGTCCTCTGACACGTCGGTGGCACCACTAATAAATTAT
131 CGCCTAACAATGATGCGGGACCACCAATGTCCTCTGACACGTCGGTGGCACCACTAATAAATTAT
1486693 TTTTTTCTGTCTCTTTTTTCTCTTCACATCTATTTTTTTCCTGACAGCCTATCATTGGTGCTGCC
196 TTTTTTCTGTCTCTTTTTTCTCTTCACATCTATTTTTTTCCTGACAGCCTATCATTGGTGCTGCC
1486758 TGATATATCAATGACACTAATTAATTT
261 TGATATATCAATGACACTAATTAATTT
1486785 AAAGAGGAGCGTGTTACCGTCCTGTCACGTTGCGGTAGGGCTGTCAGATACCAAAAACTTAAATA
1 AAAGAGGAGCGTGTTACCGTCCTGTCACGTTGCGGTAGGGCTGTCAGATACCAAAAACTTAAATA
1486850 AAAACCAAAACATTCAACAGACATAGATTTTTGGCTGAGGTGGGGTTATATATTTTGGGTGGTGT
66 AAAACCAAAACATTCAACAGACATAGATTTTTGGCTGAGGTGGGGTTATATATTTTGGGTGGTGT
1486915 CGCCTAACAATGATGCGGGACCACCAATGTCCTCTGACACGTCGGTGGCACCACTAATAAATTAT
131 CGCCTAACAATGATGCGGGACCACCAATGTCCTCTGACACGTCGGTGGCACCACTAATAAATTAT
1486980 TTTTTTCTGTCTCTTTTTTCTCTTCACATCTATTTTTTTCCTGACAGCCTATCATTGGTGCTGCC
196 TTTTTTCTGTCTCTTTTTTCTCTTCACATCTATTTTTTTCCTGACAGCCTATCATTGGTGCTGCC
1487045 TGATATATCAATGACACTAATTAATTT
261 TGATATATCAATGACACTAATTAATTT
1487072 AAA
1 AAA
1487075 AAACATTACT
Statistics
Matches: 290, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
287 290 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (287 bp):
AAAGAGGAGCGTGTTACCGTCCTGTCACGTTGCGGTAGGGCTGTCAGATACCAAAAACTTAAATA
AAAACCAAAACATTCAACAGACATAGATTTTTGGCTGAGGTGGGGTTATATATTTTGGGTGGTGT
CGCCTAACAATGATGCGGGACCACCAATGTCCTCTGACACGTCGGTGGCACCACTAATAAATTAT
TTTTTTCTGTCTCTTTTTTCTCTTCACATCTATTTTTTTCCTGACAGCCTATCATTGGTGCTGCC
TGATATATCAATGACACTAATTAATTT
Found at i:1494399 original size:7 final size:7
Alignment explanation
Indices: 1494387--1494421 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1494377 TAAAAATAGT
1494387 TTTTTTC
1 TTTTTTC
1494394 TTTTTTC
1 TTTTTTC
1494401 -TTTTTC
1 TTTTTTC
*
1494407 TTTTTTT
1 TTTTTTC
1494414 TTTTTTC
1 TTTTTTC
1494421 T
1 T
1494422 GGTTGATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:1494418 original size:13 final size:13
Alignment explanation
Indices: 1494386--1494418 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1494376 ATAAAAATAG
1494386 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
*
1494399 TCTTTTTCTTTTT
1 TTTTTTTCTTTTT
1494412 TTTTTTT
1 TTTTTTT
1494419 TCTGGTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:1499976 original size:23 final size:23
Alignment explanation
Indices: 1499949--1500024 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
1499939 TTTATGTGCA
1499949 AAATTGTCATTATATTTTAGGTG
1 AAATTGTCATTATATTTTAGGTG
** *
1499972 AAATTGAAATT-TATTTTATGTG
1 AAATTGTCATTATATTTTAGGTG
1499994 CAAAATTGTCATTATATTTTAGGTG
1 --AAATTGTCATTATATTTTAGGTG
1500019 AAATTG
1 AAATTG
1500025 AAATTTATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.23
23 15 0.34
24 9 0.20
25 10 0.23
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (23 bp):
AAATTGTCATTATATTTTAGGTG
Found at i:1499994 original size:47 final size:47
Alignment explanation
Indices: 1499938--1500032 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1499928 AAAAGTTCAT
1499938 TTTTATGTGCAAAATTGTCATTATATTTTAGGTGAAATTGAAATTTA
1 TTTTATGTGCAAAATTGTCATTATATTTTAGGTGAAATTGAAATTTA
1499985 TTTTATGTGCAAAATTGTCATTATATTTTAGGTGAAATTGAAATTTA
1 TTTTATGTGCAAAATTGTCATTATATTTTAGGTGAAATTGAAATTTA
1500032 T
1 T
1500033 CACTATATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (47 bp):
TTTTATGTGCAAAATTGTCATTATATTTTAGGTGAAATTGAAATTTA
Found at i:1501634 original size:29 final size:30
Alignment explanation
Indices: 1501591--1501648 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1501581 ATTTAACTTG
*
1501591 ATACATGAACTTT-AATTTTGTGCAATTTA
1 ATACATGAACTTTAAATTTAGTGCAATTTA
*
1501620 ATACATGAA-TATTAAATTTAGTTCAATTT
1 ATACATGAACT-TTAAATTTAGTGCAATTT
1501649 TCACAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.04
29 11 0.44
30 13 0.52
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (30 bp):
ATACATGAACTTTAAATTTAGTGCAATTTA
Found at i:1503173 original size:22 final size:22
Alignment explanation
Indices: 1503123--1503175 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1503113 TCAAGCCAAT
* *
1503123 AACAACAAAATAGTAACAATAT
1 AACAACAAAATAGTAACAAAAC
* * *
1503145 AATAACAAAATGGTAGCAAAAC
1 AACAACAAAATAGTAACAAAAC
1503167 AACAACAAA
1 AACAACAAA
1503176 TTAACTTATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.64, C:0.15, G:0.08, T:0.13
Consensus pattern (22 bp):
AACAACAAAATAGTAACAAAAC
Found at i:1504866 original size:31 final size:29
Alignment explanation
Indices: 1504831--1504907 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
1504821 TTAATAGCTC
*
1504831 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* ***
1504862 AGTGACAAAAATGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
1504891 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
1504908 CTAAAGTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 1 0.03
31 17 0.43
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.23
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:1507574 original size:12 final size:13
Alignment explanation
Indices: 1507557--1507585 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1507547 ACCATGAATA
1507557 AATTTTAAAAAT-
1 AATTTTAAAAATC
1507569 AATTTTAAAAATC
1 AATTTTAAAAATC
1507582 AATT
1 AATT
1507586 AAATTATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTTTAAAAATC
Found at i:1512989 original size:13 final size:13
Alignment explanation
Indices: 1512971--1512995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1512961 TTTTTGCCCA
1512971 AGCCTATATTTTG
1 AGCCTATATTTTG
1512984 AGCCTATATTTT
1 AGCCTATATTTT
1512996 TACCCGAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
AGCCTATATTTTG
Found at i:1513655 original size:29 final size:31
Alignment explanation
Indices: 1513619--1513679 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
1513609 AAACCTTTTT
* *
1513619 ACTTTTCCCTCAAAACTTTTACTCCT-TCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1513649 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1513680 CTCCCAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
Found at i:1514500 original size:5 final size:5
Alignment explanation
Indices: 1514490--1514521 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1514480 GAACAAATAT
*
1514490 ATTCG ATTCG ATTTG ATTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG AT
1514522 CGAATGCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.44
Consensus pattern (5 bp):
ATTCG
Found at i:1522341 original size:19 final size:19
Alignment explanation
Indices: 1522308--1522371 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 19
1522298 TAATGTTTAT
*
1522308 TAAAAATTAGAAAAAGATTA
1 TAAAAATT-GTAAAAGATTA
1522328 TAAAAATTGTAAAAGATTA
1 TAAAAATTGTAAAAGATTA
* * *
1522347 TAAAATTTTATAAAATATTA
1 TAAAA-ATTGTAAAAGATTA
1522367 TAAAA
1 TAAAA
1522372 TATATAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.38
20 24 0.62
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
TAAAAATTGTAAAAGATTA
Found at i:1522372 original size:10 final size:10
Alignment explanation
Indices: 1522319--1522384 Score: 73
Period size: 10 Copynumber: 6.7 Consensus size: 10
1522309 AAAAATTAGA
*
1522319 AAAAGATTAT
1 AAAATATTAT
*
1522329 AAAA-ATTGT
1 AAAATATTAT
*
1522338 AAAAGATTAT
1 AAAATATTAT
*
1522348 AAAATTTTAT
1 AAAATATTAT
1522358 AAAATATTAT
1 AAAATATTAT
1522368 AAAATA-TAT
1 AAAATATTAT
1522377 AGAAATAT
1 A-AAATAT
1522385 ATTTTTTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
9 12 0.25
10 36 0.75
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (10 bp):
AAAATATTAT
Found at i:1522382 original size:20 final size:20
Alignment explanation
Indices: 1522305--1522384 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 20
1522295 ATTTAATGTT
*
1522305 TATTA-AAAATTAGA-AAAA
1 TATTATAAAATTATATAAAA
* * *
1522323 GATTATAAAAAT-TGTAAAA
1 TATTATAAAATTATATAAAA
* *
1522342 GATTATAAAATTTTATAAAA
1 TATTATAAAATTATATAAAA
1522362 TATTATAAAA-TATATAGAAA
1 TATTATAAAATTATATA-AAA
1522382 TAT
1 TAT
1522385 ATTTTTTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
18 4 0.08
19 25 0.50
20 21 0.42
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (20 bp):
TATTATAAAATTATATAAAA
Found at i:1522447 original size:17 final size:18
Alignment explanation
Indices: 1522415--1522449 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1522405 AAAATGATAA
1522415 AAAAATATAAAGAATTAT
1 AAAAATATAAAGAATTAT
*
1522433 AAAATTATAAA-AATTAT
1 AAAAATATAAAGAATTAT
1522450 CGTACCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAATATAAAGAATTAT
Found at i:1522620 original size:10 final size:10
Alignment explanation
Indices: 1522607--1522660 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 10
1522597 TTTTTATGCA
1522607 TTTTATAATT
1 TTTTATAATT
1522617 TTTTATAATT
1 TTTTATAATT
**
1522627 TTTT-TAAAA
1 TTTTATAATT
**
1522636 TTTTATAAAA
1 TTTTATAATT
1522646 TTTTAT-ATT
1 TTTTATAATT
1522655 TTTTAT
1 TTTTAT
1522661 TAAAGTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
9 14 0.36
10 25 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:1522629 original size:11 final size:11
Alignment explanation
Indices: 1522607--1522639 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1522597 TTTTTATGCA
1522607 TTTTATAA-TT
1 TTTTATAATTT
1522617 TTTTATAATTT
1 TTTTATAATTT
*
1522628 TTTTAAAATTT
1 TTTTATAATTT
1522639 T
1 T
1522640 ATAAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:1522629 original size:19 final size:20
Alignment explanation
Indices: 1522606--1522678 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 20
1522596 TTTTTTATGC
1522606 ATTTTATAATTTTTTAT-AA
1 ATTTTATAATTTTTTATAAA
* * **
1522625 TTTTTTTAAAATTTTATAAA
1 ATTTTATAATTTTTTATAAA
1522645 ATTTTAT-ATTTTTTATTAAA
1 ATTTTATAATTTTTTA-TAAA
* *
1522665 GTTTAATAATTTTT
1 ATTTTATAATTTTT
1522679 ATTGATTTTG
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 19 0.46
20 16 0.39
21 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (20 bp):
ATTTTATAATTTTTTATAAA
Found at i:1522631 original size:21 final size:21
Alignment explanation
Indices: 1522607--1522649 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1522597 TTTTTATGCA
* * *
1522607 TTTTATAATTTTTTATAATTT
1 TTTTAAAATTTTATAAAATTT
1522628 TTTTAAAATTTTATAAAATTT
1 TTTTAAAATTTTATAAAATTT
1522649 T
1 T
1522650 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTAAAATTTTATAAAATTT
Found at i:1522638 original size:29 final size:30
Alignment explanation
Indices: 1522606--1522678 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 30
1522596 TTTTTTATGC
1522606 ATTTTATAATTTTTTATAATTTTT-TTAAA
1 ATTTTATAATTTTTTATAATTTTTATTAAA
** *
1522635 ATTTTATAAAATTTTATATTTTTTATTAAA
1 ATTTTATAATTTTTTATAATTTTTATTAAA
* *
1522665 GTTTAATAATTTTT
1 ATTTTATAATTTTT
1522679 ATTGATTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (30 bp):
ATTTTATAATTTTTTATAATTTTTATTAAA
Found at i:1522664 original size:20 final size:20
Alignment explanation
Indices: 1522636--1522681 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1522626 TTTTTTAAAA
* *
1522636 TTTTA-TAAAATTTTATATT
1 TTTTATTAAAATTTAATAAT
*
1522655 TTTTATTAAAGTTTAATAAT
1 TTTTATTAAAATTTAATAAT
1522675 TTTTATT
1 TTTTATT
1522682 GATTTTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATTAAAATTTAATAAT
Found at i:1522996 original size:90 final size:91
Alignment explanation
Indices: 1522827--1523024 Score: 258
Period size: 90 Copynumber: 2.2 Consensus size: 91
1522817 TGCATTTTGG
* * * *
1522827 CAATTGAATGCAAAAAAAAAAAAAGCAATGGCTTAATTGTTTTTTTTGAAAAATTTTGAGGGTCT
1 CAATTGAGTGCAAAAAAAAAAAAAGCAAGGGCTTAATTGTTTTTTTT--AAAAGTTTGAGGGACT
* *
1522892 TTTTATGCATTTTGACAA-TTTAAGTACT
64 TTTGATGCATTTTGA-AAGTTTAAGTACC
* *
1522920 CAATTGAGTGCAAAAAAAAAAAAAGCAGGGGCTTAATT-TTTTTTTT-TAAGTTTGAGGGCACTT
1 CAATTGAGTGCAAAAAAAAAAAAAGCAAGGGCTTAATTGTTTTTTTTAAAAGTTTGAGGG-ACTT
*
1522983 TTGATGCATTTTGAAAGTTTAAGTGCC
65 TTGATGCATTTTGAAAGTTTAAGTACC
1523010 CAATTGAGTGCAAAA
1 CAATTGAGTGCAAAA
1523025 CAAAGAGCAG
Statistics
Matches: 94, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
89 12 0.13
90 39 0.41
92 8 0.09
93 35 0.37
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (91 bp):
CAATTGAGTGCAAAAAAAAAAAAAGCAAGGGCTTAATTGTTTTTTTTAAAAGTTTGAGGGACTTT
TGATGCATTTTGAAAGTTTAAGTACC
Found at i:1523050 original size:90 final size:87
Alignment explanation
Indices: 1522840--1523059 Score: 234
Period size: 90 Copynumber: 2.5 Consensus size: 87
1522830 TTGAATGCAA
* * * *
1522840 AAAAAAAAAAAGCA-ATGGCTTAATTGTTTTTTTTGAAAAATTTTGAGGGTCTTTTTATGCATTT
1 AAAAAAAAAAAGCAGA-GGCTTAATT-TTTTTTTT---TAAGTTTGAGGGACTTTTGATGCATTT
*
1522904 TGACAATTTAAGTACTCAATTGAGTGC
61 TGACAATTTAAGTACCCAATTGAGTGC
*
1522931 AAAAAAAAAAAAAGCAGGGGCTTAATTTTTTTTTTTAAGTTTGAGGGCACTTTTGATGCATTTTG
1 --AAAAAAAAAAAGCAGAGGCTTAATTTTTTTTTTTAAGTTTGAGGG-ACTTTTGATGCATTTTG
*
1522996 A-AAGTTTAAGTGCCCAATTGAGTGC
63 ACAA-TTTAAGTACCCAATTGAGTGC
* * *
1523021 -AAAACAAAGAGCAGAGTCTTAA-TTTTTTTTTTAA-TTTGA
1 AAAAAAAAAAAGCAGAGGCTTAATTTTTTTTTTTAAGTTTGA
1523060 AGGTTTTTCA
Statistics
Matches: 113, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
85 5 0.04
86 12 0.11
87 18 0.16
89 12 0.11
90 35 0.31
92 8 0.07
93 23 0.20
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (87 bp):
AAAAAAAAAAAGCAGAGGCTTAATTTTTTTTTTTAAGTTTGAGGGACTTTTGATGCATTTTGACA
ATTTAAGTACCCAATTGAGTGC
Found at i:1526885 original size:49 final size:49
Alignment explanation
Indices: 1526813--1526912 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
1526803 GTCTCAGCTA
1526813 AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
1 AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
* *
1526862 AATAGTTGTAATAGTCTAATCCAAAGAAGAAAAGATAGAGCTATTATGT
1 AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
1526911 AA
1 AA
1526913 GTGAACCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (49 bp):
AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
Found at i:1530154 original size:6 final size:6
Alignment explanation
Indices: 1530143--1530176 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1530133 ATTTAATATC
1530143 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
1530177 GGAGTTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:1530407 original size:27 final size:30
Alignment explanation
Indices: 1530347--1530412 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 30
1530337 TCTAAAAAAT
*
1530347 AAAATAAAAACTAAATTTCATAAAATATAAAC
1 AAAAAAAAAACTAAATTT-ATAAAATAT-AAC
1530379 AAAAAAAAAACTAAATTT-T-AAATAT-AC
1 AAAAAAAAAACTAAATTTATAAAATATAAC
1530406 AAAAAAA
1 AAAAAAA
1530413 TATAAAGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 9 0.27
29 6 0.18
30 1 0.03
32 17 0.52
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.23
Consensus pattern (30 bp):
AAAAAAAAAACTAAATTTATAAAATATAAC
Found at i:1533133 original size:20 final size:20
Alignment explanation
Indices: 1533108--1533172 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
1533098 TTATAAATAG
* *
1533108 TTATAAAATTTATATATATT
1 TTATAAAATTTATAGAAATT
*
1533128 TTATAAAAATTATAGAAATT
1 TTATAAAATTTATAGAAATT
* *
1533148 TTAAAAAATTCTAAAGAATATT
1 TTATAAAATT-TATAGAA-ATT
1533170 TTA
1 TTA
1533173 ATTTGACATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 25 0.68
21 6 0.16
22 6 0.16
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45
Consensus pattern (20 bp):
TTATAAAATTTATAGAAATT
Found at i:1533499 original size:28 final size:29
Alignment explanation
Indices: 1533447--1533501 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1533437 TTAACAAATT
* * *
1533447 AAAATATAATTAAAATTTTAGAAAATTAC
1 AAAATATAATTAAAAATATAAAAAATTAC
1533476 AAAATA-AATTAAAAATATAAAAAATT
1 AAAATATAATTAAAAATATAAAAAATT
1533502 GAAATAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAATATAATTAAAAATATAAAAAATTAC
Found at i:1533617 original size:17 final size:17
Alignment explanation
Indices: 1533595--1533653 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1533585 GTTTCTTTTT
1533595 TTTTTTAATTTTTTGTA
1 TTTTTTAATTTTTTGTA
* *
1533612 TTTTTTAATTTTATGAA
1 TTTTTTAATTTTTTGTA
* *
1533629 TTTTCTT-CTTTTTTAT-
1 TTTT-TTAATTTTTTGTA
1533645 TTTTTTAAT
1 TTTTTTAAT
1533654 CTTAAATATA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 2 0.06
16 5 0.15
17 24 0.73
18 2 0.06
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTTTAATTTTTTGTA
Found at i:1535396 original size:25 final size:25
Alignment explanation
Indices: 1535368--1535416 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1535358 CAAACATGTA
* *
1535368 AACGAAAAGCTCTTTCGAGCCATAT
1 AACGAAAAGCTCATCCGAGCCATAT
**
1535393 AACGGGAAGCTCATCCGAGCCATA
1 AACGAAAAGCTCATCCGAGCCATA
1535417 ATTGGGAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (25 bp):
AACGAAAAGCTCATCCGAGCCATAT
Found at i:1535447 original size:24 final size:24
Alignment explanation
Indices: 1535383--1535447 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
1535373 AAAGCTCTTT
* *
1535383 CGAGCCATATAACGGGAAGCTCATC
1 CGAGCCA-ATATCGGGAAGCTCAAC
* * *
1535408 CGAGCC-ATAATTGGGAAGTTCAAG
1 CGAGCCAAT-ATCGGGAAGCTCAAC
1535432 CGAGCCAATATCGGGA
1 CGAGCCAATATCGGGA
1535448 TGGAAGCTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 2 0.06
24 22 0.69
25 8 0.25
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (24 bp):
CGAGCCAATATCGGGAAGCTCAAC
Found at i:1539123 original size:26 final size:28
Alignment explanation
Indices: 1539093--1539148 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
1539083 GTGTTTAAAA
*
1539093 ATAATATGAAAAT-AATAATGAAA-CAT
1 ATAATATGAAAATAAATAATAAAAGCAT
* *
1539119 ATAATTTGAAACTAAATAATAAAAGCAT
1 ATAATATGAAAATAAATAATAAAAGCAT
1539147 AT
1 AT
1539149 GAAATATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 9 0.36
28 5 0.20
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (28 bp):
ATAATATGAAAATAAATAATAAAAGCAT
Found at i:1548453 original size:19 final size:19
Alignment explanation
Indices: 1548426--1548465 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1548416 TTTTAGCCTT
1548426 AAAAGAAAAAAATATAATA
1 AAAAGAAAAAAATATAATA
* * *
1548445 AAAATAAAATAATATTATA
1 AAAAGAAAAAAATATAATA
1548464 AA
1 AA
1548466 TTATAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAAGAAAAAAATATAATA
Found at i:1548552 original size:48 final size:49
Alignment explanation
Indices: 1548462--1548554 Score: 120
Period size: 48 Copynumber: 1.9 Consensus size: 49
1548452 AATAATATTA
*
1548462 TAAATTATAAGAAAACATCAATATTCTCAGTAAAATCGTAATTAAATAC
1 TAAATTATAAGAAAACATCAATATTCTCAGTAAAATCATAATTAAATAC
**
1548511 TAAATTATTAA-AAAA-ATCAATATTCTTGGTAAAAGT-ATAATTAA
1 TAAATTA-TAAGAAAACATCAATATTCTCAGTAAAA-TCATAATTAA
1548555 CATTATGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
48 24 0.62
49 12 0.31
50 3 0.08
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (49 bp):
TAAATTATAAGAAAACATCAATATTCTCAGTAAAATCATAATTAAATAC
Found at i:1550159 original size:2 final size:2
Alignment explanation
Indices: 1550152--1550181 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1550142 CTTGTAACAA
1550152 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1550182 TGTGACATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1552355 original size:7 final size:7
Alignment explanation
Indices: 1552345--1552369 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1552335 CTTGTCAAGT
1552345 TTTGAAA
1 TTTGAAA
1552352 TTTGAAA
1 TTTGAAA
1552359 TTTGAAA
1 TTTGAAA
1552366 TTTG
1 TTTG
1552370 GGTTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (7 bp):
TTTGAAA
Found at i:1564010 original size:16 final size:18
Alignment explanation
Indices: 1563978--1564010 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1563968 TGTTATAGAA
1563978 TAAATTTAGTGTTAATTG
1 TAAATTTAGTGTTAATTG
1563996 TAAATTT-GT-TTAATT
1 TAAATTTAGTGTTAATT
1564011 TTGTGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
TAAATTTAGTGTTAATTG
Found at i:1568964 original size:31 final size:31
Alignment explanation
Indices: 1568926--1568988 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1568916 ATTTGATAAC
1568926 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1568957 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1568988 T
1 T
1568989 AAATTTGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (31 bp):
TTAGAATATTTGTTTTGTTAGTTAGAATAGT
Found at i:1574782 original size:14 final size:16
Alignment explanation
Indices: 1574763--1574795 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1574753 TTAAGTTAAA
1574763 ATAATA-TAAA-CTTT
1 ATAATATTAAACCTTT
1574777 ATAATATTAAACCTTT
1 ATAATATTAAACCTTT
1574793 ATA
1 ATA
1574796 TCTAATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 4 0.24
16 7 0.41
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATATTAAACCTTT
Found at i:1577368 original size:26 final size:26
Alignment explanation
Indices: 1577331--1577380 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1577321 GAATATTTTA
*
1577331 TTATTATCATATTATT-ATTAATTATT
1 TTATTATAATATT-TTAATTAATTATT
1577357 TTATTATAATATTTTAATTAATTA
1 TTATTATAATATTTTAATTAATTA
1577381 AATTCAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATTATAATATTTTAATTAATTATT
Found at i:1577376 original size:14 final size:13
Alignment explanation
Indices: 1577322--1577372 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
1577312 TAATTGGTGG
1577322 AATATTTTATTAT
1 AATATTTTATTAT
* *
1577335 TATCATATTATTATT
1 AAT-ATTTTATTA-T
1577350 AATTATTTTATTAT
1 AA-TATTTTATTAT
1577364 AATATTTTA
1 AATATTTTA
1577373 ATTAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 9 0.29
14 11 0.35
15 10 0.32
16 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
AATATTTTATTAT
Found at i:1579433 original size:20 final size:21
Alignment explanation
Indices: 1579398--1579438 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1579388 ATATATTAAA
1579398 ATTTATTATATTTTTTAGAAT
1 ATTTATTATATTTTTTAGAAT
*
1579419 ATTTA-TATTTTTTTTAGAAT
1 ATTTATTATATTTTTTAGAAT
1579439 TAAAATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (21 bp):
ATTTATTATATTTTTTAGAAT
Found at i:1580243 original size:18 final size:19
Alignment explanation
Indices: 1580208--1580246 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1580198 AATAAACACC
1580208 AAAAAATTATTTTAAAAAT
1 AAAAAATTATTTTAAAAAT
*
1580227 AAAAAGTTATTTTAAAAAT
1 AAAAAATTATTTTAAAAAT
1580246 A
1 A
1580247 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAAAATTATTTTAAAAAT
Found at i:1585700 original size:2 final size:2
Alignment explanation
Indices: 1585695--1585722 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1585685 TTTTATGCAG
1585695 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1585723 ATTGTTGGGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1594516 original size:14 final size:14
Alignment explanation
Indices: 1594497--1594531 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1594487 CCATCATCTC
1594497 TCTCTCTCTCTCTT
1 TCTCTCTCTCTCTT
*
1594511 TCTCTCACTCTCTT
1 TCTCTCTCTCTCTT
*
1594525 TTTCTCT
1 TCTCTCT
1594532 GTTCTCACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (14 bp):
TCTCTCTCTCTCTT
Found at i:1594516 original size:16 final size:16
Alignment explanation
Indices: 1594495--1594531 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1594485 GCCCATCATC
*
1594495 TCTCTCTCTCTCTCTT
1 TCTCTCACTCTCTCTT
*
1594511 TCTCTCACTCTCTTTT
1 TCTCTCACTCTCTCTT
1594527 TCTCT
1 TCTCT
1594532 GTTCTCACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.57
Consensus pattern (16 bp):
TCTCTCACTCTCTCTT
Found at i:1600376 original size:16 final size:16
Alignment explanation
Indices: 1600357--1600391 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1600347 TTTAGATGGC
* *
1600357 TTTGTGTTTGGGTTAT
1 TTTGTATTTGAGTTAT
1600373 TTTGTATTTGAGTTAT
1 TTTGTATTTGAGTTAT
1600389 TTT
1 TTT
1600392 AGGTCATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.23, T:0.66
Consensus pattern (16 bp):
TTTGTATTTGAGTTAT
Found at i:1606150 original size:137 final size:137
Alignment explanation
Indices: 1605892--1606165 Score: 415
Period size: 137 Copynumber: 2.0 Consensus size: 137
1605882 CAAAGTAAAA
*
1605892 AAATACTCACTTTATACTACACTTGAGTTGTCCTGAAAACATGTCTAGATTGTTGTCCAAAAGTT
1 AAATACTCACTTTATACTACACTTGAGTTGTCCTGAAAACATGTCTAGATTGTGGTCCAAAAGTT
* * *
1605957 AGTCTAGACAACTGTTCAAACAATGGATTAAACACAATGACAAAACATACAATTCAAGGAGCTAT
66 AGCCTAGACAACTGTTCAAACAAGGGATTAAACACAATGACAAAACATACAATTCAAGAAGCTAT
1606022 CAAACAT
131 CAAACAT
* * * *
1606029 AAATGCTCACTTTATGCTACACTTGAGTTTTCCTGAAAGCATGTCTAGACTT-TGGTCCAAAAGT
1 AAATACTCACTTTATACTACACTTGAGTTGTCCTGAAAACATGTCTAGA-TTGTGGTCCAAAAGT
* * * * *
1606093 TAGCCTAGGCAACTGTTCAAATAAGGGATTAAACACAATGACAAATCATGCAGTTCAAGAAGCTA
65 TAGCCTAGACAACTGTTCAAACAAGGGATTAAACACAATGACAAAACATACAATTCAAGAAGCTA
1606158 TCAAACAT
130 TCAAACAT
1606166 GAAGAAAAAC
Statistics
Matches: 123, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
137 121 0.98
138 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (137 bp):
AAATACTCACTTTATACTACACTTGAGTTGTCCTGAAAACATGTCTAGATTGTGGTCCAAAAGTT
AGCCTAGACAACTGTTCAAACAAGGGATTAAACACAATGACAAAACATACAATTCAAGAAGCTAT
CAAACAT
Done.