Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012182.1 Kokia drynarioides strain JFW-HI SEQ_127183, 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: 127265
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:620 original size:58 final size:59
Alignment explanation
Indices: 510--879 Score: 541
Period size: 59 Copynumber: 6.3 Consensus size: 59
500 TCCCTAAACT
510 TTCTAAAAATTACCA-TTTACCCTCGAACTTCCAAAAATCCCATTTTTGGCCCCGAACC
1 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGGCCCCGAACC
* * * *
568 TTCTAAAAATTACAATTTTACCCTTGAACTTCTAAAAATCCCA-TTTTAGCCCCGAACC
1 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGGCCCCGAACC
626 TTCTAAAAATTACCATTTTACCC-CTGAACTTCCAAAAATCCCATTTTTGGCCCCGAACC
1 TTCTAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGGCCCCGAACC
*
685 TTCTAAAAATTACCATTTTACCCTCGAGCTTCCAAAAATCCCATTTTTGGCCCCGAACC
1 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGGCCCCGAACC
* * * *
744 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCAATTTTTGACCCCTAACC
1 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGGCCCCGAACC
* * * * * *
803 TTCTAAAAATTACCATTTTACCCCCGAGCGTCCAAAAATCTCATTTTTGACTCCGAACC
1 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGGCCCCGAACC
* * *
862 CTC-CAAAACTACCATTTT
1 TTCTAAAAATTACCATTTT
880 GCCCCCATGC
Statistics
Matches: 283, Mismatches: 25, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
58 80 0.28
59 202 0.71
60 1 0.00
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGGCCCCGAACC
Found at i:783 original size:29 final size:28
Alignment explanation
Indices: 510--826 Score: 277
Period size: 29 Copynumber: 10.9 Consensus size: 28
500 TCCCTAAACT
510 TTCTAAAAATTACCA-TTTACCCTCGAAC
1 TTCTAAAAATTACCATTTTACCC-CGAAC
* * *
538 TTCCAAAAA-TCCCATTTTTGGCCCCGAACC
1 TTCTAAAAATTACCA-TTTT-ACCCCGAA-C
* *
568 TTCTAAAAATTACAATTTTACCCTTGAAC
1 TTCTAAAAATTACCATTTTACCC-CGAAC
*
597 TTCTAAAAA-TCCCATTTTAGCCCCGAACC
1 TTCTAAAAATTACCATTTTA-CCCCGAA-C
626 TTCTAAAAATTACCATTTTACCCCTGAAC
1 TTCTAAAAATTACCATTTTACCCC-GAAC
* * *
655 TTCCAAAAA-TCCCATTTTTGGCCCCGAACC
1 TTCTAAAAATTACCA-TTTT-ACCCCGAA-C
*
685 TTCTAAAAATTACCATTTTACCCTCGAGC
1 TTCTAAAAATTACCATTTTACCC-CGAAC
* * *
714 TTCCAAAAA-TCCCATTTTTGGCCCCGAACC
1 TTCTAAAAATTACCA-TTTT-ACCCCGAA-C
744 TTCTAAAAATTACCATTTTACCCTCGAAC
1 TTCTAAAAATTACCATTTTACCC-CGAAC
* * *
773 TTCCAAAAATT-CAATTTTTGACCCCTAACC
1 TTCTAAAAATTACCA-TTTT-ACCCCGAA-C
803 TTCTAAAAATTACCATTTTACCCC
1 TTCTAAAAATTACCATTTTACCCC
827 CGAGCGTCCA
Statistics
Matches: 234, Mismatches: 31, Indels: 47
0.75 0.10 0.15
Matches are distributed among these distances:
27 4 0.02
28 29 0.12
29 98 0.42
30 90 0.38
31 13 0.06
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.32
Consensus pattern (28 bp):
TTCTAAAAATTACCATTTTACCCCGAAC
Found at i:1235 original size:96 final size:96
Alignment explanation
Indices: 1127--1388 Score: 375
Period size: 104 Copynumber: 2.7 Consensus size: 96
1117 CGGGTTTCGA
*
1127 AAAT-TTGCGCCTTAACTCACTAGGTTCAAATTTTCTTCAAATCGAAATAATCGAATACCCTTAA
1 AAATATTGCGCCTTAACTCACTAGGTGCAAATTTTCTTCAAATCGAAATAATCGAATACCCTTAA
1191 TCGAGGCAATGTTTCCTTATCTTCGATTCTG
66 TCGAGGCAATGTTTCCTTATCTTCGATTCTG
**
1222 AAATATTGCGCCTTAACTCACTAGGTGCANNNNNNNNNNTTTTCTTCAAATCGAAATAATCGAAT
1 AAATATTGCGCCTTAACTCACTAGGTGCA--------AATTTTCTTCAAATCGAAATAATCGAAT
1287 ACCCTTAATCGAGGCAATGTTTCCTTATCTTCGATTCTG
58 ACCCTTAATCGAGGCAATGTTTCCTTATCTTCGATTCTG
** *
1326 AAATATTGCGCCTTAACTCACTAGGTGC-AATCTTTCTTCAAATCGGGATAATCGAATATCCTT
1 AAATATTGCGCCTTAACTCACTAGGTGCAAAT-TTTCTTCAAATCGAAATAATCGAATACCCTT
1389 TTCCCGAAAA
Statistics
Matches: 149, Mismatches: 8, Indels: 19
0.85 0.05 0.11
Matches are distributed among these distances:
95 5 0.03
96 51 0.34
104 93 0.62
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.34
Consensus pattern (96 bp):
AAATATTGCGCCTTAACTCACTAGGTGCAAATTTTCTTCAAATCGAAATAATCGAATACCCTTAA
TCGAGGCAATGTTTCCTTATCTTCGATTCTG
Found at i:4773 original size:22 final size:22
Alignment explanation
Indices: 4718--4775 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
4708 CTCATTTCTG
* * *
4718 GTAGATCCTTTTAGTGCATCAA
1 GTAGATCCTTCTAGCGCATAAA
**
4740 GTAGATATTTCTAGCGCATAAA
1 GTAGATCCTTCTAGCGCATAAA
4762 GTAGATCCTTCTAG
1 GTAGATCCTTCTAG
4776 TACTTCGTAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (22 bp):
GTAGATCCTTCTAGCGCATAAA
Found at i:6601 original size:2 final size:2
Alignment explanation
Indices: 6594--6620 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6584 CCAACATCTT
6594 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6621 TTACATACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14870 original size:18 final size:18
Alignment explanation
Indices: 14847--14881 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
14837 ACGACAGGGC
*
14847 AACCAAAATACACAAATA
1 AACCAAAACACACAAATA
14865 AACCAAAACACACAAAT
1 AACCAAAACACACAAAT
14882 GACACGACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.26, G:0.00, T:0.09
Consensus pattern (18 bp):
AACCAAAACACACAAATA
Found at i:17208 original size:18 final size:20
Alignment explanation
Indices: 17170--17209 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
17160 AAATAGCTAG
17170 AATTATGAAATAAGAAAAAA
1 AATTATGAAATAAGAAAAAA
*
17190 AATT-TGAAA-AAGAAGAAA
1 AATTATGAAATAAGAAAAAA
17208 AA
1 AA
17210 GACGATTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (20 bp):
AATTATGAAATAAGAAAAAA
Found at i:17865 original size:14 final size:16
Alignment explanation
Indices: 17836--17868 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
17826 CTCTTATGTT
17836 CTTTTTGTTCTTTTTG
1 CTTTTTGTTCTTTTTG
17852 CTTTTT-TT-TTTTTG
1 CTTTTTGTTCTTTTTG
17866 CTT
1 CTT
17869 GAGGACAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 2 0.12
16 6 0.35
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (16 bp):
CTTTTTGTTCTTTTTG
Found at i:18500 original size:30 final size:30
Alignment explanation
Indices: 18466--18523 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
18456 CTTAGTTTTA
18466 CATACCTTTTCTCTTAGCTTATTCCCTTTG
1 CATACCTTTTCTCTTAGCTTATTCCCTTTG
*
18496 CATACCTTTTCTCTTAGCTTATTTCCTT
1 CATACCTTTTCTCTTAGCTTATTCCCTT
18524 CTTGTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.14, C:0.29, G:0.05, T:0.52
Consensus pattern (30 bp):
CATACCTTTTCTCTTAGCTTATTCCCTTTG
Found at i:32428 original size:43 final size:41
Alignment explanation
Indices: 32367--32447 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 41
32357 AATCCCAAAT
*
32367 CTCAAGGCTCAAGGTTTGGATTTAGGATTTAAGGTTTAGGG
1 CTCAAGGCTCAAGGTTTGGATTTAGGATTTAAGATTTAGGG
* * *
32408 CTCAAGGTTTCAAGGGTTTGGGTTTAGGGTTTAAGATTTA
1 CTCAAGG-CTCAA-GGTTTGGATTTAGGATTTAAGATTTA
32448 AAGTAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 7 0.21
42 4 0.12
43 23 0.68
ACGTcount: A:0.23, C:0.09, G:0.31, T:0.37
Consensus pattern (41 bp):
CTCAAGGCTCAAGGTTTGGATTTAGGATTTAAGATTTAGGG
Found at i:32888 original size:4 final size:4
Alignment explanation
Indices: 32881--32915 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
32871 TGATGCATGC
32881 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
32916 GTTATTATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:34120 original size:60 final size:61
Alignment explanation
Indices: 34048--34208 Score: 175
Period size: 60 Copynumber: 2.7 Consensus size: 61
34038 TTAGTATCTG
* *
34048 AACTTGACACTTTTTCCTAATTTGATACCTAAACTTTTTTTTCG-TCCAATTTGGTACCTA
1 AACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGCGATCCAATTTGGTACCTA
* ** * * * * *
34108 AACTTGAAACTTTTTTTTTAAGTTGGTACTTAAAC--TTTTTGGGATTCAATTTGGTACCTG
1 AACTTGACAC-TTTTTCCTAATTTGGTACCTAAACTTTTTTTGCGATCCAATTTGGTACCTA
* * *
34168 AACTTGACCCTTTTTCCTAATTCGGTACCTAATCTTTTTTT
1 AACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTT
34209 AATATTAATT
Statistics
Matches: 79, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
59 24 0.30
60 31 0.39
61 24 0.30
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.47
Consensus pattern (61 bp):
AACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGCGATCCAATTTGGTACCTA
Found at i:34418 original size:32 final size:31
Alignment explanation
Indices: 34382--34478 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 31
34372 CTTAGGTATA
34382 AAATTAGGAAAAAATTGTCAAGTTCAGGTACC
1 AAATTAGGAAAAAA-TGTCAAGTTCAGGTACC
* *
34414 AAATT-GGATCCAAAA----AAGTTTAGGTACC
1 AAATTAGGA--AAAAATGTCAAGTTCAGGTACC
* *
34442 AAATTAGAAAAAAAATGTCAAGTTCAAGTACC
1 AAATTAG-GAAAAAATGTCAAGTTCAGGTACC
34474 AAATT
1 AAATT
34479 GGGTCTAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
28 21 0.41
29 1 0.02
30 1 0.02
31 3 0.06
32 21 0.41
33 4 0.08
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (31 bp):
AAATTAGGAAAAAATGTCAAGTTCAGGTACC
Found at i:34502 original size:61 final size:60
Alignment explanation
Indices: 34349--34503 Score: 211
Period size: 60 Copynumber: 2.5 Consensus size: 60
34339 TAAATTTAGA
* * ** * * *
34349 TACCAAATTGAATCTAAAAAAAGCTTAGGTATAAAATTAGGAAAAAATTGTCAAGTTCAGG
1 TACCAAATTGGATCT-AAAAAAGTTTAGGTACCAAATTAGAAAAAAAATGTCAAGTTCAAG
*
34410 TACCAAATTGGATCCAAAAAAGTTTAGGTACCAAATTAGAAAAAAAATGTCAAGTTCAAG
1 TACCAAATTGGATCTAAAAAAGTTTAGGTACCAAATTAGAAAAAAAATGTCAAGTTCAAG
*
34470 TACCAAATTGGGTCTAAAATAAGTTTAGGTACCA
1 TACCAAATTGGATCTAAAA-AAGTTTAGGTACCA
34504 TAAGGCTATT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 56 0.67
61 27 0.33
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (60 bp):
TACCAAATTGGATCTAAAAAAGTTTAGGTACCAAATTAGAAAAAAAATGTCAAGTTCAAG
Found at i:36007 original size:7 final size:7
Alignment explanation
Indices: 35991--36039 Score: 91
Period size: 7 Copynumber: 7.1 Consensus size: 7
35981 GATCCACTTA
35991 TTTTTA-
1 TTTTTAT
35997 TTTTTAT
1 TTTTTAT
36004 TTTTTAT
1 TTTTTAT
36011 TTTTTAT
1 TTTTTAT
36018 TTTTTAT
1 TTTTTAT
36025 TTTTTAT
1 TTTTTAT
36032 TTTTTAT
1 TTTTTAT
36039 T
1 T
36040 AAAGAAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 6 0.14
7 36 0.86
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTAT
Found at i:38830 original size:28 final size:27
Alignment explanation
Indices: 38771--38847 Score: 73
Period size: 31 Copynumber: 2.7 Consensus size: 27
38761 AAAAGTGACC
*
38771 AATTACGGGGTATGATATGTAAATGGAT
1 AATTACAGGGTATGATATGTAAAT-GAT
38799 AATTACAGGGTATGGATATGTGAATATGAAT
1 AATTACAGGGTAT-GATATGT-AA-ATG-AT
* * *
38830 TATTACAAGGTTTGATAT
1 AATTACAGGGTATGATAT
38848 TGCAATTATG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 12 0.29
29 7 0.17
30 8 0.20
31 14 0.34
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (27 bp):
AATTACAGGGTATGATATGTAAATGAT
Found at i:44084 original size:25 final size:23
Alignment explanation
Indices: 44056--44101 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
44046 GTTGAATCCA
44056 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
44081 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
44102 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:47538 original size:16 final size:16
Alignment explanation
Indices: 47507--47549 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
47497 CCAAGTTTTT
47507 AAAA-GAAAAT-ATAA
1 AAAAGGAAAATAATAA
*
47521 AAAGGGAAAATAATAA
1 AAAAGGAAAATAATAA
47537 AAAAGGAAAATAA
1 AAAAGGAAAATAA
47550 CAAGAGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 3 0.12
15 6 0.24
16 16 0.64
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (16 bp):
AAAAGGAAAATAATAA
Found at i:54577 original size:17 final size:17
Alignment explanation
Indices: 54547--54626 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
54537 GGCCTATTGG
*
54547 AATTTGAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
54564 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
54581 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
*
54598 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
54615 AATTTAAATTTA
1 AATTTAAATTTA
54627 AAATATCCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:54602 original size:7 final size:6
Alignment explanation
Indices: 54547--54628 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
54537 GGCCTATTGG
* * * * *
54547 AATTTG AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
54592 -ATTTGA AATTTA AATTT- -ATTATA AATTTA AATTTA AA
1 AATTT-A AATTTA AATTTA AATT-TA AATTTA AATTTA AA
54629 ATATCCAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
4 7 0.11
5 9 0.15
6 38 0.62
7 7 0.11
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:54732 original size:15 final size:15
Alignment explanation
Indices: 54705--54743 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
54695 CTAACCTAAG
54705 CCCAAATTCTAAAAGA
1 CCCAAA-TCTAAAAGA
* *
54721 CCCAAATCTAAATGG
1 CCCAAATCTAAAAGA
54736 CCCAAATC
1 CCCAAATC
54744 AGCCCAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.18
Consensus pattern (15 bp):
CCCAAATCTAAAAGA
Found at i:56451 original size:30 final size:29
Alignment explanation
Indices: 56388--56833 Score: 374
Period size: 29 Copynumber: 15.1 Consensus size: 29
56378 GGAGGTCCCT
* *
56388 AAACTGTCCAGAAACTCCA-TTTTTACCCTC
1 AAACT-TCCAAAAATTCCATTTTTTACCC-C
*
56418 GAACTTCCAAAAATTCCATTTTTTTACCCC
1 AAACTTCCAAAAATTCCA-TTTTTTACCCC
* * * *
56448 GAACTTCCAAAAA-ACCTATTTTTGACCTCA
1 AAACTTCCAAAAATTCC-ATTTTTTACC-CC
*
56478 AAACTTCCAAAATTTCCA-TTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTTACCC-C
* * *
56507 GAACTTCCAAAAATCCCATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTTTACCCC
* *
56536 AAAACTTCC-AAAATTTC-TATTTTACCCCC
1 -AAACTTCCAAAAATTCCATTTTTTA-CCCC
* *
56565 AAACTTCCAAAAATCCCATTTTTGACCCCC
1 AAACTTCCAAAAATTCCATTTTTTA-CCCC
56595 AAAACTTCCAAAAATTCCA-TTTTTACACCC
1 -AAACTTCCAAAAATTCCATTTTTTAC-CCC
* * *
56625 AAACTTCCAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTTACCC-C
*
56655 AAACTTCCAAAATTTCCA-TTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTTACCCC
* *
56683 TAAACTTCCAAAAA-TCTCATTTTTAACCCTA
1 -AAACTTCCAAAAATTC-CATTTTTTACCC-C
*
56714 AAACTTCCAAAAATTCTA-TTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTTACCC-C
* * * *
56743 GAACTTCTAAAAATCCCATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTTTACCCC
* * *
56772 AAAACTCCCAAAAATTCTA-TTTTTACCCT
1 -AAACTTCCAAAAATTCCATTTTTTACCCC
*
56801 AGAACTT-CAAAAATTCCCATTTTTAACCCC
1 A-AACTTCCAAAAATT-CCATTTTTTACCCC
56831 AAA
1 AAA
56834 ACTCCTAAAA
Statistics
Matches: 336, Mismatches: 55, Indels: 51
0.76 0.12 0.12
Matches are distributed among these distances:
28 25 0.07
29 142 0.42
30 139 0.41
31 30 0.09
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTTACCCC
Found at i:56510 original size:59 final size:58
Alignment explanation
Indices: 56419--56845 Score: 554
Period size: 59 Copynumber: 7.2 Consensus size: 58
56409 TTTACCCTCG
* * * *
56419 AACTTCCAAAAATTCCATTTTTTTACCCCGAACTTCCAAAAAACCTATTTTTGACCTCAA
1 AACTTCCAAAAATTCCA--TTTTTACCCCGAACTTCCAAAAATCCCATTTTTAACCCCAA
*
56479 AACTTCCAAAATTTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATCCCATTTTTAACCCCAA
* * * *
56538 AACTTCCAAAATTTCTA-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCCAA
1 AACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTT-AACCCCAA
* *
56597 AACTTCCAAAAATTCCATTTTTACACCCAAACTTCCAAAAATCCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTTAC-CCCGAACTTCCAAAAATCCCATTTTTAACCCCAA
* * * *
56656 AACTTCCAAAATTTCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTTACCCC-GAACTTCCAAAAATCCCATTTTTAACCCCAA
* *
56715 AACTTCCAAAAATTCTATTTTTACCCTCGAACTTCTAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATCCCATTTTTAACCCCAA
* * *
56774 AACTCCCAAAAATTCTATTTTTACCCTAGAACTT-CAAAAATTCCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAA-TCCCATTTTTAACCCCAA
56833 AAC-TCCTAAAAAT
1 AACTTCC-AAAAAT
56846 AACATTTTAA
Statistics
Matches: 334, Mismatches: 24, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
58 47 0.14
59 239 0.72
60 48 0.14
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.32
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCCCATTTTTAACCCCAA
Found at i:56853 original size:29 final size:29
Alignment explanation
Indices: 56419--56884 Score: 361
Period size: 30 Copynumber: 15.7 Consensus size: 29
56409 TTTACCCTCG
* * *
56419 AACTTCCAAAAATTCCATTTTTTTACCCC-G
1 AACTTCCAAAAATCCCA--TTTTAACCCCAA
* * * *
56449 AACTTCCAAAAAACCTATTTTTGACCTCAA
1 AACTTCCAAAAATCCCA-TTTTAACCCCAA
* * * *
56479 AACTTCCAAAATTTCCATTTTTACCCTC-G
1 AACTTCCAAAAATCCCATTTTAACCC-CAA
56508 AACTTCCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCA-TTTTAACCCCAA
* * * *
56538 AACTTCCAAAATTTCTATTTT-ACCCCCA
1 AACTTCCAAAAATCCCATTTTAACCCCAA
*
56566 AACTTCCAAAAATCCCATTTTTGACCCCCAA
1 AACTTCCAAAAATCCCA-TTTT-AACCCCAA
* *
56597 AACTTCCAAAAATTCCATTTTTACACCC-A
1 AACTTCCAAAAATCCCATTTTAAC-CCCAA
*
56626 AACTTCCAAAAATCCCATTTTTAACCCTAA
1 AACTTCCAAAAATCCCA-TTTTAACCCCAA
* * * *
56656 AACTTCCAAAATTTCCATTTTTACCCCTA
1 AACTTCCAAAAATCCCATTTTAACCCCAA
* *
56685 AACTTCCAAAAATCTCATTTTTAACCCTAA
1 AACTTCCAAAAATCCCA-TTTTAACCCCAA
* * * *
56715 AACTTCCAAAAATTCTATTTTTACCCTC-G
1 AACTTCCAAAAATCCCATTTTAACCC-CAA
*
56744 AACTTCTAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCA-TTTTAACCCCAA
* * * * * *
56774 AACTCCCAAAAATTCTATTTTTACCCTAG
1 AACTTCCAAAAATCCCATTTTAACCCCAA
56803 AACTT-CAAAAATTCCCATTTTTAACCCCAA
1 AACTTCCAAAAA-TCCCA-TTTTAACCCCAA
** *
56833 AAC-TCCTAAAAATAACATTTTAAACCCAA
1 AACTTCC-AAAAATCCCATTTTAACCCCAA
* *
56862 AATCTTTCCAAAATTACCATTTT
1 AA-C-TTCCAAAAATCCCATTTT
56885 GCCCTCGGGT
Statistics
Matches: 343, Mismatches: 72, Indels: 41
0.75 0.16 0.09
Matches are distributed among these distances:
28 26 0.08
29 136 0.40
30 140 0.41
31 38 0.11
32 3 0.01
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTAACCCCAA
Found at i:68984 original size:206 final size:206
Alignment explanation
Indices: 68629--69178 Score: 944
Period size: 206 Copynumber: 2.7 Consensus size: 206
68619 AAATGACGCA
* * *
68629 GTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACTCACGCTCGATGCGAGTAAATC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGCGAGCAAATC
68694 TTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCC
66 TTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCC
*
68759 TGATGAGATACTGAGAAGTGAACCAAATTCAG-CTTCCTGA-TGAGATACAGAGAAGCGGATTGA
131 TGATGAGATACTAAGAAGTGAACCAAATTC-GTCTTCCTGATTG-GATACAGAGAAGCGGATTGA
68822 AACAAGCGATGCG
194 AACAAGCGATGCG
* *
68835 GTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAATGCGAGCAAATC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGCGAGCAAATC
*
68900 TTCAAACCCCAGCTTCCTGATGAGATA-TCGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTC
66 TTCGAACCCCAGCTTCCTGATGAGATACT-GAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTC
*
68964 CTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCTTGATTGGATACAGAGAAGCGGATTGAA
130 CTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATTGGATACAGAGAAGCGGATTGAA
69029 ACAAGCGATGCG
195 ACAAGCGATGCG
* *
69041 GTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGCGAGCAAATC
* *
69106 TTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATAATAAAATGGTTAGCCTCC
66 TTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCC
69171 TGATGAGA
131 TGATGAGA
69179 CACAGAGAAG
Statistics
Matches: 325, Mismatches: 15, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
205 2 0.01
206 320 0.98
207 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.22
Consensus pattern (206 bp):
GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGCGAGCAAATC
TTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCC
TGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATTGGATACAGAGAAGCGGATTGAAA
CAAGCGATGCG
Found at i:69652 original size:17 final size:17
Alignment explanation
Indices: 69624--69703 Score: 124
Period size: 17 Copynumber: 4.7 Consensus size: 17
69614 GGCCTATTGG
69624 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* *
69641 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTTTA
*
69658 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTTA
*
69675 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
69692 AATTTAAATTTA
1 AATTTAAATTTA
69704 AAATGTCCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:69679 original size:7 final size:6
Alignment explanation
Indices: 69624--69705 Score: 68
Period size: 6 Copynumber: 14.3 Consensus size: 6
69614 GGCCTATTGG
* * * *
69624 AATTTA AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
69669 -ATTTGA AATTTA AATTT- -ATTATA AATTTA AATTTA AA
1 AATTT-A AATTTA AATTTA AATT-TA AATTTA AATTTA AA
69706 ATGTCCAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
4 7 0.11
5 9 0.15
6 38 0.62
7 7 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:70665 original size:6 final size:6
Alignment explanation
Indices: 70654--70705 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
70644 NNNNNNNNNN
70654 TTTAAA TTTAAA TTT--A TTTGAAA TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TT-TAAA TTTAAA
70700 TTTAAA
1 TTTAAA
70706 ATGTCCAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
4 7 0.17
5 1 0.03
6 25 0.62
7 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:70679 original size:17 final size:17
Alignment explanation
Indices: 70656--70703 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
70646 NNNNNNNNTT
70656 TAAATTTAAATTTATT-
1 TAAATTTAAATTTATTA
70672 TGAAATTTAAATTTATTA
1 T-AAATTTAAATTTATTA
70690 TAAATTTAAATTTA
1 TAAATTTAAATTTA
70704 AAATGTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.03
17 28 0.93
18 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTA
Found at i:71593 original size:1000 final size:990
Alignment explanation
Indices: 69653--71643 Score: 3892
Period size: 1000 Copynumber: 2.0 Consensus size: 990
69643 ATTAAGTTTA
69653 TTTTAAATTTAAATTTATTTGAAATTTAAATTTATTATAAATTTAAATTTAAAATGTCCAATTAA
1 TTTTAAATTTAAATTTATTTGAAATTTAAATTTATTATAAATTTAAATTTAAAATGTCCAATTAA
69718 AAGTCCAAAACAAGTACAGATGTCCACTTTACAAACTCAAATTGGGCCCAAATGCTAACCTAAGT
66 AAGTCCAAAACAAGTACAGATGTCCACTTTACAAACTCAAATTGGGCCCAAATGCTAACCTAAGT
69783 CCAAATTCTAAAAGACCCAAACCTAAATGGCCCAAATCAGCCCAAAACCATTACACCCAAAAAAC
131 CCAAATTCTAAAAGACCCAAACCTAAATGGCCCAAATCAGCCCAAAACCATTACACCCAAAAAAC
69848 CTAATCTGCTAAGTGTCACTGCTGCTACCTCTACCCCAGCCAACCAGAGACCACCACGTCATCAG
196 CTAATCTGCTAAGTGTCACTGCTGCTACCTCTACCCCAGCCAACCAGAGACCACCACGTCATCAG
69913 CAACTTGCCACCATCTTCAGCATCCACTTGCCTCTACAATAACCGCCACTGTTACAAGCCACTGC
261 CAACTTGCCACCATCTTCAGCATCCACTTGCCTCTACAATAACCGCCACTGTTACAAGCCACTGC
69978 CATAGCCGAACCTGCAAAAGGAAAAGAAGACGAGCATTAAATTGTAAAACGACTTTTGTTCATAT
326 CATAGCCGAACCTGCAAAAGGAAAAGAAGACGAGCATTAAATTGTAAAACGACTTTTGTTCATAT
70043 GAATACCACAAATCAATAGCAAGCAGAGATATCGAAATAGACCTAAGGCAACAAACACAAGTTCG
391 GAATACCACAAATCAATAGCAAGCAGAGATATCGAAATAGACCTAAGGCAACAAACACAAGTTCG
70108 AACCGGATCTCAAAACCAGAGTGCGTCGAAACATTCAAGTACAGTTTCAATGTGTTTATTACTAT
456 AACCGGATCTCAAAACCAGAGTGCGTCGAAACATTCAAGTACAGTTTCAATGTGTTTATTACTAT
70173 TCATGATTCACACGTCTAAACTCAACAGTCTCTAACACACCCATTAATGCATGTTAAGAGTCTAT
521 TCATGATTCACACGTCTAAACTCAACAGTCTCTAACACACCCATTAATGCATGTTAAGAGTCTAT
70238 ACTGTCACCATTTATTACTTTTTTTCGTTTTAAAAAGCGTAATAAATATATATATTAAATGCTTT
586 ACTGTCACCATTTATTACTTTTTTTCGTTTTAAAAAGCGTAATAAATATATATATTAAATGCTTT
70303 AATAATTTTAATAATAATACCTCTAATAACAGACGGTGGTAATATATGACATTAATATTAATAAT
651 AATAATTTTAATAATAATACCTCTAATAACAGACGGTGGTAATATATGACATTAATATTAATAAT
70368 AAAATTTTAATTAATAATAACTGTTAGTAATTAATAATAAAGAAGAGAGAAATTCGAATGGACGT
716 AAAATTTTAATTAATAATAACTGTTAGTAATTAATAATAAAGAAGAGAGAAATTCGAATGGACGT
70433 ATCTGGGTCGGAACCGCTCTCGGAGCCGTCACCGTCGCAAAACCACGAACCTCGCCAACGCTTCG
781 ATCTGGGTCGGAACCGCTCTCGGAGCCGTCACCGTCGCAAAACCACGAACCTCGCCAACGCTTCG
70498 TCATCCGTGGATCTGCAAAAAAAAAAACAAAGAATCAAAATGATCAATATTAAAATAAAAAACAG
846 TCATCCGTGGATCTGCAAAAAAAAAAACAAAGAATCAAAATGATCAATATTAAAATAAAAAACAG
70563 TTTAAAAATGGGGAGTTTTAAAGAAAGGTTTAAAACACAAAAAAAAAAAAAACAGGGAGAAAAAG
911 TTTAAAAATGGGGAGTTTTAAAGAAAGGTTTAAAACACAAAAAAAAAAAAAACAGGGAGAAAAAG
70628 GAACGGTTTTTACCT
976 GAACGGTTTTTACCT
70643 TNNNNNNNNNNTTTAAATTTAAATTTATTTGAAATTTAAATTTATTATAAATTTAAATTTAAAAT
1 T----------TTTAAATTTAAATTTATTTGAAATTTAAATTTATTATAAATTTAAATTTAAAAT
70708 GTCCAATTAAAAGTCCAAAACAAGTACAGATGTCCACTTTACAAACTCAAATTGGGCCCAAATGC
56 GTCCAATTAAAAGTCCAAAACAAGTACAGATGTCCACTTTACAAACTCAAATTGGGCCCAAATGC
70773 TAACCTAAGTCCAAATTCTAAAAGACCCAAACCTAAATGGCCCAAATCAGCCCAAAACCATTACA
121 TAACCTAAGTCCAAATTCTAAAAGACCCAAACCTAAATGGCCCAAATCAGCCCAAAACCATTACA
70838 CCCAAAAAACCTAATCTGCTAAGTGTCACTGCTGCTACCTCTACCCCAGCCAACCAGAGACCACC
186 CCCAAAAAACCTAATCTGCTAAGTGTCACTGCTGCTACCTCTACCCCAGCCAACCAGAGACCACC
70903 ACGTCATCAGCAACTTGCCACCATCTTCAGCATCCACTTGCCTCTACAATAACCGCCACTGTTAC
251 ACGTCATCAGCAACTTGCCACCATCTTCAGCATCCACTTGCCTCTACAATAACCGCCACTGTTAC
70968 AAGCCACTGCCATAGCCGAACCTGCAAAAGGAAAAGAAGACGAGCATTAAATTGTAAAACGACTT
316 AAGCCACTGCCATAGCCGAACCTGCAAAAGGAAAAGAAGACGAGCATTAAATTGTAAAACGACTT
71033 TTGTTCATATGAATACCACAAATCAATAGCAAGCAGAGATATCGAAATAGACCTAAGGCAACAAA
381 TTGTTCATATGAATACCACAAATCAATAGCAAGCAGAGATATCGAAATAGACCTAAGGCAACAAA
71098 CACAAGTTCGAACCGGATCTCAAAACCAGAGTGCGTCGAAACATTCAAGTACAGTTTCAATGTGT
446 CACAAGTTCGAACCGGATCTCAAAACCAGAGTGCGTCGAAACATTCAAGTACAGTTTCAATGTGT
71163 TTATTACTATTCATGATTCACACGTCTAAACTCAACAGTCTCTAACACACCCATTAATGCATGTT
511 TTATTACTATTCATGATTCACACGTCTAAACTCAACAGTCTCTAACACACCCATTAATGCATGTT
71228 AAGAGTCTATACTGTCACCATTTATTACTTTTTTTCGTTTTAAAAAGCGTAATAAATATATATAT
576 AAGAGTCTATACTGTCACCATTTATTACTTTTTTTCGTTTTAAAAAGCGTAATAAATATATATAT
71293 TAAATGCTTTAATAATTTTAATAATAATACCTCTAATAACAGACGGTGGTAATATATGACATTAA
641 TAAATGCTTTAATAATTTTAATAATAATACCTCTAATAACAGACGGTGGTAATATATGACATTAA
71358 TATTAATAATAAAATTTTAATTAATAATAACTGTTAGTAATTAATAATAAAGAAGAGAGAAATTC
706 TATTAATAATAAAATTTTAATTAATAATAACTGTTAGTAATTAATAATAAAGAAGAGAGAAATTC
71423 GAATGGACGTATCTGGGTCGGAACCGCTCTCGGAGCCGTCACCGTCGCAAAACCACGAACCTCGC
771 GAATGGACGTATCTGGGTCGGAACCGCTCTCGGAGCCGTCACCGTCGCAAAACCACGAACCTCGC
71488 CAACGCTTCGTCATCCGTGGATCTGCAAAAAAAAAAACAAAGAATCAAAATGATCAATATTAAAA
836 CAACGCTTCGTCATCCGTGGATCTGCAAAAAAAAAAACAAAGAATCAAAATGATCAATATTAAAA
71553 TAAAAAACAGTTTAAAAATGGGGAGTTTTAAAGAAAGGTTTAAAACACAAAAAAAAAAAAAACAG
901 TAAAAAACAGTTTAAAAATGGGGAGTTTTAAAGAAAGGTTTAAAACACAAAAAAAAAAAAAACAG
71618 GGAGAAAAAGGAACGGTTTTTACCT
966 GGAGAAAAAGGAACGGTTTTTACCT
71643 T
1 T
71644 NNNNNNNNNN
Statistics
Matches: 991, Mismatches: 0, Indels: 10
0.99 0.00 0.01
Matches are distributed among these distances:
990 1 0.00
1000 990 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (990 bp):
TTTTAAATTTAAATTTATTTGAAATTTAAATTTATTATAAATTTAAATTTAAAATGTCCAATTAA
AAGTCCAAAACAAGTACAGATGTCCACTTTACAAACTCAAATTGGGCCCAAATGCTAACCTAAGT
CCAAATTCTAAAAGACCCAAACCTAAATGGCCCAAATCAGCCCAAAACCATTACACCCAAAAAAC
CTAATCTGCTAAGTGTCACTGCTGCTACCTCTACCCCAGCCAACCAGAGACCACCACGTCATCAG
CAACTTGCCACCATCTTCAGCATCCACTTGCCTCTACAATAACCGCCACTGTTACAAGCCACTGC
CATAGCCGAACCTGCAAAAGGAAAAGAAGACGAGCATTAAATTGTAAAACGACTTTTGTTCATAT
GAATACCACAAATCAATAGCAAGCAGAGATATCGAAATAGACCTAAGGCAACAAACACAAGTTCG
AACCGGATCTCAAAACCAGAGTGCGTCGAAACATTCAAGTACAGTTTCAATGTGTTTATTACTAT
TCATGATTCACACGTCTAAACTCAACAGTCTCTAACACACCCATTAATGCATGTTAAGAGTCTAT
ACTGTCACCATTTATTACTTTTTTTCGTTTTAAAAAGCGTAATAAATATATATATTAAATGCTTT
AATAATTTTAATAATAATACCTCTAATAACAGACGGTGGTAATATATGACATTAATATTAATAAT
AAAATTTTAATTAATAATAACTGTTAGTAATTAATAATAAAGAAGAGAGAAATTCGAATGGACGT
ATCTGGGTCGGAACCGCTCTCGGAGCCGTCACCGTCGCAAAACCACGAACCTCGCCAACGCTTCG
TCATCCGTGGATCTGCAAAAAAAAAAACAAAGAATCAAAATGATCAATATTAAAATAAAAAACAG
TTTAAAAATGGGGAGTTTTAAAGAAAGGTTTAAAACACAAAAAAAAAAAAAACAGGGAGAAAAAG
GAACGGTTTTTACCT
Found at i:72543 original size:29 final size:29
Alignment explanation
Indices: 72511--72988 Score: 504
Period size: 29 Copynumber: 16.2 Consensus size: 29
72501 CAGAAACTCT
*
72511 ATTTTTACCCTCGAACTTCCAAAAATTCC
1 ATTTTTACCCTCAAACTTCCAAAAATTCC
*
72540 ATTTTTGA-CCTCAAAACTTCCAAAAATTCT
1 ATTTTT-ACCCTC-AAACTTCCAAAAATTCC
*
72570 ATTTTTAACCC-CAAACTTCCAAAAATTCT
1 ATTTTT-ACCCTCAAACTTCCAAAAATTCC
* **
72599 ATTTTTGA-CCTCGAAACTTCCAAAATTTTT
1 ATTTTT-ACCCTC-AAACTTCCAAAAATTCC
* * *
72629 GTTTTTACCCCCAAACTTCCAAAAATCCC
1 ATTTTTACCCTCAAACTTCCAAAAATTCC
72658 ATTTTTAACCC-CGAAACTTCCAAAAATTCC
1 ATTTTT-ACCCTC-AAACTTCCAAAAATTCC
* *
72688 ATTTTTACCCCCAAACTTCCAAAAATCCC
1 ATTTTTACCCTCAAACTTCCAAAAATTCC
*
72717 ATTTTGA-CCTCGAAACTTCCAAAAATTCC
1 ATTTTTACCCTC-AAACTTCCAAAAATTCC
*
72746 ATTTTTACCCTCAAACTTCCAAAAATCCC
1 ATTTTTACCCTCAAACTTCCAAAAATTCC
* *
72775 ATTTTTAACCCTAAAACTCCCAAAAATTCC
1 ATTTTT-ACCCTCAAACTTCCAAAAATTCC
* *
72805 ATTTTTACCCCTAAAACTCCCAAAAATTCC
1 ATTTTTA-CCCTCAAACTTCCAAAAATTCC
*
72835 ATTTTTACCCTCGAACTTCCAAAAA-TCTC
1 ATTTTTACCCTCAAACTTCCAAAAATTC-C
*
72864 ATTTTTAACCC-CAAAACTCCCAAAAATTCC
1 ATTTTT-ACCCTC-AAACTTCCAAAAATTCC
* *
72894 ATTTTTACCCTCGAACTTCCAAAAATCCC
1 ATTTTTACCCTCAAACTTCCAAAAATTCC
* * *
72923 ATTTTTAACCTCAAAAC-TCCAAAAAATCT
1 ATTTTTACCCTC-AAACTTCCAAAAATTCC
* * *
72952 ATTTTTAAACCTCGAATCTTCCCAAAATTACC
1 ATTTTT-ACCCTC-AAACTTCCAAAAATT-CC
72984 ATTTT
1 ATTTT
72989 GCCTTCGGGT
Statistics
Matches: 386, Mismatches: 41, Indels: 41
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.02
29 193 0.50
30 168 0.44
31 12 0.03
32 6 0.02
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (29 bp):
ATTTTTACCCTCAAACTTCCAAAAATTCC
Found at i:72603 original size:59 final size:59
Alignment explanation
Indices: 72511--72988 Score: 542
Period size: 59 Copynumber: 8.1 Consensus size: 59
72501 CAGAAACTCT
* * * *
72511 ATTTTT-ACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCT
1 ATTTTTAACCC-CAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCC
* * * **
72570 ATTTTTAACCCCAAACTTCCAAAAATTCTATTTTTGACCTCGAAACTTCCAAAATTTTT
1 ATTTTTAACCCCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCC
* * * *
72629 GTTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATTCC
1 ATTTTTAACCCCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCC
* * *
72688 ATTTTTACCCCCAAACTTCCAAAAATCCCA-TTTTGACCTCGAAACTTCCAAAAATTCC
1 ATTTTTAACCCCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCC
* * *
72746 ATTTTT-ACCCTCAAACTTCCAAAAATCCCATTTTTAACC-CTAAAACTCCCAAAAATTCC
1 ATTTTTAACCC-CAAACTTCCAAAAATTCCATTTTTAACCTC-GAAACTTCCAAAAATTCC
* *
72805 ATTTTT-ACCCCTAAAACTCCCAAAAATTCCATTTTTACCCTCG-AACTTCCAAAAA-TCTC
1 ATTTTTAACCCC--AAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTC-C
* * *
72864 ATTTTTAACCCCAAAACTCCCAAAAATTCCATTTTTACCCTCG-AACTTCCAAAAATCCC
1 ATTTTTAACCCC-AAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCC
* * * * *
72923 ATTTTTAACCTCAAAAC-TCCAAAAAATCTATTTTTAAACCTCGAATCTTCCCAAAATTACC
1 ATTTTTAACC-CCAAACTTCCAAAAATTCCATTTTT-AACCTCGAAACTTCCAAAAATT-CC
72984 ATTTT
1 ATTTT
72989 GCCTTCGGGT
Statistics
Matches: 370, Mismatches: 35, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
57 3 0.01
58 70 0.19
59 243 0.66
60 46 0.12
61 8 0.02
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (59 bp):
ATTTTTAACCCCAAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCC
Found at i:73407 original size:96 final size:96
Alignment explanation
Indices: 73221--73395 Score: 230
Period size: 96 Copynumber: 1.8 Consensus size: 96
73211 AAAACTTTAA
* * **
73221 AATCGAGGCAATATTCTTTTATTTCGAGTTTCAAAAATTTGTGCCTTAACTCACCAGGTGCAATT
1 AATCGAGGCAATATTCTCTTATTTCGAGTTTCAAAAATTTGCGCCTTAACTCACCAGGTGCAACC
73286 TTTCTTCAAATCGAAATAACCGAATACCCTT
66 TTTCTTCAAATCGAAATAACCGAATACCCTT
** * *
73317 AATCGAGGCAATATT-TCCTTATCTTCGA--TTCTGAAATATTGCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTCT-CTTAT-TTCGAGTTTCAAAAAT-TTGCGCCTTAACTCACCAGGTGCA
73379 ACCTTTCTTCAAATCGA
63 ACCTTTCTTCAAATCGA
73396 GATAGTCGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 8 0.12
96 55 0.81
97 5 0.07
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (96 bp):
AATCGAGGCAATATTCTCTTATTTCGAGTTTCAAAAATTTGCGCCTTAACTCACCAGGTGCAACC
TTTCTTCAAATCGAAATAACCGAATACCCTT
Found at i:75031 original size:21 final size:21
Alignment explanation
Indices: 75007--75143 Score: 75
Period size: 21 Copynumber: 6.5 Consensus size: 21
74997 CTATACTGGT
*
75007 TGTTGTTTTTGTTGTTTTTAC
1 TGTTATTTTTGTTGTTTTTAC
** * * *
75028 TGTT-TTGATGCTATTTTTAT
1 TGTTATTTTTGTTGTTTTTAC
** *
75048 TGAAATTTTTATTGTTTTTAC
1 TGTTATTTTTGTTGTTTTTAC
* *
75069 TGCTATTTGTTGTT-ATTTTAC
1 TGTTATTT-TTGTTGTTTTTAC
75090 TGTTATTTTTGCTACTG-TTTTAC
1 TGTTATTTTTG-T--TGTTTTTAC
* **
75113 TTGTTGTTTTTGTTGTTTGGA-
1 -TGTTATTTTTGTTGTTTTTAC
75134 TGTTATTTTT
1 TGTTATTTTT
75144 TTATACGTTT
Statistics
Matches: 86, Mismatches: 22, Indels: 17
0.69 0.18 0.14
Matches are distributed among these distances:
20 25 0.29
21 36 0.42
22 7 0.08
23 8 0.09
24 10 0.12
ACGTcount: A:0.12, C:0.06, G:0.16, T:0.66
Consensus pattern (21 bp):
TGTTATTTTTGTTGTTTTTAC
Found at i:80542 original size:12 final size:12
Alignment explanation
Indices: 80525--80554 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
80515 TGACACACTG
80525 TATAAAAAAACA
1 TATAAAAAAACA
80537 TATAAAAAAACA
1 TATAAAAAAACA
80549 TA-AAAA
1 TATAAAA
80555 GATGATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (12 bp):
TATAAAAAAACA
Found at i:96808 original size:18 final size:18
Alignment explanation
Indices: 96781--96821 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
96771 CTGTATATGT
*
96781 TATATGATATGAA-AAAAA
1 TATATAATAT-AATAAAAA
96799 TATATAATATAATAAAAA
1 TATATAATATAATAAAAA
96817 TATAT
1 TATAT
96822 TAAGTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
TATATAATATAATAAAAA
Found at i:102103 original size:24 final size:26
Alignment explanation
Indices: 102075--102128 Score: 85
Period size: 24 Copynumber: 2.1 Consensus size: 26
102065 ATGTCTAGCA
102075 AAAGATCAAGTGG-A-AGAAGCAATG
1 AAAGATCAAGTGGCACAGAAGCAATG
102099 AAAGATCAAGTGGCAGCAGAAGCAATG
1 AAAGATCAAGTGGCA-CAGAAGCAATG
102126 AAA
1 AAA
102129 ACGAAGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 13 0.48
25 1 0.04
27 13 0.48
ACGTcount: A:0.50, C:0.11, G:0.28, T:0.11
Consensus pattern (26 bp):
AAAGATCAAGTGGCACAGAAGCAATG
Found at i:107329 original size:13 final size:13
Alignment explanation
Indices: 107311--107335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
107301 ATTGTAAAGC
107311 ATGTGAAAGTGTT
1 ATGTGAAAGTGTT
107324 ATGTGAAAGTGT
1 ATGTGAAAGTGT
107336 AAAAGTGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (13 bp):
ATGTGAAAGTGTT
Found at i:110063 original size:29 final size:30
Alignment explanation
Indices: 110031--110088 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
110021 ACAAAATAAT
*
110031 TATTGAATTAAT-AAAATTTTTTATTTAAA
1 TATTGAACTAATCAAAATTTTTTATTTAAA
* *
110060 TATTGAACTATTCGAAATTTTTTATTTAA
1 TATTGAACTAATCAAAATTTTTTATTTAA
110089 GTCATTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (30 bp):
TATTGAACTAATCAAAATTTTTTATTTAAA
Found at i:110983 original size:69 final size:69
Alignment explanation
Indices: 110907--111045 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
110897 AAAAGATTAG
*
110907 AAGTATATCTATTATTTAATCAGAATTGTTAAGTTCATTTCATTGGAAAATGTTTATTTTTTATG
1 AAGTATATCTATTATTTAATCAGAATTGTTAAGCTCATTTCATTGGAAAATGTTTATTTTTTATG
110972 CTGA
66 CTGA
*
110976 AAGTATATCTGTTATTTAATCAGAATTGTTAAGCTCATTTCATTGGAAAATGTTTATTTTTTATG
1 AAGTATATCTATTATTTAATCAGAATTGTTAAGCTCATTTCATTGGAAAATGTTTATTTTTTATG
111041 CTGA
66 CTGA
111045 A
1 A
111046 TTTTGAACCA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (69 bp):
AAGTATATCTATTATTTAATCAGAATTGTTAAGCTCATTTCATTGGAAAATGTTTATTTTTTATG
CTGA
Found at i:112930 original size:18 final size:18
Alignment explanation
Indices: 112893--112935 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
112883 GTTCAAGATA
112893 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
112911 TACTTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
112929 TAATTAA
1 TAATTAA
112936 AAACTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:113197 original size:31 final size:30
Alignment explanation
Indices: 113159--113279 Score: 98
Period size: 31 Copynumber: 3.9 Consensus size: 30
113149 CTTAATATAA
*
113159 AATTTGGTACTTGAACTTAATACTTTTTCCT
1 AATTTGGTACTTAAACTT-ATACTTTTTCCT
* * ** *
113190 AATTTGGTACCTAAACTTTTTTTTTTTGTCT
1 AATTTGGTACTTAAACTTATACTTTTT-CCT
* * *
113221 AATTTGGTACTCAAACTTGACACGTTTTCCT
1 AATTTGGTACTTAAACTT-ATACTTTTTCCT
* * *
113252 AATTTGATACTTAACCTTGACACTTTTT
1 AATTTGGTACTTAAACTT-ATACTTTTT
113280 TTTAAAGTTG
Statistics
Matches: 70, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
30 6 0.09
31 60 0.86
32 4 0.06
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (30 bp):
AATTTGGTACTTAAACTTATACTTTTTCCT
Found at i:113679 original size:59 final size:59
Alignment explanation
Indices: 113515--113703 Score: 265
Period size: 58 Copynumber: 3.2 Consensus size: 59
113505 TAATACATTT
* * * * *
113515 AGGTACCAAATTGAATCTAAAATAAAGCTTAGGTGCCAAATTAGGAAAATATGCCAAGTTT
1 AGGTACCAAATTGAGTCTAAAA-AAAG-TTAGGTACCAAATTAGGAAAAAATGTCAAGTTC
*
113576 AGGTACCAAATTGGGTCTAAAAAAA-TTAGGTACCAAATTAGGAAAAAATGTCAAGTTC
1 AGGTACCAAATTGAGTCTAAAAAAAGTTAGGTACCAAATTAGGAAAAAATGTCAAGTTC
* *
113634 AGGTATCAAATTGAGTC-AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTGAGTCTAAAAAAAG-TTAGGTACCAAATTAGGAAAAAATGTCAAGTTC
113693 AGGTACCAAAT
1 AGGTACCAAAT
113704 ATTATATTAA
Statistics
Matches: 116, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
57 7 0.06
58 44 0.38
59 42 0.36
60 3 0.03
61 20 0.17
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (59 bp):
AGGTACCAAATTGAGTCTAAAAAAAGTTAGGTACCAAATTAGGAAAAAATGTCAAGTTC
Found at i:116266 original size:11 final size:11
Alignment explanation
Indices: 116238--116269 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
116228 GCAAAAAGAA
*
116238 CGAAAAACGAG
1 CGAAAATCGAG
116249 CGAAAATCGAG
1 CGAAAATCGAG
116260 CGAAAATCGA
1 CGAAAATCGA
116270 AGCAGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (11 bp):
CGAAAATCGAG
Found at i:117660 original size:19 final size:18
Alignment explanation
Indices: 117611--117660 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
117601 AAAATAATAA
117611 ATTTTTATTTTTTTAAAT
1 ATTTTTATTTTTTTAAAT
*
117629 ATTTTTGAGTTTTTTT-TAT
1 ATTTTT-A-TTTTTTTAAAT
117648 ATATTTTATTTTT
1 AT-TTTTATTTTT
117661 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 11 0.39
19 6 0.21
20 11 0.39
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (18 bp):
ATTTTTATTTTTTTAAAT
Found at i:117850 original size:31 final size:29
Alignment explanation
Indices: 117815--117875 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
117805 ACTAATTTCA
117815 ATTTTGAATTTAATCAAAATAAAAAAAAATT
1 ATTTTGAATTTAAT-AAAA-AAAAAAAAATT
* * **
117846 ATTTTTATTTTTGTAAAAAAAAAAAAATT
1 ATTTTGAATTTAATAAAAAAAAAAAAATT
117875 A
1 A
117876 ATCAATTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 12 0.46
30 4 0.15
31 10 0.38
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
ATTTTGAATTTAATAAAAAAAAAAAAATT
Found at i:118236 original size:23 final size:22
Alignment explanation
Indices: 118197--118248 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
118187 AATTTCGTGT
* *
118197 TCAAATTTGCAAATAAAAAAAC
1 TCAATTTTGCAAATAAAAAAAA
118219 TCCAATTTTG-AAATTAAAAAAAA
1 T-CAATTTTGCAAA-TAAAAAAAA
118242 TCAATTT
1 TCAATTT
118249 GGCTCCTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.31
Consensus pattern (22 bp):
TCAATTTTGCAAATAAAAAAAA
Found at i:120838 original size:24 final size:24
Alignment explanation
Indices: 120805--120857 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
120795 ACAACGAGGC
120805 AAGAT-TGGTTAAGTTGCAGACAG
1 AAGATGTGGTTAAGTTGCAGACAG
120828 AAGATGTGGTTAAGTTGCAGACAG
1 AAGATGTGGTTAAGTTGCAGACAG
120852 AAGATG
1 AAGATG
120858 GGATTGGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.25
Consensus pattern (24 bp):
AAGATGTGGTTAAGTTGCAGACAG
Found at i:121094 original size:144 final size:144
Alignment explanation
Indices: 120828--121163 Score: 564
Period size: 144 Copynumber: 2.3 Consensus size: 144
120818 TTGCAGACAG
* *
120828 AAGATGTGGTTAAGTTGCAGACAGAAGATGGGATTGGACCAACAAGCCTATTGTAGGATAGATCC
1 AAGAT-TGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGCCTATTGGAGGATAGATCC
* * * ** *
120893 AATTTAACCAAATTCGTTAGTCTCCCAATATTTTCTGGAATGGATCCATTAAGTTGGTTGCTTTG
65 AATTCAACCAAATTCCTTAGTCTCCCAATATCTTCTGGAATGGAAACATCAAGTTGGTTGCTTTG
*
120958 AAGGAACAAGGAGGT
130 AAGGAACAAGGAGGC
*
120973 AAGATTGGTTAAGTTGCTGACAGAAGATGGGATTGAACCAACAAGCCTATTGGAGGATAGATCCA
1 AAGATTGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGCCTATTGGAGGATAGATCCA
*
121038 ATTCAACCAAATTCCTTAGTCTCCTAATATCTTCTGGAATGGAAACATCAAGTTGGTTGCTTTGA
66 ATTCAACCAAATTCCTTAGTCTCCCAATATCTTCTGGAATGGAAACATCAAGTTGGTTGCTTTGA
121103 AGGAACAAGGAGGC
131 AGGAACAAGGAGGC
121117 AAGATTGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGCC
1 AAGATTGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGCC
121164 CGTTATTTGA
Statistics
Matches: 179, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
144 174 0.97
145 5 0.03
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (144 bp):
AAGATTGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGCCTATTGGAGGATAGATCCA
ATTCAACCAAATTCCTTAGTCTCCCAATATCTTCTGGAATGGAAACATCAAGTTGGTTGCTTTGA
AGGAACAAGGAGGC
Found at i:121211 original size:144 final size:142
Alignment explanation
Indices: 120828--121211 Score: 463
Period size: 144 Copynumber: 2.7 Consensus size: 142
120818 TTGCAGACAG
* * * * *
120828 AAGATGTGGTTAAGTTGCAGACAGAAGATGGGATTGGACCAACAAGCCTATTGTAGGATAGATCC
1 AAGAT-TGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGCC-CTTATTGGAGAGATCC
* * * ** *
120893 AATTTAACCAAATTCGT-TAGTCTCCCAATATTTTCTGGAATGGATCCATTAAGTTGGTTGCTTT
64 AATTCAACCAAATTC-TCTAGT-TTCCAATATCTTCTGGAATGGAAACATCAAGTTGGTTGCTTT
*
120957 GAAGGAACAAGGAGGT
127 GAAGGAACAAGGAGGC
*
120973 AAGATTGGTTAAGTTGCTGACAGAAGATGGGATTGAACCAACAAG-CC-TATTGGAGGATAGATC
1 AAGATTGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGCCCTTATTGGA-G--AGATC
*
121036 CAATTCAACCAAATTC-CTTAGTCTCCTAATATCTTCTGGAATGGAAACATCAAGTTGGTTGCTT
63 CAATTCAACCAAATTCTC-TAGTTTCC-AATATCTTCTGGAATGGAAACATCAAGTTGGTTGCTT
121100 TGAAGGAACAAGGAGGC
126 TGAAGGAACAAGGAGGC
*
121117 AAGATTGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGCCCGTTATTTGAGAGAT-CA
1 AAGATTGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGCCC-TTATTGGAGAGATCCA
* * *
121181 AGATCAACCATACTCTCTAGCTTTCCAATAT
65 A-TTCAACCAAATTCTCTAG-TTTCCAATAT
121212 TTGGTGGAAT
Statistics
Matches: 207, Mismatches: 20, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
141 5 0.02
143 6 0.03
144 177 0.86
145 12 0.06
146 1 0.00
147 6 0.03
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (142 bp):
AAGATTGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGCCCTTATTGGAGAGATCCAA
TTCAACCAAATTCTCTAGTTTCCAATATCTTCTGGAATGGAAACATCAAGTTGGTTGCTTTGAAG
GAACAAGGAGGC
Found at i:123678 original size:44 final size:45
Alignment explanation
Indices: 123630--123722 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 45
123620 TATTGACCGT
* * *
123630 TTTTTATTAGTATATTGTTAGTGTAG-TTTTAAACTTCATTAATA
1 TTTTTATTAATATATTGTTAATGTAGTTTTTAAACTTCACTAATA
123674 TTTTTATTAATATATTGTTAATGTAGTTTTTAAACTTCACTAATA
1 TTTTTATTAATATATTGTTAATGTAGTTTTTAAACTTCACTAATA
123719 TTTT
1 TTTT
123723 AATATATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 24 0.53
45 21 0.47
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (45 bp):
TTTTTATTAATATATTGTTAATGTAGTTTTTAAACTTCACTAATA
Found at i:124470 original size:17 final size:17
Alignment explanation
Indices: 124443--124538 Score: 102
Period size: 17 Copynumber: 5.5 Consensus size: 17
124433 AACTTTTAAT
*
124443 TTTTAAAATTTTAATTTA
1 TTTT-AAATTTAAATTTA
*
124461 TTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
**
124478 TTTTTAAATTTAAATTCG
1 -TTTTAAATTTAAATTTA
* *
124496 TTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
124513 CTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
124530 TTTTAAATT
1 TTTTAAATT
124539 AAAAAAATTG
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
17 46 0.72
18 18 0.28
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:126517 original size:59 final size:59
Alignment explanation
Indices: 126438--126678 Score: 247
Period size: 59 Copynumber: 4.1 Consensus size: 59
126428 CTGAAGTCTT
* *
126438 CAAAAATTACA-TTTTGACCTCGAAACTTCTAAAAATTACCATTTTACCCCCGAATGTC
1 CAAAAATTCCATTTTTGACCTCGAAACTTCTAAAAATTACCATTTTACCCCCAAATGTC
* * * * *
126496 CAAAAATTCAATTTTTAACCTCGAAACCTCTAAAAATTACTATTTTACACCCAAATAG-C
1 CAAAAATTCCATTTTTGACCTCGAAACTTCTAAAAATTACCATTTTACCCCCAAAT-GTC
* * * * **
126555 CAAAAATTCCATTTTCGACCCCAAAACTT-TCAAAAATTGCCATTTTACCCTTAAATGTC
1 CAAAAATTCCATTTTTGACCTCGAAACTTCT-AAAAATTACCATTTTACCCCCAAATGTC
* * * * * *
126614 CAAAAATACCATTTTTGACACT-TAAATTTCCAAAAATTACCATTTTACCCCTAAATTATC
1 CAAAAATTCCATTTTTGAC-CTCGAAACTTCTAAAAATTACCATTTTACCCCCAAA-TGTC
126674 CAAAA
1 CAAAA
126679 TTACCGTTTT
Statistics
Matches: 149, Mismatches: 27, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
58 11 0.07
59 128 0.86
60 10 0.07
ACGTcount: A:0.39, C:0.25, G:0.04, T:0.32
Consensus pattern (59 bp):
CAAAAATTCCATTTTTGACCTCGAAACTTCTAAAAATTACCATTTTACCCCCAAATGTC
Found at i:126676 original size:30 final size:29
Alignment explanation
Indices: 126438--126693 Score: 166
Period size: 29 Copynumber: 8.7 Consensus size: 29
126428 CTGAAGTCTT
* * *
126438 CAAAAATTA-CATTTTGACCTCGAAACTTC
1 CAAAAATTACCATTTT-ACCCCTAAATTTC
* ** *
126467 TAAAAATTACCATTTTACCCCCGAATGTC
1 CAAAAATTACCATTTTACCCCTAAATTTC
* * * **
126496 CAAAAATT-CAATTTTTAACCTCGAAACCTC
1 CAAAAATTACCA-TTTT-ACCCCTAAATTTC
* * **
126526 TAAAAATTACTATTTTACACCC-AAATAGC
1 CAAAAATTACCATTTTAC-CCCTAAATTTC
*
126555 CAAAAATT-CCATTTTCGACCCCAAAACTTT-
1 CAAAAATTACCATTTT--ACCCCTAAA-TTTC
* * *
126585 CAAAAATTGCCATTTTACCCTTAAATGTC
1 CAAAAATTACCATTTTACCCCTAAATTTC
* *
126614 CAAAAA-TACCATTTTTGACACTTAAATTTC
1 CAAAAATTACCA-TTTT-ACCCCTAAATTTC
126644 CAAAAATTACCATTTTACCCCTAAATTATC
1 CAAAAATTACCATTTTACCCCTAAATT-TC
*
126674 C-AAAATTACCGTTTTACCCC
1 CAAAAATTACCATTTTACCCC
126694 CATGCATCCA
Statistics
Matches: 180, Mismatches: 32, Indels: 30
0.74 0.13 0.12
Matches are distributed among these distances:
28 14 0.08
29 87 0.48
30 64 0.36
31 15 0.08
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCTAAATTTC
Done.