Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001175.1 Hibiscus syriacus cultivar Beakdansim tig00002341_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 212349
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:127680 original size:49 final size:51
Alignment explanation
Indices: 127622--127727 Score: 189
Period size: 49 Copynumber: 2.1 Consensus size: 51
127612 GTATCCTTAT
*
127622 TTATTTATCTATCTTATTTATTTTATTAGTATTATATTAGTA-TTTTTT-A
1 TTATTTATCTATCTTATTCATTTTATTAGTATTATATTAGTATTTTTTTAA
127671 TTATTTATCTATCTTATTCATTTTATTAGTATTATATTAGTATTTTTTTAA
1 TTATTTATCTATCTTATTCATTTTATTAGTATTATATTAGTATTTTTTTAA
127722 TTATTT
1 TTATTT
127728 TTTTCATATA
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
49 41 0.76
50 6 0.11
51 7 0.13
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (51 bp):
TTATTTATCTATCTTATTCATTTTATTAGTATTATATTAGTATTTTTTTAA
Found at i:127743 original size:49 final size:48
Alignment explanation
Indices: 127622--127743 Score: 158
Period size: 49 Copynumber: 2.5 Consensus size: 48
127612 GTATCCTTAT
*
127622 TTATTTATCTATCTTATTTATTTTATTAGTATTATATTAGTATTTTTTA
1 TTATTTATCTATCATA-TTATTTTATTAGTATTATATTAGTATTTTTTA
*
127671 TTATTTATCTATCTTATTCATTTTATTAGTATTATATTAGTATTTTTTTAA
1 TTATTTATCTATCATATT-ATTTTATTAGTATTATATTAGTA-TTTTTT-A
*
127722 TTATTT-T-TTTCATATATATTTT
1 TTATTTATCTATCATAT-TATTTT
127744 TATTTTTTAA
Statistics
Matches: 67, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
48 2 0.03
49 50 0.75
50 8 0.12
51 7 0.10
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (48 bp):
TTATTTATCTATCATATTATTTTATTAGTATTATATTAGTATTTTTTA
Found at i:134445 original size:9 final size:9
Alignment explanation
Indices: 134423--134472 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
134413 CCGGTTTTCA
134423 ACCGGTTCTG
1 ACCGGTT-TG
134433 ACCGGTTTG
1 ACCGGTTTG
*
134442 ACCGGTCTG
1 ACCGGTTTG
134451 AACCGGTTTG
1 -ACCGGTTTG
*
134461 ACCGGTCTG
1 ACCGGTTTG
134470 ACC
1 ACC
134473 CGACCCGACC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
9 21 0.58
10 15 0.42
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:134447 original size:19 final size:18
Alignment explanation
Indices: 134423--134472 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
134413 CCGGTTTTCA
134423 ACCGGTTCTGACCGGTTTG
1 ACCGG-TCTGACCGGTTTG
134442 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTG-ACCGGTTTG
134461 ACCGGTCTGACC
1 ACCGGTCTGACC
134473 CGACCCGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.26
Consensus pattern (18 bp):
ACCGGTCTGACCGGTTTG
Found at i:134479 original size:5 final size:5
Alignment explanation
Indices: 134469--134538 Score: 59
Period size: 5 Copynumber: 12.8 Consensus size: 5
134459 TGACCGGTCT
* *
134469 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
134518 GACCGTT GACCC GACCC GACC
1 GACC--C GACCC GACCC GACC
134539 GTTGACCGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
5 41 0.77
7 12 0.23
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:134490 original size:17 final size:17
Alignment explanation
Indices: 134468--134545 Score: 111
Period size: 17 Copynumber: 4.3 Consensus size: 17
134458 TTGACCGGTC
134468 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
134485 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
134507 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
134524 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
134541 TGACC
1 TGACC
134546 GTTGACCGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
17 39 0.70
22 17 0.30
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:134495 original size:22 final size:22
Alignment explanation
Indices: 134469--134552 Score: 106
Period size: 22 Copynumber: 4.0 Consensus size: 22
134459 TGACCGGTCT
134469 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
134491 GACCCGACCCGACCGTT-----
1 GACCCGACCCGACCGTTGACCC
134508 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
134530 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
134553 GTTGACTTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
17 17 0.31
22 26 0.48
24 11 0.20
ACGTcount: A:0.18, C:0.46, G:0.24, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:141754 original size:10 final size:9
Alignment explanation
Indices: 141739--141817 Score: 86
Period size: 10 Copynumber: 8.3 Consensus size: 9
141729 CCGGTTTTCA
141739 ACCGGTTCTG
1 ACCGGTT-TG
141749 ACCGGTTTG
1 ACCGGTTTG
*
141758 ACCGGTTTCA
1 ACCGGTTT-G
*
141768 ACCGGTTCG
1 ACCGGTTTG
141777 AACCGGTTTG
1 -ACCGGTTTG
*
141787 ACCGGTCTG
1 ACCGGTTTG
141796 AACCGGTTTG
1 -ACCGGTTTG
*
141806 ACCGGTCTG
1 ACCGGTTTG
141815 ACC
1 ACC
141818 CGACCCGACC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
9 29 0.49
10 30 0.51
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:141763 original size:19 final size:19
Alignment explanation
Indices: 141738--141815 Score: 97
Period size: 19 Copynumber: 4.1 Consensus size: 19
141728 ACCGGTTTTC
*
141738 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
141758 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
141777 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
141796 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
141815 A
1 A
141816 CCCGACCCGA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.04
19 41 0.79
20 9 0.17
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:141781 original size:29 final size:28
Alignment explanation
Indices: 141719--141817 Score: 117
Period size: 29 Copynumber: 3.4 Consensus size: 28
141709 GCTGCTGGAA
**
141719 ACCGGTTAAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
141749 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
141777 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
*
141806 ACCGGTCTGACC
1 ACCGGTTTGACC
141818 CGACCCGACC
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 12 0.19
29 38 0.61
30 12 0.19
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.27
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:141824 original size:5 final size:5
Alignment explanation
Indices: 141814--141883 Score: 59
Period size: 5 Copynumber: 12.8 Consensus size: 5
141804 TGACCGGTCT
* *
141814 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
141863 GACCGTT GACCC GACCC GACC
1 GACC--C GACCC GACCC GACC
141884 GTTGACCGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
5 41 0.77
7 12 0.23
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:141835 original size:17 final size:17
Alignment explanation
Indices: 141813--141890 Score: 111
Period size: 17 Copynumber: 4.3 Consensus size: 17
141803 TTGACCGGTC
141813 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
141830 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
141852 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
141869 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
141886 TGACC
1 TGACC
141891 GTTGACCGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
17 39 0.70
22 17 0.30
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:141840 original size:22 final size:22
Alignment explanation
Indices: 141814--141897 Score: 106
Period size: 22 Copynumber: 4.0 Consensus size: 22
141804 TGACCGGTCT
141814 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
141836 GACCCGACCCGACCGTT-----
1 GACCCGACCCGACCGTTGACCC
141853 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
141875 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
141898 GTTGACTTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
17 17 0.31
22 26 0.48
24 11 0.20
ACGTcount: A:0.18, C:0.46, G:0.24, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:166920 original size:3 final size:3
Alignment explanation
Indices: 166912--166973 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
166902 AATATATATT
*
166912 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
166960 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
166974 TGGGTAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:167774 original size:228 final size:227
Alignment explanation
Indices: 167109--167869 Score: 1089
Period size: 228 Copynumber: 3.3 Consensus size: 227
167099 ATTGAATAAA
* * ** * *
167109 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGCTGATCCATC
167173 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
65 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* * * *
167238 AGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCA
130 AGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAATTGATGAATTCA
* * * *
167303 AGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
193 GGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * * *
167338 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTAGCAAAGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT-A--AGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCC
167402 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
62 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
167467 TTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGAA
127 TTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAA-TTGATGAA
*
167532 TTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
189 TTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
167571 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGACTGATCCATC
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG-CTGATCCATC
* ** * * *
167636 AAATGATGGATTCGGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
65 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* *
167701 AGAT-GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCA
130 AGATAGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCCATCAA-TTGATGAATTCA
*
167764 GGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
193 GGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * **
167799 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCTTTCA
1 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
167864 AATGAT
66 AATGAT
167870 AGATTTGAAT
Statistics
Matches: 487, Mismatches: 36, Indels: 20
0.90 0.07 0.04
Matches are distributed among these distances:
227 17 0.03
228 138 0.28
229 8 0.02
230 39 0.08
231 72 0.15
232 130 0.27
233 81 0.17
234 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (227 bp):
TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
AATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATAGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAATTGATGAATTCAGGA
AAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:167858 original size:114 final size:113
Alignment explanation
Indices: 167109--167852 Score: 1003
Period size: 116 Copynumber: 6.5 Consensus size: 113
167099 ATTGAATAAA
* ** *
167109 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGATGATCCATC
*
167173 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AAATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
* * * *
167222 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCC
*
167286 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
* * * *
167338 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTAGCAAAGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCC
*
167402 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
* * *
167454 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCC
* * *
167518 ATCAACTTGATGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
62 ATCAA-ATGATGAATTCAAG-CAAAAGATTGAACAAATTCTTCTCATTATGAAC
*
167571 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGACTGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGA-TGATCCATC
* ** * *
167636 AAATGATGGATTCGGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 AAATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
* *
167685 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
* * * *
167750 ATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-ATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
167799 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
167853 CTAATCTTTC
Statistics
Matches: 591, Mismatches: 29, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
113 18 0.03
114 232 0.39
115 11 0.02
116 247 0.42
117 81 0.14
118 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
AATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
Found at i:168741 original size:83 final size:83
Alignment explanation
Indices: 168602--169077 Score: 787
Period size: 83 Copynumber: 5.7 Consensus size: 83
168592 GTAGTTCTTA
*
168602 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
168667 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
168685 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATTTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
168750 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * * *
168768 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
168833 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
168851 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCC
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCA
168915 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* * *
168934 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
168999 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
169017 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTT
169078 TCATTTAATG
Statistics
Matches: 365, Mismatches: 24, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
82 1 0.00
83 361 0.99
84 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:168861 original size:166 final size:166
Alignment explanation
Indices: 168604--169079 Score: 875
Period size: 166 Copynumber: 2.9 Consensus size: 166
168594 AGTTCTTACC
*
168604 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAAT
168669 TCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
168733 GCATATTCATTTTCCCAATTCAATGATTGGTTCTGCT
130 GCATATTCATTTTCCCAATTCAATGATTGGTTCTGCT
*
168770 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAAT
168835 TCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
66 TCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
*
168900 CATATTCATCTTCCCAATTCAATGATTGGTTCTGCT
131 CATATTCATTTTCCCAATTCAATGATTGGTTCTGCT
168936 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAAT
169001 TCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-
66 TCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGA
*
169065 GCAAATTCATCTTTC
130 GCATATTCAT-TTTC
169080 ATTTAATGTT
Statistics
Matches: 301, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
166 294 0.98
167 7 0.02
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (166 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAAT
TCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
CATATTCATTTTCCCAATTCAATGATTGGTTCTGCT
Found at i:170129 original size:1 final size:1
Alignment explanation
Indices: 170125--170199 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
170115 TTTTCTTCTC
** * * * * * * * *
170125 TTTTTTTTTTCATTTTCTATTTTTTTTCTTTTCTTTTTTTTTTATTTTCTTTCTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
170190 TTTCTTTTTT
1 TTTTTTTTTT
170200 CTTCAAGCAT
Statistics
Matches: 53, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:170135 original size:16 final size:16
Alignment explanation
Indices: 170114--170202 Score: 108
Period size: 16 Copynumber: 5.5 Consensus size: 16
170104 ACCCCCTTTC
*
170114 TTTTTCTTCTCTTTTT
1 TTTTTCTTTTCTTTTT
*
170130 TTTTTCATTTTCTATTT
1 TTTTTC-TTTTCTTTTT
170147 TTTTTCTTTTCTTTTT
1 TTTTTCTTTTCTTTTT
* *
170163 TTTTTATTTTC-TTTC
1 TTTTTCTTTTCTTTTT
*
170178 TTTTTCTTTTTTTTTCT
1 TTTTTCTTTTCTTTT-T
170195 TTTTTCTT
1 TTTTTCTT
170203 CAAGCATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
15 12 0.19
16 28 0.45
17 22 0.35
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTT
Found at i:170140 original size:10 final size:9
Alignment explanation
Indices: 170110--170199 Score: 65
Period size: 10 Copynumber: 9.1 Consensus size: 9
170100 CTTGACCCCC
170110 TTTCTTTTT
1 TTTCTTTTT
170119 CTTCTCTTTTT
1 -TT-TCTTTTT
170130 TTT-TTCATTT
1 TTTCTT--TTT
* *
170140 TCTATTTTT
1 TTTCTTTTT
170149 TTTCTTTTCTT
1 TTTC-TTT-TT
*
170160 TTTTTTTTAT
1 TTTCTTTT-T
170170 TTTCTTTCTT
1 TTTCTTT-TT
170180 TTTCTTTTTT
1 TTTC-TTTTT
170190 TTTCTTTTT
1 TTTCTTTTT
170199 T
1 T
170200 CTTCAAGCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
8 2 0.03
9 13 0.20
10 33 0.50
11 18 0.27
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:170153 original size:33 final size:32
Alignment explanation
Indices: 170109--170200 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 32
170099 CCTTGACCCC
*
170109 CTTTCTTTTTCTTCTCTTTTTTTTTTCATTTT
1 CTTTCTTTTTCTTTTCTTTTTTTTTTCATTTT
*
170141 CTATTTTTTTTCTTTTCTTTTTTTTTT-ATTTT
1 CT-TTCTTTTTCTTTTCTTTTTTTTTTCATTTT
*
170173 CTTTCTTTTTCTTTTTTTTTCTTTTTTC
1 CTTTCTTTTTCTTTTCTTTT-TTTTTTC
170201 TTCAAGCATA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
31 16 0.30
32 15 0.28
33 22 0.42
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (32 bp):
CTTTCTTTTTCTTTTCTTTTTTTTTTCATTTT
Found at i:170165 original size:25 final size:25
Alignment explanation
Indices: 170114--170199 Score: 84
Period size: 25 Copynumber: 3.2 Consensus size: 25
170104 ACCCCCTTTC
*
170114 TTTTTCTTCTCTTTTTTTTTTCATTTTCTA
1 TTTTT-TT-TCTTTTTCTTTT--TTTT-TA
170144 TTTTTTTTC-TTTTCTTTTTTTTTTA
1 TTTTTTTTCTTTTTC-TTTTTTTTTA
* *
170169 TTTTCTTTCTTTTTCTTTTTTTTTC
1 TTTTTTTTCTTTTTCTTTTTTTTTA
170194 TTTTTT
1 TTTTTT
170200 CTTCAAGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
25 24 0.48
26 9 0.18
27 4 0.08
28 6 0.12
29 2 0.04
30 5 0.10
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (25 bp):
TTTTTTTTCTTTTTCTTTTTTTTTA
Found at i:180821 original size:13 final size:15
Alignment explanation
Indices: 180799--180835 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
180789 TTTGACAGAA
180799 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
180811 AAATAAAATACTTGC
1 AAATAAAATACTTGC
180826 AAATAAAATA
1 AAATAAAATA
180836 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:180874 original size:18 final size:17
Alignment explanation
Indices: 180826--180876 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
180816 AAATACTTGC
*
180826 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
180844 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
180862 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
180877 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:181629 original size:20 final size:20
Alignment explanation
Indices: 181606--181644 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
181596 AAATATAAAC
*
181606 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
181626 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
181645 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:183052 original size:3 final size:3
Alignment explanation
Indices: 183044--183111 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
183034 AATATATATT
*
183044 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
183092 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
183112 TGGGTAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:184831 original size:9 final size:9
Alignment explanation
Indices: 184811--184848 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
184801 TTTAATGTGA
184811 AAAAATAA-
1 AAAAATAAG
*
184819 AAAAATATG
1 AAAAATAAG
184828 AAAAATAAG
1 AAAAATAAG
184837 AAAAATAAG
1 AAAAATAAG
184846 AAA
1 AAA
184849 TTACCTCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (9 bp):
AAAAATAAG
Found at i:189466 original size:2 final size:2
Alignment explanation
Indices: 189459--189500 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
189449 CGTACATGCC
189459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
189501 CAGAAAGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:191961 original size:58 final size:58
Alignment explanation
Indices: 191871--192038 Score: 225
Period size: 58 Copynumber: 2.9 Consensus size: 58
191861 AGAGGCATAG
* *
191871 TAATGGTTCGTTATT-GACATGTAGGATCATGCATTATACAAAATAAGCATTGGCAAAA
1 TAATGATTCATTATTCG-CATGTAGGATCATGCATTATACAAAATAAGCATTGGCAAAA
*
191929 TAATGATTCATTATTCGCATGTAGGATCATGCATGATACAAAATAAGCATTGGCAAAA
1 TAATGATTCATTATTCGCATGTAGGATCATGCATTATACAAAATAAGCATTGGCAAAA
* * * *
191987 TAATGATTCACTATTCACATATAGGATTC-TGCA-TAGTACAAGATAAGCATTG
1 TAATGATTCATTATTCGCATGTAGGA-TCATGCATTA-TACAAAATAAGCATTG
192039 AGTTGCTTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
57 1 0.01
58 95 0.96
59 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (58 bp):
TAATGATTCATTATTCGCATGTAGGATCATGCATTATACAAAATAAGCATTGGCAAAA
Found at i:193868 original size:6 final size:6
Alignment explanation
Indices: 193857--193903 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
193847 TTCTCAACAA
* *
193857 AATTAG AATTAG GATTAG GATTA- AGATTAG AAATTAG AATTAG AATT
1 AATTAG AATTAG AATTAG AATTAG A-ATTAG -AATTAG AATTAG AATT
193904 TATCAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 30 0.83
7 5 0.14
8 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (6 bp):
AATTAG
Found at i:197121 original size:11 final size:11
Alignment explanation
Indices: 197098--197129 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
197088 TGTAATTAAT
197098 TATTTATATATA
1 TATTTA-ATATA
197110 TATTTAATATA
1 TATTTAATATA
197121 TATTTAATA
1 TATTTAATA
197130 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:197133 original size:3 final size:3
Alignment explanation
Indices: 197125--197204 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
197115 AATATATATT
* *
197125 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
197173 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
197205 TGGATAAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:197783 original size:113 final size:113
Alignment explanation
Indices: 197519--198064 Score: 896
Period size: 113 Copynumber: 4.8 Consensus size: 113
197509 GATAGAATTA
* * *
197519 TTGAACAAGTTCTTCTTATCATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
197584 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGCAAAAGG
66 CTTTCTCTGGAAAAGATGATCCATCAA-ATGATGAATTCAGGTAAAAGG
*
197633 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
197698 CTTTCTCTGGAAAAGCTGATCCCTCAAGTAATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGG
197746 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
197811 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
66 CTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGG
197859 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
197924 CTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGG
*
197972 TTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
198037 CCTTCTCTGGCAAAA-ACTAATCCATCAA
66 CTTTCTCTGG-AAAAGA-TGATCCATCAA
198065 GTGGATTCGA
Statistics
Matches: 407, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
113 308 0.76
114 99 0.24
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGG
Found at i:198786 original size:83 final size:83
Alignment explanation
Indices: 198654--199209 Score: 1012
Period size: 83 Copynumber: 6.7 Consensus size: 83
198644 GTAGTTCTTA
*
198654 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
198719 ATTCAATGATTGTTCTGT
66 ATTCAATGATTGTTCTGT
198737 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
198802 ATTCAATGATTGTTCTGT
66 ATTCAATGATTGTTCTGT
198820 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
198885 ATTCAATGATTGTTCTGT
66 ATTCAATGATTGTTCTGT
198903 CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
198967 ATTCAATGATTGTTCTGT
66 ATTCAATGATTGTTCTGT
* * *
198985 CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
199049 ATTCAATGATTGGTTCTG-
66 ATTCAATGATT-GTTCTGT
*
199067 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
199132 ATTCAATGATTGTTCTGT
66 ATTCAATGATTGTTCTGT
**
199150 CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
199210 TCAATTAATG
Statistics
Matches: 459, Mismatches: 11, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
82 215 0.47
83 244 0.53
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
ATTCAATGATTGTTCTGT
Found at i:199076 original size:165 final size:164
Alignment explanation
Indices: 198657--199209 Score: 975
Period size: 165 Copynumber: 3.4 Consensus size: 164
198647 GTTCTTACCA
* *
198657 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCTAAATT
*
198722 CAATGATTGTTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
66 CAATGATTGTTCTG-CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
198787 AAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
130 AAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
*
198822 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
1 -AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCTAAAT
*
198887 TCAATGATTGTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAA
65 TCAATGATTGTTCTGCT-AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAA
198951 CAAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
129 CAAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
* *
198987 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCTAAATT
199052 CAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
66 CAATGATT-GTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
199117 AAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
130 AAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
*
199152 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACAAATTCATCTT
199210 TCAATTAATG
Statistics
Matches: 375, Mismatches: 8, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
164 70 0.19
165 224 0.60
166 81 0.22
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (164 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCTAAATT
CAATGATTGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACA
AATTCATCTTCTAAATTCAATGATTGTTCTGTCC
Found at i:199094 original size:247 final size:248
Alignment explanation
Indices: 198657--199209 Score: 1020
Period size: 247 Copynumber: 2.2 Consensus size: 248
198647 GTTCTTACCA
198657 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
*
198722 CAATGATTGTTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAC
66 CAATGATTGTTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAAC
198787 AAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTT
131 AAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTT
198852 CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
196 CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
*
198905 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
*
198970 CAATGATTGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
66 CAATGATTGTTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAAC
* *
199034 ACATTCATCTTCTAAATTCAATGATTGGTTCTG-CTAAACCAGATCAGATAACTCAAAGAACACT
131 AAATTCATCTTCTAAATTCAATGATT-GTTCTGTCCAAACCAGATCAGATAACTCAAAGAACACT
199098 TCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
195 TCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
**
199152 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
199210 TCAATTAATG
Statistics
Matches: 297, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
247 210 0.71
248 87 0.29
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (248 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
CAATGATTGTTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAAC
AAATTCATCTTCTAAATTCAATGATTGTTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
Found at i:200343 original size:11 final size:11
Alignment explanation
Indices: 200327--200369 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
200317 CTTGACCCCC
200327 CTTTTTCTTTT
1 CTTTTTCTTTT
*
200338 CTTTTTTTTTT
1 CTTTTTCTTTT
200349 CTTTTTTCTCTTT
1 C-TTTTTCT-TTT
200362 -TTTTTCTT
1 CTTTTTCTT
200370 CAAGCATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 1 0.04
11 18 0.64
12 6 0.21
13 3 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
CTTTTTCTTTT
Found at i:200353 original size:9 final size:9
Alignment explanation
Indices: 200328--200369 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
200318 TTGACCCCCC
200328 TTTTTC-TT
1 TTTTTCTTT
*
200336 TTCTT-TTT
1 TTTTTCTTT
200344 TTTTTCTTT
1 TTTTTCTTT
*
200353 TTTCTCTTT
1 TTTTTCTTT
200362 TTTTTCTT
1 TTTTTCTT
200370 CAAGCATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 10 0.36
9 18 0.64
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:200357 original size:18 final size:18
Alignment explanation
Indices: 200334--200369 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
200324 CCCCTTTTTC
*
200334 TTTTCTTTTTTTTTTCTT
1 TTTTCTCTTTTTTTTCTT
200352 TTTTCTCTTTTTTTTCTT
1 TTTTCTCTTTTTTTTCTT
200370 CAAGCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTCTCTTTTTTTTCTT
Found at i:203907 original size:9 final size:10
Alignment explanation
Indices: 203869--203902 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
203859 ATTTATGAAA
*
203869 TAAATAAATG
1 TAAAAAAATG
203879 TAAAAAAATG
1 TAAAAAAATG
203889 TAAAAAAATG
1 TAAAAAAATG
203899 TAAA
1 TAAA
203903 GAATGATTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (10 bp):
TAAAAAAATG
Done.