Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_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: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 16
Found at i:1043309 original size:20 final size:21
Alignment explanation
Indices: 1043261--1043316 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
1043251 TTGCGAAAGT
*
1043261 CAAA-TCGCATTGCGATTTTC
1 CAAATTCGCATTGCGATTTTA
1043281 CAAATTCGCATTGCGA-TTTA
1 CAAATTCGCATTGCGATTTTA
**
1043301 CTTATTCGCATTGCGA
1 CAAATTCGCATTGCGA
1043317 ATTAGGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (21 bp):
CAAATTCGCATTGCGATTTTA
Found at i:1043532 original size:12 final size:12
Alignment explanation
Indices: 1043513--1043546 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1043503 CTCTCCGGCG
1043513 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1043525 ATATCCGTTCCT
1 ACATCCGTTCCT
1043537 ACATCC-TTCC
1 ACATCCGTTCC
1043547 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1044127 original size:24 final size:24
Alignment explanation
Indices: 1044100--1044153 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1044090 AGTATTCGAA
*
1044100 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1044124 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1044148 TTTGAT
1 TTTGAT
1044154 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1044345 original size:12 final size:12
Alignment explanation
Indices: 1044328--1044352 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1044318 ATATAATCCT
1044328 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1044340 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1044352 G
1 G
1044353 TCCCCAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1046666 original size:19 final size:19
Alignment explanation
Indices: 1046644--1046774 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
1046634 GGAAATTACT
1046644 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1046663 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1046677 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1046696 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1046710 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1046729 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1046743 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1046762 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1046775 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1046686 original size:33 final size:33
Alignment explanation
Indices: 1046644--1046770 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
1046634 GGAAATTACT
1046644 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1046677 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1046709 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1046743 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1046771 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1046751 original size:66 final size:66
Alignment explanation
Indices: 1046645--1046777 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1046635 GAAATTACTA
*
1046645 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1046710 T
66 T
*
1046711 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1046776 T
66 T
1046777 T
1 T
1046778 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1046792 original size:19 final size:19
Alignment explanation
Indices: 1046770--1046844 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
1046760 AAATCGCAAC
*
1046770 GCGAATTTAATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
*
1046789 GCG-A-TTCA---CTCGTT
1 GCGAATTTCATTTCGCGTT
*
1046803 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
* *
1046822 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
1046841 GCGA
1 GCGA
1046845 TAGTACGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 8 0.17
16 4 0.09
17 3 0.07
18 1 0.02
19 30 0.65
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:1046845 original size:19 final size:19
Alignment explanation
Indices: 1046801--1046845 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1046791 GATTCACTCG
*
1046801 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1046820 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1046839 TTGCGAT
1 TTGCGAT
1046846 AGTACGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1046971 original size:14 final size:14
Alignment explanation
Indices: 1046952--1046988 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1046942 CATCAATTAA
1046952 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1046966 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1046980 ACAAATCAA
1 ACAAATCAA
1046989 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1048410 original size:21 final size:21
Alignment explanation
Indices: 1048344--1048410 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1048334 GTGAATCGGG
*
1048344 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1048364 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1048386 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1048407 CTCT
1 CTCT
1048411 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1048429 original size:42 final size:41
Alignment explanation
Indices: 1048344--1048466 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1048334 GTGAATCGGG
* * * *
1048344 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1048386 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1048428 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1048467 CGAGTTGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1048858 original size:91 final size:90
Alignment explanation
Indices: 1048684--1048868 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
1048674 ATTTCAAACT
*
1048684 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACACTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACACTGTT--A-AATAAACAGTTTAGC
1048749 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
1048777 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACACTGTTAAATAAACAGTTTAGCA
*
1048841 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1048868 T
1 T
1048869 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACACTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1050636 original size:33 final size:33
Alignment explanation
Indices: 1050579--1050677 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1050569 ACGAGATAAT
1050579 GAGAATCGCAACGCGGAAATAACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATAACTATCGCAACGA
1050613 GAGAATCGCAACGCGAAATAACTATCGCAACGA
1 GAGAATCGCAACGCGAAATAACTATCGCAACGA
*
1050646 GAGAATCGCAACGCGAAATGAA-AATCGCAACG
1 GAGAATCGCAACGCGAAAT-AACTATCGCAACG
1050678 CGAAATAAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
33 47 0.75
34 16 0.25
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATAACTATCGCAACGA
Found at i:1050641 original size:19 final size:17
Alignment explanation
Indices: 1050561--1050718 Score: 94
Period size: 19 Copynumber: 8.8 Consensus size: 17
1050551 GTTGAAATGA
*
1050561 AAATCGCAACGAGATAAT
1 AAATCGCAACGCGA-AAT
1050579 GAGAATCGCAACGCGGAAAT
1 -A-AATCGCAACGC-GAAAT
*
1050599 AACTATCGCAA--CGAGA-
1 AA--ATCGCAACGCGAAAT
*
1050615 GAATCGCAACGCGAAAT
1 AAATCGCAACGCGAAAT
*
1050632 AACTATCGCAA--CGAGA-
1 AA--ATCGCAACGCGAAAT
*
1050648 GAATCGCAACGCGAAAT
1 AAATCGCAACGCGAAAT
1050665 GAAAATCGCAACGCGAAAT
1 --AAATCGCAACGCGAAAT
1050684 AAAAATCGCAACGCGAAAT
1 --AAATCGCAACGCGAAAT
*
1050703 GAAAATCGCAATGCGA
1 --AAATCGCAACGCGA
1050719 TTTTGGTTTC
Statistics
Matches: 113, Mismatches: 12, Indels: 28
0.74 0.08 0.18
Matches are distributed among these distances:
14 14 0.12
16 10 0.09
17 8 0.07
18 2 0.02
19 57 0.50
20 20 0.18
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAATCGCAACGCGAAAT
Found at i:1050747 original size:19 final size:19
Alignment explanation
Indices: 1050714--1050758 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1050704 AAAATCGCAA
*
1050714 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1050733 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1050752 TACGATT
1 TGCGATT
1050759 CTCTCGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1051338 original size:20 final size:20
Alignment explanation
Indices: 1051314--1051447 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
1051304 CGCTATGTAA
* * *
1051314 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1051334 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1051354 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1051375 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1051395 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1051415 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1051435 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1051448 TTTCCCAATT
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.03
20 84 0.83
21 12 0.12
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1051487 original size:81 final size:81
Alignment explanation
Indices: 1051314--1051468 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 81
1051304 CGCTATGTAA
* * * * ** *
1051314 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCG
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
1051379 CATTGCGATAGTAAGT
66 CATTGCGATAGTAAGT
* * *
1051395 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TC
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATC
*
1051459 GCGTTGCGAT
65 GCATTGCGAT
1051469 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
81 60 0.97
82 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (81 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
CATTGCGATAGTAAGT
Found at i:1051558 original size:21 final size:21
Alignment explanation
Indices: 1051518--1051558 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1051508 ACTGTATACC
** *
1051518 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1051539 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1051559 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1052000 original size:16 final size:17
Alignment explanation
Indices: 1051979--1052011 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1051969 ATGTAAAATT
1051979 AAATATTTAA-ATTTAA
1 AAATATTTAATATTTAA
1051995 AAATATTTAATATTTAA
1 AAATATTTAATATTTAA
1052012 TCAAGTAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATTTAATATTTAA
Found at i:1054852 original size:30 final size:30
Alignment explanation
Indices: 1054816--1054872 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1054806 AGAATATGTA
* *
1054816 AATATTAAGGACTAAAGGTATAATTATTCC
1 AATATTAAGGACCAAAGATATAATTATTCC
*
1054846 AATATTAAGGACCAAATATATAATTAT
1 AATATTAAGGACCAAAGATATAATTAT
1054873 GCCAGTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (30 bp):
AATATTAAGGACCAAAGATATAATTATTCC
Found at i:1055291 original size:64 final size:64
Alignment explanation
Indices: 1055188--1055313 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 64
1055178 TATATTATAT
* *
1055188 CATTTAACTGGAAATATTATCAAGCACAATAAAATATTAGGTAGCGCTTATATAATAAAATAGG
1 CATTTAACCGAAAATATTATCAAGCACAATAAAATATTAGGTAGCGCTTATATAATAAAATAGG
* *
1055252 CATTTAACCGAAAATATTATCAAGTACAATAACAA-ATTAGGTAGCGCTTATATAATATAATA
1 CATTTAACCGAAAATATTATCAAGCACAATAA-AATATTAGGTAGCGCTTATATAATAAAATA
1055314 AGTAGCGCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
64 55 0.96
65 2 0.04
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (64 bp):
CATTTAACCGAAAATATTATCAAGCACAATAAAATATTAGGTAGCGCTTATATAATAAAATAGG
Found at i:1055526 original size:3 final size:3
Alignment explanation
Indices: 1055518--1055543 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1055508 GAATTGGGTT
1055518 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
1055544 TCTCATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1055919 original size:198 final size:197
Alignment explanation
Indices: 1055555--1056050 Score: 547
Period size: 198 Copynumber: 2.5 Consensus size: 197
1055545 CTCATAAAAT
* * * * * * *
1055555 CGGTAAATTTAAACCGGTTACATTATAAATTGACCTATTACATTAT-GTATATCGTTTTCGATGT
1 CGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAAT-TATCGATTTCGATGA
* * * * *
1055619 TTTCGGGATCGATACAATTTT-AAATGTATCAACACTTTATGCGTGCAACTCGTTTGTGCTTTAT
65 TTTCGGGATCGATAC-TTTTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCAT
* * ** *
1055683 TTTGGAAAAAAGTAGCGACACATATTTAAAGGGTGTCGATACATAATGTAGACCTATT-TGTTAA
129 TTTGGAAAAAAGTAGCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCT-CTAA
*
1055747 TTAAC
193 TGAAC
* *
1055752 CGGTATATTTTAACCGGTTACATTGTAAATTTACCTGTTACATAATAATTATCGATTTCGATG-T
1 CGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGAT
* *
1055816 TTCGAGGATCGATACTTTTTACAAATGTATCGACACTTTATGTGTACACCTCGTTTG-CCATTCA
66 TTCG-GGATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTACAACTCGTTTGTCC-TTCA
* * * * *
1055880 TTTTGGAAAAATA-TATCGACACAAATTAAAAAAGTGTCGATACTTTATGTTGACCTATTCTCTC
128 TTTTGGAAAAA-AGTAGCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTA
1055944 ATGAAC
192 ATGAAC
* * * **
1055950 CTGGTATATTTCT-ACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTCTCTTTG
1 C-GGTATATTT-TAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATG
* *
1056014 ATTTTGGGATCGATACTTGTTATAAATGTATCGACAC
64 ATTTCGGGATCGATACTTTTTA-AAATGTATCGACAC
1056051 AAAATCTAAT
Statistics
Matches: 253, Mismatches: 36, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
196 9 0.04
197 64 0.25
198 91 0.36
199 84 0.33
200 5 0.02
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (197 bp):
CGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGAT
TTCGGGATCGATACTTTTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTT
TGGAAAAAAGTAGCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATGA
AC
Found at i:1056609 original size:182 final size:182
Alignment explanation
Indices: 1056292--1057627 Score: 2022
Period size: 182 Copynumber: 7.3 Consensus size: 182
1056282 AATACATTTA
1056292 ATCATTTCGAGATC-TGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTGT
1 ATCATTTCGAGA-CATGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTGT
* * *
1056356 ATAAAATATCGACACTTTTTAGGCGCTATAACTTATTCTCTTTTAAATATA-AAAAGTGTTGATA
65 ATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAAT-TACAAAAGTGTCGATA
* * *
1056420 ATTATATTAATTTATCGACACTTGCAATATATTCGATAGCTTTTTACCGGTTTT
129 CTTATATTAATTTATCGACACTTTCAATATATTCGGTAGCTTTTTACCGGTTTT
* * *
1056474 ATCATTTCGAGACATATTTTATCATATTATTACCTGTTATATTGCTATAGATCGATACATTTGTA
1 ATCATTTCGAGACATGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTGTA
* *
1056539 TAAAGTATCGATACTTTTTAGGCGTTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACT
66 TAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACT
* * *
1056604 TATATTAATTTATCGACACTTTCAATATATCCGGTATCTTTTTACCGATTTT
131 TATATTAATTTATCGACACTTTCAATATATTCGGTAGCTTTTTACCGGTTTT
* * * *
1056656 ATCATTTCGAGACATGTTTTGTAATATTATTACATGTTATATTGCTATGGATCAATACATATGTA
1 ATCATTTCGAGACATGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTGTA
1056721 TAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACT
66 TAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACT
* * * *
1056786 TATATTAATTTATCGACACTTTCAATATATCCAGTATCTTTTTACCGATTTT
131 TATATTAATTTATCGACACTTTCAATATATTCGGTAGCTTTTTACCGGTTTT
* * * **
1056838 ATCATTTCAAGACCTGTTTTGTCATATTATTACATGTTATATTAATATGGATCGATACATTTGTA
1 ATCATTTCGAGACATGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTGTA
*
1056903 TAAAGTATCGACAATTTTTAGGCGCTATAACTTCTTCTCTTTTAAA-TATCAAAAGTGTCGATAC
66 TAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTA-CAAAAGTGTCGATAC
*
1056967 TTATATTAATTTATCGACACTTTCAATATATTCGGTAGCTTTTTACCGATTTT
130 TTATATTAATTTATCGACACTTTCAATATATTCGGTAGCTTTTTACCGGTTTT
* * *
1057020 ATCATTTCGAGACATGTTTTGTCATATTATTACCTGTTATATTGATGTGAATCGATACATTTGTA
1 ATCATTTCGAGACATGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTGTA
* *
1057085 TAAAGTATCGACACTTTTTAGGAGCTATAACTTATTCTCTTTTAAA-TATCAAAAGTGTCGATAC
66 TAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTA-CAAAAGTGTCGATAC
* *
1057149 TTATATTAATTTATCGATACTTTCAATATATCCGGTAGCTTTTTACCGGTTTT
130 TTATATTAATTTATCGACACTTTCAATATATTCGGTAGCTTTTTACCGGTTTT
* * *
1057202 ATCATTTCGAGATC-TGTTTTGTCGTATTATTACTTGTTATATTGCTATGTATCGATACATTTGT
1 ATCATTTCGAGA-CATGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTGT
* *
1057266 ATAAAATATCGACACTTTTTAAGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATAC
65 ATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATAC
* **
1057331 TTATATTAATTTATCGACACTTTCAATATATCCGGTAGCGGTTTACCGGTTTT
130 TTATATTAATTTATCGACACTTTCAATATATTCGGTAGCTTTTTACCGGTTTT
* * **
1057384 ATCATAAT-GACACCGGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTGT
1 ATCAT-TTCGAGACATGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTGT
*
1057448 ATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATAC
65 ATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATAC
**
1057513 TTATATTAATTTATCGACACTTTCAATATA-TCTGGTAGCGGTTTACCGGTTTT
130 TTATATTAATTTATCGACACTTTCAATATATTC-GGTAGCTTTTTACCGGTTTT
* * ** * * *
1057566 ATCATAAT-GACACCGGTTTTATCATATTTTTAACTGTTATATTGCTATGGATCGATACATTT
1 ATCAT-TTCGAGACATGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTT
1057628 TTCATTTATA
Statistics
Matches: 1074, Mismatches: 72, Indels: 16
0.92 0.06 0.01
Matches are distributed among these distances:
181 7 0.01
182 1063 0.99
183 4 0.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (182 bp):
ATCATTTCGAGACATGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACATTTGTA
TAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACT
TATATTAATTTATCGACACTTTCAATATATTCGGTAGCTTTTTACCGGTTTT
Found at i:1059421 original size:37 final size:37
Alignment explanation
Indices: 1059348--1059422 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
1059338 GTTAAAAAAT
* *
1059348 ATTTATATATTTTATTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAAATTGAAAATCATAAA
* *
1059385 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTATTTAAAAAATTGAAAATCATAAA
1059422 A
1 A
1059423 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTATTTAAAAAATTGAAAATCATAAA
Found at i:1064499 original size:18 final size:17
Alignment explanation
Indices: 1064466--1064499 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1064456 GAATAATTAA
1064466 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
1064483 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
1064500 ATACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:1072531 original size:18 final size:17
Alignment explanation
Indices: 1072498--1072531 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1072488 GAATAATTAA
1072498 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
1072515 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
1072532 ATACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:1077043 original size:50 final size:50
Alignment explanation
Indices: 1076984--1077105 Score: 149
Period size: 50 Copynumber: 2.4 Consensus size: 50
1076974 TAGCAGAAAA
* * **
1076984 GCGTCCCCTGCACCGCGCTATATGCTGATTTGGCGTCACGTGGGTATAGC
1 GCGTCCCCTGCACCGCGCTATATGCTGATCTGGCGCCACGTGAATATAGC
* * *
1077034 GCGTCCCCTGCCCCGCGATATATGGTGATCTGGCGCCACGTGAATATAGC
1 GCGTCCCCTGCACCGCGCTATATGCTGATCTGGCGCCACGTGAATATAGC
1077084 GCG-CCCCTTG-ATCCGCGCTATA
1 GCGTCCCC-TGCA-CCGCGCTATA
1077106 CGCCACGTAG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
49 4 0.07
50 57 0.93
ACGTcount: A:0.16, C:0.33, G:0.28, T:0.24
Consensus pattern (50 bp):
GCGTCCCCTGCACCGCGCTATATGCTGATCTGGCGCCACGTGAATATAGC
Found at i:1081242 original size:111 final size:111
Alignment explanation
Indices: 1081106--1081327 Score: 363
Period size: 111 Copynumber: 2.0 Consensus size: 111
1081096 ATTACAAAAA
* * *
1081106 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
* * * *
1081171 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTATCGAGATAT
66 AATTAAAACATTAAAATATTACAGTATCAGCAAAGTATAGAGATAT
*
1081217 TTAATTCTTAATCTAATAGTCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
*
1081282 AATTAAAACATTAAAATATTACAGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATATTACAGTATCAGCAAAGTATAGAGATAT
1081328 ATGATTTCTA
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 102 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
AATTAAAACATTAAAATATTACAGTATCAGCAAAGTATAGAGATAT
Found at i:1081465 original size:12 final size:10
Alignment explanation
Indices: 1081451--1081491 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1081441 ACCTTAAAAA
*
1081451 GAGAGTATTT
1 GAGAGAATTT
1081461 GAGAGAAATTT
1 GAGAG-AATTT
1081472 -AGAGAATTT
1 GAGAGAATTT
1081481 GAGAGAATTT
1 GAGAGAATTT
1081491 G
1 G
1081492 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:1088581 original size:20 final size:20
Alignment explanation
Indices: 1088558--1088610 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1088548 TAACGCGATC
1088558 TCCAGAATCGCAAATCAATT
1 TCCAGAATCGCAAATCAATT
*
1088578 TCCAGAATCGCAAATCAGTT
1 TCCAGAATCGCAAATCAATT
*
1088598 CCCAGAATCGCAA
1 TCCAGAATCGCAA
1088611 TACGATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (20 bp):
TCCAGAATCGCAAATCAATT
Found at i:1088670 original size:20 final size:20
Alignment explanation
Indices: 1088645--1088920 Score: 245
Period size: 20 Copynumber: 13.7 Consensus size: 20
1088635 GATTTTCCAG
* *
1088645 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
1088665 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
1088685 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
1088704 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* * *
1088726 AATCGCAACACGTATCCGTA
1 AATCGCAACGCGAATACGTA
1088746 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
1088767 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
1088787 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
1088807 AATCGCAACGCGTATATGTA
1 AATCGCAACGCGAATACGTA
*
1088827 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
1088847 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
1088867 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
1088888 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
1088908 AATCGCAACGCGA
1 AATCGCAACGCGA
1088921 TTTTTAAAGC
Statistics
Matches: 209, Mismatches: 37, Indels: 20
0.79 0.14 0.08
Matches are distributed among these distances:
18 1 0.00
19 2 0.01
20 151 0.72
21 53 0.25
22 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:1088751 original size:41 final size:41
Alignment explanation
Indices: 1088706--1088917 Score: 338
Period size: 41 Copynumber: 5.2 Consensus size: 41
1088696 GATTCTGACT
* * *
1088706 ATCGCAACGAGTATCCGTAAAATCGCAACACGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
1088747 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
**
1088788 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATATGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
1088828 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
1088868 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
1088909 ATCGCAACG
1 ATCGCAACG
1088918 CGATTTTTAA
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 74 0.47
41 84 0.53
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:1089502 original size:20 final size:19
Alignment explanation
Indices: 1089477--1089548 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
1089467 TTCTAAACTT
1089477 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
*
1089497 AAAATCGCAATACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
1089517 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
1089538 AAAATCGCAAC
1 AAAATCGCAAC
1089549 GCGAAACCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:1089564 original size:40 final size:40
Alignment explanation
Indices: 1089477--1089565 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 40
1089467 TTCTAAACTT
* **
1089477 AAAATCGCAACATGAAAATGAAAATCGCAATACGAAAATG
1 AAAATCGCAACATGAAAATGAAAATCGCAACACGAAAACC
** *
1089517 ACTATCGCAACGA-GAGAAATGAAAATCGCAACGCG-AAACC
1 AAAATCGCAAC-ATGA-AAATGAAAATCGCAACACGAAAACC
1089557 AAAATCGCA
1 AAAATCGCA
1089566 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
40 21 0.54
41 18 0.46
ACGTcount: A:0.51, C:0.20, G:0.17, T:0.12
Consensus pattern (40 bp):
AAAATCGCAACATGAAAATGAAAATCGCAACACGAAAACC
Found at i:1089583 original size:19 final size:19
Alignment explanation
Indices: 1089561--1089644 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
1089551 GAAACCAAAA
*
1089561 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1089580 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1089594 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
1089613 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1089632 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1089645 CTCTAGTTGC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 40 0.73
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1089666 original size:52 final size:52
Alignment explanation
Indices: 1089561--1089698 Score: 177
Period size: 52 Copynumber: 2.6 Consensus size: 52
1089551 GAAACCAAAA
* **
1089561 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTAATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTAGTTGCGATAGTAATT
* * *
1089613 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTCTCTAGTTGCGATAGTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTAGTTGCGATAGTAATT
** *
1089665 TCCGCATTGCGATAGTCATTCTCTCGTTGCGATT
1 T-CGCATTGCGATTTTCATT-TCGCGTTGCGATT
1089699 TTCATTTCAA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 47 0.64
53 14 0.19
54 12 0.16
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTAGTTGCGATAGTAATT
Found at i:1089694 original size:20 final size:20
Alignment explanation
Indices: 1089642--1089697 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1089632 TCGCGTTGCG
*
1089642 ATTCTCTAGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
1089662 ATT-TC-CGCATTGCGATAGTC
1 ATTCTCTCG--TTGCGATAGTC
1089682 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
1089698 TTTCATTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 24 0.77
21 2 0.06
22 2 0.06
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:1089703 original size:20 final size:19
Alignment explanation
Indices: 1089566--1089706 Score: 88
Period size: 19 Copynumber: 7.8 Consensus size: 19
1089556 CAAAATCGCA
*
1089566 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
1089585 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
* *
1089599 TTGCGATTTTAATTTCGCG
1 TTGCGATTTTCATTTCTCG
* *
1089618 TTGCGATTTTTATTTCGCG
1 TTGCGATTTTCATTTCTCG
*
1089637 TTGCGA--TTC---TCTAG
1 TTGCGATTTTCATTTCTCG
**
1089651 TTGCGATAGTCATTTC-CG
1 TTGCGATTTTCATTTCTCG
**
1089669 CATTGCGATAGTCATTCTCTCG
1 --TTGCGATTTTCATT-TCTCG
1089691 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1089707 AACCAAAAGA
Statistics
Matches: 97, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.20
16 4 0.04
17 5 0.05
18 1 0.01
19 38 0.39
20 26 0.27
21 2 0.02
22 2 0.02
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:1091011 original size:18 final size:18
Alignment explanation
Indices: 1090966--1091013 Score: 80
Period size: 17 Copynumber: 2.7 Consensus size: 18
1090956 CTCCACTTCG
*
1090966 AGAGCCATCACCTCGCCC
1 AGAGCCATCACCTCACCC
1090984 AGAG-CATCACCTCACCC
1 AGAGCCATCACCTCACCC
1091001 AGAGCCATCACCT
1 AGAGCCATCACCT
1091014 GATCGACCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.27, C:0.46, G:0.15, T:0.12
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:1091562 original size:94 final size:94
Alignment explanation
Indices: 1091401--1091780 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
1091391 TAGATTGCTT
* *
1091401 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1091466 ATTTGTCTTTTTTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
1091495 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1091560 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1091589 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1091654 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
1091683 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1091748 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1091776 AGTAA
1 AGTAA
1091781 TGCAATCCAT
Statistics
Matches: 272, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 25 0.09
94 247 0.91
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1091946 original size:19 final size:19
Alignment explanation
Indices: 1091828--1091948 Score: 118
Period size: 19 Copynumber: 6.2 Consensus size: 19
1091818 TAGTTTATTT
*
1091828 TCGCAACACGAAACATAAAA
1 TCGCAACGCGAAAC-TAAAA
* * **
1091848 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG-AAACT-AAAA
*
1091869 TCGCAACGAGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
1091888 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
*
1091907 TCGCAACGCGAAACAAAAA
1 TCGCAACGCGAAACTAAAA
*
1091926 TCGCAACGCGAAACTATAA
1 TCGCAACGCGAAACTAAAA
1091945 TCGC
1 TCGC
1091949 GTTGTGATTT
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
19 59 0.69
20 12 0.14
21 14 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:1092011 original size:20 final size:20
Alignment explanation
Indices: 1091986--1092029 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1091976 TCTCTCGTTA
1091986 CGATAGTCAAATTCGCATTG
1 CGATAGTCAAATTCGCATTG
** *
1092006 CGATAGTCATTTTCGCGTTG
1 CGATAGTCAAATTCGCATTG
1092026 CGAT
1 CGAT
1092030 TTTAAGTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (20 bp):
CGATAGTCAAATTCGCATTG
Found at i:1092604 original size:21 final size:21
Alignment explanation
Indices: 1092509--1092616 Score: 83
Period size: 21 Copynumber: 5.1 Consensus size: 21
1092499 GCCCGACTCA
*
1092509 CCTGTCATAGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1092530 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
1092551 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
1092572 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* * *
1092593 ACTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
1092614 CCT
1 CCT
1092617 CCAAACATTC
Statistics
Matches: 64, Mismatches: 21, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 1 0.02
21 62 0.97
22 1 0.02
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.24
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:1092617 original size:42 final size:42
Alignment explanation
Indices: 1092510--1092618 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 42
1092500 CCCGACTCAC
* * * *
1092510 CTGTCATAGTTCAAGAGG-CCTCTCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGTCC-CTCCCACCGTTCAAGAGGCCA
* **
1092552 CTATCATCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCA
*
1092594 CTGTCATCGTTGAAGAGGTCCCTCC
1 CTGTCATCGTTCAAGAGGTCCCTCC
1092619 AAACATTCTA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
41 1 0.02
42 48 0.91
43 4 0.08
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCA
Found at i:1093994 original size:14 final size:15
Alignment explanation
Indices: 1093975--1094011 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1093965 ATTGTTTAAT
1093975 TGATTTGTAAAA-GA
1 TGATTTGTAAAATGA
*
1093989 TGATTTGTAAAATGT
1 TGATTTGTAAAATGA
1094004 TGATTTGT
1 TGATTTGT
1094012 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (15 bp):
TGATTTGTAAAATGA
Found at i:1094201 original size:34 final size:34
Alignment explanation
Indices: 1094133--1094242 Score: 195
Period size: 34 Copynumber: 3.3 Consensus size: 34
1094123 AGAAATGACT
*
1094133 ATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
*
1094166 ATCGCAACGAGTGAATCGTAATGCGAAAATGAAA
1 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1094200 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1094234 ATCGCAACG
1 ATCGCAACG
1094243 CGAAACTAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 23 0.32
34 50 0.68
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (34 bp):
ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
Found at i:1094238 original size:20 final size:19
Alignment explanation
Indices: 1094146--1094247 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 19
1094136 GCAACGAGAG
1094146 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1094165 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
*
1094179 AATCGTAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
1094199 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
1094213 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
1094233 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
1094248 CTAATTTCGC
Statistics
Matches: 64, Mismatches: 7, Indels: 24
0.67 0.07 0.25
Matches are distributed among these distances:
14 15 0.23
16 10 0.16
17 2 0.03
18 8 0.12
19 11 0.17
20 18 0.28
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1094293 original size:33 final size:33
Alignment explanation
Indices: 1094251--1094332 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
1094241 CGCGAAACTA
* **
1094251 ATTTCGCATTGCGATTCACGCGTTGTGATTTTC
1 ATTTCGCATTGCGATTCACGCGTTGCGATAGTC
* *
1094284 ATTTCGCATTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCATTGCGATTCACGCGTTGCGATAGTC
*
1094317 ATTTCCGCGTTGCGAT
1 ATTT-CGCATTGCGAT
1094333 AGTCAATTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 32 0.76
34 10 0.24
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.40
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCACGCGTTGCGATAGTC
Found at i:1094329 original size:20 final size:20
Alignment explanation
Indices: 1094304--1094392 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
1094294 GCGATTCTCT
1094304 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1094324 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
1094344 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1094364 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
1094384 CGTTGCGAT
1 CGTTGCGAT
1094393 TTCCGCGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1096842 original size:24 final size:24
Alignment explanation
Indices: 1096808--1096861 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1096798 CTGAAAAATC
1096808 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1096832 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1096856 ATCAAA
1 ATCAAA
1096862 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1096875 original size:24 final size:24
Alignment explanation
Indices: 1096808--1096875 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1096798 CTGAAAAATC
* * *
1096808 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1096832 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1096856 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1096876 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1097736 original size:20 final size:20
Alignment explanation
Indices: 1097723--1097773 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1097713 CAGAATCTCG
1097723 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAGATTCGCA
* *
1097743 TTACGATTTACATATTCGCA
1 TTGCGATTTACAGATTCGCA
1097763 TTGCGATTTAC
1 TTGCGATTTAC
1097774 GTAATCACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACAGATTCGCA
Found at i:1097904 original size:20 final size:20
Alignment explanation
Indices: 1097860--1098092 Score: 222
Period size: 20 Copynumber: 11.6 Consensus size: 20
1097850 TACCGGAGAT
*
1097860 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
*
1097879 CGCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1097899 CGCGTTACGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
1097919 TGTCGTTGCGATTTACAGATA
1 CG-CGTTGCGATTTACGGATA
* * *
1097940 CGCATTGCGATTTACGAATT
1 CGCGTTGCGATTTACGGATA
* *
1097960 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
1097980 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
1098000 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1098020 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
1098040 TGTTGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
1098061 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1098082 CTCGTTGCGAT
1 CGCGTTGCGAT
1098093 AGTCAGAATC
Statistics
Matches: 173, Mismatches: 32, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
18 1 0.01
19 15 0.09
20 106 0.61
21 51 0.29
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1097965 original size:40 final size:41
Alignment explanation
Indices: 1097881--1098092 Score: 311
Period size: 41 Copynumber: 5.2 Consensus size: 41
1097871 TTATCGATCG
* * *
1097881 CGTTACGATTTACGGATACGCGTTACGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
1097922 CGTTGCGATTTACAGATACGCATTGCGA-TTTACGAATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1097962 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1098002 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
1098043 TGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
1098084 CGTTGCGAT
1 CGTTGCGAT
1098093 AGTCAGAATC
Statistics
Matches: 155, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 75 0.48
41 80 0.52
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1098147 original size:20 final size:20
Alignment explanation
Indices: 1097859--1098149 Score: 188
Period size: 20 Copynumber: 14.4 Consensus size: 20
1097849 ATACCGGAGA
*
1097859 TCGCGTTGCGAATTATC-GA-
1 TCGCGTTGCGATTTA-CAGAT
* *
1097878 TCGCGTTACGATTTACGGAT
1 TCGCGTTGCGATTTACAGAT
* *
1097898 ACGCGTTACGATTTTAC-GTAT
1 TCGCGTTGCGA-TTTACAG-AT
1097919 T-GTCGTTGCGATTTACAGAT
1 TCG-CGTTGCGATTTACAGAT
* *
1097939 ACGCATTGCGATTTAC-GAAT
1 TCGCGTTGCGATTTACAG-AT
*
1097959 TCTCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTACAGAT
*
1097979 ACGCGTTGCGATTTAC-GTAT
1 TCGCGTTGCGATTTACAG-AT
* *
1097999 TCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACAGAT
*
1098019 ACGCGTTGCGATTTTAC-GTAT
1 TCGCGTTGCGA-TTTACAG-AT
* *
1098040 T-GTTGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTACAGAT
* *
1098060 ACGCGTTGCGATTTTACGGAT
1 TCGCGTTGCGA-TTTACAGAT
* * * *
1098081 ACTCGTTGCGATAGT-CAGAA
1 TCGCGTTGCGAT-TTACAGAT
*
1098101 TCGCGTTGCGATTTATATG-T
1 TCGCGTTGCGATTTACA-GAT
* *
1098121 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACAGAT
*
1098141 TCTCGTTGC
1 TCGCGTTGC
1098150 AATTCTGGAA
Statistics
Matches: 218, Mismatches: 33, Indels: 41
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.00
19 18 0.08
20 144 0.66
21 55 0.25
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTACAGAT
Found at i:1101014 original size:64 final size:64
Alignment explanation
Indices: 1100946--1101072 Score: 227
Period size: 64 Copynumber: 2.0 Consensus size: 64
1100936 ATGTTATATT
1100946 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGC
1 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGC
* * *
1101010 ATTTAACCGGAAATATTATCAAGTACAATAAGATATTAGGTAGCTCTTATATAATGTAATAGG
1 ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGG
1101073 TAGCGCTTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (64 bp):
ATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGC
Found at i:1106433 original size:21 final size:21
Alignment explanation
Indices: 1106408--1106494 Score: 149
Period size: 21 Copynumber: 4.1 Consensus size: 21
1106398 CCCCCTTATG
*
1106408 TCTCTCAAGTGT-ATCTTCGAC
1 TCTCTCAAGT-TCCTCTTCGAC
1106429 TCTCTCAAGTTCCTCTTCGAC
1 TCTCTCAAGTTCCTCTTCGAC
1106450 TCTCTCAAGTTCCTCTTCGAC
1 TCTCTCAAGTTCCTCTTCGAC
1106471 TCTCTCAAGTTCCTCTTCGAC
1 TCTCTCAAGTTCCTCTTCGAC
1106492 TCT
1 TCT
1106495 TGATTGTCTT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 1 0.02
21 63 0.98
ACGTcount: A:0.15, C:0.36, G:0.10, T:0.39
Consensus pattern (21 bp):
TCTCTCAAGTTCCTCTTCGAC
Found at i:1106596 original size:15 final size:15
Alignment explanation
Indices: 1106576--1106622 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
1106566 ACTCTGTTTT
1106576 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
*
1106591 CCCTCACCATCATCC
1 CCCTCACCGTCATCC
1106606 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
1106621 CC
1 CC
1106623 TAATACAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.15, C:0.62, G:0.04, T:0.19
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:1109282 original size:18 final size:18
Alignment explanation
Indices: 1109261--1109311 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1109251 AGAGGGAGGA
1109261 AAAAAATAATAATAATAG-
1 AAAAAAT-ATAATAATAGT
1109279 AAAAAATA-AATAAT-GT
1 AAAAAATATAATAATAGT
1109295 AAATAAATATAATAATA
1 AAA-AAATATAATAATA
1109312 AAGAAGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.03
16 9 0.31
17 6 0.21
18 13 0.45
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (18 bp):
AAAAAATATAATAATAGT
Found at i:1109283 original size:19 final size:19
Alignment explanation
Indices: 1109259--1109316 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 19
1109249 TAAGAGGGAG
1109259 GAAAAAAATAATAATAATA
1 GAAAAAAATAATAATAATA
1109278 G-AAAAAAT-A-AATAAT-
1 GAAAAAAATAATAATAATA
1109293 GTAAATAAATATAATAATAA-A
1 G-AAA-AAA-ATAATAATAATA
1109314 GAA
1 GAA
1109317 GTAAAAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 13
0.71 0.00 0.29
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 3 0.09
18 10 0.31
19 3 0.09
20 3 0.09
21 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (19 bp):
GAAAAAAATAATAATAATA
Found at i:1109495 original size:193 final size:189
Alignment explanation
Indices: 1109289--1109682 Score: 569
Period size: 204 Copynumber: 2.0 Consensus size: 189
1109279 AAAAAATAAA
1109289 TAATGTAAATAAATATAATAATAAAGAAGTAAA-AATAGGGTAAAATACAAAATGTG-TAC-ATA
1 TAATGTAAATAAATATAATAATAAAGAAGTAAACAATAGGGTAAAATACAAAATGTGATACAATA
* *
1109351 TATATATATAATATAACATATAAATGAAATAATACTATACTAATAATAAATGTATACGAATGTAT
66 TATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAATGTAT
*
1109416 AAAAAACTAATAATAGTATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAA
131 AAAAAA-AAATAATA--ATAAAA-ATATAT-AA-ATTATAATGTAATAT-AAAAGATAATTAAAA
1109481 C
189 C
*
1109482 TAATGTAAATAAATATGATAATAAAGAAGTAAACAATAGGGTAAAATACAAAATGTGTACATATA
1 TAATGTAAATAAATATAATAATAAAGAAGTAAACAATAGGGTAAAATACAAAATGTG-------A
*
1109547 TACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATAC
59 TACA-ATATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATAC
* *
1109612 GAATGTGTAAAAAAAAATAATAATATAAATATATAAATTATAATGTAATATAAAAGATAATTAAA
123 GAATGTATAAAAAAAAATAATAATAAAAATATATAAATTATAATGTAATATAAAAGATAATTAAA
1109677 AC
188 AC
1109679 TAAT
1 TAAT
1109683 ATCCCGAGAA
Statistics
Matches: 183, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
193 32 0.17
194 23 0.13
197 20 0.11
198 15 0.08
199 2 0.01
200 6 0.03
201 5 0.03
202 3 0.02
203 7 0.04
204 70 0.38
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (189 bp):
TAATGTAAATAAATATAATAATAAAGAAGTAAACAATAGGGTAAAATACAAAATGTGATACAATA
TATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAATGTAT
AAAAAAAAATAATAATAAAAATATATAAATTATAATGTAATATAAAAGATAATTAAAAC
Found at i:1109552 original size:8 final size:8
Alignment explanation
Indices: 1109539--1109576 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1109529 ACAAAATGTG
1109539 TACATATA
1 TACATATA
1109547 TACATATA
1 TACATATA
*
1109555 TATATATA
1 TACATATA
1109563 TA-ATATA
1 TACATATA
1109570 -ACATATA
1 TACATATA
1109577 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:1111027 original size:20 final size:20
Alignment explanation
Indices: 1111004--1111045 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1110994 GAATCCTTCG
1111004 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
1111024 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
1111044 TC
1 TC
1111046 AGAGTTCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:1111300 original size:105 final size:105
Alignment explanation
Indices: 1111125--1111630 Score: 942
Period size: 105 Copynumber: 4.8 Consensus size: 105
1111115 AATTGTTTAT
* * *
1111125 TGACAACCAGCGGTCCCTTCGTCGCGAAGTTGAACTTGCGCTGTCTGGAGTCCAATATCCTTCGT
1 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC
*
1111190 TGTGAAGTTGAAATTGGCTCTGAAA-TTGAGAAATGTTTGT
66 TGTGAAGTTGAAATTGGCTCT-AAATTTGAGAAATGTTTGG
1111230 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC
1 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC
1111295 TGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGG
66 TGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGG
1111335 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC
1 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC
*
1111400 TGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTAG
66 TGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGG
1111440 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC
1 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC
1111505 TGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGG
66 TGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGG
*
1111545 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGT
1 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC
1111610 TGTGAAGTTGAAATTGGCTCT
66 TGTGAAGTTGAAATTGGCTCT
1111631 GGGTAAAACC
Statistics
Matches: 393, Mismatches: 7, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
104 3 0.01
105 390 0.99
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (105 bp):
TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC
TGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGG
Found at i:1111829 original size:1 final size:1
Alignment explanation
Indices: 1111823--1111849 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1111813 TGTTTGATGA
1111823 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1111850 GAAGATGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1112475 original size:60 final size:60
Alignment explanation
Indices: 1112379--1112493 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
1112369 TTTTCTCTTC
* ** *
1112379 TTTTTTCTCTTTTTTCTTTTTCAATTTAGGGTGCCCTTTCGGGTTTTCACCCTAAAAGTT
1 TTTTTTCTCTTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAAAGTT
* * * *
1112439 TTTTTTTTTTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTTCTCTTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
1112494 GCGAAGTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.13, C:0.20, G:0.12, T:0.55
Consensus pattern (60 bp):
TTTTTTCTCTTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAAAGTT
Found at i:1123235 original size:23 final size:21
Alignment explanation
Indices: 1123192--1123252 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1123182 TAAGAGGGAG
1123192 GAAAAAAATATAATAATAATA
1 GAAAAAAATATAATAATAATA
*
1123213 GAAAAAAATA-AATAAT-GT-
1 GAAAAAAATATAATAATAATA
*
1123231 -AAATAAATATAATAATAA-A
1 GAAAAAAATATAATAATAATA
1123250 GAA
1 GAA
1123253 GTAAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
17 8 0.24
18 6 0.18
19 1 0.03
20 8 0.24
21 10 0.30
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
GAAAAAAATATAATAATAATA
Found at i:1123492 original size:8 final size:8
Alignment explanation
Indices: 1123479--1123516 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1123469 ACAAAATGTG
1123479 TACATATA
1 TACATATA
1123487 TACATATA
1 TACATATA
*
1123495 TATATATA
1 TACATATA
1123503 TA-ATATA
1 TACATATA
1123510 -ACATATA
1 TACATATA
1123517 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:1123513 original size:205 final size:194
Alignment explanation
Indices: 1123225--1123627 Score: 653
Period size: 205 Copynumber: 2.0 Consensus size: 194
1123215 AAAAAATAAA
1123225 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
1 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
* *
1123290 TATATATATAATATAACATATAAATGAAATAATACTATACTAATAATAAATGTATACGAATGTAT
66 TATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAATGTAT
*
1123355 AAAAAACTAATAATAGTATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAA
131 AAAAAA--AATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAA
1123420 C
194 C
*
1123421 TAATGTAAATAAATATGATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTACATAT
1 TAATGTAAATAAATATAATAATAAAGAAGTAAA-AAATAGGGTAAAATACAAAATGTG-------
*
1123486 ATACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAATATATA
58 -TACATATATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATA
*
1123551 CGAATGTGTAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATA
122 CGAATGTATAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATA
1123616 ATTAAAAC
187 ATTAAAAC
1123624 TAAT
1 TAAT
1123628 ATCCCGAGAA
Statistics
Matches: 192, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
196 32 0.17
197 24 0.12
203 61 0.32
205 75 0.39
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.31
Consensus pattern (194 bp):
TAATGTAAATAAATATAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTACATATA
TATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAATGTAT
AAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATTAAAAC
Found at i:1124724 original size:12 final size:12
Alignment explanation
Indices: 1124698--1124742 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
1124688 AGAAAAAATG
1124698 TAATA-AATATA
1 TAATATAATATA
*
1124709 TAATATAATTTA
1 TAATATAATATA
1124721 TAATATAAATATA
1 TAATAT-AATATA
1124734 TATATATAA
1 TA-ATATAA
1124743 GGACGAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 9 0.31
14 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:1124946 original size:20 final size:20
Alignment explanation
Indices: 1124921--1124971 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1124911 GCGCTTTACT
1124921 GGTTTTATCATTTTGATACC
1 GGTTTTATCATTTTGATACC
1124941 GGTTTTATCATTTTGATACC
1 GGTTTTATCATTTTGATACC
*
1124961 GATTTTATCAT
1 GGTTTTATCAT
1124972 ATTTTTACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (20 bp):
GGTTTTATCATTTTGATACC
Found at i:1128937 original size:131 final size:131
Alignment explanation
Indices: 1128708--1129216 Score: 878
Period size: 131 Copynumber: 3.9 Consensus size: 131
1128698 TAAACATATG
* * *
1128708 TTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACC-AAAAA-ATATATT
1 TTTTAAATATATATTCTTACCTCAAATAATAAACTTGGCATACTTTAAACCAAAAAATATATATT
*
1128771 TGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAATATTTTAAAAT
66 TGATAAATAAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAATATTTTAAAAT
1128836 A
131 A
* * *
1128837 TTTTAAATATATATTCTTACCTCAAATAATAAACTTAGCCTACTTTAAACCAAAATATATATATT
1 TTTTAAATATATATTCTTACCTCAAATAATAAACTTGGCATACTTTAAACCAAAAAATATATATT
*
1128902 TGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAATATTTTAAAAT
66 TGATAAATAAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAATATTTTAAAAT
1128967 A
131 A
1128968 TTTTAAATATATATTCTTACCTCAAATAATAAACTTGGCATACTTTAAACCAAAAAATATATATT
1 TTTTAAATATATATTCTTACCTCAAATAATAAACTTGGCATACTTTAAACCAAAAAATATATATT
* *
1129033 TGATAAATAAAGAAAAAATAACAAAATAAATATTTTTATAGTTAAGAATTTAAATATTTTAAAAT
66 TGATAAATAAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAATATTTTAAAAT
1129098 A
131 A
* * *
1129099 TTTTTAATAAATATTATTACCTCAAATAATAAACTTGGCATACTTTAAACCAAAAAATATATATT
1 TTTTAAATATATATTCTTACCTCAAATAATAAACTTGGCATACTTTAAACCAAAAAATATATATT
*
1129164 TGATAAATAAAGAAAAAATAATAAATTATATATTTTTATAGTTAAGAATTTAA
66 TGATAAATAAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAA
1129217 GATTATACTA
Statistics
Matches: 362, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
129 48 0.13
130 4 0.01
131 310 0.86
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (131 bp):
TTTTAAATATATATTCTTACCTCAAATAATAAACTTGGCATACTTTAAACCAAAAAATATATATT
TGATAAATAAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAATATTTTAAAAT
A
Found at i:1129096 original size:262 final size:254
Alignment explanation
Indices: 1128637--1129216 Score: 883
Period size: 262 Copynumber: 2.3 Consensus size: 254
1128627 ATAATATTTT
** * * * *
1128637 AAAATATATATTCAATGAATTAAG-AAAAATAATAAAATGTATATTTTTATAATTAAAAATTTAA
1 AAAATATATATTTGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAA
* * *
1128701 ACATATGTTTTAAATATATATTCTTAACTTAAATAATAAACTTGGCCTACTTTAAACCAAAAAAT
66 ACATATATTTTAAATATATATTCTTAACTCAAATAATAAACTTGGCATACTTTAAACCAAAAAAT
* * *
1128766 ATATTTGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAATATTTT
131 ATATTTGATAAATAAAGAAAAAATAACAAAATAAATATTTTTATAGTTAAGAATTTAAATATTTT
* * *
1128831 AAAATATTTTAAATATATATTCTTACCTCAAATAATAAACTTAGCCTACTTTAAACCAA
196 AAAATATTTTAAATAAATATTATTACCTCAAATAATAAACTTAGCATACTTTAAACCAA
*
1128890 AATATATATATTTGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAA
1 AAAATATATATTTGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAA
* *
1128955 ATATTTTAAAATATTTTAAATATATATTCTTACCTCAAATAATAAACTTGGCATACTTTAAACCA
66 ACA---T---ATATTTTAAATATATATTCTTAACTCAAATAATAAACTTGGCATACTTTAAACC-
1129020 AAAAATATATATTTGATAAATAAAGAAAAAATAACAAAATAAATATTTTTATAGTTAAGAATTTA
124 AAAAA-ATATATTTGATAAATAAAGAAAAAATAACAAAATAAATATTTTTATAGTTAAGAATTTA
* *
1129085 AATATTTTAAAATATTTTTAATAAATATTATTACCTCAAATAATAAACTTGGCATACTTTAAACC
188 AATATTTTAAAATATTTTAAATAAATATTATTACCTCAAATAATAAACTTAGCATACTTTAAACC
1129150 AA
253 AA
* *
1129152 AAAATATATATTTGATAAATAAAGAAAAAATAATAAATTATATATTTTTATAGTTAAGAATTTAA
1 AAAATATATATTTGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAA
1129217 GATTATACTA
Statistics
Matches: 295, Mismatches: 23, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
253 20 0.07
254 39 0.13
257 1 0.00
260 50 0.17
261 5 0.02
262 180 0.61
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.38
Consensus pattern (254 bp):
AAAATATATATTTGATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAA
ACATATATTTTAAATATATATTCTTAACTCAAATAATAAACTTGGCATACTTTAAACCAAAAAAT
ATATTTGATAAATAAAGAAAAAATAACAAAATAAATATTTTTATAGTTAAGAATTTAAATATTTT
AAAATATTTTAAATAAATATTATTACCTCAAATAATAAACTTAGCATACTTTAAACCAA
Found at i:1133375 original size:50 final size:50
Alignment explanation
Indices: 1133314--1133416 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 50
1133304 AAAATTATTG
* *
1133314 AATACAAAACAAGATATCCCACTAATCAATTTTAAAATAAATACATGCTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1133364 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1133414 AAT
1 AAT
1133417 TAGGATAAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (50 bp):
AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
Found at i:1133614 original size:33 final size:33
Alignment explanation
Indices: 1133572--1133669 Score: 160
Period size: 33 Copynumber: 3.0 Consensus size: 33
1133562 GCGACCTTCA
* *
1133572 TTGGTCGCCCAGAACACCCGGCGACCTTCATTT
1 TTGGTCGCCCAGACCACCCGGCGACCTTCATTG
*
1133605 TTGGTCGCCCAGACCACCCGACGACCTTCATTG
1 TTGGTCGCCCAGACCACCCGGCGACCTTCATTG
*
1133638 TTGGTCGCCCAGACCACCCGGCGATCTTCATT
1 TTGGTCGCCCAGACCACCCGGCGACCTTCATT
1133670 CGAACTGTAG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.17, C:0.38, G:0.21, T:0.23
Consensus pattern (33 bp):
TTGGTCGCCCAGACCACCCGGCGACCTTCATTG
Found at i:1134055 original size:43 final size:44
Alignment explanation
Indices: 1134008--1134097 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 44
1133998 TTTATTGTAT
* *
1134008 ATTATTAAAATAAAAGTATAATATTATATATTAT-AAT-AATATA
1 ATTATAAAAATAAAAGTATAATATTA-AAATTATCAATAAATATA
* * * *
1134051 ATTATAAAAATGATATTATATTATTAAAATTATCAATAAATATA
1 ATTATAAAAATAAAAGTATAATATTAAAATTATCAATAAATATA
1134095 ATT
1 ATT
1134098 TAATAATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
42 6 0.15
43 24 0.62
44 9 0.23
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (44 bp):
ATTATAAAAATAAAAGTATAATATTAAAATTATCAATAAATATA
Found at i:1135872 original size:50 final size:50
Alignment explanation
Indices: 1135811--1135913 Score: 179
Period size: 50 Copynumber: 2.1 Consensus size: 50
1135801 AAAATTATTG
* *
1135811 AATACAAAACAAAATATCCCACTAATCAATTTTAAAATAAATACATGCTA
1 AATACAAAACAAAATATCCCAATAATCAATTTTAAAATAAATACATACTA
*
1135861 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAAATATCCCAATAATCAATTTTAAAATAAATACATACTA
1135911 AAT
1 AAT
1135914 TAGGATAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.26
Consensus pattern (50 bp):
AATACAAAACAAAATATCCCAATAATCAATTTTAAAATAAATACATACTA
Found at i:1136111 original size:33 final size:33
Alignment explanation
Indices: 1136069--1136166 Score: 160
Period size: 33 Copynumber: 3.0 Consensus size: 33
1136059 GCGACCTTCA
* *
1136069 TTGGTCGCCCAGAACACCCGGCGACCTTCATTT
1 TTGGTCGCCCAGACCACCCGGCGACCTTCATTG
*
1136102 TTGGTCGCCCAGACCACCCGACGACCTTCATTG
1 TTGGTCGCCCAGACCACCCGGCGACCTTCATTG
*
1136135 TTGGTCGCCCAGACCACCCGGCGATCTTCATT
1 TTGGTCGCCCAGACCACCCGGCGACCTTCATT
1136167 CGAACTGTAG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.17, C:0.38, G:0.21, T:0.23
Consensus pattern (33 bp):
TTGGTCGCCCAGACCACCCGGCGACCTTCATTG
Found at i:1136552 original size:43 final size:44
Alignment explanation
Indices: 1136505--1136594 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 44
1136495 TTTATTGTAT
* *
1136505 ATTATTAAAATAAAAGTATAATATTATATATTAT-AAT-AATATA
1 ATTATAAAAATAAAAGTATAATATTA-AAATTATCAATAAATATA
* * * *
1136548 ATTATAAAAATGATATTATATTATTAAAATTATCAATAAATATA
1 ATTATAAAAATAAAAGTATAATATTAAAATTATCAATAAATATA
1136592 ATT
1 ATT
1136595 TAATAATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
42 6 0.15
43 24 0.62
44 9 0.23
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (44 bp):
ATTATAAAAATAAAAGTATAATATTAAAATTATCAATAAATATA
Found at i:1139413 original size:9 final size:9
Alignment explanation
Indices: 1139399--1139484 Score: 91
Period size: 9 Copynumber: 9.3 Consensus size: 9
1139389 GCTGCTGGAA
1139399 ACCGGTTTG
1 ACCGGTTTG
1139408 ACCGGTTTG
1 ACCGGTTTG
1139417 ACCGGTTTG
1 ACCGGTTTG
*
1139426 ACCGGTTTA
1 ACCGGTTTG
**
1139435 ACCGGTTCAA
1 ACCGGTT-TG
1139445 ACCGGTTTG
1 ACCGGTTTG
* * *
1139454 ATCGATCTG
1 ACCGGTTTG
1139463 AACCGGTTTG
1 -ACCGGTTTG
*
1139473 ACCGGTCTG
1 ACCGGTTTG
1139482 ACC
1 ACC
1139485 CGACCGACCC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
9 50 0.78
10 14 0.22
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1139422 original size:18 final size:18
Alignment explanation
Indices: 1139399--1139484 Score: 91
Period size: 19 Copynumber: 4.7 Consensus size: 18
1139389 GCTGCTGGAA
1139399 ACCGGTTTGACCGGTTTG
1 ACCGGTTTGACCGGTTTG
*
1139417 ACCGGTTTGACCGGTTTA
1 ACCGGTTTGACCGGTTTG
**
1139435 ACCGGTTCAAACCGGTTTG
1 ACCGGTT-TGACCGGTTTG
* * *
1139454 ATCGATCTGAACCGGTTTG
1 ACCGGTTTG-ACCGGTTTG
*
1139473 ACCGGTCTGACC
1 ACCGGTTTGACC
1139485 CGACCGACCC
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
18 27 0.49
19 28 0.51
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (18 bp):
ACCGGTTTGACCGGTTTG
Found at i:1139513 original size:22 final size:22
Alignment explanation
Indices: 1139488--1139532 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1139478 TCTGACCCGA
*
1139488 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACAGTTGAC
*
1139510 CCGACCCGACCGGACAGTTGAC
1 CCGACCCGACCCGACAGTTGAC
1139532 C
1 C
1139533 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.47, G:0.24, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCCGACAGTTGAC
Found at i:1139538 original size:7 final size:7
Alignment explanation
Indices: 1139526--1139552 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1139516 CGACCGGACA
1139526 GTTGACC
1 GTTGACC
1139533 GTTGACC
1 GTTGACC
1139540 GTTGACC
1 GTTGACC
1139547 GTTGAC
1 GTTGAC
1139553 TTTCTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.30
Consensus pattern (7 bp):
GTTGACC
Found at i:1142620 original size:2 final size:2
Alignment explanation
Indices: 1142613--1142647 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1142603 TCAACTAATC
1142613 TA TA TA TA 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 TA TA TA TA T
1142648 GGTAAATCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1144100 original size:2 final size:2
Alignment explanation
Indices: 1144091--1144122 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1144081 AAATTTAATA
1144091 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1144123 GTACACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1145386 original size:19 final size:19
Alignment explanation
Indices: 1145351--1145388 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1145341 CCATTTATTT
*
1145351 TCATATTAAATATATATAA
1 TCATATTAAATAAATATAA
1145370 TCAT-TTAATATAAATATAA
1 TCATATTAA-ATAAATATAA
1145389 AATGATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
TCATATTAAATAAATATAA
Found at i:1145415 original size:17 final size:18
Alignment explanation
Indices: 1145395--1145436 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
1145385 ATAAAATGAT
1145395 ATTAAA-TTGATAAAAAA
1 ATTAAAGTTGATAAAAAA
*
1145412 ATTAATAGTTTATAAAAAA
1 ATTAA-AGTTGATAAAAAA
1145431 ATTAAA
1 ATTAAA
1145437 ACTTTCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 2 0.09
19 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
ATTAAAGTTGATAAAAAA
Found at i:1151899 original size:45 final size:45
Alignment explanation
Indices: 1151845--1151939 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
1151835 ACAAATAATT
*
1151845 AGTAGACCTATTAGTTAGAAGTTTGATTTGATTCTATAATAGTTA
1 AGTAGACCTATTAGTTAAAAGTTTGATTTGATTCTATAATAGTTA
1151890 AGTAGACCTATTAGTTAAAAGTTTGATTTGATTCTATAATAGTTA
1 AGTAGACCTATTAGTTAAAAGTTTGATTTGATTCTATAATAGTTA
1151935 AGTAG
1 AGTAG
1151940 GATTTGGATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (45 bp):
AGTAGACCTATTAGTTAAAAGTTTGATTTGATTCTATAATAGTTA
Found at i:1151963 original size:45 final size:44
Alignment explanation
Indices: 1151845--1151966 Score: 131
Period size: 45 Copynumber: 2.7 Consensus size: 44
1151835 ACAAATAATT
* * *
1151845 AGTAGACCTATTAGTTAGAAGTTTGATTTGATTCTATAATAGTTA
1 AGTAGA-CTATTAGATAAAACTTTGATTTGATTCTATAATAGTTA
* *
1151890 AGTAGACCTATTAGTTAAAAGTTTGATTTGATTCTATAATAGTTA
1 AGTAGA-CTATTAGATAAAACTTTGATTTGATTCTATAATAGTTA
*
1151935 AGTAGGA-T-TTGGATAAAACTTTGGGATTTGAT
1 AGTA-GACTATTAGATAAAACTTT--GATTTGAT
1151967 ATGGAAGAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
43 11 0.16
44 1 0.01
45 56 0.80
46 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.41
Consensus pattern (44 bp):
AGTAGACTATTAGATAAAACTTTGATTTGATTCTATAATAGTTA
Found at i:1155255 original size:20 final size:21
Alignment explanation
Indices: 1155227--1155275 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1155217 AATTGCGGCC
*
1155227 ATAGTGGGCGC-ATTACCGGT
1 ATAGCGGGCGCTATTACCGGT
*
1155247 ATAGCGGGCGCTATTACGGGT
1 ATAGCGGGCGCTATTACCGGT
1155268 ATAGCGGG
1 ATAGCGGG
1155276 TATAATGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.20, C:0.18, G:0.39, T:0.22
Consensus pattern (21 bp):
ATAGCGGGCGCTATTACCGGT
Found at i:1155803 original size:24 final size:24
Alignment explanation
Indices: 1155771--1155816 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1155761 TATGGTTGGA
1155771 GAAGAAGAGAGAAGAGGAAGCATC
1 GAAGAAGAGAGAAGAGGAAGCATC
*
1155795 GAAGAAGAGAGACGAGGAAGCA
1 GAAGAAGAGAGAAGAGGAAGCA
1155817 GGAGCAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.39, T:0.02
Consensus pattern (24 bp):
GAAGAAGAGAGAAGAGGAAGCATC
Found at i:1164811 original size:22 final size:22
Alignment explanation
Indices: 1164783--1164843 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
1164773 TTCGCTATCA
*
1164783 CCTTTTCATCAAATCCGTCGAT
1 CCTTTTCATCAAATCCGCCGAT
* **
1164805 CCTTTTCGAGCACCTCCGCCGAT
1 CCTTTTC-ATCAAATCCGCCGAT
1164828 CC-TTTCATCAAATCCG
1 CCTTTTCATCAAATCCG
1164844 GTAACCCGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 7 0.23
22 11 0.35
23 13 0.42
ACGTcount: A:0.20, C:0.38, G:0.11, T:0.31
Consensus pattern (22 bp):
CCTTTTCATCAAATCCGCCGAT
Found at i:1172983 original size:34 final size:35
Alignment explanation
Indices: 1172938--1173005 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
1172928 AATAGGAATT
* *
1172938 ACAATTTCTCTC-GATCTAACAAGGAGAAAACAATG
1 ACAATTTCTCTCTGAT-AAAAAAGGAGAAAACAATG
1172973 ACAA-TTCTCTCTTGATAAAAAAGGAGAAAACAA
1 ACAATTTCTCTC-TGATAAAAAAGGAGAAAACAA
1173006 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 7 0.24
35 19 0.66
36 3 0.10
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (35 bp):
ACAATTTCTCTCTGATAAAAAAGGAGAAAACAATG
Found at i:1181085 original size:2 final size:2
Alignment explanation
Indices: 1181078--1181121 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
1181068 GTCACTGAAT
*
1181078 TA TA TA TA TA AA TA -A T- TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1181117 TA TA T
1 TA TA T
1181122 TTTTGGTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1186270 original size:24 final size:24
Alignment explanation
Indices: 1186243--1186352 Score: 102
Period size: 24 Copynumber: 4.6 Consensus size: 24
1186233 GTAAACGGAG
*
1186243 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
1186267 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
1186291 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
1186314 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
*
1186338 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
1186353 TAAAATATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 16 0.23
24 50 0.71
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:1186274 original size:12 final size:12
Alignment explanation
Indices: 1186247--1186338 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
1186237 ACGGAGATAT
* *
1186247 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
1186259 CAGAATTCATAT
1 CAGAATTCAGAA
1186271 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1186283 CAGAATCCAGAT
1 CAGAATTCAGAA
1186295 CAGAA-TCAGAA
1 CAGAATTCAGAA
1186306 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
1186320 C-GTA-TCAGAA
1 CAGAATTCAGAA
1186330 CAGAATTCA
1 CAGAATTCA
1186339 ATTCGGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1186326 original size:47 final size:48
Alignment explanation
Indices: 1186245--1186335 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
1186235 AAACGGAGAT
*
1186245 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
*
1186293 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAAT
1186336 TCAATTCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 30 0.77
48 6 0.15
49 3 0.08
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:1188788 original size:13 final size:13
Alignment explanation
Indices: 1188770--1188799 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1188760 GGTCAACGCC
1188770 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1188783 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1188796 GGTC
1 GGTC
1188800 GGGTTATGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1191588 original size:39 final size:40
Alignment explanation
Indices: 1191544--1191637 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 40
1191534 CTTAAAATAC
1191544 GCTCATTGTTTTGAGAA-TTTTTTTCGGACTTGAACTGAA
1 GCTCATTGTTTTGAGAATTTTTTTTCGGACTTGAACTGAA
* *
1191583 GCTCATTGTTTTGAGAATTTTTTTTTTCGGATTTGAACTGAG
1 GCTCATTGTTTTGAGAA--TTTTTTTTCGGACTTGAACTGAA
1191625 GCTCATTGTTTTG
1 GCTCATTGTTTTG
1191638 GGTTTGAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 17 0.34
42 33 0.66
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (40 bp):
GCTCATTGTTTTGAGAATTTTTTTTCGGACTTGAACTGAA
Found at i:1203730 original size:3 final size:3
Alignment explanation
Indices: 1203715--1203780 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
1203705 TCAGATGATA
* * ** * *
1203715 CAG CAG CAA CAG CAG CAG CAA TTG CAA CAA CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
*
1203763 CAG CCA- CCG CAG CAG CAG
1 CAG -CAG CAG CAG CAG CAG
1203781 GTACAAATGC
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
2 1 0.02
3 46 0.94
4 2 0.04
ACGTcount: A:0.36, C:0.35, G:0.26, T:0.03
Consensus pattern (3 bp):
CAG
Found at i:1203732 original size:12 final size:12
Alignment explanation
Indices: 1203715--1203779 Score: 64
Period size: 12 Copynumber: 5.7 Consensus size: 12
1203705 TCAGATGATA
1203715 CAGCAGCAACAG
1 CAGCAGCAACAG
**
1203727 CAGCAGCAATTG
1 CAGCAGCAACAG
1203739 CA--A-CAACAG
1 CAGCAGCAACAG
*
1203748 CAGCAGCAGCAG
1 CAGCAGCAACAG
* *
1203760 CAGCAGCCACCG
1 CAGCAGCAACAG
1203772 CAGCAGCA
1 CAGCAGCA
1203780 GGTACAAATG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
9 6 0.15
10 1 0.02
11 1 0.02
12 33 0.80
ACGTcount: A:0.37, C:0.35, G:0.25, T:0.03
Consensus pattern (12 bp):
CAGCAGCAACAG
Found at i:1205189 original size:2 final size:2
Alignment explanation
Indices: 1205182--1205225 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1205172 ACATTTAAGA
1205182 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
1205224 AT
1 AT
1205226 TTTCAATTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1209694 original size:2 final size:2
Alignment explanation
Indices: 1209687--1209723 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1209677 TCTGTATCTT
1209687 TA TA TA TA TA 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 TA TA TA TA TA T
1209724 TCCCTTATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1217095 original size:33 final size:33
Alignment explanation
Indices: 1217057--1217159 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 33
1217047 CGAGCTGCTT
1217057 CCAACTGAGACATCTCTGCATCCAACGTGTTCA
1 CCAACTGAGACATCTCTGCATCCAACGTGTTCA
* * * ** * *
1217090 CCAACTCCA-ACACCTCCGGTTCGAGC-TGCTT--
1 CCAACT-GAGACATCTCTGCATCCAACGTG-TTCA
1217121 CCAACTGAGACATCTCTGCATCCAACGTGTTCA
1 CCAACTGAGACATCTCTGCATCCAACGTGTTCA
1217154 CCAACT
1 CCAACT
1217160 CCAACACCTC
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
30 1 0.02
31 19 0.38
32 4 0.08
33 25 0.50
34 1 0.02
ACGTcount: A:0.25, C:0.37, G:0.15, T:0.23
Consensus pattern (33 bp):
CCAACTGAGACATCTCTGCATCCAACGTGTTCA
Found at i:1217146 original size:64 final size:64
Alignment explanation
Indices: 1217045--1217173 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
1217035 GAATATATTC
1217045 TTCGAGCTGCTTCCAACTGAGACATCTCTGCATCCAACGTGTTCACCAACTCCAACACCTCCGG
1 TTCGAGCTGCTTCCAACTGAGACATCTCTGCATCCAACGTGTTCACCAACTCCAACACCTCCGG
1217109 TTCGAGCTGCTTCCAACTGAGACATCTCTGCATCCAACGTGTTCACCAACTCCAACACCTCCGG
1 TTCGAGCTGCTTCCAACTGAGACATCTCTGCATCCAACGTGTTCACCAACTCCAACACCTCCGG
1217173 T
1 T
1217174 GTACTAACAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.24
Consensus pattern (64 bp):
TTCGAGCTGCTTCCAACTGAGACATCTCTGCATCCAACGTGTTCACCAACTCCAACACCTCCGG
Found at i:1219451 original size:2 final size:2
Alignment explanation
Indices: 1219444--1219477 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1219434 TAAATGAATA
1219444 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
1219478 GGAGCGTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1219937 original size:25 final size:24
Alignment explanation
Indices: 1219878--1219937 Score: 57
Period size: 26 Copynumber: 2.3 Consensus size: 24
1219868 ATCTAATTTT
* * *
1219878 TTAAAATAGAAATGAAAAATAGTTA
1 TTAAAAT-TAAATCAAAAATAATTA
1219903 TTAAATAATTAAATCAAAATATAATTA
1 TT-AA-AATTAAATCAAAA-ATAATTA
1219930 TTAAAATT
1 TTAAAATT
1219938 TTTCTTTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 6 0.21
26 12 0.41
27 11 0.38
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (24 bp):
TTAAAATTAAATCAAAAATAATTA
Found at i:1220663 original size:43 final size:43
Alignment explanation
Indices: 1220616--1220698 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
1220606 TTTGTGGCAT
** * *
1220616 TTTGTCCCAAAAATGCCGCTAGATGTTCTGACATATAGTGACA
1 TTTGTCCCAAAAAAACCGCTAAATGTTATGACATATAGTGACA
* * *
1220659 TTTGTTCCAAAAAAATCGCTAAATGTTATGTCATATAGTG
1 TTTGTCCCAAAAAAACCGCTAAATGTTATGACATATAGTG
1220699 GTATTTGTGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (43 bp):
TTTGTCCCAAAAAAACCGCTAAATGTTATGACATATAGTGACA
Found at i:1220979 original size:21 final size:21
Alignment explanation
Indices: 1220920--1220981 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1220910 ATTATCCAAT
* * *
1220920 AAACTTGACATTTATAACAAC
1 AAACTTGAAATTCATAATAAC
* * *
1220941 AAATTTGAAATCCATAATAAG
1 AAACTTGAAATTCATAATAAC
1220962 AAACTTGAAATTCATAATAA
1 AAACTTGAAATTCATAATAA
1220982 TAAATCAAAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (21 bp):
AAACTTGAAATTCATAATAAC
Found at i:1221885 original size:116 final size:116
Alignment explanation
Indices: 1221681--1221914 Score: 468
Period size: 116 Copynumber: 2.0 Consensus size: 116
1221671 GAACGATAAC
1221681 ATTGGATTGGACAATGGAAAAAACAAAAGATTATACCATTTGAATGGCTGCCAAAGATGACAGTA
1 ATTGGATTGGACAATGGAAAAAACAAAAGATTATACCATTTGAATGGCTGCCAAAGATGACAGTA
1221746 CCACCTCCATTCATCTCAGCTCGTCGAATCGCGACAACACTCGCAAATTCT
66 CCACCTCCATTCATCTCAGCTCGTCGAATCGCGACAACACTCGCAAATTCT
1221797 ATTGGATTGGACAATGGAAAAAACAAAAGATTATACCATTTGAATGGCTGCCAAAGATGACAGTA
1 ATTGGATTGGACAATGGAAAAAACAAAAGATTATACCATTTGAATGGCTGCCAAAGATGACAGTA
1221862 CCACCTCCATTCATCTCAGCTCGTCGAATCGCGACAACACTCGCAAATTCT
66 CCACCTCCATTCATCTCAGCTCGTCGAATCGCGACAACACTCGCAAATTCT
1221913 AT
1 AT
1221915 GTAGGGATAC
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (116 bp):
ATTGGATTGGACAATGGAAAAAACAAAAGATTATACCATTTGAATGGCTGCCAAAGATGACAGTA
CCACCTCCATTCATCTCAGCTCGTCGAATCGCGACAACACTCGCAAATTCT
Found at i:1225220 original size:40 final size:40
Alignment explanation
Indices: 1225132--1225243 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 40
1225122 TGTAAACTTG
* * * * *
1225132 CTTTAGCGGCGTTTGTATGAAAACGTCACTAAAGTATGAGT
1 CTTTAGC-GCGTTTGTATAAAAACGCCACTAAAATACGAAT
* * *
1225173 CTATAGCGTGTTTATATAAAAACGCCACTAAAATACGAAT
1 CTTTAGCGCGTTTGTATAAAAACGCCACTAAAATACGAAT
* *
1225213 CTTTAGCGACGTTTGTATACAAACGCAACTA
1 CTTTAGCG-CGTTTGTATAAAAACGCCACTA
1225244 GTGTATTGAT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 33 0.58
41 24 0.42
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (40 bp):
CTTTAGCGCGTTTGTATAAAAACGCCACTAAAATACGAAT
Found at i:1225439 original size:36 final size:38
Alignment explanation
Indices: 1225341--1225451 Score: 120
Period size: 36 Copynumber: 2.9 Consensus size: 38
1225331 TGTGTCCTCT
* *
1225341 TATGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
1 TATGGCGTTTATATAAAAACACCACTAAAGTAC-AGTC-A
**
1225381 TAGTGGCGTTTATA-ATTTAACACCACTAAAGTACAGTC-
1 TA-TGGCGTTTATATA-AAAACACCACTAAAGTACAGTCA
*
1225419 T-TGGCGTTTATATAAAAACACCACTAAAATACA
1 TATGGCGTTTATATAAAAACACCACTAAAGTACA
1225452 AGTATTTAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
36 27 0.44
37 1 0.02
38 1 0.02
40 7 0.11
41 25 0.41
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (38 bp):
TATGGCGTTTATATAAAAACACCACTAAAGTACAGTCA
Found at i:1225467 original size:41 final size:38
Alignment explanation
Indices: 1225345--1225468 Score: 101
Period size: 41 Copynumber: 3.2 Consensus size: 38
1225335 TCCTCTTATG
* * *
1225345 GCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGT
1 GCGTTTATATAAAAACACCACTAAAGTAC-AGT-TTTAGT
** *
1225385 GGCGTTTATA-ATTTAACACCACTAAAGTACAGTCTT-G-
1 -GCGTTTATATA-AAAACACCACTAAAGTACAGTTTTAGT
*
1225422 GCGTTTATATAAAAACACCACTAAAATACAAGTATTTAGTT
1 GCGTTTATATAAAAACACCACTAAAGTAC-AGT-TTTAG-T
1225463 GCGTTT
1 GCGTTT
1225469 TTGCTTAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
36 24 0.36
37 4 0.06
38 3 0.05
39 2 0.03
40 4 0.06
41 29 0.44
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (38 bp):
GCGTTTATATAAAAACACCACTAAAGTACAGTTTTAGT
Found at i:1229739 original size:2 final size:2
Alignment explanation
Indices: 1229734--1229809 Score: 102
Period size: 2 Copynumber: 39.0 Consensus size: 2
1229724 TATATTTTCA
*
1229734 AT AT AT A- AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1229774 AT AT AT AT AT CT AT CT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1229810 CAACTAAACT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
1 2 0.03
2 62 0.97
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1229769 original size:31 final size:31
Alignment explanation
Indices: 1229734--1229802 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
1229724 TATATTTTCA
1229734 ATATATAATAAATATATATATATATATATAT
1 ATATATAATAAATATATATATATATATATAT
* * *
1229765 ATATATAATATATATATATCTATCTATATAT
1 ATATATAATAAATATATATATATATATATAT
1229796 ATATATA
1 ATATATA
1229803 TCTATATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
ATATATAATAAATATATATATATATATATAT
Found at i:1229949 original size:16 final size:16
Alignment explanation
Indices: 1229928--1229994 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
1229918 TGAAAGAATT
*
1229928 CGAACCGAAAGTAATC
1 CGAACCGAAAGTAACC
**
1229944 CGAACCGAAAACAA-C
1 CGAACCGAAAGTAACC
*
1229959 CGAACCGAAAATAACC
1 CGAACCGAAAGTAACC
1229975 CGAACCGAAAGTAACC
1 CGAACCGAAAGTAACC
1229991 CGAA
1 CGAA
1229995 TTTAATTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.30
16 32 0.70
ACGTcount: A:0.48, C:0.30, G:0.16, T:0.06
Consensus pattern (16 bp):
CGAACCGAAAGTAACC
Found at i:1230636 original size:31 final size:31
Alignment explanation
Indices: 1230577--1230637 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1230567 ATATTAACTC
*
1230577 GACCCGAAAATCAACTGATCCGACTTGATCT
1 GACCCGAAAATCAACTGATCCGAATTGATCT
* *
1230608 GACCC-AAAATCAATTGATCTGATATTGATC
1 GACCCGAAAATCAACTGATCCGA-ATTGATC
1230638 CAAACTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (31 bp):
GACCCGAAAATCAACTGATCCGAATTGATCT
Found at i:1231418 original size:14 final size:15
Alignment explanation
Indices: 1231401--1231430 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1231391 AAATTCAGGT
1231401 AAATAAT-ATTATAA
1 AAATAATAATTATAA
1231415 AAATAATAATTATAA
1 AAATAATAATTATAA
1231430 A
1 A
1231431 CTGTTAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATAATAATTATAA
Done.