Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 8 of 25
Found at i:1137497 original size:19 final size:20
Alignment explanation
Indices: 1137454--1137506 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1137444 TGCCAGTTTT
* **
1137454 ATGTATAGATACAATTGTCC
1 ATGTATCGATACAATTGAAC
1137474 ATGTATCGATACAA-TGAAC
1 ATGTATCGATACAATTGAAC
1137493 ATGTATCGATACAA
1 ATGTATCGATACAA
1137507 ATCATAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAC
Found at i:1137518 original size:20 final size:19
Alignment explanation
Indices: 1137473--1137522 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1137463 TACAATTGTC
*
1137473 CATGTATCGATACAATGAA
1 CATGTATCGATACAATCAA
1137492 CATGTATCGATACAAATCATA
1 CATGTATCGATAC-AATCA-A
1137513 -ATGTATCGAT
1 CATGTATCGAT
1137523 TCATCTGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.46
20 14 0.50
21 1 0.04
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATCAA
Found at i:1142218 original size:98 final size:99
Alignment explanation
Indices: 1142036--1142218 Score: 212
Period size: 98 Copynumber: 1.9 Consensus size: 99
1142026 CCTTCGAGGG
* * ** *
1142036 GATACTCCAACCCTGTTTTTTAAAACTTGTCAAGATTTAAATCTTGTTTTCACTTAAATTATCAT
1 GATACTCCAACCCTGATTTTTAAAACTTATCAAGATTTAAATCTTCCTTGCACTTAAATTATCAT
* * *
1142101 TATCGGGGATACTCCAACCCCATTCCTCCTAAGA
66 CATCAGGGACACTCCAACCCCATTCCTCCTAAGA
* *
1142135 GATACTCCAACCCT-ATTTTTAAAACTTATCAAGATTTGAATCTTACCCTTGC-C-TAAATTGTC
1 GATACTCCAACCCTGATTTTTAAAACTTATCAAGATTTAAATCTT--CCTTGCACTTAAATTATC
*
1142197 ATCATTAGGGACAC-CCTAACCC
64 ATCATCAGGGACACTCC-AACCC
1142219 TATTTTTCAA
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
97 2 0.03
98 50 0.71
99 15 0.21
100 3 0.04
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (99 bp):
GATACTCCAACCCTGATTTTTAAAACTTATCAAGATTTAAATCTTCCTTGCACTTAAATTATCAT
CATCAGGGACACTCCAACCCCATTCCTCCTAAGA
Found at i:1146032 original size:18 final size:18
Alignment explanation
Indices: 1146009--1146045 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1145999 TCTGGGTTTT
1146009 ACCCAGATGTATCGATAC
1 ACCCAGATGTATCGATAC
1146027 ACCCAGATGTATCGATAC
1 ACCCAGATGTATCGATAC
1146045 A
1 A
1146046 TTATTCATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (18 bp):
ACCCAGATGTATCGATAC
Found at i:1146059 original size:20 final size:20
Alignment explanation
Indices: 1146034--1146147 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
1146024 TACACCCAGA
*
1146034 TGTATCGATACATTATTCAT
1 TGTATCGATACATTGTTCAT
1146054 TGTATCGATACATTGTTCAT
1 TGTATCGATACATTGTTCAT
*
1146074 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGTTCAT
*
1146094 TGTATCAATACATTGTTCAT
1 TGTATCGATACATTGTTCAT
* * *
1146114 TTTATCAATACATTATTCAT
1 TGTATCGATACATTGTTCAT
1146134 TGTATCGATACATT
1 TGTATCGATACATT
1146148 CTGGGTTTAC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTGTTCAT
Found at i:1148727 original size:130 final size:129
Alignment explanation
Indices: 1148492--1148732 Score: 297
Period size: 130 Copynumber: 1.9 Consensus size: 129
1148482 ATTTTTCATC
* * * * *
1148492 TCGGGGATACTCCAACCTCGGTTTTATTTCCAAAACATTAATTTTTCATAATCGGGGATACTCTA
1 TCGGGGATACTCCAACCCCGATTTTATTTCCAAAACA-TAATTTTTCACAATCGAGGATACTCCA
** * **
1148557 ATTCCGTTATTTCCGACGGGATACTCCAACCTCGGCTTTATTTCTAAAATATTGATTTCTCACAA
65 ACCCCGTTATTTCCAACGGGATACTCCAACCTCAACTTTATTTCTAAAATATTGATTTCTCACAA
* *
1148622 TCGGGGATACTCCAACCCCGATTTTATTTCTAAAACCA-AATCTTTTCACAATCGAGGATATTCC
1 TCGGGGATACTCCAACCCCGATTTTATTTCCAAAA-CATAAT-TTTTCACAATCGAGGATACTCC
* * *
1148686 AACCCCGTTATTTTCAAGGGGATACTCCAACC-CTAATTTTATTTCTA
64 AACCCCGTTATTTCCAACGGGATACTCCAACCTC-AACTTTATTTCTA
1148733 GAACACCGAT
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
129 4 0.04
130 87 0.94
131 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (129 bp):
TCGGGGATACTCCAACCCCGATTTTATTTCCAAAACATAATTTTTCACAATCGAGGATACTCCAA
CCCCGTTATTTCCAACGGGATACTCCAACCTCAACTTTATTTCTAAAATATTGATTTCTCACAA
Found at i:1150852 original size:4 final size:4
Alignment explanation
Indices: 1150843--1150869 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1150833 TTTTGAGGTG
1150843 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1150870 GTTTTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1161172 original size:11 final size:11
Alignment explanation
Indices: 1161152--1161180 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1161142 CTTCTTTTTT
1161152 AAAA-AAAAAC
1 AAAACAAAAAC
1161162 AAAACAAAAAC
1 AAAACAAAAAC
1161173 AAAACAAA
1 AAAACAAA
1161181 GAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAC
Found at i:1162402 original size:61 final size:62
Alignment explanation
Indices: 1162274--1162427 Score: 213
Period size: 61 Copynumber: 2.5 Consensus size: 62
1162264 TTCACCCATT
* * *
1162274 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAAGCCCACACAAGTTGGTGGCACCTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAAGCCCACACAAGTTGATGGCACCTTCC
* * *
1162336 AGTCCTTAAATAGCAGGACGCCTTCTCCTTTT-AAAGCCCACACAAGTTGATGGCACTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAAGCCCACACAAGTTGATGGCACCTTCC
* *
1162397 AGTCCTCAAAGAGTAGGATG-CTCTCTCCTTT
1 AGTCCTCAAAGAGCAGGACGCCT-TCTCCTTT
1162428 CACCCTTTAG
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
60 2 0.02
61 50 0.62
62 29 0.36
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (62 bp):
AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAAGCCCACACAAGTTGATGGCACCTTCC
Found at i:1162452 original size:162 final size:162
Alignment explanation
Indices: 1162174--1162577 Score: 657
Period size: 162 Copynumber: 2.5 Consensus size: 162
1162164 TTCACTTTTC
*
1162174 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTCCCACT
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CCAGT
*
1162238 CCTCAAAGAGCAGGAAGCTCTCTCCTTTCACCCATTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
65 CCTCAAAGAGTAGGAAGCTCTCTCCTTTCACCCATTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
1162303 TTTAAAAGCCCACACAAGTTGGTGGCACCTTCT
130 TTTAAAAGCCCACACAAGTTGGTGGCACCTTCT
* * *
1162336 AGTCCTTAAATAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGATGGCACTTTCCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTC
* * * *
1162401 CTCAAAGAGTAGGATGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCCTT
66 CTCAAAGAGTAGGAAGCTCTCTCCTTTCACCCATTAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
* *
1162466 TTAAAAGCCCACATAAGTTGGTGTCACCTTCT
131 TTAAAAGCCCACACAAGTTGGTGGCACCTTCT
* * *
1162498 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTACAGCCCACACAAGTTGGTGGCACTTTTCTAGT
1 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCCAGT
1162563 CCTCAAAGAGTAGGA
65 CCTCAAAGAGTAGGA
1162578 CGCCTTAGAA
Statistics
Matches: 223, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
162 198 0.89
163 25 0.11
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (162 bp):
AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTC
CTCAAAGAGTAGGAAGCTCTCTCCTTTCACCCATTAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
TTAAAAGCCCACACAAGTTGGTGGCACCTTCT
Found at i:1162506 original size:62 final size:61
Alignment explanation
Indices: 1162431--1162583 Score: 218
Period size: 62 Copynumber: 2.5 Consensus size: 61
1162421 CTCCTTTCAC
* * * *
1162431 CCTT-TAGTCCTCAAAGAGCAGGATGCTTTTTCCTTTTAAAAGCCCACATAAGTTGGTGTCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
*
1162492 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTACAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1162553 CTTTTCTAGTCCTCAAAGAGTAGGACGCCTT
1 C-CTTCTAGTCCTCAAAGAGCAGGACGCCTT
1162584 AGAAAATCCG
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
61 25 0.30
62 58 0.70
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (61 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1162509 original size:101 final size:101
Alignment explanation
Indices: 1162330--1162515 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 101
1162320 GTTGGTGGCA
* * *
1162330 CCTTCTAGTCCTTAAATAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGATGGCACTTT
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGATGGCACCTT
*
1162395 CCAGTCCTCAAAGAGTAGGATGCTCTCTCCTTTCAC
66 CCAGTCCTCAAAGAGCAGGATGCTCTCTCCTTTCAC
* * * * * *
1162431 CCTT-TAGTCCTCAAAGAGCAGGATGCTTTTTCCTTTTAAAAGCCCACATAAGTTGGTGTCACCT
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT-AAAGCCCACACAAGTTGATGGCACCT
*
1162495 TCTAGTCCTCAAAGAGCAGGA
65 TCCAGTCCTCAAAGAGCAGGA
1162516 CGCCTTTTCC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
100 28 0.38
101 45 0.62
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (101 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGATGGCACCTT
CCAGTCCTCAAAGAGCAGGATGCTCTCTCCTTTCAC
Found at i:1165661 original size:51 final size:51
Alignment explanation
Indices: 1165599--1165715 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
1165589 TATTTCCAAA
* * *
1165599 GGGATATTCCAACCCC-AGCTTTATTTCTAAAA-TATTGAT-TTCTCACAATCG
1 GGGATACTCCAACCCCGA-CTTTATTTCTAAAACCA--AATCTTCTCACAATCG
* *
1165650 GGGATACTCCAACCCCGATTTTATTTCTAAAACCAAATCTTTTCACAATCG
1 GGGATACTCCAACCCCGACTTTATTTCTAAAACCAAATCTTCTCACAATCG
1165701 GGGATACTCCAACCC
1 GGGATACTCCAACCC
1165716 TGTTATTTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
50 2 0.03
51 54 0.93
52 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACCCCGACTTTATTTCTAAAACCAAATCTTCTCACAATCG
Found at i:1165769 original size:130 final size:129
Alignment explanation
Indices: 1165521--1165791 Score: 304
Period size: 130 Copynumber: 2.1 Consensus size: 129
1165511 TTTTCATCTC
* * * *
1165521 GGGATGCTCCAACCCCGGTTTTTTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAATCT
1 GGGATACTCCAACCCCGATTTTTTTCTAAAACA-CAATTTTTCACAATCGGGGATACTCCAACCT
* * **
1165586 CGTTATTTCCAAAGGGATATTCCAACCCCAGCTTTATTTCTAAAATATTGATTTCTCACA-A-TC
65 CGTTATTTCCAAAGGGATACTCCAACCCCAGCTTTATTTCTAAAACACCGATTT-TC-CATAGTC
1165649 -G
128 AG
1165650 GGGATACTCCAACCCCGATTTTATTTCTAAAAC-CAAATCTTTTCACAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCCGATTTT-TTTCTAAAACAC-AAT-TTTTCACAATCGGGGATACTCCAAC
* * * *
1165714 C-CTGTTATTTTC-AAGGGTATACTCCAA-CCCTGATTTTATTTCTAGAACACCGATTTTCCATA
63 CTC-GTTATTTCCAAAGGG-ATACTCCAACCCCAG-CTTTATTTCTAAAACACCGATTTTCCATA
1165776 GTCAG
125 GTCAG
1165781 GGGATACTCCA
1 GGGATACTCCA
1165792 GCCTCGTTGT
Statistics
Matches: 121, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
128 3 0.02
129 36 0.30
130 70 0.58
131 12 0.10
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (129 bp):
GGGATACTCCAACCCCGATTTTTTTCTAAAACACAATTTTTCACAATCGGGGATACTCCAACCTC
GTTATTTCCAAAGGGATACTCCAACCCCAGCTTTATTTCTAAAACACCGATTTTCCATAGTCAG
Found at i:1172185 original size:19 final size:19
Alignment explanation
Indices: 1172138--1172186 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1172128 ATTATTTTTT
*
1172138 AAAATTTAAT-AAAAATAA
1 AAAATTAAATAAAAAATAA
* * *
1172156 TATATTCAATAAAAAATAA
1 AAAATTAAATAAAAAATAA
1172175 AAAATTAAATAA
1 AAAATTAAATAA
1172187 TTTTAAATAG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATTAAATAAAAAATAA
Found at i:1173501 original size:17 final size:18
Alignment explanation
Indices: 1173481--1173514 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1173471 TAATTAATGC
1173481 AATAGTAAAATT-AAGTA
1 AATAGTAAAATTCAAGTA
*
1173498 AATATTAAAATTCAAGT
1 AATAGTAAAATTCAAGT
1173515 GTTTGTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (18 bp):
AATAGTAAAATTCAAGTA
Found at i:1175475 original size:34 final size:34
Alignment explanation
Indices: 1175411--1175593 Score: 251
Period size: 34 Copynumber: 5.4 Consensus size: 34
1175401 AGATGGAAGA
* * *
1175411 TGTTGATTAAAT-GGTGATGTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1175444 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1175478 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1175512 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1175546 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1175580 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1175594 TGGTTTTTAC
Statistics
Matches: 131, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 11 0.08
34 120 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.39
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1175954 original size:19 final size:19
Alignment explanation
Indices: 1175898--1175960 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1175888 TGGTTGTCGA
**
1175898 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1175917 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1175936 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1175955 GTTACT
1 GGTACT
1175961 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1180092 original size:34 final size:34
Alignment explanation
Indices: 1180026--1180210 Score: 255
Period size: 34 Copynumber: 5.5 Consensus size: 34
1180016 AAGTGGGAGA
* * *
1180026 ATTGTTGATTAAAT-GGTGATGTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1180059 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1180093 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1180127 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1180161 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1180195 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1180211 TGGTTTTTAC
Statistics
Matches: 133, Mismatches: 18, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
33 13 0.10
34 120 0.90
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.39
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1180839 original size:11 final size:11
Alignment explanation
Indices: 1180797--1180839 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1180787 AATACTATTA
* *
1180797 ATAATTTATTG
1 ATAATTTTTTT
*
1180808 ATAATTATTTT
1 ATAATTTTTTT
1180819 ATAATATTTTTT
1 ATAAT-TTTTTT
1180831 ATAATTTTT
1 ATAATTTTT
1180840 ATTTTTGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
ATAATTTTTTT
Found at i:1184387 original size:3 final size:3
Alignment explanation
Indices: 1184379--1184405 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1184369 CAATATGTAA
1184379 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1184406 TTAAGAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1184791 original size:25 final size:24
Alignment explanation
Indices: 1184748--1184800 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1184738 TTCGATAATT
* * *
1184748 TTTTATTATTTTAGGATTTTATTTC
1 TTTTATTATTTTA-CAATTTATTAC
*
1184773 TTTTATTATTTTTCAATTTATTAC
1 TTTTATTATTTTACAATTTATTAC
1184797 TTTT
1 TTTT
1184801 CATCGTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTATTATTTTACAATTTATTAC
Found at i:1185361 original size:11 final size:11
Alignment explanation
Indices: 1185345--1185387 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1185335 TTTTACGTCT
*
1185345 TAATATATTTA
1 TAATATAATTA
*
1185356 TAATATAAATA
1 TAATATAATTA
1185367 TAATCATAAATTA
1 TAAT-AT-AATTA
1185380 TAATATAA
1 TAATATAA
1185388 ATAAACAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 15 0.56
12 4 0.15
13 8 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATATAATTA
Found at i:1185377 original size:12 final size:11
Alignment explanation
Indices: 1185354--1185390 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
1185344 TTAATATATT
1185354 TATAATATAAA
1 TATAATATAAA
1185365 TATAATCATAAA
1 TATAAT-ATAAA
1185377 TTATAATATAAA
1 -TATAATATAAA
1185389 TA
1 TA
1185391 AACAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 10 0.42
13 6 0.25
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAATATAAA
Found at i:1189244 original size:13 final size:13
Alignment explanation
Indices: 1189226--1189251 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1189216 TACACAAAAG
1189226 ATGTATCGATACA
1 ATGTATCGATACA
1189239 ATGTATCGATACA
1 ATGTATCGATACA
1189252 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1189268 original size:33 final size:32
Alignment explanation
Indices: 1189208--1189271 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1189198 CTTAACTGTT
1189208 TGTATCGATACACAAAAGATGTATCGATACAA
1 TGTATCGATACACAAAAGATGTATCGATACAA
*
1189240 TGTATCGATACATCCCAAA-ATGTATCGATACA
1 TGTATCGATACA--CAAAAGATGTATCGATACA
1189272 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 13 0.45
34 4 0.14
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACAAAAGATGTATCGATACAA
Found at i:1194051 original size:52 final size:52
Alignment explanation
Indices: 1193970--1194094 Score: 241
Period size: 52 Copynumber: 2.4 Consensus size: 52
1193960 ATATGAAAAG
1193970 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
*
1194022 TTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1194074 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1194095 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1194105 original size:52 final size:51
Alignment explanation
Indices: 1193970--1194114 Score: 229
Period size: 52 Copynumber: 2.8 Consensus size: 51
1193960 ATATGAAAAG
1193970 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1194022 TTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1194074 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1194115 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1194121 original size:13 final size:13
Alignment explanation
Indices: 1194103--1194127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1194093 CAAAGATCAG
1194103 TGTATCGATACAA
1 TGTATCGATACAA
1194116 TGTATCGATACA
1 TGTATCGATACA
1194128 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1194207 original size:13 final size:13
Alignment explanation
Indices: 1194189--1194246 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
1194179 ACAAAAAATA
1194189 TGTATCGATACAT
1 TGTATCGATACAT
1194202 TGTATCGATACAAAAAAAT
1 TGTATCGATAC------AT
1194221 ATGTATCGATACAT
1 -TGTATCGATACAT
1194235 TGTATCGATACA
1 TGTATCGATACA
1194247 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 23 0.61
14 2 0.05
19 2 0.05
20 11 0.29
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1194223 original size:33 final size:33
Alignment explanation
Indices: 1194168--1194266 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1194158 AGTAGCTTAA
1194168 ATTGTATCGATAC-AAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1194200 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1194233 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1194266 A
1 A
1194267 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 13 0.21
33 49 0.79
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1195873 original size:49 final size:49
Alignment explanation
Indices: 1195754--1195876 Score: 228
Period size: 49 Copynumber: 2.5 Consensus size: 49
1195744 ATATGCGGCT
* *
1195754 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1195803 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1195852 AGCGACATTGGACTTAAAGATGAAG
1 AGCGACATTGGACTTAAAGATGAAG
1195877 ATGAGAAAAG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 72 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (49 bp):
AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
Found at i:1196059 original size:43 final size:44
Alignment explanation
Indices: 1195997--1196406 Score: 414
Period size: 43 Copynumber: 8.9 Consensus size: 44
1195987 TTAAAGATGG
1195997 AAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
1196041 -AAAAGTGTCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
1196084 AAAGAAGAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGACTT
1 --A-AA-AA-GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
** * *
1196133 AGAAGGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 A-AAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
1196178 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGT
1 -AA-A--AAG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
*
1196233 GAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -AAAAA-GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
1196279 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
1196322 -AAAGGTGCCAATGTGCTGATTCAAGGCC-GCTACATTGGACTT
1 AAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1196364 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATT
1 -AA-A--AA-GTGCCAATATGCTGATTCAAGGCCAGCTATATT
1196407 AGGCTTAGAA
Statistics
Matches: 316, Mismatches: 25, Indels: 45
0.82 0.06 0.12
Matches are distributed among these distances:
42 12 0.04
43 106 0.34
44 4 0.01
45 39 0.12
46 3 0.01
47 7 0.02
48 26 0.08
49 76 0.24
50 1 0.00
51 1 0.00
52 36 0.11
53 1 0.00
54 1 0.00
55 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (44 bp):
AAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:1196271 original size:22 final size:22
Alignment explanation
Indices: 1196246--1196314 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
1196236 AAAGGTGCCA
1196246 ATATGCTGATTCAAGGCCAGCG
1 ATATGCTGATTCAAGGCCAGCG
*
1196268 ATAT--TGGACTTAAAGGTGCCA---
1 ATATGCT-GA-TTCAA-G-GCCAGCG
1196289 ATATGCTGATTCAAGGCCAGCG
1 ATATGCTGATTCAAGGCCAGCG
1196311 ATAT
1 ATAT
1196315 TGGACTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 10 0.28
22 14 0.39
23 2 0.06
24 4 0.11
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (22 bp):
ATATGCTGATTCAAGGCCAGCG
Found at i:1196304 original size:21 final size:21
Alignment explanation
Indices: 1196237--1196304 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
1196227 AAAGGTGAAA
1196237 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
*
1196258 AA-G-GCCAGCGATAT--TGGACTTA
1 AAGGTGCCA---ATATGCT-GA-TTC
1196280 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
1196301 AAGG
1 AAGG
1196305 CCAGCGATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 14 0.39
22 10 0.28
23 2 0.06
24 4 0.11
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:1196320 original size:238 final size:233
Alignment explanation
Indices: 1195947--1196402 Score: 648
Period size: 238 Copynumber: 1.9 Consensus size: 233
1195937 GATGAGAAAA
* *
1195947 AAGATGTCAATGTGCTGATTCAAGGCCAGCTACATTAAACTTAAAGATGGAAAAAGTGCCAATAT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTACATTAAACTTAAAGATGGAAAAAGTGCCAATAT
* * * *
1196012 GCTGATTCAAGGCCAGCTATATTGGACTTAAAAGTGTCAATGTGCTGATTCAAGGCCAGCTACAT
66 GCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATATGCTGATTCAAGGCCAGCGACAT
*
1196077 TGGACTTAAAGAAGAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGACTT-AGA-AGGG
131 TGGACTT-----A-AAGGTGCCAATGTGCTAATTCAAGGCC-GCGACATTGGACTTAAGAGAAGG
*
1196140 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
189 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* *** *
1196185 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGT-GAAAAAGGTGCCAATA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTACATTAAACTTAAAGATGGAAAAA-GTGCCAATA
* *
1196249 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA
65 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATATGCTGATTCAAGGCCAGCGACA
* *
1196314 TTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCGCTACATTGGACTTAAAGATGAAGGTGCC
130 TTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCGCGACATTGGACTT-AAGA-GAAGGTGCC
1196379 AATATGCTGATTCAAGGCCAGCTA
193 AATATGCTGATTCAAGGCCAGCTA
1196403 TATTAGGCTT
Statistics
Matches: 196, Mismatches: 17, Indels: 13
0.87 0.08 0.06
Matches are distributed among these distances:
231 13 0.07
232 26 0.13
233 4 0.02
235 30 0.15
237 6 0.03
238 117 0.60
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (233 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCTACATTAAACTTAAAGATGGAAAAAGTGCCAATAT
GCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATATGCTGATTCAAGGCCAGCGACAT
TGGACTTAAAGGTGCCAATGTGCTAATTCAAGGCCGCGACATTGGACTTAAGAGAAGGTGCCAAT
ATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
Found at i:1196326 original size:22 final size:22
Alignment explanation
Indices: 1196258--1196326 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
1196248 ATGCTGATTC
1196258 AAGGCCAGCGATATTGGACTTA
1 AAGGCCAGCGATATTGGACTTA
*
1196280 AAGGTGCCA---ATA-TGCTGA-TTC
1 AA-G-GCCAGCGATATTG--GACTTA
1196301 AAGGCCAGCGATATTGGACTTA
1 AAGGCCAGCGATATTGGACTTA
1196323 AAGG
1 AAGG
1196327 TGCCAATGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 9 0.25
22 13 0.36
23 3 0.08
24 4 0.11
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (22 bp):
AAGGCCAGCGATATTGGACTTA
Found at i:1196362 original size:186 final size:188
Alignment explanation
Indices: 1195954--1196418 Score: 637
Period size: 186 Copynumber: 2.5 Consensus size: 188
1195944 AAAAAGATGT
** *
1195954 CAATGTGCTGATTCAAGGCCAGCTACATTAAACTTAAAGATGGAAAAAGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAGA-TGCCAATATGCTGATT
* * * *
1196019 CAAGGCCAGCTATATTGGAC-T-----TAAAAGTGTCAATGTGCTGATTCAAGGCCAGCTACATT
63 CAAGGCCAGCTATATTGGGCTTAAAGGTAAAAGTGCCAATATGCTGATTCAAGGCCAGCGACATT
*
1196078 GGACTTAAAGAAGAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGACTTAGAAGGGTGC
128 GGACTT----AAGAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTAGAAGGGTGC
1196143 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAA
*
1196208 GGCCAGCTATATTGGGCTTAAAGGTGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT
66 GGCCAGCTATATTGGGCTTAAAGGT--AAAA-GTGCCAATATGCTGATTCAAGGCCAGCGACATT
* *
1196273 GGACTT-A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AA-GGTGC
128 GGACTTAAGAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTAGAAGGGTGC
*
1196330 CAATGTGCTGATTCAAGGCC-GCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAA
*
1196394 GGCCAGCTATATTAGGCTTAGAAGG
66 GGCCAGCTATATTGGGCTTA-AAGG
1196419 GTTGCCACCG
Statistics
Matches: 253, Mismatches: 13, Indels: 22
0.88 0.05 0.08
Matches are distributed among these distances:
186 97 0.38
187 33 0.13
188 3 0.01
189 79 0.31
190 1 0.00
192 1 0.00
194 4 0.02
195 35 0.14
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (188 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAA
GGCCAGCTATATTGGGCTTAAAGGTAAAAGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGA
CTTAAGAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTAGAAGGGTGC
Found at i:1196574 original size:95 final size:96
Alignment explanation
Indices: 1196413--1196706 Score: 497
Period size: 95 Copynumber: 3.1 Consensus size: 96
1196403 TATTAGGCTT
* *
1196413 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAGGG-TTACCACCGACTTGTGTGGGCTTTG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GAG-GGGATTGCCACCAACTTGTGTGGGCTTTG
1196477 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
64 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1196510 AGAA-GGTTGCCACCAACTTGTGTGGGCTTTGAGGGGATTGCCACCAACTTGTGTGGGCTTTGAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAGGGGATTGCCACCAACTTGTGTGGGCTTTGAG
1196574 AAGGGTTGCCACCGACTTGTGTGGGCTTT-G
66 AAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1196604 AGAAGGGTTGCTACCGACTTGTGTGGGCTTTGAGGGGATTGCCACCAACTTGTGTGGGCTTTGAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAGGGGATTGCCACCAACTTGTGTGGGCTTTGAG
1196669 AAGGGTTGCCACCGACTTGTGTGGGCTTTA-
66 AAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1196699 AAAAGGGT
1 AGAAGGGT
1196707 GAAAGATGCC
Statistics
Matches: 188, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
94 8 0.04
95 151 0.80
96 25 0.13
97 4 0.02
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.28
Consensus pattern (96 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAGGGGATTGCCACCAACTTGTGTGGGCTTTGAG
AAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1196678 original size:127 final size:127
Alignment explanation
Indices: 1196413--1196698 Score: 472
Period size: 127 Copynumber: 2.3 Consensus size: 127
1196403 TATTAGGCTT
1196413 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAGGGTTACCACCGACTTGTGTGGGCTTTGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGA-AGGGTTACCACCGACTTGTGTGGGCTTTGA
1196478 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCAACTTGTGTGGGCTTTG
65 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCAACTTGTGTGGGCTTTG
* *
1196541 AG--GGGATTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTT-AGAAGGGTTACCACCGACTTGTGTGGGCTTTG
* *
1196604 AGAAGGGTTGCTACCGACTTGTGTGGGCTTT-GAG-GGGATTGCCACCAACTTGTGTGGGCTTTG
64 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGG-TTGCCACCAACTTGTGTGGGCTTTG
1196667 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
1196699 AAAAGGGTGA
Statistics
Matches: 148, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
125 2 0.01
126 34 0.23
127 104 0.70
128 8 0.05
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.29
Consensus pattern (127 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGGGTTACCACCGACTTGTGTGGGCTTTGAG
AAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCAACTTGTGTGGGCTTTG
Found at i:1196705 original size:32 final size:32
Alignment explanation
Indices: 1196413--1196706 Score: 447
Period size: 32 Copynumber: 9.2 Consensus size: 32
1196403 TATTAGGCTT
1196413 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1196444 AGAGAGGGTTACCACCGACTTGTGTGGGCTTTG
1 AGA-AGGGTTGCCACCGACTTGTGTGGGCTTTG
1196477 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
*
1196510 AGAA-GGTTGCCACCAACTTGTGTGGGCTTTG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1196541 AG--GGGATTGCCACCAACTTGTGTGGGCTTTG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTG
1196572 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1196604 AGAAGGGTTGCTACCGACTTGTGTGGGCTTTG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1196636 AG--GGGATTGCCACCAACTTGTGTGGGCTTTG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTG
*
1196667 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
*
1196699 AAAAGGGT
1 AGAAGGGT
1196707 GAAAGATGCC
Statistics
Matches: 243, Mismatches: 10, Indels: 19
0.89 0.04 0.07
Matches are distributed among these distances:
30 5 0.02
31 58 0.24
32 166 0.68
33 14 0.06
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.28
Consensus pattern (32 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
Found at i:1196769 original size:34 final size:33
Alignment explanation
Indices: 1196708--1197331 Score: 599
Period size: 34 Copynumber: 18.8 Consensus size: 33
1196698 AAAAAGGGTG
* *
1196708 AAAGATGCCACGAAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * **
1196741 CAAGGTGCCACGGAGTTGTGGGCTTTAAAAAAAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
*
1196775 AAAGGTGCCACGGAGTTGTAGACTTAAAAGG--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
1196806 -AAGGTGCCACGGAGTCGCGGACTTTGAAAGG--
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
* *
1196837 -AAGGTGCCACGGAGTCGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1196869 CAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAA-GGAA
* * * **
1196904 ACAGAGTGCCACAGAGTTGTGGGCTTTGAA--AA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
1196936 GAAGGTGCCACAGAGTCGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1196969 CAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAA-GGAA
*
1197004 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1197038 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGG-AA
* * *
1197073 AAAAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1197106 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
1197140 AAAGAGTGGCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1197174 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
1197208 AAGGAGTGCCACAGAGTTGTGGGCTT-TAA--AA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1197239 AGA-GTGCCACGGAGTTGTGGACTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* *
1197272 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
*
1197306 AAAGGGTGCCACGGAGTCGTGGACTT
1 AAA-GGTGCCACGGAGTTGTGGACTT
1197332 TGAGACAAAA
Statistics
Matches: 513, Mismatches: 56, Indels: 43
0.84 0.09 0.07
Matches are distributed among these distances:
29 17 0.03
30 27 0.05
31 52 0.10
32 6 0.01
33 82 0.16
34 250 0.49
35 44 0.09
36 35 0.07
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:1197091 original size:68 final size:68
Alignment explanation
Indices: 1196840--1197425 Score: 512
Period size: 68 Copynumber: 8.8 Consensus size: 68
1196830 TGAAAGGAAG
* * * * * * *
1196840 GTGCCACGGAGTCGTGGACTTAAAAAG-AACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGAA
1 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGAC-TTAGAA-GGAA
*
1196904 ACAGA
64 AAAGA
* * * * * * * * *
1196909 GTGCCACAGAGTTGTGGGCTTTG-A--AAAGAAGGTGCCACAGAGTCGTGGACTTAAAAGGAACA
1 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
1196971 AG-
66 AGA
* *
1196973 GTGCCACGGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 GTGCCACGGAGTTGTGGAC-TTAGAA-GGAAAAAAAGTGCCACGGAGTTGTGGACTTAGAAGGAA
1197038 AAAGA
64 AAAGA
* *
1197043 GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAA
1 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
1197108 AGA
66 AGA
* * * *
1197111 GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGGCACGGAGTTGTGGGCTTAGAAGGAAAA
1 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
1197176 AGA
66 AGA
* ** * * *
1197179 GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAGGAGTGCCACAGAGTTGTGGGCTT-----TAAAA
1 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
1197239 AGA
66 AGA
* * * *
1197242 GTGCCACGGAGTTGTGGACTTTGAA--AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 GTGCCACGGAGTTGTGGACTTAGAAGGAA-AAAAA-GTGCCACGGAGTTGTGGAC-TTAGAAGGA
*
1197305 AAAAGG
63 AAAAGA
* * * * * *
1197311 GTGCCACGGAGTCGTGGACTTTG-A-G-ACAAAA-TGCCACTGAGTCGTGGACTTTGAA-GAAAA
1 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
*
1197371 GGA
66 AGA
* * ** * *
1197374 -TGCCACTGAGTCGTGGACCTTA-AA-GAAAAGGA-TGCCACTGAGTCGTGGACTT
1 GTGCCACGGAGTTGTGGA-CTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGACTT
1197426 TGAGAAGAGA
Statistics
Matches: 445, Mismatches: 53, Indels: 43
0.82 0.10 0.08
Matches are distributed among these distances:
61 2 0.00
62 19 0.04
63 59 0.13
64 46 0.10
65 23 0.05
66 7 0.02
67 25 0.06
68 162 0.36
69 84 0.19
70 18 0.04
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.19
Consensus pattern (68 bp):
GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGACTTAGAAGGAAAA
AGA
Found at i:1197123 original size:102 final size:102
Alignment explanation
Indices: 1196708--1197425 Score: 618
Period size: 102 Copynumber: 7.3 Consensus size: 102
1196698 AAAAAGGGTG
* * * *
1196708 AAAGA-TGCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTA-AA-
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGGTGCCACGGAGTTGTGGAC-TTAGAAG
* *
1196770 AAAAAAAAGGTGCCACGGAGTTGTAGAC-TTAAAAGG--
65 GAAAAAAA-GTGCCACGGAGTTGTGGACTTTAAAAGGAA
* * * * * *
1196806 -AAG-GTGCCACGGAGTCGCGGACTTTGAAAGG---AAGGTGCCACGGAGTCGTGGACTTAAAAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAG-AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAG
* * *
1196866 G-AACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGAA
65 GAAAAAAAGTGCCACGGAGTTGTGGACTTTAAAA-GGAA
* * * * * * * *
1196904 ACAGAGTGCCACAGAGTTGTGGGCTTTGAA--AAGAAGGTGCCACAGAGTCGTGGACTTAAAAGG
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGG
* *
1196967 -AACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAA
66 AAAAAAAGTGCCACGGAGTTGTGGACTTTAAAA-GGAA
*
1197004 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAG-GTGCCACGGAGTTGTGGACTTAGAAG
* *
1197069 GAAAAAAAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
65 GAAAAAAAGTGCCACGGAGTTGTGGACTTTAAAAGGAA
* * *
1197106 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGGCACGGAGTTGTGGGCTTAGAAG
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAG-GTGCCACGGAGTTGTGGACTTAGAAG
* * *
1197171 GAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
65 GAAAAAAAGTGCCACGGAGTTGTGGACTTTAAAAGGAA
* * * * * *
1197208 AAGGAGTGCCACAGAGTTGTGGGCTT-TAA--AAAGA-GTGCCACGGAGTTGTGGACTTTGAA--
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGG
* *
1197267 AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
66 AA-AAAAA-GTGCCACGGAGTTGTGGACTTTAAAAGGAA
* * * * * *
1197306 AAAGGGTGCCACGGAGTCGTGGACTTTG-A-GACAAAA--TGCCACTGAGTCGTGGACTTTGAA-
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGA-AAAAGGTGCCACGGAGTTGTGGACTTAGAAG
** * * *
1197366 GAAAAGGA-TGCCACTGAGTCGTGGACCTT-AAA-GAA
65 GAAAAAAAGTGCCACGGAGTTGTGGACTTTAAAAGGAA
* * *
1197401 AAGGA-TGCCACTGAGTCGTGGACTT
1 AAAGAGTGCCACGGAGTTGTGGACTT
1197426 TGAGAAGAGA
Statistics
Matches: 532, Mismatches: 64, Indels: 52
0.82 0.10 0.08
Matches are distributed among these distances:
94 39 0.07
95 40 0.08
96 9 0.02
97 78 0.15
98 34 0.06
99 34 0.06
100 114 0.21
101 2 0.00
102 132 0.25
103 28 0.05
104 22 0.04
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.19
Consensus pattern (102 bp):
AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGG
AAAAAAAGTGCCACGGAGTTGTGGACTTTAAAAGGAA
Found at i:1197463 original size:31 final size:31
Alignment explanation
Indices: 1197205--1197462 Score: 206
Period size: 32 Copynumber: 8.1 Consensus size: 31
1197195 GGCTTAGAAG
* * *
1197205 GAAAAGGAGTGCCACAGAGTTGTGGGCTTT-A
1 GAAAAGGA-TGCCACTGAGTCGTGGACTTTAA
* *
1197236 -AAAA-GAGTGCCACGGAGTTGTGGACTTTGAAAA
1 GAAAAGGA-TGCCACTGAGTCGTGGACTTT---AA
* * *
1197269 GAAAAAGG-TGCCACGGAGTTGTGGGCTTTAAAAA
1 G-AAAAGGATGCCACTGAGTCGTGGACTTT---AA
* * *
1197303 GAAAAAGGGTGCCACGGAGTCGTGGACTTTGA
1 G-AAAAGGATGCCACTGAGTCGTGGACTTTAA
1197335 GACAAA--ATGCCACTGAGTCGTGGACTTTGAA
1 GA-AAAGGATGCCACTGAGTCGTGGACTTT-AA
*
1197366 GAAAAGGATGCCACTGAGTCGTGGACCTTAAA
1 GAAAAGGATGCCACTGAGTCGTGGA-CTTTAA
*
1197398 GAAAAGGATGCCACTGAGTCGTGGACTTTGA
1 GAAAAGGATGCCACTGAGTCGTGGACTTTAA
* *
1197429 GAAGA-GATTACCACTGAGTCGTGGACTTTAA
1 GAAAAGGA-TGCCACTGAGTCGTGGACTTTAA
1197460 GAA
1 GAA
1197463 GGTATTTGAA
Statistics
Matches: 197, Mismatches: 16, Indels: 28
0.82 0.07 0.12
Matches are distributed among these distances:
29 22 0.11
30 29 0.15
31 36 0.18
32 50 0.25
33 4 0.02
34 32 0.16
35 23 0.12
36 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (31 bp):
GAAAAGGATGCCACTGAGTCGTGGACTTTAA
Found at i:1205789 original size:52 final size:52
Alignment explanation
Indices: 1205708--1205832 Score: 241
Period size: 52 Copynumber: 2.4 Consensus size: 52
1205698 ATATGAAAAG
1205708 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
*
1205760 TTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1205812 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1205833 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1205843 original size:52 final size:51
Alignment explanation
Indices: 1205708--1205852 Score: 229
Period size: 52 Copynumber: 2.8 Consensus size: 51
1205698 ATATGAAAAG
1205708 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1205760 TTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1205812 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1205853 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1205859 original size:13 final size:13
Alignment explanation
Indices: 1205841--1205865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1205831 CAAAGATCAG
1205841 TGTATCGATACAA
1 TGTATCGATACAA
1205854 TGTATCGATACA
1 TGTATCGATACA
1205866 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1205943 original size:33 final size:33
Alignment explanation
Indices: 1205906--1205972 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1205896 AGTAGCTTAA
1205906 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1205939 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1205972 A
1 A
1205973 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1205946 original size:13 final size:13
Alignment explanation
Indices: 1205928--1205952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1205918 CAAAAAAATA
1205928 TGTATCGATACAT
1 TGTATCGATACAT
1205941 TGTATCGATACA
1 TGTATCGATACA
1205953 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1210830 original size:13 final size:13
Alignment explanation
Indices: 1210812--1210849 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1210802 CAACATTCTC
*
1210812 TGTATCGATACAT
1 TGTATCGATACAG
1210825 TGTATCGATACAG
1 TGTATCGATACAG
1210838 TGTATCGATACA
1 TGTATCGATACA
1210850 AAGGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1213300 original size:13 final size:13
Alignment explanation
Indices: 1213282--1213306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1213272 AGATTGCATA
1213282 GTATCGATACATT
1 GTATCGATACATT
1213295 GTATCGATACAT
1 GTATCGATACAT
1213307 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1213424 original size:13 final size:13
Alignment explanation
Indices: 1213406--1213431 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1213396 TACACACAAG
1213406 ATGTATCGATACA
1 ATGTATCGATACA
1213419 ATGTATCGATACA
1 ATGTATCGATACA
1213432 TCTCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1213448 original size:33 final size:32
Alignment explanation
Indices: 1213388--1213451 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1213378 CTTAACTGTT
*
1213388 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1213420 TGTATCGATACATCTCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1213452 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1221060 original size:22 final size:21
Alignment explanation
Indices: 1221026--1221066 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1221016 AATTTATGAT
*
1221026 ATTTTATTATTAATAAATATA
1 ATTTTATAATTAATAAATATA
1221047 ATTTTCATAATTAATAAATA
1 ATTTT-ATAATTAATAAATA
1221067 AATATATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTTATAATTAATAAATATA
Found at i:1221656 original size:32 final size:33
Alignment explanation
Indices: 1221620--1221686 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
1221610 CGAATAGATA
* *
1221620 AATATATCAAATTTTATGTAAA-ATAA-ATTATT
1 AATATATCAAAATTTATATAAATATAATATT-TT
*
1221652 AATATGTCAAAATTTATATAAATATAATATTTT
1 AATATATCAAAATTTATATAAATATAATATTTT
1221685 AA
1 AA
1221687 ATACAATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 19 0.63
33 8 0.27
34 3 0.10
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (33 bp):
AATATATCAAAATTTATATAAATATAATATTTT
Found at i:1226968 original size:2 final size:2
Alignment explanation
Indices: 1226961--1226992 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1226951 CTACACATTC
*
1226961 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1226993 GTATGTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1228970 original size:13 final size:13
Alignment explanation
Indices: 1228952--1228977 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1228942 AATTTTTTTG
1228952 TGTATCGATACAT
1 TGTATCGATACAT
1228965 TGTATCGATACAT
1 TGTATCGATACAT
1228978 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1229656 original size:30 final size:30
Alignment explanation
Indices: 1229620--1229679 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1229610 AAAATAAATT
*
1229620 TAACAAATTTGTACATTCTCCCCTTTAATG
1 TAACAAATTTGTACATTCTCCCCCTTAATG
1229650 TAACAAATTTGTACATTCTCCCCCTTAATG
1 TAACAAATTTGTACATTCTCCCCCTTAATG
1229680 AAATAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
TAACAAATTTGTACATTCTCCCCCTTAATG
Found at i:1231568 original size:13 final size:13
Alignment explanation
Indices: 1231550--1231588 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1231540 ATAATCACCC
*
1231550 TGTATCGATACAT
1 TGTATCGATACAA
1231563 TGTATCGATACAA
1 TGTATCGATACAA
1231576 TGTATCGATACAA
1 TGTATCGATACAA
1231589 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1233687 original size:15 final size:15
Alignment explanation
Indices: 1233667--1233697 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1233657 ATTTCGTTTG
*
1233667 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1233682 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1233697 G
1 G
1233698 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1235531 original size:21 final size:21
Alignment explanation
Indices: 1235502--1235546 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1235492 AAGTTTTCAT
*
1235502 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1235522 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1235544 TTT
1 TTT
1235547 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1242837 original size:49 final size:49
Alignment explanation
Indices: 1242648--1243019 Score: 192
Period size: 49 Copynumber: 7.9 Consensus size: 49
1242638 AGATGCGAAG
* * * *
1242648 AATGACAATGTGCTGATTCATGGCCAGCGACATTAGAT-TTAAAGA--AG
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGATGAA
** * **
1242695 AATGCCAATGTGCTGAGACAAGGCCAGCGACATTGGGCTTAGGGATGTTAA
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATG--AA
* * * * ** *
1242746 AGATGCCAATATGCTAATTCAAGGCCAACGATATCAGACTTAAAGATGAA
1 A-ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAA
* *
1242796 AATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAA
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAA
** * * * * * *
1242844 GGTGCCAATATGCCGATTCAAAGCCAACGATATTGGGC-T-----T---
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAA
* **
1242884 -ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGATGTC
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAA
** * * * * *
1242932 GGTACCAATATGGTGATTCAAGGCCAACGACATT-GACTTAAAG--G--
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAA
* * * *
1242976 --TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAGAAGA
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA-AAGA
1243020 AGATGCCACC
Statistics
Matches: 249, Mismatches: 56, Indels: 42
0.72 0.16 0.12
Matches are distributed among these distances:
39 29 0.12
40 1 0.00
42 29 0.12
43 6 0.02
44 3 0.01
45 1 0.00
46 2 0.01
47 36 0.14
48 39 0.16
49 63 0.25
50 3 0.01
51 2 0.01
52 35 0.14
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (49 bp):
AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAA
Found at i:1242918 original size:39 final size:39
Alignment explanation
Indices: 1242846--1242923 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
1242836 AAAGACAAGG
* *
1242846 TGCCAATATGCCGATTCAAAGCCAACGATATTGGGCTTA
1 TGCCAATATGCCGATTCAAAGCCAACAACATTGGGCTTA
* * * * *
1242885 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTA
1 TGCCAATATGCCGATTCAAAGCCAACAACATTGGGCTTA
1242924 AAGATGTCGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (39 bp):
TGCCAATATGCCGATTCAAAGCCAACAACATTGGGCTTA
Found at i:1243094 original size:28 final size:29
Alignment explanation
Indices: 1243036--1243305 Score: 263
Period size: 28 Copynumber: 9.5 Consensus size: 29
1243026 CACCAACTTA
* *
1243036 TGTGGGGTTTTGAAAGGGTTG-CA-TCAACT
1 TGTGGGCTTTTGAAA-GGTTGCCACT-GACT
*
1243065 TGTGTGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * * *
1243093 TGTGAGCTTTCGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* *
1243122 TGTGGGC--TTGAAAGGGGTGCC-CTTGGCT
1 TGTGGGCTTTTGAAA-GGTTGCCAC-TGACT
*
1243150 TATGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * * *
1243178 TGTGGGCTTTGGAAAAGATGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
1243207 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * * *
1243235 TGTGGGCTTTGGAAAAGATGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
1243264 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
*
1243292 TGTGAGC-TTTGAAA
1 TGTGGGCTTTTGAAA
1243306 AGGTGAAGAA
Statistics
Matches: 197, Mismatches: 33, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
27 15 0.08
28 97 0.49
29 82 0.42
30 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.33
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGTTGCCACTGACT
Found at i:1243228 original size:57 final size:56
Alignment explanation
Indices: 1243082--1243307 Score: 294
Period size: 57 Copynumber: 4.0 Consensus size: 56
1243072 TTTTGAAGGT
* * * * * * *
1243082 TGCCACTGACTTGTGAGCTTTCGAAAAGATGCCACTGACTTGTGGGC-TTGAAAGGGG
1 TGCCACTAACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGAAA-AGA
** *
1243139 TGCC-CTTGGCTTATGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCAC-TAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT-GAAAAGA
1243196 TGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT-GAAAAGA
*
1243253 TGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGAGCTTTGAAAAG
1 TGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAG
1243308 GTGAAGAATG
Statistics
Matches: 153, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
56 28 0.18
57 120 0.78
58 5 0.03
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (56 bp):
TGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:1243241 original size:85 final size:87
Alignment explanation
Indices: 1243019--1243305 Score: 295
Period size: 85 Copynumber: 3.3 Consensus size: 87
1243009 GACTTAGAAG
* * * *
1243019 AAGATGCCACCAACTTATGTGGGGTTTTGAAAGGGTTG-CA-TCAACTTGTGTGCTTTTGAAGGT
1 AAGATGCCACTAAC-T-TGTGGGCTTTTGAAAGGGTTGCCACT-GACTTGTGGGCTTTTGAAGGT
*
1243082 TGCCACTGACTTGTGAGCTTTCGAA
63 TGCCACTGACTTGTGGGCTTTCGAA
* * * *
1243107 AAGATGCCACTGACTTGTGGGC--TTGAAAGGGGTGCC-CTTGGCTTATGGGCTTTTGAAGGTTG
1 AAGATGCCACTAACTTGTGGGCTTTTGAAAGGGTTGCCAC-TGACTTGTGGGCTTTTGAAGGTTG
*
1243169 CCACTGACTTGTGGGCTTTGGAA
65 CCACTGACTTGTGGGCTTTCGAA
* * *
1243192 AAGATGCCACTAACTTGTGGGCTTTTG-AA-GGTTGCCACTGACTTGTGGGCTTTGGAAAAGATG
1 AAGATGCCACTAACTTGTGGGCTTTTGAAAGGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTG
* *
1243255 CCACTAACTTGTGGGCTTTTG-A
65 CCACTGACTTGTGGGCTTTCGAA
* * * *
1243277 AGGTTGCCACTGACTTGTGAGC-TTTGAAA
1 AAGATGCCACTAACTTGTGGGCTTTTGAAA
1243306 AGGTGAAGAA
Statistics
Matches: 168, Mismatches: 23, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
84 15 0.09
85 103 0.61
86 34 0.20
87 4 0.02
88 12 0.07
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (87 bp):
AAGATGCCACTAACTTGTGGGCTTTTGAAAGGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGC
CACTGACTTGTGGGCTTTCGAA
Found at i:1244777 original size:35 final size:33
Alignment explanation
Indices: 1244728--1244812 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 33
1244718 ATCCGGACCC
* * *
1244728 TTTTTGTTGTTTTTTTTTGTTT-TGTTTGTCTCTTT
1 TTTTTTTTGGTTTTTTTTGTTTAT-TTTGT-T-ATT
1244763 TTTTTTTTGGTTTTTTTTGTTTATTTTGTTATT
1 TTTTTTTTGGTTTTTTTTGTTTATTTTGTTATT
*
1244796 TTTTGTTT-GTTTTTTTT
1 TTTTTTTTGGTTTTTTTT
1244813 CTTCTTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
32 9 0.20
33 9 0.20
34 1 0.02
35 25 0.56
36 1 0.02
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.82
Consensus pattern (33 bp):
TTTTTTTTGGTTTTTTTTGTTTATTTTGTTATT
Found at i:1244799 original size:23 final size:22
Alignment explanation
Indices: 1244773--1244834 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
1244763 TTTTTTTTGG
1244773 TTTTTTTTGTTTATTTTGTTATT
1 TTTTTTTTGTTT-TTTTGTTATT
* * *
1244796 TTTTGTTTGTTTTTTTTCTTCTT
1 TTTTTTTTG-TTTTTTTGTTATT
*
1244819 TCTTTTTT-TTTTTTTG
1 TTTTTTTTGTTTTTTTG
1244835 CGGAGGACGC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 7 0.22
23 22 0.69
24 3 0.09
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.84
Consensus pattern (22 bp):
TTTTTTTTGTTTTTTTGTTATT
Found at i:1244850 original size:1 final size:1
Alignment explanation
Indices: 1244737--1244833 Score: 50
Period size: 1 Copynumber: 97.0 Consensus size: 1
1244727 CTTTTTGTTG
* * * * * ** * * * * *
1244737 TTTTTTTTTGTTTTGTTTGTCTCTTTTTTTTTTTGGTTTTTTTTGTTTATTTTGTTATTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
1244802 TTGTTTTTTTTCTTCTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1244834 GCGGAGGACG
Statistics
Matches: 66, Mismatches: 30, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (1 bp):
T
Found at i:1246956 original size:11 final size:11
Alignment explanation
Indices: 1246927--1246978 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
1246917 TTCCTTTCTA
1246927 TCTTTTCCTTGTT
1 TCTTTT-CTT-TT
*
1246940 TTTTTTCTTTT
1 TCTTTTCTTTT
1246951 TCTTTTCTATTT
1 TCTTTTCT-TTT
*
1246963 TCTTTCTATTTT
1 TCTTT-TCTTTT
1246975 TCTT
1 TCTT
1246979 CTTTTCTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 9 0.26
12 18 0.53
13 7 0.21
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:1247013 original size:25 final size:26
Alignment explanation
Indices: 1246974--1247039 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
1246964 CTTTCTATTT
*
1246974 TTCTTCTTTTCTTCTTACTGTTT-CGA
1 TTCTT-TTTTCTTCTTACTGTTTGCAA
* *
1247000 TTTTTTTTTCTTCTTGCTGTTTGCAA
1 TTCTTTTTTCTTCTTACTGTTTGCAA
1247026 TTCTTTTTT-TTCTT
1 TTCTTTTTTCTTCTT
1247040 TTGTTTTGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 21 0.60
26 14 0.40
ACGTcount: A:0.06, C:0.18, G:0.08, T:0.68
Consensus pattern (26 bp):
TTCTTTTTTCTTCTTACTGTTTGCAA
Found at i:1248003 original size:62 final size:62
Alignment explanation
Indices: 1247910--1248034 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 62
1247900 CCATGCATGA
* *
1247910 AATGCAATGCAATGCAATGACAACTAGAAAGCTTA-GATGGCAACAAATTAAATATGAAATCC
1 AATGCAATGCAATGCAATGACAACTAAAAAGCTTAGGA-GGCAACAAATTAAACATGAAATCC
* * *
1247972 AATGCAATGCAATGCAATGACACCTAAAAAGCTTAGGAGGCAATAAATTAAGCATGAAATCC
1 AATGCAATGCAATGCAATGACAACTAAAAAGCTTAGGAGGCAACAAATTAAACATGAAATCC
1248034 A
1 A
1248035 CCAAATTCGG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 55 0.96
63 2 0.04
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (62 bp):
AATGCAATGCAATGCAATGACAACTAAAAAGCTTAGGAGGCAACAAATTAAACATGAAATCC
Found at i:1249585 original size:23 final size:23
Alignment explanation
Indices: 1249555--1249600 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1249545 CACCCCCTCA
1249555 AGAATAGGA-CGCAATAATAGAGC
1 AGAATAGGAGC-CAATAATAGAGC
1249578 AGAATAGGAGCCAATAATAGAGC
1 AGAATAGGAGCCAATAATAGAGC
1249601 GCACATCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.48, C:0.13, G:0.26, T:0.13
Consensus pattern (23 bp):
AGAATAGGAGCCAATAATAGAGC
Found at i:1251433 original size:36 final size:36
Alignment explanation
Indices: 1251386--1251460 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
1251376 CAGAGCAGGA
1251386 TTCTTTCAAGATATCACAAGCAATTCTTTCTTTTGG
1 TTCTTTCAAGATATCACAAGCAATTCTTTCTTTTGG
1251422 TTCTTTCAAGATATCACAAGCAATTCTTTCTTTTGG
1 TTCTTTCAAGATATCACAAGCAATTCTTTCTTTTGG
1251458 TTC
1 TTC
1251461 GAGAGGAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (36 bp):
TTCTTTCAAGATATCACAAGCAATTCTTTCTTTTGG
Found at i:1253422 original size:21 final size:21
Alignment explanation
Indices: 1253397--1253440 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1253387 GATTATGTCA
1253397 TATTTATAATAATTATAAATG
1 TATTTATAATAATTATAAATG
* * *
1253418 TATTTATAGTAATTGTATATG
1 TATTTATAATAATTATAAATG
1253439 TA
1 TA
1253441 ATAAATCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (21 bp):
TATTTATAATAATTATAAATG
Found at i:1257464 original size:32 final size:32
Alignment explanation
Indices: 1257420--1257492 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
1257410 CAAATTTAAA
1257420 ATATTATTTAAATTTTAACATA-TTAATAATTT
1 ATATTATTTAAATTTTAACATATTTAAT-ATTT
*
1257452 ATATT-TTATAAATTTTAATATATTTAATATTT
1 ATATTATT-TAAATTTTAACATATTTAATATTT
*
1257484 AAATTATTT
1 ATATTATTT
1257493 TTTATTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 2 0.06
32 27 0.75
33 7 0.19
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (32 bp):
ATATTATTTAAATTTTAACATATTTAATATTT
Found at i:1257508 original size:35 final size:32
Alignment explanation
Indices: 1257469--1257545 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
1257459 ATAAATTTTA
*
1257469 ATATATTTAATATTTAAATTATTTTTTATTATATT
1 ATATATTTAATAATT-AATTA-TTTTT-TTATATT
*
1257504 ATATATTTTATTAATTAATTATTTTTTTATATT
1 ATATA-TTTAATAATTAATTATTTTTTTATATT
*
1257537 ATATTTTTA
1 ATATATTTA
1257546 TCTTATCGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 4 0.11
33 11 0.29
34 5 0.13
35 10 0.26
36 8 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (32 bp):
ATATATTTAATAATTAATTATTTTTTTATATT
Found at i:1257514 original size:17 final size:17
Alignment explanation
Indices: 1257492--1257546 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 17
1257482 TTAAATTATT
1257492 TTTTATTATATTATATA
1 TTTTATTATATTATATA
1257509 TTTTATTA-ATTA-ATTA
1 TTTTATTATATTATA-TA
*
1257525 TTTTTTTATATTATAT-
1 TTTTATTATATTATATA
1257541 TTTTAT
1 TTTTAT
1257547 CTTATCGACA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
15 1 0.03
16 18 0.55
17 13 0.39
18 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTATTATATTATATA
Found at i:1258316 original size:21 final size:21
Alignment explanation
Indices: 1258282--1258342 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
1258272 AGATTTATTG
*
1258282 AATTGTTAAT-TTAATTAAAAT
1 AATT-TTAATATTAAATAAAAT
*
1258303 -ATTTTAAATATTAAGT-AAAT
1 AATTTT-AATATTAAATAAAAT
1258323 AATTTTAATATTAAATAAAA
1 AATTTTAATATTAAATAAAA
1258343 AATAAGTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.06
20 19 0.56
21 13 0.38
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
AATTTTAATATTAAATAAAAT
Found at i:1260135 original size:18 final size:18
Alignment explanation
Indices: 1260108--1260142 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1260098 AAACTTAAAA
* *
1260108 ATAATTTTTTTTAAGTGG
1 ATAATCTTTTTAAAGTGG
1260126 ATAATCTTTTTAAAGTG
1 ATAATCTTTTTAAAGTG
1260143 AATAGAGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.51
Consensus pattern (18 bp):
ATAATCTTTTTAAAGTGG
Found at i:1260997 original size:21 final size:20
Alignment explanation
Indices: 1260973--1261027 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
1260963 GTAAGTTGAT
1260973 TTAATTTAAATTATTATTTAA
1 TTAATTTAAATTATT-TTTAA
* * *
1260994 TTAATTAAAAATATTTTTAT
1 TTAATTTAAATTATTTTTAA
1261014 TTAAATTT-AATTAT
1 TT-AATTTAAATTAT
1261028 AAAAAAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTTAAATTATTTTTAA
Found at i:1264683 original size:17 final size:17
Alignment explanation
Indices: 1264661--1264699 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1264651 AATATATTAT
1264661 TTAAAAATAAATAAAAA
1 TTAAAAATAAATAAAAA
*
1264678 TTAAAAATAATTAAAAA
1 TTAAAAATAAATAAAAA
*
1264695 ATAAA
1 TTAAA
1264700 TTTCTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TTAAAAATAAATAAAAA
Found at i:1268217 original size:11 final size:11
Alignment explanation
Indices: 1268168--1268218 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
1268158 ATCATCTTTA
1268168 TTTT-TATTAT
1 TTTTATATTAT
1268178 GTTTTA-ATTAAT
1 -TTTTATATT-AT
1268190 TTTTATATTAT
1 TTTTATATTAT
*
1268201 ATTTATATTAT
1 TTTTATATTAT
1268212 TTTTATA
1 TTTTATA
1268219 CATAAATTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 30 0.86
12 5 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:1269274 original size:20 final size:19
Alignment explanation
Indices: 1269228--1269280 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 19
1269218 TTTGAAAGGA
*
1269228 AAATTGTATCGATACATTG
1 AAATTGTATCGATACATAG
1269247 -AA--GTATCGATACATAAG
1 AAATTGTATCGATACAT-AG
1269264 AAATTGTATCGATACAT
1 AAATTGTATCGATACAT
1269281 TTTAGGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 12 0.41
17 1 0.03
18 4 0.14
20 12 0.41
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (19 bp):
AAATTGTATCGATACATAG
Found at i:1272803 original size:149 final size:149
Alignment explanation
Indices: 1272541--1272811 Score: 373
Period size: 149 Copynumber: 1.8 Consensus size: 149
1272531 AATTTCGCTT
* * * * *
1272541 ACTTCGTTGTGACCATCGATGATCAATTAGATACGTGATTTATCTACCGATTTTTCCTACTTTAA
1 ACTTCGTTGTGACCATCGAGGATCAATTAGATACGTGATTTATCTACCAATCTTCCCCACTTTAA
* *
1272606 TCAATATACCTTTTATCATACTATAGAAATCCCCAAATCACGAGGGATATCAAGTCGGCTGTGCT
66 TCAATATAACTTTTATCATACTATAAAAATCCCCAAATCACGAGGGATATCAAGTCGGCTGTGCT
1272671 TCACTCCAAATTTTCGATC
131 TCACTCCAAATTTTCGATC
** * * *
1272690 ACTTCGTTGTGACTGTTGAGGATCGATTAGATAGGTGATTTATCTACCAATCTTCCCCA-TTTCA
1 ACTTCGTTGTGACCATCGAGGATCAATTAGATACGTGATTTATCTACCAATCTTCCCCACTTT-A
* * * * *
1272754 ATCAATGTAACTTTTATCATGCTATAAAAATCCCTAAATCATGAGGGATATTAAGTCG
65 ATCAATATAACTTTTATCATACTATAAAAATCCCCAAATCACGAGGGATATCAAGTCG
1272812 AGCGTGCCCC
Statistics
Matches: 104, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
148 3 0.03
149 101 0.97
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (149 bp):
ACTTCGTTGTGACCATCGAGGATCAATTAGATACGTGATTTATCTACCAATCTTCCCCACTTTAA
TCAATATAACTTTTATCATACTATAAAAATCCCCAAATCACGAGGGATATCAAGTCGGCTGTGCT
TCACTCCAAATTTTCGATC
Found at i:1273612 original size:28 final size:27
Alignment explanation
Indices: 1273564--1273616 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
1273554 TAAAAAATTA
*
1273564 AAATTAATGTTAAATTTTAATTTATTT
1 AAATTAATATTAAATTTTAATTTATTT
1273591 AAATT-ATATTAATATTTATAATTTAT
1 AAATTAATATTAA-ATTT-TAATTTAT
1273617 ATTTATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 9 0.39
28 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
AAATTAATATTAAATTTTAATTTATTT
Found at i:1273616 original size:19 final size:17
Alignment explanation
Indices: 1273586--1273625 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
1273576 AATTTTAATT
1273586 TATTTAAATTATATTAA
1 TATTTAAATTATATTAA
*
1273603 TATTTATAATTTATATTTA
1 TATTTA-AA-TTATATTAA
1273622 TATT
1 TATT
1273626 AAAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 2 0.10
19 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTAAATTATATTAA
Found at i:1273945 original size:27 final size:28
Alignment explanation
Indices: 1273914--1274018 Score: 97
Period size: 28 Copynumber: 3.6 Consensus size: 28
1273904 TAACACTAAC
1273914 ATAAATAAAATATAAAAAATAAT-TAAA
1 ATAAATAAAATATAAAAAATAATATAAA
* *
1273941 ATAAAATATAATAT-AAAAATAATATAATT
1 AT-AAATAAAATATAAAAAATAATATAA-A
* *
1273970 ATAATATAAATATATATTAAAATTTATATAAA
1 ATAA-ATAAA-ATATA--AAAAATAATATAAA
*
1274002 ATAAATATAATATAAAA
1 ATAAATAAAATATAAAA
1274019 TTAAAAATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
27 11 0.17
28 18 0.29
29 6 0.10
30 9 0.14
31 4 0.06
32 4 0.06
33 11 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAAATAAAATATAAAAAATAATATAAA
Found at i:1273946 original size:16 final size:16
Alignment explanation
Indices: 1273925--1273992 Score: 75
Period size: 16 Copynumber: 4.1 Consensus size: 16
1273915 TAAATAAAAT
*
1273925 ATAAAAAATAATTAAA
1 ATAAAATATAATTAAA
1273941 ATAAAATATAATATAAA
1 ATAAAATATAAT-TAAA
* *
1273958 A-ATAATATAATTATA
1 ATAAAATATAATTAAA
1273973 ATATAAATATATATTAAA
1 ATA-AAATATA-ATTAAA
1273991 AT
1 AT
1273993 TTATATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 4 0.09
16 21 0.49
17 11 0.26
18 7 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAAATATAATTAAA
Found at i:1273991 original size:33 final size:31
Alignment explanation
Indices: 1273940--1274040 Score: 105
Period size: 33 Copynumber: 3.1 Consensus size: 31
1273930 AAATAATTAA
*
1273940 AATA-AAATATAATATAAAAATAATATAATTAT
1 AATATAAATATAAT-TAAAAATTATATAA-TAT
* *
1273972 AATATAAATATATATTAAAATTTATATAAAAT
1 AATATAAATATA-ATTAAAAATTATATAATAT
*
1274004 AAATATAATATAAAATTAAAAATTATACTAATAT
1 -AATATAA-ATATAATTAAAAATTATA-TAATAT
1274038 AAT
1 AAT
1274041 TTAATCACAT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
32 6 0.10
33 41 0.71
34 11 0.19
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (31 bp):
AATATAAATATAATTAAAAATTATATAATAT
Found at i:1273992 original size:32 final size:32
Alignment explanation
Indices: 1273932--1274018 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
1273922 AATATAAAAA
1273932 ATAATTAAAATAAAATATAATATAAAAATAAT
1 ATAATTAAAATAAAATATAATATAAAAATAAT
* * *
1273964 ATAATTATAATATAAATAT-ATATTAAAAT-TT
1 ATAATTAAAATA-AAATATAATATAAAAATAAT
1273995 AT-A-TAAAAT-AAATATAATATAAAA
1 ATAATTAAAATAAAATATAATATAAAA
1274019 TTAAAAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 6 0.12
28 7 0.15
29 5 0.10
30 1 0.02
31 3 0.06
32 20 0.42
33 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (32 bp):
ATAATTAAAATAAAATATAATATAAAAATAAT
Found at i:1274006 original size:16 final size:17
Alignment explanation
Indices: 1273985--1274030 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1273975 ATAAATATAT
1273985 ATTAAAATTTATATAAA
1 ATTAAAATTTATATAAA
*
1274002 A-T-AAATATAATATAAA
1 ATTAAAAT-TTATATAAA
*
1274018 ATTAAAAATTATA
1 ATTAAAATTTATA
1274031 CTAATATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
17 6 0.26
18 3 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTAAAATTTATATAAA
Found at i:1274016 original size:11 final size:11
Alignment explanation
Indices: 1273940--1274017 Score: 68
Period size: 11 Copynumber: 6.7 Consensus size: 11
1273930 AAATAATTAA
1273940 AATA-AAATAT
1 AATATAAATAT
*
1273950 AATATAAAAAT
1 AATATAAATAT
*
1273961 AATATAATTAT
1 AATATAAATAT
1273972 AATATAAATAT
1 AATATAAATAT
*
1273983 ATATTAAAATTTATAT
1 A-A-TATAA---ATAT
*
1273999 AAAATAAATAT
1 AATATAAATAT
1274010 AATATAAA
1 AATATAAA
1274018 ATTAAAAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
10 4 0.07
11 36 0.67
12 1 0.02
13 4 0.07
14 3 0.06
15 1 0.02
16 5 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATAAATAT
Found at i:1274019 original size:27 final size:27
Alignment explanation
Indices: 1273969--1274020 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
1273959 ATAATATAAT
*
1273969 TATAATATAAATATATATTAAAATTTA
1 TATAAAATAAATATATATTAAAATTTA
1273996 TATAAAATAAATATA-ATATAAAATT
1 TATAAAATAAATATATAT-TAAAATT
1274021 AAAAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TATAAAATAAATATATATTAAAATTTA
Found at i:1275813 original size:20 final size:22
Alignment explanation
Indices: 1275771--1275821 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
1275761 TAAACTCCTC
1275771 TTAAATTATAATAATAAGTAAAA
1 TTAAATTATAATAATAAG-AAAA
*
1275794 TTAAATTATAA-ATTAA-AAAA
1 TTAAATTATAATAATAAGAAAA
*
1275814 TAAAATTA
1 TTAAATTA
1275822 ACAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 11 0.42
22 4 0.15
23 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TTAAATTATAATAATAAGAAAA
Found at i:1283455 original size:34 final size:35
Alignment explanation
Indices: 1283398--1283463 Score: 125
Period size: 34 Copynumber: 1.9 Consensus size: 35
1283388 CGTGTTCTGT
1283398 TTTTTCCCTTCTCTTTTTCTTCATAAATGATTCAG
1 TTTTTCCCTTCTCTTTTTCTTCATAAATGATTCAG
1283433 TTTTTCCCTTCTC-TTTTCTTCATAAATGATT
1 TTTTTCCCTTCTCTTTTTCTTCATAAATGATT
1283464 TATCAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.17, C:0.23, G:0.05, T:0.56
Consensus pattern (35 bp):
TTTTTCCCTTCTCTTTTTCTTCATAAATGATTCAG
Found at i:1286367 original size:36 final size:36
Alignment explanation
Indices: 1286320--1286438 Score: 229
Period size: 36 Copynumber: 3.3 Consensus size: 36
1286310 ACATTTTATT
1286320 CTCTTGAATTTCTTCAATGCAGAAAAGTATAAAGTA
1 CTCTTGAATTTCTTCAATGCAGAAAAGTATAAAGTA
1286356 CTCTTGAATTTCTTCAATGCAGAAAAGTATAAAGTA
1 CTCTTGAATTTCTTCAATGCAGAAAAGTATAAAGTA
1286392 CTCTTGAATTTCTTCAATGCAGAAAAGTATAAAGTA
1 CTCTTGAATTTCTTCAATGCAGAAAAGTATAAAGTA
*
1286428 CTCTTGCATTT
1 CTCTTGAATTT
1286439 ACTGTTGTGT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (36 bp):
CTCTTGAATTTCTTCAATGCAGAAAAGTATAAAGTA
Found at i:1286734 original size:8 final size:8
Alignment explanation
Indices: 1286721--1286755 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1286711 ATCTAAATGC
1286721 TTCTTTCA
1 TTCTTTCA
1286729 TTCTTTCA
1 TTCTTTCA
*
1286737 TTCATTCA
1 TTCTTTCA
*
1286745 TTCGTTCA
1 TTCTTTCA
1286753 TTC
1 TTC
1286756 ATCTGTCAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.14, C:0.26, G:0.03, T:0.57
Consensus pattern (8 bp):
TTCTTTCA
Found at i:1289803 original size:17 final size:15
Alignment explanation
Indices: 1289778--1289823 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 15
1289768 TATATTTAAA
1289778 AATAATTTATATTTT
1 AATAATTTATATTTT
*
1289793 TATAAATTTTAATATTTT
1 AAT-AA-TTT-ATATTTT
1289811 AATAATTTATATT
1 AATAATTTATATT
1289824 ATATATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.27
16 5 0.19
17 5 0.19
18 9 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATAATTTATATTTT
Found at i:1289836 original size:33 final size:34
Alignment explanation
Indices: 1289778--1289842 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
1289768 TATATTTAAA
*
1289778 AATAATTTATATTTTTATAAATTTT-AATATTTT
1 AATAATTTATATTTATATAAATTTTAAATATTTT
*
1289811 AATAATTTATA-TTATATATATTTTTAAATATT
1 AATAATTTATATTTATATA-AATTTTAAATATT
1289843 CATATAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 6 0.21
33 16 0.57
34 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
AATAATTTATATTTATATAAATTTTAAATATTTT
Found at i:1291221 original size:2 final size:2
Alignment explanation
Indices: 1291214--1291252 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1291204 AAGATTAGCC
1291214 AT AT AT AT AT AT 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 AT AT AT A
1291253 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1298852 original size:42 final size:42
Alignment explanation
Indices: 1298796--1298914 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
1298786 TTCTTCTCTC
* * *
1298796 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTGTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1298838 CTCTTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* * *
1298880 CTCCTCCTATCATCCCTCTTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1298915 TTGAGGGTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.08, C:0.44, G:0.03, T:0.45
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1298889 original size:21 final size:21
Alignment explanation
Indices: 1298824--1298890 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1298814 CTCTCTCTAT
* *
1298824 TATCTGTCCTGTCTCTCTTCC
1 TATCTCTCCTGTCTCTCCTCC
* * *
1298845 TATCATC-CCT-CCTATCTCTAC
1 TATC-TCTCCTGTCTCTC-CTCC
1298866 TATCTCTCCTGTCTCTCCTCC
1 TATCTCTCCTGTCTCTCCTCC
1298887 TATC
1 TATC
1298891 ATCCCTCTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
20 6 0.18
21 23 0.68
22 5 0.15
ACGTcount: A:0.10, C:0.42, G:0.04, T:0.43
Consensus pattern (21 bp):
TATCTCTCCTGTCTCTCCTCC
Found at i:1300550 original size:10 final size:10
Alignment explanation
Indices: 1300532--1300565 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1300522 TCACTTAACA
1300532 AAAAAAAAAG
1 AAAAAAAAAG
*
1300542 AATAAAAAAG
1 AAAAAAAAAG
1300552 AGAAAAAAAAG
1 A-AAAAAAAAG
1300563 AAA
1 AAA
1300566 GTATCTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:1300968 original size:27 final size:27
Alignment explanation
Indices: 1300905--1300961 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1300895 TATCCCATGT
* *
1300905 CATACTTTTTGTATGCTATGTATAATG
1 CATACATTTTCTATGCTATGTATAATG
*
1300932 CATACATTTTCTATGCTATGTATGATG
1 CATACATTTTCTATGCTATGTATAATG
1300959 CAT
1 CAT
1300962 GTATTTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (27 bp):
CATACATTTTCTATGCTATGTATAATG
Found at i:1301594 original size:58 final size:57
Alignment explanation
Indices: 1301441--1301630 Score: 172
Period size: 58 Copynumber: 3.3 Consensus size: 57
1301431 TAGTATATAC
* * *
1301441 TTTCATGCATTCTAGCATTATTTTAGTCATTTTCCATGACTTAAAGACT-TTTATGTC-A
1 TTTCATGCATTTTAGGATTATTTTAGT-ATTTACCATGACTT-AAGACTATTTATG-CAA
* * * * *
1301499 TTTCATGCATTGTTTGG-TCATTCTAACTATTTGCCATGACTTAAGACTATTTATGCAA
1 TTTCATGCATT-TTAGGATTATT-TTAGTATTTACCATGACTTAAGACTATTTATGCAA
* * * * *
1301557 TTTCATGCATTTTAGGATTGTTTTAGTAATTCACCATGATTTAGGA-TCATATATGCAA
1 TTTCATGCATTTTAGGATTATTTTAGT-ATTTACCATGACTTAAGACT-ATTTATGCAA
1301615 TTTCATGCATTTTAGG
1 TTTCATGCATTTTAGG
1301631 TCATTTAAGG
Statistics
Matches: 108, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
57 15 0.14
58 88 0.81
59 5 0.05
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (57 bp):
TTTCATGCATTTTAGGATTATTTTAGTATTTACCATGACTTAAGACTATTTATGCAA
Found at i:1301670 original size:58 final size:58
Alignment explanation
Indices: 1301532--1301688 Score: 135
Period size: 58 Copynumber: 2.7 Consensus size: 58
1301522 TAACTATTTG
* ** * *
1301532 CCATGACTTA-AGACTATTTATGCAATTTCATGCATTTTAGGATTGTTTTAGTAATTCA
1 CCATGATTTAGAGACTA-TTATGCAATTTCATGCATTTTAGGATCATTTAAGGAATTCA
* **
1301590 CCATGATTTAG-GA-TCATATATGCAATTTCATGCATTTTAGG-TCATTTAAGGCATTTT
1 CCATGATTTAGAGACT-AT-TATGCAATTTCATGCATTTTAGGATCATTTAAGGAATTCA
* *
1301647 CCTTGCATTTAGAGACTATTATGCCATTTTCTATGC-TTTTAG
1 CCATG-ATTTAGAGACTATTATG-CAATTTC-ATGCATTTTAG
1301689 AGATTATTAC
Statistics
Matches: 81, Mismatches: 10, Indels: 15
0.76 0.09 0.14
Matches are distributed among these distances:
57 15 0.19
58 45 0.56
59 16 0.20
60 5 0.06
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (58 bp):
CCATGATTTAGAGACTATTATGCAATTTCATGCATTTTAGGATCATTTAAGGAATTCA
Found at i:1301675 original size:30 final size:30
Alignment explanation
Indices: 1301641--1301705 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1301631 TCATTTAAGG
*
1301641 CATTTTCCT-TGCATTTAGAGACTATTATGC
1 CATTTT-CTATGCATTTAGAGACTATTACGC
* *
1301671 CATTTTCTATGCTTTTAGAGATTATTACGC
1 CATTTTCTATGCATTTAGAGACTATTACGC
1301701 CATTT
1 CATTT
1301706 CATTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.46
Consensus pattern (30 bp):
CATTTTCTATGCATTTAGAGACTATTACGC
Found at i:1304103 original size:34 final size:35
Alignment explanation
Indices: 1304035--1304106 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
1304025 AGTGTTTGTA
*
1304035 AAAGAATAAGCATAAAGAAATACAAATGAGCTTTG
1 AAAGAATAAGCATAAAGAAATACAAAAGAGCTTTG
**
1304070 AAAGAATAA-CAATAAAG-AATACAAAAGCTCTTTG
1 AAAGAATAAGC-ATAAAGAAATACAAAAGAGCTTTG
1304104 AAA
1 AAA
1304107 TGTAGAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (35 bp):
AAAGAATAAGCATAAAGAAATACAAAAGAGCTTTG
Found at i:1304480 original size:33 final size:32
Alignment explanation
Indices: 1304427--1304490 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1304417 CGATTCAGTG
*
1304427 TGTATCGATACCAAGAATATGTATCGATACAA
1 TGTATCAATACCAAGAATATGTATCGATACAA
*
1304459 TGTATCAATACTAAGCAATATGTATCGATACA
1 TGTATCAATACCAAG-AATATGTATCGATACA
1304491 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (32 bp):
TGTATCAATACCAAGAATATGTATCGATACAA
Found at i:1306894 original size:17 final size:17
Alignment explanation
Indices: 1306872--1306909 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1306862 CAAAAGAGTA
1306872 AAAGCTAGAAAG-GAAAG
1 AAAGCT-GAAAGAGAAAG
1306889 AAAGCTGAAAGAGAAAG
1 AAAGCTGAAAGAGAAAG
1306906 AAAG
1 AAAG
1306910 AGACATTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.61, C:0.05, G:0.29, T:0.05
Consensus pattern (17 bp):
AAAGCTGAAAGAGAAAG
Found at i:1307446 original size:11 final size:11
Alignment explanation
Indices: 1307430--1307454 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1307420 TTTGTTATTT
1307430 TTTTAATTGAG
1 TTTTAATTGAG
1307441 TTTTAATTGAG
1 TTTTAATTGAG
1307452 TTT
1 TTT
1307455 GAGTTTAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTTAATTGAG
Found at i:1307889 original size:77 final size:78
Alignment explanation
Indices: 1307721--1307903 Score: 185
Period size: 77 Copynumber: 2.4 Consensus size: 78
1307711 CTCTCTTTTG
* * * *
1307721 TTCATGTTGAAATATCTCGATT-AGGGCTATTTAGGTAATACGACTTTCAAATTGAATCTTTAGG
1 TTCATGTTGAAACATATCTATTAAGGG-TATTTAAGTAATACGACTTTCAAATTGAATCTTTAGG
* *
1307785 ATCATGTGTGGACC
65 ATCATGTGAGAACC
** * * *
1307799 TTCATGTCAAAACATATCTATTAAGGGTATTTAAGTAATACTA-TCTT-AAATTGAGTTTTTAGG
1 TTCATGTTGAAACATATCTATTAAGGGTATTTAAGTAATACGACT-TTCAAATTGAATCTTTAGG
*
1307862 ATCATGTGAGAACT
65 ATCATGTGAGAACC
* *
1307876 TTTATGTTGAAACATGTCCT-TTAAGGGT
1 TTCATGTTGAAACATAT-CTATTAAGGGT
1307904 TTTTTTTTTG
Statistics
Matches: 86, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
77 47 0.55
78 35 0.41
79 4 0.05
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.39
Consensus pattern (78 bp):
TTCATGTTGAAACATATCTATTAAGGGTATTTAAGTAATACGACTTTCAAATTGAATCTTTAGGA
TCATGTGAGAACC
Found at i:1311452 original size:19 final size:17
Alignment explanation
Indices: 1311415--1311448 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1311405 TTGATTTAAA
*
1311415 TATAATTATAAAAAAAT
1 TATAATGATAAAAAAAT
*
1311432 TATAATGATAGAAAAAT
1 TATAATGATAAAAAAAT
1311449 ATTAGAAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
TATAATGATAAAAAAAT
Found at i:1312347 original size:6 final size:6
Alignment explanation
Indices: 1312336--1312374 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1312326 GATATGAGAC
*
1312336 AATATA AATATA AATATA AATATA AATATG AATATA AAT
1 AATATA AATATA AATATA AATATA AATATA AATATA AAT
1312375 TTTAAGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:1313395 original size:32 final size:32
Alignment explanation
Indices: 1313336--1313403 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
1313326 GAGTATTAGC
* * *
1313336 TATTTTAAACATAGATTGTTTCTAACAA-AAGT
1 TATTCTAAACATAAATTGTTTCGAACAATAA-T
1313368 TATTCTAAACATAAATTGTCTT-GAACAATAAT
1 TATTCTAAACATAAATTGT-TTCGAACAATAAT
1313400 TATT
1 TATT
1313404 TTGATTACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 27 0.87
33 4 0.13
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (32 bp):
TATTCTAAACATAAATTGTTTCGAACAATAAT
Found at i:1316574 original size:24 final size:22
Alignment explanation
Indices: 1316527--1316574 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1316517 CAATTGGTTT
*
1316527 ATTTTTTTAAAAATAATAATTA
1 ATTTTTTTAAAAATAATAAATA
1316549 ATTTTTTTATATAAA-AATAACATA
1 ATTTTTTTA-A-AAATAATAA-ATA
1316573 AT
1 AT
1316575 ATATTTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 9 0.41
23 6 0.27
24 7 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTTTTAAAAATAATAAATA
Found at i:1319653 original size:20 final size:20
Alignment explanation
Indices: 1319601--1319682 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 20
1319591 AAAAAAAAAA
1319601 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
1319620 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
1319641 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
1319661 ATTCTACAAATGTATCGATAC
1 ATTC-ACAAATGTATCGATAC
1319682 A
1 A
1319683 GGGTCCCAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.05
20 18 0.33
21 34 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:1319662 original size:41 final size:40
Alignment explanation
Indices: 1319601--1319682 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
1319591 AAAAAAAAAA
* *
1319601 ATTCCAAATGTATCGATACATTTGTA-GAATGTATCGATAC
1 ATTCCAAATGTATCGATACA-TTCTACAAATGTATCGATAC
1319641 ATTCACAAATGTATCGATACATTCTACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATTCTACAAATGTATCGATAC
1319682 A
1 A
1319683 GGGTCCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTCTACAAATGTATCGATAC
Done.