Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold173
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: 1189743
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 33358 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:1056582 original size:143 final size:143
Alignment explanation
Indices: 1056316--1056634 Score: 388
Period size: 143 Copynumber: 2.2 Consensus size: 143
1056306 CACGAAAGAG
* * * *
1056316 TTTGCGCCCAGCACTAGTCGGATAAACCGACAAATGTGTGCCCAGCACTAGTCAGATAAATTCAC
1 TTTGCGCCCAGCGCTAGTCGAATAAACCGACGAATGTGTGCCCAGCACTAGTCAGATAAACTCAC
* *
1056381 AGAGGTTGCACCCAACACTAGTCGAATAAACCGACGAATAATTAGTGAGCCCAACTCTAGTTGGA
66 AGAAGTTGCACCCAACACTAGTCGAATAAACCAACGAATAATTAGTGAGCCCAACTCTAGTTGGA
* * *
1056446 TAAATCAACGATA
131 TAAACCAACAAAA
** * * * *
1056459 TTTTTGCCCAGCGCTAGTCAAATAAACCGACGAATGTGTGCCGAGCGCTAGTCAGATAAACTGA-
1 TTTGCGCCCAGCGCTAGTCGAATAAACCGACGAATGTGTGCCCAGCACTAGTCAGATAAACTCAC
* * * * * * * * *
1056523 TGAAAGTTGCGCGCAGCACTAGTCGGATAAACTAACTAATAATTAGTGAGCCTAGCTCTAGTTGG
66 AG-AAGTTGCACCCAACACTAGTCGAATAAACCAACGAATAATTAGTGAGCCCAACTCTAGTTGG
1056588 ATAAACCAACAAAA
130 ATAAACCAACAAAA
* *
1056602 TTTGCGCCCAGCGCTAGTCGAACAAATCGACGA
1 TTTGCGCCCAGCGCTAGTCGAATAAACCGACGA
1056635 TGTCAATTAC
Statistics
Matches: 146, Mismatches: 29, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
142 1 0.01
143 145 0.99
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (143 bp):
TTTGCGCCCAGCGCTAGTCGAATAAACCGACGAATGTGTGCCCAGCACTAGTCAGATAAACTCAC
AGAAGTTGCACCCAACACTAGTCGAATAAACCAACGAATAATTAGTGAGCCCAACTCTAGTTGGA
TAAACCAACAAAA
Found at i:1064693 original size:33 final size:33
Alignment explanation
Indices: 1064650--1064727 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
1064640 AGCTAATATG
*
1064650 CTTGATTTCCAACAGCAGATACAACGACAAACT
1 CTTGATTTCCAACAGCAAATACAACGACAAACT
* * *
1064683 GTTGATTTCCAGCAGTAAATACAACGACAAACT
1 CTTGATTTCCAACAGCAAATACAACGACAAACT
1064716 CTTGATTTCCAA
1 CTTGATTTCCAA
1064728 AAGGAAACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (33 bp):
CTTGATTTCCAACAGCAAATACAACGACAAACT
Found at i:1066131 original size:18 final size:18
Alignment explanation
Indices: 1066108--1066159 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1066098 AGGCAACCCA
1066108 ATTTTATTTTTATTTTTT
1 ATTTTATTTTTATTTTTT
1066126 ATTTTATTTATATATTTTTT
1 ATTTTATTT-T-TATTTTTT
*
1066146 -TATT-TTTTTATTTT
1 ATTTTATTTTTATTTT
1066160 CTTGCATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 6 0.19
17 1 0.03
18 12 0.39
19 4 0.13
20 8 0.26
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (18 bp):
ATTTTATTTTTATTTTTT
Found at i:1066149 original size:8 final size:8
Alignment explanation
Indices: 1066109--1066159 Score: 57
Period size: 8 Copynumber: 6.1 Consensus size: 8
1066099 GGCAACCCAA
1066109 TTTTATTT
1 TTTTATTT
*
1066117 TTATTTTTT
1 TT-TTATTT
1066126 ATTTTATTT
1 -TTTTATTT
* *
1066135 ATATATTT
1 TTTTATTT
1066143 TTTTATTT
1 TTTTATTT
1066151 TTTTATTT
1 TTTTATTT
1066159 T
1 T
1066160 CTTGCATGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 23 0.66
9 10 0.29
10 2 0.06
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTATTT
Found at i:1067152 original size:18 final size:20
Alignment explanation
Indices: 1067116--1067158 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
1067106 ATATATTATT
1067116 AAGAAAAAAAAGAATGAAAA
1 AAGAAAAAAAAGAATGAAAA
*
1067136 AAGAAAAGAAA-AA-GAAAA
1 AAGAAAAAAAAGAATGAAAA
1067154 AAGAA
1 AAGAA
1067159 GTAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 2 0.09
20 10 0.45
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (20 bp):
AAGAAAAAAAAGAATGAAAA
Found at i:1072844 original size:6 final size:6
Alignment explanation
Indices: 1072835--1072875 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
1072825 AATAAATAAT
1072835 TATTTA TATTTA TATTTA TATTTA TATTTA TATTT- TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1072876 AAAATTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:1081160 original size:27 final size:28
Alignment explanation
Indices: 1081119--1081172 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
1081109 AGGTTGAAGG
1081119 TTTAAGGTTCAGGGTTC-GAGTTCAAAA
1 TTTAAGGTTCAGGGTTCAGAGTTCAAAA
* *
1081146 TTTAAGGTTCTGGGTTCAGGGTTCAAA
1 TTTAAGGTTCAGGGTTCAGAGTTCAAA
1081173 GTAAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (28 bp):
TTTAAGGTTCAGGGTTCAGAGTTCAAAA
Found at i:1081829 original size:18 final size:19
Alignment explanation
Indices: 1081802--1081837 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1081792 TTAGTAATAG
*
1081802 TAATATTTAAT-TTTTTTA
1 TAATACTTAATATTTTTTA
1081820 TAATACTTAATATTTTTT
1 TAATACTTAATATTTTTT
1081838 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATACTTAATATTTTTTA
Found at i:1081830 original size:25 final size:26
Alignment explanation
Indices: 1081785--1081834 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1081775 TTTTCTTGTT
1081785 ATTTTTATTAGTAATAGTAATATTTA
1 ATTTTTATTAGTAATAGTAATATTTA
*
1081811 ATTTTT-TTA-TAATACTTAATATTT
1 ATTTTTATTAGTAATA-GTAATATTT
1081835 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 11 0.50
26 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTTTTATTAGTAATAGTAATATTTA
Found at i:1082085 original size:43 final size:43
Alignment explanation
Indices: 1082037--1082370 Score: 449
Period size: 43 Copynumber: 7.8 Consensus size: 43
1082027 TTTTAGAAAT
* * * **
1082037 AAACGCTGCTATAGACCATGACCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* *
1082080 AAACGCCACTATAGATCAGGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
1082123 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTT-CAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
*
1082165 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * *
1082208 AAACGCCACTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * *
1082251 AAATGCCGCTATAAATCAAGACCTTTAGCGGCGATTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* ** * *
1082294 AAACGCCACTATATCTCAAGACCTTTAGCAGCGTTTTTTCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* *
1082337 AAACGCCGCTATAGAACAA-A-CTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
1082371 CTCGCAAAAA
Statistics
Matches: 258, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
41 11 0.04
42 42 0.16
43 205 0.79
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
Found at i:1082201 original size:128 final size:129
Alignment explanation
Indices: 1082037--1082384 Score: 477
Period size: 128 Copynumber: 2.7 Consensus size: 129
1082027 TTTTAGAAAT
* * * * *
1082037 AAACGCTGCTATAGACCATGACCTTTAGCGGCGCTTTACCCACAAACGCCACTATAGATCAGGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGATCAAGAC
* * * *
1082102 CTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTT-CAC
66 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAAATCAAGACCTTTAGCGGCGATTTTTCCAC
*
1082165 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGCTCAAGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGATCAAGAC
*
1082230 CTTTAGCGGCGCTTTTCCCAAAAATGCCGCTATAAATCAAGACCTTTAGCGGCGATTTTTCCAC
66 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAAATCAAGACCTTTAGCGGCGATTTTTCCAC
* ** * * * * *
1082294 AAACGCCACTATATCTCAAGACCTTTAGCAGCGTTTTTTCCACAAACGCCGCTATAGAACAA-A-
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGATCAAGAC
* * *
1082357 CTTTAGCGACGCTTCTCGCAAAAACGCC
66 CTTTAGCGGCGCTTTTCCCAAAAACGCC
1082385 ACTAAAAACA
Statistics
Matches: 195, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
127 24 0.12
128 115 0.59
129 56 0.29
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (129 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTATAGATCAAGAC
CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTATAAATCAAGACCTTTAGCGGCGATTTTTCCAC
Found at i:1085445 original size:24 final size:24
Alignment explanation
Indices: 1085413--1085460 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1085403 GAAGATGATC
1085413 AAAATTATAATTAAAAATCTATAT
1 AAAATTATAATTAAAAATCTATAT
*
1085437 AAAATTATAATTAAACATCTATAT
1 AAAATTATAATTAAAAATCTATAT
1085461 GGAATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAATTATAATTAAAAATCTATAT
Found at i:1086246 original size:7 final size:7
Alignment explanation
Indices: 1086236--1086273 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
1086226 CACTAACTCT
*
1086236 TAACCTC
1 TAACCCC
1086243 TAACCCC
1 TAACCCC
1086250 TAACCCC
1 TAACCCC
*
1086257 TAACCAC
1 TAACCCC
1086264 TAACCCC
1 TAACCCC
1086271 TAA
1 TAA
1086274 ACTTTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.18
Consensus pattern (7 bp):
TAACCCC
Found at i:1086374 original size:193 final size:186
Alignment explanation
Indices: 1085984--1086330 Score: 460
Period size: 186 Copynumber: 1.8 Consensus size: 186
1085974 AATTCAAAAA
* * *
1085984 ACTAGTTAATCTAAACCCAAAACCCTAACCCGACCCTGAATTTCTAAACCCTAAATCACTAACCA
1 ACTAATTAATCTAAACCCAAAACCCTAACCCGACCCCGAATCTCTAAACCCTAAATCACTAACCA
** * *
1086049 CAAACCTTTAACCCCTAACTACTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAA
66 CAAACCCCTAACCCCTAACCACTAACCCCTAAACCTTATTTAATATATAAATAAAAAAACACTAA
* * ** *
1086114 TTAATCTAAATCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAT
131 TTAATCTAAACCCTAAACCCTAAACATTATCGAATACATAAATTAAAACACACTAT
** *
1086170 ACTAATTAATCTAAACCTTAAACCCTAACCCGACCCCGAATCTCTAAATCCTAAATCACTAACTC
1 ACTAATTAATCTAAACCCAAAACCCTAACCCGACCCCGAATCTCTAAACCCTAAATCACTAAC-C
* *
1086235 TTAACCTCTAACCCCTAACCCCTAACCACTAACCCCTAAACTTTATTTAATATATAAATCAAAAA
65 ---A---CAAACCCCTAACCCCTAACCACTAACCCCTAAACCTTATTTAATATATAAAT-AAAAA
*
1086300 AATACTAATTAATCTAAACCCTAAACCCTAA
123 AACACTAATTAATCTAAACCCTAAACCCTAA
1086331 CTTGACATCG
Statistics
Matches: 138, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
186 57 0.41
187 1 0.01
190 1 0.01
193 47 0.34
194 32 0.23
ACGTcount: A:0.43, C:0.29, G:0.01, T:0.27
Consensus pattern (186 bp):
ACTAATTAATCTAAACCCAAAACCCTAACCCGACCCCGAATCTCTAAACCCTAAATCACTAACCA
CAAACCCCTAACCCCTAACCACTAACCCCTAAACCTTATTTAATATATAAATAAAAAAACACTAA
TTAATCTAAACCCTAAACCCTAAACATTATCGAATACATAAATTAAAACACACTAT
Found at i:1086402 original size:133 final size:137
Alignment explanation
Indices: 1086119--1086408 Score: 380
Period size: 133 Copynumber: 2.2 Consensus size: 137
1086109 ACTAATTAAT
*
1086119 CTAAATC-CTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTATACTAATTAATCTA
1 CTAAATCACTAACCCCTAAACATTATTTAATATATAAATCAAAACACAC-ATACTAATTAATCTA
* *
1086183 AACCTTAAACCCTAACCCGACCCCGAATCTCTAAATCCTAAATCACTAACTCTTAACCTCTAACC
65 AACCCTAAACCCTAACCCGACACCGAATCTCTAAATCCTAAATCACTAACTCTTAACCTCTAACC
*
1086248 CCTAACCC
130 ACTAACCC
* *
1086256 CT-AACCACTAACCCCTAAACTTTATTTAATATATAAATCAAAA-A-A-ATACTAATTAATCTAA
1 CTAAATCACTAACCCCTAAACATTATTTAATATATAAATCAAAACACACATACTAATTAATCTAA
** * * *
1086317 ACCCTAAACCCTAACTTGACATCGAATC-CATAAA-CCTTAAATCCCTAACTCTTAATCTCTAAC
66 ACCCTAAACCCTAACCCGACACCGAATCTC-TAAATCC-TAAATCACTAACTCTTAACCTCTAAC
1086380 CACTAACCC
129 CACTAACCC
* *
1086389 TTAAATCAC-AACCCTTAAAC
1 CTAAATCACTAACCCCTAAAC
1086409 CAGAATCCCT
Statistics
Matches: 135, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
132 3 0.02
133 86 0.64
134 5 0.04
135 1 0.01
136 4 0.03
137 36 0.27
ACGTcount: A:0.41, C:0.30, G:0.01, T:0.27
Consensus pattern (137 bp):
CTAAATCACTAACCCCTAAACATTATTTAATATATAAATCAAAACACACATACTAATTAATCTAA
ACCCTAAACCCTAACCCGACACCGAATCTCTAAATCCTAAATCACTAACTCTTAACCTCTAACCA
CTAACCC
Found at i:1086424 original size:7 final size:7
Alignment explanation
Indices: 1086412--1086442 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1086402 CTTAAACCAG
1086412 AATCCCT
1 AATCCCT
1086419 AATCCCT
1 AATCCCT
1086426 AATCCCT
1 AATCCCT
1086433 AATCCCT
1 AATCCCT
1086440 AAT
1 AAT
1086443 TCCATAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (7 bp):
AATCCCT
Found at i:1086910 original size:41 final size:41
Alignment explanation
Indices: 1086850--1087162 Score: 364
Period size: 41 Copynumber: 7.6 Consensus size: 41
1086840 AAATGTTTTT
* ** * *
1086850 GCGGCGCTTTATCAAAAACGCCGCTAAATTCCCGAGCACTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
*
1086891 GCTGCGCTTTTTCAAAAACGCCGCT-AAAGCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGC-CTGAGCATTA
* *
1086932 GCGGCGCTTTTTCAAAAATGACGCT-AAAGCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGC-CTGAGCATTA
* *
1086973 GCGGCGC-TCTTGAAAAAGCGCCGCTAAAAGCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAA-CGCCGCTAAAAGCCTGAGCATTA
* * *
1087014 GCGGTGCTTTTTCAAAATCGCCGCTAAAAGCTTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
** * * *
1087055 GCATCGCTTTTTTAAAAATGCCGTTAAAAGCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
* * * *
1087096 ACGGCGCTATTTT-AAAAACGCAGTTAAAAGCCTAAGCATTA
1 GCGGCGCT-TTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
1087137 GCGGCGCTTTTTCAAAAACGCCGCTA
1 GCGGCGCTTTTTCAAAAACGCCGCTA
1087163 CAGCCCCAAA
Statistics
Matches: 231, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
40 15 0.06
41 200 0.87
42 16 0.07
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
Found at i:1089724 original size:6 final size:6
Alignment explanation
Indices: 1089703--1089736 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
1089693 AAATAAAGAC
1089703 AATTAA AATTGCAA AATTAA AATTAA AATTAA AA
1 AATTAA AATT--AA AATTAA AATTAA AATTAA AA
1089737 ACTTTTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.77
8 6 0.23
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (6 bp):
AATTAA
Found at i:1096559 original size:15 final size:16
Alignment explanation
Indices: 1096538--1096575 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1096528 AGATTTGAAG
1096538 AATGAGGGAT-ATTGA
1 AATGAGGGATGATTGA
*
1096553 GATGAGGGATGATTGA
1 AATGAGGGATGATTGA
1096569 AATGAGG
1 AATGAGG
1096576 AGTGAGTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.39, T:0.24
Consensus pattern (16 bp):
AATGAGGGATGATTGA
Found at i:1098366 original size:12 final size:12
Alignment explanation
Indices: 1098346--1098375 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1098336 CTTCATGTCA
1098346 CACACGGCCTGG
1 CACACGGCCTGG
*
1098358 CACATGGCCTGG
1 CACACGGCCTGG
1098370 CACACG
1 CACACG
1098376 ACCGTGTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.20, C:0.40, G:0.30, T:0.10
Consensus pattern (12 bp):
CACACGGCCTGG
Found at i:1098555 original size:63 final size:62
Alignment explanation
Indices: 1098482--1098602 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 62
1098472 CACACGTTCA
* * * * * *
1098482 TGTCTCTGGCCTGTATGACTCTAATTC-CAAAATAATGAGTTACATGGCCTGGACACACGACCG
1 TGTCCCTGGCCCGTAGGACACTAATTCAC-AAACAATGAGTTACACGGCCTGG-CACACGACCG
* *
1098545 TGTCCCTGGCCCGTGGGACACTAATTCACAAACAGTGAGTTACACGGCCTGGCACACG
1 TGTCCCTGGCCCGTAGGACACTAATTCACAAACAATGAGTTACACGGCCTGGCACACG
1098603 GCTATGTGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 6 0.12
63 42 0.86
64 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (62 bp):
TGTCCCTGGCCCGTAGGACACTAATTCACAAACAATGAGTTACACGGCCTGGCACACGACCG
Found at i:1099117 original size:14 final size:14
Alignment explanation
Indices: 1099098--1099144 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
1099088 TGTGAAAACC
1099098 AAAAAGAATAAGAG
1 AAAAAGAATAAGAG
1099112 AAAAAGAAT-A-A-
1 AAAAAGAATAAGAG
*
1099123 CAAAAGAATAAGAG
1 AAAAAGAATAAGAG
1099137 AAAAAGAA
1 AAAAAGAA
1099145 CAAACGGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 8 0.29
12 2 0.07
13 2 0.07
14 16 0.57
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.06
Consensus pattern (14 bp):
AAAAAGAATAAGAG
Found at i:1099528 original size:4 final size:4
Alignment explanation
Indices: 1099519--1099565 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
1099509 TGGGCGTTAC
1099519 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
1099566 ATGCCTAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (4 bp):
AGAT
Found at i:1100181 original size:28 final size:28
Alignment explanation
Indices: 1100141--1100198 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1100131 CAAATCAAAA
1100141 GTAGTTTAAATACTTGAGATTTGTATAG
1 GTAGTTTAAATACTTGAGATTTGTATAG
1100169 GTAGTTTAAATACTTGAGATTTGTATAG
1 GTAGTTTAAATACTTGAGATTTGTATAG
1100197 GT
1 GT
1100199 TTTATACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.43
Consensus pattern (28 bp):
GTAGTTTAAATACTTGAGATTTGTATAG
Found at i:1100205 original size:24 final size:26
Alignment explanation
Indices: 1100149--1100206 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
1100139 AAGTAGTTTA
1100149 AATACTTGAGATTTGTATAGGTAGTTT
1 AATACTTGAGATTTGTATAGGTA-TTT
1100176 AAATACTTGAGATTTGTATAGGT-TTT
1 -AATACTTGAGATTTGTATAGGTATTT
1100202 -ATACT
1 AATACT
1100207 AAGAGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.17
26 3 0.10
28 22 0.73
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (26 bp):
AATACTTGAGATTTGTATAGGTATTT
Found at i:1104909 original size:72 final size:72
Alignment explanation
Indices: 1104813--1104995 Score: 350
Period size: 72 Copynumber: 2.6 Consensus size: 72
1104803 ATTTCCAATT
1104813 AGACACCCTA-TTGTTTCCTCCTTTAGTCCCGAAATTATTAATGAAAATTAGGTAAATTACCAAA
1 AGACACCCTATTTGTTTCCTCCTTTAGTCCCGAAATTATTAATGAAAATTAGGTAAATTACCAAA
1104877 CCTACCA
66 CCTACCA
1104884 AGACACCCTATTTGTTTCCTCCTTTAGTCCCGAAATTATTAATGAAAATTAGGTAAATTACCAAA
1 AGACACCCTATTTGTTTCCTCCTTTAGTCCCGAAATTATTAATGAAAATTAGGTAAATTACCAAA
1104949 CCTACCA
66 CCTACCA
*
1104956 AGACACCCTATTTGTTTCCTCCTTTAGTCCCCAAATTATT
1 AGACACCCTATTTGTTTCCTCCTTTAGTCCCGAAATTATT
1104996 TTTTTTTCTT
Statistics
Matches: 110, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
71 10 0.09
72 100 0.91
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.33
Consensus pattern (72 bp):
AGACACCCTATTTGTTTCCTCCTTTAGTCCCGAAATTATTAATGAAAATTAGGTAAATTACCAAA
CCTACCA
Found at i:1106061 original size:9 final size:10
Alignment explanation
Indices: 1106047--1106089 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
1106037 ATTAATATCC
1106047 AAAT-AAGTA
1 AAATAAAGTA
*
1106056 AAATAAAATA
1 AAATAAAGTA
1106066 AAATAAAGTAA
1 AAATAAAGT-A
1106077 TAAATAAAGTA
1 -AAATAAAGTA
1106088 AA
1 AA
1106090 GAAAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 14 0.48
11 2 0.07
12 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (10 bp):
AAATAAAGTA
Found at i:1112504 original size:44 final size:44
Alignment explanation
Indices: 1112441--1112526 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
1112431 CCTATCCGTG
*
1112441 AACACCTTACCCTGAACCGGTCTAGATTGTGAGGTCGAGAGATA
1 AACACCTTACCCTGAACCGGTCTAGACTGTGAGGTCGAGAGATA
*
1112485 AACACCTTACCCTGAACCGGTCTGGACTGTGAGGTCGAGAGA
1 AACACCTTACCCTGAACCGGTCTAGACTGTGAGGTCGAGAGA
1112527 AAAATAGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (44 bp):
AACACCTTACCCTGAACCGGTCTAGACTGTGAGGTCGAGAGATA
Found at i:1137883 original size:1 final size:1
Alignment explanation
Indices: 1137877--1137906 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1137867 TTTTGGCTGC
1137877 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1137907 CTGTACTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1137967 original size:1 final size:1
Alignment explanation
Indices: 1137963--1138016 Score: 90
Period size: 1 Copynumber: 54.0 Consensus size: 1
1137953 ACCTTGTACC
* *
1137963 TTTTTTTTTTTTTTTTTTTTTTTGTGTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1138017 GTGCGTAGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (1 bp):
T
Found at i:1137987 original size:28 final size:28
Alignment explanation
Indices: 1137956--1138013 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
1137946 TGTTTTTACC
1137956 TTGTACCTTTTTTTTTTTTTTTTTTTTT
1 TTGTACCTTTTTTTTTTTTTTTTTTTTT
***
1137984 TTGTGTTTTTTTTTTTTTTTTTTTTTTT
1 TTGTACCTTTTTTTTTTTTTTTTTTTTT
1138012 TT
1 TT
1138014 TTTGTGCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.02, C:0.03, G:0.05, T:0.90
Consensus pattern (28 bp):
TTGTACCTTTTTTTTTTTTTTTTTTTTT
Found at i:1150437 original size:18 final size:18
Alignment explanation
Indices: 1150414--1150475 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
1150404 GATGATATCA
1150414 ATATTGATGCTAGTGACG
1 ATATTGATGCTAGTGACG
*
1150432 ATATTGATGCTAGTAACG
1 ATATTGATGCTAGTGACG
* * *
1150450 CTATTGATGATAGTGGCG
1 ATATTGATGCTAGTGACG
*
1150468 CTATTGAT
1 ATATTGAT
1150476 AATGACCTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.35
Consensus pattern (18 bp):
ATATTGATGCTAGTGACG
Found at i:1150719 original size:18 final size:18
Alignment explanation
Indices: 1150679--1150721 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1150669 GTTCAAGGTG
1150679 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
1150697 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
1150715 TAATTAA
1 TAATTAA
1150722 AAACTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:1156593 original size:13 final size:13
Alignment explanation
Indices: 1156577--1156619 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
1156567 ATAAAAAGCC
1156577 ATAATAATAATTA
1 ATAATAATAATTA
*
1156590 ATAATTATAATT-
1 ATAATAATAATTA
1156602 ATAATAATAAATTA
1 ATAATAAT-AATTA
1156616 ATAA
1 ATAA
1156620 CAAAATCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.27
13 15 0.58
14 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATAATAATTA
Found at i:1157488 original size:40 final size:41
Alignment explanation
Indices: 1157433--1157528 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 41
1157423 ATCCACTAGC
* *
1157433 ACCTCCCAC-AGTACCACCCACACCATGATTCCTAATGGTA
1 ACCTCCCACGAGTACCACCCACACCATGATTCCTAACGATA
***
1157473 ACCTCCCACGA-TACCACCCATGGCATGATTCCTAACGATA
1 ACCTCCCACGAGTACCACCCACACCATGATTCCTAACGATA
*
1157513 ACCTTCCACGAGTACC
1 ACCTCCCACGAGTACC
1157529 CTCCCACGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 43 0.90
41 5 0.10
ACGTcount: A:0.29, C:0.40, G:0.11, T:0.20
Consensus pattern (41 bp):
ACCTCCCACGAGTACCACCCACACCATGATTCCTAACGATA
Found at i:1157586 original size:39 final size:39
Alignment explanation
Indices: 1157538--1157637 Score: 110
Period size: 39 Copynumber: 2.6 Consensus size: 39
1157528 CCTCCCACGG
* * **
1157538 TAACCATCCACAAGTACCTCTTGCGATACCCTCCCATAA
1 TAACCATCCACGAGTACCACCCGCGATACCCTCCCATAA
* * * **
1157577 TAACAATCCAGGAGTACCACCCGCGATACCTTCCCATGG
1 TAACCATCCACGAGTACCACCCGCGATACCCTCCCATAA
*
1157616 TAACCATCCACGAGTACTACCC
1 TAACCATCCACGAGTACCACCC
1157638 ACTGAACCAT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.30, C:0.38, G:0.12, T:0.20
Consensus pattern (39 bp):
TAACCATCCACGAGTACCACCCGCGATACCCTCCCATAA
Found at i:1167316 original size:30 final size:30
Alignment explanation
Indices: 1167264--1167326 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1167254 TCCTTTTCCG
*
1167264 CTTTTTGATAAATGACCCAATAT-TTTTTA
1 CTTTTTGATAAATGACCCAATATGTTTATA
*
1167293 CTTTTTGCATAAAT-AGCCTAATATGTTTATA
1 CTTTTTG-ATAAATGA-CCCAATATGTTTATA
1167324 CTT
1 CTT
1167327 CTTCTCCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.28
30 13 0.45
31 8 0.28
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (30 bp):
CTTTTTGATAAATGACCCAATATGTTTATA
Found at i:1168050 original size:3 final size:3
Alignment explanation
Indices: 1168044--1168073 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1168034 CTCCTCCTCC
1168044 TCT TCT TCT TCT TCT TC- TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1168074 TTACCGCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1168064 original size:14 final size:14
Alignment explanation
Indices: 1168047--1168073 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1168037 CTCCTCCTCT
1168047 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
1168061 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
1168074 TTACCGCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTCTTCTTCTTC
Found at i:1168070 original size:17 final size:17
Alignment explanation
Indices: 1168029--1168073 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1168019 GCATCTCCAT
* *
1168029 TTCTTCTCCTCCTCCTC
1 TTCTTCTTCTTCTCCTC
*
1168046 TTCTTCTTCTTCTTCTC
1 TTCTTCTTCTTCTCCTC
1168063 TTCTTCTTCTT
1 TTCTTCTTCTT
1168074 TTACCGCCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (17 bp):
TTCTTCTTCTTCTCCTC
Found at i:1168391 original size:23 final size:21
Alignment explanation
Indices: 1168341--1168391 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
1168331 ATTTATAATG
1168341 ATAA-TAATTAAAAACAATTT
1 ATAATTAATTAAAAACAATTT
*
1168361 ATTAAATTAATTTAAAACTATATTT
1 A-T-AATTAATTAAAAAC-A-ATTT
1168386 ATAATT
1 ATAATT
1168392 TTAAAAGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.04
21 1 0.04
22 2 0.08
23 14 0.56
24 2 0.08
25 5 0.20
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATTAATTAAAAACAATTT
Found at i:1183163 original size:12 final size:13
Alignment explanation
Indices: 1183148--1183176 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1183138 TATATGAATC
1183148 AGCAACATTTA-A
1 AGCAACATTTAGA
1183160 AGCAACATTTAGA
1 AGCAACATTTAGA
1183173 AGCA
1 AGCA
1183177 GTCCAAGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (13 bp):
AGCAACATTTAGA
Found at i:1186784 original size:25 final size:25
Alignment explanation
Indices: 1186756--1186816 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
1186746 ATTTAGAAAA
* *
1186756 TAAATTTTCATTGCT-ATTTTACATT
1 TAAATTTTAATTGATAATTTTACA-T
* *
1186781 TAAATATTAATTGATAATTTTATAT
1 TAAATTTTAATTGATAATTTTACAT
*
1186806 TAAATTATAAT
1 TAAATTTTAAT
1186817 ATATTTACAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.52
Consensus pattern (25 bp):
TAAATTTTAATTGATAATTTTACAT
Done.