Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008259.1 Hibiscus syriacus cultivar Beakdansim tig00110912_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2373650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2250291 original size:15 final size:13
Alignment explanation
Indices: 2250247--2250295 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
2250237 TTCTATTATG
*
2250247 TTAATTTCAGCCT
1 TTAATTTCAGCAT
*
2250260 TTGAAATTCAGCAT
1 TT-AATTTCAGCAT
2250274 TTACATTTCAGTCAT
1 TTA-ATTTCAG-CAT
2250289 TTAATTT
1 TTAATTT
2250296 TTGCATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 3 0.10
14 21 0.70
15 6 0.20
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (13 bp):
TTAATTTCAGCAT
Found at i:2265022 original size:18 final size:18
Alignment explanation
Indices: 2265001--2265038 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2264991 ACATCACGAT
* *
2265001 GAACAAGCTCTACCAGAG
1 GAACAAGCACGACCAGAG
2265019 GAACAAGCACGACCAGAG
1 GAACAAGCACGACCAGAG
2265037 GA
1 GA
2265039 TCACATGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.26, G:0.26, T:0.05
Consensus pattern (18 bp):
GAACAAGCACGACCAGAG
Found at i:2274137 original size:2 final size:2
Alignment explanation
Indices: 2274130--2274160 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2274120 ATGCTTAAAT
2274130 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2274161 TATATATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2274320 original size:22 final size:22
Alignment explanation
Indices: 2274292--2274335 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2274282 TTGACTTTTT
* *
2274292 GGTCAAAGTCAACGCTGGTCAA
1 GGTCAAAATCAACGCTAGTCAA
*
2274314 GGTCAAAATCAACTCTAGTCAA
1 GGTCAAAATCAACGCTAGTCAA
2274336 AGTTAACAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (22 bp):
GGTCAAAATCAACGCTAGTCAA
Found at i:2278128 original size:14 final size:14
Alignment explanation
Indices: 2278098--2278138 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
2278088 AGTTTGAAAT
2278098 AAAATGTAATTATGCA
1 AAAATGTAA--ATGCA
*
2278114 AAGATGTAAATGCA
1 AAAATGTAAATGCA
2278128 AAAATGTAAAT
1 AAAATGTAAAT
2278139 ATGTGAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 15 0.65
16 8 0.35
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.27
Consensus pattern (14 bp):
AAAATGTAAATGCA
Found at i:2278219 original size:26 final size:27
Alignment explanation
Indices: 2278156--2278219 Score: 62
Period size: 26 Copynumber: 2.4 Consensus size: 27
2278146 TGTAACAATA
* *
2278156 AAAATGCAAATTATGCAATACAAAAGC
1 AAAATGCAAAGTATGAAATACAAAAGC
*
2278183 AAACAT-AAAAGTAT-AAATACAAAATG-
1 AAA-ATGCAAAGTATGAAATACAAAA-GC
2278209 AAAATGCAAAG
1 AAAATGCAAAG
2278220 ATACAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
25 2 0.07
26 16 0.53
27 10 0.33
28 2 0.07
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.17
Consensus pattern (27 bp):
AAAATGCAAAGTATGAAATACAAAAGC
Found at i:2281701 original size:15 final size:15
Alignment explanation
Indices: 2281683--2281793 Score: 71
Period size: 15 Copynumber: 7.4 Consensus size: 15
2281673 TGCTATGAGT
2281683 AAATGTTCTATGTGA
1 AAATGTTCTATGTGA
* * * *
2281698 AAATATGCTAAGTTA
1 AAATGTTCTATGTGA
* *
2281713 ATATGTTCTACT-CGA
1 AAATGTTCTA-TGTGA
* *
2281728 AAATGATATATGTGA
1 AAATGTTCTATGTGA
* *
2281743 ATATGTTCTACGTGA
1 AAATGTTCTATGTGA
* *
2281758 AAATGATATATGTGA
1 AAATGTTCTATGTGA
* * *
2281773 ATATGTTATACGTGA
1 AAATGTTCTATGTGA
2281788 AAATGT
1 AAATGT
2281794 GAATATGTTC
Statistics
Matches: 68, Mismatches: 26, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
14 1 0.01
15 67 0.99
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (15 bp):
AAATGTTCTATGTGA
Found at i:2281719 original size:30 final size:30
Alignment explanation
Indices: 2281685--2281792 Score: 112
Period size: 30 Copynumber: 3.6 Consensus size: 30
2281675 CTATGAGTAA
* *
2281685 ATGTTCTATGTGAAAAT-ATGCTAAGTTAAT
1 ATGTTCTATGTGAAAATGAT-ATAAGTGAAT
* *
2281715 ATGTTCTACT-CGAAAATGATATATGTGAAT
1 ATGTTCTA-TGTGAAAATGATATAAGTGAAT
* *
2281745 ATGTTCTACGTGAAAATGATATATGTGAAT
1 ATGTTCTATGTGAAAATGATATAAGTGAAT
* *
2281775 ATGTTATACGTGAAAATG
1 ATGTTCTATGTGAAAATG
2281793 TGAATATGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
30 65 0.96
31 3 0.04
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (30 bp):
ATGTTCTATGTGAAAATGATATAAGTGAAT
Found at i:2281997 original size:47 final size:47
Alignment explanation
Indices: 2281915--2282037 Score: 167
Period size: 48 Copynumber: 2.6 Consensus size: 47
2281905 GAGTCGAGGG
* *
2281915 TTCTACGCGGTCCTTCGGGACAAATCTATGTGGTCCTTC-GGGACAA
1 TTCTACGCGGTCCTTCGGGACAAATCTATGCGGTCCTTCGGGGAAAA
* * * *
2281961 TTCTTCGTGGTCCTTCTGGATAAATTCTATGCGGTCCTTCGGGGAAAA
1 TTCTACGCGGTCCTTCGGGACAAA-TCTATGCGGTCCTTCGGGGAAAA
2282009 TTCTACGCGGTCCTTCGGGACAAAGTCTA
1 TTCTACGCGGTCCTTCGGGACAAA-TCTA
2282038 CGTGGCACTT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 20 0.31
47 14 0.22
48 30 0.47
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (47 bp):
TTCTACGCGGTCCTTCGGGACAAATCTATGCGGTCCTTCGGGGAAAA
Found at i:2282038 original size:24 final size:24
Alignment explanation
Indices: 2281915--2282039 Score: 148
Period size: 24 Copynumber: 5.3 Consensus size: 24
2281905 GAGTCGAGGG
2281915 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
* *
2281939 -TCTATGTGGTCCTTCGGGAC-AA
1 TTCTACGCGGTCCTTCGGGACAAA
* * * *
2281961 TTCTTCGTGGTCCTTCTGGATAAA
1 TTCTACGCGGTCCTTCGGGACAAA
*
2281985 TTCTATGCGGTCCTTCGGGGA-AAA
1 TTCTACGCGGTCCTTC-GGGACAAA
2282009 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
*
2282033 GTCTACG
1 TTCTACG
2282040 TGGCACTTTG
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
22 2 0.02
23 38 0.45
24 42 0.49
25 3 0.04
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGACAAA
Found at i:2282163 original size:19 final size:19
Alignment explanation
Indices: 2282139--2282175 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2282129 ACATTGGGCT
2282139 AATTAAATAAATGAATATA
1 AATTAAATAAATGAATATA
*
2282158 AATTAAATAAATGGATAT
1 AATTAAATAAATGAATAT
2282176 GGATTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
AATTAAATAAATGAATATA
Found at i:2283695 original size:17 final size:16
Alignment explanation
Indices: 2283673--2283716 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
2283663 ATATTCTTGC
2283673 TTTTGTTTTTTCTACTT
1 TTTTGTTTTTTCTAC-T
* *
2283690 TTTTGTTTCTTCTTCT
1 TTTTGTTTTTTCTACT
2283706 TTTTGTTTTTT
1 TTTTGTTTTTT
2283717 TTCATACTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.80
Consensus pattern (16 bp):
TTTTGTTTTTTCTACT
Found at i:2288241 original size:140 final size:139
Alignment explanation
Indices: 2288042--2288894 Score: 998
Period size: 138 Copynumber: 6.1 Consensus size: 139
2288032 ATTTTTAATA
* * * * *
2288042 AATTATTGAGTTGAATAATTAAAATAGAACCTCGAGCATAAAAACGAGGACCAAATAAAAAATT-
1 AATTATTGAATCGAATAATTAAAATGGAACCTCGAGCAT--AAGCGAGGACCAAATTAAAAATTC
* * * * *
2288106 CTCATAAATTTAAGGACTAAATATGAAATTAAGCCTAAAATAGAGGCTCTAATTATTGACTTATT
64 CTCATAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTATT
*
2288171 CATTTTTAACC
129 CAATTTTAACC
* * * *
2288182 AATTTATTGAATCAAATAATTAGAATGGAACCTTGAGCATAAGCGTGGACCAAATTAAAAATTCC
1 AA-TTATTGAATCGAATAATTAAAATGGAACCTCGAGCATAAGCGAGGACCAAATTAAAAATTCC
* * * * * *
2288247 CCCTAAATTAAAGGACTAAGTATAAAATTAGGCCTATAATGGAGGTTCTAATTATTAACCTAGTT
65 TCATAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTA-TT
2288312 CAA-TTTAACC
129 CAATTTTAACC
* * * * * * **
2288322 AATTA-TCAATTTGAATAATTAAAATGGGACCTTGAGTAAAAGAAAGGACCAAATTAAAAATTAA
1 AATTATTGAA-TCGAATAATTAAAATGGAACCTCGAGCATAAGCGAGGACCAAATTAAAAATT--
*
2288386 GCCTACATTCCCTTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAGTGGAGGCTCTAATTAT
63 -CCT-CA------TAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGCTCTAATTAT
2288451 TAACCTATTCAATTTTAACC
120 TAACCTATTCAATTTTAACC
* * *
2288471 AATTTATTGAATCAAATAATTAAAATGGAACCTCGACCATAAGCGAGGGCCAAATTAAAAAATTC
1 AA-TTATTGAATCGAATAATTAAAATGGAACCTCGAGCATAAGCGAGGACCAAATT-AAAAATTC
*
2288536 CTC-TAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTAGT
64 CTCATAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTATT
*
2288600 CAATTTTAATC
129 CAATTTTAACC
* * * * * *
2288611 AATTATTGATTCGAATAATTAAAATGTAACCTCGAGCAAAAGCAAGGAACAAATTAAAAATTCCC
1 AATTATTGAATCGAATAATTAAAATGGAACCTCGAGCATAAGCGAGGACCAAATTAAAAATTCCT
* * * *
2288676 CA-AAATTAAAGGACTAAGTATGAAATTAAGCCTAAAGTGGGGGTTCTAATTATTAACCTAGTCA
66 CATAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTATTCA
*
2288740 ATTTTAATC
131 ATTTTAACC
* * * * * * *
2288749 AATTATTGGATCGAATAATCAAAATGAAACCTCGAGTAGAAGTGAAGACCAAATTAAAAATTCCT
1 AATTATTGAATCGAATAATTAAAATGGAACCTCGAGCATAAGCGAGGACCAAATTAAAAATTCCT
* *
2288814 CA-AAATTAAAGGACTAAGTATGAAACTAAGCCTAAAGTGGAGGCTCTAATTATTAACCTATTCA
66 CATAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTATTCA
* *
2288878 ATTTGAATC
131 ATTTTAACC
2288887 AATTATTG
1 AATTATTG
2288895 GATATTCATC
Statistics
Matches: 614, Mismatches: 80, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
138 211 0.34
139 111 0.18
140 134 0.22
141 35 0.06
142 2 0.00
143 1 0.00
147 1 0.00
148 8 0.01
149 63 0.10
150 38 0.06
151 10 0.02
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (139 bp):
AATTATTGAATCGAATAATTAAAATGGAACCTCGAGCATAAGCGAGGACCAAATTAAAAATTCCT
CATAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTATTCA
ATTTTAACC
Found at i:2288636 original size:289 final size:277
Alignment explanation
Indices: 2288034--2288894 Score: 1073
Period size: 289 Copynumber: 3.1 Consensus size: 277
2288024 TCCAAATCAT
* * *
2288034 TTTTAATAAATTATTGAGTT-GAATAATTAAAATAGAACCTCGAGCATAAA-AACGAGGACCAAA
1 TTTTAATCAATTATTGA-TTCGAATAATTAAAATGGAACCTCGAGCA-AAAGAA--AGGAACAAA
* * * * * * *
2288097 TAAAAAATTCTCATAAATTTAAGGACTAAATATGAAATTAAGCCTAAAATAGAGGCTCTAATTAT
62 TTAAAAATTCCCCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAGTGGAGGCTCTAATTAT
* * * * *
2288162 TGACTTATTCATTTTTAACCAATTTATTGAATCAAATAATTAGAATGGAACCTTGAGCATAAGCG
127 TAACCTATTCAATTTTAACCAATTTATTGAATCAAATAATTAAAATGGAACCTCGAGCATAAGCG
* * * * *
2288227 TGGACCAAATTAAAAATTCCCCCTAAATTAAAGGACTAAGTATAAAATTAGGCCTATAATGGAGG
192 AGGACCAAATTAAAAATT-CCTCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGG
*
2288292 TTCTAATTATTAACCTAGTTCAA
256 CTCTAATTATTAACCTAG-TCAA
* ** * * * * *
2288315 -TTTAACCAATTATCAATTTGAATAATTAAAATGGGACCTTGAGTAAAAGAAAGGACCAAATTAA
1 TTTTAATCAATTATTGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGAAAGGAACAAATTAA
2288379 AAATTAAGCCTACATTCCCTTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAGTGGAGGCTC
66 AAA-T-----T-C---CCC-TAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAGTGGAGGCTC
*
2288444 TAATTATTAACCTATTCAATTTTAACCAATTTATTGAATCAAATAATTAAAATGGAACCTCGACC
120 TAATTATTAACCTATTCAATTTTAACCAATTTATTGAATCAAATAATTAAAATGGAACCTCGAGC
*
2288509 ATAAGCGAGGGCCAAATTAAAAAATTCCTCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAA
185 ATAAGCGAGGACCAAATT-AAAAATTCCTCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAA
2288574 ATGGAGGCTCTAATTATTAACCTAGTCAA
249 ATGGAGGCTCTAATTATTAACCTAGTCAA
* *
2288603 TTTTAATCAATTATTGATTCGAATAATTAAAATGTAACCTCGAGCAAAAGCAAGGAACAAATTAA
1 TTTTAATCAATTATTGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGAAAGGAACAAATTAA
* * *
2288668 AAATTCCCCAAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAGTGGGGGTTCTAATTATTAAC
66 AAATTCCCCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAGTGGAGGCTCTAATTATTAAC
* * * * * * * * * *
2288733 CTAGTCAATTTTAATCAA-TTATTGGATCGAATAATCAAAATGAAACCTCGAGTAGAAGTGAAGA
131 CTATTCAATTTTAACCAATTTATTGAATCAAATAATTAAAATGGAACCTCGAGCATAAGCGAGGA
* * *
2288797 CCAAATTAAAAATTCCTCAAAATTAAAGGACTAAGTATGAAACTAAGCCTAAAGTGGAGGCTCTA
196 CCAAATTAAAAATTCCTCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGCTCTA
*
2288862 ATTATTAACCTATTCAA
261 ATTATTAACCTAGTCAA
*
2288879 TTTGAATCAATTATTG
1 TTTTAATCAATTATTG
2288895 GATATTCATC
Statistics
Matches: 507, Mismatches: 58, Indels: 35
0.85 0.10 0.06
Matches are distributed among these distances:
276 86 0.17
277 43 0.08
278 84 0.17
279 9 0.02
280 36 0.07
282 1 0.00
283 1 0.00
284 1 0.00
285 1 0.00
288 6 0.01
289 232 0.46
290 7 0.01
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (277 bp):
TTTTAATCAATTATTGATTCGAATAATTAAAATGGAACCTCGAGCAAAAGAAAGGAACAAATTAA
AAATTCCCCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAGTGGAGGCTCTAATTATTAAC
CTATTCAATTTTAACCAATTTATTGAATCAAATAATTAAAATGGAACCTCGAGCATAAGCGAGGA
CCAAATTAAAAATTCCTCTAAATTAAAGGACTAAGTATGAAATTAAGCCTAAAATGGAGGCTCTA
ATTATTAACCTAGTCAA
Found at i:2291751 original size:16 final size:16
Alignment explanation
Indices: 2291710--2291744 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2291700 ATAATTTAAA
2291710 ATTAATTTAAAATAAT
1 ATTAATTTAAAATAAT
*
2291726 ATTAATTTAAAATATT
1 ATTAATTTAAAATAAT
2291742 ATT
1 ATT
2291745 GTTTTAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAATTTAAAATAAT
Found at i:2293261 original size:21 final size:20
Alignment explanation
Indices: 2293199--2293261 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
2293189 TTATAATAAA
2293199 ATATTAATTATGATAATTA-
1 ATATTAATTATGATAATTAT
* *
2293218 A-ATTAATAAAT-ATACTTAAT
1 ATATTAAT-TATGATAATT-AT
2293238 ATATTAATTATGATAATTAGT
1 ATATTAATTATGATAATTA-T
2293259 ATA
1 ATA
2293262 CTTTTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 11 0.32
19 4 0.12
20 4 0.12
21 15 0.44
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
ATATTAATTATGATAATTAT
Found at i:2293311 original size:21 final size:21
Alignment explanation
Indices: 2293287--2293326 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2293277 TTATATCCAA
2293287 ACACTTTATA-TATATATATAC
1 ACAC-TTATACTATATATATAC
*
2293308 ACACTTATACTTTATATAT
1 ACACTTATACTATATATAT
2293327 GTATATAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (21 bp):
ACACTTATACTATATATATAC
Found at i:2293455 original size:25 final size:24
Alignment explanation
Indices: 2293407--2293453 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2293397 TTGATGAGGG
2293407 ATGAAATTGAATTAATTATAAAAT
1 ATGAAATTGAATTAATTATAAAAT
*
2293431 ATGAAGTTGATATTAA-TATAAAA
1 ATGAAATTGA-ATTAATTATAAAA
2293454 ATGGACTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (24 bp):
ATGAAATTGAATTAATTATAAAAT
Found at i:2293840 original size:6 final size:6
Alignment explanation
Indices: 2293826--2295025 Score: 2165
Period size: 6 Copynumber: 200.8 Consensus size: 6
2293816 CATTATACTT
* * * *
2293826 TATATA TATACA TATACA TATACA TACATA CATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2293874 TATAC- TATACA TACATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA T--ATACA TATACA TATACA TATACA TATACA TATACA
2293923 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2293971 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294019 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * *
2294067 TATACA TATACA TACATA CATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294115 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294163 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294211 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATAC-
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294258 -ATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294305 TATACA TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294351 TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294397 TATACA TATACA TATACA TATACA TATAC- -ATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294443 TATACA TATACA TATACA TATACA TATACA TATACATA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATAC--A TATACA TATACA
2294493 TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294539 TATACA TATACA TATACATA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATAC--A TATACA TATACA TATACA TATACA TATACA
2294589 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294637 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294685 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294733 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294781 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294829 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATAC-
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294876 -ATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2294923 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
2294971 TATACA TATACA TATACA TATACA TATACA TGTACA TATACA TTTATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA --TATACA
2295021 TATAC
1 TATAC
2295026 TTTATATATG
Statistics
Matches: 1158, Mismatches: 15, Indels: 42
0.95 0.01 0.03
Matches are distributed among these distances:
4 24 0.02
5 5 0.00
6 1105 0.95
8 24 0.02
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:2293856 original size:8 final size:8
Alignment explanation
Indices: 2293845--2293894 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
2293835 ACATATACAT
2293845 ATACATAC
1 ATACATAC
2293853 ATACATAC
1 ATACATAC
2293861 AT--ATAC
1 ATACATAC
* * *
2293867 ATATACAT
1 ATACATAC
2293875 ATACTATAC
1 ATAC-ATAC
2293884 ATACATAC
1 ATACATAC
2293892 ATA
1 ATA
2293895 TACATATACA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
6 6 0.18
8 22 0.65
9 6 0.18
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (8 bp):
ATACATAC
Found at i:2295144 original size:24 final size:24
Alignment explanation
Indices: 2295112--2295157 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2295102 GGATGAGGGA
2295112 TGAAATTGA-ATTAATTATAAAATG
1 TGAAATTGATATTAATT-TAAAATG
* *
2295136 TGAAGTTGATTTTAATTTAAAA
1 TGAAATTGATATTAATTTAAAA
2295158 ATGGACTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (24 bp):
TGAAATTGATATTAATTTAAAATG
Found at i:2297122 original size:20 final size:21
Alignment explanation
Indices: 2297080--2297126 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2297070 ATATATAATA
*
2297080 ATATAAAGTATATAAGTATAT
1 ATATAAACTATATAAGTATAT
2297101 ATATAAACTATA-AAGTTGATAT
1 ATATAAACTATATAAG-T-ATAT
2297123 ATAT
1 ATAT
2297127 TGTCGCAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 3 0.13
21 12 0.52
22 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (21 bp):
ATATAAACTATATAAGTATAT
Found at i:2297124 original size:2 final size:2
Alignment explanation
Indices: 2296230--2297105 Score: 236
Period size: 2 Copynumber: 436.0 Consensus size: 2
2296220 GTTTAAAGTG
* * *
2296230 TA TA TA TA TA TA AA CTA TA TA T- TA TA AA TA TA TA TA TA AA CTA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
2296273 TA -A TA TA TA TA TA TA T- TA T- TC TA -A AA T- TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2296310 T- TA TA TA CTT TA TA T- TT TA TA CT- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
2296351 TA AA GT- TT TA GTA TA TA GTA TA CA TA CA TA TA TA -A TA TA AA
1 TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2296392 GTA TA -A GTA TA T- TA TA TA TA TA AA AA TA -A T- TA TA AA GA CTA
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
2296433 -A TG TA TA TA -A GTA TA TA -A TA TA AA GTA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
2296474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * ** *
2296516 TT TA -A TA TA AA GTG TA TA TA GG TA TA TA TA -A TA TA AA GTA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
2296558 TA TA AA CTA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
2296600 AA GTA TA -A T- TA TA AA GA CTA -A GTA TA TA -A GTA TA TA -A TA
1 TA -TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA -TA TA TA TA TA
* * * * ** * *
2296639 TA AA GTA TA TA AA GTT TT TA TA CG TA TA AA GTA CA -A GTA TA TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* *
2296682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA GT- TT TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * *
2296725 AA GTA TA TA TA CA TA TA TA -A TA -A TA TA AA CTA TA -A GTA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * * *
2296765 -A GTA TA CTA TA TA TA AA AA GTA TA -A T- TA TA AA CA CTA AA GTA
1 TA -TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA -TA
* * * ** * *
2296807 TA TA AA TA TA AA GTA TA TC TA CG TA TA TA -A GCA T- TA AA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
2296849 TA TA -A GTA T- TA AA TA TA AA GTA TA TA -A GTA TA TA TA TA AA
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA
*
2296889 CTA TA AA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GT- TA
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
2296931 TA GT- TA TA TA AA GT- TT TA GTA TA AA GTA TA TA TA TA TA CTA TA
1 TA -TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA
* * *
2296974 TA TA TA GT- TA TA TA AA GT- TT TA GTA TA AA GTA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA
* * * *
2297016 TA TA TG TA TA TA -A TA -A TA TA AA GCA TA TA -A GTA T- TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* * *
2297056 TA AA GTA TA TA TA CA TA TA TA -A TA -A TA TA AA GTA TA TA -A GTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
2297098 TA TA TA TA
1 TA TA TA TA
2297106 AACTATAAAG
Statistics
Matches: 643, Mismatches: 123, Indels: 216
0.65 0.13 0.22
Matches are distributed among these distances:
1 52 0.08
2 535 0.83
3 56 0.09
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (2 bp):
TA
Found at i:2297125 original size:49 final size:49
Alignment explanation
Indices: 2296721--2297114 Score: 143
Period size: 49 Copynumber: 8.3 Consensus size: 49
2296711 AAAGTTTTAG
* * *
2296721 TATAAAGTATATATACATATATAATAATATAAA-C-TATAAGTA-TAAG
1 TATAAACTATAAATACATATATAATAATATAAAGCATATAAGTATTAAA
* * *
2296767 TAT--ACTATATATAAAAAGTATAAT--TATAAA-CACTA-AAGTATATAAA
1 TATAAACTATAAATACATA-TATAATAATATAAAGCA-TATAAGTAT-TAAA
* ** * ** **
2296813 TATAAAGTATATCTACGTATATAAGCAT-TAAATATATATAAGTATTAAA
1 TATAAACTATAAATACATATATAATAATATAAA-GCATATAAGTATTAAA
* * * * *
2296862 TATAAAGTATATAAGTATATATATAA-ACTATAAAGTATAT-A-TA-TATA
1 TATAAACTATA-AA-TACATATATAATAATATAAAGCATATAAGTATTAAA
* * * * * * *
2296909 TATATA-TATATATATATAGTTATAGTTATATAAAG--TTTTAGTA-TAAA
1 TATAAACTATAAATACATA--TATAATAATATAAAGCATATAAGTATTAAA
* * * * * * *
2296956 GTATATA-TATATACTATATATATAGTTATATAAAG--TTTTAGTA-TAAA
1 -TATAAACTATA-AATACATATATAATAATATAAAGCATATAAGTATTAAA
* **
2297003 GTATATATA-TATATATATGTATATAATAATATAAAGCATATAAGTATTAAA
1 -TATA-A-ACTATAAATACATATATAATAATATAAAGCATATAAGTATTAAA
* * * *
2297054 TATAAAGTATATATACATATATAATAATATAAAGTATATAAGTA-TATA
1 TATAAACTATAAATACATATATAATAATATAAAGCATATAAGTATTAAA
2297102 TATAAACTATAAA
1 TATAAACTATAAA
2297115 GTTGATATAT
Statistics
Matches: 278, Mismatches: 42, Indels: 54
0.74 0.11 0.14
Matches are distributed among these distances:
43 7 0.03
44 22 0.08
45 11 0.04
46 18 0.06
47 57 0.21
48 58 0.21
49 65 0.23
50 23 0.08
51 17 0.06
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (49 bp):
TATAAACTATAAATACATATATAATAATATAAAGCATATAAGTATTAAA
Found at i:2297681 original size:33 final size:34
Alignment explanation
Indices: 2297646--2297732 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
2297636 AAAATAAAAG
*
2297646 GAAAATAAAAAAGAATAGAAACAAAAAAAGAAGGAA
1 GAAAAT-AATAAGAATA-AAACAAAAAAAGAAGGAA
* **
2297682 GAAAATAATAATAATAAAACAAAAACAA-AACAAA
1 GAAAATAATAAGAATAAAACAAAAA-AAGAAGGAA
* *
2297716 GAAAATAGTAATAATAA
1 GAAAATAATAAGAATAA
2297733 TAATAAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
34 29 0.64
35 10 0.22
36 6 0.13
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.11
Consensus pattern (34 bp):
GAAAATAATAAGAATAAAACAAAAAAAGAAGGAA
Found at i:2297711 original size:40 final size:40
Alignment explanation
Indices: 2297664--2297739 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
2297654 AAAAGAATAG
2297664 AAACAAAA-AAAGAAGGAAGA-AAATAATAATAATAAAACAA
1 AAACAAAACAAAGAA--AAGAGAAATAATAATAATAAAACAA
* *
2297704 AAACAAAACAAAGAAAATAGTAATAATAATAATAAA
1 AAACAAAACAAAGAAAAGAGAAATAATAATAATAAA
2297740 TATAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 3 0.09
40 23 0.72
41 6 0.19
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (40 bp):
AAACAAAACAAAGAAAAGAGAAATAATAATAATAAAACAA
Found at i:2297744 original size:6 final size:6
Alignment explanation
Indices: 2297735--2298941 Score: 1995
Period size: 6 Copynumber: 207.3 Consensus size: 6
2297725 AATAATAATA
2297735 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2297783 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2297831 ATAAAT ATAAAT ATAAAT ATAAAT AT-AAT ATAAATAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AA-AT ATAAAT ATAAAT
2297880 ATAAAT ATAAAAT ATAAAT ATAAAT AT-AA- ATAAAT ATAAAT ATAAAT
1 ATAAAT AT-AAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2297927 ATAAAT ATAAAT AAATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AA-
1 ATAAAT ATAAAT --ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2297975 ATAAA- ATAAAT ATAAAT ATAAAT ATAAAT AT-AA- ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298020 ATAAAT ATAATAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAA- ATAAATAT
1 ATAAAT ATAA-AT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AA-AT
2298070 ATAAAT ATAAAT AT-AAT ATAAAT ATAAAT AT-AAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298116 ATAAAT ATAAAT ATAAAT ATAAAT AT-AAT ATAAAT AT-AAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298162 ATAAAT ATAAAT ATAAAT ATAAAT AT-AAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298209 ATAAA- ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298256 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT A-AAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298303 ATAAAT AT-AA- ATAAAT ATAAAT ATAAAT ATAAAT AT-AA- ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298347 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298395 ATAAAT ATAAAT ATAAAT AT-AAT ATAAAT ATAAAT AT-AA- ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298440 ATAAAT ATAAAT A-AAAT ATAAAT ATAAAT ATAAAT ATAAAT A-AAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298486 AT-AA- ATAAAT ATAAAT ATAAAT AT-AA- AT-AAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298529 AT-AA- AT-AAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298574 ATAAAT A-AAAT ATAAAT AT-AAT AT-AA- ATAAA- ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298617 ATAAAT ATAAAT ATAAAT ATAAATAT ATAAAT ATAAAT ATAAAT AT-AA-
1 ATAAAT ATAAAT ATAAAT AT-AA-AT ATAAAT ATAAAT ATAAAT ATAAAT
2298665 ATAAAT AT-AAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298712 AT-AAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298758 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT-AAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298805 ATAAAT AT-AAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT--AT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298850 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
2298898 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
2298942 GTTAAGTAAA
Statistics
Matches: 1149, Mismatches: 0, Indels: 104
0.92 0.00 0.08
Matches are distributed among these distances:
4 30 0.03
5 146 0.13
6 935 0.81
7 22 0.02
8 16 0.01
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:2301490 original size:6 final size:6
Alignment explanation
Indices: 2301474--2301505 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2301464 ACCCACCTTA
2301474 TTTTC- TTTTCT TTTTCT TTTTC- TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
2301506 TCGATTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:2301490 original size:11 final size:12
Alignment explanation
Indices: 2301474--2301505 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2301464 ACCCACCTTA
2301474 TTTTC-TTTTCT
1 TTTTCTTTTTCT
2301485 TTTTCTTTTTC-
1 TTTTCTTTTTCT
2301496 TTTTCTTTTT
1 TTTTCTTTTT
2301506 TCGATTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:2301570 original size:9 final size:10
Alignment explanation
Indices: 2301544--2301569 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2301534 ACCCTAAACA
2301544 TTTTTTTCTT
1 TTTTTTTCTT
2301554 TTTTTTTCTT
1 TTTTTTTCTT
2301564 TTTTTT
1 TTTTTT
2301570 CCGACTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:2312035 original size:12 final size:12
Alignment explanation
Indices: 2312026--2312050 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2312016 TTATAAAAAT
2312026 AAATAAAAAAGA
1 AAATAAAAAAGA
2312038 AAATAAAAAAGA
1 AAATAAAAAAGA
2312050 A
1 A
2312051 TGAAGAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAATAAAAAAGA
Found at i:2312079 original size:40 final size:37
Alignment explanation
Indices: 2312018--2312112 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 37
2312008 AAACTAAATT
* * *
2312018 ATAAAAATAAATAAAAAAGAAAATAAAAAAGAATGAAGAAA
1 ATAATAAT-AATAAAAAAG-AAACAAAAAA-AAGGAA-AAA
* *
2312059 ATAATAATAATAAAACAGAAACAAAACAAAGGAAAAA
1 ATAATAATAATAAAAAAGAAACAAAAAAAAGGAAAAA
*
2312096 TTAATAATAATAAAAAA
1 ATAATAATAATAAAAAA
2312113 TATAAATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 18 0.38
38 5 0.11
39 8 0.17
40 9 0.19
41 7 0.15
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (37 bp):
ATAATAATAATAAAAAAGAAACAAAAAAAAGGAAAAA
Found at i:2313797 original size:19 final size:19
Alignment explanation
Indices: 2313773--2313825 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
2313763 ATAGTTTATA
2313773 TATATATATACTTACAGTT
1 TATATATATACTTACAGTT
*
2313792 TATATATATACTTTATAGTT
1 TATATATATAC-TTACAGTT
*
2313812 TATGTATATACTTA
1 TATATATATACTTA
2313826 TATACTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.51
Consensus pattern (19 bp):
TATATATATACTTACAGTT
Found at i:2313828 original size:28 final size:22
Alignment explanation
Indices: 2313790--2313873 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
2313780 ATACTTACAG
* *
2313790 TTTATATAT-ATACTT-TATAG
1 TTTATATTTAATACTTATATAC
* *
2313810 TTTATGTAT-ATACTTATATAC
1 TTTATATTTAATACTTATATAC
2313831 TTTATATTTAATACTTATATAC
1 TTTATATTTAATACTTATATAC
2313853 TTTATA-TTATATACTTTATAT
1 TTTATATTTA-ATAC-TTATAT
2313874 TATTATTTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
20 14 0.25
21 14 0.25
22 22 0.39
23 6 0.11
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTATATTTAATACTTATATAC
Found at i:2313835 original size:41 final size:41
Alignment explanation
Indices: 2313749--2314249 Score: 218
Period size: 43 Copynumber: 12.1 Consensus size: 41
2313739 AAAGTATATA
* * *
2313749 TATATTTACACTTTATAGTTTATATATATA--TATACTTACAGTT
1 TATATATATACTTTATACTTTATATATATACTTATA--TAC--TT
* *
2313792 TATATATATACTTTATAGTTTATGTATATACTTATATACTT
1 TATATATATACTTTATACTTTATATATATACTTATATACTT
* *
2313833 TATATTTAATACTTATATACTTTATATTATATACTT-TATATTAT
1 TATATAT-ATACTT-TATACTTTATA-TATATACTTATATACT-T
* * *
2313877 TATTTACATA-TATATA-TTATACTATATATACTT-TATA-TT
1 TATATATATACTTTATACTT-TA-TATATATACTTATATACTT
*
2313916 TA-ATACTTATATTTTATA--TTATATTATATACTTATAT--TT
1 TATATA--TATACTTTATACTTTATA-TATATACTTATATACTT
* * *
2313955 TATAT-TATGCTTATATACTTTAGTCT-TATAATTATAT--TT
1 TATATATATACTT-TATACTTTA-TATATATACTTATATACTT
*
2313994 ATATATCTAATAAC-TTATACTTTATATTATATAC-TATATACTTTT
1 -TATATAT-AT-ACTTTATACTTTATA-TATATACTTATATAC--TT
* * *
2314039 CTTTATAATTATACATTATATACTTTATATTTAATACTTATATATTT
1 -TATAT-A-TATAC-TT-TATACTTTATATAT-ATACTTATATACTT
*
2314086 TATAT-TATAATTTATATACTTTATATTATATACTTATATACTT
1 TATATATAT-ACTT-TATACTTTATA-TATATACTTATATACTT
* *
2314129 TAGTCTTATTATACTTTATA---AATATATATAC-T-TATACTT
1 TA-T-ATA-TATACTTTATACTTTATATATATACTTATATACTT
* * * *
2314168 TATATATATA-TATATA-TATATATATAATA-ATATTTA-TT
1 TATATATATACTTTATACTTTATATAT-ATACTTATATACTT
* *
2314206 GTTTATATATACTTATATACTTTATAT-TAAAC-TATATA-TT
1 -TATATATATACTT-TATACTTTATATATATACTTATATACTT
2314246 TATA
1 TATA
2314250 CATAATATAT
Statistics
Matches: 364, Mismatches: 43, Indels: 106
0.71 0.08 0.21
Matches are distributed among these distances:
35 5 0.01
36 4 0.01
37 13 0.04
38 15 0.04
39 54 0.15
40 33 0.09
41 61 0.17
42 25 0.07
43 80 0.22
44 18 0.05
45 17 0.05
46 9 0.02
47 9 0.02
48 15 0.04
49 6 0.02
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (41 bp):
TATATATATACTTTATACTTTATATATATACTTATATACTT
Found at i:2313857 original size:43 final size:42
Alignment explanation
Indices: 2313790--2314249 Score: 225
Period size: 41 Copynumber: 11.1 Consensus size: 42
2313780 ATACTTACAG
* * *
2313790 TTTATATAT-ATACTT-TATAGTTTATGTATATACTTATATAC
1 TTTATATTTAATACTTATATACTTTATAT-TATACTTATATAC
2313831 TTTATATTTAATACTTATATAC----T-TTATA-TTATATAC
1 TTTATATTTAATACTTATATACTTTATATTATACTTATATAC
* * * *
2313867 TTTATA-TTATTATTTACATA-TATATATTATACTATATATAC
1 TTTATATTTAATACTTATATACTTTATATTATACT-TATATAC
2313908 TTTATATTTAATACTTATAT--TTTATATTATA-TTATATAC
1 TTTATATTTAATACTTATATACTTTATATTATACTTATATAC
* *
2313947 -TTATATTTTATATTATGCTTATATACTTTAGTCTTATAATTATAT--
1 TTTATA-TTTA-A-TA--CTTATATACTTTA-TATTATACTTATATAC
* *
2313992 TTATATATCTAATAAC-T-TATACTTTATATTATATACTATATACTTTTC
1 TT-TATATTTAAT-ACTTATATACTTTATA-T-TATACT-TATA---TAC
* *
2314040 TTTATAATT-ATACATTATATACTTTATATTTAATACTTATATAT
1 TTTATATTTAATAC-TTATATACTTTATA-TT-ATACTTATATAC
2314084 TTTATATTATAAT--TTATATACTTTATATTATATACTTATATAC
1 TTTATATT-TAATACTTATATACTTTATA-T-TATACTTATATAC
* * **
2314127 TTTAGTCTTATTATACTT-TATA-AATATA-TATAC-T-TATAC
1 TTTA-TATT-TAATACTTATATACTTTATATTATACTTATATAC
* * * **
2314166 TTTATATATATATA-TATATATA-TATATAATAATA-TT-TATTG
1 TTTATATTTA-ATACT-TATATACTTTAT-ATTATACTTATATAC
*
2314207 TTTATA--T-ATACTTATATACTTTATATTAAAC-TATATA-
1 TTTATATTTAATACTTATATACTTTATATTATACTTATATAC
2314244 TTTATA
1 TTTATA
2314250 CATAATATAT
Statistics
Matches: 335, Mismatches: 34, Indels: 104
0.71 0.07 0.22
Matches are distributed among these distances:
35 11 0.03
36 14 0.04
37 26 0.08
38 21 0.06
39 35 0.10
40 6 0.02
41 61 0.18
42 22 0.07
43 47 0.14
44 21 0.06
45 13 0.04
46 17 0.05
47 21 0.06
48 20 0.06
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (42 bp):
TTTATATTTAATACTTATATACTTTATATTATACTTATATAC
Found at i:2313896 original size:25 final size:25
Alignment explanation
Indices: 2313853--2314183 Score: 118
Period size: 25 Copynumber: 12.6 Consensus size: 25
2313843 ACTTATATAC
2313853 TTTATAT-TATATACTTTATATTATTA
1 TTTATATATATATAC-TTATATT-TTA
*
2313879 TTTACATATATATA-TTATACTATATATA
1 TTTATATATATATACTTATA-T-T-T-TA
*
2313907 CTTTATATTTA-ATACTTATATTTTA
1 -TTTATATATATATACTTATATTTTA
2313932 TATTATAT-TATATACTTATATTTTA
1 T-TTATATATATATACTTATATTTTA
*
2313957 TATTATGCT-TATATACTT-TAGTCTTATA
1 T-TTAT-ATATATATACTTATA-T-TT-TA
* * * *
2313985 ATTATATTTATATATCTAATAACTTATA
1 TTTATATATATATA-CTTAT-A-TTTTA
*
2314013 CTTTATAT-TATATACTATATACTTTTC
1 -TTTATATATATATACT-TATA-TTTTA
2314040 TTTATA-AT-TATACATTATA---TA
1 TTTATATATATATAC-TTATATTTTA
*
2314061 CTTTATATTTA-ATACTTATATATTTTA
1 -TTTATATATATATAC-T-TATATTTTA
*
2314088 TATTATAATTTATATACTTTATATTATATA
1 T-TTAT-ATATATATAC-TTATATT-T-TA
* *
2314118 CTTATATACTTTAGT-CTTATTATACTTTA
1 TTTATATA-TATA-TACTTA-TAT--TTTA
* *
2314147 --TAAATATATATACTTATACTTTA
1 TTTATATATATATACTTATATTTTA
*
2314170 TATATATATATATA
1 TTTATATATATATA
2314184 TATATATATA
Statistics
Matches: 242, Mismatches: 23, Indels: 81
0.70 0.07 0.23
Matches are distributed among these distances:
21 1 0.00
22 6 0.02
23 10 0.04
24 7 0.03
25 58 0.24
26 36 0.15
27 40 0.17
28 36 0.15
29 41 0.17
30 6 0.02
31 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.55
Consensus pattern (25 bp):
TTTATATATATATACTTATATTTTA
Found at i:2313913 original size:7 final size:7
Alignment explanation
Indices: 2313893--2314171 Score: 84
Period size: 7 Copynumber: 39.7 Consensus size: 7
2313883 CATATATATA
2313893 TTATACT
1 TTATACT
2313900 ATATATACT
1 -T-TATACT
2313909 TTATA-T
1 TTATACT
2313915 TTAATAC-
1 TT-ATACT
*
2313922 TTATATT
1 TTATACT
2313929 TTATA--
1 TTATACT
2313934 TTATA-T
1 TTATACT
2313940 TATATAC-
1 T-TATACT
*
2313947 TTATATT
1 TTATACT
2313954 TTATA--
1 TTATACT
*
2313959 TTATGCT
1 TTATACT
2313966 TATATACT
1 T-TATACT
2313974 TTAGT-C-
1 TTA-TACT
*
2313980 TTATA-A
1 TTATACT
2313986 TTATA-T
1 TTATACT
2313992 TTATA-T
1 TTATACT
2313998 ATCTAATAAC-
1 -T-T-AT-ACT
2314008 TTATACT
1 TTATACT
2314015 TTATA-T
1 TTATACT
2314021 TATATACT
1 T-TATACT
*
2314029 ATATACT
1 TTATACT
2314036 TT-T-CT
1 TTATACT
*
2314041 TTATA-A
1 TTATACT
2314047 TTATACAT
1 TTATAC-T
2314055 TATATACT
1 T-TATACT
2314063 TTATA-T
1 TTATACT
2314069 TTAATACT
1 TT-ATACT
*
2314077 TATATATT
1 T-TATACT
2314085 TTATA--
1 TTATACT
*
2314090 TTATAATT
1 TTAT-ACT
2314098 TATATACT
1 T-TATACT
2314106 TTATA-T
1 TTATACT
2314112 TATATACT
1 T-TATACT
2314120 TATATACT
1 T-TATACT
2314128 TTAGT-CTT
1 TTA-TAC-T
2314136 ATTATACT
1 -TTATACT
*
2314144 TTATAAAT
1 TTAT-ACT
2314152 ATATATAC-
1 -T-TATACT
2314160 TTATACT
1 TTATACT
2314167 TTATA
1 TTATA
2314172 TATATATATA
Statistics
Matches: 214, Mismatches: 13, Indels: 89
0.68 0.04 0.28
Matches are distributed among these distances:
5 18 0.08
6 47 0.22
7 79 0.37
8 42 0.20
9 24 0.11
10 4 0.02
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.55
Consensus pattern (7 bp):
TTATACT
Found at i:2314064 original size:22 final size:22
Alignment explanation
Indices: 2314039--2314130 Score: 109
Period size: 22 Copynumber: 4.2 Consensus size: 22
2314029 ATATACTTTT
2314039 CTTTATAATTATACA-TTATATA
1 CTTTAT-ATTATACACTTATATA
*
2314061 CTTTATATT-TAATACTTATATA
1 CTTTATATTAT-ACACTTATATA
* *
2314083 TTTTATATTATA-ATTTATATA
1 CTTTATATTATACACTTATATA
*
2314104 CTTTATATTATATACTTATATA
1 CTTTATATTATACACTTATATA
2314126 CTTTA
1 CTTTA
2314131 GTCTTATTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.02
21 24 0.39
22 35 0.57
23 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (22 bp):
CTTTATATTATACACTTATATA
Found at i:2314163 original size:23 final size:23
Alignment explanation
Indices: 2314137--2314181 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2314127 TTTAGTCTTA
2314137 TTATACTTTATAAATATATATAC
1 TTATACTTTATAAATATATATAC
*
2314160 TTATACTTTATATATATATATA
1 TTATACTTTATAAATATATATA
2314182 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATACTTTATAAATATATATAC
Found at i:2314170 original size:70 final size:67
Alignment explanation
Indices: 2313796--2314187 Score: 210
Period size: 66 Copynumber: 6.0 Consensus size: 67
2313786 ACAGTTTATA
* * * *
2313796 TATATACTTTATAGTTTAT-GTATATACTTATATACTTTATA-TTTA-ATACTTATATACTT-TA
1 TATATACTTTATATTTTATACTTTATAATTATATAC-TTATACTTTATATACTT-TATA-TTATA
2313857 T--AT
63 TACAT
* * *
2313860 TATATACTTTATATTAT-TA-TTTA-CATATATATA-TTATACTATATATACTTTATATT-TAAT
1 TATATACTTTATATTTTATACTTTATAAT-TATATACTTATACTTTATATACTTTATATTAT-AT
2313920 AC-T
64 ACAT
* * * *
2313923 TATATTTTA-TATTATATTATATAC-TTAT-ATTTTATA-TTATGC-TTATATACTTTAGTCTTA
1 TATA---TACT-TTATATTTTATACTTTATAATTATATACTTATACTTTATATACTTTA-TATTA
*
2313983 TAATTATATT
61 T-A-TACA-T
* ** *
2313993 TATATA-TCTAATAACTTATACTTTAT-ATTATATACTATATAC-TT-T-T-CTTTATAAT-TAT
1 TATATACT-TTATATTTTATACTTTATAATTATATACT-TATACTTTATATACTTTATATTATAT
2314051 ACAT
64 ACAT
* * *
2314055 TATATACTTTATATTTAATAC-TTATATATTTTATA-TTATAATTTATATACTTTATATTATATA
1 TATATACTTTATATTTTATACTTTATA-ATTATATACTTATACTTTATATACTTTATATTATATA
2314118 C-T
65 CAT
* *
2314120 TATATACTTTAGTCTTATTATACTTTATAAATATATATACTTATACTTTATATA-TATATATATA
1 TATATACTTTA-TATT-TTATACTTTAT-AAT-TATATACTTATACTTTATATACTTTATAT-TA
2314184 TATA
61 TATA
2314188 TATATAATAA
Statistics
Matches: 258, Mismatches: 33, Indels: 68
0.72 0.09 0.19
Matches are distributed among these distances:
61 16 0.06
62 29 0.11
63 33 0.13
64 17 0.07
65 33 0.13
66 34 0.13
67 32 0.12
68 20 0.08
69 14 0.05
70 30 0.12
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.55
Consensus pattern (67 bp):
TATATACTTTATATTTTATACTTTATAATTATATACTTATACTTTATATACTTTATATTATATAC
AT
Found at i:2314212 original size:154 final size:155
Alignment explanation
Indices: 2313848--2314214 Score: 414
Period size: 154 Copynumber: 2.3 Consensus size: 155
2313838 TTAATACTTA
* * *
2313848 TATACTTTATATTATATACTTTATATTATTATTTACATATATATATTATACTATATATACTTTAT
1 TATACTTTATATTATATACTATATACTA-TA-TTA-ATA-ATAT-TTATACTTTATATACTTTAT
*
2313913 ATTTAATACTTATATTTTATATTATATTATATACTTATATTTTATATTATGCTTATATACTTTAG
61 ATTTAATACTTATATTTTATATTATATTATATACTTATATATTATATTA-GCTTATATACTTTAG
* *
2313978 TCTTATAATTATATTTATATATCTAATAACT
125 TCTTATAATTATATTTATAAATATAATAACT
** * * *
2314009 TATACTTTATATTATATACTATATACT-T-TTCTTTATAATTATACATTATATACTTTATATTTA
1 TATACTTTATATTATATACTATATACTATATTAATAATATTTATACTTTATATACTTTATATTTA
2314072 ATACTTATATATTTTATATTATAATTTATATACTT-TATATTATA-TA-CTTATATACTTTAGTC
66 ATAC-T-TATATTTTATATTAT-A-TTATATACTTATATATTATATTAGCTTATATACTTTAGTC
2314134 -T-T-ATTATACTTTATAAATAT-ATATACT
127 TTATAATTATA-TTTATAAATATAATA-ACT
**
2314161 TATACTTTATATATATATA-TATATA-TATATATAATAATATTTATTGTTTATATA
1 TATACTTTATAT-TATATACTATATACTATAT-TAATAATATTTATACTTTATATA
2314215 TACTTATATA
Statistics
Matches: 178, Mismatches: 18, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
151 10 0.06
152 32 0.18
153 8 0.04
154 59 0.33
155 4 0.02
156 18 0.10
157 11 0.06
158 10 0.06
159 1 0.01
161 25 0.14
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (155 bp):
TATACTTTATATTATATACTATATACTATATTAATAATATTTATACTTTATATACTTTATATTTA
ATACTTATATTTTATATTATATTATATACTTATATATTATATTAGCTTATATACTTTAGTCTTAT
AATTATATTTATAAATATAATAACT
Found at i:2314244 original size:154 final size:166
Alignment explanation
Indices: 2313848--2314260 Score: 363
Period size: 161 Copynumber: 2.6 Consensus size: 166
2313838 TTAATACTTA
*
2313848 TATACTTTATATTATATACT-T-TA-TAT-TAT-T-AT-TTACA-TATATA--TAT-TATACTAT
1 TATACTTTATATTATATACTATATACTATATATATAATAATACATTATATACTTATATATACT-T
* *
2313902 ATATACTTTATATTTAATACTTATATTTTATATTATATTATATACTTATATTTTATATTATGCTT
65 ATATACTTTATA-TTAA-AC-TATATATTATA-TATATTATATACTTATATATTATATTA-GCTT
* *
2313967 ATATACTTTAGTCTTATAATTATATTTATATATCTAATAACT
125 ATATACTTTAGTCTTATAATTATATTTATAAATATAATAACT
* * * *
2314009 TATACTTTATATTATATACTATATACTTTTCTTTATAATTATACATTATATACTT-TATAT--TT
1 TATACTTTATATTATATACTATATAC-TATATATATAATAATACATTATATACTTATATATACTT
2314071 A-ATACTTATATATT----T-TATATTATA-AT-TTATATACTT-TATATTATA-TA-CTTATAT
65 ATATACTT-TATATTAAACTATATATTATATATATTATATACTTATATATTATATTAGCTTATAT
2314125 ACTTTAGTC-T-T-ATTATACTTTATAAATAT-ATATACT
129 ACTTTAGTCTTATAATTATA-TTTATAAATATAATA-ACT
* **
2314161 TATACTTTATA-TATATA-TATATA-TATATATATAATAATA-TTTAT-TGTTTATATATACTTA
1 TATACTTTATATTATATACTATATACTATATATATAATAATACATTATATACTTATATATACTTA
* *
2314221 TATACTTTATATTAAACTATATATTTATACATAATATATA
66 TATACTTTATATTAAACTATATA-TTATATATATTATATA
2314261 AATAAGTTGT
Statistics
Matches: 210, Mismatches: 15, Indels: 58
0.74 0.05 0.20
Matches are distributed among these distances:
146 3 0.01
147 9 0.04
148 12 0.06
149 9 0.04
150 12 0.06
151 15 0.07
152 24 0.11
153 2 0.01
154 20 0.10
155 5 0.02
156 4 0.02
157 14 0.07
158 10 0.05
159 2 0.01
161 28 0.13
162 2 0.01
163 2 0.01
165 2 0.01
166 2 0.01
167 1 0.00
168 10 0.05
169 10 0.05
170 7 0.03
171 1 0.00
172 4 0.02
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (166 bp):
TATACTTTATATTATATACTATATACTATATATATAATAATACATTATATACTTATATATACTTA
TATACTTTATATTAAACTATATATTATATATATTATATACTTATATATTATATTAGCTTATATAC
TTTAGTCTTATAATTATATTTATAAATATAATAACT
Found at i:2314276 original size:2 final size:2
Alignment explanation
Indices: 2314145--2314260 Score: 57
Period size: 2 Copynumber: 59.0 Consensus size: 2
2314135 TATTATACTT
* *
2314145 TA TA AA TA TA TA TA CT- TA TA CTT TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * *
2314188 TA TA TA -A TA -A TA TT TA T- TG TT TA TA TA TA CT- TA TA TA CTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
* * *
2314228 TA TA T- TA AA CTA TA TA TT TA TA CA TA -A TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
2314261 AATAAGTTGT
Statistics
Matches: 86, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
1 7 0.08
2 74 0.86
3 5 0.06
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2314314 original size:16 final size:16
Alignment explanation
Indices: 2314290--2314337 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
2314280 AATATAATTC
2314290 ATATATAATTTATATA
1 ATATATAATTTATATA
2314306 A-ACTATAA-TTATATTA
1 ATA-TATAATTTATA-TA
*
2314322 ATATATAGTTTATATA
1 ATATATAATTTATATA
2314338 TACTTCAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATATAATTTATATA
Found at i:2314338 original size:11 final size:10
Alignment explanation
Indices: 2314076--2314339 Score: 62
Period size: 11 Copynumber: 24.9 Consensus size: 10
2314066 TATTTAATAC
2314076 TTATATAT-T
1 TTATATATAT
2314085 TTATATTATAAT
1 TTATA-TAT-AT
2314097 TTATATACT-T
1 TTATATA-TAT
2314107 TATATTATATACT
1 T-TA-TATATA-T
*
2314120 TATATACTTTAGT
1 T-TATA-TATA-T
2314133 CTTAT-TATACT
1 -TTATATATA-T
*
2314144 TTATAAATAT
1 TTATATATAT
*
2314154 ATATACTTATACT
1 TTATA--TATA-T
2314167 TTATATATAT
1 TTATATATAT
*
2314177 ATATATATAT
1 TTATATATAT
*
2314187 ATATATAATAAT
1 TTATAT-AT-AT
*
2314199 ATT-TAT-TGT
1 -TTATATATAT
*
2314208 TTATATATAC
1 TTATATATAT
*
2314218 TTATATA-CT
1 TTATATATAT
2314227 TTATAT-TA-
1 TTATATATAT
*
2314235 -AACTATATAT
1 TTA-TATATAT
*
2314245 TTATACATAAT
1 TTATATAT-AT
* * *
2314256 ATATAAATAAG
1 TTATATAT-AT
*
2314267 TTGTATATAT
1 TTATATATAT
*
2314277 TTAAATATAAT
1 TTATATAT-AT
*
2314288 TCATATATAAT
1 TTATATAT-AT
*
2314299 TTATATA-AA
1 TTATATATAT
*
2314308 CTATAATTATAT
1 TTAT-A-TATAT
*
2314320 TAATATATAGT
1 TTATATATA-T
2314331 TTATATATA
1 TTATATATA
2314340 CTTCAATAGT
Statistics
Matches: 188, Mismatches: 37, Indels: 58
0.66 0.13 0.20
Matches are distributed among these distances:
7 1 0.01
8 5 0.03
9 21 0.11
10 55 0.29
11 63 0.34
12 24 0.13
13 18 0.10
14 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (10 bp):
TTATATATAT
Found at i:2314387 original size:2 final size:2
Alignment explanation
Indices: 2314380--2314596 Score: 52
Period size: 2 Copynumber: 111.0 Consensus size: 2
2314370 TTATACTTGG
* * *
2314380 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA GTT TA TA TA TA -A TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
2314422 TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA T- TA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * *
2314462 T- TA TA T- TT TA TA TA -A T- TA TA TA GTT TA TA T- TA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
2314499 TA -A TA TA TA CTT TA CA CA TA -A TA TA TA TA GTT TA TA TA TA GTA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* * * * *
2314542 TA TA -A T- TA TA TA AA TA TA AA CTA TA TA GTT TA TA TA CA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA
2314585 TA TA TA TA TA TA
1 TA TA TA TA TA TA
2314597 GTTTATATTA
Statistics
Matches: 153, Mismatches: 35, Indels: 54
0.63 0.14 0.22
Matches are distributed among these distances:
1 16 0.10
2 125 0.82
3 12 0.08
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2314387 original size:20 final size:20
Alignment explanation
Indices: 2314322--2314575 Score: 136
Period size: 20 Copynumber: 12.7 Consensus size: 20
2314312 AATTATATTA
* *
2314322 ATATATAGTTTATATATACT
1 ATATATAGTTTATACATAAT
*
2314342 -TCA-ATAGTTCATACATAA-
1 AT-ATATAGTTTATACATAAT
* * **
2314360 ACTCTATAGTTTATACTTGGT
1 A-TATATAGTTTATACATAAT
2314381 ATATATAGTTTATACATAAT
1 ATATATAGTTTATACATAAT
*
2314401 ATATATAGTTTATATATAAT
1 ATATATAGTTTATACATAAT
* * * *
2314421 ATATAATAATATAAATATAA-
1 ATAT-ATAGTTTATACATAAT
2314441 ACTATATAGTTTATTA-ATAA-
1 A-TATATAGTTTA-TACATAAT
*
2314461 AT-TATA-TTT-TATATAAT
1 ATATATAGTTTATACATAAT
*
2314478 -TATATAGTTTATATTAATAAAT
1 ATATATAGTTTATA--CAT-AAT
* *
2314500 AATATATACTTTACACATAAT
1 -ATATATAGTTTATACATAAT
* *
2314521 ATATATAGTTTATATATAGT
1 ATATATAGTTTATACATAAT
* *
2314541 ATATA-A-TTATATAAATATAA
1 ATATATAGTT-TATACATA-AT
2314561 ACTATATAGTTTATA
1 A-TATATAGTTTATA
2314576 TACATAGTTT
Statistics
Matches: 181, Mismatches: 30, Indels: 44
0.71 0.12 0.17
Matches are distributed among these distances:
15 2 0.01
16 5 0.03
17 7 0.04
18 9 0.05
19 24 0.13
20 85 0.47
21 26 0.14
22 10 0.06
23 2 0.01
24 11 0.06
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ATATATAGTTTATACATAAT
Found at i:2314423 original size:9 final size:9
Alignment explanation
Indices: 2314391--2314568 Score: 61
Period size: 9 Copynumber: 19.7 Consensus size: 9
2314381 ATATATAGTT
*
2314391 TATACATAA
1 TATATATAA
*
2314400 TATATATAGTT
1 TATATATA--A
2314411 TATATATAA
1 TATATATAA
2314420 TATATAATAA
1 TATAT-ATAA
2314430 TATAAATATAA
1 TAT--ATATAA
*
2314441 -ACTATATAG
1 TA-TATATAA
*
2314450 TTTAT-TAA
1 TATATATAA
* *
2314458 TAAATTATAT
1 TATA-TATAA
*
2314468 TTTATATAA
1 TATATATAA
*
2314477 T-TATATAG
1 TATATATAA
*
2314485 TTTATATTAA
1 TATATA-TAA
2314495 TA-A-ATAA
1 TATATATAA
*
2314502 TATATACT-T
1 TATATA-TAA
* *
2314511 TACACATAA
1 TATATATAA
*
2314520 TATATATAG
1 TATATATAA
*
2314529 TTTATAT-A
1 TATATATAA
2314537 TAGTATATAA
1 TA-TATATAA
2314547 T-TATATAA
1 TATATATAA
2314555 -ATATA-AA
1 TATATATAA
2314562 CTATATA
1 -TATATA
2314569 GTTTATATAC
Statistics
Matches: 124, Mismatches: 25, Indels: 40
0.66 0.13 0.21
Matches are distributed among these distances:
7 7 0.06
8 26 0.21
9 58 0.47
10 18 0.15
11 13 0.10
12 2 0.02
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (9 bp):
TATATATAA
Found at i:2314425 original size:11 final size:11
Alignment explanation
Indices: 2314399--2314440 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2314389 TTTATACATA
*
2314399 ATATATATAGT
1 ATATATATAAT
*
2314410 TTATATATAAT
1 ATATATATAAT
2314421 ATATA-ATAAT
1 ATATATATAAT
*
2314431 ATAAATATAA
1 ATATATATAA
2314441 ACTATATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
ATATATATAAT
Found at i:2314453 original size:61 final size:61
Alignment explanation
Indices: 2314382--2314575 Score: 247
Period size: 61 Copynumber: 3.2 Consensus size: 61
2314372 ATACTTGGTA
*
2314382 TATATAGTTTATACATAATATATATAGTTTATATATAATATATAATAATATAAATATAAAC
1 TATATAGTTTATACATAATATATATAGTTTATATATAATATATAATTATATAAATATAAAC
* * *
2314443 TATATAGTTTATTA-ATAA-AT-TATA-TTT-TATATAATTATATAGTTTATATTAATA-AATAA
1 TATATAGTTTA-TACATAATATATATAGTTTATATATAA-TATATA-ATTATATAAATATAA-AC
* * *
2314502 TATATACTTTACACATAATATATATAGTTTATATATAGTATATAATTATATAAATATAAAC
1 TATATAGTTTATACATAATATATATAGTTTATATATAATATATAATTATATAAATATAAAC
2314563 TATATAGTTTATA
1 TATATAGTTTATA
2314576 TACATAGTTT
Statistics
Matches: 111, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
57 7 0.06
58 12 0.11
59 28 0.25
60 4 0.04
61 41 0.37
62 13 0.12
63 6 0.05
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (61 bp):
TATATAGTTTATACATAATATATATAGTTTATATATAATATATAATTATATAAATATAAAC
Found at i:2314453 original size:120 final size:119
Alignment explanation
Indices: 2314323--2314577 Score: 304
Period size: 120 Copynumber: 2.1 Consensus size: 119
2314313 ATTATATTAA
* * **
2314323 TATATAGTTTATATAT-ACTTCAATAGTTCATACATAAACTCTATAGTTTATACT-T-GGT-ATA
1 TATATAGTTTATATATAAATT--ATA-TT-ATACAT-AACTATATAGTTTATACTATAAATAATA
* *
2314384 TATAGTTTATACATAATATATATAGTTTATATATAATATATAATAATATAAATATAAAC
61 TATACTTTACACATAATATATATAGTTTATATATAATATATAATAATATAAATATAAAC
* * * *
2314443 TATATAGTTTAT-TAATAAATTATATTTTATATAATTATATAGTTTATATTAATAAATAATATAT
1 TATATAGTTTATAT-ATAAATTATATTATACATAACTATATAGTTTATACT-ATAAATAATATAT
* *
2314507 ACTTTACACATAATATATATAGTTTATATATAGTATATAATTATATAAATATAAAC
64 ACTTTACACATAATATATATAGTTTATATATAATATATAATAATATAAATATAAAC
2314563 TATATAGTTTATATA
1 TATATAGTTTATATA
2314578 CATAGTTTAT
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
116 15 0.13
117 4 0.03
118 3 0.03
119 5 0.04
120 85 0.73
121 4 0.03
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (119 bp):
TATATAGTTTATATATAAATTATATTATACATAACTATATAGTTTATACTATAAATAATATATAC
TTTACACATAATATATATAGTTTATATATAATATATAATAATATAAATATAAAC
Found at i:2314454 original size:41 final size:41
Alignment explanation
Indices: 2314402--2314577 Score: 163
Period size: 41 Copynumber: 4.4 Consensus size: 41
2314392 ATACATAATA
2314402 TATATAGTTTATATATAATATATAATAATATAAATATAAAC
1 TATATAGTTTATATATAATATATAATAATATAAATATAAAC
** *
2314443 TATATAGTTTAT-TAATAA-AT-T-AT-AT-TTTATAT-AAT
1 TATATAGTTTATAT-ATAATATATAATAATATAAATATAAAC
* * *
2314478 TATATAGTTTATAT-TAATAAATAATATATACTTTACACATAATA-
1 TATATAGTTTATATATAATATATAATA-ATA---TAAATATAA-AC
* *
2314522 TATATAGTTTATATATAGTATATAATTATATAAATATAAAC
1 TATATAGTTTATATATAATATATAATAATATAAATATAAAC
2314563 TATATAGTTTATATA
1 TATATAGTTTATATA
2314578 CATAGTTTAT
Statistics
Matches: 108, Mismatches: 12, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
34 3 0.03
35 15 0.14
36 7 0.06
37 4 0.04
38 2 0.02
39 3 0.03
40 4 0.04
41 38 0.35
43 4 0.04
44 18 0.17
45 10 0.09
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (41 bp):
TATATAGTTTATATATAATATATAATAATATAAATATAAAC
Found at i:2314537 original size:13 final size:13
Alignment explanation
Indices: 2314519--2314604 Score: 59
Period size: 15 Copynumber: 6.3 Consensus size: 13
2314509 TTTACACATA
2314519 ATATATATAG-TT
1 ATATATATAGTTT
*
2314531 -TATATATAGTAT
1 ATATATATAGTTT
* *
2314543 ATAATTATATAAATAT
1 AT-A-TATAT-AGTTT
*
2314559 AAACTATATAGTTT
1 ATA-TATATAGTTT
*
2314573 ATATACATAGTTTAT
1 ATATATATAG-TT-T
2314588 ATATATATAGTTT
1 ATATATATAGTTT
2314601 ATAT
1 ATAT
2314605 TAAATAAACT
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
11 9 0.16
12 1 0.02
13 12 0.21
14 10 0.17
15 21 0.36
16 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (13 bp):
ATATATATAGTTT
Found at i:2314640 original size:51 final size:51
Alignment explanation
Indices: 2314531--2314653 Score: 135
Period size: 51 Copynumber: 2.4 Consensus size: 51
2314521 ATATATAGTT
*
2314531 TATATATAGTATATAATTATATAAATATAAACTATATAGTTTATATACATAG
1 TATATATA-TATATAATTATATAAATATAAACTATATAGTTTAAATACATAG
* * * *
2314583 TTTATATATATATAGTTTATATTAA-ATAAACTATATATTTTAAACGTA-ATA-
1 TATATATATATATA-ATTATATAAATATAAACTATATAGTTTAAA--TACATAG
2314634 TATATATATATTATAATTAT
1 TATATATATA-TATAATTAT
2314654 TTCAATTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
51 36 0.60
52 22 0.37
53 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (51 bp):
TATATATATATATAATTATATAAATATAAACTATATAGTTTAAATACATAG
Found at i:2314644 original size:120 final size:119
Alignment explanation
Indices: 2314394--2314612 Score: 315
Period size: 120 Copynumber: 1.9 Consensus size: 119
2314384 TATAGTTTAT
2314394 ACATAATATATATAGTTTATATATAATATATAATAATATAAATATAAACTATATAGTTTATTAAT
1 ACATAATATATATAGTTTATATATAATATATAATAATATAAATATAAACTATATAGTTTATTAAT
* * * * *
2314459 AAATTATATTTTATATAATTATATAGTTTATATTAATAAATAATATATACTTTAC
66 -AATCATAGTTTATATAATTATATAGTTTATATTAATAAATAATATAAACGTAAC
* *
2314514 ACATAATATATATAGTTTATATATAGTATATAATTATATAAATATAAACTATATAGTTTA-T-AT
1 ACATAATATATATAGTTTATATATAATATATAATAATATAAATATAAACTATATAGTTTATTAAT
2314577 -A-CATAGTTTATAT-A-TATATAGTTTATATTAAATAAA
66 AATCATAGTTTATATAATTATATAGTTTATATT-AATAAA
2314613 CTATATATTT
Statistics
Matches: 94, Mismatches: 4, Indels: 8
0.89 0.04 0.08
Matches are distributed among these distances:
113 15 0.16
114 7 0.07
115 10 0.11
116 1 0.01
118 2 0.02
119 1 0.01
120 58 0.62
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (119 bp):
ACATAATATATATAGTTTATATATAATATATAATAATATAAATATAAACTATATAGTTTATTAAT
AATCATAGTTTATATAATTATATAGTTTATATTAATAAATAATATAAACGTAAC
Found at i:2316012 original size:17 final size:17
Alignment explanation
Indices: 2315990--2316022 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2315980 CCAATCCTCT
2315990 CAAACCATCTTAAAGCC
1 CAAACCATCTTAAAGCC
*
2316007 CAAACCCTCTTAAAGC
1 CAAACCATCTTAAAGC
2316023 TCAACCCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.36, G:0.06, T:0.18
Consensus pattern (17 bp):
CAAACCATCTTAAAGCC
Found at i:2317832 original size:21 final size:21
Alignment explanation
Indices: 2317808--2317848 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2317798 CTGCTGTACA
* *
2317808 CTCCGTAGCTATTTCAGATGG
1 CTCCGTAGCCATATCAGATGG
2317829 CTCCGTAGCCATATCAGATG
1 CTCCGTAGCCATATCAGATG
2317849 CTACCACCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
CTCCGTAGCCATATCAGATGG
Found at i:2318173 original size:3 final size:3
Alignment explanation
Indices: 2318165--2318189 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2318155 GTATCTGCTC
2318165 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
2318190 GAGTGAGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:2319956 original size:64 final size:63
Alignment explanation
Indices: 2319874--2320030 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 63
2319864 TTCAGTGTGT
* * *
2319874 ATCGATGCA-CAGGAAGTGCATCGATGCACCCCTTAAAAATGGAAACATT-GAATGCAATTAGTG
1 ATCGATGCATAAGG-AGTGCATCGATGCACCCCTT-AAAATGAAAAC-TTCGAAGGCAATTAGTG
2319937 C
63 C
* ** * *
2319938 ATCGATGCATAAGGAGTGCATCGATACACCCCCTTAAAATGAAAACTTCGAAGGTGATTTGTGT
1 ATCGATGCATAAGGAGTGCATCGATGCA-CCCCTTAAAATGAAAACTTCGAAGGCAATTAGTGC
* *
2320002 ATCGATGCATGAGTAGTGCATCGATGCAC
1 ATCGATGCATAAGGAGTGCATCGATGCAC
2320031 ATGTTAAAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
63 3 0.04
64 67 0.85
65 9 0.11
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAAGGAGTGCATCGATGCACCCCTTAAAATGAAAACTTCGAAGGCAATTAGTGC
Found at i:2320600 original size:2 final size:2
Alignment explanation
Indices: 2320595--2320646 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
2320585 TATATATATA
*
2320595 TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2320637 TG TG TG TG TG
1 TG TG TG TG TG
2320647 AACATAAGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2321617 original size:23 final size:23
Alignment explanation
Indices: 2321553--2321609 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
2321543 TTTATATGGT
*
2321553 ACTTTGGTGCAATTCTACGCGGC
1 ACTTCGGTGCAATTCTACGCGGC
* *
2321576 ACTACGGTGCAATTCTACGTGGC
1 ACTTCGGTGCAATTCTACGCGGC
2321599 ACTTCGGTGCA
1 ACTTCGGTGCA
2321610 TTTATACGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACGCGGC
Found at i:2326260 original size:20 final size:20
Alignment explanation
Indices: 2326232--2326273 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2326222 ACCCTTTTTA
*
2326232 TTTTGATTATTA-TAAATATT
1 TTTTAATTATTACT-AATATT
2326252 TTTTAATTATTACTAATATT
1 TTTTAATTATTACTAATATT
2326272 TT
1 TT
2326274 ATGAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTAATTATTACTAATATT
Found at i:2329600 original size:24 final size:24
Alignment explanation
Indices: 2329571--2329620 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2329561 TGGTGGTTGA
*
2329571 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
2329595 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
2329619 TT
1 TT
2329621 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:2339867 original size:24 final size:24
Alignment explanation
Indices: 2339838--2339887 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2339828 TGGTGGTTGA
*
2339838 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
2339862 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
2339886 TT
1 TT
2339888 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:2342286 original size:15 final size:15
Alignment explanation
Indices: 2342266--2342300 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2342256 AATTACATGC
2342266 CAACATCATTTAGTA
1 CAACATCATTTAGTA
2342281 CAACATCATTTAGTA
1 CAACATCATTTAGTA
2342296 CAACA
1 CAACA
2342301 AAATAGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (15 bp):
CAACATCATTTAGTA
Found at i:2342699 original size:24 final size:23
Alignment explanation
Indices: 2342667--2342717 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
2342657 ACTGCCACAA
* *
2342667 AGAATTGCACCGAAGTGTCGCGT
1 AGAATTGCACCGAAGTGCCACGT
2342690 AGAATATGCACCGAAGTGCCACGT
1 AGAAT-TGCACCGAAGTGCCACGT
2342714 AGAA
1 AGAA
2342718 ACGTCTCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAATTGCACCGAAGTGCCACGT
Found at i:2342762 original size:23 final size:23
Alignment explanation
Indices: 2342687--2342809 Score: 124
Period size: 23 Copynumber: 5.3 Consensus size: 23
2342677 CGAAGTGTCG
2342687 CGTAGAATATG-CACCGAAGTG-CCA
1 CGTAGAA-ATGTC-CCGAAG-GACCA
* * *
2342711 CGTAGAAACGTCTCGAAGGACAA
1 CGTAGAAATGTCCCGAAGGACCA
* * * *
2342734 CATAGATATGTCTCGAAGGACCG
1 CGTAGAAATGTCCCGAAGGACCA
*
2342757 CGTAGAAATATCCCGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
*
2342780 CGTAGAATTGTCCCGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
2342803 CGTAGAA
1 CGTAGAA
2342810 CCCTCGACTC
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
22 1 0.01
23 73 0.89
24 8 0.10
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGTCCCGAAGGACCA
Found at i:2345192 original size:23 final size:23
Alignment explanation
Indices: 2345138--2345222 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
2345128 ACATTTGTCA
* **
2345138 CGAAGGACCACATAGGTTTGTCC
1 CGAAGGACCACATAGATTTGTTT
* *
2345161 CAAATGACCACATAGATTTGTTT
1 CGAAGGACCACATAGATTTGTTT
*
2345184 TGAAGGACCACATAGATTT-TTCT
1 CGAAGGACCACATAGATTTGTT-T
*
2345207 CGAAGGACTACATAGA
1 CGAAGGACCACATAGA
2345223 ACCCTCGACT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 2 0.04
23 49 0.96
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (23 bp):
CGAAGGACCACATAGATTTGTTT
Found at i:2348706 original size:19 final size:18
Alignment explanation
Indices: 2348663--2348707 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2348653 TAAGCACATG
*
2348663 TTATTTTTATCTTTTAAA
1 TTATTTTTATCTTTAAAA
*
2348681 TTGATTTTTTTCTCTTAAAA
1 TT-ATTTTTATCT-TTAAAA
2348701 TTATTTT
1 TTATTTT
2348708 AAAATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
20 7 0.30
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (18 bp):
TTATTTTTATCTTTAAAA
Found at i:2352160 original size:19 final size:19
Alignment explanation
Indices: 2352120--2352162 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2352110 TAGTTATGCC
*
2352120 AAATTGGTTTTAAAATTCA
1 AAATTGGTTTTAAAATTAA
*
2352139 AAATT-GTTTTAAACTGTAA
1 AAATTGGTTTTAAAAT-TAA
2352158 AAATT
1 AAATT
2352163 AATTTGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (19 bp):
AAATTGGTTTTAAAATTAA
Found at i:2359456 original size:22 final size:22
Alignment explanation
Indices: 2359431--2359474 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2359421 GAAAGATTAA
* *
2359431 TTTTATTCATGATTGTTGTTTT
1 TTTTAATCATGATTATTGTTTT
2359453 TTTTAATCATGATTATTGTTTT
1 TTTTAATCATGATTATTGTTTT
2359475 CTCGTTGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (22 bp):
TTTTAATCATGATTATTGTTTT
Found at i:2359657 original size:13 final size:13
Alignment explanation
Indices: 2359629--2359660 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2359619 AGTGTTGTAG
2359629 AAAAA-TATTTTT
1 AAAAAGTATTTTT
2359641 -AAAAGTATTTTT
1 AAAAAGTATTTTT
2359653 AAAAAGTA
1 AAAAAGTA
2359661 AAATTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 7 0.39
13 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (13 bp):
AAAAAGTATTTTT
Found at i:2359944 original size:2 final size:2
Alignment explanation
Indices: 2359937--2360014 Score: 135
Period size: 2 Copynumber: 40.5 Consensus size: 2
2359927 ACTGATTAGT
2359937 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2359977 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2360015 TCTCCTGCTT
Statistics
Matches: 73, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 70 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2362923 original size:20 final size:16
Alignment explanation
Indices: 2362874--2362913 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
2362864 ATAACGACGA
2362874 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
2362890 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
2362906 AACCAGAG
1 AACCAGAG
2362914 TCTAAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.30, G:0.15, T:0.05
Consensus pattern (16 bp):
AACCAGAGAAATCCAC
Done.