Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007805.1 Hibiscus syriacus cultivar Beakdansim tig00110123_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: 2708727
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2562374 original size:80 final size:80
Alignment explanation
Indices: 2562237--2562459 Score: 394
Period size: 80 Copynumber: 2.8 Consensus size: 80
2562227 ATACCAAGTT
2562237 AGGTAAATA-TATGATCATGTCAATAACAAGTCGGATCATTTACAGGTTTGGTCAATTACAGGTC
1 AGGTAAATATTA-GATCATGTCAATAACAAGTCGGATCATTTACAGGTTTGGTCAATTACAGGTC
2562301 AGGTTCATAACAGGTC
65 AGGTTCATAACAGGTC
*
2562317 AGGTAAATATTAGATCATGTCAATAACAAGTCGGATCATTTACAGGTTTGGTAAATTACAGGTCA
1 AGGTAAATATTAGATCATGTCAATAACAAGTCGGATCATTTACAGGTTTGGTCAATTACAGGTCA
2562382 GGTTCATAACAGGTC
66 GGTTCATAACAGGTC
* * *
2562397 AGATAAATATTAGATCATGTCAATAACAAGTCGGATCATTTACATGTTGGGTCAATTACAGGT
1 AGGTAAATATTAGATCATGTCAATAACAAGTCGGATCATTTACAGGTTTGGTCAATTACAGGT
2562460 AGGGTAATAC
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
80 135 0.99
81 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (80 bp):
AGGTAAATATTAGATCATGTCAATAACAAGTCGGATCATTTACAGGTTTGGTCAATTACAGGTCA
GGTTCATAACAGGTC
Found at i:2564076 original size:22 final size:22
Alignment explanation
Indices: 2564035--2564076 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2564025 AATTTAATTT
* *
2564035 ATTTTATTTTATTTTTATTCTA
1 ATTTTATTTTAGTTTGATTCTA
*
2564057 ATTTTATTTTGGTTTGATTC
1 ATTTTATTTTAGTTTGATTC
2564077 ATCGTATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.69
Consensus pattern (22 bp):
ATTTTATTTTAGTTTGATTCTA
Found at i:2564134 original size:14 final size:13
Alignment explanation
Indices: 2564114--2564145 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
2564104 TCTCTTTGTT
2564114 TTTATTATTATTA
1 TTTATTATTATTA
2564127 TATTATTATTATTA
1 T-TTATTATTATTA
2564141 TTTAT
1 TTTAT
2564146 CTCATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:2564172 original size:15 final size:16
Alignment explanation
Indices: 2564152--2564186 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2564142 TTATCTCATA
2564152 TTTTTTCCT-TTTCCT
1 TTTTTTCCTCTTTCCT
2564167 TTTTTTCCTCTTTCCT
1 TTTTTTCCTCTTTCCT
2564183 TTTT
1 TTTT
2564187 GATTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTCCTCTTTCCT
Found at i:2567363 original size:13 final size:12
Alignment explanation
Indices: 2567323--2567382 Score: 54
Period size: 13 Copynumber: 5.0 Consensus size: 12
2567313 AAATCAGAAC
2567323 AAAAAGAGAAAA
1 AAAAAGAGAAAA
*
2567335 AATAA-A-AAAA
1 AAAAAGAGAAAA
*
2567345 ACAAAGAGAAAA
1 AAAAAGAGAAAA
2567357 TAAAAAGAGAAAA
1 -AAAAAGAGAAAA
2567370 CAACAAAGA-AAAA
1 -AA-AAAGAGAAAA
2567383 TTGAAGAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 7 0.18
11 2 0.05
12 8 0.21
13 17 0.44
14 5 0.13
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:2568528 original size:32 final size:32
Alignment explanation
Indices: 2568477--2568601 Score: 205
Period size: 32 Copynumber: 3.9 Consensus size: 32
2568467 AATGAGGAAC
*
2568477 ATTGGGGTCATTCTTGGAGATTCAACATCGAAT
1 ATTGGGG-CATTTTTGGAGATTCAACATCGAAT
2568510 ATTGGGGCATTTTTGGAGATTCAACATCGAAT
1 ATTGGGGCATTTTTGGAGATTCAACATCGAAT
2568542 ATTGGGGCATTTTTGGAGATTCAACATCGAAT
1 ATTGGGGCATTTTTGGAGATTCAACATCGAAT
* * *
2568574 ATCGGGGCATCTTTGGGGATTCAACATC
1 ATTGGGGCATTTTTGGAGATTCAACATC
2568602 CTGATACGAA
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 81 0.92
33 7 0.08
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (32 bp):
ATTGGGGCATTTTTGGAGATTCAACATCGAAT
Found at i:2569388 original size:106 final size:106
Alignment explanation
Indices: 2569238--2569555 Score: 519
Period size: 106 Copynumber: 3.0 Consensus size: 106
2569228 GTTCCACCCG
* *
2569238 AGACAACACAAGTTTAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAGTTT
*
2569303 CAGAGCCAATTTCAACTTCAAAGCGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
*
2569344 AGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAGTTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAGTTT
* * *
2569409 CAAAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * * *
2569450 AGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTAGTTGTCAACAAACAATTTCCCAGTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAGTTT
* *
2569515 CAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
2569556 GAACAATACA
Statistics
Matches: 195, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 195 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAGTTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
Found at i:2569969 original size:65 final size:64
Alignment explanation
Indices: 2569861--2570056 Score: 214
Period size: 65 Copynumber: 3.0 Consensus size: 64
2569851 AAACATTCCC
* * * * *
2569861 CTTGAAACACAAATATTTGAATCAATTCCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC
1 CTTGAAACA-AAACATTTAAAAC-ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTC
2569926 T
64 T
** * *
2569927 CTTGAAACATAAACATTTAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCT
1 CTTGAAACA-AAACATTTAAAACATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCT
* ** * *
2569992 CTTGAAACAAAATC-TTTGAATATGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATTTTC
1 CTTGAAACAAAA-CATTT-AAAACATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTC
2570056 T
64 T
2570057 GTTGGAACTA
Statistics
Matches: 109, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
64 6 0.06
65 84 0.77
66 19 0.17
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (64 bp):
CTTGAAACAAAACATTTAAAACATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCT
Found at i:2570040 original size:130 final size:129
Alignment explanation
Indices: 2569859--2570292 Score: 341
Period size: 130 Copynumber: 3.3 Consensus size: 129
2569849 GAAAACATTC
* * *
2569859 CCCTTGAAACACAAATATTTGAATCAATTCCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
1 CCCTTGAAACA-AAATCTTTGAAT-AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
*
2569924 TCTCTTGAAACATAAACATTTAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATT
64 TCTCTTGAAACATAAACATTTAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAAAATT
2569989 T
129 T
* * *
2569990 CTCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATTTT
1 CCCTTGAAACAAAATCTTTGAATA-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTT
* * * ** * * ** * **
2570055 CTGTTGGAAC-T-AA-GTTT----TGTTTCTCTTGAGATAGTTTCTCTTGAAACATAAACATT-A
65 CTCTTGAAACATAAACATTTAAAACATTTCCCTTGAAAT-GAAT-T-TTG--TC-T-CTC-TTGA
*
2570112 AAAACATTT
122 GAAA-ATTT
** * *
2570121 CCCTT-ATAA-TGAAT-TTTGAGATAGGTTCCCTTAAAACAAAATTTTGTCTCCCTTGAGACAGT
1 CCCTTGA-AACAAAATCTTTGA-ATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGT
* * *
2570183 TTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGGTCTCTCTTGAGACAG
63 TTCTCTTGAAACATAAACATTTAAAACATTTCCCTTGAAATGAATTTT-GTCTCTCTTGAGAAAA
2570248 TTT
127 TTT
** * *
2570251 CCCTTGAAACTTCAATCGTTGAATATAGTTTCTCTTGAAACA
1 CCCTTGAAAC-AAAATCTTTG-A-ATAGTTTCCCTTGAAACA
2570293 CAAAAAACCT
Statistics
Matches: 227, Mismatches: 49, Indels: 52
0.69 0.15 0.16
Matches are distributed among these distances:
123 11 0.05
124 2 0.01
125 1 0.00
126 3 0.01
127 3 0.01
128 3 0.01
129 20 0.09
130 110 0.48
131 28 0.12
132 7 0.03
133 7 0.03
134 17 0.07
135 2 0.01
136 2 0.01
137 11 0.05
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (129 bp):
CCCTTGAAACAAAATCTTTGAATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTC
TCTTGAAACATAAACATTTAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAAAATTT
Found at i:2570275 original size:262 final size:262
Alignment explanation
Indices: 2569705--2570292 Score: 871
Period size: 262 Copynumber: 2.2 Consensus size: 262
2569695 AGTTTCCAAG
* * *
2569705 TTTTGTCTCTCTTAAGACAGTTTCTCTTGAAACAAAATCTTTGAATATCTTTTCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAA
* *
2569770 TTTAGTCTCCCTTGAGATATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTT
66 TTTAGTCTCCCTTGAGACATTTTCTGTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTT
* * * *
2569835 GAAGCATAAACTTTGAAAACATTCCCCTTGAAACACAAATATTTGAATCAATTCCCCTTGAAACA
131 GAAACATAAACATTAAAAACATTCCCCTTGAAACACAAATATTTGAATCAATTCCCCTTAAAACA
*
2569900 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTTAAAACATTTCCCTTGAAATG
196 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
2569965 AA
261 AA
* *
2569967 TTTTGTCTCTCTTGAGATAATTTCTCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAA
* *
2570032 TTTCGTCTCCCTTGAGACATTTTCTGTTGGAACTAAGTTTTGTTTCTCTTGAGATAGTTTCTCTT
66 TTTAGTCTCCCTTGAGACATTTTCTGTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTT
* * ** *
2570097 GAAACATAAACATTAAAAACATTTCCCTT-ATA-ATGAAT-TTTGAGAT-AGGTT-CCCTTAAAA
131 GAAACATAAACATTAAAAACATTCCCCTTGAAACACAAATATTTGA-ATCA-ATTCCCCTTAAAA
2570157 CAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAA
194 C-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAA
2570222 ATGAA
258 ATGAA
* ** * *
2570227 TTTTGGTCTCTCTTGAGACAGTTTCCCTTGAAACTTCAATCGTTGAATATAGTTTCTCTTGAAAC
1 TTTT-GTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAAATCTTTGAATAT-GTTTCCCTTGAAAC
2570292 A
63 A
2570293 CAAAAAACCT
Statistics
Matches: 294, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
259 15 0.05
260 79 0.27
261 28 0.10
262 158 0.54
263 14 0.05
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (262 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATATGTTTCCCTTGAAACAAA
TTTAGTCTCCCTTGAGACATTTTCTGTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTT
GAAACATAAACATTAAAAACATTCCCCTTGAAACACAAATATTTGAATCAATTCCCCTTAAAACA
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
AA
Found at i:2571593 original size:16 final size:17
Alignment explanation
Indices: 2571574--2571610 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2571564 AAAATTTAAT
*
2571574 TTTTTATTTC-ATTTTA
1 TTTTTATTCCAATTTTA
2571590 TTTTTATTCCAATTTTA
1 TTTTTATTCCAATTTTA
2571607 TTTT
1 TTTT
2571611 GGTTTGATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTCCAATTTTA
Found at i:2571676 original size:3 final size:3
Alignment explanation
Indices: 2571658--2571705 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
2571648 CTCTTTGTTT
*
2571658 TTA TCA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2571705 T
1 T
2571706 ATCTCATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2580909 original size:14 final size:14
Alignment explanation
Indices: 2580890--2580916 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2580880 ATTAATAGTG
2580890 TACATATATATATA
1 TACATATATATATA
2580904 TACATATATATAT
1 TACATATATATAT
2580917 TGATAAAATA
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:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TACATATATATATA
Found at i:2581067 original size:23 final size:23
Alignment explanation
Indices: 2581029--2581076 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
2581019 ATATATTTAT
2581029 TATATATATAAAAATA-AAA-AA
1 TATATATATAAAAATACAAATAA
2581050 TATATATATACAATAATACAAATAA
1 TATATATATA-AA-AATACAAATAA
2581075 TA
1 TA
2581077 AAAGGAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 10 0.43
22 2 0.09
23 4 0.17
24 3 0.13
25 4 0.17
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
TATATATATAAAAATACAAATAA
Found at i:2581289 original size:14 final size:14
Alignment explanation
Indices: 2581270--2581304 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
2581260 GCTTCCAGCT
2581270 GGGTCGGGTCGCAC
1 GGGTCGGGTCGCAC
2581284 GGGTCGGGTCGCAC
1 GGGTCGGGTCGCAC
2581298 GGGTCGG
1 GGGTCGG
2581305 TTCGGGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.06, C:0.26, G:0.54, T:0.14
Consensus pattern (14 bp):
GGGTCGGGTCGCAC
Found at i:2582820 original size:34 final size:34
Alignment explanation
Indices: 2582775--2582843 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
2582765 AGATTTTGTG
*
2582775 TTTCAAAAGAAA-TCGTCTCAAGGGAGACAAAATT
1 TTTCAAAAGAAACT-GTCTCAAGAGAGACAAAATT
* * *
2582809 TTTCAAGAGAAACTGTCTCGAGAGAGACGAAATT
1 TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
2582843 T
1 T
2582844 GTTTAAAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (34 bp):
TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:2582901 original size:65 final size:65
Alignment explanation
Indices: 2582817--2582976 Score: 241
Period size: 65 Copynumber: 2.5 Consensus size: 65
2582807 TTTTTCAAGA
* *
2582817 GAAACTGTCTCGAGAGAGACGAAATTTGTTT-AAAGGAAAACAAATTAAAAGATTTTGTTTAAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGG-AAACAAATTAAAAGATTTTGTTTAAAG
2582881 G
65 G
* * * * *
2582882 GAAACTGTCTCAATAGAGACAAAATTTGTTTCAAAGGAAATAGATTCAAAGATTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACAAATTAAAAGATTTTGTTTAAAGG
2582947 GAAACTGTCTCAAGAGAGACAAAATTTGTT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTT
2582977 AAGAGAAAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
65 81 0.94
66 5 0.06
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (65 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACAAATTAAAAGATTTTGTTTAAAGG
Found at i:2582921 original size:36 final size:35
Alignment explanation
Indices: 2582789--2583192 Score: 319
Period size: 36 Copynumber: 11.7 Consensus size: 35
2582779 AAAAGAAATC
* *
2582789 GTCTCAAGGGAGACAAAA-TT-TTTCAAGAGAAACT
1 GTCTCAAGAGAGACAAAATTTGTTTAAAG-GAAACT
* *
2582823 GTCTCGAGAGAGACGAAATTTGTTTAAAGGAAA--
1 GTCTCAAGAGAGACAAAATTTGTTTAAAGGAAACT
* * *
2582856 ---ACAA-ATTA-A-AAGATTTTGTTTAAAGGGAAACT
1 GTCTCAAGA-GAGACAA-AATTTGTTTAAA-GGAAACT
*
2582888 GTCTCAATAGAGACAAAATTTGTTTCAAAGGAAA-T
1 GTCTCAAGAGAGACAAAATTTGTTT-AAAGGAAACT
* *
2582923 AGAT-TC-A-A-AG----ATTTTGTTTCAAGGGAAACT
1 -G-TCTCAAGAGAGACAAAATTTGTTT-AAAGGAAACT
*
2582953 GTCTCAAGAGAGACAAAATTTG-TT-AAGAGAAAAT
1 GTCTCAAGAGAGACAAAATTTGTTTAAAG-GAAACT
*
2582987 GTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACT
1 GTCTCAAGAGAGACAAAATTTG-TTTAAAGGAAACT
* * * *
2583023 GTCTCAAGGGATACGAAATTTGTTTCAAGGGAAACT
1 GTCTCAAGAGAGACAAAATTTGTTT-AAAGGAAACT
* *
2583059 GTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAAT
1 GTCTCAAGAGAGACAAAATTTGTTTAAAG-GAAACT
* *
2583095 GTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAAT
1 GTCTCAAGAGAGACAAAATTTGTTTAAAG-GAAACT
* * *
2583131 GTTTCAAGAGAGACAAAATTTGTTTTAAGAGAAACC
1 GTCTCAAGAGAGACAAAATTTGTTTAAAG-GAAACT
2583167 GTCTCAAGAGAGACAAAACTTTGTTT
1 GTCTCAAGAGAGACAAAA-TTTGTTT
2583193 TGAGTAAATT
Statistics
Matches: 304, Mismatches: 34, Indels: 61
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.01
29 32 0.11
30 10 0.03
31 1 0.00
32 2 0.01
33 4 0.01
34 43 0.14
35 19 0.06
36 176 0.58
37 15 0.05
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.28
Consensus pattern (35 bp):
GTCTCAAGAGAGACAAAATTTGTTTAAAGGAAACT
Found at i:2582982 original size:19 final size:19
Alignment explanation
Indices: 2582958--2583010 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 19
2582948 AAACTGTCTC
2582958 AAGAGAGACAAAATTTGTT
1 AAGAGAGACAAAATTTGTT
* * *
2582977 -A-AGAG--AAAATGTCTC
1 AAGAGAGACAAAATTTGTT
2582992 AAGAGAGACAAAATTTGTT
1 AAGAGAGACAAAATTTGTT
2583011 TTAAAAGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 8
0.63 0.16 0.21
Matches are distributed among these distances:
15 7 0.29
16 1 0.04
17 8 0.33
18 1 0.04
19 7 0.29
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.25
Consensus pattern (19 bp):
AAGAGAGACAAAATTTGTT
Found at i:2583085 original size:72 final size:71
Alignment explanation
Indices: 2582935--2583192 Score: 383
Period size: 72 Copynumber: 3.6 Consensus size: 71
2582925 ATTCAAAGAT
* *
2582935 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG-TTAAGAGAAAATGTCTCAAGAGAG
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAGAGAAAATGTCTCAAGAGAG
2582999 ACAAAA
66 ACAAAA
* * * * * *
2583005 TTTGTTTTAAAAGAAACTGTCTCAAGGGATACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT-AAGAGAAAATGTCTCAAGAGA
2583070 GACAAAA
65 GACAAAA
* *
2583077 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTTTCAAGAGA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTG-TTTAAGAGAAAATGTCTCAAGAGA
2583142 GACAAAA
65 GACAAAA
*
2583149 TTTGTTTTAAGAGAAACCGTCTCAAGAGAGACAAAACTTTGTTT
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTT
2583193 TGAGTAAATT
Statistics
Matches: 166, Mismatches: 18, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
70 34 0.20
71 2 0.01
72 123 0.74
73 7 0.04
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (71 bp):
TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAGAGAAAATGTCTCAAGAGAG
ACAAAA
Found at i:2583125 original size:19 final size:19
Alignment explanation
Indices: 2583067--2583162 Score: 73
Period size: 19 Copynumber: 5.3 Consensus size: 19
2583057 CTGTCTCAAG
2583067 AGAGACAAAATTTGTTTTA
1 AGAGACAAAATTTGTTTTA
**
2583086 AGAG--AAAA--TGTCTCAA
1 AGAGACAAAATTTGT-TTTA
2583102 GAGAGACAAAATTTGTTTTA
1 -AGAGACAAAATTTGTTTTA
*
2583122 AGAG--AAAA--TGTTTCAA
1 AGAGACAAAATTTGTTT-TA
2583138 GAGAGACAAAATTTGTTTTA
1 -AGAGACAAAATTTGTTTTA
2583158 AGAGA
1 AGAGA
2583163 AACCGTCTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 24
0.66 0.07 0.27
Matches are distributed among these distances:
15 8 0.14
16 3 0.05
17 16 0.27
19 21 0.36
20 3 0.05
21 8 0.14
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (19 bp):
AGAGACAAAATTTGTTTTA
Found at i:2583128 original size:108 final size:108
Alignment explanation
Indices: 2582935--2583193 Score: 414
Period size: 108 Copynumber: 2.4 Consensus size: 108
2582925 ATTCAAAGAT
2582935 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG--TTAAGAGAAAATGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
* * * *
2582998 GACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGATACGAAA
66 GACAAAATTTGTTTTAAAAGAAAATGTCTCAAGAGAGACAAAA
2583041 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
* *
2583106 GACAAAATTTGTTTTAAGAGAAAATGTTTCAAGAGAGACAAAA
66 GACAAAATTTGTTTTAAAAGAAAATGTCTCAAGAGAGACAAAA
* * *
2583149 TTTGTTTTAAGAGAAACCGTCTCAAGAGAGACAAAACTTTGTTTT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTT
2583194 GAGTAAATTA
Statistics
Matches: 141, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
106 40 0.28
108 93 0.66
109 8 0.06
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.29
Consensus pattern (108 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
GACAAAATTTGTTTTAAAAGAAAATGTCTCAAGAGAGACAAAA
Found at i:2588706 original size:21 final size:21
Alignment explanation
Indices: 2588680--2588732 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2588670 GTTTCCAAAT
*
2588680 TCGCAACGTGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
2588701 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
2588722 TCGCAATGCGA
1 TCGCAACGCGA
2588733 TTTACACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:2588771 original size:21 final size:21
Alignment explanation
Indices: 2588741--2588877 Score: 120
Period size: 21 Copynumber: 6.6 Consensus size: 21
2588731 GATTTACACA
*
2588741 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
**
2588762 TTCGCGTTGCGATAGTTAAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
2588783 TTCGCATTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* *
2588804 TT--CGTTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
2588823 TTCGCGTTGCGATTTATTCTAAA
1 TTCGCGTTGCGA--TAGTCCAAG
2588846 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
2588865 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
2588878 TTATTCTAAA
Statistics
Matches: 88, Mismatches: 22, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
19 21 0.24
21 59 0.67
23 8 0.09
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:2588863 original size:61 final size:60
Alignment explanation
Indices: 2588747--2588868 Score: 140
Period size: 61 Copynumber: 2.0 Consensus size: 60
2588737 CACATTCGCA
* **
2588747 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTTAAAGTTCGCATTGCGATTTTCCAAATTCG
1 TTGCAATAGTCCAAGTTCGCGTTGCGATAGTTAAAGTTCG-ATTGCGATAGTCCAAATTCG
* * *
2588808 TTGCAATAGTCGAAGTTCGCGTTGCGATTTATTCTAAA-TTCG-TTGCGATAGTCCAAGTTCG
1 TTGCAATAGTCCAAGTTCGCGTTGCGA--TAGT-TAAAGTTCGATTGCGATAGTCCAAATTCG
2588869 CGTTGCGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
61 41 0.79
63 7 0.13
64 4 0.08
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (60 bp):
TTGCAATAGTCCAAGTTCGCGTTGCGATAGTTAAAGTTCGATTGCGATAGTCCAAATTCG
Found at i:2588893 original size:21 final size:21
Alignment explanation
Indices: 2588827--2588898 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
2588817 TCGAAGTTCG
2588827 CGTTGCGATTTATTCTAAATT
1 CGTTGCGATTTATTCTAAATT
* * *
2588848 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCTAAATT
2588867 CGCGTTGCGATTTATTCTAAATT
1 --CGTTGCGATTTATTCTAAATT
2588890 CGTTGCGAT
1 CGTTGCGAT
2588899 AGTCCAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 8 0.20
21 25 0.61
23 8 0.20
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTATTCTAAATT
Found at i:2588903 original size:42 final size:42
Alignment explanation
Indices: 2588766--2588905 Score: 212
Period size: 42 Copynumber: 3.4 Consensus size: 42
2588756 TCCAAGTTCG
** * *
2588766 CGTTGCGATAGTTAAAGTTCGCATTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATT
* *
2588806 CGTTGCAATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATT
2588848 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATT
2588890 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
2588906 AATCGCAACG
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 25 0.27
41 2 0.02
42 64 0.70
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATT
Found at i:2589006 original size:6 final size:6
Alignment explanation
Indices: 2588995--2589019 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2588985 GACACGTATT
2588995 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
2589020 GACGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2589517 original size:5 final size:5
Alignment explanation
Indices: 2589503--2589533 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2589493 TCGCCGCCGG
2589503 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
2589534 ACTCATGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:2589735 original size:42 final size:42
Alignment explanation
Indices: 2589653--2589927 Score: 397
Period size: 42 Copynumber: 6.5 Consensus size: 42
2589643 TGTGATTTTG
* * * * **
2589653 GACTATCACAAAGAATTTGGAATAAATCGGAACGTAAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
2589695 GACAATCGCAACGAACTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
2589737 GACTATCACAACGAAATTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
2589779 GACTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
2589821 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
2589863 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
2589905 GACTATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
2589928 CTATCGCAAT
Statistics
Matches: 209, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 200 0.96
44 9 0.04
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:2590361 original size:2 final size:2
Alignment explanation
Indices: 2590354--2590413 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
2590344 AATAGTGTAC
*
2590354 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2590396 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2590414 GATAAAATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2592191 original size:2 final size:2
Alignment explanation
Indices: 2592184--2592252 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
2592174 GAGAAAACAA
2592184 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2592226 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2592253 ATTTCGCACT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2594427 original size:20 final size:20
Alignment explanation
Indices: 2594389--2594442 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
2594379 AATGGACTTT
*
2594389 AGAGTTTCAAAAC-TTCACA
1 AGAGTTTCGAAACTTTCACA
2594408 AGAGTTTCGAAACTTTCACA
1 AGAGTTTCGAAACTTTCACA
2594428 AGAGTTTCGAAACTT
1 AGAGTTTCGAAACTT
2594443 CCCTTTTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (20 bp):
AGAGTTTCGAAACTTTCACA
Found at i:2596973 original size:34 final size:33
Alignment explanation
Indices: 2596939--2597001 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2596929 TATTCTTAAT
*
2596939 TTAATTTTCTT-TAGCATTTTTAAGTTGTTATAA
1 TTAATTTTCTTGTAGCATTTCTAA-TTGTTATAA
* *
2596972 TTCATTTTGTTGTAGCATTTCTAATTGTTA
1 TTAATTTTCTTGTAGCATTTCTAATTGTTA
2597002 CATTGTCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 15 0.58
34 11 0.42
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.57
Consensus pattern (33 bp):
TTAATTTTCTTGTAGCATTTCTAATTGTTATAA
Found at i:2597015 original size:34 final size:34
Alignment explanation
Indices: 2596950--2597015 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
2596940 TAATTTTCTT
* * *
2596950 TAGCATTTTTAAGTTGTTATAATTCATTTTGTTG
1 TAGCATTTCTAAGTTGTTACAATTCACTTTGTTG
*
2596984 TAGCATTTCTAA-TTGTTACATTGTCACTTTGT
1 TAGCATTTCTAAGTTGTTACAAT-TCACTTTGT
2597016 CATTGCAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 8 0.30
34 19 0.70
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.53
Consensus pattern (34 bp):
TAGCATTTCTAAGTTGTTACAATTCACTTTGTTG
Found at i:2600582 original size:28 final size:28
Alignment explanation
Indices: 2600528--2600595 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
2600518 AGAGTCGAGG
**
2600528 GTTCTACGT-GTTTTTTAGGACATATGT
1 GTTCTACGTGGTCCTTTAGGACATATGT
*
2600555 GTTCTACGTGGTCCTTTGGGACATATGT
1 GTTCTACGTGGTCCTTTAGGACATATGT
*
2600583 GTTCTATGTGGTC
1 GTTCTACGTGGTC
2600596 TGTCGGGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 9 0.25
28 27 0.75
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (28 bp):
GTTCTACGTGGTCCTTTAGGACATATGT
Found at i:2600603 original size:28 final size:28
Alignment explanation
Indices: 2600545--2600607 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
2600535 GTGTTTTTTA
*
2600545 GGACATATGTGTTCTACGTGGTCCTTTG
1 GGACATATGTGTTCTACGTGGTCCTTCG
*
2600573 GGACATATGTGTTCTATGTGGT-CTGTCG
1 GGACATATGTGTTCTACGTGGTCCT-TCG
2600601 GGACATA
1 GGACATA
2600608 GTGGTTATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 2 0.06
28 30 0.94
ACGTcount: A:0.17, C:0.16, G:0.30, T:0.37
Consensus pattern (28 bp):
GGACATATGTGTTCTACGTGGTCCTTCG
Found at i:2600767 original size:2 final size:2
Alignment explanation
Indices: 2600753--2600805 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
2600743 CCTGAATACA
*
2600753 AT AT AT GT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2600794 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2600806 GATGTGTGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2601359 original size:2 final size:2
Alignment explanation
Indices: 2601352--2601378 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2601342 GAAACTTTTC
2601352 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2601379 CAAGTATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2610248 original size:18 final size:20
Alignment explanation
Indices: 2610211--2610251 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2610201 TGAATAAGGT
2610211 ATGAATCTTCATTAAAAATC
1 ATGAATCTTCATTAAAAATC
2610231 ATGAATCTTCA-T-AAAATC
1 ATGAATCTTCATTAAAAATC
2610249 ATG
1 ATG
2610252 TGTTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.43
19 1 0.05
20 11 0.52
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (20 bp):
ATGAATCTTCATTAAAAATC
Found at i:2619745 original size:19 final size:19
Alignment explanation
Indices: 2619718--2619754 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2619708 AAATAAAAAT
*
2619718 AAAACAAAGAATAACTTTG
1 AAAACAAAGAAAAACTTTG
*
2619737 AAAATAAAGAAAAACTTT
1 AAAACAAAGAAAAACTTT
2619755 TAATAAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAACAAAGAAAAACTTTG
Found at i:2626449 original size:22 final size:21
Alignment explanation
Indices: 2626409--2626467 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
2626399 GGGTTTAAGT
* *
2626409 TTTATGGTTTAAA-TGTTATTAG
1 TTTAGGGTTTAAAGT-TTA-TAA
2626431 TTTAGGGTTTAAAGTTTATAA
1 TTTAGGGTTTAAAGTTTATAA
* *
2626452 TTTAGAGTTTTAAGTT
1 TTTAGGGTTTAAAGTT
2626468 AGGGGTAGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 16 0.50
22 15 0.47
23 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.53
Consensus pattern (21 bp):
TTTAGGGTTTAAAGTTTATAA
Found at i:2626568 original size:14 final size:14
Alignment explanation
Indices: 2626549--2626577 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2626539 GAAAGTGCTT
2626549 AATTGGGTCCACTA
1 AATTGGGTCCACTA
2626563 AATTGGGTCCACTA
1 AATTGGGTCCACTA
2626577 A
1 A
2626578 GTTGAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (14 bp):
AATTGGGTCCACTA
Found at i:2628685 original size:2 final size:2
Alignment explanation
Indices: 2628678--2628705 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2628668 ATATAACATA
2628678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2628706 TAGTTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2629017 original size:20 final size:20
Alignment explanation
Indices: 2628992--2629040 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2628982 TTTTGAAGAG
2628992 TTTCGAAACGTTTCCCATAA
1 TTTCGAAACGTTTCCCATAA
** *
2629012 TTTCGAAATTTTTCTCATAA
1 TTTCGAAACGTTTCCCATAA
2629032 TTTCGAAAC
1 TTTCGAAAC
2629041 TTTGTGTGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTCGAAACGTTTCCCATAA
Found at i:2636181 original size:37 final size:39
Alignment explanation
Indices: 2636114--2636200 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 39
2636104 ATCTTACTCG
*
2636114 AATAATATTGACATAAAATTGTAAATGTAATA-TCTAAT
1 AATAATATTGACATAAAATTGTAAAAGTAATATTCTAAT
* *
2636152 AATAATATTGACAT-AAATTGTAAAAGTAATATTTTACT
1 AATAATATTGACATAAAATTGTAAAAGTAATATTCTAAT
2636190 AATAATATTGA
1 AATAATATTGA
2636201 AAAAAAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 16 0.36
38 29 0.64
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (39 bp):
AATAATATTGACATAAAATTGTAAAAGTAATATTCTAAT
Found at i:2636288 original size:11 final size:11
Alignment explanation
Indices: 2636236--2636288 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
2636226 TATTTATGAC
2636236 ATAATTATTATT
1 ATAA-TATTATT
* *
2636248 AAAACATTATT
1 ATAATATTATT
*
2636259 ATAATATAATT
1 ATAATATTATT
*
2636270 GT-ATATTATT
1 ATAATATTATT
2636280 ATAATATTA
1 ATAATATTA
2636289 AAGATATAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
10 8 0.25
11 21 0.66
12 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (11 bp):
ATAATATTATT
Found at i:2636930 original size:2 final size:2
Alignment explanation
Indices: 2636923--2636958 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2636913 TTTAGCCCAA
2636923 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2636959 CCATTTTGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2640978 original size:3 final size:3
Alignment explanation
Indices: 2640954--2641007 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
2640944 CTACAAAAGC
* * *
2640954 AAT ATT AAT ATT AAT AAAT AAT AAT AAT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2641000 AAT AAT AA
1 AAT AAT AA
2641008 CGGGATGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2641461 original size:111 final size:111
Alignment explanation
Indices: 2641208--2641675 Score: 629
Period size: 111 Copynumber: 4.2 Consensus size: 111
2641198 TTCAGGGAAG
* *** * * * * **
2641208 ATTGAATCAGGGTAGACTTGTTCTATTATCACTTATGAAATAT-AAATCTTGAAAGAGATTTGAT
1 ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGA-GGGAT
* * *
2641272 CTGTTCCACTTCTTCTGAGGGAATATATCAGATCTAGGAAAGTTGATCC
65 CTGTTCCACTTCCTCTGAGGG-A-ATATCAGATCTGGGAAAGTTGATTC
* * *
2641321 ATTGAATCAGGGTAGACTTGTTCCACTGTCGCTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
1 ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
* * *
2641386 TGTTCCGCTTCCTCTGAGGGAATATCATATCTGGGAAAGTTGATTT
66 TGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
*
2641432 ATTGAATCAAGGTAGACTTGTTCCGCTGTCATTCAGGGAATATCAAATCTTG-AA-AGAGGGATA
1 ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGAT-
2641495 C-GTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
65 CTGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
* * *
2641541 ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAAGGAATACCAAATCTTAAAAGAGAGGGATC
1 ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
* *
2641606 TGTTCCACTTTCTCTGAGGGAATATCAGATCTGGAAAAGTTGATTC
66 TGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
* *
2641652 ATTGAATCAAAGCAGACTTGTTCC
1 ATTGAATCAAGGTAGACTTGTTCC
2641676 ACTTACTCTG
Statistics
Matches: 320, Mismatches: 30, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
109 98 0.31
110 6 0.02
111 142 0.44
112 1 0.00
113 58 0.18
114 15 0.05
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (111 bp):
ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
TGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
Found at i:2641599 original size:220 final size:222
Alignment explanation
Indices: 2641274--2641675 Score: 646
Period size: 220 Copynumber: 1.8 Consensus size: 222
2641264 GATTTGATCT
* *
2641274 GTTCCACTTCTTCTGAGGGAATATATCAGATCTAGGAAAGTTGATCCATTGAATCAGGGTAGACT
1 GTTCCACTTCCTCTGAGGGAATATATCAGATCTAGGAAAGTTGATCCATTGAATCAAGGTAGACT
* * * * *
2641339 TGTTCCACTGTCGCTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCGCTTCCTCTGAG
66 TGTTCCACTGTCACTCAAGGAATACCAAATCTTAAAAGAGAGGGATCTGTTCCACTTCCTCTGAG
* * * * *
2641404 GGAATATCATATCTGGGAAAGTTGATTTATTGAATCAAGGTAGACTTGTTCCGCTGTCATTCAGG
131 GGAATATCAGATCTGGAAAAGTTGATTCATTGAATCAAAGCAGACTTGTTCCGCTGTCATTCAGG
2641469 GAATATCAAATCTTGAAAGAGGGATAC
196 GAATATCAAATCTTGAAAGAGGGATAC
* *
2641496 GTTCCACTTCCTCTGAGGG-A-ATATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACT
1 GTTCCACTTCCTCTGAGGGAATATATCAGATCTAGGAAAGTTGATCCATTGAATCAAGGTAGACT
* *
2641559 TGTTCCGCTGTCACTCAAGGAATACCAAATCTTAAAAGAGAGGGATCTGTTCCACTTTCTCTGAG
66 TGTTCCACTGTCACTCAAGGAATACCAAATCTTAAAAGAGAGGGATCTGTTCCACTTCCTCTGAG
2641624 GGAATATCAGATCTGGAAAAGTTGATTCATTGAATCAAAGCAGACTTGTTCC
131 GGAATATCAGATCTGGAAAAGTTGATTCATTGAATCAAAGCAGACTTGTTCC
2641676 ACTTACTCTG
Statistics
Matches: 164, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
220 145 0.88
221 1 0.01
222 18 0.11
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (222 bp):
GTTCCACTTCCTCTGAGGGAATATATCAGATCTAGGAAAGTTGATCCATTGAATCAAGGTAGACT
TGTTCCACTGTCACTCAAGGAATACCAAATCTTAAAAGAGAGGGATCTGTTCCACTTCCTCTGAG
GGAATATCAGATCTGGAAAAGTTGATTCATTGAATCAAAGCAGACTTGTTCCGCTGTCATTCAGG
GAATATCAAATCTTGAAAGAGGGATAC
Found at i:2641731 original size:66 final size:66
Alignment explanation
Indices: 2641606--2642318 Score: 1259
Period size: 66 Copynumber: 10.8 Consensus size: 66
2641596 GAGAGGGATC
* * * * *
2641606 TGTTCCACTTTCTCTG-AGGGAATATCAGATC-TGGAAAAGTTGATTCATTGAATCAAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2641669 T
66 T
* * *
2641670 TGTTCCACTTACTCTGAATGGAATATCAAATCTTGTAGAAATTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2641735 T
66 T
* * * *
2641736 TGTTCCACTTATTCTGAAGGGAATATCAAATCTTGGAGAAGTTGGTCCATTGAATCAAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2641801 T
66 T
2641802 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2641867 T
66 T
* *
2641868 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCAAAACAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2641933 T
66 T
*
2641934 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2641999 T
66 T
2642000 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2642065 T
66 T
*
2642066 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2642131 T
66 T
2642132 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2642197 T
66 T
2642198 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2642263 T
66 T
*
2642264 TGTTTCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAAT
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAAT
2642319 TGGGATCGAA
Statistics
Matches: 619, Mismatches: 28, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
64 15 0.02
65 13 0.02
66 591 0.95
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (66 bp):
TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
T
Found at i:2643508 original size:22 final size:21
Alignment explanation
Indices: 2643484--2643559 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 21
2643474 CCCTCTTTTA
2643484 TTTTTCTTTTCCTTTTTCCTCAT
1 TTTTTC-TTT-CTTTTTCCTCAT
**
2643507 TTTTTCTTTCTTTTTTTTCATT
1 TTTTTCTTTCTTTTTCCTCA-T
*
2643529 TTTTTCCATTCATTTTTCCATTCAT
1 TTTTT-CTTTC-TTTTTCC--TCAT
2643554 TTTTTC
1 TTTTTC
2643560 AGGCGAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 9 0.21
22 9 0.21
23 10 0.23
24 6 0.14
25 6 0.14
26 3 0.07
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTCTTTCTTTTTCCTCAT
Found at i:2643540 original size:14 final size:14
Alignment explanation
Indices: 2643523--2643558 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
2643513 TTTCTTTTTT
2643523 TTCATTTTTTTCCA
1 TTCATTTTTTTCCA
2643537 TTCA--TTTTTCCA
1 TTCATTTTTTTCCA
2643549 TTCATTTTTT
1 TTCATTTTTT
2643559 CAGGCGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (14 bp):
TTCATTTTTTTCCA
Found at i:2647114 original size:21 final size:21
Alignment explanation
Indices: 2647081--2647134 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
2647071 TCCCATATCA
*
2647081 AAATAGAATGAAAT-AATAATAT
1 AAATA-AAAGAAATAAATAA-AT
2647103 ATAA-AAAAGAAATAAATAAAT
1 A-AATAAAAGAAATAAATAAAT
2647124 AAATAAAAGAA
1 AAATAAAAGAA
2647135 TGGAAATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.07
21 17 0.61
22 7 0.25
23 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
AAATAAAAGAAATAAATAAAT
Found at i:2656906 original size:3 final size:3
Alignment explanation
Indices: 2656864--2656932 Score: 75
Period size: 3 Copynumber: 22.7 Consensus size: 3
2656854 CTACAAAAGC
* * * * *
2656864 AAT ATT AAT ATT AAT ATT AAT ATT AAT ATT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
*
2656910 AAT GAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
2656933 CGGGATGAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:2664715 original size:31 final size:29
Alignment explanation
Indices: 2664646--2664715 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 29
2664636 ATGGAATATG
* *
2664646 TAAATAT-AAATTTAAAGACTAAATTGAA
1 TAAATATAAAAGTGAAAGACTAAATTGAA
*
2664674 TACATATAAAAGTGAAAGACTTGAAATTGAAA
1 TAAATATAAAAGTGAAAGAC-T-AAATTG-AA
2664706 TAAAT-TAAAA
1 TAAATATAAAA
2664716 AAACAAAAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 6 0.18
29 10 0.29
30 1 0.03
31 11 0.32
32 6 0.18
ACGTcount: A:0.57, C:0.04, G:0.10, T:0.29
Consensus pattern (29 bp):
TAAATATAAAAGTGAAAGACTAAATTGAA
Found at i:2664828 original size:19 final size:18
Alignment explanation
Indices: 2664810--2664990 Score: 83
Period size: 18 Copynumber: 9.7 Consensus size: 18
2664800 AAACATATAA
2664810 TATATATATATATATATAA-
1 TATATAT-TATATATA-AAC
* *
2664829 TATAAAATTTTATATAAAC
1 TAT-ATATTATATATAAAC
2664848 TATAT-TTATATTATAAAC
1 TATATATTATA-TATAAAC
2664866 TATATATTAT-TATAAACC
1 TATATATTATATATAAA-C
* **
2664884 ATATATAAATTATAT-TTATG
1 -TATAT--ATTATATATAAAC
2664904 TGA-ACTA-TATATATAAAC
1 T-ATA-TATTATATATAAAC
* *
2664922 TATGTATATAAAATTATAAAC
1 TA--TATATTATA-TATAAAC
2664943 TATAT-TTATATTATAAAC
1 TATATATTATA-TATAAAC
**
2664961 TATATAATTAT-TATAAGT
1 TATAT-ATTATATATAAAC
2664979 TATATA-TATATA
1 TATATATTATATA
2664991 AATTATGTTT
Statistics
Matches: 126, Mismatches: 16, Indels: 42
0.68 0.09 0.23
Matches are distributed among these distances:
16 3 0.02
17 19 0.15
18 46 0.37
19 29 0.23
20 12 0.10
21 16 0.13
22 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.45
Consensus pattern (18 bp):
TATATATTATATATAAAC
Found at i:2665013 original size:100 final size:95
Alignment explanation
Indices: 2664841--2665033 Score: 305
Period size: 100 Copynumber: 2.0 Consensus size: 95
2664831 TAAAATTTTA
*
2664841 TATAAACTATATTTATATTATAAACTATATATTATTATAAACCATATATAAATTATATTTATGTG
1 TATAAACTATATTTATATTATAAACTATATATTATTATAAAACATATATAAATTATATTTATGTG
2664906 AACTATATATATAAACTATGTATATAAAAT
66 AACTATATATATAAACTATGTATATAAAAT
* *
2664936 TATAAACTATATTTATATTATAAACTATATAATTATTATAAGTTATATATATATAAATTATGTTT
1 TATAAACTATATTTATATTATAAACTATAT-ATTATTATAA---A-ACATATATAAATTATATTT
*
2665001 ATGTGAATTATATATATAAACTATGTATATAAA
61 ATGTGAACTATATATATAAACTATGTATATAAA
2665034 CTATATATTT
Statistics
Matches: 89, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
95 30 0.34
96 10 0.11
99 1 0.01
100 48 0.54
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (95 bp):
TATAAACTATATTTATATTATAAACTATATATTATTATAAAACATATATAAATTATATTTATGTG
AACTATATATATAAACTATGTATATAAAAT
Found at i:2665031 original size:13 final size:13
Alignment explanation
Indices: 2665009--2665053 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
2664999 TTATGTGAAT
2665009 TATATATATAAAC
1 TATATATATAAAC
*
2665022 TATGTATATAAAC
1 TATATATATAAAC
2665035 TATATATTTATAAAC
1 TATATA--TATAAAC
2665050 TATA
1 TATA
2665054 AAAAGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.61
15 11 0.39
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:2665040 original size:28 final size:27
Alignment explanation
Indices: 2664859--2665116 Score: 82
Period size: 28 Copynumber: 9.5 Consensus size: 27
2664849 ATATTTATAT
*
2664859 TATAAACTATATATTATTATAAACCA-TA
1 TATAAACTATATA-TA-TATAAACTATTA
* * * *
2664887 TATAAATTATATTTATGTGAACTATATA
1 TATAAACTATATATATATAAACTAT-TA
*
2664915 TATAAAC--TATGTATATAAA--A-T-
1 TATAAACTATATATATATAAACTATTA
2664936 TATAAACTATATTTATATTATAAACTATATAA
1 TATAAACTATA--TATA-TATAAACTAT-T-A
* *
2664968 TTATTATAAGTTATATATATATAAATTATGTTTA
1 -TA-TA-AA-CTATATATATATAAACTA---TTA
* *
2665002 TGTGAA-T-TATATATATAAACTATGTA
1 TATAAACTATATATATATAAACTAT-TA
*
2665028 TATAAACTATATATTTATAAACTA-TA
1 TATAAACTATATATATATAAACTATTA
* * *
2665054 -A-AAAGTATATAGTTTATAAAATATTA
1 TATAAACTATATA-TATATAAACTATTA
* * *
2665080 TTTATA-T-TA-ATATAGTATA-TA-TA
1 TATAAACTATATATATA-TAAACTATTA
2665103 TATAAACTATATAT
1 TATAAACTATATAT
2665117 GAATAAATTA
Statistics
Matches: 173, Mismatches: 26, Indels: 64
0.66 0.10 0.24
Matches are distributed among these distances:
21 7 0.04
22 1 0.01
23 8 0.05
24 16 0.09
25 21 0.12
26 35 0.20
27 4 0.02
28 50 0.29
29 1 0.01
30 1 0.01
31 2 0.01
32 1 0.01
33 11 0.06
34 7 0.04
35 3 0.02
36 5 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (27 bp):
TATAAACTATATATATATAAACTATTA
Found at i:2665053 original size:24 final size:25
Alignment explanation
Indices: 2665026--2665073 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2665016 ATAAACTATG
*
2665026 TATATAAACTATATA-TTTATAAAC
1 TATAAAAACTATATAGTTTATAAAC
*
2665050 TATAAAAAGTATATAGTTTATAAA
1 TATAAAAACTATATAGTTTATAAA
2665074 ATATTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
TATAAAAACTATATAGTTTATAAAC
Found at i:2665114 original size:75 final size:75
Alignment explanation
Indices: 2665026--2665178 Score: 218
Period size: 75 Copynumber: 2.0 Consensus size: 75
2665016 ATAAACTATG
** * *
2665026 TATATAAACTATATATTTATAAACTATA-AAAAGTATATAGTTTATAAAATATTATTTATATTAA
1 TATATAAACTATATATGAATAAACTATATAAAA-TACATAGTTTATAAAATATAATTTATATTAA
2665090 TATAGTATATA
65 TATAGTATATA
* ***
2665101 TATATAAACTATATATGAATAAATTATATAAAATACATAGTTTATATGTTATAATTTATATTAAT
1 TATATAAACTATATATGAATAAACTATATAAAATACATAGTTTATAAAATATAATTTATATTAAT
2665166 ATAGTATATA
66 ATAGTATATA
2665176 TAT
1 TAT
2665179 GTATGCATTA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 65 0.94
76 4 0.06
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (75 bp):
TATATAAACTATATATGAATAAACTATATAAAATACATAGTTTATAAAATATAATTTATATTAAT
ATAGTATATA
Found at i:2665563 original size:7 final size:7
Alignment explanation
Indices: 2665551--2665609 Score: 82
Period size: 7 Copynumber: 8.4 Consensus size: 7
2665541 TATACATGTA
2665551 TTAGGGT
1 TTAGGGT
2665558 TTAGGGT
1 TTAGGGT
2665565 TTAGGGT
1 TTAGGGT
2665572 TTAGGGT
1 TTAGGGT
2665579 TTAGGGT
1 TTAGGGT
* *
2665586 TTATGAT
1 TTAGGGT
*
2665593 TTAGGTT
1 TTAGGGT
*
2665600 TTAAGGT
1 TTAGGGT
2665607 TTA
1 TTA
2665610 TATAAACTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:2665952 original size:2 final size:2
Alignment explanation
Indices: 2665945--2665977 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2665935 ACTTTGAATA
2665945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2665978 ATTAAACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2666379 original size:2 final size:2
Alignment explanation
Indices: 2666372--2666400 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2666362 TATGTTTAAT
2666372 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2666401 TATTCAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2666532 original size:19 final size:20
Alignment explanation
Indices: 2666510--2666554 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2666500 TTGAGAATAT
*
2666510 AGGGAAATTGA-TAATTTAG
1 AGGGAAATTGAGAAATTTAG
2666529 AGGGAAATTGAGAAATTTAG
1 AGGGAAATTGAGAAATTTAG
2666549 AGGGAA
1 AGGGAA
2666555 TAGAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.24
Consensus pattern (20 bp):
AGGGAAATTGAGAAATTTAG
Found at i:2666547 original size:20 final size:19
Alignment explanation
Indices: 2666510--2666564 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
2666500 TTGAGAATAT
*
2666510 AGGGAAATTGATAATTTAG
1 AGGGAAATTGAAAATTTAG
2666529 AGGGAAATTGAGAAATTTAG
1 AGGGAAATTGA-AAATTTAG
*
2666549 AGGG-AATAGAAAATTT
1 AGGGAAATTGAAAATTT
2666565 TGGGAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 6 0.18
19 16 0.48
20 11 0.33
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.27
Consensus pattern (19 bp):
AGGGAAATTGAAAATTTAG
Found at i:2667065 original size:23 final size:23
Alignment explanation
Indices: 2667027--2667075 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2667017 TTATTTTTTC
* *
2667027 TTTATATAATTTAACTTTA-TAA
1 TTTATATAATTAAACTATATTAA
2667049 TTTATATAAATTAAACTATATTAA
1 TTTATAT-AATTAAACTATATTAA
2667073 TTT
1 TTT
2667076 TCCTTTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 10 0.43
24 6 0.26
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTATATAATTAAACTATATTAA
Found at i:2667371 original size:16 final size:15
Alignment explanation
Indices: 2667334--2667380 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2667324 TCATTTACAG
2667334 GTCAGGTTAAAAACA
1 GTCAGGTTAAAAACA
2667349 TGT-AGGTTAAAAACA
1 -GTCAGGTTAAAAACA
*
2667364 GATCAGGTTGAAAACA
1 G-TCAGGTTAAAAACA
2667380 G
1 G
2667381 GTCGGATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 1 0.04
15 13 0.46
16 14 0.50
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (15 bp):
GTCAGGTTAAAAACA
Found at i:2672654 original size:21 final size:22
Alignment explanation
Indices: 2672636--2672676 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2672626 ATAAATAACT
2672636 TAAA-ATTTC-TAACTCATAAA
1 TAAATATTTCTTAACTCATAAA
2672656 TAAATATTTCTTTAACTCATA
1 TAAATATTTC-TTAACTCATA
2672677 GTAAAACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
23 9 0.50
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATATTTCTTAACTCATAAA
Found at i:2672787 original size:21 final size:21
Alignment explanation
Indices: 2672758--2672797 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2672748 AAGGTTATGC
*
2672758 TTTATGGTTTATGGTTTGGTG
1 TTTAAGGTTTATGGTTTGGTG
2672779 TTTAAGGTTTATGGTTTGG
1 TTTAAGGTTTATGGTTTGG
2672798 GTTAGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (21 bp):
TTTAAGGTTTATGGTTTGGTG
Found at i:2672979 original size:2 final size:2
Alignment explanation
Indices: 2672972--2672996 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2672962 AGTCTAATCA
2672972 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2672997 AGTTTACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2673767 original size:17 final size:17
Alignment explanation
Indices: 2673740--2673778 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2673730 GATAATTATA
*
2673740 ATAATATTTTATAATTTT
1 ATAATAATTTAT-ATTTT
2673758 -TAATAATTTATATTTT
1 ATAATAATTTATATTTT
2673774 ATAAT
1 ATAAT
2673779 TTTTTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAATAATTTATATTTT
Found at i:2694996 original size:20 final size:20
Alignment explanation
Indices: 2694973--2695018 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2694963 ATGACTCCAT
2694973 TGAGCCGGAAGGAACTCCGC
1 TGAGCCGGAAGGAACTCCGC
2694993 TGAGCCGGAAGGAACTCCGC
1 TGAGCCGGAAGGAACTCCGC
2695013 TGAGCC
1 TGAGCC
2695019 AGGCTCTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.30, G:0.35, T:0.11
Consensus pattern (20 bp):
TGAGCCGGAAGGAACTCCGC
Found at i:2696092 original size:22 final size:22
Alignment explanation
Indices: 2696049--2696102 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
2696039 AACAACCATA
2696049 AGTAAAACATAATTCATTATTC
1 AGTAAAACATAATTCATTATTC
2696071 A-TAAAACATAAAATT-ATTATTC
1 AGTAAAACAT--AATTCATTATTC
2696093 AGGTAAAACA
1 A-GTAAAACA
2696103 AAGTTTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 8 0.29
22 9 0.32
23 4 0.14
24 7 0.25
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (22 bp):
AGTAAAACATAATTCATTATTC
Found at i:2702879 original size:24 final size:23
Alignment explanation
Indices: 2702852--2702896 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
2702842 CAACCTTACT
2702852 TAGATCA-ATTTGTGGTGGTATTTA
1 TAGATCATATTT-TGGT-GTATTTA
*
2702876 TAGATGATATTTTGGTGTATT
1 TAGATCATATTTTGGTGTATT
2702897 CCAAGTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 10 0.53
25 4 0.21
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (23 bp):
TAGATCATATTTTGGTGTATTTA
Found at i:2705341 original size:4 final size:4
Alignment explanation
Indices: 2705332--2705366 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2705322 CTATTAGTAA
*
2705332 GAAT GAAT GAAT GAAT GAAT GAAT AAAT GAAT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
2705367 AGGGCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (4 bp):
GAAT
Done.