Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008855.1 Hibiscus syriacus cultivar Beakdansim tig00112072_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: 1316246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1122027 original size:28 final size:28
Alignment explanation
Indices: 1121995--1122160 Score: 151
Period size: 28 Copynumber: 5.9 Consensus size: 28
1121985 CGGGTGGTAT
* *
1121995 TTTTGTAATTATTTTGAAATTGGTGGTA
1 TTTTGTAATTATTTTGAAAATGGTGATA
*
1122023 TTTTGTTAATTATTTTGAAAATGGTGCTA
1 TTTTG-TAATTATTTTGAAAATGGTGATA
* **
1122052 TTTTCATAATT-TTTTTTAAAT--TGATAA
1 TTTT-GTAATTATTTTGAAAATGGTGAT-A
* * **
1122079 TTTCGTAATTATTTTAAAAAAAGTGATA
1 TTTTGTAATTATTTTGAAAATGGTGATA
*
1122107 TTTTGTAATTATTTT-AAAAAGGTGATA
1 TTTTGTAATTATTTTGAAAATGGTGATA
* *
1122134 GTTTTGTAATTATTTTTAAAAGGGTGA
1 -TTTTGTAATTATTTTGAAAATGGTGA
1122161 GACAACCTTT
Statistics
Matches: 116, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
26 8 0.07
27 22 0.19
28 43 0.37
29 43 0.37
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.51
Consensus pattern (28 bp):
TTTTGTAATTATTTTGAAAATGGTGATA
Found at i:1129218 original size:29 final size:29
Alignment explanation
Indices: 1129184--1129373 Score: 133
Period size: 29 Copynumber: 6.8 Consensus size: 29
1129174 CCGTTGACAG
* *
1129184 GGTGGTATTTTTGTAATTATTTTGAAATT
1 GGTGGTATTTTCGTAATTATTTTGAAAAT
*
1129213 GGTGGTATTTTGGTAATTATTTTGAAAAT
1 GGTGGTATTTTCGTAATTATTTTGAAAAT
* * *
1129242 GATGCTATTTTCGTAATT-TTTTTAAAA-
1 GGTGGTATTTTCGTAATTATTTTGAAAAT
* * * *
1129269 -GTGATAATTTCTTAATTA-TTT-AAAAA
1 GGTGGTATTTTCGTAATTATTTTGAAAAT
* * * *
1129295 AGTGATATTTTCGTAATTA-TTTAAAAAA
1 GGTGGTATTTTCGTAATTATTTTGAAAAT
* * * *
1129323 GATGATAGTTTT-GTAATTATTTTTAAAAG
1 GGTGGTA-TTTTCGTAATTATTTTGAAAAT
** *
1129352 GGTGACATTTTCGTAAATATTT
1 GGTGGTATTTTCGTAATTATTT
1129374 CTTAAAAGGG
Statistics
Matches: 135, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
25 4 0.03
26 16 0.12
27 19 0.14
28 29 0.21
29 67 0.50
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (29 bp):
GGTGGTATTTTCGTAATTATTTTGAAAAT
Found at i:1129338 original size:28 final size:27
Alignment explanation
Indices: 1129218--1129373 Score: 136
Period size: 27 Copynumber: 5.6 Consensus size: 27
1129208 AAATTGGTGG
* * * *
1129218 TATTTTGGTAATTATTTTGAAAATGATGC
1 TATTTTCGTAATTA-TTTAAAAAAG-TGA
**
1129247 TATTTTCGTAATT-TTTTTAAAAGTGA
1 TATTTTCGTAATTATTTAAAAAAGTGA
* *
1129273 TAATTTCTTAATTATTTAAAAAAGTGA
1 TATTTTCGTAATTATTTAAAAAAGTGA
1129300 TATTTTCGTAATTATTTAAAAAAGATGA
1 TATTTTCGTAATTATTTAAAAAAG-TGA
**
1129328 TAGTTTT-GTAATTATTTTTAAAAGGGTGA
1 TA-TTTTCGTAATTA--TTTAAAAAAGTGA
* *
1129357 CATTTTCGTAAATATTT
1 TATTTTCGTAATTATTT
1129374 CTTAAAAGGG
Statistics
Matches: 106, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
26 13 0.12
27 43 0.41
28 16 0.15
29 26 0.25
30 8 0.08
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (27 bp):
TATTTTCGTAATTATTTAAAAAAGTGA
Found at i:1129379 original size:30 final size:28
Alignment explanation
Indices: 1129331--1129386 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 28
1129321 AAGATGATAG
*
1129331 TTTTGTAATTATTTTTAAAAGGGTGACA
1 TTTTGTAAATATTTTTAAAAGGGTGACA
1129359 TTTTCGTAAATATTTCTTAAAAGGGTGA
1 TTTT-GTAAATATTT-TTAAAAGGGTGA
1129387 TAATGTGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 4 0.16
29 9 0.36
30 12 0.48
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (28 bp):
TTTTGTAAATATTTTTAAAAGGGTGACA
Found at i:1129396 original size:29 final size:28
Alignment explanation
Indices: 1129334--1129397 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
1129324 ATGATAGTTT
* * *
1129334 TGTAATTATTTTTAAAAGGGTGACATTT
1 TGTAAATATTTTTAAAAGGGTGACAATG
*
1129362 TCGTAAATATTTCTTAAAAGGGTGATAATG
1 T-GTAAATATTT-TTAAAAGGGTGACAATG
1129392 TGTAAA
1 TGTAAA
1129398 ATGGTTGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 14 0.47
30 15 0.50
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.41
Consensus pattern (28 bp):
TGTAAATATTTTTAAAAGGGTGACAATG
Found at i:1131765 original size:28 final size:28
Alignment explanation
Indices: 1131728--1131784 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1131718 AATTGAAACG
* * *
1131728 AAAATCAAAGTTTAGTGTTATAATTGAT
1 AAAATCAAAGTTCAGTGGTATAAATGAT
*
1131756 AAAATTAAAGTTCAGTGGTATAAATGAT
1 AAAATCAAAGTTCAGTGGTATAAATGAT
1131784 A
1 A
1131785 TAACACCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.35
Consensus pattern (28 bp):
AAAATCAAAGTTCAGTGGTATAAATGAT
Found at i:1145317 original size:61 final size:61
Alignment explanation
Indices: 1145170--1145322 Score: 236
Period size: 61 Copynumber: 2.5 Consensus size: 61
1145160 TCATGTCCGA
* *
1145170 ATTAGCACTATAGCGTAAGCTTAGTACAGGTGGTGGGCAAGACCTTATGTGTATTGTCTGG
1 ATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGCAAGACCTTATGTGTATTGTCTAG
*
1145231 ATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGCACGACCTTATGTGTATTGT-TCAG
1 ATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGCAAGACCTTATGTGTATTGTCT-AG
* * *
1145292 ATTAGCACTATGGTGTAAGCTTAGTGTAGGT
1 ATTAGCACTATAGCGTAAGCTTAGTGCAGGT
1145323 TTAGCACTAC
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
60 1 0.01
61 84 0.99
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.32
Consensus pattern (61 bp):
ATTAGCACTATAGCGTAAGCTTAGTGCAGGTGGTGGGCAAGACCTTATGTGTATTGTCTAG
Found at i:1145421 original size:20 final size:20
Alignment explanation
Indices: 1145381--1145422 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1145371 TTGTATATTG
* *
1145381 GGCTATTGTCTATTGTTTAT
1 GGCTATTGTCTATGGTATAT
1145401 GGCTATTGTCTATGGTATAT
1 GGCTATTGTCTATGGTATAT
1145421 GG
1 GG
1145423 TTATGGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.48
Consensus pattern (20 bp):
GGCTATTGTCTATGGTATAT
Found at i:1145520 original size:31 final size:31
Alignment explanation
Indices: 1145482--1145545 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1145472 GAACAAATGG
*
1145482 TAAGTATATTGGTAAAATAAGCTTATGAGCT
1 TAAGTATATTGGTAAAATAAGCTTACGAGCT
1145513 TAAGTATATTGGTAAAATAAGCTTACGAGCT
1 TAAGTATATTGGTAAAATAAGCTTACGAGCT
1145544 TA
1 TA
1145546 TGGGATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (31 bp):
TAAGTATATTGGTAAAATAAGCTTACGAGCT
Found at i:1148404 original size:15 final size:15
Alignment explanation
Indices: 1148380--1148476 Score: 99
Period size: 15 Copynumber: 6.3 Consensus size: 15
1148370 ATAAGTGCTA
*
1148380 AAAAAAAAAAAAAAG
1 AAAAAGAAAAAAAAG
1148395 AAAAAGAAAAAGAAA-
1 AAAAAGAAAAA-AAAG
* *
1148410 AGAAAAGAAGAAAGAAT
1 A-AAAAGAA-AAAAAAG
1148427 AAAAAGAAAAAGAAA-
1 AAAAAGAAAAA-AAAG
* *
1148442 ACAAAGAAAAAATAG
1 AAAAAGAAAAAAAAG
1148457 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
1148472 AAAAA
1 AAAAA
1148477 AATGAGAGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
14 2 0.03
15 42 0.61
16 21 0.30
17 4 0.06
ACGTcount: A:0.84, C:0.01, G:0.13, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:1148415 original size:24 final size:24
Alignment explanation
Indices: 1148380--1148478 Score: 93
Period size: 24 Copynumber: 4.2 Consensus size: 24
1148370 ATAAGTGCTA
*
1148380 AAAAA-AAAAA-AAAAGAAA-AAG
1 AAAAAGAAAAAGAAAAAAAAGAAG
*
1148401 AAAAAG-AAAAGAAAAGAAGAAAGAAT
1 AAAAAGAAAAAG-AAA-AA-AAAGAAG
*
1148427 AAAAAGAAAAAGAAAACAAAGAA-
1 AAAAAGAAAAAGAAAAAAAAGAAG
1148450 AAAATAGAAAAAGAAAAAAAAGAA-
1 AAAA-AGAAAAAGAAAAAAAAGAAG
1148474 AAAAA
1 AAAAA
1148479 TGAGAGATGA
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
21 9 0.14
23 8 0.12
24 29 0.44
25 4 0.06
26 11 0.17
27 5 0.08
ACGTcount: A:0.84, C:0.01, G:0.13, T:0.02
Consensus pattern (24 bp):
AAAAAGAAAAAGAAAAAAAAGAAG
Found at i:1148497 original size:1 final size:1
Alignment explanation
Indices: 1148379--1148478 Score: 56
Period size: 1 Copynumber: 100.0 Consensus size: 1
1148369 CATAAGTGCT
* * * * * * * * * * *
1148379 AAAAAAAAAAAAAAAGAAAAAGAAAAAGAAAAGAAAAGAAGAAAGAATAAAAAGAAAAAGAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
1148444 AAAGAAAAAATAGAAAAAGAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1148479 TGAGAGATGA
Statistics
Matches: 67, Mismatches: 32, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.84, C:0.01, G:0.13, T:0.02
Consensus pattern (1 bp):
A
Found at i:1152565 original size:45 final size:45
Alignment explanation
Indices: 1152508--1152652 Score: 227
Period size: 45 Copynumber: 3.2 Consensus size: 45
1152498 GAATAATGAC
* *
1152508 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGAACAAATTGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGT
*
1152553 AAGTATATTGGTAAATTAAGCTTACGAGCTTATGGAACAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGT
* * *
1152598 AAGTATAGTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGT
*
1152643 AAGTAGATTG
1 AAGTATATTG
1152653 ATAAGAAATG
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (45 bp):
AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGT
Found at i:1152958 original size:22 final size:24
Alignment explanation
Indices: 1152915--1152959 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1152905 CAAGTCTCTC
1152915 CCAAGACCCAATTACAACATCCAA
1 CCAAGACCCAATTACAACATCCAA
*
1152939 CCAAG-CCCAA-TACAAGATCCA
1 CCAAGACCCAATTACAACATCCA
1152960 GCAGACCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 5 0.25
24 5 0.25
ACGTcount: A:0.44, C:0.38, G:0.07, T:0.11
Consensus pattern (24 bp):
CCAAGACCCAATTACAACATCCAA
Found at i:1160865 original size:42 final size:42
Alignment explanation
Indices: 1160806--1160894 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
1160796 AAGGATTTCT
* *
1160806 TGATGCTTAAATCCTTCGGGTTATCAATAAGTCTTTCGAGCA
1 TGATGCTTAAATCCTTCGAGTCATCAATAAGTCTTTCGAGCA
*
1160848 TGATGCTTAAATCCTTCGAGTCATCTATAAGTCTTTCGAGCA
1 TGATGCTTAAATCCTTCGAGTCATCAATAAGTCTTTCGAGCA
*
1160890 AGATG
1 TGATG
1160895 ATAAGTCCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (42 bp):
TGATGCTTAAATCCTTCGAGTCATCAATAAGTCTTTCGAGCA
Found at i:1160919 original size:41 final size:42
Alignment explanation
Indices: 1160807--1160919 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
1160797 AGGATTTCTT
* * ** * *
1160807 GATGCTTAAATCCTTCGGGTTATCAATAAGTCTTTCGAGCAT
1 GATGCATAAATCCTTCGAGCCATCCATAAGTCTTTCGAGCAA
* * *
1160849 GATGCTTAAATCCTTCGAGTCATCTATAAGTCTTTCGAGCAA
1 GATGCATAAATCCTTCGAGCCATCCATAAGTCTTTCGAGCAA
*
1160891 GATG-ATAAGTCCTTC-AGGCCATCCATAAG
1 GATGCATAAATCCTTCGA-GCCATCCATAAG
1160920 ACCTTCGGGT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.02
41 19 0.31
42 42 0.68
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (42 bp):
GATGCATAAATCCTTCGAGCCATCCATAAGTCTTTCGAGCAA
Found at i:1161208 original size:135 final size:135
Alignment explanation
Indices: 1160966--1161307 Score: 537
Period size: 135 Copynumber: 2.5 Consensus size: 135
1160956 CGACTCATGA
1160966 ATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAG
1 ATTTCGAATCAGTGACACCTCGCTTGAGGGATTGA-ATTTCCAATTGAGAGTTCATAATGAGAAG
*
1161031 AACTCATCCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTT-TTCGACCTATCACTCGATT
65 AACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATT
*
1161095 CA-TGT
130 CACGGT
* *
1161100 CATTTCAAATCAGTGACACCTCGCTTGAAGGATTGATATTTCCAATTGAGAGTTCATAATGAGAA
1 -ATTTCGAATCAGTGACACCTCGCTTGAGGGATTGA-ATTTCCAATTGAGAGTTCATAATGAGAA
*
1161165 GAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATTACTCGAT
64 GAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGAT
1161230 TCACGGT
129 TCACGGT
* ** * * *
1161237 ATTTCGAATCAATGACGTCTCGCTTGAGGGATTGAATTTCTAATT-AAAGTTTATAATGAGAAGA
1 ATTTCGAATCAGTGACACCTCGCTTGAGGGATTGAATTTCCAATTGAGAGTTCATAATGAGAAGA
1161301 ACTCATC
66 ACTCATC
1161308 ATAAAGAAGA
Statistics
Matches: 191, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
134 24 0.13
135 115 0.60
136 50 0.26
137 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (135 bp):
ATTTCGAATCAGTGACACCTCGCTTGAGGGATTGAATTTCCAATTGAGAGTTCATAATGAGAAGA
ACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTC
ACGGT
Found at i:1161532 original size:107 final size:105
Alignment explanation
Indices: 1161284--1161661 Score: 505
Period size: 107 Copynumber: 3.6 Consensus size: 105
1161274 TTCTAATTAA
* * * * *
1161284 AGTTTATAATGAGAAGAACTCATCATAAAGAAGAAATTTCATAATGAGAAGAACTTATTCCTTTC
1 AGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTC
* *
1161349 AAATTCACCACA-AAAAAGGTGAACCAACATTTCCAGAAG
66 AAATTCACCACAGAAAGAGGTGAACCAACATTTCAAGAAG
* *
1161388 AGTTCATAATGAGAAGAACTCGTCCTAAAGGATAAAGTTCATAATGAGAAGAACTTGTTCCTTTC
1 AGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTC
* *
1161453 AAATTCACCACAGAAAGAGGTGAACCGACATTTATAATGAAG
66 AAATTCACCACAGAAAGAGGTGAACCAACATTT-CAA-GAAG
*
1161495 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTC
1 AGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTC
*
1161560 AAATTCACCACAG-AAGAATGTGAACCAACATTTCCAA-AAG
66 AAATTCACCACAGAAAG-AGGTGAACCAACATTT-CAAGAAG
* * *
1161600 AGTTCATAATGAG-A-ATCTCATCCAAAGAGGAAGAATAAATTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCCTAA-AGG-AG-A-AAGTTCATAATGAGAAGAACTTGTTC
1161662 AACCTTGCAT
Statistics
Matches: 246, Mismatches: 20, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
103 9 0.04
104 74 0.30
105 36 0.15
106 5 0.02
107 122 0.50
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (105 bp):
AGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTC
AAATTCACCACAGAAAGAGGTGAACCAACATTTCAAGAAG
Found at i:1161842 original size:208 final size:208
Alignment explanation
Indices: 1161579--1162170 Score: 906
Period size: 208 Copynumber: 2.9 Consensus size: 208
1161569 ACAGAAGAAT
* * * * *
1161579 GTGAACCAACATTTCCAA--AAGAGTTCATAATGAG-A-ATCTCATCCAAAGAGGAAGAATAAAT
1 GTGAATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGT
*
1161640 TCATAATGAGAAGAACTTGTTCAACCTTGCATTAACATTTTCAGTGGAGAGTTCATAATGAGAAG
66 TCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTTCAGTGGAGAGTTCATAATGAGAAG
* * *
1161705 AACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAATAATTTTTTTAACCTTGGTTCGATTCC
131 AACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAAATTTTTCAACCTTGGTTCGATTCC
1161770 ATCACAAAAGGAG
196 ATCACAAAAGGAG
* *
1161783 GTGAATCAACATTTCTAATGGAGAGTTCATAATGAGAAGAACTAATCCAAAGAGGAAGAAGAAGT
1 GTGAATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGT
* *
1161848 TCATAATGAGAATAATTTGTTCAACCTTGCATCAACATTTTCAGTGGAGAGTTCATAATGAGAAG
66 TCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTTCAGTGGAGAGTTCATAATGAGAAG
1161913 AACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAAATTTTTCAACCTTGGTTCGATTCC
131 AACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAAATTTTTCAACCTTGGTTCGATTCC
*
1161978 ATCACAGAAGGAG
196 ATCACAAAAGGAG
*
1161991 GTGAATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGT
1 GTGAATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGT
* ** * **
1162056 TCATAATGAGAAGAACTTGTTTAACCTTGCATCAATGTTTCCAGTTAAGAGTTCATAATGAGAAG
66 TCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTTCAGTGGAGAGTTCATAATGAGAAG
* * * * *
1162121 AACTCATCCAA-CAAGAGAGAAGAAGTTTATAATGAGAAGAACTTGTTCAA
131 AACTCATCCAATGAGGA-AGAAGAAGTTCATAATGAGAAGAAATTTTTCAA
1162171 TCTAATGCTT
Statistics
Matches: 353, Mismatches: 30, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
204 16 0.05
206 15 0.04
207 4 0.01
208 318 0.90
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (208 bp):
GTGAATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACCTTGCATCAACATTTTCAGTGGAGAGTTCATAATGAGAAG
AACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAAATTTTTCAACCTTGGTTCGATTCC
ATCACAAAAGGAG
Found at i:1161903 original size:91 final size:91
Alignment explanation
Indices: 1161787--1161967 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
1161777 AAGGAGGTGA
1161787 ATCAACATTTCTAATGGAGAGTTCATAATGAGAAGAACTAATCCAAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCTAATGGAGAGTTCATAATGAGAAGAACTAATCCAAAGAGGAAGAAGAAGTTCAT
*
1161852 AATGAGAA-TAATTTGTTCAACCTTGC
66 AATGAGAAGAAATTT-TTCAACCTTGC
* * *
1161878 ATCAACATTT-TCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCA
1 ATCAACATTTCT-AATGGAGAGTTCATAATGAGAAGAACTAATCCAAAGAGGAAGAAGAAGTTCA
1161942 TAATGAGAAGAAATTTTTCAACCTTG
65 TAATGAGAAGAAATTTTTCAACCTTG
1161968 GTTCGATTCC
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
90 1 0.01
91 78 0.93
92 5 0.06
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (91 bp):
ATCAACATTTCTAATGGAGAGTTCATAATGAGAAGAACTAATCCAAAGAGGAAGAAGAAGTTCAT
AATGAGAAGAAATTTTTCAACCTTGC
Found at i:1162348 original size:3 final size:3
Alignment explanation
Indices: 1162340--1162391 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
1162330 TAAAACTTAA
* * *
1162340 TAT TAT TA- TAT TAT TAT AAT TAT AAT TAT AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1162387 TAT TA
1 TAT TA
1162392 AGTGTGTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1162477 original size:22 final size:24
Alignment explanation
Indices: 1162434--1162478 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1162424 AAAGCCTCTC
1162434 CCAAGACCCAATTACAACATCCAA
1 CCAAGACCCAATTACAACATCCAA
*
1162458 CCAAG-CCCAA-TACAAGATCCA
1 CCAAGACCCAATTACAACATCCA
1162479 GCAGACCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 5 0.25
24 5 0.25
ACGTcount: A:0.44, C:0.38, G:0.07, T:0.11
Consensus pattern (24 bp):
CCAAGACCCAATTACAACATCCAA
Found at i:1172493 original size:29 final size:29
Alignment explanation
Indices: 1172425--1172492 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
1172415 TTTTTTATCT
* *
1172425 AATTAAGTTATCAAATAAAAAAATTAAATT
1 AATTAA-TTTTCAAATAAAAAAATTAAATC
*
1172455 AATTAATTTTCAAAT-AAAAAATTACATC
1 AATTAATTTTCAAATAAAAAAATTAAATC
*
1172483 AATTATTTTT
1 AATTAATTTT
1172493 TTATTTACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 20 0.59
29 8 0.24
30 6 0.18
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (29 bp):
AATTAATTTTCAAATAAAAAAATTAAATC
Found at i:1173376 original size:14 final size:12
Alignment explanation
Indices: 1173346--1173387 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 12
1173336 TAAATAGATG
1173346 TAAA-AAAATCA
1 TAAATAAAATCA
1173357 TAAATAAAATCAA
1 TAAATAAAATC-A
1173370 TACAATAAAATCCA
1 TA-AATAAAAT-CA
1173384 TAAA
1 TAAA
1173388 AAACTACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.15
12 6 0.22
13 5 0.19
14 11 0.41
15 1 0.04
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAATAAAATCA
Found at i:1173493 original size:75 final size:74
Alignment explanation
Indices: 1173371--1173525 Score: 206
Period size: 75 Copynumber: 2.1 Consensus size: 74
1173361 TAAAATCAAT
* *
1173371 ACAATAAAATCCATAAAAAACTACAATATTAAAATGTCAAATCTCAAGA-TTCAAACCACAA-TA
1 ACAATAAAATCCATAAAAAACCACAATATTAAAATGTAAAATCTCAAGACTT-AAACCA-AATTA
1173434 TTAACTCTAGA
64 TTAACTCTAGA
* * *
1173445 ACAATAAAATCTATAAACAAACCATAATATTAAAGTGTAAAATCTCAAGACTTAAACCAAATTAT
1 ACAATAAAATCCATAAA-AAACCACAATATTAAAATGTAAAATCTCAAGACTTAAACCAAATTAT
* *
1173510 TAAGTTTAGA
65 TAACTCTAGA
1173520 ACAATA
1 ACAATA
1173526 TTAAACAATA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
74 18 0.25
75 51 0.72
76 2 0.03
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (74 bp):
ACAATAAAATCCATAAAAAACCACAATATTAAAATGTAAAATCTCAAGACTTAAACCAAATTATT
AACTCTAGA
Found at i:1173829 original size:14 final size:14
Alignment explanation
Indices: 1173812--1173841 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1173802 TAATAAATTT
*
1173812 GAGTTAAGTTATTC
1 GAGTCAAGTTATTC
1173826 GAGTCAAGTTATTC
1 GAGTCAAGTTATTC
1173840 GA
1 GA
1173842 ATTTCTATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (14 bp):
GAGTCAAGTTATTC
Found at i:1173920 original size:2 final size:2
Alignment explanation
Indices: 1173913--1173945 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1173903 TTCGACTTTC
1173913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1173946 TCTTTTCACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1174148 original size:20 final size:21
Alignment explanation
Indices: 1174123--1174170 Score: 89
Period size: 20 Copynumber: 2.3 Consensus size: 21
1174113 AGTCTAAATT
1174123 GAGTAAAATGAAAAGTTAA-G
1 GAGTAAAATGAAAAGTTAAGG
1174143 GAGTAAAATGAAAAGTTAAGG
1 GAGTAAAATGAAAAGTTAAGG
1174164 GAGTAAA
1 GAGTAAA
1174171 TAAAAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.19
Consensus pattern (21 bp):
GAGTAAAATGAAAAGTTAAGG
Found at i:1174178 original size:21 final size:20
Alignment explanation
Indices: 1174123--1174176 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1174113 AGTCTAAATT
*
1174123 GAGTAAAATGAAAAGTTAAG
1 GAGTAAAATAAAAAGTTAAG
*
1174143 GAGTAAAATGAAAAGTTAAGG
1 GAGTAAAATAAAAAGTTAA-G
1174164 GAGT-AAATAAAAA
1 GAGTAAAATAAAAA
1174177 AGAGTACCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (20 bp):
GAGTAAAATAAAAAGTTAAG
Found at i:1176853 original size:24 final size:26
Alignment explanation
Indices: 1176821--1176869 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1176811 TTAACAGTAT
*
1176821 ATGTTAAGA-CGGA-GAAGAAATTGC
1 ATGTCAAGAGCGGATGAAGAAATTGC
*
1176845 ATGTCAAGAGGGGATGAAGAAATTG
1 ATGTCAAGAGCGGATGAAGAAATTG
1176870 TTTGATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.41, C:0.06, G:0.33, T:0.20
Consensus pattern (26 bp):
ATGTCAAGAGCGGATGAAGAAATTGC
Found at i:1178931 original size:60 final size:60
Alignment explanation
Indices: 1178817--1178932 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
1178807 AGATTAGGGT
* * * *
1178817 TGAAATTAGAATATTCAAAAGTGTAAGTACTAATTTCGAATAAGAGTCCTAGTTTGAGAA
1 TGAAATTAGAATATTCAAAAGTGTAAGGACCAATTTAGAATAAGAGTACTAGTTTGAGAA
* *
1178877 TGAAATTAGAATATTTAAAAGT-TGAAGGACCAATTTAGAATGAGAGTTAC-AGTTTG
1 TGAAATTAGAATATTCAAAAGTGT-AAGGACCAATTTAGAATAAGAG-TACTAGTTTG
1178933 GGGATGCAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 1 0.02
60 45 0.94
61 2 0.04
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (60 bp):
TGAAATTAGAATATTCAAAAGTGTAAGGACCAATTTAGAATAAGAGTACTAGTTTGAGAA
Found at i:1187331 original size:119 final size:117
Alignment explanation
Indices: 1187145--1187378 Score: 389
Period size: 120 Copynumber: 2.0 Consensus size: 117
1187135 CATAAATAAC
*
1187145 TTAATATACACATCTCTGGTTTTTCTTAATTTTAAATTAGATTAATAAATTTCATTTATGAATGA
1 TTAATATACACATCTCTAGTTTTTCTTAATTTTAAATTAGATTAATAAATTTCATTTATGAATGA
1187210 ATTTCAATTGGTA-GAACTTTTACCTAAATAGTGATAATAATAATAATGATT
66 ATTTCAATTGGTATGAACTTTTACCTAAATAGTGATAATAATAATAATGATT
*
1187261 TTAATATACACATCTCTAGTTTTTTTTAAAATTTTAAATTAGATTAATAAAATTTCATTTATGAA
1 TTAATATACACATCTCTAGTTTTTCTT--AATTTTAAATTAGATTAAT-AAATTTCATTTATGAA
* * *
1187326 TGAATTTCTATTGGTATGGACTTTTACCTAAATAGTTATAATAATAATAATGA
63 TGAATTTCAATTGGTATGAACTTTTACCTAAATAGTGATAATAATAATAATGA
1187379 AATATAAAAA
Statistics
Matches: 109, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
116 25 0.23
118 19 0.17
119 31 0.28
120 34 0.31
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.44
Consensus pattern (117 bp):
TTAATATACACATCTCTAGTTTTTCTTAATTTTAAATTAGATTAATAAATTTCATTTATGAATGA
ATTTCAATTGGTATGAACTTTTACCTAAATAGTGATAATAATAATAATGATT
Found at i:1188348 original size:61 final size:61
Alignment explanation
Indices: 1188251--1188374 Score: 212
Period size: 61 Copynumber: 2.0 Consensus size: 61
1188241 AATCATAACT
*
1188251 TTTTTTTTTGATAAAAGGGTAATTTTACTCTAGTAATAAACTCAATTTATCACTCTCGCCC
1 TTTTTTTTTGATAAAAGGGTAATTTTACTCTAGTAATAAACTCAATTTATCACTCTCACCC
* * *
1188312 TTTTTTTTTGGTAAAAGGGTAATTTTACTCTTGTAATAGACTCAATTTATCACTCTCACCC
1 TTTTTTTTTGATAAAAGGGTAATTTTACTCTAGTAATAAACTCAATTTATCACTCTCACCC
1188373 TT
1 TT
1188375 ATAGTATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.44
Consensus pattern (61 bp):
TTTTTTTTTGATAAAAGGGTAATTTTACTCTAGTAATAAACTCAATTTATCACTCTCACCC
Found at i:1193014 original size:18 final size:18
Alignment explanation
Indices: 1192991--1193038 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1192981 AAATTGTCCT
*
1192991 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
1193009 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
1193026 TATTTATATATTT
1 TA-TTATATATTT
1193039 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:1195602 original size:19 final size:20
Alignment explanation
Indices: 1195561--1195603 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1195551 CAAAACTTTA
1195561 GATTTTAAAAATGCAAAGAAT
1 GATTTTAAAAAT-CAAAGAAT
* *
1195582 GATTTTAATAAT-AAAGGAT
1 GATTTTAAAAATCAAAGAAT
1195601 GAT
1 GAT
1195604 ACATTTATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (20 bp):
GATTTTAAAAATCAAAGAAT
Found at i:1198334 original size:27 final size:27
Alignment explanation
Indices: 1198269--1198484 Score: 126
Period size: 27 Copynumber: 7.7 Consensus size: 27
1198259 AATATCCATC
* **
1198269 ATTCAACTATTAATATCCATCATATTA
1 ATTCAACTATTGATATTAATCATATTA
* *
1198296 ATTCAAATATTGATATTAATCACATTA
1 ATTCAACTATTGATATTAATCATATTA
* * *
1198323 ATTCAACTATTGACATTATTCATATTT
1 ATTCAACTATTGATATTAATCATATTA
* ****
1198350 CTTTTTGTATTGATATTAATCATATTA
1 ATTCAACTATTGATATTAATCATATTA
* * * *
1198377 ATTAAAATATATCGTCAATAAATATCCATAATATTA
1 ATTCAACTAT-T-G---AT--AT-T-AATCATATTA
* *
1198413 ATTCAATTATTGATATTAATCGTATTA
1 ATTCAACTATTGATATTAATCATATTA
** ** * *
1198440 ATTTTACTATTGATATTGTTCACATTC
1 ATTCAACTATTGATATTAATCATATTA
1198467 ATTCAACTATTGATATTA
1 ATTCAACTATTGATATTA
1198485 TCCATAATAT
Statistics
Matches: 139, Mismatches: 41, Indels: 18
0.70 0.21 0.09
Matches are distributed among these distances:
27 109 0.78
28 2 0.01
29 3 0.02
31 2 0.01
32 2 0.01
34 3 0.02
35 2 0.01
36 16 0.12
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (27 bp):
ATTCAACTATTGATATTAATCATATTA
Found at i:1201566 original size:38 final size:38
Alignment explanation
Indices: 1201513--1201588 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
1201503 TTCAACCACC
* * *
1201513 AACCACTAACTTACTCGGGTTATTAATGGATAATTAAT
1 AACCACCAACCTACTCGGGTTATTAATGAATAATTAAT
1201551 AACCACCAACCTACTCGGGTTATTAATGAATAATTAAT
1 AACCACCAACCTACTCGGGTTATTAATGAATAATTAAT
1201589 TACTGGTGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (38 bp):
AACCACCAACCTACTCGGGTTATTAATGAATAATTAAT
Found at i:1201613 original size:13 final size:13
Alignment explanation
Indices: 1201595--1201641 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
1201585 TAATTACTGG
1201595 TGTCATTATTTTT
1 TGTCATTATTTTT
**
1201608 TGTCATTATAATT
1 TGTCATTATTTTT
**
1201621 AAT-ATTATTTTT
1 TGTCATTATTTTT
1201633 TGTCATTAT
1 TGTCATTAT
1201642 AATAAATATT
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (13 bp):
TGTCATTATTTTT
Found at i:1201627 original size:25 final size:25
Alignment explanation
Indices: 1201599--1201657 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
1201589 TACTGGTGTC
*
1201599 ATTATTTTTTGTCATTATAATTAAT
1 ATTATTTTTTGTCATTATAATAAAT
1201624 ATTATTTTTTGTCATTATAATAAAT
1 ATTATTTTTTGTCATTATAATAAAT
1201649 ATTATTTTT
1 ATTATTTTT
1201658 CTACTACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (25 bp):
ATTATTTTTTGTCATTATAATAAAT
Found at i:1205142 original size:15 final size:15
Alignment explanation
Indices: 1205101--1205143 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
1205091 AACCATGCAT
*
1205101 GGGTTTTGAAACCGG
1 GGGTTTTGAAATCGG
1205116 GGGTTTTGAAATCGG
1 GGGTTTTGAAATCGG
*
1205131 GGGTTTAGAAATC
1 GGGTTTTGAAATC
1205144 AATCAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.23, C:0.09, G:0.37, T:0.30
Consensus pattern (15 bp):
GGGTTTTGAAATCGG
Found at i:1205733 original size:17 final size:17
Alignment explanation
Indices: 1205711--1205748 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1205701 CGACGTGAGA
1205711 AAATTATCTACGAGCGC
1 AAATTATCTACGAGCGC
*
1205728 AAATTATCTACGATCGC
1 AAATTATCTACGAGCGC
1205745 AAAT
1 AAAT
1205749 CGCGTATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (17 bp):
AAATTATCTACGAGCGC
Found at i:1209374 original size:30 final size:29
Alignment explanation
Indices: 1209307--1209376 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
1209297 ATTTTGATTT
* * *
1209307 CATGATATCTGATTTACCGTATGTATTGG
1 CATGATATCTAATTTACCGTATCTATTGA
** *
1209336 GTTGATATCTAATTTACCGTATACTTTTGA
1 CATGATATCTAATTTACCGTAT-CTATTGA
1209366 CATGATATCTA
1 CATGATATCTA
1209377 GTTAATGTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 19 0.59
30 13 0.41
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (29 bp):
CATGATATCTAATTTACCGTATCTATTGA
Found at i:1214901 original size:34 final size:33
Alignment explanation
Indices: 1214814--1214904 Score: 85
Period size: 36 Copynumber: 2.6 Consensus size: 33
1214804 GTACACTAGT
* * *
1214814 ATATATATTCCATTGTGATTACACTTTGTGTGC
1 ATATATATTCGATTGTGATAACACTGTGTGTGC
*
1214847 ATATTGTGATTTCCGA-TGTGATAACACTGTGTGTGC
1 ATA-TAT-A-TT-CGATTGTGATAACACTGTGTGTGC
*
1214883 TTATATATTCTGATTGTGATAA
1 ATATATATTC-GATTGTGATAA
1214905 TAGCACTGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
32 1 0.02
33 7 0.15
34 11 0.24
35 3 0.07
36 22 0.48
37 2 0.04
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (33 bp):
ATATATATTCGATTGTGATAACACTGTGTGTGC
Found at i:1226253 original size:64 final size:65
Alignment explanation
Indices: 1226161--1226315 Score: 190
Period size: 65 Copynumber: 2.4 Consensus size: 65
1226151 TACACTGGGG
*
1226161 TGTGCATCGGTGCAC-AAAT-CTACTTCGATGTTTCAAAATAGCCA-AAGTGCATCGATGCATGT
1 TGTGCATCGGTGCACTAAATGC-A-TTCGATGTTTCAAAATAGCCAGAAGTGCATCGATGCATGA
1226223 CT
64 CT
* * * *** **
1226225 TGTGTATCGGTTCACTGAATGCATTCGATGTTTCAAAATATTTAGGGGTGCATCGATGCATGACT
1 TGTGCATCGGTGCACTAAATGCATTCGATGTTTCAAAATAGCCAGAAGTGCATCGATGCATGACT
1226290 TGTGCATCGGTGCACTAAATGCATTC
1 TGTGCATCGGTGCACTAAATGCATTC
1226316 AAAATTCAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 31 0.41
65 44 0.58
66 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (65 bp):
TGTGCATCGGTGCACTAAATGCATTCGATGTTTCAAAATAGCCAGAAGTGCATCGATGCATGACT
Found at i:1226324 original size:64 final size:65
Alignment explanation
Indices: 1226206--1226363 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 65
1226196 AAATAGCCAA
* * * * *** * *
1226206 AGTGCATCGATGCATGTCTTGTGTATCGGTTCACTGAATGCATTCGATGTTTCAAAATATTTAGG
1 AGTGCATCGATGCATGACTTGTGCATCGGTGCACTAAATGCATTCGAAAATTCAAAATAATTAAG
* **
1226271 GGTGCATCGATGCATGACTTGTGCATCGGTGCACTAAATGCATTC-AAAATTCAATTTAATTAAG
1 AGTGCATCGATGCATGACTTGTGCATCGGTGCACTAAATGCATTCGAAAATTCAAAATAATTAAG
*
1226335 AGTGCATCGATGCATGAACTAGTGCATCG
1 AGTGCATCGATGCATG-ACTTGTGCATCG
1226364 ATTTATTCCT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
64 27 0.35
65 51 0.65
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (65 bp):
AGTGCATCGATGCATGACTTGTGCATCGGTGCACTAAATGCATTCGAAAATTCAAAATAATTAAG
Found at i:1232124 original size:22 final size:21
Alignment explanation
Indices: 1232082--1232121 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1232072 AAGACTATTT
1232082 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
1232103 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
1232122 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:1237539 original size:30 final size:29
Alignment explanation
Indices: 1237492--1237559 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
1237482 TTAAATGTTA
*
1237492 TAATAAAATATTTATTATGAT-AATTAAAT
1 TAATAAAATACTTATTAT-ATAAATTAAAT
* *
1237521 TAATAAATATACTTATTATATAAATTTATT
1 TAATAAA-ATACTTATTATATAAATTAAAT
1237551 TAATAAAAT
1 TAATAAAAT
1237560 TGTTTAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.32
30 23 0.68
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
TAATAAAATACTTATTATATAAATTAAAT
Found at i:1237663 original size:23 final size:24
Alignment explanation
Indices: 1237621--1237674 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
1237611 CAATGATTAA
1237621 ATGTAAATTAATATAATTTAATTT
1 ATGTAAATTAATATAATTTAATTT
*
1237645 ATGTAAATT-ATATAGTTTAATTT
1 ATGTAAATTAATATAATTTAATTT
1237668 ATGTAAA
1 ATGTAAA
1237675 GAAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAATATAATTTAATTT
Found at i:1239585 original size:2 final size:2
Alignment explanation
Indices: 1239580--1239740 Score: 172
Period size: 2 Copynumber: 81.0 Consensus size: 2
1239570 TTTATTACTT
1239580 TA TA TA TA TA TA 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
* *
1239622 TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA -A TT TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1239661 CTA TA TA CTA TA TA TA TA -A T- TA TA -A TT TA TA AA CTA TA TA
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
1239701 CTT TA TA TA GTT TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1239741 AATTGTAGTT
Statistics
Matches: 134, Mismatches: 14, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
1 6 0.04
2 121 0.90
3 7 0.05
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1239722 original size:13 final size:13
Alignment explanation
Indices: 1239704--1239898 Score: 88
Period size: 13 Copynumber: 15.1 Consensus size: 13
1239694 CTATATACTT
1239704 TATATAGTTTATA
1 TATATAGTTTATA
*
1239717 TATATA-TATATA
1 TATATAGTTTATA
**
1239729 TATATA-AATATA
1 TATATAGTTTATA
* *
1239741 AATTGTAGTTTATAAA
1 TA-TATAGTTTAT--A
*
1239757 CTATATACTTT-T-
1 -TATATAGTTTATA
1239769 TA--TAGTTTATACA
1 TATATAGTTTAT--A
*
1239782 TATATAATTTATA
1 TATATAGTTTATA
*
1239795 TACATAGTTTATA
1 TATATAGTTTATA
1239808 TATATAGTTCATATA
1 TATATAGTT--TATA
* *
1239823 AACATAGTTTATA
1 TATATAGTTTATA
*
1239836 TATATAGCTTATA
1 TATATAGTTTATA
1239849 -ATA-A--TTATA
1 TATATAGTTTATA
* *
1239858 TAGTTTA-TAATATA
1 TA-TATAGT-TTATA
* *
1239872 AATATAGTTTACA
1 TATATAGTTTATA
1239885 TATATAGTTTATA
1 TATATAGTTTATA
1239898 T
1 T
1239899 TTAAACTTAC
Statistics
Matches: 136, Mismatches: 27, Indels: 38
0.68 0.13 0.19
Matches are distributed among these distances:
9 10 0.07
10 2 0.01
11 4 0.03
12 21 0.15
13 63 0.46
14 9 0.07
15 19 0.14
16 7 0.05
17 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:1239802 original size:28 final size:28
Alignment explanation
Indices: 1239770--1239871 Score: 93
Period size: 28 Copynumber: 3.5 Consensus size: 28
1239760 TATACTTTTT
*
1239770 ATAGTTTATACATATATAATT-TATATAC
1 ATAGTTTATA-ATATATAATTATATAAAC
*
1239798 ATAGTTTAT-ATATATAGTTCATATAAAC
1 ATAGTTTATAATATATAATT-ATATAAAC
* *
1239826 ATAGTTTAT-ATATATAGCTTATAATAATTAT
1 ATAGTTTATAATATATA-ATTAT-ATAA--AC
1239857 ATAGTTTATAATATA
1 ATAGTTTATAATATA
1239872 AATATAGTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
26 9 0.14
28 33 0.52
29 6 0.10
31 10 0.16
32 5 0.08
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (28 bp):
ATAGTTTATAATATATAATTATATAAAC
Found at i:1239876 original size:18 final size:18
Alignment explanation
Indices: 1239832--1239882 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
1239822 AAACATAGTT
*
1239832 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
1239850 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
1239868 TATAAATATAGTTTA
1 TATATATATAGTTTA
1239883 CATATATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:1240151 original size:11 final size:11
Alignment explanation
Indices: 1240134--1240169 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1240124 TAGTTTATTA
1240134 ATAAACTACAT
1 ATAAACTACAT
*
1240145 GTAAACTACAT
1 ATAAACTACAT
*
1240156 ATAAACTATAT
1 ATAAACTACAT
1240167 ATA
1 ATA
1240170 TTATATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (11 bp):
ATAAACTACAT
Found at i:1240189 original size:21 final size:21
Alignment explanation
Indices: 1240162--1240218 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
1240152 ACATATAAAC
* * *
1240162 TATATATATTATATATTTGTC
1 TATATATATTATATATATATA
*
1240183 TTTATATACTTTATATATATATA
1 TATATATA--TTATATATATATA
1240206 TATATATATTATA
1 TATATATATTATA
1240219 AGTGTTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 12 0.41
23 17 0.59
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
TATATATATTATATATATATA
Found at i:1242074 original size:21 final size:23
Alignment explanation
Indices: 1242049--1242090 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1242039 CAACCATCTA
*
1242049 AAACTAA-AA-ACTTTATTTTTT
1 AAACTAATAATACTTAATTTTTT
1242070 AAACTAATAATACTTAATTTT
1 AAACTAATAATACTTAATTTT
1242091 AATCAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (23 bp):
AAACTAATAATACTTAATTTTTT
Found at i:1242125 original size:18 final size:18
Alignment explanation
Indices: 1242102--1242138 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1242092 ATCAATAAAG
1242102 GAGATATGATAAAATTAT
1 GAGATATGATAAAATTAT
1242120 GAGATATGATAAAATTAT
1 GAGATATGATAAAATTAT
1242138 G
1 G
1242139 GGTAAAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (18 bp):
GAGATATGATAAAATTAT
Found at i:1244622 original size:2 final size:2
Alignment explanation
Indices: 1244615--1244649 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1244605 AAAACTGAGT
1244615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1244650 TGATTGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1251773 original size:22 final size:20
Alignment explanation
Indices: 1251741--1251791 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1251731 GATTCAACCA
*
1251741 GTATCGGTACCCAAGAAAAGGG
1 GTATCGATA-CCAAGAAAA-GG
* *
1251763 GTATCGATACCATGGAAAGG
1 GTATCGATACCAAGAAAAGG
1251783 GTATCGATA
1 GTATCGATA
1251792 TCAGTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 11 0.42
21 7 0.27
22 8 0.31
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (20 bp):
GTATCGATACCAAGAAAAGG
Found at i:1251934 original size:95 final size:93
Alignment explanation
Indices: 1251759--1251965 Score: 222
Period size: 95 Copynumber: 2.2 Consensus size: 93
1251749 ACCCAAGAAA
* * * *
1251759 AGGGGTATCGATACCATGGAAAGGGTATCGATATCAGTAAATATCGAATCTAATTTGGGTATCGA
1 AGGGGTATCGATACCATGGAAAGGGTATCGATATCAGGAAATATCAAAGCTAATTTCGGTATCGA
1251824 TACCTAGAGGAGGTATCTG-TACCATAGCAT
66 TACCTAGAGGAGGTATC-GATACCATA--AT
** ** *
1251854 AGGGGTATCGATACCATGGTGAGGGTATCGATA-CTAGGCCATATCAAAGCTAATTTCGGTATTG
1 AGGGGTATCGATACCATGGAAAGGGTATCGATATC-AGGAAATATCAAAGCTAATTTCGGTATCG
* * *
1251918 ATACATTA-AGGGGGTATCGATACCCTAAT
65 ATAC-CTAGAGGAGGTATCGATACCATAAT
1251947 AGGGTAGTATCGATACCAT
1 AGGG--GTATCGATACCAT
1251966 AAGCAGGGGT
Statistics
Matches: 95, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
93 6 0.06
94 2 0.02
95 85 0.89
96 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (93 bp):
AGGGGTATCGATACCATGGAAAGGGTATCGATATCAGGAAATATCAAAGCTAATTTCGGTATCGA
TACCTAGAGGAGGTATCGATACCATAAT
Found at i:1251959 original size:22 final size:21
Alignment explanation
Indices: 1251928--1251988 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
1251918 ATACATTAAG
* *
1251928 GGGGTATCGATACCCTAA-TA
1 GGGGTATCGATACCATAAGCA
1251948 GGGTAGTATCGATACCATAAGCA
1 GGG--GTATCGATACCATAAGCA
1251971 GGGGTATCGATACC-TAAG
1 GGGGTATCGATACCATAAG
1251989 GGTCAGAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 7 0.19
21 11 0.31
22 14 0.39
23 4 0.11
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (21 bp):
GGGGTATCGATACCATAAGCA
Found at i:1251979 original size:21 final size:20
Alignment explanation
Indices: 1251928--1251988 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 20
1251918 ATACATTAAG
*
1251928 GGGGTATCGATACCCTAA-TA
1 GGGGTATCGATA-CCTAAGCA
1251948 GGGTAGTATCGATACCATAAGCA
1 GGG--GTATCGATACC-TAAGCA
1251971 GGGGTATCGATACCTAAG
1 GGGGTATCGATACCTAAG
1251989 GGTCAGAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 7 0.19
21 13 0.36
22 12 0.33
23 4 0.11
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (20 bp):
GGGGTATCGATACCTAAGCA
Found at i:1252391 original size:57 final size:57
Alignment explanation
Indices: 1252329--1252926 Score: 955
Period size: 57 Copynumber: 10.5 Consensus size: 57
1252319 GTGCAAAATA
* *
1252329 TAAGAAATCATATTAAGTGTATGAATTTTAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
1252386 TAAGAAATCATACTAAGTGTATGGATTTCAGATAGGGCATTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1252443 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1252500 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATC-CTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTA-CGCTAAAATGT
* * *
1252557 TAAGAAATCATACTAAGTGTATGAATTTGAGATAGGGCATTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * *
1252614 TAAGAAATCATACTAAGTGTATGGATTTCAGACAGGGCGTTTCGTACGCTAAAGTAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
1252671 TAAGAAATCATACTCAGTGTATGAATTTCAGGTAGGGCGTTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1252728 TAAGAAATCATACTAAGTGTATAAATTTCAGATAGGGCGTTTTGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
1252785 TAAGAAATCATACTAAGTGTATGAATTTTAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
1252842 TAAGAAATCATACTAAGTGTATTAATTTCAGATAGGGCGTTTCTTATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1252899 TAATAAATCATACTAAGTGTAGGAATTT
1 TAAGAAATCATACTAAGTGTATGAATTT
1252927 TAATTTATTG
Statistics
Matches: 495, Mismatches: 44, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
56 1 0.00
57 494 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:1256757 original size:21 final size:21
Alignment explanation
Indices: 1256731--1256782 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1256721 GTAGGGGTAT
*
1256731 CGATACCCTATGGAATAGTAC
1 CGATACCCTATAGAATAGTAC
1256752 CGATACCCTATAGAATAGTAC
1 CGATACCCTATAGAATAGTAC
1256773 CGATACCCTA
1 CGATACCCTA
1256783 GGCAAGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (21 bp):
CGATACCCTATAGAATAGTAC
Found at i:1257459 original size:57 final size:57
Alignment explanation
Indices: 1257396--1257878 Score: 806
Period size: 57 Copynumber: 8.5 Consensus size: 57
1257386 GTGTCAAATA
* * * *
1257396 TAAGAAATCATACTAAGTGCATGGATTTCATATAGGGCGTTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
1257453 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
1257510 TAAGAAATCATACTAAGTGTATGAATTTCAGATA-GGCATTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1257566 TAAGAAATCATACTAAGTGTATGAATTTTAGATAGGGCGTTTCGTATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
1257623 TAAGAAATCGTACTAAGTGTATGAATTTCATATAGGGCGTTTTGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
1257680 TAAGAAATCATACTAAGTGTATAAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1257737 TAAGAAATCATACTAAGTGTATGAATTTCAGATAAGGCGTTTCATACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1257794 TAAGAAATCATACTAAGTGTATGAATTTCATATAGGGCCTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
1257851 TAAGAAATCATACTAAGTGAATGAATTT
1 TAAGAAATCATACTAAGTGTATGAATTT
1257879 TGGTATTTGA
Statistics
Matches: 400, Mismatches: 25, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
56 53 0.13
57 347 0.87
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:1264815 original size:20 final size:22
Alignment explanation
Indices: 1264790--1264829 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1264780 AGTCGTATAT
1264790 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1264810 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1264830 TCTGTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1265291 original size:21 final size:20
Alignment explanation
Indices: 1265267--1265320 Score: 85
Period size: 18 Copynumber: 2.8 Consensus size: 20
1265257 AAAAAGGTAG
1265267 CAATTGTTTACAAAATGATAC
1 CAATTGTTTA-AAAATGATAC
1265288 CAATTG-TTAAAAA-GATAC
1 CAATTGTTTAAAAATGATAC
1265306 CAATTGTTTAAAAAT
1 CAATTGTTTAAAAAT
1265321 ATATGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.35
19 11 0.35
20 3 0.10
21 6 0.19
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.33
Consensus pattern (20 bp):
CAATTGTTTAAAAATGATAC
Found at i:1265304 original size:18 final size:19
Alignment explanation
Indices: 1265257--1265319 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
1265247 ATGTTTAATG
* *
1265257 AAAAAGGTAGCAATTGTTT
1 AAAAAGATACCAATTGTTT
1265276 ACAAAATGATACCAATTG-TT
1 A-AAAA-GATACCAATTGTTT
1265296 AAAAAGATACCAATTGTTT
1 AAAAAGATACCAATTGTTT
1265315 AAAAA
1 AAAAA
1265320 TATATGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 11 0.28
19 12 0.31
20 7 0.18
21 9 0.23
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTT
Found at i:1268473 original size:20 final size:20
Alignment explanation
Indices: 1268448--1268485 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1268438 GAGCCTTCAT
*
1268448 GGGGTATTGATACCCAGGCA
1 GGGGTATCGATACCCAGGCA
*
1268468 GGGGTATCGGTACCCAGG
1 GGGGTATCGATACCCAGG
1268486 GTATGGATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.39, T:0.18
Consensus pattern (20 bp):
GGGGTATCGATACCCAGGCA
Found at i:1268495 original size:35 final size:33
Alignment explanation
Indices: 1268449--1268514 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
1268439 AGCCTTCATG
*
1268449 GGGTATTGATACCCAGGCAGGGGTATCGGTACCCA
1 GGGTATGGATACCCAGG--GGGGTATCGGTACCCA
**
1268484 GGGTATGGATACCCCTGGGGGTATCGGTACC
1 GGGTATGGATACCCAGGGGGGTATCGGTACC
1268515 TCTTTGCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 14 0.50
35 14 0.50
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.21
Consensus pattern (33 bp):
GGGTATGGATACCCAGGGGGGTATCGGTACCCA
Found at i:1269688 original size:19 final size:19
Alignment explanation
Indices: 1269660--1269708 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1269650 GCTAAAAATG
* *
1269660 GTATCGATAC-CAGGGGTCA
1 GTATCAATACTCA-GGGTAA
1269679 GTATCAATACTCAGGGTAA
1 GTATCAATACTCAGGGTAA
1269698 GTATCAATACT
1 GTATCAATACT
1269709 GAAGGCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (19 bp):
GTATCAATACTCAGGGTAA
Found at i:1271856 original size:14 final size:13
Alignment explanation
Indices: 1271839--1271928 Score: 117
Period size: 13 Copynumber: 6.7 Consensus size: 13
1271829 AGTCAACTCG
1271839 TTGACTTTGACCCA
1 TTGACTTTG-CCCA
* *
1271853 TTGACTTTGACCG
1 TTGACTTTGCCCA
*
1271866 TTGACTTTTGGCCA
1 TTGAC-TTTGCCCA
1271880 TTGACTTTGCCCA
1 TTGACTTTGCCCA
1271893 TTGACTTTTGCCCA
1 TTGAC-TTTGCCCA
*
1271907 TTGACTTTGCCCG
1 TTGACTTTGCCCA
1271920 TTGACTTTG
1 TTGACTTTG
1271929 ACCTAAAAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
13 35 0.51
14 33 0.49
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.41
Consensus pattern (13 bp):
TTGACTTTGCCCA
Found at i:1271880 original size:27 final size:27
Alignment explanation
Indices: 1271837--1271927 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
1271827 CGAGTCAACT
*
1271837 CGTTGAC-TTTGACCCATTGACTTTGAC
1 CGTTGACTTTTG-CCCATTGACTTTGCC
*
1271864 CGTTGACTTTTGGCCATTGACTTTGCC
1 CGTTGACTTTTGCCCATTGACTTTGCC
*
1271891 CATTGACTTTTGCCCATTGACTTTGCC
1 CGTTGACTTTTGCCCATTGACTTTGCC
1271918 CGTTGACTTT
1 CGTTGACTTT
1271928 GACCTAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 54 0.93
28 4 0.07
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.41
Consensus pattern (27 bp):
CGTTGACTTTTGCCCATTGACTTTGCC
Found at i:1279888 original size:33 final size:33
Alignment explanation
Indices: 1279845--1279907 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
1279835 CTTAGTACAG
1279845 ATGGTAGACACGACCTTATGTGTCATACGGATT
1 ATGGTAGACACGACCTTATGTGTCATACGGATT
*
1279878 ATGGTGGACACGACCTTATGTGTCATACGG
1 ATGGTAGACACGACCTTATGTGTCATACGG
1279908 GATAGCAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (33 bp):
ATGGTAGACACGACCTTATGTGTCATACGGATT
Found at i:1279989 original size:7 final size:7
Alignment explanation
Indices: 1279979--1280009 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1279969 GGCTATTGTC
1279979 TATGGTT
1 TATGGTT
1279986 TATGGTT
1 TATGGTT
1279993 TATGGTT
1 TATGGTT
*
1280000 TATAGTT
1 TATGGTT
1280007 TAT
1 TAT
1280010 TGTTAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (7 bp):
TATGGTT
Found at i:1287206 original size:28 final size:28
Alignment explanation
Indices: 1287168--1287222 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1287158 CTTCTCATCT
1287168 TCCTCCACCATATCTCTCTTCTTCTTCC
1 TCCTCCACCATATCTCTCTTCTTCTTCC
* *
1287196 TCCTCCTCCATGTCTCTCTTCTTCTTC
1 TCCTCCACCATATCTCTCTTCTTCTTC
1287223 ATCGAATGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.07, C:0.45, G:0.02, T:0.45
Consensus pattern (28 bp):
TCCTCCACCATATCTCTCTTCTTCTTCC
Found at i:1287943 original size:44 final size:44
Alignment explanation
Indices: 1287894--1287981 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
1287884 ATCCAACGTG
*
1287894 ACTTTCGGTCCTGCAATTGCCGTGGGGCCAATGAATTTTCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGCCAATGAATTTTCAATT
* * * *
1287938 ACTTTCGGTGCTGAAATTGTCGTGGGTCCAATGCATTTTCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGCCAATGAATTTTCAATT
1287982 GTTGCATTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (44 bp):
ACTTTCGGTCCTGAAATTGCCGTGGGGCCAATGAATTTTCAATT
Found at i:1289304 original size:18 final size:18
Alignment explanation
Indices: 1289278--1289312 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1289268 TCAAAAGGAC
*
1289278 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1289296 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1289313 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1292550 original size:28 final size:28
Alignment explanation
Indices: 1292507--1292561 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1292497 CTTCTCATCT
*
1292507 TCCTCCTCCATATCTCTCTTCTTCTTCC
1 TCCTCCTCAATATCTCTCTTCTTCTTCC
*
1292535 TCCTCCTCAATGTCTCTCTTCTTCTTC
1 TCCTCCTCAATATCTCTCTTCTTCTTC
1292562 ATCGAATGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.07, C:0.44, G:0.02, T:0.47
Consensus pattern (28 bp):
TCCTCCTCAATATCTCTCTTCTTCTTCC
Found at i:1293286 original size:45 final size:45
Alignment explanation
Indices: 1293236--1293325 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
1293226 ATCCAACGTG
*
1293236 ACTTTCGGTCCTGCAATTGCCGTGGGGGCCAATGAATTATCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
* * * * *
1293281 ACTTTCGGTGCTGAAATTGTCGTGGGGTCCAATGCATTTTCAATT
1 ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
1293326 GTTGCATTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (45 bp):
ACTTTCGGTCCTGAAATTGCCGTGGGGGCCAATGAATTATCAATT
Found at i:1294652 original size:18 final size:18
Alignment explanation
Indices: 1294626--1294660 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1294616 TCAAAAGGAC
*
1294626 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1294644 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1294661 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1297311 original size:33 final size:33
Alignment explanation
Indices: 1297269--1297331 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
1297259 ATTAGTACAG
1297269 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
1297302 ATGGTGGACACGACCTTATGTGTCATACGG
1 ATGGTGGACACGACCTTATGTGTCATACGG
1297332 GATAGCACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:1302242 original size:98 final size:98
Alignment explanation
Indices: 1302073--1302277 Score: 394
Period size: 98 Copynumber: 2.1 Consensus size: 98
1302063 TGCGTCGGGG
1302073 CTACTTTTTTCAGGGTATGAATATGATGCTTACTTCATTATCTGGAGATGCTGTTTACTTCTTGT
1 CTACTTTTTTCAGGGTATGAATATGATGCTTACTTCATTATCTGGAGATGCTGTTTACTTCTTGT
1302138 TTATGATGATGGAAGATTATTGAATGCTGCTTA
66 TTATGATGATGGAAGATTATTGAATGCTGCTTA
1302171 CTACTTTTTTCAGGGTATGAATATGATGCTTACTTCATTATCTGGAGATGCTGTTTACTTCTTGT
1 CTACTTTTTTCAGGGTATGAATATGATGCTTACTTCATTATCTGGAGATGCTGTTTACTTCTTGT
*
1302236 TTATGATGATGGAAGATTATTGAATGCTGTTTA
66 TTATGATGATGGAAGATTATTGAATGCTGCTTA
1302269 CTA-TTTTTT
1 CTACTTTTTT
1302278 GTTCTTATAG
Statistics
Matches: 106, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
97 6 0.06
98 100 0.94
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.46
Consensus pattern (98 bp):
CTACTTTTTTCAGGGTATGAATATGATGCTTACTTCATTATCTGGAGATGCTGTTTACTTCTTGT
TTATGATGATGGAAGATTATTGAATGCTGCTTA
Found at i:1303641 original size:2 final size:2
Alignment explanation
Indices: 1303636--1303680 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1303626 ATTAACACAC
* *
1303636 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT -T AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1303677 AT AT
1 AT AT
1303681 CAACAGGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1303885 original size:2 final size:2
Alignment explanation
Indices: 1303880--1303915 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
1303870 TTTTTTACAT
1303880 TA TA TA TA TGA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
1303916 ATTTTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1303956 original size:19 final size:19
Alignment explanation
Indices: 1303932--1303972 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1303922 AAAATATAAA
*
1303932 AATATA-TTTTTGGAGATAT
1 AATATAGTTTTT-GAAATAT
1303951 AATATAGTTTTTGAAATAT
1 AATATAGTTTTTGAAATAT
1303970 AAT
1 AAT
1303973 TTTGAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (19 bp):
AATATAGTTTTTGAAATAT
Found at i:1304013 original size:37 final size:37
Alignment explanation
Indices: 1303947--1304106 Score: 153
Period size: 37 Copynumber: 4.3 Consensus size: 37
1303937 ATTTTTGGAG
* * * **
1303947 ATATAATATAGTTTTTGAAATATAATTTTGAAAACAT
1 ATATTATATAGTTTTTAAAAAATGGTTTTGAAAACAT
** *
1303984 ATATTATATAGTTTTTTTAAAACGGTTTTGAAAACAT
1 ATATTATATAGTTTTTAAAAAATGGTTTTGAAAACAT
* * *
1304021 ATATAATATAGTTTTTGAAAAATGTTATTTTGAAAACAT
1 ATATTATATAGTTTTTAAAAAATG--GTTTTGAAAACAT
* *
1304060 ATA-TATATA-TGTTTAAAAAAATGGTTTTGAAAACGT
1 ATATTATATAGT-TTTTAAAAAATGGTTTTGAAAACAT
1304096 ATATATATATA
1 ATAT-TATATA
1304107 TAATCTTTAA
Statistics
Matches: 101, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
36 14 0.14
37 51 0.50
38 21 0.21
39 15 0.15
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (37 bp):
ATATTATATAGTTTTTAAAAAATGGTTTTGAAAACAT
Found at i:1304078 original size:36 final size:37
Alignment explanation
Indices: 1303971--1304105 Score: 121
Period size: 36 Copynumber: 3.6 Consensus size: 37
1303961 TTGAAATATA
**** *
1303971 ATTTTGAAAACATATAT-TATATAGTTTTTTTAAAACG
1 ATTTTGAAAACATATATATATAT-GTTTGAAAAAAATG
* * ** *
1304008 GTTTTGAAAACATATATAATATAGTTTTTGAAAAATGTT
1 ATTTTGAAAACATATAT-ATATA-TGTTTGAAAAAAATG
1304047 ATTTTGAAAACATATATATATATGTTT-AAAAAAATG
1 ATTTTGAAAACATATATATATATGTTTGAAAAAAATG
* *
1304083 GTTTTGAAAACGTATATATATAT
1 ATTTTGAAAACATATATATATAT
1304106 ATAATCTTTA
Statistics
Matches: 78, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
36 27 0.35
37 20 0.26
38 5 0.06
39 25 0.32
40 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (37 bp):
ATTTTGAAAACATATATATATATGTTTGAAAAAAATG
Found at i:1304144 original size:22 final size:23
Alignment explanation
Indices: 1304095--1304150 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
1304085 TTTGAAAACG
1304095 TATATATATATATAATCTTTAAA
1 TATATATATATATAATCTTTAAA
* *
1304118 AATATAT-TATATTAT-TTTGAAA
1 TATATATATATATAATCTTT-AAA
1304140 TATAT-TATATA
1 TATATATATATA
1304151 GTTTAATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.14
22 18 0.64
23 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATATATATATAATCTTTAAA
Found at i:1304994 original size:22 final size:22
Alignment explanation
Indices: 1304965--1305013 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1304955 CAACAACCAC
1304965 AACA-CGAAAAAGAATA-CAAAA
1 AACATCGAAAAA-AATAGCAAAA
* *
1304986 AACATCGAAATATATAGCAAAA
1 AACATCGAAAAAAATAGCAAAA
1305008 AACATC
1 AACATC
1305014 TCGCAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.63, C:0.16, G:0.08, T:0.12
Consensus pattern (22 bp):
AACATCGAAAAAAATAGCAAAA
Found at i:1309086 original size:34 final size:34
Alignment explanation
Indices: 1309043--1309112 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1309033 TTGAACAACT
1309043 GCCCAAGAGAGTGAATCCTGTTCCAGTAATTCTA
1 GCCCAAGAGAGTGAATCCTGTTCCAGTAATTCTA
1309077 GCCCAAGAGAGTGAATCCTGTTCCAGTAATTCTA
1 GCCCAAGAGAGTGAATCCTGTTCCAGTAATTCTA
1309111 GC
1 GC
1309113 TGAGACCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (34 bp):
GCCCAAGAGAGTGAATCCTGTTCCAGTAATTCTA
Found at i:1311697 original size:22 final size:22
Alignment explanation
Indices: 1311669--1311722 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
1311659 TATACCATTT
* *
1311669 CGGTGCATTCTACGTGGCACTA
1 CGGTGCATTCTACATGGAACTA
*
1311691 CGGTGCAATTCTACATGGAACTT
1 CGGTGC-ATTCTACATGGAACTA
*
1311714 CAGTGCATT
1 CGGTGCATT
1311723 TATAGGAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (22 bp):
CGGTGCATTCTACATGGAACTA
Done.