Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 56
Found at i:1093202 original size:46 final size:46
Alignment explanation
Indices: 1093134--1093247 Score: 185
Period size: 46 Copynumber: 2.5 Consensus size: 46
1093124 CAAAAAGCTA
*
1093134 CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
1 CCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
1093181 CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
1 CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
* *
1093227 CCTAAGG-CTTTGAAAACATCA
1 CCGAAGGTTTTTGAAAACATCA
1093248 AAAAGCTACC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 13 0.20
46 44 0.69
47 7 0.11
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (46 bp):
CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
Found at i:1093278 original size:31 final size:31
Alignment explanation
Indices: 1093235--1093309 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
1093225 ACCCTAAGGC
*
1093235 TTTGAAAACATCAAAAAGCTACCGAAGGCTT
1 TTTGGAAACATCAAAAAGCTACCGAAGGCTT
*
1093266 TTTGGAAACATCAAAAAGCTCCCGAAGGCTT
1 TTTGGAAACATCAAAAAGCTACCGAAGGCTT
1093297 TTTGGAAACATCA
1 TTTGGAAACATCA
1093310 TGCACTGAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (31 bp):
TTTGGAAACATCAAAAAGCTACCGAAGGCTT
Found at i:1093374 original size:107 final size:106
Alignment explanation
Indices: 1093180--1093385 Score: 376
Period size: 107 Copynumber: 1.9 Consensus size: 106
1093170 TTACAGATGA
*
1093180 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
1093245 TCAAAAAGCTACCGAAGGCTTTTTGGAAACATCAAAAAGCT
66 TCAAAAAGCTACCGAAGGCTTTTTGGAAACATCAAAAAGCT
* *
1093286 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1093351 ATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCA
65 ATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCA
1093386 TGCACTGAAG
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
106 8 0.08
107 88 0.92
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (106 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
TCAAAAAGCTACCGAAGGCTTTTTGGAAACATCAAAAAGCT
Found at i:1093429 original size:45 final size:46
Alignment explanation
Indices: 1093363--1093452 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 46
1093353 CAAAAAGCTA
*
1093363 CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
1 CCGAAGGC-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
*
1093410 CCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTATAGATG
1 CCGAAGGCTTTTGAAAACATCATGCACTGAAGGACTTACAGATG
1093453 TGGGAAATAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 34 0.83
47 7 0.17
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (46 bp):
CCGAAGGCTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
Found at i:1094591 original size:54 final size:54
Alignment explanation
Indices: 1094504--1094722 Score: 266
Period size: 54 Copynumber: 4.1 Consensus size: 54
1094494 TCAGAATAGC
* ** * * *
1094504 ATGTTCATAAAACATTTGACGGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTAGCTTCTGCTCAG
* * *
1094558 ATGTTCGTAAAATATTTGACAACACATTAATCCTTTCATGTAGTTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTAGCTTCTGCTCAG
* *
1094612 ATGTTTGT-AAACATTTGACAACACATTCAT-CTTCTCATGTGGCTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCCTT-TCATGTAGCTTCTGCTCAG
* * * *
1094665 ATGTT-GTAAAATA-TTGATAACACATTCATCCTTTCCTGTAGTTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTAGCTTCTGCTCAG
1094717 ATGTTC
1 ATGTTC
1094723 AAGAAAATTC
Statistics
Matches: 142, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
52 41 0.29
53 49 0.35
54 52 0.37
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (54 bp):
ATGTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTAGCTTCTGCTCAG
Found at i:1094694 original size:52 final size:52
Alignment explanation
Indices: 1094528--1094721 Score: 257
Period size: 52 Copynumber: 3.7 Consensus size: 52
1094518 TTTGACGGCG
* *
1094528 CATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTTCGTAAAATATTTGACAACA
1 CATTCATCCTTTCATGTAGCTTCTGCTCAGATGTT-GTAAAATA-TTGACAACA
* *
1094582 CATTAATCCTTTCATGTAGTTTCTGCTCAGATGTTTGTAAACAT-TTGACAACA
1 CATTCATCCTTTCATGTAGCTTCTGCTCAGATG-TTGTAAA-ATATTGACAACA
* *
1094635 CATTCAT-CTTCTCATGTGGCTTCTGCTCAGATGTTGTAAAATATTGATAACA
1 CATTCATCCTT-TCATGTAGCTTCTGCTCAGATGTTGTAAAATATTGACAACA
* *
1094687 CATTCATCCTTTCCTGTAGTTTCTGCTCAGATGTT
1 CATTCATCCTTTCATGTAGCTTCTGCTCAGATGTT
1094722 CAAGAAAATT
Statistics
Matches: 124, Mismatches: 11, Indels: 12
0.84 0.07 0.08
Matches are distributed among these distances:
51 2 0.02
52 46 0.37
53 38 0.31
54 34 0.27
55 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (52 bp):
CATTCATCCTTTCATGTAGCTTCTGCTCAGATGTTGTAAAATATTGACAACA
Found at i:1095829 original size:35 final size:34
Alignment explanation
Indices: 1095790--1095862 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
1095780 CATTACTTCT
1095790 TATTGAGATGAACCTTCAAAATGCCCAAATATTC
1 TATTGAGATGAACCTTCAAAATGCCCAAATATTC
** * *
1095824 ATATTGTTATGAGCCTTCAAAATGCCCCAATATTC
1 -TATTGAGATGAACCTTCAAAATGCCCAAATATTC
1095859 TATT
1 TATT
1095863 TCTGATTGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 4 0.12
35 30 0.88
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (34 bp):
TATTGAGATGAACCTTCAAAATGCCCAAATATTC
Found at i:1096934 original size:114 final size:114
Alignment explanation
Indices: 1096734--1096962 Score: 377
Period size: 114 Copynumber: 2.0 Consensus size: 114
1096724 GATCATGCAG
* * * *
1096734 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
1096799 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTTTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* *
1096848 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1096913 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
1096962 T
1 T
1096963 GGCACTTGCT
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1099129 original size:1 final size:1
Alignment explanation
Indices: 1099123--1099164 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
1099113 CTTGATTCAA
* *
1099123 TTTTTTTTTTTTCTTTTTTTTTTTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1099165 CCTTCTTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.02, G:0.02, T:0.95
Consensus pattern (1 bp):
T
Found at i:1099143 original size:15 final size:15
Alignment explanation
Indices: 1099123--1099165 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
1099113 CTTGATTCAA
1099123 TTTTTTTTTTTTCTT
1 TTTTTTTTTTTTCTT
*
1099138 TTTTTTTTTTTTGTT
1 TTTTTTTTTTTTCTT
1099153 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
1099166 CTTCTTTCTT
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:0.00, C:0.05, G:0.02, T:0.93
Consensus pattern (15 bp):
TTTTTTTTTTTTCTT
Found at i:1099468 original size:2 final size:2
Alignment explanation
Indices: 1099461--1099490 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1099451 ACAACAAATG
1099461 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
1099491 TAAAGGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1105737 original size:18 final size:18
Alignment explanation
Indices: 1105714--1105749 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1105704 AATAATATAC
1105714 TAATAATAATAAATTTAA
1 TAATAATAATAAATTTAA
1105732 TAATAATAATAAATTTAA
1 TAATAATAATAAATTTAA
1105750 ATGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATAATAATAAATTTAA
Found at i:1107248 original size:5 final size:5
Alignment explanation
Indices: 1107238--1107336 Score: 83
Period size: 5 Copynumber: 18.8 Consensus size: 5
1107228 AACGGTCAAC
* *
1107238 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
* * * *
1107287 GGTCG GGTCG GGTCAAC AGTCG GGTCG GGTC- AGACG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1107337 AGACCGGTCA
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
4 2 0.03
5 62 0.83
7 11 0.15
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:1107253 original size:17 final size:17
Alignment explanation
Indices: 1107231--1107337 Score: 114
Period size: 17 Copynumber: 6.3 Consensus size: 17
1107221 AACAGTCAAC
1107231 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1107248 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
* *
1107265 GGTC--GGGTCAACGGTCG
1 GGTCAACGGTC--GGGTCG
*
1107282 GGTC--GGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
1107297 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1107314 GGTCAGACGGGTCGGGTCG
1 GGTCA-AC-GGTCGGGTCG
1107333 GGTCA
1 GGTCA
1107338 GACCGGTCAA
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
15 13 0.17
17 49 0.63
18 2 0.03
19 14 0.18
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1107258 original size:7 final size:7
Alignment explanation
Indices: 1107204--1107241 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
1107194 GTCAAAGAAA
1107204 GTCAACG
1 GTCAACG
1107211 GTCAACG
1 GTCAACG
*
1107218 GTCAACA
1 GTCAACG
1107225 GTCAACG
1 GTCAACG
1107232 GTCAACG
1 GTCAACG
1107239 GTC
1 GTC
1107242 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1107266 original size:22 final size:22
Alignment explanation
Indices: 1107238--1107336 Score: 121
Period size: 22 Copynumber: 4.4 Consensus size: 22
1107228 AACGGTCAAC
1107238 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
1107260 GGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCAACGGTCG
* *
1107282 GGTCGGGTCGGGTC--GGGTCAAC
1 GGTCGGGTCGGGTCAACGGTC--G
*
1107304 AGTCGGGTCGGGTCAGACGGGTCG
1 GGTCGGGTCGGGTCA-AC-GGTCG
1107328 GGTCGGGTC
1 GGTCGGGTC
1107337 AGACCGGTCA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
20 4 0.06
22 49 0.75
24 8 0.12
26 4 0.06
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACGGTCG
Found at i:1107285 original size:27 final size:27
Alignment explanation
Indices: 1107255--1107317 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
1107245 TCGGGTCAAC
*
1107255 GGTCGGGTCGGGTCGGGTCAACGGTCG
1 GGTCGGGTCGGGTCGGGTCAACAGTCG
1107282 GGTCGGGTCGGGTCGGGTCAACAGTCG
1 GGTCGGGTCGGGTCGGGTCAACAGTCG
1107309 GGTCGGGTC
1 GGTCGGGTC
1107318 AGACGGGTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.08, C:0.22, G:0.51, T:0.19
Consensus pattern (27 bp):
GGTCGGGTCGGGTCGGGTCAACAGTCG
Found at i:1107329 original size:19 final size:19
Alignment explanation
Indices: 1107285--1107345 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1107275 ACGGTCGGGT
1107285 CGGGTCGGGTCGGGTCA-A
1 CGGGTCGGGTCGGGTCAGA
*
1107303 C-AGTCGGGTCGGGTCAGA
1 CGGGTCGGGTCGGGTCAGA
1107321 CGGGTCGGGTCGGGTCAGA
1 CGGGTCGGGTCGGGTCAGA
*
1107340 CCGGTC
1 CGGGTC
1107346 AAACCGGTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 14 0.37
18 3 0.08
19 21 0.55
ACGTcount: A:0.11, C:0.25, G:0.48, T:0.16
Consensus pattern (19 bp):
CGGGTCGGGTCGGGTCAGA
Found at i:1107345 original size:9 final size:9
Alignment explanation
Indices: 1107333--1107393 Score: 59
Period size: 9 Copynumber: 6.3 Consensus size: 9
1107323 GGTCGGGTCG
*
1107333 GGTCAGACC
1 GGTCAAACC
1107342 GGTCAAACC
1 GGTCAAACC
*
1107351 GGTCCAGACC
1 GGT-CAAACC
1107361 GGTCAAACC
1 GGTCAAACC
*
1107370 GGTCTAAAAACT
1 GGTC---AAACC
1107382 GGTCAAACC
1 GGTCAAACC
1107391 GGT
1 GGT
1107394 TTTCAGCAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 27 0.63
10 8 0.19
12 8 0.19
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1107358 original size:19 final size:19
Alignment explanation
Indices: 1107336--1107373 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1107326 CGGGTCGGGT
1107336 CAGACCGGTCAAACCGGTC
1 CAGACCGGTCAAACCGGTC
1107355 CAGACCGGTCAAACCGGTC
1 CAGACCGGTCAAACCGGTC
1107374 TAAAAACTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (19 bp):
CAGACCGGTCAAACCGGTC
Found at i:1114493 original size:16 final size:16
Alignment explanation
Indices: 1114467--1114534 Score: 79
Period size: 16 Copynumber: 4.3 Consensus size: 16
1114457 AACGGTCAAC
1114467 GGTCAACGGTCGGGTCG
1 GGTC-ACGGTCGGGTCG
1114484 GGTCACGGTCGGGTCG
1 GGTCACGGTCGGGTCG
*
1114500 GGTCAACAGTC-GGTCG
1 GGTC-ACGGTCGGGTCG
*
1114516 GGTCA--GACGGGTCG
1 GGTCACGGTCGGGTCG
1114530 GGTCA
1 GGTCA
1114535 GACCGTCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.04
14 10 0.21
15 1 0.02
16 25 0.53
17 9 0.19
ACGTcount: A:0.13, C:0.24, G:0.46, T:0.18
Consensus pattern (16 bp):
GGTCACGGTCGGGTCG
Found at i:1114557 original size:18 final size:17
Alignment explanation
Indices: 1114530--1114567 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
1114520 AGACGGGTCG
1114530 GGTCAGACCGTCAAACC
1 GGTCAGACCGTCAAACC
*
1114547 GGTCTAGACCGTTAAACC
1 GGTC-AGACCGTCAAACC
1114565 GGT
1 GGT
1114568 TCAAAACTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (17 bp):
GGTCAGACCGTCAAACC
Found at i:1115800 original size:20 final size:20
Alignment explanation
Indices: 1115756--1115845 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
1115746 TGTTAAGAAC
** *
1115756 AGTATCGATACATATGAAAGA
1 AGTATCGATAC-TATGCTAGT
*
1115777 AGTATTGATACTATGCTAGT
1 AGTATCGATACTATGCTAGT
1115797 AGTATCGATACTATGCTAGT
1 AGTATCGATACTATGCTAGT
1115817 AGTATCGATACTATGCTAGT
1 AGTATCGATACTATGCTAGT
1115837 AGTATCGAT
1 AGTATCGAT
1115846 TCCTAGCAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
20 54 0.84
21 10 0.16
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTATGCTAGT
Found at i:1116448 original size:21 final size:21
Alignment explanation
Indices: 1116422--1116473 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1116412 TTTCATAGTC
1116422 TAAAAGTTGTTGTTTCATCCA
1 TAAAAGTTGTTGTTTCATCCA
1116443 TAAAAGTTGTTGTTTCATCCA
1 TAAAAGTTGTTGTTTCATCCA
*
1116464 TAAAACTTGT
1 TAAAAGTTGT
1116474 GCACTAGTAA
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:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (21 bp):
TAAAAGTTGTTGTTTCATCCA
Found at i:1121996 original size:13 final size:15
Alignment explanation
Indices: 1121978--1122014 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1121968 TTTGAAATAT
1121978 TCGAATA-A-TTAAA
1 TCGAATATATTTAAA
1121991 TCGAATATATTTAAA
1 TCGAATATATTTAAA
1122006 TCGAATATA
1 TCGAATATA
1122015 AAATCTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 7 0.32
14 1 0.05
15 14 0.64
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (15 bp):
TCGAATATATTTAAA
Found at i:1122241 original size:2 final size:2
Alignment explanation
Indices: 1122234--1122258 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1122224 TAGCCAATTG
1122234 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
1122259 GTTTTCTAAG
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:1127294 original size:73 final size:71
Alignment explanation
Indices: 1127207--1127352 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 71
1127197 AGATTTTATT
1127207 AGATCACGATCATGATATTATTGTTTACTATTAAATCTAATTTATATTGGATACTGTATGGGTAG
1 AGATCACGATCATGATATTATTGTTTACTATTAAATCTAATTTATATTGGATACTGTATGGGTA-
1127272 GATTCTAG
65 -ATTCTAG
1127280 AGATCACGATCATGATATTATTGTTTACTATTAAATCTAATTTATATTGGATACTGTATGGGTAA
1 AGATCACGATCATGATATTATTGTTTACTATTAAATCTAATTTATATTGGATACTGTATGGGTAA
1127345 TTCTAG
66 TTCTAG
1127351 AG
1 AG
1127353 TATGGGGTTC
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 9 0.12
73 64 0.88
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (71 bp):
AGATCACGATCATGATATTATTGTTTACTATTAAATCTAATTTATATTGGATACTGTATGGGTAA
TTCTAG
Found at i:1138406 original size:31 final size:31
Alignment explanation
Indices: 1138365--1138429 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1138355 TTACCATTTA
*
1138365 TTTACAAATGATTTCCATCTATGGAGGGGAC
1 TTTACAAATGATTTCCATCTATGAAGGGGAC
*
1138396 TTTACTAATGATTTCCATCTATGAAGGGGAC
1 TTTACAAATGATTTCCATCTATGAAGGGGAC
1138427 TTT
1 TTT
1138430 TGTCCCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (31 bp):
TTTACAAATGATTTCCATCTATGAAGGGGAC
Found at i:1142817 original size:66 final size:65
Alignment explanation
Indices: 1142711--1142841 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 65
1142701 CCCTACCTAA
* *
1142711 GCTCCTTACTTAGGATTTTCCAACAAATCTACTAATTTGTTCTTTCTTTTTTCAAGGATCAAGAG
1 GCTCCTCACTTAGGATTTTCCAACAAATCCACTAATTTGTTCTTTC-TTTTTCAAGGATCAAGAG
1142776 T
65 T
1142777 GCTCCTCACTTAGGATTTTCCAACAAATCCACTAATTTGTTCTTTCTTTTTCAAGGATCAAGAGT
1 GCTCCTCACTTAGGATTTTCCAACAAATCCACTAATTTGTTCTTTCTTTTTCAAGGATCAAGAGT
1142842 AACATTTACA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 19 0.30
66 44 0.70
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (65 bp):
GCTCCTCACTTAGGATTTTCCAACAAATCCACTAATTTGTTCTTTCTTTTTCAAGGATCAAGAGT
Found at i:1143295 original size:19 final size:20
Alignment explanation
Indices: 1143245--1143296 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1143235 AATTTTAGGG
*
1143245 AAAGTTTCGAAACTCTTGAG
1 AAAGTTTCGAAACTCTTGAA
*
1143265 ATAGTTTCGAAACTCTT-AA
1 AAAGTTTCGAAACTCTTGAA
*
1143284 AAAGTATCGAAAC
1 AAAGTTTCGAAAC
1143297 ATTTTGAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (20 bp):
AAAGTTTCGAAACTCTTGAA
Found at i:1143335 original size:19 final size:20
Alignment explanation
Indices: 1143311--1143350 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1143301 TGAGAAATTG
1143311 TCTTGTA-AAGTTTCGAAAC
1 TCTTGTAGAAGTTTCGAAAC
1143330 TCTTGTAGAAGTTTCGAAAC
1 TCTTGTAGAAGTTTCGAAAC
1143350 T
1 T
1143351 TCTGGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (20 bp):
TCTTGTAGAAGTTTCGAAAC
Found at i:1144989 original size:15 final size:16
Alignment explanation
Indices: 1144964--1145003 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1144954 TGGAAACACA
1144964 TTTCTTTCTTTTCTTG
1 TTTCTTTCTTTTCTTG
*
1144980 TTTC-TTCTTTTCTTC
1 TTTCTTTCTTTTCTTG
1144995 TTGTCTTTC
1 TT-TCTTTC
1145004 CTCCTTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 12 0.57
16 6 0.29
17 3 0.14
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.72
Consensus pattern (16 bp):
TTTCTTTCTTTTCTTG
Found at i:1149731 original size:60 final size:59
Alignment explanation
Indices: 1149654--1149831 Score: 180
Period size: 60 Copynumber: 3.0 Consensus size: 59
1149644 CATATGTCCC
* *
1149654 CAAATTATGACTCTCATT-TCAAATTAGTTCTTAAACTTTTAAACATTTCAATTTCATCGT
1 CAAAATATGACTCTCATTCT-AAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATC-T
** * ** * *
1149714 CAAAATATGACTCTCATTCTTTATTAGTCCTTAAACTTTTGAGTATTCCAATTTTATCT
1 CAAAATATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCT
* * * * *
1149773 CTAAACTATGAATCTCATTCTAAATTAATCCCTAAACTTTTATATC-TTTCAATTTCATC
1 C-AAAATATGACTCTCATTCTAAATTAGTCCTTAAACTTTTA-AACATTTCAATTTCATC
1149832 CATAAATTCA
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
59 2 0.02
60 91 0.96
61 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.44
Consensus pattern (59 bp):
CAAAATATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCT
Found at i:1151726 original size:21 final size:21
Alignment explanation
Indices: 1151696--1151769 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
1151686 GATTTACATA
* *
1151696 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
1151717 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
1151738 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
1151757 TTTGCGTTGCGAT
1 TTCGCGTTGCGAT
1151770 TTATTATAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 16 0.37
21 27 0.63
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:1151782 original size:42 final size:41
Alignment explanation
Indices: 1151702--1151836 Score: 161
Period size: 42 Copynumber: 3.3 Consensus size: 41
1151692 CATATTCGCA
* *
1151702 TTGCGATAGTCGAAGTTCGCGTTGCGATT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTTGCGTTGCGATTATTCCAAATTCG
**
1151742 TTGCGATAGTCCAAGTTTGCGTTGCGATTTATTATAAATTCG
1 TTGCGATAGTCCAAGTTTGCGTTGCGA-TTATTCCAAATTCG
1151784 TTGCGATAGTCTCCAAG-TT-CGTTGCGA-TAGTCTCCAAATTCG
1 TTGCGATAG--TCCAAGTTTGCGTTGCGATTA-T-TCCAAATTCG
1151826 TTGCGATAGTC
1 TTGCGATAGTC
1151837 TCCAAATTCG
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
40 29 0.35
41 3 0.04
42 43 0.52
43 2 0.02
44 6 0.07
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCCAAGTTTGCGTTGCGATTATTCCAAATTCG
Found at i:1151804 original size:21 final size:21
Alignment explanation
Indices: 1151777--1151846 Score: 131
Period size: 21 Copynumber: 3.3 Consensus size: 21
1151767 GATTTATTAT
1151777 AAATTCGTTGCGATAGTCTCC
1 AAATTCGTTGCGATAGTCTCC
*
1151798 AAGTTCGTTGCGATAGTCTCC
1 AAATTCGTTGCGATAGTCTCC
1151819 AAATTCGTTGCGATAGTCTCC
1 AAATTCGTTGCGATAGTCTCC
1151840 AAATTCG
1 AAATTCG
1151847 CAACGACTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (21 bp):
AAATTCGTTGCGATAGTCTCC
Found at i:1152980 original size:21 final size:21
Alignment explanation
Indices: 1152955--1153075 Score: 173
Period size: 21 Copynumber: 6.0 Consensus size: 21
1152945 TGCGATTTTG
1152955 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
1152976 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
1152997 GACTA-CTGCAACGAATTTGGA
1 GACTATC-GCAACGAACTTGGA
1153018 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
1153039 GACTATCGCAACG-A--T-G-
1 GACTATCGCAACGAACTTGGA
*
1153055 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
1153076 AAATCGCAAC
Statistics
Matches: 91, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
16 13 0.14
17 2 0.02
18 1 0.01
19 1 0.01
20 3 0.03
21 70 0.77
22 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGAACTTGGA
Found at i:1154551 original size:245 final size:244
Alignment explanation
Indices: 1154119--1154838 Score: 1189
Period size: 245 Copynumber: 2.9 Consensus size: 244
1154109 AGAGAAAAAC
* *
1154119 GTGTCACGGTGACATAGATTCATATTTAAAATTGAAAAACTAAAGAAAAAAATAATGACATAGTA
1 GTGTCACGATGACATAGATTCCTATTTAAAATTG-AAAACTAAAGAAAAAAATAATGACATAGTA
1154184 TGAAAAAGAACAAGAAAAATAATAATCACCGACAATCGACAATCAATATTAAAATTAGTTATGTC
65 TGAAAAAGAACAAGAAAAATAATAATCACCGACAATCGACAATCAATATTAAAATTAGTTATGTC
1154249 AGCTACTAAACAAAAATCAAAGAAAAAAAGAGAGACAACACAAAATATTGAGAAAAGGTTTAGGT
130 AGCTACTAAACAAAAATCAAAGAAAAAAAGAGAGACAACACAAAATATTGAGAAAAGGTTTAGGT
1154314 AAGAGGAAAAAAGAGAAACCTTAATTATATATAAAATACTAAGATTTTTTAT
195 AAGAGGAAAAAAGAGAAACCTTAATTATATA-AAAATACTAAGA-TTTTTAT
1154366 GTGTCACGATGACATAGATTCCTATTTAAAATTG-AAACTAAAGAAAAAAATAATGACATAGTAT
1 GTGTCACGATGACATAGATTCCTATTTAAAATTGAAAACTAAAGAAAAAAATAATGACATAGTAT
1154430 GAAAAAGAACAAGAAAAATAATAATCACCGACAATCGACAATCAATATTAAAATTAGTTATGTCA
66 GAAAAAGAACAAGAAAAATAATAATCACCGACAATCGACAATCAATATTAAAATTAGTTATGTCA
1154495 GCTACTAAACAAAAATCAAAGAAAAAAAGAGAGACAACACAAAATATTGAGAAAAGGTTTAGGTA
131 GCTACTAAACAAAAATCAAAGAAAAAAAGAGAGACAACACAAAATATTGAGAAAAGGTTTAGGTA
1154560 AGAGGAAAAAAGA-AAACCTTAATTATATAAAAATACTAAGATTTTTAT
196 AGAGGAAAAAAGAGAAACCTTAATTATATAAAAATACTAAGATTTTTAT
*
1154608 GTGTCACGATGACATAGATTCCTATTTAAAATTGAAATAACTCAAGAAAAAAATAAATGACATAG
1 GTGTCACGATGACATAGATTCCTATTTAAAATTG-AA-AACTAAAGAAAAAAAT-AATGACATAG
* ** * *
1154673 TATGAAAAAGAACAAGAAAAATAATAATCACCAATGATCGACAATCAATATTAAAATT-GGTACC
63 TATGAAAAAGAACAAGAAAAATAATAATCACCGACAATCGACAATCAATATTAAAATTAGTTA-T
* * * * *
1154737 ATC-GACGACTAAACAAAAATCAAAGAAAAAGAGGGAGACAACACAAAAATATTGA-AATAAAGT
127 GTCAG-CTACTAAACAAAAATCAAAGAAAAAAAGAGAGACAACAC-AAAATATTGAGAA-AAGGT
*
1154800 TTAGGTAAGAGGAACAAAGAGAAACCTTAATTATATAAA
189 TTAGGTAAGAGGAAAAAAGAGAAACCTTAATTATATAAA
1154839 TATCATAAAA
Statistics
Matches: 450, Mismatches: 14, Indels: 17
0.94 0.03 0.04
Matches are distributed among these distances:
242 41 0.09
243 12 0.03
244 17 0.04
245 192 0.43
246 105 0.23
247 65 0.14
248 18 0.04
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.23
Consensus pattern (244 bp):
GTGTCACGATGACATAGATTCCTATTTAAAATTGAAAACTAAAGAAAAAAATAATGACATAGTAT
GAAAAAGAACAAGAAAAATAATAATCACCGACAATCGACAATCAATATTAAAATTAGTTATGTCA
GCTACTAAACAAAAATCAAAGAAAAAAAGAGAGACAACACAAAATATTGAGAAAAGGTTTAGGTA
AGAGGAAAAAAGAGAAACCTTAATTATATAAAAATACTAAGATTTTTAT
Found at i:1161530 original size:18 final size:18
Alignment explanation
Indices: 1161504--1161547 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1161494 ACATATAACC
*
1161504 TTATTATCCTTATTATTA
1 TTATTATCCTTATTAGTA
*
1161522 TTCTTATCCTTATTAGTA
1 TTATTATCCTTATTAGTA
1161540 TTATTATC
1 TTATTATC
1161548 ATTCATATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.02, T:0.59
Consensus pattern (18 bp):
TTATTATCCTTATTAGTA
Found at i:1161834 original size:28 final size:28
Alignment explanation
Indices: 1161793--1161865 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
1161783 ACTTAGAATT
*
1161793 TGTCCCGAATGACCACTTATAACAGATA
1 TGTCCCGAATGACCACTTATAACACATA
* *
1161821 TGTCCCAAAGGACCACTTATAACACATA
1 TGTCCCGAATGACCACTTATAACACATA
1161849 TGTCCCGAATGACCACT
1 TGTCCCGAATGACCACT
1161866 CCTTAAGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (28 bp):
TGTCCCGAATGACCACTTATAACACATA
Found at i:1163903 original size:11 final size:11
Alignment explanation
Indices: 1163887--1163917 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1163877 TTTAGGATAA
1163887 CTTAAGCTTTC
1 CTTAAGCTTTC
1163898 CTTAAGCTTTC
1 CTTAAGCTTTC
1163909 CTTAAGCTT
1 CTTAAGCTT
1163918 AAGTATCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.10, T:0.45
Consensus pattern (11 bp):
CTTAAGCTTTC
Found at i:1165138 original size:15 final size:16
Alignment explanation
Indices: 1165106--1165139 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1165096 TTTTAAGAGT
1165106 AATTTAATTATACTGA
1 AATTTAATTATACTGA
*
1165122 AATTTGATTAT-CTGA
1 AATTTAATTATACTGA
1165137 AAT
1 AAT
1165140 CTTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (16 bp):
AATTTAATTATACTGA
Found at i:1166859 original size:18 final size:18
Alignment explanation
Indices: 1166836--1166877 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1166826 TTGAGTGAAT
*
1166836 GAGCTTCCAGCAGTTTAG
1 GAGCTTCCAGCAGCTTAG
*
1166854 GAGCTTCTAGCAGCTTAG
1 GAGCTTCCAGCAGCTTAG
1166872 GAGCTT
1 GAGCTT
1166878 AAAATAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (18 bp):
GAGCTTCCAGCAGCTTAG
Found at i:1171548 original size:22 final size:20
Alignment explanation
Indices: 1171499--1171555 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1171489 GCCAAGCCTT
**
1171499 CGGTATGGATACCAAATTTC
1 CGGTATGGATACCAAATGCC
*
1171519 TGGTATGGATACCAAACTCGCC
1 CGGTATGGATACCAAA-T-GCC
1171541 CGGTATGGATACCAA
1 CGGTATGGATACCAA
1171556 CCCACTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 15 0.48
21 1 0.03
22 15 0.48
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (20 bp):
CGGTATGGATACCAAATGCC
Found at i:1192537 original size:22 final size:22
Alignment explanation
Indices: 1192507--1192833 Score: 438
Period size: 22 Copynumber: 15.2 Consensus size: 22
1192497 ATTTTAAAAT
*
1192507 TTTAATTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
1192529 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGGATTGA
* ***
1192551 TTTATTTTAAAATATTGAAAAA
1 TTTATTTTAAAATATGGATTGA
*
1192573 ATTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
1192595 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
1192617 TTTA-TTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
1192638 TTTATTTT-AAATATAGATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
1192659 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGGATTGA
1192681 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
1192703 TTTATTTT-AAA-AT--A-T-A
1 TTTATTTTAAAATATGGATTGA
1192719 -TTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
1192740 TTTATTTTAAAATACGGATTGA
1 TTTATTTTAAAATATGGATTGA
1192762 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
1192784 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
1192806 TTTATTTTTAAAATATGGATTGA
1 TTTA-TTTTAAAATATGGATTGA
1192829 TTTAT
1 TTTAT
1192834 GTTGGGATTT
Statistics
Matches: 270, Mismatches: 25, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
15 7 0.03
16 4 0.01
17 3 0.01
18 1 0.00
19 1 0.00
20 3 0.01
21 45 0.17
22 184 0.68
23 22 0.08
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
TTTATTTTAAAATATGGATTGA
Found at i:1192724 original size:15 final size:15
Alignment explanation
Indices: 1192704--1192732 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1192694 ATGGATTGAT
1192704 TTATTTTAAAATATA
1 TTATTTTAAAATATA
1192719 TTATTTTAAAATAT
1 TTATTTTAAAATAT
1192733 GGATTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTTTAAAATATA
Found at i:1192765 original size:81 final size:85
Alignment explanation
Indices: 1192507--1192833 Score: 385
Period size: 81 Copynumber: 3.8 Consensus size: 85
1192497 ATTTTAAAAT
* *** * ***
1192507 TTTAATTTAAAATATGGATTGATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATTGAAAA
1 TTTATTTTAAAATATGGATTGATTTATTTTAAAATATG-ATTGA-TTA-TTTAAAATATAGATTG
*
1192572 AATTATTTTAAAATATGGATTGA
63 ATTTATTTTAAAATATGGATTGA
*
1192595 TTTATTTTAAAATATGGATTGATTTA-TTTAAAATATGGATTGATTTATTTTAAATATAGATTGA
1 TTTATTTTAAAATATGGATTGATTTATTTTAAAATAT-GATTGA-TTATTTAAAATATAGATTGA
* ***
1192659 TTTATTTTAAAATATGAAAAAA
64 TTTATTTTAAAATATGGATTGA
*
1192681 TTTATTTTAAAATATGGATTGATTTATTTTAAAATAT-ATT-A-T-TTTAAAATATGGATTGATT
1 TTTATTTTAAAATATGGATTGATTTATTTTAAAATATGATTGATTATTTAAAATATAGATTGATT
*
1192742 TATTTTAAAATACGGATTGA
66 TATTTTAAAATATGGATTGA
*
1192762 TTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTTAAAATATGGATT
1 TTTATTTTAAAATATGGATTGATTTATTTTAAAATAT-GATTGA-TTA--TTTAAAATATAGATT
1192827 GATTTAT
62 GATTTAT
1192834 GTTGGGATTT
Statistics
Matches: 208, Mismatches: 21, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
81 69 0.33
82 1 0.00
83 3 0.01
84 2 0.01
85 3 0.01
86 56 0.27
87 26 0.12
88 26 0.12
89 22 0.11
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (85 bp):
TTTATTTTAAAATATGGATTGATTTATTTTAAAATATGATTGATTATTTAAAATATAGATTGATT
TATTTTAAAATATGGATTGA
Found at i:1194698 original size:23 final size:23
Alignment explanation
Indices: 1194672--1194724 Score: 99
Period size: 22 Copynumber: 2.3 Consensus size: 23
1194662 GTTTGAAACG
1194672 TTTAAAAATATGGATTGATTTAT
1 TTTAAAAATATGGATTGATTTAT
1194695 TTT-AAAATATGGATTGATTTAT
1 TTTAAAAATATGGATTGATTTAT
1194717 TTTAAAAA
1 TTTAAAAA
1194725 ATTTATTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (23 bp):
TTTAAAAATATGGATTGATTTAT
Found at i:1199514 original size:14 final size:13
Alignment explanation
Indices: 1199492--1199534 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
1199482 TGGGCTGAAC
1199492 ATAATCGAACATAA
1 ATAA-CGAACATAA
1199506 ATAACCGAACATAA
1 ATAA-CGAACATAA
*
1199520 ATTGACGAACATAA
1 A-TAACGAACATAA
1199534 A
1 A
1199535 AGAATGCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 24 0.92
15 2 0.08
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (13 bp):
ATAACGAACATAA
Found at i:1201812 original size:2 final size:2
Alignment explanation
Indices: 1201805--1201850 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1201795 ATAAAGCTCT
1201805 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
1201847 TA TA
1 TA TA
1201851 AGTTATTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1207519 original size:35 final size:35
Alignment explanation
Indices: 1207473--1207543 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1207463 GCAAGCTCAA
*
1207473 GTGGGGTGTCAAAGTACATAATGTAGCATCCATTT
1 GTGGGGTGTCAAAGCACATAATGTAGCATCCATTT
* *
1207508 GTGGGGTGTCAAAGCACATAATGTAGTATCCGTTT
1 GTGGGGTGTCAAAGCACATAATGTAGCATCCATTT
1207543 G
1 G
1207544 GGCCAGGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (35 bp):
GTGGGGTGTCAAAGCACATAATGTAGCATCCATTT
Found at i:1211140 original size:90 final size:90
Alignment explanation
Indices: 1211032--1211265 Score: 326
Period size: 90 Copynumber: 2.6 Consensus size: 90
1211022 CAATGTGTAT
*
1211032 TTTTAGAAACTAAGCCTTCGGGGGTGTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTT
1 TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTT
*
1211097 CAGTGCATGATGTTTTCAAATGAGA
66 CAGTGCAAGATGTTTTCAAATGAGA
* * * * *
1211122 TTTTAGAAACTAAACCTTCGAGGTTTTCTTTATTTGTAAGTCATTCGGGCCATCCATAAGACCTT
1 TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTT
* *
1211187 TAGTGCAAGATGTTTTTAAATGAGA
66 CAGTGCAAGATGTTTTCAAATGAGA
* * * * *
1211212 TTTT-GAAAATTAAGCCTTCAGGGGTTTCTTGATTTTTAAATCCTTCGGGTCATC
1 TTTTAG-AAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATC
1211266 AGTAAGTCTT
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
89 1 0.01
90 123 0.99
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (90 bp):
TTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTT
CAGTGCAAGATGTTTTCAAATGAGA
Found at i:1211292 original size:22 final size:22
Alignment explanation
Indices: 1211275--1211344 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
1211265 CAGTAAGTCT
1211275 TTCGAGCATGATGTGTAAATCC
1 TTCGAGCATGATGTGTAAATCC
* * * *
1211297 TTCGGGTCATCA---GTAAGTCT
1 TTCGAG-CATGATGTGTAAATCC
1211317 TTCGAGCATGATGTGTAAATCC
1 TTCGAGCATGATGTGTAAATCC
1211339 TTCGAG
1 TTCGAG
1211345 TCATCAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 4 0.11
20 11 0.31
22 17 0.47
23 4 0.11
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (22 bp):
TTCGAGCATGATGTGTAAATCC
Found at i:1211307 original size:42 final size:42
Alignment explanation
Indices: 1211248--1211413 Score: 262
Period size: 42 Copynumber: 4.0 Consensus size: 42
1211238 TCTTGATTTT
1211248 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGTG
1 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGTG
1211290 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGTG
1 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGTG
* * *
1211332 TAAATCCTTCGAGTCATCAATAAGTCTTTCAAGCATGATGCT-
1 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATG-TG
* * *
1211374 TAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATG
1 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATG
1211414 ATAAGACCTT
Statistics
Matches: 114, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 113 0.99
43 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGTG
Found at i:1211320 original size:20 final size:20
Alignment explanation
Indices: 1211255--1211320 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
1211245 TTTTAAATCC
1211255 TTCGGGTCATCAGTAAGTCT
1 TTCGGGTCATCAGTAAGTCT
* * * *
1211275 TTCGAG-CATGATGTGTAAATCC
1 TTCGGGTCATCA---GTAAGTCT
1211297 TTCGGGTCATCAGTAAGTCT
1 TTCGGGTCATCAGTAAGTCT
1211317 TTCG
1 TTCG
1211321 AGCATGATGT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 4 0.12
20 15 0.44
22 11 0.32
23 4 0.12
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
TTCGGGTCATCAGTAAGTCT
Found at i:1211688 original size:136 final size:136
Alignment explanation
Indices: 1211441--1211883 Score: 699
Period size: 136 Copynumber: 3.3 Consensus size: 136
1211431 AATGTTTTCA
* * * * *
1211441 ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGATATAGGGAGAATAATTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* * * *
1211506 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAATGACACCACATTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACACCTCACTTGAG
1211571 GGATTG
131 GGATTG
* *
1211577 ACATTTCCAATGGAGAGTTCACAATGAGAAGAACTCATTCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
*
1211642 GAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTTGAATCAGTGACACCTCACTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACACCTCACTTGAG
1211707 GGATTG
131 GGATTG
* *
1211713 ATATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* *
1211778 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACGCCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACACCTCACTTGAG
*
1211843 AGATT-
131 GGATTG
* * *
1211848 ACATTTCTAATGGAGACTTCATAATGAAAAGAACTC
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
1211884 GTCCTAAAAG
Statistics
Matches: 282, Mismatches: 25, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
135 31 0.11
136 251 0.89
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (136 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACACCTCACTTGAG
GGATTG
Found at i:1212123 original size:91 final size:91
Alignment explanation
Indices: 1211963--1212176 Score: 344
Period size: 91 Copynumber: 2.4 Consensus size: 91
1211953 CAATATTTCC
* *
1211963 AGAAG-AGTTCATAAAGAGAATAACTTGTTCAACCTTGCATCAGTATTTCCAATAAAGAGTTCAT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAGTATTTCCAATAAAGAGTTCAT
*
1212027 AATGAGAAGAACTCATTCAACG-AGAA
66 AATGAGAAGAACTCATCCAACGAAG-A
*
1212053 ATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAGTATTTCCAATGAAA-AGTTCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAGTATTTCCAAT-AAAGAGTTCA
*
1212117 TAATGAGAAGAACTCATCCAATGAAGA
65 TAATGAGAAGAACTCATCCAACGAAGA
1212144 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1212177 TCCAATGCTT
Statistics
Matches: 115, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
90 4 0.03
91 106 0.92
92 5 0.04
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (91 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGCATCAGTATTTCCAATAAAGAGTTCAT
AATGAGAAGAACTCATCCAACGAAGA
Found at i:1214637 original size:2 final size:2
Alignment explanation
Indices: 1214619--1214716 Score: 143
Period size: 2 Copynumber: 51.0 Consensus size: 2
1214609 ATAAAGCTCT
*
1214619 TA TA T- TA TA TA TT 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
1214660 TA TA TA TA TA GTA -A TA TA TA TA TA T- TA TA T- 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
1214700 -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1214717 AGTTATTTCA
Statistics
Matches: 88, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
1 5 0.06
2 81 0.92
3 2 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1216505 original size:22 final size:22
Alignment explanation
Indices: 1216471--1216534 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
1216461 AAATCAACCA
* *
1216471 AAACCAAAATTAACTCGAACAG
1 AAACCGAAATTAACCCGAACAG
*
1216493 AAATCGAAATTAACCCGAACAG
1 AAACCGAAATTAACCCGAACAG
1216515 AAACCGAAATTAACCCGAAC
1 AAACCGAAATTAACCCGAAC
1216535 CAAATTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.52, C:0.25, G:0.11, T:0.12
Consensus pattern (22 bp):
AAACCGAAATTAACCCGAACAG
Found at i:1216690 original size:18 final size:19
Alignment explanation
Indices: 1216644--1216706 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 19
1216634 AGTTATTTTC
*
1216644 AATAATA-AATTA-AATAA
1 AATAATAGATTTATAATAA
* *
1216661 AATTGATA-ATTTATTA-AA
1 AA-TAATAGATTTATAATAA
*
1216679 AATATTAGATTTATAATAA
1 AATAATAGATTTATAATAA
1216698 AATAATAGA
1 AATAATAGA
1216707 AAGTTTAAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
17 5 0.14
18 19 0.54
19 11 0.31
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
AATAATAGATTTATAATAA
Found at i:1227112 original size:2 final size:2
Alignment explanation
Indices: 1227105--1227134 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1227095 ATTGTTGTTG
1227105 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
1227135 GGACAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1228308 original size:155 final size:155
Alignment explanation
Indices: 1227936--1228328 Score: 452
Period size: 155 Copynumber: 2.5 Consensus size: 155
1227926 GTCATTGGTT
* * * * * * **
1227936 TCATTATTTCTTCAATTCCTCCTTCATTTTAAGTTCATTTTCACTAAATTTGAACCACATGCAAC
1 TCATTATTCCTTCAATTCATCATT-ATTTTAAGTCCATTTTTACCAAATTTGAACCACATGCTCC
* * *
1228001 TAAACCATAGAAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAACAAATTTTGTATTTTTT
65 TAAACCATAGTAGAATACATGTGTAATTTCAATTCCTCTTTTTGATAACAAATTTTGTATTTTTT
* *
1228066 TAATTTAGTCTTCATTTTTCATAATC
130 CAATTGAGTCTTCATTTTTCATAATC
* * * * ** *
1228092 TCATTTTTTCTTCAATTCGTCATTATTTTAAGTCCGTTTTTACCAAATTTGAGTCATATGCTCCT
1 TCATTATTCCTTCAATTCATCATTATTTTAAGTCCATTTTTACCAAATTTGAACCACATGCTCCT
* * *
1228157 AAACCCTAGTAGAATACATGTGTAATTTCAATTCCTC-TTTTGATAACAATTTTTTTA-TTTTTC
66 AAACCATAGTAGAATACATGTGTAATTTCAATTCCTCTTTTTGATAACAAATTTTGTATTTTTTC
1228220 AATTGAGTCCTTCAATTTTTCATAATC
131 AATTGAGT-CTTC-ATTTTTCATAATC
* **
1228247 -C-TTATTCCTTCAATTTATGGTTTATTTTAAGTCCATTTTTTACCAAATTTGAACCACATGCTC
1 TCATTATTCCTTCAATTCAT-CATTATTTTAAGTCCA-TTTTTACCAAATTTGAACCACATGCTC
* * *
1228310 ATATACCATAATAGAATAC
64 CTAAACCATAGTAGAATAC
1228329 CTATATAACT
Statistics
Matches: 199, Mismatches: 34, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
153 25 0.13
154 36 0.18
155 117 0.59
156 21 0.11
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.46
Consensus pattern (155 bp):
TCATTATTCCTTCAATTCATCATTATTTTAAGTCCATTTTTACCAAATTTGAACCACATGCTCCT
AAACCATAGTAGAATACATGTGTAATTTCAATTCCTCTTTTTGATAACAAATTTTGTATTTTTTC
AATTGAGTCTTCATTTTTCATAATC
Found at i:1228599 original size:2 final size:2
Alignment explanation
Indices: 1228592--1228625 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1228582 TATAACCATA
1228592 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
1228626 TATGGTTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1230063 original size:254 final size:252
Alignment explanation
Indices: 1229548--1230033 Score: 675
Period size: 254 Copynumber: 1.9 Consensus size: 252
1229538 TATATTCGGG
*
1229548 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTAT
1 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTAT
* *
1229613 ATATTTAGGAATAATTACAATAATACCCTCTATATATAATTTTTTTTCAATTAAGTCACTGTTTT
66 ATATTTAGAAATAATTACAATAATACCCTCTATATATAA-TTATTTTCAATTAAGTCACTGTTTT
*
1229678 TATGAATAAAATAATTTTTTTTATTATTTCGGGTCGGGTCGGTCGGATTTCTAATTATATTCGGG
130 TATGAATAAAATAATTTTTTTTATTATTTCGGGTCGGGTCGG-CGGATTTCTAATTATATTCAGG
* ***** *
1229743 TTAGGTCGAGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTTAAGTGTGCTAT
194 TGAGGTCGAGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTGGAGGTTAACTGTGCTAT
*
1229802 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCTGACCCGACCCAACAAATATATAATTTTACC
1 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGA---AA-AAATATATAATTTTACC
1229867 TTATATATTTAGAAATAATTACAATAATACCC-CTATATAT-A-TATTTTCAATTAAGTCACTGT
62 TTATATATTTAGAAATAATTACAATAATACCCTCTATATATAATTATTTTCAATTAAGTCACTGT
1229929 TTTTATTGAAT-AAA-AATATTTTTTTATTATTTCGGGTCGGGTC-G-GG-TTTCTAATTCATAT
127 TTTTA-TGAATAAAATAAT-TTTTTTTATTATTTCGGGTCGGGTCGGCGGATTTCTAA-T--TAT
* *
1229989 ATTCAGGTCGA-GTCGGGTGAAACTTTATTTTGGTTGGGTCGGGTC
187 ATTCAGGT-GAGGTCGAGTGAAACTTTATTTTGGTCGGGTCGGGTC
1230034 TCGGATGGAG
Statistics
Matches: 214, Mismatches: 8, Indels: 21
0.88 0.03 0.09
Matches are distributed among these distances:
250 7 0.03
251 3 0.01
253 46 0.21
254 95 0.44
255 5 0.02
256 1 0.00
257 10 0.05
258 47 0.22
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (252 bp):
TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTAT
ATATTTAGAAATAATTACAATAATACCCTCTATATATAATTATTTTCAATTAAGTCACTGTTTTT
ATGAATAAAATAATTTTTTTTATTATTTCGGGTCGGGTCGGCGGATTTCTAATTATATTCAGGTG
AGGTCGAGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTGGAGGTTAACTGTGCTAT
Found at i:1230361 original size:17 final size:17
Alignment explanation
Indices: 1230339--1230437 Score: 117
Period size: 17 Copynumber: 5.7 Consensus size: 17
1230329 TATGGAATTG
1230339 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
*
1230356 GATTCCAATTCCTTCACA
1 GATTCCAATTCC-TGACA
*
1230374 GATTCCAATTCCTGATA
1 GATTCCAATTCCTGACA
*
1230391 GATTCCAATTCCTGATA
1 GATTCCAATTCCTGACA
* * *
1230408 GATTCTAATTCTTTCACA
1 GATTCCAATTC-CTGACA
*
1230426 GATTCAAATTCC
1 GATTCCAATTCC
1230438 CTCAGAAACA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
17 42 0.59
18 29 0.41
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.35
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:1230418 original size:52 final size:52
Alignment explanation
Indices: 1230339--1230437 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
1230329 TATGGAATTG
*
1230339 GATTCCAATTCCTGACAGATTCCAATTCCTTCACAGATTCCAATTCCTGATA
1 GATTCCAATTCCTGACAGATTCCAATTCCTTCACAGATTCAAATTCCTGATA
* * *
1230391 GATTCCAATTCCTGATAGATTCTAATTCTTTCACAGATTCAAATTCC
1 GATTCCAATTCCTGACAGATTCCAATTCCTTCACAGATTCAAATTCC
1230438 CTCAGAAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.35
Consensus pattern (52 bp):
GATTCCAATTCCTGACAGATTCCAATTCCTTCACAGATTCAAATTCCTGATA
Found at i:1230429 original size:35 final size:35
Alignment explanation
Indices: 1230339--1230437 Score: 110
Period size: 35 Copynumber: 2.8 Consensus size: 35
1230329 TATGGAATTG
*
1230339 GATTCCAATTCCTGACAGATTCCAATTCCTTCACA
1 GATTCCAATTCCTCACAGATTCCAATTCCTTCACA
* * * *
1230374 GATTCCAATTCCTGATAGATTCCAATTCC-TGATA
1 GATTCCAATTCCTCACAGATTCCAATTCCTTCACA
* * *
1230408 GATTCTAATTCTTTCACAGATTCAAATTCC
1 GATTCCAATTC-CTCACAGATTCCAATTCC
1230438 CTCAGAAACA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 13 0.24
35 42 0.76
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.35
Consensus pattern (35 bp):
GATTCCAATTCCTCACAGATTCCAATTCCTTCACA
Found at i:1237240 original size:19 final size:19
Alignment explanation
Indices: 1237216--1237255 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1237206 ATTTCAAGCA
1237216 AAATTAACCTATCAGAAAT
1 AAATTAACCTATCAGAAAT
1237235 AAATTAACCTATCAGAAAT
1 AAATTAACCTATCAGAAAT
1237254 AA
1 AA
1237256 CTGAATGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (19 bp):
AAATTAACCTATCAGAAAT
Found at i:1248539 original size:19 final size:19
Alignment explanation
Indices: 1248515--1248552 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1248505 TTTTTTATCG
1248515 GAAATCAGGAAATCGACCC
1 GAAATCAGGAAATCGACCC
*
1248534 GAAATCTGGAAATCGACCC
1 GAAATCAGGAAATCGACCC
1248553 TAACTACCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATCAGGAAATCGACCC
Found at i:1249596 original size:2 final size:2
Alignment explanation
Indices: 1249589--1249621 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1249579 TGTATACTCA
1249589 AT AT AT AT AT -T 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
1249622 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1256256 original size:13 final size:13
Alignment explanation
Indices: 1256238--1256279 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1256228 CGCGTCATAA
1256238 ATTTATGACGCGC
1 ATTTATGACGCGC
* *
1256251 ATTTATGACACGT
1 ATTTATGACGCGC
*
1256264 ATTTATGACGCTC
1 ATTTATGACGCGC
1256277 ATT
1 ATT
1256280 GAGCGTCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:1258687 original size:17 final size:16
Alignment explanation
Indices: 1258656--1258689 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1258646 CACGTGAGGA
1258656 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1258672 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1258689 T
1 T
1258690 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1260469 original size:21 final size:21
Alignment explanation
Indices: 1260445--1260488 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1260435 TCTACTTCAA
*
1260445 TTAAGAATCAAGGAGCTTTAC
1 TTAAGAATCAAGGAGCCTTAC
* *
1260466 TTAATAGTCAAGGAGCCTTAC
1 TTAAGAATCAAGGAGCCTTAC
1260487 TT
1 TT
1260489 CAAAGCCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (21 bp):
TTAAGAATCAAGGAGCCTTAC
Found at i:1265058 original size:21 final size:21
Alignment explanation
Indices: 1265015--1265058 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1265005 TAACTTTTTC
* *
1265015 TTTTCTCTTTCTTTATTCATT
1 TTTTCTCTTTCATTATTAATT
*
1265036 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAATT
1265056 TTT
1 TTT
1265059 ACTTTTTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAATT
Found at i:1267874 original size:23 final size:23
Alignment explanation
Indices: 1267841--1267890 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1267831 AGCTGGCACT
*
1267841 GGACAGTTGTCTCTGCACGTGAA
1 GGACAGATGTCTCTGCACGTGAA
*
1267864 GGACAGATGTCTTTGCACGTGAA
1 GGACAGATGTCTCTGCACGTGAA
1267887 GGAC
1 GGAC
1267891 TGCTGTAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (23 bp):
GGACAGATGTCTCTGCACGTGAA
Found at i:1268895 original size:15 final size:15
Alignment explanation
Indices: 1268875--1268908 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1268865 TCACTGAGGA
1268875 TTATTT-TCTTCTTAT
1 TTATTTATCTT-TTAT
1268890 TTATTTATCTTTTAT
1 TTATTTATCTTTTAT
1268905 TTAT
1 TTAT
1268909 GTTTTTACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTATCTTTTAT
Found at i:1282672 original size:13 final size:13
Alignment explanation
Indices: 1282654--1282701 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
1282644 TCATAAATGC
1282654 GTCATAAATGTGT
1 GTCATAAATGTGT
1282667 GTCATAAATGTGT
1 GTCATAAATGTGT
* *
1282680 GTCATAAATGCGC
1 GTCATAAATGTGT
1282693 GTCATAAAT
1 GTCATAAAT
1282702 TTATGACGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (13 bp):
GTCATAAATGTGT
Found at i:1293153 original size:180 final size:177
Alignment explanation
Indices: 1292853--1293208 Score: 667
Period size: 180 Copynumber: 2.0 Consensus size: 177
1292843 TGTTACTATA
1292853 ATAGACCAAATAAAATAAATCCAATAAAGCAAACTAGAAAAACAAATACAAACCACTAACAGTCA
1 ATAGACCAAATAAAATAAATCCAATAAAGCAAACTAGAAAAACAAATACAAACCACTAACAGTCA
1292918 AAACTAAATCCGAGATGTCTTACTGATACAGTTAGTATCTATGATCTCCAAAAGATGCTTGGTAG
66 AAACTAAATCCGAGATGTCTTACTGATACAGTTAGTATCTATGATCTCCAAAAGATGCTTGGTAG
1292983 GCTCCTCACTGCACGTCCCTTTCTCTATCAGAACTTAACGCATGAAAT
131 GCTCCTCACTGCACGTCCCTTTCTCTATCAGAACTT-ACGCATGAAAT
*
1293031 ATAGACCAAATAAAATAAATCCAATAAAGCAAACTAGAAAAACATAATATAAACCACTAACAGTC
1 ATAGACCAAATAAAATAAATCCAATAAAGCAAACTAGAAAAACA-AATACAAACCACTAACAGTC
*
1293096 AAAAGTAACATCCGAGATGTCTTACTGATACAGTTAGTATCTATGATCTCCAAAAGATGCTTGGT
65 AAAACTAA-ATCCGAGATGTCTTACTGATACAGTTAGTATCTATGATCTCCAAAAGATGCTTGGT
1293161 AGGCTCCTCACTGCACGTCCCTTTCTCTATCAGAACTTACGCATGAAA
129 AGGCTCCTCACTGCACGTCCCTTTCTCTATCAGAACTTACGCATGAAA
1293209 ATCATCACAC
Statistics
Matches: 174, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
178 44 0.25
179 36 0.21
180 94 0.54
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (177 bp):
ATAGACCAAATAAAATAAATCCAATAAAGCAAACTAGAAAAACAAATACAAACCACTAACAGTCA
AAACTAAATCCGAGATGTCTTACTGATACAGTTAGTATCTATGATCTCCAAAAGATGCTTGGTAG
GCTCCTCACTGCACGTCCCTTTCTCTATCAGAACTTACGCATGAAAT
Found at i:1293799 original size:2 final size:2
Alignment explanation
Indices: 1293759--1293786 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1293749 ACATATAAGA
1293759 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
1293787 CCATTTCTAT
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:1294395 original size:12 final size:12
Alignment explanation
Indices: 1294378--1294402 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1294368 AGATGATAAG
1294378 TCAAATTCAACT
1 TCAAATTCAACT
1294390 TCAAATTCAACT
1 TCAAATTCAACT
1294402 T
1 T
1294403 ATCAACTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAAATTCAACT
Found at i:1295622 original size:115 final size:117
Alignment explanation
Indices: 1295453--1295685 Score: 402
Period size: 115 Copynumber: 2.0 Consensus size: 117
1295443 ACTCAATTTC
* *
1295453 TATAATTCTATTATTAAAAATTGGTTTCATGATTTTTTTTATTTTAATGAAAATAGATATAAACA
1 TATAATTCTATTATTAAAAATTGGTTTCATGATTTATTATATTTTAATGAAAATAGATATAAACA
1295518 ATGTTAATTTATTTTATATATTTTTTCATACTTATG-TTTTCATTCATTTCATA
66 ATGTTAATTTA-TTT-TATATTTTTTCATACTTATGTTTTTCATTCATTTCATA
1295571 TATAATTCTATTATT-AAAATTGGTTTCATGATTTATTAT-TTTTAATG-AAATAGATATAAACA
1 TATAATTCTATTATTAAAAATTGGTTTCATGATTTATTATATTTTAATGAAAATAGATATAAACA
1295633 ATGTTAATTTATTTTATATTTTTTCATACTTATGTTTTTCATTCATTTCATA
66 ATGTTAATTTATTTTATATTTTTTCATACTTATGTTTTTCATTCATTTCATA
1295685 T
1 T
1295686 TTTGTTAGAC
Statistics
Matches: 112, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
113 20 0.18
114 21 0.19
115 26 0.23
116 8 0.07
117 22 0.20
118 15 0.13
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (117 bp):
TATAATTCTATTATTAAAAATTGGTTTCATGATTTATTATATTTTAATGAAAATAGATATAAACA
ATGTTAATTTATTTTATATTTTTTCATACTTATGTTTTTCATTCATTTCATA
Found at i:1295971 original size:2 final size:2
Alignment explanation
Indices: 1295964--1296001 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1295954 GATATTGTTG
1295964 AT 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 AT
1296002 TTTTTTTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1296364 original size:21 final size:21
Alignment explanation
Indices: 1296306--1296365 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1296296 TACTTCGCCT
**
1296306 TAATTTAATG-TTTTTACACA
1 TAATTTAATGATTTTTATGCA
* *
1296326 CAATTTGATGATTTTTATGCA
1 TAATTTAATGATTTTTATGCA
1296347 TAATTTAATGATTTTTATG
1 TAATTTAATGATTTTTATG
1296366 ATAGTCGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 8 0.24
21 25 0.76
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.52
Consensus pattern (21 bp):
TAATTTAATGATTTTTATGCA
Found at i:1296608 original size:21 final size:23
Alignment explanation
Indices: 1296582--1296624 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1296572 TACATCCATA
1296582 TAAAAATAAATA-TA-AAAAATT
1 TAAAAATAAATATTATAAAAATT
*
1296603 TAAAAATATATATTATAAAAAT
1 TAAAAATAAATATTATAAAAAT
1296625 AAACTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAAATAAATATTATAAAAATT
Found at i:1303782 original size:21 final size:20
Alignment explanation
Indices: 1303752--1303805 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
1303742 GATAGACACT
*
1303752 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
1303773 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
1303796 TTACATTATA
1 TTACATTATA
1303806 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:1303793 original size:23 final size:23
Alignment explanation
Indices: 1303767--1303829 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1303757 ATATAACCAT
1303767 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1303790 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1303813 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1303830 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1305039 original size:19 final size:19
Alignment explanation
Indices: 1305015--1305068 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
1305005 TTTAATTTTA
1305015 CGGTTTATCATTTTGTTAC
1 CGGTTTATCATTTTGTTAC
1305034 CGGTTTTATCATATTT-TTAC
1 CGG-TTTATCAT-TTTGTTAC
* * *
1305054 CTGTATATCGTTTTG
1 CGGTTTATCATTTTG
1305069 GATCGATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.10
19 9 0.31
20 14 0.48
21 3 0.10
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.54
Consensus pattern (19 bp):
CGGTTTATCATTTTGTTAC
Found at i:1308136 original size:3 final size:3
Alignment explanation
Indices: 1308128--1308173 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
1308118 CTTTGCACCT
*
1308128 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1308174 CCAACTGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1308584 original size:9 final size:9
Alignment explanation
Indices: 1308570--1308599 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
1308560 CGGTCCATCC
1308570 TTGGTCCCA
1 TTGGTCCCA
1308579 TTGGTCCCA
1 TTGGTCCCA
1308588 TTGGTCCCA
1 TTGGTCCCA
1308597 TTG
1 TTG
1308600 TTCATTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.30, G:0.23, T:0.37
Consensus pattern (9 bp):
TTGGTCCCA
Found at i:1309592 original size:23 final size:23
Alignment explanation
Indices: 1309552--1309615 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1309542 AGAATTGTAT
* *
1309552 TGTCTTTGTGATATGTTTATCTA
1 TGTCTTTATGATACGTTTATCTA
*
1309575 TGTCTTTATGACACGTTTATCTA
1 TGTCTTTATGATACGTTTATCTA
* *
1309598 TGCCTTTATAATACGTTT
1 TGTCTTTATGATACGTTT
1309616 TTCTCTTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.52
Consensus pattern (23 bp):
TGTCTTTATGATACGTTTATCTA
Found at i:1316062 original size:22 final size:22
Alignment explanation
Indices: 1316042--1316110 Score: 113
Period size: 22 Copynumber: 3.1 Consensus size: 22
1316032 TAAATATATT
1316042 TATTAATATTTTTAATAATATAA
1 TATT-ATATTTTTAATAATATAA
1316065 TATTATATTTTTAATAATATAA
1 TATTATATTTTTAATAATATAA
*
1316087 TATTATA-TTTTAATATTATAA
1 TATTATATTTTTAATAATATAA
1316108 TAT
1 TAT
1316111 ACTTAGTTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
21 16 0.36
22 25 0.56
23 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTATATTTTTAATAATATAA
Found at i:1316071 original size:8 final size:8
Alignment explanation
Indices: 1316054--1316110 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
1316044 TTAATATTTT
*
1316054 TAATAATA
1 TAATATTA
1316062 TAATATTA
1 TAATATTA
*
1316070 T-AT-TTT
1 TAATATTA
*
1316076 TAATAATA
1 TAATATTA
1316084 TAATATTA
1 TAATATTA
1316092 T-AT-TT-
1 TAATATTA
1316097 TAATATTA
1 TAATATTA
1316105 TAATAT
1 TAATAT
1316111 ACTTAGTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
5 1 0.03
6 7 0.18
7 8 0.21
8 23 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TAATATTA
Found at i:1319062 original size:36 final size:35
Alignment explanation
Indices: 1319006--1319163 Score: 103
Period size: 36 Copynumber: 4.4 Consensus size: 35
1318996 TATATATTCT
* *
1319006 AAAATA-TATATA-TATATTTCAAAAATTATTTTA
1 AAAATATTATATATTTTTTTTCAAAAATTATTTTA
* * *
1319039 AAAATATTATATATGTTTTTTTCAAAAAATGTTTTT
1 AAAATATTATATAT-TTTTTTTCAAAAATTATTTTA
* *
1319075 AAAA-ATTATATATTATATTTTCCAAAAAATGATTTTTA
1 AAAATATTATATATT-T-TTTTTC-AAAAATTA-TTTTA
**
1319113 AAACCATA-TATTATATCATTTTTCAAAAA-TA-TTTA
1 AAA--ATATTA-TATATTTTTTTTCAAAAATTATTTTA
1319148 AAAAGCTATTATATAT
1 AAAA--TATTATATAT
1319164 AAGTTTCAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
33 7 0.07
34 7 0.07
35 24 0.25
36 27 0.28
37 6 0.06
38 12 0.12
39 5 0.05
40 3 0.03
41 6 0.06
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (35 bp):
AAAATATTATATATTTTTTTTCAAAAATTATTTTA
Found at i:1319076 original size:37 final size:37
Alignment explanation
Indices: 1319006--1319141 Score: 119
Period size: 36 Copynumber: 3.7 Consensus size: 37
1318996 TATATATTCT
*
1319006 AAAA-TATATA-TATATATTTC-AAAAAT-TATTTTAA
1 AAAATTATATATTATATTTTTCAAAAAATGT-TTTTAA
1319040 AAATATTATATATGT-T-TTTTTCAAAAAATGTTTTT-A
1 AAA-ATTATATAT-TATATTTTTCAAAAAATGTTTTTAA
*
1319076 AAAATTATATATTATATTTTCCAAAAAATGATTTTTAA
1 AAAATTATATATTATATTTTTCAAAAAATG-TTTTTAA
*
1319114 AACCA-TATAT-TATATCATTTTTCAAAAA
1 AA-AATTATATAT-TAT-ATTTTTCAAAAA
1319142 TATTTAAAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 21
0.77 0.04 0.19
Matches are distributed among these distances:
34 4 0.05
35 11 0.13
36 28 0.33
37 17 0.20
38 13 0.15
39 12 0.14
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (37 bp):
AAAATTATATATTATATTTTTCAAAAAATGTTTTTAA
Found at i:1319948 original size:84 final size:84
Alignment explanation
Indices: 1319823--1321219 Score: 1220
Period size: 84 Copynumber: 16.8 Consensus size: 84
1319813 TAAGTTGAAT
* * * * *
1319823 GTAATCAAACTCGAAGG--TTT--TTAGCAGATAGCCCTTATCGACTTAAGCTATGCTACAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
*
1319884 ATGTGCCTTAGAGCTGAGC
66 ATGTGCCTTGGAGCTGAGC
* * *
1319903 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
* *
1319968 ATATGCCTTAGAGCTGAGC
66 ATGTGCCTTGGAGCTGAGC
* * *
1319987 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
* *
1320052 ATATGCCTCGGAGCTGAGC
66 ATGTGCCTTGGAGCTGAGC
* * * * * *
1320071 ATAGTCAAACTCGAAGG--TTT--TTAGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
* *
1320132 ATGGTGCCTTTGAGCTGAGT
66 AT-GTGCCTTGGAGCTGAGC
* * * * * * *
1320152 GTAATCGAACTCGAAGGTCTTTTGG-TGACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAAT
1 GTAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
*
1320216 GATGTGCCCTT-GAGCTGAGT
65 GATGTG-CCTTGGAGCTGAGC
* * * * * ** *
1320236 GTAATCGAACTCAAAGAGTC-TTCGTTGACATATAGCTTTTCTCGACTTAATCTTGAGCTATGTT
1 GTAATCGAACTCGAAG-GTCTTTGGTTGGCAGATAACCCTTCTCGACTT-A-----AGCTATGCT
* * * * **
1320300 GTAAACTTGATCTGCCTCT-AAGTTGAAT
59 GCAAA--TGATGTGCCT-TGGAGCTGAGC
* * *
1320328 GTAATCGAACTCGAAGG--TTT--TTAGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
*
1320389 ATGTGCCTTAGAGCTGAGC
66 ATGTGCCTTGGAGCTGAGC
* * *
1320408 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
*
1320473 ATATGCCTTGGAGCTGAGC
66 ATGTGCCTTGGAGCTGAGC
* * * *
1320492 GTAGTCGAACTCGAAGG--TTT--TTAGCATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
* *
1320553 ATGGTGCCTTTGAGCTGAGT
66 AT-GTGCCTTGGAGCTGAGC
* * * * * * *
1320573 GTAATCGAACTCGAAGGTCTTTTGG-TGACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAAT
1 GTAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
* *
1320637 GATGTGCCCTTGAAGCTGAGT
65 GATGTG-CCTTGGAGCTGAGC
* * * * *
1320658 GTAATCGAACT-TAAGGGTC--T--TTGGCATATAGCCCTTCTTGACTTAAGCTATACTGCAAAT
1 GTAATCGAACTCGAA-GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
* *
1320718 GATATGCCTTGGAGCTGAGA
65 GATGTGCCTTGGAGCTGAGC
* * * * *
1320738 GTAATCGAACTCAAAGGTCTTTAGTTGGCGGATAACCCTTCTCGACTTAAGTTATGCCGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
* * *
1320803 ATGTGCCCTCGAAGCTGAGT
66 ATGTG-CCTTGGAGCTGAGC
* ** * * **
1320823 GTAATCGAACGCGGGGGTC-TT--TTGGCAGATAGCCCTTCTCGACTTAAACTACACTGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
*
1320885 ATGTGCCTTGGAGTTGAGC
66 ATGTGCCTTGGAGCTGAGC
* * * * * * * *
1320904 GTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
* * * *
1320968 ATATGCCCTCGAAGCTGAGT
66 ATGTG-CCTTGGAGCTGAGC
* ** *
1320988 GTAATCGAACTTGGGGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
* *
1321053 ATGTGTCGTT-GAGTTGAGC
66 ATGTG-CCTTGGAGCTGAGC
* * * * * * * ** *
1321072 GTAGTCGAACTCAAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATATTTCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
1321137 ATGTGCCTTGGAGCTGAGC
66 ATGTGCCTTGGAGCTGAGC
** * * * * * * * *
1321156 GTGGTTGAACTCGAAGGTCCTT-GCTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATG
1 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
1321220 CTATCTTTTT
Statistics
Matches: 1068, Mismatches: 200, Indels: 95
0.78 0.15 0.07
Matches are distributed among these distances:
79 1 0.00
80 148 0.14
81 118 0.11
82 67 0.06
83 73 0.07
84 434 0.41
85 162 0.15
87 1 0.00
88 18 0.02
90 14 0.01
91 4 0.00
92 28 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
ATGTGCCTTGGAGCTGAGC
Found at i:1320207 original size:165 final size:163
Alignment explanation
Indices: 1319822--1321219 Score: 1215
Period size: 165 Copynumber: 8.4 Consensus size: 163
1319812 CTAAGTTGAA
* * *
1319822 TGTAATCAAACTCGAAGGT-TTT-TAGCAGATAGCCCTTATCGACTTAAGCTATGCTACAAATGA
1 TGTAATCGAACTCGAAGGTCTTTGT-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* *
1319885 TGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACT
65 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGT-TTT-GTTGGCAGATAACCCTTCTCAACT
* *
1319950 TAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAG
128 TAAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAG
* * * * *
1319986 CGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
1 TGTAATCGAACTCGAAGGTCTTT-G-T-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
* * * * * * *
1320051 GATATGCCTCGGAGCTGAGCATAGTCAAACTCGAAGG-TTT-TTAGCAGATAGCCCTTCTCAACT
63 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTTTGTTGGCAGATAACCCTTCTCAACT
*
1320114 TAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAG
128 TAAGTTATGCTGCAAATGAT-GTGCCTTTGAGCTGAG
* * * * * * *
1320151 TGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAAT
1 TGTAATCGAACTCGAAGGTC-TTT-GTG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
* * * * * * **
1320216 GATGTGCCCTT-GAGCTGAGTGTAATCGAACTCAAAGAGTCTTCGTTGACATATAGCTTTTCTCG
63 GATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAG-GT-TTTGTTGGCAGATAACCCTTCT--
* * * * * * * * *
1320280 ACTTAATCTTGAGCTATGTTGTAAACTTGATCTGCCTCTAAGTTGAA
123 -C--AA-CTTAAGTTATGCTGCAAA--TGATGTGCCTTTGAGCTGAG
*
1320327 TGTAATCGAACTCGAAGGT-TTT-TAGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAATGA
1 TGTAATCGAACTCGAAGGTCTTTGT-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* *
1320390 TGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACT
65 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGT-TTT-GTTGGCAGATAACCCTTCTCAACT
* *
1320455 TAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAG
128 TAAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAG
* * *
1320491 CGTAGTCGAACTCGAAGGT-TTT-TAGCATATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 TGTAATCGAACTCGAAGGTCTTTGT-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * * * * * *
1320554 TGGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACTCTTCT-AGC
65 T-GTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGG--TTTTGTTGGCAGATAACCCTTCTCA-A
* * *
1320618 CTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAG
126 CTTAAGTTATGCTGCAAATGATGTGCCTTTG-AGCTGAG
* * * *
1320657 TGTAATCGAACT-TAAGGGTCTTTG-GCATATAGCCCTTCTTGACTTAAGCTATACTGCAAATGA
1 TGTAATCGAACTCGAA-GGTCTTTGTGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * * *
1320720 TATGCCTTGGAGCTGAGAGTAATCGAACTCAAAGGTCTTTAGTTGGCGGATAACCCTTCTCGACT
65 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGT-TTT-GTTGGCAGATAACCCTTCTCAACT
* * *
1320785 TAAGTTATGCCGCAAATGATGTGCCCTCGAAGCTGAG
128 TAAGTTATGCTGCAAATGATGTGCCTTTG-AGCTGAG
* ** * **
1320822 TGTAATCGAACGCGGGGGTCTTT-TGGCAGATAGCCCTTCTCGACTTAAACTACACTGCAAATGA
1 TGTAATCGAACTCGAAGGTCTTTGT-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * * *
1320886 TGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT-AGCCT
65 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGT-TTTGTTGGCAGATAACCCTTCTCA-ACT
* * * * * *
1320950 TGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAG
128 TAAGTTATGCTGCAAATGATGTGCCTTTG-AGCTGAG
* **
1320987 TGTAATCGAACTTGGGGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
1 TGTAATCGAACTCGAAGGTCTTT-G-T-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
* * * **
1321052 GATGTGTCGTT-GAGTTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAAATAACCCTTCTTG
63 GATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGG--TTTTGTTGGCAGATAACCCTTCTCA
* * * ** * *
1321116 CCTTGAGCTATATTTCAAATGATGTGCCTTGGAGCTGAG
125 ACTTAAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAG
* ** * * * * * * * *
1321155 CGTGGTTGAACTCGAAGGTCCTTGCTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATG
1 TGTAATCGAACTCGAAGGTCTTTG-T-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
1321220 CTATCTTTTT
Statistics
Matches: 1019, Mismatches: 170, Indels: 87
0.80 0.13 0.07
Matches are distributed among these distances:
163 1 0.00
164 132 0.13
165 334 0.33
166 157 0.15
167 40 0.04
168 156 0.15
169 61 0.06
170 1 0.00
171 9 0.01
172 73 0.07
173 1 0.00
174 5 0.00
175 15 0.01
176 30 0.03
177 4 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (163 bp):
TGTAATCGAACTCGAAGGTCTTTGTGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
GTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTTTGTTGGCAGATAACCCTTCTCAACTTAA
GTTATGCTGCAAATGATGTGCCTTTGAGCTGAG
Found at i:1320517 original size:421 final size:412
Alignment explanation
Indices: 1319782--1321219 Score: 1513
Period size: 421 Copynumber: 3.4 Consensus size: 412
1319772 TCGACTTAAT
* * * * * * *
1319782 CTTGAGCTATGCTGTAAACTTGATCTG-CCTCTAAGTTGAATGTAATCAAACTCGAAGGT-TTTT
1 CTTGAGTTATGCTGTAAA--TGATGTGCCCT-TGAGCTGAGTGTAATCGAACTCAAAGGTCTTTT
* * * * * * *
1319845 -AGCAGATAGCCCTTATCGACTTAAGCTATGCTACAAATGATGTGCCTT-AGAGCTGAGCGTAGT
63 GA-CATATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTGA-AGCTGAGAGTAAT
* * *
1319908 CGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
126 CGAACTCAAAGG-CTTT-ATTAGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
1319973 CCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
189 CCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
* * *
1320038 TTATGCTGCAAATGATATGCCTCGGAGCTGAGCATAGTCAAACTCGAAGGTTTTTAGCAGATAGC
254 TTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTAGCAGATAGC
1320103 CCTTCTCAACTTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
319 CCTTCTCAACTTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1320168 GTCTTTTGGTGACAGATAACTCTTCTAGC
384 GTCTTTTGGTGACAGATAACTCTTCTAGC
1320197 CTTGAGTTATGCTGTAAATGATGTGCCCTTGAGCTGAGTGTAATCGAACTCAAAGAGTCTTCGTT
1 CTTGAGTTATGCTGTAAATGATGTGCCCTTGAGCTGAGTGTAATCGAACTCAAAG-GTCTT--TT
** ** * * *
1320262 GACATATAGCTTTTCTCGACTTAATCTTGAGCTATGTTGTAAACTTGATCTGCCTCT-AAGTTGA
63 GACATATAGCCCTTCTCGACTT-A-----AGCTATACTGCAAA--TGATATGCCT-TGAAGCTGA
* * * *
1320326 -ATGTAATCGAACTCGAAGG-TTT-TTAGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAAT
119 GA-GTAATCGAACTCAAAGGCTTTATTAGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
1320388 GATGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA
183 GATGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA
1320453 CTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTAGCA
248 CTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTAGCA
* *
1320518 TATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTAATCGAAC
313 GATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTAATCGAAC
1320583 TCGAAGGTCTTTTGGTGACAGATAACTCTTCTAGC
378 TCGAAGGTCTTTTGGTGACAGATAACTCTTCTAGC
* * *
1320618 CTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC-TTTGG
1 CTTGAGTTATGCTGTAAATGATGTGCCCTTG-AGCTGAGTGTAATCGAACTCAAAGGTCTTTTGA
* *
1320682 CATATAGCCCTTCTTGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGAGTAATCGAA
65 CATATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTGAAGCTGAGAGTAATCGAA
* * * *
1320747 CTCAAAGGTCTTTAGTTGGCGGATAACCCTTCTCGACTTAAGTTATGCCGCAAATGATGTGCCCT
130 CTCAAAGG-CTTTA-TTAGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
* * * * *** * **
1320812 CGAAGCTGAGTGTAATCGAACGCGGGGGTC-TT--TTGGCAGATAGCCCTTCTCGACTTAAACTA
193 AG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
** * * *
1320874 CACTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGT-GACAGATAA
257 TGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT-TTT--TAG-CAGATAG
* * * * * * * * *
1320938 CCCTTCT-AGCCTTGAGTTATGTTGTAAATGAT-ATGCCCTCGAAGCTGAGTGTAATCGAACTTG
318 CCCTTCTCA-ACTTAAGCTATGCTGCAAATGATGGTGCCTTTG-AGCTGAGTGTAATCGAACTCG
** * * * * *
1321001 GGGGTC-TTTGGTTGGCAGATAGCCCTTCTCGA
381 AAGGTCTTTTGG-TGACAGATAACTCTTCTAGC
* * * * * * * *
1321033 CTTAAGCTATGCTGCAAATGATGTGTCGTTGAGTTGAGCGTAGTCGAACTCAAAGGTCTTTTGTT
1 CTTGAGTTATGCTGTAAATGATGTGCCCTTGAGCTGAGTGTAATCGAACTCAAAGGTC--TT-TT
* * * * * * * * * * * ** *
1321098 GGCAAATAACCCTTCTTGCCTTGAGCTATATTTCAAATGATGTGCCTTGGAGCTGAGCGTGGTTG
63 GACATATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTGAAGCTGAGAGTAATCG
* * ** * * * * *
1321163 AACTCGAAGGTCCTTGCTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATG
128 AACTCAAAGG-CTTTATTAGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1321220 CTATCTTTTT
Statistics
Matches: 875, Mismatches: 113, Indels: 68
0.83 0.11 0.06
Matches are distributed among these distances:
409 1 0.00
410 30 0.03
411 1 0.00
412 85 0.10
413 30 0.03
414 85 0.10
415 136 0.16
417 54 0.06
418 91 0.10
420 1 0.00
421 294 0.34
422 22 0.03
423 14 0.02
425 29 0.03
426 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (412 bp):
CTTGAGTTATGCTGTAAATGATGTGCCCTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGAC
ATATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTGAAGCTGAGAGTAATCGAAC
TCAAAGGCTTTATTAGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTAGA
GCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCT
GCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTAGCAGATAGCCCTTCTC
AACTTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTT
GGTGACAGATAACTCTTCTAGC
Found at i:1327868 original size:37 final size:35
Alignment explanation
Indices: 1327773--1327969 Score: 141
Period size: 36 Copynumber: 5.3 Consensus size: 35
1327763 TATCTTCTAA
1327773 ATATATATATATATATTTCAAAAAT-TATTTTAAAA-T
1 ATATATATATA-AT-TTTCAAAAATGT-TTTTAAAACT
* * ** *
1327809 TTATATATGTTTTTTTCAAAAAATGTTTTTAAAATT
1 ATATATATATAATTTTC-AAAAATGTTTTTAAAACT
*
1327845 ATATATTATATAATTTTCCAAAAAATGATTTTTAAAACC
1 ATATA-TATATAATTTT-C-AAAAATG-TTTTTAAAACT
* * *
1327884 ATATATTATATCATTTTTCAAAAAT-ATTTAAAAAGCT
1 ATATA-TATAT-AATTTTCAAAAATGTTTTTAAAA-CT
* *
1327921 ATATACTATATAAGTTTTC-AAATTGTTTTAAAAACT
1 ATATA-TATATAA-TTTTCAAAAATGTTTTTAAAACT
1327957 ATATAATATATAA
1 ATAT-ATATATAA
1327970 ATGTTTTCAA
Statistics
Matches: 132, Mismatches: 18, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
34 4 0.03
35 15 0.11
36 39 0.30
37 33 0.25
38 15 0.11
39 21 0.16
40 5 0.04
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (35 bp):
ATATATATATAATTTTCAAAAATGTTTTTAAAACT
Found at i:1327869 original size:39 final size:39
Alignment explanation
Indices: 1327820--1327907 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
1327810 TATATATGTT
* **
1327820 TTTTTCAAAAAATG-TTTTTAAAATTATATATTATATAA
1 TTTTCCAAAAAATGATTTTTAAAACCATATATTATATAA
*
1327858 TTTTCCAAAAAATGATTTTTAAAACCATATATTATATCA
1 TTTTCCAAAAAATGATTTTTAAAACCATATATTATATAA
*
1327897 TTTTTCAAAAA
1 TTTTCCAAAAA
1327908 TATTTAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 13 0.30
39 31 0.70
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (39 bp):
TTTTCCAAAAAATGATTTTTAAAACCATATATTATATAA
Found at i:1327988 original size:29 final size:27
Alignment explanation
Indices: 1327944--1327995 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1327934 GTTTTCAAAT
1327944 TGTTTTAAAAACTATATAATATATAAA
1 TGTTTTAAAAACTATATAATATATAAA
* *
1327971 TGTTTTCAAAACTATATATTATATA
1 TGTTTTAAAAACTATATAATATATA
1327996 TATTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (27 bp):
TGTTTTAAAAACTATATAATATATAAA
Found at i:1327996 original size:36 final size:36
Alignment explanation
Indices: 1327956--1328024 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
1327946 TTTTAAAAAC
* *
1327956 TATATA-ATATATAAATGTTTTC-AAAACTATATAT
1 TATATATATATAAAAATATTTTCAAAAACTATATAT
*
1327990 TATATATATTTAAAAATATTTTCAAAAACTATATA
1 TATATATATATAAAAATATTTTCAAAAACTATATA
1328025 AAATTTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 6 0.20
35 13 0.43
36 11 0.37
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (36 bp):
TATATATATATAAAAATATTTTCAAAAACTATATAT
Found at i:1332788 original size:348 final size:348
Alignment explanation
Indices: 1332016--1332802 Score: 1048
Period size: 348 Copynumber: 2.3 Consensus size: 348
1332006 TCTCAGTAGG
* * * * *
1332016 CACTATTTCAACTACTTTTCAGTGCTCAATTAATGCACAGTGTAAGCTAATTTTCAGAGATCATT
1 CACTATTTCAACTACTTTTCAGTTCTCAATTAATGCACAGTATCAGCTACTTTTCAGAGGTCATT
* **
1332081 TATTGCAGCAATAATGCAACGATTGACTTATTTTATTGGTCATTTACTGTAGAATTCAAGTAACT
66 TATTGTAGCAATAATGCAACGATTGACTTATTTTATTGGTCATTTACTGTAGAATTCAAACAACT
* * *
1332146 TTTCATAAAACGAGTAAAATAGTGGTGCATTATCATCTTCAGCAACTTTTCAAATGATACATCAA
131 TTTCAGAAAACAAATAAAATAGTGGTGCATTATCATCTTCAGCAACTTTTCAAATGATACATCAA
*
1332211 CTCAAATCAGAAAACATGTTTTTAACTCAGGCAAAATAATTCACCCTTCCAGCTATTGTGCAGTG
196 CTCAAATCAGAAAACATGTTTTTAACTCAGGCAAAATAATGCACCCTTCCAGCTATTGTGCAGTG
* * * *
1332276 AAATATGAACTAAAATCAAAAAACTTGTCAATGTTGAATTATCACTTCAAATTATAAAAAGTATG
261 AAATACGAACTAAAATCAAAAAACTTGTCAATGTTAAATTATCACTTCAAATCATAAAAACTATG
1332341 TATTTCAACCAGACCAAATTATT
326 TATTTCAACCAGACCAAATTATT
* * * **
1332364 CACTATTTCAACTACTTTTAAGTGT-TCAATTAATGTACAATATCATATACTTTTCAGAGGTCAT
1 CACTATTTCAACTACTTTTCAGT-TCTCAATTAATGCACAGTATCAGCTACTTTTCAGAGGTCAT
* * * *
1332428 TCATTATAGCAATAATGCAACGATTGGCTTATTTTGTTGGTCATTTACTGTAGAATTCAAACAAC
65 TTATTGTAGCAATAATGCAACGATTGACTTATTTTATTGGTCATTTACTGTAGAATTCAAACAAC
* * *
1332493 TTTTCAGAAAACAAATGAAATAGTGGTGCATTATCATCTTCAGGAACTTTTC-AATGATATATCA
130 TTTTCAGAAAACAAATAAAATAGTGGTGCATTATCATCTTCAGCAACTTTTCAAATGATACATCA
* * * *
1332557 ACTCAAAATCAGAAATCGTGTTTTTAACTCAGGCAAAATACTGCACCCTTCTAGCTATTGTTG-A
195 ACTC-AAATCAGAAAACATGTTTTTAACTCAGGCAAAATAATGCACCCTTCCAGCTATTG-TGCA
* * * * *
1332621 GTGAAATACGAACTCAAATTAAAAAACTTTTTAGTGTTAAATTATCACTTCAAATCATAAAAACT
258 GTGAAATACGAACTAAAATCAAAAAACTTGTCAATGTTAAATTATCACTTCAAATCATAAAAACT
*
1332686 -TGTATTTCAACCTAG-CCAAAATTTTT
323 ATGTATTTCAACC-AGACC-AAATTATT
* * * * * * *
1332712 CATTGTTTTAGCTACTTTTCAGTTCTCAATGAATGCATC-GTTTCAGCTACTTTGT-AGAGGTAA
1 CACTATTTCAACTACTTTTCAGTTCTCAATTAATGCA-CAGTATCAGCTACTTT-TCAGAGGTCA
*
1332775 TTTATTGTAGCAATAATGCAACGGTTGA
64 TTTATTGTAGCAATAATGCAACGATTGA
1332803 ATTTTTCAGT
Statistics
Matches: 377, Mismatches: 54, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
347 30 0.08
348 343 0.91
349 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (348 bp):
CACTATTTCAACTACTTTTCAGTTCTCAATTAATGCACAGTATCAGCTACTTTTCAGAGGTCATT
TATTGTAGCAATAATGCAACGATTGACTTATTTTATTGGTCATTTACTGTAGAATTCAAACAACT
TTTCAGAAAACAAATAAAATAGTGGTGCATTATCATCTTCAGCAACTTTTCAAATGATACATCAA
CTCAAATCAGAAAACATGTTTTTAACTCAGGCAAAATAATGCACCCTTCCAGCTATTGTGCAGTG
AAATACGAACTAAAATCAAAAAACTTGTCAATGTTAAATTATCACTTCAAATCATAAAAACTATG
TATTTCAACCAGACCAAATTATT
Found at i:1334156 original size:16 final size:16
Alignment explanation
Indices: 1334137--1334179 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1334127 ATAACATCCC
*
1334137 TAATTTAATTTTCTTT
1 TAATTTAATTTTCATT
**
1334153 TAATTGGATTTTCATT
1 TAATTTAATTTTCATT
1334169 TAA-TTAATTTT
1 TAATTTAATTTT
1334180 AGTGACCAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (16 bp):
TAATTTAATTTTCATT
Found at i:1335356 original size:5 final size:5
Alignment explanation
Indices: 1335346--1335424 Score: 56
Period size: 5 Copynumber: 15.8 Consensus size: 5
1335336 ATTAAAGATA
* * * *
1335346 AAAAT AAAAT --AAT AAAAC AAAAT AAAAT AAAAT AAAAAT AGAAT GAGAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT
* *
1335395 AAAA- AATAAA AAAAT AAAAA AAAAGT AAAA
1 AAAAT AA-AAT AAAAT AAAAT AAAA-T AAAA
1335425 CCAAGAAGAC
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
3 3 0.05
4 2 0.04
5 41 0.72
6 11 0.19
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:1335597 original size:2 final size:2
Alignment explanation
Indices: 1335592--1335625 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1335582 GGTTTAAATA
1335592 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
1335626 GCGCGTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1337567 original size:20 final size:20
Alignment explanation
Indices: 1337527--1337568 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1337517 CCAATTATAT
*
1337527 AAAAAATTTAACAAGTGAAA
1 AAAAAATTTAACAAGTCAAA
* *
1337547 AAAAAATTTATCGAGTCAAA
1 AAAAAATTTAACAAGTCAAA
1337567 AA
1 AA
1337569 TGAATTATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (20 bp):
AAAAAATTTAACAAGTCAAA
Found at i:1339162 original size:23 final size:23
Alignment explanation
Indices: 1339143--1339196 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1339133 AAATGCACAT
1339143 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
*
1339166 AAGTGCCGCGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
1339189 AAGTGCCA
1 AAGTGCCA
1339197 TATAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.17
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCG
Found at i:1339792 original size:18 final size:18
Alignment explanation
Indices: 1339771--1339812 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1339761 TGTATATAAC
*
1339771 CATATCATCATTTATATT
1 CATAACATCATTTATATT
*
1339789 CATAACCTCATTTATATT
1 CATAACATCATTTATATT
1339807 CATAAC
1 CATAAC
1339813 CCCTATCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (18 bp):
CATAACATCATTTATATT
Found at i:1339813 original size:18 final size:18
Alignment explanation
Indices: 1339778--1339813 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1339768 AACCATATCA
1339778 TCATTTATATTCATAACC
1 TCATTTATATTCATAACC
1339796 TCATTTATATTCATAACC
1 TCATTTATATTCATAACC
1339814 CCTATCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (18 bp):
TCATTTATATTCATAACC
Found at i:1340728 original size:24 final size:20
Alignment explanation
Indices: 1340671--1340733 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 20
1340661 TTCCCCTTGA
*
1340671 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
1340691 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
1340714 ATGTGCATCGATGCACTCCT
1 A-GTGCATCGATGCA-TCCT
1340734 TATGTATCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 14 0.40
21 1 0.03
22 1 0.03
23 4 0.11
24 14 0.40
25 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:1340734 original size:24 final size:22
Alignment explanation
Indices: 1340671--1340735 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 22
1340661 TTCCCCTTGA
*
1340671 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATCCTTAAC
*
1340691 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CCTTAAC
1340714 ATGTGCATCGATGCACTCCTTA
1 A-GTGCATCGATGCA-TCCTTA
1340736 TGTATCGATG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.38
21 1 0.03
22 1 0.03
23 3 0.08
24 17 0.46
25 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATCCTTAAC
Found at i:1344495 original size:23 final size:23
Alignment explanation
Indices: 1344462--1344523 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1344452 CTCATATAAA
*
1344462 TGCACCTAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
**
1344485 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
*
1344508 TGCACCGAAGTTCCAT
1 TGCACCGAAGTGCCAT
1344524 ATAAAATATC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:1349108 original size:40 final size:40
Alignment explanation
Indices: 1349053--1349136 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
1349043 ATATATGTCT
1349053 ATGAAAAGACATAAAAACAAGATATAAGCCACATGACATG
1 ATGAAAAGACATAAAAACAAGATATAAGCCACATGACATG
*
1349093 ATGAAAAGACATAAAAACAAGATATAAGCCATATGACATG
1 ATGAAAAGACATAAAAACAAGATATAAGCCACATGACATG
1349133 -TGAA
1 ATGAA
1349137 TGTGAATCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.55, C:0.13, G:0.15, T:0.17
Consensus pattern (40 bp):
ATGAAAAGACATAAAAACAAGATATAAGCCACATGACATG
Found at i:1350382 original size:23 final size:23
Alignment explanation
Indices: 1350325--1350376 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1350315 CCCCCTGTAG
*
1350325 GGTATCGGTACCTCCCTAGCTGT
1 GGTATAGGTACCTCCCTAGCTGT
*
1350348 GGTATAGGTACCTCTCTAGCTGT
1 GGTATAGGTACCTCCCTAGCTGT
1350371 GGTATA
1 GGTATA
1350377 TTTACCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (23 bp):
GGTATAGGTACCTCCCTAGCTGT
Found at i:1351879 original size:32 final size:32
Alignment explanation
Indices: 1351841--1351921 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
1351831 GATACTCTTA
* *
1351841 TGCATTATCTGAATGTAAACCTAAACATACTG
1 TGCATTATCTGAATGCAAACCTAAACATAATG
* * *
1351873 TTCATTATCT-AATTGCAAACCTGACCATAATG
1 TGCATTATCTGAA-TGCAAACCTAAACATAATG
1351905 TGCATTATCTGAATGCA
1 TGCATTATCTGAATGCA
1351922 CCCTGACTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.05
32 37 0.90
33 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (32 bp):
TGCATTATCTGAATGCAAACCTAAACATAATG
Found at i:1353024 original size:63 final size:64
Alignment explanation
Indices: 1352946--1353102 Score: 210
Period size: 63 Copynumber: 2.5 Consensus size: 64
1352936 GATTTAATTG
* *** *
1352946 AACATCGAATGCATTTCATGCACCGATGCACTCTCCATGCATCGATGCACTC-GAATA-TTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCATCGATGCAC-CAGAATATTTTTCA
* **
1353009 AACATCGAATGCATTTGATGCATCGATGCACAAGCAATGCATCGATGCACCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCATCGATGCACCAGAATATTTTTCA
*
1353073 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
1353103 TCCTAGTGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
62 1 0.01
63 47 0.57
64 35 0.42
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCATCGATGCACCAGAATATTTTTCA
Found at i:1353118 original size:63 final size:61
Alignment explanation
Indices: 1352946--1353122 Score: 189
Period size: 63 Copynumber: 2.8 Consensus size: 61
1352936 GATTTAATTG
* *
1352946 AACATCGAATGCATTTCATGCACCGATGCACTCTCCATGCATCGATGCACTCGAATATTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCA-TC-ACATGCATCGATGCACTCGAATATTTTCA
* **
1353009 AACATCGAATGCATTTGATGCATCGATGCA-CAAGCAATGCATCGATGCAC-CAGGCTATTTTTC
1 AACATCGAATGCATTTCATGCATCGATGCATC-A-C-ATGCATCGATGCACTC-GAATA-TTTTC
1353072 A
61 A
* *
1353073 AACATCGAATGCATTTTATGCATCGATGCATC-CTAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCATCAC-A-TGCATCGATGCACT
1353123 AAGTGTCCCA
Statistics
Matches: 98, Mismatches: 9, Indels: 13
0.82 0.08 0.11
Matches are distributed among these distances:
61 1 0.01
62 4 0.04
63 57 0.58
64 35 0.36
65 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (61 bp):
AACATCGAATGCATTTCATGCATCGATGCATCACATGCATCGATGCACTCGAATATTTTCA
Found at i:1354195 original size:19 final size:19
Alignment explanation
Indices: 1354114--1354265 Score: 135
Period size: 19 Copynumber: 7.8 Consensus size: 19
1354104 TGTTACCTTG
*
1354114 AGTATCGATACTCTAGGGAA
1 AGTATCGATACTCT-TGGAA
* * *
1354134 AATATTGATACT-TTAGAA
1 AGTATCGATACTCTTGGAA
* *
1354152 AGTCTCCATACTCTTGGGTAA
1 AGTATCGATACTCTT-GG-AA
*
1354173 AGTATTGATACTCTTGGAA
1 AGTATCGATACTCTTGGAA
*
1354192 AGTATCCATACTCTTGGGTAA
1 AGTATCGATACTCTT-GG-AA
*
1354213 AGTATCGATACTCTAGGAA
1 AGTATCGATACTCTTGGAA
** * *
1354232 AACATCCATACTCTTGAAA
1 AGTATCGATACTCTTGGAA
1354251 AGTATCGATACTCTT
1 AGTATCGATACTCTT
1354266 TGCCTAAAAT
Statistics
Matches: 103, Mismatches: 24, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
18 11 0.11
19 46 0.45
20 17 0.17
21 29 0.28
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (19 bp):
AGTATCGATACTCTTGGAA
Found at i:1354200 original size:40 final size:40
Alignment explanation
Indices: 1354114--1354265 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
1354104 TGTTACCTTG
* * * * *
1354114 AGTATCGATACTCTAGGG-AAAATATTGATACT-TTAGAA
1 AGTATCCATACTCTTGGGTAAAGTATCGATACTCTTGGAA
* *
1354152 AGTCTCCATACTCTTGGGTAAAGTATTGATACTCTTGGAA
1 AGTATCCATACTCTTGGGTAAAGTATCGATACTCTTGGAA
*
1354192 AGTATCCATACTCTTGGGTAAAGTATCGATACTCTAGGAA
1 AGTATCCATACTCTTGGGTAAAGTATCGATACTCTTGGAA
** *
1354232 AACATCCATACTCTT--GAAAAGTATCGATACTCTT
1 AGTATCCATACTCTTGGGTAAAGTATCGATACTCTT
1354266 TGCCTAAAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
38 32 0.32
39 13 0.13
40 55 0.55
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (40 bp):
AGTATCCATACTCTTGGGTAAAGTATCGATACTCTTGGAA
Found at i:1354316 original size:16 final size:17
Alignment explanation
Indices: 1354295--1354328 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1354285 TTGCCCTCAA
*
1354295 ATCATCC-ATTATCGAT
1 ATCATCCTAGTATCGAT
1354311 ATCATCCTAGTATCGAT
1 ATCATCCTAGTATCGAT
1354328 A
1 A
1354329 CTCGAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (17 bp):
ATCATCCTAGTATCGAT
Done.