Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000426.1 Hibiscus syriacus cultivar Beakdansim tig00000778_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: 3165331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 15
Found at i:2578133 original size:75 final size:74
Alignment explanation
Indices: 2577985--2578132 Score: 194
Period size: 75 Copynumber: 2.0 Consensus size: 74
2577975 ATATTTTAAT
* *
2577985 TTTAAATTTAAAAGTATCGATACTTTTGGAGAAGTATACATACTTTGCAACCTTCTCATTTTTTT
1 TTTAAATTCAAAAGTATCGATACTTTTGGAGAAGTATACATACTTTGCAACCTTATCA-TTTTTT
*
2578050 TATGTTTTTC
65 CATGTTTTTC
* *
2578060 TTTAAATTCGAAAGTATCGATATTTTTTGGA-AAGTAT-CGATACTTTTGCAACCTTATCA-TTT
1 TTTAAATTCAAAAGTATCGATA-CTTTTGGAGAAGTATAC-ATAC-TTTGCAACCTTATCATTTT
2578122 TTCATGTTTTT
63 TTCATGTTTTT
2578133 TTATTAGAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
74 14 0.22
75 30 0.46
76 21 0.32
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (74 bp):
TTTAAATTCAAAAGTATCGATACTTTTGGAGAAGTATACATACTTTGCAACCTTATCATTTTTTC
ATGTTTTTC
Found at i:2578250 original size:20 final size:20
Alignment explanation
Indices: 2578225--2578276 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2578215 AATTTAAGAG
*
2578225 TATCGATATTTTTAGAAAAA
1 TATCGATACTTTTAGAAAAA
*
2578245 TATCGATACTTTTAGAAAAG
1 TATCGATACTTTTAGAAAAA
*
2578265 TATAGATACTTT
1 TATCGATACTTT
2578277 GCAGCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (20 bp):
TATCGATACTTTTAGAAAAA
Found at i:2578443 original size:77 final size:76
Alignment explanation
Indices: 2578351--2578494 Score: 189
Period size: 77 Copynumber: 1.9 Consensus size: 76
2578341 TTTTTGAATT
* * **
2578351 TTTTATAATAAAAATATTGACATTTCATATTGCAACATATTTCTTAGTGAACCATAACAATCTTG
1 TTTTATAATAAAAATATTAACATTCCATATCACAACATATTTCTTAGTGAACCATAACAATCTTG
2578416 GGTAGAACTCA
66 GGTAGAACTCA
** * * * *
2578427 TTTTATTAATAAAAATATTAACATTCCATATCACAATTTATTTCTTAGTGTATCATGACATTCTT
1 TTTTA-TAATAAAAATATTAACATTCCATATCACAACATATTTCTTAGTGAACCATAACAATCTT
2578492 GGG
65 GGG
2578495 GTGCAATTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
76 5 0.09
77 52 0.91
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (76 bp):
TTTTATAATAAAAATATTAACATTCCATATCACAACATATTTCTTAGTGAACCATAACAATCTTG
GGTAGAACTCA
Found at i:2578721 original size:77 final size:73
Alignment explanation
Indices: 2578582--2578728 Score: 170
Period size: 77 Copynumber: 2.0 Consensus size: 73
2578572 TTCAACCCAC
* *
2578582 TTTATTAATAAAAAATTAACATTCCATATCAACTATTTTTTAGTAAACCATGACATTATTGGGCG
1 TTTATTAATAAAAAATTAACATTCCATATCAACTATTTCTTAATAAACCATGACATTATTGGGCG
2578647 CAACTCAT
66 CAACTCAT
* * * * *
2578655 TTTATTAATAAAAATATTAACATTTCACGTCA-CAATCTATTTCTTAATGAATCATGATATTCTT
1 TTTATTAATAAAAA-ATTAACA-TTC-CAT-ATCAA-CTATTTCTTAATAAACCATGACATTATT
*
2578719 GGGTGCAACT
61 GGGCGCAACT
2578729 ATATTTCTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
73 14 0.23
74 7 0.11
75 3 0.05
76 5 0.08
77 32 0.52
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (73 bp):
TTTATTAATAAAAAATTAACATTCCATATCAACTATTTCTTAATAAACCATGACATTATTGGGCG
CAACTCAT
Found at i:2583167 original size:19 final size:18
Alignment explanation
Indices: 2583126--2583176 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
2583116 CATAAGAAGC
*
2583126 CAGAAAAAAAAGGAAAGA
1 CAGAAAGAAAAGGAAAGA
* *
2583144 AAGAAAGAAAAGTGACAGA
1 CAGAAAGAAAAG-GAAAGA
2583163 CAGAAAGACAAAGG
1 CAGAAAGA-AAAGG
2583177 CAAGCACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 10 0.37
19 13 0.48
20 4 0.15
ACGTcount: A:0.65, C:0.08, G:0.25, T:0.02
Consensus pattern (18 bp):
CAGAAAGAAAAGGAAAGA
Found at i:2601085 original size:17 final size:17
Alignment explanation
Indices: 2601065--2601099 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2601055 TATTATATAT
*
2601065 TTGTATAATATTACAAA
1 TTGTAAAATATTACAAA
2601082 TTGTAAAATATTACAAA
1 TTGTAAAATATTACAAA
2601099 T
1 T
2601100 ATATAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (17 bp):
TTGTAAAATATTACAAA
Found at i:2603664 original size:16 final size:17
Alignment explanation
Indices: 2603630--2603665 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2603620 AATTGTTCAG
*
2603630 AAAATTGAATTAAATGA
1 AAAACTGAATTAAATGA
2603647 AAAACTGAATTAAA-GA
1 AAAACTGAATTAAATGA
2603663 AAA
1 AAA
2603666 TGACCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.64, C:0.03, G:0.11, T:0.22
Consensus pattern (17 bp):
AAAACTGAATTAAATGA
Found at i:2606398 original size:20 final size:21
Alignment explanation
Indices: 2606347--2606398 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
2606337 ACTCAGACAA
*
2606347 AAAATTAT-AAATTATTTTAT
1 AAAATTATAAAATTATATTAT
** *
2606367 AAAAGGAAAAAATTA-ATTAT
1 AAAATTATAAAATTATATTAT
2606387 AAAATTATAAAA
1 AAAATTATAAAA
2606399 AATAAAATTC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
AAAATTATAAAATTATATTAT
Found at i:2606405 original size:15 final size:17
Alignment explanation
Indices: 2606385--2606422 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
2606375 AAAATTAATT
2606385 ATAAAATT-ATAA-AAA
1 ATAAAATTCATAATAAA
*
2606400 ATAAAATTCATAATAAT
1 ATAAAATTCATAATAAA
2606417 ATAAAA
1 ATAAAA
2606423 CAATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 4 0.20
17 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATTCATAATAAA
Found at i:2607344 original size:40 final size:42
Alignment explanation
Indices: 2607249--2607407 Score: 250
Period size: 42 Copynumber: 3.8 Consensus size: 42
2607239 AAACATATTG
*
2607249 TCGTCACAAATCATCAACTAAGACTAGTGACAAAAACAACTA
1 TCGTCACAAATCACCAACTAAGACTAGTGACAAAAACAACTA
*
2607291 TCGTCACAAATCACCAACTAAGACTATTGACAAAAA-AA-TA
1 TCGTCACAAATCACCAACTAAGACTAGTGACAAAAACAACTA
* *
2607331 TCGTCACAAATCACCAATTAAGACTAGTGACAAAAACAATTA
1 TCGTCACAAATCACCAACTAAGACTAGTGACAAAAACAACTA
* *
2607373 TCATCACAAATCACCAATTAAGACTAGTGACAAAA
1 TCGTCACAAATCACCAACTAAGACTAGTGACAAAA
2607408 TGTTTTCATC
Statistics
Matches: 110, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
40 36 0.33
41 4 0.04
42 70 0.64
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.20
Consensus pattern (42 bp):
TCGTCACAAATCACCAACTAAGACTAGTGACAAAAACAACTA
Found at i:2607358 original size:82 final size:82
Alignment explanation
Indices: 2607249--2607407 Score: 264
Period size: 82 Copynumber: 1.9 Consensus size: 82
2607239 AAACATATTG
* *
2607249 TCGTCACAAATCATCAACTAAGACTAGTGACAAAAACAACTATCGTCACAAATCACCAACTAAGA
1 TCGTCACAAATCACCAACTAAGACTAGTGACAAAAACAACTATCATCACAAATCACCAACTAAGA
*
2607314 CTATTGACAAAAAAATA
66 CTAGTGACAAAAAAATA
* * *
2607331 TCGTCACAAATCACCAATTAAGACTAGTGACAAAAACAATTATCATCACAAATCACCAATTAAGA
1 TCGTCACAAATCACCAACTAAGACTAGTGACAAAAACAACTATCATCACAAATCACCAACTAAGA
2607396 CTAGTGACAAAA
66 CTAGTGACAAAA
2607408 TGTTTTCATC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.20
Consensus pattern (82 bp):
TCGTCACAAATCACCAACTAAGACTAGTGACAAAAACAACTATCATCACAAATCACCAACTAAGA
CTAGTGACAAAAAAATA
Found at i:2613164 original size:103 final size:103
Alignment explanation
Indices: 2612980--2613189 Score: 384
Period size: 103 Copynumber: 2.0 Consensus size: 103
2612970 GTCGAGGGTC
2612980 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
2613045 TTGATCCTTGGCATATGTTTATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2613083 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2613148 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2613186 TATG
1 TATG
2613190 GTCCTTATGG
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:2613279 original size:23 final size:23
Alignment explanation
Indices: 2613211--2613271 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2613201 CATTATTATA
*
2613211 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
2613234 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
2613257 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
2613272 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:2615217 original size:33 final size:33
Alignment explanation
Indices: 2615175--2615241 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2615165 CCTAGTACAG
2615175 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
2615208 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
2615241 A
1 A
2615242 ACACTACGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:2615369 original size:44 final size:44
Alignment explanation
Indices: 2615320--2615412 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
2615310 TGGTATATGG
*
2615320 TTATGGAATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
* * *
2615364 TTATGGATTAATGGTAAGTATATTGGTAAAATAAGCTTATGAGC
1 TTATGGAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
2615408 TTATG
1 TTATG
2615413 AGATAAATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.34
Consensus pattern (44 bp):
TTATGGAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:2615957 original size:20 final size:20
Alignment explanation
Indices: 2615909--2615957 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2615899 CCGATTCCCC
*
2615909 CACTGTTCACGGGTACTGTT
1 CACTGTTCACGAGTACTGTT
* *
2615929 CATTGTTCACGAGTATTGTT
1 CACTGTTCACGAGTACTGTT
*
2615949 CACTATTCA
1 CACTGTTCA
2615958 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.39
Consensus pattern (20 bp):
CACTGTTCACGAGTACTGTT
Found at i:2622590 original size:33 final size:33
Alignment explanation
Indices: 2622548--2622614 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2622538 CTTATTACAG
*
2622548 ATGGTGGACACGATCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
2622581 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
2622614 A
1 A
2622615 GCACTACAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:2622742 original size:44 final size:43
Alignment explanation
Indices: 2622693--2622791 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 43
2622683 TGGTATATGG
*
2622693 TTATGGAATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGG-ATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
* *
2622737 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGC
1 TTATGGAT-AATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
2622781 TTATGGGATAA
1 TTAT-GGATAA
2622792 ATGGTAAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
43 2 0.04
44 44 0.88
45 4 0.08
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (43 bp):
TTATGGATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:2624232 original size:18 final size:18
Alignment explanation
Indices: 2624211--2624267 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
2624201 CCGGAAAAAA
2624211 TTGTCGTGGCCAAATTTT
1 TTGTCGTGGCCAAATTTT
2624229 TTGTCGTGG-CAAATTTTT
1 TTGTCGTGGCCAAA-TTTT
*
2624247 TTGTCGT-GCC-ACTTTT
1 TTGTCGTGGCCAAATTTT
2624263 TTGTC
1 TTGTC
2624268 TTTTCTTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 9 0.25
17 6 0.17
18 21 0.58
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (18 bp):
TTGTCGTGGCCAAATTTT
Found at i:2625704 original size:29 final size:29
Alignment explanation
Indices: 2625667--2625722 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2625657 ATATATTAAT
*
2625667 TATAATATAAAATATAA-TAAGAATATACC
1 TATAATATAAAAT-TAATTAAAAATATACC
*
2625696 TATATTATAAAATTAATTAAAAATATA
1 TATAATATAAAATTAATTAAAAATATA
2625723 TTAATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.36
Consensus pattern (29 bp):
TATAATATAAAATTAATTAAAAATATACC
Found at i:2625732 original size:29 final size:29
Alignment explanation
Indices: 2625655--2625732 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 29
2625645 TATTTTATGG
2625655 AAATATATTAATTATAATATAAAATATAATAA
1 AAATATATTAATT-T--TATAAAATATAATAA
* * *
2625687 GAATATACCT-ATATTATAAAAT-TAATTAA
1 AAATATA-TTAATTTTATAAAATATAA-TAA
2625716 AAATATATTAATTTTAT
1 AAATATATTAATTTTAT
2625733 TAAAGCGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
28 4 0.11
29 23 0.62
31 1 0.03
32 8 0.22
33 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (29 bp):
AAATATATTAATTTTATAAAATATAATAA
Found at i:2626332 original size:21 final size:21
Alignment explanation
Indices: 2626306--2626345 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2626296 TAAAGCTCCC
*
2626306 AATAATAACATTTCCGGTAGA
1 AATAATAACACTTCCGGTAGA
*
2626327 AATAATAATACTTCCGGTA
1 AATAATAACACTTCCGGTA
2626346 ATATTTTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (21 bp):
AATAATAACACTTCCGGTAGA
Found at i:2627467 original size:20 final size:20
Alignment explanation
Indices: 2627439--2627496 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
2627429 ATATTTTTTT
2627439 TATTTTTTTAAAATATAAAA
1 TATTTTTTTAAAATATAAAA
* * *
2627459 TATTATTTTAATATAT-ATA
1 TATTTTTTTAAAATATAAAA
*
2627478 TATTTTTTTAAAATCTAAA
1 TATTTTTTTAAAATATAAA
2627497 CGTGAAACGC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTTTTTAAAATATAAAA
Found at i:2627473 original size:18 final size:19
Alignment explanation
Indices: 2627439--2627488 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
2627429 ATATTTTTTT
* *
2627439 TATTTTTTTAAAATATAAAA
1 TATTATTTTAATATAT-AAA
*
2627459 TATTATTTTAATATATATA
1 TATTATTTTAATATATAAA
*
2627478 TATTTTTTTAA
1 TATTATTTTAA
2627489 AATCTAAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTATTTTAATATATAAA
Found at i:2632335 original size:21 final size:21
Alignment explanation
Indices: 2632309--2632390 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
2632299 TAATATTATT
*
2632309 AATAATATATTATTTTTAAAA
1 AATAATATATTAATTTTAAAA
* * *
2632330 AATAATATATAAATGTTAATATT
1 AATAATATATTAATTTTAA-A-A
*
2632353 ATTAATA-ATATAATTTTAAAA
1 AATAATATAT-TAATTTTAAAA
* *
2632374 ATTAATATATTATTTTT
1 AATAATATATTAATTTT
2632391 TCGAATTACT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
21 29 0.60
22 6 0.12
23 13 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
AATAATATATTAATTTTAAAA
Found at i:2632370 original size:44 final size:46
Alignment explanation
Indices: 2632297--2632383 Score: 142
Period size: 47 Copynumber: 1.9 Consensus size: 46
2632287 TTAAACTTGA
2632297 GTTAATATTATTAATAATATATTATTTTTAAAAAATAATATATAAAT
1 GTTAATATTATTAATAATATA-TATTTTTAAAAAATAATATATAAAT
*
2632344 GTTAATATTATTAATAATATA-A-TTTTAAAAATTAATATAT
1 GTTAATATTATTAATAATATATATTTTTAAAAAATAATATAT
2632384 TATTTTTTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 17 0.44
45 1 0.03
47 21 0.54
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (46 bp):
GTTAATATTATTAATAATATATATTTTTAAAAAATAATATATAAAT
Found at i:2635680 original size:34 final size:35
Alignment explanation
Indices: 2635632--2635700 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
2635622 CAAAAAAAAT
*
2635632 TCTTGTATAATTAGATACATTTATATCAAACCATG
1 TCTTGTATAATTAGATACAGTTATATCAAACCATG
* * *
2635667 TCTTGT-TTATTAGATATAGTTATATCGAACCATG
1 TCTTGTATAATTAGATACAGTTATATCAAACCATG
2635701 CACTGTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 24 0.80
35 6 0.20
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (35 bp):
TCTTGTATAATTAGATACAGTTATATCAAACCATG
Found at i:2637159 original size:23 final size:24
Alignment explanation
Indices: 2637129--2637177 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2637119 TCTGTCATTC
2637129 TGACATGT-TTTTCTATGCTATTG
1 TGACATGTGTTTTCTATGCTATTG
* *
2637152 TGACATGTGTTTTCTCTGCTCTTG
1 TGACATGTGTTTTCTATGCTATTG
2637176 TG
1 TG
2637178 GCACGATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.51
Consensus pattern (24 bp):
TGACATGTGTTTTCTATGCTATTG
Found at i:2638382 original size:21 final size:20
Alignment explanation
Indices: 2638339--2638379 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2638329 ATTTTTTTTA
*
2638339 TATTTTTTATATTAATAATT
1 TATTTTTAATATTAATAATT
2638359 TATTTTTAATTATTAA-AATT
1 TATTTTTAA-TATTAATAATT
2638379 T
1 T
2638380 TATAAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTTAATATTAATAATT
Found at i:2642008 original size:21 final size:21
Alignment explanation
Indices: 2641982--2642026 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2641972 CATAAATATT
*
2641982 TAAAAA-AATTGATATTTTAGA
1 TAAAAATAA-TGATATTTTAAA
2642003 TAAAAATAATGATATTTTAAA
1 TAAAAATAATGATATTTTAAA
2642024 TAA
1 TAA
2642027 TTTTTTTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TAAAAATAATGATATTTTAAA
Found at i:2642486 original size:7 final size:7
Alignment explanation
Indices: 2642474--2642498 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2642464 ATTTAATTTT
2642474 AAAAATA
1 AAAAATA
2642481 AAAAATA
1 AAAAATA
2642488 AAAAATA
1 AAAAATA
2642495 AAAA
1 AAAA
2642499 TAATTTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2644340 original size:20 final size:20
Alignment explanation
Indices: 2644315--2644366 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2644305 TTTTTTCGAG
2644315 TTGAGTC-ATGTTTATAAAAT
1 TTGAGTCGA-GTTTATAAAAT
2644335 TTGAGTCGAGTTTATAAAAT
1 TTGAGTCGAGTTTATAAAAT
2644355 TTGAGTCGAGTT
1 TTGAGTCGAGTT
2644367 ATTCGAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGAGTCGAGTTTATAAAAT
Found at i:2646866 original size:20 final size:20
Alignment explanation
Indices: 2646825--2646866 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2646815 GTAAAATTGG
*
2646825 TACCCAGAGGTTAATATGGA
1 TACCCAGAGGTTAATATCGA
* *
2646845 TACCTAGAGGTTAGTATCGA
1 TACCCAGAGGTTAATATCGA
2646865 TA
1 TA
2646867 ATGAGGGCTT
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:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (20 bp):
TACCCAGAGGTTAATATCGA
Found at i:2648388 original size:160 final size:160
Alignment explanation
Indices: 2648118--2648441 Score: 526
Period size: 160 Copynumber: 2.0 Consensus size: 160
2648108 TATGGGAGAA
* *
2648118 GTGGATTGACAAAAACAAACGAAATCATTTAACCAATTTGGTTGTTTATGAATTCTACTGAATTT
1 GTGGATTAACAAAAACAAACAAAATCATTTAACCAATTTGGTTGTTTATGAATTCTACTGAATTT
* * * *
2648183 TTGAGTATGAACAACAAGGGTAGGAATAGAAGTAATTTGTTGATGTGAACATGAAGATG-ATGCA
66 TTGAGTAGGAACAACAAGGGTAGGAATAGAAGTAATCTATTGATGTAAACATGAAGA-GCATGCA
*
2648247 CTTGTTGAAACATAAAAATGTGAAGAAGAGT
130 CTTGTTGAAACATAAAAATGTGAAGAAGACT
2648278 GTGGATTAACAAAAACAAACAAAATCATTTAACCAATTTGGTTGTTTA-GAAATTCTACTGAATT
1 GTGGATTAACAAAAACAAACAAAATCATTTAACCAATTTGGTTGTTTATG-AATTCTACTGAATT
* *
2648342 TTTGAGTAGGAACAACAGGGGTAGGAATAGAAGTAATCTATTGATGTAAACATGAAGAGCATGTA
65 TTTGAGTAGGAACAACAAGGGTAGGAATAGAAGTAATCTATTGATGTAAACATGAAGAGCATGCA
*
2648407 CTTGTTGAAACATGAAAATGTGAAGAAGACT
130 CTTGTTGAAACATAAAAATGTGAAGAAGACT
2648438 GTGG
1 GTGG
2648442 GACTAAAGAT
Statistics
Matches: 152, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
159 2 0.01
160 150 0.99
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (160 bp):
GTGGATTAACAAAAACAAACAAAATCATTTAACCAATTTGGTTGTTTATGAATTCTACTGAATTT
TTGAGTAGGAACAACAAGGGTAGGAATAGAAGTAATCTATTGATGTAAACATGAAGAGCATGCAC
TTGTTGAAACATAAAAATGTGAAGAAGACT
Found at i:2658747 original size:23 final size:24
Alignment explanation
Indices: 2658721--2658769 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
2658711 ATAAAATACA
*
2658721 ATAACATACTAGGTA-GCGCTTAT
1 ATAACATAATAGGTAGGCGCTTAT
**
2658744 ATAATGTAATAGGTAGGCGCTTAT
1 ATAACATAATAGGTAGGCGCTTAT
2658768 AT
1 AT
2658770 TGACTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (24 bp):
ATAACATAATAGGTAGGCGCTTAT
Found at i:2659281 original size:23 final size:23
Alignment explanation
Indices: 2659246--2659318 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2659236 ATACTTTACA
*
2659246 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2659269 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
2659292 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2659315 ATAT
1 ATAT
2659319 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2659763 original size:23 final size:23
Alignment explanation
Indices: 2659736--2659808 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2659726 ATACTTTATA
2659736 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
2659759 ATATAAACACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
** *
2659782 ATATAAGTGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATT
2659805 ATAT
1 ATAT
2659809 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:2659763 original size:490 final size:489
Alignment explanation
Indices: 2658843--2661128 Score: 4051
Period size: 490 Copynumber: 4.7 Consensus size: 489
2658833 TTATAATATG
* * *
2658843 TTGAAAGTGTCTATATTTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATG
1 TTGAAAGTGTCCATA--CTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATG
*
2658908 TTTCAA-TTTTTTAATAGTGTTTTATGTTTT-TCACCTACAATATTAATTTAATAATTTCATTTG
64 TTTCAATTTTTTTAATAGTGTTTCATGTTTTCT-ACCTACAATATTAATTTAATAATTTCATTTG
* *
2658971 CATAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTATAATTTAAATTTAACAAT
128 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAAT
* *
2659036 ATTAACTAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATAT
193 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATAT
* * * ** * *
2659101 ATACCGTAACATAAAAAATAAATCATTAAATACATATAATTACTAAATTGATATCTTAAAACTCA
258 ATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCA
*
2659166 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTAAAATAAGTATGGACACTTTTATAAAAAG
323 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAG
*
2659231 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATAT
388 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACACTACCTATTACATTATAT
2659296 AAGTGCTACCTATTACATCATATTTTTACCTATTATA
453 AAGTGCTACCTATTACATCATATTTTTACCTATTATA
*
2659333 TTGAAAGTGTTCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
2659398 TCAATTTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTGCA
2659463 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
2659528 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* *
2659593 ATCGTAACGTAAAAAATAAATCATTACACGCCTATAATTATTAAATTAATATCTTAAAACTCACT
260 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
*
2659658 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGTACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGA
*
2659723 TAGATACTTTATAATATAAGCACTACCTATTACATTATATAAACACTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACACTACCTATTACATTATATAA
2659788 GTGCTACCTATTACATCATATTTTTACCTATTATA
455 GTGCTACCTATTACATCATATTTTTACCTATTATA
* *
2659823 TTGAAAGTGTTCATACTTTTTTATAAAAAGGATCTATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
2659888 TTCAATTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCTTTTGCA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTGCA
2659953 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
2660018 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
2660083 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTATTAAATTAATATCTTAAAACTCACT
260 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
* * *
2660148 CAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAATAAGTATGGACATTTTTATAAAAATGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGA
2660213 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACACTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACACTACCTATTACATTATATAA
*
2660278 GTGCTACCTATTATATCATATTTTTACCTATTATA
455 GTGCTACCTATTACATCATATTTTTACCTATTATA
* *
2660313 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATATAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* *
2660378 TCTATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTGCAC
*
2660443 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
2660508 AACCAAAGATAATAAT-AATATGT-A-ATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
2660570 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
*
2660635 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGAT
* *
2660700 AGATACTTTACAATATAAGCACTATCTATTACATTATATAAACGCTACCTATTACATTATATAAG
391 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACACTACCTATTACATTATATAAG
*
2660765 CGCTACCTATTACATCATATTTTTACCTATTATA
456 TGCTACCTATTACATCATATTTTTACCTATTATA
*
2660799 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATATTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* * *
2660864 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATGTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTGCAC
* *
2660929 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
2660994 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* * *
2661059 CCGTAACGTAAAAAATAAATCATTAGACGCCCATAATTACTAAATTAATATCTTAAAACTCACTT
261 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
2661124 AAAAG
326 AAAAG
2661129 GTGTACATAC
Statistics
Matches: 1728, Mismatches: 61, Indels: 15
0.96 0.03 0.01
Matches are distributed among these distances:
486 460 0.27
487 8 0.00
488 60 0.03
489 293 0.17
490 854 0.49
491 53 0.03
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (489 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGAT
AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACACTACCTATTACATTATATAAG
TGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:2660298 original size:23 final size:23
Alignment explanation
Indices: 2660226--2660290 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
2660216 ATACTTTACA
2660226 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
2660249 ATATAAACACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
**
2660272 ATATAAGTGCTACCTATTA
1 ATATAAGCACTACCTATTA
2660291 TATCATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:2660737 original size:21 final size:23
Alignment explanation
Indices: 2660712--2660784 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2660702 ATACTTTACA
* *
2660712 ATATAAGCACTATCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2660735 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2660758 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2660781 ATAT
1 ATAT
2660785 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2661158 original size:25 final size:25
Alignment explanation
Indices: 2661130--2661219 Score: 180
Period size: 25 Copynumber: 3.6 Consensus size: 25
2661120 ACTTAAAAGG
2661130 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
2661155 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
2661180 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
2661205 TGTACATACCTAAAT
1 TGTACATACCTAAAT
2661220 TTAATGATAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:2662377 original size:368 final size:368
Alignment explanation
Indices: 2661700--2662437 Score: 1449
Period size: 368 Copynumber: 2.0 Consensus size: 368
2661690 CTCATACGCC
2661700 AGTCACAAGAACAGGATGTAAGGCTAGAGTCGTAGTTACAGCAACAAATACAAACGATCAGTGGG
1 AGTCACAAGAACAGGATGTAAGGCTAGAGTCGTAGTTACAGCAACAAATACAAACGATCAGTGGG
*
2661765 TTATAAGTAAGTCTGATCAGAAACATAATCATGCATTGTGCACACCTGCTATGACACCATTTATG
66 TTATAAGTAAGTCTAATCAGAAACATAATCATGCATTGTGCACACCTGCTATGACACCATTTATG
2661830 CGTTCTAATAGAGCTGTAAGTAAGGCTGATATCGATGAGGCAACAACATTGAAAGAGGTCGGTGT
131 CGTTCTAATAGAGCTGTAAGTAAGGCTGATATCGATGAGGCAACAACATTGAAAGAGGTCGGTGT
2661895 TGGCACGTCACAAGTAATTAACTATTTAACGCAGCAGGCAGGGGGCTATCATAATGTTGGATTTA
196 TGGCACGTCACAAGTAATTAACTATTTAACGCAGCAGGCAGGGGGCTATCATAATGTTGGATTTA
2661960 CATCAACTGATTTTTTCGAAGACGGAATGGAATGACAACGATCTCCATATATCGTAAGTATCAAC
261 CATCAACTGATTTTTTCGAAGACGGAATGGAATGACAACGATCTCCATATATCGTAAGTATCAAC
2662025 ATGACTCCTATTGTATGTACATATAAATATTTTGAATGAAGGA
326 ATGACTCCTATTGTATGTACATATAAATATTTTGAATGAAGGA
*
2662068 AGTCACAAGAACAGGATGTAAGGCTAGAGTTGTAGTTACAGCAACAAATACAAACGATCAGTGGG
1 AGTCACAAGAACAGGATGTAAGGCTAGAGTCGTAGTTACAGCAACAAATACAAACGATCAGTGGG
2662133 TTATAAGTAAGTCTAATCAGAAACATAATCATGCATTGTGCACACCTGCTATGACACCATTTATG
66 TTATAAGTAAGTCTAATCAGAAACATAATCATGCATTGTGCACACCTGCTATGACACCATTTATG
2662198 CGTTCTAATAGAGCTGTAAGTAAGGCTGATATCGATGAGGCAACAACATTGAAAGAGGTCGGTGT
131 CGTTCTAATAGAGCTGTAAGTAAGGCTGATATCGATGAGGCAACAACATTGAAAGAGGTCGGTGT
*
2662263 TGGCACGTCACAAGTAATTAACTATTTAACGCATCAGGCAGGGGGCTATCATAATGTTGGATTTA
196 TGGCACGTCACAAGTAATTAACTATTTAACGCAGCAGGCAGGGGGCTATCATAATGTTGGATTTA
2662328 CATCAACTGATTTTTTCGAAGACGGAATGGAATGACAACGATCTCCATATATCGTAAGTATCAAC
261 CATCAACTGATTTTTTCGAAGACGGAATGGAATGACAACGATCTCCATATATCGTAAGTATCAAC
2662393 ATGACTCCTATTGTATGTACATATAAATATTTTGAATGAAGGA
326 ATGACTCCTATTGTATGTACATATAAATATTTTGAATGAAGGA
2662436 AG
1 AG
2662438 AAAAACCGCG
Statistics
Matches: 367, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
368 367 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (368 bp):
AGTCACAAGAACAGGATGTAAGGCTAGAGTCGTAGTTACAGCAACAAATACAAACGATCAGTGGG
TTATAAGTAAGTCTAATCAGAAACATAATCATGCATTGTGCACACCTGCTATGACACCATTTATG
CGTTCTAATAGAGCTGTAAGTAAGGCTGATATCGATGAGGCAACAACATTGAAAGAGGTCGGTGT
TGGCACGTCACAAGTAATTAACTATTTAACGCAGCAGGCAGGGGGCTATCATAATGTTGGATTTA
CATCAACTGATTTTTTCGAAGACGGAATGGAATGACAACGATCTCCATATATCGTAAGTATCAAC
ATGACTCCTATTGTATGTACATATAAATATTTTGAATGAAGGA
Found at i:2662777 original size:183 final size:183
Alignment explanation
Indices: 2662459--2663757 Score: 2355
Period size: 183 Copynumber: 7.1 Consensus size: 183
2662449 TACTTAAAAT
*
2662459 TACCGACACAATATTAAAAAGTGTCAATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
2662524 TATT-TACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATG
66 T-TTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATG
2662588 TCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
130 TCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
2662642 TACCGAAACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
2662707 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATT-TCGGGTTCCGATGTGTAAATA
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCT-GGGTTCCGATGTGTAAATG
2662771 TCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
130 TCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
2662825 TACCGACACAATATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
2662890 TTTATACAGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATAT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
2662955 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
2663008 TACCGACACAATATTAAAAAGTGTTGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
2663073 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCAATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
2663138 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
2663191 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
2663256 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAGTTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
2663321 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
2663374 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
2663439 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAGTTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
2663504 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
2663557 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* * *
2663622 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTTTTTTCAA
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAA
* *
2663687 --TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTCTGGAC----A-
128 TGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
2663736 TACCGACACAATATTAAAAAGT
1 TACCGACACAATATTAAAAAGT
2663758 TTGAAAACTT
Statistics
Matches: 1090, Mismatches: 20, Indels: 16
0.97 0.02 0.01
Matches are distributed among these distances:
179 22 0.02
180 1 0.00
182 3 0.00
183 1013 0.93
184 47 0.04
186 4 0.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:2664977 original size:3 final size:3
Alignment explanation
Indices: 2664969--2665025 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
2664959 ACTTGTTTGG
* * *
2664969 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC GTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
2665017 ATC TTC ATC
1 ATC ATC ATC
2665026 GTCAGCTTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:2665026 original size:12 final size:12
Alignment explanation
Indices: 2664973--2665042 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 12
2664963 GTTTGGATCA
* *
2664973 TCATCATCATCA
1 TCATCGTCATCT
* *
2664985 TCATCATCATCA
1 TCATCGTCATCT
2664997 TCATCGTCATCT
1 TCATCGTCATCT
2665009 TCATCGTCATCT
1 TCATCGTCATCT
*
2665021 TCATCGTCAGCT
1 TCATCGTCATCT
*
2665033 TCATCTTCAT
1 TCATCGTCAT
2665043 TGACCGCTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 53 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.39
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:2666862 original size:200 final size:200
Alignment explanation
Indices: 2666519--2667445 Score: 1703
Period size: 200 Copynumber: 4.6 Consensus size: 200
2666509 TTAAATTAGT
2666519 ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATG
1 ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATG
* *
2666584 TTTATGGGATCGACACTTTTTATATATGGATCGAAACTTTATTGTTGCACCCTGTTTGCCATTCA
66 TTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCA
* *
2666649 TTCTGTACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACCTATTCTCTC
131 TTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTC
2666714 ATAAA
196 ATAAA
*
2666719 ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGAGTTTC-ATT
1 ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGA-T
*
2666783 TTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTC
65 GTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTC
2666848 ATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCT
130 ATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCT
2666913 CATAAA
195 CATAAA
2666919 ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATG
1 ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATG
*
2666984 TTTATGAGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCA
66 TTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCA
*
2667049 TTCTGGACCAAAAATATCGACACAAACTACAAAAATGTCGATACATTATTTAGACCTATTCTCTC
131 TTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTC
2667114 ATAAA
196 ATAAA
* *
2667119 ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGTTT
1 ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATG
*
2667184 TTTATGGGATCGATACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCA
66 TTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCA
*
2667249 TTCTAGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTC
131 TTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTC
2667314 ATAAA
196 ATAAA
* * *
2667319 ACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTATATTATACTTTTGGGTTTCGATG
1 ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATG
2667384 TTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
66 TTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
2667446 ATTGTAAATT
Statistics
Matches: 703, Mismatches: 22, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
199 1 0.00
200 701 1.00
201 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (200 bp):
ACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATG
TTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCA
TTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTC
ATAAA
Found at i:2669421 original size:33 final size:33
Alignment explanation
Indices: 2669384--2669446 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2669374 CAACTTAATA
*
2669384 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
2669417 TCACCCCTCAACACCTCTACTTCTTTCACC
1 TCACCCCTCAACACCCCAACTTCTTTCACC
2669447 GCTCCATCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.49, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:2669508 original size:21 final size:21
Alignment explanation
Indices: 2669483--2669547 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2669473 CCCCTTATGC
* *
2669483 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2669504 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
2669525 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2669546 CT
1 CT
2669548 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:2671795 original size:17 final size:18
Alignment explanation
Indices: 2671773--2671815 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
2671763 ATATATCCGA
2671773 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
2671790 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
2671810 TATCAT
1 TATCAT
2671816 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:2671833 original size:20 final size:19
Alignment explanation
Indices: 2671778--2671824 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2671768 TCCGATATCA
2671778 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
2671797 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
2671818 TTTTACC
1 TTTTACC
2671825 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2671989 original size:20 final size:20
Alignment explanation
Indices: 2671959--2672005 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2671949 TCCGGTAACG
*
2671959 TTTTACTGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
2671978 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
2671999 TTTTACC
1 TTTTACC
2672006 TGGTATATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:2672049 original size:181 final size:182
Alignment explanation
Indices: 2671745--2672217 Score: 705
Period size: 181 Copynumber: 2.6 Consensus size: 182
2671735 CGTACTTACG
* * *
2671745 AAAGTATCGACACTTTCAATATATCCGATATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
2671810 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
2671875 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
2671926 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACTGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
2671991 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
2672056 AGGATTTAAAACTGATTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * **
2672108 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
2672173 TGTCATAGTTTTACATGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
2672218 AATTTGGATC
Statistics
Matches: 262, Mismatches: 29, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
181 165 0.63
182 97 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:2674481 original size:20 final size:20
Alignment explanation
Indices: 2674456--2674493 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2674446 TTTGGTTCAC
2674456 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
2674476 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
2674494 GAAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:2678798 original size:32 final size:32
Alignment explanation
Indices: 2678757--2678820 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2678747 ATTTCCACCC
2678757 ACCACAATCAATTAATTAACCTGTATTAAATT
1 ACCACAATCAATTAATTAACCTGTATTAAATT
*
2678789 ACCACAATCAATTAATTACCCTGTATTAAATT
1 ACCACAATCAATTAATTAACCTGTATTAAATT
2678821 GGCTTGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.34
Consensus pattern (32 bp):
ACCACAATCAATTAATTAACCTGTATTAAATT
Found at i:2680631 original size:21 final size:21
Alignment explanation
Indices: 2680580--2680632 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2680570 ATTATGACTA
*
2680580 TCGCAATGCGATTTTTCAATT
1 TCGCAATGCGATTTTCCAATT
**
2680601 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2680622 TCGCAATGCGA
1 TCGCAATGCGA
2680633 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2680647 original size:20 final size:21
Alignment explanation
Indices: 2680622--2680673 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2680612 TTTTCCCAAT
*
2680622 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2680642 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2680663 TCGCAATGCGA
1 TCGCAATGCGA
2680674 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2680686 original size:41 final size:41
Alignment explanation
Indices: 2680659--2680756 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
2680649 GCGAATTGGG
* *
2680659 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCACAACGCGATACTGACTATCGCAACGCGATAATAC
* *
2680700 AAAATCACAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCACAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
2680741 ATAATCGCAATGCGAT
1 AAAATCACAACGCGAT
2680757 TTTCAAAGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.20
Consensus pattern (41 bp):
AAAATCACAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:2680750 original size:21 final size:21
Alignment explanation
Indices: 2680661--2680756 Score: 74
Period size: 20 Copynumber: 4.7 Consensus size: 21
2680651 GAATTGGGAA
* *
2680661 AATCGCAATGCGATACTGAC-T
1 AATCGCAACGCGATAAT-ACAT
*
2680682 -ATCGCAACGCGATAATACAA
1 AATCGCAACGCGATAATACAT
* *
2680702 AATCACAACGCGATACTGAC-T
1 AATCGCAACGCGATAAT-ACAT
* *
2680723 -TTCGCAACGAGATAATACAT
1 AATCGCAACGCGATAATACAT
*
2680743 AATCGCAATGCGAT
1 AATCGCAACGCGAT
2680757 TTTCAAAGCA
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
19 4 0.07
20 27 0.47
21 24 0.42
22 2 0.04
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.21
Consensus pattern (21 bp):
AATCGCAACGCGATAATACAT
Found at i:2680953 original size:22 final size:21
Alignment explanation
Indices: 2680925--2680973 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
2680915 CTCTCTCACC
2680925 CATCTCCGACGAAATCCGTCCT
1 CATCTCCGACGAAATCCGT-CT
*
2680947 CATCTCCGGCGAAATCCGTCT
1 CATCTCCGACGAAATCCGTCT
2680968 -ATCTCC
1 CATCTCC
2680974 ATCTCTAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 6 0.23
21 2 0.08
22 18 0.69
ACGTcount: A:0.20, C:0.41, G:0.14, T:0.24
Consensus pattern (21 bp):
CATCTCCGACGAAATCCGTCT
Found at i:2681263 original size:20 final size:20
Alignment explanation
Indices: 2681215--2681272 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
2681205 TTATTCTCTC
* **
2681215 GTTGCGATAGTCAAATTCGT
1 GTTGCGATTGTCATTTTCGT
2681235 GTTGCGATTGTCATTTTCGT
1 GTTGCGATTGTCATTTTCGT
*
2681255 GTTGCGATTTTCATTTTC
1 GTTGCGATTGTCATTTTC
2681273 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.47
Consensus pattern (20 bp):
GTTGCGATTGTCATTTTCGT
Found at i:2683167 original size:20 final size:20
Alignment explanation
Indices: 2683142--2683222 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
2683132 GAAGAATAGT
*
2683142 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
2683162 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
2683182 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
** * *
2683202 TGGCTATCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
2683222 T
1 T
2683223 GGCTATCGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:2683223 original size:20 final size:20
Alignment explanation
Indices: 2683168--2683240 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
2683158 AAACTTACTT
*
2683168 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGGCTA
*
2683188 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
2683208 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
*
2683228 TCGCAATGCGAAA
1 TCGCAACGCGAAA
2683241 TGAAAATCGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGGCTA
Found at i:2683249 original size:19 final size:19
Alignment explanation
Indices: 2683227--2683281 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
2683217 GAAAATGGCT
2683227 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2683246 ATCGCAA--CG--AT-AAA
1 ATCGCAATGCGAAATGAAA
*
2683260 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2683279 ATC
1 ATC
2683282 ACAACGACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
14 10 0.33
15 2 0.07
16 1 0.03
17 2 0.07
18 2 0.07
19 13 0.43
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2683261 original size:39 final size:40
Alignment explanation
Indices: 2683168--2683254 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
2683158 AAACTTACTT
***
2683168 TCGCAACGCGAAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTATCGCAACGCGGAAATGAAAA
* *
2683208 TCGCAACGCGAAAATGGCTATCGCAATGC-GAAATGAAAA
1 TCGCAACGCGAAAATGACTATCGCAACGCGGAAATGAAAA
2683247 TCGCAACG
1 TCGCAACG
2683255 ATAAAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 15 0.36
40 27 0.64
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (40 bp):
TCGCAACGCGAAAATGACTATCGCAACGCGGAAATGAAAA
Found at i:2683314 original size:33 final size:33
Alignment explanation
Indices: 2683227--2683306 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
2683217 GAAAATGGCT
* *
2683227 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
*
2683260 ATCGCAATGTGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
*
2683293 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2683307 CACAAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGACAAA
Found at i:2683335 original size:19 final size:19
Alignment explanation
Indices: 2683313--2683409 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
2683303 GAAACACAAA
2683313 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
2683332 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
2683348 TCG--TTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2683365 TCACATTGCGATTTT-A--
1 TCGCATTGCGATTTTCATT
2683381 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2683398 TCGCATTGCGAT
1 TCGCATTGCGAT
2683410 AGCCATTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 15 0.25
15 4 0.07
16 6 0.10
17 6 0.10
18 4 0.07
19 26 0.43
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2683364 original size:33 final size:33
Alignment explanation
Indices: 2683318--2683409 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
2683308 ACAAATCGCA
* *
2683318 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTATCG
* *
2683351 TTGTGATTTTCATTTCACATTGCGATTTTATCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTATCG
2683384 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2683410 AGCCATTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.14, C:0.17, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTATCG
Found at i:2683445 original size:20 final size:20
Alignment explanation
Indices: 2683396--2683448 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2683386 GCGATTTTCA
*
2683396 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
2683416 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
2683436 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
2683449 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:2683813 original size:21 final size:20
Alignment explanation
Indices: 2683787--2683854 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
2683777 CTGTCATCCC
2683787 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
2683808 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
*
2683829 TCAAGAGTCCCCCCCA-CGT
1 TCAAGAGTCCCCTCCATCGT
2683848 TCAAGAG
1 TCAAGAG
2683855 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 8 0.22
20 2 0.05
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:2683866 original size:40 final size:42
Alignment explanation
Indices: 2683777--2683866 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
2683767 CCCGACTCAC
*
2683777 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCA
* *
2683819 CTATCATCCCTCAAGAGTCCCC-CCCA-CGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCA
2683859 CTGTCATC
1 CTGTCATC
2683867 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 20 0.45
41 3 0.07
42 21 0.48
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCA
Found at i:2683875 original size:40 final size:40
Alignment explanation
Indices: 2683780--2683866 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 40
2683770 GACTCACCTG
* *
2683780 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCA-CGTTCAAGAGGCCACTA
*
2683822 TCATCCCTCAAGAGTCCCCCCCACGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACGTTCAAGAGGCCACTA
2683862 TCATC
1 TCATC
2683867 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
40 20 0.48
41 3 0.07
42 19 0.45
ACGTcount: A:0.23, C:0.41, G:0.15, T:0.21
Consensus pattern (40 bp):
TCATCCCTCAAGAGTCCCCCCCACGTTCAAGAGGCCACTA
Found at i:2685290 original size:14 final size:14
Alignment explanation
Indices: 2685256--2685294 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2685246 TTGATTGTTT
2685256 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
2685270 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
2685284 TGTTGATTTGT
1 AATTGATTTGT
2685295 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2685523 original size:20 final size:20
Alignment explanation
Indices: 2685498--2685553 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
2685488 TCGTATTGCG
*
2685498 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
2685518 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
2685538 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
2685554 TTCCCCGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2687183 original size:12 final size:12
Alignment explanation
Indices: 2687166--2687190 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2687156 TCTTCGGGGA
2687166 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2687178 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2687190 C
1 C
2687191 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2688218 original size:20 final size:20
Alignment explanation
Indices: 2688091--2688217 Score: 173
Period size: 20 Copynumber: 6.3 Consensus size: 20
2688081 GTATTATCTT
* *
2688091 GTTGCGATAGTCAGAATCTC
1 GTTGCGAAAGTCAGAATCGC
* * *
2688111 GTTGTGAAATTCAGAATTGC
1 GTTGCGAAAGTCAGAATCGC
2688131 GTTGCGAAAGTCAGAATCGC
1 GTTGCGAAAGTCAGAATCGC
2688151 GTTGCGAAAGTCAGAATCGC
1 GTTGCGAAAGTCAGAATCGC
*
2688171 GTTGCGAAAGTCAGTATCGC
1 GTTGCGAAAGTCAGAATCGC
* *
2688191 GTTGCGATAGTCAGTATCGC
1 GTTGCGAAAGTCAGAATCGC
*
2688211 ATTGCGA
1 GTTGCGA
2688218 TTTTCCAAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 96 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (20 bp):
GTTGCGAAAGTCAGAATCGC
Found at i:2688272 original size:21 final size:20
Alignment explanation
Indices: 2688248--2688300 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
2688238 ATTTACTTAT
2688248 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
2688269 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
2688290 TCGCATTGCGA
1 TCGCATTGCGA
2688301 TAGCCATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.81
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:2688792 original size:20 final size:19
Alignment explanation
Indices: 2688764--2688818 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2688754 CAATCATCTT
*
2688764 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
2688784 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
2688803 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
2688819 AGGGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:2688806 original size:19 final size:20
Alignment explanation
Indices: 2688725--2688818 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
2688715 GGCAATCATT
*
2688725 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
2688745 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-C-GCGGAAA
*
2688766 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
2688786 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
**
2688805 TGAAAATCGCAACG
1 TGACTATCGCAACG
2688819 AGGGAATCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 16 0.28
20 27 0.47
21 13 0.23
22 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:2688847 original size:19 final size:19
Alignment explanation
Indices: 2688771--2688854 Score: 61
Period size: 19 Copynumber: 4.6 Consensus size: 19
2688761 CTTAATGTCT
* **
2688771 ATCGCAACGCGGAAATGACT
1 ATCGCAAAGC-GAAATGAAA
*
2688791 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
**
2688810 ATCGC-AA-CG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
2688824 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
2688843 ATCGCAACGCGA
1 ATCGCAAAGCGA
2688855 TTTTAGTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
14 7 0.14
15 3 0.06
16 2 0.04
17 2 0.04
18 2 0.04
19 25 0.50
20 9 0.18
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:2688873 original size:19 final size:19
Alignment explanation
Indices: 2688851--2688936 Score: 103
Period size: 19 Copynumber: 4.8 Consensus size: 19
2688841 AAATCGCAAC
2688851 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
*
2688870 GCGA-TTT--TGTCG--TT
1 GCGATTTTCATTTCGCGTT
*
2688884 GCGATTTTCATTTCACGTT
1 GCGATTTTCATTTCGCGTT
2688903 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
2688922 GCGATTTTCATTTCG
1 GCGATTTTCATTTCG
2688937 TATTGCGATA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
14 6 0.10
15 3 0.05
16 4 0.07
17 3 0.05
18 3 0.05
19 39 0.67
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.48
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:2688945 original size:19 final size:19
Alignment explanation
Indices: 2688880--2688936 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
2688870 GCGATTTTGT
*
2688880 CGTTGCGATTTTCATTTCA
1 CGTTGCGATTTTCATTTCG
2688899 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
2688918 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
2688937 TATTGCGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2688951 original size:19 final size:19
Alignment explanation
Indices: 2688891--2688953 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
2688881 GTTGCGATTT
* * **
2688891 TCATTTCACGTTGCGATTT
1 TCATTTCGCATTGCGATAG
* **
2688910 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATAG
*
2688929 TCATTTCGTATTGCGATAG
1 TCATTTCGCATTGCGATAG
2688948 TCATTT
1 TCATTT
2688954 TTGCCTTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.48
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:2688952 original size:38 final size:38
Alignment explanation
Indices: 2688880--2688953 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
2688870 GCGATTTTGT
* **
2688880 CGTTGCGATTTTCATTTCACGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCACATTGCGATAGTCATTTCG
**
2688918 CGTTGCGATTTTCATTTCGTATTGCGATAGTCATTT
1 CGTTGCGATTTTCATTTCACATTGCGATAGTCATTT
2688954 TTGCCTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (38 bp):
CGTTGCGATTTTCATTTCACATTGCGATAGTCATTTCG
Found at i:2690518 original size:42 final size:42
Alignment explanation
Indices: 2690472--2690551 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
2690462 CGATGACAGT
* * *
2690472 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
2690514 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
2690552 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:2690946 original size:20 final size:20
Alignment explanation
Indices: 2690923--2690992 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
2690913 ACTTACTTTC
*
2690923 GCAATGCGAAAATGACTATT
1 GCAACGCGAAAATGACTATT
* *
2690943 GCAACGC-AGAAATGGCTATC
1 GCAACGCGA-AAATGACTATT
* **
2690963 GCAACACG-AAATGAAAATT
1 GCAACGCGAAAATGACTATT
*
2690982 GCAATGCGAAA
1 GCAACGCGAAA
2690993 TGAAAATCGC
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 14 0.38
20 23 0.62
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATT
Found at i:2690975 original size:19 final size:20
Alignment explanation
Indices: 2690932--2690976 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2690922 CGCAATGCGA
* *
2690932 AAATGACTATTGCAACGCAG
1 AAATGACTATCGCAACACAG
*
2690952 AAATGGCTATCGCAACAC-G
1 AAATGACTATCGCAACACAG
2690971 AAATGA
1 AAATGA
2690977 AAATTGCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACACAG
Found at i:2690985 original size:19 final size:19
Alignment explanation
Indices: 2690960--2691005 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2690950 AGAAATGGCT
2690960 ATCGCAACACGAAATGAAA
1 ATCGCAACACGAAATGAAA
* **
2690979 ATTGCAATGCGAAATGAAA
1 ATCGCAACACGAAATGAAA
2690998 ATCGCAAC
1 ATCGCAAC
2691006 TACAAAATCG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAACACGAAATGAAA
Found at i:2691019 original size:33 final size:33
Alignment explanation
Indices: 2690976--2691058 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
2690966 ACACGAAATG
* *
2690976 AAAATTGCAATGCGAAATGAAAATCGCAACTAC
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAC
*
2691009 AAAATCGCAATGCGAAATGAAAATCGCAACGAT
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAC
*
2691042 AAAATCGCAACGCGAAA
1 AAAATCGCAATGCGAAA
2691059 CACAAATCGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.14
Consensus pattern (33 bp):
AAAATCGCAATGCGAAATGAAAATCGCAACGAC
Found at i:2691033 original size:19 final size:19
Alignment explanation
Indices: 2690969--2691037 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
2690959 TATCGCAACA
*
2690969 CGAAATGAAAATTGCAATG
1 CGAAATGAAAATCGCAATG
2690988 CGAAATGAAAATCGCAA--
1 CGAAATGAAAATCGCAATG
* *
2691005 C--TA-CAAAATCGCAATG
1 CGAAATGAAAATCGCAATG
2691021 CGAAATGAAAATCGCAA
1 CGAAATGAAAATCGCAA
2691038 CGATAAAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 26 0.65
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.16
Consensus pattern (19 bp):
CGAAATGAAAATCGCAATG
Found at i:2691047 original size:14 final size:14
Alignment explanation
Indices: 2690995--2691053 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
2690985 ATGCGAAATG
* *
2690995 AAAATCGCAACTAC
1 AAAATCGCAACGAT
2691009 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
2691027 GAAAATCGCAACGAT
1 -AAAATCGCAACGAT
2691042 AAAATCGCAACG
1 AAAATCGCAACG
2691054 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 2 0.05
16 1 0.03
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.22, G:0.15, T:0.14
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:2691066 original size:33 final size:33
Alignment explanation
Indices: 2690976--2691069 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
2690966 ACACGAAATG
* * * *
2690976 AAAATTGCAATGCGAAATGAAAATCGCAACTAC
1 AAAATCGCAACGCGAAATCAAAATCGCAACGAC
* * *
2691009 AAAATCGCAATGCGAAATGAAAATCGCAACGAT
1 AAAATCGCAACGCGAAATCAAAATCGCAACGAC
2691042 AAAATCGCAACGCGAAA-CACAAATCGCA
1 AAAATCGCAACGCGAAATCA-AAATCGCA
2691070 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 1 0.02
33 54 0.98
ACGTcount: A:0.49, C:0.21, G:0.16, T:0.14
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATCAAAATCGCAACGAC
Found at i:2691087 original size:19 final size:19
Alignment explanation
Indices: 2691065--2691167 Score: 108
Period size: 19 Copynumber: 5.6 Consensus size: 19
2691055 GAAACACAAA
2691065 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2691084 TCGCGTTGCGATTTT-A--
1 TCGCATTGCGATTTTCATT
2691100 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2691117 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
** ***
2691136 TCGTGTTGCGATAGCCATTT
1 TCGCATTGCGATTTTCA-TT
2691156 TCGCATTGCGAT
1 TCGCATTGCGAT
2691168 AGTCATTTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 3 0.04
17 3 0.04
18 1 0.01
19 40 0.57
20 12 0.17
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2691164 original size:20 final size:20
Alignment explanation
Indices: 2691141--2691184 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2691131 TCATTTCGTG
2691141 TTGCGATAGCCATTTTCGCA
1 TTGCGATAGCCATTTTCGCA
* *
2691161 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTTCGCA
2691181 TTGC
1 TTGC
2691185 AAAAGTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCA
Found at i:2691197 original size:20 final size:20
Alignment explanation
Indices: 2691174--2691212 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2691164 CGATAGTCAT
2691174 TTTCGCGTTGCAAAAGTAAG
1 TTTCGCGTTGCAAAAGTAAG
* *
2691194 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCAAAAGTAA
2691213 CTATTCTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
TTTCGCGTTGCAAAAGTAAG
Found at i:2693615 original size:21 final size:21
Alignment explanation
Indices: 2693583--2693657 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
2693573 CGCTTTGAAA
*
2693583 ATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* * *
2693604 ATCTCGTTGCGA--AAGTCAGT
1 ATCGCGTTGCGATTATGT-ATT
*
2693624 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTATGTATT
2693645 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
2693658 AGTCAGTATC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.07
20 13 0.30
21 25 0.58
22 2 0.05
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:2693631 original size:20 final size:20
Alignment explanation
Indices: 2693603--2693669 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
2693593 GATTATGTAT
* *
2693603 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2693623 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
2693644 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
2693664 TATCGC
1 TATCGC
2693670 ATTGTGATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.08
20 19 0.50
21 14 0.37
22 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:2693643 original size:41 final size:41
Alignment explanation
Indices: 2693583--2693680 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
2693573 CGCTTTGAAA
* *
2693583 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
2693624 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
2693665 ATCGCATTGTGATTTT
1 ATCGCATTGCGATTTT
2693681 CCAAATTCGC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.40
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:2693696 original size:41 final size:41
Alignment explanation
Indices: 2693583--2693698 Score: 99
Period size: 41 Copynumber: 2.8 Consensus size: 41
2693573 CGCTTTGAAA
* ** * * * *
2693583 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCATTGCGATAGTCAGT
* ** * *
2693624 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCATTGCGATAGTCAGT
*
2693665 ATCGCATTGTGATTTTCCAAAT-TCGCATTGCGAT
1 ATCGCATTGCGATTTT-CAAATATCGCATTGCGAT
2693699 TTACTTATTC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 62 0.97
42 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCAAATATCGCATTGCGATAGTCAGT
Found at i:2693759 original size:21 final size:22
Alignment explanation
Indices: 2693707--2693759 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
2693697 ATTTACTTAT
*
2693707 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGAAAAA
* **
2693728 TTGCAACGCGAAATT-GAAAAA
1 TCGCATTGCGAAATTGGAAAAA
2693749 TCGCATTGCGA
1 TCGCATTGCGA
2693760 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGAAAAA
Found at i:2695346 original size:19 final size:19
Alignment explanation
Indices: 2695322--2695359 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2695312 AAACTAGTCC
*
2695322 AAATCAACATTTTCATATT
1 AAATCAACATTTTAATATT
*
2695341 AAATCAATATTTTAATATT
1 AAATCAACATTTTAATATT
2695360 CGATTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATCAACATTTTAATATT
Found at i:2696365 original size:16 final size:16
Alignment explanation
Indices: 2696344--2696382 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2696334 GGTATTATCC
*
2696344 GACCTGTTTTCAACCT
1 GACCTGTTATCAACCT
*
2696360 GACCTGTTATCAATCT
1 GACCTGTTATCAACCT
2696376 GACCTGT
1 GACCTGT
2696383 AATTGACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:2697390 original size:21 final size:20
Alignment explanation
Indices: 2697364--2697407 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2697354 GATTTCTGGG
* *
2697364 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
2697385 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
2697405 CAA
1 CAA
2697408 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:2698424 original size:2 final size:2
Alignment explanation
Indices: 2698417--2698465 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2698407 GAACATGTGA
2698417 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2698458 AT AT AT AT
1 AT AT AT AT
2698466 GTCTAAGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2699107 original size:149 final size:149
Alignment explanation
Indices: 2698927--2699231 Score: 592
Period size: 149 Copynumber: 2.0 Consensus size: 149
2698917 AGAGTCGAGG
2698927 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
1 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
*
2698992 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATT
2699057 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
2699076 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
1 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
2699141 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATT
2699206 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
*
2699225 TTCTACG
1 GTCTACG
2699232 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAA
Found at i:2699254 original size:23 final size:23
Alignment explanation
Indices: 2699210--2699254 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2699200 ATCATTATAT
* *
2699210 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTACAATTATACGG
* *
2699233 GGCACTTCGGTACATTTATACG
1 GGCACTACGGTACAATTATACG
2699255 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGG
Found at i:2700276 original size:17 final size:17
Alignment explanation
Indices: 2700254--2700291 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
2700244 TTTAAATAAG
2700254 AATTTATAATGTTAAAA
1 AATTTATAATGTTAAAA
*
2700271 AATTTATAATGTTTAAA
1 AATTTATAATGTTAAAA
2700288 AATT
1 AATT
2700292 GATTTAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
AATTTATAATGTTAAAA
Found at i:2703187 original size:40 final size:39
Alignment explanation
Indices: 2703138--2703213 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 39
2703128 ATCCCTATAA
*
2703138 AATTTATATTA-A-TAAACTATTTATAATTAATATTAAAAT
1 AATTTATATTATACTAAA-TATTAAT-ATTAATATTAAAAT
*
2703177 AATTATATATTATACTTAATATTAATATTAATATTAA
1 AATT-TATATTATACTAAATATTAATATTAATATTAA
2703214 CTTATATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
39 4 0.12
40 18 0.56
41 7 0.22
42 3 0.09
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (39 bp):
AATTTATATTATACTAAATATTAATATTAATATTAAAAT
Found at i:2703203 original size:6 final size:6
Alignment explanation
Indices: 2703163--2703262 Score: 57
Period size: 6 Copynumber: 16.3 Consensus size: 6
2703153 ACTATTTATA
2703163 ATTAAT ATTAAAAT AATTATAT ATT-AT ACTTAAT ATTAAT ATTAAT ATTAA-
1 ATTAAT ATT--AAT -ATTA-AT ATTAAT A-TTAAT ATTAAT ATTAAT ATTAAT
* * * * *
2703214 CTT-AT ATTAAT A-TAAT A-TAAA ATATAGT CTATAAA ATTAAT ATTAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT AT-TAAT AT-TAAT ATTAAT ATTAAT
2703261 AT
1 AT
2703263 AAACTATATG
Statistics
Matches: 74, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
4 1 0.01
5 16 0.22
6 35 0.47
7 14 0.19
8 5 0.07
9 3 0.04
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTAAT
Found at i:2703223 original size:22 final size:24
Alignment explanation
Indices: 2703158--2703231 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 24
2703148 AATAAACTAT
*
2703158 TTATAATTAATATTAAAATAATTATATA
1 TTATACTTAATATT--AAT-ATTA-ATA
2703186 TTATACTTAATATTAATATTAATA
1 TTATACTTAATATTAATATTAATA
2703210 TTA-ACTT-ATATTAATA-TAATA
1 TTATACTTAATATTAATATTAATA
2703231 T
1 T
2703232 AAAATATAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
21 6 0.13
22 9 0.20
23 4 0.09
24 6 0.13
25 4 0.09
26 3 0.07
28 13 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATACTTAATATTAATATTAATA
Found at i:2703253 original size:52 final size:51
Alignment explanation
Indices: 2703197--2703334 Score: 133
Period size: 52 Copynumber: 2.7 Consensus size: 51
2703187 TATACTTAAT
2703197 ATTAATATTAATATTAACTTATATTAATATAATATAAAATATAGTCTATAAA
1 ATTAATATTAATATTAACTTATATTAATATAATATAAAATATAGTCTAT-AA
* * * * *
2703249 ATTAATATTAATATAAAC-TATATGTTATA-AATTATATAGTATAGTTTATAA
1 ATTAATATTAATATTAACTTATAT-TAATATAA-TATAAAATATAGTCTATAA
* *
2703300 ACT-ATAGTTAATA-TAA-TTAATATTAATATAGTATA
1 ATTAATA-TTAATATTAACTT-ATATTAATATAATATA
2703335 GTTTATAAAC
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
50 14 0.20
51 22 0.31
52 35 0.49
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (51 bp):
ATTAATATTAATATTAACTTATATTAATATAATATAAAATATAGTCTATAA
Found at i:2703297 original size:14 final size:14
Alignment explanation
Indices: 2703280--2703341 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
2703270 ATGTTATAAA
2703280 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
2703294 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
2703308 TAATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
2703323 TAATATAGTATAGT
1 TTATATAGTATAGT
2703337 TTATA
1 TTATA
2703342 AACCTTAAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.61
15 9 0.24
16 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:2703483 original size:22 final size:22
Alignment explanation
Indices: 2703458--2703527 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
2703448 AAATAGATTG
2703458 TATATATACATATACTATATG-
1 TATATATACATATACTATATGT
*
2703479 T-TATAT--ATATAGT-T-TGT
1 TATATATACATATACTATATGT
2703496 ATATATTATACATATACTATATGT
1 -TATA-TATACATATACTATATGT
2703520 TATATATA
1 TATATATA
2703528 TAGTTTGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
16 2 0.05
17 1 0.03
18 7 0.18
19 2 0.05
20 8 0.21
21 1 0.03
22 10 0.26
23 5 0.13
24 3 0.08
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (22 bp):
TATATATACATATACTATATGT
Found at i:2703485 original size:20 final size:20
Alignment explanation
Indices: 2703460--2703525 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
2703450 ATAGATTGTA
2703460 TATATACATATACTATATGT
1 TATATACATATACTATATGT
* * * *
2703480 TATATATATAGT-TTGTAT-A
1 TATATACATA-TACTATATGT
2703499 TATTATACATATACTATATGT
1 TA-TATACATATACTATATGT
2703520 TATATA
1 TATATA
2703526 TATAGTTTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
TATATACATATACTATATGT
Found at i:2703488 original size:18 final size:18
Alignment explanation
Indices: 2703462--2703529 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
2703452 AGATTGTATA
2703462 TATACATATACTATATGT
1 TATACATATACTATATGT
* * *
2703480 TATATATATAGTTTGTATATAT
1 TATACATATA----CTATATGT
2703502 TATACATATACTATATGT
1 TATACATATACTATATGT
*
2703520 TATATATATA
1 TATACATATA
2703530 GTTTGTATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 24 0.62
22 15 0.38
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (18 bp):
TATACATATACTATATGT
Found at i:2703516 original size:40 final size:39
Alignment explanation
Indices: 2703458--2703549 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 39
2703448 AAATAGATTG
2703458 TATATATACATATACTATATGTTATATATATAGTTTGTA
1 TATATATACATATACTATATGTTATATATATAGTTTGTA
2703497 TATATTATACATATACTATATGTTATATATATAGTTTGTA
1 TATA-TATACATATACTATATGTTATATATATAGTTTGTA
2703537 TATACTATACATA
1 TATA-TATACATA
2703550 GTTTATACAT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 4 0.08
40 47 0.92
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (39 bp):
TATATATACATATACTATATGTTATATATATAGTTTGTA
Found at i:2703550 original size:20 final size:19
Alignment explanation
Indices: 2703480--2703553 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
2703470 TACTATATGT
*
2703480 TATATATATAGTTTGTATA
1 TATATACATAGTTTGTATA
* * *
2703499 TATTATACATA-TACTATATGT
1 TA-TATACATAGT-TTGTAT-A
*
2703520 TATATATATAGTTTGTATA
1 TATATACATAGTTTGTATA
2703539 TACTATACATAGTTT
1 TA-TATACATAGTTT
2703554 ATACATACAT
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
19 5 0.12
20 33 0.80
21 3 0.07
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TATATACATAGTTTGTATA
Found at i:2703561 original size:20 final size:20
Alignment explanation
Indices: 2703522--2703561 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2703512 CTATATGTTA
* * *
2703522 TATATATAGTTTGTATATAC
1 TATACATAGTTTATACATAC
2703542 TATACATAGTTTATACATAC
1 TATACATAGTTTATACATAC
2703562 ATGTACTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (20 bp):
TATACATAGTTTATACATAC
Found at i:2703587 original size:35 final size:36
Alignment explanation
Indices: 2703547--2703620 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
2703537 TATACTATAC
*
2703547 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
2703582 ATAGTTTACATGTATACATATACTATAGGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
2703619 AT
1 AT
2703621 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:2703903 original size:15 final size:14
Alignment explanation
Indices: 2703885--2703977 Score: 51
Period size: 15 Copynumber: 6.0 Consensus size: 14
2703875 ATATATATAC
2703885 TATATTAATATAAAT
1 TATATT-ATATAAAT
*
2703900 TATATTTTATAAACT
1 TATATTATATAAA-T
* **
2703915 ATATATTTTTATAGTT
1 -TATA-TTATATAAAT
2703931 TATATAAATAATATAAAT
1 TATAT---T-ATATAAAT
*
2703949 TATAGTATATAAAT
1 TATATTATATAAAT
*
2703963 ATATAGTATATAAAT
1 -TATATTATATAAAT
2703978 ATAAACTATA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 15 0.24
15 26 0.41
16 5 0.08
17 8 0.13
18 9 0.14
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.47
Consensus pattern (14 bp):
TATATTATATAAAT
Found at i:2703978 original size:15 final size:15
Alignment explanation
Indices: 2703941--2704005 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 15
2703931 TATATAAATA
2703941 ATATAAAT-TATAGT
1 ATATAAATATATAGT
2703955 ATATAAATATATAGT
1 ATATAAATATATAGT
* *
2703970 ATATAAATATAAACT
1 ATATAAATATATAGT
**
2703985 ATAATTTATATATAGT
1 AT-ATAAATATATAGT
2704001 ATATA
1 ATATA
2704006 CTATATAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 8 0.19
15 23 0.55
16 11 0.26
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (15 bp):
ATATAAATATATAGT
Done.