Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002012.1 Hibiscus syriacus cultivar Beakdansim tig00004111_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: 773058
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1040 original size:35 final size:34
Alignment explanation
Indices: 959--1040 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 34
949 ATTAAACTTT
*
959 TTTTATATTTTTAATTTTGTAAAAAAATTATATAA
1 TTTTATA-ATTTAATTTTGTAAAAAAATTATATAA
* *
994 TATTATGAATTTAATTTTTTAAAGAAAA-TATATAAA
1 TTTTAT-AATTTAATTTTGTAAA-AAAATTATAT-AA
1030 TTTTATAATTT
1 TTTTATAATTT
1041 TTAATATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 28 0.70
36 12 0.30
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (34 bp):
TTTTATAATTTAATTTTGTAAAAAAATTATATAA
Found at i:15737 original size:66 final size:67
Alignment explanation
Indices: 15610--15740 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 67
15600 ATATCCTCTA
* * * * *
15610 TTTTTTCTTAAAAATCATCCTTAATGTTACATTTTATTTCTATCCTATGTTTTGATTATTAAATT
1 TTTTTTCTTAAAAATCATACTTAATATTACATTTTATTTCTATCCTATATCTTGATCATTAAATT
15675 AT
66 AT
* **
15677 TTTTTTCTT-AAAATCATACTTAATATTATATTTTATTTCTATTTTAATATCTT-ATCATTAAAT
1 TTTTTTCTTAAAAATCATACTTAATATTACATTTTATTTCTATCCT-ATATCTTGATCATTAAAT
15740 T
65 T
15741 TGACCATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
66 41 0.75
67 14 0.25
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.56
Consensus pattern (67 bp):
TTTTTTCTTAAAAATCATACTTAATATTACATTTTATTTCTATCCTATATCTTGATCATTAAATT
AT
Found at i:23693 original size:31 final size:31
Alignment explanation
Indices: 23658--23735 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
23648 GTTTCAAAAG
* *
23658 TAACAAATTGGCCACTGACATTATTGATTTA
1 TAACAAATCGACCACTGACATTATTGATTTA
* * *
23689 TAACAAATCGATCATTGACATTATTGATTTT
1 TAACAAATCGACCACTGACATTATTGATTTA
*
23720 TAACAAATCGATCACT
1 TAACAAATCGACCACT
23736 CGTTGTTAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (31 bp):
TAACAAATCGACCACTGACATTATTGATTTA
Found at i:29388 original size:3 final size:3
Alignment explanation
Indices: 29380--29407 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29370 CGAAGAGCTT
29380 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
29408 CACCGGTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:33589 original size:17 final size:17
Alignment explanation
Indices: 33567--33601 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
33557 CATTATCATG
33567 GTGGAAGAATGAGTTGC
1 GTGGAAGAATGAGTTGC
33584 GTGGAAGAATGAGTTGC
1 GTGGAAGAATGAGTTGC
33601 G
1 G
33602 GCGCAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.43, T:0.23
Consensus pattern (17 bp):
GTGGAAGAATGAGTTGC
Found at i:33767 original size:20 final size:20
Alignment explanation
Indices: 33744--33789 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
33734 TCATACATCC
33744 TAAAATT-ATGATTTAAATTT
1 TAAAATTGATGA-TTAAATTT
*
33764 T-AAATTGATTATTAAATTT
1 TAAAATTGATGATTAAATTT
33783 TCAAAAT
1 T-AAAAT
33790 ACTATAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 14 0.64
20 4 0.18
21 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (20 bp):
TAAAATTGATGATTAAATTT
Found at i:34915 original size:31 final size:31
Alignment explanation
Indices: 34880--34938 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
34870 TTTTTTAAAA
* *
34880 ATTTTATATGTTTTA-ATGTTTATTAAATCTT
1 ATTTTATATATTTTATAT-TTTATAAAATCTT
34911 ATTTTATATATTTTATATTTTATAAAAT
1 ATTTTATATATTTTATATTTTATAAAAT
34939 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (31 bp):
ATTTTATATATTTTATATTTTATAAAATCTT
Found at i:42646 original size:28 final size:28
Alignment explanation
Indices: 42606--42742 Score: 238
Period size: 28 Copynumber: 4.9 Consensus size: 28
42596 AAAGGACCAC
*
42606 TATGTCCCGAAGGACCACATAGAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
*
42634 TATGTCCCGAAGGACCACATAGAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
*
42662 TATGTCCCGAAGGACCTCGTAGAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
42690 TATGTCCCGAAGGACCACGTAGAACACA
1 TATGTCCCGAAGGACCACGTAGAACACA
*
42718 TATGTCCCGAAGGACCGCGTAGAAC
1 TATGTCCCGAAGGACCACGTAGAAC
42743 CATCGACTCT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 105 1.00
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.15
Consensus pattern (28 bp):
TATGTCCCGAAGGACCACGTAGAACACA
Found at i:44091 original size:18 final size:19
Alignment explanation
Indices: 44068--44104 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
44058 CTTCATCTCC
*
44068 TCCGA-TCTTCTCCCGCCG
1 TCCGATTCTTCCCCCGCCG
44086 TCCGATTCTTCCCCCGCCG
1 TCCGATTCTTCCCCCGCCG
44105 CCCTTCCCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.05, C:0.51, G:0.16, T:0.27
Consensus pattern (19 bp):
TCCGATTCTTCCCCCGCCG
Found at i:46292 original size:12 final size:12
Alignment explanation
Indices: 46275--46301 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
46265 AGTTCTGGAT
46275 TGGGGATCATTA
1 TGGGGATCATTA
46287 TGGGGATCATTA
1 TGGGGATCATTA
46299 TGG
1 TGG
46302 CTGCTCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.37, T:0.33
Consensus pattern (12 bp):
TGGGGATCATTA
Found at i:49171 original size:32 final size:34
Alignment explanation
Indices: 49126--49195 Score: 99
Period size: 32 Copynumber: 2.1 Consensus size: 34
49116 TATATATATA
*
49126 TTAATATTAAAATTTAAATAGAT-AGA-TATCTT
1 TTAATATTAAAATTTAAATAAATAAGAGTATCTT
* *
49158 TTAATATTCAAATTTAAATAAATAATAGTATCTT
1 TTAATATTAAAATTTAAATAAATAAGAGTATCTT
49192 TTAA
1 TTAA
49196 CCTGAGATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 21 0.64
33 2 0.06
34 10 0.30
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (34 bp):
TTAATATTAAAATTTAAATAAATAAGAGTATCTT
Found at i:49221 original size:68 final size:68
Alignment explanation
Indices: 49147--49318 Score: 179
Period size: 68 Copynumber: 2.5 Consensus size: 68
49137 ATTTAAATAG
* * *
49147 ATAGATATCTTTTAATATTCAAATTTAAATAAATAATAGTATCTTTTAACCTGAGATATTCAAAA
1 ATAGATATCTTTTAATATTCAAAATTAAATAAATAATAATATCTTTTAA-CTGAAATATTCAAAA
49212 G-AT
65 GAAT
* * * * * * *
49215 ATAGATACCTTTTAATATTCAAACTTGAAGAGAA-AATAATATCTTTTAATTTAAATATTTAAAA
1 ATAGATATCTTTTAATATTCAAAATTAAATA-AATAATAATATCTTTTAACTGAAATATTCAAAA
49279 GAAT
65 GAAT
* * *
49283 ATA-ATTATATTTCAATATTCAAAATTAAATAGATAA
1 ATAGA-TATCTTTTAATATTCAAAATTAAATAAATAA
49319 CAAATATAAT
Statistics
Matches: 84, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
67 14 0.17
68 68 0.81
69 2 0.02
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (68 bp):
ATAGATATCTTTTAATATTCAAAATTAAATAAATAATAATATCTTTTAACTGAAATATTCAAAAG
AAT
Found at i:58563 original size:13 final size:13
Alignment explanation
Indices: 58563--58625 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
58553 CCGTTGACCC
58563 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
58576 TACCCAACCCGTT
1 GACCCGACCCGTT
*
58589 TACCCGACCCGACCCATT
1 GACCCGACCCG-----TT
58607 GACCCGACCCGTT
1 GACCCGACCCGTT
58620 GACCCG
1 GACCCG
58626 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 29 0.71
18 12 0.29
ACGTcount: A:0.19, C:0.48, G:0.17, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:58564 original size:18 final size:18
Alignment explanation
Indices: 58541--58631 Score: 93
Period size: 18 Copynumber: 5.2 Consensus size: 18
58531 ACCGGTCACA
58541 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
58559 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
58577 ACCC-A----ACCCGTTT
1 ACCCGACCCGACCCGTTG
*
58590 ACCCGACCCGACCCATTG
1 ACCCGACCCGACCCGTTG
58608 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
58629 ACC
1 ACC
58632 GTTGACCCGT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
13 12 0.20
14 1 0.02
17 1 0.02
18 36 0.59
21 11 0.18
ACGTcount: A:0.19, C:0.48, G:0.18, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:58594 original size:31 final size:31
Alignment explanation
Indices: 58545--58625 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
58535 GTCACAACCC
*
58545 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCATT
* * *
58576 TACCCAACCCGTTTACCCGACCCGACCCATT
1 GACCCGACCCGTTGACCCGACCCGACCCATT
58607 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
58626 TTGACCGTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCATT
Found at i:58623 original size:8 final size:8
Alignment explanation
Indices: 58612--58653 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
58602 CCATTGACCC
58612 GACCCGTT
1 GACCCGTT
58620 GACCCGTT
1 GACCCGTT
58628 GA-CCGTT
1 GACCCGTT
58635 GACCCGTT
1 GACCCGTT
58643 GA-CCGTT
1 GACCCGTT
58650 GACC
1 GACC
58654 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.44
8 18 0.56
ACGTcount: A:0.14, C:0.36, G:0.26, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:58635 original size:7 final size:7
Alignment explanation
Indices: 58615--58654 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
58605 TTGACCCGAC
58615 CCGTTGA
1 CCGTTGA
58622 CCCGTTGA
1 -CCGTTGA
58630 CCGTTGA
1 CCGTTGA
58637 CCCGTTGA
1 -CCGTTGA
58645 CCGTTGA
1 CCGTTGA
58652 CCG
1 CCG
58655 GAGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:58635 original size:15 final size:15
Alignment explanation
Indices: 58615--58653 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
58605 TTGACCCGAC
58615 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
58630 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
58645 CCGTTGACC
1 CCGTTGACC
58654 GGAGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.36, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:63331 original size:9 final size:9
Alignment explanation
Indices: 63317--63362 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
63307 AAGGGAAAAG
63317 TGACCGGTT
1 TGACCGGTT
63326 TGACCGGTTT
1 TGACCGG-TT
* *
63336 TGAAACTGTT
1 TG-ACCGGTT
63346 TGACCGGTT
1 TGACCGGTT
63355 TGACCGGT
1 TGACCGGT
63363 CACAACCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 20 0.65
10 8 0.26
11 3 0.10
ACGTcount: A:0.15, C:0.20, G:0.30, T:0.35
Consensus pattern (9 bp):
TGACCGGTT
Found at i:63389 original size:13 final size:13
Alignment explanation
Indices: 63389--63451 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
63379 CCGTTGACCC
63389 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
63402 TACCCAACCCGTT
1 GACCCGACCCGTT
*
63415 TACCCGACCCGACCCATT
1 GACCCGACCCG-----TT
63433 GACCCGACCCGTT
1 GACCCGACCCGTT
63446 GACCCG
1 GACCCG
63452 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 29 0.71
18 12 0.29
ACGTcount: A:0.19, C:0.48, G:0.17, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:63390 original size:18 final size:18
Alignment explanation
Indices: 63367--63457 Score: 93
Period size: 18 Copynumber: 5.2 Consensus size: 18
63357 ACCGGTCACA
63367 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
63385 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
63403 ACCC-A----ACCCGTTT
1 ACCCGACCCGACCCGTTG
*
63416 ACCCGACCCGACCCATTG
1 ACCCGACCCGACCCGTTG
63434 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
63455 ACC
1 ACC
63458 GTTGACCCGT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
13 12 0.20
14 1 0.02
17 1 0.02
18 36 0.59
21 11 0.18
ACGTcount: A:0.19, C:0.48, G:0.18, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:63420 original size:31 final size:31
Alignment explanation
Indices: 63371--63451 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
63361 GTCACAACCC
*
63371 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCATT
* * *
63402 TACCCAACCCGTTTACCCGACCCGACCCATT
1 GACCCGACCCGTTGACCCGACCCGACCCATT
63433 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
63452 TTGACCGTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCATT
Found at i:63449 original size:8 final size:8
Alignment explanation
Indices: 63438--63479 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
63428 CCATTGACCC
63438 GACCCGTT
1 GACCCGTT
63446 GACCCGTT
1 GACCCGTT
63454 GA-CCGTT
1 GACCCGTT
63461 GACCCGTT
1 GACCCGTT
63469 GA-CCGTT
1 GACCCGTT
63476 GACC
1 GACC
63480 GGAGTTGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.44
8 18 0.56
ACGTcount: A:0.14, C:0.36, G:0.26, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:63461 original size:7 final size:7
Alignment explanation
Indices: 63441--63480 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
63431 TTGACCCGAC
63441 CCGTTGA
1 CCGTTGA
63448 CCCGTTGA
1 -CCGTTGA
63456 CCGTTGA
1 CCGTTGA
63463 CCCGTTGA
1 -CCGTTGA
63471 CCGTTGA
1 CCGTTGA
63478 CCG
1 CCG
63481 GAGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:63461 original size:15 final size:15
Alignment explanation
Indices: 63441--63479 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
63431 TTGACCCGAC
63441 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
63456 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
63471 CCGTTGACC
1 CCGTTGACC
63480 GGAGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.36, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:101606 original size:20 final size:20
Alignment explanation
Indices: 101581--101673 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
101571 TTTTCCCAAT
101581 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
101601 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
101621 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
101642 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
101663 TCGCAATGCGA
1 TCGCAATGCGA
101674 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:101623 original size:41 final size:41
Alignment explanation
Indices: 101578--101673 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
101568 CGATTTTCCC
*
101578 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
101619 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
101660 AAATCGCAATGCGA
1 AATTCGCAATGCGA
101674 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:101686 original size:41 final size:41
Alignment explanation
Indices: 101600--101734 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
101590 GAATAAGTAA
* * * *
101600 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
101641 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
101682 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
101723 TTCGCAACGCGA
1 ATCGCAACGCGA
101735 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:101687 original size:20 final size:20
Alignment explanation
Indices: 101662--101756 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
101652 AATTGAGAAA
*
101662 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
101682 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
101703 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
101723 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
101743 TTCGCAACGCGATA
1 ATCGCAACGCGATA
101757 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:101972 original size:22 final size:22
Alignment explanation
Indices: 101944--101987 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
101934 CACTCTCTCA
101944 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
101966 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
101988 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:102276 original size:20 final size:20
Alignment explanation
Indices: 102251--102288 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
102241 CGATTCTCTC
102251 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
102271 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
102289 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:103625 original size:18 final size:18
Alignment explanation
Indices: 103604--103648 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
103594 TCCACTTCGG
*
103604 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
103622 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
103640 GAGCCATCA
1 GAGCCATCA
103649 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:104175 original size:19 final size:20
Alignment explanation
Indices: 104121--104187 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
104111 TAGTTTACTT
* *
104121 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
104141 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
104161 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
104180 TCGCAACG
1 TCGCAACG
104188 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:104195 original size:14 final size:14
Alignment explanation
Indices: 104176--104233 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
104166 ATGCGAAATG
104176 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
104190 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
104206 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
104222 AAAATCGCAACG
1 AAAATCGCAACG
104234 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:104218 original size:32 final size:33
Alignment explanation
Indices: 104160--104250 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
104150 GGAAATGGCT
*
104160 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
104193 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
104225 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
104251 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:104244 original size:19 final size:19
Alignment explanation
Indices: 104121--104255 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
104111 TAGTTTACTT
* **
104121 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
104141 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
104161 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
104180 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
104194 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
104212 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
104226 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
104245 TCGCAATGCGA
1 TCGCAACGCGA
104256 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:104301 original size:32 final size:32
Alignment explanation
Indices: 104262--104372 Score: 204
Period size: 32 Copynumber: 3.4 Consensus size: 32
104252 GCGATTTGTG
104262 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
104294 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
104326 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
*
104359 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
104373 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 59 0.77
33 18 0.23
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:104371 original size:19 final size:18
Alignment explanation
Indices: 104262--104413 Score: 121
Period size: 14 Copynumber: 8.9 Consensus size: 18
104252 GCGATTTGTG
104262 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
104278 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
104294 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
104310 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
104326 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
104342 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
* **
104359 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
*
104378 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGAT-TTCA
104398 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
104414 TAAGTTTCGT
Statistics
Matches: 109, Mismatches: 12, Indels: 28
0.73 0.08 0.19
Matches are distributed among these distances:
14 30 0.28
15 3 0.03
16 10 0.09
17 2 0.02
18 24 0.22
19 23 0.21
20 17 0.16
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.44
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:104391 original size:20 final size:19
Alignment explanation
Indices: 104357--104411 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
104347 TTGCGATTTT
*
104357 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
104376 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
104396 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
104412 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:106297 original size:14 final size:14
Alignment explanation
Indices: 106278--106313 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
106268 ATTGTTTAAT
106278 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
106292 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
106306 TGATTTGT
1 TGATTTGT
106314 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:106881 original size:14 final size:14
Alignment explanation
Indices: 106862--106897 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
106852 ATTGTTTAAT
106862 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
106876 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
106890 TGATTTGT
1 TGATTTGT
106898 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:108168 original size:24 final size:24
Alignment explanation
Indices: 108112--108170 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
108102 AGTCAGTATT
* *
108112 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
108136 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
108160 CGAATTTTGAT
1 CGAAATTTGAT
108171 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:108362 original size:12 final size:12
Alignment explanation
Indices: 108345--108369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
108335 ATATAATCCC
108345 GAAGAAGAAAAA
1 GAAGAAGAAAAA
108357 GAAGAAGAAAAA
1 GAAGAAGAAAAA
108369 G
1 G
108370 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:110680 original size:19 final size:19
Alignment explanation
Indices: 110658--110755 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
110648 GGAAATTACT
110658 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
110677 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
110691 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
110710 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
110724 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
110743 ATCGCAACGCGAA
1 ATCGCAATGCGAA
110756 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:110700 original size:33 final size:33
Alignment explanation
Indices: 110658--110751 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
110648 GGAAATTACT
110658 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
110691 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
110724 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
110752 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:110773 original size:19 final size:20
Alignment explanation
Indices: 110751--110793 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
110741 AAATCGCAAC
110751 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
110770 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
110790 GCGA
1 GCGA
110794 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:110778 original size:14 final size:14
Alignment explanation
Indices: 110779--110812 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
110769 TGCGATTTTC
110779 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
110793 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
110807 ATTTTC
1 ATTTTC
110813 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:110952 original size:14 final size:14
Alignment explanation
Indices: 110933--110969 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
110923 CATCAATTAA
110933 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
110947 ACAAATCACCTTTT
1 ACAAATCAACTTTT
110961 ACAAATCAA
1 ACAAATCAA
110970 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:112389 original size:21 final size:21
Alignment explanation
Indices: 112323--112389 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
112313 GTGAATCGGG
*
112323 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
112343 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
112365 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
112386 CTCT
1 CTCT
112390 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:112408 original size:42 final size:41
Alignment explanation
Indices: 112323--112444 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
112313 GTGAATCGGG
* * * * *
112323 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
112365 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
112407 CTC-TCAACGATAGGAGTGGACTCTTGATGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
112445 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
41 31 0.46
42 32 0.48
43 4 0.06
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:114483 original size:20 final size:19
Alignment explanation
Indices: 114438--114578 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
114428 TCTTTTGGTT
114438 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
114457 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
114478 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
114497 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
114511 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
114530 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
114544 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
114563 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
114579 TGCGATTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 18 0.19
16 4 0.04
17 4 0.04
19 39 0.42
20 26 0.28
21 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:114520 original size:33 final size:33
Alignment explanation
Indices: 114463--114561 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
114453 ACGAGATAAT
* *
114463 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
114497 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
114530 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
114562 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:114555 original size:19 final size:19
Alignment explanation
Indices: 114533--114583 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
114523 GCGACGAGAG
114533 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
114552 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
114571 AATCGCAATGCGA
1 AATCGCAACGCGA
114584 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:114612 original size:19 final size:19
Alignment explanation
Indices: 114579--114645 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
114569 AAAATCGCAA
**
114579 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
114598 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
114617 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
114637 TGCGATTTT
1 TGCGATTTT
114646 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:115259 original size:20 final size:20
Alignment explanation
Indices: 115166--115259 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
115156 CGCTAAGTAA
*
115166 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
115186 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
115206 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
115227 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
115247 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
115260 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:115278 original size:41 final size:41
Alignment explanation
Indices: 115187--115321 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
115177 AAAGTCAGTA
* * * ** *
115187 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
115227 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
115269 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
115310 TCGCGTTGCGAT
1 TCGCGTTGCGAT
115322 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:115292 original size:20 final size:20
Alignment explanation
Indices: 115248--115340 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
115238 ATAGTCAGTA
* **
115248 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
115269 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
115289 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
115310 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
115330 TCGCATTGCGA
1 TCGCATTGCGA
115341 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:115322 original size:41 final size:41
Alignment explanation
Indices: 115248--115343 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
115238 ATAGTCAGTA
*
115248 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
115289 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
115330 TCGCATTGCGAATT
1 TCGCATTGCGAATT
115344 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:143090 original size:33 final size:34
Alignment explanation
Indices: 143048--143114 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
143038 AAAGATTTGC
*
143048 TTAACTGTATGGGTGATTTAGGGC-TTTGGATCA
1 TTAACTGTATGGGTGATTTAAGGCTTTTGGATCA
*
143081 TTAATTGTATGGGTGATTTAAGGCTTTTGGATCA
1 TTAACTGTATGGGTGATTTAAGGCTTTTGGATCA
143115 CTCTTTCTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 22 0.71
34 9 0.29
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.42
Consensus pattern (34 bp):
TTAACTGTATGGGTGATTTAAGGCTTTTGGATCA
Found at i:146222 original size:44 final size:44
Alignment explanation
Indices: 146156--146249 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
146146 TACCATTATA
* * * * *
146156 AAGGAAGTATCGGTATTGTACCTTGAATACCGATACTACTTAAT
1 AAGGAAGTATCGGTACTATACCTCGAATAACAATACTACTTAAT
* **
146200 ATGGAAGTATCGGTACTATACCTCGGGTAACAATACTACTTAAT
1 AAGGAAGTATCGGTACTATACCTCGAATAACAATACTACTTAAT
146244 AAGGAA
1 AAGGAA
146250 AATGTGAATA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (44 bp):
AAGGAAGTATCGGTACTATACCTCGAATAACAATACTACTTAAT
Found at i:146873 original size:23 final size:23
Alignment explanation
Indices: 146846--146910 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
146836 TTTATATGGC
*
146846 ACTTCAGTGCATTTCTACGCGGA
1 ACTTCGGTGCATTTCTACGCGGA
* * * *
146869 ACTTCGGTACAATTCTACGTGGC
1 ACTTCGGTGCATTTCTACGCGGA
*
146892 ACTTCGGTGCATTTATACG
1 ACTTCGGTGCATTTCTACG
146911 AGTTGTGGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGA
Found at i:150883 original size:20 final size:20
Alignment explanation
Indices: 150858--150915 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
150848 ATCATATTCC
*
150858 CTGGTAATCTTTTATTCTCA
1 CTGGTAATCTTTTATTCCCA
150878 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
* *
150898 CTGATAATCTTATATTCC
1 CTGGTAATCTTTTATTCC
150916 GTGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:161589 original size:60 final size:60
Alignment explanation
Indices: 161498--161658 Score: 137
Period size: 60 Copynumber: 2.7 Consensus size: 60
161488 ATAGTTTAGG
* ** * ** * *
161498 ATGAAATTAAAATGTTCAAAACTTTGGGGACTATTTTATAATGAAAATCGCAGATTAG-A
1 ATGAAATTACAACATTCAAAAGTTTAAGGACTATTTTAGAATGAAAATCACAGATTAGTA
* * * * * * *
161557 GATGACATTAGAACATTCAAAAGTTTAAGGACTAATTTAGAATGAGATTCATAGATTGGTA
1 -ATGAAATTACAACATTCAAAAGTTTAAGGACTATTTTAGAATGAAAATCACAGATTAGTA
* **
161618 ATGAAATTACAACATTCAAAGGTTTAAAAACTATTTT-GAAT
1 ATGAAATTACAACATTCAAAAGTTTAAGGACTATTTTAGAAT
161659 TAAAGATCGT
Statistics
Matches: 80, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
59 4 0.05
60 75 0.94
61 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (60 bp):
ATGAAATTACAACATTCAAAAGTTTAAGGACTATTTTAGAATGAAAATCACAGATTAGTA
Found at i:167696 original size:19 final size:19
Alignment explanation
Indices: 167638--167696 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
167628 TAATAATAAA
*
167638 AATTATAAATTTTGAATAT
1 AATTATAAATTCTGAATAT
* *
167657 AATTCATAAA-TGT-AACAAT
1 AATT-ATAAATTCTGAA-TAT
167676 AATTATAAATTCTGAATAT
1 AATTATAAATTCTGAATAT
167695 AA
1 AA
167697 ATGGTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 7 0.22
19 18 0.56
20 7 0.22
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
AATTATAAATTCTGAATAT
Found at i:170777 original size:4 final size:4
Alignment explanation
Indices: 170768--170797 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
170758 GATAGGTGAA
*
170768 ATAC ATAC ATAC ATAC ATGC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
170798 TTCATGTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:171968 original size:18 final size:17
Alignment explanation
Indices: 171945--171985 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
171935 ATAAATGTTT
171945 AAATTATGTATCTAAAAA
1 AAATTATGT-TCTAAAAA
*
171963 AAATTA-GTTTTAAAAA
1 AAATTATGTTCTAAAAA
171979 AAATTAT
1 AAATTAT
171986 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 13 0.62
17 2 0.10
18 6 0.29
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (17 bp):
AAATTATGTTCTAAAAA
Found at i:175232 original size:16 final size:17
Alignment explanation
Indices: 175200--175232 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
175190 CTGGATGAAA
175200 ATCTGAGAGGAAACCAT
1 ATCTGAGAGGAAACCAT
175217 ATCTGAGAGG-AACCAT
1 ATCTGAGAGGAAACCAT
175233 GGCGTTCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (17 bp):
ATCTGAGAGGAAACCAT
Found at i:178539 original size:23 final size:23
Alignment explanation
Indices: 178496--178541 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
178486 GTAAATGCAA
* *
178496 TATTCTTTTGTTTGATATTTTAT
1 TATTCTTTTATTTAATATTTTAT
*
178519 TATTCTATTTATTTAATTTTTTA
1 TATTCT-TTTATTTAATATTTTA
178542 ATTTAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (23 bp):
TATTCTTTTATTTAATATTTTAT
Found at i:183304 original size:51 final size:52
Alignment explanation
Indices: 183228--183330 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 52
183218 TTGAGGTACA
183228 TAGTATTTGAGGTCACCATGTGAAATAACTTGAAAG-AAAATAGTTCAGATG
1 TAGTATTTGAGGTCACCATGTGAAATAACTTGAAAGAAAAATAGTTCAGATG
*
183279 TAGTATTTGAGGTCACCATGTGAAATACCTTGAAAGAAAAATAGTTCAGATG
1 TAGTATTTGAGGTCACCATGTGAAATAACTTGAAAGAAAAATAGTTCAGATG
183331 ATTGATTATC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 35 0.70
52 15 0.30
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (52 bp):
TAGTATTTGAGGTCACCATGTGAAATAACTTGAAAGAAAAATAGTTCAGATG
Found at i:187202 original size:60 final size:61
Alignment explanation
Indices: 187127--187302 Score: 214
Period size: 60 Copynumber: 2.9 Consensus size: 61
187117 TTGCAACATA
* * * * ** *
187127 CATCCTTAAACTATGACTCTTATTTTAAATTACTCCCTAAACTTTTAAACATT-TTAATTT
1 CATCCCTAAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTGAACATTCCAAACTT
* * *
187187 CATCCCTAAATTATGACTCTCATTCTAAATTGGTCCCTAAACTTTTGAACATTCCAAACTT
1 CATCCCTAAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTGAACATTCCAAACTT
* *
187248 -AT-CCTCAAACTATGACTCTTACTCTAAATTAGTCCCCAAACTTTTGAACATTCCA
1 CATCCCT-AAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTGAACATTCCA
187303 TTGATAACCC
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
59 3 0.03
60 92 0.93
61 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (61 bp):
CATCCCTAAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTGAACATTCCAAACTT
Found at i:192943 original size:2 final size:2
Alignment explanation
Indices: 192931--193002 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
192921 TTTGTTCTTT
192931 TA TA T- 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
192972 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
193003 TTTTTTTTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:202873 original size:22 final size:22
Alignment explanation
Indices: 202812--202873 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
202802 CAACTAAAAA
*
202812 TCGGTGGAAAGTTTTTTTCAACTT
1 TCGGTGG-AAG-TTTTTTCAACAT
*
202836 TCGGTGG-ATTTGTTTTCAACAT
1 TCGGTGGAAGTT-TTTTCAACAT
202858 TCGGTGGAAGTTTTTT
1 TCGGTGGAAGTTTTTT
202874 TTTGACTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.06
22 21 0.64
23 3 0.09
24 7 0.21
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.47
Consensus pattern (22 bp):
TCGGTGGAAGTTTTTTCAACAT
Found at i:205981 original size:181 final size:181
Alignment explanation
Indices: 205671--206035 Score: 667
Period size: 181 Copynumber: 2.0 Consensus size: 181
205661 AGTCTCTCCC
205671 TTCAGCATGTATAAGATTGTTGCTATCTTTTCGCCTTTCAGCACCACAAGCGCTCCACGGAACAC
1 TTCAGCATGTATAAGATTGTTGCTATCTTTTCGCCTTTCAGCACCACAAGCGCTCCACGGAACAC
* * * *
205736 CTTCATGATTCCTTTCCATGTTTCAATTTTGCTTGTATTATTATCCAACAATCCGTAGGATAATA
66 CTTCATGATTCATTTCCATGTTTCAATTTTGCTTGCATTATTAACCAACAATCCGTAAGATAATA
* *
205801 ATTTTTTCTTCAGGCCTTTCACGTGTCGCACATCTCGAACAACTTTAATTG
131 AATTTTTCTTCAGGCCTTTCACGTGCCGCACATCTCGAACAACTTTAATTG
*
205852 TTCAGCATGTATAAGTTTGTTGCTATCTTTTCGCCTTTCAGCACCACAAGCGCTCCACGGAACAC
1 TTCAGCATGTATAAGATTGTTGCTATCTTTTCGCCTTTCAGCACCACAAGCGCTCCACGGAACAC
205917 CTTCATGATTCATTTCCATGTTTCAATTTTGCTTGCATTATTAACCAACAATCCGTAAGATAATA
66 CTTCATGATTCATTTCCATGTTTCAATTTTGCTTGCATTATTAACCAACAATCCGTAAGATAATA
205982 AATTTTTCTTCAGGCCTTTCACGTGCCGCACATCTCGAACAACTTTAATTG
131 AATTTTTCTTCAGGCCTTTCACGTGCCGCACATCTCGAACAACTTTAATTG
206033 TTC
1 TTC
206036 CATCATACAT
Statistics
Matches: 177, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
181 177 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (181 bp):
TTCAGCATGTATAAGATTGTTGCTATCTTTTCGCCTTTCAGCACCACAAGCGCTCCACGGAACAC
CTTCATGATTCATTTCCATGTTTCAATTTTGCTTGCATTATTAACCAACAATCCGTAAGATAATA
AATTTTTCTTCAGGCCTTTCACGTGCCGCACATCTCGAACAACTTTAATTG
Found at i:206694 original size:13 final size:13
Alignment explanation
Indices: 206676--206702 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
206666 ATAAAGTGTT
206676 TAGCGTGTTTAAC
1 TAGCGTGTTTAAC
206689 TAGCGTGTTTAAC
1 TAGCGTGTTTAAC
206702 T
1 T
206703 GCTCCGTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (13 bp):
TAGCGTGTTTAAC
Found at i:207664 original size:23 final size:23
Alignment explanation
Indices: 207634--207696 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
207624 CAACTAAAAA
*
207634 TCGGTGGAAAGTTTTTTT-AACTT
1 TCGGTGGAAA-TTTTTTTCAACAT
207657 TCGGTGG--ATTTGTTTTCAACAT
1 TCGGTGGAAATTT-TTTTCAACAT
207679 TCGGTGGAAACTTTTTTT
1 TCGGTGGAAA-TTTTTTT
207697 TTTACTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 11 0.32
23 7 0.21
24 5 0.15
25 3 0.09
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.48
Consensus pattern (23 bp):
TCGGTGGAAATTTTTTTCAACAT
Found at i:212128 original size:314 final size:315
Alignment explanation
Indices: 211571--212185 Score: 939
Period size: 314 Copynumber: 2.0 Consensus size: 315
211561 TAGGTCCTGA
* *
211571 GGAACGGTGACCTAAAAATAACACATCACCCTATGAGTATAAAATCATATATCTAAACATAAATT
1 GGAACGGTGACCTAAAAATAACACATCACCCTATGAGTATAAAACCATATATCTAAACATAAATG
* *
211636 GACCATTAAATCATTTAACAACACTTACACAAATCTCGAGACGAATGTCCGAAACTGAACTGAAT
66 GACCATTAAATCATTTAACAACACTTACACAAATCTCGAGACGAATGTCCGAAACTAAACTGAAC
* * *
211701 TGAGTGAGGACGATCGAGACATATCAGAGAGTAATGCAGAGACTCGAGCTTACCTTCAGAACATA
131 TGAGCGAGGACGATCGAGACATATCAGAGAGTAATACAGAGACTCGAGCTCACCTTCAGAACATA
* * *
211766 ATAACAAGAAGTGAGTTAAAATCCCCATAATTTACGTAACATAATTAATATTTTAAGCAATAAAT
196 ATAACAAGAAGTGAGTCAAAATCCCAATAATTTACGTAACATAATTAATAATTTAAGCAATAAAT
211831 TATGCAAAACGAGACTTTT-AGGTCAGAATTTGGCAAAACATAACTAGGTCATAC
261 TATGCAAAACGAGACTTTTGAGGTCAGAATTTGGCAAAACATAACTAGGTCATAC
* * *
211885 GGAATGGTGACCTAAAAATAACACATCAGCCTATGTGTATAAAACCATATATCTAAACATAAATG
1 GGAACGGTGACCTAAAAATAACACATCACCCTATGAGTATAAAACCATATATCTAAACATAAATG
**** *
211950 GACCATTAAATCATTTAACAACACTTATGTGAATCTCGAGACGAATGTCCGGAACTAAACTGAAC
66 GACCATTAAATCATTTAACAACACTTACACAAATCTCGAGACGAATGTCCGAAACTAAACTGAAC
* * * * *
212015 TGAGCGAGGATGATCGGGATC-TATCAGAGAGTGATACGGAGACTCGAGCTCACCTTCAGAATAT
131 TGAGCGAGGACGATCGAGA-CATATCAGAGAGTAATACAGAGACTCGAGCTCACCTTCAGAACAT
* *
212079 AATAACAAGAAGTGAGTCCAAAA-CCTAATAATTTACTTAACATAATTAATAATTTAAGCAATAA
195 AATAACAAGAAGTGAGT-CAAAATCCCAATAATTTACGTAACATAATTAATAATTTAAGCAATAA
* * *
212143 ATTATGCAAAATGAGACTTTTGGGGTTAGAATTTGGCAAAACA
259 ATTATGCAAAACGAGACTTTTGAGGTCAGAATTTGGCAAAACA
212186 GGCTGCAGAA
Statistics
Matches: 270, Mismatches: 28, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
314 246 0.91
315 24 0.09
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.25
Consensus pattern (315 bp):
GGAACGGTGACCTAAAAATAACACATCACCCTATGAGTATAAAACCATATATCTAAACATAAATG
GACCATTAAATCATTTAACAACACTTACACAAATCTCGAGACGAATGTCCGAAACTAAACTGAAC
TGAGCGAGGACGATCGAGACATATCAGAGAGTAATACAGAGACTCGAGCTCACCTTCAGAACATA
ATAACAAGAAGTGAGTCAAAATCCCAATAATTTACGTAACATAATTAATAATTTAAGCAATAAAT
TATGCAAAACGAGACTTTTGAGGTCAGAATTTGGCAAAACATAACTAGGTCATAC
Found at i:212251 original size:12 final size:12
Alignment explanation
Indices: 212234--212258 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
212224 GTAGGGGTCT
212234 ACGAAAAAGTCA
1 ACGAAAAAGTCA
212246 ACGAAAAAGTCA
1 ACGAAAAAGTCA
212258 A
1 A
212259 TAGTCAACTG
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:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (12 bp):
ACGAAAAAGTCA
Found at i:212337 original size:34 final size:34
Alignment explanation
Indices: 212299--212384 Score: 154
Period size: 34 Copynumber: 2.5 Consensus size: 34
212289 TGGTCAACTT
212299 ATTGTCATTGTTTTCTCCTTGTTAGATCGAGAGA
1 ATTGTCATTGTTTTCTCCTTGTTAGATCGAGAGA
*
212333 ATTGTCATTGTTTTCTCTTTGTTAGATCGAGAGA
1 ATTGTCATTGTTTTCTCCTTGTTAGATCGAGAGA
*
212367 ATTGTCATTGCTTTCTCC
1 ATTGTCATTGTTTTCTCC
212385 CAATACTAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.47
Consensus pattern (34 bp):
ATTGTCATTGTTTTCTCCTTGTTAGATCGAGAGA
Found at i:213581 original size:509 final size:509
Alignment explanation
Indices: 212619--214147 Score: 2851
Period size: 509 Copynumber: 3.0 Consensus size: 509
212609 CAGTTGCGAT
* ** *
212619 TTTTCTCTATCCGGTAGCCGTATTCCGTAACAATTGGTATCAAGAGCCAGATTAGAGTGTGTAAT
1 TTTTCTCTATCCGATAGTTGTATTCCGCAACAATTGGTATCAAGAGCCAGATTAGAGTGTGTAAT
*
212684 ATCTACTTATTGTCTTTTGTTTGCACCAAAAGGTGGATCCTCCAACATAAGAAAGTAAGAAGGTA
66 ATCTACTTATTGTCTTTTGTTTGCACCAAAAAGTGGATCCTCCAACATAAGAAAGTAAGAAGGTA
*
212749 TTTCCCATTCTTTGAAGGATCCAAAGAACTATTCACGATAGTGAAATAGTAGGAGCTATCCGTAA
131 TTTCCCATTCTTTGAAGGATCCAAAGAACTATTCACGATAGTGAAATAGTGGGAGCTATCCGTAA
*
212814 TAGAAGTTATGGCAACGAAATTTGATATTGAAAAGTTCAATGGGAGAAATTTCTCATTATGGAAA
196 TAGAAGTTATGGCAACGAAATTTGATATTGAAAAGTTCAATGGGAGAAATTTCTCATTGTGGAAA
212879 TTGAAAATGAAGGTCATCCTAAGGAAAGACGGTTGTCTAGCAATTATCAGTGAAAGGCCGGTAGA
261 TTGAAAATGAAGGTCATCCTAAGGAAAGACGGTTGTCTAGCAATTATCAGTGAAAGGCCGGTAGA
212944 TTTCACATATGACAACAAATGGATCGAAATGGACGGGAATGCTATGAAAAACTTTCATCTAGCAT
326 TTTCACATATGACAACAAATGGATCGAAATGGACGGGAATGCTATGAAAAACTTTCATCTAGCAT
* *
213009 TAGTAGATGAAGTATTGTCAAGCATCGAGGAGAAGAAGACAACTAAGGAGATATGTAATCATCTC
391 TAGTAGATGAAGTATTGTCAAGCATCGAGGAGAAAAAGACAACTAAGGAGATATGTGATCATCTC
213074 ACCAAACTGAACGAGGCCACATCGTTGCACAATAAAATTTTCCTTAAGAGGAAA
456 ACCAAACTGAACGAGGCCACATCGTTGCACAATAAAATTTTCCTTAAGAGGAAA
*
213128 TTTTCTCTATCCGATAGTTGTATTCCGCAACAATTGGTATCAAGAGCCAGATTAAAGTGTGTAAT
1 TTTTCTCTATCCGATAGTTGTATTCCGCAACAATTGGTATCAAGAGCCAGATTAGAGTGTGTAAT
* * *
213193 ATCTACTTATTGTCTTTTATTTGCACCAAAAAGTGGATCCTCTAACATAAGAAAGTAATAAGGTA
66 ATCTACTTATTGTCTTTTGTTTGCACCAAAAAGTGGATCCTCCAACATAAGAAAGTAAGAAGGTA
213258 TTTCCCATTCTTTGAAGGATCCAAAGAACTATTCACGATAGTGAAATAGTGGGAGCTATCCGTAA
131 TTTCCCATTCTTTGAAGGATCCAAAGAACTATTCACGATAGTGAAATAGTGGGAGCTATCCGTAA
213323 TAGAAGTTATGGCAACGAAATTTGATATTGAAAAGTTCAATGGGAGAAATTTCTCATTGTGGAAA
196 TAGAAGTTATGGCAACGAAATTTGATATTGAAAAGTTCAATGGGAGAAATTTCTCATTGTGGAAA
*
213388 TTGAAAATGAAGGTCATCCTAAGGAAAGACGGTTGTCTAGCAATTATCAGTGAAAGGTCGGTAGA
261 TTGAAAATGAAGGTCATCCTAAGGAAAGACGGTTGTCTAGCAATTATCAGTGAAAGGCCGGTAGA
* *
213453 TTTCACATATGACAACAAATGGATCGAAATAGACGGGAATGTTATGAAAAACTTTCATCTAGCAT
326 TTTCACATATGACAACAAATGGATCGAAATGGACGGGAATGCTATGAAAAACTTTCATCTAGCAT
213518 TAGTAGATGAAGTATTGTCAAGCATCGAGGAGAAAAAGACAACTAAGGAGATATGTGATCATCTC
391 TAGTAGATGAAGTATTGTCAAGCATCGAGGAGAAAAAGACAACTAAGGAGATATGTGATCATCTC
*
213583 ACCAAACTGAACGAGGCCACATCGTTGCACAATAAAATTTTTCTTAAGAGGAAA
456 ACCAAACTGAACGAGGCCACATCGTTGCACAATAAAATTTTCCTTAAGAGGAAA
*
213637 TTTTCTCTATCCGATAGTTGTATTCCGCAACAATTGGTATCAAGAGCCATATTAGAGTGTGTAAT
1 TTTTCTCTATCCGATAGTTGTATTCCGCAACAATTGGTATCAAGAGCCAGATTAGAGTGTGTAAT
213702 ATCTACTTATTGTCTTTTGTTTGCACCAAAAAGTGGATCCTCCAACATAAGAAAGTAAGAAGGTA
66 ATCTACTTATTGTCTTTTGTTTGCACCAAAAAGTGGATCCTCCAACATAAGAAAGTAAGAAGGTA
213767 TTTCCCATTCTTTGAAGGATCCAAAGAACTATTCACGATAGTGAAATAGTGGGAGCTATCCGTAA
131 TTTCCCATTCTTTGAAGGATCCAAAGAACTATTCACGATAGTGAAATAGTGGGAGCTATCCGTAA
213832 TAGAAGTTATGGCAACGAAATTTGATATTGAAAAGTTCAATGGGAGAAATTTCTCATTGTGGAAA
196 TAGAAGTTATGGCAACGAAATTTGATATTGAAAAGTTCAATGGGAGAAATTTCTCATTGTGGAAA
*
213897 TTGAAAATGAAGGTCATCCTAAGGAAAGACGGTTGTCTATCAATTATCAGTGAAAGGCCGGTAGA
261 TTGAAAATGAAGGTCATCCTAAGGAAAGACGGTTGTCTAGCAATTATCAGTGAAAGGCCGGTAGA
*
213962 TTTCACATATGACAACAAATGGATCGAAATGGACAGGAATGCTATGAAAAACTTTCATCTAGCAT
326 TTTCACATATGACAACAAATGGATCGAAATGGACGGGAATGCTATGAAAAACTTTCATCTAGCAT
* *
214027 TAGTAGATGAAGTATTGTCAAGCATCAAGGAGAATAAGACAACTAAGGAGATATGTGATCATCTC
391 TAGTAGATGAAGTATTGTCAAGCATCGAGGAGAAAAAGACAACTAAGGAGATATGTGATCATCTC
*
214092 ACCAAACTGAACGAGACCACATCGTTGCACAATAAAATTTTCCTTAAGAGGAAA
456 ACCAAACTGAACGAGGCCACATCGTTGCACAATAAAATTTTCCTTAAGAGGAAA
214146 TT
1 TT
214148 GTACACTCTC
Statistics
Matches: 989, Mismatches: 31, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
509 989 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.28
Consensus pattern (509 bp):
TTTTCTCTATCCGATAGTTGTATTCCGCAACAATTGGTATCAAGAGCCAGATTAGAGTGTGTAAT
ATCTACTTATTGTCTTTTGTTTGCACCAAAAAGTGGATCCTCCAACATAAGAAAGTAAGAAGGTA
TTTCCCATTCTTTGAAGGATCCAAAGAACTATTCACGATAGTGAAATAGTGGGAGCTATCCGTAA
TAGAAGTTATGGCAACGAAATTTGATATTGAAAAGTTCAATGGGAGAAATTTCTCATTGTGGAAA
TTGAAAATGAAGGTCATCCTAAGGAAAGACGGTTGTCTAGCAATTATCAGTGAAAGGCCGGTAGA
TTTCACATATGACAACAAATGGATCGAAATGGACGGGAATGCTATGAAAAACTTTCATCTAGCAT
TAGTAGATGAAGTATTGTCAAGCATCGAGGAGAAAAAGACAACTAAGGAGATATGTGATCATCTC
ACCAAACTGAACGAGGCCACATCGTTGCACAATAAAATTTTCCTTAAGAGGAAA
Found at i:219604 original size:19 final size:19
Alignment explanation
Indices: 219546--219604 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
219536 TAATAATAAA
*
219546 AATTATAAATTTTGAATAT
1 AATTATAAATTCTGAATAT
* *
219565 AATTCATAAA-TGT-AACAAT
1 AATT-ATAAATTCTGAA-TAT
219584 AATTATAAATTCTGAATAT
1 AATTATAAATTCTGAATAT
219603 AA
1 AA
219605 ATGGTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 7 0.22
19 18 0.56
20 7 0.22
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
AATTATAAATTCTGAATAT
Found at i:220558 original size:2 final size:2
Alignment explanation
Indices: 220553--220581 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
220543 TAAGTGTGTG
220553 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
220582 TCCATTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:227564 original size:16 final size:16
Alignment explanation
Indices: 227543--227574 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
227533 CTGGATGAAA
227543 ATCTGAGAGGAACCAT
1 ATCTGAGAGGAACCAT
227559 ATCTGAGAGGAACCAT
1 ATCTGAGAGGAACCAT
227575 GGCGTTCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.19
Consensus pattern (16 bp):
ATCTGAGAGGAACCAT
Found at i:234484 original size:51 final size:52
Alignment explanation
Indices: 234408--234510 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 52
234398 TTGAGGTACA
234408 TAGTATTTGAGGTCACCATGTGAAATAACTTGAAAG-AAAATAGTTCAGATG
1 TAGTATTTGAGGTCACCATGTGAAATAACTTGAAAGAAAAATAGTTCAGATG
*
234459 TAGTATTTGAGGTCACCATGTGAAATACCTTGAAAGAAAAATAGTTCAGATG
1 TAGTATTTGAGGTCACCATGTGAAATAACTTGAAAGAAAAATAGTTCAGATG
234511 ATTGATTATC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 35 0.70
52 15 0.30
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (52 bp):
TAGTATTTGAGGTCACCATGTGAAATAACTTGAAAGAAAAATAGTTCAGATG
Found at i:238190 original size:60 final size:61
Alignment explanation
Indices: 238115--238290 Score: 205
Period size: 60 Copynumber: 2.9 Consensus size: 61
238105 TTGCAACATA
* * * * **
238115 CATCCTTAAACTATGACTCTTATTTTAAATTACTCCCTAAACTTTTAAATATT-TTAATTT
1 CATCCCTAAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTAAACATTCCAAATTT
* * * *
238175 CATCCCTAAATTATGACTCTCATTCTAAATTGGTCCCTAAACTTTTGAACATTCCAAATTT
1 CATCCCTAAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTAAACATTCCAAATTT
* * *
238236 -AT-CCTCAAACTATGACTCTTACTCTAAATTAGTCCCCAAACTTTTGAACATTCCA
1 CATCCCT-AAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTAAACATTCCA
238291 TTGATAACCC
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
59 3 0.03
60 91 0.92
61 5 0.05
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (61 bp):
CATCCCTAAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTAAACATTCCAAATTT
Found at i:248828 original size:19 final size:20
Alignment explanation
Indices: 248790--248829 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
248780 AAGAGAATAT
*
248790 TTCATTTTTCTTTATATTTG
1 TTCAATTTTCTTTATATTTG
*
248810 TTCAATTTT-TTTATTTTTG
1 TTCAATTTTCTTTATATTTG
248829 T
1 T
248830 AGGAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.15, C:0.07, G:0.05, T:0.72
Consensus pattern (20 bp):
TTCAATTTTCTTTATATTTG
Found at i:249619 original size:35 final size:37
Alignment explanation
Indices: 249556--249655 Score: 123
Period size: 35 Copynumber: 2.8 Consensus size: 37
249546 TTTCGTCCTA
249556 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
* *
249593 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
* * * * *
249628 CTATGTTTTAAACTCTTAAAGATAGGAT
1 CTAGGATTCAAACTCTCAAAAATAGGAT
249656 CCACAAGCAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 25 0.47
36 10 0.19
37 18 0.34
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:250084 original size:2 final size:2
Alignment explanation
Indices: 250079--250111 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
250069 TTAGTGTTAT
*
250079 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
250112 TTCCTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:250238 original size:17 final size:18
Alignment explanation
Indices: 250218--250253 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
250208 TTTACTCATT
*
250218 TATTTAT-CTATTTTTTA
1 TATTTATCCTATATTTTA
250235 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
250253 T
1 T
250254 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:254048 original size:16 final size:15
Alignment explanation
Indices: 254022--254119 Score: 60
Period size: 16 Copynumber: 6.3 Consensus size: 15
254012 AGATCCAATC
254022 AAGAACAAAAAAGAAA
1 AAGAAC-AAAAAGAAA
254038 AAGAAGCAAAAAAGCAAA
1 AAGAA-C-AAAAAG-AAA
*
254056 AA-AA-AAAAA-ACA
1 AAGAACAAAAAGAAA
*
254068 AAGAA-AAAGAGAAA
1 AAGAACAAAAAGAAA
*
254082 CAAGAACAAAAGGAAAA
1 -AAGAACAAAAAG-AAA
* *
254099 AAGAGCAAAAATCAAA
1 AAGAACAAAAA-GAAA
254115 AAGAA
1 AAGAA
254120 AAAGGGACAA
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
12 4 0.06
13 6 0.09
14 7 0.11
15 5 0.08
16 25 0.38
17 13 0.20
18 5 0.08
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.01
Consensus pattern (15 bp):
AAGAACAAAAAGAAA
Found at i:254786 original size:22 final size:22
Alignment explanation
Indices: 254758--254808 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
254748 CCCCATCAAT
254758 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
254780 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
254802 CCTTTGA
1 CCTTTGA
254809 CCAAAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:255230 original size:18 final size:18
Alignment explanation
Indices: 255207--255242 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
255197 TCAACATCAA
*
255207 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
255225 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
255243 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:255870 original size:37 final size:37
Alignment explanation
Indices: 255807--255878 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
255797 CATTGAAAAC
* *
255807 ATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAAAAAATTTTCGTCTCTATTGAGATA
255844 ATTTCCCTTGAAACAAAATTTT-GTCTCTATTGAGA
1 ATTTCCCTTGAAA-AAAATTTTCGTCTCTATTGAGA
255879 CCGTTTCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (37 bp):
ATTTCCCTTGAAAAAAATTTTCGTCTCTATTGAGATA
Found at i:256733 original size:105 final size:105
Alignment explanation
Indices: 256531--257893 Score: 1450
Period size: 105 Copynumber: 13.0 Consensus size: 105
256521 ATATTGTGGC
* * * *
256531 ACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAAC-AACAAATTCCC
*
256596 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
256637 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAAATTCTCA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAACAACAAATTCCCA
*
256702 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
256742 ACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCC
1 AC-TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAACAACAAATTCCC
* *
256806 AATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * *
256847 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAACAACAAATTCCCA
* *
256912 ATCTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
256952 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAATAATTTCCCA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAACAACAAATTCCCA
* *
257017 GTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
257057 ACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGAC-TGT---CGAC-AA---GC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTG-CTTGTCAACAACAAATTCCC
* *
257114 AATTTCGGAGCCAATCTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
257155 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAAC-AACAAATTCCC
* *
257220 AGTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
257261 ACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGACGGCTGAC-TGT---CGAC-AA---GC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTG-CTTGTCAACAACAAATTCCC
* *
257318 AATTTCGGAGCCAATCTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
257359 ACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAAC-AACAAATTCCC
* * * *
257424 AATTCCAGAGCCAATTTCAACTCCAC-GACGGAGGATATCGTGCT
65 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATAT--TG-G
* * * * **
257468 ACCCGAGACAACACAAGTTCAACATCACAACGAAGGGACGGTTGGTTGTCAACGAA-AAACTTTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAAC-AACAAA-TTCC
* ** * * *
257532 CAGTTTCA-TCCGCGATTTCAAC-TCTAC-GACGGAGGATATCGTGCC
64 CAATTTCAGAGC-CAATTTCAACTTC-ACAG-CGAAGGATAT--TG-G
* ** * *
257577 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAAC-AACAAATTCCC
** *
257642 AATTTCAGAGCCAATTTCAACTTCGTAGCGAAGGATATTAG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
257683 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-A-AGATT-TC-
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAACAACAAATTCCCA
* * * * *
257744 -GTTCAGTGTCAATTTCATCTTCACAGCGAAGGATATTAG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
257783 ACTCGAGACAGCACAAGCTCAACTTCACAGCAAAGGGGCGACTGAC-TGTCAACAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTG-CTTGTCAAC-AACAAATTCC
* * * *
257847 CAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
257889 ACTCG
1 ACTCG
257894 GAACAATATT
Statistics
Matches: 1077, Mismatches: 140, Indels: 80
0.83 0.11 0.06
Matches are distributed among these distances:
98 160 0.15
100 78 0.07
101 4 0.00
102 9 0.01
103 9 0.01
104 4 0.00
105 384 0.36
106 251 0.23
107 1 0.00
108 6 0.01
109 166 0.15
110 5 0.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (105 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAACAACAAATTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:258417 original size:35 final size:35
Alignment explanation
Indices: 258354--258453 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
258344 TTTCGTCCTA
*
258354 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
258391 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
258426 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
258454 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:258984 original size:20 final size:20
Alignment explanation
Indices: 258959--258996 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
258949 ATTATTATTA
258959 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
258979 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
258997 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:259027 original size:17 final size:18
Alignment explanation
Indices: 259007--259042 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
258997 TTTACTCATT
*
259007 TATTTAT-CTATTTTTTA
1 TATTTATCCTATATTTTA
259024 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
259042 T
1 T
259043 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:265525 original size:20 final size:21
Alignment explanation
Indices: 265500--265560 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
265490 TTTTTGTGCA
*
265500 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
265520 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
265541 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
265561 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.29
21 8 0.23
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:265568 original size:20 final size:20
Alignment explanation
Indices: 265543--265580 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
265533 CCCCCTTTGA
*
265543 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
265563 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
265581 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:272724 original size:16 final size:16
Alignment explanation
Indices: 272703--272736 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
272693 TTACTATTCA
*
272703 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
272719 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
272735 CG
1 CG
272737 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:273507 original size:15 final size:16
Alignment explanation
Indices: 273487--273518 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
273477 TGGCAGATCC
273487 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
273502 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
273518 A
1 A
273519 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:278568 original size:19 final size:20
Alignment explanation
Indices: 278546--278588 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
278536 AAGTAATCCG
278546 AAAATTCAAATATACT-AAA
1 AAAATTCAAATATACTGAAA
* *
278565 AAAATTTAAATATATTGAAA
1 AAAATTCAAATATACTGAAA
278585 AAAA
1 AAAA
278589 AGAGATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAATTCAAATATACTGAAA
Found at i:283574 original size:31 final size:31
Alignment explanation
Indices: 283501--283574 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
283491 TAAAAATTAT
* * * *
283501 AATATAATCCCCCAACATTTAGTCCGTTTGC
1 AATATGATCCCTCAACATTTAGTCCATTTAC
*
283532 AATATGATCCCTCAACATTTAGTTCATTTAC
1 AATATGATCCCTCAACATTTAGTCCATTTAC
283563 AATATGATCCCT
1 AATATGATCCCT
283575 AAATGAAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (31 bp):
AATATGATCCCTCAACATTTAGTCCATTTAC
Found at i:286876 original size:314 final size:314
Alignment explanation
Indices: 286299--286892 Score: 846
Period size: 314 Copynumber: 1.9 Consensus size: 314
286289 GATCGATAGT
* * *
286299 ACTAGGTCTTGCGAAATGGTGACCTAAAAATAACACATCACCCTATGAGTATAAAACCATATATC
1 ACTAGGTCCTACGAAATGATGACCTAAAAATAACACATCACCCTATGAGTATAAAACCATATATC
* * *
286364 TAAACATAAATGGACCATTAAATCATTTAACAACACTTACACAAATCTCGAGACAAATGTCTGAA
66 TAAACAGAAATGGACCATTAAATCATTTAACAACACTTACACAAATCTCGAGACAAATGCCCGAA
* * * *
286429 ACTGAACTGAATTGAGTGAGGACGATCGGGATCTATCAGAGAGTAATGCGGAGACTCGAGCTCAC
131 ACTGAACTGAACTAAGTGAGGACGATCGGGATCTATCAGAGAGCAATACGGAGACTCGAGCTCAC
* * * * * *
286494 CTTCATAACATAATAATAAGAAGTGATTCCAAAACCTAATAATTTACTTAACCTAATTAAGACTT
196 ATTCAGAACATAATAACAAGAAGTGAGTCCAAAACCTAATAATTCACTTAACATAATTAAGACTT
286559 TAAGCAATAAATTATGCAAAAGGAGACTTTTGGGTCAGAATTTGACAAAACATA
261 TAAGCAATAAATTATGCAAAAGGAGACTTTTGGGTCAGAATTTGACAAAACATA
* * *
286613 ACTAGGTCCTACGGAATGATGACTTAAAAATAACACATCACCCTGTGAGTATAAAACCATATATC
1 ACTAGGTCCTACGAAATGATGACCTAAAAATAACACATCACCCTATGAGTATAAAACCATATATC
* * **** *
286678 TAAGCAGAAATGGGCCATTAAATCATTTAACAACACTTATGTGAATCTCGAGACGAATGCCCGAA
66 TAAACAGAAATGGACCATTAAATCATTTAACAACACTTACACAAATCTCGAGACAAATGCCCGAA
* * * * *
286743 ATTGAGCTGAACTAAGTGAGGATGATCGGGATCTATCAGAGAGCGATACGGAGACTTGAGCTCAC
131 ACTGAACTGAACTAAGTGAGGACGATCGGGATCTATCAGAGAGCAATACGGAGACTCGAGCTCAC
* * * * * *
286808 ATTCGGAACATAATAACAAGAAGTGAGTCCAAAATCTCATAATTCGCTTAACATAATTTAGGCTT
196 ATTCAGAACATAATAACAAGAAGTGAGTCCAAAACCTAATAATTCACTTAACATAATTAAGACTT
*
286873 TAAGTAATAAATTATGCAAA
261 TAAGCAATAAATTATGCAAA
286893 GACTTTTGAG
Statistics
Matches: 242, Mismatches: 38, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
314 242 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (314 bp):
ACTAGGTCCTACGAAATGATGACCTAAAAATAACACATCACCCTATGAGTATAAAACCATATATC
TAAACAGAAATGGACCATTAAATCATTTAACAACACTTACACAAATCTCGAGACAAATGCCCGAA
ACTGAACTGAACTAAGTGAGGACGATCGGGATCTATCAGAGAGCAATACGGAGACTCGAGCTCAC
ATTCAGAACATAATAACAAGAAGTGAGTCCAAAACCTAATAATTCACTTAACATAATTAAGACTT
TAAGCAATAAATTATGCAAAAGGAGACTTTTGGGTCAGAATTTGACAAAACATA
Found at i:286987 original size:12 final size:12
Alignment explanation
Indices: 286970--286996 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
286960 GTAGAGGTCT
286970 ACGAAAAAGTCA
1 ACGAAAAAGTCA
286982 ACGAAAAAGTCA
1 ACGAAAAAGTCA
286994 ACG
1 ACG
286997 GTCAACGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.19, G:0.19, T:0.07
Consensus pattern (12 bp):
ACGAAAAAGTCA
Found at i:288451 original size:12 final size:12
Alignment explanation
Indices: 288436--288460 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
288426 TTTCATTTTT
288436 ATTTTATTTTAA
1 ATTTTATTTTAA
288448 ATTTTATTTTAA
1 ATTTTATTTTAA
288460 A
1 A
288461 CATGCTAAGT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTTATTTTAA
Found at i:293250 original size:28 final size:28
Alignment explanation
Indices: 293218--293281 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
293208 TATAAACGAT
293218 GGACCAAACATAATTTACCTTGTACACG
1 GGACCAAACATAATTTACCTTGTACACG
293246 GGACCAAACATAATTTACCTTGTACACG
1 GGACCAAACATAATTTACCTTGTACACG
293274 GGACCAAA
1 GGACCAAA
293282 TCCACCTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.22
Consensus pattern (28 bp):
GGACCAAACATAATTTACCTTGTACACG
Found at i:305923 original size:9 final size:9
Alignment explanation
Indices: 305909--305977 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
305899 GCTGCTGGAA
305909 ACCGGTTTG
1 ACCGGTTTG
*
305918 ACCGGTTTCA
1 ACCGGTTT-G
*
305928 ACCGGTTCG
1 ACCGGTTTG
305937 AACCGGTTTG
1 -ACCGGTTTG
*
305947 ACCGGTCTG
1 ACCGGTTTG
*
305956 AATCGGTTTG
1 -ACCGGTTTG
*
305966 ACCGGTCTG
1 ACCGGTTTG
305975 ACC
1 ACC
305978 CGACCCGACC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 26 0.54
10 22 0.46
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:305950 original size:19 final size:19
Alignment explanation
Indices: 305909--305971 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
305899 GCTGCTGGAA
* *
305909 ACCGGTTTG-ACCGGTTTCA
1 ACCGGTTCGAACCGGTTT-G
305928 ACCGGTTCGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTG
*
305947 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTC-GAACCGGTTTG
305966 ACCGGT
1 ACCGGT
305972 CTGACCCGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 2 0.05
19 28 0.74
20 8 0.21
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (19 bp):
ACCGGTTCGAACCGGTTTG
Found at i:305962 original size:29 final size:29
Alignment explanation
Indices: 305908--305977 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
305898 GGCTGCTGGA
*
305908 AACCGGTTTGACCGGTTTCAACCGGTTCG
1 AACCGGTTTGACCGGTCTCAACCGGTTCG
* * *
305937 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 AACCGGTTTGACCGGTCTCAACCGGTTCG
*
305966 -ACCGGTCTGACC
1 AACCGGTTTGACC
305978 CGACCCGACC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 11 0.31
29 25 0.69
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (29 bp):
AACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:306000 original size:22 final size:22
Alignment explanation
Indices: 305974--306038 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
305964 TGACCGGTCT
305974 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
* *
305996 GACCCAACCTGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
306018 GACCCGACCCGACTGTTGACC
1 GACCCGACCCGACCGTTGACC
306039 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.20, C:0.46, G:0.22, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:306044 original size:7 final size:7
Alignment explanation
Indices: 306032--306058 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
306022 CGACCCGACT
306032 GTTGACC
1 GTTGACC
306039 GTTGACC
1 GTTGACC
306046 GTTGACC
1 GTTGACC
306053 GTTGAC
1 GTTGAC
306059 TTTCTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.30
Consensus pattern (7 bp):
GTTGACC
Found at i:313587 original size:2 final size:2
Alignment explanation
Indices: 313580--313613 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
313570 TAATTTATTC
313580 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
313614 GTGTGTGTGC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:317127 original size:20 final size:20
Alignment explanation
Indices: 317104--317143 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
317094 TTTGGGAAAA
* *
317104 ATCGGTTTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
317124 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
317144 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:317202 original size:12 final size:12
Alignment explanation
Indices: 317187--317233 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
317177 CCGGTTTTTT
*
317187 AACCGGCTAAAA
1 AACCGGTTAAAA
317199 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
317214 AACCGGTTAAAA
1 AACCGGTTAAAA
317226 AACCGGTT
1 AACCGGTT
317234 TTTATCCGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 2 0.06
15 10 0.32
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:319547 original size:21 final size:21
Alignment explanation
Indices: 319523--319562 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
319513 TTTATTTTAT
319523 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
319544 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
319563 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:319614 original size:33 final size:33
Alignment explanation
Indices: 319551--319692 Score: 160
Period size: 33 Copynumber: 4.6 Consensus size: 33
319541 GTAAACTTTG
319551 TTTCAA-TTATCGAACTT-GAAG-TTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
*
319581 TTTGAATTTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
* * *
319614 TTTGAATTTATCAAACTTGGAAGTATTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
*
319647 TTTCAA-TTAT-G---TT-G-AGTTAATTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTT-TTTAAGTA
319674 TTTCAATTTATCGAACTTG
1 TTTCAATTTATCGAACTTG
319693 AGGTTTGATG
Statistics
Matches: 95, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
26 3 0.03
27 14 0.15
28 6 0.06
29 1 0.01
30 5 0.05
31 11 0.12
32 10 0.11
33 45 0.47
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (33 bp):
TTTCAATTTATCGAACTTGGAAGTTTTTAAGTA
Found at i:320101 original size:15 final size:15
Alignment explanation
Indices: 320083--320131 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
320073 ATATTAAAAT
320083 CGGTTTTTTTATAAC
1 CGGTTTTTTTATAAC
* *
320098 CGGTTTTTTAAAAAAAC
1 CGGTTTTTT--TATAAC
*
320115 CGGTTTTTTTTTAAC
1 CGGTTTTTTTATAAC
320130 CG
1 CG
320132 AAACCGGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 14 0.52
17 13 0.48
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (15 bp):
CGGTTTTTTTATAAC
Found at i:320248 original size:15 final size:17
Alignment explanation
Indices: 320222--320253 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
320212 TTCTATGGGA
320222 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
320238 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
320254 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:328750 original size:26 final size:27
Alignment explanation
Indices: 328699--328750 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
328689 TTATTAATAA
* * *
328699 AAATAAAAATATTGGTATATTTTATTG
1 AAATAAAAATATTGATAAATTATATTG
328726 AAATAAAAATATT-ATAAATTATATT
1 AAATAAAAATATTGATAAATTATATT
328751 AATTATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (27 bp):
AAATAAAAATATTGATAAATTATATTG
Found at i:328809 original size:23 final size:23
Alignment explanation
Indices: 328780--328824 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
328770 AGTGTTATAT
328780 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
328803 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
328825 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Done.