Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 38
Found at i:428923 original size:39 final size:38
Alignment explanation
Indices: 428833--429009 Score: 222
Period size: 36 Copynumber: 4.7 Consensus size: 38
428823 ATATATATAT
* *
428833 ATATATATATTATATAATTTTGAAAACATTTTG-AAA-
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAAAC
428869 ATATATATGA-TATATAGTTTTTAAAACATTTTTGAAAAC
1 ATATATAT-ATTATATAGTTTTTAAAACA-TTTTGAAAAC
* *
428908 ATATATATATTATATAGTTTTTAAAATATTTTGAAAAT
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAAAC
*
428946 ATATA-ATA-TATA-ATTTTTTAAAAAGCATTTTGAAAAC
1 ATATATATATTATATAGTTTTT-AAAA-CATTTTGAAAAC
428983 ATATATATATTATATAGTTTTTTAAAA
1 ATATATATATTATATAG-TTTTTAAAA
429010 AAACCCTTTT
Statistics
Matches: 122, Mismatches: 8, Indels: 18
0.82 0.05 0.12
Matches are distributed among these distances:
35 6 0.05
36 32 0.26
37 24 0.20
38 21 0.17
39 29 0.24
40 5 0.04
41 5 0.04
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (38 bp):
ATATATATATTATATAGTTTTTAAAACATTTTGAAAAC
Found at i:428963 original size:73 final size:73
Alignment explanation
Indices: 428833--429062 Score: 265
Period size: 75 Copynumber: 3.1 Consensus size: 73
428823 ATATATATAT
* * * *
428833 ATATATATATTATATAATTTTGAAAACATTTTGAAAATATATATGATATATAGTTTTTAAAACAT
1 ATATATATATTATATAGTTTTTAAAAAATTTTGAAAATATATA--ATATATAATTTTTAAAACAT
428898 TTTTGAAAAC
64 TTTTGAAAAC
*
428908 ATATATATATTATATAGTTTTTAAAATATTTTGAAAATATATAATATATAATTTTTTAAAAAGCA
1 ATATATATATTATATAGTTTTTAAAAAATTTTGAAAATATATAATATATAA-TTTTT-AAAA-CA
428973 -TTTTGAAAAC
63 TTTTTGAAAAC
* *
428983 ATATATATATTATATAGTTTTTTAAAAAAACCCTTTTGAAAA-ACATAA-ACAT-A-TTTTAAAA
1 ATATATATATTATATAG-TTTTT-AAAAAA---TTTTGAAAATATATAATATATAATTTTTAAAA
429044 CATTTTTGAAAAC
61 CATTTTTGAAAAC
429057 -TATATA
1 ATATATA
429063 ATTTTGAAAA
Statistics
Matches: 139, Mismatches: 7, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
73 15 0.11
74 19 0.14
75 75 0.54
76 7 0.05
77 6 0.04
78 3 0.02
79 5 0.04
80 9 0.06
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (73 bp):
ATATATATATTATATAGTTTTTAAAAAATTTTGAAAATATATAATATATAATTTTTAAAACATTT
TTGAAAAC
Found at i:429083 original size:28 final size:28
Alignment explanation
Indices: 429035--429092 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
429025 ACATAAACAT
** **
429035 ATTTTAAAACATTTTTGAAAACTATATA
1 ATTTTAAAACATTTTAAAAAAAAATATA
429063 ATTTTGAAAACA-TTTAAAAAAAAATATA
1 ATTTT-AAAACATTTTAAAAAAAAATATA
429091 AT
1 AT
429093 ATATAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (28 bp):
ATTTTAAAACATTTTAAAAAAAAATATA
Found at i:429134 original size:33 final size:34
Alignment explanation
Indices: 429081--429148 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
429071 AACATTTAAA
* *
429081 AAAAAATATAATATATAATTT-TAAAATATTTTT
1 AAAAAATATAATATAGAATTTAGAAAATATTTTT
* *
429114 AAAATATATTATATAGAATTTCAGAAAATATTTTT
1 AAAAAATATAATATAGAATTT-AGAAAATATTTTT
429149 TAGTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 18 0.62
35 11 0.38
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (34 bp):
AAAAAATATAATATAGAATTTAGAAAATATTTTT
Found at i:429170 original size:24 final size:24
Alignment explanation
Indices: 429156--429219 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
429146 TTTTAGTTTA
429156 TTTTTATTTTAATTTATTTACCTT
1 TTTTTATTTTAATTTATTTACCTT
*
429180 TTTTTA-TTTATTATTATTATTACC-T
1 TTTTTATTTTAAT-TTA-T-TTACCTT
*
429205 TTTTTATTTTTATTT
1 TTTTTATTTTAATTT
429220 TCATTTTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 5 0.15
24 9 0.27
25 10 0.30
26 9 0.27
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTATTTTAATTTATTTACCTT
Found at i:430449 original size:5 final size:5
Alignment explanation
Indices: 430428--430462 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
430418 GTCATTTTTC
430428 TTATT TTCATGT TTATT TTATT TTATT TTATT TTA
1 TTATT TT-AT-T TTATT TTATT TTATT TTATT TTA
430463 ATCTCGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 21 0.75
6 4 0.14
7 3 0.11
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:430521 original size:3 final size:3
Alignment explanation
Indices: 430513--430538 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
430503 ATATATACAT
430513 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
430539 TACTTCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:430580 original size:2 final size:2
Alignment explanation
Indices: 430573--430608 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
430563 TTTATCTTAT
*
430573 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
430609 ATCTTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:430693 original size:26 final size:25
Alignment explanation
Indices: 430648--430696 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
430638 TATCTTTATT
430648 TATTTATTTTAATTTCATTTTTAAA
1 TATTTATTTTAATTTCATTTTTAAA
* *
430673 TATTTTTTTATAATTTTATTTTTA
1 TATTTATTT-TAATTTCATTTTTA
430697 GTTTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TATTTATTTTAATTTCATTTTTAAA
Found at i:432422 original size:24 final size:24
Alignment explanation
Indices: 432378--432423 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
432368 CCATTTCTAA
* *
432378 AGTTTCATGTGACATTTTGTTAAG
1 AGTTTCATGTCACATTCTGTTAAG
*
432402 AGTTTCATGTCACCTTCTGTTA
1 AGTTTCATGTCACATTCTGTTA
432424 CGAAAATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (24 bp):
AGTTTCATGTCACATTCTGTTAAG
Found at i:437095 original size:39 final size:39
Alignment explanation
Indices: 437047--437123 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
437037 TCAAACATAG
437047 AATACACTCATTCATTTGAAGCTTGCAATAGCAAAACAC
1 AATACACTCATTCATTTGAAGCTTGCAATAGCAAAACAC
437086 AATACACTCATTCATTTGAAGCTTGCAATAGCAAAACA
1 AATACACTCATTCATTTGAAGCTTGCAATAGCAAAACA
437124 TGTGTCTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (39 bp):
AATACACTCATTCATTTGAAGCTTGCAATAGCAAAACAC
Found at i:442668 original size:20 final size:21
Alignment explanation
Indices: 442626--442682 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
442616 CCTGTGGGAC
442626 GAATCGGTTCCCCTTCAAAGGGG
1 GAATCGGTT-CCC-TCAAAGGGG
442649 GAATCGGTTCCCTC-AAGGGG
1 GAATCGGTTCCCTCAAAGGGG
* *
442669 GGATCGATTCCCTC
1 GAATCGGTTCCCTC
442683 TGCACCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 18 0.56
21 2 0.06
22 3 0.09
23 9 0.28
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.23
Consensus pattern (21 bp):
GAATCGGTTCCCTCAAAGGGG
Found at i:449143 original size:13 final size:13
Alignment explanation
Indices: 449125--449159 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
449115 TATTTAAAAT
449125 AATTTACAATTCA
1 AATTTACAATTCA
449138 AATTTACAATTCA
1 AATTTACAATTCA
449151 AATTTACAA
1 AATTTACAA
449160 AATAGAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
AATTTACAATTCA
Found at i:454933 original size:11 final size:11
Alignment explanation
Indices: 454908--454946 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
454898 AAAATATAAG
454908 TAATTAATT-A
1 TAATTAATTAA
*
454918 TAATTTATTAA
1 TAATTAATTAA
454929 TAATTAATTAA
1 TAATTAATTAA
*
454940 TGATTAA
1 TAATTAA
454947 CCATTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (11 bp):
TAATTAATTAA
Found at i:455833 original size:41 final size:40
Alignment explanation
Indices: 455765--455845 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 40
455755 TATACATATA
*
455765 TAAGATATCTTTTTATAATACTTACCAGAACTCTTAACAC
1 TAAGATATCTTTTTATAATACTCACCAGAACTCTTAACAC
455805 TAAGATATCTTTTTTATAATACTCACCAGAACTCTTAACAC
1 TAAGATATC-TTTTTATAATACTCACCAGAACTCTTAACAC
455846 CTACGCTTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 9 0.23
41 30 0.77
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (40 bp):
TAAGATATCTTTTTATAATACTCACCAGAACTCTTAACAC
Found at i:455923 original size:20 final size:20
Alignment explanation
Indices: 455898--455935 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
455888 TTTGGTTCAC
455898 GGAATGTAAGATTACCAGTA
1 GGAATGTAAGATTACCAGTA
455918 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
455936 GGAATAGGAT
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:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTA
Found at i:456619 original size:15 final size:16
Alignment explanation
Indices: 456568--456612 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
456558 TCACGGAATG
456568 TAAGATTACCAGTGTGAA
1 TAAGATTACCAG-G-GAA
456586 TAAAAGATTACCAGGGAA
1 T--AAGATTACCAGGGAA
456604 TAAGATTAC
1 TAAGATTAC
456613 TGGGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 5 0.20
19 1 0.04
20 11 0.44
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.24
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Found at i:459448 original size:26 final size:28
Alignment explanation
Indices: 459392--459449 Score: 66
Period size: 31 Copynumber: 2.0 Consensus size: 28
459382 ATTGCTGAGC
*
459392 TCGACTCGACTCGAAAACTCTGAAATGGAGT
1 TCGACTCGACTCGAAAACTCTG--A-CGAGT
459423 TCGACTCGACTCGAAAACTC-G-CGAGT
1 TCGACTCGACTCGAAAACTCTGACGAGT
459449 T
1 T
459450 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 5 0.19
30 1 0.04
31 20 0.77
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (28 bp):
TCGACTCGACTCGAAAACTCTGACGAGT
Found at i:461527 original size:14 final size:14
Alignment explanation
Indices: 461508--461543 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
461498 GTGAGAGATT
461508 AAAGTAAATAAACG
1 AAAGTAAATAAACG
461522 AAAGTAAATAAACG
1 AAAGTAAATAAACG
461536 AAAGTAAA
1 AAAGTAAA
461544 AAATTGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.67, C:0.06, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAGTAAATAAACG
Found at i:464397 original size:30 final size:30
Alignment explanation
Indices: 464361--464421 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
464351 AGTCGAGGGT
*
464361 TACCTATGTTCTTC-GAGACATATGGATAGG
1 TACCTATATTCTTCAGA-ACATATGGATAGG
464391 TACCTATATTCTTCAGAACATATGGATAGG
1 TACCTATATTCTTCAGAACATATGGATAGG
464421 T
1 T
464422 CCTTCAGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (30 bp):
TACCTATATTCTTCAGAACATATGGATAGG
Found at i:470549 original size:20 final size:20
Alignment explanation
Indices: 470524--470572 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
470514 ATTCATGAGG
470524 TATCGATACTTGAAGAACAA
1 TATCGATACTTGAAGAACAA
* *
470544 TATCGATATTTGAAGAACAG
1 TATCGATACTTGAAGAACAA
470564 TATCGATAC
1 TATCGATAC
470573 CAAGGGTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (20 bp):
TATCGATACTTGAAGAACAA
Found at i:473863 original size:10 final size:11
Alignment explanation
Indices: 473850--473878 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
473840 TAAATAAAAG
473850 AAACAAAAC-A
1 AAACAAAACGA
473860 AAACAAAACGA
1 AAACAAAACGA
473871 AAACAAAA
1 AAACAAAA
473879 ATGGGTTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.79, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AAACAAAACGA
Found at i:474275 original size:14 final size:14
Alignment explanation
Indices: 474230--474302 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
474220 GTGAGAGATC
474230 AAAGTAAATAAACG
1 AAAGTAAATAAACG
** * *
474244 AAAGT-TTTTATC-
1 AAAGTAAATAAACG
474256 AAAGTAAATAAACG
1 AAAGTAAATAAACG
474270 AAAGTAAA-AAACTG
1 AAAGTAAATAAAC-G
*
474284 -AAGTAAAATAAATG
1 AAAGT-AAATAAACG
474298 AAAGT
1 AAAGT
474303 GGTAAATAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
12 5 0.11
13 14 0.32
14 18 0.41
15 7 0.16
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (14 bp):
AAAGTAAATAAACG
Found at i:485035 original size:31 final size:32
Alignment explanation
Indices: 484997--485088 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 32
484987 ATAATTTTTA
* * *
484997 ACTAATTTCAAT-CAAAGAGTCAACTTCATGT
1 ACTAATTTCAATAAAAAAAGTCAACTTCATAT
* * *
485028 ACTAATTTGAATAAAAAAAGTTAACTTCTTAT
1 ACTAATTTCAATAAAAAAAGTCAACTTCATAT
* *
485060 ACTAATTTGAATAAAAAAAAGTCATCTTC
1 ACTAATTTCAAT-AAAAAAAGTCAACTTC
485089 GTGTATATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 11 0.22
32 26 0.51
33 14 0.27
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.34
Consensus pattern (32 bp):
ACTAATTTCAATAAAAAAAGTCAACTTCATAT
Found at i:485063 original size:32 final size:32
Alignment explanation
Indices: 485018--485078 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
485008 TCAAAGAGTC
*
485018 AACTTCATGTACTAATTTGAATAAAAAAAGTT
1 AACTTCATATACTAATTTGAATAAAAAAAGTT
*
485050 AACTTCTTATACTAATTTGAATAAAAAAA
1 AACTTCATATACTAATTTGAATAAAAAAA
485079 AGTCATCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (32 bp):
AACTTCATATACTAATTTGAATAAAAAAAGTT
Found at i:485437 original size:2 final size:2
Alignment explanation
Indices: 485432--485463 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
485422 AAACATTGTA
485432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
485464 GGCCATGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:494604 original size:14 final size:14
Alignment explanation
Indices: 494570--494613 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
494560 AATACCTTTT
494570 AAAATAATTTTAAGA
1 AAAATAATTTTAA-A
494585 AAAATAATTTTAAA
1 AAAATAATTTTAAA
*
494599 ATAATAATTTTAAA
1 AAAATAATTTTAAA
494613 A
1 A
494614 GATAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AAAATAATTTTAAA
Found at i:502317 original size:134 final size:133
Alignment explanation
Indices: 502148--502886 Score: 811
Period size: 134 Copynumber: 5.5 Consensus size: 133
502138 ATTCCACTTT
* * * * * * *
502148 TCTTCAGTGAATATTGAATCAGAATTGATTTGCTTCACTGTTCTTCAGGAAGACCAAATCTAAAA
1 TCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAA
* * *
502213 GAAGAAGAATTTGTTCCACTACTCTTTAGGGAAGATTAGACTCGAGAAAACTTTAATCCACTTCA
66 GAAGAAGAATTTGCTCCACTACTCTTTAGGG-AGATCAGACTCGAGAAAATTTTAATCCACTTCA
**
502278 CTAT
130 CTGC
* *
502282 TCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAGGAATACCAAATTTGAAA
1 TCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAA
* * * * * *
502347 GAACAAGAATTTGCTCTACTACTCTTTAGGGGAGATTAGACTTGAG-AAATATTTCATCCACTTA
66 GAAGAAGAATTTGCTCCACTACTCTTTA-GGGAGATCAGACTCGAGAAAAT-TTTAATCCACTTC
502411 ACTGC
129 ACTGC
* * *
502416 TCTTCAGGAAAGATTGAATCAGAATCGATTTGTTTCACTGCTCTTCAGGAAGACCAAATATGAAA
1 TCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAA
* * ** * * *
502481 GAAGAAGAATTCGCTCCGCTACTCTTTAAGGGAGGCCAGACTAGATG-AAATTTTGATCTACTTC
66 GAAGAAGAATTTGCTCCACTACTCTTT-AGGGAGATCAGACTCGA-GAAAATTTTAATCCACTTC
*
502545 ATTGC
129 ACTGC
* * * *
502550 TCTTCAGGGAAGATTGAATCAAACTTGATTTGCTTCACTGCTCTTCAGGAAAACCAAATATAAAA
1 TCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAA
* ** * * * *
502615 GAA-AGAGAATCTAATCCACAACTCTTTAGGGAGATCAAACTCGAGAAAATTTTGATCCACTTCG
66 GAAGA-AGAATTTGCTCCACTACTCTTTAGGGAGATCAGACTCGAGAAAATTTTAATCCACTTCA
* *
502679 TTGT
130 CTGC
* * *
502683 TCTTCAGCGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
1 TCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAA
* * * * * * *
502748 GAAGAAAAATATGATTCGCTACTCTTTAGGGGAGGTCAGACTCGTGAAAATTTTAATCCACTTCA
66 GAAGAAGAATTTGCTCCACTACTCTTTA-GGGAGATCAGACTCGAGAAAATTTTAATCCACTTCA
*
502813 TTGC
130 CTGC
* * ** * *
502817 TCTTCAAGGAAGATTGAATCAAACGT-GATTTGCTTCGTTGCTCTTTAGGAAGCCCAAAATATTG
1 TCTTCAGGGAAGATTGAATCAAA-ATCGATTTGCTTCACTGCTCTTCAGGAAGACC-AAATA-TG
502881 AAAGAA
63 AAAGAA
502887 AAATAGGGAT
Statistics
Matches: 512, Mismatches: 82, Indels: 20
0.83 0.13 0.03
Matches are distributed among these distances:
132 1 0.00
133 114 0.22
134 375 0.73
135 14 0.03
136 8 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (133 bp):
TCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAA
GAAGAAGAATTTGCTCCACTACTCTTTAGGGAGATCAGACTCGAGAAAATTTTAATCCACTTCAC
TGC
Found at i:502641 original size:268 final size:267
Alignment explanation
Indices: 502148--502867 Score: 905
Period size: 267 Copynumber: 2.7 Consensus size: 267
502138 ATTCCACTTT
* * * * *
502148 TCTTCAGTGAATATTGAATCAGAATTGATTTGCTTCACTGTTCTTCAGGAAGACCAAATCTAAAA
1 TCTTCAGCGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
* * * * *
502213 GAAGAAGAATTTGTTCCACTACTCTTT-AGGGAAGATTAGACTCGA-GAAAACTTTAATCCACTT
66 GAAGAAGAA-TTGATCCGCTACTCTTTAAGGG-AGGTCAGACTCGATGAAAATTTTAATCCACTT
* ** * * *
502276 CACTATTCTTCAGGGAAGATTGAATCAAAATCGATTTGCTTCACTGCTCTTCAGGAATACCAAAT
129 CATTGCTCTTCAGGGAAGATTGAATCAAACTTGATTTGCTTCACTGCTCTTCAGGAAAACCAAAT
* * * ** * * * * *
502341 TTGAAAGAACAAGAATTTGCTCTACTACTCTTTAGGGGAGATTAGACTTGAG-AAATATTTCATC
194 ATAAAAGAACAAGAATCTAATCCACAACTCTTTA-GGGAGATCAAACTCGAGAAAAT-TTTCATC
502405 CACTTAACTGC
257 CACTTAACTGC
* *
502416 TCTTCAG-GAAAGATTGAATCAGAATCGATTTGTTTCACTGCTCTTCAGGAAGACCAAATATGAA
1 TCTTCAGCG-AAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAA
* * * * *
502480 AGAAGAAGAATTCGCTCCGCTACTCTTTAAGGGAGGCCAGACTAGATG-AAATTTTGATCTACTT
65 AGAAGAAGAATT-GATCCGCTACTCTTTAAGGGAGGTCAGACTCGATGAAAATTTTAATCCACTT
502544 CATTGCTCTTCAGGGAAGATTGAATCAAACTTGATTTGCTTCACTGCTCTTCAGGAAAACCAAAT
129 CATTGCTCTTCAGGGAAGATTGAATCAAACTTGATTTGCTTCACTGCTCTTCAGGAAAACCAAAT
*
502609 ATAAAAGAA-AGAGAATCTAATCCACAACTCTTTAGGGAGATCAAACTCGAGAAAATTTTGATCC
194 ATAAAAGAACA-AGAATCTAATCCACAACTCTTTAGGGAGATCAAACTCGAGAAAATTTTCATCC
*** *
502673 ACTTCGTTGT
258 ACTTAACTGC
502683 TCTTCAGCGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
1 TCTTCAGCGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
* * *
502748 GAAGAAAAATATGATTCGCTACTCTTTAGGGGAGGTCAGACTCG-TGAAAATTTTAATCCACTTC
66 GAAGAAGAAT-TGATCCGCTACTCTTTAAGGGAGGTCAGACTCGATGAAAATTTTAATCCACTTC
* * ** *
502812 ATTGCTCTTCAAGGAAGATTGAATCAAACGTGATTTGCTTCGTTGCTCTTTAGGAA
130 ATTGCTCTTCAGGGAAGATTGAATCAAACTTGATTTGCTTCACTGCTCTTCAGGAA
502868 GCCCAAAATA
Statistics
Matches: 392, Mismatches: 51, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
266 2 0.01
267 194 0.49
268 191 0.49
269 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (267 bp):
TCTTCAGCGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAA
GAAGAAGAATTGATCCGCTACTCTTTAAGGGAGGTCAGACTCGATGAAAATTTTAATCCACTTCA
TTGCTCTTCAGGGAAGATTGAATCAAACTTGATTTGCTTCACTGCTCTTCAGGAAAACCAAATAT
AAAAGAACAAGAATCTAATCCACAACTCTTTAGGGAGATCAAACTCGAGAAAATTTTCATCCACT
TAACTGC
Found at i:503650 original size:45 final size:44
Alignment explanation
Indices: 503601--503836 Score: 217
Period size: 45 Copynumber: 5.2 Consensus size: 44
503591 TCTTCATAAT
* * *
503601 AAAGTAAAAAAGGACAACATTAAACTATCGACTTCTCTTCGCGAG
1 AAAGTAAAGAAGGACAACATTAAA-TATTGACTTCTCTTCACGAG
* *
503646 AAAGTCAAGAAGGACAACACTAAAATATTGAC-TCATCTTCACGAG
1 AAAGTAAAGAAGGACAACA-TTAAATATTGACTTC-TCTTCACGAG
* * * * * *
503691 AAAGTCAAGGAA-AACAATACTGAAAGATTGACTTCTCTTCGCGAG
1 AAAGT-AAAGAAGGACAACA-TTAAATATTGACTTCTCTTCACGAG
* * * *
503736 AAAGTTAAGAAGGACAACATTAAAAGATTGACTCCTCTTCACAAG
1 AAAGTAAAGAAGGACAACATT-AAATATTGACTTCTCTTCACGAG
* * *
503781 AAAGTCAAGGAA-GACAACATTGAAATATTGACTCCTTTTCACGAG
1 AAAGT-AAAGAAGGACAACATT-AAATATTGACTTCTCTTCACGAG
503826 AAAGTAAAGAA
1 AAAGTAAAGAA
503837 TAACGAAGAT
Statistics
Matches: 157, Mismatches: 27, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
44 12 0.08
45 131 0.83
46 14 0.09
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.22
Consensus pattern (44 bp):
AAAGTAAAGAAGGACAACATTAAATATTGACTTCTCTTCACGAG
Found at i:503729 original size:90 final size:90
Alignment explanation
Indices: 503630--503836 Score: 297
Period size: 90 Copynumber: 2.3 Consensus size: 90
503620 TTAAACTATC
* * *
503630 GACTTCTCTTCGCGAGAAAGTCAAGAAGGACAACACTAAAATATTGACTCATCTTCACGAGAAAG
1 GACTTCTCTTCGCGAGAAAGTAAAGAAGGACAACACTAAAAGATTGACTCATCTTCACAAGAAAG
*
503695 TCAAGGAAAACAATACTGAAAGATT
66 TCAAGGAAAACAACACTGAAAGATT
* * *
503720 GACTTCTCTTCGCGAGAAAGTTAAGAAGGACAACATTAAAAGATTGACTCCTCTTCACAAGAAAG
1 GACTTCTCTTCGCGAGAAAGTAAAGAAGGACAACACTAAAAGATTGACTCATCTTCACAAGAAAG
* * *
503785 TCAAGGAAGACAACATTGAAATATT
66 TCAAGGAAAACAACACTGAAAGATT
* * *
503810 GACTCCTTTTCACGAGAAAGTAAAGAA
1 GACTTCTCTTCGCGAGAAAGTAAAGAA
503837 TAACGAAGAT
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 104 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (90 bp):
GACTTCTCTTCGCGAGAAAGTAAAGAAGGACAACACTAAAAGATTGACTCATCTTCACAAGAAAG
TCAAGGAAAACAACACTGAAAGATT
Found at i:503860 original size:38 final size:38
Alignment explanation
Indices: 503807--504246 Score: 513
Period size: 38 Copynumber: 11.4 Consensus size: 38
503797 ACATTGAAAT
* * * * *
503807 ATTGACTCCTTTTCACGAGAAAGTAAAGAATAACGAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
503845 ATTGATTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
503883 ATCGACTTCTCTTCACGAGGAAGTCAAGAATAACAATG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
** * *
503921 ACCGACTTCTCTTCATGAGAAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
**
503959 ACCGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
*** * *
504001 ATTGAC-TCATCTTCGTAAGGGAGTCAGGAATAACAAAG
1 ATTGACTTC-TCTTCACGAGGAAGTCAAGAATAACAAAG
*
504039 ATTGACTTCTCTTCACGAAGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *** * *
504077 ATTAACTTCTCTTCGTAAGGAAGTCAGGAATAACAAAT
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
504115 ATTGACTTCTCTTCACGAGGAAATCAAGAGTAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
504153 ATTGACTTCTCTTCATGAGGAAGTCAAGAACAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
504191 ATTGACTTCTCTTAACGAGGAAGTCAAGAATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
504233 ATTGACTTCTCTTC
1 ATTGACTTCTCTTC
504247 GCTATGGAAT
Statistics
Matches: 341, Mismatches: 51, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
38 292 0.86
39 2 0.01
41 2 0.01
42 45 0.13
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (38 bp):
ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
Found at i:504064 original size:194 final size:194
Alignment explanation
Indices: 503834--504187 Score: 523
Period size: 194 Copynumber: 1.8 Consensus size: 194
503824 AGAAAGTAAA
* * * *
503834 GAATAACGAAGATTGATTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGACTTCTCTTCAC
1 GAATAACAAAGATTGACTTCTCTTCACGAAGAAGTCAAGAATAACAAAGATCAACTTCTCTTCAC
* *
503899 GAGGAAGTCAAGAATAAC-AATGACCGACTTCTCTTCATGA-GAAAGTCAAGAATAACAAAGACC
66 AAGGAAGTCAAGAATAACAAAT-ACCGACTTCTCTTCACGAGGAAA-TCAAGAATAACAAAGACC
*
503962 GACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCATCTTCGTAAGGGAGTCA
129 GACTTCTCTTCACGAGGAAGTCAAGAACAACATTGAAAGATTGACTCATCTTCGTAAGGGAGTCA
504027 G
194 G
* **
504028 GAATAACAAAGATTGACTTCTCTTCACGAAGAAGTCAAGAATAACAAAGATTAACTTCTCTTCGT
1 GAATAACAAAGATTGACTTCTCTTCACGAAGAAGTCAAGAATAACAAAGATCAACTTCTCTTCAC
* ** * **
504093 AAGGAAGTCAGGAATAACAAATATTGACTTCTCTTCACGAGGAAATCAAGAGTAACAAAGATTGA
66 AAGGAAGTCAAGAATAACAAATACCGACTTCTCTTCACGAGGAAATCAAGAATAACAAAGACCGA
*
504158 CTTCTCTTCATGAGGAAGTCAAGAACAACA
131 CTTCTCTTCACGAGGAAGTCAAGAACAACA
504188 AAGATTGACT
Statistics
Matches: 141, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
194 134 0.95
195 7 0.05
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (194 bp):
GAATAACAAAGATTGACTTCTCTTCACGAAGAAGTCAAGAATAACAAAGATCAACTTCTCTTCAC
AAGGAAGTCAAGAATAACAAATACCGACTTCTCTTCACGAGGAAATCAAGAATAACAAAGACCGA
CTTCTCTTCACGAGGAAGTCAAGAACAACATTGAAAGATTGACTCATCTTCGTAAGGGAGTCAG
Found at i:504213 original size:232 final size:232
Alignment explanation
Indices: 503807--504247 Score: 652
Period size: 232 Copynumber: 1.9 Consensus size: 232
503797 ACATTGAAAT
* * * * *
503807 ATTGACTCCTTTTCACGAGAAAGTAAAGAATAACGAAGATTGATTTCTCTTCACGAGGAAGTCAA
1 ATTGACTCCTCTTCACGAGAAAGTAAAGAATAACAAAGATTAACTTCTCTTCACAAGGAAGTCAA
* *
503872 GAATAACAAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAACAATGACCGACTTCTCTTCAT
66 GAATAACAAAGATCGACTTCTCTTCACGAGGAAATCAAGAATAACAAAGACCGACTTCTCTTCAT
* *
503937 GAGAAAGTCAAGAATAACAAAGACCGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGA
131 GAGAAAGTCAAGAACAACAAAGACCGACTTCTCTTAACGAGGAAGTCAAGAATAACATTGAAAGA
504002 TTGAC-TCATCTTCGTAAGGGAGTCAGGAATAACAAAG
196 TTGACTTC-TCTTCGTAAGGGAGTCAGGAATAACAAAG
* * **
504039 ATTGACTTCTCTTCACGA-AGAAGTCAAGAATAACAAAGATTAACTTCTCTTCGTAAGGAAGTCA
1 ATTGACTCCTCTTCACGAGA-AAGTAAAGAATAACAAAGATTAACTTCTCTTCACAAGGAAGTCA
* * * * **
504103 GGAATAACAAATATTGACTTCTCTTCACGAGGAAATCAAGAGTAACAAAGATTGACTTCTCTTCA
65 AGAATAACAAAGATCGACTTCTCTTCACGAGGAAATCAAGAATAACAAAGACCGACTTCTCTTCA
* **
504168 TGAGGAAGTCAAGAACAACAAAGATTGACTTCTCTTAACGAGGAAGTCAAGAATAACATTGAAAG
130 TGAGAAAGTCAAGAACAACAAAGACCGACTTCTCTTAACGAGGAAGTCAAGAATAACATTGAAAG
504233 ATTGACTTCTCTTCG
195 ATTGACTTCTCTTCG
504248 CTATGGAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
231 1 0.01
232 182 0.98
233 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (232 bp):
ATTGACTCCTCTTCACGAGAAAGTAAAGAATAACAAAGATTAACTTCTCTTCACAAGGAAGTCAA
GAATAACAAAGATCGACTTCTCTTCACGAGGAAATCAAGAATAACAAAGACCGACTTCTCTTCAT
GAGAAAGTCAAGAACAACAAAGACCGACTTCTCTTAACGAGGAAGTCAAGAATAACATTGAAAGA
TTGACTTCTCTTCGTAAGGGAGTCAGGAATAACAAAG
Found at i:506254 original size:13 final size:13
Alignment explanation
Indices: 506238--506375 Score: 54
Period size: 13 Copynumber: 9.9 Consensus size: 13
506228 ACTTTATTTA
506238 TTTTCTTTCT-TAT
1 TTTTCTTTCTCT-T
*
506251 TTTTTTTTCTCTT
1 TTTTCTTTCTCTT
*
506264 TTTTTTAATCTCTCTT
1 TTTTCT--T-TCTCTT
506280 TTTTCTTTCT-TT
1 TTTTCTTTCTCTT
*
506292 CTTTTCTTCTTCTATAT
1 -TTTTC-T-TTCTCT-T
*
506309 TTTTCTTTTTCTGTT
1 TTTTC--TTTCTCTT
506324 TTTATCCTTTCTCTT
1 TTT-T-CTTTCTCTT
*
506339 ATCTTCTCTT-TC-T
1 -TTTTCT-TTCTCTT
506352 TTTTC-TTCT-TT
1 TTTTCTTTCTCTT
506363 TTTTCTTCTCTCT
1 TTTTCTT-TCTCT
506376 CCTTTTTATC
Statistics
Matches: 100, Mismatches: 6, Indels: 37
0.70 0.04 0.26
Matches are distributed among these distances:
10 2 0.02
11 7 0.07
12 7 0.07
13 28 0.28
14 8 0.08
15 19 0.19
16 25 0.25
17 4 0.04
ACGTcount: A:0.05, C:0.21, G:0.01, T:0.73
Consensus pattern (13 bp):
TTTTCTTTCTCTT
Found at i:506294 original size:15 final size:15
Alignment explanation
Indices: 506239--506371 Score: 54
Period size: 15 Copynumber: 9.1 Consensus size: 15
506229 CTTTATTTAT
506239 TTTCTTTCTTATTTT-
1 TTTCTTTCTT-TTTTC
506254 TTT-TTCTCTTTTTT-
1 TTTCTT-TCTTTTTTC
*
506268 TTAATCTCTCTTTTTTC
1 TT--TCTTTCTTTTTTC
506285 TTTCTTTCTTTTCTTC
1 TTTCTTTCTTTT-TTC
* *
506301 -TTCTAT-ATTTTTC
1 TTTCTTTCTTTTTTC
506314 -TT-TTTCTGTTTTT-
1 TTTCTTTCT-TTTTTC
* * * *
506327 ATCCTTTCTCTTATC
1 TTTCTTTCTTTTTTC
506342 TTCTCTTTC-TTTTTC
1 TT-TCTTTCTTTTTTC
506357 -TTCTTT-TTTTCTTC
1 TTTCTTTCTTTT-TTC
506371 T
1 T
506372 CTCTCCTTTT
Statistics
Matches: 90, Mismatches: 13, Indels: 30
0.68 0.10 0.23
Matches are distributed among these distances:
12 2 0.02
13 13 0.14
14 24 0.27
15 31 0.34
16 17 0.19
17 3 0.03
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (15 bp):
TTTCTTTCTTTTTTC
Found at i:507844 original size:14 final size:15
Alignment explanation
Indices: 507825--507904 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 15
507815 GCATGTTAAG
507825 ATGCAATGTATAT-T
1 ATGCAATGTATATGT
507839 ATGCAATGTATGATGT
1 ATGCAATGTAT-ATGT
*
507855 AT--AGATGTAAATGT
1 ATGCA-ATGTATATGT
507869 AAAGATGCAATGTATAT-T
1 ----ATGCAATGTATATGT
507887 ATGCAATGTATGATGT
1 ATGCAATGTAT-ATGT
507903 AT
1 AT
507905 AGATGTAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 20
0.71 0.03 0.27
Matches are distributed among these distances:
14 27 0.51
15 9 0.17
16 6 0.11
18 3 0.06
19 7 0.13
20 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (15 bp):
ATGCAATGTATATGT
Found at i:507856 original size:21 final size:21
Alignment explanation
Indices: 507830--507905 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 21
507820 TTAAGATGCA
507830 ATGTATATTATGCAATGTATG
1 ATGTATATTATGCAATGTATG
* *
507851 ATGTATA-GATGTAAATGTAAAGATG
1 ATGTATATTATG-CAATGT----ATG
507876 CAATGTATATTATGCAATGTATG
1 --ATGTATATTATGCAATGTATG
507899 ATGTATA
1 ATGTATA
507906 GATGTAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
20 3 0.07
21 19 0.44
23 3 0.07
25 3 0.07
27 12 0.28
28 3 0.07
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (21 bp):
ATGTATATTATGCAATGTATG
Found at i:507893 original size:48 final size:48
Alignment explanation
Indices: 507817--507923 Score: 205
Period size: 48 Copynumber: 2.2 Consensus size: 48
507807 TGATTAATGC
*
507817 ATGTTAAGATGCAATGTATATTATGCAATGTATGATGTATAGATGTAA
1 ATGTAAAGATGCAATGTATATTATGCAATGTATGATGTATAGATGTAA
507865 ATGTAAAGATGCAATGTATATTATGCAATGTATGATGTATAGATGTAA
1 ATGTAAAGATGCAATGTATATTATGCAATGTATGATGTATAGATGTAA
507913 ATGTAAAGATG
1 ATGTAAAGATG
507924 TAAAATGTAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (48 bp):
ATGTAAAGATGCAATGTATATTATGCAATGTATGATGTATAGATGTAA
Found at i:507916 original size:14 final size:15
Alignment explanation
Indices: 507899--507934 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
507889 GCAATGTATG
507899 ATGTATAGATGT-AA
1 ATGTATAGATGTAAA
*
507913 ATGTAAAGATGTAAA
1 ATGTATAGATGTAAA
507928 ATGTATA
1 ATGTATA
507935 TATGAATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (15 bp):
ATGTATAGATGTAAA
Found at i:511135 original size:3 final size:3
Alignment explanation
Indices: 511121--511170 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
511111 TACAAACGAA
* *
511121 AAT AAG AAT AAT AAT AAT AAT AAAT AAT AAT GAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
511166 AAT AA
1 AAT AA
511171 AAGTGGGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:511156 original size:22 final size:22
Alignment explanation
Indices: 511120--511166 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
511110 CTACAAACGA
511120 AAATAAGAATAATAATAATAAT
1 AAATAAGAATAATAATAATAAT
* *
511142 AAATAATAATGATAATAATAAT
1 AAATAAGAATAATAATAATAAT
511164 AAA
1 AAA
511167 ATAAAAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (22 bp):
AAATAAGAATAATAATAATAAT
Found at i:512086 original size:18 final size:20
Alignment explanation
Indices: 512043--512080 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
512033 TTTGGTTCAC
* *
512043 GGAATATAATATTACCATTG
1 GGAATAAAAGATTACCATTG
512063 GGAATAAAAGATTACCAT
1 GGAATAAAAGATTACCAT
512081 GGAATAGGAT
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:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (20 bp):
GGAATAAAAGATTACCATTG
Found at i:512254 original size:15 final size:15
Alignment explanation
Indices: 512236--512266 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
512226 AAATTCTAAA
512236 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
512251 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
512266 T
1 T
512267 CATCGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:516150 original size:22 final size:21
Alignment explanation
Indices: 516099--516150 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
516089 AATTATAATG
*
516099 TATATATATAGATAAACTATG
1 TATATATATAGATAAACTATA
* * *
516120 TAGTGTATATATATGAACTATA
1 TA-TATATATAGATAAACTATA
516142 -ATATATATA
1 TATATATATA
516151 ATTTATATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 7 0.28
21 3 0.12
22 15 0.60
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (21 bp):
TATATATATAGATAAACTATA
Found at i:516267 original size:24 final size:24
Alignment explanation
Indices: 516233--516280 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
516223 CTATATAGAC
516233 TATATAATTTACAT-ATGAACTATA
1 TATATAATTTA-ATAATGAACTATA
* *
516257 TATATAGTTTATTAATGAACTATA
1 TATATAATTTAATAATGAACTATA
516281 AAAACTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (24 bp):
TATATAATTTAATAATGAACTATA
Found at i:516309 original size:2 final size:2
Alignment explanation
Indices: 516292--516393 Score: 50
Period size: 2 Copynumber: 49.0 Consensus size: 2
516282 AAACTATTTG
* * * *
516292 TA TA GTA TA TA CTA TA TA CA TA AA TA TA GTT TA TA TT TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
516335 T- TA TA TA -A TA TA GT- TGA TA TT TA TA TA CTA TA TA T- TA TA
1 TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA -TA TA TA TA TA TA
*
516374 TA TA TA AA CTA TA TA CTA TA
1 TA TA TA TA -TA TA TA -TA TA
516394 ATTGATATTG
Statistics
Matches: 76, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
1 4 0.05
2 60 0.79
3 12 0.16
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:516344 original size:27 final size:27
Alignment explanation
Indices: 516304--516447 Score: 153
Period size: 27 Copynumber: 5.7 Consensus size: 27
516294 TAGTATATAC
*
516304 TATATAC-ATA-AATATAGTTTATATT
1 TATATACTATATAATATAGTTGATATT
*
516329 TATATATTATATAATATAGTTGATATT
1 TATATACTATATAATATAGTTGATATT
516356 TATATACTATAT-AT-TA--T-ATA--
1 TATATACTATATAATATAGTTGATATT
* * *
516376 TATAAACTATATACTATAATTGATATT
1 TATATACTATATAATATAGTTGATATT
** *
516403 GGTATATTATATAATATAGTTGATATT
1 TATATACTATATAATATAGTTGATATT
516430 TATATACTATATAATATA
1 TATATACTATATAATATA
516448 ATTTATACTA
Statistics
Matches: 96, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
20 11 0.11
21 1 0.01
22 5 0.05
23 1 0.01
24 1 0.01
25 11 0.11
26 5 0.05
27 61 0.64
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (27 bp):
TATATACTATATAATATAGTTGATATT
Found at i:516374 original size:47 final size:52
Alignment explanation
Indices: 516314--516450 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 52
516304 TATATACATA
* * *
516314 AATATAGTTTATATTTATATATTATATAATATAGTTGATATT-TATA-TA-CT
1 AATATAG-TTATATTTATATACTATATAATATAATTGATATTGTATATTATAT
* * *
516364 -ATATA-TTATATATATAAACTATATACTATAATTGATATTGGTATATTATAT
1 AATATAGTTATATTTATATACTATATAATATAATTGATATT-GTATATTATAT
516415 AATATAGTTGATATTTATATACTATATAATATAATT
1 AATATAGTT-ATATTTATATACTATATAATATAATT
516451 TATACTATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
47 29 0.41
49 9 0.13
50 2 0.03
51 1 0.01
52 5 0.07
53 2 0.03
54 23 0.32
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (52 bp):
AATATAGTTATATTTATATACTATATAATATAATTGATATTGTATATTATAT
Found at i:516589 original size:26 final size:26
Alignment explanation
Indices: 516553--516604 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
516543 ATATATAAAC
*
516553 TATATAGTTTACAT-ATGAACTATATA
1 TATATAATTTA-ATAATGAACTATATA
*
516579 TATATAATTTATTAATGAACTATATA
1 TATATAATTTAATAATGAACTATATA
516605 AACTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (26 bp):
TATATAATTTAATAATGAACTATATA
Found at i:516627 original size:18 final size:18
Alignment explanation
Indices: 516601--516635 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
516591 TAATGAACTA
*
516601 TATAAACTATTTATATAG
1 TATAAACTATATATATAG
*
516619 TATATACTATATATATA
1 TATAAACTATATATATA
516636 AACTATAGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (18 bp):
TATAAACTATATATATAG
Found at i:516635 original size:20 final size:20
Alignment explanation
Indices: 516612--516773 Score: 63
Period size: 20 Copynumber: 8.0 Consensus size: 20
516602 ATAAACTATT
516612 TATATAGTATATACTATATA
1 TATATAGTATATACTATATA
* * * *
516632 TATAAACTATA-GCTTATATT
1 TATATAGTATATAC-TATATA
*
516652 TATATACTATATACTATAGT-
1 TATATAGTATATACTATA-TA
*
516672 TGATAT-TTATATACTATACACTA
1 T-ATATAGTATATACTAT--A-TA
*
516695 TAGTTGATATTAATATACTATATA
1 TA--T-ATAGT-ATATACTATATA
*
516719 -ATATAGTTTATACT-TATA
1 TATATAGTATATACTATATA
516737 TA-AT--T-TATACTATATA
1 TATATAGTATATACTATATA
* *
516753 AATTCAAAGTATATACTATAT
1 TA-T-ATAGTATATACTATAT
516774 GTATGAATAC
Statistics
Matches: 110, Mismatches: 12, Indels: 38
0.69 0.08 0.24
Matches are distributed among these distances:
15 6 0.05
16 6 0.05
18 6 0.05
19 9 0.08
20 43 0.39
21 8 0.07
22 13 0.12
23 2 0.02
24 3 0.03
25 3 0.03
26 2 0.02
27 9 0.08
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
TATATAGTATATACTATATA
Found at i:516662 original size:7 final size:7
Alignment explanation
Indices: 516612--516669 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
516602 ATAAACTATT
*
516612 TATATAG
1 TATATAC
516619 TATATAC
1 TATATAC
516626 TATATA-
1 TATATAC
*
516632 TATAAAC
1 TATATAC
*
516639 TATA-GC
1 TATATAC
*
516645 T-TATATT
1 TATATA-C
516652 TATATAC
1 TATATAC
516659 TATATAC
1 TATATAC
516666 TATA
1 TATA
516670 GTTGATATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
5 2 0.05
6 7 0.17
7 28 0.68
8 4 0.10
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (7 bp):
TATATAC
Found at i:516749 original size:54 final size:54
Alignment explanation
Indices: 516613--516750 Score: 165
Period size: 54 Copynumber: 2.6 Consensus size: 54
516603 TAAACTATTT
* *
516613 ATATAGTATATAC-TATAT-ATATAAACTATAGCTTATATTTATATACTATATA
1 ATATAGTTTATACTTATATAATATAAACTATAGCTTATATTAATATACTATATA
* * * * *
516665 CTATAGTTGATATTTATATACTATACACTATAG-TTGATATTAATATACTATATA
1 ATATAGTTTATACTTATATAATATAAACTATAGCTT-ATATTAATATACTATATA
* *
516719 ATATAGTTTATACTTATATAATTTATACTATA
1 ATATAGTTTATACTTATATAATATAAACTATA
516751 TAAATTCAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
52 9 0.13
53 7 0.10
54 54 0.77
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (54 bp):
ATATAGTTTATACTTATATAATATAAACTATAGCTTATATTAATATACTATATA
Found at i:516750 original size:27 final size:27
Alignment explanation
Indices: 516601--516750 Score: 146
Period size: 27 Copynumber: 5.7 Consensus size: 27
516591 TAATGAACTA
* * *
516601 TATAAACTATTTA-TATAGTATATAC-
1 TATATACTATATACTATAGTTTATACT
* * *
516626 TATATA-TATAAACTATAGCTTATATT
1 TATATACTATATACTATAGTTTATACT
* *
516652 TATATACTATATACTATAGTTGATATT
1 TATATACTATATACTATAGTTTATACT
* *
516679 TATATACTATACACTATAGTTGATA-T
1 TATATACTATATACTATAGTTTATACT
*
516705 TAATATACTATATAATATAGTTTATACT
1 T-ATATACTATATACTATAGTTTATACT
* *
516733 TATATAATTTATACTATA
1 TATATACTATATACTATA
516751 TAAATTCAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
24 4 0.04
25 14 0.13
26 8 0.08
27 76 0.73
28 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (27 bp):
TATATACTATATACTATAGTTTATACT
Found at i:516756 original size:15 final size:15
Alignment explanation
Indices: 516719--516753 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
516709 ATACTATATA
*
516719 ATATAGTTTATACTT
1 ATATAATTTATACTT
516734 ATATAATTTATAC-T
1 ATATAATTTATACTT
516748 ATATAA
1 ATATAA
516754 ATTCAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATAATTTATACTT
Found at i:523006 original size:20 final size:19
Alignment explanation
Indices: 522981--523039 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
522971 TTTTGGTGTA
*
522981 GAGGGAATTGATACCCCCAT
1 GAGGGAATCGATACCCCC-T
* *
523001 GAGGGAACCGATTCCCCCT
1 GAGGGAATCGATACCCCCT
523020 -AGGAGAATCGATACCCCCT
1 GAGG-GAATCGATACCCCCT
523039 G
1 G
523040 GGGTTCTGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.09
19 14 0.44
20 15 0.47
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (19 bp):
GAGGGAATCGATACCCCCT
Found at i:525869 original size:123 final size:123
Alignment explanation
Indices: 525731--525973 Score: 468
Period size: 123 Copynumber: 2.0 Consensus size: 123
525721 GTAACGATTC
525731 CCCCCCAGTGTAACGGTCGAAATATTTGAATTTTACAATTAGGGAACCGATTCCCCATAGGGGGT
1 CCCCCCAGTGTAACGGTCGAAATATTTGAATTTTACAATTAGGGAACCGATTCCCCATAGGGGGT
525796 ACCAATTCCGCCCACGCTCCAAACTGTTTTATTAATTGATTTCAAACTAAAACGGGTT
66 ACCAATTCCGCCCACGCTCCAAACTGTTTTATTAATTGATTTCAAACTAAAACGGGTT
525854 CCCCCCAGTGTAACGGTCGAAATATTTGAATTTTACAATTAGGGAACCGATTCCCCATAGGGGGT
1 CCCCCCAGTGTAACGGTCGAAATATTTGAATTTTACAATTAGGGAACCGATTCCCCATAGGGGGT
* *
525919 ACCGATTCCGCCCACGCTCCAAACTGTTTTATTAATTGATTTCACACTAAAACGG
66 ACCAATTCCGCCCACGCTCCAAACTGTTTTATTAATTGATTTCAAACTAAAACGG
525974 CTATATTATC
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 118 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (123 bp):
CCCCCCAGTGTAACGGTCGAAATATTTGAATTTTACAATTAGGGAACCGATTCCCCATAGGGGGT
ACCAATTCCGCCCACGCTCCAAACTGTTTTATTAATTGATTTCAAACTAAAACGGGTT
Found at i:527440 original size:30 final size:28
Alignment explanation
Indices: 527392--527468 Score: 75
Period size: 30 Copynumber: 2.7 Consensus size: 28
527382 ACTATATAGT
* * * *
527392 ATATACTAACTATATAATATAAACCATGTA
1 ATATAGTAATTATTTAATATAAA--ATATA
*
527422 ATATAGTAATTATTTAATATCAAATATA
1 ATATAGTAATTATTTAATATAAAATATA
*
527450 ATAT-GTAATTATTTGATAT
1 ATATAGTAATTATTTAATAT
527469 GAAGCTATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 14 0.34
28 8 0.20
30 19 0.46
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (28 bp):
ATATAGTAATTATTTAATATAAAATATA
Found at i:528130 original size:21 final size:21
Alignment explanation
Indices: 528105--528169 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
528095 AACATAAGAA
528105 TAATAATATAATAATCATAAT
1 TAATAATATAATAATCATAAT
* *
528126 TAAT-ATA-ATTAAT-ATATT
1 TAATAATATAATAATCATAAT
* * *
528144 TATTAATTTAATTATCATAAT
1 TAATAATATAATAATCATAAT
528165 TAATA
1 TAATA
528170 TTTTATTATA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 7 0.21
19 7 0.21
20 7 0.21
21 12 0.36
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATAATATAATAATCATAAT
Found at i:528174 original size:21 final size:20
Alignment explanation
Indices: 528113--528178 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 20
528103 AATAATAATA
*
528113 TAATAATCATAATTAATA--
1 TAATTATCATAATTAATATT
* *
528131 TAATTAAT-ATATTTATTAATT
1 TAATT-ATCATAATTAAT-ATT
528152 TAATTATCATAATTAATATT
1 TAATTATCATAATTAATATT
*
528172 TTATTAT
1 TAATTAT
528179 AACATTTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
18 11 0.30
19 3 0.08
20 11 0.30
21 12 0.32
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTATCATAATTAATATT
Found at i:528773 original size:26 final size:26
Alignment explanation
Indices: 528744--528812 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
528734 AATCATAGTC
*
528744 CAGTAAATCTCATAAAAATTGTACTG
1 CAGTAAATCTCATAAAAATTGTACTA
528770 CAGTAAATCTCATAAAAATTGTACTA
1 CAGTAAATCTCATAAAAATTGTACTA
528796 CAGTAAATCTCATAAAA
1 CAGTAAATCTCATAAAA
528813 GAGTTACCCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (26 bp):
CAGTAAATCTCATAAAAATTGTACTA
Found at i:528913 original size:32 final size:31
Alignment explanation
Indices: 528875--528951 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
528865 TTGGGGCCGT
*
528875 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
528907 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
528938 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
528952 GTCATATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:529640 original size:25 final size:25
Alignment explanation
Indices: 529611--529661 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
529601 AAACATAAAG
529611 TATGACTTTTCAAAAATTCAAATTC
1 TATGACTTTTCAAAAATTCAAATTC
529636 TATGACTTTTCAAAAATTCAAATTC
1 TATGACTTTTCAAAAATTCAAATTC
529661 T
1 T
529662 TGGTCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TATGACTTTTCAAAAATTCAAATTC
Found at i:529904 original size:29 final size:28
Alignment explanation
Indices: 529861--530022 Score: 152
Period size: 29 Copynumber: 5.6 Consensus size: 28
529851 TCCACATTCG
*
529861 AAAATTACCAAAATGTCACATTTTTCAA
1 AAAATTACCAGAATGTCACATTTTTCAA
* *
529889 AATAATTCCCAGAATGTCAC-CTTTTCACA
1 AA-AATTACCAGAATGTCACATTTTTCA-A
*
529918 AAAATTACC-GAAATGTCA-TTTTTTCAAAAA
1 AAAATTACCAG-AATGTCACATTTTTC---AA
529948 AAAATT-CCAGAATGTCACATTTTTCACA
1 AAAATTACCAGAATGTCACATTTTTCA-A
* *
529976 AAAATTCCCAAAATGTCACATTTTTCAA
1 AAAATTACCAGAATGTCACATTTTTCAA
**
530004 AATAATTTTCAGAATGTCA
1 AA-AATTACCAGAATGTCA
530023 TCGGGTCGGG
Statistics
Matches: 112, Mismatches: 10, Indels: 23
0.77 0.07 0.16
Matches are distributed among these distances:
27 2 0.02
28 36 0.32
29 59 0.53
30 14 0.12
31 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (28 bp):
AAAATTACCAGAATGTCACATTTTTCAA
Found at i:529958 original size:57 final size:58
Alignment explanation
Indices: 529861--530022 Score: 213
Period size: 58 Copynumber: 2.8 Consensus size: 58
529851 TCCACATTCG
*
529861 AAAATTACCAAAATGTCACATTTTTC-AAAATAATTCCCAGAATGTCAC-CTTTTCACA
1 AAAATTACCAAAATGTCACATTTTTCAAAAAAAATT-CCAGAATGTCACACTTTTCACA
* * *
529918 AAAATTACCGAAATGTCA-TTTTTTCAAAAAAAAATTCCAGAATGTCACATTTTTCACA
1 AAAATTACCAAAATGTCACATTTTTC-AAAAAAAATTCCAGAATGTCACACTTTTCACA
* * * *
529976 AAAATTCCCAAAATGTCACATTTTTCAAAATAATTTTCAGAATGTCA
1 AAAATTACCAAAATGTCACATTTTTCAAAAAAAATTCCAGAATGTCA
530023 TCGGGTCGGG
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
56 6 0.07
57 29 0.32
58 50 0.55
59 6 0.07
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (58 bp):
AAAATTACCAAAATGTCACATTTTTCAAAAAAAATTCCAGAATGTCACACTTTTCACA
Found at i:535540 original size:26 final size:26
Alignment explanation
Indices: 535511--535579 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
535501 AATCATAGTC
535511 CAGTAAATCTCATAAAAATTGTACTG
1 CAGTAAATCTCATAAAAATTGTACTG
535537 CAGTAAATCTCATAAAAATTGTACTG
1 CAGTAAATCTCATAAAAATTGTACTG
535563 CAGTAAATCTCATAAAA
1 CAGTAAATCTCATAAAA
535580 GAGTTACCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (26 bp):
CAGTAAATCTCATAAAAATTGTACTG
Found at i:536671 original size:58 final size:58
Alignment explanation
Indices: 536597--536761 Score: 203
Period size: 58 Copynumber: 2.8 Consensus size: 58
536587 AACACATTCG
*
536597 AAAATTACCAAAATGTCACATTTTTCAAAATAATTCCTAGAATGTCACCTTTTTCACA
1 AAAATTTCCAAAATGTCACATTTTTCAAAATAATTCCTAGAATGTCACCTTTTTCACA
* * **
536655 AAAA-TTCTCGAAATGT--CATTTTTCCAAAAAAAAATT-CTAGAATGTCATATTTTTCACA
1 AAAATTTC-CAAAATGTCACATTTTT-C--AAAATAATTCCTAGAATGTCACCTTTTTCACA
* *
536713 AAAATTTCCAAAATGTCACCTTTTTCAAAATAATTCCCAGAATGTCACC
1 AAAATTTCCAAAATGTCACATTTTTCAAAATAATTCCTAGAATGTCACC
536762 GGGTCGGGTC
Statistics
Matches: 88, Mismatches: 11, Indels: 16
0.77 0.10 0.14
Matches are distributed among these distances:
56 7 0.08
57 11 0.12
58 52 0.59
59 12 0.14
60 6 0.07
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (58 bp):
AAAATTTCCAAAATGTCACATTTTTCAAAATAATTCCTAGAATGTCACCTTTTTCACA
Found at i:536690 original size:30 final size:30
Alignment explanation
Indices: 536654--536716 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
536644 CCTTTTTCAC
*
536654 AAAAATTCTCGAAATGTCAT-TTTTCCAAAA
1 AAAAATTCTAG-AATGTCATATTTTCCAAAA
* *
536684 AAAAATTCTAGAATGTCATATTTTTCACAA
1 AAAAATTCTAGAATGTCATATTTTCCAAAA
536714 AAA
1 AAA
536717 TTTCCAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (30 bp):
AAAAATTCTAGAATGTCATATTTTCCAAAA
Found at i:536761 original size:29 final size:28
Alignment explanation
Indices: 536597--536761 Score: 131
Period size: 29 Copynumber: 5.7 Consensus size: 28
536587 AACACATTCG
* * *
536597 AAAATTACCAAAATGTCACATTTTTCAA
1 AAAATTCCCAGAATGTCACCTTTTTCAA
*
536625 AATAATTCCTAGAATGTCACCTTTTTCACA
1 AA-AATTCCCAGAATGTCACCTTTTTCA-A
*
536655 AAAATTCTC-GAAATGTCA--TTTTTCCAAAAA
1 AAAATTCCCAG-AATGTCACCTTTTT-C---AA
* **
536685 AAAATT-CTAGAATGTCATATTTTTCACA
1 AAAATTCCCAGAATGTCACCTTTTTCA-A
* *
536713 AAAATTTCCAAAATGTCACCTTTTTCAA
1 AAAATTCCCAGAATGTCACCTTTTTCAA
536741 AATAATTCCCAGAATGTCACC
1 AA-AATTCCCAGAATGTCACC
536762 GGGTCGGGTC
Statistics
Matches: 110, Mismatches: 14, Indels: 25
0.74 0.09 0.17
Matches are distributed among these distances:
27 6 0.05
28 14 0.13
29 72 0.65
30 12 0.11
31 6 0.05
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (28 bp):
AAAATTCCCAGAATGTCACCTTTTTCAA
Found at i:540287 original size:27 final size:27
Alignment explanation
Indices: 540225--540287 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
540215 GTACTAGCAA
* * **
540225 ACCCATGCAGAATTTACAAGCCAATTC
1 ACCCATGCAAAATATACAAGCCAAGCC
* * *
540252 TCTCGTGCAAAATATACAAGCCAAGCC
1 ACCCATGCAAAATATACAAGCCAAGCC
540279 ACCCATGCA
1 ACCCATGCA
540288 GATGCAAGTC
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.19
Consensus pattern (27 bp):
ACCCATGCAAAATATACAAGCCAAGCC
Found at i:541738 original size:22 final size:21
Alignment explanation
Indices: 541706--541758 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
541696 AAATAATAAT
* *
541706 AAAATATTATTTTTATTCAATA
1 AAAATAATATTTTAATTCAA-A
*
541728 AAAATAATATTTTAATTGAAA
1 AAAATAATATTTTAATTCAAA
541749 AAAATAATAT
1 AAAATAATAT
541759 ATAGAGAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAATAATATTTTAATTCAAA
Found at i:552408 original size:13 final size:13
Alignment explanation
Indices: 552392--552418 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
552382 GAATACTACT
552392 TGGGAAAACTATA
1 TGGGAAAACTATA
552405 TGGGAAAACTATA
1 TGGGAAAACTATA
552418 T
1 T
552419 TGTGTTGAAT
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:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (13 bp):
TGGGAAAACTATA
Found at i:554439 original size:54 final size:54
Alignment explanation
Indices: 554381--554886 Score: 683
Period size: 54 Copynumber: 9.4 Consensus size: 54
554371 TTCTATAGGG
* * * * * *
554381 TGCACACGTAGTGCCGATACGATCATTTATAAACTCATTATGAATTCAGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGT
* * *
554435 TGCACACCTAGTGTCGATACGATCGTTCATAAACTTATTATGAATTCTGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGT
* * * *
554489 TGCACACTTATTGTCGATACGGTCGTTTATAAACTTGTTATGAATTCTGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGT
* *
554543 TGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGT
*
554597 TGCACATTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATT-TCGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCT-GTGGGT
* * **
554651 TGCACACTTAATGCCGATATGGTTATTCATAAACTTATTATGAACTT-TGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA-TTCTGTGGGT
* **
554705 TGCACACTTAGAGCCGATACGGTCGTTCATAAACTTATTATGAATTCCATGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGT
* * * * * *
554759 TGCACACTTAGTCCCGATATGATTGTTCATAGACTTATTATGAATTATGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGT
* * *
554813 TGCACACTTAGTGTCAATACGGTCGTTCATAAACTTGTTATGAATTCTGTGGGT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGT
*
554867 TGCACACTTAGTGTCGATAC
1 TGCACACTTAGTGCCGATAC
554887 ATAAAAAAAT
Statistics
Matches: 400, Mismatches: 49, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
53 2 0.00
54 395 0.99
55 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (54 bp):
TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGT
Found at i:555601 original size:20 final size:21
Alignment explanation
Indices: 555558--555601 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
555548 CAACTAACTT
** *
555558 ACATCCATAAATCTCCTTATA
1 ACATCCATAAATCTCCAAAGA
555579 ACATCCA-AAATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
555599 ACA
1 ACA
555602 CTCAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:557330 original size:21 final size:21
Alignment explanation
Indices: 557285--557324 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
557275 TAGAGTTTTT
*
557285 GTTTAGAGGTTATGATTTAGC
1 GTTTAGAGGTTATAATTTAGC
*
557306 GTTTAGAGTTTATAATTTA
1 GTTTAGAGGTTATAATTTA
557325 AGGTTTTAAG
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:0.28, C:0.03, G:0.23, T:0.47
Consensus pattern (21 bp):
GTTTAGAGGTTATAATTTAGC
Found at i:558357 original size:33 final size:33
Alignment explanation
Indices: 558320--558389 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
558310 GATTTTGAAA
558320 AAAAAATTAAAAATTTAAGTACTTAATCAAATC
1 AAAAAATTAAAAATTTAAGTACTTAATCAAATC
558353 AAAAAATTAAAAATTTAAGTACTTAATCAAATC
1 AAAAAATTAAAAATTTAAGTACTTAATCAAATC
558386 AAAA
1 AAAA
558390 CTGATAGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (33 bp):
AAAAAATTAAAAATTTAAGTACTTAATCAAATC
Found at i:558597 original size:2 final size:2
Alignment explanation
Indices: 558590--558620 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
558580 ATTAATTAAT
558590 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
558621 TCAAGAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:560702 original size:36 final size:36
Alignment explanation
Indices: 560654--560736 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
560644 TCAAACAGGT
*
560654 GGGGAGCAATCTGAGAAATCGGATTCAAGTAGCAGT
1 GGGGAGCAATCTGAGAAATCGGATTCAAGTAGCAGC
* *
560690 TGGGAGCAATCTGAGAAATCGGATTCAAGTGGCAGC
1 GGGGAGCAATCTGAGAAATCGGATTCAAGTAGCAGC
560726 GGGGAGCAATC
1 GGGGAGCAATC
560737 AGACTCAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.31, C:0.16, G:0.35, T:0.18
Consensus pattern (36 bp):
GGGGAGCAATCTGAGAAATCGGATTCAAGTAGCAGC
Found at i:561353 original size:132 final size:135
Alignment explanation
Indices: 561125--561381 Score: 405
Period size: 132 Copynumber: 1.9 Consensus size: 135
561115 TGCAACAGAC
* *
561125 AATGCAGCTTCAGATGTTACTCAAAAGGACAACAATTTGAATGAAAATGAACATGCTGCTCAGAG
1 AATGCAACTGCAGATGTTACTCAAAAGGACAACAATTTGAATG-AAA-GAACA-GCTGCTCAGAG
* * *
561190 CAACACCGAAAACAATGAAAATGCAGTTCAGAATGAGAACAATGCCACTCAGAGCAACACAGACA
63 CAACACCGAAAACAATGAAAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAACACAGACA
561255 ATAATGAA
128 ATAATGAA
561263 AATGCAACTGCAGATGTTACTCAAAAGGACAACAATTTGAATG-AA-AAC-GCTGCTCAGAGCAA
1 AATGCAACTGCAGATGTTACTCAAAAGGACAACAATTTGAATGAAAGAACAGCTGCTCAGAGCAA
561325 CACCGAAAACAAT-AACAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAACAC
66 CACCGAAAACAATGAA-AATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAACAC
561382 CGGAAGCAAT
Statistics
Matches: 113, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
131 2 0.02
132 65 0.58
134 3 0.03
136 2 0.02
138 41 0.36
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (135 bp):
AATGCAACTGCAGATGTTACTCAAAAGGACAACAATTTGAATGAAAGAACAGCTGCTCAGAGCAA
CACCGAAAACAATGAAAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAACACAGACAATA
ATGAA
Found at i:561379 original size:54 final size:54
Alignment explanation
Indices: 561315--561705 Score: 480
Period size: 54 Copynumber: 7.2 Consensus size: 54
561305 GAAAACGCTG
*
561315 CTCAGAGCAACACCGAAAACAATAACAATGCAGGTCAGAACGAGAACAAGGCCA
1 CTCAGAGCAACACCGAAAGCAATAACAATGCAGGTCAGAACGAGAACAAGGCCA
* * * * *
561369 CTCAGAGCAACACCGGAAGCAATGACAATGAAGGTCAGGATGAGAACAAGGCCA
1 CTCAGAGCAACACCGAAAGCAATAACAATGCAGGTCAGAACGAGAACAAGGCCA
* * * * * *
561423 CTCAAAGCAACACCGGAAGCAATGACAATGCAGGTCAGGATGAGAACATGGCCA
1 CTCAGAGCAACACCGAAAGCAATAACAATGCAGGTCAGAACGAGAACAAGGCCA
* * * *
561477 CTCAAAGCAACACCGAAAGCAATGAA-AATGCAGGTCAGAATGAGAATAAGACCA
1 CTCAGAGCAACACCGAAAGCAAT-AACAATGCAGGTCAGAACGAGAACAAGGCCA
* ** *
561531 CTCAGAGCTACACCGACGGCAATGACAATGCAGGTCAGAACGAGAACAAGGCCA
1 CTCAGAGCAACACCGAAAGCAATAACAATGCAGGTCAGAACGAGAACAAGGCCA
* ** * * *
561585 CTCAGAGCAACACTGATGGCAATGATAATGCAGGTCATAACGAGAACAAGGCCA
1 CTCAGAGCAACACCGAAAGCAATAACAATGCAGGTCAGAACGAGAACAAGGCCA
* *
561639 CTCAGAGCAACAGC-AACAGCAATAACAATGCAGGTCAGAACGAGAACAAGGTCA
1 CTCAGAGCAACACCGAA-AGCAATAACAATGCAGGTCAGAACGAGAACAAGGCCA
* *
561693 CTCAAACCAACAC
1 CTCAGAGCAACAC
561706 TGACAACAAT
Statistics
Matches: 295, Mismatches: 39, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
53 2 0.01
54 292 0.99
55 1 0.00
ACGTcount: A:0.42, C:0.25, G:0.23, T:0.10
Consensus pattern (54 bp):
CTCAGAGCAACACCGAAAGCAATAACAATGCAGGTCAGAACGAGAACAAGGCCA
Found at i:561754 original size:162 final size:162
Alignment explanation
Indices: 561315--561738 Score: 541
Period size: 162 Copynumber: 2.6 Consensus size: 162
561305 GAAAACGCTG
*
561315 CTCAGAGCAACACCGAAAACAATAACAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAAC
1 CTCAGAGCAACACCGAAAGCAATAACAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAAC
* *
561380 ACCGGA-AGCAATGACAATGAAGGTCAGGATGAGAACAAGGCCACTCAAAGCAACACCGGAAGCA
66 ACC-GACAGCAATGACAATGAAGGTCAGAATGAGAACAAGGCCACTCAGAGCAACACCGGAAGCA
* * *
561444 ATGACAATGCAGGTCAGGATGAGAACATGGCCA
130 ATGACAATGCAGGTCAGAACGAGAACAAGGCCA
* * * * *
561477 CTCAAAGCAACACCGAAAGCAATGAA-AATGCAGGTCAGAATGAGAATAAGACCACTCAGAGCTA
1 CTCAGAGCAACACCGAAAGCAAT-AACAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAA
* * * * *
561541 CACCGACGGCAATGACAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAACA-CTGATGGC
65 CACCGACAGCAATGACAATGAAGGTCAGAATGAGAACAAGGCCACTCAGAGCAACACCGGA-AGC
* *
561605 AATGATAATGCAGGTCATAACGAGAACAAGGCCA
129 AATGACAATGCAGGTCAGAACGAGAACAAGGCCA
* * * *
561639 CTCAGAGCAACAGC-AACAGCAATAACAATGCAGGTCAGAACGAGAACAAGGTCACTCAAACCAA
1 CTCAGAGCAACACCGAA-AGCAATAACAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAA
* * * * *
561703 CACTGACAACAATGAAAATGTAGGCCAGAATGAGAA
65 CACCGACAGCAATGACAATGAAGGTCAGAATGAGAA
561739 TAATGCTTCT
Statistics
Matches: 223, Mismatches: 34, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
161 9 0.04
162 212 0.95
163 2 0.01
ACGTcount: A:0.43, C:0.24, G:0.23, T:0.11
Consensus pattern (162 bp):
CTCAGAGCAACACCGAAAGCAATAACAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAAC
ACCGACAGCAATGACAATGAAGGTCAGAATGAGAACAAGGCCACTCAGAGCAACACCGGAAGCAA
TGACAATGCAGGTCAGAACGAGAACAAGGCCA
Found at i:561774 original size:108 final size:105
Alignment explanation
Indices: 561338--561776 Score: 370
Period size: 108 Copynumber: 4.1 Consensus size: 105
561328 CGAAAACAAT
* * * * *
561338 AACAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAACACCGGAAGCAATGACAATGAAGG
1 AACAATGCAGGTCAGAACGAGAACAAGGCCACTCAAAGCAACA-CTGAAACAATGAAAATGCAGG
* * * * * *
561403 TCAGGATGAGAACAAGGCCACTCAAAGCAAC-AC-CGGAAGCAA
65 TCAGAATGAGAATAA-GCCACTCAGAGCTACGACGC-CAA-TAA
* * * * *
561445 TGACAATGCAGGTCAGGATGAGAACATGGCCACTCAAAGCAACACCGAAAGCAATGAAAATGCAG
1 -AACAATGCAGGTCAGAACGAGAACAAGGCCACTCAAAGCAACACTGAAA-CAATGAAAATGCAG
*
561510 GTCAGAATGAGAATAAGACCACTCAGAGCTACACCGACGGCAAT--
64 GTCAGAATGAGAATAAG-CCACTCAGAGCT--A-CGACGCCAATAA
* * ** *
561554 GACAATGCAGGTCAGAACGAGAACAAGGCCACTCAGAGCAACACTGATGGCAATGATAATGCAGG
1 AACAATGCAGGTCAGAACGAGAACAAGGCCACTCAAAGCAACACTGA-AACAATGAAAATGCAGG
* * * *
561619 TCATAACGAGAACAAGGCCACTCAGAGCAACAGCAACAG-CAAT--
65 TCAGAATGAGAATAA-GCCACTCAGAGCTAC-G--AC-GCCAATAA
* * *
561662 AACAATGCAGGTCAGAACGAGAACAAGGTCACTCAAACCAACACTGACAACAATGAAAATGTAGG
1 AACAATGCAGGTCAGAACGAGAACAAGGCCACTCAAAGCAACACTGA-AACAATGAAAATGCAGG
* **
561727 CCAGAATGAGAATAATGCTTCTCAGAGCTACGACGCCAATAA
65 TCAGAATGAGAATAA-GCCACTCAGAGCTACGACGCCAATAA
561769 CAACAATG
1 -AACAATG
561777 AAAATACAAG
Statistics
Matches: 269, Mismatches: 45, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
104 1 0.00
105 7 0.03
106 2 0.01
107 6 0.02
108 245 0.91
109 2 0.01
110 1 0.00
111 1 0.00
112 4 0.01
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (105 bp):
AACAATGCAGGTCAGAACGAGAACAAGGCCACTCAAAGCAACACTGAAACAATGAAAATGCAGGT
CAGAATGAGAATAAGCCACTCAGAGCTACGACGCCAATAA
Found at i:567336 original size:15 final size:15
Alignment explanation
Indices: 567316--567352 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
567306 ATATTTAATT
*
567316 GGGCGGGCAGATGTG
1 GGGCGGGCAGATGCG
*
567331 GGGCGGGCGGATGCG
1 GGGCGGGCAGATGCG
567346 GGGCGGG
1 GGGCGGG
567353 TAATGTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.68, T:0.08
Consensus pattern (15 bp):
GGGCGGGCAGATGCG
Found at i:569075 original size:29 final size:31
Alignment explanation
Indices: 569043--569106 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
569033 TAATTTAAAT
569043 ATATAATA-AAAATAAAAA-AATATAATATA
1 ATATAATATAAAATAAAAACAATATAATATA
** * *
569072 ATATAATATTTAATAAAAACTATATAATATT
1 ATATAATATAAAATAAAAACAATATAATATA
569103 ATAT
1 ATAT
569107 TTTCAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.28
30 8 0.28
31 13 0.45
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (31 bp):
ATATAATATAAAATAAAAACAATATAATATA
Found at i:569155 original size:17 final size:17
Alignment explanation
Indices: 569097--569155 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 17
569087 AAAACTATAT
*
569097 AATAT-TATATTTTCAA
1 AATATATATGTTTTCAA
569113 AA-ATAATATGTTTTCGAAA
1 AATAT-ATATGTTTTC--AA
569132 ATTATATATATGTTTTCAA
1 A--ATATATATGTTTTCAA
569151 AATAT
1 AATAT
569156 TTTAAAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
15 2 0.06
16 2 0.06
17 12 0.34
19 6 0.17
21 11 0.31
22 2 0.06
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (17 bp):
AATATATATGTTTTCAA
Found at i:569188 original size:13 final size:13
Alignment explanation
Indices: 569170--569196 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
569160 AAAACTCTAT
569170 ATATGTTTTCAAA
1 ATATGTTTTCAAA
569183 ATATGTTTTCAAA
1 ATATGTTTTCAAA
569196 A
1 A
569197 CTATATTATA
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:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATGTTTTCAAA
Found at i:569201 original size:31 final size:32
Alignment explanation
Indices: 569117--569202 Score: 106
Period size: 31 Copynumber: 2.7 Consensus size: 32
569107 TTTCAAAAAT
*
569117 AATATGTTTTCGAAAATTATATATATGTTTTCAA
1 AATATGTTTTC-AAAA-TCTATATATGTTTTCAA
*
569151 AATA--TTTTAAAAACTCTATATATGTTTTCAA
1 AATATGTTTTCAAAA-TCTATATATGTTTTCAA
569182 AATATGTTTTCAAAA-CTATAT
1 AATATGTTTTCAAAATCTATAT
569203 TATATATGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
31 30 0.65
32 4 0.09
33 8 0.17
34 4 0.09
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (32 bp):
AATATGTTTTCAAAATCTATATATGTTTTCAA
Found at i:569208 original size:36 final size:36
Alignment explanation
Indices: 569085--569472 Score: 247
Period size: 36 Copynumber: 10.8 Consensus size: 36
569075 TAATATTTAA
* *
569085 TAAAAACTATATAATATTATATTTTCAAAAATAATATGTTT
1 TAAAAACTATATATTA-TATGTTTTC---AA-AATATGTTT
*
569126 TCGAAAA-T-TATA-TATATGTTTTCAAAATA--TTT
1 T-AAAAACTATATATTATATGTTTTCAAAATATGTTT
*
569158 TAAAAAC--TCTA-TATATGTTTTCAAAATATGTTT
1 TAAAAACTATATATTATATGTTTTCAAAATATGTTT
* ** *
569191 TCAAAACTATAT-TATATATGTTTTTCGAAAACCTTTTT
1 TAAAAACTATATAT-TATATG-TTTTC-AAAATATGTTT
** *
569229 TTTAAATTATATATTATATGTTTTCAAAAT-TGTTT
1 TAAAAACTATATATTATATGTTTTCAAAATATGTTT
*
569264 TAAAAACTATATATTATATGCTTTCAAAATTAT-TTT
1 TAAAAACTATATATTATATGTTTTCAAAA-TATGTTT
**
569300 TAAAAAAACTATATATTATACT-TTATTTTAAATAT-TTT
1 T--AAAAACTATATATTATA-TGTT-TTCAAAATATGTTT
* * * *
569338 TAAAAATTATACACTATACT-TTTTCAAAA-ATTGATT
1 TAAAAACTATATATTATA-TGTTTTCAAAATA-TGTTT
* *
569374 TAAAAACTATATA-T-TATGTATTCAAAACCAT-TTT
1 TAAAAACTATATATTATATGTTTTCAAAA-TATGTTT
* *
569408 TAAAAACTATATATTATACGTTTTCAAAAATACGTTT
1 TAAAAACTATATATTATATGTTTTC-AAAATATGTTT
* * **
569445 TCAAAAC-ATATACTATATACTTTCAAAA
1 TAAAAACTATATATTATATGTTTTCAAAA
569473 ATTACGTTTG
Statistics
Matches: 281, Mismatches: 40, Indels: 58
0.74 0.11 0.15
Matches are distributed among these distances:
31 24 0.09
32 4 0.01
33 10 0.04
34 30 0.11
35 46 0.16
36 68 0.24
37 24 0.09
38 56 0.20
39 9 0.03
40 4 0.01
41 2 0.01
42 4 0.01
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (36 bp):
TAAAAACTATATATTATATGTTTTCAAAATATGTTT
Found at i:569216 original size:106 final size:106
Alignment explanation
Indices: 569087--569472 Score: 228
Period size: 106 Copynumber: 3.6 Consensus size: 106
569077 ATATTTAATA
569087 AAAACTATATAATATTATATTTTCAAAAATAATATGTTTTCGAAAAT-TATA-TATATGTTTTCA
1 AAAACTATATAATATTATATTTTCAAAAA-AAT-T-TTTTCGAAAATATATATTATATGTTTTCA
*
569150 AAA-TATTTTAAAAACTCTATATATGTTTTCAAAATATGTTTTC
63 AAATTATTTTAAAAACTATATATATGTTTTCAAAATATGTTTTC
* * * ** ** *
569193 AAAACTATATTATA-TATGTTTTTCGAAAACCTTTTTTTTAAATTATATATTATATGTTTTCAAA
1 AAAACTATATAATATTAT-ATTTTCAAAAAAATTTTTTCGAAAATATATATTATATGTTTTCAAA
* * *
569257 ATTGTTTTAAAAACTATATATTATATGCTTTCAAAATTAT-TTTTAAA
65 ATTATTTTAAAAAC--TATA-TATATGTTTTCAAAA-TATGTTTT--C
* * * *
569304 AAAACTATATATTATACTT-TATTTT---AAATA-TTTTT-AAAAATTATACACTATACT-TTTT
1 AAAACTATATA--ATA-TTATATTTTCAAAAAAATTTTTTCGAAAA-TATATATTATA-TGTTTT
* * *
569362 CAAAAATTGA-TTTAAAAACTATATATTATGTATTCAAAACCAT-TTTTA
61 C-AAAATT-ATTTTAAAAACTATATA-TATGTTTTCAAAA-TATGTTTTC
* ** * ** * * **
569410 AAAACTATATATTA-TACGTTTTCAAAAATACGTTTTC-AAAACATATACTATATACTTTCAAAA
1 AAAACTATATAATATTATATTTTCAAAAAAATTTTTTCGAAAATATATATTATATGTTTTCAAAA
569473 ATTACGTTTG
Statistics
Matches: 222, Mismatches: 32, Indels: 53
0.72 0.10 0.17
Matches are distributed among these distances:
102 1 0.00
103 12 0.05
104 7 0.03
105 24 0.11
106 63 0.28
107 10 0.05
108 27 0.12
109 37 0.17
110 22 0.10
111 10 0.05
113 7 0.03
114 1 0.00
115 1 0.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (106 bp):
AAAACTATATAATATTATATTTTCAAAAAAATTTTTTCGAAAATATATATTATATGTTTTCAAAA
TTATTTTAAAAACTATATATATGTTTTCAAAATATGTTTTC
Found at i:569442 original size:14 final size:14
Alignment explanation
Indices: 569423--569450 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
569413 ACTATATATT
569423 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
569437 ATACGTTTTCAAAA
1 ATACGTTTTCAAAA
569451 CATATACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
ATACGTTTTCAAAA
Found at i:569457 original size:108 final size:108
Alignment explanation
Indices: 569232--569475 Score: 256
Period size: 106 Copynumber: 2.3 Consensus size: 108
569222 CCTTTTTTTT
* * **
569232 AAATTATA-TATTATATGTTTTC-AAAATTGTTTTAAAAACTATATATTATATGCTTTCAAAATT
1 AAATTATACTA-TATA-CTTTTCAAAAATTGATTTAAAAACTATATATTATATGCTTTCAAAACC
*** *
569295 ATTTTTAAAAAAACTATATATTATACTTTATTTTAAATATTTTTAA
64 ATTTTT-AAAAAACTATATATTATACTTTATCAAAAATATTTTCAA
569341 AAATTATAC-ACTATACTTTTTCAAAAATTGATTTAAAAACTATATA-T-TATG-TATTCAAAAC
1 AAATTATACTA-TATAC-TTTTCAAAAATTGATTTAAAAACTATATATTATATGCT-TTCAAAAC
569402 CATTTTT-AAAAACTATATATTATACGTTT-TCAAAAATACGTTTTCAA
63 CATTTTTAAAAAACTATATATTATAC-TTTATCAAAAATA--TTTTCAA
569449 AACA-TATACTATATAC-TTTCAAAAATT
1 AA-ATTATACTATATACTTTTCAAAAATT
569476 ACGTTTGAAA
Statistics
Matches: 117, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
106 35 0.30
107 4 0.03
108 35 0.30
109 21 0.18
110 22 0.19
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.44
Consensus pattern (108 bp):
AAATTATACTATATACTTTTCAAAAATTGATTTAAAAACTATATATTATATGCTTTCAAAACCAT
TTTTAAAAAACTATATATTATACTTTATCAAAAATATTTTCAA
Found at i:572957 original size:12 final size:12
Alignment explanation
Indices: 572937--572970 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
572927 ATCACACTCT
*
572937 ATTTCACGCAGAA
1 ATTT-ACGCAAAA
572950 ATTTACGCAAAA
1 ATTTACGCAAAA
572962 ATTTACGCA
1 ATTTACGCA
572971 CAACCATCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (12 bp):
ATTTACGCAAAA
Found at i:573240 original size:2 final size:2
Alignment explanation
Indices: 573233--573265 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
573223 GCAAGCCACA
573233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
573266 AATCGAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:574431 original size:23 final size:22
Alignment explanation
Indices: 574393--574439 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
574383 CATTTTATTG
574393 TTTTTTTTTTACTGTT-TTCTTA
1 TTTTTTTTTTACTGTTATT-TTA
*
574415 TTTTTTTTATTATTGTTATTTTA
1 TTTTTTTT-TTACTGTTATTTTA
574438 TT
1 TT
574440 ATTTCAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 12 0.55
24 2 0.09
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTTTTTTTACTGTTATTTTA
Found at i:574438 original size:14 final size:12
Alignment explanation
Indices: 574385--574443 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
574375 GAATGATGCA
*
574385 TTTTATTGTTTT
1 TTTTATTATTTT
* *
574397 TTTT-TTA-CTG
1 TTTTATTATTTT
*
574407 TTTTCTTATTTT
1 TTTTATTATTTT
574419 TTTTATTATTGTT
1 TTTTATTATT-TT
574432 ATTTTATTATTT
1 -TTTTATTATTT
574444 CAATTATGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
10 5 0.14
11 5 0.14
12 14 0.38
13 3 0.08
14 10 0.27
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (12 bp):
TTTTATTATTTT
Found at i:579985 original size:75 final size:76
Alignment explanation
Indices: 579895--580056 Score: 240
Period size: 76 Copynumber: 2.1 Consensus size: 76
579885 ATCTCATTGG
*
579895 AGATTGTTTTTCTTAAAAC-GGACTTTGTCTCACTTGAGACT-G-TTTTACTCGAAAGAAGACAT
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCACTTGAGA-TAGTTTTTACTCGAAAGAAGACAT
*
579957 TTCATTTGACTCA
64 TTCATTTCACTCA
* * *
579970 AGATTGTTTTTCTTAAAACAAGATTTGTCTCTCTTGAGATAGTTTTTACTCGAAATAATACATTT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGATAGTTTTTACTCGAAAGAAGACATTT
580035 CATTTCACTCA
66 CATTTCACTCA
580046 AGATTGTTTTT
1 AGATTGTTTTT
580057 AAAGAATATT
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
74 1 0.01
75 35 0.44
76 43 0.54
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGATAGTTTTTACTCGAAAGAAGACATTT
CATTTCACTCA
Found at i:580122 original size:39 final size:39
Alignment explanation
Indices: 580059--580406 Score: 452
Period size: 39 Copynumber: 9.0 Consensus size: 39
580049 TTGTTTTTAA
* * * *
580059 AGAATATTATATCTCGCTTGAGATAGTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
580098 AGATGATTTTATCTCGCTTGAGATAGTTTCCATCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
580137 ATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
580176 AGAAGA-TTTATCTCGCTTGAGATAGTTTCCCTCAAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
580214 AGAATATTTTGTCTCACTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
580253 ATAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
580292 AGAAGATTTTGTCTCGCTTGAGATAGTTTCTCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
580331 AGAAGATTTTTTCTCGCTTGAGACAATTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
580370 --AA-ATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
580406 A
1 A
580407 CAAAATCTTT
Statistics
Matches: 277, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
36 31 0.11
37 2 0.01
38 35 0.13
39 209 0.75
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:580268 original size:155 final size:156
Alignment explanation
Indices: 580059--580406 Score: 488
Period size: 155 Copynumber: 2.3 Consensus size: 156
580049 TTGTTTTTAA
* * * *
580059 AGAATATTATATCTCGCTTGAGATAGTTTTCCTTGAAACAGATGATTTTATCTCGCTTGAGATAG
1 AGAATATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAG
* *
580124 TTTCCATCGAAACATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAGAAGA-TTTATC
66 TTTCCATCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATC
* *
580188 TCGCTTGAGATAGTTTCCCTCAAAAC
131 TCGCTTGAGACAATTTCCCTCAAAAC
* * * *
580214 AGAATATTTTGTCTCACTTGAGATAGTTTCCCTCGAAACATAAGATTTTGTCTCGCTTGAGATAG
1 AGAATATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAG
* * * *
580279 TTTCCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCTCTCGAAACAGAAGATTTTTTC
66 TTTCCATCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATC
**
580344 TCGCTTGAGACAATTTCCCTTGAAAC
131 TCGCTTGAGACAATTTCCCTCAAAAC
* *
580370 --AA-ATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
1 AGAATATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACA
580407 CAAAATCTTT
Statistics
Matches: 170, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
153 31 0.18
154 2 0.01
155 110 0.65
156 27 0.16
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (156 bp):
AGAATATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAG
TTTCCATCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATC
TCGCTTGAGACAATTTCCCTCAAAAC
Found at i:580470 original size:67 final size:66
Alignment explanation
Indices: 580357--580609 Score: 258
Period size: 66 Copynumber: 3.7 Consensus size: 66
580347 CTTGAGACAA
*
580357 TTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGA-AT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAAATCTTTGAGA-
*
580421 ATG
64 ACG
* *
580424 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGACC
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGAAC
580489 G
66 G
* * ** * ****
580490 TTTCCCTTGAAACAAATTTTTTCTCTCTAAAGACAGTTTCCCTTGAAACGAGTTTTGCCTCTCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-A----AAAATCT-TT
*
580555 GAG-ACAA
60 GAGAAC-G
* * *
580562 TTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACAGTTTCCCTTGAAA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
580610 GAATAAATGT
Statistics
Matches: 160, Mismatches: 18, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
66 55 0.34
67 50 0.31
71 4 0.03
72 51 0.32
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (66 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGAAC
G
Found at i:581262 original size:132 final size:132
Alignment explanation
Indices: 581020--581790 Score: 1040
Period size: 132 Copynumber: 5.8 Consensus size: 132
581010 AATAGATATA
* * * * * * *
581020 TCAACTTTTTACTCGATTTTATCACAGAAAGAGATAGATCAACACCGACGTCTCGTTCGATTTCC
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGA-TTCC
* * * *
581085 ATCACAGAAGAAGGTGGATCGATATTTTTATTTCGCTCAAATCCATCGCAGAAGGAGTTGGATTA
65 ATCACAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCA
581150 GCG
130 GCG
* * * *
581153 TCAATTTTTTGCACGATTCTACCACAGAAGGATGTAGATCAGCATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * * *
581218 TCATAGAAGGATGTGGATTGACATTTTTATTTTGCTCAAATCCATCGCAGAAGGAGATGGATCAG
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
*
581283 CA
131 CG
* * * * *
581285 CCAA-TATTTTGCTCGATTCTATCATAGAATGAGGTAGATCAGCATCGACATCTTGTTTGATTCC
1 TCAACT-TTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCC
* *
581349 ATTACAGAATGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCA
65 ATCACAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCA
581414 GCG
130 GCG
* * *
581417 TCAACTTTTTGCTCGATTCTATCACAGAATGAGGTAGATCATCATCGACATCTGGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * *
581482 TCAAAGAAGGAGGTGGATCAACATTTTTATTTTGCTCAAATCCATCGCAGAAAGAGTTGGATCAG
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
581547 CG
131 CG
* * * *
581549 TCAACTTTTTACGCAATTCTATCACAGAAGTAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* * * * * *
581614 TCACAGAATGAGGTGGATCGATATTTTTATTTTCACTCAAATTCATCGCAGAAGAAGTTGGATTA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTT-GCTCAAATCCATCGCAGAAGGAGTTGGATCA
581679 GCG
130 GCG
* * * * * *
581682 TCAACTTTTAGCTCGATTCTATCCCAAAAGCAGGTAGATCAGCATTGACATATCGTTCGATTTCC
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGA-TTCC
*
581747 ATCACAGAAGGAGGTGGATCGACATTTCTATTTTCGCTCAAATC
65 ATCACAGAAGGAGGTGGATCGACATTTTTATTTT-GCTCAAATC
581791 AGCGTCAACT
Statistics
Matches: 559, Mismatches: 75, Indels: 7
0.87 0.12 0.01
Matches are distributed among these distances:
131 1 0.00
132 385 0.69
133 130 0.23
134 43 0.08
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (132 bp):
TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAG
CG
Found at i:581325 original size:44 final size:44
Alignment explanation
Indices: 581245--581632 Score: 199
Period size: 44 Copynumber: 8.8 Consensus size: 44
581235 TTGACATTTT
* * * * * * *
581245 TATTTTGCTCAAATCCATCGCAGAAGGAGATGGATCAGCACCAA
1 TATTTTGCTCGATTCCATCACAGAATGAGGTAGATCAGCATCAA
* * *
581289 TATTTTGCTCGATTCTATCATAGAATGAGGTAGATCAGCATCGA
1 TATTTTGCTCGATTCCATCACAGAATGAGGTAGATCAGCATCAA
* * * * * * ***
581333 CATCTTGTTTGATTCCATTACAGAATGAGGTGGATC-GACATTTT
1 TATTTTGCTCGATTCCATCACAGAATGAGGTAGATCAG-CATCAA
* * * * * * *
581377 TATTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAA
1 TATTTTGCTCGATTCCATCACAGAATGAGGTAGATCAGCATCAA
* * *
581421 CT-TTTTGCTCGATTCTATCACAGAATGAGGTAGATCATCATCGA
1 -TATTTTGCTCGATTCCATCACAGAATGAGGTAGATCAGCATCAA
* * * * * * * * ***
581465 CATCTGGTTCGATTCCATCAAAGAAGGAGGTGGATCAACATTTT
1 TATTTTGCTCGATTCCATCACAGAATGAGGTAGATCAGCATCAA
* * * * * * *
581509 TATTTTGCTCAAATCCATCGCAGAAAGAGTTGGATCAGCGTCAA
1 TATTTTGCTCGATTCCATCACAGAATGAGGTAGATCAGCATCAA
* * * * *
581553 CT-TTTTACGCAATTCTATCACAGAA-GTAGGTAGATCAGCATCGA
1 -TATTTTGCTCGATTCCATCACAGAATG-AGGTAGATCAGCATCAA
* * * * *
581597 CATCTCGTTCGATTCCATCACAGAATGAGGTGGATC
1 TATTTTGCTCGATTCCATCACAGAATGAGGTAGATC
581633 GATATTTTTA
Statistics
Matches: 246, Mismatches: 90, Indels: 16
0.70 0.26 0.05
Matches are distributed among these distances:
43 2 0.01
44 240 0.98
45 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
TATTTTGCTCGATTCCATCACAGAATGAGGTAGATCAGCATCAA
Found at i:581570 original size:264 final size:264
Alignment explanation
Indices: 581020--581953 Score: 1168
Period size: 264 Copynumber: 3.6 Consensus size: 264
581010 AATAGATATA
* * * *
581020 TCAACTTTTTACTCGATTTTATCACAGAAAGAGATAGATCAACACCGACGTCTCGTTCGATTTCC
1 TCAACTTTTTACTCGATTCTATCACAG-AAGAGGTAGATCAACATCGACATCTCGTTCGATTTCC
*
581085 ATCACAGAA-GAAGGTGGATCGATATTTTTA-TTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT
65 ATCACAGAATG-AGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT
* * * * * *
581148 TAGCGTCAATTTTTTGCACGATTCTACCACAGAAGGATGTAGATCAGCATCGACATCTCGTTCGA
129 CAGCGTCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGA
* * * *
581213 TTCCATCATAGAAGGATGTGGATTGACATTTTTATTTTGCTCAAATCCATCGCAGAAGGAGATGG
194 TTCCATCAAAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAAGAG-TGG
*
581278 ATCAGCA
258 ATCAGCG
* * * * * *
581285 CCAA-TATTTTGCTCGATTCTATCATAGAATGAGGTAGATCAGCATCGACATCTTGTTTGA-TTC
1 TCAACT-TTTTACTCGATTCTATCACAGAA-GAGGTAGATCAACATCGACATCTCGTTCGATTTC
*
581348 CATTACAGAATGAGGTGGATCGACATTTTTATTTT-GCTCAAATCCATCGCAGAAGGAGTTGGAT
64 CATCACAGAATGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT
* * *
581412 CAGCGTCAACTTTTTGCTCGATTCTATCACAGAATGAGGTAGATCATCATCGACATCTGGTTCGA
129 CAGCGTCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGA
*
581477 TTCCATCAAAGAAGGAGGTGGATCAACATTTTTATTTTGCTCAAATCCATCGCAGAAAGAGTTGG
194 TTCCATCAAAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAAGAG-TGG
581542 ATCAGCG
258 ATCAGCG
* * *
581549 TCAACTTTTTACGCAATTCTATCACAGAAGTAGGTAGATCAGCATCGACATCTCGTTCGA-TTCC
1 TCAACTTTTTACTCGATTCTATCACAGAAG-AGGTAGATCAACATCGACATCTCGTTCGATTTCC
* * * * *
581613 ATCACAGAATGAGGTGGATCGATATTTTTATTTTCACTCAAATTCATCGCAGAAGAAGTTGGATT
65 ATCACAGAATGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
* * * *
581678 AGCGTCAACTTTTAGCTCGATTCTATCCCA-AAAGCAGGTAGATCAGCATTGACATATCGTTCGA
130 AGCGTCAACTTTTTGCTCGATTCTATCACAGAAAG-AGGTAGATCAGCATCGACATCTCGTTCGA
* * *
581742 TTTCCATCACAGAAGGAGGTGGATCGACATTTCTA-TTT--TC----GC-T--C----A-A----
194 -TTCCATCAAAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAAGAGTGG
581788 ATCAGCG
258 ATCAGCG
*
581795 TCAAC-TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATATCGTTCGATTTC
1 TCAACTTTTTA-CTCGATTCTATCACAGAA-GAGGTAGATCAACATCGACATCTCGTTCGATTTC
*
581859 CATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT
64 CATCACAGAATGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT
*
581924 CAGCGTCAACTTCTTGCTCGATTC-ATCACA
129 CAGCGTCAACTTTTTGCTCGATTCTATCACA
581954 TATGGAGTTG
Statistics
Matches: 593, Mismatches: 64, Indels: 43
0.85 0.09 0.06
Matches are distributed among these distances:
245 5 0.01
246 60 0.10
247 85 0.14
251 1 0.00
252 1 0.00
256 1 0.00
258 1 0.00
259 1 0.00
263 3 0.01
264 272 0.46
265 132 0.22
266 31 0.05
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (264 bp):
TCAACTTTTTACTCGATTCTATCACAGAAGAGGTAGATCAACATCGACATCTCGTTCGATTTCCA
TCACAGAATGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
GCGTCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATT
CCATCAAAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATCGCAGAAAGAGTGGATC
AGCG
Found at i:581876 original size:113 final size:113
Alignment explanation
Indices: 581678--581903 Score: 398
Period size: 113 Copynumber: 2.0 Consensus size: 113
581668 AAGTTGGATT
* * *
581678 AGCGTCAACTTTTAGCTCGATTCTATCCCAAAAGCAGGTAGATCAGCATTGACATATCGTTCGAT
1 AGCGTCAACTTTTAGCTCGATTCTATCACAAAAGCAGGTAGATCAACATCGACATATCGTTCGAT
581743 TTCCATCACAGAAGGAGGTGGATCGACATTTCTATTTTCGCTCAAATC
66 TTCCATCACAGAAGGAGGTGGATCGACATTTCTATTTTCGCTCAAATC
* *
581791 AGCGTCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATATCGTTCGAT
1 AGCGTCAACTTTTAGCTCGATTCTATCACAAAAGCAGGTAGATCAACATCGACATATCGTTCGAT
*
581856 TTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATC
66 TTCCATCACAGAAGGAGGTGGATCGACATTTCTATTTTCGCTCAAATC
581904 CATCGCAGAA
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 107 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (113 bp):
AGCGTCAACTTTTAGCTCGATTCTATCACAAAAGCAGGTAGATCAACATCGACATATCGTTCGAT
TTCCATCACAGAAGGAGGTGGATCGACATTTCTATTTTCGCTCAAATC
Found at i:582709 original size:2 final size:2
Alignment explanation
Indices: 582702--582728 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
582692 GCAAGCCACA
582702 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
582729 AATCGAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:589328 original size:20 final size:23
Alignment explanation
Indices: 589275--589328 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
589265 ACCTAGGCAT
589275 GGTACCGATACCACAACTAGGGA
1 GGTACCGATACCACAACTAGGGA
* * *
589298 AGTATCGATACC-CTAC-AGGG-
1 GGTACCGATACCACAACTAGGGA
589318 GGTACCGATAC
1 GGTACCGATAC
589329 TACTTCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 9 0.35
21 4 0.15
22 3 0.12
23 10 0.38
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
GGTACCGATACCACAACTAGGGA
Found at i:597154 original size:36 final size:36
Alignment explanation
Indices: 597065--597446 Score: 256
Period size: 36 Copynumber: 10.6 Consensus size: 36
597055 AATAAAATCT
*
597065 CTATAATATTATA--TTTTCAAAA-ATATTTTAAAAA
1 CTAT-ATATTATATGTTTTCAAAATATGTTTTAAAAA
* *
597099 C--TATA-TATACGTTTTCAAAATATGTTTTCAAAA
1 CTATATATTATATGTTTTCAAAATATGTTTTAAAAA
* * **
597132 CTATAT-TATATATGTTTCCAAAA-ACCGTTTTTTTAAA
1 CTATATAT-TATATGTTTTCAAAATA-TG-TTTTAAAAA
* *
597169 TTATATATTATACGTTTT-AAAA-ACTGTTTTAAAAA
1 CTATATATTATATGTTTTCAAAATA-TGTTTTAAAAA
*
597204 CTATATATTATATGTTTTCAAAATTAT-TTTTTAAAA
1 CTATATATTATATGTTTTCAAAA-TATGTTTTAAAAA
* *
597240 CTATATATTATACTTTTTTTTAAAATAT-TTTTAAAAA
1 CTATATATTATA--TGTTTTCAAAATATGTTTTAAAAA
*
597277 CTATATATTATATGTTTTCAAAA-ACCGTTTTAAAAAA
1 CTATATATTATATGTTTTCAAAATA-TGTTTT-AAAAA
* * * ** *
597314 C-ATTTATTATACGTCTTCAAAA-CCGTTTTTAAAA
1 CTATATATTATATGTTTTCAAAATATGTTTTAAAAA
* *
597348 CTTATATATTATACGTTTTCAAAACTATTTTTTAAAAAAA
1 C-TATATATTATATGTTTTCAAAA-TATGTTTT--AAAAA
* * ** *
597388 TTATGTATTATATGTTTTCAAAAATACATTTTCAAAA
1 CTATATATTATATGTTTTC-AAAATATGTTTTAAAAA
* **
597425 C-ATATACTATATACTTTCAAAA
1 CTATATATTATATGTTTTCAAAA
597447 ATTACGTTTA
Statistics
Matches: 279, Mismatches: 44, Indels: 49
0.75 0.12 0.13
Matches are distributed among these distances:
30 4 0.01
31 3 0.01
32 10 0.04
33 11 0.04
34 7 0.03
35 46 0.16
36 99 0.35
37 54 0.19
38 15 0.05
39 22 0.08
40 8 0.03
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (36 bp):
CTATATATTATATGTTTTCAAAATATGTTTTAAAAA
Found at i:597281 original size:73 final size:71
Alignment explanation
Indices: 597065--597384 Score: 259
Period size: 71 Copynumber: 4.5 Consensus size: 71
597055 AATAAAATCT
* *
597065 CTATAATATTATA--TTTTCAAAA--ATATTTTAAAA--ACTATA-TATACGTTTTCAAAATATG
1 CTAT-ATATTATATGTTTTCAAAACCATTTTTTAAAACTA-TATATTATAC-TTTTTAAAATATG
*
597123 TTTTCAAAA
63 TTTTAAAAA
* * * * *
597132 CTATAT-TATATATGTTTCCAAAAACCGTTTTTTTAAATTATATATTATACGTTTTAAAA-ACTG
1 CTATATAT-TATATGTTTTC-AAAACCATTTTTTAAAACTATATATTATACTTTTTAAAATA-TG
597195 TTTTAAAAA
63 TTTTAAAAA
**
597204 CTATATATTATATGTTTTCAAAATTATTTTTTAAAACTATATATTATACTTTTTTTTAAAATAT-
1 CTATATATTATATGTTTTCAAAACCATTTTTTAAAACTATATATTATAC---TTTTTAAAATATG
597268 TTTTAAAAA
63 TTTTAAAAA
* ** * * * **
597277 CTATATATTATATGTTTTCAAAAACCGTTTTAAAAAAC-ATTTATTATACGTCTTCAAAA-CCGT
1 CTATATATTATATGTTTTC-AAAACCATTTTTTAAAACTATATATTATAC-TTTTTAAAATATGT
*
597340 TTTTAAAA
64 TTTAAAAA
* *
597348 CTTATATATTATACGTTTTCAAAACTATTTTTTAAAA
1 C-TATATATTATATGTTTTCAAAACCATTTTTTAAAA
597385 AAATTATGTA
Statistics
Matches: 204, Mismatches: 31, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
65 1 0.00
66 6 0.03
67 4 0.02
68 4 0.02
69 4 0.02
71 63 0.31
72 54 0.26
73 45 0.22
74 22 0.11
75 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (71 bp):
CTATATATTATATGTTTTCAAAACCATTTTTTAAAACTATATATTATACTTTTTAAAATATGTTT
TAAAAA
Found at i:597354 original size:109 final size:110
Alignment explanation
Indices: 597065--597411 Score: 303
Period size: 108 Copynumber: 3.2 Consensus size: 110
597055 AATAAAATCT
** *
597065 CTATAATATTATA--TTTTCAAAAA-TATTTTAAAAAC--TATA-TATACGTTTTCAAAAT-ATG
1 CTAT-ATATTATATGTTTTCAAAAACCGTTTTAAAAACTATATATTATACGTCTTCAAAATCA-G
* * * ** *
597123 TTTTCAAAACTATAT-TATATATGTTTCCAAAAACCGTTTTTT--TAAA
64 TTTTTAAAACTATATAT-TATACGTTTTC-AAAACTATTTTTTAAAAAA
* * * * * * *
597169 TTATATATTATACGTTTT-AAAAACTGTTTTAAAAACTATATATTATATGTTTTCAAAATTATTT
1 CTATATATTATATGTTTTCAAAAACCGTTTTAAAAACTATATATTATACGTCTTCAAAATCAGTT
* *
597233 TTTAAAACTATATATTATACTTTTTTTTAAAA-TA-TTTTT-AAAAA
66 TTTAAAACTATATATTATAC--GTTTTCAAAACTATTTTTTAAAAAA
* *
597277 CTATATATTATATGTTTTCAAAAACCGTTTTAAAAAAC-ATTTATTATACGTCTTCAAAA-CCGT
1 CTATATATTATATGTTTTCAAAAACCGTTTT-AAAAACTATATATTATACGTCTTCAAAATCAGT
597340 TTTTAAAACTTATATATTATACGTTTTCAAAACTATTTTTTAAAAAAA
65 TTTTAAAAC-TATATATTATACGTTTTCAAAACTATTTTTT-AAAAAA
* *
597388 TTATGTATTATATGTTTTCAAAAA
1 CTATATATTATATGTTTTCAAAAA
597412 TACATTTTCA
Statistics
Matches: 200, Mismatches: 25, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
103 8 0.04
104 8 0.04
105 15 0.08
107 17 0.09
108 64 0.32
109 52 0.26
110 9 0.05
111 27 0.14
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (110 bp):
CTATATATTATATGTTTTCAAAAACCGTTTTAAAAACTATATATTATACGTCTTCAAAATCAGTT
TTTAAAACTATATATTATACGTTTTCAAAACTATTTTTTAAAAAA
Found at i:597974 original size:31 final size:33
Alignment explanation
Indices: 597918--597981 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
597908 TTAAAAAAAT
597918 TATATTACATTTAAAAGTTTATTTTAA-TCTTTC
1 TATATTACATTTAAAAG-TTATTTTAATTCTTTC
*
597951 TATATTATATTTAAAA-TTATTTTAATTCTTT
1 TATATTACATTTAAAAGTTATTTTAATTCTTT
597982 TTATTGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.31
32 5 0.17
33 15 0.52
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (33 bp):
TATATTACATTTAAAAGTTATTTTAATTCTTTC
Found at i:598642 original size:118 final size:121
Alignment explanation
Indices: 598426--598672 Score: 383
Period size: 118 Copynumber: 2.0 Consensus size: 121
598416 TTTATTGTTT
* *
598426 TATTTATGAATTTTTACATGAATCTTCTTAATACTTATGAAATCTAAACGTGTGTTTAAATTTTA
1 TATTT-TGAATTTTTAAATGAATCTTCTTAATACATATGAAATCTAAACG-GTGTTTAAATTTTA
*
598491 ATTATCTTTTAGATTTCATAAATGTTTAAATTTTTTAT-ATAAAAATTAACAAAAA-A
64 ATTATCTTTTAGATTTCATAAATGTTTAAATTTTTTATAAAAAAAATTAACAAAAAGA
* *
598547 TATTTTGAATTTTTAAATGAATTTTCTTAATACATATGAAATTTAAAC-GTGTTTAAATTTTAAT
1 TATTTTGAATTTTTAAATGAATCTTCTTAATACATATGAAATCTAAACGGTGTTTAAATTTTAAT
* * *
598611 TATTTTTTAGATTTCATAGATGTTTAAATTTTTTATAAAAAAAATTAATAAAAAGA
66 TATCTTTTAGATTTCATAAATGTTTAAATTTTTTATAAAAAAAATTAACAAAAAGA
598667 TATTTT
1 TATTTT
598673 AAAGAAAATT
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
118 50 0.43
119 15 0.13
120 46 0.40
121 5 0.04
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (121 bp):
TATTTTGAATTTTTAAATGAATCTTCTTAATACATATGAAATCTAAACGGTGTTTAAATTTTAAT
TATCTTTTAGATTTCATAAATGTTTAAATTTTTTATAAAAAAAATTAACAAAAAGA
Found at i:604781 original size:12 final size:12
Alignment explanation
Indices: 604766--604827 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
604756 TGTATTTTTA
604766 TTATTAAATATT
1 TTATTAAATATT
604778 TTATTAAATATT
1 TTATTAAATATT
604790 TT-TATAAATA-T
1 TTAT-TAAATATT
* *
604801 ATAATAATAGTATT
1 TTATTAA-A-TATT
*
604815 TTTTTAAATATT
1 TTATTAAATATT
604827 T
1 T
604828 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
11 6 0.15
12 26 0.65
13 3 0.08
14 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:604837 original size:13 final size:12
Alignment explanation
Indices: 604769--604838 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
604759 ATTTTTATTA
*
604769 TTAAATATTTTA
1 TTAAATATTTTT
604781 TTAAATATTTTT
1 TTAAATATTTTT
* * *
604793 ATAAATA-TATA
1 TTAAATATTTTT
*
604804 ATAATAGTATTTTT
1 TTAA-A-TATTTTT
604818 TTAAATATTTATT
1 TTAAATATTT-TT
*
604831 TTTAATAT
1 TTAAATAT
604839 CGAAGAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
11 6 0.13
12 23 0.50
13 12 0.26
14 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (12 bp):
TTAAATATTTTT
Found at i:616516 original size:16 final size:16
Alignment explanation
Indices: 616497--616533 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
616487 CAATTCTATC
*
616497 TATTTCAAATTCAATT
1 TATTTCAAATTAAATT
*
616513 TATTTGAAATTAAATT
1 TATTTCAAATTAAATT
616529 TATTT
1 TATTT
616534 TTGGAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (16 bp):
TATTTCAAATTAAATT
Found at i:617336 original size:83 final size:83
Alignment explanation
Indices: 617230--617766 Score: 936
Period size: 83 Copynumber: 6.5 Consensus size: 83
617220 GAATTTACCA
617230 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAATT
617295 TGGAAGATGAATGTG-CC
66 TGGAAGATGAATGTGTCC
617312 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAAT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAAT
617377 TTGGAAGATGAATGTGTCC
65 TTGGAAGATGAATGTGTCC
617396 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAATT
617461 TGGAAGATGAATGTGTCC
66 TGGAAGATGAATGTGTCC
* *
617479 ATAGCATCTTCTGGAAGCGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAATT
*
617544 TGGAAGATGAATGTGTTC
66 TGGAAGATGAATGTGTCC
*
617562 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAATT
617627 TGGAAGATGAATGTG-CC
66 TGGAAGATGAATGTGTCC
* * * *
617644 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTTGACAAA-ACAATCATTGAGT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAAT
** *
617708 TTAAAAGATGAATGTGTTC
65 TTGGAAGATGAATGTGTCC
617727 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
617767 ATTCAGTAGG
Statistics
Matches: 435, Mismatches: 16, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
82 65 0.15
83 368 0.85
84 2 0.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAATCCAATCATTGAATT
TGGAAGATGAATGTGTCC
Found at i:618946 original size:113 final size:113
Alignment explanation
Indices: 618520--618930 Score: 779
Period size: 113 Copynumber: 3.6 Consensus size: 113
618510 TTCCAGTTCG
618520 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
*
618585 AACCTTTTACTTGAATTCATCACTTGATGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGAA
618633 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
618698 AACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGAA
618746 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
618811 AACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGAA
* * *
618859 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
618924 AA-CTTTT
66 AACCTTTT
618931 GGCATAATTC
Statistics
Matches: 294, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
112 5 0.02
113 289 0.98
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGAA
Found at i:619262 original size:3 final size:3
Alignment explanation
Indices: 619249--619362 Score: 196
Period size: 3 Copynumber: 38.7 Consensus size: 3
619239 TTTTTATCCA
*
619249 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
619296 TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
619344 TAT TAT T-T TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
619363 AATATATTAA
Statistics
Matches: 105, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
2 4 0.04
3 101 0.96
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:619402 original size:20 final size:19
Alignment explanation
Indices: 619361--619405 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
619351 TTATTATTAT
* *
619361 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
619380 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
619400 TAAATA
1 TAAATA
619406 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:620823 original size:12 final size:12
Alignment explanation
Indices: 620808--620870 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
620798 TGTATTTTTA
620808 TTATTAAATATT
1 TTATTAAATATT
620820 TTATTAAATATT
1 TTATTAAATATT
*
620832 TT-TATAAATATA
1 TTAT-TAAATATT
* *
620844 TAATAAATAGTATT
1 TTATTAA-A-TATT
*
620858 TTTTTAAATATT
1 TTATTAAATATT
620870 T
1 T
620871 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 1 0.03
12 29 0.73
13 3 0.08
14 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:620880 original size:13 final size:12
Alignment explanation
Indices: 620811--620881 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
620801 ATTTTTATTA
*
620811 TTAAATATTTTA
1 TTAAATATTTTT
620823 TTAAATATTTTT
1 TTAAATATTTTT
* * **
620835 ATAAATATATAA
1 TTAAATATTTTT
*
620847 TAAATAGTATTTTT
1 TTAA-A-TATTTTT
620861 TTAAATATTTATT
1 TTAAATATTT-TT
*
620874 TTTAATAT
1 TTAAATAT
620882 CGAAGAAAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
12 26 0.59
13 11 0.25
14 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (12 bp):
TTAAATATTTTT
Done.