Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 119 of 345
Found at i:39455466 original size:46 final size:46
Alignment explanation
Indices: 39455291--39455466 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
39455281 TGTAACCCGC
* *
39455291 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
39455337 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
39455383 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
39455430 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
39455467 TGCCCAAATA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:39482895 original size:22 final size:22
Alignment explanation
Indices: 39482863--39482909 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
39482853 TGATGCAGGT
*
39482863 ATGTACGTAAAACTCATACGTA
1 ATGTACATAAAACTCATACGTA
39482885 ATGTACATAAAACTCATACGTA
1 ATGTACATAAAACTCATACGTA
39482907 ATG
1 ATG
39482910 AGCTCGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.28
Consensus pattern (22 bp):
ATGTACATAAAACTCATACGTA
Found at i:39487522 original size:41 final size:41
Alignment explanation
Indices: 39487465--39487610 Score: 195
Period size: 41 Copynumber: 3.6 Consensus size: 41
39487455 GGTTTAAATT
39487465 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
1 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
*
39487506 CGAGCTTGGTCTCGAAGGGCTTTTAAGCCAGTGTCATAA-C
1 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
* *** * * * * *
39487546 CGAACCAAGTTTCGAAGGGCCTTCGGGCCAATGTCATAATC
1 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
39487587 CGAGCTTGGTCTCGAAGGGCTTTT
1 CGAGCTTGGTCTCGAAGGGCTTTT
39487611 TGAGTCAGCG
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 30 0.35
41 56 0.65
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.27
Consensus pattern (41 bp):
CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
Found at i:39495632 original size:41 final size:41
Alignment explanation
Indices: 39495575--39495724 Score: 212
Period size: 41 Copynumber: 3.7 Consensus size: 41
39495565 TCGGGGTTTA
39495575 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
*
39495616 AATCCGAGCTTGGTCTCGAAGGGCTTTTAAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * * *
39495657 AAT-CGAACCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
39495697 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
39495725 TGAGTCAGCG
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
40 31 0.34
41 61 0.66
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:39505107 original size:43 final size:43
Alignment explanation
Indices: 39505059--39505209 Score: 198
Period size: 43 Copynumber: 3.5 Consensus size: 43
39505049 TATCTCAAAT
*
39505059 ATGGTCTTACATGTTATCACATATCGATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
* * * *
39505102 ATGGTCTTACATGAAATCATATAACGATGCCAATGTCTCAGAC
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
* * *
39505145 ATGGCCTTACATGTAATCACA-ATACAATACCAATG-CCCTAGAC
1 ATGGTCTTACATGTAATCACATAT-CGATGCCAATGTCCC-AGAC
39505188 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
39505210 CTTGGTAATC
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.03
43 89 0.97
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAC
Found at i:39510162 original size:40 final size:40
Alignment explanation
Indices: 39510111--39510236 Score: 216
Period size: 40 Copynumber: 3.1 Consensus size: 40
39510101 CCCGGATGTT
* *
39510111 ATTCCAGCACGAAGCCTGTGGATCTTTAAGCCCGAATACA
1 ATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGGATACA
* *
39510151 ATTCCAACACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
1 ATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGGATACA
39510191 ATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGGATACA
1 ATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGGATACA
39510231 ATTCCA
1 ATTCCA
39510237 CATCAAATAA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (40 bp):
ATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGGATACA
Found at i:39510216 original size:80 final size:79
Alignment explanation
Indices: 39510084--39510236 Score: 234
Period size: 80 Copynumber: 1.9 Consensus size: 79
39510074 TATCTAGCAC
* *** *
39510084 AGCCTGCAGGTTTTTAACCCGGATGTTATTCCAGCACGAAGCCTGTGGATCTTTAAGCCCGAATA
1 AGCCTGCAGGTCTTTAACCCGGATACAATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGAATA
39510149 CAATTCCAACACGA
66 CAATTCCAACACGA
* *
39510163 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGGAT
1 AGCCTGCAGGTCTTTAA-CCCGGATACAATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGAAT
39510228 ACAATTCCA
65 ACAATTCCA
39510237 CATCAAATAA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
79 15 0.23
80 51 0.77
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
AGCCTGCAGGTCTTTAACCCGGATACAATTCCAGCACGAAGCCTGCGGATCTTTAAGCCCGAATA
CAATTCCAACACGA
Found at i:39517417 original size:40 final size:40
Alignment explanation
Indices: 39517346--39517498 Score: 247
Period size: 40 Copynumber: 3.9 Consensus size: 40
39517336 TATCTAGCAC
* * *
39517346 AGCCTGCAGGTTTTTAA-CCCGGATGTC-ATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGAT-ACAATTCCAGCACGA
*
39517385 AGCCTGCGAGTCTTTAAGCCCGGATACAATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
39517425 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
39517465 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCA
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCA
39517499 CATCAAATAA
Statistics
Matches: 107, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
39 15 0.14
40 92 0.86
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
Found at i:39520230 original size:9 final size:9
Alignment explanation
Indices: 39520216--39520274 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
39520206 AAATCTTGTA
39520216 ATATATAAT
1 ATATATAAT
39520225 ATATATGATAT
1 ATATAT-A-AT
39520236 ATATTATAAT
1 ATA-TATAAT
*
39520246 ATATATAAA
1 ATATATAAT
39520255 ATA-ATAAT
1 ATATATAAT
*
39520263 GT-TAT-AT
1 ATATATAAT
39520270 ATATA
1 ATATA
39520275 ACTTTAACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
7 3 0.07
8 9 0.22
9 14 0.34
10 6 0.15
11 6 0.15
12 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
ATATATAAT
Found at i:39520258 original size:14 final size:14
Alignment explanation
Indices: 39520216--39520260 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
39520206 AAATCTTGTA
39520216 ATATATAATATATAT
1 ATATATAATATA-AT
*
39520231 GATATATATTATAAT
1 -ATATATAATATAAT
*
39520246 ATATATAAAATAAT
1 ATATATAATATAAT
39520260 A
1 A
39520261 ATGTTATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 13 0.50
15 2 0.08
16 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATATATAATATAAT
Found at i:39520416 original size:23 final size:23
Alignment explanation
Indices: 39520390--39520457 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
39520380 TTGCATATAT
*
39520390 TATATATTATTATATATAAATAC
1 TATATATTACTATATATAAATAC
39520413 TATATATTACTATATATAAATAC
1 TATATATTACTATATATAAATAC
* *
39520436 TATATGTTACTATATGTAAATA
1 TATATATTACTATATATAAATA
39520458 ATAAATAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (23 bp):
TATATATTACTATATATAAATAC
Found at i:39520418 original size:13 final size:13
Alignment explanation
Indices: 39520400--39520440 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
39520390 TATATATTAT
39520400 TATATATAAATAC
1 TATATATAAATAC
39520413 TATATAT---TAC
1 TATATATAAATAC
39520423 TATATATAAATAC
1 TATATATAAATAC
39520436 TATAT
1 TATAT
39520441 GTTACTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.40
13 15 0.60
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATATAAATAC
Found at i:39520452 original size:10 final size:10
Alignment explanation
Indices: 39520384--39520450 Score: 57
Period size: 10 Copynumber: 6.4 Consensus size: 10
39520374 TTTCTCTTGC
39520384 ATATATTA-T
1 ATATATTACT
39520393 ATATTATTA-T
1 ATA-TATTACT
*
39520403 ATATAAATACT
1 ATAT-ATTACT
39520414 ATATATTACT
1 ATATATTACT
39520424 ATATATAAATACT
1 ATATAT---TACT
*
39520437 ATATGTTACT
1 ATATATTACT
39520447 ATAT
1 ATAT
39520451 GTAAATAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
9 4 0.08
10 31 0.63
11 5 0.10
13 9 0.18
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (10 bp):
ATATATTACT
Found at i:39523376 original size:18 final size:18
Alignment explanation
Indices: 39523353--39523389 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39523343 TTTCTTCCAA
39523353 AAGTGCTTTTGGAGTCAG
1 AAGTGCTTTTGGAGTCAG
39523371 AAGTGCTTTTGGAGTCAG
1 AAGTGCTTTTGGAGTCAG
39523389 A
1 A
39523390 TAAACAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.32
Consensus pattern (18 bp):
AAGTGCTTTTGGAGTCAG
Found at i:39528318 original size:46 final size:48
Alignment explanation
Indices: 39528210--39528331 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 48
39528200 TGTCTTCGAC
** * * *
39528210 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATATA
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATAGATA
*
39528258 ATAAGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATA-ACT-GAT-
1 AT--GGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATA-TAGATA
*
39528306 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
39528332 CTGTCCTGTC
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
46 22 0.35
48 4 0.06
49 3 0.05
50 34 0.54
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATAGATA
Found at i:39542542 original size:11 final size:11
Alignment explanation
Indices: 39542528--39542629 Score: 53
Period size: 11 Copynumber: 8.8 Consensus size: 11
39542518 TAAATATCTT
39542528 TAAAATAATAA
1 TAAAATAATAA
*
39542539 TAAAATTAACAA
1 TAAAA-TAATAA
*
39542551 TAAAATAAGAA
1 TAAAATAATAA
*
39542562 TTATATATATATCCAA
1 -TA-AAATA-AT--AA
* *
39542578 -ATAATAACAA
1 TAAAATAATAA
39542588 TAAAATAATAA
1 TAAAATAATAA
* * *
39542599 CAATATAATTA
1 TAAAATAATAA
*
39542610 TAAAATAATAG
1 TAAAATAATAA
*
39542621 TAGAATAAT
1 TAAAATAAT
39542630 GAGAAATAAG
Statistics
Matches: 67, Mismatches: 17, Indels: 14
0.68 0.17 0.14
Matches are distributed among these distances:
10 2 0.03
11 41 0.61
12 13 0.19
13 7 0.10
14 2 0.03
16 2 0.03
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:39542595 original size:14 final size:14
Alignment explanation
Indices: 39542576--39542617 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
39542566 ATATATATCC
39542576 AAATAATAACAATA
1 AAATAATAACAATA
39542590 AAATAATAACAATA
1 AAATAATAACAATA
* *
39542604 TAATTATAA-AATA
1 AAATAATAACAATA
39542617 A
1 A
39542618 TAGTAGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:39546578 original size:23 final size:23
Alignment explanation
Indices: 39546552--39546645 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
39546542 AAGTTAGAAG
39546552 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
39546575 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
39546598 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
39546621 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
39546644 AG
1 AG
39546646 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:39548502 original size:15 final size:17
Alignment explanation
Indices: 39548472--39548503 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
39548462 TAAAGCAATG
39548472 AAAATATATATTAAAAT
1 AAAATATATATTAAAAT
39548489 AAAATA-AT-TTAAAAT
1 AAAATATATATTAAAAT
39548504 TTTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATATATATTAAAAT
Found at i:39552212 original size:19 final size:20
Alignment explanation
Indices: 39552188--39552225 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39552178 GGTACCACCA
39552188 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
39552207 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
39552226 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:39552614 original size:93 final size:93
Alignment explanation
Indices: 39552455--39552625 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
39552445 GCCCCTAAGT
* * *
39552455 GAACTCAGACTGAACTCAACGAGCTCGGGCGTTCACATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
39552520 CGAGCTCGGATGCCTAGTTACATTTCAC
66 CGAGCTCGGATGCCTAGTTACATTTCAC
* * * *
39552548 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
*
39552613 CGAGTTCGGATGC
66 CGAGCTCGGATGC
39552626 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATTTCAC
Found at i:39552622 original size:46 final size:46
Alignment explanation
Indices: 39552450--39552622 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
39552440 AACCCGCCCC
* * * *
39552450 TAAGTGAACTCAGACTGAACTCAACGAGCTCGGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCA
* *
39552496 TAAATGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCACATCCA
* * * *
39552544 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCA
*
39552589 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
39552623 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 59 0.56
47 28 0.27
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCA
Found at i:39552641 original size:46 final size:45
Alignment explanation
Indices: 39552548--39552633 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
39552538 TACATTTCAC
* *
39552548 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGA-ATGCGCAACCATAAGT
*
39552594 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
1 GAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAACCAT
39552634 CCTAGTGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 9 0.24
46 28 0.76
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGAATGCGCAACCATAAGT
Found at i:39558294 original size:40 final size:40
Alignment explanation
Indices: 39558175--39558393 Score: 232
Period size: 40 Copynumber: 5.5 Consensus size: 40
39558165 ACCCAAGTAT
* ** * *
39558175 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
39558213 CTTCGGGTCTTAGCCTGGAT-TGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
39558252 CTTCGGGACTTAGCCCGTATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
39558292 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
39558332 CTTC-GGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
*
39558372 CTTCGGGACTTAGCCTGGATAT
1 CTTCGGGACTTAGCCCGGATAT
39558394 CATTCGAATA
Statistics
Matches: 148, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
38 19 0.13
39 29 0.20
40 96 0.65
41 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:39562275 original size:28 final size:27
Alignment explanation
Indices: 39562193--39562276 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 27
39562183 ATTATCCGGT
*
39562193 ACACGTAGTAGCCTGCACTTATTACTAC
1 ACACGTAGTAGCCTACACTTA-TACTAC
* *
39562221 ACACGT-G-A-CCTA-AC-CAT-CTGAT
1 ACACGTAGTAGCCTACACTTATACT-AC
39562243 ACACGTAGTAGCCTACACTTAGTACTAC
1 ACACGTAGTAGCCTACACTTA-TACTAC
39562271 ACACGT
1 ACACGT
39562277 GATCACAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 7 0.16
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (27 bp):
ACACGTAGTAGCCTACACTTATACTAC
Found at i:39566341 original size:31 final size:30
Alignment explanation
Indices: 39566306--39566366 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
39566296 ATTTAAGAGC
*
39566306 CTAGGGGTAAAATCATAATTTTTGTAAAAGT
1 CTAGGGGCAAAATCATAA-TTTTGTAAAAGT
** *
39566337 CTAGGGGCAAAATGGTCATTTTGTAAAAGT
1 CTAGGGGCAAAATCATAATTTTGTAAAAGT
39566367 ATAAATTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (30 bp):
CTAGGGGCAAAATCATAATTTTGTAAAAGT
Found at i:39567040 original size:50 final size:50
Alignment explanation
Indices: 39566881--39567152 Score: 255
Period size: 50 Copynumber: 5.7 Consensus size: 50
39566871 TGACATGTGT
* *
39566881 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCA-T-A-TTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GGCATTGAGATATGAGA
* * ** * * *
39566927 GCCAATACAAGACCATGTCTGGGGCATGGCATCGACATTGAG--ACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATATGAGA
* *
39566975 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGGC-TTGAGATATGAAA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GGCATTGAGATATGAGA
* * *
39567025 GCTACTGTAAGACCATGTCTGGGACATGTCATCGGC-TT--GATATGTG-
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATATGAGA
* * * * *
39567071 TC-AGTGTAAGACCATGTCTGGGACATGGCATCAGCACTGACAGATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATATGAGA
*
39567120 GCTAGTGTAAGACCATGTCTAGGACATGGCATC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC
39567153 TGCCTCGATA
Statistics
Matches: 182, Mismatches: 31, Indels: 22
0.77 0.13 0.09
Matches are distributed among these distances:
45 30 0.16
46 10 0.05
47 22 0.12
48 48 0.26
49 9 0.05
50 63 0.35
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (50 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATATGAGA
Found at i:39567083 original size:95 final size:95
Alignment explanation
Indices: 39566978--39567152 Score: 253
Period size: 95 Copynumber: 1.8 Consensus size: 95
39566968 GACGAGAGCT
* * * * *
39566978 AGTGTAAGACCATGTTTGGGACATGGCATCGGGC-TTGAGATATGAAAGCTACTGTAAGACCATG
1 AGTGTAAGACCATGTCTGGGACATGGCATC-AGCACTGACAGATGAAAGCTACTGTAAGACCATG
* *
39567042 TCTGGGACATGTCATCGGCTTGATATGTGTC
65 TCTAGGACATGGCATCGGCTTGATATGTGTC
* *
39567073 AGTGTAAGACCATGTCTGGGACATGGCATCAGCACTGACAGATGAGAGCTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCACTGACAGATGAAAGCTACTGTAAGACCATGT
39567138 CTAGGACATGGCATC
66 CTAGGACATGGCATC
39567153 TGCCTCGATA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
94 2 0.03
95 68 0.97
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (95 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCACTGACAGATGAAAGCTACTGTAAGACCATGT
CTAGGACATGGCATCGGCTTGATATGTGTC
Found at i:39575223 original size:40 final size:39
Alignment explanation
Indices: 39575179--39575402 Score: 263
Period size: 40 Copynumber: 5.7 Consensus size: 39
39575169 GCCACTAGCT
*
39575179 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
39575219 CAAATGCCTTC-GGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * * *
39575257 CAAATGCCTTCGGGACTTAGCCCGGACATAATAGCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * *
39575297 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* ** * *
39575337 CAAATGCCTTCGGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
39575377 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
39575403 TATCATCCGA
Statistics
Matches: 161, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
38 23 0.14
39 29 0.18
40 109 0.68
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:39575299 original size:78 final size:80
Alignment explanation
Indices: 39575179--39575362 Score: 264
Period size: 78 Copynumber: 2.3 Consensus size: 80
39575169 GCCACTAGCT
** * ** *
39575179 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTC-GGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGACATAATAACTCACACAAACGCCTTCGGGACTTAGCCCGG
39575243 -TATAATAACTCGCA
66 ATATAATAACTCGCA
*
39575257 CAAATGCCTTCGGGACTTAGCCCGGACATAATAGCTCACACAAACGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGACATAATAACTCACACAAACGCCTTCGGGACTTAGCCCGG
* * *
39575322 ATATAGTAGCTCGTA
66 ATATAATAACTCGCA
39575337 CAAATGCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39575363 ATTAGCCACT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 44 0.47
79 13 0.14
80 37 0.39
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGACATAATAACTCACACAAACGCCTTCGGGACTTAGCCCGG
ATATAATAACTCGCA
Found at i:39614328 original size:80 final size:77
Alignment explanation
Indices: 39614233--39614416 Score: 233
Period size: 80 Copynumber: 2.3 Consensus size: 77
39614223 CTACTTGCTC
* **
39614233 AATGCCTTCGAGACTTAGCCCGTTATAGTAACTCGGCACCAATGCCTTCGAGACTTAACCCAGTT
1 AATGCCTTCG-GACTTAGCCCGTTATAGTAACTC-GCACAAATGCCTTCGAGACTTAACCC-GAA
*
39614298 TATAGTAACTCGCACA
63 T-TAGTAACTAGCACA
* * *
39614314 AATGCCTTCGGACTTAGCCCGGTTATAGTAACTCTCACAAATGCCTTCGGGACTTAGCCCGAATT
1 AATGCCTTCGGACTTAGCCC-GTTATAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGAATT
*
39614379 AGTCACTAGCACA
65 AGTAACTAGCACA
* *
39614392 AATGCCTTTGGACTTAGCCGGTTAT
1 AATGCCTTCGGACTTAGCCCGTTAT
39614417 CATCCGTTTA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
77 5 0.05
78 30 0.33
79 2 0.02
80 32 0.35
81 23 0.25
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (77 bp):
AATGCCTTCGGACTTAGCCCGTTATAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGAATTA
GTAACTAGCACA
Found at i:39614353 original size:39 final size:39
Alignment explanation
Indices: 39614233--39614416 Score: 221
Period size: 39 Copynumber: 4.7 Consensus size: 39
39614223 CTACTTGCTC
*
39614233 AATGCCTTCGAGACTTAGCCC-GTTATAGTAACTCGGCACC
1 AATGCCTTCG-GACTTAGCCCGGTTATAGTAACTC-GCACA
* *
39614273 AATGCCTTCGAGACTTAACCCAGTTTATAGTAACTCGCACA
1 AATGCCTTCG-GACTTAGCCC-GGTTATAGTAACTCGCACA
*
39614314 AATGCCTTCGGACTTAGCCCGGTTATAGTAACTCTCACA
1 AATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCACA
** * *
39614353 AATGCCTTCGGGACTTAGCCCGAAT-TAGTCACTAGCACA
1 AATGCCTTC-GGACTTAGCCCGGTTATAGTAACTCGCACA
*
39614392 AATGCCTTTGGACTTAG-CCGGTTAT
1 AATGCCTTCGGACTTAGCCCGGTTAT
39614417 CATCCGTTTA
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
37 4 0.03
38 9 0.07
39 45 0.36
40 42 0.33
41 14 0.11
42 12 0.10
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (39 bp):
AATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCACA
Found at i:39625394 original size:53 final size:54
Alignment explanation
Indices: 39625327--39625532 Score: 216
Period size: 53 Copynumber: 3.8 Consensus size: 54
39625317 TCCTTTTTAT
* * * *
39625327 ACTTACCATTGCCATGTCTTGATATGGTCTTACGTGGTATCCTTGCCTTAT-GA
1 ACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGA
* * * * *
39625380 ACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTA
1 ACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG-A
** * * * * * *
39625435 GTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAA
1 ACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGA
* * *
39625489 ACTTACCAATGCCATGCCTTGGCATGGTCTCACTTGGTATCCTT
1 ACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
39625533 AAACCCTAAT
Statistics
Matches: 122, Mismatches: 29, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 44 0.36
54 37 0.30
55 41 0.34
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.37
Consensus pattern (54 bp):
ACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGA
Found at i:39640781 original size:17 final size:17
Alignment explanation
Indices: 39640759--39640792 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
39640749 ACGTATTAAA
39640759 GAAAATTAATTTTTTAG
1 GAAAATTAATTTTTTAG
39640776 GAAAATTAATTTTTTAG
1 GAAAATTAATTTTTTAG
39640793 TCGAAGATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
GAAAATTAATTTTTTAG
Found at i:39641555 original size:20 final size:18
Alignment explanation
Indices: 39641522--39641558 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
39641512 TGTGATGTTG
39641522 ATATGTTTAATTTAATTA
1 ATATGTTTAATTTAATTA
39641540 ATATGATTTAAATTTAATT
1 ATATG-TTT-AATTTAATT
39641559 CGTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
ATATGTTTAATTTAATTA
Found at i:39649041 original size:144 final size:144
Alignment explanation
Indices: 39648775--39649101 Score: 372
Period size: 144 Copynumber: 2.3 Consensus size: 144
39648765 ATTGCCAATT
* * * * * * ** * * *
39648775 CCATGTTCCAAACATGGTCTTACACTGGCTCACATGTTGAGGCCGATGCCGTGTCCCAGACATGG
1 CCATGTCCCAGACATAGTCTTACACTAGCACACATATCAATGCCGACGCCATGTCCCAGACATGG
* * *
39648840 TCTTACACTAGCTCTCATCTCTATGGAGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA
66 TCTTACACTAGCTCTCATCACTATGCAGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCA
*
39648905 TAAT-GTGGTCGATG
131 T-ATCGTGGCCGATG
* * * *
39648919 TCATGTCCTAGACATAGTCTTACATTAGCGCACATATCAATGCCGACGCCATGTCCCAGACATGG
1 CCATGTCCCAGACATAGTCTTACACTAGCACACATATCAATGCCGACGCCATGTCCCAGACATGG
* * * * *
39648984 TCTTATACTGGCTCTCA-CAAC-ATCGCCGATGCCATGTTCCAAACATGGTCTTGCACTGGCTCT
66 TCTTACACTAGCTCTCATC-ACTAT-GCAGATGCCATGTCCCAAACATGGTCTTACACTGGCTCT
39649047 CATATCGTGGCCGATG
129 CATATCGTGGCCGATG
* *
39649063 CCATGTCCCAGACATGGTCTTACACTGGCACACATATCA
1 CCATGTCCCAGACATAGTCTTACACTAGCACACATATCA
39649102 CCCAAATGTC
Statistics
Matches: 151, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
143 5 0.03
144 146 0.97
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (144 bp):
CCATGTCCCAGACATAGTCTTACACTAGCACACATATCAATGCCGACGCCATGTCCCAGACATGG
TCTTACACTAGCTCTCATCACTATGCAGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCA
TATCGTGGCCGATG
Found at i:39649100 original size:48 final size:48
Alignment explanation
Indices: 39648775--39649101 Score: 329
Period size: 48 Copynumber: 6.8 Consensus size: 48
39648765 ATTGCCAATT
* * * * *
39648775 CCATGTTCCAAACATGGTCTTACACTGGCTCACATGTTGA-GGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATCATGGCCGATG
* * * *
39648823 CCGTGTCCCAGACATGGTCTTACACTAGCTCTCATCTCTATGG-AGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATATC-ATGGCCGATG
* *
39648871 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATCATGGCCGATG
* * * * * * * *
39648919 TCATGTCCTAGACATAGTCTTACATTAGCGCACATATCAAT-GCCGACG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATATC-ATGGCCGATG
* * * *
39648967 CCATGTCCCAGACATGGTCTTATACTGGCTCTCACAACATCGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCATGGCCGATG
* * * *
39649015 CCATGTTCCAAACATGGTCTTGCACTGGCTCTCATATCGTGGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCATGGCCGATG
* *
39649063 CCATGTCCCAGACATGGTCTTACACTGGCACACATATCA
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCA
39649102 CCCAAATGTC
Statistics
Matches: 224, Mismatches: 48, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
47 8 0.04
48 212 0.95
49 4 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCATGGCCGATG
Found at i:39657409 original size:40 final size:40
Alignment explanation
Indices: 39657347--39657593 Score: 208
Period size: 40 Copynumber: 6.2 Consensus size: 40
39657337 CGGATGATAA
*
39657347 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAAT-T
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCTAGT-GCTAATAT
* * *
39657387 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGCTAATAT
* ** * * *
39657427 TCGGGCTAAGTCCCGAAGGTGTTTGTAC--GAGCTATTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTA--ATAT
* *
39657467 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT--TATTAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTAATAT
* * *
39657505 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT-ATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGCTAATAT
*
39657546 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GCTAATAT
39657586 CC-GGCTAA
1 CCGGGCTAA
39657594 ACTTCGAAGG
Statistics
Matches: 170, Mismatches: 24, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
37 2 0.01
38 3 0.02
39 39 0.23
40 119 0.70
41 5 0.03
42 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTAATAT
Found at i:39657552 original size:79 final size:80
Alignment explanation
Indices: 39657388--39657570 Score: 260
Period size: 79 Copynumber: 2.3 Consensus size: 80
39657378 TGGCTAATTT
* **
39657388 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATTCGGGCTAAGTCCCGAAGGTGTTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
* * **
39657453 ACGAGCTATTATGTC
66 ACAAGCTACTATAAC
* *
39657468 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
* *
39657532 GCAAGTTACTATAAC
66 ACAAGCTACTATAAC
39657547 CGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
39657571 AGCTAGTGGC
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 56 0.61
80 36 0.39
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
ACAAGCTACTATAAC
Found at i:39657592 original size:79 final size:78
Alignment explanation
Indices: 39657388--39657593 Score: 243
Period size: 79 Copynumber: 2.6 Consensus size: 78
39657378 TGGCTAATTT
* **
39657388 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATTCGGGCTAAGTCCCGAAGGTGTTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATA-TCCGGCTAAGTCCCGAAGGCATTTGT
* * **
39657453 ACGAGCTATTATGTC
64 ACAAGCTACTATAAC
*
39657468 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCC-GGCTAAGTCCCGAAGGCATTTGT
* *
39657532 GCAAGTTACTATAAC
64 ACAAGCTACTATAAC
* * *
39657547 CGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGCTAA
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATATCCGGCTAA
39657594 ACTTCGAAGG
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
78 2 0.02
79 68 0.63
80 38 0.35
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (78 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCCGGCTAAGTCCCGAAGGCATTTGTAC
AAGCTACTATAAC
Found at i:39660293 original size:28 final size:29
Alignment explanation
Indices: 39660238--39660304 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 29
39660228 ATACCAGGGA
*
39660238 ACACACGGCCGTTTCACCTGGCTGTGTGTC
1 ACACACGACCGTTTCACCTGGC-GTGTGTC
39660268 ACACACGACCGTTTCACCTGGC-TGTGTC
1 ACACACGACCGTTTCACCTGGCGTGTGTC
39660296 ACACACGAC
1 ACACACGAC
39660305 TAAGACACAC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 15 0.42
30 21 0.58
ACGTcount: A:0.19, C:0.36, G:0.22, T:0.22
Consensus pattern (29 bp):
ACACACGACCGTTTCACCTGGCGTGTGTC
Found at i:39662349 original size:52 final size:53
Alignment explanation
Indices: 39662293--39662415 Score: 171
Period size: 52 Copynumber: 2.4 Consensus size: 53
39662283 GGGAAATTTC
* *
39662293 TCACTTAGCACCA-TGTCATGGACTTATTTCACTTAGATGCCATGGACTTATT
1 TCACTTAGCACCATTGCCATGGACTTATTTCACTTAGATGCCACGGACTTATT
* * *
39662345 TCACTTAGCA-CATTGCCATGGACTTATTTCACTTCGATGCCACGGTCTTGTT
1 TCACTTAGCACCATTGCCATGGACTTATTTCACTTAGATGCCACGGACTTATT
*
39662397 TCACTTAGCA-CAATGCCAT
1 TCACTTAGCACCATTGCCAT
39662416 ATCCTAGATA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 2 0.03
52 62 0.97
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (53 bp):
TCACTTAGCACCATTGCCATGGACTTATTTCACTTAGATGCCACGGACTTATT
Found at i:39662362 original size:28 final size:27
Alignment explanation
Indices: 39662293--39662415 Score: 132
Period size: 24 Copynumber: 4.7 Consensus size: 27
39662283 GGGAAATTTC
*
39662293 TCACTTAGCACCATGTCATGGACTTATT
1 TCACTTAGCA-CATGCCATGGACTTATT
39662321 TCACTTAG---ATGCCATGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
39662345 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
* * * *
39662373 TCACTT--C-GATGCCACGGTCTTGTT
1 TCACTTAGCACATGCCATGGACTTATT
39662397 TCACTTAGCACAATGCCAT
1 TCACTTAGCAC-ATGCCAT
39662416 ATCCTAGATA
Statistics
Matches: 80, Mismatches: 7, Indels: 16
0.78 0.07 0.16
Matches are distributed among these distances:
24 41 0.51
25 1 0.01
26 2 0.03
27 1 0.01
28 35 0.44
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:39666252 original size:23 final size:23
Alignment explanation
Indices: 39666198--39666338 Score: 214
Period size: 23 Copynumber: 6.1 Consensus size: 23
39666188 CCTAGCCTCT
39666198 TTTAATAACTGGGGCGA-AAGCCC
1 TTTAATAACTGGGGC-ATAAGCCC
* *
39666221 TTTTAATAACTAGGGCATAAGCCG
1 -TTTAATAACTGGGGCATAAGCCC
39666245 TTTAATAACT-GGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
39666267 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
39666290 TTCAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
39666313 TTTAATAACTGAGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
39666336 TTT
1 TTT
39666339 TGCACTTCCT
Statistics
Matches: 109, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
22 21 0.19
23 69 0.63
24 19 0.17
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:39666414 original size:20 final size:20
Alignment explanation
Indices: 39666389--39666453 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
39666379 ATGAATACAC
39666389 CATGTGCATATCATACATAT
1 CATGTGCATATCATACATAT
*
39666409 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAT
* *
39666429 CATGCGCATATCATACATAC
1 CATGTGCATATCATACATAT
39666449 CATGT
1 CATGT
39666454 TTATCAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (20 bp):
CATGTGCATATCATACATAT
Found at i:39669204 original size:21 final size:21
Alignment explanation
Indices: 39669178--39669229 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
39669168 TATACGAGTA
39669178 AATTTAACATCAATTCAATAC
1 AATTTAACATCAATTCAATAC
*
39669199 AATTTAAACA-CAATTCAATCC
1 AATTT-AACATCAATTCAATAC
39669220 AATTT-ACATC
1 AATTTAACATC
39669230 TTAGGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.11
20 1 0.04
21 20 0.71
22 4 0.14
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTAACATCAATTCAATAC
Found at i:39671738 original size:24 final size:24
Alignment explanation
Indices: 39671711--39671761 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
39671701 GCCATAATCG
*
39671711 GGAAGTTCATAAAGAACCATATTA
1 GGAAGTTCACAAAGAACCATATTA
*
39671735 GGAAGTTCACAAAGGACCATATTA
1 GGAAGTTCACAAAGAACCATATTA
39671759 GGA
1 GGA
39671762 GCTCTAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (24 bp):
GGAAGTTCACAAAGAACCATATTA
Found at i:39685138 original size:45 final size:45
Alignment explanation
Indices: 39685050--39685211 Score: 238
Period size: 45 Copynumber: 3.6 Consensus size: 45
39685040 CCGAATTCAT
* * *
39685050 TCACCGGC-ATTTCGCCTGCTAGGCTC-GAGGCCCGAATAATATC
1 TCACCGGCAATATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
*
39685093 TCACCGGCAATATAGCCTGCTAGGCTCAAAGGCCCGAATATTATC
1 TCACCGGCAATATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* * *
39685138 TCACCGGCATTATAGCCTGCTAGGCTTAAATGCCCGAATAATATC
1 TCACCGGCAATATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
*
39685183 TCACCGGCATTATAGCCTGCTAGGCTCAA
1 TCACCGGCAATATAGCCTGCTAGGCTCAA
39685212 CGGACCAAAT
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
43 8 0.07
44 16 0.15
45 84 0.78
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (45 bp):
TCACCGGCAATATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
Found at i:39685186 original size:90 final size:86
Alignment explanation
Indices: 39685008--39685211 Score: 259
Period size: 90 Copynumber: 2.3 Consensus size: 86
39684998 TTTTATCAAA
* * *
39685008 TCACCGGC-AT-TCAGCCTGCTAGGTTTAAAAACCCGAATTCATTCACCGGCATTTCGCCTGCTA
1 TCACCGGCAATAT-AGCCTGCTAGGCTCAAAAACCCGAATTCATTCACCGGCATTTAGCCTGCTA
**
39685071 GGCTCGAGGCCCGAATAATATC
65 GGCTAAAGGCCCGAATAATATC
** *
39685093 TCACCGGCAATATAGCCTGCTAGGCTCAAAGGCCCGAATATTATCTCACCGGCATTATAGCCTGC
1 TCACCGGCAATATAGCCTGCTAGGCTCAAAAACCCGAAT-TCAT-TCACCGGCATT-TAGCCTGC
*
39685158 TAGGCTTAAATGCCCGAATAATATC
63 TAGGC-TAAAGGCCCGAATAATATC
*
39685183 TCACCGGCATTATAGCCTGCTAGGCTCAA
1 TCACCGGCAATATAGCCTGCTAGGCTCAA
39685212 CGGACCAAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
85 8 0.08
86 24 0.23
87 4 0.04
88 11 0.11
89 12 0.12
90 44 0.43
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (86 bp):
TCACCGGCAATATAGCCTGCTAGGCTCAAAAACCCGAATTCATTCACCGGCATTTAGCCTGCTAG
GCTAAAGGCCCGAATAATATC
Found at i:39693567 original size:45 final size:45
Alignment explanation
Indices: 39693485--39693612 Score: 179
Period size: 45 Copynumber: 2.9 Consensus size: 45
39693475 CCGAATTTAT
* * *
39693485 TCACCGGCATT-TCGCCTGCTAGGCTC-GAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCTGAATAATATC
* * *
39693528 TCACCAGCATTATAGCCTACTAGGCTCAAAGGCCTGAATATTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCTGAATAATATC
*
39693573 TCACCGGCATTATAGCCTGCTAGGCTCAAAAGCCTGAATA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCTGAATA
39693613 GTACTGCACA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 10 0.14
44 13 0.18
45 51 0.69
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCTGAATAATATC
Found at i:39696630 original size:31 final size:30
Alignment explanation
Indices: 39696561--39696634 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
39696551 GGGCCGTGTG
* * *
39696561 GACCACACAGGCGCGTGGGCCCATACGGGT
1 GACCACACGGGCACGTGGGCCCACACGGGT
* *
39696591 GCAGCACACGGGCATGTGGGCCCACACGGGT
1 G-ACCACACGGGCACGTGGGCCCACACGGGT
39696622 AGACCACACGGGC
1 -GACCACACGGGC
39696635 GTGAGCCGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 1 0.03
31 34 0.94
32 1 0.03
ACGTcount: A:0.22, C:0.34, G:0.36, T:0.08
Consensus pattern (30 bp):
GACCACACGGGCACGTGGGCCCACACGGGT
Found at i:39702982 original size:16 final size:16
Alignment explanation
Indices: 39702961--39702993 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39702951 CCCTCAATTT
39702961 CGTCATAACCTTATGG
1 CGTCATAACCTTATGG
39702977 CGTCATAACCTTATGG
1 CGTCATAACCTTATGG
39702993 C
1 C
39702994 TCAGTGCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (16 bp):
CGTCATAACCTTATGG
Found at i:39711349 original size:23 final size:22
Alignment explanation
Indices: 39711314--39711362 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
39711304 TAACTAACAT
* *
39711314 TTCACAACTTAAT-AAACATTCA
1 TTCACAACATAATCAAA-ATCCA
39711336 TTCACAATCATAATCAAAATCCA
1 TTCACAA-CATAATCAAAATCCA
39711359 TTCA
1 TTCA
39711363 TATGAATCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 13 0.57
24 3 0.13
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (22 bp):
TTCACAACATAATCAAAATCCA
Found at i:39711815 original size:30 final size:30
Alignment explanation
Indices: 39711779--39711837 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
39711769 CCCCAAGGGA
* * *
39711779 CACACAGCCGTGTAACATGACCGTGTGTCG
1 CACACAGCCGAGAAACATGACCATGTGTCG
*
39711809 CACACAGCTGAGAAACATGACCATGTGTC
1 CACACAGCCGAGAAACATGACCATGTGTC
39711838 ACGCCCGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (30 bp):
CACACAGCCGAGAAACATGACCATGTGTCG
Found at i:39724358 original size:22 final size:23
Alignment explanation
Indices: 39724328--39724371 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
39724318 AAAGTTAACC
39724328 TAAACACAAATAGAATTA-ATTAG
1 TAAACACAAATA-AATTATATTAG
39724351 TAAA-ACAAATAAATTATATTA
1 TAAACACAAATAAATTATATTA
39724372 CAAAAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (23 bp):
TAAACACAAATAAATTATATTAG
Found at i:39724377 original size:22 final size:22
Alignment explanation
Indices: 39724333--39724377 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39724323 TAACCTAAAC
**
39724333 ACAAATAGAATTAATTAGTAAA
1 ACAAATAGAATTAATTACAAAA
39724355 ACAAATA-AATTATATTACAAAA
1 ACAAATAGAATTA-ATTACAAAA
39724377 A
1 A
39724378 ATCATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (22 bp):
ACAAATAGAATTAATTACAAAA
Found at i:39743303 original size:19 final size:19
Alignment explanation
Indices: 39743256--39743293 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
39743246 TTTCTTGATC
39743256 TAAATATAATCAAAATTAA
1 TAAATATAATCAAAATTAA
39743275 TAAATATAATCAAAATTAA
1 TAAATATAATCAAAATTAA
39743294 CTTATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAATATAATCAAAATTAA
Found at i:39746645 original size:14 final size:14
Alignment explanation
Indices: 39746626--39746657 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39746616 GAGCATTAGT
39746626 TAACAAAAAATTCA
1 TAACAAAAAATTCA
39746640 TAACAAAAAATTCA
1 TAACAAAAAATTCA
39746654 TAAC
1 TAAC
39746658 GCCCATACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (14 bp):
TAACAAAAAATTCA
Found at i:39757887 original size:220 final size:220
Alignment explanation
Indices: 39757505--39757946 Score: 857
Period size: 220 Copynumber: 2.0 Consensus size: 220
39757495 ACTTTTTAAC
39757505 TTGTGGTTTGATACTGATTGATAAGACGTATCATCAAAAGCAAAAGTTTCTTCACAATGTGAAGT
1 TTGTGGTTTGATACTGATTGATAAGACGTATCATCAAAAGCAAAAGTTTCTTCACAATGTGAAGT
*
39757570 ACTATTTCTAGGAAGATTCATGTTTGTTTAAAAAGTGCACAGATCAAATGATCAGGAGATGCGTG
66 ACTATTTCTAGGAAGATTCATGTTTGTTTAAAAAGTGCACAGATCAAATGATCAGGAGATGCATG
*
39757635 GTAGAAGATGAAGTACAAAAGATTCTATACCATTGTCATTCAGCTCCAAGTGGAGGACATTTTGG
131 GTAGAAGATGAAGTACAAAAGATTCTATACCATTGTCACTCAGCTCCAAGTGGAGGACATTTTGG
39757700 AAGTACTCGTATTGCGGCCAAAGTA
196 AAGTACTCGTATTGCGGCCAAAGTA
39757725 TTGTGGTTTGATACTGATTGATAAGACGTATCATCAAAAGCAAAAGTTTCTTCACAATGTGAAGT
1 TTGTGGTTTGATACTGATTGATAAGACGTATCATCAAAAGCAAAAGTTTCTTCACAATGTGAAGT
*
39757790 ACTATTTCTGGGAAGATTCATGTTTGTTTAAAAAGTGCACAGATCAAATGATCAGGAGATGCATG
66 ACTATTTCTAGGAAGATTCATGTTTGTTTAAAAAGTGCACAGATCAAATGATCAGGAGATGCATG
39757855 GTAGAAGATGAAGTACAAAAGATTCTATACCATTGTCACTCAGCTCCAAGTGGAGGACATTTTGG
131 GTAGAAGATGAAGTACAAAAGATTCTATACCATTGTCACTCAGCTCCAAGTGGAGGACATTTTGG
39757920 AAGTACTCGTATTGCGGCCAAAGTA
196 AAGTACTCGTATTGCGGCCAAAGTA
39757945 TT
1 TT
39757947 ACAAGCTGGA
Statistics
Matches: 219, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
220 219 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (220 bp):
TTGTGGTTTGATACTGATTGATAAGACGTATCATCAAAAGCAAAAGTTTCTTCACAATGTGAAGT
ACTATTTCTAGGAAGATTCATGTTTGTTTAAAAAGTGCACAGATCAAATGATCAGGAGATGCATG
GTAGAAGATGAAGTACAAAAGATTCTATACCATTGTCACTCAGCTCCAAGTGGAGGACATTTTGG
AAGTACTCGTATTGCGGCCAAAGTA
Found at i:39758290 original size:142 final size:142
Alignment explanation
Indices: 39758034--39758317 Score: 559
Period size: 142 Copynumber: 2.0 Consensus size: 142
39758024 TCAGAAATGT
*
39758034 CACCAACATAAATGAGATGCCTCGAACAAACATTATTGAGGTAGAATTGTTCGATGTATAGGGTA
1 CACCAACATAAATGAGATGCCTCGAACAAACATTATTGAGGTAGAATTGTTCGATGTATAAGGTA
39758099 TTGACTTTCTTGGTCCTTTCCCTCCGTCCTTTGATCACAAGTATTTATTGGTAGCAGTAGACTAT
66 TTGACTTTCTTGGTCCTTTCCCTCCGTCCTTTGATCACAAGTATTTATTGGTAGCAGTAGACTAT
39758164 GTGTCTAAGTGG
131 GTGTCTAAGTGG
39758176 CACCAACATAAATGAGATGCCTCGAACAAACATTATTGAGGTAGAATTGTTCGATGTATAAGGTA
1 CACCAACATAAATGAGATGCCTCGAACAAACATTATTGAGGTAGAATTGTTCGATGTATAAGGTA
39758241 TTGACTTTCTTGGTCCTTTCCCTCCGTCCTTTGATCACAAGTATTTATTGGTAGCAGTAGACTAT
66 TTGACTTTCTTGGTCCTTTCCCTCCGTCCTTTGATCACAAGTATTTATTGGTAGCAGTAGACTAT
39758306 GTGTCTAAGTGG
131 GTGTCTAAGTGG
39758318 GTCAAGGCTG
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (142 bp):
CACCAACATAAATGAGATGCCTCGAACAAACATTATTGAGGTAGAATTGTTCGATGTATAAGGTA
TTGACTTTCTTGGTCCTTTCCCTCCGTCCTTTGATCACAAGTATTTATTGGTAGCAGTAGACTAT
GTGTCTAAGTGG
Found at i:39759766 original size:17 final size:18
Alignment explanation
Indices: 39759740--39759773 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39759730 ATTTTTTTTA
39759740 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
39759757 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
39759774 ATATTTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:39760406 original size:25 final size:25
Alignment explanation
Indices: 39760372--39760431 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
39760362 TTCTCCTAAA
* *
39760372 TTTTAATTTATTTAATTATT-TAAT
1 TTTTAATTTATTGAATCATTATAAT
39760396 TTTTCAATTTATTGAATCATTAATAAT
1 TTTT-AATTTATTGAATCATT-ATAAT
39760423 TTTT-ATTTA
1 TTTTAATTTA
39760432 ATTAAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 4 0.13
25 19 0.61
27 8 0.26
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTAATTTATTGAATCATTATAAT
Found at i:39767679 original size:23 final size:22
Alignment explanation
Indices: 39767652--39767710 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
39767642 TAGCCATGGT
39767652 TAATTA-TTTTAATTGTGAAATA
1 TAATTACTTTTAATT-TGAAATA
* * *
39767674 TAAATTAGTTTCAATTTTAAATA
1 T-AATTACTTTTAATTTGAAATA
*
39767697 TTATTACTTTTAAT
1 TAATTACTTTTAAT
39767711 CCAGATCTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 11 0.37
23 12 0.40
24 7 0.23
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (22 bp):
TAATTACTTTTAATTTGAAATA
Found at i:39768356 original size:35 final size:35
Alignment explanation
Indices: 39768286--39768357 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
39768276 AGTGAACATT
* *
39768286 ATAATTATAATTTAACTTACAATTATTAGTTAAAA
1 ATAATTATAATTAAACTTACAATTATTAGTAAAAA
*
39768321 ATAATTATAATTAAATTTTA-ACATTATTA-TAAAAA
1 ATAATTATAATTAAA-CTTACA-ATTATTAGTAAAAA
39768356 AT
1 AT
39768358 GACTTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 22 0.69
36 10 0.31
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (35 bp):
ATAATTATAATTAAACTTACAATTATTAGTAAAAA
Found at i:39771494 original size:23 final size:24
Alignment explanation
Indices: 39771479--39771531 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
39771469 GTACATGTAT
39771479 GCTCATACGAGTTGTAAATGGTAA
1 GCTCATACGAGTTGTAAATGGTAA
* * * *
39771503 GCTCCTACGAGCTGAATAACGGTAA
1 GCTCATACGAGTTGTA-AATGGTAA
39771528 GCTC
1 GCTC
39771532 CTCCAAGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (24 bp):
GCTCATACGAGTTGTAAATGGTAA
Found at i:39771582 original size:25 final size:25
Alignment explanation
Indices: 39771479--39771584 Score: 106
Period size: 25 Copynumber: 4.3 Consensus size: 25
39771469 GTACATGTAT
* * *
39771479 GCTCATACGAGTTGTA-AATGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
*
39771503 GCTCCTACGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* * * *
39771528 GCTCCTCCAAGCTGAATAACGATAA
1 GCTCATACGAGCTGAATAACGGTAA
* * *
39771553 GCTCATATGAGCTGAGTATCGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
39771578 GCTCATA
1 GCTCATA
39771585 AAAGCTAAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
24 13 0.19
25 54 0.81
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:39777393 original size:18 final size:18
Alignment explanation
Indices: 39777370--39777415 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
39777360 TTTTAAGATA
39777370 AGAGCTTACTAAGCTTTC
1 AGAGCTTACTAAGCTTTC
39777388 AGAGCTTACTAAGCTTTC
1 AGAGCTTACTAAGCTTTC
*
39777406 AAAGCTTACT
1 AGAGCTTACT
39777416 CTGTGTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (18 bp):
AGAGCTTACTAAGCTTTC
Found at i:39786263 original size:51 final size:51
Alignment explanation
Indices: 39786187--39786470 Score: 317
Period size: 51 Copynumber: 5.6 Consensus size: 51
39786177 CTTATACAGG
*
39786187 TAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGTTGTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGTTGTCGGGTACACA
*
39786238 TAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGTTGCCGGGTACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGTTGTCGGGTACACA
* * *** * * *
39786289 TAGTAGCCTGCACTTAGTACTACATA-GTGACCT-AA-CCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGTTGTCGGGTACACA
* *
39786338 TAGTAGCTTGCACTTAGTACTACACACGTGATTGAAGTTGTCAGGTACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGTTGTCGGGTACACA
* * * * * * * **
39786389 TAGTAGCTTTGCACTTAGTACTACACATGCGACCT-AA-CTATCTGGTACATG
1 TAGTAGC-CTGCACTTAGTACTACACACGTGA-TTGAAGTTGTCGGGTACACA
39786440 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
39786471 CCTAAAACCA
Statistics
Matches: 196, Mismatches: 31, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
49 32 0.16
50 33 0.17
51 106 0.54
52 24 0.12
53 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (51 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGTTGTCGGGTACACA
Found at i:39786355 original size:151 final size:152
Alignment explanation
Indices: 39786080--39786517 Score: 568
Period size: 151 Copynumber: 2.9 Consensus size: 152
39786070 GAAGCTATCT
* * *
39786080 GGTACTCATAGTAGCT-TGCACTTAGTACTACACATGCGACCAATAA-TAT--GATACATATAGT
1 GGTACACATAGTAGCTCTGCACTTAGTACTACACACGCGACC--TAACTATCGGGTACATATAGT
* *
39786141 AGCCTGCACTTAGTACTACACACATGACCTAACCATCTTATACAGGTAGTAGCCTGCACTTAGTA
64 AGCCTGCACTTAGTACTACACACGTGACCTAACCATCTTATACACGTAGTAGCCTGCACTTAGTA
*
39786206 CTACACACGTGATTGAAGTTGTCG
129 CTACACACGTGATTGAAGTTGTCA
* * * * *
39786230 GGTACGCATAGTAGC-CTGCACTTAGTACTACACACGTGA-TTGAAGT-TGCCGGGTACACATAG
1 GGTACACATAGTAGCTCTGCACTTAGTACTACACACGCGACCT-AACTAT--CGGGTACATATAG
* * *
39786292 TAGCCTGCACTTAGTACTACATA-GTGACCTAACCATCTGATACACGTAGTAGCTTGCACTTAGT
63 TAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTTATACACGTAGTAGCCTGCACTTAGT
39786356 ACTACACACGTGATTGAAGTTGTCA
128 ACTACACACGTGATTGAAGTTGTCA
* * * *
39786381 GGTACACATAGTAGCTTTGCACTTAGTACTACACATGCGACCTAACTATCTGGTACATGTAGTAG
1 GGTACACATAGTAGCTCTGCACTTAGTACTACACACGCGACCTAACTATCGGGTACATATAGTAG
* * *
39786446 CCTGCACTTAGTACTACACACGTGACCTAAAACCATCTTAAACACATAGTAGCCTGCACATAGTA
66 CCTGCACTTAGTACTACACACGTGACCT--AACCATCTTATACACGTAGTAGCCTGCACTTAGTA
39786511 CTACACA
129 CTACACA
39786518 TGTGTTCTCA
Statistics
Matches: 248, Mismatches: 27, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
147 1 0.00
148 3 0.01
149 1 0.00
150 35 0.14
151 107 0.43
152 62 0.25
153 2 0.01
154 37 0.15
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (152 bp):
GGTACACATAGTAGCTCTGCACTTAGTACTACACACGCGACCTAACTATCGGGTACATATAGTAG
CCTGCACTTAGTACTACACACGTGACCTAACCATCTTATACACGTAGTAGCCTGCACTTAGTACT
ACACACGTGATTGAAGTTGTCA
Found at i:39786504 original size:102 final size:101
Alignment explanation
Indices: 39786067--39786519 Score: 387
Period size: 102 Copynumber: 4.5 Consensus size: 101
39786057 CACCCTTGTA
* * * * * *
39786067 ACTGAAGCTATCTGGTACTCATAGTAGCTTGCACTTAGTACTACACATGCGACC-AA-TAATATG
1 ACTGAAACCATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACT-ATCTG
* *
39786130 ATACATATAGTAGCCTGCACTTAGTACTACACACATG
65 ATACACATAGTAGCCTGCACTTAGTACTACACACGTG
* ** * * * * *
39786167 ACCT--AACCATCTTATACAGGTAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGTTGTC
1 A-CTGAAACCATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCT-AA-CTATC
* * *
39786229 GGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTG
63 TGATACACATAGTAGCCTGCACTTAGTACTACACACGTG
* ***** * * * * *
39786268 ATTGAAGTTGCCGGGTACACATAGTAGCCTGCACTTAGTACTACATA-GTGACCTAACCATCTGA
1 ACTGAAACCATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATCTGA
* *
39786332 TACACGTAGTAGCTTGCACTTAGTACTACACACGTG
66 TACACATAGTAGCCTGCACTTAGTACTACACACGTG
* **** * * *
39786368 ATTGAAGTTGTCAGGTACACATAGTAGCTTTGCACTTAGTACTACACATGCGACCTAACTATCTG
1 ACTGAAACCATCTGATACACATAGTAGC-CTGCACTTAGTACTACACATGCGACCTAACTATCTG
* **
39786433 GTACATGTAGTAGCCTGCACTTAGTACTACACACGTG
65 ATACACATAGTAGCCTGCACTTAGTACTACACACGTG
* * * *
39786470 ACCTAAAACCATCTTAAACACATAGTAGCCTGCACATAGTACTACACATG
1 A-CTGAAACCATCTGATACACATAGTAGCCTGCACTTAGTACTACACATG
39786520 TGTTCTCACA
Statistics
Matches: 282, Mismatches: 60, Indels: 20
0.78 0.17 0.06
Matches are distributed among these distances:
99 37 0.13
100 66 0.23
101 61 0.22
102 101 0.36
103 17 0.06
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (101 bp):
ACTGAAACCATCTGATACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATCTGA
TACACATAGTAGCCTGCACTTAGTACTACACACGTG
Found at i:39789194 original size:3 final size:3
Alignment explanation
Indices: 39789181--39789227 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
39789171 AAGTAAAAGA
* * *
39789181 TAT TGT TAT TAT TAT TAT TGT TAT TGT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39789228 ATGTTAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39965240 original size:46 final size:46
Alignment explanation
Indices: 39965173--39965347 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
39965163 TGTAACCCGC
* *
39965173 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
* * *
39965219 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C-ATTTGCAT
* * ** *
39965269 -C-TCA-CGAACTCGGACTCAAGTCAACGAGTTCGAACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
*
39965312 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
39965348 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 2 0.02
46 60 0.57
47 26 0.25
48 3 0.03
49 2 0.02
50 5 0.05
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
Found at i:39965293 original size:93 final size:93
Alignment explanation
Indices: 39965180--39965351 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
39965170 CGCCCATAAG
** * *
39965180 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
39965245 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
39965273 CGAACTCGGACTCAAGTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
39965338 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
39965352 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:39973256 original size:24 final size:24
Alignment explanation
Indices: 39973221--39973266 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
39973211 AACTCACCAC
* *
39973221 AGCTCGTAAGAGTTTATTGTTTTT
1 AGCTCGTAAGAGCTTATCGTTTTT
*
39973245 AGCTCGTTAGAGCTTATCGTTT
1 AGCTCGTAAGAGCTTATCGTTT
39973267 CAGCTCAACA
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:0.20, C:0.13, G:0.22, T:0.46
Consensus pattern (24 bp):
AGCTCGTAAGAGCTTATCGTTTTT
Found at i:39987978 original size:16 final size:16
Alignment explanation
Indices: 39987957--39987989 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39987947 TAAACTCTTG
39987957 TCTCTAGTCAATAGGC
1 TCTCTAGTCAATAGGC
39987973 TCTCTAGTCAATAGGC
1 TCTCTAGTCAATAGGC
39987989 T
1 T
39987990 TTTAAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (16 bp):
TCTCTAGTCAATAGGC
Found at i:39988561 original size:16 final size:15
Alignment explanation
Indices: 39988540--39988569 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39988530 AATACTCCTT
39988540 ATTCTTTCCTCTTTCA
1 ATTCTTTCCT-TTTCA
39988556 ATTCTTTCCTTTTC
1 ATTCTTTCCTTTTC
39988570 CTTCACCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTCTTTCCTTTTCA
Found at i:40002894 original size:40 final size:40
Alignment explanation
Indices: 40002770--40002969 Score: 243
Period size: 39 Copynumber: 5.1 Consensus size: 40
40002760 CGGAATTTAA
* * *
40002770 CCGGATATAGCT-ACTCGCTCGAATGCCTTC--GACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
40002808 CC-GATTATAGTAACTCGCACAAATGCC-TCGGGACTTAGC
1 CCGGA-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40002847 CCAGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40002887 CCGGATATAATAACTCGCACAATTGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40002926 CCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
40002966 CCGG
1 CCGG
40002970 TTATCATCCG
Statistics
Matches: 142, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
37 5 0.04
38 21 0.15
39 63 0.44
40 53 0.37
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40002924 original size:79 final size:79
Alignment explanation
Indices: 40002773--40002973 Score: 245
Period size: 79 Copynumber: 2.6 Consensus size: 79
40002763 AATTTAACCG
* * *
40002773 GATATAGCTACTCGCTCGAATGCCTTC--GACATAGCCC-GATTATAGTAACTCGCACAAATGCC
1 GATATAG-TACTCGCACGAATGCCTTCGGGACTTAGCCCGGATTATAATAACTCGCACAAATGCC
40002835 TCGGGACTTAGCCCA
65 TCGGGACTTAGCCCA
*
40002850 GATATAGTAACTCGCACGAATGCCTTCGGGACTTAGCCCGGA-TATAATAACTCGCACAATTGCC
1 GATATAGT-ACTCGCACGAATGCCTTCGGGACTTAGCCCGGATTATAATAACTCGCACAAATGCC
*
40002914 TTCGGG-CTTAGCCCG
65 -TCGGGACTTAGCCCA
* *
40002929 GA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG-TTAT
1 GATA-TAGT-ACTCGCACGAATGCCTTCGGGACTTAGCCCGGATTAT
40002974 CATCCGAATA
Statistics
Matches: 109, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
76 1 0.01
77 24 0.22
78 1 0.01
79 76 0.70
80 7 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
GATATAGTACTCGCACGAATGCCTTCGGGACTTAGCCCGGATTATAATAACTCGCACAAATGCCT
CGGGACTTAGCCCA
Found at i:40009348 original size:45 final size:45
Alignment explanation
Indices: 40009288--40009390 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
40009278 CCAACATTTG
*
40009288 TTTTCGTGTAAGACCACATCTGGGATGTTGGCATCGATATATGTT
1 TTTTCGTGTAAGACCACATCTGGGACGTTGGCATCGATATATGTT
* ** *
40009333 TTTTCTTGTAAGACCATGTCTGGGACGTTGGCATCGATATATGTG
1 TTTTCGTGTAAGACCACATCTGGGACGTTGGCATCGATATATGTT
* *
40009378 GTTACGTGTAAGA
1 TTTTCGTGTAAGA
40009391 TCATGGCTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (45 bp):
TTTTCGTGTAAGACCACATCTGGGACGTTGGCATCGATATATGTT
Found at i:40009401 original size:45 final size:45
Alignment explanation
Indices: 40009292--40009413 Score: 136
Period size: 45 Copynumber: 2.7 Consensus size: 45
40009282 CATTTGTTTT
*** * ** *
40009292 CGTGTAAGACCACATCTGGGATGTTGGCATCGATATATGTTTTTT
1 CGTGTAAGACCATGGCTGGGACGTTGGCATCGATATATGTGGTTA
* *
40009337 CTTGTAAGACCATGTCTGGGACGTTGGCATCGATATATGTGGTTA
1 CGTGTAAGACCATGGCTGGGACGTTGGCATCGATATATGTGGTTA
* * *
40009382 CGTGTAAGATCATGGCTGGGACATCGGCATCG
1 CGTGTAAGACCATGGCTGGGACGTTGGCATCG
40009414 TATTTGATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (45 bp):
CGTGTAAGACCATGGCTGGGACGTTGGCATCGATATATGTGGTTA
Found at i:40013491 original size:17 final size:17
Alignment explanation
Indices: 40013459--40013505 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
40013449 TCTTTTTGCT
40013459 TTAA-TTAAATCAATTAA
1 TTAATTTAAA-CAATTAA
* *
40013476 TTAGTTTAAACAATTAG
1 TTAATTTAAACAATTAA
*
40013493 TTAATTAAAACAA
1 TTAATTTAAACAA
40013506 ACATTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38
Consensus pattern (17 bp):
TTAATTTAAACAATTAA
Found at i:40017701 original size:12 final size:12
Alignment explanation
Indices: 40017686--40017718 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
40017676 ATATGTGGCT
40017686 ATATATATATAA
1 ATATATATATAA
40017698 ATATATATATAA
1 ATATATATATAA
*
40017710 ACATATATA
1 ATATATATA
40017719 CATATTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATATATATAA
Found at i:40019511 original size:27 final size:27
Alignment explanation
Indices: 40019464--40019553 Score: 119
Period size: 27 Copynumber: 3.4 Consensus size: 27
40019454 GGGGGCATTT
*
40019464 TAGTCATTT-ACCACATTAGGGCAAAA
1 TAGTCATTTAACCACATAAGGGCAAAA
* *
40019490 CAATCATTTAACCACATAAGGGCAAAA
1 TAGTCATTTAACCACATAAGGGCAAAA
* * *
40019517 TAGTCATTTTAGCACATAAGGGAAAAA
1 TAGTCATTTAACCACATAAGGGCAAAA
40019544 TAGTCATTTA
1 TAGTCATTTA
40019554 TCAAATTTGG
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 7 0.13
27 47 0.87
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (27 bp):
TAGTCATTTAACCACATAAGGGCAAAA
Found at i:40022610 original size:51 final size:49
Alignment explanation
Indices: 40022551--40022695 Score: 182
Period size: 49 Copynumber: 2.9 Consensus size: 49
40022541 TAGCCGAAGC
*
40022551 TATCTGGTACACGTAGTAGCCAGCACTTAGTACTACACACGTGATCAAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CAAA-T
* * * * * * *
40022602 TTTTTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACAAAT
* *
40022651 TATCCGGTACACGTAGTAGTCTGCACTTAGTACTACACACGTGAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAC
40022696 CTCACAATAG
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
49 38 0.49
50 3 0.04
51 37 0.47
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACAAAT
Found at i:40022676 original size:49 final size:51
Alignment explanation
Indices: 40022551--40022691 Score: 178
Period size: 51 Copynumber: 2.8 Consensus size: 51
40022541 TAGCCGAAGC
* *
40022551 TATCTGGTACACGTAGTAGCCAGCACTTAGTACTACACACGTGATCAAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGATCAAAGT
* * * * * *
40022602 TTTTTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-T
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGATCAAAGT
* *
40022651 TATCCGGTACACGTAGTAGTCTGCACTTAGTACTACACACG
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACG
40022692 TGACCTCACA
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
49 35 0.47
50 3 0.04
51 37 0.49
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (51 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGATCAAAGT
Found at i:40032713 original size:16 final size:16
Alignment explanation
Indices: 40032692--40032722 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40032682 CGGCAAATCC
*
40032692 TGAAATGTCGAAAAGT
1 TGAAATGCCGAAAAGT
40032708 TGAAATGCCGAAAAG
1 TGAAATGCCGAAAAG
40032723 CCGAAAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (16 bp):
TGAAATGCCGAAAAGT
Found at i:40032981 original size:29 final size:29
Alignment explanation
Indices: 40032939--40033057 Score: 204
Period size: 29 Copynumber: 4.1 Consensus size: 29
40032929 GAAAGCATGT
40032939 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
40032968 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
40032997 ATACGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
40033026 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
40033054 ATAT
1 ATAT
40033058 TCATGTATGT
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
28 19 0.22
29 67 0.78
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.29
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:40034787 original size:49 final size:49
Alignment explanation
Indices: 40034731--40034957 Score: 274
Period size: 49 Copynumber: 4.6 Consensus size: 49
40034721 CTAGTATGCA
* *
40034731 TAGTAGCCTGCACTTAGTACTACACATGCGATTAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATCTGGTACACG
* * *** *
40034780 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAGCCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CTAATTATCTGGTACACG
* * * * * * *
40034830 TAGTAGCCTGCAGTTAGTACTACACACGTGATCAAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CTAA-TTATCTGGTACACG
*
40034881 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATCTGGTACACG
*
40034930 TAGTAGCCTACACTTAGTACTACACATG
1 TAGTAGCCTGCACTTAGTACTACACATG
40034958 TGACCTCACA
Statistics
Matches: 150, Mismatches: 26, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
49 67 0.45
50 47 0.31
51 36 0.24
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATCTGGTACACG
Found at i:40034904 original size:101 final size:98
Alignment explanation
Indices: 40034731--40034960 Score: 307
Period size: 100 Copynumber: 2.3 Consensus size: 98
40034721 CTAGTATGCA
* * *
40034731 TAGTAGCCTGCACTTAGTACTACACATGCGATTAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGTGATAAATTATCCGGTACACATAGTAGCCTGCACTTA
* *
40034796 GTACTACACACGTGACCTAGCCATCTGATACACG
66 GTACTACACACGCGACC-AACCATCTGATACACG
* * * *
40034830 TAGTAGCCTGCAGTTAGTACTACACACGTGATCAAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACATGTGAT-AAA-TTATCCGGTACACATAGTAGCCTGCACT
* ** *
40034895 TAGTACTACACATGCGACCAATTATCTGGTACACG
64 TAGTACTACACACGCGACCAACCATCTGATACACG
*
40034930 TAGTAGCCTACACTTAGTACTACACATGTGA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA
40034961 CCTCACAATA
Statistics
Matches: 113, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
99 29 0.26
100 42 0.37
101 42 0.37
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGATAAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCAACCATCTGATACACG
Found at i:40036506 original size:17 final size:17
Alignment explanation
Indices: 40036484--40036520 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
40036474 GGGTATTACA
40036484 TAATTGCTCAAAATCTT
1 TAATTGCTCAAAATCTT
*
40036501 TAATTGCTCGAAATCTT
1 TAATTGCTCAAAATCTT
40036518 TAA
1 TAA
40036521 AATTTTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (17 bp):
TAATTGCTCAAAATCTT
Found at i:40040639 original size:20 final size:20
Alignment explanation
Indices: 40040610--40040654 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
40040600 AACACGTGTA
* *
40040610 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
40040630 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
40040650 TTCAT
1 TTCAT
40040655 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:40044267 original size:42 final size:40
Alignment explanation
Indices: 40044181--40044347 Score: 235
Period size: 40 Copynumber: 4.1 Consensus size: 40
40044171 CTCGATATAT
* *
40044181 TATATATCTGGGTTAAATCCCGCAAGCTTCGTGCTGGTAA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
*
40044221 TATATATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGTAA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* *
40044261 TATATATCCGGGTTAAATCCCACAGGCTTTGTGCTGGTAAA
1 TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGT-AA
* * * *
40044302 GTATATATCCGGGTTAAATCCCGTAGGCTTAGTGCTAGTAC
1 -TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
40044343 TATAT
1 TATAT
40044348 CCGAGCTTAA
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 77 0.68
41 3 0.03
42 34 0.30
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (40 bp):
TATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
Found at i:40044348 original size:80 final size:80
Alignment explanation
Indices: 40044181--40044373 Score: 255
Period size: 82 Copynumber: 2.4 Consensus size: 80
40044171 CTCGATATAT
* * *
40044181 TATATATCTGGGTTAAATCCCGCAAGCTTCGTGCTGGTAATATATATCCGGGTTAAATCCCGTAG
1 TATATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATATATATCCGGGTTAAATCCCGTAG
* *
40044246 GCTTCGTGCTGGTAA
66 GCTTAGTGCTAGTAA
*
40044261 TATATATCCGGGTTAAATCCCACAGGCTTTGTGCTGGTAAAGTATATATCCGGGTTAAATCCCGT
1 TATATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGT-AA-TATATATCCGGGTTAAATCCCGT
40044326 AGGCTTAGTGCTAGT-A
64 AGGCTTAGTGCTAGTAA
* * *
40044342 -CTATATCCGAGCTTAAAGTTCCGCAGGCTTTG
1 TATATATCCG-GGTTAAA-TCCCGCAGGCTTTG
40044374 AGCTAGTGAC
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
80 42 0.42
81 9 0.09
82 48 0.48
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (80 bp):
TATATATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATATATATCCGGGTTAAATCCCGTAG
GCTTAGTGCTAGTAA
Found at i:40044370 original size:40 final size:37
Alignment explanation
Indices: 40044221--40044380 Score: 95
Period size: 40 Copynumber: 4.0 Consensus size: 37
40044211 GTGCTGGTAA
* * * * *
40044221 TATATATCCGGGTTAAATCCCGTAGGCTTCGTGCTGGTAA
1 TATATATCCGGCTTAAATCCCGCAGGCTTAGAGC---TAG
* * * *
40044261 TATATATCCGGGTTAAATCCCACAGGCTTTGTGCTGGTAAAG
1 TATATATCCGGCTTAAATCCCGCAGGCTTAGAGC---T--AG
* * *
40044303 TATATATCCGGGTTAAATCCCGTAGGCTTAGTGCTAG
1 TATATATCCGGCTTAAATCCCGCAGGCTTAGAGCTAG
* *
40044340 TACTATATCCGAGCTTAAAGTTCCGCAGGCTTTGAGCTAG
1 TA-TATATCCG-GCTTAAA-TCCCGCAGGCTTAGAGCTAG
40044380 T
1 T
40044381 GACTGGATTC
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
37 4 0.04
38 8 0.08
39 7 0.07
40 52 0.50
42 32 0.31
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (37 bp):
TATATATCCGGCTTAAATCCCGCAGGCTTAGAGCTAG
Found at i:40079553 original size:20 final size:20
Alignment explanation
Indices: 40079524--40079568 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
40079514 AGTACATATA
* *
40079524 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
40079544 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
40079564 TTCAT
1 TTCAT
40079569 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:40080385 original size:25 final size:25
Alignment explanation
Indices: 40080357--40080405 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
40080347 TATCTAGGCT
*
40080357 ATATAACGGGAAGCTCATAAGAGCC
1 ATATAACGAGAAGCTCATAAGAGCC
* *
40080382 ATATATCGAGATGCTCATAAGAGC
1 ATATAACGAGAAGCTCATAAGAGC
40080406 TAAGGTGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (25 bp):
ATATAACGAGAAGCTCATAAGAGCC
Found at i:40080663 original size:18 final size:17
Alignment explanation
Indices: 40080640--40080675 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
40080630 GACATGTGGG
*
40080640 ATACATAATCAATTTCAT
1 ATACATAAT-AAATTCAT
40080658 ATACATAATAAATTCAT
1 ATACATAATAAATTCAT
40080675 A
1 A
40080676 ATTCACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (17 bp):
ATACATAATAAATTCAT
Found at i:40097826 original size:19 final size:19
Alignment explanation
Indices: 40097792--40097836 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
40097782 CAATTCTAAC
*
40097792 TCATAACCATTTATCATG-T
1 TCAT-ACCATTTATCAAGTT
40097811 TCATACCATTTCATCAAGTT
1 TCATACCATTT-ATCAAGTT
40097831 TCATAC
1 TCATAC
40097837 ACATAGTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 9 0.39
20 7 0.30
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.40
Consensus pattern (19 bp):
TCATACCATTTATCAAGTT
Found at i:40100199 original size:27 final size:27
Alignment explanation
Indices: 40100166--40100260 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
40100156 CCTTAGGGGA
40100166 ATTTCGGTAATTTTACAAGTTGAGGGT
1 ATTTCGGTAATTTTACAAGTTGAGGGT
* * *
40100193 ATTTCGGTAATTGTACAGGTCGAGGGT
1 ATTTCGGTAATTTTACAAGTTGAGGGT
* * *
40100220 ATTTCAGTAATTTCACAAATT-AGAGGT
1 ATTTCGGTAATTTTACAAGTTGAG-GGT
*
40100247 ATTTTGGTAATTTT
1 ATTTCGGTAATTTT
40100261 CCTTTATTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
26 2 0.04
27 53 0.96
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.41
Consensus pattern (27 bp):
ATTTCGGTAATTTTACAAGTTGAGGGT
Found at i:40100602 original size:28 final size:29
Alignment explanation
Indices: 40100554--40100644 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
40100544 AAGTCTACAT
* *
40100554 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
**
40100582 TTATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
40100611 ACATTCATATGGCCCATCT-GGCCCGAATC
1 ACATTCATATGGCCCAT-TAGGCCCAAATC
40100640 A-ATTC
1 ACATTC
40100645 CAAGCCATGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 24 0.44
29 29 0.54
30 1 0.02
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:40111718 original size:52 final size:50
Alignment explanation
Indices: 40111639--40111822 Score: 235
Period size: 50 Copynumber: 3.6 Consensus size: 50
40111629 ATTGTGAGAA
* * * *
40111639 CACATTTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGTTGTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGG-T-TAGGT
* * *
40111691 CACATGTGTAGTACTAAGTGCAAGCTACTATGTGTACCAGATAGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTTAGGT
**
40111741 GGCATGTGTAGTACTAAGTGCAGGCTACTACT-TGTATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTA-TGTGTATCAGATGGTTAGGT
* *
40111791 CACGTGTGTAGTACTAAGTGCAGGATACTATG
1 CACATGTGTAGTACTAAGTGCAGGCTACTATG
40111823 CGTACCAAAT
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 74 0.65
51 2 0.02
52 37 0.32
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTTAGGT
Found at i:40111820 original size:100 final size:102
Alignment explanation
Indices: 40111645--40111834 Score: 278
Period size: 100 Copynumber: 1.9 Consensus size: 102
40111635 AGAACACATT
* *
40111645 TGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGTTGTAGGTCACATGTGTAGTACTAAGT
1 TGTAGTACTAAGTGCAGGCTACTATGTGTATAAGATGGTTGTAGGTCACATGTGTAGTACTAAGT
* * *
40111710 GCAAGCTACTATGTGTACCAGATAGTTAGGTGGCATG
66 GCAAGATACTATGCGTACCAAATAGTTAGGTGGCATG
* *
40111747 TGTAGTACTAAGTGCAGGCTACTACT-TGTATCAGATGG-T-TAGGTCACGTGTGTAGTACTAAG
1 TGTAGTACTAAGTGCAGGCTACTA-TGTGTATAAGATGGTTGTAGGTCACATGTGTAGTACTAAG
*
40111809 TGCAGGATACTATGCGTACCAAATAG
65 TGCAAGATACTATGCGTACCAAATAG
40111835 CTTCGGTGAC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 44 0.56
101 1 0.01
102 33 0.42
103 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (102 bp):
TGTAGTACTAAGTGCAGGCTACTATGTGTATAAGATGGTTGTAGGTCACATGTGTAGTACTAAGT
GCAAGATACTATGCGTACCAAATAGTTAGGTGGCATG
Found at i:40122473 original size:24 final size:26
Alignment explanation
Indices: 40122446--40122498 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 26
40122436 TTATACCAAA
40122446 TCATTATGC-CAAAA-TCATCACAT-T
1 TCATTAT-CACAAAACTCATCACATCT
*
40122470 TCA-TATCACAAAACTCATCATATCT
1 TCATTATCACAAAACTCATCACATCT
40122495 TCAT
1 TCAT
40122499 CTCAAACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
22 1 0.04
23 8 0.33
24 11 0.46
25 4 0.17
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (26 bp):
TCATTATCACAAAACTCATCACATCT
Found at i:40125157 original size:28 final size:29
Alignment explanation
Indices: 40125125--40125181 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
40125115 ATCTGAAATA
* *
40125125 CTGATAT-CATGGCCTGAAGCCACATCAG
1 CTGATATGCATGGCCAGAAGCCAAATCAG
40125153 CTGATATGCATGGCCAGAAGCCAAATCAG
1 CTGATATGCATGGCCAGAAGCCAAATCAG
40125182 TTTATCTCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (29 bp):
CTGATATGCATGGCCAGAAGCCAAATCAG
Found at i:40133357 original size:15 final size:15
Alignment explanation
Indices: 40133334--40133368 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
40133324 ATTCACATTG
*
40133334 AACACTCGGAATAAT
1 AACAGTCGGAATAAT
40133349 AACAGTCGGAATAAT
1 AACAGTCGGAATAAT
40133364 AACAG
1 AACAG
40133369 ATACTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (15 bp):
AACAGTCGGAATAAT
Found at i:40138076 original size:27 final size:29
Alignment explanation
Indices: 40138046--40138105 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 29
40138036 TAAAGGCTAA
* *
40138046 TATTTTCAATTAGTTAGTA-TTTAAATT-
1 TATTTTCAATTAATTAGTACTTGAAATTG
* *
40138073 TATTTTTATTTAATTAGTACTTGAAATTG
1 TATTTTCAATTAATTAGTACTTGAAATTG
40138102 TATT
1 TATT
40138106 CTGTCACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 16 0.59
28 7 0.26
29 4 0.15
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (29 bp):
TATTTTCAATTAATTAGTACTTGAAATTG
Found at i:40138337 original size:19 final size:19
Alignment explanation
Indices: 40138313--40138350 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40138303 TACTATAAGA
40138313 TTGACCAACATTGTAACAT
1 TTGACCAACATTGTAACAT
40138332 TTGACCAACATTGTAACAT
1 TTGACCAACATTGTAACAT
40138351 CAACACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (19 bp):
TTGACCAACATTGTAACAT
Found at i:40141006 original size:3 final size:3
Alignment explanation
Indices: 40140998--40141022 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40140988 ACGTAATAGC
40140998 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
40141023 ATAAGTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40141820 original size:31 final size:31
Alignment explanation
Indices: 40141782--40141851 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
40141772 CGACTCAAAC
*
40141782 TCAAAAAACTGAATTACTTATTCAAGTTTAT
1 TCAAAAAACTAAATTACTTATTCAAGTTTAT
* * **
40141813 TCGAAAAATTAAATTTTTTATTCAAGTTTAT
1 TCAAAAAACTAAATTACTTATTCAAGTTTAT
40141844 TCAAAAAA
1 TCAAAAAA
40141852 TCGAATAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (31 bp):
TCAAAAAACTAAATTACTTATTCAAGTTTAT
Found at i:40143708 original size:26 final size:26
Alignment explanation
Indices: 40143654--40143708 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
40143644 AATATCATAT
*
40143654 TGATAAATAGAATGTGTAAGAAAATG
1 TGATAAATAGAATATGTAAGAAAATG
* *
40143680 TGATGAAATAGTATATGTATGAAAA-G
1 TGAT-AAATAGAATATGTAAGAAAATG
40143706 TGA
1 TGA
40143709 AAGAGAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (26 bp):
TGATAAATAGAATATGTAAGAAAATG
Found at i:40147668 original size:49 final size:47
Alignment explanation
Indices: 40147526--40147746 Score: 159
Period size: 49 Copynumber: 4.7 Consensus size: 47
40147516 TTATAAGAGC
* * *
40147526 CAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGAGATAT-ACAAG-
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGGCCT--TGATATGA-AAGT
* ** * ***
40147573 CTAGTGTAAGACCT-ACTGGGACATGGTGTCAG-CTTG-T-TGTGTGT
1 C-AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTTGATATGAAAGT
* *
40147617 CAGTGTAAGACCTGTCTGGGACACGACATCGGCCTTGATATACGAAAGT
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTTGATAT--GAAAGT
* * * * **
40147666 CAGTGTAAGACCTGTTTGGGACATGGCATCGACTTTGATGTGCTAGT
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTTGATATGAAAGT
*
40147713 CAGTGTAAGACAATGTCTGGGACATGGCATCGGC
1 CAGTGTAAGAC-CTGTCTGGGACATGGCATCGGC
40147747 ATCTTATCCC
Statistics
Matches: 135, Mismatches: 28, Indels: 21
0.73 0.15 0.11
Matches are distributed among these distances:
43 14 0.10
44 14 0.10
45 5 0.04
46 1 0.01
47 28 0.21
48 35 0.26
49 38 0.28
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (47 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTTGATATGAAAGT
Found at i:40151072 original size:49 final size:50
Alignment explanation
Indices: 40150951--40151074 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
40150941 TATCGGATTA
* ** *
40150951 GTGTAGTACTAAGTGC-AGTCTACTACGTGTATCAGATGGTTAGGTCACGT
1 GTGTAGTACTAAGTGCAAG-CTACTACGTGTACCAGATAATTAGGTCACAT
* * * *
40151001 GTGTAGTACTAACTGCAGGCTACTACGTGTACCGGATAATT-GGTCGCAT
1 GTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTAGGTCACAT
40151050 GTGTAGTACTAAGTGCAAGCTACTA
1 GTGTAGTACTAAGTGCAAGCTACTA
40151075 TGCATACCAG
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
49 29 0.46
50 33 0.52
51 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
GTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTAGGTCACAT
Found at i:40171997 original size:49 final size:48
Alignment explanation
Indices: 40171937--40172113 Score: 162
Period size: 49 Copynumber: 3.6 Consensus size: 48
40171927 TGTTGTGTGT
* * * *
40171937 CAGTGCAAGACCTGTCTGGGACATGGCATCGACACTGGTAGATGAGAGC
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGAC-CTGATAGATGAAAGC
* * * *
40171986 CAGTGTAAGACCTATCTAGGACACGGCATC-AGCCTCGATATATGAAAGT
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGA-CCT-GATAGATGAAAGC
* * * * * *
40172035 TAGTGTAAGACCTGTCTGGGAAATGACATCGACTTTGAT-G-TGATAGC
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGAC-CTGATAGATGAAAGC
40172082 CAGTGTAAGACCATGTCTAGGACATGGCATCG
1 CAGTGTAAGACC-TGTCTAGGACATGGCATCG
40172114 GCATCTTATC
Statistics
Matches: 101, Mismatches: 22, Indels: 11
0.75 0.16 0.08
Matches are distributed among these distances:
47 16 0.16
48 19 0.19
49 64 0.63
50 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (48 bp):
CAGTGTAAGACCTGTCTAGGACATGGCATCGACCTGATAGATGAAAGC
Found at i:40172044 original size:142 final size:138
Alignment explanation
Indices: 40171799--40172053 Score: 323
Period size: 142 Copynumber: 1.8 Consensus size: 138
40171789 TTATAAGAGC
* * * * * * *
40171799 CAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTTTGG
1 CAGTGCAAGACATGTCTGGGACATGCATCGACATGGAGACGAGAGCCAGTGTAAGACATATCTAG
*
40171864 GAAATGCATCAGCCTCGAGATATACAAGCTAGTGTAAGACCTATCTGGTACATGGTCTTAGCTTG
66 GAAAGGCATCAGCCTCGAGATATACAAGCTAGTGTAAGACCTATCTGGTACATGGTCTTAGCTTG
40171929 TTGTGTGT
131 TTGTGTGT
* * *
40171937 CAGTGCAAGACCTGTCTGGGACATGGCATCGACACTGGTAGATGAGAGCCAGTGTAAGACCTATC
1 CAGTGCAAGACATGTCTGGGACAT-GCATCGACA-TGG-AGACGAGAGCCAGTGTAAGACATATC
* * * *
40172002 TAGGACACGGCATCAGCCTCGATATATGA-AAGTTAGTGTAAGACCTGTCTGG
63 TAGGA-AAGGCATCAGCCTCGAGATAT-ACAAGCTAGTGTAAGACCTATCTGG
40172054 GAAATGACAT
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
138 22 0.23
139 8 0.08
140 2 0.02
141 25 0.26
142 39 0.40
143 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (138 bp):
CAGTGCAAGACATGTCTGGGACATGCATCGACATGGAGACGAGAGCCAGTGTAAGACATATCTAG
GAAAGGCATCAGCCTCGAGATATACAAGCTAGTGTAAGACCTATCTGGTACATGGTCTTAGCTTG
TTGTGTGT
Found at i:40172360 original size:31 final size:31
Alignment explanation
Indices: 40172325--40172387 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
40172315 GTTGAGTAAC
40172325 ACAGGTATGTATGCCAAACTCATGAGAAATG
1 ACAGGTATGTATGCCAAACTCATGAGAAATG
*
40172356 ACAGGTATGTATGCCGAACTCATGAGAAATG
1 ACAGGTATGTATGCCAAACTCATGAGAAATG
40172387 A
1 A
40172388 TTTCGGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (31 bp):
ACAGGTATGTATGCCAAACTCATGAGAAATG
Found at i:40182037 original size:20 final size:20
Alignment explanation
Indices: 40182012--40182059 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
40182002 GTGTGGACTC
*
40182012 ACACGCTCGTATATCTTGGG
1 ACACGCCCGTATATCTTGGG
*
40182032 ACACGCCCGTGTATCTTGGG
1 ACACGCCCGTATATCTTGGG
*
40182052 GCACGCCC
1 ACACGCCC
40182060 ATGCCCTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (20 bp):
ACACGCCCGTATATCTTGGG
Found at i:40189126 original size:23 final size:23
Alignment explanation
Indices: 40189096--40189141 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
40189086 GTTAAGGGTT
40189096 AGATTGAATAATACGTAACAATC
1 AGATTGAATAATACGTAACAATC
*
40189119 AGATTGAATAATATGTAACAATC
1 AGATTGAATAATACGTAACAATC
40189142 CTCCCTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (23 bp):
AGATTGAATAATACGTAACAATC
Found at i:40189590 original size:37 final size:37
Alignment explanation
Indices: 40189540--40189619 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
40189530 TCTATTAAGA
40189540 TAGTGATCTACCCAGATCATTTCAGAATTATATTCAT
1 TAGTGATCTACCCAGATCATTTCAGAATTATATTCAT
* *
40189577 TAGTGATCTACCCAGATCATTTCAGGATTATATTCGT
1 TAGTGATCTACCCAGATCATTTCAGAATTATATTCAT
40189614 TA-TGAT
1 TAGTGAT
40189620 GTGACTTGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 4 0.10
37 37 0.90
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (37 bp):
TAGTGATCTACCCAGATCATTTCAGAATTATATTCAT
Found at i:40210304 original size:55 final size:53
Alignment explanation
Indices: 40210181--40210377 Score: 160
Period size: 55 Copynumber: 3.7 Consensus size: 53
40210171 AGGGTTTAAG
* * * * * * ** *
40210181 GATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTATAAGGCAAG
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGATAA-CTACATAAGGCAAA
* * * *
40210235 GAAATCATGTAAGACCATGTCAAGACGTGGCATTGATAAACTACGATAAGGCAAA
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGAT-AACTAC-ATAAGGCAAA
* * * * * * * *
40210290 GATCCCATGTAAGACCACGCCAAGGCATGGCAATGGTAAGTTCATAAGGCAAG
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGATAACTACATAAGGCAAA
* *
40210343 GATACCACGTAAGACCATGTCAAGACATGGTAATG
1 GATACCATGTAAGACCATGTCAAGACATGGCAATG
40210378 GTAAGTTTAA
Statistics
Matches: 112, Mismatches: 29, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
53 38 0.34
54 35 0.31
55 39 0.35
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (53 bp):
GATACCATGTAAGACCATGTCAAGACATGGCAATGATAACTACATAAGGCAAA
Found at i:40210358 original size:53 final size:53
Alignment explanation
Indices: 40210178--40210384 Score: 216
Period size: 53 Copynumber: 3.8 Consensus size: 53
40210168 ATTAGGGTTT
* * * *
40210178 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * * *
40210232 AAGGAAATCATGTAAGACCATGTCAAGACGTGGCATTGATAAACTACGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
40210287 AAAGATCCCATGTAAGACCACGCCAAGGCATGGCAATGGTAAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* * *
40210340 AAGGATACCACGTAAGACCATGTCAAGACATGGTAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
40210385 TAAAAAGGAA
Statistics
Matches: 122, Mismatches: 29, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
53 45 0.37
54 38 0.31
55 39 0.32
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Done.