Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 16
Found at i:2600511 original size:22 final size:20
Alignment explanation
Indices: 2600465--2600512 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
2600455 TATATATTAC
2600465 AATATAAATTTATAATTTAT
1 AATATAAATTTATAATTTAT
* *
2600485 TATATAAATTAATATTATTTAT
1 AATATAAATT--TATAATTTAT
2600507 AATATA
1 AATATA
2600513 TTTATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 9 0.39
22 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATATAAATTTATAATTTAT
Found at i:2601946 original size:20 final size:21
Alignment explanation
Indices: 2601923--2601974 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
2601913 TCCCTATATA
2601923 TTATAATATAAATT-TATAAT
1 TTATAATATAAATTATATAAT
* *
2601943 TTATTATATAAATTAATATTAT
1 TTATAATATAAATT-ATATAAT
2601965 TTATAATATA
1 TTATAATATA
2601975 TTTATATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 13 0.48
22 14 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATAATATAAATTATATAAT
Found at i:2601951 original size:30 final size:29
Alignment explanation
Indices: 2601917--2601986 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2601907 CTGTTGTCCC
*
2601917 TATATATTATAATATAAATTTATAATTTAT
1 TATATATTATAATAT-AATTTATAATATAT
* *
2601947 TATATA-AATTAATATTATTTATAATATAT
1 TATATATTA-TAATATAATTTATAATATAT
2601976 T-TATATTATAA
1 TATATATTATAA
2601987 GTAATATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 7 0.21
29 15 0.44
30 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TATATATTATAATATAATTTATAATATAT
Found at i:2601983 original size:20 final size:20
Alignment explanation
Indices: 2601923--2601984 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
2601913 TCCCTATATA
2601923 TTATAATATAAATTTATA--AT
1 TTATAATAT--ATTTATATTAT
* *
2601943 TTATTATATAAATTAATATTAT
1 TTA-TA-ATATATTTATATTAT
2601965 TTATAATATATTTATATTAT
1 TTATAATATATTTATATTAT
2601985 AAGTAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 22 0.65
21 4 0.12
22 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATAATATATTTATATTAT
Found at i:2603185 original size:28 final size:29
Alignment explanation
Indices: 2603132--2603186 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
2603122 GGGTTTTATG
*
2603132 GAATTTGAGGGTTCTTTTTAGGATTTTGT
1 GAATTTGAGGGTTCTTTTTAGAATTTTGT
*
2603161 GAATTT-AGGG-TGTTTTTAGTAATTTT
1 GAATTTGAGGGTTCTTTTTAG-AATTTT
2603187 ACGATGAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.35
28 9 0.39
29 6 0.26
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.53
Consensus pattern (29 bp):
GAATTTGAGGGTTCTTTTTAGAATTTTGT
Found at i:2603416 original size:20 final size:21
Alignment explanation
Indices: 2603393--2603444 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
2603383 TCCATATATA
2603393 TTATAATATAAATT-TATAAT
1 TTATAATATAAATTATATAAT
* *
2603413 TTATTATATAAATTAATATTAT
1 TTATAATATAAATT-ATATAAT
2603435 TTATAATATA
1 TTATAATATA
2603445 TTTATATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 13 0.48
22 14 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATAATATAAATTATATAAT
Found at i:2603421 original size:30 final size:29
Alignment explanation
Indices: 2603387--2603456 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2603377 TTGTTGTCCA
*
2603387 TATATATTATAATATAAATTTATAATTTAT
1 TATATATTATAATAT-AATTTATAATATAT
* *
2603417 TATATA-AATTAATATTATTTATAATATAT
1 TATATATTA-TAATATAATTTATAATATAT
2603446 T-TATATTATAA
1 TATATATTATAA
2603457 GTAATATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 7 0.21
29 15 0.44
30 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TATATATTATAATATAATTTATAATATAT
Found at i:2603453 original size:20 final size:20
Alignment explanation
Indices: 2603393--2603454 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
2603383 TCCATATATA
2603393 TTATAATATAAATTTATA--AT
1 TTATAATAT--ATTTATATTAT
* *
2603413 TTATTATATAAATTAATATTAT
1 TTA-TA-ATATATTTATATTAT
2603435 TTATAATATATTTATATTAT
1 TTATAATATATTTATATTAT
2603455 AAGTAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 22 0.65
21 4 0.12
22 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATAATATATTTATATTAT
Found at i:2608075 original size:17 final size:19
Alignment explanation
Indices: 2608029--2608068 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2608019 ACTATTAAAT
* *
2608029 TTTAAGATTTTATATTCGA
1 TTTAAAATTATATATTCGA
2608048 TTTAAAATTATATATTCGA
1 TTTAAAATTATATATTCGA
2608067 TT
1 TT
2608069 AAATTATTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (19 bp):
TTTAAAATTATATATTCGA
Found at i:2613229 original size:52 final size:52
Alignment explanation
Indices: 2613132--2613235 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 52
2613122 ATTTATATTC
* * *
2613132 TATGATACTTGATTTTGTTAATATTTAAAATGATTATGATGAGTGAATGATA
1 TATGATACTTGATTGTGATAATATTTAAAATGATTATGATGAGTGAAAGATA
* * * *
2613184 TATGATACTTGATTGTGATGATGTTTGAAAA-GATTTTGATTAGTGAAAGATA
1 TATGATACTTGATTGTGATAATATTT-AAAATGATTATGATGAGTGAAAGATA
2613236 AAGGATTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 40 0.91
53 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.42
Consensus pattern (52 bp):
TATGATACTTGATTGTGATAATATTTAAAATGATTATGATGAGTGAAAGATA
Found at i:2613455 original size:43 final size:45
Alignment explanation
Indices: 2613358--2613481 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 45
2613348 ATTATATTTG
2613358 TAGCACGAGTCTGACATT-TGTGTGACGGTGGTGCTATTATATGATACT
1 TAGCACGAGTCTGAC-TTCTGTGTGACGGTGGTG---TTATATGATACT
* * * *
2613406 GAGCACGAGTCTGACTTCTGTGTGATGGTGGTG-TGT-TGGTACT
1 TAGCACGAGTCTGACTTCTGTGTGACGGTGGTGTTATATGATACT
*
2613449 TAGCACGAGTCTGACGTCTGTGTGACGGTGGTG
1 TAGCACGAGTCTGACTTCTGTGTGACGGTGGTG
2613482 CTAAAGTATC
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
43 36 0.53
44 2 0.03
47 2 0.03
48 28 0.41
ACGTcount: A:0.18, C:0.15, G:0.34, T:0.33
Consensus pattern (45 bp):
TAGCACGAGTCTGACTTCTGTGTGACGGTGGTGTTATATGATACT
Found at i:2613735 original size:30 final size:30
Alignment explanation
Indices: 2613663--2613740 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
2613653 GAGATGAAAC
* * *
2613663 TGAATGATATAGGCTACGAAATAAATTAAA
1 TGAATGATACATGCTATGAAATAAATTAAA
*
2613693 TGAATGATACATGTTATGAAATAAA-TAAA
1 TGAATGATACATGCTATGAAATAAATTAAA
2613722 GTGAATGGA-ACATGCTATG
1 -TGAAT-GATACATGCTATG
2613741 CTATGATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 4 0.10
30 35 0.85
31 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
TGAATGATACATGCTATGAAATAAATTAAA
Found at i:2615276 original size:42 final size:42
Alignment explanation
Indices: 2615215--2615298 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
2615205 GAATAGCATA
* * * * *
2615215 TCAGGCCTTATTCTTCTGAGCTTTTGTTGTACTGGCTTGCAC
1 TCAGGCCTCATTATCCTGAGCTTTTGCTGCACTGGCTTGCAC
2615257 TCAGGCCTCATTATCCTGAGCTTTTGCTGCACTGGCTTGCAC
1 TCAGGCCTCATTATCCTGAGCTTTTGCTGCACTGGCTTGCAC
2615299 CCATGCCTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.13, C:0.27, G:0.21, T:0.38
Consensus pattern (42 bp):
TCAGGCCTCATTATCCTGAGCTTTTGCTGCACTGGCTTGCAC
Found at i:2632024 original size:18 final size:17
Alignment explanation
Indices: 2632003--2632072 Score: 70
Period size: 18 Copynumber: 4.0 Consensus size: 17
2631993 AGTATAATCT
2632003 TTCATTCAA-TAAAGCTAG
1 TTCATT-AATTAAA-CTAG
*
2632021 TTCACTAATTAAACTAG
1 TTCATTAATTAAACTAG
* * *
2632038 TTCATCCATTTAAACTGG
1 TTCAT-TAATTAAACTAG
2632056 TTCATTAATTAAACTAG
1 TTCATTAATTAAACTAG
2632073 CTCTTTATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 19 0.45
18 23 0.55
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:2636020 original size:17 final size:19
Alignment explanation
Indices: 2635983--2636020 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2635973 TCTTTTTTTC
*
2635983 TTTCGAACAGTCTCTCTTT
1 TTTCGAACAGTCTCGCTTT
2636002 TTTCGAACAG-CT-GCTTT
1 TTTCGAACAGTCTCGCTTT
2636019 TT
1 TT
2636021 GTTTTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.16, C:0.24, G:0.13, T:0.47
Consensus pattern (19 bp):
TTTCGAACAGTCTCGCTTT
Found at i:2642709 original size:24 final size:24
Alignment explanation
Indices: 2642663--2642709 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2642653 TGATTTTATA
* *
2642663 AAAGTTTTTCTTTTCTTTTTTTTC
1 AAAGTTCTTCTTTTCTTTATTTTC
2642687 AAAGTTCTTCTTTGT-TTTATTTT
1 AAAGTTCTTCTTT-TCTTTATTTT
2642710 TATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.15, C:0.11, G:0.06, T:0.68
Consensus pattern (24 bp):
AAAGTTCTTCTTTTCTTTATTTTC
Found at i:2643357 original size:18 final size:18
Alignment explanation
Indices: 2643331--2643373 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2643321 TTTAAATTTA
* *
2643331 TTTAATTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
2643349 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
2643367 TTTATTT
1 TTTATTT
2643374 TGAAAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:2643665 original size:21 final size:20
Alignment explanation
Indices: 2643637--2643675 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2643627 ACATATCAGT
*
2643637 TTTAATTATTATTATATAAA
1 TTTAATTATAATTATATAAA
2643657 TTTATATTATAATTATATA
1 TTTA-ATTATAATTATATA
2643676 TAAGTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAATTATAATTATATAAA
Found at i:2644313 original size:17 final size:17
Alignment explanation
Indices: 2644288--2644326 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2644278 CAGTAATCGG
*
2644288 GTATATGGATTTTGCGA
1 GTATCTGGATTTTGCGA
*
2644305 GTATCTGGATTTTGCGG
1 GTATCTGGATTTTGCGA
2644322 GTATC
1 GTATC
2644327 CGTATTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.10, G:0.31, T:0.41
Consensus pattern (17 bp):
GTATCTGGATTTTGCGA
Found at i:2644333 original size:17 final size:17
Alignment explanation
Indices: 2644294--2644335 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2644284 TCGGGTATAT
*
2644294 GGATTTTGCGAGTATCT
1 GGATTTTGCGAGTATCC
*
2644311 GGATTTTGCGGGTATCC
1 GGATTTTGCGAGTATCC
*
2644328 GTATTTTG
1 GGATTTTG
2644336 GGTACCCGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.14, C:0.12, G:0.31, T:0.43
Consensus pattern (17 bp):
GGATTTTGCGAGTATCC
Found at i:2645106 original size:15 final size:15
Alignment explanation
Indices: 2645065--2645107 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2645055 TTGTTTAATT
*
2645065 TAAT-ATATAATATT
1 TAATAATATAATATA
2645079 TAATAAT-TAAATATA
1 TAATAATAT-AATATA
2645094 TAATAATATAATAT
1 TAATAATATAATAT
2645108 TATTTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.20
15 19 0.76
16 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATAATATAATATA
Found at i:2645109 original size:22 final size:22
Alignment explanation
Indices: 2645060--2645106 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2645050 ATTAGTTGTT
* *
2645060 TAATTTAATATATAATATTTAA
1 TAATTAAATATATAATATATAA
2645082 TAATTAAATATATAATAATATAA
1 TAATTAAATATATAAT-ATATAA
2645105 TA
1 TA
2645107 TTATTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATTAAATATATAATATATAA
Found at i:2664410 original size:134 final size:133
Alignment explanation
Indices: 2664213--2664911 Score: 832
Period size: 134 Copynumber: 5.2 Consensus size: 133
2664203 TGATTCATTC
* * * * *
2664213 CACTGCTCTTGAGGAAGACCAAATCTGAAAGAAGGAGAATATTG-TCCACTATTCTTTAAGGGAG
1 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAAT-CTGCTCCACTACTCTTTAGGGGAG
* * *
2664277 ATCAAATTCGAGAAAATTTTGATCCACTTCGCTACTCTTCAGGGAAGATTGAAT-AGAACATGAT
65 ATCAGACTCGAGAAAATTTTGATCCACTTCACTACTCTTCAGGGAAGATTGAATCA-AA-ATGAT
*
2664341 TTTCTT
128 TTGCTT
* * ** *
2664347 CGCTGCTATTCAGGAAGATTAAATCTGAAAGAAGAATAATCTGCTCCACTACTCTTTAGGGGAGA
1 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGA
* * * *
2664412 TCAGACTCGAGAAAACTTTAATCCACTTCACTATTCTTCAGGGAAGATTGAATCATAATTGATTT
66 TCAGACTCGAGAAAATTTTGATCCACTTCACTACTCTTCAGGGAAGATTGAATCA-AAATGATTT
*
2664477 GTTT
130 GCTT
** * * * *
2664481 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGTTCCATTAATCTTT-GGGGAGA
1 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGA
* * *
2664545 TCAGACT-GAAGAAAATTTTGATCCACTTCACTGCTCTTTAGGGAATATTGAATCAAAATTGATT
66 TCAGACTCG-AGAAAATTTTGATCCACTTCACTACTCTTCAGGGAAGATTGAATCAAAA-TGATT
2664609 TGCTT
129 TGCTT
* *
2664614 CACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCTACTACTCTTTAGGGGAGA
1 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGA
* * * * *
2664679 TCAGACTCGAGAAAACTTTGATCCATTTCACTATTCTTTAGGAAAGATTGAATCAAAATCGATTT
66 TCAGACTCGAGAAAATTTTGATCCACTTCACTACTCTTCAGGGAAGATTGAATCAAAAT-GATTT
2664744 GCTT
130 GCTT
* * * * * * * *
2664748 TACTACTATTCGGGAAGACCAAATTTCAAAGAAGAA-ACGTCTGCTCCACTACTTTTTAGGGGAG
1 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGA-ATCTGCTCCACTACTCTTTAGGGGAG
* * * ** *
2664812 ATCAGGCTCAAGAAAATTTTGATCCACTTCACTACTCTTCTGGGAAGATTGAATCGAATGTGGTT
65 ATCAGACTCGAGAAAATTTTGATCCACTTCACTACTCTTCAGGGAAGATTGAATC-AAAATGATT
2664877 TGCTT
129 TGCTT
*
2664882 CGCTGCTCTTCAGGAAGACCAAATCTGAAA
1 CACTGCTCTTCAGGAAGACCAAATCTGAAA
2664912 TCAAACATTG
Statistics
Matches: 477, Mismatches: 79, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
132 3 0.01
133 116 0.24
134 351 0.74
135 7 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (133 bp):
CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGA
TCAGACTCGAGAAAATTTTGATCCACTTCACTACTCTTCAGGGAAGATTGAATCAAAATGATTTG
CTT
Found at i:2664689 original size:267 final size:269
Alignment explanation
Indices: 2664213--2664911 Score: 912
Period size: 267 Copynumber: 2.6 Consensus size: 269
2664203 TGATTCATTC
* * ** * *
2664213 CACTGCTCTTGAGGAAGACCAAATCTGAAAGAAGGAGAATAT-TGTCCACTATTCTTTAAGGGAG
1 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGT-TCCACTAATCTTTAGGGGAG
* * * *
2664277 ATCAAATTCG-AGAAAATTTTGATCCACTTCGCTACTCTTCAGGGAAGATTGAAT-AGAACA-TG
65 ATCAGACT-GAAGAAAATTTTGATCCACTTCACTACTCTTTAGGGAAGATTGAATCA-AA-ATTG
* * ** *
2664339 ATTTTCTTCGCTGCTATTCAGGAAGATTAAATCTGAAAGAAGAATAATCTGCTCCACTACTCTTT
127 ATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTT
* *
2664404 AGGGGAGATCAGACTCGAGAAAACTTTAATCCACTTCACTATTCTTCAGGGAAGATTGAATCATA
192 AGGGGAGATCAGACTCGAGAAAACTTTAATCCACTTCACTATTCTTCAGGAAAGATTGAATCAAA
*
2664469 ATTGATTTG-TTT
257 ATCGATTTGCTTT
*
2664481 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGTTCCATTAATCTTT-GGGGAGA
1 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGTTCCACTAATCTTTAGGGGAGA
* *
2664545 TCAGACTGAAGAAAATTTTGATCCACTTCACTGCTCTTTAGGGAATATTGAATCAAAATTGATTT
66 TCAGACTGAAGAAAATTTTGATCCACTTCACTACTCTTTAGGGAAGATTGAATCAAAATTGATTT
* * *
2664610 GCTTCACTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCTACTACTCTTTAGGG
131 GCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGG
* * *
2664675 GAGATCAGACTCGAGAAAACTTTGATCCATTTCACTATTCTTTAGGAAAGATTGAATCAAAATCG
196 GAGATCAGACTCGAGAAAACTTTAATCCACTTCACTATTCTTCAGGAAAGATTGAATCAAAATCG
2664740 ATTTGCTTT
261 ATTTGCTTT
* * * * * * * * * *
2664749 -ACTACTATTCGGGAAGACCAAATTTCAAAGAAGAAACGTCTGCTCCACTACTTTTTAGGGGAGA
1 CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGTTCCACTAATCTTTAGGGGAGA
* * * *
2664813 TCAGGCTCAAGAAAATTTTGATCCACTTCACTACTCTTCT-GGGAAGATTGAATC-GAATGTGGT
66 TCAGACTGAAGAAAATTTTGATCCACTTCACTACTCTT-TAGGGAAGATTGAATCAAAAT-TGAT
2664876 TTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAA
129 TTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAA
2664912 TCAAACATTG
Statistics
Matches: 377, Mismatches: 46, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
266 2 0.01
267 228 0.60
268 145 0.38
269 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (269 bp):
CACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGCGTATGTTCCACTAATCTTTAGGGGAGA
TCAGACTGAAGAAAATTTTGATCCACTTCACTACTCTTTAGGGAAGATTGAATCAAAATTGATTT
GCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGG
GAGATCAGACTCGAGAAAACTTTAATCCACTTCACTATTCTTCAGGAAAGATTGAATCAAAATCG
ATTTGCTTT
Found at i:2665539 original size:45 final size:44
Alignment explanation
Indices: 2665469--2665576 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 44
2665459 GATACTACTG
*
2665469 AAAGGTTGACTCTTCTTCGTGAGAAAGTCAAAAAGGACAACACTA
1 AAAGATTGACT-TTCTTCGTGAGAAAGTCAAAAAGGACAACACTA
* * * *
2665514 AAAGATTGACTTATCTTCGTTAGAAAGTCAAGAATGACAACACTG
1 AAAGATTGACTT-TCTTCGTGAGAAAGTCAAAAAGGACAACACTA
* *
2665559 AATGATTGAATTTTCTTC
1 AAAGATTG-ACTTTCTTC
2665577 ACAAGAAAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 1 0.02
45 50 0.93
46 3 0.06
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (44 bp):
AAAGATTGACTTTCTTCGTGAGAAAGTCAAAAAGGACAACACTA
Found at i:2665584 original size:45 final size:45
Alignment explanation
Indices: 2665490--2665638 Score: 140
Period size: 45 Copynumber: 3.3 Consensus size: 45
2665480 CTTCTTCGTG
* * * * ***
2665490 AGAAAGTCAAAAAGGACAACACTAAAAGATTGACTTATCTTCGTT
1 AGAAAGTCAAGAATGACAACACTAAAAGATTGAATTTTCTTCACA
* *
2665535 AGAAAGTCAAGAATGACAACACTGAATGATTGAATTTTCTTCACA
1 AGAAAGTCAAGAATGACAACACTAAAAGATTGAATTTTCTTCACA
* * * * *
2665580 AGAAAGTCAAGAATGACAATACTTAACGATT-AACTTCTT-ATCACG
1 AGAAAGTCAAGAATGACAACACTAAAAGATTGAA-TT-TTCTTCACA
2665625 AGAAAGTCAAGAAT
1 AGAAAGTCAAGAAT
2665639 AACATTGAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
44 2 0.02
45 84 0.95
46 2 0.02
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (45 bp):
AGAAAGTCAAGAATGACAACACTAAAAGATTGAATTTTCTTCACA
Found at i:2665863 original size:38 final size:38
Alignment explanation
Indices: 2665607--2666352 Score: 540
Period size: 38 Copynumber: 18.8 Consensus size: 38
2665597 AATACTTAAC
* *
2665607 GATTAACTTCT-TATCACGAGAAAGTCAAGAATAACATTGAAA
1 GATTGACTTCTCT-TCACGAGGAAGTCAAGAATAAC----AAA
*
2665649 GATTGAC-TCGTCTTCACGA-GAGAGTCAAGAACAACAAA
1 GATTGACTTC-TCTTCACGAGGA-AGTCAAGAATAACAAA
* ** * * * * *
2665687 TATTGTTTTCTCTTTATG-GGAAATCAATAATAGCATTGAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATA--A--CAAA
* * * *
2665728 GATTGACTCCTCTTCACGAGGGAGTCAGGAATGATATTGAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-A--CAAA
* * * *
2665770 GATCGACTTCTCTTTACGAGGAAGTCGATAATAACATTGAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAA
* * *
2665812 GATTGACTCCTCTTCGCGA-GAGAGTCAGGAATAACAAA
1 GATTGACTTCTCTTCACGAGGA-AGTCAAGAATAACAAA
*
2665850 GATTGACTTCTCTTCACAAGGAAGTCAAGAATAACAAAGAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAA
* * * * * * *
2665892 GATTGACTCCTCTTCACAAGCG-AGTTAGGATTGACATA
1 GATTGACTTCTCTTCACGAG-GAAGTCAAGAATAACAAA
* * *
2665930 TATTGACTTCTCTTAATGAGGAAGTCAAGAATAACATTGAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAA
* * *
2665972 GATT-ATCTCCTCTTCGCGAGGGAGTCAAGAATAACAAA
1 GATTGA-CTTCTCTTCACGAGGAAGTCAAGAATAACAAA
*
2666010 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAAAAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAA
* * *
2666048 GATTGACTCCTCTTTAAGAGGAAGTCAAGAATAACATTGAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAA
* *
2666090 GATTGAC-TCATCTTCGCGAGGGAGTCAAGAATAACAAA
1 GATTGACTTC-TCTTCACGAGGAAGTCAAGAATAACAAA
* * * *
2666128 TATTGACTTCTTTTCACGAGGAAGTCAAGAAAAAAATTGAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAG--AATAA--CAAA
*
2666170 GATTGA-TTCCTCTTCACGAGGGAGTCAAGAATAACAAA
1 GATTGACTT-CTCTTCACGAGGAAGTCAAGAATAACAAA
* *
2666208 GATTGAGTTCTTTTCACGAGGAAGTCAAGAATAACAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAA
* * *
2666246 GTTTAACTTCTCTTCACGAGGAAGTCAAGAATAACCAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAA
* * *
2666284 GATTGACTTATCTTCATGAGGAAGTCAAGAATAATAAAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-ACAAA
2666324 GATTGACTTCTCTTCACGAAGG-AGTCAAG
1 GATTGACTTCTCTTCACG-AGGAAGTCAAG
2666353 TTGAAGCTTC
Statistics
Matches: 557, Mismatches: 103, Indels: 90
0.74 0.14 0.12
Matches are distributed among these distances:
37 9 0.02
38 260 0.47
39 11 0.02
40 35 0.06
41 28 0.05
42 211 0.38
43 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (38 bp):
GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAA
Found at i:2665892 original size:80 final size:79
Alignment explanation
Indices: 2665607--2666352 Score: 609
Period size: 80 Copynumber: 9.4 Consensus size: 79
2665597 AATACTTAAC
* * *
2665607 GATTAACTTCT-TATCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTCGTCTTCACGAGAG
1 GATTGACTTCTCT-TCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAG-G
*
2665671 AGTCAAGAACAACAAA
64 AGTCAAGAATAACAAA
* ** * * * * *
2665687 TATTGTTTTCTCTTTATG-GGAAATCAATAATAGCATTGAAAGATTGACTCCTCTTCACGAGGGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGA-GGA
* *
2665751 GTCAGGAATGATATTGAAA
65 GTCAAGAAT-A-A--CAAA
* * * * *
2665770 GATCGACTTCTCTTTACGAGGAAGTCGATAATAACATTGAAAGATTGACTCCTCTTCGCGAGAGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAG-GA
*
2665835 GTCAGGAATAACAAA
65 GTCAAGAATAACAAA
* ** *
2665850 GATTGACTTCTCTTCACAAGGAAGTCAAGAATAACAAAGAAAGATTGACTCCTCTTCACAAGCGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAG-GA
* * * * *
2665915 GTTAGGATTGACATA
65 GTCAAGAATAACAAA
* * * *
2665930 TATTGACTTCTCTTAATGAGGAAGTCAAGAATAACATTGAAAGATT-ATCTCCTCTTCGCGAGGG
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGA-CTCCTCTTCACGA-GG
2665994 AGTCAAGAATAACAAA
64 AGTCAAGAATAACAAA
* *
2666010 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAA-A---AAAGATTGACTCCTCTTTAAGAGGAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG-A
2666071 GTCAAGAATAACATTGAAA
65 GTCAAGAATAAC----AAA
* * * * *
2666090 GATTGAC-TCATCTTCGCGAGGGAGTCAAGAATAAC----AAATATTGACTTCTTTTCACGAGGA
1 GATTGACTTC-TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG-
* *
2666150 AGTCAAGAAAAAAATTGAAA
64 AGTCAAG--AATAA--CAAA
* * * *
2666170 GATTGA-TTCCTCTTCACGAGGGAGTCAAGAATAAC----AAAGATTGAGTTCTTTTCACGAGGA
1 GATTGACTT-CTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG-
2666230 AGTCAAGAATAACAAA
64 AGTCAAGAATAACAAA
* * * ** *
2666246 GTTTAACTTCTCTTCACGAGGAAGTCAAGAATAAC----CAAGATTGACTTATCTTCATGAGGAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG-A
*
2666307 GTCAAGAATAATAAAAA
65 GTCAAGAAT-A-ACAAA
2666324 GATTGACTTCTCTTCACGAAGG-AGTCAAG
1 GATTGACTTCTCTTCACG-AGGAAGTCAAG
2666353 TTGAAGCTTC
Statistics
Matches: 556, Mismatches: 82, Indels: 58
0.80 0.12 0.08
Matches are distributed among these distances:
75 2 0.00
76 92 0.17
77 4 0.01
78 31 0.06
79 53 0.10
80 298 0.54
81 4 0.01
82 5 0.01
83 18 0.03
84 49 0.09
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (79 bp):
GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGAG
TCAAGAATAACAAA
Found at i:2666017 original size:118 final size:118
Alignment explanation
Indices: 2665646--2666352 Score: 482
Period size: 118 Copynumber: 5.9 Consensus size: 118
2665636 AATAACATTG
* * * * ** * *
2665646 AAAGATTGAC-TCGTCTTCACGA-GAGAGTCAAGAACAACAAATATTGTTTTCTCTTTATG-GGA
1 AAAGATTGACTTC-TCTTCACAAGGA-AGTCAAGAATAAAAAAGATTGACTCCTCTTTAAGAGGA
* * * * * * *
2665708 AATCAATAATAGCATTGAAAGATTGACTCCTCTTCACGAGGGAGTCAGGAATGATATTG
64 AGTCAAGAATAACATTGAAAGATTGACTCATCTTCGCGAGGGAGTCAAGAAT-A-A--C
* * * * * ***
2665767 AAAGATCGACTTCTCTTTACGAGGAAGTCGATAATAACATTGAAAGATTGACTCCTCTTCGCGA-
1 AAAGATTGACTTCTCTTCACAAGGAAGTCAAGAATAA-A---AAAGATTGACTCCTCTTTAAGAG
* * * *
2665831 GAGAGTCAGGAATAAC----AAAGATTGACTTC-TCTTCACAAGGAAGTCAAGAATAAC
62 GA-AGTCAAGAATAACATTGAAAGATTGAC-TCATCTTCGCGAGGGAGTCAAGAATAAC
* * * * * * * * *
2665885 AAAGAAAGATTGACTCCTCTTCACAAGCG-AGTTAGGATTGACATATATTGACTTCTC-TTAATG
1 ----AAAGATTGACTTCTCTTCACAAG-GAAGTCAAGAATAAAAAAGATTGACTCCTCTTTAA-G
*
2665948 AGGAAGTCAAGAATAACATTGAAAGATT-ATCTCCTCTTCGCGAGGGAGTCAAGAATAAC
60 AGGAAGTCAAGAATAACATTGAAAGATTGA-CTCATCTTCGCGAGGGAGTCAAGAATAAC
*
2666007 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAAAAAGATTGACTCCTCTTTAAGAGGAAG
1 AAAGATTGACTTCTCTTCACAAGGAAGTCAAGAATAAAAAAGATTGACTCCTCTTTAAGAGGAAG
2666072 TCAAGAATAACATTGAAAGATTGACTCATCTTCGCGAGGGAGTCAAGAATAAC
66 TCAAGAATAACATTGAAAGATTGACTCATCTTCGCGAGGGAGTCAAGAATAAC
* * * * * * *
2666125 AAATATTGACTTCTTTTCACGAGGAAGTCAAGAAAAAAATTGAAAGATTGATTCCTCTTCACGAG
1 AAAGATTGACTTCTCTTCACAAGGAAGTCAAG-AATAAA---AAAGATTGACTCCTCTTTAAGAG
* * * * *
2666190 GGAGTCAAGAATAAC----AAAGATTGAGTTC-TTTTCACGAGGAAGTCAAGAATAAC
62 GAAGTCAAGAATAACATTGAAAGATTGA-CTCATCTTCGCGAGGGAGTCAAGAATAAC
* * * ** ** * *
2666243 AAAGTTTAACTTCTCTTCACGAGGAAGTCAAGAATAACCAAGATTGACTTATCTTCATGAGGAAG
1 AAAGATTGACTTCTCTTCACAAGGAAGTCAAGAATAAAAAAGATTGACTCCTCTTTAAGAGGAAG
** * *
2666308 TCAAGAAT-A-ATAAAAAGATTGACTTC-TCTTCACGAAGGAGTCAAG
66 TCAAGAATAACATTGAAAGATTGAC-TCATCTTCGCGAGGGAGTCAAG
2666353 TTGAAGCTTC
Statistics
Matches: 471, Mismatches: 80, Indels: 75
0.75 0.13 0.12
Matches are distributed among these distances:
113 1 0.00
114 29 0.06
116 27 0.06
117 6 0.01
118 213 0.45
119 14 0.03
120 1 0.00
121 30 0.06
122 122 0.26
123 3 0.01
125 16 0.03
126 9 0.02
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (118 bp):
AAAGATTGACTTCTCTTCACAAGGAAGTCAAGAATAAAAAAGATTGACTCCTCTTTAAGAGGAAG
TCAAGAATAACATTGAAAGATTGACTCATCTTCGCGAGGGAGTCAAGAATAAC
Found at i:2666072 original size:198 final size:198
Alignment explanation
Indices: 2665729--2666352 Score: 647
Period size: 198 Copynumber: 3.1 Consensus size: 198
2665719 GCATTGAAAG
* * * * ** * * * *
2665729 ATTGACTCCTCTTCACGAGGGAGTCAGGAATGATATTGAAAGATCGACTT-CTCTTTACGAGGAA
1 ATTGACTTCTCTTAACGAGGAAGTCAAGAAAAAAATTGAAAGATTGA-TTCCTCTTCACGAGGGA
* * * * *
2665793 GTCGATAATAACATTGAAAGATTGACTCCTCTTCGCGA-GAGAGTCAGGAATAACAAAGATTGAC
65 GTCAAGAATAAC----AAAGATTGACTTCTCTTCACGAGGA-AGTCAAGAATAACAAAGATTGAC
* * *
2665857 TTCTCTTCACA-AGGAAGTCAAGAATAACAAAGAAAGATTGACTCCTCTTCACAAGCGAGTTAGG
125 TTCTCTTCA-AGAGGAAGTCAAGAATAACAAAGAAAGATTGACTCATCTTCACAAGCGAGTCAAG
* * *
2665921 ATTGACATAT
189 AATAACAAAT
* * * *
2665931 ATTGACTTCTCTTAATGAGGAAGTCAAGAATAACATTGAAAGATT-ATCTCCTCTTCGCGAGGGA
1 ATTGACTTCTCTTAACGAGGAAGTCAAGAAAAAAATTGAAAGATTGAT-TCCTCTTCACGAGGGA
* *
2665995 GTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAAAAAGATTGACTCCTC
65 GTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTC
* ** * * *
2666060 TTTAAGAGGAAGTCAAGAATAACATTGAAAGATTGACTCATCTTCGCGAGGGAGTCAAGAATAAC
130 TTCAAGAGGAAGTCAAGAATAACAAAGAAAGATTGACTCATCTTCACAAGCGAGTCAAGAATAAC
2666125 AAAT
195 AAAT
* *
2666129 ATTGACTTCTTTTCACGAGGAAGTCAAGAAAAAAATTGAAAGATTGATTCCTCTTCACGAGGGAG
1 ATTGACTTCTCTTAACGAGGAAGTCAAGAAAAAAATTGAAAGATTGATTCCTCTTCACGAGGGAG
* * * *
2666194 TCAAGAATAACAAAGATTGAGTTCTTTTCACGAGGAAGTCAAGAATAACAAAGTTTAACTTCTCT
66 TCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCT
* * * **
2666259 TCACGAGGAAGTCAAGAATAAC----CAAGATTGACTTATCTTCATGAG-GAAGTCAAGAATAAT
131 TCAAGAGGAAGTCAAGAATAACAAAGAAAGATTGACTCATCTTCACAAGCG-AGTCAAGAAT-A-
* *
2666319 AAAAAG
193 ACAAAT
*
2666325 ATTGACTTCTCTTCACGAAGG-AGTCAAG
1 ATTGACTTCTCTTAACG-AGGAAGTCAAG
2666353 TTGAAGCTTC
Statistics
Matches: 362, Mismatches: 51, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
193 1 0.00
194 29 0.08
195 1 0.00
196 27 0.07
197 4 0.01
198 235 0.65
199 4 0.01
200 1 0.00
201 2 0.01
202 58 0.16
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (198 bp):
ATTGACTTCTCTTAACGAGGAAGTCAAGAAAAAAATTGAAAGATTGATTCCTCTTCACGAGGGAG
TCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCT
TCAAGAGGAAGTCAAGAATAACAAAGAAAGATTGACTCATCTTCACAAGCGAGTCAAGAATAACA
AAT
Found at i:2668331 original size:17 final size:16
Alignment explanation
Indices: 2668286--2668367 Score: 77
Period size: 16 Copynumber: 5.3 Consensus size: 16
2668276 ACTTGATTTA
2668286 TTTTCTTTC-TC-T-T
1 TTTTCTTTCTTCTTCT
*
2668299 TTTTCTTT-TTCCTCT
1 TTTTCTTTCTTCTTCT
2668314 TTTTCTTTTCTTCTTCT
1 TTTTC-TTTCTTCTTCT
*
2668331 TTTTCTATCTT-TTCT
1 TTTTCTTTCTTCTTCT
2668346 CTTTT-TTTCTTTCTTCT
1 -TTTTCTTTC-TTCTTCT
2668363 TTTTC
1 TTTTC
2668368 AATCTTTTCC
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
13 10 0.18
14 1 0.02
15 13 0.23
16 18 0.32
17 15 0.26
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTTTCTTCTTCT
Found at i:2668348 original size:23 final size:22
Alignment explanation
Indices: 2668322--2668496 Score: 64
Period size: 23 Copynumber: 7.6 Consensus size: 22
2668312 CTTTTTCTTT
2668322 TCTTCTTCTTTTTCTATCTTTTC
1 TCTTCTTCTTTTTCT-TCTTTTC
*
2668345 TCTT-TTTTTCTTTCTTCTTTTTC
1 TCTTCTTCTT-TTTCTTC-TTTTC
2668368 AATCTT-TTCCCTTTTTC--CTTTTC
1 --TCTTCTT--CTTTTTCTTCTTTTC
* *
2668391 ATTTTC-TCTTTTTTCCTTCTTTTT
1 -TCTTCTTC-TTTTT-CTTCTTTTC
* *
2668415 TTTTCTATCTTTTCCTAT-TTTTC
1 TCTTCT-TCTTTTTCT-TCTTTTC
* *
2668438 TTTTTCCTTCTTTTTCTTCTTTTT
1 -TCTT-CTTCTTTTTCTTCTTTTC
2668462 TCCTT-TT-TTTTAATCTT-TTTTC
1 T-CTTCTTCTTTT--TCTTCTTTTC
2668484 -CTTCTTCTTTTTC
1 TCTTCTTCTTTTTC
2668497 AATATTTTCT
Statistics
Matches: 120, Mismatches: 10, Indels: 47
0.68 0.06 0.27
Matches are distributed among these distances:
20 6 0.05
21 11 0.09
22 22 0.18
23 36 0.30
24 29 0.24
25 10 0.08
26 4 0.03
27 2 0.02
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (22 bp):
TCTTCTTCTTTTTCTTCTTTTC
Found at i:2668360 original size:32 final size:31
Alignment explanation
Indices: 2668286--2668461 Score: 116
Period size: 32 Copynumber: 5.5 Consensus size: 31
2668276 ACTTGATTTA
*
2668286 TTTTCTTTC-TCTTTTTTCT-TTTTCCTCTTT
1 TTTTCTTTCTTC-TTTTTCTATTTTTCTCTTT
*
2668316 TTCTTTTCTTCTTCTTTTTCTATCTTTTCTCTTT
1 TT-TTCT-TTCTTCTTTTTCTAT-TTTTCTCTTT
* *
2668350 TTTTCTTTCTTCTTTTTCAATCTTTTC-C-CT
1 TTTTCTTTCTTCTTTTTCTAT-TTTTCTCTTT
*
2668380 TTTTCCTT-TTCATTTTCTCT-TTTTTC-CTTCT
1 TTTTCTTTCTTC-TTTT-TCTATTTTTCTCTT-T
* *
2668411 TTTTTTTTCTATCTTTTCCTATTTTTCT-TTT
1 TTTTCTTTCT-TCTTTTTCTATTTTTCTCTTT
*
2668442 TCCTTCTTTTTCTTCTTTTT
1 T--TT-TCTTTCTTCTTTTT
2668462 TCCTTTTTTT
Statistics
Matches: 118, Mismatches: 12, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
29 9 0.08
30 15 0.13
31 17 0.14
32 43 0.36
33 16 0.14
34 18 0.15
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (31 bp):
TTTTCTTTCTTCTTTTTCTATTTTTCTCTTT
Found at i:2668373 original size:17 final size:16
Alignment explanation
Indices: 2668289--2668374 Score: 54
Period size: 17 Copynumber: 5.3 Consensus size: 16
2668279 TGATTTATTT
2668289 TCTTTC-TCTTTTTTC-
1 TCTTTCTTC-TTTTTCA
* * *
2668304 TTTTTCCTCTTTTTCT
1 TCTTTCTTCTTTTTCA
*
2668320 TTTCTTCTTCTTTTTCTA
1 TCT-TTCTTCTTTTTC-A
*
2668338 TCTTT-TCTCTTTTT-T
1 TCTTTCT-TCTTTTTCA
2668353 TCTTTCTTCTTTTTCAA
1 TCTTTCTTCTTTTTC-A
2668370 TCTTT
1 TCTTT
2668375 TCCCTTTTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
15 23 0.40
16 7 0.12
17 25 0.44
18 2 0.04
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (16 bp):
TCTTTCTTCTTTTTCA
Found at i:2668401 original size:52 final size:53
Alignment explanation
Indices: 2668340--2668443 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 53
2668330 TTTTTCTATC
* *
2668340 TTTTCTCTTTTTTTCTT-TCTTCTTTTTCAATCTTTTCC-CTTTTTCCTTTTCA
1 TTTTCTCTTTTTTCCTTCT-TTCTTTTTCAATCTTTTCCTATTTTTCCTTTTCA
* * *
2668392 TTTTCTCTTTTTTCCTTCTTTTTTTTTCTATCTTTTCCTATTTTTCTTTTTC
1 TTTTCTCTTTTTTCCTTCTTTCTTTTTCAATCTTTTCCTATTTTTCCTTTTC
2668444 CTTCTTTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
52 33 0.73
53 12 0.27
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (53 bp):
TTTTCTCTTTTTTCCTTCTTTCTTTTTCAATCTTTTCCTATTTTTCCTTTTCA
Found at i:2668461 original size:9 final size:9
Alignment explanation
Indices: 2668286--2668461 Score: 80
Period size: 9 Copynumber: 20.4 Consensus size: 9
2668276 ACTTGATTTA
2668286 TTTTCTTTCT
1 TTTTC-TTCT
2668296 CTTTT-TTCT
1 -TTTTCTTCT
*
2668305 TTTTCCTCT
1 TTTTCTTCT
2668314 TTTTCTT-T
1 TTTTCTTCT
*
2668322 TCTTCTTCT
1 TTTTCTTCT
2668331 TTTTCTATC-
1 TTTTCT-TCT
2668340 TTTTC-TCT
1 TTTTCTTCT
2668348 TTTT-TTC-
1 TTTTCTTCT
2668355 -TTTCTTCT
1 TTTTCTTCT
*
2668363 TTTTCAATC-
1 TTTTC-TTCT
*
2668372 TTTTC-CCT
1 TTTTCTTCT
*
2668380 TTTTCCTTTTCA
1 TTTT-C--TTCT
2668392 TTTTC-TCT
1 TTTTCTTCT
*
2668400 TTTT-TCCT
1 TTTTCTTCT
*
2668408 TCTT-TT-T
1 TTTTCTTCT
2668415 TTTTCTATC-
1 TTTTCT-TCT
2668424 TTTTC--CT
1 TTTTCTTCT
*
2668431 ATTT-TTCT
1 TTTTCTTCT
2668439 TTTTCCTTCT
1 TTTT-CTTCT
2668449 TTTTCTTCT
1 TTTTCTTCT
2668458 TTTT
1 TTTT
2668462 TCCTTTTTTT
Statistics
Matches: 127, Mismatches: 15, Indels: 48
0.67 0.08 0.25
Matches are distributed among these distances:
6 4 0.03
7 13 0.10
8 39 0.31
9 49 0.39
10 12 0.09
11 5 0.04
12 5 0.04
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:2668471 original size:20 final size:20
Alignment explanation
Indices: 2668379--2668486 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
2668369 ATCTTTTCCC
2668379 TTTTTCCTTTTCATTTTC-TCT
1 TTTTTCCTTTT--TTTTCTTCT
*
2668400 TTTTTCCTTCTTTTTTTTTCT
1 TTTTTCCTT-TTTTTTCTTCT
*
2668421 ATCTTTTCC---TATTT-TTC-
1 -T-TTTTCCTTTTTTTTCTTCT
*
2668438 TTTTTCCTTCTTTTTCTTCT
1 TTTTTCCTTTTTTTTCTTCT
**
2668458 TTTTTCCTTTTTTTTAATCT
1 TTTTTCCTTTTTTTTCTTCT
2668478 TTTTTCCTT
1 TTTTTCCTT
2668487 CTTCTTTTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
15 6 0.08
16 1 0.01
18 7 0.10
19 7 0.10
20 30 0.42
21 12 0.17
22 3 0.04
23 6 0.08
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCCTTTTTTTTCTTCT
Found at i:2668492 original size:53 final size:57
Alignment explanation
Indices: 2668378--2668496 Score: 140
Period size: 57 Copynumber: 2.1 Consensus size: 57
2668368 AATCTTTTCC
** *
2668378 CTTTTTCCTTTTCATTTTCTCTTTTTTCCTTCTTTTTTTTTCTATCTTTTCCTATTTTT
1 CTTTTTCC-TTTCATTTTCTCTTTTTTCCTTCTTTTTTAATCTATCTTTTCC-ATTCTT
*
2668437 CTTTTTCC-TTCTTTTTCTTCTTTTTTCCTT-TTTTTTAATCT-T-TTTTCC-TTCTT
1 CTTTTTCCTTTCATTTTC-TCTTTTTTCCTTCTTTTTTAATCTATCTTTTCCATTCTT
2668490 CTTTTTC
1 CTTTTTC
2668497 AATATTTTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
53 11 0.20
55 6 0.11
56 1 0.02
57 17 0.31
58 12 0.22
59 8 0.15
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (57 bp):
CTTTTTCCTTTCATTTTCTCTTTTTTCCTTCTTTTTTAATCTATCTTTTCCATTCTT
Found at i:2673892 original size:11 final size:11
Alignment explanation
Indices: 2673878--2673909 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2673868 GAAATGGGAC
2673878 TAAAATAAAAT
1 TAAAATAAAAT
2673889 TAAAATAAAAT
1 TAAAATAAAAT
*
2673900 AAAAATAAAA
1 TAAAATAAAA
2673910 ACAATATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
TAAAATAAAAT
Found at i:2675252 original size:3 final size:3
Alignment explanation
Indices: 2675244--2675277 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
2675234 AAAAATTAGT
2675244 TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
2675278 ATAAAGATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2676517 original size:17 final size:18
Alignment explanation
Indices: 2676495--2676532 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2676485 CATTAATTGT
*
2676495 TTCCTCCTT-TATAGTAG
1 TTCCTCCTTGTATACTAG
*
2676512 TTCCTCTTTGTATACTAG
1 TTCCTCCTTGTATACTAG
2676530 TTC
1 TTC
2676533 ACGGTCGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.16, C:0.24, G:0.11, T:0.50
Consensus pattern (18 bp):
TTCCTCCTTGTATACTAG
Found at i:2678113 original size:21 final size:19
Alignment explanation
Indices: 2678062--2678113 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
2678052 AGTCAGAGAG
2678062 AAAAAATTATA-AAACATA
1 AAAAAATTATATAAACATA
* *
2678080 AACAATTTCATATATAACATA
1 AAAAAATT-ATATA-AACATA
2678101 AAAAAATTGATAT
1 AAAAAATT-ATAT
2678114 CAAAACATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.23
19 3 0.12
20 1 0.04
21 16 0.62
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAAATTATATAAACATA
Found at i:2678120 original size:22 final size:21
Alignment explanation
Indices: 2678069--2678122 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2678059 GAGAAAAAAT
* *
2678069 TATAAAACATAAACAATTTCA
1 TATAAAACATAAAAAAATTCA
* *
2678090 TATATAACATAAAAAAATTGA
1 TATAAAACATAAAAAAATTCA
2678111 TATCAAAACATA
1 TAT-AAAACATA
2678123 TAAATACATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (21 bp):
TATAAAACATAAAAAAATTCA
Found at i:2687294 original size:22 final size:23
Alignment explanation
Indices: 2687261--2687308 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
2687251 TGCTTCAACT
2687261 TTTCTTTCTTTTCTT-TTCTCTTC
1 TTTCTTTCTTTT-TTGTTCTCTTC
*
2687284 TTTC-TTCTTTTTTGTTTTCTTC
1 TTTCTTTCTTTTTTGTTCTCTTC
2687306 TTT
1 TTT
2687309 TGAGTGCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.09
22 17 0.74
23 4 0.17
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTCTTTCTTTTTTGTTCTCTTC
Found at i:2687303 original size:19 final size:19
Alignment explanation
Indices: 2687259--2687309 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2687249 AGTGCTTCAA
2687259 CTTTTCTTTCTTTTCTTTT
1 CTTTTCTTTCTTTTCTTTT
*
2687278 CTCTTCTTTCTTCTT-TTTT
1 CTTTTCTTTCTT-TTCTTTT
*
2687297 GTTTTC-TTCTTTT
1 CTTTTCTTTCTTTT
2687310 GAGTGCTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.07
18 5 0.18
19 19 0.68
20 2 0.07
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (19 bp):
CTTTTCTTTCTTTTCTTTT
Found at i:2687901 original size:15 final size:15
Alignment explanation
Indices: 2687881--2687910 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2687871 AGGTGTGTTT
2687881 ACAAATGAATAGGAC
1 ACAAATGAATAGGAC
*
2687896 ACAAATGAATTGGAC
1 ACAAATGAATAGGAC
2687911 TAGAATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.20, T:0.17
Consensus pattern (15 bp):
ACAAATGAATAGGAC
Found at i:2690473 original size:30 final size:30
Alignment explanation
Indices: 2690438--2690521 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
2690428 ATTTATTTAA
* *
2690438 TGATCAAATTATAAATTTGGTAAAGTTT-GG
1 TGATCAAAATATAAATTTGG-AAAATTTAGG
*
2690468 TGATCAAAGTATAAACTTTGGAAAATTTAGG
1 TGATCAAAATATAAA-TTTGGAAAATTTAGG
*
2690499 -GATCAAAATATAATTTTGGAAAA
1 TGATCAAAATATAAATTTGGAAAA
2690522 ATTACAAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 9 0.19
30 32 0.67
31 7 0.15
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.35
Consensus pattern (30 bp):
TGATCAAAATATAAATTTGGAAAATTTAGG
Found at i:2692652 original size:46 final size:46
Alignment explanation
Indices: 2692554--2692731 Score: 200
Period size: 46 Copynumber: 3.9 Consensus size: 46
2692544 ATAAACTGGC
* * * ** * *
2692554 AAATAAGCTTACGAACTTATGGAA-T-AACGACAAGTATATTGGTA
1 AAATAAGCTTATGAGCTTATGGAATTAAATGGTAAGTGTATTGATA
* **
2692598 AAATAAGCTTATGAGCTTATGAAATTAAATGGTAAGTGTATTTTTA
1 AAATAAGCTTATGAGCTTATGGAATTAAATGGTAAGTGTATTGATA
*
2692644 AAATAAGCTTATGAGCTTATGGAATTAAATGGTAAGTGTACTGATA
1 AAATAAGCTTATGAGCTTATGGAATTAAATGGTAAGTGTATTGATA
** * *
2692690 AAATAAGCTTACAAGCTTATGGGA-TAAATGGTAAGTATATTG
1 AAATAAGCTTATGAGCTTATGGAATTAAATGGTAAGTGTATTG
2692732 GATATGCTAA
Statistics
Matches: 114, Mismatches: 18, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
44 21 0.18
45 17 0.15
46 76 0.67
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTATGGAATTAAATGGTAAGTGTATTGATA
Found at i:2695563 original size:19 final size:18
Alignment explanation
Indices: 2695521--2695576 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
2695511 AATATTATAT
2695521 AAGAAAAGAAA-AAAAAG-
1 AAGAAAA-AAACAAAAAGA
*
2695538 AAGAAAATAACAAAAAGA
1 AAGAAAAAAACAAAAAGA
*
2695556 AAGAAAAAAAAGAAAAAGA
1 AAG-AAAAAAACAAAAAGA
2695575 AA
1 AA
2695577 ATGAAGAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 2 0.06
17 13 0.39
18 3 0.09
19 15 0.45
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAACAAAAAGA
Found at i:2695609 original size:42 final size:40
Alignment explanation
Indices: 2695521--2695626 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 40
2695511 AATATTATAT
*
2695521 AAGAAAAGAAAAA-AAAGAAGAAAATAACAAAAAGAAAGAA
1 AAGAAAAGAAAAAGAAA-AAGAAAAGAACAAAAAGAAAGAA
* *
2695561 AA-AAAAGAAAAAGAAAATGAAGAAGAA-AAAAATAATAGAAA
1 AAGAAAAGAAAAAGAAAAAGAA-AAGAACAAAAAGAA-AG-AA
2695602 AAGAAAAGAAAAAGAAAAAGGAAAA
1 AAGAAAAGAAAAAGAAAAA-GAAAA
2695627 AAACTGAGAG
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
39 21 0.38
40 11 0.20
41 4 0.07
42 17 0.30
43 3 0.05
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (40 bp):
AAGAAAAGAAAAAGAAAAAGAAAAGAACAAAAAGAAAGAA
Found at i:2695625 original size:7 final size:6
Alignment explanation
Indices: 2695524--2695627 Score: 88
Period size: 6 Copynumber: 16.7 Consensus size: 6
2695514 ATTATATAAG
* *
2695524 AAAAGA AAAA-A AAGAAGAA AATAACA AAAAGA AAGAAAA AAAAGA AAAAGA
1 AAAAGA AAAAGA AA-AAG-A AA-AAGA AAAAGA AA-AAGA AAAAGA AAAAGA
* *
2695575 AAATGA AGAAGA AAAA-A ATAATAGA AAAAG- AAAAGA AAAAGA AAAAGGA
1 AAAAGA AAAAGA AAAAGA A-AA-AGA AAAAGA AAAAGA AAAAGA AAAA-GA
2695624 AAAA
1 AAAA
2695628 AACTGAGAGA
Statistics
Matches: 80, Mismatches: 9, Indels: 17
0.75 0.08 0.16
Matches are distributed among these distances:
5 10 0.12
6 46 0.57
7 17 0.21
8 7 0.09
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:2697559 original size:30 final size:30
Alignment explanation
Indices: 2697499--2697571 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
2697489 AATGGATTTA
* * *
2697499 TTTAATGACCAAATTATAAATTTGTTAAAG
1 TTTAATGATCAAAGTATAAATTTGTGAAAG
*
2697529 TTTATTGATCAAAGTATAAACTTTG-GAAAG
1 TTTAATGATCAAAGTATAAA-TTTGTGAAAG
**
2697559 TTTAGGGATCAAA
1 TTTAATGATCAAA
2697572 ATGTAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (30 bp):
TTTAATGATCAAAGTATAAATTTGTGAAAG
Found at i:2699684 original size:36 final size:40
Alignment explanation
Indices: 2699644--2699743 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 40
2699634 TAAGCTTACG
2699644 AGCTTATGGAATAATGACAAGTATATTGGTAAAATAAGCTTAC
1 AGCTTATGGAATAATGACAAGTATATTGGT-AAATAA-C-TAC
2699687 GAGCTTATGGAATAATGACAAGTATATTGGTAAAATAAGCTTAC
1 -AGCTTATGGAATAATGACAAGTATATTGGT-AAATAA-C-TAC
2699731 GAGCTTATGGAAT
1 -AGCTTATGGAAT
2699744 TAAATGGTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (40 bp):
AGCTTATGGAATAATGACAAGTATATTGGTAAATAACTAC
Found at i:2699784 original size:46 final size:45
Alignment explanation
Indices: 2699630--2699853 Score: 308
Period size: 46 Copynumber: 5.0 Consensus size: 45
2699620 GATAAACTGG
**
2699630 AAAATAAGCTTACGAGCTTATGGAAT-AATGACAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
**
2699674 AAAATAAGCTTACGAGCTTATGGAAT-AATGACAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* **
2699718 AAAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTGTATTTTT
1 AAAATAAGCTTACGAGCTTATGGAA-TAAATGGTAAGTATATTGGT
* * *
2699764 AAAATAAGCTTACGAGCTTATAGAATTAAATGGTAAGTTTATTGAT
1 AAAATAAGCTTACGAGCTTATGGAA-TAAATGGTAAGTATATTGGT
* *
2699810 AAAATAAGCTTACAAGCTTATGGGATAAATGGTAAGTATATTGG
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGG
2699854 ATATGCTAAT
Statistics
Matches: 164, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
44 69 0.42
45 18 0.11
46 77 0.47
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:2699830 original size:92 final size:89
Alignment explanation
Indices: 2699630--2699853 Score: 306
Period size: 90 Copynumber: 2.5 Consensus size: 89
2699620 GATAAACTGG
**
2699630 AAAATAAGCTTACGAGCTTATGGAAT-AATGACAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
2699694 TGGAATAATGACAAGTATATTGGT
66 TAGAATAATGACAAGTATATTGAT
* **
2699718 AAAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTGTATTTTTAAAATAAGCTTACGAGCTT
1 AAAATAAGCTTACGAGCTTATGGAA-TAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTT
** *
2699783 ATAGAATTAAATGGTAAGTTTATTGAT
65 ATAGAA-T-AATGACAAGTATATTGAT
* *
2699810 AAAATAAGCTTACAAGCTTATGGGATAAATGGTAAGTATATTGG
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGG
2699854 ATATGCTAAT
Statistics
Matches: 117, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
88 25 0.21
89 1 0.01
90 37 0.32
91 17 0.15
92 37 0.32
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (89 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
TAGAATAATGACAAGTATATTGAT
Found at i:2702581 original size:20 final size:20
Alignment explanation
Indices: 2702552--2702590 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2702542 TTTCCACGAC
*
2702552 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2702572 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
2702591 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:2704776 original size:17 final size:18
Alignment explanation
Indices: 2704754--2704788 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2704744 TAAATCCATT
2704754 TTATATTTTCA-TTATAA
1 TTATATTTTCATTTATAA
2704771 TTATATTTTCATTTATAA
1 TTATATTTTCATTTATAA
2704789 ATTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTTTCATTTATAA
Found at i:2704841 original size:14 final size:14
Alignment explanation
Indices: 2704822--2704848 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2704812 TTTTAAATAT
2704822 TATTAATATATTTA
1 TATTAATATATTTA
2704836 TATTAATATATTT
1 TATTAATATATTT
2704849 TTAATTTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTAATATATTTA
Found at i:2717518 original size:54 final size:54
Alignment explanation
Indices: 2717449--2717774 Score: 438
Period size: 54 Copynumber: 6.0 Consensus size: 54
2717439 GCACACCCAC
** * * *
2717449 TGCCAATACATAAATTCATAAACTTATTATGAATTTCTTAAGTTGAATACATAG
1 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
* * * ** *
2717503 TGCTAGTATGGAAATTCATACTCTCATTATGAGTTTCTTAAGTTGCACACATAG
1 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
* *
2717557 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTTCATACATAG
1 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
** *
2717611 TAG-CAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGAACACATAG
1 T-GCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
** * * *
2717665 CACCAATACGAAAATTCATAAACTCATTATGAATTTTTTAAGCTGCACACATAG
1 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
*
2717719 TACCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
1 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
2717773 TG
1 TG
2717775 TGATGTAAGG
Statistics
Matches: 235, Mismatches: 35, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
54 234 1.00
55 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (54 bp):
TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
Found at i:2717620 original size:162 final size:162
Alignment explanation
Indices: 2717452--2717773 Score: 491
Period size: 162 Copynumber: 2.0 Consensus size: 162
2717442 CACCCACTGC
* * * ** * * * *
2717452 CAATACATAAATTCATAAACTTATTATGAATTTCTTAAGTTGAATACATAGTGCTAGTATGGAAA
1 CAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGAACACATAGCACCAATACGAAAA
** * * *
2717517 TTCATACTCTCATTATGAGTTTCTTAAGTTGCACACATAGTGCCAATACGGAAATTCATAAACTC
66 TTCATAAACTCATTATGAATTTCTTAAGCTGCACACATAGTACCAATACGGAAATTCATAAACTC
* *
2717582 ATTATGAATTTCTTAAGTTTCATACATAGTAG
131 ATTATGAATTTCTTAAGTTGCACACATAGTAG
2717614 CAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGAACACATAGCACCAATACGAAAA
1 CAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGAACACATAGCACCAATACGAAAA
*
2717679 TTCATAAACTCATTATGAATTTTTTAAGCTGCACACATAGTACCAATACGGAAATTCATAAACTC
66 TTCATAAACTCATTATGAATTTCTTAAGCTGCACACATAGTACCAATACGGAAATTCATAAACTC
2717744 ATTATGAATTTCTTAAGTTGCACACATAGT
131 ATTATGAATTTCTTAAGTTGCACACATAGT
2717774 GTGATGTAAG
Statistics
Matches: 143, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
162 143 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (162 bp):
CAATACAAAAATTCATAAACTCATTATGAATTTCTTAAGTTGAACACATAGCACCAATACGAAAA
TTCATAAACTCATTATGAATTTCTTAAGCTGCACACATAGTACCAATACGGAAATTCATAAACTC
ATTATGAATTTCTTAAGTTGCACACATAGTAG
Found at i:2721634 original size:11 final size:11
Alignment explanation
Indices: 2721618--2721642 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2721608 TTGTTTTTCT
2721618 TTCACTTGCAC
1 TTCACTTGCAC
2721629 TTCACTTGCAC
1 TTCACTTGCAC
2721640 TTC
1 TTC
2721643 TTTTTGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:2724292 original size:19 final size:19
Alignment explanation
Indices: 2724270--2724311 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2724260 TCAAACTCTT
*
2724270 CTTTACTTATCCCAACTAA
1 CTTTACTTAACCCAACTAA
* *
2724289 CTTTCCTTAACTCAACTAA
1 CTTTACTTAACCCAACTAA
2724308 CTTT
1 CTTT
2724312 CCTTCATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (19 bp):
CTTTACTTAACCCAACTAA
Found at i:2734859 original size:90 final size:89
Alignment explanation
Indices: 2734750--2734924 Score: 244
Period size: 90 Copynumber: 2.0 Consensus size: 89
2734740 TCCCGAATAT
* *
2734750 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCATAATACG-TCTA
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCATAATACGAT-TA
*
2734814 GGGTAACTTGGATATAAAAGGATTA
65 GGCTAACTTGGATATAAAAGGATTA
* * * * *
2734839 TTAAATTCTAATTAATTAAATATATATTTAATTATTTTGAAATAATAAAAACCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCATAATACGATTA
*
2734904 GGCTAACTTGGCTATAAAAGG
65 GGCTAACTTGGATATAAAAGG
2734925 GGGTGTTAGG
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
89 7 0.09
90 67 0.89
91 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCATAATACGATTAG
GCTAACTTGGATATAAAAGGATTA
Found at i:2756230 original size:59 final size:59
Alignment explanation
Indices: 2756153--2756273 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
2756143 AATAGATGGA
* * *
2756153 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGAAAATTTGATAATATGGCTC
1 TAAGTGTCCCATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTTGATAATATGGCTC
*
2756212 TAAGTGTCCCATCAAACCCTCCTAGTCGCAATGAAAAGGCAAACTTGATAATATGGCTC
1 TAAGTGTCCCATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTTGATAATATGGCTC
2756271 TAA
1 TAA
2756274 CCAACCCTCC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (59 bp):
TAAGTGTCCCATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTTGATAATATGGCTC
Found at i:2773764 original size:20 final size:19
Alignment explanation
Indices: 2773735--2773774 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2773725 AAATCATTTC
* *
2773735 ATTAGTTCATATGCATTCAT
1 ATTAGCTCATAGGC-TTCAT
2773755 ATTAGCTCATAGGCTTCAT
1 ATTAGCTCATAGGCTTCAT
2773774 A
1 A
2773775 CATTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (19 bp):
ATTAGCTCATAGGCTTCAT
Found at i:2781672 original size:23 final size:23
Alignment explanation
Indices: 2781646--2781691 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2781636 TCTAAACATC
2781646 ATTTCCATTCATATACAATCAAG
1 ATTTCCATTCATATACAATCAAG
2781669 ATTTCCATTCATATACAATCAAG
1 ATTTCCATTCATATACAATCAAG
2781692 TCCTTACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (23 bp):
ATTTCCATTCATATACAATCAAG
Found at i:2783083 original size:31 final size:30
Alignment explanation
Indices: 2783026--2783083 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
2783016 TGGTTCCTAA
*
2783026 AACTTCATAAGCTTCTAAATTGATCCAAAC
1 AACTTCATAAGCTTCTAAATTCATCCAAAC
*
2783056 AACTTTATAAAGCTTGCTAAA-TCATCCA
1 AACTTCAT-AAGCTT-CTAAATTCATCCA
2783084 TTCATCATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.29
31 12 0.50
32 5 0.21
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (30 bp):
AACTTCATAAGCTTCTAAATTCATCCAAAC
Found at i:2785957 original size:45 final size:45
Alignment explanation
Indices: 2785893--2786344 Score: 636
Period size: 45 Copynumber: 10.0 Consensus size: 45
2785883 TGAAAATAAT
* * * * * * *
2785893 AATGCATATGGGTGCATTATCAGCATGAAAGGATACCACAATTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
** *
2785938 AATGCATATGGGTGCATTATCTTCAGAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* *
2785983 AATGCATATGGGTACATTATCAACATAAAAGTATGCGATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* ** * *
2786028 AATGCATATAGGTTTATTATCAACAGAAAAGTATGCTACAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* * *
2786073 AATGCATATTGGTGCATTATCAACAGAAAAGTAT-CATAGAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGC-TATAGTTGA
* *
2786118 AATGCATATGGGTGTATTATCAACATAAAAGTATGCGATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* *
2786163 AATGCATATGGGTGCATTATCAACAAAAAAGTATGTTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
2786208 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTAA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
2786253 AATGCATAAGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* *
2786298 AATGCATATAGGTGCATTTTCAACATAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
2786343 AA
1 AA
2786345 ATGTAGAATG
Statistics
Matches: 364, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
44 1 0.00
45 362 0.99
46 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
Found at i:2793000 original size:45 final size:45
Alignment explanation
Indices: 2792914--2793339 Score: 597
Period size: 45 Copynumber: 9.4 Consensus size: 45
2792904 TGAAAATAAT
* * * * *
2792914 AATGAATATGGGTGCATTATCAGCATGAAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* * *
2792959 AATGCCTATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTTA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
2793004 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTACAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* * * *
2793049 AATGTATATGGGTGCATTATCAATAGAAAAGTATGCTACAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
*
2793094 AATGCATATGGGTGCATTATCAACATAAAGGTATG-TGATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCT-ATAGTTGA
*
2793139 AATGCATTTGGGTGCATTATCAACATAAAAGTATG-TGATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCT-ATAGTTGA
2793184 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* * *
2793229 AATGCATATGGGTGAATTATCAAAATAAAAGTATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* * *
2793274 AATGCATATGAGTGCATTTTTAACATAAAAGTATGCTATAGTTGAAA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTG--A
2793321 AATGCATAAT-GGTGCATTA
1 AATGCAT-ATGGGTGCATTA
2793340 CAAACATGAA
Statistics
Matches: 342, Mismatches: 34, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
44 1 0.00
45 323 0.94
46 1 0.00
47 15 0.04
48 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
Found at i:2799029 original size:39 final size:39
Alignment explanation
Indices: 2798975--2799187 Score: 223
Period size: 39 Copynumber: 5.4 Consensus size: 39
2798965 AATATACAAT
* * *
2798975 TTATTTTCTTTTACAAAACAGGAAATTAAACCCAATGAA
1 TTATTTCCTTTTACAAAACAGGAAAATAAATCCAATGAA
* * * *
2799014 TTATTTCCTTTTACAAAATAGAAAAATATATCCAATGAT
1 TTATTTCCTTTTACAAAACAGGAAAATAAATCCAATGAA
* * **
2799053 TTATTTCCTTCTACAAAATAGGAAAATAAAT-CAAAAAA
1 TTATTTCCTTTTACAAAACAGGAAAATAAATCCAATGAA
* * * *
2799091 TTTATTTCCTTTTACAAAACATGAAAATATATCCAACGAT
1 -TTATTTCCTTTTACAAAACAGGAAAATAAATCCAATGAA
* * *
2799131 TTATTTTTCTTTTACAAATCAGGAAAATAAATCCAA-CAA
1 TTA-TTTCCTTTTACAAAACAGGAAAATAAATCCAATGAA
2799170 TTTATTTCCTTTTACAAA
1 -TTATTTCCTTTTACAAA
2799188 CTAGAATCAT
Statistics
Matches: 143, Mismatches: 27, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
38 4 0.03
39 104 0.73
40 35 0.24
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.37
Consensus pattern (39 bp):
TTATTTCCTTTTACAAAACAGGAAAATAAATCCAATGAA
Found at i:2799172 original size:79 final size:78
Alignment explanation
Indices: 2798973--2799187 Score: 283
Period size: 78 Copynumber: 2.7 Consensus size: 78
2798963 AAAATATACA
* * * * *
2798973 ATTTATTTTCTTTTACAAAACAGGAAATTAAACCCAATGAA-TTATTTCCTTTTACAAAATAGAA
1 ATTTATTTTCTTTTACAAATCAGGAAAATAAATCCAA-AAATTTATTTCCTTTTACAAAACAGAA
*
2799037 AAATATATCCAATG
65 AAATATATCCAACG
* * *
2799051 ATTTATTTCCTTCTACAAAAT-AGGAAAATAAATCAAAAAATTTATTTCCTTTTACAAAACATG-
1 ATTTATTTTCTTTTAC-AAATCAGGAAAATAAATCCAAAAATTTATTTCCTTTTACAAAACA-GA
2799114 AAAATATATCCAACG
64 AAAATATATCCAACG
*
2799129 ATTTATTTTTCTTTTACAAATCAGGAAAATAAATCCAACAATTTATTTCCTTTTACAAA
1 ATTTA-TTTTCTTTTACAAATCAGGAAAATAAATCCAAAAATTTATTTCCTTTTACAAA
2799188 CTAGAATCAT
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
77 2 0.02
78 69 0.58
79 48 0.40
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.37
Consensus pattern (78 bp):
ATTTATTTTCTTTTACAAATCAGGAAAATAAATCCAAAAATTTATTTCCTTTTACAAAACAGAAA
AATATATCCAACG
Found at i:2799354 original size:57 final size:58
Alignment explanation
Indices: 2799155--2799401 Score: 175
Period size: 58 Copynumber: 4.1 Consensus size: 58
2799145 CAAATCAGGA
*
2799155 AAATAAATCCAACAATTTATTTCCTTTTACAAACTAGAATCA-TCTAAGATTCATTTTACAAAAG
1 AAATAAATCCAACAATTTATTTCCTTTTACAAAATAGAATCATTC-AAGATTC----T-C-AAAG
* * * * * *
2799219 AGGAA-AAATTCAATAATTTATTTCCTTTTTTCATAATAGGATCCTTCAAGA-T-TCATAAG
1 A--AATAAATCCAACAATTTATTTCC-TTTTACAAAATAGAATCATTCAAGATTCTCA-AAG
* ** *
2799278 AAAATAAATTCGCCAATTTATTTACTTTTACAAAATAGAATCATT-AAGATTCTCAAAG
1 -AAATAAATCCAACAATTTATTTCCTTTTACAAAATAGAATCATTCAAGATTCTCAAAG
* * * * *
2799336 AAATAAATCCAACTATTTATTTCC-CTTACAAATTTATAATCATTCAAGTTTCTCAATA-
1 AAATAAATCCAACAATTTATTTCCTTTTACAAA-ATAGAATCATTCAAGATTCTCAA-AG
2799394 AAATAAAT
1 AAATAAAT
2799402 TTAACGGTTA
Statistics
Matches: 147, Mismatches: 24, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
56 7 0.05
57 32 0.22
58 41 0.28
59 24 0.16
60 2 0.01
64 1 0.01
65 19 0.13
66 19 0.13
67 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (58 bp):
AAATAAATCCAACAATTTATTTCCTTTTACAAAATAGAATCATTCAAGATTCTCAAAG
Found at i:2799547 original size:45 final size:44
Alignment explanation
Indices: 2799480--2799715 Score: 244
Period size: 45 Copynumber: 5.2 Consensus size: 44
2799470 TTAGCAATAT
* * *
2799480 AATAATCAAAATGAATTAATCCTTTGACGTTAACTTTCGCAACTC
1 AATAATCAAAAGGAACTAATCCTTTGA-TTTAACTTTCGCAACTC
* * * * *
2799525 AGTAATCGAAAGGAACTAATCCTTTGATTTTACTTTTGGCAACCC
1 AATAATCAAAAGGAACTAATCCTTTGATTTAAC-TTTCGCAACTC
2799570 AATAATCAAAAGGAACTAATCCTTTGATTTTAA-TTTCTGCAACTC
1 AATAATCAAAAGGAACTAATCCTTTGA-TTTAACTTTC-GCAACTC
* * *
2799615 AGTAATCGAAAGGAACCAATCCTTTGAATTTAACTTT-GACAACTC
1 AATAATCAAAAGGAACTAATCCTTTG-ATTTAACTTTCG-CAACTC
* * *
2799660 AATAATCAAAAGGAACTAATCAC-TTGATTTTACTTTTGACAACCC
1 AATAATCAAAAGGAACTAATC-CTTTGATTTAACTTTCG-CAACTC
*
2799705 AATAATAAAAA
1 AATAATCAAAA
2799716 ACATTGGATT
Statistics
Matches: 161, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
44 17 0.11
45 135 0.84
46 9 0.06
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (44 bp):
AATAATCAAAAGGAACTAATCCTTTGATTTAACTTTCGCAACTC
Found at i:2799687 original size:90 final size:90
Alignment explanation
Indices: 2799480--2799695 Score: 305
Period size: 90 Copynumber: 2.4 Consensus size: 90
2799470 TTAGCAATAT
* * ** *
2799480 AATAATCAAAATGAATTAATCCTTTGACGTTAACTTTCGCAACTCAGTAATCGAAAGGAACTAAT
1 AATAATCAAAAGGAACTAATCCTTTGATTTTAACTTTCGCAACTCAGTAATCGAAAGGAACCAAT
* *
2799545 CCTTTGATTTTACTTTTGGCAACCC
66 CCTTTGATTTAACTTTTGACAACCC
2799570 AATAATCAAAAGGAACTAATCCTTTGATTTTAA-TTTCTGCAACTCAGTAATCGAAAGGAACCAA
1 AATAATCAAAAGGAACTAATCCTTTGATTTTAACTTTC-GCAACTCAGTAATCGAAAGGAACCAA
*
2799634 TCCTTTGAATTTAAC-TTTGACAACTC
65 TCCTTTG-ATTTAACTTTTGACAACCC
2799660 AATAATCAAAAGGAACTAATCAC-TTGATTTT-ACTTT
1 AATAATCAAAAGGAACTAATC-CTTTGATTTTAACTTT
2799696 TGACAACCCA
Statistics
Matches: 114, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
89 5 0.04
90 102 0.89
91 7 0.06
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (90 bp):
AATAATCAAAAGGAACTAATCCTTTGATTTTAACTTTCGCAACTCAGTAATCGAAAGGAACCAAT
CCTTTGATTTAACTTTTGACAACCC
Found at i:2800053 original size:14 final size:14
Alignment explanation
Indices: 2800034--2800061 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2800024 TTTGCAAAAG
2800034 GCTAATCACCATGC
1 GCTAATCACCATGC
2800048 GCTAATCACCATGC
1 GCTAATCACCATGC
2800062 ATTTGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (14 bp):
GCTAATCACCATGC
Found at i:2805581 original size:20 final size:20
Alignment explanation
Indices: 2805532--2805585 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
2805522 TACTGGAAGG
* *
2805532 GGGTATCGGTACCATAGTAC
1 GGGTATCGATACCATAGTAA
*
2805552 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
2805574 GGGTATCGATAC
1 GGGTATCGATAC
2805586 TAGGCAACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
22 17 0.59
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:2805654 original size:95 final size:95
Alignment explanation
Indices: 2805460--2805684 Score: 290
Period size: 95 Copynumber: 2.4 Consensus size: 95
2805450 CCAAAGAGGT
* * * ** * *
2805460 AGTATCGATACCATGATAAGGGTATCAATACCAAACAACATCGAATCTAAAATAGGTATCGATAC
1 AGTATCGATACCATGGTAAGGGTATCGATACTAGGCAACATCGAACCTAAAATAGGTATCAATAC
** * *
2805525 TGGAAGGGGGTATCGGTACCATAGTACGGT
66 TGGAAGGGGGTATCAATACCATAGTACAGA
*
2805555 AGTATCGATACCATGGTAAGGGTATCGATACTAGGCAACATCGAACCTAAAATTGGTATCAATAC
1 AGTATCGATACCATGGTAAGGGTATCGATACTAGGCAACATCGAACCTAAAATAGGTATCAATAC
*
2805620 TGGAAGGGGGTATCAATACCATAGTATAGA
66 TGGAAGGGGGTATCAATACCATAGTACAGA
* * *
2805650 AGTATCGGTACCAGGGT-AGTAGTATCGATACTAGG
1 AGTATCGATACCATGGTAAG-GGTATCGATACTAGG
2805685 AAGCCAAAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 2 0.02
95 111 0.98
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (95 bp):
AGTATCGATACCATGGTAAGGGTATCGATACTAGGCAACATCGAACCTAAAATAGGTATCAATAC
TGGAAGGGGGTATCAATACCATAGTACAGA
Found at i:2806076 original size:59 final size:59
Alignment explanation
Indices: 2805999--2806447 Score: 600
Period size: 59 Copynumber: 7.6 Consensus size: 59
2805989 GGTGATTACC
* * * *
2805999 AAATCTTAAGGAATTCATACTAAGTGTTTGAATTTCCATATAGGGCACTTCATGTGCTA
1 AAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTA
* * * *
2806058 AAATGCTAAGTAATTCATACTAAGTGTATGAATTTCCATATAGGGAACTTCGTGTGCTA
1 AAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTA
* * *
2806117 AATTGTTAAGGAATTCATACTAAGTATATGAATTTTCGTATAGGGCACTTCGTGTGCTA
1 AAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTA
** *
2806176 AAATGTTAAATAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTCGTGTGCTA
1 AAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTA
*
2806235 AAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCGTATGGGGCACTAT-GTGTGCTA
1 AAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACT-TCGTGTGCTA
* * *
2806294 AAATGTTAAGGAATTCATACTAAGTGTATGAATTCCCGTATGGGGCACTTTGTGTGCTA
1 AAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTA
* * * * *
2806353 AAATGTTAAGAAATTCATACTAAGTGTATTAATTTCCTGAATA-GGCATTTTGTGTGC-A
1 AAATGTTAAGGAATTCATACTAAGTGTATGAATTTCC-GTATAGGGCACTTCGTGTGCTA
* * * *
2806411 AATTGTT-ATGAGAGTCATACTAAATGTATGAATTTCC
1 AAATGTTAAGGA-ATTCATACTAAGTGTATGAATTTCC
2806448 ATATGGGAAA
Statistics
Matches: 352, Mismatches: 34, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
57 2 0.01
58 30 0.09
59 316 0.90
60 4 0.01
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (59 bp):
AAATGTTAAGGAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTA
Found at i:2806882 original size:44 final size:45
Alignment explanation
Indices: 2806819--2806937 Score: 150
Period size: 44 Copynumber: 2.6 Consensus size: 45
2806809 TAGGTATAAC
* * * *
2806819 AATGTATAATGGTGTATAAAAGGCATGAAAGGATG-CTTAAGTGA
1 AATGTATAATAGTGTATAAAAGGCATGAAAAGATGCCCTAAATGA
* *
2806863 AATGTATAATAGAGTATAAAAGACATGAAAAGATGCCCTAAATGA
1 AATGTATAATAGTGTATAAAAGGCATGAAAAGATGCCCTAAATGA
* *
2806908 AATCTATAGTAGTGTATAAAAAGGCATGAA
1 AATGTATAATAGTGTAT-AAAAGGCATGAA
2806938 CAATTGTCAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 31 0.49
45 21 0.33
46 11 0.17
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.25
Consensus pattern (45 bp):
AATGTATAATAGTGTATAAAAGGCATGAAAAGATGCCCTAAATGA
Found at i:2807756 original size:24 final size:22
Alignment explanation
Indices: 2807715--2807758 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
2807705 CAGGATGATA
2807715 TATTATCTTTTAGAATTAGATT
1 TATTATCTTTTAGAATTAGATT
*
2807737 TATTATTTTATTAGGAATTAGA
1 TATTATCTT-TTA-GAATTAGA
2807759 ATTAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (22 bp):
TATTATCTTTTAGAATTAGATT
Found at i:2809053 original size:30 final size:30
Alignment explanation
Indices: 2809018--2809075 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2809008 ATTTATTTAA
* * *
2809018 TGACCAAATTATAAATTTTGTAAAGTTTGG
1 TGACCAAAGTATAAACTTTGAAAAGTTTGG
2809048 TGACCAAAGTATAAACTTTGAAAAGTTT
1 TGACCAAAGTATAAACTTTGAAAAGTTT
2809076 ACGGACCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (30 bp):
TGACCAAAGTATAAACTTTGAAAAGTTTGG
Found at i:2809083 original size:30 final size:30
Alignment explanation
Indices: 2809018--2809085 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2809008 ATTTATTTAA
* * * *
2809018 TGACCAAATTATAAATTTTGTAAAGTTTGG
1 TGACCAAAGTATAAACTTTGAAAAGTTTCG
2809048 TGACCAAAGTATAAACTTTGAAAAGTTTACG
1 TGACCAAAGTATAAACTTTGAAAAGTTT-CG
2809079 -GACCAAA
1 TGACCAAA
2809086 ATGTAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (30 bp):
TGACCAAAGTATAAACTTTGAAAAGTTTCG
Found at i:2811647 original size:15 final size:16
Alignment explanation
Indices: 2811627--2811669 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2811617 GGTTATCATC
2811627 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
2811642 ATAATATA-TATAGATG
1 ATAATA-ACTATAGATG
*
2811658 AAAATAACTATA
1 ATAATAACTATA
2811670 TTAAAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:2812615 original size:90 final size:88
Alignment explanation
Indices: 2812490--2812661 Score: 247
Period size: 90 Copynumber: 1.9 Consensus size: 88
2812480 ATAAACTGGC
* *
2812490 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTAAAATAATCATACGAGCTTATG
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATAATGGTAAAATAAGCATACGAGCTTATG
* *
2812555 TGATTAAATGGTAAGTATAATGGTA
66 GGA--AAATGGTAAATATAATGGTA
* * *
2812580 AAATAAG-TTACGAGCTTATGGGATAAATGGTAAGTATAATGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATAATGGTAAAATAAGCATACGAGCTTAT
2812644 GGGAAAATGGTAAATATA
65 GGGAAAATGGTAAATATA
2812662 TTGTATATGC
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 13 0.18
89 16 0.22
90 45 0.61
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (88 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATAATGGTAAAATAAGCATACGAGCTTATG
GGAAAATGGTAAATATAATGGTA
Found at i:2812636 original size:45 final size:45
Alignment explanation
Indices: 2812490--2812661 Score: 251
Period size: 44 Copynumber: 3.9 Consensus size: 45
2812480 ATAAACTGGC
* * *
2812490 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATAATGGTA
* * *
2812534 AAATAATCATACGAGCTTATGTGATTAAATGGTAAGTATAATGGTA
1 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTATAATGGTA
2812580 AAATAAG-TTACGAGCTTATGGGATAAATGGTAAGTATAATGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATAATGGTA
*
2812624 AAATAAGCTTACGAGCTTATGGGA-AAATGGTAAATATA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATA
2812662 TTGTATATGC
Statistics
Matches: 115, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
44 61 0.53
45 31 0.27
46 23 0.20
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATAATGGTA
Found at i:2816024 original size:49 final size:49
Alignment explanation
Indices: 2815924--2816031 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 49
2815914 AACGTCCATG
* *
2815924 TGACAATGGTGCTAATATATGATGCTGAGCAAGTAATATGTCGTCTATA
1 TGACAATGGTGCTAATATATGATACTGAGCAACTAATATGTCGTCTATA
* * * * * *
2815973 TGACAGTGGTGCTAATATATGATACTGCGCACCTAATCT-TACGTTTGTA
1 TGACAATGGTGCTAATATATGATACTGAGCAACTAATATGT-CGTCTATA
2816022 TGACAATGGT
1 TGACAATGGT
2816032 CGTTGGTACT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 1 0.02
49 48 0.98
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (49 bp):
TGACAATGGTGCTAATATATGATACTGAGCAACTAATATGTCGTCTATA
Found at i:2816110 original size:49 final size:44
Alignment explanation
Indices: 2816037--2816169 Score: 124
Period size: 44 Copynumber: 2.9 Consensus size: 44
2816027 ATGGTCGTTG
**
2816037 GTACTTATAACGTAATCTGATGTCTGTGTGATGATT-GTGCTAATATAT
1 GTACTTAGCACGTAATCTGATGTCTGTGTGATG-TTGGTGC--AT-T-T
* * *
2816085 GATACTTAGCACGTAAACTGATGTCTATATGATGTTGGTGCATTT
1 G-TACTTAGCACGTAATCTGATGTCTGTGTGATGTTGGTGCATTT
* * * *
2816130 GTACTTAGCACGTAATCTGACGTTTGTGTGAAGGTGGTGC
1 GTACTTAGCACGTAATCTGATGTCTGTGTGATGTTGGTGC
2816170 TGAAGACCAG
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
44 32 0.45
45 2 0.03
46 1 0.01
47 2 0.03
48 3 0.04
49 31 0.44
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (44 bp):
GTACTTAGCACGTAATCTGATGTCTGTGTGATGTTGGTGCATTT
Found at i:2818394 original size:18 final size:20
Alignment explanation
Indices: 2818371--2818408 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2818361 GGATTAAATA
*
2818371 TGAAT-ATG-TATATCTGTG
1 TGAATAATGTTATATATGTG
2818389 TGAATAATGTTATATATGTG
1 TGAATAATGTTATATATGTG
2818409 AAAGAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (20 bp):
TGAATAATGTTATATATGTG
Found at i:2854900 original size:45 final size:45
Alignment explanation
Indices: 2854849--2854939 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
2854839 CTCCTAACTA
2854849 AGTGTCTTGAATCTTTTGATTCATTTAAAAACTTAACACCGTCCT
1 AGTGTCTTGAATCTTTTGATTCATTTAAAAACTTAACACCGTCCT
*
2854894 AGTGTCTTGAATCTTTTGATTCATTTAATAACTTAACACCGTCCT
1 AGTGTCTTGAATCTTTTGATTCATTTAAAAACTTAACACCGTCCT
2854939 A
1 A
2854940 TGTTATTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.41
Consensus pattern (45 bp):
AGTGTCTTGAATCTTTTGATTCATTTAAAAACTTAACACCGTCCT
Found at i:2857388 original size:138 final size:139
Alignment explanation
Indices: 2857220--2857497 Score: 549
Period size: 138 Copynumber: 2.0 Consensus size: 139
2857210 CTTACAATCA
2857220 TATTAAACATGATTATCTTATATACATCAAGGCACCATCATTATAATTCATTTCATTAGTTCATA
1 TATTAAACATGATTATCTTATATACATCAAGGCACCATCATTATAATTCATTTCATTAGTTCATA
2857285 TGCATTCATATTAGCTCTTAAGCTTCATACATTTTCTTAAAAATATTATGAGATGATATA-TTAG
66 TGCATTCATATTAGCTCTTAAGCTTCATACATTTTCTTAAAAATATTATGAGATGATATATTTAG
2857349 CTCATGACC
131 CTCATGACC
2857358 TATTAAACATGATTATCTTATATACATCAAGGCACCATCATTATAATTCATTTCATTAGTTCATA
1 TATTAAACATGATTATCTTATATACATCAAGGCACCATCATTATAATTCATTTCATTAGTTCATA
2857423 TGCATTCATATTAGCTCTTAAGCTTCATACATTTTCTTAAAAATATTATGAGATGATATATTTAG
66 TGCATTCATATTAGCTCTTAAGCTTCATACATTTTCTTAAAAATATTATGAGATGATATATTTAG
2857488 CTCATGACC
131 CTCATGACC
2857497 T
1 T
2857498 TCAATCATAG
Statistics
Matches: 139, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
138 125 0.90
139 14 0.10
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.40
Consensus pattern (139 bp):
TATTAAACATGATTATCTTATATACATCAAGGCACCATCATTATAATTCATTTCATTAGTTCATA
TGCATTCATATTAGCTCTTAAGCTTCATACATTTTCTTAAAAATATTATGAGATGATATATTTAG
CTCATGACC
Found at i:2859146 original size:64 final size:64
Alignment explanation
Indices: 2859067--2859196 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
2859057 ATTTTAAATC
2859067 TGAAACAACATCTCTATTATCTAATAGTATCATAGTGTTTCGGTTGGGACATTGGCTGGCAACA
1 TGAAACAACATCTCTATTATCTAATAGTATCATAGTGTTTCGGTTGGGACATTGGCTGGCAACA
2859131 TGAAACAACATCTCTATTATCTAATAGTATCATAGTGTTTCGGTTGGGACATTGGCTGGCAACA
1 TGAAACAACATCTCTATTATCTAATAGTATCATAGTGTTTCGGTTGGGACATTGGCTGGCAACA
2859195 TG
1 TG
2859197 TCCTTTCCCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (64 bp):
TGAAACAACATCTCTATTATCTAATAGTATCATAGTGTTTCGGTTGGGACATTGGCTGGCAACA
Found at i:2863832 original size:13 final size:13
Alignment explanation
Indices: 2863810--2863839 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2863800 ACTAAACACC
2863810 TTTC-ACATACCT
1 TTTCAACATACCT
2863822 TTTCAACATACCT
1 TTTCAACATACCT
2863835 TTTCA
1 TTTCA
2863840 TCTTTGGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:2868298 original size:23 final size:23
Alignment explanation
Indices: 2868270--2868313 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2868260 TTTTCTTCTT
2868270 TTTGAGTGCTTTCAATTTCTTAA
1 TTTGAGTGCTTTCAATTTCTTAA
* * *
2868293 TTTGAGTTCTTTTATTTTCTT
1 TTTGAGTGCTTTCAATTTCTT
2868314 TGCTGGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.61
Consensus pattern (23 bp):
TTTGAGTGCTTTCAATTTCTTAA
Found at i:2870447 original size:32 final size:32
Alignment explanation
Indices: 2870386--2870452 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
2870376 ACAAAATTAA
* *
2870386 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATAAAAAT-GAAAATGGATAG
2870418 AAGAAAGGAAATGATAAGAAAT-AAAATGGATAG
1 AAGAAA-GAAATGATAA-AAATGAAAATGGATAG
2870451 AA
1 AA
2870453 ATGTTATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 13 0.43
33 13 0.43
34 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (32 bp):
AAGAAAGAAATGATAAAAATGAAAATGGATAG
Found at i:2870631 original size:35 final size:35
Alignment explanation
Indices: 2870591--2870704 Score: 151
Period size: 35 Copynumber: 3.2 Consensus size: 35
2870581 TGGTAAAGGA
* *
2870591 ATGGTGGTTATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATTATATAGGCGTGAAATGGTGATGGAAG
* *
2870626 ATGGTGATGATATAGGCGTGCAATGGTGATGGAAG
1 ATGGTGATTATATAGGCGTGAAATGGTGATGGAAG
2870661 ATGGTGATGT-TATA-GCGTGAAAAATGGTGATGGAAG
1 ATGGTGAT-TATATAGGCGTG--AAATGGTGATGGAAG
2870697 ATGGTGAT
1 ATGGTGAT
2870705 GAACAGATAG
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
34 5 0.07
35 43 0.61
36 22 0.31
ACGTcount: A:0.31, C:0.04, G:0.38, T:0.28
Consensus pattern (35 bp):
ATGGTGATTATATAGGCGTGAAATGGTGATGGAAG
Found at i:2872953 original size:44 final size:45
Alignment explanation
Indices: 2872833--2872958 Score: 173
Period size: 48 Copynumber: 2.8 Consensus size: 45
2872823 ATAAAATCCA
* *
2872833 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATAC
* *
2872878 TTACCATTTAAAATTCCATAAGCTCATAAGCTTATTTTTCCAATATAC
1 TTACCATTT---ATTCCATAAGCTCATAAGCTTATTTTACCAAAATAC
*
2872926 TTGCCA-TTATTCCATAAGCTCATAAGCTTATTT
1 TTACCATTTATTCCATAAGCTCATAAGCTTATTT
2872959 ACATTGTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
44 25 0.34
45 9 0.12
47 2 0.03
48 37 0.51
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATAC
Found at i:2880673 original size:17 final size:16
Alignment explanation
Indices: 2880642--2880677 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2880632 AACAACATAA
*
2880642 TATGTTATTTATTATT
1 TATGTTATATATTATT
2880658 TATGTTATAATATTATT
1 TATGTTAT-ATATTATT
2880675 TAT
1 TAT
2880678 TATTATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TATGTTATATATTATT
Found at i:2880699 original size:18 final size:17
Alignment explanation
Indices: 2880651--2880699 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
2880641 ATATGTTATT
*
2880651 TATTATTTATGTTATAA
1 TATTATTTATATTATAA
2880668 TATTATTTATTATTATAA
1 TATTATTTA-TATTATAA
2880686 -ATTAAATTTATATT
1 TATT--ATTTATATT
2880700 TTTGAGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 12 0.43
18 11 0.39
19 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TATTATTTATATTATAA
Found at i:2882121 original size:16 final size:16
Alignment explanation
Indices: 2882097--2882129 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2882087 GTTACTGTTT
*
2882097 ATTACTATTGAATTCC
1 ATTAATATTGAATTCC
2882113 ATTAATATTGAATTCC
1 ATTAATATTGAATTCC
2882129 A
1 A
2882130 CCTCTCAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTAATATTGAATTCC
Found at i:2883221 original size:20 final size:22
Alignment explanation
Indices: 2883175--2883221 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2883165 GATCCTCATC
2883175 CGATTCAACTTTTCTTGTAATT
1 CGATTCAACTTTTCTTGTAATT
2883197 C-ATTCAAACTTTT-TT-TAA-T
1 CGATTC-AACTTTTCTTGTAATT
2883216 CGATTC
1 CGATTC
2883222 TTTTGACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.09
20 7 0.30
21 6 0.26
22 8 0.35
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (22 bp):
CGATTCAACTTTTCTTGTAATT
Found at i:2886193 original size:30 final size:30
Alignment explanation
Indices: 2886169--2886227 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2886159 TTTGGTCCTT
*
2886169 AAACTTT-TCAAAGTTTATAATTTGGTCACC
1 AAACTTTACCAAA-TTTATAATTTGGTCACC
*
2886199 AAACTTTACCAAATTTATAATTTGATCAC
1 AAACTTTACCAAATTTATAATTTGGTCAC
2886228 TAAATGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTTGGTCACC
Found at i:2888757 original size:10 final size:10
Alignment explanation
Indices: 2888737--2888768 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
2888727 CCTCCCCTAT
2888737 TTCTT-TTCC
1 TTCTTCTTCC
2888746 TTCTTCTTCC
1 TTCTTCTTCC
2888756 TTCTTCTTCC
1 TTCTTCTTCC
2888766 TTC
1 TTC
2888769 GTTTCCCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:2889768 original size:14 final size:13
Alignment explanation
Indices: 2889738--2889840 Score: 100
Period size: 14 Copynumber: 7.5 Consensus size: 13
2889728 GATTACACCA
* *
2889738 TAAACCTAAATCT
1 TAAACCTAAACCC
2889751 TAAATCCTAAACCC
1 TAAA-CCTAAACCC
*
2889765 TAAACTCTAAACTC
1 TAAAC-CTAAACCC
2889779 TAAA-CTCAAACCC
1 TAAACCT-AAACCC
* *
2889792 CAAACCTCAAATCC
1 TAAACCT-AAACCC
2889806 TAAACACTAAACCC
1 TAAAC-CTAAACCC
2889820 TAAATCCTAAACCC
1 TAAA-CCTAAACCC
2889834 TAAACCT
1 TAAACCT
2889841 TTAATCCAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
12 2 0.03
13 16 0.21
14 55 0.72
15 3 0.04
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAACCTAAACCC
Found at i:2889838 original size:7 final size:7
Alignment explanation
Indices: 2889738--2889839 Score: 84
Period size: 7 Copynumber: 14.9 Consensus size: 7
2889728 GATTACACCA
2889738 TAAA-CC
1 TAAACCC
* *
2889744 TAAATCT
1 TAAACCC
*
2889751 TAAATCC
1 TAAACCC
2889758 TAAACCC
1 TAAACCC
*
2889765 TAAACTC
1 TAAACCC
*
2889772 TAAACTC
1 TAAACCC
*
2889779 TAAACTC
1 TAAACCC
2889786 -AAACCC
1 TAAACCC
*
2889792 CAAA-CC
1 TAAACCC
*
2889798 TCAAATCC
1 T-AAACCC
*
2889806 TAAACAC
1 TAAACCC
2889813 TAAACCC
1 TAAACCC
*
2889820 TAAATCC
1 TAAACCC
2889827 TAAACCC
1 TAAACCC
2889834 TAAACC
1 TAAACC
2889840 TTTAATCCAA
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
6 11 0.14
7 67 0.83
8 3 0.04
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:2891453 original size:19 final size:20
Alignment explanation
Indices: 2891429--2891467 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
2891419 GAAAAACTAC
2891429 GAAAGAGAAA-GGGAGAGAG
1 GAAAGAGAAATGGGAGAGAG
2891448 GAAAGAGAAATTGGGAGAGA
1 GAAAGAGAAA-TGGGAGAGA
2891468 CAAAGACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.44, T:0.05
Consensus pattern (20 bp):
GAAAGAGAAATGGGAGAGAG
Found at i:2891713 original size:30 final size:31
Alignment explanation
Indices: 2891651--2891716 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2891641 CAAACTATTG
* *
2891651 AATTTTTTTTGAGTTCGAGTCGAGTTTTAAT
1 AATTTATTTTGAGTTCGAGTCGAGTCTTAAT
*
2891682 AATTTATTTTGAGTTTGAG-CTGAG-CTTAAT
1 AATTTATTTTGAGTTCGAGTC-GAGTCTTAAT
2891712 AATTT
1 AATTT
2891717 TTAGCTCGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.26, C:0.06, G:0.18, T:0.50
Consensus pattern (31 bp):
AATTTATTTTGAGTTCGAGTCGAGTCTTAAT
Found at i:2891796 original size:27 final size:27
Alignment explanation
Indices: 2891766--2891861 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
2891756 ACAGTTTTCA
2891766 AGTTTGAGTCGAGCTCAGTAATACTCG
1 AGTTTGAGTCGAGCTCAGTAATACTCG
*
2891793 AGTTTGAGTTGAGCTCAGTAATACTCG
1 AGTTTGAGTCGAGCTCAGTAATACTCG
2891820 AGTTTGAGTCGAGCTCAGTAATACTCG
1 AGTTTGAGTCGAGCTCAGTAATACTCG
*
2891847 AGTTTGACTCG-GCTC
1 AGTTTGAGTCGAGCTC
2891862 GTTTATACCC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
26 4 0.06
27 62 0.94
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (27 bp):
AGTTTGAGTCGAGCTCAGTAATACTCG
Found at i:2894133 original size:12 final size:12
Alignment explanation
Indices: 2894111--2894136 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2894101 TATTTATTCA
2894111 TTATTTTATTTT
1 TTATTTTATTTT
2894123 TTATTTTATTTT
1 TTATTTTATTTT
2894135 TT
1 TT
2894137 TTCCATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:2894983 original size:21 final size:21
Alignment explanation
Indices: 2894957--2894997 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2894947 ACACCAAAAC
2894957 TCAACAAAACAA-TTCTTCACT
1 TCAAC-AAACAAGTTCTTCACT
2894978 TCAACAAACAAGTTCTTCAC
1 TCAACAAACAAGTTCTTCAC
2894998 CTCTTCCGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.27
Consensus pattern (21 bp):
TCAACAAACAAGTTCTTCACT
Found at i:2897972 original size:3 final size:3
Alignment explanation
Indices: 2897964--2897999 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
2897954 ATTTGTTTAT
2897964 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
2898000 TTTAGCATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2904890 original size:18 final size:18
Alignment explanation
Indices: 2904867--2904901 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2904857 AGAAAAATTC
2904867 AATTTCTTAATGAAAAAT
1 AATTTCTTAATGAAAAAT
2904885 AATTTCTTAATGAAAAA
1 AATTTCTTAATGAAAAA
2904902 GGGGGAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTTCTTAATGAAAAAT
Found at i:2904965 original size:19 final size:19
Alignment explanation
Indices: 2904941--2905018 Score: 120
Period size: 19 Copynumber: 4.0 Consensus size: 19
2904931 CAACAATTTG
2904941 TAACAATTGATATCTTTTT
1 TAACAATTGATATCTTTTT
*
2904960 TAACAATTGATATATTTTT
1 TAACAATTGATATCTTTTT
2904979 TAACAATTGATATCCTTTTGT
1 TAACAATTGATAT-CTTTT-T
*
2905000 TAACAATTGCTATCTTTTT
1 TAACAATTGATATCTTTTT
2905019 CATTAAACAT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
19 32 0.59
20 9 0.17
21 13 0.24
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (19 bp):
TAACAATTGATATCTTTTT
Found at i:2904992 original size:38 final size:40
Alignment explanation
Indices: 2904941--2905018 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
2904931 CAACAATTTG
2904941 TAACAATTGATAT-CTTTT-TTAACAATTGATATATTTTT
1 TAACAATTGATATCCTTTTGTTAACAATTGATATATTTTT
* *
2904979 TAACAATTGATATCCTTTTGTTAACAATTGCTATCTTTTT
1 TAACAATTGATATCCTTTTGTTAACAATTGATATATTTTT
2905019 CATTAAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 13 0.36
39 5 0.14
40 18 0.50
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (40 bp):
TAACAATTGATATCCTTTTGTTAACAATTGATATATTTTT
Found at i:2910858 original size:88 final size:87
Alignment explanation
Indices: 2910704--2910882 Score: 234
Period size: 88 Copynumber: 2.0 Consensus size: 87
2910694 TATATATAAC
* * ** *
2910704 TAAAATACCTCAGTATTCTAATAAGTGTATTAGAAAGATGACTTAACATCCTTCATAGAAGTTGT
1 TAAAATAACTCAGGATTCTAATAAGTGTATTAGAAAGA-GACCCAACATCCTTCATAGAAGATGT
* * *
2910769 ATAATTCTTCTCATTTACGTAGG
65 ATAATCCTCCTCACTTACGTAGG
* *
2910792 TAAAATAACTCGGGATTTTAATAAGTGTATTA-AGAAGAGAACCCAACATCCTTCATAGAAGATG
1 TAAAATAACTCAGGATTCTAATAAGTGTATTAGA-AAGAG-ACCCAACATCCTTCATAGAAGATG
2910856 TATAATCCTCCTCACTTACGTAGG
64 TATAATCCTCCTCACTTACGTAGG
2910880 TAA
1 TAA
2910883 TTTCATTAAG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
87 2 0.03
88 77 0.97
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (87 bp):
TAAAATAACTCAGGATTCTAATAAGTGTATTAGAAAGAGACCCAACATCCTTCATAGAAGATGTA
TAATCCTCCTCACTTACGTAGG
Found at i:2912341 original size:15 final size:15
Alignment explanation
Indices: 2912321--2912350 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2912311 AAATATATTA
*
2912321 ATTATAATATTAATT
1 ATTATAATAATAATT
2912336 ATTATAATAATAATT
1 ATTATAATAATAATT
2912351 TAATAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAATAATAATT
Found at i:2912476 original size:28 final size:28
Alignment explanation
Indices: 2912419--2912493 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
2912409 AATAATTGAG
2912419 ATTAT-TTTAAAATATAAACATATAAAT
1 ATTATATTTAAAATATAAACATATAAAT
*
2912446 ATTAATATTTAAACATA-AAACAT-TAATT
1 ATT-ATATTTAAA-ATATAAACATATAAAT
*
2912474 ATTATATTTTAAAAAATAAA
1 ATTATA-TTTAAAATATAAA
2912494 AAAATTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
27 8 0.20
28 18 0.44
29 12 0.29
30 3 0.07
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
ATTATATTTAAAATATAAACATATAAAT
Found at i:2912503 original size:30 final size:30
Alignment explanation
Indices: 2912421--2912503 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 30
2912411 TAATTGAGAT
* * * *
2912421 TATTTTAAAATATAAACATA-TAAATATTA
1 TATTTTAAAAAATAAAAAAATTAATTATTA
* *
2912450 -ATATTT-AAACAT-AAAACATTAATTATTA
1 TAT-TTTAAAAAATAAAAAAATTAATTATTA
2912478 TATTTTAAAAAATAAAAAAATTAATT
1 TATTTTAAAAAATAAAAAAATTAATT
2912504 TAATTTAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
27 4 0.09
28 18 0.42
29 10 0.23
30 11 0.26
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (30 bp):
TATTTTAAAAAATAAAAAAATTAATTATTA
Found at i:2913491 original size:21 final size:20
Alignment explanation
Indices: 2913463--2913501 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2913453 GTGTCGTACA
2913463 ATAAATTTGTCACAAAAGGT
1 ATAAATTTGTCACAAAAGGT
*
2913483 ATAATATTTGTGACAAAAG
1 ATAA-ATTTGTCACAAAAG
2913502 TACTCAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (20 bp):
ATAAATTTGTCACAAAAGGT
Found at i:2915022 original size:162 final size:162
Alignment explanation
Indices: 2914817--2915193 Score: 553
Period size: 162 Copynumber: 2.3 Consensus size: 162
2914807 CTTTGGGGTG
* * * * * *
2914817 CACACATAGTGCCGATACGATAGTTCACAAACCTATTATGAATTTTGTGGGTTGCACACTTAGTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGCACACTTAGTG
*
2914882 AC-AATACGGTCGTTCATAAACATATTATCAATTTCGTGGGTTGCACACTTAGTGTCGATACGGT
66 -CTAATACGGTCGTTCATAAACATATTATCAATTCCGTGGGTTGCACACTTAGTGTCGATACGGT
* *
2914946 CATTCATAAACTTATAATGAATT-C-TGCGAGTTC
130 CATTAATAAACTTATAATGAATTCCATG-G-GTTA
*
2914979 CACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGCACACTTAGTG
1 CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGCACACTTAGTG
* * *
2915044 CTGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTGCACACTTAGTGTCGTTACGGTC
66 CTAATACGGTCGTTCATAAACATATTATCAATTCCGTGGGTTGCACACTTAGTGTCGATACGGTC
* *
2915109 GTTAATAAACTTATTATGAATTCCATGGGTTA
131 ATTAATAAACTTATAATGAATTCCATGGGTTA
* *
2915141 CACACTCAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTT
1 CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTT
2915194 AAAAAATCAG
Statistics
Matches: 194, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
161 1 0.01
162 189 0.97
163 2 0.01
164 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (162 bp):
CACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGCACACTTAGTG
CTAATACGGTCGTTCATAAACATATTATCAATTCCGTGGGTTGCACACTTAGTGTCGATACGGTC
ATTAATAAACTTATAATGAATTCCATGGGTTA
Found at i:2915206 original size:54 final size:54
Alignment explanation
Indices: 2914797--2915193 Score: 492
Period size: 54 Copynumber: 7.4 Consensus size: 54
2914787 TTTTCATAAC
* * * * * * *
2914797 ATTAT-AAGTTCTTTGGGGTGCACACATAGTGCCGATACGATAGTTCACAAACCT
1 ATTATGAA-TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * * *
2914851 ATTATGAATTTTGTGGGTTGCACACTTAGTGACAATACGGTCGTTCATAAACAT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * *
2914905 ATTATCAATT-TCGTGGGTTGCACACTTAGTGTCGATACGGTCATTCATAAACTT
1 ATTATGAATTCT-GTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * * * *
2914959 ATAATGAATTCTGCGAGTTCCACACTTAGTGTCGATACGGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * *
2915013 ATTATGAATTATGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCATAAACAT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * * *
2915067 ATTATGAATTCCGTGGGTTGCACACTTAGTGTCGTTACGGTCGTTAATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
** * *
2915121 ATTATGAATTCCATGGGTTACACACTCAGTGCCGATACGGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
2915175 ATTATGAATTCTGTGGGTT
1 ATTATGAATTCTGTGGGTT
2915194 AAAAAATCAG
Statistics
Matches: 296, Mismatches: 44, Indels: 6
0.86 0.13 0.02
Matches are distributed among these distances:
53 1 0.00
54 292 0.99
55 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (54 bp):
ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
Done.