Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009628.1 Hibiscus syriacus cultivar Beakdansim tig00117021_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: 2284295
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:2176859 original size:12 final size:12
Alignment explanation
Indices: 2176842--2176878 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
2176832 TCTTCGGGGA
2176842 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2176854 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2176866 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2176878 C
1 C
2176879 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2177916 original size:20 final size:21
Alignment explanation
Indices: 2177891--2177942 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2177881 TTTTCCTAAT
*
2177891 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
2177911 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2177932 TCGCAATGCGA
1 TCGCAATGCGA
2177943 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2178018 original size:20 final size:20
Alignment explanation
Indices: 2177927--2178018 Score: 58
Period size: 20 Copynumber: 4.5 Consensus size: 20
2177917 TGCGAATTTG
* *
2177927 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
2177947 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* * *
2177967 ACAAAATCACAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** * *
2177988 GACTTTTGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
2178008 GAAAATCGCAA
1 GAAAATCGCAA
2178019 TCATCTTCAA
Statistics
Matches: 50, Mismatches: 21, Indels: 2
0.68 0.29 0.03
Matches are distributed among these distances:
20 36 0.72
21 14 0.28
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:2178256 original size:20 final size:20
Alignment explanation
Indices: 2178231--2178298 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
2178221 CAACGGGGAA
2178231 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
2178251 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
2178271 ATCGCAGCGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
2178291 ATCGCAAC
1 ATCGCAAC
2178299 TAGAAAATCG
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
19 5 0.15
20 24 0.71
21 5 0.15
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:2178515 original size:14 final size:14
Alignment explanation
Indices: 2178496--2178532 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2178486 CATCAATTAA
2178496 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2178510 ACAAATCATCTTTT
1 ACAAATCAACATTT
2178524 ACAAATCAA
1 ACAAATCAA
2178533 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2180422 original size:20 final size:19
Alignment explanation
Indices: 2180399--2180466 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
2180389 GAAACTTAAA
2180399 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
2180419 ATCGCAACGTGGAAATGGCT
1 ATCGCAACG-CGAAATGACT
* **
2180439 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
2180458 ATCGCAACG
1 ATCGCAACG
2180467 ATAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:2180474 original size:14 final size:14
Alignment explanation
Indices: 2180455--2180545 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
2180445 ATGCGAAATG
2180455 AAAATCGCAACGAT
1 AAAATCGCAACGAT
2180469 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
*
2180487 GAAAATCGCAACGAC
1 -AAAATCGCAACGAT
2180502 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
* *
2180520 GAAATCGCAACGAC
1 AAAATCGCAACGAT
2180534 AAAATCGCAACG
1 AAAATCGCAACG
2180546 CGAAACACAA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 32 0.51
15 1 0.02
16 6 0.10
17 2 0.03
18 12 0.19
19 10 0.16
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:2180530 original size:32 final size:33
Alignment explanation
Indices: 2180439--2180550 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
2180429 GGAAATGGCT
*
2180439 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2180472 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2180505 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2180537 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2180551 CACAAATCGC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 29 0.38
33 48 0.62
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2180558 original size:65 final size:66
Alignment explanation
Indices: 2180439--2180561 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 66
2180429 GGAAATGGCT
* * *
2180439 ATCGCAATGCGAAATGAAAATCGCAACGATAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
2180504 A
66 A
2180505 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
2180562 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 1 0.02
65 36 0.68
66 16 0.30
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:2180592 original size:18 final size:18
Alignment explanation
Indices: 2180557--2180656 Score: 127
Period size: 18 Copynumber: 5.7 Consensus size: 18
2180547 GAAACACAAA
2180557 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
2180576 TCGCGTTGCGATTTCATT
1 TCGCATTGCGATTTCATT
2180594 TCGCATTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
2180612 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
2180628 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
2180645 TCCCATTGCGAT
1 TCGCATTGCGAT
2180657 AGCCATTTCC
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 4 0.06
17 3 0.04
18 39 0.55
19 16 0.23
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:2180693 original size:20 final size:20
Alignment explanation
Indices: 2180641--2180684 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2180631 TTGCGATTTT
*
2180641 CATTTCC-CATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
2180660 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
2180680 CATTT
1 CATTT
2180685 TCGTGTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:2181203 original size:18 final size:18
Alignment explanation
Indices: 2181177--2181222 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2181167 GTCGATCAGA
*
2181177 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
2181195 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2181213 TGATGGCTCT
1 TGATGGCTCT
2181223 CGAAGTGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.43, T:0.28
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:2182874 original size:22 final size:22
Alignment explanation
Indices: 2182847--2182890 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2182837 GATGGAGATA
2182847 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2182869 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2182891 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2183164 original size:20 final size:20
Alignment explanation
Indices: 2183058--2183192 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
2183048 TGCTTTGAAA
*
2183058 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
2183079 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
2183099 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
2183119 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
2183140 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
2183160 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2183180 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2183193 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2183164 original size:61 final size:61
Alignment explanation
Indices: 2183058--2183195 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
2183048 TGCTTTGAAA
* * * *
2183058 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
2183119 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
2183180 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
2183196 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:2183211 original size:61 final size:61
Alignment explanation
Indices: 2183058--2183213 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
2183048 TGCTTTGAAA
* ** * * * *
2183058 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
2183119 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
2183180 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
2183214 TTACTTATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:2183303 original size:21 final size:21
Alignment explanation
Indices: 2183263--2183303 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2183253 ACTGTAGACC
** *
2183263 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
2183284 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
2183304 GCGAATTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:2187437 original size:43 final size:43
Alignment explanation
Indices: 2187376--2187461 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
2187366 TTGAAATTGT
2187376 AAAATAATCACAATTACAGCATTGCAGCCAGCCTAATTTTACA
1 AAAATAATCACAATTACAGCATTGCAGCCAGCCTAATTTTACA
2187419 AAAATAATCACAATTACAGCATTGCAGCCAGCCTAATTTTACA
1 AAAATAATCACAATTACAGCATTGCAGCCAGCCTAATTTTACA
2187462 TTCCAATCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (43 bp):
AAAATAATCACAATTACAGCATTGCAGCCAGCCTAATTTTACA
Found at i:2189365 original size:26 final size:26
Alignment explanation
Indices: 2189310--2189367 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
2189300 TTGAGAGAAC
* *
2189310 TTATTTATTATAAAAAAATTAAAATT
1 TTATTTATAATAAAAAAATTAAAATA
2189336 TTATTTA-AATAAAAAAATATAAACA-A
1 TTATTTATAATAAAAAAAT-TAAA-ATA
2189362 TTATTT
1 TTATTT
2189368 GGTTATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 10 0.36
26 17 0.61
27 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TTATTTATAATAAAAAAATTAAAATA
Found at i:2189977 original size:2 final size:2
Alignment explanation
Indices: 2189970--2190017 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2189960 TGTTTTACCC
2189970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2190012 AT AT AT
1 AT AT AT
2190018 CATTTTCAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2194472 original size:30 final size:33
Alignment explanation
Indices: 2194436--2194510 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 33
2194426 AAGTAATATA
2194436 TTAGCCCA-C-CTTCTTCC-TTTTTAACAGATT
1 TTAGCCCATCTCTTCTTCCTTTTTTAACAGATT
*
2194466 TTAGCCCATCTTCTTCTTCCTTTTTTAATAGATT
1 TTAGCCCATC-TCTTCTTCCTTTTTTAACAGATT
*
2194500 TTAGCCTATCT
1 TTAGCCCATCT
2194511 TCTCGAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 8 0.21
31 1 0.03
33 9 0.23
34 21 0.54
ACGTcount: A:0.19, C:0.27, G:0.07, T:0.48
Consensus pattern (33 bp):
TTAGCCCATCTCTTCTTCCTTTTTTAACAGATT
Found at i:2194487 original size:33 final size:34
Alignment explanation
Indices: 2194445--2194513 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
2194435 ATTAGCCCAC
2194445 CTTCTTCC-TTTTTAACAGATTTTAGCCCATCTT
1 CTTCTTCCTTTTTTAACAGATTTTAGCCCATCTT
* *
2194478 CTTCTTCCTTTTTTAATAGATTTTAGCCTATCTT
1 CTTCTTCCTTTTTTAACAGATTTTAGCCCATCTT
2194512 CT
1 CT
2194514 CGAATAAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.17, C:0.25, G:0.06, T:0.52
Consensus pattern (34 bp):
CTTCTTCCTTTTTTAACAGATTTTAGCCCATCTT
Found at i:2200290 original size:15 final size:15
Alignment explanation
Indices: 2200267--2200296 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2200257 ATTACTTGAT
2200267 GAGAGGGAGCAGGCC
1 GAGAGGGAGCAGGCC
*
2200282 GAGATGGAGCAGGCC
1 GAGAGGGAGCAGGCC
2200297 AGAAGCACAA
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:0.27, C:0.20, G:0.50, T:0.03
Consensus pattern (15 bp):
GAGAGGGAGCAGGCC
Found at i:2203194 original size:23 final size:23
Alignment explanation
Indices: 2203168--2203212 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2203158 CACCACAGCT
*
2203168 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
2203191 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2203213 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:2205058 original size:21 final size:21
Alignment explanation
Indices: 2205016--2205060 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2205006 TTTTGTTCGT
* * *
2205016 TTGAAGGGGTATCGGTTTCCC
1 TTGAAGGGGTACCGATTCCCC
*
2205037 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2205058 TTG
1 TTG
2205061 CCCATAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2208351 original size:23 final size:23
Alignment explanation
Indices: 2208325--2208369 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2208315 CACCACAGCT
*
2208325 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
2208348 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2208370 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:2208511 original size:25 final size:26
Alignment explanation
Indices: 2208475--2208525 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
2208465 TCCAAAGAAT
2208475 ATATATATCCCGAAGGACCGCGTAGA
1 ATATATATCCCGAAGGACCGCGTAGA
2208501 ATAT-TATCCCGAAGGACCGCGTAGA
1 ATATATATCCCGAAGGACCGCGTAGA
2208526 CCCTCTACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (26 bp):
ATATATATCCCGAAGGACCGCGTAGA
Found at i:2210173 original size:21 final size:21
Alignment explanation
Indices: 2210149--2210193 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2210139 TTTTGTTCGT
* *
2210149 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2210170 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2210191 TTG
1 TTG
2210194 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2212076 original size:279 final size:277
Alignment explanation
Indices: 2211571--2212129 Score: 893
Period size: 278 Copynumber: 2.0 Consensus size: 277
2211561 GGAAGTTATG
*
2211571 CAAACTTGGCCGAAGCCTAAAACCCTTAAATCTCTTAAGGGTTCTAGGTCTAACAGGTTATTACA
1 CAAACTTGGCCGAAGCCTAAAACCCTTAAATCTCTAAAGGGTTCTAGGTCTAACAGGTTATTACA
* *
2211636 GAAGATTTATTCGAAATTGTGGCATTCTTAGCAGACCATTGACATTACTATTAAAGAAGGTGGCT
66 GAAGATTTATTCAAAATTATGGCATTCTTAGCAGACCATTGACATTA-TATTAAAGAAGGTGGCT
*
2211701 TCCAATGGAATTCTGCTGCTCATACTGCTTTGAAAATCTTAAGAAACTGTGTGTTCTGCTCCATT
130 TCCAATGGAATTATGCTGCTCA-ACTGCTTTGAAAATCTTAAGAAAC-GTGTGTTCTGCTCCATT
2211766 TTAGCACTGCCTGATTTTTCTAAGATTTTTTTTCT-GAAACAGATGCTAGTTCT-GGGGTATTGG
193 TTAG-ACTGCCTGATTTTTCTAAGATTTTTTTTCTGGAAAC--ATGCTAGTTCTGGGGGTATTGG
2211829 GGTTGTTCTTTCACATGAAAGAA
255 GGTTGTTCTTTCACATGAAAGAA
2211852 CAAACTTGGCCGAAGCCT-AAA-CCTTAAATCTCTCAAAGGGTTTCTAGGTCTAACAGGTTTATT
1 CAAACTTGGCCGAAGCCTAAAACCCTTAAATCTCT-AAAGGG-TTCTAGGTCTAACAGG-TTATT
2211915 ACAGAAGATTTATTCAAAATTATGGCATTCTTAGCAGACCATTGACA-T-TATTAAAGAAGGATG
63 ACAGAAGATTTATTCAAAATTATGGCATTCTTAGCAGACCATTGACATTATATTAAAGAAGG-TG
2211978 GCTTCCAATGGAATTATGCTGCTC-ACTGCATTTGAAAATCTTAAGAAAAC-TGTGTTCTGCTCC
127 GCTTCCAATGGAATTATGCTGCTCAACTGC-TTTGAAAATCTTAAG-AAACGTGTGTTCTGCTCC
2212041 AGTTTTAG-CTGCCTGATTTTTCTAAGAATTTTTTTTCTGGAAACATGCTAGTTCTGGGGGTATT
190 A-TTTTAGACTGCCTGATTTTTCTAAG-ATTTTTTTTCTGGAAACATGCTAGTTCTGGGGGTATT
2212105 GGGGTTGTTCTTTCACATGAAAGAA
253 GGGGTTGTTCTTTCACATGAAAGAA
2212130 GACCAATTGA
Statistics
Matches: 264, Mismatches: 4, Indels: 23
0.91 0.01 0.08
Matches are distributed among these distances:
277 29 0.11
278 63 0.24
279 50 0.19
280 37 0.14
281 35 0.13
282 50 0.19
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (277 bp):
CAAACTTGGCCGAAGCCTAAAACCCTTAAATCTCTAAAGGGTTCTAGGTCTAACAGGTTATTACA
GAAGATTTATTCAAAATTATGGCATTCTTAGCAGACCATTGACATTATATTAAAGAAGGTGGCTT
CCAATGGAATTATGCTGCTCAACTGCTTTGAAAATCTTAAGAAACGTGTGTTCTGCTCCATTTTA
GACTGCCTGATTTTTCTAAGATTTTTTTTCTGGAAACATGCTAGTTCTGGGGGTATTGGGGTTGT
TCTTTCACATGAAAGAA
Found at i:2225108 original size:21 final size:22
Alignment explanation
Indices: 2225076--2225252 Score: 158
Period size: 20 Copynumber: 8.5 Consensus size: 22
2225066 CATTTAAATC
*
2225076 TATTTT-AAATATAGA-TGATT
1 TATTTTAAAATATGGATTGATT
*
2225096 TATTTTAAAATATGAATTG-TT
1 TATTTTAAAATATGGATTGATT
*
2225117 TA-TTTAAAATA-GAATTGATT
1 TATTTTAAAATATGGATTGATT
* **
2225137 TATTTTAAAAATATGGA--AAAA
1 TATTTT-AAAATATGGATTGATT
2225158 TATTTTAAAATATGGATTGA-T
1 TATTTTAAAATATGGATTGATT
* ***
2225179 T-TTTTAAAATATGAAAAAATT
1 TATTTTAAAATATGGATTGATT
*
2225200 TATTTTAAAATATGGATTTATT
1 TATTTTAAAATATGGATTGATT
* *
2225222 TATTTT-ACATATGGCTTGATT
1 TATTTTAAAATATGGATTGATT
2225243 TATTTTAAAA
1 TATTTTAAAA
2225253 ATTTATTATT
Statistics
Matches: 126, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
19 6 0.05
20 43 0.34
21 42 0.33
22 33 0.26
23 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (22 bp):
TATTTTAAAATATGGATTGATT
Found at i:2225165 original size:42 final size:42
Alignment explanation
Indices: 2225076--2225228 Score: 156
Period size: 42 Copynumber: 3.7 Consensus size: 42
2225066 CATTTAAATC
* ***
2225076 TATTTT-AAATATAGA-TGATTTATTTTAAAATAT-GAATTG
1 TATTTTAAAATATGGATTGATTTATTTTAAAATATGGAAAAA
* *
2225115 TTTATTTAAAATA-GAATTGATTTATTTTAAAAATATGGAAAAA
1 TAT-TTTAAAATATGGATTGATTTATTTT-AAAATATGGAAAAA
*
2225158 TATTTTAAAATATGGATTGA-TT-TTTTAAAATATGAAAAAA
1 TATTTTAAAATATGGATTGATTTATTTTAAAATATGGAAAAA
*
2225198 TTTATTTTAAAATATGGATTTATTTATTTTA
1 --TATTTTAAAATATGGATTGATTTATTTTA
2225229 CATATGGCTT
Statistics
Matches: 94, Mismatches: 10, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
39 2 0.02
40 17 0.18
41 20 0.21
42 37 0.39
43 13 0.14
44 5 0.05
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (42 bp):
TATTTTAAAATATGGATTGATTTATTTTAAAATATGGAAAAA
Found at i:2225185 original size:62 final size:62
Alignment explanation
Indices: 2225096--2225215 Score: 172
Period size: 62 Copynumber: 1.9 Consensus size: 62
2225086 ATAGATGATT
***
2225096 TATTTTAAAATATGAATTGTTTATTTAAAATA-GAATTGATTTATTTTAAAAATATGGAAAAA
1 TATTTTAAAATATGAATTGTTTATTTAAAATATGAAAAAATTTATTTT-AAAATATGGAAAAA
*
2225158 TATTTTAAAATATGGATTGATTT-TTTAAAATATGAAAAAATTTATTTTAAAATATGGA
1 TATTTTAAAATATGAATTG-TTTATTTAAAATATGAAAAAATTTATTTTAAAATATGGA
2225216 TTTATTTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
62 37 0.71
63 15 0.29
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (62 bp):
TATTTTAAAATATGAATTGTTTATTTAAAATATGAAAAAATTTATTTTAAAATATGGAAAAA
Found at i:2226010 original size:20 final size:20
Alignment explanation
Indices: 2225963--2226019 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
2225953 ATTGCGATTT
*
2225963 TCAAGAATCGCAACGCGAATA
1 TCAA-AATCGCAACGCGAACA
*
2225984 TGAAAATCGCAACGCGAACA
1 TCAAAATCGCAACGCGAACA
*
2226004 -CATAAATCACAACGCG
1 TCA-AAATCGCAACGCG
2226020 TATCCGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 27 0.87
21 3 0.10
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.12
Consensus pattern (20 bp):
TCAAAATCGCAACGCGAACA
Found at i:2226029 original size:20 final size:20
Alignment explanation
Indices: 2226006--2226215 Score: 228
Period size: 20 Copynumber: 10.6 Consensus size: 20
2225996 CGCGAACACA
* *
2226006 TAAATCACAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
2226026 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
2226046 TAAATAGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
2226066 TAAATCGCAATGTGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
2226086 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
2226106 TAAATCGCAACGA-TAATCCG
1 TAAATCGCAACGAGT-ATCCG
* *
2226126 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGAGTATCCG
* *
2226146 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGAGTATCCG
2226166 TAAATCGCAACGA-TAATCCG
1 TAAATCGCAACGAGT-ATCCG
* *
2226186 T-AATCGCAACGAGAATCTG
1 TAAATCGCAACGAGTATCCG
*
2226205 TAAATCACAAC
1 TAAATCGCAAC
2226216 ACTGAAATTT
Statistics
Matches: 164, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.10
20 147 0.90
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGAGTATCCG
Found at i:2226178 original size:60 final size:60
Alignment explanation
Indices: 2225968--2226215 Score: 241
Period size: 60 Copynumber: 4.2 Consensus size: 60
2225958 GATTTTCAAG
** * ** * * * *
2225968 AATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACATAAATCACAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGATAATC-CGTAAATCGCAACGAGAATCCGTA
* * * * * * * *
2226028 AACCGCAACGTGTATCCGTAAATAGCAACGCGT-ATCCGTAAATCGCAATGTGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCCGTA
* * *
2226088 TATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTA
* * *
2226148 AATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT-AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTA
*
2226207 AATCACAAC
1 AATCGCAAC
2226216 ACTGAAATTT
Statistics
Matches: 158, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
59 29 0.18
60 128 0.81
61 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCCGTA
Found at i:2226940 original size:24 final size:24
Alignment explanation
Indices: 2226901--2226947 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2226891 AAATTTGGTC
2226901 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2226925 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2226948 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2229517 original size:72 final size:71
Alignment explanation
Indices: 2229423--2229656 Score: 266
Period size: 72 Copynumber: 3.3 Consensus size: 71
2229413 GCAACGAGAG
*
2229423 AATCGCAATGCAAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAA-GCG
2229488 AAATGAA
65 AAATGAA
* * * *
2229495 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGGAAATGAAAATCGCAAAGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGC-AAGCG
2229560 AAATGAA
65 AAATGAA
* * * * * *
2229567 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA-C
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAAGC
*
2229628 G--A-GAG
64 GAAATGAA
2229633 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
2229657 GCAATGCGAA
Statistics
Matches: 137, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
70 2 0.01
71 14 0.10
72 87 0.64
73 10 0.07
74 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAAGCGA
AATGAA
Found at i:2229538 original size:105 final size:104
Alignment explanation
Indices: 2229409--2229678 Score: 388
Period size: 105 Copynumber: 2.6 Consensus size: 104
2229399 CGGAAATTAC
* *
2229409 AATCGCAACGAGAGAATCGCAATGC-AAAATGAAAATC-CCAA-C-AA-GAAAATCGCAATGCGG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAAAGCAAATGAAAATCGCAA--C-G
2229469 AAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 --A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2229514 AATCGCAACGAGAGAATCACAATGCGGAAATGAAAATCGCAAAGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAAAGC-AAATGAAAATCGCAACGAG
*
2229579 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
65 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2229619 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAAAGC-AAATGAAAATCGCA
2229679 TTGCGATTCT
Statistics
Matches: 153, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
105 122 0.80
106 12 0.08
107 3 0.02
108 2 0.01
109 1 0.01
110 2 0.01
111 11 0.07
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (104 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAAAGCAAATGAAAATCGCAACGAGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2229544 original size:53 final size:52
Alignment explanation
Indices: 2229409--2229678 Score: 388
Period size: 53 Copynumber: 5.1 Consensus size: 52
2229399 CGGAAATTAC
* *
2229409 AATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
2229456 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
2229514 AATCGCAACGAGAGAATCACAATGCGGAAATGAAAATCGCAAAGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
2229567 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
2229619 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
2229672 AATCGCA
1 AATCGCA
2229679 TTGCGATTCT
Statistics
Matches: 202, Mismatches: 8, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 64 0.32
53 112 0.55
55 2 0.01
56 1 0.00
57 2 0.01
58 11 0.05
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:2229683 original size:19 final size:19
Alignment explanation
Indices: 2229423--2229684 Score: 285
Period size: 19 Copynumber: 14.7 Consensus size: 19
2229413 GCAACGAGAG
*
2229423 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
*
2229442 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
2229456 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
2229476 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2229495 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2229514 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
2229528 AATCACAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
2229548 AATCGCAAAGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2229567 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2229581 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2229600 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2229619 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2229633 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
2229653 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2229672 AATCGCATTGCGA
1 AATCGCAATGCGA
2229685 TTCTCTCGTT
Statistics
Matches: 208, Mismatches: 12, Indels: 46
0.78 0.05 0.17
Matches are distributed among these distances:
14 39 0.19
15 5 0.02
16 5 0.02
17 9 0.04
18 1 0.00
19 111 0.53
20 38 0.18
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2229684 original size:72 final size:68
Alignment explanation
Indices: 2229390--2229683 Score: 258
Period size: 72 Copynumber: 4.2 Consensus size: 68
2229380 GCATTTGACT
** * * * *
2229390 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCCCAAC-AAG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
2229454 AAA
66 AAA
*
2229457 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
2229522 CG-AGAGA
61 CGAAGAAA
* * * * * *
2229529 ATCACAATGCGGAAATGAAAATCGCAAAGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
2229591 CGAAATGAAA
61 CG-AA-GAAA
2229601 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
2229665 AAATGAAA
63 -AA-GAAA
*
2229673 ATCGCATTGCG
1 ATCGCAATGCG
2229684 ATTCTCTCGT
Statistics
Matches: 186, Mismatches: 22, Indels: 32
0.77 0.09 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 33 0.18
69 4 0.02
70 1 0.01
71 21 0.11
72 105 0.56
73 3 0.02
74 5 0.03
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (68 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
AAA
Found at i:2229718 original size:53 final size:52
Alignment explanation
Indices: 2229655--2229770 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
2229645 GAAATGAAAA
*
2229655 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
2229707 TCCGCATTGCGACTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
2229760 TCGCATTGCGA
1 TCGCATTGCGA
2229771 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2229733 original size:19 final size:19
Alignment explanation
Indices: 2229693--2229780 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
2229683 GATTCTCTCG
2229693 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
2229713 TTGCGACTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2229732 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2229746 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2229765 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2229781 AACATAATGC
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 7 0.12
19 26 0.43
20 14 0.23
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2229887 original size:14 final size:14
Alignment explanation
Indices: 2229870--2229906 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2229860 CATCAATTAC
2229870 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2229884 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2229898 ACAAATCAA
1 ACAAATCAA
2229907 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2231328 original size:21 final size:21
Alignment explanation
Indices: 2231298--2231360 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
2231288 GTGAATCGGG
2231298 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
* * ** *
2231319 CTCTTCAATGATGACAGTGAC
1 CTCTTGAATGGTGGGAGGGAC
*
2231340 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
2231361 TCTCGAGGAA
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGAC
Found at i:2231871 original size:37 final size:37
Alignment explanation
Indices: 2231828--2231912 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
2231818 CACGAACTTA
*
2231828 AAATCGCAACGCGAAATG-AGAATCGCAACGAGAAACC
1 AAATCGCAACGCGAAA-GCAAAATCGCAACGAGAAACC
* **
2231865 AAATCGCAACGCGAAAGCAAAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAAGCAAAATCGCAACGAGAAACC
2231902 AAATCGCAACG
1 AAATCGCAACG
2231913 ACAGAATCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 1 0.02
37 42 0.98
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.08
Consensus pattern (37 bp):
AAATCGCAACGCGAAAGCAAAATCGCAACGAGAAACC
Found at i:2231922 original size:14 final size:14
Alignment explanation
Indices: 2231903--2231959 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2231893 CGCGAAATGA
*
2231903 AATCGCAACGACAG
1 AATCGCAACGAAAG
2231917 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
2231934 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
2231950 AATCGCAACG
1 AATCGCAACG
2231960 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2231939 original size:51 final size:54
Alignment explanation
Indices: 2231827--2231945 Score: 158
Period size: 51 Copynumber: 2.2 Consensus size: 54
2231817 ACACGAACTT
2231827 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAATCGCAACGCGAAAGC
1 AAAATCGCAACGCGAAATGAGAATCGCAAC-AG-AACCAAATCGCAACGCGAAAGC
*
2231883 AAAATCGCAACGCGAAATGA-AATCGCAAC-G-A-CAGAATCGCAATGCGAAATG-
1 AAAATCGCAACGCGAAATGAGAATCGCAACAGAACCA-AATCGCAACGCGAAA-GC
2231934 AAAATCGCAACG
1 AAAATCGCAACG
2231946 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
50 2 0.03
51 27 0.45
52 1 0.02
53 1 0.02
55 9 0.15
56 20 0.33
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.09
Consensus pattern (54 bp):
AAAATCGCAACGCGAAATGAGAATCGCAACAGAACCAAATCGCAACGCGAAAGC
Found at i:2231944 original size:33 final size:33
Alignment explanation
Indices: 2231885--2231976 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
2231875 GCGAAAGCAA
2231885 AATCGCAACGCGAAATG-AAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
2231917 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
2231950 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2231977 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 16 0.29
33 40 0.71
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:2231981 original size:19 final size:18
Alignment explanation
Indices: 2231827--2231981 Score: 130
Period size: 19 Copynumber: 8.8 Consensus size: 18
2231817 ACACGAACTT
2231827 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAA-G
* * *
2231846 AGAATCGCAACGAGAAAC
1 AAAATCGCAACGCGAAAG
*
2231864 CAAATCGCAACGCGAAAG
1 AAAATCGCAACGCGAAAG
2231882 CAAAATCGCAACGCGAAATG
1 -AAAATCGCAACGCGAAA-G
*
2231902 -AAATCGCAA--CGACAG
1 AAAATCGCAACGCGAAAG
*
2231917 --AATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAA-G
2231934 AAAATCGCAA--CG--AG
1 AAAATCGCAACGCGAAAG
*
2231948 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAA-G
*
2231967 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
2231982 TTTTGGTTTC
Statistics
Matches: 111, Mismatches: 13, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
14 18 0.16
15 2 0.02
16 10 0.09
17 3 0.03
18 24 0.22
19 53 0.48
20 1 0.01
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.10
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAG
Found at i:2232012 original size:14 final size:14
Alignment explanation
Indices: 2231993--2232051 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2231983 TTTGGTTTCG
2231993 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
2232007 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
2232024 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
2232040 CGTTGCGATTTT
1 CGTTGCGATTTT
2232052 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2232019 original size:33 final size:33
Alignment explanation
Indices: 2231977--2232100 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
2231967 AAAATCGCAA
*
2231977 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
2232010 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
2232043 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
2232076 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
2232101 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2232031 original size:19 final size:18
Alignment explanation
Indices: 2231977--2232068 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
2231967 AAAATCGCAA
2231977 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2231996 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
2232010 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
2232029 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
2232043 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
2232062 TGCGATT
1 TGCGATT
2232069 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:2232078 original size:14 final size:14
Alignment explanation
Indices: 2232026--2232082 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2232016 TTTGGTTTCG
*
2232026 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
2232040 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2232059 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2232073 CGTTGCGATT
1 CGTTGCGATT
2232083 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2232478 original size:94 final size:93
Alignment explanation
Indices: 2232197--2232510 Score: 580
Period size: 94 Copynumber: 3.4 Consensus size: 93
2232187 TCAGGGTATT
2232197 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAAC-AAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2232260 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
2232288 AGTTTAGCAGAATTGGCAGCAACCGAAC-AATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
2232352 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
2232380 AGTTTAGTAGAATTGGCAGCAACCGAACAAATTTACTTTCAAACCAAAAGACAAAACAAAGACAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTC-AACCAAAAGACAAAACAAAGACAA
2232445 ATACTATTTCACAGTGTTAAAGAATACAC
65 ATACTATTTCACAGTGTTAAAGAATACAC
*
2232474 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
2232511 AAGCAATCTA
Statistics
Matches: 216, Mismatches: 3, Indels: 5
0.96 0.01 0.02
Matches are distributed among these distances:
90 22 0.10
91 32 0.15
92 63 0.29
93 11 0.05
94 88 0.41
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.23
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:2234217 original size:20 final size:20
Alignment explanation
Indices: 2234186--2234247 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
2234176 TTTTGGTTGA
2234186 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
2234206 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2234226 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
2234247 A
1 A
2234248 TCGCAATGCG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.47, C:0.16, G:0.26, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2234238 original size:21 final size:21
Alignment explanation
Indices: 2234184--2234247 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
2234174 TCTTTTGGTT
2234184 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
2234205 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2234225 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
2234246 GA
1 GA
2234248 TCGCAATGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.47, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:2234271 original size:19 final size:19
Alignment explanation
Indices: 2234247--2234296 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
2234237 GCAACGAGAG
2234247 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2234266 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2234285 ATCGCAATGCGA
1 ATCGCAATGCGA
2234297 TTTTGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2234344 original size:21 final size:21
Alignment explanation
Indices: 2234319--2234390 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
2234309 GTTGCGATTC
2234319 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
2234340 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
2234361 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
2234382 TCTCGTTGC
1 TCTCGTTGC
2234391 AACTCTTCTG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 6 0.14
21 30 0.71
22 6 0.14
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.49
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:2234514 original size:33 final size:33
Alignment explanation
Indices: 2234472--2234542 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2234462 AATACTAACT
2234472 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
2234505 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
2234538 TGAAA
1 TGAAA
2234543 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:2234947 original size:20 final size:20
Alignment explanation
Indices: 2234922--2235114 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
2234912 CTTTAAAAAT
2234922 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2234942 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2234962 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
2234983 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2235003 CGCATTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
2235023 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2235043 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2235063 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2235083 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2235103 CGCGTTGCGATT
1 CGCGTTGCGATT
2235115 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2247043 original size:17 final size:17
Alignment explanation
Indices: 2247016--2247054 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
2247006 AACGTCCTTT
2247016 AAAATATTTTTAAGA-A
1 AAAATATTTTTAAGACA
2247032 AAAATCATTTTTAAGACA
1 AAAAT-ATTTTTAAGACA
2247050 AAAAT
1 AAAAT
2247055 TGGTTTGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 10 0.48
18 6 0.29
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (17 bp):
AAAATATTTTTAAGACA
Found at i:2249254 original size:17 final size:17
Alignment explanation
Indices: 2249232--2249275 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
2249222 AAAATGTAGT
*
2249232 AATAATACTATTAATAA
1 AATAATAATATTAATAA
*
2249249 AATAATAATATTAATAGT
1 AATAATAATATTAATA-A
2249267 AATAATAAT
1 AATAATAAT
2249276 TAAAACACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AATAATAATATTAATAA
Found at i:2249614 original size:30 final size:31
Alignment explanation
Indices: 2249578--2249643 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
2249568 TTTTGGCTCT
2249578 AACGTCTTATTTTAGGAT-AAAATAGTCTCC
1 AACGTCTTATTTTAGGATAAAAATAGTCTCC
*
2249608 AACGTCTTATTTTAGGATAAAAATAGTCTCT
1 AACGTCTTATTTTAGGATAAAAATAGTCTCC
2249639 AACGT
1 AACGT
2249644 TTGATCTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (31 bp):
AACGTCTTATTTTAGGATAAAAATAGTCTCC
Found at i:2252020 original size:13 final size:14
Alignment explanation
Indices: 2252002--2252031 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2251992 CGCCTTTTTC
2252002 AAATTTTCCT-GGA
1 AAATTTTCCTGGGA
2252015 AAATTTTCCTGGGA
1 AAATTTTCCTGGGA
2252029 AAA
1 AAA
2252032 ATTAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (14 bp):
AAATTTTCCTGGGA
Found at i:2254392 original size:17 final size:16
Alignment explanation
Indices: 2254342--2254399 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 16
2254332 AACTCTAAGA
2254342 AAAATATAATAACTAAAT
1 AAAATATAATAACT--AT
2254360 AAAATATAAGTAACTAT
1 AAAATATAA-TAACTAT
*
2254377 AGAAATAGAATAACTAT
1 A-AAATATAATAACTAT
2254394 AAAATA
1 AAAATA
2254400 AAAAAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 5 0.14
17 11 0.30
18 16 0.43
19 5 0.14
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (16 bp):
AAAATATAATAACTAT
Found at i:2254684 original size:19 final size:19
Alignment explanation
Indices: 2254660--2254701 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
2254650 ATATCCTGTC
* *
2254660 AATAAAATATTATTTTAAA
1 AATAAAAGATTAATTTAAA
2254679 AAT-AAAGATTAATTTAAA
1 AATAAAAGATTAATTTAAA
2254697 AATAA
1 AATAA
2254702 TTTTCATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AATAAAAGATTAATTTAAA
Found at i:2257934 original size:24 final size:24
Alignment explanation
Indices: 2257907--2258011 Score: 138
Period size: 24 Copynumber: 4.4 Consensus size: 24
2257897 TATATCAAAA
* * *
2257907 ATCAAATCATAATTCACGTCAAGT
1 ATCAGATCATAATCCAAGTCAAGT
* * *
2257931 ATCATATCAAAATCCAGGTCAAGT
1 ATCAGATCATAATCCAAGTCAAGT
*
2257955 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAGATCATAATCCAAGTCAAGT
*
2257979 ATCAGATCATAATCCATGTCAAGT
1 ATCAGATCATAATCCAAGTCAAGT
2258003 ATCAGATCA
1 ATCAGATCA
2258012 GAAATCAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (24 bp):
ATCAGATCATAATCCAAGTCAAGT
Found at i:2258031 original size:48 final size:48
Alignment explanation
Indices: 2257925--2258031 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
2257915 ATAATTCACG
* * *
2257925 TCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAG
1 TCAAGAATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAA
* * *
2257973 TCAAGTATCAGATCATAATCCATGTCAAGTATCAGATCAGAAAT-CAAA
1 TCAAGAATCAGATCAAAATCCAGGTCAAGTATCAGATCAG-AATCCAAA
2258021 TCGAA-AATCAG
1 TC-AAGAATCAG
2258032 GTAAAATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 47 0.90
49 5 0.10
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (48 bp):
TCAAGAATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAA
Found at i:2260432 original size:22 final size:19
Alignment explanation
Indices: 2260407--2260454 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 19
2260397 TAATGCCCGA
2260407 TCAACGTCGGTCAAAGTTCCAG
1 TCAACGT-GGTCAAAG--CCAG
*
2260429 TCAACTGTGGTCAACGCCAG
1 TCAAC-GTGGTCAAAGCCAG
2260449 TCAACG
1 TCAACG
2260455 ATCGACTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 9 0.38
22 12 0.50
23 2 0.08
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (19 bp):
TCAACGTGGTCAAAGCCAG
Found at i:2275548 original size:2 final size:2
Alignment explanation
Indices: 2275541--2275579 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2275531 ATTAGACCGT
2275541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2275580 TTAACTCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2281390 original size:14 final size:14
Alignment explanation
Indices: 2281371--2281398 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2281361 AAAATTTCAC
2281371 TTGTAACGTTTGCT
1 TTGTAACGTTTGCT
2281385 TTGTAACGTTTGCT
1 TTGTAACGTTTGCT
2281399 CCCATCGTGC
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:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (14 bp):
TTGTAACGTTTGCT
Found at i:2283467 original size:21 final size:21
Alignment explanation
Indices: 2283441--2283483 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2283431 CATCATCGAT
2283441 TCAATTTCCACAGAACTCAAC
1 TCAATTTCCACAGAACTCAAC
2283462 TCAATTTCCACAGAACTCAAC
1 TCAATTTCCACAGAACTCAAC
2283483 T
1 T
2283484 GGGTTGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.33, G:0.05, T:0.26
Consensus pattern (21 bp):
TCAATTTCCACAGAACTCAAC
Found at i:2283991 original size:16 final size:16
Alignment explanation
Indices: 2283967--2284000 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2283957 TATCGCCGAC
*
2283967 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2283983 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2283999 CG
1 CG
2284001 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Done.