Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000426.1 Hibiscus syriacus cultivar Beakdansim tig00000778_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: 3165331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 15
Found at i:2337851 original size:22 final size:22
Alignment explanation
Indices: 2337810--2337877 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
2337800 CTCGTATAAA
2337810 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
2337833 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2337855 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2337877 T
1 T
2337878 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2338138 original size:30 final size:31
Alignment explanation
Indices: 2338097--2338156 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2338087 TAGACATAGT
*
2338097 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
2338127 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
2338157 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:2338213 original size:29 final size:28
Alignment explanation
Indices: 2338171--2338241 Score: 115
Period size: 29 Copynumber: 2.5 Consensus size: 28
2338161 TTTTCTGCAT
*
2338171 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATA-CA
*
2338200 ATTCATGTCATGTAATACATTTAATACA
1 ATTCATGTCATGTAATACATATAATACA
2338228 ATTCATGTCATGTA
1 ATTCATGTCATGTA
2338242 TCATAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 15 0.38
29 25 0.62
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATACA
Found at i:2338580 original size:18 final size:19
Alignment explanation
Indices: 2338543--2338579 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2338533 CTTTTTCTCA
*
2338543 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
2338562 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2338580 TCAAGCAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:2338707 original size:67 final size:66
Alignment explanation
Indices: 2338544--2338715 Score: 229
Period size: 68 Copynumber: 2.6 Consensus size: 66
2338534 TTTTTCTCAT
* * *
2338544 GGGGGAATCGGTTCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATG
1 GGGGGTATCGGTTCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
2338609 A
66 A
* * *
2338610 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCAATCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTT--CCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
2338674 TGA
64 TGA
* *
2338677 GGGGGTATCGGTTCCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCTG--GGGGTACCGATTCCCCT
2338716 AACCCAGAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
65 6 0.06
66 12 0.13
67 35 0.37
68 41 0.44
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
A
Found at i:2342293 original size:15 final size:15
Alignment explanation
Indices: 2342275--2342350 Score: 70
Period size: 15 Copynumber: 5.3 Consensus size: 15
2342265 ATGAAATTCT
2342275 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
2342290 AATTATTTATATAAA
1 AATTATTTAAATAAA
**
2342305 AATTCA--TCGAT-AA
1 AATT-ATTTAAATAAA
*
2342318 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
*
2342332 AATTATTTATATAAA
1 AATTATTTAAATAAA
2342347 AATT
1 AATT
2342351 CATCGATAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.12
14 6 0.12
15 33 0.69
16 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:2342325 original size:42 final size:41
Alignment explanation
Indices: 2342274--2342361 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 41
2342264 AATGAAATTC
2342274 TAATTATTTAAATAAAAATTATTTATATAAAAATTCATCGA
1 TAATTATTTAAATAAAAATTATTTATATAAAAATTCATCGA
2342315 TAATATATTTAAATAAAAATTATTTATATAAAAATTCATCGA
1 TAAT-TATTTAAATAAAAATTATTTATATAAAAATTCATCGA
2342357 TAATT
1 TAATT
2342362 TATTATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 5 0.11
42 41 0.89
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (41 bp):
TAATTATTTAAATAAAAATTATTTATATAAAAATTCATCGA
Found at i:2342674 original size:31 final size:32
Alignment explanation
Indices: 2342623--2342688 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
2342613 ATTCCTCGAA
2342623 AGATGATTTCTACCGAGTCGGACACTTGTTAC
1 AGATGATTTCTACCGAGTCGGACACTTGTTAC
*
2342655 AGATGATTTCTA-CGAGTCGGACTCTTGTTAC
1 AGATGATTTCTACCGAGTCGGACACTTGTTAC
2342686 AGA
1 AGA
2342689 CGCTATGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 21 0.64
32 12 0.36
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (32 bp):
AGATGATTTCTACCGAGTCGGACACTTGTTAC
Found at i:2349573 original size:21 final size:21
Alignment explanation
Indices: 2349547--2349589 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2349537 TCGCTTCTTC
2349547 TTCGTAAGCTGATATTTCCTT
1 TTCGTAAGCTGATATTTCCTT
2349568 TTCGTAAGCTGATATTTCCTT
1 TTCGTAAGCTGATATTTCCTT
2349589 T
1 T
2349590 GTCAAAGTTT
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:0.19, C:0.19, G:0.14, T:0.49
Consensus pattern (21 bp):
TTCGTAAGCTGATATTTCCTT
Found at i:2350483 original size:154 final size:154
Alignment explanation
Indices: 2350189--2350511 Score: 511
Period size: 154 Copynumber: 2.1 Consensus size: 154
2350179 GCTGTCCAAA
* ** *
2350189 GGTTTGCTTGATGGATGTTCATTGGCTTCTCGACTGGCCATATTGACATCCTGTTCTGTCTAGTG
1 GGTTTGC-TCATGGATGTTCATTGGCTTCTCGACTACCCATATTGACATCCTGATCTGTCTAGTG
** * * *
2350254 ATCACCAGTTTGTCAGCCTTGCAACCTTGGTTGCTTGAGGTCCTTTCTGACTCGGTAATTGGTAT
65 ATCACCAGTTTGTCAGCCTTGCAACCTAAGTTGCTTGAGGTCCTTTCCGACTCGATAACTGGTAT
* *
2350319 TTGGCAGCTACTTGCAGTGCCAGTT
130 TTGGAAGCTACTTGCAGTGCCAGGT
*
2350344 GGTTTGCTCATGTATGTTCATTGGCTTCTCGACTACCCATATTGACATCCTGATCTGTCTAGTGA
1 GGTTTGCTCATGGATGTTCATTGGCTTCTCGACTACCCATATTGACATCCTGATCTGTCTAGTGA
*
2350409 TCACCTGTTTGTCAGCCTTGCAACCTAAGTTGCTTGAGGTCCTTTCCGACTCGATAACTGGTATT
66 TCACCAGTTTGTCAGCCTTGCAACCTAAGTTGCTTGAGGTCCTTTCCGACTCGATAACTGGTATT
2350474 TGGAAGCTACTTGCAGTGCCAGGT
131 TGGAAGCTACTTGCAGTGCCAGGT
2350498 GGTTTGCTCCATGG
1 GGTTTGCT-CATGG
2350512 TCATGCTGAG
Statistics
Matches: 153, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
154 142 0.93
155 11 0.07
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (154 bp):
GGTTTGCTCATGGATGTTCATTGGCTTCTCGACTACCCATATTGACATCCTGATCTGTCTAGTGA
TCACCAGTTTGTCAGCCTTGCAACCTAAGTTGCTTGAGGTCCTTTCCGACTCGATAACTGGTATT
TGGAAGCTACTTGCAGTGCCAGGT
Found at i:2356492 original size:20 final size:20
Alignment explanation
Indices: 2356467--2356506 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2356457 AGTGTTACAT
2356467 AATATCCCTTGAAGATCGAC
1 AATATCCCTTGAAGATCGAC
*
2356487 AATATCCCTTGCAGATCGAC
1 AATATCCCTTGAAGATCGAC
2356507 CTTATGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (20 bp):
AATATCCCTTGAAGATCGAC
Found at i:2362447 original size:37 final size:37
Alignment explanation
Indices: 2362406--2362508 Score: 197
Period size: 37 Copynumber: 2.8 Consensus size: 37
2362396 TGTTATAACT
2362406 GGAGTAGGCTTCTGGTTCTTTCCCTTTTTATAGTACA
1 GGAGTAGGCTTCTGGTTCTTTCCCTTTTTATAGTACA
2362443 GGAGTAGGCTTCTGGTTCTTTCCCTTTTTATAGTACA
1 GGAGTAGGCTTCTGGTTCTTTCCCTTTTTATAGTACA
*
2362480 GGAGTAGGCTTCTGTTTCTTTCCCTTTTT
1 GGAGTAGGCTTCTGGTTCTTTCCCTTTTT
2362509 CTGCTAGTAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (37 bp):
GGAGTAGGCTTCTGGTTCTTTCCCTTTTTATAGTACA
Found at i:2368493 original size:37 final size:37
Alignment explanation
Indices: 2368419--2368501 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 37
2368409 TACGTTTAAC
*
2368419 CTGAAGACGCCAAACAATCATGGAGTCTTATCGATTGG
1 CTGAAGACGCCAAACAATCAT-GAGTCTTATCCATTGG
2368457 TCTGAAGACGCCAAACAATCAT-AGTCTTATCCATTGG
1 -CTGAAGACGCCAAACAATCATGAGTCTTATCCATTGG
2368494 CTTGAAGA
1 C-TGAAGA
2368502 AATCGTACAC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 1 0.02
37 20 0.48
39 21 0.50
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (37 bp):
CTGAAGACGCCAAACAATCATGAGTCTTATCCATTGG
Found at i:2369058 original size:2 final size:2
Alignment explanation
Indices: 2369053--2369084 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2369043 TGTGTGTGTG
2369053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2369085 AAAGTTCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2370608 original size:35 final size:37
Alignment explanation
Indices: 2370537--2370608 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 37
2370527 GTTTAAAAAT
* * *
2370537 ATTTATATATTTTCTTTGAAAAATTTAAATTCATAAA
1 ATTTATATATATTCTTTGAAAAATTGAAAATCATAAA
2370574 ATTTATATATATT-TTT-ACAAAATTGAAAAT-ATAAA
1 ATTTATATATATTCTTTGA-AAAATTGAAAATCATAAA
2370609 GAGGTTTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 6 0.19
36 13 0.42
37 12 0.39
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (37 bp):
ATTTATATATATTCTTTGAAAAATTGAAAATCATAAA
Found at i:2375713 original size:22 final size:22
Alignment explanation
Indices: 2375687--2375731 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
2375677 GAAGATCAGC
2375687 TATTAGGTTTAG-TTTAATATAT
1 TATTAGGTTTAGTTTTAA-ATAT
2375709 TATTAGGTTTAGTTTTAAATAT
1 TATTAGGTTTAGTTTTAAATAT
2375731 T
1 T
2375732 GGTAATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (22 bp):
TATTAGGTTTAGTTTTAAATAT
Found at i:2388982 original size:8 final size:8
Alignment explanation
Indices: 2388969--2389016 Score: 69
Period size: 8 Copynumber: 6.0 Consensus size: 8
2388959 TCGTTTACTT
*
2388969 CACACACA
1 CACACATA
2388977 CACACATA
1 CACACATA
2388985 CACACATA
1 CACACATA
2388993 CACACATA
1 CACACATA
*
2389001 CATACATA
1 CACACATA
*
2389009 CATACATA
1 CACACATA
2389017 TAATTGTCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (8 bp):
CACACATA
Found at i:2389005 original size:4 final size:4
Alignment explanation
Indices: 2388980--2389016 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
2388970 ACACACACAC
* *
2388980 ACAT ACAC ACAT ACAC ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
2389017 TAATTGTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (4 bp):
ACAT
Found at i:2390991 original size:2 final size:2
Alignment explanation
Indices: 2390984--2391013 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2390974 AATTTAATTC
2390984 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
2391014 TAATTTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2392937 original size:21 final size:21
Alignment explanation
Indices: 2392911--2392979 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
2392901 ACCGAAAACA
* *
2392911 TTATTATTTCTATCGGTTTTG
1 TTATTATTTCTACCGATTTTG
*** *
2392932 TTATTA-TT-GGGCGCTTTTG
1 TTATTATTTCTACCGATTTTG
*
2392951 TTATTTTTTCTACCGATTTTG
1 TTATTATTTCTACCGATTTTG
2392972 TTATTATT
1 TTATTATT
2392980 GGACACTTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 12 0.33
20 4 0.11
21 20 0.56
ACGTcount: A:0.14, C:0.10, G:0.14, T:0.61
Consensus pattern (21 bp):
TTATTATTTCTACCGATTTTG
Found at i:2395096 original size:33 final size:33
Alignment explanation
Indices: 2395050--2395116 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
2395040 CTGTCAGGGA
2395050 TAGAGTCAAAATTAAACTATGACGGAGGCAAGT
1 TAGAGTCAAAATTAAACTATGACGGAGGCAAGT
* *
2395083 TAGAGTCAGAATTAAACTATGACGGAGGTAAGT
1 TAGAGTCAAAATTAAACTATGACGGAGGCAAGT
2395116 T
1 T
2395117 GTAAACAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.24
Consensus pattern (33 bp):
TAGAGTCAAAATTAAACTATGACGGAGGCAAGT
Found at i:2401646 original size:20 final size:20
Alignment explanation
Indices: 2401608--2401647 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2401598 TAATCCTATT
**
2401608 CCCTGATAATCTTTTATTCC
1 CCCTGATAATCTTACATTCC
*
2401628 CCCTGGTAATCTTACATTCC
1 CCCTGATAATCTTACATTCC
2401648 GTAAACCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (20 bp):
CCCTGATAATCTTACATTCC
Found at i:2402891 original size:19 final size:20
Alignment explanation
Indices: 2402867--2402905 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
2402857 GAACGCTGGA
2402867 AACCGGTTTTG-ACCGGTTT
1 AACCGGTTTTGAACCGGTTT
2402886 AACCGGTTTTGAACCGGTTT
1 AACCGGTTTTGAACCGGTTT
2402906 TGACCGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
AACCGGTTTTGAACCGGTTT
Found at i:2402902 original size:11 final size:11
Alignment explanation
Indices: 2402867--2402912 Score: 64
Period size: 10 Copynumber: 4.5 Consensus size: 11
2402857 GAACGCTGGA
2402867 AACCGGTTTTG
1 AACCGGTTTTG
2402878 -ACCGG-TTT-
1 AACCGGTTTTG
2402886 AACCGGTTTTG
1 AACCGGTTTTG
2402897 AACCGGTTTTG
1 AACCGGTTTTG
2402908 -ACCGG
1 AACCGG
2402913 GTTGACCGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.25
10 13 0.41
11 11 0.34
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:2402915 original size:11 final size:10
Alignment explanation
Indices: 2402868--2402922 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
2402858 AACGCTGGAA
2402868 ACCGGTTTTG
1 ACCGGTTTTG
*
2402878 ACCGG-TTTA
1 ACCGGTTTTG
2402887 ACCGGTTTTG
1 ACCGGTTTTG
2402897 AACCGGTTTTG
1 -ACCGGTTTTG
*
2402908 ACCGG-GTTG
1 ACCGGTTTTG
2402917 ACCGGT
1 ACCGGT
2402923 CACGACCCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
9 16 0.41
10 13 0.33
11 10 0.26
ACGTcount: A:0.15, C:0.22, G:0.31, T:0.33
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:2402944 original size:13 final size:13
Alignment explanation
Indices: 2402926--2403007 Score: 59
Period size: 13 Copynumber: 6.3 Consensus size: 13
2402916 GACCGGTCAC
2402926 GACCCGACCCGTT
1 GACCCGACCCGTT
2402939 GACCCGACCCGACTGTT
1 GACCCGA-CC--C-GTT
2402956 GACCCGACCC---
1 GACCCGACCCGTT
*
2402966 GACCGTTGACCCG--
1 GACC--CGACCCGTT
2402979 -ACCCGACCCGTT
1 GACCCGACCCGTT
2402991 GACCCGACCCGTT
1 GACCCGACCCGTT
2403004 GACC
1 GACC
2403008 GGTGCTATTC
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
10 10 0.18
12 8 0.14
13 23 0.40
14 3 0.05
16 3 0.05
17 10 0.18
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2402958 original size:17 final size:18
Alignment explanation
Indices: 2402925--2403001 Score: 131
Period size: 17 Copynumber: 4.4 Consensus size: 18
2402915 TGACCGGTCA
2402925 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
2402943 CGACCCGA-CTGTTGACC
1 CGACCCGACCCGTTGACC
2402960 CGACCCGA-CCGTTGACC
1 CGACCCGACCCGTTGACC
2402977 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
2402995 CGACCCG
1 CGACCCG
2403002 TTGACCGGTG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
17 32 0.57
18 24 0.43
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:2403069 original size:29 final size:30
Alignment explanation
Indices: 2403037--2403105 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
2403027 ATTCGGTTTT
2403037 GGTGCTATTTTGGGAATTAATTCT-AAAAG
1 GGTGCTATTTTGGGAATTAATTCTAAAAAG
* * * *
2403066 GGTGCTATATTGGTAATTATTTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTCTAAAAAG
2403096 GGTGCTATTT
1 GGTGCTATTT
2403106 GTGTAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (30 bp):
GGTGCTATTTTGGGAATTAATTCTAAAAAG
Found at i:2403839 original size:24 final size:24
Alignment explanation
Indices: 2403807--2403875 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
2403797 ATAGTTTATC
*
2403807 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * * *
2403831 TGATATTTGATCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
2403855 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
2403876 TTTTGTACTT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:2410116 original size:19 final size:19
Alignment explanation
Indices: 2410092--2410147 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
2410082 GAACGCTGGA
2410092 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
2410111 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
2410132 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
2410148 CACGACCCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:2410127 original size:11 final size:11
Alignment explanation
Indices: 2410092--2410140 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
2410082 GAACGCTGGA
2410092 AACCGGTTTTG
1 AACCGGTTTTG
2410103 -ACCGG-TTT-
1 AACCGGTTTTG
2410111 AACCGGTTTTG
1 AACCGGTTTTG
2410122 AACCGGTTTTG
1 AACCGGTTTTG
2410133 -ACCGGTTT
1 AACCGGTTT
2410141 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:2410143 original size:9 final size:10
Alignment explanation
Indices: 2410093--2410147 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
2410083 AACGCTGGAA
2410093 ACCGGTTTTG
1 ACCGGTTTTG
*
2410103 ACCGG-TTTA
1 ACCGGTTTTG
2410112 ACCGGTTTTG
1 ACCGGTTTTG
2410122 AACCGGTTTTG
1 -ACCGGTTTTG
2410133 ACCGG-TTTG
1 ACCGGTTTTG
2410142 ACCGGT
1 ACCGGT
2410148 CACGACCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:2410169 original size:13 final size:13
Alignment explanation
Indices: 2410151--2410232 Score: 59
Period size: 13 Copynumber: 6.3 Consensus size: 13
2410141 GACCGGTCAC
2410151 GACCCGACCCGTT
1 GACCCGACCCGTT
2410164 GACCCGACCCGACTGTT
1 GACCCGA-CC--C-GTT
2410181 GACCCGACCC---
1 GACCCGACCCGTT
*
2410191 GACCGTTGACCCG--
1 GACC--CGACCCGTT
2410204 -ACCCGACCCGTT
1 GACCCGACCCGTT
2410216 GACCCGACCCGTT
1 GACCCGACCCGTT
2410229 GACC
1 GACC
2410233 GGTGCTATTC
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
10 10 0.18
12 8 0.14
13 23 0.40
14 3 0.05
16 3 0.05
17 10 0.18
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2410183 original size:17 final size:18
Alignment explanation
Indices: 2410150--2410226 Score: 131
Period size: 17 Copynumber: 4.4 Consensus size: 18
2410140 TGACCGGTCA
2410150 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
2410168 CGACCCGA-CTGTTGACC
1 CGACCCGACCCGTTGACC
2410185 CGACCCGA-CCGTTGACC
1 CGACCCGACCCGTTGACC
2410202 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
2410220 CGACCCG
1 CGACCCG
2410227 TTGACCGGTG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
17 32 0.57
18 24 0.43
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:2410321 original size:29 final size:29
Alignment explanation
Indices: 2410262--2410317 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2410252 ATTCTGTTTT
*
2410262 GGTGCTATTTTGGGAATTAATTCTAAAAG
1 GGTGCTATATTGGGAATTAATTCTAAAAG
* *
2410291 GGTGCTATATTGGTAATT-ATTTTAAAA
1 GGTGCTATATTGGGAATTAATTCTAAAA
2410318 AGGGGTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.41
Consensus pattern (29 bp):
GGTGCTATATTGGGAATTAATTCTAAAAG
Found at i:2411065 original size:24 final size:24
Alignment explanation
Indices: 2411033--2411101 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
2411023 ATAGTTTATC
*
2411033 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * * *
2411057 TGATATTTGATCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
2411081 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
2411102 TTTTGTACTT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:2418052 original size:11 final size:11
Alignment explanation
Indices: 2418038--2418113 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
2418028 ATAACTTAAT
2418038 AATAATAATAA
1 AATAATAATAA
*
2418049 AATAATCATGAA
1 AATAATAAT-AA
*
2418061 GATAATAATTTAA
1 AATAATAA--TAA
2418074 ACAT-AT-ATCAA
1 A-ATAATAAT-AA
2418085 AAGTAATAATAA
1 AA-TAATAATAA
2418097 AATAA-AATAA
1 AATAATAATAA
2418107 TAATAAT
1 -AATAAT
2418114 TAAAATGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
10 7 0.14
11 20 0.39
12 15 0.29
13 6 0.12
14 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:2419438 original size:3 final size:3
Alignment explanation
Indices: 2419430--2419494 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
2419420 TTGTAATATT
2419430 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2419477 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
2419495 ATTTAAATGA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2419870 original size:76 final size:76
Alignment explanation
Indices: 2419626--2420645 Score: 1869
Period size: 76 Copynumber: 13.4 Consensus size: 76
2419616 GAAATGTTGA
* *
2419626 AAACATCAGGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGCTCCCG
2419691 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
2419703 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGCTCCCG
2419768 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
2419780 AAACATCATGCACTGAAGGACTTACAGATGATCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2419845 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2419856 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTCTGAAAACACCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2419921 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2419932 AAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2419997 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2420008 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2420073 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2420084 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACACCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2420149 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2420160 AAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2420225 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2420236 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACACCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2420301 AGGCTTTTTGG
66 AGGCTTTTTGG
2420312 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2420377 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2420388 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2420453 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2420464 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACACCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2420529 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2420540 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACACCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2420605 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2420616 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
2420646 TGGGAAATAG
Statistics
Matches: 917, Mismatches: 26, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
76 804 0.88
77 113 0.12
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:2421346 original size:22 final size:22
Alignment explanation
Indices: 2421321--2421376 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
2421311 CATAAAGCTT
* *
2421321 TCATCTTTGAAAAGAGAATTTG
1 TCATCTTTGAAAAGAGAATCTA
* *
2421343 TCATCTTTTAAAAAGGGAATCTA
1 TCATC-TTTGAAAAGAGAATCTA
2421366 TCATCTTTGAA
1 TCATCTTTGAA
2421377 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2423912 original size:114 final size:114
Alignment explanation
Indices: 2423704--2424134 Score: 704
Period size: 114 Copynumber: 3.8 Consensus size: 114
2423694 GATCATGCAG
* * *** * * * *
2423704 TTCATTTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCATATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTAATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
* * *
2423769 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGC-AAA
* * *
2423819 TTCATCTTTCAAATCCAATGATTGATTTTGGAATTCA-ACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTAATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
2423883 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
2423932 TTCATCTTTCAAATCCAATGATTAATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTAATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
2423997 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
2424046 TTCATCTTTCAAATCCAATGATTAATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTAATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
2424111 ACACTTCCAGAAGATGCTA-TGAGC
66 ACACTTCCAGAAGATGCTATTGAGC
2424135 ACATTCATCT
Statistics
Matches: 299, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
113 42 0.14
114 228 0.76
115 29 0.10
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.30
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTAATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
Found at i:2424211 original size:93 final size:93
Alignment explanation
Indices: 2424037--2424317 Score: 431
Period size: 94 Copynumber: 3.0 Consensus size: 93
2424027 TATTTCTACC
* * * * *
2424037 ATGAGCAAATTCATCTTTCAAATCCAATGATTAATTCTG-GAG-TTCATACCAAATCAGATCAGA
1 ATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTG-GTTTCATACCAAACCAGATCAGA
2424100 TAACTCAAAGAACACTTCCAGAAGATGCT
65 TAACTCAAAGAACACTTCCAGAAGATGCT
*
2424129 ATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAAATCAGAT
1 ATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGAT
* *
2424194 AACTTAAAGAACACTTCCCAAAAGATGCT
66 AACTCAAAGAACACTT-CCAGAAGATGCT
* *
2424223 ATGAGCACATTCATCTTCCAAATTCAATGAGTGGTTCTGTGGTTTCATACCAAACCAGATCAGAT
1 ATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGAT
*
2424288 AACTCAAAGAACACTTCCAGAAGATACT
66 AACTCAAAGAACACTTCCAGAAGATGCT
2424316 AT
1 AT
2424318 TGGGTCTTCT
Statistics
Matches: 172, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
92 36 0.21
93 48 0.28
94 88 0.51
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (93 bp):
ATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGAT
AACTCAAAGAACACTTCCAGAAGATGCT
Found at i:2426621 original size:15 final size:15
Alignment explanation
Indices: 2426597--2426629 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2426587 TTGATTCAAT
2426597 TTTTCTTTTTC-TTC
1 TTTTCTTTTTCTTTC
2426611 TTTTCTTTTTTCTTTC
1 TTTTC-TTTTTCTTTC
2426627 TTT
1 TTT
2426630 GTTGGATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTCTTTC
Found at i:2426930 original size:2 final size:2
Alignment explanation
Indices: 2426923--2426988 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
2426913 ACAACAAAGG
2426923 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
2426965 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
2426989 TAAAGGATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2429236 original size:14 final size:14
Alignment explanation
Indices: 2429219--2429257 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2429209 TAAAAGTATG
2429219 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
2429233 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
2429248 AATG-AAAATG
1 AATGCAAAATG
2429258 CATGTATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:2432472 original size:11 final size:11
Alignment explanation
Indices: 2432458--2432533 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
2432448 ATAACTTAAT
2432458 AATAATAATAA
1 AATAATAATAA
*
2432469 AATAATCATGAA
1 AATAATAAT-AA
*
2432481 GATAATAATTTAA
1 AATAATAA--TAA
2432494 ACAT-AT-ATCAA
1 A-ATAATAAT-AA
2432505 AAGTAATAATAA
1 AA-TAATAATAA
2432517 AATAA-AATAA
1 AATAATAATAA
2432527 TAATAAT
1 -AATAAT
2432534 TAAAATGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
10 7 0.14
11 20 0.39
12 15 0.29
13 6 0.12
14 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:2433869 original size:3 final size:3
Alignment explanation
Indices: 2433850--2433905 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
2433840 TTGTAATATT
* **
2433850 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAA TTT TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2433897 TAA TAA TAA
1 TAA TAA TAA
2433906 ATTTAAATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2433883 original size:15 final size:15
Alignment explanation
Indices: 2433850--2433903 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
2433840 TTGTAATATT
2433850 TAATAAATAA-TAT-A
1 TAAT-AATAATTATAA
2433864 TAATAATAATTATAA
1 TAATAATAATTATAA
*
2433879 TAATAATAATTTTAA
1 TAATAATAATTATAA
2433894 TAATAATAAT
1 TAATAATAAT
2433904 AAATTTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
13 5 0.14
14 7 0.19
15 25 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATTATAA
Found at i:2435366 original size:21 final size:20
Alignment explanation
Indices: 2435323--2435367 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2435313 ATCAATTTTT
**
2435323 TTAAATGAACAATGTGGGAA
1 TTAAATGAACAATGAAGGAA
*
2435343 TTAAATGAACAATGCAATGAA
1 TTAAATGAACAATG-AAGGAA
2435364 TTAA
1 TTAA
2435368 GCTGTATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.27
Consensus pattern (20 bp):
TTAAATGAACAATGAAGGAA
Found at i:2435367 original size:83 final size:83
Alignment explanation
Indices: 2435158--2435407 Score: 351
Period size: 83 Copynumber: 3.0 Consensus size: 83
2435148 TACCACGAAA
* * *
2435158 TTAAATGAACAATATGAGAATTGAAA-GAACAATGCAATGAATTAAGTTGTATTAATTAAATACC
1 TTAAATGAACAATGTGGGAATT-AAATGAACAATGCAATGAATTAAGCTGTATTAATTAAATACC
2435222 ATGCATTAAATCAA-TTTT
65 ATGCATTAAATCAATTTTT
* * * * * * * *
2435240 TTAAGTGAACAGTGTGGGAATTAAATTAACACTACAAAGAATTAAGCTGCATTAATTAAATATCA
1 TTAAATGAACAATGTGGGAATTAAATGAACAATGCAATGAATTAAGCTGTATTAATTAAATACCA
* *
2435305 TGCGTTCAATCAATTTTT
66 TGCATTAAATCAATTTTT
*
2435323 TTAAATGAACAATGTGGGAATTAAATGAACAATGCAATGAATTAAGCTGTATTAATTAAACACCA
1 TTAAATGAACAATGTGGGAATTAAATGAACAATGCAATGAATTAAGCTGTATTAATTAAATACCA
2435388 TGCATTAAATCAATTTTT
66 TGCATTAAATCAATTTTT
2435406 TT
1 TT
2435408 TTGAGTTTCA
Statistics
Matches: 142, Mismatches: 24, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
81 3 0.02
82 61 0.43
83 78 0.55
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (83 bp):
TTAAATGAACAATGTGGGAATTAAATGAACAATGCAATGAATTAAGCTGTATTAATTAAATACCA
TGCATTAAATCAATTTTT
Found at i:2436391 original size:23 final size:23
Alignment explanation
Indices: 2436356--2436418 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
2436346 TTGTTAACTA
* *
2436356 TTGATCGACGTTAACTTCGATCG
1 TTGATCAATGTTAACTTCGATCG
2436379 TTGATCAATGTTAACTTCGATCG
1 TTGATCAATGTTAACTTCGATCG
2436402 TTGATCAATGTTAACTT
1 TTGATCAATGTTAACTT
2436419 TTTTTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (23 bp):
TTGATCAATGTTAACTTCGATCG
Found at i:2437218 original size:2 final size:2
Alignment explanation
Indices: 2437211--2437242 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
2437201 ATACATCCAA
2437211 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
2437243 CATACATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2439167 original size:20 final size:20
Alignment explanation
Indices: 2439142--2439195 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2439132 GAAATATTGA
2439142 TGCATCGATGCACCCCTTAC
1 TGCATCGATGCACCCCTTAC
2439162 TGCATCGATGCACCCCTTAC
1 TGCATCGATGCACCCCTTAC
*
2439182 TACATCGATGCACC
1 TGCATCGATGCACC
2439196 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.39, G:0.15, T:0.24
Consensus pattern (20 bp):
TGCATCGATGCACCCCTTAC
Found at i:2443554 original size:4 final size:4
Alignment explanation
Indices: 2443545--2443582 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
2443535 AAAACAAAAG
2443545 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
2443583 GTATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:2448817 original size:2 final size:2
Alignment explanation
Indices: 2448810--2448849 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2448800 GTCTTTGGAT
2448810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2448850 ATTGGTTATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2450813 original size:2 final size:2
Alignment explanation
Indices: 2450801--2450833 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
2450791 CATGAAATGC
2450801 AT AT CAT 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
2450834 GGTTATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2453480 original size:39 final size:39
Alignment explanation
Indices: 2453437--2453519 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 39
2453427 AGACAAATAT
*
2453437 GAAGACTAC-ACGACTGCATGATATCTTCAGGCAAATGAA
1 GAAGAC-ACTACGACTGCATGACATCTTCAGGCAAATGAA
* *
2453476 GAAGACCCTACGACTGCATGACATCTTCAGGCAAATGGA
1 GAAGACACTACGACTGCATGACATCTTCAGGCAAATGAA
2453515 GAAGA
1 GAAGA
2453520 TCCCAAGAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 1 0.03
39 39 0.98
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (39 bp):
GAAGACACTACGACTGCATGACATCTTCAGGCAAATGAA
Found at i:2453702 original size:2 final size:2
Alignment explanation
Indices: 2453695--2453719 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2453685 GCAAGAAAAT
2453695 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 T
2453720 TATTAGTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2456066 original size:16 final size:17
Alignment explanation
Indices: 2456041--2456084 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
2456031 ATCCGAAGGT
2456041 AATT-TTTATTTATTT-
1 AATTATTTATTTATTTG
*
2456056 AGTTATTTATTT-TTTG
1 AATTATTTATTTATTTG
2456072 AATTATTTATTTA
1 AATTATTTATTTA
2456085 ATTTTTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
AATTATTTATTTATTTG
Found at i:2458154 original size:39 final size:38
Alignment explanation
Indices: 2458097--2458198 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 38
2458087 GGCTCGTCGG
* * * * *
2458097 CTTTGTGCTCAAGGTAAGTCCTTACCGCAAGTTCCTATT
1 CTTTGTGCAC-AGATAAGTCCTTACCGCAAGCTCATATA
* *
2458136 CTTTGTGCACATGATAAGTCCTTACTGCAAGCTCATCTA
1 CTTTGTGCACA-GATAAGTCCTTACCGCAAGCTCATATA
*
2458175 CTTTGTGCATAGAGTAAGTCCTTA
1 CTTTGTGCACAGA-TAAGTCCTTA
2458199 TTGAGTGTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 3 0.06
39 50 0.94
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (38 bp):
CTTTGTGCACAGATAAGTCCTTACCGCAAGCTCATATA
Found at i:2459653 original size:293 final size:293
Alignment explanation
Indices: 2459126--2459711 Score: 1091
Period size: 293 Copynumber: 2.0 Consensus size: 293
2459116 GGGACACCAT
*
2459126 TAATAGAGATGTCTTTCGTATGTTCAGGAGAGCTTCTCGAGTCCCTGGTAATATGTCTGCTGTTG
1 TAATAGAGATGTCTTTCGTATATTCAGGAGAGCTTCTCGAGTCCCTGGTAATATGTCTGCTGTTG
*
2459191 AGATTTCAAAGTCTTTGGTAGCCGCTGGAGTAGTTCATTTCGAAGGCATTACTGGTTGACCTCTG
66 AGATTTCAAAGTCTTTGGTAGCCACTGGAGTAGTTCATTTCGAAGGCATTACTGGTTGACCTCTG
2459256 ACTGACATTGAGTATTGGTTGGAGGATTCAAAGAGAATTATGGATGAGATGGATTTTATGCATGA
131 ACTGACATTGAGTATTGGTTGGAGGATTCAAAGAGAATTATGGATGAGATGGATTTTATGCATGA
* *
2459321 GAAAAAGTTAAAAGGGGCCCTAATTATGCTAAAGAAAGAGAGTTTTTTGTGGTGGCAATCAATTT
196 GAAAAAGTTAAAAGGGGCCCTAATTATGATAAAGAAAGAGAGTTTTTGGTGGTGGCAATCAATTT
*
2459386 CTGGTAGTATTTTAGGAAATTAGTTGAATTGGG
261 CTGGTAGTATTCTAGGAAATTAGTTGAATTGGG
*
2459419 TAATAGAGTTGTCTTTCGTATATTCAGGAGAGCTTCTCGAGTCCCTGGTAATATGTCTGCTGTTG
1 TAATAGAGATGTCTTTCGTATATTCAGGAGAGCTTCTCGAGTCCCTGGTAATATGTCTGCTGTTG
**
2459484 AGATTTTGAAGTCTTTGGTAGCCACTGGAGTAGTTCATTTCGAAGGCATTACTGGTTGACCTCTG
66 AGATTTCAAAGTCTTTGGTAGCCACTGGAGTAGTTCATTTCGAAGGCATTACTGGTTGACCTCTG
*
2459549 ACTGACATTGAGTATTGGTTGGAGGATTCAAAGAGAATTATGGATTAGATGGATTTTATGCATGA
131 ACTGACATTGAGTATTGGTTGGAGGATTCAAAGAGAATTATGGATGAGATGGATTTTATGCATGA
2459614 GAAAAAGTTAAAAGGGGCCCTAATTATGATAAAGAAAGAGAGTTTTTGGTGGTGGCAATCAATTT
196 GAAAAAGTTAAAAGGGGCCCTAATTATGATAAAGAAAGAGAGTTTTTGGTGGTGGCAATCAATTT
2459679 CTGGTAGTATTCTAGGAAATTAGTTGAATTGGG
261 CTGGTAGTATTCTAGGAAATTAGTTGAATTGGG
2459712 ATCTTCTCAA
Statistics
Matches: 284, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
293 284 1.00
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (293 bp):
TAATAGAGATGTCTTTCGTATATTCAGGAGAGCTTCTCGAGTCCCTGGTAATATGTCTGCTGTTG
AGATTTCAAAGTCTTTGGTAGCCACTGGAGTAGTTCATTTCGAAGGCATTACTGGTTGACCTCTG
ACTGACATTGAGTATTGGTTGGAGGATTCAAAGAGAATTATGGATGAGATGGATTTTATGCATGA
GAAAAAGTTAAAAGGGGCCCTAATTATGATAAAGAAAGAGAGTTTTTGGTGGTGGCAATCAATTT
CTGGTAGTATTCTAGGAAATTAGTTGAATTGGG
Found at i:2482222 original size:24 final size:24
Alignment explanation
Indices: 2482194--2482243 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2482184 ACTAACTAAT
2482194 CTCTCTCTATATATGGGTAAACTA
1 CTCTCTCTATATATGGGTAAACTA
2482218 CTCTCTCTATATATGGGTAAACTA
1 CTCTCTCTATATATGGGTAAACTA
2482242 CT
1 CT
2482244 TCAATTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (24 bp):
CTCTCTCTATATATGGGTAAACTA
Found at i:2482223 original size:26 final size:25
Alignment explanation
Indices: 2482187--2482241 Score: 94
Period size: 24 Copynumber: 2.2 Consensus size: 25
2482177 AATACCAACT
2482187 AACTAATCTCTCTCTATATATGGGTA
1 AACT-ATCTCTCTCTATATATGGGTA
2482213 AACTA-CTCTCTCTATATATGGGTA
1 AACTATCTCTCTCTATATATGGGTA
2482237 AACTA
1 AACTA
2482242 CTTCAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 24 0.83
25 1 0.03
26 4 0.14
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (25 bp):
AACTATCTCTCTCTATATATGGGTA
Found at i:2483171 original size:164 final size:166
Alignment explanation
Indices: 2482966--2483542 Score: 476
Period size: 180 Copynumber: 3.4 Consensus size: 166
2482956 CTCATTCAAT
* * * **
2482966 TTTAGCTTCATCTTTTATCTCAAACTGAGAAT-CAATTTTCACTCTAATTTGACGCTCTTTAGCT
1 TTTAGCTTTATCTTTTAGCTGAAACTGAGAATCCTTTTTTCACTCTAATTTGACGCTCTTTAGCT
** * * *
2483030 ATATCG-TTTA-CTTGAAAATCTATATGTTTTTCAC-CAAGT-GTTGGCGCTATC-TAGCTCTAT
66 -T-TCGCTGAAGC-TGAAAATCTATATGTTTTTCACTCAACTAGTTAGCGCTATCTTAGCTCTAA
* *
2483090 CTAAAAATCTTTTTGTTTTTGCACTCAATTCTAACGCTA
128 CCAAAAATCTGTTTGTTTTTGCACTCAATTCTAACGCTA
* * * *
2483129 TTTAGCTTTATCTTTTAGCTGAAACTAAGAATCCTTTTTTCACTCTGATTTGACGCTCCTTATCG
1 TTTAGCTTTATCTTTTAGCTGAAACTGAGAATCCTTTTTTCACTCTAATTTGACGCTCTTTAGC-
** * * *
2483194 TTTCGCTGAAGCTGAAAATCTATATGTTTTTCACTCGCCTATTTAGCTCTATCTTTTAGCTGTAA
65 TTTCGCTGAAGCTGAAAATCTATATGTTTTTCACTCAACTAGTTAGCGCTATC--TTAGCTCTAA
* * * * *
2483259 CCAAAAATCTGTTTGTTTTTTCATTCGATTTTGACGCTA
128 CCAAAAATCTGTTTGTTTTTGCACTCAATTCTAACGCTA
* **
2483298 TTTAGC--TGTCTTAAAGCTGAAACTGAGAATCCTTTTTTTCACTCTAATTTGACGCTCTTTAGC
1 TTTAGCTTTATCTTTTAGCTGAAACTGAGAATCC-TTTTTTCACTCTAATTTGACGCTCTTTAGC
* * *
2483361 TTAATTGTGTAGCTGAAGCTGAAAATC--TATGTTTTTCACTCAGTGTTGACTCTATTTAGCTCT
65 -----T-T-TCGCTGAAGCTGAAAATCTATATGTTTTTCACTCA------A--CTAGTTAGCGCT
* * * * * *
2483424 ATCTTTTAGCTGTAACCAAAAATCTGTTTGTTTTTTCATTCGATTTTGACGCTA
115 ATC--TTAGCTCTAACCAAAAATCTGTTTGTTTTTGCACTCAATTCTAACGCTA
* **
2483478 TTTAGC--TGTCTTAAAGCTGAAACTGAGAATCCTTTTTTTCACTCTAATTTGACGCTCTTTAGC
1 TTTAGCTTTATCTTTTAGCTGAAACTGAGAATCC-TTTTTTCACTCTAATTTGACGCTCTTTAGC
2483541 TT
65 TT
2483543 AATTGTGTAG
Statistics
Matches: 353, Mismatches: 37, Indels: 37
0.83 0.09 0.09
Matches are distributed among these distances:
163 31 0.09
164 51 0.14
165 4 0.01
166 9 0.03
167 22 0.06
168 27 0.08
169 45 0.13
172 15 0.04
173 1 0.00
174 18 0.05
175 1 0.00
180 129 0.37
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (166 bp):
TTTAGCTTTATCTTTTAGCTGAAACTGAGAATCCTTTTTTCACTCTAATTTGACGCTCTTTAGCT
TTCGCTGAAGCTGAAAATCTATATGTTTTTCACTCAACTAGTTAGCGCTATCTTAGCTCTAACCA
AAAATCTGTTTGTTTTTGCACTCAATTCTAACGCTA
Found at i:2483410 original size:60 final size:58
Alignment explanation
Indices: 2483288--2483605 Score: 213
Period size: 60 Copynumber: 5.4 Consensus size: 58
2483278 TTCATTCGAT
* * ** * * *
2483288 TTTGACGCTATTTAGCTGT-CTTAAAGCTGAAACTGAGAATCCT-T-TTTTTCACTCTAA
1 TTTGACGCTATTTAGCTCTATTTGTAGCTGAAGCTGAAAAT-CTATGTTTTTCACTC-AG
*
2483345 TTTGACGCTCTTTAGCT-TAATTGTGTAGCTGAAGCTGAAAATCTATGTTTTTCACTCAG
1 TTTGACGCTATTTAGCTCT-ATT-TGTAGCTGAAGCTGAAAATCTATGTTTTTCACTCAG
* * ** * * *
2483404 TGTTGACTCTATTTAGCTCTATCTTTTAGCTGTAA-CCAAAAATCTGTTTGTTTTTTCATTCGAT
1 T-TTGACGCTATTTAGCTCTAT-TTGTAGCTG-AAGCTGAAAATC--TATG-TTTTTCACTC-AG
* * ** * * *
2483468 TTTGACGCTATTTAGCTGT-CTTAAAGCTGAAACTGAGAATCCT-T-TTTTTCACTCTAA
1 TTTGACGCTATTTAGCTCTATTTGTAGCTGAAGCTGAAAAT-CTATGTTTTTCACTC-AG
*
2483525 TTTGACGCTCTTTAGCT-TAATTGTGTAGCTGAAGCTGAAAATCTATGTTTTTCACTCAG
1 TTTGACGCTATTTAGCTCT-ATT-TGTAGCTGAAGCTGAAAATCTATGTTTTTCACTCAG
*
2483584 TGTTGACTCTATTTAGCTCTAT
1 T-TTGACGCTATTTAGCTCTAT
2483606 CATTTTAATG
Statistics
Matches: 204, Mismatches: 35, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
56 2 0.01
57 42 0.21
58 6 0.03
59 37 0.18
60 69 0.34
61 17 0.08
62 4 0.02
63 25 0.12
64 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (58 bp):
TTTGACGCTATTTAGCTCTATTTGTAGCTGAAGCTGAAAATCTATGTTTTTCACTCAG
Found at i:2483481 original size:63 final size:61
Alignment explanation
Indices: 2483232--2483484 Score: 200
Period size: 60 Copynumber: 4.2 Consensus size: 61
2483222 TTTCACTCGC
*
2483232 CTATTTAGCTCTATCTTTTAGCTGTAACCAAAAATCTGTTTGTTTTTTCATTCGATTTTGACG
1 CTATTTAGCTCTATCTTTTAGCTGTAACCAAAAATC--TTTGTTTTTTCACTCGATTTTGACG
* ** * ** * * * *
2483295 CTATTTAG--CTGTCTTAAAGCTGAAACTGAGAATC-CT-TTTTTTCACTCTAATTTGACG
1 CTATTTAGCTCTATCTTTTAGCTGTAACCAAAAATCTTTGTTTTTTCACTCGATTTTGACG
* * ** * * *
2483352 CTCTTTAGCT-TAAT-TGTGTAGCTG-AAGCTGAAAATCTATG-TTTTTCACTC-AGTGTTGACT
1 CTATTTAGCTCT-ATCT-TTTAGCTGTAA-CCAAAAATCTTTGTTTTTTCACTCGA-TTTTGACG
*
2483412 CTATTTAGCTCTATCTTTTAGCTGTAACCAAAAATCTGTTTGTTTTTTCATTCGATTTTGACG
1 CTATTTAGCTCTATCTTTTAGCTGTAACCAAAAATC--TTTGTTTTTTCACTCGATTTTGACG
2483475 CTATTTAGCT
1 CTATTTAGCT
2483485 GTCTTAAAGC
Statistics
Matches: 147, Mismatches: 28, Indels: 30
0.72 0.14 0.15
Matches are distributed among these distances:
57 25 0.17
58 5 0.03
59 16 0.11
60 41 0.28
61 23 0.16
62 3 0.02
63 33 0.22
64 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (61 bp):
CTATTTAGCTCTATCTTTTAGCTGTAACCAAAAATCTTTGTTTTTTCACTCGATTTTGACG
Found at i:2483494 original size:180 final size:180
Alignment explanation
Indices: 2483092--2483612 Score: 766
Period size: 180 Copynumber: 3.0 Consensus size: 180
2483082 AGCTCTATCT
* * * * * * * ** *
2483092 AAAAATCTTTTTGTTTTTGCACTCAATTCTAACGCTATTTAGCTTTATCTTTTAGCTGAAACTAA
1 AAAAATCTGTTTGTTTTTTCATTCGATTTTGACGCTATTTAGC--TGTCTTAAAGCTGAAACTGA
* * * *
2483157 GAATCC-TTTTTTCACTCTGATTTGACGCTC-----CTT-ATCGTTTCGCTGAAGCTGAAAATCT
64 GAATCCTTTTTTTCACTCTAATTTGACGCTCTTTAGCTTAATTGTGTAGCTGAAGCTGAAAATC-
2483215 ATATGTTTTTCACTC------G-C-CTATTTAGCTCTATCTTTTAGCTGTAACC
128 -TATGTTTTTCACTCAGTGTTGACTCTATTTAGCTCTATCTTTTAGCTGTAACC
2483261 AAAAATCTGTTTGTTTTTTCATTCGATTTTGACGCTATTTAGCTGTCTTAAAGCTGAAACTGAGA
1 AAAAATCTGTTTGTTTTTTCATTCGATTTTGACGCTATTTAGCTGTCTTAAAGCTGAAACTGAGA
2483326 ATCCTTTTTTTCACTCTAATTTGACGCTCTTTAGCTTAATTGTGTAGCTGAAGCTGAAAATCTAT
66 ATCCTTTTTTTCACTCTAATTTGACGCTCTTTAGCTTAATTGTGTAGCTGAAGCTGAAAATCTAT
2483391 GTTTTTCACTCAGTGTTGACTCTATTTAGCTCTATCTTTTAGCTGTAACC
131 GTTTTTCACTCAGTGTTGACTCTATTTAGCTCTATCTTTTAGCTGTAACC
2483441 AAAAATCTGTTTGTTTTTTCATTCGATTTTGACGCTATTTAGCTGTCTTAAAGCTGAAACTGAGA
1 AAAAATCTGTTTGTTTTTTCATTCGATTTTGACGCTATTTAGCTGTCTTAAAGCTGAAACTGAGA
2483506 ATCCTTTTTTTCACTCTAATTTGACGCTCTTTAGCTTAATTGTGTAGCTGAAGCTGAAAATCTAT
66 ATCCTTTTTTTCACTCTAATTTGACGCTCTTTAGCTTAATTGTGTAGCTGAAGCTGAAAATCTAT
2483571 GTTTTTCACTCAGTGTTGACTCTATTTAGCTCTATCATTTTA
131 GTTTTTCACTCAGTGTTGACTCTATTTAGCTCTATC-TTTTA
2483613 ATGAAGCTGA
Statistics
Matches: 322, Mismatches: 14, Indels: 20
0.90 0.04 0.06
Matches are distributed among these distances:
167 22 0.07
168 23 0.07
169 37 0.11
172 14 0.04
173 3 0.01
174 21 0.07
178 1 0.00
179 1 0.00
180 195 0.61
181 5 0.02
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.44
Consensus pattern (180 bp):
AAAAATCTGTTTGTTTTTTCATTCGATTTTGACGCTATTTAGCTGTCTTAAAGCTGAAACTGAGA
ATCCTTTTTTTCACTCTAATTTGACGCTCTTTAGCTTAATTGTGTAGCTGAAGCTGAAAATCTAT
GTTTTTCACTCAGTGTTGACTCTATTTAGCTCTATCTTTTAGCTGTAACC
Found at i:2483618 original size:60 final size:60
Alignment explanation
Indices: 2483332--2483673 Score: 181
Period size: 60 Copynumber: 5.7 Consensus size: 60
2483322 GAGAATCCTT
* * * *
2483332 TTTTTCACTCTAAT-TTGACGCTCTTTAGCT-TAAT-TGTGTAGCTGAAGCTGAAAATCTATG
1 TTTTTCACTC-AGTGTTGACGCTATTTAGCTCT-ATCT-TTTAGATGAAGCTGAAAATCTATG
* * ** *
2483392 TTTTTCACTCAGTGTTGACTCTATTTAGCTCTATCTTTTAGCTGTAA-CCAAAAATCTGTTTG
1 TTTTTCACTCAGTGTTGACGCTATTTAGCTCTATCTTTTAGATG-AAGCTGAAAATC--TATG
* * * ** * * *
2483454 TTTTTTCATTC-GATTTTGACGCTATTTAG--CTGTCTTAAAGCTGAAACTGAGAATCCT-T-
1 -TTTTTCACTCAG-TGTTGACGCTATTTAGCTCTATCTTTTAGATGAAGCTGAAAAT-CTATG
* * * *
2483512 TTTTTCACTCTAAT-TTGACGCTCTTTAGCT-TAAT-TGTGTAGCTGAAGCTGAAAATCTATG
1 TTTTTCACTC-AGTGTTGACGCTATTTAGCTCT-ATCT-TTTAGATGAAGCTGAAAATCTATG
* ** *
2483572 TTTTTCACTCAGTGTTGACTCTATTTAGCTCTATCATTTTA-ATGAAGCTGAATTTTTTTAATG
1 TTTTTCACTCAGTGTTGACGCTATTTAGCTCTATC-TTTTAGATGAAGCTGAA--AATCT-ATG
* * *
2483635 TTTGTTCACTC-CTTTTGACGCTATTTAGCTCCATCTTTT
1 TTT-TTCACTCAGTGTTGACGCTATTTAGCTCTATCTTTT
2483674 TTTCACTCAA
Statistics
Matches: 220, Mismatches: 36, Indels: 50
0.72 0.12 0.16
Matches are distributed among these distances:
57 22 0.10
58 5 0.02
59 22 0.10
60 79 0.36
61 24 0.11
62 12 0.05
63 49 0.22
64 7 0.03
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (60 bp):
TTTTTCACTCAGTGTTGACGCTATTTAGCTCTATCTTTTAGATGAAGCTGAAAATCTATG
Found at i:2487471 original size:158 final size:157
Alignment explanation
Indices: 2487269--2487654 Score: 449
Period size: 158 Copynumber: 2.4 Consensus size: 157
2487259 TGTAGTATAT
* * * *
2487269 GAGCATGTGATTCAAATTTGGTAAAAAAAAGTG-ACTTAAAATAAATCAAAAATTGAAGGAATAA
1 GAGCATGTGACTCAAATTT-G-ACAAAAATG-GAACTTAAAATAAATCAAAAATTGAAGAAATAA
* * *
2487333 GGAGATTATAAAAAATT-GAAGGACTAAATTGAAAAATAAAAAATTTGTTATAAAAAAAAGGAAT
63 GAAAATTATAAAAAATTGGAA-GACTAAATTAAAAAATAAAAAATTTGTTATAAAAAAAAGGAA-
* *
2487397 TGAAAGTACACATATACTCTACTATGGTTTAG
126 TAAAAGTACACATATACTCTACTATGGTTTAA
* **
2487429 GAGCATGTTG-CTCAAATTTGACAAAAATGGAACTTAAAATAAATGATGAATTGAAGAAATAAGA
1 GAGCATG-TGACTCAAATTTGACAAAAATGGAACTTAAAATAAATCAAAAATTGAAGAAATAAGA
* * *
2487493 AAATTATAAAAAATTGGAAGACTAAATTAAAAAATAAATAATTTGTTATCAAAAAGAGGAATAAA
65 AAATTATAAAAAATTGGAAGACTAAATTAAAAAATAAAAAATTTGTTATAAAAAAAAGGAATAAA
* *
2487558 AGTACGCATGTACTCTACTATGGTTTAA
130 AGTACACATATACTCTACTATGGTTTAA
* * * *
2487586 GAGCATGTGATTCAAATTTGATAAAAAAAATAG-ACTTAAAATGAAA-GAAAAATTGAAGAAATA
1 GAGCATGTGACTCAAATTTG---ACAAAAATGGAACTTAAAAT-AAATCAAAAATTGAAGAAATA
2487649 ATGAAA
62 A-GAAA
2487655 TTAGAGATTA
Statistics
Matches: 195, Mismatches: 22, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
156 2 0.01
157 45 0.23
158 87 0.45
159 29 0.15
160 30 0.15
161 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.26
Consensus pattern (157 bp):
GAGCATGTGACTCAAATTTGACAAAAATGGAACTTAAAATAAATCAAAAATTGAAGAAATAAGAA
AATTATAAAAAATTGGAAGACTAAATTAAAAAATAAAAAATTTGTTATAAAAAAAAGGAATAAAA
GTACACATATACTCTACTATGGTTTAA
Found at i:2491070 original size:21 final size:21
Alignment explanation
Indices: 2490955--2491070 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
2490945 GCGAAATAAA
**
2490955 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
2490975 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
2490995 AATCGCAACGCGATTCTT-AAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
2491016 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
2491036 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
2491058 AATCGCAACGCGA
1 AATCGCAACGCGA
2491071 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:2491132 original size:20 final size:20
Alignment explanation
Indices: 2491058--2491209 Score: 189
Period size: 20 Copynumber: 7.6 Consensus size: 20
2491048 GATTTTCCAG
* ** *
2491058 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2491078 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2491098 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2491118 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2491138 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2491158 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2491178 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2491198 AATCGCAACGCG
1 AATCGCAACGCG
2491210 ATTTTTAAAG
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 1 0.01
20 110 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2491628 original size:33 final size:33
Alignment explanation
Indices: 2491589--2491659 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2491579 TTCACTTAGA
2491589 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2491622 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2491655 TTTCA
1 TTTCA
2491660 AGTTAGTATT
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:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2491765 original size:21 final size:20
Alignment explanation
Indices: 2491739--2491812 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
2491729 TGCAGAAGAG
2491739 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
2491760 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
2491780 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
2491802 TCGCAACGAGA
1 TCGCAACGAGA
2491813 GAATCGCAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.22
21 25 0.56
22 10 0.22
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:2491857 original size:19 final size:19
Alignment explanation
Indices: 2491835--2491947 Score: 94
Period size: 19 Copynumber: 6.1 Consensus size: 19
2491825 GAAACCAAAA
*
2491835 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2491854 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2491873 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2491887 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
2491907 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
2491927 CTCTCGTTGCGA-TTTCATT
1 -TCGCGTTGCGATTTTCATT
2491946 TC
1 TC
2491948 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
18 2 0.03
19 34 0.43
20 14 0.17
21 14 0.17
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2491910 original size:21 final size:20
Alignment explanation
Indices: 2491884--2491947 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
2491874 CGCGTTGCGA
2491884 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGA-TTTCAT
**
2491905 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGA-TTTCAT
2491925 TTCTCTCGTTGCGATTTCAT
1 TTCTCTCGTTGCGATTTCAT
2491945 TTC
1 TTC
2491948 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 3 0.08
20 17 0.46
21 17 0.46
ACGTcount: A:0.11, C:0.27, G:0.16, T:0.47
Consensus pattern (20 bp):
TTCTCTCGTTGCGATTTCAT
Found at i:2491930 original size:20 final size:20
Alignment explanation
Indices: 2491883--2491938 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
2491873 TCGCGTTGCG
***
2491883 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
2491903 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGACAGTC
2491924 ATTCTCTCGTTGCGA
1 ATTCTCTCGTTGCGA
2491939 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:2493788 original size:93 final size:93
Alignment explanation
Indices: 2493629--2494037 Score: 800
Period size: 93 Copynumber: 4.4 Consensus size: 93
2493619 TAGATTGCTT
*
2493629 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2493694 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2493722 AGTAAATTTGTTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2493787 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2493815 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2493880 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2493908 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2493973 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2494001 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2494038 AATACCCTGA
Statistics
Matches: 313, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 313 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2494172 original size:14 final size:14
Alignment explanation
Indices: 2494153--2494209 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2494143 CGAAACTTAA
2494153 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2494167 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
2494186 AATCGCAACGACAG
1 AATCGCAACGAGAG
2494200 AATCGCAACG
1 AATCGCAACG
2494210 CGAAACAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2494191 original size:19 final size:18
Alignment explanation
Indices: 2494167--2494258 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
2494157 GCAACGAGAG
2494167 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
2494186 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
2494200 AATCGCAACGCGAAACAAA
1 AATCGCAACGCGAAA-GAA
*
2494219 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
2494233 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
2494252 AATCGCA
1 AATCGCA
2494259 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 18 0.31
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.44
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:2494193 original size:33 final size:33
Alignment explanation
Indices: 2494135--2494258 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
2494125 TAGTTTACTT
* * *
2494135 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-AAAAATCGCAACGACAGAA
**
2494169 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACAAAAATCGCAACGACAGAA
*
2494202 TCGCAACGCGAAACAAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACAAAAATCGCAACGACAGAA
*
2494235 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACAAAAATCGCA
2494259 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 70 0.85
34 12 0.15
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACAAAAATCGCAACGACAGAA
Found at i:2494236 original size:14 final size:14
Alignment explanation
Indices: 2494184--2494242 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2494174 ACGCGAAATG
2494184 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2494198 AGAATCGCAACGCGAAAC
1 AAAATCGCAA--CG--AC
2494216 AAAAATCGCAACGAC
1 -AAAATCGCAACGAC
2494231 AAAATCGCAACG
1 AAAATCGCAACG
2494243 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.55
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
19 9 0.24
ACGTcount: A:0.49, C:0.27, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2494276 original size:19 final size:19
Alignment explanation
Indices: 2494254--2494393 Score: 146
Period size: 19 Copynumber: 7.6 Consensus size: 19
2494244 GAAACCAAAA
*
2494254 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2494273 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2494289 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2494306 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
2494325 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
2494344 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
2494363 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2494383 TCGTGTTGCGA
1 TCGCGTTGCGA
2494394 AAGTAAACTA
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
14 8 0.08
16 5 0.05
17 5 0.05
19 72 0.71
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2496333 original size:14 final size:14
Alignment explanation
Indices: 2496314--2496349 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2496304 ATTGTTTAAT
2496314 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2496328 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2496342 TGATTTGT
1 TGATTTGT
2496350 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2496464 original size:19 final size:19
Alignment explanation
Indices: 2496440--2496527 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
2496430 GCATTATGTT
2496440 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
2496459 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
2496476 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
2496492 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
2496511 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
2496528 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:2496559 original size:53 final size:53
Alignment explanation
Indices: 2496440--2496546 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
2496430 GCATTATGTT
2496440 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
2496492 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
2496545 GA
1 GA
2496547 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:2496621 original size:33 final size:33
Alignment explanation
Indices: 2496560--2496753 Score: 151
Period size: 33 Copynumber: 5.6 Consensus size: 33
2496550 TCATTTCGCA
*
2496560 TTGCGATTTTCATTTCCGCATTACGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
2496594 TTGCGATTTTCATTTCGCATTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
** *
2496627 TTGCGATTTTTTTTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
2496664 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
* *
2496699 TTGCGATTTTCATTTCCGCATTGCGATTTTCTTG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
2496733 TTGAGATTTTCATTTCGCATT
1 TTGCGATTTTCATTTCGCATT
2496754 CTCTCGTTGC
Statistics
Matches: 127, Mismatches: 20, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
31 4 0.03
32 6 0.05
33 56 0.44
34 31 0.24
35 4 0.03
36 3 0.02
37 2 0.02
38 2 0.02
39 8 0.06
40 3 0.02
41 8 0.06
ACGTcount: A:0.13, C:0.22, G:0.16, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:2496666 original size:53 final size:53
Alignment explanation
Indices: 2496594--2496753 Score: 259
Period size: 53 Copynumber: 3.0 Consensus size: 53
2496584 GATTCTCTCG
* **
2496594 TTGCGATTTTCATTT-CGCATTGTGATTCTCTCGTTGCGATTTTTTTTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
2496646 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
* * *
2496699 TTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGAGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
2496752 TT
1 TT
2496754 CTCTCGTTGC
Statistics
Matches: 101, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
52 15 0.15
53 86 0.85
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.49
Consensus pattern (53 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:2496667 original size:86 final size:86
Alignment explanation
Indices: 2496542--2496706 Score: 294
Period size: 86 Copynumber: 1.9 Consensus size: 86
2496532 AGAATCGCAA
2496542 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTACGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTACGATTCTCTCGTTGCGATTTTCAT
*
2496607 TTCGCATTGTGATTCTCTCGT
66 TTCGCATTGCGATTCTCTCGT
** *
2496628 TGCGATTTTTTTTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTACGATTCTCTCGTTGCGATTTTCAT
2496693 TTCGCATTGCGATT
66 TTCGCATTGCGATT
2496707 TTCATTTCCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 75 1.00
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.47
Consensus pattern (86 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTACGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTCTCTCGT
Found at i:2496752 original size:86 final size:84
Alignment explanation
Indices: 2496554--2496753 Score: 237
Period size: 86 Copynumber: 2.3 Consensus size: 84
2496544 CGATTTTCAT
* *
2496554 TTCGCATTGCGATTTTCATTTCCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGTGA
1 TTCG-ATTGAGATTTTCATTTCCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
*
2496619 TTCTCTCGTTGCGATTTTTTT
65 TTCTCTCGTTGCGA-TTTTTC
* *
2496640 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 TTCG-ATTGAGATTTTCATTTCCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
*
2496705 TTTTCATTTCCGCATTGCGA-TTTTC
65 --TTC-TCT-CG--TTGCGATTTTTC
2496730 TT-G-TTGAGATTTTCATTT-CGCATT
1 TTCGATTGAGATTTTCATTTCCGCATT
2496754 CTCTCGTTGC
Statistics
Matches: 103, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
86 69 0.67
87 14 0.14
88 3 0.03
89 3 0.03
90 8 0.08
92 6 0.06
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.48
Consensus pattern (84 bp):
TTCGATTGAGATTTTCATTTCCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
TCTCTCGTTGCGATTTTTC
Found at i:2499068 original size:12 final size:12
Alignment explanation
Indices: 2499051--2499075 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2499041 TCTTCGGGGA
2499051 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2499063 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2499075 C
1 C
2499076 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2499284 original size:24 final size:24
Alignment explanation
Indices: 2499250--2499296 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2499240 CTGAAACATC
2499250 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2499274 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2499297 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2500017 original size:20 final size:20
Alignment explanation
Indices: 2499989--2500217 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
2499979 AAATTTCAGT
* * *
2499989 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2500009 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2500029 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2500049 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
2500069 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2500089 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2500109 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
2500129 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
2500149 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
2500169 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
2500189 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
2500209 GTTGCGATT
1 GTTGCGATT
2500218 CTTGAAAGTC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2509110 original size:20 final size:19
Alignment explanation
Indices: 2509060--2509130 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
2509050 ATATAAAACA
2509060 CATGAGTCCATGCCAGCTC
1 CATGAGTCCATGCCAGCTC
2509079 CATGAGTCCATGCCAGCTC
1 CATGAGTCCATGCCAGCTC
2509098 CATGAGTTCCATGCCAGCTC
1 CATGAG-TCCATGCCAGCTC
2509118 CATGAGTCCATGC
1 CATGAGTCCATGC
2509131 TATGAAATAG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 32 0.63
20 19 0.37
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (19 bp):
CATGAGTCCATGCCAGCTC
Found at i:2509818 original size:37 final size:38
Alignment explanation
Indices: 2509755--2509826 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
2509745 AATAATTATT
2509755 ATATATATATAAATATTGATAAATTTAATTTAAATTAA
1 ATATATATATAAATATTGATAAATTTAATTTAAATTAA
* *
2509793 ATATATATAT-AATATTTATATATTTAATTTAAAT
1 ATATATATATAAATATTGATAAATTTAATTTAAAT
2509827 ATATATACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 22 0.69
38 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (38 bp):
ATATATATATAAATATTGATAAATTTAATTTAAATTAA
Found at i:2510123 original size:2 final size:2
Alignment explanation
Indices: 2510116--2510143 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2510106 TTGTTGTGTA
2510116 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
2510144 GAGTTAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2511473 original size:19 final size:18
Alignment explanation
Indices: 2511450--2511501 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 18
2511440 AAATTTAAAA
2511450 AAAAATTATAAATTATCGAT
1 AAAAATTATAAATTAT--AT
2511470 AAAAATATATAAATTATAT
1 AAAAAT-TATAAATTATAT
*
2511489 AAAATTTA-AAATT
1 AAAAATTATAAATT
2511502 TTCATAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 2 0.07
19 7 0.23
20 6 0.20
21 10 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAAATTATAAATTATAT
Found at i:2517536 original size:18 final size:18
Alignment explanation
Indices: 2517508--2517554 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2517498 ATTTGTATCA
2517508 TGAATCAAAATGTCAAATG
1 TGAA-CAAAATGTCAAATG
* *
2517527 TGACCAAAATGTCAAGTG
1 TGAACAAAATGTCAAATG
2517545 TGAACAAAAT
1 TGAACAAAAT
2517555 AATTCCATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACAAAATGTCAAATG
Found at i:2519444 original size:44 final size:44
Alignment explanation
Indices: 2519346--2519456 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 44
2519336 TGTTCAAGTG
* * * **
2519346 GTACCAATACAGGTATCGATACCAATGTGTAAAAATACACTGCA
1 GTACCAATACTGGTAACGATACTAATGTGTAAAAATACACTAAA
* * * * *
2519390 GTATCGATACTGATAACGATACTAGTGTGTAAGAATACACTAAA
1 GTACCAATACTGGTAACGATACTAATGTGTAAAAATACACTAAA
*
2519434 GTACCAATACTGGTACCGATACT
1 GTACCAATACTGGTAACGATACT
2519457 CCTATTAAGT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (44 bp):
GTACCAATACTGGTAACGATACTAATGTGTAAAAATACACTAAA
Found at i:2521524 original size:22 final size:21
Alignment explanation
Indices: 2521486--2521527 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2521476 GCTTGAAAAT
*
2521486 AAAAGAAAAATAAAAAACTTG
1 AAAAGAAAAAGAAAAAACTTG
*
2521507 AAAAGTAAAAAGAGAAAACTT
1 AAAAG-AAAAAGAAAAAACTT
2521528 TTATAAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (21 bp):
AAAAGAAAAAGAAAAAACTTG
Found at i:2528481 original size:38 final size:37
Alignment explanation
Indices: 2528396--2528511 Score: 151
Period size: 38 Copynumber: 3.0 Consensus size: 37
2528386 GTTAGTTTAT
*
2528396 TAACTTAAATAAATAAATATTAATAATTTTTTTTATTGA
1 TAACTTAAATAAATAAGTATTAATAA--TTTTTTATTGA
** *
2528435 TAGGTTAAATAAATAAGTATTAACAGATTTTTTATTGA
1 TAACTTAAATAAATAAGTATTAATA-ATTTTTTATTGA
*
2528473 TAACTTAAATAAATAAGTAATAATAAATTTTTTATTGA
1 TAACTTAAATAAATAAGTATTAAT-AATTTTTTATTGA
2528511 T
1 T
2528512 GGCGTCTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
38 44 0.66
39 22 0.33
40 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TAACTTAAATAAATAAGTATTAATAATTTTTTATTGA
Found at i:2531284 original size:22 final size:20
Alignment explanation
Indices: 2531250--2531297 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
2531240 ATAATTATTT
2531250 AAAAAATTAAATAAAAATATC
1 AAAAAATTAAATAAAAA-ATC
* *
2531271 AAAAATATTTAATAAAAAATT
1 AAAAA-ATTAAATAAAAAATC
2531292 AAAAAA
1 AAAAAA
2531298 AAATTAGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 11 0.46
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAATTAAATAAAAAATC
Found at i:2531372 original size:10 final size:10
Alignment explanation
Indices: 2531357--2531383 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2531347 GCTGGTTCGA
2531357 ACGGTTCCTT
1 ACGGTTCCTT
2531367 ACGGTTCCTT
1 ACGGTTCCTT
2531377 ACGGTTC
1 ACGGTTC
2531384 ACTAAAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.30, G:0.22, T:0.37
Consensus pattern (10 bp):
ACGGTTCCTT
Found at i:2532309 original size:27 final size:25
Alignment explanation
Indices: 2532279--2532344 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
2532269 TGGCGACTTC
2532279 AAATTTCAAATTAATTCAAAATAAATA
1 AAATTTCAAATT-ATTCAAAA-AAATA
* *
2532306 AAATTTCAAGTTTTTCAAAAAAAT-
1 AAATTTCAAATTATTCAAAAAAATA
2532330 AAA-TTCATAATTATT
1 AAATTTCA-AATTATT
2532345 TTTAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.12
24 8 0.24
25 4 0.12
26 7 0.21
27 11 0.32
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.38
Consensus pattern (25 bp):
AAATTTCAAATTATTCAAAAAAATA
Found at i:2546279 original size:50 final size:50
Alignment explanation
Indices: 2546203--2546301 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
2546193 TCTGTTTCGA
*
2546203 AAACATAAGAAATACAATCAACCACAACAAATAATTTAATCCAAGTAGCG
1 AAACATAAGAAATACAATCAAACACAACAAATAATTTAATCCAAGTAGCG
2546253 AAACATAAGAAATACAATCAAACACAACAAATAATTTAATCCAAGTAGC
1 AAACATAAGAAATACAATCAAACACAACAAATAATTTAATCCAAGTAGC
2546302 AACACTAAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.56, C:0.19, G:0.07, T:0.18
Consensus pattern (50 bp):
AAACATAAGAAATACAATCAAACACAACAAATAATTTAATCCAAGTAGCG
Found at i:2553216 original size:31 final size:31
Alignment explanation
Indices: 2553176--2553246 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
2553166 AAAAATAGTA
2553176 TTTGAATCACGTATGCTATCAGTTCT-TTAC-AT
1 TTTG-ATCACGTA-GCTATCAGTT-TATTACAAT
* *
2553208 TTTGATCACTTAGTTATCAGTTTATTACAAT
1 TTTGATCACGTAGCTATCAGTTTATTACAAT
2553239 TTTG-TCAC
1 TTTGATCAC
2553247 TGATTCGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 1 0.03
30 17 0.49
31 13 0.37
32 4 0.11
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46
Consensus pattern (31 bp):
TTTGATCACGTAGCTATCAGTTTATTACAAT
Found at i:2554126 original size:19 final size:20
Alignment explanation
Indices: 2554100--2554153 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2554090 AGTTTCCCAA
*
2554100 AAAGTTTTGATACTTT-TC-
1 AAAGTTTTGATACTTTCCCT
*
2554118 AAGAGTTTTGAAACTTTCCCT
1 AA-AGTTTTGATACTTTCCCT
2554139 AAAGTTTTGATACTT
1 AAAGTTTTGATACTT
2554154 GGGCTCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 2 0.07
19 13 0.43
20 13 0.43
21 2 0.07
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
AAAGTTTTGATACTTTCCCT
Found at i:2555115 original size:20 final size:21
Alignment explanation
Indices: 2555090--2555133 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2555080 TGGGTATCAG
* *
2555090 TACTGAA-GGATCTATATTGA
1 TACTGAAGGGATCAATATCGA
2555110 TACTGAAGGGATCAATATCGA
1 TACTGAAGGGATCAATATCGA
2555131 TAC
1 TAC
2555134 CATCATATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (21 bp):
TACTGAAGGGATCAATATCGA
Found at i:2556143 original size:31 final size:31
Alignment explanation
Indices: 2556108--2556207 Score: 132
Period size: 31 Copynumber: 3.3 Consensus size: 31
2556098 AACATCTAAA
* *
2556108 TGACCAAAACTTAATAAAAAGATAATACAAG
1 TGACCAAAACTTAATAAAAAGATAACATAAG
* *
2556139 TGACCAAAACTTAATAAAACGATAACATGAG
1 TGACCAAAACTTAATAAAAAGATAACATAAG
* *
2556170 TGATC-AAACTTAAT-AAATGATAACATAAG
1 TGACCAAAACTTAATAAAAAGATAACATAAG
2556199 TGACCAAAA
1 TGACCAAAA
2556208 TTTATGTTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
29 17 0.28
30 12 0.20
31 31 0.52
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (31 bp):
TGACCAAAACTTAATAAAAAGATAACATAAG
Found at i:2556600 original size:15 final size:15
Alignment explanation
Indices: 2556580--2556627 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 15
2556570 TTCTTGTATA
2556580 TTTTATATTTTCATG
1 TTTTATATTTTCATG
*
2556595 -TTT-TATGTT-ATG
1 TTTTATATTTTCATG
2556607 TTTTATATTTTCATG
1 TTTTATATTTTCATG
*
2556622 ATTTAT
1 TTTTAT
2556628 GTTATGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 3 0.11
13 8 0.30
14 8 0.30
15 8 0.30
ACGTcount: A:0.21, C:0.04, G:0.08, T:0.67
Consensus pattern (15 bp):
TTTTATATTTTCATG
Found at i:2556610 original size:27 final size:27
Alignment explanation
Indices: 2556580--2556637 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
2556570 TTCTTGTATA
*
2556580 TTTTATATTTTCATGTTTTATGTTATG
1 TTTTATATTTTCATGATTTATGTTATG
2556607 TTTTATATTTTCATGATTTATGTTATG
1 TTTTATATTTTCATGATTTATGTTATG
2556634 TTTT
1 TTTT
2556638 GATTTGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.03, G:0.10, T:0.67
Consensus pattern (27 bp):
TTTTATATTTTCATGATTTATGTTATG
Found at i:2557381 original size:23 final size:24
Alignment explanation
Indices: 2557339--2557388 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2557329 AATATATGTT
* *
2557339 TTTTAAAAAATCAATATTAAACTA
1 TTTTAAAAAATAAATATTAAAATA
*
2557363 TTTTAAAAATTAAAT-TTAAAATA
1 TTTTAAAAAATAAATATTAAAATA
2557386 TTT
1 TTT
2557389 ATTTATGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTTAAAAAATAAATATTAAAATA
Found at i:2558280 original size:20 final size:20
Alignment explanation
Indices: 2558242--2558281 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2558232 CATCCATATC
*
2558242 TTTGTTTTCCATTTCTTTTA
1 TTTGTTTTCCATTTATTTTA
2558262 TTTGTTTT-CACTTTATTTTA
1 TTTGTTTTCCA-TTTATTTTA
2558282 AGCAATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.12, C:0.12, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTGTTTTCCATTTATTTTA
Found at i:2564019 original size:18 final size:17
Alignment explanation
Indices: 2563989--2564028 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
2563979 GTTTTTAAAA
2563989 ATTTTAAATTTTTATAT
1 ATTTTAAATTTTTATAT
2564006 ATTTTAGATATTTTT-TAT
1 ATTTTA-A-ATTTTTATAT
2564024 ATTTT
1 ATTTT
2564029 TATTAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 9 0.43
19 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTAAATTTTTATAT
Found at i:2564056 original size:22 final size:24
Alignment explanation
Indices: 2564018--2564064 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
2564008 TTTAGATATT
2564018 TTTTATATTTTTATTAAAAGTTTA
1 TTTTATATTTTTATTAAAAGTTTA
*
2564042 TTTT-TATTTTT-TTAAAATTTTA
1 TTTTATATTTTTATTAAAAGTTTA
2564064 T
1 T
2564065 AAATATGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 7 0.32
24 4 0.18
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTATATTTTTATTAAAAGTTTA
Found at i:2567412 original size:22 final size:22
Alignment explanation
Indices: 2567378--2567448 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
2567368 TCAGTATTTA
* *
2567378 TCCCGAAGGACCACTGAATATG
1 TCCCGAAGGACCACTGGATACG
* *
2567400 TCCCAAAGAACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
2567422 TCCCGAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
2567444 TCCCG
1 TCCCG
2567449 GATGACTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.30, C:0.32, G:0.23, T:0.15
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATACG
Found at i:2568847 original size:5 final size:5
Alignment explanation
Indices: 2568837--2568862 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2568827 ATGATTTATT
2568837 TTTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA T
2568863 ATTTATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:2572173 original size:13 final size:13
Alignment explanation
Indices: 2572155--2572181 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2572145 GGGCGTTGCA
2572155 TAATCTTATTTGG
1 TAATCTTATTTGG
2572168 TAATCTTATTTGG
1 TAATCTTATTTGG
2572181 T
1 T
2572182 CGGATTCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TAATCTTATTTGG
Found at i:2574633 original size:197 final size:197
Alignment explanation
Indices: 2574227--2575206 Score: 953
Period size: 197 Copynumber: 5.0 Consensus size: 197
2574217 TAATTTTCAA
* * * *
2574227 AAGTATCGACACTAATTTAA-AAAGTGTCGATACAT-TCTGTAGACCTATTTTCTCATAAAACTG
1 AAGTATCGACAC-AAATGAATAAAGTGTCGACACATAT-TGTAGACCTATTTT-TCATAAAACCG
* *
2574290 GTAAATTTAAACCGGTTACATTGTAAAATGACCTATTACATTATAATTACGGGTTCGATGTTTTT
63 GTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGTTTCGATGTTTTT
* *
2574355 AGGATCG--ACTTTTTCTAAATGTATCGAC-CTTTTTCGTGAACTT-GTTTGGAAAATTTATTAT
128 AGGATCGACACTTTTTATAAATGTATCGACACTTTTTCGTGAACTTGGTTTGGAAAA--CATTAT
2574416 GGACATA-
191 GGACA-AC
* * * * * * **
2574423 AAGTGTCGACACAAATGTATAAAGTATCGATACAT-TATGTATACCT-TTTTTTA-AATAACCAA
1 AAGTATCGACACAAATGAATAAAGTGTCGACACATAT-TGTAGACCTATTTTTCATAA-AACCGG
* * * * * * * *
2574485 TATATTTAGACCGGTTACATTGTTATGTTACCGATTACATTATAATTATGTGTTTCGATGTTTGT
64 TAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACG-GTTTCGATGTTTTT
*
2574550 ATGATCGACACTTTTTATAAATGTATCGACACTTTGTTCGT-ACACTTGGTTTGGAAATACA-T-
128 AGGATCGACACTTTTTATAAATGTATCGACACTTT-TTCGTGA-ACTTGGTTTGGAAA-ACATTA
2574612 TGGACAAC
190 TGGACAAC
*
2574620 ATGTATCGACACAAATGAATAAAGTGTCGACACATATTGTAGACCTA-TTTTCATAAAACCGGTA
1 AAGTATCGACACAAATGAATAAAGTGTCGACACATATTGTAGACCTATTTTTCATAAAACCGGTA
* * *
2574684 AATTTAAACCGATTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTGG
66 AATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTAC-GGTTTCGATGTTTTTAG
* *
2574749 GATCGACAC--TTGATAAATGTGTCGACACTTATTT-GTGAACTTGTTTTGTTTGGAAAACATTA
130 GATCGACACTTTTTATAAATGTATCGACACTT-TTTCGTGAACTTG----GTTTGGAAAACATTA
2574811 TGGAC-AC
190 TGGACAAC
** ** * * * * *
2574818 AAAGTATCGGTACAAATTTATAAAGTGTCGATACTTA-TGAATACCTCTTTTCTCAT-AAACC-G
1 -AAGTATCGACACAAATGAATAAAGTGTCGACACATATTGTAGACCTATTTT-TCATAAAACCGG
* * * * ** *
2574880 TATATTTAGACCGATTACATTGTTATTTTACCTATTACA-T-TAATTACGGATTTCGATGTTTTT
64 TAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGG-TTTCGATGTTTTT
* * * *
2574943 GGGATCGATACTTTTTATAAATGTATCGACACTTTGTTCGTGCACTTGGTTTGG-AAA-A-T-TC
128 AGGATCGACACTTTTTATAAATGTATCGACACTTT-TTCGTGAACTTGGTTTGGAAAACATTATG
2575004 GACAAC
192 GACAAC
*
2575010 ATGTATCGACACAAATGAATAAA--GTCGACACATATTGTAGA-CTATTTTCTCATAAAACCGGT
1 AAGTATCGACACAAATGAATAAAGTGTCGACACATATTGTAGACCTATTTT-TCATAAAACCGGT
* *
2575072 AAATTTAAACTGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTA
65 AAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTAC-GGTTTCGATGTTTTTA
** * *
2575137 GGATCGACACTTGATATAAATGTGTCGACACTTATT--TGAACTTGTTTGTTTGGAAAACACATT
129 GGATCGACACTTTTTATAAATGTATCGACACTTTTTCGTGAACTTG---GTTTGG-AAA-ACATT
2575200 ATGGACA
189 ATGGACA
2575207 CTTTGCCTTT
Statistics
Matches: 641, Mismatches: 96, Indels: 91
0.77 0.12 0.11
Matches are distributed among these distances:
189 20 0.03
190 16 0.02
191 54 0.08
192 6 0.01
193 57 0.09
194 59 0.09
195 58 0.09
196 66 0.10
197 141 0.22
198 85 0.13
199 65 0.10
200 13 0.02
201 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (197 bp):
AAGTATCGACACAAATGAATAAAGTGTCGACACATATTGTAGACCTATTTTTCATAAAACCGGTA
AATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGTTTCGATGTTTTTAGG
ATCGACACTTTTTATAAATGTATCGACACTTTTTCGTGAACTTGGTTTGGAAAACATTATGGACA
AC
Found at i:2574958 original size:393 final size:394
Alignment explanation
Indices: 2574229--2575207 Score: 1345
Period size: 393 Copynumber: 2.5 Consensus size: 394
2574219 ATTTTCAAAA
* * * *
2574229 GTATCGACACTAATTTAA-AAAGTGTCGATACAT-TCTGTAGACCTATTTTCTCATAAAACTGGT
1 GTATCGACAC-AAATGAATAAAGTGTCGACACATAT-TGTAGACCTATTTTCTCATAAAACCGGT
* *
2574292 AAATTTAAACCGGTTACATTGTAAAATGACCTATTACATTATAATTACGGG-TTCGATGTTTTTA
64 AAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTA
** ** * *
2574356 GGATCGACTTTTTCTAAATGTATCGAC-CTT-TTTCGTGAAC----TTGTTTGGAAAATTTATTA
129 GGATCGACACTTGATAAATGTGTCGACACTTATTT-GTGAACTTGTTTGTTTGGAAAA--CATTA
* * * *
2574415 TGGACATAAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTAAATA
191 TGGACACAAAGTATCGACACAAATGTATAAAGTATCGATACATTATGAATACCTTTTTTCAAATA
* *
2574480 ACCAATATATTTAGACCGGTTACATTGTTATGTTACCGATTACATTATAATTATGTGTTTCGATG
256 ACCAATATATTTAGACCGATTACATTGTTATGTTACCGATTACATTATAATTACGTGTTTCGATG
*
2574545 TTTGTATGATCGACACTTTTTATAAATGTATCGACACTTTGTTCGTACACTTGGTTTGGAAATAC
321 TTTGTAGGATCGACACTTTTTATAAATGTATCGACACTTTGTTCGTACACTTGGTTTGG-AA-A-
*
2574610 ATTGGACAACAT
383 ATTCGACAACAT
2574622 GTATCGACACAAATGAATAAAGTGTCGACACATATTGTAGACCTA-TTT-TCATAAAACCGGTAA
1 GTATCGACACAAATGAATAAAGTGTCGACACATATTGTAGACCTATTTTCTCATAAAACCGGTAA
* *
2574685 ATTTAAACCGATTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTGGG
66 ATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTAGG
2574750 ATCGACACTTGATAAATGTGTCGACACTTATTTGTGAACTTGTTTTGTTTGGAAAACATTATGGA
131 ATCGACACTTGATAAATGTGTCGACACTTATTTGTGAACTTG-TTTGTTTGGAAAACATTATGGA
** * * *
2574815 CACAAAGTATCGGTACAAATTTATAAAGTGTCGATAC-TTATGAATACCTCTTTTCTCATA-AAC
195 CACAAAGTATCGACACAAATGTATAAAGTATCGATACATTATGAATACCT-TTTT-TCAAATAAC
* * *
2574878 C-GTATATTTAGACCGATTACATTGTTATTTTACCTATTACA-T-TAATTACG-GATTTCGATGT
258 CAATATATTTAGACCGATTACATTGTTATGTTACCGATTACATTATAATTACGTG-TTTCGATGT
* * * *
2574939 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTGTTCGTGCACTTGGTTTGGAAAATTC
322 TTGTAGGATCGACACTTTTTATAAATGTATCGACACTTTGTTCGTACACTTGGTTTGGAAAATTC
2575004 GACAACAT
387 GACAACAT
2575012 GTATCGACACAAATGAATAAA--GTCGACACATATTGTAGA-CTATTTTCTCATAAAACCGGTAA
1 GTATCGACACAAATGAATAAAGTGTCGACACATATTGTAGACCTATTTTCTCATAAAACCGGTAA
*
2575074 ATTTAAACTGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTAGG
66 ATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTAGG
2575139 ATCGACACTTGATATAAATGTGTCGACACTTA-TT-TGAACTTGTTTGTTTGGAAAACACATTAT
131 ATCGACACTTG--ATAAATGTGTCGACACTTATTTGTGAACTTGTTTGTTTGG-AAA-ACATTAT
2575202 GGACAC
192 GGACAC
2575208 TTTGCCTTTG
Statistics
Matches: 530, Mismatches: 37, Indels: 41
0.87 0.06 0.07
Matches are distributed among these distances:
387 3 0.01
388 30 0.06
389 99 0.19
390 47 0.09
391 80 0.15
392 45 0.08
393 112 0.21
394 5 0.01
395 47 0.09
396 47 0.09
397 3 0.01
398 12 0.02
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (394 bp):
GTATCGACACAAATGAATAAAGTGTCGACACATATTGTAGACCTATTTTCTCATAAAACCGGTAA
ATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTAGG
ATCGACACTTGATAAATGTGTCGACACTTATTTGTGAACTTGTTTGTTTGGAAAACATTATGGAC
ACAAAGTATCGACACAAATGTATAAAGTATCGATACATTATGAATACCTTTTTTCAAATAACCAA
TATATTTAGACCGATTACATTGTTATGTTACCGATTACATTATAATTACGTGTTTCGATGTTTGT
AGGATCGACACTTTTTATAAATGTATCGACACTTTGTTCGTACACTTGGTTTGGAAAATTCGACA
ACAT
Found at i:2577538 original size:182 final size:182
Alignment explanation
Indices: 2576891--2577538 Score: 878
Period size: 182 Copynumber: 3.6 Consensus size: 182
2576881 TATTAAAGTA
* * * * *
2576891 CGAC-CTTTCAACATAACCGGTAGCACTTTACCGATTTTATCATTTCGATACCGGTTTTATCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCAT-
* * * *
2576955 ATT-TTACC-ATTATATTGTTATGGATCGATACATTTTCT-TAAAGTATCGACACTTTTTAGATG
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTTT-TATAAAGTATCGACACCTTTTAGGTG
* *
2577017 CTATAATTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
129 CTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* * ** *
2577071 CGACACTTTCAATATATCCGGTATCTTTTTACCGGTTTTATCATTTCGAGACCTCTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCATA
* * * *
2577136 TTATTACCGGATATATTACTATGGATCGATACATTTGTATAAAGTATCGACA-CTTTTCAGGTGC
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACCTTTT-AGGTGC
2577200 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* * * *
2577253 CGACACTTTCAATATATCTGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCATA
* * *
2577318 TTATTACCTGTTATATTGCTATGGATCGACATATTTTTATAAAGTATCAACACCTTTTAGGCT-C
66 TTATTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACCTTTTAGG-TGC
* *
2577382 TATAACTTCTTCTCTTTTAAATTATAAAAGTGTCGACACTTATATTAATTTAT
130 TATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
* * * * **
2577435 CGATACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCATAAT-GTCACCGGTTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCAT-TTCGAGACCGGTTTTATCAT
*
2577499 ATTTTTACCTGTTATATTGCTATGGATCGATACATTTTTA
65 ATTATTACCTGTTATATTGCTATGGATCGATACATTTTTA
2577539 ATTTGTATCG
Statistics
Matches: 418, Mismatches: 42, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
180 7 0.02
181 59 0.14
182 345 0.83
183 7 0.02
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.43
Consensus pattern (182 bp):
CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTATCATA
TTATTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACCTTTTAGGTGCT
ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
Done.