Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold41
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: 2798036
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 10448 characters in sequence are not A, C, G, or T
File 18 of 21
Found at i:2240822 original size:25 final size:27
Alignment explanation
Indices: 2240773--2240834 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 27
2240763 ATTTAAAAGT
*
2240773 TAATTTTATTGTTTATTATATTATTAA
1 TAATTTTATTGTTTATTATACTATTAA
2240800 -AATTTTATT-TTTA-TATTACTATTAA
1 TAATTTTATTGTTTATTA-TACTATTAA
2240825 TATATTTTAT
1 TA-ATTTTAT
2240835 ACTTTAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 2 0.06
25 12 0.39
26 10 0.32
27 7 0.23
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (27 bp):
TAATTTTATTGTTTATTATACTATTAA
Found at i:2242989 original size:90 final size:90
Alignment explanation
Indices: 2242836--2243016 Score: 290
Period size: 90 Copynumber: 2.0 Consensus size: 90
2242826 GATAAAAGCT
* * *
2242836 CTGATGAGGCAAAAGGTGATGGGCAGGTTAAAAAACAGAGCTCAAATGAAGTTTTCCTATCTGGT
1 CTGATGAGGCAAAAGATGATGGGCAGGTGAAAAAACAGAGCTCAAAAGAAGTTTTCCTATCTGGT
*
2242901 GCTCAGTCTGAACTTTTGAATGAAA
66 GCACAGTCTGAACTTTTGAATGAAA
* * * *
2242926 CTGATGAGGCAATAGATGATGGTCAGGTGAAAAACCAGAGCTCAAAAGAAGTTTTTCTATCTGGT
1 CTGATGAGGCAAAAGATGATGGGCAGGTGAAAAAACAGAGCTCAAAAGAAGTTTTCCTATCTGGT
2242991 GCACAGTCTGAACTTTTGAATGAAA
66 GCACAGTCTGAACTTTTGAATGAAA
2243016 C
1 C
2243017 CATGACTCAG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.27
Consensus pattern (90 bp):
CTGATGAGGCAAAAGATGATGGGCAGGTGAAAAAACAGAGCTCAAAAGAAGTTTTCCTATCTGGT
GCACAGTCTGAACTTTTGAATGAAA
Found at i:2246595 original size:119 final size:119
Alignment explanation
Indices: 2246384--2246614 Score: 417
Period size: 119 Copynumber: 1.9 Consensus size: 119
2246374 CATAAATTGA
*
2246384 CTGACTACACTTACAGCATAAGCTATGTTCAGTCTTGTGTGTGAAAGATAAATCAGTTTGCCAAC
1 CTGACTACACTTACAGCATAAGCTATGTTCAGTCTTGTGTGCGAAAGATAAATCAGTTTGCCAAC
*
2246449 TAACTTCTGGTACCTTTCTCTATCAACCATAAGATCTTTTAGTGCTTTTCCAAG
66 TAACTTCTGGTACCTTTCTCTATCAACCATAAGATCCTTTAGTGCTTTTCCAAG
*
2246503 CTGACTACACTTACAGCATAAGCTATGTTCAGTCTTGTGTGCGAGAGATAAATCAGTTTGCCAAC
1 CTGACTACACTTACAGCATAAGCTATGTTCAGTCTTGTGTGCGAAAGATAAATCAGTTTGCCAAC
* *
2246568 TAACTTTTGGTACCTTTCTCTATCAACCATAGGATCCTTTAGTGCTT
66 TAACTTCTGGTACCTTTCTCTATCAACCATAAGATCCTTTAGTGCTT
2246615 CTCCCAGTTT
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
119 107 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (119 bp):
CTGACTACACTTACAGCATAAGCTATGTTCAGTCTTGTGTGCGAAAGATAAATCAGTTTGCCAAC
TAACTTCTGGTACCTTTCTCTATCAACCATAAGATCCTTTAGTGCTTTTCCAAG
Found at i:2247832 original size:36 final size:35
Alignment explanation
Indices: 2247760--2247838 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 35
2247750 TGGGGACAAA
* * * *
2247760 GGTATTGACTCAGCTTGGTTTGAGACTTAGATTGT
1 GGTAGTGACTCAGCTTGGTTTGAGACTCAAAATGT
*
2247795 GGTAGTGACTTAGCTTGGTTTTGAGACTCAAAATGT
1 GGTAGTGACTCAGCTTGG-TTTGAGACTCAAAATGT
*
2247831 GGCAGTGA
1 GGTAGTGA
2247839 GAGATTTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 16 0.43
36 21 0.57
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.35
Consensus pattern (35 bp):
GGTAGTGACTCAGCTTGGTTTGAGACTCAAAATGT
Found at i:2252571 original size:16 final size:16
Alignment explanation
Indices: 2252550--2252589 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2252540 AAAAACTATT
*
2252550 TAAAATGA-TCTAAATA
1 TAAAATGAGT-TAAACA
2252566 TAAAATGAGTTAAACA
1 TAAAATGAGTTAAACA
2252582 TAAAATGA
1 TAAAATGA
2252590 CTTCAGCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (16 bp):
TAAAATGAGTTAAACA
Found at i:2253124 original size:17 final size:18
Alignment explanation
Indices: 2253104--2253139 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2253094 AATAGAACTC
2253104 TTTTATTTATTAT-TATT
1 TTTTATTTATTATATATT
*
2253121 TTTTATTTTTTATATATT
1 TTTTATTTATTATATATT
2253139 T
1 T
2253140 GCACATGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATTTATTATATATT
Found at i:2258343 original size:36 final size:36
Alignment explanation
Indices: 2258293--2258362 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
2258283 CTAAAATCTT
** *
2258293 TGGATATACCACCAAATTCTTTTAAATCTAGATATG
1 TGGATATACCACCAAAGACTTTGAAATCTAGATATG
** *
2258329 TGGATATATTACCAAAGACTTTGAATTCTAGATA
1 TGGATATACCACCAAAGACTTTGAAATCTAGATA
2258363 GCCCTACTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (36 bp):
TGGATATACCACCAAAGACTTTGAAATCTAGATATG
Found at i:2258455 original size:59 final size:59
Alignment explanation
Indices: 2258392--2258676 Score: 241
Period size: 59 Copynumber: 4.9 Consensus size: 59
2258382 TATATCAACT
* * *
2258392 AAAGACTTGACTTCTAGAATATTCTGGTCACCACCACCAGAAACTTTGGATACACCATC
1 AAAGACTTGACTTCTAGAATATTCTAGTTACCACCACCAGAAACTTTGGATACACCACC
* * * * *
2258451 AAAGACTTGACTTCTAGAATAATT-TAGTTAACGCCATCAGAAGCCTTGGATACACCACC
1 AAAGACTTGACTTCTAGAAT-ATTCTAGTTACCACCACCAGAAACTTTGGATACACCACC
* * * *
2258510 AATGACTTGGCTTCTAAGAATATTCTAGTTACCACCACTAGAATCTTTGGATACACCACC
1 AAAGACTTGACTTCT-AGAATATTCTAGTTACCACCACCAGAAACTTTGGATACACCACC
* ** *
2258570 -AA-A--T-A--TCTAGAATATT-TCGATTACCACCACC-GAAAGCTTTTAATATACCACC
1 AAAGACTTGACTTCTAGAATATTCTAG-TTACCACCACCAGAAA-CTTTGGATACACCACC
* * * ** * *
2258622 AAAGACTTAACTTCTAAAACATT-TCAGTTACCACCATTAGAAGCTTTAGATACAC
1 AAAGACTTGACTTCTAGAATATTCT-AGTTACCACCACCAGAAACTTTGGATACAC
2258677 TAACTTGACT
Statistics
Matches: 179, Mismatches: 33, Indels: 28
0.75 0.14 0.12
Matches are distributed among these distances:
51 5 0.03
52 31 0.17
53 5 0.03
54 1 0.01
56 2 0.01
57 1 0.01
58 1 0.01
59 92 0.51
60 41 0.23
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.28
Consensus pattern (59 bp):
AAAGACTTGACTTCTAGAATATTCTAGTTACCACCACCAGAAACTTTGGATACACCACC
Found at i:2263315 original size:19 final size:19
Alignment explanation
Indices: 2263291--2263358 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
2263281 AATTCAACAA
2263291 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2263310 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
2263325 --TGTATCGATACATCAGT
1 TTTGTATCGATACATAAGT
*
2263342 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2263359 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 11 0.27
15 1 0.02
17 2 0.05
19 27 0.66
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2263330 original size:13 final size:13
Alignment explanation
Indices: 2263312--2263336 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2263302 ACATAAGTTT
2263312 TGTATCGATACAA
1 TGTATCGATACAA
2263325 TGTATCGATACA
1 TGTATCGATACA
2263337 TCAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2263334 original size:32 final size:32
Alignment explanation
Indices: 2263293--2263355 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2263283 TTCAACAATT
*
2263293 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
2263325 TGTATCGATACATCAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2263356 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2263416 original size:13 final size:13
Alignment explanation
Indices: 2263398--2263436 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
2263388 CATTTTTCTA
2263398 TGTATCGATACAT
1 TGTATCGATACAT
2263411 TGTATCGATACAT
1 TGTATCGATACAT
2263424 TGTATCGATACAT
1 TGTATCGATACAT
2263437 GGATCTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2266027 original size:52 final size:50
Alignment explanation
Indices: 2265960--2266127 Score: 142
Period size: 52 Copynumber: 3.2 Consensus size: 50
2265950 TTTCCGAGGA
*
2265960 GATACTCTAACCCCGGTTTTATCGCTAAAACACTAATTTTTCCACAATCGGG
1 GATACTCCAA-CCCGGTTTTATC-CTAAAACACTAATTTTTCCACAATCGGG
** * **
2266012 GATACTCCAATCCCGGTTTTATTTTCAAAACGCTAA-TTTTCCTTTAATCGGG
1 GATACTCCAA-CCCGGTTTTATCCT-AAAACACTAATTTTTCC-ACAATCGGG
* * * * **
2266064 GATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCTAG
1 GATACTCCAAC-CCGGTTTTA--TCCTAAAACACTAATTTTTCCACAATCGGG
2266116 GATACTCCAACC
1 GATACTCCAACC
2266128 TCGTTATTTC
Statistics
Matches: 92, Mismatches: 18, Indels: 13
0.75 0.15 0.11
Matches are distributed among these distances:
51 9 0.10
52 70 0.76
53 8 0.09
54 5 0.05
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (50 bp):
GATACTCCAACCCGGTTTTATCCTAAAACACTAATTTTTCCACAATCGGG
Found at i:2266147 original size:28 final size:28
Alignment explanation
Indices: 2266115--2266186 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
2266105 TCACAATCTA
* * **
2266115 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
2266143 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
2266171 GGATACTCCAATCCCG
1 GGATACTCCAACCCCG
2266187 ATTTTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:2266155 original size:212 final size:212
Alignment explanation
Indices: 2265788--2266178 Score: 608
Period size: 212 Copynumber: 1.8 Consensus size: 212
2265778 TTCTCAATTC
* * *
2265788 TCCACAATCGGGGATATTCCAACTTCGATTTTATTTTCAAAACACTAATTTTCTATAATTGGGAA
1 TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGAA
* *
2265853 TACTCTAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAACCC
*
2265918 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGAGATACTCTAACCCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGAGATACTCTAACCCCGGTTTTATC
2265983 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * *
2266000 TCCACAATCGGGGATACTCCAA-TCCCGGTTTTATTTTCAAAACGCTAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGG
* *
2266064 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCTAGGATACTCCAAC
64 AATACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAAC
* * *
2266127 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTC
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGAGATACTC
2266179 CAATCCCGAT
Statistics
Matches: 162, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 28 0.17
212 101 0.62
213 33 0.20
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (212 bp):
TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGAA
TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGAGATACTCTAACCCCGGTTTTATC
GCTAAAACACTAATTTT
Found at i:2276622 original size:11 final size:10
Alignment explanation
Indices: 2276592--2276667 Score: 57
Period size: 10 Copynumber: 7.6 Consensus size: 10
2276582 CATTCTCTTC
2276592 AAAAAAGAAA
1 AAAAAAGAAA
**
2276602 GCAAAAGAAA
1 AAAAAAGAAA
2276612 AAAAAAGGAAA
1 AAAAAA-GAAA
*
2276623 AAAAAA-CAA
1 AAAAAAGAAA
*
2276632 AAAAAA-CAA
1 AAAAAAGAAA
*
2276641 AACAAAGAAA
1 AAAAAAGAAA
* *
2276651 AAGAGAGAAA
1 AAAAAAGAAA
2276661 AGAAAAA
1 A-AAAAA
2276668 AACCTACTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
9 16 0.31
10 23 0.44
11 13 0.25
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:2277842 original size:55 final size:54
Alignment explanation
Indices: 2277636--2278330 Score: 824
Period size: 55 Copynumber: 12.3 Consensus size: 54
2277626 TCCGCTTTTT
2277636 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
2277689 TAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 -AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTC
* *
2277745 AGTCCCCAAAGAG-AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-C
*
2277799 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTTTAGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAA----G-TT-GGTGGCACTTT-C
*
2277860 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-C
* *
2277915 AGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTC
* * *
2277969 AGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* * * *
2278028 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCACTTTC
* * *
2278087 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAATTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * *
2278148 AGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTC
2278203 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * * *
2278258 AGTCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACTAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTC
* *
2278313 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
2278331 TACACTTTAT
Statistics
Matches: 573, Mismatches: 34, Indels: 67
0.85 0.05 0.10
Matches are distributed among these distances:
53 5 0.01
54 115 0.20
55 242 0.42
56 10 0.02
57 1 0.00
58 2 0.00
59 96 0.17
60 23 0.04
61 74 0.13
64 4 0.01
65 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (54 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
Found at i:2278256 original size:110 final size:110
Alignment explanation
Indices: 2277636--2278820 Score: 1210
Period size: 110 Copynumber: 10.7 Consensus size: 110
2277626 TCCGCTTTTT
2277636 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA--TTTCTAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAA
* *
2277699 AGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
65 AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTC
* *
2277745 AGTCCCCAAAGAG-AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAA
*
2277808 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTTTAGGTGGCAT-TTTCC
65 AGAGCAGGACACCTTTTAAAGCCCACACAA----G-TT-GGTGGCATCTTT-C
* *
2277860 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAG
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAA
* *
2277924 AGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-CCTTC
65 AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTC
* *
2277969 AGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCC
1 AGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* * * *
2278033 TCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCA-CCTTC
61 TCAAAGAGCAGGAC-AC----CTTTTAAAGCCCACACAAGTTGGTGGCATCTTTC
* * *
2278087 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTC
1 AGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* *
2278152 CCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTC
60 CTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTC
*
2278203 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTTAA
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* * * *
2278267 AGAGCAGGACGCCTTTCAAAGCCCACACTAGTTGGTGGCA-CTTTTT
65 AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATC-TTTC
* * * **** * *
2278313 ACTCCTCAATGAGCAGGATACACTTT--ATTTTC-CTC---TT--T-----CTTT--GTCCTCAG
1 AGTCCTCAAAGAGCAGGACAC-CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* *
2278363 AGAGCAGGACATCTTTCAAAGCCCACACAAGTTGGTGGCAT-TTTCC
65 AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATCTTT-C
* *
2278409 AGTCCTTAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* *
2278472 AGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTC
65 AGAGCAGGACAC-----CTTTTAAAGCCCACACAAGTTGGTGGCATCTTTC
* *
2278522 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 AGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* * * * * * *
2278587 CCCAAAGAGTAGAACCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTG
60 CTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTC
* *
2278638 AGT-CTCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCA
1 AGTCCT-CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCA
* *
2278701 AAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
64 AAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTC
* ** * * * *
2278748 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATGAGTTGGTGGCACTTTTTACTCCTCAAT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
2278813 GAGCAGGA
66 GAGCAGGA
2278821 TACACTTTAT
Statistics
Matches: 910, Mismatches: 97, Indels: 137
0.80 0.08 0.12
Matches are distributed among these distances:
95 5 0.01
96 61 0.07
97 2 0.00
98 6 0.01
101 2 0.00
103 2 0.00
105 2 0.00
107 2 0.00
108 38 0.04
109 95 0.10
110 241 0.26
111 12 0.01
112 1 0.00
113 36 0.04
114 66 0.07
115 77 0.08
116 116 0.13
118 50 0.05
119 55 0.06
120 40 0.04
124 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (110 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
GAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTC
Found at i:2278439 original size:55 final size:55
Alignment explanation
Indices: 2278355--2278820 Score: 532
Period size: 55 Copynumber: 8.3 Consensus size: 55
2278345 CTCTTTCTTT
* * *
2278355 GTCCTCAGAGAGCAGGACATCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCA
1 GTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CA
* *
2278410 GTCCTTAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC-TTCA
1 GTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
* *
2278464 GTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCA
1 GTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
* *
2278523 GTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
1 GTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
* * * * *
2278584 GTCCCCAAAGAGTAGAACCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTGA
1 GTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
* *
2278639 GT-CTCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCA
1 GTCCT-CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CA
2278694 GTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCA
1 GTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
* ** * *
2278749 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATGAGTTGGTGGCACTTTTTA
1 GTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
* *
2278804 CTCCTCAATGAGCAGGA
1 GTCCTCAAAGAGCAGGA
2278821 TACACTTTAT
Statistics
Matches: 359, Mismatches: 31, Indels: 42
0.83 0.07 0.10
Matches are distributed among these distances:
54 25 0.07
55 227 0.63
56 9 0.03
58 2 0.01
59 48 0.13
60 28 0.08
61 19 0.05
65 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (55 bp):
GTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
Found at i:2278802 original size:490 final size:491
Alignment explanation
Indices: 2277861--2278862 Score: 1760
Period size: 490 Copynumber: 2.0 Consensus size: 491
2277851 GCATTTTCCA
*
2277861 GTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAGAG
1 GTCCTCAGAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAGAG
2277926 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACA
66 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACA
*
2277991 TTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCT
131 TTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCT
* * * * *
2278056 TTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAA
196 TTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCCCAAAGAGCAGGATAC---TCCCTTTCAA
2278121 AGCCCACACAAATTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACA
258 AGCCCACACAAATTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACA
*
2278186 AGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGC
323 AGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGC
*
2278251 ACCTTTCAGTCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACTAGTTGGTGGCACTTTTTACT
388 ACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACTAGTTGGTGGCACTTTTTACT
2278316 CCTCAATGAGCAGGATACACTTTATTTTCCTCTTTCTTT
453 CCTCAATGAGCAGGATACACTTTATTTTCCTCTTTCTTT
* *
2278355 GTCCTCAGAGAGCAGGACATCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTTAGAG
1 GTCCTCAGAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAGAG
2278420 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACA
66 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACA
* *
2278485 TTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCT
131 TTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCT
*
2278550 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGTA-GA-AC-CCCTTTCAAA
196 TTT-AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCCCAAAGAGCAGGATACTCCCTTTCAAA
* * *
2278612 GCCCACACAAGTTGGTGGCACCTTTGAGTCTCCAAAGAGCAGGACACCTTTTAAAGCCCACACAA
259 GCCCACACAAATTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAA
2278677 GTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA
324 GTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA
2278742 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACA-TGAGTTGGTGGCACTTTTTACT
389 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACT-AGTTGGTGGCACTTTTTACT
*
2278806 CCTCAATGAGCAGGATACACTTTATTTTCCTTTTTCTTT
453 CCTCAATGAGCAGGATACACTTTATTTTCCTCTTTCTTT
2278845 GTCCTCAGAGAGCAGGAC
1 GTCCTCAGAGAGCAGGAC
2278863 GTATTTCATT
Statistics
Matches: 487, Mismatches: 18, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
489 1 0.00
490 251 0.52
494 193 0.40
495 26 0.05
496 16 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (491 bp):
GTCCTCAGAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAGAG
AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACA
TTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCT
TTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCCCAAAGAGCAGGATACTCCCTTTCAAAGC
CCACACAAATTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGT
TGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACC
TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACTAGTTGGTGGCACTTTTTACTCCT
CAATGAGCAGGATACACTTTATTTTCCTCTTTCTTT
Found at i:2278857 original size:435 final size:433
Alignment explanation
Indices: 2277658--2278862 Score: 1317
Period size: 435 Copynumber: 2.7 Consensus size: 433
2277648 GCAGGACACC
*
2277658 TTTCAAAGCCCACACAAGTTGGTGGCA--TTTCTAGTCCTCAAAGAGCAGGACACCTCTTAAAGC
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCCCAAAGAGCAGGACACCT-TTAAAGC
*
2277721 CCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG-AGGACACCTTTCAAAGCCCACACAAGT
64 CCACACAAGTTGGTGGCACCTTTCAGT-CCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGT
2277785 TGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTTTAGGT
128 TGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAA----G-TT-GGT
*
2277850 GGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
187 GGCACTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCACTTTT
* * **
2277913 CCAGTCCTCAGAGAGCAGGACAC-CTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCA
251 -CACTCCTCA-AGAGCAGGACACACT-TT--A-CCTAC-C---TT--T---TTCTT-AGTCCTCA
* * *
2277977 AAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC
300 GAGAGCAGGACAC----TCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC
* * *
2278042 GGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATG
361 GGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATG
2278107 CTTTTTCT
426 CTTTTTCT
*
2278115 TTTCAAAGCCCACACAAATTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACC-TTTAAAGCC
** *
2278180 CACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTT
65 CACACAAGTTGGTGGCACCTTTCAGTCC-CAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTT
* * * *
2278245 GGTGGCACCTTT-CAGTCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACTAGTTGGTGGCACT
129 GGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACT
* * * * **** * * *** * ****
2278309 TTTTACTCCTCAATGAGCAGGATACACTTT-ATTTTCCTCTTTCTTTGTCCTCAGAG-AGCAGGA
193 TTTCAGTCCTCAAAGAGCAGGACAC-CTTTCAAAGCCCACATAAGTTG--GT--G-GCA-CTTTT
* ** ** ** ** * * *
2278372 CA-TCTTTCAA-AGC-CCACACAAGTT-GGTGGCATTTTC-CAGTCCTTAGAGAGCAGGACAC-C
251 CACTC-CTCAAGAGCAGGACACACTTTACCTACCTTTTTCTTAGTCCTCAGAGAGCAGGACACTC
2278431 TCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAA
315 TCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAA
2278496 AGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCT
380 AGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCT
* * *
2278550 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGTAGAACCCCTTTCAAAGCC
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTT-AAAGCC
*
2278615 CACACAAGTTGGTGGCACCTTTGAGTCTCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTT
65 CACACAAGTTGGTGGCACCTTTCAGTC-CCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTT
*
2278680 GGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
129 GGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACT
* * *
2278744 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATGAGTTGGTGGCACTTTTTACTCCT
193 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCACTTTTCACTCCT
* ** * *
2278809 CAATGAGCAGGATACACTTTATTTTCCTTTTTCTTTGTCCTCAGAGAGCAGGAC
258 CAA-GAGCAGGACACACTTTACCTACCTTTTTCTTAGTCCTCAGAGAGCAGGAC
2278863 GTATTTCATT
Statistics
Matches: 622, Mismatches: 97, Indels: 80
0.78 0.12 0.10
Matches are distributed among these distances:
430 7 0.01
431 4 0.01
432 3 0.00
433 7 0.01
434 17 0.03
435 329 0.53
436 3 0.00
440 18 0.03
442 1 0.00
445 1 0.00
447 1 0.00
450 1 0.00
453 32 0.05
454 10 0.02
455 8 0.01
456 3 0.00
457 33 0.05
458 66 0.11
459 75 0.12
460 3 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (433 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTAAAGCCC
ACACAAGTTGGTGGCACCTTTCAGTCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGG
TGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT
CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCACTTTTCACTCCTCAA
GAGCAGGACACACTTTACCTACCTTTTTCTTAGTCCTCAGAGAGCAGGACACTCTCTTAAAGCCC
ACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAA
GTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCT
Found at i:2279586 original size:13 final size:13
Alignment explanation
Indices: 2279568--2279592 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2279558 ACATAAGTTT
2279568 TGTATCGATACAA
1 TGTATCGATACAA
2279581 TGTATCGATACA
1 TGTATCGATACA
2279593 TAATTAGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2279653 original size:13 final size:13
Alignment explanation
Indices: 2279635--2279660 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2279625 CATTTTTCTG
2279635 TGTATCGATACAT
1 TGTATCGATACAT
2279648 TGTATCGATACAT
1 TGTATCGATACAT
2279661 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2279657 original size:33 final size:33
Alignment explanation
Indices: 2279615--2279681 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2279605 GCCAAGGAAA
***
2279615 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2279648 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2279681 T
1 T
2279682 TGAAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2282239 original size:52 final size:51
Alignment explanation
Indices: 2282156--2282324 Score: 157
Period size: 52 Copynumber: 3.3 Consensus size: 51
2282146 ATTTCCGAGG
* * * *
2282156 GGATACTCCAACCCCGG-TTTTATCGCTAAAACACTAATTTTTCCACAATCGG
1 GGATACTCCAA-CCCGGTTTTTTTC-CAAAAACACCAATTTTTCCACAATCGA
* * **
2282208 GGATACTCCAATCCCGGTTTTGTTTTC-AAAACGCCAA-TTTTCCTTTAATCGA
1 GGATACTCCAA-CCCGGTTTT-TTTCCAAAAACACCAATTTTTCC-ACAATCGA
* *
2282260 GGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCGA
1 GGATACTCCAAC-CCGGTTTT-TTTCCAAAAACACCAATTTTTCCACAATCGA
2282312 GGATACTCCAACC
1 GGATACTCCAACC
2282325 TCGTTATTTC
Statistics
Matches: 96, Mismatches: 15, Indels: 13
0.77 0.12 0.10
Matches are distributed among these distances:
51 8 0.08
52 69 0.72
53 13 0.14
54 6 0.06
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
GGATACTCCAACCCGGTTTTTTTCCAAAAACACCAATTTTTCCACAATCGA
Found at i:2282339 original size:28 final size:29
Alignment explanation
Indices: 2282307--2282363 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
2282297 ATTTTTCACA
*
2282307 ATCGAGGATACTCCAACCTCGTTA-TTTC
1 ATCGAGGATACTCCAACCCCGTTACTTTC
2282335 ATCGAGGATACTCCAACCCCGTTACTTTC
1 ATCGAGGATACTCCAACCCCGTTACTTTC
2282364 GAGGGGATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.30
Consensus pattern (29 bp):
ATCGAGGATACTCCAACCCCGTTACTTTC
Found at i:2282352 original size:184 final size:184
Alignment explanation
Indices: 2282012--2282355 Score: 516
Period size: 185 Copynumber: 1.9 Consensus size: 184
2282002 TTCTCAATTC
* * *
2282012 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGA
* * *
2282077 TACTCTAACTCCGATTTTATTTCCAAAAAATATCAATTTTTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTTTTCACAATCGAGGATACTCCAACCC
2282142 CGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCGCTAAAACACTAATTTT
131 CGTTATTTCCGA-GGGATACTCCAACCCCGGTTTTATCGCTAAAACACTAATTTT
* * * *
2282197 TCCACAATCGGGGATACTCCAA-TCCCGGTTTTGTTTTCAAAACGCCAATTTTCCTTTAATCGAG
1 TCCACAATCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGAG
2282261 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAA-TTTTTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTTTTCACAATCGAGGATACTCCAAC
*
2282324 CTCGTTATTTCATCGA-GGATACTCCAACCCCG
129 CCCGTTATTTC--CGAGGGATACTCCAACCCCG
2282356 TTACTTTCGA
Statistics
Matches: 144, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
184 52 0.36
185 55 0.38
186 37 0.26
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (184 bp):
TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGA
TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTTTTCACAATCGAGGATACTCCAACCC
CGTTATTTCCGAGGGATACTCCAACCCCGGTTTTATCGCTAAAACACTAATTTT
Found at i:2282371 original size:28 final size:27
Alignment explanation
Indices: 2282309--2282378 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 27
2282299 TTTTCACAAT
*
2282309 CGAGGATACTCCAACCTCGTTATTTCA
1 CGAGGATACTCCAACCCCGTTATTTCA
2282336 TCGAGGATACTCCAACCCCGTTACTTTCGA
1 -CGAGGATACTCCAACCCCGTTA-TTTC-A
*
2282366 -GGGGATACTCCAA
1 CGAGGATACTCCAA
2282379 TCCTGATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 33 0.87
29 4 0.11
30 1 0.03
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (27 bp):
CGAGGATACTCCAACCCCGTTATTTCA
Found at i:2292826 original size:18 final size:17
Alignment explanation
Indices: 2292794--2292827 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2292784 TTTGTTTTCA
*
2292794 AAAAAAATAAAAAAAGG
1 AAAAAAAGAAAAAAAGG
2292811 AAAAAAAGAAAGAAAAG
1 AAAAAAAGAAA-AAAAG
2292828 ATGTGCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAGG
Found at i:2294682 original size:16 final size:15
Alignment explanation
Indices: 2294657--2294690 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2294647 ATAATTGAGT
*
2294657 AAAAAAGTAAGTAAA
1 AAAAAAGTAAATAAA
2294672 AAAAGAAGTAAATAAA
1 AAAA-AAGTAAATAAA
2294688 AAA
1 AAA
2294691 TTAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAAAAGTAAATAAA
Found at i:2294995 original size:2 final size:2
Alignment explanation
Indices: 2294990--2295025 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
2294980 TTTCTTTAGT
*
2294990 TC TC TC TC TC TC TC TC TC TC TC TC TGC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC T
2295026 TCACCAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (2 bp):
TC
Found at i:2299228 original size:10 final size:10
Alignment explanation
Indices: 2299213--2299254 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
2299203 AATGCTTGGA
*
2299213 TTTCTTGATG
1 TTTCTTGTTG
2299223 TTTCTTGTTG
1 TTTCTTGTTG
* *
2299233 GTTCTTGTTC
1 TTTCTTGTTG
2299243 TTTCTTGTTG
1 TTTCTTGTTG
2299253 TT
1 TT
2299255 CTTCAACTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.02, C:0.12, G:0.19, T:0.67
Consensus pattern (10 bp):
TTTCTTGTTG
Found at i:2299543 original size:20 final size:19
Alignment explanation
Indices: 2299498--2299546 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2299488 CTTTTCAAGG
*
2299498 TGTATCGATACTACGAACA
1 TGTATCGATACTAAGAACA
* *
2299517 CGTATCGATACTAAGCAATA
1 TGTATCGATACTAAG-AACA
2299537 TGTATCGATA
1 TGTATCGATA
2299547 TATCTGGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (19 bp):
TGTATCGATACTAAGAACA
Found at i:2299681 original size:23 final size:22
Alignment explanation
Indices: 2299647--2299690 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
2299637 ACTTTGAATT
*
2299647 ATTTTTACTTGAAAAATATTTG
1 ATTTTTACTTGAAAAACATTTG
2299669 ATTTATTACTTGAAAAACATTT
1 ATTT-TTACTTGAAAAACATTT
2299691 ATACTTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTTTTACTTGAAAAACATTTG
Found at i:2302075 original size:20 final size:20
Alignment explanation
Indices: 2302050--2302087 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2302040 TTGTTGATGA
2302050 TTTTGATG-AAAAACAGATAG
1 TTTTGATGCAAAAA-AGATAG
2302070 TTTTGATGCAAAAAAGAT
1 TTTTGATGCAAAAAAGAT
2302088 GAAATTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (20 bp):
TTTTGATGCAAAAAAGATAG
Found at i:2303315 original size:19 final size:19
Alignment explanation
Indices: 2303291--2303358 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2303281 AATTCAACAA
2303291 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2303310 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2303325 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2303342 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2303359 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2303330 original size:13 final size:13
Alignment explanation
Indices: 2303312--2303336 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2303302 ACATAAGTTT
2303312 TGTATCGATACAA
1 TGTATCGATACAA
2303325 TGTATCGATACA
1 TGTATCGATACA
2303337 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2303334 original size:32 final size:32
Alignment explanation
Indices: 2303293--2303355 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2303283 TTCAACAATT
*
2303293 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2303325 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2303356 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2303416 original size:13 final size:13
Alignment explanation
Indices: 2303398--2303423 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2303388 CATTTTTCTG
2303398 TGTATCGATACAT
1 TGTATCGATACAT
2303411 TGTATCGATACAT
1 TGTATCGATACAT
2303424 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2303420 original size:33 final size:33
Alignment explanation
Indices: 2303378--2303444 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2303368 GCCAAGGAAA
***
2303378 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2303411 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2303444 T
1 T
2303445 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2305955 original size:28 final size:27
Alignment explanation
Indices: 2305884--2305956 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
2305874 AATTTTCACA
2305884 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
* *
2305911 ATCGGGGATACTACAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
2305937 TTCGAGGGGATACTCCAACC
1 ATC--GGGGATACTCCAACC
2305957 TCGACTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 4 0.10
27 22 0.55
28 14 0.35
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:2306097 original size:52 final size:53
Alignment explanation
Indices: 2305942--2306163 Score: 242
Period size: 51 Copynumber: 4.3 Consensus size: 53
2305932 TTATTTTCGA
* * * ***
2305942 GGGGATACTCCAACCTCGACTTTATTTCC-AAAATATTGATTTTT-CATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCCATAATC
* * *
2305993 GGGGATACTCCAACCCCGGTTTTA--TCGCTAAAACACTAATTTTTCCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTC-CAAAAACACCAATTTTTCCATAATC
* *
2306045 -GGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCC-ATAATC
* * *
2306097 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCCATAATC
*
2306149 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2306164 TCGTTATCTC
Statistics
Matches: 146, Mismatches: 17, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
49 2 0.01
50 1 0.01
51 71 0.49
52 30 0.21
53 28 0.19
54 14 0.10
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (53 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCCATAATC
Found at i:2306182 original size:28 final size:28
Alignment explanation
Indices: 2306146--2306219 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
2306136 ATTTTTCACA
*
2306146 ATCGAGGATACTCCAACCTCGTTA-TCTC
1 ATCGGGGATACTCCAACCTCGTTACT-TC
2306174 ATCGGGGATACTCCAACCTCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTACTTC
***
2306202 CGAGGGGATACTCCAACC
1 ATCGGGGATACTCCAACC
2306220 CCGGCTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 40 0.98
29 1 0.02
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTACTTC
Found at i:2306245 original size:263 final size:261
Alignment explanation
Indices: 2305791--2306273 Score: 752
Period size: 263 Copynumber: 1.8 Consensus size: 261
2305781 TCGGGGTAAT
* * * *
2305791 TCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATTGAGGATACTCCAACTCCGATTT
1 TCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGATACTCCAACTCCGATTT
*
2305856 TATTTCCAAAAAACACCAAATTTTCACAATCGGGGATACTCCAACCCCGTTAATCATCGGGGATA
66 TATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCCGTTAATCATCGGGGATA
* * * * *
2305921 CTACAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTTT
131 CTACAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATTGATTTCT
2305986 CATAATCGGGGATACTCCAACCCCGGTTTTATCGCTAAAACACTAATTTTTCCATAATCGGGATA
196 CATAATCGGGGATACTCCAACCCCGGTTTTATCGCTAAAACACTAATTTTTCCATAATCGGGATA
2306051 C
261 C
* *
2306052 TCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCCTTTAATCGGGGATACTCCAACTCCGAT
1 TCCAACCCCGATTTTATTTTCAAAACACCAA-TTTT-CTATAATCGAGGATACTCCAACTCCGAT
* * * *
2306117 TTTATTTCC-AAAAATACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATCTCATCGGGG
64 TTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCCGTTA-ATCATCGGGG
* * *
2306181 ATACTCCAACCTCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATT
128 ATACTACAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATTGATT
*
2306246 TCTCATAATTGGGGATACTCCAACCCCG
193 TCTCATAATCGGGGATACTCCAACCCCG
2306274 TTATTTTCGA
Statistics
Matches: 199, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
261 28 0.14
262 44 0.22
263 127 0.64
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (261 bp):
TCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGATACTCCAACTCCGATTT
TATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCCGTTAATCATCGGGGATA
CTACAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATTGATTTCT
CATAATCGGGGATACTCCAACCCCGGTTTTATCGCTAAAACACTAATTTTTCCATAATCGGGATA
C
Found at i:2318593 original size:12 final size:12
Alignment explanation
Indices: 2318576--2318631 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
2318566 ACCTTCTCTT
2318576 CAAAAAAAAAAA
1 CAAAAAAAAAAA
2318588 CAAAAAAAAAAA
1 CAAAAAAAAAAA
*
2318600 C--AAAACAAAA
1 CAAAAAAAAAAA
**
2318610 CAAAAAGCAAAA
1 CAAAAAAAAAAA
2318622 CAAAGAAAAA
1 CAAA-AAAAA
2318632 GAGAGAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 9 0.24
12 25 0.68
13 3 0.08
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:2318599 original size:17 final size:17
Alignment explanation
Indices: 2318577--2318631 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
2318567 CCTTCTCTTC
2318577 AAAAAAA-AAAACAAAA
1 AAAAAAACAAAACAAAA
2318593 AAAAAAACAAAACAAAA
1 AAAAAAACAAAACAAAA
* *
2318610 CAAAAAGCAAAACAAAGA
1 AAAAAAACAAAACAAA-A
2318628 AAAA
1 AAAA
2318632 GAGAGAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 7 0.21
17 23 0.68
18 4 0.12
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAACAAAA
Found at i:2318631 original size:22 final size:21
Alignment explanation
Indices: 2318580--2318631 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
2318570 TCTCTTCAAA
2318580 AAAAAAAACAAAAAAAAAAAC
1 AAAAAAAACAAAAAAAAAAAC
**
2318601 AAAACAAAACAAAAAGCAAAAC
1 AAAA-AAAACAAAAAAAAAAAC
2318623 AAAGAAAAA
1 AAA-AAAAA
2318632 GAGAGAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 4 0.15
22 22 0.81
23 1 0.04
ACGTcount: A:0.85, C:0.12, G:0.04, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAAAAAAAAAC
Found at i:2319833 original size:55 final size:54
Alignment explanation
Indices: 2319608--2320207 Score: 549
Period size: 55 Copynumber: 10.4 Consensus size: 54
2319598 TCTCCTTCCG
* * *
2319608 CTTTCCAGTCCTCAAAGAGCAGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGTCA
1 CTTT-CAGTCCTCAAAGAGCAGGA--CA---CCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
2319668 TTTTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCA
* *
2319728 CCTTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
2319788 CCTTTCAGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
2319843 CCTTTCAGTCCCCAAAGAGCAGGACACCTTTCGAAGCCCACACAAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
2319898 CTTCCCAGTCCTCAGAGAGCAGGATGCCTTCACCTTTCAAA-CCCACACAAGTTGGTGGCA
1 CTT-TCAGTCCTCAAAGAGCAGGA------CACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
2319958 TTTTCCAGTCCTCAAAGAACAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
2320013 CCTTTTAGTCCCCAAAGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
2320068 TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTAGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * * *
2320123 CTTCCCAGTCCTCAGAGAGCAGGATGCCTTCGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTT-TCAGTCCTCAAAGAGCAGGA------CACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
2320184 CTTCTTAGTCCTCAAAGAGCAGGA
1 CTT-TCAGTCCTCAAAGAGCAGGA
2320208 TACACTTTAT
Statistics
Matches: 456, Mismatches: 51, Indels: 64
0.80 0.09 0.11
Matches are distributed among these distances:
54 16 0.04
55 223 0.49
56 8 0.02
58 1 0.00
59 18 0.04
60 107 0.23
61 78 0.17
64 4 0.01
65 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.23
Consensus pattern (54 bp):
CTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:2319845 original size:29 final size:29
Alignment explanation
Indices: 2319763--2319845 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 29
2319753 CTTTTTCTTT
*
2319763 TCAAAGCCCACACAAGTTGGTGGCACCTT
1 TCAAAGCCCACACAAGTTGGTGGCACCTC
* **
2319792 TC--AGTCCC-CA-AAG-AGCAGGACACCTC
1 TCAAAG-CCCACACAAGTTGGTGG-CACCTC
2319818 TCAAAGCCCACACAAGTTGGTGGCACCT
1 TCAAAGCCCACACAAGTTGGTGGCACCT
2319846 TTCAGTCCCC
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
25 3 0.08
26 10 0.25
27 7 0.17
28 7 0.17
29 10 0.25
30 3 0.08
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (29 bp):
TCAAAGCCCACACAAGTTGGTGGCACCTC
Found at i:2319856 original size:29 final size:29
Alignment explanation
Indices: 2319769--2319856 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
2319759 CTTTTCAAAG
2319769 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
** * * ***
2319798 CCCA-A-AGAG-CAG-GACACCTCTCAAAG
1 CCCACACA-AGTTGGTGGCACCTTTCAGTC
2319824 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
2319853 CCCA
1 CCCA
2319857 AAGAGCAGGA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 13 0.32
27 5 0.12
28 5 0.12
29 17 0.43
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.18
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:2319874 original size:26 final size:26
Alignment explanation
Indices: 2319786--2319874 Score: 83
Period size: 26 Copynumber: 3.3 Consensus size: 26
2319776 AAGTTGGTGG
2319786 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * **
2319812 CACCTCTCAAAG-CCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCC-CA-AAG-AGCAGGA
2319841 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
2319867 CACCTTTC
1 CACCTTTC
2319875 GAAGCCCACA
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
25 3 0.06
26 18 0.38
27 7 0.15
28 7 0.15
29 10 0.21
30 3 0.06
ACGTcount: A:0.28, C:0.36, G:0.18, T:0.18
Consensus pattern (26 bp):
CACCTTTCAGTCCCCAAAGAGCAGGA
Found at i:2319955 original size:170 final size:170
Alignment explanation
Indices: 2319645--2320207 Score: 617
Period size: 170 Copynumber: 3.3 Consensus size: 170
2319635 ATTTTCTTTT
* ** * * * *
2319645 AAAGCCCACACAAGTTGGTGTCATTTTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACC-TTTC----GAAGC
* * * * ** *
2319710 CCACCCGAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCAC
61 CCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGATGCCTTCACCTTTCAAAGCCCAC
*
2319774 ACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACACCTCTC
125 ACAAGTTGGTGGCA-CTTTCCAGTCCCCAAAGAACAGGACACCTCTC
2319820 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCGAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCGAAGCCCACA
*
2319885 CAAGTTGGTGGCACTTCCCAGTCCTCAGAGAGCAGGATGCCTTCACCTTTCAAA-CCCACACAAG
66 CAAGTTGGTGGCACTT-CCAGTCCTCAAAGAGCAGGATGCCTTCACCTTTCAAAGCCCACACAAG
* *
2319949 TTGGTGGCATTTTCCAGTCCTCAAAGAACAGGACACCTCTC
130 TTGGTGGCACTTTCCAGTCCCCAAAGAACAGGACACCTCTC
* *
2319990 AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCCCAAAGAGCAGGACCCCTTTCGAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCGAAGCCCACA
*
2320055 CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA------CACCTCTT-AAAGCCCACACAA
66 CAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGATGCCTTCACCT-TTCAAAGCCCACACAA
* * * * * * * *
2320113 GTTGGTAGCACTTCCCAGTCCTCAGAGAGCAGGATGCCTTCGCCTTTT
129 GTTGGTGGCACTTTCCAGTCCCCAAAGAACAGGA------CACCTCTC
* *
2320161 AAAGCCCACACAAGTTGGTGGCA-CTTCTTAGTCCTCAAAGAGCAGGA
1 AAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCCCAAAGAGCAGGA
2320208 TACACTTTAT
Statistics
Matches: 344, Mismatches: 31, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
164 8 0.02
165 40 0.12
169 6 0.02
170 162 0.47
171 79 0.23
174 4 0.01
175 45 0.13
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (170 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCGAAGCCCACA
CAAGTTGGTGGCACTTCCAGTCCTCAAAGAGCAGGATGCCTTCACCTTTCAAAGCCCACACAAGT
TGGTGGCACTTTCCAGTCCCCAAAGAACAGGACACCTCTC
Found at i:2320027 original size:225 final size:226
Alignment explanation
Indices: 2319643--2320207 Score: 732
Period size: 225 Copynumber: 2.5 Consensus size: 226
2319633 GCATTTTCTT
* ** * * * ** *
2319643 TTAAAGCCCACACAAGTTGGT-GTCATTTTTCAGTCCTCAAAGAGCGGGACGCCTT-TTCTTTTA
1 TTAAAGCCCACACAAGTTGGTAG-CACTTCCCAGTCCTCAGAGAGCAGGATGCCTTCACCTTTCA
* * * * * * *
2319706 AAGCCCACCCGAGTTGGTGGCACCT-TTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGC
65 AAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAACAGGA--C----ACCTCTCAAAGC
2319770 CCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGT
124 CCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGT
2319835 TGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACACCT-
189 TGGTGGCA-CTTTCCAGTCCCCAAAGAGCAGGACACCTC
* *
2319872 TTCGAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAGAGAGCAGGATGCCTTCACCTTTCA
1 TT-AAAGCCCACACAAGTTGGTAGCACTTCCCAGTCCTCAGAGAGCAGGATGCCTTCACCTTTCA
2319937 AA-CCCACACAAGTTGGTGGCA-TT-TTCCAGTCCTCAAAGAACAGGACACCTCTCAAAGCCCAC
65 AAGCCCACACAAGTTGGTGGCACTTCTT--AGTCCTCAAAGAACAGGACACCTCTCAAAGCCCAC
* * * *
2319999 ACAAGTTGGTGGCACCTTTTAGTCCCCAAAGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGT
128 ACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGT
* *
2320064 GGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
193 GGCACTTTCCAGTCCCCAAAGAGCAGGACACCTC
* *
2320098 TTAAAGCCCACACAAGTTGGTAGCACTTCCCAGTCCTCAGAGAGCAGGATGCCTTCGCCTTTTAA
1 TTAAAGCCCACACAAGTTGGTAGCACTTCCCAGTCCTCAGAGAGCAGGATGCCTTCACCTTTCAA
*
2320163 AGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGCAGGA
66 AGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAACAGGA
2320208 TACACTTTAT
Statistics
Matches: 298, Mismatches: 28, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
224 3 0.01
225 161 0.54
226 38 0.13
227 2 0.01
228 2 0.01
229 6 0.02
230 61 0.20
231 25 0.08
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (226 bp):
TTAAAGCCCACACAAGTTGGTAGCACTTCCCAGTCCTCAGAGAGCAGGATGCCTTCACCTTTCAA
AGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAACAGGACACCTCTCAAAGCCCACACA
AGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGC
ACTTTCCAGTCCCCAAAGAGCAGGACACCTC
Found at i:2320967 original size:19 final size:20
Alignment explanation
Indices: 2320920--2320975 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
2320910 AAAAAAAAAT
*
2320920 CAAATGTATCGATACATTTG
1 CAAATGTATCGATACATTTA
* *
2320940 TAGAATGTATTGATACA-TTA
1 CA-AATGTATCGATACATTTA
2320960 CAAATGTATCGATACA
1 CAAATGTATCGATACA
2320976 GGGTCCCAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (20 bp):
CAAATGTATCGATACATTTA
Found at i:2321035 original size:19 final size:19
Alignment explanation
Indices: 2321011--2321078 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2321001 AATTCAATAA
2321011 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2321030 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2321045 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2321062 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2321079 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2321049 original size:32 final size:32
Alignment explanation
Indices: 2321013--2321075 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2321003 TTCAATAATT
*
2321013 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2321045 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2321076 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2321050 original size:13 final size:13
Alignment explanation
Indices: 2321032--2321056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2321022 ACATAAGTTT
2321032 TGTATCGATACAA
1 TGTATCGATACAA
2321045 TGTATCGATACA
1 TGTATCGATACA
2321057 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2321155 original size:33 final size:33
Alignment explanation
Indices: 2321098--2321164 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2321088 GCCAAGGAAA
*** *
2321098 TGTATCGATACATTTTTCTGTGTATCGATGCAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2321131 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2321164 T
1 T
2321165 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2323572 original size:51 final size:52
Alignment explanation
Indices: 2323517--2323889 Score: 201
Period size: 51 Copynumber: 7.1 Consensus size: 52
2323507 TCGAGGTAAT
* *
2323517 TCCAACTCCGATTTTATTTTC-AAGACACTAATTTTCTATAATCGGGGATAC
1 TCCAACCCCGATTTTATTTTCAAAAACACTAATTTTCTATAATCGGGGATAC
* * * *
2323568 TCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTC-ACAATCGGGGATAC
1 TCCAACCCCGATTTTATTTTC-AAAAACA-CTAATTTTCTATAATCGGGGATAC
* ** ** * * * *** **
2323621 TCCAACCCCG--TTAATCATCGGGGATACTCCAA-CCCCGTTATTTTCGAGGGGATAC
1 TCCAACCCCGATTTTATTTTC--AAAAACACTAATTTTC--TATAATC--GGGGATAC
* * * * * *
2323676 TCCAACCCCAACTTTA-TTTCCAAAATATTGATTTT-TCATAATCGGGGATAC
1 TCCAACCCCGATTTTATTTTCAAAAACACTAATTTTCT-ATAATCGGGGATAC
* ** * * *
2323727 TCCAACCCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATC-GGGATAC
1 TCCAACCCCGATTTTATTTTCAAAAACACTAA-TTTTCTATAATCGGGGATAC
* *
2323778 TCCAACCCCGGTTTTATTTTC-AAAACACTAATTTTTCCTTTAATCGGGGATAC
1 TCCAACCCCGATTTTATTTTCAAAAACACTAA-TTTT-CTATAATCGGGGATAC
* * * * * *
2323831 TCCAACTCCGATTTTATTTCCAAAAATACCAATTTT-TCACAATCGAGGATAC
1 TCCAACCCCGATTTTATTTTCAAAAACACTAATTTTCT-ATAATCGGGGATAC
2323883 TCCAACC
1 TCCAACC
2323890 TCGTTATCTC
Statistics
Matches: 239, Mismatches: 63, Indels: 39
0.70 0.18 0.11
Matches are distributed among these distances:
50 1 0.00
51 97 0.41
52 37 0.15
53 63 0.26
54 19 0.08
55 17 0.07
56 2 0.01
57 3 0.01
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (52 bp):
TCCAACCCCGATTTTATTTTCAAAAACACTAATTTTCTATAATCGGGGATAC
Found at i:2323680 original size:28 final size:27
Alignment explanation
Indices: 2323610--2323684 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 27
2323600 AATTTTCACA
2323610 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
2323637 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
2323663 TTCGAGGGGATACTCCAACCCC
1 ATC--GGGGATACTCCAACCCC
2323685 AACTTTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 4 0.09
27 23 0.52
28 17 0.39
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:2323908 original size:28 final size:28
Alignment explanation
Indices: 2323872--2323948 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
2323862 ATTTTTCACA
* *
2323872 ATCGAGGATACTCCAACCTCGTTA-TCTC
1 ATCGGGGATACTCCAACCCCGTTACT-TC
2323900 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2323928 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2323949 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 42 0.98
29 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2323966 original size:263 final size:262
Alignment explanation
Indices: 2323500--2323999 Score: 781
Period size: 263 Copynumber: 1.9 Consensus size: 262
2323490 TTCTCAATTC
* * *
2323500 TCCACAATCGAGGTAATTCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGTAACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
*
2323565 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGGGGATACTCCAACCCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
* * *
2323630 GTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAACTTTATTT
131 GTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCAACTTTATTC
* *
2323695 CCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATCGCTAAAACACTAATT
196 CCAAAATATTGATTTCTCATAATCGGGGATAATCCAACCCCGGTTTTATCGCTAAAACACTAATT
2323760 TT
261 TT
* *
2323762 TCCACAATCG-GG-ATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTTCCTTTAATCGG
1 TCCACAATCGAGGTA-ACTCCAACCCCGATTTTATTTTCAAAACACTAA-TTTT-CTATAATCGG
* *
2323825 GGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTTTTCACAATCGAGGATACTCCAAC
63 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAAC
* * **
2323889 CTCGTTATCTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
128 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCAACTTT
*
2323954 ATTCCCAAAATATTGATTTCTCATAATTGGGGATAATCCAACCCCG
192 ATTCCCAAAATATTGATTTCTCATAATCGGGGATAATCCAACCCCG
2324000 TTATTTTCGA
Statistics
Matches: 216, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
260 1 0.00
261 31 0.14
262 54 0.25
263 130 0.60
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (262 bp):
TCCACAATCGAGGTAACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
GTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCAACTTTATTC
CCAAAATATTGATTTCTCATAATCGGGGATAATCCAACCCCGGTTTTATCGCTAAAACACTAATT
TT
Found at i:2327407 original size:79 final size:79
Alignment explanation
Indices: 2327269--2327838 Score: 718
Period size: 79 Copynumber: 7.2 Consensus size: 79
2327259 GGAGATGACG
* * * * * * **
2327269 ACGGGGCTGGAGTACCCCTGATTATG-GAAAATCGATGTTCTGGAAATAAAATCGGGGTTGGAGT
1 ACGGGGTTGGAGTATCCCTGATTATGAG-AAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGT
*
2327333 ATCCCCTTGGAAATA
65 ATCCCCTCGGAAATA
* * *** * * ** *
2327348 ACAGGGTTGGAGTATCCCTAATTAT-AGAAAATTGGTGTTTTAAAAATAAAATCGCGGTTGGAGT
1 ACGGGGTTGGAGTATCCCTGATTATGAG-AAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGT
**
2327412 ATCCCCTCAAAAATA
65 ATCCCCTCGGAAATA
* *
2327427 ACGGGGTTGGAGTAT-CCTCGATTATGAGAAATCAATATTTTAGGAATAAAGCCGGGATTGGAGT
1 ACGGGGTTGGAGTATCCCT-GATTATGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGT
*
2327491 ATCCCCTTGGAAATA
65 ATCCCCTCGGAAATA
* * * *
2327506 ATGGGATTGGAGTATCCCTGATTGTGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTGGAGTA
1 ACGGGGTTGGAGTATCCCTGATTATGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTA
2327571 TCCCCTCGGAAATA
66 TCCCCTCGGAAATA
* * *
2327585 ACGAGGTTGGAGCATCTCC-GATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGT
1 ACGGGGTTGGAGTATC-CCTGATTATGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGT
2327649 ATCCCCTCGGAAATA
65 ATCCCCTCGGAAATA
* * ** *
2327664 AC-GGGTTGAAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAATCGGGGTTGGAATA
1 ACGGGGTTGGAGTATCCCTGATTATGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTA
2327728 TCCCCTCGGAAATA
66 TCCCCTCGGAAATA
* *
2327742 ACGGGGTTGGAGTATTCCTGATTATGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTAGAGTA
1 ACGGGGTTGGAGTATCCCTGATTATGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTA
*
2327807 TCCCCTTGGAAATA
66 TCCCCTCGGAAATA
2327821 ACGGGGTTGGAGTATCCC
1 ACGGGGTTGGAGTATCCC
2327839 CGATGATTAA
Statistics
Matches: 430, Mismatches: 54, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
77 2 0.00
78 71 0.17
79 350 0.81
80 7 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
ACGGGGTTGGAGTATCCCTGATTATGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTA
TCCCCTCGGAAATA
Found at i:2327772 original size:236 final size:236
Alignment explanation
Indices: 2327269--2327838 Score: 727
Period size: 236 Copynumber: 2.4 Consensus size: 236
2327259 GGAGATGACG
* * * * * **
2327269 ACGGGGCTGGAGTACCCCTGATTATG-GAAAATCGATGTTCT-GGAAATAAAATCGGGGTTGGAG
1 ACGGGGTTGGAGTATCCCTGATTATGAG-AAATCAATATTTTAGG-AATAAAGCCGGGGTTGGAG
* *** *
2327332 TATCCCCTTGGAAATAAC-AGGGTTGGAGTATCCCTAATTATAGAAAATTGGTGTTTTAAAAATA
64 TATCCCCTTGGAAATAACGA-GGTTGGAGTATCCC-GATTATAGAAAATCAATATTTTAAAAATA
* * *
2327396 AAATCGCGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCTCGATTATGAGAAATCA
127 AAACCGCGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGAAGTATCCCCGATTATGAGAAATCA
* * * *
2327461 ATATTTTAGGAATAAAGCCGGGATTGGAGTATCCCCTTGGAAATA
192 ATATTTTAGAAATAAAACCGGGATTGGAATATCCCCTCGGAAATA
* * *
2327506 ATGGGATTGGAGTATCCCTGATTGTGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTGGAGTA
1 ACGGGGTTGGAGTATCCCTGATTATGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTGGAGTA
* * * *
2327571 TCCCCTCGGAAATAACGAGGTTGGAGCATCTCCGATTGT-GAGAAATCAATATTTTAGAAATAAA
66 TCCCCTTGGAAATAACGAGGTTGGAGTATC-CCGATTATAGA-AAATCAATATTTTAAAAATAAA
* * **
2327635 GCCGGGGTTGGAGTATCCCCTCGGAAATAAC-GGGTTGAAGTATCCCCGATTATGAGAAATCAAT
129 ACCGCGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGAAGTATCCCCGATTATGAGAAATCAAT
* *
2327699 ATTTTAGAAATAAAATCGGGGTTGGAATATCCCCTCGGAAATA
194 ATTTTAGAAATAAAACCGGGATTGGAATATCCCCTCGGAAATA
* * *
2327742 ACGGGGTTGGAGTATTCCTGATTATGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTAGAGTA
1 ACGGGGTTGGAGTATCCCTGATTATGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTGGAGTA
*
2327807 TCCCCTTGGAAATAACGGGGTTGGAGTATCCC
66 TCCCCTTGGAAATAACGAGGTTGGAGTATCCC
2327839 CGATGATTAA
Statistics
Matches: 287, Mismatches: 41, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
235 2 0.01
236 156 0.54
237 123 0.43
238 6 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (236 bp):
ACGGGGTTGGAGTATCCCTGATTATGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTGGAGTA
TCCCCTTGGAAATAACGAGGTTGGAGTATCCCGATTATAGAAAATCAATATTTTAAAAATAAAAC
CGCGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGAAGTATCCCCGATTATGAGAAATCAATAT
TTTAGAAATAAAACCGGGATTGGAATATCCCCTCGGAAATA
Found at i:2327828 original size:28 final size:27
Alignment explanation
Indices: 2327794--2327869 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
2327784 GAAATAAAGC
* *
2327794 CGGGGTTAGAGTATCCCC-TTGGAAATAA
1 CGGGGTTGGAGTATCCCCGAT-G-AATAA
*
2327822 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATGAATAA
2327849 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2327870 TATGAAAAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 18 0.41
29 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATGAATAA
Found at i:2330306 original size:13 final size:13
Alignment explanation
Indices: 2330288--2330312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2330278 ACAAAGATCG
2330288 ATGTATCGATACC
1 ATGTATCGATACC
2330301 ATGTATCGATAC
1 ATGTATCGATAC
2330313 ATTCAATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACC
Found at i:2331069 original size:42 final size:41
Alignment explanation
Indices: 2330993--2331190 Score: 172
Period size: 42 Copynumber: 4.7 Consensus size: 41
2330983 AAAAAGAGTA
* *
2330993 CGTCCTGCT-TTTCGAGGATAAAGGAAAAAAGGAAAACGAAA-TG
1 CGTCCTGCTCTTT-GAGGACAAA-G-AAAGAGGAAAA-GAAAGTG
*
2331036 CGTCCTGCTCTTTGAGGACAGAAGAAAGAGGAAAATAAAGTG
1 CGTCCTGCTCTTTGAGGACA-AAGAAAGAGGAAAAGAAAGTG
* *
2331078 CGTCCTGCTCTTTGAGGACAAA-AGAGA-AAATAAGGGAATGAGGTG
1 CGTCCTGCTCTTTGAGGACAAAGAAAGAGGAA-AA--GAA--A-GTG
* * * *
2331123 TGTCCTGCTCTTTGAAGACAAAGGAGAGAGGAAAATAAAGTG
1 CGTCCTGCTCTTTGAGGACAAA-GAAAGAGGAAAAGAAAGTG
2331165 CGTCCTGCTCTTTGAGGACAAA-AAAG
1 CGTCCTGCTCTTTGAGGACAAAGAAAG
2331191 TGCCACCAAC
Statistics
Matches: 130, Mismatches: 13, Indels: 27
0.76 0.08 0.16
Matches are distributed among these distances:
39 2 0.02
40 9 0.07
41 5 0.04
42 57 0.44
43 17 0.13
44 6 0.05
45 25 0.19
47 7 0.05
48 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (41 bp):
CGTCCTGCTCTTTGAGGACAAAGAAAGAGGAAAAGAAAGTG
Found at i:2331304 original size:55 final size:55
Alignment explanation
Indices: 2331164--2331630 Score: 679
Period size: 55 Copynumber: 8.4 Consensus size: 55
2331154 AAAATAAAGT
** *
2331164 GCGTCCTGCTCTTTGAGGAC-AAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAAGAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT----AAG--AG
* * * *
2331225 GCGTCCTACTCTTTGAAGACTGGAAAATGCCATCAACTTGTGCGGGCTTTGAA-AG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAG
*
2331280 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAG
*
2331335 GCGTCCTGCTCTTTGAGGACTGGAAAATGTCACCAACTTGTGTGGGCTTTAAGAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAG
* *
2331390 GCGTCCTGCTCTTTGAGGACTGGAAAATGGCACCAACTTGTGTGGGCTTTAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAG
* *
2331445 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGGTTTGAA-AG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAG
*
2331500 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCCTTAAGAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAG
* *
2331555 GCGTCCTGCTTTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTAAGAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAG
*
2331610 GCGTCATGCTCTTTGAGGACT
1 GCGTCCTGCTCTTTGAGGACT
2331631 AAAGGGCGAA
Statistics
Matches: 374, Mismatches: 28, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
54 4 0.01
55 324 0.87
56 2 0.01
58 2 0.01
61 38 0.10
62 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (55 bp):
GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAG
Found at i:2332710 original size:1 final size:1
Alignment explanation
Indices: 2332704--2332774 Score: 70
Period size: 1 Copynumber: 71.0 Consensus size: 1
2332694 TTCTTTTCTC
* * * * * * * *
2332704 TTTTTTTCTTTGTTTTGTTTTTTTTTTTGTTTTTTTTTTTTGTGTTTTTTTTTTCTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2332769 TTTTTT
1 TTTTTT
2332775 AGAAGAGGAG
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (1 bp):
T
Found at i:2332726 original size:17 final size:16
Alignment explanation
Indices: 2332704--2332774 Score: 99
Period size: 17 Copynumber: 4.4 Consensus size: 16
2332694 TTCTTTTCTC
*
2332704 TTTTTTTCTTTGTTTT
1 TTTTTTTTTTTGTTTT
2332720 GTTTTTTTTTTTG-TTT
1 -TTTTTTTTTTTGTTTT
*
2332736 TTTTTTTTTGTGTTTT
1 TTTTTTTTTTTGTTTT
2332752 TTTTTTCTTTTTGTTTT
1 TTTTTT-TTTTTGTTTT
2332769 TTTTTT
1 TTTTTT
2332775 AGAAGAGGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
15 11 0.22
16 12 0.24
17 26 0.53
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (16 bp):
TTTTTTTTTTTGTTTT
Found at i:2332736 original size:27 final size:26
Alignment explanation
Indices: 2332692--2332771 Score: 88
Period size: 26 Copynumber: 2.9 Consensus size: 26
2332682 AAGCAGGTTC
* *
2332692 TTTTCTTTTCTCTTTTTTTCTTTGTTTTG
1 TTTT-TTTTTTCTTTTTTT-TTT-TTGTG
*
2332721 TTTTTTTTTTTGTTTTTTTTTTTTGTG
1 -TTTTTTTTTTCTTTTTTTTTTTTGTG
2332748 TTTTTTTTTTCTTTTTGTTTTTTT
1 TTTTTTTTTTCTTTTT-TTTTTTT
2332772 TTTAGAAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
26 15 0.33
27 11 0.24
28 3 0.07
29 12 0.27
30 4 0.09
ACGTcount: A:0.00, C:0.06, G:0.07, T:0.86
Consensus pattern (26 bp):
TTTTTTTTTTCTTTTTTTTTTTTGTG
Found at i:2332750 original size:32 final size:31
Alignment explanation
Indices: 2332704--2332774 Score: 108
Period size: 32 Copynumber: 2.3 Consensus size: 31
2332694 TTCTTTTCTC
*
2332704 TTTTTTTCTTTGTTTTGTTTTTT-TTTTTGTT
1 TTTTTTTTTTTGTTTT-TTTTTTCTTTTTGTT
2332735 TTTTTTTTTTGTGTTTTTTTTTTCTTTTTGTT
1 TTTTTTTTTT-TGTTTTTTTTTTCTTTTTGTT
2332767 TTTTTTTT
1 TTTTTTTT
2332775 AGAAGAGGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 15 0.41
32 22 0.59
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (31 bp):
TTTTTTTTTTTGTTTTTTTTTTCTTTTTGTT
Found at i:2332773 original size:30 final size:31
Alignment explanation
Indices: 2332692--2332774 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
2332682 AAGCAGGTTC
2332692 TTTTCTTTTCTCTTTTTTTCTTTGTTTTGTTT
1 TTTTCTTTTCTCTTTTTTT-TTTGTTTTGTTT
* *
2332724 TTTT-TTTTGTTTTTTTTTTTTGTGTTT-TTT
1 TTTTCTTTTCTCTTTTTTTTTTGT-TTTGTTT
*
2332754 TTTTCTTTT-TGTTTTTTTTTT
1 TTTTCTTTTCTCTTTTTTTTTT
2332775 AGAAGAGGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 23 0.50
31 19 0.41
32 4 0.09
ACGTcount: A:0.00, C:0.06, G:0.07, T:0.87
Consensus pattern (31 bp):
TTTTCTTTTCTCTTTTTTTTTTGTTTTGTTT
Found at i:2347267 original size:20 final size:20
Alignment explanation
Indices: 2347214--2347268 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2347204 AACTTCCTAG
**
2347214 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
2347234 ATGTATCGATACATTGAAT-A
1 ATGTATCGATACATTG-ATCA
2347254 ATGTATCGATACATT
1 ATGTATCGATACATT
2347269 TCCTTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:2347345 original size:21 final size:19
Alignment explanation
Indices: 2347298--2347350 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 19
2347288 AGCGATACAC
2347298 TGTATCGATACAATACTTA
1 TGTATCGATACAATACTTA
* * *
2347317 TATATCGATACATTTACTGTT
1 TGTATCGATACA-ATACT-TA
2347338 TGTATCGATACAA
1 TGTATCGATACAA
2347351 ATTATTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (19 bp):
TGTATCGATACAATACTTA
Found at i:2360220 original size:22 final size:21
Alignment explanation
Indices: 2360186--2360226 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2360176 GGTGAAACTC
2360186 AAATTACTATTTATATAATAAA
1 AAATTACTATTTAT-TAATAAA
2360208 AAATTA-TATTTTATTAATA
1 AAATTACTA-TTTATTAATA
2360227 TTTATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATTACTATTTATTAATAAA
Found at i:2360225 original size:21 final size:22
Alignment explanation
Indices: 2360186--2360226 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
2360176 GGTGAAACTC
2360186 AAATTACTATTTATATAATAAA
1 AAATTACTATTTATATAATAAA
2360208 AAATTA-TATTT-TATTAATA
1 AAATTACTATTTATA-TAATA
2360227 TTTATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATTACTATTTATATAATAAA
Found at i:2360245 original size:32 final size:32
Alignment explanation
Indices: 2360188--2360250 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
2360178 TGAAACTCAA
* *
2360188 ATTACTATTTATATAATAAAAAATTATATTTT
1 ATTAATATTTATATAATAAAAAATTAAATTTT
* * *
2360220 ATTAATATTTATATATTATATAATTAAATTT
1 ATTAATATTTATATAATAAAAAATTAAATTT
2360251 AAATAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTAATATTTATATAATAAAAAATTAAATTTT
Found at i:2362731 original size:2 final size:2
Alignment explanation
Indices: 2362724--2362756 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2362714 TCCAAGAACT
2362724 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2362757 GTTAGGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2363049 original size:20 final size:21
Alignment explanation
Indices: 2363018--2363056 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2363008 AGGTCAAAAT
2363018 CCTAGAAAGTATCGATACAGA
1 CCTAGAAAGTATCGATACAGA
2363039 CCTAG-AAGTATCGATACA
1 CCTAGAAAGTATCGATACA
2363057 TATTACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (21 bp):
CCTAGAAAGTATCGATACAGA
Found at i:2363218 original size:33 final size:33
Alignment explanation
Indices: 2363162--2363227 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2363152 CCACTATTTG
* * ** *
2363162 TATCGATACATGGTACACTGTATCGATATATTA
1 TATCGATACATAGTAAAAAGTATCGATACATTA
2363195 TATCGATACATAGTAAAAAGTATCGATACATTA
1 TATCGATACATAGTAAAAAGTATCGATACATTA
2363228 GACCCAACAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (33 bp):
TATCGATACATAGTAAAAAGTATCGATACATTA
Found at i:2366686 original size:15 final size:15
Alignment explanation
Indices: 2366655--2366695 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2366645 ATTCGTAAAT
*
2366655 TTATATTATATTCATA
1 TTATATTTTA-TCATA
*
2366671 TTATTTTTTATCATA
1 TTATATTTTATCATA
2366686 TTATATTTTA
1 TTATATTTTA
2366696 ATTATTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATATTTTATCATA
Found at i:2367877 original size:33 final size:32
Alignment explanation
Indices: 2367814--2367881 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
2367804 CCTTAACTGT
* *
2367814 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCAATACATACAAAATGTATCGATACA
*
2367846 TTGTATCAATACATGACAAAATGTATTGATACA
1 TTGTATCAATACAT-ACAAAATGTATCGATACA
2367879 TTG
1 TTG
2367882 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTATCAATACATACAAAATGTATCGATACA
Found at i:2374064 original size:13 final size:13
Alignment explanation
Indices: 2374046--2374083 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2374036 CAGCATTCTC
* *
2374046 TGTATCTATACAT
1 TGTATCGATACAG
2374059 TGTATCGATACAG
1 TGTATCGATACAG
2374072 TGTATCGATACA
1 TGTATCGATACA
2374084 AAGGGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2376012 original size:20 final size:21
Alignment explanation
Indices: 2375974--2376016 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
2375964 GATTAAAGGA
2375974 AATTGTTTTATTAAGGGGGAG
1 AATTGTTTTATTAAGGGGGAG
2375995 AATT-TTTTAATTAAGGGGGAG
1 AATTGTTTT-ATTAAGGGGGAG
2376016 A
1 A
2376017 GAAAAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (21 bp):
AATTGTTTTATTAAGGGGGAG
Found at i:2376694 original size:13 final size:13
Alignment explanation
Indices: 2376676--2376701 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2376666 ACATACAAGA
2376676 TGTATCGATACAT
1 TGTATCGATACAT
2376689 TGTATCGATACAT
1 TGTATCGATACAT
2376702 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2376697 original size:32 final size:33
Alignment explanation
Indices: 2376656--2376723 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2376646 CCTTAACTGT
2376656 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1 TTGTATCGATACATGACCAA-ATGTATCGATACA
*
2376688 TTGTATCGATACATGACCAAATGTATTGATACA
1 TTGTATCGATACATGACCAAATGTATCGATACA
2376721 TTG
1 TTG
2376724 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCGATACA
Found at i:2378494 original size:6 final size:6
Alignment explanation
Indices: 2378464--2378511 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
2378454 TTTGCTACTA
* * * *
2378464 CATATT AATATT AATATT CATATT CATATT CATACT CATCTT CATATT
1 CATATT CATATT CATATT CATATT CATATT CATATT CATATT CATATT
2378512 TTGCTTTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
CATATT
Found at i:2379206 original size:21 final size:21
Alignment explanation
Indices: 2379182--2379238 Score: 98
Period size: 20 Copynumber: 2.8 Consensus size: 21
2379172 ACATTGAGTA
2379182 ATTTTAAAAAATATAGTGATC
1 ATTTTAAAAAATATAGTGATC
2379203 ATTTT-AAAAATATAGTGATC
1 ATTTTAAAAAATATAGTGATC
*
2379223 ATTTTAAATAATATAG
1 ATTTTAAAAAATATAG
2379239 AGATTAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (21 bp):
ATTTTAAAAAATATAGTGATC
Found at i:2380281 original size:27 final size:27
Alignment explanation
Indices: 2380235--2380302 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
2380225 ATACTTATGT
*
2380235 AATATTTAAATT-TTTGTAAAAATAATAA
1 AATATTAAAATTATTTGT--AAATAATAA
*
2380263 AATA-TAAAATTATTT-TAAATTATAA
1 AATATTAAAATTATTTGTAAATAATAA
2380288 AATATTTAAAATTAT
1 AATA-TTAAAATTAT
2380303 ATTTTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
25 12 0.34
27 16 0.46
28 7 0.20
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
AATATTAAAATTATTTGTAAATAATAA
Found at i:2380293 original size:17 final size:18
Alignment explanation
Indices: 2380260--2380303 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
2380250 GTAAAAATAA
*
2380260 TAAAATATAAAATTATTT
1 TAAATTATAAAATTATTT
2380278 TAAATTATAAAA-TATTT
1 TAAATTATAAAATTATTT
*
2380295 AAAATTATA
1 TAAATTATA
2380304 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATTATAAAATTATTT
Found at i:2380602 original size:18 final size:20
Alignment explanation
Indices: 2380566--2380603 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2380556 TTATATGATT
*
2380566 AATATTTTTTAAATTATAAA
1 AATATTTTTTAAATAATAAA
2380586 AATA-TTTTTAAA-AATAAA
1 AATATTTTTTAAATAATAAA
2380604 TAAAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATTTTTTAAATAATAAA
Found at i:2381253 original size:29 final size:29
Alignment explanation
Indices: 2381216--2381282 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
2381206 ATTAAAATGA
* *
2381216 TAAAAAAATATATAT-TTTATTATTTTATT
1 TAAATAAATATATATATTT-TTATTATATT
*
2381245 TAAATAAATATTTATATTTTTATTATATT
1 TAAATAAATATATATATTTTTATTATATT
2381274 TAAATAAAT
1 TAAATAAAT
2381283 TTTAAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 31 0.91
30 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TAAATAAATATATATATTTTTATTATATT
Found at i:2381293 original size:29 final size:30
Alignment explanation
Indices: 2381229--2381324 Score: 99
Period size: 29 Copynumber: 3.2 Consensus size: 30
2381219 AAAAATATAT
* *
2381229 ATTTTATTATTTTATTTAAATAAATATTTAT
1 ATTTT-TTATTATATTTAAATAAATATTTAA
2381260 A-TTTTTATTATATTTAAATAAAT-TTTAA
1 ATTTTTTATTATATTTAAATAAATATTTAA
* * *
2381288 ATTTTTTAATTTATTTTTAAATATATCTTT-A
1 ATTTTTT-A-TTATATTTAAATAAATATTTAA
2381319 ATTTTT
1 ATTTTT
2381325 AAATTATACC
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
28 5 0.09
29 23 0.40
30 4 0.07
31 22 0.39
32 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTTTTTATTATATTTAAATAAATATTTAA
Found at i:2381310 original size:31 final size:32
Alignment explanation
Indices: 2381229--2381329 Score: 99
Period size: 31 Copynumber: 3.3 Consensus size: 32
2381219 AAAAATATAT
*
2381229 ATTTTATT-ATTT-TATTTAAATAAATATTTAT
1 ATTTT-TTAATTTATATTTAAATAAATATTTAA
2381260 A-TTTTT-A-TTATATTTAAATAAAT-TTTAA
1 ATTTTTTAATTTATATTTAAATAAATATTTAA
* * *
2381288 ATTTTTTAATTTATTTTTAAATATATCTTT-A
1 ATTTTTTAATTTATATTTAAATAAATATTTAA
*
2381319 ATTTTTAAATT
1 ATTTTTTAATT
2381330 ATACCTAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
28 7 0.11
29 21 0.34
30 4 0.07
31 26 0.43
32 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (32 bp):
ATTTTTTAATTTATATTTAAATAAATATTTAA
Found at i:2381526 original size:22 final size:20
Alignment explanation
Indices: 2381498--2381538 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
2381488 AAACGTAAAA
2381498 ATATTTTATATATTAATATTTT
1 ATATTTTATA-ATTAA-ATTTT
2381520 ATATTTTATAATTAAATTT
1 ATATTTTATAATTAAATTT
2381539 AAATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTTTATAATTAAATTTT
Found at i:2381764 original size:16 final size:15
Alignment explanation
Indices: 2381688--2381764 Score: 59
Period size: 16 Copynumber: 4.7 Consensus size: 15
2381678 AAATTTTTTT
2381688 TAATATTTTAATTAAA
1 TAAT-TTTTAATTAAA
2381704 TAATTTTTATATT-AA
1 TAATTTTTA-ATTAAA
*
2381719 TAATTTATATAATT-TA
1 TAATTT-T-TAATTAAA
2381735 TAATTTAATTTAATTAAAA
1 TAA-TT--TTTAATT-AAA
2381754 TAATTTTTAAT
1 TAATTTTTAAT
2381765 AAGTAATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
15 13 0.25
16 21 0.41
17 9 0.18
18 3 0.06
19 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTTTAATTAAA
Found at i:2381774 original size:36 final size:36
Alignment explanation
Indices: 2381717--2381797 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
2381707 TTTTTATATT
* *
2381717 AATAATTTATATAATTTATAATTTAATTT-AATTAA
1 AATAATTTATATAAGTAATAATTTAATTTAAATTAA
* *
2381752 AATAATTTTTAATAAGTAATAATTTTATTTAAATTAA
1 AATAATTTAT-ATAAGTAATAATTTAATTTAAATTAA
*
2381789 ATTAATTTA
1 AATAATTTA
2381798 AATTAAGAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 9 0.24
36 16 0.42
37 13 0.34
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (36 bp):
AATAATTTATATAAGTAATAATTTAATTTAAATTAA
Found at i:2388009 original size:22 final size:22
Alignment explanation
Indices: 2387973--2388029 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
2387963 AAAGGGACAA
* * * *
2387973 AAAAAAAAAAAAAGGAATGGAG
1 AAAAGAAAAAGAAGGAAAGAAG
* *
2387995 AAAAGAAGAAGAAGGAAAGAAT
1 AAAAGAAAAAGAAGGAAAGAAG
2388017 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
2388030 AATTTTCTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.04
Consensus pattern (22 bp):
AAAAGAAAAAGAAGGAAAGAAG
Found at i:2389502 original size:21 final size:21
Alignment explanation
Indices: 2389469--2389509 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2389459 CTAAGTAAAA
2389469 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
2389490 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
2389510 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:2389574 original size:20 final size:19
Alignment explanation
Indices: 2389549--2389619 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
2389539 ACCCTGAAAA
2389549 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
2389569 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
2389588 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
2389609 GTATCGATACA
1 GTATCGATACA
2389620 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:2389646 original size:34 final size:34
Alignment explanation
Indices: 2389602--2389687 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
2389592 TCGATACACA
*
2389602 CAAATATGTATCGATACAGGACATTGGCAGTAGC
1 CAAATTTGTATCGATACAGGACATTGGCAGTAGC
* *
2389636 CAAATTTGTATTGATACAGGTCATTGGCAGTAGC
1 CAAATTTGTATCGATACAGGACATTGGCAGTAGC
2389670 CAAATTTGTATCGATACA
1 CAAATTTGTATCGATACA
2389688 CAAAATATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (34 bp):
CAAATTTGTATCGATACAGGACATTGGCAGTAGC
Found at i:2389782 original size:21 final size:22
Alignment explanation
Indices: 2389748--2389803 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
2389738 CTTCACTATT
2389748 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
2389770 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
2389791 CATCACTGTTCAT
1 CATCACTGTTCAT
2389804 ACATCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:2389807 original size:14 final size:14
Alignment explanation
Indices: 2389788--2389816 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2389778 TCATGTATCG
2389788 ATACATCACTGTTC
1 ATACATCACTGTTC
2389802 ATACATCACTGTTC
1 ATACATCACTGTTC
2389816 A
1 A
2389817 CACTGTTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (14 bp):
ATACATCACTGTTC
Found at i:2389821 original size:23 final size:23
Alignment explanation
Indices: 2389794--2389839 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2389784 ATCGATACAT
* *
2389794 CACTGTTCATACATCACTGTTCA
1 CACTGTTCACACATCACTATTCA
*
2389817 CACTGTTCACATATCACTATTCA
1 CACTGTTCACACATCACTATTCA
2389840 TGTTTCGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (23 bp):
CACTGTTCACACATCACTATTCA
Found at i:2389911 original size:13 final size:13
Alignment explanation
Indices: 2389893--2389918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2389883 ACATATTTGT
2389893 GTGTATCGATACA
1 GTGTATCGATACA
2389906 GTGTATCGATACA
1 GTGTATCGATACA
2389919 TCATAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:2390460 original size:34 final size:35
Alignment explanation
Indices: 2390397--2390463 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2390387 CTAAGTGATT
2390397 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
2390433 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
2390464 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:2393225 original size:21 final size:19
Alignment explanation
Indices: 2393201--2393242 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
2393191 ATTTAATCTT
2393201 TATATGATATAAATTAAATAA
1 TATATGATAT-AATTAAA-AA
*
2393222 TATATTATATAATTAAAAA
1 TATATGATATAATTAAAAA
2393241 TA
1 TA
2393243 GGTCAAGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
21 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TATATGATATAATTAAAAA
Found at i:2394148 original size:18 final size:18
Alignment explanation
Indices: 2394116--2394167 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
2394106 GTGATTAAAG
2394116 TATATATTTACATAAATTTT
1 TATATA-TTA-ATAAATTTT
2394136 TATATATTAAT-AATTTT
1 TATATATTAATAAATTTT
2394153 TAT-TA-T-ATAAATTTT
1 TATATATTAATAAATTTT
2394168 GAAACAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.06
15 7 0.23
16 2 0.06
17 9 0.29
18 2 0.06
19 3 0.10
20 6 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATATTAATAAATTTT
Found at i:2394583 original size:3 final size:3
Alignment explanation
Indices: 2394575--2394604 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2394565 AGGAACAAGT
2394575 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2394605 GTCTAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2394689 original size:16 final size:17
Alignment explanation
Indices: 2394658--2394700 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2394648 TTTAATATTT
*
2394658 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
2394675 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
*
2394690 TTAAAATTTAT
1 ATAAAATTTAT
2394701 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:2395657 original size:19 final size:19
Alignment explanation
Indices: 2395601--2395661 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
2395591 ATACAAAAAA
* *
2395601 ATAAATATGACATAAATAT
1 ATAAATATTACATAAATTT
* * *
2395620 ACAAATA-TAAAAAATATTT
1 ATAAATATTACATAA-ATTT
2395639 ATAAATATTACATAAATTT
1 ATAAATATTACATAAATTT
2395658 ATAA
1 ATAA
2395662 TATGTTTAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 4 0.12
19 23 0.72
20 5 0.16
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAAATATTACATAAATTT
Found at i:2395792 original size:25 final size:24
Alignment explanation
Indices: 2395715--2395795 Score: 64
Period size: 25 Copynumber: 3.4 Consensus size: 24
2395705 TTTCTCCCAT
* *
2395715 ATATAA-AATAAAATATACATAAAA
1 ATATAATATTAAAATA-AAATAAAA
2395739 ATAT-ATA-TAAAATAAAAT-AAA
1 ATATAATATTAAAATAAAATAAAA
*
2395760 TTATTAATATGTAAAA-AAATATAAAA
1 ATA-TAATAT-TAAAATAAA-ATAAAA
2395786 ATATAATATT
1 ATATAATATT
2395796 TTAAATACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
21 5 0.11
22 4 0.09
23 11 0.23
24 9 0.19
25 13 0.28
26 5 0.11
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (24 bp):
ATATAATATTAAAATAAAATAAAA
Found at i:2396264 original size:12 final size:12
Alignment explanation
Indices: 2396247--2396287 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
2396237 TTGTATTATA
2396247 TTTATACTATTT
1 TTTATACTATTT
2396259 TTTATACTATATT
1 TTTATACTAT-TT
*
2396272 TTTA-ATTATTT
1 TTTATACTATTT
2396283 TTTAT
1 TTTAT
2396288 GTTGTGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 6 0.23
12 14 0.54
13 6 0.23
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATACTATTT
Found at i:2396270 original size:23 final size:24
Alignment explanation
Indices: 2396243--2396287 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2396233 TTATTTGTAT
2396243 TATATTTAT-ACTATTTTTTATAC
1 TATATTTATAACTATTTTTTATAC
* *
2396266 TATATTTTTAATTATTTTTTAT
1 TATATTTATAACTATTTTTTAT
2396288 GTTGTGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
TATATTTATAACTATTTTTTATAC
Found at i:2396792 original size:16 final size:17
Alignment explanation
Indices: 2396765--2396805 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2396755 ATTTTTAAAT
2396765 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
2396780 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
2396797 AAATTTTAT
1 AAATTTTAT
2396806 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:2397098 original size:25 final size:26
Alignment explanation
Indices: 2397047--2397120 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
2397037 CATGAAAATA
* * *
2397047 ATATACACATAATATAAA-TATATGT
1 ATATATACATAAAATAAATTATAAGT
2397072 ATATATACATAAAATAAATTA-AAGT
1 ATATATACATAAAATAAATTATAAGT
* *
2397097 AT-TAATATATAAAAAAAATTATAA
1 ATAT-ATACATAAAATAAATTATAA
2397121 AAATATAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 1 0.02
25 36 0.88
26 4 0.10
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (26 bp):
ATATATACATAAAATAAATTATAAGT
Found at i:2397178 original size:4 final size:4
Alignment explanation
Indices: 2397169--2397211 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
2397159 ATATATAAAA
2397169 TTTC TTTC TTTC TTTC TTTC TTT- TTT- TTCTCC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTTC TTTC TTT
2397212 TTTTTTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 5 0.14
4 28 0.78
5 1 0.03
6 2 0.06
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:2397190 original size:16 final size:17
Alignment explanation
Indices: 2397169--2397213 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
2397159 ATATATAAAA
2397169 TTTCTTTCTTTCTT-T-C
1 TTTCTTTCTTT-TTCTCC
2397185 TTTCTTT-TTTTTCTCC
1 TTTCTTTCTTTTTCTCC
2397201 TTTCTTTCTTTTT
1 TTTCTTTCTTTTT
2397214 TTTTTTTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.08
15 4 0.15
16 15 0.58
17 5 0.19
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTCTTTTTCTCC
Found at i:2397204 original size:24 final size:24
Alignment explanation
Indices: 2397176--2397221 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2397166 AAATTTCTTT
2397176 CTTTCTTTCTTTCTTTTTTTTCTC
1 CTTTCTTTCTTTCTTTTTTTTCTC
*
2397200 CTTTCTTTCTTTTTTTTTTTTC
1 CTTTCTTTCTTTCTTTTTTTTC
2397222 AGCCCATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (24 bp):
CTTTCTTTCTTTCTTTTTTTTCTC
Done.