Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 20
Found at i:2197174 original size:2 final size:2
Alignment explanation
Indices: 2197167--2197217 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
2197157 CTATACCATA
* *
2197167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2197209 AT AG AT AT A
1 AT AT AT AT A
2197218 CTTAGTGACA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2197218 original size:14 final size:14
Alignment explanation
Indices: 2197158--2197218 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
2197148 TTCATTTGTC
2197158 TATACCATA-ATATA
1 TATA-CATATATATA
*
2197172 TATATATATATATA
1 TATACATATATATA
*
2197186 TATATATATATATA
1 TATACATATATATA
* *
2197200 TATACATACATAGA
1 TATACATATATATA
2197214 TATAC
1 TATAC
2197219 TTAGTGACAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
13 3 0.07
14 39 0.93
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (14 bp):
TATACATATATATA
Found at i:2200689 original size:7 final size:8
Alignment explanation
Indices: 2200677--2200739 Score: 67
Period size: 8 Copynumber: 7.6 Consensus size: 8
2200667 TGATTTTTAC
2200677 ATTTTTTT
1 ATTTTTTT
2200685 ATTTTTTT
1 ATTTTTTT
2200693 ATTTTTTT
1 ATTTTTTT
2200701 ATTTTTTT
1 ATTTTTTT
2200709 -TCCTTTTTCT
1 AT--TTTTT-T
*
2200719 CTTTTTTT
1 ATTTTTTT
2200727 -TGTTTTTT
1 AT-TTTTTT
2200735 ATTTT
1 ATTTT
2200740 CTTTTTGACG
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
7 2 0.04
8 34 0.69
9 11 0.22
10 1 0.02
11 1 0.02
ACGTcount: A:0.08, C:0.06, G:0.02, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:2200690 original size:9 final size:9
Alignment explanation
Indices: 2200678--2200734 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
2200668 GATTTTTACA
2200678 TTTTTTTA-
1 TTTTTTTAT
2200686 TTTTTTTA-
1 TTTTTTTAT
2200694 TTTTTTTAT
1 TTTTTTTAT
**
2200703 TTTTTTTCC
1 TTTTTTTAT
* *
2200712 TTTTTCTCT
1 TTTTTTTAT
*
2200721 TTTTTTTGT
1 TTTTTTTAT
2200730 TTTTT
1 TTTTT
2200735 ATTTTCTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
8 16 0.38
9 26 0.62
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:2200690 original size:16 final size:16
Alignment explanation
Indices: 2200669--2200706 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2200659 TTTATTTGTG
2200669 ATTTTTACATTTTTTT
1 ATTTTTACATTTTTTT
**
2200685 ATTTTTTTATTTTTTT
1 ATTTTTACATTTTTTT
2200701 ATTTTT
1 ATTTTT
2200707 TTTCCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
ATTTTTACATTTTTTT
Found at i:2200739 original size:12 final size:11
Alignment explanation
Indices: 2200678--2200745 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
2200668 GATTTTTACA
*
2200678 TTTTTTTATTT
1 TTTTTTTCTTT
2200689 TTTTATTT-TTT
1 TTTT-TTTCTTT
*
2200700 TATTTTT-TTT
1 TTTTTTTCTTT
** *
2200710 CCTTTTTCTCT
1 TTTTTTTCTTT
*
2200721 TTTTTTTGTTT
1 TTTTTTTCTTT
2200732 TTTATTTTCTTT
1 TTT-TTTTCTTT
2200744 TT
1 TT
2200746 GACGAAAACC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
10 11 0.24
11 22 0.49
12 12 0.27
ACGTcount: A:0.06, C:0.07, G:0.01, T:0.85
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:2205482 original size:11 final size:11
Alignment explanation
Indices: 2205468--2205495 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2205458 CTAAAACATA
2205468 AAAATAATAAT
1 AAAATAATAAT
2205479 AAAATAATAAT
1 AAAATAATAAT
2205490 AAAATA
1 AAAATA
2205496 CTATCTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:2207917 original size:2 final size:2
Alignment explanation
Indices: 2207910--2207935 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2207900 CTTTCTAATC
2207910 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2207936 TAATGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2208188 original size:21 final size:20
Alignment explanation
Indices: 2208140--2208190 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
2208130 AATTGAATAA
2208140 AATAAAAAAATAAAAAATTT
1 AATAAAAAAATAAAAAATTT
*
2208160 AATCAAAAAATAAAAAAATGTT
1 AATAAAAAAAT-AAAAAAT-TT
2208182 -ATAAAAAAA
1 AATAAAAAAA
2208191 GAATTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 15 0.56
22 2 0.07
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (20 bp):
AATAAAAAAATAAAAAATTT
Found at i:2217809 original size:31 final size:31
Alignment explanation
Indices: 2217774--2217840 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
2217764 AAAAACATGT
2217774 GTTTTAGTCACTTACGTTATCATTTTATTAA
1 GTTTTAGTCACTTACGTTATCATTTTATTAA
*
2217805 GTTTTAGTCACTTACGTTATCGTTTTATTAA
1 GTTTTAGTCACTTACGTTATCATTTTATTAA
2217836 GTTTT
1 GTTTT
2217841 GGCCACTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (31 bp):
GTTTTAGTCACTTACGTTATCATTTTATTAA
Found at i:2217848 original size:31 final size:31
Alignment explanation
Indices: 2217774--2217848 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
2217764 AAAAACATGT
*
2217774 GTTTTAGTCACTTACGTTATCATTTTATTAA
1 GTTTTAGCCACTTACGTTATCATTTTATTAA
* *
2217805 GTTTTAGTCACTTACGTTATCGTTTTATTAA
1 GTTTTAGCCACTTACGTTATCATTTTATTAA
*
2217836 GTTTTGGCCACTT
1 GTTTTAGCCACTT
2217849 GGATGTTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (31 bp):
GTTTTAGCCACTTACGTTATCATTTTATTAA
Found at i:2224006 original size:20 final size:20
Alignment explanation
Indices: 2223963--2224006 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2223953 AAATTTTTTC
* *
2223963 GAGTCAAGTCTAAGAAATTA
1 GAGTCAAGTCGAACAAATTA
2223983 GAGTCAAGTCGAATCAAATT-
1 GAGTCAAGTCGAA-CAAATTA
2224003 GAGT
1 GAGT
2224007 TTTCTAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (20 bp):
GAGTCAAGTCGAACAAATTA
Found at i:2226496 original size:133 final size:132
Alignment explanation
Indices: 2226224--2226475 Score: 321
Period size: 133 Copynumber: 1.9 Consensus size: 132
2226214 TATAAATTAT
**
2226224 TTATTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTGCTTTAAGACAGCTCTTTTCTTCGATAT
1 TTATTTATTTAGAAATATCAGAAAAGAACTTCTAGGTGCTTTAAGACAGCTCTTTTCTTCGATAT
* * * **
2226289 TAATAAATAAATAACTAAAAAAAGCATTTTTTTAAAAAAATAATTAATTTATAAAAAAAACAAGA
66 TAATAAATAAATAACTAAAAAAAACAATTTTTCAAAAAAATAATT-ATAGATAAAAAAAACAAGA
2226354 TAA
130 TAA
* * *
2226357 TTATTTATTTA-AGAATATCATAAAAGAACTTCTAGGTGTTTTAAGACAGTTCTTTTCTTCGATA
1 TTATTTATTTAGA-AATATCAGAAAAGAACTTCTAGGTGCTTTAAGACAGCTCTTTTCTTCGATA
* * * *
2226421 TTAATAAATAAAT-ATTAAAAATATAATAATTTTTCATAAAAATGATT-TAGATAAA
65 TTAATAAATAAATAACTAAAAA-A-AACAATTTTTCAAAAAAATAATTATAGATAAA
2226476 TTATAATTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
132 14 0.14
133 71 0.70
134 17 0.17
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (132 bp):
TTATTTATTTAGAAATATCAGAAAAGAACTTCTAGGTGCTTTAAGACAGCTCTTTTCTTCGATAT
TAATAAATAAATAACTAAAAAAAACAATTTTTCAAAAAAATAATTATAGATAAAAAAAACAAGAT
AA
Found at i:2227926 original size:3 final size:3
Alignment explanation
Indices: 2227907--2227971 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
2227897 TTGTAATATT
* *
2227907 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TTA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
2227954 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
2227972 ACTTAAAATG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2227928 original size:24 final size:23
Alignment explanation
Indices: 2227900--2227971 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 23
2227890 ATGGGCTTTG
2227900 TAATATTTAATAAATAATATATAA
1 TAATATTTAATAAATAATA-ATAA
2227924 TAATAATTATAATAATTATAATAATAA
1 TAAT-ATT-TAATAA--ATAATAATAA
2227951 TAAT-TTTAAT-AATAATAATAA
1 TAATATTTAATAAATAATAATAA
2227972 ACTTAAAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
21 10 0.23
23 1 0.02
24 8 0.18
25 5 0.11
26 6 0.14
27 8 0.18
28 6 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATATTTAATAAATAATAATAA
Found at i:2228261 original size:76 final size:76
Alignment explanation
Indices: 2228101--2229278 Score: 2113
Period size: 76 Copynumber: 15.5 Consensus size: 76
2228091 GATGGAAATG
* * *
2228101 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
2228166 TCCCGAAGGCTT
65 TCCCGAAGGCTT
2228178 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
2228243 CTCGAAGGCTT
66 CCCGAAGGCTT
*
2228254 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2228319 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
2228330 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATTAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2228395 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2228406 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATTAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2228471 CCCGAAGGCTT
66 CCCGAAGGCTT
2228482 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
2228547 CCTGAAGGCTT
66 CCCGAAGGCTT
*
2228558 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2228623 CCCGAAGGCTT
66 CCCGAAGGCTT
2228634 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2228699 CCCGAAGGCTT
66 CCCGAAGGCTT
**
2228710 TTTGGAAACATCATGCACTGAAGGGTTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2228775 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2228786 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTCGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-GAAAACATCAAAAAGC
2228851 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
2228863 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2228928 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
2228939 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTCGAAAACATAAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-GAAAACATCAAAAAGC
2229004 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
2229016 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2229081 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2229092 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2229157 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2229168 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2229233 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2229244 TTTGGAAACATCATGCACTGAAGGGCTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
2229279 TGAGAAATAG
Statistics
Matches: 1071, Mismatches: 28, Indels: 5
0.97 0.03 0.00
Matches are distributed among these distances:
76 882 0.82
77 189 0.18
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:2229968 original size:22 final size:22
Alignment explanation
Indices: 2229940--2229994 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2229930 CATAAAGCTT
*
2229940 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAACCTA
*
2229962 TCATCTTTAAAAAGAGAACCTA
1 TCATCTTTGAAAAGAGAACCTA
2229984 TCATCTTTGAA
1 TCATCTTTGAA
2229995 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAACCTA
Found at i:2230427 original size:54 final size:54
Alignment explanation
Indices: 2230345--2230500 Score: 249
Period size: 54 Copynumber: 2.9 Consensus size: 54
2230335 AGAATAGCAG
*** *
2230345 GTTCGTAAAACATTTGACAGTGCATTCATCATTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* *
2230399 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
2230453 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
2230501 CAAGATTTCT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:2231633 original size:45 final size:45
Alignment explanation
Indices: 2231569--2231658 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
2231559 AAGTGTGCTC
*
2231569 AACATTACTTCTTGTTGAGATGAGCCTCCAAAAATACTCAAATAT
1 AACATTACTTCTTGTTGAGATGAGCCCCCAAAAATACTCAAATAT
2231614 AACATTACTTCTTGTTGAGATGAGCCCCCAAAAATACTCAAATAT
1 AACATTACTTCTTGTTGAGATGAGCCCCCAAAAATACTCAAATAT
2231659 TCATATTGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (45 bp):
AACATTACTTCTTGTTGAGATGAGCCCCCAAAAATACTCAAATAT
Found at i:2242067 original size:3 final size:3
Alignment explanation
Indices: 2242048--2242111 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
2242038 TTGTAATATT
2242048 TAA TAAA TAA TATA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
2242094 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
2242112 ACTTAAAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 46 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2245212 original size:3 final size:3
Alignment explanation
Indices: 2245204--2245278 Score: 82
Period size: 3 Copynumber: 24.3 Consensus size: 3
2245194 TTTTACTTTA
* *
2245204 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT AAT AAT ATCT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT AT-T ATT
2245251 A-T ATAT ATT A-T ATAT ATT ATT ATT ATT A
1 ATT AT-T ATT ATT AT-T ATT ATT ATT ATT A
2245279 AATAAAGAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
2 4 0.06
3 48 0.75
4 12 0.19
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:2246283 original size:21 final size:21
Alignment explanation
Indices: 2246258--2246306 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
2246248 ATATTTTTAA
2246258 ATAAATAAATATCT-TACTTTT
1 ATAAATAAATAT-TGTACTTTT
2246279 ATAAATAAATATTGTACTTTT
1 ATAAATAAATATTGTACTTTT
2246300 ATAAATA
1 ATAAATA
2246307 TTATTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (21 bp):
ATAAATAAATATTGTACTTTT
Found at i:2246346 original size:135 final size:134
Alignment explanation
Indices: 2246180--2246422 Score: 314
Period size: 135 Copynumber: 1.8 Consensus size: 134
2246170 AATATAAATC
*
2246180 ATGTTTTAATATTTATTTTTCAATATTAAGAAA-AGGCAGTCTTAAAACAAC-AGGATGTCCATT
1 ATGTTTTAATATTTATTTTTCAATATTAAGAAATAGGCAGTCTTAAAACAACTA-GAAGT-CATT
* *
2246243 TTCTGATATTTTTAAATAAATAAATATCTTACTTT-TATAAATAAATATTGTACTTTTATAAATA
64 TTCTGATATTTCTAAATAAATAAATATCTTA-TTTATAAAAATAAATATTGTACTTTTATAAATA
2246307 TTATTTT
128 TTATTTT
* * ** ** *
2246314 ATGTTTTATTTATTTATTTCTT-AATATTAAGAAATTGGTTGTCTTAAAGTACCTAGAAGTCATT
1 ATGTTTTA-ATATTTATTT-TTCAATATTAAGAAATAGGCAGTCTTAAAACAACTAGAAGTCATT
*
2246378 TTCTGATATTTCTAAGTAAATAAATATCTTATTTATAAAAATAAA
64 TTCTGATATTTCTAAATAAATAAATATCTTATTTATAAAAATAAA
2246423 AAATATATAT
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
134 11 0.12
135 63 0.68
136 18 0.19
137 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (134 bp):
ATGTTTTAATATTTATTTTTCAATATTAAGAAATAGGCAGTCTTAAAACAACTAGAAGTCATTTT
CTGATATTTCTAAATAAATAAATATCTTATTTATAAAAATAAATATTGTACTTTTATAAATATTA
TTTT
Found at i:2252188 original size:13 final size:13
Alignment explanation
Indices: 2252170--2252221 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2252160 ATTATACTTG
2252170 AAGAAGAAGAAAA
1 AAGAAGAAGAAAA
2252183 AAGAAGAAGAAAGA
1 AAGAAGAAGAAA-A
2252197 AA-AA-AAGAAAA
1 AAGAAGAAGAAAA
*
2252208 AA-AAGGA-AAAA
1 AAGAAGAAGAAAA
2252219 AAG
1 AAG
2252222 GAAAAAATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 11 0.31
12 7 0.20
13 14 0.40
14 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAAA
Found at i:2252190 original size:16 final size:17
Alignment explanation
Indices: 2252169--2252219 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
2252159 TATTATACTT
2252169 GAAGAAG-AAGAAAAAA
1 GAAGAAGAAAGAAAAAA
2252185 GAAGAAGAAAGAAAAAAA
1 GAAGAAGAAAG-AAAAAA
*
2252203 GAA-AAAAAAGGAAAAAA
1 GAAGAAGAAA-GAAAAAA
2252220 AGGAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 7 0.23
17 14 0.45
18 10 0.32
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
GAAGAAGAAAGAAAAAA
Found at i:2252207 original size:7 final size:8
Alignment explanation
Indices: 2252179--2252228 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 8
2252169 GAAGAAGAAG
2252179 AAAAAAGA
1 AAAAAAGA
2252187 AGAAGAAAGA
1 A-AA-AAAGA
2252197 AAAAAAGAA
1 AAAAAAG-A
2252206 AAAAAAGGA
1 AAAAAA-GA
2252215 AAAAAAGGA
1 AAAAAA-GA
2252224 AAAAA
1 AAAAA
2252229 TTGAATCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
8 5 0.13
9 26 0.68
10 7 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:2252210 original size:9 final size:9
Alignment explanation
Indices: 2252173--2252228 Score: 60
Period size: 10 Copynumber: 6.0 Consensus size: 9
2252163 ATACTTGAAG
2252173 AAGAAGAAAA
1 AAGAA-AAAA
*
2252183 AAGAAGAAGA
1 AAGAA-AAAA
2252193 AAG-AAAAA
1 AAGAAAAAA
2252201 AAGAAAAAA
1 AAGAAAAAA
2252210 AAGGAAAAAA
1 AA-GAAAAAA
*
2252220 AGGAAAAAA
1 AAGAAAAAA
2252229 TTGAATCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
8 6 0.15
9 15 0.37
10 20 0.49
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:2252721 original size:32 final size:32
Alignment explanation
Indices: 2252685--2252746 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
2252675 TCTGGAAACA
**
2252685 AGAAGTATCTCTA-CAAGATGAGCATAACAACG
1 AGAAGTATCTCTAGC-AGAAAAGCATAACAACG
2252717 AGAAGTATCTCTAGCAGAAAAGCATAACAA
1 AGAAGTATCTCTAGCAGAAAAGCATAACAA
2252747 TTATTTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (32 bp):
AGAAGTATCTCTAGCAGAAAAGCATAACAACG
Found at i:2257366 original size:45 final size:45
Alignment explanation
Indices: 2257317--2257472 Score: 249
Period size: 46 Copynumber: 3.4 Consensus size: 45
2257307 GAGCTTTTTG
2257317 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
*
2257362 GTTTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 G-TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
* * *
2257408 GTTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
2257453 GTTTTCAAAAAGCCTTCGGG
1 GTTTTC-AAAA-CCTTCGGG
2257473 AGATTTTTGG
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
45 47 0.46
46 48 0.47
47 7 0.07
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
Found at i:2257492 original size:74 final size:73
Alignment explanation
Indices: 2257408--2257545 Score: 240
Period size: 74 Copynumber: 1.9 Consensus size: 73
2257398 AGTGCATGAT
2257408 GTTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGG
1 GTTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAA-CCTTCGGG
2257473 AGATTTTTG
65 AGATTTTTG
* * *
2257482 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGG
1 GTTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAACCTTCGGG
2257546 TCATCTGTAA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
73 8 0.13
74 53 0.87
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (73 bp):
GTTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAACCTTCGGGA
GATTTTTG
Found at i:2257509 original size:119 final size:120
Alignment explanation
Indices: 2257364--2257582 Score: 395
Period size: 119 Copynumber: 1.8 Consensus size: 120
2257354 TGCATGATGT
2257364 TTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGAGTC
1 TTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGAGTC
2257428 ATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGG
66 ATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGG
* *
2257483 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTC
1 TTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGAGTC
* *
2257548 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
66 ATCTGTAAGACCTACAGTGCATGATGTTTTCAAAA
2257583 CCTTCGAGTC
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
119 49 0.52
120 46 0.48
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (120 bp):
TTTTAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGAGTC
ATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGG
Found at i:2257538 original size:46 final size:45
Alignment explanation
Indices: 2257482--2257762 Score: 454
Period size: 45 Copynumber: 6.2 Consensus size: 45
2257472 GAGATTTTTG
2257482 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
2257527 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
*
2257573 GTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
2257618 GTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
1 GTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
* * *
2257664 GTTTTCAAAATCTTCGGATCATTTGTAAGCCCTTCAGTGCATGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
* * * * * *
2257709 GTTCTCAAAACCTCCGGGTCATTTATAAGACCTTCAGTGCAGGAT
1 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
2257754 GTTTTCAAA
1 GTTTTCAAA
2257763 TGAGATTTTA
Statistics
Matches: 221, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
45 132 0.60
46 89 0.40
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (45 bp):
GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
Found at i:2257539 original size:165 final size:165
Alignment explanation
Indices: 2257262--2257636 Score: 689
Period size: 165 Copynumber: 2.3 Consensus size: 165
2257252 CTATTTCATA
* * *
2257262 CATCTGTAAGACCTACAGTGCATGATGTTTTCCAAAAGCCTTCGAGAGCTTTTTGGTTTTCAAAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGGTTTTCAAAA
*
2257327 CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAAACCTTCGGGTCATCTGTAAG
66 CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAG
2257392 CCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
131 CCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
2257427 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGGTTTTCAAAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGGTTTTCAAAA
2257492 CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAG
66 CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAG
2257557 CCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
131 CCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
* *
2257592 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAA-CCTTCGGG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGG
2257637 TCATCTGTAA
Statistics
Matches: 204, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
164 8 0.04
165 196 0.96
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (165 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGGTTTTCAAAA
CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAG
CCCTTCAGTGCATGATGTTTTCAAAACCTTCGAGT
Found at i:2257637 original size:91 final size:90
Alignment explanation
Indices: 2257482--2257762 Score: 456
Period size: 91 Copynumber: 3.1 Consensus size: 90
2257472 GAGATTTTTG
2257482 GTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 GTTTTCAAAACCTTC-GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
2257547 CATCTGTAAGCCCTTCAGTGCATGAT
65 CATCTGTAAGCCCTTCAGTGCATGAT
2257573 GTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 GTTTTCAAAACCTTCG-GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
2257638 CATCTGTAAGCCCTTCAGTGCATGAT
65 CATCTGTAAGCCCTTCAGTGCATGAT
* * * *
2257664 GTTTTCAAAATCTTCGGATCATTTGTAAGCCCTTCAGTGCATGATGTTCTC-AAAACCTCCGGGT
1 GTTTTCAAAACCTTCGG-TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * * *
2257728 CATTTATAAGACCTTCAGTGCAGGAT
65 CATCTGTAAGCCCTTCAGTGCATGAT
2257754 GTTTTCAAA
1 GTTTTCAAA
2257763 TGAGATTTTA
Statistics
Matches: 180, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
90 45 0.25
91 135 0.75
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (90 bp):
GTTTTCAAAACCTTCGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTC
ATCTGTAAGCCCTTCAGTGCATGAT
Found at i:2258026 original size:3 final size:3
Alignment explanation
Indices: 2258020--2258089 Score: 70
Period size: 3 Copynumber: 22.3 Consensus size: 3
2258010 TTTTACTTTA
* * *
2258020 ATT ATT ATT ATT ATT TTT ATT ATT ATT ATTT AAT AAT ATCT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT AT-T ATT ATT
2258066 ATAT ATT ATAT ATT ATT ATT ATT A
1 AT-T ATT AT-T ATT ATT ATT ATT A
2258090 AATAAAGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
2 2 0.03
3 44 0.76
4 12 0.21
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:2258064 original size:32 final size:32
Alignment explanation
Indices: 2258000--2258082 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
2257990 GTAAACACTA
* *
2258000 ATTTTTTTTATT-TTACTTTAATTATTATTATT
1 ATTTTTATTATTATTA-TTTAATTAATATTATT
2258032 ATTTTTATTATTATTATTTAA-TAATATCTATT
1 ATTTTTATTATTATTATTTAATTAATAT-TATT
* *
2258064 ATATATATTATATATTATT
1 ATTTTTATTAT-TATTATT
2258083 ATTATTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
31 5 0.11
32 29 0.66
33 10 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (32 bp):
ATTTTTATTATTATTATTTAATTAATATTATT
Found at i:2259152 original size:2 final size:2
Alignment explanation
Indices: 2259145--2259213 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
2259135 TCCTTATCTG
2259145 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2259187 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 T
2259214 TTAGGGTAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2259868 original size:21 final size:21
Alignment explanation
Indices: 2259843--2259891 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
2259833 ATATTTTTAA
2259843 ATAAATAAATATCT-TACTTTT
1 ATAAATAAATAT-TGTACTTTT
2259864 ATAAATAAATATTGTACTTTT
1 ATAAATAAATATTGTACTTTT
2259885 ATAAATA
1 ATAAATA
2259892 TTATTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (21 bp):
ATAAATAAATATTGTACTTTT
Found at i:2259931 original size:135 final size:133
Alignment explanation
Indices: 2259765--2260007 Score: 312
Period size: 135 Copynumber: 1.8 Consensus size: 133
2259755 AATATAAATC
* *
2259765 ATGTTTTAATATTTATTTTTCAATATTAAGAAA-GGTCAGTCTTAAAGCAACTGGATGTCCATTT
1 ATGTTTTAATATTTATTTTTCAATATTAAGAAATGGT-AGTCTTAAAGCAACTAGAAGT-CATTT
* *
2259829 TCTGATATTTTTAAATAAATAAATATCTTACTTT-TATAAATAAATATTGTACTTTTATAAATAT
64 TCTGATATTTCTAAATAAATAAATATCTTA-TTTATAAAAATAAATATTGTACTTTTATAAATAT
2259893 TATTTT
128 TATTTT
* * ** **
2259899 ATGTTTTATTTATTTATTTCTT-AATATTAAGAAATTGGTTGTCTTAAAGCATTTAGAAGTTTTT
1 ATGTTTTA-ATATTTATTT-TTCAATATTAAGAAA-TGGTAGTCTTAAAGCAACTAGAAGTCATT
*
2259963 TTCTGATATTTCTAAGTAAATAAATATCTTATTTATAAAAATAAA
63 TTCTGATATTTCTAAATAAATAAATATCTTATTTATAAAAATAAA
2260008 AATATATATA
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
134 11 0.12
135 61 0.66
136 18 0.19
137 3 0.03
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (133 bp):
ATGTTTTAATATTTATTTTTCAATATTAAGAAATGGTAGTCTTAAAGCAACTAGAAGTCATTTTC
TGATATTTCTAAATAAATAAATATCTTATTTATAAAAATAAATATTGTACTTTTATAAATATTAT
TTT
Found at i:2266403 original size:7 final size:7
Alignment explanation
Indices: 2266391--2266465 Score: 141
Period size: 7 Copynumber: 10.7 Consensus size: 7
2266381 ATCCATTCTT
2266391 TTCTTTC
1 TTCTTTC
2266398 TTCTTTC
1 TTCTTTC
*
2266405 TTTTTTC
1 TTCTTTC
2266412 TTCTTTC
1 TTCTTTC
2266419 TTCTTTC
1 TTCTTTC
2266426 TTCTTTC
1 TTCTTTC
2266433 TTCTTTC
1 TTCTTTC
2266440 TTCTTTC
1 TTCTTTC
2266447 TTCTTTC
1 TTCTTTC
2266454 TTCTTTC
1 TTCTTTC
2266461 TTCTT
1 TTCTT
2266466 CCTTTCTTTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 66 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTTC
Found at i:2266417 original size:21 final size:21
Alignment explanation
Indices: 2266391--2266474 Score: 141
Period size: 21 Copynumber: 4.0 Consensus size: 21
2266381 ATCCATTCTT
*
2266391 TTCTTTCTTCTTTCTTTTTTC
1 TTCTTTCTTCTTTCTTCTTTC
2266412 TTCTTTCTTCTTTCTTCTTTC
1 TTCTTTCTTCTTTCTTCTTTC
2266433 TTCTTTCTTCTTTCTTCTTTC
1 TTCTTTCTTCTTTCTTCTTTC
*
2266454 TTCTTTCTTCTTCCTTTCTTT
1 TTCTTTCTTCTTTC-TTCTTT
2266475 GTGTTTAAGC
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
21 54 0.90
22 6 0.10
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCTTTCTTCTTTCTTCTTTC
Found at i:2268420 original size:83 final size:83
Alignment explanation
Indices: 2268262--2268427 Score: 262
Period size: 83 Copynumber: 2.0 Consensus size: 83
2268252 GTGTATATAT
*
2268262 ATATTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAATATATGT
1 ATATTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAAAATATGT
*
2268327 GGTTGAAGTAAATCTCTC
66 GGTTGAAGTAAAACTCTC
* * *
2268345 ATATTTAATATTTTAAATTTAAAAGATATTATTATCTTTTTAAATTTATATATTAAAAAATATTT
1 ATATTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAAAATATGT
*
2268410 AGG-TGGAGTAAAACTCTC
66 -GGTTGAAGTAAAACTCTC
2268428 TCGAAATTTC
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
83 74 0.97
84 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.46
Consensus pattern (83 bp):
ATATTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAAAATATGT
GGTTGAAGTAAAACTCTC
Found at i:2268521 original size:20 final size:22
Alignment explanation
Indices: 2268496--2268538 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
2268486 TTCTTCTCTT
2268496 GAAAATATT-TTATCT-CCTTA
1 GAAAATATTCTTATCTCCCTTA
*
2268516 GAAAATATTCTTTTCTCCCTTA
1 GAAAATATTCTTATCTCCCTTA
2268538 G
1 G
2268539 TTTTTCTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 5 0.25
22 6 0.30
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (22 bp):
GAAAATATTCTTATCTCCCTTA
Found at i:2269995 original size:57 final size:56
Alignment explanation
Indices: 2269912--2270065 Score: 166
Period size: 57 Copynumber: 2.7 Consensus size: 56
2269902 AATCTAGATC
* * ***
2269912 GATTTTATTTTGTAGAACAAAATAAATTGTTAAATTTATTTT-CATGGAATTTTGTAT
1 GATTCTATTTTGTA-AA-AAAATAAATTGTTAAATTTATTTTCCATAGAATCAAGTAT
* ** * *
2269969 GATTCTATTTTGTAAAAGAAATTAAATCGTTGGATTTTTTTTCCTTAGAATCAAGTAT
1 GATTCTATTTTGTAAAA-AAA-TAAATTGTTAAATTTATTTTCCATAGAATCAAGTAT
*
2270027 GATTCTATCTTGTAAAAAAATAAATTGTTAAATTTATTT
1 GATTCTATTTTGTAAAAAAATAAATTGTTAAATTTATTT
2270066 CTTGAACGTC
Statistics
Matches: 79, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
55 1 0.01
56 20 0.25
57 32 0.41
58 26 0.33
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.47
Consensus pattern (56 bp):
GATTCTATTTTGTAAAAAAATAAATTGTTAAATTTATTTTCCATAGAATCAAGTAT
Found at i:2271554 original size:15 final size:15
Alignment explanation
Indices: 2271517--2271548 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2271507 ACTATTGTAA
*
2271517 CAAATTTAATTTTTT
1 CAAAATTAATTTTTT
2271532 CAAAATTAATTTTTT
1 CAAAATTAATTTTTT
2271547 CA
1 CA
2271549 CTATTAGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (15 bp):
CAAAATTAATTTTTT
Found at i:2272510 original size:21 final size:21
Alignment explanation
Indices: 2272485--2272526 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2272475 AGGGATTAAA
2272485 CCACTAAATTATAAATGGATT
1 CCACTAAATTATAAATGGATT
*
2272506 CCACTAAATTCTAAATGGATT
1 CCACTAAATTATAAATGGATT
2272527 TTCAAATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
CCACTAAATTATAAATGGATT
Found at i:2274530 original size:24 final size:24
Alignment explanation
Indices: 2274476--2274530 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
2274466 ATATCTATTT
*
2274476 AATATTTTAAATTTAAAAGATATTAT
1 AATATTTTAAATTT--AAGATATTAA
*
2274502 TATATGTTTAAATTT-AGATATTAA
1 AATAT-TTTAAATTTAAGATATTAA
2274526 AATAT
1 AATAT
2274531 ATCTAGTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 12 0.48
26 4 0.16
27 9 0.36
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (24 bp):
AATATTTTAAATTTAAGATATTAA
Found at i:2277576 original size:19 final size:19
Alignment explanation
Indices: 2277503--2277577 Score: 66
Period size: 19 Copynumber: 4.0 Consensus size: 19
2277493 GGAGGGCTGG
*
2277503 AAACCGGTTTGACCGGTTTT
1 AAACCGGTTTGACCGG-TCT
* *
2277523 CAACC-G-CTGACCGGT-T
1 AAACCGGTTTGACCGGTCT
* *
2277539 CGAACCGATTTGACCGGTCT
1 -AAACCGGTTTGACCGGTCT
2277559 AAACCGGTTTGACCGGTCT
1 AAACCGGTTTGACCGGTCT
2277578 GACCCGACCC
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
16 1 0.02
17 5 0.11
18 7 0.16
19 26 0.59
20 5 0.11
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.27
Consensus pattern (19 bp):
AAACCGGTTTGACCGGTCT
Found at i:2277588 original size:5 final size:5
Alignment explanation
Indices: 2277578--2277624 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
2277568 TGACCGGTCT
* *
2277578 GACCC GACCC GACCC GA-CT GACCC GACCC GA-CT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
2277625 GTTGACTGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 6 0.17
5 30 0.83
ACGTcount: A:0.21, C:0.53, G:0.21, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:2277600 original size:14 final size:14
Alignment explanation
Indices: 2277583--2277623 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
2277573 GGTCTGACCC
2277583 GACCCGACCCGACT
1 GACCCGACCCGACT
2277597 GACCCGACCCGACT
1 GACCCGACCCGACT
2277611 GACCCGACCCGAC
1 GACCCGACCCGAC
2277624 CGTTGACTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.22, C:0.51, G:0.22, T:0.05
Consensus pattern (14 bp):
GACCCGACCCGACT
Found at i:2283650 original size:6 final size:7
Alignment explanation
Indices: 2283627--2283655 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2283617 ACCCGACCCA
2283627 ACCGTTG
1 ACCGTTG
2283634 ACCGTTG
1 ACCGTTG
2283641 ACCG-TG
1 ACCGTTG
2283647 ACCGTTG
1 ACCGTTG
2283654 AC
1 AC
2283656 TTCCTTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.17, C:0.31, G:0.28, T:0.24
Consensus pattern (7 bp):
ACCGTTG
Found at i:2283650 original size:13 final size:14
Alignment explanation
Indices: 2283627--2283655 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2283617 ACCCGACCCA
2283627 ACCGTTGACCGTTG
1 ACCGTTGACCGTTG
2283641 ACCG-TGACCGTTG
1 ACCGTTGACCGTTG
2283654 AC
1 AC
2283656 TTCCTTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.17, C:0.31, G:0.28, T:0.24
Consensus pattern (14 bp):
ACCGTTGACCGTTG
Found at i:2290578 original size:19 final size:19
Alignment explanation
Indices: 2290554--2290591 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2290544 ACGCGCCACA
*
2290554 CGACCCGACTGATCCGACC
1 CGACCCGACTGACCCGACC
2290573 CGACCCGACTGACCCGACC
1 CGACCCGACTGACCCGACC
2290592 GTTGACCGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.08
Consensus pattern (19 bp):
CGACCCGACTGACCCGACC
Found at i:2290600 original size:7 final size:7
Alignment explanation
Indices: 2290588--2290624 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
2290578 CGACTGACCC
2290588 GACCGTT
1 GACCGTT
2290595 GACCGTT
1 GACCGTT
2290602 GACCG-T
1 GACCGTT
*
2290608 GACGGTT
1 GACCGTT
2290615 GACCGTT
1 GACCGTT
2290622 GAC
1 GAC
2290625 TTCCTTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.16, C:0.27, G:0.32, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:2292836 original size:20 final size:20
Alignment explanation
Indices: 2292811--2292870 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
2292801 CTTGGTTTAC
2292811 AGCAAAGATTATACAAACAA
1 AGCAAAGATTATACAAACAA
* * * * *
2292831 AGCAAACATCACACTAAGAA
1 AGCAAAGATTATACAAACAA
*
2292851 AACAAAGCATTATACAAACA
1 AGCAAAG-ATTATACAAACA
2292871 TTATGAATTA
Statistics
Matches: 28, Mismatches: 11, Indels: 1
0.70 0.28 0.03
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.58, C:0.20, G:0.08, T:0.13
Consensus pattern (20 bp):
AGCAAAGATTATACAAACAA
Found at i:2293549 original size:28 final size:30
Alignment explanation
Indices: 2293518--2293577 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
2293508 ATGCCTGTTC
*
2293518 TTTTAATTTAGTGT-TAATATTTT-TTTTG
1 TTTTAATTTAGCGTCTAATATTTTATTTTG
* *
2293546 TTTTAGTTTGGCGTCTAATATTTTATTTTG
1 TTTTAATTTAGCGTCTAATATTTTATTTTG
2293576 TT
1 TT
2293578 ATTTAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 11 0.41
29 9 0.33
30 7 0.26
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.65
Consensus pattern (30 bp):
TTTTAATTTAGCGTCTAATATTTTATTTTG
Found at i:2295395 original size:20 final size:21
Alignment explanation
Indices: 2295366--2295408 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2295356 TAATAAAGCG
*
2295366 TTATCTAAAACATT-ATTTTT
1 TTATCGAAAACATTAATTTTT
*
2295386 TTATCGAAAATATTAATTTTT
1 TTATCGAAAACATTAATTTTT
2295407 TT
1 TT
2295409 TACCTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TTATCGAAAACATTAATTTTT
Found at i:2295519 original size:80 final size:79
Alignment explanation
Indices: 2295433--2295593 Score: 196
Period size: 79 Copynumber: 2.0 Consensus size: 79
2295423 TAGAAAAAAT
* * *** *
2295433 AACATTTTAGGTAGCGCCCAATATTAATAATTTTTTGTATAAAAAATAATATTTTAAATAACGCT
1 AACATTTTAGGTAGCACCAAATATTAA-AATTTCCAGTAGAAAAAATAATATTTTAAATAACGCT
2295498 TTACCAAAAATGTTA
65 TTACCAAAAATGTTA
* * * ** *
2295513 AACATTTTAGGTAGCACTAAATATTAACATTTCCAGTAGAAAAAATAATGTTTTAGGTAGCGCTT
1 AACATTTTAGGTAGCACCAAATATTAAAATTTCCAGTAGAAAAAATAATATTTTAAATAACGCTT
*
2295578 TACCCAAAATGTTA
66 TACCAAAAATGTTA
2295592 AA
1 AA
2295594 AAAAATATTA
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
79 44 0.65
80 24 0.35
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (79 bp):
AACATTTTAGGTAGCACCAAATATTAAAATTTCCAGTAGAAAAAATAATATTTTAAATAACGCTT
TACCAAAAATGTTA
Found at i:2298960 original size:17 final size:17
Alignment explanation
Indices: 2298928--2298973 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2298918 AAAGAAACTA
2298928 AAAATATAATG-A-AAAT
1 AAAATA-AATGTATAAAT
2298944 -AAATAAATAGTATAAAT
1 AAAATAAAT-GTATAAAT
2298961 AAAATAAATGTAT
1 AAAATAAATGTAT
2298974 GTATAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.12
15 6 0.23
16 1 0.04
17 8 0.31
18 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (17 bp):
AAAATAAATGTATAAAT
Found at i:2298962 original size:26 final size:25
Alignment explanation
Indices: 2298933--2299023 Score: 77
Period size: 25 Copynumber: 3.7 Consensus size: 25
2298923 AACTAAAAAT
2298933 ATAATGAAAATAAATAAATAGTAT--
1 ATAAT-AAAATAAATAAATAGTATAA
**
2298957 A-AATAAAATAAATGTAT-GTATAA
1 ATAATAAAATAAATAAATAGTATAA
*
2298980 TATAATAAAAT-ACTAAATAGTA-ATA
1 -ATAATAAAATAAATAAATAGTATA-A
2299005 ATAATAATAATAAATAAAT
1 ATAATAA-AATAAATAAAT
2299024 GAAAAATAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
21 4 0.08
22 11 0.21
23 3 0.06
24 14 0.26
25 15 0.28
26 6 0.11
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (25 bp):
ATAATAAAATAAATAAATAGTATAA
Found at i:2298979 original size:17 final size:18
Alignment explanation
Indices: 2298940--2298973 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2298930 AATATAATGA
2298940 AAAT-AAATAAATAGTAT
1 AAATAAAATAAATAGTAT
2298957 AAATAAAATAAAT-GTAT
1 AAATAAAATAAATAGTAT
2298974 GTATAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AAATAAAATAAATAGTAT
Found at i:2298988 original size:29 final size:31
Alignment explanation
Indices: 2298955--2299022 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
2298945 AATAAATAGT
*
2298955 ATAAATAAAATAAAT-GT-ATGTATAAT-ATA
1 ATAAATAAAATAAATAGTAAT-AATAATAATA
* *
2298984 ATAAA-ATACTAAATAGTAATAATAATAATA
1 ATAAATAAAATAAATAGTAATAATAATAATA
2299014 ATAAATAAA
1 ATAAATAAA
2299023 TGAAAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
28 7 0.23
29 12 0.39
30 10 0.32
31 2 0.06
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (31 bp):
ATAAATAAAATAAATAGTAATAATAATAATA
Found at i:2299164 original size:21 final size:19
Alignment explanation
Indices: 2299119--2299166 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
2299109 TAACGTTAGG
*
2299119 AAAATATAGTAAAAAAATAG
1 AAAATA-AGTAAAAAAATAA
*
2299139 TAAATAAGTAAACATAAATAA
1 AAAATAAGTAAA-A-AAATAA
2299160 AAAATAA
1 AAAATAA
2299167 TAATATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
21 11 0.48
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (19 bp):
AAAATAAGTAAAAAAATAA
Found at i:2300011 original size:2 final size:2
Alignment explanation
Indices: 2300004--2300047 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
2299994 ATTGGACATG
2300004 TA TA TA TA TA TA TA TA T- TA TA -A TA TGA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
2300044 TA TA
1 TA TA
2300048 ACATAACATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2300961 original size:253 final size:252
Alignment explanation
Indices: 2300461--2301102 Score: 1011
Period size: 253 Copynumber: 2.5 Consensus size: 252
2300451 AATCGTATAG
* * * * *
2300461 GGCCCCTTCGTCGTGAAGTTGAGCATGGGTATTGGATATCCTTCGTTGTGAAGTTGAAATCCAAT
1 GGCCCCTTCGTCGTGAAGTTGAGCCTGAG-ACTGGATATCCTTCATAGTGAAGTTGAAATCCAAT
* *
2300526 GTAAGTTG-TGCTGTTTCGAGGCCAATATCTCTCGCCGTGAAGTTGAAATTGACTCTGAAACTGG
65 GTAGGTTGCT-TTGTTTCGAGGCCAATATCTC-CGCCGTGAAGTTGAAATTGACTCTGAAACTGG
* *
2300590 AAAGTTTTGTTGACATGCACTCATTCTTTGAGTTGAATATCTTTCGTCATGAAATTGAAATCCAA
128 AAA-ATTTGTTGACATGCACTCATTCTTTGAGTTGAATATCCTTCGTCATGAAATTGAAATCCAA
*
2300655 TCTAAAGATGGATGCTGCTTGTATGCACGATTCCCTTCGCCGTGAAGTTGAAACCGCGGGT
192 TCTAAAGATGGATGCTGCTTGTATGCACGATTCCCTTCGCCGTGAAATTGAAACCGCGGGT
*
2300716 GGCCCCTTCGTCGTGAAGTTGAGCCTGAGACTGGATATCCTTCATAGTGAAGTTGAAATTCAATG
1 GGCCCCTTCGTCGTGAAGTTGAGCCTGAGACTGGATATCCTTCATAGTGAAGTTGAAATCCAATG
2300781 TAGGTTGCTTTGTTTCGAGGCCAATATCTTCCGCCGTGAAGTTGAAATTGACTCTGAAACTGGAA
66 TAGGTTGCTTTGTTTCGAGGCCAATATC-TCCGCCGTGAAGTTGAAATTGACTCTGAAACTGGAA
* *
2300846 AATTTGTTGACA-GACACTTC-TTCTTTGAGTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAT
130 AATTTGTTGACATG-CAC-TCATTCTTTGAGTTGAATATCCTTCGTCATGAAATTGAAATCCAAT
*
2300909 CTAAAGATGGATGCTGCTTGTATGCACGATTCCCTTCTCCGTGAAATTGAAACCGCGGGT
193 CTAAAGATGGATGCTGCTTGTATGCACGATTCCCTTCGCCGTGAAATTGAAACCGCGGGT
2300969 GGCCCCTTCGTCGTGAAGTTGAGCCTGAGACTGGATATCCTTCATAGTGAAGTTGAAATCCAATG
1 GGCCCCTTCGTCGTGAAGTTGAGCCTGAGACTGGATATCCTTCATAGTGAAGTTGAAATCCAATG
* * * * * *
2301034 TAGGTTGCTTTGTTCCAAGTCCAATATCCTCCACCATGAAGTTGAAATTGACTCTGAAACTGGGA
66 TAGGTTGCTTTGTTTCGAGGCCAATAT-CTCCGCCGTGAAGTTGAAATTGACTCTGAAACTGGAA
2301099 AATT
130 AATT
2301103 GTTTGTTGAC
Statistics
Matches: 361, Mismatches: 21, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
252 1 0.00
253 236 0.65
254 94 0.26
255 30 0.08
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (252 bp):
GGCCCCTTCGTCGTGAAGTTGAGCCTGAGACTGGATATCCTTCATAGTGAAGTTGAAATCCAATG
TAGGTTGCTTTGTTTCGAGGCCAATATCTCCGCCGTGAAGTTGAAATTGACTCTGAAACTGGAAA
ATTTGTTGACATGCACTCATTCTTTGAGTTGAATATCCTTCGTCATGAAATTGAAATCCAATCTA
AAGATGGATGCTGCTTGTATGCACGATTCCCTTCGCCGTGAAATTGAAACCGCGGGT
Found at i:2301240 original size:106 final size:106
Alignment explanation
Indices: 2301051--2301265 Score: 306
Period size: 106 Copynumber: 2.0 Consensus size: 106
2301041 CTTTGTTCCA
*
2301051 AGTCCAATATCCTCCACCATGAAGTTGAAATTGACTCTGAAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTCCACCATGAAGTTGAAATTGACTCTGAAACTGGGAAATTATTTGTTGACAAC
* * *
2301116 CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CACTCGTCCCTTCATTGTGAAGTTAAACTTGTGTTGTCTCG
* * ** * * *
2301157 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAGAAC
1 AGTCCAATATCCTCCACCATGAAGTTGAAATTGACTCTGAAACTGGGAAATTATTTGTTGACAAC
*
2301222 CAACT-GTCCCTTCATTGTGAAGTTAAACTTGTGTTGTCTTG
66 C-ACTCGTCCCTTCATTGTGAAGTTAAACTTGTGTTGTCTCG
2301263 AGT
1 AGT
2301266 GGCACGATAT
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 94 0.98
107 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (106 bp):
AGTCCAATATCCTCCACCATGAAGTTGAAATTGACTCTGAAACTGGGAAATTATTTGTTGACAAC
CACTCGTCCCTTCATTGTGAAGTTAAACTTGTGTTGTCTCG
Found at i:2302983 original size:9 final size:9
Alignment explanation
Indices: 2302969--2303037 Score: 53
Period size: 8 Copynumber: 8.4 Consensus size: 9
2302959 TTTTTGTTCT
2302969 TTCTTTTTG
1 TTCTTTTTG
2302978 TTC-TTTTG
1 TTCTTTTTG
2302986 TTC-TTTTG
1 TTCTTTTTG
2302994 ---TTTTT-
1 TTCTTTTTG
*
2302999 TCCTTTTT-
1 TTCTTTTTG
*
2303007 TTCTTTTTT
1 TTCTTTTTG
2303016 TTCTTTTTG
1 TTCTTTTTG
**
2303025 CCCTTTTTG
1 TTCTTTTTG
2303034 TTCT
1 TTCT
2303038 GATTGAATCT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
6 4 0.08
8 25 0.51
9 20 0.41
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (9 bp):
TTCTTTTTG
Found at i:2302984 original size:21 final size:20
Alignment explanation
Indices: 2302960--2303017 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
2302950 TTCTTTCAAT
2302960 TTTTGTTCTTTCTTTTTGTT-C
1 TTTTGTTCTTT-TTTTT-TTCC
2302981 TTTTGTTCTTTTGTTTTTTCC
1 TTTTGTTCTTTT-TTTTTTCC
*
2303002 TTTTTTTCTTTTTTTT
1 TTTTGTTCTTTTTTTT
2303018 CTTTTTGCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 7 0.21
21 27 0.79
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (20 bp):
TTTTGTTCTTTTTTTTTTCC
Found at i:2302997 original size:13 final size:13
Alignment explanation
Indices: 2302959--2302983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2302949 TTTCTTTCAA
2302959 TTTTTGTTCTTTC
1 TTTTTGTTCTTTC
2302972 TTTTTGTTCTTT
1 TTTTTGTTCTTT
2302984 TGTTCTTTTG
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:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTTGTTCTTTC
Found at i:2303324 original size:29 final size:29
Alignment explanation
Indices: 2303284--2303353 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
2303274 AAATGAAACC
*
2303284 AATAATAATAAACATAAAAT-AATTGGATGAA
1 AATAA-AATAAA-ATAAAATAAATTGAAT-AA
2303315 AA-AAAAT-AAATAAAATGAAATTGAATAA
1 AATAAAATAAAATAAAAT-AAATTGAATAA
2303343 AATAAAATAAA
1 AATAAAATAAA
2303354 TGAAGATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
27 7 0.21
28 6 0.18
29 15 0.44
30 4 0.12
31 2 0.06
ACGTcount: A:0.69, C:0.01, G:0.07, T:0.23
Consensus pattern (29 bp):
AATAAAATAAAATAAAATAAATTGAATAA
Found at i:2303470 original size:22 final size:22
Alignment explanation
Indices: 2303444--2303560 Score: 64
Period size: 22 Copynumber: 4.9 Consensus size: 22
2303434 AAACTAAAAA
2303444 TATAATTAAAATAAATAAATAG
1 TATAATTAAAATAAATAAATAG
*
2303466 TATAAATAAAAT-AATAAAATA-
1 TATAATTAAAATAAAT-AAATAG
2303487 TATATATATAAAAATATAA-AAATGTATG
1 TATA-AT-T-AAAATA-AATAAA--TA-G
2303515 TATAATATAATAA-AATACTAAATAG
1 TATAAT-TAA-AATAA-A-TAAATAG
2303540 TAATAA-TAATAATAAATAAAT
1 T-ATAATTAA-AATAAATAAAT
2303561 GAAAAATAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 31
0.70 0.02 0.28
Matches are distributed among these distances:
21 7 0.09
22 17 0.22
23 6 0.08
24 15 0.19
25 5 0.06
26 14 0.18
27 6 0.08
28 7 0.09
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (22 bp):
TATAATTAAAATAAATAAATAG
Found at i:2303508 original size:24 final size:24
Alignment explanation
Indices: 2303473--2303555 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 24
2303463 TAGTATAAAT
2303473 AAAATAATAAAATATATATATATA
1 AAAATAATAAAATATATATATATA
* *
2303497 AAAAT-ATAAAA-ATGTATGTAT-
1 AAAATAATAAAATATATATATATA
* *
2303518 AATATAATAAAATACTAAATAGTAATA
1 AAAATAATAAAATA-TATATA-T-ATA
*
2303545 ATAATAATAAA
1 AAAATAATAAA
2303556 TAAATGAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
21 4 0.09
22 14 0.31
23 7 0.16
24 8 0.18
25 1 0.02
26 2 0.04
27 9 0.20
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAATAATAAAATATATATATATA
Found at i:2303676 original size:74 final size:73
Alignment explanation
Indices: 2303591--2303734 Score: 170
Period size: 74 Copynumber: 1.9 Consensus size: 73
2303581 ATATTAACTA
* **
2303591 AAAAAATAGTAATTATAG-AA-ATATA-AAATAAAATGAAGTAAGAATATATATATATA-ATGTT
1 AAAAAATAGTAAATA-AGAAACATATATAAA-AAAAT-AA-T-AGAATATATATATATATATAAT
2303652 AGGAAAATATAGT
61 AGGAAAATATAGT
*
2303665 AAAAAATAGTAAATAAGTAAACATATATAAAAAAATAATATAATATATATATATATATAATAGGA
1 AAAAAATAGTAAATAAG-AAACATATATAAAAAAATAATAGAATATATATATATATATAATAGGA
2303730 AAATA
65 AAATA
2303735 ATATAATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
73 17 0.28
74 27 0.44
75 4 0.07
76 10 0.16
77 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.09, T:0.29
Consensus pattern (73 bp):
AAAAAATAGTAAATAAGAAACATATATAAAAAAATAATAGAATATATATATATATATAATAGGAA
AATATAGT
Found at i:2303809 original size:2 final size:2
Alignment explanation
Indices: 2303796--2303825 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2303786 AAAATATAAT
*
2303796 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2303826 AATAATAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2304573 original size:2 final size:2
Alignment explanation
Indices: 2304566--2304613 Score: 66
Period size: 2 Copynumber: 25.0 Consensus size: 2
2304556 ATAAATAAAT
2304566 TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TGA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
2304606 TA TA TA TA
1 TA TA TA TA
2304614 ACATAACATT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.07
2 37 0.88
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2306448 original size:3 final size:3
Alignment explanation
Indices: 2306423--2306472 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
2306413 TTGAGTCTTT
2306423 TTA TT- TTA -TA TT- TTA TCTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
2306466 TTA TTA T
1 TTA TTA T
2306473 GTTAACATCT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.14
3 34 0.79
4 3 0.07
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2311402 original size:134 final size:134
Alignment explanation
Indices: 2311162--2311445 Score: 367
Period size: 134 Copynumber: 2.1 Consensus size: 134
2311152 GCTGTCATTT
* * * *
2311162 AGGGAATATTAGATCTGAGGATGTTGATCCATTTCACTGTTCTTCAGGGAAGATTGGATCAGGGT
1 AGGGAATATCAGATCTGAGGATGTTGATCCATTCCACTGTTCCTCAGGGAAGATTGAATCAGGGT
* * *
2311227 AGACTTGTTCCAATGTCACTCAGGGAATATAAAATCTTGAAAAATAGGGATCTGTTTTGCTT-CT
66 AGACTTGTTCCAATGTCACTCAGGGAATATAAAATCTTGAAAAAGAAGGATCTGTTCTGCTTAC-
2311291 TCTGA
130 TCTGA
* * **
2311296 AGGGAATATCAGATCTGGATGA-GTTGATCCATTCCGCTG-TCACTCAGGGAAGATTGAATCATT
1 AGGGAATATCAGATCT-GAGGATGTTGATCCATTCCACTGTTC-CTCAGGGAAGATTGAATCAGG
* * * * *
2311359 GTAGACTTGTTCCACTGTCACTTAGGGAATATCAAATCTTGAAAGAGAATGATCTGTTCTGCTTA
64 GTAGACTTGTTCCAATGTCACTCAGGGAATATAAAATCTTGAAAAAGAAGGATCTGTTCTGCTTA
2311424 CTCTGA
129 CTCTGA
*
2311430 AGGAAATATCAGATCT
1 AGGGAATATCAGATCT
2311446 TGGAGAAGAG
Statistics
Matches: 130, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
133 2 0.02
134 123 0.95
135 5 0.04
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (134 bp):
AGGGAATATCAGATCTGAGGATGTTGATCCATTCCACTGTTCCTCAGGGAAGATTGAATCAGGGT
AGACTTGTTCCAATGTCACTCAGGGAATATAAAATCTTGAAAAAGAAGGATCTGTTCTGCTTACT
CTGA
Found at i:2311438 original size:48 final size:47
Alignment explanation
Indices: 2311382--2311625 Score: 245
Period size: 48 Copynumber: 5.2 Consensus size: 47
2311372 ACTGTCACTT
*
2311382 AGGGAATATCAAATCTTGA-AAGAGAATGATCTGTTCTGCTTACTCTGA
1 AGGGAATATCAAATCTTGAGAAGAG-A-GATCTGTTCTACTTACTCTGA
* * * *
2311430 AGGAAATATCAGATCTTGGAGAAGAGAGATTTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTT-GAGAAGAGAGATCTGTTCTACTTACTCTGA
* * *
2311478 AGGGAATATCAAATCTTTGAGAAGAGAGATCTGTT-TCGCTCACTTTGA
1 AGGGAATATCAAATC-TTGAGAAGAGAGATCTGTTCT-ACTTACTCTGA
* * * *
2311526 AGGGAATATCAGATC-TG-G--CAGA-CT-TGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGAGAAGAGAGATCTGTTCTACTTACTCTGA
2311567 AGGGAATATCAAATCTTGGAGAAGAGAGA-CATGTTCTACTTACTCTGA
1 AGGGAATATCAAATCTT-GAGAAGAGAGATC-TGTTCTACTTACTCTGA
*
2311615 AGGAAATATCA
1 AGGGAATATCA
2311626 GATATGGGGG
Statistics
Matches: 159, Mismatches: 24, Indels: 26
0.76 0.11 0.12
Matches are distributed among these distances:
41 26 0.16
42 2 0.01
43 4 0.03
44 1 0.01
45 1 0.01
46 5 0.03
48 110 0.69
49 5 0.03
50 5 0.03
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (47 bp):
AGGGAATATCAAATCTTGAGAAGAGAGATCTGTTCTACTTACTCTGA
Found at i:2311616 original size:89 final size:89
Alignment explanation
Indices: 2311460--2311628 Score: 261
Period size: 89 Copynumber: 1.9 Consensus size: 89
2311450 GAAGAGAGAT
* * *
2311460 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTTGAGAAGAGAGATCTGTTTCGCTCACTTTG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGATCTGTTTCACTCACTCTG
*
2311525 AAGGGAATATCAGATCTGGCAGAC
66 AAGGAAATATCAGATCTGGCAGAC
*
2311549 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGA-CATG-TTCTACTTACTC
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGATC-TGTTTC-ACTCACTC
2311612 TGAAGGAAATATCAGAT
64 TGAAGGAAATATCAGAT
2311629 ATGGGGGAGT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
88 4 0.05
89 69 0.95
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (89 bp):
TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGATCTGTTTCACTCACTCTG
AAGGAAATATCAGATCTGGCAGAC
Found at i:2329849 original size:15 final size:15
Alignment explanation
Indices: 2329819--2329915 Score: 74
Period size: 15 Copynumber: 6.3 Consensus size: 15
2329809 AAATAAATAG
2329819 AAAAA-CAAAGAGAA
1 AAAAATCAAAGAGAA
*
2329833 AAGAATCAAAG-GAAA
1 AAAAATCAAAGAG-AA
*
2329848 AACAAATTGCAAAGAGGA
1 AA-AAA-T-CAAAGAGAA
2329866 AAAAATCAAAGAGAA
1 AAAAATCAAAGAGAA
* *
2329881 AAAAAGCAAAGGAAAGA
1 AAAAATCAAA-GAGA-A
*
2329898 AAAAAGCAAA-AGAA
1 AAAAATCAAAGAGAA
2329912 AAAA
1 AAAA
2329916 GCAAAGAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
14 10 0.15
15 28 0.41
16 6 0.09
17 15 0.22
18 8 0.12
19 1 0.01
ACGTcount: A:0.71, C:0.07, G:0.18, T:0.04
Consensus pattern (15 bp):
AAAAATCAAAGAGAA
Found at i:2329876 original size:48 final size:44
Alignment explanation
Indices: 2329819--2329930 Score: 129
Period size: 48 Copynumber: 2.5 Consensus size: 44
2329809 AAATAAATAG
* *
2329819 AAAAACAAAGAGAAAAGAATCAAAGGAAA-AACAAATTGCAAAGAGGA
1 AAAAACAAAGAGAAAAGAAGCAAAGGAAAGAA-AAA-AGCAAA-A-GA
*
2329866 AAAAATCAAAGAGAAAAAAAGCAAAGGAAAGAAAAAAGCAAAAGA
1 AAAAA-CAAAGAGAAAAGAAGCAAAGGAAAGAAAAAAGCAAAAGA
2329911 AAAAAGCAAAGA-AAAAGAAG
1 AAAAA-CAAAGAGAAAAGAAG
2329931 ACAATAAGCA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
44 7 0.12
45 13 0.22
46 1 0.02
47 10 0.17
48 25 0.43
49 2 0.03
ACGTcount: A:0.71, C:0.07, G:0.19, T:0.04
Consensus pattern (44 bp):
AAAAACAAAGAGAAAAGAAGCAAAGGAAAGAAAAAAGCAAAAGA
Found at i:2329900 original size:18 final size:17
Alignment explanation
Indices: 2329880--2329912 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2329870 ATCAAAGAGA
*
2329880 AAAAAAGCAAAGGAAAG
1 AAAAAAGCAAAAGAAAG
2329897 AAAAAAGCAAAAGAAA
1 AAAAAAGCAAAAGAAA
2329913 AAAGCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAGCAAAAGAAAG
Found at i:2329913 original size:12 final size:12
Alignment explanation
Indices: 2329888--2329926 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2329878 GAAAAAAAGC
*
2329888 AAAGGAAAGAAA
1 AAAGCAAAGAAA
2329900 AAAGCAAAAGAAA
1 AAAGC-AAAGAAA
2329913 AAAGCAAAGAAA
1 AAAGCAAAGAAA
2329925 AA
1 AA
2329927 GAAGACAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAGCAAAGAAA
Found at i:2329925 original size:17 final size:17
Alignment explanation
Indices: 2329880--2329925 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 17
2329870 ATCAAAGAGA
*
2329880 AAAAAAGCAAAGGAAAG
1 AAAAAAGCAAAGAAAAG
2329897 AAAAAAGC----AAAAG
1 AAAAAAGCAAAGAAAAG
2329910 AAAAAAGCAAAGAAAA
1 AAAAAAGCAAAGAAAA
2329926 AGAAGACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
13 12 0.50
17 12 0.50
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAGCAAAGAAAAG
Found at i:2331355 original size:37 final size:38
Alignment explanation
Indices: 2331263--2331356 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
2331253 TTTTCTTGAG
* **
2331263 AAATCTTTGAGTCCGTTTCACTTTAAACGAAACAAAAA
1 AAATCTTTGAGTCTGTTTCACTCGAAACGAAACAAAAA
* *
2331301 AAATCTTTGGGTCTGTTTCACTCGAAAC-AAA-ATGAAA
1 AAATCTTTGAGTCTGTTTCACTCGAAACGAAACA-AAAA
*
2331338 AAATCTTTGAGTTTGTTTC
1 AAATCTTTGAGTCTGTTTC
2331357 TTTGGTAACA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 1 0.02
37 23 0.48
38 24 0.50
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (38 bp):
AAATCTTTGAGTCTGTTTCACTCGAAACGAAACAAAAA
Found at i:2331458 original size:62 final size:63
Alignment explanation
Indices: 2331336--2331458 Score: 185
Period size: 63 Copynumber: 2.0 Consensus size: 63
2331326 AACAAAATGA
* * * * *
2331336 AAAAATCTTTGAGTTTGTTTCTTTGGTAACAAAATTTTGTCTCTTTTGATACAGTTTCTTTTG
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGTATCTTTTG
*
2331399 AAAATTCTTTGAGTCTGTTTCTTTGGAAACAAAA-TTTGTCTCTCTTGAGACAGTATCTTT
1 AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGTATCTTT
2331459 GAGTTTGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 23 0.43
63 31 0.57
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (63 bp):
AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGTATCTTTTG
Found at i:2331490 original size:30 final size:30
Alignment explanation
Indices: 2331454--2331510 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2331444 TGAGACAGTA
* * * *
2331454 TCTTTGAGTTTGTTTCTCTTGAAACAAAAG
1 TCTTTGAGTCTATTTCTATTAAAACAAAAG
2331484 TCTTTGAGTCTATTTCTATTAAAACAA
1 TCTTTGAGTCTATTTCTATTAAAACAA
2331511 GAAACAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (30 bp):
TCTTTGAGTCTATTTCTATTAAAACAAAAG
Found at i:2331834 original size:129 final size:130
Alignment explanation
Indices: 2331582--2331862 Score: 314
Period size: 129 Copynumber: 2.1 Consensus size: 130
2331572 TCCCTTGAAA
* * *
2331582 TATTATCCCTAAAGATGGCATGTCGTCCTCATCACGTAGGAACCGTGTCATCTCCCGACCAGACC
1 TATTATCCCTAAAGATGGCATATCGTCCTCATCACGTAGGAACCATGTCATCTCCCAACCAGACC
* * * * * * *
2331647 TCCTCATTATATAAGAGCCGTGTCACCCCAAATAACCAATCGTGCTCATCATGAAGGAATCGTGT
66 TCCTCATCATATAAGAGCCGTGTCACCCCAAATAACCAACCGTCCACATCACGAAGGAACCGAGT
* *
2331712 TATTATCCCTAAAGATGG-TTATCGTCCTCATCATGTAGGAACCATGTCATC-CCCAACCAGACC
1 TATTATCCCTAAAGATGGCATATCGTCCTCATCACGTAGGAACCATGTCATCTCCCAACCAGACC
* * * * * * ** *
2331775 TCCTCATCATGTAGGAGTCGTGTCACCCTTAGATAACCAGCCGTCCACATTGCGTAGGAACCGAG
66 TCCTCATCATATAAGAGCCGTGTCACCC-CAAATAACCAACCGTCCACATCACGAAGGAACCGAG
2331840 T
130 T
*
2331841 TATCACTATTCCTAAAGATGGC
1 TAT---TATCCCTAAAGATGGC
2331863 CAGAACTCTT
Statistics
Matches: 124, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
128 35 0.28
129 57 0.46
130 18 0.15
132 14 0.11
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (130 bp):
TATTATCCCTAAAGATGGCATATCGTCCTCATCACGTAGGAACCATGTCATCTCCCAACCAGACC
TCCTCATCATATAAGAGCCGTGTCACCCCAAATAACCAACCGTCCACATCACGAAGGAACCGAGT
Found at i:2332143 original size:16 final size:16
Alignment explanation
Indices: 2332119--2332167 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2332109 TTGTCGGGTC
*
2332119 TTTTTTATTTTATTTA
1 TTTTATATTTTATTTA
*
2332135 TTTTATATTTTATCTA
1 TTTTATATTTTATTTA
2332151 TTATTATTATTATTATT
1 TT-TTA-TATT-TTATT
2332168 ATGTTAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 16 0.59
17 3 0.11
18 4 0.15
19 4 0.15
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATATTTTATTTA
Found at i:2332168 original size:9 final size:8
Alignment explanation
Indices: 2332119--2332169 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 8
2332109 TTGTCGGGTC
2332119 TTTT-TTA
1 TTTTATTA
2332126 TTTTATTTA
1 TTTTA-TTA
2332135 TTTTA-TA
1 TTTTATTA
2332142 TTTTATCTA
1 TTTTAT-TA
2332151 TTATTATTA
1 TT-TTATTA
2332160 TTATTATTA
1 TT-TTATTA
2332169 T
1 T
2332170 GTTAACATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
7 11 0.28
9 24 0.62
10 4 0.10
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTATTA
Found at i:2332738 original size:18 final size:16
Alignment explanation
Indices: 2332711--2332745 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2332701 GATTCAGTGG
2332711 GGGAAGAAAAATACAGA
1 GGGAAG-AAAATACAGA
2332728 GGGAGAGAAAATACAGA
1 GGGA-AGAAAATACAGA
2332745 G
1 G
2332746 AAACTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.34, T:0.06
Consensus pattern (16 bp):
GGGAAGAAAATACAGA
Found at i:2333658 original size:30 final size:30
Alignment explanation
Indices: 2333624--2333697 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
2333614 ATTTTTACTG
*
2333624 TTTTAG-CTCTTTAAATTTTTGTTTGTGCCA
1 TTTTAGTC-CTTTAAATTTTGGTTTGTGCCA
* * *
2333654 TTTTAGTCCTTTAAGTTTTGGTTTTTGCTA
1 TTTTAGTCCTTTAAATTTTGGTTTGTGCCA
* *
2333684 TTTTGGTCATTTAA
1 TTTTAGTCCTTTAA
2333698 GTTGTTGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.16, C:0.11, G:0.15, T:0.58
Consensus pattern (30 bp):
TTTTAGTCCTTTAAATTTTGGTTTGTGCCA
Found at i:2333697 original size:60 final size:60
Alignment explanation
Indices: 2333593--2333707 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
2333583 TTTTAATACT
* *
2333593 ATTTTAGACCTTTAAGTTTCTATTTTTACTGTTTTAGCTCTTTAAATTTTTGTTTGTGCC
1 ATTTTAGACCTTTAAGTTTCTATTTTTACTATTTTAGCTCTTTAAATTGTTGTTTGTGCC
* * * * *
2333653 ATTTTAGTCCTTTAAGTTT-TGGTTTTTGCTATTTT-GGTCATTTAAGTTGTTGTTT
1 ATTTTAGACCTTTAAGTTTCT-ATTTTTACTATTTTAGCTC-TTTAAATTGTTGTTT
2333708 TTCTCATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 4 0.09
60 42 0.91
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.58
Consensus pattern (60 bp):
ATTTTAGACCTTTAAGTTTCTATTTTTACTATTTTAGCTCTTTAAATTGTTGTTTGTGCC
Found at i:2333698 original size:30 final size:29
Alignment explanation
Indices: 2333640--2333721 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
2333630 CTCTTTAAAT
* * * *
2333640 TTTTGTTTGTGCCATTTTAGTCCTTTAAG
1 TTTTGTTTTTGCTATTTTGGTCATTTAAG
2333669 TTTTGGTTTTTGCTATTTTGGTCATTTAAG
1 TTTT-GTTTTTGCTATTTTGGTCATTTAAG
2333699 TTGTTGTTTTT-CTCATTTTGGTC
1 TT-TTGTTTTTGCT-ATTTTGGTC
2333722 CATGTTATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 6 0.13
30 38 0.83
31 2 0.04
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.60
Consensus pattern (29 bp):
TTTTGTTTTTGCTATTTTGGTCATTTAAG
Found at i:2338633 original size:23 final size:23
Alignment explanation
Indices: 2338596--2338640 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2338586 GTTGTGTATC
* *
2338596 GATACAGTTAAATTGATCATACT
1 GATACAGGTAAATTGAGCATACT
*
2338619 GATACAGGTACATTGAGCATAC
1 GATACAGGTAAATTGAGCATAC
2338641 CAATATAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (23 bp):
GATACAGGTAAATTGAGCATACT
Found at i:2341075 original size:21 final size:21
Alignment explanation
Indices: 2341051--2341101 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2341041 ATATGCTCAC
*
2341051 TAATTTTTTAAATTGGTCATT
1 TAATTTTTTAAATTGATCATT
* * *
2341072 TAATATTTCAAATTGATCTTT
1 TAATTTTTTAAATTGATCATT
2341093 TAATTTTTT
1 TAATTTTTT
2341102 GATACAAACT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (21 bp):
TAATTTTTTAAATTGATCATT
Found at i:2348316 original size:21 final size:21
Alignment explanation
Indices: 2348292--2348337 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2348282 CTCGCTGAAA
*
2348292 GCCAGCAACCCCATCATTCCG
1 GCCAGCAACCCCATCACTCCG
* *
2348313 GCCAGTAACCCCATCGCTCCG
1 GCCAGCAACCCCATCACTCCG
2348334 GCCA
1 GCCA
2348338 CCACACACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.48, G:0.17, T:0.13
Consensus pattern (21 bp):
GCCAGCAACCCCATCACTCCG
Found at i:2349971 original size:42 final size:41
Alignment explanation
Indices: 2349878--2349989 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 41
2349868 CACTGAAGGT
* * *
2349878 CTTATGGATGACCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* *
2349919 CTTATAGATGGCCCTAATGACTTATGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTAT-CATCATGCTCGAAAGA
*
2349961 TTTACT-GATGGCCCGAAGGACTTACTCAT
1 CTTA-TAGATGGCCCGAAGGACTTA-TCAT
2349990 TAAAAAACCC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
41 21 0.35
42 37 0.62
43 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:2350248 original size:236 final size:236
Alignment explanation
Indices: 2349834--2350729 Score: 1036
Period size: 236 Copynumber: 3.8 Consensus size: 236
2349824 CCCCCAAAAG
* * * * * * * *
2349834 CTTAGTTTCTAAAATCTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGAC
1 CTTAGTTTCTAAAAACACAGTTGAAAACATCCTAC-CCGAAGGTCTTATGGATGGCCCGAAGAAC
* * * * *
2349899 TTATCATCTTGCTCGAAAGACTTATAGATGGCCCTAATGACTTATGCATCATGCTCGAAAGATTT
65 TTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGACTT
*
2349964 ACTGATGGCCCGAAGGACTTACTCATTAAAAAACCCTTGAAAATCAAGCTCAGATTCCTTTTAAA
130 ACTGATGGCCCGAAGGACTTACTCATTAAGAAACCCTTGAAAATCAAGCTCAGATTCCTTTTAAA
2350029 AACTCTTAGTAGATAATCATCAAGAAACCTCTGAAAATCAGA
195 AACTCTTAGTAGATAATCATCAAGAAACCTCTGAAAATCAGA
* *
2350071 CTTAGTTTCTAAAAACACAGTTGAAAACATCCTACCTGAAGGTCTTATGGATGGCCCGAATAACT
1 CTTAGTTTCTAAAAACACAGTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGAACT
* *
2350136 TATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATGTTCGAAAGACTTA
66 TATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGACTTA
* * * * * * *
2350201 CTGATGGCCTGAAAGACTTACTCTTTAAGAAACTCTTGAAAATCAAGCTCAGTTTCTACATATCA
131 CTGATGGCCCGAAGGACTTACTCATTAAGAAACCCTTGAAAATCAAGCTCAGATTC--C-TTTTA
*** * * * ** * *** * ** *
2350266 CATTGGTCCCTCGAGTGAGGTGTTGC-TGATTTAA-CTC-CATATGTGAAGA
193 -A--AAACTCT-TAGT-AGATAAT-CATCAAGAAACCTCTGA-AAAT-CAGA
* * * * * * * *
2350315 ATCGAGTATC--AGAA-A-TGTTGAAAACACCCTACCCAAAGGTCTTATGGATGGCCCAAAGAAC
1 CT-TAGTTTCTAAAAACACAGTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGAAC
* *
2350376 TTATCATCTTGCTCGAAAGACTTATAGATGGCCCGAAGGACTTATGCATCATGCTCGAAAGACTT
65 TTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGACTT
*
2350441 ACTGATGGCCCGAAGGATTTACTCATTAAGAAACCCTTGAAAATCAAGCTCA-ATTTCCTTTTAA
130 ACTGATGGCCCGAAGGACTTACTCATTAAGAAACCCTTGAAAATCAAGCTCAGA-TTCCTTTTAA
*
2350505 AAACTCTTAGTAGATAATCATCAAGAAACCCCTGAAAATCAGA
194 AAACTCTTAGTAGATAATCATCAAGAAACCTCTGAAAATCAGA
* * * *
2350548 CTTAGTTTCTAAAAACACAGTTGAAAACATCTTTCCCGAAGGTCTTATGGATGTCTCGAATG-AC
1 CTTAGTTTCTAAAAACACAGTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAA-GAAC
* * *
2350612 TTATCATCTTGTTCGAAAGACTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAGACTT
65 TTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGACTT
* *
2350677 ACTGATGGCCCGAAGGACTTACTCTTTAAGAAACTCTTGAAAATCAAGCTCAG
130 ACTGATGGCCCGAAGGACTTACTCATTAAGAAACCCTTGAAAATCAAGCTCAG
2350730 TTTCTTAGTT
Statistics
Matches: 539, Mismatches: 98, Indels: 44
0.79 0.14 0.06
Matches are distributed among these distances:
232 6 0.01
233 12 0.02
234 10 0.02
235 5 0.01
236 280 0.52
237 32 0.06
238 4 0.01
239 4 0.01
240 1 0.00
241 151 0.28
242 5 0.01
243 11 0.02
244 12 0.02
245 6 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (236 bp):
CTTAGTTTCTAAAAACACAGTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGAACT
TATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGACTTA
CTGATGGCCCGAAGGACTTACTCATTAAGAAACCCTTGAAAATCAAGCTCAGATTCCTTTTAAAA
ACTCTTAGTAGATAATCATCAAGAAACCTCTGAAAATCAGA
Found at i:2350439 original size:22 final size:21
Alignment explanation
Indices: 2350369--2350441 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
2350359 TGGATGGCCC
2350369 AAAGAACTTAT-CATCTTGCTCG
1 AAAG-ACTTATGCATC-TGCTCG
* *
2350391 AAAGACTTATAG-AT-GGCCCG
1 AAAGACTTAT-GCATCTGCTCG
*
2350411 AAGGACTTATGCATCATGCTCG
1 AAAGACTTATGCATC-TGCTCG
2350433 AAAGACTTA
1 AAAGACTTA
2350442 CTGATGGCCC
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 1 0.03
20 15 0.38
21 6 0.15
22 18 0.45
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (21 bp):
AAAGACTTATGCATCTGCTCG
Found at i:2350441 original size:42 final size:40
Alignment explanation
Indices: 2350355--2350466 Score: 143
Period size: 42 Copynumber: 2.7 Consensus size: 40
2350345 ACCCAAAGGT
* * *
2350355 CTTATGGATGGCCCAAAGAACTTATCATCTTGCTCGAAAGA
1 CTTAT-GATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
2350396 CTTATAGATGGCCCGAAGGACTTATGCATCATGCTCGAAAGA
1 CTTAT-GATGGCCCGAAGGACTTAT-CATCATGCTCGAAAGA
*
2350438 CTTACTGATGGCCCGAAGGATTTACTCAT
1 CTTA-TGATGGCCCGAAGGACTTA-TCAT
2350467 TAAGAAACCC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 22 0.35
42 39 0.62
43 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (40 bp):
CTTATGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:2350636 original size:41 final size:42
Alignment explanation
Indices: 2350591--2350697 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 42
2350581 TCCCGAAGGT
* * * * * *
2350591 CTTATGGATGTCTCGAATGACTT-ATCATCTTGTTCGAAAGA
1 CTTATAGATGACTCGAAGGACTTAAGCATCATGCTCGAAAGA
*
2350632 CTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACTCGAAGGACTTAAGCATCATGCTCGAAAGA
* *
2350674 CTTACT-GATGGCCCGAAGGACTTA
1 CTTA-TAGATGACTCGAAGGACTTA
2350698 CTCTTTAAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 19 0.35
42 34 0.63
43 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (42 bp):
CTTATAGATGACTCGAAGGACTTAAGCATCATGCTCGAAAGA
Found at i:2352168 original size:28 final size:28
Alignment explanation
Indices: 2352128--2352190 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
2352118 GATAAAAGGC
2352128 TCAGGTTAATTTGGGGAGGTAATGTGCT
1 TCAGGTTAATTTGGGGAGGTAATGTGCT
*
2352156 TCAGGTTAATTTGGGGAGGTAATGTGTT
1 TCAGGTTAATTTGGGGAGGTAATGTGCT
*
2352184 TTAGGTT
1 TCAGGTT
2352191 GGCTTCTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.21, C:0.05, G:0.35, T:0.40
Consensus pattern (28 bp):
TCAGGTTAATTTGGGGAGGTAATGTGCT
Found at i:2352846 original size:17 final size:16
Alignment explanation
Indices: 2352824--2352934 Score: 95
Period size: 17 Copynumber: 6.9 Consensus size: 16
2352814 GATCTGTCTA
*
2352824 TTTTCTTCTTTCTTCTT
1 TTTTCTTCTTTTTTC-T
2352841 TTTTCTAT-TTTTTTCT
1 TTTTCT-TCTTTTTTCT
*
2352857 TTTTCTT-TTTTTCTCG
1 TTTTCTTCTTTTT-TCT
*
2352873 TTTTCTTCTGTTTTCT
1 TTTTCTTCTTTTTTCT
*
2352889 CTTTC-T-TTTTTTCT
1 TTTTCTTCTTTTTTCT
* *
2352903 TATTCTCTCTTTTTTAT
1 TTTTCT-TCTTTTTTCT
2352920 TTTTCTCTCTTTTTT
1 TTTTCT-TCTTTTTT
2352935 TCCTATTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.13
15 7 0.09
16 23 0.29
17 37 0.47
18 1 0.01
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTCTTCTTTTTTCT
Found at i:2352847 original size:24 final size:22
Alignment explanation
Indices: 2352825--2352933 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 22
2352815 ATCTGTCTAT
2352825 TTTCTTCTTTCTTCTTTTTTCTAT
1 TTTCTTCTTT-TTCTTTTTTCT-T
*
2352849 TTTTTTCTTTTTCTTTTTTTCTCGT
1 TTTCTTCTTTTTC-TTTTTTCT--T
2352874 TTTCTTCTGTTTTCTCTTTCTT-TT
1 TTTCTTCT-TTTTCT-TTT-TTCTT
* * *
2352898 TTTCTTATTCTCTCTTTTTTATT
1 TTTCTTCTT-TTTCTTTTTTCTT
2352921 TTTCTCTCTTTTT
1 TTTCT-TCTTTTT
2352934 TTCCTATTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
22 2 0.03
23 16 0.23
24 32 0.46
25 9 0.13
26 9 0.13
27 2 0.03
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTCTTCTTTTTCTTTTTTCTT
Found at i:2352859 original size:16 final size:15
Alignment explanation
Indices: 2352824--2352925 Score: 80
Period size: 16 Copynumber: 6.4 Consensus size: 15
2352814 GATCTGTCTA
*
2352824 TTTTCTTCTTTCTTCTT
1 TTTTCTT-TTTTTTC-T
2352841 TTTTCTATTTTTTTCT
1 TTTTCT-TTTTTTTCT
*
2352857 TTTTCTTTTTTTCTCG
1 TTTTCTTTTTTT-TCT
*
2352873 TTTTCTTCTGTTTTCT
1 TTTTCTT-TTTTTTCT
*
2352889 CTTTC-TTTTTTTCT
1 TTTTCTTTTTTTTCT
* *
2352903 TATTCTCTCTTTTTTAT
1 T-TT-TCTTTTTTTTCT
2352920 TTTTCT
1 TTTTCT
2352926 CTCTTTTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.10
15 12 0.17
16 26 0.37
17 24 0.34
18 1 0.01
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTTTTTCT
Found at i:2352909 original size:38 final size:35
Alignment explanation
Indices: 2352824--2352941 Score: 91
Period size: 35 Copynumber: 3.3 Consensus size: 35
2352814 GATCTGTCTA
* *
2352824 TTTTCTTCTT-TCTTCTTTTTTCTATTTT-TTTCTTT
1 TTTTCTTATTCTC-TCTTTTTTAT-TTTTCTTTCTTT
* *
2352859 TTCTT-TTTTTCTCGT-TTTCTTCTGTTTTCTCTTTCTTT
1 TT-TTCTTATTCTC-TCTTT-TT-TATTTT-TCTTTCTTT
*
2352897 TTTTCTTATTCTCTCTTTTTTATTTTTCTCTCTTT
1 TTTTCTTATTCTCTCTTTTTTATTTTTCTTTCTTT
*
2352932 TTTTCCTATT
1 TTTTCTTATT
2352942 TTTAGTTTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
35 26 0.38
36 15 0.22
37 8 0.12
38 19 0.28
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.75
Consensus pattern (35 bp):
TTTTCTTATTCTCTCTTTTTTATTTTTCTTTCTTT
Found at i:2352932 original size:10 final size:9
Alignment explanation
Indices: 2352827--2352934 Score: 64
Period size: 10 Copynumber: 11.9 Consensus size: 9
2352817 CTGTCTATTT
*
2352827 TCTTCTTTC
1 TCTTTTTTC
2352836 TTCTTTTTTC
1 -TCTTTTTTC
*
2352846 TATTTTTT-
1 TCTTTTTTC
2352854 TC-TTTTTC
1 TCTTTTTTC
2352862 T-TTTTTTC
1 TCTTTTTTC
2352870 TCGTTTTCTTC
1 TC-TTTT-TTC
* *
2352881 TGTTTTCTCTT
1 TCTTTT-T-TC
2352892 TCTTTTTT-
1 TCTTTTTTC
*
2352900 TCTTATTCTC
1 TCTT-TTTTC
*
2352910 TCTTTTTTA
1 TCTTTTTTC
*
2352919 T-TTTTCTC
1 TCTTTTTTC
2352927 TCTTTTTT
1 TCTTTTTT
2352935 TCCTATTTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
7 5 0.06
8 19 0.25
9 20 0.26
10 23 0.30
11 10 0.13
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (9 bp):
TCTTTTTTC
Found at i:2352944 original size:46 final size:43
Alignment explanation
Indices: 2352832--2352944 Score: 106
Period size: 46 Copynumber: 2.5 Consensus size: 43
2352822 TATTTTCTTC
*
2352832 TTTCTTC-TTTTTT-CTATTTTTTTCTTTTTCTTTTTTTCTCGT
1 TTTCTTCTTTTTTTCCTATTTTTTTCTTTTTCTTTTTTTATC-T
* * *
2352874 TTTCTTCTGTTTTCTCTTTCTTTTTTTCTTATTCTCTCTTTTTTAT-T
1 TTTCTTCT-TTTTTTC-CTATTTTTTTCTT-TT-TCT-TTTTTTATCT
2352921 TTTCTCTCTTTTTTTCCTATTTTT
1 TTTCT-TCTTTTTTTCCTATTTTT
2352945 AGTTTCTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
42 7 0.12
44 5 0.09
46 17 0.30
47 14 0.25
48 6 0.11
49 7 0.12
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.76
Consensus pattern (43 bp):
TTTCTTCTTTTTTTCCTATTTTTTTCTTTTTCTTTTTTTATCT
Found at i:2353623 original size:22 final size:22
Alignment explanation
Indices: 2353595--2353645 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
2353585 TAATGTTATT
2353595 GAAAGGTTATTTCTGTCTGGAA
1 GAAAGGTTATTTCTGTCTGGAA
2353617 GAAAGGTTATTTCTGTCTGGAA
1 GAAAGGTTATTTCTGTCTGGAA
*
2353639 GGAAGGT
1 GAAAGGT
2353646 CTAATCTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.08, G:0.31, T:0.33
Consensus pattern (22 bp):
GAAAGGTTATTTCTGTCTGGAA
Found at i:2358001 original size:27 final size:27
Alignment explanation
Indices: 2357950--2358001 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2357940 GATGAAAATG
* **
2357950 ACACAAACAAAAGAAATAAGTTAGTGT
1 ACACAAACAAAAGAAAAAAAATAGTGT
2357977 ACACAAACAAAAGAAAAAAAATAGT
1 ACACAAACAAAAGAAAAAAAATAGT
2358002 TAGTACAGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.63, C:0.12, G:0.12, T:0.13
Consensus pattern (27 bp):
ACACAAACAAAAGAAAAAAAATAGTGT
Found at i:2380966 original size:14 final size:14
Alignment explanation
Indices: 2380943--2380975 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2380933 TGAACAATAA
2380943 AATA-CGTATAAAC
1 AATACCGTATAAAC
*
2380956 AGTACCGTATAAAC
1 AATACCGTATAAAC
2380970 AATACC
1 AATACC
2380976 TACTACAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.48, C:0.21, G:0.09, T:0.21
Consensus pattern (14 bp):
AATACCGTATAAAC
Found at i:2381056 original size:21 final size:22
Alignment explanation
Indices: 2381018--2381059 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2381008 ATTCAAAGAG
*
2381018 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATTACCCTGCTACA
2381040 GGGAACCGA-TACCCTGCTAC
1 GGGAACCGATTACCCTGCTAC
2381060 GGTACTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.17
Consensus pattern (22 bp):
GGGAACCGATTACCCTGCTACA
Found at i:2381794 original size:24 final size:24
Alignment explanation
Indices: 2381767--2381907 Score: 141
Period size: 23 Copynumber: 6.0 Consensus size: 24
2381757 CACCACAGCT
*
2381767 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
2381791 CGTAGAAATTATC-CCGAAG-GACCA
1 CGTAGAAATT-GCACCGAAGTG-CCA
*
2381815 CGTAGAGA-TGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
** *
2381838 CGTAGAAATTGTC-CCGAAGAACCG
1 CGTAGAAATTG-CACCGAAGTGCCA
*
2381862 CGTAGAGA-TGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
2381885 CGTAG-AATTGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
2381908 TATAATATGT
Statistics
Matches: 95, Mismatches: 14, Indels: 17
0.75 0.11 0.13
Matches are distributed among these distances:
22 3 0.03
23 47 0.49
24 43 0.45
25 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.17
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:2381845 original size:47 final size:47
Alignment explanation
Indices: 2381776--2381891 Score: 205
Period size: 47 Copynumber: 2.5 Consensus size: 47
2381766 TCGTATAAAT
*
2381776 TGCACCGAAGTGCCACGTAGAAATTATCCCGAAGGACCACGTAGAGA
1 TGCACCGAAGTGCCACGTAGAAATTATCCCGAAGAACCACGTAGAGA
* *
2381823 TGCACCGAAGTGCCACGTAGAAATTGTCCCGAAGAACCGCGTAGAGA
1 TGCACCGAAGTGCCACGTAGAAATTATCCCGAAGAACCACGTAGAGA
2381870 TGCACCGAAGTGCCACGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
2381892 TTGCACCGTA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.33, C:0.26, G:0.27, T:0.15
Consensus pattern (47 bp):
TGCACCGAAGTGCCACGTAGAAATTATCCCGAAGAACCACGTAGAGA
Found at i:2384763 original size:2 final size:2
Alignment explanation
Indices: 2384747--2384810 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
2384737 TCAATTAATC
* *
2384747 AT AT AT TT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2384789 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2384811 TCAATCAGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2388392 original size:24 final size:24
Alignment explanation
Indices: 2388365--2388505 Score: 116
Period size: 23 Copynumber: 6.0 Consensus size: 24
2388355 CACCACGGCT
*
2388365 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
2388389 CGTAGAAATTATC-CCGAAG-GACCG
1 CGTAGAAATT-GCACCGAAGTG-CCA
*
2388413 CGTAGAGA-TGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
** *
2388436 CGTAGAAATTGTC-CCGAAGAACCG
1 CGTAGAAATTG-CACCGAAGTGCCA
* *
2388460 CGTAGAGA-TGCACCGAAGTACCA
1 CGTAGAAATTGCACCGAAGTGCCA
2388483 CGTAG-AATTGCACC-ATAGTGCCA
1 CGTAGAAATTGCACCGA-AGTGCCA
2388506 TATAATATGT
Statistics
Matches: 93, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
22 4 0.04
23 45 0.48
24 42 0.45
25 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.17
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:2388443 original size:47 final size:47
Alignment explanation
Indices: 2388374--2388489 Score: 205
Period size: 47 Copynumber: 2.5 Consensus size: 47
2388364 TCGTATAAAT
*
2388374 TGCACCGAAGTGCCACGTAGAAATTATCCCGAAGGACCGCGTAGAGA
1 TGCACCGAAGTGCCACGTAGAAATTATCCCGAAGAACCGCGTAGAGA
*
2388421 TGCACCGAAGTGCCACGTAGAAATTGTCCCGAAGAACCGCGTAGAGA
1 TGCACCGAAGTGCCACGTAGAAATTATCCCGAAGAACCGCGTAGAGA
*
2388468 TGCACCGAAGTACCACGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
2388490 TTGCACCATA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.33, C:0.26, G:0.27, T:0.15
Consensus pattern (47 bp):
TGCACCGAAGTGCCACGTAGAAATTATCCCGAAGAACCGCGTAGAGA
Found at i:2395063 original size:6 final size:6
Alignment explanation
Indices: 2395047--2395078 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2395037 CAGTTAAACC
*
2395047 CTTTGA ATTTGA CTTTGA CTTTGA CTTTGA CT
1 CTTTGA CTTTGA CTTTGA CTTTGA CTTTGA CT
2395079 AAGAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (6 bp):
CTTTGA
Found at i:2405079 original size:103 final size:103
Alignment explanation
Indices: 2404854--2405068 Score: 403
Period size: 103 Copynumber: 2.1 Consensus size: 103
2404844 GTCGAGGGTC
2404854 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
2404919 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2404957 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2405022 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2405060 TATGTGGTC
1 TATGTGGTC
2405069 ATTATGGACA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Done.