Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008301.1 Hibiscus syriacus cultivar Beakdansim tig00110987_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: 3376434
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 18
Found at i:2124454 original size:106 final size:104
Alignment explanation
Indices: 2124266--2124580 Score: 479
Period size: 106 Copynumber: 3.0 Consensus size: 104
2124256 ATACAGATAA
* * *
2124266 AATACTTCAGTCAAAATTAGTTTATCAAACATGTTTTAAAAAATATGGACACTACCCCCATCCGA
1 AATACTTCAGT-AAAATCAGTTTATCAAACATGTTTT-AAAAATATGAACACTACCCCCATCTGA
* *
2124331 TCACCAAAATGTCTAGGTTCCCTAGAACCATACACCCACCTG
64 TCACCAGAATGTGTAGGTTCCC-AGAACCATACACCCACCTG
*
2124373 AATACTTCAGTAAGAATCAGTTTATCAAACATGTTTTAAAAATATGAACACTACTCCCATCTGAT
1 AATACTTCAGTAA-AATCAGTTTATCAAACATGTTTTAAAAATATGAACACTACCCCCATCTGAT
*
2124438 CACCAGAATCTGTAGGTTCCCCAGAACCATACACCCACCTG
65 CACCAGAATGTGTAGGTT-CCCAGAACCATACACCCACCTG
*
2124479 AATACTTCAGTAAAAATCAGTTTATCAAACATGTTTTAAAAATATGAACATTACCCCCATCCT-A
1 AATACTTCAGT-AAAATCAGTTTATCAAACATGTTTTAAAAATATGAACACTACCCCCAT-CTGA
2124543 TCACCAGAATGTGTAGGTTCCGCAGAACCATACACCCA
64 TCACCAGAATGTGTAGGTTCC-CAGAACCATACACCCA
2124581 TCTGTACACC
Statistics
Matches: 193, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
105 2 0.01
106 151 0.78
107 40 0.21
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (104 bp):
AATACTTCAGTAAAATCAGTTTATCAAACATGTTTTAAAAATATGAACACTACCCCCATCTGATC
ACCAGAATGTGTAGGTTCCCAGAACCATACACCCACCTG
Found at i:2124709 original size:39 final size:39
Alignment explanation
Indices: 2124627--2124747 Score: 119
Period size: 39 Copynumber: 3.2 Consensus size: 39
2124617 AAGGGTCTAT
* **
2124627 GGTAAGGACTTACCCTGAGCACAAAGTTAAGGAGATTGT
1 GGTAAGGACTTACCCTGAGCACAAAGTTAAGGAGACTAC
*
2124666 GGTAAGGACTTACCCTGAGCACAAAGTCT-AGGAGCCTAC
1 GGTAAGGACTTACCCTGAGCACAAAGT-TAAGGAGACTAC
* * *
2124705 GGT-A--A-TGACCCTGAGCACAAAGCTAAGGA-ACATGC
1 GGTAAGGACTTACCCTGAGCACAAAGTTAAGGAGAC-TAC
2124740 GGTAAGGA
1 GGTAAGGA
2124748 ACATGCGGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
34 2 0.03
35 25 0.37
36 2 0.03
38 2 0.03
39 36 0.53
40 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (39 bp):
GGTAAGGACTTACCCTGAGCACAAAGTTAAGGAGACTAC
Found at i:2124743 original size:35 final size:35
Alignment explanation
Indices: 2124677--2124744 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
2124667 GTAAGGACTT
* *
2124677 ACCCTGAGCACAAAGTCTAGGAGCCTACGGTAATG
1 ACCCTGAGCACAAAGTCTAGGAACATACGGTAATG
*
2124712 ACCCTGAGCACAAAG-CTAAGGAACATGCGGTAA
1 ACCCTGAGCACAAAGTCT-AGGAACATACGGTAA
2124745 GGAACATGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 2 0.07
35 27 0.93
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (35 bp):
ACCCTGAGCACAAAGTCTAGGAACATACGGTAATG
Found at i:2124747 original size:14 final size:14
Alignment explanation
Indices: 2124728--2124761 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
2124718 AGCACAAAGC
2124728 TAAGGAACATGCGG
1 TAAGGAACATGCGG
2124742 TAAGGAACATGCGG
1 TAAGGAACATGCGG
2124756 TAAGGA
1 TAAGGA
2124762 CTTACATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.35, T:0.15
Consensus pattern (14 bp):
TAAGGAACATGCGG
Found at i:2126154 original size:29 final size:30
Alignment explanation
Indices: 2126121--2126178 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
2126111 ACTTTCAGAA
*
2126121 TTTGGA-TCCGAATTTAATCAAAATTTCAC
1 TTTGGACTCCAAATTTAATCAAAATTTCAC
* * *
2126150 TTTGGACTCTAAATTTAGTTAAAATTTCA
1 TTTGGACTCCAAATTTAATCAAAATTTCA
2126179 ATTTAGTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (30 bp):
TTTGGACTCCAAATTTAATCAAAATTTCAC
Found at i:2128496 original size:108 final size:107
Alignment explanation
Indices: 2128368--2128563 Score: 320
Period size: 107 Copynumber: 1.8 Consensus size: 107
2128358 CCATTCAGGT
** **
2128368 AAAATACTTCAGTAAAAATCAGTTTATCAAACATGTTTTAAAAAAATATGAACACAACCCTTATC
1 AAAATACTTCAGTAAAAATCAGTTTATCAAACATGTTTT-AAAAAATACAAACACAACCCCCATC
2128433 CAATCACCAGAATGTGTAGGTTCCTCATAACCATACACCCATA
65 CAATCACCAGAATGTGTAGGTTCCTCATAACCATACACCCATA
* *
2128476 AAAATACTTCAGTAAAAATCAGTTTATCAAACATGTTTTAAAAAATACAAACACTACCCCCATTC
1 AAAATACTTCAGTAAAAATCAGTTTATCAAACATGTTTTAAAAAATACAAACACAACCCCCATCC
*
2128541 GATCACCAGAATGTGTAGGTTCC
66 AATCACCAGAATGTGTAGGTTCC
2128564 CCAGAACTAT
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
107 42 0.52
108 39 0.48
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (107 bp):
AAAATACTTCAGTAAAAATCAGTTTATCAAACATGTTTTAAAAAATACAAACACAACCCCCATCC
AATCACCAGAATGTGTAGGTTCCTCATAACCATACACCCATA
Found at i:2128664 original size:39 final size:38
Alignment explanation
Indices: 2128621--2128792 Score: 150
Period size: 39 Copynumber: 4.4 Consensus size: 38
2128611 TAACATAAGG
* *
2128621 GCCTACAGTAATGACTTACCCTTAGCACAAAGTACAGGA
1 GCCTACAGTAAGGACTTACCCTGAGCACAAAG-ACAGGA
* * *
2128660 GCCTAC-GATATGGACCTACCCTGAGCACAAAG-CTGATGA
1 GCCTACAG-TAAGGACTTACCCTGAGCACAAAGAC--AGGA
* * * * *
2128699 GCTTGCGGTAAGGACTTACCTTGAGCACAAAGATGAGGA
1 GCCTACAGTAAGGACTTACCCTGAGCACAAAGA-CAGGA
* * *
2128738 GCCTGCAGTAAGGACTTACCCTGAGCATAAAGCCGAGGA
1 GCCTACAGTAAGGACTTACCCTGAGCACAAAGAC-AGGA
*
2128777 GCCTACGGTAAGGACT
1 GCCTACAGTAAGGACT
2128793 AACAAGTCAT
Statistics
Matches: 106, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 103 0.97
40 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (38 bp):
GCCTACAGTAAGGACTTACCCTGAGCACAAAGACAGGA
Found at i:2128762 original size:78 final size:78
Alignment explanation
Indices: 2128621--2128792 Score: 197
Period size: 78 Copynumber: 2.2 Consensus size: 78
2128611 TAACATAAGG
* * *
2128621 GCCTACAGTAATGACTTACCCTTAGCACAAAGTACAGGAGCCTACGATATGGACCTACCCTGAGC
1 GCCTACGGTAAGGACTTACCCTTAGCACAAAGTACAGGAGCCTACGATAAGGACCTACCCTGAGC
* *
2128686 ACAAAGCTGATGA
66 ACAAAGCCGAGGA
* * * * *
2128699 GCTTGCGGTAAGGACTTA-CCTTGAGCACAAAG-ATGAGGAGCCTGC-AGTAAGGACTTACCCTG
1 GCCTACGGTAAGGACTTACCCTT-AGCACAAAGTA-CAGGAGCCTACGA-TAAGGACCTACCCTG
*
2128761 AGCATAAAGCCGAGGA
63 AGCACAAAGCCGAGGA
2128777 GCCTACGGTAAGGACT
1 GCCTACGGTAAGGACT
2128793 AACAAGTCAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
77 6 0.08
78 72 0.92
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (78 bp):
GCCTACGGTAAGGACTTACCCTTAGCACAAAGTACAGGAGCCTACGATAAGGACCTACCCTGAGC
ACAAAGCCGAGGA
Found at i:2132536 original size:14 final size:14
Alignment explanation
Indices: 2132517--2132549 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2132507 TGAACAAGTT
2132517 CTTCTCATTATGAA
1 CTTCTCATTATGAA
2132531 CTTCTCATTATGAA
1 CTTCTCATTATGAA
2132545 CTTCT
1 CTTCT
2132550 TCTTTCGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (14 bp):
CTTCTCATTATGAA
Found at i:2132551 original size:17 final size:16
Alignment explanation
Indices: 2132515--2132552 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
2132505 ATTGAACAAG
2132515 TTCTTCTCATTATGAA
1 TTCTTCTCATTATGAA
2132531 --CTTCTCATTATGAA
1 TTCTTCTCATTATGAA
2132545 CTTCTTCT
1 -TTCTTCT
2132553 TTCGAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
14 14 0.74
17 5 0.26
ACGTcount: A:0.21, C:0.24, G:0.05, T:0.50
Consensus pattern (16 bp):
TTCTTCTCATTATGAA
Found at i:2147233 original size:22 final size:22
Alignment explanation
Indices: 2147208--2147249 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2147198 TCACGTAATG
*
2147208 CTTTACTTGGTATTTTGATGCA
1 CTTTACTTGGTATTTCGATGCA
**
2147230 CTTTGTTTGGTATTTCGATG
1 CTTTACTTGGTATTTCGATG
2147250 GTTTTCCGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.12, G:0.21, T:0.52
Consensus pattern (22 bp):
CTTTACTTGGTATTTCGATGCA
Found at i:2147988 original size:39 final size:38
Alignment explanation
Indices: 2147794--2148043 Score: 168
Period size: 39 Copynumber: 6.6 Consensus size: 38
2147784 TCAAAAATTA
*
2147794 TATATATTATATATGTTT-ACAAAAACCG-TTTTAAAAAC
1 TATATATTATATGT-TTTCA-AAAAACCGTTTTTAAAAAC
** * *
2147832 TATA-CGTATATGTTTTCAAAATA--TTTTTTCAAAAA-
1 TATATATTATATGTTTTCAAAAAACCGTTTTT-AAAAAC
*
2147867 T-TATATTATATACGTTTTC-AAAAACCG-TTTTAATATATATA
1 TATATATTATAT--GTTTTCAAAAAACCGTTTTTAA-A-A-A-C
* *
2147908 TATATATTATATATGTTTTC-AAAAATCGTTTTTTAAGAAC
1 TATATA-T-TATATGTTTTCAAAAAACCG-TTTTTAAAAAC
*
2147948 TATATATTATATGTTTTCAAAAAACCATTTTCTAAAAAC
1 TATATATTATATGTTTTCAAAAAACCGTTTT-TAAAAAC
* * *
2147987 TATATATTATATGTCTTC--AAAACCCTTTTT--TAAC
1 TATATATTATATGTTTTCAAAAAACCGTTTTTAAAAAC
*
2148021 TATATAGTATATGTTTTCAAAAA
1 TATATATTATATGTTTTCAAAAA
2148044 CTATACTATA
Statistics
Matches: 170, Mismatches: 20, Indels: 46
0.72 0.08 0.19
Matches are distributed among these distances:
34 21 0.12
35 10 0.06
36 22 0.13
37 28 0.16
38 20 0.12
39 31 0.18
40 6 0.04
41 2 0.01
42 18 0.11
43 1 0.01
44 11 0.06
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.44
Consensus pattern (38 bp):
TATATATTATATGTTTTCAAAAAACCGTTTTTAAAAAC
Found at i:2148046 original size:24 final size:21
Alignment explanation
Indices: 2148018--2148076 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 21
2148008 ACCCTTTTTT
*
2148018 AACTATATAGTATATGTTTTCAAA
1 AACTATATA-TATA--TCTTCAAA
2148042 AACTATACTATATATCTTCAAA
1 AACTATA-TATATATCTTCAAA
2148064 AAGCTATATATAT
1 AA-CTATATATAT
2148077 TATTATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 14 0.44
23 5 0.16
24 11 0.34
25 2 0.06
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (21 bp):
AACTATATATATATCTTCAAA
Found at i:2148097 original size:14 final size:12
Alignment explanation
Indices: 2148068--2148099 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2148058 TTCAAAAAGC
2148068 TATATATATTAT
1 TATATATATTAT
2148080 TATATATATTAT
1 TATATATATTAT
*
2148092 CATATATA
1 TATATATA
2148100 CTATATAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TATATATATTAT
Found at i:2153041 original size:13 final size:14
Alignment explanation
Indices: 2153014--2153061 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
2153004 ATATAACTAA
2153014 AATTTTATTTTAAT
1 AATTTTATTTTAAT
2153028 -ATTTT-TTTTCAAT
1 AATTTTATTTT-AAT
*
2153041 AATTTTA-GTTAAT
1 AATTTTATTTTAAT
2153054 AATTTTAT
1 AATTTTAT
2153062 AAAATTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
12 4 0.14
13 18 0.62
14 7 0.24
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
AATTTTATTTTAAT
Found at i:2153593 original size:28 final size:28
Alignment explanation
Indices: 2153533--2153591 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
2153523 TATAATAAAA
** *
2153533 TTTAAAATTTAATATCTATCATATAATT
1 TTTAAAATTTAATATCTAAAAAATAATT
*
2153561 TTTAAAATTTTAATATCTAAAAAATCATT
1 TTTAAAA-TTTAATATCTAAAAAATAATT
2153590 TT
1 TT
2153592 AATATAGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTAAAATTTAATATCTAAAAAATAATT
Found at i:2155654 original size:23 final size:22
Alignment explanation
Indices: 2155628--2155672 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2155618 TTGATTGCAA
2155628 TTCAATTCCTATT-TTTATTTTAT
1 TTCAATT--TATTCTTTATTTTAT
2155651 TTCAATTTATTCTTTATTTTAT
1 TTCAATTTATTCTTTATTTTAT
2155673 ATTATTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 10 0.48
23 7 0.33
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (22 bp):
TTCAATTTATTCTTTATTTTAT
Found at i:2155662 original size:27 final size:27
Alignment explanation
Indices: 2155595--2155679 Score: 64
Period size: 28 Copynumber: 3.1 Consensus size: 27
2155585 TTTAATAAAA
* * * *
2155595 TTCAATTTAGTCCATAATTTTAATTGAT
1 TTCAATTTATTCC-TATTTTTATTTTAT
* *
2155623 TGCAATTCAATTCCTATTTTTATTTTAT
1 TTCAATT-TATTCCTATTTTTATTTTAT
* *
2155651 TTCAATTTATT-CTTTATTTTATATTAT
1 TTCAATTTATTCCTAT-TTTTATTTTAT
2155678 TT
1 TT
2155680 TACTAATTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
26 3 0.07
27 15 0.33
28 23 0.51
29 4 0.09
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.59
Consensus pattern (27 bp):
TTCAATTTATTCCTATTTTTATTTTAT
Found at i:2175277 original size:132 final size:132
Alignment explanation
Indices: 2175103--2175369 Score: 489
Period size: 132 Copynumber: 2.0 Consensus size: 132
2175093 TTGCATATGT
2175103 TGAATGATATGGGTGAATACATGTTTATATGATATATATTATGTGATATGATATATGGACAAGAA
1 TGAATGATATGGGTGAATACATGTTTATATGATATATATTATGTGATATGATATATGGACAAGAA
* *
2175168 ATATGAAATGACTCAGTAAGTTAATATCAGCTATGTGAAAGTAATGTAGGTGTATATATGTGGTA
66 ATATGAAATGACTCAGTAAGCTAATATCAGCAATGTGAAAGTAATGTAGGTGTATATATGTGGTA
2175233 AG
131 AG
*
2175235 TGAATGATATGGGTGAATACATGTTTATATGATATATGTTATGTGATATGATATATGGACAAGAA
1 TGAATGATATGGGTGAATACATGTTTATATGATATATATTATGTGATATGATATATGGACAAGAA
* *
2175300 ATATGAAATGACTCGGTAAGCTAATATCAGCAATGTGAAAGTAATGTAGGTGTCTATATGTGGTA
66 ATATGAAATGACTCAGTAAGCTAATATCAGCAATGTGAAAGTAATGTAGGTGTATATATGTGGTA
2175365 AG
131 AG
2175367 TGA
1 TGA
2175370 TTCATATAAA
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 130 1.00
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (132 bp):
TGAATGATATGGGTGAATACATGTTTATATGATATATATTATGTGATATGATATATGGACAAGAA
ATATGAAATGACTCAGTAAGCTAATATCAGCAATGTGAAAGTAATGTAGGTGTATATATGTGGTA
AG
Found at i:2175620 original size:2 final size:2
Alignment explanation
Indices: 2175564--2175604 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2175554 AGATTTTATG
2175564 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2175605 GTTACTTGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2176162 original size:31 final size:31
Alignment explanation
Indices: 2176124--2176234 Score: 98
Period size: 40 Copynumber: 3.3 Consensus size: 31
2176114 GAGTCGAGGG
2176124 TTACCTATGTCTTTTGAGACATATGGATAGTT
1 TTACCTATGTCTTTTGAGACATATGGATAG-T
2176156 TACCTATGTCCTTTATGTCTTTTGAGACATATGGATAGT
1 T---TA---CC--TATGTCTTTTGAGACATATGGATAGT
* * * *
2176195 TTACCTATGTCCTTCGGGACATATGGACAG-
1 TTACCTATGTCTTTTGAGACATATGGATAGT
2176225 TTACCTATGT
1 TTACCTATGT
2176235 TCTCCAGAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
30 10 0.15
31 21 0.31
32 1 0.01
33 2 0.03
35 2 0.03
36 2 0.03
38 2 0.03
39 2 0.03
40 25 0.37
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (31 bp):
TTACCTATGTCTTTTGAGACATATGGATAGT
Found at i:2176184 original size:40 final size:40
Alignment explanation
Indices: 2176129--2176208 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
2176119 GAGGGTTACC
2176129 TATGTCTTTTGAGACATATGGATAGTTTACCTATGTCCTT
1 TATGTCTTTTGAGACATATGGATAGTTTACCTATGTCCTT
2176169 TATGTCTTTTGAGACATATGGATAGTTTACCTATGTCCTT
1 TATGTCTTTTGAGACATATGGATAGTTTACCTATGTCCTT
2176209 CGGGACATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (40 bp):
TATGTCTTTTGAGACATATGGATAGTTTACCTATGTCCTT
Found at i:2176247 original size:30 final size:31
Alignment explanation
Indices: 2176182--2176251 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
2176172 GTCTTTTGAG
* * * *
2176182 ACATATGGATAGTTTACCTATGTCCTTCGGG
1 ACATATGGACAGTTTACCTATGTCCTCCAGA
*
2176213 ACATATGGACAG-TTACCTATGTTCTCCAGA
1 ACATATGGACAGTTTACCTATGTCCTCCAGA
2176243 ACATATGGA
1 ACATATGGA
2176252 TAGGTCCTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 23 0.68
31 11 0.32
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (31 bp):
ACATATGGACAGTTTACCTATGTCCTCCAGA
Found at i:2176310 original size:24 final size:24
Alignment explanation
Indices: 2176283--2176330 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2176273 TTCATATGCC
2176283 ACTTAGTGGATTTTATACGAGCTG
1 ACTTAGTGGATTTTATACGAGCTG
2176307 ACTTAGTGGATTTTATACGAGCTG
1 ACTTAGTGGATTTTATACGAGCTG
2176331 TGGTGATAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (24 bp):
ACTTAGTGGATTTTATACGAGCTG
Found at i:2180111 original size:19 final size:19
Alignment explanation
Indices: 2180087--2180129 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
2180077 AAGAAATGTT
*
2180087 TATACGATGAACATATATA
1 TATACGATAAACATATATA
2180106 TATACGATAAACATATATA
1 TATACGATAAACATATATA
2180125 TATAC
1 TATAC
2180130 ATACATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.33
Consensus pattern (19 bp):
TATACGATAAACATATATA
Found at i:2185507 original size:209 final size:208
Alignment explanation
Indices: 2185146--2185560 Score: 539
Period size: 209 Copynumber: 2.0 Consensus size: 208
2185136 CCAAACAATA
* * *
2185146 TGATGTTTTCAAATGAATTTTGAAAGCAATTAAGCCTAATTTTTAGGCATTTCTTGATGTTTTCA
1 TGATGTTTTCAAATGAATTTTGAAAGAAAATAAGCCTAATTTTCAGGCATTTCTTGATGTTTTCA
* ** * *
2185211 AATGAATATTTAAAGGAGCTAAGCCTGGTTTTCATGGGTTTCTTGATGTCTTTAAATGAATTTTG
66 AATGAATATTTAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTTAAATAAATTTTG
* * * *
2185276 AAAGAATCTAAGCCTAATTTTTAGGGGATTCTTGATGATAACTGTAAATGATTTTTTTAAGAAAC
131 AAAGAAGCTAAGCCTAATTTTTA-GGGATTCTTGATGATAACTATAAATGAATTTTTAAAGAAAC
2185341 TAAGCCTAATTTCT
195 TAAGCCTAATTTCT
** ** *
2185355 TGATGTTTTCAAATGAATTTTGAAAGAAAATAAGCCTTGTTTTCAGGGGTTTCTTGATGTTTTTA
1 TGATGTTTTCAAATGAATTTTGAAAGAAAATAAGCCTAATTTTCAGGCATTTCTTGATGTTTTCA
* * *
2185420 AATGACT-TTTAAAAGAAGTTAAGCCTAATTTTTAGGGGTTTCTTGATGT-TTTCAAATAAATGT
66 AATGAATATTT-AAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTT-AAATAAAT-T
* * * *
2185483 TT-AAAGGAGCTAAGCCTGATTTTTAGGGTTTCTTGATGATTACTATAAATGAATTTTTAAAGAA
128 TTGAAAGAAGCTAAGCCTAATTTTTAGGGATTCTTGATGATAACTATAAATGAATTTTTAAAGAA
* *
2185547 GCTAAGCCTGATTT
193 ACTAAGCCTAATTT
2185561 TTAGGGGTTT
Statistics
Matches: 177, Mismatches: 26, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
208 52 0.29
209 122 0.69
210 3 0.02
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (208 bp):
TGATGTTTTCAAATGAATTTTGAAAGAAAATAAGCCTAATTTTCAGGCATTTCTTGATGTTTTCA
AATGAATATTTAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTTAAATAAATTTTG
AAAGAAGCTAAGCCTAATTTTTAGGGATTCTTGATGATAACTATAAATGAATTTTTAAAGAAACT
AAGCCTAATTTCT
Found at i:2185553 original size:56 final size:53
Alignment explanation
Indices: 2185146--2185577 Score: 359
Period size: 54 Copynumber: 8.1 Consensus size: 53
2185136 CCAAACAATA
* * * **
2185146 TGATGTTTTCAAATGAATTTTGAAAGCAA-TTAAGCCTAATTTTTAGGCATTTCT
1 TGATGTTTT-AAATGAATTTTTAAAG-AAGCTAAGCCTGATTTTTAGGGGTTTCT
* * * * *
2185200 TGATGTTTTCAAATGAATATTTAAAGGAGCTAAGCCTGGTTTTCATGGGTTTCT
1 TGATGTTTT-AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCT
* * * *
2185254 TGATGTCTTTAAATGAATTTTGAAAGAATCTAAGCCTAATTTTTAGGGGATTCT
1 TGATGT-TTTAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCT
* * * *
2185308 TGATGATAACTGTAAATGATTTTTTTAAGAAACTAAGCCT-A-----A----TTTCT
1 TGATG-T---TTTAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCT
* ** *
2185355 TGATGTTTTCAAATGAATTTTGAAAGAAAATAAGCCTTG-TTTTCAGGGGTTTCT
1 TGATGTTTT-AAATGAATTTTTAAAGAAGCTAAGCC-TGATTTTTAGGGGTTTCT
* * * *
2185409 TGATGTTTTTAAATGACTTTTAAAAGAAGTTAAGCCTAATTTTTAGGGGTTTCT
1 TGATG-TTTTAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCT
* * *
2185463 TGATGTTTTCAAATAAATGTTTAAAGGAGCTAAGCCTGATTTTTA-GGGTTTCT
1 TGATGTTTT-AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCT
*
2185516 TGATGATTACTATAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCA
1 TGATG-TT--T-TAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCT
2185573 TGATG
1 TGATG
2185578 ATAACTGTAA
Statistics
Matches: 306, Mismatches: 47, Indels: 47
0.76 0.12 0.12
Matches are distributed among these distances:
43 2 0.01
44 22 0.07
45 1 0.00
46 1 0.00
47 9 0.03
50 1 0.00
51 1 0.00
53 19 0.06
54 169 0.55
55 8 0.03
56 34 0.11
57 39 0.13
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (53 bp):
TGATGTTTTAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCT
Found at i:2185561 original size:110 final size:108
Alignment explanation
Indices: 2185350--2185577 Score: 291
Period size: 110 Copynumber: 2.1 Consensus size: 108
2185340 CTAAGCCTAA
*
2185350 TTTCTTGATGTTTTCAAATGAATTTTGAAAGAAAATAAGCCTTGTTTTCAGGGGTTTCTTGATGT
1 TTTCTTGATGTTTTCAAATAAATTTTGAAAGAAAATAAGCCTTGTTTTCAGGGGTTTCTTGATGT
* * *
2185415 TTTTAAATGACTTTTAAAAGAAGTTAAGCCTAATTTTTAGGGG
66 TTATAAATGAATTTTAAAAGAAGCTAAGCCTAATTTTTAGGGG
* ** *
2185458 TTTCTTGATGTTTTCAAATAAATGTTT-AAAGGAGCTAAGCC-TGATTTTTA-GGGTTTCTTGAT
1 TTTCTTGATGTTTTCAAATAAAT-TTTGAAAGAAAATAAGCCTTG-TTTTCAGGGGTTTCTTGAT
* *
2185520 GATTACTATAAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGG
64 G-TT--TATAAATGAATTTTAAAAGAAGCTAAGCCTAATTTTTAGGGG
*
2185568 TTTCATGATG
1 TTTCTTGATG
2185578 ATAACTGTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
107 15 0.14
108 40 0.38
109 3 0.03
110 46 0.44
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (108 bp):
TTTCTTGATGTTTTCAAATAAATTTTGAAAGAAAATAAGCCTTGTTTTCAGGGGTTTCTTGATGT
TTATAAATGAATTTTAAAAGAAGCTAAGCCTAATTTTTAGGGG
Found at i:2185635 original size:58 final size:57
Alignment explanation
Indices: 2185473--2185639 Score: 147
Period size: 58 Copynumber: 2.9 Consensus size: 57
2185463 TGATGTTTTC
* * * * * ** *
2185473 AAATAAATGTTTAAAGGAGCTAAGCCTGATTTT-TAGGGTTTCTTGATGATTACTAT
1 AAATGAATTTTTAAAGAAGCCAAGCCTGATTTTCAAAAGTTTCTTGATGATAACTAT
* * *** * *
2185529 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCATGATGATAACTGT
1 AAATGAATTTTTAAAGAAGCCAAGCCTGATTTTCAAAAGTTTCTTGATGATAACTAT
* * **
2185586 AAATGAATTTTTTGAATAAGCCAAGTTTGATTTTCAAAAGTTTCTTGATGATAA
1 AAATGAA-TTTTTAAAGAAGCCAAGCCTGATTTTCAAAAGTTTCTTGATGATAA
2185640 GTCATTCAAG
Statistics
Matches: 91, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
56 30 0.33
57 25 0.27
58 36 0.40
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (57 bp):
AAATGAATTTTTAAAGAAGCCAAGCCTGATTTTCAAAAGTTTCTTGATGATAACTAT
Found at i:2187382 original size:20 final size:17
Alignment explanation
Indices: 2187342--2187374 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2187332 AATGGAAGGA
2187342 TTCATAATAAGAAGAAG
1 TTCATAATAAGAAGAAG
*
2187359 TTCATAATGAGAAGAA
1 TTCATAATAAGAAGAA
2187375 CTTGTTCAAC
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:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
TTCATAATAAGAAGAAG
Found at i:2190601 original size:28 final size:28
Alignment explanation
Indices: 2190584--2190651 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
2190574 GTCATAGAGT
*
2190584 CAGTGCTTGAAATATTATACCATCCAGC
1 CAGTGCTTGAAATATTATACCATACAGC
*
2190612 CAGTGCTTGAAATATTATACCATCCAGC
1 CAGTGCTTGAAATATTATACCATACAGC
2190640 CAGTGCTTGAAA
1 CAGTGCTTGAAA
2190652 GCAATGATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (28 bp):
CAGTGCTTGAAATATTATACCATACAGC
Found at i:2193652 original size:52 final size:52
Alignment explanation
Indices: 2193582--2193688 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 52
2193572 CTATAATTAG
*
2193582 GTGAACATTGGTTATTTGCTTCAAT-TCTTGGAATAATACTACAAATAATGAT
1 GTGAACATTGGTTATTTGCTTCAATGT-TCGGAATAATACTACAAATAATGAT
** * *
2193634 GTGAACATTGGTTATTTGCTTTGATGTTCGGAATAGTACTACAAATAATTAT
1 GTGAACATTGGTTATTTGCTTCAATGTTCGGAATAATACTACAAATAATGAT
2193686 GTG
1 GTG
2193689 TTCCATTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
52 48 0.98
53 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (52 bp):
GTGAACATTGGTTATTTGCTTCAATGTTCGGAATAATACTACAAATAATGAT
Found at i:2198551 original size:53 final size:53
Alignment explanation
Indices: 2198443--2198551 Score: 137
Period size: 53 Copynumber: 2.1 Consensus size: 53
2198433 CTAGTTTCTT
* * * * * * *
2198443 GTTTTCACTGGAAAATATGAACGTTCTAGATTTATGAATCATGAGATCGACTG
1 GTTTTCACTAGAAAATATAAACATTCCACATTTATGAATCATGAAATCAACTG
* *
2198496 GTTTTCACTAGAAAATATAAACATTCCACATTTATGGATCATGAAATCAATTG
1 GTTTTCACTAGAAAATATAAACATTCCACATTTATGAATCATGAAATCAACTG
2198549 GTT
1 GTT
2198552 ACTACTTGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (53 bp):
GTTTTCACTAGAAAATATAAACATTCCACATTTATGAATCATGAAATCAACTG
Found at i:2198719 original size:32 final size:32
Alignment explanation
Indices: 2198652--2198719 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
2198642 AAGGTGACCA
* **
2198652 TTGGGTAGGCTTTGAGGCCCCAAGAAACTTTC
1 TTGGGTAAGCTTTGAGGCCCCAAGAAACTCCC
**
2198684 TTGGGTAAGCTCTT-AGGCCCCAAGGCACTCCC
1 TTGGGTAAGCT-TTGAGGCCCCAAGAAACTCCC
2198716 TTGG
1 TTGG
2198720 ATTAATCATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (32 bp):
TTGGGTAAGCTTTGAGGCCCCAAGAAACTCCC
Found at i:2215442 original size:21 final size:21
Alignment explanation
Indices: 2215400--2215442 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2215390 TTTATGGGCT
*
2215400 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
2215421 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
2215442 A
1 A
2215443 ACGGATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2216161 original size:103 final size:103
Alignment explanation
Indices: 2215977--2216398 Score: 751
Period size: 103 Copynumber: 4.1 Consensus size: 103
2215967 GTAGAGGGTC
*
2215977 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
2216042 TTGATCCTT-GTCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGT-ATATGTATATGATTCTTAAGGAATGA
*
2216080 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
2216145 TTGATCCTTGGTATATGTATATGATTCTTAAGGAAT-A
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
* *
2216182 -ATATGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
2216246 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
* *
2216284 TATGTGGTCCTTCGGGGCATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2216349 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
2216387 TATGTGGTCCTT
1 TATGTGGTCCTT
2216399 ATGGACATTA
Statistics
Matches: 306, Mismatches: 10, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
101 97 0.32
102 2 0.01
103 205 0.67
104 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:2216331 original size:204 final size:204
Alignment explanation
Indices: 2215981--2216390 Score: 741
Period size: 204 Copynumber: 2.0 Consensus size: 204
2215971 AGGGTCTATG
2215981 TGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
*
2216046 TCCTTGTCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGATATATATGTATTCT
66 TCCTTGTCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATATATGTATTCT
*
2216111 TTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGTATATGTATATGATTCTTAA
131 TTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTATATGATTCTTAA
2216176 GGAATAATA
196 GGAATAATA
* *
2216185 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
*
2216250 TCCTTGGT-ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGGCATATATGTATTC
66 TCCTT-GTCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATATATGTATTC
*
2216314 TTTGGAATATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTATATGATTCTTA
130 TTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTATATGATTCTTA
*
2216379 AGGAATGATA
195 AGGAATAATA
2216389 TG
1 TG
2216391 TGGTCCTTAT
Statistics
Matches: 198, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
204 196 0.99
205 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (204 bp):
TGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
TCCTTGTCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATATATGTATTCT
TTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTATATGATTCTTAA
GGAATAATA
Found at i:2216448 original size:23 final size:23
Alignment explanation
Indices: 2216415--2216477 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
2216405 ATTATTATAT
*
2216415 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2216438 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
2216461 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
2216478 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2216715 original size:14 final size:15
Alignment explanation
Indices: 2216690--2216718 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2216680 TACTTTATGT
2216690 TTATTGATATTATTA
1 TTATTGATATTATTA
2216705 TTATT-ATATTATTA
1 TTATTGATATTATTA
2216719 CCTCACTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTATTGATATTATTA
Found at i:2222562 original size:21 final size:21
Alignment explanation
Indices: 2222520--2222562 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2222510 TTTCTGGGCT
*
2222520 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
2222541 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
2222562 A
1 A
2222563 ACGGATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2223530 original size:103 final size:103
Alignment explanation
Indices: 2223099--2223522 Score: 785
Period size: 103 Copynumber: 4.1 Consensus size: 103
2223089 GTAGAGGGTT
2223099 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
2223164 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
2223202 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2223267 TTGATCCTTGGCATATGTTTATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
** *
2223305 TATGTGGTCCTTCAAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2223370 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
2223408 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2223473 TTGATCCTTGGCATATGTATATAATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
2223511 TATGTGGTCCTT
1 TATGTGGTCCTT
2223523 ATGGACATTA
Statistics
Matches: 309, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 309 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:2223598 original size:23 final size:23
Alignment explanation
Indices: 2223538--2223601 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
2223528 CATTATTATA
*
2223538 TGGCAC-TACGGTGTAATTCTACG
1 TGGCACTTA-GGTGCAATTCTACG
* ** *
2223561 CGGCACTCCGATGCAATTCTACG
1 TGGCACTTAGGTGCAATTCTACG
2223584 TGGCACTTAGGTGCAATT
1 TGGCACTTAGGTGCAATT
2223602 ATATGAGCTG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:2231571 original size:22 final size:22
Alignment explanation
Indices: 2231546--2231587 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2231536 ACATCATATC
2231546 AACATTATCACATGGCATTTGG
1 AACATTATCACATGGCATTTGG
2231568 AACATTATCACATGGCATTT
1 AACATTATCACATGGCATTT
2231588 TCCAAATGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (22 bp):
AACATTATCACATGGCATTTGG
Found at i:2238148 original size:65 final size:64
Alignment explanation
Indices: 2238079--2238202 Score: 151
Period size: 65 Copynumber: 1.9 Consensus size: 64
2238069 TACATTGAGG
* * * * * *
2238079 GTGCATCGATGCATAAAATCAATTCGATGTTTTAA-TAATACATGGAGTGCATCGATGCATAGTA
1 GTGCATCGATACACAAAAGCAATTCGATG-TTCAATTAAAACAAGG-GTGCATCGATGCATAGTA
2238143 T
64 T
* *
2238144 GTGCATCGGTACACAAAAGCCATTCGATGTTCAATTAAAACAAGGGTGCATCGATGCAT
1 GTGCATCGATACACAAAAGCAATTCGATGTTCAATTAAAACAAGGGTGCATCGATGCAT
2238203 TGATTCATGC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
64 18 0.36
65 32 0.64
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (64 bp):
GTGCATCGATACACAAAAGCAATTCGATGTTCAATTAAAACAAGGGTGCATCGATGCATAGTAT
Found at i:2240894 original size:10 final size:10
Alignment explanation
Indices: 2240879--2240912 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2240869 GTTTGATGCT
2240879 TTCTCTTTGA
1 TTCTCTTTGA
2240889 TTCTCTTTGA
1 TTCTCTTTGA
2240899 TTCT-TGTTGA
1 TTCTCT-TTGA
2240909 TTCT
1 TTCT
2240913 TGTTTCTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 1 0.04
10 22 0.96
ACGTcount: A:0.09, C:0.18, G:0.12, T:0.62
Consensus pattern (10 bp):
TTCTCTTTGA
Found at i:2241211 original size:65 final size:64
Alignment explanation
Indices: 2241142--2241265 Score: 151
Period size: 65 Copynumber: 1.9 Consensus size: 64
2241132 TACATTGAGG
* * * * * *
2241142 GTGCATCGATGCATAAAATCAATTCGATGTTTTAA-TAATACATGGAGTGCATCGATGCATAGTA
1 GTGCATCGATACACAAAAGCAATTCGATG-TTCAATTAAAACAAGG-GTGCATCGATGCATAGTA
2241206 T
64 T
* *
2241207 GTGCATCGGTACACAAAAGCCATTCGATGTTCAATTAAAACAAGGGTGCATCGATGCAT
1 GTGCATCGATACACAAAAGCAATTCGATGTTCAATTAAAACAAGGGTGCATCGATGCAT
2241266 TGATTCATGC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
64 18 0.36
65 32 0.64
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (64 bp):
GTGCATCGATACACAAAAGCAATTCGATGTTCAATTAAAACAAGGGTGCATCGATGCATAGTAT
Found at i:2244253 original size:65 final size:64
Alignment explanation
Indices: 2244184--2244306 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 64
2244174 ACATTGAGGG
* * * * * *
2244184 TGCATCGATGCATAAAATCAATTCGATGTTTTAA-TAATACATGGAGTGCATCGATGCATATTAT
1 TGCATCGATACACAAAAGCAATTCGATG-TTCAATTAAAACAAGG-GTGCATCGATGCATATTAT
2244248 A
64 A
* *
2244249 TGCATCGGTACACAAAAGCCATTCGATGTTCAATTAAAACAAGGGTGCATCGATGCAT
1 TGCATCGATACACAAAAGCAATTCGATGTTCAATTAAAACAAGGGTGCATCGATGCAT
2244307 TGATTCATGC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
64 18 0.37
65 31 0.63
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (64 bp):
TGCATCGATACACAAAAGCAATTCGATGTTCAATTAAAACAAGGGTGCATCGATGCATATTATA
Found at i:2244675 original size:16 final size:15
Alignment explanation
Indices: 2244643--2244672 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2244633 CCCCCTTACT
2244643 TTAACACGTCTCCCC
1 TTAACACGTCTCCCC
*
2244658 TTAACACTTCTCCCC
1 TTAACACGTCTCCCC
2244673 CTTTTTGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.47, G:0.03, T:0.30
Consensus pattern (15 bp):
TTAACACGTCTCCCC
Found at i:2246939 original size:23 final size:22
Alignment explanation
Indices: 2246909--2246990 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 22
2246899 GCATGGCAGT
2246909 GTGCATCGATGCACATTCAAGTA
1 GTGCATCGATGCACATTCAAG-A
* *
2246932 GTGCATCGGTGCATC-TTCATGA
1 GTGCATCGATGCA-CATTCAAGA
* *
2246954 -TGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGA
2246976 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
2246991 TATTTAGTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 3 0.06
23 17 0.36
24 13 0.28
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGA
Found at i:2251216 original size:124 final size:124
Alignment explanation
Indices: 2251060--2251305 Score: 381
Period size: 124 Copynumber: 2.0 Consensus size: 124
2251050 TGTGGAAAAA
* *
2251060 CATTCAAGATTCCCTGTAACACCAAAACAAAGATGAATGGTAA-TACATGATAATGGATCAAGAA
1 CATTCAAGATTCCCTATAACACCAAAACAAAGATGAATAGTAACT-CATGATAATGGATCAAGAA
** *
2251124 ATACAAGTTTAAA-ATTATTGTTCCTACAAGCCATGATGAAA-CAAATAGTAAAAGTTGTAG
65 ATACAAG-CAAAACACTATTGTTCCTACAAGCCATGAT-AAAGCAAATAGTAAAAGTTGTAG
2251184 CATTCAAGATTCCCTATAACACCAAAACAAAGATGAATAGTAACTCATGATAATGGATCAAGAAA
1 CATTCAAGATTCCCTATAACACCAAAACAAAGATGAATAGTAACTCATGATAATGGATCAAGAAA
* *
2251249 TGCAAGCAAAACACTATTGTTGCTACAAGCCATGATAAAGCAAATAGTAAAAGTTGT
66 TACAAGCAAAACACTATTGTTCCTACAAGCCATGATAAAGCAAATAGTAAAAGTTGT
2251306 TCTCATTACA
Statistics
Matches: 112, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
123 6 0.05
124 105 0.94
125 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (124 bp):
CATTCAAGATTCCCTATAACACCAAAACAAAGATGAATAGTAACTCATGATAATGGATCAAGAAA
TACAAGCAAAACACTATTGTTCCTACAAGCCATGATAAAGCAAATAGTAAAAGTTGTAG
Found at i:2256937 original size:23 final size:23
Alignment explanation
Indices: 2256882--2256947 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 23
2256872 TGAACAAAGG
* *
2256882 GTTTT-TTCGTTCATTTACGTTC
1 GTTTTATTTGTTCATTTATGTTC
* *
2256904 G-ATTATATGTTCATTTATGTTC
1 GTTTTATTTGTTCATTTATGTTC
* *
2256926 GTTTTATTTGTTTAATTATGTT
1 GTTTTATTTGTTCATTTATGTT
2256948 TGTTCATTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
21 2 0.06
22 16 0.47
23 16 0.47
ACGTcount: A:0.17, C:0.09, G:0.14, T:0.61
Consensus pattern (23 bp):
GTTTTATTTGTTCATTTATGTTC
Found at i:2257378 original size:16 final size:16
Alignment explanation
Indices: 2257353--2257384 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2257343 AAAAAAAAAA
2257353 TTATTCGTTTATGTTC
1 TTATTCGTTTATGTTC
*
2257369 TTATTTGTTTATGTTC
1 TTATTCGTTTATGTTC
2257385 ATACATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.66
Consensus pattern (16 bp):
TTATTCGTTTATGTTC
Found at i:2259244 original size:20 final size:20
Alignment explanation
Indices: 2259206--2259245 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2259196 TTTTTTAGAT
*
2259206 TACAAGAAAAATAATAAAAA
1 TACAAGAAAAATAAAAAAAA
*
2259226 TACAAG-AAAAGAAAAAAAA
1 TACAAGAAAAATAAAAAAAA
2259245 T
1 T
2259246 CAAATTAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (20 bp):
TACAAGAAAAATAAAAAAAA
Found at i:2259727 original size:24 final size:25
Alignment explanation
Indices: 2259700--2259762 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
2259690 GGTTTATTTG
*
2259700 ATTTTTTAAATA-AAAATGTTTAAA
1 ATTTTTAAAATATAAAATGTTTAAA
2259724 A--TTTAAAATATTAAAATGTTTAAA
1 ATTTTTAAAATA-TAAAATGTTTAAA
2259748 A--TTTAAAATATAAAA
1 ATTTTTAAAATATAAAA
2259763 ATATAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 8 0.22
23 5 0.14
24 23 0.64
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTTTTAAAATATAAAATGTTTAAA
Found at i:2259730 original size:7 final size:7
Alignment explanation
Indices: 2259718--2259762 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
2259708 AATAAAAATG
2259718 TTTAAAA
1 TTTAAAA
2259725 TTTAAAA
1 TTTAAAA
2259732 TATTAAAA
1 T-TTAAAA
2259740 TGTTTAAAA
1 --TTTAAAA
2259749 TTTAAAA
1 TTTAAAA
*
2259756 TATAAAA
1 TTTAAAA
2259763 ATATAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 21 0.62
8 6 0.18
9 6 0.18
10 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (7 bp):
TTTAAAA
Found at i:2259739 original size:8 final size:8
Alignment explanation
Indices: 2259719--2259775 Score: 64
Period size: 8 Copynumber: 7.2 Consensus size: 8
2259709 ATAAAAATGT
2259719 TTAAAAT-
1 TTAAAATA
2259726 TTAAAATA
1 TTAAAATA
*
2259734 TTAAAATGT
1 TTAAAAT-A
2259743 TTAAAAT-
1 TTAAAATA
2259750 TTAAAATA
1 TTAAAATA
*
2259758 TAAAAATA
1 TTAAAATA
*
2259766 TAAAAATA
1 TTAAAATA
2259774 TT
1 TT
2259776 TTAAAAATAC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
7 14 0.32
8 23 0.52
9 7 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
TTAAAATA
Found at i:2259755 original size:16 final size:17
Alignment explanation
Indices: 2259725--2259756 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2259715 ATGTTTAAAA
2259725 TTTAAAATATTAAAATG
1 TTTAAAATATTAAAATG
2259742 TTTAAAAT-TTAAAAT
1 TTTAAAATATTAAAAT
2259757 ATAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTAAAATATTAAAATG
Found at i:2259763 original size:24 final size:24
Alignment explanation
Indices: 2259709--2259764 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
2259699 GATTTTTTAA
2259709 ATAAAAATGTTTAAAATTTAAAAT
1 ATAAAAATGTTTAAAATTTAAAAT
*
2259733 ATTAAAATGTTTAAAATTTAAAAT
1 ATAAAAATGTTTAAAATTTAAAAT
2259757 ATAAAAAT
1 ATAAAAAT
2259765 ATAAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
ATAAAAATGTTTAAAATTTAAAAT
Found at i:2260428 original size:15 final size:13
Alignment explanation
Indices: 2260367--2260429 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
2260357 ATTTTTTAAA
2260367 ATATTTAATTTTT
1 ATATTTAATTTTT
*
2260380 AT-TTTTATTTTT
1 ATATTTAATTTTT
*
2260392 -T-TGT-ATTTTT
1 ATATTTAATTTTT
2260402 ATATTTAATTTTT
1 ATATTTAATTTTT
*
2260415 ATATTGTAAATTTT
1 ATATT-TAATTTTT
2260429 A
1 A
2260430 AATATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 6 0.14
11 4 0.10
12 11 0.26
13 13 0.31
14 8 0.19
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
ATATTTAATTTTT
Found at i:2263927 original size:3 final size:3
Alignment explanation
Indices: 2263919--2263943 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2263909 ATGGAAATAC
2263919 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2263944 TGTAACACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2265091 original size:60 final size:58
Alignment explanation
Indices: 2265018--2265152 Score: 132
Period size: 59 Copynumber: 2.3 Consensus size: 58
2265008 TTTATAGGGT
* * * *
2265018 AAAG-TACACAAATGGTCCCCTGACTATATGATA-TTGCTTTGTTGAGT-TTCTCGACTATTA
1 AAAGTTACA-AAATGATCCCC-GACTATAGGA-AGCTGCTTTATTGAGTATT-T-GACTATTA
* * *
2265078 AAAGTTACAAAATGATTCTCGATTATAGGAAGCTGCTTTATTGAGTCATTTGACTATTA
1 AAAGTTACAAAATGATCCCCGACTATAGGAAGCTGCTTTATTGAGT-ATTTGACTATTA
2265137 AAAGTTACAAAATGAT
1 AAAGTTACAAAATGAT
2265153 TACCTGACTA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
58 1 0.02
59 44 0.69
60 13 0.20
61 6 0.09
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (58 bp):
AAAGTTACAAAATGATCCCCGACTATAGGAAGCTGCTTTATTGAGTATTTGACTATTA
Found at i:2265495 original size:25 final size:24
Alignment explanation
Indices: 2265448--2265507 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 24
2265438 AGTTTAAACA
2265448 TTTTGAAAACTATATAATATATAG
1 TTTTGAAAACTATATAATATATAG
*
2265472 TTTTGAAAACATTTATATATTATATAG
1 TTTTGAAAAC---TATATAATATATAG
*
2265499 TTTTTAAAA
1 TTTTGAAAA
2265508 AACGTTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 10 0.32
27 21 0.68
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (24 bp):
TTTTGAAAACTATATAATATATAG
Found at i:2265538 original size:37 final size:35
Alignment explanation
Indices: 2265492--2265615 Score: 137
Period size: 36 Copynumber: 3.5 Consensus size: 35
2265482 ATTTATATAT
2265492 TATATAGTTTTTAAAAAACGTTTTGAAATATATGTAA
1 TATATAGTTTTT-AAAAACGTTTTGAAA-ATATGTAA
* * * *
2265529 TATATAG-TTTTAAAGACATTTTTGAAAATATATATT
1 TATATAGTTTTTAAAAAC-GTTTTGAAAATATGTA-A
*
2265565 TATATAGTTTTT-AAAACGTTTTTGAAAATACGTAA
1 TATATAGTTTTTAAAAACG-TTTTGAAAATATGTAA
2265600 -ATATAGTTTTTAAAAA
1 TATATAGTTTTTAAAAA
2265616 AACATTTCGG
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
34 11 0.15
35 15 0.21
36 36 0.49
37 11 0.15
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (35 bp):
TATATAGTTTTTAAAAACGTTTTGAAAATATGTAA
Found at i:2265635 original size:72 final size:73
Alignment explanation
Indices: 2265482--2265653 Score: 203
Period size: 73 Copynumber: 2.4 Consensus size: 73
2265472 TTTTGAAAAC
* *
2265482 ATTTATATATTATATAGTTTTTAAAAAACGTTTTGAAATATATGTAATATATAGTTTTAAAGACA
1 ATTTATATATTATATAGTTTTT-AAAAACGTTTTGAAATATACGTAATATATAGTTTTAAAAACA
*
2265547 TTTTTGAAA
65 TTTTCGAAA
*
2265556 ATATATAT-TTATATAGTTTTT-AAAACGTTTTTGAAA-ATACGTAA-ATATAGTTTTTAAAAAA
1 ATTTATATATTATATAGTTTTTAAAAACG-TTTTGAAATATACGTAATATATAG-TTTT--AAAA
*
2265617 ACA-TTTCGGAA
62 ACATTTTCGAAA
*
2265628 ATTTATATATTATAT-GTTTTTGAAAA
1 ATTTATATATTATATAGTTTTTAAAAA
2265654 TATTTATATA
Statistics
Matches: 86, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
70 6 0.07
71 17 0.20
72 27 0.31
73 29 0.34
74 7 0.08
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (73 bp):
ATTTATATATTATATAGTTTTTAAAAACGTTTTGAAATATACGTAATATATAGTTTTAAAAACAT
TTTCGAAA
Found at i:2267066 original size:12 final size:13
Alignment explanation
Indices: 2267040--2267072 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
2267030 TGTTCCGTTT
2267040 TTATTTTTTCTTA
1 TTATTTTTTCTTA
2267053 TTATTTTTTC-TA
1 TTATTTTTTCTTA
2267065 TTATTTTT
1 TTATTTTT
2267073 CTGTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTTTCTTA
Found at i:2267548 original size:6 final size:6
Alignment explanation
Indices: 2267537--2267562 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2267527 GCGAAAGTTA
2267537 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
2267563 TTTATTCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:2272393 original size:84 final size:84
Alignment explanation
Indices: 2272252--2272836 Score: 680
Period size: 84 Copynumber: 7.0 Consensus size: 84
2272242 TTAAAAACAA
*
2272252 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
2272317 GCTCAGCTCCAAGGCATAT
66 GCTCAGCTCCAAGGCACAT
* * * * * *
2272336 CATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
2272401 GCTCAGCT-CAACGGTACAT
66 GCTCAGCTCCAA-GGCACAT
* * * ** *
2272420 CATTTGCAGCATAGCTTAAGTAGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * *
2272481 ACTCAGCTTCGAGGGCATAT
66 GCTCAGC-TCCAAGGCACAT
* * * * * * *
2272501 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
2272565 GCTCAGCT-CAACGCACAT
66 GCTCAGCTCCAAGGCACAT
* *
2272583 CATTTGCAGTATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
2272648 ACTCAGCTCTAAGGCATAT
66 GCTCAGCTCCAAGGCACAT
* * *
2272667 CATTTGCAGCATAACTTAACTCGAGAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
2272732 GCTCAGCTCCAAGGCACAT
66 GCTCAGCTCCAAGGCACAT
** * * * * * * *
2272751 CACCTGCAGCATAGCTTAAGTCGAGAAGAGCTATCTGCCAACCGAGGACCTTTGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
2272816 ACTCAGCTCAAAGGCAAAT
66 GCTCAGCTCCAAGGCACAT
2272835 CA
1 CA
2272837 AGTTCACAGC
Statistics
Matches: 414, Mismatches: 79, Indels: 16
0.81 0.16 0.03
Matches are distributed among these distances:
80 24 0.06
81 35 0.08
82 38 0.09
83 35 0.08
84 282 0.68
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACAT
Found at i:2273530 original size:38 final size:36
Alignment explanation
Indices: 2273483--2273728 Score: 192
Period size: 38 Copynumber: 6.8 Consensus size: 36
2273473 AAAAAACACA
2273483 TATATAATATATAGTTTTTAAAAAACATTTTGAAAACT
1 TATATAATATATAGTTTTT-AAAAACATTTTGAAAA-T
*
2273521 TATATAATATATAG-TTTTGAAAACA-TTT----A-
1 TATATAATATATAGTTTTTAAAAACATTTTGAAAAT
*
2273550 TATAT--TATATAGTTTTTAAAAAACGTTTTGAAAAT
1 TATATAATATATAGTTTTT-AAAAACATTTTGAAAAT
*
2273585 ATATATAATATATAGTTTTTAAAGACATTTTTGAAAAT
1 -TATATAATATATAGTTTTTAAAAACA-TTTTGAAAAT
* *
2273623 ATATATATTATATAGTTTTT-AAAACGTTTTTGAAAA-
1 -TATATAATATATAGTTTTTAAAAAC-ATTTTGAAAAT
* * *
2273659 TACGTATAATAAATAGTTTTTTAAAAAAACATTTCAGAAATT
1 TA--TATAATATATAG-TTTTT--AAAAACATTT-TGAAAAT
* * *
2273701 TATATATTATAT-GATTTTGAAAACATTT
1 TATATAATATATAGTTTTTAAAAACATTT
2273729 ATATATATAA
Statistics
Matches: 170, Mismatches: 17, Indels: 44
0.74 0.07 0.19
Matches are distributed among these distances:
27 7 0.04
28 4 0.02
29 10 0.06
30 3 0.02
31 1 0.01
34 1 0.01
35 5 0.03
36 20 0.12
37 32 0.19
38 64 0.38
39 1 0.01
40 11 0.06
41 9 0.05
42 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAAACATTTTGAAAAT
Found at i:2273544 original size:25 final size:26
Alignment explanation
Indices: 2273510--2273570 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
2273500 TTAAAAAACA
2273510 TTTTGAAAAC-TTATATAATATATAG
1 TTTTGAAAACATTATATAATATATAG
*
2273535 TTTTGAAAACATTTATATATTATATAG
1 TTTTGAAAACA-TTATATAATATATAG
*
2273562 TTTTTAAAA
1 TTTTGAAAA
2273571 AACGTTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 10 0.31
27 22 0.69
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (26 bp):
TTTTGAAAACATTATATAATATATAG
Found at i:2273579 original size:65 final size:66
Alignment explanation
Indices: 2273483--2273614 Score: 214
Period size: 65 Copynumber: 2.0 Consensus size: 66
2273473 AAAAAACACA
2273483 TATATAATATATAGTTTTTAAAAAACATTTTGAAAACT-TATATAATATATAGTTTTGAAA-ACA
1 TATATAATATATAGTTTTTAAAAAACATTTTGAAAA-TATATATAATATATAGTTTTGAAAGACA
2273546 TT
65 TT
* * *
2273548 TATATATTATATAGTTTTTAAAAAACGTTTTGAAAATATATATAATATATAGTTTTTAAAGACAT
1 TATATAATATATAGTTTTTAAAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAGACAT
2273613 T
66 T
2273614 T
1 T
2273615 TTGAAAATAT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
64 1 0.02
65 55 0.89
66 6 0.10
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (66 bp):
TATATAATATATAGTTTTTAAAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAGACAT
T
Found at i:2275034 original size:26 final size:25
Alignment explanation
Indices: 2275005--2275056 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
2274995 TTTTTATTCC
2275005 TTTACTATTTCTTTAAATTATCTTTT
1 TTTACTATTTCTTTAAATTAT-TTTT
* * * *
2275031 TTTATTCTTTTTTTAATTTATTTTT
1 TTTACTATTTCTTTAAATTATTTTT
2275056 T
1 T
2275057 ATTCAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTACTATTTCTTTAAATTATTTTT
Found at i:2276605 original size:2 final size:2
Alignment explanation
Indices: 2276594--2276622 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2276584 ATGTTCAAAC
2276594 AT AT -T 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
2276623 TACAAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2280509 original size:60 final size:62
Alignment explanation
Indices: 2280425--2280585 Score: 165
Period size: 60 Copynumber: 2.7 Consensus size: 62
2280415 TTTAAAATGA
* * *
2280425 TCCCTAAACTTTT-AAATATTTCAATTTCATCCCTAAACTATG-AC-TTCCATTCTAAATTAG
1 TCCCCAAACTTTTTGAACATTTCAATTTCATCCCTAAACTATGTACATT-CATTCTAAATTAG
* * * * *
2280485 TCCTCATAC-TTTTGTACATTTCAATTTCAT-CCTCAAAATA-GTACATTCATTCTAAATTGG
1 TCCCCAAACTTTTTGAACATTTCAATTTCATCCCT-AAACTATGTACATTCATTCTAAATTAG
* *
2280545 TCCCCAAACTTTTTGAACATTCCAATTTTATCCC-AAACTAT
1 TCCCCAAACTTTTTGAACATTTCAATTTCATCCCTAAACTAT
2280586 ACGTATGTAC
Statistics
Matches: 80, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
59 7 0.09
60 51 0.64
61 20 0.25
62 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (62 bp):
TCCCCAAACTTTTTGAACATTTCAATTTCATCCCTAAACTATGTACATTCATTCTAAATTAG
Found at i:2283401 original size:12 final size:12
Alignment explanation
Indices: 2283384--2283413 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2283374 TTCTTAATTC
2283384 TATTTATTTTTA
1 TATTTATTTTTA
*
2283396 TTTTTATTTTTA
1 TATTTATTTTTA
2283408 TATTTA
1 TATTTA
2283414 CATATTACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TATTTATTTTTA
Found at i:2285076 original size:19 final size:19
Alignment explanation
Indices: 2285052--2285091 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2285042 CATAACACTT
*
2285052 TTGTATCTAATAAGGTTTA
1 TTGTATCCAATAAGGTTTA
2285071 TTGTATCCAATAAGGTTTA
1 TTGTATCCAATAAGGTTTA
2285090 TT
1 TT
2285092 TATAATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (19 bp):
TTGTATCCAATAAGGTTTA
Found at i:2286271 original size:98 final size:95
Alignment explanation
Indices: 2286010--2286272 Score: 339
Period size: 95 Copynumber: 2.7 Consensus size: 95
2286000 AGATTATAAT
* * * * * *
2286010 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGCTTAAACACCCCAGCTTTA
1 ATTATA-ATATACAATAAAGATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
*
2286075 TGGATAAGATTTAGCTAGCTTGATAAAGGTG
65 TGGATAAGATTCAGCTAGCTTGATAAAGGTG
* * * *
2286106 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGTAATTTGTTAAACGCCCCGGCTTTAT
1 ATTATAATATACAATAAAGATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
*
2286171 GGATAATATTCAGCTAGCTTGATAAAGGTG
66 GGATAAGATTCAGCTAGCTTGATAAAGGTG
* * *
2286201 ATTATAATAT-CTATACAATGATATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCTCGGTT
1 ATTATAATATACAATA-AA-G--ATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCT
2286265 TTATGGAT
62 TTATGGAT
2286273 CTAGCTAGCC
Statistics
Matches: 148, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
94 4 0.03
95 93 0.63
96 7 0.05
98 44 0.30
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (95 bp):
ATTATAATATACAATAAAGATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
GGATAAGATTCAGCTAGCTTGATAAAGGTG
Found at i:2287939 original size:244 final size:238
Alignment explanation
Indices: 2287515--2287972 Score: 672
Period size: 244 Copynumber: 1.9 Consensus size: 238
2287505 CATCTACACA
*
2287515 AGATTGGATTTTAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAAGGGGC
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAAGGGGC
*
2287580 TTCCCAGTTTTATTCAAAGCCAATTTCAACTTCACGGCGAAAGATATTAGACTCGAAACAATACA
66 TTCCCAGTTTCATTCAAAGCCAATTTCAACTTCACGGCGAAAGATATTAGACTCGAAACAATACA
* * * *
2287645 AGCTTGGATTTTAACTTTACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGC
131 AGATTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAA--GGC
2287710 CATCCAC-GATTTCAACTTCACAGTAAAGGATATCATACCAACTCT
194 CATCCACAG-TTTCAACTTCACAGTAAAGGATATCATACCAACTCT
*
2287755 AGATTGGATTTCAACTTCACGATGAA-GATATCCAATTCAAAGCTCAACTTCACGGCGAA-GGGC
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAAGGGGC
* * * * **
2287818 TTCCCAGTTTCATTCAGAG-CAATTTCAACTTCACGGTGAAGGATATTGGACTCGAAGTAATATT
66 TTCCCAGTTTCATTCAAAGCCAATTTCAACTTCACGGCGAAAGATATTAGACTCGAAACAATA--
*
2287882 CATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACG
129 CA-----AGATTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACAACG
2287947 AAGGCCATCCACAGTTTCAACTTCAC
189 AAGGCCATCCACAGTTTCAACTTCAC
2287973 GACGAAGGAA
Statistics
Matches: 196, Mismatches: 14, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
237 38 0.19
238 21 0.11
239 35 0.18
240 24 0.12
242 22 0.11
243 1 0.01
244 55 0.28
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (238 bp):
AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAAGGGGC
TTCCCAGTTTCATTCAAAGCCAATTTCAACTTCACGGCGAAAGATATTAGACTCGAAACAATACA
AGATTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAAGGCCA
TCCACAGTTTCAACTTCACAGTAAAGGATATCATACCAACTCT
Found at i:2288054 original size:105 final size:107
Alignment explanation
Indices: 2287914--2288114 Score: 302
Period size: 107 Copynumber: 1.9 Consensus size: 107
2287904 TTCACGACGA
2287914 AGGATATCCAATTCAAGGCTCAACTTCACAACGAA-GGCCATCCACAGTTTCAACTTCACGACGA
1 AGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGCCATCCAC-GTTTCAACTTCACGACGA
2287978 A-GGAATC-TGCTCACCAACAACATTCATCTTTATATGGATTGG
65 AGGGAATCGTGC-CACCAACAACATTCATCTTTATATGGATTGG
* * *
2288020 AGGATAT-CAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCTACGTTTCAACTTCATGATGA
1 AGGATATCCAATTCAAGGCTCAACTTCACAACGAA-GGGCCATCCACGTTTCAACTTCACGACGA
**
2288084 AGGGAATCGTGCCACCAGTAACATTCATCTT
65 AGGGAATCGTGCCACCAACAACATTCATCTT
2288115 CAGATTGGAT
Statistics
Matches: 86, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
105 27 0.31
106 24 0.28
107 32 0.37
108 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (107 bp):
AGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGCCATCCACGTTTCAACTTCACGACGAA
GGGAATCGTGCCACCAACAACATTCATCTTTATATGGATTGG
Found at i:2288405 original size:82 final size:82
Alignment explanation
Indices: 2288266--2288538 Score: 359
Period size: 82 Copynumber: 3.3 Consensus size: 82
2288256 GATATCGTGT
* * *
2288266 TCATTTGCAACATAGCTCAAGGCAAGAAGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTAC
1 TCATTTGCAACATAACTCAAGGCAAAAAGGTTATATGCCAACAAAAGACCTTCGAGTTCGACTAC
*
2288331 GCTCAGCTCAAGGCATA
66 GCTCAGCTCAAGGCAAA
* * **
2288348 TTATTTGCAGCATAACTCAAGGCAAAAAGGTTATATGCCAACTGAAGACCTTCGAGTTCGACTAC
1 TCATTTGCAACATAACTCAAGGCAAAAAGGTTATATGCCAACAAAAGACCTTCGAGTTCGACTAC
*
2288413 GCTTAGCTCCAAGGCAAA
66 GCTCAGCT-CAAGGCAAA
* * * *
2288431 TCATTTGCAACATAACTCAATGCAGAAGGGTTATCA-GCCAACAAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAACATAACTCAAGGCAAAAAGGTTAT-ATGCCAACAAAAGACCTTCGAGTTCGACTA
* *
2288495 CACTCAGCTCAAGGCACA
65 CGCTCAGCTCAAGGCAAA
* * *
2288513 TCATTTGCAGCTTATCTCAAGGCAAA
1 TCATTTGCAACATAACTCAAGGCAAA
2288539 GGTTATCTTT
Statistics
Matches: 164, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
82 94 0.57
83 69 0.42
84 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (82 bp):
TCATTTGCAACATAACTCAAGGCAAAAAGGTTATATGCCAACAAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCAAGGCAAA
Found at i:2291527 original size:148 final size:144
Alignment explanation
Indices: 2291252--2291541 Score: 445
Period size: 148 Copynumber: 2.0 Consensus size: 144
2291242 TAGTGGTCGC
*
2291252 AAAATAAAATAAATCAAGATTTTATGTGAAAATTCTTTAAATAAAATTATGGGAAAAAGAGAAAA
1 AAAATAAAATAAATCAAGATTTTATGTGAAAATTCTTTAAATAAAATTATGGAAAAAAGAGAAAA
* * *
2291317 AAAATTCTTTAAAGTTAAAAAAGAAAAATATAAAAGAATTGCATCTTTACATAGACATGATGCTA
66 AAAATTCATTAAAGTTAAAAAAGAAAAATATAAAAGAATTGCAGCTTTACATAGACACGATGCTA
2291382 CGAATGGCGCAAGT
131 CGAATGGCGCAAGT
* ***
2291396 AAAATAAAATAAATATCAAGGTTTTATGTGAGAAATTCTTTTGGTAACAATTATGGAAAAAAGAG
1 AAAATAAAAT-AA-ATCAAGATTTTATGTGA-AAATTCTTTAAATAA-AATTATGGAAAAAAGAG
* *
2291461 AAAAAAAATTCATTAAAGTTAAAATAGAAAAATATAGAAGAATTGCAGCTTTACATAGACACGAT
62 AAAAAAAATTCATTAAAGTTAAAAAAGAAAAATATAAAAGAATTGCAGCTTTACATAGACACGAT
*
2291526 GCTATGAATGGCGCAA
127 GCTACGAATGGCGCAA
2291542 TTGCACACTA
Statistics
Matches: 131, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
144 10 0.08
145 2 0.02
146 16 0.12
147 12 0.09
148 91 0.69
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (144 bp):
AAAATAAAATAAATCAAGATTTTATGTGAAAATTCTTTAAATAAAATTATGGAAAAAAGAGAAAA
AAAATTCATTAAAGTTAAAAAAGAAAAATATAAAAGAATTGCAGCTTTACATAGACACGATGCTA
CGAATGGCGCAAGT
Found at i:2297478 original size:13 final size:13
Alignment explanation
Indices: 2297460--2297490 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2297450 ATAGTCAAGG
2297460 AACTCAACAAAAT
1 AACTCAACAAAAT
*
2297473 AACTCAACAAAGT
1 AACTCAACAAAAT
2297486 AACTC
1 AACTC
2297491 TCTATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.26, G:0.03, T:0.16
Consensus pattern (13 bp):
AACTCAACAAAAT
Found at i:2298533 original size:179 final size:183
Alignment explanation
Indices: 2298058--2298696 Score: 781
Period size: 182 Copynumber: 3.6 Consensus size: 183
2298048 GTCGATAAAA
*
2298058 ATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCA-GTTTCATTATG
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA-CATGTTTCATTATG
* * * * ** *
2298122 ATAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTATCGATTAGATT-ATAATTAGTATCGAC
65 ACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATTCCATTGA-AATAAGTATCGAC
* * * * **
2298186 ATTTTTAGAATTTAAAAGAGAAGCAGTAAT-AGTACCAATAAAGTGTCGATAC-AA
129 ACTTTTGGAATTTAAAAGAGAAGCAGTAATAACT-CCTATAAAGTGTCGATACTTT
* *
2298240 ATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCTGTTTCATTATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCATTATGA
* * * *
2298305 CAAAACCGGTAAATCGCTACTAGATATGTTGAATGTGTCGATACCATTGAAATAAGTATCGACAC
66 CAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATTCCATTGAAATAAGTATCGACAC
2298370 TTTTGGAATTTAAAAGAGAAGCAGTAATAACTCCTATAAAGTGTCGATACTTT
131 TTTTGGAATTTAAAAGAGAAGCAGTAATAACTCCTATAAAGTGTCGATACTTT
** * * *
2298423 ATAAAAATGTATCGATTTATAA-AA-ATAACAAGT-AAAA-ATGACAAAACATGTATAATTATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCATTATGA
** * *
2298484 CAAAATGGGTAAAGCGCTACTAGATATGTTGAAATTGTCGATTCCATTGAAATAAGTATCGACAC
66 CAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATTCCATTGAAATAAGTATCGACAC
* * * *
2298549 TTTTGGAATTTAAAAGAAAAGCAG---TAGCGCCTATAAAGTGTCGATGCTTT
131 TTTTGGAATTTAAAAGAGAAGCAGTAATAACTCCTATAAAGTGTCGATACTTT
* * * *
2298599 AT-AAAATGTATCTAT--AT-A-TA-ATAACTGGTAAAAATATGACAAAACAAGTTTCATTATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCATTATGA
* *
2298658 CAAAATCGGTAAAGCGCTACCGGATATGTTGAAAGTGTC
66 CAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTC
2298697 TATACTTTAA
Statistics
Matches: 404, Mismatches: 47, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
172 9 0.02
173 6 0.01
174 56 0.14
175 12 0.03
176 25 0.06
179 103 0.25
180 4 0.01
181 9 0.02
182 157 0.39
183 23 0.06
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (183 bp):
ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACATGTTTCATTATGA
CAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATTCCATTGAAATAAGTATCGACAC
TTTTGGAATTTAAAAGAGAAGCAGTAATAACTCCTATAAAGTGTCGATACTTT
Found at i:2300872 original size:15 final size:15
Alignment explanation
Indices: 2300852--2300882 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2300842 TGATAGTAGA
2300852 GGGATGACGATGAGG
1 GGGATGACGATGAGG
*
2300867 GGGATGACGGTGAGG
1 GGGATGACGATGAGG
2300882 G
1 G
2300883 AAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.58, T:0.13
Consensus pattern (15 bp):
GGGATGACGATGAGG
Found at i:2301130 original size:66 final size:65
Alignment explanation
Indices: 2301004--2301130 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 65
2300994 GGGAAGTGGA
** * *
2301004 TGGAAAAATAGATGGAGTGGTGAAGAAGTTGAGGTGTTGAGGGGTGAACTTAAGATGGTGATGGG
1 TGGAAAAATAGATGGAGTGGTGAAGAAGTTGAGGAATTGAGGAGTGAACTTAAGAGGGTGATGGG
* * * *
2301069 TGGAAAAATTGATGGAGTGGTGAAGGAAGTTGTGGAATTGAGGAGTGAACTTACGGGGGTGA
1 TGGAAAAATAGATGGAGTGGTGAA-GAAGTTGAGGAATTGAGGAGTGAACTTAAGAGGGTGA
2301131 AGGGGGTGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
65 23 0.43
66 30 0.57
ACGTcount: A:0.31, C:0.02, G:0.43, T:0.24
Consensus pattern (65 bp):
TGGAAAAATAGATGGAGTGGTGAAGAAGTTGAGGAATTGAGGAGTGAACTTAAGAGGGTGATGGG
Found at i:2301174 original size:14 final size:16
Alignment explanation
Indices: 2301155--2301187 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2301145 AAAAAGTTGG
2301155 ATGAAGGG-GAAA-AA
1 ATGAAGGGTGAAATAA
2301169 ATGAAGGGTGAAATAA
1 ATGAAGGGTGAAATAA
2301185 ATG
1 ATG
2301188 CGATGAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (16 bp):
ATGAAGGGTGAAATAA
Found at i:2302530 original size:20 final size:20
Alignment explanation
Indices: 2302492--2302532 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2302482 AGCAATAAAT
* * *
2302492 CATAAACCATAGCCTATAGC
1 CATAAACAATAGACAATAGC
2302512 CATAAACAATAGACAATAGC
1 CATAAACAATAGACAATAGC
2302532 C
1 C
2302533 CAATACAACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.27, G:0.10, T:0.17
Consensus pattern (20 bp):
CATAAACAATAGACAATAGC
Found at i:2306701 original size:123 final size:123
Alignment explanation
Indices: 2306477--2306722 Score: 384
Period size: 123 Copynumber: 2.0 Consensus size: 123
2306467 AGCATAACTG
* * * * * *
2306477 ACTTGACGTTGCACGTAGAGTAGTGAGCCTTTCCATTTGCATTACTTCTTGAGGCACATTCAAGT
1 ACTTGACGTTGCACGTAGAGCAGCGAACCTTGCCATTTGCATTACTTCTGGAGGCACATTCAAGC
* * * *
2306542 CAACAAAACTGGGTGCCCAAGGCTTCGTATCCTTAGTCCACCTACTTTGAATCAAAGA
66 CAACAAAACTAGGTGCCCAAGCCTTCGCATCATTAGTCCACCTACTTTGAATCAAAGA
*
2306600 ACTTGACGTTGCACGTAGAGCAGCGAACCTTGCCATTTGTATTACTTCTGGAGGCACATTCAAGC
1 ACTTGACGTTGCACGTAGAGCAGCGAACCTTGCCATTTGCATTACTTCTGGAGGCACATTCAAGC
*
2306665 CAACAAAACTAGGTGCCCAAGCCTTTGCATCATTAGTCCACCTACTTTGAATCAAAGA
66 CAACAAAACTAGGTGCCCAAGCCTTCGCATCATTAGTCCACCTACTTTGAATCAAAGA
2306723 CCCGGGAAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
123 111 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (123 bp):
ACTTGACGTTGCACGTAGAGCAGCGAACCTTGCCATTTGCATTACTTCTGGAGGCACATTCAAGC
CAACAAAACTAGGTGCCCAAGCCTTCGCATCATTAGTCCACCTACTTTGAATCAAAGA
Found at i:2309401 original size:198 final size:196
Alignment explanation
Indices: 2309001--2309746 Score: 925
Period size: 198 Copynumber: 3.8 Consensus size: 196
2308991 AAAATATGTA
*
2309001 TCGATA-ATTTTAAAATTTTATCGATCCCAAAAATATCGAAACCGATAATTATAAA-GTAATAGG
1 TCGATACA-TTTAAAATTGTATCGATCCCAAAAATATCGAAACCGATAATTA-AAATGTAATAGG
* * * * * *
2309064 TAAATTTACAATGTACTGGT--AAAATACCAGTTTTATGACAGAATAGG-GAACATATTATGTCG
64 TAAATTTACAATGTACTGGTAAAAAATACCAGTTTAATTAGAAAATAGGTCAACATATTATATCG
* * * * *
2309126 ATACTTTTTAAATTGTGTTGATACTTTTGGTCCAGAATAAATGCCCAACAAGGTGCATGCATAAA
129 ACACTTTTTAAATTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAA
2309191 GTG
194 GTG
* * *
2309194 TCGATACATTTAAAATTGTATCGATCCCGAAAACATCGAAACCAATAATTAAAATGTAATAGGTA
1 TCGATACATTTAAAATTGTATCGATCCCAAAAATATCGAAACCGATAATTAAAATGTAATAGGTA
* * * *
2309259 AATTTACAATGTAACCGGTAGAAAAATACCGGTTTAATTAGAAAATAGGTCAACATAATGTATCG
66 AATTTACAATGT-ACTGGTA-AAAAATACCAGTTTAATTAGAAAATAGGTCAACATATTATATCG
* * *
2309324 ACACTTTTTAAATTGTGTCGATACTTTTGGTCCATAATGAATGTCGAACGAGGTGCACGCATAAA
129 ACACTTTTTAAATTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAA
2309389 GTG
194 GTG
* * * *
2309392 TCGATACATTTAAAATTGTATCGATCCCTAAAATATCAAAATCGAT-ATTATAATGTAATAGGTA
1 TCGATACATTTAAAATTGTATCGATCCCAAAAATATCGAAACCGATAATTAAAATGTAATAGGT-
* * * * *
2309456 AAATTTGCAATATACTGGTAGAAATATACCAGTTTAATTAGAAAAAATAGGTCCACATAGTATAT
65 AAATTTACAATGTACTGGTA-AAAAATACCAGTTTAATTAG--AAAATAGGTCAACATATTATAT
* * *
2309521 CGACAC-TTTTAAATT-TGTTCGACAACTTTTGGTCAAGAATGAATGCCCAACGAGGTGCACGGA
127 CGACACTTTTTAAATTGTG-TCGA-TACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCA
2309584 TAAAGTG
190 TAAAGTG
* *
2309591 TCGATACATTTAAAATTGTATCGATCCCAAAAATATCGAAATCGATAATTATAATGTAATAGGTA
1 TCGATACATTTAAAATTGTATCGATCCCAAAAATATCGAAACCGATAATTAAAATGTAATAGGTA
* * * * * * *
2309656 ATTTTACAATGTA-TGGTAAAAATATACCGGTTTTATTAGAGAATAGGTAAACATATTGTATCAA
66 AATTTACAATGTACTGGTAAAAA-ATACCAGTTTAATTAGAAAATAGGTCAACATATTATATCGA
* *
2309720 TACTTTTTAAATTGTATCGATACTTTT
130 CACTTTTTAAATTGTGTCGATACTTTT
2309747 TGAATACGCG
Statistics
Matches: 478, Mismatches: 59, Indels: 29
0.84 0.10 0.05
Matches are distributed among these distances:
192 3 0.01
193 67 0.14
194 6 0.01
196 27 0.06
197 81 0.17
198 156 0.33
199 121 0.25
200 17 0.04
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (196 bp):
TCGATACATTTAAAATTGTATCGATCCCAAAAATATCGAAACCGATAATTAAAATGTAATAGGTA
AATTTACAATGTACTGGTAAAAAATACCAGTTTAATTAGAAAATAGGTCAACATATTATATCGAC
ACTTTTTAAATTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGT
G
Found at i:2309735 original size:20 final size:20
Alignment explanation
Indices: 2309710--2309747 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2309700 AGGTAAACAT
2309710 ATTGTATCAATACTTTTTAA
1 ATTGTATCAATACTTTTTAA
*
2309730 ATTGTATCGATACTTTTT
1 ATTGTATCAATACTTTTT
2309748 GAATACGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (20 bp):
ATTGTATCAATACTTTTTAA
Found at i:2309818 original size:15 final size:15
Alignment explanation
Indices: 2309798--2309828 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2309788 GATTCGATAT
*
2309798 AAACCCTAAATCGAA
1 AAACCCTAAACCGAA
2309813 AAACCCTAAACCGAA
1 AAACCCTAAACCGAA
2309828 A
1 A
2309829 GGCAGAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.29, G:0.06, T:0.10
Consensus pattern (15 bp):
AAACCCTAAACCGAA
Found at i:2310084 original size:18 final size:16
Alignment explanation
Indices: 2310040--2310098 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 16
2310030 AACCTTAAAT
2310040 CTTCTTCTCAACCAAC
1 CTTCTTCTCAACCAAC
2310056 C-TCTTCTCAACGACAAC
1 CTTCTTCTCAAC--CAAC
*
2310073 CTTCTCCTCAACCAAGC
1 CTTCTTCTCAACCAA-C
2310090 GCTTCTTCT
1 -CTTCTTCT
2310099 GAACAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 10 0.28
16 4 0.11
17 6 0.17
18 16 0.44
ACGTcount: A:0.22, C:0.42, G:0.05, T:0.31
Consensus pattern (16 bp):
CTTCTTCTCAACCAAC
Found at i:2310834 original size:159 final size:161
Alignment explanation
Indices: 2310544--2310862 Score: 624
Period size: 159 Copynumber: 2.0 Consensus size: 161
2310534 ATAGCGATTA
2310544 TTGGTGGTTAGCAAAGTATAGATCCAAAATGGCTCTAAACATTGCTAAACTGATATTAAGATAAT
1 TTGGTGGTTAGCAAAGTATAGATCCAAAATGGCTCTAAACATTGCTAAACTGATATTAAGATAAT
2310609 TGTATATATGGTCACAAAGGGAACATCAATTTCAACTTCACTACCATATGGATGTGTCATCACCC
66 TGTATATATGGTCACAAAGGGAACATCAATTTCAACTTCACTACCATATGGATGTGTCATCACCC
2310674 ATCTGTTGAAG-AGCATGAAGTTGATTTTTG
131 ATCTGTTGAAGAAGCATGAAGTTGATTTTTG
2310704 TTGGTGGTTAGCAAAGTATAGATCC-AAATGGCTCTAAACATTGCTAAACTGATATTAAGATAAT
1 TTGGTGGTTAGCAAAGTATAGATCCAAAATGGCTCTAAACATTGCTAAACTGATATTAAGATAAT
2310768 TGTATATATGGTCACAAAGGGAACATCAATTTCAACTTCACTACCATATGGATGTGTCATCACCC
66 TGTATATATGGTCACAAAGGGAACATCAATTTCAACTTCACTACCATATGGATGTGTCATCACCC
2310833 ATCTGTTGAAGAAGCATGAAGTTGATTTTT
131 ATCTGTTGAAGAAGCATGAAGTTGATTTTT
2310863 TGCAAGACTC
Statistics
Matches: 158, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
159 115 0.73
160 43 0.27
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (161 bp):
TTGGTGGTTAGCAAAGTATAGATCCAAAATGGCTCTAAACATTGCTAAACTGATATTAAGATAAT
TGTATATATGGTCACAAAGGGAACATCAATTTCAACTTCACTACCATATGGATGTGTCATCACCC
ATCTGTTGAAGAAGCATGAAGTTGATTTTTG
Found at i:2312685 original size:24 final size:23
Alignment explanation
Indices: 2312654--2312698 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2312644 TTCATTTCAT
2312654 ATTTAATTGGAGTTTGAATTTAA
1 ATTTAATTGGAGTTTGAATTTAA
*
2312677 ATTTCAATTTGAGTTTGAATTT
1 ATTT-AATTGGAGTTTGAATTT
2312699 TGATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (23 bp):
ATTTAATTGGAGTTTGAATTTAA
Found at i:2312709 original size:24 final size:24
Alignment explanation
Indices: 2312658--2312710 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2312648 TTTCATATTT
* * *
2312658 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
**
2312682 AATTTGAGTTTGAATTTTGATATA
1 AATTTGAGTTTGAATTTAAATATA
2312706 AATTT
1 AATTT
2312711 CAGCTATACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:2314584 original size:192 final size:197
Alignment explanation
Indices: 2314070--2314614 Score: 763
Period size: 192 Copynumber: 2.8 Consensus size: 197
2314060 GAATAGGTAA
* *
2314070 ACATAATGTATCGATA-ATTT-TTAAAATTGTATAGATCCCAAAAACATCGAAACCGATAATTAT
1 ACATAAAGTGTCGATACATTTATTAAAA--GTATAGATCCCAAAAACATCGAAACCGATAATTAT
2314133 AATGTAATA-GTAAATTTACAATGTAACCGATAGAAATATACCGATTTAATTAGAAAAATAGGTC
64 AATGTAATAGGTAAATTTACAATGTAACCGATAG-AATATACCGA-TTAATTAG-AAAATAGGTC
2314197 AAC---A--TATCGATACA--TTTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGTCAAACG
126 AACATAATGTATCGATACATTTTTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGTCAAAC-
2314255 AGGTGCAC
190 AGGTGCAC
2314263 ACATAAAGTGTCG--ACATTTATTAAAAGTATAGATCCCAAAAACATCGAAACCGATAATTATAA
1 ACATAAAGTGTCGATACATTTATTAAAAGTATAGATCCCAAAAACATCGAAACCGATAATTATAA
2314326 TGTAATAGGTAAATTTACAATGTAACCGGTATA-AATATACCGATTAATTAGAAAATAGGTCAAC
66 TGTAATAGGTAAATTTACAATGTAACC-G-ATAGAATATACCGATTAATTAGAAAATAGGTCAAC
* *
2314390 ATAATGTATCGATACATTTTTAAATTGTGTCGATACTTTTTG-CCTATAATGAATG-CCAA-AGG
129 ATAATGTATCGATACATTTTTAAATTGTGTCGATACTTTTTGTCC-AGAATGAATGTCAAACAGG
2314452 TGCAC
193 TGCAC
* * * * *
2314457 GCATAAAGTGTCGATACATTTATTAAAAGTATCGACCCCAAAAA-ATTGAAACCTATAA-T-TAA
1 ACATAAAGTGTCGATACATTTATTAAAAGTATAGATCCCAAAAACATCGAAACCGATAATTATAA
* *
2314519 TGTAATAGGTAAATTTACAATGTAACCGATAGAATATACCGGTTAATTAGAAAATAAGTCAACAT
66 TGTAATAGGTAAATTTACAATGTAACCGATAGAATATACCGATTAATTAGAAAATAGGTCAACAT
2314584 AATGTATC-ATAC-TTTTTAAATTGTGTCGATA
131 AATGTATCGATACATTTTTAAATTGTGTCGATA
2314615 AAAAGTGCAC
Statistics
Matches: 325, Mismatches: 11, Indels: 35
0.88 0.03 0.09
Matches are distributed among these distances:
190 32 0.10
191 60 0.18
192 73 0.22
193 49 0.15
194 24 0.07
195 22 0.07
196 32 0.10
197 33 0.10
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (197 bp):
ACATAAAGTGTCGATACATTTATTAAAAGTATAGATCCCAAAAACATCGAAACCGATAATTATAA
TGTAATAGGTAAATTTACAATGTAACCGATAGAATATACCGATTAATTAGAAAATAGGTCAACAT
AATGTATCGATACATTTTTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGTCAAACAGGTGC
AC
Found at i:2314784 original size:21 final size:21
Alignment explanation
Indices: 2314758--2314799 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2314748 GTCAACATAA
2314758 TGTATCGACACTTTTTAAATT
1 TGTATCGACACTTTTTAAATT
* *
2314779 TGTATCGATATTTTTTAAATT
1 TGTATCGACACTTTTTAAATT
2314800 AGGCGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (21 bp):
TGTATCGACACTTTTTAAATT
Found at i:2316604 original size:2 final size:2
Alignment explanation
Indices: 2316599--2316624 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2316589 AAATATATCG
2316599 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
2316625 TCCATACTTA
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:2317245 original size:22 final size:23
Alignment explanation
Indices: 2317219--2317272 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
2317209 AACCTATTTA
2317219 TTATATAAGCGCTA-CTATTACG
1 TTATATAAGCGCTACCTATTACG
2317241 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTATTACG
2317264 -TATATAAGC
1 TTATATAAGC
2317273 TATCTAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 23 0.74
23 8 0.26
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (23 bp):
TTATATAAGCGCTACCTATTACG
Found at i:2323009 original size:3 final size:3
Alignment explanation
Indices: 2323001--2323083 Score: 130
Period size: 3 Copynumber: 27.7 Consensus size: 3
2322991 ACATGTAAAT
* *
2323001 AAC AAC AAC AAC AAC AAC AAC AAC AAA AAC AAC AAC AAT AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* *
2323049 AAC AAC AAC AAC AAT AAT AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
2323084 TAATAATAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.69, C:0.28, G:0.00, T:0.04
Consensus pattern (3 bp):
AAC
Found at i:2323627 original size:37 final size:35
Alignment explanation
Indices: 2323585--2323704 Score: 119
Period size: 37 Copynumber: 3.5 Consensus size: 35
2323575 ATCTTTAGGG
2323585 ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
1 ATTTGTTTCAAGAGAAACTGTCT-AAGAGAGACAAA
* * *
2323621 ACTTTGTTTCAAGGGAAACAGACT-----A-A-AAA
1 A-TTTGTTTCAAGAGAAACTGTCTAAGAGAGACAAA
*
2323650 ATTTGTGTTACAAGGGAAACTGTCTAAGAGAGACAAA
1 ATTTGT-TT-CAAGAGAAACTGTCTAAGAGAGACAAA
2323687 ATTTGTTTCAAGAGAAAC
1 ATTTGTTTCAAGAGAAAC
2323705 AATCTCAATG
Statistics
Matches: 68, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
28 5 0.07
29 6 0.09
30 14 0.21
31 1 0.01
35 10 0.15
36 4 0.06
37 28 0.41
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (35 bp):
ATTTGTTTCAAGAGAAACTGTCTAAGAGAGACAAA
Found at i:2323744 original size:65 final size:65
Alignment explanation
Indices: 2323590--2323798 Score: 269
Period size: 65 Copynumber: 3.2 Consensus size: 65
2323580 TAGGGATTTG
* * **
2323590 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGA-CTAAAAAATTT
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACA-ATCT-AAATGTTT
*
2323654 GTG
63 GTA
* * **
2323657 TTACAAGGGAAACTGTCT-AAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAATGTTCATA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTAAATGTTTGTA
* * *
2323721 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAACTTATTTCAAGAGAAACAATCTAAATGTTTGTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTAAATGTTTGTA
2323786 TTTCAAGGGAAAC
1 TTTCAAGGGAAAC
2323799 AACTTCTGGA
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
64 23 0.19
65 72 0.58
66 13 0.10
67 16 0.13
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (65 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTAAATGTTTGTA
Found at i:2329581 original size:55 final size:56
Alignment explanation
Indices: 2329520--2329628 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 56
2329510 ATAAAAAATA
2329520 CATAGTTTACAGTGACCAAAATAAACACGCGTAAAATAAT-AGACCAAATGAGAAT
1 CATAGTTTACAGTGACCAAAATAAACACGCGTAAAATAATAAGACCAAATGAGAAT
2329575 CATAGTTTACAGTGACCAAAATAAACACGCGTAAAATAATAAGACCAAATGAGA
1 CATAGTTTACAGTGACCAAAATAAACACGCGTAAAATAATAAGACCAAATGAGA
2329629 TCAATAATCT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 40 0.75
56 13 0.25
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.19
Consensus pattern (56 bp):
CATAGTTTACAGTGACCAAAATAAACACGCGTAAAATAATAAGACCAAATGAGAAT
Found at i:2331201 original size:2 final size:2
Alignment explanation
Indices: 2331196--2331221 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2331186 GCGCGCGCGC
2331196 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
2331222 TATGATTAGA
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:2337780 original size:20 final size:20
Alignment explanation
Indices: 2337755--2337794 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2337745 TTTTTTCATG
2337755 TGGATTGAATATTGGTGTAT
1 TGGATTGAATATTGGTGTAT
2337775 TGGATTGAATATTGGTGTAT
1 TGGATTGAATATTGGTGTAT
2337795 GGGGAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (20 bp):
TGGATTGAATATTGGTGTAT
Found at i:2338436 original size:76 final size:77
Alignment explanation
Indices: 2338310--2338466 Score: 307
Period size: 76 Copynumber: 2.1 Consensus size: 77
2338300 AGTGGATTTG
2338310 TCATCTTAAGTATTATTATGTCTATGGTTATATCATTAAATTATATACTATTTTGTGTGTTTAAT
1 TCATCTTAAGTATTATTATGTCTATGGTTATATCATTAAATTATATACTATTTTGTGTGTTTAAT
2338375 G-TTTTAGGACA
66 GTTTTTAGGACA
2338386 TCATCTTAAGTATTATTATGTCTATGGTTATATCATTAAATTATATACTATTTTGTGTGTTTAAT
1 TCATCTTAAGTATTATTATGTCTATGGTTATATCATTAAATTATATACTATTTTGTGTGTTTAAT
2338451 GTTTTTAGGACA
66 GTTTTTAGGACA
2338463 TCAT
1 TCAT
2338467 GTTGTATAGA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 66 0.82
77 14 0.17
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (77 bp):
TCATCTTAAGTATTATTATGTCTATGGTTATATCATTAAATTATATACTATTTTGTGTGTTTAAT
GTTTTTAGGACA
Found at i:2342131 original size:17 final size:17
Alignment explanation
Indices: 2342102--2342146 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2342092 CTTATTTTTC
2342102 TTTTCT-TTCTTTTGCTCT
1 TTTTCTCTT-TTTTG-TCT
*
2342120 TTTTCTCTTTTTTGTTT
1 TTTTCTCTTTTTTGTCT
2342137 TTTTCTCTTT
1 TTTTCTCTTT
2342147 CCTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 12 0.48
18 11 0.44
19 2 0.08
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTTCTCTTTTTTGTCT
Found at i:2342137 original size:23 final size:23
Alignment explanation
Indices: 2342096--2342154 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
2342086 ACCCACCTTA
2342096 TTTTTCT-TTTCTTTCTTTTGCTC
1 TTTTTCTCTTT-TTTCTTTTGCTC
* **
2342119 TTTTTCTCTTTTTTGTTTTTTTC
1 TTTTTCTCTTTTTTCTTTTGCTC
*
2342142 TCTTTC-CTTTTTT
1 TTTTTCTCTTTTTT
2342155 TTCCGACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 7 0.23
23 21 0.68
24 3 0.10
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (23 bp):
TTTTTCTCTTTTTTCTTTTGCTC
Found at i:2342154 original size:17 final size:17
Alignment explanation
Indices: 2342119--2342157 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2342109 TCTTTTGCTC
*
2342119 TTTTTCTCTTTTTTGTT
1 TTTTTCTCTTTCTTGTT
*
2342136 TTTTTCTCTTTCCT-TT
1 TTTTTCTCTTTCTTGTT
2342152 TTTTTC
1 TTTTTC
2342158 CGACTTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTCTCTTTCTTGTT
Found at i:2342765 original size:21 final size:21
Alignment explanation
Indices: 2342732--2342771 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2342722 ATATATGTAT
*
2342732 ATATATATATTTATAAATAAG
1 ATATATATATTTAGAAATAAG
* *
2342753 ATATTTATTTTTAGAAATA
1 ATATATATATTTAGAAATA
2342772 TCAGAAAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATATATATTTAGAAATAAG
Found at i:2342932 original size:120 final size:117
Alignment explanation
Indices: 2342739--2342955 Score: 294
Period size: 120 Copynumber: 1.8 Consensus size: 117
2342729 TATATATATA
* * *
2342739 TATTTATAAATAAGATATTTATTTTTAGAAATATCAGAAAATGGCTTCTAGGTGCTTTAAGACAG
1 TATTTATAAATAAGATATTTATTTTTAAAAATATCAGAAAATGGCATCCAGGTGCTTTAAGACAG
* * *
2342804 CTCTTTTCTTAATATTAAATATAAATAAATATTAATAAAACATTTATTAAAAT
66 CTCCTTTCTTAATATGAAAAAT-AATAAATATTAATAAAACATTTATTAAAAT
*
2342857 TATTTATAAAGTAA-ATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGCTTTAAG
1 TATTTATAAA-TAAGATATTTA-TT-TTTAAAAATATCAGAAAATGG-CATCCAGGTGCTTTAAG
* *
2342921 ACTGC-CCTTTCTTAATATGAAAAATAATATATATT
62 ACAGCTCCTTTCTTAATATGAAAAATAATAAATATT
2342956 TAAATATAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 17 0.20
119 14 0.16
120 37 0.43
121 18 0.21
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (117 bp):
TATTTATAAATAAGATATTTATTTTTAAAAATATCAGAAAATGGCATCCAGGTGCTTTAAGACAG
CTCCTTTCTTAATATGAAAAATAATAAATATTAATAAAACATTTATTAAAAT
Found at i:2343187 original size:19 final size:18
Alignment explanation
Indices: 2343143--2343187 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2343133 TGACTAATAA
*
2343143 AATAATAATTAAAGCAAT
1 AATAAAAATTAAAGCAAT
* *
2343161 AATTAAAATATAAAGTAAT
1 AATAAAAAT-TAAAGCAAT
2343180 AATAAAAA
1 AATAAAAA
2343188 AGATTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AATAAAAATTAAAGCAAT
Found at i:2343201 original size:88 final size:87
Alignment explanation
Indices: 2343092--2343274 Score: 332
Period size: 88 Copynumber: 2.1 Consensus size: 87
2343082 ATATTTGAAA
2343092 AATAAATAAAGTTATTAATTTAAACCAATATATATATTTAT-TGACTAATAAAATAATAATTAAA
1 AATAAA-AAAGTTATTAATTT-AACCAATATATATATTTATATGACTAATAAAATAATAATTAAA
2343156 GCAATAATTAAAATATAAAGTAAT
64 GCAATAATTAAAATATAAAGTAAT
2343180 AATAAAAAAGATTATTAATTTAACCAATATATATATTTATATGACTAATAAAATAATAATTAAAG
1 AATAAAAAAG-TTATTAATTTAACCAATATATATATTTATATGACTAATAAAATAATAATTAAAG
2343245 CAATAATTAAAATATAAAGTAAT
65 CAATAATTAAAATATAAAGTAAT
2343268 AATAAAA
1 AATAAAA
2343275 TAATATTGCA
Statistics
Matches: 93, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
87 23 0.25
88 70 0.75
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (87 bp):
AATAAAAAAGTTATTAATTTAACCAATATATATATTTATATGACTAATAAAATAATAATTAAAGC
AATAATTAAAATATAAAGTAAT
Found at i:2343275 original size:18 final size:18
Alignment explanation
Indices: 2343231--2343276 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
2343221 TGACTAATAA
2343231 AATAATAAT-TAAAGCAAT
1 AATAA-AATATAAAGCAAT
*
2343249 AATTAAAATATAAAGTAAT
1 AA-TAAAATATAAAGCAAT
2343268 AATAAAATA
1 AATAAAATA
2343277 ATATTGCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (18 bp):
AATAAAATATAAAGCAAT
Found at i:2344586 original size:3 final size:3
Alignment explanation
Indices: 2344578--2344628 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
2344568 ATTTTTTAGT
*
2344578 TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2344626 TAA
1 TAA
2344629 AACGAAATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2344899 original size:26 final size:25
Alignment explanation
Indices: 2344871--2345011 Score: 86
Period size: 25 Copynumber: 6.0 Consensus size: 25
2344861 GAAGGCTTTT
* *
2344871 TTTTTAAAACATCATGCACTGAAGG
1 TTTTGAAAACATCAAGCACTGAAGG
*
2344896 TTTTGAAAACATTAAGCACTGAAGG
1 TTTTGAAAACATCAAGCACTGAAGG
** * * *
2344921 GCTT--ACAGAT-GAGC-C-GAAGG
1 TTTTGAAAACATCAAGCACTGAAGG
2344941 TTTTTGAAAACATCAAGCACTGAAGG
1 -TTTTGAAAACATCAAGCACTGAAGG
** * * *
2344967 GCTT--ACAGAT-GA-C-CTGAAGG
1 TTTTGAAAACATCAAGCACTGAAGG
2344987 TTTTGAAAACATCAAGCACTGAAGG
1 TTTTGAAAACATCAAGCACTGAAGG
2345012 GCTTACAGAT
Statistics
Matches: 82, Mismatches: 23, Indels: 22
0.65 0.18 0.17
Matches are distributed among these distances:
20 14 0.17
21 4 0.05
22 8 0.10
23 13 0.16
24 4 0.05
25 34 0.41
26 5 0.06
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (25 bp):
TTTTGAAAACATCAAGCACTGAAGG
Found at i:2345029 original size:46 final size:45
Alignment explanation
Indices: 2344889--2345025 Score: 240
Period size: 45 Copynumber: 3.0 Consensus size: 45
2344879 ACATCATGCA
*
2344889 CTGAAGGTTTTGAAAACATTAAGCACTGAAGGGCTTACAGATGAGC
1 CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA-C
2344935 C-GAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
1 CTGAAGG-TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
2344980 CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
1 CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
2345025 C
1 C
2345026 CTGAGGCTTT
Statistics
Matches: 88, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
45 46 0.52
46 42 0.48
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (45 bp):
CTGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
Found at i:2345126 original size:46 final size:46
Alignment explanation
Indices: 2345059--2345646 Score: 1009
Period size: 46 Copynumber: 12.8 Consensus size: 46
2345049 TCTCAAACTC
*
2345059 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
2345105 TTTTTGATAACATCATGCACTGAAGGGCTTACAGATGACCCGGAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
2345151 -TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
2345196 TTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
2345242 TTTTTGATAACATCATGCACTGAAGGGCTTACAGATGACCCGGAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
2345288 -TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
2345333 TTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* * *
2345379 TTTTTGAAAATATCATGCACTGAAGAGCTTACAGATAACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
2345425 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
2345471 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
2345517 TTTTTGAAAATATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
2345563 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGGCCCGAAGG
1 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
2345609 TTTTTTGAAAATATCATGCACTGAAGGGCTTACAGATG
1 -TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
2345647 TTGGAAATAG
Statistics
Matches: 512, Mismatches: 27, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
45 85 0.17
46 391 0.76
47 36 0.07
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (46 bp):
TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:2345305 original size:137 final size:138
Alignment explanation
Indices: 2345059--2345646 Score: 1018
Period size: 137 Copynumber: 4.3 Consensus size: 138
2345049 TCTCAAACTC
*
2345059 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAACATCATGCA
1 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCA
*
2345124 CTGAAGGGCTTACAGATGACCCGGAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
66 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
2345188 CCCAAAGG
131 CCCGAAGG
* *
2345196 TTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAACATCATGCA
1 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCA
*
2345261 CTGAAGGGCTTACAGATGACCCGGAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
66 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
2345325 CCCGAAGG
131 CCCGAAGG
* *
2345333 TTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAATATCATGCA
1 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCA
* *
2345398 CTGAAGAGCTTACAGATAACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
66 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
2345463 CCCGAAGG
131 CCCGAAGG
* *
2345471 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAATATCATGCA
1 TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCA
*
2345536 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGG
66 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
2345601 CCCGAAGG
131 CCCGAAGG
* *
2345609 TTTTTTGAAAATATCATGCACTGAAGGGCTTACAGATG
1 -TTTTTGAAAACATCATGCACTGAAGGACTTACAGATG
2345647 TTGGAAATAG
Statistics
Matches: 436, Mismatches: 13, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
137 222 0.51
138 178 0.41
139 36 0.08
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (138 bp):
TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCA
CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
CCCGAAGG
Found at i:2346373 original size:22 final size:22
Alignment explanation
Indices: 2346322--2346379 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
2346312 GATAAAGCTT
* *
2346322 TCATCTTCGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2346344 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2346366 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
2346380 TGTAGATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:2346849 original size:54 final size:54
Alignment explanation
Indices: 2346746--2346895 Score: 136
Period size: 54 Copynumber: 2.9 Consensus size: 54
2346736 TGACTAGTTC
* * * *
2346746 GTAAAACATTTGTCAATACATTCATCATCTCATGTGGTTTATGCTCAGATGCAA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCAA
* * * *
2346800 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAGAT---A
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCAA
* * * *
2346851 CT-----AGTTGACAACACATTCATCATTTCATGTGACTTATGCACAGAT
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGAT
2346896 TTCTGGTCAG
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
46 38 0.46
51 2 0.02
54 42 0.51
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCAA
Done.