Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold179
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: 2991183
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.31
Warning! 65816 characters in sequence are not A, C, G, or T
File 10 of 18
Found at i:1156268 original size:1 final size:1
Alignment explanation
Indices: 1156264--1156393 Score: 125
Period size: 1 Copynumber: 130.0 Consensus size: 1
1156254 CGGACCCCCC
* * * * * * *
1156264 TTTTTTTGTTTTTGTTTGTTTTTTTTTTGTTTTTTTTTTGTTTTTTTTTGTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * ** * * * *
1156329 TTTGTTTTTTTTTGTTTTTTTCATTTTTTTTGTTTTTTTTTGTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1156394 GGAGGACGTC
Statistics
Matches: 100, Mismatches: 29, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 100 1.00
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:1156283 original size:10 final size:9
Alignment explanation
Indices: 1156264--1156393 Score: 138
Period size: 9 Copynumber: 13.7 Consensus size: 9
1156254 CGGACCCCCC
1156264 TTTTTTTGT
1 TTTTTTTGT
1156273 TTTTGTTTGTTT
1 TTTT-TTTG--T
1156285 TTTTTTTGTTT
1 TTTTTTTG--T
1156296 TTTTTTTGTT
1 TTTTTTTG-T
1156306 TTTTTTTGT
1 TTTTTTTGT
1156315 TTTTTTTGTT
1 TTTTTTTG-T
1156325 TTTTTTTGTT
1 TTTTTTTG-T
1156335 TTTTTTTGT
1 TTTTTTTGT
**
1156344 TTTTTTCAT
1 TTTTTTTGT
1156353 TTTTTTTGT
1 TTTTTTTGT
1156362 TTTTTTT-T
1 TTTTTTTGT
*
1156370 GTTTTGTT-T
1 -TTTTTTTGT
1156379 TTTTTTTGT
1 TTTTTTTGT
1156388 TTTTTT
1 TTTTTT
1156394 GGAGGACGTC
Statistics
Matches: 109, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
8 7 0.06
9 49 0.45
10 33 0.30
11 15 0.14
12 5 0.05
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:1156292 original size:11 final size:11
Alignment explanation
Indices: 1156264--1156393 Score: 159
Period size: 10 Copynumber: 12.4 Consensus size: 11
1156254 CGGACCCCCC
1156264 TTTTTTTG-TT
1 TTTTTTTGTTT
*
1156274 TTTGTTTGTTT
1 TTTTTTTGTTT
1156285 TTTTTTTGTTT
1 TTTTTTTGTTT
1156296 TTTTTTTG-TT
1 TTTTTTTGTTT
1156306 TTTTTTTG--T
1 TTTTTTTGTTT
1156315 TTTTTTTG-TT
1 TTTTTTTGTTT
1156325 TTTTTTTG-TT
1 TTTTTTTGTTT
1156335 TTTTTTTGTTT
1 TTTTTTTGTTT
1156346 TTTTCATTT-TTT
1 TTTT--TTTGTTT
*
1156358 TTGTTTT-TTT
1 TTTTTTTGTTT
*
1156368 TTGTTTTGTTT
1 TTTTTTTGTTT
1156379 TTTTTTTGTTT
1 TTTTTTTGTTT
1156390 TTTT
1 TTTT
1156394 GGAGGACGTC
Statistics
Matches: 110, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
9 9 0.08
10 49 0.45
11 43 0.39
12 6 0.05
13 3 0.03
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:1156394 original size:19 final size:18
Alignment explanation
Indices: 1156264--1156393 Score: 149
Period size: 19 Copynumber: 7.2 Consensus size: 18
1156254 CGGACCCCCC
*
1156264 TTTTTTTGTTTTTGTTTGT
1 TTTTTTTTTTTTTGTTT-T
*
1156283 TTTTTTTTTGTTT-TTTT
1 TTTTTTTTTTTTTGTTTT
*
1156300 TTTGTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTGTTTT
1156318 TTTTGTTTTTTTTTGTTTT
1 TTTT-TTTTTTTTTGTTTT
**
1156337 TTTTTGTTTTTTTCATTTT
1 TTTTT-TTTTTTTTGTTTT
1156356 TTTTGTTTTTTTTTG--TT
1 TTTT-TTTTTTTTTGTTTT
*
1156373 TTGTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTGTTTT
1156391 TTT
1 TTT
1156394 GGAGGACGTC
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.11
17 17 0.18
18 15 0.16
19 51 0.54
20 1 0.01
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (18 bp):
TTTTTTTTTTTTTGTTTT
Found at i:1167251 original size:52 final size:52
Alignment explanation
Indices: 1167166--1167290 Score: 187
Period size: 52 Copynumber: 2.4 Consensus size: 52
1167156 ATATGAAAAG
* * *
1167166 TTGCTTGCATGTATCGATATATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
* *
1167218 TTTCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
* *
1167270 TTGCCTTCATGTATCAATACA
1 TTGCCTGCATGTATCGATACA
1167291 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1167303 original size:52 final size:52
Alignment explanation
Indices: 1167191--1167310 Score: 161
Period size: 52 Copynumber: 2.3 Consensus size: 52
1167181 GATATATTTA
* * ***
1167191 ATAGTGTATCGATACATCTGGGCAAATTTTCCTGCATGTATCGATACATTTT
1 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCAATACATAAG
* *
1167243 ATAATGTATCGATACATCTGGGCAAATTTGCCTTCATGTATCAATACA-AAG
1 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCAATACATAAG
1167294 ATCAGTGTATCGATACA
1 AT-AGTGTATCGATACA
1167311 ATGTATCGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
51 2 0.03
52 57 0.97
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (52 bp):
ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCAATACATAAG
Found at i:1167317 original size:13 final size:13
Alignment explanation
Indices: 1167299--1167323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1167289 CAAAGATCAG
1167299 TGTATCGATACAA
1 TGTATCGATACAA
1167312 TGTATCGATACA
1 TGTATCGATACA
1167324 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1167401 original size:33 final size:33
Alignment explanation
Indices: 1167364--1167430 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1167354 AGTAGCTTAA
1167364 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1167397 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1167430 A
1 A
1167431 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1167404 original size:13 final size:13
Alignment explanation
Indices: 1167386--1167410 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1167376 CAAAAAAATA
1167386 TGTATCGATACAT
1 TGTATCGATACAT
1167399 TGTATCGATACA
1 TGTATCGATACA
1167411 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1171761 original size:19 final size:19
Alignment explanation
Indices: 1171737--1171793 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1171727 TGTACCAATA
1171737 CATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
* *
1171756 CATTGTATCGATACACGGT
1 CATTGTATCGATACATGAT
*
1171775 CAATTGTATCGATATATGA
1 C-ATTGTATCGATACATGA
1171794 AACTAGCAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:1171845 original size:19 final size:20
Alignment explanation
Indices: 1171821--1171873 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1171811 CTACCACTGT
1171821 TTGTATCGATACATG-GACA
1 TTGTATCGATACATGAGACA
**
1171840 TTGTATCGATACATGAGGGA
1 TTGTATCGATACATGAGACA
1171860 TTGTATCGATACAT
1 TTGTATCGATACAT
1171874 TGCTTCTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (20 bp):
TTGTATCGATACATGAGACA
Found at i:1171932 original size:19 final size:20
Alignment explanation
Indices: 1171908--1171945 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1171898 ATATTTTCTA
1171908 ATGAA-TGTATCGATACATT
1 ATGAATTGTATCGATACATT
1171927 ATGAATTGTATCGATACAT
1 ATGAATTGTATCGATACAT
1171946 AGCTACGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGAATTGTATCGATACATT
Found at i:1173947 original size:20 final size:19
Alignment explanation
Indices: 1173919--1173993 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
1173909 TTTTACCTTG
*
1173919 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTAT-A
* *
1173939 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTAT-A
*
1173959 ATGTATCGATATATTCTATA
1 ATGTATCGATACATT-TATA
1173979 ATGTATCGATACATT
1 ATGTATCGATACATT
1173994 ATGTCTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTTATA
Found at i:1173986 original size:40 final size:39
Alignment explanation
Indices: 1173919--1173996 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
1173909 TTTTACCTTG
*
1173919 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTTATCAATATATCGATACAT-TATGA
* *
1173959 ATGTATCGATATATTCTAT-AATGTATCGATACATTATG
1 ATGTATCGATACATT-TATCAATATATCGATACATTATG
1173997 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 28 0.82
41 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTTATCAATATATCGATACATTATGA
Found at i:1174933 original size:22 final size:22
Alignment explanation
Indices: 1174907--1174961 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1174897 AGCCTTTGAC
1174907 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1174929 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1174951 CATGCATTTTT
1 CATGCATTTTT
1174962 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:1174968 original size:20 final size:21
Alignment explanation
Indices: 1174907--1174968 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1174897 AGCCTTTGAC
**
1174907 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
1174929 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
1174951 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
1174969 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
22 28 0.74
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.58
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:1181134 original size:21 final size:21
Alignment explanation
Indices: 1181110--1181156 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1181100 AAATGAAAAG
1181110 AAAAAGTGCAAAAAC-AAAATAA
1 AAAAAG-G-AAAAACAAAAATAA
*
1181132 AAAAAGGAACAACAAAAATAA
1 AAAAAGGAAAAACAAAAATAA
1181153 AAAA
1 AAAA
1181157 TGAGGACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 12 0.52
22 6 0.26
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.06
Consensus pattern (21 bp):
AAAAAGGAAAAACAAAAATAA
Found at i:1182445 original size:27 final size:27
Alignment explanation
Indices: 1182407--1182844 Score: 651
Period size: 27 Copynumber: 16.0 Consensus size: 27
1182397 ACTGTGACCT
*
1182407 CTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
1182434 CTTTTAAGTCCACAATTCTGTGGCATCA
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1182462 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1182489 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1182516 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1182544 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1182571 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1182598 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1182625 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1182652 CTTTTAAGTCCACAACTCCATGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1182679 CTTTTAAGTCTACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1182706 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1182733 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1182761 CTTTTGAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1182788 CTTTTAAAATCCACAACTCCGTGGCACT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1182816 CTTTTAAAATCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
1182844 C
1 C
1182845 ACTTCAAAGC
Statistics
Matches: 372, Mismatches: 35, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
27 256 0.69
28 116 0.31
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1182549 original size:82 final size:81
Alignment explanation
Indices: 1182407--1182844 Score: 651
Period size: 82 Copynumber: 5.3 Consensus size: 81
1182397 ACTGTGACCT
* * * *
1182407 CTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAATTCTGTGGCATCACTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
1182472 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
1182489 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
1182554 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
*
1182571 CTTTTTAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1182636 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
* * * *
1182652 CTTTTAAGTCCACAACTCCATGGCATCCTTTTAAGTCTACAACTCCGTGGCACCCTTTTAAGACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1182717 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
* * * * *
1182733 CTTTTAAGTCCATAACTCCGTGGCATCTCTTTTGAGTCCACAACTCTGTGGCACCCTTTTAAAAT
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
*
1182798 CCACAACTCCGTGGCACT
64 CCACAACTCCGTGGCACC
* *
1182816 CTTTTAAAATCCACAACTCTGTGGCACCC
1 CTTTT-AAGTCCACAACTCCGTGGCACCC
1182845 ACTTCAAAGC
Statistics
Matches: 324, Mismatches: 29, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
81 126 0.39
82 155 0.48
83 26 0.08
84 17 0.05
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:1182886 original size:32 final size:31
Alignment explanation
Indices: 1182847--1183616 Score: 867
Period size: 32 Copynumber: 25.2 Consensus size: 31
1182837 TGGCACCCAC
1182847 TTCAAAGCCCACACAAGTCGGTGGCAACCCAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
* *
1182879 TTTAAAGCCCACACAAGTCGGTGGCAACACTT
1 TTCAAAGCCCACACAAGTCGGTGGCAAC-CCT
1182911 TTCAAAGCCCACACAAGTCGGTGGC-ACCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
*
1182941 TTCAAAG-CC-CACAAGTCAGTGGC-ACTCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAAC-CCT
* *
1182970 TTCAAAG-CC-CACAAGTCAGTGGC-ACTCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAAC-CCT
* **
1182999 TTCAAAGCCCACA-AA-TCAGTGGC-ACTTTT
1 TTCAAAGCCCACACAAGTCGGTGGCAAC-CCT
*
1183028 TTCAAAG-CC-CACAAGTCAGTGGC-ACCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
**
1183056 TTCAAAG-CC-CACAAGTTAGTGGC-ACCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
* *
1183084 TTCAGAG-CC-CACAAGTCAGTGGC-ACCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
* * *
1183112 TTCGAAG-CC-CACAAGTCAGTGGC-ACCAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
*
1183140 TGCAAAGCCCACACAAGTCGGTGGCAACCCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
* **
1183172 TTCAAAGCCCACACAAGTCGGTGAC-ACTAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
**
1183202 TTCAAAGCCCACGTAAGTCGGTGGCAACCCAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
1183234 TTCAAAGCCCACACAAGTCGGTGGCAACCCAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
1183266 TTCAAAGCCCACACAAGTCGGTGGCAACCCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
1183298 TTCAAAGCCCACACAAGTCGGTGGCAACCCAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
* *
1183330 TTCAAAGCCCAAACAAGTCGATGGCAACCCAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
*
1183362 TTCAAAGCCCACACAAGTCGGTGGCAATCCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAA-CCCT
* *
1183394 TTCAAAG-CC-CACAAGTCAGTGGC-ACCAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
* **
1183422 TTCAAAGCCCACACAAGTCGATGGC-ACTAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
**
1183452 TTCAAAGCCCACGTAAGTCGGTGGCAACCCAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
*
1183484 TTCAAAGCCCACACAAGTCGGTGGAAACCCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
1183516 TTCAAAGCCCACACAAGTCGGTGGCAACCCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
*
1183548 TTCAAAGCCCACACAAGTCGGTGGCAACCTAT
1 TTCAAAGCCCACACAAGTCGGTGGCAACC-CT
* *
1183580 TTCAAA-CCCACGCAAGTCAGTGGCAACCCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
1183611 TTCAAA
1 TTCAAA
1183617 CCACCATTTT
Statistics
Matches: 663, Mismatches: 56, Indels: 39
0.87 0.07 0.05
Matches are distributed among these distances:
27 2 0.00
28 113 0.17
29 75 0.11
30 100 0.15
31 42 0.06
32 328 0.49
33 3 0.00
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.19
Consensus pattern (31 bp):
TTCAAAGCCCACACAAGTCGGTGGCAACCCT
Found at i:1182962 original size:28 final size:28
Alignment explanation
Indices: 1182407--1183616 Score: 722
Period size: 32 Copynumber: 41.3 Consensus size: 28
1182397 ACTGTGACCT
* * *
1182407 CTTT-AAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* * * * *
1182434 CTTT-TAAGTCCACAATTCTGTGGCATCA
1 CTTTCAAAGCCCACAAGTCGGTGGCA-CC
* * * *
1182462 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* * * *
1182489 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* * * * * *
1182516 CTTT-TAAGTCCATAACTCCGTGGCATCT
1 CTTTCAAAGCCCACAAGTCGGTGGCA-CC
* * * *
1182544 CTTT-TAAGTCCACAACTCTGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
** * * *
1182571 CTTT-TTAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* * * *
1182598 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* * * *
1182625 CTTT-TAAGTCCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* * * ** *
1182652 CTTT-TAAGTCCACAACTCCATGGCATC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* * * * *
1182679 CTTT-TAAGTCTACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* * * *
1182706 CTTT-TAAGACCACAACTCCGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* * * * * *
1182733 CTTT-TAAGTCCATAACTCCGTGGCATCT
1 CTTTCAAAGCCCACAAGTCGGTGGCA-CC
** * * *
1182761 CTTT-TGAGTCCACAACTCTGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* ** * * *
1182788 CTTTTAAAATCCACAACTCCGTGGCACT
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* ** * *
1182816 CTTTTAAAATCCACAACTCTGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
*
1182844 CACTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTTCAAAG-CC-CACAAGTCGGTGGC-ACC
*
1182876 CATTTTAAAGCCCACACAAGTCGGTGGCAACAC
1 C-TTTCAAAG-CC-CACAAGTCGGTGGC-AC-C
*
1182909 TTTTCAAAGCCCACACAAGTCGGTGGCACC
1 CTTTCAAAG-CC-CACAAGTCGGTGGCACC
*
1182939 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCGGTGGCAC-C
*
1182968 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCGGTGGCAC-C
* * * *
1182997 TTTTCAAAGCCCACAAATCAGTGGCACTT
1 CTTTCAAAGCCCACAAGTCGGTGGCAC-C
* *
1183026 TTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
**
1183054 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* *
1183082 CTTTCAGAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* *
1183110 CTTTCGAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* *
1183138 ATTGCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTCAAAG-CC-CACAAGTCGGTGGC-ACC
* *
1183169 CTTTTCAAAGCCCACACAAGTCGGTGACACT
1 C-TTTCAAAG-CC-CACAAGTCGGTGGCACC
*
1183200 ATTTCAAAGCCCACGTAAGTCGGTGGCAACC
1 CTTTCAAAGCCCAC--AAGTCGGTGGC-ACC
1183231 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTTCAAAG-CC-CACAAGTCGGTGGC-ACC
1183263 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTTCAAAG-CC-CACAAGTCGGTGGC-ACC
1183295 CTTTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTTCAAAG-CC-CACAAGTCGGTGGC-ACC
*
1183327 CATTTCAAAGCCCAAACAAGTCGATGGCAACC
1 C-TTTCAAAGCCC--ACAAGTCGGTGGC-ACC
1183359 CATTTCAAAGCCCACACAAGTCGGTGGCAATCC
1 C-TTTCAAAG-CC-CACAAGTCGGTGGC-A-CC
* *
1183392 TTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCGGTGGCACC
* * *
1183420 ATTTCAAAGCCCACACAAGTCGATGGCACT
1 CTTTCAAAG-CC-CACAAGTCGGTGGCACC
*
1183450 ATTTCAAAGCCCACGTAAGTCGGTGGCAACC
1 CTTTCAAAGCCCAC--AAGTCGGTGGC-ACC
*
1183481 CATTTCAAAGCCCACACAAGTCGGTGGAAACC
1 C-TTTCAAAG-CC-CACAAGTCGGTGG-CACC
1183513 CTTTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTTCAAAG-CC-CACAAGTCGGTGGC-ACC
1183545 CTTTTCAAAGCCCACACAAGTCGGTGGCAACC
1 C-TTTCAAAG-CC-CACAAGTCGGTGGC-ACC
* *
1183577 TATTTCAAA-CCCACGCAAGTCAGTGGCAACC
1 -CTTTCAAAGCCCA--CAAGTCGGTGGC-ACC
1183608 CTTTTCAAA
1 C-TTTCAAA
1183617 CCACCATTTT
Statistics
Matches: 1054, Mismatches: 90, Indels: 74
0.87 0.07 0.06
Matches are distributed among these distances:
27 255 0.24
28 231 0.22
29 100 0.09
30 90 0.09
31 49 0.05
32 313 0.30
33 9 0.01
34 7 0.01
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.23
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCGGTGGCACC
Found at i:1183454 original size:250 final size:250
Alignment explanation
Indices: 1182827--1183616 Score: 1031
Period size: 250 Copynumber: 3.2 Consensus size: 250
1182817 TTTTAAAATC
* * * * *
1182827 CACAACTCTGTGGCACCCACTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTTAAAGCCCACA
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACA
*
1182892 CAAGTCGGTGGCAACACTTTTCAAAGCCCACACAAGTCGGTGGCACCCTTTCAAAG-CC-CACAA
66 CAAGTCGGTGGCAAC-CTTTTCAAAGCCCACACAAGTCGGTGGCACCATTTCAAAGCCCACACAA
* * * *
1182955 GTC-AGTGGCACTCCTTTCAAAGCCCAC--AAGTCAGTGGC-ACTCTTTTCAAAGCCCACA-AA-
130 GTCGA-TGGCACT-ATTTCAAAGCCCACGTAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAG
* ** *
1183014 TCAGTGGC-ACTTTTTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-
193 TCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
** * *
1183065 CACAAGTTAGTGGCACCC-TTTCAGAG-CC-CACAAGTCAGTGGC-ACCC-TTTCGAAG-CC-CA
1 CACAAGTCGGTGGCACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACA
* * * *
1183123 CAAGTCAGTGGC-ACCATTGCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACA
66 CAAGTCGGTGGCAACCTTTTCAAAGCCCACACAAGTCGGTGGC-A-CCATTTCAAAGCCCACACA
* *
1183187 AGTCGGTGACACTATTTCAAAGCCCACGTAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGT
129 AGTCGATGGCACTATTTCAAAGCCCACGTAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGT
*
1183252 CGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
194 CGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
*
1183309 CACAAGTCGGTGGCAACCCATTTCAAAGCCCAAACAAGTC-GATGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCACACAAGTCAG-TGGCAACCCATTTCAAAGCCCA
*
1183373 CACAAGTCGGTGGCAATCCTTTTCAAAG-CC-CACAAGTCAGTGGCACCATTTCAAAGCCCACAC
64 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCACACAAGTCGGTGGCACCATTTCAAAGCCCACAC
1183436 AAGTCGATGGCACTATTTCAAAGCCCACGTAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAG
128 AAGTCGATGGCACTATTTCAAAGCCCACGTAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAG
*
1183501 TCGGTGGAAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
193 TCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
* * *
1183559 CACAAGTCGGTGGCAACCTATTTCAAA-CCCACGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGC-ACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAA
1183617 CCACCATTTT
Statistics
Matches: 482, Mismatches: 41, Indels: 47
0.85 0.07 0.08
Matches are distributed among these distances:
229 26 0.05
230 3 0.01
231 23 0.05
232 17 0.04
233 20 0.04
234 14 0.03
235 30 0.06
236 4 0.01
237 13 0.03
238 25 0.05
239 2 0.00
240 13 0.03
241 4 0.01
242 8 0.02
243 2 0.00
244 12 0.02
245 4 0.01
246 7 0.01
247 3 0.01
248 11 0.02
249 30 0.06
250 170 0.35
251 3 0.01
252 26 0.05
253 3 0.01
254 9 0.02
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (250 bp):
CACAAGTCGGTGGCACCCATTTCAAAGCCCACACAAGTCAGTGGCAACCCATTTCAAAGCCCACA
CAAGTCGGTGGCAACCTTTTCAAAGCCCACACAAGTCGGTGGCACCATTTCAAAGCCCACACAAG
TCGATGGCACTATTTCAAAGCCCACGTAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCG
GTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCA
Found at i:1183717 original size:45 final size:46
Alignment explanation
Indices: 1183653--1183769 Score: 137
Period size: 49 Copynumber: 2.5 Consensus size: 46
1183643 GATATCGTTA
*
1183653 GCCTTGAATCAGCATATTGGCACCTTT-CTAAGCCCAATGTCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTTCCTAAGCCCAATGTCGCTG
* * *
1183698 GCCTTGAGTCAGCACATTGGTCTACTTTTCCCTTAGCCCAATGTCGCTG
1 GCCTTGAATCAGCACATTGG-C-ACCTTT-CCTAAGCCCAATGTCGCTG
* **
1183747 GCTTTGAATTGGCACATTGGCAC
1 GCCTTGAATCAGCACATTGGCAC
1183770 TCCTCTCATC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
45 18 0.30
46 1 0.02
47 7 0.12
48 1 0.02
49 33 0.55
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.31
Consensus pattern (46 bp):
GCCTTGAATCAGCACATTGGCACCTTTCCTAAGCCCAATGTCGCTG
Found at i:1184172 original size:20 final size:20
Alignment explanation
Indices: 1184144--1184218 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1184134 TTTTACCTTG
1184144 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1184164 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1184184 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1184204 ATGTATCGATACATT
1 ATGTATCGATACATT
1184219 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1184211 original size:40 final size:39
Alignment explanation
Indices: 1184144--1184221 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1184134 TTTTACCTTG
* *
1184144 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1184184 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1184222 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1185151 original size:22 final size:22
Alignment explanation
Indices: 1185125--1185179 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1185115 AGCCTTTGAC
1185125 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1185147 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1185169 CATGCATTTTT
1 CATGCATTTTT
1185180 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:1185186 original size:20 final size:21
Alignment explanation
Indices: 1185125--1185186 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1185115 AGCCTTTGAC
**
1185125 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
1185147 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
1185169 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
1185187 CCAGCATGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
22 28 0.74
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.58
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:1189162 original size:2 final size:2
Alignment explanation
Indices: 1189155--1189224 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
1189145 ACATACATAC
* *
1189155 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1189197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1189225 GAGGAACGTA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1190334 original size:21 final size:21
Alignment explanation
Indices: 1190310--1190354 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1190300 AAGAATGAGT
*
1190310 TAATCTTATAATTTTAAAATA
1 TAATCTTATAATTTTAAAAGA
* **
1190331 TAATTTTATTTTTTTAAAAGA
1 TAATCTTATAATTTTAAAAGA
1190352 TAA
1 TAA
1190355 AATATTTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATCTTATAATTTTAAAAGA
Found at i:1193156 original size:52 final size:51
Alignment explanation
Indices: 1193062--1193200 Score: 154
Period size: 51 Copynumber: 2.7 Consensus size: 51
1193052 TCTGGAAAAA
* * * *
1193062 AAATGTATCGATACATTTTTTATTGTATCAATACATTATGGGTTTTTGACCC
1 AAATATATCGATACATTATTCATCGTATCAATACATTATGGG-TTTTGACCC
** * *
1193114 AAATATATCGATACATTATTCATCGTATTGATATATTTTGGGTTTTGACCC
1 AAATATATCGATACATTATTCATCGTATCAATACATTATGGGTTTTGACCC
* * *
1193165 AAATATATCCATACATTCTTCAAT-GTATCGATACAT
1 AAATATATCGATACATTATTC-ATCGTATCAATACAT
1193201 GCAAGCAATT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
51 38 0.51
52 36 0.49
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (51 bp):
AAATATATCGATACATTATTCATCGTATCAATACATTATGGGTTTTGACCC
Found at i:1194095 original size:18 final size:18
Alignment explanation
Indices: 1194064--1194103 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1194054 TTTGTTGGTG
*
1194064 CATTTTTTTACTATGTTT
1 CATTTTTTTACTATGCTT
1194082 CATTTATTTT-CTATGCTT
1 CATTT-TTTTACTATGCTT
1194100 CATT
1 CATT
1194104 CATGCACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.17, C:0.15, G:0.05, T:0.62
Consensus pattern (18 bp):
CATTTTTTTACTATGCTT
Found at i:1205967 original size:15 final size:15
Alignment explanation
Indices: 1205947--1205977 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1205937 ATTTCGTTTG
*
1205947 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1205962 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1205977 G
1 G
1205978 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1210066 original size:13 final size:13
Alignment explanation
Indices: 1210048--1210073 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1210038 CAATTTTTTG
1210048 TGTATCGATACAT
1 TGTATCGATACAT
1210061 TGTATCGATACAT
1 TGTATCGATACAT
1210074 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1210088 original size:32 final size:33
Alignment explanation
Indices: 1210028--1210091 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1210018 TACAAGCTAA
** *
1210028 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1210061 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1210092 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1210196 original size:20 final size:20
Alignment explanation
Indices: 1210144--1210198 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1210134 CATATTTTTG
*
1210144 ATGTATCGATACATTGCAAT
1 ATGTATCGATACTTTGCAAT
1210164 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-T
*
1210184 GTGTATCGATACTTT
1 ATGTATCGATACTTT
1210199 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAT
Found at i:1219367 original size:21 final size:19
Alignment explanation
Indices: 1219343--1219398 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
1219333 CAGGGTAGTT
1219343 TGTATCGATACATTTCTGGTA
1 TGTATCGATACATTTCT--TA
* *
1219364 TGTATCGATAAATTCACTTA
1 TGTATCGATACATT-TCTTA
1219384 TGTATCGATACATTT
1 TGTATCGATACATTT
1219399 TGTTAGGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 15 0.50
21 13 0.43
22 2 0.07
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTTCTTA
Found at i:1219798 original size:19 final size:19
Alignment explanation
Indices: 1219774--1219838 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
1219764 TAGCTAAACT
1219774 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
1219793 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
1219806 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
1219827 TGTATCGATACA
1 TGTATCGATACA
1219839 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:1219810 original size:13 final size:13
Alignment explanation
Indices: 1219792--1219817 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1219782 TACACAAAAT
1219792 ATGTATCGATACA
1 ATGTATCGATACA
1219805 ATGTATCGATACA
1 ATGTATCGATACA
1219818 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1219815 original size:32 final size:33
Alignment explanation
Indices: 1219774--1219838 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
1219764 TAGCTAAACT
1219774 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
1219806 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
1219839 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:1225551 original size:20 final size:20
Alignment explanation
Indices: 1225508--1225553 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1225498 AAATCTTTTG
1225508 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1225529 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1225549 CAAAA
1 CAAAA
1225554 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1225869 original size:21 final size:20
Alignment explanation
Indices: 1225827--1225869 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1225817 GGCAGCACCA
* * *
1225827 CCAGGTCGCGACCGGCATTC
1 CCAGGTCACAACCGGCAGTC
1225847 CCAGGTCACAACCGGGCAGTC
1 CCAGGTCACAACC-GGCAGTC
1225868 CC
1 CC
1225870 CACACTAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.19, C:0.42, G:0.28, T:0.12
Consensus pattern (20 bp):
CCAGGTCACAACCGGCAGTC
Found at i:1227944 original size:19 final size:19
Alignment explanation
Indices: 1227920--1227984 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
1227910 TAGCCAAACT
1227920 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
1227939 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
1227952 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
1227973 TGTATCGATACA
1 TGTATCGATACA
1227985 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:1227956 original size:13 final size:13
Alignment explanation
Indices: 1227938--1227963 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1227928 TACACAAAAT
1227938 ATGTATCGATACA
1 ATGTATCGATACA
1227951 ATGTATCGATACA
1 ATGTATCGATACA
1227964 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1227961 original size:32 final size:33
Alignment explanation
Indices: 1227920--1227984 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
1227910 TAGCCAAACT
1227920 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
1227952 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
1227985 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:1230039 original size:48 final size:46
Alignment explanation
Indices: 1229983--1230110 Score: 148
Period size: 48 Copynumber: 2.7 Consensus size: 46
1229973 TAAAGTTTTT
*
1229983 TGTATTAATACAATGAATAATGTATCAATACATTTGGGTTTTCCAAAA
1 TGTATTAATACAAT-AATAATGTATCAATACATATGGG-TTTCCAAAA
** * *
1230031 TGTATTAATACAATAATAATGTATTGATACATATGGGTTTCCAGAT
1 TGTATTAATACAATAATAATGTATCAATACATATGGGTTTCCAAAA
* * *
1230077 TGTATCAATTACACTCATTAATGTATCAATACAT
1 TGTATTAA-TACAAT-AATAATGTATCAATACAT
1230111 GCATAGTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 14 0.21
47 25 0.37
48 29 0.43
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (46 bp):
TGTATTAATACAATAATAATGTATCAATACATATGGGTTTCCAAAA
Found at i:1230227 original size:20 final size:19
Alignment explanation
Indices: 1230196--1230233 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1230186 CATCAACTCT
1230196 CACAAATTCATCAAATTGC
1 CACAAATTCATCAAATTGC
1230215 CACAAATTTCATCAAATTG
1 CACAAA-TTCATCAAATTG
1230234 TTCCTCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (19 bp):
CACAAATTCATCAAATTGC
Found at i:1235696 original size:15 final size:15
Alignment explanation
Indices: 1235676--1235709 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1235666 GCTTATAATG
*
1235676 TTTGCATTATTTTGT
1 TTTGCATTATTTTAT
1235691 TTTGCATTATTTTAT
1 TTTGCATTATTTTAT
1235706 TTTG
1 TTTG
1235710 ATTTAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.68
Consensus pattern (15 bp):
TTTGCATTATTTTAT
Found at i:1238031 original size:20 final size:19
Alignment explanation
Indices: 1238006--1238056 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1237996 ACCAATTTCG
**
1238006 TGTATCGATACAATTGTGCA
1 TGTATCGATACAATAAT-CA
*
1238026 TGTATCGATTCAATAATCA
1 TGTATCGATACAATAATCA
1238045 TGTATCGATACA
1 TGTATCGATACA
1238057 GTGTATCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAATAATCA
Found at i:1238063 original size:13 final size:13
Alignment explanation
Indices: 1238045--1238069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1238035 TCAATAATCA
1238045 TGTATCGATACAG
1 TGTATCGATACAG
1238058 TGTATCGATACA
1 TGTATCGATACA
1238070 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1241468 original size:20 final size:22
Alignment explanation
Indices: 1241440--1241495 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
1241430 CTGTTAGGCT
*
1241440 AATTGTATCGATACAATTTTGG
1 AATTGTATCGATACAATTCTGG
*
1241462 -A-TGTATCAATAC-ATTCTGG
1 AATTGTATCGATACAATTCTGG
1241481 AATTGTATCGATACA
1 AATTGTATCGATACA
1241496 CTCCTATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 6 0.21
20 11 0.39
21 11 0.39
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (22 bp):
AATTGTATCGATACAATTCTGG
Found at i:1241488 original size:21 final size:21
Alignment explanation
Indices: 1241440--1241495 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1241430 CTGTTAGGCT
*
1241440 AATTGTATCGATACAATTTTGG
1 AATTGTATCGATAC-ATTCTGG
*
1241462 -A-TGTATCAATACATTCTGG
1 AATTGTATCGATACATTCTGG
1241481 AATTGTATCGATACA
1 AATTGTATCGATACA
1241496 CTCCTATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 6 0.21
20 11 0.38
21 12 0.41
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (21 bp):
AATTGTATCGATACATTCTGG
Found at i:1241598 original size:20 final size:20
Alignment explanation
Indices: 1241544--1241637 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
1241534 TGTCAATGAC
*
1241544 TTGTATCGATAC-TTTCACAT
1 TTGTATCGATACATTGCA-AT
* * *
1241564 AATGTATCAACACATTGCAAT
1 -TTGTATCGATACATTGCAAT
*
1241585 TTGTATCGATACATTACAACT
1 TTGTATCGATACATTGCAA-T
1241606 TT-TATCGATACATCTGC-AT
1 TTGTATCGATACAT-TGCAAT
* *
1241625 GTGTATTGATACA
1 TTGTATCGATACA
1241638 AATAAGGGTT
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.03
20 36 0.62
21 16 0.28
22 4 0.07
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (20 bp):
TTGTATCGATACATTGCAAT
Found at i:1244562 original size:17 final size:17
Alignment explanation
Indices: 1244540--1244573 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1244530 ACATTATCAC
* *
1244540 CAAAAATTTGATCAAAA
1 CAAAAATATGAACAAAA
1244557 CAAAAATATGAACAAAA
1 CAAAAATATGAACAAAA
1244574 TTCCATATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.18
Consensus pattern (17 bp):
CAAAAATATGAACAAAA
Found at i:1247837 original size:20 final size:19
Alignment explanation
Indices: 1247772--1247843 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
1247762 CTACCAGTTT
1247772 CATGTATCGATACTTTAA-AA
1 CATGTATCGATAC--TAAGAA
** *
1247792 GGTGTATCGATACTATGAA
1 CATGTATCGATACTAAGAA
*
1247811 CATGTATCGATAGTAAGCAA
1 CATGTATCGATACTAAG-AA
*
1247831 TATGTATCGATAC
1 CATGTATCGATAC
1247844 ATCTAGGTCT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
18 2 0.05
19 15 0.37
20 24 0.59
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACTAAGAA
Found at i:1250732 original size:18 final size:19
Alignment explanation
Indices: 1250686--1250732 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
1250676 ATTCCTTAAC
*
1250686 AAATAAGCACAATCATCAA
1 AAATAAGCAAAATCATCAA
*
1250705 AAATCA-CAAAATCAT-AA
1 AAATAAGCAAAATCATCAA
*
1250722 AATTAAGCAAA
1 AAATAAGCAAA
1250733 TAAATTATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 5 0.22
ACGTcount: A:0.62, C:0.17, G:0.04, T:0.17
Consensus pattern (19 bp):
AAATAAGCAAAATCATCAA
Found at i:1255032 original size:3 final size:3
Alignment explanation
Indices: 1255024--1255055 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1255014 GCTAACTTTT
*
1255024 TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1255056 TTTGATGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:1256772 original size:32 final size:33
Alignment explanation
Indices: 1256731--1256795 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1256721 ACTTTTTATG
*
1256731 GTGTATCGAT-GCTATG-AACATGTATCGATACA
1 GTGTATCGATAG-TAAGCAACATGTATCGATACA
*
1256763 GTGTATCGATAGTAAGCAATATGTATCGATACA
1 GTGTATCGATAGTAAGCAACATGTATCGATACA
1256796 TCTAGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.31
Consensus pattern (33 bp):
GTGTATCGATAGTAAGCAACATGTATCGATACA
Found at i:1260673 original size:28 final size:29
Alignment explanation
Indices: 1260613--1260694 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 29
1260603 TTTTGGAGAT
*
1260613 AATAACGGGGTTGGAGTATCCCC--TCGA
1 AATAACGGGGTTCGAGTATCCCCGATCGA
1260640 AGATAACGGGGTTCGAGTATCCCCGAT-GA
1 A-ATAACGGGGTTCGAGTATCCCCGATCGA
* * *
1260669 AATAATGAGGTTCGAGTATCCTCGAT
1 AATAACGGGGTTCGAGTATCCCCGAT
1260695 TGTGAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 1 0.02
28 43 0.90
29 3 0.06
30 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (29 bp):
AATAACGGGGTTCGAGTATCCCCGATCGA
Found at i:1260827 original size:51 final size:51
Alignment explanation
Indices: 1260677--1260947 Score: 303
Period size: 51 Copynumber: 5.3 Consensus size: 51
1260667 GAAATAATGA
* * * * ** * * *
1260677 GGTTCGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTAAAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAATG-TTTTAGAAATAAAACCGG
* * **
1260729 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTT-GAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAATTAATGTTTTAG-AAATAAAACCGG
1260781 GGTTGGAGTATCCCCGATTATGGAAAATTAATGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAATGTTTTAGAAATAAAACCGG
* *
1260832 GGTTGGAGTATCCTCGATTATGGAAAATTAATGTTTTAGAAATAAAACCAG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAATGTTTTAGAAATAAAACCGG
* * * * **
1260883 GGTTGGAGTATCCCCGATTAT-GAGGAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGGA-AAATTAATGTTTTAGAAATAAAACCGG
1260934 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
1260948 TTCGGAAATA
Statistics
Matches: 192, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.01
51 130 0.68
52 49 0.26
53 11 0.06
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGGAAAATTAATGTTTTAGAAATAAAACCGG
Found at i:1261015 original size:79 final size:79
Alignment explanation
Indices: 1260882--1261057 Score: 291
Period size: 79 Copynumber: 2.2 Consensus size: 79
1260872 AATAAAACCA
* *
1260882 GGGTTGGAGTATCCCCGATTATGAGGAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAGGAATCAATATTTTAGAAATAAAGTAGGGGTTGGAGTATCC
*
1260947 CTTCGGAAATAACG
66 CCTCGGAAATAACG
* *
1260961 GGGTTGGAGTATCCCTGATTATGAGGAATCAATATTTTA-AGAATAATGTAGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTATGAGGAATCAATATTTTAGA-AATAAAGTAGGGGTTGGAGTATC
1261025 CCCTCGGAAATAACG
65 CCCTCGGAAATAACG
1261040 GGGTTGGAGTATCCCCGA
1 GGGTTGGAGTATCCCCGA
1261058 CGATTAACGG
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
78 1 0.01
79 89 0.99
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCGATTATGAGGAATCAATATTTTAGAAATAAAGTAGGGGTTGGAGTATCC
CCTCGGAAATAACG
Found at i:1261073 original size:27 final size:29
Alignment explanation
Indices: 1261011--1261084 Score: 109
Period size: 27 Copynumber: 2.7 Consensus size: 29
1261001 GAATAATGTA
*
1261011 GGGGTTGGAGTATCCCC-TCGGAAATAAC
1 GGGGTTGGAGTATCCCCGACGGAAATAAC
*
1261039 GGGGTTGGAGTATCCCCGAC-G-ATTAAC
1 GGGGTTGGAGTATCCCCGACGGAAATAAC
1261066 GGGGTTGGAGTATCCCCGA
1 GGGGTTGGAGTATCCCCGA
1261085 TTGTGAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 24 0.56
28 18 0.42
29 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.22
Consensus pattern (29 bp):
GGGGTTGGAGTATCCCCGACGGAAATAAC
Found at i:1261149 original size:53 final size:51
Alignment explanation
Indices: 1261069--1261190 Score: 165
Period size: 51 Copynumber: 2.4 Consensus size: 51
1261059 GATTAACGGG
* * *
1261069 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG--TTTTGAAAATAAAATCGGA
1261122 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGAAAATAAAATCGGA
* *
1261173 GTGGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
1261191 GCAGAGAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
51 34 0.54
52 1 0.02
53 28 0.44
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:1263573 original size:13 final size:13
Alignment explanation
Indices: 1263555--1263580 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1263545 CAAAGAATAG
1263555 ATGTATCGATACA
1 ATGTATCGATACA
1263568 ATGTATCGATACA
1 ATGTATCGATACA
1263581 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1263576 original size:34 final size:33
Alignment explanation
Indices: 1263533--1263600 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
1263523 AAACTTCCTA
*
1263533 AATGTATCGATACAAAGAATAGATGTATCGATAC
1 AATGTATCGATACAAAGAA-AAATGTATCGATAC
*
1263567 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1263600 A
1 A
1263601 TTTCCTTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.44
34 18 0.56
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1263642 original size:13 final size:13
Alignment explanation
Indices: 1263624--1263675 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
1263614 AGCTTCCTAG
1263624 CGATACATTGTAT
1 CGATACATTGTAT
1263637 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1263656 CGATACATTGTAT
1 CGATACATTGTAT
1263669 CGATACA
1 CGATACA
1263676 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1263656 original size:19 final size:19
Alignment explanation
Indices: 1263632--1263717 Score: 76
Period size: 19 Copynumber: 4.7 Consensus size: 19
1263622 AGCGATACAT
1263632 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1263651 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1263664 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
1263683 TGTATCGATACATTTACTAAA
1 TGTATCGATACA-AAACT-TA
1263704 TGTATCGATACAAA
1 TGTATCGATACAAA
1263718 TTATTAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 11 0.20
14 1 0.02
16 2 0.04
18 1 0.02
19 23 0.43
20 3 0.06
21 13 0.24
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1263665 original size:32 final size:32
Alignment explanation
Indices: 1263624--1263696 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1263614 AGCTTCCTAG
1263624 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1263656 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1263688 CGATACATT
1 CGATACATT
1263697 TACTAAATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1264923 original size:20 final size:22
Alignment explanation
Indices: 1264893--1264936 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
1264883 TGATTTCCCG
1264893 TGTGAATGTATCGATACA-ATT
1 TGTGAATGTATCGATACATATT
1264914 TGTG-ATGTATCGATACATATT
1 TGTGAATGTATCGATACATATT
1264935 TG
1 TG
1264937 AAAATATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (22 bp):
TGTGAATGTATCGATACATATT
Found at i:1265013 original size:19 final size:20
Alignment explanation
Indices: 1264970--1265021 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1264960 TACAAGCCAA
*
1264970 TGTATCGATACAATTTTTGG
1 TGTATCGATACAATCTTTGG
1264990 TGTATCGATAC-ATACTTT-G
1 TGTATCGATACAAT-CTTTGG
1265009 TGTATCGATACAA
1 TGTATCGATACAA
1265022 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATCTTTGG
Found at i:1265866 original size:22 final size:20
Alignment explanation
Indices: 1265840--1265883 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 20
1265830 TTATAGGTTA
1265840 AAAAATCAAAGTACAATGCAAAT
1 AAAAA-CAAAGT-CAA-GCAAAT
1265863 AAAAACAAAGTCAAGCAAAT
1 AAAAACAAAGTCAAGCAAAT
1265883 A
1 A
1265884 CATTAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 3 0.14
22 6 0.29
23 5 0.24
ACGTcount: A:0.64, C:0.14, G:0.09, T:0.14
Consensus pattern (20 bp):
AAAAACAAAGTCAAGCAAAT
Found at i:1271464 original size:21 final size:21
Alignment explanation
Indices: 1271409--1271465 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
1271399 TGAATCATGC
*
1271409 AAGTTTTTATTTTTC-TTAGCT
1 AAGTTTTT-TATTTCATTAGCT
**
1271430 AA-TTCATTATTTTCATTAGCT
1 AAGTTTTTTA-TTTCATTAGCT
1271451 AAGTTTTTTATTTCA
1 AAGTTTTTTATTTCA
1271466 ACTTGCAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 1 0.04
20 7 0.25
21 15 0.54
22 5 0.18
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.58
Consensus pattern (21 bp):
AAGTTTTTTATTTCATTAGCT
Found at i:1273625 original size:20 final size:22
Alignment explanation
Indices: 1273595--1273638 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
1273585 TGATTTCCCG
1273595 TGTGAATGTATCAATACA-ATT
1 TGTGAATGTATCAATACATATT
*
1273616 TGTG-ATGTATCGATACATATT
1 TGTGAATGTATCAATACATATT
1273637 TG
1 TG
1273639 AAAATATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (22 bp):
TGTGAATGTATCAATACATATT
Found at i:1273701 original size:20 final size:20
Alignment explanation
Indices: 1273672--1273723 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1273662 TACAAGCCAA
* *
1273672 TGTATTGATACAAT-TTTTGG
1 TGTATCGATACAATACTTT-G
1273692 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
1273711 TGTATCGATACAA
1 TGTATCGATACAA
1273724 GTTTGGTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:1274831 original size:21 final size:21
Alignment explanation
Indices: 1274789--1274846 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
1274779 GTGTATTTAC
1274789 TTGAAAAACATTATTTCTTTGT
1 TTGAAAAACATT-TTTCTTTGT
1274811 TTGAAAAACATTTGTTC-TTGT
1 TTGAAAAACATTT-TTCTTTGT
* *
1274832 CTCAAAAACATTTTT
1 TTGAAAAACATTTTT
1274847 ATATTAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 15 0.45
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.47
Consensus pattern (21 bp):
TTGAAAAACATTTTTCTTTGT
Found at i:1276606 original size:18 final size:17
Alignment explanation
Indices: 1276573--1276611 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1276563 GACATTGACT
*
1276573 TAATTTTTTAAGAATTC
1 TAATTTTTTAAAAATTC
*
1276590 TAATTTTATTAAAAATTT
1 TAATTTT-TTAAAAATTC
1276608 TAAT
1 TAAT
1276612 AAATATCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TAATTTTTTAAAAATTC
Found at i:1277564 original size:21 final size:21
Alignment explanation
Indices: 1277539--1277581 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1277529 AATTTACACA
*
1277539 AAAAAACATCATGAAAAATCAT
1 AAAAACCAT-ATGAAAAATCAT
1277561 AAAAACCATATGAAAAATCAT
1 AAAAACCATATGAAAAATCAT
1277582 GATAATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.63, C:0.14, G:0.05, T:0.19
Consensus pattern (21 bp):
AAAAACCATATGAAAAATCAT
Found at i:1278410 original size:20 final size:19
Alignment explanation
Indices: 1278364--1278419 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1278354 TTGCATCGAT
* *
1278364 ACATTGTATTGATACATGT
1 ACATTGTATCGATACATGG
*
1278383 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
1278402 ACAATTGTATCGATACAT
1 AC-ATTGTATCGATACAT
1278420 AAGATTGGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1278486 original size:13 final size:13
Alignment explanation
Indices: 1278465--1278517 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1278455 CGATACATGG
*
1278465 TACAATGTATCGA
1 TACATTGTATCGA
1278478 TACATTGTATCGA
1 TACATTGTATCGA
1278491 TACA-TG-AT-G-
1 TACATTGTATCGA
1278500 -A-ATTGTATCGA
1 TACATTGTATCGA
1278511 TACATTG
1 TACATTG
1278518 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1278491 original size:33 final size:33
Alignment explanation
Indices: 1278449--1278517 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1278439 CTACCACTAT
*
1278449 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
1278482 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
1278515 TTG
1 TTG
1278518 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:1281658 original size:20 final size:20
Alignment explanation
Indices: 1281635--1281690 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
1281625 TAGGACACGC
1281635 AAGGTTAAATTTGATTACCT
1 AAGGTTAAATTTGATTACCT
1281655 AAGGTTAAATTTGATTACCT
1 AAGGTTAAATTTGATTACCT
1281675 AAGGTTAAATTTGATT
1 AAGGTTAAATTTGATT
1281691 GTGATAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (20 bp):
AAGGTTAAATTTGATTACCT
Found at i:1283693 original size:13 final size:13
Alignment explanation
Indices: 1283675--1283700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1283665 CAATTTTTTG
1283675 TGTATCGATACAT
1 TGTATCGATACAT
1283688 TGTATCGATACAT
1 TGTATCGATACAT
1283701 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1284473 original size:21 final size:21
Alignment explanation
Indices: 1284410--1284473 Score: 87
Period size: 20 Copynumber: 3.1 Consensus size: 21
1284400 CTCCCCTTTA
* *
1284410 TCTCCCCCGTTTATTAA-TAAT
1 TCTCCCCC-TTAATCAAGTAAT
1284431 TCTCCCCCTTAATCAAGT-AT
1 TCTCCCCCTTAATCAAGTAAT
1284451 TCTCCCCCTTAATCAAGTAAT
1 TCTCCCCCTTAATCAAGTAAT
1284472 TC
1 TC
1284474 ATATCAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 26 0.67
21 13 0.33
ACGTcount: A:0.25, C:0.33, G:0.05, T:0.38
Consensus pattern (21 bp):
TCTCCCCCTTAATCAAGTAAT
Found at i:1286294 original size:13 final size:13
Alignment explanation
Indices: 1286276--1286300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1286266 ATAATCACCC
1286276 TGTATCGATACAT
1 TGTATCGATACAT
1286289 TGTATCGATACA
1 TGTATCGATACA
1286301 AAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1292682 original size:52 final size:52
Alignment explanation
Indices: 1292597--1292721 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1292587 ATATGAAAAG
* *
1292597 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1292649 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1292701 TTTCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1292722 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1292734 original size:52 final size:51
Alignment explanation
Indices: 1292597--1292741 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
1292587 ATATGAAAAG
*
1292597 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1292649 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1292701 TTTCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1292742 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1292748 original size:13 final size:13
Alignment explanation
Indices: 1292730--1292754 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1292720 CAAAGATCAG
1292730 TGTATCGATACAA
1 TGTATCGATACAA
1292743 TGTATCGATACA
1 TGTATCGATACA
1292755 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1292837 original size:33 final size:33
Alignment explanation
Indices: 1292795--1292864 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1292785 GGCAGTAGCT
1292795 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
1292828 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
1292861 TACA
1 TACA
1292865 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:1292838 original size:13 final size:13
Alignment explanation
Indices: 1292820--1292844 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1292810 CAAAAAAATA
1292820 TGTATCGATACAT
1 TGTATCGATACAT
1292833 TGTATCGATACA
1 TGTATCGATACA
1292845 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1295886 original size:13 final size:13
Alignment explanation
Indices: 1295868--1295893 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1295858 CAATTTTTTG
1295868 TGTATCGATACAT
1 TGTATCGATACAT
1295881 TGTATCGATACAT
1 TGTATCGATACAT
1295894 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1298038 original size:13 final size:13
Alignment explanation
Indices: 1298020--1298059 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1298010 ACAATATTCC
1298020 TTGTATCGATACA
1 TTGTATCGATACA
1298033 TTGTATCGATACA
1 TTGTATCGATACA
*
1298046 TGGTATCGATACA
1 TTGTATCGATACA
1298059 T
1 T
1298060 AGGGTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1300462 original size:19 final size:20
Alignment explanation
Indices: 1300440--1300490 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1300430 ATACTTCAAA
**
1300440 GTATCGATACATGTTC-ATT
1 GTATCGATACATGGACAATT
1300459 GTATCGATACATGGACAATT
1 GTATCGATACATGGACAATT
1300479 GTATCGATACAT
1 GTATCGATACAT
1300491 AAGATTAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (20 bp):
GTATCGATACATGGACAATT
Found at i:1300557 original size:13 final size:13
Alignment explanation
Indices: 1300536--1300566 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1300526 CGATACATGG
*
1300536 TACAATGTATCGA
1 TACATTGTATCGA
1300549 TACATTGTATCGA
1 TACATTGTATCGA
1300562 TACAT
1 TACAT
1300567 GATGAATTGT
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:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1300578 original size:33 final size:33
Alignment explanation
Indices: 1300520--1300588 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1300510 GTACCACTAT
*
1300520 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGATACAATGTATCGATACA
* *
1300553 TTGTATCGATACATGATGA-ATTGTATTGATACA
1 TTGTATCGATACATGAT-ACAATGTATCGATACA
1300586 TTG
1 TTG
1300589 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATGTATCGATACA
Found at i:1302516 original size:25 final size:22
Alignment explanation
Indices: 1302488--1302545 Score: 55
Period size: 25 Copynumber: 2.5 Consensus size: 22
1302478 TAAAAAATTA
1302488 AATTTTAAAAAAATAATTGAATATG
1 AATTTTAAAAAAATAATTG---ATG
* *
1302513 AA-TTTAATGAAAATATTTGATG
1 AATTTTAA-AAAAATAATTGATG
1302535 AATTTTAAAAA
1 AATTTTAAAAA
1302546 TTATAACTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 7 0.25
23 5 0.18
24 5 0.18
25 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (22 bp):
AATTTTAAAAAAATAATTGATG
Found at i:1305498 original size:20 final size:21
Alignment explanation
Indices: 1305462--1305500 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1305452 GTACAAATGT
1305462 TTTTCAAGCATAAAAATAAAG
1 TTTTCAAGCATAAAAATAAAG
*
1305483 TTTTCAAGTA-AAAAATAA
1 TTTTCAAGCATAAAAATAA
1305501 TCTAAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (21 bp):
TTTTCAAGCATAAAAATAAAG
Found at i:1305596 original size:21 final size:20
Alignment explanation
Indices: 1305570--1305608 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1305560 AGGTCAAAAC
1305570 CCTAGAAAGTATCGATACACA
1 CCTAG-AAGTATCGATACACA
*
1305591 CCTAGATGTATCGATACA
1 CCTAGAAGTATCGATACA
1305609 TATTGTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CCTAGAAGTATCGATACACA
Found at i:1305656 original size:52 final size:52
Alignment explanation
Indices: 1305578--1305692 Score: 221
Period size: 52 Copynumber: 2.2 Consensus size: 52
1305568 ACCCTAGAAA
*
1305578 GTATCGATACACACCTAGATGTATCGATACATATTGTTAGTATCAATACATT
1 GTATCGATACACACCTAGATGTATCGATACATACTGTTAGTATCAATACATT
1305630 GTATCGATACACACCTAGATGTATCGATACATACTGTTAGTATCAATACATT
1 GTATCGATACACACCTAGATGTATCGATACATACTGTTAGTATCAATACATT
1305682 GTATCGATACA
1 GTATCGATACA
1305693 TGTTCATAGT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (52 bp):
GTATCGATACACACCTAGATGTATCGATACATACTGTTAGTATCAATACATT
Found at i:1305778 original size:13 final size:13
Alignment explanation
Indices: 1305760--1305807 Score: 80
Period size: 13 Copynumber: 3.7 Consensus size: 13
1305750 AATTCACTTA
1305760 GTATCGATACATT
1 GTATCGATACATT
1305773 GTATCGATACAGTT
1 GTATCGATACA-TT
1305787 -TATCGATACATT
1 GTATCGATACATT
1305799 GTATCGATA
1 GTATCGATA
1305808 TATGGTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.06
13 29 0.88
14 2 0.06
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1311991 original size:20 final size:20
Alignment explanation
Indices: 1311968--1312013 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1311958 TATTGTATCA
* *
1311968 ATACATGAAGGATTGTATTG
1 ATACATGAAGAAATGTATTG
**
1311988 ATACATGGTGAAATGTATTG
1 ATACATGAAGAAATGTATTG
1312008 ATACAT
1 ATACAT
1312014 TGAGCCCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.35
Consensus pattern (20 bp):
ATACATGAAGAAATGTATTG
Found at i:1317252 original size:13 final size:13
Alignment explanation
Indices: 1317234--1317258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1317224 ATATTGCTTA
1317234 GTATCGATACATT
1 GTATCGATACATT
1317247 GTATCGATACAT
1 GTATCGATACAT
1317259 GTTCATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1317255 original size:33 final size:32
Alignment explanation
Indices: 1317213--1317276 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1317203 CACACCCAGA
*
1317213 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATT-CATAGTATCGATACAT
* *
1317246 TGTATCGATACATGTTCATAGTATTGATACA
1 TGTATCGATACATATTCATAGTATCGATACA
1317277 CATTAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATATTCATAGTATCGATACAT
Found at i:1317294 original size:20 final size:19
Alignment explanation
Indices: 1317244--1317296 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
1317234 GTATCGATAC
** *
1317244 ATTGTATCGATACATGTTC
1 ATTGTATCGATACACATTA
* *
1317263 ATAGTATTGATACACATTAA
1 ATTGTATCGATACACATT-A
1317283 ATTGTATCGATACA
1 ATTGTATCGATACA
1317297 TGAAACTGGC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (19 bp):
ATTGTATCGATACACATTA
Found at i:1321356 original size:20 final size:19
Alignment explanation
Indices: 1321308--1321356 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1321298 GATTTAAGCA
*
1321308 TTTTATTTTTATTTTATAT
1 TTTTATTTTTATTTGATAT
* *
1321327 TTATAATTTTAATTTGATAT
1 TT-TTATTTTTATTTGATAT
1321347 TTTTATTTTT
1 TTTTATTTTT
1321357 TTAATTGAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTATTTTTATTTGATAT
Found at i:1321610 original size:10 final size:10
Alignment explanation
Indices: 1321595--1321628 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1321585 TTTATCATAC
*
1321595 TATAATATAA
1 TATAATGTAA
1321605 TATAATGTAA
1 TATAATGTAA
*
1321615 TGTAATGTAA
1 TATAATGTAA
1321625 TATA
1 TATA
1321629 GTAAAGTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (10 bp):
TATAATGTAA
Found at i:1328343 original size:32 final size:32
Alignment explanation
Indices: 1328303--1328365 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1328293 CTCACTCAGA
1328303 TGTATCGATACATTATATCGATACATGTTCAT
1 TGTATCGATACATTATATCGATACATGTTCAT
*
1328335 TGTATCGATACATTGTATCGATACATGTTCA
1 TGTATCGATACATTATATCGATACATGTTCA
1328366 GGACAATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATTATATCGATACATGTTCAT
Found at i:1328441 original size:20 final size:20
Alignment explanation
Indices: 1328416--1328468 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1328406 TACCACTATT
*
1328416 TGTATCGATACATGGT-ACAA
1 TGTATCGATACATGATGA-AA
*
1328436 TGTATCGATACATGATGAAT
1 TGTATCGATACATGATGAAA
1328456 TGTATCGATACAT
1 TGTATCGATACAT
1328469 TGCTTGTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGATGAAA
Found at i:1336521 original size:22 final size:22
Alignment explanation
Indices: 1336490--1336531 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1336480 TTTTTAAAGA
1336490 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAGGGGGAGAAATGC
*
1336512 TTTGATAAAGGGGGAGAAAT
1 TTTGACAAAGGGGGAGAAAT
1336532 ATGTTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (22 bp):
TTTGACAAAGGGGGAGAAATGC
Found at i:1337149 original size:19 final size:19
Alignment explanation
Indices: 1337106--1337177 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
1337096 CTCACCCAAA
*
1337106 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
1337126 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
1337145 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
1337165 TGTATCGATACAT
1 TGTATCGATACAT
1337178 AAAATTGGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
19 17 0.36
20 29 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1337265 original size:33 final size:33
Alignment explanation
Indices: 1337210--1337275 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1337200 CCACTATTTA
* *
1337210 TATCGATACATGGTACAATGTATTGATACATTG
1 TATCGATACATGATACAATGTATCGATACATTG
*
1337243 TATCGATACATGATGA-ATTGTATCGATACATTG
1 TATCGATACATGAT-ACAATGTATCGATACATTG
1337276 CTTGTAACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (33 bp):
TATCGATACATGATACAATGTATCGATACATTG
Found at i:1338074 original size:17 final size:17
Alignment explanation
Indices: 1338038--1338079 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1338028 TTTCTCTTAG
*
1338038 TTTTATTTTTGCTTTGA
1 TTTTATTTTTGCTTCGA
1338055 TTTTATTTTT-CTTCGCA
1 TTTTATTTTTGCTTCG-A
1338072 TTTT-TTTT
1 TTTTATTTT
1338080 CATTTTGCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.74
Consensus pattern (17 bp):
TTTTATTTTTGCTTCGA
Found at i:1338749 original size:20 final size:20
Alignment explanation
Indices: 1338726--1338771 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1338716 CATTGTCTCA
* *
1338726 ATACATGAAGGATTGTATCG
1 ATACATGAAGAAATGTATCG
**
1338746 ATACATGGTGAAATGTATCG
1 ATACATGAAGAAATGTATCG
1338766 ATACAT
1 ATACAT
1338772 TGAGCCTAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (20 bp):
ATACATGAAGAAATGTATCG
Found at i:1339202 original size:23 final size:23
Alignment explanation
Indices: 1339167--1339210 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1339157 GTATTCAACC
*
1339167 TTGGGTTACAATTTCTT-AAGAAT
1 TTGGGATACAA-TTCTTGAAGAAT
*
1339190 TTGGGATATAATTCTTGAAGA
1 TTGGGATACAATTCTTGAAGA
1339211 GATTGAGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (23 bp):
TTGGGATACAATTCTTGAAGAAT
Found at i:1339979 original size:33 final size:33
Alignment explanation
Indices: 1339921--1339984 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1339911 TACACCCAAA
* *
1339921 TGTATTGATACAAATTGCTAAGTATCGATACAT
1 TGTATCGATACAAATTGCTAAGTATCAATACAT
**
1339954 TGTATCGATACAAATTGCTTTGTATCAATAC
1 TGTATCGATACAAATTGCTAAGTATCAATAC
1339985 TCTATGGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (33 bp):
TGTATCGATACAAATTGCTAAGTATCAATACAT
Found at i:1343993 original size:84 final size:84
Alignment explanation
Indices: 1343851--1344016 Score: 314
Period size: 84 Copynumber: 2.0 Consensus size: 84
1343841 AAGATACTAA
1343851 TATGGCTCCTAGCAAACAAAGTTTCTCCCTTTTAAAGGTTTTTTAGATTACTTATATGGATAACC
1 TATGGCTCCTAGCAAACAAAGTTTCTCCCTTTTAAAGGTTTTTTAGATTACTTATATGGATAACC
1343916 ATTAGAGGCTGAACACTGG
66 ATTAGAGGCTGAACACTGG
*
1343935 TATGGCTCCTAGCAAACAAAGTTTCTCCCTTTTAAAGGTTTTTTAGATTACTTGTATGGATAACC
1 TATGGCTCCTAGCAAACAAAGTTTCTCCCTTTTAAAGGTTTTTTAGATTACTTATATGGATAACC
*
1344000 ATTAGAGGCTGGACACT
66 ATTAGAGGCTGAACACT
1344017 TGGACAACTT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (84 bp):
TATGGCTCCTAGCAAACAAAGTTTCTCCCTTTTAAAGGTTTTTTAGATTACTTATATGGATAACC
ATTAGAGGCTGAACACTGG
Found at i:1347106 original size:12 final size:12
Alignment explanation
Indices: 1347089--1347115 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1347079 TAAAAATTAA
1347089 AAATTCAAATTC
1 AAATTCAAATTC
1347101 AAATTCAAATTC
1 AAATTCAAATTC
1347113 AAA
1 AAA
1347116 AAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTCAAATTC
Found at i:1347313 original size:50 final size:50
Alignment explanation
Indices: 1347237--1347400 Score: 267
Period size: 50 Copynumber: 3.3 Consensus size: 50
1347227 AATAGAAAAT
*
1347237 GCATGCATGGGAAAGCATAAAGATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
* * *
1347287 GCATGCATGGGAAAACACAAAAATTGCAATTGGAGACAAAGCATGC-GAAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAG-AG
1347337 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
*
1347387 ACATGCATGGGAAA
1 GCATGCATGGGAAA
1347401 TGAAAAAAGC
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
49 1 0.01
50 102 0.98
51 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.27, T:0.15
Consensus pattern (50 bp):
GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
Found at i:1347943 original size:47 final size:43
Alignment explanation
Indices: 1347892--1347984 Score: 105
Period size: 47 Copynumber: 2.1 Consensus size: 43
1347882 AAAGAATGAG
*
1347892 CAGCAAAAAACAACAGCAACAGCTCCAGTAGCCAACGACTGCAACTC
1 CAGCAAAAAACAACAGCAACAACTCC---AG-CAACGACTGCAACTC
*** *
1347939 CAGCACGCAACAACAGCAGCAACTCCAGCAACGACTGCAACTC
1 CAGCAAAAAACAACAGCAACAACTCCAGCAACGACTGCAACTC
1347982 CAG
1 CAG
1347985 AACGCAACAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 18 0.44
44 2 0.05
47 21 0.51
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.08
Consensus pattern (43 bp):
CAGCAAAAAACAACAGCAACAACTCCAGCAACGACTGCAACTC
Found at i:1349060 original size:53 final size:51
Alignment explanation
Indices: 1348958--1349075 Score: 134
Period size: 53 Copynumber: 2.3 Consensus size: 51
1348948 TCGTAATCGA
*
1348958 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCCTTTAATCGAGG
1 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-CTTCAATCG-GG
* **
1349011 GGATACTCCAACCCCGGTTTTA-TTTCTAAAATATTAATTT-TTCACAATCGGG
1 GGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTCTT--CAATCGGG
1349063 GG-TACTCCAACCC
1 GGATACTCCAACCC
1349076 TGTTATTTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
51 13 0.22
52 8 0.14
53 37 0.64
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (51 bp):
GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTTCAATCGGG
Found at i:1349227 original size:79 final size:79
Alignment explanation
Indices: 1349006--1349304 Score: 474
Period size: 79 Copynumber: 3.8 Consensus size: 79
1348996 TTCCTTTAAT
* * *
1349006 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGGTACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
* *
1349071 AACCCTGTTATTTT
66 AACCCCGTTATTTC
* * * *
1349085 CGAGGGGATACTCCAA-CCCGATTTTATCTCTAAAATATTAATTTTTCACAATCGGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
1349149 AACCCCGTTATTTC
66 AACCCCGTTATTTC
* *
1349163 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
1349228 AACCCCGTTATTTC
66 AACCCCGTTATTTC
* *
1349242 CGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACT
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACT
1349305 TTAATCCCGA
Statistics
Matches: 206, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
78 73 0.35
79 133 0.65
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (79 bp):
CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
AACCCCGTTATTTC
Found at i:1362906 original size:62 final size:61
Alignment explanation
Indices: 1362803--1363588 Score: 1085
Period size: 60 Copynumber: 12.9 Consensus size: 61
1362793 GAGCAGGACG
* * * *
1362803 CCTTTTAAAGCCCACACAAGTTAGTGGCACTTTTCCGGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTT
* * * **
1362865 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTCAGTCCTCAAAAAGCAGGACACCTTCG
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACC-TTTCAGTCCTCAAAGAGCAGGACGCCTTTT
1362927 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* *
1362987 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTT-AGTCTTCAAAGAGCAGGACG-CTTTCG
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT-T
* *
1363047 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCAC-CTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* * **
1363109 -CTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTCAGTCCTCAAAAAGCAGGACACCTTCG
1 CCTTTT-AAAGCCCACACAAGCTGGTGGCACC-TTTCAGTCCTCAAAGAGCAGGACGCCTTTT
*
1363171 CCTTTTAAAGCCCACACAAGCTGGT-GCACCTTT-AGTCCTCAAAGAGTAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
*
1363230 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGACG-CTTTCG
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT-T
1363290 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* *
1363350 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTT-AGTCTTCAAAGAGCAGGACG-CTTTCG
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT-T
* * *
1363410 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCAC-CTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1363472 -CTTTTCAAAGCCCACGCAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTT-AAAGCCCACACAAGCTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1363534 -CTTTTCAAAAAGCCCACACGAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGA
1 CCTTTT---AAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
1363589 TACACTTTAT
Statistics
Matches: 657, Mismatches: 48, Indels: 37
0.89 0.06 0.05
Matches are distributed among these distances:
59 58 0.09
60 269 0.41
61 31 0.05
62 240 0.37
63 35 0.05
64 24 0.04
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTT
Done.