Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold194
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: 3945165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1023 characters in sequence are not A, C, G, or T
File 12 of 24
Found at i:1955234 original size:22 final size:25
Alignment explanation
Indices: 1955208--1955255 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1955198 GTTGAAGTTG
*
1955208 TTATTT-A-TATAAAAA-ATTATTT
1 TTATTTAATTATAAAAATAATATTT
1955230 TTATTTAATTATAAAAATAATATTT
1 TTATTTAATTATAAAAATAATATTT
1955255 T
1 T
1955256 AATATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 1 0.05
24 8 0.36
25 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATTTAATTATAAAAATAATATTT
Found at i:1955413 original size:253 final size:255
Alignment explanation
Indices: 1954950--1955444 Score: 599
Period size: 253 Copynumber: 1.9 Consensus size: 255
1954940 AATTATTATT
1954950 TTTATAATAAAAAATTATTTATATTTAATTATAAATTATATATTTTATATTTTAATATTATTAAA
1 TTTATAATAAAAAATTATTTATATTTAATTATAAA-TATATA---TATATTTTAATATTATTAAA
* * * * * * * * ***
1955015 TAATGATTCAAGTTTATAAGAGAGGACAAATTTCAATTTGAATAAAAAATTAAAAAATTTTTTAA
62 CAATGACTCAAGCTTACAAGAGAGGACAAATTCCAAATTAAACAAAAAATTAAAAAAAAATTTAA
* * * * * * *
1955080 TTACGATCTAATCTAACATATTTTTAAACTTTTAAATTCAAGTTGCGTAGAGCTGGTGACTATTT
127 CTACGATCTAATATAACAGA--TTGAAACCTTTAAATTCAAGTTGCGTAAAGCTGATGACTATTT
* * * *
1955145 GGTTCCAATATATTTTAAACAAACTTTTATAATTACTGTATATTTTTTGTTTAGTTGAAGTTGTT
190 GGTTCCAACATATTTTAAACAAAATTTTATAATTACTATACATTTTTTGTTTAGTTGAAGTTGTT
1955210 A
255 A
*
1955211 TTTAT-ATAAAAAATTATTTTTATTTAATTATAAA-A-ATA-ATATTTTAATATTATTAAACAAT
1 TTTATAATAAAAAATTATTTATATTTAATTATAAATATATATATATTTTAATATTATTAAACAAT
1955272 GACTCAAGCTTACAAGAGAGGACAAATTCCAAATTAAACAAAAAATTAAAAAAAAAATTTAGACT
66 GACTCAAGCTTACAAGAGAGGACAAATTCCAAATTAAACAAAAAATT-AAAAAAAAATTTA-ACT
* * *
1955337 ACGATCTAATATAGCAGA-TGAACACCTTTAATTTCAAGTTG-GATAAAGTTGATGA-TGATTTG
129 ACGATCTAATATAACAGATTGAA-ACCTTTAAATTCAAGTTGCG-TAAAGCTGATGACT-ATTTG
*
1955399 GTTCCGACATATTTTAAACAAAATTTTATAATTACTATACATTTTT
191 GTTCCAACATATTTTAAACAAAATTTTATAATTACTATACATTTTT
1955445 GTAAAAATTT
Statistics
Matches: 202, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
252 5 0.02
253 133 0.66
254 10 0.05
255 17 0.08
257 3 0.01
258 1 0.00
260 28 0.14
261 5 0.02
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (255 bp):
TTTATAATAAAAAATTATTTATATTTAATTATAAATATATATATATTTTAATATTATTAAACAAT
GACTCAAGCTTACAAGAGAGGACAAATTCCAAATTAAACAAAAAATTAAAAAAAAATTTAACTAC
GATCTAATATAACAGATTGAAACCTTTAAATTCAAGTTGCGTAAAGCTGATGACTATTTGGTTCC
AACATATTTTAAACAAAATTTTATAATTACTATACATTTTTTGTTTAGTTGAAGTTGTTA
Found at i:1955515 original size:21 final size:21
Alignment explanation
Indices: 1955491--1955531 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1955481 AGAGGGTTTA
*
1955491 TATTTACGTATATTTATATCG
1 TATTTACATATATTTATATCG
* *
1955512 TATTTATATATTTTTATATC
1 TATTTACATATATTTATATC
1955532 ATAATTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (21 bp):
TATTTACATATATTTATATCG
Found at i:1955606 original size:2 final size:2
Alignment explanation
Indices: 1955601--1955657 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
1955591 ATAAATTTTG
*
1955601 AT AT AT AT AT AT -T TT AT AT -T AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1955640 TT TT AT A- AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT
1955658 TTTATATCGT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
1 5 0.11
2 42 0.89
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
AT
Found at i:1955609 original size:16 final size:16
Alignment explanation
Indices: 1955583--1955639 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
1955573 AAATTAATAA
1955583 TATATTATATAAATTT
1 TATATTATATAAATTT
*
1955599 TGATA-TATATATATTT
1 T-ATATTATATAAATTT
* *
1955615 TATATTATATATATATA
1 TATATTATATAAAT-TT
1955632 TATATTAT
1 TATATTAT
1955640 TTTTATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
15 3 0.08
16 21 0.58
17 12 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TATATTATATAAATTT
Found at i:1955623 original size:12 final size:12
Alignment explanation
Indices: 1955602--1955698 Score: 61
Period size: 12 Copynumber: 7.7 Consensus size: 12
1955592 TAAATTTTGA
1955602 TATATATATATTT
1 TATAT-TATATTT
*
1955615 TATATTATATATA
1 TATATTATAT-TT
1955628 TATATATATTATTTT
1 TATAT-TA-TA-TTT
* *
1955643 TATAATATATTA
1 TATATTATATTT
* **
1955655 TATTTTATATCG
1 TATATTATATTT
*
1955667 TATTTTA-ATTTT
1 TATATTATA-TTT
1955679 TATATTATATTT
1 TATATTATATTT
*
1955691 AATATTAT
1 TATATTAT
1955699 TTAAATTATC
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
11 1 0.02
12 39 0.59
13 14 0.21
14 4 0.06
15 7 0.11
16 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (12 bp):
TATATTATATTT
Found at i:1955650 original size:26 final size:26
Alignment explanation
Indices: 1955601--1955657 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
1955591 ATAAATTTTG
*
1955601 ATATATATATATTTTATATTATATAT
1 ATATATATATATTTTATATAATATAT
1955627 ATATATATATTATTTT-TATAATATAT
1 ATATATATA-TATTTTATATAATATAT
1955653 -TATAT
1 ATATAT
1955658 TTTATATCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 5 0.17
26 18 0.62
27 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATATATATATTTTATATAATATAT
Found at i:1956256 original size:16 final size:16
Alignment explanation
Indices: 1956221--1956290 Score: 50
Period size: 20 Copynumber: 3.9 Consensus size: 16
1956211 TAGGATCTCG
* *
1956221 ATTTAAATTTAAATTGA
1 ATTTAATTTTAAA-TAA
1956238 ATTTAATTTTAAATAA
1 ATTTAATTTTAAATAA
1956254 ATTTATATAATTTTAAATAA
1 A--T-T-TAATTTTAAATAA
*
1956274 ATTAAATGATTTAAATA
1 ATTTAAT--TTTAAATA
1956291 TTATTTAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 6 0.14
17 13 0.30
18 10 0.23
19 1 0.02
20 14 0.32
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTTAATTTTAAATAA
Found at i:1956258 original size:10 final size:10
Alignment explanation
Indices: 1956245--1956302 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
1956235 TGAATTTAAT
1956245 TTTAAATAAA
1 TTTAAATAAA
* *
1956255 TTTATATAAT
1 TTTAAATAAA
1956265 TTTAAATAAA
1 TTTAAATAAA
*
1956275 -TTAAAT-GA
1 TTTAAATAAA
*
1956283 TTTAAATATTA
1 TTTAAATA-AA
1956294 TTTAAATAA
1 TTTAAATAA
1956303 TATAAATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
8 1 0.03
9 12 0.32
10 16 0.42
11 9 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:1956300 original size:20 final size:19
Alignment explanation
Indices: 1956275--1956316 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1956265 TTTAAATAAA
* *
1956275 TTAAATGATTTAAATATTAT
1 TTAAATAATATAAATATT-T
1956295 TTAAATAATATAAATATTT
1 TTAAATAATATAAATATTT
1956314 TTA
1 TTA
1956317 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TTAAATAATATAAATATTT
Found at i:1956355 original size:13 final size:14
Alignment explanation
Indices: 1956320--1956347 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1956310 ATTTTTATTT
1956320 AAATTTAATTATAA
1 AAATTTAATTATAA
1956334 AAATTTAATTATAA
1 AAATTTAATTATAA
1956348 TTTTTAATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTTAATTATAA
Found at i:1956877 original size:3 final size:3
Alignment explanation
Indices: 1956860--1956901 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
1956850 AAAACAATCA
1956860 TAT TAAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1956902 ATTTTAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1957327 original size:18 final size:18
Alignment explanation
Indices: 1957291--1957330 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
1957281 ACTTAGATTT
1957291 AAAAAAAATTTAAATTAA
1 AAAAAAAATTTAAATTAA
1957309 AAAAATAAATTTAAA-TAA
1 AAAAA-AAATTTAAATTAA
1957327 AAAA
1 AAAA
1957331 TTTATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAAAAATTTAAATTAA
Found at i:1957339 original size:19 final size:19
Alignment explanation
Indices: 1957296--1957351 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1957286 GATTTAAAAA
*
1957296 AAATTTAAATTAAAAAA-AT
1 AAATTTAAA-TAAAAAATTT
1957315 AAATTTAAATAAAAAATTT
1 AAATTTAAATAAAAAATTT
* **
1957334 ATATTTATTTAAAAAATT
1 AAATTTAAATAAAAAATT
1957352 GATAAATCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 7 0.22
19 25 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTTAAATAAAAAATTT
Found at i:1957486 original size:17 final size:17
Alignment explanation
Indices: 1957454--1957510 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 17
1957444 AATTTATACA
*
1957454 ATATAAAATT-TAATAT
1 ATATAATATTATAATAT
1957470 ATATAATATTAT-A-AT
1 ATATAATATTATAATAT
*
1957485 ATA-AATATTAAAATAT
1 ATATAATATTATAATAT
1957501 AT-TAA-ATTAT
1 ATATAATATTAT
1957511 TTATATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 7 0.21
15 10 0.29
16 16 0.47
17 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATATTATAATAT
Found at i:1957491 original size:14 final size:14
Alignment explanation
Indices: 1957433--1957501 Score: 56
Period size: 14 Copynumber: 4.9 Consensus size: 14
1957423 CCTGTATATT
1957433 TATTATAATAT-AA
1 TATTATAATATAAA
1957446 T-TTATACAATATAAA
1 TATTAT--AATATAAA
1957461 -ATT-TAATATATATAA
1 TATTAT-A-ATATA-AA
1957476 TATTATAATATAAA
1 TATTATAATATAAA
*
1957490 TATTAAAATATA
1 TATTATAATATA
1957502 TTAAATTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
12 4 0.09
13 2 0.04
14 24 0.52
15 11 0.24
16 4 0.09
17 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTATAATATAAA
Found at i:1958010 original size:19 final size:17
Alignment explanation
Indices: 1957976--1958021 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
1957966 TAAATTTAGT
*
1957976 ATATTATTTAGATAATA
1 ATATTATTTAAATAATA
1957993 ATATTATATTAAATTAATA
1 ATATTAT-TTAAA-TAATA
*
1958012 ATTTTATTTA
1 ATATTATTTA
1958022 TTATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 7 0.28
19 11 0.44
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATATTATTTAAATAATA
Found at i:1958482 original size:26 final size:26
Alignment explanation
Indices: 1958421--1958483 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
1958411 TGTTAACAAA
* * * *
1958421 ATTAAAAAAATAGTAATTTTTTTATT
1 ATTAAAAAAATAATAAATTTATTAAT
*
1958447 ATT-AATAAATAATAAATTTATTAAT
1 ATTAAAAAAATAATAAATTTATTAAT
*
1958472 CTTAAAAAAATA
1 ATTAAAAAAATA
1958484 TCTTTTAAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAAAAAAATAATAAATTTATTAAT
Found at i:1958516 original size:17 final size:16
Alignment explanation
Indices: 1958490--1958521 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1958480 AATATCTTTT
1958490 AAGACACTTGATAACA
1 AAGACACTTGATAACA
1958506 AAGATCACTTGATAAC
1 AAGA-CACTTGATAAC
1958522 CAAAATCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (16 bp):
AAGACACTTGATAACA
Found at i:1958765 original size:6 final size:7
Alignment explanation
Indices: 1958748--1958790 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
1958738 TAATCCACCC
1958748 AAAAAAT
1 AAAAAAT
1958755 AAAAAAT
1 AAAAAAT
1958762 AAAAAAT
1 AAAAAAT
1958769 -AAAAAT
1 AAAAAAT
1958775 -AAAAAT
1 AAAAAAT
1958781 AAAAAAT
1 AAAAAAT
1958788 AAA
1 AAA
1958791 GGCAAACTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 12 0.34
7 23 0.66
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:1958772 original size:13 final size:13
Alignment explanation
Indices: 1958749--1958790 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
1958739 AATCCACCCA
1958749 AAAAATAAAAAAT
1 AAAAATAAAAAAT
1958762 AAAAA-ATAAAAAT
1 AAAAATA-AAAAAT
1958775 AAAAATAAAAAAT
1 AAAAATAAAAAAT
1958788 AAA
1 AAA
1958791 GGCAAACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.04
13 25 0.93
14 1 0.04
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:1970587 original size:20 final size:20
Alignment explanation
Indices: 1970562--1970638 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 20
1970552 TTTTACCTAG
*
1970562 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
*** * *
1970582 ATGTATCGATACGCGTATGA
1 ATGTATCGATACATTTTTCA
* *
1970602 CTGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
1970622 ATGTATCAATACATTTT
1 ATGTATCGATACATTTT
1970639 GTCTTTTTTT
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1977154 original size:19 final size:19
Alignment explanation
Indices: 1977114--1977155 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1977104 AGTTGCCTTG
* *
1977114 TTTTTATTTTTTTTCAATT
1 TTTTTATTTTTTATCAACT
1977133 TTTTTATTTTTTCAT-AACT
1 TTTTTATTTTTT-ATCAACT
1977152 TTTT
1 TTTT
1977156 CTTTTGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTTTATCAACT
Found at i:1977866 original size:28 final size:29
Alignment explanation
Indices: 1977834--1978564 Score: 757
Period size: 28 Copynumber: 25.6 Consensus size: 29
1977824 CATCAACCTG
* *
1977834 TGTGGGCATTG-AAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
1977862 TGTGGGCTTTGAAAA-GATGCCACTTACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
1977890 TGTGGGCTTT-AAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* ** *
1977918 TGTGGG-TTTTAAAAATATACCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
1977946 TGTGGGCTTTGAAAATG-TGCCACTGACC
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
1977974 TGTGGGCTTTGAAAAGGGTTGTCACTAACT
1 TGTGGGCTTTGAAAA-GGATGCCACTGACT
* * * *
1978004 TATGGGCTTTGAAAAGAGTTGCCATTAACT
1 TGTGGGCTTTGAAAAG-GATGCCACTGACT
* *
1978034 TGTGGGCTTTGAAAA-GATACCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
1978062 TGTGGGCTTTGAGAAGG-TGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
1978090 TGTGGGCTTTGAAAAAGG-TCGCCACTGACT
1 TGTGGGCTTTG-AAAAGGAT-GCCACTGACT
* * *
1978120 TGTGAGCTTTGAAAATG-TGCCACTGATT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
1978148 TGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
1978176 TGTGGGCTTTGAAAAAAGTTGCCACTGACT
1 TGTGGGCTTTG-AAAAGGATGCCACTGACT
*
1978206 TGTGGGCTTTGAAAAGGGTTGCCACTGACT
1 TGTGGGCTTTGAAAA-GGATGCCACTGACT
* *
1978236 TGTGGGCTTTGAAAAGAGTTGCTACTGACT
1 TGTGGGCTTTGAAAAG-GATGCCACTGACT
1978266 TGTGGGCTTTGAAAA-GATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * *
1978294 TGTGAGCTTTGAGAATGA-GCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* * * * *
1978322 TGTGGGCTTTGAGAATG-TGTCATTGATT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
1978350 TGTGGGCTTTGAAAAGGGTTGCCACTGA--
1 TGTGGGCTTTGAAAA-GGATGCCACTGACT
* * *
1978378 -GTGGGCTTCG-AAAGGAGGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
1978405 TATGGGCTTTGAAAAAGGTTGCCACTGACT
1 TGTGGGCTTTG-AAAAGGATGCCACTGACT
*
1978435 TGTGGGCTTTGAGAAA-G-TGCTACTGACT
1 TGTGGGCTTTGA-AAAGGATGCCACTGACT
*
1978463 TGTGTGCTTTGAAAAGGA-GCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
1978491 TGTGGGCTTTG-AAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
1978519 TGTGGGATTTGAAAAAGGTTGCCACTGACT
1 TGTGGGCTTTG-AAAAGGATGCCACTGACT
1978549 TGTGGGCTTTGAAAAG
1 TGTGGGCTTTGAAAAG
1978565 AAGTCGTATT
Statistics
Matches: 602, Mismatches: 72, Indels: 57
0.82 0.10 0.08
Matches are distributed among these distances:
25 9 0.01
26 3 0.00
27 24 0.04
28 320 0.53
29 45 0.07
30 201 0.33
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACT
Found at i:1978130 original size:86 final size:86
Alignment explanation
Indices: 1977845--1978565 Score: 826
Period size: 86 Copynumber: 8.4 Consensus size: 86
1977835 GTGGGCATTG
* * *
1977845 AAAGGATGCCACTAACTTGTGGGCTTTGAAAAGATGCCACTTACTTGTGGGCTTT-AAAAGGGTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAA-GGTG
*
1977909 CCACTAACTTGTGGG-TTTTAA
65 CCACTAACTTGTGGGCTTTGAA
* *
1977930 AAA--TATACCACTGACTTGTGGGCTTTGAAAATG-TGCCACTGACCTGTGGGCTTTGAAAAGGG
1 AAAGGT-TGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAA-GG
* *
1977992 TTGTCACTAACTTATGGGCTTTG-A
63 -TGCCACTAACTTGTGGGCTTTGAA
* * * * *
1978016 AAAGAGTTGCCATTAACTTGTGGGCTTTGAAAAGATACCACTAACTTGTGGGCTTTGAGAAGGTG
1 AAAG-GTTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTG
1978081 CCACTAACTTGTGGGCTTTGAA
65 CCACTAACTTGTGGGCTTTGAA
* * *
1978103 AAAGGTCGCCACTGACTTGTGAGCTTTGAAAATG-TGCCACTGATTTGTGGGCTTTGAAAAGGTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAAGGTG
1978167 CCACTAACTTGTGGGCTTTGAA
65 CCACTAACTTGTGGGCTTTGAA
* *
1978189 AAAAGTTGCCACTGACTTGTGGGCTTTGAAAAGGGTTGCCACTGACTTGTGGGCTTTGAAAAGAG
1 AAAGGTTGCCACTGACTTGTGGGCTTTGAAAA--GATGCCACTGACTTGTGGGCTTTGAAAAG-G
* *
1978254 TTGCTACTGACTTGTGGGCTTTG-A
63 -TGCCACTAACTTGTGGGCTTTGAA
* * * * *
1978278 AAA-GATGCCACTGACTTGTGAGCTTTGAGAATGA-GCCACTGACTTGTGGGCTTTGAGAATGTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTGA-AAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTG
* * * *
1978341 TCATTGATTTGTGGGCTTTGAA
65 CCACTAACTTGTGGGCTTTGAA
* * * * * *
1978363 AAGGGTTGCCACTGA---GTGGGCTTCGAAAGGAGGCCACTAACTTATGGGCTTTGAAAAAGGTT
1 AAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTG-AAAAGG-T
* *
1978425 GCCACTGACTTGTGGGCTTTGAG
64 GCCACTAACTTGTGGGCTTTGAA
* * *
1978448 AAA-G-TGCTACTGACTTGTGTGCTTTGAAAAGGA-GCCACTGACTTGTGGGCTTTGAAAGGGTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAAGGTG
*
1978510 CCACTAACTTGTGGGATTTGAA
65 CCACTAACTTGTGGGCTTTGAA
1978532 AAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGA
1 AAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGA
1978566 AGTCGTATTG
Statistics
Matches: 541, Mismatches: 68, Indels: 54
0.82 0.10 0.08
Matches are distributed among these distances:
82 4 0.01
83 36 0.07
84 90 0.17
85 45 0.08
86 228 0.42
87 16 0.03
88 94 0.17
89 8 0.01
90 20 0.04
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (86 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGC
CACTAACTTGTGGGCTTTGAA
Found at i:1980833 original size:28 final size:28
Alignment explanation
Indices: 1980773--1980847 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
1980763 AAATAAAACT
1980773 GGGGTTGGAGTATCCCTC-A-AAAATAAC
1 GGGGTTGGAGTATCCC-CGATAAAATAAC
** *
1980800 AAGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGATAAAATAAC
*
1980828 GGGGTTGGAGTATCCTCGAT
1 GGGGTTGGAGTATCCCCGAT
1980848 TGTGAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.03
27 15 0.38
28 24 0.60
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATAAAATAAC
Found at i:1980885 original size:106 final size:108
Alignment explanation
Indices: 1980715--1980950 Score: 307
Period size: 106 Copynumber: 2.2 Consensus size: 108
1980705 ATCTTCTTGA
* * *
1980715 AAATAACGGGGTTAGAGTATCCACGATTGTGAAAAATCGGTGTTCTGGAAATAAAACTGGGGTTG
1 AAATAACGGGGTTGGAGTATCCACGATTGTGAAAAATCGGTGTTCTAGAAATAAAACTGAGGTTG
*
1980780 GAGTATCC-CTCAAAAATAACAAGGTTGGAGTATCCCCG-ATG
66 GAGTATCCTCTCAAAAATAACAAGGTTCGAGTATCCCCGTATG
* * *
1980821 AAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTAGAAATAAAA-TCGAGGTT
1 AAATAACGGGGTTGGAGTATCCACGATTGTGAAAAATCGGTGTTCTAGAAATAAAACT-GAGGTT
* ** * *
1980885 GGAGTATCCTTTCGGAAATAACGAGGTTCGAGTGTCCCCGATTATG
65 GGAGTATCCTCTCAAAAATAACAAGGTTCGAGTATCCCCG--TATG
*
1980931 AAATAATGGGGTTGGAGTAT
1 AAATAACGGGGTTGGAGTAT
1980951 TCCTGAGATG
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
105 1 0.01
106 65 0.58
107 24 0.21
110 22 0.20
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.28
Consensus pattern (108 bp):
AAATAACGGGGTTGGAGTATCCACGATTGTGAAAAATCGGTGTTCTAGAAATAAAACTGAGGTTG
GAGTATCCTCTCAAAAATAACAAGGTTCGAGTATCCCCGTATG
Found at i:1983345 original size:13 final size:13
Alignment explanation
Indices: 1983298--1983327 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1983288 GTAAACCCAG
1983298 AATGTATCGATAC
1 AATGTATCGATAC
*
1983311 AATGTATCGATAT
1 AATGTATCGATAC
1983324 AATG
1 AATG
1983328 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1984009 original size:61 final size:61
Alignment explanation
Indices: 1983905--1984482 Score: 687
Period size: 61 Copynumber: 9.4 Consensus size: 61
1983895 ATGAAATGGG
* * * * ** *
1983905 TCCTGCTCTTTGGGGACT-AGAAGGTGCCACCAGCTTGTATGGGCTTTGCATGGAGAAA-GCA
1 TCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCA
* * * *
1983966 TCCTTCTCTTTAAGGACTGAAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
** *
1984027 TCCTATTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACA
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * * * * *
1984089 TCCTGCTCTTTGAGGACT-ATAAGGTGCCAACAACTTGTATGAGCTTTAAAAGGAAAAGACG
1 TCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * * *
1984150 TCCTGGTCCTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * * * *
1984211 TCCTACTCCTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * * * * *
1984272 TCTTGCTCTTTGAGGA-TTAGAAGGGCCACCAACATGTGTGGGCTTTAAAAGGAAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAAGGCA
*
1984333 TCCTGCTCTTTGAGGACTAGAAAAGTGCCAACAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * * * *
1984395 TCCTACTCTTTGAGGACTAGAAAATTGCCACCAACTTGTGTGGGCTGTAAAAGGAAAACGCG
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
*
1984457 TCCTGCTCTTTGAAGACTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTG
1984483 AAATGAGAAA
Statistics
Matches: 452, Mismatches: 57, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
60 35 0.08
61 249 0.55
62 138 0.31
63 30 0.07
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
Found at i:1984163 original size:123 final size:122
Alignment explanation
Indices: 1983891--1984482 Score: 712
Period size: 123 Copynumber: 4.8 Consensus size: 122
1983881 TAAGGAAAAA
* * * * * * **
1983891 TAAAATGAAATGG-GTCCTGCTCTTTGGGGACTAG-AAGGTGCCACCAGCTTGTATGGGCTTTGC
1 TAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * * * *
1983954 ATGGAGAAAGCATCCTTCTCTTTAAGGACTGAAAGGTGCC-ACTAACTTGTGTGGGCTT
66 AAGGA-AAAGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCAAC-AACTTGTGTGGGCTT
* **
1984012 TAAAAGGAAAAGGCATCCTATTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
1 TAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
1984077 AAGGAAAAGACATCCTGCTCTTTGAGGACT-ATAAGGTGCCAACAACTTGTATGAGCTT
66 AAGGAAAAG-CGTCCTGCTCTTTGAGGACTGA-AAAGTGCCAACAACTTGTGTGGGCTT
* * * *
1984135 TAAAAGGAAAAGACGTCCTGGTCCTTGAGGA-TTGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
1 TAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
* * * *
1984199 AAGGAAAAGGCGTCCTACTCCTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTT
66 AAGGAAAA-GCGTCCTGCTCTTTGAGGACTGAAAAGTGCCAACAACTTGTGTGGGCTT
* * * * *
1984257 TAAAAAGAAAAGGCGTCTTGCTCTTTGAGGATTAG--AAGGGCCACCAACATGTGTGGGCTTTAA
1 TAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
1984320 AAGGAAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCAACAACTTGTGTGGGCTT
66 AAGG-AAAA-GCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCAACAACTTGTGTGGGCTT
* * * *
1984380 TAAAAGGAAAAGGCATCCTACTCTTTGAGGACTAGAAAATTGCCACCAACTTGTGTGGGCTGTAA
1 TAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
*
1984445 AAGGAAAACGCGTCCTGCTCTTTGAAGACTGAAAAGTG
66 AAGGAAAA-GCGTCCTGCTCTTTGAGGACTGAAAAGTG
1984483 AAATGAGAAA
Statistics
Matches: 406, Mismatches: 53, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
121 41 0.10
122 149 0.37
123 162 0.40
124 26 0.06
125 28 0.07
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (122 bp):
TAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAA
AAGGAAAAGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCAACAACTTGTGTGGGCTT
Found at i:1984226 original size:184 final size:182
Alignment explanation
Indices: 1983904--1984474 Score: 777
Period size: 184 Copynumber: 3.1 Consensus size: 182
1983894 AATGAAATGG
* * ** * *
1983904 GTCCTGCTCTTTGGGGACTAGAAGGTGCCACCAGCTTGTATGGGCTTTGCATGGAGAAAGCATCC
1 GTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGA-AAAGCGTCC
* * * * * *
1983969 TTCTCTTTAAGGACTGAAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTATT
65 TGCTCTTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACT
1984034 CTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
130 CTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG-C
* * * *
1984088 ATCCTGCTCTTTGAGGACTATAAGGTGCCAACAACTTGTATGAGCTTTAAAAGGAAAAGACGTCC
1 GTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAG-CGTCC
* * *
1984153 TGGTCCTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACT
65 TGCTCTTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACT
* * *
1984218 CCTTGAGGA-TTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGC
130 CTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GC
* * * *
1984271 GTCTTGCTCTTTGAGGATTAGAAGG-GCCACCAACATGTGTGGGCTTTAAAAGGAAAAAGGCGTC
1 GTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGG-AAAA-GCGTC
* *
1984335 CTGCTCTTTGAGGACTAGAAAAGTGCCAACAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTA
64 CTGCTCTTTGAGGA-TTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTA
* *
1984400 CTCTTTGAGGACTAGAAAATTGCCACCAACTTGTGTGGGCTGTAAAAGGAAAACGC
128 CTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GC
*
1984456 GTCCTGCTCTTTGAAGACT
1 GTCCTGCTCTTTGAGGACT
1984475 GAAAAGTGAA
Statistics
Matches: 337, Mismatches: 44, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
182 24 0.07
183 85 0.25
184 173 0.51
185 55 0.16
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (182 bp):
GTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGCGTCCT
GCTCTTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTACTC
TTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGC
Found at i:1985478 original size:13 final size:12
Alignment explanation
Indices: 1985462--1985507 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
1985452 TTCTTTTCTC
1985462 TTTTTTTTCTTTG
1 TTTTTTTT-TTTG
*
1985475 TTTTGTTTTTTTA
1 TTTT-TTTTTTTG
*
1985488 TTTTGTTTTTTG
1 TTTTTTTTTTTG
1985500 TTTTTTTT
1 TTTTTTTT
1985508 AAAAAAAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
12 13 0.46
13 11 0.39
14 4 0.14
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.87
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:1985485 original size:18 final size:18
Alignment explanation
Indices: 1985462--1985507 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
1985452 TTCTTTTCTC
1985462 TTTTTTTTCTTTG-TTTTG
1 TTTTTTTT-TTTGTTTTTG
1985480 TTTTTTTATTTTGTTTTTTG
1 TTTTTTT-TTTTG-TTTTTG
1985500 TTTTTTTT
1 TTTTTTTT
1985508 AAAAAAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 11 0.44
19 2 0.08
20 12 0.48
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.87
Consensus pattern (18 bp):
TTTTTTTTTTTGTTTTTG
Found at i:1998031 original size:20 final size:20
Alignment explanation
Indices: 1998006--1998161 Score: 120
Period size: 20 Copynumber: 8.8 Consensus size: 20
1997996 TTTTCACAAT
*
1998006 TTGTATTGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
1998026 TTGTATCGATACATCGTTCA
1 TTGTATCGATACATTGTTCA
1998046 TTGTATCGAT--A-----CA
1 TTGTATCGATACATTGTTCA
*
1998059 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
1998079 TTGTATCGAT--A-----CA
1 TTGTATCGATACATTGTTCA
*
1998092 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
1998112 TTGTATCGAT--A-----CA
1 TTGTATCGATACATTGTTCA
*
1998125 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
1998145 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
1998162 ATCGATATAT
Statistics
Matches: 112, Mismatches: 3, Indels: 42
0.71 0.02 0.27
Matches are distributed among these distances:
13 36 0.32
15 3 0.03
18 3 0.03
20 70 0.62
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1998062 original size:13 final size:13
Alignment explanation
Indices: 1998044--1998168 Score: 124
Period size: 13 Copynumber: 11.0 Consensus size: 13
1998034 ATACATCGTT
1998044 CATTGTATCGATA
1 CATTGTATCGATA
1998057 CATTGTATCGATA
1 CATTGTATCGATA
1998070 CATTG---C--T-
1 CATTGTATCGATA
1998077 CATTGTATCGATA
1 CATTGTATCGATA
1998090 CATTGTATCGATA
1 CATTGTATCGATA
1998103 CATTG---C--T-
1 CATTGTATCGATA
1998110 CATTGTATCGATA
1 CATTGTATCGATA
1998123 CATTGTATCGATA
1 CATTGTATCGATA
1998136 CATTG---C--T-
1 CATTGTATCGATA
1998143 CATTGTATCGATA
1 CATTGTATCGATA
1998156 CATTGTATCGATA
1 CATTGTATCGATA
1998169 TATGGCTCAT
Statistics
Matches: 94, Mismatches: 0, Indels: 36
0.72 0.00 0.28
Matches are distributed among these distances:
7 15 0.16
8 3 0.03
10 6 0.06
12 3 0.03
13 67 0.71
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1998066 original size:33 final size:33
Alignment explanation
Indices: 1998024--1998188 Score: 294
Period size: 33 Copynumber: 5.0 Consensus size: 33
1998014 ATACATTGTT
* *
1998024 CATTGTATCGATACATCGTTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
1998057 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
1998090 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
1998123 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
* *
1998156 CATTGTATCGATATATGGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
1998189 TATTTTACAA
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 128 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTGTATCGATA
Found at i:2000650 original size:28 final size:28
Alignment explanation
Indices: 2000614--2000687 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
2000604 TTTCATAATC
* **
2000614 GGGGGTACTCCAACCCCGTTATTTCATT
1 GGGGATACTCCAACCCCGTTATTTCAGA
* * *
2000642 GGGGATACTCCAATCCCATTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCAGA
2000670 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2000688 ATTTTATTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCAGA
Found at i:2000740 original size:51 final size:51
Alignment explanation
Indices: 2000670--2000787 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 51
2000660 TTATTTCCGA
* * *
2000670 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTT-TCCACAATT
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCT-CACAATC
* ** *
2000721 GGGGATACTCTAATTCCGATTTTATTTCCAAAACACCAATTTCTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
2000772 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
2000788 TGTTATTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
Found at i:2000804 original size:79 final size:78
Alignment explanation
Indices: 2000721--2000940 Score: 262
Period size: 79 Copynumber: 2.8 Consensus size: 78
2000711 TTCCACAATT
* * *
2000721 GGGGATACTCTAATTCCGATTTTATTTCCAAAACACCAATTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAATCCCGATTTTATTTCCAAAACACCGATTT-TCATAATCGGGGATACTCCAAC
* * *
2000786 CCTGTTATTTTTGC
65 CCTATTATTTTCGA
* * *
2000800 GGGGATACTCCAACCCCGATTTTATATT-CAAAATACCGATTTTCTATAATCAGGGATACTCCAA
1 GGGGATACTCCAATCCCGATTTTAT-TTCCAAAACACCGATTTTC-ATAATCGGGGATACTCCAA
*
2000864 CTCTATTATTTTCGA
64 CCCTATTATTTTCGA
* * *
2000879 GGGGATACTCCAATCCCGATTTTTTATTTCTAGAACACTGATTTTCCATAATCGGGGATACT
1 GGGGATACTCCAATCCCGA--TTTTATTTCCAAAACACCGATTTT-CATAATCGGGGATACT
2000941 TTAGCCCCGT
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.02
79 81 0.68
80 4 0.03
81 31 0.26
82 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (78 bp):
GGGGATACTCCAATCCCGATTTTATTTCCAAAACACCGATTTTCATAATCGGGGATACTCCAACC
CTATTATTTTCGA
Found at i:2002091 original size:13 final size:13
Alignment explanation
Indices: 2002073--2002102 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2002063 ATAATTCTTC
*
2002073 ATGTATCGATATA
1 ATGTATCGATACA
2002086 ATGTATCGATACA
1 ATGTATCGATACA
2002099 ATGT
1 ATGT
2002103 GCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2002109 original size:33 final size:32
Alignment explanation
Indices: 2002050--2002119 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 32
2002040 GTCATTTGGG
* *
2002050 ATAATGTATCGATATAATTCTTCATGTATCGAT
1 ATAATGTATCGATACAATTC-TCATGTATCGAA
2002083 ATAATGTATCGATACAATGTGC-CATGTATCGAA
1 ATAATGTATCGATACAAT-T-CTCATGTATCGAA
2002116 ATAA
1 ATAA
2002120 ATAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 31 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (32 bp):
ATAATGTATCGATACAATTCTCATGTATCGAA
Found at i:2002195 original size:19 final size:20
Alignment explanation
Indices: 2002148--2002201 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
2002138 CTGCCAGTTT
**
2002148 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
2002168 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
2002187 CATGCATCGATACAA
1 CATGTATCGATACAA
2002202 AGCATAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:2004392 original size:33 final size:32
Alignment explanation
Indices: 2004335--2004399 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
2004325 CATTAGAAGC
*
2004335 AATGTATCGATACAATTCATCATGTCTCGATAT
1 AATGTATCGATACAATTCA-CATGTATCGATAT
2004368 AATGTATCGATACAATGTGC-CATGTATCGATA
1 AATGTATCGATACAAT-T-CACATGTATCGATA
2004400 CAAACAGCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (32 bp):
AATGTATCGATACAATTCACATGTATCGATAT
Found at i:2006475 original size:80 final size:79
Alignment explanation
Indices: 2006364--2006561 Score: 270
Period size: 79 Copynumber: 2.5 Consensus size: 79
2006354 CTGACTATGG
* * *
2006364 AAAATCGGTGTTCTAGAAATAAAATTAGGGTTGGAGTATCCCCTTGAAAATAATGGGGTTGGAGT
1 AAAATCGGTGTTCTAGAAATAAAATTAGGGTTGGAGTAT-CCCTCGAAAATAACGGAGTTGGAGT
*
2006429 ATCTCCGAGTGTGAA
65 ATCCCCGAGTGTGAA
* * *
2006444 AAAATCGGTGTTCTGGAAATAAAACTGGGGTTGGAGTATCCCTCGAAAATAACGGAGTTGGAGTA
1 AAAATCGGTGTTCTAGAAATAAAATTAGGGTTGGAGTATCCCTCGAAAATAACGGAGTTGGAGTA
*
2006509 TCCCCGATTGTGAA
66 TCCCCGAGTGTGAA
* ** * *
2006523 AAGATTAGTGTTTTAGAAATGAAATTAGGGTTGGAGTAT
1 AAAATCGGTGTTCTAGAAATAAAATTAGGGTTGGAGTAT
2006562 TCCCAATTGT
Statistics
Matches: 102, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 66 0.65
80 36 0.35
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.29
Consensus pattern (79 bp):
AAAATCGGTGTTCTAGAAATAAAATTAGGGTTGGAGTATCCCTCGAAAATAACGGAGTTGGAGTA
TCCCCGAGTGTGAA
Found at i:2008446 original size:49 final size:50
Alignment explanation
Indices: 2008369--2008502 Score: 207
Period size: 49 Copynumber: 2.7 Consensus size: 50
2008359 AAAAATACCT
* * * *
2008369 GAATATATCGATACATTGAAAAATGTATCGATACATCTGGGT-AAGCCCA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCCA
2008418 GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCCA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCCA
* *
2008468 AAATGTATCGATACAATGAACAATGTATCGTTACA
1 GAATGTATCGATACAATGAACAATGTATCGATACA
2008503 AATTGTGAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 39 0.50
50 39 0.50
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (50 bp):
GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCCA
Found at i:2008491 original size:50 final size:49
Alignment explanation
Indices: 2008374--2008502 Score: 204
Period size: 50 Copynumber: 2.6 Consensus size: 49
2008364 TACCTGAATA
* * * *
2008374 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAGCCCAGAATG
1 TATCGATACAATGAACAATGTATCGATACATCTGGGTAAACCCAAAATG
2008423 TATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCCAAAATG
1 TATCGATACAATGAACAATGTATCGATACATCTGGGT-AAACCCAAAATG
*
2008473 TATCGATACAATGAACAATGTATCGTTACA
1 TATCGATACAATGAACAATGTATCGATACA
2008503 AATTGTGAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 35 0.47
50 39 0.53
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (49 bp):
TATCGATACAATGAACAATGTATCGATACATCTGGGTAAACCCAAAATG
Found at i:2010342 original size:20 final size:20
Alignment explanation
Indices: 2010317--2010355 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2010307 TATTTGAGAC
2010317 ATGTATCGACACATTCACTT
1 ATGTATCGACACATTCACTT
* *
2010337 ATGTATTGATACATTCACT
1 ATGTATCGACACATTCACT
2010356 AGTTTTATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGTATCGACACATTCACTT
Found at i:2011362 original size:20 final size:20
Alignment explanation
Indices: 2011312--2011365 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2011302 TTTACCCAGA
* *
2011312 TGTATCGATAAACTGTTCAT
1 TGTATCGATACATTGTTCAT
2011332 TGTATCGATACATTGTTCAT
1 TGTATCGATACATTGTTCAT
2011352 TGTATCGATACATT
1 TGTATCGATACATT
2011366 CTAGGTTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTGTTCAT
Found at i:2011413 original size:69 final size:70
Alignment explanation
Indices: 2011269--2011414 Score: 240
Period size: 69 Copynumber: 2.1 Consensus size: 70
2011259 ATTTGTATTA
* *
2011269 ATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATAAACTGTTCATTG
1 ATACATTGTTCATTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATAAACTGTTCAATG
2011334 TATCG
66 TATCG
* * *
2011339 ATACATTGTTCATTGTATCGATACATTCTAGG-TTTACCCAGATGTATCGATACATTTTTCAATG
1 ATACATTGTTCATTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATAAACTGTTCAATG
2011403 TATCG
66 TATCG
2011408 ATACATT
1 ATACATT
2011415 CAGGCATTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
69 40 0.56
70 31 0.44
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (70 bp):
ATACATTGTTCATTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATAAACTGTTCAATG
TATCG
Found at i:2013129 original size:130 final size:126
Alignment explanation
Indices: 2012908--2013307 Score: 463
Period size: 130 Copynumber: 3.1 Consensus size: 126
2012898 ATTTTTAATC
* * * *
2012908 TCGGGG-TACTCCAA-CCCTGGTTTTATATCCAAAACATCAATTTTTTATAATCGGGGATACTCC
1 TCGGGGATACTCCAACCCCT-ATTTTATTTCTAAAACACCAATTTTTTA-AATCGGGGATACTCC
* *
2012971 AATCTCCTTATTTCTGAGGGAATACTCCAACCCTGGCTTTATTTCTAAAATATTGATTTTTCACA
64 AATC-CCTTATTTCCGAGAG-ATACTCCAACCC-GGCTTTATTTCTAAAATATTGATTTTTCACA
2013036 A
126 A
* * * *
2013037 TCGGGGATACTCTAACCCCTATTTTATTTCTAAAACACCAATCTTTTCACAATCGAGGATACTCT
1 TCGGGGATACTCCAACCCCTATTTTATTTCTAAAACACCAAT-TTTTTA-AATCGGGGATACTCC
* * *
2013102 AATCCCATTATTTCCGAGAGATGCTCCAACCCCAGCTTTATTTCTAAAATATTGATTTCTCACAA
64 AATCCC-TTATTTCCGAGAGATACTCCAA-CCCGGCTTTATTTCTAAAATATTGATTTTTCACAA
2013167 TCGGGGATACTCCAACCCCTA---T-TTT-TAAAACACCAATTTTTTAAATCGGGGATACTCCAA
1 TCGGGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATTTTTTAAATCGGGGATACTCCAA
* * * ** **
2013227 CCCCGTTATTTTCGAGAGGATACTCCAGTCCCGGCCGTATTTCTAAAGCATTGATTTTTCACAA
66 TCCC-TTATTTCCGAGA-GATACTCCA-ACCCGGCTTTATTTCTAAAATATTGATTTTTCACAA
2013291 TCGGGGATACTCCAACC
1 TCGGGGATACTCCAACC
2013308 TCGTTATTTT
Statistics
Matches: 235, Mismatches: 29, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
123 29 0.12
124 59 0.25
125 12 0.05
126 3 0.01
127 1 0.00
129 6 0.03
130 85 0.36
131 40 0.17
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (126 bp):
TCGGGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATTTTTTAAATCGGGGATACTCCAA
TCCCTTATTTCCGAGAGATACTCCAACCCGGCTTTATTTCTAAAATATTGATTTTTCACAA
Found at i:2013365 original size:79 final size:80
Alignment explanation
Indices: 2013186--2013392 Score: 208
Period size: 80 Copynumber: 2.6 Consensus size: 80
2013176 CTCCAACCCC
* **
2013186 TATTTTTAAAACACCAATTTTT-TA-AATCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATA
1 TATTTCTAAAACACTGATTTTTCTACAATCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATA
** *
2013249 CTCCAGTCCCGGCCG
66 CTCCAACCCCGACCG
* * * **
2013264 TATTTCTAAAGCATTGATTTTTC-ACAATCGGGGATACTCCAACCTCGTTATTTTTTAGAGAGAT
1 TATTTCTAAAACACTGATTTTTCTACAATCGGGGATACTCCAACCCCGTTATTTTCGAGAG-GAT
* ***
2013328 ACTTCAACCCCGATTT
65 ACTCCAACCCCGACCG
* *
2013344 TAGTTTC-AAAACACTGA-TTTTCTATAATCGGGGATACTCCAGCCCCGTT
1 TA-TTTCTAAAACACTGATTTTTCTACAATCGGGGATACTCCAACCCCGTT
2013393 GTTATCCCCA
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
78 18 0.17
79 37 0.36
80 45 0.43
81 4 0.04
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (80 bp):
TATTTCTAAAACACTGATTTTTCTACAATCGGGGATACTCCAACCCCGTTATTTTCGAGAGGATA
CTCCAACCCCGACCG
Found at i:2022527 original size:166 final size:164
Alignment explanation
Indices: 2022168--2022608 Score: 435
Period size: 166 Copynumber: 2.7 Consensus size: 164
2022158 GATAAGGGAC
* * * * * * *
2022168 ATTTCAA-AGAAAAATCAAAAACTTATGAAAATGAATTAATTTTTTAAAACTGATTTAATTTGAA
1 ATTTCAAGAAAAAAATGAAAAATTTATGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAA
* * * * * * *** **
2022232 TCAAATGACA-GTATTTCATGAGTTTTAAAAATCAAAAACCAAGAAAAATCTTTCTGAAAATTTA
66 TTAAAT-AAATATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAATTTA
* * *
2022296 TGAAGTAGAAAACTTCGTATTTTAGAAATGAGAAA
130 CGAAGTAGAAAACTTCATATTTTAGAAAAGAGAAA
* * * * ** * *
2022331 ATTTTAAGAAAAAATTGAAACATTTATGAAAAT-AAGTGAGTTTTTGCAAATTGATTTAATAT-A
1 ATTTCAAGAAAAAAATGAAAAATTTATGAAAATGAA-TGAATTTTTAAAAACTAATTTAATATGA
* *
2022394 GATTAAAT-AATAATATTTGGTGAATTTTAAAAATTAAAAACTAAGAAAAATCCCCCCAAAAATA
65 -ATTAAATAAAT-ATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAAT-
* * *
2022458 ATTACGAAGTAGAAAACTTTATATTTTTGAAACAGAG-GA
127 -TTACGAAGTAGAAAACTTCATATTTTAGAAA-AGAGAAA
2022497 ATTTCAAGAAAAAAATGAAAAATTTATGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAA
1 ATTTCAAGAAAAAAATGAAAAATTTATGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAA
* * *
2022562 TTAAATAAATATATTTGATGAATTTAAAAAATTTTAAAACCATGAAA
66 TTAAATAAATATATTTGATGAATTTTAAAAA-TTAAAAACCAAGAAA
2022609 TCCTTTCAAA
Statistics
Matches: 222, Mismatches: 44, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
162 1 0.00
163 9 0.04
164 86 0.39
166 105 0.47
167 21 0.09
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (164 bp):
ATTTCAAGAAAAAAATGAAAAATTTATGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAA
TTAAATAAATATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAATTTAC
GAAGTAGAAAACTTCATATTTTAGAAAAGAGAAA
Found at i:2029406 original size:61 final size:61
Alignment explanation
Indices: 2029331--2029469 Score: 224
Period size: 61 Copynumber: 2.3 Consensus size: 61
2029321 TAGCAGTTTG
* * *
2029331 TAATCTGAGCTTTATGGTCATGTTTTTTTTGGTTGCAATGTAGAACATAACCTAAATGAAA
1 TAATCTGAGCTTTATGGTCAAGTTTTTGTTGGTTGCAATATAGAACATAACCTAAATGAAA
* *
2029392 TAATCTGAGCTTTATGGTCAAGTTTTTGTTGGTTGCAATATGGAACATAACCTAAATTAAA
1 TAATCTGAGCTTTATGGTCAAGTTTTTGTTGGTTGCAATATAGAACATAACCTAAATGAAA
2029453 TAATCTGAGCTTCTATG
1 TAATCTGAGCTT-TATG
2029470 TTTATTTCTT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
61 68 0.94
62 4 0.06
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (61 bp):
TAATCTGAGCTTTATGGTCAAGTTTTTGTTGGTTGCAATATAGAACATAACCTAAATGAAA
Found at i:2032682 original size:12 final size:12
Alignment explanation
Indices: 2032665--2032689 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2032655 AGAGTGTTTG
2032665 AAAAAAAAAATT
1 AAAAAAAAAATT
2032677 AAAAAAAAAATT
1 AAAAAAAAAATT
2032689 A
1 A
2032690 TCCAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAAAAATT
Found at i:2032720 original size:21 final size:21
Alignment explanation
Indices: 2032694--2032774 Score: 110
Period size: 21 Copynumber: 3.9 Consensus size: 21
2032684 AAATTATCCA
2032694 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2032715 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
** *
2032736 AATGTATCGATACA-TCCTACA
1 AATGTATCGATACATTTGTA-G
2032757 AATGTATCGATACATTTG
1 AATGTATCGATACATTTG
2032775 GATAATTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.04
21 48 0.94
22 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2032794 original size:12 final size:12
Alignment explanation
Indices: 2032777--2032811 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2032767 TACATTTGGA
2032777 TAATTTTTTTTT
1 TAATTTTTTTTT
2032789 TAA--TTTTTTT
1 TAATTTTTTTTT
2032799 TAATTTTTTTTT
1 TAATTTTTTTTT
2032811 T
1 T
2032812 CAAACACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.48
12 11 0.52
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TAATTTTTTTTT
Found at i:2032795 original size:10 final size:10
Alignment explanation
Indices: 2032782--2032809 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2032772 TTGGATAATT
2032782 TTTTTTTTAA
1 TTTTTTTTAA
2032792 TTTTTTTTAA
1 TTTTTTTTAA
2032802 TTTTTTTT
1 TTTTTTTT
2032810 TTCAAACACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:2032901 original size:19 final size:19
Alignment explanation
Indices: 2032877--2032976 Score: 107
Period size: 19 Copynumber: 5.9 Consensus size: 19
2032867 AATTCAACAA
2032877 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2032896 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2032911 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2032928 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2032943 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2032960 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2032977 TTAGCTACTG
Statistics
Matches: 69, Mismatches: 0, Indels: 24
0.74 0.00 0.26
Matches are distributed among these distances:
13 22 0.32
15 4 0.06
17 4 0.06
19 39 0.57
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2032916 original size:13 final size:13
Alignment explanation
Indices: 2032898--2032954 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
2032888 ACATAAGTTT
2032898 TGTATCGATACAA
1 TGTATCGATACAA
2032911 TGTATCGATACATAA
1 TGTATCGATAC--AA
2032926 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
2032943 TGTATCGATACA
1 TGTATCGATACA
2032955 TAAGTATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2032920 original size:32 final size:32
Alignment explanation
Indices: 2032879--2032973 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
2032869 TTCAACAATT
2032879 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
2032911 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
2032943 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTTTTGTATCGATACA
2032974 TAATTAGCTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:2033034 original size:13 final size:13
Alignment explanation
Indices: 2033016--2033041 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2033006 CATTTTTCTG
2033016 TGTATCGATACAT
1 TGTATCGATACAT
2033029 TGTATCGATACAT
1 TGTATCGATACAT
2033042 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2033038 original size:33 final size:33
Alignment explanation
Indices: 2032996--2033062 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2032986 GCCAAGGAAA
***
2032996 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2033029 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2033062 T
1 T
2033063 TTACAATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2035493 original size:54 final size:51
Alignment explanation
Indices: 2035361--2035704 Score: 171
Period size: 51 Copynumber: 6.6 Consensus size: 51
2035351 TTGAGTTGCT
* * * * *
2035361 CAATTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACAT
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* * *
2035412 TAATT-TTCTATAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAAACAC
1 CAATTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACAC
* * * * ** * *
2035465 CAATTTCTTCACAATCGGGGACACTCCAACCCCG--TTAATCATCGGGGATACTC
1 CAA-TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC--CAAAACAC
** *** * * *
2035518 CAACCCCGTT-ATTTTCGAGGGGATACTCCAAC-CTCGACTTTATTTCCAAAATAT
1 CAA-TTC-TTCACAATC--GGGGATACTCCAACTC-CGATTTTATTTCCAAAACAC
** * * * * *
2035572 TGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* * *
2035623 CAATT-TTC-CTTTAATTGGGGATACTCCAACACCGATTTTATTTCCAAAAATAC
1 CAATTCTTCAC---AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACAC
* *
2035676 CAATTTTTCACAATCGAGGATACTCCAAC
1 CAATTCTTCACAATCGGGGATACTCCAAC
2035705 CTCGTTATTT
Statistics
Matches: 215, Mismatches: 56, Indels: 43
0.68 0.18 0.14
Matches are distributed among these distances:
50 5 0.02
51 66 0.31
52 52 0.24
53 36 0.17
54 31 0.14
55 19 0.09
56 2 0.01
57 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
Found at i:2035548 original size:28 final size:27
Alignment explanation
Indices: 2035478--2035550 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
2035468 TTTCTTCACA
*
2035478 ATCGGGGACACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
2035505 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
2035531 TTCGAGGGGATACTCCAACC
1 ATC--GGGGATACTCCAACC
2035551 TCGACTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 4 0.10
27 22 0.54
28 15 0.37
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.22
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:2035596 original size:51 final size:51
Alignment explanation
Indices: 2035536--2035708 Score: 195
Period size: 52 Copynumber: 3.4 Consensus size: 51
2035526 TTATTTTCGA
* ***
2035536 GGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTCATAATC
* * * * * * *
2035587 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATT
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTC-ATAATC
*
2035639 GGGGATACTCCAACAC-CGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAAC-CTCGATTTTATTTCC-AAAATACCAATTTTTCATAATC
*
2035691 GAGGATACTCCAACCTCG
1 GGGGATACTCCAACCTCG
2035709 TTATTTCATC
Statistics
Matches: 99, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
51 37 0.37
52 47 0.47
53 15 0.15
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:2035724 original size:28 final size:28
Alignment explanation
Indices: 2035688--2035769 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
2035678 ATTTTTCACA
* *
2035688 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
2035716 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
2035744 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCCGTTATT
2035770 ATCTCCAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 42 0.89
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:2035759 original size:211 final size:211
Alignment explanation
Indices: 2035372--2035761 Score: 577
Period size: 211 Copynumber: 1.8 Consensus size: 211
2035362 AATTCTCCAC
* * **
2035372 AATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACATTAATTTTCTATAATCGGGGATACTC
1 AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* * *
2035437 CAACTCTGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
* * * *
2035502 ATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCGACTTTATTTCCAA
131 ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCTCGACTTTATTTCCAA
2035567 AATATTGATTTTTCAT
196 AATATTGATTTTTCAT
* * * *
2035583 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATTGGGGATACT
1 AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACT
* * *
2035648 CCAACACCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCGTT
65 CCAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTT
*
2035711 ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACC
130 A-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACC
2035762 CCGTTATTAT
Statistics
Matches: 158, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
210 27 0.17
211 98 0.62
212 33 0.21
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (211 bp):
AATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCTCGACTTTATTTCCAA
AATATTGATTTTTCAT
Found at i:2038235 original size:19 final size:20
Alignment explanation
Indices: 2038211--2038263 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
2038201 ATCGATATAA
**
2038211 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGGACAAT
2038230 TGTATCGATACATGGACAAT
1 TGTATCGATACATGGACAAT
*
2038250 TGTATCAATACATG
1 TGTATCGATACATG
2038264 AAACTGGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGGACAAT
Found at i:2038238 original size:32 final size:33
Alignment explanation
Indices: 2038178--2038239 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2038168 CACACCCAGG
*
2038178 TGTATCGATACATTATGCTTTGTATCGATATAA
1 TGTATCGATACATTATGCATTGTATCGATATAA
2038211 TGTATCGATACATGT-T-CATTGTATCGATA
1 TGTATCGATACAT-TATGCATTGTATCGATA
2038240 CATGGACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTATGCATTGTATCGATATAA
Found at i:2038317 original size:20 final size:19
Alignment explanation
Indices: 2038292--2038345 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
2038282 CTACCACTGT
2038292 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
2038312 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGA-GAA
2038332 TTGTATCGATACAT
1 TTGTATCGATACAT
2038346 TGCTTCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:2044631 original size:21 final size:21
Alignment explanation
Indices: 2044593--2044632 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2044583 ATCAAATCTT
* *
2044593 CTTCAAATTTCTTAATTTTCA
1 CTTCAAAATACTTAATTTTCA
*
2044614 CTTCAAAATACTTCATTTT
1 CTTCAAAATACTTAATTTT
2044633 TCATCAAAAT
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:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (21 bp):
CTTCAAAATACTTAATTTTCA
Found at i:2046387 original size:21 final size:23
Alignment explanation
Indices: 2046344--2046395 Score: 81
Period size: 21 Copynumber: 2.3 Consensus size: 23
2046334 TTGAAAATAA
2046344 TTTTTTATCAAAGGGGGAGAAATT
1 TTTTTTATCAAA-GGGGAGAAATT
2046368 TTTTTTATCAAA-GGGA-AAATT
1 TTTTTTATCAAAGGGGAGAAATT
2046389 TTTTTTA
1 TTTTTTA
2046396 ATGAAAGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.43
22 4 0.14
24 12 0.43
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (23 bp):
TTTTTTATCAAAGGGGAGAAATT
Found at i:2048739 original size:79 final size:80
Alignment explanation
Indices: 2048588--2048740 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 80
2048578 CTTCTCCCGA
* * *** * *
2048588 TGAAAATTTTGATATTTTGGAAATAAAATTGGGGTTGGAGTATCCTATCAGAAATAATGGGGTTG
1 TGAAAATTTTGATATTTTGGAAATAAAACTGAGGTTGGAGTATCCTATCAGAAATAACAAGCTTA
*
2048653 GAGTATCCCCAATGG
66 GAATATCCCCAATGG
*
2048668 TGAAAA-TTTGATATTTTGGAAATAAAACTGAGGTTGGAGTATCCCT-TCGGAAATAACAAGCTT
1 TGAAAATTTTGATATTTTGGAAATAAAACTGAGGTTGGAGTAT-CCTATCAGAAATAACAAGCTT
2048731 AGAATATCCC
65 AGAATATCCC
2048741 TAAATGCTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
79 54 0.86
80 9 0.14
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (80 bp):
TGAAAATTTTGATATTTTGGAAATAAAACTGAGGTTGGAGTATCCTATCAGAAATAACAAGCTTA
GAATATCCCCAATGG
Found at i:2048817 original size:28 final size:28
Alignment explanation
Indices: 2048784--2048838 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2048774 ACCAGAGTTC
* *
2048784 GAGTATTCCTTCAAAAATAACGGGGTTA
1 GAGTATCCCCTCAAAAATAACGGGGTTA
* *
2048812 GAGTATCCCCTCATAACTAACGGGGTT
1 GAGTATCCCCTCAAAAATAACGGGGTT
2048839 GAAATATTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (28 bp):
GAGTATCCCCTCAAAAATAACGGGGTTA
Found at i:2050061 original size:5 final size:5
Alignment explanation
Indices: 2050051--2050075 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2050041 ACATTTTTAT
2050051 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
2050076 AAACTAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:2051563 original size:13 final size:13
Alignment explanation
Indices: 2051545--2051570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2051535 TACAGCAAGT
2051545 ATGTATCGATACA
1 ATGTATCGATACA
2051558 ATGTATCGATACA
1 ATGTATCGATACA
2051571 CAAAAAATTG
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:2051655 original size:20 final size:21
Alignment explanation
Indices: 2051625--2051663 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2051615 CTATATTTTC
2051625 AAATATGTATCGATACATTAA
1 AAATATGTATCGATACATTAA
2051646 AAAT-TGTATCGATACATT
1 AAATATGTATCGATACATT
2051664 TACACGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
AAATATGTATCGATACATTAA
Found at i:2055665 original size:15 final size:15
Alignment explanation
Indices: 2055645--2055675 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2055635 TAAAAATGTC
*
2055645 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2055660 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2055675 C
1 C
2055676 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2061914 original size:65 final size:68
Alignment explanation
Indices: 2061801--2061941 Score: 180
Period size: 65 Copynumber: 2.1 Consensus size: 68
2061791 AGGCTTTTTA
* * *
2061801 AAAAGAAAAAGAAAAAGGAGTCCTGCTCTTTAAGGACTAGAAGTTGCCACCAGCTTGTGTGGGCT
1 AAAAGAAAAAGAAAAAGGAGTCCTACTCTTTAAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCT
2061866 T-T
66 TCT
* * * * *
2061868 AAAAGAAAAA-AGAAA-GTGTCCTACTCTTTGAGGGCTAAAAGGTGCCACTAGCTTGTGTGGGCT
1 AAAAGAAAAAGAAAAAGGAGTCCTACTCTTTAAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCT
2061931 TCT
66 TCT
*
2061934 AAAGGAAA
1 AAAAGAAA
2061942 GTGTCCTGCT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
65 42 0.66
66 12 0.19
67 10 0.16
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (68 bp):
AAAAGAAAAAGAAAAAGGAGTCCTACTCTTTAAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCT
TCT
Found at i:2062037 original size:61 final size:60
Alignment explanation
Indices: 2061886--2062401 Score: 498
Period size: 61 Copynumber: 8.4 Consensus size: 60
2061876 AAAGAAAGTG
* * * *
2061886 TCCTACTCTTTGAGGGCTAAAAGGTGCCACTAGCTTGTGTGGGCTTCT-AAAGGAAAGTG--
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTT-TAAAAGGAAAG-GCA
* * * * * *
2061945 TCCTGCTTTTTTAGGACTAAAAGGTGTCACCAACTTATGTGGGTTTTTAAAAGGGAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGG-CTTTAAAAGGAAAGGCA
* * * *
2062006 TCTTGCTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGTGCTTTGAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGCA
* * * * * *
2062067 TCTTGCTCTTTGAGGAATAAAAAATGGTGCCACTAACTTATGTTGGCTTTAAAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACT--AAAA-GGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAGGCA
** * * * * * *
2062131 TCCTATTCTTTGAAGATTGAAAGTTGCCACCAACTTGTGTAGGCTTTGAAAGGAAATGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA-GGCA
* * * * *
2062192 TCATACTCTTTGAAGACTAACAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGCA
* * * *
2062253 TCCCGCTCTTTGAGGAATAAAAAAGAGTGCCACTAACTTTTGTGGGCTTTAAAAGGGAAAGGCA
1 TCCTGCTCTTTGAGGACT--AAAAG-GTGCCACCAACTTGTGTGGGCTTTAAAA-GGAAAGGCA
* * * **
2062317 TCCTACTCTTTGAGGACCAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGCA
2062378 TCCTGCTCTTTGAGGACTAAAAGG
1 TCCTGCTCTTTGAGGACTAAAAGG
2062402 ATAAAAAGTT
Statistics
Matches: 372, Mismatches: 69, Indels: 30
0.79 0.15 0.06
Matches are distributed among these distances:
59 37 0.10
60 28 0.08
61 196 0.53
62 11 0.03
63 8 0.02
64 85 0.23
65 7 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCA
Found at i:2062159 original size:125 final size:121
Alignment explanation
Indices: 2061962--2062400 Score: 412
Period size: 125 Copynumber: 3.5 Consensus size: 121
2061952 TTTTTAGGAC
* * * * * *
2061962 TAAAAGGTGTCACCAACTTATGTGGGTTTTTAAAAGGGAAGGCATCTTGCTCTTTGAGGACTAAA
1 TAAAAGGTGCCACCAACTTATGTGGG-CTTTAAAAGGAAAGGCATCCTACTCTTTGAAGACTAAA
* * *
2062027 AGATGCCACCAACTTGTGT-GTGCTTTGAAAGGAAAAGGCATCTTGCTCTTTGAGGAA
65 AGATGCCACCAACTTGTGTAG-GCTTTGAAAGGAAAAGGCATCATACTCTTTGAAGAA
* * * * *
2062084 TAAAAAATGGTGCCACTAACTTATGTTGGCTTTAAAAAGGAAAGGCGTCCTATTCTTTGAAGATT
1 T--AAAA-GGTGCCACCAACTTATGTGGGCTTT-AAAAGGAAAGGCATCCTACTCTTTGAAGACT
* * * *
2062149 GAAAGTTGCCACCAACTTGTGTAGGCTTTGAAAGGAAATGGCATCATACTCTTTGAAGAC
62 AAAAGATGCCACCAACTTGTGTAGGCTTTGAAAGGAAAAGGCATCATACTCTTTGAAGAA
* * * ** * *
2062209 TAACAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCCATCCCGCTCTTTGAGGAATAAA
1 TAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGG-AAAGGCATCCTACTCTTTGAAGACT--A
* * * * * * * *
2062274 AAAGAGTGCCACTAACTTTTGTGGGCTTTAAAAGGGAAAGGCATCCTACTCTTTGAGGAC
63 AAAGA-TGCCACCAACTTGTGTAGGCTTTGAAAGGAAAAGGCATCATACTCTTTGAAGAA
* * * ** * *
2062334 CAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGTGTCCTGCTCTTTGAGGACTAAA
1 TAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGG-AAAGGCATCCTACTCTTTGAAGACTAAA
2062399 AG
65 AG
2062401 GATAAAAAGT
Statistics
Matches: 261, Mismatches: 47, Indels: 17
0.80 0.14 0.05
Matches are distributed among these distances:
121 6 0.02
122 41 0.16
123 8 0.03
124 11 0.04
125 194 0.74
126 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (121 bp):
TAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAGGCATCCTACTCTTTGAAGACTAAAA
GATGCCACCAACTTGTGTAGGCTTTGAAAGGAAAAGGCATCATACTCTTTGAAGAA
Found at i:2062222 original size:186 final size:185
Alignment explanation
Indices: 2061826--2062400 Score: 547
Period size: 186 Copynumber: 3.1 Consensus size: 185
2061816 AGGAGTCCTG
* * * * ** *
2061826 CTCTTT-AAGGACTAGAAGTTGCCACCAGCTTGTGTGGGCTTTAAAAGAAAAAAGAAAGTGTCCT
1 CTCTTTGAA-GACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAG-GAAAAGCCA---TCCC
* ** * *
2061890 ACTCTTTGAGGGCT--AAAAG-GTGCCACTAGCTTGTGTGGGCTTCT--AAAGGAAAGTG--TCC
61 GCTCTTTGAGGAATAAAAAAGAGTGCCACTAACTTATGTGGGCTT-TAAAAAGGAAAG-GCATCC
* * * * * * * * * * * * *
2061948 TGCTTTTTTAGGACTAAAAGGTGTCACCAACTTATGTGGGTTTTTAAAAGGGAAGGCATCTTG
124 TACTCTTTGAAGACCAAAAGGTGCCACCAACTTGTGTAGG-CTTTGAAAGGAAAGGCATCATA
* * * * **
2062011 CTCTTTGAGGACTAAAAGATGCCACCAACTTGTGTGTGCTTTGAAAGGAAAAGGCATCTTGCTCT
1 CTCTTTGAAGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCCATCCCGCTCT
* * *
2062076 TTGAGGAATAAAAAATG-GTGCCACTAACTTATGTTGGCTTTAAAAAGGAAAGGCGTCCTATTCT
66 TTGAGGAATAAAAAA-GAGTGCCACTAACTTATGTGGGCTTTAAAAAGGAAAGGCATCCTACTCT
*** *
2062140 TTGAAGATTGAAAGTTGCCACCAACTTGTGTAGGCTTTGAAAGGAAATGGCATCATA
130 TTGAAGACCAAAAGGTGCCACCAACTTGTGTAGGCTTTGAAAGGAAA-GGCATCATA
* *
2062197 CTCTTTGAAGACTAACAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCCATCCCGCTCT
1 CTCTTTGAAGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCCATCCCGCTCT
* *
2062262 TTGAGGAATAAAAAAGAGTGCCACTAACTTTTGTGGGCTTTAAAAGGGAAAGGCATCCTACTCTT
66 TTGAGGAATAAAAAAGAGTGCCACTAACTTATGTGGGCTTTAAAAAGGAAAGGCATCCTACTCTT
* * ** * *
2062327 TGAGGACCAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGTGTCCTG
131 TGAAGACCAAAAGGTGCCACCAACTTGTGTAGGCTTTGAAAGG-AAAGGCATCATA
*
2062383 CTCTTTGAGGACTAAAAG
1 CTCTTTGAAGACTAAAAG
2062401 GATAAAAAGT
Statistics
Matches: 322, Mismatches: 57, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
181 14 0.04
183 5 0.02
184 28 0.09
185 59 0.18
186 213 0.66
187 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (185 bp):
CTCTTTGAAGACTAAAAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCCATCCCGCTCT
TTGAGGAATAAAAAAGAGTGCCACTAACTTATGTGGGCTTTAAAAAGGAAAGGCATCCTACTCTT
TGAAGACCAAAAGGTGCCACCAACTTGTGTAGGCTTTGAAAGGAAAGGCATCATA
Found at i:2069094 original size:52 final size:51
Alignment explanation
Indices: 2069016--2069165 Score: 237
Period size: 52 Copynumber: 2.9 Consensus size: 51
2069006 CGAAATATGA
2069016 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
2069068 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
2069120 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACAT
2069166 TTAAGTGATG
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:2070721 original size:79 final size:79
Alignment explanation
Indices: 2070583--2071196 Score: 549
Period size: 79 Copynumber: 7.8 Consensus size: 79
2070573 TTGGAATATT
* *
2070583 CCCTCAAAGATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGCTTTAGAAATAAAATC
1 CCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATC
*
2070648 GGGGTTAGAGTATT
66 GGGGTTAGAGTATC
* * * ** * *
2070662 CCTTCAAAAATAACGGGGTTGGAATATCCTCGATAATGAAAAATCGATATTTTAAAAATAAAATC
1 CCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATC
** * * *
2070727 GAAGTTGGAGTGTT
66 GGGGTTAGAGTATC
* ** * * *
2070741 CCCTCAGAAATAAAAGGGTTGGAGTATGCCCAATGGTGAAAAATCG-TGTTTTAGAAATAAAACC
1 CCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATC
2070805 GGGGTTAGAGTATC
66 GGGGTTAGAGTATC
** * ** * * *
2070819 CCCTTGAAATTAACTAGGTAGAAGTAT-CCCGATGATGAAAAATC-AGTGTTTTAGAAATAAAAT
1 CCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGA-TGTTTTAGAAATAAAAT
** *
2070882 TAGGGCTAGAGTATC
65 CGGGGTTAGAGTATC
* * * ** * * *
2070897 CCCTCAAAAA-AATGAGGTTGGAGTATCCCCAATCATGGAAAATCGATATTTTAGAAATAAAACC
1 CCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATC
** * *
2070961 AAGGTTGGAGTGTC
66 GGGGTTAGAGTATC
* * * * * * *
2070975 CCCTCAAAAATAACGGGGTTAGAGTATCCCCGTTCGTGGAAAATTGGTGTTTTAAAAATAAAA-C
1 CCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATC
2071039 TGGGGTTAGAGTATC
66 -GGGGTTAGAGTATC
** * * *
2071054 CCCTCAAAAATAACAAGGTTGAAGTATCCCCGATGGTGGAAAAT-TAGTGTTTTAGAAATAAAAT
1 CCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGA-TGTTTTAGAAATAAAAT
* *
2071118 CGAGGTTAAAGTATC
65 CGGGGTTAGAGTATC
** * * * * * *
2071133 CTTTTAGAAATAATGGGGTTAGAGTATCCCC-ACTGGTGGAAAATCGATATTTTAGAAATAAAAT
1 CCCTCAAAAATAACGGGGTTGGAGTATCCCCGA-TGGTGAAAAATCGATGTTTTAGAAATAAAAT
2071197 ATCAATGAAA
Statistics
Matches: 426, Mismatches: 99, Indels: 20
0.78 0.18 0.04
Matches are distributed among these distances:
77 27 0.06
78 128 0.30
79 269 0.63
80 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (79 bp):
CCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAATC
GGGGTTAGAGTATC
Found at i:2071161 original size:28 final size:30
Alignment explanation
Indices: 2071103--2071161 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
2071093 AAAATTAGTG
2071103 TTTTAGAAATAAAATCGAGGTTAAAGTATCC
1 TTTTAGAAAT-AAATCGAGGTTAAAGTATCC
* *
2071134 TTTTAGAAAT-AAT-GGGGTTAGAGTATCC
1 TTTTAGAAATAAATCGAGGTTAAAGTATCC
2071162 CCACTGGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 3 0.12
31 10 0.38
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (30 bp):
TTTTAGAAATAAATCGAGGTTAAAGTATCC
Found at i:2073679 original size:13 final size:13
Alignment explanation
Indices: 2073661--2073687 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2073651 ATTTTAGGCA
2073661 TGTATCAATACAT
1 TGTATCAATACAT
2073674 TGTATCAATACAT
1 TGTATCAATACAT
2073687 T
1 T
2073688 TACTATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:2074567 original size:42 final size:42
Alignment explanation
Indices: 2074359--2074884 Score: 359
Period size: 42 Copynumber: 12.3 Consensus size: 42
2074349 AGGCATCCGA
* * * * * *
2074359 CTCTTTAAGGGCAAAGG-AAAAAGGAGAATAAAATGGGTCTTG
1 CTCTTTGAGGACAAAGGAAAAAAAGA-AATAAAGTGCGTCCTG
* *
2074401 CT-TCTTGAGGACAAAGG-AAAAAAGAAA-AAAGAAAGTGTCCTG
1 CTCT-TTGAGGACAAAGGAAAAAAAGAAATAAAG--TGCGTCCTG
* * * * *
2074443 CTAC-TTGACGACAAAGG-GAAAAGGGAATAAAGTGCGTCCTA
1 CT-CTTTGAGGACAAAGGAAAAAAAGAAATAAAGTGCGTCCTG
* * ** * *
2074484 CTTTTTAAGGACAAAAGGGAAAAAAAAGGAAACGAAGTGCATCCTA
1 CTCTTTGAGGAC-AAA-GG-AAAAAAA-GAAATAAAGTGCGTCCTG
* * *
2074530 CTCTTTGAGGACAAAGGAAAAAAAGAAATAAAATGCATCATG
1 CTCTTTGAGGACAAAGGAAAAAAAGAAATAAAGTGCGTCCTG
* * * * **
2074572 CTATTTGAGGACAAAAGAAAAAAGGAAATAAAGTGCATGTTG
1 CTCTTTGAGGACAAAGGAAAAAAAGAAATAAAGTGCGTCCTG
* * *
2074614 CTCTTTTAGGACAAAAAGAAAAAAAAGGAAATGAAGTGCGTCCTG
1 CTCTTTGAGGAC--AAAGGAAAAAAA-GAAATAAAGTGCGTCCTG
** * * *
2074659 CTCTTTGAGGGTAAAGGAAAAAAAGAAATGAAGTGCAT-CTT
1 CTCTTTGAGGACAAAGGAAAAAAAGAAATAAAGTGCGTCCTG
* * * * * *
2074700 CGTTTTTGAGGACAAAGGGAAAAGAAG-GA-AACGATGCATCCTA
1 C-TCTTTGAGGACAAA-GGAAAAAAAGAAATAAAG-TGCGTCCTG
* * * * *
2074743 TTCTTTGAGGACAAAAGGAAAAGAAGGAAATGAAGTACGTCTTG
1 CTCTTTGAGGAC-AAAGGAAAA-AAAGAAATAAAGTGCGTCCTG
2074787 CTCTTTGAGGACAAAGGAAAAAGAAGGAAATAAAGTGCGTCCTG
1 CTCTTTGAGGACAAAGGAAAAA-AA-GAAATAAAGTGCGTCCTG
* * * *
2074831 CTCTTTGAGGACAAAAGATAAAAAGAAATAAAGTGTGTCCTA
1 CTCTTTGAGGACAAAGGAAAAAAAGAAATAAAGTGCGTCCTG
2074873 CTCTTTGAGGAC
1 CTCTTTGAGGAC
2074885 CTAAAAGGTG
Statistics
Matches: 380, Mismatches: 79, Indels: 50
0.75 0.16 0.10
Matches are distributed among these distances:
40 3 0.01
41 22 0.06
42 184 0.48
43 52 0.14
44 63 0.17
45 32 0.08
46 24 0.06
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.20
Consensus pattern (42 bp):
CTCTTTGAGGACAAAGGAAAAAAAGAAATAAAGTGCGTCCTG
Found at i:2074574 original size:129 final size:129
Alignment explanation
Indices: 2074405--2074884 Score: 456
Period size: 129 Copynumber: 3.7 Consensus size: 129
2074395 GTCTTGCTTC
* * ** * * *
2074405 TTGAGGACAAAGG-AAAAAAGAAAAAAGAAAGTGTCCTGCTACTTGACGAC-AAAGGGAAAAGGG
1 TTGAGGACAAAGGAAAAAAAGAAATAA-AATGCATCCTGCTACTTGAGGACAAAAGAGAAAAGGA
* * * * *
2074468 AATAAAGTGCGTCCTACTTTTTAAGGACAAAAGGGAAAAAAAAGGAAACGAAGTGCATCCTACTC
65 AATAAAGTGCATCCTACTTTTTGAGGACAAAA-GGAAAAAAAAGGAAATGAAGTGCGTCCTGCTC
2074533 T
129 T
* * *
2074534 TTGAGGACAAAGGAAAAAAAGAAATAAAATGCATCATGCTATTTGAGGACAAAAGAAAAAAGGAA
1 TTGAGGACAAAGGAAAAAAAGAAATAAAATGCATCCTGCTACTTGAGGACAAAAGAGAAAAGGAA
** * *
2074599 ATAAAGTGCATGTTGCTCTTTT-AGGACAAAAAGAAAAAAAAGGAAATGAAGTGCGTCCTGCTCT
66 ATAAAGTGCATCCTACT-TTTTGAGGACAAAAGGAAAAAAAAGGAAATGAAGTGCGTCCTGCTCT
** * * * ** *
2074663 TTGAGGGTAAAGGAAAAAAAGAAATGAAGTGCAT-CTTCGTTTTTGAGGAC-AAAGGGAAAA-GA
1 TTGAGGACAAAGGAAAAAAAGAAATAAAATGCATCCTGC-TACTTGAGGACAAAAGAGAAAAGGA
** * * *
2074725 AGGAAACGATGCATCCTA-TTCTTTGAGGACAAAAGG-AAAAGAAGGAAATGAAGTACGTCTTGC
65 AATAAA-G-TGCATCCTACTT-TTTGAGGACAAAAGGAAAAAAAAGGAAATGAAGTGCGTCCTGC
2074788 TCT
127 TCT
* * * *
2074791 TTGAGGACAAAGGAAAAAGAAGGAAATAAAGTGCGTCCTGCT-CTTTGAGGACAAAAGATAAAAA
1 TTGAGGACAAAGGAAAAA-AA-GAAATAAAATGCATCCTGCTAC-TTGAGGACAAAAGAGAAAAG
** *
2074855 GAAATAAAGTGTGTCCTACTCTTTGAGGAC
63 GAAATAAAGTGCATCCTACTTTTTGAGGAC
2074885 CTAAAAGGTG
Statistics
Matches: 287, Mismatches: 49, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
127 7 0.02
128 58 0.20
129 117 0.41
130 82 0.29
131 17 0.06
132 6 0.02
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.20
Consensus pattern (129 bp):
TTGAGGACAAAGGAAAAAAAGAAATAAAATGCATCCTGCTACTTGAGGACAAAAGAGAAAAGGAA
ATAAAGTGCATCCTACTTTTTGAGGACAAAAGGAAAAAAAAGGAAATGAAGTGCGTCCTGCTCT
Found at i:2074794 original size:86 final size:85
Alignment explanation
Indices: 2074491--2074884 Score: 350
Period size: 86 Copynumber: 4.6 Consensus size: 85
2074481 CTACTTTTTA
* * *
2074491 AGGACAAAAGGGAAAAAAAAGGAAACGAAGTGCATCCTACTCTTTGAGGACAAAGG-AAAAAAAG
1 AGGACAAAA-GG--AAAAAAGGAAATGAAGTGCATCTTGCTCTTTGAGGACAAAGGAAAAAAAAG
* * * *
2074555 AAATAAAATGCATCATGCTATTTG
63 GAA-AAGATGCATCCTGCTCTTTG
* * * *
2074579 AGGACAAAA-GAAAAAAGGAAATAAAGTGCATGTTGCTCTTTTAGGACAAAAAGAAAAAAAAGGA
1 AGGACAAAAGGAAAAAAGGAAATGAAGTGCATCTTGCTCTTTGAGGAC-AAAGGAAAAAAAAGGA
* *
2074643 AATGAAGTGCGTCCTGCTCTTTG
65 AAAG-A-TGCATCCTGCTCTTTG
** * * * *
2074666 AGG-GTAAAGGAAAAAAAGAAATGAAGTGCATCTT-CGTTTTTGAGGACAAAGGGAAAAGAAGGA
1 AGGACAAAAGGAAAAAAGGAAATGAAGTGCATCTTGC-TCTTTGAGGACAAAGGAAAAAAAAGGA
* **
2074729 AACGATGCATCCTATTCTTTG
65 AAAGATGCATCCTGCTCTTTG
* * *
2074750 AGGACAAAAGGAAAAGAAGGAAATGAAGTACGTCTTGCTCTTTGAGGACAAAGGAAAAAGAAGGA
1 AGGACAAAAGGAAAA-AAGGAAATGAAGTGCATCTTGCTCTTTGAGGACAAAGGAAAAAAAAGGA
* *
2074815 AATAAAGTGCGTCCTGCTCTTTG
65 AA-AGA-TGCATCCTGCTCTTTG
* ** * *
2074838 AGGACAAAA-GATAAAAA-GAAATAAAGTGTGTCCTACTCTTTGAGGAC
1 AGGACAAAAGGA-AAAAAGGAAATGAAGTGCATCTTGCTCTTTGAGGAC
2074885 CTAAAAGGTG
Statistics
Matches: 250, Mismatches: 44, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
84 47 0.19
85 15 0.06
86 101 0.40
87 53 0.21
88 34 0.14
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.20
Consensus pattern (85 bp):
AGGACAAAAGGAAAAAAGGAAATGAAGTGCATCTTGCTCTTTGAGGACAAAGGAAAAAAAAGGAA
AAGATGCATCCTGCTCTTTG
Found at i:2074962 original size:60 final size:62
Alignment explanation
Indices: 2074868--2075016 Score: 194
Period size: 60 Copynumber: 2.4 Consensus size: 62
2074858 ATAAAGTGTG
* * **
2074868 TCCTACTCTTTGAGGACCTAAAAGGTGCCACCAACTTATGTGGGCTTTGGAAAGG-AAA-GCA
1 TCCTACTCTTTGAGGA-CTAAAAGGTGCCACCAACTTATGTAGGCATTAAAAAGGAAAAGGCA
* *
2074929 TCCTACTCTTTGAGGACTAAAAGTTGCCACCAACTTGTGTAGGCATTAAAAAGGAAAAAGGCA
1 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTAGGCATTAAAAAGG-AAAAGGCA
* *
2074992 TCCTGCTCTTTAAGGACTAAAAGGT
1 TCCTACTCTTTGAGGACTAAAAGGT
2075017 TAAAAAAGGT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
60 32 0.42
61 16 0.21
62 3 0.04
63 25 0.33
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (62 bp):
TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTAGGCATTAAAAAGGAAAAGGCA
Found at i:2076309 original size:25 final size:26
Alignment explanation
Indices: 2076280--2076332 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
2076270 CTTTTTGATA
2076280 TTTG-TCATTCC-TTTTTTATTCTTTT
1 TTTGTTCATTCCTTTTTTTATT-TTTT
*
2076305 TTTGTTTCTTTCCTTTTTTTATTTTTT
1 TTTG-TTCATTCCTTTTTTTATTTTTT
2076332 T
1 T
2076333 CATATTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 4 0.17
27 11 0.46
28 9 0.38
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.77
Consensus pattern (26 bp):
TTTGTTCATTCCTTTTTTTATTTTTT
Found at i:2076333 original size:17 final size:17
Alignment explanation
Indices: 2076300--2076333 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2076290 CTTTTTTATT
*
2076300 CTTTTTTTGTTTCTTTC
1 CTTTTTTTATTTCTTTC
*
2076317 CTTTTTTTATTTTTTTC
1 CTTTTTTTATTTCTTTC
2076334 ATATTTGTTT
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:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (17 bp):
CTTTTTTTATTTCTTTC
Found at i:2084255 original size:33 final size:32
Alignment explanation
Indices: 2084210--2084273 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
2084200 CACAACCAGA
*
2084210 TGTATCGGTACATATTGCTTAGTATCAATACAT
1 TGTATCGATACATATT-CTTAGTATCAATACAT
* *
2084243 TGTATCGATACATATTCTTTGTATCGATACA
1 TGTATCGATACATATTCTTAGTATCAATACA
2084274 CCATAAAATG
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:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATATTCTTAGTATCAATACAT
Found at i:2084843 original size:35 final size:34
Alignment explanation
Indices: 2084797--2084919 Score: 100
Period size: 35 Copynumber: 3.7 Consensus size: 34
2084787 AATGATTGAG
2084797 AGGTTCTATCTTAGCCTTGAAAAAGATGGGGAGAA
1 AGGTTCTATCTTAGCCTTGAAAAAGAT-GGGAGAA
*
2084832 AGGTTCTATCTT--CACTTGTGAAAAGATAGGGA-AGA
1 AGGTTCTATCTTAGC-CTTG-AAAAAGAT-GGGAGA-A
* *
2084867 A-GTTTTATCTTAGCCTGTG-AAAAGATAGG-G--
1 AGGTTCTATCTTAGCCT-TGAAAAAGATGGGAGAA
*
2084897 AGGTTCTATCTTAGCCTTCAAAA
1 AGGTTCTATCTTAGCCTTGAAAA
2084920 GATATTGTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
30 2 0.03
31 17 0.23
33 3 0.04
34 21 0.29
35 27 0.37
36 3 0.04
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (34 bp):
AGGTTCTATCTTAGCCTTGAAAAAGATGGGAGAA
Found at i:2084886 original size:34 final size:32
Alignment explanation
Indices: 2084794--2084923 Score: 131
Period size: 34 Copynumber: 3.9 Consensus size: 32
2084784 CGAAATGATT
* *
2084794 GAGAGGTTCTATCTTAGCCTTGAAAAAGATGGG
1 GAGAAGTTCTATCTTAGCCTTG-AAAAGATAGG
*
2084827 GAGAAAGGTTCTATCTTCA-CTTGTGAAAAGATAGG
1 GAG-AA-GTTCTATCTT-AGCCT-TGAAAAGATAGG
*
2084862 GAAGAAGTTTTATCTTAGCCTGTGAAAAGATAGG
1 G-AGAAGTTCTATCTTAGCCT-TGAAAAGATAGG
*
2084896 GAG--GTTCTATCTTAGCCTTCAAAAGATA
1 GAGAAGTTCTATCTTAGCCTTGAAAAGATA
2084924 TTGTTGTAAG
Statistics
Matches: 84, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
30 9 0.11
31 14 0.17
33 6 0.07
34 26 0.31
35 24 0.29
36 5 0.06
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (32 bp):
GAGAAGTTCTATCTTAGCCTTGAAAAGATAGG
Found at i:2089520 original size:27 final size:27
Alignment explanation
Indices: 2089483--2089579 Score: 130
Period size: 27 Copynumber: 3.7 Consensus size: 27
2089473 TATAACAAAA
*
2089483 TGGGAGAGAAGAGTCTATAAATAAATT
1 TGGGGGAGAAGAGTCTATAAATAAATT
2089510 TGGGGGAGAAGAGTCTATAAATAAATT
1 TGGGGGAGAAGAGTCTATAAATAAATT
* *
2089537 TGGAGGAGAAGAGT-T-T--ATAAGTT
1 TGGGGGAGAAGAGTCTATAAATAAATT
*
2089560 TGGGGGAGAAGAGTTTATAA
1 TGGGGGAGAAGAGTCTATAA
2089580 GTTTGAGGGA
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
23 19 0.31
24 1 0.02
25 2 0.03
26 1 0.02
27 39 0.63
ACGTcount: A:0.39, C:0.02, G:0.32, T:0.27
Consensus pattern (27 bp):
TGGGGGAGAAGAGTCTATAAATAAATT
Found at i:2089616 original size:27 final size:23
Alignment explanation
Indices: 2089503--2089616 Score: 93
Period size: 27 Copynumber: 4.6 Consensus size: 23
2089493 GAGTCTATAA
*
2089503 ATAAATTTGGGGGAGAAGAGTCTAT
1 ATAAGTTTGGGGGAGAAGAGTC--T
* * *
2089528 AAATAAATTTGGAGGAGAAGAGTTT
1 --ATAAGTTTGGGGGAGAAGAGTCT
*
2089553 ATAAGTTTGGGGGAGAAGAGTTT
1 ATAAGTTTGGGGGAGAAGAGTCT
*
2089576 ATAAGTTTGAGGGAGAAAAGTTAGTCT
1 ATAAGTTTG-GGG-GAGAAG--AGTCT
*
2089603 ATAATTTTGGGGGA
1 ATAAGTTTGGGGGA
2089617 AATATTTGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
23 30 0.39
24 3 0.04
25 8 0.11
26 3 0.04
27 32 0.42
ACGTcount: A:0.36, C:0.02, G:0.32, T:0.30
Consensus pattern (23 bp):
ATAAGTTTGGGGGAGAAGAGTCT
Found at i:2090432 original size:20 final size:20
Alignment explanation
Indices: 2090407--2090444 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2090397 TTACCCTAAT
*
2090407 TAAATTGTATCGATACATGG
1 TAAATTATATCGATACATGG
2090427 TAAATTATATCGATACAT
1 TAAATTATATCGATACAT
2090445 TAAGCCCAAC
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:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAATTATATCGATACATGG
Found at i:2090995 original size:34 final size:33
Alignment explanation
Indices: 2090914--2091033 Score: 145
Period size: 34 Copynumber: 3.6 Consensus size: 33
2090904 GAAGTGATTG
* * * *
2090914 AGAGGTTCTATCGTAGCCTTTGAAAAAGACAAGA
1 AGAGGTTCTATCTTAGCCTGTG-AAAAGATAGGA
2090948 AGAAAGGTTCTATCTTAGCCTGTGAAAAGATAGCGA
1 AG--AGGTTCTATCTTAGCCTGTGAAAAGATAG-GA
2090984 AGAGGTTCTATCTTAGCCTGTGAAAAGATAGG-
1 AGAGGTTCTATCTTAGCCTGTGAAAAGATAGGA
*
2091016 -GAGGTTTTATCTTAGCCT
1 AGAGGTTCTATCTTAGCCT
2091034 TTAGAAGATA
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
31 17 0.22
33 1 0.01
34 31 0.40
35 7 0.09
36 22 0.28
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (33 bp):
AGAGGTTCTATCTTAGCCTGTGAAAAGATAGGA
Found at i:2097379 original size:33 final size:33
Alignment explanation
Indices: 2097337--2097402 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2097327 GCCAAGGGAA
***
2097337 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
* *
2097370 TGTATCGATAGATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2097403 CTAGGAAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2099874 original size:27 final size:28
Alignment explanation
Indices: 2099844--2099914 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
2099834 TCACAATCGA
*
2099844 GGATACTCCAACCCCGTTA-ATCAT-TGG
1 GGATACTCCAACCCCGTTATATC-TGAGG
* *
2099871 GGATACTCCGACCCCGTTATTTCTGAGG
1 GGATACTCCAACCCCGTTATATCTGAGG
2099899 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
2099915 ACTTTATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 19 0.50
28 19 0.50
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATATCTGAGG
Found at i:2099963 original size:51 final size:51
Alignment explanation
Indices: 2099897--2100118 Score: 228
Period size: 52 Copynumber: 4.3 Consensus size: 51
2099887 TTATTTCTGA
* * *** *
2099897 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
* * * *
2099948 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT-CACAATC
* * * * **
2100000 GGGGAAACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-ACAATC
* ** *
2100052 GGGGATACTCTAACTTCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTTCACAATC
*
2100104 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2100119 TCGTTATTTC
Statistics
Matches: 139, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
51 38 0.27
52 87 0.63
53 14 0.10
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
Found at i:2100016 original size:52 final size:50
Alignment explanation
Indices: 2099730--2100118 Score: 203
Period size: 52 Copynumber: 7.4 Consensus size: 50
2099720 CTCAATTCTC
* * * *
2099730 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAA-TTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTCT-AAAACACCAATTTTT
* * *
2099780 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTA-TT-C-TAAAACACCAATTT-TT
* * * *** **
2099835 CACAATCGAGGATACTCCAACCCCG-TTAATCATTGGGGATACTCCGACCCCGTTATTT
1 CACAATCGGGGATACTCCAACCCCGATT--TTATT----CTAAAAC-A-CCAATT-TTT
** * * * ***
2099893 C-TGA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTA-TTCTAAAACACCAATTTTT
* * *
2099941 CATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATT-CTAAAACACCAATTTTT
* * * *
2099992 CCACAATCGGGGAAACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTC
1 -CACAATCGGGGATACTCCAACCCCGATTTTATTCT-AAAACACCAATTTTT
** * ** * *
2100044 CTTTAATCGGGGATACTCTAACTTCGATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTA-TT-CTAAAACACCAATTTTT
*
2100097 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
2100119 TCGTTATTTC
Statistics
Matches: 254, Mismatches: 60, Indels: 48
0.70 0.17 0.13
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
50 4 0.02
51 66 0.26
52 85 0.33
53 27 0.11
54 27 0.11
55 24 0.09
56 3 0.01
57 2 0.01
58 7 0.03
59 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTCTAAAACACCAATTTTT
Found at i:2100137 original size:28 final size:28
Alignment explanation
Indices: 2100101--2100177 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
2100091 ATTTTTCACA
* * *
2100101 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2100129 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2100157 --CGAGAGGATACTCCAACCCCG
1 ATCG-G-GGATACTCCAACCCCG
2100178 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 41 0.93
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2100195 original size:263 final size:263
Alignment explanation
Indices: 2099728--2100228 Score: 781
Period size: 263 Copynumber: 1.9 Consensus size: 263
2099718 TTCTCAATTC
* * * *
2099728 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGAAACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
2099793 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * * * *
2099858 CGTTAATCATTGGGGATACTCCGACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATT
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGAGGATACTCCAACCCCGACTTTATT
* *
2099923 TCCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
196 CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
2099988 TTT
261 TTT
* *
2099991 TCCACAATCGGGGAAACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGG
1 TCCACAATCGGGGAAACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGG
* * *
2100056 ATACTCTAACTTCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACC
65 ATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACC
* * *
2100119 TCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGAGGATACTCCAACCCCGGCTTTA
130 CCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGAGGATACTCCAACCCCGACTTTA
* *
2100184 TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCTAACCCCG
194 TTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
2100229 TTATTTTCGA
Statistics
Matches: 215, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
262 29 0.13
263 152 0.71
264 34 0.16
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (263 bp):
TCCACAATCGGGGAAACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGAGGATACTCCAACCCCGACTTTATT
CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
TTT
Found at i:2103532 original size:20 final size:20
Alignment explanation
Indices: 2103507--2103591 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
2103497 TTTCAACTAG
2103507 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
2103527 ATGTATTGATACATATGGGCAAAA
1 ATGTATCGATACAT-T--G-AAAA
2103551 GGATAGAATGTATCGATACATTGAAAA
1 --AT-G--T--ATCGATACATTGAAAA
2103578 ATGTATCGATACAT
1 ATGTATCGATACAT
2103592 CTGGGTACTT
Statistics
Matches: 52, Mismatches: 2, Indels: 22
0.68 0.03 0.29
Matches are distributed among these distances:
20 23 0.44
21 1 0.02
22 1 0.02
23 1 0.02
24 5 0.10
25 2 0.04
26 2 0.04
27 5 0.10
28 1 0.02
29 1 0.02
30 1 0.02
31 9 0.17
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:2106513 original size:28 final size:27
Alignment explanation
Indices: 2106481--2106542 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
2106471 CAAAAAAATT
* * *
2106481 AAGAAAAGGGCTAATCCCTAGTGGAATC
1 AAGAAAAGGGC-AATCCCCAATAGAATC
*
2106509 AAGAAAAAGTGCAATCCCCAATAGAATC
1 AAG-AAAAGGGCAATCCCCAATAGAATC
2106537 AAGAAA
1 AAGAAA
2106543 CTTGCAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 19 0.66
29 7 0.24
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.15
Consensus pattern (27 bp):
AAGAAAAGGGCAATCCCCAATAGAATC
Found at i:2106835 original size:21 final size:21
Alignment explanation
Indices: 2106811--2106853 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2106801 GTCATCTTTC
*
2106811 GTTCCAATGTTGTTGACCTTA
1 GTTCCAATATTGTTGACCTTA
2106832 GTTCCAATATTGTTGACCTTA
1 GTTCCAATATTGTTGACCTTA
2106853 G
1 G
2106854 ATCAGCACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (21 bp):
GTTCCAATATTGTTGACCTTA
Found at i:2107300 original size:32 final size:31
Alignment explanation
Indices: 2107264--2107349 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 31
2107254 TATCCTTTTG
*
2107264 AAGCCCACATAAGCTGGTGGCAACCTTCCTC-A
1 AAGCCCACACAAG-TGGTGGCAACCTT-CTCAA
*
2107296 AAGCCCACACAAGTCGGTGGGAACCTTCTCAA
1 AAGCCCACACAAGT-GGTGGCAACCTTCTCAA
2107328 AAGCCCACACAAGTTGGTGGCA
1 AAGCCCACACAAG-TGGTGGCA
2107350 TCCCTTTCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
31 4 0.08
32 43 0.90
33 1 0.02
ACGTcount: A:0.30, C:0.31, G:0.22, T:0.16
Consensus pattern (31 bp):
AAGCCCACACAAGTGGTGGCAACCTTCTCAA
Found at i:2107993 original size:20 final size:20
Alignment explanation
Indices: 2107970--2108024 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
2107960 AAGTACCTAG
*
2107970 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCATCA
* *
2107990 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTCATCA
2108010 ATGTATCGATACATT
1 ATGTATCGATACATT
2108025 TTGTCTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCATCA
Found at i:2111649 original size:52 final size:52
Alignment explanation
Indices: 2111520--2111665 Score: 159
Period size: 52 Copynumber: 2.8 Consensus size: 52
2111510 TTAACATTCG
* * * * ** *
2111520 TAAGCCCAATGTCTCTGATCTTGAATTAGTACATTAGCGCTCTTCTCATCTT
1 TAAGCCCAATGTCACTGACCTTGAATTAGCACATTGGCATTCTTCGCATCTT
* * * * *
2111572 CAAGTCTAATGTCACT-AGCTGTGAATTAACACATTGGCATTCTTCGCATCTT
1 TAAGCCCAATGTCACTGACCT-TGAATTAGCACATTGGCATTCTTCGCATCTT
*
2111624 TAAGCCCAATGTCACTGACCTTGAATCAGCACATTGGCATTC
1 TAAGCCCAATGTCACTGACCTTGAATTAGCACATTGGCATTC
2111666 GTTTCATATT
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
51 3 0.04
52 69 0.92
53 3 0.04
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (52 bp):
TAAGCCCAATGTCACTGACCTTGAATTAGCACATTGGCATTCTTCGCATCTT
Found at i:2111678 original size:52 final size:52
Alignment explanation
Indices: 2111486--2111680 Score: 155
Period size: 52 Copynumber: 3.8 Consensus size: 52
2111476 ATATCGCTGG
* * * *
2111486 CCTTGAATCAGCATATTGGCA-TCTT-TAACATTCGTAAGCCCAATGTCTCTGA
1 CCTTGAATCAGCACATTGGCATTCTTCTCATATT--TAAGCCCAATGTCACTGA
* * * * ** * * * *
2111538 TCTTGAATTAGTACATTAGCGCTCTTCTCATCTTCAAGTCTAATGTCACT-A
1 CCTTGAATCAGCACATTGGCATTCTTCTCATATTTAAGCCCAATGTCACTGA
* * * * *
2111589 GCTGTGAATTAACACATTGGCATTCTTCGCATCTTTAAGCCCAATGTCACTGA
1 CCT-TGAATCAGCACATTGGCATTCTTCTCATATTTAAGCCCAATGTCACTGA
2111642 CCTTGAATCAGCACATTGGCATTCGTT-TCATATTTAAGC
1 CCTTGAATCAGCACATTGGCATTC-TTCTCATATTTAAGC
2111681 GCACTAGCGC
Statistics
Matches: 110, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
51 3 0.03
52 94 0.85
53 9 0.08
54 4 0.04
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (52 bp):
CCTTGAATCAGCACATTGGCATTCTTCTCATATTTAAGCCCAATGTCACTGA
Found at i:2116786 original size:20 final size:20
Alignment explanation
Indices: 2116763--2116814 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
2116753 CACACCTAGA
*
2116763 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCAT
*
2116783 TGTATCGATACA-TATTCAT
1 TGTATCGATACATTATGCAT
2116802 TGTATCGATACAT
1 TGTATCGATACAT
2116815 GAAACTGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTATGCAT
Found at i:2116872 original size:20 final size:20
Alignment explanation
Indices: 2116847--2116897 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
2116837 CCACTGTTTC
2116847 TATCGATACAT-AGGACATTG
1 TATCGATACATGAGGA-ATTG
*
2116867 TATCGATACATGATGAATTG
1 TATCGATACATGAGGAATTG
2116887 TATCGATACAT
1 TATCGATACAT
2116898 TGCTTATAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (20 bp):
TATCGATACATGAGGAATTG
Found at i:2119145 original size:21 final size:20
Alignment explanation
Indices: 2119111--2119153 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2119101 TATTAAAAAT
*
2119111 TTAGCTAAAGAAAATAATGAA
1 TTAGCTAAAGAAAACAA-GAA
2119132 TTAGCT-AAGAAAAACAAGAA
1 TTAGCTAAAG-AAAACAAGAA
2119152 TT
1 TT
2119154 TGCATGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (20 bp):
TTAGCTAAAGAAAACAAGAA
Found at i:2119152 original size:20 final size:21
Alignment explanation
Indices: 2119111--2119153 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2119101 TATTAAAAAT
*
2119111 TTAGCTAAAGAAAATAATGAA
1 TTAGCTAAAGAAAATAAAGAA
2119132 TTAGCT-AAGAAAA-ACAAGAA
1 TTAGCTAAAGAAAATA-AAGAA
2119152 TT
1 TT
2119154 TGCATGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 13 0.65
21 6 0.30
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (21 bp):
TTAGCTAAAGAAAATAAAGAA
Found at i:2123082 original size:13 final size:13
Alignment explanation
Indices: 2123064--2123090 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2123054 AGAACATTTC
2123064 TTGTATCGATACA
1 TTGTATCGATACA
2123077 TTGTATCGATACA
1 TTGTATCGATACA
2123090 T
1 T
2123091 GAGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2125571 original size:13 final size:13
Alignment explanation
Indices: 2125553--2125578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2125543 CACACCCAAA
2125553 TGTATCGATACAT
1 TGTATCGATACAT
2125566 TGTATCGATACAT
1 TGTATCGATACAT
2125579 ATTCATTGTA
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:2125608 original size:20 final size:19
Alignment explanation
Indices: 2125562--2125618 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
2125552 ATGTATCGAT
**
2125562 ACATTGTATCGATACATAT
1 ACATTGTATCGATACATGG
*
2125581 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
2125600 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
2125619 AAACTAGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:2125679 original size:20 final size:20
Alignment explanation
Indices: 2125647--2125700 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
2125637 CTACCACTGT
2125647 TTGTATC-AGTACAT-AGGACA
1 TTGTATCGA-TACATGAGGA-A
*
2125667 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGAGGAA
2125687 TTGTATCGATACAT
1 TTGTATCGATACAT
2125701 TGCTTATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGAGGAA
Done.