Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold469
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: 257357
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:145827 original size:24 final size:24
Alignment explanation
Indices: 145755--145827 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 24
145745 ACCTTCATGT
***
145755 ATCACTGTTCA-CACTATTCACGT
1 ATCACTGTTCATCACTATTCAAAA
* **
145778 ATCACTATTCATGCACCGTT-AAAA
1 ATCACTGTTCAT-CACTATTCAAAA
*
145802 ATCACTGTTCATCACTATTCATAA
1 ATCACTGTTCATCACTATTCAAAA
145826 AT
1 AT
145828 TGTATCGATA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
23 15 0.41
24 17 0.46
25 5 0.14
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (24 bp):
ATCACTGTTCATCACTATTCAAAA
Found at i:145845 original size:20 final size:20
Alignment explanation
Indices: 145820--145862 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
145810 TCATCACTAT
145820 TCATAAATTGTATCGATACA
1 TCATAAATTGTATCGATACA
145840 TCATAAATTGTATCGATACA
1 TCATAAATTGTATCGATACA
145860 TCA
1 TCA
145863 CTGTTCACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (20 bp):
TCATAAATTGTATCGATACA
Found at i:152043 original size:21 final size:21
Alignment explanation
Indices: 152017--152083 Score: 102
Period size: 20 Copynumber: 3.3 Consensus size: 21
152007 CACGACAATT
*
152017 TGTATCGATACAATAAGTTAA
1 TGTATCGATACAATAAGTGAA
*
152038 TGTATCGATACAA-AAGAGAA
1 TGTATCGATACAATAAGTGAA
152058 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
152078 TGTATC
1 TGTATC
152084 AATATTGGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.02
20 28 0.67
21 13 0.31
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:160393 original size:52 final size:52
Alignment explanation
Indices: 160323--160443 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
160313 GAAAATTTAT
*
160323 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
160375 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
160427 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
160444 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:160456 original size:52 final size:51
Alignment explanation
Indices: 160323--160463 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
160313 GAAAATTTAT
160323 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
160375 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
160427 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
160464 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:160470 original size:13 final size:13
Alignment explanation
Indices: 160452--160489 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
160442 CAAAGATCAG
160452 TGTATCGATACAA
1 TGTATCGATACAA
160465 TGTATCGATACAA
1 TGTATCGATACAA
160478 TGTATCGATACA
1 TGTATCGATACA
160490 TGTGAGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:160559 original size:20 final size:20
Alignment explanation
Indices: 160530--160587 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
160520 GCAGTAGCTT
160530 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
160549 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
160569 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
160588 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:169050 original size:27 final size:28
Alignment explanation
Indices: 168988--169053 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
168978 AAATTGAAAT
*
168988 ATAAAAATTAAATAATAAATAGTATTTA
1 ATAAAAATTAAATAATAAATACTATTTA
*
169016 A-AATAAATATAAA-AATAATTACT-TTTA
1 ATAA-AAAT-TAAATAATAAATACTATTTA
169043 ATAAAAATTAA
1 ATAAAAATTAA
169054 TAACTGACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 3 0.09
27 11 0.33
28 15 0.45
29 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (28 bp):
ATAAAAATTAAATAATAAATACTATTTA
Found at i:171180 original size:79 final size:78
Alignment explanation
Indices: 171046--171505 Score: 449
Period size: 79 Copynumber: 5.8 Consensus size: 78
171036 AGATAAAAAT
* * * *** *
171046 GGGGTTGAAGTATCACCGATGGTGGAAAATTGGCATTTTAGAAATAAAACTGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATGGT-GAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
171111 CCCTCAAAAATAAC
65 CCCTCAAAAATAAC
*** * * *
171125 GGGGTTGGAGTATTTTCGATTGTCGAAAATCAATGTTTTAGAAATAAAACCGGGGTTGGAGTATT
1 GGGGTTGGAGTATCCCCGATGGT-GAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
* * *
171190 CCCTTAGAAATAAT
65 CCCTCAAAAATAAC
* * * * **
171204 GGGGTTGGAGTATCCTCGATGGTGAAAAATTGATGTTTTAGATATAAAACCAGGGTTAAAGTATC
1 GGGGTTGGAGTATCCCCGATGGTG-AAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
*
171269 CCCTAAAAAATAAC
65 CCCTCAAAAATAAC
* * * * * *
171283 GGGATTGGAGTATCCCCGATTGTGGAAAATCAATATTTT-GAAAATAAAACCAGAGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATGGT-GAAAATCGATGTTTTAG-AAATAAAACCGGGGTTGGAGTAT
* *
171347 CCCTTCGAAAATAAC
64 CCCCTCAAAAATAAC
* * * * * *
171362 GGGATTGGAGTATCCCCGATGGTAAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAATATC
1 GGGGTTGGAGTATCCCCGATGGT-GAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
* *
171427 CTCTC-GAAATAAAC
65 CCCTCAAAAAT-AAC
* * *
171441 GAGGTTGGAGTATCCCCGATGGTGAAAATCGATGTTTT-GAAAATAAAATCGAGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATGGTGAAAATCGATGTTTTAG-AAATAAAACCGGGGTTGGAGTATC
171505 C
65 C
171506 TCGATAGTGA
Statistics
Matches: 314, Mismatches: 61, Indels: 13
0.81 0.16 0.03
Matches are distributed among these distances:
77 1 0.00
78 42 0.13
79 269 0.86
80 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (78 bp):
GGGGTTGGAGTATCCCCGATGGTGAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCC
CCTCAAAAATAAC
Found at i:171235 original size:158 final size:157
Alignment explanation
Indices: 171043--171503 Score: 536
Period size: 158 Copynumber: 2.9 Consensus size: 157
171033 TGGAGATAAA
* * ***
171043 AATGGGGTTGAAGTATCACCGATGGTGGAAAATTGGCATTTTAGAAATAAAACTGGGGTTGGAGT
1 AATGGGGTTGGAGTATC-CCGATGGTGAAAAATTGATGTTTTAGAAATAAAACTGGGGTTGGAGT
***
171108 ATCCCCTCAAAAATAACGGGGTTGGAGTATTTTCGATTGTCGAAAATCAATGTTTT-AGAAATAA
65 ATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGT-GAAAATCAATGTTTTGA-AAATAA
171172 AACCGGGGTTGGAGTATTCCCTTAG-AAAT
128 AACCGGGGTTGGAGTATTCCCTTAGAAAAT
* ** **
171201 AATGGGGTTGGAGTATCCTCGATGGTGAAAAATTGATGTTTTAGATATAAAACCAGGGTTAAAGT
1 AATGGGGTTGGAGTATCC-CGATGGTGAAAAATTGATGTTTTAGAAATAAAACTGGGGTTGGAGT
* * *
171266 ATCCCCTAAAAAATAACGGGATTGGAGTATCCCCGATTGTGGAAAATCAATATTTTGAAAATAAA
65 ATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGT-GAAAATCAATGTTTTGAAAATAAA
* * *
171331 ACCAGAGTTGGAGTA-TCCCTTCGAAAAT
129 ACCGGGGTTGGAGTATTCCCTTAGAAAAT
* * * * *
171359 AACGGGATTGGAGTATCCCCGATGGTAAAAAATTGATGTTTTGGAAATAAAA-TCGGGGTTGGAA
1 AATGGGGTTGGAGTAT-CCCGATGGTGAAAAATTGATGTTTTAGAAATAAAACT-GGGGTTGGAG
* * * * *
171423 TATCCTCTC-GAAATAAACGAGGTTGGAGTATCCCCGATGGTGAAAATCGATGTTTTGAAAATAA
64 TATCCCCTCAAAAAT-AACGGGGTTGGAGTATCCCCGATTGTGAAAATCAATGTTTTGAAAATAA
* *
171487 AATCGAGGTTGGAGTAT
128 AACCGGGGTTGGAGTAT
171504 CCTCGATAGT
Statistics
Matches: 254, Mismatches: 42, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
157 45 0.18
158 206 0.81
159 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.28
Consensus pattern (157 bp):
AATGGGGTTGGAGTATCCCGATGGTGAAAAATTGATGTTTTAGAAATAAAACTGGGGTTGGAGTA
TCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAATCAATGTTTTGAAAATAAAAC
CGGGGTTGGAGTATTCCCTTAGAAAAT
Found at i:171516 original size:50 final size:50
Alignment explanation
Indices: 171432--171539 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
171422 ATATCCTCTC
*
171432 GAAAT-AAACGAGGTTGGAGTATCCCCGATGGTG-AAAATC-GATGTTTT-
1 GAAATAAAACGAGGTTGGAGTATCCCCGATAGTGAAAAATCAG-TGTTTTA
*
171479 GAAAATAAAATCGAGGTTGGAGTATCCTCGATAGTGAAAAATCAGTGTTTTA
1 G-AAATAAAA-CGAGGTTGGAGTATCCCCGATAGTGAAAAATCAGTGTTTTA
171531 GAAATAAAA
1 GAAATAAAA
171540 ACATTAATGA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
47 1 0.02
48 4 0.08
49 3 0.06
50 23 0.43
51 20 0.38
52 2 0.04
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (50 bp):
GAAATAAAACGAGGTTGGAGTATCCCCGATAGTGAAAAATCAGTGTTTTA
Found at i:177505 original size:79 final size:79
Alignment explanation
Indices: 177406--177608 Score: 273
Period size: 79 Copynumber: 2.6 Consensus size: 79
177396 GAGATAATAA
* ** *
177406 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCAATGA
1 CGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAAT-A
*
177471 -TTAGAAAATAAAAT
65 TTTAGAAAATAAAAC
* *
177485 CGGGATTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
* * *
177550 TTTGGAAATAAAGC
66 TTAGAAAATAAAAC
* **
177564 CGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCC
177609 TGATGAAATA
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
78 1 0.01
79 108 0.99
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
TTAGAAAATAAAAC
Found at i:177620 original size:28 final size:27
Alignment explanation
Indices: 177564--177639 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 27
177554 GAAATAAAGC
**
177564 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTAT-CCCTCGGAAATAA
177592 CGGGGTTGGAGTATCCCT-GATGAAATAA
1 CGGGGTTGGAGTATCCCTCG--GAAATAA
*
177620 CGAGGTTGGAGTAT-CCTCGG
1 CGGGGTTGGAGTATCCCTCGG
177640 TTGTGAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
26 2 0.05
27 7 0.17
28 33 0.79
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCGGAAATAA
Found at i:177713 original size:52 final size:53
Alignment explanation
Indices: 177646--177746 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 53
177636 TCGGTTGTGA
* * **
177646 AAAATTGGTGTTTTTGGAAATAAAATTGGAGTTGGAGTATCCCAGATTAAAGG
1 AAAATCGGTGTTTTTGAAAATAAAACCGGAGTTGGAGTATCCCAGATTAAAGG
* * *
177699 AAAATCGGTG-TTTTGAAAATATAACCGGGGTTGGAGTATCCCCGATTA
1 AAAATCGGTGTTTTTGAAAATAAAACCGGAGTTGGAGTATCCCAGATTA
177747 TGAACAATTG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
52 32 0.78
53 9 0.22
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.31
Consensus pattern (53 bp):
AAAATCGGTGTTTTTGAAAATAAAACCGGAGTTGGAGTATCCCAGATTAAAGG
Found at i:180133 original size:13 final size:13
Alignment explanation
Indices: 180115--180139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
180105 ACAAAGATCG
180115 ATGTATCGATACA
1 ATGTATCGATACA
180128 ATGTATCGATAC
1 ATGTATCGATAC
180140 TTTTCCTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:180151 original size:21 final size:21
Alignment explanation
Indices: 180127--180168 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
180117 GTATCGATAC
*
180127 AATGTATCGATACTTTTCCTT
1 AATGTATCGATACATTTCCTT
180148 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
180169 GGCAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:180219 original size:19 final size:18
Alignment explanation
Indices: 180195--180287 Score: 89
Period size: 19 Copynumber: 5.6 Consensus size: 18
180185 CGATACATTC
180195 TATCGATACAAAACTTATG
1 TATCGATAC-AAACTTATG
180214 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
180227 TATCGATACAACACTTATG
1 TATCGATACAA-ACTTATG
180246 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
180259 TATCGATACAACACTTATG
1 TATCGATACAA-ACTTATG
180278 TATCGATACA
1 TATCGATACA
180288 TTTTCTATTT
Statistics
Matches: 62, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.35
14 2 0.03
16 4 0.06
18 2 0.03
19 32 0.52
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TATCGATACAAACTTATG
Found at i:180230 original size:13 final size:13
Alignment explanation
Indices: 180212--180268 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
180202 ACAAAACTTA
180212 TGTATCGATACAT
1 TGTATCGATACAT
180225 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
180243 ATGTATCGATACAT
1 -TGTATCGATACAT
180257 TGTATCGATACA
1 TGTATCGATACA
180269 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:180231 original size:32 final size:32
Alignment explanation
Indices: 180185--180289 Score: 192
Period size: 32 Copynumber: 3.3 Consensus size: 32
180175 AGCTTCGTAG
* *
180185 CGATACATTCTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
180217 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
180249 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
180281 CGATACATT
1 CGATACATT
180290 TTCTATTTGT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:182511 original size:53 final size:51
Alignment explanation
Indices: 182430--182777 Score: 371
Period size: 53 Copynumber: 6.8 Consensus size: 51
182420 ACATTGGCAC
* * *
182430 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCTCCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCAT
182482 CTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCAT
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCAT
* * * * * *
182532 CTTTAAGTCCAATATTGCTGGCCTTGAATCAACATATTAGCGCCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCAT
*
182584 CTTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACC-T-TCAT
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCAT
* * * *
182634 CTTTAAGTCCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT-GTCAT
** * * * * *
182686 CTTTAAAACCCAATGTTGTTGGCCTTGAATCAACACATTGGCATTCTTCTCAT
1 CTTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTGTCAT
* * ** *
182739 CTTCAAGTCTAATGTCGCTAACCGTGAATCAGCACATTG
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
182778 ACATCGTTTT
Statistics
Matches: 246, Mismatches: 40, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
49 75 0.30
50 11 0.04
51 3 0.01
52 40 0.16
53 114 0.46
54 3 0.01
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (51 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCAT
Found at i:182568 original size:102 final size:102
Alignment explanation
Indices: 182217--182728 Score: 650
Period size: 102 Copynumber: 5.2 Consensus size: 102
182207 GGGGACGAAT
* * *
182217 TTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATA
1 TTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA
* *
182282 TTGGCACC-TT-T-ATC-TTTAAGTCCACTGTAGCTGGCC
63 TTGGCGCCTTTGTCATCTTTTAAGTCCAATGTAGCTGGCC
* *
182318 TTGAATCAGCACATTGGCACC-TC--C---AAGTCCAATATCGCTGGCCTTGAATCAACATATAG
1 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
**
182377 G-TACTTT-T-ATC-TTTAAGTCCAATGTAGCTGGCC
66 GCGCCTTTGTCATCTTTTAAGTCCAATGTAGCTGGCC
182410 TTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
1 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
* *
182469 GCTCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCC
66 GCGCCTTTGTCATCTTTTAAGTCCAATGTAGCTGGCC
* * *
182506 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAACATATTA
1 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
*
182571 GCGCCTTTGTCATCTTTTAAGTCCAATGTTGCTGGCC
66 GCGCCTTTGTCATCTTTTAAGTCCAATGTAGCTGGCC
*
182608 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAGTATCGCTGGCCTTGAATCAGCATATTG
1 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
* * ** * *
182673 GCGCCTTCGTCATCTTTAAAACCCAATGTTGTTGGCC
66 GCGCCTTTGTCATCTTTTAAGTCCAATGTAGCTGGCC
*
182710 TTGAATCAACACATTGGCA
1 TTGAATCAGCACATTGGCA
182729 TTCTTCTCAT
Statistics
Matches: 370, Mismatches: 27, Indels: 27
0.87 0.06 0.06
Matches are distributed among these distances:
89 2 0.01
91 1 0.00
92 113 0.31
93 5 0.01
94 1 0.00
95 4 0.01
96 40 0.11
97 2 0.01
100 1 0.00
101 19 0.05
102 182 0.49
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (102 bp):
TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
GCGCCTTTGTCATCTTTTAAGTCCAATGTAGCTGGCC
Found at i:182680 original size:49 final size:49
Alignment explanation
Indices: 182217--182680 Score: 502
Period size: 49 Copynumber: 9.5 Consensus size: 49
182207 GGGGACGAAT
*
182217 TTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATATCGCTGGCC
1 TTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCC
* * * * *
182269 TTGAATTAGCATATTGGCACCTTTATCTTTAAGTCCACTGTAGCTGGCC
1 TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCC
*
182318 TTGAATCAGCACATTGGCACC-TC--C---AAGTCCAATATCGCTGGCC
1 TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCC
* * * * * * *
182361 TTGAATCAACATATAGGTACTTTTATCTTTAAGTCCAATGTAGCTGGCC
1 TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCC
*
182410 TTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCC
1 TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCC
* *
182453 TTGAATCAGCATATTGGCTCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCC
1 TTGAATCAGCATATTGGCACC--T-TCATC-TTTAAGTCCAATATCGCTGGCC
* *
182506 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATTGCTGGCC
1 TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCC
* * * * *
182555 TTGAATCAACATATTAGCGCCTTTGTCATCTTTTAAGTCCAATGTTGCTGGCC
1 TTGAATCAGCATATTGGCACC--T-TCATC-TTTAAGTCCAATATCGCTGGCC
* *
182608 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAGTATCGCTGGCC
1 TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCC
*
182657 TTGAATCAGCATATTGGCGCCTTC
1 TTGAATCAGCATATTGGCACCTTC
182681 GTCATCTTTA
Statistics
Matches: 344, Mismatches: 48, Indels: 43
0.79 0.11 0.10
Matches are distributed among these distances:
43 70 0.20
44 1 0.00
46 2 0.01
48 1 0.00
49 152 0.44
50 12 0.03
51 3 0.01
52 25 0.07
53 78 0.23
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
TTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCC
Found at i:183382 original size:49 final size:52
Alignment explanation
Indices: 183283--183389 Score: 157
Period size: 49 Copynumber: 2.1 Consensus size: 52
183273 GGGGATGAAT
* *
183283 TTGAATAAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATATCGCTGGCC
1 TTGAATAAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATAGCTGGCC
* *
183335 TTGAATCAGCATATTGGCACC-TT-T-ATCTTTAAGTCCAATGTAGCTGGCC
1 TTGAATAAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATAGCTGGCC
183384 TTGAAT
1 TTGAAT
183390 GTGTGTTCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 29 0.57
50 1 0.02
51 2 0.04
52 19 0.37
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (52 bp):
TTGAATAAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATAGCTGGCC
Found at i:183572 original size:13 final size:13
Alignment explanation
Indices: 183554--183610 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
183544 TTCAATGATT
183554 TGTATCGATACAA
1 TGTATCGATACAA
183567 TGTATCGATACATAA
1 TGTATCGATAC--AA
183582 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
183599 TGTATCGATACA
1 TGTATCGATACA
183611 TAAGTTTTGT
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:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:183591 original size:19 final size:18
Alignment explanation
Indices: 183567--183629 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
183557 ATCGATACAA
183567 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
183586 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
183599 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
183618 TGTATCGATACA
1 TGTATCGATACA
183630 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:183594 original size:32 final size:32
Alignment explanation
Indices: 183553--183637 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
183543 TTTCAATGAT
183553 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
183585 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
183617 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
183638 CTACGAAGCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:183700 original size:13 final size:13
Alignment explanation
Indices: 183682--183706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183672 ATTACTCAAA
183682 TGTATCGATACAT
1 TGTATCGATACAT
183695 TGTATCGATACA
1 TGTATCGATACA
183707 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:183756 original size:52 final size:52
Alignment explanation
Indices: 183718--183843 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
183708 TGATCTTTGC
* *
183718 ATCGATACATGCAGGCGAATTTGCCTAGATGTATCGATACACTATGAAATGT
1 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGT
** *
183770 ATCGATACATATAGGCAAATTTGCCCAGATGTATTGATACACTATGAAATGT
1 ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGT
183822 ATCGATACATGCAGGCAAATTT
1 ATCGATACATGCAGGCAAATTT
183844 TCATATTTCG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (52 bp):
ATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGT
Found at i:192772 original size:50 final size:49
Alignment explanation
Indices: 192697--192877 Score: 254
Period size: 49 Copynumber: 3.7 Consensus size: 49
192687 CCAGTGTGTA
* **
192697 AATTCAAGGCCTGCAACATTGGACTTAAAGGTGAAGGTGTTAATGTGCT
1 AATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCCAATGTGCT
* * * *
192746 AATTCAAGGCCAAGCGACATTGGACTTAAAGATAAAGATGCCAATGTGCT
1 AATTCAAGGCC-AGCAACATTGGACTTAAAGGTGAAGGTGCCAATGTGCT
*
192796 GATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCCAATGTGCT
1 AATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCCAATGTGCT
* * *
192845 GATTCAAGGCTAGCAACATTGGGCTTAAAGGTG
1 AATTCAAGGCCAGCAACATTGGACTTAAAGGTG
192878 CTAATATGCT
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
49 76 0.65
50 41 0.35
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.24
Consensus pattern (49 bp):
AATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCCAATGTGCT
Found at i:192890 original size:43 final size:43
Alignment explanation
Indices: 192738--192914 Score: 165
Period size: 49 Copynumber: 3.8 Consensus size: 43
192728 TGAAGGTGTT
* *
192738 AATGTGCTAATTCAAGGCCAAGCGACATTGGACTTAAAGATAAAGATGCC
1 AATGTGCTGATTCAAGGCC-AGCAACATTGGACTTAAAG-----G-TGCC
192788 AATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCAACATTGGACTT--A----AAGGTGCC
* * *
192837 AATGTGCTGATTCAAGGCTAGCAACATTGGGCTTAAAGGTGCT
1 AATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGCC
* * *
192880 AATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 AATGTGCTGATTCAAGGCCAGCAACATTGGACTTA
192915 GAAGAAGATG
Statistics
Matches: 111, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
43 37 0.33
47 1 0.01
49 50 0.45
50 19 0.17
51 1 0.01
55 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (43 bp):
AATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGCC
Found at i:193030 original size:28 final size:28
Alignment explanation
Indices: 192958--193437 Score: 518
Period size: 28 Copynumber: 16.9 Consensus size: 28
192948 TGTGCTTTTG
*
192958 AAGGTTGCCACTGCCTTGTGGGCTTTG--
1 AAGG-TGCCACTGACTTGTGGGCTTTGAA
192985 AAGGTTGCCACTGACTTGTGGGCTTTGAA
1 AAGG-TGCCACTGACTTGTGGGCTTTGAA
**
193014 AAGGTGCCACAAACTTGTGGGCTTTTG--
1 AAGGTGCCACTGACTTGTGGGC-TTTGAA
193041 AAGGTTGCCACTGACTTGTGGGCTTTGAA
1 AAGG-TGCCACTGACTTGTGGGCTTTGAA
* *
193070 AAGGTGCCACTAACGTGTGGGCTTTTGAA
1 AAGGTGCCACTGACTTGTGGGC-TTTGAA
*
193099 AAGATGCCACTGACTTGTGGGCTTTGAA
1 AAGGTGCCACTGACTTGTGGGCTTTGAA
* *
193127 AAGGTGTCACTGACATGTGGGCTTTGAA
1 AAGGTGCCACTGACTTGTGGGCTTTGAA
* *
193155 AAGATGCCACTAACTTGTGGGCTTTTG--
1 AAGGTGCCACTGACTTGTGGGC-TTTGAA
193182 AAGGTTGCCACTGACTTGTGGGCTTTGAA
1 AAGG-TGCCACTGACTTGTGGGCTTTGAA
* *
193211 AGGGGTGCCACCGACTTGTGGGCTTCTG--
1 A-AGGTGCCACTGACTTGTGGGCTT-TGAA
* *
193239 AAGGTTGCCACTGACTTATGAGCTTTGAA
1 AAGG-TGCCACTGACTTGTGGGCTTTGAA
*
193268 AAGATGCCACTGACTTGTGGGCTTTTG--
1 AAGGTGCCACTGACTTGTGGGC-TTTGAA
*
193295 AAGGTTGCTACTGACTTGTGGGCTTTGAA
1 AAGG-TGCCACTGACTTGTGGGCTTTGAA
* *
193324 AGGGGTGCCACCGACTTGTGGGCTTCT--A
1 A-AGGTGCCACTGACTTGTGGGCTT-TGAA
193352 AAGGTTGCCACTGACTTGTGGGCTTTTGAA
1 AAGG-TGCCACTGACTTGTGGGC-TTTGAA
193382 AAGGGTGCCA-TCGACTTGTGGGCTTTTGAA
1 AA-GGTGCCACT-GACTTGTGGGC-TTTGAA
* *
193412 AAGATGTCACTGACTTGTGGGCTTTG
1 AAGGTGCCACTGACTTGTGGGCTTTG
193438 GAAGGCGAGG
Statistics
Matches: 387, Mismatches: 37, Indels: 57
0.80 0.08 0.12
Matches are distributed among these distances:
27 54 0.14
28 189 0.49
29 106 0.27
30 36 0.09
31 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (28 bp):
AAGGTGCCACTGACTTGTGGGCTTTGAA
Found at i:193138 original size:85 final size:86
Alignment explanation
Indices: 192945--193436 Score: 541
Period size: 85 Copynumber: 5.8 Consensus size: 86
192935 GTGTGGGCTT
* *
192945 TTGTGTGCTTTTG--AAGGTTGCCACTGCCTTGTGGGCTTTG--AAGGTTGCCACTGACTTGTGG
1 TTGTGGGCTTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGG
* **
193006 GC-TTTGAAAAGGTGCCACAAAC
64 GCTTTTGAAAAGATGCCACTGAC
* *
193028 TTGTGGGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACGTGTGGG
1 TTGTGGGCTTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGG
193091 CTTTTGAAAAGATGCCACTGAC
65 CTTTTGAAAAGATGCCACTGAC
* * * *
193113 TTGTGGGC-TTTGAAAAGGTGTCACTGACATGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGC
1 TTGTGGGCTTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGC
* *
193177 TTTTG-AAGGTTGCCACTGAC
66 TTTTGAAAAGATGCCACTGAC
* * *
193197 TTGTGGGC-TTTGAAAGGGGTGCCACCGACTTGTGGGCTTCTG--AAGGTTGCCACTGACTTATG
1 TTGTGGGCTTTTGAAA-AGGTGCCACTGACTTGTGGGCTT-TGAAAAGG-TGCCACTGACTTGTG
*
193259 AGC-TTTGAAAAGATGCCACTGAC
63 GGCTTTTGAAAAGATGCCACTGAC
* * *
193282 TTGTGGGCTTTTG--AAGGTTGCTACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGG
1 TTGTGGGCTTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAA-AGGTGCCACTGACTTGTGG
* * *
193345 GCTTCT-AAAGGTTGCCACTGAC
64 GCTTTTGAAAAGATGCCACTGAC
* *
193367 TTGTGGGCTTTTGAAAAGGGTGCCA-TCGACTTGTGGGCTTTTGAAAAGATGTCACTGACTTGTG
1 TTGTGGGCTTTTGAAAA-GGTGCCACT-GACTTGTGGGC-TTTGAAAAGGTGCCACTGACTTGTG
193431 GGCTTT
63 GGCTTT
193437 GGAAGGCGAG
Statistics
Matches: 350, Mismatches: 39, Indels: 36
0.82 0.09 0.08
Matches are distributed among these distances:
83 42 0.12
84 74 0.21
85 174 0.50
86 15 0.04
87 36 0.10
88 9 0.03
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.32
Consensus pattern (86 bp):
TTGTGGGCTTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGC
TTTTGAAAAGATGCCACTGAC
Found at i:193146 original size:113 final size:114
Alignment explanation
Indices: 192945--193442 Score: 599
Period size: 113 Copynumber: 4.4 Consensus size: 114
192935 GTGTGGGCTT
* * * *
192945 TTGTGTGCTTTTGAAGGTTGCCACTGCCTTGTGGGCTTTG-AA-GGTTGCCACTGACTTGTGGGC
1 TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGGGC
** * *
193008 TT-TGAAAAGG-TGCCACAAACTTGTGGGCTTTTG-AAGGTTGCCACTGAC
66 TTCTG-AAAGGTTGCCACTGACTTGTGGGC-TTTGAAAAGATGCCACTGAC
* * * * *
193056 TTGTGGGC-TTTGAAAAGG-TGCCACTAACGTGTGGGCTTTTGAAA-AGATGCCACTGACTTGTG
1 TTGTGGGCTTTTG--AAGGTTGCCACTGACTTGTGGGC-TTTGAAAGGGGTGCCACCGACTTGTG
* * *
193118 GGCTT-TGAAAAGG-TGTCACTGACATGTGGGCTTTGAAAAGATGCCACTAAC
63 GGCTTCTG-AAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGAC
193169 TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGGGC
1 TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGGGC
* *
193234 TTCTG-AAGGTTGCCACTGACTTATGAGCTTTGAAAAGATGCCACTGAC
66 TTCTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGAC
*
193282 TTGTGGGCTTTTGAAGGTTGCTACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGGGC
1 TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGGGC
*
193347 TTCT-AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCA-TCGAC
66 TTCTGAAAGGTTGCCACTGACTTGTGGGC-TTTGAAAA-GATGCCACT-GAC
* * * *
193397 TTGTGGGCTTTTGAAAAGATGTCACTGACTTGTGGGCTTTGGAAGG
1 TTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGAAAGG
193443 CGAGGAATGT
Statistics
Matches: 340, Mismatches: 32, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
110 4 0.01
111 22 0.06
112 27 0.08
113 223 0.66
114 15 0.04
115 22 0.06
116 27 0.08
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (114 bp):
TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGGGC
TTCTGAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGAC
Found at i:194894 original size:13 final size:12
Alignment explanation
Indices: 194873--194930 Score: 64
Period size: 13 Copynumber: 4.6 Consensus size: 12
194863 ATCTAGACCC
194873 TTTTTGTTTTTT-
1 TTTTT-TTTTTTG
194885 TTTGTTGTTTTTTG
1 TTT-TT-TTTTTTG
*
194899 TTTTTGTTTTTG
1 TTTTTTTTTTTG
194911 TTTTTTTTGTTTG
1 TTTTTTTT-TTTG
194924 TTTTTTT
1 TTTTTTT
194931 ATGGAAGATG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
12 16 0.39
13 22 0.54
14 3 0.07
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:194923 original size:19 final size:20
Alignment explanation
Indices: 194873--194928 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 20
194863 ATCTAGACCC
*
194873 TTTTTGTTTTTTTTTGTTGT
1 TTTTTGTTTGTTTTTGTTGT
194893 TTTTTGTTTTTGTTTTTGTT-T
1 TTTTTG--TTTGTTTTTGTTGT
194914 TTTTTGTTTGTTTTT
1 TTTTTGTTTGTTTTT
194929 TTATGGAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 9 0.27
20 6 0.18
21 7 0.21
22 11 0.33
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (20 bp):
TTTTTGTTTGTTTTTGTTGT
Found at i:202563 original size:17 final size:17
Alignment explanation
Indices: 202541--202573 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
202531 ATACTATGTA
202541 ATCACAACAGGGACAAT
1 ATCACAACAGGGACAAT
202558 ATCACAACAGGGACAA
1 ATCACAACAGGGACAA
202574 CACGATTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.09
Consensus pattern (17 bp):
ATCACAACAGGGACAAT
Found at i:208875 original size:13 final size:13
Alignment explanation
Indices: 208857--208882 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
208847 AGGGTAGCTT
208857 TTGTATCGATACA
1 TTGTATCGATACA
208870 TTGTATCGATACA
1 TTGTATCGATACA
208883 ACACTTATGT
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):
TTGTATCGATACA
Found at i:216103 original size:20 final size:20
Alignment explanation
Indices: 216080--216127 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
216070 TAGATGTACC
* *
216080 GATACATTGAATAATGTATG
1 GATACATCGAATAACGTATG
216100 GATACATCGAATAACGTATG
1 GATACATCGAATAACGTATG
216120 GATACATC
1 GATACATC
216128 TAGGTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (20 bp):
GATACATCGAATAACGTATG
Found at i:216195 original size:20 final size:20
Alignment explanation
Indices: 216143--216197 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
216133 AAAAAGACAG
* *
216143 AATGTATCGATGCATTCATA
1 AATGTATCGATACATTCAAA
* ** *
216163 CATGTATTAATACATTGAAA
1 AATGTATCGATACATTCAAA
216183 AATGTATCGATACAT
1 AATGTATCGATACAT
216198 CTGGGTAAAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:216197 original size:71 final size:71
Alignment explanation
Indices: 216073--216268 Score: 212
Period size: 71 Copynumber: 2.8 Consensus size: 71
216063 TTTTAACTAG
* * * ** * * * *
216073 ATGTACCGATACATTGAATAATGTATGGATACATCGAATAACGTATGGATACATCTAGGTAAAAA
1 ATGTATCGATACATTCAAAAATGTATCAATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
216138 GACAGA
66 GACAGA
* * * * *
216144 ATGTATCGATGCATTCATACATGTATTAATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACATTCAAAAATGTATCAATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
*
216209 TACAGA
66 GACAGA
* * * * *
216215 ATGTATCGATACATTGAAAAATGTATCGATACATTCATACATGTATCGATACAT
1 ATGTATCGATACATTCAAAAATGTATCAATACATTGAAAAATGTATCGATACAT
216269 TGAAAAATGT
Statistics
Matches: 102, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
71 102 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (71 bp):
ATGTATCGATACATTCAAAAATGTATCAATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
GACAGA
Found at i:216303 original size:24 final size:20
Alignment explanation
Indices: 216214--216289 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
216204 AAAAATACAG
216214 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
* *
216234 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
*
216254 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
216274 AATGTATCGATACATT
1 AATGTATCGATACATT
216290 TGGGTAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:217224 original size:20 final size:21
Alignment explanation
Indices: 217199--217253 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
217189 TAAAACCTAG
**
217199 AATGTATCGATACAATGA-AA
1 AATGTATCGATACAAACAGAA
*
217219 AATGTATCGATACAAACAGTA
1 AATGTATCGATACAAACAGAA
217240 AATGTATCGATACA
1 AATGTATCGATACA
217254 TTTACTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (21 bp):
AATGTATCGATACAAACAGAA
Found at i:217840 original size:28 final size:28
Alignment explanation
Indices: 217803--217913 Score: 105
Period size: 29 Copynumber: 3.9 Consensus size: 28
217793 GTAAGCTAAA
* *
217803 GAATTAAAAATCAATTAAAACACTAAAAG
1 GAATTAAAAGTCAACT-AAACACTAAAAG
* * *
217832 GAATTAAAAGTCAATTAAACTACAAAAAA
1 GAATTAAAAGTCAACTAAAC-ACTAAAAG
* *
217861 TAATTAAAAGTCAACTAAACACTATAAG
1 GAATTAAAAGTCAACTAAACACTAAAAG
* * *
217889 AAATTAGAAGTTAACTAAAACACTA
1 GAATTAAAAGTCAACT-AAACACTA
217914 TAACTTCCCT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 22 0.32
29 47 0.68
ACGTcount: A:0.59, C:0.12, G:0.07, T:0.23
Consensus pattern (28 bp):
GAATTAAAAGTCAACTAAACACTAAAAG
Found at i:224055 original size:11 final size:10
Alignment explanation
Indices: 224039--224088 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 10
224029 TTTGCAAGTG
224039 AAGAAAAATAA
1 AAGAAAAA-AA
224050 AAGAAAAAAA
1 AAGAAAAAAA
224060 AAGAGAAAAAA
1 AAGA-AAAAAA
* *
224071 GAGAGAAATAA
1 AAGA-AAAAAA
224082 AAGAAAA
1 AAGAAAA
224089 CTCTTGCACC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
10 9 0.26
11 26 0.74
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:225189 original size:144 final size:140
Alignment explanation
Indices: 225031--225385 Score: 405
Period size: 144 Copynumber: 2.5 Consensus size: 140
225021 TATCATCTCA
* * *
225031 ATTTTTTT-AAATTTCTAATATTTTCATGAGTATCCGTGAGGGTATAGAAATTTTTAAAACTTTT
1 ATTTTTTTCAGATTTCTAATATTTT-ATGAGTTTTCGTGAGGGTATAGAAATTTTTAAAACTTTT
** * * * *
225095 CGTATCTTTTTGGATCTCTATTAAAATGCGAAATAAATTTTTTGAAAATTAAAAAATTAAATAAA
65 CGTATCTTTTCAGATCTCCATTAAAATACAAAATAAATTTTTTAAAAATT-AAAAATTAAATAAA
225160 AATTATTATCTT
129 AATTATTATCTT
* *
225172 ATTTTTTTTTCAGATTTCTAATATTCTTATG-GTTTTC-TGTAGGGATATAGAAATTTTCAAAAT
1 A--TTTTTTTCAGATTTCTAATATT-TTATGAGTTTTCGTG-AGGG-TATAGAAATTTTTAAAAC
* * ** *
225235 TTTTTGTATCTTTTCAGTTCTCCATTAAGGTACAAAATGAATTTTTTAAAAATTAAAAATTAAAT
61 TTTTCGTATCTTTTCAGATCTCCATTAAAATACAAAATAAATTTTTTAAAAATTAAAAATTAAAT
225300 AAAAATTATTATCTT
126 AAAAATTATTATCTT
* * * *
225315 A-ATTTTTCAAGATTTTTAATATTTTTATGATTTTTCGT-ATAGGTATAGAAATTTTTAAAACTT
1 ATTTTTTTC-AGATTTCTAATA-TTTTATGAGTTTTCGTGA-GGGTATAGAAATTTTTAAAACTT
225378 TTCGTATC
63 TTCGTATC
225386 CCTTGGTTTT
Statistics
Matches: 180, Mismatches: 23, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
140 6 0.03
141 43 0.24
142 11 0.06
143 43 0.24
144 75 0.42
145 2 0.01
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (140 bp):
ATTTTTTTCAGATTTCTAATATTTTATGAGTTTTCGTGAGGGTATAGAAATTTTTAAAACTTTTC
GTATCTTTTCAGATCTCCATTAAAATACAAAATAAATTTTTTAAAAATTAAAAATTAAATAAAAA
TTATTATCTT
Found at i:227759 original size:34 final size:32
Alignment explanation
Indices: 227721--227789 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
227711 CGTTACAAGC
227721 CAATGTATCGATACAAT-TTGGTCATGTATCGATA
1 CAATGTATCGATAC-ATCTT-GT-ATGTATCGATA
*
227755 CAATGTATCGATACATCTTGTATGTATTGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
227787 CAA
1 CAA
227790 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 13 0.39
33 4 0.12
34 16 0.48
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:227762 original size:13 final size:13
Alignment explanation
Indices: 227721--227769 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
227711 CGTTACAAGC
227721 CAATGTATCGATA
1 CAATGTATCGATA
*
227734 CAAT-T-T-GGT-
1 CAATGTATCGATA
227743 C-ATGTATCGATA
1 CAATGTATCGATA
227755 CAATGTATCGATA
1 CAATGTATCGATA
227768 CA
1 CA
227770 TCTTGTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 3 0.10
11 3 0.10
12 2 0.07
13 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:230140 original size:8 final size:8
Alignment explanation
Indices: 230122--230152 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
230112 ATTTCAACAT
230122 CAAACATCA
1 CAAA-ATCA
230131 CAAAATCA
1 CAAAATCA
230139 CAAAATCA
1 CAAAATCA
230147 CAAAAT
1 CAAAAT
230153 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:233008 original size:68 final size:65
Alignment explanation
Indices: 232823--233473 Score: 510
Period size: 68 Copynumber: 9.9 Consensus size: 65
232813 GGGGATGAAT
* ** * *
232823 TCCACCACTCCGTGGCACTCTTTTTCCCTTTTTAAGCCCACAACTCCATGGCACTCCTTTTCCTT
1 TCCACAACTCCGTGGCAC-CTTTTT--CTTTCAAAGCCCACAACTCCGTGGCA--CCTTTTTCTT
232888 CT-AAG
61 -TAAAG
* * * *
232893 TCCACAAC-CTCGTGGCACC-TTTTCTTT-TAAGTCCACGACTCCATGGCACCTTTTTCTTTCCA
1 TCCACAACTC-CGTGGCACCTTTTTCTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT--A
232955 AAG
63 AAG
* * * *
232958 TCCACGACTCCGTGGTACCTTTTTCTTTCCAAAGTCCACGACTCCGTGGCACCTTTTTCTTTTCA
1 TCCACAACTCCGTGGCACCTTTTTCTTT-CAAAGCCCACAACTCCGTGGCACCTTTTTC-TTT-A
233023 AAG
63 AAG
* *
233026 TCCACAACTCCGTGGCA--TTCTT-TTT-AAAGCCCACAACTCCGTGGCACC-----CTTTGAAG
1 TCCACAACTCCGTGGCACCTTTTTCTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTAAAG
* * * * * ** * *
233082 CCCACAACACCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGTGCCTTCTT-TTCAAA
1 TCCACAACTCCGTGGCAC-CTTTTTCTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTAAA
233146 G
65 G
* * *
233147 CCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTTT
1 TCCACAACTCCGTGGCAC-CTTTTT--CTTTCAAAGCCCACAACTCCGTGGCACCTT-TTTCTTT
*
233212 TAAG
62 AAAG
* * * * *
233216 TCCACGACTCCGTGGCATC-TTCT-TTTCAAAGCCCACCACTCCGTGGCACC-TTTTCTTTTTAA
1 TCCACAACTCCGTGGCACCTTTTTCTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC-TTTAAA
233278 G
65 G
* * *
233279 TCCACGACCCCGTGGCACCTTGTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTGTTCCTTT
1 TCCACAACTCCGTGGCACCTTTTTC-TTTCAAAGCCCACAACTCCGTGGCAC-CTTT-TT-CTTT
*
233344 TAAG
62 AAAG
* * * * * *
233348 TCCACGACCCCGTGGCATCTTGTTCCTTT-TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTA
1 TCCACAACTCCGTGGCACCTT-TTTCTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC--TTTA
233412 AAG
63 AAG
* * * * *
233415 CCCACAACTCCGTGGCAGCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTTTTTTC
1 TCCACAACTCCGTGGCACCTTTTTC-TTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
233474 CTCTCAAAGC
Statistics
Matches: 483, Mismatches: 62, Indels: 74
0.78 0.10 0.12
Matches are distributed among these distances:
56 18 0.04
57 3 0.01
58 1 0.00
59 4 0.01
60 2 0.00
61 19 0.04
62 4 0.01
63 55 0.11
64 27 0.06
65 70 0.14
66 47 0.10
67 58 0.12
68 100 0.21
69 57 0.12
70 18 0.04
ACGTcount: A:0.19, C:0.34, G:0.14, T:0.33
Consensus pattern (65 bp):
TCCACAACTCCGTGGCACCTTTTTCTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTAAAG
Found at i:233094 original size:27 final size:27
Alignment explanation
Indices: 233052--233104 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
233042 ATTCTTTTTA
*
233052 AAGCCCACAACTCCGTGGCACCCTTTG
1 AAGCCCACAACACCGTGGCACCCTTTG
*
233079 AAGCCCACAACACCGTGGCACTCTTT
1 AAGCCCACAACACCGTGGCACCCTTT
233105 TTCCTTCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.40, G:0.17, T:0.19
Consensus pattern (27 bp):
AAGCCCACAACACCGTGGCACCCTTTG
Found at i:233162 original size:92 final size:91
Alignment explanation
Indices: 233001--233327 Score: 309
Period size: 100 Copynumber: 3.4 Consensus size: 91
232991 GTCCACGACT
* * * *
233001 CCGTGGCACCTTTTTCTTTTCAAAGTCCACAACTCCGT-GGCATTCTTTTTAAAGCCCACAACTC
1 CCGTGGCACCTTTTTC-CTTCTAAGTCCACAACTCCGTGGGCCTTCTTTTCAAAGCCCACAACTC
*
233065 CGTGGCACCC-TTTGAAGCCCACAACA
65 CGTGGCACCCTTTTAAAGCCCACAACA
233091 CCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGTGCCTTCTTTTCAAAGCCCACAACT
1 CCGTGGCAC-CTTTTTCCTTCTAAGTCCACAACTCCGTGG-GCCTTCTTTTCAAAGCCCACAACT
*
233156 CCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACT
64 CCGTGGCA--------CCCTTTTAAAGCCCACAACA
* * * *
233192 CCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGT-GGCATCTTCTTTTCAAAGCCCACCACT
1 CCGTGGCACCTTTTTCCTTCTAAGTCCACAACTCCGTGGGC--CTTCTTTTCAAAGCCCACAACT
* * * *
233256 CCGTGGCACCTTTTCTTTTTAAGTCCACGACC
64 CCGTGGCACC----CTTTTAAAGCCCACAACA
* * * *
233288 CCGTGGCACCTTGTTCTTTTCAAAGCCCACAACTCCGTGG
1 CCGTGGCACCTTTTTC-CTTCTAAGTCCACAACTCCGTGG
233328 CACTCTTTGT
Statistics
Matches: 198, Mismatches: 19, Indels: 32
0.80 0.08 0.13
Matches are distributed among these distances:
90 28 0.14
91 8 0.04
92 32 0.16
96 30 0.15
97 16 0.08
98 3 0.02
99 1 0.01
100 57 0.29
101 23 0.12
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (91 bp):
CCGTGGCACCTTTTTCCTTCTAAGTCCACAACTCCGTGGGCCTTCTTTTCAAAGCCCACAACTCC
GTGGCACCCTTTTAAAGCCCACAACA
Found at i:233394 original size:102 final size:97
Alignment explanation
Indices: 232850--233470 Score: 563
Period size: 102 Copynumber: 6.3 Consensus size: 97
232840 CTCTTTTTCC
* *
232850 CTTTTT-AAGCCCACAACTCCATGGCACTCCTTTTCCTTCTAAGTCCACAAC-CTCGTGGCACC-
1 CTTTTTAAAGCCCACAACTCCGTGGCA-T-CTTTTCCTTTTAAGTCCACAACTC-CGTGGCACCT
* *
232912 TTTTCTTTT--AAGTCCACGACTCCATGGCACCTT
63 TTTTCTTTTCAAAGTCCACAACTCCGTGGCACCTT
* * * * * * * *
232945 TTTCTTTCCAAAGTCCACGACTCCGTGGTACCTTTTTCTTTCCAAAGTCCACGACTCCGTGGCAC
1 CTT-TTT--AAAGCCCACAACTCCGTGGCATCTTTTCCTTT--TAAGTCCACAACTCCGTGGCAC
233010 CTTTTTCTTTTCAAAGTCCACAACTCCGTGGCA--TT
61 CTTTTTCTTTTCAAAGTCCACAACTCCGTGGCACCTT
* * *
233045 CTTTTTAAAGCCCACAACTCCGTGGCA-C----CCTTTGAAGCCCACAACACCGTGGCACTCTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCATCTTTTCCTTTTAAGTCCACAACTCCGTGGCAC-CTTT
* * **
233105 TTC-CTTCTAAGTCCACAACTCCGTGGTGCCTT
65 TTCTTTTCAAAGTCCACAACTCCGTGGCACCTT
* *
233137 CTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTTTAAAGCCCACAACTCCGTGGCA-TC-TTTT-CCTTTT-AAGTCCACAACTCCGTGGCACC
* * *
233202 TTGTTCCTTTT--AAGTCCACGACTCCGTGGCATCTT
62 TT-TTTCTTTTCAAAGTCCACAACTCCGTGGCACCTT
* * * * * * *
233237 CTTTTCAAAGCCCACCACTCCGTGGCACCTTTTCTTTTTAAGTCCACGACCCCGTGGCACCTTGT
1 CTTTTTAAAGCCCACAACTCCGTGGCATCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
*
233302 TCTTTTCAAAGCCCACAACTCCGTGGCACTCTTT
66 TCTTTTCAAAGTCCACAACTCCGTGGCAC-C-TT
* * * * *
233336 GTTCCTTTTAAGTCCACGACCCCGTGGCATCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCT
1 CTT--TTTAAAGCCCACAACTCCGTGGCATCTT-TTCCTTTTAAGTCCACAACTCCGTGGCACCT
* * *
233401 TTTTCTTTTTAAAGCCCACAACTCCGTGGCAGCTTTTT
63 TTTTCTTTTCAAAGTCCACAACTCCGTGGCA-C--CTT
*
233439 CTTTTTAAAGCCCACAACTCTGTGGCA-CTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCATCTTTT
233471 TTCCTCTCAA
Statistics
Matches: 429, Mismatches: 64, Indels: 62
0.77 0.12 0.11
Matches are distributed among these distances:
90 39 0.09
91 7 0.02
92 32 0.07
94 1 0.00
95 8 0.02
96 25 0.06
97 49 0.11
98 5 0.01
99 45 0.10
100 71 0.17
101 64 0.15
102 77 0.18
103 5 0.01
104 1 0.00
ACGTcount: A:0.19, C:0.34, G:0.14, T:0.33
Consensus pattern (97 bp):
CTTTTTAAAGCCCACAACTCCGTGGCATCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
TCTTTTCAAAGTCCACAACTCCGTGGCACCTT
Found at i:233483 original size:34 final size:33
Alignment explanation
Indices: 232824--233488 Score: 410
Period size: 34 Copynumber: 20.2 Consensus size: 33
232814 GGGATGAATT
* *
232824 CCACCACTCCGTGGCACTCTTTTTCCCTTTTTAAGC
1 CCACAACTCCGTGGCACT-TTTTT-CC-TTTAAAGC
* * *
232860 CCACAACTCCATGGCACTCCTTTTCCTTCT-AAGT
1 CCACAACTCCGTGGCACT-TTTTTCCTT-TAAAGC
* * *
232894 CCACAAC-CTCGTGGCAC-CTTTT-CTTTTAAGT
1 CCACAACTC-CGTGGCACTTTTTTCCTTTAAAGC
* * * *
232925 CCACGACTCCATGGCACCTTTTT-CTTTCCAAAGT
1 CCACAACTCCGTGGCACTTTTTTCCTTT--AAAGC
* * * *
232959 CCACGACTCCGTGGTACCTTTTT-CTTTCCAAAGT
1 CCACAACTCCGTGGCACTTTTTTCCTTT--AAAGC
* * * *
232993 CCACGACTCCGTGGCACCTTTTTCTTTTCAAAGT
1 CCACAACTCCGTGGCACTTTTTTCCTTT-AAAGC
*
233027 CCACAACTCCGTGGCA--TTCTT--TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCCTTTAAAGC
*
233056 CCACAACTCCGTGGCAC------CCTTTGAAGC
1 CCACAACTCCGTGGCACTTTTTTCCTTTAAAGC
* *
233083 CCACAACACCGTGGCACTCTTTTTCCTTCT-AAGT
1 CCACAACTCCGTGGCACT-TTTTTCCTT-TAAAGC
** * * *
233117 CCACAACTCCGTGGTGCCTTCTT--TTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCCTTTAAAGC
233148 CCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGC
1 CCACAACTCCGTGGCACT-TTTTT-CC-TTTAAAGC
* * * *
233184 CCACAACTCCGTGGCACCTTGTTCCTTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCCTTTAAAGC
*
233217 CCACGACTCCGTGGCATCTTCTTTT-C---AAAGC
1 CCACAACTCCGTGGCA-CTT-TTTTCCTTTAAAGC
* * * * *
233248 CCACCACTCCGTGGCAC-CTTTTCTTTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCCTTTAAAGC
* * * * *
233280 CCACGACCCCGTGGCACCTTGTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCCTTT-AAAGC
* *
233314 CCACAACTCCGTGGCACTCTTTGTTCCTTTTAAGT
1 CCACAACTCCGTGGCACT-TTT-TTCCTTTAAAGC
* * * * *
233349 CCACGACCCCGTGGCA-TCTTGTTCCTTTTAAGT
1 CCACAACTCCGTGGCACT-TTTTTCCTTTAAAGC
* *
233382 CCACAACTCCGTGGCACCTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTC-CTTTAAAGC
*
233416 CCACAACTCCGTGGCAGC-TTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCA-CTTTTTTC-CTTTAAAGC
* *
233450 CCACAACTCTGTGGCACTTTTTTCCTCTCAAAGC
1 CCACAACTCCGTGGCACTTTTTTCCT-TTAAAGC
233484 CCACA
1 CCACA
233489 CAAGTCGGTG
Statistics
Matches: 518, Mismatches: 71, Indels: 82
0.77 0.11 0.12
Matches are distributed among these distances:
27 23 0.04
28 4 0.01
29 20 0.04
30 5 0.01
31 58 0.11
32 40 0.08
33 67 0.13
34 216 0.42
35 34 0.07
36 51 0.10
ACGTcount: A:0.19, C:0.35, G:0.14, T:0.32
Consensus pattern (33 bp):
CCACAACTCCGTGGCACTTTTTTCCTTTAAAGC
Found at i:233521 original size:33 final size:33
Alignment explanation
Indices: 233474--233671 Score: 305
Period size: 32 Copynumber: 6.1 Consensus size: 33
233464 CACTTTTTTC
233474 CTCTCAAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTCT-AAAGCCCACACAAGTCGGTGGCAACCCTT
233508 CTCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
*
233540 CTTCTAAAGCCCACATAAGTCGGTGGCAACCCTT
1 C-TCTAAAGCCCACACAAGTCGGTGGCAACCCTT
* *
233574 C-CCAAAGCCCACACAAGTCGGTGGCAACCCCT
1 CTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
*
233606 C-CCAAAGCCCACACAAGTCGGTGGCAACCC-T
1 CTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
*
233637 CTCTAAAGCCCACATAAGTCGGTGGCAACCCTT
1 CTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
233670 CT
1 CT
233672 AAGCCCAATA
Statistics
Matches: 154, Mismatches: 6, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
31 2 0.01
32 90 0.58
33 53 0.34
34 9 0.06
ACGTcount: A:0.27, C:0.37, G:0.18, T:0.17
Consensus pattern (33 bp):
CTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:233778 original size:43 final size:43
Alignment explanation
Indices: 233717--234172 Score: 518
Period size: 43 Copynumber: 10.1 Consensus size: 43
233707 GCACCTTCTT
**
233717 CTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
233760 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
*
233807 TTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
233852 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C
*
233896 TTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
233941 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG---CA-C
* *
233988 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAA
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
234033 CTCCT-AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTC
1 CT-TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* * * *
234080 ATCTTTTAAGCCCAATGTCGCTAGCCTTGAATCAGCACATTGGCAC
1 --C-TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
234126 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
234169 CTTT
1 CTTT
234173 GTCATCTTTA
Statistics
Matches: 358, Mismatches: 31, Indels: 48
0.82 0.07 0.11
Matches are distributed among these distances:
43 193 0.54
44 3 0.01
45 2 0.01
46 45 0.13
47 2 0.01
49 79 0.22
50 34 0.09
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:233833 original size:92 final size:92
Alignment explanation
Indices: 233666--234223 Score: 890
Period size: 92 Copynumber: 6.0 Consensus size: 92
233656 CGGTGGCAAC
* * *
233666 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAACG
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
233731 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* *
233759 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
233824 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
233851 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-T--TCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
233913 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
233940 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
234005 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * * *
234032 ACTCCT-AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTCATCTTTTAAGCCCAAT
1 CCT-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCCAAT
* *
234096 GTCGCTAGCCTTGAATCAGCACATTGGCA
64 GTAGCTGGCCTTGAATCAGCACATTGGCA
*
234125 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAA
* *
234190 TGTCGCTGGCCTTGAATCAGCATATTGGCA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
234220 CCTT
1 CCTT
234224 CATCATCTTT
Statistics
Matches: 439, Mismatches: 17, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
89 87 0.20
90 1 0.00
91 1 0.00
92 220 0.50
93 83 0.19
95 42 0.10
96 5 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (92 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:233983 original size:181 final size:182
Alignment explanation
Indices: 233666--234223 Score: 886
Period size: 181 Copynumber: 3.0 Consensus size: 182
233656 CGGTGGCAAC
* *
233666 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAACG
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--CTTCTTTAAGTCCAATG
*
233731 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
63 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA
*
233796 TTGGCACCTTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
128 TTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
*
233851 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTCTTTAAGTCCAATGTAG
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTTTAAGTCCAATGTAG
233915 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
66 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
*
233980 GCACCATCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
131 GCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* * *
234032 ACTCCT-AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTCATCTTTTAAGCCCAAT
1 CCT-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCT--TC-TTTAAGTCCAAT
* *
234096 GTCGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
62 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
* * *
234161 ATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
127 ATTGGCACC--T-TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
234220 CCTT
1 CCTT
234224 CATCATCTTT
Statistics
Matches: 347, Mismatches: 18, Indels: 14
0.92 0.05 0.04
Matches are distributed among these distances:
181 171 0.49
182 4 0.01
183 1 0.00
184 39 0.11
185 86 0.25
188 46 0.13
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (182 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTTCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
GCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
Found at i:234204 original size:52 final size:52
Alignment explanation
Indices: 234126--234330 Score: 221
Period size: 52 Copynumber: 3.9 Consensus size: 52
234116 ACATTGGCAC
* * * *
234126 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCAT
* *
234178 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCAT
** * * * ** *
234230 CTTTAAAACCTAATGTTGTTGGCCTTGAATTAGCACATTGGCATTTTTCTCAT
1 CTTTAAGTCC-AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCAT
* * * * *
234283 CTTCAAGTCTAATGTCGCTGACCGTGAATCAGCACATTGACATCCTTT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTT
234331 TTCTTATCTT
Statistics
Matches: 125, Mismatches: 26, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
52 82 0.66
53 43 0.34
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCAT
Found at i:234505 original size:10 final size:10
Alignment explanation
Indices: 234490--234525 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
234480 TCCTTTCCAA
234490 AATCTACACC
1 AATCTACACC
234500 AATCTACACC
1 AATCTACACC
*
234510 AACCTACACC
1 AATCTACACC
*
234520 TATCTA
1 AATCTA
234526 AAGAGGTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (10 bp):
AATCTACACC
Found at i:234929 original size:13 final size:13
Alignment explanation
Indices: 234911--234935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234901 CATAAAGTGT
234911 TGTATCGATACAA
1 TGTATCGATACAA
234924 TGTATCGATACA
1 TGTATCGATACA
234936 TATTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:234951 original size:32 final size:33
Alignment explanation
Indices: 234891--234956 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
234881 TTCAACGATT
234891 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
** *
234924 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
234956 T
1 T
234957 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:235015 original size:13 final size:13
Alignment explanation
Indices: 234997--235021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234987 ATTACTCAAA
234997 TGTATCGATACAT
1 TGTATCGATACAT
235010 TGTATCGATACA
1 TGTATCGATACA
235022 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:235070 original size:52 final size:53
Alignment explanation
Indices: 235010--235147 Score: 174
Period size: 52 Copynumber: 2.7 Consensus size: 53
235000 ATCGATACAT
*** * *
235010 TGTATCGATACACTGAT-CTTTGTATTGATACATGCAGGTAAATTTGCCCAAA
1 TGTATCGATACACTGATAAAATGTATCGATACATGCAGGGAAATTTGCCCAAA
* * *
235062 TGTATCGATACA-TTATAAAATGTATCGATACATGCAGGGAAATTTGCCTAGA
1 TGTATCGATACACTGATAAAATGTATCGATACATGCAGGGAAATTTGCCCAAA
*
235114 TGTATCGATACACT-ATTAAATGTATCGATACATG
1 TGTATCGATACACTGATAAAATGTATCGATACATG
235148 TAGGAACTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 3 0.04
52 71 0.95
53 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (53 bp):
TGTATCGATACACTGATAAAATGTATCGATACATGCAGGGAAATTTGCCCAAA
Found at i:243271 original size:17 final size:17
Alignment explanation
Indices: 243251--243289 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
243241 ACTCCATAAA
243251 TTTTTGAAATAGAGAGT
1 TTTTTGAAATAGAGAGT
*
243268 TTTTTGAAATATAGAGT
1 TTTTTGAAATAGAGAGT
243285 TTTTT
1 TTTTT
243290 ACTCCATACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (17 bp):
TTTTTGAAATAGAGAGT
Found at i:243305 original size:49 final size:48
Alignment explanation
Indices: 243232--243352 Score: 152
Period size: 48 Copynumber: 2.5 Consensus size: 48
243222 TCATTTTAAT
* *
243232 GAGTTTTTTACTCCATAAATTTTTGAAATAGAGAGTTTTTTGAAATATA
1 GAGTTTTTTACTCCATAAACTTTTGAAA-AGACAGTTTTTTGAAATATA
** ** **
243281 GAGTTTTTTACTCCATACCCTTTTGAAAATCCCTTTTTTTGAAATATA
1 GAGTTTTTTACTCCATAAACTTTTGAAAAGACAGTTTTTTGAAATATA
*
243329 GAGTTTTTTACTCCATAAATTTTT
1 GAGTTTTTTACTCCATAAACTTTT
243353 TCGAGAAGAT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
48 36 0.59
49 25 0.41
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (48 bp):
GAGTTTTTTACTCCATAAACTTTTGAAAAGACAGTTTTTTGAAATATA
Found at i:243366 original size:48 final size:47
Alignment explanation
Indices: 243232--243366 Score: 139
Period size: 48 Copynumber: 2.8 Consensus size: 47
243222 TCATTTTAAT
*
243232 GAGTTTTTTACTCCATAAA-TTTTTGAAATAGAGAGTTTTTTGAAATATA
1 GAGTTTTTTACTCCATAAATTTTTTG-AA-A-AGATTTTTTTGAAATATA
*** **
243281 GAGTTTTTTACTCCAT-ACCCTTTTGAAAATCCCTTTTTTTGAAATATA
1 GAGTTTTTTACTCCATAAATTTTTTGAAAA--GATTTTTTTGAAATATA
*
243329 GAGTTTTTTACTCCATAAATTTTTTCGAGAAGATTTTT
1 GAGTTTTTTACTCCATAAATTTTTT-GAAAAGATTTTT
243367 CTTAGTTTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
46 1 0.01
47 1 0.01
48 38 0.54
49 26 0.37
50 4 0.06
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (47 bp):
GAGTTTTTTACTCCATAAATTTTTTGAAAAGATTTTTTTGAAATATA
Found at i:243514 original size:166 final size:164
Alignment explanation
Indices: 243330--243897 Score: 544
Period size: 166 Copynumber: 3.5 Consensus size: 164
243320 TGAAATATAG
* *
243330 AGTTTTTTACTCCATAAATTTTTTCGAGAAGATTTTTCTTAGTTTTAAATTTTTAAAATTCATAA
1 AGTTTTCTACTCCATAAATTTTTTCGAGGAGATTTTTCTTAGTTTTAAATTTTTAAAATTCATAA
* *
243395 AATATTATTATTTAATTCCTTTTAAATCAATTTTCAAAAATTCATTCATTTTCAATCATTTTTCT
66 AATATTATTATTTAATTCATATTAAATCAATTTTCAAAAATTCATTCATTTTCAATCATTTTTCT
* *
243460 TTTTCTCTTTGAAAATCTCCTCTTTCTGAAATACGG
131 TTTTCTCTTTG-AAATCTCCT-TTTCTGAAAAACGA
* *
243496 AGTTTTCTACTCCATAAATTTTTTCGAGGA-ATTTTTCTTGGTTTTTAAA-TTTTAAAATTCATC
1 AGTTTTCTACTCCATAAATTTTTTCGAGGAGATTTTTCTTAG-TTTTAAATTTTTAAAATTCATA
*
243559 AAATATTATTATTTAATTCATATTAAAT-AATTTTTCAAAAATTCACTCATTTT---TCA----T
65 AAATATTATTATTTAATTCATATTAAATCAA-TTTTCAAAAATTCATTCATTTTCAATCATTTTT
* ** *
243616 -TTTTTC-C-TTGAAATTTCCCTATTTCCAAAAAATGA
129 CTTTTTCTCTTTGAAATCT-CCT-TTTCTGAAAAACGA
* ** * * *
243651 AGTTTTTTTGTTCCGTAAATGTTTTT-GAGG-GTATTTTT-TTGGGTTTTTAATTTTTAAAATTC
1 AG-TTTTCTACTCCATAAAT-TTTTTCGAGGAG-ATTTTTCTT-AGTTTTAAATTTTTAAAATTC
* * * * *
243713 ATCAAATATTGTTATTTAATTCATATTAAAACAA-TTTCAAAAAATTCATTAATTTTCATGAT-T
62 ATAAAATATTATTATTTAATTCATATTAAATCAATTTTC-AAAAATTCATTCATTTTCA--ATCA
* * *
243776 TTTTTCTTTTT-TCTTTGAAATCCCCTTATTTTCGAAAAACCA
124 TTTTTCTTTTTCTCTTTGAAATCTCCTT-TTCT-GAAAAACGA
* * * * * ** *
243818 AGTTTTCTACTCCGTAAATGTTTTCAAGGAGATTTTTCTTAGTTTGAAATTCTTAAAATTTGTAT
1 AGTTTTCTACTCCATAAATTTTTTCGAGGAGATTTTTCTTAGTTTTAAATTTTTAAAATTCATAA
*
243883 AATATTGTTATTTAA
66 AATATTATTATTTAA
243898 CTCCCCATTA
Statistics
Matches: 330, Mismatches: 44, Indels: 56
0.77 0.10 0.13
Matches are distributed among these distances:
154 5 0.02
155 17 0.05
156 30 0.09
157 74 0.22
158 3 0.01
162 4 0.01
164 2 0.01
165 76 0.23
166 101 0.31
167 18 0.05
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (164 bp):
AGTTTTCTACTCCATAAATTTTTTCGAGGAGATTTTTCTTAGTTTTAAATTTTTAAAATTCATAA
AATATTATTATTTAATTCATATTAAATCAATTTTCAAAAATTCATTCATTTTCAATCATTTTTCT
TTTTCTCTTTGAAATCTCCTTTTCTGAAAAACGA
Found at i:243574 original size:165 final size:163
Alignment explanation
Indices: 243330--243877 Score: 538
Period size: 165 Copynumber: 3.4 Consensus size: 163
243320 TGAAATATAG
* * *
243330 AGTTTTTTACTCCATAAATTTTTTCGAGAAGATTTTTCTTAGTTTTAAATTTTTAAAATTCATAA
1 AGTTTTCTACTCCATAAATTTTTTCGAGGAGATTTTTCTTAGTTTTAAA-TTTTAAAATTCATCA
* *
243395 AATATTATTATTTAATTCCTTTTAAATCAATTTTCAAAAATTCATTCATTTTCAATCATTTTTCT
65 AATATTATTATTTAATTCATATTAAATCAATTTTCAAAAATTCATTCATTTTCAATCATTTTTCT
* *
243460 TTTTCTCTTTGAAAATCTCCTCTTTCTGAAATACGG
130 TTTTCTCTTTG-AAATCTCCT-TTTCTGAAAAACGA
*
243496 AGTTTTCTACTCCATAAATTTTTTCGAGGA-ATTTTTCTTGGTTTTTAAATTTTAAAATTCATCA
1 AGTTTTCTACTCCATAAATTTTTTCGAGGAGATTTTTCTTAG-TTTTAAATTTTAAAATTCATCA
*
243560 AATATTATTATTTAATTCATATTAAAT-AATTTTTCAAAAATTCACTCATTTT---TCA----T-
65 AATATTATTATTTAATTCATATTAAATCAA-TTTTCAAAAATTCATTCATTTTCAATCATTTTTC
* ** *
243616 TTTTTC-C-TTGAAATTTCCCTATTTCCAAAAAATGA
129 TTTTTCTCTTTGAAATCT-CCT-TTTCTGAAAAACGA
* ** * * *
243651 AGTTTTTTTGTTCCGTAAATGTTTTT-GAGG-GTATTTTT-TTGGGTTTTTAATTTTTAAAATTC
1 AG-TTTTCTACTCCATAAAT-TTTTTCGAGGAG-ATTTTTCTT-AG-TTTTAAATTTTAAAATTC
* * * *
243713 ATCAAATATTGTTATTTAATTCATATTAAAACAA-TTTCAAAAAATTCATTAATTTTCATGAT-T
61 ATCAAATATTATTATTTAATTCATATTAAATCAATTTTC-AAAAATTCATTCATTTTCA--ATCA
* * *
243776 TTTTTCTTTTT-TCTTTGAAATCCCCTTATTTTCGAAAAACCA
123 TTTTTCTTTTTCTCTTTGAAATCTCCTT-TTCT-GAAAAACGA
* * * *
243818 AGTTTTCTACTCCGTAAATGTTTTCAAGGAGATTTTTCTTAGTTTGAAATTCTTAAAATT
1 AGTTTTCTACTCCATAAATTTTTTCGAGGAGATTTTTCTTAGTTTTAAATT-TTAAAATT
243878 TGTATAATAT
Statistics
Matches: 315, Mismatches: 39, Indels: 56
0.77 0.10 0.14
Matches are distributed among these distances:
154 5 0.02
155 17 0.05
156 24 0.08
157 81 0.26
158 3 0.01
162 4 0.01
164 2 0.01
165 83 0.26
166 78 0.25
167 18 0.06
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (163 bp):
AGTTTTCTACTCCATAAATTTTTTCGAGGAGATTTTTCTTAGTTTTAAATTTTAAAATTCATCAA
ATATTATTATTTAATTCATATTAAATCAATTTTCAAAAATTCATTCATTTTCAATCATTTTTCTT
TTTCTCTTTGAAATCTCCTTTTCTGAAAAACGA
Found at i:244290 original size:4 final size:4
Alignment explanation
Indices: 244268--244314 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
244258 GCTGAAAAAC
* * *
244268 AAGA GAGA AAAA AAAA AAGA AAGGA AAGA AAGA AAGA AAGA AA-A AAG
1 AAGA AAGA AAGA AAGA AAGA AA-GA AAGA AAGA AAGA AAGA AAGA AAG
244315 GAAAAAATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 3 0.08
4 30 0.81
5 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:244294 original size:17 final size:16
Alignment explanation
Indices: 244262--244313 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
244252 AGTTTAGCTG
* *
244262 AAAAACAAGAGAGAAA
1 AAAAAAAAGAAAGAAA
244278 AAAAAAAAGAAAGGAAA
1 AAAAAAAAGAAA-GAAA
* *
244295 GAAAGAAAGAAAGAAA
1 AAAAAAAAGAAAGAAA
244311 AAA
1 AAA
244314 GGAAAAAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAGAAA
Found at i:244318 original size:12 final size:13
Alignment explanation
Indices: 244283--244318 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
244273 AGAAAAAAAA
244283 AAAGAAAGGAAAG
1 AAAGAAAGGAAAG
244296 AAAGAAA-GAAAG
1 AAAGAAAGGAAAG
244308 AAA-AAAGGAAA
1 AAAGAAAGGAAA
244319 AAATGGTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 12 0.55
13 7 0.32
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AAAGAAAGGAAAG
Found at i:246244 original size:153 final size:153
Alignment explanation
Indices: 245934--246328 Score: 383
Period size: 154 Copynumber: 2.6 Consensus size: 153
245924 ATCCCTTTGG
* * * *
245934 GGCATTTTAGT-ATTTTTCTAGAACCGAGTCCTAGTTTATCACTGGGTCTACTTTTATGTTGAAG
1 GGCATTTTAGTAATTTTT-TAGAATCGAGTCCTAGGTTGTCACTGGGTC-ACTTTTATGTCGAAG
* *
245998 GTGGGTATTTAGGATAGGTTCA-CCCTTTTTCTAATCCTTTAAAGTCCTTTAAGGGTATTGAGCA
64 GTGGGTATTTAGGATAAGTTCATCCC-TTTTCTAATCCTTTAAAGTCCTTTAAGGGTATCGAGCA
** * * * *
246062 CTTCTACGTTGAAGGTATCCTTTAGA
128 CTTCTACGACGAAAGTAACCTCTAAA
* * * * *
246088 GGCATTTTGGTAATTTTTTAGAATCAAGTCCTAGGTTGTCACCGGGTCACTATTATGCCGAAGGT
1 GGCATTTTAGTAATTTTTTAGAATCGAGTCCTAGGTTGTCACTGGGTCACTTTTATGTCGAAGGT
* * *
246153 GGGTATTTAGGATAAGTTCATCCC-TTTCATAATTCTCTT-AAGT-CTTTTAGGGTAATCGAGAT
66 GGGTATTTAGGATAAGTTCATCCCTTTTC-TAATCCT-TTAAAGTCCTTTAAGGGT-ATCGAG-C
*
246215 ACTTTTACGACGAAAGTAACC-CTAAA
127 ACTTCTACGACGAAAGTAACCTCTAAA
* * * ** **
246241 GGCATTTTTA-TAATTTTTTAAAATCGATTCCT-GAGTTGCCACTGCATTTGCTTTTATGTCGAA
1 GGCA-TTTTAGTAATTTTTTAGAATCGAGTCCTAG-GTTGTCACTG-GGTCACTTTTATGTCGAA
*
246304 GGTGGGTATTGAGGATAAGTTCATC
63 GGTGGGTATTTAGGATAAGTTCATC
246329 TAATCCATAA
Statistics
Matches: 198, Mismatches: 34, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
152 14 0.07
153 82 0.41
154 96 0.48
155 6 0.03
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (153 bp):
GGCATTTTAGTAATTTTTTAGAATCGAGTCCTAGGTTGTCACTGGGTCACTTTTATGTCGAAGGT
GGGTATTTAGGATAAGTTCATCCCTTTTCTAATCCTTTAAAGTCCTTTAAGGGTATCGAGCACTT
CTACGACGAAAGTAACCTCTAAA
Found at i:256497 original size:167 final size:164
Alignment explanation
Indices: 255967--256567 Score: 502
Period size: 165 Copynumber: 3.6 Consensus size: 164
255957 CGATATATAT
* * * ** * ** *
255967 AAAAAATT-TAAAATTTATGAAATAAATAGAATATTTCAAAACTGATTTAATGGGAGTTAAATAA
1 AAAAAATTCAAAAATTTATGAAAAAAAT-GAATTTTTGTAGACTGATTTAATATGAATTAAATAA
* ** * ** * **
256031 CAATA-TTAGATGAATTTTAAACATTTTAAATCAAGAAAAA-TCACCTCAAAAATATTTATTGAG
65 CAATATTTA-ATGAATTTTAAAAATTAAAAACCAAGAAAAATTC-CCTTGAAAACATTTACAGAG
**
256094 TAGAAAACTTAGTTTTTTGAAAAAAGGGCATTTTAAAG
128 TAGAAAACTTA-TTTTTTGAAAAAAGGAAATTTTAAAG
* * * * * * ** *
256132 AAAAAA-TCCAAAACTTATAAAAATAAATTAATTTTT-TAAAACTAATTTAATATGAATCCAATG
1 AAAAAATTCAAAAATTTATGAAAA-AAATGAATTTTTGT-AGACTGATTTAATATGAATTAAATA
* * ** * *
256195 ACAATATTTTAT-AAGTTTTAAAAA-TCAAAACCAAGAAAAATTCCAGTGAAAGCATTTACGGAG
64 ACAATATTTAATGAA-TTTTAAAAATTAAAAACCAAGAAAAATTCCCTTGAAAACATTTACAGAG
* * * * * *
256258 TAAAAAACTTCA-TATTTAAAAAATAAGAAAATTTCAAG
128 TAGAAAACTT-ATTTTTTGAAAAA-AGGAAATTTTAAAG
* * * * * *
256296 GAAAAATTGAAAAATTTATGAAAATAAGTGAATTTTTGTAGACTGATTTAATGTGAATAAAATGA
1 AAAAAATTCAAAAATTTATGAAAA-AAATGAATTTTTGTAGACTGATTTAATATGAATTAAATAA
* *
256361 TAATATTTAATGAATTTTAAAAATTAAAAACCAAGAAAAATTCCCTTGAAAACATTTACAAAGTA
65 CAATATTTAATGAATTTTAAAAATTAAAAACCAAGAAAAATTCCCTTGAAAACATTTACAGAGTA
*
256426 GAAAACTCTATTTTTTGGAAACAAGGAAATTTTAAAG
130 GAAAACT-TATTTTTT-GAAAAAAGGAAATTTTAAAG
* * *
256463 AAAAAATTCAAAAATTTATGAATAAGAATGAATTTTTG-AGAATTGATTTTATATGAATTAAATA
1 AAAAAATTCAAAAATTTATGAA-AAAAATGAATTTTTGTAG-ACTGATTTAATATGAATTAAATA
* * *
256527 ATAATATTTGATGAATTTTAAAAATTAAATACCAA-AAAAAT
64 ACAATATTTAATGAATTTTAAAAATTAAAAACCAAGAAAAAT
256568 CCTATTGAAA
Statistics
Matches: 346, Mismatches: 73, Indels: 33
0.77 0.16 0.07
Matches are distributed among these distances:
163 9 0.03
164 51 0.15
165 123 0.36
166 59 0.17
167 98 0.28
168 6 0.02
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (164 bp):
AAAAAATTCAAAAATTTATGAAAAAAATGAATTTTTGTAGACTGATTTAATATGAATTAAATAAC
AATATTTAATGAATTTTAAAAATTAAAAACCAAGAAAAATTCCCTTGAAAACATTTACAGAGTAG
AAAACTTATTTTTTGAAAAAAGGAAATTTTAAAG
Done.