Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1335
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: 53465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:2048 original size:9 final size:9
Alignment explanation
Indices: 2034--2064 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2024 TCTGAGTCAC
*
2034 CATCATCAT
1 CATCATCTT
2043 CATCATCTT
1 CATCATCTT
2052 CATCATCTT
1 CATCATCTT
2061 CATC
1 CATC
2065 GTCCTTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (9 bp):
CATCATCTT
Found at i:3694 original size:19 final size:20
Alignment explanation
Indices: 3651--3701 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3641 TACAAGCCAA
*
3651 TGTATCGATACATTTTATGG
1 TGTATCGATACATCTTATGG
3671 TGTATCGATACATACTT-T-G
1 TGTATCGATACAT-CTTATGG
3690 TGTATCGATACA
1 TGTATCGATACA
3702 AGTTTAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.45
20 14 0.48
21 2 0.07
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATCTTATGG
Found at i:3781 original size:20 final size:20
Alignment explanation
Indices: 3756--3808 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3746 TATTTTTTAA
3756 GTATCGATACAATGCAACAT
1 GTATCGATACAATGCAACAT
**
3776 GTATCGATACTGTGCAACAT
1 GTATCGATACAATGCAACAT
3796 GTATCGATACAAT
1 GTATCGATACAAT
3809 TAAATGTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (20 bp):
GTATCGATACAATGCAACAT
Found at i:4911 original size:13 final size:13
Alignment explanation
Indices: 4893--4918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4883 ATAGTAACCC
4893 ATGTATCGATACA
1 ATGTATCGATACA
4906 ATGTATCGATACA
1 ATGTATCGATACA
4919 TCTGGGTTTT
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:8822 original size:33 final size:33
Alignment explanation
Indices: 8780--8846 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
8770 TTCTTTTTAC
8780 AGCATGCAAATGAGACTCCTTAGGTGCGGATTA
1 AGCATGCAAATGAGACTCCTTAGGTGCGGATTA
8813 AGCATGCAAATGAGACTCCTTAGGTGCGGATTA
1 AGCATGCAAATGAGACTCCTTAGGTGCGGATTA
8846 A
1 A
8847 AAATGAGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (33 bp):
AGCATGCAAATGAGACTCCTTAGGTGCGGATTA
Found at i:14064 original size:19 final size:20
Alignment explanation
Indices: 14019--14070 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
14009 TTACAAGCCA
*
14019 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
14039 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
14059 -TGTATCGATACA
1 ATGTATCGATACA
14071 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:14159 original size:20 final size:21
Alignment explanation
Indices: 14112--14164 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
14102 GCCAATGACC
*
14112 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
14133 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
14153 TGTATCGATACA
1 TGTATCGATACA
14165 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:14170 original size:13 final size:13
Alignment explanation
Indices: 14152--14176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14142 ACATTTGGTC
14152 ATGTATCGATACA
1 ATGTATCGATACA
14165 ATGTATCGATAC
1 ATGTATCGATAC
14177 TGTGCAATCT
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:15850 original size:155 final size:155
Alignment explanation
Indices: 15476--17059 Score: 1447
Period size: 155 Copynumber: 10.3 Consensus size: 155
15466 GTTATCAGGA
* * * * * * *
15476 TACTTTCACGTCAAAAGTATCTCC-AGAGGTATTTTTGTAATTTTTTAAAACCAACT-TTAGGTT
1 TACTTTTACGTCGAAAGTATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGGTT
** * * *
15539 GTCG-TTGGTCTACTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAAT-TT
66 GTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCT
* *
15602 TTTTAAGTTCTTTAGGGGTATCGAG
131 TTTTAAGTCCTTTAGGGGTACCGAG
* * * * * * * *
15627 TACTTGTACATTGAAAGTATCCCCCATGGGCATTTTCATAATTTTTTAGAACCAACTCATAGGTT
1 TACTTTTACGTCGAAAGTATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGGTT
* * *
15692 GTCGCCGGGTCTGCTTTTATACCAAAGGTGGGCAGTTAGGATAGGTTTATCCCTTTTATAGTCAT
66 GTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCT
* * * *
15757 TTTAAAGTCCTTTAAGGCTACCAAG
131 TTTTAAGTCCTTTAGGGGTACCGAG
** * * *
15782 TACTTTTACGTCGAAAGTATCCCCTAGGGGTATTTTTATAATTTTATAGAACCAACTCTTAAGTT
1 TACTTTTACGTCGAAAGTATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGGTT
** * * * *
15847 GTCGTTGGGTCCGCTTTTAGGCCAAAGGT-GGCAGTTAGGATAGGTTCATCCCATTTCA-A-ACC
66 GTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCC-TTTTATAGTCC
* ** *
15909 TTTTTTAGTCCTTTAAAGGTAGCGAG
130 TTTTTAAGTCCTTTAGGGGTACCGAG
* *
15935 TACTTTTACGTC-AAAGGTATCCCCTAGGGGTATTTTTGTAATTTTTTAGAACTAACTCCTAGGT
1 TACTTTTACGTCGAAA-GTATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGGT
* * * * * *
15999 TGTCACCGGAT-TCGC--TTATGCCAAAGGTGAG-TGTTTAGGATAGGTTCATTCC-TTTATAAT
65 TGTCGCCGGGTCT-GCTTTTATGCCAAAGGTGGGCAG-TTAGGATAGGTTCATCCCTTTTATAGT
* * *
16059 CATTTTTAAGTCCTTTAAGGGTACCAAG
128 CCTTTTTAAGTCCTTTAGGGGTACCGAG
* * * * * *
16087 ATACGTTCATGTCG-AAGATATCCCTTAGGGGCATTTTCGTAATTTTTTAGAACCAACACCTAGG
1 -TACTTTTACGTCGAAAG-TATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGG
* * **
16151 TTGTCGCCGGGTCTGCATTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCGT-CCTATTT-TAAA
64 TTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCT-TTTATAGT
* * *
16214 CCTTTTAAAGTCCTTTAGGGGTATCGGG
128 CCTTTTTAAGTCCTTTAGGGGTACCGAG
* * * * * *
16242 TACTTATACATCGAAGGTATCCCATAAGGGTATTTTCGTAA-TTTTTAGAACCAACTCATAGGTT
1 TACTTTTACGTCGAAAGTATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGGTT
* **
16306 GTCGCCAGGTCCACTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCT
66 GTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCT
* *
16371 TTTTAAGTCATTTAGGGGTACCGTG
131 TTTTAAGTCCTTTAGGGGTACCGAG
* * * * * *
16396 TACTTGTATGTCGAAGGTATCCCCTAGAGGTATTTTTGTAACTTTTTAGAACCAACTCCTAGGTT
1 TACTTTTACGTCGAAAGTATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGGTT
* * * * * *
16461 ATCGTCGGGTCCGCTTTTATGCCAAAGGTGGGCAATTAGGATAGGTTCATCCCATTTCA-A-ACC
66 GTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCC-TTTTATAGTCC
*
16524 TTTTTAAGTCCTTTAGGGGTATC-AGG
130 TTTTTAAGTCCTTTAGGGGTACCGA-G
* * * * * *
16550 TACTTTTATGTC-AAAG-GTCCTC-AAGGGTCTTTTCGTAATTTTTTAGAACCAACTCTTAGGTT
1 TACTTTTACGTCGAAAGTATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGGTT
* * * * * * *
16612 GTCACCGAGTCCGCTTTTATGCCGATA-GTGGGCATTTAGGATAGGTTCATTCCTTTTATAGTCT
66 GTCGCCGGGTCTGCTTTTATGCC-AAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCC
* *
16676 TTTTTAAGTCTTTTAGGGGTACCTAG
130 TTTTTAAGTCCTTTAGGGGTACCGAG
* ** * * * * * * * *
16702 ATACTTTCATATCG-AAGATATCCCCTAAGGGCATTTTCATAATTTTTTAGAATCGATTCTTAAG
1 -TACTTTTACGTCGAAAG-TATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGG
* * * * * * *
16766 TTATCACCGGGTCTGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCATTCCTTTTATAGTC
64 TTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTC
* * *
16831 CTTTTTAAGTCTTTTAGGGGTAACAAG
129 CTTTTTAAGTCCTTTAGGGGTACCGAG
* * ** * ** *
16858 ATACTTTCATGTCGAAAGTATCCTTTAGTGGTATTTTCGTAATTTTTTAGAACTGAGTCCTAGGT
1 -TACTTTTACGTCGAAAGTATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGGT
* ** * * * ** * * * *
16923 TATAACTGGGCCTGCTTTTATGCCGAATATGAGTATTTAAGATAGGTTCATCCCTTTTATAGTCC
65 TGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCC
* * ** *
16988 TTTTTAAGTCCTTTAAGAGTATTGGG
130 TTTTTAAGTCCTTTAGGGGTACCGAG
* * * *
17014 TACTTATACGTC-AAAGATATCCCCTAAGGGCATTTTTGTAATTTTT
1 TACTTTTACGTCGAAAG-TATCCCCTAGGGGTATTTTCGTAATTTTT
17060 CTTGAACTTA
Statistics
Matches: 1186, Mismatches: 209, Indels: 72
0.81 0.14 0.05
Matches are distributed among these distances:
150 7 0.01
151 110 0.09
152 100 0.08
153 245 0.21
154 208 0.18
155 267 0.23
156 246 0.21
157 3 0.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.38
Consensus pattern (155 bp):
TACTTTTACGTCGAAAGTATCCCCTAGGGGTATTTTCGTAATTTTTTAGAACCAACTCCTAGGTT
GTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCT
TTTTAAGTCCTTTAGGGGTACCGAG
Found at i:16482 original size:308 final size:307
Alignment explanation
Indices: 15500--17059 Score: 1554
Period size: 308 Copynumber: 5.1 Consensus size: 307
15490 AAGTATCTCC
* * * *
15500 AGAGGTATTTTTGTAATTTTTTAAAACCAACT-TTAGGTTGTCGT-TGGTCTACTTTTATGCCAA
1 AGAGGCATTTTTGTAATTTTTTAGAACCAACTCTTAGGTTGTCGTCGGGTCTGCTTTTATGCCAA
** * *
15563 AGGTGGGCAGTTAGGATAGGTTCATCCC-TTTTATAATTTTTTTAAGTTCTTTAGGGGTATCGAG
66 AGGTGGGCAGTTAGGATAGGTTCATCCCATTTTA-AACCTTTTTAAGTCCTTTAGGGGTATCGGG
* * * * * * *
15627 TACTTGTACATTGAAAGTATCCCCCATGGGCATTTTCATAATTTTTTAGAACCAACTCATAGGTT
130 TACTTTTACATCGAAGGTATCCCCTAAGGGTATTTTCGTAATTTTTTAGAACCAACTCATAGGTT
* * * *
15692 GTCGCCGGGTCTGCTTTTATACCAAAGGTGGGCAGTTAGGATAGGTTTATCCCTTTTATAGTCAT
195 GTCACC-GGTCCGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCAT
* * *
15757 TTTAAAGTCCTTTAAGGCTACCAAGTACTTTTACGTCGAA-AGTATCCCCT
259 TTTTAAGTCCTTTAAGGGTACCAAGTAC-TTTATGTCGAAGA-TATCCCCT
* * * * * * * *
15807 AGGGGTATTTTTATAATTTTATAGAACCAACTCTTAAGTTGTCGTTGGGTCCGCTTTTAGGCCAA
1 AGAGGCATTTTTGTAATTTTTTAGAACCAACTCTTAGGTTGTCGTCGGGTCTGCTTTTATGCCAA
* * ** * *
15872 AGGT-GGCAGTTAGGATAGGTTCATCCCATTTCAAACCTTTTTTAGTCCTTTAAAGGTAGCGAGT
66 AGGTGGGCAGTTAGGATAGGTTCATCCCATTTTAAACCTTTTTAAGTCCTTTAGGGGTATCGGGT
* * * * * *
15936 ACTTTTACGTCAAAGGTATCCCCTAGGGGTATTTTTGTAATTTTTTAGAACTAACTCCTAGGTTG
131 ACTTTTACATCGAAGGTATCCCCTAAGGGTATTTTCGTAATTTTTTAGAACCAACTCATAGGTTG
* * * * *
16001 TCACCGGATTCGC--TTATGCCAAAGGTGAG-TGTTTAGGATAGGTTCATTCC-TTTATAATCAT
196 TCACCGG-TCCGCTTTTATGCCAAAGGTGGGCAG-TTAGGATAGGTTCATCCCTTTTATAGTCAT
* *
16062 TTTTAAGTCCTTTAAGGGTACCAAGATACGTTCATGTCGAAGATATCCCTT
259 TTTTAAGTCCTTTAAGGGTACCAAG-TAC-TTTATGTCGAAGATATCCCCT
* * * * * *
16113 AGGGGCATTTTCGTAATTTTTTAGAACCAACACCTAGGTTGTCGCCGGGTCTGCATTTATGCCAA
1 AGAGGCATTTTTGTAATTTTTTAGAACCAACTCTTAGGTTGTCGTCGGGTCTGCTTTTATGCCAA
* * *
16178 AGGTGGGCAGTTAGGATAGGTTCGTCCTATTTTAAACCTTTTAAAGTCCTTTAGGGGTATCGGGT
66 AGGTGGGCAGTTAGGATAGGTTCATCCCATTTTAAACCTTTTTAAGTCCTTTAGGGGTATCGGGT
* *
16243 ACTTATACATCGAAGGTATCCCATAAGGGTATTTTCGTAA-TTTTTAGAACCAACTCATAGGTTG
131 ACTTTTACATCGAAGGTATCCCCTAAGGGTATTTTCGTAATTTTTTAGAACCAACTCATAGGTTG
* * *
16307 TCGCCAGGTCCACTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCTT
196 TCACC-GGTCCGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCATT
* * ** *
16372 TTTAAGTCATTTAGGGGTACCGTGTACTTGTATGTCGAAGGTATCCCCT
260 TTTAAGTCCTTTAAGGGTACCAAGTACTT-TATGTCGAAGATATCCCCT
* * * * *
16421 AGAGGTATTTTTGTAACTTTTTAGAACCAACTCCTAGGTTATCGTCGGGTCCGCTTTTATGCCAA
1 AGAGGCATTTTTGTAATTTTTTAGAACCAACTCTTAGGTTGTCGTCGGGTCTGCTTTTATGCCAA
* * *
16486 AGGTGGGCAATTAGGATAGGTTCATCCCATTTCAAACCTTTTTAAGTCCTTTAGGGGTATCAGGT
66 AGGTGGGCAGTTAGGATAGGTTCATCCCATTTTAAACCTTTTTAAGTCCTTTAGGGGTATCGGGT
** * * * *
16551 ACTTTTATGTCAAAGG--TCCTC-AAGGGTCTTTTCGTAATTTTTTAGAACCAACTCTTAGGTTG
131 ACTTTTACATCGAAGGTATCCCCTAAGGGTATTTTCGTAATTTTTTAGAACCAACTCATAGGTTG
* * * *
16613 TCACCGAGTCCGCTTTTATGCCGATA-GTGGGCATTTAGGATAGGTTCATTCCTTTTATAGTCTT
196 TCACCG-GTCCGCTTTTATGCC-AAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCAT
* * * *
16677 TTTTAAGTCTTTTAGGGGTACCTAGATACTTTCATATCGAAGATATCCCCT
259 TTTTAAGTCCTTTAAGGGTACCAAG-TACTTT-ATGTCGAAGATATCCCCT
** * * * * * ** *
16728 A-AGGGCATTTTCATAATTTTTTAGAATCGATTCTTAAGTTATCACCGGGTCTGCTTTTATGCCG
1 AGA-GGCATTTTTGTAATTTTTTAGAACCAACTCTTAGGTTGTCGTCGGGTCTGCTTTTATGCCA
* * * * * * *
16792 AATGTGGGTATTTAGGATAGGTTCATTCC-TTTTATAGTCCTTTTTAAGTCTTTTAGGGGTAACA
65 AAGGTGGGCAGTTAGGATAGGTTCATCCCATTTTA-A-ACCTTTTTAAGTCCTTTAGGGGTATC-
* * * ** * * * ** * *
16856 AGATACTTTCATGTCGAAAGTAT-CCTTTAGTGGTATTTTCGTAATTTTTTAGAACTGAGTCCTA
127 GGGTACTTTTACATCGAAGGTATCCCCTAAG-GGTATTTTCGTAATTTTTTAGAACCAACTCATA
* * * * * ** * * * *
16920 GGTTATAACTGGGCCTGCTTTTATGCCGAATATGAGTATTTAAGATAGGTTCATCCCTTTTATAG
191 GGTTGTCACCGGTCC-GCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAG
* * **** * *
16985 TCCTTTTTAAGTCCTTTAAGAGTATTGGGTACTTATACGTCAAAGATATCCCCT
255 TCATTTTTAAGTCCTTTAAGGGTACCAAGTACTT-TATGTCGAAGATATCCCCT
17039 A-AGGGCATTTTTGTAATTTTT
1 AGA-GGCATTTTTGTAATTTTT
17060 CTTGAACTTA
Statistics
Matches: 1044, Mismatches: 179, Indels: 56
0.82 0.14 0.04
Matches are distributed among these distances:
305 50 0.05
306 242 0.23
307 218 0.21
308 319 0.31
309 70 0.07
310 1 0.00
311 46 0.04
312 98 0.09
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (307 bp):
AGAGGCATTTTTGTAATTTTTTAGAACCAACTCTTAGGTTGTCGTCGGGTCTGCTTTTATGCCAA
AGGTGGGCAGTTAGGATAGGTTCATCCCATTTTAAACCTTTTTAAGTCCTTTAGGGGTATCGGGT
ACTTTTACATCGAAGGTATCCCCTAAGGGTATTTTCGTAATTTTTTAGAACCAACTCATAGGTTG
TCACCGGTCCGCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCATTT
TTAAGTCCTTTAAGGGTACCAAGTACTTTATGTCGAAGATATCCCCT
Found at i:16750 original size:615 final size:610
Alignment explanation
Indices: 15513--17059 Score: 1793
Period size: 615 Copynumber: 2.5 Consensus size: 610
15503 GGTATTTTTG
* * ** *
15513 TAATTTTTTAAAACCAACTTTAGGTTGTCG-TTGGTCTACTTTTATGCCAAAGGTGGGCAGTTAG
1 TAATTTTTTAGAACCAACCTTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAG
* ** * * *
15577 GATAGGTTCATCCCTTTTATAATTTTTTTAAGTTCTTTAGGGGTATCGAGTACTTGTACATTGAA
66 GATAGGTTCATCCTTTTTA-AACCTTTTTAAGTCCTTTAGGGGTATCGGGTACTT-TACATCGAA
** * * * * *
15642 AGTATCCCCCATGGGCATTTTCATAATTTTTTAGAACCAACTCATAGGTTGTCGCCGGGTCTGCT
129 AGTATCCCATAAGGGTATTTTCGTAATTTTTTAGAACCAACTCATAGGTTGTCGCCAGGTCCGCT
* * * *
15707 TTTATACCAAAGGTGGGCAGTTAGGATAGGTTTATCCCTTTTATAGTCATTTTAAAGTCCTTTAA
194 TTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAGTCCTTTAA
* * * * * *
15772 GGCTACCAAGTACTTTTACGTCGAAAGTATCCCCTAGGGGTATTTTTATAATTTTATAGAACCAA
259 GGGTACCGAGTACTTATACGTCGAAGGTATCCCCTAGAGGTATTTTTGTAATTTT-TAGAACCAA
* * * *
15837 CTCTTAAGTTGTCGTTGGGTCCGCTTTTAGGCCAAAGGTGGCAGTTAGGATAGGTTCATCCCATT
323 CTCCTAAGTTATCGTCGGGTCCGCTTTTAGGCCAAAGGTGGCAATTAGGATAGGTTCATCCCATT
* *
15902 TCAAACCTTTTTTAGTCCTTTAAAGGTAGCGAGTACTTTTACGTCAAAGGTATCCCCTAGGGGTA
388 TCAAACCTTTTTAAGTCCTTTAAAGGTAGCGAGTACTTTTACGTCAAAGG-ATCCCCTAAGGGTA
* * * **
15967 TTTTTGTAATTTTTTAGAACTAACTCCTAGGTTGTCACCGGATTCGCTTATGCCAAAGGTGAGTG
452 TTTTCGTAATTTTTTAGAACCAACTCCTAGGTTGTCACCGGATCCGCTTATGCCAAAGGTGAGCA
16032 TTTAGGATAGGTTCATTCCTTTATAATCATTTTTAAGTCCTTTAAGGGTACCAAGATACGTTCAT
517 TTTAGGATAGGTTCATTCCTTTATAATCATTTTTAAGTCCTTTAAGGGTACCAAGATACGTTCAT
* * * *
16097 GTCGAAGATATCCCTTAGGGGCATTTTCG
582 ATCGAAGATATCCCCTAAGGGCATTTTCA
* *
16126 TAATTTTTTAGAACCAACACCTAGGTTGTCGCCGGGTCTGCATTTATGCCAAAGGTGGGCAGTTA
1 TAATTTTTTAGAACCAAC-CTTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTA
* *
16191 GGATAGGTTCGTCCTATTTTAAACCTTTTAAAGTCCTTTAGGGGTATCGGGTACTTATACATCGA
65 GGATAGGTTCATCCT-TTTTAAACCTTTTTAAGTCCTTTAGGGGTATCGGGTACTT-TACATCGA
* *
16256 AGGTATCCCATAAGGGTATTTTCGTAA-TTTTTAGAACCAACTCATAGGTTGTCGCCAGGTCCAC
128 AAGTATCCCATAAGGGTATTTTCGTAATTTTTTAGAACCAACTCATAGGTTGTCGCCAGGTCCGC
*
16320 TTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAGTCATTTA
193 TTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAGTCCTTTA
* * * *
16385 GGGGTACCGTGTACTTGTATGTCGAAGGTATCCCCTAGAGGTATTTTTGTAACTTTTTAGAACCA
258 AGGGTACCGAGTACTTATACGTCGAAGGTATCCCCTAGAGGTATTTTTGTAA-TTTTTAGAACCA
* *
16450 ACTCCTAGGTTATCGTCGGGTCCGCTTTTATGCCAAAGGTGGGCAATTAGGATAGGTTCATCCCA
322 ACTCCTAAGTTATCGTCGGGTCCGCTTTTAGGCCAAAGGT-GGCAATTAGGATAGGTTCATCCCA
** * * *
16515 TTTCAAACCTTTTTAAGTCCTTTAGGGGTATC-AGGTACTTTTATGTCAAAGG-TCCTC-AAGGG
386 TTTCAAACCTTTTTAAGTCCTTTAAAGGTAGCGA-GTACTTTTACGTCAAAGGATCCCCTAAGGG
* * *
16577 TCTTTTCGTAATTTTTTAGAACCAACTCTTAGGTTGTCACC-GAGTCCGCTTTTATGCCGATA-G
450 TATTTTCGTAATTTTTTAGAACCAACTCCTAGGTTGTCACCGGA-TCCGC--TTATGCC-AAAGG
* * * * * *
16640 TGGGCATTTAGGATAGGTTCATTCCTTTTATAGTCTTTTTTAAGTCTTTTAGGGGTACCTAGATA
511 TGAGCATTTAGGATAGGTTCATTCC-TTTATAATCATTTTTAAGTCCTTTAAGGGTACCAAGATA
*
16705 CTTTCATATCGAAGATATCCCCTAAGGGCATTTTCA
575 CGTTCATATCGAAGATATCCCCTAAGGGCATTTTCA
* ** * * * * * * *
16741 TAATTTTTTAGAATCGATTCTTAAGTTATCACCGGGTCTGCTTTTATGCCGAATGTGGGTATTTA
1 TAATTTTTTAGAA-CCAACCTTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTA
** * * * *
16806 GGATAGGTTCATTCCTTTTATAGTCCTTTTTAAGTCTTTTAGGGGTAACAAGATACTTT-CATGT
65 GGATAGGTTCA-TCCTTTT-TAAACCTTTTTAAGTCCTTTAGGGGTATC-GGGTACTTTACA--T
* * ** * * * ** * *
16870 CGAAAGTAT-CCTTTAGTGGTATTTTCGTAATTTTTTAGAACTGAGTCCTAGGTTAT-AACTGGG
125 CGAAAGTATCCCATAAG-GGTATTTTCGTAATTTTTTAGAACCAACTCATAGGTTGTCGCCAGGT
* ** * * * *
16933 CCTGCTTTTATGCCGAATATGAGTATTTAAGATAGGTTCATCCCTTTTATAGTCCTTTTTAAGTC
189 CC-GCTTTTATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAGTC
* ** * * * *
16998 CTTTAAGAGTATTGGGTACTTATACGTCAAAGATATCCCCTA-AGGGCATTTTTGTAATTTTT
253 CTTTAAGGGTACCGAGTACTTATACGTCGAAGGTATCCCCTAGA-GGTATTTTTGTAATTTTT
17060 CTTGAACTTA
Statistics
Matches: 791, Mismatches: 122, Indels: 38
0.83 0.13 0.04
Matches are distributed among these distances:
611 2 0.00
612 45 0.06
613 21 0.03
614 221 0.28
615 304 0.38
616 41 0.05
617 39 0.05
618 118 0.15
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.38
Consensus pattern (610 bp):
TAATTTTTTAGAACCAACCTTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAG
GATAGGTTCATCCTTTTTAAACCTTTTTAAGTCCTTTAGGGGTATCGGGTACTTTACATCGAAAG
TATCCCATAAGGGTATTTTCGTAATTTTTTAGAACCAACTCATAGGTTGTCGCCAGGTCCGCTTT
TATGCCAAAGGTGGGCAGTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAGTCCTTTAAGG
GTACCGAGTACTTATACGTCGAAGGTATCCCCTAGAGGTATTTTTGTAATTTTTAGAACCAACTC
CTAAGTTATCGTCGGGTCCGCTTTTAGGCCAAAGGTGGCAATTAGGATAGGTTCATCCCATTTCA
AACCTTTTTAAGTCCTTTAAAGGTAGCGAGTACTTTTACGTCAAAGGATCCCCTAAGGGTATTTT
CGTAATTTTTTAGAACCAACTCCTAGGTTGTCACCGGATCCGCTTATGCCAAAGGTGAGCATTTA
GGATAGGTTCATTCCTTTATAATCATTTTTAAGTCCTTTAAGGGTACCAAGATACGTTCATATCG
AAGATATCCCCTAAGGGCATTTTCA
Found at i:18820 original size:42 final size:41
Alignment explanation
Indices: 18753--18997 Score: 169
Period size: 41 Copynumber: 5.9 Consensus size: 41
18743 TTCTTTCCTT
* *
18753 TTAGTCCCAGTCAA-CTTTTATCCTTTGTTCACTTGTCGAC
1 TTAGTCCCAGTAAATCTTTTATCCTTTGTTGACTTGTCGAC
* *
18793 TTAGTCCCAAGTAAATCTCTTATCCTTTGTTGA-TTCGTCG-G
1 TTAGTCCC-AGTAAATCTTTTATCCTTTGTTGACTT-GTCGAC
* * * * * * *
18834 TTCAATCCCATTTAATCTTTCATTCTTTGTTTACTTGTCGGC
1 TT-AGTCCCAGTAAATCTTTTATCCTTTGTTGACTTGTCGAC
*
18876 TTAGTCCCGGGTAAACTCTTTTAT-CTTTGGTTGACTTGTCGA-
1 TTAGTCCC-AGTAAA-TCTTTTATCCTTT-GTTGACTTGTCGAC
* * ** * *
18918 TTGATTCCCGGTCGACCTTTTATCCTTTGTTTACTTGTCGAC
1 TT-AGTCCCAGTAAATCTTTTATCCTTTGTTGACTTGTCGAC
* * * *
18960 TTAGTCCTAGGTGAATCCTTCTATCCTTT-TTAACTTGT
1 TTAGTCCCA-GTAAAT-CTTTTATCCTTTGTTGACTTGT
18998 TGGTTTATTC
Statistics
Matches: 159, Mismatches: 32, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
40 8 0.05
41 59 0.37
42 58 0.36
43 34 0.21
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (41 bp):
TTAGTCCCAGTAAATCTTTTATCCTTTGTTGACTTGTCGAC
Found at i:18956 original size:84 final size:83
Alignment explanation
Indices: 18757--18966 Score: 237
Period size: 84 Copynumber: 2.5 Consensus size: 83
18747 TTCCTTTTAG
*
18757 TCCCAGTCAA-CTTTTATCCTTTGTTCACTTGTCGACTTAGTCCCAAGTAAATCTCTTATCCTTT
1 TCCCAGTCAACCTTTTATCCTTTGTTTACTTGTCGACTTAGTCCCAAGTAAATCTCTTATCCTTT
*
18821 GTTGATTCGTCGGTTCAA
66 GTTGATTCGTCGATTCAA
* * * * * * ** *
18839 TCCCATTTAATCTTTCATTCTTTGTTTACTTGTCGGCTTAGTCCCGGGTAAACTCTTTTAT-CTT
1 TCCCAGTCAACCTTTTATCCTTTGTTTACTTGTCGACTTAGTCCCAAGTAAA-TCTCTTATCCTT
* *
18903 TGGTTGACTT-GTCGATTGAT
65 T-GTTGA-TTCGTCGATTCAA
* *
18923 TCCCGGTCGACCTTTTATCCTTTGTTTACTTGTCGACTTAGTCC
1 TCCCAGTCAACCTTTTATCCTTTGTTTACTTGTCGACTTAGTCC
18967 TAGGTGAATC
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
82 8 0.08
83 39 0.38
84 55 0.53
85 2 0.02
ACGTcount: A:0.16, C:0.24, G:0.15, T:0.44
Consensus pattern (83 bp):
TCCCAGTCAACCTTTTATCCTTTGTTTACTTGTCGACTTAGTCCCAAGTAAATCTCTTATCCTTT
GTTGATTCGTCGATTCAA
Found at i:20500 original size:14 final size:15
Alignment explanation
Indices: 20481--20510 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
20471 AAATTTTATC
20481 TTAATTTTTA-AATT
1 TTAATTTTTACAATT
20495 TTAATTTTTACAATT
1 TTAATTTTTACAATT
20510 T
1 T
20511 AATCATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAATTTTTACAATT
Found at i:20836 original size:23 final size:23
Alignment explanation
Indices: 20792--20836 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20782 CTAAGGATGA
**
20792 GGAGAAGAAGAAGAAAGGAAAAG
1 GGAGAAGAAGAAGAAAAAAAAAG
20815 GGAGAAAGAA-AAGAAAAAAAAA
1 GGAG-AAGAAGAAGAAAAAAAAA
20837 AGATGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (23 bp):
GGAGAAGAAGAAGAAAAAAAAAG
Found at i:20851 original size:11 final size:11
Alignment explanation
Indices: 20831--20857 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20821 AGAAAAGAAA
20831 AAAAAAAGATG
1 AAAAAAAGATG
20842 AAAAAAAGATG
1 AAAAAAAGATG
20853 AAAAA
1 AAAAA
20858 TAGCATCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (11 bp):
AAAAAAAGATG
Found at i:21746 original size:22 final size:22
Alignment explanation
Indices: 21721--21764 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21711 AGAAAGTGAG
21721 GAAAGAAGAAACAGCAAGCAAA
1 GAAAGAAGAAACAGCAAGCAAA
* *
21743 GAAAGAAGAAATAGTAAGCAAA
1 GAAAGAAGAAACAGCAAGCAAA
21765 AGCAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.64, C:0.09, G:0.23, T:0.05
Consensus pattern (22 bp):
GAAAGAAGAAACAGCAAGCAAA
Found at i:23315 original size:154 final size:152
Alignment explanation
Indices: 23308--24549 Score: 855
Period size: 154 Copynumber: 8.0 Consensus size: 152
23298 GGTATTTTTG
* * * *
23308 TAATTTTTTAAAACCAACTCTTAGGTTGTTGTCGGGTCTGCTTTTATGCCAAAAGTGGGCAGTTA
1 TAATTTTTTAAAACCAACTCCTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTA
* * * * * ** *
23373 GGATAGGTTCATCCCATTTCAAACCTTTTTAAGTCTTTTACGGGTATCGAGTA-TTTTTTGTCAA
66 GGATAGGTTCAT-CCATTTTAAACCTTTTTAAGTCCTTTAGGGGTACCG-GTACTTGTACGTCGA
23437 AGGTATCCCCTA-AGGGTATTTTCA
129 AGGTATCCCCTAGA-GGTATTTTCA
* * * * * * * *
23461 TAATTTTTTAAAACCAATTCCTAGGTTATCACCGAGT-TCGCTTTTATGCCGAATGTGGGTATTT
1 TAATTTTTTAAAACCAACTCCTAGGTTGTCGCCGGGTCT-GCTTTTATGCCAAAGGTGGGCAGTT
* ** * *
23525 AGGATAGGTTCAGTCC-TTCTATAGTCATTTTAAGTCCTTTAGGGGTACCGAGATACTT-TCATG
65 AGGATAGGTTCA-TCCATTTTA-AACCTTTTTAAGTCCTTTAGGGGTACCG-G-TACTTGT-ACG
* * **
23588 TCGAAGGTATCTCCTA-AGAGCATTTTTG
125 TCGAAGGTATCCCCTAGAG-GTATTTTCA
* ** * * *
23616 CAATTTTTTAAAACCAACTCCTAGGTTGTCGTTGGGTCCGCTTTTATGTCAAAGGTGGGCAATTA
1 TAATTTTTTAAAACCAACTCCTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTA
* * *
23681 GGATAGATTCATCTCATCTTAAACCTTTTTAAGTCCTTTAGGGGTACCGGGTACTTGTACATCGA
66 GGATAGGTTCATC-CATTTTAAACCTTTTTAAGTCCTTTAGGGGTACC-GGTACTTGTACGTCGA
*
23746 AGGTATCCCCTA-AGGATATTTTTA
129 AGGTATCCCCTAGAGG-TATTTTCA
* * * * * * * ** *
23770 TAATTTTTTAGAACTAACTCGTAAGTTATCGTCGGCTCCACTTTTATGCCAAAGGTGGGTAGTTA
1 TAATTTTTTAAAACCAACTCCTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTA
* * *** * *
23835 TGATAGGTTCATCCTTTTTATAGTGTTTTTTAAGTCTTTTAGGGGTACCGGGTACTTGTACAT-G
66 GGATAGGTTCATCCATTTTA-A-ACCTTTTTAAGTCCTTTAGGGGTACC-GGTACTTGTACGTCG
* *
23899 AAGGTATCCCCTAAAGGCATTTTCA
128 AAGGTATCCCCTAGAGGTATTTTCA
* * * *
23924 TAATTTTTTAAAACCAACTCTTAGGTTGTCGCCGGGTCTGTTTTTACGCCAAAAGTGGGCAGTTA
1 TAATTTTTTAAAACCAACTCCTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTA
* * * * * * *
23989 TGATAGGTTCATCCTATTTCAAACCTTTTTATA-TCCTTTAGGAGTATCGAGTACTTTTACATCA
66 GGATAGGTTCATCC-ATTTTAAACCTTTTTA-AGTCCTTTAGGGGTACCG-GTACTTGTACGTCG
*
24053 AAGGTATCCCCTAGGGGTATTTTCA
128 AAGGTATCCCCTAGAGGTATTTTCA
* * * * *
24078 TAATTTTTTAGAACCAACTCCTAGGTTGTCACCAGGTCTGCTTTTATGCCGAAA-GTGGGTATTT
1 TAATTTTTTAAAACCAACTCCTAGGTTGTCGCCGGGTCTGCTTTTATGCC-AAAGGTGGGCAGTT
* * * *
24142 AGGATAGGTTCATTCTTTTTATAGTCCTTTTTAAGTCCTTTAGGGGTACCGAGATACTTTTATC-
65 AGGATAGGTTCATCCATTTTA-A-ACCTTTTTAAGTCCTTTAGGGGTACCG-G-TACTTGTA-CG
* *
24206 TTGAAGGTATCCCCTACG-GGCATTTTCA
125 TCGAAGGTATCCCCTA-GAGGTATTTTCA
* * * * * * ** * * * * * * *
24234 TAATTTTTTAGAATCGAGTCCTAAGTTATCATCGGGTCTACTTTTGTGCCGATGGTAGGTATTTA
1 TAATTTTTTAAAACCAACTCCTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTA
* * ** * *
24299 GGATAGGTTCATTCC-TTTTATAGTCCTTTTTAAGTCTTTTAAAGGTACCAAGATACTT-TCATG
66 GGATAGGTTCA-TCCATTTTA-A-ACCTTTTTAAGTCCTTTAGGGGTACC--GGTACTTGT-ACG
* *
24362 TCGAAGGTATCCCCTAG-GAGCATTTTCG
125 TCGAAGGTATCCCCTAGAG-GTATTTTCA
* * * * * ** ** * * * * * *
24390 TAA-TTTTCAGAACCGAGTCCTAGGTTATAACTAGGTCCGCTTTTATGTCGAATGTGGGTATTTA
1 TAATTTTTTAAAACCAACTCCTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTA
* * * * * *
24454 GGATAGGTTCTTTCC-TTTTATAGTCATTTTTAAGTCTTTTAGGGGTATCGGGTACTTATACGTC
66 GGATAGGTTC-ATCCATTTTA-A-ACCTTTTTAAGTCCTTTAGGGGTA-CCGGTACTTGTACGTC
* * * *
24518 AAAGGTATCTCTTAG-GAGTATTTTCG
127 GAAGGTATCCCCTAGAG-GTATTTTCA
24544 TAATTT
1 TAATTT
24550 GTCTTGAATT
Statistics
Matches: 891, Mismatches: 160, Indels: 74
0.79 0.14 0.07
Matches are distributed among these distances:
152 5 0.01
153 128 0.14
154 313 0.35
155 279 0.31
156 161 0.18
157 4 0.00
158 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (152 bp):
TAATTTTTTAAAACCAACTCCTAGGTTGTCGCCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTA
GGATAGGTTCATCCATTTTAAACCTTTTTAAGTCCTTTAGGGGTACCGGTACTTGTACGTCGAAG
GTATCCCCTAGAGGTATTTTCA
Found at i:23506 original size:308 final size:307
Alignment explanation
Indices: 22935--24549 Score: 1526
Period size: 308 Copynumber: 5.2 Consensus size: 307
22925 ATCTCTAATC
* * * * *
22935 TTTTTAAGTCCTTTAAGGTTACC-GGAATACTT-TCATGTTGAAGGTATC-CTCTAAGGGTATTT
1 TTTTTAAGTCCTTTAGGGGTACCAGG--TACTTGT-ACGTCGAAGGTATCTC-CT-AGGGCATTT
* * * * * *
22997 TTGTAATTTTTTAGAACTAACTCCTAGGTTGTTGTCGGGT-TCGTTTTTATGCGAAAGGTGGGCA
61 TCGTAATTTTTTAAAACCAACTCCTAGGTTGTCGTCGGGTCT-GCTTTTATGCCAAAGGTGGGCA
** *
23061 GTTAGGATAGGTTTGTCCCATTTCAAACCTTTTTAAGTCCTTTAGGGGTATCCG-GTACTTGTAC
125 GTTAGGATAGGTTCATCCCATTTCAAACCTTTTTAAGTCCTTTAGGGGTAT-CGAGTACTTTTAC
* * * * * * * *
23125 GTCGAAGGTAT-ACCTAGGGGCATTTTCATAATTTTTTGGAACCAATTCCTAGGTTGTCGCCCAG
189 GTCGAAGGTATCCCCTAAGGGTATTTTCATAATTTTTTAGAACCAACTCCTAGGTTATCACCGAG
* * *
23189 -TCTGCTTTTATGCCAAAGGTGGGCAATTATGATAGGTTCATCCATTTTATAGTCT
254 TTC-GCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCC-TTTTATAGTCT
* * * * *
23244 TTTTTAAGTCCTTTGGGGGTACCAGGTACTTGTGCGTCGAAGGTATCTCTTAGAGGTATTTTTGT
1 TTTTTAAGTCCTTTAGGGGTACCAGGTACTTGTACGTCGAAGGTATCTCCTAG-GGCATTTTCGT
* * *
23309 AATTTTTTAAAACCAACTCTTAGGTTGTTGTCGGGTCTGCTTTTATGCCAAAAGTGGGCAGTTAG
65 AATTTTTTAAAACCAACTCCTAGGTTGTCGTCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAG
* * ** *
23374 GATAGGTTCATCCCATTTCAAACCTTTTTAAGTCTTTTACGGGTATCGAGTA-TTTTTTGTCAAA
130 GATAGGTTCATCCCATTTCAAACCTTTTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTCGAA
* *
23438 GGTATCCCCTAAGGGTATTTTCATAATTTTTTAAAACCAATTCCTAGGTTATCACCGAGTTCGCT
195 GGTATCCCCTAAGGGTATTTTCATAATTTTTTAGAACCAACTCCTAGGTTATCACCGAGTTCGCT
* * *
23503 TTTATGCCGAATGTGGGTATTTAGGATAGGTTCAGTCCTTCTATAGTC-
260 TTTATGCCAAAGGTGGGTATTTAGGATAGGTTCA-TCCTTTTATAGTCT
* * * * *
23551 ATTTTAAGTCCTTTAGGGGTACCGAGATACTT-TCATGTCGAAGGTATCTCCTAAGAGCATTTTT
1 TTTTTAAGTCCTTTAGGGGTACC-AGGTACTTGT-ACGTCGAAGGTATCTCCT-AGGGCATTTTC
* * * * *
23615 GCAATTTTTTAAAACCAACTCCTAGGTTGTCGTTGGGTCCGCTTTTATGTCAAAGGTGGGCAATT
63 GTAATTTTTTAAAACCAACTCCTAGGTTGTCGTCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTT
* * * * * *
23680 AGGATAGATTCATCTCATCTT-AAACCTTTTTAAGTCCTTTAGGGGTACCGGGTACTTGTACATC
128 AGGATAGGTTCATCCCAT-TTCAAACCTTTTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTC
* * * * * ** *
23744 GAAGGTATCCCCTAAGGATATTTTTATAATTTTTTAGAACTAACTCGTAAGTTATCGTCG-GCTC
192 GAAGGTATCCCCTAAGGGTATTTTCATAATTTTTTAGAACCAACTCCTAGGTTATCACCGAG-TT
* * * *
23808 CACTTTTATGCCAAAGGTGGGTAGTTATGATAGGTTCATCCTTTTTATAGTGT
256 CGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCC-TTTTATAGTCT
* * * * * *
23861 TTTTTAAGTCTTTTAGGGGTACCGGGTACTTGTACAT-GAAGGTATCCCCTAAAGGCATTTTCAT
1 TTTTTAAGTCCTTTAGGGGTACCAGGTACTTGTACGTCGAAGGTATCTCCT-AGGGCATTTTCGT
* * * * * *
23925 AATTTTTTAAAACCAACTCTTAGGTTGTCGCCGGGTCTGTTTTTACGCCAAAAGTGGGCAGTTAT
65 AATTTTTTAAAACCAACTCCTAGGTTGTCGTCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAG
* * * *
23990 GATAGGTTCATCCTATTTCAAACCTTTTTATA-TCCTTTAGGAGTATCGAGTACTTTTACATCAA
130 GATAGGTTCATCCCATTTCAAACCTTTTTA-AGTCCTTTAGGGGTATCGAGTACTTTTACGTCGA
* * *
24054 AGGTATCCCCTAGGGGTATTTTCATAATTTTTTAGAACCAACTCCTAGGTTGTCACC-AGGTCTG
194 AGGTATCCCCTAAGGGTATTTTCATAATTTTTTAGAACCAACTCCTAGGTTATCACCGAGTTC-G
* *
24118 CTTTTATGCCGAAA-GTGGGTATTTAGGATAGGTTCATTCTTTTTATAGTCC
258 CTTTTATGCC-AAAGGTGGGTATTTAGGATAGGTTCA-TCCTTTTATAGTCT
* * * *
24169 TTTTTAAGTCCTTTAGGGGTACCGAGATACTTTTATC-TTGAAGGTATCCCCTACGGGCATTTTC
1 TTTTTAAGTCCTTTAGGGGTACC-AGGTACTTGTA-CGTCGAAGGTATCTCCTA-GGGCATTTTC
* * * * * * * * * * * * * * *
24233 ATAATTTTTTAGAATCGAGTCCTAAGTTATCATCGGGTCTACTTTTGTGCCGATGGTAGGTATTT
63 GTAATTTTTTAAAACCAACTCCTAGGTTGTCGTCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTT
* * * * ** * * * *
24298 AGGATAGGTTCATTCC-TTTTATAGTCCTTTTTAAGTCTTTTAAAGGTACCAAGATACTTTCATG
128 AGGATAGGTTCATCCCATTTCA-A-ACCTTTTTAAGTCCTTTAGGGGTATCGAG-TACTTTTACG
* * * * * * *
24362 TCGAAGGTATCCCCT-AGGAGCATTTTCGTAA-TTTTCAGAACCGAGTCCTAGGTTAT-AACTAG
190 TCGAAGGTATCCCCTAAGG-GTATTTTCATAATTTTTTAGAACCAACTCCTAGGTTATCACCGA-
* * * * * *
24424 GTCCGCTTTTATGTCGAATGTGGGTATTTAGGATAGGTTCTTTCCTTTTATAGTCA
253 GTTCGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTC-ATCCTTTTATAGTCT
* * * * * * *
24480 TTTTTAAGTCTTTTAGGGGTATCGGGTACTTATACGTCAAAGGTATCTCTTAGGAGTATTTTCGT
1 TTTTTAAGTCCTTTAGGGGTACCAGGTACTTGTACGTCGAAGGTATCTCCTAGG-GCATTTTCGT
24545 AATTT
65 AATTT
24550 GTCTTGAATT
Statistics
Matches: 1076, Mismatches: 191, Indels: 77
0.80 0.14 0.06
Matches are distributed among these distances:
307 42 0.04
308 588 0.55
309 160 0.15
310 145 0.13
311 108 0.10
312 33 0.03
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (307 bp):
TTTTTAAGTCCTTTAGGGGTACCAGGTACTTGTACGTCGAAGGTATCTCCTAGGGCATTTTCGTA
ATTTTTTAAAACCAACTCCTAGGTTGTCGTCGGGTCTGCTTTTATGCCAAAGGTGGGCAGTTAGG
ATAGGTTCATCCCATTTCAAACCTTTTTAAGTCCTTTAGGGGTATCGAGTACTTTTACGTCGAAG
GTATCCCCTAAGGGTATTTTCATAATTTTTTAGAACCAACTCCTAGGTTATCACCGAGTTCGCTT
TTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCTTTTATAGTCT
Found at i:24490 original size:155 final size:155
Alignment explanation
Indices: 23126--24494 Score: 790
Period size: 155 Copynumber: 8.9 Consensus size: 155
23116 TACTTGTACG
* * * * * * *
23126 TCGAAGGTAT-ACCTAGGGGCATTTTCATAATTTTTTGGAACCAATTCCTAGGTTGTCGCCCA-G
1 TCGAAGGTATCCCCTA-GGGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTATC-ACTAGG
* * * * * *
23189 TCTGCTTTTATGCCAAAGGTGGGCAATTATGATAGGTTCA-TCCATTTTATAGTCTTTTTTAAGT
64 TCTGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCATTCC-TTTTATAGTCCTTTTTAAGT
* *** * *
23253 CCTTTGGGGGTACC-AGGTACTTGTGC--G
128 CTTTTAAAGGTACCAAGATACTT-T-CATC
* * * ** * * * * * ** *
23280 TCGAAGGTATCTCTTAGAGGTATTTTTGTAATTTTTTAAAACCAACTCTTAGGTTGT-TGTCGGG
1 TCGAAGGTATCCCCTAG-GGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTATCACT-AGG
* * * * * * *
23344 TCTGCTTTTATGCCAAAAGTGGGCAGTTAGGATAGGTTCATCCCATTTCA-A-ACCTTTTTAAGT
64 TCTGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCATTCC-TTTTATAGTCCTTTTTAAGT
** * * ** *
23407 CTTTTACGGGTATCGAG-TA-TTTTTTG
128 CTTTTAAAGGTACCAAGATACTTTCATC
* * * * * * *
23433 TCAAAGGTATCCCCTAAGGGTATTTTCATAATTTTTTAAAACCAATTCCTAGGTTATCACCGAGT
1 TCGAAGGTATCCCCT-AGGGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTATCA-CTAGG
* * *
23498 TC-GCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCAGTCCTTCTATAGT-CATTTTAAGTC
64 TCTGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCATTCCTTTTATAGTCCTTTTTAAGTC
* ** * *
23561 CTTTAGGGGTACCGAGATACTTTCATG
129 TTTTAAAGGTACCAAGATACTTTCATC
* * *** * * * * ** *
23588 TCGAAGGTATCTCCTAAGAGCATTTTTGCAATTTTTTAAAACCAACTCCTAGGTTGTCGTTGGGT
1 TCGAAGGTATCCCCT-AGGGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTATCACTAGGT
* * * * * * * * * *
23653 CCGCTTTTATGTCAAAGGTGGGCAATTAGGATAGATTCATCTCATCTTA-A-ACCTTTTTAAGTC
65 CTGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCAT-TCCTTTTATAGTCCTTTTTAAGTC
* ** * *
23716 CTTTAGGGGTACC-GGGTACTTGT-A-C
129 TTTTAAAGGTACCAAGATACTT-TCATC
** * ** * * * * *
23741 ATCGAAGGTATCCCCTAAGGATATTTTTATAATTTTTTAGAACTAACTCGTAAGTTATC-GTCGG
1 -TCGAAGGTATCCCCT-AGGGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTATCACTAGG
** * * * * **
23805 CTCCACTTTTATGCCAAAGGTGGGTAGTTATGATAGGTTCA-TCCTTTTTATAGTGTTTTTTAAG
64 -TCTGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCATTCC-TTTTATAGTCCTTTTTAAG
** * *
23869 TCTTTTAGGGGTACC-GGGTACTTGT-A-C
127 TCTTTTAAAGGTACCAAGATACTT-TCATC
* * * * * * * **
23896 AT-GAAGGTATCCCCTAAAGGCATTTTCATAATTTTTTAAAACCAACTCTTAGGTTGTCGCCGGG
1 -TCGAAGGTATCCCCT-AGGGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTATCACTAGG
* * * * * * * *
23960 TCTGTTTTTACGCCAAAAGTGGGCAGTTATGATAGGTTCA-TCCTATTTCA-A-ACCTTTTTATA
64 TCTGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCATTCCT-TTT-ATAGTCCTTTTTA-A
* * * * *
24022 -TCCTTT-AGGAGTATCGAG-TACTTTTA-C
126 GTCTTTTAAAG-GTACCAAGATACTTTCATC
* * * * * *
24049 ATCAAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTAGAACCAACTCCTAGGTTGTCACCAGG
1 -TCGAAGGTATCCCCTA-GGGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTATCACTAGG
* *
24114 TCTGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATTCTTTTTATAGTCCTTTTTAAGTC
64 TCTGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCATTCCTTTTATAGTCCTTTTTAAGTC
* ** * *
24179 CTTTAGGGGTACCGAGATACTTTTATC
129 TTTTAAAGGTACCAAGATACTTTCATC
* * * *
24206 TTGAAGGTATCCCCTACGGGCATTTTCATAATTTTTTAGAATCGAGTCCTAAGTTATCA-TCGGG
1 TCGAAGGTATCCCCTA-GGGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTATCACT-AGG
* * *
24270 TCTACTTTTGTGCCG-ATGGTAGGTATTTAGGATAGGTTCATTCCTTTTATAGTCCTTTTTAAGT
64 TCTGCTTTTATGCCGAAT-GTGGGTATTTAGGATAGGTTCATTCCTTTTATAGTCCTTTTTAAGT
*
24334 CTTTTAAAGGTACCAAGATACTTTCATG
128 CTTTTAAAGGTACCAAGATACTTTCATC
* * *
24362 TCGAAGGTATCCCCTAGGAGCATTTTCGTAA-TTTTCAGAACCGAGTCCTAGGTTATAACTAGGT
1 TCGAAGGTATCCCCTAGG-GCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTATCACTAGGT
* * * *
24426 CCGCTTTTATGTCGAATGTGGGTATTTAGGATAGGTTCTTTCCTTTTATAGTCATTTTTAAGTCT
65 CTGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCATTCCTTTTATAGTCCTTTTTAAGTCT
24491 TTTA
130 TTTA
24495 GGGGTATCGG
Statistics
Matches: 985, Mismatches: 185, Indels: 89
0.78 0.15 0.07
Matches are distributed among these distances:
152 9 0.01
153 142 0.14
154 314 0.32
155 337 0.34
156 182 0.18
157 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (155 bp):
TCGAAGGTATCCCCTAGGGCATTTTCATAATTTTTTAGAACCGAGTCCTAGGTTATCACTAGGTC
TGCTTTTATGCCGAATGTGGGTATTTAGGATAGGTTCATTCCTTTTATAGTCCTTTTTAAGTCTT
TTAAAGGTACCAAGATACTTTCATC
Found at i:33592 original size:11 final size:11
Alignment explanation
Indices: 33576--33625 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
33566 TAAACTTTTA
33576 ATTAAATTAAT
1 ATTAAATTAAT
*
33587 ATTAAA-T-AC
1 ATTAAATTAAT
33596 ATTAACATTAAT
1 ATTAA-ATTAAT
*
33608 ATTAAAATAAT
1 ATTAAATTAAT
*
33619 ATCAAAT
1 ATTAAAT
33626 ACATAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 17 0.55
12 6 0.19
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTAAATTAAT
Found at i:33612 original size:32 final size:31
Alignment explanation
Indices: 33576--33637 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
33566 TAAACTTTTA
* *
33576 ATTAAATTAATATTAAATACATTAACATTAAT
1 ATTAAAATAATATCAAATACA-TAACATTAAT
*
33608 ATTAAAATAATATCAAATACATAATATTAA
1 ATTAAAATAATATCAAATACATAACATTAA
33638 ACACATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.37
Consensus pattern (31 bp):
ATTAAAATAATATCAAATACATAACATTAAT
Found at i:33815 original size:23 final size:24
Alignment explanation
Indices: 33789--33836 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
33779 AATTAAATTC
* *
33789 TTAATTTTA-AAAAAAGAAAAAAA
1 TTAATTTAATAAAAAACAAAAAAA
*
33812 TTAATTTAATAAAAAACAAATAAA
1 TTAATTTAATAAAAAACAAAAAAA
33836 T
1 T
33837 GCTTTTGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
TTAATTTAATAAAAAACAAAAAAA
Found at i:37667 original size:12 final size:12
Alignment explanation
Indices: 37650--37675 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37640 ATCCATATCT
37650 TGCTCATCTTCA
1 TGCTCATCTTCA
37662 TGCTCATCTTCA
1 TGCTCATCTTCA
37674 TG
1 TG
37676 TTATGGTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.31, G:0.12, T:0.42
Consensus pattern (12 bp):
TGCTCATCTTCA
Found at i:39138 original size:20 final size:20
Alignment explanation
Indices: 39113--39167 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
39103 GGTTTTCCAG
*
39113 ATGTATCGATACATTGCATA
1 ATGTATCGATGCATTGCATA
39133 ATGTATCGATGCATTGCATA
1 ATGTATCGATGCATTGCATA
39153 ATGTATCGATGCATT
1 ATGTATCGATGCATT
39168 CTAGGAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (20 bp):
ATGTATCGATGCATTGCATA
Found at i:40299 original size:21 final size:22
Alignment explanation
Indices: 40259--40310 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
40249 AGTTAATCCA
40259 TCATTTTCTTCTTGCAACTCATT
1 TCATTTTCTTCTTGCAACTCA-T
*
40282 TC-TTTTCTT-TTTCAACTCAT
1 TCATTTTCTTCTTGCAACTCAT
40302 TCATTTTCT
1 TCATTTTCT
40311 CCTCTAGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 15 0.56
22 7 0.26
23 2 0.07
ACGTcount: A:0.15, C:0.25, G:0.02, T:0.58
Consensus pattern (22 bp):
TCATTTTCTTCTTGCAACTCAT
Found at i:41955 original size:31 final size:31
Alignment explanation
Indices: 41904--41999 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 31
41894 CCTTACAACA
* *
41904 CTATCTTTTGAAGGCTAAGATAGAACCTC-C
1 CTATCTTTTCAAAGCTAAGATAGAACCTCTC
41934 CTATCTTTTCACAAGCTAAGATAGAACCTCTCTC
1 CTATCTTTTCA-AAGCTAAGATAGAA-C-CTCTC
*
41968 CTTACCTTTTTCAAAGGCTAAGATAGAACCTC
1 C-TATC-TTTTCAAA-GCTAAGATAGAACCTC
42000 ACAATCACTT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
30 10 0.18
31 13 0.23
32 1 0.02
33 3 0.05
34 5 0.09
35 6 0.11
36 18 0.32
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (31 bp):
CTATCTTTTCAAAGCTAAGATAGAACCTCTC
Found at i:41988 original size:36 final size:34
Alignment explanation
Indices: 41914--41999 Score: 108
Period size: 36 Copynumber: 2.6 Consensus size: 34
41904 CTATCTTTTG
*
41914 AAGGCTAAGATAGAA-C-CTCCCTATCTTTTCAC
1 AAGGCTAAGATAGAACCTCTCCCTACCTTTTCAC
41946 AA-GCTAAGATAGAACCTCTCTCCTTACCTTTTTCA-
1 AAGGCTAAGATAGAACCTCTC-CC-TACC-TTTTCAC
41981 AAGGCTAAGATAGAACCTC
1 AAGGCTAAGATAGAACCTC
42000 ACAATCACTT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
31 12 0.26
32 3 0.06
33 3 0.06
34 2 0.04
35 5 0.11
36 22 0.47
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (34 bp):
AAGGCTAAGATAGAACCTCTCCCTACCTTTTCAC
Found at i:42405 original size:20 final size:20
Alignment explanation
Indices: 42377--42429 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
42367 TTACACACTT
* *
42377 TAATTTATCGATTCAATTCA
1 TAATGTATCGATACAATTCA
42397 TAATGTATCGATACAATTCA
1 TAATGTATCGATACAATTCA
*
42417 TAATGTATTGATA
1 TAATGTATCGATA
42430 TAATGCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (20 bp):
TAATGTATCGATACAATTCA
Found at i:46307 original size:20 final size:19
Alignment explanation
Indices: 46231--46307 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 19
46221 AAAAAGACAG
* *
46231 AATGTATCGATACATTGAAG
1 AATGTATCGATACATT-TAT
*
46251 AATGTATCGATACATTCAT
1 AATGTATCGATACATTTAT
*
46270 ACATGTATCGATACATTTTT
1 A-ATGTATCGATACATTTAT
46290 CAATGTATCGATACATTT
1 -AATGTATCGATACATTT
46308 GGGTAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.04
20 48 0.94
21 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (19 bp):
AATGTATCGATACATTTAT
Found at i:46352 original size:20 final size:20
Alignment explanation
Indices: 46320--46376 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
46310 GTAAAAAGAC
*
46320 AAAATGTATCGATACATTCA
1 AAAATGCATCGATACATTCA
* * *
46340 TACATGCATCGATACATTGA
1 AAAATGCATCGATACATTCA
*
46360 AAAATGTATCGATACAT
1 AAAATGCATCGATACAT
46377 CTAAGTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (20 bp):
AAAATGCATCGATACATTCA
Found at i:46356 original size:91 final size:92
Alignment explanation
Indices: 46200--46376 Score: 250
Period size: 91 Copynumber: 1.9 Consensus size: 92
46190 TTTTAACTAG
* * * *
46200 ATGTATCGATACATTATTCGTAAAAAGACAGAATGTATCGATACATTGAAGAATGTATCGATACA
1 ATGTATCGATACATTATGCGTAAAAAGACAAAATGTATCGATACATTCAAGAATGCATCGATACA
* *
46265 TTCATACATGTATCGATACATTTTTCA
66 TTCAAAAATGTATCGATACATTTTTCA
* *
46292 ATGTATCGATACATT-TGGGTAAAAAGACAAAATGTATCGATACATTCATA-CATGCATCGATAC
1 ATGTATCGATACATTATGCGTAAAAAGACAAAATGTATCGATACATTCA-AGAATGCATCGATAC
*
46355 ATTGAAAAATGTATCGATACAT
65 ATTCAAAAATGTATCGATACAT
46377 CTAAGTAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
91 59 0.79
92 16 0.21
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (92 bp):
ATGTATCGATACATTATGCGTAAAAAGACAAAATGTATCGATACATTCAAGAATGCATCGATACA
TTCAAAAATGTATCGATACATTTTTCA
Found at i:46385 original size:71 final size:71
Alignment explanation
Indices: 46251--46387 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 71
46241 TACATTGAAG
* **** * **
46251 AATGTATCGATACATTCATACATGTATCGATACATTTTTCAATGTATCGATACATTTGGGTAAAA
1 AATGTATCGATACATTCATACATGCATCGATACATTGAAAAATGTATCGATACATCTAAGTAAAA
46316 AGACAA
66 AGACAA
46322 AATGTATCGATACATTCATACATGCATCGATACATTGAAAAATGTATCGATACATCTAAGTAAAA
1 AATGTATCGATACATTCATACATGCATCGATACATTGAAAAATGTATCGATACATCTAAGTAAAA
46387 A
66 A
46388 TATGACTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (71 bp):
AATGTATCGATACATTCATACATGCATCGATACATTGAAAAATGTATCGATACATCTAAGTAAAA
AGACAA
Found at i:46998 original size:59 final size:59
Alignment explanation
Indices: 46901--47018 Score: 148
Period size: 59 Copynumber: 2.0 Consensus size: 59
46891 GGTGTCTATA
* *
46901 GTCCTTAGATTATATAAAGTAACCCAAATGACCCTAAAATGCAT-GAAAATTGCTAAATG
1 GTCCTTAGATTATATAAAATAACCCAAATGACCCTAAAATGCATAG-AAATTGATAAATG
* * * ** *
46960 GTCCTTAGATTATATAAAATAACCTAGATGGCTTTAAAATGTATAGAAATTGATAAATG
1 GTCCTTAGATTATATAAAATAACCCAAATGACCCTAAAATGCATAGAAATTGATAAATG
47019 ATCCCTAGTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
59 49 0.98
60 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (59 bp):
GTCCTTAGATTATATAAAATAACCCAAATGACCCTAAAATGCATAGAAATTGATAAATG
Found at i:50630 original size:19 final size:19
Alignment explanation
Indices: 50608--50645 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
50598 TATTTAATCA
* *
50608 TTAAAAATTAAAAACATAT
1 TTAAAAAATAAAAAAATAT
50627 TTAAAAAATAAAAAAATAT
1 TTAAAAAATAAAAAAATAT
50646 ACTATAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
TTAAAAAATAAAAAAATAT
Found at i:50926 original size:20 final size:20
Alignment explanation
Indices: 50885--50924 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
50875 TTTATATCAT
* *
50885 ATTTTATATTGTGTTTCTAA
1 ATTTTATATTATGCTTCTAA
50905 ATTTTATATTAT-CTTCTAA
1 ATTTTATATTATGCTTCTAA
50924 A
1 A
50925 ATGTATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTATATTATGCTTCTAA
Found at i:51121 original size:19 final size:19
Alignment explanation
Indices: 51097--51144 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
51087 TTTTATAAAA
51097 ACTTTTT-TTATTTTTCTTT-
1 ACTTTTTCTT-TTTTT-TTTC
51116 ACTTTTTCTTTTTTTTTTC
1 ACTTTTTCTTTTTTTTTTC
*
51135 ACTTTATCTT
1 ACTTTTTCTT
51145 CATCATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 21 0.81
20 2 0.08
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (19 bp):
ACTTTTTCTTTTTTTTTTC
Found at i:51196 original size:16 final size:15
Alignment explanation
Indices: 51161--51219 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
51151 AAATAAACTA
*
51161 AAAAATAATTTAAATTT
1 AAAAATAATTTTAA--T
51178 AAAAATTAATTTTAAT
1 AAAAA-TAATTTTAAT
*
51194 -AAAATAATATTTTAT
1 AAAAATAAT-TTTAAT
51209 AAAAATAATTT
1 AAAAATAATTT
51220 AAATCATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 4 0.11
15 11 0.30
16 9 0.24
17 5 0.14
18 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAAATAATTTTAAT
Found at i:51210 original size:15 final size:17
Alignment explanation
Indices: 51177--51217 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
51167 AATTTAAATT
*
51177 TAAAAATTA-ATTTTAA
1 TAAAAATAATATTTTAA
51193 T-AAAATAATATTTT-A
1 TAAAAATAATATTTTAA
51208 TAAAAATAAT
1 TAAAAATAAT
51218 TTAAATCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAAATAATATTTTAA
Found at i:51455 original size:12 final size:13
Alignment explanation
Indices: 51429--51470 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
51419 GAAGGAAATA
51429 TTAAAAATAATTT
1 TTAAAAATAATTT
*
51442 TTAAAATTAATTT
1 TTAAAAATAATTT
51455 TTAATAAAT-ATTT
1 TTAA-AAATAATTT
51468 TTA
1 TTA
51471 GTTTATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 23 0.88
14 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAAAATAATTT
Found at i:51994 original size:15 final size:15
Alignment explanation
Indices: 51948--51996 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
51938 TTCATCTTCA
*
51948 TTTATAATATATAATAT
1 TTTATAAT-TA-ATTAT
**
51965 TTTATAATTTTTTAT
1 TTTATAATTAATTAT
51980 TTTATAATTAATTAT
1 TTTATAATTAATTAT
51995 TT
1 TT
51997 AAGAGTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 18 0.67
16 1 0.04
17 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATAATTAATTAT
Done.