Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003395.1 Hibiscus syriacus cultivar Beakdansim tig00007142_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 97828
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:939 original size:3 final size:3
Alignment explanation
Indices: 925--990 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
915 CCGGGTTTTG
* * * * *
925 TAA TAT TAA TAA TAA T-A TATA TAA TAA TAA TAA TAT TAT TATT TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA
971 TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
991 ACATTAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 44 0.83
4 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:959 original size:30 final size:30
Alignment explanation
Indices: 925--989 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
915 CCGGGTTTTG
925 TAATATTAATAATAATAT-ATATAATAATAA
1 TAATATT-ATAATAATATAATATAATAATAA
* **
955 TAATATTATTATTTTATAATATAATAATAA
1 TAATATTATAATAATATAATATAATAATAA
985 TAATA
1 TAATA
990 AACATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAATATTATAATAATATAATATAATAATAA
Found at i:5642 original size:11 final size:11
Alignment explanation
Indices: 5609--5644 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
5599 ACAATAATAA
5609 AAAAAATAAA-
1 AAAAAATAAAT
5619 AAAAAATAGAAT
1 AAAAAATA-AAT
5631 AAAAAATAAAT
1 AAAAAATAAAT
5642 AAA
1 AAA
5645 CACAAGTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.33
11 8 0.33
12 8 0.33
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:7496 original size:42 final size:42
Alignment explanation
Indices: 7403--7516 Score: 137
Period size: 42 Copynumber: 2.7 Consensus size: 42
7393 ACCCAGATGT
* *
7403 CTTATGGATGGCCC-AAAGGACTTA-TCATCTTGTTCGAAAGA
1 CTTATAGATGGCCCGAAA-GACTTACTCATCATGTTCGAAAGA
*
7444 CTTATAGATGGCCCGAAAGACTTACACATCATGCTT-GAAAGA
1 CTTATAGATGGCCCGAAAGACTTACTCATCATG-TTCGAAAGA
*
7486 CTTACT-GATGGCCCGAAGGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAAGACTTACTCATCA
7517 AGAAACCCTT
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
41 19 0.30
42 42 0.66
43 3 0.05
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (42 bp):
CTTATAGATGGCCCGAAAGACTTACTCATCATGTTCGAAAGA
Found at i:7725 original size:41 final size:41
Alignment explanation
Indices: 7662--7793 Score: 131
Period size: 42 Copynumber: 3.2 Consensus size: 41
7652 CTTATTTGAA
* * * * *
7662 ATCATCATGCTCGAAGGTCTTATGGATGGCCCTAAGGACTT
1 ATCATCATGCTCGAAAGACTTATAGATGACCCGAAGGACTT
* * *
7703 ATCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGATTT
1 ATCATCATGCTCGAAAGACTTATAGATGACCCGAAGGACTT
* * *
7744 AAGCATCATGGTCGAAAGACTTACTA-ATGACACGAAGGACTT
1 -ATCATCATGCTCGAAAGACTTA-TAGATGACCCGAAGGACTT
7786 ACTCATCA
1 A-TCATCA
7794 AGAAACCCTT
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
41 34 0.47
42 37 0.51
43 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (41 bp):
ATCATCATGCTCGAAAGACTTATAGATGACCCGAAGGACTT
Found at i:7917 original size:277 final size:278
Alignment explanation
Indices: 7401--8219 Score: 1179
Period size: 277 Copynumber: 2.9 Consensus size: 278
7391 CTACCCAGAT
* * *
7401 GTCTTATGGATGGCCCAAAGGACTTATCATCTTG-TTCGAAAGACTTATAGATGGCCCGAAAGAC
1 GTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTT-GAAAGACTTATAGATGACCCGAAGGAT
*
7465 TTACA-CATCATGCTTGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGA
65 TTA-AGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGA
* * * *
7529 AAATCAAGCTTAGCTTCTTAGTTTTCATTAAGGAACCCCTAAAAGTTAGGCTTAAATTCCTTTTA
129 AAATCAAGCTTAGTTTCTTAGTTTTCATCAAGGAACCCCTAAAAATTAGGCTTAGATTCCTTTTA
* *
7594 AAAACTCTTTGGATATAATCATCAAGAAA-CCCTGAAAATAAGGCTTAGTTTCTAAAAACTTATT
194 AAAACTCTTTGGATATAATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATT
7658 TGAAATCAT-CATGCTC-GAAG
259 TGAAATCATCCA-GC-CAGAAG
*
7678 GTCTTATGGATGGCCCTAAGGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGATT
1 GTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGATT
* * * *
7743 TAAGCATCATGGTCGAAAGACTTACTAATGACACGAAGGACTTACTCATCAAGAAACCCTTGAAA
66 TAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAA
*
7808 ATCAAGC-TAGTTTCTTAGTTTTCATCAAGGAACCCCTAAAAATTAGGCTTAGTTTCCTTTTAAA
131 ATCAAGCTTAGTTTCTTAGTTTTCATCAAGGAACCCCTAAAAATTAGGCTTAGATTCCTTTTAAA
7872 AACTCTTTGGATATAATCATCAAGAAACCCCT-ATAAATCAGGCTTAGTTTCTAAAAACTCATTT
196 AACTCTTTGGATATAATCATCAAGAAACCCCTGA-AAATCAGGCTTAGTTTCTAAAAACTCATTT
7936 GAAATCATCCAGCCAGAAG
260 GAAATCATCCAGCCAGAAG
* * *
7955 GTCTTATTGATGGCCCGGAA-GACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGAT
1 GTCTTATGGATGGCCC-AAAGGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGAT
* * * *
8019 TTAAGCATCATCCTCGAAAGACTTACTGATGGCCCGAAGGACTTACGCATCAAGAAACCCATAAA
65 TTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAA
* * * * *
8084 AATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTAAAAATT-TGATTTGCTTCCTTTTTA
130 AATCAAGCTTAGTTTCTTAGTTTTCATCAAGGAACCCCTAAAAATTAGGCTTAGATTCC-TTTTA
* * * * * * *
8148 AAAACTCATTGAAAATCATCATCAAGAAACCCCTGAAAATCAGACTTAGTTTCTTTAAAAATTCT
194 AAAACTCTTTGGATATAATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTC--TAAAAACTCA
8213 TTTGAAA
257 TTTGAAA
8220 ATATCATGTT
Statistics
Matches: 491, Mismatches: 39, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
276 82 0.17
277 300 0.61
278 93 0.19
279 1 0.00
280 15 0.03
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (278 bp):
GTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTTGAAAGACTTATAGATGACCCGAAGGATT
TAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAA
ATCAAGCTTAGTTTCTTAGTTTTCATCAAGGAACCCCTAAAAATTAGGCTTAGATTCCTTTTAAA
AACTCTTTGGATATAATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTG
AAATCATCCAGCCAGAAG
Found at i:8036 original size:42 final size:42
Alignment explanation
Indices: 7989--8070 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
7979 TATCATCTTG
*
7989 CTCGAAAGACTTA-TAGATGACCCGAAGGATTTAAGCATCATC
1 CTCGAAAGACTTACT-GATGACCCGAAGGACTTAAGCATCATC
* *
8031 CTCGAAAGACTTACTGATGGCCCGAAGGACTTACGCATCA
1 CTCGAAAGACTTACTGATGACCCGAAGGACTTAAGCATCA
8071 AGAAACCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (42 bp):
CTCGAAAGACTTACTGATGACCCGAAGGACTTAAGCATCATC
Found at i:9531 original size:28 final size:28
Alignment explanation
Indices: 9499--9600 Score: 141
Period size: 28 Copynumber: 3.6 Consensus size: 28
9489 TTAGGCTGTC
* * * *
9499 TTGGGAAGGTAATGTGCTTCATGTTATT
1 TTGGGGAGGTAATGTGTTTCACGTTAAT
* *
9527 TTGGGGTGGTAATGTGTTTCAGGTTAAT
1 TTGGGGAGGTAATGTGTTTCACGTTAAT
*
9555 TTGGTGAGGTAATGTGTTTCACGTTAAT
1 TTGGGGAGGTAATGTGTTTCACGTTAAT
9583 TTGGGGAGGTAATGTGTT
1 TTGGGGAGGTAATGTGTT
9601 ACAGGTTGGA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.20, C:0.05, G:0.33, T:0.42
Consensus pattern (28 bp):
TTGGGGAGGTAATGTGTTTCACGTTAAT
Found at i:10262 original size:10 final size:9
Alignment explanation
Indices: 10240--10337 Score: 64
Period size: 9 Copynumber: 10.9 Consensus size: 9
10230 TTCTTTCTTT
10240 TCATTTTTC
1 TCATTTTTC
10249 TCATTTTCTC
1 TCATTTT-TC
*
10259 TCATTTTTT
1 TCATTTTTC
*
10268 TCTTTTTTTCC
1 TC-ATTTTT-C
*
10279 TCTTTTTTCTC
1 TC-ATTTT-TC
10290 TCATTTTT-
1 TCATTTTTC
10298 TC-TTTTTC
1 TCATTTTTC
*
10306 T--TTTTTT
1 TCATTTTTC
10313 TCATTTGTT-
1 TCATTT-TTC
10322 TCATTTTTC
1 TCATTTTTC
10331 T-ATTTTT
1 TCATTTTT
10338 TTCTTTCTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
7 11 0.15
8 11 0.15
9 21 0.28
10 20 0.27
11 11 0.15
12 1 0.01
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.73
Consensus pattern (9 bp):
TCATTTTTC
Found at i:10264 original size:19 final size:20
Alignment explanation
Indices: 10240--10289 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
10230 TTCTTTCTTT
10240 TCATTTTTCTCATTTTCT-C
1 TCATTTTTCTCATTTTCTCC
* * *
10259 TCATTTTTTTCTTTTTTTCC
1 TCATTTTTCTCATTTTCTCC
*
10279 TCTTTTTTCTC
1 TCATTTTTCTC
10290 TCATTTTTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (20 bp):
TCATTTTTCTCATTTTCTCC
Found at i:10297 original size:73 final size:73
Alignment explanation
Indices: 10219--10359 Score: 207
Period size: 73 Copynumber: 1.9 Consensus size: 73
10209 TTTGATCGAT
*
10219 TTTTTTCTTCTTTCTTTCTTTTCATTT-TTCTCATTTTCTCTCATTTTTTTCTTT-TTTTC-CTC
1 TTTTTTCTT-TTTCTTTCTTTTCATTTGTT-TCATTTT-TCT-ATTTTTTTCTTTCTTTTCTATC
10281 TTTTTTCTCTCA
62 TTTTTTCTCTCA
*
10293 TTTTTTCTTTTTCTTTTTTTTCATTTGTTTCATTTTTCTATTTTTTTCTTTCTTTTCTATCTTTT
1 TTTTTTCTTTTTCTTTCTTTTCATTTGTTTCATTTTTCTATTTTTTTCTTTCTTTTCTATCTTTT
10358 TT
66 TT
10360 ATGTTTCATT
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
71 12 0.19
72 8 0.13
73 31 0.50
74 11 0.18
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (73 bp):
TTTTTTCTTTTTCTTTCTTTTCATTTGTTTCATTTTTCTATTTTTTTCTTTCTTTTCTATCTTTT
TTCTCTCA
Found at i:10304 original size:20 final size:18
Alignment explanation
Indices: 10263--10359 Score: 62
Period size: 18 Copynumber: 5.3 Consensus size: 18
10253 TTTCTCTCAT
*
10263 TTTTTTCTTTTTTTCCTC
1 TTTTTTCTTTTTTTCTTC
*
10281 TTTTTTCTCTCATTTT-TTC
1 TTTTTTCT-T-TTTTTCTTC
10300 -TTTTTC-TTTTTT-TTC
1 TTTTTTCTTTTTTTCTTC
*
10315 ATTTGTTTC-ATTTTTCTAT-
1 -TTT-TTTCTTTTTTTCT-TC
10334 TTTTTTCTTTCTTTTCTATC
1 TTTTTTCTTT-TTTTCT-TC
10354 TTTTTT
1 TTTTTT
10360 ATGTTTCATT
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
15 7 0.11
16 1 0.02
17 6 0.09
18 27 0.42
19 12 0.19
20 11 0.17
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.77
Consensus pattern (18 bp):
TTTTTTCTTTTTTTCTTC
Found at i:10326 original size:63 final size:60
Alignment explanation
Indices: 10218--10375 Score: 160
Period size: 62 Copynumber: 2.5 Consensus size: 60
10208 ATTTGATCGA
* * * *
10218 TTTTTTTCTTCTTTCTTTC-TTTTCATTTTTCTCATTTTCTCTCATTTTTTTCTTTTTTTCC
1 TTTTTTTCTTCTTT-TTTCTTTTTCTTTTTTTTCATTTTCTCTCATTTTTCTATTTTTTT-C
10279 TCTTTTTTCTCTCATTTTTTCTTTTTCTTTTTTTTCATTTGT-T-TCATTTTTCTATTTTTTTC
1 T-TTTTTTCT-TC-TTTTTTCTTTTTCTTTTTTTTCATTT-TCTCTCATTTTTCTATTTTTTTC
* *
10341 TTTCTTTTCTATCTTTTTTATGTTTCATTTTTTTT
1 TTT-TTTTCT-TCTTTTTTCTTTTTC-TTTTTTTT
10376 TATATCTTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 13
0.81 0.07 0.13
Matches are distributed among these distances:
61 14 0.17
62 26 0.31
63 22 0.27
64 20 0.24
65 1 0.01
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.75
Consensus pattern (60 bp):
TTTTTTTCTTCTTTTTTCTTTTTCTTTTTTTTCATTTTCTCTCATTTTTCTATTTTTTTC
Found at i:10338 original size:9 final size:9
Alignment explanation
Indices: 10243--10358 Score: 50
Period size: 10 Copynumber: 12.6 Consensus size: 9
10233 TTTCTTTTCA
10243 TTTTTCTCAT
1 TTTTTCT-AT
*
10253 TTTCTCTCATT
1 TTTTTCT-A-T
10264 TTTTTCT-T
1 TTTTTCTAT
*
10272 TTTTTCCTCTT
1 TTTTT-CT-AT
10283 TTTTCTCTCAT
1 TTTT-TCT-AT
10294 TTTTTC---
1 TTTTTCTAT
*
10300 TTTTTCTTT
1 TTTTTCTAT
10309 TTTTTC-AT
1 TTTTTCTAT
10317 TTGTTTC-A-
1 TT-TTTCTAT
10325 TTTTTCTATT
1 TTTTTCTA-T
10335 TTTTTCT-T
1 TTTTTCTAT
10343 TCTTTTCTAT
1 T-TTTTCTAT
10353 CTTTTT
1 -TTTTT
10359 TATGTTTCAT
Statistics
Matches: 87, Mismatches: 4, Indels: 30
0.72 0.03 0.25
Matches are distributed among these distances:
6 6 0.07
7 4 0.05
8 14 0.16
9 19 0.22
10 22 0.25
11 21 0.24
12 1 0.01
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTTTCTAT
Found at i:10340 original size:10 final size:10
Alignment explanation
Indices: 10243--10359 Score: 53
Period size: 9 Copynumber: 12.5 Consensus size: 10
10233 TTTCTTTTCA
10243 TTTTTCTCA-T
1 TTTTTCT-ATT
*
10253 TTTCTCTCATT
1 TTTTTCT-ATT
10264 TTTTTCT-TT
1 TTTTTCTATT
* *
10273 TTTTCCTCTT
1 TTTTTCTATT
10283 TTTTCTCTCA-T
1 TTTT-TCT-ATT
10294 TTTTTC----
1 TTTTTCTATT
10300 TTTTTCT-TT
1 TTTTTCTATT
10309 TTTTTC-ATT
1 TTTTTCTATT
*
10318 TGTTTC-A--
1 TTTTTCTATT
10325 TTTTTCTATT
1 TTTTTCTATT
10335 TTTTTCT-TT
1 TTTTTCTATT
*
10344 CTTTTCTATCT
1 TTTTTCTAT-T
10355 TTTTT
1 TTTTT
10360 ATGTTTCATT
Statistics
Matches: 85, Mismatches: 9, Indels: 25
0.71 0.08 0.21
Matches are distributed among these distances:
6 6 0.07
7 5 0.06
8 1 0.01
9 30 0.35
10 24 0.28
11 19 0.22
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (10 bp):
TTTTTCTATT
Found at i:13616 original size:30 final size:29
Alignment explanation
Indices: 13580--13641 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
13570 GTTGAACAGT
* *
13580 AAATACATAAAGTTAAAGGACCAAAATAAC
1 AAATACAGAAACTTAAAGGACCAAAA-AAC
13610 AAATACAGAAACTTAAAGGACCAAAAAAC
1 AAATACAGAAACTTAAAGGACCAAAAAAC
13639 AAA
1 AAA
13642 AATAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.63, C:0.15, G:0.10, T:0.13
Consensus pattern (29 bp):
AAATACAGAAACTTAAAGGACCAAAAAAC
Found at i:13658 original size:30 final size:30
Alignment explanation
Indices: 13592--13655 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
13582 ATACATAAAG
* *
13592 TTAAAGGACCAAAATAACAAATACAGAAAC
1 TTAAAGGACCAAAATAACAAAAACAAAAAC
* *
13622 TTAAAGGACCAAAA-AACAAAAATAAAAAT
1 TTAAAGGACCAAAATAACAAAAACAAAAAC
13651 TTAAA
1 TTAAA
13656 AGGTCTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.64, C:0.12, G:0.08, T:0.16
Consensus pattern (30 bp):
TTAAAGGACCAAAATAACAAAAACAAAAAC
Found at i:13712 original size:29 final size:30
Alignment explanation
Indices: 13649--13756 Score: 94
Period size: 29 Copynumber: 3.6 Consensus size: 30
13639 AAAAATAAAA
*
13649 ATTTAAAAGGTCTAAAATAGTAAAAAAAGAC
1 ATTT-AAAGGACTAAAATAGTAAAAAAAGAC
* * * * *
13680 ATTTAAGGGATTAAAATAG-CAAAATAGAT
1 ATTTAAAGGACTAAAATAGTAAAAAAAGAC
* *
13709 ATTTAAAGGACTAAAATAATAAAAATAGA-
1 ATTTAAAGGACTAAAATAGTAAAAAAAGAC
*
13738 ATCTTAAAGGGTCTAAAAT
1 AT-TTAAA-GGACTAAAAT
13757 GGTATTAACA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
29 25 0.40
30 25 0.40
31 13 0.21
ACGTcount: A:0.55, C:0.06, G:0.14, T:0.26
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAGTAAAAAAAGAC
Found at i:13755 original size:60 final size:61
Alignment explanation
Indices: 13592--13756 Score: 144
Period size: 60 Copynumber: 2.8 Consensus size: 61
13582 ATACATAAAG
* * * * * * *
13592 TTAAAGGACCAAAATAACAAATACAGAAACTTAAA-GGACCAAAA-AACAAAAATAAAAAT
1 TTAAAGGACTAAAATAATAAAAAAAGAATCTTAAAGGGTCTAAAATAACAAAAATAAAAAT
* * * * *
13651 TTAAAAGGTCTAAAATAGTAAAAAAAGACAT-TT-AAGGGAT-TAAAATAGC-AAAATAGATAT
1 TT-AAAGGACTAAAATAATAAAAAAAGA-ATCTTAAAGGG-TCTAAAATAACAAAAATAAAAAT
*
13711 TTAAAGGACTAAAATAATAAAAATAGAATCTTAAAGGGTCTAAAAT
1 TTAAAGGACTAAAATAATAAAAAAAGAATCTTAAAGGGTCTAAAAT
13757 GGTATTAACA
Statistics
Matches: 83, Mismatches: 15, Indels: 15
0.73 0.13 0.13
Matches are distributed among these distances:
58 2 0.02
59 29 0.35
60 49 0.59
61 3 0.04
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.21
Consensus pattern (61 bp):
TTAAAGGACTAAAATAATAAAAAAAGAATCTTAAAGGGTCTAAAATAACAAAAATAAAAAT
Found at i:14521 original size:3 final size:3
Alignment explanation
Indices: 14513--14577 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
14503 TAAGTATGTA
*
14513 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
14561 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
14578 CATAATTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:15087 original size:130 final size:131
Alignment explanation
Indices: 14866--15131 Score: 362
Period size: 130 Copynumber: 2.0 Consensus size: 131
14856 ATATTTAAAG
* **
14866 AGGG-TGATAACACAGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGTCTCCTA
1 AGGGATGATAACACAGTTCCTACACGATGAGGACGGCTGGTTATCTAGGGGTGACACAACTCCTA
* * ** *
14930 CGTGATGAGGAGGTCTGGTTGGTGGATGACACGGTACCTACGTGATGAGG-ATGATATGCCATCT
66 CGTGATGAGGAGGTCTAGTAGGTGGATGACACGGTACCTACACGATGAGGAAAG-TATGCCATCT
14994 TT
130 TT
*
14996 AGGGATGATAACAC-GATTCCTACATGATGAGGACGGCTGGTTAT-TAGGGGTGACACAACTCCT
1 AGGGATGATAACACAG-TTCCTACACGATGAGGACGGCTGGTTATCTAGGGGTGACACAACTCCT
* * *
15059 ACGTGATGAGGAGGTCTAGTCAGG-GGATGACATGGTTCCTATACGATGAGGAAAGTATGCCATC
65 ACGTGATGAGGAGGTCTAGT-AGGTGGATGACACGGTACCTACACGATGAGGAAAGTATGCCATC
15123 TTT
129 TTT
15126 AGGGAT
1 AGGGAT
15132 AATGGTTTCA
Statistics
Matches: 120, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
130 81 0.68
131 39 0.32
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (131 bp):
AGGGATGATAACACAGTTCCTACACGATGAGGACGGCTGGTTATCTAGGGGTGACACAACTCCTA
CGTGATGAGGAGGTCTAGTAGGTGGATGACACGGTACCTACACGATGAGGAAAGTATGCCATCTT
T
Found at i:15234 original size:30 final size:32
Alignment explanation
Indices: 15198--15256 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
15188 AGAGACAAAA
*
15198 TTTGTTTCAAG-GAAAC-GACTCAAAGATGGT
1 TTTGTTTCAAGAGAAACAAACTCAAAGATGGT
15228 TTTGTTTCAAGAGAAACAAACTCAAAGAT
1 TTTGTTTCAAGAGAAACAAACTCAAAGAT
15257 TTTGCGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 11 0.42
31 5 0.19
32 10 0.38
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (32 bp):
TTTGTTTCAAGAGAAACAAACTCAAAGATGGT
Found at i:15266 original size:31 final size:30
Alignment explanation
Indices: 15201--15275 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
15191 GACAAAATTT
* *
15201 GTTTCAAG-GAAACGACTCAAAGATGGTTTT
1 GTTTCAAGAGAAACAACTCAAAGAT-GTTTC
15231 GTTTCAAGAGAAACAAACTCAAAGAT-TTTGC
1 GTTTCAAGAGAAAC-AACTCAAAGATGTTT-C
15262 GTTTCGAA-AGAAAC
1 GTTTC-AAGAGAAAC
15276 TGCCTCAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
30 11 0.28
31 16 0.41
32 12 0.31
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (30 bp):
GTTTCAAGAGAAACAACTCAAAGATGTTTC
Found at i:15600 original size:32 final size:32
Alignment explanation
Indices: 15559--15622 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
15549 TTCACATCAA
*
15559 GATGTTGAATCCCCAAAGATGCCCCAACATTC
1 GATGTTGAATCCCCAAAGATACCCCAACATTC
* * *
15591 GATGTTGAATCTCCAATGATACCCCATCATTC
1 GATGTTGAATCCCCAAAGATACCCCAACATTC
15623 ATCGTTTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.27
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGATACCCCAACATTC
Found at i:21470 original size:31 final size:31
Alignment explanation
Indices: 21370--21579 Score: 114
Period size: 30 Copynumber: 7.0 Consensus size: 31
21360 AAGAGGGTTG
* * * *
21370 AATAGTAAATACATAAAGTTAAAGGA-CCAA
1 AATAGTAAAAACAGAAATTTAAAGGATCTAA
** * * *
21400 AATAACAAATACAGAAACTTAAAGGA-CCAA
1 AATAGTAAAAACAGAAATTTAAAGGATCTAA
** * *
21430 AA-AACAAAAATAGAAATTTAAAAGATCTAA
1 AATAGTAAAAACAGAAATTTAAAGGATCTAA
* * *
21460 AATAGTAAAAACAGACATTTAAGGGAT-TGA
1 AATAGTAAAAACAGAAATTTAAAGGATCTAA
*
21490 AATAG-CAAAACA-AATATTTAAAGGA-CTAA
1 AATAGTAAAAACAGAA-ATTTAAAGGATCTAA
* * *
21519 AACAATAAAAACA-AAATCTTAAAGGGTCTAA
1 AATAGTAAAAACAGAAAT-TTAAAGGATCTAA
* ** * *
21550 AATGGTATTAATAGAAATTAAAAGG-TCTAA
1 AATAGTAAAAACAGAAATTTAAAGGATCTAA
21580 CAAACAAATA
Statistics
Matches: 141, Mismatches: 31, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
28 1 0.01
29 41 0.29
30 60 0.43
31 35 0.25
32 4 0.03
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (31 bp):
AATAGTAAAAACAGAAATTTAAAGGATCTAA
Found at i:25687 original size:37 final size:37
Alignment explanation
Indices: 25594--25915 Score: 168
Period size: 37 Copynumber: 8.8 Consensus size: 37
25584 AAAATATCGA
* * *
25594 TTTTTGAAAATATATATAATATGATTTTGAAAATAC-G
1 TTTTTGAAAACATATATTATATAATTTTGAAAA-ACAG
* *
25631 -ATTTAAAAACATATATTATATAATTTTGAAAACACA-
1 TTTTTGAAAACATATATTATATAATTTTGAAAA-ACAG
* * * *
25667 TTTTTTAAAACATGTTTTATATAGTTTTGAAAAACAG
1 TTTTTGAAAACATATATTATATAATTTTGAAAAACAG
* * * * * *
25704 TTTTTGAAAATGTATATAATATATAGTTTTTAAAATCGG
1 TTTTTGAAAA--CATATATTATATAATTTTGAAAAACAG
** * * *
25743 TTTTAAAAAACATATAATATATAGTTTT--AAAATA-
1 TTTTTGAAAACATATATTATATAATTTTGAAAAACAG
* *
25777 TATTTAAAAACATATATATAATATAATTTTTG-AAAAC-G
1 TTTTTGAAAACATATAT-T-ATATAA-TTTTGAAAAACAG
* * * * *
25815 TTTTTGTAAACATAAAATATATATATTTT--AATATA-
1 TTTTTGAAAACATATATTATATA-ATTTTGAAAAACAG
*
25850 TTTTT-AAAACGTATATATAATATAAATTTTG-AAAAC-G
1 TTTTTGAAAAC--ATATATTATAT-AATTTTGAAAAACAG
* *
25887 TTTTTTGAAAACATATAATATATAGTTTT
1 -TTTTTGAAAACATATATTATATAATTTT
25916 TATGCATATT
Statistics
Matches: 220, Mismatches: 46, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
34 18 0.08
35 12 0.05
36 64 0.29
37 72 0.33
38 21 0.10
39 33 0.15
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (37 bp):
TTTTTGAAAACATATATTATATAATTTTGAAAAACAG
Found at i:25834 original size:72 final size:72
Alignment explanation
Indices: 25632--25915 Score: 265
Period size: 72 Copynumber: 3.9 Consensus size: 72
25622 GAAAATACGA
* * **
25632 TTTAAAAACATATAT-T-ATAT-AATTTTGAAAACACATTTTTT-AAAACATGTTTTATATAGTT
1 TTTAAAAACATATATATAATATAAATTTTG-AAA-ACGTTTTTTGAAAACATATAATATATAGTT
*
25693 TTGAAAAACAGT
64 TT--AAAATA-T
** * * * * **
25705 TTTTGAAA-ATGTATATAATATATAGTTTTTAAAATCGGTTTTAAAAAACATATAATATATAGTT
1 TTTAAAAACATATATATAATATA-AATTTTGAAAA-CGTTTTTTGAAAACATATAATATATAGTT
25769 TTAAAATAT
64 TTAAAATAT
* * * *
25778 ATTTAAAAACATATATATAATATAATTTTTGAAAACG-TTTTTGTAAACATAAAATATATATATT
1 -TTTAAAAACATATATATAATATAAATTTTGAAAACGTTTTTTGAAAACATATAATATATA-GTT
*
25842 TTAATATAT
64 TTAAAATAT
* *
25851 TTTTAAAACGTATATATAATATAAATTTTGAAAACGTTTTTTGAAAACATATAATATATAGTTTT
1 TTTAAAAACATATATATAATATAAATTTTGAAAACGTTTTTTGAAAACATATAATATATAGTTTT
25916 TATGCATATT
Statistics
Matches: 172, Mismatches: 29, Indels: 21
0.77 0.13 0.09
Matches are distributed among these distances:
72 61 0.35
73 41 0.24
74 25 0.15
75 21 0.12
76 24 0.14
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (72 bp):
TTTAAAAACATATATATAATATAAATTTTGAAAACGTTTTTTGAAAACATATAATATATAGTTTT
AAAATAT
Found at i:25917 original size:73 final size:73
Alignment explanation
Indices: 25594--25917 Score: 263
Period size: 73 Copynumber: 4.4 Consensus size: 73
25584 AAAATATCGA
* * *
25594 TTTTTGAAAATATAT-ATA-ATATGATTTTGAAAATACGATTTAAAAACATATAT-T-ATAT-AA
1 TTTTTGAAAACATATAATATATA-G-TTTTTAAAATA-TATTTAAAAACATATATATAATATAAA
*
25654 TTTTGAAAACACA
63 TTTTG-AAA-ACG
* * ** * * ** * *
25667 TTTTTTAAAACATGTTTTATATAGTTTTGAAAA-ACAGTTTTTGAAA-ATGTATATAATATATAG
1 TTTTTGAAAACATATAATATATAGTTTTTAAAATATA--TTTAAAAACATATATATAATATA-AA
*
25730 TTTTTAAAATCGG
63 TTTTGAAAA-C-G
** *
25743 TTTTAAAAAACATATAATATATAG-TTTTAAAATATATTTAAAAACATATATATAATATAATTTT
1 TTTTTGAAAACATATAATATATAGTTTTTAAAATATATTTAAAAACATATATATAATATAAATTT
25807 TGAAAACG
66 TGAAAACG
* * * * *
25815 TTTTTGTAAACATAAAATATATA-TATTTTAATATAT-TTTTAAAACGTATATATAATATAAATT
1 TTTTTGAAAACATATAATATATAGT-TTTTAAAATATATTTAAAAACATATATATAATATAAATT
25878 TTGAAAACG
65 TTGAAAACG
25887 TTTTTTGAAAACATATAATATATAGTTTTTA
1 -TTTTTGAAAACATATAATATATAGTTTTTA
25918 TGCATATTTT
Statistics
Matches: 202, Mismatches: 33, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
71 1 0.00
72 59 0.29
73 65 0.32
74 24 0.12
75 27 0.13
76 26 0.13
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (73 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAATATATTTAAAAACATATATATAATATAAATTT
TGAAAACG
Found at i:25946 original size:73 final size:69
Alignment explanation
Indices: 25705--25946 Score: 234
Period size: 72 Copynumber: 3.3 Consensus size: 69
25695 GAAAAACAGT
* * * **
25705 TTTTGAAAATGTATATAATATATAGTTTTTAAAATCGGTTTTAAAAAACATATAATATATAGTTT
1 TTTTGAAAATATATATAATATA-AATTTTGAAAA-C-GTTTTTGAAAACATATAATATATAGTTT
*
25770 TAAAATATA
63 T--TATATA
** * * *
25779 TTTAAAAACATATATATAATATAATTTTTGAAAACGTTTTTGTAAACATAAAATATATA-TATTT
1 TTTTGAAA-ATATATATAATATAAATTTTGAAAACGTTTTTGAAAACATATAATATATAGT-TTT
25843 TAATATA
64 T-ATATA
*
25850 TTTTTAAAACGTATATATAATATAAATTTTGAAAACGTTTTTTGAAAACATATAATATATAGTTT
1 TTTTGAAAA--TATATATAATATAAATTTTGAAAACG-TTTTTGAAAACATATAATATATAGTTT
25915 TTATGCATA
63 TTAT--ATA
*
25924 TTTTGAATATATATATATATATA
1 TTTTGAAAATATATATA-ATATA
25947 GTCTTTTTAA
Statistics
Matches: 141, Mismatches: 17, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
70 1 0.01
71 12 0.09
72 58 0.41
73 31 0.22
74 26 0.18
75 13 0.09
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (69 bp):
TTTTGAAAATATATATAATATAAATTTTGAAAACGTTTTTGAAAACATATAATATATAGTTTTTA
TATA
Found at i:26079 original size:28 final size:27
Alignment explanation
Indices: 26025--26099 Score: 71
Period size: 31 Copynumber: 2.6 Consensus size: 27
26015 AAATATAATG
*
26025 TTATATAATTTTTATTATATATTA-TTATT
1 TTATTTAATTTTT-TTAT-TATTACTTA-T
26054 GATTATTTCATATTTTTTTATTATTACTTAT
1 --TTATTT-A-ATTTTTTTATTATTACTTAT
26085 TTATTTAATTTTTTT
1 TTATTTAATTTTTTT
26100 GTTCTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
27 8 0.20
28 1 0.03
29 6 0.15
31 11 0.28
32 8 0.20
33 6 0.15
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (27 bp):
TTATTTAATTTTTTTATTATTACTTAT
Found at i:26789 original size:4 final size:4
Alignment explanation
Indices: 26780--26815 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
26770 TAACATTTCT
26780 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
26816 CTTTTTCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:26967 original size:8 final size:8
Alignment explanation
Indices: 26954--26990 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
26944 TTTAAAAATC
26954 TTTTTTTA
1 TTTTTTTA
26962 TTTTTTTA
1 TTTTTTTA
26970 TTTTTTT-
1 TTTTTTTA
26977 TATTTTTTA
1 T-TTTTTTA
26986 TTTTT
1 TTTTT
26991 ACAATCTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.04
8 25 0.93
9 1 0.04
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:26968 original size:9 final size:9
Alignment explanation
Indices: 26954--26984 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
26944 TTTAAAAATC
26954 TTTTTTTA-
1 TTTTTTTAT
26962 TTTTTTTAT
1 TTTTTTTAT
26971 TTTTTTTAT
1 TTTTTTTAT
26980 TTTTT
1 TTTTT
26985 ATTTTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:26974 original size:17 final size:16
Alignment explanation
Indices: 26954--26990 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 16
26944 TTTAAAAATC
26954 TTTTTTTATTTTTTTAT
1 TTTTTTTA-TTTTTTAT
26971 TTTTTTTATTTTTTAT
1 TTTTTTTATTTTTTAT
26987 TTTT
1 TTTT
26991 ACAATCTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTTTTATTTTTTAT
Found at i:27953 original size:42 final size:42
Alignment explanation
Indices: 27883--27988 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 42
27873 GAAAACATAT
**
27883 ATATATATATATATATATTTTTTGAAACA-ATT-TTTTTGGAAAC
1 ATATATA-ATATATA-ATTTTTAAAAACATATTATTTTT-GAAAC
*
27926 ATATATAATATATAATTTTATAAAAACATATTATTTTTGAAAT
1 ATATATAATATATAATTTT-TAAAAACATATTATTTTTGAAAC
**
27969 ATA-ATGTTATATAATTTTTA
1 ATATATAATATATAATTTTTA
27989 TTATATATCA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
41 7 0.13
42 26 0.47
43 17 0.31
44 5 0.09
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (42 bp):
ATATATAATATATAATTTTTAAAAACATATTATTTTTGAAAC
Found at i:28122 original size:22 final size:22
Alignment explanation
Indices: 28095--28141 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
28085 AGCAGAAACT
28095 CAATCGGGTAAAAGGCCTGACC
1 CAATCGGGTAAAAGGCCTGACC
* *
28117 CAATCGGGTAAAGGGCTTGACC
1 CAATCGGGTAAAAGGCCTGACC
28139 CAA
1 CAA
28142 CCTTAACCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.28, T:0.15
Consensus pattern (22 bp):
CAATCGGGTAAAAGGCCTGACC
Found at i:28710 original size:5 final size:5
Alignment explanation
Indices: 28700--28726 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28690 TTTAAGTTTC
28700 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
28727 TCCCTACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:29064 original size:13 final size:13
Alignment explanation
Indices: 29046--29075 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29036 TGAATCGAGT
29046 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
29059 TTTTAATTTTTAA
1 TTTTAAATTTTAA
29072 TTTT
1 TTTT
29076 CACAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:30690 original size:14 final size:14
Alignment explanation
Indices: 30655--30690 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
30645 GTCACGAGTG
30655 TTTTATTTCTATTC
1 TTTTATTTCTATTC
* *
30669 ATTGATTTCTATTC
1 TTTTATTTCTATTC
30683 TTTTATTT
1 TTTTATTT
30691 TACTTTTATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTATTTCTATTC
Found at i:31811 original size:110 final size:112
Alignment explanation
Indices: 31441--31839 Score: 649
Period size: 112 Copynumber: 3.6 Consensus size: 112
31431 TTGTCGGTTT
** *
31441 GTGTCGATACTTTATAAAAATATATTAATCCATAACAATATAACAGGTAAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
31506 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
31554 GTGTCGACACTTTATAAAAATATGTTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
31619 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGTATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
31666 GTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAATGAAAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
31730 GGTTTATAAATGACAAAACAGGTAAAGCGCTA-CGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
** *
31776 GTGTCGATACTTTATAAAAATATATCGATTTATAACAATATAACATGTAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
31840 AGGTAAAGCG
Statistics
Matches: 266, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
110 56 0.21
111 60 0.23
112 105 0.39
113 45 0.17
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:31876 original size:92 final size:91
Alignment explanation
Indices: 31737--31931 Score: 327
Period size: 92 Copynumber: 2.1 Consensus size: 91
31727 ACCGGTTTAT
*
31737 AAATGACAAAACAGGTAAAGCGCTACGGATATATTGAAAGTGTCGATACTTTATAAAAATATATC
1 AAATGACAAAACAGGTAAAGCGCTACGGATATATTGAAAGTGCCGATACTTTATAAAAATATATC
** *
31802 GATTTATAACAATATAACATGTAAAA
66 GATCCATAACAATATAACAGGTAAAA
*
31828 AAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGCCGATACTTTATAAAAATGTAT
1 AAATGACAAAACAGGTAAAGCGCTA-CGGATATATTGAAAGTGCCGATACTTTATAAAAATATAT
31893 CGATCCATAACAATATAACAGGTAAAA
65 CGATCCATAACAATATAACAGGTAAAA
*
31920 AAATAACAAAAC
1 AAATGACAAAAC
31932 CGGTCTATAA
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 25 0.26
92 72 0.74
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.24
Consensus pattern (91 bp):
AAATGACAAAACAGGTAAAGCGCTACGGATATATTGAAAGTGCCGATACTTTATAAAAATATATC
GATCCATAACAATATAACAGGTAAAA
Found at i:32179 original size:182 final size:182
Alignment explanation
Indices: 31865--32502 Score: 1026
Period size: 182 Copynumber: 3.5 Consensus size: 182
31855 GGATATATTG
* * *
31865 AAAGTGCCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* ** * *
31930 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACC-AGATATGTTGATAGTGTCGATACTTTA
66 ACCAGTCTCGAAATGACAAAACAGGTAAAGAGCTACCGA-ATATGTTGAAAGTGTCGATACTTTA
* * *
31994 TTATAAGTATCGACACTTTTGAAATTTAAAAGAGAAGAAGTTATATCGCTAAT
130 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAAT
** *
32047 AAAGTGTCGATACTTTATAAAAATGTATTAATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
32112 ACCAGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTAT
66 ACCAGTCTCGAAATGACAAAACAGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTAT
*
32177 TATAAGTATCGAAACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAAT
32229 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * * *
32294 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTATCGGATATGTTGAAAGTGTCGATACTTTAT
66 ACCAGTCTCGAAATGACAAAACAGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTAT
* * *
32359 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCACCAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAAT
*
32411 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAAAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
32476 ATCAGTCACGAAATGACAAAACAGGTA
66 ACCAGTCTCGAAATGACAAAACAGGTA
32503 GTAAAAAAGT
Statistics
Matches: 424, Mismatches: 31, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
182 423 1.00
183 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCAGTCTCGAAATGACAAAACAGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAAT
Found at i:34445 original size:49 final size:50
Alignment explanation
Indices: 34368--34468 Score: 134
Period size: 49 Copynumber: 2.0 Consensus size: 50
34358 TTCTATAATG
*
34368 TTATTGAAACTCGTCACGTCGATATGACGAGTTCCAATAAAAAAT-ATTT
1 TTATTCAAACTCGTCACGTCGATATGACGAGTTCCAATAAAAAATAATTT
* * * *
34417 TTATTCAAACTCTTCACG-CTGATGTGACGAGTTCGAATAAAATATAATTT
1 TTATTCAAACTCGTCACGTC-GATATGACGAGTTCCAATAAAAAATAATTT
34467 TT
1 TT
34469 TTTATTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 1 0.02
49 38 0.84
50 6 0.13
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (50 bp):
TTATTCAAACTCGTCACGTCGATATGACGAGTTCCAATAAAAAATAATTT
Found at i:36455 original size:32 final size:32
Alignment explanation
Indices: 36411--36487 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
36401 AATGTCATGT
* *
36411 TAACTCTGTTGTGCATTATTTGATTGCAATAC
1 TAACTCTGTTGTGCATTATCTGAATGCAATAC
* *
36443 TAACTCTATTGTGCATTATCTGAATGCAATAT
1 TAACTCTGTTGTGCATTATCTGAATGCAATAC
36475 TAACTCTGTTGTG
1 TAACTCTGTTGTG
36488 ACTCATACAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.43
Consensus pattern (32 bp):
TAACTCTGTTGTGCATTATCTGAATGCAATAC
Found at i:41671 original size:23 final size:23
Alignment explanation
Indices: 41645--41691 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
41635 GCTTTATCCA
41645 TGAGAAGAGATTAGGTTCATCAC
1 TGAGAAGAGATTAGGTTCATCAC
41668 TGAGAAGAGATTAGGTTCATCAC
1 TGAGAAGAGATTAGGTTCATCAC
41691 T
1 T
41692 CGAACCTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (23 bp):
TGAGAAGAGATTAGGTTCATCAC
Found at i:46155 original size:135 final size:134
Alignment explanation
Indices: 45975--46557 Score: 568
Period size: 134 Copynumber: 4.4 Consensus size: 134
45965 TCGAGAAATG
* * * * * *
45975 TTGACTCATTCCACTGTTCTTCAGGGAAGACTGAATCGAGGTAGACTTGTTCCATTGTCACTTAG
1 TTGACTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCAACTGTTACTCAG
* * **
46040 GGAATGTCAAATCTTGAAAGAGATGGATATGTTCCACTTCTTATTGA-GGAAATATCAGATCTTG
66 GGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTATTGAGGGAAA-ATCAGATC-TG
*
46104 GGGACT
129 GGGACA
* * * * * * *
46110 TTGATTCATTTCACTGTTAC-TCAAGGAAGATTGAATCGAGGTAGACATGTTTAACTGTTACTTA
1 TTGACTCATTCCACTGTT-CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCAACTGTTACTCA
* * * * * * * *
46174 GGAAATATCAAATCTTGGAAGAGAGTGATCTATTCTGCTTCTTCTTGAGGGAAAATCATATCTAG
65 GGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTATTGAGGGAAAATCAGATCTGG
46239 GGACA
130 GGACA
* * * * *
46244 TTGATTCATTCCACTGTTAATT-ATGGAAGATTGAATCAAGGCATACTTGTTCAACTGTTACTCA
1 TTGACTCATTCCACTGTT-CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCAACTGTTACTCA
* * * * *
46308 GGTAATATCAAATCTTGAAAGAGAGGGATTTGTTATGCTTTTTATTGAGGGAAAATAAGATCTGG
65 GGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTATTGAGGGAAAATCAGATCTGG
46373 GGACA
130 GGACA
** * *
46378 TCAACTCATTCCATTGTTCTTCAGGGAAGATTGAATCGAGGCATACTTGTTCCAA-TGTTACTCA
1 TTGACTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTT-CAACTGTTACTCA
* * * * * * * *
46442 GGGAATATCTAATCTTGAAATAGAGGGATCTATT-T--TTTTTCTTGAGGGAAAATCAGGTATGG
65 GGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTATTGAGGGAAAATCAGATCTGG
**
46504 GGATG
130 GGACA
* * * * * *
46509 TTGAGTTATTCCATTGTTCTTTAAGGAAGATTGAATCAAGGCAGACTTG
1 TTGACTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
46558 CTTCTCTTGT
Statistics
Matches: 375, Mismatches: 68, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
131 67 0.18
133 3 0.01
134 197 0.53
135 102 0.27
136 6 0.02
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (134 bp):
TTGACTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCAACTGTTACTCAG
GGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTATTGAGGGAAAATCAGATCTGGG
GACA
Found at i:54853 original size:131 final size:131
Alignment explanation
Indices: 54489--54854 Score: 398
Period size: 131 Copynumber: 2.8 Consensus size: 131
54479 AATTTTAAGG
* * * * *
54489 GAGAAAATAATAATATCTAATTATTTCCAATCGAGAATAAATGACTTTTCATGCCTTAAAACGGT
1 GAGAAAATAATAATATCGAATTATTTCCAATCGAGAATAAATGACCTTTCATGCCTTAGAGCAGT
* * * * *
54554 TATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCATCTTAAAATTAAATATCAATTCT
66 CATTTATTACTCCAATCAAAATGAAGAGATATTACTATTACATCCTAAAAATAAATATCAATTCT
54619 A
131 A
* * * * * * * * **
54620 GTGAAAACAATAATATATG-ATGATTTTCAATTGAGAATATATGACCTCTCACACCTT-GAAGCA
1 GAGAAAATAATAATAT-CGAATTATTTCCAATCGAGAATAAATGACCTTTCATGCCTTAG-AGCA
* * * * *
54683 GTCATTTATTGCTCCAATCAAACTGAAGAGATATCACTATTACATCCTAAAAATCAATATTAATT
64 GTCATTTATTACTCCAATCAAAATGAAGAGATATTACTATTACATCCTAAAAATAAATATCAATT
54748 -TGA
129 CT-A
* *
54751 GAGATAATGATAATATCGAATTATTTCCAATCGAGAATAAATGACCTTTCATGCCTTAGAGCAGT
1 GAGAAAATAATAATATCGAATTATTTCCAATCGAGAATAAATGACCTTTCATGCCTTAGAGCAGT
* * *
54816 CATTTATTACCCCAA-CTAAAATGAAAATATATTACTATT
66 CATTTATTACTCCAATC-AAAATGAAGAGATATTACTATT
54855 TGCAATATCG
Statistics
Matches: 186, Mismatches: 43, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
130 3 0.02
131 182 0.98
132 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.34
Consensus pattern (131 bp):
GAGAAAATAATAATATCGAATTATTTCCAATCGAGAATAAATGACCTTTCATGCCTTAGAGCAGT
CATTTATTACTCCAATCAAAATGAAGAGATATTACTATTACATCCTAAAAATAAATATCAATTCT
A
Found at i:56738 original size:3 final size:3
Alignment explanation
Indices: 56730--56780 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
56720 GGATTTGTAA
*
56730 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56777 AAT A
1 AAT A
56781 TTAAAAAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:60272 original size:6 final size:6
Alignment explanation
Indices: 60261--60288 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
60251 TAATGACTCC
60261 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
60289 TCGGGTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:60771 original size:21 final size:20
Alignment explanation
Indices: 60747--60905 Score: 146
Period size: 21 Copynumber: 7.7 Consensus size: 20
60737 GACTATCGCA
60747 TTGCGATAGTCCAAGTTCGTG
1 TTGCGATAGTCCAAGTTCG-G
60768 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCG-G
** *
60789 TTGCGATTTTCCAAATTC-G
1 TTGCGATAGTCCAAGTTCGG
*
60808 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCG-G
*
60829 TTGCGATTTATTCC-AGATTC-G
1 TTGCGA--TAGTCCAAG-TTCGG
*
60850 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCG-G
*
60871 TTGCGATTTATTCCAAGTTC-G
1 TTGCGA--TAGTCCAAGTTCGG
60892 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
60906 AATCGCAACG
Statistics
Matches: 113, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
19 29 0.26
20 2 0.02
21 63 0.56
22 2 0.02
23 17 0.15
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCGG
Found at i:60808 original size:42 final size:42
Alignment explanation
Indices: 60767--60905 Score: 228
Period size: 42 Copynumber: 3.4 Consensus size: 42
60757 CCAAGTTCGT
60767 GTTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
* *
60807 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAGATTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
* *
60849 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTC
1 GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
60891 GTTGCGATAGTCCAA
1 GTTGCGATAGTCCAA
60906 AATCGCAACG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 27 0.29
41 2 0.02
42 63 0.68
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (42 bp):
GTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC
Found at i:61050 original size:5 final size:6
Alignment explanation
Indices: 61000--61047 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
60990 GACACGTATT
61000 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
61045 ACC
1 ACC
61048 CGAGACGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:61535 original size:18 final size:18
Alignment explanation
Indices: 61509--61551 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
61499 TCGTCTCGGG
61509 TCGTGGTCGTGGTCGTTC
1 TCGTGGTCGTGGTCGTTC
* * *
61527 TCGTTGTCGTTGTCGTTG
1 TCGTGGTCGTGGTCGTTC
61545 TCGTGGT
1 TCGTGGT
61552 AATACGTGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.37, T:0.44
Consensus pattern (18 bp):
TCGTGGTCGTGGTCGTTC
Found at i:61727 original size:40 final size:41
Alignment explanation
Indices: 61644--61818 Score: 282
Period size: 40 Copynumber: 4.3 Consensus size: 41
61634 TGCGATTTTG
*
61644 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTG-GATAAATCGCAACGCGAACTTC
*
61686 GACTATCGCAACGAATTTGGA-AAATGGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGATAAATCGCAACGCGAACTTC
*
61726 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGG-ATAAATCGCAACGCGAACTTC
*
61768 GACTATCGCAACGAATTTGGA-AAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGATAAATCGCAACGCGAACTTC
61808 GACTATCGCAA
1 GACTATCGCAA
61819 TCGCATTGCG
Statistics
Matches: 125, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
40 66 0.53
41 3 0.02
42 56 0.45
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (41 bp):
GACTATCGCAACGAATTTGGATAAATCGCAACGCGAACTTC
Found at i:61781 original size:82 final size:82
Alignment explanation
Indices: 61644--61818 Score: 314
Period size: 82 Copynumber: 2.1 Consensus size: 82
61634 TGCGATTTTG
61644 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
*
61709 ATGGCAACGCGAACTTC
66 ATCGCAACGCGAACTTC
* *
61726 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
*
61791 ATCGCAATGCGAACTTC
66 ATCGCAACGCGAACTTC
61808 GACTATCGCAA
1 GACTATCGCAA
61819 TCGCATTGCG
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 89 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (82 bp):
GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
ATCGCAACGCGAACTTC
Found at i:61819 original size:21 final size:20
Alignment explanation
Indices: 61641--61818 Score: 121
Period size: 21 Copynumber: 8.7 Consensus size: 20
61631 CGTTGCGATT
*
61641 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
* *
61660 TTGAAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* *
61683 TTCGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
** *
61702 TTGGAAAATGGCAACGCGAAC
1 TTGGACTATCGCAA-GCGAAC
* *
61723 TTCGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
61742 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
61765 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
**
61784 TTGGAAAATCGCAATGCGAAC
1 TTGGACTATCGCAA-GCGAAC
*
61805 TTCGACTATCGCAA
1 TTGGACTATCGCAA
61819 TCGCATTGCG
Statistics
Matches: 119, Mismatches: 28, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
19 44 0.37
21 57 0.48
23 18 0.15
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:61848 original size:21 final size:21
Alignment explanation
Indices: 61819--61868 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
61809 ACTATCGCAA
61819 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
61840 TCGCGTTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
61861 TCGCATTG
1 TCGCATTG
61869 TGAATCTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:66593 original size:20 final size:20
Alignment explanation
Indices: 66551--66593 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
66541 AGATCAATCT
* * *
66551 TTTTATTAAGGAATCGATTC
1 TTTTACTAAGAAATCGATCC
*
66571 TTTTACTAAGAAATTGATCC
1 TTTTACTAAGAAATCGATCC
66591 TTT
1 TTT
66594 AAGTCAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTTACTAAGAAATCGATCC
Found at i:66654 original size:21 final size:21
Alignment explanation
Indices: 66630--66673 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
66620 CTTTTAAACG
*
66630 TTAAAACAATT-GATTAATTAT
1 TTAAAA-AATTCGACTAATTAT
*
66651 TTAAAAGATTCGACTAATTAT
1 TTAAAAAATTCGACTAATTAT
66672 TT
1 TT
66674 TTTAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (21 bp):
TTAAAAAATTCGACTAATTAT
Found at i:70417 original size:124 final size:124
Alignment explanation
Indices: 70197--70445 Score: 498
Period size: 124 Copynumber: 2.0 Consensus size: 124
70187 AGGTTATTGT
70197 AGTAAATTTTTTATTTCATTCTAGAGGAGTGACTGATGGTTTAACACCTCCTAGACTGGTGTCCT
1 AGTAAATTTTTTATTTCATTCTAGAGGAGTGACTGATGGTTTAACACCTCCTAGACTGGTGTCCT
70262 CAATTAACTCCAAAGCATACTTGCACTGATTCATGAGAATACCCTCATTCGACCTTAAA
66 CAATTAACTCCAAAGCATACTTGCACTGATTCATGAGAATACCCTCATTCGACCTTAAA
70321 AGTAAATTTTTTATTTCATTCTAGAGGAGTGACTGATGGTTTAACACCTCCTAGACTGGTGTCCT
1 AGTAAATTTTTTATTTCATTCTAGAGGAGTGACTGATGGTTTAACACCTCCTAGACTGGTGTCCT
70386 CAATTAACTCCAAAGCATACTTGCACTGATTCATGAGAATACCCTCATTCGACCTTAAA
66 CAATTAACTCCAAAGCATACTTGCACTGATTCATGAGAATACCCTCATTCGACCTTAAA
70445 A
1 A
70446 CCTCAAACCA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (124 bp):
AGTAAATTTTTTATTTCATTCTAGAGGAGTGACTGATGGTTTAACACCTCCTAGACTGGTGTCCT
CAATTAACTCCAAAGCATACTTGCACTGATTCATGAGAATACCCTCATTCGACCTTAAA
Found at i:74197 original size:21 final size:21
Alignment explanation
Indices: 74171--74210 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
74161 TCTGCTCTGA
74171 TATAGTCCAAGAAATAAAAAT
1 TATAGTCCAAGAAATAAAAAT
* *
74192 TATAGTCGAAGACATAAAA
1 TATAGTCCAAGAAATAAAA
74211 GTGGGGGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
TATAGTCCAAGAAATAAAAAT
Found at i:78379 original size:20 final size:20
Alignment explanation
Indices: 78342--78379 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
78332 AGTTAGTATA
*
78342 GATACCTAGGGATCAATATT
1 GATACCTAGGGATAAATATT
78362 GATACCTAGAGG-TAAATA
1 GATACCTAG-GGATAAATA
78380 CCGATACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (20 bp):
GATACCTAGGGATAAATATT
Found at i:79929 original size:264 final size:265
Alignment explanation
Indices: 79458--79989 Score: 1057
Period size: 264 Copynumber: 2.0 Consensus size: 265
79448 TCTATCTATA
79458 GTTAGCTTATGTTACTCTTTACATTGATTTTAACGACAGATGATCAAATTTTATGCATTGTCCGA
1 GTTAGCTTATGTTACTCTTTACATTGATTTTAACGACAGATGATCAAATTTTATGCATTGTCCGA
79523 TTGAAAAGCATTTAGGCTTCGTTTTCCATTCGCATATAAAACCAAAAGCAATGGTTTTATATTGG
66 TTGAAAAGCATTTAGGCTTCGTTTTCCATTCGCATATAAAACCAAAAGCAATGGTTTTATATTGG
79588 CACCAAACTCTTCTTGGATGATTTCGGGGACCAACAGGGGTGTTGCGTGGGATACAGACCATCAG
131 CACCAAACTCTTCTTGGATGATTTCGGGGACCAACAGGGGTGTTGCGTGGGATACAGACCATCAG
79653 TTTCCATACCATAGGCACAGTCGGAATCACTTGGACAGACAACCACTGTCCACTGTGATGGATCA
196 TTTCCATACCATAGGCACAGTCGGAATCACTTGGACAGACAACCACTGTCCACTGTGATGGATCA
79718 AAGGC
261 AAGGC
79723 GTTAGCTTATGTTACTCTTTACATTGATTTTAACGACAGATGATCAAATTTTATGCATTGTCCGA
1 GTTAGCTTATGTTACTCTTTACATTGATTTTAACGACAGATGATCAAATTTTATGCATTGTCCGA
79788 TTG-AAAGCATTTAGGCTTCGTTTTCCATTCGCATATAAAACCAAAAGCAATGGTTTTATATTGG
66 TTGAAAAGCATTTAGGCTTCGTTTTCCATTCGCATATAAAACCAAAAGCAATGGTTTTATATTGG
79852 CACCAAACTCTTCTTGGATGATTTCGGGGACCAACAGGGGTGTTGCGTGGGATACAGACCATCAG
131 CACCAAACTCTTCTTGGATGATTTCGGGGACCAACAGGGGTGTTGCGTGGGATACAGACCATCAG
79917 TTTCCATACCATAGGCACAGTCGGAATCACTTGGACAGACAACCACTGTCCACTGTGATGGATCA
196 TTTCCATACCATAGGCACAGTCGGAATCACTTGGACAGACAACCACTGTCCACTGTGATGGATCA
79982 AAGGC
261 AAGGC
79987 GTT
1 GTT
79990 CCATTTGTTT
Statistics
Matches: 267, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
264 199 0.75
265 68 0.25
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (265 bp):
GTTAGCTTATGTTACTCTTTACATTGATTTTAACGACAGATGATCAAATTTTATGCATTGTCCGA
TTGAAAAGCATTTAGGCTTCGTTTTCCATTCGCATATAAAACCAAAAGCAATGGTTTTATATTGG
CACCAAACTCTTCTTGGATGATTTCGGGGACCAACAGGGGTGTTGCGTGGGATACAGACCATCAG
TTTCCATACCATAGGCACAGTCGGAATCACTTGGACAGACAACCACTGTCCACTGTGATGGATCA
AAGGC
Found at i:80647 original size:3 final size:3
Alignment explanation
Indices: 80636--80696 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
80626 TTTTTTCCCG
** *
80636 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
80681 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
80697 CAATTGTTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:94287 original size:1 final size:1
Alignment explanation
Indices: 94281--94328 Score: 69
Period size: 1 Copynumber: 48.0 Consensus size: 1
94271 TATTACACTT
** *
94281 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
94329 TAAATAAAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.94, C:0.00, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:95865 original size:3 final size:3
Alignment explanation
Indices: 95854--95908 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
95844 TTTTTTCCCG
* * *
95854 TTA TT- TTA TTA TTA TTA TTA TTA TTC GTA -TC TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
95899 TTA TTTA TTA
1 TTA -TTA TTA
95909 CAATTGTTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
2 5 0.12
3 35 0.81
4 3 0.07
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Done.