Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008754.1 Hibiscus syriacus cultivar Beakdansim tig00111845_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: 290996
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:161 original size:49 final size:50
Alignment explanation
Indices: 57--162 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 50
47 TCAAAAAGGT
57 AAAATGAGCCTCAACAGCTTCTAAGACTTTGGTCACATTTGATCCTGTTTG
1 AAAATGAGCCTCAACAGCTTCTAAGACTTT-GTCACATTTGATCCTGTTTG
108 AAAATGAGCCTCAACAGCTTCTAAGACTTT-TCACATTTGATCCTGTTTG
1 AAAATGAGCCTCAACAGCTTCTAAGACTTTGTCACATTTGATCCTGTTTG
157 AAAATG
1 AAAATG
163 TTTTTCTCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 25 0.45
51 30 0.55
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (50 bp):
AAAATGAGCCTCAACAGCTTCTAAGACTTTGTCACATTTGATCCTGTTTG
Found at i:333 original size:26 final size:26
Alignment explanation
Indices: 297--358 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
287 AAAGGAATCA
297 ATAGCTCTTTTAAGGCTTTCAGAGTT
1 ATAGCTCTTTTAAGGCTTTCAGAGTT
323 ATAGCTCTTTTAAGGCTTTCAGAGTT
1 ATAGCTCTTTTAAGGCTTTCAGAGTT
349 ATAGCTCTTT
1 ATAGCTCTTT
359 GAAAAATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.44
Consensus pattern (26 bp):
ATAGCTCTTTTAAGGCTTTCAGAGTT
Found at i:916 original size:93 final size:92
Alignment explanation
Indices: 738--919 Score: 265
Period size: 93 Copynumber: 2.0 Consensus size: 92
728 CAGCTCAATA
* * * *
738 TTATAATCACCTTTATCACGCTAGCTAAATCTTATCCATAAAGTCGGGCGTTTAACCAATTTCTT
1 TTATAATCACCTTTATCACGCTAGCTAAATCTCATCCATAAAGCCGGGCGTTTAACCAATTGCTC
*
803 TAGAGGGACAACTCACGCTTTATTGTG
66 TAGAGGGACAACTCAAGCTTTATTGTG
* * * * *
830 TTATAATCACTTTTATCAGGCTAGTTGAATCTCATCCTTAAAGCCTGGGCGTTTAACCAATTGCT
1 TTATAATCACCTTTATCACGCTAGCTAAATCTCATCCATAAAGCC-GGGCGTTTAACCAATTGCT
895 CTAGAGGGACAACTCAAGCTTTATT
65 CTAGAGGGACAACTCAAGCTTTATT
920 ATATACATAT
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
92 38 0.48
93 41 0.52
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (92 bp):
TTATAATCACCTTTATCACGCTAGCTAAATCTCATCCATAAAGCCGGGCGTTTAACCAATTGCTC
TAGAGGGACAACTCAAGCTTTATTGTG
Found at i:2337 original size:61 final size:61
Alignment explanation
Indices: 2269--2394 Score: 234
Period size: 61 Copynumber: 2.1 Consensus size: 61
2259 ACTCCCCCTT
*
2269 ACTTTAACACTTCTCCCATTTATCATTTTAAAAACACACACACTTAAACACATTTAAAAAC
1 ACTTTAACACTTCTCCCATTTATCATTTTAAAAACACACACACTTAAACACACTTAAAAAC
*
2330 ACTTTAACACTTCTCCCATTTATCATTTTAAAAACACACACACTTAAACACACTTAAACAC
1 ACTTTAACACTTCTCCCATTTATCATTTTAAAAACACACACACTTAAACACACTTAAAAAC
2391 ACTT
1 ACTT
2395 CTTCTCCCCC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (61 bp):
ACTTTAACACTTCTCCCATTTATCATTTTAAAAACACACACACTTAAACACACTTAAAAAC
Found at i:2390 original size:8 final size:10
Alignment explanation
Indices: 2367--2394 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2357 TTAAAAACAC
2367 ACACACTTAA
1 ACACACTTAA
2377 ACACACTTAA
1 ACACACTTAA
2387 ACACACTT
1 ACACACTT
2395 CTTCTCCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.21
Consensus pattern (10 bp):
ACACACTTAA
Found at i:4607 original size:21 final size:21
Alignment explanation
Indices: 4581--4620 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4571 CAGAACCCCA
*
4581 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
4602 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
4621 TCAAAGGGGA
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:4654 original size:20 final size:20
Alignment explanation
Indices: 4601--4662 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
4591 GATTCCCCTG
4601 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGG-ATCGGTT-CCC-TCA
** *
4624 AAGGGGAATCGGTTCCCTCA
1 TGGGGGGATCGGTTCCCTCA
*
4644 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
4663 TGCACAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 18 0.56
21 3 0.09
22 7 0.22
23 4 0.12
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGGATCGGTTCCCTCA
Found at i:14193 original size:14 final size:14
Alignment explanation
Indices: 14174--14200 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14164 AAAAAATGAA
14174 ATAAAGAAGATAAG
1 ATAAAGAAGATAAG
14188 ATAAAGAAGATAA
1 ATAAAGAAGATAA
14201 AAAAATGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (14 bp):
ATAAAGAAGATAAG
Found at i:14236 original size:5 final size:5
Alignment explanation
Indices: 14211--14290 Score: 60
Period size: 5 Copynumber: 15.8 Consensus size: 5
14201 AAAAATGAAG
* *
14211 TAAAGA TAAAA TAGTAAA TAAAA T-AAG TAAAA CAAAA -AAAA -AAAA
1 TAAA-A TAAAA TA--AAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
*
14256 -AAAA AAAAA TAAAAA TAAAA TAAAA TAAAAA TAAA
1 TAAAA TAAAA T-AAAA TAAAA TAAAA T-AAAA TAAA
14291 GAAACATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
4 15 0.23
5 30 0.47
6 14 0.22
7 5 0.08
ACGTcount: A:0.80, C:0.01, G:0.04, T:0.15
Consensus pattern (5 bp):
TAAAA
Found at i:14238 original size:27 final size:28
Alignment explanation
Indices: 14185--14241 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
14175 TAAAGAAGAT
14185 AAGATAAAGAAGATAAAAAAATGAAGTA
1 AAGATAAAGAAGATAAAAAAATGAAGTA
14213 AAGATAAA-ATAG-TAAATAAAAT-AAGTA
1 AAGATAAAGA-AGATAAA-AAAATGAAGTA
14240 AA
1 AA
14242 ACAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (28 bp):
AAGATAAAGAAGATAAAAAAATGAAGTA
Found at i:14247 original size:14 final size:14
Alignment explanation
Indices: 14202--14278 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 14
14192 AGAAGATAAA
14202 AAAATGAAGTAAAGAT
1 AAAAT-AAGTAAA-AT
14218 AAAAT-AGT-AAAT
1 AAAATAAGTAAAAT
*
14230 AAAATAAGTAAAAC
1 AAAATAAGTAAAAT
** *
14244 AAAA-AAAAAAAAA
1 AAAATAAGTAAAAT
* *
14257 AAAAAAAATAAAAAT
1 AAAATAAGT-AAAAT
14272 AAAATAA
1 AAAATAA
14279 AATAAAAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
12 7 0.14
13 15 0.30
14 13 0.26
15 10 0.20
16 5 0.10
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (14 bp):
AAAATAAGTAAAAT
Found at i:14258 original size:11 final size:11
Alignment explanation
Indices: 14239--14309 Score: 72
Period size: 11 Copynumber: 6.5 Consensus size: 11
14229 TAAAATAAGT
*
14239 AAAACAAAAAA
1 AAAATAAAAAA
*
14250 AAAAAAAAAAA
1 AAAATAAAAAA
*
14261 AAAATAAAAAT
1 AAAATAAAAAA
*
14272 AAAATAAAATA
1 AAAATAAAAAA
*
14283 AAAAT-AAAGA
1 AAAATAAAAAA
*
14293 AACATAAAAAA
1 AAAATAAAAAA
*
14304 ATAATA
1 AAAATA
14310 GTAAAAATAT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
10 8 0.16
11 41 0.84
ACGTcount: A:0.85, C:0.03, G:0.01, T:0.11
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:14258 original size:16 final size:16
Alignment explanation
Indices: 14239--14304 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 16
14229 TAAAATAAGT
14239 AAAACAAAAAAAAAAA
1 AAAACAAAAAAAAAAA
14255 AAAA-AAAAAATAAAAA
1 AAAACAAAAAA-AAAAA
*
14271 TAAAATAAAATAAAAATAA
1 -AAAACAAAA-AAAAA-AA
14290 AGAAACATAAAAAAA
1 A-AAACA-AAAAAAA
14305 TAATAGTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
15 6 0.14
16 9 0.21
17 4 0.10
18 8 0.19
19 12 0.29
20 3 0.07
ACGTcount: A:0.86, C:0.03, G:0.02, T:0.09
Consensus pattern (16 bp):
AAAACAAAAAAAAAAA
Found at i:14287 original size:6 final size:6
Alignment explanation
Indices: 14239--14290 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
14229 TAAAATAAGT
* *
14239 AAAACA AAAA-A AAAA-A AAAAAA AAAATA AAAAT- AAAAT- AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
14283 AAAATA AA
1 AAAATA AA
14291 GAAACATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
5 20 0.47
6 23 0.53
ACGTcount: A:0.88, C:0.02, G:0.00, T:0.10
Consensus pattern (6 bp):
AAAATA
Found at i:14304 original size:1 final size:1
Alignment explanation
Indices: 14239--14286 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
14229 TAAAATAAGT
* * * * *
14239 AAAACAAAAAAAAAAAAAAAAAAAAATAAAAATAAAATAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14287 TAAAGAAACA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.02, G:0.00, T:0.08
Consensus pattern (1 bp):
A
Found at i:14336 original size:4 final size:4
Alignment explanation
Indices: 14329--14380 Score: 61
Period size: 4 Copynumber: 12.8 Consensus size: 4
14319 TTATATATAT
* *
14329 AATA AATAA AATA AAAA AATA AA-A AATTA AATA AATA AATA AATA TATA
1 AATA AAT-A AATA AATA AATA AATA AA-TA AATA AATA AATA AATA AATA
14378 AAT
1 AAT
14381 TAGAATATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 3 0.07
4 31 0.76
5 7 0.17
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:14341 original size:9 final size:9
Alignment explanation
Indices: 14225--14371 Score: 82
Period size: 9 Copynumber: 16.9 Consensus size: 9
14215 GATAAAATAG
14225 TAAATAAAA
1 TAAATAAAA
*
14234 TAAGTAAAA
1 TAAATAAAA
*
14243 CAAA-AAAA
1 TAAATAAAA
14251 -AAA-AAAA
1 TAAATAAAA
14258 -AAA-AAAA
1 TAAATAAAA
14265 TAAAAATAAAA
1 T--AAATAAAA
14276 TAAAATAAAAA
1 T-AAAT-AAAA
*
14287 TAAAGAAACA
1 TAAATAAA-A
14297 TAAA-AAAA
1 TAAATAAAA
*
14305 T-AATAGTAA
1 TAAATA-AAA
**
14314 -AAATATTA
1 TAAATAAAA
* *
14322 TATATATAA
1 TAAATAAAA
14331 TAAATAAAA
1 TAAATAAAA
14340 TAAA-AAAA
1 TAAATAAAA
*
14348 TAAA-AAAT
1 TAAATAAAA
14356 TAAAT-AAA
1 TAAATAAAA
14364 TAAATAAA
1 TAAATAAA
14372 TATATAAATT
Statistics
Matches: 114, Mismatches: 12, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
7 16 0.14
8 31 0.27
9 41 0.36
10 16 0.14
11 10 0.09
ACGTcount: A:0.77, C:0.01, G:0.02, T:0.20
Consensus pattern (9 bp):
TAAATAAAA
Found at i:14371 original size:20 final size:20
Alignment explanation
Indices: 14226--14371 Score: 82
Period size: 20 Copynumber: 7.0 Consensus size: 20
14216 ATAAAATAGT
*
14226 AAATAAAATAAGTAAAACAAAAA
1 AAATAAAATAA--AAAA-ATAAA
* *
14249 AAAAAAAAAAAAAAAAT-AA
1 AAATAAAATAAAAAAATAAA
*
14268 AAATAAAATAAAATAAA-AAT
1 AAATAAAATAAAA-AAATAAA
*
14288 AAAGAAACATAAAAAAATAATA
1 AAATAAA-ATAAAAAAATAA-A
* * * * *
14310 GTAAA-AATATTATATATATAAT
1 --AAATAA-AATAAAAAAATAAA
14332 AAATAAAATAAAAAAATAAA
1 AAATAAAATAAAAAAATAAA
* *
14352 AAATTAAATAAATAAATAAA
1 AAATAAAATAAAAAAATAAA
14372 TATATAAATT
Statistics
Matches: 94, Mismatches: 20, Indels: 21
0.70 0.15 0.16
Matches are distributed among these distances:
19 13 0.14
20 44 0.47
21 14 0.15
23 19 0.20
24 4 0.04
ACGTcount: A:0.77, C:0.01, G:0.02, T:0.19
Consensus pattern (20 bp):
AAATAAAATAAAAAAATAAA
Found at i:14378 original size:16 final size:16
Alignment explanation
Indices: 14250--14380 Score: 71
Period size: 16 Copynumber: 8.4 Consensus size: 16
14240 AAACAAAAAA
* * *
14250 AAAAAAAAAAAAAAAT
1 AAAAATAAATAAATAT
14266 AAAAATAAAATAAA-AT
1 AAAAAT-AAATAAATAT
* *
14282 AAAAATAAAGAAACAT
1 AAAAATAAATAAATAT
14298 -AAAA-AAAT-AATAGT
1 AAAAATAAATAAATA-T
* *
14312 AAAAAT-ATTATATAT
1 AAAAATAAATAAATAT
* *
14327 -ATAATAAATAAAATAA
1 AAAAATAAAT-AAATAT
14343 AAAAATAAA-AAAT-T
1 AAAAATAAATAAATAT
14357 AAATAAATAAATAAATAT
1 -AA-AAATAAATAAATAT
*
14375 ATAAAT
1 AAAAAT
14381 TAGAATATTA
Statistics
Matches: 88, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
13 3 0.03
14 8 0.09
15 25 0.28
16 33 0.38
17 18 0.20
18 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.22
Consensus pattern (16 bp):
AAAAATAAATAAATAT
Found at i:21932 original size:15 final size:15
Alignment explanation
Indices: 21909--21946 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
21899 AGATATATGG
*
21909 AGATAGGGCCTGAGA
1 AGATTGGGCCTGAGA
*
21924 AGATTGGGCCTGAGC
1 AGATTGGGCCTGAGA
21939 AGATTGGG
1 AGATTGGG
21947 TATATTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.42, T:0.18
Consensus pattern (15 bp):
AGATTGGGCCTGAGA
Found at i:30963 original size:3 final size:3
Alignment explanation
Indices: 30955--30998 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
30945 GTAGACACTA
*
30955 ATT ATT ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT A
30999 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:30987 original size:19 final size:19
Alignment explanation
Indices: 30963--31002 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
30953 TAATTATTAT
30963 TATTATTATTATTATTAAA
1 TATTATTATTATTATTAAA
30982 TATTATTATTATTATTAAA
1 TATTATTATTATTATTAAA
31001 TA
1 TA
31003 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATTATTATTATTAAA
Found at i:32338 original size:11 final size:11
Alignment explanation
Indices: 32315--32346 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
32305 TTAAATTCAA
32315 TATTTTAATTAT
1 TATTTT-ATTAT
32327 TATTTTATTAT
1 TATTTTATTAT
32338 TATTTTATT
1 TATTTTATT
32347 TCAGTCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:33650 original size:22 final size:21
Alignment explanation
Indices: 33625--33683 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
33615 GGGTCAATTG
33625 TAAGACCTACAGTGCAAGATGA
1 TAAGACCTACAGTGC-AGATGA
* * *
33647 TAAGACCT-CAGGGC-CATCCA
1 TAAGACCTACAGTGCAGAT-GA
33667 TAAGACCTACAGTGCAG
1 TAAGACCTACAGTGCAG
33684 GATGTTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.07
20 9 0.31
21 10 0.34
22 8 0.28
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (21 bp):
TAAGACCTACAGTGCAGATGA
Found at i:35229 original size:15 final size:15
Alignment explanation
Indices: 35202--35236 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
35192 AATTTTATTC
35202 TTTAAATTTCAATAT
1 TTTAAATTTCAATAT
35217 GTTTAAA-TTCAATAT
1 -TTTAAATTTCAATAT
35232 TTTAA
1 TTTAA
35237 TTATTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 8 0.42
16 6 0.32
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (15 bp):
TTTAAATTTCAATAT
Found at i:35252 original size:11 final size:11
Alignment explanation
Indices: 35229--35260 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
35219 TTAAATTCAA
35229 TATTTTAATTAT
1 TATTTT-ATTAT
35241 TATTTTATTAT
1 TATTTTATTAT
35252 TATTTTATT
1 TATTTTATT
35261 TCAGTCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:38642 original size:31 final size:31
Alignment explanation
Indices: 38571--38673 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 31
38561 TCAGATTCAT
* * * *
38571 GGGTTAAATTGATGTTTTAGCTAAAGTTCAA
1 GGGTTAAATTGATATTTTATCTAAAATTTAA
* *
38602 GGGTAAAATTGATATTTTATCTAAAATTTAT
1 GGGTTAAATTGATATTTTATCTAAAATTTAA
* *
38633 GGGTTAAATT-AGTTTTTTATCTTAAATTTAA
1 GGGTTAAATTGA-TATTTTATCTAAAATTTAA
38664 GGGTTAAATT
1 GGGTTAAATT
38674 AAAAATGAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
30 1 0.02
31 60 0.98
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (31 bp):
GGGTTAAATTGATATTTTATCTAAAATTTAA
Found at i:41391 original size:2 final size:2
Alignment explanation
Indices: 41386--41420 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41376 CTCCTAACGT
41386 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41421 TTATTTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41520 original size:8 final size:8
Alignment explanation
Indices: 41496--41532 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
41486 TTAAATACTA
41496 TATTTTAT
1 TATTTTAT
41504 T-TTTCTAT
1 TATTT-TAT
41512 TATTTTAT
1 TATTTTAT
41520 TATTTT-T
1 TATTTTAT
41527 TATTTT
1 TATTTT
41533 TGTTTTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 10 0.37
8 14 0.52
9 3 0.11
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (8 bp):
TATTTTAT
Found at i:41527 original size:21 final size:21
Alignment explanation
Indices: 41456--41527 Score: 51
Period size: 21 Copynumber: 3.3 Consensus size: 21
41446 TTTCCTTTTC
41456 TTTTTTTCTATTA-TTTATTTA
1 TTTTTTTCTATTATTTTA-TTA
* *
41477 TTTTATT-TATTAAATACTATATT-
1 TTTTTTTCTATT--AT--TTTATTA
41500 TTATTTTTCTATTATTTTATTA
1 TT-TTTTTCTATTATTTTATTA
41522 TTTTTT
1 TTTTTT
41528 ATTTTTGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
20 4 0.10
21 15 0.38
22 3 0.08
23 4 0.10
24 6 0.15
25 7 0.18
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTTTCTATTATTTTATTA
Found at i:41675 original size:12 final size:13
Alignment explanation
Indices: 41652--41686 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
41642 TAGATTAATC
41652 TTTTATTATTATT
1 TTTTATTATTATT
41665 TTTTATT-TTATT
1 TTTTATTATTATT
*
41677 TATTATTATT
1 TTTTATTATT
41687 TTGATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTATTATT
Found at i:41679 original size:22 final size:21
Alignment explanation
Indices: 41653--41698 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
41643 AGATTAATCT
*
41653 TTTATTATTATTTTTTATTTTA
1 TTTATTATTA-TTTTGATTTTA
41675 TTTATTATTATTTTGATTTTA
1 TTTATTATTATTTTGATTTTA
41696 TTT
1 TTT
41699 GGGGTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTATTATTATTTTGATTTTA
Found at i:45084 original size:21 final size:21
Alignment explanation
Indices: 45060--45099 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
45050 ATACTTTGCA
45060 TTTT-TATTTTTCCATGTTTAT
1 TTTTCTATTTTT-CATGTTTAT
45081 TTTTCTATTTTTCATGTTT
1 TTTTCTATTTTTCATGTTT
45100 TTACATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTCTATTTTTCATGTTTAT
Found at i:52178 original size:60 final size:59
Alignment explanation
Indices: 52114--52229 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 59
52104 AATACTTCGC
* * * *
52114 TTAGGACGAAAACCCGAGAGGGCGTCCTAAGTCGAAAAAGAAAAAG-AAAAGAAAAAACGT
1 TTAGGACGAAAACCCGAAAAGG-GACCTAAATCG-AAAAGAAAAAGAAAAAGAAAAAACGT
** *
52174 TTAGGGTGAAAACCCGAAAAGGGACCTAAATTGAAAAGAAAAAGAAAAAGAAAAAA
1 TTAGGACGAAAACCCGAAAAGGGACCTAAATCGAAAAGAAAAAGAAAAAGAAAAAA
52230 GGAAAAAGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 11 0.23
59 19 0.40
60 18 0.38
ACGTcount: A:0.54, C:0.12, G:0.23, T:0.10
Consensus pattern (59 bp):
TTAGGACGAAAACCCGAAAAGGGACCTAAATCGAAAAGAAAAAGAAAAAGAAAAAACGT
Found at i:52221 original size:5 final size:6
Alignment explanation
Indices: 52207--52261 Score: 65
Period size: 6 Copynumber: 8.3 Consensus size: 6
52197 ACCTAAATTG
52207 AAAAGA AAAAGA AAAAGAA AAAAGGA AAAAGAA AAAATTGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAG-A AAAA-GA AAAAG-A AAAA--GA AAAAGA AAAAGA
52260 AA
1 AA
52262 GGAAAATAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
6 22 0.50
7 15 0.34
8 6 0.14
9 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:52234 original size:8 final size:7
Alignment explanation
Indices: 52207--52261 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
52197 ACCTAAATTG
52207 AAAAG-A
1 AAAAGAA
52213 AAAAG-A
1 AAAAGAA
52219 AAAAGAA
1 AAAAGAA
*
52226 AAAAGGA
1 AAAAGAA
52233 AAAAGAA
1 AAAAGAA
52240 AAAATTG-A
1 AAAA--GAA
52248 AAAAG-A
1 AAAAGAA
52254 AAAAGAA
1 AAAAGAA
52261 A
1 A
52262 GGAAAATAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
6 18 0.42
7 19 0.44
8 5 0.12
9 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:52234 original size:14 final size:13
Alignment explanation
Indices: 52207--52261 Score: 69
Period size: 14 Copynumber: 4.2 Consensus size: 13
52197 ACCTAAATTG
52207 AAAAG-AAAAAGA
1 AAAAGAAAAAAGA
52219 AAAAGAAAAAAGGA
1 AAAAGAAAAAA-GA
52233 AAAAGAAAAAATTGA
1 AAAAGAAAAAA--GA
52248 AAAAG-AAAAAGA
1 AAAAGAAAAAAGA
52260 AA
1 AA
52262 GGAAAATAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
12 9 0.23
13 5 0.13
14 18 0.46
15 7 0.18
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:52242 original size:15 final size:15
Alignment explanation
Indices: 52212--52267 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
52202 AATTGAAAAG
52212 AAAAA-GAAAAAG-A
1 AAAAAGGAAAAAGAA
52225 AAAAAGGAAAAAGAA
1 AAAAAGGAAAAAGAA
**
52240 AAAATTGAAAAAGAAA
1 AAAAAGGAAAAAG-AA
52256 AAGAAAGGAAAA
1 AA-AAAGGAAAA
52268 TAAGGCGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
13 5 0.14
14 7 0.20
15 12 0.34
16 4 0.11
17 7 0.20
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (15 bp):
AAAAAGGAAAAAGAA
Found at i:55106 original size:21 final size:19
Alignment explanation
Indices: 55075--55133 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
55065 TTAGCACTTT
55075 TTTTATTATTTATTTTTTTAC
1 TTTT-TTATTTATTTTTTT-C
55096 TATTTTTA-TT-TTTTTTTC
1 T-TTTTTATTTATTTTTTTC
*
55114 TTTTTTATTAATTTTTTTC
1 TTTTTTATTTATTTTTTTC
55133 T
1 T
55134 CCTAACGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 6 0.18
18 3 0.09
19 16 0.47
20 2 0.06
21 4 0.12
22 3 0.09
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTATTTATTTTTTTC
Found at i:55111 original size:18 final size:18
Alignment explanation
Indices: 55078--55122 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
55068 GCACTTTTTT
55078 TATTATTTA-TTTTTTTAC
1 TATT-TTTATTTTTTTTAC
*
55096 TATTTTTATTTTTTTTTC
1 TATTTTTATTTTTTTTAC
55114 T-TTTTTATT
1 TATTTTTATT
55123 AATTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (18 bp):
TATTTTTATTTTTTTTAC
Found at i:55119 original size:17 final size:17
Alignment explanation
Indices: 55072--55133 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
55062 AATTTAGCAC
* *
55072 TTTTTTTATTATTTA-T
1 TTTTTTTCTTTTTTATT
*
55088 TTTTTTACTATTTTTATT
1 TTTTTTTCT-TTTTTATT
55106 TTTTTTTCTTTTTTATT
1 TTTTTTTCTTTTTTATT
55123 AATTTTTTTCT
1 --TTTTTTTCT
55134 CCTAACGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
16 7 0.18
17 13 0.34
18 9 0.24
19 9 0.24
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTCTTTTTTATT
Found at i:55250 original size:16 final size:17
Alignment explanation
Indices: 55219--55250 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
55209 AAAATTTTCA
55219 TCCTTATTATTGTTTTT
1 TCCTTATTATTGTTTTT
55236 TCCTT-TTATT-TTTTT
1 TCCTTATTATTGTTTTT
55251 CTATTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.75
Consensus pattern (17 bp):
TCCTTATTATTGTTTTT
Found at i:55287 original size:21 final size:21
Alignment explanation
Indices: 55263--55313 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
55253 ATTATTTATT
55263 TATTTTATTTAT-TAAATACTA
1 TATTTTATTTATATAAATA-TA
*
55284 TATTTTA-TTATATATATATA
1 TATTTTATTTATATAAATATA
*
55304 TATTTCATTT
1 TATTTTATTT
55314 CATTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTATTTATATAAATATA
Found at i:55324 original size:15 final size:16
Alignment explanation
Indices: 55306--55343 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
55296 TATATATATA
55306 TTTCATTTCATTTT-T
1 TTTCATTTCATTTTGT
*
55321 TTTCTTTTCATTTTGT
1 TTTCATTTCATTTTGT
55337 TTT-ATTT
1 TTTCATTT
55344 TTTGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTCATTTCATTTTGT
Found at i:55339 original size:20 final size:21
Alignment explanation
Indices: 55306--55344 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
55296 TATATATATA
55306 TTTCATTTCATTTT-TTTTCT
1 TTTCATTTCATTTTATTTTCT
**
55326 TTTCATTTTGTTTTATTTT
1 TTTCATTTCATTTTATTTT
55345 TTGTTTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTCATTTCATTTTATTTTCT
Found at i:55453 original size:14 final size:14
Alignment explanation
Indices: 55394--55454 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
55384 TTTTTCCTTA
55394 TTTTTATTTTTATCT
1 TTTTTATTTTT-TCT
*
55409 TATTCTATTTTGTT-T
1 T-TTTTATTTT-TTCT
* **
55424 TGTTTATTTTACCT
1 TTTTTATTTTTTCT
55438 TTTTTATTTTTTCT
1 TTTTTATTTTTTCT
55452 TTT
1 TTT
55455 ATTGTGGTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
14 22 0.63
15 3 0.09
16 9 0.26
17 1 0.03
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTATTTTTTCT
Found at i:55487 original size:3 final size:3
Alignment explanation
Indices: 55479--55519 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
55469 GATTAGTCTT
55479 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
55520 TAATTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:55497 original size:15 final size:15
Alignment explanation
Indices: 55478--55530 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
55468 AGATTAGTCT
55478 TTTATTATTATTATTA
1 TTTATTATTATT-TTA
55494 -TTATTATTATTTTA
1 TTTATTATTATTTTA
*
55508 TTTATTATTATTTAA
1 TTTATTATTATTTTA
55523 TTT-TTATT
1 TTTATTATT
55531 TGGGTATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
14 8 0.23
15 27 0.77
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTATTATTTTA
Found at i:55527 original size:21 final size:21
Alignment explanation
Indices: 55480--55531 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
55470 ATTAGTCTTT
*
55480 TATTATTA-TTATTATTATTAT
1 TATT-TTATTTATTATTATTAA
55501 TATTTTATTTATTATTATTTAA
1 TATTTTATTTATTATTA-TTAA
55523 T-TTTTATTT
1 TATTTTATTT
55532 GGGTATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 21 0.75
22 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTTATTTATTATTATTAA
Found at i:59199 original size:18 final size:18
Alignment explanation
Indices: 59176--59231 Score: 112
Period size: 18 Copynumber: 3.1 Consensus size: 18
59166 AACAATACAT
59176 CATTACCTTTTGGTCCAA
1 CATTACCTTTTGGTCCAA
59194 CATTACCTTTTGGTCCAA
1 CATTACCTTTTGGTCCAA
59212 CATTACCTTTTGGTCCAA
1 CATTACCTTTTGGTCCAA
59230 CA
1 CA
59232 AAATTTTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.38
Consensus pattern (18 bp):
CATTACCTTTTGGTCCAA
Found at i:60271 original size:37 final size:37
Alignment explanation
Indices: 60196--60476 Score: 282
Period size: 37 Copynumber: 7.2 Consensus size: 37
60186 ATATACATAA
60196 TTTTGAAAACATTTTTTTGAAATTATATATATAATATATAG
1 TTTTGAAAACA--TTTTTGAAA-T-TATATATAATATATAG
*
60237 TTTTGAAAACATTTTTGAAATTATATATAATATATAT
1 TTTTGAAAACATTTTTGAAATTATATATAATATATAG
*
60274 TTTTGAAAACATTTTTGAAATTATATATATAACATATAG
1 TTTTGAAAACATTTTTGAAA-T-TATATATAATATATAG
* *
60313 TTTTGAAAACTTTTTTGAAAAATATATATATATATATATATAATA
1 TTTTGAAAACATTTTTG---AA-AT-TATATATA-ATATAT-A-G
* *
60358 TAGTTTTGAAAACATTTTTGAAAATATATATAATATATAG
1 T--TTTG-AAAACATTTTTGAAATTATATATAATATATAG
*
60398 TTTTGAAAACATTTTCG-AA--ATATATAATATATAG
1 TTTTGAAAACATTTTTGAAATTATATATAATATATAG
** *
60432 TTTTGAAAACA-TTTTGAAAAGATATATATTATATAG
1 TTTTGAAAACATTTTTGAAATTATATATAATATATAG
*
60468 TTTTAAAAA
1 TTTTGAAAA
60477 AATATTTTTT
Statistics
Matches: 210, Mismatches: 15, Indels: 35
0.81 0.06 0.13
Matches are distributed among these distances:
33 4 0.02
34 28 0.13
36 24 0.11
37 46 0.22
38 5 0.02
39 39 0.19
40 1 0.00
41 12 0.06
42 18 0.09
43 14 0.07
44 2 0.01
45 3 0.01
47 3 0.01
48 11 0.05
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTGAAAACATTTTTGAAATTATATATAATATATAG
Found at i:60350 original size:85 final size:84
Alignment explanation
Indices: 60258--60430 Score: 260
Period size: 85 Copynumber: 2.0 Consensus size: 84
60248 TTTTTGAAAT
*
60258 TATATATA-AT-ATATATTTTTGAAAACATTTTTGAAATTATATATATAACATATAGTTTTGAAA
1 TATATATATATAATATAGTTTTGAAAACATTTTTGAAA--ATATATATAACATATAGTTTTGAAA
* *
60321 ACTTTTTTGAAAAATATATATA
64 ACATTTTCGAAAAATATA-ATA
*
60343 TATATATATATAATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
1 TATATATATATAATATAGTTTTGAAAACATTTTTGAAAATATATATAACATATAGTTTTGAAAAC
*
60408 ATTTTCGAAATATATAATA
66 ATTTTCGAAAAATATAATA
60427 TATA
1 TATA
60431 GTTTTGAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
84 7 0.09
85 47 0.58
86 2 0.02
87 25 0.31
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (84 bp):
TATATATATATAATATAGTTTTGAAAACATTTTTGAAAATATATATAACATATAGTTTTGAAAAC
ATTTTCGAAAAATATAATA
Found at i:60351 original size:48 final size:47
Alignment explanation
Indices: 60295--60396 Score: 163
Period size: 48 Copynumber: 2.2 Consensus size: 47
60285 TTTTTGAAAT
*
60295 TATATATATA-ACATATAGTTTTGAAAACTTTTTTGAAAAATATATATA
1 TATATATATATA-ATATAGTTTTGAAAACATTTTTG-AAAATATATATA
60343 TATATATATATAATATAGTTTTGAAAACATTTTTGAAAATATATATA
1 TATATATATATAATATAGTTTTGAAAACATTTTTGAAAATATATATA
60390 -ATATATA
1 TATATATA
60397 GTTTTGAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
46 7 0.13
47 12 0.23
48 32 0.62
49 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (47 bp):
TATATATATATAATATAGTTTTGAAAACATTTTTGAAAATATATATA
Found at i:60361 original size:124 final size:117
Alignment explanation
Indices: 60219--60466 Score: 374
Period size: 124 Copynumber: 2.1 Consensus size: 117
60209 TTTTTGAAAT
* *
60219 TATATATATAATATATAGTTTTGAAAACATTTTTGAAATTATATATAATATATATTTTTGAAAAC
1 TATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
* *
60284 ATTTTTGAAATTATATATATAACATATAGTTTTGAAAACTTTTTTGAAAA-ATATATA
66 ATTTTCGAAA-TATATA-AT---ATATAGTTTTGAAAAC-ATTTTGAAAAGATATATA
60341 TATATATATATATAATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAA
1 TATATATATA-AT-ATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAA
60406 ACATTTTCGAAATATATAATATATAGTTTTGAAAACATTTTGAAAAGATATATA
64 ACATTTTCGAAATATATAATATATAGTTTTGAAAACATTTTGAAAAGATATATA
60460 T-TATATA
1 TATATATA
60467 GTTTTAAAAA
Statistics
Matches: 119, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
118 15 0.13
119 24 0.20
122 12 0.10
123 8 0.07
124 60 0.50
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (117 bp):
TATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
ATTTTCGAAATATATAATATATAGTTTTGAAAACATTTTGAAAAGATATATA
Found at i:60426 original size:34 final size:35
Alignment explanation
Indices: 60344--60476 Score: 171
Period size: 34 Copynumber: 3.7 Consensus size: 35
60334 ATATATATAT
*
60344 ATATATATATAATATAGTTTTGAAAACATTTTTGAAAAT
1 ATATATA-AT-ATATAGTTTTGAAAACA-TTTTG-AAAG
60383 ATATATAATATATAGTTTTGAAAACATTTTCG-AA-
1 ATATATAATATATAGTTTTGAAAACATTTT-GAAAG
60417 ATATATAATATATAGTTTTGAAAACATTTTGAAAAG
1 ATATATAATATATAGTTTTGAAAACATTTTG-AAAG
* *
60453 ATATATATTATATAGTTTTAAAAA
1 ATATATAATATATAGTTTTGAAAA
60477 AATATTTTTT
Statistics
Matches: 88, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
33 1 0.01
34 30 0.34
35 4 0.05
36 26 0.30
37 18 0.20
38 2 0.02
39 7 0.08
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (35 bp):
ATATATAATATATAGTTTTGAAAACATTTTGAAAG
Found at i:61324 original size:150 final size:149
Alignment explanation
Indices: 61133--61435 Score: 561
Period size: 150 Copynumber: 2.0 Consensus size: 149
61123 AAGTGTCGCG
61133 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
* *
61198 TATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGTTCCACAGAATATAT
66 TATACATATACTAGGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGTTCCAAAGAATATAC
61263 ATATATCCCGAAGGACCGCA
130 ATATATCCCGAAGGACCGCA
61283 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
61348 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
* *
61413 TATGTCCCGAAGGACCGCG
131 TATATCCCGAAGGACCGCA
61432 TAGA
1 TAGA
61436 CCCTCTACCC
Statistics
Matches: 149, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
149 51 0.34
150 98 0.66
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
TATATCCCGAAGGACCGCA
Found at i:68055 original size:23 final size:23
Alignment explanation
Indices: 68029--68073 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
68019 CACCACAGCT
*
68029 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
68052 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
68074 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:68238 original size:150 final size:149
Alignment explanation
Indices: 68041--68356 Score: 571
Period size: 150 Copynumber: 2.1 Consensus size: 149
68031 TATAAATGCA
*
68041 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAA
68105 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTT-CAAGACTTCACACATGT
* *
68170 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
68191 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAAT
68256 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
68321 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
68340 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
68357 CCCTCTACCC
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
149 53 0.33
150 108 0.67
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAAGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:69693 original size:5 final size:5
Alignment explanation
Indices: 69683--69749 Score: 66
Period size: 5 Copynumber: 13.0 Consensus size: 5
69673 AAAACATGTA
*
69683 ATTTT ATTTT A-TTT ATTATTT ATTTT ATTTT A-TTT AGTTT ATTTT ATTTATT
1 ATTTT ATTTT ATTTT A-T-TTT ATTTT ATTTT ATTTT ATTTT ATTTT A-TT-TT
*
69735 ATTTT ATTTA ATTTT
1 ATTTT ATTTT ATTTT
69750 TTTGTCCAGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
4 8 0.15
5 33 0.62
6 5 0.09
7 7 0.13
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:69712 original size:26 final size:26
Alignment explanation
Indices: 69685--69744 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 26
69675 AACATGTAAT
69685 TTTATTTTATTTATTA-TTTATTTTA
1 TTTATTTTATTTATTATTTTATTTTA
*
69710 TTT-TATTTA-GT-TTATTTTA-TTTA
1 TTTAT-TTTATTTATTATTTTATTTTA
69733 -TTATTTTATTTA
1 TTTATTTTATTTA
69745 ATTTTTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
22 6 0.21
23 9 0.32
24 6 0.21
25 7 0.25
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTATTTTATTTATTATTTTATTTTA
Found at i:71927 original size:3 final size:3
Alignment explanation
Indices: 71916--71947 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
71906 TGTTTTTTTA
71916 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT A
71948 GTCTTACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:75268 original size:7 final size:7
Alignment explanation
Indices: 75256--75346 Score: 51
Period size: 7 Copynumber: 13.3 Consensus size: 7
75246 TTTTATAATG
75256 AACCCTA
1 AACCCTA
75263 AACCCT-
1 AACCCTA
* *
75269 AACCATT
1 AACCCTA
*
75276 AACCTTA
1 AACCCTA
75283 AACCCTA
1 AACCCTA
***
75290 AAATATA
1 AACCCTA
*
75297 AACCATA
1 AACCCTA
**
75304 AAATCTA
1 AACCCTA
*
75311 AACCTTA
1 AACCCTA
*
75318 AACTCTA
1 AACCCTA
*
75325 AATCCTA
1 AACCCTA
*
75332 AACCATA
1 AACCCTA
75339 AA-CCTA
1 AACCCTA
75345 AA
1 AA
75347 TTGCACTTAC
Statistics
Matches: 61, Mismatches: 22, Indels: 3
0.71 0.26 0.03
Matches are distributed among these distances:
6 10 0.16
7 51 0.84
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (7 bp):
AACCCTA
Found at i:75319 original size:21 final size:21
Alignment explanation
Indices: 75269--75346 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
75259 CCTAAACCCT
* * *
75269 AACCATTAACCTTAAACCCTA
1 AACCATAAACCTAAAATCCTA
**
75290 AAATATAAACCATAAAAT-CTA
1 AACCATAAACC-TAAAATCCTA
*
75311 AACCTTAAACTCT-AAATCCTA
1 AACCATAAAC-CTAAAATCCTA
75332 AACCATAAACCTAAA
1 AACCATAAACCTAAA
75347 TTGCACTTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 6 0.14
21 33 0.75
22 5 0.11
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCATAAACCTAAAATCCTA
Found at i:77808 original size:17 final size:17
Alignment explanation
Indices: 77786--77822 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
77776 ATTTGAGTTT
77786 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
77803 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
77820 GAG
1 GAG
77823 CTCCTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:79058 original size:21 final size:20
Alignment explanation
Indices: 79034--79074 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
79024 AAACATGAGC
*
79034 AATTCGAAAATTCAATAAGTA
1 AATTAGAAAATTCAA-AAGTA
*
79055 AATTAGAAAATTTAAAAGTA
1 AATTAGAAAATTCAAAAGTA
79075 CAATGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (20 bp):
AATTAGAAAATTCAAAAGTA
Found at i:85881 original size:17 final size:18
Alignment explanation
Indices: 85838--85878 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
85828 GAATTATATT
85838 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
85855 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
85873 ATTAAA
1 AGTAAA
85879 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:87196 original size:24 final size:24
Alignment explanation
Indices: 87169--87231 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
87159 AAATTTTAAA
**
87169 TATTCTATAATTTTATTTCATTTT
1 TATTCTATAATTTTATTTCAAATT
* *
87193 TATTTTGATAA-TTAATTTCAAATT
1 TATTCT-ATAATTTTATTTCAAATT
*
87217 TATTCTTTAATTTTA
1 TATTCTATAATTTTA
87232 ATTAATAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
23 3 0.10
24 23 0.77
25 4 0.13
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (24 bp):
TATTCTATAATTTTATTTCAAATT
Found at i:87375 original size:16 final size:17
Alignment explanation
Indices: 87356--87395 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
87346 ATAAAAAATA
*
87356 ATTAATTTTTATT-AAT
1 ATTAATTTTAATTGAAT
*
87372 ATTAATTTTAATTGGAT
1 ATTAATTTTAATTGAAT
87389 ATTAATT
1 ATTAATT
87396 AAGATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTAATTTTAATTGAAT
Found at i:89110 original size:18 final size:18
Alignment explanation
Indices: 89087--89124 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
89077 CTTAAAATTT
89087 TGTTGGACCAAAAGGTAA
1 TGTTGGACCAAAAGGTAA
89105 TGTTGGACCAAAAGGTAA
1 TGTTGGACCAAAAGGTAA
89123 TG
1 TG
89125 ATGTATCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (18 bp):
TGTTGGACCAAAAGGTAA
Found at i:93277 original size:21 final size:21
Alignment explanation
Indices: 93253--93299 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
93243 TGGAGCCTTA
93253 GAAGTGATTGAAAACATGTTT
1 GAAGTGATTGAAAACATGTTT
93274 GAAGTGATTGAAAACATGTTT
1 GAAGTGATTGAAAACATGTTT
93295 GAAGT
1 GAAGT
93300 TTTGGTGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (21 bp):
GAAGTGATTGAAAACATGTTT
Found at i:94323 original size:48 final size:48
Alignment explanation
Indices: 94261--94409 Score: 221
Period size: 48 Copynumber: 3.1 Consensus size: 48
94251 ACATACTTTG
94261 TGTATGATGGTTATCGATCAATTTTGTTTAATGCATAAGGTT-CATTTT
1 TGTATGATGGTTATCGATCAATTTTGTTTAATGCATAA-GTTGCATTTT
*
94309 TGTATGATGATTATCGATCGAA-TTTGTTTAATGCATAAGTTGCATTTT
1 TGTATGATGGTTATCGATC-AATTTTGTTTAATGCATAAGTTGCATTTT
* * *
94357 CGTATGATGGTTATCGATCGATTTTGTTTAATGCATATGTTGCATTTT
1 TGTATGATGGTTATCGATCAATTTTGTTTAATGCATAAGTTGCATTTT
*
94405 CGTAT
1 TGTAT
94410 CAGTACTATA
Statistics
Matches: 93, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
47 4 0.04
48 87 0.94
49 2 0.02
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.47
Consensus pattern (48 bp):
TGTATGATGGTTATCGATCAATTTTGTTTAATGCATAAGTTGCATTTT
Found at i:94510 original size:51 final size:51
Alignment explanation
Indices: 94438--94538 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
94428 TGGTACTATG
* *
94438 TGTGCACCCATGGTATTCATAATGAGTTTATGAATGACCATTTCGGCACTA
1 TGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGACACTA
* * *
94489 TGTGCATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGACACT
1 TGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGACACT
94539 TAGGTGCAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (51 bp):
TGTGCACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGACACTA
Found at i:100579 original size:20 final size:20
Alignment explanation
Indices: 100554--100598 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
100544 TAATTTAATC
* *
100554 GAATATATAATTTTAAAATT
1 GAATATAAAATCTTAAAATT
100574 GAATATAAAATCTTAAAATT
1 GAATATAAAATCTTAAAATT
*
100594 CAATA
1 GAATA
100599 GTACTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
GAATATAAAATCTTAAAATT
Found at i:102936 original size:23 final size:22
Alignment explanation
Indices: 102908--102965 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
102898 TACACTTTGG
102908 GATGTATCGATACACATTCA-A
1 GATGTATCGATACACATTCATA
* *
102929 GGAATGTATCGGTACATATTCATA
1 -G-ATGTATCGATACACATTCATA
102953 G-TGTATCGATACA
1 GATGTATCGATACA
102966 TAGCGAGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 11 0.35
22 1 0.03
23 18 0.58
24 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (22 bp):
GATGTATCGATACACATTCATA
Found at i:110659 original size:24 final size:24
Alignment explanation
Indices: 110632--110750 Score: 150
Period size: 24 Copynumber: 5.0 Consensus size: 24
110622 TTCGACTTGA
110632 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
110656 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* * *
110680 ATTCTGATCTAATACTTTACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
110704 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
110728 ATTTTGATATGATATTTGACATG
1 ATTCTGATCTGATACTTGACATG
110751 AATTATGCTT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:110668 original size:48 final size:49
Alignment explanation
Indices: 110614--110716 Score: 129
Period size: 48 Copynumber: 2.1 Consensus size: 49
110604 TAAATATTTT
* * *
110614 ATATGATTTTC-GACTTGAATTCTGATCTGATACTTGACATGGATTCTG
1 ATATGATTATCTGACATGAATTCTGATCTAATACTTGACATGGATTCTG
* * *
110662 ATATGA-TATCTGACATGGATTCTGATCTAATACTTTACTTGGATTCTG
1 ATATGATTATCTGACATGAATTCTGATCTAATACTTGACATGGATTCTG
*
110710 ATCTGAT
1 ATATGAT
110717 ACTTGACCTG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
47 3 0.07
48 43 0.93
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (49 bp):
ATATGATTATCTGACATGAATTCTGATCTAATACTTGACATGGATTCTG
Found at i:110685 original size:12 final size:12
Alignment explanation
Indices: 110648--110686 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
110638 ATCTGATACT
110648 TGACATGGATTC
1 TGACATGGATTC
*
110660 TGATAT-GATATC
1 TGACATGGAT-TC
110672 TGACATGGATTC
1 TGACATGGATTC
110684 TGA
1 TGA
110687 TCTAATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:112592 original size:17 final size:19
Alignment explanation
Indices: 112550--112592 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
112540 GGGAGCGTAG
112550 GTGTATCGGTACACTATCAAA
1 GTGTATCGGTACAC-ATC-AA
112571 GTGTATCGGTACAC-TC-A
1 GTGTATCGGTACACATCAA
112588 GTGTA
1 GTGTA
112593 AAATTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
19 2 0.09
21 14 0.64
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (19 bp):
GTGTATCGGTACACATCAA
Found at i:112891 original size:20 final size:20
Alignment explanation
Indices: 112866--112909 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
112856 AATTTAATCA
* * *
112866 AATATATAATTTTAAAATTG
1 AATATAAAATCTTAAAATTC
112886 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
112906 AATA
1 AATA
112910 GTACTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:114881 original size:24 final size:23
Alignment explanation
Indices: 114853--114927 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 23
114843 TATCGATCAA
114853 TTTTGTTTAATGCATAAGTTGCAT
1 TTTTGTTTAATGCATAAGTTG-AT
* * *
114877 TTTTGTATGATG-ATTA-TTGAT
1 TTTTGTTTAATGCATAAGTTGAT
114898 TGAATTTGTTTAATGCATAAGTTGTAT
1 T---TTTGTTTAATGCATAAGTTG-AT
114925 TTT
1 TTT
114928 CATATTATGG
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 3 0.08
22 3 0.08
23 3 0.08
24 21 0.54
25 3 0.08
26 3 0.08
27 3 0.08
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.53
Consensus pattern (23 bp):
TTTTGTTTAATGCATAAGTTGAT
Found at i:114976 original size:48 final size:48
Alignment explanation
Indices: 114834--114980 Score: 197
Period size: 48 Copynumber: 3.1 Consensus size: 48
114824 ATACTTTGTG
* **
114834 TATGATGGTTATCGATCAATTTTGTTTAATGCATAAGTTGCATTTTTG
1 TATGATGGTTATCGATCAATTTTGTTTAATGCATAAGTTGTATTTTCA
* * *
114882 TATGATGATTATTGATTGAA-TTTGTTTAATGCATAAGTTGTATTTTCA
1 TATGATGGTTATCGA-TCAATTTTGTTTAATGCATAAGTTGTATTTTCA
* * *
114930 TATTATGGTTATCGATCCATTTTGTTTAATGCATATGTTGTATTTTCA
1 TATGATGGTTATCGATCAATTTTGTTTAATGCATAAGTTGTATTTTCA
114978 TAT
1 TAT
114981 CTGTACTATA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
47 2 0.02
48 80 0.94
49 3 0.04
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.50
Consensus pattern (48 bp):
TATGATGGTTATCGATCAATTTTGTTTAATGCATAAGTTGTATTTTCA
Found at i:133226 original size:26 final size:27
Alignment explanation
Indices: 133175--133275 Score: 86
Period size: 26 Copynumber: 3.9 Consensus size: 27
133165 AACACAAAGC
*
133175 AAAA-AAAAAAA-AAAAAACAAATAGA
1 AAAAGAAAAAAAGAAAAAACAAAGAGA
* *
133200 AAAGGAAAAAAAGACAAAA-AAAGAGA
1 AAAAGAAAAAAAGAAAAAACAAAGAGA
* ** *
133226 AAAACAAAAAAAGGGAAAATAAAGA-A
1 AAAAGAAAAAAAGAAAAAACAAAGAGA
133252 AAAAGAAAATAAA-AAAAGAACAAA
1 AAAAGAAAA-AAAGAAAA-AACAAA
133276 TTAATATTTC
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
25 3 0.05
26 39 0.65
27 18 0.30
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.03
Consensus pattern (27 bp):
AAAAGAAAAAAAGAAAAAACAAAGAGA
Found at i:133232 original size:16 final size:17
Alignment explanation
Indices: 133208--133244 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
133198 GAAAAGGAAA
133208 AAAAGACAAAAAAAGAG
1 AAAAGACAAAAAAAGAG
*
133225 AAAA-ACAAAAAAAGGG
1 AAAAGACAAAAAAAGAG
133241 AAAA
1 AAAA
133245 TAAAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAGACAAAAAAAGAG
Found at i:133253 original size:16 final size:15
Alignment explanation
Indices: 133215--133270 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
133205 AAAAAAAGAC
*
133215 AAAAAAAGAGAAAAAC
1 AAAAAAAGAG-AAAAT
*
133231 AAAAAAAGGGAAAAT
1 AAAAAAAGAGAAAAT
*
133246 AAAGAAAAAAGAAAAT
1 AAA-AAAAGAGAAAAT
133262 AAAAAAAGA
1 AAAAAAAGA
133271 ACAAATTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 12 0.35
16 22 0.65
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (15 bp):
AAAAAAAGAGAAAAT
Found at i:137065 original size:137 final size:137
Alignment explanation
Indices: 136804--137293 Score: 461
Period size: 130 Copynumber: 3.6 Consensus size: 137
136794 ATTAGATCTT
* * * * *
136804 TCAACGCGAAGGAGTAGTGTCATCCTAAGACAATCAGACTTCCTTAACGCGAAAGAATCGTGTTT
1 TCAACGCGAAGGAGCAGTGTCATCCT-A-ACAATCAAACTTCCTCAACGCGAAGGAATCATG-TT
* * * * **
136869 TTCTCCAAATTATCTCCAAAT-AGG-TAGATGTCCTCAATATAAAGGAACAATGTCATCCACGAC
63 GTCTCTAAATTATCTCCAAATAAGGCTAGACGTCCTCAACACGAAGGAACAATGTCATCCACGAC
136932 CAAATCTTCA
128 CAAATCTTCA
* * *
136942 T-AACGCGAATGAGCAGTTTCATCCTTATACAATCAAACTTCCTCAACGCGAAGGAATCACGTTG
1 TCAACGCGAAGGAGCAGTGTCATCC-TA-ACAATCAAACTTCCTCAACGCGAAGGAATCATGTTG
*
137006 TCTCTAAATTATCTCCAAATAAGGCTAGACGTCCTCAACACGAAGGAACAATGT-GTCCACTGAC
64 TCTCTAAATTATCTCCAAATAAGGCTAGACGTCCTCAACACGAAGGAACAATGTCATCCAC-GAC
* * *
137070 TAGATC-TCT
128 CAAATCTTCA
* * * * ** *
137079 TCAATGTGAAGGAGCAGTGTCAT-C--A-GA-C-AACTTTCTCAACGTAAAGGAACCATGTTGTC
1 TCAACGCGAAGGAGCAGTGTCATCCTAACAATCAAACTTCCTCAACGCGAAGGAATCATGTTGTC
*
137138 TCTAAATTATCTCCAAATACGGCTAGACGTCCTCAACACGAAGGAACAATGTCATCCACCGACCA
66 TCTAAATTATCTCCAAATAAGGCTAGACGTCCTCAACACGAAGGAACAATGTCATCCA-CGACCA
*
137203 AATCTAC-
130 AATCTTCA
* * * * * * * *
137210 TCAATGTGAAGGAGAAGTGTCATCTTCAGATAACCAAACTTCCTCAACACTAAGGAA-CTATGTT
1 TCAACGCGAAGGAGCAGTGTCATCCT-A-ACAATCAAACTTCCTCAACGCGAAGGAATC-ATGTT
*
137274 GTCTCCAAATTA-C-CCAAATA
63 GTCTCTAAATTATCTCCAAATA
137294 CTTCTAGAAC
Statistics
Matches: 293, Mismatches: 42, Indels: 35
0.79 0.11 0.09
Matches are distributed among these distances:
130 77 0.26
131 34 0.12
132 3 0.01
133 1 0.00
136 22 0.08
137 69 0.24
138 54 0.18
139 33 0.11
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (137 bp):
TCAACGCGAAGGAGCAGTGTCATCCTAACAATCAAACTTCCTCAACGCGAAGGAATCATGTTGTC
TCTAAATTATCTCCAAATAAGGCTAGACGTCCTCAACACGAAGGAACAATGTCATCCACGACCAA
ATCTTCA
Found at i:147819 original size:21 final size:19
Alignment explanation
Indices: 147793--147837 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
147783 GGCCAGTACT
147793 GATACTCTAGTCCAGGGTATC
1 GATAC-CTAG-CCAGGGTATC
*
147814 GATA-CTAGCTAGGGTATC
1 GATACCTAGCCAGGGTATC
147832 GATACC
1 GATACC
147838 GATTTTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 13 0.59
19 5 0.23
21 4 0.18
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (19 bp):
GATACCTAGCCAGGGTATC
Found at i:147821 original size:19 final size:18
Alignment explanation
Indices: 147799--147836 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
147789 TACTGATACT
147799 CTAGTCCAGGGTATCGATA
1 CTAG-CCAGGGTATCGATA
*
147818 CTAGCTAGGGTATCGATA
1 CTAGCCAGGGTATCGATA
147836 C
1 C
147837 CGATTTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (18 bp):
CTAGCCAGGGTATCGATA
Found at i:153696 original size:3 final size:3
Alignment explanation
Indices: 153684--153731 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
153674 TATCCCATAT
*
153684 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
153731 T
1 T
153732 GTACTTCCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:155074 original size:21 final size:19
Alignment explanation
Indices: 155050--155334 Score: 183
Period size: 21 Copynumber: 13.7 Consensus size: 19
155040 CATATTCGCA
155050 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
155071 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
155092 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
*
155113 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
*
155134 TTGCGATAGTCGAAGTTTGCG
1 TTGCGATAGTCCAAG-TT-CG
* *
155155 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* *
155176 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* *
155197 TTGCAATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
155218 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* * *
155239 TTGTGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
155260 TTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCG
155279 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* * *
155300 TTGCGATTTATTCCAAATTCA
1 TTGCGA--TAGTCCAAGTTCG
155321 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
155335 AATTGCAACG
Statistics
Matches: 224, Mismatches: 26, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
19 50 0.22
20 2 0.01
21 139 0.62
22 2 0.01
23 31 0.14
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:155096 original size:42 final size:41
Alignment explanation
Indices: 155044--155334 Score: 206
Period size: 42 Copynumber: 7.0 Consensus size: 41
155034 GATTTACATA
* * *
155044 TTCGCATTGCGATAGTCCAAGTTCGCGTTGCGA-TAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAATT--CGTTGCGATTAGTCCAAG
* *
155086 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAATTCGTTGCGA-TTAGTCCAAG
* * * *
155130 TT--CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGATAGTCCAA-ATT-CGTTGCGA-TTAGTCCAAG
* * *
155172 TT--CGTTGCGATTTATTCCAAATTCGTTGC-AATAGTCGAAG
1 TTCGCGTTGCGA--TAGTCCAAATTCGTTGCGATTAGTCCAAG
* * * *
155212 TTCGCGTTGCGATTTATTCCAAATTCGTTGTGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAATTCGTTGCGA-TTAGTCCAAG
*
155256 TT--CGTTGCGATAGTCCAAGTTCGTTGCGA-TAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAATTCGTTGCGATTAGTCCAAG
* *
155294 TTCGCGTTGCGATTTATTCCAAATTCATTGCGA-TAGTCCAA
1 TTCGCGTTGCGA--TAGTCCAAATTCGTTGCGATTAGTCCAA
155335 AATTGCAACG
Statistics
Matches: 204, Mismatches: 29, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
38 9 0.04
40 38 0.19
41 3 0.01
42 119 0.58
43 3 0.01
44 32 0.16
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTCCAAATTCGTTGCGATTAGTCCAAG
Found at i:155139 original size:63 final size:63
Alignment explanation
Indices: 155069--155331 Score: 408
Period size: 63 Copynumber: 4.2 Consensus size: 63
155059 TCCAAGTTCG
*
155069 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
*
155132 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* *
155195 CGTTGCAATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGTGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
* * *
155258 CGTTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATT
*
155319 CATTGCGATAGTC
1 CGTTGCGATAGTC
155332 CAAAATTGCA
Statistics
Matches: 187, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
59 9 0.05
61 40 0.21
63 138 0.74
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (63 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
Found at i:155295 original size:82 final size:83
Alignment explanation
Indices: 155153--155327 Score: 280
Period size: 82 Copynumber: 2.1 Consensus size: 83
155143 TCGAAGTTTG
* *
155153 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCAATAGTCGAAGTTCGCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGA-TTAGTCCAAATTCGTTGCAATAGTCCAAGTTCGCG
155218 TTGCGATTTATTCCAAATT
65 TTGCGATTTATTCCAAATT
* * *
155237 CGTTGTGATTTATTCCAAATTCGTTGCGA-TAGTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAATTCGTTGCAATAGTCCAAGTTCGCGT
155301 TGCGATTTATTCCAAATT
66 TGCGATTTATTCCAAATT
*
155319 CATTGCGAT
1 CGTTGCGAT
155328 AGTCCAAAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
82 56 0.67
84 28 0.33
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (83 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATTAGTCCAAATTCGTTGCAATAGTCCAAGTTCGCGT
TGCGATTTATTCCAAATT
Found at i:155955 original size:6 final size:6
Alignment explanation
Indices: 155934--155976 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
155924 GTCCGTCTCG
155934 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
155977 AATACGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:156681 original size:17 final size:17
Alignment explanation
Indices: 156659--156692 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
156649 ATTATGTTGC
156659 ATAACAGAAATCTTTGA
1 ATAACAGAAATCTTTGA
*
156676 ATAACAGAATTCTTTGA
1 ATAACAGAAATCTTTGA
156693 TATCTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (17 bp):
ATAACAGAAATCTTTGA
Found at i:157514 original size:58 final size:55
Alignment explanation
Indices: 157452--157688 Score: 160
Period size: 58 Copynumber: 4.1 Consensus size: 55
157442 TAAATCATTG
* *
157452 AATTTATTTTCCTATGAATCTTATATGATTCTGTTTGGTAAAAGAAAAGAAATTGTCA
1 AATTTATTTTCATA-GAATCTTATATGATTCTGTTT-GTAAAAGAAAATAAATTGT-A
* * * * * * *
157510 AATTTATTTTCTTGGGAATCTTGAT-CGATTTCAT-CTTATAGAAGAAAATAAATAGATA
1 AATTTATTTTCAT-AGAATCTT-ATATGA-TTC-TGTTTGTAAAAGAAAATAAATTG-TA
* * *
157568 AATTTATTTTCATAGAATCTTATATGATTATGTTTGTAAAAGAAATTAAATTGTTG
1 AATTTATTTTCATAGAATCTTATATGATTCTGTTTGTAAAAGAAAATAAATTG-TA
* * * * *
157624 GATTTA-TTTCTTTAGAATC-AAGTATGATTCTATCTTGTAAAA-AGAAATAAATTGTTG
1 AATTTATTTTC-ATAGAATCTTA-TATGATTCTGT-TTGTAAAAGA-AAATAAATTG-TA
157681 AATTTATT
1 AATTTATT
157689 ACTTGAAAGT
Statistics
Matches: 141, Mismatches: 26, Indels: 24
0.74 0.14 0.13
Matches are distributed among these distances:
55 6 0.04
56 43 0.30
57 34 0.24
58 49 0.35
59 8 0.06
60 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (55 bp):
AATTTATTTTCATAGAATCTTATATGATTCTGTTTGTAAAAGAAAATAAATTGTA
Found at i:160377 original size:20 final size:20
Alignment explanation
Indices: 160323--160378 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 20
160313 CTCAGAGGGA
160323 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATT-CCCCCC-AGGGGGT
160345 ACCGATTCCCCCCAGGGGGT
1 ACCGATTCCCCCCAGGGGGT
160365 ACCGATTCCCCCCA
1 ACCGATTCCCCCCA
160379 CTGTTCAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 21 0.62
21 6 0.18
22 7 0.21
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (20 bp):
ACCGATTCCCCCCAGGGGGT
Found at i:169199 original size:24 final size:24
Alignment explanation
Indices: 169172--169300 Score: 161
Period size: 24 Copynumber: 5.4 Consensus size: 24
169162 ATTTGATTTA
169172 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
169196 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
169220 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
169244 TGATCTGTTACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTC
** * *
169268 TGAAATGATACTTGACATGAATTA
1 TGATCTGATACTTGACATGGATTC
*
169292 TGATTTGAT
1 TGATCTGAT
169301 TTTTTGATAT
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 1 0.01
24 89 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:174295 original size:82 final size:83
Alignment explanation
Indices: 174209--174370 Score: 245
Period size: 83 Copynumber: 2.0 Consensus size: 83
174199 GAAAATATAT
* * *
174209 GTTTAATATTT-AAATTTAAAAGACATTATAATCTTTTTAAATTTAGATATTAAAAGAATTTTGG
1 GTTTAATATTTAAAATTTAAAAGACATTATAATATGTTTAAATTTAGATATTAAAAGAATTTTAG
174273 TTGAAGTAAAACTCTTAG
66 TTGAAGTAAAACTCTTAG
* * * *
174291 GTTTAATATTTAAAATTTAAAAGATATTATTATATGTTTAAATTTAGATATTAAAATAGTTTTAG
1 GTTTAATATTTAAAATTTAAAAGACATTATAATATGTTTAAATTTAGATATTAAAAGAATTTTAG
*
174356 TTGGAGTAAAACTCT
66 TTGAAGTAAAACTCT
174371 CTCGAAATTC
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 11 0.15
83 60 0.85
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (83 bp):
GTTTAATATTTAAAATTTAAAAGACATTATAATATGTTTAAATTTAGATATTAAAAGAATTTTAG
TTGAAGTAAAACTCTTAG
Found at i:175620 original size:21 final size:21
Alignment explanation
Indices: 175596--175654 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
175586 TTCGAAATAA
175596 GGGTGTATCGGTACATCAGAG
1 GGGTGTATCGGTACATCAGAG
175617 GGGTGTATCGGTACATCAGAG
1 GGGTGTATCGGTACATCAGAG
*
175638 GAGTGTATCGGTACATC
1 GGGTGTATCGGTACATC
175655 CCTTTATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.15, G:0.36, T:0.25
Consensus pattern (21 bp):
GGGTGTATCGGTACATCAGAG
Found at i:175967 original size:13 final size:13
Alignment explanation
Indices: 175951--176010 Score: 70
Period size: 12 Copynumber: 4.8 Consensus size: 13
175941 TAAGATTTTC
*
175951 TTTTTGAAAATTA
1 TTTTTGAAAATCA
175964 TTTTTG-AAATCA
1 TTTTTGAAAATCA
* *
175976 ATTTTGAAAATTA
1 TTTTTGAAAATCA
175989 TTTTTG-AAATCA
1 TTTTTGAAAATCA
*
176001 ATTTTGAAAA
1 TTTTTGAAAA
176011 ATTACTCCCC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
12 20 0.51
13 19 0.49
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:175985 original size:25 final size:25
Alignment explanation
Indices: 175952--176010 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
175942 AAGATTTTCT
175952 TTTTGAAAATTATTTTTGAAATCAA
1 TTTTGAAAATTATTTTTGAAATCAA
175977 TTTTGAAAATTATTTTTGAAATCAA
1 TTTTGAAAATTATTTTTGAAATCAA
176002 TTTTGAAAA
1 TTTTGAAAA
176011 ATTACTCCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTGAAAATTATTTTTGAAATCAA
Found at i:177156 original size:15 final size:15
Alignment explanation
Indices: 177136--177165 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
177126 ATTTCTCTCT
177136 CGTTATCTAAACCAA
1 CGTTATCTAAACCAA
177151 CGTTATCTAAACCAA
1 CGTTATCTAAACCAA
177166 ATGTCCTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (15 bp):
CGTTATCTAAACCAA
Found at i:178268 original size:23 final size:22
Alignment explanation
Indices: 178241--178317 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 22
178231 CACTTCAGAG
178241 TGTATCGATACACATTCAAGGAA
1 TGTATCGATACACATTCAAGG-A
*
178264 TGTATCGGTACACATTCATA-G-
1 TGTATCGATACACATTCA-AGGA
* * *
178285 TGTATCGATATATA-GCAAGGA
1 TGTATCGATACACATTCAAGGA
178306 TGTATCGATACA
1 TGTATCGATACA
178318 TAGGTATCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 22 0.49
23 18 0.40
24 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (22 bp):
TGTATCGATACACATTCAAGGA
Found at i:178304 original size:43 final size:42
Alignment explanation
Indices: 178221--178317 Score: 115
Period size: 44 Copynumber: 2.3 Consensus size: 42
178211 ACCCAACGGG
* *
178221 TGTATTGGTACACTTCAGAGTGTATCGATACACATTCAAGGAA
1 TGTATCGGTACACTTCAGAGTGTATCGATACACATGCAAGG-A
* * *
178264 TGTATCGGTACACATTCATAGTGTATCGATATATA-GCAAGGA
1 TGTATCGGTACAC-TTCAGAGTGTATCGATACACATGCAAGGA
*
178306 TGTATCGATACA
1 TGTATCGGTACA
178318 TAGGTATCGA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 12 0.26
43 17 0.36
44 18 0.38
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (42 bp):
TGTATCGGTACACTTCAGAGTGTATCGATACACATGCAAGGA
Found at i:180184 original size:12 final size:12
Alignment explanation
Indices: 180167--180191 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
180157 ATGATGGTTC
180167 TCCAACGCCATG
1 TCCAACGCCATG
180179 TCCAACGCCATG
1 TCCAACGCCATG
180191 T
1 T
180192 GCATTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (12 bp):
TCCAACGCCATG
Found at i:185528 original size:19 final size:19
Alignment explanation
Indices: 185504--185553 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
185494 TTTGTTCAAT
185504 GCATAATGGTGTATTTTCG
1 GCATAATGGTGTATTTTCG
*
185523 GCATAATGGTATATTTTCG
1 GCATAATGGTGTATTTTCG
185542 GCATAAATGGTG
1 GCAT-AATGGTG
185554 CCACCCATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (19 bp):
GCATAATGGTGTATTTTCG
Found at i:185780 original size:20 final size:20
Alignment explanation
Indices: 185748--185801 Score: 99
Period size: 20 Copynumber: 2.6 Consensus size: 20
185738 TTTGACATAC
185748 ATTGGGCAAAAATAAAAGATA
1 ATTGGG-AAAAATAAAAGATA
185769 ATTGGGAAAAATAAAAGATA
1 ATTGGGAAAAATAAAAGATA
185789 ATTGGGAAAAATA
1 ATTGGGAAAAATA
185802 TACAGAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 27 0.82
21 6 0.18
ACGTcount: A:0.57, C:0.02, G:0.20, T:0.20
Consensus pattern (20 bp):
ATTGGGAAAAATAAAAGATA
Found at i:186889 original size:132 final size:129
Alignment explanation
Indices: 186633--186890 Score: 358
Period size: 132 Copynumber: 2.0 Consensus size: 129
186623 TATTTATAAA
* *
186633 GAATTTGATTCTTTCTTTTATTTTTCTTAGGTTCCAATTTTGTCTCTGATTAACTCTCAGTCAAC
1 GAATTTGATTCTTTCTTTTATTTTTCTCAGGTTCCAATTTTGTCTCGGATTAACTCTCAGTCAAC
* * *
186698 GAATCAAACTAGAATTGTATAACCAAAGAGACACTAACCAATGGCTCCGGGGATGAACCAAGCTC
66 GAATCAAACTAGAACTGTATAACCAAAGAGA-ACTAACCAATGGCTCCGAGGATAAACCAAGCTC
*
186763 GAATTTGATTCTTTCTTTTTATTTTTTCTCAGGTTCCAATTTTGTCTCGGATTATTACTCTCGGT
1 GAATTTGATTCTTTC-TTTTA-TTTTTCTCAGGTTCCAATTTTGTCTCGGATTA--ACTCTCAGT
* * * *
186828 CAACATAATCAAACTAGAACTGTATGACCAAAGAG-ACTGATCAATGGCTCC-AGGATAAACCAA
62 CAAC-GAATCAAACTAGAACTGTATAACCAAAGAGAACTAACCAATGGCTCCGAGGATAAACCAA
186891 ACTTGAACAG
Statistics
Matches: 113, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
130 15 0.13
131 5 0.04
132 40 0.35
133 14 0.12
134 12 0.11
135 27 0.24
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (129 bp):
GAATTTGATTCTTTCTTTTATTTTTCTCAGGTTCCAATTTTGTCTCGGATTAACTCTCAGTCAAC
GAATCAAACTAGAACTGTATAACCAAAGAGAACTAACCAATGGCTCCGAGGATAAACCAAGCTC
Found at i:196360 original size:142 final size:142
Alignment explanation
Indices: 196104--196387 Score: 559
Period size: 142 Copynumber: 2.0 Consensus size: 142
196094 AGCCACTCGA
196104 GCACGAGCAACCTGTTCACATAGTCTCCGTCCACGCTACAACACACTTTCTGTTTCGATAAACTC
1 GCACGAGCAACCTGTTCACATAGTCTCCGTCCACGCTACAACACACTTTCTGTTTCGATAAACTC
*
196169 CGAGTCAAAGATGAATTTTTTTCTCTCTATCTAGAGGCACCAAAGGATTGATCCAAACATAAGGT
66 CGAGTCAAAGATGAATTTTTTTCTCTCTATCCAGAGGCACCAAAGGATTGATCCAAACATAAGGT
196234 CTTAATCATTTC
131 CTTAATCATTTC
196246 GCACGAGCAACCTGTTCACATAGTCTCCGTCCACGCTACAACACACTTTCTGTTTCGATAAACTC
1 GCACGAGCAACCTGTTCACATAGTCTCCGTCCACGCTACAACACACTTTCTGTTTCGATAAACTC
196311 CGAGTCAAAGATGAATTTTTTTCTCTCTATCCAGAGGCACCAAAGGATTGATCCAAACATAAGGT
66 CGAGTCAAAGATGAATTTTTTTCTCTCTATCCAGAGGCACCAAAGGATTGATCCAAACATAAGGT
196376 CTTAATCATTTC
131 CTTAATCATTTC
196388 CATTGATCGG
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (142 bp):
GCACGAGCAACCTGTTCACATAGTCTCCGTCCACGCTACAACACACTTTCTGTTTCGATAAACTC
CGAGTCAAAGATGAATTTTTTTCTCTCTATCCAGAGGCACCAAAGGATTGATCCAAACATAAGGT
CTTAATCATTTC
Found at i:197610 original size:29 final size:29
Alignment explanation
Indices: 197567--197649 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
197557 CTCACCTAAC
197567 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
197597 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
197626 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
197650 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:201028 original size:15 final size:15
Alignment explanation
Indices: 201008--201037 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
200998 CTTTCTCATA
201008 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
201023 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
201038 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:202368 original size:29 final size:29
Alignment explanation
Indices: 202325--202407 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
202315 CTCACCTAAC
202325 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
202355 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
202384 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
202408 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:206690 original size:3 final size:3
Alignment explanation
Indices: 206665--206719 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
206655 TTTTAATTTC
* * * *
206665 TTA TT- TTA TT- TTA TTA GTA TTA TTA TCA TTA TTA TTA GTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
206711 TTA TTA TTA
1 TTA TTA TTA
206720 ATTTATATGT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:206721 original size:15 final size:15
Alignment explanation
Indices: 206676--206725 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
206666 TATTTTATTT
*
206676 TATTAGTATTATT-A
1 TATTATTATTATTAA
*
206690 TCATTATTATTAGTAA
1 T-ATTATTATTATTAA
206706 TATTATTATTATTAA
1 TATTATTATTATTAA
206721 T-TTAT
1 TATTAT
206726 ATGTTACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 5 0.16
15 24 0.77
16 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (15 bp):
TATTATTATTATTAA
Found at i:208458 original size:12 final size:12
Alignment explanation
Indices: 208441--208465 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
208431 TTTAGTCCAT
208441 TATGTATGTGTA
1 TATGTATGTGTA
208453 TATGTATGTGTA
1 TATGTATGTGTA
208465 T
1 T
208466 TTGTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (12 bp):
TATGTATGTGTA
Found at i:211425 original size:20 final size:20
Alignment explanation
Indices: 211400--211460 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
211390 ACATTCCCTC
*
211400 TCTTTGAGACCTTGAAATAT
1 TCTTTGAGACCTTGAAACAT
211420 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
* * *
211440 TTTTTGCGGCCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
211460 T
1 T
211461 GCATTTATCC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (20 bp):
TCTTTGAGACCTTGAAACAT
Found at i:212068 original size:22 final size:24
Alignment explanation
Indices: 212042--212107 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
212032 GTCCAAAGAT
*
212042 AAAATAAAAGTG-AAGAAA-AAAG
1 AAAATAAAAGAGAAAGAAACAAAG
*
212064 AAAATCAAAGAGAAAGAAACAAAG
1 AAAATAAAAGAGAAAGAAACAAAG
*
212088 AGAAA-ACAAGCAGAAAGAAA
1 A-AAATAAAAG-AGAAAGAAA
212108 AGAAAAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.28
23 6 0.17
24 8 0.22
25 12 0.33
ACGTcount: A:0.71, C:0.06, G:0.18, T:0.05
Consensus pattern (24 bp):
AAAATAAAAGAGAAAGAAACAAAG
Found at i:212104 original size:25 final size:23
Alignment explanation
Indices: 212054--212135 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 23
212044 AATAAAAGTG
*
212054 AAGAAAAAAGAAAATCAAAGAGA
1 AAGAAAAAAGAAAAACAAAGAGA
212077 AAGAAACAAAGAGAAAAC-AAGCAGA
1 AAGAAA-AAAGA-AAAACAAAG-AGA
* *
212102 AAGAAAAGAA-AAAAGA-AAAAACA
1 AAGAAAA-AAGAAAA-ACAAAGAGA
212125 AAGAAAAAAGA
1 AAGAAAAAAGA
212136 GGACAAGAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
22 2 0.04
23 19 0.39
24 13 0.27
25 15 0.31
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.01
Consensus pattern (23 bp):
AAGAAAAAAGAAAAACAAAGAGA
Found at i:213340 original size:4 final size:4
Alignment explanation
Indices: 213331--217417 Score: 6823
Period size: 4 Copynumber: 1032.5 Consensus size: 4
213321 ATACATCAAC
*
213331 ACAT ACAT ACAT -CAAC ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
213379 ACAT AACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT GCAT GCAT GCAT
1 ACAT -ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
213428 GCAT GCAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
213476 ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT GCAT GCAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
213521 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
213568 ACAT ACAT ACAT ACAT -CAT ACAT ATGCAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT A--CAT ACAT ACAT ACAT ACAT ACAT
*
213617 ACAT ACAT ACAT ACAT -CAT ACAT ACAT ACAT ACAT GCAT -CAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
213663 ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
213709 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
213757 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
213805 ACAT ACAT ACAT ACAT ACAT GCAT ACAT ACAT -CAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
213852 ACAT GCAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
213900 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -CAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
213947 ACAT ACAT ACAT ACAT ACAT ACAT ACCAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT A-CAT ACAT ACAT ACAT ACAT ACAT
213996 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214044 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214091 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
214139 ACAT ACAT -CAT ACAT ACAT --AT ACAT AC-G ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214183 ACAT ACAT ACAT ACAT ACAT ACAT -CAT ACAT -CAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
214229 ACAT ACAT ACAT ACAT GCAT ACA- ACAT CACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT -ACAT ACAT ACAT ACAT ACAT
* *
214277 ACAT GCAT ACAT AGCAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT
1 ACAT ACAT ACAT A-CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214326 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214374 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214422 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214470 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214518 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
214566 ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
214614 GCAT CACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT
1 ACAT -ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214662 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214710 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214758 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214806 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214854 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214902 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214950 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
214998 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T -CAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
215044 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
215092 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
215140 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
215188 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
215236 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -CAAC ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT
* * * *
215284 ACAT ACAT ACAT ACAT ACAT GCAT GCAT AGAT GCAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
215332 ACAT ACAT GCAT ACAT ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
215380 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * *
215428 ACAT ACAT ACAT ACAT ACAT A-AT ACAT GCAT GCAT GCAT GCAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * *
215475 ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT GCAT GCAT GCAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
215523 GCAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
215571 ACAT ACAT GCAT ACAT ACAT --AT ACAT ACAT ACAT ACAC ATAC ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
215617 ACAT ACCT ACAT ACAT CCAT ACAT ACAT ACAT -CATT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-T ACAT ACAT ACAT
*
215665 ACAT ACAT ACA- AAAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT AC-T
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
215710 ACAT AC-T ACAT ACAT ACAT ACAT A-AT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
215756 ACAT ACA- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACATT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-T ACAT ACAT
215804 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -CAT AC-T ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
215850 A-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACA- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
215895 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
215943 ACAT ACAG ACAT ACAT ACAT AC-T ACAT AC-T ACAT ACAT AACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -ACAT ACAT
215990 ACAT ACAT ACAT ACAT A-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
216037 ACAT ACAT ACAT ACAT ACA- ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
216082 ACAT ACAT ACATT GCAT -CAT AGAT GCAT ACAT ACAT ACAT ACAAT GCAT
1 ACAT ACAT ACA-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-AT ACAT
216131 ACAT ATGCAT ACAT ACAT ACAT ACAT ACAT AGCAT ACAT AGCAT ACAT
1 ACAT A--CAT ACAT ACAT ACAT ACAT ACAT A-CAT ACAT A-CAT ACAT
*
216179 ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACTAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT
216228 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
216274 ACAT ACAT -CAT ACAT ACAT ACCAT GCAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT A-CAT ACAT ACAT ACAT ACAT ACAT ACAT
216322 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT -ACAT ACAT ACAT ACAT ACAT
216371 ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
216418 ACAT ACAT CAAAC ACAT ACCT ACAT ACAT ACAT ACAT ACAT AC-- ACAT
1 ACAT ACAT -ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
216465 ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT -CAT GCAT AGAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
216511 ACAT ACAT ACAT ACAT ACAT GCACAT ACAT GCAT ACAT ACAT AC-T ACAT
1 ACAT ACAT ACAT ACAT ACAT --ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
216560 ACAT -CAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ATAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
216607 ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * *
216653 GCA- GCAT GCAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
216700 GCAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
216748 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA- AAAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
216795 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
216843 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
216891 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
216939 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
216987 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
217035 ATAT ACAT ACAT ACAT ACAT ACAT ACAT -CAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
217082 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-A- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
217128 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
217176 AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
217222 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
217270 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
217318 ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
217364 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
217412 ACAT AC
1 ACAT AC
217418 TTTCTGAAAT
Statistics
Matches: 3897, Mismatches: 95, Indels: 182
0.93 0.02 0.04
Matches are distributed among these distances:
2 22 0.01
3 125 0.03
4 3680 0.94
5 58 0.01
6 12 0.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:217638 original size:102 final size:103
Alignment explanation
Indices: 217462--217647 Score: 338
Period size: 102 Copynumber: 1.8 Consensus size: 103
217452 TTTTACTACA
*
217462 GGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
1 GGTTTTGTCATTTCGAGATCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACA
217527 TTTTTATAAAGTAT-GACATATCCGGTAGTTCTTTACC
66 TTTTTATAAAGTATCGACATATCCGGTAGTTCTTTACC
* *
217564 GGTTTTGTCATTTCGAGATCGGTTTTATCATATTTTTACTTGTTATATTGTTATGGATCGATACA
1 GGTTTTGTCATTTCGAGATCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACA
217629 TTTTTATAAAGTATCGACA
66 TTTTTATAAAGTATCGACA
217648 CTTTATTAGC
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 76 0.95
103 4 0.05
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (103 bp):
GGTTTTGTCATTTCGAGATCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACA
TTTTTATAAAGTATCGACATATCCGGTAGTTCTTTACC
Done.