Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008460.1 Hibiscus syriacus cultivar Beakdansim tig00111273_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: 2854393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 15
Found at i:189364 original size:33 final size:33
Alignment explanation
Indices: 189311--189408 Score: 155
Period size: 32 Copynumber: 3.0 Consensus size: 33
189301 TTTGTTTCAA
189311 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
189343 TTATCGAACTTGGAAGTTTTT-AGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
189375 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
189408 T
1 T
189409 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 41 0.67
33 20 0.33
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:189437 original size:13 final size:13
Alignment explanation
Indices: 189394--189448 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
189384 TTGGAAGTAT
189394 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
189407 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
189421 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
189434 TTAAGTATTTGAA
1 TTAAGTATTTCAA
189447 TT
1 TT
189449 TATCGACTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:189669 original size:21 final size:21
Alignment explanation
Indices: 189643--189699 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
189633 TCGAGCGTGG
*
189643 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
189664 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
189685 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
189700 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:189889 original size:15 final size:15
Alignment explanation
Indices: 189864--189919 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
189854 ATCTGGAATA
*
189864 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
189879 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
189894 TTAAAAAACCGATTTTT
1 TT--AAAACCGGTTTTT
189911 TTAAAACCG
1 TTAAAACCG
189920 AAACCGGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 22 0.63
17 13 0.37
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:189903 original size:17 final size:17
Alignment explanation
Indices: 189866--189916 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
189856 CTGGAATATT
*
189866 AAAATCGGTTTTTTT--
1 AAAACCGGTTTTTTTAA
*
189881 ATAACCGGTTTTTTTAA
1 AAAACCGGTTTTTTTAA
*
189898 AAAACCGATTTTTTTAA
1 AAAACCGGTTTTTTTAA
189915 AA
1 AA
189917 CCGAAACCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 13 0.43
17 17 0.57
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (17 bp):
AAAACCGGTTTTTTTAA
Found at i:197069 original size:30 final size:30
Alignment explanation
Indices: 197029--197088 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
197019 ATCGCAGAAA
197029 ATTAATTGAACTGTAAGAAATAAATAAAAT
1 ATTAATTGAACTGTAAGAAATAAATAAAAT
* *
197059 ATTAGTTGAACTGTAAGAAATAGATAAAAT
1 ATTAATTGAACTGTAAGAAATAAATAAAAT
197089 CAGGACAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.30
Consensus pattern (30 bp):
ATTAATTGAACTGTAAGAAATAAATAAAAT
Found at i:200168 original size:15 final size:15
Alignment explanation
Indices: 200148--200178 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
200138 CAACAGAGAG
200148 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
200163 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
200178 A
1 A
200179 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:203579 original size:2 final size:2
Alignment explanation
Indices: 203572--203606 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
203562 ATTAAAAATC
203572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
203607 ACCAGGTCGG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:204079 original size:2 final size:2
Alignment explanation
Indices: 204074--204116 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
204064 TATAAAAAAT
204074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
204116 T
1 T
204117 GAGTTTACGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:206217 original size:29 final size:29
Alignment explanation
Indices: 206174--206256 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
206164 CTCACCTAAC
206174 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
206204 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
*
206233 TAAATGATGTAAGCAATGTCATCA
1 TAAATGATGTAAGCAATGACATCA
206257 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:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:209644 original size:15 final size:15
Alignment explanation
Indices: 209624--209653 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
209614 CTTTCTCATA
209624 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
209639 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
209654 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:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:210983 original size:29 final size:30
Alignment explanation
Indices: 210940--211027 Score: 135
Period size: 29 Copynumber: 2.9 Consensus size: 30
210930 CTCACCTAAC
210940 TAAATTGATGTAAGCAATGACATCA-TTACT
1 TAAA-TGATGTAAGCAATGACATCATTTACT
210970 TAAATGATGTAAGCAATGACAT-ATTTACT
1 TAAATGATGTAAGCAATGACATCATTTACT
*
210999 TAAATGATGTAAGCAATGATATCAATTTA
1 TAAATGATGTAAGCAATGACATC-ATTTA
211028 GTTTGGGTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
28 1 0.02
29 44 0.81
30 4 0.07
31 5 0.09
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (30 bp):
TAAATGATGTAAGCAATGACATCATTTACT
Found at i:215999 original size:118 final size:118
Alignment explanation
Indices: 215791--216028 Score: 467
Period size: 118 Copynumber: 2.0 Consensus size: 118
215781 AGATTCACCT
215791 TGTACCGACTAACCACTCCCACTGCTTGTACAATGTCTGGTCTTGTGCGTATCATAGCGAACATT
1 TGTACCGACTAACCACTCCCACTGCTTGTACAATGTCTGGTCTTGTGCGTATCATAGCGAACATT
*
215856 AAATTTCCCACTGCTGATGCATACGGTACTCGAGACATCTCCATCATCTGAAG
66 AAATTTCCCACTACTGATGCATACGGTACTCGAGACATCTCCATCATCTGAAG
215909 TGTACCGACTAACCACTCCCACTGCTTGTACAATGTCTGGTCTTGTGCGTATCATAGCGAACATT
1 TGTACCGACTAACCACTCCCACTGCTTGTACAATGTCTGGTCTTGTGCGTATCATAGCGAACATT
215974 AAATTTCCCACTACTGATGCATACGGTACTCGAGACATCTCCATCATCTGAAG
66 AAATTTCCCACTACTGATGCATACGGTACTCGAGACATCTCCATCATCTGAAG
216027 TG
1 TG
216029 CTTGCGGTAT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 119 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (118 bp):
TGTACCGACTAACCACTCCCACTGCTTGTACAATGTCTGGTCTTGTGCGTATCATAGCGAACATT
AAATTTCCCACTACTGATGCATACGGTACTCGAGACATCTCCATCATCTGAAG
Found at i:218238 original size:23 final size:23
Alignment explanation
Indices: 218210--218259 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
218200 AATCGACCCT
218210 TAAATTTTAATATTCAATCAATA
1 TAAATTTTAATATTCAATCAATA
218233 TAAATTTTAATATTCAATCAATA
1 TAAATTTTAATATTCAATCAATA
218256 TAAA
1 TAAA
218260 ATTTGACTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATTTTAATATTCAATCAATA
Found at i:218544 original size:23 final size:23
Alignment explanation
Indices: 218518--218566 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
218508 TAAGCTACCA
* *
218518 AAAGGCAGATAAAAACGTGTCAT
1 AAAGGCAGAGAAAAACGAGTCAT
* *
218541 AAAGGTAGAGATAAACGAGTCAT
1 AAAGGCAGAGAAAAACGAGTCAT
218564 AAA
1 AAA
218567 AGTAGAAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.16
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACGAGTCAT
Found at i:219102 original size:31 final size:31
Alignment explanation
Indices: 219031--219108 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
219021 CTTTTAAAAC
** *
219031 TTGCAATACAATCCCCCAACATTTAGTTCGT
1 TTGCAATATGATCCCCCAACATTTAGTCCGT
** * *
219062 TTGTTATATGATCCCTCAATATTTAGTCCGT
1 TTGCAATATGATCCCCCAACATTTAGTCCGT
*
219093 TTGCAATATGGTCCCC
1 TTGCAATATGATCCCC
219109 GACATAACTA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (31 bp):
TTGCAATATGATCCCCCAACATTTAGTCCGT
Found at i:220458 original size:31 final size:31
Alignment explanation
Indices: 220418--220489 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
220408 AACTTTTAAA
* *
220418 ATTTACAATACAATCCCCCAATATTTAATT-C
1 ATTTGCAATACAATCCCCCAACATTT-ATTCC
** *
220449 ATTTGCAATATGATCCCTCAACATTTATTCC
1 ATTTGCAATACAATCCCCCAACATTTATTCC
220480 ATTTGCAATA
1 ATTTGCAATA
220490 TGGTCCCTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 3 0.09
31 32 0.91
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (31 bp):
ATTTGCAATACAATCCCCCAACATTTATTCC
Found at i:220490 original size:31 final size:31
Alignment explanation
Indices: 220430--220497 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
220420 TTACAATACA
* *
220430 ATCCCCCAATATTTAATTCATTTGCAATATG
1 ATCCCTCAACATTTAATTCATTTGCAATATG
220461 ATCCCTCAACATTT-ATTCCATTTGCAATATG
1 ATCCCTCAACATTTAATT-CATTTGCAATATG
*
220492 GTCCCT
1 ATCCCT
220498 GACGTAACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 3 0.09
31 30 0.91
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.38
Consensus pattern (31 bp):
ATCCCTCAACATTTAATTCATTTGCAATATG
Found at i:229661 original size:26 final size:25
Alignment explanation
Indices: 229632--229709 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 25
229622 AAAAAGTGAT
*
229632 GAAAATAAATTAAAAATAAAAATAAA
1 GAAAATAAATGAAAAA-AAAAATAAA
* *
229658 GAAAATGAAATGAAGAACAAAATAAA
1 GAAAAT-AAATGAAAAAAAAAATAAA
* *
229684 TAAAATAAATGATAAACAATAAATAA
1 GAAAATAAATGA-AAA-AAAAAATAA
229710 CATAATCAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
25 6 0.14
26 21 0.50
27 15 0.36
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (25 bp):
GAAAATAAATGAAAAAAAAAATAAA
Found at i:229933 original size:2 final size:2
Alignment explanation
Indices: 229926--229960 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
229916 GAATTAAATA
229926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
229961 AATGTTAAAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:230045 original size:2 final size:2
Alignment explanation
Indices: 230033--230099 Score: 77
Period size: 2 Copynumber: 34.5 Consensus size: 2
230023 TAATAAAAAC
* * *
230033 AT AT GT AT AT AT AT -T A- AT AA AA AT A- AT ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
230073 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
230100 ATAATAGCTA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
1 3 0.05
2 52 0.91
3 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:230169 original size:18 final size:18
Alignment explanation
Indices: 230135--230169 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
230125 AATGATAGAG
*
230135 AAATAAAATAATGAAAAT
1 AAATAAAATAATAAAAAT
*
230153 AAATATAATAATAAAAA
1 AAATAAAATAATAAAAA
230170 AGGTAAAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AAATAAAATAATAAAAAT
Found at i:231372 original size:16 final size:16
Alignment explanation
Indices: 231351--231391 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
231341 TGGTTAAAAA
231351 ATAATA-ATACATATAT
1 ATAATATATA-ATATAT
231367 ATAATATATAATATAT
1 ATAATATATAATATAT
231383 A-AATATATA
1 ATAATATATA
231392 TATGTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.33
16 13 0.54
17 3 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATATATAATATAT
Found at i:234086 original size:19 final size:20
Alignment explanation
Indices: 234046--234087 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
234036 ATTATTATAG
*
234046 AATATTTTTTTCTTAATGAT
1 AATATTTTTTTCTTAATAAT
*
234066 AATATTTTTTTGTTAA-AAT
1 AATATTTTTTTCTTAATAAT
234085 AAT
1 AAT
234088 GAGAATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (20 bp):
AATATTTTTTTCTTAATAAT
Found at i:234410 original size:2 final size:2
Alignment explanation
Indices: 234403--234460 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
234393 GATAACTATG
* * *
234403 AT AT AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
234445 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
234461 CATAAAAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:238215 original size:17 final size:17
Alignment explanation
Indices: 238189--238224 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
238179 TATTTTTTAC
*
238189 TGTTGGAAATTCTAGAT
1 TGTTGAAAATTCTAGAT
238206 TGTTGAAAATTCTAGAT
1 TGTTGAAAATTCTAGAT
238223 TG
1 TG
238225 GCAGCCGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (17 bp):
TGTTGAAAATTCTAGAT
Found at i:246604 original size:16 final size:16
Alignment explanation
Indices: 246583--246616 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
246573 ATATGTTTGA
* *
246583 AAAGAATATAGCAAGT
1 AAAGAATAAAGAAAGT
246599 AAAGAATAAAGAAAGT
1 AAAGAATAAAGAAAGT
246615 AA
1 AA
246617 GGATTTTGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAGAATAAAGAAAGT
Found at i:248923 original size:63 final size:64
Alignment explanation
Indices: 248784--248945 Score: 170
Period size: 63 Copynumber: 2.5 Consensus size: 64
248774 ATTGTTCAAG
* * *** *
248784 GTGTATCGATGCACATGAAGTGCATCGATGCATTACTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
* * *
248848 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAATAG-GATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAAT-GCCA-TC
248911 A
64 A
* *
248912 -TGTATCGATGCA-TAGATAGTACATCGATGCACCC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCC
248946 GTCAAGGGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.02
63 46 0.55
64 36 0.43
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:249654 original size:23 final size:23
Alignment explanation
Indices: 249594--249646 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
249584 TATGGTACTA
249594 CGGTGCAATTCTACGCGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
*
249617 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
249640 CGGTGCA
1 CGGTGCA
249647 TTTATACGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.26
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTT
Found at i:251874 original size:17 final size:17
Alignment explanation
Indices: 251852--251890 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
251842 TTCAAGTGGG
*
251852 AGATTGTTGGAAATTCT
1 AGATTGTTGAAAATTCT
251869 AGATTGTTGAAAATTCT
1 AGATTGTTGAAAATTCT
251886 AGATT
1 AGATT
251891 TTCTAGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (17 bp):
AGATTGTTGAAAATTCT
Found at i:252949 original size:21 final size:21
Alignment explanation
Indices: 252924--252963 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
252914 TTGAGTAAAC
252924 AATAATATGAATTATAAAGCT
1 AATAATATGAATTATAAAGCT
252945 AATAATATGAATTATAAAG
1 AATAATATGAATTATAAAG
252964 TTAAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (21 bp):
AATAATATGAATTATAAAGCT
Found at i:255825 original size:50 final size:50
Alignment explanation
Indices: 255637--255825 Score: 279
Period size: 50 Copynumber: 3.8 Consensus size: 50
255627 TTCATACTAC
*
255637 AAAAAAGTGTAGCACTTAACACATACTTACACCGATGTAGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAGTGAATAAAAT
* * * *
255687 AAAAAAGTCTAGCACTTAACACATACCTATATCGGTGTAGTGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAGTGAATAAAAT
* * * *
255737 AAAAAAGTATAGTACTTAACACATACTTACACCAGTGTAATGAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAGTGAATAAAAT
* *
255787 AAAAAAGTGTAGCACTTAATACATACTTACATCGGTGTA
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTA
255826 TGTACATCTC
Statistics
Matches: 122, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 122 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (50 bp):
AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAGTGAATAAAAT
Found at i:256097 original size:25 final size:27
Alignment explanation
Indices: 256052--256102 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
256042 TTATAAAATT
256052 AATTTATTAACCATTAACCTTAACCGA
1 AATTTATTAACCATTAACCTTAACCGA
*
256079 AATTTA-TAACTA-TAACCTTAACCG
1 AATTTATTAACCATTAACCTTAACCG
256103 TTAAACATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 5 0.22
27 6 0.26
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (27 bp):
AATTTATTAACCATTAACCTTAACCGA
Found at i:267699 original size:19 final size:19
Alignment explanation
Indices: 267675--267762 Score: 95
Period size: 19 Copynumber: 4.5 Consensus size: 19
267665 TCTACAGTTA
*
267675 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
267694 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
267713 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
267734 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
*
267754 TCTTTGCGA
1 TCGTTGCGA
267763 AAATTCGTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 36 0.64
20 5 0.09
21 5 0.09
22 10 0.18
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:267728 original size:60 final size:60
Alignment explanation
Indices: 267634--267762 Score: 197
Period size: 60 Copynumber: 2.1 Consensus size: 60
267624 TTGAAAATCG
* *
267634 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTTCAAATT
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATT
*
267695 CGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCC-AATTCCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATT
*
267755 CTTTGCGA
1 CGTTGCGA
267763 AAATTCGTTG
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
60 46 0.73
61 14 0.22
62 3 0.05
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (60 bp):
CGTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATT
Found at i:268547 original size:22 final size:22
Alignment explanation
Indices: 268519--268653 Score: 147
Period size: 22 Copynumber: 6.4 Consensus size: 22
268509 AATTTGGAAA
268519 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
268541 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
268563 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
268582 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
268604 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
268623 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
268645 ATGGCAACG
1 ATCGCAACG
268654 CGATTTTCAA
Statistics
Matches: 90, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
19 26 0.29
20 4 0.04
21 4 0.04
22 56 0.62
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:268586 original size:41 final size:41
Alignment explanation
Indices: 268541--268653 Score: 217
Period size: 41 Copynumber: 2.8 Consensus size: 41
268531 ACTGTAGACT
268541 ATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAA
268582 ATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAA
*
268623 ATCGCAACGACAACTGTAGACTATGGCAACG
1 ATCGCAACGACAACTGTAGACTATCGCAACG
268654 CGATTTTCAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (41 bp):
ATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAA
Found at i:268587 original size:19 final size:19
Alignment explanation
Indices: 268563--268632 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
268553 ACTGTAGACT
268563 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* * **
268582 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG--AA-TTTGGAAA
268604 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
268623 ATCGCAACGA
1 ATCGCAACGA
268633 CAACTGTAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 23 0.57
20 2 0.05
21 2 0.05
22 13 0.32
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:268685 original size:21 final size:21
Alignment explanation
Indices: 268642--268685 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
268632 ACAACTGTAG
* ** *
268642 ACTATGGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
268663 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
268684 AC
1 AC
268686 GCGAATTTGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:275823 original size:43 final size:42
Alignment explanation
Indices: 275770--276128 Score: 367
Period size: 43 Copynumber: 8.6 Consensus size: 42
275760 AAAAAAAAAT
* *
275770 GCCGCAATAGGTCGAGATCTATAGCGGCGTTTCTGGGACAAAC
1 GCCGTAATAGGTCGAGATCTATAGCGGCGTTT-TGGAACAAAC
* * *
275813 ACTGTAATAGGTCGAGATCTATAGC-G-G---T-GAAAAAAC
1 GCCGTAATAGGTCGAGATCTATAGCGGCGTTTTGGAACAAAC
*
275849 GCCGTAATAGGTCGAGATCTATAGCGGCGCTTTTGGGACAAAC
1 GCCGTAATAGGTCGAGATCTATAGCGGCG-TTTTGGAACAAAC
*
275892 GTCGTAATAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAAC
1 GCCGTAATAGGTCGAGATCTATAGCGGCG-TTTTGGAACAAAC
** *
275935 GCCACAATAGGTCGAGATCTATAGCGGCATTTTTGGAACAAAC
1 GCCGTAATAGGTCGAGATCTATAGCGGC-GTTTTGGAACAAAC
* * * * * *
275978 ACCGCAATAGGTCAAAATCTATAGCAGCGTTTTAGAACAAAC
1 GCCGTAATAGGTCGAGATCTATAGCGGCGTTTTGGAACAAAC
* * * *
276020 GCCGCAATAGATCGATATCTATAGCGGCGTTTTTGGAATAAAC
1 GCCGTAATAGGTCGAGATCTATAGCGGCG-TTTTGGAACAAAC
** *
276063 GCCGTAA-ATTTC-AGATCTATAGCGGCGTTTTTAGAACAAAC
1 GCCGTAATAGGTCGAGATCTATAGCGGCG-TTTTGGAACAAAC
* * *
276104 GCCGCAAAAGGTC-AAATCTATAGCG
1 GCCGTAATAGGTCGAGATCTATAGCG
276129 ACATTTTTGT
Statistics
Matches: 266, Mismatches: 40, Indels: 21
0.81 0.12 0.06
Matches are distributed among these distances:
36 29 0.11
37 2 0.01
38 1 0.00
41 33 0.12
42 55 0.21
43 146 0.55
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (42 bp):
GCCGTAATAGGTCGAGATCTATAGCGGCGTTTTGGAACAAAC
Found at i:275990 original size:86 final size:85
Alignment explanation
Indices: 275770--276149 Score: 411
Period size: 86 Copynumber: 4.5 Consensus size: 85
275760 AAAAAAAAAT
* * * * *
275770 GCCGCAATAGGTCGAGATCTATAGCGGCGTTTCTGGGACAAACACTGTAATAGGTCGAGATCTAT
1 GCCGCAATAGGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCCGTAATAGGTC-AGATCTAT
*
275835 AGC-G-G----T-GAAAAAAC
65 AGCGGCGTTTTTAGAACAAAC
* ** * *
275849 GCCGTAATAGGTCGAGATCTATAGCGGCGCTTTTGGGACAAACGTCGTAATAGGTCGAGATCTAT
1 GCCGCAATAGGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCCGTAATAGGTC-AGATCTAT
*
275914 AGCGGCGTTTTTGGAACAAAC
65 AGCGGCGTTTTTAGAACAAAC
* * * *
275935 GCCACAATAGGTCGAGATCTATAGCGGCATTTTTGGAACAAACACCGCAATAGGTCAAAATCTAT
1 GCCGCAATAGGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCCGTAATAGGTC-AGATCTAT
*
276000 AGCAGCG-TTTTAGAACAAAC
65 AGCGGCGTTTTTAGAACAAAC
* * * * **
276020 GCCGCAATAGATCGATATCTATAGCGGCGTTTTTGGAATAAACGCCGTAA-ATTTCAGATCTATA
1 GCCGCAATAGGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCCGTAATAGGTCAGATCTATA
276084 GCGGCGTTTTTAGAACAAAC
66 GCGGCGTTTTTAGAACAAAC
* * * *
276104 GCCGCAAAAGGTC-AAATCTATAGCGACATTTTTGTATACAAACGCC
1 GCCGCAATAGGTCGAGATCTATAGCGGCATTTTTGGA-ACAAACGCC
276150 ACTAATGACC
Statistics
Matches: 255, Mismatches: 37, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
79 62 0.24
80 1 0.00
81 1 0.00
83 32 0.13
84 35 0.14
85 56 0.22
86 68 0.27
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (85 bp):
GCCGCAATAGGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCCGTAATAGGTCAGATCTATA
GCGGCGTTTTTAGAACAAAC
Found at i:279435 original size:27 final size:27
Alignment explanation
Indices: 279404--279455 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
279394 GAAAAAAAAT
*
279404 AGATTGAACGGCCAAAAACCAAATTCC
1 AGATTGAACGACCAAAAACCAAATTCC
279431 AGATTGAACGACCAAAAACCAAATT
1 AGATTGAACGACCAAAAACCAAATT
279456 GAAGCAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.15
Consensus pattern (27 bp):
AGATTGAACGACCAAAAACCAAATTCC
Found at i:280024 original size:64 final size:66
Alignment explanation
Indices: 279905--280035 Score: 176
Period size: 65 Copynumber: 2.0 Consensus size: 66
279895 AACGCCACTA
* * * *
279905 TATATATGGGCTATTACGACGTTTTATACATAAACGCCACTAAAGTACG-TTTTTTTGTGGCGTT
1 TATATATGGCCTATTACGACGTTTTATACATAAACGCCACTAAAGAACGCATTTTTTATGGCGTT
279969 T
66 T
* * * *
279970 TATATCTGGCCTATTACGGCGTTTT-TGCATAAACGCCACTAAAGAATGCATTTTTTATGGCGTT
1 TATATATGGCCTATTACGACGTTTTATACATAAACGCCACTAAAGAACGCATTTTTTATGGCGTT
280034 T
66 T
280035 T
1 T
280036 CACAAAAACG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 20 0.35
65 37 0.65
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (66 bp):
TATATATGGCCTATTACGACGTTTTATACATAAACGCCACTAAAGAACGCATTTTTTATGGCGTT
T
Found at i:280107 original size:82 final size:82
Alignment explanation
Indices: 279970--280238 Score: 332
Period size: 82 Copynumber: 3.3 Consensus size: 82
279960 TGTGGCGTTT
*
279970 TATATCTGGCCTATTACGGCGTTTTTGCATAAACGCCACTAAAGAATGCATTTTTTATGGCGTTT
1 TATATCTGGCCTATTACGGCGTTTTTGCATAAACGCCACTAAAGTATGCATTTTTTATGGCGTTT
*
280035 TCACAAAAACGCTGCTA
66 TCACAAAAACGCCGCTA
* * *
280052 TATATCTGGCCTATTACAGCGTTTTTGCATAAAC-CCTACTAAAGTATGCATTTTTTACGGTGTT
1 TATATCTGGCCTATTACGGCGTTTTTGCATAAACGCC-ACTAAAGTATGCATTTTTTATGGCGTT
280116 TTCACAAAAACGCCGCTA
65 TTCACAAAAACGCCGCTA
* ** * * * *
280134 TATAT-TAGG-ATATTGTGGTGTGTTTTACACAAACGCCACTAAAGTACGCA-TTTTTAGTGGCG
1 TATATCT-GGCCTATTACGGCGT-TTTTGCATAAACGCCACTAAAGTATGCATTTTTTA-TGGCG
280196 TTTTCACAAAAACGCCGCTA
63 TTTTCACAAAAACGCCGCTA
* * *
280216 TATAT-TTGCATATAACGGCGTTT
1 TATATCTGGCCTATTACGGCGTTT
280239 GTACAAAAAT
Statistics
Matches: 161, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
81 19 0.12
82 140 0.87
83 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (82 bp):
TATATCTGGCCTATTACGGCGTTTTTGCATAAACGCCACTAAAGTATGCATTTTTTATGGCGTTT
TCACAAAAACGCCGCTA
Found at i:281646 original size:32 final size:32
Alignment explanation
Indices: 281597--281693 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 32
281587 GCACAATGAT
* * *
281597 AGAAAATTTTCAATGATATATCACTTCGTTTC
1 AGAAACTTTTCAATGATATATAACTTCATTTC
* * *
281629 AGAAACTTTTTAGTGATA-AGTAACTTCATTTT
1 AGAAACTTTTCAATGATATA-TAACTTCATTTC
*
281661 AGAAACTTTTCAATGATATATTACTTCATTTC
1 AGAAACTTTTCAATGATATATAACTTCATTTC
281693 A
1 A
281694 AACAAATATT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
31 1 0.02
32 51 0.96
33 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (32 bp):
AGAAACTTTTCAATGATATATAACTTCATTTC
Found at i:281794 original size:32 final size:32
Alignment explanation
Indices: 281758--281870 Score: 129
Period size: 32 Copynumber: 3.5 Consensus size: 32
281748 GTGCCCAATT
* * *
281758 ACTTCACTTCAGAAAAATTTCAATTATATATC
1 ACTTCATTTCAGAAAAATTTCAGTGATATATC
* *
281790 ACTTCATTTTAG-AAAATTTCTAGTGATATGTC
1 ACTTCATTTCAGAAAAATTTC-AGTGATATATC
** *
281822 ACTTCATTTCAGAAACTTTTCAGTGATATATT
1 ACTTCATTTCAGAAAAATTTCAGTGATATATC
*
281854 ACTTCATTTAAGAAAAA
1 ACTTCATTTCAGAAAAA
281871 ATGTCATTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
31 8 0.12
32 52 0.79
33 6 0.09
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (32 bp):
ACTTCATTTCAGAAAAATTTCAGTGATATATC
Found at i:281948 original size:171 final size:170
Alignment explanation
Indices: 281596--281989 Score: 515
Period size: 171 Copynumber: 2.3 Consensus size: 170
281586 TGCACAATGA
* * * * * *
281596 TAGAAAATTTTCAATGATATATCACTTCGTTTCAGAAACTTTTTAGTGATAAGTAACTTCATTTT
1 TAGAAAATTTTCAATAATATATCACTTCATTTTAGAAA-ATTTTAGTGATATGTAACTTCATTTC
* * *
281661 AGAAACTTTTCAATGATATATTACTTCATTTCAAACAAATATTCTTTTCTTATGTACAATTTAAT
65 AGAAACTTTTCAATGATATATTACTTCATTTCAAACAAAAATTCTTTTCTCATATACAATTTAAT
* * * *
281726 GCACACTAATAAAAACTTTTTAGTGCCCAATTACTTCACTT
130 GCACACTAACAAAAACTTTTCAGTGCACAATCACTTCACTT
* * * *
281767 CAGAAAAATTTCAATTATATATCACTTCATTTTAGAAAATTTCTAGTGATATGTCACTTCATTTC
1 TAGAAAATTTTCAATAATATATCACTTCATTTTAGAAAATTT-TAGTGATATGTAACTTCATTTC
*
281832 AGAAACTTTTCAGTGATATATTACTTCATTT-AAGA-AAAAATGTCATTTTCTCATATACAATTT
65 AGAAACTTTTCAATGATATATTACTTCATTTCAA-ACAAAAAT-TC-TTTTCTCATATACAATTT
* *
281895 AATGCACGCTGACAAAAACTTTTCAGTGCACAATCACTTCACTT
127 AATGCACACTAACAAAAACTTTTCAGTGCACAATCACTTCACTT
* *
281939 TAGAAAATTTTTAGTAATATATCACTTCA-TTTAGAAAATTTTCAGTGATAT
1 TAGAAAATTTTCAATAATATATCACTTCATTTTAGAAAATTTT-AGTGATAT
281990 AATATTTCAT
Statistics
Matches: 194, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
170 11 0.06
171 105 0.54
172 78 0.40
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.40
Consensus pattern (170 bp):
TAGAAAATTTTCAATAATATATCACTTCATTTTAGAAAATTTTAGTGATATGTAACTTCATTTCA
GAAACTTTTCAATGATATATTACTTCATTTCAAACAAAAATTCTTTTCTCATATACAATTTAATG
CACACTAACAAAAACTTTTCAGTGCACAATCACTTCACTT
Found at i:281975 original size:31 final size:32
Alignment explanation
Indices: 281927--281990 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
281917 TCAGTGCACA
*
281927 ATCACTTCACTTTAGAAAATTTTTAGTAATAT
1 ATCACTTCACTTTAGAAAATTTTCAGTAATAT
*
281959 ATCACTTCA-TTTAGAAAATTTTCAGTGATAT
1 ATCACTTCACTTTAGAAAATTTTCAGTAATAT
281990 A
1 A
281991 ATATTTCATC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (32 bp):
ATCACTTCACTTTAGAAAATTTTCAGTAATAT
Found at i:282048 original size:137 final size:138
Alignment explanation
Indices: 281787--282238 Score: 559
Period size: 139 Copynumber: 3.3 Consensus size: 138
281777 TCAATTATAT
* * *
281787 ATCACTTCATTTTAGAAAATTTCT-AGTGATATGTCACTTCATTTCAGAAACTTTTCAGTGATAT
1 ATCACTTCACTTCAGAAAATTT-TAAGTGATATATCACTTCATTT-AGAAACTTTTCAGTGATAT
* * * *
281851 ATTACTTCATTTAAGAAAAAATGTCATTTTCTCATATACAATTTAATGCACGCTGACAAAAACTT
64 AATACTTCATTTAAG-AAAAACGTCATTTTCTCATAGACAATTTAATGAACGCTGACAAAAACTT
*
281916 TTCAGTGCACA
128 TTCAGTGCCCA
* * * *
281927 ATCACTTCACTTTAGAAAATTTTTAGTAATATATCACTTCATTTAGAAAATTTTCAGTGATATAA
1 ATCACTTCACTTCAGAAAATTTTAAGTGATATATCACTTCATTTAGAAACTTTTCAGTGATATAA
* * * **
281992 TATTTCATCTAA-TAAAACGTCATTTTCTCATAGACAATTTAATGAACGCTGACAAAAACGGTTC
66 TACTTCATTTAAGAAAAACGTCATTTTCTCATAGACAATTTAATGAACGCTGACAAAAACTTTTC
282056 AGTGCCCA
131 AGTGCCCA
* * *
282064 TTCACTTCACTTCAGAAACTTTTAAGTGATATATCACTTTATTTTAGAAACTTTTCAGTGATAT-
1 ATCACTTCACTTCAGAAAATTTTAAGTGATATATCACTTCA-TTTAGAAACTTTTCAGTGATATA
* * * * * * * **
282128 ATCACTTCGTTTCAGAAAAACATCATTTTCTAATAGACCATTTAGTAAACAATGACAAAAACTTT
65 AT-ACTTCATTTAAGAAAAACGTCATTTTCTCATAGACAATTTAATGAACGCTGACAAAAACTTT
282193 TCAGTGCCCA
129 TCAGTGCCCA
* *
282203 TTCACTTCACTTCAGAAACTTTTAAGTGATATATCA
1 ATCACTTCACTTCAGAAAATTTTAAGTGATATATCA
282239 GACAATTGAA
Statistics
Matches: 273, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
137 90 0.33
138 28 0.10
139 116 0.42
140 39 0.14
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (138 bp):
ATCACTTCACTTCAGAAAATTTTAAGTGATATATCACTTCATTTAGAAACTTTTCAGTGATATAA
TACTTCATTTAAGAAAAACGTCATTTTCTCATAGACAATTTAATGAACGCTGACAAAAACTTTTC
AGTGCCCA
Found at i:282145 original size:32 final size:32
Alignment explanation
Indices: 282065--282145 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
282055 CAGTGCCCAT
*
282065 TCACTTCACTTCAGAAACTTTTAAGTGATATA
1 TCACTTCATTTCAGAAACTTTTAAGTGATATA
* * *
282097 TCACTTTATTTTAGAAACTTTTCAGTGATATA
1 TCACTTCATTTCAGAAACTTTTAAGTGATATA
*
282129 TCACTTCGTTTCAGAAA
1 TCACTTCATTTCAGAAA
282146 AACATCATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (32 bp):
TCACTTCATTTCAGAAACTTTTAAGTGATATA
Found at i:282880 original size:26 final size:26
Alignment explanation
Indices: 282850--282905 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
282840 TATTGTATTG
*
282850 TAATGTAATGTAAGG-GTTAATGTTTC
1 TAATGTAACGT-AGGAGTTAATGTTTC
*
282876 TAATGTAACGTAGGATTTAATGTTTC
1 TAATGTAACGTAGGAGTTAATGTTTC
282902 TAAT
1 TAAT
282906 ATGTGTGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (26 bp):
TAATGTAACGTAGGAGTTAATGTTTC
Found at i:288469 original size:4 final size:4
Alignment explanation
Indices: 288460--288484 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
288450 TGTCCATGAA
288460 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
288485 GCTGTCCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:288884 original size:26 final size:27
Alignment explanation
Indices: 288854--288928 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 27
288844 ATTTTCCTCA
*
288854 ACTCGTGCTCGTTAAGAAAATTTGTTG
1 ACTCGTGCTCGTTAAGAAAATTTCTTG
* **
288881 -CTCGTTAAGATCGTTAA-AATTTTTCTTG
1 ACTCG-T--GCTCGTTAAGAAAATTTCTTG
288909 ACTCGTGCTCGTTAAGAAAA
1 ACTCGTGCTCGTTAAGAAAA
288929 ATTTATTACT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
26 12 0.33
27 3 0.08
28 9 0.25
29 12 0.33
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (27 bp):
ACTCGTGCTCGTTAAGAAAATTTCTTG
Found at i:288888 original size:55 final size:55
Alignment explanation
Indices: 288823--288928 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
288813 ACTCAACTCA
288823 TTGCTCGTTAAGATAATTAAAATTTTCCTCAACTCGTGCTCGTTAAGAAAATTTG
1 TTGCTCGTTAAGATAATTAAAATTTTCCTCAACTCGTGCTCGTTAAGAAAATTTG
** * **
288878 TTGCTCGTTAAGATCGTTAAAATTTTTCTTGACTCGTGCTCGTTAAGAAAA
1 TTGCTCGTTAAGATAATTAAAATTTTCCTCAACTCGTGCTCGTTAAGAAAA
288929 ATTTATTACT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (55 bp):
TTGCTCGTTAAGATAATTAAAATTTTCCTCAACTCGTGCTCGTTAAGAAAATTTG
Found at i:288932 original size:30 final size:33
Alignment explanation
Indices: 288896--288957 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
288886 TAAGATCGTT
288896 AAAATTT-TT-CTTGACTCG-TGCTCGTTAAGA
1 AAAATTTATTACTTGACTCGTTGCTCGTTAAGA
*
288926 AAAATTTATTACTTGACTTGTTGCTCGTTAAG
1 AAAATTTATTACTTGACTCGTTGCTCGTTAAG
288958 CTCATTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.25
31 2 0.07
32 8 0.29
33 11 0.39
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (33 bp):
AAAATTTATTACTTGACTCGTTGCTCGTTAAGA
Found at i:290288 original size:2 final size:2
Alignment explanation
Indices: 290281--290314 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
290271 TTTGTCATCT
290281 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
290315 TAAAACTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:292496 original size:23 final size:23
Alignment explanation
Indices: 292461--292540 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
292451 TAAACTACCA
*
292461 AAAGACGGA-AAAAACGTGCCAC
1 AAAGACAGAGAAAAACGTGCCAC
* *
292483 AAAGACAGAGAAAAATGTGTCAC
1 AAAGACAGAGAAAAACGTGCCAC
* * * *
292506 AAAAGA-ATATATAAACGTGCCAT
1 -AAAGACAGAGAAAAACGTGCCAC
292529 AAAGACAGAGAA
1 AAAGACAGAGAA
292541 TATGTAACAA
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
22 13 0.30
23 25 0.58
24 5 0.12
ACGTcount: A:0.54, C:0.15, G:0.20, T:0.11
Consensus pattern (23 bp):
AAAGACAGAGAAAAACGTGCCAC
Found at i:293378 original size:17 final size:18
Alignment explanation
Indices: 293338--293378 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
293328 CTCTGTTGTT
**
293338 TTAAAAACAAATGTCAAA
1 TTAAAAACAAATGGAAAA
293356 TT-AAAAC-AATGGAAAA
1 TTAAAAACAAATGGAAAA
293372 TTAAAAA
1 TTAAAAA
293379 TATCTATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 9 0.45
17 9 0.45
18 2 0.10
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (18 bp):
TTAAAAACAAATGGAAAA
Found at i:294712 original size:51 final size:51
Alignment explanation
Indices: 294633--294747 Score: 169
Period size: 51 Copynumber: 2.3 Consensus size: 51
294623 GTAACTATTA
* *
294633 AATAAAATAATAATAAACTAAAATTAATATTTTGATTATATCCTAATTCCT
1 AATAAAATAATAATAAACTAAAATTAATATTTTAACTATATCCTAATTCCT
*
294684 AATAAAATAATAATAAACTAAAGA-TAATATTTTAACTATATCTTAATTCCT
1 AATAAAATAATAATAAACTAAA-ATTAATATTTTAACTATATCCTAATTCCT
* *
294735 AGTAAAATGATAA
1 AATAAAATAATAA
294748 ATCTAATCCT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 57 0.98
52 1 0.02
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAATTAATATTTTAACTATATCCTAATTCCT
Found at i:296556 original size:19 final size:20
Alignment explanation
Indices: 296534--296582 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
296524 TTAGTTGCAA
296534 TTTTATAATTTT-ATTTTAT
1 TTTTATAATTTTAATTTTAT
*
296553 TTTTATACTTTTAAATTTTAT
1 TTTTATAATTTT-AATTTTAT
296574 TTTTA-AATT
1 TTTTATAATT
296583 ATGATATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 11 0.42
20 3 0.12
21 12 0.46
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATAATTTTAATTTTAT
Found at i:296591 original size:21 final size:21
Alignment explanation
Indices: 296534--296591 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
296524 TTAGTTGCAA
296534 TTTTATAATTT--TATTTTAT
1 TTTTATAATTTGATATTTTAT
* * *
296553 TTTTATACTTTTAAATTTTAT
1 TTTTATAATTTGATATTTTAT
296574 TTTTA-AATTATGATATTT
1 TTTTATAATT-TGATATTT
296592 GAATTTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 10 0.32
20 3 0.10
21 18 0.58
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATAATTTGATATTTTAT
Found at i:296597 original size:22 final size:21
Alignment explanation
Indices: 296572--296612 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
296562 TTTAAATTTT
*
296572 ATTTTTAAATTATGATATTTGA
1 ATTTATAAATT-TGATATTTGA
*
296594 ATTTATAAATTTTATATTT
1 ATTTATAAATTTGATATTT
296613 ATGTTATGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTATAAATTTGATATTTGA
Found at i:296700 original size:17 final size:17
Alignment explanation
Indices: 296677--296715 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
296667 TGGATTTTTT
*
296677 ATAAAAAATAATATAAA
1 ATAAAAAATAAAATAAA
*
296694 TTAAAAAATAAAATAAA
1 ATAAAAAATAAAATAAA
296711 ATAAA
1 ATAAA
296716 TATTAACCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAAAAAATAAAATAAA
Found at i:297791 original size:205 final size:204
Alignment explanation
Indices: 297289--297811 Score: 561
Period size: 205 Copynumber: 2.6 Consensus size: 204
297279 GAAAATTATC
* *
297289 ATAATTTATAAGCTTAGAGGTGTAGTATTGCAACATATCTTTCATTTGAGGGTAATATCAGCATA
1 ATAATTTTTAAGCTTAGAGGCGTAGTATTGCAACATATCTTTCATTTGAGGGTAATATCAGCATA
* * * *
297354 TACGAGACATTGTAAAAAAGATAAAAATCATGTTGAAAATGATTCGAAAGCTTGATTTTAAGCAT
66 TACGAGACATTATAAACAAGGTAAAAATCATGTTGAAAATGGTTC-AAAGCTTGATTTTAAGCAT
* * * * *** *
297419 GAAGATCAAGCTAAAATGACTTTGTAAACATTTTTGAGGTATTTTTCTGGGAAGTTAATTGAAAA
130 GAAGAACAAGCTAAAATGACTTTGTAAACATGTTCGAGGTATTTTACTAAAAAGTTAATTCAAAA
297484 TATTTTTTTT
195 TATTTTTTTT
* * * * * ** *
297494 ATAATTTTTAAGCTTAAAGGCATGGTATTACAACGTATCTTTCATTTGAGGGTAATATCAATACA
1 ATAATTTTTAAGCTTAGAGGCGTAGTATTGCAACATATCTTTCATTTGAGGGTAATATCAGCATA
* * * * * **
297559 TATGAGACATCATAAAC-GGGATAAAAATCATGTTAAAAATGGTTTCAAAGCTTGGTTTTGTGCA
66 TACGAGACATTATAAACAAGG-TAAAAATCATGTTGAAAATGG-TTCAAAGCTTGATTTTAAGCA
* **
297623 TGAAGAACAAGCTAAAATGGC-TTGATAGGCATGTTCGAGTGGTA-TTTAC-AAAAAGTTAA-TC
129 TGAAGAACAAGCTAAAATGACTTTG-TAAACATGTTCGA--GGTATTTTACTAAAAAGTTAATTC
* *
297684 AAACCTTTTTTTTTT
191 AAA-ATATTTTTTTT
* * * *
297699 GTAATTTTTAAGCTTAGAGGCGTAGTATTGCAACTTATCTTGCATTTGAAGGTAATATCAGCATA
1 ATAATTTTTAAGCTTAGAGGCGTAGTATTGCAACATATCTTTCATTTGAGGGTAATATCAGCATA
* * * **
297764 TACGATACATTATAAGCATGGTAAAAATCGCGTTGAAAATGGTTCAAA
66 TACGAGACATTATAAACAAGGTAAAAATCATGTTGAAAATGGTTCAAA
297812 ACCATTTAAA
Statistics
Matches: 258, Mismatches: 53, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
204 14 0.05
205 231 0.90
206 9 0.03
207 4 0.02
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (204 bp):
ATAATTTTTAAGCTTAGAGGCGTAGTATTGCAACATATCTTTCATTTGAGGGTAATATCAGCATA
TACGAGACATTATAAACAAGGTAAAAATCATGTTGAAAATGGTTCAAAGCTTGATTTTAAGCATG
AAGAACAAGCTAAAATGACTTTGTAAACATGTTCGAGGTATTTTACTAAAAAGTTAATTCAAAAT
ATTTTTTTT
Found at i:298006 original size:73 final size:73
Alignment explanation
Indices: 297887--298034 Score: 224
Period size: 73 Copynumber: 2.0 Consensus size: 73
297877 TTTAGTTAAT
* * * *
297887 TAGAAAGTTAAAGTATCTATAGTTATCCTCTAATGTTCAATACATTTAAATTTGAAAAAGTTGAT
1 TAGAAAGTTAAAATATCGATACTTATACTCTAATGTTCAATACATTTAAATTTGAAAAAGTTGAT
297952 GAAGGTAA
66 GAAGGTAA
* * *
297960 TAGAAAGTTAAAATATCGATACTTATACTTTGATGTTCAATACATTTACATTTGAAAAAGTTGAT
1 TAGAAAGTTAAAATATCGATACTTATACTCTAATGTTCAATACATTTAAATTTGAAAAAGTTGAT
*
298025 GAATGTAA
66 GAAGGTAA
298033 TA
1 TA
298035 CAAAATGTTG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.36
Consensus pattern (73 bp):
TAGAAAGTTAAAATATCGATACTTATACTCTAATGTTCAATACATTTAAATTTGAAAAAGTTGAT
GAAGGTAA
Found at i:303020 original size:13 final size:14
Alignment explanation
Indices: 303000--303035 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
302990 TTTCAAAATT
303000 ATAAATAAATAATC
1 ATAAATAAATAATC
303014 A-AAATAAATAATC
1 ATAAATAAATAATC
303027 ATAAATAAA
1 ATAAATAAA
303036 AATTATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (14 bp):
ATAAATAAATAATC
Found at i:303891 original size:22 final size:24
Alignment explanation
Indices: 303842--303891 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
303832 TAAAATTTTT
303842 CTATTTTTATTTATTCATGTATTA
1 CTATTTTTATTTATTCATGTATTA
303866 -TATTTTTAGTTT-TT-ATGTA-TA
1 CTATTTTTA-TTTATTCATGTATTA
303887 CTATT
1 CTATT
303892 AAAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 2 0.08
22 9 0.38
23 10 0.42
24 3 0.12
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (24 bp):
CTATTTTTATTTATTCATGTATTA
Found at i:303950 original size:18 final size:19
Alignment explanation
Indices: 303926--303966 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
303916 AAAAAAAATC
*
303926 ATTTTTTTT-TATTTTTT-
1 ATTTTTTTTCCATTTTTTA
303943 ATTTTTTTTCCATTTTTTA
1 ATTTTTTTTCCATTTTTTA
303962 ATTTT
1 ATTTT
303967 CTTTAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 7 0.33
19 5 0.24
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (19 bp):
ATTTTTTTTCCATTTTTTA
Found at i:304461 original size:3 final size:3
Alignment explanation
Indices: 304453--304509 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
304443 AACAAATAAT
304453 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
304501 TTA TCTA TT
1 TTA T-TA TT
304510 TTTAGTAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:307354 original size:27 final size:26
Alignment explanation
Indices: 307308--307398 Score: 100
Period size: 26 Copynumber: 3.5 Consensus size: 26
307298 AGTGAAACTG
*
307308 AAATAAA-AAAATA-AG-GACAAAAT
1 AAATAAATAAAATACAGAAACAAAAT
*
307331 AGAATAAGATAAAA-AGAGAAACAAAGAT
1 A-AATAA-ATAAAATACAGAAACAAA-AT
307359 AAATAAATAAAATACAGAAACAAAAT
1 AAATAAATAAAATACAGAAACAAAAT
*
307385 AAATAAAAAAAATA
1 AAATAAATAAAATA
307399 AGGGGAAAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
23 1 0.02
24 5 0.09
25 2 0.03
26 27 0.47
27 20 0.34
28 3 0.05
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (26 bp):
AAATAAATAAAATACAGAAACAAAAT
Found at i:307368 original size:26 final size:25
Alignment explanation
Indices: 307324--307396 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 25
307314 AAAAATAAGG
*
307324 ACAAAATAGAATAAGATAAAAAGAGAA
1 ACAAAATA-AATAA-ATAAAAACAGAA
307351 ACAAAGATAAATAAATAAAATACAGAA
1 ACAAA-ATAAATAAATAAAA-ACAGAA
307378 ACAAAATAAATAAA-AAAAA
1 ACAAAATAAATAAATAAAAA
307397 TAAGGGGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
24 1 0.02
25 4 0.09
26 15 0.35
27 20 0.47
28 3 0.07
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.12
Consensus pattern (25 bp):
ACAAAATAAATAAATAAAAACAGAA
Found at i:307385 original size:13 final size:13
Alignment explanation
Indices: 307347--307399 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
307337 AGATAAAAAG
307347 AGAAACAAAGATAA
1 AGAAACAAA-ATAA
* * *
307361 ATAAATAAAATAC
1 AGAAACAAAATAA
307374 AGAAACAAAATAA
1 AGAAACAAAATAA
* *
307387 ATAAAAAAAATAA
1 AGAAACAAAATAA
307400 GGGGAAAGGA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 24 0.77
14 7 0.23
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.13
Consensus pattern (13 bp):
AGAAACAAAATAA
Found at i:307397 original size:26 final size:25
Alignment explanation
Indices: 307308--307400 Score: 93
Period size: 27 Copynumber: 3.6 Consensus size: 25
307298 AGTGAAACTG
*
307308 AAAT-AAAAAAATAAG-GACAAAAT
1 AAATAAAAAAAATAAGAAACAAAAT
*
307331 AGAATAAGATAAAAA-GAGAAACAAAGAT
1 A-AATAA-A-AAAAATAAGAAACAAA-AT
*
307359 AAATAAATAAAATACAGAAACAAAAT
1 AAATAAAAAAAATA-AGAAACAAAAT
307385 AAATAAAAAAAATAAG
1 AAATAAAAAAAATAAG
307401 GGGAAAGGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
23 1 0.02
24 3 0.05
25 7 0.12
26 19 0.33
27 24 0.42
28 3 0.05
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.13
Consensus pattern (25 bp):
AAATAAAAAAAATAAGAAACAAAAT
Found at i:307499 original size:6 final size:6
Alignment explanation
Indices: 307490--307514 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
307480 TATATATAAT
307490 ATAGAA ATAGAA ATAGAA ATAGAA A
1 ATAGAA ATAGAA ATAGAA ATAGAA A
307515 CATATCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
ATAGAA
Found at i:307580 original size:15 final size:13
Alignment explanation
Indices: 307536--307581 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
307526 AATAAAATAA
*
307536 AATACATATA-AT
1 AATATATATATAT
307548 AATATATATATAT
1 AATATATATATAT
307561 AATATATATATAT
1 AATATATATATAT
*
307574 AACATATA
1 AATATATA
307582 ATAAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 9 0.29
13 22 0.71
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (13 bp):
AATATATATATAT
Found at i:307605 original size:15 final size:16
Alignment explanation
Indices: 307580--307609 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
307570 ATATAACATA
307580 TAATAAAAAATAAAAG
1 TAATAAAAAATAAAAG
307596 TAAT-AAAAATAAAA
1 TAATAAAAAATAAAA
307610 TAGTACAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
TAATAAAAAATAAAAG
Found at i:309591 original size:103 final size:100
Alignment explanation
Indices: 309440--309676 Score: 287
Period size: 103 Copynumber: 2.3 Consensus size: 100
309430 GGTTTTTTTG
* * * * *
309440 TGTTTCAAGAGAAAATGTCTCGAGTGAGACGAAATTTGTTTAATGGAAAACAGATTCAAAGATTT
1 TGTTCCAAAAGAAAATGTCTCAAGAGAGAC-AAATTTGTTTAATGGAAAACAAATTCAAAGA-TT
** *
309505 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
64 TTGTTTCAAAAGAAACTATCTCAAGAGAGACAAAATT
* * *
309542 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACACAATTTGTTTCAA-GGAAAACAAATTCAGAGAT
1 T-GTTCCAAAAGAAAATGTCTCAAGAGAGACA-AATTTGTTT-AATGGAAAACAAATTCAAAGAT
309606 TTTGTTTCAAAAGAAACTATCTCAAGAGAGACAAAATT
63 TTTGTTTCAAAAGAAACTATCTCAAGAGAGACAAAATT
** **
309644 TGTTTTACGAGAAAATGTCTCAAGAGAGACAAA
1 TGTTCCAAAAGAAAATGTCTCAAGAGAGACAAA
309677 ATTTAGTTCT
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
100 2 0.02
101 24 0.21
102 39 0.34
103 49 0.42
104 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (100 bp):
TGTTCCAAAAGAAAATGTCTCAAGAGAGACAAATTTGTTTAATGGAAAACAAATTCAAAGATTTT
GTTTCAAAAGAAACTATCTCAAGAGAGACAAAATT
Found at i:309646 original size:36 final size:36
Alignment explanation
Indices: 309606--309996 Score: 268
Period size: 36 Copynumber: 11.2 Consensus size: 36
309596 ATTCAGAGAT
* *
309606 TTTGTTTCAAAAGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
309642 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
309678 TTTAG-TTCTAAAAGAAAATGTCTCAAGAGAGACAAAA
1 TTT-GTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
* **
309715 TTTGTTTAAAG-GAAA-------AA-AGATTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-A
*
309743 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * * *
309780 TTTGTTTTACGAGAAAATGTCTCAAGAGAGCCTACA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
309816 TTTAG-TTCTAAAAGAAACTGTCTCAAGAGAGACAAAA
1 TTT-GTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
** **
309853 CTTTGTTTCAAG-GAAAACAAAT-TC-A-A-AG----TT
1 -TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
* *
309883 TTTGTTTCAAGGGAAACCGTCTCAAGAGA-A-AAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
309917 TTTGTTTTAAGAGAAAATGTCTCAAGAGATATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
309953 TTTGTTTTAAGAGAAACTGTCTCAAGAAAGACAAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
309990 TTTGTTT
1 TTTGTTT
309997 TGAGTAAATT
Statistics
Matches: 278, Mismatches: 46, Indels: 61
0.72 0.12 0.16
Matches are distributed among these distances:
27 7 0.03
28 4 0.01
29 27 0.10
30 6 0.02
31 1 0.00
32 1 0.00
34 27 0.10
35 6 0.02
36 107 0.38
37 78 0.28
38 14 0.05
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:309673 original size:138 final size:138
Alignment explanation
Indices: 309516--309996 Score: 718
Period size: 138 Copynumber: 3.5 Consensus size: 138
309506 TGTTTCAAGG
* * * *
309516 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACACAATTTG
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAATTTG
* ** *
309581 TTTCAAGGAAAACAAATTCAGAGATTTTGTTTCAAAAGAAACTATCTCAAGAGAGACAAAATTTG
66 TTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
309646 TTTTACGA
131 TTTTACGA
*
309654 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAAATGTCTCAAGAGAGACAAAATTTG
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAATTTG
*
309719 TTTAAAGGAAAA-AAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
66 TTTCAAGGAAAACAA-ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
309783 GTTTTACGA
130 GTTTTACGA
* * *
309792 GAAAATGTCTCAAGAGAGCCTACATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAACTTT
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAA-TTT
* *
309857 GTTTCAAGGAAAACAAATTCAAAGTTTTTGTTTCAAGGGAAACCGTCTCAAGAGA-A-AAAATTT
65 GTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
309920 GTTTTAAGA
130 GTTTTACGA
* * * * *
309929 GAAAATGTCTCAAGAGATATAAAATTT-GTTTTAAGAGAAACTGTCTCAAGAAAGACAAAAATTT
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGAC-AAAATTT
309993 GTTT
65 GTTT
309997 TGAGTAAATT
Statistics
Matches: 313, Mismatches: 26, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
136 33 0.11
137 43 0.14
138 183 0.58
139 52 0.17
140 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (138 bp):
GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAATTTG
TTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
TTTTACGA
Found at i:309703 original size:37 final size:35
Alignment explanation
Indices: 309516--309996 Score: 227
Period size: 36 Copynumber: 13.9 Consensus size: 35
309506 TGTTTCAAGG
* *
309516 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAA
1 GAAAATGTCTCAAGAGAGACAAAATTT-GTT-TAAAA
* * * * *
309553 GAAACTGTCTCAAGGGAGACACAATTTGTTTCAAG
1 GAAAATGTCTCAAGAGAGACAAAATTTGTTTAAAA
*** * * *
309588 GAAAA-----CAA-ATTCAGAGATTTTGTTTCAAAA
1 GAAAATGTCTCAAGAGAGACAAAATTTGTTT-AAAA
* * **
309618 GAAACTATCTCAAGAGAGACAAAATTTGTTTTACGA
1 GAAAATGTCTCAAGAGAGACAAAATTTG-TTTAAAA
309654 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAAATGTCTCAAGAGAGACAAAATTT-GTT-TAAAA
*
309691 GAAAATGTCTCAAGAGAGACAAAATTTGTTTAAAG
1 GAAAATGTCTCAAGAGAGACAAAATTTGTTTAAAA
* * **
309726 GAAAAAAGAT-TC-A-A-AG----ATTTTGTTTCAAGG
1 G-AAAATG-TCTCAAGAGAGACAAAATTTGTTT-AAAA
* **
309756 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGA
1 GAAAATGTCTCAAGAGAGACAAAATTTG-TTTAAAA
* * *
309792 GAAAATGTCTCAAGAGAGCCTACATTTAGTTCTAAAA
1 GAAAATGTCTCAAGAGAGACAAAATTT-GTT-TAAAA
* * *
309829 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAG
1 GAAAATGTCTCAAGAGAGACAAAA-TTTGTTTAAAA
** * **
309865 GAAAA-----C-A-A-ATTCAAAGTTTTTGTTTCAAGG
1 GAAAATGTCTCAAGAGAGACAAA--ATTTGTTT-AAAA
** *
309895 GAAACCGTCTCAAGAGA-A-AAAATTTGTTTTAAGA
1 GAAAATGTCTCAAGAGAGACAAAATTTG-TTTAAAA
* * *
309929 GAAAATGTCTCAAGAGATATAAAATTTGTTTTAAGA
1 GAAAATGTCTCAAGAGAGACAAAATTTG-TTTAAAA
* *
309965 GAAACTGTCTCAAGAAAGACAAAAATTTGTTT
1 GAAAATGTCTCAAGAGAGAC-AAAATTTGTTT
309997 TGAGTAAATT
Statistics
Matches: 339, Mismatches: 65, Indels: 81
0.70 0.13 0.17
Matches are distributed among these distances:
28 6 0.02
29 32 0.09
30 21 0.06
31 2 0.01
32 2 0.01
33 2 0.01
34 23 0.07
35 20 0.06
36 128 0.38
37 99 0.29
38 4 0.01
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (35 bp):
GAAAATGTCTCAAGAGAGACAAAATTTGTTTAAAA
Found at i:309930 original size:19 final size:19
Alignment explanation
Indices: 309906--309968 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
309896 AAACCGTCTC
309906 AAGAGAAAAAATTTGTTTT
1 AAGAGAAAAAATTTGTTTT
* *
309925 AAGAG--AAAA--TGTCTC
1 AAGAGAAAAAATTTGTTTT
309940 AAGAGATATAAAATTTGTTTT
1 AAGAGA-A-AAAATTTGTTTT
309961 AAGAGAAA
1 AAGAGAAA
309969 CTGTCTCAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 9 0.26
17 4 0.12
19 10 0.29
20 1 0.03
21 10 0.29
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.30
Consensus pattern (19 bp):
AAGAGAAAAAATTTGTTTT
Found at i:311415 original size:83 final size:86
Alignment explanation
Indices: 311306--311532 Score: 221
Period size: 95 Copynumber: 2.6 Consensus size: 86
311296 GGCTAGCTGG
* * * *
311306 ATCCAAAAAGCCGGGGCGTTTTACCAATTACTCTAGAGGGACAACTCAATAT-GTA-AAT-ACCT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATAGTATAATCACCT
* * * *
311368 TTATTAGGTTAGTTGAATCTT
66 TTATCAGGCTAGCTGAATATT
* *
311389 ATCCATAAAGCTGGGGCGTTTAACCAATTGC-CATAGAGGGATATCTCAAACTTTATTGTATAGT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTC-TAGAGGG--A---C-AAC-TCA--ATATAGT
311453 ATAATCACCTTTATCAGGCTAGCTGAATATT
56 ATAATCACCTTTATCAGGCTAGCTGAATATT
*
311484 ATCCATAAAG-TCGGGGCGTTTAACTAATTGCTCTAGAGGGACAACTCAA
1 ATCCATAAAGCT-GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
311533 GCTTTATTAT
Statistics
Matches: 116, Mismatches: 13, Indels: 27
0.74 0.08 0.17
Matches are distributed among these distances:
82 1 0.01
83 34 0.29
85 1 0.01
88 3 0.03
89 6 0.05
90 3 0.03
92 3 0.03
93 4 0.03
94 4 0.03
95 56 0.48
96 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (86 bp):
ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATAGTATAATCACCT
TTATCAGGCTAGCTGAATATT
Found at i:311532 original size:95 final size:95
Alignment explanation
Indices: 311364--311545 Score: 251
Period size: 95 Copynumber: 1.9 Consensus size: 95
311354 ATATGTAAAT
* * * *
311364 ACCTTTATTAGGTTAGTTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAATTGCCATAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGGGGCGTTTAACCAATTGCCATAGAGGG
* * *
311429 ATATCTCAAACTTTATTGTATAGTATAATC
66 ACAACTCAAACTTTATTATATAGTATAATC
*
311459 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAG-TCGGGGCGTTTAACTAATTGCTC-TAGAG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCT-GGGGCGTTTAACCAATTGC-CATAGAG
*
311522 GGACAACTCAAGCTTTATTATATA
64 GGACAACTCAAACTTTATTATATA
311546 TAAATAATAT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
94 1 0.01
95 74 0.97
96 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGGGGCGTTTAACCAATTGCCATAGAGGG
ACAACTCAAACTTTATTATATAGTATAATC
Found at i:312666 original size:64 final size:62
Alignment explanation
Indices: 312571--312710 Score: 149
Period size: 64 Copynumber: 2.2 Consensus size: 62
312561 CACATTGAAT
*
312571 GTGCATCGATGCAATCTTTAAAGAAGAAACATCGAATGCAAATGATGCATCGATGCATAAGG-A
1 GTGCATCGATGC-ATCTTTAAAGAAGAAACATCGAAGGCAAATGATGCATCGATGCAT-AGGTA
* * * ** * *
312634 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTCTGTATCGATGCATGGGTA
1 GTGCATCGATGCAT--CTTTAAAGAAG-AAACATCGAAGGCAAATGATGCATCGATGCATAGGTA
312698 GTGCATCGATGCA
1 GTGCATCGATGCA
312711 CAAGTTAAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
62 2 0.03
63 16 0.25
64 47 0.72
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATCTTTAAAGAAGAAACATCGAAGGCAAATGATGCATCGATGCATAGGTA
Found at i:312731 original size:24 final size:20
Alignment explanation
Indices: 312699--312755 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 20
312689 GCATGGGTAG
312699 TGCATCGATGCACAAGTTAAAGAA
1 TGCATCGATGCAC-AG-T--AGAA
*
312723 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACAGTAGAA
312743 TGCATCGATGCAC
1 TGCATCGATGCAC
312756 TTCAAGGGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 1 0.03
24 13 0.41
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (20 bp):
TGCATCGATGCACAGTAGAA
Found at i:312744 original size:20 final size:20
Alignment explanation
Indices: 312719--312756 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
312709 CACAAGTTAA
312719 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
312739 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
312757 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:313576 original size:31 final size:31
Alignment explanation
Indices: 313538--313602 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
313528 AGAGTCGAGG
*
313538 GTTTACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
** * *
313569 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
313600 GTT
1 GTT
313603 ACCGAGGATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGACA
Found at i:313622 original size:30 final size:30
Alignment explanation
Indices: 313561--313657 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
313551 CTAAGGAACA
* * ***
313561 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
313592 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
313622 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
313652 TCTGGA
1 TATGGA
313658 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:313658 original size:30 final size:30
Alignment explanation
Indices: 313588--313660 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
313578 GGTTCTTCGG
* *
313588 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
313618 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
313648 GACCTCTGGATAG
1 GACCTCTGGATAG
313661 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:314844 original size:19 final size:19
Alignment explanation
Indices: 314820--314953 Score: 110
Period size: 19 Copynumber: 6.6 Consensus size: 19
314810 AGATGATATA
314820 TGTTTATGTGATATAAAAG
1 TGTTTATGTGATATAAAAG
314839 TGTTTATGTGATATAAAAG
1 TGTTTATGTGATATAAAAG
*
314858 TGTATATGTGAATGATATAATAAG
1 TGT-T-TATG--TGATATAA-AAG
* * *
314882 AAG-CTATGTGATA-AGATGATATA
1 -TGTTTATGTGATATA-A--A-A-G
314905 TGTTTATGTGATATAAAAG
1 TGTTTATGTGATATAAAAG
314924 TGTTTATGTGATATAAAAG
1 TGTTTATGTGATATAAAAG
*
314943 TGTATATGTGA
1 TGTTTATGTGA
314954 AATGTCATGA
Statistics
Matches: 93, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
19 52 0.56
20 8 0.09
21 5 0.05
22 5 0.05
23 18 0.19
24 4 0.04
25 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.22, T:0.40
Consensus pattern (19 bp):
TGTTTATGTGATATAAAAG
Found at i:314879 original size:85 final size:85
Alignment explanation
Indices: 314777--314954 Score: 347
Period size: 85 Copynumber: 2.1 Consensus size: 85
314767 GATATTGAAG
314777 TATGTGAATGATATAATAAGAAGCTAAGTGATAAGATGATATATGTTTATGTGATATAAAAGTGT
1 TATGTGAATGATATAATAAGAAGCTAAGTGATAAGATGATATATGTTTATGTGATATAAAAGTGT
314842 TTATGTGATATAAAAGTGTA
66 TTATGTGATATAAAAGTGTA
*
314862 TATGTGAATGATATAATAAGAAGCTATGTGATAAGATGATATATGTTTATGTGATATAAAAGTGT
1 TATGTGAATGATATAATAAGAAGCTAAGTGATAAGATGATATATGTTTATGTGATATAAAAGTGT
314927 TTATGTGATATAAAAGTGTA
66 TTATGTGATATAAAAGTGTA
314947 TATGTGAA
1 TATGTGAA
314955 ATGTCATGAT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.37
Consensus pattern (85 bp):
TATGTGAATGATATAATAAGAAGCTAAGTGATAAGATGATATATGTTTATGTGATATAAAAGTGT
TTATGTGATATAAAAGTGTA
Found at i:317117 original size:64 final size:62
Alignment explanation
Indices: 317022--317161 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 62
317012 CACATTCAAT
*
317022 GTGCATCGATGCAATCTTTAAAGAAGAAACATCGAATGCAAATGGTGAATCGATGCATAAGG-A
1 GTGCATCGATGC-ATCTTTAAAGAAGAAACATCGAAGGCAAATGGTGAATCGATGCAT-AGGTA
* * * * * *
317085 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCAT--CTTTAAAGAAG-AAACATCGAAGGCAAATGGTGAATCGATGCATAGGTA
317149 GTGCATCGATGCA
1 GTGCATCGATGCA
317162 CAAGTTAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
62 2 0.03
63 16 0.24
64 48 0.73
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATCTTTAAAGAAGAAACATCGAAGGCAAATGGTGAATCGATGCATAGGTA
Found at i:318612 original size:21 final size:21
Alignment explanation
Indices: 318586--318627 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
318576 CCAGAATGGG
*
318586 GGGAATCGGTACCCCCTCATA
1 GGGAATCGATACCCCCTCATA
*
318607 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCCTCATA
318628 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.21
Consensus pattern (21 bp):
GGGAATCGATACCCCCTCATA
Found at i:318757 original size:19 final size:19
Alignment explanation
Indices: 318733--318780 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
318723 GAGCCTCGGG
*
318733 TTACTGTTCAAACAGTAAT
1 TTACTGTTCAAACAGTAAA
* *
318752 TTACTGTCCAAATAGTAAA
1 TTACTGTTCAAACAGTAAA
*
318771 TTACTATTCA
1 TTACTGTTCA
318781 TAAAAACATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAA
Found at i:320159 original size:19 final size:20
Alignment explanation
Indices: 320116--320163 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
320106 TCTAAATCCT
*
320116 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
320136 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
320155 TTTTCAAAA
1 TTTTCAAAA
320164 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:321408 original size:21 final size:22
Alignment explanation
Indices: 321374--321416 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
321364 CCCAGAATGG
*
321374 GGGGAATCGGTACCCCTTCATA
1 GGGGAATCGATACCCCTTCATA
321396 GGGG-ATCGATACCCCTTCATA
1 GGGGAATCGATACCCCTTCATA
321417 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (22 bp):
GGGGAATCGATACCCCTTCATA
Found at i:322236 original size:4 final size:4
Alignment explanation
Indices: 322229--322266 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
322219 TGATAATGAC
322229 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
322267 TTGTTACATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:326416 original size:26 final size:25
Alignment explanation
Indices: 326372--326457 Score: 86
Period size: 26 Copynumber: 3.2 Consensus size: 25
326362 AAAAATAAAG
326372 ACAAAATAGAATAAGATAAAAAGAGAA
1 ACAAAATA-AATAA-ATAAAAAGAGAA
326399 ACAAAGATAAATAAATAAAATACG-GAA
1 ACAAA-ATAAATAAATAAAA-A-GAGAA
*
326426 ACAAAATAAATAAAAATAAAAA-AAAA
1 ACAAAATAAAT--AAATAAAAAGAGAA
326452 ACAAAA
1 ACAAAA
326458 ATGAGGGGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 13
0.79 0.02 0.20
Matches are distributed among these distances:
26 20 0.38
27 20 0.38
28 12 0.23
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (25 bp):
ACAAAATAAATAAATAAAAAGAGAA
Found at i:326624 original size:16 final size:16
Alignment explanation
Indices: 326571--326650 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
326561 TAGAAATAGA
326571 AACATAT-AA-AAAAT
1 AACATATAAATAAAAT
* *
326585 AAAATA-AAAT-ATAT
1 AACATATAAATAAAAT
*
326599 ATACATATATATATAATAT
1 A-ACATATA-A-ATAAAAT
326618 AACATATAAATAAAAT
1 AACATATAAATAAAAT
*
326634 AA-ATAAATAATAAAAT
1 AACATATA-AATAAAAT
326650 A
1 A
326651 GTACAGGTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
14 11 0.21
15 8 0.15
16 18 0.34
17 2 0.04
18 9 0.17
19 5 0.09
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
AACATATAAATAAAAT
Found at i:326693 original size:2 final size:2
Alignment explanation
Indices: 326686--326717 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
326676 AAGAAAACTA
326686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
326718 ATGTAATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:327678 original size:28 final size:29
Alignment explanation
Indices: 327641--327696 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
327631 ATGTTTGTTA
327641 ATAACAATAATAATACATATA-ATATATAC
1 ATAACAATAATAA-ACATATATATATATAC
327670 ATAA-AATAATAAACATATATATATATA
1 ATAACAATAATAAACATATATATATATA
327697 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 7 0.27
28 15 0.58
29 4 0.15
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (29 bp):
ATAACAATAATAAACATATATATATATAC
Found at i:327691 original size:2 final size:2
Alignment explanation
Indices: 327684--327715 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
327674 AATAATAAAC
327684 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
327716 GCATTCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:335983 original size:20 final size:20
Alignment explanation
Indices: 335958--335995 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
335948 ACATAATATA
*
335958 AATATTTATAATTATTTTTC
1 AATATTAATAATTATTTTTC
*
335978 AATATTAATTATTATTTT
1 AATATTAATAATTATTTT
335996 ACTAAGTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
AATATTAATAATTATTTTTC
Found at i:337961 original size:20 final size:21
Alignment explanation
Indices: 337909--338010 Score: 79
Period size: 20 Copynumber: 5.0 Consensus size: 21
337899 ACGTTACGAT
* *
337909 TTTCTAAATTCGCAACACTGAA
1 TTTCTGAATTCGCAACTC-GAA
*
337931 TTTC-AAATTCGCAACTCG-A
1 TTTCTGAATTCGCAACTCGAA
337950 TTTCTGAATTCGCAACGT-GAA
1 TTTCTGAATTCGCAAC-TCGAA
** *
337971 TTT-TGTTTTCGCAACTCGAT
1 TTTCTGAATTCGCAACTCGAA
* *
337991 TTTC-GAATTCACAACACGAA
1 TTTCTGAATTCGCAACTCGAA
338011 ATTTAATTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
19 6 0.09
20 38 0.58
21 17 0.26
22 4 0.06
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (21 bp):
TTTCTGAATTCGCAACTCGAA
Found at i:338021 original size:40 final size:41
Alignment explanation
Indices: 337905--338024 Score: 129
Period size: 40 Copynumber: 3.0 Consensus size: 41
337895 AATCACGTTA
* *
337905 CGATTTTCTAAATTCGCAACACTG-AATTTCAAATTCGCAACT
1 CGATTTTCTGAATTCGCAACAC-GAAATTT-AATTTCGCAACT
** * **
337947 CGA-TTTCTGAATTCGCAACGTGAATTTTGTTTTCGCAACT
1 CGATTTTCTGAATTCGCAACACGAAATTTAATTTCGCAACT
*
337987 CGATTTTC-GAATTCACAACACGAAATTTAATTTCGCAA
1 CGATTTTCTGAATTCGCAACACGAAATTTAATTTCGCAA
338025 TAGGTTTTAG
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
40 37 0.59
41 23 0.37
42 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (41 bp):
CGATTTTCTGAATTCGCAACACGAAATTTAATTTCGCAACT
Found at i:338213 original size:15 final size:14
Alignment explanation
Indices: 338182--338218 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
338172 TCCCCATCTC
*
338182 TAATTTTTTTTATA
1 TAATTTTTTTCATA
338196 TAATTTTATTTCATA
1 TAATTTT-TTTCATA
338211 TAATTTTT
1 TAATTTTT
338219 CAATGATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TAATTTTTTTCATA
Found at i:338829 original size:12 final size:12
Alignment explanation
Indices: 338808--338841 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
338798 CACACATTTC
*
338808 CAATACCAAACA
1 CAATATCAAACA
338820 CAATATCAAACA
1 CAATATCAAACA
*
338832 CAATCTCAAA
1 CAATATCAAA
338842 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:338994 original size:24 final size:24
Alignment explanation
Indices: 338967--339020 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
338957 GTATTCGAAA
*
338967 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAAAACCCGGAC
* *
338991 TTTGATCTTGGTCAAAACTCGGAT
1 TTTGATCTTGGTCAAAACCCGGAC
339015 TTTGAT
1 TTTGAT
339021 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGTCAAAACCCGGAC
Found at i:339302 original size:24 final size:24
Alignment explanation
Indices: 339275--339328 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
339265 GTATTCGAAA
*
339275 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAAAACCCGGAC
* *
339299 TTTGATCTTGGTCAAAACTCGGAT
1 TTTGATCTTGGTCAAAACCCGGAC
339323 TTTGAT
1 TTTGAT
339329 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGTCAAAACCCGGAC
Found at i:339510 original size:3 final size:3
Alignment explanation
Indices: 339502--339529 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
339492 ATATAACCCT
339502 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
339530 TCCACGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:339518 original size:308 final size:309
Alignment explanation
Indices: 338925--339542 Score: 1170
Period size: 308 Copynumber: 2.0 Consensus size: 309
338915 AGACGATTAT
338925 GAGCCAATAGAAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTGGTCAATACCCGGA
1 GAGCCAATAGAAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTGGTCAATACCCGGA
338990 CTTTGATCTTGGTCAAAACTCGGATTTTGATGATGTTTCAGAAGAAGAAATAGACCCTACGTGTA
66 CTTTGATCTTGGTCAAAACTCGGATTTTGATGATGTTTCAGAAGAAGAAATAGACCCTACGTGTA
339055 ATGATTTTGATATTGGTCAATACCCAATTTTGATGATGAAACAGTCGTTGCCGAGGAAGATGTTG
131 ATGATTTTGATATTGGTCAATACCCAATTTTGATGATGAAACAGTCGTTGCCGAGGAAGATGTTG
339120 TTGATAATAATGAGAGGAAGTTACGACTGTGAATGAACATGTTGAACATCCATTTTGTAATCATA
196 TTGATAATAATGAGAGGAAGTTACGACTGTGAATGAACATGTTGAACATCCATTTTGTAATCATA
339185 TAACCCT-GAAGAAGAAGAAAAGAAGAA-AAGAAGTCCACGAAGAAAATA
261 TAACCCTAGAAGAAGAAG-AAAGAAGAAGAAGAAGTCCACGAAGAAAATA
339233 GAGCCAATAGAAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTGGTCAATACCCGGA
1 GAGCCAATAGAAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTGGTCAATACCCGGA
339298 CTTTGATCTTGGTCAAAACTCGGATTTTGATGATGTTTCAGAAGAAGAAATAGACCCTACGTGTA
66 CTTTGATCTTGGTCAAAACTCGGATTTTGATGATGTTTCAGAAGAAGAAATAGACCCTACGTGTA
339363 ATGATTTTGATATTGGTCAATACCCGAATTTTGATGATGAAACAGTCGTTGCCGAGGAAGATGTT
131 ATGATTTTGATATTGGTCAATACCC-AATTTTGATGATGAAACAGTCGTTGCCGAGGAAGATGTT
339428 GTTGATAATAATGAGAGGAAGTTACGACTGTGAATGAACATGTTGAACATCCATTTTGTAATTCA
195 GTTGATAATAATGAGAGGAAGTTACGACTGTGAATGAACATGTTGAACATCCATTTTGTAA-TCA
339493 TATAACCCT-GAAGAAGAAGAAGAAGAAGAAGAAGAAGTCCACGAAGAAAA
259 TATAACCCTAGAAGAAGAAG-A-AAGAAGAAGAAGAAGTCCACGAAGAAAA
339543 GAAAAAGAAG
Statistics
Matches: 306, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
308 155 0.51
309 100 0.33
310 24 0.08
311 8 0.03
312 19 0.06
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (309 bp):
GAGCCAATAGAAAAAATTGTGAGTACTAGTCAGTATTCGAAATTTGATCTTGGTCAATACCCGGA
CTTTGATCTTGGTCAAAACTCGGATTTTGATGATGTTTCAGAAGAAGAAATAGACCCTACGTGTA
ATGATTTTGATATTGGTCAATACCCAATTTTGATGATGAAACAGTCGTTGCCGAGGAAGATGTTG
TTGATAATAATGAGAGGAAGTTACGACTGTGAATGAACATGTTGAACATCCATTTTGTAATCATA
TAACCCTAGAAGAAGAAGAAAGAAGAAGAAGAAGTCCACGAAGAAAATA
Found at i:341844 original size:20 final size:20
Alignment explanation
Indices: 341814--341880 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
341804 AACGCGAAAA
341814 TCGCAACGCGAATTTGACTT
1 TCGCAACGCGAATTTGACTT
*** *
341834 TCGCGTTGCGAATTTGACTA
1 TCGCAACGCGAATTTGACTT
341854 TCGCAACGCGAATTTGACTT
1 TCGCAACGCGAATTTGACTT
341874 TCGCAAC
1 TCGCAAC
341881 CATCGCAACG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (20 bp):
TCGCAACGCGAATTTGACTT
Found at i:342095 original size:64 final size:64
Alignment explanation
Indices: 341994--342142 Score: 244
Period size: 64 Copynumber: 2.3 Consensus size: 64
341984 AATTTAAAAC
341994 AACAAATCAACTTTTACAAATCAATTAAAAAAGCAAAAAAGAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAAAAAGCAAAAAAGAAGAATTATTTACACATCAATTA
* * *** *
342058 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAAAAAGCAAAAAAGAAGAATTATTTACACATCAATTA
342122 AACAAATCAACTTTTACAAAT
1 AACAAATCAACTTTTACAAAT
342143 ACATCAATTT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 79 1.00
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.28
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAAAAAGCAAAAAAGAAGAATTATTTACACATCAATTA
Found at i:343231 original size:24 final size:23
Alignment explanation
Indices: 343204--343271 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 23
343194 AGCTCGTATA
343204 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACC-AAGTGCCACGTAG
*
343228 AATTTGTC-CCAAAG-GACCGCGTAG
1 AATTTG-CACC-AAGTG-CCACGTAG
343252 AATTTTGCACCATAGTGCCA
1 AA-TTTGCACCA-AGTGCCA
343272 TATAATATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
23 1 0.03
24 22 0.63
25 11 0.31
26 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (23 bp):
AATTTGCACCAAGTGCCACGTAG
Found at i:343301 original size:48 final size:48
Alignment explanation
Indices: 343206--343301 Score: 108
Period size: 48 Copynumber: 2.0 Consensus size: 48
343196 CTCGTATAAA
* *
343206 TTTGCACCGAAGTGCCACGTAGAATTTGTCCCAAAGGACCGCGTAGAAT
1 TTTGCACCGAAGTGCCAC-TAGAATTTGTCCCAAAGGACCACATAGAAT
*
343255 TTTGCACC-ATAGTGCCA-TATAATATTGT-CCATAAGGACCACATAGAA
1 TTTGCACCGA-AGTGCCACTAGAAT-TTGTCCCA-AAGGACCACATAGAA
343302 ATTCCTTAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
47 8 0.20
48 18 0.44
49 15 0.37
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (48 bp):
TTTGCACCGAAGTGCCACTAGAATTTGTCCCAAAGGACCACATAGAAT
Found at i:343673 original size:34 final size:29
Alignment explanation
Indices: 343594--343665 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
343584 TTTTCTGCAT
343594 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
343623 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
343652 ATTCATGTCATGTA
1 ATTCATGTCATGTA
343666 TCATAATATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATGA
Found at i:350625 original size:30 final size:30
Alignment explanation
Indices: 350580--350638 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
350570 ATCGCGTAGA
* *
350580 CATATTATTTCCATACCTTTATCACATAGG
1 CATATCATTTACATACCTTTATCACATAGG
350610 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
350639 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGG
Found at i:350739 original size:34 final size:29
Alignment explanation
Indices: 350660--350731 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
350650 TTTTCTGCAT
350660 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
350689 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATGA
350718 ATTCATGTCATGTA
1 ATTCATGTCATGTA
350732 TCATAATATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATGA
Found at i:352900 original size:21 final size:20
Alignment explanation
Indices: 352871--352988 Score: 128
Period size: 21 Copynumber: 5.7 Consensus size: 20
352861 GTGAATCGGG
* *
352871 CTCTCGAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGG-C
**
352892 CTCTTGAACGATGAAAAGGGC
1 CTCTTGAACGATG-GGAGGGC
352913 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGGGA-GGGC
* *
352934 CTCTTGAAGGATGAGAGGGGC
1 CTCTTGAACGATGGGA-GGGC
*
352955 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGGGAG-GGC
352976 CTCTTGAACGATG
1 CTCTTGAACGATG
352989 ACAGGTGAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.02
21 76 0.93
22 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.19
Consensus pattern (20 bp):
CTCTTGAACGATGGGAGGGC
Found at i:352937 original size:42 final size:42
Alignment explanation
Indices: 352871--352989 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
352861 GTGAATCGGG
* * *
352871 CTCTCGAACGGTGGGAGGGACCTCTTGAACGATGAAAAGGGC
1 CTCTTGAACGATGGGAGGGGCCTCTTGAACGATGAAAAGGGC
* * *
352913 CTCTTGAACGATGGGAGGGGCCTCTTGAAGGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGCCTCTTGAACGATGAAAAGGGC
* *
352955 CTCTTGAACGATAGGAGAGGCCTCTTGAACGATGA
1 CTCTTGAACGATGGGAGGGGCCTCTTGAACGATGA
352990 CAGGTGAATC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.19
Consensus pattern (42 bp):
CTCTTGAACGATGGGAGGGGCCTCTTGAACGATGAAAAGGGC
Done.