Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008919.1 Hibiscus syriacus cultivar Beakdansim tig00112223_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: 1453011
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 5
Found at i:364797 original size:20 final size:19
Alignment explanation
Indices: 364750--364799 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
364740 AGCCAAGAGC
* *
364750 ATGTATTTTCATTAAAGTT
1 ATGTATTTTCATTAAAATA
* *
364769 GTATATTTTCATTAACAATA
1 ATGTATTTTCATTAA-AATA
364789 ATGTATTTTCA
1 ATGTATTTTCA
364800 AAGAGATTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (19 bp):
ATGTATTTTCATTAAAATA
Found at i:369181 original size:31 final size:33
Alignment explanation
Indices: 369116--369185 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 33
369106 CACCTATTCC
* *
369116 TTCTTTGCTTTCATTCATTTTGCTTTTAACCAT
1 TTCTTTGCTTTCATTCATTTTGCCTTAAACCAT
369149 TTCTTT-CTTTTCATTCA-TTT-CCTTAAACCAT
1 TTCTTTGC-TTTCATTCATTTTGCCTTAAACCAT
369180 TTCTTT
1 TTCTTT
369186 ATCTTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 15 0.44
32 4 0.12
33 15 0.44
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.59
Consensus pattern (33 bp):
TTCTTTGCTTTCATTCATTTTGCCTTAAACCAT
Found at i:370200 original size:17 final size:18
Alignment explanation
Indices: 370169--370202 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
370159 GATGGTCTTG
*
370169 ATGGATGATGTTGATGAA
1 ATGGATGATGGTGATGAA
370187 ATGGA-GATGGTGATGA
1 ATGGATGATGGTGATGA
370203 TGTTGTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (18 bp):
ATGGATGATGGTGATGAA
Found at i:373404 original size:15 final size:14
Alignment explanation
Indices: 373377--373411 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
373367 TATAAAATGG
373377 ATATATTCATCTAT
1 ATATATTCATCTAT
373391 ATATATTACATCTAT
1 ATATATT-CATCTAT
*
373406 AGATAT
1 ATATAT
373412 GATGATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (14 bp):
ATATATTCATCTAT
Found at i:375180 original size:30 final size:30
Alignment explanation
Indices: 375144--375226 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 30
375134 CTAAACCTTC
375144 TTTTCTTTCATTCCTTTTCTTAAAATC-A-TT
1 TTTTCTTTCATT-CTTTTCTTAAAA-CAATTT
*
375174 TTTTCTTTTCATTCATTTCTT-AAACAATTT
1 TTTTC-TTTCATTCTTTTCTTAAAACAATTT
375204 TTTATCTTTCCATTCTTTTCTTA
1 TTT-TCTTT-CATTCTTTTCTTA
375227 TTCTATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
28 1 0.02
29 4 0.09
30 20 0.44
31 20 0.44
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTCTTTCATTCTTTTCTTAAAACAATTT
Found at i:375187 original size:31 final size:31
Alignment explanation
Indices: 375144--375226 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
375134 CTAAACCTTC
375144 TTTTC-TTTCATTCCTTTTCTTAAAATC-A-TT
1 TTTTCTTTTCATT-CTTTTCTTAAAA-CAATTT
*
375174 TTTTCTTTTCATTCATTTCTT-AAACAATTT
1 TTTTCTTTTCATTCTTTTCTTAAAACAATTT
*
375204 TTTATCTTTCCATTCTTTTCTTA
1 TTT-TCTTTTCATTCTTTTCTTA
375227 TTCTATATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 1 0.02
29 4 0.09
30 17 0.38
31 23 0.51
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTCTTTTCATTCTTTTCTTAAAACAATTT
Found at i:389127 original size:22 final size:22
Alignment explanation
Indices: 389086--389132 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
389076 TGTTTCTTCT
*
389086 TTTTGAGTGCTTGATTTTTTTC
1 TTTTGAGTGCTTGATCTTTTTC
389108 TTTTGAGTGCTTGCA-CTTTTTC
1 TTTTGAGTGCTTG-ATCTTTTTC
389130 TTT
1 TTT
389133 CCTGAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.62
Consensus pattern (22 bp):
TTTTGAGTGCTTGATCTTTTTC
Found at i:391311 original size:13 final size:13
Alignment explanation
Indices: 391276--391347 Score: 60
Period size: 13 Copynumber: 5.8 Consensus size: 13
391266 ATGGTAAGGG
*
391276 AATGGTGATAGAA
1 AATGGTGATGGAA
*
391289 GATGGTGATGGAA
1 AATGGTGATGGAA
**
391302 AATGGTGATGTTA
1 AATGGTGATGGAA
* *
391315 TA-GGCG-T-GAA
1 AATGGTGATGGAA
391325 AATGGTGATGGAA
1 AATGGTGATGGAA
*
391338 GATGGTGATG
1 AATGGTGATG
391348 AACAGATAGT
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 2 0.05
11 4 0.09
12 4 0.09
13 34 0.77
ACGTcount: A:0.33, C:0.01, G:0.39, T:0.26
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:395264 original size:29 final size:26
Alignment explanation
Indices: 395221--395289 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 26
395211 TATATTGTGC
*
395221 TTTTCTTTATACTTTGCAACTTTCTTCACT
1 TTTTCTTT-TTCTTTG-AA-TTT-TTCACT
**
395251 TTTTCTTTTTCTTTGAATTTTTCTTT
1 TTTTCTTTTTCTTTGAATTTTTCACT
395277 TTTTC-TTTTCTTT
1 TTTTCTTTTTCTTT
395290 CTTTTGCACT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 8 0.22
26 9 0.25
27 3 0.08
28 2 0.06
29 6 0.17
30 8 0.22
ACGTcount: A:0.10, C:0.17, G:0.03, T:0.70
Consensus pattern (26 bp):
TTTTCTTTTTCTTTGAATTTTTCACT
Found at i:395734 original size:35 final size:35
Alignment explanation
Indices: 395695--395805 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
395685 AATAGTTATT
* * **
395695 ATATAAGCGTGAAATGGGGATACAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
* *
395730 ATATAGGCGTGCAATGGTGATGGAAAATGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
* *
395765 TTATAGGTGTGAAAATGGTGATGGAAGATGGTGATG
1 ATATAGGCGTG-AAATGGTGATGGAAGATGGTGATG
395801 A-ATAG
1 ATATAG
395806 ATAGTATCTT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 42 0.66
36 22 0.34
ACGTcount: A:0.34, C:0.04, G:0.36, T:0.26
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTGATG
Found at i:395760 original size:13 final size:13
Alignment explanation
Indices: 395742--395800 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
395732 ATAGGCGTGC
395742 AATGGTGATGGAA
1 AATGGTGATGGAA
**
395755 AATGGTGATGTTA
1 AATGGTGATGGAA
*
395768 TA-GGTG-T-GAA
1 AATGGTGATGGAA
395778 AATGGTGATGGAA
1 AATGGTGATGGAA
*
395791 GATGGTGATG
1 AATGGTGATG
395801 AATAGATAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 5 0.14
13 24 0.67
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:403796 original size:5 final size:5
Alignment explanation
Indices: 403786--403851 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
403776 GAACTTCTCT
* * ** *
403786 TTTTC TTTTC TTTTC TTTTT TTCTTT TTTTC TGAT- TTTTC TCTTC -TTT-
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTTC
403834 TTTTC TTTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTT
403852 TGCACTCTGA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
4 11 0.23
5 32 0.67
6 5 0.10
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:403807 original size:8 final size:8
Alignment explanation
Indices: 403780--403852 Score: 62
Period size: 8 Copynumber: 9.0 Consensus size: 8
403770 CCTTTTGAAC
*
403780 TTCTCTTT
1 TTCTTTTT
403788 TTCTTTTCTT
1 TTC-TTT-TT
403798 TTCTTTTT
1 TTCTTTTT
403806 TTCTTTTT
1 TTCTTTTT
*
403814 TTCTGATTT
1 TTCT-TTTT
*
403823 TTC---TC
1 TTCTTTTT
403828 TTCTTTTT
1 TTCTTTTT
403836 TTCTTTTCT
1 TTCTTTT-T
403845 TTCTTTTT
1 TTCTTTTT
403853 GCACTCTGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
5 4 0.07
8 26 0.48
9 19 0.35
10 5 0.09
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (8 bp):
TTCTTTTT
Found at i:403823 original size:17 final size:17
Alignment explanation
Indices: 403780--403851 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 17
403770 CCTTTTGAAC
*
403780 TTCTCTTTTTCTTTTCTT
1 TTCTATTTTTC-TTTCTT
*
403798 TTCTTTTTTTCTTT-TT
1 TTCTATTTTTCTTTCTT
403814 TTCTGATTTTTCTCTTCTT
1 TTCT-ATTTTTCT-TTCTT
*
403833 TT-TTTCTTTTCTTTCTT
1 TTCTAT-TTTTCTTTCTT
403850 TT
1 TT
403852 TGCACTCTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
16 6 0.13
17 18 0.38
18 19 0.40
19 4 0.09
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (17 bp):
TTCTATTTTTCTTTCTT
Found at i:403832 original size:30 final size:31
Alignment explanation
Indices: 403791--403848 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
403781 TCTCTTTTTC
*
403791 TTTTCTTTTCTTTTTTTCTTTT-TTTCTGAT
1 TTTTCTCTTCTTTTTTTCTTTTCTTTCTGAT
403821 TTTTCTCTTCTTTTTTTCTTTTCTTTCT
1 TTTTCTCTTCTTTTTTTCTTTTCTTTCT
403849 TTTTGCACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (31 bp):
TTTTCTCTTCTTTTTTTCTTTTCTTTCTGAT
Found at i:409820 original size:2 final size:2
Alignment explanation
Indices: 409809--409858 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
409799 TAACTATAGG
409809 TA TA -A 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
409850 TA TA TA TA T
1 TA TA TA TA T
409859 GAAAATAACT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:418948 original size:8 final size:8
Alignment explanation
Indices: 418921--419015 Score: 52
Period size: 8 Copynumber: 11.0 Consensus size: 8
418911 CCTTTTGAAA
*
418921 TTCTCTTT
1 TTCTTTTT
418929 TTCTTTTCTT
1 TTC-TTT-TT
418939 TTCTTTTT
1 TTCTTTTT
418947 TTCTTTTT
1 TTCTTTTT
*
418955 TTCTGATTT
1 TTCT-TTTT
*
418964 TTC---TC
1 TTCTTTTT
418969 TTCTTTTT
1 TTCTTTTT
418977 TTCTGATTTT
1 TTCT--TTTT
418987 TCTCTTCTTTT
1 T-TC-T-TTTT
418998 TGTCTTTTCT
1 T-TCTTTT-T
419008 TTCTTTTT
1 TTCTTTTT
419016 GCACTCTAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 22
0.71 0.06 0.22
Matches are distributed among these distances:
5 4 0.06
8 23 0.33
9 20 0.29
10 13 0.19
11 9 0.13
12 1 0.01
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (8 bp):
TTCTTTTT
Found at i:418964 original size:17 final size:17
Alignment explanation
Indices: 418921--419014 Score: 66
Period size: 18 Copynumber: 5.1 Consensus size: 17
418911 CCTTTTGAAA
*
418921 TTCTCTTTTTCTTTTCTT
1 TTCTATTTTTC-TTTCTT
*
418939 TTCTTTTTTTCTTT-TT
1 TTCTATTTTTCTTTCTT
418955 TTCTGATTTTTCTCTTCTTTTT
1 TTCT-ATTTTTCT-TTC---TT
418977 TTCTGATTTTTCTCTTCTT
1 TTCT-ATTTTTCT-TTCTT
*
418996 TT-TGTCTTTTCTTTCTT
1 TTCTAT-TTTTCTTTCTT
419013 TT
1 TT
419015 TGCACTCTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 15
0.79 0.04 0.18
Matches are distributed among these distances:
16 6 0.09
17 18 0.27
18 19 0.29
19 4 0.06
22 19 0.29
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (17 bp):
TTCTATTTTTCTTTCTT
Found at i:418973 original size:30 final size:31
Alignment explanation
Indices: 418932--418989 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
418922 TCTCTTTTTC
* *
418932 TTTTCTTTTCTTTTTTTCT-TTTTTTCTGAT
1 TTTTCTCTTCTTTTTTTCTGATTTTTCTGAT
418962 TTTTCTCTTCTTTTTTTCTGATTTTTCT
1 TTTTCTCTTCTTTTTTTCTGATTTTTCT
418990 CTTCTTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (31 bp):
TTTTCTCTTCTTTTTTTCTGATTTTTCTGAT
Found at i:419011 original size:22 final size:22
Alignment explanation
Indices: 418947--418998 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
418937 TTTTCTTTTT
418947 TTCTTTTTTTCTGATTTTTCTC
1 TTCTTTTTTTCTGATTTTTCTC
418969 TTCTTTTTTTCTGATTTTTCTC
1 TTCTTTTTTTCTGATTTTTCTC
418991 TTCTTTTT
1 TTCTTTTT
418999 GTCTTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (22 bp):
TTCTTTTTTTCTGATTTTTCTC
Found at i:424943 original size:35 final size:34
Alignment explanation
Indices: 424839--424944 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 34
424829 CTACCTAAAC
424839 ATCACCATCTTCCATCACCATTTTCACGCCTATAAT
1 ATCACCATCTTCCATCACCA-TTTCACGCCTAT-AT
* * *
424875 ATCACCATCTTCCATTACCATTGCATGCCTATAT
1 ATCACCATCTTCCATCACCATTTCACGCCTATAT
* * *
424909 GATTACCATCTTCTAGCACCATTTCACGCCTATAT
1 -ATCACCATCTTCCATCACCATTTCACGCCTATAT
424944 A
1 A
424945 ACTACCAATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
34 3 0.05
35 38 0.63
36 19 0.32
ACGTcount: A:0.27, C:0.33, G:0.06, T:0.34
Consensus pattern (34 bp):
ATCACCATCTTCCATCACCATTTCACGCCTATAT
Found at i:430421 original size:35 final size:35
Alignment explanation
Indices: 430380--430493 Score: 131
Period size: 35 Copynumber: 3.2 Consensus size: 35
430370 TGGTAAGGGA
** *
430380 ATGGTGATTATATATAAGTGAAATGGTGATAGAAG
1 ATGGTGATTATATAGGAGTGAAATGGTGATGGAAG
* * * *
430415 ATGGTGATGATATAGGCGTGCAATGGTGATGGAAA
1 ATGGTGATTATATAGGAGTGAAATGGTGATGGAAG
*
430450 ATGGTGATGT-TATAGGTGTGAAAATGGTGATGGAAG
1 ATGGTGAT-TATATAGGAGTG-AAATGGTGATGGAAG
430486 ATGGTGAT
1 ATGGTGAT
430494 GAATAGATAG
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
35 45 0.68
36 21 0.32
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (35 bp):
ATGGTGATTATATAGGAGTGAAATGGTGATGGAAG
Found at i:430454 original size:13 final size:13
Alignment explanation
Indices: 430436--430494 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
430426 ATAGGCGTGC
430436 AATGGTGATGGAA
1 AATGGTGATGGAA
**
430449 AATGGTGATGTTA
1 AATGGTGATGGAA
*
430462 TA-GGTG-T-GAA
1 AATGGTGATGGAA
430472 AATGGTGATGGAA
1 AATGGTGATGGAA
*
430485 GATGGTGATG
1 AATGGTGATG
430495 AATAGATAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 5 0.14
13 24 0.67
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:436618 original size:24 final size:21
Alignment explanation
Indices: 436591--436636 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
436581 AGAATTGTTG
436591 TTGAGTGCTTACAAATTTCTTCTT
1 TTGAGTG-TTAC-AATTT-TTCTT
*
436615 TTGAGTGTTTCAATTTTTCTT
1 TTGAGTGTTACAATTTTTCTT
436636 T
1 T
436637 GTTGAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 5 0.24
23 3 0.14
24 7 0.33
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (21 bp):
TTGAGTGTTACAATTTTTCTT
Found at i:439421 original size:22 final size:22
Alignment explanation
Indices: 439395--439436 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
439385 TATTTATAGT
*
439395 TATGATGATGATATTATGAATG
1 TATGAAGATGATATTATGAATG
* *
439417 TATGAAGTTGTTATTATGAA
1 TATGAAGATGATATTATGAA
439437 CCACATATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (22 bp):
TATGAAGATGATATTATGAATG
Found at i:456805 original size:15 final size:14
Alignment explanation
Indices: 456778--456808 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
456768 TATAACATGG
456778 ATATATTCATCTAT
1 ATATATTCATCTAT
456792 ATATATTACATCTAT
1 ATATATT-CATCTAT
456807 AT
1 AT
456809 CTATGATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATTCATCTAT
Found at i:458607 original size:32 final size:32
Alignment explanation
Indices: 458565--458646 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
458555 TTCCTTCTTT
458565 TCTTTCATTCATTTTCTTAAAACCATTTATTTA
1 TCTTTCATTCATTTTCTT-AAACCATTTATTTA
* *
458598 T-TTTCATTCATTTCCTTAAACCATTTCTTTA
1 TCTTTCATTCATTTTCTTAAACCATTTATTTA
458629 TCTTTCCATTC-TTTTCTT
1 TCTTT-CATTCATTTTCTT
458647 CTTCCAGCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
31 14 0.32
32 24 0.55
33 6 0.14
ACGTcount: A:0.21, C:0.22, G:0.00, T:0.57
Consensus pattern (32 bp):
TCTTTCATTCATTTTCTTAAACCATTTATTTA
Found at i:462832 original size:23 final size:23
Alignment explanation
Indices: 462805--462866 Score: 92
Period size: 22 Copynumber: 2.7 Consensus size: 23
462795 AAAGTGAAGA
462805 ACTCAAAAGAAAGAAAAATCAGC
1 ACTCAAAAGAAAGAAAAATCAGC
462828 ACTCAAAAGAAAG-AAAATCAGC
1 ACTCAAAAGAAAGAAAAATCAGC
*
462850 GCTCAAAA-AGAAGAAAA
1 ACTCAAAAGA-AAGAAAA
462867 GCAAAGAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 1 0.03
22 19 0.53
23 16 0.44
ACGTcount: A:0.61, C:0.16, G:0.15, T:0.08
Consensus pattern (23 bp):
ACTCAAAAGAAAGAAAAATCAGC
Found at i:464193 original size:24 final size:21
Alignment explanation
Indices: 464159--464201 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
464149 TTTTGGTGAT
*
464159 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
464181 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
464202 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:474406 original size:19 final size:20
Alignment explanation
Indices: 474380--474427 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
474370 ATTTTTTTCT
* *
474380 CAAAAAAAATAAGAAAAAGG
1 CAAAAAAAAAAAGAAAAAGC
474400 CAAAAAAAAAAAGAAAAAGC
1 CAAAAAAAAAAAGAAAAAGC
474420 CAAAAAAA
1 CAAAAAAA
474428 GTCAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.79, C:0.08, G:0.10, T:0.02
Consensus pattern (20 bp):
CAAAAAAAAAAAGAAAAAGC
Found at i:481496 original size:17 final size:17
Alignment explanation
Indices: 481431--481526 Score: 81
Period size: 17 Copynumber: 5.5 Consensus size: 17
481421 CACTTCGTTG
481431 ATTAAACTAGTTCATTCAA
1 ATTAAACTAGTTCATT--A
*
481450 GATT--ACAAGTTCATTGA
1 -ATTAAACTAGTTCATT-A
*
481467 A-TAAATTTAGTTCATTA
1 ATTAAA-CTAGTTCATTA
*
481484 ATTAAACTAGTTCATTC
1 ATTAAACTAGTTCATTA
* *
481501 ATCAAACTAGTTCATTT
1 ATTAAACTAGTTCATTA
481518 ATTAAACTA
1 ATTAAACTA
481527 ACTTTTAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
15 1 0.02
16 1 0.02
17 36 0.57
18 22 0.35
20 3 0.05
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (17 bp):
ATTAAACTAGTTCATTA
Found at i:484261 original size:15 final size:15
Alignment explanation
Indices: 484250--484278 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
484240 ACTCAAAAAG
484250 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
484265 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
484279 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:488390 original size:21 final size:22
Alignment explanation
Indices: 488365--488405 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
488355 GGAGTGTTTG
488365 GTGAGGTT-TTTCCTTTTATTT
1 GTGAGGTTATTTCCTTTTATTT
*
488386 GTGAGGTTATTTCTTTTTAT
1 GTGAGGTTATTTCCTTTTAT
488406 AACTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.12, C:0.07, G:0.20, T:0.61
Consensus pattern (22 bp):
GTGAGGTTATTTCCTTTTATTT
Found at i:490271 original size:29 final size:29
Alignment explanation
Indices: 490238--490306 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
490228 TGAAATTAGG
*
490238 AAGGAAATGAAATGATAGTGAAAAGATGA
1 AAGGAAATGAAATGATAATGAAAAGATGA
490267 AAGGAAATGAAATGATAATGAAAAGATGA
1 AAGGAAATGAAATGATAATGAAAAGATGA
490296 AAGGAAA-GAAA
1 AAGGAAATGAAA
490307 AGGTTATCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 4 0.10
29 35 0.90
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.14
Consensus pattern (29 bp):
AAGGAAATGAAATGATAATGAAAAGATGA
Found at i:501104 original size:23 final size:23
Alignment explanation
Indices: 501064--501108 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
501054 ATATATATAT
501064 ATATGAAAATAACTATCTTATAAC
1 ATATGAAAATAACTATC-TATAAC
501088 ATATG-AAATAAGC-ATCTATAA
1 ATATGAAAATAA-CTATCTATAA
501109 GTATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (23 bp):
ATATGAAAATAACTATCTATAAC
Found at i:501850 original size:17 final size:17
Alignment explanation
Indices: 501815--501850 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
501805 TTACATCGGC
*
501815 TATAGAAATGGTTAGGG
1 TATAGAAATGGATAGGG
*
501832 TATAGAAATGGATATGG
1 TATAGAAATGGATAGGG
501849 TA
1 TA
501851 GGATAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (17 bp):
TATAGAAATGGATAGGG
Found at i:502073 original size:25 final size:24
Alignment explanation
Indices: 502045--502097 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
502035 TTTGAGCGTA
502045 CTTTGCAACTTT-TTCTTTTCTTTTT
1 CTTTG-AACTTTCTTCTTTTC-TTTT
*
502070 CTTTGAATTTTCTTCTTTTCTTTT
1 CTTTGAACTTTCTTCTTTTCTTTT
502094 CTTT
1 CTTT
502098 CTCTTGTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.08, C:0.19, G:0.04, T:0.70
Consensus pattern (24 bp):
CTTTGAACTTTCTTCTTTTCTTTT
Found at i:502138 original size:6 final size:6
Alignment explanation
Indices: 502127--502171 Score: 65
Period size: 6 Copynumber: 7.3 Consensus size: 6
502117 ATGTATGAGT
502127 TTTTTC TTTTTC TTTTTC TTTTTAC -TTTTC TTCTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTT-C TTTTTC TT-TTTC TTTTTC TT
502172 GTTTGATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.03
6 28 0.78
7 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:512574 original size:17 final size:18
Alignment explanation
Indices: 512547--512582 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
512537 TTGCGTCGGC
*
512547 TATAGGAAATGGTTATGG
1 TATAGGAAATGGATATGG
512565 TATA-GAAATGGATATGG
1 TATAGGAAATGGATATGG
512582 T
1 T
512583 CAAGGTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (18 bp):
TATAGGAAATGGATATGG
Found at i:513233 original size:35 final size:35
Alignment explanation
Indices: 513188--513300 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 35
513178 TTATAAGGGA
*
513188 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
* *
513223 ATGGTGATGATATAGGCATGACATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
* ** *
513258 ATGGTGATGTTATATACGTGAAAATAGTGATGGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATGGAAG
513294 ATGGTGA
1 ATGGTGA
513301 CGAACAAATA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 48 0.71
36 20 0.29
ACGTcount: A:0.34, C:0.04, G:0.35, T:0.27
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
Found at i:517714 original size:28 final size:28
Alignment explanation
Indices: 517683--517736 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
517673 AATTGCAACT
517683 TTTCTTCACTTTC-TTCTTTTGCTTTTAA
1 TTTCTTC-CTTTCTTTCTTTTGCTTTTAA
* *
517711 TTTCTTCTTTTCTTTCTTTTTCTTTT
1 TTTCTTCCTTTCTTTCTTTTGCTTTT
517737 TGTACTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.72
Consensus pattern (28 bp):
TTTCTTCCTTTCTTTCTTTTGCTTTTAA
Found at i:522680 original size:17 final size:17
Alignment explanation
Indices: 522658--522710 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
522648 TGAATAAAGT
522658 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
522675 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
522692 TAGTTCATTTAA-TAAAC
1 TAGTTCA-TTAATTAAAC
522709 TA
1 TA
522711 ATTCTTGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 28 0.90
18 3 0.10
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:526474 original size:17 final size:16
Alignment explanation
Indices: 526433--526504 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 16
526423 ATTCATGCAT
526433 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
*
526450 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
*
526468 CTAGTTCATTCATCAAA
1 CTAGTTCATTAAT-AAA
526485 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
526502 CTA
1 CTA
526505 ACTCTTAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
16 1 0.02
17 29 0.62
18 17 0.36
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:529590 original size:24 final size:24
Alignment explanation
Indices: 529563--529615 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
529553 TCAAAACATC
529563 AAGAGACATGTCTTGTGAATCACA
1 AAGAGACATGTCTTGTGAATCACA
* *
529587 AAGAGACATGTCTTGTGGATCACG
1 AAGAGACATGTCTTGTGAATCACA
529611 AAGAG
1 AAGAG
529616 TCACTCCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (24 bp):
AAGAGACATGTCTTGTGAATCACA
Found at i:530957 original size:30 final size:29
Alignment explanation
Indices: 530923--530988 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
530913 TTTGAGAATA
*
530923 TTTTGCATATT-TTCTTTTCCTTTCTTTTGT
1 TTTTGCAT-TTCTTCTTTTCCTTTC-TTTCT
* *
530953 TTTTGAATTTCTTCTTTTCTTTTCTTTCT
1 TTTTGCATTTCTTCTTTTCCTTTCTTTCT
530982 TTTTGCA
1 TTTTGCA
530989 CTCCAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.08, C:0.17, G:0.06, T:0.70
Consensus pattern (29 bp):
TTTTGCATTTCTTCTTTTCCTTTCTTTCT
Found at i:531042 original size:13 final size:12
Alignment explanation
Indices: 531018--531050 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
531008 GTCTTTTCTC
531018 TTTCTTTTTGTT
1 TTTCTTTTTGTT
531030 TTTCTTCTTTGTT
1 TTTCTT-TTTGTT
531043 TTTCTTTT
1 TTTCTTTT
531051 GTTACAGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (12 bp):
TTTCTTTTTGTT
Found at i:531044 original size:19 final size:18
Alignment explanation
Indices: 531011--531050 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
531001 TGTAGGAGTC
*
531011 TTTTCTCTTTCTTTTTGT
1 TTTTCTCTTTCTTTTTCT
*
531029 TTTTCTTCTTTGTTTTTCT
1 TTTTC-TCTTTCTTTTTCT
531048 TTT
1 TTT
531051 GTTACAGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTCTCTTTCTTTTTCT
Found at i:531392 original size:11 final size:12
Alignment explanation
Indices: 531375--531407 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
531365 AGGATGGCAT
531375 TATGGTGATGGA
1 TATGGTGATGGA
531387 -ATGGTGATGGA
1 TATGGTGATGGA
*
531398 TATGATGATG
1 TATGGTGATG
531408 TTGTAGGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.27, C:0.00, G:0.39, T:0.33
Consensus pattern (12 bp):
TATGGTGATGGA
Found at i:542359 original size:17 final size:17
Alignment explanation
Indices: 542337--542373 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
542327 AGCTTGTGAG
542337 CTAGTTCATTCATCAAA
1 CTAGTTCATTCATCAAA
* *
542354 CTAGTTCATTTATTAAA
1 CTAGTTCATTCATCAAA
542371 CTA
1 CTA
542374 ACTCTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (17 bp):
CTAGTTCATTCATCAAA
Found at i:545780 original size:6 final size:6
Alignment explanation
Indices: 545769--545811 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
545759 GTGCTACAAC
*
545769 AAAAAG AAAAAG AAAAATTAA AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG -AAAA--AG AAAAAG AAAAAG AAAAAG AAAA
545812 GAATCCTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 23 0.72
7 4 0.12
8 4 0.12
9 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:545858 original size:11 final size:11
Alignment explanation
Indices: 545842--545872 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
545832 AGTGCAAAAG
545842 AAAGAAAAGAA
1 AAAGAAAAGAA
545853 AAAGAAAAGAA
1 AAAGAAAAGAA
545864 AAAGAAAAG
1 AAAGAAAAG
545873 CGAAGCAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:546030 original size:5 final size:5
Alignment explanation
Indices: 546020--546055 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
546010 TTTTCTCTTT
*
546020 ATTTC ATTTC ATTTC CTCTTC ATTTC ATTTC ATTTC
1 ATTTC ATTTC ATTTC AT-TTC ATTTC ATTTC ATTTC
546056 CTTTTCATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTTC
Found at i:546032 original size:21 final size:21
Alignment explanation
Indices: 546006--546064 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
545996 GTAAGTTGTC
* *
546006 TTCATTTTCTCTTTATTTCAT
1 TTCATTTCCTCTTCATTTCAT
546027 TTCATTTCCTCTTCATTTCAT
1 TTCATTTCCTCTTCATTTCAT
*
546048 TTCATTTCCTTTTCATT
1 TTCATTTCCTCTTCATT
546065 CATCTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.63
Consensus pattern (21 bp):
TTCATTTCCTCTTCATTTCAT
Found at i:546061 original size:16 final size:16
Alignment explanation
Indices: 546006--546064 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
545996 GTAAGTTGTC
*
546006 TTCATTTTC-TCTTTAT
1 TTCATTTTCAT-TTCAT
*
546022 TTCA-TTTCATTTCCT
1 TTCATTTTCATTTCAT
546037 CTTCA-TTTCATTTCAT
1 -TTCATTTTCATTTCAT
*
546053 TTCCTTTTCATT
1 TTCATTTTCATT
546065 CATCTTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 10 0.28
16 26 0.72
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.63
Consensus pattern (16 bp):
TTCATTTTCATTTCAT
Found at i:550134 original size:15 final size:15
Alignment explanation
Indices: 550097--550126 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
550087 GTGCTTCAAC
550097 TTTCTTTG-TTTTCT
1 TTTCTTTGATTTTCT
550111 TTTCTTTGATTTTCT
1 TTTCTTTGATTTTCT
550126 T
1 T
550127 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.03, C:0.13, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTCTTTGATTTTCT
Found at i:556405 original size:21 final size:21
Alignment explanation
Indices: 556381--556420 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
556371 GAAACGAGAG
556381 TTGAAAA-AGACATTGAGAGCA
1 TTGAAAAGAGA-ATTGAGAGCA
556402 TTGAAAAGAGAATTGAGAG
1 TTGAAAAGAGAATTGAGAG
556421 TGAAAATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.20
Consensus pattern (21 bp):
TTGAAAAGAGAATTGAGAGCA
Found at i:561189 original size:21 final size:20
Alignment explanation
Indices: 561165--561216 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
561155 GAAACCCCTT
561165 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGA-TTTTAAA
*
561186 TGAAAATACATTATTTTAAA
1 TGAAAATACATGATTTTAAA
*
561206 -GAAGATACATG
1 TGAAAATACATG
561217 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 9 0.32
20 7 0.25
21 12 0.43
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:562034 original size:26 final size:25
Alignment explanation
Indices: 562005--562053 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
561995 ATAATATCAG
*
562005 CTAAGTATATGAATTATTATAAAGTA
1 CTAAGAATATGAA-TATTATAAAGTA
* *
562031 CTAAGAATGTGCATATTATAAAG
1 CTAAGAATATGAATATTATAAAG
562054 ATATGAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (25 bp):
CTAAGAATATGAATATTATAAAGTA
Found at i:564413 original size:13 final size:13
Alignment explanation
Indices: 564365--564429 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
564355 TTTGAAATTC
564365 TTCTATTTTTT-TT
1 TTCT-TTTTTTATT
* *
564378 TTCTTTTCTTATA
1 TTCTTTTTTTATT
564391 TTCTGATTTTTTATT
1 TTCT--TTTTTTATT
* *
564406 TTCTTTTTGTCTT
1 TTCTTTTTTTATT
564419 TTCTTTCTTTT
1 TTCTTT-TTTT
564430 TGCACTCCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
12 5 0.12
13 22 0.54
14 3 0.07
15 11 0.27
ACGTcount: A:0.08, C:0.12, G:0.03, T:0.77
Consensus pattern (13 bp):
TTCTTTTTTTATT
Found at i:564790 original size:20 final size:21
Alignment explanation
Indices: 564753--564791 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
564743 GATGGTCTTG
*
564753 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
564774 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
564792 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:573927 original size:25 final size:25
Alignment explanation
Indices: 573884--573933 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
573874 TCTTGGCTTG
573884 CTTTCTCTTTTTGAATTTTCTTTTT
1 CTTTCTCTTTTTGAATTTTCTTTTT
* *
573909 CTTT-TCTTTTCTGACTTTTTTTTTT
1 CTTTCTCTTTT-TGAATTTTCTTTTT
573934 GCACTCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.74
Consensus pattern (25 bp):
CTTTCTCTTTTTGAATTTTCTTTTT
Found at i:582067 original size:17 final size:17
Alignment explanation
Indices: 582024--582071 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
582014 AAGATAGTGA
*
582024 AATAAGAAAATACGAAAG
1 AATAAGAAAA-ATGAAAG
582042 AATAA-AAAAATGAAATG
1 AATAAGAAAAATGAAA-G
582059 -ATAAGAAAAATGA
1 AATAAGAAAAATGA
582072 TGATAACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.33
17 13 0.48
18 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.15, T:0.15
Consensus pattern (17 bp):
AATAAGAAAAATGAAAG
Found at i:593507 original size:15 final size:15
Alignment explanation
Indices: 593477--593518 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
593467 GGATAATTAA
593477 GAAAGGAAATTGAAATG
1 GAAA-GAAA-TGAAATG
593494 GAAAGAAATGAAATG
1 GAAAGAAATGAAATG
*
593509 GATAGAAATG
1 GAAAGAAATG
593519 TTATCAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 16 0.67
16 4 0.17
17 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.17
Consensus pattern (15 bp):
GAAAGAAATGAAATG
Found at i:600622 original size:16 final size:15
Alignment explanation
Indices: 600590--600638 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
600580 TGATTAATTG
600590 GAAA-AAAAT-GAAA
1 GAAATAAAATGGAAA
* *
600603 GAAATAGAATTGATAA
1 GAAATAAAATGGA-AA
600619 GAAATAAAATGGAAA
1 GAAATAAAATGGAAA
600634 GAAAT
1 GAAAT
600639 TATATCAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 9 0.30
16 13 0.43
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.16
Consensus pattern (15 bp):
GAAATAAAATGGAAA
Found at i:600637 original size:15 final size:14
Alignment explanation
Indices: 600590--600638 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
600580 TGATTAATTG
600590 GAAA-AAAATGAAA
1 GAAATAAAATGAAA
*
600603 GAAATAGAATTGATAA
1 GAAATA-AAATGA-AA
600619 GAAATAAAATGGAAA
1 GAAATAAAAT-GAAA
600634 GAAAT
1 GAAAT
600639 TATATCAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 4 0.13
14 1 0.03
15 15 0.50
16 10 0.33
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.16
Consensus pattern (14 bp):
GAAATAAAATGAAA
Found at i:606548 original size:2 final size:2
Alignment explanation
Indices: 606532--606599 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
606522 TCATAATAAC
*
606532 TA TA GA TA TA T- 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
606573 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 T
606600 GTTAATAACT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:612561 original size:24 final size:25
Alignment explanation
Indices: 612534--612580 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
612524 GATGTAGGAG
* *
612534 TCTTTTTTC-TTTTCTTTTTGTTTT
1 TCTTCTTTCATTTGCTTTTTGTTTT
612558 TCTTCTTTCATTTGCTTTTTGTT
1 TCTTCTTTCATTTGCTTTTTGTT
612581 GCAACACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (25 bp):
TCTTCTTTCATTTGCTTTTTGTTTT
Found at i:616739 original size:13 final size:13
Alignment explanation
Indices: 616701--616741 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
616691 GATGTATGAG
*
616701 TCTTTTTTC-TTT
1 TCTTCTTTCATTT
*
616713 TCTTC-TTGATTT
1 TCTTCTTTCATTT
616725 TCTTCTTTCATTT
1 TCTTCTTTCATTT
616738 TCTT
1 TCTT
616742 TTTGTTGCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 2 0.08
12 12 0.50
13 10 0.42
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (13 bp):
TCTTCTTTCATTT
Found at i:616979 original size:15 final size:14
Alignment explanation
Indices: 616935--616982 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 14
616925 TTGGAATTAA
616935 GAAATGAAAGAAAT
1 GAAATGAAAGAAAT
616949 GGAAATTGATAAGAAAT
1 -GAAA-TGA-AAGAAAT
616966 GAAATGGAAAGAAAT
1 GAAAT-GAAAGAAAT
616981 GA
1 GA
616983 TATCAAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 14 0.47
16 9 0.30
17 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (14 bp):
GAAATGAAAGAAAT
Found at i:616979 original size:26 final size:24
Alignment explanation
Indices: 616932--616984 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
616922 TAATTGGAAT
616932 TAAGAAATGAAAGAAATGGAAATTGA
1 TAAGAAATGAAAGAAA-GGAAA-TGA
616958 TAAGAAATGAAATGGAAA-GAAATGA
1 TAAGAAATGAAA--GAAAGGAAATGA
616983 TA
1 TA
616985 TCAAGGTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 5 0.20
26 16 0.64
28 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (24 bp):
TAAGAAATGAAAGAAAGGAAATGA
Found at i:630768 original size:19 final size:19
Alignment explanation
Indices: 630746--630782 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
630736 AACTTAATTT
*
630746 TTTTGATGAAAATACATGA
1 TTTTAATGAAAATACATGA
*
630765 TTTTAATGAAGATACATG
1 TTTTAATGAAAATACATG
630783 CTCTTGGCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:630983 original size:21 final size:21
Alignment explanation
Indices: 630950--631001 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
630940 TGCTTGAATG
630950 ATGCACATGGAAGCCTACATGA
1 ATGCACAT-GAAGCCTACATGA
*
630972 ATGCACATGAAGCCTATATGA
1 ATGCACATGAAGCCTACATGA
630993 ATGCACATG
1 ATGCACATG
631002 GTCTTCTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (21 bp):
ATGCACATGAAGCCTACATGA
Found at i:632893 original size:13 final size:13
Alignment explanation
Indices: 632839--632897 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 13
632829 ACTATATGTT
*
632839 CATCACCATCTTC
1 CATCACCATTTTC
632852 CATCACCATTTT-
1 CATCACCATTTTC
* * **
632864 CA-CGCC-TATAA
1 CATCACCATTTTC
632875 CATCACCATTTTC
1 CATCACCATTTTC
632888 CATCACCATT
1 CATCACCATT
632898 GCACGCCTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 5 0.14
13 23 0.66
ACGTcount: A:0.27, C:0.39, G:0.02, T:0.32
Consensus pattern (13 bp):
CATCACCATTTTC
Found at i:632914 original size:35 final size:35
Alignment explanation
Indices: 632838--632953 Score: 169
Period size: 35 Copynumber: 3.3 Consensus size: 35
632828 TACTATATGT
632838 TCATCACCATCTTCCATCACCATTTTCACGCCTATA
1 TCATCACCATCTTCCATCACCA-TTTCACGCCTATA
* * *
632874 ACATCACCATTTTCCATCACCATTGCACGCCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
* *
632909 TCATCACCATCTTCTATTACCATTTCACGCCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
*
632944 TAATCACCAT
1 TCATCACCAT
632954 TCCCTTACCA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 51 0.72
36 20 0.28
ACGTcount: A:0.28, C:0.36, G:0.03, T:0.33
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTTCACGCCTATA
Found at i:633773 original size:13 final size:13
Alignment explanation
Indices: 633755--633779 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
633745 AATCGAGCGA
633755 AAAATGGTGATGG
1 AAAATGGTGATGG
633768 AAAATGGTGATG
1 AAAATGGTGATG
633780 TTATAGGCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (13 bp):
AAAATGGTGATGG
Found at i:635800 original size:19 final size:20
Alignment explanation
Indices: 635776--635826 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
635766 CAGCCAAGAG
* *
635776 CATGTATCTTCCT-TAAAAT
1 CATGTATCTTCATCAAAAAT
*
635795 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
*
635815 CATGTATTTTCA
1 CATGTATCTTCA
635827 AAGGGGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:636583 original size:13 final size:12
Alignment explanation
Indices: 636536--636592 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 12
636526 GTGCAAAAAG
*
636536 AAAGAAAAAGACA
1 AAAG-AAAAGAAA
*
636549 AAAGAAGAGAAA
1 AAAGAAAAGAAA
636561 AATCAGAAAAGAAGA
1 AA--AGAAAAGAA-A
636576 AAAGAAAAGAAA
1 AAAGAAAAGAAA
636588 AAAGA
1 AAAGA
636593 GAAGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 14 0.37
13 13 0.34
14 8 0.21
15 3 0.08
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:636595 original size:27 final size:26
Alignment explanation
Indices: 636536--636595 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
636526 GTGCAAAAAG
*
636536 AAAGA-AAAAGACAAAAGAAGAGAAA
1 AAAGAGAAAAGACAAAAGAAAAGAAA
** *
636561 AATCAGAAAAGAAGAAAAGAAAAGAAA
1 AAAGAGAAAAG-ACAAAAGAAAAGAAA
636588 AAAGAGAA
1 AAAGAGAA
636596 GTTCAAAAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
25 3 0.11
26 5 0.19
27 19 0.70
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (26 bp):
AAAGAGAAAAGACAAAAGAAAAGAAA
Found at i:637910 original size:24 final size:24
Alignment explanation
Indices: 637830--637911 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
637820 GACCTTCGGT
* * *
637830 GTTCCACAAGACATGTCATTTGAC
1 GTTCCAAAAGACATGTCACTTGAA
* ** *
637854 GTTCCAACAGTTATGCCACTTGAA
1 GTTCCAAAAGACATGTCACTTGAA
* *
637878 ATTCAAAAAGACATGTCACTTGAA
1 GTTCCAAAAGACATGTCACTTGAA
*
637902 GTGCCAAAAG
1 GTTCCAAAAG
637912 TTATGATCAT
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (24 bp):
GTTCCAAAAGACATGTCACTTGAA
Found at i:641697 original size:19 final size:19
Alignment explanation
Indices: 641673--641714 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
641663 AAAACCCCTT
* *
641673 TGAAAACATATTATTTTAA
1 TGAAAACACATAATTTTAA
*
641692 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
641711 TGAA
1 TGAA
641715 GATAAATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:647435 original size:15 final size:15
Alignment explanation
Indices: 647415--647447 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
647405 GTGCTTCAAC
647415 TTTCTTTCCTTTCCT
1 TTTCTTTCCTTTCCT
*
647430 TTTCTTTCCTTTTCT
1 TTTCTTTCCTTTCCT
647445 TTT
1 TTT
647448 TTTTAAGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTTCCTTTCCT
Found at i:647436 original size:10 final size:10
Alignment explanation
Indices: 647414--647446 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
647404 AGTGCTTCAA
*
647414 CTTT-CTTTC
1 CTTTCCTTTT
647423 CTTTCCTTTT
1 CTTTCCTTTT
647433 CTTTCCTTTT
1 CTTTCCTTTT
647443 CTTT
1 CTTT
647447 TTTTTAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:650333 original size:16 final size:18
Alignment explanation
Indices: 650302--650345 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
650292 AAGGTAATGA
650302 AATAAGAAAGAATGAAAG
1 AATAAGAAAGAATGAAAG
*
650320 AATAA-AAA-AATGAAAT
1 AATAAGAAAGAATGAAAG
*
650336 AGTAAGAAAG
1 AATAAGAAAG
650346 TGAAGATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 11 0.50
17 6 0.27
18 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (18 bp):
AATAAGAAAGAATGAAAG
Found at i:650506 original size:14 final size:14
Alignment explanation
Indices: 650476--650524 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
650466 TTGCAACTTG
*
650476 CTTCTATTT-TTTT
1 CTTCTTTTTCTTTT
650489 -TTCTTTTTCTTTT
1 CTTCTTTTTCTTTT
650502 CTTCTTTTTCTTTT
1 CTTCTTTTTCTTTT
650516 CTTTCTTTT
1 C-TTCTTTT
650525 GCACTCCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 7 0.22
13 4 0.12
14 14 0.44
15 7 0.22
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTCTTTTTCTTTT
Found at i:653293 original size:19 final size:18
Alignment explanation
Indices: 653269--653332 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 18
653259 CGGCCAATAG
* *
653269 CATGTATCTTCATTAAAAT
1 CATGTAT-TTCATAAAAAC
*
653288 CATGTA-TTCATCAAAAC
1 CATGTATTTCATAAAAAC
653305 CATGTATTTCATCAAAAAC
1 CATGTATTTCAT-AAAAAC
653324 CATGTATTT
1 CATGTATTT
653333 TCAAAGGGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.38
18 5 0.12
19 20 0.50
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (18 bp):
CATGTATTTCATAAAAAC
Found at i:653303 original size:17 final size:17
Alignment explanation
Indices: 653277--653331 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
653267 AGCATGTATC
* *
653277 TTCATTAAAATCATGTA
1 TTCATCAAAACCATGTA
653294 TTCATCAAAACCATGTA
1 TTCATCAAAACCATGTA
653311 TTTCATCAAAAACCATGTA
1 -TTCATC-AAAACCATGTA
653330 TT
1 TT
653332 TTCAAAGGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 15 0.44
18 8 0.24
19 11 0.32
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.36
Consensus pattern (17 bp):
TTCATCAAAACCATGTA
Found at i:658536 original size:19 final size:20
Alignment explanation
Indices: 658512--658554 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
658502 AGCATTTATC
*
658512 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
658531 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
658551 TTCA
1 TTCA
658555 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:659099 original size:15 final size:15
Alignment explanation
Indices: 659079--659110 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
659069 TTGATAACTT
659079 TTCTTTCCATTTCAA
1 TTCTTTCCATTTCAA
659094 TTCTTTCCATTTCAA
1 TTCTTTCCATTTCAA
659109 TT
1 TT
659111 TCCTTTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (15 bp):
TTCTTTCCATTTCAA
Found at i:662696 original size:19 final size:19
Alignment explanation
Indices: 662672--662711 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
662662 AGCATTTATC
*
662672 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTATT
*
662691 TTCATTAAAATCATGTGTT
1 TTCATTAAAATCATGTATT
662710 TT
1 TT
662712 TAAAGGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:675922 original size:17 final size:17
Alignment explanation
Indices: 675900--675932 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
675890 TCGGCTTAAA
675900 AGAAATGGTTAGGGTAT
1 AGAAATGGTTAGGGTAT
*
675917 AGAAATGGTTATGGTA
1 AGAAATGGTTAGGGTA
675933 GAGGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (17 bp):
AGAAATGGTTAGGGTAT
Found at i:676683 original size:35 final size:35
Alignment explanation
Indices: 676639--676750 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
676629 AATGGAATGC
* **
676639 TGATTATATAGGCGTGAAATGGTGATATAAGATGG
1 TGATGATATAGGCGTGAAATGGTGATGGAAGATGG
*
676674 TGATGATATAGGCGTGCAATGGTGATGGAAGATGG
1 TGATGATATAGGCGTGAAATGGTGATGGAAGATGG
*
676709 TGATGTTATAGGCGTGAAAATGGTGATGGAAGATGG
1 TGATGATATAGGCGTG-AAATGGTGATGGAAGATGG
676745 TGATGA
1 TGATGA
676751 ACAGATAGTA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 46 0.67
36 23 0.33
ACGTcount: A:0.31, C:0.04, G:0.37, T:0.29
Consensus pattern (35 bp):
TGATGATATAGGCGTGAAATGGTGATGGAAGATGG
Found at i:676710 original size:13 final size:13
Alignment explanation
Indices: 676692--676749 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
676682 TAGGCGTGCA
676692 ATGGTGATGGAAG
1 ATGGTGATGGAAG
** *
676705 ATGGTGATGTTAT
1 ATGGTGATGGAAG
* *
676718 A-GGCG-T-GAAA
1 ATGGTGATGGAAG
676728 ATGGTGATGGAAG
1 ATGGTGATGGAAG
676741 ATGGTGATG
1 ATGGTGATG
676750 AACAGATAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 23 0.70
ACGTcount: A:0.29, C:0.02, G:0.41, T:0.28
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:677219 original size:29 final size:29
Alignment explanation
Indices: 677194--677249 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
677184 TTTTTGGCTG
677194 AATAGAGAGAAGCCTATTCACTTTGGCCA
1 AATAGAGAGAAGCCTATTCACTTTGGCCA
*
677223 AATAGAGAGAAGCCTCTTCACTTTGGC
1 AATAGAGAGAAGCCTATTCACTTTGGC
677250 GCCCATTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (29 bp):
AATAGAGAGAAGCCTATTCACTTTGGCCA
Found at i:685421 original size:13 final size:12
Alignment explanation
Indices: 685405--685446 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
685395 GTGCAAAAAT
685405 AAAGAAAATCATA
1 AAAGAAAATCA-A
*
685418 AAAGAAAA-GAA
1 AAAGAAAATCAA
685429 AAAGAAAATTCAA
1 AAAGAAAA-TCAA
685442 AAAGA
1 AAAGA
685447 GAAAGCAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.74, C:0.05, G:0.12, T:0.10
Consensus pattern (12 bp):
AAAGAAAATCAA
Found at i:685436 original size:24 final size:25
Alignment explanation
Indices: 685405--685451 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
685395 GTGCAAAAAT
685405 AAAGAAAA-TCATAAAAGA-AAAGAA
1 AAAGAAAATTCA-AAAAGAGAAAGAA
685429 AAAGAAAATTCAAAAAGAGAAAG
1 AAAGAAAATTCAAAAAGAGAAAG
685452 CAAGCCAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.72, C:0.04, G:0.15, T:0.09
Consensus pattern (25 bp):
AAAGAAAATTCAAAAAGAGAAAGAA
Found at i:688343 original size:2 final size:2
Alignment explanation
Indices: 688336--688371 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
688326 AGTTATTTTC
688336 AT AT 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 AT AT A
688372 CCTATAGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:695356 original size:666 final size:667
Alignment explanation
Indices: 694085--695419 Score: 2332
Period size: 666 Copynumber: 2.0 Consensus size: 667
694075 TAAGTTCCGC
* * *
694085 TACATGCTAGCTCCTCCAGATAAGTTGAGCTTTTCTTAGTGTTCCACGAGCTGCCATGACATTTT
1 TACATGCTAACTCCTCCAGATAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCATGACATTTG
694150 TGAGCTGTTTGGGAGCTGCATATGACATCCAAATACTCTACCAAGCTGCATCATCGTGCATCACA
66 TGAGCTGTTTGGGAGCTGCATATGACATCCAAATACTCTACCAAGCTGCATCATCGTGCATCACA
* * * * *
694215 CTCCAATATACCTATTTGTGCAAGGATACAAGGTAAGTCCATTATATTGAGTTGTTTTGAGCTAA
131 CTCCAATATACCTATATGTGCAAGGAAACAAAGTAAATCCATTATATTGAGATGTTTTGAGCTAA
*
694280 ATACCTTGCTGCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTCATTATA
196 ATACCTTGCTGCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
* * * *
694345 TTATCTCAAAATATTTGTAAGATAATGCATGAAGCTTAAGAGCTAATATGAATGTATATGAACTA
261 TCATCTCAAAATATGTGTAAGATAATGCATGAAGCTTAAAAGCTAATATGAATGCATATGAACTA
* *
694410 ATGAAATTATTTATAATGATGTTGCCTTGATGTATATATGATAATCATGCTTAATATGATTATAA
326 ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGATAATCATGCTTAATATGATTATAA
694475 GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACGTTGTATGCA
391 GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACGTTGTATGCA
* * *
694540 TGAATATCATATAACATGGTATTCATAAATGATAAATTGAAACATGTAATAATATTATCCTAAGA
456 TGAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATGTAACAATAATATCCTAAGA
*
694605 AATGATATGTAATCATAGCATGTATTTGAATAATATGAAAAACAAGATCAAATAAGCATAGGATG
521 AATGATATGTAATCATAGCATATATTTGAATAATATGAAAAACAAGATCAAATAAGCATAGGATG
694670 GAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATA
586 GAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATA
694735 AATGATA-AGTATAAGA
651 AATGATATAGTATAAGA
* * *
694751 TACATGCTAACTCCTTCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCATGATATTTG
1 TACATGCTAACTCCTCCAGATAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCATGACATTTG
* * *
694816 TGAGCTGTTTGTGAGCTGCATATGACGTCCAAATACTCTACCAAGCTGCCTCATCGTGCATCACA
66 TGAGCTGTTTGGGAGCTGCATATGACATCCAAATACTCTACCAAGCTGCATCATCGTGCATCACA
*
694881 CTCCAATGTACCTATATGTGCAAGGAAACAAAGTAAATCCATTATATTGAGATGTTTTGAGCTAA
131 CTCCAATATACCTATATGTGCAAGGAAACAAAGTAAATCCATTATATTGAGATGTTTTGAGCTAA
*
694946 ATACCTTGCTGCCATGTATGATTATGGTGATGTGAGTTATGTTTGAAGGTCATGAGCTAATTATA
196 ATACCTTGCTGCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
* *
695011 TCATCTCCAAATATGTGTAAGATAATGCATGTAGCTTAAAAGCTAATATGAATGCATATGAACTA
261 TCATCTCAAAATATGTGTAAGATAATGCATGAAGCTTAAAAGCTAATATGAATGCATATGAACTA
*
695076 ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGATAATCTTGCTTAATATGATTATAA
326 ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGATAATCATGCTTAATATGATTATAA
* *
695141 GACTATTCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATATGTTGTATGCA
391 GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACGTTGTATGCA
695206 TGAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATGTAACAATAATATCCTAAGA
456 TGAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATGTAACAATAATATCCTAAGA
* * *
695271 GATGATATGTAATCATA-CTATATATTTGAATAATATGAAAAACATGATCAAATAAGCATATGAT
521 AATGATATGTAATCATAGC-ATATATTTGAATAATATGAAAAACAAGATCAAATAAGCATAGGAT
695335 GGAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTAT
585 GGAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTAT
695400 AAATGATATAGTATAAGA
650 AAATGATATAGTATAAGA
695418 TA
1 TA
695420 GGGTAATGAA
Statistics
Matches: 632, Mismatches: 35, Indels: 3
0.94 0.05 0.00
Matches are distributed among these distances:
665 1 0.00
666 620 0.98
667 11 0.02
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (667 bp):
TACATGCTAACTCCTCCAGATAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCATGACATTTG
TGAGCTGTTTGGGAGCTGCATATGACATCCAAATACTCTACCAAGCTGCATCATCGTGCATCACA
CTCCAATATACCTATATGTGCAAGGAAACAAAGTAAATCCATTATATTGAGATGTTTTGAGCTAA
ATACCTTGCTGCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
TCATCTCAAAATATGTGTAAGATAATGCATGAAGCTTAAAAGCTAATATGAATGCATATGAACTA
ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGATAATCATGCTTAATATGATTATAA
GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACGTTGTATGCA
TGAATATCATATAACATGGTATTCATAAATGATAAATGGAAACATGTAACAATAATATCCTAAGA
AATGATATGTAATCATAGCATATATTTGAATAATATGAAAAACAAGATCAAATAAGCATAGGATG
GAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATA
AATGATATAGTATAAGA
Found at i:697857 original size:666 final size:667
Alignment explanation
Indices: 696586--697920 Score: 2357
Period size: 666 Copynumber: 2.0 Consensus size: 667
696576 TAAGTTCCGC
* * *
696586 TACATGCTAGCTCCTCCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTTCCATGACATTTT
1 TACATGCTAACTCCTCCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCATGACATTTG
696651 TGAGCTGTTTGGGAGCTGCATATGACATCCAAATACTCTACCAAGCTGCATCATCGTGCATCACA
66 TGAGCTGTTTGGGAGCTGCATATGACATCCAAATACTCTACCAAGCTGCATCATCGTGCATCACA
* * * * *
696716 CTCCAATATACCTATTTGTGCAAGGATACAAGGTAAGTCCATTATATTGAGTTGTTTTGAGCTAA
131 CTCCAATATACCTATATGTGCAAGGAAACAAAGTAAATCCATTATATTGAGATGTTTTGAGCTAA
696781 ATACCTTGCTGCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
196 ATACCTTGCTGCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
* * *
696846 TCATCTCAAAATATTTGTAAGATAATGCATGAAGCTTAAGAGCTAATATGAATGTATATGAACTA
261 TCATCTCAAAATATGTGTAAGATAATGCATGAAGCTTAAAAGCTAATATGAATGCATATGAACTA
* * *
696911 ATGAAATTATTTATAATGATGTTGCCTTGATGTATATATGATAATCATGCTTAATATGATTATAA
326 ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGAGAATCATGCTTAATATGATTATAA
696976 GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACGTTGTATGCA
391 GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACGTTGTATGCA
* * *
697041 TGAATATCATATAACATGGTATTCATAAATGATAAATTGAAACATGTAATAATATTATCCTAAGA
456 TGAATATAATATAACATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGA
* *
697106 AATGATATGTAATCATAGCATGTATTTGAATAATATGAAAAACAAGATCAAATAAGCATAGGATG
521 AATGATATGTAATAATAGCATATATTTGAATAATATGAAAAACAAGATCAAATAAGCATAGGATG
*
697171 GAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATA
586 GAAATAATAATATGATAATTTATAATAACATGTGAATGCATGCTTATGATAGAATAGAATGTATA
697236 AATGATA-AGTATAAGA
651 AATGATATAGTATAAGA
* *
697252 TACATGCTAACTCCTTCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCATGATATTTG
1 TACATGCTAACTCCTCCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCATGACATTTG
* * *
697317 TGAGCTGTTTGTGAGCTGCATATGACGTCCAAATACTCTACCAAGCTGCCTCATCGTGCATCACA
66 TGAGCTGTTTGGGAGCTGCATATGACATCCAAATACTCTACCAAGCTGCATCATCGTGCATCACA
*
697382 CTCCAATGTACCTATATGTGCAAGGAAACAAAGTAAATCCATTATATTGAGATGTTTTGAGCTAA
131 CTCCAATATACCTATATGTGCAAGGAAACAAAGTAAATCCATTATATTGAGATGTTTTGAGCTAA
*
697447 ATACCTTGCTGCCATGTATGATTATGGTGATGTGAGTTATGTTTGAAGGTCATGAGCTAATTATA
196 ATACCTTGCTGCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
* * *
697512 TCATCTCCAAATATGTGTAATATAATGCATGTAGCTTAAAAGCTAATATGAATGCATATGAACTA
261 TCATCTCAAAATATGTGTAAGATAATGCATGAAGCTTAAAAGCTAATATGAATGCATATGAACTA
697577 ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGAGAATCATGCTTAATATGATTATAA
326 ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGAGAATCATGCTTAATATGATTATAA
* *
697642 GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGTGTATATGTTGTATGCA
391 GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACGTTGTATGCA
*
697707 TGGATATAATATAACATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGA
456 TGAATATAATATAACATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGA
*
697772 AATGATATGTAATAATAGCATATATTTGAATAATATGAAAAACATGATCAAATAAGCATAGGATG
521 AATGATATGTAATAATAGCATATATTTGAATAATATGAAAAACAAGATCAAATAAGCATAGGATG
697837 GAAATAATAATATGATAATTTATAATAACATGTGAATGCATGCTTATGATAGAATAGAATGTATA
586 GAAATAATAATATGATAATTTATAATAACATGTGAATGCATGCTTATGATAGAATAGAATGTATA
697902 AATGATATAGTATAAGA
651 AATGATATAGTATAAGA
697919 TA
1 TA
697921 GGGTAATGAT
Statistics
Matches: 634, Mismatches: 34, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
666 623 0.98
667 11 0.02
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33
Consensus pattern (667 bp):
TACATGCTAACTCCTCCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCATGACATTTG
TGAGCTGTTTGGGAGCTGCATATGACATCCAAATACTCTACCAAGCTGCATCATCGTGCATCACA
CTCCAATATACCTATATGTGCAAGGAAACAAAGTAAATCCATTATATTGAGATGTTTTGAGCTAA
ATACCTTGCTGCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
TCATCTCAAAATATGTGTAAGATAATGCATGAAGCTTAAAAGCTAATATGAATGCATATGAACTA
ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGAGAATCATGCTTAATATGATTATAA
GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACGTTGTATGCA
TGAATATAATATAACATGGTATTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGA
AATGATATGTAATAATAGCATATATTTGAATAATATGAAAAACAAGATCAAATAAGCATAGGATG
GAAATAATAATATGATAATTTATAATAACATGTGAATGCATGCTTATGATAGAATAGAATGTATA
AATGATATAGTATAAGA
Found at i:700361 original size:667 final size:665
Alignment explanation
Indices: 699088--700648 Score: 2800
Period size: 667 Copynumber: 2.4 Consensus size: 665
699078 TAAGTTCAGC
*
699088 TACATGCTAGCTCCTCCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCATGATATTTC
1 TACATGCTAGCTCCTCCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCCTGATATTT-
* *
699153 TGAGCTGTTTGTGAGCTGCATATGACGTCCAAATACTCTACCAAACTGCCTCATCGTGCATCACA
65 TGAGCTGTTTGTGAGCTGTATATGACGTCCAAATACTCTACCAAGCTGCCTCATCGTGCATCACA
* * *** * *
699218 CTCCAATATACCTATATGTGCAAGGAAACAAGGTAAGTCCATTATATTGAGCTATTTTGAGCTAA
130 TTCCAATGTACCTATATGTGCAAGGAAACAAGGTAAGTCCATGGCATTGAGCTGTTATGAGCTAA
*
699283 ATACCTTGCTTCCATGTATGATTATTGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
195 ATACCTTG-TTCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
699348 TCATCTCAAAATATGTGTAAGATAATGCATGAAGCTCAAGAGCTAATATGAATGCATATGAACTA
259 TCATCTCAAAATATGTGTAAGATAATGCATGAAGCTCAAGAGCTAATATGAATGCATATGAACTA
*
699413 ATGAAATGATTTATAATGATGTTGCCTTGATGTATATATGATAATCATGCTTAATATGATTATAA
324 ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGATAATCATGCTTAATATGATTATAA
* *
699478 GACTATCCTAACATGCTTATAACGTTGTGTATCAATCATAAAGATATGGGTATACGTTGTATGCA
389 GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACATTGTATGCA
699543 TGAATATCATATAACATGGTATTCATAAATGATAAATTGAAACATGTAATAATAATATCCTAAGA
454 TGAATATCATATAACATGGTATTCATAAATGATAAATTGAAACATGTAATAATAATATCCTAAGA
699608 AATGATATGTAATCATAGCATATATTTGAATAATATGAAAAACATGATCAAATAAGCATAGGATG
519 AATGATATGTAATCATAGCATATATTTGAATAATATGAAAAACATGATCAAATAAGCATAGGATG
* *
699673 GAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATATAATGTATA
584 GAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATAAAATGAATA
699738 AATGATATAGTATAAGA
649 AATGATATAGTATAAGA
699755 TACATGCTAGCTCCTCCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCCTGATATTTG
1 TACATGCTAGCTCCTCCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCCTGATATTT-
*
699820 TGAGCTGTTTGTGAGCTGTATATGACGTCCAAATACTATACCAAGCTGCCTCATCGTGCATCACA
65 TGAGCTGTTTGTGAGCTGTATATGACGTCCAAATACTCTACCAAGCTGCCTCATCGTGCATCACA
* *
699885 TTCCAATGTACATATATGTGCAAGGAAACAAGGTAAGTCCATGGCATTGAGCTGTTATAAGCTAA
130 TTCCAATGTACCTATATGTGCAAGGAAACAAGGTAAGTCCATGGCATTGAGCTGTTATGAGCTAA
699950 ATACCTTGTTGCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
195 ATACCTTGTT-CCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATA
*
700015 TCATCTCAAAATATGTGTAAGATAATGCATGAAGCTTAAGAGCTAATATGAATGCATATGAACTA
259 TCATCTCAAAATATGTGTAAGATAATGCATGAAGCTCAAGAGCTAATATGAATGCATATGAACTA
700080 ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGATAATCATGCTTAATATGATTATAA
324 ATGAAATGATTTATAATGATGCTGCCTTGATGTATATATGATAATCATGCTTAATATGATTATAA
*
700145 GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACATTTTATGCA
389 GACTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACATTGTATGCA
700210 TGAATATCATATAACATGGTATTCATAAATGATAAATTGAAACATGTAATAATAATATCCTAAGA
454 TGAATATCATATAACATGGTATTCATAAATGATAAATTGAAACATGTAATAATAATATCCTAAGA
700275 AATGATATGTAATCATAGCATATATTTGAATAATATGAAAAACATGATCAAATAAGCATAGGATG
519 AATGATATGTAATCATAGCATATATTTGAATAATATGAAAAACATGATCAAATAAGCATAGGATG
700340 GAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATAAAATGAATA
584 GAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATAAAATGAATA
700405 AATGATATAGTATAAGA
649 AATGATATAGTATAAGA
*
700422 TACATGCTAGCTCCTCCAGCTAAGTTGAGCTTTCCTTAGTCTTCCACGAGCTGCCCTG--A---T
1 TACATGCTAGCTCCTCCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCCTGATATTTT
700482 -A----TTTGTGAGCTGTATATGACGTCCAAATACTCTACCAAGCTGCCTCATCGTGCATCACAT
66 GAGCTGTTTGTGAGCTGTATATGACGTCCAAATACTCTACCAAGCTGCCTCATCGTGCATCACAT
700542 TCCAATGTACCTATATGTGCAAGGAAACAAGGTAAGTCCATGGCATTGAGCTGTTATGAGCTAAA
131 TCCAATGTACCTATATGTGCAAGGAAACAAGGTAAGTCCATGGCATTGAGCTGTTATGAGCTAAA
*
700607 TACCTTGTTTCCATATATGATTATGGTGATGTGAGCTATGTT
196 TACCTTG-TTCCATGTATGATTATGGTGATGTGAGCTATGTT
700649 AAAGTCATCA
Statistics
Matches: 865, Mismatches: 27, Indels: 15
0.95 0.03 0.02
Matches are distributed among these distances:
656 159 0.18
657 2 0.00
660 1 0.00
661 1 0.00
665 1 0.00
666 2 0.00
667 699 0.81
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (665 bp):
TACATGCTAGCTCCTCCAGCTAAGTTGAGCTTTCCTTAGTGTTCCACGAGCTGCCCTGATATTTT
GAGCTGTTTGTGAGCTGTATATGACGTCCAAATACTCTACCAAGCTGCCTCATCGTGCATCACAT
TCCAATGTACCTATATGTGCAAGGAAACAAGGTAAGTCCATGGCATTGAGCTGTTATGAGCTAAA
TACCTTGTTCCATGTATGATTATGGTGATGTGAGCTATGTTTGAAGGTCATGAGCTAATTATATC
ATCTCAAAATATGTGTAAGATAATGCATGAAGCTCAAGAGCTAATATGAATGCATATGAACTAAT
GAAATGATTTATAATGATGCTGCCTTGATGTATATATGATAATCATGCTTAATATGATTATAAGA
CTATCCTAACATGCTTATAACATTGTGTATCAATCATAAAGATATGGGTATACATTGTATGCATG
AATATCATATAACATGGTATTCATAAATGATAAATTGAAACATGTAATAATAATATCCTAAGAAA
TGATATGTAATCATAGCATATATTTGAATAATATGAAAAACATGATCAAATAAGCATAGGATGGA
AATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGATAGAATAAAATGAATAAA
TGATATAGTATAAGA
Found at i:702966 original size:13 final size:13
Alignment explanation
Indices: 702948--702973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
702938 AAAACCTCTC
702948 ACATACCTTTTCA
1 ACATACCTTTTCA
702961 ACATACCTTTTCA
1 ACATACCTTTTCA
702974 TCTTTGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:709574 original size:19 final size:20
Alignment explanation
Indices: 709550--709601 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
709540 CGGCCAAGAG
* *
709550 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
709569 CATGTATTTTCATAAAAAAAT
1 CATGTATTTTCAT-AAAAAAT
709590 CATGTATTTTCA
1 CATGTATTTTCA
709602 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
21 17 0.59
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:710350 original size:21 final size:19
Alignment explanation
Indices: 710304--710373 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
710294 AATTGGAGTG
710304 CAAAAAGAAAAGAAAAATA
1 CAAAAAGAAAAGAAAAATA
*
710323 CAAAAAGAAGAAGAAAATTCA
1 CAAAAAGAA-AAGAAAAAT-A
*
710344 GAAAAAGAAAGAGAAGAAA-A
1 CAAAAAGAAA-AGAA-AAATA
*
710364 GAAAAAGAAA
1 CAAAAAGAAA
710374 TTCAAAAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 9 0.20
20 20 0.45
21 13 0.30
22 2 0.05
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.04
Consensus pattern (19 bp):
CAAAAAGAAAAGAAAAATA
Found at i:710350 original size:35 final size:32
Alignment explanation
Indices: 710311--710385 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 32
710301 GTGCAAAAAG
* *
710311 AAAAGAAAAATACA-AAAAGAAGAAGAAAATTCAGA
1 AAAAGAAAAAGA-AGAAAAGAAAAAG-AAATTC--A
*
710346 AAAAGAAAGAGAAGAAAAGAAAAAGAAATTCA
1 AAAAGAAAAAGAAGAAAAGAAAAAGAAATTCA
710378 AAAAGAAA
1 AAAAGAAA
710386 GCAAGCCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 9 0.25
34 7 0.19
35 20 0.56
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (32 bp):
AAAAGAAAAAGAAGAAAAGAAAAAGAAATTCA
Found at i:713636 original size:19 final size:20
Alignment explanation
Indices: 713612--713662 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
713602 CGGCCAAGAG
* *
713612 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
713631 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
713651 CATGTATTTTCA
1 CATGTATTTTCA
713663 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:715780 original size:22 final size:22
Alignment explanation
Indices: 715754--715795 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
715744 ATATTAAATT
715754 ATATT-AAAATTAATCAATATAA
1 ATATTGAAAATTAA-CAATATAA
*
715776 ATATTGAAAATTCACAATAT
1 ATATTGAAAATTAACAATAT
715796 TTACAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATTGAAAATTAACAATATAA
Found at i:717813 original size:16 final size:16
Alignment explanation
Indices: 717788--717829 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
717778 AGAGATGTCT
717788 AGTGGAGACAAAGCCA
1 AGTGGAGACAAAGCCA
*
717804 AGTGGGGACAAAGCCA
1 AGTGGAGACAAAGCCA
*
717820 ACTGGAGACA
1 AGTGGAGACA
717830 TGCTCCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.19, G:0.33, T:0.07
Consensus pattern (16 bp):
AGTGGAGACAAAGCCA
Found at i:718067 original size:23 final size:23
Alignment explanation
Indices: 718027--718071 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
718017 TAATATATAT
**
718027 ATATGAAAATAATTATCTTATAAC
1 ATATGAAAATAAGCATC-TATAAC
718051 ATATG-AAATAAGCATCTATAA
1 ATATGAAAATAAGCATCTATAA
718072 GTATAAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (23 bp):
ATATGAAAATAAGCATCTATAAC
Found at i:720967 original size:13 final size:12
Alignment explanation
Indices: 720949--720990 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
720939 GCTTTCTTTC
720949 TCTTTTTGAATTT
1 TCTTTTTG-ATTT
*
720962 TCTTTTT-CTTT
1 TCTTTTTGATTT
720973 TCTTTTCTGATTT
1 TCTTTT-TGATTT
720986 TCTTT
1 TCTTT
720991 CTTTTTGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (12 bp):
TCTTTTTGATTT
Found at i:720985 original size:24 final size:25
Alignment explanation
Indices: 720941--720990 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
720931 TTTCCTTGGC
720941 TTTCTTTCTCTTTTTGAATTTTCTT
1 TTTCTTTCTCTTTTTGAATTTTCTT
720966 TTTCTTT-TCTTTTCTG-ATTTTCTT
1 TTTCTTTCTCTTTT-TGAATTTTCTT
720990 T
1 T
720991 CTTTTTGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTCTTTCTCTTTTTGAATTTTCTT
Found at i:722476 original size:23 final size:23
Alignment explanation
Indices: 722436--722480 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
722426 TAATATATAT
722436 ATATGAAAATAACTATCTTATAAC
1 ATATGAAAATAACTATC-TATAAC
722460 ATATG-AAATAAGC-ATCTATAA
1 ATATGAAAATAA-CTATCTATAA
722481 GTATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (23 bp):
ATATGAAAATAACTATCTATAAC
Found at i:724628 original size:16 final size:16
Alignment explanation
Indices: 724607--724645 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
724597 AGAGATGTCT
724607 AGTGGAGACAAAGCCA
1 AGTGGAGACAAAGCCA
724623 AGTGGAGACAAAGCCA
1 AGTGGAGACAAAGCCA
*
724639 ACTGGAG
1 AGTGGAG
724646 TCAAGTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.33, T:0.08
Consensus pattern (16 bp):
AGTGGAGACAAAGCCA
Found at i:725742 original size:17 final size:17
Alignment explanation
Indices: 725699--725765 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
725689 CAATAAAGGA
* **
725699 TTAATAAATGAACTGGT
1 TTAATTAATGAACTACT
* *
725716 TTGATGAATGAACTACT
1 TTAATTAATGAACTACT
725733 TTAATTAATGAACTAACT
1 TTAATTAATGAACT-ACT
725751 TT-ATTCAATGAACTA
1 TTAATT-AATGAACTA
725766 GATACTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
17 29 0.69
18 13 0.31
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (17 bp):
TTAATTAATGAACTACT
Found at i:725753 original size:18 final size:18
Alignment explanation
Indices: 725722--725765 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
725712 TGGTTTGATG
725722 AATGAACT-ACTTTAATT-
1 AATGAACTAACTTT-ATTC
725739 AATGAACTAACTTTATTC
1 AATGAACTAACTTTATTC
725757 AATGAACTA
1 AATGAACTA
725766 GATACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTATTC
Found at i:728305 original size:16 final size:16
Alignment explanation
Indices: 728284--728328 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
728274 CAAGAGATGT
728284 CTAGTGGAGACAAAGC
1 CTAGTGGAGACAAAGC
*
728300 CTAGTGGAGATAAAGC
1 CTAGTGGAGACAAAGC
*
728316 CAAGTGGAGACAA
1 CTAGTGGAGACAA
728329 GTAATCTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.31, T:0.13
Consensus pattern (16 bp):
CTAGTGGAGACAAAGC
Found at i:729420 original size:17 final size:17
Alignment explanation
Indices: 729377--729443 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
729367 CAATTAAGGA
* **
729377 TTAATAAATGAACTGGT
1 TTAATTAATGAACTACT
* *
729394 TTGATGAATGAACTACT
1 TTAATTAATGAACTACT
729411 TTAATTAATGAACTAACT
1 TTAATTAATGAACT-ACT
729429 TT-ATTCAATGAACTA
1 TTAATT-AATGAACTA
729444 GATACTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
17 29 0.69
18 13 0.31
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (17 bp):
TTAATTAATGAACTACT
Found at i:729431 original size:18 final size:18
Alignment explanation
Indices: 729400--729443 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
729390 TGGTTTGATG
729400 AATGAACT-ACTTTAATT-
1 AATGAACTAACTTT-ATTC
729417 AATGAACTAACTTTATTC
1 AATGAACTAACTTTATTC
729435 AATGAACTA
1 AATGAACTA
729444 GATACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTATTC
Found at i:732169 original size:24 final size:24
Alignment explanation
Indices: 732123--732169 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
732113 TCTTGGCACT
* * *
732123 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAGCTGTTGGAACA
*
732147 TCAAGTGGCATAGCTGTTGGAAC
1 TCAAGTGGCACAGCTGTTGGAAC
732170 GTTAAAGGAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (24 bp):
TCAAGTGGCACAGCTGTTGGAACA
Found at i:743776 original size:19 final size:20
Alignment explanation
Indices: 743752--743802 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
743742 CGGCCAAGAG
* *
743752 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
743771 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
743791 CATGTATTTTCA
1 CATGTATTTTCA
743803 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:744541 original size:22 final size:22
Alignment explanation
Indices: 744516--744567 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
744506 GTGCAAAATG
744516 AAAGAAAAAGACA-AAAAGAAGA
1 AAAGAAAAA-ACAGAAAAGAAGA
*
744538 AAAGAAAAATCAGAAAAGAAGA
1 AAAGAAAAAACAGAAAAGAAGA
744560 AAAGAAAA
1 AAAGAAAA
744568 GAAAAAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAGAAAAAACAGAAAAGAAGA
Found at i:746636 original size:30 final size:31
Alignment explanation
Indices: 746584--746643 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
746574 CTTAGCTTTA
**
746584 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
746614 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
746644 GGAAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Done.