Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009458.1 Hibiscus syriacus cultivar Beakdansim tig00113719_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: 1407308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:2414 original size:8 final size:8
Alignment explanation
Indices: 2401--2441 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2391 CTCATTTTCA
2401 GAGAATTT
1 GAGAATTT
2409 GAGAATTT
1 GAGAATTT
*
2417 -AGAGTTT
1 GAGAATTT
*
2424 GGGAATTT
1 GAGAATTT
2432 GAGAATTT
1 GAGAATTT
2440 GA
1 GA
2442 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:2748 original size:125 final size:125
Alignment explanation
Indices: 2509--3105 Score: 1139
Period size: 125 Copynumber: 4.8 Consensus size: 125
2499 CTATAATCGG
2509 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
2573 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTAT
2634 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
2699 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTAT
2759 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
2824 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTAT
2884 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
2949 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTAT
3010 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTC--AGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
3072 TCATTGCCCTATTATGTCACTCATGTCCCTCGGG
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGG
3106 GAATAACTTA
Statistics
Matches: 469, Mismatches: 1, Indels: 7
0.98 0.00 0.01
Matches are distributed among these distances:
122 3 0.01
123 39 0.08
125 303 0.65
126 124 0.26
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.33
Consensus pattern (125 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTAT
Found at i:3556 original size:33 final size:34
Alignment explanation
Indices: 3495--3593 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
3485 AAATTTAATG
*
3495 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * *
3529 TTAAATTT-GAATAATATTATTTTTATTTT-ATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
3561 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
3594 AACATTTATC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 10 0.18
33 37 0.66
34 9 0.16
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:4193 original size:21 final size:21
Alignment explanation
Indices: 4105--4198 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
4095 TATGGTATAA
*
4105 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
4126 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
4147 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
4168 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
4189 AACCCTGCGG
1 AACCCTGCGG
4199 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:4228 original size:21 final size:21
Alignment explanation
Indices: 4202--4249 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4192 CCTGCGGAGA
*
4202 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
4223 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
4244 GGGCAT
1 TGGCAT
4250 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:6056 original size:15 final size:15
Alignment explanation
Indices: 5990--6058 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
5980 TATTATTTTA
*
5990 ATAAAAAATATTTAC
1 ATAAAAAATATTAAC
* *
6005 AT-AAATATATTAAT
1 ATAAAAAATATTAAC
*
6019 ATAAAAAATAATAAC
1 ATAAAAAATATTAAC
*
6034 TATTTAAAAAATACTAAC
1 -A--TAAAAAATATTAAC
6052 ATAAAAA
1 ATAAAAA
6059 TAAATTTCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
14 11 0.26
15 17 0.40
16 1 0.02
17 1 0.02
18 13 0.30
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAAAAATATTAAC
Found at i:6780 original size:19 final size:20
Alignment explanation
Indices: 6766--6844 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 20
6756 TTATTTTCGC
*
6766 AACGCGTTGCGATTTTGGAG
1 AACGCGTTGCGATTTTAGAG
6786 AATCGCGTTGCGATTTTAGAG
1 AA-CGCGTTGCGATTTTAGAG
6807 AACTGCGTTGCGATTTTAGAG
1 AAC-GCGTTGCGATTTTAGAG
*
6828 AACCGCGTTACGATTTT
1 AA-CGCGTTGCGATTTT
6845 GCAGAACCGT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
20 3 0.06
21 50 0.93
22 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (20 bp):
AACGCGTTGCGATTTTAGAG
Found at i:6793 original size:21 final size:21
Alignment explanation
Indices: 6768--6903 Score: 106
Period size: 21 Copynumber: 6.8 Consensus size: 21
6758 ATTTTCGCAA
6768 CGCGTTGCGATTTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAT
*
6789 CGCGTTGCGATTTTAGAGAA-
1 CGCGTTGCGATTTTGGAGAAT
* *
6809 CTGCGTTGCGATTTTAGAGAAC
1 C-GCGTTGCGATTTTGGAGAAT
* * *
6831 CGCGTTACGATTTTGCAGAAC
1 CGCGTTGCGATTTTGGAGAAT
** * * *
6852 CGTATTGTGAATTT-GAAAAT
1 CGCGTTGCGATTTTGGAGAAT
6872 --C---GCGATTTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAT
*
6888 CGCGTTGTGATTTTGG
1 CGCGTTGCGATTTTGG
6904 GAACTGTATT
Statistics
Matches: 90, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
15 6 0.07
16 5 0.06
18 1 0.01
20 4 0.04
21 73 0.81
22 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.34
Consensus pattern (21 bp):
CGCGTTGCGATTTTGGAGAAT
Found at i:7216 original size:31 final size:31
Alignment explanation
Indices: 7175--7263 Score: 144
Period size: 31 Copynumber: 2.9 Consensus size: 31
7165 GTGACAGTCG
*
7175 ATCTGTCATGTTTGAGTTGTCAATTTAATTA
1 ATCTGACATGTTTGAGTTGTCAATTTAATTA
*
7206 ATCTGACATGTTTGAGTTGTCAATTTACTTA
1 ATCTGACATGTTTGAGTTGTCAATTTAATTA
7237 ATCTGACATGTTTGAGTT-TCCAATTTA
1 ATCTGACATGTTTGAGTTGT-CAATTTA
7264 GCCAATATGA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
30 1 0.02
31 54 0.98
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (31 bp):
ATCTGACATGTTTGAGTTGTCAATTTAATTA
Found at i:7275 original size:31 final size:30
Alignment explanation
Indices: 7175--7278 Score: 129
Period size: 31 Copynumber: 3.4 Consensus size: 30
7165 GTGACAGTCG
* *
7175 ATCTGTCATGTTTGAGTTGTCAATTTAATTA
1 ATCTGACATGTTTGAGTTGTCAATTT-ACTA
7206 ATCTGACATGTTTGAGTTGTCAATTTACTTA
1 ATCTGACATGTTTGAGTTGTCAATTTAC-TA
*
7237 ATCTGACATGTTTGAGTT-TCCAATTTAGCCA
1 ATCTGACATGTTTGAGTTGT-CAATTTA-CTA
*
7268 ATATGACATGT
1 ATCTGACATGT
7279 CATCCGTCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
30 2 0.03
31 63 0.95
32 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.43
Consensus pattern (30 bp):
ATCTGACATGTTTGAGTTGTCAATTTACTA
Found at i:29597 original size:2 final size:2
Alignment explanation
Indices: 29590--29621 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
29580 TTTGAGGTGA
29590 AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
29622 GCCTTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33778 original size:18 final size:18
Alignment explanation
Indices: 33745--33789 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
33735 TCATTTGAAG
*
33745 TATATGA-AATAATAATT
1 TATATGATAAAAATAATT
33762 TATATGATAAAAATAATT
1 TATATGATAAAAATAATT
* *
33780 AATATAATAA
1 TATATGATAA
33790 TTATATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
TATATGATAAAAATAATT
Found at i:34996 original size:31 final size:31
Alignment explanation
Indices: 34961--35027 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
34951 ATTTGTACAT
*
34961 TTTTGCTCACTTATATTGTCGTTTTA-TAAA
1 TTTTGCTCACTTATATTATCGTTTTATTAAA
* * * *
34991 GTTTTGGTTATTTATGTTATCGTTTTATTAAA
1 -TTTTGCTCACTTATATTATCGTTTTATTAAA
35023 TTTTG
1 TTTTG
35028 GTTATTTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.21, C:0.07, G:0.13, T:0.58
Consensus pattern (31 bp):
TTTTGCTCACTTATATTATCGTTTTATTAAA
Found at i:45455 original size:21 final size:21
Alignment explanation
Indices: 45429--45473 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
45419 TCCTAGTTTG
*
45429 GATCTTTCTTTGGTGGAATGT
1 GATCTTTCTTTAGTGGAATGT
* *
45450 GATCTTTTTTTAGTGGAGTGT
1 GATCTTTCTTTAGTGGAATGT
45471 GAT
1 GAT
45474 AGTGCTTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.07, G:0.29, T:0.49
Consensus pattern (21 bp):
GATCTTTCTTTAGTGGAATGT
Found at i:46025 original size:20 final size:20
Alignment explanation
Indices: 46000--46038 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
45990 TTAGGAACAT
*
46000 GAATTACAATCATTA-TCATC
1 GAATTA-AAACATTAGTCATC
46020 GAATTAAAACATTAGTCAT
1 GAATTAAAACATTAGTCAT
46039 ATGATTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (20 bp):
GAATTAAAACATTAGTCATC
Found at i:51024 original size:32 final size:32
Alignment explanation
Indices: 50988--51053 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
50978 GGGTAATTAA
50988 AATTAAAATGCTTCTCTGGATAGA-TTGATTGT
1 AATTAAAATGCTTCTCTGGATAGAGTT-ATTGT
*
51020 AATTAAAATGCTTGTCTGGATAGAGTTATTGT
1 AATTAAAATGCTTCTCTGGATAGAGTTATTGT
51052 AA
1 AA
51054 ATAGTAGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (32 bp):
AATTAAAATGCTTCTCTGGATAGAGTTATTGT
Found at i:52562 original size:11 final size:11
Alignment explanation
Indices: 52546--52587 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 11
52536 ACTTAAAAAA
52546 TTAATTTTTAT
1 TTAATTTTTAT
*
52557 TTAA-TTTTAA
1 TTAATTTTTAT
52567 TTAATTTTTAGT
1 TTAATTTTTA-T
52579 TATAATTTT
1 T-TAATTTT
52588 ATAAATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 9 0.35
11 9 0.35
12 1 0.04
13 7 0.27
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TTAATTTTTAT
Found at i:52568 original size:21 final size:23
Alignment explanation
Indices: 52544--52588 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
52534 CGACTTAAAA
52544 AATTAATTTTTA-TT-TAATTTT
1 AATTAATTTTTAGTTATAATTTT
52565 AATTAATTTTTAGTTATAATTTT
1 AATTAATTTTTAGTTATAATTTT
52588 A
1 A
52589 TAAATTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.55
22 2 0.09
23 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
AATTAATTTTTAGTTATAATTTT
Found at i:57704 original size:8 final size:8
Alignment explanation
Indices: 57691--57723 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
57681 TCATTTCGGC
57691 ATAATAAA
1 ATAATAAA
57699 ATAATAAA
1 ATAATAAA
57707 ATAATAAA
1 ATAATAAA
57715 ATAATAAA
1 ATAATAAA
57723 A
1 A
57724 CCTTAATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAATAAA
Found at i:64125 original size:216 final size:216
Alignment explanation
Indices: 63749--64181 Score: 618
Period size: 216 Copynumber: 2.0 Consensus size: 216
63739 TGTAATGCTT
* * ** * * *
63749 AGCAATAATGATTGATGGTGTGTTGTTTTCTGAGTTCTTGCTTGAAGTTCAGTTTGCAACTATAG
1 AGCAATAATGATTGAAGGTGTGCTGTTGGCTGAATTCTTGCTTGAAGTTCAGTATACAACTATAG
* * *
63814 GTTCTTTGTGTGTGTGTGTCTGTAGGATCATGCATAGTCCGTTCAGCCGAAAATCATGCTATCTT
66 GTTC-TTCTGTGTCTGTGTCTGTAGGATCATGCATAGTCCGTTCAGCCGAAAATCATGCTATATT
* * *
63879 CGACCGTGTCTAATTGTCATTCATGCTTCAGATTGCGATACTCTGATATGGTCGAAAATCTGATT
130 CGACCATGTCTAATGGTCATTCATGCTTCAGATTGCGATACTC-GATATGGTCGAAAATCTGAGT
*
63944 AAAGATTTGATTTTGATTAACTG
194 AAAGATTTGATCTTGATTAACTG
*
63967 AGCAATAATGATTGAAGGTGTGCTGTTGGCTGAATTCTTGCTT-AAGGTTTAGTATACAACTATA
1 AGCAATAATGATTGAAGGTGTGCTGTTGGCTGAATTCTTGCTTGAA-GTTCAGTATACAACTATA
** * *
64031 GGTTC-TCTGTGTCTGTGTCTGTAGGATCATGGTTCGTCCGTTTAGCCGAAAATCATGCTATATT
65 GGTTCTTCTGTGTCTGTGTCTGTAGGATCATGCATAGTCCGTTCAGCCGAAAATCATGCTATATT
* * * *
64095 CGACCATGTCTAATGGTCATTCATGCTTCAGATTGTGATATTCGATATGGTCTAAAGTCTGAGTA
130 CGACCATGTCTAATGGTCATTCATGCTTCAGATTGCGATACTCGATATGGTCGAAAATCTGAGTA
64160 AAGATTTGATCTTGATTAACTG
195 AAGATTTGATCTTGATTAACTG
64182 TTGCAGAGCC
Statistics
Matches: 191, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
215 40 0.21
216 91 0.48
217 2 0.01
218 58 0.30
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (216 bp):
AGCAATAATGATTGAAGGTGTGCTGTTGGCTGAATTCTTGCTTGAAGTTCAGTATACAACTATAG
GTTCTTCTGTGTCTGTGTCTGTAGGATCATGCATAGTCCGTTCAGCCGAAAATCATGCTATATTC
GACCATGTCTAATGGTCATTCATGCTTCAGATTGCGATACTCGATATGGTCGAAAATCTGAGTAA
AGATTTGATCTTGATTAACTG
Found at i:72209 original size:15 final size:15
Alignment explanation
Indices: 72189--72222 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
72179 CGCTGGGCAT
72189 CCGAGGGCCATCCGA
1 CCGAGGGCCATCCGA
72204 CCGA-GGCCATCCGA
1 CCGAGGGCCATCCGA
*
72218 ACGAG
1 CCGAG
72223 CTATGCGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.24, C:0.38, G:0.32, T:0.06
Consensus pattern (15 bp):
CCGAGGGCCATCCGA
Found at i:72286 original size:33 final size:33
Alignment explanation
Indices: 72204--72288 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
72194 GGCCATCCGA
* * * *
72204 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
** *
72237 CCGAGGGCAATTGAGCGAGCTATGTGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
72270 CCGAGGG-AAGCCGAGCGAG
1 CCGAGGGCAA-CCGAGCGAG
72289 GGTAGGTCGC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
32 2 0.05
33 40 0.95
ACGTcount: A:0.26, C:0.24, G:0.39, T:0.12
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:72325 original size:29 final size:29
Alignment explanation
Indices: 72292--72347 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
72282 GAGCGAGGGT
*
72292 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
72321 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
72348 TTTGTTAGGA
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:0.20, C:0.30, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:72451 original size:29 final size:29
Alignment explanation
Indices: 72406--72462 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
72396 GAGCAAGGGT
*
72406 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAATGCATGGCGACCTACA
*
72435 AGGTCGCTCGGAATGCATGGCGACCTAC
1 AGGTCGCCCGGAATGCATGGCGACCTAC
72463 GGCCAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGAATGCATGGCGACCTACA
Found at i:76172 original size:2 final size:2
Alignment explanation
Indices: 76165--76198 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
76155 TTAATAAAGA
*
76165 AT AT AT AT AT AT AT AT AT AT AT AT AA AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76199 ATTTTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:81141 original size:2 final size:2
Alignment explanation
Indices: 81134--81178 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
81124 GGAGGTGACT
81134 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
81176 TA T
1 TA T
81179 GGGTATATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:81795 original size:19 final size:19
Alignment explanation
Indices: 81752--81788 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
81742 ATAAAAAAAA
*
81752 TAAATAATAAAAAAAATTC
1 TAAAAAATAAAAAAAATTC
*
81771 TAAAAAATAAATAAAATT
1 TAAAAAATAAAAAAAATT
81789 TTGAAAATAT
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:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAAAAATAAAAAAAATTC
Found at i:82433 original size:132 final size:132
Alignment explanation
Indices: 82183--82436 Score: 298
Period size: 132 Copynumber: 1.9 Consensus size: 132
82173 GAAAAATTGA
*
82183 AAGTTTAAGTATTAAAACAGATTAAAATTAATAGTTTAAGTACTAAACGTGTAATTTACCCAAAA
1 AAGTTTAAGTATTAAAACAGATTAAAAGTAATAGTTTAAGTACTAAACGTGTAATTTACCCAAAA
* *** * * ***
82248 AATTATAATTTGGTTTTGACCATTGGATTTGACCCTGAGTGATGAGGTCATGAACTGATTGTGAA
66 AATTATAATTTGGTTCTGACCATTGGACCGGACCATGAGTCATGAGAAAATGAACTGATTGTGAA
82313 AC
131 AC
* * * *
82315 AAGTTTAAGTATTAAAATAGATTAAAAGTAATAGTTTAAGTATTAAACGTGTAATTTATCTAAAA
1 AAGTTTAAGTATTAAAACAGATTAAAAGTAATAGTTTAAGTACTAAACGTGTAATTTACCCAAAA
* * * *
82380 ATTTATACTTTGGTTCTGA-CATT-GACCCCGGGCGATGAGGTCATGA-AAAATGAACTG
66 AATTATAATTTGGTTCTGACCATTGGA--CCGGACCATGA-GTCATGAGAAAATGAACTG
82437 CGAAACAAGT
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
130 2 0.02
131 4 0.04
132 89 0.88
133 6 0.06
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (132 bp):
AAGTTTAAGTATTAAAACAGATTAAAAGTAATAGTTTAAGTACTAAACGTGTAATTTACCCAAAA
AATTATAATTTGGTTCTGACCATTGGACCGGACCATGAGTCATGAGAAAATGAACTGATTGTGAA
AC
Found at i:86433 original size:2 final size:2
Alignment explanation
Indices: 86426--86450 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
86416 AAAGAATCAT
86426 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 T
86451 TTTTTTCCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90598 original size:89 final size:89
Alignment explanation
Indices: 90497--90670 Score: 348
Period size: 89 Copynumber: 2.0 Consensus size: 89
90487 GGGTGGGATA
90497 GATATAAATTTAGTAGATAGTGGGCAAGAGTGGATGTAAAAAGTTATACCCGTTGTAGATAGTGA
1 GATATAAATTTAGTAGATAGTGGGCAAGAGTGGATGTAAAAAGTTATACCCGTTGTAGATAGTGA
90562 GTACTTAATGGGACCTCACCGATG
66 GTACTTAATGGGACCTCACCGATG
90586 GATATAAATTTAGTAGATAGTGGGCAAGAGTGGATGTAAAAAGTTATACCCGTTGTAGATAGTGA
1 GATATAAATTTAGTAGATAGTGGGCAAGAGTGGATGTAAAAAGTTATACCCGTTGTAGATAGTGA
90651 GTACTTAATGGGACCTCACC
66 GTACTTAATGGGACCTCACC
90671 CACCCCACAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (89 bp):
GATATAAATTTAGTAGATAGTGGGCAAGAGTGGATGTAAAAAGTTATACCCGTTGTAGATAGTGA
GTACTTAATGGGACCTCACCGATG
Found at i:91025 original size:30 final size:30
Alignment explanation
Indices: 90989--91089 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 30
90979 ATAATTTATG
*
90989 TAAAATGGATTACCTGAAAACTGTTTTACA
1 TAAAATGAATTACCTGAAAACTGTTTTACA
*** * *
91019 TAAAATGAATTATAAGAAAATTGTTTTACG
1 TAAAATGAATTACCTGAAAACTGTTTTACA
* * **
91049 TAAAATGAATTACCT-AATATTGTTTTATG
1 TAAAATGAATTACCTGAAAACTGTTTTACA
*
91078 TCAAATGAATTA
1 TAAAATGAATTA
91090 TATTTTTCGA
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
29 23 0.39
30 36 0.61
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.38
Consensus pattern (30 bp):
TAAAATGAATTACCTGAAAACTGTTTTACA
Found at i:91525 original size:33 final size:32
Alignment explanation
Indices: 91488--91567 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
91478 ATACAATATC
91488 ATATATTATTATAATATATT-TGAGTGTATATTA
1 ATATATTATTATAATATATTAT-A-TGTATATTA
* *
91521 ATATAATATTAAAATTATATTATATGTATATTA
1 ATATATTATTATAA-TATATTATATGTATATTA
91554 A-ATATT-TTAATAAT
1 ATATATTATT-ATAAT
91568 TAATATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
31 3 0.08
32 7 0.17
33 22 0.55
34 7 0.17
35 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (32 bp):
ATATATTATTATAATATATTATATGTATATTA
Found at i:91539 original size:22 final size:23
Alignment explanation
Indices: 91514--91574 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
91504 TATTTGAGTG
91514 TATATTAATATAATATTAAA-AT
1 TATATTAATATAATATTAAATAT
*
91536 TATATT-ATATGTATATTAAATAT
1 TATATTAATAT-AATATTAAATAT
* *
91559 TTTAATAAT-TAATATT
1 TATATTAATATAATATT
91575 TTTATTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 4 0.12
22 19 0.59
23 7 0.22
24 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TATATTAATATAATATTAAATAT
Found at i:91599 original size:19 final size:18
Alignment explanation
Indices: 91577--91624 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
91567 TTAATATTTT
*
91577 TATTAAAATGATATTAAAA
1 TATTAAAATAATATT-AAA
**
91596 TATTAATTTAATATTAAA
1 TATTAAAATAATATTAAA
91614 TATATAAAATA
1 TAT-TAAAATA
91625 TTTTTTGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
TATTAAAATAATATTAAA
Found at i:95032 original size:24 final size:24
Alignment explanation
Indices: 94938--95032 Score: 91
Period size: 24 Copynumber: 4.0 Consensus size: 24
94928 ATTTCCGACT
* *
94938 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATATATGATC
* * * * *
94962 TGAATTTTGTTCTGATTTCTTATA
1 TGAATTCTGTTCTGATATATGATC
* *
94986 TGGATTCTGTTCTGATATCTGATC
1 TGAATTCTGTTCTGATATATGATC
* *
95010 TGAATTCTGTTTTGATTTATGAT
1 TGAATTCTGTTCTGATATATGAT
95033 ATCTTCGTTT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATATGATC
Found at i:109756 original size:13 final size:13
Alignment explanation
Indices: 109738--109763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
109728 CTCCTATTCC
109738 ATACATTGGACAT
1 ATACATTGGACAT
109751 ATACATTGGACAT
1 ATACATTGGACAT
109764 GACCATCCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATACATTGGACAT
Found at i:117864 original size:263 final size:265
Alignment explanation
Indices: 117411--117892 Score: 618
Period size: 263 Copynumber: 1.8 Consensus size: 265
117401 TATTTGGGTC
* * *
117411 ATCATATTAACGTCCAGCTTAGACAATCGCTAATTTTTTAATGAAAAAATGGTAAGTTTAGAACA
1 ATCATATTAACGTCCAGCTTAAACAACCGC--ATTTTTTAATGAAAAAATGATAAGTTTAGAACA
** *
117476 TGATAAATAGTCGAGTGACTATTTTGTAACTTTAATAGCCAAAGGACTTAACAAAGCAATACTCT
64 AAATAAACAGTCGAGTGACTATTTTGTAACTTTAATAGCCAAAGGACTTAACAAAGCAATACTCT
* * * * *
117541 ATAGTCGAATGATCATTTTATAACTTTCAACATTATAATAACTTAATAAAGTACTACCCTATAAT
129 ATAGTAGAATGATCATTTTATAACTTTCAACAGTAGAAGAACTTAATAAAATACTACCCTATAAT
*
117606 C-AGGAGATCATTTGTC-TACTTTACGCTAAAAATAAATATCAAACAACTATCTAACAACTATCT
194 CAAGG-GACCATTT-TCGTACTTTACGCTAAAAATAAATATCAAACAACTATCTAACAACTATCT
117669 ATCACAGTT
257 ATCACAGTT
* * * *
117678 ATCATGTTAACGTCCAGCTTAAATAACCGC-TTTTTTAATG-AAAAATGATGAGTTTATAACAAA
1 ATCATATTAACGTCCAGCTTAAACAACCGCATTTTTTAATGAAAAAATGATAAGTTTAGAACAAA
** * *
117741 ATGGACAGTCG-GATGACTATTTTGTAACTTTTAATAGCC-GAGGACTTAACAAAGCAATATTCT
66 ATAAACAGTCGAG-TGACTATTTTGTAAC-TTTAATAGCCAAAGGACTTAACAAAGCAATACTCT
* * * * * *
117804 ATAGTTAG-ATGATCATTTTATAACTTTTAACAGTCGAGGGACTTAATAAAATAGTACCCTATAG
129 ATAG-TAGAATGATCATTTTATAACTTTCAACAGTAGAAGAACTTAATAAAATACTACCCTATAA
117868 TCAAGGGACCATTTTCGTACTTTAC
193 TCAAGGGACCATTTTCGTACTTTAC
117893 CCGTTTATTT
Statistics
Matches: 184, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
262 3 0.02
263 130 0.71
264 25 0.14
267 26 0.14
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (265 bp):
ATCATATTAACGTCCAGCTTAAACAACCGCATTTTTTAATGAAAAAATGATAAGTTTAGAACAAA
ATAAACAGTCGAGTGACTATTTTGTAACTTTAATAGCCAAAGGACTTAACAAAGCAATACTCTAT
AGTAGAATGATCATTTTATAACTTTCAACAGTAGAAGAACTTAATAAAATACTACCCTATAATCA
AGGGACCATTTTCGTACTTTACGCTAAAAATAAATATCAAACAACTATCTAACAACTATCTATCA
CAGTT
Found at i:120296 original size:30 final size:31
Alignment explanation
Indices: 120261--120320 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
120251 TAGTTACGTT
*
120261 GGGGACCATATTACAAACAGA-TTAATATTG
1 GGGGACCATATTACAAACAGACTAAATATTG
* *
120291 GGGGACTATATTGCAAACAGACTAAATATT
1 GGGGACCATATTACAAACAGACTAAATATT
120321 AAAGGACTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (31 bp):
GGGGACCATATTACAAACAGACTAAATATTG
Found at i:122247 original size:37 final size:37
Alignment explanation
Indices: 122205--122278 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
122195 TCATTACACC
* *
122205 TTTTTAT-ATTTTCAATTTTGTAAAAAAAATTATATAA
1 TTTTTATGAATTTAAATTTTGTAAAAAAAA-TATATAA
* *
122242 TTTTTATGAATTTAAATTTTTTAAAGAAAATATATAA
1 TTTTTATGAATTTAAATTTTGTAAAAAAAATATATAA
122279 ATATTTTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (37 bp):
TTTTTATGAATTTAAATTTTGTAAAAAAAATATATAA
Found at i:122890 original size:12 final size:12
Alignment explanation
Indices: 122873--122905 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
122863 ACCGGTCAAC
122873 CCGTTGACTCGA
1 CCGTTGACTCGA
122885 CCGTTGACTCGA
1 CCGTTGACTCGA
122897 CCGTTGACT
1 CCGTTGACT
122906 TTGACCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.24, T:0.27
Consensus pattern (12 bp):
CCGTTGACTCGA
Found at i:129068 original size:15 final size:15
Alignment explanation
Indices: 129048--129080 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
129038 ATTAGATCGA
129048 GTATAAAAAATTCGG
1 GTATAAAAAATTCGG
129063 GTATAAAAAATTCGG
1 GTATAAAAAATTCGG
129078 GTA
1 GTA
129081 GATTTAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (15 bp):
GTATAAAAAATTCGG
Found at i:141730 original size:39 final size:39
Alignment explanation
Indices: 141682--141758 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
141672 CGAGTTTGTT
* ** *
141682 GATGACGAAGATGACGCCGATGATGACTGGGAAGATGAA
1 GATGACGAAGATGAAGCCGACAACGACTGGGAAGATGAA
* *
141721 GATGGCGAAGGTGAAGCCGACAACGACTGGGAAGATGA
1 GATGACGAAGATGAAGCCGACAACGACTGGGAAGATGA
141759 TGAATCTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.38, T:0.13
Consensus pattern (39 bp):
GATGACGAAGATGAAGCCGACAACGACTGGGAAGATGAA
Found at i:158846 original size:21 final size:21
Alignment explanation
Indices: 158820--158873 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
158810 GCGTTGCATT
158820 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
* *
158841 TCGCGTTACGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
158862 TCGCATTGCGAT
1 TCGCGTTGCGAT
158874 TTTCCATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:159013 original size:21 final size:19
Alignment explanation
Indices: 158972--159020 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 19
158962 TTTTTTAACT
*
158972 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTAGAAA
158991 ATCGCAACGACATTGTAGAAA
1 ATCGCAACGA-ATT-TAGAAA
159012 ATCGCAACG
1 ATCGCAACG
159021 CGAAATGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 10 0.37
20 3 0.11
21 14 0.52
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (19 bp):
ATCGCAACGAATTTAGAAA
Found at i:159033 original size:20 final size:20
Alignment explanation
Indices: 159006--159080 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
158996 AACGACATTG
159006 TAGAAAATCGCAACGCGAAA
1 TAGAAAATCGCAACGCGAAA
* * **
159026 TGGAAAATCGCAACACGATT
1 TAGAAAATCGCAACGCGAAA
** *
159046 TTCAACTATCGCAACGCGAAA
1 TAGAA-AATCGCAACGCGAAA
159067 TAGAAAATCGCAAC
1 TAGAAAATCGCAAC
159081 ACGATTTTCA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (20 bp):
TAGAAAATCGCAACGCGAAA
Found at i:159034 original size:41 final size:41
Alignment explanation
Indices: 158985--159109 Score: 146
Period size: 41 Copynumber: 3.0 Consensus size: 41
158975 GCAACGAATT
158985 TGGAAAATCGCAACGAC-ATTGT-AGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAAC-ACGATTGTCA-AAAATCGCAACGCGAAA
* **
159026 TGGAAAATCGCAACACGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACACGATTGTCAAAAATCGCAACGCGAAA
* * ** *
159067 TAGAAAATCGCAACACGATTTTCAACTATCACAACGCGAAA
1 TGGAAAATCGCAACACGATTGTCAAAAATCGCAACGCGAAA
159108 TG
1 TG
159110 CAACGCGAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.03
41 73 0.96
42 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (41 bp):
TGGAAAATCGCAACACGATTGTCAAAAATCGCAACGCGAAA
Found at i:159058 original size:21 final size:21
Alignment explanation
Indices: 159032--159101 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
159022 GAAATGGAAA
159032 ATCGCAACACGATTTTCAACT
1 ATCGCAACACGATTTTCAACT
* ** ** *
159053 ATCGCAACGCGAAATAGAA-A
1 ATCGCAACACGATTTTCAACT
159073 ATCGCAACACGATTTTCAACT
1 ATCGCAACACGATTTTCAACT
*
159094 ATCACAAC
1 ATCGCAAC
159102 GCGAAATGCA
Statistics
Matches: 35, Mismatches: 13, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.21
Consensus pattern (21 bp):
ATCGCAACACGATTTTCAACT
Found at i:166765 original size:14 final size:12
Alignment explanation
Indices: 166737--166761 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
166727 TATTAATTTT
166737 TTTAAAATTATA
1 TTTAAAATTATA
166749 TTTAAAATTATA
1 TTTAAAATTATA
166761 T
1 T
166762 ATTTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAAAATTATA
Found at i:170255 original size:16 final size:17
Alignment explanation
Indices: 170224--170256 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
170214 AAATTTTTAC
*
170224 TTTTATTGAATAATATT
1 TTTTATTAAATAATATT
170241 TTTTATTAAAT-ATATT
1 TTTTATTAAATAATATT
170257 ATTTCGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTATTAAATAATATT
Found at i:172527 original size:48 final size:48
Alignment explanation
Indices: 172427--172554 Score: 134
Period size: 48 Copynumber: 2.7 Consensus size: 48
172417 CGATCACCAA
* * * *
172427 AATTCGAACACATGACCTTGCTTAAGGGATCTGATGACTCATTAACGG
1 AATTCGAACCCATGACCTTGCTTAAGGGATCTAATGACTCATCAACAG
* * * *
172475 AATTCGAACCCCTGACCTTGCTTAAGGAATCTAAT-ACCTCATCAATAT
1 AATTCGAACCCATGACCTTGCTTAAGGGATCTAATGA-CTCATCAACAG
* **
172523 AATTCGGA-CCATGAAATTGCTTAAGGGATCTA
1 AATTCGAACCCATGACCTTGCTTAAGGGATCTA
172555 GCGAGAATAC
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
47 21 0.32
48 45 0.68
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (48 bp):
AATTCGAACCCATGACCTTGCTTAAGGGATCTAATGACTCATCAACAG
Found at i:173713 original size:31 final size:30
Alignment explanation
Indices: 173678--173765 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 30
173668 TCAAAAAAAC
173678 TTAAGATTTTGTCACTTTCGTTTCGTTTTAA
1 TTAAGATTTTGTCACTTTCGTTTCGTTTT-A
* *
173709 TTAAGA-TTTGATCAC-TTCATTTTGTTTTA
1 TTAAGATTTTG-TCACTTTCGTTTCGTTTTA
*
173738 TTAAG-TTTTGGTCACTTACGTTATCGTT
1 TTAAGATTTT-GTCACTTTCGTT-TCGTT
173766 AAAGGTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
29 13 0.28
30 20 0.43
31 14 0.30
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.53
Consensus pattern (30 bp):
TTAAGATTTTGTCACTTTCGTTTCGTTTTA
Found at i:173752 original size:29 final size:30
Alignment explanation
Indices: 173678--173754 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
173668 TCAAAAAAAC
*
173678 TTAAGATTTT-GTCACTTTCGTTTCGTTTTAA
1 TTAAG-TTTTGGTCAC-TTCATTTCGTTTTAA
* * *
173709 TTAAGATTTGATCACTTCATTTTGTTTT-A
1 TTAAGTTTTGGTCACTTCATTTCGTTTTAA
173738 TTAAGTTTTGGTCACTT
1 TTAAGTTTTGGTCACTT
173755 ACGTTATCGT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 16 0.41
30 14 0.36
31 9 0.23
ACGTcount: A:0.21, C:0.12, G:0.13, T:0.55
Consensus pattern (30 bp):
TTAAGTTTTGGTCACTTCATTTCGTTTTAA
Found at i:179075 original size:16 final size:16
Alignment explanation
Indices: 179054--179084 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
179044 GATGAAGAGA
*
179054 AAACCCTAAAGCCGCC
1 AAACCCTAAAACCGCC
179070 AAACCCTAAAACCGC
1 AAACCCTAAAACCGC
179085 TGTTTCCGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.42, G:0.10, T:0.06
Consensus pattern (16 bp):
AAACCCTAAAACCGCC
Found at i:179803 original size:70 final size:70
Alignment explanation
Indices: 179727--179869 Score: 191
Period size: 70 Copynumber: 2.0 Consensus size: 70
179717 CCAGAATTCT
* *
179727 AGTTCAAAGGGGCAAAGTATAATTAACAAT-AAAAAT-GAGAGGGAAAAAATCAAAATAAACCAA
1 AGTTCAAAGGGGAAAAATATAATTAACAATAAAAAATGGA-AGGG-AAAAATCAAAATAAACCAA
179790 AACTTGA
64 AACTTGA
* * * *
179797 AGTTCAATGGGGAAAAATTTAATTAACAATAAAAAAATGGAAGGGCAAAATCAAAATAAATCAAA
1 AGTTCAAAGGGGAAAAATATAATTAACAAT-AAAAAATGGAAGGGAAAAATCAAAATAAACCAAA
179862 ACTTGA
65 ACTTGA
179868 AG
1 AG
179870 GACCAAATAG
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
70 26 0.41
71 26 0.41
72 10 0.16
73 2 0.03
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (70 bp):
AGTTCAAAGGGGAAAAATATAATTAACAATAAAAAATGGAAGGGAAAAATCAAAATAAACCAAAA
CTTGA
Found at i:179862 original size:71 final size:70
Alignment explanation
Indices: 179727--179869 Score: 191
Period size: 71 Copynumber: 2.0 Consensus size: 70
179717 CCAGAATTCT
* *
179727 AGTTCAAAGGGGCAAAGTATAATTAACAATAAAAATGAGAGGGAAAAAATCAAAATAAACCAAAA
1 AGTTCAAAGGGGAAAAATATAATTAACAATAAAAATGAGAGGGAAAAAATCAAAATAAACCAAAA
179792 CTTGA
66 CTTGA
* * * *
179797 AGTTCAATGGGGAAAAATTTAATTAACAATAAAAAAATG-GAAGGG-CAAAATCAAAATAAATCA
1 AGTTCAAAGGGGAAAAATATAATTAACAAT--AAAAATGAG-AGGGAAAAAATCAAAATAAACCA
179860 AAACTTGA
63 AAACTTGA
179868 AG
1 AG
179870 GACCAAATAG
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
70 26 0.41
71 27 0.42
72 11 0.17
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (70 bp):
AGTTCAAAGGGGAAAAATATAATTAACAATAAAAATGAGAGGGAAAAAATCAAAATAAACCAAAA
CTTGA
Found at i:180136 original size:76 final size:76
Alignment explanation
Indices: 180052--180208 Score: 226
Period size: 76 Copynumber: 2.1 Consensus size: 76
180042 AATGGAGGAA
* * *
180052 AAGAGTACACTCTCCCGACAAAAGGAAATAGAAAGAGACGCTTAAAGACACAAAACCAACACAGA
1 AAGAGTACACTCTCCCAACAAAAGGAAATAAAAAGAGACGATTAAAGACACAAAACCAACACAGA
180117 CAGAAAA-GATT
66 CA-AAAAGGATT
* * * * *
180128 AAGAGTACACTCTCCCAACAAAAGGAAATAAAAATAGACGATTAAGGACGCAAAACCAACATAGT
1 AAGAGTACACTCTCCCAACAAAAGGAAATAAAAAGAGACGATTAAAGACACAAAACCAACACAGA
180193 CAAAAAGGATT
66 CAAAAAGGATT
180204 AAGAG
1 AAGAG
180209 CCCCCGAGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 4 0.06
76 68 0.94
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (76 bp):
AAGAGTACACTCTCCCAACAAAAGGAAATAAAAAGAGACGATTAAAGACACAAAACCAACACAGA
CAAAAAGGATT
Found at i:180576 original size:29 final size:29
Alignment explanation
Indices: 180541--180612 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
180531 ACAAATTATT
180541 ATAGTCAGAGGACTATTTTGTAACTTTTA
1 ATAGTCAGAGGACTATTTTGTAACTTTTA
180570 ATAGTCAGAGGACTATTTTGTAACTTTTA
1 ATAGTCAGAGGACTATTTTGTAACTTTTA
*
180599 ATAGTCAGGGGACT
1 ATAGTCAGAGGACT
180613 TAATAAAACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (29 bp):
ATAGTCAGAGGACTATTTTGTAACTTTTA
Found at i:181437 original size:21 final size:21
Alignment explanation
Indices: 181411--181454 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
181401 AAATTATACA
*
181411 TTTAGTACTTAAACTATC-AAT
1 TTTAGTACCTAAACT-TCTAAT
181432 TTTAGTACCTAAACTTCTAAT
1 TTTAGTACCTAAACTTCTAAT
181453 TT
1 TT
181455 CTTCAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTAGTACCTAAACTTCTAAT
Found at i:188984 original size:12 final size:13
Alignment explanation
Indices: 188948--188991 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
188938 GCCCCGATTA
188948 CCCGATTACCCGC
1 CCCGATTACCCGC
188961 CCCGATTACCCGC
1 CCCGATTACCCGC
*
188974 CCCGA-TACCCGA
1 CCCGATTACCCGC
188986 CCCGAT
1 CCCGAT
188992 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:189043 original size:30 final size:30
Alignment explanation
Indices: 188993--189081 Score: 71
Period size: 30 Copynumber: 3.0 Consensus size: 30
188983 CGACCCGATA
188993 AATATTAA-AAATAATT-ATTTATATATATAT
1 AATATTAATAAAT--TTAATTTATATATATAT
* *
189023 AATATTAATAAATTTAATTTA-A-ATAAAA
1 AATATTAATAAATTTAATTTATATATATAT
* * *
189051 AATATATATTTAATTTAA-ATATATATATAT
1 AATAT-TAATAAATTTAATTTATATATATAT
189081 A
1 A
189082 CCCGGCCCGA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
28 11 0.23
29 14 0.30
30 18 0.38
31 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AATATTAATAAATTTAATTTATATATATAT
Found at i:189048 original size:24 final size:26
Alignment explanation
Indices: 189021--189081 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
189011 TTATATATAT
*
189021 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
189045 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
*
189069 AT-ATATATATATA
1 ATAATATAAATATA
189082 CCCGGCCCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 4 0.13
23 3 0.10
24 18 0.58
25 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:189063 original size:19 final size:19
Alignment explanation
Indices: 189039--189078 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
189029 AATAAATTTA
189039 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
189058 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
189077 AT
1 AT
189079 ATACCCGGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:189123 original size:12 final size:12
Alignment explanation
Indices: 189099--189141 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
189089 CGATTCCCAG
189099 CCCAATA-CCGA
1 CCCAATACCCGA
189110 CCCAATACCCGA
1 CCCAATACCCGA
* *
189122 CCCAATACCTGG
1 CCCAATACCCGA
189134 CCCAATAC
1 CCCAATAC
189142 TCGTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.33, C:0.47, G:0.09, T:0.12
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:189607 original size:21 final size:21
Alignment explanation
Indices: 189582--189623 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
189572 AAATTTTAAA
* * *
189582 AAATATTAATGTTTTAGGTAG
1 AAATAATAACGTTTTAAGTAG
189603 AAATAATAACGTTTTAAGTAG
1 AAATAATAACGTTTTAAGTAG
189624 TTTTTTTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (21 bp):
AAATAATAACGTTTTAAGTAG
Found at i:192375 original size:20 final size:22
Alignment explanation
Indices: 192333--192375 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
192323 TTAATAAAAA
*
192333 TAATATATTTTTATTTTTGTCT
1 TAATATATTTTTACTTTTGTCT
*
192355 TAATATGTTTTT-CTTTT-TCT
1 TAATATATTTTTACTTTTGTCT
192375 T
1 T
192376 TTTCTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 11 0.58
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (22 bp):
TAATATATTTTTACTTTTGTCT
Found at i:192377 original size:5 final size:6
Alignment explanation
Indices: 192362--192386 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
192352 TCTTAATATG
192362 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
192387 CTAAAACTAT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:192758 original size:2 final size:2
Alignment explanation
Indices: 192751--192798 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
192741 AGAATATGAA
192751 AT AT AT AT AT 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 AT AT AT AT AT
192793 AT AT AT
1 AT AT AT
192799 CTTATATGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:193102 original size:26 final size:27
Alignment explanation
Indices: 193068--193125 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
193058 AAAAAATCAA
*
193068 AAATCAGG-AAAAATTCCTCAACATTC
1 AAATCAGGAAAAAAATCCTCAACATTC
*
193094 AAATCAGGAAAAAAAATCCTCAACGTTC
1 AAATCAGG-AAAAAAATCCTCAACATTC
193122 AAAT
1 AAAT
193126 TAAAAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 8 0.29
28 20 0.71
ACGTcount: A:0.50, C:0.21, G:0.09, T:0.21
Consensus pattern (27 bp):
AAATCAGGAAAAAAATCCTCAACATTC
Found at i:193135 original size:28 final size:29
Alignment explanation
Indices: 193075--193137 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
193065 CAAAAATCAG
* *
193075 GAAAAATTCCTCAACATTCAAATCAGGAA
1 GAAAAAATCCTCAACATTCAAATCAGAAA
* *
193104 -AAAAAATCCTCAACGTTCAAATTA-AAA
1 GAAAAAATCCTCAACATTCAAATCAGAAA
193131 GAAAAAA
1 GAAAAAA
193138 CCAAAAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.19
Consensus pattern (29 bp):
GAAAAAATCCTCAACATTCAAATCAGAAA
Found at i:193373 original size:20 final size:20
Alignment explanation
Indices: 193336--193374 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
193326 ATATTTAATA
*
193336 TTTTCTTTTTGTATATTTTT
1 TTTTCTTTTTGTACATTTTT
193356 TTTTCTTTTT-TAACATTTT
1 TTTTCTTTTTGT-ACATTTT
193375 GCAATCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTTGTACATTTTT
Found at i:197410 original size:59 final size:58
Alignment explanation
Indices: 197253--197430 Score: 203
Period size: 59 Copynumber: 3.0 Consensus size: 58
197243 GATAAATTCA
* *
197253 GGATGAAATTGGAATATTCAAAAGTTTAGGGACCAATTTATAAATAGGGTCATAGTTTAG
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTA-AAATAGAGTCATAGTTT-G
* * * ** * ** *
197313 GAATGATATTAGAATGCTCAAAAGTTGAAGGATTAATTTAGAATGAGAGTCATAGTTTG
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAAAAT-AGAGTCATAGTTTG
* *
197372 GGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAAAATTAAAGTTATAGTTTG
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAAAA-TAGAGTCATAGTTTG
197431 AGGACATATT
Statistics
Matches: 94, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
59 50 0.53
60 44 0.47
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.33
Consensus pattern (58 bp):
GGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAAAATAGAGTCATAGTTTG
Found at i:197463 original size:2 final size:2
Alignment explanation
Indices: 197456--197491 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
197446 ATTAACTCTT
197456 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
197492 CAGTAACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:210355 original size:330 final size:330
Alignment explanation
Indices: 209754--210417 Score: 1292
Period size: 330 Copynumber: 2.0 Consensus size: 330
209744 TTCTATAAAA
209754 GATTGGTATGGTAATGAATTTGTGGTCTAACAATGTTCAAATATAAGAATTCCTAGCCATTTGAT
1 GATTGGTATGGTAATGAATTTGTGGTCTAACAATGTTCAAATATAAGAATTCCTAGCCATTTGAT
*
209819 CTCAGAATTGCCCCATGCTTTAGGGTTTAGGGAACTTTTCATCCATTGCTAACAGACAAGAGAGC
66 CTCAGAATCGCCCCATGCTTTAGGGTTTAGGGAACTTTTCATCCATTGCTAACAGACAAGAGAGC
209884 TAAGCTATATCTTAATAGCATCCCAACAGTTATTGTCAATACATATATGTAAGATATACACATCT
131 TAAGCTATATCTTAATAGCATCCCAACAGTTATTGTCAATACATATATGTAAGATATACACATCT
209949 AGCAAACAAGGTGGACCCAAAATTTCCTTTTGGCTCTTTCTTCACCATTGACAGAGCCACATGCT
196 AGCAAACAAGGTGGACCCAAAATTTCCTTTTGGCTCTTTCTTCACCATTGACAGAGCCACATGCT
210014 TGTCCAAGTCAAATATAATGAATAATATTAAGAGTCGAACTTTGATTTATAATACCAATAAAAAA
261 TGTCCAAGTCAAATATAATGAATAATATTAAGAGTCGAACTTTGATTTATAATACCAATAAAAAA
210079 ATAAT
326 ATAAT
210084 GATTGGTATGGTAATGAATTTGTGGTCTAACAATGTTCAAATATAAGAATTCCTAGCCATTTGAT
1 GATTGGTATGGTAATGAATTTGTGGTCTAACAATGTTCAAATATAAGAATTCCTAGCCATTTGAT
*
210149 CTCAGAATCGCCCTATGCTTTAGGGTTTAGGGAACTTTTCATCCATTGCTAACAGACAAGAGAGC
66 CTCAGAATCGCCCCATGCTTTAGGGTTTAGGGAACTTTTCATCCATTGCTAACAGACAAGAGAGC
* *
210214 TAAGTTATATCTTAATAGCATCCCAACAGTTATTGTCAATACATATATGTAAGATATACACATTT
131 TAAGCTATATCTTAATAGCATCCCAACAGTTATTGTCAATACATATATGTAAGATATACACATCT
210279 AGCAAACAAGGTGGACCCAAAATTTCCTTTTGGCTCTTTCTTCACCATTGACAGAGCCACATGCT
196 AGCAAACAAGGTGGACCCAAAATTTCCTTTTGGCTCTTTCTTCACCATTGACAGAGCCACATGCT
210344 TGTCCAAGTCAAATATAATGAATAATATTAAGAGTCGAACTTTGATTTATAATACCAATAAAAAA
261 TGTCCAAGTCAAATATAATGAATAATATTAAGAGTCGAACTTTGATTTATAATACCAATAAAAAA
210409 ATAAT
326 ATAAT
210414 GATT
1 GATT
210418 TTATCCCTTC
Statistics
Matches: 330, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
330 330 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (330 bp):
GATTGGTATGGTAATGAATTTGTGGTCTAACAATGTTCAAATATAAGAATTCCTAGCCATTTGAT
CTCAGAATCGCCCCATGCTTTAGGGTTTAGGGAACTTTTCATCCATTGCTAACAGACAAGAGAGC
TAAGCTATATCTTAATAGCATCCCAACAGTTATTGTCAATACATATATGTAAGATATACACATCT
AGCAAACAAGGTGGACCCAAAATTTCCTTTTGGCTCTTTCTTCACCATTGACAGAGCCACATGCT
TGTCCAAGTCAAATATAATGAATAATATTAAGAGTCGAACTTTGATTTATAATACCAATAAAAAA
ATAAT
Found at i:210701 original size:28 final size:29
Alignment explanation
Indices: 210646--210711 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 29
210636 TTTTAGTCGA
210646 TAAATTT-TAAATGTTATAAAATGATCAT
1 TAAATTTATAAATGTTATAAAATGATCAT
210674 TAAATTTTATAAATAGTTA-AAAA-G-TCAT
1 TAAA-TTTATAAAT-GTTATAAAATGATCAT
210702 TAAAATTTAT
1 T-AAATTTAT
210712 CATACTATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
28 14 0.41
29 7 0.21
30 9 0.26
31 4 0.12
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (29 bp):
TAAATTTATAAATGTTATAAAATGATCAT
Found at i:211763 original size:55 final size:56
Alignment explanation
Indices: 211658--211763 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 56
211648 TATAATATTA
* * * * *
211658 TTTTATTAAATCTTTCAATTATTAAAAGTTATAAAATGATATTCTGACTATAGATG
1 TTTTATTAAATCTTCCAACTATTAAAAGTTACAAAATAATACTCTGACTATAGATG
*
211714 TTTTATTAAATC-TCCGACTATTAAAAGTTACAAAATAATCACTCT-ACTAT
1 TTTTATTAAATCTTCCAACTATTAAAAGTTACAAAATAAT-ACTCTGACTAT
211764 TTTTTATGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
55 27 0.63
56 16 0.37
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (56 bp):
TTTTATTAAATCTTCCAACTATTAAAAGTTACAAAATAATACTCTGACTATAGATG
Found at i:218718 original size:13 final size:14
Alignment explanation
Indices: 218700--218733 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
218690 CTATACTCTG
*
218700 CCCTAACTTA-AAA
1 CCCTAAATTACAAA
218713 CCCTAAATTACAAA
1 CCCTAAATTACAAA
218727 CCCTAAA
1 CCCTAAA
218734 CCCTAACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (14 bp):
CCCTAAATTACAAA
Found at i:221019 original size:32 final size:32
Alignment explanation
Indices: 220983--221085 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
220973 TATACCGTTC
220983 ATATGATGTTCGTTTGTTAATCAATATAAACA
1 ATATGATGTTCGTTTGTTAATCAATATAAACA
221015 ATATGATGTTCGTTTGTTAATCAATATAAACA
1 ATATGATGTTCGTTTGTTAATCAATATAAACA
* *
221047 ATATAATGTTCATTTGTTAATCAATATAAACAA
1 ATATGATGTTCGTTTGTTAATCAATATAAAC-A
221080 ATATGA
1 ATATGA
221086 CTAAAGATTT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 61 0.91
33 6 0.09
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.40
Consensus pattern (32 bp):
ATATGATGTTCGTTTGTTAATCAATATAAACA
Found at i:232369 original size:2 final size:2
Alignment explanation
Indices: 232362--232401 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
232352 CCAGTTAATT
232362 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
232402 TTTAAGAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:232436 original size:20 final size:19
Alignment explanation
Indices: 232413--232485 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 19
232403 TTAAGAATTT
232413 TATT-TTTATATTAATAAAAA
1 TATTATTTA-ATT-ATAAAAA
*
232433 TATTATTTAATTATTAAAA
1 TATTATTTAATTATAAAAA
***
232452 TATTAAAAATATTATAAAATA
1 TATTATTTA-ATTATAAAA-A
232473 TATTAATTTAATT
1 TATT-ATTTAATT
232486 GTTTAAAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
19 12 0.29
20 15 0.37
21 12 0.29
22 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTATTTAATTATAAAAA
Found at i:233202 original size:29 final size:29
Alignment explanation
Indices: 233160--233236 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
233150 AGTATTGGTC
*
233160 GTAGGTCGCCATGCACTCCGGACGACCTT
1 GTAGGTCGCCATGCACTCCGGACGACCAT
* *
233189 GTAGGTCGCCATGCACTTCGGGCGACCAT
1 GTAGGTCGCCATGCACTCCGGACGACCAT
233218 GTAGGTCGCCATGCACTCC
1 GTAGGTCGCCATGCACTCC
233237 TGGCGACTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.17, C:0.34, G:0.29, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGACGACCAT
Found at i:233336 original size:29 final size:29
Alignment explanation
Indices: 233303--233359 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
233293 GTCCCAACAC
*
233303 ATAGGTCGCCATGCCCTCCGGGCGACCTT
1 ATAGGTCGCCATGCACTCCGGGCGACCTT
233332 ATAGGTCGCCATGCACTCCGGGCGACCT
1 ATAGGTCGCCATGCACTCCGGGCGACCT
233360 ACCCTCGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.37, G:0.28, T:0.19
Consensus pattern (29 bp):
ATAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:233404 original size:33 final size:33
Alignment explanation
Indices: 233363--233432 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
233353 GCGACCTACC
* *
233363 CTCGCTCGGCTT-CTCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
233396 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
233429 CTCG
1 CTCG
233433 TTCAGATGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.09, C:0.40, G:0.24, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:233446 original size:33 final size:33
Alignment explanation
Indices: 233377--233447 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
233367 CTCGGCTTCT
* * *
233377 CTCGGATTCCCTCGCATAGCTCGCTCGGTTGCC
1 CTCGGATGCCCTCGCATAGCTCGCTCAGATGCC
* *
233410 CTCGGATGCCCTCGCATAGCTCGTTCAGATGGC
1 CTCGGATGCCCTCGCATAGCTCGCTCAGATGCC
233443 CTCGG
1 CTCGG
233448 TCAGATGGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.11, C:0.37, G:0.27, T:0.25
Consensus pattern (33 bp):
CTCGGATGCCCTCGCATAGCTCGCTCAGATGCC
Found at i:233451 original size:14 final size:14
Alignment explanation
Indices: 233429--233461 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
233419 CCTCGCATAG
*
233429 CTCGTTCAGATGGC
1 CTCGGTCAGATGGC
233443 CTCGGTCAGATGGC
1 CTCGGTCAGATGGC
233457 CTCGG
1 CTCGG
233462 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.30, G:0.33, T:0.24
Consensus pattern (14 bp):
CTCGGTCAGATGGC
Found at i:233567 original size:29 final size:29
Alignment explanation
Indices: 233535--233610 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
233525 TAGCTCATCG
*
233535 GGAAGACATGGCGACCTAGTAGGTCGCCC
1 GGAAGGCATGGCGACCTAGTAGGTCGCCC
233564 GGAAGGCATGGCGACCTAGTAGGTCGCCC
1 GGAAGGCATGGCGACCTAGTAGGTCGCCC
*
233593 GGAAGGCATGACGACCTA
1 GGAAGGCATGGCGACCTA
233611 TGGCCAACAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.25, C:0.26, G:0.36, T:0.13
Consensus pattern (29 bp):
GGAAGGCATGGCGACCTAGTAGGTCGCCC
Found at i:243259 original size:29 final size:30
Alignment explanation
Indices: 243216--243295 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
243206 AACTTAGATG
243216 AAAAAATAAATATTTTAAATATTA-TTTAATT
1 AAAAAAT-AA-ATTTTAAATATTATTTTAATT
*
243247 AAAAAATAAATTTCT--ATACTTATTTTGATT
1 AAAAAATAAATTT-TAAATA-TTATTTTAATT
243277 AAAAAAT-AA-TTTAAATATT
1 AAAAAATAAATTTTAAATATT
243296 GCAATGAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
27 1 0.02
28 7 0.16
29 12 0.28
30 16 0.37
31 7 0.16
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (30 bp):
AAAAAATAAATTTTAAATATTATTTTAATT
Found at i:244012 original size:2 final size:2
Alignment explanation
Indices: 244007--244036 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
243997 AATAAAAGTA
244007 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
244037 CGATGGTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:258455 original size:3 final size:3
Alignment explanation
Indices: 258447--258520 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
258437 TTTTTATCCA
* * *
258447 TAT TAT TAT TAT TAG TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
258495 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
258521 AATATATATT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:271073 original size:18 final size:18
Alignment explanation
Indices: 271050--271141 Score: 87
Period size: 19 Copynumber: 4.7 Consensus size: 18
271040 ATTATGCTTG
271050 AAGAAAAAAGAAAAAAAA
1 AAGAAAAAAGAAAAAAAA
271068 AAGAAAAGAAAGAAAAGAAAA
1 AAG-AAA-AAAGAAAA-AAAA
271089 AA-AAGAAAAGAAAAAAAA
1 AAGAA-AAAAGAAAAAAAA
* *
271107 AATAGAAAATGAAAAAAAA
1 AAGA-AAAAAGAAAAAAAA
271126 AGAGAAGAAAAAGAAA
1 A-AG-A-AAAAAGAAA
271142 GGGGGTCAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
18 9 0.14
19 27 0.43
20 11 0.17
21 16 0.25
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAGAAAAAAAA
Found at i:271096 original size:34 final size:35
Alignment explanation
Indices: 271048--271141 Score: 122
Period size: 34 Copynumber: 2.7 Consensus size: 35
271038 GTATTATGCT
* *
271048 TGAAGAAAAAAGAAAAAAAAAAGAAAAGAAAGAAAA
1 TGAAAAAAAAAGAAAAGAAAAAGAAAA-AAAGAAAA
*
271084 -G-AAAAAAAAGAAAAGAAAAA-AAAAATAGAAAA
1 TGAAAAAAAAAGAAAAGAAAAAGAAAAAAAGAAAA
*
271116 TGAAAAAAAAAGAGAAGAAAAAGAAA
1 TGAAAAAAAAAGAAAAGAAAAAGAAA
271142 GGGGGTCAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
32 7 0.14
33 5 0.10
34 35 0.69
35 4 0.08
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (35 bp):
TGAAAAAAAAAGAAAAGAAAAAGAAAAAAAGAAAA
Found at i:272647 original size:83 final size:83
Alignment explanation
Indices: 272174--272649 Score: 785
Period size: 83 Copynumber: 5.7 Consensus size: 83
272164 CATTAAATGA
*
272174 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
**
272238 AACCAATCATTGAATTTAA
65 AACCAATCATTGAATTTGG
* *
272257 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
272322 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTGG
* * *
272340 AAGATGAATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
272404 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTGG
* *
272423 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
272488 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTGG
* *
272506 AAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
272571 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
272589 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
272650 TAAGAACTAC
Statistics
Matches: 363, Mismatches: 27, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
82 3 0.01
83 354 0.98
84 6 0.02
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAATTTGG
Found at i:273495 original size:113 final size:112
Alignment explanation
Indices: 273292--273962 Score: 943
Period size: 113 Copynumber: 5.9 Consensus size: 112
273282 ATTCAAATCT
*
273292 ATCATTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
273357 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG-CTGAATTC
* * *
273405 ATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAA
1 ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * *
273470 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTGAATTC
* *
273517 TATCATTTGATGGATTAACATTCCCAGAGAA-GTTCATAATGAGAAGAATTCATCTGAAGAAGGA
1 -ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
273581 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTGAATTC
* *** * *
273629 TATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 -ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
273694 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-TGAATTC
* * *
273743 ATCATTTGATGAATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCATTTGATGGATTAACATTGCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAA
*
273807 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCATGAATTC
62 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-TGAATTC
* * * ** *
273859 ATCAATTGATGGATCAACATTTCTGGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
273923 GAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
273963 ATAATTCTAT
Statistics
Matches: 510, Mismatches: 40, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
112 164 0.32
113 237 0.46
114 5 0.01
115 18 0.04
116 84 0.16
117 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (112 bp):
ATCATTTGATGGATTAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTGAATTC
Found at i:273601 original size:24 final size:23
Alignment explanation
Indices: 273558--273602 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
273548 GTTCATAATG
*
273558 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
273581 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
273603 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:273676 original size:225 final size:225
Alignment explanation
Indices: 273284--273962 Score: 981
Period size: 225 Copynumber: 3.0 Consensus size: 225
273274 TAGCAAAGAT
* *
273284 TCAAATCTATCATTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCATTTGATGGATTAACATTGCCAGAGAA-GTTCATAATGAGAAGAATTCATCTGA
* **
273349 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAAT-TCATCACTTG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCT-ATCACTTG
* * *
273413 ATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGT
129 ATGGATTATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
273478 TCATAATGAGAAGAATTTGTTCAACCTTTTGC
194 TCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
273510 TCAAATCTATCATTTGATGGATTAACATTCCCAGAGAAGTTCATAATGAGAAGAATTCATCTGAA
1 TCAAATCTATCATTTGATGGATTAACATTGCCAGAGAAGTTCATAATGAGAAGAATTCATCTGAA
273575 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGAT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGAT
**
273640 GGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
131 GGATTATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
*
273705 ATAATGAGAAGAACTTGTTCAATCTTTTGC
196 ATAATGAGAAGAACTTGTTCAACCTTTTGC
** * *
273735 TTGAAT-TCATCATTTGATGAATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCA
1 TCAAATCT-ATCATTTGATGGATTAACATTGCCAGAG-A-AGTTCATAATGAGAAGAA-T--TCA
* * * *
273798 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCATGAATTC-ATC
60 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAAATCTATC
* * * ** *
273862 AATTGATGGATCAACATTTCTGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAA
124 ACTTGATGGATTATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
* *
273926 GAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
189 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
273963 ATAATTCTAT
Statistics
Matches: 412, Mismatches: 33, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
224 2 0.00
225 202 0.49
226 55 0.13
227 1 0.00
228 72 0.17
229 75 0.18
230 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (225 bp):
TCAAATCTATCATTTGATGGATTAACATTGCCAGAGAAGTTCATAATGAGAAGAATTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGAT
GGATTATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:273725 original size:338 final size:340
Alignment explanation
Indices: 273284--273962 Score: 1060
Period size: 338 Copynumber: 2.0 Consensus size: 340
273274 TAGCAAAGAT
* *
273284 TCAAATCTATCATTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCACTTGATGGATTATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
273349 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGA
* * *
273414 TGGATTATCATTGCCAGAGAAG-GTTCATAATGAGAAGAAC-C-CATCTGAAGAAGGAAGAAGAA
131 TGAATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGCATCTGAAGAAGGAAGAAGAA
* * *
273476 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAAATCTATCATTTGATGGATTAACATTC
195 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATCAAATC-ATCAATTGATGGATCAACATTC
* * *
273540 CCAGAGAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
259 CCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAA
*
273605 TTTGTTCAACCTTTTGC
324 CTTGTTCAACCTTTTGC
** *
273622 TCAAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCTATCACTTGATGGATTATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
273687 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGA
*
273752 TGAATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAA
131 TGAATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCG-CATCTGAAGAAGGAAGAAGAA
* * * *
273817 GTTCATAATGAGAAGAACTTGTTCAATCTTTTGCATGAATTCATCAATTGATGGATCAACATTTC
195 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATCAAATCATCAATTGATGGATCAACATTCC
**
273882 TGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAAC
260 CAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAAC
*
273947 TTGTTCAACTTTTTGC
325 TTGTTCAACCTTTTGC
273963 ATAATTCTAT
Statistics
Matches: 309, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
337 3 0.01
338 153 0.50
339 1 0.00
341 147 0.48
342 5 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (340 bp):
TCAAATCTATCACTTGATGGATTATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGA
TGAATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGCATCTGAAGAAGGAAGAAGAAG
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCATCAAATCATCAATTGATGGATCAACATTCCC
AGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACT
TGTTCAACCTTTTGC
Found at i:274287 original size:3 final size:3
Alignment explanation
Indices: 274279--274370 Score: 148
Period size: 3 Copynumber: 30.7 Consensus size: 3
274269 TTTTTATCCA
* * *
274279 TAT TAT TAT TAT TAG TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
274327 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
274371 AATATATATT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:278864 original size:18 final size:19
Alignment explanation
Indices: 278829--278865 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
278819 CACGGACTTT
278829 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
278849 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
278866 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:285495 original size:16 final size:16
Alignment explanation
Indices: 285476--285508 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
285466 CCTTAACTTG
285476 ACCCGTTATCATCCCT
1 ACCCGTTATCATCCCT
285492 ACCCGTTATCATCCCT
1 ACCCGTTATCATCCCT
285508 A
1 A
285509 ATCCTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.42, G:0.06, T:0.30
Consensus pattern (16 bp):
ACCCGTTATCATCCCT
Found at i:286317 original size:59 final size:59
Alignment explanation
Indices: 286234--286361 Score: 175
Period size: 59 Copynumber: 2.2 Consensus size: 59
286224 AAGGGTAAAC
* * * *
286234 TACACAAATGGTCCTTTGACTATAATATGTTATTTTATTAAGTCCCCGACTATCAAAAGT
1 TACA-AAATGATCCCTTGACTATAAGATGTTACTTTATTAAGTCCCCGACTATCAAAAGT
* * * *
286294 TACAAAATGATCCCTTGATTATAAGATGTTGCTTTGTTGAGTCCCCGACTATCAAAAGT
1 TACAAAATGATCCCTTGACTATAAGATGTTACTTTATTAAGTCCCCGACTATCAAAAGT
286353 TACAAAATG
1 TACAAAATG
286362 GATACCTAGC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 56 0.93
60 4 0.07
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (59 bp):
TACAAAATGATCCCTTGACTATAAGATGTTACTTTATTAAGTCCCCGACTATCAAAAGT
Found at i:290682 original size:4 final size:4
Alignment explanation
Indices: 290673--290703 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
290663 CTGCAAAATA
*
290673 TAAT TAAT TAAT TAGT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
290704 ATCGTGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:291003 original size:18 final size:18
Alignment explanation
Indices: 290961--291012 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
290951 AGAAAATAAA
* *
290961 TTACTTATAAATATGATG
1 TTACTTATAATTATTATG
290979 TTACTTATAATTATTATAG
1 TTACTTATAATTATTAT-G
290998 TT-CTTA-AATTTATTA
1 TTACTTATAA-TTATTA
291013 GGGTGTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 25 0.83
19 3 0.10
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (18 bp):
TTACTTATAATTATTATG
Found at i:300220 original size:6 final size:6
Alignment explanation
Indices: 300068--300217 Score: 255
Period size: 6 Copynumber: 25.0 Consensus size: 6
300058 AATACAATCA
* * * *
300068 ATATAT ATATAT ATATAT ATATAT ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
300116 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
300164 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
*
300212 TTATAC
1 ATATAC
300218 TTACCATGAT
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 142 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:300480 original size:22 final size:22
Alignment explanation
Indices: 300455--300505 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
300445 TTCATGTTGA
* * * *
300455 CGACGATCCGTCGTTAATCTTC
1 CGACGATACGTCCTCAACCTTC
300477 CGACGATACGTCCTCAACCTTC
1 CGACGATACGTCCTCAACCTTC
300499 CGACGAT
1 CGACGAT
300506 TAAAAGATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (22 bp):
CGACGATACGTCCTCAACCTTC
Found at i:302260 original size:60 final size:59
Alignment explanation
Indices: 302120--302262 Score: 180
Period size: 60 Copynumber: 2.4 Consensus size: 59
302110 TCGGGTAACC
* *
302120 ATTTTGTAACTTTTAATAGTAGAAACACTCAACAAAGCAACACTCTATAGTCGGATAATC
1 ATTTTGTAACTTTTAATAGTCGAAACACTCAACAAAGCAACACTCTATAGTC-GATAATA
* * * * *
302180 ATTTTGTAACTTTTAATAGTCTAGAGACTCAACAAATCAACACTCTATGGTC-ATAAGATA
1 ATTTTGTAACTTTTAATAGTCGAAACACTCAACAAAGCAACACTCTATAGTCGAT-A-ATA
*
302240 ATTTTATAACTTTTAATAGTCGA
1 ATTTTGTAACTTTTAATAGTCGA
302263 TGAACTTAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
58 2 0.03
59 1 0.01
60 69 0.96
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCGAAACACTCAACAAAGCAACACTCTATAGTCGATAATA
Found at i:306873 original size:24 final size:25
Alignment explanation
Indices: 306821--306873 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
306811 GGTTAAAATA
* *
306821 ATAAACGAGCATAAATGAACGATAG
1 ATAAACGAACATAAATGAACGAAAG
*
306846 -TAAATGAACATAAATGAAC-AAAG
1 ATAAACGAACATAAATGAACGAAAG
306869 ATAAA
1 ATAAA
306874 ATTAATTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.58, C:0.09, G:0.15, T:0.17
Consensus pattern (25 bp):
ATAAACGAACATAAATGAACGAAAG
Found at i:306965 original size:19 final size:21
Alignment explanation
Indices: 306921--306965 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
306911 TAATTCAAGG
306921 GTTTATATTTTCTTTAATTAT
1 GTTTATATTTTCTTTAATTAT
* *
306942 TTTTATA-TTT-TTTAATTGT
1 GTTTATATTTTCTTTAATTAT
306961 GTTTA
1 GTTTA
306966 AAATTAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 12 0.57
20 3 0.14
21 6 0.29
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (21 bp):
GTTTATATTTTCTTTAATTAT
Found at i:309866 original size:22 final size:22
Alignment explanation
Indices: 309841--309892 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
309831 TGACACATGT
*
309841 CATTTAACGAGATTTTTAATTA
1 CATTTAACGAGATTTTTAACTA
*
309863 CATTTAACGAGGTTTTTAACTA
1 CATTTAACGAGATTTTTAACTA
309885 CATTTAAC
1 CATTTAAC
309893 ATCTAGGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
CATTTAACGAGATTTTTAACTA
Found at i:310777 original size:24 final size:21
Alignment explanation
Indices: 310730--310770 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
310720 AATAAAAATG
*
310730 TTACTAATTTTAAAAAAAAGT
1 TTACTAAGTTTAAAAAAAAGT
*
310751 TTACTAAGTTTAAGAAAAAG
1 TTACTAAGTTTAAAAAAAAG
310771 ATTTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (21 bp):
TTACTAAGTTTAAAAAAAAGT
Found at i:329342 original size:60 final size:60
Alignment explanation
Indices: 329234--329347 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
329224 ATTTGTGACA
* * * * *
329234 ATTTTGTAACTTTTAATATTCAAGGGACTCGACAAAGAAATTTCCTATAGTCGGATGATC
1 ATTTTATAACTTTTAATAATCAAAGGACTCAACAAAGAAATTTCCTATAATCGGATGATC
* *
329294 ATTTTATAACTTTTAATAATCAAATGACTCAATAAA-ATAATATT-CTATAATCGG
1 ATTTTATAACTTTTAATAATCAAAGGACTCAACAAAGA-AAT-TTCCTATAATCGG
329348 GAACCATTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
59 1 0.02
60 42 0.93
61 2 0.04
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAATCAAAGGACTCAACAAAGAAATTTCCTATAATCGGATGATC
Found at i:331124 original size:19 final size:21
Alignment explanation
Indices: 331081--331123 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
331071 CAGTAAAATA
*
331081 TTTATCTAAAATATTATTATT
1 TTTATCTAAAATATCATTATT
*
331102 TTTATTTAAAATATCATT-TT
1 TTTATCTAAAATATCATTATT
331122 TT
1 TT
331124 AACATTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATCTAAAATATCATTATT
Found at i:335861 original size:15 final size:13
Alignment explanation
Indices: 335831--335862 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
335821 TTACAAAAAA
335831 AAAATCTATAATT
1 AAAATCTATAATT
335844 AAAATCTATAATT
1 AAAATCTATAATT
335857 ATAAAT
1 A-AAAT
335863 TTATGCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATCTATAATT
Found at i:336056 original size:20 final size:20
Alignment explanation
Indices: 336027--336086 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
336017 AGTAATACTA
336027 TTCC-CTGATAATCTTTTAT
1 TTCCACTGATAATCTTTTAT
336046 TTCCACTGATAATCTTTTAT
1 TTCCACTGATAATCTTTTAT
* *
336066 TTCAACT-AGTAATTTTTTAT
1 TTCCACTGA-TAATCTTTTAT
336086 T
1 T
336087 CCTATTAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 5 0.14
20 32 0.86
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (20 bp):
TTCCACTGATAATCTTTTAT
Found at i:337327 original size:298 final size:304
Alignment explanation
Indices: 336802--338559 Score: 2365
Period size: 298 Copynumber: 5.6 Consensus size: 304
336792 AGCTACTTGA
* *
336802 TACTAGACTCGAAAAGTTCACGAGTAACTCGAATATATAATATATTAAGATTTTATTATTTTTAA
1 TACT-GACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTATTTTTAA
* * *
336867 AAATAAATTATTAATAATATTAACATTTATGTTTTGATTT-AAAAAACAATATAAAATTTTAATT
65 AAATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAATTTTAATG
336931 TATTTAAGGTTCATATTCGAGTTAAATTTAAGATTCTTTTTACAATTGTGGGGTTTATAGTGCAT
130 TATTTAAGGTTCATATTCGAGTTAAATTTAAGATTCTTTTTACAATTGTGGGGTTTATAGTGCAT
* * *
336996 GGTTATGTCTATGGCTGTAAATGAGATTAGATCGATCGTGAGCTACTTGAGATCAACTCAGTCAA
195 GGTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGATCGACTCAGTCAA
337061 AGTTCGATAAATACTCGACTCAAGCTCGAGCT-A-CTT-GA-TAC
260 AGTTCGATAAATACTCGACTCAAGCTCGAGCTGAGCTTAGAGTAC
337102 T-C-GACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTATTTTTAAA
1 TACTGACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTATTTTTAAA
*
337165 AATAAACTATAAATAATATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAATTTTAATGT
66 AATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAATTTTAATGT
* *
337230 ATTTAAGGTTCAGATTCGAGCTAAATTTAAGATTCTTTTTACAATTGTGGGGTTTATAGTGCATG
131 ATTTAAGGTTCATATTCGAGTTAAATTTAAGATTCTTTTTACAATTGTGGGGTTTATAGTGCATG
*
337295 GTTATGTCTATGGCCGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGATCGACTCAGTCAAA
196 GTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGATCGACTCAGTCAAA
*
337360 GTTCGATAAATACTCGACTCAAGCTCGAGCTTGACTCGAGTGTTTAACGAGTCGAAACGAGCTAC
261 GTTCGATAAATACTCGACTCAAGCTCGA----G-CT-GA--G-----C---T---TA-GAG-TAC
* *
337425 TTGATACTAGACTCGAAAAGTTCACGAGTAACTCGAATATATAATATATTAAGATTTTATTATTT
1 ----TACT-GACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTATTT
*
337490 TTAAAAATAAATTATTAATAATATTAACATTTATGTGTTGATTT-AAAAAACAATATAAAATTTT
61 TTAAAAATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAATTTT
*
337554 AATTTATTTAAGGTTCATATTCGAGTTAAATTTAAGATTCTTTTTACAATTGTGGGGTTTATAGT
126 AATGTATTTAAGGTTCATATTCGAGTTAAATTTAAGATTCTTTTTACAATTGTGGGGTTTATAGT
* * *
337619 GCATGGTTATGTCTATGGCTGTAAATGAGATTAGATCGATCGTGAGCTACTTGAGATCAACTCAG
191 GCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGATCGACTCAG
337684 TCAAAGTTCGATAAATACTCGACTCAAGCTCGAGCT-A-CTT-GA-TAC
256 TCAAAGTTCGATAAATACTCGACTCAAGCTCGAGCTGAGCTTAGAGTAC
337729 T-C-GACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTATTTTTAAA
1 TACTGACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTATTTTTAAA
*
337792 AATAAACTATTAATATTATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAATTTTAATGT
66 AATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAATTTTAATGT
* *
337857 ATATAAGGTTCATATTCGAGTTAAATTTAAGATTGTTTTTACAATTGTGGGGTTTATAGTGCATG
131 ATTTAAGGTTCATATTCGAGTTAAATTTAAGATTCTTTTTACAATTGTGGGGTTTATAGTGCATG
*
337922 GTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGTTACTCGAGATCGACTCAGTCAAA
196 GTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGATCGACTCAGTCAAA
*
337987 GTTCGATAAATACTCGATTCAAGCTCGAGCTTGACTCGAGTGCTTAACGAGTCGAAACGAGC
261 GTTCGATAAATACTCGACTCAAGCTCGA----G-CT-GA--GCTT-A-GAGT-------A-C
338049 TACTTGATACTCAACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTA
1 TAC-TG-------ACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTA
*
338114 TTTTTAAAAATAAACTATTAATAATATTAATATTTATGTGTTGATTTAAAAAAAACAATATAAAA
58 TTTTTAAAAATAAACTATTAATAATATTAACATTTATGTGTTGATTT-AAAAAAACAATATAAAA
* *
338179 TTTTAATGTATTTAAGGTTTATATTCGAGTTAAATTTAAGATTGTTTTTACAATTGTGGGGTTTA
122 TTTTAATGTATTTAAGGTTCATATTCGAGTTAAATTTAAGATTCTTTTTACAATTGTGGGGTTTA
338244 TAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGATCGAC
187 TAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGATCGAC
*
338309 TCAGTCAAAGTTCAATAAATACTCGACTCAAGCTCGAGCTTGACTCGAGTGCTTAACGAGTCGAA
252 TCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGA----G-CT-GA--GC-T------T----
338374 ACGAGCTAC
298 A-GAG-TAC
* *
338383 TTGATACTAGACTCGAAAAGTTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTTTTT
1 ----TACT-GACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTATTT
* *
338448 TTAAAAATAAATTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAAAACAATATAAGATT
61 TTAAAAATAAACTATTAATAATATTAACATTTATGTGTTGATTT--AAAAAAACAATATAAAATT
* *
338513 TTCATGTATTTAAGGTTCAAATTCGAGTTAAATTTAAGATTCTTTTT
124 TTAATGTATTTAAGGTTCATATTCGAGTTAAATTTAAGATTCTTTTT
338560 CATTTCGAGT
Statistics
Matches: 1321, Mismatches: 53, Indels: 136
0.87 0.04 0.09
Matches are distributed among these distances:
297 191 0.14
298 351 0.27
299 2 0.00
300 2 0.00
302 2 0.00
303 4 0.00
304 3 0.00
305 2 0.00
306 2 0.00
308 3 0.00
311 3 0.00
312 1 0.00
313 1 0.00
314 1 0.00
316 1 0.00
319 1 0.00
320 2 0.00
321 3 0.00
322 1 0.00
323 4 0.00
324 2 0.00
325 1 0.00
327 1 0.00
328 1 0.00
329 176 0.13
330 193 0.15
331 289 0.22
332 63 0.05
334 1 0.00
335 1 0.00
337 1 0.00
338 5 0.00
341 6 0.00
342 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (304 bp):
TACTGACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTATTTTTAAA
AATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAATTTTAATGT
ATTTAAGGTTCATATTCGAGTTAAATTTAAGATTCTTTTTACAATTGTGGGGTTTATAGTGCATG
GTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGATCGACTCAGTCAAA
GTTCGATAAATACTCGACTCAAGCTCGAGCTGAGCTTAGAGTAC
Found at i:337831 original size:627 final size:627
Alignment explanation
Indices: 336638--338559 Score: 3112
Period size: 627 Copynumber: 3.0 Consensus size: 627
336628 AAGGTCCTTT
* * * * * * **
336638 TTTTTACAATTGTGGGGTTTATAGTACATGGTTATGT-TGGAT-GATTTAAATAAGACGAAATAA
1 TTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCT--ATGGCTGTAAATGAGACTAGATCG
* * * *
336701 ATTGTGAGTTACTCGAGATCGATTTAGTCAAAGTTCGATAAATACTTGACTCAAGCTCGAGCTTG
64 ATCGTGAGTTACTCGAGATCGACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGAGCTTG
336766 ACTCGAGTGTTTAACGAGTCGAAACGAGCTACTTGATACTAGACTCGAAAAGTTCACGAGTAACT
129 ACTCGAGTGTTTAACGAGTCGAAACGAGCTACTTGATACTAGACTCGAAAAGTTCACGAGTAACT
336831 CGAATATATAATATATTAAGATTTTATTATTTTTAAAAATAAATTATTAATAATATTAACATTTA
194 CGAATATATAATATATTAAGATTTTATTATTTTTAAAAATAAATTATTAATAATATTAACATTTA
*
336896 TGTTTTGATTTAAAAAACAATATAAAATTTTAATTTATTTAAGGTTCATATTCGAGTTAAATTTA
259 TGTGTTGATTTAAAAAACAATATAAAATTTTAATTTATTTAAGGTTCATATTCGAGTTAAATTTA
336961 AGATTCTTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGATTAG
324 AGATTCTTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGATTAG
337026 ATCGATCGTGAGCTACTTGAGATCAACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGAG
389 ATCGATCGTGAGCTACTTGAGATCAACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGAG
337091 CTACTTGATACTCGACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATT
454 CTACTTGATACTCGACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATT
*
337156 ATTTTTAAAAATAAACTATAAATAATATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAA
519 ATTTTTAAAAATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAA
* *
337221 TTTTAATGTATTTAAGGTTCAGATTCGAGCTAAATTTAAGATTC
584 TTTTAATGTATTTAAGGTTCAAATTCGAGTTAAATTTAAGATTC
*
337265 TTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCCGTAAATGAGACTAGATCGAT
1 TTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGAT
*
337330 CGTGAGCTACTCGAGATCGACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGAGCTTGAC
66 CGTGAGTTACTCGAGATCGACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGAGCTTGAC
337395 TCGAGTGTTTAACGAGTCGAAACGAGCTACTTGATACTAGACTCGAAAAGTTCACGAGTAACTCG
131 TCGAGTGTTTAACGAGTCGAAACGAGCTACTTGATACTAGACTCGAAAAGTTCACGAGTAACTCG
337460 AATATATAATATATTAAGATTTTATTATTTTTAAAAATAAATTATTAATAATATTAACATTTATG
196 AATATATAATATATTAAGATTTTATTATTTTTAAAAATAAATTATTAATAATATTAACATTTATG
337525 TGTTGATTTAAAAAACAATATAAAATTTTAATTTATTTAAGGTTCATATTCGAGTTAAATTTAAG
261 TGTTGATTTAAAAAACAATATAAAATTTTAATTTATTTAAGGTTCATATTCGAGTTAAATTTAAG
337590 ATTCTTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGATTAGAT
326 ATTCTTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGATTAGAT
337655 CGATCGTGAGCTACTTGAGATCAACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGAGCT
391 CGATCGTGAGCTACTTGAGATCAACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGAGCT
337720 ACTTGATACTCGACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTAT
456 ACTTGATACTCGACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTAT
*
337785 TTTTAAAAATAAACTATTAATATTATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAATT
521 TTTTAAAAATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAATT
* * *
337850 TTAATGTATATAAGGTTCATATTCGAGTTAAATTTAAGATTG
586 TTAATGTATTTAAGGTTCAAATTCGAGTTAAATTTAAGATTC
337892 TTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGAT
1 TTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGAT
*
337957 CGTGAGTTACTCGAGATCGACTCAGTCAAAGTTCGATAAATACTCGATTCAAGCTCGAGCTTGAC
66 CGTGAGTTACTCGAGATCGACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGAGCTTGAC
* *
338022 TCGAGTGCTTAACGAGTCGAAACGAGCTACTTGATACTCA-ACTCGAAAAGCTCACGAGTAACTC
131 TCGAGTGTTTAACGAGTCGAAACGAGCTACTTGATACT-AGACTCGAAAAGTTCACGAGTAACTC
* * *
338086 GAAAATATAATATATTAAGATTTTATTATTTTTAAAAATAAACTATTAATAATATTAATATTTAT
195 GAATATATAATATATTAAGATTTTATTATTTTTAAAAATAAATTATTAATAATATTAACATTTAT
* *
338151 GTGTTGATTTAAAAAAAACAATATAAAATTTTAATGTATTTAAGGTTTATATTCGAGTTAAATTT
260 GTGTTGATTT--AAAAAACAATATAAAATTTTAATTTATTTAAGGTTCATATTCGAGTTAAATTT
* *
338216 AAGATTGTTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTA
323 AAGATTCTTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGATTA
* * *
338281 GATCGATCGTGAGCTACTCGAGATCGACTCAGTCAAAGTTCAATAAATACTCGACTCAAGCTCGA
388 GATCGATCGTGAGCTACTTGAGATCAACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGA
*
338346 GCTTGACTCGAGTGCTTAACGAGTCGAAACGAGCTACTTGATACTAGACTCGAAAAGTTCACGAG
453 ----G-CT--A---C-T------T------GA--TAC----T-C--GACTCGAAAAGCTCACGAG
* *
338411 TAACTCGAAAATATAATATATTAAGATTTTATTTTTTTTAAAAATAAATTATTAATAATATTAAC
486 TAACTCGAAAATATAATATATTAAGATTTTATTATTTTTAAAAATAAACTATTAATAATATTAAC
* *
338476 ATTTATGTGTTGATTTAAAAAAAAACAATATAAGATTTTCATGTATTTAAGGTTCAAATTCGAGT
551 ATTTATGTGTTGATTT--AAAAAAACAATATAAAATTTTAATGTATTTAAGGTTCAAATTCGAGT
338541 TAAATTTAAGATTC
614 TAAATTTAAGATTC
338555 TTTTT
1 TTTTT
338560 CATTTCGAGT
Statistics
Matches: 1211, Mismatches: 45, Indels: 42
0.93 0.03 0.03
Matches are distributed among these distances:
626 2 0.00
627 860 0.71
628 2 0.00
629 176 0.15
633 1 0.00
634 2 0.00
636 1 0.00
639 1 0.00
640 1 0.00
646 1 0.00
652 2 0.00
654 3 0.00
658 1 0.00
659 1 0.00
661 96 0.08
663 61 0.05
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (627 bp):
TTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGAT
CGTGAGTTACTCGAGATCGACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGAGCTTGAC
TCGAGTGTTTAACGAGTCGAAACGAGCTACTTGATACTAGACTCGAAAAGTTCACGAGTAACTCG
AATATATAATATATTAAGATTTTATTATTTTTAAAAATAAATTATTAATAATATTAACATTTATG
TGTTGATTTAAAAAACAATATAAAATTTTAATTTATTTAAGGTTCATATTCGAGTTAAATTTAAG
ATTCTTTTTACAATTGTGGGGTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGATTAGAT
CGATCGTGAGCTACTTGAGATCAACTCAGTCAAAGTTCGATAAATACTCGACTCAAGCTCGAGCT
ACTTGATACTCGACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTTTATTAT
TTTTAAAAATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAACAATATAAAATT
TTAATGTATTTAAGGTTCAAATTCGAGTTAAATTTAAGATTC
Found at i:338315 original size:331 final size:331
Alignment explanation
Indices: 337714--338559 Score: 1525
Period size: 331 Copynumber: 2.6 Consensus size: 331
337704 GACTCAAGCT
*
337714 CGAGCTACTTGATACTCGACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTT
1 CGAGCTACTTGATACTCAACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTT
*
337779 TATTATTTTTAAAAATAAACTATTAATATTATTAACATTTATGTGTTGATTT-AAAAAAACAATA
66 TATTATTTTTAAAAATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAAACAATA
*
337843 TAAAATTTTAATGTATATAAGGTTCATATTCGAGTTAAATTTAAGATTGTTTTTACAATTGTGGG
131 TAAAATTTTAATGTATTTAAGGTTCATATTCGAGTTAAATTTAAGATTGTTTTTACAATTGTGGG
*
337908 GTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGTTACTCGAGA
196 GTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGA
* *
337973 TCGACTCAGTCAAAGTTCGATAAATACTCGATTCAAGCTCGAGCTTGACTCGAGTGCTTAACGAG
261 TCGACTCAGTCAAAGTTCAATAAATACTCGACTCAAGCTCGAGCTTGACTCGAGTGCTTAACGAG
338038 TCGAAA
326 TCGAAA
338044 CGAGCTACTTGATACTCAACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTT
1 CGAGCTACTTGATACTCAACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTT
*
338109 TATTATTTTTAAAAATAAACTATTAATAATATTAATATTTATGTGTTGATTTAAAAAAAACAATA
66 TATTATTTTTAAAAATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAAACAATA
*
338174 TAAAATTTTAATGTATTTAAGGTTTATATTCGAGTTAAATTTAAGATTGTTTTTACAATTGTGGG
131 TAAAATTTTAATGTATTTAAGGTTCATATTCGAGTTAAATTTAAGATTGTTTTTACAATTGTGGG
338239 GTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGA
196 GTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGA
338304 TCGACTCAGTCAAAGTTCAATAAATACTCGACTCAAGCTCGAGCTTGACTCGAGTGCTTAACGAG
261 TCGACTCAGTCAAAGTTCAATAAATACTCGACTCAAGCTCGAGCTTGACTCGAGTGCTTAACGAG
338369 TCGAAA
326 TCGAAA
*
338375 CGAGCTACTTGATACT-AGACTCGAAAAGTTCACGAGTAACTCGAAAATATAATATATTAAGATT
1 CGAGCTACTTGATACTCA-ACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATT
* *
338439 TTATTTTTTTTAAAAATAAATTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAAAACAA
65 TTATTATTTTTAAAAATAAACTATTAATAATATTAACATTTATGTGTTGATTT-AAAAAAAACAA
* * * *
338504 TATAAGATTTTCATGTATTTAAGGTTCAAATTCGAGTTAAATTTAAGATTCTTTTT
129 TATAAAATTTTAATGTATTTAAGGTTCATATTCGAGTTAAATTTAAGATTGTTTTT
338560 CATTTCGAGT
Statistics
Matches: 496, Mismatches: 17, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
330 115 0.23
331 319 0.64
332 62 0.12
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (331 bp):
CGAGCTACTTGATACTCAACTCGAAAAGCTCACGAGTAACTCGAAAATATAATATATTAAGATTT
TATTATTTTTAAAAATAAACTATTAATAATATTAACATTTATGTGTTGATTTAAAAAAAACAATA
TAAAATTTTAATGTATTTAAGGTTCATATTCGAGTTAAATTTAAGATTGTTTTTACAATTGTGGG
GTTTATAGTGCATGGTTATGTCTATGGCTGTAAATGAGACTAGATCGATCGTGAGCTACTCGAGA
TCGACTCAGTCAAAGTTCAATAAATACTCGACTCAAGCTCGAGCTTGACTCGAGTGCTTAACGAG
TCGAAA
Found at i:339294 original size:116 final size:115
Alignment explanation
Indices: 339077--339308 Score: 324
Period size: 116 Copynumber: 2.0 Consensus size: 115
339067 GCTCAAGCCC
* *
339077 CCAATTTTTTATTTATAATTAGGGCCCCTAATTTTTATAATTTCATAAAAATTTTAGTTTTTAAC
1 CCAATTTTTTATTTATAATTAGGGCCCCTAATTTTTATAATTTCAT-AAAATATTAGCTTTTAAC
** *
339142 CATCCTTTTCCATTTCTCTTATTGGTTCATTCAATTTTGAATTAAACTTAA
65 CATCCTTTTCCATTTCTCTTATTCATTAATTCAATTTTGAATTAAACTTAA
* *
339193 CCAATTTTTAATATTTATAA-TAGGGCCCCTAATTTTTATATTTTCAT-AAATGATTAGCTTTTG
1 CCAATTTTT--TATTTATAATTAGGGCCCCTAATTTTTATAATTTCATAAAAT-ATTAGCTTTTA
* * *
339256 ACCATCTTTTTCCATTTCTCTTATTCATTAATTTAATTTTGAATTAAATTTAA
63 ACCATCCTTTTCCATTTCTCTTATTCATTAATTCAATTTTGAATTAAACTTAA
339309 TCATGTTTTC
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
115 4 0.04
116 64 0.62
117 26 0.25
118 9 0.09
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.50
Consensus pattern (115 bp):
CCAATTTTTTATTTATAATTAGGGCCCCTAATTTTTATAATTTCATAAAATATTAGCTTTTAACC
ATCCTTTTCCATTTCTCTTATTCATTAATTCAATTTTGAATTAAACTTAA
Found at i:351942 original size:2 final size:2
Alignment explanation
Indices: 351935--351960 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
351925 TTTATTCTGG
351935 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
351961 TAAACTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:352212 original size:46 final size:46
Alignment explanation
Indices: 352159--352247 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
352149 TCGTCTTTGT
* * * * *
352159 CGTTAAAAAATTGATGATAGTCTAAGCTTGATGTTAACTTATTGAC
1 CGTTAAAAAATCGATAACAATCTAAGCTTGATGTTAACATATTGAC
352205 CGTTAAAAAATCGATAACAATCTAAGCTTGATGTTAACATATT
1 CGTTAAAAAATCGATAACAATCTAAGCTTGATGTTAACATATT
352248 TAATGAGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (46 bp):
CGTTAAAAAATCGATAACAATCTAAGCTTGATGTTAACATATTGAC
Found at i:359840 original size:17 final size:17
Alignment explanation
Indices: 359818--359850 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
359808 TTAAATTATT
359818 AATAAATTTTTAAATAC
1 AATAAATTTTTAAATAC
359835 AATAAATTTTTAAATA
1 AATAAATTTTTAAATA
359851 ATTTTTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAATTTTTAAATAC
Found at i:373766 original size:14 final size:14
Alignment explanation
Indices: 373743--373953 Score: 218
Period size: 14 Copynumber: 16.1 Consensus size: 14
373733 GCAGACGGGG
373743 CGGCGG-CGACGGA
1 CGGCGGTCGACGGA
373756 CGGCGGTCGACGGA
1 CGGCGGTCGACGGA
373770 ---C-G--G-CGGA
1 CGGCGGTCGACGGA
373777 CGGCGGTCGACGGA
1 CGGCGGTCGACGGA
* * *
373791 CGGCAGACGGCGGA
1 CGGCGGTCGACGGA
373805 CGGCGGTCGACGGA
1 CGGCGGTCGACGGA
* * *
373819 CGGCAGACGGCGGA
1 CGGCGGTCGACGGA
373833 CGGCGGTCGACGGA
1 CGGCGGTCGACGGA
* * *
373847 CGGCAGACGGCGGA
1 CGGCGGTCGACGGA
373861 CGGCGGTCGACGGA
1 CGGCGGTCGACGGA
373875 ---CGG-C-A--GA
1 CGGCGGTCGACGGA
* *
373882 CGGCGGACGGCGGA
1 CGGCGGTCGACGGA
373896 CGGCGGTCGACGGA
1 CGGCGGTCGACGGA
373910 CGGCGGTCGACGGA
1 CGGCGGTCGACGGA
373924 CGGCGGTCGACGGA
1 CGGCGGTCGACGGA
373938 CGGCGGTCGACGGA
1 CGGCGGTCGACGGA
373952 CG
1 CG
373954 ACGGACGGCG
Statistics
Matches: 162, Mismatches: 21, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
7 6 0.04
8 1 0.01
9 1 0.01
10 6 0.04
11 6 0.04
13 7 0.04
14 135 0.83
ACGTcount: A:0.16, C:0.29, G:0.51, T:0.04
Consensus pattern (14 bp):
CGGCGGTCGACGGA
Done.