Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1727
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: 95211
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6239 original size:19 final size:19
Alignment explanation
Indices: 6217--6277 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
6207 AATAAATTCA
6217 AGATTTGCTTAAAAATAAG
1 AGATTTGCTTAAAAATAAG
*
6236 AGATTTG-TGT--GAA-AAG
1 AGATTTGCT-TAAAAATAAG
*
6252 ATATTTGCTTAAAAATAAG
1 AGATTTGCTTAAAAATAAG
6271 AGATTTG
1 AGATTTG
6278 TGTGAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
16 10 0.30
17 3 0.09
18 3 0.09
19 17 0.52
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (19 bp):
AGATTTGCTTAAAAATAAG
Found at i:6260 original size:35 final size:35
Alignment explanation
Indices: 6219--6288 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
6209 TAAATTCAAG
6219 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
1 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
6254 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
1 ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
6289 TTTAGAGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (35 bp):
ATTTGCTTAAAAATAAGAGATTTGTGTGAAAAGAT
Found at i:6285 original size:19 final size:19
Alignment explanation
Indices: 6228--6285 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
6218 GATTTGCTTA
6228 AAAATAAGAGATTTGTGTG
1 AAAATAAGAGATTTGTGTG
* *
6247 --AA-AAGATATTTGCT-TA
1 AAAATAAGAGATTTG-TGTG
6263 AAAATAAGAGATTTGTGTG
1 AAAATAAGAGATTTGTGTG
6282 AAAA
1 AAAA
6286 GATTTTAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 10 0.33
17 3 0.10
18 3 0.10
19 14 0.47
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.31
Consensus pattern (19 bp):
AAAATAAGAGATTTGTGTG
Found at i:7131 original size:70 final size:70
Alignment explanation
Indices: 7018--7160 Score: 241
Period size: 70 Copynumber: 2.0 Consensus size: 70
7008 TGAATAAGTA
* * *
7018 TAAATGATATTAGTACTCTACTTAGGCCAATCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
1 TAAATGATATTAATACTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
7083 TATTT
66 TATTT
* *
7088 TAAATGATATTAATGCTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATTTTTGGAC
1 TAAATGATATTAATACTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
7153 TATTT
66 TATTT
7158 TAA
1 TAA
7161 CTTAGTAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (70 bp):
TAAATGATATTAATACTATACTTAGGCCAACCCCATGAGCTTCTAGTTGGAAGACATCTTTGGAC
TATTT
Found at i:12061 original size:187 final size:187
Alignment explanation
Indices: 11746--12120 Score: 714
Period size: 187 Copynumber: 2.0 Consensus size: 187
11736 TCGTTGTTGA
11746 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
1 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
*
11811 TACATGCATTTGAAATTTATAGCCGTTAGGAGAATGTATCGATACTTTTCATTATGTATCAATAA
66 TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
* *
11876 AATGTACTACGTATCGATACCAACAATGGTAGGGTAGCTACTGCCAGTTTCATGTAT
131 AATGTACTACGTATCGATACAAACAATAGTAGGGTAGCTACTGCCAGTTTCATGTAT
11933 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
1 CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
11998 TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
66 TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
*
12063 AATGTACTACGTATCGATACAAATAATAGTAGGGTAGCTACTGCCAGTTTCATGTAT
131 AATGTACTACGTATCGATACAAACAATAGTAGGGTAGCTACTGCCAGTTTCATGTAT
12120 C
1 C
12121 GATACAATTG
Statistics
Matches: 184, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
187 184 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (187 bp):
CTTGTTTGGTGCTTGTTTCCATGCATTCCCGTTAGTATGCATCGATACTTTTCATAATGTATCGA
TACATGCATTTGAAATTTATAGCCGTTAGGACAATGTATCGATACTTTTCATTATGTATCAATAA
AATGTACTACGTATCGATACAAACAATAGTAGGGTAGCTACTGCCAGTTTCATGTAT
Found at i:12153 original size:13 final size:13
Alignment explanation
Indices: 12135--12159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12125 CAATTGAGTA
12135 TGTATCGATACAT
1 TGTATCGATACAT
12148 TGTATCGATACA
1 TGTATCGATACA
12160 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17057 original size:56 final size:54
Alignment explanation
Indices: 16931--17072 Score: 151
Period size: 56 Copynumber: 2.6 Consensus size: 54
16921 AGGTAGTGTT
* * * * *
16931 AAAAAAATAGACA-GAAACCCAAAATGGGCATCTATAATAAAAAGAAATAAAAAACA
1 AAAAAAATA-A-ATGAAACCTAAAA-AGGCATCCAAAATAAAAAGAAACAAAAAACA
** *
16987 AAAAAAATGGATGAAAACCTAAGAAAGGCATCCAAAATAAAAGGAAACAAAAAACA
1 AAAAAAATAAATG-AAACCTAA-AAAGGCATCCAAAATAAAAAGAAACAAAAAACA
*
17043 AAAAAATTAAATGAAACCTAAAAAGGCATC
1 AAAAAAATAAATGAAACCTAAAAAGGCATC
17073 TAATCCAAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
54 10 0.14
55 9 0.12
56 51 0.71
57 2 0.03
ACGTcount: A:0.63, C:0.13, G:0.12, T:0.12
Consensus pattern (54 bp):
AAAAAAATAAATGAAACCTAAAAAGGCATCCAAAATAAAAAGAAACAAAAAACA
Found at i:18481 original size:66 final size:64
Alignment explanation
Indices: 18409--18551 Score: 164
Period size: 66 Copynumber: 2.2 Consensus size: 64
18399 AGTTGGTTTG
* ** * * *
18409 TATGGTTTCGTCTCGATTAACCCTTTTTCAACTTAGGTTTCA-CTTTGCTCATCCAAAGTT-AGT
1 TATGGTTTCGTCCCGACCAACCCTTTTT-AACTCAAGTTTCACCTTAG-TCA-CCAAAGTTGA-T
18472 TCA
62 TCA
*
18475 TATGGTTTCGTCCCGGCCAACCCTTTTTAACTCAAGTTTCACCTTAGTCACCAAAGTTGATTCA
1 TATGGTTTCGTCCCGACCAACCCTTTTTAACTCAAGTTTCACCTTAGTCACCAAAGTTGATTCA
*
18539 TATGGTTTTGTCC
1 TATGGTTTCGTCC
18552 TGGTCAACTC
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
64 24 0.36
65 15 0.22
66 28 0.42
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (64 bp):
TATGGTTTCGTCCCGACCAACCCTTTTTAACTCAAGTTTCACCTTAGTCACCAAAGTTGATTCA
Found at i:19077 original size:65 final size:62
Alignment explanation
Indices: 18990--19163 Score: 152
Period size: 64 Copynumber: 2.7 Consensus size: 62
18980 TTCAGTTGGC
** * * * * *
18990 TCATATGGTTTCATTCTAACTAACTCTTTTCTGACTTAGGTTCCATCTTGGTCAACAAAGTTGGT
1 TCATATGGTTTC-GCCTTACTAACCCTTTT-TGACTTAGGTTCCA-CCTGGCCAACAAAGTTAGT
* * *
19055 TCGTATGGTTTCGCCTTGACTAACCCTTTTTAGACTCTA-GTTCTACCTGGCCACCAAAGTTAGT
1 TCATATGGTTTCGCCTT-ACTAACCCTTTTT-GACT-TAGGTTCCACCTGGCCAACAAAGTTAGT
* * *
19119 TCATATGGTTTTGTCTTAGCCAACCCTTTTTTGACTTAGGTTCCA
1 TCATATGGTTTCGCCTTA-CTAACCC-TTTTTGACTTAGGTTCCA
19164 ACCTAGTCAC
Statistics
Matches: 88, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
63 3 0.03
64 47 0.53
65 36 0.41
66 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (62 bp):
TCATATGGTTTCGCCTTACTAACCCTTTTTGACTTAGGTTCCACCTGGCCAACAAAGTTAGT
Found at i:19152 original size:195 final size:195
Alignment explanation
Indices: 18815--19226 Score: 442
Period size: 195 Copynumber: 2.1 Consensus size: 195
18805 TCACCCTTAT
* * * * * * *
18815 CAACCCTTTTTGACTTAGGTTCCTCATTGGTCACTCAGAGCTGGTTTGTATGGTTTTGTCTTGGC
1 CAACTCTTTTTGACTTAGGTTCCTCATTGGTCACACAAAGCTGGTTCGTATGGTTTCGCCTTGAC
* ** ** *
18880 TAACCCTTTTTGACTTAGGTTTTACCCGGGTTACCTTTAGTTGGTTCATATGGTTTCATCTCAGC
66 TAACCCTTTTTGACTTAGGTTCTACCCGGGCCACCTAAAGTTAGTTCATATGGTTTCATCTCAGC
**** *
18945 CAACACTTTTTGACTTAGGTTTTGCCCTAGTCA-GCTTCAGTTGGCTCATATGGTTTCAT-TCTA
131 CAACACTTTTTGACTTAGGTTCCAACCTAGTCACCCTT-AGTTGGCTCATATGGTTTCATCTC-A
19008 AC
194 AC
* *
19010 TAACTCTTTTCTGACTTAGGTTCCATC-TTGGTCA-ACAAAGTTGGTTCGTATGGTTTCGCCTTG
1 CAACTCTTTT-TGACTTAGGTTCC-TCATTGGTCACACAAAGCTGGTTCGTATGGTTTCGCCTTG
* **
19073 ACTAACCCTTTTTAGACTCTA-GTTCTA-CCTGGCCACC-AAAGTTAGTTCATATGGTTTTGTCT
64 ACTAACCCTTTTT-GACT-TAGGTTCTACCCGGGCCACCTAAAGTTAGTTCATATGGTTTCATCT
* * * **
19135 TAGCCAACCCTTTTTTGACTTAGGTTCCAACCTAGTCACCCTTAGTTGGTTTGTATGGTTTCATC
127 CAGCCAACAC-TTTTTGACTTAGGTTCCAACCTAGTCACCCTTAGTTGGCTCATATGGTTTCATC
*
19200 TCAGC
191 TCAAC
19205 CAACTCTTTTTTGACTTAGGTT
1 CAACTC-TTTTTGACTTAGGTT
19227 TTGCCTTAGT
Statistics
Matches: 179, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
194 28 0.16
195 109 0.61
196 38 0.21
197 4 0.02
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (195 bp):
CAACTCTTTTTGACTTAGGTTCCTCATTGGTCACACAAAGCTGGTTCGTATGGTTTCGCCTTGAC
TAACCCTTTTTGACTTAGGTTCTACCCGGGCCACCTAAAGTTAGTTCATATGGTTTCATCTCAGC
CAACACTTTTTGACTTAGGTTCCAACCTAGTCACCCTTAGTTGGCTCATATGGTTTCATCTCAAC
Found at i:19237 original size:66 final size:64
Alignment explanation
Indices: 18881--19279 Score: 252
Period size: 65 Copynumber: 6.1 Consensus size: 64
18871 TGTCTTGGCT
* ** *
18881 AACCC-TTTTTGACTTAGGTTTTACCCGGGTTACCTTTAGTTGGTTCATATGGTTTCATCTCAGC
1 AACCCTTTTTTGACTTAGGTTCTA-CCTAGTCACC-TTAGTTGGTTCATATGGTTTCATCTCAGC
18945 C
64 C
* * * * * *
18946 AACAC-TTTTTGACTTAGGTTTTGCCCTAGTCAGCTTCAGTTGGCTCATATGGTTTCAT-TCTAA
1 AACCCTTTTTTGACTTAGGTTCT-ACCTAGTCACCTT-AGTTGGTTCATATGGTTTCATCTC-AG
*
19009 CT
63 CC
* * * * * * ** * ** *
19011 AACTCTTTTCTGACTTAGGTTCCATCTTGGTCAACAAAGTTGGTTCGTATGGTTTCGCCT-TGAC
1 AACCCTTTTTTGACTTAGGTTCTA-CCTAGTCACCTTAGTTGGTTCATATGGTTTCATCTCAG-C
*
19075 T
64 C
* * * ** * ** *
19076 AACCCTTTTTAGACTCTA-GTTCTACCTGGCCACCAAAGTTAGTTCATATGGTTTTGTCTTAGCC
1 AACCCTTTTTTGACT-TAGGTTCTACCTAGTCACCTTAGTTGGTTCATATGGTTTCATCTCAGCC
* **
19140 AACCCTTTTTTGACTTAGGTTCCAACCTAGTCACCCTTAGTTGGTTTGTATGGTTTCATCTCAGC
1 AACCCTTTTTTGACTTAGGTT-CTACCTAGTCA-CCTTAGTTGGTTCATATGGTTTCATCTCAGC
19205 C
64 C
* * * ** * * *
19206 AACTCTTTTTTGACTTAGGTTTTGCCTTAGTCACCAAAGTTGGTTCACT-TAGTTTCATCCCAAC
1 AACCCTTTTTTGACTTAGGTTCTACC-TAGTCACCTTAGTTGGTTCA-TATGGTTTCATCTCAGC
19270 C
64 C
19271 AACCCTTTT
1 AACCCTTTT
19280 AGACATTGGT
Statistics
Matches: 258, Mismatches: 62, Indels: 28
0.74 0.18 0.08
Matches are distributed among these distances:
63 2 0.01
64 50 0.19
65 131 0.51
66 75 0.29
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.40
Consensus pattern (64 bp):
AACCCTTTTTTGACTTAGGTTCTACCTAGTCACCTTAGTTGGTTCATATGGTTTCATCTCAGCC
Found at i:25503 original size:20 final size:20
Alignment explanation
Indices: 25478--25531 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
25468 TTTACCGAGA
*
25478 TGTATCGAAACATTGTTCAT
1 TGTATCGATACATTGTTCAT
25498 TGTATCGATACATTGTTCAT
1 TGTATCGATACATTGTTCAT
25518 TGTATCGATACATT
1 TGTATCGATACATT
25532 CTAGGTTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTGTTCAT
Found at i:25578 original size:69 final size:70
Alignment explanation
Indices: 25428--25580 Score: 227
Period size: 69 Copynumber: 2.2 Consensus size: 70
25418 TTTCACAATT
* * *
25428 TGTATCGATACATGGCTCATTGTATCGATACATTCTGAGTTTTACCGAGATGTATCGAAACATTG
1 TGTATCGATACATTGCTCATTGTATCGATACATTCTGAGGTTTACCCAGATGTATCGAAACATTG
*
25493 TTCAT
66 TTCAA
* * *
25498 TGTATCGATACATTGTTCATTGTATCGATACATTCT-AGGTTTACCCAGATGTATCGATACATTT
1 TGTATCGATACATTGCTCATTGTATCGATACATTCTGAGGTTTACCCAGATGTATCGAAACATTG
*
25562 TTTAA
66 TTCAA
25567 TGTATCGATACATT
1 TGTATCGATACATT
25581 CAGGCATTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
69 41 0.55
70 34 0.45
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (70 bp):
TGTATCGATACATTGCTCATTGTATCGATACATTCTGAGGTTTACCCAGATGTATCGAAACATTG
TTCAA
Found at i:26486 original size:10 final size:10
Alignment explanation
Indices: 26471--26509 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
26461 CACATCTTGA
26471 GCATGATCAT
1 GCATGATCAT
*
26481 GCATGATTAAT
1 GCATGA-TCAT
26492 AGCATGATCAT
1 -GCATGATCAT
26503 GCATGAT
1 GCATGAT
26510 TAATATCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 13 0.52
11 6 0.24
12 6 0.24
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (10 bp):
GCATGATCAT
Found at i:26521 original size:22 final size:22
Alignment explanation
Indices: 26470--26514 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
26460 ACACATCTTG
26470 AGCATGATCATGCATGATTAAT
1 AGCATGATCATGCATGATTAAT
26492 AGCATGATCATGCATGATTAAT
1 AGCATGATCATGCATGATTAAT
26514 A
1 A
26515 TCTTGATAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (22 bp):
AGCATGATCATGCATGATTAAT
Found at i:27880 original size:50 final size:49
Alignment explanation
Indices: 27793--27919 Score: 130
Period size: 50 Copynumber: 2.5 Consensus size: 49
27783 TAAATTTCTA
* * * * *
27793 GATTTTTCATCTCGGGGATACTCCATCCCCTACTTTATTTCTAAAATATT
1 GATTTTTCATCTC-GGGATACTCTAACCCCTACTTTATTTCCAAAACATC
*
27843 GATTTTTCATCTCGGGAATACTCTAACCCC-AGTTTTATTTCCAAAACATC
1 GATTTTTCATCTCGGG-ATACTCTAACCCCTA-CTTTATTTCCAAAACATC
* *
27893 AATTTTTCATAATCAGGGATACTCTAA
1 GATTTTTCAT-CTC-GGGATACTCTAA
27920 TCCCGTTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
49 4 0.06
50 47 0.72
51 11 0.17
52 3 0.05
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (49 bp):
GATTTTTCATCTCGGGATACTCTAACCCCTACTTTATTTCCAAAACATC
Found at i:27991 original size:79 final size:79
Alignment explanation
Indices: 27860--28188 Score: 315
Period size: 79 Copynumber: 4.2 Consensus size: 79
27850 CATCTCGGGA
* * * * * *
27860 ATACTCTAACCCCAGTTTTATTTCCAAAACATCAATTTTTCATAATCAGGGATACTCTAATCCCG
1 ATACTCCAACCCCAGCTTTATTTCTAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCG
*
27925 TTATTTTTGAGGGG
66 TTATTTTCGAGGGG
* * * * * *
27939 ATACTCCAACCCCTGCTTTATTTCTAAAATATTGATTTCTCATGATCGGGGATACTCCAACCCCG
1 ATACTCCAACCCCAGCTTTATTTCTAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCG
* * *
28004 TTATTTTGGCGTGG
66 TTATTTTCGAGGGG
* * * * * *
28018 ATACTCCAACCCCGGCCTTATTTCTAAAGCATCGATTTTTCACAATCCGAGATACTCCAACCCCG
1 ATACTCCAACCCCAGCTTTATTTCTAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCG
28083 TTATTTTCGAGGGG
66 TTATTTTCGAGGGG
* * * * * *
28097 ATACTCCAA-CCCTGATTTTATTT-TCAAA-GTGCCGA-TTTTCTATAATTAGGGATACTCTAAC
1 ATACTCCAACCCCAG-CTTTATTTCTAAAACAT--CGATTTTTC-ATAATCAGGGATACTCCAAC
* * *
28158 CCTGTTATTTTCAAAGGG
62 CCCGTTATTTTCGAGGGG
28176 ATACTCCAACCCC
1 ATACTCCAACCCC
28189 GATTTTATTT
Statistics
Matches: 203, Mismatches: 42, Indels: 9
0.80 0.17 0.04
Matches are distributed among these distances:
77 1 0.00
78 12 0.06
79 187 0.92
80 3 0.01
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (79 bp):
ATACTCCAACCCCAGCTTTATTTCTAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCG
TTATTTTCGAGGGG
Found at i:28149 original size:158 final size:158
Alignment explanation
Indices: 27877--28168 Score: 365
Period size: 158 Copynumber: 1.8 Consensus size: 158
27867 AACCCCAGTT
* * * * *
27877 TTATTTCCAAAACATCAATTTTTCATAATCAGGGATACTCTAATCCCGTTATTTTTGAGGGGATA
1 TTATTTCCAAAACATCAATTTTTCACAATCAGAGATACTCCAACCCCGTTATTTTCGAGGGGATA
** * *
27942 CTCCAACCCCTGCTTTATTTCTAAAATATTGATTTCTCATGATCGGGGATACTCCAACCCCGTTA
66 CTCCAACCCCTGCTTTATTTCTAAAATACCGATTTCTCATAATCAGGGATACTCCAACCCCGTTA
28007 TTTTGGCGTGGATACTCCAACCCCGGCC
131 TTTTGGCGTGGATACTCCAACCCCGGCC
* * * *
28035 TTATTTCTAAAGCATCGATTTTTCACAATCCGAGATACTCCAACCCCGTTATTTTCGAGGGGATA
1 TTATTTCCAAAACATCAATTTTTCACAATCAGAGATACTCCAACCCCGTTATTTTCGAGGGGATA
* * * * * *
28100 CTCCAA-CCCTGATTTTATTT-TCAAAGTGCCGATTT-TCTATAATTAGGGATACTCTAACCCTG
66 CTCCAACCCCTG-CTTTATTTCT-AAAATACCGATTTCTC-ATAATCAGGGATACTCCAACCCCG
28162 TTATTTT
128 TTATTTT
28169 CAAAGGGATA
Statistics
Matches: 112, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
157 8 0.07
158 104 0.93
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (158 bp):
TTATTTCCAAAACATCAATTTTTCACAATCAGAGATACTCCAACCCCGTTATTTTCGAGGGGATA
CTCCAACCCCTGCTTTATTTCTAAAATACCGATTTCTCATAATCAGGGATACTCCAACCCCGTTA
TTTTGGCGTGGATACTCCAACCCCGGCC
Found at i:28230 original size:79 final size:79
Alignment explanation
Indices: 27989--28234 Score: 230
Period size: 79 Copynumber: 3.1 Consensus size: 79
27979 CATGATCGGG
*** *** *
27989 GATACTCCAACCCCGTTATTTT-GGCGTGGATACTCCAACCCCGGCCTTA-TTTCTAAAGCATCG
1 GATACTCCAACCCCGTTATTTTCAAAG-GGATACTCCAACCCCGATTTTATTTTC-AAAGCACCG
* * **
28052 ATTTTTCACAATCCGA
64 ATTTTCCATAATGAGA
* * * **
28068 GATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGATTTTATTTTCAAAGTGCCGAT
1 GATACTCCAACCCCGTTATTTTCAAAGGGATACTCCAACCCCGATTTTATTTTCAAAGCACCGAT
* * *
28133 TTTCTATAATTAGG
66 TTTCCATAATGAGA
* *
28147 GATACTCTAACCCTGTTATTTTCAAAGGGATACTCCAACCCCGATTTTATTTTCAGAA-CACCGA
1 GATACTCCAACCCCGTTATTTTCAAAGGGATACTCCAACCCCGATTTTATTTTCA-AAGCACCGA
*
28211 TTTTCCGTAATCGA-A
65 TTTTCCATAAT-GAGA
28226 GATACTCCA
1 GATACTCCA
28235 GCCCTATTGT
Statistics
Matches: 136, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
79 127 0.93
80 9 0.07
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (79 bp):
GATACTCCAACCCCGTTATTTTCAAAGGGATACTCCAACCCCGATTTTATTTTCAAAGCACCGAT
TTTCCATAATGAGA
Found at i:34030 original size:13 final size:13
Alignment explanation
Indices: 34012--34036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34002 CATAAAGTGT
34012 TGTATCGATACAA
1 TGTATCGATACAA
34025 TGTATCGATACA
1 TGTATCGATACA
34037 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:34119 original size:13 final size:13
Alignment explanation
Indices: 34101--34125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34091 ATTACTCAAA
34101 TGTATCGATACAT
1 TGTATCGATACAT
34114 TGTATCGATACA
1 TGTATCGATACA
34126 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:43819 original size:13 final size:13
Alignment explanation
Indices: 43801--43826 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43791 TACACAAAGT
43801 ATGTATCGATACA
1 ATGTATCGATACA
43814 ATGTATCGATACA
1 ATGTATCGATACA
43827 CAAAAAAATT
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):
ATGTATCGATACA
Found at i:43845 original size:34 final size:32
Alignment explanation
Indices: 43783--43847 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
43773 TAGCCAAACT
**
43783 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
43815 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
43848 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:47916 original size:15 final size:15
Alignment explanation
Indices: 47896--47926 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47886 TAAAAATGTC
47896 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
47911 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
47926 C
1 C
47927 CAAACGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:50173 original size:20 final size:20
Alignment explanation
Indices: 50130--50175 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
50120 AAATCTTTTG
50130 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
50151 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
50171 CAAAA
1 CAAAA
50176 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:52571 original size:13 final size:13
Alignment explanation
Indices: 52553--52578 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52543 TACACAAAGT
52553 ATGTATCGATACA
1 ATGTATCGATACA
52566 ATGTATCGATACA
1 ATGTATCGATACA
52579 CAAAAAAATT
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):
ATGTATCGATACA
Found at i:52597 original size:34 final size:32
Alignment explanation
Indices: 52535--52599 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
52525 TAGCCAAACT
**
52535 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
52567 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
52600 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:54199 original size:17 final size:15
Alignment explanation
Indices: 54174--54247 Score: 58
Period size: 17 Copynumber: 4.5 Consensus size: 15
54164 TTTCTTTTTT
*
54174 AAAAAAAAAAGCAAAA
1 AAAAAAAAAAAC-AAA
*
54190 AAATAAAAAAAACAACC
1 AAA-AAAAAAAACAA-A
54207 AAAAAAAAAAACAAA
1 AAAAAAAAAAACAAA
*
54222 ACAAAGAAAAAAGAGAGAA
1 A-AAA-AAAAAA-ACA-AA
54241 AAAAAAA
1 AAAAAAA
54248 CCTACTTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
15 1 0.02
16 19 0.40
17 20 0.42
18 5 0.10
19 3 0.06
ACGTcount: A:0.84, C:0.08, G:0.07, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAAACAAA
Found at i:54200 original size:21 final size:20
Alignment explanation
Indices: 54174--54247 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
54164 TTTCTTTTTT
54174 AAAAAAAAAAGCAAAAAAATA
1 AAAAAAAAAAGCAAAAAAA-A
* *
54195 AAAAAAACAACCAAAAAAAA
1 AAAAAAAAAAGCAAAAAAAA
54215 AAACAAAACAAAG-AAAAAAGAGA
1 AAA-AAAA-AAAGCAAAAAA-A-A
54238 GAAAAAAAAA
1 -AAAAAAAAA
54248 CCTACTTAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
20 4 0.09
21 27 0.61
22 5 0.11
23 5 0.11
24 3 0.07
ACGTcount: A:0.84, C:0.08, G:0.07, T:0.01
Consensus pattern (20 bp):
AAAAAAAAAAGCAAAAAAAA
Found at i:55404 original size:26 final size:26
Alignment explanation
Indices: 55374--55456 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 26
55364 TGGTGGCACT
55374 TTTCAGTCCTCAAAGAGCAGGACGCC
1 TTTCAGTCCTCAAAGAGCAGGACGCC
* **
55400 TTTCAAAGTCCAT-ATA-AGCAGGTGGCAC
1 TTTC--AGTCC-TCAAAGAGCAGGACGC-C
*
55428 CTTCAGTCCTCAAAGAGCAGGACGCC
1 TTTCAGTCCTCAAAGAGCAGGACGCC
55454 TTT
1 TTT
55457 TCCTTTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
25 1 0.02
26 14 0.33
27 16 0.37
28 11 0.26
29 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (26 bp):
TTTCAGTCCTCAAAGAGCAGGACGCC
Found at i:55446 original size:27 final size:27
Alignment explanation
Indices: 55365--55448 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
55355 CACACAAGCT
55365 GGTGGCACTTTTCAGTCCTCAAAGAGCA
1 GGTGGCAC-TTTCAGTCCTCAAAGAGCA
** *
55393 GGACGC-CTTTCAAAGTCCAT-ATA-AGCA
1 GGTGGCACTTTC--AGTCC-TCAAAGAGCA
*
55420 GGTGGCACCTTCAGTCCTCAAAGAGCA
1 GGTGGCACTTTCAGTCCTCAAAGAGCA
55447 GG
1 GG
55449 ACGCCTTTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
25 1 0.02
26 11 0.26
27 15 0.35
28 15 0.35
29 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.21
Consensus pattern (27 bp):
GGTGGCACTTTCAGTCCTCAAAGAGCA
Found at i:55511 original size:61 final size:60
Alignment explanation
Indices: 55344--56783 Score: 1667
Period size: 61 Copynumber: 23.9 Consensus size: 60
55334 AACAGGACAT
* *
55344 CTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCC-TTT-
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * ** **
55403 C----AAAGTCCATATAAGCAGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* *
55459 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAGAGAGAAGGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
*
55520 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTTAAAGAGCAGGACGCC-TTT-
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * ** *
55579 C----AAGGCCTACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGGCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
** *
55635 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
* * * * *
55696 CTTTTAAAGCTCACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGGGCAGGACACTTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * *
55757 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGGGCAGGACACCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * **
55818 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGATGCCCTCGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * ** *
55879 CTTTCAAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * *
55939 CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCTAGTCCTCAAAGAGCGGGACACCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
* ** *
56000 CTTTTAAAGGCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
*
56061 CTTTTAAAGCCCACACAAGTTGGT-GCACTTTTCCAGTCCTCAAAGAGGAGGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTC
* * ** * *
56122 CTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGTGCGGGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * ** *
56182 CTTTTAAAGCCCACACATGTTGATGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTCT-
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
* *
56242 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTC
1 CTTTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
56304 CTTTGAAAGCCCACGCAAGTTGGTAGCACCTTTT-AGTCCTCAAAGAGCAGGACGTCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCA--TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* **
56365 CTTTTAAAGCCCACACAAATTGGTGG-ACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
56425 CTTTTAAAGCCAACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGCAGGACACATTTT-
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
56485 CTTTGTAAAGCCCACACAAGTTAGTGGCACTTTTCTAGTCCTCAAAGAGTAGGGCACCTTTTC
1 CTTT-TAAAGCCCACACAAGTTGGTGGCA-TTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
** *
56548 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGGCGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
* * *
56609 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAATCCTC-AAGAAGTAGGATGCCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAG-AGCAGGACGCCTTTTC
* * * *
56670 CTTTTAAAGCCCGCACAAGTTGGTGGCACCTTTCAGTCCTTAAAGAGCAGGATG-CTTTCTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGACGCCTTT-TC
** * ** * *
56731 CTTGCAAAGCCCATACAAGTTGGTGGCACCTTCTAGTCCCCAAAGAGTAGGAC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCTCAAAGAGCAGGAC
56784 CTATTTCACT
Statistics
Matches: 1199, Mismatches: 146, Indels: 70
0.85 0.10 0.05
Matches are distributed among these distances:
54 48 0.04
55 45 0.04
56 2 0.00
58 2 0.00
59 2 0.00
60 227 0.19
61 798 0.67
62 71 0.06
63 4 0.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (60 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
Found at i:55960 original size:243 final size:243
Alignment explanation
Indices: 55344--56783 Score: 1814
Period size: 243 Copynumber: 6.0 Consensus size: 243
55334 AACAGGACAT
* *
55344 CTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG------CCTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
* * * *
55403 CAAAGTCCATATAAGCAGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAG
66 CAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAG
* * * *
55468 CCCACACAAGTTGGTGGCATTTTTCAGTCCTCAGAGAGAAGGACGCCTTTTCCTTTTAAAGCCCA
131 CCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCA
* *
55533 CACAAGTTGGTGGCATTTTTCAGTCCTTAAAGAGCAGGACGCC-TTT-
196 CACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * * *
55579 C----AAGGCCTACACAAGCTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGGCTTTTCCTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
* * *
55639 TAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCCTTTTCCTTTTAAA
66 CAAAGCCCACACAAGCTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAA
* * * *
55704 GCTCACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGGGCAGGACACTTTTTCCTTTTAAAGCCC
130 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCC
* * *
55769 ACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGGGCAGGACACCTTTTC
195 ACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * **
55818 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGATGCCCTCGCCTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
* *
55883 CAAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCCTTTTAAAG
66 CAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAG
* * *
55948 CCCACACAAGTTGGTGGCA-TCTTCTAGTCCTCAAAGAGCGGGACACCTTTTCCTTTTAAAGGCC
131 CCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCC
* *
56012 ACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGTAGGACGCCTTTTC
195 ACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
*
56061 CTTTTAAAGCCCACACAAGTTGGT-GCACTTTTCCAGTCCTCAAAGAGGAGGACGCCTTTTCCTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
* *
56125 TCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGTGCGGGACGCCTTTTCCTTTTAAA
65 TCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAA
* * * * *
56190 GCCCACACATGTTGATGGCAC-CTTCTAGTCCTCAAAGAGCAGGACGCCTTCT-CTTTTCAAAGC
130 GCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACACCTTTTCCTTTT-AAAGC
* * *
56253 CCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTC
193 CCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
* * * *
56304 CTTTGAAAGCCCACGCAAGTTGGTAGCACCTTTT-AGTCCTCAAAGAGCAGGACGTCTTTTCCTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
* **
56368 TTAAAGCCCACACAAATTGGTGG-ACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAA
65 TCAAAGCCCACACAAGCTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAA
* * *
56432 AGCCAACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGCAGGACACATTTT-CTTTGTAAAGC
129 AGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTT-TAAAGC
* * * *
56496 CCACACAAGTTAGTGGCACTTTTCTAGTCCTCAAAGAGTAGGGCACCTTTTC
193 CCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTC
* *
56548 CTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAGGGCGCCTTTTCCTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTT
* * ** * * *
56612 TTAAAGCCCACACAAGTTGGTGGCATTTTTCAATCCTC-AAGAAGTAGGATGCCTTTTCCTTTTA
65 TCAAAGCCCACACAAGCTGGTGGCA-CCTTCAGTCCTCAAAG-AGCAGGACGCCTTTTCCTTTTA
* * * ** **
56676 AAGCCCGCACAAGTTGGTGGCACCTTTCAGTCCTTAAAGAGCAGGA-TGCTTTCTCCTTGCAAAG
128 AAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTT-TCCTTTTAAAG
* * * *
56740 CCCATACAAGTTGGTGGCAC-CTTCTAGTCCCCAAAGAGTAGGAC
192 CCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGAC
56784 CTATTTCACT
Statistics
Matches: 1052, Mismatches: 120, Indels: 57
0.86 0.10 0.05
Matches are distributed among these distances:
230 23 0.02
231 22 0.02
235 1 0.00
236 28 0.03
237 130 0.12
238 3 0.00
239 1 0.00
242 28 0.03
243 526 0.50
244 188 0.18
245 96 0.09
246 6 0.01
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (243 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
CAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAG
CCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCA
CACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTC
Found at i:57402 original size:20 final size:20
Alignment explanation
Indices: 57377--57500 Score: 70
Period size: 20 Copynumber: 5.7 Consensus size: 20
57367 TTTTCACAAT
57377 TTGTATCGATACATGGTTTA
1 TTGTATCGATACATGGTTTA
57397 TTGTATCGATACATTCTGAGTTTTA
1 TTGTATCGATACA---TG-G-TTTA
* * *
57422 TCCAGATGTATCGAAACATTGTTCA
1 T-----TGTATCGATACATGGTTTA
* * *
57447 TTGTATCAATACATTGTTCA
1 TTGTATCGATACATGGTTTA
*
57467 TTGTATCGATACAT-TTTTCA
1 TTGTATCGATACATGGTTT-A
*
57487 ATGTATCGATACAT
1 TTGTATCGATACAT
57501 TCAGATATTT
Statistics
Matches: 84, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.02
20 57 0.68
23 2 0.02
24 1 0.01
25 9 0.11
26 1 0.01
27 1 0.01
30 11 0.13
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATGGTTTA
Found at i:57501 original size:20 final size:20
Alignment explanation
Indices: 57427--57501 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
57417 TTTTATCCAG
*
57427 ATGTATCGAAACATTGTTCA
1 ATGTATCGATACATTGTTCA
* *
57447 TTGTATCAATACATTGTTCA
1 ATGTATCGATACATTGTTCA
* *
57467 TTGTATCGATACATTTTTCA
1 ATGTATCGATACATTGTTCA
57487 ATGTATCGATACATT
1 ATGTATCGATACATT
57502 CAGATATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTGTTCA
Found at i:59849 original size:50 final size:50
Alignment explanation
Indices: 59786--59909 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 50
59776 TAAATTTTTA
** * *
59786 GATTTTT-ATTCTCGGGGATACTCCGACCCCGGGTTTA-TTTCTAAAATATT
1 GATTTTTCA-TCTCGGGGATACTCAAACCCCGGGTTTATTTTC-AAAACATC
* *
59836 GATTTTTCATCTCGGGGATACTCAAACCTCGGTTTTATTTTCAAAACATC
1 GATTTTTCATCTCGGGGATACTCAAACCCCGGGTTTATTTTCAAAACATC
* *
59886 AATTTTTCATAATCGGGGATACTC
1 GATTTTTCAT-CTCGGGGATACTC
59910 TAATCCCATT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
50 46 0.73
51 17 0.27
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (50 bp):
GATTTTTCATCTCGGGGATACTCAAACCCCGGGTTTATTTTCAAAACATC
Found at i:59932 original size:79 final size:79
Alignment explanation
Indices: 59849--60230 Score: 360
Period size: 79 Copynumber: 4.9 Consensus size: 79
59839 TTTTCATCTC
* * * * *
59849 GGGGATACTCAAACCTCGGTTTTATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCTAAT
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
59914 CCCATTATTTTCGA
66 CCCATTATTTTCGA
* ** * *
59928 GGGGATACTCCAACCCCGATTTTA-TTTCTAAAATATTTATTTCTCATGATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACATCAATTTTTCATAATCGGGGATACTCCAA
* * *
59992 CCCCGTTATTTTGGC
65 CCCCATTATTTTCGA
*** * * * * ** *
60007 GGGGATACTCCAACCCCGGCCTTA-TTTCTAAAGCATCGATTTTCCACAATTAGTGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACATCAATTTTTCATAATCGGGGATACTCCAA
*
60071 CCCCATTATTTTCGG
65 CCCCATTATTTTCGA
* ** * *
60086 GGGGATACT-CAACCCCGATTTTATTTTCAAAACATGAA-TTTTCTATAATTAGGCATACTCTAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTC-ATAATCGGGGATACTCCAA
**
60149 CCCTGTTA-TTTCGA
65 CCCCATTATTTTCGA
* * * * * * *
60163 GGAGATACTCCAACCCTGATTTTATTTTCAGAACACCAATTTTCCATAATCGGAGATACTCCAGC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
60228 CCC
66 CCC
60231 GTGTTGTTAT
Statistics
Matches: 241, Mismatches: 57, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
77 17 0.07
78 84 0.35
79 140 0.58
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
CCCATTATTTTCGA
Found at i:61197 original size:13 final size:13
Alignment explanation
Indices: 61179--61204 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61169 TACACACAAG
61179 ATGTATCGATACA
1 ATGTATCGATACA
61192 ATGTATCGATACA
1 ATGTATCGATACA
61205 TCCCAAAATG
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):
ATGTATCGATACA
Found at i:61221 original size:33 final size:32
Alignment explanation
Indices: 61161--61224 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
61151 CTTAACTGTT
* *
61161 TGTATTGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
61193 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
61225 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:67312 original size:19 final size:20
Alignment explanation
Indices: 67269--67319 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
67259 AACCCTACAA
*
67269 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCAT
67289 TGTATCGATACATGT-T-CAT
1 TGTATCGATACAT-TATGCAT
*
67308 TGTATTGATACA
1 TGTATCGATACA
67320 CACTCAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.46
20 14 0.50
21 1 0.04
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATGCAT
Found at i:67395 original size:20 final size:20
Alignment explanation
Indices: 67370--67423 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
67360 CTACCACTAT
*
67370 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATAGTGA-A
67390 TTGTATCGATACATAGTGAA
1 TTGTATCGATACATAGTGAA
*
67410 ATGTATCGATACAT
1 TTGTATCGATACAT
67424 TGTCCTAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATAGTGAA
Found at i:69633 original size:79 final size:82
Alignment explanation
Indices: 69483--69667 Score: 200
Period size: 79 Copynumber: 2.3 Consensus size: 82
69473 AGAAGAAAAA
* * * *
69483 AAAATCGGGATTGGAGTATCCCC--TCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAA
1 AAAACCGGGGTTGGAGTATCCCCGATCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAA
*
69546 TCAATA-TTTTGGGAAT
66 TCAATATTTTTGGAAAT
* * * *
69562 AAAGCCGGGGTTGGAGTATCCCCGAT-G-AAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAA
1 AAAACCGGGGTTGGAGTATCCCCGATCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAA
***
69625 TTGGTATTTTTGGAAAT
66 TCAATATTTTTGGAAAT
* * *
69642 AAAATCAGAGTTGGAGTATCCCCGAT
1 AAAACCGGGGTTGGAGTATCCCCGAT
69668 TAAAGAAAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
79 54 0.62
80 32 0.37
81 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (82 bp):
AAAACCGGGGTTGGAGTATCCCCGATCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAA
TCAATATTTTTGGAAAT
Found at i:69739 original size:52 final size:51
Alignment explanation
Indices: 69598--69739 Score: 176
Period size: 52 Copynumber: 2.7 Consensus size: 51
69588 GAAATAACGA
* * * *
69598 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGAAAATAAAACCAG
* ** *
69650 AGTTGGAGTATCCCCGATTAAAGAAAAATTGGCGTTTTGAAAATAAAACCAG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGAAAATAAAACCAG
*
69702 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTT
69740 AGCGATAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
52 65 0.87
53 10 0.13
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCAG
Found at i:69748 original size:52 final size:49
Alignment explanation
Indices: 69598--69767 Score: 151
Period size: 52 Copynumber: 3.3 Consensus size: 49
69588 GAAATAACGA
* *
69598 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGG--ATAAAATCAG
* ** * * *
69650 AGTTGGAGTATCCCCGATTAAAGAAAAATTGGCGTTTTGAAAATAAAACCAG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG--GATAAAATCAG
* **
69702 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCGATAAAATTGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTT-G-GATAAAATCAG
*
69754 GGTTTGAGTATCCC
1 GGTTGGAGTATCCC
69768 TTCAGAAATA
Statistics
Matches: 94, Mismatches: 19, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
52 83 0.88
53 11 0.12
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.31
Consensus pattern (49 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGATAAAATCAG
Found at i:72290 original size:13 final size:13
Alignment explanation
Indices: 72272--72297 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
72262 ACAAAGATCC
72272 ATGTATCGATACA
1 ATGTATCGATACA
72285 ATGTATCGATACA
1 ATGTATCGATACA
72298 CAGAAAAATG
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):
ATGTATCGATACA
Found at i:72293 original size:33 final size:33
Alignment explanation
Indices: 72251--72317 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
72241 AAAATTTCCA
***
72251 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
72284 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
72317 A
1 A
72318 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:72361 original size:19 final size:18
Alignment explanation
Indices: 72337--72404 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
72327 CAGTAGCTAA
72337 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
72356 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
72371 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
72388 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
72405 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:72377 original size:13 final size:13
Alignment explanation
Indices: 72359--72383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
72349 ACAATACTTA
72359 TGTATCGATACAT
1 TGTATCGATACAT
72372 TGTATCGATACA
1 TGTATCGATACA
72384 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:72381 original size:32 final size:32
Alignment explanation
Indices: 72340--72402 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
72330 TAGCTAATTA
*
72340 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
72372 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
72403 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:72466 original size:21 final size:21
Alignment explanation
Indices: 72440--72516 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
72430 GTTGGGACCC
* *
72440 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
*
72461 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
72482 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
*
72503 AGTATCGATACATT
1 TGTATCGATACATT
72517 TGAATTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 3 0.06
21 47 0.94
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:75380 original size:3 final size:3
Alignment explanation
Indices: 75372--75409 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
75362 TGCGTCAACT
*
75372 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
75410 TTTGACACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:80850 original size:20 final size:20
Alignment explanation
Indices: 80822--80861 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
80812 AAGAATAACG
80822 CATGCTAGTCTTTGACCATT
1 CATGCTAGTCTTTGACCATT
* *
80842 CATGGTAGTCTTTGAGCATT
1 CATGCTAGTCTTTGACCATT
80862 GCTAATAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
CATGCTAGTCTTTGACCATT
Found at i:82582 original size:58 final size:58
Alignment explanation
Indices: 82510--82881 Score: 292
Period size: 57 Copynumber: 6.5 Consensus size: 58
82500 GGATCATTTA
* * * * * *
82510 CAATTTCATACATTTTAGGGTCGTTTAAATAATTTTTCATGTTTTAAGGATTATTTTG
1 CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACTATTTTG
* * * * *
82568 CAATTTCATGCATTTTAGGTTTATTTAAGCCA-TTTTCATGATTTAAGAATTAATTTT-
1 CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACT-ATTTTG
* * * *
82625 TAATTTCATGCATTTTTGGTTCATTTAAGTCATTTTTCATGATTTAGGGACTATTTTG
1 CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACTATTTTG
* * ** * *
82683 CAATATT-AGGCATTTTAGGGTCATTTAATTCATTTCCCATGATTTAAGGACCATTTTT
1 CAAT-TTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACTATTTTG
* ** * * *
82741 CAATTTCAT-TATTTTATAGTCATTTAAGTCA-TTTTCTATGGTTT-AGAGACCATTTTA
1 CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTC-ATGATTTAAG-GACTATTTTG
* *** * * * *
82798 CAATTTTATTTGTTTTAGGGTCATATAAGTCATTTTCCAGGATTT-AGGA-TCATTTTA
1 CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACT-ATTTTG
* * * *
82855 TAATTTTATGCATTTTAAGATCATTTA
1 CAATTTCATGCATTTTAGGGTCATTTA
82882 TTTAGGACTA
Statistics
Matches: 253, Mismatches: 51, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
56 5 0.02
57 121 0.48
58 121 0.48
59 6 0.02
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (58 bp):
CAATTTCATGCATTTTAGGGTCATTTAAGTCATTTTTCATGATTTAAGGACTATTTTG
Found at i:82631 original size:57 final size:58
Alignment explanation
Indices: 82510--82775 Score: 218
Period size: 58 Copynumber: 4.6 Consensus size: 58
82500 GGATCATTTA
* * * *** * *
82510 CAATTTCATACATTTTAGGGTCGTTTAAATAATTTTTCATGTTTTAAGGATTATTTTG
1 CAATTTCATGCATTTTAGGTTCATTTAAGCCATTTTTCATGATTTAAGAATTATTTTG
*
82568 CAATTTCATGCATTTTAGGTTTATTTAAGCCA-TTTTCATGATTTAAGAATTAATTTT-
1 CAATTTCATGCATTTTAGGTTCATTTAAGCCATTTTTCATGATTTAAGAATT-ATTTTG
* * * * * *
82625 TAATTTCATGCATTTTTGGTTCATTTAAGTCATTTTTCATGATTTAGGGACTATTTTG
1 CAATTTCATGCATTTTAGGTTCATTTAAGCCATTTTTCATGATTTAAGAATTATTTTG
* * ** ** * ** *
82683 CAATATT-AGGCATTTTAGGGTCATTTAATTCATTTCCCATGATTTAAGGACCATTTTT
1 CAAT-TTCATGCATTTTAGGTTCATTTAAGCCATTTTTCATGATTTAAGAATTATTTTG
* * *
82741 CAATTTCAT-TATTTTATAG-TCATTTAAGTCATTTT
1 CAATTTCATGCATTTTA-GGTTCATTTAAGCCATTTT
82776 CTATGGTTTA
Statistics
Matches: 171, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
57 72 0.42
58 97 0.57
59 2 0.01
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.49
Consensus pattern (58 bp):
CAATTTCATGCATTTTAGGTTCATTTAAGCCATTTTTCATGATTTAAGAATTATTTTG
Found at i:82717 original size:115 final size:112
Alignment explanation
Indices: 82500--82870 Score: 334
Period size: 115 Copynumber: 3.2 Consensus size: 112
82490 TGCGTATTAT
** * * * * * * * *
82500 GGATCATTTACAATTTCATACATTTTAGGGTCGTTTAAATAATTTTTCATGTTTTAAGGATTATT
1 GGATCATTTTTAATTTCATGCATTTT-TGGTCATTTAAGTCATTTTTCATGATTTAGGGACTATT
* * *
82565 TTGCAATTTCATGCATTTTAGGTTTATTTAAGCCATTTTCATGATTTAA
65 TTGCAATTT-ATGCATTTTAGGGTCATTTAAGTCATTTTCATGATTTAA
* *
82614 GAATTAATTTTTAATTTCATGCATTTTTGGTTCATTTAAGTCATTTTTCATGATTTAGGGACTAT
1 GGA-TCATTTTTAATTTCATGCATTTTTGG-TCATTTAAGTCATTTTTCATGATTTAGGGACTAT
* * *
82679 TTTGCAATATTAGGCATTTTAGGGTCATTTAATTCATTTCCCATGATTTAA
64 TTTGCAAT-TTATGCATTTTAGGGTCATTTAAGTCATTT-TCATGATTTAA
* * * * * *
82730 GGACCATTTTTCAATTTCAT-TATTTTATAGTCATTTAAGTCA-TTTTCTATGGTTTAGAGACCA
1 GGATCATTTTT-AATTTCATGCATTTT-TGGTCATTTAAGTCATTTTTC-ATGATTTAGGGACTA
* *** * *
82793 TTTTACAATTTTATTTGTTTTAGGGTCATATAAGTCATTTTCCAGGATTT-A
63 TTTTGCAA-TTTATGCATTTTAGGGTCATTTAAGTCATTTT-CATGATTTAA
*
82844 GGATCATTTTATAATTTTATGCATTTT
1 GGATCATTTT-TAATTTCATGCATTTT
82871 AAGATCATTT
Statistics
Matches: 208, Mismatches: 38, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
114 26 0.12
115 157 0.75
116 25 0.12
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (112 bp):
GGATCATTTTTAATTTCATGCATTTTTGGTCATTTAAGTCATTTTTCATGATTTAGGGACTATTT
TGCAATTTATGCATTTTAGGGTCATTTAAGTCATTTTCATGATTTAA
Found at i:82792 original size:57 final size:58
Alignment explanation
Indices: 82510--82853 Score: 201
Period size: 58 Copynumber: 6.0 Consensus size: 58
82500 GGATCATTTA
* * * * ** *
82510 CAATTTCA-TACATTTTAGGGTCGTTTAAATAATTTT-TCATGTTTTA-AGGATTATTTTG
1 CAATTTCAGT-CATTTTAGGGTCATTTAAGTCATTTTCT-ATGATTTAGA-GACCATTTTT
* * * **
82568 CAATTTCA-TGCATTTTAGGTTTATTTAAGCCATTTTC-ATGATTTA-AGAATTAATTTTT
1 CAATTTCAGT-CATTTTAGGGTCATTTAAGTCATTTTCTATGATTTAGAG-A-CCATTTTT
* * * * *
82626 -AATTTCA-TGCATTTTTGGTTCATTTAAGTCATTTT-TCATGATTTAGGGACTATTTTG
1 CAATTTCAGT-CATTTTAGGGTCATTTAAGTCATTTTCT-ATGATTTAGAGACCATTTTT
* * * *
82683 CAATATT-AGGCATTTTAGGGTCATTTAATTCATTTCCCATGATTTA-AGGACCATTTTT
1 CAAT-TTCAGTCATTTTAGGGTCATTTAAGTCATTTTCTATGATTTAGA-GACCATTTTT
* ** * *
82741 CAATTTCA-TTATTTTATAGTCATTTAAGTCATTTTCTATGGTTTAGAGACCATTTTA
1 CAATTTCAGTCATTTTAGGGTCATTTAAGTCATTTTCTATGATTTAGAGACCATTTTT
* * ** * * * *
82798 CAATTTTATTTGTTTTAGGGTCATATAAGTCATTTTCCAGGATTTAG-GATCATTTT
1 CAATTTCAGTCATTTTAGGGTCATTTAAGTCATTTTCTATGATTTAGAGACCATTTT
82854 ATAATTTTAT
Statistics
Matches: 228, Mismatches: 44, Indels: 29
0.76 0.15 0.10
Matches are distributed among these distances:
56 1 0.00
57 101 0.44
58 123 0.54
59 3 0.01
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (58 bp):
CAATTTCAGTCATTTTAGGGTCATTTAAGTCATTTTCTATGATTTAGAGACCATTTTT
Found at i:82913 original size:99 final size:101
Alignment explanation
Indices: 82782--82971 Score: 240
Period size: 99 Copynumber: 1.9 Consensus size: 101
82772 TTTTCTATGG
* ** * *
82782 TTTAGAGACCATTTTACAATTTTATTTGTTTTAGGGTCATATAAGTCATTTTCCAGGATTTAGGA
1 TTTAGAGACCATTTTACAATTTCATTCATTTTAGAGTCATATAAGTCATTTTCCAGGATTTAAGA
* * *
82847 TC-ATTTTATAATTTTATGCATTTTAAGATCATTTA
66 ACTATTTAATAATTTTATACATTTTAAGATCATTTA
* * * * * *
82882 TTTAG-GACTATTTTGCAATTTCATTCATTTTAGAGTTATTTAAGTCATTTTCTATGATTTAAGA
1 TTTAGAGACCATTTTACAATTTCATTCATTTTAGAGTCATATAAGTCATTTTCCAGGATTTAAGA
82946 ACTATTTAATAATTTTATACATTTTA
66 ACTATTTAATAATTTTATACATTTTA
82972 GAGTCTTTTA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
99 49 0.65
100 26 0.35
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.49
Consensus pattern (101 bp):
TTTAGAGACCATTTTACAATTTCATTCATTTTAGAGTCATATAAGTCATTTTCCAGGATTTAAGA
ACTATTTAATAATTTTATACATTTTAAGATCATTTA
Found at i:84976 original size:58 final size:58
Alignment explanation
Indices: 84913--85031 Score: 193
Period size: 58 Copynumber: 2.1 Consensus size: 58
84903 CATATCCAAA
* * *
84913 GTATTACGCAAAGATATTACTATATATAGTGACCTTAAAAAATGTCTTTATGACACTT
1 GTATTACACAAAGAGATTACTATATATAGTGACCTTAAAAAATGTCCTTATGACACTT
* *
84971 GTATTATACAAAGAGATTACTATATATAGTGACCTTAAAAAATGTCCTTATGACGCTT
1 GTATTACACAAAGAGATTACTATATATAGTGACCTTAAAAAATGTCCTTATGACACTT
85029 GTA
1 GTA
85032 AGCAAAATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (58 bp):
GTATTACACAAAGAGATTACTATATATAGTGACCTTAAAAAATGTCCTTATGACACTT
Found at i:85525 original size:13 final size:13
Alignment explanation
Indices: 85507--85531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85497 CATAAAATGT
85507 TGTATCGATACAA
1 TGTATCGATACAA
85520 TGTATCGATACA
1 TGTATCGATACA
85532 TATTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:85547 original size:32 final size:33
Alignment explanation
Indices: 85487--85552 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
85477 TTCAACGATT
85487 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
** *
85520 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
85552 T
1 T
85553 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:85615 original size:13 final size:13
Alignment explanation
Indices: 85597--85621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85587 ATTACTCACA
85597 TGTATCGATACAT
1 TGTATCGATACAT
85610 TGTATCGATACA
1 TGTATCGATACA
85622 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:85686 original size:52 final size:52
Alignment explanation
Indices: 85630--85758 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
85620 CACTGATCTT
* *
85630 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
*
85682 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
85734 TGTATCGATACATGCA-GATAAATTT
1 TGTATCGATACATGCAGGA-AAATTT
85759 TCATATTTCG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
51 2 0.03
52 71 0.97
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:90430 original size:21 final size:21
Alignment explanation
Indices: 90379--90433 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
90369 GAGGGCCCGG
* *
90379 GCTCCGCCACAGCCATCATCA
1 GCTCCTCCACCGCCATCATCA
90400 GCTCCTCCACCGCCATCATCA
1 GCTCCTCCACCGCCATCATCA
90421 GCT-CTCCCACCGC
1 GCTCCT-CCACCGC
90434 TTCCCATGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.18, C:0.53, G:0.13, T:0.16
Consensus pattern (21 bp):
GCTCCTCCACCGCCATCATCA
Found at i:92360 original size:2 final size:2
Alignment explanation
Indices: 92353--92383 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
92343 GCGTTATTGG
92353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
92384 GTGGTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:93323 original size:72 final size:71
Alignment explanation
Indices: 93169--93323 Score: 197
Period size: 72 Copynumber: 2.2 Consensus size: 71
93159 TTAAAATATT
* * *
93169 TTTATTAACAATAGAATTTATCACATTGATAAATAAAAATTCTAAATATATTAAAAATTTGGTTC
1 TTTATTAATAATAGAATTTATCACATTGATAAATAAAAATTCTAAATATATTAAAAATTTGGGTA
*
93234 AATTAA
66 AATAAA
* * *
93240 TTTATTGAATAATAGAATTTATCACATT-ATAAATAAAAATTTTAATTTTATTGAAAAATTATGG
1 TTTATT-AATAATAGAATTTATCACATTGATAAATAAAAATTCTAAATATATT-AAAAATT-TGG
93304 GTAAATCAAA
63 GTAAAT-AAA
93314 TTTA-TAATAA
1 TTTATTAATAA
93324 ATAAAAAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
71 27 0.37
72 32 0.44
73 8 0.11
74 6 0.08
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (71 bp):
TTTATTAATAATAGAATTTATCACATTGATAAATAAAAATTCTAAATATATTAAAAATTTGGGTA
AATAAA
Found at i:93469 original size:2 final size:2
Alignment explanation
Indices: 93462--93488 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
93452 TTTCTATTTT
93462 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
93489 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:93493 original size:2 final size:2
Alignment explanation
Indices: 93488--93530 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
93478 ACACACACAC
93488 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
93530 A
1 A
93531 CAATAGTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.