Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000637.1 Hibiscus syriacus cultivar Beakdansim tig00001234_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: 67597
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4043 original size:20 final size:20
Alignment explanation
Indices: 4020--4146 Score: 182
Period size: 20 Copynumber: 6.3 Consensus size: 20
4010 GAATATGTAA
* * *
4020 ATCGCAATGCGAGTATGACT
1 ATCGCAACGCGATTCTGACT
4040 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
4060 ATCGCAACGAGATTTTGACT
1 ATCGCAACGCGATTCTGACT
*
4080 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
4100 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
4120 GTCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
4140 ATCGCAA
1 ATCGCAA
4147 TGCAATTTTC
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 97 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:4066 original size:60 final size:60
Alignment explanation
Indices: 3996--4131 Score: 166
Period size: 60 Copynumber: 2.3 Consensus size: 60
3986 GCGATTTTCC
* * *
3996 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGAGTATGACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGAATATG-ACAATCGCAACGAGAGTATGACTATCGCAACGCGATTCT
* * * * * *
4056 GACTATCGCAACGAGATTTTGACTATCGCAACGAGATTCTGACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGAATATGACAATCGCAACGAGAGTATGACTATCGCAACGCGATTCT
*
4116 GACTGTCGCAACGCGA
1 GACTATCGCAACGCGA
4132 TGCTGACTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 63 0.98
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (60 bp):
GACTATCGCAACGCGAATATGACAATCGCAACGAGAGTATGACTATCGCAACGCGATTCT
Found at i:4364 original size:22 final size:23
Alignment explanation
Indices: 4319--4364 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4309 CACTCTCTAA
* *
4319 GACGACATCCGTCCCCAATCTCC
1 GACGAAATCAGTCCCCAATCTCC
4342 GACGAAATCAGTCCCC-ATCTCC
1 GACGAAATCAGTCCCCAATCTCC
4364 G
1 G
4365 GCAAAATCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.24, C:0.43, G:0.15, T:0.17
Consensus pattern (23 bp):
GACGAAATCAGTCCCCAATCTCC
Found at i:4371 original size:22 final size:23
Alignment explanation
Indices: 4329--4372 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
4319 GACGACATCC
*
4329 GTCCCCAATCTCCGACGAAATCA
1 GTCCCCAATCTCCGACAAAATCA
*
4352 GTCCCC-ATCTCCGGCAAAATC
1 GTCCCCAATCTCCGACAAAATC
4373 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.27, C:0.41, G:0.14, T:0.18
Consensus pattern (23 bp):
GTCCCCAATCTCCGACAAAATCA
Found at i:4838 original size:20 final size:20
Alignment explanation
Indices: 4775--4840 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
4765 TTTGGCATTT
*
4775 CGATTTTCA-TTTCGCGTTG
1 CGATTTTCATTTTCGTGTTG
**
4794 CGATAGTCATTTTCGTGTTG
1 CGATTTTCATTTTCGTGTTG
4814 CGATTTTCATTTTCGTGTTG
1 CGATTTTCATTTTCGTGTTG
4834 CGATTTT
1 CGATTTT
4841 AAGTTTCAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 7 0.17
20 34 0.83
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (20 bp):
CGATTTTCATTTTCGTGTTG
Found at i:4847 original size:20 final size:20
Alignment explanation
Indices: 4804--4847 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4794 CGATAGTCAT
* *
4804 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
4824 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
4844 TTTC
1 TTTC
4848 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:6767 original size:20 final size:20
Alignment explanation
Indices: 6742--6807 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
6732 GTTTACTTTT
6742 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
6762 GCAACGCGAAAATAACTATC
1 GCAACGCGAAAATGACTATC
*
6782 GCAACGTGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
6802 GCAACG
1 GCAACG
6808 AAAGAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:6875 original size:20 final size:20
Alignment explanation
Indices: 6850--6925 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
6840 ACGATTCTCT
**
6850 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
6870 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
6890 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
6910 CGTTACGATAGTCATT
1 CGTTGCGATAGTCATT
6926 CGTGTTACGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:6932 original size:18 final size:19
Alignment explanation
Indices: 6850--6936 Score: 95
Period size: 20 Copynumber: 4.5 Consensus size: 19
6840 ACGATTCTCT
* *
6850 CGTTGCGATAGTCAAATTCG
1 CGTTACGATAGTC-ATTTCG
*
6870 CGTTGCGATAGTCATTTTCG
1 CGTTACGATAGTCA-TTTCG
*
6890 CGTTGCGATAGTCATTTTCG
1 CGTTACGATAGTCA-TTTCG
6910 CGTTACGATAGTCA-TTCG
1 CGTTACGATAGTCATTTCG
*
6928 TGTTACGAT
1 CGTTACGAT
6937 TTTAAGTTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
18 12 0.19
19 1 0.02
20 50 0.79
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTACGATAGTCATTTCG
Found at i:7517 original size:21 final size:21
Alignment explanation
Indices: 7426--7524 Score: 67
Period size: 21 Copynumber: 4.7 Consensus size: 21
7416 GACTCACCTG
7426 TCATCGTTCAAGAGG--ACTCC
1 TCATCGTTCAAGAGGCCACT-C
* * *
7446 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCACTC
** * *
7468 TCATCCCTCAAGAGTCCTCTC
1 TCATCGTTCAAGAGGCCACTC
* * *
7489 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCACTC
*
7510 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
7525 TCCCTCCCAA
Statistics
Matches: 57, Mismatches: 19, Indels: 5
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 53 0.93
22 1 0.02
23 2 0.04
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCACTC
Found at i:7523 original size:42 final size:42
Alignment explanation
Indices: 7423--7533 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
7413 CCCGACTCAC
** * *
7423 CTGTCATCGTTCAAGAGGACTC-CCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCCTCTCCC-ACCGTTCAAGAGGCCA
* **
7465 CTATCATCCCTCAAGAGTCCTCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCTCTCCCACCGTTCAAGAGGCCA
*
7507 CTGTCATCGTTGAAGAGGTCC-CTCCCA
1 CTGTCATCGTTCAAGA-GTCCTCTCCCA
7534 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 49 0.88
43 7 0.12
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCTCTCCCACCGTTCAAGAGGCCA
Found at i:8950 original size:14 final size:14
Alignment explanation
Indices: 8913--8974 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
8903 TTTCTTGTTT
*
8913 AATTGATTTATAAA
1 AATTGATTTGTAAA
8927 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
8941 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
8956 TATTGATGTGTAAA
1 AATTGATTTGTAAA
8970 TAATT
1 -AATT
8975 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:9098 original size:20 final size:20
Alignment explanation
Indices: 9073--9125 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
9063 AGGTACACTT
* **
9073 TCGCAACGCTAAACTTAAAA
1 TCGCAACGCGAAACACAAAA
* *
9093 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAACACAAAA
9113 TCGCAACGCGAAA
1 TCGCAACGCGAAA
9126 GTCAATTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACACAAAA
Found at i:9126 original size:20 final size:20
Alignment explanation
Indices: 9089--9126 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9079 CGCTAAACTT
*
9089 AAAATCGCAATGCGAAAGAC
1 AAAATCGCAACGCGAAAGAC
9109 AAAATCGCAACGCGAAAG
1 AAAATCGCAACGCGAAAG
9127 TCAATTCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAGAC
Found at i:9142 original size:19 final size:20
Alignment explanation
Indices: 9120--9161 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
9110 AAATCGCAAC
*
9120 GCGAAAGTC-AATTCGCGTT
1 GCGAAAGTCTAATACGCGTT
* *
9139 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCGTT
9159 GCG
1 GCG
9162 CTTTTCTCGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCGTT
Found at i:9194 original size:20 final size:20
Alignment explanation
Indices: 9169--9413 Score: 255
Period size: 20 Copynumber: 12.8 Consensus size: 20
9159 GCGCTTTTCT
* *
9169 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
9189 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
9209 CGTTGCAATACTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
9229 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
9249 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
9263 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
*
9282 TCATTGCGATAGTCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
*
9303 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
9323 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
9343 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
9357 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
9377 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
9397 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
9414 GAATGTGTAA
Statistics
Matches: 186, Mismatches: 25, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
14 23 0.12
16 2 0.01
18 2 0.01
19 1 0.01
20 156 0.84
21 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:9267 original size:74 final size:74
Alignment explanation
Indices: 9189--9331 Score: 198
Period size: 74 Copynumber: 1.9 Consensus size: 74
9179 GTCAAATACC
* * *
9189 CGTTGCGATAATCAAATTCG-CGTTGCAATACTCAAATTTGCGTTGCGATAGTCAAATTCGCGTT
1 CGTTGCGATAATCAAA-TAGTCATTGCAATACTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
9253 GCGATTTTCT
65 GCGATTTTCT
* * * * *
9263 CGTTGCGATAGTCAAATAGTCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGTGTTG
1 CGTTGCGATAATCAAATAGTCATTGCAATACTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
9328 CGAT
66 CGAT
9332 AGTCAAATTC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 2 0.03
74 58 0.97
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (74 bp):
CGTTGCGATAATCAAATAGTCATTGCAATACTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
CGATTTTCT
Found at i:9278 original size:54 final size:56
Alignment explanation
Indices: 9169--9413 Score: 177
Period size: 54 Copynumber: 4.3 Consensus size: 56
9159 GCGCTTTTCT
* * * * * *
9169 CGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCAATACTCAAATTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT-AT-ATATT--CGTTGCGATAGTCAAATTAG
9229 CGTTGCGATAGTCAAATTCGCGTTGCGAT-T-T-TCTCGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATATATAT-TCGTTGCGATAGTCAAATTAG
* *
9282 TCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCG
1 -CGTTGCGATAGTCAAATTCGCGTTGCGATA-T-ATATTC--GTTGCGATAGTCAAATTAG
* * * *
9343 CGTTGCGAT--T----TTTGAGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT-AT-ATATT--CGTTGCGATAGTCAAATTAG
*
9397 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
9414 GAATGTGTAA
Statistics
Matches: 154, Mismatches: 12, Indels: 38
0.75 0.06 0.19
Matches are distributed among these distances:
53 2 0.01
54 87 0.56
55 2 0.01
56 4 0.03
58 5 0.03
59 1 0.01
60 51 0.33
61 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (56 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATATATATTCGTTGCGATAGTCAAATTAG
Found at i:9298 original size:94 final size:93
Alignment explanation
Indices: 9129--9413 Score: 383
Period size: 94 Copynumber: 3.0 Consensus size: 93
9119 CGCGAAAGTC
* * * * *
9129 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGCTTTTCTCGTTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATA-GCGTTG
* *
9194 CGATAATCAAATTCGCGTTGCAATACTCA
65 CGATAGTCAAATTCGCGTTGCGATACTCA
* *
9223 AATTTGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAGTCATTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAG-CGTTG
*
9288 CGATAGTCAAATTCGCGTTGCGATAGTCA
65 CGATAGTCAAATTCGCGTTGCGATACTCA
* * * * *
9317 TATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGAGTTGCGATAATCAAATTCGCGTT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-CGTTGCGATAGTCAAA-TAGCGTT
*
9381 GCGATAGTCAAATTCGCGTTGCGATATTCA
64 GCGATAGTCAAATTCGCGTTGCGATACTCA
9411 AAT
1 AAT
9414 GAATGTGTAA
Statistics
Matches: 169, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
93 1 0.01
94 166 0.98
95 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (93 bp):
AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAGCGTTGC
GATAGTCAAATTCGCGTTGCGATACTCA
Found at i:9636 original size:140 final size:140
Alignment explanation
Indices: 9384--9653 Score: 540
Period size: 140 Copynumber: 1.9 Consensus size: 140
9374 TCGCGTTGCG
9384 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
9449 TAGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
9514 AATACACATA
131 AATACACATA
9524 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
9589 TAGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
9654 TACAACGTTT
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 130 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:9736 original size:18 final size:18
Alignment explanation
Indices: 9713--9747 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9703 AAGCCGGTTG
*
9713 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
9731 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
9748 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:11798 original size:14 final size:15
Alignment explanation
Indices: 11779--11815 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
11769 TCCCGTGGCA
11779 TTTTCTTCGGGGA-C
1 TTTTCTTCGGGGATC
*
11793 TTTTCTTCGGGGATT
1 TTTTCTTCGGGGATC
11808 TTTTCTTC
1 TTTTCTTC
11816 TTTTTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.05, C:0.19, G:0.22, T:0.54
Consensus pattern (15 bp):
TTTTCTTCGGGGATC
Found at i:12036 original size:24 final size:24
Alignment explanation
Indices: 12002--12055 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
11992 CTGAAACATC
12002 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
12026 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
12050 ATCAAA
1 ATCAAA
12056 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:12920 original size:40 final size:40
Alignment explanation
Indices: 12891--13026 Score: 236
Period size: 40 Copynumber: 3.4 Consensus size: 40
12881 ACAGTCAGAA
12891 TCGCGTTGCGATAGTCATAATCGCATTGCGATTTACATAT
1 TCGCGTTGCGATAGTCATAATCGCATTGCGATTTACATAT
*
12931 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
1 TCGCGTTGCGATAGTCATAATCGCATTGCGATTTACATAT
* *
12971 TCGCGTTTCGATAGTCATACTCGCATTGCGATTTACATAT
1 TCGCGTTGCGATAGTCATAATCGCATTGCGATTTACATAT
*
13011 TCGCATTGCGATAGTC
1 TCGCGTTGCGATAGTC
13027 GGAAAATCGC
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 90 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (40 bp):
TCGCGTTGCGATAGTCATAATCGCATTGCGATTTACATAT
Found at i:12922 original size:20 final size:20
Alignment explanation
Indices: 12876--13026 Score: 146
Period size: 20 Copynumber: 7.5 Consensus size: 20
12866 AAATTTAGTG
* * *
12876 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
12896 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* *
12916 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
12936 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* * *
12956 TTGCGAT-TTACATATTCGCG
1 TTGCGATAGT-CATAATCGCA
* *
12976 TTTCGATAGTCATACTCGCA
1 TTGCGATAGTCATAATCGCA
* *
12996 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
13016 TTGCGATAGTC
1 TTGCGATAGTC
13027 GGAAAATCGC
Statistics
Matches: 107, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.03
20 101 0.94
21 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:13088 original size:41 final size:40
Alignment explanation
Indices: 13040--13127 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
13030 AAATCGCAAC
*
13040 GCGAATTTGGAAAATCGCA-ATGCGATAGTCAGA-ATCGCGTT
1 GCGAATTTGGAAAAT-G-ATATGCGATA-CCAGAGATCGCGTT
* *
13081 GCGAATTTGGAAACTGATTTGCGATACCAGAGATCGCGTT
1 GCGAATTTGGAAAATGATATGCGATACCAGAGATCGCGTT
13121 GCGAATT
1 GCGAATT
13128 ATCGATCACA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 5 0.12
40 23 0.55
41 14 0.33
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (40 bp):
GCGAATTTGGAAAATGATATGCGATACCAGAGATCGCGTT
Found at i:17423 original size:54 final size:54
Alignment explanation
Indices: 17334--17595 Score: 285
Period size: 54 Copynumber: 4.8 Consensus size: 54
17324 TCGATACGGT
* * * ** * * *
17334 AATTCACAAACTCATTATGAATTACGTGGAG-TGCACATATAATGCCAAAACGAA
1 AATTCATAAACTAATTATGAATTTC-TTAAGTTGCACACACAATGCCAATACGAA
*
17388 AATTCATAAACTAATTATGAATTTCTTAAGTTGCACACACACAGTGCCAATACGGA
1 AATTCATAAACTAATTATGAATTTCTTAAGTTGCACACACA-A-TGCCAATACGAA
* * * * *
17444 AATTCATAAACCAATTATGAATTTCTTATGTTGCACACATAGTGTCAATACGAA
1 AATTCATAAACTAATTATGAATTTCTTAAGTTGCACACACAATGCCAATACGAA
* * * * *
17498 AATTCATAAATTAATTATGAATTTCTTAGGATGCACATACAGTG-CATATACGAA
1 AATTCATAAACTAATTATGAATTTCTTAAGTTGCACACACAATGCCA-ATACGAA
* *
17552 AATTCATAAACTAATTATGAATTTTTTAGGTTGCACACACAATG
1 AATTCATAAACTAATTATGAATTTCTTAAGTTGCACACACAATG
17596 TCATTCGGTA
Statistics
Matches: 178, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
53 5 0.03
54 124 0.70
55 1 0.01
56 48 0.27
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (54 bp):
AATTCATAAACTAATTATGAATTTCTTAAGTTGCACACACAATGCCAATACGAA
Found at i:18415 original size:12 final size:12
Alignment explanation
Indices: 18397--18437 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
18387 ACTATACGGT
18397 ATGAACAATACC
1 ATGAACAATACC
*
18409 GTGAACAATA--
1 ATGAACAATACC
18419 ATGAACAATACC
1 ATGAACAATACC
18431 ATGAACA
1 ATGAACA
18438 GTGCTACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.17
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:18465 original size:21 final size:21
Alignment explanation
Indices: 18439--18479 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
18429 CCATGAACAG
*
18439 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCACCGATGCAT
18460 TGCTACAGTGCACCGATGCA
1 TGCTACAGTGCACCGATGCA
18480 CTAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCTACAGTGCACCGATGCAT
Found at i:20046 original size:2 final size:2
Alignment explanation
Indices: 20039--20091 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
20029 TACTTATGTT
20039 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
20081 TA TA TA TA TA T
1 TA TA TA TA TA T
20092 CACACGACAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21252 original size:42 final size:42
Alignment explanation
Indices: 21124--21414 Score: 359
Period size: 42 Copynumber: 6.8 Consensus size: 42
21114 CTGTACACCA
* * * *
21124 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCTTTGCACACAGCAAAGGGA-CCT-GGGAAACT
* * * *
21168 GTAAGGCTTACCCTTGCACATAACAAAAGGGACATGGGAAACT
1 GTAAGGCTTACCTTTGCACACAGC-AAAGGGACCTGGGAAACT
21211 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT
* *
21253 GTAAGGCTTACCTTTGCACACAACAAAAGGGACATGGGAAACT
1 GTAAGGCTTACCTTTGCACACAGC-AAAGGGACCTGGGAAACT
* * *
21296 GTAAGTCTTACCTTTGCACACAGTAAATGGACCTGGGAAACT
1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT
* * *
21338 GTAAGGTTTACCTTTGCACACATCAAAGGGACATGGGAAACT
1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT
* * *
21380 GTATGGCTTACCTTTGCATACAGCAAAGAGACCTG
1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTG
21415 ATAATACTTC
Statistics
Matches: 214, Mismatches: 30, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
42 121 0.57
43 77 0.36
44 13 0.06
45 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (42 bp):
GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:21270 original size:85 final size:85
Alignment explanation
Indices: 21124--21414 Score: 415
Period size: 85 Copynumber: 3.4 Consensus size: 85
21114 CTGTACACCA
* * * * *
21124 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGCTTACCCTTGCACA
1 GTAAGGCTT-ACCTTTGCACACAGCAAAGGGA-CCT-GGGAAACTGTAAGGCTTACCTTTGCACA
*
21188 TAACAAAAGGGACATGGGAAACT
63 CAACAAAAGGGACATGGGAAACT
21211 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCACACAA
1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCACACAA
21276 CAAAAGGGACATGGGAAACT
66 CAAAAGGGACATGGGAAACT
* * * * *
21296 GTAAGTCTTACCTTTGCACACAGTAAATGGACCTGGGAAACTGTAAGGTTTACCTTTGCACACAT
1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCACACAA
21361 C-AAAGGGACATGGGAAACT
66 CAAAAGGGACATGGGAAACT
* * *
21380 GTATGGCTTACCTTTGCATACAGCAAAGAGACCTG
1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTG
21415 ATAATACTTC
Statistics
Matches: 186, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
84 47 0.25
85 109 0.59
86 18 0.10
87 12 0.06
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (85 bp):
GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCACACAA
CAAAAGGGACATGGGAAACT
Found at i:21358 original size:127 final size:128
Alignment explanation
Indices: 21163--21406 Score: 364
Period size: 127 Copynumber: 1.9 Consensus size: 128
21153 GAGCCTAGGA
21163 AAACTGTAAGGCTTACCCTTGCACATAACAAAAGGGACATGGGAAACTGTAAGGCTTACCTTTGC
1 AAACTGTAAGGCTTACCCTTGCACATAACAAAAGGGACATGGGAAACTGTAAGGCTTACCTTTGC
*
21228 ACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAAGGGACATGGG
66 ACACAGCAAAGGGACATGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAAGGGACATGGG
* * * ** * * *
21291 AAACTGTAAGTCTTACCTTTGCACA-CAGTAAATGGACCTGGGAAACTGTAAGGTTTACCTTTGC
1 AAACTGTAAGGCTTACCCTTGCACATAACAAAAGGGACATGGGAAACTGTAAGGCTTACCTTTGC
* * * *
21355 ACACATCAAAGGGACATGGGAAACTGTATGGCTTACCTTTGCATACAGCAAA
66 ACACAGCAAAGGGACATGGGAAACTGTAAGGCTTACCTTTGCACACAACAAA
21407 GAGACCTGAT
Statistics
Matches: 103, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
127 80 0.78
128 23 0.22
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (128 bp):
AAACTGTAAGGCTTACCCTTGCACATAACAAAAGGGACATGGGAAACTGTAAGGCTTACCTTTGC
ACACAGCAAAGGGACATGGGAAACTGTAAGGCTTACCTTTGCACACAACAAAAGGGACATGGG
Found at i:22394 original size:30 final size:28
Alignment explanation
Indices: 22357--22563 Score: 227
Period size: 29 Copynumber: 7.1 Consensus size: 28
22347 CAATTATTAC
* * *
22357 CCTTTTAAGAAATATTTAAGAAACTATCA
1 CCTTTTAA-AAATATTTACGAAAATAACA
22386 CTCTTTTAAAAATATTTACGAAAATAACA
1 C-CTTTTAAAAATATTTACGAAAATAACA
22415 CCATTTTAAAAATATTTACGAAAATAACA
1 CC-TTTTAAAAATATTTACGAAAATAACA
* * *
22444 CTTTTTTTAAAAAATAATTACGAAAATAGCA
1 C--CTTTT-AAAAATATTTACGAAAATAACA
* *
22475 CCATTTTAAAAATAATTACGAAAATAGCA
1 CC-TTTTAAAAATATTTACGAAAATAACA
*
22504 CCATTTTAAAAATAATTACGAAAATAACA
1 CC-TTTTAAAAATATTTACGAAAATAACA
*
22533 CCATTTTAAAAATAATTAC-AAAACTAACA
1 CC-TTTTAAAAATATTTACGAAAA-TAACA
22562 CC
1 CC
22564 CGGTCAACGG
Statistics
Matches: 163, Mismatches: 8, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
28 5 0.03
29 122 0.75
30 15 0.09
31 21 0.13
ACGTcount: A:0.50, C:0.14, G:0.04, T:0.31
Consensus pattern (28 bp):
CCTTTTAAAAATATTTACGAAAATAACA
Found at i:22401 original size:29 final size:29
Alignment explanation
Indices: 22389--22563 Score: 262
Period size: 29 Copynumber: 6.0 Consensus size: 29
22379 ACTATCACTC
*
22389 TTTTAAAAATATTTACGAAAATAACACCA
1 TTTTAAAAATAATTACGAAAATAACACCA
* **
22418 TTTTAAAAATATTTACGAAAATAACACTTT
1 TTTTAAAAATAATTACGAAAATAACAC-CA
*
22448 TTTTAAAAAATAATTACGAAAATAGCACCA
1 TTTT-AAAAATAATTACGAAAATAACACCA
*
22478 TTTTAAAAATAATTACGAAAATAGCACCA
1 TTTTAAAAATAATTACGAAAATAACACCA
22507 TTTTAAAAATAATTACGAAAATAACACCA
1 TTTTAAAAATAATTACGAAAATAACACCA
22536 TTTTAAAAATAATTAC-AAAACTAACACC
1 TTTTAAAAATAATTACGAAAA-TAACACC
22564 CGGTCAACGG
Statistics
Matches: 136, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
28 4 0.03
29 103 0.76
30 8 0.06
31 21 0.15
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.30
Consensus pattern (29 bp):
TTTTAAAAATAATTACGAAAATAACACCA
Found at i:22510 original size:89 final size:86
Alignment explanation
Indices: 22389--22555 Score: 262
Period size: 89 Copynumber: 1.9 Consensus size: 86
22379 ACTATCACTC
* * **
22389 TTTTAAAAATATTTACGAAAATAACACCATTTTAAAAATATTTACGAAAATAACACTTTTTTTAA
1 TTTTAAAAATAATTACGAAAATAACACCATTTTAAAAATAATTACGAAAATAACAC-CATTTT-A
22454 AAAATAATTACGAAAATAGCACCA
64 AAAATAATTAC-AAAATAGCACCA
*
22478 TTTTAAAAATAATTACGAAAATAGCACCATTTTAAAAATAATTACGAAAATAACACCATTTTAAA
1 TTTTAAAAATAATTACGAAAATAACACCATTTTAAAAATAATTACGAAAATAACACCATTTTAAA
22543 AATAATTACAAAA
66 AATAATTACAAAA
22556 CTAACACCCG
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
86 4 0.05
87 12 0.16
88 4 0.05
89 53 0.73
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.31
Consensus pattern (86 bp):
TTTTAAAAATAATTACGAAAATAACACCATTTTAAAAATAATTACGAAAATAACACCATTTTAAA
AATAATTACAAAATAGCACCA
Found at i:22601 original size:13 final size:13
Alignment explanation
Indices: 22583--22607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22573 GTCAACGATT
22583 AACGGGTCGGGTC
1 AACGGGTCGGGTC
22596 AACGGGTCGGGT
1 AACGGGTCGGGT
22608 TGGAACCGGT
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:0.16, C:0.20, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTC
Found at i:36276 original size:2 final size:2
Alignment explanation
Indices: 36271--36311 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
36261 TTTCCCCCCA
36271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36312 GAATTTTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37396 original size:8 final size:8
Alignment explanation
Indices: 37385--37480 Score: 51
Period size: 8 Copynumber: 12.4 Consensus size: 8
37375 ACCCTTTATA
37385 TTTTTAA-
1 TTTTTAAT
37392 TTTTT-AT
1 TTTTTAAT
*
37399 TAATTT-AT
1 T-TTTTAAT
37407 TTTTTAA-
1 TTTTTAAT
37414 TTTTTAAT
1 TTTTTAAT
**
37422 TAATTAAT
1 TTTTTAAT
37430 TTTTTAA-
1 TTTTTAAT
37437 TTTTT-AT
1 TTTTTAAT
* * *
37444 GTTATGAT
1 TTTTTAAT
* *
37452 ATTTATATT
1 -TTTTTAAT
37461 TTTTTAAT
1 TTTTTAAT
37469 TTTTTATAT
1 TTTTTA-AT
37478 TTT
1 TTT
37481 AAAAAAATTA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
6 2 0.03
7 24 0.35
8 32 0.47
9 10 0.15
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
TTTTTAAT
Found at i:37413 original size:22 final size:22
Alignment explanation
Indices: 37379--37443 Score: 103
Period size: 23 Copynumber: 2.9 Consensus size: 22
37369 AATAGTACCC
37379 TTTATATTTTTAATTTTTATTAA
1 TTTAT-TTTTTAATTTTTATTAA
37402 TTTATTTTTTAATTTTTAATTAA
1 TTTATTTTTTAATTTTT-ATTAA
*
37425 TTAATTTTTTAATTTTTAT
1 TTTATTTTTTAATTTTTAT
37444 GTTATGATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 14 0.35
23 26 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTATTTTTTAATTTTTATTAA
Found at i:39658 original size:14 final size:14
Alignment explanation
Indices: 39639--39666 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39629 TGAGAGGTTA
39639 AAATCTTTGAGTCT
1 AAATCTTTGAGTCT
39653 AAATCTTTGAGTCT
1 AAATCTTTGAGTCT
39667 TTCTTTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
AAATCTTTGAGTCT
Found at i:46804 original size:21 final size:21
Alignment explanation
Indices: 46746--46804 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
46736 GTCTGAGTTA
*
46746 CCCGCGAAAGCCGCAATAGCG
1 CCCGCGACAGCCGCAATAGCG
* * *
46767 TCCGCGACAGCCACAATAGTG
1 CCCGCGACAGCCGCAATAGCG
* *
46788 CCCGCGACGGTCGCAAT
1 CCCGCGACAGCCGCAAT
46805 CACAATAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.37, G:0.27, T:0.10
Consensus pattern (21 bp):
CCCGCGACAGCCGCAATAGCG
Found at i:47102 original size:6 final size:6
Alignment explanation
Indices: 47091--47120 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
47081 GCAAGCTCTT
47091 AACATG AACATG AACATG AACATG AACATG
1 AACATG AACATG AACATG AACATG AACATG
47121 GTGGATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
AACATG
Found at i:52764 original size:28 final size:28
Alignment explanation
Indices: 52724--52781 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
52714 TGGTTTTTTA
52724 CTTAAAGGCTTGATACAAAAATAAGTGC
1 CTTAAAGGCTTGATACAAAAATAAGTGC
*
52752 CTTAAATGCTTGATACAAAAATAAGTGC
1 CTTAAAGGCTTGATACAAAAATAAGTGC
52780 CT
1 CT
52782 AAACTTTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (28 bp):
CTTAAAGGCTTGATACAAAAATAAGTGC
Found at i:53032 original size:21 final size:21
Alignment explanation
Indices: 52992--53032 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52982 AGCTCACGTC
*
52992 TCCCTCTCCCCTATCTCTTTT
1 TCCCTCTCCCCTATCCCTTTT
* *
53013 TCCCTTTCCCCTTTCCCTTT
1 TCCCTCTCCCCTATCCCTTT
53033 CTATGGTCGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (21 bp):
TCCCTCTCCCCTATCCCTTTT
Found at i:54173 original size:33 final size:33
Alignment explanation
Indices: 54115--54231 Score: 200
Period size: 33 Copynumber: 3.6 Consensus size: 33
54105 CTTTATTTTG
* *
54115 TTCGGGTTGGGTCAGG-TTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
54147 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
54180 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
*
54213 TTCGGGTTGGGTCGGGTTT
1 TTCGGGTCGGGTCGGGTTT
54232 GGGTTTAGGG
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 14 0.17
33 67 0.83
ACGTcount: A:0.11, C:0.09, G:0.38, T:0.43
Consensus pattern (33 bp):
TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:54863 original size:43 final size:43
Alignment explanation
Indices: 54739--54863 Score: 187
Period size: 44 Copynumber: 2.9 Consensus size: 43
54729 TCTGACATGT
* * *
54739 CTGCGAACTAAACAAAATATGAAATTGGATTCCAATTCCATTTC
1 CTGCCAACCAAAC-AAATATGGAATTGGATTCCAATTCCATTTC
*
54783 TTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCCATTTC
1 CTGCCAACCAAACA-AATATGGAATTGGATTCCAATTCCATTTC
*
54827 CTGCCAACCAAACAAATATGGAATTGGATTCTAATTC
1 CTGCCAACCAAACAAATATGGAATTGGATTCCAATTC
54864 TTGACAGATT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
43 23 0.31
44 51 0.69
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.29
Consensus pattern (43 bp):
CTGCCAACCAAACAAATATGGAATTGGATTCCAATTCCATTTC
Found at i:54890 original size:18 final size:18
Alignment explanation
Indices: 54853--54899 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
54843 TATGGAATTG
* *
54853 GATTCTAATT-CTTGACA
1 GATTCCAATTCCTTCACA
54870 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
54888 GATTCCAATTCC
1 GATTCCAATTCC
54900 CTCATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:64563 original size:16 final size:16
Alignment explanation
Indices: 64529--64563 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
64519 CAAGGGTGTG
* *
64529 TTTCTTCTGATTTTGT
1 TTTCTTCTGATTCTCT
64545 TTTCTTCTGATTCTCT
1 TTTCTTCTGATTCTCT
64561 TTT
1 TTT
64564 ACTTAGCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.17, G:0.09, T:0.69
Consensus pattern (16 bp):
TTTCTTCTGATTCTCT
Done.