Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011630.1 Kokia drynarioides strain JFW-HI SEQ_126621, 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: 38657
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1625 original size:138 final size:138
Alignment explanation
Indices: 1317--1736 Score: 574
Period size: 138 Copynumber: 3.0 Consensus size: 138
1307 TAGAAAAATG
* * * *
1317 AATTATATTCTTTTCAAAAGAATATTAA-TTTCTTTGTTTTTTGTATTTTGATCGAAATTAATTA
1 AATTATATTCTTTACAAAAGAATATTAATTTTC-ATGTCTTTTATATTTTGATCGAAATTAATTA
* * * * * *
1381 ATATAACTGTTTATGTTAATAAATTTGGTAAAACACATATGCAATTAATACTTTGTATGAATCAA
65 ATATAACTATTTATATTAATAAATTCGGT-AAA-ATATATACAATTAATAATTTGTATGAATCAA
*
1446 ATTAATATATT
128 ATTCATATATT
* *
1457 AATTATATTCTTTACAAAAGAATTTTAATTTTCATGTCTTTTATATTTTAATCGAAATTAATTAA
1 AATTATATTCTTTACAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
* * *
1522 TATAACTATTTATATTAATAAATTCAGTAAAATATATACAATTAATAATTTGTATGAATTAAGTT
66 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTGTATGAATCAAATT
1587 CATATATT
131 CATATATT
* * *
1595 AATTATATTCTTTCCAAAAGAATATTAATTTTCACGTCTTTTATATTTTGA-CTAAAATTAATTA
1 AATTATATTCTTTACAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATC-GAAATTAATTA
* * * * *
1659 ATATAATTTTTTATATTAATAAATTCGGTAAAATATATAAAATTAATATTTTGCATGAATCAAAT
65 ATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTGTATGAATCAAAT
1724 TCATATATT
130 TCATATATT
1733 AATT
1 AATT
1737 TTATCTATGT
Statistics
Matches: 249, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
137 1 0.00
138 163 0.65
139 3 0.01
140 78 0.31
141 4 0.02
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTACAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAA
TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTGTATGAATCAAATT
CATATATT
Found at i:1842 original size:21 final size:21
Alignment explanation
Indices: 1803--1842 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1793 TTAACTATCA
*
1803 AATTTAATTAATTTAACAATT
1 AATTTAATTAATATAACAATT
* *
1824 AATTTAATTCATATGACAA
1 AATTTAATTAATATAACAA
1843 CAAAATACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (21 bp):
AATTTAATTAATATAACAATT
Found at i:3231 original size:20 final size:19
Alignment explanation
Indices: 3151--3237 Score: 66
Period size: 20 Copynumber: 4.4 Consensus size: 19
3141 TGGCCTGGAG
3151 TTATTTTGACTTGTTTGAAAA
1 TTATTTTGACTTG-TT-AAAA
* **
3172 ATATTTTGAAGTGTTAAAA
1 TTATTTTGACTTGTTAAAA
* * *
3191 TGAGTTTGACTTAGTTCAAA
1 TTATTTTGACTT-GTTAAAA
*
3211 TTATTTTCACTTGTTTAAAA
1 TTATTTTGACTTG-TTAAAA
*
3231 TCATTTT
1 TTATTTT
3238 AAATTAATTT
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
19 12 0.24
20 28 0.56
21 10 0.20
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (19 bp):
TTATTTTGACTTGTTAAAA
Found at i:4074 original size:138 final size:138
Alignment explanation
Indices: 3764--4185 Score: 589
Period size: 138 Copynumber: 3.0 Consensus size: 138
3754 TAGAAAAATG
* * *
3764 AATTATATTATTTTCAAAAGAATATTAATTTTCATGTCTTTTATATTTTAACTGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
3829 TATAATTGTTTGTATTAATAAATTCGAATATATATATATATACAATTAATATTTTGTATGAATCA
66 TATAACTGTTTATATTAATAAATTCG-ATA-A-A-ATATATACAATTAATATTTTGTATGAATCA
3894 AATTCATATATT
127 AATTCATATATT
* *
3906 AATTATATTCTTTTCAAAAGAATATTAATTTTTATGTCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
3971 TATAACTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
4036 CCTATATT
131 CATATATT
* ** * * *
4044 AATTATATTCTTTCCAAAAGAATACCAATTTTCA-GACCTTTTATAGTTTGACCGAAATTAAATA
1 AATTATATTCTTTTCAAAAGAATATTAATTTTCATG-TCTTTTATATTTTGACCGAAATTAATTA
* * * * *
4108 ATAT-ACT-TAGTTATATTAATAAATTCGGTAATATATATAAAATTAATATTTTGAATGAATAAA
65 ATATAACTGT--TTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAA
4171 ATTCATATATT
128 ATTCATATATT
4182 AATT
1 AATT
4186 TTATATATGT
Statistics
Matches: 255, Mismatches: 22, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
136 1 0.00
137 4 0.02
138 161 0.63
139 1 0.00
140 1 0.00
141 3 0.01
142 84 0.33
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTTCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:6865 original size:28 final size:28
Alignment explanation
Indices: 6746--6864 Score: 141
Period size: 28 Copynumber: 4.2 Consensus size: 28
6736 CGACCAATTC
*
6746 CAGAATAATGCTCTTTTGAGCCAAAATA
1 CAGAATAACGCTCTTTTGAGCCAAAATA
* *
6774 CAGAATAACGTTCTTTCT-AGCCAGAATA
1 CAGAATAACGCTCTTT-TGAGCCAAAATA
** *
6802 CAGAATAACGCTCTTTCAAGCCATAATA
1 CAGAATAACGCTCTTTTGAGCCAAAATA
* *
6830 TAGAATATCGCTCTTTTGAGCCAAAATA
1 CAGAATAACGCTCTTTTGAGCCAAAATA
*
6858 CATAATA
1 CAGAATA
6865 TTTCTTAAGC
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
28 75 0.99
29 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.29
Consensus pattern (28 bp):
CAGAATAACGCTCTTTTGAGCCAAAATA
Found at i:7838 original size:27 final size:27
Alignment explanation
Indices: 7806--7862 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
7796 AATGAGACTT
*
7806 TTTGGA-TACCCGGGGGTAAAATGGTAA
1 TTTGGACT-CCCGGGGGCAAAATGGTAA
**
7833 TTTGGACTCTTGGGGGCAAAATGGTAA
1 TTTGGACTCCCGGGGGCAAAATGGTAA
7860 TTT
1 TTT
7863 TGGGAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.32
Consensus pattern (27 bp):
TTTGGACTCCCGGGGGCAAAATGGTAA
Found at i:8009 original size:59 final size:62
Alignment explanation
Indices: 7938--8159 Score: 172
Period size: 60 Copynumber: 3.8 Consensus size: 62
7928 ATCAGGATCT
* * *
7938 AAAACGAA-TTTTTTGGAC-GTCTAGGGGTAAAATGGTAA-TTTTGAAAG-TTTCGAGGTTA
1 AAAATGAAGTTTTTTGGACAGTCGAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGAGGTTA
* * * *
7996 AAAATGGAG-TTTTTGGACATTCGGGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGGTTA
1 AAAATGAAGTTTTTTGGACAGTCGAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGAGGTTA
* * ** *
8057 AAAATGAAG--TTTTAGAAAGTTC-AGGGGTAAAAAT-GTAATTTTCAAAAATTTTAG-GGTT-
1 AAAATGAAGTTTTTTGGACAG-TCGAGGGGT-AAAATGGTAATTTTTGAAAGTTTTAGAGGTTA
*
8115 AAAATGGAA--TTTTTGGA-AGTTC-A-GGGAAAAAT-GTAATTTTTGAAA
1 AAAAT-GAAGTTTTTTGGACAG-TCGAGGGGTAAAATGGTAATTTTTGAAA
8160 AAATCGAGGT
Statistics
Matches: 137, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
56 16 0.12
57 3 0.02
58 26 0.19
59 30 0.22
60 38 0.28
61 24 0.18
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (62 bp):
AAAATGAAGTTTTTTGGACAGTCGAGGGGTAAAATGGTAATTTTTGAAAGTTTTAGAGGTTA
Found at i:8098 original size:29 final size:29
Alignment explanation
Indices: 7960--8227 Score: 133
Period size: 30 Copynumber: 9.1 Consensus size: 29
7950 TTGGACGTCT
7960 AGGGGT-AAAATGGTAA-TTTTGAAAGTTTC
1 AGGGGTAAAAAT-GTAATTTTTGAAAG-TTC
* * * *
7989 -GAGGTTAAAAATGGAGTTTTTGGACA-TTC
1 AG-GGGTAAAAATGTAATTTTT-GAAAGTTC
* *
8018 GGGGGGT-AAAATGGTAATTTTTGAAAGTTTT
1 -AGGGGTAAAAAT-GTAATTTTTGAAAG-TTC
*
8049 AGGGGTTAAAAATG-AAGTTTTAGAAAGTTC
1 AGGGG-TAAAAATGTAA-TTTTTGAAAGTTC
** * *
8079 AGGGGTAAAAATGTAATTTTCAAAAATTTT
1 AGGGGTAAAAATGTAATTTT-TGAAAGTTC
* * *
8109 A-GGGTTAAAATGGAATTTTTGGAAGTTC
1 AGGGGTAAAAATGTAATTTTTGAAAGTTC
**
8137 A-GGG-AAAAATGTAATTTTTGAAAAAATC
1 AGGGGTAAAAATGTAATTTTTG-AAAGTTC
* * * *
8165 -GAGGTAAAAAATGGAATTTTGGAAAGTTT
1 AGGGGT-AAAAATGTAATTTTTGAAAGTTC
* * * *
8194 AGGGGTCAAAATATGATTTTTGAACAGTTT
1 AGGGGTAAAAATGTAATTTTTGAA-AGTTC
8224 AGGG
1 AGGG
8228 ACCTTTAGGG
Statistics
Matches: 180, Mismatches: 39, Indels: 39
0.70 0.15 0.15
Matches are distributed among these distances:
27 14 0.08
28 15 0.08
29 61 0.34
30 68 0.38
31 17 0.09
32 5 0.03
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (29 bp):
AGGGGTAAAAATGTAATTTTTGAAAGTTC
Found at i:8162 original size:58 final size:61
Alignment explanation
Indices: 8020--8217 Score: 175
Period size: 57 Copynumber: 3.4 Consensus size: 61
8010 GGACATTCGG
*
8020 GGGGT-AAAATGGTAATTTTTG-AAAGTTTTAGGGGTTAAAAATGAAGTTTTAGAAAGTTCA
1 GGGGTAAAAAT-GTAATTTTTGAAAAATTTTAGGGGTTAAAAATGAAGTTTTAGAAAGTTCA
* * *
8080 GGGGTAAAAATGTAA-TTTTCAAAAATTTTA-GGGTT-AAAATGGAA-TTTTTGGAAGTTCA
1 GGGGTAAAAATGTAATTTTTGAAAAATTTTAGGGGTTAAAAAT-GAAGTTTTAGAAAGTTCA
* * * * * *
8138 -GGG-AAAAATGTAATTTTTGAAAAA--ATCGAGGTAAAAAATGGAA-TTTTGGAAAGTTTA
1 GGGGTAAAAATGTAATTTTTGAAAAATTTTAGGGGTTAAAAAT-GAAGTTTTAGAAAGTTCA
* * *
8195 GGGGTCAAAATATGATTTTTGAA
1 GGGGTAAAAATGTAATTTTTGAA
8218 CAGTTTAGGG
Statistics
Matches: 115, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
55 1 0.01
56 13 0.11
57 32 0.28
58 20 0.17
59 27 0.23
60 17 0.15
61 5 0.04
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (61 bp):
GGGGTAAAAATGTAATTTTTGAAAAATTTTAGGGGTTAAAAATGAAGTTTTAGAAAGTTCA
Found at i:10000 original size:17 final size:17
Alignment explanation
Indices: 9980--10056 Score: 100
Period size: 17 Copynumber: 4.5 Consensus size: 17
9970 AATAATTTTT
*
9980 AATTCAAAATAAATTCA
1 AATTTAAAATAAATTCA
*
9997 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
* * * *
10014 AATTCAACATGAATTTA
1 AATTTAAAATAAATTCA
10031 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
10048 AATTTAAAA
1 AATTTAAAA
10057 ATTAAAAGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:10008 original size:34 final size:34
Alignment explanation
Indices: 9970--10056 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 34
9960 TTTTAATATT
* *
9970 AATAATTTTTAATTCAAAATAAATTCAAATTTAA
1 AATAAATTTAAATTCAAAATAAATTCAAATTTAA
* * *
10004 AATAAATTTAAATTCAACATGAATTTAAATTTAA
1 AATAAATTTAAATTCAAAATAAATTCAAATTTAA
* *
10038 AATAAATTCAAATTTAAAA
1 AATAAATTTAAATTCAAAA
10057 ATTAAAAGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (34 bp):
AATAAATTTAAATTCAAAATAAATTCAAATTTAA
Found at i:10731 original size:205 final size:205
Alignment explanation
Indices: 10379--10782 Score: 569
Period size: 205 Copynumber: 2.0 Consensus size: 205
10369 TCTGGTTTCA
* * * **
10379 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAATGGCCGCGTCGCTTGTTTTGATCCACTTC
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAATGACCGCATCACTTGTTTCAATCCACTTC
* * ** *
10444 TCTGTGTTTCATCAAGAAGACGGATTTGGTTCACTTCTCAATATCTCATCAAGAAGCAAACCACT
66 TCTGTATCTCATCAAGAAGACAAATTTGGTCCACTTCTCAATATCTCATCAAGAAGCAAACCACT
* *
10509 TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATT
131 TTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACATT
10574 GAGCGTGGGT
196 GAGCGTGGGT
** *
10584 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATTGCATCACTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAA-ATGACCGCATCACTTGTTTCAATCCACTT
* * * * * *
10649 CT-TTTATCTCATTAGGAAGGCAAATTTGGTCCACTTCTCAGTATCTCATC-AGAAAGCTAACCA
65 CTCTGTATCTCATCAAGAAGACAAATTTGGTCCACTTCTCAATATCTCATCAAG-AAGCAAACCA
* *
10712 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACT
129 CTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACA
10777 TTGAGC
194 TTGAGC
10783 CTTGAGTTGG
Statistics
Matches: 174, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
204 2 0.01
205 149 0.86
206 23 0.13
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (205 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAATGACCGCATCACTTGTTTCAATCCACTTC
TCTGTATCTCATCAAGAAGACAAATTTGGTCCACTTCTCAATATCTCATCAAGAAGCAAACCACT
TTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACATT
GAGCGTGGGT
Found at i:10877 original size:115 final size:115
Alignment explanation
Indices: 10681--10890 Score: 357
Period size: 115 Copynumber: 1.8 Consensus size: 115
10671 AATTTGGTCC
*
10681 ACTTCTCAGTATCTCATCAGAAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGAAAGCTAACCATTTTAATACTTCGACCTGCTTCTCAGTATCTCAT
10746 CAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGGTAT
66 CAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGGTAT
* * *
10796 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTAATGCTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGAAAGCTAACCATTTTAATACTTCGACCTGCTTCTCAGTATCTCAT
* * *
10861 TAGGAAGCTGGTGTTCGAAGATTTGCTCAC
66 CAAGAAGCTGGGGTTCGAAGATTTGCTCAC
10891 ATCGAGAATG
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
115 88 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (115 bp):
ACTTCTCAGTATCTCATCAGAAAGCTAACCATTTTAATACTTCGACCTGCTTCTCAGTATCTCAT
CAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGGTAT
Found at i:11132 original size:321 final size:320
Alignment explanation
Indices: 10476--11140 Score: 1114
Period size: 320 Copynumber: 2.1 Consensus size: 320
10466 GATTTGGTTC
* * *
10476 ACTTCTCAATATCTCATCAAGAAGCAAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCTATATCTCATCAGGAAGCAAACCACTTTAATGCTTCGACCTGCTTCTCAGTATCTCAT
* **
10541 CAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGT
66 CAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGAATGGGTTTGATTTGGTCTTCTTCTCAGT
* **
10606 ATCTCATCAGGAAGATGATTGCATCACTTGTTTCAATCCGCTTCTTTTATCTCATTAGGAAGGCA
131 ATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTTTTATCTCATTAGGAAGGCA
* * *
10671 AATTTGGTCCACTTCTCAGTATCTCATCAGAAAGCTAACCATTTTATTACTTCGACCTGCTTCTC
196 AATTTGGTCCACTTCTCAGTATCTCATCAGAAAGCTAACCATATTATTACCTCGACCGGCTTCTC
*
10736 AGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGGTAT
261 AGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGCTAT
* * *
10796 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTAATGCTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCTATATCTCATCAGGAAGCAAACCACTTTAATGCTTCGACCTGCTTCTCAGTATCTCAT
* *
10861 TAGGAAGCTGGTGTTCGAAGATTTGCTCACATCGAGAATGGGTTTGATTTGGTCTTCTTCTCAGT
66 CAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGAATGGGTTTGATTTGGTCTTCTTCTCAGT
10926 ATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTTTGTATCTCATTAGGAAGGC
131 ATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTTT-TATCTCATTAGGAAGGC
* * *
10991 GAATTTGGTCCACTTCTCGGTATCTCATCAGGAAGCTAACCATATTATTACCTCGACCGGCTTCT
195 AAATTTGGTCCACTTCTCAGTATCTCATCAGAAAGCTAACCATATTATTACCTCGACCGGCTTCT
*
11056 CAGTATCTCATCAAGAAGTTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGCTAT
260 CAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGCTAT
*
11117 ACTTCTCTATATCTCATTAGGAAG
1 ACTTCTCTATATCTCATCAGGAAG
11141 ATGATCGCCT
Statistics
Matches: 320, Mismatches: 24, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
320 163 0.51
321 157 0.49
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (320 bp):
ACTTCTCTATATCTCATCAGGAAGCAAACCACTTTAATGCTTCGACCTGCTTCTCAGTATCTCAT
CAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGAATGGGTTTGATTTGGTCTTCTTCTCAGT
ATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTTTTATCTCATTAGGAAGGCA
AATTTGGTCCACTTCTCAGTATCTCATCAGAAAGCTAACCATATTATTACCTCGACCGGCTTCTC
AGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGCTAT
Found at i:11207 original size:201 final size:201
Alignment explanation
Indices: 10796--11358 Score: 750
Period size: 201 Copynumber: 2.8 Consensus size: 201
10786 GAGTTGGTAT
* *
10796 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTAATGCTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
* * * ** * * *
10861 TAGGAAGCTGGTGTTCGAAGATTTGCTCACATCGAG-AATGGGTTTGATTTGGTCTTCTTCTCAG
66 CAGGAAGCTGGTGTTCGAAGATTTGCTCACTTTGAGCCTTGAG-TTGATAT--ACTTC-TCT-A-
* * * **
10925 TATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTTTGTATCTCATTAGGAAGG
125 TATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCACCAGGAAGG
10990 CGAATTTGGTCC
190 CGAATTTGGTCC
* * * * *
11002 ACTTCTCGGTATCTCATCAGGAAGCTAACCATATTATTACCTCGACCGGCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
* * * *
11067 CAAGAAGTTGGGGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGCTATACTTCTCTATATCTC
66 CAGGAAGCTGGTGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGATATACTTCTCTATATCTC
* * * *
11132 ATTAGGAAGATGATCGCCTCATTTGTTTCAATTCGCTTCTCTGTATCTCACCAGGAAGGCGAATT
131 ATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCACCAGGAAGGCGAATT
11197 TGGTCC
196 TGGTCC
* * *
11203 ACTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTTAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
* * * *
11268 CAGGAAACTGGTGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGGTATACTTCTCTGTATATC
66 CAGGAAGCTGGTGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGATATACTTCTCTATATCTC
11333 ATCAGGAAGATGACCGCCTCACTTGT
131 ATCAGGAAGATGACCGCCTCACTTGT
11359 GGATAATCGC
Statistics
Matches: 311, Mismatches: 45, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
201 206 0.66
202 1 0.00
203 3 0.01
204 4 0.01
206 94 0.30
207 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (201 bp):
ACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
CAGGAAGCTGGTGTTCGAAGATTTGCTCACTTTGAGCCTTGAGTTGATATACTTCTCTATATCTC
ATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCACCAGGAAGGCGAATT
TGGTCC
Found at i:11504 original size:39 final size:38
Alignment explanation
Indices: 11408--11593 Score: 126
Period size: 39 Copynumber: 4.8 Consensus size: 38
11398 TGGTTGATGG
* * * * * *
11408 TGATCTGCCCCAGGCTTGGGGTAAGAGATCGAATGACTA
1 TGATCTGCCCCAAGCTCGGGGTAAAAGATCG-GTTACGA
* * ** *
11447 TAATCTACCCCTGGCTCGGGGTAAGAGATCGGTTAACGA
1 TGATCTGCCCCAAGCTCGGGGTAAAAGATCGGTT-ACGA
*
11486 TGATCTGCCCCAAACTCGGGGTAAAAGATCAAATGGTTAC-A
1 TGATCTGCCCCAAGCTCGGGGTAAAAGATC----GGTTACGA
* * * *
11527 --ATCTGCCCCAAGCTCGAGGTAAGAGATTGGTTGATGA
1 TGATCTGCCCCAAGCTCGGGGTAAAAGATCGGTT-ACGA
* *
11564 TGATCTGCCCCAGGCTCAGGGTAAAAGATC
1 TGATCTGCCCCAAGCTCGGGGTAAAAGATC
11594 AAATGGCTGC
Statistics
Matches: 115, Mismatches: 23, Indels: 18
0.74 0.15 0.12
Matches are distributed among these distances:
35 4 0.03
36 1 0.01
37 1 0.01
38 1 0.01
39 101 0.88
41 1 0.01
42 2 0.02
43 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (38 bp):
TGATCTGCCCCAAGCTCGGGGTAAAAGATCGGTTACGA
Found at i:11637 original size:78 final size:78
Alignment explanation
Indices: 11393--11643 Score: 322
Period size: 78 Copynumber: 3.2 Consensus size: 78
11383 TTAGGGTGAG
* * * * * * *
11393 GAGATTGGTTGATGGTGATCTGCCCCAGGCTTGGGGTAAGAGATCGAATGACTATAATCTACCCC
1 GAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTACAATCTGCCCC
*
11458 TGGCTCGGGGTAA
66 AGGCTCGGGGTAA
* * * ** *
11471 GAGATCGGTTAACGATGATCTGCCCCAAACTCGGGGTAAAAGATCAAATGGTTACAATCTGCCCC
1 GAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTACAATCTGCCCC
* *
11536 AAGCTCGAGGTAA
66 AGGCTCGGGGTAA
* * *
11549 GAGATTGGTTGATGATGATCTGCCCCAGGCTCAGGGTAAAAGATCAAATGGCTGCAACCTGCCCC
1 GAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTACAATCTGCCCC
11614 AGGCTCGGGGTAA
66 AGGCTCGGGGTAA
*
11627 TAGATTGGTTGATGATG
1 GAGATTGGTTGATGATG
11644 TAACTTCACT
Statistics
Matches: 145, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
78 145 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
GAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTACAATCTGCCCC
AGGCTCGGGGTAA
Found at i:11858 original size:103 final size:102
Alignment explanation
Indices: 11733--11990 Score: 430
Period size: 100 Copynumber: 2.5 Consensus size: 102
11723 TGATGTCGAG
*
11733 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGATATTGTTTTTAATCCAACTT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCAACTT
*
11798 TACTGTAACTTCAAGAGGATAGGAATTAATGTTTTGAA
66 TACTGCAACTTCAAGAGGATAGGAATTAATG-TTTGAA
*
11836 GCTTCATCTTGCTCTTACTACAACTTCAGAGAAATAAAGACTTGCTATTG--TTTAATCCAACTT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCAACTT
* *
11899 TACTGCAACTTTAAGAGGATAGGAATTGATGTTTGAA
66 TACTGCAACTTCAAGAGGATAGGAATTAATGTTTGAA
* *
11936 GCTTCATTTTGCTCTTGCTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTT
11991 TTTTATCTAA
Statistics
Matches: 145, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
100 53 0.37
101 41 0.28
102 3 0.02
103 48 0.33
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (102 bp):
GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCAACTT
TACTGCAACTTCAAGAGGATAGGAATTAATGTTTGAA
Found at i:12167 original size:48 final size:48
Alignment explanation
Indices: 12101--12337 Score: 303
Period size: 48 Copynumber: 4.9 Consensus size: 48
12091 TCCCTTCAAA
* * * *
12101 TCTTCGTGATACTGGATCCGCTGTCGCGGCTTAGATCTTTCCCTTGTG
1 TCTTCGCGGTACTGGATCCGCCGTCGTGGCTTAGATCTTTCCCTTGTG
* *
12149 TCTTCGCGGTACTAGATCCGCCGTTGTGGTCTTAGATCTTTCCCTTGTG
1 TCTTCGCGGTACTGGATCCGCCGTCGTGG-CTTAGATCTTTCCCTTGTG
* * *
12198 TCTTCGCAGTATTGGATTCGCCGTCGTGGCTTAGATCTTTCCCTTGTG
1 TCTTCGCGGTACTGGATCCGCCGTCGTGGCTTAGATCTTTCCCTTGTG
* * * **
12246 TCTTCGTGGTACTAGATCCGTCGTCACGGCTTAGATCTTTCCCTTGTG
1 TCTTCGCGGTACTGGATCCGCCGTCGTGGCTTAGATCTTTCCCTTGTG
* * *
12294 TCTTCGCAGAACTGGATCCGCCGTTGTGGTCTTAGATCTTTCCC
1 TCTTCGCGGTACTGGATCCGCCGTCGTGG-CTTAGATCTTTCCC
12338 GTCGTGTTTT
Statistics
Matches: 160, Mismatches: 27, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
48 103 0.64
49 57 0.36
ACGTcount: A:0.11, C:0.27, G:0.24, T:0.38
Consensus pattern (48 bp):
TCTTCGCGGTACTGGATCCGCCGTCGTGGCTTAGATCTTTCCCTTGTG
Found at i:12236 original size:97 final size:96
Alignment explanation
Indices: 12111--12337 Score: 337
Period size: 97 Copynumber: 2.3 Consensus size: 96
12101 TCTTCGTGAT
* * ***
12111 ACTGGATCCGCTGTCGCGGCTTAGATCTTTCCCTTGTGTCTTCGCGGTACTAGATCCGCCGTTGT
1 ACTGGATCCGCCGTCGTGGCTTAGATCTTTCCCTTGTGTCTTCGCGGTACTAGATCCGCCGTCAC
*
12176 GGTCTTAGATCTTTCCCTTGTGTCTTCGCAGT
66 GG-CTTAGATCTTTCCCTTGTGTCTTCGCAGA
* * * *
12208 ATTGGATTCGCCGTCGTGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTAGATCCGTCGTCAC
1 ACTGGATCCGCCGTCGTGGCTTAGATCTTTCCCTTGTGTCTTCGCGGTACTAGATCCGCCGTCAC
12273 GGCTTAGATCTTTCCCTTGTGTCTTCGCAGA
66 GGCTTAGATCTTTCCCTTGTGTCTTCGCAGA
*
12304 ACTGGATCCGCCGTTGTGGTCTTAGATCTTTCCC
1 ACTGGATCCGCCGTCGTGG-CTTAGATCTTTCCC
12338 GTCGTGTTTT
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
96 44 0.38
97 72 0.62
ACGTcount: A:0.11, C:0.27, G:0.24, T:0.37
Consensus pattern (96 bp):
ACTGGATCCGCCGTCGTGGCTTAGATCTTTCCCTTGTGTCTTCGCGGTACTAGATCCGCCGTCAC
GGCTTAGATCTTTCCCTTGTGTCTTCGCAGA
Found at i:12976 original size:100 final size:102
Alignment explanation
Indices: 12859--13058 Score: 296
Period size: 106 Copynumber: 1.9 Consensus size: 102
12849 CGCAAGGCGA
*
12859 ATGAAATTTATTGGAGGCAAAGCTCACATGAATG-GA-AAAAGTGACCCATATTGGTCAAAGGAT
1 ATGAAATTTATTGGAGGCAAAGCTCACATGAATGAGATAAAAGTGACCCATATTGGTCAAAAGAT
*
12922 GCCAAATATAAAGTGAGCAAAGAATAGAGTTAGGTGG
66 GCCAAACATAAAGTGAGCAAAGAATAGAGTTAGGTGG
* * *
12959 ATGAATTTTATTGGAGGCAATGCTCGCATGAATGAAAAGATTAAAAGTGACCCATATTGGTCAAA
1 ATGAAATTTATTGGAGGCAAAGCTCACATGAATG---AGA-TAAAAGTGACCCATATTGGTCAAA
*
13024 AGATGCCAAACATAAGGTGAGCAAAGAATAGAGTT
62 AGATGCCAAACATAAAGTGAGCAAAGAATAGAGTT
13059 TGGAGGCAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
100 31 0.35
104 2 0.02
106 55 0.62
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (102 bp):
ATGAAATTTATTGGAGGCAAAGCTCACATGAATGAGATAAAAGTGACCCATATTGGTCAAAAGAT
GCCAAACATAAAGTGAGCAAAGAATAGAGTTAGGTGG
Found at i:13630 original size:7 final size:6
Alignment explanation
Indices: 13597--13661 Score: 51
Period size: 7 Copynumber: 10.2 Consensus size: 6
13587 TCAACTTCTC
* *
13597 CTTTTT -TTTTT CATTTTT TTATTTT CTTTATT CTTTTT CTTCTTT TTTCTTT
1 CTTTTT CTTTTT C-TTTTT CT-TTTT CTTT-TT CTTTTT CTT-TTT CTT-TTT
*
13649 CTTCTT CTTTTT C
1 CTTTTT CTTTTT C
13662 CTTTGTTCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
5 5 0.10
6 16 0.33
7 27 0.56
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:13642 original size:27 final size:26
Alignment explanation
Indices: 13603--13661 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
13593 TCTCCTTTTT
13603 TTTTTCATTTTTTTAT-TTTCTTTATTC
1 TTTTTCATTTTTTT-TCTTTC-TTATTC
*
13630 TTTTTC-TTCTTTTTTCTTTCTTCTTC
1 TTTTTCATT-TTTTTTCTTTCTTATTC
13656 TTTTTC
1 TTTTTC
13662 CTTTGTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTCATTTTTTTTCTTTCTTATTC
Found at i:13655 original size:17 final size:16
Alignment explanation
Indices: 13620--13665 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
13610 TTTTTTTATT
*
13620 TTCTTTATTCTTTTTC
1 TTCTTTTTTCTTTTTC
13636 TTCTTTTTTCTTTCTTC
1 TTCTTTTTTCTTT-TTC
*
13653 TTCTTTTTCCTTT
1 TTCTTTTTTCTTT
13666 GTTCATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTTTTCTTTTTC
Found at i:13659 original size:16 final size:15
Alignment explanation
Indices: 13620--13661 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 15
13610 TTTTTTTATT
13620 TTCTTTATTCTTTTTC
1 TTCTTT-TTCTTTTTC
13636 TTCTTTTTTCTTTCTTC
1 TTC-TTTTTCTTT-TTC
13653 TTCTTTTTC
1 TTCTTTTTC
13662 CTTTGTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTTTTCTTTTTC
Found at i:15823 original size:25 final size:25
Alignment explanation
Indices: 15789--15838 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
15779 TTGTCAAGTA
15789 AGCCAAACAAATTTACAACTGCGTC
1 AGCCAAACAAATTTACAACTGCGTC
15814 AGCCAAACAAATTTACAACTGCGTC
1 AGCCAAACAAATTTACAACTGCGTC
15839 CCTTACGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (25 bp):
AGCCAAACAAATTTACAACTGCGTC
Found at i:19347 original size:28 final size:28
Alignment explanation
Indices: 19246--19349 Score: 86
Period size: 28 Copynumber: 3.6 Consensus size: 28
19236 GGATACATAG
* ** *
19246 GGGTAAAATGGTAATTTTGGACCCTCGA
1 GGGTAAAATGGTAATTTTAGACATTCAA
* * **
19274 GGGCAAAATGGTAATTTTGAGAAAATT-TG
1 GGGTAAAATGGTAATTTT-AG-ACATTCAA
19303 GGGTTAAAAATGG-AATTTTAGACATTCAA
1 GGG-T-AAAATGGTAATTTTAGACATTCAA
19332 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
19350 TAGAAAAATC
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
27 7 0.12
28 28 0.47
29 9 0.15
30 8 0.14
31 7 0.12
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.32
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTAGACATTCAA
Found at i:19376 original size:58 final size:59
Alignment explanation
Indices: 19273--19408 Score: 152
Period size: 58 Copynumber: 2.3 Consensus size: 59
19263 TGGACCCTCG
* * ** * *
19273 AGGGCAAAATGGTAATTTTGAGAAAATTTGGGGTTAAAAATGGAA-TTTTAGACAT-TCA
1 AGGGTAAAATGGTAATTTTGAGAAAAATCAGGATTAAAAACGGAATTTTTAGACATCT-A
* *
19331 AGGGTAAAATGGTAATTTTTAGAAAAATCAGGATCT-AAAACGGAATTTTTGGACATCTA
1 AGGGTAAAATGGTAATTTTGAGAAAAATCAGGAT-TAAAAACGGAATTTTTAGACATCTA
*
19390 GGGGTAAAATGGTAATTTT
1 AGGGTAAAATGGTAATTTT
19409 AAAAGTTTCG
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
58 36 0.55
59 29 0.44
60 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.32
Consensus pattern (59 bp):
AGGGTAAAATGGTAATTTTGAGAAAAATCAGGATTAAAAACGGAATTTTTAGACATCTA
Found at i:19408 original size:28 final size:28
Alignment explanation
Indices: 19243--19408 Score: 83
Period size: 28 Copynumber: 5.8 Consensus size: 28
19233 TTTGGATACA
*
19243 TAGGGGTAAAATGGTAATTTTGGAC-CC
1 TAGGGGTAAAATGGTAATTTTGGACATC
* * *
19270 TCGAGGGCAAAATGGTAATTTTGAGAAAAT-
1 TAG-GGGTAAAATGGTAATTTTG-G-ACATC
* *
19300 TTGGGGTTAAAAATGG-AATTTTAGACAT-
1 TAGGGG-T-AAAATGGTAATTTTGGACATC
* * *
19328 TCAAGGGTAAAATGGTAATTTTTAGAAAAATC
1 T-AGGGGTAAAATGGTAA-TTTT-G-GACATC
** *
19360 -AGGATCTAAAACGG-AATTTTTGGACATC
1 TAGG-GGTAAAATGGTAA-TTTTGGACATC
19388 TAGGGGTAAAATGGTAATTTT
1 TAGGGGTAAAATGGTAATTTT
19409 AAAAGTTTCG
Statistics
Matches: 102, Mismatches: 22, Indels: 29
0.67 0.14 0.19
Matches are distributed among these distances:
27 9 0.09
28 40 0.39
29 18 0.18
30 18 0.18
31 17 0.17
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (28 bp):
TAGGGGTAAAATGGTAATTTTGGACATC
Found at i:19504 original size:60 final size:57
Alignment explanation
Indices: 19436--19643 Score: 203
Period size: 60 Copynumber: 3.5 Consensus size: 57
19426 AAATGGAATA
19436 TAGGGGTAAAATGGTAATTTTTGAAAGTTTCATAGGTCAAAAATGGTGTTTTGGAAAGTT
1 TAGGGGTAAAAT-GTAATTTTTGAAAGTTT-ATAGGTCAAAAATGGT-TTTTGGAAAGTT
*
19496 TAGGGGTAAAAATGTAATTTTTGAAAGTTT-TAGGGTTAAAAATGGAATTTTTGG-AAGTT
1 TAGGGGT-AAAATGTAATTTTTGAAAGTTTATA-GGTCAAAAATGG--TTTTTGGAAAGTT
* * * *
19555 CAGGGGTAAAATGTAATTTTCAGAAA-ATTA-AGGTCAAAAATGGAATTTTGGAAAGTT
1 TAGGGGTAAAATGTAATTTT-TGAAAGTTTATAGGTCAAAAATGG-TTTTTGGAAAGTT
*
19612 T-GGTGGTCAAA-GTATGATTTTTGAACAGTTTA
1 TAGG-GGTAAAATGTA--ATTTTTGAA-AGTTTA
19644 GGGACCTCTA
Statistics
Matches: 126, Mismatches: 10, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
56 12 0.10
57 25 0.20
58 24 0.19
59 29 0.23
60 30 0.24
61 6 0.05
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (57 bp):
TAGGGGTAAAATGTAATTTTTGAAAGTTTATAGGTCAAAAATGGTTTTTGGAAAGTT
Found at i:19528 original size:30 final size:29
Alignment explanation
Indices: 19436--19646 Score: 146
Period size: 29 Copynumber: 7.2 Consensus size: 29
19426 AAATGGAATA
19436 TAGGGGT-AAAATGGTAATTTTTGAAAGTT
1 TAGGGGTAAAAAT-GTAATTTTTGAAAGTT
** * *
19465 TCATAGGTCAAAAATGGT-GTTTTGGAAAGTT
1 T-AGGGGT-AAAAAT-GTAATTTTTGAAAGTT
19496 TAGGGGTAAAAATGTAATTTTTGAAAGTTT
1 TAGGGGTAAAAATGTAATTTTTGAAAG-TT
* * *
19526 TAGGGTTAAAAATGGAATTTTTGGAAGTT
1 TAGGGGTAAAAATGTAATTTTTGAAAGTT
* * *
19555 CAGGGGT-AAAATGTAATTTTCAGAAA-AT
1 TAGGGGTAAAAATGTAATTTT-TGAAAGTT
* * *
19583 TA-AGGTCAAAAATGGAATTTTGGAAAGTT
1 TAGGGGT-AAAAATGTAATTTTTGAAAGTT
* * * *
19612 T-GGTGGTCAAAGTATGATTTTTGAACAGTT
1 TAGG-GGTAAAAATGTAATTTTTGAA-AGTT
19642 TAGGG
1 TAGGG
19647 ACCTCTAGGG
Statistics
Matches: 140, Mismatches: 29, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
27 3 0.02
28 20 0.14
29 52 0.37
30 43 0.31
31 14 0.10
32 8 0.06
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
TAGGGGTAAAAATGTAATTTTTGAAAGTT
Found at i:21420 original size:17 final size:17
Alignment explanation
Indices: 21400--21476 Score: 100
Period size: 17 Copynumber: 4.5 Consensus size: 17
21390 AATAATTTTT
*
21400 AATTCAAAATAAATTCA
1 AATTTAAAATAAATTCA
*
21417 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
* * * *
21434 AATTCAACATGAATTTA
1 AATTTAAAATAAATTCA
21451 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
21468 AATTTAAAA
1 AATTTAAAA
21477 ATTAAAAGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:21428 original size:34 final size:34
Alignment explanation
Indices: 21390--21476 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 34
21380 TTTTAATATT
* *
21390 AATAATTTTTAATTCAAAATAAATTCAAATTTAA
1 AATAAATTTAAATTCAAAATAAATTCAAATTTAA
* * *
21424 AATAAATTTAAATTCAACATGAATTTAAATTTAA
1 AATAAATTTAAATTCAAAATAAATTCAAATTTAA
* *
21458 AATAAATTCAAATTTAAAA
1 AATAAATTTAAATTCAAAA
21477 ATTAAAAGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (34 bp):
AATAAATTTAAATTCAAAATAAATTCAAATTTAA
Found at i:37476 original size:157 final size:158
Alignment explanation
Indices: 37189--37515 Score: 431
Period size: 157 Copynumber: 2.1 Consensus size: 158
37179 TAACATCTCC
* * *
37189 ATAACCTATAATGCTCACAAGGGCTATGAAATGGGCCTGCTCACATGAGCTGTGGGTCAAGATGT
1 ATAACCTGTAATGCTCACAAGAGCTATGAAATGAGCCTGCTCACATGAGCTGTGGGTCAAGATGT
* * * * * * * *
37254 TGGGCTACATGATGCTGCTTATAGGAGCTATGGAGAAACCGTAATAAATGTCGGATCTCATCCAT
66 TAGGCTACACGATACTGCTCACACGAGCTATGGAGAAACCGCAATAAATGTCGGATCTCAGCCAT
* *
37319 C-GTAGGACATCTAGGACCAGCACCCAT
131 CAGTAAGACATCTAAGACCAGCACCCAT
* * *
37346 ATAACCTGTAATGCTCACATGAGCTATGAAATGAGTCTGCTCACATGAGCTGTGGGTCGAGATGT
1 ATAACCTGTAATGCTCACAAGAGCTATGAAATGAGCCTGCTCACATGAGCTGTGGGTCAAGATGT
* * * * *
37411 TAGGCTACACGATACTTCTCACACGAGCTGTGGAGAATCTGCGATAAATGTCGGATCTCAGCCAT
66 TAGGCTACACGATACTGCTCACACGAGCTATGGAGAAACCGCAATAAATGTCGGATCTCAGCCAT
* *
37476 CAGTAAGACATCTAAGACCAGCACTCGT
131 CAGTAAGACATCTAAGACCAGCACCCAT
*
37504 ATAACATGTAAT
1 ATAACCTGTAAT
37516 CCCAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
157 112 0.77
158 33 0.23
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (158 bp):
ATAACCTGTAATGCTCACAAGAGCTATGAAATGAGCCTGCTCACATGAGCTGTGGGTCAAGATGT
TAGGCTACACGATACTGCTCACACGAGCTATGGAGAAACCGCAATAAATGTCGGATCTCAGCCAT
CAGTAAGACATCTAAGACCAGCACCCAT
Done.