Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012178.1 Kokia drynarioides strain JFW-HI SEQ_127179, 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: 17813
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Found at i:1078 original size:96 final size:96
Alignment explanation
Indices: 897--1083 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 96
887 GGGAAAAAGA
**
897 TATTCGATTATCTTGATTTGAAGAAAGGTAGCACCTAGTAAGTTAAGACGCAAATTTTCAGAATC
1 TATTCGATTATCTTGATTTGAAGAAAAATAGCACCTAGTAAGTTAAGACGCAAATTTTCAGAATC
** *
962 GAAGATAATGAAACATTGCCTCGATTAAGGG
66 GAAGATAAAAAAACACTGCCTCGATTAAGGG
* * *
993 TATTCGATTAT-TTCGATTTGAAGAAAAATTGTACCTAGTAAGTTAAGGCGCAAATTTTC-GAAA
1 TATTCGATTATCTT-GATTTGAAGAAAAATAGCACCTAGTAAGTTAAGACGCAAATTTTCAG-AA
*
1056 CTCGAA-ATAAAAAAATACTGCCTCGATT
64 -TCGAAGATAAAAAAACACTGCCTCGATT
1084 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
95 3 0.04
96 71 0.90
97 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (96 bp):
TATTCGATTATCTTGATTTGAAGAAAAATAGCACCTAGTAAGTTAAGACGCAAATTTTCAGAATC
GAAGATAAAAAAACACTGCCTCGATTAAGGG
Found at i:1331 original size:29 final size:27
Alignment explanation
Indices: 1298--1359 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
1288 AAATAAGACT
1298 TTTTGGATACCCGGGGGGTAAAATGGTAA
1 TTTTGGAT--CCGGGGGGTAAAATGGTAA
****
1327 TTTTGGATTTTTGGGGTAAAATGGTAA
1 TTTTGGATCCGGGGGGTAAAATGGTAA
1354 TTTTGG
1 TTTTGG
1360 GAAAATTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 21 0.72
29 8 0.28
ACGTcount: A:0.24, C:0.05, G:0.32, T:0.39
Consensus pattern (27 bp):
TTTTGGATCCGGGGGGTAAAATGGTAA
Found at i:1447 original size:59 final size:59
Alignment explanation
Indices: 1375--1622 Score: 152
Period size: 59 Copynumber: 4.2 Consensus size: 59
1365 TTTAGGGTTT
* * * * *
1375 AAAAGGGAATTTTTAGACATTTGGGGGTAAAAAGGGTAA-TTTCGAGAGTTTCGAGGTCG
1 AAAATGGAATTTTTAGACATTCGAGGG-AAAAAGGGTAATTTTCGAAAGTTTCGAGGTCA
* * * * *
1434 AAAATGGAGTTTTTGGACATTCGAGGGCAAAATGGTAATTTTTGAAAGTTTCGAGGTCA
1 AAAATGGAATTTTTAGACATTCGAGGGAAAAAGGGTAATTTTCGAAAGTTTCGAGGTCA
* * * ** * * * * * *
1493 AAAATGTAAATTTTGGAGGTT-TAGGGGTAAAATGG-AATTTTTGGAAGGTTCGAGGTCA
1 AAAATGGAATTTTTAGACATTCGA-GGGAAAAAGGGTAATTTTCGAAAGTTTCGAGGTCA
* * * * *
1551 AAAATGGAATTTTTGGA-AGTTTCG-GGGTTGAAAA-TGTAATTTTTGGAAGTTT-GAGGT-A
1 AAAATGGAATTTTTAGACA--TTCGAGGG--AAAAAGGGTAATTTTCGAAAGTTTCGAGGTCA
1609 AAAATGGAATTTTT
1 AAAATGGAATTTTT
1623 GGAAGTTTCG
Statistics
Matches: 155, Mismatches: 26, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
58 64 0.41
59 73 0.47
60 18 0.12
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAATGGAATTTTTAGACATTCGAGGGAAAAAGGGTAATTTTCGAAAGTTTCGAGGTCA
Found at i:1489 original size:30 final size:29
Alignment explanation
Indices: 1421--1767 Score: 273
Period size: 30 Copynumber: 11.9 Consensus size: 29
1411 TAATTTCGAG
* *
1421 AGTTTCGAGGTCGAAAATGGAGTTTTTGGA
1 AGTTTCGAGGGC-AAAATGGAATTTTTGGA
*
1451 CA--TTCGAGGGCAAAATGGTAATTTTTGAA
1 -AGTTTCGAGGGCAAAATGG-AATTTTTGGA
* * *
1480 AGTTTCGAGGTCAAAAATGTAAATTTTGGA
1 AGTTTCGAGGGC-AAAATGGAATTTTTGGA
* * *
1510 GGTTTAG-GGGTAAAATGGAATTTTTGGA
1 AGTTTCGAGGGCAAAATGGAATTTTTGGA
* *
1538 AGGTTCGAGGTCAAAAATGGAATTTTTGGA
1 AGTTTCGAGGGC-AAAATGGAATTTTTGGA
* *
1568 AGTTTCG-GGGTTGAAAATGTAATTTTTGGA
1 AGTTTCGAGGG--CAAAATGGAATTTTTGGA
**
1598 AGTTT-GAGGTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGGCAAAATGGAATTTTTGGA
*
1626 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
1 AGTTTCGAGGGC-AAAATGGAATTTTTGGA
* * * *
1656 AG-TTCGGGGGTGAAAATAGAATTTTTAGA
1 AGTTTCGAGGG-CAAAATGGAATTTTTGGA
* *
1685 AGTTTCAAGGTCAAAAATGG-ATTTTTGGA
1 AGTTTCGAGGGC-AAAATGGAATTTTTGGA
*
1714 AG-TTCAAGGATG-AAAATGGAATTTTTGGA
1 AGTTTCGAGG--GCAAAATGGAATTTTTGGA
* * *
1743 AG-CTCGAGGGTAGAAATGTAATTTT
1 AGTTTCGAGGGCA-AAATGGAATTTT
1768 CAAACAGTTT
Statistics
Matches: 256, Mismatches: 41, Indels: 40
0.76 0.12 0.12
Matches are distributed among these distances:
27 1 0.00
28 63 0.25
29 88 0.34
30 97 0.38
31 7 0.03
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
AGTTTCGAGGGCAAAATGGAATTTTTGGA
Found at i:1552 original size:58 final size:58
Alignment explanation
Indices: 1424--1767 Score: 319
Period size: 58 Copynumber: 5.9 Consensus size: 58
1414 TTTCGAGAGT
* * * *
1424 TTCGAGGTCGAAAATGGAGTTTTTGGACA--TTCGAGGG-CAAAATGGTAATTTTTGAAAG
1 TTCGAGGTCAAAAATGGAATTTTTGGA-AGTTTCG-GGGTAAAAATGG-AATTTTTGGAAG
* * * *
1482 TTTCGAGGTCAAAAATGTAAATTTTGGAGGTTTAGGGGT-AAAATGGAATTTTTGGAAGG
1 -TTCGAGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTGGAA-G
* *
1541 TTCGAGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTTGAAAATGTAATTTTTGGAAG
1 TTCGAGGTCAAAAATGGAATTTTTGGAAGTTTCGGGG-TAAAAATGGAATTTTTGGAAG
* *
1600 TTTGAGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG
1 TTCGAGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGT-AAAAATGGAATTTTTGGAAG
* * * * **
1658 TTCGGGGGT-GAAAATAGAATTTTTAGAAGTTTCAAGGTCAAAAATGG-ATTTTTGGAAG
1 TTC-GAGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGT-AAAAATGGAATTTTTGGAAG
* * * * *
1716 TTCAAGGAT-GAAAATGGAATTTTTGGAAG-CTCGAGGGTAGAAATGTAATTTT
1 TTCGAGG-TCAAAAATGGAATTTTTGGAAGTTTCG-GGGTAAAAATGGAATTTT
1768 CAAACAGTTT
Statistics
Matches: 243, Mismatches: 31, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
57 11 0.05
58 131 0.54
59 81 0.33
60 20 0.08
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (58 bp):
TTCGAGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTTGGAAG
Found at i:1553 original size:88 final size:87
Alignment explanation
Indices: 1434--1744 Score: 332
Period size: 88 Copynumber: 3.6 Consensus size: 87
1424 TTCGAGGTCG
* * *
1434 AAAATGGAGTTTTTGGACA-TTCGAGGGC-AAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAA
1 AAAATGGAATTTTTGGA-AGTTCGAGGTCAAAAATGG-AATTTTTGGAAGTTTCGAGGTCAAAAA
* *
1497 TGTAAATTTTGGAGGTTTAGGGGT-
64 TGTAAATTTTGGAAGTTT-GAGGTA
* **
1521 AAAATGGAATTTTTGGAAGGTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTTGAAAAT
1 AAAATGGAATTTTTGGAA-GTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAAT
*
1586 GTAATTTTTGGAAGTTTGAGGTA
65 GTAAATTTTGGAAGTTTGAGGTA
* *
1609 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG-TTCGGGGGT-GAAAA
1 AAAATGGAATTTTTGGAAG-TTCGAGGTCAAAAATGGAATTTTTGGAAGTTTC-GAGGTCAAAAA
* * *
1672 TAG-AATTTTTAGAAGTTTCAAGGTCA
64 T-GTAAATTTTGGAAGTTT-GAGGT-A
* *
1698 AAAATGG-ATTTTTGGAAGTTCAAGGAT-GAAAATGGAATTTTTGGAAG
1 AAAATGGAATTTTTGGAAGTTCGAGG-TCAAAAATGGAATTTTTGGAAG
1745 CTCGAGGGTA
Statistics
Matches: 201, Mismatches: 13, Indels: 20
0.86 0.06 0.09
Matches are distributed among these distances:
86 1 0.00
87 69 0.34
88 116 0.58
89 15 0.07
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (87 bp):
AAAATGGAATTTTTGGAAGTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATG
TAAATTTTGGAAGTTTGAGGTA
Found at i:2853 original size:3 final size:3
Alignment explanation
Indices: 2847--2872 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2837 TTATTAAAAA
2847 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2873 ATTGTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3511 original size:17 final size:17
Alignment explanation
Indices: 3480--3538 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
3470 TAAATTTAAT
* * *
3480 TTTAATTTTATAATAGA
1 TTTAAATTTAAAATAAA
*
3497 TTTAAATTTCAAATAAA
1 TTTAAATTTAAAATAAA
* *
3514 CTTAACTTTAAAATAAA
1 TTTAAATTTAAAATAAA
3531 TTTAAATT
1 TTTAAATT
3539 CTGTTGGGCC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:4274 original size:205 final size:205
Alignment explanation
Indices: 3851--4552 Score: 902
Period size: 205 Copynumber: 3.4 Consensus size: 205
3841 TCTGGTTTCA
* * * *** * * **
3851 TTGACTTGGCCTTCTTCTCAGTATCTCATCAGGAAGACGACCATATCA-TTTGTTTTGATCCACT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGT-AGTTCGCTTCAATCCACT
*** * * ** * ** * *
3915 TCTCTGTGTTTCATCTGGAAGATGGTTTTGGTTCACTTCCCTTTATTTCGTCAGGAAGCTAACCA
65 TCTCTGTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACC-
** * * * * * *
3980 TTTTATTATTTTGACTTGCTTCTCAATAACTCATCAGGAAGCTGGGGTTCGAGGATTTGCTCACA
129 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACA
* *
4045 TCAAGCATGGGT
194 TCGAGCGTGGGT
* *
4057 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTAGTTTGCTTCAATTCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTAGTTCGCTTCAATCCACTT
* *
4122 CTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTACCTCATCAGGAAGCTAACCTT
66 CTCTGTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTT
4187 TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACATC
131 TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACATC
*
4252 GAGTGTGGGT
196 GAGCGTGGGT
* * *
4262 TTGATTTGGTCTTCTTCTCAGTAACTCATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTAGTTCGCTTCAATCCACTT
* * *
4327 CTCTGTACCTTATCAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCTT
66 CTCTGTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTT
* ** *
4392 TTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAATTGGGATTCGAAGATTTACTCACATC
131 TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACATC
4457 GAGCGTGGGT
196 GAGCGTGGGT
* * * * *
4467 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGGCCGCGTCGTTCACTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTAGTTCGCTTCAATCCACTT
*
4532 CTCTGTACCTTATCAGGAAGA
66 CTCTGTACCTCATCAGGAAGA
4553 TGACCGCGTC
Statistics
Matches: 443, Mismatches: 52, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
205 339 0.77
206 104 0.23
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (205 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTAGTTCGCTTCAATCCACTT
CTCTGTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTT
TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACATC
GAGCGTGGGT
Found at i:4552 original size:49 final size:49
Alignment explanation
Indices: 4480--4601 Score: 181
Period size: 49 Copynumber: 2.5 Consensus size: 49
4470 ATTTGGTCTT
* * * *
4480 CTTCTCAGTATCTCATCAGGAAGATGGCCGCGTCGTTCACTTCAATTCG
1 CTTCTCTGTACCTCATCAGGAAGATGACCGCGTCGTTCACTTCAATCCG
* * *
4529 CTTCTCTGTACCTTATCAGGAAGATGACCGCGTCGTTCGCTTTAATCCG
1 CTTCTCTGTACCTCATCAGGAAGATGACCGCGTCGTTCACTTCAATCCG
4578 CTTCTCTGTACCTCATCAGGAAGA
1 CTTCTCTGTACCTCATCAGGAAGA
4602 CGAATTTAGT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (49 bp):
CTTCTCTGTACCTCATCAGGAAGATGACCGCGTCGTTCACTTCAATCCG
Found at i:4720 original size:133 final size:133
Alignment explanation
Indices: 4528--5203 Score: 738
Period size: 133 Copynumber: 5.2 Consensus size: 133
4518 ACTTCAATTC
* * * * *
4528 GCTTCTCTGTACCTTATCAGGAAGATGACCGCGTCGTTCGCTTTAATCCGCTTCTCTGTACCTCA
1 GCTTCTCAGTATCTCATCAGGAAGATGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCA
* * * * *
4593 TCAGGAAGACGAATTTAGTCCACTTCTCAGTTTCTCATCAGGAAGCTAACCTTTTATTGCTTCAA
66 TCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCGA
4658 CCT
131 CCT
*
4661 GCTTCTCAGTATCTCATCAGGAAGTTGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCA
1 GCTTCTCAGTATCTCATCAGGAAGATGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCA
* * * *
4726 TCAAGAAGATGAATTT-GTCCACTTCTCAGTATCTCATCATGAAGTTAACATTTTATTGCTTCGA
66 TCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCGA
4790 CCT
131 CCT
* ** ** * * * * * * *
4793 GCTTCTCAGTATCTCATCAGGAAGCTGG--GATTCG-AAGATT---TGCTCATATC-G-A--GCG
1 GCTTCTCAGTATCTCATCAGGAAGATGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCA
* * ** * * ** ** *
4848 T--GG--GTTTG-ATATGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTTCACTT
66 TCAGGAAG-ATGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACC-TTTTATT-GCTT
**
4908 C-AATT
128 CGACCT
* * * *
4913 CGCTTCTCTGTACCTTATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTC
1 -GCTTCTCAGTATCTCATCAGGAAGATGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTC
* *
4978 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTTTCTCATCAAGAAGCTAACCTTTTATTGCTTCG
65 ATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCG
5043 ACCT
130 ACCT
* *
5047 GCTTCTCAGTATCTCATCAGGAAGTTGGCCGCATCGTTCGCTTCAATCCGCTTCTCTGTACCTCA
1 GCTTCTCAGTATCTCATCAGGAAGATGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCA
* * *
5112 TCAAGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCATGAAGCTAACATTTTATTGCTTCGA
66 TCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCGA
5177 CCT
131 CCT
5180 GCTTCTCAGTATCTCATCAGGAAG
1 GCTTCTCAGTATCTCATCAGGAAG
5204 CTGGGATTCG
Statistics
Matches: 439, Mismatches: 83, Indels: 42
0.78 0.15 0.07
Matches are distributed among these distances:
118 4 0.01
119 30 0.07
120 6 0.01
121 27 0.06
122 2 0.00
123 4 0.01
124 4 0.01
125 1 0.00
126 6 0.01
127 6 0.01
128 1 0.00
129 4 0.01
130 4 0.01
131 2 0.00
132 73 0.17
133 225 0.51
134 6 0.01
135 34 0.08
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (133 bp):
GCTTCTCAGTATCTCATCAGGAAGATGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCA
TCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCGA
CCT
Found at i:4938 original size:49 final size:49
Alignment explanation
Indices: 4866--4987 Score: 190
Period size: 49 Copynumber: 2.5 Consensus size: 49
4856 ATATGGTCTT
* * * *
4866 CTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTTCACTTCAATTCG
1 CTTCTCTGTACCTCATCAGGAAGATGACCGCGTCGTTCACTTCAATCCG
* *
4915 CTTCTCTGTACCTTATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCG
1 CTTCTCTGTACCTCATCAGGAAGATGACCGCGTCGTTCACTTCAATCCG
4964 CTTCTCTGTACCTCATCAGGAAGA
1 CTTCTCTGTACCTCATCAGGAAGA
4988 CGAATTTGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 66 1.00
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (49 bp):
CTTCTCTGTACCTCATCAGGAAGATGACCGCGTCGTTCACTTCAATCCG
Found at i:4989 original size:386 final size:387
Alignment explanation
Indices: 4275--5325 Score: 1798
Period size: 386 Copynumber: 2.7 Consensus size: 387
4265 ATTTGGTCTT
* * * *
4275 CTTCTCAGTAACTCATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTTAT
1 CTTCTCAGTATCTCATCAGGAAGTTGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
* * * * * *
4340 CAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCAAC
66 CAAGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCATGAAGCTAACATTTTATTGCTTCGAC
** * *
4405 CTGCTTCTCAGTATCTCATCAGGAAATTGGGATTCGAAGATTTACTCACATCGAGCGTGGGTTTG
131 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCATATCGAGCGTGGGTTTG
* *
4470 ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGGCCGCGTCGTTCACTTCAATTCGCTTCTC
196 ATATGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCACTTCAATTCGCTTCTC
*
4535 TGTACCTTATCAGGAAGATGACCGCGTCGTTCGCTTTAATCCGCTTCTCTGTACCTCATCAGGAA
261 TGTACCTTATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCATCAGGAA
*
4600 GACGAATTTAGTCCACTTCTCAGTTTCTCATCAGGAAGCTAACCTTTTATTGCTTCAACCTG
326 GACGAATTTAGTCCACTTCTCAGTTTCTCATCAAGAAGCTAACCTTTTATTGCTTCAACCTG
4662 CTTCTCAGTATCTCATCAGGAAGTTGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
1 CTTCTCAGTATCTCATCAGGAAGTTGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
*
4727 CAAGAAGATGAATTT-GTCCACTTCTCAGTATCTCATCATGAAGTTAACATTTTATTGCTTCGAC
66 CAAGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCATGAAGCTAACATTTTATTGCTTCGAC
4791 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCATATCGAGCGTGGGTTTG
131 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCATATCGAGCGTGGGTTTG
*
4856 ATATGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTTCACTTCAATTCGCTTCTC
196 ATATGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCACTTCAATTCGCTTCTC
4921 TGTACCTTATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCATCAGGAA
261 TGTACCTTATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCATCAGGAA
* *
4986 GACGAATTTGGTCCACTTCTCAGTTTCTCATCAAGAAGCTAACCTTTTATTGCTTCGACCTG
326 GACGAATTTAGTCCACTTCTCAGTTTCTCATCAAGAAGCTAACCTTTTATTGCTTCAACCTG
*
5048 CTTCTCAGTATCTCATCAGGAAGTTGGCCGCATCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
1 CTTCTCAGTATCTCATCAGGAAGTTGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
5113 CAAGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCATGAAGCTAACATTTTATTGCTTCGAC
66 CAAGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCATGAAGCTAACATTTTATTGCTTCGAC
* *
5178 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCATATTGAGTGTGGGTTTG
131 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCATATCGAGCGTGGGTTTG
* *** * *
5243 ATATGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTTAGTTCGCTTCTC
196 ATATGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCACTTCAATTCGCTTCTC
* *
5308 TGTATCTCATCAGGAAGA
261 TGTACCTTATCAGGAAGA
5326 CGAATTTGGT
Statistics
Matches: 628, Mismatches: 35, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
386 369 0.59
387 259 0.41
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (387 bp):
CTTCTCAGTATCTCATCAGGAAGTTGGCCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
CAAGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCATGAAGCTAACATTTTATTGCTTCGAC
CTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCATATCGAGCGTGGGTTTG
ATATGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCACTTCAATTCGCTTCTC
TGTACCTTATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCATCAGGAA
GACGAATTTAGTCCACTTCTCAGTTTCTCATCAAGAAGCTAACCTTTTATTGCTTCAACCTG
Found at i:5400 original size:205 final size:207
Alignment explanation
Indices: 5048--5495 Score: 618
Period size: 205 Copynumber: 2.2 Consensus size: 207
5038 CTTCGACCTG
* *
5048 CTTCTCAGTATCTCATCAGGAAGTTGGCCGCATCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
* * *
5113 CAAGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCATGAAGCTAACATTTTATTGCTTCGAC
66 CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCAAC
* * **
5178 CTGCTTCTCAGTATCTCATCAGGAAGCTGG-GATTCGAAGATTTGCTCATATTGAG-T-GTGGGT
131 CTGCTTCTCAGTATCTCATCAGGAAGCTGGAG-TTCGAAGATTTGCTCACATCGAGCTCGTGGCA
5240 TTGATATGGTCTT-
195 TTGATATGGT-TTA
* * * * * * * *
5253 CTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTTAGTTCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
* *
5318 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTAG-TTCAA
66 CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTATT-GCTTCAA
* **
5382 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGATTTTCTCACATCGAGCCTCGTTTC
130 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGATTTGCTCACATCGAG-CTCGTGGC
*
5447 ATTGATTTGGTTTA
194 ATTGATATGGTTTA
5461 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCG
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCG
5496 CTGTTTGTGG
Statistics
Matches: 212, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
205 163 0.77
206 2 0.01
207 3 0.01
208 44 0.21
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (207 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
CAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCAAC
CTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGATTTGCTCACATCGAGCTCGTGGCAT
TGATATGGTTTA
Found at i:16217 original size:21 final size:20
Alignment explanation
Indices: 16193--16231 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
16183 AAAAAAATGC
*
16193 AAAATACAAGTGCATAATAGT
1 AAAATACAAATGCA-AATAGT
*
16214 AAAATTCAAATGCAAATA
1 AAAATACAAATGCAAATA
16232 TTGATGATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (20 bp):
AAAATACAAATGCAAATAGT
Found at i:16480 original size:59 final size:59
Alignment explanation
Indices: 16322--16663 Score: 172
Period size: 58 Copynumber: 5.9 Consensus size: 59
16312 GATTTTTAGG
* * * * ***
16322 GGCAAAATGGTAATTTTGGGAAA-ATTTAAGGTTAAAAAGGGAATTTTCAAACATTCAGA
1 GGCAAAATGGTAATTTT-CGAAAGTTTTGAGGTTAAAAATGGAATTTTTGGACATTCAGA
* * * * * *
16381 GGTAAAAGGGTAA-TTTCGAGAGTTTTGAGGTTGAAAATGGAGTTTTTGGACA-TCTGA
1 GGCAAAATGGTAATTTTCGAAAGTTTTGAGGTTAAAAATGGAATTTTTGGACATTCAGA
* * ** *
16438 GAGCAAAATGGTAATTTTTGAAAGTTTTGAGGTTAAAAATGGAAATTTTGGAGGTTC-GG
1 G-GCAAAATGGTAATTTTCGAAAGTTTTGAGGTTAAAAATGGAATTTTTGGACATTCAGA
* * * * * ** *
16497 GGTAAAAATGG-ATTTTTTGGAAGTTTTGGGGTTAAAAATAGG-ATTTTTGGA-AGTTTTGG
1 GG-CAAAATGGTAATTTTCGAAAGTTTTGAGGTTAAAAAT-GGAATTTTTGGACA-TTCAGA
* * * ** *
16556 GGTCGAAAATGG-AATTTT-TAGAAG-TTTAAGG-TAAAAATGGAATTTTTTGA-AGTTTTGG
1 GG-C-AAAATGGTAATTTTCGA-AAGTTTTGAGGTTAAAAATGGAATTTTTGGACA-TTCAGA
* * * *
16614 GGTCAAAATGG-AATTTTTGGAAGTTTAG-GGGTAAAAATGGAATTTTTGGA
1 GG-CAAAATGGTAATTTTCGAAAGTTTTGAGGTTAAAAATGGAATTTTTGGA
16664 AGTTTTGGTG
Statistics
Matches: 227, Mismatches: 42, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
57 28 0.12
58 118 0.52
59 64 0.28
60 17 0.07
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (59 bp):
GGCAAAATGGTAATTTTCGAAAGTTTTGAGGTTAAAAATGGAATTTTTGGACATTCAGA
Found at i:16528 original size:29 final size:29
Alignment explanation
Indices: 16442--16758 Score: 320
Period size: 29 Copynumber: 10.8 Consensus size: 29
16432 ATCTGAGAGC
* *
16442 AAAATGGTAATTTTTGAAAGTTTTGAGGTTA
1 AAAATGG-AATTTTTGGAAGTTTTG-GGGTA
* * *
16473 AAAATGGAAATTTTGG-AGGTTCGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
*
16501 AAAATGGATTTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTGGGG-TA
*
16531 AAAATAGG-ATTTTTGGAAGTTTTGGGGTCG
1 AAAAT-GGAATTTTTGGAAGTTTTGGGGT-A
* **
16561 AAAATGGAATTTTTAGAAG-TTTAAGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
* *
16589 AAAATGGAATTTTTTGAAGTTTTGGGGTC
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
*
16618 AAAATGGAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
*
16647 AAAATGGAATTTTTGGAAGTTTTGGTGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-A
* * *
16677 AAAATGAAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-A
* *
16707 AAAAT-GAATTTTTTGGAAG-CTCGAGGGTA
1 AAAATGGAA-TTTTTGGAAGTTTTG-GGGTA
* *
16736 GAAATGTAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
16759 AGGGACCTCT
Statistics
Matches: 240, Mismatches: 34, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
28 36 0.15
29 98 0.41
30 96 0.40
31 10 0.04
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTA
Found at i:16533 original size:58 final size:58
Alignment explanation
Indices: 16401--16719 Score: 308
Period size: 59 Copynumber: 5.5 Consensus size: 58
16391 TAATTTCGAG
* * ** * * * *
16401 AGTTTTGAGGTTGAAAATGGAGTTTTTGGACATCTGAGAG-CAAAATGGTAATTTTTGAA
1 AGTTTTGAGGTTAAAAATGGAATTTTTGGAGTTTTG-GGGTAAAAATGG-AATTTTTGGA
* * * *
16460 AGTTTTGAGGTTAAAAATGGAAATTTTGGAGGTTCGGGGTAAAAATGGATTTTTTGGA
1 AGTTTTGAGGTTAAAAATGGAATTTTTGGAGTTTTGGGGTAAAAATGGAATTTTTGGA
* * *
16518 AGTTTTGGGGTTAAAAATAGG-ATTTTTGGAAGTTTTGGGGTCGAAAATGGAATTTTTAGA
1 AGTTTTGAGGTTAAAAAT-GGAATTTTTGG-AGTTTTGGGGT-AAAAATGGAATTTTTGGA
* * *
16578 AG-TTTAAGG-TAAAAATGGAATTTTTTGAAGTTTTGGGGTCAAAATGGAATTTTTGGA
1 AGTTTTGAGGTTAAAAATGGAA-TTTTTGGAGTTTTGGGGTAAAAATGGAATTTTTGGA
* * * *
16635 AGTTTAG-GGGTAAAAATGGAATTTTTGGAAGTTTTGGTGTCAAAAATGAAATTTTTGGA
1 AGTTTTGAGGTTAAAAATGGAATTTTTGG-AGTTTTGGGGT-AAAAATGGAATTTTTGGA
* *
16694 AGTTTCGAGGTCAAAAAT-GAATTTTT
1 AGTTTTGAGGTTAAAAATGGAATTTTT
16720 TGGAAGCTCG
Statistics
Matches: 217, Mismatches: 32, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
57 28 0.13
58 76 0.35
59 88 0.41
60 25 0.12
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (58 bp):
AGTTTTGAGGTTAAAAATGGAATTTTTGGAGTTTTGGGGTAAAAATGGAATTTTTGGA
Found at i:16535 original size:30 final size:30
Alignment explanation
Indices: 16442--16725 Score: 305
Period size: 30 Copynumber: 9.6 Consensus size: 30
16432 ATCTGAGAGC
* *
16442 AAAATGGTAATTTTTGAAAGTTTTGAGGTTA
1 AAAATGG-AATTTTTGGAAGTTTTGGGGTTA
* * *
16473 AAAATGGAAATTTTGG-AGGTTCGGGG-TA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
*
16501 AAAATGGATTTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
**
16531 AAAATAGG-ATTTTTGGAAGTTTTGGGGTCG
1 AAAAT-GGAATTTTTGGAAGTTTTGGGGTTA
* **
16561 AAAATGGAATTTTTAGAAG-TTTAAGG-TA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
* *
16589 AAAATGGAATTTTTTGAAGTTTTGGGG-TC
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
*
16618 AAAATGGAATTTTTGGAAGTTTAGGGG-TA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
* *
16647 AAAATGGAATTTTTGGAAGTTTTGGTGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
* * * *
16677 AAAATGAAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
16707 AAAAT-GAATTTTTTGGAAG
1 AAAATGGAA-TTTTTGGAAG
16726 CTCGAGGGTA
Statistics
Matches: 214, Mismatches: 32, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
28 34 0.16
29 81 0.38
30 90 0.42
31 9 0.04
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.37
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTTA
Found at i:16762 original size:29 final size:28
Alignment explanation
Indices: 16442--16762 Score: 277
Period size: 30 Copynumber: 10.9 Consensus size: 28
16432 ATCTGAGAGC
* *
16442 AAAATGGTAATTTTTGAAAGTTTTGAGGTTA
1 AAAATGG-AATTTTTGGAAG-TTT-AGGGTA
* * **
16473 AAAATGGAAATTTTGGAGGTTCGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGTA
* *
16501 AAAATGGATTTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAG-TTTAGGG-TA
* *
16531 AAAATAGG-ATTTTTGGAAGTTTTGGGGTCG
1 AAAAT-GGAATTTTTGGAAG-TTTAGGGT-A
* *
16561 AAAATGGAATTTTTAGAAGTTTAAGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGTA
* * *
16589 AAAATGGAATTTTTTGAAGTTTTGGGGTC
1 AAAATGGAATTTTTGGAAG-TTTAGGGTA
16618 AAAATGGAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTA-GGGTA
*
16647 AAAATGGAATTTTTGGAAGTTTTGGTGTCA
1 AAAATGGAATTTTTGGAAGTTTAGG-GT-A
* *
16677 AAAATGAAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTAG-GGT-A
**
16707 AAAAT-GAATTTTTTGGAAGCTCGAGGGTA
1 AAAATGGAA-TTTTTGGAAG-TTTAGGGTA
* *
16736 GAAATGTAATTTTTGGACAGTTTAGGG
1 AAAATGGAATTTTTGGA-AGTTTAGGG
16763 ACCTCTAGGG
Statistics
Matches: 242, Mismatches: 34, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
28 43 0.18
29 89 0.37
30 98 0.40
31 12 0.05
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTAGGGTA
Found at i:17369 original size:30 final size:30
Alignment explanation
Indices: 17335--17400 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
17325 AATCGGTTAC
*
17335 CACGCGCACCCGTCCCGT-AGTCCTTCGGTG
1 CACGCGCACCCGTCCC-TCAGTCCTCCGGTG
***
17365 CACGCGCTGTCGTCCCTCAGTCCTCCGGTG
1 CACGCGCACCCGTCCCTCAGTCCTCCGGTG
17395 CACGCG
1 CACGCG
17401 TCACTGCTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.09, C:0.44, G:0.27, T:0.20
Consensus pattern (30 bp):
CACGCGCACCCGTCCCTCAGTCCTCCGGTG
Found at i:17791 original size:3 final size:3
Alignment explanation
Indices: 17785--17813 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17775 TTTTATTTAT
17785 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Done.