Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013544.1 Kokia drynarioides strain JFW-HI SEQ_128570, 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: 7841
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Found at i:1251 original size:29 final size:28
Alignment explanation
Indices: 1129--1693 Score: 172
Period size: 29 Copynumber: 19.4 Consensus size: 28
1119 GAAAAATTAT
* * *
1129 AATTTTGGGAAATTTTGGGGTTAAAAATGG
1 AATTTTTGG-AATTTCGGGGGT-AAAATGG
* *
1159 AATTTTTAGACATTT-GGGGGTAAAAGGG
1 AATTTTTGGA-ATTTCGGGGGTAAAATGG
* **
1187 TAA-TTTTGAGAGTTTC-GAAGTCGAAAATGG
1 -AATTTTTG-GAATTTCGGGGGT--AAAATGG
* *
1217 AGTTTTTGGACTTTCGGGGGTAAAATGG
1 AATTTTTGGAATTTCGGGGGTAAAATGG
*
1245 TAATTTTTGGAAGTTT-AGGGGTCAAAATGG
1 -AATTTTTGGAA-TTTCGGGGGT-AAAATGG
* *** *
1275 AATTTTTGGAAGTTCGAGGCCAAAAATTG
1 AATTTTTGGAATTTCG-GGGGTAAAATGG
* *
1304 AATTTTTGGAAGTTCGAGGGTAAAAATGGG
1 AATTTTTGGAATTTCGGGGGT-AAAAT-GG
* * ***
1334 ATTTTTTGGAAGTTCGGGGGTAAAAACAA
1 AATTTTTGGAATTTCGGGGGT-AAAATGG
* *
1363 AATTTTTGGAAGTTC-GAGGTCAAAAAT-G
1 AATTTTTGGAATTTCGGGGGT--AAAATGG
* * *
1391 AGATTTTTTGAAGTTCGGGCGTAAAAATGG
1 A-ATTTTTGGAATTTCGGGGGT-AAAATGG
* * *
1421 AATTTTTAGAAGTTT-TGGTGTAAAAAAT-G
1 AATTTTTGGAA-TTTCGGGGGT--AAAATGG
* *
1450 AGATTTTTGAAAGTTT-AGGGGTAAAAATGG
1 A-ATTTTTGGAA-TTTCGGGGGT-AAAATGG
* ** * *
1480 GATTTTTAAAAGTTT-TGTGGTAAAAAT-G
1 AATTTTTGGAA-TTTCGGGGGT-AAAATGG
* *
1508 AGATTTTTAGAAGTTT-TGGGGTCAAAATGG
1 A-ATTTTTGGAA-TTTCGGGGGT-AAAATGG
* * *
1538 GATTTTTGGAAGTTT-TGGGGTCAAAATGA
1 AATTTTTGGAA-TTTCGGGGGT-AAAATGG
* **
1567 AATTTTTAGAAGTTT-TAGGGTCAAAATGG
1 AATTTTTGGAA-TTTCGGGGGT-AAAATGG
* *
1596 GATTTTTGGAAGTTT-AGGGGTAAAAATGG
1 AATTTTTGGAA-TTTCGGGGGT-AAAATGG
* * * *
1625 AATTTTTAGAAGTTTTGGAGTTAAAAAT-G
1 AATTTTTGGAA-TTTCGGGGGT-AAAATGG
* *
1654 AGATTTTTGGAAGTTCGAGGGTAAAAATGG
1 A-ATTTTTGGAATTTCGGGGGT-AAAATGG
*
1684 AATTCTTGGA
1 AATTTTTGGA
1694 TAGTTTAGGG
Statistics
Matches: 428, Mismatches: 79, Indels: 57
0.76 0.14 0.10
Matches are distributed among these distances:
28 32 0.07
29 283 0.66
30 113 0.26
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (28 bp):
AATTTTTGGAATTTCGGGGGTAAAATGG
Found at i:1272 original size:58 final size:57
Alignment explanation
Indices: 1129--1693 Score: 360
Period size: 58 Copynumber: 9.7 Consensus size: 57
1119 GAAAAATTAT
* * * *
1129 AATTTTGGGAAATTTTGGGGTTAAAAATGGAATTTTTAGACATTTGGGGGT-AAAAGGG
1 AATTTTTGGAAGTTTTGGGG-TAAAAATGGAATTTTTGGA-ATTTGGGGGTAAAAATGG
* ** * * *
1187 TAA-TTTT-GAGAGTTTCGAAGTCGAAAATGGAGTTTTTGGACTTTCGGGGGT-AAAATGG
1 -AATTTTTGGA-AGTTTTGGGGT-AAAAATGGAATTTTTGGAATTT-GGGGGTAAAAATGG
* * * * ** *
1245 TAATTTTTGGAAGTTTAGGGGTCAAAATGGAATTTTTGGAAGTTCGAGGCCAAAAATTG
1 -AATTTTTGGAAGTTTTGGGGTAAAAATGGAATTTTTGGAA-TTTGGGGGTAAAAATGG
* * * ***
1304 AATTTTTGGAAG-TTCGAGGGTAAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAAACAA
1 AATTTTTGGAAGTTTTG-GGGTAAAAAT-GGAATTTTTGGAA-TTTGGGGGTAAAAATGG
* * * * *
1363 AATTTTTGGAAG-TTCGAGGTCAAAAAT-GAGATTTTTTGAAGTTCGGGCGTAAAAATGG
1 AATTTTTGGAAGTTTTGGGGT-AAAAATGGA-ATTTTTGGAA-TTTGGGGGTAAAAATGG
* * * *
1421 AATTTTTAGAAGTTTTGGTGTAAAAAAT-GAGATTTTTGAAAGTTTAGGGGTAAAAATGG
1 AATTTTTGGAAGTTTTGGGGT-AAAAATGGA-ATTTTTGGAA-TTTGGGGGTAAAAATGG
* ** * * * *
1480 GATTTTTAAAAGTTTTGTGGTAAAAAT-GAGATTTTTAGAAGTTTTGGGGTCAAAATGG
1 AATTTTTGGAAGTTTTGGGGTAAAAATGGA-ATTTTTGGAA-TTTGGGGGTAAAAATGG
* * * * ** *
1538 GATTTTTGGAAGTTTTGGGGTCAAAATGAAATTTTTAGAAGTTTTAGGGTCAAAATGG
1 AATTTTTGGAAGTTTTGGGGTAAAAATGGAATTTTTGGAA-TTTGGGGGTAAAAATGG
* * * * *
1596 GATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTAGAAGTTTTGGAGTTAAAAAT-G
1 AATTTTTGGAAGTTTTGGGGTAAAAATGGAATTTTTGGAA--TTTGGGGGTAAAAATGG
* *
1654 AGATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTCTTGGA
1 A-ATTTTTGGAAGTTTTG-GGGTAAAAATGGAATTTTTGGA
1694 TAGTTTAGGG
Statistics
Matches: 416, Mismatches: 74, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
57 11 0.03
58 239 0.57
59 164 0.39
60 2 0.00
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (57 bp):
AATTTTTGGAAGTTTTGGGGTAAAAATGGAATTTTTGGAATTTGGGGGTAAAAATGG
Found at i:1279 original size:87 final size:87
Alignment explanation
Indices: 1150--1703 Score: 321
Period size: 88 Copynumber: 6.3 Consensus size: 87
1140 ATTTTGGGGT
* * * *
1150 TAAAAATGGAATTTTTAGACA-TTTGGGGGTAAAAGGGTAA-TTTT-GAGAGTTTCGAAGTCGAA
1 TAAAAATGGAATTTTTGGA-AGTTTAGGGGTAAAAGGGTAATTTTTGGA-AG-TTCGAAGCCAAA
* ** *
1212 AATGGAGTTTTTGGACTTTCGGGGG
63 AATGGAATTTTTGGAAGTTCGAGGG
* *
1237 T-AAAATGGTAATTTTTGGAAGTTTAGGGGTCAAAATGG-AATTTTTGGAAGTTCGAGGCCAAAA
1 TAAAAATGG-AATTTTTGGAAGTTTAGGGGT-AAAAGGGTAATTTTTGGAAGTTCGAAGCCAAAA
*
1300 ATTGAATTTTTGGAAGTTCGAGGG
64 ATGGAATTTTTGGAAGTTCGAGGG
* ** **** * *
1324 TAAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAAACAAAATTTTTGGAAGTTCGAGGTCAAAAA
1 TAAAAAT-GGAATTTTTGGAAGTTTAGGGGTAAAAGGGTAATTTTTGGAAGTTCGAAGCCAAAAA
*
1389 T-GAGATTTTTTGAAGTTCG-GGCG
65 TGGA-ATTTTTGGAAGTTCGAGG-G
* * * ** * * * **
1412 TAAAAATGGAATTTTTAGAAGTTTTGGTGTAAAA-AATGAGATTTTTGAAAGTT-TAGGGGTAAA
1 TAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAGGGT-A-ATTTTTGGAAGTTCGA-AGCCAAA
* ** * *
1475 AATGGGATTTTTAAAAGTTTTG-TGG
63 AATGGAATTTTTGGAAG-TTCGAGGG
* * * ** *
1500 TAAAAAT-GAGATTTTTAGAAGTTTTGGGGTCAAAATGGG--ATTTTTGGAAGTTTTGGGGTC-A
1 TAAAAATGGA-ATTTTTGGAAGTTTAGGGGT-AAAA-GGGTAATTTTTGGAAG-TTCGAAGCCAA
* * **
1561 AAATGAAATTTTTAGAAGTTTTAGGG
62 AAATGGAATTTTTGGAAGTTCGAGGG
* * * * * * **
1587 TCAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGG-AATTTTTAGAAGTTTTGGAGTTAAAA
1 TAAAAATGGAATTTTTGGAAGTTTAGGGGT-AAAAGGGTAATTTTTGGAAG-TTCGAAGCCAAAA
1651 AT-GAGATTTTTGGAAGTTCGAGGG
64 ATGGA-ATTTTTGGAAGTTCGAGGG
*
1675 TAAAAATGGAATTCTTGGATAGTTTAGGG
1 TAAAAATGGAATTTTTGGA-AGTTTAGGG
1704 ACCTCTAAGG
Statistics
Matches: 376, Mismatches: 64, Indels: 52
0.76 0.13 0.11
Matches are distributed among these distances:
86 14 0.04
87 159 0.42
88 181 0.48
89 22 0.06
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (87 bp):
TAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAGGGTAATTTTTGGAAGTTCGAAGCCAAAAAT
GGAATTTTTGGAAGTTCGAGGG
Found at i:1352 original size:117 final size:116
Alignment explanation
Indices: 1210--1698 Score: 388
Period size: 117 Copynumber: 4.2 Consensus size: 116
1200 TTCGAAGTCG
** *
1210 AAAAT-GGAGTTTTTGGACTTTCGGGGGT-AAAATGGTAATTTTTGGAAGTTTAGGGGTCAAAAT
1 AAAATGGGA-TTTTTGGAAGTTCGGGGGTAAAAATGG-AATTTTTGGAAGTTTAGGGGTAAAAAT
* *
1273 G-GAATTTTTGGAAG-TTCGAGGCCAAAAATTGAATTTTTGGAAG-TTCGAGGGTA
64 GAG-ATTTTTAGAAGTTTCG-GGCCAAAAATGGAATTTTTGGAAGTTTCG-GGGTA
*** * *
1326 AAAATGGGATTTTTTGGAAGTTCGGGGGTAAAAACAAAATTTTTGGAAG-TTCGAGGTCAAAAAT
1 AAAATGGGA-TTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTAGGGGT-AAAAAT
* * * * *
1390 GAGATTTTTTGAAG-TTCGGGCGTAAAAATGGAATTTTTAGAAGTTTTGGTGTAA
64 GAGATTTTTAGAAGTTTCGGGC-CAAAAATGGAATTTTTGGAAGTTTCGGGGT-A
* * ** * ** * *
1444 AAAATGAGATTTTTGAAAGTTTAGGGGTAAAAATGGGATTTTTAAAAGTTTTGTGGTAAAAATGA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGA
* * * * *
1509 GATTTTTAGAAGTTTTGGGGTC-AAAATGGGATTTTTGGAAGTTTTGGGGTC
66 GATTTTTAGAAG-TTTCGGGCCAAAAATGGAATTTTTGGAAGTTTCGGGGTA
** * *** * *
1560 AAAATGAAATTTTTAGAAGTTTTAGGGTCAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATG-
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGA
* **
1624 GAATTTTTAGAAGTTTTGGAGTTAAAAAT-GAGATTTTTGGAAG-TTCGAGGGTA
66 G-ATTTTTAGAAGTTTCGG-GCCAAAAATGGA-ATTTTTGGAAGTTTCG-GGGTA
* *
1677 AAAATGGAATTCTTGGATAGTT
1 AAAATGGGATTTTTGGA-AGTT
1699 TAGGGACCTC
Statistics
Matches: 304, Mismatches: 53, Indels: 30
0.79 0.14 0.08
Matches are distributed among these distances:
115 6 0.02
116 85 0.28
117 181 0.60
118 27 0.09
119 5 0.02
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (116 bp):
AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGA
GATTTTTAGAAGTTTCGGGCCAAAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:1703 original size:29 final size:28
Alignment explanation
Indices: 1234--1703 Score: 340
Period size: 29 Copynumber: 16.1 Consensus size: 28
1224 GGACTTTCGG
1234 GGGT-AAAATGGTAATTTTTGGAAGTTTA
1 GGGTAAAAATGG-AATTTTTGGAAGTTTA
* *
1262 GGGGTCAAAATGGAATTTTTGGAAGTTCGA
1 -GGGTAAAAATGGAATTTTTGGAAGTT-TA
** * *
1292 GGCCAAAAATTGAATTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTT-TA
* **
1321 GGGTAAAAATGGGATTTTTTGGAAGTTCGG
1 GGGTAAAAAT-GGAATTTTTGGAAGTT-TA
*** *
1351 GGGTAAAAACAAAATTTTTGGAAG-TTC
1 GGGTAAAAATGGAATTTTTGGAAGTTTA
* **
1378 GAGGTCAAAAAT-GAGATTTTTTGAAGTTCG
1 G-GGT-AAAAATGGA-ATTTTTGGAAGTTTA
* *
1408 GGCGTAAAAATGGAATTTTTAGAAGTTTT
1 GG-GTAAAAATGGAATTTTTGGAAGTTTA
*
1437 GGTGTAAAAAAT-GAGATTTTTGAAAGTTTA
1 GG-GT-AAAAATGGA-ATTTTTGGAAGTTTA
* ** *
1467 GGGGTAAAAATGGGATTTTTAAAAGTTTT
1 -GGGTAAAAATGGAATTTTTGGAAGTTTA
* *
1496 GTGGTAAAAAT-GAGATTTTTAGAAGTTTTG
1 G-GGTAAAAATGGA-ATTTTTGGAAG-TTTA
* * *
1526 GGGTCAAAATGGGATTTTTGGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAG-TTTA
* * *
1555 GGGTCAAAATGAAATTTTTAGAAGTTTTA
1 GGGTAAAAATGGAATTTTTGGAAG-TTTA
* *
1584 GGGTCAAAATGGGATTTTTGGAAGTTTA
1 GGGTAAAAATGGAATTTTTGGAAGTTTA
* *
1612 GGGGTAAAAATGGAATTTTTAGAAGTTTT
1 -GGGTAAAAATGGAATTTTTGGAAGTTTA
*
1641 GGAGTTAAAAAT-GAGATTTTTGGAAGTTCGA
1 GG-G-TAAAAATGGA-ATTTTTGGAAGTT-TA
*
1672 GGGTAAAAATGGAATTCTTGGATAGTTTA
1 GGGTAAAAATGGAATTTTTGGA-AGTTTA
1701 GGG
1 GGG
1704 ACCTCTAAGG
Statistics
Matches: 364, Mismatches: 53, Indels: 48
0.78 0.11 0.10
Matches are distributed among these distances:
27 1 0.00
28 13 0.04
29 255 0.70
30 91 0.25
31 4 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (28 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTA
Found at i:2750 original size:15 final size:16
Alignment explanation
Indices: 2725--2757 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2715 CCCTTTTTTT
2725 TATTAATTATTAATAA
1 TATTAATTATTAATAA
*
2741 TATT-ATTATTATTAA
1 TATTAATTATTAATAA
2756 TA
1 TA
2758 AAACATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATTATTAATAA
Found at i:3506 original size:6 final size:6
Alignment explanation
Indices: 3463--3545 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
3453 TTTTAATTAA
* * * *
3463 TTAAATT TTAAAT TCAAA- TTAATT TTAAAC TT-AAT TTAAAT TTAAAC
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* **
3510 TTAAAA GAAAAGT TTAAACT TTAAA- TTAAAT TTAAA
1 TTAAAT TTAAA-T TTAAA-T TTAAAT TTAAAT TTAAA
3546 CCCAAAATGA
Statistics
Matches: 58, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
5 12 0.21
6 32 0.55
7 14 0.24
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:3545 original size:18 final size:18
Alignment explanation
Indices: 3461--3546 Score: 86
Period size: 17 Copynumber: 4.8 Consensus size: 18
3451 TTTTTTAATT
*
3461 AATTAAATTTTAAA-TTCA
1 AATTAAA-TTTAAACTTTA
*
3479 AATTAATTTTAAAC-TTA
1 AATTAAATTTAAACTTTA
* *
3496 ATTTAAATTTAAACTTAA
1 AATTAAATTTAAACTTTA
**
3514 AAGAAAAGTTTAAACTTTA
1 AATTAAA-TTTAAACTTTA
3533 AATTAAATTTAAAC
1 AATTAAATTTAAAC
3547 CCAAAATGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
17 20 0.37
18 19 0.35
19 15 0.28
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (18 bp):
AATTAAATTTAAACTTTA
Found at i:4349 original size:205 final size:203
Alignment explanation
Indices: 3950--4478 Score: 718
Period size: 204 Copynumber: 2.6 Consensus size: 203
3940 ACCATATCAC
* * * * * * * ** * * *
3950 TTGTTTTAATCCACTTCTCTGTATTTCATCAGGAAGATGATTTTGGTTTACTTCCCCGTATTTCA
1 TTGTTTTAATTCGCTTTTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
* * * *
4015 TCAGGAAGTTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAGGCTGGGGTTA
66 TCAGGAAGCTAACC-GTTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTA
*
4080 GAAGATTTGTTCATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGTAAGATGA
130 GAAGATTTGTTCATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGA
* *
4145 TCGCGTTGT
195 CCGCGTCGT
4154 TTGTTTTAATTCGCTTTTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
1 TTGTTTTAATTCGCTTTTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
* * * * * *
4219 TCAGGAAGCTAACCGTTTGTTGCTTCGACTTGCTTCTTAGTGTCTCATCAAGAAGCTGGGGTTCG
66 TCAGGAAGCTAACCGTTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTAG
** * *
4284 AAGATTTGTTCACATCGAGGGTGGGTTTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATG
131 AAGATTTGTT--CATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATG
4349 ACCGCGTCGT
194 ACCGCGTCGT
4359 TTGTTTTAATTCGC-TTTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
1 TTGTTTTAATTCGCTTTTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
* ** *
4423 TCAAGAAGCTAATTGTTTTATTACTTCGACCTGCTTCTCATTGTCTCATCAGGAAG
66 TCAGGAAGCTAACCG-TTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAG
4479 ACGAATTTGG
Statistics
Matches: 284, Mismatches: 38, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
203 52 0.18
204 128 0.45
205 104 0.37
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (203 bp):
TTGTTTTAATTCGCTTTTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
TCAGGAAGCTAACCGTTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTAG
AAGATTTGTTCATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGAC
CGCGTCGT
Found at i:4470 original size:85 final size:85
Alignment explanation
Indices: 4381--4733 Score: 430
Period size: 85 Copynumber: 4.2 Consensus size: 85
4371 GCTTTTTGTA
*
4381 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAATTGTTTTATTA
1 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAATCGTTTTATTA
*
4446 CTTCGACCTGCTTCTCATTG
66 CTTCGACCTGCTTCTCAGTG
* *
4466 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAAGAAGCTAACCGTTTTATTA
1 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAATCGTTTTATTA
*
4531 CTTCAACCTGCTTCTCAGTG
66 CTTCGACCTGCTTCTCAGTG
* * * * * *
4551 TCTCATCAAGAAGACAAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGATGACCGCGTCGTTT
1 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCT-A----ATCGTTT
* * * * *
4616 GTTTTAATT--A---GCTTTTCTGTA
61 -TATTACTTCGACCTGCTTCTCAGTG
* * * *
4637 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAATC-ATTTGTTG
1 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAATCGTTTTATTA
4701 CTTCGACCTGCTTCTCAGTG
66 CTTCGACCTGCTTCTCAGTG
4721 TCTCATCAGGAAG
1 TCTCATCAGGAAG
4734 CTGGGGTTCG
Statistics
Matches: 227, Mismatches: 30, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
79 5 0.02
80 2 0.01
81 3 0.01
84 21 0.09
85 127 0.56
86 57 0.25
89 1 0.00
90 5 0.02
91 6 0.03
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (85 bp):
TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAATCGTTTTATTA
CTTCGACCTGCTTCTCAGTG
Found at i:5340 original size:27 final size:27
Alignment explanation
Indices: 5310--5368 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
5300 TCAAAAATTC
*
5310 TATTAAAAAGAGGATAAAAGGAAACAA
1 TATTAAAAAGAAGATAAAAGGAAACAA
*
5337 TATT-AAAAGAAGATCAAAGGAAACAA
1 TATTAAAAAGAAGATAAAAGGAAACAA
5363 TCATTA
1 T-ATTA
5369 GTTGAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.19
Consensus pattern (27 bp):
TATTAAAAAGAAGATAAAAGGAAACAA
Found at i:6990 original size:11 final size:11
Alignment explanation
Indices: 6974--7000 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6964 TCCTCTGTCT
6974 CAATATCACAA
1 CAATATCACAA
6985 CAATATCACAA
1 CAATATCACAA
6996 CAATA
1 CAATA
7001 AGCAGGAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.19
Consensus pattern (11 bp):
CAATATCACAA
Done.