Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018319.1 Corchorus olitorius cultivar O-4 contig18352, 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: 42593
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1173 original size:20 final size:20
Alignment explanation
Indices: 1136--1174 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1126 TACTTTTATT
1136 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
1156 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
1175 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:1368 original size:22 final size:22
Alignment explanation
Indices: 1340--1572 Score: 109
Period size: 22 Copynumber: 10.5 Consensus size: 22
1330 TGTCTCTATG
1340 TGGTTATCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAAAA
* * **
1362 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAAA
* **
1385 -GGTTATCAAAATTCCATAATG
1 TGGTTATCAAAATTTCATAAAA
* **
1406 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AAA
* *
1429 -GGTCATCAAAATTTCATGGGAAA
1 TGGTTATCAAAATTTCAT--AAAA
* ***
1452 --GTTATCAAAATATCATATTG
1 TGGTTATCAAAATTTCATAAAA
*
1472 TGGTTACCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAAAA
* *
1494 TCAGGTTATTAAAATTTCTTAGAAA
1 T--GGTTATCAAAATTTCATA-AAA
** ***
1519 -GGTTATTGAAATTTCATAGCT
1 TGGTTATCAAAATTTCATAAAA
* * *
1540 TGGTTATCACAATTTTATGGAAA
1 TGGTTATCAAAATTTCAT-AAAA
1563 T-GTTATCAAA
1 TGGTTATCAAA
1573 GAGATTATCA
Statistics
Matches: 151, Mismatches: 48, Indels: 24
0.68 0.22 0.11
Matches are distributed among these distances:
21 1 0.01
22 128 0.85
23 4 0.03
24 15 0.10
25 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAAA
Found at i:1410 original size:44 final size:44
Alignment explanation
Indices: 1341--1494 Score: 125
Period size: 44 Copynumber: 3.5 Consensus size: 44
1331 GTCTCTATGT
* ** *
1341 GGTTATCAAAATTTCATAAAATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTCCATAAAATGGTTACCAAAATTTCAT-ATGGA
**
1385 GGTTATCAAAATTCCATAATGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTCCATAAAATGGTTACCAAAATTTCATATGGA
* * * * * * *
1429 GGTCATCAAAATTTCATGGGAAA--GTTATCAAAATATCATATTGT
1 GGTTATCAAAATTCCAT--AAAATGGTTACCAAAATTTCATATGGA
* *
1473 GGTTACCAAAATTTCATAAAAT
1 GGTTATCAAAATTCCATAAAAT
1495 CAGGTTATTA
Statistics
Matches: 88, Mismatches: 18, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
42 3 0.03
43 1 0.01
44 83 0.94
46 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (44 bp):
GGTTATCAAAATTCCATAAAATGGTTACCAAAATTTCATATGGA
Found at i:1443 original size:66 final size:66
Alignment explanation
Indices: 1337--1494 Score: 196
Period size: 66 Copynumber: 2.4 Consensus size: 66
1327 TCTTGTCTCT
* * * * *
1337 ATGTGGTTATCAAAATTTCATAAAATGGTTATTATAATTTCATGAGG-AGGTTATCAAAAT-TCC
1 ATGTGGTTACCAAAATTTCATAAAATGGTCATCAAAATTTCATG-GGAAAGTTATCAAAATAT-C
1400 ATA
64 ATA
**
1403 ATGTGGTTACCAAAATTTCATATGGA-GGTCATCAAAATTTCATGGGAAAGTTATCAAAATATCA
1 ATGTGGTTACCAAAATTTCATA-AAATGGTCATCAAAATTTCATGGGAAAGTTATCAAAATATCA
1467 TA
65 TA
*
1469 TTGTGGTTACCAAAATTTCATAAAAT
1 ATGTGGTTACCAAAATTTCATAAAAT
1495 CAGGTTATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
65 3 0.04
66 73 0.94
67 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (66 bp):
ATGTGGTTACCAAAATTTCATAAAATGGTCATCAAAATTTCATGGGAAAGTTATCAAAATATCAT
A
Found at i:1613 original size:22 final size:21
Alignment explanation
Indices: 1581--1739 Score: 68
Period size: 22 Copynumber: 7.0 Consensus size: 21
1571 AAGAGATTAT
*
1581 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAG-GAGGTTA-A
* *
1604 -AGAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAG-GAGGTTAA
1625 CAAAATTTCATAAGGAGGTTAGTA
1 CAAAATTTCAT-AGGAGGTTA--A
** *
1649 CTATTATTTCATCATGGGGAGGTTAT
1 C-AAAATTTCAT-A---GGAGGTTAA
* *
1675 CAAAATTTCATAGTGTGGTTAT
1 CAAAATTTCATAG-GAGGTTAA
** * *
1697 CAAAATTTTTTAGTGCGGTTAT
1 CAAAATTTCATAG-GAGGTTAA
*
1719 CAAAATTTCATATGAAGGTTA
1 CAAAATTTCATA-GGAGGTTA
1740 TAAAAGTCTC
Statistics
Matches: 106, Mismatches: 20, Indels: 21
0.72 0.14 0.14
Matches are distributed among these distances:
21 2 0.02
22 72 0.68
23 3 0.03
24 3 0.03
25 17 0.16
26 1 0.01
28 8 0.08
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.36
Consensus pattern (21 bp):
CAAAATTTCATAGGAGGTTAA
Found at i:1740 original size:22 final size:21
Alignment explanation
Indices: 1668--1996 Score: 139
Period size: 22 Copynumber: 14.8 Consensus size: 21
1658 CATCATGGGG
*
1668 AGGTTATCAAAATTTCATAGTG
1 AGGTTATCAAAATTTCATAG-A
* ** *
1690 TGGTTATCAAAATTTTTTAGTG
1 AGGTTATCAAAATTTCATAG-A
*
1712 CGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
1734 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
1759 AGGAATACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
**
1781 AGGTTATC-AAACCTCATAG-
1 AGGTTATCAAAATTTCATAGA
*
1800 AGTGATTATCGAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
*
1823 GATCGAATTATCAAAATTT-ATAAGA
1 -A--G-GTTATCAAAATTTCAT-AGA
* *
1848 AGATTATCAAAATTTAATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
1868 TGTTGTTATCAAAATTTCAGAGCG
1 AG--GTTATCAAAATTTCATAG-A
*
1892 AGGTTATCAAAATTACATATCG-
1 AGGTTATCAAAATTTCATA--GA
* *
1914 TGATTATCAAAATTTCATAGA
1 AGGTTATCAAAATTTCATAGA
* * * *
1935 GGGGTCAACAAAATTTTATAGA
1 -AGGTTATCAAAATTTCATAGA
*
1957 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
1979 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
1997 AAATGTGATT
Statistics
Matches: 236, Mismatches: 46, Indels: 50
0.71 0.14 0.15
Matches are distributed among these distances:
19 2 0.01
20 11 0.05
21 27 0.11
22 157 0.67
23 3 0.01
24 6 0.03
25 20 0.08
26 6 0.03
27 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:1947 original size:44 final size:43
Alignment explanation
Indices: 1829--2020 Score: 167
Period size: 44 Copynumber: 4.4 Consensus size: 43
1819 TAGAGATCGA
* *
1829 ATTATCAAAATTT-ATA-AGAAGATTATCAAAATTTAATAGTGTTG
1 ATTATCAAAATTTCATAGAG-AGGTTATCAAAATTTCATA-TG-TG
* * *
1873 -TTATCAAAATTTCAGAGCGAGGTTATCAAAATTACATATCGTG
1 ATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAT-GTG
* * * * *
1916 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATA-GAG
1 ATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATATGTG
* * *
1958 AGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTG
1 A--TTATCAAAATTTCATAGAGAGGTTATCAAAATTTC-ATATGTG
*
2004 ATTACCAAAATTTCATA
1 ATTATCAAAATTTCATA
2021 ATAGTATTTT
Statistics
Matches: 118, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
42 3 0.03
43 15 0.13
44 94 0.80
45 3 0.03
46 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (43 bp):
ATTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATATGTG
Found at i:1987 original size:66 final size:66
Alignment explanation
Indices: 1830--1996 Score: 176
Period size: 66 Copynumber: 2.5 Consensus size: 66
1820 AGAGATCGAA
* * ** * * *
1830 TTATCAAAATTT-AT-AAGAAGATTATCAAAATTTAATAGTGTTGTTATCAAAATTTCAGAGCGA
1 TTATCAAAATTTCATAAAG-AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAGAGAGA
1893 GG
65 GG
* ** * * *
1895 TTATCAAAATTACATATCGTGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAG
1 TTATCAAAATTTCATAAAGAGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAGAGAGAG
1960 G
66 G
* *
1961 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 TTATCAAAATTTCATAAAGAGATTATCAAAATTTCA
1997 AAATGTGATT
Statistics
Matches: 81, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
65 11 0.14
66 69 0.85
67 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (66 bp):
TTATCAAAATTTCATAAAGAGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAGAGAGAG
G
Found at i:2149 original size:22 final size:22
Alignment explanation
Indices: 2036--2285 Score: 146
Period size: 22 Copynumber: 11.7 Consensus size: 22
2026 ATTTTTGGGG
*
2036 AGGTTATCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGGA
* *
2058 TGGTTA-CCAAA--T--TAGGA
1 AGGTTATCAAAATTTCATAGGA
* * *
2075 AGGTTATTAAACTATCATTATGG-
1 AGGTTATCAAAATTTCA-TA-GGA
* *
2098 A-GTAATCAAAATTTC--AGGG
1 AGGTTATCAAAATTTCATAGGA
* * *
2117 AGGATATCAAAATTTCACATGA
1 AGGTTATCAAAATTTCATAGGA
**
2139 AGGTTATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG-GA
*
2162 A-GTTTTCAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
* *
2183 GGGTTATCAAAATTTCATA-GT
1 AGGTTATCAAAATTTCATAGGA
* * *
2204 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATAGGA
* * *
2227 AGATTAACAAAATTTCATAATG-
1 AGGTTATCAAAATTTCAT-AGGA
** *
2249 AGGTTATCAAAAAATCATAGGG
1 AGGTTATCAAAATTTCATAGGA
2271 AGGTTATCAAAATTT
1 AGGTTATCAAAATTT
2286 GTAGTTATCA
Statistics
Matches: 169, Mismatches: 42, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
17 9 0.05
18 4 0.02
19 3 0.02
20 13 0.08
21 9 0.05
22 120 0.71
23 9 0.05
24 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:2334 original size:22 final size:22
Alignment explanation
Indices: 2102--2345 Score: 170
Period size: 22 Copynumber: 11.5 Consensus size: 22
2092 TTATGGAGTA
*
2102 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* * *
2122 ATCAAAATTTCACATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
2144 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
*
2166 TTCAAAATTTCATA-GGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
2188 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
2210 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
2232 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
2254 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
2276 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
** *
2292 ATCATGA-TTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
2313 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
2336 AGCAAAATTT
1 ATCAAAATTT
2346 ATAAGAAGGT
Statistics
Matches: 173, Mismatches: 37, Indels: 25
0.74 0.16 0.11
Matches are distributed among these distances:
16 10 0.06
17 2 0.01
18 1 0.01
19 1 0.01
20 14 0.08
21 11 0.06
22 119 0.69
23 15 0.09
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:2355 original size:22 final size:23
Alignment explanation
Indices: 2302--2355 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
2292 ATCATGATTC
*
2302 ATAAGGAGG-TTATCAAAATTTT
1 ATAAGGAGGTTTAGCAAAATTTT
*
2324 ATAGGGAGGTTTAGCAAAA-TTT
1 ATAAGGAGGTTTAGCAAAATTTT
*
2346 ATAAGAAGGT
1 ATAAGGAGGT
2356 GTTGCGCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (23 bp):
ATAAGGAGGTTTAGCAAAATTTT
Found at i:4808 original size:12 final size:13
Alignment explanation
Indices: 4786--4813 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4776 CTTTGAGGCC
4786 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
4799 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
4812 AA
1 AA
4814 GGGTAATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:24231 original size:28 final size:28
Alignment explanation
Indices: 24200--24253 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
24190 TTAGACTTAT
*
24200 ATAATATA-ATATAAAATAAACTAAAATA
1 ATAATATATA-ATAAAATAAAATAAAATA
*
24228 ATAATCTATAATAAAATAAAATAAAA
1 ATAATATATAATAAAATAAAATAAAA
24254 ATCTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (28 bp):
ATAATATATAATAAAATAAAATAAAATA
Found at i:24240 original size:23 final size:23
Alignment explanation
Indices: 24205--24260 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
24195 CTTATATAAT
* * *
24205 ATAATATAAAATAAACTAAAATA
1 ATAATCTATAATAAAATAAAATA
24228 ATAATCTATAATAAAATAAAATA
1 ATAATCTATAATAAAATAAAATA
*
24251 AAAATCTATA
1 ATAATCTATA
24261 TTTATACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (23 bp):
ATAATCTATAATAAAATAAAATA
Found at i:24912 original size:129 final size:131
Alignment explanation
Indices: 24768--25009 Score: 389
Period size: 131 Copynumber: 1.9 Consensus size: 131
24758 ATTTAAGAAA
* * * *
24768 TATATTTTAAGAATTCTAATATATCTAAG-TTTTTAATTAAATTATTGAAATGGTAAAAATAAAA
1 TATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTGAAATGGTAAAAATAAAA
24832 TAGGTATAAGGATATTAGATTAAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
66 TAGGTATAAGGATATTAGATTAAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
24897 G
131 G
24898 TATA-TTTAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTGAAATGGTAAAAATAAA
1 TATATTTTAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTGAAATGGTAAAAATAAA
* * * *
24962 ATAGTTATAAGGATATTAGATTTAATTATATACAAATAGAGTTTTTAG
65 ATAGGTATAAGGATATTAGATTAAATTAAATAAAAATAGAGTTTTTAG
25010 CTAAATTTAT
Statistics
Matches: 102, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
129 22 0.22
130 4 0.04
131 76 0.75
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (131 bp):
TATATTTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTGAAATGGTAAAAATAAAA
TAGGTATAAGGATATTAGATTAAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
G
Found at i:26239 original size:169 final size:163
Alignment explanation
Indices: 25949--26282 Score: 578
Period size: 165 Copynumber: 2.0 Consensus size: 163
25939 GAATAAGTAC
25949 ATAAATTTCCTTTTAATTTGTAAACGTATTTGATATTTATTCAATATATTAGTTGAGACTTATCA
1 ATAAATTTCCTTTTAATTTGTAAACGTATTTGATATTTATTCAATATATTAGTTGAGACTTATCA
26014 TCAACAAAATTTCCAGGTCCATAGGCCAAATTAAAAATTGTGAACCACAAGACTTTTTTTTTATC
66 TCAACAAAATTTCCAGGTCCATAGGCCAAATTAAAAATTGTGAACCACAAGAC--TTTTTTTATC
26079 GTGGTGATAAATTGTTCTATATATATGAAAATGAA
129 GTGGTGATAAATTGTTCTATATATATGAAAATGAA
*
26114 ATAAATTTCTTTTTAATTTGTAAACGTATTTGATATTTATTCAATATATTAGTTGAGACTTACAT
1 ATAAATTTCCTTTTAATTTGTAAACGTATTTGATATTTATTCAATATATTAGTTGAGAC-T---T
* *
26179 ATCATCAACAAAATTTCCAGGTCCATAGGCCAAATTAGAAATTGTGAACCACAAGACTTTTTTTG
62 ATCATCAACAAAATTTCCAGGTCCATAGGCCAAATTAAAAATTGTGAACCACAAGACTTTTTTTA
*
26244 TCGTGGTGATAAATTGTTCTGTATATATGAAAATGAA
127 TCGTGGTGATAAATTGTTCTATATATATGAAAATGAA
26281 AT
1 AT
26283 TTGACAATAC
Statistics
Matches: 161, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
165 58 0.36
166 1 0.01
167 45 0.28
169 57 0.35
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (163 bp):
ATAAATTTCCTTTTAATTTGTAAACGTATTTGATATTTATTCAATATATTAGTTGAGACTTATCA
TCAACAAAATTTCCAGGTCCATAGGCCAAATTAAAAATTGTGAACCACAAGACTTTTTTTATCGT
GGTGATAAATTGTTCTATATATATGAAAATGAA
Found at i:28494 original size:13 final size:13
Alignment explanation
Indices: 28476--28503 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28466 ATATATCTCC
28476 TCGCTCCCTTCGT
1 TCGCTCCCTTCGT
28489 TCGCTCCCTTCGT
1 TCGCTCCCTTCGT
28502 TC
1 TC
28504 ATATTAGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.46, G:0.14, T:0.39
Consensus pattern (13 bp):
TCGCTCCCTTCGT
Found at i:31218 original size:157 final size:157
Alignment explanation
Indices: 30918--31222 Score: 361
Period size: 157 Copynumber: 1.9 Consensus size: 157
30908 CCGGGATATG
* **
30918 AAAAAATTTGGTGGGAAAAATTTTCCACCAAAATTATTCATTTTTTCCCGTTCTATTATTTTTTT
1 AAAAAATTTGGTGGGAAAAATTTTCCACCAAAATAATTCATTTTTTCCCGTTCTACCATTTTTTT
* * * *
30983 TATAAAATTGTATAAAACATTTATGGTGGCGTTTCTTTGGTTGAAACACCACTATATGGTGGCAT
66 AATAAAATAGTATAAAACATTTATGGTGGCGTTTCTTTGGATGAAACACCACCATATGGTGGCAT
* *
31048 TTTGTCTTCAAAACGCCGCCATACTAA
131 TTTGTCGTAAAAACGCCGCCATACTAA
* * * *
31075 AAAAAATTTGGTGGGAAAAA-TTTCCGCCCAAATAATTCTTTTTTTTTCCGTT-TAACCA-TTTT
1 AAAAAATTTGGTGGGAAAAATTTTCCACCAAAATAATTC-ATTTTTTCCCGTTCT-ACCATTTTT
* **
31137 TTAATAAAATAGTATAAAACATTTATGGTGGC-TTTTTTGATGGATGAAAGGCCACCATACT-GT
64 TTAATAAAATAGTATAAAACATTTATGGTGGCGTTTCTT--TGGATGAAACACCACCATA-TGGT
*
31200 GGCGTTTTTGT-GTAAAAACGCCG
126 GGC-ATTTTGTCGTAAAAACGCCG
31223 GTATATGGAA
Statistics
Matches: 125, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
155 5 0.04
156 50 0.40
157 63 0.50
158 7 0.06
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (157 bp):
AAAAAATTTGGTGGGAAAAATTTTCCACCAAAATAATTCATTTTTTCCCGTTCTACCATTTTTTT
AATAAAATAGTATAAAACATTTATGGTGGCGTTTCTTTGGATGAAACACCACCATATGGTGGCAT
TTTGTCGTAAAAACGCCGCCATACTAA
Done.