Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020845.1 Corchorus olitorius cultivar O-4 contig20878, 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: 49767
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:726 original size:156 final size:156
Alignment explanation
Indices: 487--796 Score: 534
Period size: 156 Copynumber: 2.0 Consensus size: 156
477 TAATCCAGCG
* * *
487 CTAAAAAGATTTAAGGGCTTTTTATGCTTCAAATATGGCTCTTCTTTTTTTTTATCCAATTAATT
1 CTAAAAACATTTAAGGGCTTTTTATGCTTCAAATATGGCTCTTCTCTTTTTTTATCCAATTAACT
552 TCTGATAAACCGAATGAAGATTTCGATGCTCGTAAAAACATATCCTTAAATCCATTATAGT-TGA
66 TCTGATAAACCGAATGAAGATTTCGATGCTCGTAAAAACATATCCTTAAATCCATTATA-TCTGA
616 GATTTGATTAGATTCATATAGATATCC
130 GATTTGATTAGATTCATATAGATATCC
* *
643 CTAAAAACATTTCAGGGCTTTTTATGCTTCAAATATGGCTTTTC-CTTTTTTTATCCAATTAACT
1 CTAAAAACATTTAAGGGCTTTTTATGCTTCAAATATGGCTCTTCTCTTTTTTTATCCAATTAACT
*
707 TCTGATAAAACCGAATGAAGATTTTGATGCTCGTAAAAACATATCCTTAAATCCATTATATCTGA
66 TCTGAT-AAACCGAATGAAGATTTCGATGCTCGTAAAAACATATCCTTAAATCCATTATATCTGA
772 GATTTGATTAGATTCATATAGATAT
130 GATTTGATTAGATTCATATAGATAT
797 TTCAACAAGT
Statistics
Matches: 146, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
155 25 0.17
156 121 0.83
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (156 bp):
CTAAAAACATTTAAGGGCTTTTTATGCTTCAAATATGGCTCTTCTCTTTTTTTATCCAATTAACT
TCTGATAAACCGAATGAAGATTTCGATGCTCGTAAAAACATATCCTTAAATCCATTATATCTGAG
ATTTGATTAGATTCATATAGATATCC
Found at i:1301 original size:333 final size:330
Alignment explanation
Indices: 645--1879 Score: 1453
Period size: 333 Copynumber: 3.7 Consensus size: 330
635 AGATATCCCT
* * * * *
645 AAAAACATTTCAGGGCTTTTTATGCTTCAAATATGGCTTTTCCTTTTTTTATCCAATTAACTTCT
1 AAAAAGATTTCAAGGCTTTTCATGCTTCAAATATGGTTTTTCCTTTTTTTATCCAATTAATTTCT
* ** * * *
710 GATAAAACCGAATGAAGATTTTGATGCTCGTAAAAACATATCCTTAAATCCATTATATCTGAGAT
66 GATAAAACCGAATCAAGATTCAGAAGCTCGTAAAAACATATCCTTAAATCCATTGTAGCTGAGAT
** * *
775 TTGATTAGATTCATATAGATATTTCAACAAGTCTCGATGCCAAAAATCTAGCAAAACTGAGCCGG
131 TTGATTAGATTCATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTTGCAAAACTGAGCCGG
* * * *
840 GGCCCTGAAACGCATTTTCAGCCAGAAACCGTGATGGTTAGTATACAATTTCAGCTAAAATTTTG
196 GGCCCTGGAACGCGTTTTCAGCCAGAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTG
* * * * * *
905 CAAAAACTGATCATAAATTTTTTTTCACAATTTTTGGCCACAGTGCTGTTAA-AAAATATATAAT
261 CAAAAACTAATCAGAAATTTTTTTTCTCAATTTTTGGCCACAATAC--TCAATAAAA-ATATAAT
969 TCAACGCC
323 TCAACGCC
* *
977 AAAAAGATTTCAAGCCTTTTCATGCTTCAAATATGGTTTTTCATTTTTTTATCCAATTAATTTCT
1 AAAAAGATTTCAAGGCTTTTCATGCTTCAAATATGGTTTTTCCTTTTTTTATCCAATTAATTTCT
* * * * *
1042 GATAAAACCCGAATCAACATTCAGAGGCTCGTTAAAACATATCCTTTAATCCATTGTAGCTGATA
66 GATAAAA-CCGAATCAAGATTCAGAAGCTCGTAAAAACATATCCTTAAATCCATTGTAGCTGAGA
*
1107 TTTGATTAGATTCATATAGATATTTCAAGGAGTCTCGACGCCCAAAATCTTGCAAAACTGAGCCG
130 TTTGATTAGATTCATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTTGCAAAACTGAGCCG
** * *
1172 GGGCCCTGGAACGCGTTTTTGGCCAGAAACTGTTATGGTTAGTACACGATTTCAGCTAAAATTTT
195 GGGCCCTGGAACGCGTTTTCAGCCAGAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTT
* *
1237 GCAAGAACTAATGCA-AAATTTTTTTTTCTCATTTTTTGGCCACAATACTCAATATAAAATATAA
260 GCAAAAACTAAT-CAGAAA-TTTTTTTTCTCAATTTTTGGCCACAATACTCAATA-AAAATATAA
1301 TTCAACGCC
322 TTCAACGCC
* * * *
1310 -AAAAGATATTTAATGGATTTTCATGCTTCAAATATGGTTTTCCCTTTTTTT-TCCAA-AAATTT
1 AAAAAGAT-TTCAA-GGCTTTTCATGCTTCAAATATGGTTTTTCCTTTTTTTATCCAATTAA-TT
* * * * * *
1372 TCTGACAAAACCGAATCAAGATTCAGAAGCTCATAAAGACATATCTCTT-AATCCAATGTGGTTG
63 TCTGATAAAACCGAATCAAGATTCAGAAGCTCGTAAAAACATATC-CTTAAATCCATTGTAGCTG
* * * * * * * ** *
1436 AGATTTAATTAGATTAATATTGATATTTTAAGGAGTTTAGACGTCTGAAATCATGCAAAACTGAG
127 AGATTTGATTAGATTCATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTTGCAAAACTGAG
** * * * * *
1501 TCC-GTTCCCCGGAACGCTTTTTTAGGCAGAAACC---A----T--T-CACGATTTCAGATAAAA
192 -CCGGGGCCCTGGAACGCGTTTTCAGCCAGAAACCGTGATGGTTAGTACACGATTTCAGCTAAAA
* *
1555 TTTTGCAAAAACTTATCAGAAATTTCTTTTCTCAATTTTTGGCCACAATACTC-ATAAAAAATAA
256 TTTTGCAAAAACTAATCAGAAATTTTTTTTCTCAATTTTTGGCCACAATACTCAAT-AAAAAT--
**
1619 ATAATTCAACTTC
318 ATAATTCAACGCC
* *
1632 AAAAAGATTTCAAGGCTTTTCAGGCTTCAAATTTGGTTTTTCCTTTTTTTTTATCCAATTAATTT
1 AAAAAGATTTCAAGGCTTTTCATGCTTCAAATATGGTTTTTCC--TTTTTTTATCCAATTAATTT
* * * * * *
1697 CTAATAAAATCGAATCAAGATTTAGAAGCTCGTAAAAACATATTCTTAAATCCATTGTAGCTTAT
64 CTGATAAAACCGAATCAAGATTCAGAAGCTCGTAAAAACATATCCTTAAATCCATTGTAGCTGAG
* *
1762 ATTTGATTAGATTCATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTTGCAAAATTGAGCT
129 ATTTGATTAGATTCATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTTGCAAAACTGAGCC
* *
1827 GGGGCCCTGTAACGCGTTTTCAGCCAGAAACCATGATGGTTAGTACACGATTT
194 GGGGCCCTGGAACGCGTTTTCAGCCAGAAACCGTGATGGTTAGTACACGATTT
1880 TTTTTGATAA
Statistics
Matches: 758, Mismatches: 114, Indels: 60
0.81 0.12 0.06
Matches are distributed among these distances:
320 7 0.01
321 58 0.08
322 48 0.06
323 19 0.03
324 133 0.18
325 3 0.00
327 1 0.00
329 1 0.00
331 1 0.00
332 197 0.26
333 219 0.29
334 71 0.09
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35
Consensus pattern (330 bp):
AAAAAGATTTCAAGGCTTTTCATGCTTCAAATATGGTTTTTCCTTTTTTTATCCAATTAATTTCT
GATAAAACCGAATCAAGATTCAGAAGCTCGTAAAAACATATCCTTAAATCCATTGTAGCTGAGAT
TTGATTAGATTCATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTTGCAAAACTGAGCCGG
GGCCCTGGAACGCGTTTTCAGCCAGAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTG
CAAAAACTAATCAGAAATTTTTTTTCTCAATTTTTGGCCACAATACTCAATAAAAATATAATTCA
ACGCC
Found at i:2436 original size:631 final size:621
Alignment explanation
Indices: 1269--2510 Score: 1610
Period size: 631 Copynumber: 2.0 Consensus size: 621
1259 TTTTTCTCAT
* * *
1269 TTTTTGGCCACAATACTCAATATAAAATATAATTCAACGCCAAAAGATATTTAATGGATTTTCAT
1 TTTTTGGCCACAATACTCAATAAAAAATATAATTCAACGCCAAAAGATATTCAATGCATTTTCAT
1334 GCTTCAAATATGGTTTTCCCTTTTTTTTCCAAAAATTTTCTGACAAAACCGAATCAAGATTCAGA
66 GCTTCAAATATGGTTTTCCCTTTTTTTTCCAAAAATTTTCTGACAAAACCGAATCAAGATTCAGA
* ** *
1399 AGCTCATAAAGACATATCTCTTAATCCAATGTGGTTGAGATTTAATTAGATTAATATTGATATTT
131 AACTCATAAAGACATATCTCTTAATCCAATGTGACTGAGATTTAATTAGATTAATATAGATATTT
* * *** * * *
1464 TAAGGAGTTTAGACGTCTGAAATCATGCAAAACTGAGTCCGTTCCCCGGAACGCTTTTTTAGGCA
196 CAAGGAGTTTAGACGTCAGAAATCATGCAAAACTGAGTCCGGGACCCGGAACGCGTTTTCAGCCA
* *
1529 GAAACCATTCACGATTTCAGATAAAATTTTGCAAAAACTTATCAGAAATTTCTTTTCTCAATTTT
261 GAAACCATTCACGATTTCAGATAAAATTTTGCAAAAACTGATCAGAAATTTATTTTCTCAATTTT
* * *
1594 TGGCCACAATACTCATAAAAAATAAATAATTCAACTTCAAAAAGATTTCAAGGCTTTTCAGGCTT
326 TGGCCACAATACTCACAAAAAATAAATAACTCAACTGCAAAAAGATTTCAAGGCTTTTCAGGCTT
*** * *
1659 CAAATTTGGTTTTTCCTTTTTTTTTATCCAATTAATTTCTAATAAAATCGAATCAAGATTTAGAA
391 CAAATACAGTTTTTCCTATTTTTTTATCCAATTAATTTCTAATAAAACCGAATCAAGATTTAGAA
* *
1724 GCTCGTAAAAACATATTCTTAAATCCATTGTAGCTTATATTTGATTAGATTCATATAGATATTTC
456 GCTCGTAAAAACATATCCTTAAATCCATTGTAGCTTAGATTTGATTAGATTCATATAGATATTTC
* * * * *
1789 AAGGAGTCTCGACGCCAAAAATCTTGCAAAATTGAGCTGGGGCCCTGTAACGCGTTTTCAGCCAG
521 AAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGGCCCTGGAACGCGTCTTCAGCCAG
1854 AAACCATGATGGTTAGTACACGATTTTTTTTGATAA
586 AAACCATGATGGTTAGTACACGATTTTTTTTGATAA
* * *
1890 TTTTTGGCCACAGTGCTC-ATAAAAAATATATAATTCAACGCCAAAAAGAT-TTCAA-GCCTTTT
1 TTTTTGGCCACAATACTCAAT-AAAAA-ATATAATTCAACGCC-AAAAGATATTCAATGCATTTT
* * * *
1952 CATGCTTCAAATATGGTTTTTCGTTTTTTTATCCAATTAA-TTTCTGATAAAACCCGAATCAAGA
63 CATGCTTCAAATATGGTTTTCCCTTTTTTT-TCCAA-AAATTTTCTGACAAAA-CCGAATCAAGA
* *
2016 TTCAGAAACTCGTTAAA-ACATATC-CTTAAAT-CAATGTGACTGCA-ATTTGATTAGATTAATA
125 TTCAGAAACTC-ATAAAGACATATCTCTT-AATCCAATGTGACTG-AGATTTAATTAGATTAATA
* * * * *
2077 TAGATATTTCAAGGAGTTTCGACGTCAGAAATCATGGAAAACTGAGTCGGGGATCCGGAATGCGT
187 TAGATATTTCAAGGAGTTTAGACGTCAGAAATCATGCAAAACTGAGTCCGGGACCCGGAACGCGT
* * *
2142 TTTCAGCCAGAAACCGTGATGTAATACACGATTTCAGCTCAAATTTTGCAAAAACTGATCCGATA
252 TTTCAGCCAGAAACC---A--T--T-CACGATTTCAGATAAAATTTTGCAAAAACTGATCAGA-A
* * * * * *
2207 TTTTATTTTTTCTATATTTTTGGCCCCAATACTTACAGAAAATATATAACTCAA-TGCTAAAAAG
308 ATTTATTTTCTC-A-ATTTTTGGCCACAATACTCACAAAAAATAAATAACTCAACTGC-AAAAAG
* *
2271 ATTT-AAGGGCTTTTCATGCTTCAAATACAGTTTTT-C-ATTTTTTTATCCAATTAATTTCTGAT
370 ATTTCAA-GGCTTTTCAGGCTTCAAATACAGTTTTTCCTATTTTTTTATCCAATTAATTTCTAAT
* * *
2333 AAAACCGAATGAAGATTTCGATGCTCGTAAAAACATATCCTTAAATCCATTGTAG-TTGAGATTT
434 AAAACCGAATCAAGATTTAGAAGCTCGTAAAAACATATCCTTAAATCCATTGTAGCTT-AGATTT
*
2397 GGTTAGATTCATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGG
498 GATTAGATTCATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGG
* * *
2462 CCCTGGAACGTGTCTTCAGCCAGAAACCGTGATGGTTAGTATACGATTT
563 CCCTGGAACGCGTCTTCAGCCAGAAACCATGATGGTTAGTACACGATTT
2511 CAGTTAAAAT
Statistics
Matches: 534, Mismatches: 64, Indels: 36
0.84 0.10 0.06
Matches are distributed among these distances:
620 2 0.00
621 53 0.10
622 129 0.24
623 41 0.08
624 4 0.01
625 1 0.00
627 1 0.00
629 1 0.00
630 35 0.07
631 194 0.36
632 6 0.01
633 67 0.13
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (621 bp):
TTTTTGGCCACAATACTCAATAAAAAATATAATTCAACGCCAAAAGATATTCAATGCATTTTCAT
GCTTCAAATATGGTTTTCCCTTTTTTTTCCAAAAATTTTCTGACAAAACCGAATCAAGATTCAGA
AACTCATAAAGACATATCTCTTAATCCAATGTGACTGAGATTTAATTAGATTAATATAGATATTT
CAAGGAGTTTAGACGTCAGAAATCATGCAAAACTGAGTCCGGGACCCGGAACGCGTTTTCAGCCA
GAAACCATTCACGATTTCAGATAAAATTTTGCAAAAACTGATCAGAAATTTATTTTCTCAATTTT
TGGCCACAATACTCACAAAAAATAAATAACTCAACTGCAAAAAGATTTCAAGGCTTTTCAGGCTT
CAAATACAGTTTTTCCTATTTTTTTATCCAATTAATTTCTAATAAAACCGAATCAAGATTTAGAA
GCTCGTAAAAACATATCCTTAAATCCATTGTAGCTTAGATTTGATTAGATTCATATAGATATTTC
AAGGAGTCTCGACGCCAAAAATCTAGCAAAACTGAGCCGGGGCCCTGGAACGCGTCTTCAGCCAG
AAACCATGATGGTTAGTACACGATTTTTTTTGATAA
Found at i:2495 original size:333 final size:335
Alignment explanation
Indices: 1912--2532 Score: 864
Period size: 333 Copynumber: 1.9 Consensus size: 335
1902 GTGCTCATAA
* ** *
1912 AAAATATATAATTCAACGCCAAAAAGATTTCAAGCCTTTTCATGCTTCAAATATGGTTTTTCGTT
1 AAAATATATAACTCAACGCCAAAAAGATTTCAAGCCTTTTCATGCTTCAAATACAGTTTTTCATT
*
1977 TTTTTATCCAATTAATTTCTGATAAAACCCGAATCAAGATTCAGAAACTCGTTAAAACATATCCT
66 TTTTTATCCAATTAATTTCTGATAAAACCCGAATCAAGATTCAGAAACTCGTAAAAACATATCCT
* * *
2042 TAAATCAATGTGACTGCAATTTGATTAGATTAATATAGATATTTCAAGGAGTTTCGACGTCAGAA
131 TAAATCAATGTGACTGCAATTTGATTAGATTAATATAGATATTTCAAGGAGTCTCGACGCCAAAA
* * * * *
2107 ATCATGGAAAACTGAGTCGGGGATCCGGAATGCGTTTTCAGCCAGAAACCGTGAT-G-TAATACA
196 ATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTCTTCAGCCAGAAACCGTGATGGTTAATACA
*
2170 CGATTTCAGCTCAAATTTTGCAAAAACTGATCCGATATTTTATTTTTTCTATATTTTTGGCCCCA
261 CGATTTCAGCTAAAATTTTGCAAAAACTGATCCGATATTTTATTTTTTCTATATTTTTGGCCCCA
2235 ATACTTACAG
326 ATACTTACAG
* * *
2245 AAAATATATAACTCAATGCTAAAAAGATTT-AAGGGCTTTTCATGCTTCAAATACAGTTTTTCAT
1 AAAATATATAACTCAACGCCAAAAAGATTTCAA-GCCTTTTCATGCTTCAAATACAGTTTTTCAT
* **
2309 TTTTTTATCCAATTAATTTCTGATAAAA-CCGAATGAAGATTTC-GATGCTCGTAAAAACATATC
65 TTTTTTATCCAATTAATTTCTGATAAAACCCGAATCAAGA-TTCAGAAACTCGTAAAAACATATC
* * * *
2372 CTTAAATCCAT-TGTAGTTG-AGATTTGGTTAGATTCATATAGATATTTCAAGGAGTCTCGACGC
129 CTTAAATCAATGTG-A-CTGCA-ATTTGATTAGATTAATATAGATATTTCAAGGAGTCTCGACGC
*
2435 CAAAAATC-TAGCAAAACTGAGCCGGGG-CCCTGGAACGTGTCTTCAGCCAGAAACCGTGATGGT
191 CAAAAATCAT-GCAAAACTGAGCCGGGGACCC-GGAACGCGTCTTCAGCCAGAAACCGTGATGGT
* * *
2498 TAGTATACGATTTCAGTTAAAATTTTGCAAAAACT
254 TAATACACGATTTCAGCTAAAATTTTGCAAAAACT
2533 TAACCCACAG
Statistics
Matches: 251, Mismatches: 28, Indels: 16
0.85 0.09 0.05
Matches are distributed among these distances:
331 2 0.01
332 44 0.18
333 173 0.69
334 1 0.00
335 31 0.12
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (335 bp):
AAAATATATAACTCAACGCCAAAAAGATTTCAAGCCTTTTCATGCTTCAAATACAGTTTTTCATT
TTTTTATCCAATTAATTTCTGATAAAACCCGAATCAAGATTCAGAAACTCGTAAAAACATATCCT
TAAATCAATGTGACTGCAATTTGATTAGATTAATATAGATATTTCAAGGAGTCTCGACGCCAAAA
ATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTCTTCAGCCAGAAACCGTGATGGTTAATACA
CGATTTCAGCTAAAATTTTGCAAAAACTGATCCGATATTTTATTTTTTCTATATTTTTGGCCCCA
ATACTTACAG
Found at i:4808 original size:11 final size:11
Alignment explanation
Indices: 4792--4816 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4782 TTAGTGGGAT
4792 CATATGACCAG
1 CATATGACCAG
4803 CATATGACCAG
1 CATATGACCAG
4814 CAT
1 CAT
4817 TAAACTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (11 bp):
CATATGACCAG
Found at i:4897 original size:18 final size:18
Alignment explanation
Indices: 4874--4954 Score: 76
Period size: 18 Copynumber: 4.5 Consensus size: 18
4864 TCCTCTCCTT
4874 CCTCCGCC-ACGTCCTCTG
1 CCTCCGCCTACG-CCTCTG
*
4892 CCTCCGCCTCCGCCTCTG
1 CCTCCGCCTACGCCTCTG
* **
4910 CCTCTGCCT-CTGCCTCCA
1 CCTCCGCCTAC-GCCTCTG
*
4928 CCTCCGCCTCCGCCTCTG
1 CCTCCGCCTACGCCTCTG
*
4946 CCTCTGCCT
1 CCTCCGCCT
4955 CTGCCCCGGC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
17 1 0.02
18 48 0.92
19 3 0.06
ACGTcount: A:0.02, C:0.58, G:0.15, T:0.25
Consensus pattern (18 bp):
CCTCCGCCTACGCCTCTG
Found at i:4900 original size:6 final size:6
Alignment explanation
Indices: 4886--4974 Score: 81
Period size: 6 Copynumber: 14.8 Consensus size: 6
4876 TCCGCCACGT
* * * * *
4886 CCTCTG CCTCCG CCTCCG CCTCTG CCTCTG CCTCTG CCTCCA CCTCCG
1 CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG
* * * *
4934 CCTCCG CCTCTG CCTCTG CCTCTG CC-CCGG CCTCGG CCTCC
1 CCTCCG CCTCCG CCTCCG CCTCCG CCTCC-G CCTCCG CCTCC
4975 AAACATTGAT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
5 1 0.01
6 70 0.97
7 1 0.01
ACGTcount: A:0.01, C:0.58, G:0.17, T:0.24
Consensus pattern (6 bp):
CCTCCG
Found at i:4901 original size:12 final size:12
Alignment explanation
Indices: 4886--4974 Score: 99
Period size: 12 Copynumber: 7.4 Consensus size: 12
4876 TCCGCCACGT
* *
4886 CCTCTGCCTCCG
1 CCTCCGCCTCTG
4898 CCTCCGCCTCTG
1 CCTCCGCCTCTG
*
4910 CCTCTGCCTCTG
1 CCTCCGCCTCTG
* *
4922 CCTCCACCTCCG
1 CCTCCGCCTCTG
4934 CCTCCGCCTCTG
1 CCTCCGCCTCTG
*
4946 CCTCTGCCTCTG
1 CCTCCGCCTCTG
*
4958 CC-CCGGCCTCGG
1 CCTCC-GCCTCTG
4970 CCTCC
1 CCTCC
4975 AAACATTGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
11 1 0.02
12 61 0.95
13 2 0.03
ACGTcount: A:0.01, C:0.58, G:0.17, T:0.24
Consensus pattern (12 bp):
CCTCCGCCTCTG
Found at i:4920 original size:30 final size:30
Alignment explanation
Indices: 4886--4973 Score: 124
Period size: 30 Copynumber: 2.9 Consensus size: 30
4876 TCCGCCACGT
*
4886 CCTCTGCCTCCGCCTCCGCCTCTGCCTCTG
1 CCTCTGCCTCCGCCTCCGCCTCCGCCTCTG
*
4916 CCTCTGCCTCCACCTCCGCCTCCGCCTCTG
1 CCTCTGCCTCCGCCTCCGCCTCCGCCTCTG
* *
4946 CCTCTGCCTCTGCC-CCGGCCTCGGCCTC
1 CCTCTGCCTCCGCCTCC-GCCTCCGCCTC
4974 CAAACATTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
29 2 0.04
30 50 0.96
ACGTcount: A:0.01, C:0.58, G:0.17, T:0.24
Consensus pattern (30 bp):
CCTCTGCCTCCGCCTCCGCCTCCGCCTCTG
Found at i:4973 original size:36 final size:36
Alignment explanation
Indices: 4886--4974 Score: 135
Period size: 36 Copynumber: 2.5 Consensus size: 36
4876 TCCGCCACGT
*
4886 CCTCTGCCTCCGCCTCCGCCTCTGCCTCTGCCTCTG
1 CCTCCGCCTCCGCCTCCGCCTCTGCCTCTGCCTCTG
*
4922 CCTCCACCTCCGCCTCCGCCTCTGCCTCTGCCTCTG
1 CCTCCGCCTCCGCCTCCGCCTCTGCCTCTGCCTCTG
*
4958 CC-CCGGCCTCGGCCTCC
1 CCTCC-GCCTCCGCCTCC
4975 AAACATTGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 2 0.04
36 46 0.96
ACGTcount: A:0.01, C:0.58, G:0.17, T:0.24
Consensus pattern (36 bp):
CCTCCGCCTCCGCCTCCGCCTCTGCCTCTGCCTCTG
Found at i:15551 original size:86 final size:86
Alignment explanation
Indices: 15362--15537 Score: 257
Period size: 86 Copynumber: 2.0 Consensus size: 86
15352 ACAGATCAGG
*
15362 ATTCCAGTTAAAAAGGTGCATCTGCTTTCATACATTAATTAATTTGATTATAATCAAATGATCTG
1 ATTCCAGTTAAAAAGGTGCATCTGCTTTCATACATTAATTAATTTGATAATAATCAAATGATCTG
* *
15427 ACCTTTAGTTTTAGCAAGCTA
66 ACCTTTAGTTTGAGAAAGCTA
15448 ATTCCAGTTAAAAAGGTGCATCTGCTTT-ACTACATTAATTAATTTGATAATAATCAAATGATCG
1 ATTCCAGTTAAAAAGGTGCATCTGCTTTCA-TACATTAATTAATTTGATAATAATCAAATGATC-
15512 ATCAGACCTTTAGTCTTGA-AAAGCTA
64 -T--GACCTTTAGT-TTGAGAAAGCTA
15538 TCTTTAGGAA
Statistics
Matches: 81, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
85 1 0.01
86 60 0.74
88 1 0.01
90 16 0.20
91 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (86 bp):
ATTCCAGTTAAAAAGGTGCATCTGCTTTCATACATTAATTAATTTGATAATAATCAAATGATCTG
ACCTTTAGTTTGAGAAAGCTA
Found at i:21693 original size:14 final size:14
Alignment explanation
Indices: 21674--21708 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
21664 GAAAATCCTC
21674 TGCCCCAATTTTGG
1 TGCCCCAATTTTGG
21688 TGCCCCAATTTTGG
1 TGCCCCAATTTTGG
21702 TGCCCCA
1 TGCCCCA
21709 CTTGTGCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.34, G:0.20, T:0.31
Consensus pattern (14 bp):
TGCCCCAATTTTGG
Found at i:30398 original size:33 final size:33
Alignment explanation
Indices: 30358--30441 Score: 168
Period size: 33 Copynumber: 2.5 Consensus size: 33
30348 ACGTAATTTT
30358 AGAAAGGAAAACCATGATTTTAACCAGAAAAAA
1 AGAAAGGAAAACCATGATTTTAACCAGAAAAAA
30391 AGAAAGGAAAACCATGATTTTAACCAGAAAAAA
1 AGAAAGGAAAACCATGATTTTAACCAGAAAAAA
30424 AGAAAGGAAAACCATGAT
1 AGAAAGGAAAACCATGAT
30442 ATGAAGTTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.14
Consensus pattern (33 bp):
AGAAAGGAAAACCATGATTTTAACCAGAAAAAA
Found at i:34647 original size:81 final size:84
Alignment explanation
Indices: 34545--34769 Score: 321
Period size: 81 Copynumber: 2.7 Consensus size: 84
34535 AGCAACAGCT
* *
34545 TTGCTGTCCTGGCTTTCTTTACAAGTCTTCTCTCCCTGAAATGCCTGGTCAATGTTAAAAACTTC
1 TTGCTATCCTGGCTTTTTTTACAAGTCTTCTCTCCCTGAAATGCCTGGTCAATGTTAAAAACTTC
*
34610 ACTA-CC-CTCCAA-TGCC
66 ACTACCCACTCCAACGGCC
*
34626 TTGCTATCCTGGCTTTTTTTACAAGTCTTCTCTCCCTGAAATGCCTGGTCAATGTTAAAAATTTC
1 TTGCTATCCTGGCTTTTTTTACAAGTCTTCTCTCCCTGAAATGCCTGGTCAATGTTAAAAACTTC
*
34691 ACTACTCTCCACTGCAACGGCC
66 ACTA--C-CCACTCCAACGGCC
* * **
34713 ATGCTATCCTGGCTTTTCTTACAAGTCTTCTCTCCCTGAGGTGCCTGGTCAATGTTA
1 TTGCTATCCTGGCTTTTTTTACAAGTCTTCTCTCCCTGAAATGCCTGGTCAATGTTA
34770 GAAATCTCAC
Statistics
Matches: 129, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
81 66 0.51
85 2 0.02
86 5 0.04
87 56 0.43
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.36
Consensus pattern (84 bp):
TTGCTATCCTGGCTTTTTTTACAAGTCTTCTCTCCCTGAAATGCCTGGTCAATGTTAAAAACTTC
ACTACCCACTCCAACGGCC
Found at i:34767 original size:87 final size:87
Alignment explanation
Indices: 34506--34834 Score: 384
Period size: 87 Copynumber: 3.9 Consensus size: 87
34496 AAGTGTCTCA
* * * * * *
34506 TCAATGTTAGAAATTGCACAACTCTCCAAAGCAACAGCTTTGCTGTCCTGGC-TTTCTTTACAAG
1 TCAATGTTAAAAATTTCACTACTCTCCAAAGCAACGGCCTTGCTATCCTGGCTTTTC-TTACAAG
34570 TCTTCTCTCCCTGAAATGCCTGG
65 TCTTCTCTCCCTGAAATGCCTGG
* * * *
34593 TCAATGTTAAAAACTTCACTACCCT-C----CAA-TGCCTTGCTATCCTGGCTTTTTTTACAAGT
1 TCAATGTTAAAAATTTCACTACTCTCCAAAGCAACGGCCTTGCTATCCTGGCTTTTCTTACAAGT
34652 CTTCTCTCCCTGAAATGCCTGG
66 CTTCTCTCCCTGAAATGCCTGG
** *
34674 TCAATGTTAAAAATTTCACTACTCTCCACTGCAACGGCCATGCTATCCTGGCTTTTCTTACAAGT
1 TCAATGTTAAAAATTTCACTACTCTCCAAAGCAACGGCCTTGCTATCCTGGCTTTTCTTACAAGT
**
34739 CTTCTCTCCCTGAGGTGCCTGG
66 CTTCTCTCCCTGAAATGCCTGG
* * * * * * ***
34761 TCAATGTTAGAAATCTCACTAATCTCTAAAGCAATGGCCTTGCTTTCCTCATTTTTCTTACAAGT
1 TCAATGTTAAAAATTTCACTACTCTCCAAAGCAACGGCCTTGCTATCCTGGCTTTTCTTACAAGT
34826 CTTCTCTCC
66 CTTCTCTCC
34835 TTTTGTTAGG
Statistics
Matches: 207, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
81 67 0.32
82 7 0.03
86 4 0.02
87 129 0.62
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.35
Consensus pattern (87 bp):
TCAATGTTAAAAATTTCACTACTCTCCAAAGCAACGGCCTTGCTATCCTGGCTTTTCTTACAAGT
CTTCTCTCCCTGAAATGCCTGG
Found at i:36847 original size:14 final size:14
Alignment explanation
Indices: 36828--36855 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36818 ACAGAGAGAC
36828 GCAACAAATTTCGA
1 GCAACAAATTTCGA
36842 GCAACAAATTTCGA
1 GCAACAAATTTCGA
36856 AGTCAATTCC
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:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
GCAACAAATTTCGA
Found at i:45474 original size:131 final size:132
Alignment explanation
Indices: 45336--45600 Score: 435
Period size: 132 Copynumber: 2.0 Consensus size: 132
45326 TTGTTTAGAC
45336 TTTTATAGTTTTACTCAACTAAAAACTCTA-TTTTTATTTAATTAAATATAATATCCTTATAACT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATATAATATCCTTATAACT
* * * * *
45400 ATTTAATTTTTACCATTTTACTATTTTAATTAAAATA-TATATATATATTAGAATTTTTTAAATA
66 ATTTAATTTTTACCAATTTACTAATTTAATTAAAAAACT-TAGATATATTAGAATTTTTAAAATA
45464 TAT
130 TAT
*
45467 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATATAATATCCTTATAACT
* *
45532 ATTTTATTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATAT
66 ATTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATAT
45597 AT
131 AT
45599 TT
1 TT
45601 CTTAAATGAC
Statistics
Matches: 124, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
131 30 0.24
132 93 0.75
133 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.51
Consensus pattern (132 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATATAATATCCTTATAACT
ATTTAATTTTTACCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATAT
AT
Done.